From 8bfdad3fbf0382e657bd72e83830722dd44aa716 Mon Sep 17 00:00:00 2001
From: fizwit <john@fuzzdog.com>
Date: Thu, 23 Jun 2022 07:00:06 -0700
Subject: [PATCH 001/835] adding easyconfigs: Regenie-3.1.1-GCC-11.2.0.eb,
 BGEN-enkre-1.1.7-GCC-11.2.0.eb, Boost-1.55.0-GCC-11.2.0.eb and patches:
 regenie-3.1.1_Makefile.patch, 3rd-party-removal.patch,
 BGEN-enkre_streampos.patch

---
 .../b/BGEN-enkre/3rd-party-removal.patch      | 176 ++++++++++++++++++
 .../BGEN-enkre/BGEN-enkre-1.1.7-GCC-11.2.0.eb |  71 +++++++
 .../b/BGEN-enkre/BGEN-enkre_streampos.patch   |  12 ++
 .../b/Boost/Boost-1.55.0-GCC-11.2.0.eb        |  21 +++
 .../r/Regenie/Regenie-3.1.1-GCC-11.2.0.eb     |  45 +++++
 .../r/Regenie/regenie-3.1.1_Makefile.patch    |  41 ++++
 6 files changed, 366 insertions(+)
 create mode 100644 easybuild/easyconfigs/b/BGEN-enkre/3rd-party-removal.patch
 create mode 100644 easybuild/easyconfigs/b/BGEN-enkre/BGEN-enkre-1.1.7-GCC-11.2.0.eb
 create mode 100644 easybuild/easyconfigs/b/BGEN-enkre/BGEN-enkre_streampos.patch
 create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.55.0-GCC-11.2.0.eb
 create mode 100644 easybuild/easyconfigs/r/Regenie/Regenie-3.1.1-GCC-11.2.0.eb
 create mode 100644 easybuild/easyconfigs/r/Regenie/regenie-3.1.1_Makefile.patch

diff --git a/easybuild/easyconfigs/b/BGEN-enkre/3rd-party-removal.patch b/easybuild/easyconfigs/b/BGEN-enkre/3rd-party-removal.patch
new file mode 100644
index 00000000000..83f35651997
--- /dev/null
+++ b/easybuild/easyconfigs/b/BGEN-enkre/3rd-party-removal.patch
@@ -0,0 +1,176 @@
+Removal of sqlite3, boost and zstd from 3-party modules
+Author: J. Sassmannshausen
+diff --git a/bgen.tgz.orig/3rd_party/wscript b/bgen.tgz/3rd_party/wscript
+index 220728a..e69de29 100644
+--- a/bgen.tgz.orig/3rd_party/wscript
++++ b/bgen.tgz/3rd_party/wscript
+@@ -1,2 +0,0 @@
+-def build( bld ):
+-	bld.recurse( [ 'boost_1_55_0', 'sqlite3', 'zstd-1.1.0' ] )
+diff --git a/bgen.tgz.orig/Makefile b/bgen.tgz/Makefile
+index a7b0ac8..c62ac16 100644
+--- a/bgen.tgz.orig/Makefile
++++ b/bgen.tgz/Makefile
+@@ -1,14 +1,9 @@
+ FLAGS = -g -std=c++11 -lz \
+ -I genfile/include \
+ -I db/include \
+--I 3rd_party/boost_1_55_0 \
+--I 3rd_party/zstd-1.1.0 \
+--I 3rd_party/zstd-1.1.0/lib \
+--I 3rd_party/zstd-1.1.0/lib/common \
+--I 3rd_party/zstd-1.1.0/lib/compress \
+--I 3rd_party/zstd-1.1.0/lib/decompress \
+--I 3rd_party/sqlite3 \
+--I include/3rd_party/sqlite3 \
++-I ${EBBOST}/include \
++-I ${EBDEVELZSTD}/include \
++-I ${EBSQLITE3}/include \
+ -D SQLITE_ENABLE_COLUMN_METADATA \
+ -D SQLITE_ENABLE_STAT4 \
+ -D SQLITE_MAX_EXPR_DEPTH=10000 \
+diff --git a/bgen.tgz.orig/db/include/db/SQLStatement.hpp b/bgen.tgz/db/include/db/SQLStatement.hpp
+index e107bd2..fca5957 100644
+--- a/bgen.tgz.orig/db/include/db/SQLStatement.hpp
++++ b/bgen.tgz/db/include/db/SQLStatement.hpp
+@@ -12,7 +12,7 @@
+ #include <vector>
+ #include <exception>
+ #include <stdint.h>
+-#include "sqlite3/sqlite3.h"
++#include "sqlite3.h"
+ #include "db/SQLite3Connection.hpp"
+ 
+ namespace db {
+diff --git a/bgen.tgz.orig/db/include/db/SQLite3Connection.hpp b/bgen.tgz/db/include/db/SQLite3Connection.hpp
+index b4bd219..cfbbd3a 100644
+--- a/bgen.tgz.orig/db/include/db/SQLite3Connection.hpp
++++ b/bgen.tgz/db/include/db/SQLite3Connection.hpp
+@@ -10,7 +10,7 @@
+ #include <cassert>
+ #include <string>
+ #include <exception>
+-#include "sqlite3/sqlite3.h"
++#include "sqlite3.h"
+ #include "db/Connection.hpp"
+ #include "db/Transaction.hpp"
+ #include "db/Error.hpp"
+diff --git a/bgen.tgz.orig/db/include/db/SQLite3Statement.hpp b/bgen.tgz/db/include/db/SQLite3Statement.hpp
+index d41a710..76dbfb6 100644
+--- a/bgen.tgz.orig/db/include/db/SQLite3Statement.hpp
++++ b/bgen.tgz/db/include/db/SQLite3Statement.hpp
+@@ -11,7 +11,7 @@
+ #include <string>
+ #include <exception>
+ 
+-#include "sqlite3/sqlite3.h"
++#include "sqlite3.h"
+ #include "db/SQLite3Connection.hpp"
+ #include "db/SQLStatement.hpp"
+ 
+diff --git a/bgen.tgz.orig/db/src/SQLStatement.cpp b/bgen.tgz/db/src/SQLStatement.cpp
+index 60168c6..32576ca 100644
+--- a/bgen.tgz.orig/db/src/SQLStatement.cpp
++++ b/bgen.tgz/db/src/SQLStatement.cpp
+@@ -7,7 +7,7 @@
+ #include <cassert>
+ #include <string>
+ #include <stdint.h>
+-#include "sqlite3/sqlite3.h"
++#include "sqlite3.h"
+ #include "db/SQLStatement.hpp"
+ 
+ namespace db {
+diff --git a/bgen.tgz.orig/db/src/SQLite3Statement.cpp b/bgen.tgz/db/src/SQLite3Statement.cpp
+index 84e0658..03b3d5e 100644
+--- a/bgen.tgz.orig/db/src/SQLite3Statement.cpp
++++ b/bgen.tgz/db/src/SQLite3Statement.cpp
+@@ -9,7 +9,7 @@
+ #include <string>
+ #include <exception>
+ #include <boost/lexical_cast.hpp>
+-#include "sqlite3/sqlite3.h"
++#include "sqlite3.h"
+ #include "db/SQLite3Connection.hpp"
+ #include "db/SQLStatement.hpp"
+ #include "db/SQLite3Statement.hpp"
+diff --git a/bgen.tgz.orig/db/wscript b/bgen.tgz/db/wscript
+index 7b0b617..a3861f0 100644
+--- a/bgen.tgz.orig/db/wscript
++++ b/bgen.tgz/db/wscript
+@@ -5,8 +5,8 @@ def build( bld ):
+ 	bld.stlib(
+ 		target = 'db',
+ 		source = sources,
+-		includes='./include',
++		includes='${EBSQLITE}/include ./include',
+ 		cxxflags = [],
+ 		use = 'boost sqlite3',
+-		export_includes = './include'
++		export_includes = '${EBSQLITE}/include ./include'
+ 	)
+diff --git a/bgen.tgz.orig/wscript b/bgen.tgz/wscript
+index a6385d9..47b9fc9 100644
+--- a/bgen.tgz.orig/wscript
++++ b/bgen.tgz/wscript
+@@ -63,7 +63,7 @@ def build( bld ):
+ 		use = 'zlib zstd sqlite3 db',
+ 		export_includes = 'genfile/include'
+ 	)
+-	bld.recurse( [ '3rd_party', 'appcontext', 'genfile', 'db', 'apps', 'example', 'test', 'R' ] )
++	bld.recurse( [ 'appcontext', 'genfile', 'db', 'apps', 'example', 'test', 'R' ] )
+ 	# Copy files into rbgen package directory
+ 	for source in bgen_sources:
+ 		bld( rule = 'cp ${SRC} ${TGT}', source = source, target = 'R/rbgen/src/bgen/' + os.path.basename( source.abspath() ), always = True )
+@@ -126,12 +126,12 @@ class ReleaseBuilder:
+ 		shutil.copytree( 'R/package/', rbgen_dir )
+ 		os.makedirs( os.path.join( rbgen_dir, "src", "include" ))
+ 		os.makedirs( os.path.join( rbgen_dir, "src", "include", "boost" ))
+-		os.makedirs( os.path.join( rbgen_dir, "src", "include", "zstd-1.1.0" ))
++		os.makedirs( os.path.join( rbgen_dir, "src", "include", "zstd" ))
+ 		os.makedirs( os.path.join( rbgen_dir, "src", "db" ))
+ 		os.makedirs( os.path.join( rbgen_dir, "src", "bgen" ))
+ 		os.makedirs( os.path.join( rbgen_dir, "src", "boost" ))
+ 		os.makedirs( os.path.join( rbgen_dir, "src", "sqlite3" ))
+-		os.makedirs( os.path.join( rbgen_dir, "src", "zstd-1.1.0" ))
++		os.makedirs( os.path.join( rbgen_dir, "src", "zstd" ))
+ 
+ 		# Copy source files in
+ 		from glob import glob
+@@ -141,11 +141,11 @@ class ReleaseBuilder:
+ 		for filename in glob( 'db/src/*.cpp' ):
+ 			shutil.copy( filename, os.path.join( rbgen_dir, "src", "db", os.path.basename( filename ) ) )
+ 
+-		for filename in glob( '3rd_party/sqlite3/sqlite3/sqlite3.c' ):
+-			shutil.copy( filename, os.path.join( rbgen_dir, "src", "sqlite3", os.path.basename( filename ) ) )
++#		for filename in glob( '3rd_party/sqlite3/sqlite3/sqlite3.c' ):
++#			shutil.copy( filename, os.path.join( rbgen_dir, "src", "sqlite3", os.path.basename( filename ) ) )
+ 
+-		for filename in glob( '3rd_party/zstd-1.1.0/lib/common/*.c' ) + glob( '3rd_party/zstd-1.1.0/lib/compress/*.c' ) + glob( '3rd_party/zstd-1.1.0/lib/decompress/*.c' ):
+-			shutil.copy( filename, os.path.join( rbgen_dir, "src", "zstd-1.1.0", os.path.basename( filename ) ) )
++#		for filename in glob( '3rd_party/zstd-1.1.0/lib/common/*.c' ) + glob( '3rd_party/zstd-1.1.0/lib/compress/*.c' ) + glob( '3rd_party/zstd-1.1.0/lib/decompress/*.c' ):
++#			shutil.copy( filename, os.path.join( rbgen_dir, "src", "zstd-1.1.0", os.path.basename( filename ) ) )
+ 
+ 		boostGlobs = [
+ 			'libs/system/src/*.cpp',
+@@ -160,14 +160,14 @@ class ReleaseBuilder:
+ 			'libs/chrono/src/*.cpp',
+ 		]
+ 
+-		for pattern in boostGlobs:
+-			for filename in glob( '3rd_party/boost_1_55_0/%s' % pattern ):
+-				shutil.copy( filename, os.path.join( rbgen_dir, "src", "boost", os.path.basename( filename ) ) )
++#		for pattern in boostGlobs:
++#			for filename in glob( '3rd_party/boost_1_55_0/%s' % pattern ):
++#				shutil.copy( filename, os.path.join( rbgen_dir, "src", "boost", os.path.basename( filename ) ) )
+ 
+ 		include_paths = [
+-			"3rd_party/boost_1_55_0/boost/",
+-			"3rd_party/zstd-1.1.0/",
+-			"3rd_party/sqlite3/",
++			"${EBBOOST}",
++			"${EBROOTZSTD}",
++			"${EBROOTSQLITE}",
+ 			"genfile/include/genfile",
+ 			"db/include/db"
+ 		]
diff --git a/easybuild/easyconfigs/b/BGEN-enkre/BGEN-enkre-1.1.7-GCC-11.2.0.eb b/easybuild/easyconfigs/b/BGEN-enkre/BGEN-enkre-1.1.7-GCC-11.2.0.eb
new file mode 100644
index 00000000000..a4bb6387868
--- /dev/null
+++ b/easybuild/easyconfigs/b/BGEN-enkre/BGEN-enkre-1.1.7-GCC-11.2.0.eb
@@ -0,0 +1,71 @@
+# Contribution from the NIHR Biomedical Research Centre
+# Guy's and St Thomas' NHS Foundation Trust and King's College London
+# uploaded by J. Sassmannshausen
+# we recommend to use --download-timeout=1000 when fetching the files
+
+easyblock = 'CmdCp'
+
+name = 'BGEN-enkre'
+version = '1.1.7'
+
+homepage = 'https://enkre.net/cgi-bin/code/bgen/dir?ci=trunk'
+description = """This repository contains a reference implementation 
+of the BGEN format, written in C++. The library can be used as the 
+basis for BGEN support in other software, or as a reference for 
+developers writing their own implementations of the BGEN format.
+Please cite:
+Band, G. and Marchini, J., "BGEN: a binary file format for imputed genotype and haplotype data", 
+bioArxiv 308296; doi: https://doi.org/10.1101/308296
+"""
+
+toolchain = {'name': 'GCC', 'version': '11.2.0'}
+
+source_urls = ['https://code.enkre.net/bgen/tarball/release/']
+sources = ['%(version)s.tgz']
+patches = [
+    '3rd-party-removal.patch',
+    'BGEN-enkre_streampos.patch',
+]
+checksums = [
+    '8173d614ae629f00c84c0e6edd7d16f56a61af2e5a8717e8fe0167f530a6aabb',  # 1.1.7.tgz
+    '0269b91d21976f38a9cf9bf7811375d16bf35be587d903ab1d846b2001b7d767',  # 3rd-party-removal.patch
+    '61c05ae5f7363d5b7b6015f0a015b93f149dbda4b23b9f48f9517a6ce93d5869',  # BGEN-enkre_streampos.patch
+]
+
+builddependencies = [
+    ('Python', '3.9.6'),
+]
+
+dependencies = [
+    ('SQLite', '3.36'),
+    ('zstd', '1.5.0'),
+    ('Boost', '1.55.0'),
+]
+
+cmds_map = [
+    ('.*', "./waf configure && echo LIB_zstd = [\\'zstd\\'] >> build/c4che/_cache.py &&"
+     " echo LIB_sqlite3 = [\\'sqlite3\\'] >> build/c4che/_cache.py &&"
+     "echo LIB_boost = [\\'boost_system\\', \\'boost_filesystem\\', \\'boost_thread\\', \\'boost_timer\\'] "
+     " >> build/c4che/_cache.py && ./waf"),
+]
+
+files_to_copy = [
+    (['build/apps/edit-bgen', 'build/apps/bgenix', 'build/apps/cat-bgen'], 'bin'),
+    (['build/db/libdb.a', 'build/libbgen.a'], 'lib'),
+    (['genfile/include/*', 'db/include/*'], 'include'),
+]
+
+postinstallcmds = ['./build/test/unit/test_bgen']
+
+sanity_check_paths = {
+    'files': ['bin/edit-bgen', 'bin/bgenix', 'bin/cat-bgen'],
+    'dirs': ['bin', 'lib', 'include'],
+}
+
+sanity_check_commands = [
+    'bgenix -help',
+    'cat-bgen -help',
+    'edit-bgen -help',
+]
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/b/BGEN-enkre/BGEN-enkre_streampos.patch b/easybuild/easyconfigs/b/BGEN-enkre/BGEN-enkre_streampos.patch
new file mode 100644
index 00000000000..5d7c0e471c3
--- /dev/null
+++ b/easybuild/easyconfigs/b/BGEN-enkre/BGEN-enkre_streampos.patch
@@ -0,0 +1,12 @@
+diff -ruN 1.1.7.tgz.orig/src/View.cpp 1.1.7.tgz/src/View.cpp
+--- 1.1.7.tgz.orig/src/View.cpp	2020-06-29 01:19:43.000000000 -0700
++++ 1.1.7.tgz/src/View.cpp	2022-06-06 18:05:10.650577000 -0700
+@@ -177,7 +177,7 @@
+ 
+ 			// get file size
+ 			{
+-				std::ios::streampos origin = m_stream->tellg() ;
++				std::streampos origin = m_stream->tellg() ;
+ 				m_stream->seekg( 0, std::ios::end ) ;
+ 				m_file_metadata.size = m_stream->tellg() - origin ;
+ 				m_stream->seekg( 0, std::ios::beg ) ;
diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.55.0-GCC-11.2.0.eb b/easybuild/easyconfigs/b/Boost/Boost-1.55.0-GCC-11.2.0.eb
new file mode 100644
index 00000000000..1814c8648e9
--- /dev/null
+++ b/easybuild/easyconfigs/b/Boost/Boost-1.55.0-GCC-11.2.0.eb
@@ -0,0 +1,21 @@
+name = 'Boost'
+version = '1.55.0'
+
+homepage = 'http://www.boost.org/'
+description = """Boost provides free peer-reviewed portable C++ source libraries."""
+
+toolchain = {'name': 'GCC', 'version': '11.2.0'}
+toolchainopts = {'pic': True}
+
+source_urls = [SOURCEFORGE_SOURCE]
+sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))]
+checksums = ['19c4305cd6669f2216260258802a7abc73c1624758294b2cad209d45cc13a767']
+
+dependencies = [
+    ('bzip2', '1.0.8'),
+    ('zlib', '1.2.11'),
+]
+
+configopts = '--without-libraries=python'
+
+moduleclass = 'devel'
diff --git a/easybuild/easyconfigs/r/Regenie/Regenie-3.1.1-GCC-11.2.0.eb b/easybuild/easyconfigs/r/Regenie/Regenie-3.1.1-GCC-11.2.0.eb
new file mode 100644
index 00000000000..7f008d0c180
--- /dev/null
+++ b/easybuild/easyconfigs/r/Regenie/Regenie-3.1.1-GCC-11.2.0.eb
@@ -0,0 +1,45 @@
+# Contribution from the NIHR Biomedical Research Centre
+# Guy's and St Thomas' NHS Foundation Trust and King's College London
+# uploaded by J. Sassmannshausen
+# we recommend to use --download-timeout=1000 when fetching the files
+
+easyblock = 'MakeCp'
+
+name = 'Regenie'
+version = '3.1.1'
+
+homepage = 'https://rgcgithub.github.io/regenie'
+description = """Regenie is a C++ program for whole genome regression modelling of large genome-wide 
+association studies.  It is developed and supported by a team of scientists at the Regeneron Genetics Center."""
+
+toolchain = {'name': 'GCC', 'version': '11.2.0'}
+
+source_urls = ['https://github.com/rgcgithub/regenie/archive/']
+sources = ['v%(version)s.tar.gz']
+patches = ['%(namelower)s-%(version)s_Makefile.patch']
+
+checksums = []
+
+dependencies = [
+    ('Boost', '1.55.0'),
+    ('BGEN-enkre', '1.1.7'),
+    ('OpenBLAS', '0.3.18'),
+]
+
+build_cmd = "make BGEN_PATH=$EBROOTBGENMINENKRE HAS_BOOST_IOSTREAM=1 "
+build_cmd += "OPENBLAS_ROOT=$EBROOTOPENBLAS BOOST=$EBROOTBOOST STATIC=0"
+
+files_to_copy = [
+    (['regenie'], 'bin'),
+    (['example/*'], 'example'),
+    (['docs/*'], 'docs'),
+]
+
+sanity_check_commands = ['regenie --help']
+
+sanity_check_paths = {
+    'files': ['bin/regenie'],
+    'dirs': ['bin', 'example', 'docs'],
+}
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/r/Regenie/regenie-3.1.1_Makefile.patch b/easybuild/easyconfigs/r/Regenie/regenie-3.1.1_Makefile.patch
new file mode 100644
index 00000000000..3fc4820cc4d
--- /dev/null
+++ b/easybuild/easyconfigs/r/Regenie/regenie-3.1.1_Makefile.patch
@@ -0,0 +1,41 @@
+Patch to remove 3rd party software and replace lapack(e) with openblas and boost 1.55
+base on the work of Author: J. Sassmannshausen NHS/GSTT
+diff -ruN regenie-3.1.1.orig/Makefile regenie-3.1.1/Makefile
+--- regenie-3.1.1.orig/Makefile	2022-05-05 10:59:29.000000000 -0700
++++ regenie-3.1.1/Makefile	2022-06-21 13:34:54.464076000 -0700
+@@ -44,7 +44,7 @@
+ # detect OS architecture and add flags
+ UNAME_S      := $(shell uname -s)
+ ifeq ($(UNAME_S),Linux)
+- INC          = -I${BGEN_PATH}/3rd_party/boost_1_55_0
++ INC          = -I${BOOST}
+  CFLAGS      += -fopenmp
+  ifeq ($(strip $(STATIC)),1)
+   LPATHS      = -static-libgcc -static-libstdc++
+@@ -103,10 +103,10 @@
+   INC        += -I${OPENBLAS_ROOT}/include/
+   # static linking
+   ifeq ($(strip $(STATIC)),1)
+-   SLIBS     += -Wl,-rpath=${OPENBLAS_ROOT}/lib/ -llapack -llapacke -lopenblas
++   SLIBS     += -Wl,-rpath=${OPENBLAS_ROOT}/lib/ -lopenblas
+   # dynamic linking
+   else
+-   DLIBS     += -Wl,-rpath=${OPENBLAS_ROOT}/lib/ -llapack -llapacke -lopenblas
++   DLIBS     += -Wl,-rpath=${OPENBLAS_ROOT}/lib/ -lopenblas -lgfortran
+   endif
+  endif
+ endif
+@@ -119,11 +119,10 @@
+ OBJECTS       = $(patsubst %.cpp,%.o,$(wildcard ./src/*.cpp))
+ 
+ PGEN_PATH     = ./external_libs/pgenlib/
+-INC          += -I${PGEN_PATH} -I${PGEN_PATH}/simde/ -I${PGEN_PATH}/include/ -I./external_libs/cxxopts/include/ -I./external_libs/LBFGSpp/include/ -I${BGEN_PATH} -I./external_libs/eigen-3.4.0/ -I${BGEN_PATH}/genfile/include/ -I${BGEN_PATH}/3rd_party/boost_1_55_0/ -I${BGEN_PATH}/3rd_party/zstd-1.1.0/lib -I${BGEN_PATH}/db/include/ -I${BGEN_PATH}/3rd_party/sqlite3 -I./external_libs/
++INC          += -I${PGEN_PATH} -I${PGEN_PATH}/simde/ -I${PGEN_PATH}/include/ -I./external_libs/cxxopts/include/ -I./external_libs/LBFGSpp/include/ -I./external_libs/eigen-3.4.0/ -I${BGEN_PATH}/include/ -I${BOOST}/include -I./external_libs/
+ 
+-LPATHS       += ${LIBMKL} -L${BGEN_PATH}/build/ -L${BGEN_PATH}/build/3rd_party/zstd-1.1.0/ -L${BGEN_PATH}/build/db/ -L${BGEN_PATH}/build/3rd_party/sqlite3/ -L${BGEN_PATH}/build/3rd_party/boost_1_55_0 -L/usr/lib/
+ 
+-LIBS         += ${SLIBS} -lbgen -lzstd -ldb  -lsqlite3 -lboost
++LIBS         += ${SLIBS} -lbgen -lzstd -ldb  -lsqlite3 -lboost_system -lboost_filesystem -lboost_thread -lboost_timer
+ LIBS         += -lz ${DLIBS} -lm -ldl -lgfortran
+ 
+ 

From f1b3396edbfe16fba1d4f55cc65b6682a6e1e699 Mon Sep 17 00:00:00 2001
From: fizwit <john@fuzzdog.com>
Date: Tue, 12 Jul 2022 15:08:55 -0700
Subject: [PATCH 002/835] bump version

---
 ...ie-3.1.1-GCC-11.2.0.eb => Regenie-3.1.2-GCC-11.2.0.eb} | 8 +++++---
 ...-3.1.1_Makefile.patch => regenie-3.1.2_Makefile.patch} | 0
 2 files changed, 5 insertions(+), 3 deletions(-)
 rename easybuild/easyconfigs/r/Regenie/{Regenie-3.1.1-GCC-11.2.0.eb => Regenie-3.1.2-GCC-11.2.0.eb} (84%)
 rename easybuild/easyconfigs/r/Regenie/{regenie-3.1.1_Makefile.patch => regenie-3.1.2_Makefile.patch} (100%)

diff --git a/easybuild/easyconfigs/r/Regenie/Regenie-3.1.1-GCC-11.2.0.eb b/easybuild/easyconfigs/r/Regenie/Regenie-3.1.2-GCC-11.2.0.eb
similarity index 84%
rename from easybuild/easyconfigs/r/Regenie/Regenie-3.1.1-GCC-11.2.0.eb
rename to easybuild/easyconfigs/r/Regenie/Regenie-3.1.2-GCC-11.2.0.eb
index 7f008d0c180..09b2ac462d6 100644
--- a/easybuild/easyconfigs/r/Regenie/Regenie-3.1.1-GCC-11.2.0.eb
+++ b/easybuild/easyconfigs/r/Regenie/Regenie-3.1.2-GCC-11.2.0.eb
@@ -6,7 +6,7 @@
 easyblock = 'MakeCp'
 
 name = 'Regenie'
-version = '3.1.1'
+version = '3.1.2'
 
 homepage = 'https://rgcgithub.github.io/regenie'
 description = """Regenie is a C++ program for whole genome regression modelling of large genome-wide 
@@ -17,8 +17,10 @@ toolchain = {'name': 'GCC', 'version': '11.2.0'}
 source_urls = ['https://github.com/rgcgithub/regenie/archive/']
 sources = ['v%(version)s.tar.gz']
 patches = ['%(namelower)s-%(version)s_Makefile.patch']
-
-checksums = []
+checksums = [
+    'b2e5e98bb310d9b9071ae5c63c5207be853bb1ec7918574e1acfdd0c83e744ff',  # v3.1.2.tar.gz
+    '8be5d4b3b237d7a1820727061227857770554970aa136da614b71c14767e655e',  # regenie-3.1.2_Makefile.patch
+]
 
 dependencies = [
     ('Boost', '1.55.0'),
diff --git a/easybuild/easyconfigs/r/Regenie/regenie-3.1.1_Makefile.patch b/easybuild/easyconfigs/r/Regenie/regenie-3.1.2_Makefile.patch
similarity index 100%
rename from easybuild/easyconfigs/r/Regenie/regenie-3.1.1_Makefile.patch
rename to easybuild/easyconfigs/r/Regenie/regenie-3.1.2_Makefile.patch

From 96250473b1efa8111780f9116b26a8308f038757 Mon Sep 17 00:00:00 2001
From: Simon Pinches <Simon.Pinches@iter.org>
Date: Thu, 27 Apr 2023 15:26:07 +0200
Subject: [PATCH 003/835] adding easyconfigs: pygmo-2.19.5-foss-2022b.eb,
 pagmo-2.19.0-foss-2022b.eb

---
 .../p/pagmo/pagmo-2.19.0-foss-2022b.eb        | 36 ++++++++++++
 .../p/pygmo/pygmo-2.19.5-foss-2022b.eb        | 58 +++++++++++++++++++
 2 files changed, 94 insertions(+)
 create mode 100644 easybuild/easyconfigs/p/pagmo/pagmo-2.19.0-foss-2022b.eb
 create mode 100644 easybuild/easyconfigs/p/pygmo/pygmo-2.19.5-foss-2022b.eb

diff --git a/easybuild/easyconfigs/p/pagmo/pagmo-2.19.0-foss-2022b.eb b/easybuild/easyconfigs/p/pagmo/pagmo-2.19.0-foss-2022b.eb
new file mode 100644
index 00000000000..c497bd406af
--- /dev/null
+++ b/easybuild/easyconfigs/p/pagmo/pagmo-2.19.0-foss-2022b.eb
@@ -0,0 +1,36 @@
+easyblock = 'CMakeMake'
+
+name = 'pagmo'
+version = '2.19.0'
+
+homepage = 'https://esa.github.io/pagmo2'
+description = "pagmo is a C++ scientific library for massively parallel optimization."
+
+toolchain = {'name': 'foss', 'version': '2022b'}
+toolchainopts = {'usempi': True}
+
+source_urls = ['https://github.com/esa/pagmo2/archive/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['701ada528de7d454201e92a5d88903dd1c22ea64f43861d9694195ddfef82a70']
+
+builddependencies = [
+    ('CMake', '3.24.3'),
+]
+
+dependencies = [
+    ('Boost', '1.81.0'),
+    ('tbb', '2021.9.0'),
+    ('Eigen', '3.4.0'),
+    ('NLopt', '2.7.1'),
+]
+
+configopts = "-DPAGMO_WITH_EIGEN3=ON -DPAGMO_WITH_NLOPT=ON -DPAGMO_BUILD_TESTS=ON"
+
+runtest = 'test'
+
+sanity_check_paths = {
+    'files': ['lib/libpagmo.%s' % SHLIB_EXT],
+    'dirs': ['include/pagmo', 'lib/cmake/pagmo'],
+}
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/p/pygmo/pygmo-2.19.5-foss-2022b.eb b/easybuild/easyconfigs/p/pygmo/pygmo-2.19.5-foss-2022b.eb
new file mode 100644
index 00000000000..f6b56bc229a
--- /dev/null
+++ b/easybuild/easyconfigs/p/pygmo/pygmo-2.19.5-foss-2022b.eb
@@ -0,0 +1,58 @@
+easyblock = 'CMakePythonPackage'
+
+name = 'pygmo'
+version = '2.19.5'
+
+homepage = 'https://esa.github.io/pygmo2'
+description = "pygmo is a scientific Python library for massively parallel optimization."
+
+toolchain = {'name': 'foss', 'version': '2022b'}
+
+source_urls = ['https://github.com/esa/pygmo2/archive/refs/tags/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['742ff0c3d535cb2af94d5095968d8f29c23ed7bdbd4ddd8259ca787eef881aa2']
+
+builddependencies = [
+    ('CMake', '3.24.3'),
+    ('pybind11', '2.10.3'),
+]
+
+dependencies = [
+    ('Python', '3.10.8'),
+    ('SciPy-bundle', '2023.02'),
+    ('Boost', '1.81.0'),
+    ('pagmo', '2.19.0'),
+    ('matplotlib', '3.7.0'),
+    ('networkx', '3.0'),
+]
+
+# make sure that all files are installed in the correct location (-DCMAKE_INSTALL_PREFIX is not enough)...
+configopts = "-DPYGMO_INSTALL_PATH=%(installdir)s/lib/python%(pyshortver)s/site-packages"
+
+runtest = False
+
+exts_defaultclass = 'PythonPackage'
+
+exts_default_options = {
+    'source_urls': [PYPI_SOURCE],
+    'download_dep_fail': True,
+    'use_pip': True,
+}
+
+exts_list = [
+    ('cloudpickle', '2.2.1', {
+        'checksums': ['d89684b8de9e34a2a43b3460fbca07d09d6e25ce858df4d5a44240403b6178f5'],
+    }),
+    ('dill', '0.3.6', {
+        'checksums': ['e5db55f3687856d8fbdab002ed78544e1c4559a130302693d839dfe8f93f2373'],
+    }),
+]
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['lib/python%(pyshortver)s/site-packages/pygmo'],
+}
+
+sanity_pip_check = True
+
+moduleclass = 'lib'

From 517ab5c28c7614af843a788eeb5b5f866509d898 Mon Sep 17 00:00:00 2001
From: Simon Pinches <Simon.Pinches@iter.org>
Date: Thu, 27 Apr 2023 15:52:21 +0200
Subject: [PATCH 004/835] tbb/2021.9.0 for GCCcore/12.2.0

---
 .../t/tbb/tbb-2021.9.0-GCCcore-12.2.0.eb      | 32 +++++++++++++++++++
 1 file changed, 32 insertions(+)
 create mode 100644 easybuild/easyconfigs/t/tbb/tbb-2021.9.0-GCCcore-12.2.0.eb

diff --git a/easybuild/easyconfigs/t/tbb/tbb-2021.9.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/t/tbb/tbb-2021.9.0-GCCcore-12.2.0.eb
new file mode 100644
index 00000000000..1a7a522f8bf
--- /dev/null
+++ b/easybuild/easyconfigs/t/tbb/tbb-2021.9.0-GCCcore-12.2.0.eb
@@ -0,0 +1,32 @@
+easyblock = 'CMakeNinja'
+
+name = 'tbb'
+version = '2021.9.0'
+
+homepage = 'https://github.com/oneapi-src/oneTBB'
+description = """Intel(R) Threading Building Blocks (Intel(R) TBB) lets you easily write parallel C++ programs that
+ take full advantage of multicore performance, that are portable, composable and have future-proof scalability."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+toolchainopts = {'cstd': 'c++11'}
+
+source_urls = ['https://github.com/oneapi-src/oneTBB/archive/refs/tags/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['1ce48f34dada7837f510735ff1172f6e2c261b09460e3bf773b49791d247d24e']
+
+builddependencies = [
+    ('binutils', '2.39'),
+    ('CMake', '3.24.3'),
+    ('Ninja', '1.11.1'),
+]
+
+dependencies = [('hwloc', '2.8.0')]
+
+configopts = '-DTBB_TEST=OFF '
+
+sanity_check_paths = {
+    'files': ['lib/libtbb.%s' % SHLIB_EXT, 'lib/libtbbmalloc.%s' % SHLIB_EXT],
+    'dirs': ['lib', 'include', 'share'],
+}
+
+moduleclass = 'lib'

From 0814b6de499c16825ce01d046a99d5a773386bda Mon Sep 17 00:00:00 2001
From: eylenbt <eylenbt@by0owl.eu.seeds.basf.net>
Date: Thu, 15 Jun 2023 12:12:15 +0200
Subject: [PATCH 005/835] adding easyconfigs: Bowtie-1.3.1-GCC-12.2.0.eb

---
 .../b/Bowtie/Bowtie-1.3.1-GCC-12.2.0.eb       | 30 +++++++++++++++++++
 1 file changed, 30 insertions(+)
 create mode 100644 easybuild/easyconfigs/b/Bowtie/Bowtie-1.3.1-GCC-12.2.0.eb

diff --git a/easybuild/easyconfigs/b/Bowtie/Bowtie-1.3.1-GCC-12.2.0.eb b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.3.1-GCC-12.2.0.eb
new file mode 100644
index 00000000000..202b84a2953
--- /dev/null
+++ b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.3.1-GCC-12.2.0.eb
@@ -0,0 +1,30 @@
+##
+# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia
+# Homepage: 	https://staff.flinders.edu.au/research/deep-thought
+#
+# Authors::	Robert Qiao <rob.qiao@flinders.edu.au>
+# License::	Artistic v2.0
+#
+# Notes::
+##
+
+name = 'Bowtie'
+version = '1.3.1'
+
+homepage = 'http://bowtie-bio.sourceforge.net/index.shtml'
+description = """Bowtie is an ultrafast, memory-efficient short read aligner.
+ It aligns short DNA sequences (reads) to the human genome."""
+
+toolchain = {'name': 'GCC', 'version': '12.2.0'}
+toolchainopts = {'pic': True, 'cstd': 'gnu++98'}
+
+source_urls = ['https://sourceforge.net/projects/bowtie-bio/files/bowtie/%(version)s/']
+sources = ['%(namelower)s-%(version)s-src.zip']
+checksums = ['e23517aa53846ef828172be911750cd05748522117efcbbe5a36f3241fb40761']
+
+dependencies = [
+    ('tbb', '2021.9.0'),
+    ('zlib', '1.2.12'),
+]
+
+moduleclass = 'bio'

From a87884ef98f776bbc1ef5d289aa5d406ca5ba7ca Mon Sep 17 00:00:00 2001
From: Simon Pinches <Simon.Pinches@iter.org>
Date: Sat, 24 Jun 2023 18:15:06 +0200
Subject: [PATCH 006/835] pagmo,pygmo: foss/2022b -> gfbf/2022b; tbb: Ninja ->
 CMakeMake

---
 ...{pagmo-2.19.0-foss-2022b.eb => pagmo-2.19.0-gfbf-2022b.eb} | 3 +--
 ...{pygmo-2.19.5-foss-2022b.eb => pygmo-2.19.5-gfbf-2022b.eb} | 2 +-
 easybuild/easyconfigs/t/tbb/tbb-2021.9.0-GCCcore-12.2.0.eb    | 4 +---
 3 files changed, 3 insertions(+), 6 deletions(-)
 rename easybuild/easyconfigs/p/pagmo/{pagmo-2.19.0-foss-2022b.eb => pagmo-2.19.0-gfbf-2022b.eb} (90%)
 rename easybuild/easyconfigs/p/pygmo/{pygmo-2.19.5-foss-2022b.eb => pygmo-2.19.5-gfbf-2022b.eb} (96%)

diff --git a/easybuild/easyconfigs/p/pagmo/pagmo-2.19.0-foss-2022b.eb b/easybuild/easyconfigs/p/pagmo/pagmo-2.19.0-gfbf-2022b.eb
similarity index 90%
rename from easybuild/easyconfigs/p/pagmo/pagmo-2.19.0-foss-2022b.eb
rename to easybuild/easyconfigs/p/pagmo/pagmo-2.19.0-gfbf-2022b.eb
index c497bd406af..6f64905045c 100644
--- a/easybuild/easyconfigs/p/pagmo/pagmo-2.19.0-foss-2022b.eb
+++ b/easybuild/easyconfigs/p/pagmo/pagmo-2.19.0-gfbf-2022b.eb
@@ -6,8 +6,7 @@ version = '2.19.0'
 homepage = 'https://esa.github.io/pagmo2'
 description = "pagmo is a C++ scientific library for massively parallel optimization."
 
-toolchain = {'name': 'foss', 'version': '2022b'}
-toolchainopts = {'usempi': True}
+toolchain = {'name': 'gfbf', 'version': '2022b'}
 
 source_urls = ['https://github.com/esa/pagmo2/archive/']
 sources = ['v%(version)s.tar.gz']
diff --git a/easybuild/easyconfigs/p/pygmo/pygmo-2.19.5-foss-2022b.eb b/easybuild/easyconfigs/p/pygmo/pygmo-2.19.5-gfbf-2022b.eb
similarity index 96%
rename from easybuild/easyconfigs/p/pygmo/pygmo-2.19.5-foss-2022b.eb
rename to easybuild/easyconfigs/p/pygmo/pygmo-2.19.5-gfbf-2022b.eb
index f6b56bc229a..20109f00554 100644
--- a/easybuild/easyconfigs/p/pygmo/pygmo-2.19.5-foss-2022b.eb
+++ b/easybuild/easyconfigs/p/pygmo/pygmo-2.19.5-gfbf-2022b.eb
@@ -6,7 +6,7 @@ version = '2.19.5'
 homepage = 'https://esa.github.io/pygmo2'
 description = "pygmo is a scientific Python library for massively parallel optimization."
 
-toolchain = {'name': 'foss', 'version': '2022b'}
+toolchain = {'name': 'gfbf', 'version': '2022b'}
 
 source_urls = ['https://github.com/esa/pygmo2/archive/refs/tags/']
 sources = ['v%(version)s.tar.gz']
diff --git a/easybuild/easyconfigs/t/tbb/tbb-2021.9.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/t/tbb/tbb-2021.9.0-GCCcore-12.2.0.eb
index 1a7a522f8bf..68c8f42e14c 100644
--- a/easybuild/easyconfigs/t/tbb/tbb-2021.9.0-GCCcore-12.2.0.eb
+++ b/easybuild/easyconfigs/t/tbb/tbb-2021.9.0-GCCcore-12.2.0.eb
@@ -1,4 +1,4 @@
-easyblock = 'CMakeNinja'
+easyblock = 'CMakeMake'
 
 name = 'tbb'
 version = '2021.9.0'
@@ -8,7 +8,6 @@ description = """Intel(R) Threading Building Blocks (Intel(R) TBB) lets you easi
  take full advantage of multicore performance, that are portable, composable and have future-proof scalability."""
 
 toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
-toolchainopts = {'cstd': 'c++11'}
 
 source_urls = ['https://github.com/oneapi-src/oneTBB/archive/refs/tags/']
 sources = ['v%(version)s.tar.gz']
@@ -17,7 +16,6 @@ checksums = ['1ce48f34dada7837f510735ff1172f6e2c261b09460e3bf773b49791d247d24e']
 builddependencies = [
     ('binutils', '2.39'),
     ('CMake', '3.24.3'),
-    ('Ninja', '1.11.1'),
 ]
 
 dependencies = [('hwloc', '2.8.0')]

From 929f42a244690ac950294cd0a95351d960fcb4da Mon Sep 17 00:00:00 2001
From: Stefan Wolfsheimer <stefan.wolfsheimer@surf.nl>
Date: Thu, 7 Sep 2023 18:46:25 +0200
Subject: [PATCH 007/835] adding easyconfigs: WRF-4.5.1-foss-2023a-dmpar.eb and
 patches: WRF-4.5.1_netCDF-Fortran_separate_path.patch

---
 .../w/WRF/WRF-4.5.1-foss-2023a-dmpar.eb       |  51 +++
 ...F-4.5.1_netCDF-Fortran_separate_path.patch | 298 ++++++++++++++++++
 2 files changed, 349 insertions(+)
 create mode 100644 easybuild/easyconfigs/w/WRF/WRF-4.5.1-foss-2023a-dmpar.eb
 create mode 100644 easybuild/easyconfigs/w/WRF/WRF-4.5.1_netCDF-Fortran_separate_path.patch

diff --git a/easybuild/easyconfigs/w/WRF/WRF-4.5.1-foss-2023a-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-4.5.1-foss-2023a-dmpar.eb
new file mode 100644
index 00000000000..04ca4736994
--- /dev/null
+++ b/easybuild/easyconfigs/w/WRF/WRF-4.5.1-foss-2023a-dmpar.eb
@@ -0,0 +1,51 @@
+name = 'WRF'
+version = '4.5.1'
+buildtype = 'dmpar'
+versionsuffix = '-%s' % buildtype
+
+homepage = 'https://www.wrf-model.org'
+description = """The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale
+ numerical weather prediction system designed to serve both operational forecasting and atmospheric
+ research needs."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+toolchainopts = {'opt': False}  # don't use agressive optimization, stick to -O2
+
+source_urls = ['https://github.com/wrf-model/WRF/archive/']
+# sources = ['v%(version)s.tar.gz']
+sources = [{
+    'filename': 'v%(version)s.tar.gz',
+    'git_config': {
+        'url': 'https://github.com/wrf-model',
+        'repo_name': 'WRF',
+        'tag': 'v%(version)s',
+        'clone_into': 'WRF-%(version)s',
+        'recursive': True,
+    },
+}]
+patches = [
+    'WRF-4.5.1_netCDF-Fortran_separate_path.patch',
+]
+checksums = [
+    '9d557c34c105db4d41e727843ecb19199233c7cf82c5369b34a2ce8efe65e2d1',  # v4.5.1.tar.gz
+    '3cc30b1dca275719a1bcfa4fb911c25baaa943456e2d57a4e3fc34842929629b',  # WRF-5.1_netCDF-Fortran_separate_path.patch
+]
+
+# csh is used by WRF install scripts
+builddependencies = [
+    ('Autotools', '20220317'),
+    ('tcsh', '6.24.10'),
+    ('time', '1.9'),
+    ('Perl', '5.36.1'),
+]
+
+dependencies = [
+    ('JasPer', '4.0.0'),
+    ('netCDF', '4.9.2'),
+    ('netCDF-Fortran', '4.6.1'),
+]
+
+# limit parallel build to 20
+maxparallel = 20
+
+moduleclass = 'geo'
diff --git a/easybuild/easyconfigs/w/WRF/WRF-4.5.1_netCDF-Fortran_separate_path.patch b/easybuild/easyconfigs/w/WRF/WRF-4.5.1_netCDF-Fortran_separate_path.patch
new file mode 100644
index 00000000000..ac5c261db07
--- /dev/null
+++ b/easybuild/easyconfigs/w/WRF/WRF-4.5.1_netCDF-Fortran_separate_path.patch
@@ -0,0 +1,298 @@
+# Allow netCDF library with separate directories for C and Fortran
+# ============================================================================
+# This patch has been around in EasyBuild since WRF3.5; it was committed by
+# @boegel then.  Adapted by @andreas-h to accomodate WRFv4 and foss toolchain
+#
+# updated for WPS v4.4 by Maxim Masterov (SURF)
+# updated for WRF v4.5.1 by Stefan Wolfsheimer (SURF)
+
+
+diff -Nru WRFV4.5.1.orig/arch/Config.pl WRFV4.5.1/arch/Config.pl
+--- WRFV4.5.1.orig/arch/Config.pl	2023-07-25 23:14:55.214200451 +0200
++++ WRFV4.5.1/arch/Config.pl	2023-09-07 18:29:05.423831752 +0200
+@@ -11,6 +11,7 @@
+ select((select(STDOUT), $|=1)[0]);
+ $sw_perl_path = perl ;
+ $sw_netcdf_path = "" ;
++$sw_netcdff_path = "" ;
+ $sw_pnetcdf_path = "" ;
+ $sw_netcdfpar_path = "" ;
+ $sw_adios2_path = "" ;
+@@ -96,6 +97,10 @@
+           }
+       }
+   }
++  if ( substr( $ARGV[0], 1, 8 ) eq "netcdff=" )
++  {
++      $sw_netcdff_path = substr( $ARGV[0], 9 ) ;
++  }
+   if ( substr( $ARGV[0], 1, 8 ) eq "pnetcdf=" )
+   {
+     $sw_pnetcdf_path = substr( $ARGV[0], 9 ) ;
+@@ -130,7 +135,8 @@
+   }
+   if ( substr( $ARGV[0], 1, 11 ) eq "USENETCDFF=" )
+   {
+-    $sw_usenetcdff = substr( $ARGV[0], 12 ) ;
++     $sw_usenetcdff = substr( $ARGV[0], 12 ) ;
++     $sw_usenetcdff =~ s/!/ /g ;
+   }
+   if ( substr( $ARGV[0], 1, 10 ) eq "USENETCDF=" )
+   {
+@@ -615,6 +621,7 @@
+   {
+     $_ =~ s/CONFIGURE_PERL_PATH/$sw_perl_path/g ;
+     $_ =~ s/CONFIGURE_NETCDF_PATH/$sw_netcdf_path/g ;
++    $_ =~ s/CONFIGURE_NETCDFF_PATH/$sw_netcdff_path/g ;
+     $_ =~ s/CONFIGURE_PNETCDF_PATH/$sw_pnetcdf_path/g ;
+     $_ =~ s/CONFIGURE_NETCDFPAR_PATH/$sw_netcdfpar_path/g ;
+     $_ =~ s/CONFIGURE_ADIOS2_PATH/$sw_adios2_path/g ;
+@@ -666,7 +673,7 @@
+         } elsif ( $sw_os eq "Interix" ) {
+           $_ =~ s:CONFIGURE_NETCDFPAR_LIB_PATH:\$\(WRF_SRC_ROOT_DIR\)/external/io_netcdfpar/libwrfio_nfpar.a -L$sw_netcdfpar_path/lib $sw_usenetcdff $sw_usenetcdf : ;
+         } else {
+-          $_ =~ s:CONFIGURE_NETCDFPAR_LIB_PATH:-L\$\(WRF_SRC_ROOT_DIR\)/external/io_netcdfpar -lwrfio_nfpar -L$sw_netcdfpar_path/lib $sw_usenetcdff $sw_usenetcdf : ;
++	  $_ =~ s:CONFIGURE_NETCDFPAR_LIB_PATH:-L\$\(WRF_SRC_ROOT_DIR\)/external/io_netcdfpar -lwrfio_nfpar -L$sw_netcdfpar_path/lib $sw_usenetcdff $sw_usenetcdf : ;
+         }
+          }
+     else
+@@ -684,7 +691,7 @@
+         } elsif ( $sw_os eq "Interix" ) {
+ 	  $_ =~ s:CONFIGURE_NETCDF_LIB_PATH:\$\(WRF_SRC_ROOT_DIR\)/external/io_netcdf/libwrfio_nf.a -L$sw_netcdf_path/lib $sw_usenetcdff $sw_usenetcdf : ;
+         } else {
+-	  $_ =~ s:CONFIGURE_NETCDF_LIB_PATH:-L\$\(WRF_SRC_ROOT_DIR\)/external/io_netcdf -lwrfio_nf -L$sw_netcdf_path/lib $sw_usenetcdff $sw_usenetcdf : ;
++	  $_ =~ s:CONFIGURE_NETCDF_LIB_PATH:-L\$\(WRF_SRC_ROOT_DIR\)/external/io_netcdf -lwrfio_nf -L$sw_netcdff_path/lib -L$sw_netcdf_path/lib64 $sw_usenetcdff $sw_usenetcdf : ;
+         }
+ 	 }
+     else                   
+@@ -1072,7 +1079,7 @@
+         } elsif ( $sw_os eq "Interix" ) {
+ 	  $_ =~ s:CONFIGURE_NETCDF_LIB_PATH:\$\(WRF_SRC_ROOT_DIR\)/external/io_netcdf/libwrfio_nf.a -L$sw_netcdf_path/lib $sw_usenetcdff $sw_usenetcdf : ;
+         } else {
+-	  $_ =~ s:CONFIGURE_NETCDF_LIB_PATH:-L\$\(WRF_SRC_ROOT_DIR\)/external/io_netcdf -lwrfio_nf -L$sw_netcdf_path/lib $sw_usenetcdff $sw_usenetcdf : ;
++	  $_ =~ s:CONFIGURE_NETCDF_LIB_PATH:-L\$\(WRF_SRC_ROOT_DIR\)/external/io_netcdf -lwrfio_nf -L$sw_netcdff_path/lib -L$sw_netcdf_path/lib $sw_usenetcdff $sw_usenetcdf : ;
+         }
+ 	 }
+     else
+diff -Nru WRFV4.5.1.orig/arch/configure.defaults WRFV4.5.1/arch/configure.defaults
+--- WRFV4.5.1.orig/arch/configure.defaults	2023-07-25 23:14:55.215890637 +0200
++++ WRFV4.5.1/arch/configure.defaults	2023-09-07 14:20:06.651406753 +0200
+@@ -1638,6 +1638,7 @@
+ 
+ LIB_EXTERNAL    = \
+                      ../external/io_netcdf/libwrfio_nf.a CONFIGURE_NETCDF_PATH/lib/libnetcdf.lib \
++                     CONFIGURE_NETCDFF_PATH/lib/libnetcdff.lib \
+                      ../external/wavelet/libWavelet.a ../external/wavelet/lib_wavelet.a
+ ESMF_IO_LIB     =    ../external/esmf_time_f90/libesmf_time.a
+ LIB_BUNDLED     = \
+diff -Nru WRFV4.5.1.orig/arch/conf_tokens WRFV4.5.1/arch/conf_tokens
+--- WRFV4.5.1.orig/arch/conf_tokens	2023-07-25 23:14:55.215165000 +0200
++++ WRFV4.5.1/arch/conf_tokens	2023-09-07 14:20:50.194754577 +0200
+@@ -5,6 +5,7 @@
+        CONFIGURE_DMPARALLEL
+ CONFIGURE_RWORDSIZE
+ CONFIGURE_NETCDF_FLAG
++CONFIGURE_NETCDFF_FLAG
+ CONFIGURE_GRIB2_FLAG
+ CONFIGURE_NETCDF_LIB_PATH
+ CONFIGURE_GRIB2_LIB
+@@ -13,4 +14,5 @@
+ CONFIGURE_WRFIO_NF 
+ CONFIGURE_WRFIO_GRIB2 
+ CONFIGURE_NETCDF_PATH
++CONFIGURE_NETCDFF_PATH
+ CONFIGURE_GRIB2_INC
+diff -Nru WRFV4.5.1.orig/arch/postamble WRFV4.5.1/arch/postamble
+--- WRFV4.5.1.orig/arch/postamble	2023-07-25 23:14:55.219090000 +0200
++++ WRFV4.5.1/arch/postamble	2023-09-07 16:01:17.500706228 +0200
+@@ -54,6 +54,7 @@
+                       -I$(WRF_SRC_ROOT_DIR)/phys \
+                       -I$(WRF_SRC_ROOT_DIR)/wrftladj \
+                       -I$(WRF_SRC_ROOT_DIR)/chem -I$(WRF_SRC_ROOT_DIR)/inc \
++                      -I$(NETCDFPATH)/include -I$(NETCDFFPATH)/include \
+                       -I$(NETCDFPATH)/include \
+                       CONFIGURE_RTTOV_INC CONFIGURE_CTSM_INC
+ REGISTRY        =    Registry
+@@ -64,6 +65,7 @@
+ ENVCOMPDEFS     =    CONFIGURE_COMPILEFLAGS
+ CPPFLAGS        =    $(ARCHFLAGS) $(ENVCOMPDEFS) -I$(LIBINCLUDE) $(TRADFLAG) CONFIGURE_COMMS_INCLUDE
+ NETCDFPATH      =    CONFIGURE_NETCDF_PATH
++NETCDFFPATH     =    CONFIGURE_NETCDFF_PATH
+ HDF5PATH        =    CONFIGURE_HDF5_PATH
+ WRFPLUSPATH     =    CONFIGURE_WRFPLUS_PATH
+ RTTOVPATH       =    CONFIGURE_RTTOV_PATH
+@@ -96,18 +98,18 @@
+ 
+ wrfio_nf : 
+ 	( cd $(WRF_SRC_ROOT_DIR)/external/io_netcdf ; \
+-          make $(J) NETCDFPATH="$(NETCDFPATH)" RANLIB="$(RANLIB)" CPP="$(CPP)" \
++          make $(J) NETCDFPATH="$(NETCDFPATH)" NETCDFFPATH="$(NETCDFFPATH)" RANLIB="$(RANLIB)" CPP="$(CPP)" \
+           CC="$(SCC)" CFLAGS="$(CFLAGS)" \
+           FC="$(SFC) $(PROMOTION) $(OMP) $(FCFLAGS)" TRADFLAG="$(TRADFLAG)" AR="$(AR)" ARFLAGS="$(ARFLAGS)" )
+ 
+ wrfio_nfpar : 
+ 	( cd $(WRF_SRC_ROOT_DIR)/external/io_netcdfpar ; \
+-          make $(J) NETCDFPARPATH="$(NETCDFPATH)" RANLIB="$(RANLIB)" CPP="$(CPP) $(ARCHFLAGS)" \
++          make $(J) NETCDFPARPATH="$(NETCDFPATH)" NETCDFFPATH="$(NETCDFFPATH)" RANLIB="$(RANLIB)" CPP="$(CPP) $(ARCHFLAGS)" \
+           FC="$(FC) $(PROMOTION) $(OMP) $(FCFLAGS)" TRADFLAG="$(TRADFLAG)" AR="$(AR)" ARFLAGS="$(ARFLAGS)" )
+ 
+ wrfio_pnf : 
+ 	( cd $(WRF_SRC_ROOT_DIR)/external/io_pnetcdf ; \
+-          make $(J) NETCDFPATH="$(PNETCDFPATH)" RANLIB="$(RANLIB)" CPP="$(CPP) $(ARCHFLAGS)" \
++          make $(J) NETCDFPATH="$(PNETCDFPATH)" NETCDFFPATH="$(PNETCDFPATH)" RANLIB="$(RANLIB)" CPP="$(CPP) $(ARCHFLAGS)" \
+           FC="$(FC) $(PROMOTION) $(OMP) $(FCFLAGS)" TRADFLAG="$(TRADFLAG)" AR="$(AR)" ARFLAGS="$(ARFLAGS)" )
+ 
+ wrfio_adios2 : 
+diff -Nru WRFV4.5.1.orig/configure WRFV4.5.1/configure
+--- WRFV4.5.1.orig/configure	2023-07-25 23:14:55.692864209 +0200
++++ WRFV4.5.1/configure	2023-09-07 14:30:41.177727094 +0200
+@@ -214,7 +214,11 @@
+   unset NETCDF4
+ fi
+ 
+-USENETCDFF=""
++if [ -f "$NETCDFF/lib/libnetcdff.a" -o -f "$NETCDFF/lib/libnetcdff.so" -o -f "$NETCDFF/lib64/libnetcdff.so" -o -f "$NETCDFF/lib64/libnetcdff.so" ] ; then
++    USENETCDFF="-L$NETCDFF/lib!-L$NETCDFF/lib64!-lnetcdff" # ! will be replaced with space
++else
++    USENETCDFF=" "
++fi
+ USENETCDF=""
+ if [ -n "$NETCDF" ] ; then
+   echo "Will use NETCDF in dir: $NETCDF"
+@@ -224,7 +228,7 @@
+   else
+     USENETCDFF=" "
+   fi
+-  if [ -f "$NETCDF/lib/libnetcdf.a" -o -f "$NETCDF/lib/libnetcdf.so" -o -f "$NETCDF/lib/libnetcdf.dll.a" ] ; then
++  if [ -f "$NETCDF/lib/libnetcdf.a" -o -f "$NETCDF/lib/libnetcdf.so" -o -f "$NETCDF/lib64/libnetcdf.a" -o -f "$NETCDF/lib64/libnetcdf.so" ] ; then
+     USENETCDF="-lnetcdf"
+   else
+     USENETCDF=" "
+@@ -572,7 +576,7 @@
+    srch=`grep -i "^#ARCH.*$os" arch/configure.defaults | grep -i "$mach"`
+    if [ -n "$srch" ] ; then
+      $PERL arch/Config.pl -dmparallel=$COMMLIB -ompparallel=$OMP -perl=$PERL \
+-          -netcdf=$NETCDF -pnetcdf=$PNETCDF -netcdfpar=$NETCDFPAR -adios2=$ADIOS2 -hdf5=$HDF5 -phdf5=$PHDF5 -os=$os -mach=$mach -ldflags=$ldflags \
++          -netcdf=$NETCDF -netcdff=$NETCDFF -pnetcdf=$PNETCDF -netcdfpar=$NETCDFPAR -hdf5=$HDF5 -phdf5=$PHDF5 -os=$os -mach=$mach -ldflags=$ldflags \
+           -compileflags=$compileflags -opt_level=$opt_level -USENETCDFF=$USENETCDFF -USENETCDF=$USENETCDF \
+           -time=$FORTRAN_COMPILER_TIMER -tfl="$TFL" -cfl="$CFL" -config_line="$config_line" \
+           -wrf_core=$wrf_core -gpfs=$GPFS_PATH -curl=$CURL_PATH -dep_lib_path="$DEP_LIB_PATH"
+@@ -654,14 +658,14 @@
+ echo "If you wish to change the default options, edit the file:"
+ echo "     arch/configure.defaults"
+ 
+-if test -n "$NETCDF" ; then
+-  if [ ! -f $NETCDF/include/netcdf.inc ] ; then
++if test -n "$NETCDFF" ; then
++  if [ ! -f $NETCDFF/include/netcdf.inc ] ; then
+     echo
+-    echo "Error : Not found $NETCDF/include/netcdf.inc"
++    echo "Error : Not found $NETCDFF/include/netcdf.inc"
+     echo "        Please check this installation of NetCDF and re-run this configure script"
+     exit -1
+   fi
+-  grep nf_format_64bit $NETCDF/include/netcdf.inc > /dev/null
++  grep nf_format_64bit $NETCDFF/include/netcdf.inc > /dev/null
+   configure_aaaa=$? ; export configure_aaaa
+   if [ $configure_aaaa -a -z "$WRFIO_NCD_NO_LARGE_FILE_SUPPORT" ] ; then
+     echo "NetCDF users note:"
+diff -Nru WRFV4.5.1.orig/external/io_netcdf/makefile WRFV4.5.1/external/io_netcdf/makefile
+--- WRFV4.5.1.orig/external/io_netcdf/makefile	2023-07-25 23:14:55.935985000 +0200
++++ WRFV4.5.1/external/io_netcdf/makefile	2023-09-07 14:33:23.630405047 +0200
+@@ -3,9 +3,9 @@
+ OBJSL   = wrf_io.o field_routines.o module_wrfsi_static.o
+ OBJS    = $(OBJSL)
+ CODE    = ext_ncd_get_dom_ti.code ext_ncd_get_var_td.code ext_ncd_get_var_ti.code ext_ncd_put_dom_ti.code ext_ncd_put_var_td.code ext_ncd_put_var_ti.code transpose.code 
+-FFLAGS  =  $(FCFLAGS) -I$(NETCDFPATH)/include -I../ioapi_share
+-LIBS    = $(LIB_LOCAL) -L$(NETCDFPATH)/lib -lnetcdf
+-LIBFFS  = $(LIB_LOCAL) -L$(NETCDFPATH)/lib -lnetcdff -lnetcdf $(NETCDF4_DEP_LIB)
++FFLAGS  =  $(FCFLAGS) -I$(NETCDFFPATH)/include -I../ioapi_share
++LIBS    = $(LIB_LOCAL) -L$(NETCDFPATH)/lib -L$(NETCDFPATH)/lib64 -lnetcdf
++LIBFFS  = $(LIB_LOCAL) -L$(NETCDFPATH)/lib -L$(NETCDFPATH)/lib64 -L$(NETCDFFPATH)/lib -L$(NETCDFFPATH)/lib64 -lnetcdff -lnetcdf $(NETCDF4_DEP_LIB)
+ CPP1    = $(CPP) -P $(TRADFLAG)
+ M4      = m4 -Uinclude -Uindex -Ulen
+ AR      = ar
+@@ -24,7 +24,7 @@
+ 			$(RANLIB) $@
+ 
+ wrf_io.o:               wrf_io.F90 $(CODE)
+-			grep nf_format_64bit $(NETCDFPATH)/include/netcdf.inc ;\
++			grep nf_format_64bit $(NETCDFFPATH)/include/netcdf.inc ;\
+                         a=$$? ; export a ; \
+ 			if [ $$a -a "$$WRFIO_NCD_LARGE_FILE_SUPPORT" = "1" ] ; then \
+                           $(CPP1) -DWRFIO_NCD_LARGE_FILE_SUPPORT -I../ioapi_share wrf_io.F90 | $(M4) - > wrf_io.f ; \
+@@ -43,14 +43,14 @@
+ 	x=`echo "$(FC)" | awk '{print $$1}'` ; export x ; \
+ 	if [ $$x = "gfortran" ] ; then \
+            echo removing external declaration of iargc for gfortran ; \
+-	   $(CPP1) -I$(NETCDFPATH)/include -I../ioapi_share diffwrf.F90 | sed '/integer *, *external.*iargc/d' > diffwrf.f ;\
++	   $(CPP1) -I$(NETCDFFPATH)/include -I../ioapi_share diffwrf.F90 | sed '/integer *, *external.*iargc/d' > diffwrf.f ;\
+         else \
+-	   $(CPP1) -I$(NETCDFPATH)/include -I../ioapi_share diffwrf.F90 > diffwrf.f ; \
++	   $(CPP1) -I$(NETCDFFPATH)/include -I../ioapi_share diffwrf.F90 > diffwrf.f ; \
+         fi
+ 	$(FC) -c $(FFLAGS) diffwrf.f
+ 	@if [ \( -f ../../frame/wrf_debug.o \) -a \( -f ../../frame/module_wrf_error.o \) -a \( -f $(ESMF_MOD_DEPENDENCE) \) -a \( -f ../../frame/clog.o \) ] ; then \
+ 	  echo "diffwrf io_netcdf is being built now. " ; \
+-          if [ \( -f $(NETCDFPATH)/lib/libnetcdff.a -o -f $(NETCDFPATH)/lib/libnetcdff.so -o -f $(NETCDFPATH)/lib/libnetcdff.dll.a \) ] ; then \
++          if [ \( -f $(NETCDFFPATH)/lib/libnetcdff.a -o -f $(NETCDFFPATH)/lib/libnetcdff.so -o -f $(NETCDFFPATH)/lib/libnetcdff.dll.a \) ] ; then \
+             $(FC) $(FFLAGS) $(LDFLAGS) -o diffwrf diffwrf.o $(OBJSL) ../../frame/wrf_debug.o ../../frame/module_wrf_error.o ../../frame/clog.o $(ESMF_IO_LIB_EXT) $(LIBFFS) ;\
+           else \
+             $(FC) $(FFLAGS) $(LDFLAGS) -o diffwrf diffwrf.o $(OBJSL) ../../frame/wrf_debug.o ../../frame/module_wrf_error.o ../../frame/clog.o $(ESMF_IO_LIB_EXT) $(LIBS) ;\
+diff -Nru WRFV4.5.1.orig/external/io_pnetcdf/Makefile WRFV4.5.1/external/io_pnetcdf/Makefile
+--- WRFV4.5.1.orig/external/io_pnetcdf/Makefile	2023-07-25 23:14:55.952757000 +0200
++++ WRFV4.5.1/external/io_pnetcdf/Makefile	2023-09-07 14:34:31.077960575 +0200
+@@ -9,8 +9,8 @@
+ 	  ext_pnc_put_var_td.code \
+ 	  ext_pnc_put_var_ti.code \
+ 	  transpose.code 
+-FFLAGS  = $(FCFLAGS) -I$(NETCDFPATH)/include -I../ioapi_share
+-LIBS    = -L$(NETCDFPATH)/lib -lpnetcdf
++FFLAGS  = $(FCFLAGS) -I$(NETCDFFPATH)/include -I../ioapi_share
++LIBS    = -L$(NETCDFFPATH)/lib -lpnetcdf
+ CPP1    = $(CPP) -P $(TRADFLAG)
+ M4      = m4 -Uinclude -Uindex -Ulen
+ AR      = ar
+@@ -25,15 +25,15 @@
+ 			$(RANLIB) libwrfio_pnf.a
+ 
+ wrf_io.o:               wrf_io.F90 $(CODE)
+-			$(CPP1) -I$(NETCDFPATH)/include -I../ioapi_share wrf_io.F90 | $(M4) - > wrf_io.f
++			$(CPP1) -I$(NETCDFFPATH)/include -I../ioapi_share wrf_io.F90 | $(M4) - > wrf_io.f
+ 			$(FC) $(FFLAGS) -c wrf_io.f
+ 
+ module_wrfsi_static.o:  module_wrfsi_static.F90
+-			$(CPP1) -I$(NETCDFPATH)/include -I../ioapi_share module_wrfsi_static.F90 > module_wrfsi_static.f
++			$(CPP1) -I$(NETCDFFPATH)/include -I../ioapi_share module_wrfsi_static.F90 > module_wrfsi_static.f
+ 			$(FC) $(FFLAGS) -c module_wrfsi_static.f
+ 
+ field_routines.o:	field_routines.F90 wrf_io.o
+-			$(CPP1) -I$(NETCDFPATH)/include -I../ioapi_share field_routines.F90 > field_routines.f
++			$(CPP1) -I$(NETCDFFPATH)/include -I../ioapi_share field_routines.F90 > field_routines.f
+ 			$(FC) $(FFLAGS) -c field_routines.f
+ 
+ superclean:
+diff -Nru WRFV4.5.1.orig/Makefile WRFV4.5.1/Makefile
+--- WRFV4.5.1.orig/Makefile	2023-07-25 23:14:55.185289891 +0200
++++ WRFV4.5.1/Makefile	2023-09-07 14:36:58.707252929 +0200
+@@ -923,7 +923,7 @@
+ 	@ echo '--------------------------------------'
+ 	( cd frame ; $(MAKE) $(J) LLIST="$(LINKLIST)" framework ; \
+           cd ../external/io_netcdf ; \
+-          $(MAKE) NETCDFPATH="$(NETCDFPATH)" \
++          $(MAKE) NETCDFPATH="$(NETCDFPATH)" NETCDFFPATH="$(NETCDFFPATH)" \
+                FC="$(FC) $(FCBASEOPTS) $(PROMOTION) $(FCDEBUG) $(OMP)" RANLIB="$(RANLIB)" \
+                CPP="$(CPP)" LDFLAGS="$(LDFLAGS)" TRADFLAG="$(TRADFLAG)" ESMF_IO_LIB_EXT="$(ESMF_IO_LIB_EXT)" \
+                LIB_LOCAL="$(LIB_LOCAL)" \
+@@ -1070,9 +1070,9 @@
+ # rule used by configure to test if this will compile with netcdf4
+ nc4_test:
+ 	if [ $(USENETCDFPAR) -eq 0 ] ; then \
+-	 ( cd tools ; /bin/rm -f nc4_test.{exe,nc,o} ; $(SCC) -o nc4_test.exe nc4_test.c -I$(NETCDF)/include -L$(NETCDF)/lib -lnetcdf $(NETCDF4_DEP_LIB) ; cd .. ) ; \
++	 ( cd tools ; /bin/rm -f nc4_test.{exe,nc,o} ; $(SCC) -o nc4_test.exe nc4_test.c -I$(NETCDF)/include -L$(NETCDF)/lib64 -lnetcdf $(NETCDF4_DEP_LIB) ; cd .. ) ; \
+ 	else \
+-	 ( cd tools ; /bin/rm -f nc4_test.{exe,nc,o} ; $(DM_CC) -o nc4_test.exe nc4_test.c -I$(NETCDF)/include -L$(NETCDF)/lib -lnetcdf $(NETCDF4_DEP_LIB) ; cd ..  ) ; \
++	 ( cd tools ; /bin/rm -f nc4_test.{exe,nc,o} ; $(DM_CC) -o nc4_test.exe nc4_test.c -I$(NETCDF)/include -L$(NETCDF)/lib64 -lnetcdf $(NETCDF4_DEP_LIB) ; cd ..  ) ; \
+ 	fi
+ 
+ # rule used by configure to test if Fortran 2003 IEEE signaling is available

From 81052529ebcc66a618b1d563d3701bf893f5ea45 Mon Sep 17 00:00:00 2001
From: Stefan Wolfsheimer <stefan.wolfsheimer@surf.nl>
Date: Fri, 8 Sep 2023 11:48:21 +0200
Subject: [PATCH 008/835] fixed patch file, enable tests

---
 .../w/WRF/WRF-4.5.1-foss-2023a-dmpar.eb          |  4 +++-
 .../WRF-4.5.1_netCDF-Fortran_separate_path.patch | 16 +++++++++-------
 2 files changed, 12 insertions(+), 8 deletions(-)

diff --git a/easybuild/easyconfigs/w/WRF/WRF-4.5.1-foss-2023a-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-4.5.1-foss-2023a-dmpar.eb
index 04ca4736994..6f8b8d751e6 100644
--- a/easybuild/easyconfigs/w/WRF/WRF-4.5.1-foss-2023a-dmpar.eb
+++ b/easybuild/easyconfigs/w/WRF/WRF-4.5.1-foss-2023a-dmpar.eb
@@ -28,7 +28,7 @@ patches = [
 ]
 checksums = [
     '9d557c34c105db4d41e727843ecb19199233c7cf82c5369b34a2ce8efe65e2d1',  # v4.5.1.tar.gz
-    '3cc30b1dca275719a1bcfa4fb911c25baaa943456e2d57a4e3fc34842929629b',  # WRF-5.1_netCDF-Fortran_separate_path.patch
+    '951bff9a3fc651482b287cc03a9f3197979b7800d515fe61cc9c932d9e0dc62e',  # WRF-5.1_netCDF-Fortran_separate_path.patch
 ]
 
 # csh is used by WRF install scripts
@@ -45,6 +45,8 @@ dependencies = [
     ('netCDF-Fortran', '4.6.1'),
 ]
 
+runtest = True
+
 # limit parallel build to 20
 maxparallel = 20
 
diff --git a/easybuild/easyconfigs/w/WRF/WRF-4.5.1_netCDF-Fortran_separate_path.patch b/easybuild/easyconfigs/w/WRF/WRF-4.5.1_netCDF-Fortran_separate_path.patch
index ac5c261db07..2e35f0dbb86 100644
--- a/easybuild/easyconfigs/w/WRF/WRF-4.5.1_netCDF-Fortran_separate_path.patch
+++ b/easybuild/easyconfigs/w/WRF/WRF-4.5.1_netCDF-Fortran_separate_path.patch
@@ -145,8 +145,8 @@ diff -Nru WRFV4.5.1.orig/arch/postamble WRFV4.5.1/arch/postamble
  wrfio_adios2 : 
 diff -Nru WRFV4.5.1.orig/configure WRFV4.5.1/configure
 --- WRFV4.5.1.orig/configure	2023-07-25 23:14:55.692864209 +0200
-+++ WRFV4.5.1/configure	2023-09-07 14:30:41.177727094 +0200
-@@ -214,7 +214,11 @@
++++ WRFV4.5.1/configure	2023-09-08 11:40:15.875789587 +0200
+@@ -214,17 +214,19 @@
    unset NETCDF4
  fi
  
@@ -159,16 +159,18 @@ diff -Nru WRFV4.5.1.orig/configure WRFV4.5.1/configure
  USENETCDF=""
  if [ -n "$NETCDF" ] ; then
    echo "Will use NETCDF in dir: $NETCDF"
-@@ -224,7 +228,7 @@
-   else
-     USENETCDFF=" "
+ # Oh UNIDATA, why make it so hard ...
+   if [ -f "$NETCDF/lib/libnetcdff.a" -o -f "$NETCDF/lib/libnetcdff.so" -o -f "$NETCDF/lib/libnetcdff.dll.a" ] ; then
+     USENETCDFF="-lnetcdff"
+-  else
+-    USENETCDFF=" "
    fi
 -  if [ -f "$NETCDF/lib/libnetcdf.a" -o -f "$NETCDF/lib/libnetcdf.so" -o -f "$NETCDF/lib/libnetcdf.dll.a" ] ; then
 +  if [ -f "$NETCDF/lib/libnetcdf.a" -o -f "$NETCDF/lib/libnetcdf.so" -o -f "$NETCDF/lib64/libnetcdf.a" -o -f "$NETCDF/lib64/libnetcdf.so" ] ; then
      USENETCDF="-lnetcdf"
    else
      USENETCDF=" "
-@@ -572,7 +576,7 @@
+@@ -572,7 +574,7 @@
     srch=`grep -i "^#ARCH.*$os" arch/configure.defaults | grep -i "$mach"`
     if [ -n "$srch" ] ; then
       $PERL arch/Config.pl -dmparallel=$COMMLIB -ompparallel=$OMP -perl=$PERL \
@@ -177,7 +179,7 @@ diff -Nru WRFV4.5.1.orig/configure WRFV4.5.1/configure
            -compileflags=$compileflags -opt_level=$opt_level -USENETCDFF=$USENETCDFF -USENETCDF=$USENETCDF \
            -time=$FORTRAN_COMPILER_TIMER -tfl="$TFL" -cfl="$CFL" -config_line="$config_line" \
            -wrf_core=$wrf_core -gpfs=$GPFS_PATH -curl=$CURL_PATH -dep_lib_path="$DEP_LIB_PATH"
-@@ -654,14 +658,14 @@
+@@ -654,14 +656,14 @@
  echo "If you wish to change the default options, edit the file:"
  echo "     arch/configure.defaults"
  

From e5413f92af8e786e7b510ece74d1160a54292060 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 2 Jan 2024 15:39:28 +0100
Subject: [PATCH 009/835] use None as checksum for WRF 4.5.1 source tarball

---
 easybuild/easyconfigs/w/WRF/WRF-4.5.1-foss-2023a-dmpar.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/w/WRF/WRF-4.5.1-foss-2023a-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-4.5.1-foss-2023a-dmpar.eb
index 6f8b8d751e6..cd811672d43 100644
--- a/easybuild/easyconfigs/w/WRF/WRF-4.5.1-foss-2023a-dmpar.eb
+++ b/easybuild/easyconfigs/w/WRF/WRF-4.5.1-foss-2023a-dmpar.eb
@@ -27,7 +27,7 @@ patches = [
     'WRF-4.5.1_netCDF-Fortran_separate_path.patch',
 ]
 checksums = [
-    '9d557c34c105db4d41e727843ecb19199233c7cf82c5369b34a2ce8efe65e2d1',  # v4.5.1.tar.gz
+    None,  # v4.5.1.tar.gz
     '951bff9a3fc651482b287cc03a9f3197979b7800d515fe61cc9c932d9e0dc62e',  # WRF-5.1_netCDF-Fortran_separate_path.patch
 ]
 

From ad2faf9865ff518dace68136d6a1fd8bebf87ec1 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 2 Jan 2024 15:42:09 +0100
Subject: [PATCH 010/835] fix name of patch file for WRF 4.5.1

---
 easybuild/easyconfigs/w/WRF/WRF-4.5.1-foss-2023a-dmpar.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/w/WRF/WRF-4.5.1-foss-2023a-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-4.5.1-foss-2023a-dmpar.eb
index cd811672d43..399ee9f1ff4 100644
--- a/easybuild/easyconfigs/w/WRF/WRF-4.5.1-foss-2023a-dmpar.eb
+++ b/easybuild/easyconfigs/w/WRF/WRF-4.5.1-foss-2023a-dmpar.eb
@@ -28,7 +28,7 @@ patches = [
 ]
 checksums = [
     None,  # v4.5.1.tar.gz
-    '951bff9a3fc651482b287cc03a9f3197979b7800d515fe61cc9c932d9e0dc62e',  # WRF-5.1_netCDF-Fortran_separate_path.patch
+    '951bff9a3fc651482b287cc03a9f3197979b7800d515fe61cc9c932d9e0dc62e',  # WRF-4.5.1_netCDF-Fortran_separate_path.patch
 ]
 
 # csh is used by WRF install scripts

From 40e198313727ca526b1567d6f4d43a69a3f9f114 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 2 Jan 2024 18:21:40 +0100
Subject: [PATCH 011/835] use prepared source tarball for WRF 4.5.1 rather than
 creating our own via git_config

---
 .../w/WRF/WRF-4.5.1-foss-2023a-dmpar.eb         | 17 ++++-------------
 1 file changed, 4 insertions(+), 13 deletions(-)

diff --git a/easybuild/easyconfigs/w/WRF/WRF-4.5.1-foss-2023a-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-4.5.1-foss-2023a-dmpar.eb
index 399ee9f1ff4..2d0cd78573a 100644
--- a/easybuild/easyconfigs/w/WRF/WRF-4.5.1-foss-2023a-dmpar.eb
+++ b/easybuild/easyconfigs/w/WRF/WRF-4.5.1-foss-2023a-dmpar.eb
@@ -12,23 +12,14 @@ toolchain = {'name': 'foss', 'version': '2023a'}
 toolchainopts = {'opt': False}  # don't use agressive optimization, stick to -O2
 
 source_urls = ['https://github.com/wrf-model/WRF/archive/']
-# sources = ['v%(version)s.tar.gz']
-sources = [{
-    'filename': 'v%(version)s.tar.gz',
-    'git_config': {
-        'url': 'https://github.com/wrf-model',
-        'repo_name': 'WRF',
-        'tag': 'v%(version)s',
-        'clone_into': 'WRF-%(version)s',
-        'recursive': True,
-    },
-}]
+sources = ['v%(version)s.tar.gz']
 patches = [
     'WRF-4.5.1_netCDF-Fortran_separate_path.patch',
 ]
 checksums = [
-    None,  # v4.5.1.tar.gz
-    '951bff9a3fc651482b287cc03a9f3197979b7800d515fe61cc9c932d9e0dc62e',  # WRF-4.5.1_netCDF-Fortran_separate_path.patch
+    {'v4.5.1.tar.gz': '91d7dc84f6a41e1243f0b56b2f2c86b10d860610a2c686dfea599aecab02e8f8'},
+    {'WRF-4.5.1_netCDF-Fortran_separate_path.patch':
+     '951bff9a3fc651482b287cc03a9f3197979b7800d515fe61cc9c932d9e0dc62e'},
 ]
 
 # csh is used by WRF install scripts

From 02dd7f10cd3754656683f6d555f358b0e446b2f0 Mon Sep 17 00:00:00 2001
From: Stefan Wolfsheimer <stefan.wolfsheimer@surf.nl>
Date: Thu, 4 Jan 2024 16:58:54 +0100
Subject: [PATCH 012/835] added libdap-3.20.11-GCCco NCO-5.1.9-foss-2023.eb
 ESMF-8.6.0-foss-2023a.eb ANTLR-2.7.7-GCCcore-12.3.0-Java-11.eb

---
 .../ANTLR-2.7.7-GCCcore-12.3.0-Java-11.eb     | 36 +++++++++++++++
 .../e/ESMF/ESMF-8.6.0-foss-2023a.eb           | 37 ++++++++++++++++
 .../l/libdap/libdap-3.20.11-GCCcore-12.3.0.eb | 37 ++++++++++++++++
 .../easyconfigs/n/NCO/NCO-5.1.9-foss-2023.eb  | 44 +++++++++++++++++++
 4 files changed, 154 insertions(+)
 create mode 100644 easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-12.3.0-Java-11.eb
 create mode 100644 easybuild/easyconfigs/e/ESMF/ESMF-8.6.0-foss-2023a.eb
 create mode 100644 easybuild/easyconfigs/l/libdap/libdap-3.20.11-GCCcore-12.3.0.eb
 create mode 100644 easybuild/easyconfigs/n/NCO/NCO-5.1.9-foss-2023.eb

diff --git a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-12.3.0-Java-11.eb b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-12.3.0-Java-11.eb
new file mode 100644
index 00000000000..4f76242d899
--- /dev/null
+++ b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-12.3.0-Java-11.eb
@@ -0,0 +1,36 @@
+easyblock = 'ConfigureMake'
+
+name = 'ANTLR'
+version = '2.7.7'
+versionsuffix = '-Java-%(javaver)s'
+
+homepage = 'https://www.antlr2.org/'
+description = """ANTLR, ANother Tool for Language Recognition, (formerly PCCTS)
+ is a language tool that provides a framework for constructing recognizers,
+ compilers, and translators from grammatical descriptions containing
+ Java, C#, C++, or Python actions."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+source_urls = ['https://www.antlr2.org/download/']
+sources = [SOURCELOWER_TAR_GZ]
+patches = ['%(name)s-%(version)s_includes.patch']
+checksums = [
+    '853aeb021aef7586bda29e74a6b03006bcb565a755c86b66032d8ec31b67dbb9',  # antlr-2.7.7.tar.gz
+    'd167d3248a03301bc93efcb37d5df959aae6794968e42231af0b0dd26d6a2e66',  # ANTLR-2.7.7_includes.patch
+]
+
+builddependencies = [('binutils', '2.40')]
+
+dependencies = [('Java', '11', '', SYSTEM)]
+
+configopts = '--disable-examples --disable-csharp --disable-python'
+
+sanity_check_paths = {
+    'files': ['bin/antlr', 'bin/antlr-config'],
+    'dirs': ['include'],
+}
+
+sanity_check_commands = ["antlr --help"]
+
+moduleclass = 'tools'
diff --git a/easybuild/easyconfigs/e/ESMF/ESMF-8.6.0-foss-2023a.eb b/easybuild/easyconfigs/e/ESMF/ESMF-8.6.0-foss-2023a.eb
new file mode 100644
index 00000000000..356f3864756
--- /dev/null
+++ b/easybuild/easyconfigs/e/ESMF/ESMF-8.6.0-foss-2023a.eb
@@ -0,0 +1,37 @@
+name = 'ESMF'
+version = '8.6.0'
+
+homepage = 'https://www.earthsystemcog.org/projects/esmf/'
+description = """The Earth System Modeling Framework (ESMF) is a suite of software tools for developing
+ high-performance, multi-component Earth science modeling applications."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+toolchainopts = {'usempi': True, 'openmp': True, 'cstd': 'c++11', 'pic': True}
+
+source_urls = ['https://github.com/esmf-org/esmf/archive/']
+sources = ['v%(version)s.tar.gz']
+patches = ['ESMF-6.1.1_libopts.patch']
+checksums = [
+    'ed057eaddb158a3cce2afc0712b49353b7038b45b29aee86180f381457c0ebe7',  # v8.6.0.tar.gz
+    '3851627f07c32a7da55d99072d619942bd3a1d9dd002e1557716158e7aacdaf4',  # ESMF-6.1.1_libopts.patch
+]
+
+builddependencies = [('CMake', '3.26.3')]
+
+dependencies = [
+    ('netCDF', '4.9.2'),
+    ('netCDF-Fortran', '4.6.1'),
+    ('netCDF-C++4', '4.3.1'),
+    ('libarchive', '3.6.2'),
+]
+
+# disable errors from GCC 10 on mismatches between actual and dummy argument lists (GCC 9 behaviour)
+prebuildopts = 'ESMF_F90COMPILEOPTS="${ESMF_F90COMPILEOPTS} -fallow-argument-mismatch"'
+
+buildopts = 'ESMF_NETCDF_INCLUDE=$EBROOTNETCDFMINFORTRAN/include '
+buildopts += 'ESMF_NETCDF_LIBS="`nc-config --libs` `nf-config --flibs` `ncxx4-config --libs`"'
+
+# too parallel causes the build to become really slow
+maxparallel = 8
+
+moduleclass = 'geo'
diff --git a/easybuild/easyconfigs/l/libdap/libdap-3.20.11-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libdap/libdap-3.20.11-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..1f3f87a6d66
--- /dev/null
+++ b/easybuild/easyconfigs/l/libdap/libdap-3.20.11-GCCcore-12.3.0.eb
@@ -0,0 +1,37 @@
+easyblock = 'ConfigureMake'
+
+name = 'libdap'
+version = '3.20.11'
+
+homepage = 'https://www.opendap.org/software/libdap'
+description = """A C++ SDK which contains an implementation of DAP 2.0 and
+ DAP4.0. This includes both Client- and Server-side support classes."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+source_urls = ['https://www.opendap.org/pub/source/']
+sources = [SOURCE_TAR_GZ]
+checksums = ['850debf6ee6991350bf31051308093bee35ddd2121e4002be7e130a319de1415']
+
+builddependencies = [
+    ('binutils', '2.40'),
+    ('Bison', '3.8.2'),
+    ('flex', '2.6.4'),
+]
+dependencies = [
+    ('cURL', '8.0.1'),
+    ('libxml2', '2.11.4'),
+    ('libtirpc', '1.3.3'),
+    ('PCRE', '8.45'),
+    ('util-linux', '2.39'),
+]
+
+configopts = 'TIRPC_LIBS="-ltirpc"'
+
+
+sanity_check_paths = {
+    'files': ['bin/getdap', 'bin/getdap4', 'bin/dap-config', 'lib/%(name)s.a', 'lib/%(name)s.so'],
+    'dirs': ['include'],
+}
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/n/NCO/NCO-5.1.9-foss-2023.eb b/easybuild/easyconfigs/n/NCO/NCO-5.1.9-foss-2023.eb
new file mode 100644
index 00000000000..0e7dd9be31a
--- /dev/null
+++ b/easybuild/easyconfigs/n/NCO/NCO-5.1.9-foss-2023.eb
@@ -0,0 +1,44 @@
+easyblock = 'ConfigureMake'
+
+name = 'NCO'
+version = '5.1.9'
+
+homepage = "https://github.com/nco/nco"
+description = """The NCO toolkit manipulates and analyzes data stored in netCDF-accessible formats, 
+including DAP, HDF4, and HDF5."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+source_urls = ['https://github.com/nco/nco/archive/']
+sources = ['%(version)s.tar.gz']
+checksums = ['9cd90345c1e3860a690b53fd6c08b721d631a646d169431927884c99841c34e9']
+
+builddependencies = [
+    ('Bison', '3.8.2'),
+    ('flex', '2.6.4'),
+]
+
+dependencies = [
+    ('UDUNITS', '2.2.28'),
+    ('expat', '2.5.0'),
+    ('ANTLR', '2.7.7', '-Java-11'),
+    ('libdap', '3.20.11'),
+    ('GSL', '2.7'),
+    ('netCDF', '4.9.2'),
+    ('ESMF', '8.6.0'),  # ncremap needs ESMF_RegridWeightGen
+]
+
+configopts = "--enable-nco_cplusplus"
+
+sanity_check_paths = {
+    'files': ['bin/nc%s' % x for x in ('ap2', 'atted', 'bo', 'diff', 'ea', 'ecat', 'es',
+                                       'flint', 'ks', 'pdq', 'ra', 'rcat', 'rename', 'wa')] +
+             ['lib/libnco.a', 'lib/libnco.%s' % SHLIB_EXT, 'lib/libnco_c++.a', 'lib/libnco_c++.%s' % SHLIB_EXT],
+    'dirs': ['include'],
+}
+sanity_check_commands = [
+    "ncks -O -7 --cnk_dmn time,10 "
+    "%(builddir)s/%(namelower)s-%(version)s/data/in.nc %(builddir)s/%(namelower)s-%(version)s/data/in4.cdl"
+]
+
+moduleclass = 'tools'

From 22c00b466113a63b7c5d155921ac795b11df6980 Mon Sep 17 00:00:00 2001
From: Stefan Wolfsheimer <stefan.wolfsheimer@surf.nl>
Date: Thu, 4 Jan 2024 17:15:07 +0100
Subject: [PATCH 013/835] fixed name

---
 .../n/NCO/{NCO-5.1.9-foss-2023.eb => NCO-5.1.9-foss-2023a.eb}     | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename easybuild/easyconfigs/n/NCO/{NCO-5.1.9-foss-2023.eb => NCO-5.1.9-foss-2023a.eb} (100%)

diff --git a/easybuild/easyconfigs/n/NCO/NCO-5.1.9-foss-2023.eb b/easybuild/easyconfigs/n/NCO/NCO-5.1.9-foss-2023a.eb
similarity index 100%
rename from easybuild/easyconfigs/n/NCO/NCO-5.1.9-foss-2023.eb
rename to easybuild/easyconfigs/n/NCO/NCO-5.1.9-foss-2023a.eb

From ca5fa192916b41522baf2ba21ebfa505dbac0d36 Mon Sep 17 00:00:00 2001
From: stefan-wolfsheimer <stefan.wolfsheimer@gmail.com>
Date: Fri, 5 Jan 2024 10:11:09 +0100
Subject: [PATCH 014/835] Update libdap-3.20.11-GCCcore-12.3.0.eb: SHLIB_EXT
 variable instead of hard-coded extension

---
 easybuild/easyconfigs/l/libdap/libdap-3.20.11-GCCcore-12.3.0.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/l/libdap/libdap-3.20.11-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libdap/libdap-3.20.11-GCCcore-12.3.0.eb
index 1f3f87a6d66..ae260fd0348 100644
--- a/easybuild/easyconfigs/l/libdap/libdap-3.20.11-GCCcore-12.3.0.eb
+++ b/easybuild/easyconfigs/l/libdap/libdap-3.20.11-GCCcore-12.3.0.eb
@@ -30,7 +30,7 @@ configopts = 'TIRPC_LIBS="-ltirpc"'
 
 
 sanity_check_paths = {
-    'files': ['bin/getdap', 'bin/getdap4', 'bin/dap-config', 'lib/%(name)s.a', 'lib/%(name)s.so'],
+    'files': ['bin/getdap', 'bin/getdap4', 'bin/dap-config', 'lib/%(name)s.a', 'lib/lib%%(name)s.%s' % SHLIB_EXT],
     'dirs': ['include'],
 }
 

From 40de60f6294554de04aa6d0fc50e18461e2231d7 Mon Sep 17 00:00:00 2001
From: Alan O'Cais <a.ocais@fz-juelich.de>
Date: Fri, 8 Mar 2024 10:19:34 +0000
Subject: [PATCH 015/835] Correct configuration of QuantumESPRESSO for 6.7/7.2

---
 .../q/QuantumESPRESSO/QuantumESPRESSO-6.7-foss-2021a.eb      | 3 ++-
 .../q/QuantumESPRESSO/QuantumESPRESSO-6.7-intel-2021a.eb     | 3 ++-
 .../q/QuantumESPRESSO/QuantumESPRESSO-7.2-foss-2022b.eb      | 5 +++++
 .../q/QuantumESPRESSO/QuantumESPRESSO-7.2-foss-2023a.eb      | 3 +++
 .../q/QuantumESPRESSO/QuantumESPRESSO-7.2-intel-2022b.eb     | 3 +++
 5 files changed, 15 insertions(+), 2 deletions(-)

diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-foss-2021a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-foss-2021a.eb
index 5438527c158..627a096a2d8 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-foss-2021a.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-foss-2021a.eb
@@ -29,7 +29,8 @@ checksums = [
 
 dependencies = [
     ('HDF5', '1.10.7'),
-    ('ELPA', '2021.05.001'),
+# From the QE configure help, this version of ELPA is not compatible
+#    ('ELPA', '2021.05.001'),
     ('libxc', '5.1.5'),
 ]
 
diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-intel-2021a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-intel-2021a.eb
index 90cb839d1f7..7d5de7397f3 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-intel-2021a.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-intel-2021a.eb
@@ -29,7 +29,8 @@ checksums = [
 
 dependencies = [
     ('HDF5', '1.10.7'),
-    ('ELPA', '2021.05.001'),
+# From the QE configure help, this version of ELPA is not compatible
+#    ('ELPA', '2021.05.001'),
     ('libxc', '5.1.5'),
 ]
 
diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-foss-2022b.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-foss-2022b.eb
index 376073c6808..80b1a8863b7 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-foss-2022b.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-foss-2022b.eb
@@ -40,11 +40,16 @@ dependencies = [
     ('libxc', '6.1.0'),
 ]
 
+
 # The third party packages should be installed separately and added as
 # dependencies.  The exception is w90, which is force built, and gipaw
 # which depends on qe source
 buildopts = 'all gwl xspectra couple epw gipaw w90'
 
+# building gipaw requires FoX
+with_fox = True
+
+
 # parallel build tends to fail
 parallel = 1
 
diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-foss-2023a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-foss-2023a.eb
index 4a79d7df97a..2bf29814216 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-foss-2023a.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-foss-2023a.eb
@@ -46,6 +46,9 @@ dependencies = [
 # which depends on qe source
 buildopts = "all gwl xspectra couple epw gipaw w90"
 
+# building gipaw requires FoX
+with_fox = True
+
 # parallel build tends to fail
 parallel = 1
 
diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-intel-2022b.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-intel-2022b.eb
index 8b78a44b1f6..4101e1e3282 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-intel-2022b.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-intel-2022b.eb
@@ -45,6 +45,9 @@ dependencies = [
 # which depends on qe source
 buildopts = 'all gwl xspectra couple epw gipaw w90'
 
+# building gipaw requires FoX
+with_fox = True
+
 # parallel build tends to fail
 parallel = 1
 

From 08ec5b29aab662c56b9273d9448915b834cda039 Mon Sep 17 00:00:00 2001
From: ocaisa <alan.ocais@cecam.org>
Date: Fri, 8 Mar 2024 11:20:18 +0100
Subject: [PATCH 016/835] Update QuantumESPRESSO-7.2-foss-2022b.eb

---
 .../q/QuantumESPRESSO/QuantumESPRESSO-7.2-foss-2022b.eb          | 1 -
 1 file changed, 1 deletion(-)

diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-foss-2022b.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-foss-2022b.eb
index 80b1a8863b7..d4430331437 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-foss-2022b.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-foss-2022b.eb
@@ -49,7 +49,6 @@ buildopts = 'all gwl xspectra couple epw gipaw w90'
 # building gipaw requires FoX
 with_fox = True
 
-
 # parallel build tends to fail
 parallel = 1
 

From 9ebcd49cbbe1f4905c0494e52427de5046ee3f2e Mon Sep 17 00:00:00 2001
From: ocaisa <alan.ocais@cecam.org>
Date: Fri, 8 Mar 2024 12:24:05 +0100
Subject: [PATCH 017/835] Update QuantumESPRESSO-7.2-foss-2022b.eb

---
 .../q/QuantumESPRESSO/QuantumESPRESSO-7.2-foss-2022b.eb          | 1 -
 1 file changed, 1 deletion(-)

diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-foss-2022b.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-foss-2022b.eb
index d4430331437..bc13fda0984 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-foss-2022b.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-foss-2022b.eb
@@ -40,7 +40,6 @@ dependencies = [
     ('libxc', '6.1.0'),
 ]
 
-
 # The third party packages should be installed separately and added as
 # dependencies.  The exception is w90, which is force built, and gipaw
 # which depends on qe source

From e102d887e1f3dd73b8ad6aba096b682a8412a2b1 Mon Sep 17 00:00:00 2001
From: ocaisa <alan.ocais@cecam.org>
Date: Mon, 11 Mar 2024 12:04:53 +0100
Subject: [PATCH 018/835] Switching on OpenMP causes may test failures for QE
 7.2 and Intel

---
 .../q/QuantumESPRESSO/QuantumESPRESSO-7.2-intel-2022b.eb      | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-intel-2022b.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-intel-2022b.eb
index 4101e1e3282..ca89c1f70f4 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-intel-2022b.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-intel-2022b.eb
@@ -9,7 +9,9 @@ It is based on density-functional theory, plane waves, and pseudopotentials
 """
 
 toolchain = {'name': 'intel', 'version': '2022b'}
-toolchainopts = {'usempi': True, 'openmp': True}
+# Switching on OpenMP causes may test failures for QE 7.2 and Intel 
+# toolchainopts = {'usempi': True, 'openmp': True}
+toolchainopts = {'usempi': True}
 
 sources = [
     {

From 5ef1d0870cf20141be2172d83be3eb29476d8b4b Mon Sep 17 00:00:00 2001
From: ocaisa <alan.ocais@cecam.org>
Date: Mon, 11 Mar 2024 12:10:39 +0100
Subject: [PATCH 019/835] Update QuantumESPRESSO-7.2-intel-2022b.eb

---
 .../q/QuantumESPRESSO/QuantumESPRESSO-7.2-intel-2022b.eb        | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-intel-2022b.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-intel-2022b.eb
index ca89c1f70f4..028fee4349c 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-intel-2022b.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-intel-2022b.eb
@@ -9,7 +9,7 @@ It is based on density-functional theory, plane waves, and pseudopotentials
 """
 
 toolchain = {'name': 'intel', 'version': '2022b'}
-# Switching on OpenMP causes may test failures for QE 7.2 and Intel 
+# OpenMP is not working with Intel ifort/ifx compilers (Fortran) starting from version 2021.2.0 
 # toolchainopts = {'usempi': True, 'openmp': True}
 toolchainopts = {'usempi': True}
 

From 9a12aa24f2f4c7d04202c30e4301719de379ed4d Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Wed, 13 Mar 2024 11:29:45 +0100
Subject: [PATCH 020/835] add wrapper for Julia with linking safeguards and
 delegate environment setup to JuliaPackage

---
 .../j/Julia/Julia-1.10.0-linux-x86_64.eb      | 21 +++++++++----------
 .../j/Julia/Julia-1.6.0-linux-aarch64.eb      | 20 +++++++++---------
 .../j/Julia/Julia-1.6.5-linux-x86_64.eb       | 20 +++++++++---------
 .../j/Julia/Julia-1.6.6-linux-x86_64.eb       | 21 +++++++++----------
 .../j/Julia/Julia-1.6.7-linux-x86_64.eb       | 21 +++++++++----------
 .../j/Julia/Julia-1.7.0-linux-x86_64.eb       | 21 +++++++++----------
 .../j/Julia/Julia-1.7.1-linux-x86_64.eb       | 21 +++++++++----------
 .../j/Julia/Julia-1.7.2-linux-x86_64.eb       | 21 +++++++++----------
 .../j/Julia/Julia-1.7.3-linux-x86_64.eb       | 21 +++++++++----------
 .../j/Julia/Julia-1.8.0-linux-x86_64.eb       | 21 +++++++++----------
 .../j/Julia/Julia-1.8.2-linux-x86_64.eb       | 21 +++++++++----------
 .../j/Julia/Julia-1.8.5-linux-x86_64.eb       | 19 ++++++++---------
 .../j/Julia/Julia-1.9.0-linux-x86_64.eb       | 21 +++++++++----------
 .../j/Julia/Julia-1.9.2-linux-x86_64.eb       | 19 ++++++++---------
 .../j/Julia/Julia-1.9.3-linux-x86_64.eb       | 21 +++++++++----------
 15 files changed, 148 insertions(+), 161 deletions(-)

diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.10.0-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.10.0-linux-x86_64.eb
index 6671e1cd4ff..a7320c2365f 100644
--- a/easybuild/easyconfigs/j/Julia/Julia-1.10.0-linux-x86_64.eb
+++ b/easybuild/easyconfigs/j/Julia/Julia-1.10.0-linux-x86_64.eb
@@ -11,21 +11,20 @@ toolchain = SYSTEM
 
 source_urls = ['https://julialang-s3.julialang.org/bin/linux/x64/%(version_major_minor)s/']
 sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz']
-checksums = ['a7298207f72f2b27b2ab1ce392a6ea37afbd1fbee0f1f8d190b054dcaba878fe']
+patches = [('julia.wrapper', 'bin/')]
+checksums = [
+    {'julia-1.10.0-linux-x86_64.tar.gz': 'a7298207f72f2b27b2ab1ce392a6ea37afbd1fbee0f1f8d190b054dcaba878fe'},
+    {'julia.wrapper': 'a36a3e0cb98ab4d2b05e0ca8f0bf2724baafbd669a0db318a00e40737d2f02f9'},
+]
+
+# install wrapper with linking safeguards for Julia libraries
+postinstallcmds = ["cd %(installdir)s/bin && mv julia julia.bin && mv julia.wrapper julia"]
 
 sanity_check_paths = {
-    'files': ['bin/julia', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT],
-    'dirs': ['bin', 'etc', 'include', 'lib', 'share']
+    'files': ['bin/julia', 'bin/julia.bin', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT],
+    'dirs': ['bin', 'etc', 'include', 'lib', 'lib/julia', 'share']
 }
 
 sanity_check_commands = ['julia --help']
 
-modextrapaths_append = {
-    # Use default DEPOT_PATH where first entry is user's depot.
-    # JULIA_DEPOT_PATH must be set to be able to load other JuliaPackage modules and have
-    # those installations appended to DEPOT_PATH without disabling any of the default paths.
-    # Appending ':' to make sure we don't override the user's custom JULIA_DEPOT_PATH if set.
-    'JULIA_DEPOT_PATH': ':',
-}
-
 moduleclass = 'lang'
diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.6.0-linux-aarch64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.6.0-linux-aarch64.eb
index 225d86de75a..dee7717b5a0 100644
--- a/easybuild/easyconfigs/j/Julia/Julia-1.6.0-linux-aarch64.eb
+++ b/easybuild/easyconfigs/j/Julia/Julia-1.6.0-linux-aarch64.eb
@@ -15,20 +15,20 @@ toolchain = SYSTEM
 
 source_urls = ['https://julialang-s3.julialang.org/bin/linux/aarch64/%(version_major_minor)s/']
 sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz']
-checksums = ['0f496972d26cea88151204d03e6bd87702aa1ff983de3b1e4f320c48ef67325f']
+patches = [('julia.wrapper', 'bin/')]
+checksums = [
+    {'julia-1.6.0-linux-aarch64.tar.gz': '0f496972d26cea88151204d03e6bd87702aa1ff983de3b1e4f320c48ef67325f'},
+    {'julia.wrapper': 'a36a3e0cb98ab4d2b05e0ca8f0bf2724baafbd669a0db318a00e40737d2f02f9'},
+]
+
+# install wrapper with linking safeguards for Julia libraries
+postinstallcmds = ["cd %(installdir)s/bin && mv julia julia.bin && mv julia.wrapper julia"]
 
 sanity_check_paths = {
-    'files': ['bin/julia', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT],
-    'dirs': ['bin', 'etc', 'include', 'lib', 'share']
+    'files': ['bin/julia', 'bin/julia.bin', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT],
+    'dirs': ['bin', 'etc', 'include', 'lib', 'lib/julia', 'share']
 }
 
 sanity_check_commands = ['julia --help']
 
-modextravars = {
-    # Use default DEPOT_PATH where first entry is user's depot
-    # JULIA_DEPOT_PATH must be set to be able to load other JuliaPackage modules and have
-    # those installations appended to DEPOT_PATH without disabling any of the default paths
-    'JULIA_DEPOT_PATH': ':',
-}
-
 moduleclass = 'lang'
diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.6.5-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.6.5-linux-x86_64.eb
index 45b365aa65d..9bf44e78f13 100644
--- a/easybuild/easyconfigs/j/Julia/Julia-1.6.5-linux-x86_64.eb
+++ b/easybuild/easyconfigs/j/Julia/Julia-1.6.5-linux-x86_64.eb
@@ -19,20 +19,20 @@ toolchain = SYSTEM
 
 source_urls = ['https://julialang-s3.julialang.org/bin/linux/x64/%(version_major_minor)s/']
 sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz']
-checksums = ['b8fe23ee547254a2fe14be587284ed77c78c06c2d8e9aad5febce0d21cab8e2c']
+patches = [('julia.wrapper', 'bin/')]
+checksums = [
+    {'julia-1.6.5-linux-x86_64.tar.gz': 'b8fe23ee547254a2fe14be587284ed77c78c06c2d8e9aad5febce0d21cab8e2c'},
+    {'julia.wrapper': 'a36a3e0cb98ab4d2b05e0ca8f0bf2724baafbd669a0db318a00e40737d2f02f9'},
+]
+
+# install wrapper with linking safeguards for Julia libraries
+postinstallcmds = ["cd %(installdir)s/bin && mv julia julia.bin && mv julia.wrapper julia"]
 
 sanity_check_paths = {
-    'files': ['bin/julia', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT],
-    'dirs': ['bin', 'etc', 'include', 'lib', 'share']
+    'files': ['bin/julia', 'bin/julia.bin', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT],
+    'dirs': ['bin', 'etc', 'include', 'lib', 'lib/julia', 'share']
 }
 
 sanity_check_commands = ['julia --help']
 
-modextravars = {
-    # Use default DEPOT_PATH where first entry is user's depot
-    # JULIA_DEPOT_PATH must be set to be able to load other JuliaPackage modules and have
-    # those installations appended to DEPOT_PATH without disabling any of the default paths
-    'JULIA_DEPOT_PATH': ':',
-}
-
 moduleclass = 'lang'
diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.6.6-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.6.6-linux-x86_64.eb
index 48c2259422e..6430a94ca59 100644
--- a/easybuild/easyconfigs/j/Julia/Julia-1.6.6-linux-x86_64.eb
+++ b/easybuild/easyconfigs/j/Julia/Julia-1.6.6-linux-x86_64.eb
@@ -19,20 +19,19 @@ toolchain = SYSTEM
 
 source_urls = ['https://julialang-s3.julialang.org/bin/linux/x64/%(version_major_minor)s/']
 sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz']
-checksums = ['c25ff71a4242207ab2681a0fcc5df50014e9d99f814e77cacbc5027e20514945']
+patches = [('julia.wrapper', 'bin/')]
+checksums = [
+    {'julia-1.6.6-linux-x86_64.tar.gz': 'c25ff71a4242207ab2681a0fcc5df50014e9d99f814e77cacbc5027e20514945'},
+    {'julia.wrapper': 'a36a3e0cb98ab4d2b05e0ca8f0bf2724baafbd669a0db318a00e40737d2f02f9'},
+]
+
+# install wrapper with linking safeguards for Julia libraries
+postinstallcmds = ["cd %(installdir)s/bin && mv julia julia.bin && mv julia.wrapper julia"]
 
 sanity_check_paths = {
-    'files': ['bin/julia', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT],
-    'dirs': ['bin', 'etc', 'include', 'lib', 'share']
+    'files': ['bin/julia', 'bin/julia.bin', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT],
+    'dirs': ['bin', 'etc', 'include', 'lib', 'lib/julia', 'share']
 }
-
 sanity_check_commands = ['julia --help']
 
-modextravars = {
-    # Use default DEPOT_PATH where first entry is user's depot
-    # JULIA_DEPOT_PATH must be set to be able to load other JuliaPackage modules and have
-    # those installations appended to DEPOT_PATH without disabling any of the default paths
-    'JULIA_DEPOT_PATH': ':',
-}
-
 moduleclass = 'lang'
diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.6.7-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.6.7-linux-x86_64.eb
index f5d1446913f..6935d34d151 100644
--- a/easybuild/easyconfigs/j/Julia/Julia-1.6.7-linux-x86_64.eb
+++ b/easybuild/easyconfigs/j/Julia/Julia-1.6.7-linux-x86_64.eb
@@ -19,20 +19,19 @@ toolchain = SYSTEM
 
 source_urls = ['https://julialang-s3.julialang.org/bin/linux/x64/%(version_major_minor)s/']
 sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz']
-checksums = ['6c4522d595e4cbcd00157ac458a72f8aec01757053d2073f99daa39e442b2a36']
+patches = [('julia.wrapper', 'bin/')]
+checksums = [
+    {'julia-1.6.7-linux-x86_64.tar.gz': '6c4522d595e4cbcd00157ac458a72f8aec01757053d2073f99daa39e442b2a36'},
+    {'julia.wrapper': 'a36a3e0cb98ab4d2b05e0ca8f0bf2724baafbd669a0db318a00e40737d2f02f9'},
+]
+
+# install wrapper with linking safeguards for Julia libraries
+postinstallcmds = ["cd %(installdir)s/bin && mv julia julia.bin && mv julia.wrapper julia"]
 
 sanity_check_paths = {
-    'files': ['bin/julia', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT],
-    'dirs': ['bin', 'etc', 'include', 'lib', 'share']
+    'files': ['bin/julia', 'bin/julia.bin', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT],
+    'dirs': ['bin', 'etc', 'include', 'lib', 'lib/julia', 'share']
 }
-
 sanity_check_commands = ['julia --help']
 
-modextravars = {
-    # Use default DEPOT_PATH where first entry is user's depot
-    # JULIA_DEPOT_PATH must be set to be able to load other JuliaPackage modules and have
-    # those installations appended to DEPOT_PATH without disabling any of the default paths
-    'JULIA_DEPOT_PATH': ':',
-}
-
 moduleclass = 'lang'
diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.7.0-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.7.0-linux-x86_64.eb
index ecc3020f4c0..45655ab233d 100644
--- a/easybuild/easyconfigs/j/Julia/Julia-1.7.0-linux-x86_64.eb
+++ b/easybuild/easyconfigs/j/Julia/Julia-1.7.0-linux-x86_64.eb
@@ -19,20 +19,19 @@ toolchain = SYSTEM
 
 source_urls = ['https://julialang-s3.julialang.org/bin/linux/x64/%(version_major_minor)s/']
 sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz']
-checksums = ['7299f3a638aec5e0b9e14eaf0e6221c4fe27189aa0b38ac5a36f03f0dc4c0d40']
+patches = [('julia.wrapper', 'bin/')]
+checksums = [
+    {'julia-1.7.0-linux-x86_64.tar.gz': '7299f3a638aec5e0b9e14eaf0e6221c4fe27189aa0b38ac5a36f03f0dc4c0d40'},
+    {'julia.wrapper': 'a36a3e0cb98ab4d2b05e0ca8f0bf2724baafbd669a0db318a00e40737d2f02f9'},
+]
+
+# install wrapper with linking safeguards for Julia libraries
+postinstallcmds = ["cd %(installdir)s/bin && mv julia julia.bin && mv julia.wrapper julia"]
 
 sanity_check_paths = {
-    'files': ['bin/julia', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT],
-    'dirs': ['bin', 'etc', 'include', 'lib', 'share']
+    'files': ['bin/julia', 'bin/julia.bin', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT],
+    'dirs': ['bin', 'etc', 'include', 'lib', 'lib/julia', 'share']
 }
-
 sanity_check_commands = ['julia --help']
 
-modextravars = {
-    # Use default DEPOT_PATH where first entry is user's depot
-    # JULIA_DEPOT_PATH must be set to be able to load other JuliaPackage modules and have
-    # those installations appended to DEPOT_PATH without disabling any of the default paths
-    'JULIA_DEPOT_PATH': ':',
-}
-
 moduleclass = 'lang'
diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.7.1-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.7.1-linux-x86_64.eb
index b8b0a744c04..3dbb49f7345 100644
--- a/easybuild/easyconfigs/j/Julia/Julia-1.7.1-linux-x86_64.eb
+++ b/easybuild/easyconfigs/j/Julia/Julia-1.7.1-linux-x86_64.eb
@@ -19,20 +19,19 @@ toolchain = SYSTEM
 
 source_urls = ['https://julialang-s3.julialang.org/bin/linux/x64/%(version_major_minor)s/']
 sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz']
-checksums = ['44658e9c7b45e2b9b5b59239d190cca42de05c175ea86bc346c294a8fe8d9f11']
+patches = [('julia.wrapper', 'bin/')]
+checksums = [
+    {'julia-1.7.1-linux-x86_64.tar.gz': '44658e9c7b45e2b9b5b59239d190cca42de05c175ea86bc346c294a8fe8d9f11'},
+    {'julia.wrapper': 'a36a3e0cb98ab4d2b05e0ca8f0bf2724baafbd669a0db318a00e40737d2f02f9'},
+]
+
+# install wrapper with linking safeguards for Julia libraries
+postinstallcmds = ["cd %(installdir)s/bin && mv julia julia.bin && mv julia.wrapper julia"]
 
 sanity_check_paths = {
-    'files': ['bin/julia', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT],
-    'dirs': ['bin', 'etc', 'include', 'lib', 'share']
+    'files': ['bin/julia', 'bin/julia.bin', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT],
+    'dirs': ['bin', 'etc', 'include', 'lib', 'lib/julia', 'share']
 }
-
 sanity_check_commands = ['julia --help']
 
-modextravars = {
-    # Use default DEPOT_PATH where first entry is user's depot
-    # JULIA_DEPOT_PATH must be set to be able to load other JuliaPackage modules and have
-    # those installations appended to DEPOT_PATH without disabling any of the default paths
-    'JULIA_DEPOT_PATH': ':',
-}
-
 moduleclass = 'lang'
diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.7.2-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.7.2-linux-x86_64.eb
index e88e509e098..1742ac0b42b 100644
--- a/easybuild/easyconfigs/j/Julia/Julia-1.7.2-linux-x86_64.eb
+++ b/easybuild/easyconfigs/j/Julia/Julia-1.7.2-linux-x86_64.eb
@@ -19,20 +19,19 @@ toolchain = SYSTEM
 
 source_urls = ['https://julialang-s3.julialang.org/bin/linux/x64/%(version_major_minor)s/']
 sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz']
-checksums = ['a75244724f3b2de0e7249c861fbf64078257c16fb4203be78f1cf4dd5973ba95']
+patches = [('julia.wrapper', 'bin/')]
+checksums = [
+    {'julia-1.7.2-linux-x86_64.tar.gz': 'a75244724f3b2de0e7249c861fbf64078257c16fb4203be78f1cf4dd5973ba95'},
+    {'julia.wrapper': 'a36a3e0cb98ab4d2b05e0ca8f0bf2724baafbd669a0db318a00e40737d2f02f9'},
+]
+
+# install wrapper with linking safeguards for Julia libraries
+postinstallcmds = ["cd %(installdir)s/bin && mv julia julia.bin && mv julia.wrapper julia"]
 
 sanity_check_paths = {
-    'files': ['bin/julia', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT],
-    'dirs': ['bin', 'etc', 'include', 'lib', 'share']
+    'files': ['bin/julia', 'bin/julia.bin', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT],
+    'dirs': ['bin', 'etc', 'include', 'lib', 'lib/julia', 'share']
 }
-
 sanity_check_commands = ['julia --help']
 
-modextravars = {
-    # Use default DEPOT_PATH where first entry is user's depot
-    # JULIA_DEPOT_PATH must be set to be able to load other JuliaPackage modules and have
-    # those installations appended to DEPOT_PATH without disabling any of the default paths
-    'JULIA_DEPOT_PATH': ':',
-}
-
 moduleclass = 'lang'
diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.7.3-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.7.3-linux-x86_64.eb
index dac9088825a..61ab7eb2bdf 100644
--- a/easybuild/easyconfigs/j/Julia/Julia-1.7.3-linux-x86_64.eb
+++ b/easybuild/easyconfigs/j/Julia/Julia-1.7.3-linux-x86_64.eb
@@ -19,20 +19,19 @@ toolchain = SYSTEM
 
 source_urls = ['https://julialang-s3.julialang.org/bin/linux/x64/%(version_major_minor)s/']
 sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz']
-checksums = ['9b2f4fa12d92b4dcc5d11dc66fb118c47681a76d3df8da064cc97573f2f5c739']
+patches = [('julia.wrapper', 'bin/')]
+checksums = [
+    {'julia-1.7.3-linux-x86_64.tar.gz': '9b2f4fa12d92b4dcc5d11dc66fb118c47681a76d3df8da064cc97573f2f5c739'},
+    {'julia.wrapper': 'a36a3e0cb98ab4d2b05e0ca8f0bf2724baafbd669a0db318a00e40737d2f02f9'},
+]
+
+# install wrapper with linking safeguards for Julia libraries
+postinstallcmds = ["cd %(installdir)s/bin && mv julia julia.bin && mv julia.wrapper julia"]
 
 sanity_check_paths = {
-    'files': ['bin/julia', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT],
-    'dirs': ['bin', 'etc', 'include', 'lib', 'share']
+    'files': ['bin/julia', 'bin/julia.bin', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT],
+    'dirs': ['bin', 'etc', 'include', 'lib', 'lib/julia', 'share']
 }
-
 sanity_check_commands = ['julia --help']
 
-modextravars = {
-    # Use default DEPOT_PATH where first entry is user's depot
-    # JULIA_DEPOT_PATH must be set to be able to load other JuliaPackage modules and have
-    # those installations appended to DEPOT_PATH without disabling any of the default paths
-    'JULIA_DEPOT_PATH': ':',
-}
-
 moduleclass = 'lang'
diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.8.0-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.8.0-linux-x86_64.eb
index c7f6214e4a8..77e3fee2212 100644
--- a/easybuild/easyconfigs/j/Julia/Julia-1.8.0-linux-x86_64.eb
+++ b/easybuild/easyconfigs/j/Julia/Julia-1.8.0-linux-x86_64.eb
@@ -19,20 +19,19 @@ toolchain = SYSTEM
 
 source_urls = ['https://julialang-s3.julialang.org/bin/linux/x64/%(version_major_minor)s/']
 sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz']
-checksums = ['e80d732ccb7f79e000d798cb8b656dc3641ab59516d6e4e52e16765017892a00']
+patches = [('julia.wrapper', 'bin/')]
+checksums = [
+    {'julia-1.8.0-linux-x86_64.tar.gz': 'e80d732ccb7f79e000d798cb8b656dc3641ab59516d6e4e52e16765017892a00'},
+    {'julia.wrapper': 'a36a3e0cb98ab4d2b05e0ca8f0bf2724baafbd669a0db318a00e40737d2f02f9'},
+]
+
+# install wrapper with linking safeguards for Julia libraries
+postinstallcmds = ["cd %(installdir)s/bin && mv julia julia.bin && mv julia.wrapper julia"]
 
 sanity_check_paths = {
-    'files': ['bin/julia', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT],
-    'dirs': ['bin', 'etc', 'include', 'lib', 'share']
+    'files': ['bin/julia', 'bin/julia.bin', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT],
+    'dirs': ['bin', 'etc', 'include', 'lib', 'lib/julia', 'share']
 }
-
 sanity_check_commands = ['julia --help']
 
-modextravars = {
-    # Use default DEPOT_PATH where first entry is user's depot
-    # JULIA_DEPOT_PATH must be set to be able to load other JuliaPackage modules and have
-    # those installations appended to DEPOT_PATH without disabling any of the default paths
-    'JULIA_DEPOT_PATH': ':',
-}
-
 moduleclass = 'lang'
diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.8.2-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.8.2-linux-x86_64.eb
index 37b817f557e..fd619b4de39 100644
--- a/easybuild/easyconfigs/j/Julia/Julia-1.8.2-linux-x86_64.eb
+++ b/easybuild/easyconfigs/j/Julia/Julia-1.8.2-linux-x86_64.eb
@@ -19,20 +19,19 @@ toolchain = SYSTEM
 
 source_urls = ['https://julialang-s3.julialang.org/bin/linux/x64/%(version_major_minor)s/']
 sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz']
-checksums = ['671cf3a450b63a717e1eedd7f69087e3856f015b2e146cb54928f19a3c05e796']
+patches = [('julia.wrapper', 'bin/')]
+checksums = [
+    {'julia-1.8.2-linux-x86_64.tar.gz': '671cf3a450b63a717e1eedd7f69087e3856f015b2e146cb54928f19a3c05e796'},
+    {'julia.wrapper': 'a36a3e0cb98ab4d2b05e0ca8f0bf2724baafbd669a0db318a00e40737d2f02f9'},
+]
+
+# install wrapper with linking safeguards for Julia libraries
+postinstallcmds = ["cd %(installdir)s/bin && mv julia julia.bin && mv julia.wrapper julia"]
 
 sanity_check_paths = {
-    'files': ['bin/julia', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT],
-    'dirs': ['bin', 'etc', 'include', 'lib', 'share']
+    'files': ['bin/julia', 'bin/julia.bin', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT],
+    'dirs': ['bin', 'etc', 'include', 'lib', 'lib/julia', 'share']
 }
-
 sanity_check_commands = ['julia --help']
 
-modextravars = {
-    # Use default DEPOT_PATH where first entry is user's depot
-    # JULIA_DEPOT_PATH must be set to be able to load other JuliaPackage modules and have
-    # those installations appended to DEPOT_PATH without disabling any of the default paths
-    'JULIA_DEPOT_PATH': ':',
-}
-
 moduleclass = 'lang'
diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.8.5-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.8.5-linux-x86_64.eb
index 1d5fa47c96c..d69227cc952 100644
--- a/easybuild/easyconfigs/j/Julia/Julia-1.8.5-linux-x86_64.eb
+++ b/easybuild/easyconfigs/j/Julia/Julia-1.8.5-linux-x86_64.eb
@@ -19,20 +19,19 @@ toolchain = SYSTEM
 
 source_urls = ['https://julialang-s3.julialang.org/bin/linux/x64/%(version_major_minor)s/']
 sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz']
-checksums = ['e71a24816e8fe9d5f4807664cbbb42738f5aa9fe05397d35c81d4c5d649b9d05']
+patches = [('julia.wrapper', 'bin/')]
+checksums = [
+    {'julia-1.8.5-linux-x86_64.tar.gz': 'e71a24816e8fe9d5f4807664cbbb42738f5aa9fe05397d35c81d4c5d649b9d05'},
+    {'julia.wrapper': 'a36a3e0cb98ab4d2b05e0ca8f0bf2724baafbd669a0db318a00e40737d2f02f9'},
+]
+
+postinstallcmds = ["cd %(installdir)s/bin && mv julia julia.bin && mv julia.wrapper julia"]
 
 sanity_check_paths = {
-    'files': ['bin/julia', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT],
-    'dirs': ['bin', 'etc', 'include', 'lib', 'share']
+    'files': ['bin/julia', 'bin/julia.bin', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT],
+    'dirs': ['bin', 'etc', 'include', 'lib', 'lib/julia', 'share']
 }
 
 sanity_check_commands = ['julia --help']
 
-modextravars = {
-    # Use default DEPOT_PATH where first entry is user's depot
-    # JULIA_DEPOT_PATH must be set to be able to load other JuliaPackage modules and have
-    # those installations appended to DEPOT_PATH without disabling any of the default paths
-    'JULIA_DEPOT_PATH': ':',
-}
-
 moduleclass = 'lang'
diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.9.0-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.9.0-linux-x86_64.eb
index 2ee4230cbb9..7469924860b 100644
--- a/easybuild/easyconfigs/j/Julia/Julia-1.9.0-linux-x86_64.eb
+++ b/easybuild/easyconfigs/j/Julia/Julia-1.9.0-linux-x86_64.eb
@@ -19,20 +19,19 @@ toolchain = SYSTEM
 
 source_urls = ['https://julialang-s3.julialang.org/bin/linux/x64/%(version_major_minor)s/']
 sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz']
-checksums = ['00c614466ef9809c2eb23480e38d196a2c577fff2730c4f83d135b913d473359']
+patches = [('julia.wrapper', 'bin/')]
+checksums = [
+    {'julia-1.9.0-linux-x86_64.tar.gz': '00c614466ef9809c2eb23480e38d196a2c577fff2730c4f83d135b913d473359'},
+    {'julia.wrapper': 'a36a3e0cb98ab4d2b05e0ca8f0bf2724baafbd669a0db318a00e40737d2f02f9'},
+]
+
+# install wrapper with linking safeguards for Julia libraries
+postinstallcmds = ["cd %(installdir)s/bin && mv julia julia.bin && mv julia.wrapper julia"]
 
 sanity_check_paths = {
-    'files': ['bin/julia', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT],
-    'dirs': ['bin', 'etc', 'include', 'lib', 'share']
+    'files': ['bin/julia', 'bin/julia.bin', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT],
+    'dirs': ['bin', 'etc', 'include', 'lib', 'lib/julia', 'share']
 }
-
 sanity_check_commands = ['julia --help']
 
-modextravars = {
-    # Use default DEPOT_PATH where first entry is user's depot
-    # JULIA_DEPOT_PATH must be set to be able to load other JuliaPackage modules and have
-    # those installations appended to DEPOT_PATH without disabling any of the default paths
-    'JULIA_DEPOT_PATH': ':',
-}
-
 moduleclass = 'lang'
diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.9.2-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.9.2-linux-x86_64.eb
index a0d92b7aacb..01939dc25f7 100644
--- a/easybuild/easyconfigs/j/Julia/Julia-1.9.2-linux-x86_64.eb
+++ b/easybuild/easyconfigs/j/Julia/Julia-1.9.2-linux-x86_64.eb
@@ -19,20 +19,19 @@ toolchain = SYSTEM
 
 source_urls = ['https://julialang-s3.julialang.org/bin/linux/x64/%(version_major_minor)s/']
 sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz']
-checksums = ['4c2d799f442d7fe718827b19da2bacb72ea041b9ce55f24eee7b1313f57c4383']
+patches = [('julia.wrapper', 'bin/')]
+checksums = [
+    {'julia-1.9.2-linux-x86_64.tar.gz': '4c2d799f442d7fe718827b19da2bacb72ea041b9ce55f24eee7b1313f57c4383'},
+    {'julia.wrapper': 'a36a3e0cb98ab4d2b05e0ca8f0bf2724baafbd669a0db318a00e40737d2f02f9'},
+]
+
+postinstallcmds = ["cd %(installdir)s/bin && mv julia julia.bin && mv julia.wrapper julia"]
 
 sanity_check_paths = {
-    'files': ['bin/julia', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT],
-    'dirs': ['bin', 'etc', 'include', 'lib', 'share']
+    'files': ['bin/julia', 'bin/julia.bin', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT],
+    'dirs': ['bin', 'etc', 'include', 'lib', 'lib/julia', 'share']
 }
 
 sanity_check_commands = ['julia --help']
 
-modextravars = {
-    # Use default DEPOT_PATH where first entry is user's depot
-    # JULIA_DEPOT_PATH must be set to be able to load other JuliaPackage modules and have
-    # those installations appended to DEPOT_PATH without disabling any of the default paths
-    'JULIA_DEPOT_PATH': ':',
-}
-
 moduleclass = 'lang'
diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.9.3-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.9.3-linux-x86_64.eb
index 7b207dc635c..d5e1511d63e 100644
--- a/easybuild/easyconfigs/j/Julia/Julia-1.9.3-linux-x86_64.eb
+++ b/easybuild/easyconfigs/j/Julia/Julia-1.9.3-linux-x86_64.eb
@@ -19,20 +19,19 @@ toolchain = SYSTEM
 
 source_urls = ['https://julialang-s3.julialang.org/bin/linux/x64/%(version_major_minor)s/']
 sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz']
-checksums = ['d76670cc9ba3e0fd4c1545dd3d00269c0694976a1176312795ebce1692d323d1']
+patches = [('julia.wrapper', 'bin/')]
+checksums = [
+    {'julia-1.9.3-linux-x86_64.tar.gz': 'd76670cc9ba3e0fd4c1545dd3d00269c0694976a1176312795ebce1692d323d1'},
+    {'julia.wrapper': 'a36a3e0cb98ab4d2b05e0ca8f0bf2724baafbd669a0db318a00e40737d2f02f9'},
+]
+
+# install wrapper with linking safeguards for Julia libraries
+postinstallcmds = ["cd %(installdir)s/bin && mv julia julia.bin && mv julia.wrapper julia"]
 
 sanity_check_paths = {
-    'files': ['bin/julia', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT],
-    'dirs': ['bin', 'etc', 'include', 'lib', 'share']
+    'files': ['bin/julia', 'bin/julia.bin', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT],
+    'dirs': ['bin', 'etc', 'include', 'lib', 'lib/julia', 'share']
 }
-
 sanity_check_commands = ['julia --help']
 
-modextravars = {
-    # Use default DEPOT_PATH where first entry is user's depot
-    # JULIA_DEPOT_PATH must be set to be able to load other JuliaPackage modules and have
-    # those installations appended to DEPOT_PATH without disabling any of the default paths
-    'JULIA_DEPOT_PATH': ':',
-}
-
 moduleclass = 'lang'

From 36fdc535eb94f43f97721d03a77b49006c0d1ffc Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Wed, 13 Mar 2024 11:40:02 +0100
Subject: [PATCH 021/835] adding file julia.wrapper

---
 easybuild/easyconfigs/j/Julia/julia.wrapper | 2 ++
 1 file changed, 2 insertions(+)
 create mode 100755 easybuild/easyconfigs/j/Julia/julia.wrapper

diff --git a/easybuild/easyconfigs/j/Julia/julia.wrapper b/easybuild/easyconfigs/j/Julia/julia.wrapper
new file mode 100755
index 00000000000..625ec57ab49
--- /dev/null
+++ b/easybuild/easyconfigs/j/Julia/julia.wrapper
@@ -0,0 +1,2 @@
+#!/bin/bash
+LD_LIBRARY_PATH="$EBROOTJULIA/lib:$EBROOTJULIA/lib/julia:$LD_LIBRARY_PATH" julia.bin "$@"

From 6bb1bcb21ae67f04e106bd83301241b4c7e61630 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Thu, 14 Mar 2024 15:03:53 +0100
Subject: [PATCH 022/835] adding easyconfigs:
 Single-cell-python-bundle-2024.02-foss-2023a.eb

---
 ...e-cell-python-bundle-2024.02-foss-2023a.eb | 58 +++++++++++++++++++
 1 file changed, 58 insertions(+)
 create mode 100644 easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb

diff --git a/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb b/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb
new file mode 100644
index 00000000000..fd51741e663
--- /dev/null
+++ b/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb
@@ -0,0 +1,58 @@
+easyblock = 'PythonBundle'
+
+name = 'Single-cell-python-bundle'
+version = '2024.02'
+
+homepage = 'xxx'
+description = """Bundle for single-cell ???"""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('Python-bundle-PyPI', '2023.06'),
+    ('SciPy-bundle', '2023.07'),
+    ('matplotlib', '3.7.2'),
+    ('Seaborn', '0.13.2'),
+    ('PyTorch', '2.1.2'),
+    ('scanpy', '1.9.8'),
+    # scvi-tools TODO
+    # scArches TODO
+    # scib-metrics TODO
+    ('scib', '1.1.4'),
+    ('scVelo', '0.3.1'),  # imports loompy
+    ('CellTypist', '1.6.2'),
+    # loompy in scVelo
+    ('epiScanpy', '0.4.0'),
+    ('CellRank', '2.0.2'),
+    ('scCODA', '0.1.9'),  # imports rpy2
+    # rpy2 in scCODA
+    ('infercnvpy', '4.0.3'),
+    ('pySCENIC', '0.12.1-20240311'),
+    ('Squidpy', '1.4.1'),
+    ('umap-learn', '0.5.5'),  # bbknn dep
+    ('scikit-learn', '1.3.1'),  # bbknn dep
+]
+
+# DEPS to add:
+# Anndata2ri
+# Cassiopeia
+# Sc_toolbox
+# Altair
+# Pertpy
+# Tasccoda
+# Liana-py 
+# Harmonypy
+# Scirpy
+# CellPhoneDB
+# Decoupler
+# contrastiveVI
+# Schist
+
+exts_list = [
+    ('pynndescent', '0.5.11'),
+    ('annoy', '1.17.3'),
+    ('bbknn', '1.6.0'),  # requested
+]
+
+moduleclass = 'bio'

From 248a561ed299b36c26c53befaf23cf38441fcdb3 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Fri, 15 Mar 2024 10:23:43 +0100
Subject: [PATCH 023/835] update1 bundle

---
 ...e-cell-python-bundle-2024.02-foss-2023a.eb | 55 +++++++++++++++----
 1 file changed, 43 insertions(+), 12 deletions(-)

diff --git a/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb b/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb
index fd51741e663..8629de7f8be 100644
--- a/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb
+++ b/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb
@@ -8,6 +8,8 @@ description = """Bundle for single-cell ???"""
 
 toolchain = {'name': 'foss', 'version': '2023a'}
 
+builddependencies = [('poetry', '1.5.1')]
+
 dependencies = [
     ('Python', '3.11.3'),
     ('Python-bundle-PyPI', '2023.06'),
@@ -20,23 +22,22 @@ dependencies = [
     # scArches TODO
     # scib-metrics TODO
     ('scib', '1.1.4'),
-    ('scVelo', '0.3.1'),  # imports loompy
+    # ('scVelo', '0.3.1'),  # imports loompy
     ('CellTypist', '1.6.2'),
     # loompy in scVelo
     ('epiScanpy', '0.4.0'),
-    ('CellRank', '2.0.2'),
+    # ('CellRank', '2.0.2'),
     ('scCODA', '0.1.9'),  # imports rpy2
     # rpy2 in scCODA
-    ('infercnvpy', '4.0.3'),
-    ('pySCENIC', '0.12.1-20240311'),
-    ('Squidpy', '1.4.1'),
-    ('umap-learn', '0.5.5'),  # bbknn dep
-    ('scikit-learn', '1.3.1'),  # bbknn dep
+    ('infercnvpy', '0.4.3'),
+    # ('pySCENIC', '0.12.1-20240311'),
+    # ('Squidpy', '1.4.1'),
+    ('umap-learn', '0.5.5'),  # bbknn
+    ('scikit-learn', '1.3.1'),  # bbknn
+    ('Pillow', '10.0.0'),  # cassiopeia
 ]
 
 # DEPS to add:
-# Anndata2ri
-# Cassiopeia
 # Sc_toolbox
 # Altair
 # Pertpy
@@ -50,9 +51,39 @@ dependencies = [
 # Schist
 
 exts_list = [
-    ('pynndescent', '0.5.11'),
-    ('annoy', '1.17.3'),
-    ('bbknn', '1.6.0'),  # requested
+    ('arrow', '0.17.0', {
+        'checksums': ['ff08d10cda1d36c68657d6ad20d74fbea493d980f8b2d45344e00d6ed2bf6ed4'],
+    }),
+    ('datapipelines', '1.0.7', {
+        'checksums': ['752bc71a1e03a45d723fc4d9b56c641ed0b872ed1df73b08896ee34d93c56e8f'],
+    }),
+    ('merakicommons', '1.0.10', {
+        'checksums': ['fc99ebe0cb85c4af0093a9454294adcb97c0792f8a8dd03898242ab2446aa77e'],
+    }),
+    ('flake8', '7.0.0', {
+        'checksums': ['33f96621059e65eec474169085dc92bf26e7b2d47366b70be2f67ab80dc25132'],
+    }),
+    ('pynndescent', '0.5.11', {
+        'checksums': ['6f44ced9d5a9da2c87d9b2fff30bb5308540c0657605e4d5cde7ed3275bbad50'],
+    }),
+    ('annoy', '1.17.3', {
+        'checksums': ['9cbfebefe0a5f843eba29c6be4c84d601f4f41ad4ded0486f1b88c3b07739c15'],
+    }),
+    ('tzlocal', '5.2', {
+        'checksums': ['8d399205578f1a9342816409cc1e46a93ebd5755e39ea2d85334bea911bf0e6e'],
+    }),
+    ('anndata2ri', '1.3.1', {
+        'checksums': ['0e3fa2f81789f682d19ef452fabdb401ec27899db9abe5a78e45e21dcc7caa42'],
+    }),
+    ('bbknn', '1.6.0', {
+        'checksums': ['1c01a9d6df2fc52a527de8a403617897a4b672724863299a7026f2132f1b041b'],
+    }),
+    ('cassiopeia', '5.0.3', {
+        'checksums': ['18adfc81f795f807ce6e6674da5c81c801d28ecf42f9ce94e23fc018b6840d63'],
+    }),
+    # ('sc_toolbox', '0.12.3', {
+    #     'checksums': ['6ca22a364c269a095114e620eb3c6da8aac1950d8f43f58ceea08005a09cc2cb'],
+    # }),
 ]
 
 moduleclass = 'bio'

From 12d3670f2ac49d1085cab694383ce92eaaeccbc9 Mon Sep 17 00:00:00 2001
From: crivella <davide.grassano@epfl.ch>
Date: Mon, 18 Mar 2024 16:05:30 +0100
Subject: [PATCH 024/835] Added Econf for QE 7.3.1 with cmake foss/intel

---
 .../QuantumESPRESSO-7.3.1-foss-2023a.eb       | 57 ++++++++++++++++++
 .../QuantumESPRESSO-7.3.1-intel-2023a.eb      | 58 +++++++++++++++++++
 2 files changed, 115 insertions(+)
 create mode 100644 easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-foss-2023a.eb
 create mode 100644 easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-intel-2023a.eb

diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-foss-2023a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-foss-2023a.eb
new file mode 100644
index 00000000000..5ae5b6db043
--- /dev/null
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-foss-2023a.eb
@@ -0,0 +1,57 @@
+name = 'QuantumESPRESSO'
+version = '7.3'
+
+homepage = 'https://www.quantum-espresso.org'
+description = """Quantum ESPRESSO  is an integrated suite of computer codes
+for electronic-structure calculations and materials modeling at the nanoscale.
+It is based on density-functional theory, plane waves, and pseudopotentials
+(both norm-conserving and ultrasoft).
+"""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+toolchainopts = {
+    'usempi': True,
+    'openmp': True,
+    }
+
+sources = [
+    {
+        'filename': 'q-e-qe-%(version)s.tar.gz',
+        'extract_cmd': 'mkdir -p %(builddir)s/qe-%(version)s && tar xzvf %s --strip-components=1 -C $_',
+        'source_urls': ['https://gitlab.com/QEF/q-e/-/archive/qe-%(version)s']
+    },
+    {
+        'filename': 'qe-gipaw-%(version)s.tar.gz',
+        'source_urls': ['https://github.com/dceresoli/qe-gipaw/releases/download/%(version)s/']},
+    {
+        'filename': 'wannier90-3.1.0.tar.gz',
+        'download_filename': 'v3.1.0.tar.gz',
+        'source_urls': ['https://github.com/wannier-developers/wannier90/archive/']
+    },
+]
+checksums = [
+    {'q-e-qe-%(version)s.tar.gz': 'edc2a0f3315c69966df4f82ec86ab9f682187bc9430ef6d2bacad5f27f08972c'},
+    {'qe-gipaw-%(version)s.tar.gz': 'a24d328ec068043d36fdf69fe4f8d1904d7befeba7962cb85be059ea0fe6f026'},
+    {'wannier90-3.1.0.tar.gz': '40651a9832eb93dec20a8360dd535262c261c34e13c41b6755fa6915c936b254'},
+]
+
+builddependencies = [
+    ('M4', '1.4.19'),
+]
+dependencies = [
+    ('HDF5', '1.14.0'),
+    ('ELPA', '2023.05.001'),
+    ('libxc', '6.2.2'),
+]
+
+# The third party packages should be installed separately and added as
+# dependencies.  The exception is w90, which is force built, and gipaw
+# which depends on qe source
+buildopts = "all gwl xspectra couple epw gipaw w90"
+with_fox = True # Needed from QE7.2 to build GIPAW
+
+# parallel build tends to fail
+parallel = 1
+
+
+moduleclass = 'chem'
diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-intel-2023a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-intel-2023a.eb
new file mode 100644
index 00000000000..f4f49d2223e
--- /dev/null
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-intel-2023a.eb
@@ -0,0 +1,58 @@
+easyblock = 'EB_QuantumESPRESSOcmake'
+
+name = 'QuantumESPRESSO'
+version = '7.3.1'
+
+homepage = 'https://www.quantum-espresso.org'
+description = """Quantum ESPRESSO  is an integrated suite of computer codes
+for electronic-structure calculations and materials modeling at the nanoscale.
+It is based on density-functional theory, plane waves, and pseudopotentials
+(both norm-conserving and ultrasoft).
+"""
+
+toolchain = {'name': 'intel', 'version': '2023a'}
+toolchainopts = {
+    'usempi': True,
+    'openmp': False # QE not linking FFTW and ELPA correctly with OpenMP + cmake
+    }
+
+sources = [
+    {
+        'filename': 'q-e-qe-%(version)s.tar.gz',
+        'extract_cmd': 'mkdir -p %(builddir)s/qe-%(version)s && tar xzvf %s --strip-components=1 -C $_',
+        'source_urls': ['https://gitlab.com/QEF/q-e/-/archive/qe-%(version)s']
+    },
+]
+checksums = [
+    {'q-e-qe-%(version)s.tar.gz': '2c58b8fadfe4177de5a8b69eba447db5e623420b070dea6fd26c1533b081d844'},
+]
+
+builddependencies = [
+    ('M4', '1.4.19'),
+    ('CMake', '3.26.3'),
+]
+dependencies = [
+    ('HDF5', '1.14.0'),
+    ('ELPA', '2023.05.001'),
+    ('libxc', '6.2.2'),
+]
+
+# Disabled because of https://gitlab.com/QEF/q-e/-/issues/667
+# Trouble in linking with shared libraries and intel toolchain
+build_shared_libs = False
+with_scalapack = True
+with_gipaw = False # https://github.com/dceresoli/qe-gipaw/issues/19
+with_d3q = False # https://gitlab.com/QEF/q-e/-/issues/666
+with_qmcpack = True
+
+moduleclass = 'chem'
+
+test_suite_threshold = 0.4 # Low threshold because of https://gitlab.com/QEF/q-e/-/issues/665
+test_suite_max_failed = 5 # Allow for some flaky tests (failed due to strict thresholds)
+test_suite_allow_failures = [
+    'test_qe_xclib_',  # 7.3.1:  https://gitlab.com/QEF/q-e/-/issues/640
+    '--hp_',  # 7.3.1:  Broken testsuite (https://gitlab.com/QEF/q-e/-/issues/665)
+    '--ph_',  # 7.3.1:  Broken testsuite (https://gitlab.com/QEF/q-e/-/issues/665)
+    '--epw_',  # 7.3.1:  Broken testsuite (https://gitlab.com/QEF/q-e/-/issues/665)
+    '--tddfpt_',  # 7.3.1:  Broken testsuite (https://gitlab.com/QEF/q-e/-/issues/665)
+]

From 6f04b7fde1cc62217e9596e0cfff8be5d588b8d4 Mon Sep 17 00:00:00 2001
From: crivella <davide.grassano@epfl.ch>
Date: Mon, 18 Mar 2024 16:11:30 +0100
Subject: [PATCH 025/835] Updated wrong copy

---
 .../QuantumESPRESSO-7.3.1-foss-2023a.eb       | 47 ++++++++++---------
 1 file changed, 24 insertions(+), 23 deletions(-)

diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-foss-2023a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-foss-2023a.eb
index 5ae5b6db043..39bca0aefae 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-foss-2023a.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-foss-2023a.eb
@@ -1,5 +1,7 @@
+easyblock = 'EB_QuantumESPRESSOcmake'
+
 name = 'QuantumESPRESSO'
-version = '7.3'
+version = '7.3.1'
 
 homepage = 'https://www.quantum-espresso.org'
 description = """Quantum ESPRESSO  is an integrated suite of computer codes
@@ -8,10 +10,10 @@ It is based on density-functional theory, plane waves, and pseudopotentials
 (both norm-conserving and ultrasoft).
 """
 
-toolchain = {'name': 'foss', 'version': '2023a'}
+toolchain = {'name': 'intel', 'version': '2023a'}
 toolchainopts = {
     'usempi': True,
-    'openmp': True,
+    'openmp': False # QE not linking FFTW and ELPA correctly with OpenMP + cmake
     }
 
 sources = [
@@ -20,23 +22,14 @@ sources = [
         'extract_cmd': 'mkdir -p %(builddir)s/qe-%(version)s && tar xzvf %s --strip-components=1 -C $_',
         'source_urls': ['https://gitlab.com/QEF/q-e/-/archive/qe-%(version)s']
     },
-    {
-        'filename': 'qe-gipaw-%(version)s.tar.gz',
-        'source_urls': ['https://github.com/dceresoli/qe-gipaw/releases/download/%(version)s/']},
-    {
-        'filename': 'wannier90-3.1.0.tar.gz',
-        'download_filename': 'v3.1.0.tar.gz',
-        'source_urls': ['https://github.com/wannier-developers/wannier90/archive/']
-    },
 ]
 checksums = [
-    {'q-e-qe-%(version)s.tar.gz': 'edc2a0f3315c69966df4f82ec86ab9f682187bc9430ef6d2bacad5f27f08972c'},
-    {'qe-gipaw-%(version)s.tar.gz': 'a24d328ec068043d36fdf69fe4f8d1904d7befeba7962cb85be059ea0fe6f026'},
-    {'wannier90-3.1.0.tar.gz': '40651a9832eb93dec20a8360dd535262c261c34e13c41b6755fa6915c936b254'},
+    {'q-e-qe-%(version)s.tar.gz': '2c58b8fadfe4177de5a8b69eba447db5e623420b070dea6fd26c1533b081d844'},
 ]
 
 builddependencies = [
     ('M4', '1.4.19'),
+    ('CMake', '3.26.3'),
 ]
 dependencies = [
     ('HDF5', '1.14.0'),
@@ -44,14 +37,22 @@ dependencies = [
     ('libxc', '6.2.2'),
 ]
 
-# The third party packages should be installed separately and added as
-# dependencies.  The exception is w90, which is force built, and gipaw
-# which depends on qe source
-buildopts = "all gwl xspectra couple epw gipaw w90"
-with_fox = True # Needed from QE7.2 to build GIPAW
-
-# parallel build tends to fail
-parallel = 1
-
+# Disabled because of https://gitlab.com/QEF/q-e/-/issues/667
+# Trouble in linking with shared libraries and intel toolchain
+build_shared_libs = False 
+with_scalapack = True
+with_gipaw = False # https://github.com/dceresoli/qe-gipaw/issues/19
+with_d3q = False # https://gitlab.com/QEF/q-e/-/issues/666
+with_qmcpack = True
 
 moduleclass = 'chem'
+
+test_suite_threshold = 0.4 # Low threshold because of https://gitlab.com/QEF/q-e/-/issues/665
+test_suite_max_failed = 5 # Allow for some flaky tests (failed due to strict thresholds)
+test_suite_allow_failures = [
+    'test_qe_xclib_',  # 7.3.1:  https://gitlab.com/QEF/q-e/-/issues/640
+    '--hp_',  # 7.3.1:  Broken testsuite (https://gitlab.com/QEF/q-e/-/issues/665)
+    '--ph_',  # 7.3.1:  Broken testsuite (https://gitlab.com/QEF/q-e/-/issues/665)
+    '--epw_',  # 7.3.1:  Broken testsuite (https://gitlab.com/QEF/q-e/-/issues/665)
+    '--tddfpt_',  # 7.3.1:  Broken testsuite (https://gitlab.com/QEF/q-e/-/issues/665)
+]

From d3972cd586e2cc2a3c70f35293b9c5f8f5cfaf2f Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Mon, 18 Mar 2024 22:20:09 +0100
Subject: [PATCH 026/835] Allow for some failing tests in old easyconfigs

---
 .../q/QuantumESPRESSO/QuantumESPRESSO-6.7-foss-2021a.eb        | 3 +++
 .../q/QuantumESPRESSO/QuantumESPRESSO-6.7-intel-2021a.eb       | 3 +++
 .../q/QuantumESPRESSO/QuantumESPRESSO-6.8-intel-2021a.eb       | 3 +++
 .../q/QuantumESPRESSO/QuantumESPRESSO-7.0-foss-2021b.eb        | 3 +++
 .../q/QuantumESPRESSO/QuantumESPRESSO-7.1-intel-2022a.eb       | 3 +++
 5 files changed, 15 insertions(+)

diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-foss-2021a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-foss-2021a.eb
index 627a096a2d8..d167e57e541 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-foss-2021a.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-foss-2021a.eb
@@ -42,4 +42,7 @@ buildopts = 'all gwl xspectra couple epw gipaw w90'
 # parallel build tends to fail
 parallel = 1
 
+# allow some test failures (not investigated for old easyconfig)
+test_suite_max_failed = 4
+
 moduleclass = 'chem'
diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-intel-2021a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-intel-2021a.eb
index 7d5de7397f3..55923f47c1b 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-intel-2021a.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-intel-2021a.eb
@@ -42,4 +42,7 @@ buildopts = 'all gwl xspectra couple epw gipaw w90'
 # parallel build tends to fail
 parallel = 1
 
+# allow some test failures (not investigated for old easyconfig)
+test_suite_max_failed = 2
+
 moduleclass = 'chem'
diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.8-intel-2021a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.8-intel-2021a.eb
index 4b187cd70ee..5982b4efde6 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.8-intel-2021a.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.8-intel-2021a.eb
@@ -41,4 +41,7 @@ buildopts = 'all gwl xspectra couple epw gipaw w90'
 # parallel build tends to fail
 parallel = 1
 
+# allow some test failures (not investigated for old easyconfig)
+test_suite_max_failed = 4
+
 moduleclass = 'chem'
diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.0-foss-2021b.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.0-foss-2021b.eb
index a0a1ebea9ea..9f62ca5ad84 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.0-foss-2021b.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.0-foss-2021b.eb
@@ -41,4 +41,7 @@ buildopts = 'all gwl xspectra couple epw gipaw w90'
 # parallel build tends to fail
 parallel = 1
 
+# allow some test failures (not investigated for old easyconfig)
+test_suite_max_failed = 3
+
 moduleclass = 'chem'
diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-intel-2022a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-intel-2022a.eb
index a81be226c25..a7ed17a2f6b 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-intel-2022a.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-intel-2022a.eb
@@ -48,4 +48,7 @@ buildopts = 'all gwl xspectra couple epw gipaw w90'
 # parallel build tends to fail
 parallel = 1
 
+# allow some test failures (not investigated for old easyconfig)
+test_suite_max_failed = 6
+
 moduleclass = 'chem'

From 1e6c7262b218bd1ee16b712d1c64fcedb3c13a74 Mon Sep 17 00:00:00 2001
From: ocaisa <alan.ocais@cecam.org>
Date: Tue, 19 Mar 2024 16:21:33 +0100
Subject: [PATCH 027/835] Update QuantumESPRESSO-6.7-foss-2021a.eb

---
 .../q/QuantumESPRESSO/QuantumESPRESSO-6.7-foss-2021a.eb       | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-foss-2021a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-foss-2021a.eb
index d167e57e541..bdff659a888 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-foss-2021a.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-foss-2021a.eb
@@ -29,8 +29,8 @@ checksums = [
 
 dependencies = [
     ('HDF5', '1.10.7'),
-# From the QE configure help, this version of ELPA is not compatible
-#    ('ELPA', '2021.05.001'),
+    # From the QE configure help, this version of ELPA is not compatible
+    # ('ELPA', '2021.05.001'),
     ('libxc', '5.1.5'),
 ]
 

From 279d8533ca467599aa404d1c3783945cde18d8d3 Mon Sep 17 00:00:00 2001
From: ocaisa <alan.ocais@cecam.org>
Date: Tue, 19 Mar 2024 16:22:17 +0100
Subject: [PATCH 028/835] Update QuantumESPRESSO-6.7-intel-2021a.eb

---
 .../q/QuantumESPRESSO/QuantumESPRESSO-6.7-intel-2021a.eb      | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-intel-2021a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-intel-2021a.eb
index 55923f47c1b..99d05042d92 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-intel-2021a.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-intel-2021a.eb
@@ -29,8 +29,8 @@ checksums = [
 
 dependencies = [
     ('HDF5', '1.10.7'),
-# From the QE configure help, this version of ELPA is not compatible
-#    ('ELPA', '2021.05.001'),
+    # From the QE configure help, this version of ELPA is not compatible
+    # ('ELPA', '2021.05.001'),
     ('libxc', '5.1.5'),
 ]
 

From 6a42985e50fd8e880a6ebae42f245ca7ac2536f0 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Tue, 19 Mar 2024 18:20:27 +0100
Subject: [PATCH 029/835] update bundle + add adjustText pycodestyle

---
 .../adjustText/adjustText-1.1.1-foss-2023a.eb | 27 +++++++
 .../pycodestyle-2.11.1-foss-2023a.eb          | 24 ++++++
 ...e-cell-python-bundle-2024.02-foss-2023a.eb | 81 +++++++++++++++----
 3 files changed, 118 insertions(+), 14 deletions(-)
 create mode 100644 easybuild/easyconfigs/a/adjustText/adjustText-1.1.1-foss-2023a.eb
 create mode 100644 easybuild/easyconfigs/p/pycodestyle/pycodestyle-2.11.1-foss-2023a.eb

diff --git a/easybuild/easyconfigs/a/adjustText/adjustText-1.1.1-foss-2023a.eb b/easybuild/easyconfigs/a/adjustText/adjustText-1.1.1-foss-2023a.eb
new file mode 100644
index 00000000000..f109d19d3aa
--- /dev/null
+++ b/easybuild/easyconfigs/a/adjustText/adjustText-1.1.1-foss-2023a.eb
@@ -0,0 +1,27 @@
+easyblock = 'PythonBundle'
+
+name = 'adjustText'
+version = '1.1.1'
+
+homepage = 'https://github.com/Phlya/adjustText'
+description = "A small library for automatically adjustment of text position in matplotlib plots to minimize overlaps."
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('matplotlib', '3.7.2'),
+    ('SciPy-bundle', '2023.07'),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    (name, version, {
+        'modulename': 'adjustText',
+        'checksums': ['e2c0975ef2c642478e60f4c03c5e9afbdeda7764336907ef69a9205bfa2d9896'],
+    }),
+]
+
+moduleclass = 'tools'
diff --git a/easybuild/easyconfigs/p/pycodestyle/pycodestyle-2.11.1-foss-2023a.eb b/easybuild/easyconfigs/p/pycodestyle/pycodestyle-2.11.1-foss-2023a.eb
new file mode 100644
index 00000000000..c704acc3b36
--- /dev/null
+++ b/easybuild/easyconfigs/p/pycodestyle/pycodestyle-2.11.1-foss-2023a.eb
@@ -0,0 +1,24 @@
+easyblock = 'PythonBundle'
+
+name = 'pycodestyle'
+version = '2.11.1'
+
+homepage = "https://pycodestyle.readthedocs.io"
+description = """pycodestyle is a tool to check your Python code against some of the style conventions in PEP 8."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+dependencies = [
+    ('Python', '3.11.3'),
+]
+
+exts_list = [
+    (name, version, {
+        'checksums': ['41ba0e7afc9752dfb53ced5489e89f8186be00e599e712660695b7a75ff2663f'],
+    }),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb b/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb
index 8629de7f8be..a3c7011d4ac 100644
--- a/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb
+++ b/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb
@@ -8,7 +8,7 @@ description = """Bundle for single-cell ???"""
 
 toolchain = {'name': 'foss', 'version': '2023a'}
 
-builddependencies = [('poetry', '1.5.1')]
+# builddependencies = [('poetry', '1.5.1')]
 
 dependencies = [
     ('Python', '3.11.3'),
@@ -22,7 +22,7 @@ dependencies = [
     # scArches TODO
     # scib-metrics TODO
     ('scib', '1.1.4'),
-    # ('scVelo', '0.3.1'),  # imports loompy
+    ('scVelo', '0.3.1'),  # imports loompy
     ('CellTypist', '1.6.2'),
     # loompy in scVelo
     ('epiScanpy', '0.4.0'),
@@ -32,13 +32,29 @@ dependencies = [
     ('infercnvpy', '0.4.3'),
     # ('pySCENIC', '0.12.1-20240311'),
     # ('Squidpy', '1.4.1'),
-    ('umap-learn', '0.5.5'),  # bbknn
-    ('scikit-learn', '1.3.1'),  # bbknn
+    # deps for exts:
     ('Pillow', '10.0.0'),  # cassiopeia
+    ('pycodestyle', '2.11.1'),  # cassiopeia, created
+    ('umap-learn', '0.5.5'),  # bbknn
+    ('scikit-learn', '1.3.1'),  # bbknn, sc_toolbox
+    ('PyYAML', '6.0'),  # sc_toolbox
+    ('typing-extensions', '4.9.0'),  # sc_toolbox
+    ('adjustText', '1.1.1'),  
 ]
 
 # DEPS to add:
-# Sc_toolbox
+# Cassiopeia OK
+    # arrow, datapipelines,merakicommons, flake8, Pillow
+    # flake8: mccabe, pycodestyle (created for 2023a), pyflakes
+# Bbknn OK
+    # umap-learn, scikit-learn, pynndescent, annoy, flit_core 
+# Anndata2ri OK
+    # rpy2, anndata, tzlocal
+# Sc_toolbox - adjustText (created), rich, PyYAML, questionary, cookiecutter (in eb, not 2023b), matplotlib, scanpy, seaborn, scikit-learn, typing-extensions, pypi-latest
+    # OK cookiecutter - binaryornot, python-slugify
+    # OK questionary 2.0.1 has requirement prompt_toolkit<=3.0.36,>=2.0, but you have prompt-toolkit 3.0.39 -> 3.0.36 to exts_list
+    # OKpython-slugify 8.0.4 requires text-unidecode, which is not installed.
+    # questionary needs poetry-core?
 # Altair
 # Pertpy
 # Tasccoda
@@ -51,6 +67,12 @@ dependencies = [
 # Schist
 
 exts_list = [
+    ('pyflakes', '3.2.0', {
+        'checksums': ['1c61603ff154621fb2a9172037d84dca3500def8c8b630657d1701f026f8af3f'],
+    }),
+    ('mccabe', '0.7.0', {
+        'checksums': ['348e0240c33b60bbdf4e523192ef919f28cb2c3d7d5c7794f74009290f236325'],
+    }),
     ('arrow', '0.17.0', {
         'checksums': ['ff08d10cda1d36c68657d6ad20d74fbea493d980f8b2d45344e00d6ed2bf6ed4'],
     }),
@@ -63,27 +85,58 @@ exts_list = [
     ('flake8', '7.0.0', {
         'checksums': ['33f96621059e65eec474169085dc92bf26e7b2d47366b70be2f67ab80dc25132'],
     }),
-    ('pynndescent', '0.5.11', {
-        'checksums': ['6f44ced9d5a9da2c87d9b2fff30bb5308540c0657605e4d5cde7ed3275bbad50'],
+    ('cassiopeia', '5.0.3', {
+        'checksums': ['18adfc81f795f807ce6e6674da5c81c801d28ecf42f9ce94e23fc018b6840d63'],
+    }),
+    ('flit_core', '3.9.0', {
+        'checksums': ['72ad266176c4a3fcfab5f2930d76896059851240570ce9a98733b658cb786eba'],
     }),
     ('annoy', '1.17.3', {
         'checksums': ['9cbfebefe0a5f843eba29c6be4c84d601f4f41ad4ded0486f1b88c3b07739c15'],
     }),
+    ('pynndescent', '0.5.11', {
+        'checksums': ['6f44ced9d5a9da2c87d9b2fff30bb5308540c0657605e4d5cde7ed3275bbad50'],
+    }),
+    ('bbknn', '1.6.0', {
+        'checksums': ['1c01a9d6df2fc52a527de8a403617897a4b672724863299a7026f2132f1b041b'],
+    }),
     ('tzlocal', '5.2', {
         'checksums': ['8d399205578f1a9342816409cc1e46a93ebd5755e39ea2d85334bea911bf0e6e'],
     }),
     ('anndata2ri', '1.3.1', {
         'checksums': ['0e3fa2f81789f682d19ef452fabdb401ec27899db9abe5a78e45e21dcc7caa42'],
     }),
-    ('bbknn', '1.6.0', {
-        'checksums': ['1c01a9d6df2fc52a527de8a403617897a4b672724863299a7026f2132f1b041b'],
+    ('pypi-latest', '0.1.2', {
+        'checksums': ['b195654567e6abaac6acfec37638d8e000838f419bc6b129962a896eedc4ed4e'],
     }),
-    ('cassiopeia', '5.0.3', {
-        'checksums': ['18adfc81f795f807ce6e6674da5c81c801d28ecf42f9ce94e23fc018b6840d63'],
+    ('text-unidecode', '1.3', {
+        'checksums': ['bad6603bb14d279193107714b288be206cac565dfa49aa5b105294dd5c4aab93'],
+    }),
+    ('python-slugify', '8.0.4', {
+        'modulename': 'slugify',
+        'checksums': ['59202371d1d05b54a9e7720c5e038f928f45daaffe41dd10822f3907b937c856'],
+    }),
+    ('prompt_toolkit', '3.0.36', {
+        'checksums': ['3e163f254bef5a03b146397d7c1963bd3e2812f0964bb9a24e6ec761fd28db63'],
+    }),
+    ('binaryornot', '0.4.4', {
+        'checksums': ['359501dfc9d40632edc9fac890e19542db1a287bbcfa58175b66658392018061'],
+    }),
+    ('cookiecutter', '2.6.0', {
+        'checksums': ['db21f8169ea4f4fdc2408d48ca44859349de2647fbe494a9d6c3edfc0542c21c'],
+    }),
+    ('questionary', '2.0.1', {
+        'checksums': ['bcce898bf3dbb446ff62830c86c5c6fb9a22a54146f0f5597d3da43b10d8fc8b'],
+    }),
+    ('rich', '13.7.1', {
+        'checksums': ['9be308cb1fe2f1f57d67ce99e95af38a1e2bc71ad9813b0e247cf7ffbcc3a432'],
+    }),
+    ('sc_toolbox', '0.12.3', {
+        'checksums': ['6ca22a364c269a095114e620eb3c6da8aac1950d8f43f58ceea08005a09cc2cb'],
     }),
-    # ('sc_toolbox', '0.12.3', {
-    #     'checksums': ['6ca22a364c269a095114e620eb3c6da8aac1950d8f43f58ceea08005a09cc2cb'],
-    # }),
 ]
 
+use_pip = True
+sanity_pip_check = True
+
 moduleclass = 'bio'

From f1c8e26f0bfe036c24e4bd4bd8c1c17daa841bc2 Mon Sep 17 00:00:00 2001
From: ocaisa <alan.ocais@cecam.org>
Date: Wed, 20 Mar 2024 20:14:19 +0100
Subject: [PATCH 030/835] Update
 easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-foss-2022b.eb
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Mikael Öhman <micketeer@gmail.com>
---
 .../q/QuantumESPRESSO/QuantumESPRESSO-7.2-foss-2022b.eb          | 1 -
 1 file changed, 1 deletion(-)

diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-foss-2022b.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-foss-2022b.eb
index bc13fda0984..9362d5a9fb8 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-foss-2022b.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-foss-2022b.eb
@@ -45,7 +45,6 @@ dependencies = [
 # which depends on qe source
 buildopts = 'all gwl xspectra couple epw gipaw w90'
 
-# building gipaw requires FoX
 with_fox = True
 
 # parallel build tends to fail

From 11eaaa573c00e0cc1062184088bfc95283cb1e4b Mon Sep 17 00:00:00 2001
From: ocaisa <alan.ocais@cecam.org>
Date: Wed, 20 Mar 2024 20:14:27 +0100
Subject: [PATCH 031/835] Update
 easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-foss-2023a.eb
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Mikael Öhman <micketeer@gmail.com>
---
 .../q/QuantumESPRESSO/QuantumESPRESSO-7.2-foss-2023a.eb          | 1 -
 1 file changed, 1 deletion(-)

diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-foss-2023a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-foss-2023a.eb
index 2bf29814216..8369f3fb31a 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-foss-2023a.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-foss-2023a.eb
@@ -46,7 +46,6 @@ dependencies = [
 # which depends on qe source
 buildopts = "all gwl xspectra couple epw gipaw w90"
 
-# building gipaw requires FoX
 with_fox = True
 
 # parallel build tends to fail

From 611bb5d6a2ab9b2d50d609c10b2a761f7a217414 Mon Sep 17 00:00:00 2001
From: ocaisa <alan.ocais@cecam.org>
Date: Wed, 20 Mar 2024 20:14:38 +0100
Subject: [PATCH 032/835] Update
 easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-intel-2022b.eb
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Mikael Öhman <micketeer@gmail.com>
---
 .../q/QuantumESPRESSO/QuantumESPRESSO-7.2-intel-2022b.eb         | 1 -
 1 file changed, 1 deletion(-)

diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-intel-2022b.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-intel-2022b.eb
index 028fee4349c..53852bd770b 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-intel-2022b.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-intel-2022b.eb
@@ -47,7 +47,6 @@ dependencies = [
 # which depends on qe source
 buildopts = 'all gwl xspectra couple epw gipaw w90'
 
-# building gipaw requires FoX
 with_fox = True
 
 # parallel build tends to fail

From d6889a4eaa512d5d3e9887392f067fab97883afc Mon Sep 17 00:00:00 2001
From: crivella <davide.grassano@epfl.ch>
Date: Fri, 22 Mar 2024 16:01:29 +0100
Subject: [PATCH 033/835] Added manual downloads for all sbumodules

---
 .../QuantumESPRESSO-7.3.1-foss-2023a.eb       | 168 ++++++++++++++----
 .../QuantumESPRESSO-7.3.1-intel-2023a.eb      | 121 ++++++++++++-
 2 files changed, 250 insertions(+), 39 deletions(-)

diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-foss-2023a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-foss-2023a.eb
index 39bca0aefae..084d212d95e 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-foss-2023a.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-foss-2023a.eb
@@ -1,58 +1,166 @@
-easyblock = 'EB_QuantumESPRESSOcmake'
+easyblock = "EB_QuantumESPRESSOcmake"
 
-name = 'QuantumESPRESSO'
-version = '7.3.1'
+name = "QuantumESPRESSO"
+version = "7.3.1"
 
-homepage = 'https://www.quantum-espresso.org'
+homepage = "https://www.quantum-espresso.org"
 description = """Quantum ESPRESSO  is an integrated suite of computer codes
 for electronic-structure calculations and materials modeling at the nanoscale.
 It is based on density-functional theory, plane waves, and pseudopotentials
 (both norm-conserving and ultrasoft).
 """
 
-toolchain = {'name': 'intel', 'version': '2023a'}
+toolchain = {"name": "foss", "version": "2023a"}
 toolchainopts = {
-    'usempi': True,
-    'openmp': False # QE not linking FFTW and ELPA correctly with OpenMP + cmake
-    }
+    "usempi": True,
+    "openmp": False,  # QE not linking FFTW and ELPA correctly with OpenMP + cmake
+}
+
+# Check hashes inside external/submodule_commit_hash_records when making file for new version
+local_lapack_hash = "12d825396fcef1e0a1b27be9f119f9e554621e55"
+local_mbd_hash = "82005cbb65bdf5d32ca021848eec8f19da956a77"
+local_devxlib_hash = "a6b89ef77b1ceda48e967921f1f5488d2df9226d"
+local_fox_hash = "3453648e6837658b747b895bb7bef4b1ed2eac40"
+# Different from the one at tag qe-7.3.1 because of:
+# https://gitlab.com/QEF/q-e/-/issues/666
+local_d3q_hash = "de4718351e7bbb9d1d12aad2b7ca232d06775b83"
+local_qe_gipaw_hash = "75b01b694c9ba4df55d294cacc27cf28591b2161"
+local_pw2qmcpack_hash = "f72ab25fa4ea755c1b4b230ae8074b47d5509c70"
+local_wannier90_hash = "1d6b187374a2d50b509e5e79e2cab01a79ff7ce1"
+
 
 sources = [
     {
-        'filename': 'q-e-qe-%(version)s.tar.gz',
-        'extract_cmd': 'mkdir -p %(builddir)s/qe-%(version)s && tar xzvf %s --strip-components=1 -C $_',
-        'source_urls': ['https://gitlab.com/QEF/q-e/-/archive/qe-%(version)s']
+        "filename": "q-e-qe-%(version)s.tar.gz",
+        "extract_cmd": "mkdir -p %(builddir)s/qe-%(version)s && tar xzvf %s --strip-components=1 -C $_",
+        "source_urls": ["https://gitlab.com/QEF/q-e/-/archive/qe-%(version)s"],
+    },
+    {
+        "filename": "lapack-%s.tar.gz" % local_lapack_hash,
+        "git_config": {
+            "url": "https://github.com/Reference-LAPACK",
+            "repo_name": "lapack",
+            "commit": "%s" % local_lapack_hash,
+            "keep_git_dir": True,
+        },
+    },
+    {
+        "filename": "mbd-%s.tar.gz" % local_mbd_hash,
+        "git_config": {
+            "url": "https://github.com/libmbd",
+            "repo_name": "libmbd",
+            "commit": "%s" % local_mbd_hash,
+            'clone_into': 'mbd',
+            "keep_git_dir": True,
+        },
+    },
+    {
+        "filename": "devxlib-%s.tar.gz" % local_devxlib_hash,
+        "git_config": {
+            "url": "https://gitlab.com/max-centre/components",
+            "repo_name": "devicexlib",
+            "commit": "%s" % local_devxlib_hash,
+            'clone_into': 'devxlib',
+            "keep_git_dir": True,
+        },
+    },
+    {
+        "filename": "d3q-%s.tar.gz" % local_d3q_hash,
+        "git_config": {
+            "url": "https://github.com/anharmonic",
+            "repo_name": "d3q",
+            "commit": "%s" % local_d3q_hash,
+            "keep_git_dir": True,
+        },
+    },
+    {
+        "filename": "fox-%s.tar.gz" % local_fox_hash,
+        "git_config": {
+            "url": "https://github.com/pietrodelugas",
+            "repo_name": "fox",
+            "commit": "%s" % local_fox_hash,
+            "keep_git_dir": True,
+        },
+    },
+    {
+        "filename": "qe-gipaw-%s.tar.gz" % local_qe_gipaw_hash,
+        "git_config": {
+            "url": "https://github.com/dceresoli",
+            "repo_name": "qe-gipaw",
+            "commit": "%s" % local_qe_gipaw_hash,
+            "keep_git_dir": True,
+        },
+    },
+    {
+        "filename": "pw2qmcpack-%s.tar.gz" % local_pw2qmcpack_hash,
+        "git_config": {
+            "url": "https://github.com/QMCPACK",
+            "repo_name": "pw2qmcpack",
+            "commit": "%s" % local_pw2qmcpack_hash,
+            "keep_git_dir": True,
+        },
+    },
+    {
+        "filename": "wannier90-%s.tar.gz" % local_wannier90_hash,
+        "git_config": {
+            "url": "https://github.com/wannier-developers",
+            "repo_name": "wannier90",
+            "commit": "%s" % local_wannier90_hash,
+            "keep_git_dir": True,
+        },
     },
 ]
 checksums = [
-    {'q-e-qe-%(version)s.tar.gz': '2c58b8fadfe4177de5a8b69eba447db5e623420b070dea6fd26c1533b081d844'},
+    {'q-e-qe-7.3.1.tar.gz': '2c58b8fadfe4177de5a8b69eba447db5e623420b070dea6fd26c1533b081d844'},
+    {'lapack-12d825396fcef1e0a1b27be9f119f9e554621e55.tar.gz':
+     'c05532ae0e5fe35f473206dda12970da5f2e2214620487d71837ddcf0ea6b21d'},
+    {'mbd-82005cbb65bdf5d32ca021848eec8f19da956a77.tar.gz':
+     'a180682c00bb890c9b1e26a98addbd68e32f970c06439acf7582415f4c589800'},
+    {'devxlib-a6b89ef77b1ceda48e967921f1f5488d2df9226d.tar.gz':
+     '76da8fe5a2050f58efdc92fa8831efec25c19190df7f4e5e39c173a5fbae83b4'},
+    {'d3q-de4718351e7bbb9d1d12aad2b7ca232d06775b83.tar.gz':
+     '43e50753a56af05d181b859d3e29d842fb3fc4352f00cb7fe229a435a1f20c31'},
+    {'fox-3453648e6837658b747b895bb7bef4b1ed2eac40.tar.gz':
+     '99b6a899a3f947d7763aa318e86f9f08db684568bfdcd293f3318bee9d7f1948'},
+    {'qe-gipaw-75b01b694c9ba4df55d294cacc27cf28591b2161.tar.gz':
+     '9ac8314363d29cc2f1ce85abd8f26c1a3ae311d54f6e6034d656442dd101c928'},
+    {'pw2qmcpack-f72ab25fa4ea755c1b4b230ae8074b47d5509c70.tar.gz':
+     'a8136da8429fc49ab560ef7356cd6f0a2714dfbb137baff7961f46dfe32061eb'},
+    {'wannier90-1d6b187374a2d50b509e5e79e2cab01a79ff7ce1.tar.gz':
+     'f989497790ec9777bdc159945bbf42156edb7268011f972874dec67dd4f58658'},
 ]
 
 builddependencies = [
-    ('M4', '1.4.19'),
-    ('CMake', '3.26.3'),
+    ("M4", "1.4.19"),
+    ("CMake", "3.26.3"),
 ]
 dependencies = [
-    ('HDF5', '1.14.0'),
-    ('ELPA', '2023.05.001'),
-    ('libxc', '6.2.2'),
+    ("HDF5", "1.14.0"),
+    ("ELPA", "2023.05.001"),
+    ("libxc", "6.2.2"),
 ]
 
-# Disabled because of https://gitlab.com/QEF/q-e/-/issues/667
-# Trouble in linking with shared libraries and intel toolchain
-build_shared_libs = False 
+# Disabled because of
+# https://gitlab.com/QEF/q-e/-/issues/667
+# https://github.com/anharmonic/d3q/issues/15
+build_shared_libs = False
 with_scalapack = True
-with_gipaw = False # https://github.com/dceresoli/qe-gipaw/issues/19
-with_d3q = False # https://gitlab.com/QEF/q-e/-/issues/666
+with_gipaw = False  # https://github.com/dceresoli/qe-gipaw/issues/19
+with_d3q = True
 with_qmcpack = True
 
-moduleclass = 'chem'
+moduleclass = "chem"
 
-test_suite_threshold = 0.4 # Low threshold because of https://gitlab.com/QEF/q-e/-/issues/665
-test_suite_max_failed = 5 # Allow for some flaky tests (failed due to strict thresholds)
+test_suite_threshold = (
+    0.4  # Low threshold because of https://gitlab.com/QEF/q-e/-/issues/665
+)
+test_suite_max_failed = (
+    5  # Allow for some flaky tests (failed due to strict thresholds)
+)
 test_suite_allow_failures = [
-    'test_qe_xclib_',  # 7.3.1:  https://gitlab.com/QEF/q-e/-/issues/640
-    '--hp_',  # 7.3.1:  Broken testsuite (https://gitlab.com/QEF/q-e/-/issues/665)
-    '--ph_',  # 7.3.1:  Broken testsuite (https://gitlab.com/QEF/q-e/-/issues/665)
-    '--epw_',  # 7.3.1:  Broken testsuite (https://gitlab.com/QEF/q-e/-/issues/665)
-    '--tddfpt_',  # 7.3.1:  Broken testsuite (https://gitlab.com/QEF/q-e/-/issues/665)
+    "test_qe_xclib_",  # 7.3.1:  https://gitlab.com/QEF/q-e/-/issues/640
+    "--hp_",  # 7.3.1:  Broken testsuite (https://gitlab.com/QEF/q-e/-/issues/665)
+    "--ph_",  # 7.3.1:  Broken testsuite (https://gitlab.com/QEF/q-e/-/issues/665)
+    "--epw_",  # 7.3.1:  Broken testsuite (https://gitlab.com/QEF/q-e/-/issues/665)
+    "--tddfpt_",  # 7.3.1:  Broken testsuite (https://gitlab.com/QEF/q-e/-/issues/665)
 ]
diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-intel-2023a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-intel-2023a.eb
index f4f49d2223e..a0ae8b2c58f 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-intel-2023a.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-intel-2023a.eb
@@ -13,8 +13,20 @@ It is based on density-functional theory, plane waves, and pseudopotentials
 toolchain = {'name': 'intel', 'version': '2023a'}
 toolchainopts = {
     'usempi': True,
-    'openmp': False # QE not linking FFTW and ELPA correctly with OpenMP + cmake
-    }
+    'openmp': False  # QE not linking FFTW and ELPA correctly with OpenMP + cmake
+}
+
+# Check hashes inside external/submodule_commit_hash_records when making file for new version
+local_lapack_hash = "12d825396fcef1e0a1b27be9f119f9e554621e55"
+local_mbd_hash = "82005cbb65bdf5d32ca021848eec8f19da956a77"
+local_devxlib_hash = "a6b89ef77b1ceda48e967921f1f5488d2df9226d"
+local_fox_hash = "3453648e6837658b747b895bb7bef4b1ed2eac40"
+# Different from the one at tag qe-7.3.1 because of:
+# https://gitlab.com/QEF/q-e/-/issues/666
+local_d3q_hash = "de4718351e7bbb9d1d12aad2b7ca232d06775b83"
+local_qe_gipaw_hash = "75b01b694c9ba4df55d294cacc27cf28591b2161"
+local_pw2qmcpack_hash = "f72ab25fa4ea755c1b4b230ae8074b47d5509c70"
+local_wannier90_hash = "1d6b187374a2d50b509e5e79e2cab01a79ff7ce1"
 
 sources = [
     {
@@ -22,9 +34,99 @@ sources = [
         'extract_cmd': 'mkdir -p %(builddir)s/qe-%(version)s && tar xzvf %s --strip-components=1 -C $_',
         'source_urls': ['https://gitlab.com/QEF/q-e/-/archive/qe-%(version)s']
     },
+    {
+        "filename": "lapack-%s.tar.gz" % local_lapack_hash,
+        "git_config": {
+            "url": "https://github.com/Reference-LAPACK",
+            "repo_name": "lapack",
+            "commit": "%s" % local_lapack_hash,
+            "keep_git_dir": True,
+        },
+    },
+    {
+        "filename": "mbd-%s.tar.gz" % local_mbd_hash,
+        "git_config": {
+            "url": "https://github.com/libmbd",
+            "repo_name": "libmbd",
+            "commit": "%s" % local_mbd_hash,
+            'clone_into': 'mbd',
+            "keep_git_dir": True,
+        },
+    },
+    {
+        "filename": "devxlib-%s.tar.gz" % local_devxlib_hash,
+        "git_config": {
+            "url": "https://gitlab.com/max-centre/components",
+            "repo_name": "devicexlib",
+            "commit": "%s" % local_devxlib_hash,
+            'clone_into': 'devxlib',
+            "keep_git_dir": True,
+        },
+    },
+    {
+        "filename": "d3q-%s.tar.gz" % local_d3q_hash,
+        "git_config": {
+            "url": "https://github.com/anharmonic",
+            "repo_name": "d3q",
+            "commit": "%s" % local_d3q_hash,
+            "keep_git_dir": True,
+        },
+    },
+    {
+        "filename": "fox-%s.tar.gz" % local_fox_hash,
+        "git_config": {
+            "url": "https://github.com/pietrodelugas",
+            "repo_name": "fox",
+            "commit": "%s" % local_fox_hash,
+            "keep_git_dir": True,
+        },
+    },
+    {
+        "filename": "qe-gipaw-%s.tar.gz" % local_qe_gipaw_hash,
+        "git_config": {
+            "url": "https://github.com/dceresoli",
+            "repo_name": "qe-gipaw",
+            "commit": "%s" % local_qe_gipaw_hash,
+            "keep_git_dir": True,
+        },
+    },
+    {
+        "filename": "pw2qmcpack-%s.tar.gz" % local_pw2qmcpack_hash,
+        "git_config": {
+            "url": "https://github.com/QMCPACK",
+            "repo_name": "pw2qmcpack",
+            "commit": "%s" % local_pw2qmcpack_hash,
+            "keep_git_dir": True,
+        },
+    },
+    {
+        "filename": "wannier90-%s.tar.gz" % local_wannier90_hash,
+        "git_config": {
+            "url": "https://github.com/wannier-developers",
+            "repo_name": "wannier90",
+            "commit": "%s" % local_wannier90_hash,
+            "keep_git_dir": True,
+        },
+    },
 ]
 checksums = [
-    {'q-e-qe-%(version)s.tar.gz': '2c58b8fadfe4177de5a8b69eba447db5e623420b070dea6fd26c1533b081d844'},
+    {'q-e-qe-7.3.1.tar.gz': '2c58b8fadfe4177de5a8b69eba447db5e623420b070dea6fd26c1533b081d844'},
+    {'lapack-12d825396fcef1e0a1b27be9f119f9e554621e55.tar.gz':
+     'c05532ae0e5fe35f473206dda12970da5f2e2214620487d71837ddcf0ea6b21d'},
+    {'mbd-82005cbb65bdf5d32ca021848eec8f19da956a77.tar.gz':
+     'a180682c00bb890c9b1e26a98addbd68e32f970c06439acf7582415f4c589800'},
+    {'devxlib-a6b89ef77b1ceda48e967921f1f5488d2df9226d.tar.gz':
+     '76da8fe5a2050f58efdc92fa8831efec25c19190df7f4e5e39c173a5fbae83b4'},
+    {'d3q-de4718351e7bbb9d1d12aad2b7ca232d06775b83.tar.gz':
+     '43e50753a56af05d181b859d3e29d842fb3fc4352f00cb7fe229a435a1f20c31'},
+    {'fox-3453648e6837658b747b895bb7bef4b1ed2eac40.tar.gz':
+     '99b6a899a3f947d7763aa318e86f9f08db684568bfdcd293f3318bee9d7f1948'},
+    {'qe-gipaw-75b01b694c9ba4df55d294cacc27cf28591b2161.tar.gz':
+     '9ac8314363d29cc2f1ce85abd8f26c1a3ae311d54f6e6034d656442dd101c928'},
+    {'pw2qmcpack-f72ab25fa4ea755c1b4b230ae8074b47d5509c70.tar.gz':
+     'a8136da8429fc49ab560ef7356cd6f0a2714dfbb137baff7961f46dfe32061eb'},
+    {'wannier90-1d6b187374a2d50b509e5e79e2cab01a79ff7ce1.tar.gz':
+     'f989497790ec9777bdc159945bbf42156edb7268011f972874dec67dd4f58658'},
 ]
 
 builddependencies = [
@@ -37,18 +139,19 @@ dependencies = [
     ('libxc', '6.2.2'),
 ]
 
-# Disabled because of https://gitlab.com/QEF/q-e/-/issues/667
-# Trouble in linking with shared libraries and intel toolchain
+# Disabled because of
+# https://gitlab.com/QEF/q-e/-/issues/667
+# https://github.com/anharmonic/d3q/issues/15
 build_shared_libs = False
 with_scalapack = True
-with_gipaw = False # https://github.com/dceresoli/qe-gipaw/issues/19
-with_d3q = False # https://gitlab.com/QEF/q-e/-/issues/666
+with_gipaw = False  # https://github.com/dceresoli/qe-gipaw/issues/19
+with_d3q = True
 with_qmcpack = True
 
 moduleclass = 'chem'
 
-test_suite_threshold = 0.4 # Low threshold because of https://gitlab.com/QEF/q-e/-/issues/665
-test_suite_max_failed = 5 # Allow for some flaky tests (failed due to strict thresholds)
+test_suite_threshold = 0.4  # Low threshold because of https://gitlab.com/QEF/q-e/-/issues/665
+test_suite_max_failed = 5  # Allow for some flaky tests (failed due to strict thresholds)
 test_suite_allow_failures = [
     'test_qe_xclib_',  # 7.3.1:  https://gitlab.com/QEF/q-e/-/issues/640
     '--hp_',  # 7.3.1:  Broken testsuite (https://gitlab.com/QEF/q-e/-/issues/665)

From bb925f351b68d52471b99721cf53700612447555 Mon Sep 17 00:00:00 2001
From: crivella <davide.grassano@epfl.ch>
Date: Fri, 22 Mar 2024 16:19:48 +0100
Subject: [PATCH 034/835] No need for formatting

---
 .../QuantumESPRESSO-7.3.1-foss-2023a.eb          | 16 ++++++++--------
 .../QuantumESPRESSO-7.3.1-intel-2023a.eb         | 16 ++++++++--------
 2 files changed, 16 insertions(+), 16 deletions(-)

diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-foss-2023a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-foss-2023a.eb
index 084d212d95e..ed44a934d0d 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-foss-2023a.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-foss-2023a.eb
@@ -40,7 +40,7 @@ sources = [
         "git_config": {
             "url": "https://github.com/Reference-LAPACK",
             "repo_name": "lapack",
-            "commit": "%s" % local_lapack_hash,
+            "commit": local_lapack_hash,
             "keep_git_dir": True,
         },
     },
@@ -49,7 +49,7 @@ sources = [
         "git_config": {
             "url": "https://github.com/libmbd",
             "repo_name": "libmbd",
-            "commit": "%s" % local_mbd_hash,
+            "commit": local_mbd_hash,
             'clone_into': 'mbd',
             "keep_git_dir": True,
         },
@@ -59,7 +59,7 @@ sources = [
         "git_config": {
             "url": "https://gitlab.com/max-centre/components",
             "repo_name": "devicexlib",
-            "commit": "%s" % local_devxlib_hash,
+            "commit": local_devxlib_hash,
             'clone_into': 'devxlib',
             "keep_git_dir": True,
         },
@@ -69,7 +69,7 @@ sources = [
         "git_config": {
             "url": "https://github.com/anharmonic",
             "repo_name": "d3q",
-            "commit": "%s" % local_d3q_hash,
+            "commit": local_d3q_hash,
             "keep_git_dir": True,
         },
     },
@@ -78,7 +78,7 @@ sources = [
         "git_config": {
             "url": "https://github.com/pietrodelugas",
             "repo_name": "fox",
-            "commit": "%s" % local_fox_hash,
+            "commit": local_fox_hash,
             "keep_git_dir": True,
         },
     },
@@ -87,7 +87,7 @@ sources = [
         "git_config": {
             "url": "https://github.com/dceresoli",
             "repo_name": "qe-gipaw",
-            "commit": "%s" % local_qe_gipaw_hash,
+            "commit": local_qe_gipaw_hash,
             "keep_git_dir": True,
         },
     },
@@ -96,7 +96,7 @@ sources = [
         "git_config": {
             "url": "https://github.com/QMCPACK",
             "repo_name": "pw2qmcpack",
-            "commit": "%s" % local_pw2qmcpack_hash,
+            "commit": local_pw2qmcpack_hash,
             "keep_git_dir": True,
         },
     },
@@ -105,7 +105,7 @@ sources = [
         "git_config": {
             "url": "https://github.com/wannier-developers",
             "repo_name": "wannier90",
-            "commit": "%s" % local_wannier90_hash,
+            "commit": local_wannier90_hash,
             "keep_git_dir": True,
         },
     },
diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-intel-2023a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-intel-2023a.eb
index a0ae8b2c58f..e897a4a8192 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-intel-2023a.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-intel-2023a.eb
@@ -39,7 +39,7 @@ sources = [
         "git_config": {
             "url": "https://github.com/Reference-LAPACK",
             "repo_name": "lapack",
-            "commit": "%s" % local_lapack_hash,
+            "commit": local_lapack_hash,
             "keep_git_dir": True,
         },
     },
@@ -48,7 +48,7 @@ sources = [
         "git_config": {
             "url": "https://github.com/libmbd",
             "repo_name": "libmbd",
-            "commit": "%s" % local_mbd_hash,
+            "commit": local_mbd_hash,
             'clone_into': 'mbd',
             "keep_git_dir": True,
         },
@@ -58,7 +58,7 @@ sources = [
         "git_config": {
             "url": "https://gitlab.com/max-centre/components",
             "repo_name": "devicexlib",
-            "commit": "%s" % local_devxlib_hash,
+            "commit": local_devxlib_hash,
             'clone_into': 'devxlib',
             "keep_git_dir": True,
         },
@@ -68,7 +68,7 @@ sources = [
         "git_config": {
             "url": "https://github.com/anharmonic",
             "repo_name": "d3q",
-            "commit": "%s" % local_d3q_hash,
+            "commit": local_d3q_hash,
             "keep_git_dir": True,
         },
     },
@@ -77,7 +77,7 @@ sources = [
         "git_config": {
             "url": "https://github.com/pietrodelugas",
             "repo_name": "fox",
-            "commit": "%s" % local_fox_hash,
+            "commit": local_fox_hash,
             "keep_git_dir": True,
         },
     },
@@ -86,7 +86,7 @@ sources = [
         "git_config": {
             "url": "https://github.com/dceresoli",
             "repo_name": "qe-gipaw",
-            "commit": "%s" % local_qe_gipaw_hash,
+            "commit": local_qe_gipaw_hash,
             "keep_git_dir": True,
         },
     },
@@ -95,7 +95,7 @@ sources = [
         "git_config": {
             "url": "https://github.com/QMCPACK",
             "repo_name": "pw2qmcpack",
-            "commit": "%s" % local_pw2qmcpack_hash,
+            "commit": local_pw2qmcpack_hash,
             "keep_git_dir": True,
         },
     },
@@ -104,7 +104,7 @@ sources = [
         "git_config": {
             "url": "https://github.com/wannier-developers",
             "repo_name": "wannier90",
-            "commit": "%s" % local_wannier90_hash,
+            "commit": local_wannier90_hash,
             "keep_git_dir": True,
         },
     },

From bf119b340a7f4ed7934c38b2010a3829ae96014d Mon Sep 17 00:00:00 2001
From: crivella <davide.grassano@epfl.ch>
Date: Fri, 22 Mar 2024 18:36:21 +0100
Subject: [PATCH 035/835] Tested and enabled OpenMP support

---
 .../q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-foss-2023a.eb       | 2 +-
 .../q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-intel-2023a.eb      | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-foss-2023a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-foss-2023a.eb
index ed44a934d0d..65827acf805 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-foss-2023a.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-foss-2023a.eb
@@ -13,7 +13,7 @@ It is based on density-functional theory, plane waves, and pseudopotentials
 toolchain = {"name": "foss", "version": "2023a"}
 toolchainopts = {
     "usempi": True,
-    "openmp": False,  # QE not linking FFTW and ELPA correctly with OpenMP + cmake
+    "openmp": True,
 }
 
 # Check hashes inside external/submodule_commit_hash_records when making file for new version
diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-intel-2023a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-intel-2023a.eb
index e897a4a8192..be1bc77e808 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-intel-2023a.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-intel-2023a.eb
@@ -13,7 +13,7 @@ It is based on density-functional theory, plane waves, and pseudopotentials
 toolchain = {'name': 'intel', 'version': '2023a'}
 toolchainopts = {
     'usempi': True,
-    'openmp': False  # QE not linking FFTW and ELPA correctly with OpenMP + cmake
+    'openmp': True,
 }
 
 # Check hashes inside external/submodule_commit_hash_records when making file for new version

From 06537c9a9e4ab3b62f51d2a04b24eab77c1c67b3 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Mon, 25 Mar 2024 11:07:06 +0100
Subject: [PATCH 036/835] tascCODA added, cassiopeia remove

---
 ...e-cell-python-bundle-2024.02-foss-2023a.eb | 139 +++++++++++++-----
 1 file changed, 106 insertions(+), 33 deletions(-)

diff --git a/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb b/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb
index a3c7011d4ac..f7976233e97 100644
--- a/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb
+++ b/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb
@@ -4,7 +4,7 @@ name = 'Single-cell-python-bundle'
 version = '2024.02'
 
 homepage = 'xxx'
-description = """Bundle for single-cell ???"""
+description = """Bundle of softwares for single-cell research ???"""
 
 toolchain = {'name': 'foss', 'version': '2023a'}
 
@@ -33,31 +33,56 @@ dependencies = [
     # ('pySCENIC', '0.12.1-20240311'),
     # ('Squidpy', '1.4.1'),
     # deps for exts:
-    ('Pillow', '10.0.0'),  # cassiopeia
-    ('pycodestyle', '2.11.1'),  # cassiopeia, created
+    # ('Pillow', '10.0.0'),  # cassiopeia
+    # ('pycodestyle', '2.11.1'),  # cassiopeia, created
     ('umap-learn', '0.5.5'),  # bbknn
     ('scikit-learn', '1.3.1'),  # bbknn, sc_toolbox
     ('PyYAML', '6.0'),  # sc_toolbox
     ('typing-extensions', '4.9.0'),  # sc_toolbox
-    ('adjustText', '1.1.1'),  
+    ('adjustText', '1.1.1'),  # sc_toolbox, created
 ]
 
 # DEPS to add:
-# Cassiopeia OK
+# Cassiopeia-lineage
+# Cassiopeia NO! do it again for https://pypi.org/project/cassiopeia-lineage/
     # arrow, datapipelines,merakicommons, flake8, Pillow
     # flake8: mccabe, pycodestyle (created for 2023a), pyflakes
 # Bbknn OK
     # umap-learn, scikit-learn, pynndescent, annoy, flit_core 
 # Anndata2ri OK
     # rpy2, anndata, tzlocal
-# Sc_toolbox - adjustText (created), rich, PyYAML, questionary, cookiecutter (in eb, not 2023b), matplotlib, scanpy, seaborn, scikit-learn, typing-extensions, pypi-latest
-    # OK cookiecutter - binaryornot, python-slugify
+# Sc_toolbox OK
+    # adjustText (created), rich, PyYAML, questionary, cookiecutter (in eb, not 2023b), matplotlib, scanpy, seaborn, scikit-learn, typing-extensions, pypi-latest
+    # OK cookiecutter - binaryornot, python-slugify, arrow
     # OK questionary 2.0.1 has requirement prompt_toolkit<=3.0.36,>=2.0, but you have prompt-toolkit 3.0.39 -> 3.0.36 to exts_list
-    # OKpython-slugify 8.0.4 requires text-unidecode, which is not installed.
-    # questionary needs poetry-core?
-# Altair
-# Pertpy
-# Tasccoda
+    # OK python-slugify 8.0.4 requires text-unidecode, which is not installed.
+    # questionary needs poetry-core? Seems NOT
+    # arrow 1.3.0 requires types-python-dateutil OK exts
+# Altair OK
+    # altair 5.2.0 requires toolz OK exts
+# Pertpy NO - needs scvi-tools
+    # pertpy 0.6.0 requires decoupler, which is not installed. -> Do decoupler first
+    # pertpy 0.6.0 requires ipywidgets, which is not installed.
+    # pertpy 0.6.0 requires muon, which is not installed.
+    # pertpy 0.6.0 requires numpyro, which is not installed.
+    # pertpy 0.6.0 requires ott-jax, which is not installed.
+    # pertpy 0.6.0 requires plotnine, which is not installed.
+    # pertpy 0.6.0 requires scvi-tools, which is not installed.
+    # pertpy 0.6.0 requires sparsecca, which is not installed.
+    # pertpy 0.6.0 requires toytree OK exts
+    # ('pertpy', '0.6.0', {
+    #     'checksums': ['0f9ed443a74a07ab8cd0fb6d2d06275df30ec836c161124b83c9505b7cab182b'],
+    # }),
+# tascCODA OK
+    # tasccoda 0.1.3 requires tensorflow-probability OK in scCoda -> delete TF-prob. from setup.py as in scCoda
+        # strip out tensorflow-probability as required dependency, to ensure that 'pip check' passes
+    # tasccoda 0.1.3 requires toytree OK exts
+    # toytree 2.0.5 requires toyplot OK exts
+    # toyplot 1.0.3 requires arrow OK exts
+    # toyplot 1.0.3 requires custom-inherit OK exts
+    # toyplot 1.0.3 requires multipledispatch OK exts
+    # toyplot 1.0.3 requires pypng OK exts
+    # toyplot 1.0.3 requires reportlab OK exts
 # Liana-py 
 # Harmonypy
 # Scirpy
@@ -66,28 +91,18 @@ dependencies = [
 # contrastiveVI
 # Schist
 
+# cassiopeia-lineage Error:
+# gcc -DNDEBUG -g -fwrapv -O3 -Wall -O2 -ftree-vectorize -march=native -fno-math-errno -fPIC -O2 -ftree-vectorize -march=native -fno-math-errn
+# O2 -ftree-vectorize -march=native -fno-math-errno -I/apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-12.3.0/include -I/apps/gent/RHEL8/cas
+# ib/software/FlexiBLAS/3.3.1-GCC-12.3.0/include -I/apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.3.1-GCC-12.3.0/include/flexiblas -fPIC -I/sc
+# t/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/Python/3.11.3-GCCcore-12.3.0/include/python3.11 -c cassiopeia/TreeSolver/lineage_
+# lver_utils.c -o build/temp.linux-x86_64-cpython-311/cassiopeia/TreeSolver/lineage_solver/solver_utils.o
+#       cassiopeia/TreeSolver/lineage_solver/solver_utils.c:208:12: fatal error: longintrepr.h: No such file or directory
+#         208 |   #include "longintrepr.h"
+#             |            ^~~~~~~~~~~~~~~
+#       compilation terminated.
+      
 exts_list = [
-    ('pyflakes', '3.2.0', {
-        'checksums': ['1c61603ff154621fb2a9172037d84dca3500def8c8b630657d1701f026f8af3f'],
-    }),
-    ('mccabe', '0.7.0', {
-        'checksums': ['348e0240c33b60bbdf4e523192ef919f28cb2c3d7d5c7794f74009290f236325'],
-    }),
-    ('arrow', '0.17.0', {
-        'checksums': ['ff08d10cda1d36c68657d6ad20d74fbea493d980f8b2d45344e00d6ed2bf6ed4'],
-    }),
-    ('datapipelines', '1.0.7', {
-        'checksums': ['752bc71a1e03a45d723fc4d9b56c641ed0b872ed1df73b08896ee34d93c56e8f'],
-    }),
-    ('merakicommons', '1.0.10', {
-        'checksums': ['fc99ebe0cb85c4af0093a9454294adcb97c0792f8a8dd03898242ab2446aa77e'],
-    }),
-    ('flake8', '7.0.0', {
-        'checksums': ['33f96621059e65eec474169085dc92bf26e7b2d47366b70be2f67ab80dc25132'],
-    }),
-    ('cassiopeia', '5.0.3', {
-        'checksums': ['18adfc81f795f807ce6e6674da5c81c801d28ecf42f9ce94e23fc018b6840d63'],
-    }),
     ('flit_core', '3.9.0', {
         'checksums': ['72ad266176c4a3fcfab5f2930d76896059851240570ce9a98733b658cb786eba'],
     }),
@@ -122,6 +137,13 @@ exts_list = [
     ('binaryornot', '0.4.4', {
         'checksums': ['359501dfc9d40632edc9fac890e19542db1a287bbcfa58175b66658392018061'],
     }),
+    ('types-python-dateutil', '2.9.0.20240316', {
+        'modulename': False,
+        'checksums': ['5d2f2e240b86905e40944dd787db6da9263f0deabef1076ddaed797351ec0202'],
+    }),
+    ('arrow', '1.3.0', {
+        'checksums': ['d4540617648cb5f895730f1ad8c82a65f2dad0166f57b75f3ca54759c4d67a85'],
+    }),
     ('cookiecutter', '2.6.0', {
         'checksums': ['db21f8169ea4f4fdc2408d48ca44859349de2647fbe494a9d6c3edfc0542c21c'],
     }),
@@ -134,8 +156,59 @@ exts_list = [
     ('sc_toolbox', '0.12.3', {
         'checksums': ['6ca22a364c269a095114e620eb3c6da8aac1950d8f43f58ceea08005a09cc2cb'],
     }),
+    ('toolz', '0.12.1', {
+        'checksums': ['ecca342664893f177a13dac0e6b41cbd8ac25a358e5f215316d43e2100224f4d'],
+    }),
+    ('altair', '5.2.0', {
+        'checksums': ['2ad7f0c8010ebbc46319cc30febfb8e59ccf84969a201541c207bc3a4fa6cf81'],
+    }),
+    ('custom_inherit', '2.4.1', {
+        'checksums': ['7052eb337bcce83551815264391cc4efc2bf70b295a3c52aba64f1ab57c3a8a2'],
+    }),
+    ('multipledispatch', '1.0.0', {
+        'checksums': ['5c839915465c68206c3e9c473357908216c28383b425361e5d144594bf85a7e0'],
+    }),
+    ('pypng', '0.20220715.0', {
+        'modulename': 'png',
+        'checksums': ['739c433ba96f078315de54c0db975aee537cbc3e1d0ae4ed9aab0ca1e427e2c1'],
+    }),
+    ('reportlab', '4.1.0', {
+        'checksums': ['3a99faf412691159c068b3ff01c15307ce2fd2cf6b860199434874e002040a84'],
+    }),
+    ('toyplot', '1.0.3', {
+        'checksums': ['7b7b2bc5784fd75e5c695300bffc80d568c83bebef543bb54e6e6c2229912edd'],
+    }),
+    ('toytree', '2.0.5', {
+        'checksums': ['7be04ca310067e0e9737449700d6ab1b68b4379b64e2d22f2f7697a70030ceb0'],
+    }),
+    ('tascCODA', '0.1.3', {
+        'preinstallopts': "sed -i '28d' setup.py && ",
+        'checksums': ['8c12ddccb72c41c96c6a5abceb52e7a76f439a9ab94fb092aa86ee3c1292383a'],
+    }),
+    # ('cassiopeia-lineage', '1.0.4', {
+    #     'checksums': ['c341f6f4f0e4cb422c657387336f001a9e5d4eaff8fe0b40a00508b307de27aa'],
+    # }),
 ]
 
+    # ('pyflakes', '3.2.0', {
+    #     'checksums': ['1c61603ff154621fb2a9172037d84dca3500def8c8b630657d1701f026f8af3f'],
+    # }),
+    # ('mccabe', '0.7.0', {
+    #     'checksums': ['348e0240c33b60bbdf4e523192ef919f28cb2c3d7d5c7794f74009290f236325'],
+    # }),
+    # ('arrow', '0.17.0', {
+    #     'checksums': ['ff08d10cda1d36c68657d6ad20d74fbea493d980f8b2d45344e00d6ed2bf6ed4'],
+    # }),
+    # ('datapipelines', '1.0.7', {
+    #     'checksums': ['752bc71a1e03a45d723fc4d9b56c641ed0b872ed1df73b08896ee34d93c56e8f'],
+    # }),
+    # ('merakicommons', '1.0.10', {
+    #     'checksums': ['fc99ebe0cb85c4af0093a9454294adcb97c0792f8a8dd03898242ab2446aa77e'],
+    # }),
+    # ('flake8', '7.0.0', {
+    #     'checksums': ['33f96621059e65eec474169085dc92bf26e7b2d47366b70be2f67ab80dc25132'],
+    # }),
+    
 use_pip = True
 sanity_pip_check = True
 

From bebfd24d418f9cf1eabd3ff54da6b32cc43e840e Mon Sep 17 00:00:00 2001
From: crivella <davide.grassano@epfl.ch>
Date: Mon, 25 Mar 2024 12:58:38 +0100
Subject: [PATCH 037/835] Generalized injected checksums

---
 .../QuantumESPRESSO-7.3.1-foss-2023a.eb       | 30 +++++++------------
 .../QuantumESPRESSO-7.3.1-intel-2023a.eb      | 30 +++++++------------
 2 files changed, 22 insertions(+), 38 deletions(-)

diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-foss-2023a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-foss-2023a.eb
index 65827acf805..eed5e0c4e40 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-foss-2023a.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-foss-2023a.eb
@@ -25,7 +25,7 @@ local_fox_hash = "3453648e6837658b747b895bb7bef4b1ed2eac40"
 # https://gitlab.com/QEF/q-e/-/issues/666
 local_d3q_hash = "de4718351e7bbb9d1d12aad2b7ca232d06775b83"
 local_qe_gipaw_hash = "75b01b694c9ba4df55d294cacc27cf28591b2161"
-local_pw2qmcpack_hash = "f72ab25fa4ea755c1b4b230ae8074b47d5509c70"
+local_qmcpack_hash = "f72ab25fa4ea755c1b4b230ae8074b47d5509c70"
 local_wannier90_hash = "1d6b187374a2d50b509e5e79e2cab01a79ff7ce1"
 
 
@@ -92,11 +92,11 @@ sources = [
         },
     },
     {
-        "filename": "pw2qmcpack-%s.tar.gz" % local_pw2qmcpack_hash,
+        "filename": "pw2qmcpack-%s.tar.gz" % local_qmcpack_hash,
         "git_config": {
             "url": "https://github.com/QMCPACK",
             "repo_name": "pw2qmcpack",
-            "commit": local_pw2qmcpack_hash,
+            "commit": local_qmcpack_hash,
             "keep_git_dir": True,
         },
     },
@@ -112,22 +112,14 @@ sources = [
 ]
 checksums = [
     {'q-e-qe-7.3.1.tar.gz': '2c58b8fadfe4177de5a8b69eba447db5e623420b070dea6fd26c1533b081d844'},
-    {'lapack-12d825396fcef1e0a1b27be9f119f9e554621e55.tar.gz':
-     'c05532ae0e5fe35f473206dda12970da5f2e2214620487d71837ddcf0ea6b21d'},
-    {'mbd-82005cbb65bdf5d32ca021848eec8f19da956a77.tar.gz':
-     'a180682c00bb890c9b1e26a98addbd68e32f970c06439acf7582415f4c589800'},
-    {'devxlib-a6b89ef77b1ceda48e967921f1f5488d2df9226d.tar.gz':
-     '76da8fe5a2050f58efdc92fa8831efec25c19190df7f4e5e39c173a5fbae83b4'},
-    {'d3q-de4718351e7bbb9d1d12aad2b7ca232d06775b83.tar.gz':
-     '43e50753a56af05d181b859d3e29d842fb3fc4352f00cb7fe229a435a1f20c31'},
-    {'fox-3453648e6837658b747b895bb7bef4b1ed2eac40.tar.gz':
-     '99b6a899a3f947d7763aa318e86f9f08db684568bfdcd293f3318bee9d7f1948'},
-    {'qe-gipaw-75b01b694c9ba4df55d294cacc27cf28591b2161.tar.gz':
-     '9ac8314363d29cc2f1ce85abd8f26c1a3ae311d54f6e6034d656442dd101c928'},
-    {'pw2qmcpack-f72ab25fa4ea755c1b4b230ae8074b47d5509c70.tar.gz':
-     'a8136da8429fc49ab560ef7356cd6f0a2714dfbb137baff7961f46dfe32061eb'},
-    {'wannier90-1d6b187374a2d50b509e5e79e2cab01a79ff7ce1.tar.gz':
-     'f989497790ec9777bdc159945bbf42156edb7268011f972874dec67dd4f58658'},
+    {'lapack-%s.tar.gz' % local_lapack_hash: 'c05532ae0e5fe35f473206dda12970da5f2e2214620487d71837ddcf0ea6b21d'},
+    {'mbd-%s.tar.gz' % local_mbd_hash: 'a180682c00bb890c9b1e26a98addbd68e32f970c06439acf7582415f4c589800'},
+    {'devxlib-%s.tar.gz' % local_devxlib_hash: '76da8fe5a2050f58efdc92fa8831efec25c19190df7f4e5e39c173a5fbae83b4'},
+    {'d3q-%s.tar.gz' % local_d3q_hash: '43e50753a56af05d181b859d3e29d842fb3fc4352f00cb7fe229a435a1f20c31'},
+    {'fox-%s.tar.gz' % local_fox_hash: '99b6a899a3f947d7763aa318e86f9f08db684568bfdcd293f3318bee9d7f1948'},
+    {'qe-gipaw-%s.tar.gz' % local_qe_gipaw_hash: '9ac8314363d29cc2f1ce85abd8f26c1a3ae311d54f6e6034d656442dd101c928'},
+    {'pw2qmcpack-%s.tar.gz' % local_qmcpack_hash: 'a8136da8429fc49ab560ef7356cd6f0a2714dfbb137baff7961f46dfe32061eb'},
+    {'wannier90-%s.tar.gz' % local_wannier90_hash: 'f989497790ec9777bdc159945bbf42156edb7268011f972874dec67dd4f58658'},
 ]
 
 builddependencies = [
diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-intel-2023a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-intel-2023a.eb
index be1bc77e808..888fd27916c 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-intel-2023a.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-intel-2023a.eb
@@ -25,7 +25,7 @@ local_fox_hash = "3453648e6837658b747b895bb7bef4b1ed2eac40"
 # https://gitlab.com/QEF/q-e/-/issues/666
 local_d3q_hash = "de4718351e7bbb9d1d12aad2b7ca232d06775b83"
 local_qe_gipaw_hash = "75b01b694c9ba4df55d294cacc27cf28591b2161"
-local_pw2qmcpack_hash = "f72ab25fa4ea755c1b4b230ae8074b47d5509c70"
+local_qmcpack_hash = "f72ab25fa4ea755c1b4b230ae8074b47d5509c70"
 local_wannier90_hash = "1d6b187374a2d50b509e5e79e2cab01a79ff7ce1"
 
 sources = [
@@ -91,11 +91,11 @@ sources = [
         },
     },
     {
-        "filename": "pw2qmcpack-%s.tar.gz" % local_pw2qmcpack_hash,
+        "filename": "pw2qmcpack-%s.tar.gz" % local_qmcpack_hash,
         "git_config": {
             "url": "https://github.com/QMCPACK",
             "repo_name": "pw2qmcpack",
-            "commit": local_pw2qmcpack_hash,
+            "commit": local_qmcpack_hash,
             "keep_git_dir": True,
         },
     },
@@ -111,22 +111,14 @@ sources = [
 ]
 checksums = [
     {'q-e-qe-7.3.1.tar.gz': '2c58b8fadfe4177de5a8b69eba447db5e623420b070dea6fd26c1533b081d844'},
-    {'lapack-12d825396fcef1e0a1b27be9f119f9e554621e55.tar.gz':
-     'c05532ae0e5fe35f473206dda12970da5f2e2214620487d71837ddcf0ea6b21d'},
-    {'mbd-82005cbb65bdf5d32ca021848eec8f19da956a77.tar.gz':
-     'a180682c00bb890c9b1e26a98addbd68e32f970c06439acf7582415f4c589800'},
-    {'devxlib-a6b89ef77b1ceda48e967921f1f5488d2df9226d.tar.gz':
-     '76da8fe5a2050f58efdc92fa8831efec25c19190df7f4e5e39c173a5fbae83b4'},
-    {'d3q-de4718351e7bbb9d1d12aad2b7ca232d06775b83.tar.gz':
-     '43e50753a56af05d181b859d3e29d842fb3fc4352f00cb7fe229a435a1f20c31'},
-    {'fox-3453648e6837658b747b895bb7bef4b1ed2eac40.tar.gz':
-     '99b6a899a3f947d7763aa318e86f9f08db684568bfdcd293f3318bee9d7f1948'},
-    {'qe-gipaw-75b01b694c9ba4df55d294cacc27cf28591b2161.tar.gz':
-     '9ac8314363d29cc2f1ce85abd8f26c1a3ae311d54f6e6034d656442dd101c928'},
-    {'pw2qmcpack-f72ab25fa4ea755c1b4b230ae8074b47d5509c70.tar.gz':
-     'a8136da8429fc49ab560ef7356cd6f0a2714dfbb137baff7961f46dfe32061eb'},
-    {'wannier90-1d6b187374a2d50b509e5e79e2cab01a79ff7ce1.tar.gz':
-     'f989497790ec9777bdc159945bbf42156edb7268011f972874dec67dd4f58658'},
+    {'lapack-%s.tar.gz' % local_lapack_hash: 'c05532ae0e5fe35f473206dda12970da5f2e2214620487d71837ddcf0ea6b21d'},
+    {'mbd-%s.tar.gz' % local_mbd_hash: 'a180682c00bb890c9b1e26a98addbd68e32f970c06439acf7582415f4c589800'},
+    {'devxlib-%s.tar.gz' % local_devxlib_hash: '76da8fe5a2050f58efdc92fa8831efec25c19190df7f4e5e39c173a5fbae83b4'},
+    {'d3q-%s.tar.gz' % local_d3q_hash: '43e50753a56af05d181b859d3e29d842fb3fc4352f00cb7fe229a435a1f20c31'},
+    {'fox-%s.tar.gz' % local_fox_hash: '99b6a899a3f947d7763aa318e86f9f08db684568bfdcd293f3318bee9d7f1948'},
+    {'qe-gipaw-%s.tar.gz' % local_qe_gipaw_hash: '9ac8314363d29cc2f1ce85abd8f26c1a3ae311d54f6e6034d656442dd101c928'},
+    {'pw2qmcpack-%s.tar.gz' % local_qmcpack_hash: 'a8136da8429fc49ab560ef7356cd6f0a2714dfbb137baff7961f46dfe32061eb'},
+    {'wannier90-%s.tar.gz' % local_wannier90_hash: 'f989497790ec9777bdc159945bbf42156edb7268011f972874dec67dd4f58658'},
 ]
 
 builddependencies = [

From ea076ae1def18d26b63fa2153e2be088d8d41bca Mon Sep 17 00:00:00 2001
From: mssmzs <mssmzs@login01.avon.hpc>
Date: Wed, 3 Apr 2024 22:59:26 +0100
Subject: [PATCH 038/835] adding easyconfigs: libzip-1.10.1-GCCcore-13.2.0.eb

---
 .../l/libzip/libzip-1.10.1-GCCcore-13.2.0.eb  | 32 +++++++++++++++++++
 1 file changed, 32 insertions(+)
 create mode 100755 easybuild/easyconfigs/l/libzip/libzip-1.10.1-GCCcore-13.2.0.eb

diff --git a/easybuild/easyconfigs/l/libzip/libzip-1.10.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/libzip/libzip-1.10.1-GCCcore-13.2.0.eb
new file mode 100755
index 00000000000..e0998b1c6a6
--- /dev/null
+++ b/easybuild/easyconfigs/l/libzip/libzip-1.10.1-GCCcore-13.2.0.eb
@@ -0,0 +1,32 @@
+easyblock = 'CMakeMake'
+
+name = 'libzip'
+version = '1.10.1'
+
+homepage = 'https://libzip.org/'
+description = "libzip is a C library for reading, creating, and modifying zip archives."
+
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
+
+source_urls = ['https://github.com/nih-at/libzip/archive/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['d56d857d1c3ad4a7f3a4c01a51c6a6e5530e35ab93503f62276e8ba2b306186a']
+
+builddependencies = [
+    ('binutils', '2.40'),
+    ('CMake', '3.27.6'),
+]
+
+dependencies = [('zlib', '1.2.13')]
+
+sanity_check_paths = {
+    'files': [
+        'bin/zipcmp',
+        'bin/zipmerge',
+        'bin/ziptool',
+        'lib64/libzip.%s' % SHLIB_EXT,
+    ],
+    'dirs': ['include', 'lib/pkgconfig'],
+}
+
+moduleclass = 'lib'

From ccb9c6942a2838782d7ef256443ec2260afb7abf Mon Sep 17 00:00:00 2001
From: mssmzs <mssmzs@login01.avon.hpc>
Date: Thu, 4 Apr 2024 11:26:09 +0100
Subject: [PATCH 039/835] fix permissions

---
 easybuild/easyconfigs/l/libzip/libzip-1.10.1-GCCcore-13.2.0.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/l/libzip/libzip-1.10.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/libzip/libzip-1.10.1-GCCcore-13.2.0.eb
index e0998b1c6a6..99be49a252a 100755
--- a/easybuild/easyconfigs/l/libzip/libzip-1.10.1-GCCcore-13.2.0.eb
+++ b/easybuild/easyconfigs/l/libzip/libzip-1.10.1-GCCcore-13.2.0.eb
@@ -4,7 +4,7 @@ name = 'libzip'
 version = '1.10.1'
 
 homepage = 'https://libzip.org/'
-description = "libzip is a C library for reading, creating, and modifying zip archives."
+description = "libzip is a C library for reading, creating, and modifying zip archives.."
 
 toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
 

From 6a0d3bdb8e5624ffd9afe0ab82de0bf744a934f5 Mon Sep 17 00:00:00 2001
From: mssmzs <mssmzs@login01.avon.hpc>
Date: Thu, 4 Apr 2024 19:39:29 +0100
Subject: [PATCH 040/835] adding sanity check commands as per reviewer's
 request

---
 .../easyconfigs/l/libzip/libzip-1.10.1-GCCcore-13.2.0.eb    | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/easybuild/easyconfigs/l/libzip/libzip-1.10.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/libzip/libzip-1.10.1-GCCcore-13.2.0.eb
index 99be49a252a..887eaf37405 100755
--- a/easybuild/easyconfigs/l/libzip/libzip-1.10.1-GCCcore-13.2.0.eb
+++ b/easybuild/easyconfigs/l/libzip/libzip-1.10.1-GCCcore-13.2.0.eb
@@ -29,4 +29,10 @@ sanity_check_paths = {
     'dirs': ['include', 'lib/pkgconfig'],
 }
 
+sanity_check_commands = [
+    "zipcmp -h",
+    "zipmerge -h",
+    "ziptool -h"
+]
+
 moduleclass = 'lib'

From 3e3ae363e7acfd6a3d3ae51bfebab915571af888 Mon Sep 17 00:00:00 2001
From: crivella <davide.grassano@epfl.ch>
Date: Fri, 5 Apr 2024 11:29:53 +0200
Subject: [PATCH 041/835] Non reproducible checksums

---
 .../QuantumESPRESSO-7.3.1-foss-2023a.eb       | 25 +++++++++++--------
 .../QuantumESPRESSO-7.3.1-intel-2023a.eb      | 25 +++++++++++--------
 2 files changed, 28 insertions(+), 22 deletions(-)

diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-foss-2023a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-foss-2023a.eb
index eed5e0c4e40..4386cebd5d2 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-foss-2023a.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-foss-2023a.eb
@@ -26,7 +26,7 @@ local_fox_hash = "3453648e6837658b747b895bb7bef4b1ed2eac40"
 local_d3q_hash = "de4718351e7bbb9d1d12aad2b7ca232d06775b83"
 local_qe_gipaw_hash = "75b01b694c9ba4df55d294cacc27cf28591b2161"
 local_qmcpack_hash = "f72ab25fa4ea755c1b4b230ae8074b47d5509c70"
-local_wannier90_hash = "1d6b187374a2d50b509e5e79e2cab01a79ff7ce1"
+local_w90_hash = "1d6b187374a2d50b509e5e79e2cab01a79ff7ce1"
 
 
 sources = [
@@ -101,25 +101,28 @@ sources = [
         },
     },
     {
-        "filename": "wannier90-%s.tar.gz" % local_wannier90_hash,
+        "filename": "wannier90-%s.tar.gz" % local_w90_hash,
         "git_config": {
             "url": "https://github.com/wannier-developers",
             "repo_name": "wannier90",
-            "commit": local_wannier90_hash,
+            "commit": local_w90_hash,
             "keep_git_dir": True,
         },
     },
 ]
 checksums = [
     {'q-e-qe-7.3.1.tar.gz': '2c58b8fadfe4177de5a8b69eba447db5e623420b070dea6fd26c1533b081d844'},
-    {'lapack-%s.tar.gz' % local_lapack_hash: 'c05532ae0e5fe35f473206dda12970da5f2e2214620487d71837ddcf0ea6b21d'},
-    {'mbd-%s.tar.gz' % local_mbd_hash: 'a180682c00bb890c9b1e26a98addbd68e32f970c06439acf7582415f4c589800'},
-    {'devxlib-%s.tar.gz' % local_devxlib_hash: '76da8fe5a2050f58efdc92fa8831efec25c19190df7f4e5e39c173a5fbae83b4'},
-    {'d3q-%s.tar.gz' % local_d3q_hash: '43e50753a56af05d181b859d3e29d842fb3fc4352f00cb7fe229a435a1f20c31'},
-    {'fox-%s.tar.gz' % local_fox_hash: '99b6a899a3f947d7763aa318e86f9f08db684568bfdcd293f3318bee9d7f1948'},
-    {'qe-gipaw-%s.tar.gz' % local_qe_gipaw_hash: '9ac8314363d29cc2f1ce85abd8f26c1a3ae311d54f6e6034d656442dd101c928'},
-    {'pw2qmcpack-%s.tar.gz' % local_qmcpack_hash: 'a8136da8429fc49ab560ef7356cd6f0a2714dfbb137baff7961f46dfe32061eb'},
-    {'wannier90-%s.tar.gz' % local_wannier90_hash: 'f989497790ec9777bdc159945bbf42156edb7268011f972874dec67dd4f58658'},
+    # Holding off checksum checks untill 5.0.x
+    # https://github.com/easybuilders/easybuild-framework/pull/4248
+
+    # {'lapack-%s.tar.gz' % local_lapack_hash: 'c05532ae0e5fe35f473206dda12970da5f2e2214620487d71837ddcf0ea6b21d'},
+    # {'mbd-%s.tar.gz' % local_mbd_hash: 'a180682c00bb890c9b1e26a98addbd68e32f970c06439acf7582415f4c589800'},
+    # {'devxlib-%s.tar.gz' % local_devxlib_hash: '76da8fe5a2050f58efdc92fa8831efec25c19190df7f4e5e39c173a5fbae83b4'},
+    # {'d3q-%s.tar.gz' % local_d3q_hash: '43e50753a56af05d181b859d3e29d842fb3fc4352f00cb7fe229a435a1f20c31'},
+    # {'fox-%s.tar.gz' % local_fox_hash: '99b6a899a3f947d7763aa318e86f9f08db684568bfdcd293f3318bee9d7f1948'},
+    # {'qe-gipaw-%s.tar.gz' % local_qe_gipaw_hash: '9ac8314363d29cc2f1ce85abd8f26c1a3ae311d54f6e6034d656442dd101c928'},
+    # {'pw2qmcpack-%s.tar.gz' % local_qmcpack_hash: 'a8136da8429fc49ab560ef7356cd6f0a2714dfbb137baff7961f46dfe32061eb'},
+    # {'wannier90-%s.tar.gz' % local_w90_hash: 'f989497790ec9777bdc159945bbf42156edb7268011f972874dec67dd4f58658'},
 ]
 
 builddependencies = [
diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-intel-2023a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-intel-2023a.eb
index 888fd27916c..fd33e950151 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-intel-2023a.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-intel-2023a.eb
@@ -26,7 +26,7 @@ local_fox_hash = "3453648e6837658b747b895bb7bef4b1ed2eac40"
 local_d3q_hash = "de4718351e7bbb9d1d12aad2b7ca232d06775b83"
 local_qe_gipaw_hash = "75b01b694c9ba4df55d294cacc27cf28591b2161"
 local_qmcpack_hash = "f72ab25fa4ea755c1b4b230ae8074b47d5509c70"
-local_wannier90_hash = "1d6b187374a2d50b509e5e79e2cab01a79ff7ce1"
+local_w90_hash = "1d6b187374a2d50b509e5e79e2cab01a79ff7ce1"
 
 sources = [
     {
@@ -100,25 +100,28 @@ sources = [
         },
     },
     {
-        "filename": "wannier90-%s.tar.gz" % local_wannier90_hash,
+        "filename": "wannier90-%s.tar.gz" % local_w90_hash,
         "git_config": {
             "url": "https://github.com/wannier-developers",
             "repo_name": "wannier90",
-            "commit": local_wannier90_hash,
+            "commit": local_w90_hash,
             "keep_git_dir": True,
         },
     },
 ]
 checksums = [
     {'q-e-qe-7.3.1.tar.gz': '2c58b8fadfe4177de5a8b69eba447db5e623420b070dea6fd26c1533b081d844'},
-    {'lapack-%s.tar.gz' % local_lapack_hash: 'c05532ae0e5fe35f473206dda12970da5f2e2214620487d71837ddcf0ea6b21d'},
-    {'mbd-%s.tar.gz' % local_mbd_hash: 'a180682c00bb890c9b1e26a98addbd68e32f970c06439acf7582415f4c589800'},
-    {'devxlib-%s.tar.gz' % local_devxlib_hash: '76da8fe5a2050f58efdc92fa8831efec25c19190df7f4e5e39c173a5fbae83b4'},
-    {'d3q-%s.tar.gz' % local_d3q_hash: '43e50753a56af05d181b859d3e29d842fb3fc4352f00cb7fe229a435a1f20c31'},
-    {'fox-%s.tar.gz' % local_fox_hash: '99b6a899a3f947d7763aa318e86f9f08db684568bfdcd293f3318bee9d7f1948'},
-    {'qe-gipaw-%s.tar.gz' % local_qe_gipaw_hash: '9ac8314363d29cc2f1ce85abd8f26c1a3ae311d54f6e6034d656442dd101c928'},
-    {'pw2qmcpack-%s.tar.gz' % local_qmcpack_hash: 'a8136da8429fc49ab560ef7356cd6f0a2714dfbb137baff7961f46dfe32061eb'},
-    {'wannier90-%s.tar.gz' % local_wannier90_hash: 'f989497790ec9777bdc159945bbf42156edb7268011f972874dec67dd4f58658'},
+    # Holding off checksum checks untill 5.0.x
+    # https://github.com/easybuilders/easybuild-framework/pull/4248
+
+    # {'lapack-%s.tar.gz' % local_lapack_hash: 'c05532ae0e5fe35f473206dda12970da5f2e2214620487d71837ddcf0ea6b21d'},
+    # {'mbd-%s.tar.gz' % local_mbd_hash: 'a180682c00bb890c9b1e26a98addbd68e32f970c06439acf7582415f4c589800'},
+    # {'devxlib-%s.tar.gz' % local_devxlib_hash: '76da8fe5a2050f58efdc92fa8831efec25c19190df7f4e5e39c173a5fbae83b4'},
+    # {'d3q-%s.tar.gz' % local_d3q_hash: '43e50753a56af05d181b859d3e29d842fb3fc4352f00cb7fe229a435a1f20c31'},
+    # {'fox-%s.tar.gz' % local_fox_hash: '99b6a899a3f947d7763aa318e86f9f08db684568bfdcd293f3318bee9d7f1948'},
+    # {'qe-gipaw-%s.tar.gz' % local_qe_gipaw_hash: '9ac8314363d29cc2f1ce85abd8f26c1a3ae311d54f6e6034d656442dd101c928'},
+    # {'pw2qmcpack-%s.tar.gz' % local_qmcpack_hash: 'a8136da8429fc49ab560ef7356cd6f0a2714dfbb137baff7961f46dfe32061eb'},
+    # {'wannier90-%s.tar.gz' % local_w90_hash: 'f989497790ec9777bdc159945bbf42156edb7268011f972874dec67dd4f58658'},
 ]
 
 builddependencies = [

From a09e4c4ade604088befa507e000e49bb459a18bf Mon Sep 17 00:00:00 2001
From: crivella <davide.grassano@epfl.ch>
Date: Fri, 5 Apr 2024 11:31:46 +0200
Subject: [PATCH 042/835] `keep_git_dir` would always cause non reproducible
 hashes

---
 .../q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-foss-2023a.eb | 8 --------
 .../QuantumESPRESSO/QuantumESPRESSO-7.3.1-intel-2023a.eb  | 8 --------
 2 files changed, 16 deletions(-)

diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-foss-2023a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-foss-2023a.eb
index 4386cebd5d2..88dd142f976 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-foss-2023a.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-foss-2023a.eb
@@ -41,7 +41,6 @@ sources = [
             "url": "https://github.com/Reference-LAPACK",
             "repo_name": "lapack",
             "commit": local_lapack_hash,
-            "keep_git_dir": True,
         },
     },
     {
@@ -51,7 +50,6 @@ sources = [
             "repo_name": "libmbd",
             "commit": local_mbd_hash,
             'clone_into': 'mbd',
-            "keep_git_dir": True,
         },
     },
     {
@@ -61,7 +59,6 @@ sources = [
             "repo_name": "devicexlib",
             "commit": local_devxlib_hash,
             'clone_into': 'devxlib',
-            "keep_git_dir": True,
         },
     },
     {
@@ -70,7 +67,6 @@ sources = [
             "url": "https://github.com/anharmonic",
             "repo_name": "d3q",
             "commit": local_d3q_hash,
-            "keep_git_dir": True,
         },
     },
     {
@@ -79,7 +75,6 @@ sources = [
             "url": "https://github.com/pietrodelugas",
             "repo_name": "fox",
             "commit": local_fox_hash,
-            "keep_git_dir": True,
         },
     },
     {
@@ -88,7 +83,6 @@ sources = [
             "url": "https://github.com/dceresoli",
             "repo_name": "qe-gipaw",
             "commit": local_qe_gipaw_hash,
-            "keep_git_dir": True,
         },
     },
     {
@@ -97,7 +91,6 @@ sources = [
             "url": "https://github.com/QMCPACK",
             "repo_name": "pw2qmcpack",
             "commit": local_qmcpack_hash,
-            "keep_git_dir": True,
         },
     },
     {
@@ -106,7 +99,6 @@ sources = [
             "url": "https://github.com/wannier-developers",
             "repo_name": "wannier90",
             "commit": local_w90_hash,
-            "keep_git_dir": True,
         },
     },
 ]
diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-intel-2023a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-intel-2023a.eb
index fd33e950151..8235b0731f0 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-intel-2023a.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-intel-2023a.eb
@@ -40,7 +40,6 @@ sources = [
             "url": "https://github.com/Reference-LAPACK",
             "repo_name": "lapack",
             "commit": local_lapack_hash,
-            "keep_git_dir": True,
         },
     },
     {
@@ -50,7 +49,6 @@ sources = [
             "repo_name": "libmbd",
             "commit": local_mbd_hash,
             'clone_into': 'mbd',
-            "keep_git_dir": True,
         },
     },
     {
@@ -60,7 +58,6 @@ sources = [
             "repo_name": "devicexlib",
             "commit": local_devxlib_hash,
             'clone_into': 'devxlib',
-            "keep_git_dir": True,
         },
     },
     {
@@ -69,7 +66,6 @@ sources = [
             "url": "https://github.com/anharmonic",
             "repo_name": "d3q",
             "commit": local_d3q_hash,
-            "keep_git_dir": True,
         },
     },
     {
@@ -78,7 +74,6 @@ sources = [
             "url": "https://github.com/pietrodelugas",
             "repo_name": "fox",
             "commit": local_fox_hash,
-            "keep_git_dir": True,
         },
     },
     {
@@ -87,7 +82,6 @@ sources = [
             "url": "https://github.com/dceresoli",
             "repo_name": "qe-gipaw",
             "commit": local_qe_gipaw_hash,
-            "keep_git_dir": True,
         },
     },
     {
@@ -96,7 +90,6 @@ sources = [
             "url": "https://github.com/QMCPACK",
             "repo_name": "pw2qmcpack",
             "commit": local_qmcpack_hash,
-            "keep_git_dir": True,
         },
     },
     {
@@ -105,7 +98,6 @@ sources = [
             "url": "https://github.com/wannier-developers",
             "repo_name": "wannier90",
             "commit": local_w90_hash,
-            "keep_git_dir": True,
         },
     },
 ]

From 7d8e8cd5c2cb3a303ae8d7e223393b8827bc6c57 Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Fri, 5 Apr 2024 14:32:05 +0200
Subject: [PATCH 043/835] foss build of QE 7.3 has seen a single failure in
 test suites on some architectures

---
 .../q/QuantumESPRESSO/QuantumESPRESSO-7.3-foss-2023a.eb        | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3-foss-2023a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3-foss-2023a.eb
index 208c3041689..d0089ef7bc7 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3-foss-2023a.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3-foss-2023a.eb
@@ -52,4 +52,7 @@ buildopts = "all gwl xspectra couple epw gipaw w90"
 # parallel build tends to fail
 parallel = 1
 
+# allow some test failures (see https://github.com/EESSI/software-layer/pull/504#issuecomment-2039605740)
+test_suite_max_failed = 1
+
 moduleclass = 'chem'

From 22e9d452c8f0c1f1cce6f1a3c5e1ba728067b4cc Mon Sep 17 00:00:00 2001
From: ocaisa <alan.ocais@cecam.org>
Date: Fri, 5 Apr 2024 20:39:22 +0200
Subject: [PATCH 044/835] Update
 easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-intel-2023a.eb

---
 .../q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-intel-2023a.eb       | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-intel-2023a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-intel-2023a.eb
index 8235b0731f0..57e35f427c9 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-intel-2023a.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-intel-2023a.eb
@@ -119,6 +119,7 @@ checksums = [
 builddependencies = [
     ('M4', '1.4.19'),
     ('CMake', '3.26.3'),
+    ("pkgconf", "1.9.5"),
 ]
 dependencies = [
     ('HDF5', '1.14.0'),

From 2ef25a0b99e3ba35747b87940208398f08391929 Mon Sep 17 00:00:00 2001
From: ocaisa <alan.ocais@cecam.org>
Date: Fri, 5 Apr 2024 20:39:33 +0200
Subject: [PATCH 045/835] Update
 easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-foss-2023a.eb

---
 .../q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-foss-2023a.eb        | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-foss-2023a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-foss-2023a.eb
index 88dd142f976..6f577cb5e91 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-foss-2023a.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-foss-2023a.eb
@@ -120,6 +120,7 @@ checksums = [
 builddependencies = [
     ("M4", "1.4.19"),
     ("CMake", "3.26.3"),
+    ("pkgconf", "1.9.5"),
 ]
 dependencies = [
     ("HDF5", "1.14.0"),

From f988b1d6072749c2ca5708abbbe333ff3b03ce59 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Mon, 8 Apr 2024 11:03:20 +0200
Subject: [PATCH 046/835] cassiopeia added, homepage, description

---
 ...e-cell-python-bundle-2024.02-foss-2023a.eb | 46 +++----------------
 1 file changed, 6 insertions(+), 40 deletions(-)

diff --git a/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb b/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb
index f7976233e97..9f0a5b02b36 100644
--- a/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb
+++ b/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb
@@ -3,8 +3,8 @@ easyblock = 'PythonBundle'
 name = 'Single-cell-python-bundle'
 version = '2024.02'
 
-homepage = 'xxx'
-description = """Bundle of softwares for single-cell research ???"""
+homepage = (None)
+description = """Bundle of tools for single-cell sequence analysis."""
 
 toolchain = {'name': 'foss', 'version': '2023a'}
 
@@ -26,15 +26,14 @@ dependencies = [
     ('CellTypist', '1.6.2'),
     # loompy in scVelo
     ('epiScanpy', '0.4.0'),
-    # ('CellRank', '2.0.2'),
     ('scCODA', '0.1.9'),  # imports rpy2
     # rpy2 in scCODA
     ('infercnvpy', '0.4.3'),
-    # ('pySCENIC', '0.12.1-20240311'),
+    ('pySCENIC', '0.12.1-20240311'),
+    # ('CellRank', '2.0.2'),
     # ('Squidpy', '1.4.1'),
+    # ('Cassiopeia', '2.0.0'),
     # deps for exts:
-    # ('Pillow', '10.0.0'),  # cassiopeia
-    # ('pycodestyle', '2.11.1'),  # cassiopeia, created
     ('umap-learn', '0.5.5'),  # bbknn
     ('scikit-learn', '1.3.1'),  # bbknn, sc_toolbox
     ('PyYAML', '6.0'),  # sc_toolbox
@@ -43,7 +42,7 @@ dependencies = [
 ]
 
 # DEPS to add:
-# Cassiopeia-lineage
+# Cassiopeia-lineage OK deps
 # Cassiopeia NO! do it again for https://pypi.org/project/cassiopeia-lineage/
     # arrow, datapipelines,merakicommons, flake8, Pillow
     # flake8: mccabe, pycodestyle (created for 2023a), pyflakes
@@ -90,17 +89,6 @@ dependencies = [
 # Decoupler
 # contrastiveVI
 # Schist
-
-# cassiopeia-lineage Error:
-# gcc -DNDEBUG -g -fwrapv -O3 -Wall -O2 -ftree-vectorize -march=native -fno-math-errno -fPIC -O2 -ftree-vectorize -march=native -fno-math-errn
-# O2 -ftree-vectorize -march=native -fno-math-errno -I/apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-12.3.0/include -I/apps/gent/RHEL8/cas
-# ib/software/FlexiBLAS/3.3.1-GCC-12.3.0/include -I/apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.3.1-GCC-12.3.0/include/flexiblas -fPIC -I/sc
-# t/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/Python/3.11.3-GCCcore-12.3.0/include/python3.11 -c cassiopeia/TreeSolver/lineage_
-# lver_utils.c -o build/temp.linux-x86_64-cpython-311/cassiopeia/TreeSolver/lineage_solver/solver_utils.o
-#       cassiopeia/TreeSolver/lineage_solver/solver_utils.c:208:12: fatal error: longintrepr.h: No such file or directory
-#         208 |   #include "longintrepr.h"
-#             |            ^~~~~~~~~~~~~~~
-#       compilation terminated.
       
 exts_list = [
     ('flit_core', '3.9.0', {
@@ -185,29 +173,7 @@ exts_list = [
         'preinstallopts': "sed -i '28d' setup.py && ",
         'checksums': ['8c12ddccb72c41c96c6a5abceb52e7a76f439a9ab94fb092aa86ee3c1292383a'],
     }),
-    # ('cassiopeia-lineage', '1.0.4', {
-    #     'checksums': ['c341f6f4f0e4cb422c657387336f001a9e5d4eaff8fe0b40a00508b307de27aa'],
-    # }),
 ]
-
-    # ('pyflakes', '3.2.0', {
-    #     'checksums': ['1c61603ff154621fb2a9172037d84dca3500def8c8b630657d1701f026f8af3f'],
-    # }),
-    # ('mccabe', '0.7.0', {
-    #     'checksums': ['348e0240c33b60bbdf4e523192ef919f28cb2c3d7d5c7794f74009290f236325'],
-    # }),
-    # ('arrow', '0.17.0', {
-    #     'checksums': ['ff08d10cda1d36c68657d6ad20d74fbea493d980f8b2d45344e00d6ed2bf6ed4'],
-    # }),
-    # ('datapipelines', '1.0.7', {
-    #     'checksums': ['752bc71a1e03a45d723fc4d9b56c641ed0b872ed1df73b08896ee34d93c56e8f'],
-    # }),
-    # ('merakicommons', '1.0.10', {
-    #     'checksums': ['fc99ebe0cb85c4af0093a9454294adcb97c0792f8a8dd03898242ab2446aa77e'],
-    # }),
-    # ('flake8', '7.0.0', {
-    #     'checksums': ['33f96621059e65eec474169085dc92bf26e7b2d47366b70be2f67ab80dc25132'],
-    # }),
     
 use_pip = True
 sanity_pip_check = True

From 0f03e0cbff1bc6955aad67ced9fea1ca23b329f3 Mon Sep 17 00:00:00 2001
From: mssmzs <mssmzs@login01.avon.hpc>
Date: Wed, 10 Apr 2024 13:10:42 +0100
Subject: [PATCH 047/835] fix permissions

---
 easybuild/easyconfigs/l/libzip/libzip-1.10.1-GCCcore-13.2.0.eb | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 mode change 100755 => 100644 easybuild/easyconfigs/l/libzip/libzip-1.10.1-GCCcore-13.2.0.eb

diff --git a/easybuild/easyconfigs/l/libzip/libzip-1.10.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/libzip/libzip-1.10.1-GCCcore-13.2.0.eb
old mode 100755
new mode 100644

From 07bb12db55c15482dc123803270ddf24a51d27ff Mon Sep 17 00:00:00 2001
From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com>
Date: Thu, 11 Apr 2024 15:41:26 +0200
Subject: [PATCH 048/835] Update
 easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a-CUDA-12.1.1.eb

Co-authored-by: Alexander Grund <Flamefire@users.noreply.github.com>
---
 .../easyconfigs/j/jax/jax-0.4.25-gfbf-2023a-CUDA-12.1.1.eb      | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a-CUDA-12.1.1.eb
index 6b5b930524e..23d51500542 100644
--- a/easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a-CUDA-12.1.1.eb
+++ b/easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a-CUDA-12.1.1.eb
@@ -41,6 +41,8 @@ local_xla_commit = '4ccfe33c71665ddcbca5b127fefe8baa3ed632d4'
 local_tfrt_commit = '0aeefb1660d7e37964b2bb71b1f518096bda9a25'
 local_repo_opt = '--bazel_options="--override_repository=xla=%%(builddir)s/xla-%s" ' % local_xla_commit
 local_repo_opt += '--bazel_options="--override_repository=runtime=%%(builddir)s/tf_runtime-%s" ' % local_xla_commit
+local_repo_opt += '-bazel_options="--action_env=TF_SYSTEM_LIBS=pybind11" '
+local_repo_opt += '--bazel_options="--action_env=CPATH=$EBROOTPYBIND11/include"'
 
 
 # Some tests require an isolated run:

From 7809bd3377fe8d875d0983f77015191ea6c8425e Mon Sep 17 00:00:00 2001
From: Alexander Grund <alexander.grund@tu-dresden.de>
Date: Thu, 11 Apr 2024 18:16:42 +0200
Subject: [PATCH 049/835] Fix usage of system Pybind11

---
 .../j/jax/jax-0.4.25-gfbf-2023a-CUDA-12.1.1.eb |  7 ++++---
 .../jax-0.4.25_fix-pybind11-systemlib.patch    | 18 ++++++++++++++++++
 2 files changed, 22 insertions(+), 3 deletions(-)
 create mode 100644 easybuild/easyconfigs/j/jax/jax-0.4.25_fix-pybind11-systemlib.patch

diff --git a/easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a-CUDA-12.1.1.eb
index 23d51500542..04db9ad33e1 100644
--- a/easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a-CUDA-12.1.1.eb
+++ b/easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a-CUDA-12.1.1.eb
@@ -41,8 +41,8 @@ local_xla_commit = '4ccfe33c71665ddcbca5b127fefe8baa3ed632d4'
 local_tfrt_commit = '0aeefb1660d7e37964b2bb71b1f518096bda9a25'
 local_repo_opt = '--bazel_options="--override_repository=xla=%%(builddir)s/xla-%s" ' % local_xla_commit
 local_repo_opt += '--bazel_options="--override_repository=runtime=%%(builddir)s/tf_runtime-%s" ' % local_xla_commit
-local_repo_opt += '-bazel_options="--action_env=TF_SYSTEM_LIBS=pybind11" '
-local_repo_opt += '--bazel_options="--action_env=CPATH=$EBROOTPYBIND11/include"'
+local_repo_opt += '--bazel_options="--action_env=TF_SYSTEM_LIBS=pybind11" '
+local_repo_opt += '--bazel_options="--action_env=CPATH=$EBROOTPYBIND11/include" '
 
 
 # Some tests require an isolated run:
@@ -51,7 +51,6 @@ local_isolated_tests = [
     'tests/host_callback_test.py::HostCallbackTapTest::test_tap_transforms_doc',
     'tests/lax_scipy_special_functions_test.py::LaxScipySpcialFunctionsTest' +
     '::testScipySpecialFun_gammainc_s_2x1x4_float32_float32',
-    'tests/lax_numpy_test.py::NumpyUfuncTests::testUfuncInputTypes763'
 ]
 # deliberately not testing in parallel, as that results in (additional) failing tests;
 # use XLA_PYTHON_CLIENT_ALLOCATOR=platform to allocate and deallocate GPU memory during testing,
@@ -105,6 +104,7 @@ components = [
             'https://github.com/tensorflow/runtime/archive',
             'https://github.com/openxla/xla/archive'
         ],
+        'patches': [('jax-0.4.25_fix-pybind11-systemlib.patch', '../xla-' + local_xla_commit)],
         'checksums': [
             {'jaxlib-v0.4.25.tar.gz':
              'fc1197c401924942eb14185a61688d0c476e3e81ff71f9dc95e620b57c06eec8'},
@@ -112,6 +112,7 @@ components = [
              '8a59b9af7d0850059d7043f7043c780066d61538f3af536e8a10d3d717f35089'},
             {'tf_runtime-0aeefb1660d7e37964b2bb71b1f518096bda9a25.tar.gz':
              'a3df827d7896774cb1d80bf4e1c79ab05c268f29bd4d3db1fb5a4b9c2079d8e3'},
+            {'jax-0.4.25_fix-pybind11-systemlib.patch': '4cdc97ce05b708b16e161082428e5413c89c2852edb4262cd19d16618ddad9b6'},
         ],
         'start_dir': 'jax-jaxlib-v%(version)s',
         # Avoid warning (treated as error) in upb/table.c
diff --git a/easybuild/easyconfigs/j/jax/jax-0.4.25_fix-pybind11-systemlib.patch b/easybuild/easyconfigs/j/jax/jax-0.4.25_fix-pybind11-systemlib.patch
new file mode 100644
index 00000000000..620acb11d0a
--- /dev/null
+++ b/easybuild/easyconfigs/j/jax/jax-0.4.25_fix-pybind11-systemlib.patch
@@ -0,0 +1,18 @@
+Add missing value for System Pybind11 Bazel config
+
+Author: Alexander Grund (TU Dresden)
+
+--- xla-orig/third_party/tsl/third_party/systemlibs/pybind11.BUILD
++++ xla-4ccfe33c71665ddcbca5b127fefe8baa3ed632d4/third_party/tsl/third_party/systemlibs/pybind11.BUILD
+@@ -6,3 +6,10 @@
+         "@tsl//third_party/python_runtime:headers",
+     ],
+ )
++
++# Needed by pybind11_bazel.
++config_setting(
++    name = "osx",
++    constraint_values = ["@platforms//os:osx"],
++)
++
+

From 65e87a6dd94b4bf1b14b3a1479db9846ad93dd40 Mon Sep 17 00:00:00 2001
From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com>
Date: Fri, 12 Apr 2024 11:53:34 +0200
Subject: [PATCH 050/835] Update jax-0.4.25-gfbf-2023a-CUDA-12.1.1.eb

fix checksum
---
 .../easyconfigs/j/jax/jax-0.4.25-gfbf-2023a-CUDA-12.1.1.eb      | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a-CUDA-12.1.1.eb
index 04db9ad33e1..af2e1b2ec5c 100644
--- a/easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a-CUDA-12.1.1.eb
+++ b/easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a-CUDA-12.1.1.eb
@@ -112,7 +112,7 @@ components = [
              '8a59b9af7d0850059d7043f7043c780066d61538f3af536e8a10d3d717f35089'},
             {'tf_runtime-0aeefb1660d7e37964b2bb71b1f518096bda9a25.tar.gz':
              'a3df827d7896774cb1d80bf4e1c79ab05c268f29bd4d3db1fb5a4b9c2079d8e3'},
-            {'jax-0.4.25_fix-pybind11-systemlib.patch': '4cdc97ce05b708b16e161082428e5413c89c2852edb4262cd19d16618ddad9b6'},
+            {'jax-0.4.25_fix-pybind11-systemlib.patch': 'ec93de5628e4d40d3378b92784f7d1e5b0b43bd207a86badeffd44a42e0b1d47'},
         ],
         'start_dir': 'jax-jaxlib-v%(version)s',
         # Avoid warning (treated as error) in upb/table.c

From c5f0711b146fa13de8768ef07a27e915be23b1ef Mon Sep 17 00:00:00 2001
From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com>
Date: Fri, 12 Apr 2024 12:18:50 +0200
Subject: [PATCH 051/835] Update jax-0.4.25-gfbf-2023a-CUDA-12.1.1.eb

fix style; add PyBind11 builddep
---
 .../easyconfigs/j/jax/jax-0.4.25-gfbf-2023a-CUDA-12.1.1.eb    | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a-CUDA-12.1.1.eb
index af2e1b2ec5c..d7ed71d94d6 100644
--- a/easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a-CUDA-12.1.1.eb
+++ b/easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a-CUDA-12.1.1.eb
@@ -22,6 +22,7 @@ builddependencies = [
     ('git', '2.41.0', '-nodocs'),
     ('matplotlib', '3.7.2'),  # required for tests/lobpcg_test.py
     ('poetry', '1.5.1'),
+    ('pybind11', '2.11.1'),
 ]
 
 dependencies = [
@@ -112,7 +113,8 @@ components = [
              '8a59b9af7d0850059d7043f7043c780066d61538f3af536e8a10d3d717f35089'},
             {'tf_runtime-0aeefb1660d7e37964b2bb71b1f518096bda9a25.tar.gz':
              'a3df827d7896774cb1d80bf4e1c79ab05c268f29bd4d3db1fb5a4b9c2079d8e3'},
-            {'jax-0.4.25_fix-pybind11-systemlib.patch': 'ec93de5628e4d40d3378b92784f7d1e5b0b43bd207a86badeffd44a42e0b1d47'},
+            {'jax-0.4.25_fix-pybind11-systemlib.patch':
+             'ec93de5628e4d40d3378b92784f7d1e5b0b43bd207a86badeffd44a42e0b1d47'},
         ],
         'start_dir': 'jax-jaxlib-v%(version)s',
         # Avoid warning (treated as error) in upb/table.c

From 47967f77f1251515ee16c02850f5b0971efb0ce7 Mon Sep 17 00:00:00 2001
From: ocaisa <alan.ocais@cecam.org>
Date: Sun, 14 Apr 2024 12:28:39 +0200
Subject: [PATCH 052/835] Update QuantumESPRESSO-7.3.1-foss-2023a.eb

---
 .../q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-foss-2023a.eb       | 2 --
 1 file changed, 2 deletions(-)

diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-foss-2023a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-foss-2023a.eb
index 6f577cb5e91..95de4bc7834 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-foss-2023a.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-foss-2023a.eb
@@ -1,5 +1,3 @@
-easyblock = "EB_QuantumESPRESSOcmake"
-
 name = "QuantumESPRESSO"
 version = "7.3.1"
 

From 5c3d0d92967a200ff00eb7fc5a6e8fa5b5e434c4 Mon Sep 17 00:00:00 2001
From: ocaisa <alan.ocais@cecam.org>
Date: Sun, 14 Apr 2024 12:29:05 +0200
Subject: [PATCH 053/835] Update QuantumESPRESSO-7.3.1-intel-2023a.eb

---
 .../q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-intel-2023a.eb      | 2 --
 1 file changed, 2 deletions(-)

diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-intel-2023a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-intel-2023a.eb
index 57e35f427c9..b9d0f3ab624 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-intel-2023a.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-intel-2023a.eb
@@ -1,5 +1,3 @@
-easyblock = 'EB_QuantumESPRESSOcmake'
-
 name = 'QuantumESPRESSO'
 version = '7.3.1'
 

From 6a4f58ea7b44d41287d7d5fe6d207a5a9d9a793f Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Sun, 14 Apr 2024 12:50:21 +0200
Subject: [PATCH 054/835] Move all legacy QuantumESPRESSO easyconfigs to the
 legacy easyblock

---
 .../QuantumESPRESSO-5.3.0-intel-2016.02-GCC-4.9.eb              | 2 ++
 .../QuantumESPRESSO/QuantumESPRESSO-5.4.0-foss-2016b-hybrid.eb  | 2 ++
 .../QuantumESPRESSO-5.4.0-intel-2016.02-GCC-4.9.eb              | 2 ++
 .../q/QuantumESPRESSO/QuantumESPRESSO-6.0-intel-2016b.eb        | 2 ++
 .../q/QuantumESPRESSO/QuantumESPRESSO-6.1-intel-2017a.eb        | 2 ++
 .../q/QuantumESPRESSO/QuantumESPRESSO-6.2-intel-2017b.eb        | 2 ++
 .../q/QuantumESPRESSO/QuantumESPRESSO-6.2.1-iomkl-2017b.eb      | 2 ++
 .../q/QuantumESPRESSO/QuantumESPRESSO-6.3-foss-2018b.eb         | 2 ++
 .../q/QuantumESPRESSO/QuantumESPRESSO-6.3-intel-2018b.eb        | 2 ++
 .../q/QuantumESPRESSO/QuantumESPRESSO-6.4.1-intel-2019a.eb      | 2 ++
 .../q/QuantumESPRESSO/QuantumESPRESSO-6.5-intel-2019a.eb        | 2 ++
 .../q/QuantumESPRESSO/QuantumESPRESSO-6.5-intel-2019b.eb        | 2 ++
 .../q/QuantumESPRESSO/QuantumESPRESSO-6.6-foss-2019b.eb         | 2 ++
 .../q/QuantumESPRESSO/QuantumESPRESSO-6.6-foss-2020a.eb         | 2 ++
 .../q/QuantumESPRESSO/QuantumESPRESSO-6.6-foss-2020b.eb         | 2 ++
 .../q/QuantumESPRESSO/QuantumESPRESSO-6.6-intel-2019b.eb        | 2 ++
 .../q/QuantumESPRESSO/QuantumESPRESSO-6.6-intel-2020a.eb        | 2 ++
 .../q/QuantumESPRESSO/QuantumESPRESSO-6.7-foss-2019b.eb         | 2 ++
 .../q/QuantumESPRESSO/QuantumESPRESSO-6.7-foss-2020b.eb         | 2 ++
 .../q/QuantumESPRESSO/QuantumESPRESSO-6.7-foss-2021a.eb         | 2 ++
 .../q/QuantumESPRESSO/QuantumESPRESSO-6.7-intel-2019b.eb        | 2 ++
 .../q/QuantumESPRESSO/QuantumESPRESSO-6.7-intel-2021a.eb        | 2 ++
 .../q/QuantumESPRESSO/QuantumESPRESSO-6.7-iomkl-2019b.eb        | 2 ++
 .../q/QuantumESPRESSO/QuantumESPRESSO-6.8-foss-2021a.eb         | 2 ++
 .../q/QuantumESPRESSO/QuantumESPRESSO-6.8-foss-2021b.eb         | 2 ++
 .../q/QuantumESPRESSO/QuantumESPRESSO-6.8-intel-2021a.eb        | 2 ++
 .../q/QuantumESPRESSO/QuantumESPRESSO-7.0-foss-2021b.eb         | 2 ++
 .../q/QuantumESPRESSO/QuantumESPRESSO-7.0-intel-2021b.eb        | 2 ++
 .../q/QuantumESPRESSO/QuantumESPRESSO-7.1-foss-2022a.eb         | 2 ++
 .../q/QuantumESPRESSO/QuantumESPRESSO-7.1-intel-2022a.eb        | 2 ++
 .../q/QuantumESPRESSO/QuantumESPRESSO-7.2-foss-2022b.eb         | 2 ++
 .../q/QuantumESPRESSO/QuantumESPRESSO-7.2-foss-2023a.eb         | 2 ++
 .../q/QuantumESPRESSO/QuantumESPRESSO-7.2-intel-2022b.eb        | 2 ++
 .../q/QuantumESPRESSO/QuantumESPRESSO-7.3-foss-2023a.eb         | 2 ++
 .../q/QuantumESPRESSO/QuantumESPRESSO-7.3-intel-2023a.eb        | 2 ++
 35 files changed, 70 insertions(+)

diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.3.0-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.3.0-intel-2016.02-GCC-4.9.eb
index 35cd35ceaed..e456ec0bf5c 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.3.0-intel-2016.02-GCC-4.9.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.3.0-intel-2016.02-GCC-4.9.eb
@@ -1,3 +1,5 @@
+easyblock = "EB_QuantumESPRESSO_autotools"
+
 name = 'QuantumESPRESSO'
 version = '5.3.0'
 
diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0-foss-2016b-hybrid.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0-foss-2016b-hybrid.eb
index 2b285f6ff8b..b37dc5e6097 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0-foss-2016b-hybrid.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0-foss-2016b-hybrid.eb
@@ -1,3 +1,5 @@
+easyblock = "EB_QuantumESPRESSO_autotools"
+
 name = 'QuantumESPRESSO'
 version = '5.4.0'
 versionsuffix = '-hybrid'
diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0-intel-2016.02-GCC-4.9.eb
index 185719e2b8b..6890a8c39c4 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0-intel-2016.02-GCC-4.9.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0-intel-2016.02-GCC-4.9.eb
@@ -1,3 +1,5 @@
+easyblock = "EB_QuantumESPRESSO_autotools"
+
 name = 'QuantumESPRESSO'
 version = '5.4.0'
 
diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.0-intel-2016b.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.0-intel-2016b.eb
index 1e47f214d6a..b163c87b805 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.0-intel-2016b.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.0-intel-2016b.eb
@@ -1,3 +1,5 @@
+easyblock = "EB_QuantumESPRESSO_autotools"
+
 name = 'QuantumESPRESSO'
 version = '6.0'
 
diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.1-intel-2017a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.1-intel-2017a.eb
index 6eed0d5280f..4616a8ca038 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.1-intel-2017a.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.1-intel-2017a.eb
@@ -1,3 +1,5 @@
+easyblock = "EB_QuantumESPRESSO_autotools"
+
 name = 'QuantumESPRESSO'
 version = '6.1'
 
diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.2-intel-2017b.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.2-intel-2017b.eb
index be1a20b60bd..aa3688bff39 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.2-intel-2017b.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.2-intel-2017b.eb
@@ -1,3 +1,5 @@
+easyblock = "EB_QuantumESPRESSO_autotools"
+
 name = 'QuantumESPRESSO'
 version = '6.2'
 
diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.2.1-iomkl-2017b.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.2.1-iomkl-2017b.eb
index 2d5b3eb9707..b2ad6ab82e3 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.2.1-iomkl-2017b.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.2.1-iomkl-2017b.eb
@@ -1,3 +1,5 @@
+easyblock = "EB_QuantumESPRESSO_autotools"
+
 name = 'QuantumESPRESSO'
 version = '6.2.1'
 
diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.3-foss-2018b.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.3-foss-2018b.eb
index 2fa04e3d676..70449ce8a60 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.3-foss-2018b.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.3-foss-2018b.eb
@@ -1,3 +1,5 @@
+easyblock = "EB_QuantumESPRESSO_autotools"
+
 name = 'QuantumESPRESSO'
 version = '6.3'
 
diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.3-intel-2018b.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.3-intel-2018b.eb
index b9f585b351f..2a277c38bda 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.3-intel-2018b.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.3-intel-2018b.eb
@@ -1,3 +1,5 @@
+easyblock = "EB_QuantumESPRESSO_autotools"
+
 name = 'QuantumESPRESSO'
 version = '6.3'
 
diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.4.1-intel-2019a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.4.1-intel-2019a.eb
index 98ab9f1f280..f3927d3c15a 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.4.1-intel-2019a.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.4.1-intel-2019a.eb
@@ -1,3 +1,5 @@
+easyblock = "EB_QuantumESPRESSO_autotools"
+
 name = 'QuantumESPRESSO'
 version = '6.4.1'
 
diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.5-intel-2019a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.5-intel-2019a.eb
index 870805c92b5..a0adef65227 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.5-intel-2019a.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.5-intel-2019a.eb
@@ -1,3 +1,5 @@
+easyblock = "EB_QuantumESPRESSO_autotools"
+
 name = 'QuantumESPRESSO'
 version = '6.5'
 
diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.5-intel-2019b.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.5-intel-2019b.eb
index 195349a44c6..e99fad4bfe3 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.5-intel-2019b.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.5-intel-2019b.eb
@@ -1,3 +1,5 @@
+easyblock = "EB_QuantumESPRESSO_autotools"
+
 name = 'QuantumESPRESSO'
 version = '6.5'
 
diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.6-foss-2019b.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.6-foss-2019b.eb
index 55bef0c0fb3..07eef2aa5c7 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.6-foss-2019b.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.6-foss-2019b.eb
@@ -1,3 +1,5 @@
+easyblock = "EB_QuantumESPRESSO_autotools"
+
 name = 'QuantumESPRESSO'
 version = '6.6'
 
diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.6-foss-2020a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.6-foss-2020a.eb
index e28840d75ad..438b3e98374 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.6-foss-2020a.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.6-foss-2020a.eb
@@ -1,3 +1,5 @@
+easyblock = "EB_QuantumESPRESSO_autotools"
+
 name = 'QuantumESPRESSO'
 version = '6.6'
 
diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.6-foss-2020b.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.6-foss-2020b.eb
index 02147ccb84a..c954f1ce9a7 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.6-foss-2020b.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.6-foss-2020b.eb
@@ -1,3 +1,5 @@
+easyblock = "EB_QuantumESPRESSO_autotools"
+
 name = 'QuantumESPRESSO'
 version = '6.6'
 
diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.6-intel-2019b.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.6-intel-2019b.eb
index cd2e199f59d..2e6a5d86a52 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.6-intel-2019b.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.6-intel-2019b.eb
@@ -1,3 +1,5 @@
+easyblock = "EB_QuantumESPRESSO_autotools"
+
 name = 'QuantumESPRESSO'
 version = '6.6'
 
diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.6-intel-2020a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.6-intel-2020a.eb
index 9f590db57c1..068aa1ddfe6 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.6-intel-2020a.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.6-intel-2020a.eb
@@ -1,3 +1,5 @@
+easyblock = "EB_QuantumESPRESSO_autotools"
+
 name = 'QuantumESPRESSO'
 version = '6.6'
 
diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-foss-2019b.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-foss-2019b.eb
index 74d36c967cb..29c301d5dff 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-foss-2019b.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-foss-2019b.eb
@@ -1,3 +1,5 @@
+easyblock = "EB_QuantumESPRESSO_autotools"
+
 name = 'QuantumESPRESSO'
 version = '6.7'
 
diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-foss-2020b.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-foss-2020b.eb
index 43a880080ad..f34b824285f 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-foss-2020b.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-foss-2020b.eb
@@ -1,6 +1,8 @@
 ##
 # Author:    Robert Mijakovic <robert.mijakovic@lxp.lu>
 ##
+easyblock = "EB_QuantumESPRESSO_autotools"
+
 name = 'QuantumESPRESSO'
 version = '6.7'
 
diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-foss-2021a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-foss-2021a.eb
index bdff659a888..72f5a65efd3 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-foss-2021a.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-foss-2021a.eb
@@ -1,3 +1,5 @@
+easyblock = "EB_QuantumESPRESSO_autotools"
+
 name = 'QuantumESPRESSO'
 version = '6.7'
 
diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-intel-2019b.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-intel-2019b.eb
index d52fb661c17..d565ea1ea7c 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-intel-2019b.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-intel-2019b.eb
@@ -1,3 +1,5 @@
+easyblock = "EB_QuantumESPRESSO_autotools"
+
 name = 'QuantumESPRESSO'
 version = '6.7'
 
diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-intel-2021a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-intel-2021a.eb
index 99d05042d92..1a8428bec18 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-intel-2021a.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-intel-2021a.eb
@@ -1,3 +1,5 @@
+easyblock = "EB_QuantumESPRESSO_autotools"
+
 name = 'QuantumESPRESSO'
 version = '6.7'
 
diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-iomkl-2019b.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-iomkl-2019b.eb
index d35f44ab478..5ba6f0bcdb0 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-iomkl-2019b.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-iomkl-2019b.eb
@@ -1,3 +1,5 @@
+easyblock = "EB_QuantumESPRESSO_autotools"
+
 name = 'QuantumESPRESSO'
 version = '6.7'
 
diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.8-foss-2021a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.8-foss-2021a.eb
index 36c8fdf64b0..850af4acd68 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.8-foss-2021a.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.8-foss-2021a.eb
@@ -1,3 +1,5 @@
+easyblock = "EB_QuantumESPRESSO_autotools"
+
 name = 'QuantumESPRESSO'
 version = '6.8'
 
diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.8-foss-2021b.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.8-foss-2021b.eb
index fc8ad317547..a5df2d14198 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.8-foss-2021b.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.8-foss-2021b.eb
@@ -1,3 +1,5 @@
+easyblock = "EB_QuantumESPRESSO_autotools"
+
 name = 'QuantumESPRESSO'
 version = '6.8'
 
diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.8-intel-2021a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.8-intel-2021a.eb
index 5982b4efde6..2a06371e99c 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.8-intel-2021a.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.8-intel-2021a.eb
@@ -1,3 +1,5 @@
+easyblock = "EB_QuantumESPRESSO_autotools"
+
 name = 'QuantumESPRESSO'
 version = '6.8'
 
diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.0-foss-2021b.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.0-foss-2021b.eb
index 9f62ca5ad84..4399027df12 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.0-foss-2021b.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.0-foss-2021b.eb
@@ -1,3 +1,5 @@
+easyblock = "EB_QuantumESPRESSO_autotools"
+
 name = 'QuantumESPRESSO'
 version = '7.0'
 
diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.0-intel-2021b.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.0-intel-2021b.eb
index febc60c8c61..562b85e742f 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.0-intel-2021b.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.0-intel-2021b.eb
@@ -1,3 +1,5 @@
+easyblock = "EB_QuantumESPRESSO_autotools"
+
 name = 'QuantumESPRESSO'
 version = '7.0'
 
diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-foss-2022a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-foss-2022a.eb
index 87066c6ae6d..fe65f088760 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-foss-2022a.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-foss-2022a.eb
@@ -1,3 +1,5 @@
+easyblock = "EB_QuantumESPRESSO_autotools"
+
 name = 'QuantumESPRESSO'
 version = '7.1'
 
diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-intel-2022a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-intel-2022a.eb
index a7ed17a2f6b..8de5eeefdb0 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-intel-2022a.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-intel-2022a.eb
@@ -1,3 +1,5 @@
+easyblock = "EB_QuantumESPRESSO_autotools"
+
 name = 'QuantumESPRESSO'
 version = '7.1'
 
diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-foss-2022b.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-foss-2022b.eb
index 9362d5a9fb8..d165c425a69 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-foss-2022b.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-foss-2022b.eb
@@ -1,3 +1,5 @@
+easyblock = "EB_QuantumESPRESSO_autotools"
+
 name = 'QuantumESPRESSO'
 version = '7.2'
 
diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-foss-2023a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-foss-2023a.eb
index 8369f3fb31a..0e6d9fd967c 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-foss-2023a.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-foss-2023a.eb
@@ -1,3 +1,5 @@
+easyblock = "EB_QuantumESPRESSO_autotools"
+
 name = 'QuantumESPRESSO'
 version = '7.2'
 
diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-intel-2022b.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-intel-2022b.eb
index 53852bd770b..797592734a7 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-intel-2022b.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-intel-2022b.eb
@@ -1,3 +1,5 @@
+easyblock = "EB_QuantumESPRESSO_autotools"
+
 name = 'QuantumESPRESSO'
 version = '7.2'
 
diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3-foss-2023a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3-foss-2023a.eb
index d0089ef7bc7..2ea617dcbb9 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3-foss-2023a.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3-foss-2023a.eb
@@ -1,3 +1,5 @@
+easyblock = "EB_QuantumESPRESSO_autotools"
+
 name = 'QuantumESPRESSO'
 version = '7.3'
 
diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3-intel-2023a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3-intel-2023a.eb
index 2f3ccd6da68..4a3e56e47b9 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3-intel-2023a.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3-intel-2023a.eb
@@ -1,3 +1,5 @@
+easyblock = "EB_QuantumESPRESSO_autotools"
+
 name = 'QuantumESPRESSO'
 version = '7.3'
 

From 7576c039389ffb7fcc18784eda4a294cc93e0606 Mon Sep 17 00:00:00 2001
From: jfgrimm <jasper.grimm@york.ac.uk>
Date: Mon, 15 Apr 2024 12:35:09 +0100
Subject: [PATCH 055/835] adding easyconfigs:
 OpenMM-8.0.0-foss-2023a-CUDA-12.1.1.eb

---
 .../OpenMM-8.0.0-foss-2023a-CUDA-12.1.1.eb    | 70 +++++++++++++++++++
 1 file changed, 70 insertions(+)
 create mode 100644 easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2023a-CUDA-12.1.1.eb

diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2023a-CUDA-12.1.1.eb
new file mode 100644
index 00000000000..8cf271071e7
--- /dev/null
+++ b/easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2023a-CUDA-12.1.1.eb
@@ -0,0 +1,70 @@
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+# Author: Pablo Escobar Lopez
+# sciCORE - University of Basel
+# SIB Swiss Institute of Bioinformatics
+# Update to 7.5.1
+# J. Sassmannshausen / GSTT
+
+easyblock = 'CMakeMake'
+
+name = 'OpenMM'
+version = '8.0.0'
+versionsuffix = '-CUDA-%(cudaver)s'
+
+homepage = 'https://openmm.org'
+description = "OpenMM is a toolkit for molecular simulation."
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+toolchainopts = {'opt': True}
+
+source_urls = ['https://github.com/openmm/openmm/archive/']
+sources = ['%(version)s.tar.gz']
+patches = ['OpenMM-8.0.0_add_no_tree_vectorize.patch']
+checksums = [
+    'dc63d7b47c8bb7b169c409cfd63d909ed0ce1ae114d37c627bf7a4231acf488e',  # 8.0.0.tar.gz
+    '4bacf45443a2472e59798743f27d07481e065d784cbbea7be22aa6427af0d2bd',  # OpenMM-8.0.0_add_no_tree_vectorize.patch
+]
+
+builddependencies = [
+    ('CMake', '3.26.3'),
+    ('Doxygen', '1.9.7'),
+]
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('SWIG', '4.1.1'),
+    ('CUDA', '12.1.1', '', SYSTEM),
+]
+
+# Set the OPENMM_CUDA_COMPILER variable to make sure that all tests use the right nvcc,
+# Otherwise they will use the wrong path: `/usr/local/cuda/bin/nvcc`
+pretestopts = ' export OPENMM_CUDA_COMPILER=${EBROOTCUDA}/bin/nvcc && '
+pretestopts += " CTEST_OUTPUT_ON_FAILURE=1"
+# Skip CudaCompiler test as it doesn't work when the OPENMM_CUDA_COMPILER variable is set
+local_ignore_pattern = "(Integrator)|(Thermostat)|(Barostat)|(Rpmd)|(Amoeba)|(CudaCompiler)"
+runtest = """test -e ARGS="-E \'%s\'" """ % local_ignore_pattern
+
+preinstallopts = ' export OPENMM_INCLUDE_PATH=%(installdir)s/include && '
+preinstallopts += ' export OPENMM_LIB_PATH=%(installdir)s/lib && '
+
+# required to install the python API
+installopts = ' && cd python && python setup.py build && python setup.py install --prefix=%(installdir)s'
+
+sanity_check_paths = {
+    'files': ['lib/libOpenMM.%s' % SHLIB_EXT],
+    'dirs': ['lib/python%(pyshortver)s/site-packages']
+}
+
+sanity_check_commands = [
+    "python -c 'import simtk.openmm'",
+    "python -m openmm.testInstallation",
+]
+
+modextrapaths = {
+    'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages/OpenMM-%(version)s-py%(pyshortver)s-linux-%(arch)s.egg',
+    'OPENMM_INCLUDE_PATH': 'include',
+    'OPENMM_LIB_PATH': 'lib',
+}
+
+moduleclass = 'bio'

From a979c150597e208f458389ddf8a1a362300d22a1 Mon Sep 17 00:00:00 2001
From: Alexander Grund <alexander.grund@tu-dresden.de>
Date: Thu, 25 Jan 2024 13:22:17 +0100
Subject: [PATCH 056/835] adding easyconfigs: molmod-1.4.8-foss-2022a.eb,
 molmod-1.4.8-gfbf-2022b.eb, TAMkin-1.2.6-foss-2022a.eb,
 TAMkin-1.2.6-foss-2022b.eb

---
 .../m/molmod/molmod-1.4.8-foss-2022a.eb       | 37 +++++++++++++++
 .../m/molmod/molmod-1.4.8-gfbf-2022b.eb       | 42 +++++++++++++++++
 .../n/nose3/nose3-1.3.8-GCCcore-12.2.0.eb     | 34 ++++++++++++++
 .../t/TAMkin/TAMkin-1.2.6-foss-2022a.eb       | 46 +++++++++++++++++++
 .../t/TAMkin/TAMkin-1.2.6-foss-2022b.eb       | 46 +++++++++++++++++++
 5 files changed, 205 insertions(+)
 create mode 100644 easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2022a.eb
 create mode 100644 easybuild/easyconfigs/m/molmod/molmod-1.4.8-gfbf-2022b.eb
 create mode 100644 easybuild/easyconfigs/n/nose3/nose3-1.3.8-GCCcore-12.2.0.eb
 create mode 100644 easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6-foss-2022a.eb
 create mode 100644 easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6-foss-2022b.eb

diff --git a/easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2022a.eb b/easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2022a.eb
new file mode 100644
index 00000000000..e2e6b2f69cd
--- /dev/null
+++ b/easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2022a.eb
@@ -0,0 +1,37 @@
+easyblock = 'PythonPackage'
+
+name = 'molmod'
+version = '1.4.8'
+
+homepage = 'https://molmod.github.io/molmod/'
+description = "MolMod is a Python library with many compoments that are useful to write molecular modeling programs."
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+source_urls = ['https://github.com/molmod/molmod/releases/download/%(version)s']
+sources = [SOURCE_TAR_GZ]
+patches = ['molmod-1.4.8_fix-git-version-check.patch']
+checksums = [
+    {'molmod-1.4.8.tar.gz': '759f8894f8a206e8d83f3f88882f29fcf73a7f9be375026e03c58e19496f42e8'},
+    {'molmod-1.4.8_fix-git-version-check.patch': '6d1455f9dc3af07b723b05d144f6d8c3c0e5184e094eced1a6f59822f97dcf47'},
+]
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('matplotlib', '3.5.2'),
+]
+
+use_pip = True
+download_dep_fail = True
+sanity_pip_check = True
+
+# disable tests that require X11 by specifying "backend: agg" in matplotlibrc
+runtest = "export MATPLOTLIBRC=$PWD; echo 'backend: agg' > $MATPLOTLIBRC/matplotlibrc;"
+runtest += "python setup.py build_ext -i && pytest -ra"
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+moduleclass = 'math'
diff --git a/easybuild/easyconfigs/m/molmod/molmod-1.4.8-gfbf-2022b.eb b/easybuild/easyconfigs/m/molmod/molmod-1.4.8-gfbf-2022b.eb
new file mode 100644
index 00000000000..3f20a89299f
--- /dev/null
+++ b/easybuild/easyconfigs/m/molmod/molmod-1.4.8-gfbf-2022b.eb
@@ -0,0 +1,42 @@
+easyblock = 'PythonPackage'
+
+name = 'molmod'
+version = '1.4.8'
+
+homepage = 'https://molmod.github.io/molmod/'
+description = "MolMod is a Python library with many compoments that are useful to write molecular modeling programs."
+
+toolchain = {'name': 'gfbf', 'version': '2022b'}
+
+source_urls = ['https://github.com/molmod/molmod/releases/download/%(version)s']
+sources = [SOURCE_TAR_GZ]
+patches = [
+    'molmod-1.4.8_fix-git-version-check.patch',
+    'molmod-1.4.8_fix-np-unicode.patch',
+]
+checksums = [
+    {'molmod-1.4.8.tar.gz': '759f8894f8a206e8d83f3f88882f29fcf73a7f9be375026e03c58e19496f42e8'},
+    {'molmod-1.4.8_fix-git-version-check.patch': '6d1455f9dc3af07b723b05d144f6d8c3c0e5184e094eced1a6f59822f97dcf47'},
+    {'molmod-1.4.8_fix-np-unicode.patch':
+     '85bd2e2981d2cdd8cfab5d1c2cf37432e2967ff82de603700383d7c31530327c'},
+]
+
+dependencies = [
+    ('Python', '3.10.8'),
+    ('matplotlib', '3.7.0'),
+]
+
+use_pip = True
+download_dep_fail = True
+sanity_pip_check = True
+
+# disable tests that require X11 by specifying "backend: agg" in matplotlibrc
+runtest = "export MATPLOTLIBRC=$PWD; echo 'backend: agg' > $MATPLOTLIBRC/matplotlibrc;"
+runtest += "python setup.py build_ext -i && pytest -ra"
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+moduleclass = 'math'
diff --git a/easybuild/easyconfigs/n/nose3/nose3-1.3.8-GCCcore-12.2.0.eb b/easybuild/easyconfigs/n/nose3/nose3-1.3.8-GCCcore-12.2.0.eb
new file mode 100644
index 00000000000..3fb61c98db7
--- /dev/null
+++ b/easybuild/easyconfigs/n/nose3/nose3-1.3.8-GCCcore-12.2.0.eb
@@ -0,0 +1,34 @@
+easyblock = 'PythonPackage'
+
+name = 'nose3'
+version = '1.3.8'
+
+homepage = 'https://nose.readthedocs.io/'
+description = """Nose extends unittest to make testing easier."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+
+sources = [SOURCE_TAR_GZ]
+checksums = ['762aae22cadb898b00b9d4f4bbb9f8e87f8e0dde6c49a88cd0c554f4e5925b76']
+
+builddependencies = [('binutils', '2.39')]
+
+dependencies = [
+    ('Python', '3.10.8'),
+    ('coverage', '7.2.3'),
+]
+
+use_pip = True
+sanity_pip_check = True
+download_dep_fail = True
+
+sanity_check_paths = {
+    'files': ['bin/nosetests'],
+    'dirs': [],
+}
+
+options = {'modulename': 'nose'}
+
+sanity_check_commands = ["nosetests --help"]
+
+moduleclass = 'devel'
diff --git a/easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6-foss-2022a.eb b/easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6-foss-2022a.eb
new file mode 100644
index 00000000000..c672ef52e80
--- /dev/null
+++ b/easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6-foss-2022a.eb
@@ -0,0 +1,46 @@
+easyblock = 'PythonPackage'
+
+name = 'TAMkin'
+version = '1.2.6'
+
+homepage = 'https://molmod.github.io/tamkin/'
+description = """TAMkin is a post-processing toolkit for normal mode analysis,
+ thermochemistry and reaction kinetics. It uses a Hessian computation from a
+ standard computational chemistry program as its input."""
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+source_urls = ['https://github.com/molmod/tamkin/releases/download/%(version)s']
+sources = [SOURCE_TAR_GZ]
+patches = [
+    'TAMkin-1.2.6_fix-python38.patch',
+    'TAMkin-1.2.6_fix-test_vsa_no_mass.patch',
+]
+checksums = [
+    {'TAMkin-1.2.6.tar.gz': '1bde275a09be91e5241616aaa9fedc60cb359a263f5c5909bb14431c3a4ed5fd'},
+    {'TAMkin-1.2.6_fix-python38.patch': '1633d5b24b012f8c4b6731491e4072c819ebbba65574966b7185ecca52eeac9b'},
+    {'TAMkin-1.2.6_fix-test_vsa_no_mass.patch': '67d8b8671d7c71123e8ee9a7b9ebea6562e9711edb41555d1926b1b51d549066'},
+]
+
+builddependencies = [('nose3', '1.3.8')]
+dependencies = [
+    ('Python', '3.10.4'),
+    ('matplotlib', '3.5.2'),
+    ('molmod', '1.4.8'),
+]
+
+download_dep_fail = True
+use_pip = True
+
+# disable tests that require X11 by specifying "backend: agg" in matplotlibrc
+runtest = 'export MATPLOTLIBRC=$PWD; echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc; '
+runtest += 'export OMP_NUM_THREADS=1; nosetests -v tamkin'
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_pip_check = True
+
+moduleclass = 'chem'
diff --git a/easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6-foss-2022b.eb b/easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6-foss-2022b.eb
new file mode 100644
index 00000000000..f0ac1c8820c
--- /dev/null
+++ b/easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6-foss-2022b.eb
@@ -0,0 +1,46 @@
+easyblock = 'PythonPackage'
+
+name = 'TAMkin'
+version = '1.2.6'
+
+homepage = 'https://molmod.github.io/tamkin/'
+description = """TAMkin is a post-processing toolkit for normal mode analysis,
+ thermochemistry and reaction kinetics. It uses a Hessian computation from a
+ standard computational chemistry program as its input."""
+
+toolchain = {'name': 'foss', 'version': '2022b'}
+
+source_urls = ['https://github.com/molmod/tamkin/releases/download/%(version)s']
+sources = [SOURCE_TAR_GZ]
+patches = [
+    'TAMkin-1.2.6_fix-python38.patch',
+    'TAMkin-1.2.6_fix-test_vsa_no_mass.patch',
+]
+checksums = [
+    {'TAMkin-1.2.6.tar.gz': '1bde275a09be91e5241616aaa9fedc60cb359a263f5c5909bb14431c3a4ed5fd'},
+    {'TAMkin-1.2.6_fix-python38.patch': '1633d5b24b012f8c4b6731491e4072c819ebbba65574966b7185ecca52eeac9b'},
+    {'TAMkin-1.2.6_fix-test_vsa_no_mass.patch': '67d8b8671d7c71123e8ee9a7b9ebea6562e9711edb41555d1926b1b51d549066'},
+]
+
+builddependencies = [('nose3', '1.3.8')]
+dependencies = [
+    ('Python', '3.10.8'),
+    ('matplotlib', '3.7.0'),
+    ('molmod', '1.4.8'),
+]
+
+download_dep_fail = True
+use_pip = True
+
+# disable tests that require X11 by specifying "backend: agg" in matplotlibrc
+runtest = 'export MATPLOTLIBRC=$PWD; echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc; '
+runtest += 'export OMP_NUM_THREADS=1; nosetests -v tamkin'
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_pip_check = True
+
+moduleclass = 'chem'

From 07812133646be2c42d59d8f7b045258cd4a1e11e Mon Sep 17 00:00:00 2001
From: crivella <davide.grassano@epfl.ch>
Date: Tue, 16 Apr 2024 15:38:05 +0200
Subject: [PATCH 057/835] Fix for checksums

---
 .../QuantumESPRESSO-7.3.1-foss-2023a.eb       | 27 ++++++++++---------
 .../QuantumESPRESSO-7.3.1-intel-2023a.eb      | 27 ++++++++++---------
 2 files changed, 30 insertions(+), 24 deletions(-)

diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-foss-2023a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-foss-2023a.eb
index 95de4bc7834..58193947e6c 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-foss-2023a.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-foss-2023a.eb
@@ -100,19 +100,22 @@ sources = [
         },
     },
 ]
+# Holding off checksum checks untill 5.0.x
+# https://github.com/easybuilders/easybuild-framework/pull/4248
+# checksums = [
+#     {'q-e-qe-7.3.1.tar.gz': '2c58b8fadfe4177de5a8b69eba447db5e623420b070dea6fd26c1533b081d844'},
+#     {'lapack-%s.tar.gz' % local_lapack_hash: 'c05532ae0e5fe35f473206dda12970da5f2e2214620487d71837ddcf0ea6b21d'},
+#     {'mbd-%s.tar.gz' % local_mbd_hash: 'a180682c00bb890c9b1e26a98addbd68e32f970c06439acf7582415f4c589800'},
+#     {'devxlib-%s.tar.gz' % local_devxlib_hash: '76da8fe5a2050f58efdc92fa8831efec25c19190df7f4e5e39c173a5fbae83b4'},
+#     {'d3q-%s.tar.gz' % local_d3q_hash: '43e50753a56af05d181b859d3e29d842fb3fc4352f00cb7fe229a435a1f20c31'},
+#     {'fox-%s.tar.gz' % local_fox_hash: '99b6a899a3f947d7763aa318e86f9f08db684568bfdcd293f3318bee9d7f1948'},
+#     {'qe-gipaw-%s.tar.gz' % local_qe_gipaw_hash: '9ac8314363d29cc2f1ce85abd8f26c1a3ae311d54f6e6034d656442dd101c928'},
+#     {'pw2qmcpack-%s.tar.gz' % local_qmcpack_hash: 'a8136da8429fc49ab560ef7356cd6f0a2714dfbb137baff7961f46dfe32061eb'},
+#     {'wannier90-%s.tar.gz' % local_w90_hash: 'f989497790ec9777bdc159945bbf42156edb7268011f972874dec67dd4f58658'},
+# ]
 checksums = [
-    {'q-e-qe-7.3.1.tar.gz': '2c58b8fadfe4177de5a8b69eba447db5e623420b070dea6fd26c1533b081d844'},
-    # Holding off checksum checks untill 5.0.x
-    # https://github.com/easybuilders/easybuild-framework/pull/4248
-
-    # {'lapack-%s.tar.gz' % local_lapack_hash: 'c05532ae0e5fe35f473206dda12970da5f2e2214620487d71837ddcf0ea6b21d'},
-    # {'mbd-%s.tar.gz' % local_mbd_hash: 'a180682c00bb890c9b1e26a98addbd68e32f970c06439acf7582415f4c589800'},
-    # {'devxlib-%s.tar.gz' % local_devxlib_hash: '76da8fe5a2050f58efdc92fa8831efec25c19190df7f4e5e39c173a5fbae83b4'},
-    # {'d3q-%s.tar.gz' % local_d3q_hash: '43e50753a56af05d181b859d3e29d842fb3fc4352f00cb7fe229a435a1f20c31'},
-    # {'fox-%s.tar.gz' % local_fox_hash: '99b6a899a3f947d7763aa318e86f9f08db684568bfdcd293f3318bee9d7f1948'},
-    # {'qe-gipaw-%s.tar.gz' % local_qe_gipaw_hash: '9ac8314363d29cc2f1ce85abd8f26c1a3ae311d54f6e6034d656442dd101c928'},
-    # {'pw2qmcpack-%s.tar.gz' % local_qmcpack_hash: 'a8136da8429fc49ab560ef7356cd6f0a2714dfbb137baff7961f46dfe32061eb'},
-    # {'wannier90-%s.tar.gz' % local_w90_hash: 'f989497790ec9777bdc159945bbf42156edb7268011f972874dec67dd4f58658'},
+    '2c58b8fadfe4177de5a8b69eba447db5e623420b070dea6fd26c1533b081d844',
+    None, None, None, None, None, None, None, None
 ]
 
 builddependencies = [
diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-intel-2023a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-intel-2023a.eb
index b9d0f3ab624..d6ffe3c80c1 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-intel-2023a.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-intel-2023a.eb
@@ -99,19 +99,22 @@ sources = [
         },
     },
 ]
+# Holding off checksum checks untill 5.0.x
+# https://github.com/easybuilders/easybuild-framework/pull/4248
+# checksums = [
+#     {'q-e-qe-7.3.1.tar.gz': '2c58b8fadfe4177de5a8b69eba447db5e623420b070dea6fd26c1533b081d844'},
+#     {'lapack-%s.tar.gz' % local_lapack_hash: 'c05532ae0e5fe35f473206dda12970da5f2e2214620487d71837ddcf0ea6b21d'},
+#     {'mbd-%s.tar.gz' % local_mbd_hash: 'a180682c00bb890c9b1e26a98addbd68e32f970c06439acf7582415f4c589800'},
+#     {'devxlib-%s.tar.gz' % local_devxlib_hash: '76da8fe5a2050f58efdc92fa8831efec25c19190df7f4e5e39c173a5fbae83b4'},
+#     {'d3q-%s.tar.gz' % local_d3q_hash: '43e50753a56af05d181b859d3e29d842fb3fc4352f00cb7fe229a435a1f20c31'},
+#     {'fox-%s.tar.gz' % local_fox_hash: '99b6a899a3f947d7763aa318e86f9f08db684568bfdcd293f3318bee9d7f1948'},
+#     {'qe-gipaw-%s.tar.gz' % local_qe_gipaw_hash: '9ac8314363d29cc2f1ce85abd8f26c1a3ae311d54f6e6034d656442dd101c928'},
+#     {'pw2qmcpack-%s.tar.gz' % local_qmcpack_hash: 'a8136da8429fc49ab560ef7356cd6f0a2714dfbb137baff7961f46dfe32061eb'},
+#     {'wannier90-%s.tar.gz' % local_w90_hash: 'f989497790ec9777bdc159945bbf42156edb7268011f972874dec67dd4f58658'},
+# ]
 checksums = [
-    {'q-e-qe-7.3.1.tar.gz': '2c58b8fadfe4177de5a8b69eba447db5e623420b070dea6fd26c1533b081d844'},
-    # Holding off checksum checks untill 5.0.x
-    # https://github.com/easybuilders/easybuild-framework/pull/4248
-
-    # {'lapack-%s.tar.gz' % local_lapack_hash: 'c05532ae0e5fe35f473206dda12970da5f2e2214620487d71837ddcf0ea6b21d'},
-    # {'mbd-%s.tar.gz' % local_mbd_hash: 'a180682c00bb890c9b1e26a98addbd68e32f970c06439acf7582415f4c589800'},
-    # {'devxlib-%s.tar.gz' % local_devxlib_hash: '76da8fe5a2050f58efdc92fa8831efec25c19190df7f4e5e39c173a5fbae83b4'},
-    # {'d3q-%s.tar.gz' % local_d3q_hash: '43e50753a56af05d181b859d3e29d842fb3fc4352f00cb7fe229a435a1f20c31'},
-    # {'fox-%s.tar.gz' % local_fox_hash: '99b6a899a3f947d7763aa318e86f9f08db684568bfdcd293f3318bee9d7f1948'},
-    # {'qe-gipaw-%s.tar.gz' % local_qe_gipaw_hash: '9ac8314363d29cc2f1ce85abd8f26c1a3ae311d54f6e6034d656442dd101c928'},
-    # {'pw2qmcpack-%s.tar.gz' % local_qmcpack_hash: 'a8136da8429fc49ab560ef7356cd6f0a2714dfbb137baff7961f46dfe32061eb'},
-    # {'wannier90-%s.tar.gz' % local_w90_hash: 'f989497790ec9777bdc159945bbf42156edb7268011f972874dec67dd4f58658'},
+    '2c58b8fadfe4177de5a8b69eba447db5e623420b070dea6fd26c1533b081d844',
+    None, None, None, None, None, None, None, None
 ]
 
 builddependencies = [

From 9be216723e30155da1be2080663ae86e7b0c3d11 Mon Sep 17 00:00:00 2001
From: WilleBell <cintiawillemyns@gmail.com>
Date: Tue, 16 Apr 2024 16:28:08 +0200
Subject: [PATCH 058/835] adding easyconfigs: Ray-project-2.9.1-foss-2023a.eb

---
 .../Ray-project-2.9.1-foss-2023a.eb           | 58 +++++++++++++++++++
 1 file changed, 58 insertions(+)
 create mode 100644 easybuild/easyconfigs/r/Ray-project/Ray-project-2.9.1-foss-2023a.eb

diff --git a/easybuild/easyconfigs/r/Ray-project/Ray-project-2.9.1-foss-2023a.eb b/easybuild/easyconfigs/r/Ray-project/Ray-project-2.9.1-foss-2023a.eb
new file mode 100644
index 00000000000..c0e9bc15437
--- /dev/null
+++ b/easybuild/easyconfigs/r/Ray-project/Ray-project-2.9.1-foss-2023a.eb
@@ -0,0 +1,58 @@
+# Author: Pavel Grochal (INUITS)
+# License: GPLv2
+
+easyblock = 'PythonBundle'
+
+name = 'Ray-project'
+version = '2.9.1'
+
+homepage = "https://docs.ray.io/en/latest/"
+description = "Ray is a fast and simple framework for building and running distributed applications."
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+toolchainopts = {'usempi': True}
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('protobuf-python', '4.24.0'),
+    ('PyYAML', '6.0'),
+    ('redis-py', '5.0.1'),
+    ('hatchling', '1.18.0'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('grpcio', '1.62.1', {
+        'modulename': 'grpc',
+        'preinstallopts': "export GRPC_PYTHON_BUILD_EXT_COMPILER_JOBS=%(parallel)s && ",
+        'checksums': ['6c455e008fa86d9e9a9d85bb76da4277c0d7d9668a3bfa70dbe86e9f3c759947'],
+    }),
+    ('aiosignal', '1.3.1', {
+        'checksums': ['54cd96e15e1649b75d6c87526a6ff0b6c1b0dd3459f43d9ca11d48c339b68cfc'],
+    }),
+    ('expandvars', '0.12.0', {
+        'checksums': ['7d1adfa55728cf4b5d812ece3d087703faea953e0c0a1a78415de9df5024d844'],
+    }),
+    ('frozenlist', '1.4.1', {
+        'checksums': ['c037a86e8513059a2613aaba4d817bb90b9d9b6b69aace3ce9c877e8c8ed402b'],
+    }),
+    ('Ray', version, {
+        'source_tmpl': '%(namelower)s-%(version)s-cp311-cp311-manylinux2014_x86_64.whl',
+        'checksums': ['fabc520990c1b98dde592813d62737e5e817460e0ac359f32ba029ace292cbe2'],
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['bin/ray'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = [
+    'ray --help'
+]
+
+sanity_pip_check = True
+
+moduleclass = 'tools'

From 9eb89b6f7f56f0032f4dcc44ec000cfb113f123a Mon Sep 17 00:00:00 2001
From: ocaisa <alan.ocais@cecam.org>
Date: Wed, 17 Apr 2024 12:09:32 +0200
Subject: [PATCH 059/835] Update QuantumESPRESSO-7.0-intel-2021b.eb

---
 .../q/QuantumESPRESSO/QuantumESPRESSO-7.0-intel-2021b.eb      | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.0-intel-2021b.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.0-intel-2021b.eb
index 562b85e742f..64d469187e0 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.0-intel-2021b.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.0-intel-2021b.eb
@@ -11,7 +11,9 @@ It is based on density-functional theory, plane waves, and pseudopotentials
 """
 
 toolchain = {'name': 'intel', 'version': '2021b'}
-toolchainopts = {'usempi': True, 'openmp': True}
+# OpenMP is not working with Intel ifort/ifx compilers (Fortran) starting from version 2021.2.0 
+# toolchainopts = {'usempi': True, 'openmp': True}
+toolchainopts = {'usempi': True}
 
 source_urls = [
     'https://github.com/QEF/q-e/releases/download/qe-%(version)s/',

From 752ee2d7f5f53070592e897879d4aaa5ca470ce0 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Wed, 17 Apr 2024 16:20:25 +0000
Subject: [PATCH 060/835] adding easyconfigs:
 mm-common-1.0.6-GCCcore-11.3.0.eb, mm-common-1.0.6-GCCcore-12.2.0.eb,
 mm-common-1.0.6-GCCcore-12.3.0.eb, mm-common-1.0.6-GCCcore-13.2.0.eb,
 libsigc++-3.6.0-GCCcore-11.3.0.eb, libsigc++-3.6.0-GCCcore-12.2.0.eb,
 libsigc++-3.6.0-GCCcore-12.3.0.eb, libsigc++-3.6.0-GCCcore-13.2.0.eb,
 GLibmm-2.72.1-GCCcore-11.3.0.eb, GLibmm-2.75.0-GCCcore-12.2.0.eb,
 GLibmm-2.77.0-GCCcore-12.3.0.eb, GLibmm-2.78.1-GCCcore-13.2.0.eb

---
 .../g/GLibmm/GLibmm-2.72.1-GCCcore-11.3.0.eb  | 34 +++++++++++++++++++
 .../g/GLibmm/GLibmm-2.75.0-GCCcore-12.2.0.eb  | 34 +++++++++++++++++++
 .../g/GLibmm/GLibmm-2.77.0-GCCcore-12.3.0.eb  | 34 +++++++++++++++++++
 .../g/GLibmm/GLibmm-2.78.1-GCCcore-13.2.0.eb  | 34 +++++++++++++++++++
 .../libsigc++-3.6.0-GCCcore-11.3.0.eb         | 34 +++++++++++++++++++
 .../libsigc++-3.6.0-GCCcore-12.2.0.eb         | 34 +++++++++++++++++++
 .../libsigc++-3.6.0-GCCcore-12.3.0.eb         | 34 +++++++++++++++++++
 .../libsigc++-3.6.0-GCCcore-13.2.0.eb         | 34 +++++++++++++++++++
 .../mm-common-1.0.6-GCCcore-11.3.0.eb         | 33 ++++++++++++++++++
 .../mm-common-1.0.6-GCCcore-12.2.0.eb         | 33 ++++++++++++++++++
 .../mm-common-1.0.6-GCCcore-12.3.0.eb         | 33 ++++++++++++++++++
 .../mm-common-1.0.6-GCCcore-13.2.0.eb         | 33 ++++++++++++++++++
 12 files changed, 404 insertions(+)
 create mode 100644 easybuild/easyconfigs/g/GLibmm/GLibmm-2.72.1-GCCcore-11.3.0.eb
 create mode 100644 easybuild/easyconfigs/g/GLibmm/GLibmm-2.75.0-GCCcore-12.2.0.eb
 create mode 100644 easybuild/easyconfigs/g/GLibmm/GLibmm-2.77.0-GCCcore-12.3.0.eb
 create mode 100644 easybuild/easyconfigs/g/GLibmm/GLibmm-2.78.1-GCCcore-13.2.0.eb
 create mode 100644 easybuild/easyconfigs/l/libsigc++/libsigc++-3.6.0-GCCcore-11.3.0.eb
 create mode 100644 easybuild/easyconfigs/l/libsigc++/libsigc++-3.6.0-GCCcore-12.2.0.eb
 create mode 100644 easybuild/easyconfigs/l/libsigc++/libsigc++-3.6.0-GCCcore-12.3.0.eb
 create mode 100644 easybuild/easyconfigs/l/libsigc++/libsigc++-3.6.0-GCCcore-13.2.0.eb
 create mode 100644 easybuild/easyconfigs/m/mm-common/mm-common-1.0.6-GCCcore-11.3.0.eb
 create mode 100644 easybuild/easyconfigs/m/mm-common/mm-common-1.0.6-GCCcore-12.2.0.eb
 create mode 100644 easybuild/easyconfigs/m/mm-common/mm-common-1.0.6-GCCcore-12.3.0.eb
 create mode 100644 easybuild/easyconfigs/m/mm-common/mm-common-1.0.6-GCCcore-13.2.0.eb

diff --git a/easybuild/easyconfigs/g/GLibmm/GLibmm-2.72.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/GLibmm/GLibmm-2.72.1-GCCcore-11.3.0.eb
new file mode 100644
index 00000000000..75a9c993725
--- /dev/null
+++ b/easybuild/easyconfigs/g/GLibmm/GLibmm-2.72.1-GCCcore-11.3.0.eb
@@ -0,0 +1,34 @@
+easyblock = 'MesonNinja'
+
+name = 'GLibmm'
+version = '2.72.1'
+
+homepage = 'https://www.gtk.org/'
+description = """C++ bindings for Glib"""
+
+toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://ftp.gnome.org/pub/gnome/sources/glibmm/%(version_major_minor)s/']
+sources = ['%(namelower)s-%(version)s.tar.xz']
+checksums = ['2a7649a28ab5dc53ac4dabb76c9f61599fbc628923ab6a7dd74bf675d9155cd8']
+
+builddependencies = [
+    ('binutils', '2.38'),
+    ('pkgconf', '1.8.0'),
+    ('Meson', '0.62.1'),
+    ('Ninja', '1.10.2'),
+]
+
+dependencies = [
+    ('GLib', '2.72.1'),
+    ('libsigc++', '3.6.0'),
+]
+
+sanity_check_paths = {
+    'files': ['lib/libglibmm-2.68.%s' % SHLIB_EXT, 'lib/libgiomm-2.68.%s' % SHLIB_EXT,
+              'include/glibmm-2.68/glibmm.h', 'include/giomm-2.68/giomm.h'],
+    'dirs': ['lib/pkgconfig'],
+}
+
+moduleclass = 'vis'
diff --git a/easybuild/easyconfigs/g/GLibmm/GLibmm-2.75.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/GLibmm/GLibmm-2.75.0-GCCcore-12.2.0.eb
new file mode 100644
index 00000000000..ba2c86f4057
--- /dev/null
+++ b/easybuild/easyconfigs/g/GLibmm/GLibmm-2.75.0-GCCcore-12.2.0.eb
@@ -0,0 +1,34 @@
+easyblock = 'MesonNinja'
+
+name = 'GLibmm'
+version = '2.75.0'
+
+homepage = 'https://www.gtk.org/'
+description = """C++ bindings for Glib"""
+
+toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://ftp.gnome.org/pub/gnome/sources/glibmm/%(version_major_minor)s/']
+sources = ['%(namelower)s-%(version)s.tar.xz']
+checksums = ['60bb12e66488aa8ce41f0eb2f3612f89f5ddc887e3e4d45498524bf60b266b3d']
+
+builddependencies = [
+    ('binutils', '2.39'),
+    ('pkgconf', '1.9.3'),
+    ('Meson', '0.64.0'),
+    ('Ninja', '1.11.1'),
+]
+
+dependencies = [
+    ('GLib', '2.75.0'),
+    ('libsigc++', '3.6.0'),
+]
+
+sanity_check_paths = {
+    'files': ['lib/libglibmm-2.68.%s' % SHLIB_EXT, 'lib/libgiomm-2.68.%s' % SHLIB_EXT,
+              'include/glibmm-2.68/glibmm.h', 'include/giomm-2.68/giomm.h'],
+    'dirs': ['lib/pkgconfig'],
+}
+
+moduleclass = 'vis'
diff --git a/easybuild/easyconfigs/g/GLibmm/GLibmm-2.77.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/GLibmm/GLibmm-2.77.0-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..768bdcbb2ed
--- /dev/null
+++ b/easybuild/easyconfigs/g/GLibmm/GLibmm-2.77.0-GCCcore-12.3.0.eb
@@ -0,0 +1,34 @@
+easyblock = 'MesonNinja'
+
+name = 'GLibmm'
+version = '2.77.0'
+
+homepage = 'https://www.gtk.org/'
+description = """C++ bindings for Glib"""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://ftp.gnome.org/pub/gnome/sources/glibmm/%(version_major_minor)s/']
+sources = ['%(namelower)s-%(version)s.tar.xz']
+checksums = ['7cb34684e7ac6dfbf83492a52dff3f919e2fff63eb7810613bf71eb272d5450e']
+
+builddependencies = [
+    ('binutils', '2.40'),
+    ('pkgconf', '1.9.5'),
+    ('Meson', '1.1.1'),
+    ('Ninja', '1.11.1'),
+]
+
+dependencies = [
+    ('GLib', '2.77.1'),
+    ('libsigc++', '3.6.0'),
+]
+
+sanity_check_paths = {
+    'files': ['lib/libglibmm-2.68.%s' % SHLIB_EXT, 'lib/libgiomm-2.68.%s' % SHLIB_EXT,
+              'include/glibmm-2.68/glibmm.h', 'include/giomm-2.68/giomm.h'],
+    'dirs': ['lib/pkgconfig'],
+}
+
+moduleclass = 'vis'
diff --git a/easybuild/easyconfigs/g/GLibmm/GLibmm-2.78.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/g/GLibmm/GLibmm-2.78.1-GCCcore-13.2.0.eb
new file mode 100644
index 00000000000..1cfbeec1c85
--- /dev/null
+++ b/easybuild/easyconfigs/g/GLibmm/GLibmm-2.78.1-GCCcore-13.2.0.eb
@@ -0,0 +1,34 @@
+easyblock = 'MesonNinja'
+
+name = 'GLibmm'
+version = '2.78.1'
+
+homepage = 'https://www.gtk.org/'
+description = """C++ bindings for Glib"""
+
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://ftp.gnome.org/pub/gnome/sources/glibmm/%(version_major_minor)s/']
+sources = ['%(namelower)s-%(version)s.tar.xz']
+checksums = ['f473f2975d26c3409e112ed11ed36406fb3843fa975df575c22d4cb843085f61']
+
+builddependencies = [
+    ('binutils', '2.40'),
+    ('pkgconf', '2.0.3'),
+    ('Meson', '1.2.3'),
+    ('Ninja', '1.11.1'),
+]
+
+dependencies = [
+    ('GLib', '2.78.1'),
+    ('libsigc++', '3.6.0'),
+]
+
+sanity_check_paths = {
+    'files': ['lib/libglibmm-2.68.%s' % SHLIB_EXT, 'lib/libgiomm-2.68.%s' % SHLIB_EXT,
+              'include/glibmm-2.68/glibmm.h', 'include/giomm-2.68/giomm.h'],
+    'dirs': ['lib/pkgconfig'],
+}
+
+moduleclass = 'vis'
diff --git a/easybuild/easyconfigs/l/libsigc++/libsigc++-3.6.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libsigc++/libsigc++-3.6.0-GCCcore-11.3.0.eb
new file mode 100644
index 00000000000..78c10c800de
--- /dev/null
+++ b/easybuild/easyconfigs/l/libsigc++/libsigc++-3.6.0-GCCcore-11.3.0.eb
@@ -0,0 +1,34 @@
+easyblock = 'CMakeMake'
+
+name = 'libsigc++'
+version = '3.6.0'
+
+homepage = 'https://libsigcplusplus.github.io/libsigcplusplus/'
+description = """The libsigc++ package implements a typesafe callback system 
+for standard C++."""
+
+toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
+toolchainopts = {'pic': True}
+
+source_urls = [FTPGNOME_SOURCE]
+sources = [SOURCELOWER_TAR_XZ]
+checksums = ['c3d23b37dfd6e39f2e09f091b77b1541fbfa17c4f0b6bf5c89baef7229080e17']
+
+builddependencies = [
+    ('binutils', '2.38'),
+    ('libxslt', '1.1.34'),
+    ('mm-common', '1.0.6'),
+    ('CMake', '3.24.3'),
+]
+
+#configopts = '-Dbuild-documentation=false'
+
+test_cmd = 'ctest'
+runtest = '-j'
+
+sanity_check_paths = {
+    'files': ['lib/libsigc-%%(version_major)s.0.%s' % SHLIB_EXT],
+    'dirs': [],
+}
+
+moduleclass = 'devel'
diff --git a/easybuild/easyconfigs/l/libsigc++/libsigc++-3.6.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/libsigc++/libsigc++-3.6.0-GCCcore-12.2.0.eb
new file mode 100644
index 00000000000..77bcf5b1dbf
--- /dev/null
+++ b/easybuild/easyconfigs/l/libsigc++/libsigc++-3.6.0-GCCcore-12.2.0.eb
@@ -0,0 +1,34 @@
+easyblock = 'CMakeMake'
+
+name = 'libsigc++'
+version = '3.6.0'
+
+homepage = 'https://libsigcplusplus.github.io/libsigcplusplus/'
+description = """The libsigc++ package implements a typesafe callback system 
+for standard C++."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+toolchainopts = {'pic': True}
+
+source_urls = [FTPGNOME_SOURCE]
+sources = [SOURCELOWER_TAR_XZ]
+checksums = ['c3d23b37dfd6e39f2e09f091b77b1541fbfa17c4f0b6bf5c89baef7229080e17']
+
+builddependencies = [
+    ('binutils', '2.39'),
+    ('libxslt', '1.1.37'),
+    ('mm-common', '1.0.6'),
+    ('CMake', '3.24.3'),
+]
+
+#configopts = '-Dbuild-documentation=false'
+
+test_cmd = 'ctest'
+runtest = '-j'
+
+sanity_check_paths = {
+    'files': ['lib/libsigc-%%(version_major)s.0.%s' % SHLIB_EXT],
+    'dirs': [],
+}
+
+moduleclass = 'devel'
diff --git a/easybuild/easyconfigs/l/libsigc++/libsigc++-3.6.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libsigc++/libsigc++-3.6.0-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..8ec02b3e43e
--- /dev/null
+++ b/easybuild/easyconfigs/l/libsigc++/libsigc++-3.6.0-GCCcore-12.3.0.eb
@@ -0,0 +1,34 @@
+easyblock = 'CMakeMake'
+
+name = 'libsigc++'
+version = '3.6.0'
+
+homepage = 'https://libsigcplusplus.github.io/libsigcplusplus/'
+description = """The libsigc++ package implements a typesafe callback system 
+for standard C++."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+toolchainopts = {'pic': True}
+
+source_urls = [FTPGNOME_SOURCE]
+sources = [SOURCELOWER_TAR_XZ]
+checksums = ['c3d23b37dfd6e39f2e09f091b77b1541fbfa17c4f0b6bf5c89baef7229080e17']
+
+builddependencies = [
+    ('binutils', '2.40'),
+    ('libxslt', '1.1.38'),
+    ('mm-common', '1.0.6'),
+    ('CMake', '3.26.3'),
+]
+
+#configopts = '-Dbuild-documentation=false'
+
+test_cmd = 'ctest'
+runtest = '-j'
+
+sanity_check_paths = {
+    'files': ['lib/libsigc-%%(version_major)s.0.%s' % SHLIB_EXT],
+    'dirs': [],
+}
+
+moduleclass = 'devel'
diff --git a/easybuild/easyconfigs/l/libsigc++/libsigc++-3.6.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/libsigc++/libsigc++-3.6.0-GCCcore-13.2.0.eb
new file mode 100644
index 00000000000..741dcf51c4f
--- /dev/null
+++ b/easybuild/easyconfigs/l/libsigc++/libsigc++-3.6.0-GCCcore-13.2.0.eb
@@ -0,0 +1,34 @@
+easyblock = 'CMakeMake'
+
+name = 'libsigc++'
+version = '3.6.0'
+
+homepage = 'https://libsigcplusplus.github.io/libsigcplusplus/'
+description = """The libsigc++ package implements a typesafe callback system 
+for standard C++."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
+toolchainopts = {'pic': True}
+
+source_urls = [FTPGNOME_SOURCE]
+sources = [SOURCELOWER_TAR_XZ]
+checksums = ['c3d23b37dfd6e39f2e09f091b77b1541fbfa17c4f0b6bf5c89baef7229080e17']
+
+builddependencies = [
+    ('binutils', '2.40'),
+    ('libxslt', '1.1.38'),
+    ('mm-common', '1.0.6'),
+    ('CMake', '3.27.6'),
+]
+
+#configopts = '-Dbuild-documentation=false'
+
+test_cmd = 'ctest'
+runtest = '-j'
+
+sanity_check_paths = {
+    'files': ['lib/libsigc-%%(version_major)s.0.%s' % SHLIB_EXT],
+    'dirs': [],
+}
+
+moduleclass = 'devel'
diff --git a/easybuild/easyconfigs/m/mm-common/mm-common-1.0.6-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/mm-common/mm-common-1.0.6-GCCcore-11.3.0.eb
new file mode 100644
index 00000000000..9a06d985675
--- /dev/null
+++ b/easybuild/easyconfigs/m/mm-common/mm-common-1.0.6-GCCcore-11.3.0.eb
@@ -0,0 +1,33 @@
+easyblock = 'MesonNinja'
+
+name = 'mm-common'
+version = '1.0.6'
+
+homepage = 'https://gitlab.gnome.org/GNOME/mm-common'
+description = """The mm-common module provides the build infrastructure and 
+utilities shared among the GNOME C++ binding libraries."""
+
+toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
+
+source_urls = [FTPGNOME_SOURCE]
+sources = [SOURCELOWER_TAR_XZ]
+checksums = ['b55c46037dbcdabc5cee3b389ea11cc3910adb68ebe883e9477847aa660862e7']
+
+builddependencies = [
+    ('binutils', '2.38'),
+    ('Meson', '0.62.1'),
+    ('Ninja', '1.10.2'),
+]
+
+dependencies = [
+    ('Python', '3.10.4'),
+]
+
+sanity_check_paths = {
+    'files': ['bin/mm-common-get', 'bin/mm-common-prepare', 'share/pkgconfig/mm-common-util.pc'],
+    'dirs': ['share/man/man1'],
+}
+
+sanity_check_commands = ["mm-common-prepare --help"]
+
+moduleclass = 'devel'
diff --git a/easybuild/easyconfigs/m/mm-common/mm-common-1.0.6-GCCcore-12.2.0.eb b/easybuild/easyconfigs/m/mm-common/mm-common-1.0.6-GCCcore-12.2.0.eb
new file mode 100644
index 00000000000..48aae0caae0
--- /dev/null
+++ b/easybuild/easyconfigs/m/mm-common/mm-common-1.0.6-GCCcore-12.2.0.eb
@@ -0,0 +1,33 @@
+easyblock = 'MesonNinja'
+
+name = 'mm-common'
+version = '1.0.6'
+
+homepage = 'https://gitlab.gnome.org/GNOME/mm-common'
+description = """The mm-common module provides the build infrastructure and 
+utilities shared among the GNOME C++ binding libraries."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+
+source_urls = [FTPGNOME_SOURCE]
+sources = [SOURCELOWER_TAR_XZ]
+checksums = ['b55c46037dbcdabc5cee3b389ea11cc3910adb68ebe883e9477847aa660862e7']
+
+builddependencies = [
+    ('binutils', '2.39'),
+    ('Meson', '0.64.0'),
+    ('Ninja', '1.11.1'),
+]
+
+dependencies = [
+    ('Python', '3.10.8'),
+]
+
+sanity_check_paths = {
+    'files': ['bin/mm-common-get', 'bin/mm-common-prepare', 'share/pkgconfig/mm-common-util.pc'],
+    'dirs': ['share/man/man1'],
+}
+
+sanity_check_commands = ["mm-common-prepare --help"]
+
+moduleclass = 'devel'
diff --git a/easybuild/easyconfigs/m/mm-common/mm-common-1.0.6-GCCcore-12.3.0.eb b/easybuild/easyconfigs/m/mm-common/mm-common-1.0.6-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..0078e0948e9
--- /dev/null
+++ b/easybuild/easyconfigs/m/mm-common/mm-common-1.0.6-GCCcore-12.3.0.eb
@@ -0,0 +1,33 @@
+easyblock = 'MesonNinja'
+
+name = 'mm-common'
+version = '1.0.6'
+
+homepage = 'https://gitlab.gnome.org/GNOME/mm-common'
+description = """The mm-common module provides the build infrastructure and 
+utilities shared among the GNOME C++ binding libraries."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+source_urls = [FTPGNOME_SOURCE]
+sources = [SOURCELOWER_TAR_XZ]
+checksums = ['b55c46037dbcdabc5cee3b389ea11cc3910adb68ebe883e9477847aa660862e7']
+
+builddependencies = [
+    ('binutils', '2.40'),
+    ('Meson', '1.1.1'),
+    ('Ninja', '1.11.1'),
+]
+
+dependencies = [
+    ('Python', '3.11.3'),
+]
+
+sanity_check_paths = {
+    'files': ['bin/mm-common-get', 'bin/mm-common-prepare', 'share/pkgconfig/mm-common-util.pc'],
+    'dirs': ['share/man/man1'],
+}
+
+sanity_check_commands = ["mm-common-prepare --help"]
+
+moduleclass = 'devel'
diff --git a/easybuild/easyconfigs/m/mm-common/mm-common-1.0.6-GCCcore-13.2.0.eb b/easybuild/easyconfigs/m/mm-common/mm-common-1.0.6-GCCcore-13.2.0.eb
new file mode 100644
index 00000000000..f545595fd96
--- /dev/null
+++ b/easybuild/easyconfigs/m/mm-common/mm-common-1.0.6-GCCcore-13.2.0.eb
@@ -0,0 +1,33 @@
+easyblock = 'MesonNinja'
+
+name = 'mm-common'
+version = '1.0.6'
+
+homepage = 'https://gitlab.gnome.org/GNOME/mm-common'
+description = """The mm-common module provides the build infrastructure and 
+utilities shared among the GNOME C++ binding libraries."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
+
+source_urls = [FTPGNOME_SOURCE]
+sources = [SOURCELOWER_TAR_XZ]
+checksums = ['b55c46037dbcdabc5cee3b389ea11cc3910adb68ebe883e9477847aa660862e7']
+
+builddependencies = [
+    ('binutils', '2.40'),
+    ('Meson', '1.2.3'),
+    ('Ninja', '1.11.1'),
+]
+
+dependencies = [
+    ('Python', '3.11.5'),
+]
+
+sanity_check_paths = {
+    'files': ['bin/mm-common-get', 'bin/mm-common-prepare', 'share/pkgconfig/mm-common-util.pc'],
+    'dirs': ['share/man/man1'],
+}
+
+sanity_check_commands = ["mm-common-prepare --help"]
+
+moduleclass = 'devel'

From 57d826d6719148209663ae8a66338d62c2752cde Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Wed, 17 Apr 2024 16:26:36 +0000
Subject: [PATCH 061/835] Fix style

---
 .../easyconfigs/l/libsigc++/libsigc++-3.6.0-GCCcore-11.3.0.eb   | 2 --
 .../easyconfigs/l/libsigc++/libsigc++-3.6.0-GCCcore-12.2.0.eb   | 2 --
 .../easyconfigs/l/libsigc++/libsigc++-3.6.0-GCCcore-12.3.0.eb   | 2 --
 .../easyconfigs/l/libsigc++/libsigc++-3.6.0-GCCcore-13.2.0.eb   | 2 --
 4 files changed, 8 deletions(-)

diff --git a/easybuild/easyconfigs/l/libsigc++/libsigc++-3.6.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libsigc++/libsigc++-3.6.0-GCCcore-11.3.0.eb
index 78c10c800de..52518f5a054 100644
--- a/easybuild/easyconfigs/l/libsigc++/libsigc++-3.6.0-GCCcore-11.3.0.eb
+++ b/easybuild/easyconfigs/l/libsigc++/libsigc++-3.6.0-GCCcore-11.3.0.eb
@@ -21,8 +21,6 @@ builddependencies = [
     ('CMake', '3.24.3'),
 ]
 
-#configopts = '-Dbuild-documentation=false'
-
 test_cmd = 'ctest'
 runtest = '-j'
 
diff --git a/easybuild/easyconfigs/l/libsigc++/libsigc++-3.6.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/libsigc++/libsigc++-3.6.0-GCCcore-12.2.0.eb
index 77bcf5b1dbf..8657a57fde1 100644
--- a/easybuild/easyconfigs/l/libsigc++/libsigc++-3.6.0-GCCcore-12.2.0.eb
+++ b/easybuild/easyconfigs/l/libsigc++/libsigc++-3.6.0-GCCcore-12.2.0.eb
@@ -21,8 +21,6 @@ builddependencies = [
     ('CMake', '3.24.3'),
 ]
 
-#configopts = '-Dbuild-documentation=false'
-
 test_cmd = 'ctest'
 runtest = '-j'
 
diff --git a/easybuild/easyconfigs/l/libsigc++/libsigc++-3.6.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libsigc++/libsigc++-3.6.0-GCCcore-12.3.0.eb
index 8ec02b3e43e..4f452cbc432 100644
--- a/easybuild/easyconfigs/l/libsigc++/libsigc++-3.6.0-GCCcore-12.3.0.eb
+++ b/easybuild/easyconfigs/l/libsigc++/libsigc++-3.6.0-GCCcore-12.3.0.eb
@@ -21,8 +21,6 @@ builddependencies = [
     ('CMake', '3.26.3'),
 ]
 
-#configopts = '-Dbuild-documentation=false'
-
 test_cmd = 'ctest'
 runtest = '-j'
 
diff --git a/easybuild/easyconfigs/l/libsigc++/libsigc++-3.6.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/libsigc++/libsigc++-3.6.0-GCCcore-13.2.0.eb
index 741dcf51c4f..e64e49e0f74 100644
--- a/easybuild/easyconfigs/l/libsigc++/libsigc++-3.6.0-GCCcore-13.2.0.eb
+++ b/easybuild/easyconfigs/l/libsigc++/libsigc++-3.6.0-GCCcore-13.2.0.eb
@@ -21,8 +21,6 @@ builddependencies = [
     ('CMake', '3.27.6'),
 ]
 
-#configopts = '-Dbuild-documentation=false'
-
 test_cmd = 'ctest'
 runtest = '-j'
 

From fd1e75d870a69e5835f298f41fe72e6b8e22b96b Mon Sep 17 00:00:00 2001
From: WilleBell <cintiawillemyns@gmail.com>
Date: Fri, 19 Apr 2024 17:13:47 +0200
Subject: [PATCH 062/835] move hatchling and redis builddep and use %(arch)s
 template

---
 .../r/Ray-project/Ray-project-2.9.1-foss-2023a.eb        | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/easybuild/easyconfigs/r/Ray-project/Ray-project-2.9.1-foss-2023a.eb b/easybuild/easyconfigs/r/Ray-project/Ray-project-2.9.1-foss-2023a.eb
index c0e9bc15437..81a18f68d8a 100644
--- a/easybuild/easyconfigs/r/Ray-project/Ray-project-2.9.1-foss-2023a.eb
+++ b/easybuild/easyconfigs/r/Ray-project/Ray-project-2.9.1-foss-2023a.eb
@@ -12,13 +12,16 @@ description = "Ray is a fast and simple framework for building and running distr
 toolchain = {'name': 'foss', 'version': '2023a'}
 toolchainopts = {'usempi': True}
 
+builddependencies = [
+    ('redis-py', '5.0.1'),
+    ('hatchling', '1.18.0'),
+]
+
 dependencies = [
     ('Python', '3.11.3'),
     ('SciPy-bundle', '2023.07'),
     ('protobuf-python', '4.24.0'),
     ('PyYAML', '6.0'),
-    ('redis-py', '5.0.1'),
-    ('hatchling', '1.18.0'),
 ]
 
 use_pip = True
@@ -39,7 +42,7 @@ exts_list = [
         'checksums': ['c037a86e8513059a2613aaba4d817bb90b9d9b6b69aace3ce9c877e8c8ed402b'],
     }),
     ('Ray', version, {
-        'source_tmpl': '%(namelower)s-%(version)s-cp311-cp311-manylinux2014_x86_64.whl',
+        'source_tmpl': '%(namelower)s-%(version)s-cp311-cp311-manylinux2014_%(arch)s.whl',
         'checksums': ['fabc520990c1b98dde592813d62737e5e817460e0ac359f32ba029ace292cbe2'],
     }),
 ]

From 6bfc0b2cf8476817111a716d92e1f7fd7f737a34 Mon Sep 17 00:00:00 2001
From: WilleBell <cintiawillemyns@gmail.com>
Date: Mon, 22 Apr 2024 21:07:25 +0200
Subject: [PATCH 063/835] adding easyconfigs: OpenAI-Gym-0.26.2-foss-2023a.eb,
 Arcade-Learning-Environment-0.8.1-foss-2023a.eb

---
 ...e-Learning-Environment-0.8.1-foss-2023a.eb | 63 +++++++++++++++++++
 .../OpenAI-Gym-0.26.2-foss-2023a.eb           | 53 ++++++++++++++++
 2 files changed, 116 insertions(+)
 create mode 100644 easybuild/easyconfigs/a/Arcade-Learning-Environment/Arcade-Learning-Environment-0.8.1-foss-2023a.eb
 create mode 100644 easybuild/easyconfigs/o/OpenAI-Gym/OpenAI-Gym-0.26.2-foss-2023a.eb

diff --git a/easybuild/easyconfigs/a/Arcade-Learning-Environment/Arcade-Learning-Environment-0.8.1-foss-2023a.eb b/easybuild/easyconfigs/a/Arcade-Learning-Environment/Arcade-Learning-Environment-0.8.1-foss-2023a.eb
new file mode 100644
index 00000000000..aca8f2dca72
--- /dev/null
+++ b/easybuild/easyconfigs/a/Arcade-Learning-Environment/Arcade-Learning-Environment-0.8.1-foss-2023a.eb
@@ -0,0 +1,63 @@
+easyblock = 'CMakeMake'
+
+name = 'Arcade-Learning-Environment'
+version = '0.8.1'
+
+homepage = 'https://github.com/mgbellemare/Arcade-Learning-Environment'
+description = """The Arcade Learning Environment (ALE) is a simple framework that allows
+researchers and hobbyists to develop AI agents for Atari 2600 games. It is
+built on top of the Atari 2600 emulator Stella and separates the details of
+emulation from agent design. This video depicts over 50 games currently
+supported in the ALE."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+github_account = 'mgbellemare'
+source_urls = [GITHUB_SOURCE]
+sources = ['v%(version)s.tar.gz']
+checksums = ['28960616cd89c18925ced7bbdeec01ab0b2ebd2d8ce5b7c88930e97381b4c3b5']
+
+builddependencies = [
+    ('CMake', '3.26.3'),
+]
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('pybind11', '2.11.1'),
+    ('SciPy-bundle', '2023.07'),
+    ('SDL2', '2.28.2'),
+    ('zlib', '1.2.13'),
+]
+
+# main build of C++ libraries
+configopts = "-DBUILD_PYTHON_LIB=OFF"
+
+# install Python bindings and its dependencies
+exts_defaultclass = 'PythonPackage'
+exts_default_options = {
+    'download_dep_fail': True,
+    'use_pip': True,
+    'sanity_pip_check': True,
+}
+exts_list = [
+    ('ale-py', version, {
+        'patches': ['%(name)s-%(version)s_fix_version.patch'],
+        'preinstallopts': 'ALE_BUILD_VERSION=%(version)s',
+        'source_tmpl': 'v%(version)s.tar.gz',
+        'checksums': [
+            {'v0.8.1.tar.gz': '28960616cd89c18925ced7bbdeec01ab0b2ebd2d8ce5b7c88930e97381b4c3b5'},
+            {'ale-py-0.8.1_fix_version.patch': '3ad39a05eb82c3aacf34a6de562ad2d76c254a906963bdef6a810f0b5ce0d22f'},
+        ],
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['bin/ale-import-roms', 'lib64/libale.a'],
+    'dirs': ['include/ale', 'lib/python%(pyshortver)s/site-packages/'],
+}
+
+sanity_check_commands = ["ale-import-roms --help"]
+
+modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'}
+
+moduleclass = 'tools'
diff --git a/easybuild/easyconfigs/o/OpenAI-Gym/OpenAI-Gym-0.26.2-foss-2023a.eb b/easybuild/easyconfigs/o/OpenAI-Gym/OpenAI-Gym-0.26.2-foss-2023a.eb
new file mode 100644
index 00000000000..c7ad7c7c04f
--- /dev/null
+++ b/easybuild/easyconfigs/o/OpenAI-Gym/OpenAI-Gym-0.26.2-foss-2023a.eb
@@ -0,0 +1,53 @@
+easyblock = 'PythonBundle'
+
+name = 'OpenAI-Gym'
+version = '0.26.2'
+
+homepage = 'https://gym.openai.com'
+description = "A toolkit for developing and comparing reinforcement learning algorithms."
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+builddependencies = [
+    ('CMake', '3.26.3'),
+    ('SWIG', '4.1.1'),
+]
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('Arcade-Learning-Environment', '0.8.1'),
+    ('OpenCV', '4.8.1', '-contrib'),
+    ('lz4', '1.9.4'),
+    ('pygame', '2.5.2'),
+    ('MuJoCo', '3.1.4'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('cloudpickle', '3.0.0', {
+        'checksums': ['996d9a482c6fb4f33c1a35335cf8afd065d2a56e973270364840712d9131a882'],
+    }),
+    ('gym-notices', '0.0.8', {
+        'checksums': ['ad25e200487cafa369728625fe064e88ada1346618526102659b4640f2b4b911'],
+    }),
+    ('box2d-py', '2.3.8', {
+        'modulename': 'Box2D',
+        'checksums': ['bdacfbbc56079bb317548efe49d3d5a86646885cc27f4a2ee97e4b2960921ab7'],
+    }),
+    ('lz4', '4.3.3', {
+        'checksums': ['01fe674ef2889dbb9899d8a67361e0c4a2c833af5aeb37dd505727cf5d2a131e'],
+    }),
+    ('gym', version, {
+        'use_pip_extras': 'all',
+        'checksums': ['e0d882f4b54f0c65f203104c24ab8a38b039f1289986803c7d02cdbe214fbcc4'],
+    }),
+]
+
+local_envs = ['box2d', 'classic_control', 'mujoco', 'toy_text']
+sanity_check_commands = ["python -c 'import gym.envs.%s'" % e for e in local_envs]
+
+sanity_pip_check = True
+
+moduleclass = 'tools'

From 9733121f1bbeebc06af5d28dec68ff25d36f81aa Mon Sep 17 00:00:00 2001
From: Adam Huffman <12435+verdurin@users.noreply.github.com>
Date: Tue, 23 Apr 2024 09:15:28 +0000
Subject: [PATCH 064/835] adding easyconfigs: SKA2-0.3.7-GCCcore-12.2.0.eb

---
 .../s/SKA2/SKA2-0.3.7-GCCcore-12.2.0.eb       | 32 +++++++++++++++++++
 1 file changed, 32 insertions(+)
 create mode 100644 easybuild/easyconfigs/s/SKA2/SKA2-0.3.7-GCCcore-12.2.0.eb

diff --git a/easybuild/easyconfigs/s/SKA2/SKA2-0.3.7-GCCcore-12.2.0.eb b/easybuild/easyconfigs/s/SKA2/SKA2-0.3.7-GCCcore-12.2.0.eb
new file mode 100644
index 00000000000..094972fec6a
--- /dev/null
+++ b/easybuild/easyconfigs/s/SKA2/SKA2-0.3.7-GCCcore-12.2.0.eb
@@ -0,0 +1,32 @@
+easyblock = 'Binary'
+
+name = 'SKA2'
+version = '0.3.7'
+
+homepage = 'https://docs.rs/ska/latest/ska/'
+description = """Split k-mer analysis (version 2) uses exact matching of split k-mer sequences to align closely
+ related sequences, typically small haploid genomes such as bacteria and viruses."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+
+source_urls = ['https://github.com/bacpop/ska.rust/archive']
+sources = ['v%(version)s.tar.gz']
+checksums = ['ea7234428f253638b2093abdd6c8b1e8362ecad0ba56e3b29700af9a4481d911']
+
+builddependencies = [
+    ('binutils', '2.39'),
+    ('Rust', '1.75.0'),
+]
+
+extract_sources = True
+
+install_cmd = "cargo install --root %(installdir)s --path ."
+
+sanity_check_paths = {
+    'files': ['bin/ska'],
+    'dirs': [],
+}
+
+sanity_check_commands = ["ska --help"]
+
+moduleclass = 'bio'

From 1172d644dac2263e599f152c7415699a1da6c5ef Mon Sep 17 00:00:00 2001
From: Adam Huffman <12435+verdurin@users.noreply.github.com>
Date: Tue, 23 Apr 2024 09:18:36 +0000
Subject: [PATCH 065/835] adding easyconfigs: Gubbins-3.3.5-foss-2022b.eb,
 rapidNJ-2.3.3-GCCcore-12.2.0.eb, FastTree-2.1.11-GCCcore-12.2.0.eb,
 multiprocess-0.70.15-gfbf-2022b.eb,
 Autoconf-archive-2023.02.20-GCCcore-12.2.0.eb

---
 ...oconf-archive-2023.02.20-GCCcore-12.2.0.eb | 53 +++++++++++++++
 .../FastTree-2.1.11-GCCcore-12.2.0.eb         | 42 ++++++++++++
 .../g/Gubbins/Gubbins-3.3.5-foss-2022b.eb     | 64 +++++++++++++++++++
 .../multiprocess-0.70.15-gfbf-2022b.eb        | 24 +++++++
 .../r/rapidNJ/rapidNJ-2.3.3-GCCcore-12.2.0.eb | 41 ++++++++++++
 5 files changed, 224 insertions(+)
 create mode 100644 easybuild/easyconfigs/a/Autoconf-archive/Autoconf-archive-2023.02.20-GCCcore-12.2.0.eb
 create mode 100644 easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-12.2.0.eb
 create mode 100644 easybuild/easyconfigs/g/Gubbins/Gubbins-3.3.5-foss-2022b.eb
 create mode 100644 easybuild/easyconfigs/m/multiprocess/multiprocess-0.70.15-gfbf-2022b.eb
 create mode 100644 easybuild/easyconfigs/r/rapidNJ/rapidNJ-2.3.3-GCCcore-12.2.0.eb

diff --git a/easybuild/easyconfigs/a/Autoconf-archive/Autoconf-archive-2023.02.20-GCCcore-12.2.0.eb b/easybuild/easyconfigs/a/Autoconf-archive/Autoconf-archive-2023.02.20-GCCcore-12.2.0.eb
new file mode 100644
index 00000000000..73e0608725b
--- /dev/null
+++ b/easybuild/easyconfigs/a/Autoconf-archive/Autoconf-archive-2023.02.20-GCCcore-12.2.0.eb
@@ -0,0 +1,53 @@
+##
+# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia
+# Homepage: 	https://staff.flinders.edu.au/research/deep-thought
+#
+# Authors::	Robert Qiao <rob.qiao@flinders.edu.au>
+# License::	GNU Free Documentation License
+#
+# Notes::
+##
+
+easyblock = 'ConfigureMake'
+
+name = 'Autoconf-archive'
+version = '2023.02.20'
+
+homepage = "https://www.gnu.org/software/autoconf-archive"
+
+description = """
+The GNU Autoconf Archive is a collection of more than 500 macros for GNU Autoconf
+that have been contributed as free software by friendly supporters of the cause from
+all over the Internet. Every single one of those macros can be re-used without
+imposing any restrictions whatsoever on the licensing of the generated configure script.
+In particular, it is possible to use all those macros in configure scripts that
+are meant for non-free software. This policy is unusual for a Free Software Foundation
+project. The FSF firmly believes that software ought to be free, and software licenses
+like the GPL are specifically designed to ensure that derivative work based on free
+software must be free as well. In case of Autoconf, however, an exception has been made,
+because Autoconf is at such a pivotal position in the software development tool chain
+that the benefits from having this tool available as widely as possible outweigh the
+disadvantage that some authors may choose to use it, too, for proprietary software.
+"""
+
+toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+
+source_urls = [GNU_SOURCE]
+sources = [SOURCELOWER_TAR_XZ]
+checksums = ['71d4048479ae28f1f5794619c3d72df9c01df49b1c628ef85fde37596dc31a33']
+
+builddependencies = [
+    ('binutils', '2.39'),
+    ('Autotools', '20220317'),
+    ('makeinfo', '7.0.3'),
+]
+
+preconfigopts = 'autoreconf -i -f &&'
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['share/%s' % x for x in
+             ['aclocal', 'doc', 'info']],
+}
+
+moduleclass = 'devel'
diff --git a/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-12.2.0.eb b/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-12.2.0.eb
new file mode 100644
index 00000000000..abb4f293128
--- /dev/null
+++ b/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-12.2.0.eb
@@ -0,0 +1,42 @@
+# Updated from previous config
+# Author: Pavel Grochal (INUITS)
+# License: GPLv2
+
+easyblock = 'CmdCp'
+
+name = 'FastTree'
+version = '2.1.11'
+
+homepage = 'http://www.microbesonline.org/fasttree/'
+description = """FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide
+ or protein sequences. FastTree can handle alignments with up to a million of sequences in a reasonable amount of
+ time and memory. """
+
+toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+toolchainopts = {'openmp': True}
+
+# HTTPS cert error:
+# hostname 'www.microbesonline.org' doesn't match either of 'genomics.lbl.gov', 'mojave.qb3.berkeley.edu', ...
+source_urls = ['http://www.microbesonline.org/fasttree/']
+sources = [{'filename': '%(name)s-%(version)s.c', 'extract_cmd': 'cp %s FastTree.c'}]
+checksums = ['9026ae550307374be92913d3098f8d44187d30bea07902b9dcbfb123eaa2050f']
+
+builddependencies = [('binutils', '2.39')]
+
+cmds_map = [('%(name)s-%(version)s.c', '$CC -DOPENMP $CFLAGS $LIBS %%(source)s -o %(name)s')]
+
+files_to_copy = [(['FastTree'], 'bin')]
+
+# as FastTree is built with OpenMP, the correct binary is FastTreeMP
+# the FastTree binary should normally be built without OpenMP, but let’s keep it as is for backward compatibility
+# see http://www.microbesonline.org/fasttree/#OpenMP
+postinstallcmds = ['cd %(installdir)s/bin && ln -s FastTree FastTreeMP']
+
+sanity_check_paths = {
+    'files': ['bin/FastTree'],
+    'dirs': [],
+}
+
+sanity_check_commands = ['FastTree 2>&1 | grep "FastTree Version %(version)s"']
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/g/Gubbins/Gubbins-3.3.5-foss-2022b.eb b/easybuild/easyconfigs/g/Gubbins/Gubbins-3.3.5-foss-2022b.eb
new file mode 100644
index 00000000000..1a19d74c757
--- /dev/null
+++ b/easybuild/easyconfigs/g/Gubbins/Gubbins-3.3.5-foss-2022b.eb
@@ -0,0 +1,64 @@
+# This easyconfig was created by the BEAR Software team at the University of Birmingham.
+easyblock = 'ConfigureMake'
+
+name = 'Gubbins'
+version = '3.3.5'
+
+homepage = "https://nickjcroucher.github.io/gubbins/"
+description = """Gubbins (Genealogies Unbiased By recomBinations In Nucleotide Sequences) is an algorithm that
+ iteratively identifies loci containing elevated densities of base substitutions, which are marked as recombinations,
+ while concurrently constructing a phylogeny based on the putative point mutations outside of these regions.
+ Simulations demonstrate the algorithm generates highly accurate reconstructions under realistic models of short-term
+ bacterial evolution, and can be run in only a few hours on alignments of hundreds of bacterial genome sequences."""
+
+toolchain = {'name': 'foss', 'version': '2022b'}
+
+source_urls = ['https://github.com/nickjcroucher/gubbins/archive/refs/tags/']
+sources = ['v%(version)s.tar.gz']
+
+builddependencies = [
+    ('Autotools', '20220317'),
+    ('Autoconf-archive', '2023.02.20'),
+    ('pkgconf', '1.9.3'),
+    ('Check', '0.15.2'),
+    ('subunit', '1.4.3'),
+]
+
+dependencies = [
+    ('Python', '3.10.8'),
+    ('Biopython', '1.81'),
+    ('DendroPy', '4.5.2'),
+    ('numba', '0.58.1'),
+    ('SciPy-bundle', '2023.02'),
+    ('FastTree', '2.1.11'),
+    ('IQ-TREE', '2.2.2.6'),
+    ('rapidNJ', '2.3.3'),
+    ('RAxML', '8.2.12', '-avx2'),
+    ('RAxML-NG', '1.2.0'),
+    ('SKA2', '0.3.7'),
+    ('dill', '0.3.7'),
+    ('multiprocess', '0.70.15'),
+]
+
+preconfigopts = "autoreconf -i && "
+# runtest = 'check'  # runs the Python tests and this causes package to be installed into the Python install
+postinstallcmds = [
+    """sed -i 's/self.executable = "iqtree"/self.executable = "iqtree2"/' python/gubbins/treebuilders.py""",
+    "cd python && python -m pip install --prefix %(installdir)s --no-build-isolation . "
+]
+
+modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'}
+
+sanity_check_paths = {
+    'files': ['bin/gubbins', 'lib/libgubbins.%s' % SHLIB_EXT],
+    'dirs': [],
+}
+
+sanity_check_commands = [
+    "gubbins --help",
+    "run_gubbins.py --version",
+    'python -c "import gubbins"',
+    'python -m pip check',
+]
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/m/multiprocess/multiprocess-0.70.15-gfbf-2022b.eb b/easybuild/easyconfigs/m/multiprocess/multiprocess-0.70.15-gfbf-2022b.eb
new file mode 100644
index 00000000000..2bac0d9bfe6
--- /dev/null
+++ b/easybuild/easyconfigs/m/multiprocess/multiprocess-0.70.15-gfbf-2022b.eb
@@ -0,0 +1,24 @@
+easyblock = 'PythonPackage'
+
+name = 'multiprocess'
+version = '0.70.15'
+
+homepage = 'https://github.com/uqfoundation/multiprocess'
+description = "better multiprocessing and multithreading in python"
+
+toolchain = {'name': 'gfbf', 'version': '2022b'}
+
+sources = [SOURCE_TAR_GZ]
+checksums = ['f20eed3036c0ef477b07a4177cf7c1ba520d9a2677870a4f47fe026f0cd6787e']
+
+dependencies = [
+    ('Python', '3.10.8'),
+    ('dill', '0.3.7'),
+    ('Arrow', '11.0.0'),  # if needed rebuild --from-pr 19758
+]
+
+download_dep_fail = True
+use_pip = True
+sanity_pip_check = True
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/r/rapidNJ/rapidNJ-2.3.3-GCCcore-12.2.0.eb b/easybuild/easyconfigs/r/rapidNJ/rapidNJ-2.3.3-GCCcore-12.2.0.eb
new file mode 100644
index 00000000000..b6fc9da5925
--- /dev/null
+++ b/easybuild/easyconfigs/r/rapidNJ/rapidNJ-2.3.3-GCCcore-12.2.0.eb
@@ -0,0 +1,41 @@
+# This seems to be actively maintained version of the code by the looks of it. 
+# See issue #5
+# https://github.com/somme89/rapidNJ/issues/5
+# why -march=native will not be used
+# Author: J. Sassmannshausen (Imperial College London/UK)
+
+easyblock = 'MakeCp'
+
+name = 'rapidNJ'
+version = '2.3.3'
+
+homepage = 'https://github.com/somme89/rapidNJ'
+description = """RapidNJ is an algorithmic engineered implementation of canonical 
+neighbour-joining. It uses an efficient search heuristic to speed-up the core 
+computations of the neighbour-joining method that enables RapidNJ to 
+outperform other state-of-the-art neighbour-joining implementations."""
+
+citing = """Rapid Neighbour Joining. Martin Simonsen, Thomas Mailund and Christian N. S. Pedersen.
+In: Proceedings of the 8th Workshop in Algorithms in Bioinformatics (WABI), LNBI 5251, 113-122,
+Springer Verlag, October 2008.
+doi: 10.1007/978-3-540-87361-7_10"""
+
+toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+
+source_urls = ['https://github.com/somme89/rapidNJ/archive/']
+sources = [{'filename': 'v%(version)s.tar.gz', 'download_filename': 'latest.tar.gz'}]
+checksums = ['662f864cc3e5bc68aea23129f02e0062cac9ebd37e414b54c5c5e616ff4f245d']
+
+builddependencies = [('binutils', '2.39')]
+
+files_to_copy = [(['bin/rapidnj'], 'bin')]
+
+# That is returning 1 instead of 0, so disabled for now
+# sanity_check_commands = ['rapidnj --help']
+
+sanity_check_paths = {
+    'files': ['bin/rapidnj'],
+    'dirs': [],
+}
+
+moduleclass = 'bio'

From 4ea706341c818df7e7d1a6429762520e9a552a1e Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Wed, 24 Apr 2024 16:22:13 +0200
Subject: [PATCH 066/835] add another dependencies

---
 .../Single-cell-python-bundle-2024.02-foss-2023a.eb    | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb b/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb
index 9f0a5b02b36..637f3767f2b 100644
--- a/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb
+++ b/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb
@@ -30,9 +30,9 @@ dependencies = [
     # rpy2 in scCODA
     ('infercnvpy', '0.4.3'),
     ('pySCENIC', '0.12.1-20240311'),
-    # ('CellRank', '2.0.2'),
-    # ('Squidpy', '1.4.1'),
-    # ('Cassiopeia', '2.0.0'),
+    ('CellRank', '2.0.2'),
+    ('Squidpy', '1.4.1'),
+    ('Cassiopeia', '2.0.0'),
     # deps for exts:
     ('umap-learn', '0.5.5'),  # bbknn
     ('scikit-learn', '1.3.1'),  # bbknn, sc_toolbox
@@ -89,7 +89,7 @@ dependencies = [
 # Decoupler
 # contrastiveVI
 # Schist
-      
+
 exts_list = [
     ('flit_core', '3.9.0', {
         'checksums': ['72ad266176c4a3fcfab5f2930d76896059851240570ce9a98733b658cb786eba'],
@@ -174,7 +174,7 @@ exts_list = [
         'checksums': ['8c12ddccb72c41c96c6a5abceb52e7a76f439a9ab94fb092aa86ee3c1292383a'],
     }),
 ]
-    
+
 use_pip = True
 sanity_pip_check = True
 

From 45ae3bc714ab7bbaf89a65758c9cfc92eef8a0e6 Mon Sep 17 00:00:00 2001
From: WilleBell <cintiawillemyns@gmail.com>
Date: Thu, 25 Apr 2024 15:52:45 +0200
Subject: [PATCH 067/835] adding easyconfigs: Gymnasium-0.29.1-foss-2023a.eb

---
 .../Gymnasium/Gymnasium-0.29.1-foss-2023a.eb  | 52 +++++++++++++++++++
 1 file changed, 52 insertions(+)
 create mode 100644 easybuild/easyconfigs/g/Gymnasium/Gymnasium-0.29.1-foss-2023a.eb

diff --git a/easybuild/easyconfigs/g/Gymnasium/Gymnasium-0.29.1-foss-2023a.eb b/easybuild/easyconfigs/g/Gymnasium/Gymnasium-0.29.1-foss-2023a.eb
new file mode 100644
index 00000000000..e389e3ef7d7
--- /dev/null
+++ b/easybuild/easyconfigs/g/Gymnasium/Gymnasium-0.29.1-foss-2023a.eb
@@ -0,0 +1,52 @@
+easyblock = 'PythonBundle'
+
+name = 'Gymnasium'
+version = '0.29.1'
+
+homepage = 'https://gymnasium.farama.org/'
+description = """
+Gymnasium is an open source Python library for developing and comparing reinforcement learning
+algorithms by providing a standard API to communicate between learning algorithms and
+environments, as well as a standard set of environments compliant with that API.
+"""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+builddependencies = [
+    ('CMake', '3.26.3'),
+    ('SWIG', '4.1.1'),
+]
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('OpenCV', '4.8.1', '-contrib'),
+    ('pygame', '2.5.2'),
+    ('MuJoCo', '3.1.4'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('cloudpickle', '3.0.0', {
+        'checksums': ['996d9a482c6fb4f33c1a35335cf8afd065d2a56e973270364840712d9131a882'],
+    }),
+    ('Farama-Notifications', '0.0.4', {
+        'checksums': ['13fceff2d14314cf80703c8266462ebf3733c7d165336eee998fc58e545efd18'],
+    }),
+    ('box2d-py', '2.3.8', {
+        'modulename': 'Box2D',
+        'checksums': ['bdacfbbc56079bb317548efe49d3d5a86646885cc27f4a2ee97e4b2960921ab7'],
+    }),
+    ('gymnasium', version, {
+        'use_pip_extras': 'all',
+        'checksums': ['1a532752efcb7590478b1cc7aa04f608eb7a2fdad5570cd217b66b6a35274bb1'],
+    }),
+]
+
+local_envs = ['box2d', 'classic_control', 'mujoco', 'toy_text']
+sanity_check_commands = ["python -c 'import gymnasium.envs.%s'" % e for e in local_envs]
+
+sanity_pip_check = True
+
+moduleclass = 'tools'

From 075f2c261ebf4b30eb723f7d89d428c835d0ee19 Mon Sep 17 00:00:00 2001
From: Cintia Willemyns <115622907+WilleBell@users.noreply.github.com>
Date: Mon, 29 Apr 2024 12:11:12 +0200
Subject: [PATCH 068/835] Update
 easybuild/easyconfigs/r/Ray-project/Ray-project-2.9.1-foss-2023a.eb

Add checksums for source aarch64

Co-authored-by: Miguel Dias Costa <migueldiascosta@gmail.com>
---
 .../r/Ray-project/Ray-project-2.9.1-foss-2023a.eb        | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/r/Ray-project/Ray-project-2.9.1-foss-2023a.eb b/easybuild/easyconfigs/r/Ray-project/Ray-project-2.9.1-foss-2023a.eb
index 81a18f68d8a..2206c458376 100644
--- a/easybuild/easyconfigs/r/Ray-project/Ray-project-2.9.1-foss-2023a.eb
+++ b/easybuild/easyconfigs/r/Ray-project/Ray-project-2.9.1-foss-2023a.eb
@@ -43,7 +43,14 @@ exts_list = [
     }),
     ('Ray', version, {
         'source_tmpl': '%(namelower)s-%(version)s-cp311-cp311-manylinux2014_%(arch)s.whl',
-        'checksums': ['fabc520990c1b98dde592813d62737e5e817460e0ac359f32ba029ace292cbe2'],
+        'checksums': [{
+            '%(namelower)s-%(version)s-cp311-cp311-manylinux2014_x86_64.whl': (
+                'fabc520990c1b98dde592813d62737e5e817460e0ac359f32ba029ace292cbe2'
+            ),
+            '%(namelower)s-%(version)s-cp311-cp311-manylinux2014_aarch64.whl': (
+                '1907649d69efdc1b9ffbc03db086f6d768216cb73908ebd4038ac5030effef9e'
+            ),
+        }],
     }),
 ]
 

From 472400a7d21a61f8ed300e45214c58bd0c8c86e8 Mon Sep 17 00:00:00 2001
From: WilleBell <cintiawillemyns@gmail.com>
Date: Mon, 29 Apr 2024 12:15:31 +0200
Subject: [PATCH 069/835] add lz4 needed for RLlib performance

---
 .../easyconfigs/r/Ray-project/Ray-project-2.9.1-foss-2023a.eb | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/easybuild/easyconfigs/r/Ray-project/Ray-project-2.9.1-foss-2023a.eb b/easybuild/easyconfigs/r/Ray-project/Ray-project-2.9.1-foss-2023a.eb
index 2206c458376..0ee7b374943 100644
--- a/easybuild/easyconfigs/r/Ray-project/Ray-project-2.9.1-foss-2023a.eb
+++ b/easybuild/easyconfigs/r/Ray-project/Ray-project-2.9.1-foss-2023a.eb
@@ -22,6 +22,7 @@ dependencies = [
     ('SciPy-bundle', '2023.07'),
     ('protobuf-python', '4.24.0'),
     ('PyYAML', '6.0'),
+    ('lz4', '1.9.4'),
 ]
 
 use_pip = True
@@ -41,6 +42,9 @@ exts_list = [
     ('frozenlist', '1.4.1', {
         'checksums': ['c037a86e8513059a2613aaba4d817bb90b9d9b6b69aace3ce9c877e8c8ed402b'],
     }),
+    ('lz4', '4.3.3', {
+        'checksums': ['01fe674ef2889dbb9899d8a67361e0c4a2c833af5aeb37dd505727cf5d2a131e'],
+    }),
     ('Ray', version, {
         'source_tmpl': '%(namelower)s-%(version)s-cp311-cp311-manylinux2014_%(arch)s.whl',
         'checksums': [{

From cf6f043765f231e0a8bfb62b306f74259c5e60ae Mon Sep 17 00:00:00 2001
From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com>
Date: Mon, 29 Apr 2024 12:59:07 +0200
Subject: [PATCH 070/835] Update
 easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a-CUDA-12.1.1.eb

Co-authored-by: Alexander Grund <Flamefire@users.noreply.github.com>
---
 .../easyconfigs/j/jax/jax-0.4.25-gfbf-2023a-CUDA-12.1.1.eb      | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a-CUDA-12.1.1.eb
index d7ed71d94d6..fcc807a7055 100644
--- a/easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a-CUDA-12.1.1.eb
+++ b/easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a-CUDA-12.1.1.eb
@@ -41,7 +41,7 @@ dependencies = [
 local_xla_commit = '4ccfe33c71665ddcbca5b127fefe8baa3ed632d4'
 local_tfrt_commit = '0aeefb1660d7e37964b2bb71b1f518096bda9a25'
 local_repo_opt = '--bazel_options="--override_repository=xla=%%(builddir)s/xla-%s" ' % local_xla_commit
-local_repo_opt += '--bazel_options="--override_repository=runtime=%%(builddir)s/tf_runtime-%s" ' % local_xla_commit
+local_repo_opt += '--bazel_options="--override_repository=tf_runtime=%%(builddir)s/runtime-%s" ' % local_tfrt_commit
 local_repo_opt += '--bazel_options="--action_env=TF_SYSTEM_LIBS=pybind11" '
 local_repo_opt += '--bazel_options="--action_env=CPATH=$EBROOTPYBIND11/include" '
 

From 23345de3862df7c9eee34c06a4d44f39d1538c4a Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 30 Apr 2024 19:10:26 +0200
Subject: [PATCH 071/835] {bio}[foss/2023a] dorado v0.6.1, kineto v0.4.0 w/
 CUDA 12.1.1

---
 .../dorado-0.6.1-foss-2023a-CUDA-12.1.1.eb    | 87 +++++++++++++++++++
 .../dorado/dorado-0.6.1_include-fstream.patch | 27 ++++++
 .../k/kineto/kineto-0.4.0-GCC-12.3.0.eb       | 35 ++++++++
 3 files changed, 149 insertions(+)
 create mode 100644 easybuild/easyconfigs/d/dorado/dorado-0.6.1-foss-2023a-CUDA-12.1.1.eb
 create mode 100644 easybuild/easyconfigs/d/dorado/dorado-0.6.1_include-fstream.patch
 create mode 100644 easybuild/easyconfigs/k/kineto/kineto-0.4.0-GCC-12.3.0.eb

diff --git a/easybuild/easyconfigs/d/dorado/dorado-0.6.1-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/d/dorado/dorado-0.6.1-foss-2023a-CUDA-12.1.1.eb
new file mode 100644
index 00000000000..22a9289b01a
--- /dev/null
+++ b/easybuild/easyconfigs/d/dorado/dorado-0.6.1-foss-2023a-CUDA-12.1.1.eb
@@ -0,0 +1,87 @@
+easyblock = 'CMakeMake'
+
+name = 'dorado'
+version = '0.6.1'
+versionsuffix = '-CUDA-%(cudaver)s'
+
+homepage = 'https://github.com/nanoporetech/dorado'
+description = """Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+toolchainopts = {'usempi': True}
+
+source_urls = ['https://github.com/nanoporetech/dorado/archive/']
+sources = [{
+    'git_config': {
+        'url': 'https://github.com/nanoporetech',
+        'repo_name': name,
+        'tag': 'v%(version)s',
+        'recursive': True,
+    },
+    'filename': SOURCE_TAR_GZ,
+}]
+patches = ['dorado-0.6.1_include-fstream.patch']
+checksums = [
+    None,
+    'a7692a2d67422d808b3b81f3a297b7b89299ab0091e5d01f0b8a9aee9b942377',
+]
+
+builddependencies = [
+    ('binutils', '2.40'),
+    ('CMake', '3.26.3'),
+]
+
+dependencies = [
+    ('CUDA', '12.1.1', '', SYSTEM),
+    ('OpenSSL', '1.1', '', SYSTEM),
+    ('PyTorch', '2.1.2', '-CUDA-%(cudaver)s'),
+    ('HDF5', '1.14.0'),
+    ('zstd', '1.5.5'),
+    ('HTSlib', '1.18'),
+    ('kineto', '0.4.0'),
+    ('libaec', '1.0.6'),
+]
+
+# don't link to OpenSSL static libraries
+# fix for CMake Error "missing: OPENSSL_CRYPTO_LIBRARY" (if only shared OpenSSL libraries are available)
+preconfigopts = "sed -i '/OPENSSL_USE_STATIC_LIBS TRUE/d' ../dorado/cmake/OpenSSL.cmake && "
+preconfigopts += "export OPENSSL_ROOT_DIR=$EBROOTOPENSSL && "
+# link in the ssl and crypto libs, to fix:
+# undefined reference to symbol 'SSL_get_peer_certificate@@OPENSSL_1_1_0'
+preconfigopts += "sed -i 's/OpenSSL::SSL/ssl\\n    crypto/g' ../dorado/dorado/utils/CMakeLists.txt && "
+
+# don't use vendored HTSlib, use provided HTSlib dependency
+preconfigopts += "rm -r ../dorado/dorado/3rdparty/htslib/ && "
+preconfigopts += "sed -i '/add_dependencies.*htslib_project/d' ../dorado/CMakeLists.txt && "
+preconfigopts += "sed -i '/add_dependencies.*htslib_project/d' ../dorado/dorado/utils/CMakeLists.txt && "
+preconfigopts += "sed -i '/Htslib.cmake/d' ../dorado/CMakeLists.txt && "
+# link with -lhts, not -lhtslib
+preconfigopts += "sed -i 's/htslib/hts/g' ../dorado/CMakeLists.txt && "
+preconfigopts += "sed -i 's/htslib/hts/g' ../dorado/dorado/utils/CMakeLists.txt && "
+
+# disable treating warnings like errors by stripping out -Werror
+# cfr. https://github.com/nanoporetech/dorado/issues/779
+# -Wno-error option is required to fix:
+# error: void {anonymous}::convert_f32_to_f16_impl(c10::Half*, const float*, std::size_t) defined but not used
+# -Wno-error=stringop-overflow is required to fix:
+# error: writing 16 bytes into a region of size 11
+# -Wno-error=maybe-uninitialized is required to fix:
+# error: ... may be used uninitialized
+#toolchainopts = {'usempi': True, 'extra_cxxflags': "-Wno-error=unused-function -Wno-error=stringop-overflow -Wno-error=maybe-uninitialized"}
+preconfigopts += "sed -i 's/-Werror//g' ../dorado/cmake/Warnings.cmake && "
+
+configopts = "-DDORADO_INSTALL_PATH=%(installdir)s "
+configopts += "-DCUDA_TOOLKIT_ROOT_DIR=$EBROOTCUDA -DCMAKE_CUDA_COMPILER=$EBROOTCUDA/bin/nvcc "
+configopts += "-DDORADO_LIBTORCH_DIR=$EBROOTPYTORCH/lib "
+# add -pthread flag (in addition to -lpthread) to avoid linking error:
+# in function `_GLOBAL__sub_I_mutex.cc': mutex.cc:(.text.startup+0x17): undefined reference to `pthread_atfork'
+configopts += '-DCMAKE_C_FLAGS="$CFLAGS -pthread" '
+
+sanity_check_paths = {
+    'files': ['bin/dorado'],
+    'dirs': [],
+}
+
+sanity_check_commands = ["dorado basecaller --help"]
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/d/dorado/dorado-0.6.1_include-fstream.patch b/easybuild/easyconfigs/d/dorado/dorado-0.6.1_include-fstream.patch
new file mode 100644
index 00000000000..c1165f3fe5c
--- /dev/null
+++ b/easybuild/easyconfigs/d/dorado/dorado-0.6.1_include-fstream.patch
@@ -0,0 +1,27 @@
+add missing include to fix compiler errors like:
+
+    error: variable std::ofstream summary_out has initializer but incomplete type
+
+see also https://github.com/nanoporetech/dorado/pull/780
+
+author: Kenneth Hoste (HPC-UGent)
+--- dorado/dorado/cli/duplex.cpp.orig	2024-04-30 17:59:15.483935823 +0200
++++ dorado/dorado/cli/duplex.cpp	2024-04-30 17:59:34.658694274 +0200
+@@ -39,6 +39,7 @@
+ #include <cstdlib>
+ #include <exception>
+ #include <filesystem>
++#include <fstream>
+ #include <memory>
+ #include <thread>
+ #include <unordered_set>
+--- dorado/dorado/cli/demux.cpp.orig	2024-04-30 18:13:40.327122548 +0200
++++ dorado/dorado/cli/demux.cpp	2024-04-30 18:15:37.576760942 +0200
+@@ -17,6 +17,7 @@
+ #include <spdlog/spdlog.h>
+ 
+ #include <chrono>
++#include <fstream>
+ #include <memory>
+ #include <optional>
+ #include <string>
diff --git a/easybuild/easyconfigs/k/kineto/kineto-0.4.0-GCC-12.3.0.eb b/easybuild/easyconfigs/k/kineto/kineto-0.4.0-GCC-12.3.0.eb
new file mode 100644
index 00000000000..4dd6b4afdf1
--- /dev/null
+++ b/easybuild/easyconfigs/k/kineto/kineto-0.4.0-GCC-12.3.0.eb
@@ -0,0 +1,35 @@
+easyblock = 'CMakeMake'
+
+name = 'kineto'
+version = '0.4.0'
+
+homepage = 'https://github.com/pytorch/kineto'
+description = "A CPU+GPU Profiling library that provides access to timeline traces and hardware performance counters"
+
+toolchain = {'name': 'GCC', 'version': '12.3.0'}
+
+source_urls = ['https://github.com/pytorch/kineto/archive/']
+sources = [{
+    'git_config': {
+        'url': 'https://github.com/pytorch',
+        'repo_name': name,
+        'tag': 'v%(version)s',
+        'recursive': True,
+    },
+    'filename': SOURCE_TAR_GZ,
+}]
+checksums = [None]
+
+builddependencies = [
+    ('CMake', '3.26.3'),
+    ('Python', '3.11.3'),
+]
+
+start_dir = 'libkineto'
+
+sanity_check_paths = {
+    'files': ['lib/libkineto.a'],
+    'dirs': ['include/kineto'],
+}
+
+moduleclass = 'perf'

From 20c400a15d346d8ff9768b7b8cf4877e46f1f500 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 30 Apr 2024 19:38:00 +0200
Subject: [PATCH 072/835] remove extra comments w.r.t. stripping out -Werror
 from dorado 0.6.1 easyconfig

---
 .../d/dorado/dorado-0.6.1-foss-2023a-CUDA-12.1.1.eb        | 7 -------
 1 file changed, 7 deletions(-)

diff --git a/easybuild/easyconfigs/d/dorado/dorado-0.6.1-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/d/dorado/dorado-0.6.1-foss-2023a-CUDA-12.1.1.eb
index 22a9289b01a..e292bfcc18b 100644
--- a/easybuild/easyconfigs/d/dorado/dorado-0.6.1-foss-2023a-CUDA-12.1.1.eb
+++ b/easybuild/easyconfigs/d/dorado/dorado-0.6.1-foss-2023a-CUDA-12.1.1.eb
@@ -61,13 +61,6 @@ preconfigopts += "sed -i 's/htslib/hts/g' ../dorado/dorado/utils/CMakeLists.txt
 
 # disable treating warnings like errors by stripping out -Werror
 # cfr. https://github.com/nanoporetech/dorado/issues/779
-# -Wno-error option is required to fix:
-# error: void {anonymous}::convert_f32_to_f16_impl(c10::Half*, const float*, std::size_t) defined but not used
-# -Wno-error=stringop-overflow is required to fix:
-# error: writing 16 bytes into a region of size 11
-# -Wno-error=maybe-uninitialized is required to fix:
-# error: ... may be used uninitialized
-#toolchainopts = {'usempi': True, 'extra_cxxflags': "-Wno-error=unused-function -Wno-error=stringop-overflow -Wno-error=maybe-uninitialized"}
 preconfigopts += "sed -i 's/-Werror//g' ../dorado/cmake/Warnings.cmake && "
 
 configopts = "-DDORADO_INSTALL_PATH=%(installdir)s "

From bc921774d5e29dec6addf5e49d0486d2f52ae0a0 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Thu, 2 May 2024 13:24:36 +0200
Subject: [PATCH 073/835] adding easyconfigs:
 empanada-napari-1.1.0-foss-2023a.eb, empanada-dl-0.1.7-foss-2023a.eb,
 connected-components-3d-3.14.1-foss-2023a.eb,
 Albumentations-1.4.0-foss-2023a.eb, imagecodecs-2023.1.23-foss-2023a.eb

---
 .../Albumentations-1.4.0-foss-2023a.eb        | 36 ++++++++++
 ...nnected-components-3d-3.14.1-foss-2023a.eb | 26 +++++++
 .../empanada-dl-0.1.7-foss-2023a.eb           | 44 ++++++++++++
 .../empanada-napari-1.1.0-foss-2023a.eb       | 38 ++++++++++
 .../imagecodecs-2023.1.23-foss-2023a.eb       | 70 +++++++++++++++++++
 5 files changed, 214 insertions(+)
 create mode 100644 easybuild/easyconfigs/a/Albumentations/Albumentations-1.4.0-foss-2023a.eb
 create mode 100644 easybuild/easyconfigs/c/connected-components-3d/connected-components-3d-3.14.1-foss-2023a.eb
 create mode 100644 easybuild/easyconfigs/e/empanada-dl/empanada-dl-0.1.7-foss-2023a.eb
 create mode 100644 easybuild/easyconfigs/e/empanada-napari/empanada-napari-1.1.0-foss-2023a.eb
 create mode 100644 easybuild/easyconfigs/i/imagecodecs/imagecodecs-2023.1.23-foss-2023a.eb

diff --git a/easybuild/easyconfigs/a/Albumentations/Albumentations-1.4.0-foss-2023a.eb b/easybuild/easyconfigs/a/Albumentations/Albumentations-1.4.0-foss-2023a.eb
new file mode 100644
index 00000000000..36b765ffdc8
--- /dev/null
+++ b/easybuild/easyconfigs/a/Albumentations/Albumentations-1.4.0-foss-2023a.eb
@@ -0,0 +1,36 @@
+easyblock = 'PythonBundle'
+
+name = 'Albumentations'
+version = '1.4.0'
+
+homepage = 'https://albumentations.ai'
+description = "Albumentations is a Python library for fast and flexible image augmentations"
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('Python-bundle-PyPI', '2023.06'),
+    ('SciPy-bundle', '2023.07'),
+    ('PyYAML', '6.0'),
+    ('scikit-image', '0.22.0'),
+    ('scikit-learn', '1.3.1'),
+    ('OpenCV', '4.8.1', '-contrib'),
+]
+
+preinstallopts = "sed -i 's|CHOOSE_INSTALL_REQUIRES),|[]),|g' setup.py && "
+
+use_pip = True
+
+exts_list = [
+    ('qudida', '0.0.4', {
+        'checksums': ['db198e2887ab0c9aa0023e565afbff41dfb76b361f85fd5e13f780d75ba18cc8'],
+    }),
+    ('albumentations', version, {
+        'checksums': ['649f8a14896f788b356ecc70083c4fb91bedab4ff4e2b39ad217a824e189ded0'],
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'vis'
diff --git a/easybuild/easyconfigs/c/connected-components-3d/connected-components-3d-3.14.1-foss-2023a.eb b/easybuild/easyconfigs/c/connected-components-3d/connected-components-3d-3.14.1-foss-2023a.eb
new file mode 100644
index 00000000000..5a366beb6d0
--- /dev/null
+++ b/easybuild/easyconfigs/c/connected-components-3d/connected-components-3d-3.14.1-foss-2023a.eb
@@ -0,0 +1,26 @@
+easyblock = 'PythonPackage'
+
+name = 'connected-components-3d'
+version = '3.14.1'
+
+homepage = 'https://github.com/seung-lab/connected-components-3d/'
+description = """cc3d is an implementation of connected components in three dimensions using a 26, 18,
+ or 6-connected neighborhood in 3D or 4 and 8-connected in 2D."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+sources = [SOURCE_TAR_GZ]
+checksums = ['fdc4099508b734b266a42ee12534ee42e29467c28506b137e8c1edc8c7513c92']
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+]
+
+download_dep_fail = True
+use_pip = True
+sanity_pip_check = True
+
+options = {'modulename': 'cc3d'}
+
+moduleclass = 'data'
diff --git a/easybuild/easyconfigs/e/empanada-dl/empanada-dl-0.1.7-foss-2023a.eb b/easybuild/easyconfigs/e/empanada-dl/empanada-dl-0.1.7-foss-2023a.eb
new file mode 100644
index 00000000000..890161c392e
--- /dev/null
+++ b/easybuild/easyconfigs/e/empanada-dl/empanada-dl-0.1.7-foss-2023a.eb
@@ -0,0 +1,44 @@
+easyblock = 'PythonBundle'
+
+name = 'empanada-dl'
+version = '0.1.7'
+
+homepage = 'https://empanada.readthedocs.io/'
+description = "Tool for panoptic segmentation of organelles in 2D and 3D electron microscopy (EM) images."
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+ 
+dependencies = [
+    ('Python', '3.11.3'),
+    ('Python-bundle-PyPI', '2023.06'),
+    ('SciPy-bundle', '2023.07'),
+    ('numba', '0.58.1'),
+    ('OpenCV', '4.8.1', '-contrib'),
+    ('PyYAML', '6.0'),
+    ('zarr', '2.17.1'),
+    ('torchvision', '0.16.0'),
+    ('Albumentations', '1.4.0'),
+    ('dask', '2023.9.2'),
+    ('connected-components-3d', '3.14.1'),
+    ('matplotlib', '3.7.2'),
+    ('imagecodecs', '2023.1.23'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('cztile', '0.1.2', {
+        'checksums': ['3e42c4a93fd7b2df985b42e66dc3c585b3ebd9c1167e9f7e7d5c34c57697b929'],
+    }),
+    (name, version, {
+        # fix requirements - numpy version and opencv-python>=4.5.3 - pip is not aware of cv2 in OpenCV from EB
+        'preinstallopts': "sed -i 's/numpy==1.22/numpy>=1.22/g' setup.cfg && "
+                                        "sed -i '34d' setup.cfg && ",
+        'modulename': 'empanada',
+        'checksums': ['4289e69842242203be77cdb656a12fb2be4ed83816969b24a0b4eab1d67c3b91'],
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'vis'
diff --git a/easybuild/easyconfigs/e/empanada-napari/empanada-napari-1.1.0-foss-2023a.eb b/easybuild/easyconfigs/e/empanada-napari/empanada-napari-1.1.0-foss-2023a.eb
new file mode 100644
index 00000000000..4130aeda884
--- /dev/null
+++ b/easybuild/easyconfigs/e/empanada-napari/empanada-napari-1.1.0-foss-2023a.eb
@@ -0,0 +1,38 @@
+easyblock = 'PythonBundle'
+
+name = 'empanada-napari'
+version = '1.1.0'
+
+homepage = 'https://empanada.readthedocs.io/'
+description = "Panoptic segmentation algorithms for 2D and 3D electron microscopy in napari."
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('Python-bundle-PyPI', '2023.06'),
+    ('SciPy-bundle', '2023.07'),
+    ('napari', '0.4.18'),
+    ('MLflow', '2.10.2'),
+    ('openpyxl', '3.1.2'),
+    ('SimpleITK', '2.3.1'),
+    ('imagecodecs', '2023.1.23'),
+    ('Albumentations', '1.4.0'),
+    ('connected-components-3d', '3.14.1'),
+    ('empanada-dl', '0.1.7'),
+]
+
+exts_list = [
+    ('ImageHash', '4.3.1', {
+        'checksums': ['7038d1b7f9e0585beb3dd8c0a956f02b95a346c0b5f24a9e8cc03ebadaf0aa70'],
+    }),
+    (name, version, {
+        'preinstallopts': "sed -i 's/numpy==1.22/numpy>=1.22/g' setup.cfg && ",
+        'checksums': ['f4890cb6f20689933e28903dd7d43238aeae32afb53fa225bdf41d4bdcfc2c71'],
+    }),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+moduleclass = 'vis'
diff --git a/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2023.1.23-foss-2023a.eb b/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2023.1.23-foss-2023a.eb
new file mode 100644
index 00000000000..a775562db42
--- /dev/null
+++ b/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2023.1.23-foss-2023a.eb
@@ -0,0 +1,70 @@
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+# Author: Denis Kristak
+# update: Thomas Hoffmann (EMBL), Denis Kristak (Inuits), Pavel Tománek (Inuits)
+easyblock = 'PythonBundle'
+
+name = 'imagecodecs'
+version = '2023.1.23'
+
+homepage = 'https://github.com/cgohlke/imagecodecs'
+description = """Imagecodecs is a Python library that provides block-oriented, in-memory buffer transformation,
+compression, and decompression functions for use in the tifffile, czifile, zarr, and other
+scientific image input/output modules."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+local_openjpeg_maj_min = '2.5'
+dependencies = [
+    ('Python', '3.11.3'),
+    ('Python-bundle-PyPI', '2023.06'),
+    ('SciPy-bundle', '2023.07'),
+    ('matplotlib', '3.7.2'),
+    ('Brotli', '1.0.9'),
+    ('bzip2', '1.0.8'),
+    ('Blosc', '1.21.5'),
+    ('Blosc2', '2.8.0'),
+    ('CFITSIO', '4.3.0'),
+    ('CharLS', '2.4.2'),
+    ('giflib', '5.2.1'),
+    ('jxrlib', '1.1'),
+    ('LittleCMS', '2.15'),
+    ('LERC', '4.0.0'),
+    ('libaec', '1.0.6'),
+    ('libavif', '1.0.4'),
+    ('libdeflate', '1.18'),
+    ('libjpeg-turbo', '2.1.5.1'),
+    ('libjxl', '0.8.2'),
+    ('LibLZF', '3.6'),
+    ('libpng', '1.6.39'),
+    ('XZ', '5.4.2'),
+    ('LibTIFF', '4.5.0'),
+    ('libwebp', '1.3.1'),
+    ('lz4', '1.9.4'),
+    ('OpenJPEG', local_openjpeg_maj_min + '.0'),
+    ('snappy', '1.1.10'),
+    ('zlib', '1.2.13'),
+    ('zlib-ng', '2.1.6'),
+    ('Zopfli', '1.0.3'),
+    ('zfp', '1.0.1'),
+    ('zstd', '1.5.5'),
+    ('Brunsli', '0.1'),
+    ('HDF5', '1.14.0'),
+    ('h5py', '3.9.0'),
+    ('libheif', '1.17.6'),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    ('bitshuffle', '0.5.1', {
+        'checksums': ['988f224739aa6858475a4c59172968c7b51cc657d2249580c8f96848708fbae3'],
+    }),
+    (name, version, {
+        'preinstallopts': "export CPATH=$EBROOTOPENJPEG/include/openjpeg-2.5/:$CPATH && ",
+        'sources': ['%(name)s-%(version)s.tar.gz'],
+        'checksums': ['1b4591839a2f5c90467e50ebe54117cbd9be42c18864abdf85fc7743223ac5b2'],
+    }),
+]
+
+moduleclass = 'lib'

From 04e3ef3e6b243708120add03150ce68d342aa9f9 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Thu, 2 May 2024 16:29:10 +0200
Subject: [PATCH 074/835] fix whitespace and indent

---
 .../e/empanada-dl/empanada-dl-0.1.7-foss-2023a.eb            | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/easybuild/easyconfigs/e/empanada-dl/empanada-dl-0.1.7-foss-2023a.eb b/easybuild/easyconfigs/e/empanada-dl/empanada-dl-0.1.7-foss-2023a.eb
index 890161c392e..cae05720108 100644
--- a/easybuild/easyconfigs/e/empanada-dl/empanada-dl-0.1.7-foss-2023a.eb
+++ b/easybuild/easyconfigs/e/empanada-dl/empanada-dl-0.1.7-foss-2023a.eb
@@ -7,7 +7,7 @@ homepage = 'https://empanada.readthedocs.io/'
 description = "Tool for panoptic segmentation of organelles in 2D and 3D electron microscopy (EM) images."
 
 toolchain = {'name': 'foss', 'version': '2023a'}
- 
+
 dependencies = [
     ('Python', '3.11.3'),
     ('Python-bundle-PyPI', '2023.06'),
@@ -32,8 +32,7 @@ exts_list = [
     }),
     (name, version, {
         # fix requirements - numpy version and opencv-python>=4.5.3 - pip is not aware of cv2 in OpenCV from EB
-        'preinstallopts': "sed -i 's/numpy==1.22/numpy>=1.22/g' setup.cfg && "
-                                        "sed -i '34d' setup.cfg && ",
+        'preinstallopts': "sed -i 's/numpy==1.22/numpy>=1.22/g' setup.cfg && sed -i '34d' setup.cfg && ",
         'modulename': 'empanada',
         'checksums': ['4289e69842242203be77cdb656a12fb2be4ed83816969b24a0b4eab1d67c3b91'],
     }),

From a7850cc0217fea2b510379e83134ff980767c543 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Fri, 3 May 2024 10:23:41 +0200
Subject: [PATCH 075/835] add imagecodecs deps

---
 .../c/CharLS/CharLS-2.4.2-GCCcore-12.3.0.eb   | 30 +++++++++++
 .../j/jxrlib/jxrlib-1.1-GCCcore-12.3.0.eb     | 39 ++++++++++++++
 .../l/LibLZF/LibLZF-3.6-GCCcore-12.3.0.eb     | 31 +++++++++++
 .../l/libavif/libavif-1.0.4-GCCcore-12.3.0.eb | 37 +++++++++++++
 .../l/libde265/libde265-1.0.15-GCC-12.3.0.eb  | 34 ++++++++++++
 .../l/libheif/libheif-1.17.6-GCC-12.3.0.eb    | 43 +++++++++++++++
 .../l/libjxl/libjxl-0.8.2-foss-2023a.eb       | 52 +++++++++++++++++++
 .../l/libwebp/libwebp-1.3.1-GCCcore-12.3.0.eb |  1 +
 .../z/Zopfli/Zopfli-1.0.3-GCCcore-12.3.0.eb   | 36 +++++++++++++
 .../z/zfp/zfp-1.0.1-GCCcore-12.3.0.eb         | 40 ++++++++++++++
 .../z/zlib-ng/zlib-ng-2.1.6-GCCcore-12.3.0.eb | 30 +++++++++++
 11 files changed, 373 insertions(+)
 create mode 100644 easybuild/easyconfigs/c/CharLS/CharLS-2.4.2-GCCcore-12.3.0.eb
 create mode 100644 easybuild/easyconfigs/j/jxrlib/jxrlib-1.1-GCCcore-12.3.0.eb
 create mode 100644 easybuild/easyconfigs/l/LibLZF/LibLZF-3.6-GCCcore-12.3.0.eb
 create mode 100644 easybuild/easyconfigs/l/libavif/libavif-1.0.4-GCCcore-12.3.0.eb
 create mode 100644 easybuild/easyconfigs/l/libde265/libde265-1.0.15-GCC-12.3.0.eb
 create mode 100644 easybuild/easyconfigs/l/libheif/libheif-1.17.6-GCC-12.3.0.eb
 create mode 100644 easybuild/easyconfigs/l/libjxl/libjxl-0.8.2-foss-2023a.eb
 create mode 100644 easybuild/easyconfigs/z/Zopfli/Zopfli-1.0.3-GCCcore-12.3.0.eb
 create mode 100644 easybuild/easyconfigs/z/zfp/zfp-1.0.1-GCCcore-12.3.0.eb
 create mode 100644 easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.1.6-GCCcore-12.3.0.eb

diff --git a/easybuild/easyconfigs/c/CharLS/CharLS-2.4.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/c/CharLS/CharLS-2.4.2-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..9d814bdfc23
--- /dev/null
+++ b/easybuild/easyconfigs/c/CharLS/CharLS-2.4.2-GCCcore-12.3.0.eb
@@ -0,0 +1,30 @@
+easyblock = 'CMakeMake'
+
+name = 'CharLS'
+version = '2.4.2'
+
+homepage = 'https://github.com/team-charls/charls'
+description = """CharLS is a C++ implementation of the JPEG-LS standard for lossless and near-lossless image
+compression and decompression. JPEG-LS is a low-complexity image compression standard that matches JPEG 2000
+compression ratios."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://github.com/team-charls/charls/archive/']
+sources = ['%(version)s.tar.gz']
+checksums = ['d1c2c35664976f1e43fec7764d72755e6a50a80f38eca70fcc7553cad4fe19d9']
+
+builddependencies = [
+    ('binutils', '2.40'),
+    ('CMake', '3.26.3')
+]
+
+configopts = '-DBUILD_SHARED_LIBS=ON '
+
+sanity_check_paths = {
+    'files': ['lib/libcharls.%s' % SHLIB_EXT],
+    'dirs': ['include'],
+}
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/j/jxrlib/jxrlib-1.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/j/jxrlib/jxrlib-1.1-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..af33ba9e3d6
--- /dev/null
+++ b/easybuild/easyconfigs/j/jxrlib/jxrlib-1.1-GCCcore-12.3.0.eb
@@ -0,0 +1,39 @@
+##
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+# Author::   Denis Kristak (INUITS)
+# Update:    Thomas Hoffmann (EMBL), Pavel Tománek (Inuits)
+##
+
+easyblock = 'CMakeMake'
+
+name = 'jxrlib'
+version = '1.1'
+
+homepage = 'https://github.com/4creators/jxrlib'
+description = """Open source implementation of jpegxr"""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+source_urls = ['https://deb.debian.org/debian/pool/main/j/jxrlib/']
+sources = ['%(name)s_%(version)s.orig.tar.gz']
+patches = [('jxrlib-%(version)s_cmake.patch', 1)]
+checksums = [
+    {'jxrlib_1.1.orig.tar.gz': 'c7287b86780befa0914f2eeb8be2ac83e672ebd4bd16dc5574a36a59d9708303'},
+    {'jxrlib-1.1_cmake.patch': 'e96ea8b418fdab10e9cbc2f4cad95ca1f59a826ce7379c6a3192882050689a74'},
+]
+
+builddependencies = [
+    ('binutils', '2.40'),
+    ('CMake', '3.26.3'),
+]
+
+sanity_check_paths = {
+    'files': ['bin/JxrDecApp', 'bin/JxrEncApp', "lib/libjpegxr.%s" % SHLIB_EXT],
+    'dirs': [],
+}
+
+sanity_check_commands = ['JxrDecApp', 'JxrEncApp']
+
+modextrapaths = {'CPATH': 'include/jxrlib'}
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/l/LibLZF/LibLZF-3.6-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/LibLZF/LibLZF-3.6-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..45bef34f6e6
--- /dev/null
+++ b/easybuild/easyconfigs/l/LibLZF/LibLZF-3.6-GCCcore-12.3.0.eb
@@ -0,0 +1,31 @@
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+# Author: Denis Kristak
+# Update: Thomas Hoffmann (EMBL), Denis Kristak, Pavel Tománek (Inuits)
+easyblock = 'ConfigureMake'
+
+name = 'LibLZF'
+version = '3.6'
+
+homepage = 'http://oldhome.schmorp.de/marc/liblzf.html'
+description = """LibLZF is a very small data compression library. It consists of only two .c and two .h files
+and is very easy to incorporate into your own programs. The compression algorithm is very, very fast, yet still
+written in portable C."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+source_urls = ['http://dist.schmorp.de/liblzf/Attic/']
+sources = ['liblzf-%(version)s.tar.gz']
+checksums = ['9c5de01f7b9ccae40c3f619d26a7abec9986c06c36d260c179cedd04b89fb46a']
+
+builddependencies = [
+    ('binutils', '2.40'),
+]
+
+sanity_check_commands = ['lzf -h']
+
+sanity_check_paths = {
+    'files': ['bin/lzf', 'lib/liblzf.a'],
+    'dirs': ['bin', 'lib'],
+}
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/l/libavif/libavif-1.0.4-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libavif/libavif-1.0.4-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..be45830f850
--- /dev/null
+++ b/easybuild/easyconfigs/l/libavif/libavif-1.0.4-GCCcore-12.3.0.eb
@@ -0,0 +1,37 @@
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+# Author: Denis Kristak (Inuits)
+# Update: Thomas Hoffmann (EMBL), Denis Kristak (Inuits), Pavel Tománek (Inuits)
+easyblock = 'CMakeMake'
+
+name = 'libavif'
+version = '1.0.4'
+
+homepage = 'https://github.com/AOMediaCodec/libavif'
+description = """This library aims to be a friendly, portable C implementation of the AV1 Image File Format,
+as described here: https://aomediacodec.github.io/av1-avif/
+"""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+source_urls = ['https://github.com/AOMediaCodec/libavif/archive/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['dc56708c83a4b934a8af2b78f67f866ba2fb568605c7cf94312acf51ee57d146']
+
+builddependencies = [
+    ('CMake', '3.26.3'),
+    ('binutils', '2.40'),
+]
+
+dependencies = [
+    ('NASM', '2.16.01'),
+    ('Meson', '1.1.1'),
+    ('Ninja', '1.11.1'),
+    ('Rust', '1.75.0'),
+]
+
+sanity_check_paths = {
+    'files': ['lib/libavif.%s' % SHLIB_EXT, 'include/avif/avif.h'],
+    'dirs': [],
+}
+
+moduleclass = 'tools'
diff --git a/easybuild/easyconfigs/l/libde265/libde265-1.0.15-GCC-12.3.0.eb b/easybuild/easyconfigs/l/libde265/libde265-1.0.15-GCC-12.3.0.eb
new file mode 100644
index 00000000000..611c9fbcf33
--- /dev/null
+++ b/easybuild/easyconfigs/l/libde265/libde265-1.0.15-GCC-12.3.0.eb
@@ -0,0 +1,34 @@
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+# Author: Denis Kristak
+# Update: Pavel Tomának (Inuits)
+easyblock = 'CMakeMake'
+
+name = 'libde265'
+version = '1.0.15'
+
+homepage = 'https://github.com/strukturag/libde265'
+description = "libde265 is an open source implementation of the h.265 video codec"
+
+toolchain = {'name': 'GCC', 'version': '12.3.0'}
+
+source_urls = ['https://github.com/strukturag/libde265/releases/download/v%(version)s/']
+sources = [SOURCE_TAR_GZ]
+checksums = ['00251986c29d34d3af7117ed05874950c875dd9292d016be29d3b3762666511d']
+
+builddependencies = [
+    ('CMake', '3.26.3'),
+]
+
+configopts = "-DENABLE_DECODER=ON -DENABLE_ENCODER=ON"
+
+sanity_check_paths = {
+    'files': ['bin/dec265', 'bin/enc265', 'lib/libde265.%s' % SHLIB_EXT, 'lib/pkgconfig/libde265.pc'],
+    'dirs': ['include/libde265', 'lib/cmake/libde265'],
+}
+
+sanity_check_commands = [
+    "dec265 --help",
+    "enc265 --help",
+]
+
+moduleclass = 'tools'
diff --git a/easybuild/easyconfigs/l/libheif/libheif-1.17.6-GCC-12.3.0.eb b/easybuild/easyconfigs/l/libheif/libheif-1.17.6-GCC-12.3.0.eb
new file mode 100644
index 00000000000..e552b35a50b
--- /dev/null
+++ b/easybuild/easyconfigs/l/libheif/libheif-1.17.6-GCC-12.3.0.eb
@@ -0,0 +1,43 @@
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+# Author: Denis Kristak
+# Update: Pavel Tománek (Inuits)
+easyblock = 'CMakeMake'
+
+name = 'libheif'
+version = '1.17.6'
+
+homepage = 'https://github.com/strukturag/libheif'
+description = "libheif is an HEIF and AVIF file format decoder and encoder"
+
+toolchain = {'name': 'GCC', 'version': '12.3.0'}
+
+source_urls = ['https://github.com/strukturag/libheif/releases/download/v%(version)s/']
+sources = [SOURCE_TAR_GZ]
+checksums = ['8390baf4913eda0a183e132cec62b875fb2ef507ced5ddddc98dfd2f17780aee']
+
+builddependencies = [
+    ('CMake', '3.26.3'),
+]
+
+dependencies = [
+    ('libpng', '1.6.39'),
+    ('libjpeg-turbo', '2.1.5.1'),
+    ('libde265', '1.0.15'),
+    ('x265', '3.5'),
+    ('Gdk-Pixbuf', '2.42.10'),
+]
+
+# build both static and shared libraries
+configopts = [
+    "-DBUILD_SHARED_LIBS=OFF",
+    "-DBUILD_SHARED_LIBS=ON",
+]
+
+sanity_check_paths = {
+    'files': ['bin/heif-info', 'lib/libheif.a', 'lib/libheif.%s' % SHLIB_EXT, 'lib/pkgconfig/libheif.pc'],
+    'dirs': ['include/libheif'],
+}
+
+sanity_check_commands = ["heif-info --help"]
+
+moduleclass = 'tools'
diff --git a/easybuild/easyconfigs/l/libjxl/libjxl-0.8.2-foss-2023a.eb b/easybuild/easyconfigs/l/libjxl/libjxl-0.8.2-foss-2023a.eb
new file mode 100644
index 00000000000..ced70b9c630
--- /dev/null
+++ b/easybuild/easyconfigs/l/libjxl/libjxl-0.8.2-foss-2023a.eb
@@ -0,0 +1,52 @@
+easyblock = 'CMakeMake'
+
+name = 'libjxl'
+version = '0.8.2'
+
+homepage = 'https://github.com/libjxl/libjxl'
+description = "JPEG XL image format reference implementation"
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+github_account = 'libjxl'
+source_urls = [GITHUB_SOURCE]
+sources = ['v%(version)s.tar.gz']
+checksums = ['c70916fb3ed43784eb840f82f05d390053a558e2da106e40863919238fa7b420']
+
+builddependencies = [
+    ('binutils', '2.40'),
+    ('CMake', '3.26.3'),
+    ('googletest', '1.13.0'),
+    ('pkgconf', '1.9.5'),
+    ('Highway', '1.0.4'),  # Highway only has a static library
+]
+
+dependencies = [
+    ('LittleCMS', '2.15'),
+    ('Brotli', '1.0.9'),
+    ('libjpeg-turbo', '2.1.5.1'),
+    ('libpng', '1.6.39'),
+    ('zlib', '1.2.13'),
+    ('giflib', '5.2.1'),
+    ('libwebp', '1.3.1'),
+    ('OpenEXR', '3.1.7'),
+    ('gperftools', '2.12'),
+]
+
+configopts = '-DJPEGXL_WARNINGS_AS_ERRORS=OFF -DJPEGXL_ENABLE_SJPEG=OFF -DJPEGXL_ENABLE_SKCMS=OFF '
+# building man pages requires/uses asciidoc (which may be installed in OS, and may fail)
+configopts += '-DJPEGXL_ENABLE_MANPAGES=OFF '
+configopts += '-DJPEGXL_FORCE_SYSTEM_BROTLI=ON -DJPEGXL_FORCE_SYSTEM_HWY=ON '
+configopts += '-DJPEGXL_FORCE_SYSTEM_GTEST=ON -DJPEGXL_FORCE_SYSTEM_LCMS2=ON '
+
+sanity_check_paths = {
+    'files': ['bin/cjxl', 'bin/djxl', 'lib/libjxl.%s' % SHLIB_EXT],
+    'dirs': ['include/jxl'],
+}
+
+sanity_check_commands = [
+    "cjxl --help",
+    "djxl --help",
+]
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/l/libwebp/libwebp-1.3.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libwebp/libwebp-1.3.1-GCCcore-12.3.0.eb
index 4ac82164e4b..bc39f91e6af 100644
--- a/easybuild/easyconfigs/l/libwebp/libwebp-1.3.1-GCCcore-12.3.0.eb
+++ b/easybuild/easyconfigs/l/libwebp/libwebp-1.3.1-GCCcore-12.3.0.eb
@@ -10,6 +10,7 @@ webmasters and web developers can create smaller, richer images that
 make the web faster."""
 
 toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+toolchainopts = {'extra_cflags': '-fPIE'}
 
 source_urls = ['https://storage.googleapis.com/downloads.webmproject.org/releases/webp']
 sources = [SOURCELOWER_TAR_GZ]
diff --git a/easybuild/easyconfigs/z/Zopfli/Zopfli-1.0.3-GCCcore-12.3.0.eb b/easybuild/easyconfigs/z/Zopfli/Zopfli-1.0.3-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..b9186e52d16
--- /dev/null
+++ b/easybuild/easyconfigs/z/Zopfli/Zopfli-1.0.3-GCCcore-12.3.0.eb
@@ -0,0 +1,36 @@
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+# Updated: Thomas Hoffmann (EMBL), Denis Kristak (Inuits), Pavel Tománek (Inuits)
+easyblock = 'CMakeMake'
+
+name = 'Zopfli'
+version = '1.0.3'
+
+homepage = 'https://github.com/google/zopfli'
+description = """Zopfli Compression Algorithm is a compression library programmed in C to perform
+very good, but slow, deflate or zlib compression."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://github.com/google/zopfli/archive/refs/tags/']
+sources = ['%(namelower)s-%(version)s.tar.gz']
+checksums = ['e955a7739f71af37ef3349c4fa141c648e8775bceb2195be07e86f8e638814bd']
+
+builddependencies = [
+    ('CMake', '3.26.3'),
+    ('binutils', '2.40'),
+]
+
+configopts = [
+    '-DBUILD_SHARED_LIBS=ON',
+    '-DBUILD_SHARED_LIBS=OFF',
+]
+
+sanity_check_paths = {
+    'files': ['bin/zopfli', 'include/zopfli.h', 'lib/libzopfli.a', 'lib/libzopfli.%s' % SHLIB_EXT],
+    'dirs': [],
+}
+
+sanity_check_commands = ["zopfli --help"]
+
+moduleclass = 'tools'
diff --git a/easybuild/easyconfigs/z/zfp/zfp-1.0.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/z/zfp/zfp-1.0.1-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..86aae25ec6e
--- /dev/null
+++ b/easybuild/easyconfigs/z/zfp/zfp-1.0.1-GCCcore-12.3.0.eb
@@ -0,0 +1,40 @@
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+# Author: Denis Kristak
+# Update: Thomas Hoffmann (EMBL), Pavel Tománek (Inuits)
+easyblock = 'MakeCp'
+
+name = 'zfp'
+version = '1.0.1'
+
+homepage = 'https://github.com/LLNL/zfp'
+description = """zfp is a compressed format for representing multidimensional floating-point and integer arrays.
+zfp provides compressed-array classes that support high throughput read and write random access to individual array
+elements. zfp also supports serial and parallel (OpenMP and CUDA) compression of whole arrays, e.g., for applications
+that read and write large data sets to and from disk."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://github.com/LLNL/zfp/archive']
+sources = ['%(version)s.tar.gz']
+checksums = ['4984db6a55bc919831966dd17ba5e47ca7ac58668f4fd278ebd98cd2200da66f']
+
+builddependencies = [
+    ('binutils', '2.40'),
+]
+
+prebuildopts = "sed -i 's/FLAGS = -O3/FLAGS = $CFLAGS/g' Makefile && "
+buildopts = 'ZFP_WITH_OPENMP=1'
+
+runtest = 'test'
+
+files_to_copy = ['bin', 'include', 'lib']
+
+sanity_check_paths = {
+    'files': ['bin/zfp', 'bin/testzfp', 'include/zfp.h', 'lib/libzfp.a'],
+    'dirs': ['include/zfp'],
+}
+
+sanity_check_commands = ["zfp --help 2>&1 | grep 'Usage: zfp'"]
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.1.6-GCCcore-12.3.0.eb b/easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.1.6-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..67dab064f7a
--- /dev/null
+++ b/easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.1.6-GCCcore-12.3.0.eb
@@ -0,0 +1,30 @@
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+# Updated: Denis Kristak (Inuits)
+# Updated: Thomas Hoffmann (EMBL), Denis Kristak (Inuits), Pavel Tománek (Inuits)
+easyblock = 'CMakeMake'
+
+name = 'zlib-ng'
+version = '2.1.6'
+
+homepage = 'https://github.com/zlib-ng/zlib-ng'
+description = """zlib data compression library for the next generation systems"""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+source_urls = ['https://github.com/zlib-ng/zlib-ng/archive/']
+sources = ['%(version)s.tar.gz']
+checksums = ['a5d504c0d52e2e2721e7e7d86988dec2e290d723ced2307145dedd06aeb6fef2']
+
+builddependencies = [
+    ('CMake', '3.26.3'),
+    ('binutils', '2.40'),
+]
+
+configopts = ' -DZLIB_ENABLE_TESTS=True '
+
+sanity_check_paths = {
+    'files': ['include/zconf-ng.h', 'include/zlib-ng.h', 'lib/libz-ng.a', 'lib/libz-ng.%s' % SHLIB_EXT],
+    'dirs': [],
+}
+
+moduleclass = 'tools'

From 90be71a02be9a6ab1e7b606261ebafcdef08c80c Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Mon, 6 May 2024 10:57:07 +0200
Subject: [PATCH 076/835] poetry as a builddep

---
 .../Single-cell-python-bundle-2024.02-foss-2023a.eb             | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb b/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb
index 637f3767f2b..eb1ab72f5f4 100644
--- a/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb
+++ b/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb
@@ -8,7 +8,7 @@ description = """Bundle of tools for single-cell sequence analysis."""
 
 toolchain = {'name': 'foss', 'version': '2023a'}
 
-# builddependencies = [('poetry', '1.5.1')]
+builddependencies = [('poetry', '1.5.1')]
 
 dependencies = [
     ('Python', '3.11.3'),

From 9b4d4824914b770e58427ebc7e571e002a5c08ad Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Mon, 6 May 2024 13:11:54 +0200
Subject: [PATCH 077/835] delete comments to let tests pass

---
 ...e-cell-python-bundle-2024.02-foss-2023a.eb | 49 -------------------
 1 file changed, 49 deletions(-)

diff --git a/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb b/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb
index eb1ab72f5f4..d99406dc627 100644
--- a/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb
+++ b/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb
@@ -41,55 +41,6 @@ dependencies = [
     ('adjustText', '1.1.1'),  # sc_toolbox, created
 ]
 
-# DEPS to add:
-# Cassiopeia-lineage OK deps
-# Cassiopeia NO! do it again for https://pypi.org/project/cassiopeia-lineage/
-    # arrow, datapipelines,merakicommons, flake8, Pillow
-    # flake8: mccabe, pycodestyle (created for 2023a), pyflakes
-# Bbknn OK
-    # umap-learn, scikit-learn, pynndescent, annoy, flit_core 
-# Anndata2ri OK
-    # rpy2, anndata, tzlocal
-# Sc_toolbox OK
-    # adjustText (created), rich, PyYAML, questionary, cookiecutter (in eb, not 2023b), matplotlib, scanpy, seaborn, scikit-learn, typing-extensions, pypi-latest
-    # OK cookiecutter - binaryornot, python-slugify, arrow
-    # OK questionary 2.0.1 has requirement prompt_toolkit<=3.0.36,>=2.0, but you have prompt-toolkit 3.0.39 -> 3.0.36 to exts_list
-    # OK python-slugify 8.0.4 requires text-unidecode, which is not installed.
-    # questionary needs poetry-core? Seems NOT
-    # arrow 1.3.0 requires types-python-dateutil OK exts
-# Altair OK
-    # altair 5.2.0 requires toolz OK exts
-# Pertpy NO - needs scvi-tools
-    # pertpy 0.6.0 requires decoupler, which is not installed. -> Do decoupler first
-    # pertpy 0.6.0 requires ipywidgets, which is not installed.
-    # pertpy 0.6.0 requires muon, which is not installed.
-    # pertpy 0.6.0 requires numpyro, which is not installed.
-    # pertpy 0.6.0 requires ott-jax, which is not installed.
-    # pertpy 0.6.0 requires plotnine, which is not installed.
-    # pertpy 0.6.0 requires scvi-tools, which is not installed.
-    # pertpy 0.6.0 requires sparsecca, which is not installed.
-    # pertpy 0.6.0 requires toytree OK exts
-    # ('pertpy', '0.6.0', {
-    #     'checksums': ['0f9ed443a74a07ab8cd0fb6d2d06275df30ec836c161124b83c9505b7cab182b'],
-    # }),
-# tascCODA OK
-    # tasccoda 0.1.3 requires tensorflow-probability OK in scCoda -> delete TF-prob. from setup.py as in scCoda
-        # strip out tensorflow-probability as required dependency, to ensure that 'pip check' passes
-    # tasccoda 0.1.3 requires toytree OK exts
-    # toytree 2.0.5 requires toyplot OK exts
-    # toyplot 1.0.3 requires arrow OK exts
-    # toyplot 1.0.3 requires custom-inherit OK exts
-    # toyplot 1.0.3 requires multipledispatch OK exts
-    # toyplot 1.0.3 requires pypng OK exts
-    # toyplot 1.0.3 requires reportlab OK exts
-# Liana-py 
-# Harmonypy
-# Scirpy
-# CellPhoneDB
-# Decoupler
-# contrastiveVI
-# Schist
-
 exts_list = [
     ('flit_core', '3.9.0', {
         'checksums': ['72ad266176c4a3fcfab5f2930d76896059851240570ce9a98733b658cb786eba'],

From 840ea01cdb8a742abc0b141489edd3970e60ef64 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Tue, 7 May 2024 12:07:00 +0200
Subject: [PATCH 078/835] update deps of libavif

---
 .../easyconfigs/l/libavif/libavif-1.0.4-GCCcore-12.3.0.eb     | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/easybuild/easyconfigs/l/libavif/libavif-1.0.4-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libavif/libavif-1.0.4-GCCcore-12.3.0.eb
index be45830f850..e4e4ee45a1d 100644
--- a/easybuild/easyconfigs/l/libavif/libavif-1.0.4-GCCcore-12.3.0.eb
+++ b/easybuild/easyconfigs/l/libavif/libavif-1.0.4-GCCcore-12.3.0.eb
@@ -20,13 +20,13 @@ checksums = ['dc56708c83a4b934a8af2b78f67f866ba2fb568605c7cf94312acf51ee57d146']
 builddependencies = [
     ('CMake', '3.26.3'),
     ('binutils', '2.40'),
+    ('Rust', '1.75.0'),
+    ('Meson', '1.1.1'),
 ]
 
 dependencies = [
     ('NASM', '2.16.01'),
-    ('Meson', '1.1.1'),
     ('Ninja', '1.11.1'),
-    ('Rust', '1.75.0'),
 ]
 
 sanity_check_paths = {

From 990da6ebfb6b5c2de57d9845c6f2795c08bcc70f Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Tue, 7 May 2024 12:56:23 +0200
Subject: [PATCH 079/835] update deps of libavif - all deps to builddeps

---
 .../easyconfigs/l/libavif/libavif-1.0.4-GCCcore-12.3.0.eb    | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/easybuild/easyconfigs/l/libavif/libavif-1.0.4-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libavif/libavif-1.0.4-GCCcore-12.3.0.eb
index e4e4ee45a1d..a5d73b0eb00 100644
--- a/easybuild/easyconfigs/l/libavif/libavif-1.0.4-GCCcore-12.3.0.eb
+++ b/easybuild/easyconfigs/l/libavif/libavif-1.0.4-GCCcore-12.3.0.eb
@@ -22,11 +22,8 @@ builddependencies = [
     ('binutils', '2.40'),
     ('Rust', '1.75.0'),
     ('Meson', '1.1.1'),
-]
-
-dependencies = [
-    ('NASM', '2.16.01'),
     ('Ninja', '1.11.1'),
+    ('NASM', '2.16.01'),
 ]
 
 sanity_check_paths = {

From 72a229901b9801de78912563263fe94417aba5b3 Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Wed, 8 May 2024 10:17:16 +0200
Subject: [PATCH 080/835] use generic posix shell in julia wrapper

---
 easybuild/easyconfigs/j/Julia/julia.wrapper | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/j/Julia/julia.wrapper b/easybuild/easyconfigs/j/Julia/julia.wrapper
index 625ec57ab49..613b8a831f1 100755
--- a/easybuild/easyconfigs/j/Julia/julia.wrapper
+++ b/easybuild/easyconfigs/j/Julia/julia.wrapper
@@ -1,2 +1,2 @@
-#!/bin/bash
+#!/bin/sh
 LD_LIBRARY_PATH="$EBROOTJULIA/lib:$EBROOTJULIA/lib/julia:$LD_LIBRARY_PATH" julia.bin "$@"

From 2e9329d58d1b2b309400c03612b918787540ceb4 Mon Sep 17 00:00:00 2001
From: Alexander Grund <alexander.grund@tu-dresden.de>
Date: Wed, 8 May 2024 16:57:35 +0200
Subject: [PATCH 081/835] Use Bazel --distdir

Don't unpack the archives just put them into a folder
Allows to verify that we used the right ones as Bazel checks the name
and checksum.
---
 .../jax/jax-0.4.25-gfbf-2023a-CUDA-12.1.1.eb  | 11 +++--
 .../jax-0.4.25_fix-pybind11-systemlib.patch   | 46 +++++++++++++------
 2 files changed, 40 insertions(+), 17 deletions(-)

diff --git a/easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a-CUDA-12.1.1.eb
index fcc807a7055..68ab99486f2 100644
--- a/easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a-CUDA-12.1.1.eb
+++ b/easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a-CUDA-12.1.1.eb
@@ -40,8 +40,9 @@ dependencies = [
 # note: this *must* be the exact same commit as used in third_party/{xla,"other"}/workspace.bzl
 local_xla_commit = '4ccfe33c71665ddcbca5b127fefe8baa3ed632d4'
 local_tfrt_commit = '0aeefb1660d7e37964b2bb71b1f518096bda9a25'
-local_repo_opt = '--bazel_options="--override_repository=xla=%%(builddir)s/xla-%s" ' % local_xla_commit
-local_repo_opt += '--bazel_options="--override_repository=tf_runtime=%%(builddir)s/runtime-%s" ' % local_tfrt_commit
+
+local_extract_cmd = 'cp %s %(builddir)s/archives'
+local_repo_opt = '--bazel_options="--distdir=%(builddir)s/archives" '
 local_repo_opt += '--bazel_options="--action_env=TF_SYSTEM_LIBS=pybind11" '
 local_repo_opt += '--bazel_options="--action_env=CPATH=$EBROOTPYBIND11/include" '
 
@@ -94,10 +95,12 @@ components = [
             {
                 'download_filename': '%s.tar.gz' % local_xla_commit,
                 'filename': 'xla-%s.tar.gz' % local_xla_commit,
+                'extract_cmd': local_extract_cmd,
             },
             {
                 'download_filename': '%s.tar.gz' % local_tfrt_commit,
                 'filename': 'tf_runtime-%s.tar.gz' % local_tfrt_commit,
+                'extract_cmd': local_extract_cmd,
             },
         ],
         'source_urls': [
@@ -105,7 +108,7 @@ components = [
             'https://github.com/tensorflow/runtime/archive',
             'https://github.com/openxla/xla/archive'
         ],
-        'patches': [('jax-0.4.25_fix-pybind11-systemlib.patch', '../xla-' + local_xla_commit)],
+        'patches': ['jax-0.4.25_fix-pybind11-systemlib.patch'],
         'checksums': [
             {'jaxlib-v0.4.25.tar.gz':
              'fc1197c401924942eb14185a61688d0c476e3e81ff71f9dc95e620b57c06eec8'},
@@ -114,7 +117,7 @@ components = [
             {'tf_runtime-0aeefb1660d7e37964b2bb71b1f518096bda9a25.tar.gz':
              'a3df827d7896774cb1d80bf4e1c79ab05c268f29bd4d3db1fb5a4b9c2079d8e3'},
             {'jax-0.4.25_fix-pybind11-systemlib.patch':
-             'ec93de5628e4d40d3378b92784f7d1e5b0b43bd207a86badeffd44a42e0b1d47'},
+             'daad5b726d1a138431b05eb60ecf4c89c7b5148eb939721800bdf43d804ca033'},
         ],
         'start_dir': 'jax-jaxlib-v%(version)s',
         # Avoid warning (treated as error) in upb/table.c
diff --git a/easybuild/easyconfigs/j/jax/jax-0.4.25_fix-pybind11-systemlib.patch b/easybuild/easyconfigs/j/jax/jax-0.4.25_fix-pybind11-systemlib.patch
index 620acb11d0a..c404ee6917f 100644
--- a/easybuild/easyconfigs/j/jax/jax-0.4.25_fix-pybind11-systemlib.patch
+++ b/easybuild/easyconfigs/j/jax/jax-0.4.25_fix-pybind11-systemlib.patch
@@ -2,17 +2,37 @@ Add missing value for System Pybind11 Bazel config
 
 Author: Alexander Grund (TU Dresden)
 
---- xla-orig/third_party/tsl/third_party/systemlibs/pybind11.BUILD
-+++ xla-4ccfe33c71665ddcbca5b127fefe8baa3ed632d4/third_party/tsl/third_party/systemlibs/pybind11.BUILD
-@@ -6,3 +6,10 @@
-         "@tsl//third_party/python_runtime:headers",
-     ],
- )
-+
-+# Needed by pybind11_bazel.
-+config_setting(
-+    name = "osx",
-+    constraint_values = ["@platforms//os:osx"],
-+)
-+
+diff --git a/third_party/xla/fix-pybind11-systemlib.patch b/third_party/xla/fix-pybind11-systemlib.patch
+new file mode 100644
+index 000000000..68bd2063d
+--- /dev/null
++++ b/third_party/xla/fix-pybind11-systemlib.patch
+@@ -0,0 +1,13 @@
++--- xla-orig/third_party/tsl/third_party/systemlibs/pybind11.BUILD
+++++ xla-4ccfe33c71665ddcbca5b127fefe8baa3ed632d4/third_party/tsl/third_party/systemlibs/pybind11.BUILD
++@@ -6,3 +6,10 @@
++         "@tsl//third_party/python_runtime:headers",
++     ],
++ )
+++
+++# Needed by pybind11_bazel.
+++config_setting(
+++    name = "osx",
+++    constraint_values = ["@platforms//os:osx"],
+++)
+++
+diff --git a/third_party/xla/workspace.bzl b/third_party/xla/workspace.bzl
+index ebc8d9838..125e1c173 100644
+--- a/third_party/xla/workspace.bzl
++++ b/third_party/xla/workspace.bzl
+@@ -29,6 +29,9 @@ def repo():
+         sha256 = XLA_SHA256,
+         strip_prefix = "xla-{commit}".format(commit = XLA_COMMIT),
+         urls = tf_mirror_urls("https://github.com/openxla/xla/archive/{commit}.tar.gz".format(commit = XLA_COMMIT)),
++        patch_file = [
++            "//third_party/xla:fix-pybind11-systemlib.patch",
++        ],
+     )
+ 
+     # For development, one often wants to make changes to the TF repository as well
 

From 97b22a899b4adcb9aa0860b79f383e124d45cf41 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Thu, 9 May 2024 15:15:20 +0200
Subject: [PATCH 082/835] update comment for tascCODA deletion in setup.py

---
 .../Single-cell-python-bundle-2024.02-foss-2023a.eb              | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb b/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb
index d99406dc627..28a63c085a6 100644
--- a/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb
+++ b/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb
@@ -121,6 +121,7 @@ exts_list = [
         'checksums': ['7be04ca310067e0e9737449700d6ab1b68b4379b64e2d22f2f7697a70030ceb0'],
     }),
     ('tascCODA', '0.1.3', {
+        # strip out tensorflow-probability as required dependency, to ensure that 'pip check' passes
         'preinstallopts': "sed -i '28d' setup.py && ",
         'checksums': ['8c12ddccb72c41c96c6a5abceb52e7a76f439a9ab94fb092aa86ee3c1292383a'],
     }),

From d8d949705db11aae374ae24fa9a5db1fc07c6432 Mon Sep 17 00:00:00 2001
From: Adam Huffman <12435+verdurin@users.noreply.github.com>
Date: Thu, 9 May 2024 15:48:19 +0000
Subject: [PATCH 083/835] adding easyconfigs: fsm-lite-1.0-GCCcore-12.2.0.eb,
 sdsl-lite-2.0.3-GCCcore-12.2.0.eb

---
 .../f/fsm-lite/fsm-lite-1.0-GCCcore-12.2.0.eb | 34 +++++++++++++++++++
 .../sdsl-lite-2.0.3-GCCcore-12.2.0.eb         | 31 +++++++++++++++++
 2 files changed, 65 insertions(+)
 create mode 100644 easybuild/easyconfigs/f/fsm-lite/fsm-lite-1.0-GCCcore-12.2.0.eb
 create mode 100644 easybuild/easyconfigs/s/sdsl-lite/sdsl-lite-2.0.3-GCCcore-12.2.0.eb

diff --git a/easybuild/easyconfigs/f/fsm-lite/fsm-lite-1.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/f/fsm-lite/fsm-lite-1.0-GCCcore-12.2.0.eb
new file mode 100644
index 00000000000..563eba10e7c
--- /dev/null
+++ b/easybuild/easyconfigs/f/fsm-lite/fsm-lite-1.0-GCCcore-12.2.0.eb
@@ -0,0 +1,34 @@
+# This easyconfig was created by the BEAR Software team at the University of Birmingham.
+easyblock = "MakeCp"
+
+name = 'fsm-lite'
+version = '1.0'
+
+homepage = "https://github.com/nvalimak/fsm-lite"
+description = """A singe-core implemetation of frequency-based substring mining."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+
+source_urls = ['https://github.com/nvalimak/%(name)s/archive/']
+sources = ['v%(version)s-stable.tar.gz']
+checksums = ['f781a9fbab5265bd09b3b5b7e1cba904582ec201c3d30baed36e28a03de3ac61']
+
+builddependencies = [
+    ('CMake', '3.24.3'),
+    ('binutils', '2.39'),
+]
+
+dependencies = [
+    ('sdsl-lite', '2.0.3'),
+]
+
+prebuildopts = "sed -i '1s/.*/SDSL_INSTALL_PREFIX=${EBROOTSDSLMINLITE}/' Makefile && make depend &&"
+
+files_to_copy = [(['fsm-lite'], 'bin')]
+
+sanity_check_paths = {
+    'files': ['bin/fsm-lite'],
+    'dirs': [],
+}
+
+moduleclass = 'tools'
diff --git a/easybuild/easyconfigs/s/sdsl-lite/sdsl-lite-2.0.3-GCCcore-12.2.0.eb b/easybuild/easyconfigs/s/sdsl-lite/sdsl-lite-2.0.3-GCCcore-12.2.0.eb
new file mode 100644
index 00000000000..d4bda3a4a9e
--- /dev/null
+++ b/easybuild/easyconfigs/s/sdsl-lite/sdsl-lite-2.0.3-GCCcore-12.2.0.eb
@@ -0,0 +1,31 @@
+# This easyconfig was created by the BEAR Software team at the University of Birmingham.
+easyblock = "CMakeMake"
+
+name = 'sdsl-lite'
+version = '2.0.3'
+
+homepage = "https://github.com/simongog/sdsl-lite"
+description = """The Succinct Data Structure Library (SDSL) is a powerful and flexible C++11 library implementing
+ succinct data structures. In total, the library contains the highlights of 40 research publications. Succinct
+ data structures can represent an object (such as a bitvector or a tree) in space close to the information-theoretic
+ lower bound of the object while supporting operations of the original object efficiently. The theoretical time
+ complexity of an operation performed on the classical data structure and the equivalent succinct data structure
+ are (most of the time) identical."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+
+source_urls = ['https://github.com/simongog/%(name)s/archive/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['08ece40ce44041906bfa425af81a20a8071d187285f674debd8816c2e3113c2f']
+
+builddependencies = [
+    ('CMake', '3.24.3'),
+    ('binutils', '2.39'),
+]
+
+sanity_check_paths = {
+    'files': ['lib/libdivsufsort64.a', 'lib/libdivsufsort.a', 'lib/libsdsl.a', 'include/divsufsort64.h'],
+    'dirs': ['include/sdsl'],
+}
+
+moduleclass = 'tools'

From 116ab0c2ff2f8bde4782440b4c439c41cc86f27d Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Fri, 10 May 2024 10:22:09 +0200
Subject: [PATCH 084/835] update checksum of julia.wrapper

---
 easybuild/easyconfigs/j/Julia/Julia-1.10.0-linux-x86_64.eb | 2 +-
 easybuild/easyconfigs/j/Julia/Julia-1.6.0-linux-aarch64.eb | 2 +-
 easybuild/easyconfigs/j/Julia/Julia-1.6.5-linux-x86_64.eb  | 2 +-
 easybuild/easyconfigs/j/Julia/Julia-1.6.6-linux-x86_64.eb  | 2 +-
 easybuild/easyconfigs/j/Julia/Julia-1.6.7-linux-x86_64.eb  | 2 +-
 easybuild/easyconfigs/j/Julia/Julia-1.7.0-linux-x86_64.eb  | 2 +-
 easybuild/easyconfigs/j/Julia/Julia-1.7.1-linux-x86_64.eb  | 2 +-
 easybuild/easyconfigs/j/Julia/Julia-1.7.2-linux-x86_64.eb  | 2 +-
 easybuild/easyconfigs/j/Julia/Julia-1.7.3-linux-x86_64.eb  | 2 +-
 easybuild/easyconfigs/j/Julia/Julia-1.8.0-linux-x86_64.eb  | 2 +-
 easybuild/easyconfigs/j/Julia/Julia-1.8.2-linux-x86_64.eb  | 2 +-
 easybuild/easyconfigs/j/Julia/Julia-1.8.5-linux-x86_64.eb  | 2 +-
 easybuild/easyconfigs/j/Julia/Julia-1.9.0-linux-x86_64.eb  | 2 +-
 easybuild/easyconfigs/j/Julia/Julia-1.9.2-linux-x86_64.eb  | 2 +-
 easybuild/easyconfigs/j/Julia/Julia-1.9.3-linux-x86_64.eb  | 2 +-
 15 files changed, 15 insertions(+), 15 deletions(-)

diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.10.0-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.10.0-linux-x86_64.eb
index a7320c2365f..6081619a331 100644
--- a/easybuild/easyconfigs/j/Julia/Julia-1.10.0-linux-x86_64.eb
+++ b/easybuild/easyconfigs/j/Julia/Julia-1.10.0-linux-x86_64.eb
@@ -14,7 +14,7 @@ sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz']
 patches = [('julia.wrapper', 'bin/')]
 checksums = [
     {'julia-1.10.0-linux-x86_64.tar.gz': 'a7298207f72f2b27b2ab1ce392a6ea37afbd1fbee0f1f8d190b054dcaba878fe'},
-    {'julia.wrapper': 'a36a3e0cb98ab4d2b05e0ca8f0bf2724baafbd669a0db318a00e40737d2f02f9'},
+    {'julia.wrapper': 'd10aeaff53cca9875f7b0ce9218eae3bd21870b654e26c4c52aa8bfcc9da702d'},
 ]
 
 # install wrapper with linking safeguards for Julia libraries
diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.6.0-linux-aarch64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.6.0-linux-aarch64.eb
index dee7717b5a0..17abf7d929c 100644
--- a/easybuild/easyconfigs/j/Julia/Julia-1.6.0-linux-aarch64.eb
+++ b/easybuild/easyconfigs/j/Julia/Julia-1.6.0-linux-aarch64.eb
@@ -18,7 +18,7 @@ sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz']
 patches = [('julia.wrapper', 'bin/')]
 checksums = [
     {'julia-1.6.0-linux-aarch64.tar.gz': '0f496972d26cea88151204d03e6bd87702aa1ff983de3b1e4f320c48ef67325f'},
-    {'julia.wrapper': 'a36a3e0cb98ab4d2b05e0ca8f0bf2724baafbd669a0db318a00e40737d2f02f9'},
+    {'julia.wrapper': 'd10aeaff53cca9875f7b0ce9218eae3bd21870b654e26c4c52aa8bfcc9da702d'},
 ]
 
 # install wrapper with linking safeguards for Julia libraries
diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.6.5-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.6.5-linux-x86_64.eb
index 9bf44e78f13..dd9ad4890db 100644
--- a/easybuild/easyconfigs/j/Julia/Julia-1.6.5-linux-x86_64.eb
+++ b/easybuild/easyconfigs/j/Julia/Julia-1.6.5-linux-x86_64.eb
@@ -22,7 +22,7 @@ sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz']
 patches = [('julia.wrapper', 'bin/')]
 checksums = [
     {'julia-1.6.5-linux-x86_64.tar.gz': 'b8fe23ee547254a2fe14be587284ed77c78c06c2d8e9aad5febce0d21cab8e2c'},
-    {'julia.wrapper': 'a36a3e0cb98ab4d2b05e0ca8f0bf2724baafbd669a0db318a00e40737d2f02f9'},
+    {'julia.wrapper': 'd10aeaff53cca9875f7b0ce9218eae3bd21870b654e26c4c52aa8bfcc9da702d'},
 ]
 
 # install wrapper with linking safeguards for Julia libraries
diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.6.6-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.6.6-linux-x86_64.eb
index 6430a94ca59..03bdc16da5a 100644
--- a/easybuild/easyconfigs/j/Julia/Julia-1.6.6-linux-x86_64.eb
+++ b/easybuild/easyconfigs/j/Julia/Julia-1.6.6-linux-x86_64.eb
@@ -22,7 +22,7 @@ sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz']
 patches = [('julia.wrapper', 'bin/')]
 checksums = [
     {'julia-1.6.6-linux-x86_64.tar.gz': 'c25ff71a4242207ab2681a0fcc5df50014e9d99f814e77cacbc5027e20514945'},
-    {'julia.wrapper': 'a36a3e0cb98ab4d2b05e0ca8f0bf2724baafbd669a0db318a00e40737d2f02f9'},
+    {'julia.wrapper': 'd10aeaff53cca9875f7b0ce9218eae3bd21870b654e26c4c52aa8bfcc9da702d'},
 ]
 
 # install wrapper with linking safeguards for Julia libraries
diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.6.7-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.6.7-linux-x86_64.eb
index 6935d34d151..7046809d33d 100644
--- a/easybuild/easyconfigs/j/Julia/Julia-1.6.7-linux-x86_64.eb
+++ b/easybuild/easyconfigs/j/Julia/Julia-1.6.7-linux-x86_64.eb
@@ -22,7 +22,7 @@ sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz']
 patches = [('julia.wrapper', 'bin/')]
 checksums = [
     {'julia-1.6.7-linux-x86_64.tar.gz': '6c4522d595e4cbcd00157ac458a72f8aec01757053d2073f99daa39e442b2a36'},
-    {'julia.wrapper': 'a36a3e0cb98ab4d2b05e0ca8f0bf2724baafbd669a0db318a00e40737d2f02f9'},
+    {'julia.wrapper': 'd10aeaff53cca9875f7b0ce9218eae3bd21870b654e26c4c52aa8bfcc9da702d'},
 ]
 
 # install wrapper with linking safeguards for Julia libraries
diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.7.0-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.7.0-linux-x86_64.eb
index 45655ab233d..39df361aa99 100644
--- a/easybuild/easyconfigs/j/Julia/Julia-1.7.0-linux-x86_64.eb
+++ b/easybuild/easyconfigs/j/Julia/Julia-1.7.0-linux-x86_64.eb
@@ -22,7 +22,7 @@ sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz']
 patches = [('julia.wrapper', 'bin/')]
 checksums = [
     {'julia-1.7.0-linux-x86_64.tar.gz': '7299f3a638aec5e0b9e14eaf0e6221c4fe27189aa0b38ac5a36f03f0dc4c0d40'},
-    {'julia.wrapper': 'a36a3e0cb98ab4d2b05e0ca8f0bf2724baafbd669a0db318a00e40737d2f02f9'},
+    {'julia.wrapper': 'd10aeaff53cca9875f7b0ce9218eae3bd21870b654e26c4c52aa8bfcc9da702d'},
 ]
 
 # install wrapper with linking safeguards for Julia libraries
diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.7.1-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.7.1-linux-x86_64.eb
index 3dbb49f7345..87f911a7da0 100644
--- a/easybuild/easyconfigs/j/Julia/Julia-1.7.1-linux-x86_64.eb
+++ b/easybuild/easyconfigs/j/Julia/Julia-1.7.1-linux-x86_64.eb
@@ -22,7 +22,7 @@ sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz']
 patches = [('julia.wrapper', 'bin/')]
 checksums = [
     {'julia-1.7.1-linux-x86_64.tar.gz': '44658e9c7b45e2b9b5b59239d190cca42de05c175ea86bc346c294a8fe8d9f11'},
-    {'julia.wrapper': 'a36a3e0cb98ab4d2b05e0ca8f0bf2724baafbd669a0db318a00e40737d2f02f9'},
+    {'julia.wrapper': 'd10aeaff53cca9875f7b0ce9218eae3bd21870b654e26c4c52aa8bfcc9da702d'},
 ]
 
 # install wrapper with linking safeguards for Julia libraries
diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.7.2-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.7.2-linux-x86_64.eb
index 1742ac0b42b..5e48ff39fbe 100644
--- a/easybuild/easyconfigs/j/Julia/Julia-1.7.2-linux-x86_64.eb
+++ b/easybuild/easyconfigs/j/Julia/Julia-1.7.2-linux-x86_64.eb
@@ -22,7 +22,7 @@ sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz']
 patches = [('julia.wrapper', 'bin/')]
 checksums = [
     {'julia-1.7.2-linux-x86_64.tar.gz': 'a75244724f3b2de0e7249c861fbf64078257c16fb4203be78f1cf4dd5973ba95'},
-    {'julia.wrapper': 'a36a3e0cb98ab4d2b05e0ca8f0bf2724baafbd669a0db318a00e40737d2f02f9'},
+    {'julia.wrapper': 'd10aeaff53cca9875f7b0ce9218eae3bd21870b654e26c4c52aa8bfcc9da702d'},
 ]
 
 # install wrapper with linking safeguards for Julia libraries
diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.7.3-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.7.3-linux-x86_64.eb
index 61ab7eb2bdf..0f1649345d9 100644
--- a/easybuild/easyconfigs/j/Julia/Julia-1.7.3-linux-x86_64.eb
+++ b/easybuild/easyconfigs/j/Julia/Julia-1.7.3-linux-x86_64.eb
@@ -22,7 +22,7 @@ sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz']
 patches = [('julia.wrapper', 'bin/')]
 checksums = [
     {'julia-1.7.3-linux-x86_64.tar.gz': '9b2f4fa12d92b4dcc5d11dc66fb118c47681a76d3df8da064cc97573f2f5c739'},
-    {'julia.wrapper': 'a36a3e0cb98ab4d2b05e0ca8f0bf2724baafbd669a0db318a00e40737d2f02f9'},
+    {'julia.wrapper': 'd10aeaff53cca9875f7b0ce9218eae3bd21870b654e26c4c52aa8bfcc9da702d'},
 ]
 
 # install wrapper with linking safeguards for Julia libraries
diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.8.0-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.8.0-linux-x86_64.eb
index 77e3fee2212..701b6bcbde7 100644
--- a/easybuild/easyconfigs/j/Julia/Julia-1.8.0-linux-x86_64.eb
+++ b/easybuild/easyconfigs/j/Julia/Julia-1.8.0-linux-x86_64.eb
@@ -22,7 +22,7 @@ sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz']
 patches = [('julia.wrapper', 'bin/')]
 checksums = [
     {'julia-1.8.0-linux-x86_64.tar.gz': 'e80d732ccb7f79e000d798cb8b656dc3641ab59516d6e4e52e16765017892a00'},
-    {'julia.wrapper': 'a36a3e0cb98ab4d2b05e0ca8f0bf2724baafbd669a0db318a00e40737d2f02f9'},
+    {'julia.wrapper': 'd10aeaff53cca9875f7b0ce9218eae3bd21870b654e26c4c52aa8bfcc9da702d'},
 ]
 
 # install wrapper with linking safeguards for Julia libraries
diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.8.2-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.8.2-linux-x86_64.eb
index fd619b4de39..c85c5bdc291 100644
--- a/easybuild/easyconfigs/j/Julia/Julia-1.8.2-linux-x86_64.eb
+++ b/easybuild/easyconfigs/j/Julia/Julia-1.8.2-linux-x86_64.eb
@@ -22,7 +22,7 @@ sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz']
 patches = [('julia.wrapper', 'bin/')]
 checksums = [
     {'julia-1.8.2-linux-x86_64.tar.gz': '671cf3a450b63a717e1eedd7f69087e3856f015b2e146cb54928f19a3c05e796'},
-    {'julia.wrapper': 'a36a3e0cb98ab4d2b05e0ca8f0bf2724baafbd669a0db318a00e40737d2f02f9'},
+    {'julia.wrapper': 'd10aeaff53cca9875f7b0ce9218eae3bd21870b654e26c4c52aa8bfcc9da702d'},
 ]
 
 # install wrapper with linking safeguards for Julia libraries
diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.8.5-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.8.5-linux-x86_64.eb
index d69227cc952..6e60397495d 100644
--- a/easybuild/easyconfigs/j/Julia/Julia-1.8.5-linux-x86_64.eb
+++ b/easybuild/easyconfigs/j/Julia/Julia-1.8.5-linux-x86_64.eb
@@ -22,7 +22,7 @@ sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz']
 patches = [('julia.wrapper', 'bin/')]
 checksums = [
     {'julia-1.8.5-linux-x86_64.tar.gz': 'e71a24816e8fe9d5f4807664cbbb42738f5aa9fe05397d35c81d4c5d649b9d05'},
-    {'julia.wrapper': 'a36a3e0cb98ab4d2b05e0ca8f0bf2724baafbd669a0db318a00e40737d2f02f9'},
+    {'julia.wrapper': 'd10aeaff53cca9875f7b0ce9218eae3bd21870b654e26c4c52aa8bfcc9da702d'},
 ]
 
 postinstallcmds = ["cd %(installdir)s/bin && mv julia julia.bin && mv julia.wrapper julia"]
diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.9.0-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.9.0-linux-x86_64.eb
index 7469924860b..2e89fb8640b 100644
--- a/easybuild/easyconfigs/j/Julia/Julia-1.9.0-linux-x86_64.eb
+++ b/easybuild/easyconfigs/j/Julia/Julia-1.9.0-linux-x86_64.eb
@@ -22,7 +22,7 @@ sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz']
 patches = [('julia.wrapper', 'bin/')]
 checksums = [
     {'julia-1.9.0-linux-x86_64.tar.gz': '00c614466ef9809c2eb23480e38d196a2c577fff2730c4f83d135b913d473359'},
-    {'julia.wrapper': 'a36a3e0cb98ab4d2b05e0ca8f0bf2724baafbd669a0db318a00e40737d2f02f9'},
+    {'julia.wrapper': 'd10aeaff53cca9875f7b0ce9218eae3bd21870b654e26c4c52aa8bfcc9da702d'},
 ]
 
 # install wrapper with linking safeguards for Julia libraries
diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.9.2-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.9.2-linux-x86_64.eb
index 01939dc25f7..fef2c5a347c 100644
--- a/easybuild/easyconfigs/j/Julia/Julia-1.9.2-linux-x86_64.eb
+++ b/easybuild/easyconfigs/j/Julia/Julia-1.9.2-linux-x86_64.eb
@@ -22,7 +22,7 @@ sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz']
 patches = [('julia.wrapper', 'bin/')]
 checksums = [
     {'julia-1.9.2-linux-x86_64.tar.gz': '4c2d799f442d7fe718827b19da2bacb72ea041b9ce55f24eee7b1313f57c4383'},
-    {'julia.wrapper': 'a36a3e0cb98ab4d2b05e0ca8f0bf2724baafbd669a0db318a00e40737d2f02f9'},
+    {'julia.wrapper': 'd10aeaff53cca9875f7b0ce9218eae3bd21870b654e26c4c52aa8bfcc9da702d'},
 ]
 
 postinstallcmds = ["cd %(installdir)s/bin && mv julia julia.bin && mv julia.wrapper julia"]
diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.9.3-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.9.3-linux-x86_64.eb
index d5e1511d63e..1d0f85d9874 100644
--- a/easybuild/easyconfigs/j/Julia/Julia-1.9.3-linux-x86_64.eb
+++ b/easybuild/easyconfigs/j/Julia/Julia-1.9.3-linux-x86_64.eb
@@ -22,7 +22,7 @@ sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz']
 patches = [('julia.wrapper', 'bin/')]
 checksums = [
     {'julia-1.9.3-linux-x86_64.tar.gz': 'd76670cc9ba3e0fd4c1545dd3d00269c0694976a1176312795ebce1692d323d1'},
-    {'julia.wrapper': 'a36a3e0cb98ab4d2b05e0ca8f0bf2724baafbd669a0db318a00e40737d2f02f9'},
+    {'julia.wrapper': 'd10aeaff53cca9875f7b0ce9218eae3bd21870b654e26c4c52aa8bfcc9da702d'},
 ]
 
 # install wrapper with linking safeguards for Julia libraries

From a563666c80665dcb70cbf748bf5f487788db3dc0 Mon Sep 17 00:00:00 2001
From: crivella <davide.grassano@epfl.ch>
Date: Fri, 10 May 2024 16:38:40 +0200
Subject: [PATCH 085/835] QE-gipaw_fix

---
 .../q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-foss-2023a.eb  | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-foss-2023a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-foss-2023a.eb
index 58193947e6c..ff3277e87b3 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-foss-2023a.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3.1-foss-2023a.eb
@@ -22,7 +22,9 @@ local_fox_hash = "3453648e6837658b747b895bb7bef4b1ed2eac40"
 # Different from the one at tag qe-7.3.1 because of:
 # https://gitlab.com/QEF/q-e/-/issues/666
 local_d3q_hash = "de4718351e7bbb9d1d12aad2b7ca232d06775b83"
-local_qe_gipaw_hash = "75b01b694c9ba4df55d294cacc27cf28591b2161"
+# Different from the one at tag qe-7.3.1 because of:
+# https://github.com/dceresoli/qe-gipaw/issues/19
+local_qe_gipaw_hash = "79d3a03b7bdc4325e66f3fad02a24c6e6e3e5806"
 local_qmcpack_hash = "f72ab25fa4ea755c1b4b230ae8074b47d5509c70"
 local_w90_hash = "1d6b187374a2d50b509e5e79e2cab01a79ff7ce1"
 
@@ -134,7 +136,8 @@ dependencies = [
 # https://github.com/anharmonic/d3q/issues/15
 build_shared_libs = False
 with_scalapack = True
-with_gipaw = False  # https://github.com/dceresoli/qe-gipaw/issues/19
+with_fox = True
+with_gipaw = True
 with_d3q = True
 with_qmcpack = True
 

From fb5442b406d70f8cfe51b86f4e0cfe5d7b1f3868 Mon Sep 17 00:00:00 2001
From: Adam Huffman <12435+verdurin@users.noreply.github.com>
Date: Fri, 10 May 2024 16:48:39 +0000
Subject: [PATCH 086/835] adding easyconfigs: bcl-convert-4.2.7-2el7.x86_64.eb

---
 .../bcl-convert-4.2.7-2el7.x86_64.eb          | 24 +++++++++++++++++++
 1 file changed, 24 insertions(+)
 create mode 100644 easybuild/easyconfigs/b/bcl-convert/bcl-convert-4.2.7-2el7.x86_64.eb

diff --git a/easybuild/easyconfigs/b/bcl-convert/bcl-convert-4.2.7-2el7.x86_64.eb b/easybuild/easyconfigs/b/bcl-convert/bcl-convert-4.2.7-2el7.x86_64.eb
new file mode 100644
index 00000000000..db6e1f9feee
--- /dev/null
+++ b/easybuild/easyconfigs/b/bcl-convert/bcl-convert-4.2.7-2el7.x86_64.eb
@@ -0,0 +1,24 @@
+easyblock = 'Rpm'
+
+name = 'bcl-convert'
+version = '4.2.7-2'
+versionsuffix = 'el7.x86_64'
+
+homepage = 'https://support.illumina.com/sequencing/sequencing_software/bcl-convert.html'
+description = """The Illumina BCL Convert v4.0 is a standalone local software app that converts the
+ Binary Base Call (BCL) files produced by Illumina sequencing systems to FASTQ files."""
+
+toolchain = SYSTEM
+
+source_urls = ['https://webdata.illumina.com/downloads/software/bcl-convert/']
+sources = ['bcl-convert-%(version)s.%(versionsuffix)s.rpm']
+checksums = ['ea508d763dc27d30d1a34f6a38d8da31ea67797d7b4971e8c10677bc48539565']
+
+sanity_check_paths = {
+    'files': ['usr/bin/bcl-convert'],
+    'dirs': [],
+}
+
+sanity_check_commands = ["bcl-convert --help"]
+
+moduleclass = 'bio'

From aff935cce22303e511e1a06bf4e1cf8dd1ab6e8f Mon Sep 17 00:00:00 2001
From: tanmoy1989 <mssmzs@login01.avon.hpc>
Date: Tue, 21 May 2024 12:36:40 +0100
Subject: [PATCH 087/835] adding easyconfigs: PLY-3.11-GCCcore-13.2.0.eb

---
 .../p/PLY/PLY-3.11-GCCcore-13.2.0.eb          | 22 +++++++++++++++++++
 1 file changed, 22 insertions(+)
 create mode 100644 easybuild/easyconfigs/p/PLY/PLY-3.11-GCCcore-13.2.0.eb

diff --git a/easybuild/easyconfigs/p/PLY/PLY-3.11-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/PLY/PLY-3.11-GCCcore-13.2.0.eb
new file mode 100644
index 00000000000..74ab008fb99
--- /dev/null
+++ b/easybuild/easyconfigs/p/PLY/PLY-3.11-GCCcore-13.2.0.eb
@@ -0,0 +1,22 @@
+easyblock = 'PythonPackage'
+
+name = 'PLY'
+version = '3.11'
+
+homepage = "https://www.dabeaz.com/ply/"
+description = """PLY is yet another implementation of lex and yacc for Python."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
+
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['00c7c1aaa88358b9c765b6d3000c6eec0ba42abca5351b095321aef446081da3']
+
+builddependencies = [('binutils', '2.40')]
+
+dependencies = [('Python', '3.11.5')]
+
+download_dep_fail = True
+use_pip = True
+sanity_pip_check = True
+
+moduleclass = 'lib'

From 0f2f3696a41ee77fd23c13c768ffb642324da3bf Mon Sep 17 00:00:00 2001
From: tanmoy1989 <mssmzs@login01.avon.hpc>
Date: Tue, 21 May 2024 12:42:26 +0100
Subject: [PATCH 088/835] adding easyconfigs: SIP-6.8.3-GCCcore-13.2.0.eb

---
 .../s/SIP/SIP-6.8.3-GCCcore-13.2.0.eb         | 42 +++++++++++++++++++
 1 file changed, 42 insertions(+)
 create mode 100644 easybuild/easyconfigs/s/SIP/SIP-6.8.3-GCCcore-13.2.0.eb

diff --git a/easybuild/easyconfigs/s/SIP/SIP-6.8.3-GCCcore-13.2.0.eb b/easybuild/easyconfigs/s/SIP/SIP-6.8.3-GCCcore-13.2.0.eb
new file mode 100644
index 00000000000..7e615a60c0a
--- /dev/null
+++ b/easybuild/easyconfigs/s/SIP/SIP-6.8.3-GCCcore-13.2.0.eb
@@ -0,0 +1,42 @@
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+# Author: Bart Verleye
+# Center for eResearch, Auckland
+# update 6.8.1: THEMBL
+easyblock = 'PythonPackage'
+
+name = 'SIP'
+version = '6.8.3'
+
+homepage = 'http://www.riverbankcomputing.com/software/sip/'
+description = """SIP is a tool that makes it very easy to create Python bindings for C and C++ libraries."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
+
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['888547b018bb24c36aded519e93d3e513d4c6aa0ba55b7cc1affbd45cf10762c']
+
+builddependencies = [
+    ('binutils', '2.40'),
+]
+dependencies = [
+    ('Python', '3.11.5'),
+    ('Python-bundle-PyPI', '2023.10'),
+    ('PLY', '3.11'),
+]
+
+download_dep_fail = True
+use_pip = True
+
+local_tools = ['build',  'distinfo',  'install',  'module', 'sdist', 'wheel']
+sanity_check_paths = {
+    'files': ['bin/sip-%s' % x for x in local_tools],
+    'dirs': ['lib/python%(pyshortver)s/site-packages/sipbuild'],
+}
+
+sanity_pip_check = True
+
+sanity_check_commands = ['sip-%s --help' % x for x in local_tools]
+
+options = {'modulename': 'sipbuild'}
+
+moduleclass = 'lang'

From 723f8f964289ee1e61ec12223a16e4881a971397 Mon Sep 17 00:00:00 2001
From: tanmoy1989 <mssmzs@login01.avon.hpc>
Date: Tue, 21 May 2024 13:33:40 +0100
Subject: [PATCH 089/835] adding easyconfigs: meshio-5.3.5-foss-2023b.eb

---
 .../m/meshio/meshio-5.3.5-foss-2023b.eb       | 37 +++++++++++++++++++
 1 file changed, 37 insertions(+)
 create mode 100644 easybuild/easyconfigs/m/meshio/meshio-5.3.5-foss-2023b.eb

diff --git a/easybuild/easyconfigs/m/meshio/meshio-5.3.5-foss-2023b.eb b/easybuild/easyconfigs/m/meshio/meshio-5.3.5-foss-2023b.eb
new file mode 100644
index 00000000000..c8cd7d931df
--- /dev/null
+++ b/easybuild/easyconfigs/m/meshio/meshio-5.3.5-foss-2023b.eb
@@ -0,0 +1,37 @@
+easyblock = 'PythonBundle'
+
+name = 'meshio'
+version = '5.3.5'
+
+homepage = 'https://github.com/nschloe/meshio'
+description = "meshio is a tool for reading/writing various mesh formats representing unstructured meshes"
+
+toolchain = {'name': 'foss', 'version': '2023b'}
+
+dependencies = [
+    ('Python', '3.11.5'),  # includes numpy
+    ('h5py', '3.11.0'),
+    ('VTK', '9.3.0'),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    ('appdirs', '1.4.4', {
+        'checksums': ['7d5d0167b2b1ba821647616af46a749d1c653740dd0d2415100fe26e27afdf41'],
+    }),
+    ('pipdate', '0.5.6', {
+        'checksums': ['1b6b7ec2c5468fb7036ec9d6b2ced7a8a538db55aaca03f30199216d3bbd264b'],
+    }),
+    (name, version, {
+        'checksums': ['f21f01abd9f29ba06ea119304b3d39e610421cfe93b9dd23362834919f87586d'],
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['bin/meshio', 'bin/pipdate'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+moduleclass = 'cae'

From 3b36e47e8450d2e0c3b432a98da5640fef7b2dd9 Mon Sep 17 00:00:00 2001
From: tanmoy1989 <mssmzs@login01.avon.hpc>
Date: Tue, 21 May 2024 14:00:43 +0100
Subject: [PATCH 090/835] adding easyconfigs: Hypre-2.31.0-foss-2023b.eb

---
 .../h/Hypre/Hypre-2.31.0-foss-2023b.eb         | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)
 create mode 100644 easybuild/easyconfigs/h/Hypre/Hypre-2.31.0-foss-2023b.eb

diff --git a/easybuild/easyconfigs/h/Hypre/Hypre-2.31.0-foss-2023b.eb b/easybuild/easyconfigs/h/Hypre/Hypre-2.31.0-foss-2023b.eb
new file mode 100644
index 00000000000..62d72e357a8
--- /dev/null
+++ b/easybuild/easyconfigs/h/Hypre/Hypre-2.31.0-foss-2023b.eb
@@ -0,0 +1,18 @@
+name = 'Hypre'
+version = '2.31.0'
+
+homepage = 'https://computation.llnl.gov/projects/hypre-scalable-linear-solvers-multigrid-methods'
+description = """Hypre is a library for solving large, sparse linear systems of equations on massively
+ parallel computers. The problems of interest arise in the simulation codes being developed at LLNL
+ and elsewhere to study physical phenomena in the defense, environmental, energy, and biological sciences."""
+
+toolchain = {'name': 'foss', 'version': '2023b'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://github.com/hypre-space/hypre/archive/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['9a7916e2ac6615399de5010eb39c604417bb3ea3109ac90e199c5c63b0cb4334']
+
+start_dir = 'src'
+
+moduleclass = 'numlib'

From 825836a0cd34ab7a4f048574ca90de8766ec776b Mon Sep 17 00:00:00 2001
From: tanmoy1989 <mssmzs@login01.avon.hpc>
Date: Tue, 21 May 2024 14:07:58 +0100
Subject: [PATCH 091/835] adding easyconfigs: SuperLU_DIST-8.2.1-foss-2023b.eb

---
 .../SuperLU_DIST-8.2.1-foss-2023b.eb          | 44 +++++++++++++++++++
 1 file changed, 44 insertions(+)
 create mode 100644 easybuild/easyconfigs/s/SuperLU_DIST/SuperLU_DIST-8.2.1-foss-2023b.eb

diff --git a/easybuild/easyconfigs/s/SuperLU_DIST/SuperLU_DIST-8.2.1-foss-2023b.eb b/easybuild/easyconfigs/s/SuperLU_DIST/SuperLU_DIST-8.2.1-foss-2023b.eb
new file mode 100644
index 00000000000..a113fb7ef50
--- /dev/null
+++ b/easybuild/easyconfigs/s/SuperLU_DIST/SuperLU_DIST-8.2.1-foss-2023b.eb
@@ -0,0 +1,44 @@
+easyblock = "EB_SuperLU"
+
+name = 'SuperLU_DIST'
+version = '8.2.1'
+
+homepage = 'https://crd-legacy.lbl.gov/~xiaoye/SuperLU/'
+description = """SuperLU is a general purpose library for the direct solution of large, sparse, nonsymmetric systems
+ of linear equations on high performance machines."""
+
+toolchain = {'name': 'foss', 'version': '2023b'}
+toolchainopts = {'pic': True, 'openmp': True}
+
+github_account = 'xiaoyeli'
+source_urls = [GITHUB_LOWER_SOURCE]
+sources = ["v%(version)s.tar.gz"]
+checksums = ['b77d065cafa6bc1a1dcc15bf23fd854f54b05762b165badcffc195835ad2bddf']
+
+builddependencies = [('CMake', '3.27.6')]
+
+dependencies = [
+    ('ParMETIS', '4.0.3'),
+]
+
+configopts = '-DTPL_PARMETIS_INCLUDE_DIRS="${EBROOTPARMETIS}/include" '
+configopts += '-DTPL_PARMETIS_LIBRARIES="${EBROOTPARMETIS}/lib/libparmetis.a;${EBROOTPARMETIS}/lib/libmetis.a" '
+
+# Some tests run longer than default 1500s timeout on fairly big machine (36 cores).
+# Include only first four tests, which should be fairly small to run
+pretestopts = 'export ARGS="$ARGS --tests-regex pdtest_[21]x1_[13]_2_8_20_SP" && '
+
+# remove broken symlink to libsuperlu.a
+postinstallcmds = [
+    "if [ -f %(installdir)s/lib64/libsuperlu.a ]; then rm %(installdir)s/lib64/libsuperlu.a; fi",
+    # This second one can be removed when https://github.com/easybuilders/easybuild-framework/pull/4435 is merged
+    # (i.e. in EasyBuild 5.0)
+    "if [ -f %(installdir)s/lib/libsuperlu.a ]; then rm %(installdir)s/lib/libsuperlu.a; fi"
+]
+
+sanity_check_paths = {
+    'files': ['lib64/libsuperlu_dist.a'],
+    'dirs': ['include']
+}
+
+moduleclass = 'numlib'

From 7a81d9530390904f871718ee02770dbcd4919688 Mon Sep 17 00:00:00 2001
From: tanmoy1989 <mssmzs@login01.avon.hpc>
Date: Tue, 21 May 2024 14:14:13 +0100
Subject: [PATCH 092/835] adding easyconfigs:
 SuiteSparse-7.7.0-foss-2023b-METIS-5.1.0.eb

---
 ...uiteSparse-7.7.0-foss-2023b-METIS-5.1.0.eb | 29 +++++++++++++++++++
 1 file changed, 29 insertions(+)
 create mode 100644 easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-7.7.0-foss-2023b-METIS-5.1.0.eb

diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-7.7.0-foss-2023b-METIS-5.1.0.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-7.7.0-foss-2023b-METIS-5.1.0.eb
new file mode 100644
index 00000000000..260ca279304
--- /dev/null
+++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-7.7.0-foss-2023b-METIS-5.1.0.eb
@@ -0,0 +1,29 @@
+name = 'SuiteSparse'
+version = '7.7.0'
+local_metis_ver = '5.1.0'
+versionsuffix = '-METIS-%s' % local_metis_ver
+
+homepage = 'https://faculty.cse.tamu.edu/davis/suitesparse.html'
+description = """SuiteSparse is a collection of libraries to manipulate sparse matrices."""
+
+toolchain = {'name': 'foss', 'version': '2023b'}
+toolchainopts = {'unroll': True, 'pic': True}
+
+source_urls = ['https://github.com/DrTimothyAldenDavis/SuiteSparse/archive']
+sources = ['v%(version)s.tar.gz']
+checksums = ['529b067f5d80981f45ddf6766627b8fc5af619822f068f342aab776e683df4f3']
+
+builddependencies = [
+    ('CMake', '3.27.6'),
+    ('M4', '1.4.19'),
+]
+
+dependencies = [
+    ('METIS', local_metis_ver),
+    ('MPFR', '4.2.1'),
+]
+
+# make sure that bin/demo can find libsuitesparseconfig.so.5 during build
+prebuildopts = "export LD_LIBRARY_PATH=%(builddir)s/SuiteSparse-%(version)s/lib:$LD_LIBRARY_PATH && "
+
+moduleclass = 'numlib'

From a643eebd36dfc0e40282c56bb1f4cb1fd1126e1d Mon Sep 17 00:00:00 2001
From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com>
Date: Wed, 22 May 2024 13:49:20 +0200
Subject: [PATCH 093/835] Update
 easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a-CUDA-12.1.1.eb

Co-authored-by: Kenneth Hoste <kenneth.hoste@ugent.be>
---
 .../easyconfigs/j/jax/jax-0.4.25-gfbf-2023a-CUDA-12.1.1.eb      | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a-CUDA-12.1.1.eb
index 68ab99486f2..33b8d5546fa 100644
--- a/easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a-CUDA-12.1.1.eb
+++ b/easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a-CUDA-12.1.1.eb
@@ -41,7 +41,7 @@ dependencies = [
 local_xla_commit = '4ccfe33c71665ddcbca5b127fefe8baa3ed632d4'
 local_tfrt_commit = '0aeefb1660d7e37964b2bb71b1f518096bda9a25'
 
-local_extract_cmd = 'cp %s %(builddir)s/archives'
+local_extract_cmd = 'cp %s %%(builddir)s/archives'
 local_repo_opt = '--bazel_options="--distdir=%(builddir)s/archives" '
 local_repo_opt += '--bazel_options="--action_env=TF_SYSTEM_LIBS=pybind11" '
 local_repo_opt += '--bazel_options="--action_env=CPATH=$EBROOTPYBIND11/include" '

From 121683f0e478d520daa8f6bd24123eb46942f3ed Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Fri, 24 May 2024 15:26:30 +0200
Subject: [PATCH 094/835] adding easyconfigs: micro-sam-1.0.1-foss-2023a.eb,
 torch_em-0.7.1-foss-2023a.eb, affogato-0.3.3-foss-2023a.eb,
 segment-anything-1.0-foss-2023a.eb, z5py-2.0.17-foss-2023a.eb,
 python-elf-0.5.1-foss-2023a.eb, nifty-1.2.1-foss-2023a.eb,
 vigra-1.11.2-foss-2023a.eb

---
 .../a/affogato/affogato-0.3.3-foss-2023a.eb   |  40 ++++++
 .../m/micro-sam/micro-sam-1.0.1-foss-2023a.eb |  43 +++++++
 .../n/nifty/nifty-1.2.1-foss-2023a.eb         |  54 ++++++++
 .../python-elf/python-elf-0.5.1-foss-2023a.eb |  72 +++++++++++
 .../segment-anything-1.0-foss-2023a.eb        |  29 +++++
 .../t/torch_em/torch_em-0.7.1-foss-2023a.eb   | 117 ++++++++++++++++++
 .../v/vigra/vigra-1.11.2-foss-2023a.eb        |  48 +++++++
 .../z/z5py/z5py-2.0.17-foss-2023a.eb          |  50 ++++++++
 8 files changed, 453 insertions(+)
 create mode 100644 easybuild/easyconfigs/a/affogato/affogato-0.3.3-foss-2023a.eb
 create mode 100644 easybuild/easyconfigs/m/micro-sam/micro-sam-1.0.1-foss-2023a.eb
 create mode 100644 easybuild/easyconfigs/n/nifty/nifty-1.2.1-foss-2023a.eb
 create mode 100644 easybuild/easyconfigs/p/python-elf/python-elf-0.5.1-foss-2023a.eb
 create mode 100644 easybuild/easyconfigs/s/segment-anything/segment-anything-1.0-foss-2023a.eb
 create mode 100644 easybuild/easyconfigs/t/torch_em/torch_em-0.7.1-foss-2023a.eb
 create mode 100644 easybuild/easyconfigs/v/vigra/vigra-1.11.2-foss-2023a.eb
 create mode 100644 easybuild/easyconfigs/z/z5py/z5py-2.0.17-foss-2023a.eb

diff --git a/easybuild/easyconfigs/a/affogato/affogato-0.3.3-foss-2023a.eb b/easybuild/easyconfigs/a/affogato/affogato-0.3.3-foss-2023a.eb
new file mode 100644
index 00000000000..391f9d95eda
--- /dev/null
+++ b/easybuild/easyconfigs/a/affogato/affogato-0.3.3-foss-2023a.eb
@@ -0,0 +1,40 @@
+easyblock = 'CMakeMakeCp'
+
+name = 'affogato'
+version = '0.3.3'
+
+homepage = 'https://github.com/constantinpape/affogato/'
+description = """Affinity based segmentation algorithms and tools."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+source_urls = ['https://github.com/constantinpape/affogato/archive/']
+sources = ['%(version)s.tar.gz']
+checksums = ['ad3bb1aca50ce9311d4e88e97e701237bce94faa6e79460f0bc2d2061f1484d2']
+
+builddependencies = [('CMake', '3.26.3')]
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('Boost', '1.82.0'),
+    ('SciPy-bundle', '2023.07'),
+    ('vigra', '1.11.2'),
+    ('xtensor', '0.24.7'),
+    ('h5py', '3.9.0'),
+]
+
+configopts = '-DBUILD_PYTHON=ON '
+# Fix path to python executable - it finds v3.6.8 from /usr/bin/ without this fix
+configopts += '-DPYTHON_EXECUTABLE="$EBROOTPYTHON/bin/python" '
+
+files_to_copy = [(['python/affogato'], 'lib/python%(pyshortver)s/site-packages')]
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['lib/python%(pyshortver)s/site-packages/affogato'],
+}
+sanity_check_commands = ["python -c 'import affogato'"]
+
+modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'}
+
+moduleclass = 'vis'
diff --git a/easybuild/easyconfigs/m/micro-sam/micro-sam-1.0.1-foss-2023a.eb b/easybuild/easyconfigs/m/micro-sam/micro-sam-1.0.1-foss-2023a.eb
new file mode 100644
index 00000000000..eb2f74f218f
--- /dev/null
+++ b/easybuild/easyconfigs/m/micro-sam/micro-sam-1.0.1-foss-2023a.eb
@@ -0,0 +1,43 @@
+easyblock = 'PythonBundle'
+
+name = 'micro-sam'
+version = '1.0.1'
+
+homepage = 'https://github.com/computational-cell-analytics/micro-sam/'
+description = "Tools for segmentation and tracking in microscopy build on top of SegmentAnything."
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('Python-bundle-PyPI', '2023.06'),
+    ('torchvision', '0.16.0'),
+    ('napari', '0.4.18'),
+    ('zarr', '2.17.1'),
+    ('vigra', '1.11.2'),
+    ('python-elf', '0.5.1'),
+    ('z5py', '2.0.17'),
+    ('python-xxhash', '3.4.1'),
+    ('segment-anything', '1.0'),
+    ('torch_em', '0.7.1'),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    (name, version, {
+        'source_urls': ['https://github.com/computational-cell-analytics/micro-sam/archive/'],
+        'sources': ['v%(version)s.tar.gz'],
+        'checksums': ['5b7cc562a639d68de4f9462f3696f17b479ea0d669eaedb34687b65ceac715e9'],
+    }),
+]
+
+sanity_check_commands = [
+    "python -c 'import affogato'",
+    "python -c 'import napari.viewer'",
+    "micro_sam.annotator_2d -h",
+    "micro_sam.annotator_3d -h",
+]
+
+moduleclass = 'vis'
diff --git a/easybuild/easyconfigs/n/nifty/nifty-1.2.1-foss-2023a.eb b/easybuild/easyconfigs/n/nifty/nifty-1.2.1-foss-2023a.eb
new file mode 100644
index 00000000000..f02aa7ac12e
--- /dev/null
+++ b/easybuild/easyconfigs/n/nifty/nifty-1.2.1-foss-2023a.eb
@@ -0,0 +1,54 @@
+easyblock = 'CMakeMakeCp'
+
+name = 'nifty'
+version = '1.2.1'
+
+homepage = 'https://github.com/DerThorsten/nifty/'
+description = """A nifty library for 2D and 3D image segmentation, graph based segmentation an opt. 
+This library provided building blocks for segmentation algorithms and complex segmentation pipelines."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+source_urls = ['https://github.com/DerThorsten/nifty/archive/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['a5fd611463336ba18be828da3154da8828b6486603e2a04f14a4520cb357661a']
+
+builddependencies = [('CMake', '3.26.3')]
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('Boost', '1.82.0'),
+    ('h5py', '3.9.0'),
+    ('nlohmann_json', '3.11.2'),
+    ('scikit-image', '0.22.0'),
+    ('vigra', '1.11.2'),
+    ('xtensor', '0.24.7'),
+    ('zlib', '1.2.13'),
+    ('HDF5', '1.14.0'),
+]
+
+# Add flags (nifty/.github/workflows/build_unix.sh)
+configopts = '-DWITH_QPBO=OFF -DWITH_HDF5=ON -DWITH_Z5=OFF -DWITH_ZLIB=ON -DWITH_CPLEX=OFF -DWITH_GUROBI=OFF '
+# Fix path to python executable - it finds v3.6.8 from /usr/bin/ without this fix
+configopts += '-DPYTHON_EXECUTABLE="$EBROOTPYTHON/bin/python" -DBUILD_NIFTY_PYTHON=ON '
+
+# export PYTHON_MODULE_INSTALL_DIR to fix make install
+preinstallopts = 'export PYTHON_MODULE_INSTALL_DIR="%(builddir)s/easybuild_obj/python/" '
+
+files_to_copy = [(['python/nifty'], 'lib/python%(pyshortver)s/site-packages'),]
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['lib/python%(pyshortver)s/site-packages/nifty'],
+}
+
+sanity_check_commands = [
+    "python -c 'import nifty'",
+    "python -c 'from nifty.graph import UndirectedGraph'",
+    "python -c 'import nifty.tools'",
+]
+
+modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'}
+
+moduleclass = 'vis'
diff --git a/easybuild/easyconfigs/p/python-elf/python-elf-0.5.1-foss-2023a.eb b/easybuild/easyconfigs/p/python-elf/python-elf-0.5.1-foss-2023a.eb
new file mode 100644
index 00000000000..c3fe23a272a
--- /dev/null
+++ b/easybuild/easyconfigs/p/python-elf/python-elf-0.5.1-foss-2023a.eb
@@ -0,0 +1,72 @@
+easyblock = 'PythonBundle'
+
+name = 'python-elf'
+version = '0.5.1'
+
+homepage = 'https://github.com/constantinpape/elf'
+description = "Utils and convenience functions for large-scale bio-image analysis."
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+builddependencies = [
+    ('scikit-build', '0.17.6'),
+    ('CMake', '3.26.3'),
+]
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('imageio', '2.33.1'),
+    ('scikit-image', '0.22.0'),
+    ('scikit-learn', '1.3.1'),
+    ('h5py', '3.9.0'),
+    ('zarr', '2.17.1'),
+    ('mrcfile', '1.5.0'),
+    ('numba', '0.58.1'),
+    ('tqdm', '4.66.1'),
+    ('vigra', '1.11.2'),
+    ('python-blosc', '1.11.0'),
+    ('openpyxl', '3.1.2'),
+    ('nifty', '1.2.1'),
+    ('z5py', '2.0.17'),
+    ('affogato', '0.3.3'),
+    ('napari', '0.4.18'),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    ('nose2', '0.14.1', {
+        'checksums': ['7f8f03a21c9de2c33015933afcef72bf8e4a2d5dfec3b40092287de6e41b093a'],
+    }),
+    ('intern', '1.4.1', {
+        'checksums': ['7cdc6caa66716760f93dbbadaa67cc8a03866d6c5f33a6a3285cb9e5f4994315'],
+    }),
+    ('skan', '0.11.1', {
+        'checksums': ['d5439c17fbf5f86386a7548acb6ab11482961164a6284047b9bdc6652a0d1faf'],
+    }),
+    (name, version, {
+        'modulename': 'elf',
+        'source_urls': ['https://github.com/constantinpape/elf/archive/'],
+        'sources': ['%(version)s.tar.gz'],
+        'checksums': ['29c542dfb953a1975e2d45f72c84b8f8a2f79fcb0cb2d855dae5493cadbbaa9d'],
+    }),
+]
+
+sanity_check_commands = [
+    "python -c 'import elf.segmentation.multicut'",
+    "python -c 'import elf.segmentation.features'",
+    "python -c 'import elf.segmentation.embeddings'",
+    "python -c 'from elf.segmentation.mutex_watershed import mutex_watershed_clustering'",
+    "python -c 'from elf.segmentation.utils import load_mutex_watershed_problem'",
+    "python -c 'import elf.htm'",
+    "python -c 'from elf.parallel.label import label'",
+    "python -c 'from elf.evaluation import rand_index'",
+    "python -c 'from elf.io import open_file'",
+    "python -c 'from elf.visualisation import visualise_edges'",
+    "python -c 'import elf.tracking.tracking_utils'",
+    "python -c 'import elf.transformation'",
+    "python -c 'import elf.util'",
+]
+
+moduleclass = 'vis'
diff --git a/easybuild/easyconfigs/s/segment-anything/segment-anything-1.0-foss-2023a.eb b/easybuild/easyconfigs/s/segment-anything/segment-anything-1.0-foss-2023a.eb
new file mode 100644
index 00000000000..23c6de38a67
--- /dev/null
+++ b/easybuild/easyconfigs/s/segment-anything/segment-anything-1.0-foss-2023a.eb
@@ -0,0 +1,29 @@
+easyblock = 'PythonPackage'
+
+name = 'segment-anything'
+version = '1.0'
+
+homepage = 'https://github.com/facebookresearch/segment-anything'
+description = """The Segment Anything Model (SAM) produces high quality object masks from input prompts
+ such as points or boxes, and it can be used to generate masks for all objects in an image.
+ It has been trained on a dataset of 11 million images and 1.1 billion masks, and has strong zero-shot
+ performance on a variety of segmentation tasks."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+sources = ['segment_anything-%(version)s.tar.gz']
+checksums = ['ed0c9f6fb07bbef9c6238a7028a13c8272f1ba6b6305ca73e3e064266503736b']
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('torchvision', '0.16.0'),
+    ('OpenCV', '4.8.1', '-contrib'),
+    ('pycocotools', '2.0.7'),
+]
+
+download_dep_fail = True
+use_pip = True
+sanity_pip_check = True
+
+moduleclass = 'ai'
diff --git a/easybuild/easyconfigs/t/torch_em/torch_em-0.7.1-foss-2023a.eb b/easybuild/easyconfigs/t/torch_em/torch_em-0.7.1-foss-2023a.eb
new file mode 100644
index 00000000000..d53c71b30d5
--- /dev/null
+++ b/easybuild/easyconfigs/t/torch_em/torch_em-0.7.1-foss-2023a.eb
@@ -0,0 +1,117 @@
+easyblock = 'PythonBundle'
+
+name = 'torch_em'
+version = '0.7.1'
+
+homepage = 'https://github.com/constantinpape/torch-em/'
+description = """Deep-learning based semantic and instance segmentation for 3D Electron Microscopy and 
+other bioimage analysis problems based on pytorch."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+builddependencies = [
+    ('maturin', '1.1.0'),
+    ('CMake', '3.26.3'),
+    ('hatchling', '1.18.0'),
+]
+dependencies = [
+    ('Python', '3.11.3'),
+    ('torchvision', '0.16.0'),
+    ('h5py', '3.9.0'),
+    ('imagecodecs', '2023.1.23'),
+    ('tensorboard', '2.15.1'),
+    ('tqdm', '4.66.1'),
+    ('napari', '0.4.18'),
+    ('vigra', '1.11.2'),
+    ('python-elf', '0.5.1'),
+    ('z5py', '2.0.17'),
+    ('pydantic', '2.5.3'),
+    ('xarray', '2023.9.0'),
+    ('affogato', '0.3.3'),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+# avoid using hatchling as build backend (since installing it for this old Python version is a nightmare)
+# copied from MONAI-1.0.1-foss-2022a.eb
+local_preinstallopts_termcolor = ' '.join([
+    r"""sed -i -e 's/^build-backend = .*/build-backend = "setuptools.build_meta"/g' """,
+    r"""-e 's/^requires = \[/requires = \["setuptools"/g' """,
+    r"""-e '/"hatch/d' """,
+    # replace dynamic version with hardcoded version
+    r"""-e '/"version"/d' """,
+    r"""-e 's/^readme = .*/version = "%(version)s"/g' """,
+    r"pyproject.toml && ",
+])
+
+exts_list = [
+    ('termcolor', '2.3.0', {
+        'checksums': ['b5b08f68937f138fe92f6c089b99f1e2da0ae56c52b78bf7075fd95420fd9a5a'],
+        'preinstallopts': local_preinstallopts_termcolor,
+    }),
+    ('dnspython', '2.6.1', {
+        'modulename': False,
+        'checksums': ['e8f0f9c23a7b7cb99ded64e6c3a6f3e701d78f50c55e002b839dea7225cff7cc'],
+    }),
+    ('kornia_rs', '0.1.3', {
+        'checksums': ['e299d110774fc10f82c547fb04b1b8bf450a0514010324e7be06206d2179ceaf'],
+    }),
+    ('email_validator', '2.1.1', {
+        'checksums': ['200a70680ba08904be6d1eef729205cc0d687634399a5924d842533efb824b84'],
+    }),
+    ('annotated_types', '0.7.0', {
+        'checksums': ['aff07c09a53a08bc8cfccb9c85b05f1aa9a2a6f23728d790723543408344ce89'],
+    }),
+    ('ruyaml', '0.91.0', {
+        'checksums': ['6ce9de9f4d082d696d3bde264664d1bcdca8f5a9dff9d1a1f1a127969ab871ab'],
+    }),
+    ('python-dotenv', '1.0.1', {
+        'modulename': 'dotenv',
+        'checksums': ['e324ee90a023d808f1959c46bcbc04446a10ced277783dc6ee09987c37ec10ca'],
+    }),
+    ('pydantic_settings', '2.2.1', {
+        'checksums': ['00b9f6a5e95553590434c0fa01ead0b216c3e10bc54ae02e37f359948643c5ed'],
+    }),
+    ('loguru', '0.7.2', {
+        'checksums': ['e671a53522515f34fd406340ee968cb9ecafbc4b36c679da03c18fd8d0bd51ac'],
+    }),
+    ('fire', '0.6.0', {
+        'checksums': ['54ec5b996ecdd3c0309c800324a0703d6da512241bc73b553db959d98de0aa66'],
+    }),
+    ('kornia', '0.7.2', {
+        'checksums': ['f834ccd51188d071ed286a6727471c94344ea2a718903cc6f0e56a92f9c66ac5'],
+    }),
+    ('tifffile', '2024.5.10', {
+        'checksums': ['aa1e1b12be952ab20717d6848bd6d4a5ee88d2aa319f1152bff4354ad728ec86'],
+    }),
+    ('bioimageio.core', '0.6.5', {
+        'checksums': ['3b2851e44a2b074536c36fe3bb05b28dc1413ed358d3edd0eb272b75e6c9ca2b'],
+    }),
+    ('bioimageio.spec', '0.5.2.post5', {
+        # delete pin of pydantic version
+        'preinstallopts': "sed -i 's/pydantic>=2.6.3,<3/pydantic/' setup.py && ",
+        'checksums': ['3007aedc4da9f77f4fb46f72c134c8367bd469f05f6dd275db1a93f0fff48e97'],
+    }),
+    (name, version, {
+        'source_urls': ['https://github.com/constantinpape/torch-em/archive/'],
+        'sources': ['%(version)s.tar.gz'],
+        'checksums': ['201aae9af1e698b5a0d8e878def4538b00b0cd8ab9165b71194a6c978ae50931'],
+    }),
+]
+
+sanity_check_commands = [
+    "python -c 'import torch_em.data.datasets.util'",
+    "python -c 'import torch_em.transform.label'",
+    "python -c 'import torch_em.data.sampler'",
+    "python -c 'import torch_em.segmentation'",
+    "python -c 'import torch_em.data.datasets.neurips_cell_seg'",
+    "python -c 'import torch_em.model'",
+    "python -c 'import torch_em.loss'",
+    "python -c 'import torch_em.trainer'",
+    # check if unpined pydantic version is woking 
+    "python -c 'import bioimageio.spec.model.v0_5'",
+    "python -c 'from bioimageio.spec import save_bioimageio_package'",
+]
+
+moduleclass = 'vis'
diff --git a/easybuild/easyconfigs/v/vigra/vigra-1.11.2-foss-2023a.eb b/easybuild/easyconfigs/v/vigra/vigra-1.11.2-foss-2023a.eb
new file mode 100644
index 00000000000..0d374d287ed
--- /dev/null
+++ b/easybuild/easyconfigs/v/vigra/vigra-1.11.2-foss-2023a.eb
@@ -0,0 +1,48 @@
+easyblock = 'CMakePythonPackage'
+
+name = 'vigra'
+version = '1.11.2'
+
+homepage = 'https://ukoethe.github.io/vigra/'
+description = """Vision with Generic Algorithms is an image processing and analysis library 
+that puts its main emphasis on customizable algorithms and data structures."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+source_urls = ['https://github.com/ukoethe/vigra/archive/']
+sources = ['Version-1-11-2.tar.gz']
+checksums = ['4841936f5c3c137611ec782e293d961df29d3b5b70ade8cb711374de0f4cb5d3']
+
+builddependencies = [
+    ('CMake', '3.26.3'),
+]
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('Boost.Python', '1.83.0'),
+    ('libjpeg-turbo', '2.1.5.1'),
+    ('OpenJPEG', '2.5.0'),
+    ('LibTIFF', '4.5.0'),
+    ('libpng', '1.6.39'),
+    ('OpenEXR', '3.1.7'),
+    ('HDF5', '1.14.0'),
+    ('FFTW', '3.3.10'),
+    ('nose3', '1.3.8'),
+]
+
+# Fix python files path in make install step
+_py_path = "%(builddir)s/%(name)s-Version-1-11-2/config/FindVIGRANUMPY_DEPENDENCIES.cmake"
+_py_add = "SET(VIGRANUMPY_INSTALL_DIR ${CMAKE_INSTALL_PREFIX}/lib/python%(pyshortver)s/site-packages)"
+preinstallopts = "sed -i '90,91d' %s && " % _py_path
+preinstallopts += "sed -i '94d' %s && " % _py_path
+preinstallopts += "sed -i '89 a\%s' %s && " % (_py_add, _py_path)
+
+sanity_check_paths = {
+    'files': ['bin/vigra-config'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages/vigra'],
+}
+
+sanity_check_commands = ["vigra-config --version", "python -c 'import vigra'"]
+
+moduleclass = 'vis'
diff --git a/easybuild/easyconfigs/z/z5py/z5py-2.0.17-foss-2023a.eb b/easybuild/easyconfigs/z/z5py/z5py-2.0.17-foss-2023a.eb
new file mode 100644
index 00000000000..7f725171c46
--- /dev/null
+++ b/easybuild/easyconfigs/z/z5py/z5py-2.0.17-foss-2023a.eb
@@ -0,0 +1,50 @@
+easyblock = 'CMakeMakeCp'
+
+name = 'z5py'
+version = '2.0.17'
+
+homepage = 'https://github.com/constantinpape/z5/'
+description = """Lightweight C++ and Python interface for datasets in zarr and N5 format."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+source_urls = ['https://github.com/constantinpape/z5/archive/']
+sources = ['%(version)s.tar.gz']
+checksums = ['76acaeec7203b8d3baec45ccce82cd260dc1893f1516640acec5de6d74c078ef']
+
+builddependencies = [('CMake', '3.26.3')]
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('bzip2', '1.0.8'),
+    ('lz4', '1.9.4'),
+    ('XZ', '5.4.2'),
+    ('zlib', '1.2.13'),
+    ('xtensor', '0.24.7'),
+    ('python-blosc', '1.11.0'),
+    ('imageio', '2.33.1'),
+    ('h5py', '3.9.0'),
+    ('nlohmann_json', '3.11.2'),
+    ('zarr', '2.17.1'),
+    ('pybind11', '2.11.1'),
+]
+
+configopts = '-DWITH_ZLIB=ON -DWITH_BZIP2=ON '
+# Fix path to python executable - it finds v3.6.8 from /usr/bin/ without this fix
+configopts += '-DPYTHON_EXECUTABLE="$EBROOTPYTHON/bin/python" '
+
+# export PYTHON_MODULE_INSTALL_DIR to fix make install
+preinstallopts = 'export PYTHON_MODULE_INSTALL_DIR="%(builddir)s/easybuild_obj/python/" '
+
+files_to_copy = [(['python/z5py'], 'lib/python%(pyshortver)s/site-packages'), 'z5-config.cmake']
+
+sanity_check_paths = {
+    'files': ['z5-config.cmake'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages/z5py'],
+}
+sanity_check_commands = ["python -c 'import z5py'"]
+
+modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'}
+
+moduleclass = 'vis'

From 7bb21b0f3dabb1a062fe918474292f9cb542bd5e Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Fri, 24 May 2024 15:34:06 +0200
Subject: [PATCH 095/835] fix vigra to pass tests

---
 easybuild/easyconfigs/v/vigra/vigra-1.11.2-foss-2023a.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/v/vigra/vigra-1.11.2-foss-2023a.eb b/easybuild/easyconfigs/v/vigra/vigra-1.11.2-foss-2023a.eb
index 0d374d287ed..68eb19c4346 100644
--- a/easybuild/easyconfigs/v/vigra/vigra-1.11.2-foss-2023a.eb
+++ b/easybuild/easyconfigs/v/vigra/vigra-1.11.2-foss-2023a.eb
@@ -36,7 +36,7 @@ _py_path = "%(builddir)s/%(name)s-Version-1-11-2/config/FindVIGRANUMPY_DEPENDENC
 _py_add = "SET(VIGRANUMPY_INSTALL_DIR ${CMAKE_INSTALL_PREFIX}/lib/python%(pyshortver)s/site-packages)"
 preinstallopts = "sed -i '90,91d' %s && " % _py_path
 preinstallopts += "sed -i '94d' %s && " % _py_path
-preinstallopts += "sed -i '89 a\%s' %s && " % (_py_add, _py_path)
+preinstallopts += r"sed -i '89 a\%s' %s && " % (_py_add, _py_path)
 
 sanity_check_paths = {
     'files': ['bin/vigra-config'],

From f71916bec7acdadb7512b393b58ec89558f810ad Mon Sep 17 00:00:00 2001
From: Samuel Moors <samuel.moors@vub.be>
Date: Sat, 25 May 2024 11:46:40 +0200
Subject: [PATCH 096/835] adding easyconfigs:
 Safetensors-0.4.3-foss-2023a-CUDA-12.1.1.eb

---
 ...afetensors-0.4.3-foss-2023a-CUDA-12.1.1.eb | 301 ++++++++++++++++++
 1 file changed, 301 insertions(+)
 create mode 100644 easybuild/easyconfigs/s/Safetensors/Safetensors-0.4.3-foss-2023a-CUDA-12.1.1.eb

diff --git a/easybuild/easyconfigs/s/Safetensors/Safetensors-0.4.3-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/s/Safetensors/Safetensors-0.4.3-foss-2023a-CUDA-12.1.1.eb
new file mode 100644
index 00000000000..c21239cfcc7
--- /dev/null
+++ b/easybuild/easyconfigs/s/Safetensors/Safetensors-0.4.3-foss-2023a-CUDA-12.1.1.eb
@@ -0,0 +1,301 @@
+easyblock = "CargoPythonBundle"
+
+name = 'Safetensors'
+version = '0.4.3'
+versionsuffix = '-CUDA-%(cudaver)s'
+_rustver = '1.75.0'
+
+homepage = 'https://huggingface.co/docs/safetensors'
+description = """Safetensors is a new simple format for storing tensors safely (as opposed to
+pickle) and that is still fast (zero-copy). Safetensors is really fast.
+
+This variant of Safetensors is installed with support for numpy and PyTorch
+"""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+builddependencies = [
+    ('Rust', _rustver),
+    ('maturin', '1.4.0', '-Rust-' + _rustver),
+]
+
+dependencies = [
+    ('CUDA', '12.1.1', '', SYSTEM),
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('PyTorch', '2.1.2', versionsuffix),  # optional
+    # ('jax', 'xxx', versionsuffix),  # optional, add 'jax' to 'use_pip_extras'
+    # ('TensorFlow', 'xxx', versionsuffix),  # optional, add 'tensorflow' to 'use_pip_extras'
+]
+
+# crates generated on 2024-05-24 from directories savetensors/ and bindings/python/
+crates = [
+    ('aho-corasick', '1.1.3'),
+    ('anes', '0.1.6'),
+    ('anstyle', '1.0.7'),
+    ('autocfg', '1.2.0'),
+    ('autocfg', '1.3.0'),
+    ('bitflags', '1.3.2'),
+    ('bitflags', '2.5.0'),
+    ('bit-set', '0.5.3'),
+    ('bit-vec', '0.6.3'),
+    ('bumpalo', '3.16.0'),
+    ('cast', '0.3.0'),
+    ('cfg-if', '1.0.0'),
+    ('ciborium', '0.2.2'),
+    ('ciborium-io', '0.2.2'),
+    ('ciborium-ll', '0.2.2'),
+    ('clap', '4.5.4'),
+    ('clap_builder', '4.5.2'),
+    ('clap_lex', '0.7.0'),
+    ('criterion', '0.5.1'),
+    ('criterion-plot', '0.5.0'),
+    ('crossbeam-deque', '0.8.5'),
+    ('crossbeam-epoch', '0.9.18'),
+    ('crossbeam-utils', '0.8.20'),
+    ('crunchy', '0.2.2'),
+    ('either', '1.12.0'),
+    ('errno', '0.3.9'),
+    ('fastrand', '2.1.0'),
+    ('fnv', '1.0.7'),
+    ('getrandom', '0.2.15'),
+    ('half', '2.4.1'),
+    ('heck', '0.4.1'),
+    ('hermit-abi', '0.3.9'),
+    ('indoc', '2.0.5'),
+    ('is-terminal', '0.4.12'),
+    ('itertools', '0.10.5'),
+    ('itoa', '1.0.11'),
+    ('js-sys', '0.3.69'),
+    ('lazy_static', '1.4.0'),
+    ('libc', '0.2.153'),
+    ('libc', '0.2.155'),
+    ('libm', '0.2.8'),
+    ('linux-raw-sys', '0.4.14'),
+    ('lock_api', '0.4.11'),
+    ('log', '0.4.21'),
+    ('memchr', '2.7.2'),
+    ('memmap2', '0.9.4'),
+    ('memoffset', '0.9.1'),
+    ('num-traits', '0.2.19'),
+    ('once_cell', '1.19.0'),
+    ('oorandom', '11.1.3'),
+    ('parking_lot', '0.12.1'),
+    ('parking_lot_core', '0.9.9'),
+    ('plotters', '0.3.6'),
+    ('plotters-backend', '0.3.6'),
+    ('plotters-svg', '0.3.6'),
+    ('portable-atomic', '1.6.0'),
+    ('ppv-lite86', '0.2.17'),
+    ('proc-macro2', '1.0.80'),
+    ('proc-macro2', '1.0.83'),
+    ('proptest', '1.4.0'),
+    ('pyo3', '0.21.1'),
+    ('pyo3-build-config', '0.21.1'),
+    ('pyo3-ffi', '0.21.1'),
+    ('pyo3-macros', '0.21.1'),
+    ('pyo3-macros-backend', '0.21.1'),
+    ('quick-error', '1.2.3'),
+    ('quote', '1.0.36'),
+    ('rand', '0.8.5'),
+    ('rand_chacha', '0.3.1'),
+    ('rand_core', '0.6.4'),
+    ('rand_xorshift', '0.3.0'),
+    ('rayon', '1.10.0'),
+    ('rayon-core', '1.12.1'),
+    ('redox_syscall', '0.4.1'),
+    ('regex', '1.10.4'),
+    ('regex-automata', '0.4.6'),
+    ('regex-syntax', '0.8.3'),
+    ('rustix', '0.38.34'),
+    ('rusty-fork', '0.3.0'),
+    ('ryu', '1.0.17'),
+    ('ryu', '1.0.18'),
+    ('same-file', '1.0.6'),
+    ('scopeguard', '1.2.0'),
+    ('serde', '1.0.197'),
+    ('serde', '1.0.202'),
+    ('serde_derive', '1.0.197'),
+    ('serde_derive', '1.0.202'),
+    ('serde_json', '1.0.115'),
+    ('serde_json', '1.0.117'),
+    ('smallvec', '1.13.2'),
+    ('syn', '2.0.59'),
+    ('syn', '2.0.66'),
+    ('target-lexicon', '0.12.14'),
+    ('tempfile', '3.10.1'),
+    ('tinytemplate', '1.2.1'),
+    ('unarray', '0.1.4'),
+    ('unicode-ident', '1.0.12'),
+    ('unindent', '0.2.3'),
+    ('wait-timeout', '0.2.0'),
+    ('walkdir', '2.5.0'),
+    ('wasi', '0.11.0+wasi-snapshot-preview1'),
+    ('wasm-bindgen', '0.2.92'),
+    ('wasm-bindgen-backend', '0.2.92'),
+    ('wasm-bindgen-macro', '0.2.92'),
+    ('wasm-bindgen-macro-support', '0.2.92'),
+    ('wasm-bindgen-shared', '0.2.92'),
+    ('web-sys', '0.3.69'),
+    ('winapi-util', '0.1.8'),
+    ('windows_aarch64_gnullvm', '0.48.5'),
+    ('windows_aarch64_gnullvm', '0.52.5'),
+    ('windows_aarch64_msvc', '0.48.5'),
+    ('windows_aarch64_msvc', '0.52.5'),
+    ('windows_i686_gnu', '0.48.5'),
+    ('windows_i686_gnu', '0.52.5'),
+    ('windows_i686_gnullvm', '0.52.5'),
+    ('windows_i686_msvc', '0.48.5'),
+    ('windows_i686_msvc', '0.52.5'),
+    ('windows-sys', '0.52.0'),
+    ('windows-targets', '0.48.5'),
+    ('windows-targets', '0.52.5'),
+    ('windows_x86_64_gnu', '0.48.5'),
+    ('windows_x86_64_gnu', '0.52.5'),
+    ('windows_x86_64_gnullvm', '0.48.5'),
+    ('windows_x86_64_gnullvm', '0.52.5'),
+    ('windows_x86_64_msvc', '0.48.5'),
+    ('windows_x86_64_msvc', '0.52.5'),
+]
+
+checksums = [
+    {'aho-corasick-1.1.3.tar.gz': '8e60d3430d3a69478ad0993f19238d2df97c507009a52b3c10addcd7f6bcb916'},
+    {'anes-0.1.6.tar.gz': '4b46cbb362ab8752921c97e041f5e366ee6297bd428a31275b9fcf1e380f7299'},
+    {'anstyle-1.0.7.tar.gz': '038dfcf04a5feb68e9c60b21c9625a54c2c0616e79b72b0fd87075a056ae1d1b'},
+    {'autocfg-1.2.0.tar.gz': 'f1fdabc7756949593fe60f30ec81974b613357de856987752631dea1e3394c80'},
+    {'autocfg-1.3.0.tar.gz': '0c4b4d0bd25bd0b74681c0ad21497610ce1b7c91b1022cd21c80c6fbdd9476b0'},
+    {'bitflags-1.3.2.tar.gz': 'bef38d45163c2f1dde094a7dfd33ccf595c92905c8f8f4fdc18d06fb1037718a'},
+    {'bitflags-2.5.0.tar.gz': 'cf4b9d6a944f767f8e5e0db018570623c85f3d925ac718db4e06d0187adb21c1'},
+    {'bit-set-0.5.3.tar.gz': '0700ddab506f33b20a03b13996eccd309a48e5ff77d0d95926aa0210fb4e95f1'},
+    {'bit-vec-0.6.3.tar.gz': '349f9b6a179ed607305526ca489b34ad0a41aed5f7980fa90eb03160b69598fb'},
+    {'bumpalo-3.16.0.tar.gz': '79296716171880943b8470b5f8d03aa55eb2e645a4874bdbb28adb49162e012c'},
+    {'cast-0.3.0.tar.gz': '37b2a672a2cb129a2e41c10b1224bb368f9f37a2b16b612598138befd7b37eb5'},
+    {'cfg-if-1.0.0.tar.gz': 'baf1de4339761588bc0619e3cbc0120ee582ebb74b53b4efbf79117bd2da40fd'},
+    {'ciborium-0.2.2.tar.gz': '42e69ffd6f0917f5c029256a24d0161db17cea3997d185db0d35926308770f0e'},
+    {'ciborium-io-0.2.2.tar.gz': '05afea1e0a06c9be33d539b876f1ce3692f4afea2cb41f740e7743225ed1c757'},
+    {'ciborium-ll-0.2.2.tar.gz': '57663b653d948a338bfb3eeba9bb2fd5fcfaecb9e199e87e1eda4d9e8b240fd9'},
+    {'clap-4.5.4.tar.gz': '90bc066a67923782aa8515dbaea16946c5bcc5addbd668bb80af688e53e548a0'},
+    {'clap_builder-4.5.2.tar.gz': 'ae129e2e766ae0ec03484e609954119f123cc1fe650337e155d03b022f24f7b4'},
+    {'clap_lex-0.7.0.tar.gz': '98cc8fbded0c607b7ba9dd60cd98df59af97e84d24e49c8557331cfc26d301ce'},
+    {'criterion-0.5.1.tar.gz': 'f2b12d017a929603d80db1831cd3a24082f8137ce19c69e6447f54f5fc8d692f'},
+    {'criterion-plot-0.5.0.tar.gz': '6b50826342786a51a89e2da3a28f1c32b06e387201bc2d19791f622c673706b1'},
+    {'crossbeam-deque-0.8.5.tar.gz': '613f8cc01fe9cf1a3eb3d7f488fd2fa8388403e97039e2f73692932e291a770d'},
+    {'crossbeam-epoch-0.9.18.tar.gz': '5b82ac4a3c2ca9c3460964f020e1402edd5753411d7737aa39c3714ad1b5420e'},
+    {'crossbeam-utils-0.8.20.tar.gz': '22ec99545bb0ed0ea7bb9b8e1e9122ea386ff8a48c0922e43f36d45ab09e0e80'},
+    {'crunchy-0.2.2.tar.gz': '7a81dae078cea95a014a339291cec439d2f232ebe854a9d672b796c6afafa9b7'},
+    {'either-1.12.0.tar.gz': '3dca9240753cf90908d7e4aac30f630662b02aebaa1b58a3cadabdb23385b58b'},
+    {'errno-0.3.9.tar.gz': '534c5cf6194dfab3db3242765c03bbe257cf92f22b38f6bc0c58d59108a820ba'},
+    {'fastrand-2.1.0.tar.gz': '9fc0510504f03c51ada170672ac806f1f105a88aa97a5281117e1ddc3368e51a'},
+    {'fnv-1.0.7.tar.gz': '3f9eec918d3f24069decb9af1554cad7c880e2da24a9afd88aca000531ab82c1'},
+    {'getrandom-0.2.15.tar.gz': 'c4567c8db10ae91089c99af84c68c38da3ec2f087c3f82960bcdbf3656b6f4d7'},
+    {'half-2.4.1.tar.gz': '6dd08c532ae367adf81c312a4580bc67f1d0fe8bc9c460520283f4c0ff277888'},
+    {'heck-0.4.1.tar.gz': '95505c38b4572b2d910cecb0281560f54b440a19336cbbcb27bf6ce6adc6f5a8'},
+    {'hermit-abi-0.3.9.tar.gz': 'd231dfb89cfffdbc30e7fc41579ed6066ad03abda9e567ccafae602b97ec5024'},
+    {'indoc-2.0.5.tar.gz': 'b248f5224d1d606005e02c97f5aa4e88eeb230488bcc03bc9ca4d7991399f2b5'},
+    {'is-terminal-0.4.12.tar.gz': 'f23ff5ef2b80d608d61efee834934d862cd92461afc0560dedf493e4c033738b'},
+    {'itertools-0.10.5.tar.gz': 'b0fd2260e829bddf4cb6ea802289de2f86d6a7a690192fbe91b3f46e0f2c8473'},
+    {'itoa-1.0.11.tar.gz': '49f1f14873335454500d59611f1cf4a4b0f786f9ac11f4312a78e4cf2566695b'},
+    {'js-sys-0.3.69.tar.gz': '29c15563dc2726973df627357ce0c9ddddbea194836909d655df6a75d2cf296d'},
+    {'lazy_static-1.4.0.tar.gz': 'e2abad23fbc42b3700f2f279844dc832adb2b2eb069b2df918f455c4e18cc646'},
+    {'libc-0.2.153.tar.gz': '9c198f91728a82281a64e1f4f9eeb25d82cb32a5de251c6bd1b5154d63a8e7bd'},
+    {'libc-0.2.155.tar.gz': '97b3888a4aecf77e811145cadf6eef5901f4782c53886191b2f693f24761847c'},
+    {'libm-0.2.8.tar.gz': '4ec2a862134d2a7d32d7983ddcdd1c4923530833c9f2ea1a44fc5fa473989058'},
+    {'linux-raw-sys-0.4.14.tar.gz': '78b3ae25bc7c8c38cec158d1f2757ee79e9b3740fbc7ccf0e59e4b08d793fa89'},
+    {'lock_api-0.4.11.tar.gz': '3c168f8615b12bc01f9c17e2eb0cc07dcae1940121185446edc3744920e8ef45'},
+    {'log-0.4.21.tar.gz': '90ed8c1e510134f979dbc4f070f87d4313098b704861a105fe34231c70a3901c'},
+    {'memchr-2.7.2.tar.gz': '6c8640c5d730cb13ebd907d8d04b52f55ac9a2eec55b440c8892f40d56c76c1d'},
+    {'memmap2-0.9.4.tar.gz': 'fe751422e4a8caa417e13c3ea66452215d7d63e19e604f4980461212f3ae1322'},
+    {'memoffset-0.9.1.tar.gz': '488016bfae457b036d996092f6cb448677611ce4449e970ceaf42695203f218a'},
+    {'num-traits-0.2.19.tar.gz': '071dfc062690e90b734c0b2273ce72ad0ffa95f0c74596bc250dcfd960262841'},
+    {'once_cell-1.19.0.tar.gz': '3fdb12b2476b595f9358c5161aa467c2438859caa136dec86c26fdd2efe17b92'},
+    {'oorandom-11.1.3.tar.gz': '0ab1bc2a289d34bd04a330323ac98a1b4bc82c9d9fcb1e66b63caa84da26b575'},
+    {'parking_lot-0.12.1.tar.gz': '3742b2c103b9f06bc9fff0a37ff4912935851bee6d36f3c02bcc755bcfec228f'},
+    {'parking_lot_core-0.9.9.tar.gz': '4c42a9226546d68acdd9c0a280d17ce19bfe27a46bf68784e4066115788d008e'},
+    {'plotters-0.3.6.tar.gz': 'a15b6eccb8484002195a3e44fe65a4ce8e93a625797a063735536fd59cb01cf3'},
+    {'plotters-backend-0.3.6.tar.gz': '414cec62c6634ae900ea1c56128dfe87cf63e7caece0852ec76aba307cebadb7'},
+    {'plotters-svg-0.3.6.tar.gz': '81b30686a7d9c3e010b84284bdd26a29f2138574f52f5eb6f794fc0ad924e705'},
+    {'portable-atomic-1.6.0.tar.gz': '7170ef9988bc169ba16dd36a7fa041e5c4cbeb6a35b76d4c03daded371eae7c0'},
+    {'ppv-lite86-0.2.17.tar.gz': '5b40af805b3121feab8a3c29f04d8ad262fa8e0561883e7653e024ae4479e6de'},
+    {'proc-macro2-1.0.80.tar.gz': 'a56dea16b0a29e94408b9aa5e2940a4eedbd128a1ba20e8f7ae60fd3d465af0e'},
+    {'proc-macro2-1.0.83.tar.gz': '0b33eb56c327dec362a9e55b3ad14f9d2f0904fb5a5b03b513ab5465399e9f43'},
+    {'proptest-1.4.0.tar.gz': '31b476131c3c86cb68032fdc5cb6d5a1045e3e42d96b69fa599fd77701e1f5bf'},
+    {'pyo3-0.21.1.tar.gz': 'a7a8b1990bd018761768d5e608a13df8bd1ac5f678456e0f301bb93e5f3ea16b'},
+    {'pyo3-build-config-0.21.1.tar.gz': '650dca34d463b6cdbdb02b1d71bfd6eb6b6816afc708faebb3bac1380ff4aef7'},
+    {'pyo3-ffi-0.21.1.tar.gz': '09a7da8fc04a8a2084909b59f29e1b8474decac98b951d77b80b26dc45f046ad'},
+    {'pyo3-macros-0.21.1.tar.gz': '4b8a199fce11ebb28e3569387228836ea98110e43a804a530a9fd83ade36d513'},
+    {'pyo3-macros-backend-0.21.1.tar.gz': '93fbbfd7eb553d10036513cb122b888dcd362a945a00b06c165f2ab480d4cc3b'},
+    {'quick-error-1.2.3.tar.gz': 'a1d01941d82fa2ab50be1e79e6714289dd7cde78eba4c074bc5a4374f650dfe0'},
+    {'quote-1.0.36.tar.gz': '0fa76aaf39101c457836aec0ce2316dbdc3ab723cdda1c6bd4e6ad4208acaca7'},
+    {'rand-0.8.5.tar.gz': '34af8d1a0e25924bc5b7c43c079c942339d8f0a8b57c39049bef581b46327404'},
+    {'rand_chacha-0.3.1.tar.gz': 'e6c10a63a0fa32252be49d21e7709d4d4baf8d231c2dbce1eaa8141b9b127d88'},
+    {'rand_core-0.6.4.tar.gz': 'ec0be4795e2f6a28069bec0b5ff3e2ac9bafc99e6a9a7dc3547996c5c816922c'},
+    {'rand_xorshift-0.3.0.tar.gz': 'd25bf25ec5ae4a3f1b92f929810509a2f53d7dca2f50b794ff57e3face536c8f'},
+    {'rayon-1.10.0.tar.gz': 'b418a60154510ca1a002a752ca9714984e21e4241e804d32555251faf8b78ffa'},
+    {'rayon-core-1.12.1.tar.gz': '1465873a3dfdaa8ae7cb14b4383657caab0b3e8a0aa9ae8e04b044854c8dfce2'},
+    {'redox_syscall-0.4.1.tar.gz': '4722d768eff46b75989dd134e5c353f0d6296e5aaa3132e776cbdb56be7731aa'},
+    {'regex-1.10.4.tar.gz': 'c117dbdfde9c8308975b6a18d71f3f385c89461f7b3fb054288ecf2a2058ba4c'},
+    {'regex-automata-0.4.6.tar.gz': '86b83b8b9847f9bf95ef68afb0b8e6cdb80f498442f5179a29fad448fcc1eaea'},
+    {'regex-syntax-0.8.3.tar.gz': 'adad44e29e4c806119491a7f06f03de4d1af22c3a680dd47f1e6e179439d1f56'},
+    {'rustix-0.38.34.tar.gz': '70dc5ec042f7a43c4a73241207cecc9873a06d45debb38b329f8541d85c2730f'},
+    {'rusty-fork-0.3.0.tar.gz': 'cb3dcc6e454c328bb824492db107ab7c0ae8fcffe4ad210136ef014458c1bc4f'},
+    {'ryu-1.0.17.tar.gz': 'e86697c916019a8588c99b5fac3cead74ec0b4b819707a682fd4d23fa0ce1ba1'},
+    {'ryu-1.0.18.tar.gz': 'f3cb5ba0dc43242ce17de99c180e96db90b235b8a9fdc9543c96d2209116bd9f'},
+    {'same-file-1.0.6.tar.gz': '93fc1dc3aaa9bfed95e02e6eadabb4baf7e3078b0bd1b4d7b6b0b68378900502'},
+    {'scopeguard-1.2.0.tar.gz': '94143f37725109f92c262ed2cf5e59bce7498c01bcc1502d7b9afe439a4e9f49'},
+    {'serde-1.0.197.tar.gz': '3fb1c873e1b9b056a4dc4c0c198b24c3ffa059243875552b2bd0933b1aee4ce2'},
+    {'serde-1.0.202.tar.gz': '226b61a0d411b2ba5ff6d7f73a476ac4f8bb900373459cd00fab8512828ba395'},
+    {'serde_derive-1.0.197.tar.gz': '7eb0b34b42edc17f6b7cac84a52a1c5f0e1bb2227e997ca9011ea3dd34e8610b'},
+    {'serde_derive-1.0.202.tar.gz': '6048858004bcff69094cd972ed40a32500f153bd3be9f716b2eed2e8217c4838'},
+    {'serde_json-1.0.115.tar.gz': '12dc5c46daa8e9fdf4f5e71b6cf9a53f2487da0e86e55808e2d35539666497dd'},
+    {'serde_json-1.0.117.tar.gz': '455182ea6142b14f93f4bc5320a2b31c1f266b66a4a5c858b013302a5d8cbfc3'},
+    {'smallvec-1.13.2.tar.gz': '3c5e1a9a646d36c3599cd173a41282daf47c44583ad367b8e6837255952e5c67'},
+    {'syn-2.0.59.tar.gz': '4a6531ffc7b071655e4ce2e04bd464c4830bb585a61cabb96cf808f05172615a'},
+    {'syn-2.0.66.tar.gz': 'c42f3f41a2de00b01c0aaad383c5a45241efc8b2d1eda5661812fda5f3cdcff5'},
+    {'target-lexicon-0.12.14.tar.gz': 'e1fc403891a21bcfb7c37834ba66a547a8f402146eba7265b5a6d88059c9ff2f'},
+    {'tempfile-3.10.1.tar.gz': '85b77fafb263dd9d05cbeac119526425676db3784113aa9295c88498cbf8bff1'},
+    {'tinytemplate-1.2.1.tar.gz': 'be4d6b5f19ff7664e8c98d03e2139cb510db9b0a60b55f8e8709b689d939b6bc'},
+    {'unarray-0.1.4.tar.gz': 'eaea85b334db583fe3274d12b4cd1880032beab409c0d774be044d4480ab9a94'},
+    {'unicode-ident-1.0.12.tar.gz': '3354b9ac3fae1ff6755cb6db53683adb661634f67557942dea4facebec0fee4b'},
+    {'unindent-0.2.3.tar.gz': 'c7de7d73e1754487cb58364ee906a499937a0dfabd86bcb980fa99ec8c8fa2ce'},
+    {'wait-timeout-0.2.0.tar.gz': '9f200f5b12eb75f8c1ed65abd4b2db8a6e1b138a20de009dacee265a2498f3f6'},
+    {'walkdir-2.5.0.tar.gz': '29790946404f91d9c5d06f9874efddea1dc06c5efe94541a7d6863108e3a5e4b'},
+    {'wasi-0.11.0+wasi-snapshot-preview1.tar.gz': '9c8d87e72b64a3b4db28d11ce29237c246188f4f51057d65a7eab63b7987e423'},
+    {'wasm-bindgen-0.2.92.tar.gz': '4be2531df63900aeb2bca0daaaddec08491ee64ceecbee5076636a3b026795a8'},
+    {'wasm-bindgen-backend-0.2.92.tar.gz': '614d787b966d3989fa7bb98a654e369c762374fd3213d212cfc0251257e747da'},
+    {'wasm-bindgen-macro-0.2.92.tar.gz': 'a1f8823de937b71b9460c0c34e25f3da88250760bec0ebac694b49997550d726'},
+    {'wasm-bindgen-macro-support-0.2.92.tar.gz': 'e94f17b526d0a461a191c78ea52bbce64071ed5c04c9ffe424dcb38f74171bb7'},
+    {'wasm-bindgen-shared-0.2.92.tar.gz': 'af190c94f2773fdb3729c55b007a722abb5384da03bc0986df4c289bf5567e96'},
+    {'web-sys-0.3.69.tar.gz': '77afa9a11836342370f4817622a2f0f418b134426d91a82dfb48f532d2ec13ef'},
+    {'winapi-util-0.1.8.tar.gz': '4d4cc384e1e73b93bafa6fb4f1df8c41695c8a91cf9c4c64358067d15a7b6c6b'},
+    {'windows_aarch64_gnullvm-0.48.5.tar.gz': '2b38e32f0abccf9987a4e3079dfb67dcd799fb61361e53e2882c3cbaf0d905d8'},
+    {'windows_aarch64_gnullvm-0.52.5.tar.gz': '7088eed71e8b8dda258ecc8bac5fb1153c5cffaf2578fc8ff5d61e23578d3263'},
+    {'windows_aarch64_msvc-0.48.5.tar.gz': 'dc35310971f3b2dbbf3f0690a219f40e2d9afcf64f9ab7cc1be722937c26b4bc'},
+    {'windows_aarch64_msvc-0.52.5.tar.gz': '9985fd1504e250c615ca5f281c3f7a6da76213ebd5ccc9561496568a2752afb6'},
+    {'windows_i686_gnu-0.48.5.tar.gz': 'a75915e7def60c94dcef72200b9a8e58e5091744960da64ec734a6c6e9b3743e'},
+    {'windows_i686_gnu-0.52.5.tar.gz': '88ba073cf16d5372720ec942a8ccbf61626074c6d4dd2e745299726ce8b89670'},
+    {'windows_i686_gnullvm-0.52.5.tar.gz': '87f4261229030a858f36b459e748ae97545d6f1ec60e5e0d6a3d32e0dc232ee9'},
+    {'windows_i686_msvc-0.48.5.tar.gz': '8f55c233f70c4b27f66c523580f78f1004e8b5a8b659e05a4eb49d4166cca406'},
+    {'windows_i686_msvc-0.52.5.tar.gz': 'db3c2bf3d13d5b658be73463284eaf12830ac9a26a90c717b7f771dfe97487bf'},
+    {'windows-sys-0.52.0.tar.gz': '282be5f36a8ce781fad8c8ae18fa3f9beff57ec1b52cb3de0789201425d9a33d'},
+    {'windows-targets-0.48.5.tar.gz': '9a2fa6e2155d7247be68c096456083145c183cbbbc2764150dda45a87197940c'},
+    {'windows-targets-0.52.5.tar.gz': '6f0713a46559409d202e70e28227288446bf7841d3211583a4b53e3f6d96e7eb'},
+    {'windows_x86_64_gnu-0.48.5.tar.gz': '53d40abd2583d23e4718fddf1ebec84dbff8381c07cae67ff7768bbf19c6718e'},
+    {'windows_x86_64_gnu-0.52.5.tar.gz': '4e4246f76bdeff09eb48875a0fd3e2af6aada79d409d33011886d3e1581517d9'},
+    {'windows_x86_64_gnullvm-0.48.5.tar.gz': '0b7b52767868a23d5bab768e390dc5f5c55825b6d30b86c844ff2dc7414044cc'},
+    {'windows_x86_64_gnullvm-0.52.5.tar.gz': '852298e482cd67c356ddd9570386e2862b5673c85bd5f88df9ab6802b334c596'},
+    {'windows_x86_64_msvc-0.48.5.tar.gz': 'ed94fce61571a4006852b7389a063ab983c02eb1bb37b47f8272ce92d06d9538'},
+    {'windows_x86_64_msvc-0.52.5.tar.gz': 'bec47e5bfd1bff0eeaf6d8b485cc1074891a197ab4225d504cb7a1ab88b02bf0'},
+]
+
+use_pip = True
+
+exts_list = [
+    ('safetensors', version, {
+        'use_pip_extras': 'numpy,torch',
+        'checksums': ['2f85fc50c4e07a21e95c24e07460fe6f7e2859d0ce88092838352b798ce711c2'],
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'ai'

From 18a60a9ee7458fa7c81522d7a52b210a7783aa90 Mon Sep 17 00:00:00 2001
From: WilleBell <cintiawillemyns@gmail.com>
Date: Mon, 27 May 2024 11:39:34 +0200
Subject: [PATCH 097/835] adding easyconfigs: MPICH-4.2.1-GCC-12.3.0.eb,
 GeoDict-2024.SP2-GCC-12.3.0.eb

---
 .../g/GeoDict/GeoDict-2024.SP2-GCC-12.3.0.eb  | 42 +++++++++++++++++++
 .../m/MPICH/MPICH-4.2.1-GCC-12.3.0.eb         | 20 +++++++++
 2 files changed, 62 insertions(+)
 create mode 100644 easybuild/easyconfigs/g/GeoDict/GeoDict-2024.SP2-GCC-12.3.0.eb
 create mode 100644 easybuild/easyconfigs/m/MPICH/MPICH-4.2.1-GCC-12.3.0.eb

diff --git a/easybuild/easyconfigs/g/GeoDict/GeoDict-2024.SP2-GCC-12.3.0.eb b/easybuild/easyconfigs/g/GeoDict/GeoDict-2024.SP2-GCC-12.3.0.eb
new file mode 100644
index 00000000000..be6419dedeb
--- /dev/null
+++ b/easybuild/easyconfigs/g/GeoDict/GeoDict-2024.SP2-GCC-12.3.0.eb
@@ -0,0 +1,42 @@
+easyblock = 'Tarball'
+
+name = 'GeoDict'
+version = '2024.SP2'
+
+homepage = 'https://www.math2market.com/geodict-software/geodict-applications.html'
+description = """
+The innovative and easy-to-use material simulator GeoDict is the most complete software
+solution for multi-scale 3D image processing, modeling of materials, visualization, material
+property characterization, simulation-based material development, and optimization of
+processes.
+"""
+
+toolchain = {'name': 'GCC', 'version': '12.3.0'}
+
+source_urls = [
+    'https://www.gddownload.de/Releases'
+]
+sources = [
+    '%(name)s2024-3-4-Linux-x86_64-ServicePack2.tar.gz',
+    '%(name)s2024-3-4-Linux-x86_64-ServicePack2-Tools.tar.gz'
+]
+checksums = [
+    {'GeoDict2024-3-4-Linux-x86_64-ServicePack2.tar.gz':
+     '049401063d892eac65696d7d1ed8d4b915c9a81bb13e325cc0657c60ce8aeb28'},
+    {'GeoDict2024-3-4-Linux-x86_64-ServicePack2-Tools.tar.gz':
+     '1b50fb840e8e78c225c748d73eaca60faedd822de33f20c716b1e98b15492eac'},
+]
+
+dependencies = [
+    ('X11', '20230603'),
+    ('MPICH', '4.2.1'),
+]
+
+modextrapaths = {'PATH': '.'}
+
+sanity_check_paths = {
+    'files': ['geodict2024'],
+    'dirs': ['Python', 'Tools'],
+}
+
+moduleclass = 'geo'
diff --git a/easybuild/easyconfigs/m/MPICH/MPICH-4.2.1-GCC-12.3.0.eb b/easybuild/easyconfigs/m/MPICH/MPICH-4.2.1-GCC-12.3.0.eb
new file mode 100644
index 00000000000..08f9b0e3d4d
--- /dev/null
+++ b/easybuild/easyconfigs/m/MPICH/MPICH-4.2.1-GCC-12.3.0.eb
@@ -0,0 +1,20 @@
+name = 'MPICH'
+version = '4.2.1'
+
+homepage = 'https://www.mpich.org/'
+description = """MPICH is a high-performance and widely portable implementation 
+of the Message Passing Interface (MPI) standard (MPI-1, MPI-2 and MPI-3)."""
+
+toolchain = {'name': 'GCC', 'version': '12.3.0'}
+
+source_urls = ['https://www.mpich.org/static/downloads/%(version)s']
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['23331b2299f287c3419727edc2df8922d7e7abbb9fd0ac74e03b9966f9ad42d7']
+
+configopts = 'FFLAGS="-w -fallow-argument-mismatch -O2" --with-devices=ch4:ucx --with-ucx=$EBROOTUCX'
+
+dependencies = [
+    ('UCX', '1.14.1'),
+]
+
+moduleclass = 'mpi'

From a3d6aac192a3a6b3272274545d10edd1b983d4d0 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com>
Date: Mon, 27 May 2024 12:42:36 +0200
Subject: [PATCH 098/835] Update nifty-1.2.1-foss-2023a.eb - fix comma

---
 easybuild/easyconfigs/n/nifty/nifty-1.2.1-foss-2023a.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/n/nifty/nifty-1.2.1-foss-2023a.eb b/easybuild/easyconfigs/n/nifty/nifty-1.2.1-foss-2023a.eb
index f02aa7ac12e..2c6c5ade6d3 100644
--- a/easybuild/easyconfigs/n/nifty/nifty-1.2.1-foss-2023a.eb
+++ b/easybuild/easyconfigs/n/nifty/nifty-1.2.1-foss-2023a.eb
@@ -36,7 +36,7 @@ configopts += '-DPYTHON_EXECUTABLE="$EBROOTPYTHON/bin/python" -DBUILD_NIFTY_PYTH
 # export PYTHON_MODULE_INSTALL_DIR to fix make install
 preinstallopts = 'export PYTHON_MODULE_INSTALL_DIR="%(builddir)s/easybuild_obj/python/" '
 
-files_to_copy = [(['python/nifty'], 'lib/python%(pyshortver)s/site-packages'),]
+files_to_copy = [(['python/nifty'], 'lib/python%(pyshortver)s/site-packages')]
 
 sanity_check_paths = {
     'files': [],

From 0442b4ea7836714ff7f59bceb8e5db3dbe5e75b8 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Mon, 27 May 2024 13:06:33 +0200
Subject: [PATCH 099/835] add ec for deps

---
 .../Boost.Python-1.83.0-GCC-12.3.0.eb         | 24 +++++++++
 .../pycocotools-2.0.7-foss-2023a.eb           | 25 ++++++++++
 .../python-blosc-1.11.0-foss-2023a.eb         | 36 ++++++++++++++
 .../x/xtensor/xtensor-0.24.7-foss-2023a.eb    | 49 +++++++++++++++++++
 4 files changed, 134 insertions(+)
 create mode 100644 easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.83.0-GCC-12.3.0.eb
 create mode 100644 easybuild/easyconfigs/p/pycocotools/pycocotools-2.0.7-foss-2023a.eb
 create mode 100644 easybuild/easyconfigs/p/python-blosc/python-blosc-1.11.0-foss-2023a.eb
 create mode 100644 easybuild/easyconfigs/x/xtensor/xtensor-0.24.7-foss-2023a.eb

diff --git a/easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.83.0-GCC-12.3.0.eb b/easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.83.0-GCC-12.3.0.eb
new file mode 100644
index 00000000000..cea3b40eb66
--- /dev/null
+++ b/easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.83.0-GCC-12.3.0.eb
@@ -0,0 +1,24 @@
+easyblock = 'EB_Boost'
+
+name = 'Boost.Python'
+version = '1.83.0'
+
+homepage = 'https://boostorg.github.io/python'
+description = """Boost.Python is a C++ library which enables seamless interoperability between C++
+ and the Python programming language."""
+
+toolchain = {'name': 'GCC', 'version': '12.3.0'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://boostorg.jfrog.io/artifactory/main/release/%(version)s/source/']
+sources = ['boost_1_83_0.tar.gz']
+checksums = ['c0685b68dd44cc46574cce86c4e17c0f611b15e195be9848dfd0769a0a207628']
+
+dependencies = [
+    ('Boost', '1.82.0'),
+    ('Python', '3.11.3'),
+]
+
+only_python_bindings = True
+
+moduleclass = 'lib'
\ No newline at end of file
diff --git a/easybuild/easyconfigs/p/pycocotools/pycocotools-2.0.7-foss-2023a.eb b/easybuild/easyconfigs/p/pycocotools/pycocotools-2.0.7-foss-2023a.eb
new file mode 100644
index 00000000000..666074add24
--- /dev/null
+++ b/easybuild/easyconfigs/p/pycocotools/pycocotools-2.0.7-foss-2023a.eb
@@ -0,0 +1,25 @@
+easyblock = 'PythonPackage'
+
+name = 'pycocotools'
+version = '2.0.7'
+
+homepage = 'https://pypi.org/project/pycocotools'
+description = "Official APIs for the MS-COCO dataset"
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+sources = [SOURCE_TAR_GZ]
+checksums = ['da8b7815196eebf0adabf67fcc459126cbc6498bbc6ab1fd144c371465d86879']
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('matplotlib', '3.7.2'),
+]
+
+download_dep_fail = True
+use_pip = True
+
+sanity_pip_check = True
+
+moduleclass = 'data'
diff --git a/easybuild/easyconfigs/p/python-blosc/python-blosc-1.11.0-foss-2023a.eb b/easybuild/easyconfigs/p/python-blosc/python-blosc-1.11.0-foss-2023a.eb
new file mode 100644
index 00000000000..3a8083cc0d5
--- /dev/null
+++ b/easybuild/easyconfigs/p/python-blosc/python-blosc-1.11.0-foss-2023a.eb
@@ -0,0 +1,36 @@
+easyblock = 'PythonBundle'
+
+name = 'python-blosc'
+version = '1.11.0'
+
+homepage = 'https://github.com/Blosc/python-blosc/'
+description = "A Python wrapper for the extremely fast Blosc compression library."
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+builddependencies = [
+    ('scikit-build', '0.17.6'),
+    ('CMake', '3.26.3'),
+]
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('Blosc', '1.21.5'),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+local_preinstallopts = 'export USE_SYSTEM_BLOSC=1 && '
+local_preinstallopts += 'export Blosc_ROOT=$EBROOTBLOSC && '
+
+exts_list = [
+    ('blosc', version, {
+        'preinstallopts': local_preinstallopts,
+        'checksums': ['c985b8f435dbc49b190fe88947539ed710ad0e9aaaf83778acc506a71ada7bd2'],
+    }),
+]
+
+sanity_check_commands = ["python -m blosc.test"]
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/x/xtensor/xtensor-0.24.7-foss-2023a.eb b/easybuild/easyconfigs/x/xtensor/xtensor-0.24.7-foss-2023a.eb
new file mode 100644
index 00000000000..8b30ddf8a2f
--- /dev/null
+++ b/easybuild/easyconfigs/x/xtensor/xtensor-0.24.7-foss-2023a.eb
@@ -0,0 +1,49 @@
+easyblock = 'Bundle'
+
+name = 'xtensor'
+version = '0.24.7'
+
+homepage = 'https://github.com/xtensor-stack/xtensor'
+description = "xtensor is a C++ library meant for numerical analysis with multi-dimensional array expressions."
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+builddependencies = [
+    ('CMake', '3.26.3'),
+    ('pybind11', '2.11.1'),
+]
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+]
+
+default_easyblock = 'CMakeMake'
+
+default_component_specs = {
+    'source_urls': ['https://github.com/xtensor-stack/%(name)s/archive/'],
+    'sources': ['%(version)s.tar.gz'],
+    'start_dir': '%(name)s-%(version)s',
+}
+
+components = [
+    ('xtl', '0.7.5', {
+        'checksums': ['3286fef5fee5d58f82f7b91375cd449c819848584bae9367893501114d923cbe'],
+    }),
+    ('xsimd', '8.0.5', {
+        'checksums': ['0e1b5d973b63009f06a3885931a37452580dbc8d7ca8ad40d4b8c80d2a0f84d7'],
+    }),
+    ('xtensor', version, {
+        'checksums': ['0fbbd524dde2199b731b6af99b16063780de6cf1d0d6cb1f3f4d4ceb318f3106'],
+    }),
+    ('xtensor-python', '0.26.1', {
+        'checksums': ['eb64155c6824be471decf93927beedae3645714c8ce92f38e037434db2c2454a'],
+        'configopts': '-DPYTHON_EXECUTABLE=$EBROOTPYTHON/bin/python',
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['include/xtensor.hpp', 'lib/pkgconfig/xsimd.pc'],
+    'dirs': ['include/xsimd', 'include/xtensor', 'include/xtensor-python', 'include/xtl', 'lib/cmake'],
+}
+
+moduleclass = 'lib'

From 7d37a7df648a6f630956baafcd198d731c3b4327 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com>
Date: Mon, 27 May 2024 13:26:11 +0200
Subject: [PATCH 100/835] Update Boost.Python-1.83.0-GCC-12.3.0.eb fix end line

---
 .../b/Boost.Python/Boost.Python-1.83.0-GCC-12.3.0.eb            | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.83.0-GCC-12.3.0.eb b/easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.83.0-GCC-12.3.0.eb
index cea3b40eb66..6a5ffcc08a7 100644
--- a/easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.83.0-GCC-12.3.0.eb
+++ b/easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.83.0-GCC-12.3.0.eb
@@ -21,4 +21,4 @@ dependencies = [
 
 only_python_bindings = True
 
-moduleclass = 'lib'
\ No newline at end of file
+moduleclass = 'lib'

From 0c95b0d8221aaa7301fc9a7ddaa5078be09559ee Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Mon, 27 May 2024 20:42:03 +0200
Subject: [PATCH 101/835] adding easyconfigs: TF-COMB-1.1-foss-2022b.eb,
 TOBIAS-0.16.1-foss-2022b.eb, svist4get-1.3.1-foss-2022b.eb,
 adjustText-0.7.3-foss-2022b.eb, python-louvain-0.16-foss-2022b.eb,
 GOATOOLS-1.4.5-foss-2022b.eb, pydot-2.0.0-GCCcore-12.2.0.eb

---
 .../adjustText/adjustText-0.7.3-foss-2022b.eb | 27 +++++++
 .../g/GOATOOLS/GOATOOLS-1.4.5-foss-2022b.eb   | 73 +++++++++++++++++++
 .../p/pydot/pydot-2.0.0-GCCcore-12.2.0.eb     | 25 +++++++
 .../python-louvain-0.16-foss-2022b.eb         | 24 ++++++
 .../s/svist4get/svist4get-1.3.1-foss-2022b.eb | 62 ++++++++++++++++
 .../t/TF-COMB/TF-COMB-1.1-foss-2022b.eb       | 52 +++++++++++++
 .../t/TOBIAS/TOBIAS-0.16.1-foss-2022b.eb      | 55 ++++++++++++++
 7 files changed, 318 insertions(+)
 create mode 100644 easybuild/easyconfigs/a/adjustText/adjustText-0.7.3-foss-2022b.eb
 create mode 100644 easybuild/easyconfigs/g/GOATOOLS/GOATOOLS-1.4.5-foss-2022b.eb
 create mode 100644 easybuild/easyconfigs/p/pydot/pydot-2.0.0-GCCcore-12.2.0.eb
 create mode 100644 easybuild/easyconfigs/p/python-louvain/python-louvain-0.16-foss-2022b.eb
 create mode 100644 easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2022b.eb
 create mode 100644 easybuild/easyconfigs/t/TF-COMB/TF-COMB-1.1-foss-2022b.eb
 create mode 100644 easybuild/easyconfigs/t/TOBIAS/TOBIAS-0.16.1-foss-2022b.eb

diff --git a/easybuild/easyconfigs/a/adjustText/adjustText-0.7.3-foss-2022b.eb b/easybuild/easyconfigs/a/adjustText/adjustText-0.7.3-foss-2022b.eb
new file mode 100644
index 00000000000..4c13c121047
--- /dev/null
+++ b/easybuild/easyconfigs/a/adjustText/adjustText-0.7.3-foss-2022b.eb
@@ -0,0 +1,27 @@
+easyblock = 'PythonPackage'
+
+name = 'adjustText'
+version = '0.7.3'
+
+homepage = 'https://github.com/Phlya/adjustText'
+description = "A small library for automatically adjustment of text position in matplotlib plots to minimize overlaps."
+
+toolchain = {'name': 'foss', 'version': '2022b'}
+
+sources = [SOURCE_TAR_GZ]
+checksums = ['b90e275a95b4d980cbbac7967914b8d66477c09bc346a0b3c9e2125bba664b06']
+
+dependencies = [
+    ('Python', '3.10.8'),
+    ('matplotlib', '3.7.0'),
+    ('SciPy-bundle', '2023.02'),
+]
+
+download_dep_fail = True
+use_pip = True
+
+sanity_pip_check = True
+
+options = {'modulename': 'adjustText'}
+
+moduleclass = 'tools'
diff --git a/easybuild/easyconfigs/g/GOATOOLS/GOATOOLS-1.4.5-foss-2022b.eb b/easybuild/easyconfigs/g/GOATOOLS/GOATOOLS-1.4.5-foss-2022b.eb
new file mode 100644
index 00000000000..1f34441c1cb
--- /dev/null
+++ b/easybuild/easyconfigs/g/GOATOOLS/GOATOOLS-1.4.5-foss-2022b.eb
@@ -0,0 +1,73 @@
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+# Author: Denis Kristak
+# Update: Pavel Tománek (Inuits)
+easyblock = 'PythonPackage'
+
+name = 'GOATOOLS'
+version = '1.4.5'
+
+homepage = 'https://github.com/tanghaibao/goatools'
+description = "A Python library for Gene Ontology analyses"
+
+toolchain = {'name': 'foss', 'version': '2022b'}
+
+# must download sources via git to preserve .git directory,
+# since setuptools-scm is used to determine version
+sources = [{
+    'git_config': {
+        'url': 'https://github.com/tanghaibao',
+        'repo_name': 'goatools',
+        'tag': 'v%(version)s',
+        'keep_git_dir': True,
+    },
+    'filename': SOURCE_TAR_GZ,
+}]
+checksums = ['ba92ad89f9c91b3aadd1c36ae58f77c1725e64dbf00e27910e5b00d3d7348c61']
+
+builddependencies = [('cURL', '7.86.0')]
+
+dependencies = [
+    ('Python', '3.10.8'),
+    ('SciPy-bundle', '2023.02'),
+    ('XlsxWriter', '3.1.2'),
+    ('statsmodels', '0.14.0'),
+    ('pydot', '2.0.0'),
+    ('openpyxl', '3.1.2'),
+]
+
+exts_defaultclass = 'PythonPackage'
+exts_default_options = {
+    'source_urls': [PYPI_SOURCE],
+    'download_dep_fail': True,
+    'use_pip': True,
+    'sanity_pip_check': True,
+}
+
+exts_list = [
+    ('ftpretty', '0.4.0', {
+        'checksums': ['61233b9212f2cceec96ee2c972738fa31cae7248e92d0874c99c04ee739bb5a9'],
+    }),
+]
+
+download_dep_fail = True
+use_pip = True
+
+postinstallcmds = ["cp -a %(builddir)s/goatools/data/ %(installdir)s/"]
+
+sanity_check_paths = {
+    'files': ['bin/find_enrichment.py'],
+    'dirs': ['data', 'lib/python%(pyshortver)s/site-packages'],
+}
+
+# example test run, see https://github.com/tanghaibao/goatools/blob/master/run.sh
+sanity_check_commands = [
+    "mkdir -p %(builddir)s",
+    "cd %(builddir)s && curl -OL http://geneontology.org/ontology/go-basic.obo",
+    "cd %(builddir)s && curl -OL http://www.geneontology.org/ontology/subsets/goslim_generic.obo",
+    "cd %(builddir)s && cp -a %(installdir)s/data .",
+    "cd %(builddir)s && find_enrichment.py --pval=0.05 --indent data/study data/population data/association",
+]
+
+sanity_pip_check = True
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/p/pydot/pydot-2.0.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/pydot/pydot-2.0.0-GCCcore-12.2.0.eb
new file mode 100644
index 00000000000..d39e368e0cd
--- /dev/null
+++ b/easybuild/easyconfigs/p/pydot/pydot-2.0.0-GCCcore-12.2.0.eb
@@ -0,0 +1,25 @@
+# updated: Denis Kristak, Pavel Tománek (INUITS)
+easyblock = 'PythonBundle'
+
+name = 'pydot'
+version = '2.0.0'
+
+homepage = 'https://github.com/pydot/pydot'
+description = "Python interface to Graphviz's Dot language."
+
+toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+
+builddependencies = [('binutils', '2.39')]
+
+dependencies = [('Python', '3.10.8')]
+
+exts_list = [
+    (name, version, {
+        'checksums': ['60246af215123fa062f21cd791be67dda23a6f280df09f68919e637a1e4f3235'],
+    }),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+moduleclass = 'vis'
diff --git a/easybuild/easyconfigs/p/python-louvain/python-louvain-0.16-foss-2022b.eb b/easybuild/easyconfigs/p/python-louvain/python-louvain-0.16-foss-2022b.eb
new file mode 100644
index 00000000000..6e61e7cf51b
--- /dev/null
+++ b/easybuild/easyconfigs/p/python-louvain/python-louvain-0.16-foss-2022b.eb
@@ -0,0 +1,24 @@
+easyblock = 'PythonPackage'
+
+name = 'python-louvain'
+version = '0.16'
+
+homepage = 'https://pypi.org/project/python-louvain'
+description = "Louvain algorithm for community detection"
+
+toolchain = {'name': 'foss', 'version': '2022b'}
+
+sources = [SOURCE_TAR_GZ]
+
+dependencies = [
+    ('Python', '3.10.8'),
+    ('networkx', '2.8.8'),
+]
+
+download_dep_fail = True
+use_pip = True
+sanity_pip_check = True
+
+options = {'modulename': 'community'}
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2022b.eb b/easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2022b.eb
new file mode 100644
index 00000000000..df059031ffe
--- /dev/null
+++ b/easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2022b.eb
@@ -0,0 +1,62 @@
+# Author: J. Sassmannshausen (Imperial College London/UK)
+# Update: Pavel Tománek (Inuits)
+
+easyblock = 'PythonBundle'
+
+name = 'svist4get'
+version = '1.3.1'
+
+homepage = 'https://github.com/art-egorov/svist4get'
+description = """Svist4get is a simple bioinformatics tool for visualization of 
+genomic signal tracks in user-defined genomic windows, either arbitrary selected 
+by genomic coordinates or anchored to particular transcripts or genes."""
+
+toolchain = {'name': 'foss', 'version': '2022b'}
+
+dependencies = [
+    ('Python', '3.10.8'),
+    ('pybedtools', '0.9.0'),
+    ('Biopython', '1.81'),
+    ('Pillow', '9.4.0'),
+    ('ImageMagick', '7.1.0-53'),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    ('reportlab', '3.6.9', {
+        'patches': ['reportlab-3.6.12-fontconfig.patch'],
+        'checksums': ['5d0cc3682456ad213150f6dbffe7d47eab737d809e517c316103376be548fb84',
+                      # reportlab-3.6.12-fontconfig.patch:
+                      '2cc9b40e09650b7404ee9c4d72b134739acc89bacac3da58131cef2308726297'],
+    }),
+    ('configs', '3.0.3', {
+        'sources': ['%(name)s-%(version)s.zip'],
+        'checksums': ['a5ab09e04e441dac6aa856a71fbf5ffc62954352630f79d311b8f8a31d9ce19c'],
+    }),
+    ('argparse', '1.4.0', {
+        'checksums': ['62b089a55be1d8949cd2bc7e0df0bddb9e028faefc8c32038cc84862aefdd6e4'],
+    }),
+    ('Wand', '0.6.10', {
+        'checksums': ['373f4a7f2866c868c31ce910e1f9b36a92d132640a20068ec17cea3284fedc57'],
+    }),
+    ('statistics', '1.0.3.5', {
+        'checksums': ['2dc379b80b07bf2ddd5488cad06b2b9531da4dd31edb04dc9ec0dc226486c138'],
+    }),
+    (name, version, {
+        'checksums': ['22311fdc956cca531dac7ba924744e8f870a57bc6f27cbe4e8ba9854117e720c'],
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['bin/svist4get', 'bin/svist4get_copier'],
+    'dirs': ['lib'],
+}
+
+sanity_check_commands = [
+    "svist4get --help",
+    "svist4get -v",
+]
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/t/TF-COMB/TF-COMB-1.1-foss-2022b.eb b/easybuild/easyconfigs/t/TF-COMB/TF-COMB-1.1-foss-2022b.eb
new file mode 100644
index 00000000000..0f8dab61983
--- /dev/null
+++ b/easybuild/easyconfigs/t/TF-COMB/TF-COMB-1.1-foss-2022b.eb
@@ -0,0 +1,52 @@
+easyblock = 'PythonBundle'
+
+name = 'TF-COMB'
+version = '1.1'
+
+homepage = 'https://github.com/loosolab/TF-COMB'
+description = """Transcription Factor Co-Occurrence using Market Basket analysis."""
+
+toolchain = {'name': 'foss', 'version': '2022b'}
+
+dependencies = [
+    ('Python', '3.10.8'),
+    ('SciPy-bundle', '2023.02'),
+    ('tqdm', '4.64.1'),
+    ('Pysam', '0.21.0'),
+    ('matplotlib', '3.7.0'),
+    ('networkx', '2.8.8'),
+    ('Graphviz', '8.1.0'),
+    ('statsmodels', '0.14.0'),
+    ('dill', '0.3.7'),
+    ('Seaborn', '0.12.2'),
+    ('IPython', '8.14.0'),
+    ('TOBIAS', '0.16.1'),
+    ('python-louvain', '0.16'),
+    ('GOATOOLS', '1.4.5'),
+    ('qnorm', '0.8.1'),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+# remove graphviz from deps - the pip check failing, should be "import gv"
+local_tfcomb_preinstallopts = "sed -i '70d' setup.py && "
+# fix "import graphviz" to "import gv"
+local_tfcomb_preinstallopts += "sed -i 's/import graphviz/import gv as graphviz/' tfcomb/plotting.py && "
+
+exts_list = [
+    ('uropa', '4.0.3', {
+        'checksums': ['e0b648881b95f301e3f3ecc924314995312f10b0cbabf96d5a5ce2fb18c53a59'],
+    }),
+    (name, version, {
+        'preinstallopts': local_tfcomb_preinstallopts,
+        'modulename': 'tfcomb',
+        'checksums': ['5b718061660e0f9f94d86459eb742ca81de5851b0defd8b08c8a7a7e3370c253'],
+    }),
+]
+
+sanity_check_commands = [
+    "python -c 'import gv'",
+]
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/t/TOBIAS/TOBIAS-0.16.1-foss-2022b.eb b/easybuild/easyconfigs/t/TOBIAS/TOBIAS-0.16.1-foss-2022b.eb
new file mode 100644
index 00000000000..9150965319e
--- /dev/null
+++ b/easybuild/easyconfigs/t/TOBIAS/TOBIAS-0.16.1-foss-2022b.eb
@@ -0,0 +1,55 @@
+easyblock = 'PythonBundle'
+
+name = 'TOBIAS'
+version = '0.16.1'
+
+homepage = 'https://github.com/loosolab/TOBIAS'
+description = """TOBIAS is a collection of command-line bioinformatics tools 
+for performing footprinting analysis on ATAC-seq data."""
+
+toolchain = {'name': 'foss', 'version': '2022b'}
+
+dependencies = [
+    ('Python', '3.10.8'),
+    ('SciPy-bundle', '2023.02'),
+    ('matplotlib', '3.7.0'),
+    ('Seaborn', '0.12.2'),
+    ('Pysam', '0.21.0'),
+    ('pybedtools', '0.9.0'),
+    ('boto3', '1.26.163'),
+    ('pyBigWig', '0.3.22'),
+    ('scikit-learn', '1.2.1'),
+    ('PyYAML', '6.0'),
+    ('XlsxWriter', '3.1.2'),
+    ('svist4get', '1.3.1'),
+    ('adjustText', '0.7.3'),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    ('kneed', '0.8.5', {
+        'checksums': ['a4847ac4f1d04852fea278d5de7aa8bfdc3beb7fbca4a182fec0f0efee43f4b1'],
+    }),
+    ('logomaker', '0.8', {
+        'checksums': ['d8c7501a7d6d7961cd68e5a44e939000ebf1b0c4197a0c9198351e1d681d3f6d'],
+    }),
+    ('MOODS-python', '1.9.4.1', {
+        'modulename': 'MOODS',
+        'checksums': ['b3b5e080cb0cd13c0fd175d0ee0d453fde3e42794fa7ac39a4f6db1ac5ddb4cc'],
+    }),
+    ('PyPDF2', '3.0.1', {
+        'modulename': 'PyPDF2',
+        'checksums': ['a74408f69ba6271f71b9352ef4ed03dc53a31aa404d29b5d31f53bfecfee1440'],
+    }),
+    ('tobias', version, {
+        # remove pyBigWig dependency - pip_check fails with "import pybigwig"
+        'preinstallopts': "sed -i '81d' setup.py && ",
+        'checksums': ['c46267c01287be06201b3e6f7a36daad1ad86d6c578f96e878501be7da7fd109'],
+    }),
+]
+
+sanity_check_commands = ["python -c 'import pyBigWig'"]
+
+moduleclass = 'bio'

From 6212ea21536f581688c7e6ff613f1a24e32a5c06 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Mon, 27 May 2024 21:34:07 +0200
Subject: [PATCH 102/835] add qnorm dep + checksum

---
 .../python-louvain-0.16-foss-2022b.eb         |  1 +
 .../q/qnorm/qnorm-0.8.1-foss-2022b.eb         | 36 +++++++++++++++++++
 2 files changed, 37 insertions(+)
 create mode 100644 easybuild/easyconfigs/q/qnorm/qnorm-0.8.1-foss-2022b.eb

diff --git a/easybuild/easyconfigs/p/python-louvain/python-louvain-0.16-foss-2022b.eb b/easybuild/easyconfigs/p/python-louvain/python-louvain-0.16-foss-2022b.eb
index 6e61e7cf51b..e69d4eb0dbe 100644
--- a/easybuild/easyconfigs/p/python-louvain/python-louvain-0.16-foss-2022b.eb
+++ b/easybuild/easyconfigs/p/python-louvain/python-louvain-0.16-foss-2022b.eb
@@ -9,6 +9,7 @@ description = "Louvain algorithm for community detection"
 toolchain = {'name': 'foss', 'version': '2022b'}
 
 sources = [SOURCE_TAR_GZ]
+checksums = ['b7ba2df5002fd28d3ee789a49532baad11fe648e4f2117cf0798e7520a1da56b']
 
 dependencies = [
     ('Python', '3.10.8'),
diff --git a/easybuild/easyconfigs/q/qnorm/qnorm-0.8.1-foss-2022b.eb b/easybuild/easyconfigs/q/qnorm/qnorm-0.8.1-foss-2022b.eb
new file mode 100644
index 00000000000..99c6ebe1e23
--- /dev/null
+++ b/easybuild/easyconfigs/q/qnorm/qnorm-0.8.1-foss-2022b.eb
@@ -0,0 +1,36 @@
+easyblock = 'PythonPackage'
+
+name = 'qnorm'
+version = '0.8.1'
+
+homepage = 'https://github.com/Maarten-vd-Sande/qnorm'
+description = "Fast-ish (and correct!) quantile normalization in Python"
+
+toolchain = {'name': 'foss', 'version': '2022b'}
+
+dependencies = [
+    ('Python', '3.10.8'),
+    ('SciPy-bundle', '2023.02'),
+    ('numba', '0.58.1'),
+]
+
+sources = [SOURCE_TAR_GZ]
+checksums = ['61b2f3ef09a9c552a4f3b83dc438cb13f191fa190164361a3a508c4777eed3c7']
+
+download_dep_fail = True
+use_pip = True
+
+# pyproject.toml included in qnorm source tarball does not include standard fields,
+# it's only there to be read by setup.py...
+preinstallopts = "sed -i 's/pyproject.toml/pyproject.toml_/g' setup.py && mv pyproject.toml pyproject.toml_ && "
+
+sanity_check_paths = {
+    'files': ['bin/qnorm'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = ["qnorm --help"]
+
+sanity_pip_check = True
+
+moduleclass = 'bio'

From 70d790457bc00847c15ae3f8cc4ac7576f47d9df Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Tue, 28 May 2024 10:57:00 +0200
Subject: [PATCH 103/835] fix svist4get - delete statistics dep

---
 .../easyconfigs/s/svist4get/svist4get-1.3.1-foss-2022b.eb    | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2022b.eb b/easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2022b.eb
index df059031ffe..72d977763e9 100644
--- a/easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2022b.eb
+++ b/easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2022b.eb
@@ -41,10 +41,9 @@ exts_list = [
     ('Wand', '0.6.10', {
         'checksums': ['373f4a7f2866c868c31ce910e1f9b36a92d132640a20068ec17cea3284fedc57'],
     }),
-    ('statistics', '1.0.3.5', {
-        'checksums': ['2dc379b80b07bf2ddd5488cad06b2b9531da4dd31edb04dc9ec0dc226486c138'],
-    }),
     (name, version, {
+        # unpin statistics dependency - it is old package and interfering with python lib statistics
+        'preinstallopts': "sed -i 's/statistics//' setup.py && ",
         'checksums': ['22311fdc956cca531dac7ba924744e8f870a57bc6f27cbe4e8ba9854117e720c'],
     }),
 ]

From 9adc2be4402836f927967c8b9808e2af7fa4064c Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Tue, 28 May 2024 13:16:05 +0200
Subject: [PATCH 104/835] fix networkx version to pass tests

---
 .../p/python-louvain/python-louvain-0.16-foss-2022b.eb          | 2 +-
 easybuild/easyconfigs/t/TF-COMB/TF-COMB-1.1-foss-2022b.eb       | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/easybuild/easyconfigs/p/python-louvain/python-louvain-0.16-foss-2022b.eb b/easybuild/easyconfigs/p/python-louvain/python-louvain-0.16-foss-2022b.eb
index e69d4eb0dbe..5c6085a41e6 100644
--- a/easybuild/easyconfigs/p/python-louvain/python-louvain-0.16-foss-2022b.eb
+++ b/easybuild/easyconfigs/p/python-louvain/python-louvain-0.16-foss-2022b.eb
@@ -13,7 +13,7 @@ checksums = ['b7ba2df5002fd28d3ee789a49532baad11fe648e4f2117cf0798e7520a1da56b']
 
 dependencies = [
     ('Python', '3.10.8'),
-    ('networkx', '2.8.8'),
+    ('networkx', '3.0'),
 ]
 
 download_dep_fail = True
diff --git a/easybuild/easyconfigs/t/TF-COMB/TF-COMB-1.1-foss-2022b.eb b/easybuild/easyconfigs/t/TF-COMB/TF-COMB-1.1-foss-2022b.eb
index 0f8dab61983..2dcd3a55fdf 100644
--- a/easybuild/easyconfigs/t/TF-COMB/TF-COMB-1.1-foss-2022b.eb
+++ b/easybuild/easyconfigs/t/TF-COMB/TF-COMB-1.1-foss-2022b.eb
@@ -14,7 +14,7 @@ dependencies = [
     ('tqdm', '4.64.1'),
     ('Pysam', '0.21.0'),
     ('matplotlib', '3.7.0'),
-    ('networkx', '2.8.8'),
+    ('networkx', '3.0'),
     ('Graphviz', '8.1.0'),
     ('statsmodels', '0.14.0'),
     ('dill', '0.3.7'),

From 8c87d280779fc084627639466ed170c492a686e5 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com>
Date: Tue, 28 May 2024 13:37:33 +0200
Subject: [PATCH 105/835] Update GOATOOLS-1.4.5-foss-2022b.eb checksum

---
 easybuild/easyconfigs/g/GOATOOLS/GOATOOLS-1.4.5-foss-2022b.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/g/GOATOOLS/GOATOOLS-1.4.5-foss-2022b.eb b/easybuild/easyconfigs/g/GOATOOLS/GOATOOLS-1.4.5-foss-2022b.eb
index 1f34441c1cb..46728a39e63 100644
--- a/easybuild/easyconfigs/g/GOATOOLS/GOATOOLS-1.4.5-foss-2022b.eb
+++ b/easybuild/easyconfigs/g/GOATOOLS/GOATOOLS-1.4.5-foss-2022b.eb
@@ -22,7 +22,7 @@ sources = [{
     },
     'filename': SOURCE_TAR_GZ,
 }]
-checksums = ['ba92ad89f9c91b3aadd1c36ae58f77c1725e64dbf00e27910e5b00d3d7348c61']
+checksums = [None]
 
 builddependencies = [('cURL', '7.86.0')]
 

From 9e61515095a6388a3aad6ac4329e906f44823cc3 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Tue, 28 May 2024 17:24:15 +0200
Subject: [PATCH 106/835] add harmonypy, cellphonedb, decoupler

---
 ...e-cell-python-bundle-2024.02-foss-2023a.eb | 29 +++++++++++++++++++
 1 file changed, 29 insertions(+)

diff --git a/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb b/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb
index 28a63c085a6..d554e9fddca 100644
--- a/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb
+++ b/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb
@@ -125,6 +125,35 @@ exts_list = [
         'preinstallopts': "sed -i '28d' setup.py && ",
         'checksums': ['8c12ddccb72c41c96c6a5abceb52e7a76f439a9ab94fb092aa86ee3c1292383a'],
     }),
+    ('harmonypy', '0.0.9', {
+        'checksums': ['85bfdd4e6ec6e0fa8816a276639358d3598a40d60ba9f7a5d9dada8706be8c4d'],
+    }),
+    ('fbpca', '1.0', {
+        'checksums': ['150677642479663f317fdbb5e06dab3f98721cf7031bb4a84113d7a631c472d1'],
+    }),
+    ('geosketch', '1.2', {
+        'checksums': ['bbfe97366b91c5927b6076d5a6738d9cfbe094efb5ac1117aab7a30b6081cc4e'],
+    }),
+    ('python_circos', '0.3.0', {
+        'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl',
+        'modulename': 'pycircos',
+        'checksums': ['410eaffc4eb2933cd688897356813da23310f5e2f14a8bceb003e9b96faa715b'],
+    }),
+    ('mizani', '0.9.3', {
+        'checksums': ['fb61339e9e4711850e902ca286b1ae75255f483823d891aa0515b426d56c606d'],
+    }),
+    ('plotnine', '0.12.4', {
+        'checksums': ['adc41a672503594445a8fa19872799253bd0784cdbd5a1cc16657a1dd20ba905'],
+    }),
+    ('ktplotspy', '0.2.3', {
+        'checksums': ['9a1e3646217e6e99f59ab2258dfd76120cf1f50880c9cb2f9005de397c00f0a9'],
+    }),
+    ('cellphonedb', '5.0.0', {
+        'checksums': ['1c96173d8527f1655216d265fc50a28ea3360d70486afa5050e3f5565fa3a8cd'],
+    }),
+    ('decoupler', '1.6.0', {
+        'checksums': ['dde501f4d3e55a260f716e51b871bee403bc8aaa6b66799df0e42dee0787b98d'],
+    }),
 ]
 
 use_pip = True

From 8c29963581daf3828cdb15d21df08083dc81bda2 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Tue, 28 May 2024 18:02:21 +0000
Subject: [PATCH 107/835] adding easyconfigs: Brunsli-0.1-GCCcore-13.2.0.eb,
 GDAL-3.9.0-foss-2023b.eb, libgeotiff-1.7.3-GCCcore-13.2.0.eb,
 GEOS-3.12.1-GCC-13.2.0.eb

---
 .../b/Brunsli/Brunsli-0.1-GCCcore-13.2.0.eb   | 53 ++++++++++++
 .../g/GDAL/GDAL-3.9.0-foss-2023b.eb           | 81 +++++++++++++++++++
 .../g/GEOS/GEOS-3.12.1-GCC-13.2.0.eb          | 26 ++++++
 .../libgeotiff-1.7.3-GCCcore-13.2.0.eb        | 36 +++++++++
 4 files changed, 196 insertions(+)
 create mode 100644 easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-13.2.0.eb
 create mode 100644 easybuild/easyconfigs/g/GDAL/GDAL-3.9.0-foss-2023b.eb
 create mode 100644 easybuild/easyconfigs/g/GEOS/GEOS-3.12.1-GCC-13.2.0.eb
 create mode 100644 easybuild/easyconfigs/l/libgeotiff/libgeotiff-1.7.3-GCCcore-13.2.0.eb

diff --git a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-13.2.0.eb
new file mode 100644
index 00000000000..75ccfd09cea
--- /dev/null
+++ b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-13.2.0.eb
@@ -0,0 +1,53 @@
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+# Author: Denis Kristak
+# update: Thomas Hoffmann (EMBL)
+easyblock = 'CMakeMake'
+
+name = 'Brunsli'
+version = '0.1'
+
+homepage = 'https://github.com/google/brunsli/'
+description = """Brunsli is a lossless JPEG repacking library."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
+
+source_urls = ['https://github.com/google/brunsli/archive/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['62762dc740f9fcc9706449c078f12c2a366416486d2882be50a9f201f99ac0bc']
+
+builddependencies = [
+    ('CMake', '3.27.6'),
+    ('binutils', '2.40'),
+]
+
+dependencies = [
+    ('Brotli', '1.1.0'),
+    ('Highway', '1.0.7'),
+]
+
+# skip use of third_party directory, since we provide Brotli via a proper dependency
+preconfigopts = "sed -i 's/add_subdirectory(third_party)//g' ../brunsli-%(version)s/CMakeLists.txt && "
+
+configopts = '-DCMAKE_CXX_FLAGS="$CXXFLAGS -lbrotlienc -lbrotlidec -lbrotlicommon" '
+
+# make sure that libraries end up in <prefix>/lib (not lib64)
+configopts += "-DCMAKE_INSTALL_LIBDIR=lib "
+
+buildopts = "BROTLI_DIR=$EBROOTBROTLI BROTLI_INCLUDE=$EBROOTBROTLI/include"
+
+# also install dbrunsli binary and missing libraries
+postinstallcmds = [
+    "mkdir %(installdir)s/bin",
+    "cp dbrunsli %(installdir)s/bin/",
+    "cp libbrunsli*.a %(installdir)s/lib/",
+    "cp libbrunsli*.%s %%(installdir)s/lib/" % SHLIB_EXT,
+]
+
+sanity_check_paths = {
+    'files': ['bin/dbrunsli'],
+    'dirs': ['include/brunsli', 'lib'],
+}
+
+sanity_check_commands = ['dbrunsli 2>&1 | grep Usage']
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.9.0-foss-2023b.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.9.0-foss-2023b.eb
new file mode 100644
index 00000000000..05c6ee60dab
--- /dev/null
+++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.9.0-foss-2023b.eb
@@ -0,0 +1,81 @@
+easyblock = 'CMakeMake'
+
+name = 'GDAL'
+version = '3.9.0'
+
+homepage = 'https://www.gdal.org'
+description = """GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style
+ Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model
+ to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for
+ data translation and processing."""
+
+toolchain = {'name': 'foss', 'version': '2023b'}
+toolchainopts = {'usempi': True}
+
+source_urls = ['https://download.osgeo.org/%(namelower)s/%(version)s/']
+sources = [SOURCELOWER_TAR_XZ]
+patches = ['%(name)s-3.6.2_fix-python-CC-CXX.patch']
+checksums = [
+    {'gdal-3.9.0.tar.xz': '577f80e9d14ff7c90b6bfbc34201652b4546700c01543efb4f4c3050e0b3fda2'},
+    {'GDAL-3.6.2_fix-python-CC-CXX.patch': '859b874b0c8ff7626a76d51f008bf05b7f89a35b325bdd1d126d2364154acc63'},
+]
+
+builddependencies = [
+    ('CMake', '3.27.6'),
+    ('pkgconf', '2.0.3'),
+    ('Bison', '3.8.2'),
+]
+dependencies = [
+    ('Python', '3.11.5'),
+    ('netCDF', '4.9.2'),
+    ('expat', '2.5.0'),
+    ('GEOS', '3.12.1'),
+    ('SQLite', '3.43.1'),
+    ('libarchive', '3.7.2'),
+    ('libxml2', '2.11.5'),
+    ('libpng', '1.6.40'),
+    ('libjpeg-turbo', '3.0.1'),
+    ('LibTIFF', '4.6.0'),
+    ('zlib', '1.2.13'),
+    ('cURL', '8.3.0'),
+    ('PCRE', '8.45'),
+    ('PROJ', '9.3.1'),
+    ('libgeotiff', '1.7.3'),
+    ('SciPy-bundle', '2023.11'),
+    ('HDF5', '1.14.3'),
+    ('HDF', '4.2.16-2'),
+    ('Armadillo', '12.8.0'),
+    ('CFITSIO', '4.3.1'),
+    ('zstd', '1.5.5'),
+    ('giflib', '5.2.1'),
+    ('json-c', '0.17'),
+    ('Xerces-C++', '3.2.5'),
+    ('PCRE2', '10.42'),
+    ('OpenEXR', '3.2.0'),
+    ('Brunsli', '0.1'),
+    ('Qhull', '2020.2'),
+    ('LERC', '4.0.0'),
+    ('OpenJPEG', '2.5.0'),
+    ('SWIG', '4.1.1'),
+]
+
+# iterative build for both static and shared libraries
+local_configopts_common = "-DGDAL_USE_INTERNAL_LIBS=OFF -DArrow_DIR=$EBROOTARROW "
+local_configopts_common += "-DGEOTIFF_INCLUDE_DIR=$EBROOTLIBGEOTIFF/include -DPython_ROOT=$EBROOTPYTHON "
+
+configopts = [
+    local_configopts_common + "-DBUILD_SHARED_LIBS=OFF",
+    local_configopts_common
+]
+
+
+sanity_check_paths = {
+    'files': ['lib/libgdal.a', 'lib/libgdal.%s' % SHLIB_EXT],
+    'dirs': ['bin', 'include', 'lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = ["python -c 'import osgeo.%(namelower)s'"]
+
+modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'}
+
+moduleclass = 'data'
diff --git a/easybuild/easyconfigs/g/GEOS/GEOS-3.12.1-GCC-13.2.0.eb b/easybuild/easyconfigs/g/GEOS/GEOS-3.12.1-GCC-13.2.0.eb
new file mode 100644
index 00000000000..8dc235ab95c
--- /dev/null
+++ b/easybuild/easyconfigs/g/GEOS/GEOS-3.12.1-GCC-13.2.0.eb
@@ -0,0 +1,26 @@
+easyblock = 'CMakeMake'
+
+name = 'GEOS'
+version = '3.12.1'
+
+homepage = 'https://trac.osgeo.org/geos'
+description = """GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS)"""
+
+toolchain = {'name': 'GCC', 'version': '13.2.0'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://download.osgeo.org/geos/']
+sources = [SOURCELOWER_TAR_BZ2]
+checksums = ['d6ea7e492224b51193e8244fe3ec17c4d44d0777f3c32ca4fb171140549a0d03']
+
+builddependencies = [('CMake', '3.27.6')]
+
+# Build static and shared libraries
+configopts = ['', '-DBUILD_SHARED_LIBS=OFF']
+
+sanity_check_paths = {
+    'files': ['bin/geos-config', 'lib/libgeos.%s' % SHLIB_EXT, 'lib/libgeos.a', 'include/geos.h'],
+    'dirs': [],
+}
+
+moduleclass = 'math'
diff --git a/easybuild/easyconfigs/l/libgeotiff/libgeotiff-1.7.3-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/libgeotiff/libgeotiff-1.7.3-GCCcore-13.2.0.eb
new file mode 100644
index 00000000000..ce66887030e
--- /dev/null
+++ b/easybuild/easyconfigs/l/libgeotiff/libgeotiff-1.7.3-GCCcore-13.2.0.eb
@@ -0,0 +1,36 @@
+easyblock = 'ConfigureMake'
+
+name = 'libgeotiff'
+version = '1.7.3'
+
+homepage = 'https://directory.fsf.org/wiki/Libgeotiff'
+description = """Library for reading and writing coordinate system information from/to GeoTIFF files"""
+
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
+
+source_urls = ['https://download.osgeo.org/geotiff/libgeotiff']
+sources = [SOURCE_TAR_GZ]
+checksums = ['ba23a3a35980ed3de916e125c739251f8e3266be07540200125a307d7cf5a704']
+
+builddependencies = [
+    ('binutils', '2.40'),
+]
+
+dependencies = [
+    ('PROJ', '9.3.1'),
+    ('libjpeg-turbo', '3.0.1'),
+    ('zlib', '1.2.13'),
+    ('SQLite', '3.43.1'),
+    ('LibTIFF', '4.6.0'),
+    ('cURL', '8.3.0'),
+]
+
+configopts = ' --with-libtiff=$EBROOTLIBTIFF --with-proj=$EBROOTPROJ --with-zlib=$EBROOTZLIB'
+configopts += ' --with-jpeg=$EBROOTLIBJPEGMINTURBO'
+
+sanity_check_paths = {
+    'files': ['bin/listgeo', 'lib/libgeotiff.a', 'lib/libgeotiff.%s' % SHLIB_EXT],
+    'dirs': ['include', 'share'],
+}
+
+moduleclass = 'lib'

From c5702f31fb01b43db04b4aed4feba300e4bd9b98 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 30 May 2024 13:20:24 +0200
Subject: [PATCH 108/835] avoid hardcoding OpenJPEG version in preinstallopts
 in easyconfig for imagecodecs 2023.1.23

---
 .../i/imagecodecs/imagecodecs-2023.1.23-foss-2023a.eb           | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2023.1.23-foss-2023a.eb b/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2023.1.23-foss-2023a.eb
index a775562db42..4255c33f1e7 100644
--- a/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2023.1.23-foss-2023a.eb
+++ b/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2023.1.23-foss-2023a.eb
@@ -61,7 +61,7 @@ exts_list = [
         'checksums': ['988f224739aa6858475a4c59172968c7b51cc657d2249580c8f96848708fbae3'],
     }),
     (name, version, {
-        'preinstallopts': "export CPATH=$EBROOTOPENJPEG/include/openjpeg-2.5/:$CPATH && ",
+        'preinstallopts': "export CPATH=$EBROOTOPENJPEG/include/openjpeg-%s/:$CPATH && " % local_openjpeg_maj_min,
         'sources': ['%(name)s-%(version)s.tar.gz'],
         'checksums': ['1b4591839a2f5c90467e50ebe54117cbd9be42c18864abdf85fc7743223ac5b2'],
     }),

From 4d3a007527f87c7f4c08be9a81d67b71b80a75d0 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Thu, 30 May 2024 14:18:18 +0200
Subject: [PATCH 109/835] add scirpy, liana, muon, mudata

---
 ...e-cell-python-bundle-2024.02-foss-2023a.eb | 54 ++++++++++++++++++-
 1 file changed, 53 insertions(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb b/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb
index d554e9fddca..0fa2bcb2cf6 100644
--- a/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb
+++ b/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb
@@ -8,7 +8,11 @@ description = """Bundle of tools for single-cell sequence analysis."""
 
 toolchain = {'name': 'foss', 'version': '2023a'}
 
-builddependencies = [('poetry', '1.5.1')]
+builddependencies = [
+    ('poetry', '1.5.1'),
+    ('CMake', '3.26.3'),
+    ('hatchling', '1.18.0'),
+]
 
 dependencies = [
     ('Python', '3.11.3'),
@@ -39,6 +43,7 @@ dependencies = [
     ('PyYAML', '6.0'),  # sc_toolbox
     ('typing-extensions', '4.9.0'),  # sc_toolbox
     ('adjustText', '1.1.1'),  # sc_toolbox, created
+    ('python-parasail', '1.3.4'),  # scirpy
 ]
 
 exts_list = [
@@ -154,6 +159,53 @@ exts_list = [
     ('decoupler', '1.6.0', {
         'checksums': ['dde501f4d3e55a260f716e51b871bee403bc8aaa6b66799df0e42dee0787b98d'],
     }),
+    ('mudata', '0.2.3', {
+        'checksums': ['45288ac150bfc598d68acb7c2c1c43c38c5c39522107e04f7efbf3360c7f2035'],
+    }),
+    ('nodeenv', '1.9.0', {
+        'checksums': ['07f144e90dae547bf0d4ee8da0ee42664a42a04e02ed68e06324348dafe4bdb1'],
+    }),
+    ('identify', '2.5.36', {
+        'checksums': ['e5e00f54165f9047fbebeb4a560f9acfb8af4c88232be60a488e9b68d122745d'],
+    }),
+    ('cfgv', '3.4.0', {
+        'checksums': ['e52591d4c5f5dead8e0f673fb16db7949d2cfb3f7da4582893288f0ded8fe560'],
+    }),
+    ('pre_commit', '3.7.1', {
+        'checksums': ['8ca3ad567bc78a4972a3f1a477e94a79d4597e8140a6e0b651c5e33899c3654a'],
+    }),
+    ('muon', '0.1.6', {
+        'checksums': ['762feeb6f52f865cf79d0d0332cc742fe91c1885f668ce15794b62b3952b02f9'],
+    }),
+    ('liana', '1.2.0', {
+        'checksums': ['be899c69bfcbf3d0f8b61c04c35f225ac6b11fe1ea80e6ed4bdc0e6212cb2379'],
+    }),
+    ('squarify', '0.4.3', {
+        'checksums': ['54091f6ad175f7f201f8934574e647ce1b50dedc478c5fd968688eb7d7469f95'],
+    }),
+    ('scikit_build_core', '0.9.3', {
+        'checksums': ['341d113e473a5409dc62522e8b1b1b8b1647a0b95557ad15f6be2a36071fd390'],
+    }),
+    ('awkward-cpp', '33', {
+        'checksums': ['550adebccd329d18d02e95226d0b89698188fd33e44f07450942c692881927d8'],
+    }),
+    ('awkward', '2.6.4', {
+        'checksums': ['ee0cb27c64150f368749983dda499c108848c64dc830912480eb37b78c04300f'],
+    }),
+    ('yamlordereddictloader', '0.4.2', {
+        'checksums': ['36af2f6210fcff5da4fc4c12e1d815f973dceb41044e795e1f06115d634bca13'],
+    }),
+    ('airr', '1.5.0', {
+        'checksums': ['febc0a881bf46b1a9c29ac6a7089dd733ff9120d114585e75dede26403f68d42'],
+    }),
+    ('scirpy', '0.17.0', {
+        'checksums': ['f61653a4f7387562ec89b00fbfd7cab762c0bf3320f21ccfc47df80a13cc5d41'],
+    }),
+    # ('schist', '0.8.3', {
+    #     'source_tmpl': 'v%(version)s.tar.gz',
+    #     'source_urls': ['https://github.com/dawe/schist/archive/'],
+    #     'checksums': ['9b98ec9d85554573288c24f18c4791ba7c4d315397cbc422ea25d4a7cdd42e6d'],
+    # }),
 ]
 
 use_pip = True

From a045edf6a863721ff8d9cc7e2a0b7db0326dd015 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 30 May 2024 14:33:50 +0200
Subject: [PATCH 110/835] revert workaround for framework bug in extract
 command in easyconfig for jax 0.4.25

---
 .../easyconfigs/j/jax/jax-0.4.25-gfbf-2023a-CUDA-12.1.1.eb      | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a-CUDA-12.1.1.eb
index 33b8d5546fa..68ab99486f2 100644
--- a/easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a-CUDA-12.1.1.eb
+++ b/easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a-CUDA-12.1.1.eb
@@ -41,7 +41,7 @@ dependencies = [
 local_xla_commit = '4ccfe33c71665ddcbca5b127fefe8baa3ed632d4'
 local_tfrt_commit = '0aeefb1660d7e37964b2bb71b1f518096bda9a25'
 
-local_extract_cmd = 'cp %s %%(builddir)s/archives'
+local_extract_cmd = 'cp %s %(builddir)s/archives'
 local_repo_opt = '--bazel_options="--distdir=%(builddir)s/archives" '
 local_repo_opt += '--bazel_options="--action_env=TF_SYSTEM_LIBS=pybind11" '
 local_repo_opt += '--bazel_options="--action_env=CPATH=$EBROOTPYBIND11/include" '

From e0bfd59cabd0bbb080c86073f179954486fe227e Mon Sep 17 00:00:00 2001
From: Julian Morillo <julian.morillo@bsc.es>
Date: Thu, 30 May 2024 16:34:31 +0200
Subject: [PATCH 111/835] Add Extrae-4.1.6-gompi.2023b.eb and make binutils
 detection more robust

---
 .../Extrae/Extrae-4.1.6-detect_binutils.patch | 43 +++++++++++++++++++
 .../e/Extrae/Extrae-4.1.6-gompi.2023b.eb      | 27 ++++++++++++
 2 files changed, 70 insertions(+)
 create mode 100644 easybuild/easyconfigs/e/Extrae/Extrae-4.1.6-detect_binutils.patch
 create mode 100644 easybuild/easyconfigs/e/Extrae/Extrae-4.1.6-gompi.2023b.eb

diff --git a/easybuild/easyconfigs/e/Extrae/Extrae-4.1.6-detect_binutils.patch b/easybuild/easyconfigs/e/Extrae/Extrae-4.1.6-detect_binutils.patch
new file mode 100644
index 00000000000..4eeac3ad4ac
--- /dev/null
+++ b/easybuild/easyconfigs/e/Extrae/Extrae-4.1.6-detect_binutils.patch
@@ -0,0 +1,43 @@
+diff -Nru extrae-4.1.6.orig/config/macros.m4 extrae-4.1.6/config/macros.m4
+--- extrae-4.1.6.orig/config/macros.m4  2024-05-30 16:23:59.684839619 +0200
++++ extrae-4.1.6/config/macros.m4       2024-05-30 16:27:08.208600097 +0200
+@@ -779,6 +779,8 @@
+          elif test -r "${binutils_home_dir}/lib/libbfd.a" -a \
+                       "${binutils_require_shared}" = "no" ; then
+             BFD_LIBSDIR="${binutils_home_dir}/lib"
++         elif test -r "${binutils_home_dir}/libbfd.so" ; then
++            BFD_LIBSDIR="${binutils_home_dir}"
+          else
+             dnl Try something more automatic using find command
+             libbfd_lib=""
+@@ -814,6 +816,8 @@
+             LIBERTY_LIBSDIR="${binutils_home_dir}/lib"
+          elif test -r "${binutils_home_dir}/lib/libiberty.a" ; then
+             LIBERTY_LIBSDIR="${binutils_home_dir}/lib"
++         elif test -r "${binutils_home_dir}/libiberty.a" ; then
++            LIBERTY_LIBSDIR="${binutils_home_dir}"
+          else
+             dnl Try something more automatic using find command
+             libiberty_lib=""
+diff -Nru extrae-4.1.6.orig/configure extrae-4.1.6/configure
+--- extrae-4.1.6.orig/configure 2024-05-30 16:23:59.716839578 +0200
++++ extrae-4.1.6/configure      2024-05-30 16:25:31.276723193 +0200
+@@ -35072,6 +35072,8 @@
+          elif test -r "${binutils_home_dir}/lib/libbfd.a" -a \
+                       "${binutils_require_shared}" = "no" ; then
+             BFD_LIBSDIR="${binutils_home_dir}/lib"
++         elif test -r "${binutils_home_dir}/libbfd.so" ; then
++            BFD_LIBSDIR="${binutils_home_dir}"
+          else
+                         libbfd_lib=""
+
+@@ -35106,6 +35108,8 @@
+             LIBERTY_LIBSDIR="${binutils_home_dir}/lib"
+          elif test -r "${binutils_home_dir}/lib/libiberty.a" ; then
+             LIBERTY_LIBSDIR="${binutils_home_dir}/lib"
++         elif test -r "${binutils_home_dir}/libiberty.a" ; then
++            LIBERTY_LIBSDIR="${binutils_home_dir}"
+          else
+                         libiberty_lib=""
+
+
diff --git a/easybuild/easyconfigs/e/Extrae/Extrae-4.1.6-gompi.2023b.eb b/easybuild/easyconfigs/e/Extrae/Extrae-4.1.6-gompi.2023b.eb
new file mode 100644
index 00000000000..66da152c916
--- /dev/null
+++ b/easybuild/easyconfigs/e/Extrae/Extrae-4.1.6-gompi.2023b.eb
@@ -0,0 +1,27 @@
+name = 'Extrae'
+version = '4.1.6'
+
+homepage = 'https://tools.bsc.es/extrae'
+description = """Extrae is the package devoted to generate Paraver trace-files for a post-mortem analysis. Extrae is a tool that uses different interposition mechanisms to inject probes into the target application so as to gather information regarding the application performance."""
+
+toolchain = {'name': 'gompi', 'version': '2023b'}
+toolchainopts = {'usempi': True}
+
+source_urls = ['https://ftp.tools.bsc.es/%(namelower)s']
+sources = ['%(namelower)s-%(version)s-src.tar.bz2']
+checksums = ['9f146e70311b8ae9d77584f6efc7b30478885cfd095f7bd3937d5b08aec19985']
+
+builddependencies = [
+    ('Automake', '1.16.5'),
+]
+
+dependencies = [
+    ('zlib', '1.2.12'),
+    ('Boost', '1.83.0', '', ('GCC', '13.2.0')),
+    ('libunwind', '1.6.2', '', ('GCCcore', '13.2.0')),
+    ('libxml2', '2.11.5', '', ('GCCcore', '13.2.0')),
+    ('libdwarf', '0.9.2', '', ('GCCcore', '13.2.0')),
+    ('PAPI', '7.1.0', '', ('GCCcore', '13.2.0')),
+]
+
+moduleclass = 'perf'

From de831e8e3e75f4feda1df09c40ac0a9cfe338fb5 Mon Sep 17 00:00:00 2001
From: Julian Morillo <julian.morillo@bsc.es>
Date: Thu, 30 May 2024 16:48:00 +0200
Subject: [PATCH 112/835] Add the use of the patch to the easyconfig file

---
 easybuild/easyconfigs/e/Extrae/Extrae-4.1.6-gompi.2023b.eb | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/e/Extrae/Extrae-4.1.6-gompi.2023b.eb b/easybuild/easyconfigs/e/Extrae/Extrae-4.1.6-gompi.2023b.eb
index 66da152c916..e6a3f0397ba 100644
--- a/easybuild/easyconfigs/e/Extrae/Extrae-4.1.6-gompi.2023b.eb
+++ b/easybuild/easyconfigs/e/Extrae/Extrae-4.1.6-gompi.2023b.eb
@@ -9,7 +9,10 @@ toolchainopts = {'usempi': True}
 
 source_urls = ['https://ftp.tools.bsc.es/%(namelower)s']
 sources = ['%(namelower)s-%(version)s-src.tar.bz2']
-checksums = ['9f146e70311b8ae9d77584f6efc7b30478885cfd095f7bd3937d5b08aec19985']
+patches = ['Extrae-4.1.6-detect_binutils.patch']
+checksums = ['9f146e70311b8ae9d77584f6efc7b30478885cfd095f7bd3937d5b08aec19985',
+    '7c4d87d12a5383ccdfdd75967a207b9d9aca27c707c499cd6ef0a27fd4989483', # Extrae-4.1.6-detect_binutils.patch
+]
 
 builddependencies = [
     ('Automake', '1.16.5'),

From ffebdadbd735cb242b2ffc10f657f50eb876cd60 Mon Sep 17 00:00:00 2001
From: Julian Morillo <julian.morillo@bsc.es>
Date: Thu, 30 May 2024 17:16:46 +0200
Subject: [PATCH 113/835] Adding checksum

---
 easybuild/easyconfigs/e/Extrae/Extrae-4.1.6-gompi.2023b.eb | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/easybuild/easyconfigs/e/Extrae/Extrae-4.1.6-gompi.2023b.eb b/easybuild/easyconfigs/e/Extrae/Extrae-4.1.6-gompi.2023b.eb
index e6a3f0397ba..03fc0fc2461 100644
--- a/easybuild/easyconfigs/e/Extrae/Extrae-4.1.6-gompi.2023b.eb
+++ b/easybuild/easyconfigs/e/Extrae/Extrae-4.1.6-gompi.2023b.eb
@@ -10,8 +10,11 @@ toolchainopts = {'usempi': True}
 source_urls = ['https://ftp.tools.bsc.es/%(namelower)s']
 sources = ['%(namelower)s-%(version)s-src.tar.bz2']
 patches = ['Extrae-4.1.6-detect_binutils.patch']
-checksums = ['9f146e70311b8ae9d77584f6efc7b30478885cfd095f7bd3937d5b08aec19985',
-    '7c4d87d12a5383ccdfdd75967a207b9d9aca27c707c499cd6ef0a27fd4989483', # Extrae-4.1.6-detect_binutils.patch
+checksums = [
+    # extrae-4.1.6-src.tar.bz2
+    ('9f146e70311b8ae9d77584f6efc7b30478885cfd095f7bd3937d5b08aec19985',
+     'f96b2c3586a0e83c6fa08d3136a8f399715969b5bb7ee6792c3fd93667d495fd'),
+    '7c4d87d12a5383ccdfdd75967a207b9d9aca27c707c499cd6ef0a27fd4989483',  # Extrae-4.1.6-detect_binutils.patch
 ]
 
 builddependencies = [

From b4386d95664d5ec4a127127c5db77520a3ce3376 Mon Sep 17 00:00:00 2001
From: Julian Morillo <julian.morillo@bsc.es>
Date: Thu, 30 May 2024 17:32:50 +0200
Subject: [PATCH 114/835] Solving "line too long" failing test

---
 easybuild/easyconfigs/e/Extrae/Extrae-4.1.6-gompi.2023b.eb | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/e/Extrae/Extrae-4.1.6-gompi.2023b.eb b/easybuild/easyconfigs/e/Extrae/Extrae-4.1.6-gompi.2023b.eb
index 03fc0fc2461..418ee07ee98 100644
--- a/easybuild/easyconfigs/e/Extrae/Extrae-4.1.6-gompi.2023b.eb
+++ b/easybuild/easyconfigs/e/Extrae/Extrae-4.1.6-gompi.2023b.eb
@@ -2,7 +2,9 @@ name = 'Extrae'
 version = '4.1.6'
 
 homepage = 'https://tools.bsc.es/extrae'
-description = """Extrae is the package devoted to generate Paraver trace-files for a post-mortem analysis. Extrae is a tool that uses different interposition mechanisms to inject probes into the target application so as to gather information regarding the application performance."""
+description = """Extrae is the package devoted to generate Paraver trace-files for a post-mortem analysis. 
+Extrae is a tool that uses different interposition mechanisms to inject probes into the target application 
+so as to gather information regarding the application performance."""
 
 toolchain = {'name': 'gompi', 'version': '2023b'}
 toolchainopts = {'usempi': True}

From aa3c8dd3f49e99514c84a0e5b9595ad2aaaa1b82 Mon Sep 17 00:00:00 2001
From: Julian Morillo <julian.morillo@bsc.es>
Date: Thu, 30 May 2024 17:47:13 +0200
Subject: [PATCH 115/835] Solve naming issue

---
 .../{Extrae-4.1.6-gompi.2023b.eb => Extrae-4.1.6-gompi-2023b.eb}  | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename easybuild/easyconfigs/e/Extrae/{Extrae-4.1.6-gompi.2023b.eb => Extrae-4.1.6-gompi-2023b.eb} (100%)

diff --git a/easybuild/easyconfigs/e/Extrae/Extrae-4.1.6-gompi.2023b.eb b/easybuild/easyconfigs/e/Extrae/Extrae-4.1.6-gompi-2023b.eb
similarity index 100%
rename from easybuild/easyconfigs/e/Extrae/Extrae-4.1.6-gompi.2023b.eb
rename to easybuild/easyconfigs/e/Extrae/Extrae-4.1.6-gompi-2023b.eb

From 92ec0829c6428df125a44628541d11111d2851fa Mon Sep 17 00:00:00 2001
From: Julian Morillo <julian.morillo@bsc.es>
Date: Thu, 30 May 2024 18:05:43 +0200
Subject: [PATCH 116/835] Solve zlib dependency

---
 easybuild/easyconfigs/e/Extrae/Extrae-4.1.6-gompi-2023b.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/e/Extrae/Extrae-4.1.6-gompi-2023b.eb b/easybuild/easyconfigs/e/Extrae/Extrae-4.1.6-gompi-2023b.eb
index 418ee07ee98..8476ba54e13 100644
--- a/easybuild/easyconfigs/e/Extrae/Extrae-4.1.6-gompi-2023b.eb
+++ b/easybuild/easyconfigs/e/Extrae/Extrae-4.1.6-gompi-2023b.eb
@@ -24,7 +24,7 @@ builddependencies = [
 ]
 
 dependencies = [
-    ('zlib', '1.2.12'),
+    ('zlib', '1.2.13', '', ('GCC', '13.2.0')),
     ('Boost', '1.83.0', '', ('GCC', '13.2.0')),
     ('libunwind', '1.6.2', '', ('GCCcore', '13.2.0')),
     ('libxml2', '2.11.5', '', ('GCCcore', '13.2.0')),

From 0eb7f74681090087c644d7527dd5d44f981f577c Mon Sep 17 00:00:00 2001
From: Julian Morillo <julian.morillo@bsc.es>
Date: Thu, 30 May 2024 18:24:17 +0200
Subject: [PATCH 117/835] Fix zlib dependency

---
 easybuild/easyconfigs/e/Extrae/Extrae-4.1.6-gompi-2023b.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/e/Extrae/Extrae-4.1.6-gompi-2023b.eb b/easybuild/easyconfigs/e/Extrae/Extrae-4.1.6-gompi-2023b.eb
index 8476ba54e13..08c2742c7ac 100644
--- a/easybuild/easyconfigs/e/Extrae/Extrae-4.1.6-gompi-2023b.eb
+++ b/easybuild/easyconfigs/e/Extrae/Extrae-4.1.6-gompi-2023b.eb
@@ -24,7 +24,7 @@ builddependencies = [
 ]
 
 dependencies = [
-    ('zlib', '1.2.13', '', ('GCC', '13.2.0')),
+    ('zlib', '1.2.13', '', ('GCCcore', '13.2.0')),
     ('Boost', '1.83.0', '', ('GCC', '13.2.0')),
     ('libunwind', '1.6.2', '', ('GCCcore', '13.2.0')),
     ('libxml2', '2.11.5', '', ('GCCcore', '13.2.0')),

From 3f44e140a8440450b3e64cc80e43f044a90e9ac1 Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Fri, 31 May 2024 10:09:31 +0200
Subject: [PATCH 118/835] adding easyconfigs: CORSIKA-77550-foss-2023a.eb

---
 .../c/CORSIKA/CORSIKA-77550-foss-2023a.eb     | 41 +++++++++++++++++++
 1 file changed, 41 insertions(+)
 create mode 100644 easybuild/easyconfigs/c/CORSIKA/CORSIKA-77550-foss-2023a.eb

diff --git a/easybuild/easyconfigs/c/CORSIKA/CORSIKA-77550-foss-2023a.eb b/easybuild/easyconfigs/c/CORSIKA/CORSIKA-77550-foss-2023a.eb
new file mode 100644
index 00000000000..0a11129ccb9
--- /dev/null
+++ b/easybuild/easyconfigs/c/CORSIKA/CORSIKA-77550-foss-2023a.eb
@@ -0,0 +1,41 @@
+easyblock = "MakeCp"
+
+name = 'CORSIKA'
+version = '77550'
+
+homepage = "https://www.iap.kit.edu/corsika"
+description = """CORSIKA (COsmic Ray SImulations for KAscade) is a program for detailed
+simulation of extensive air showers initiated by high energy cosmic ray
+particles. Protons, light nuclei up to iron, photons, and many other particles
+may be treated as primaries."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+toolchainopts = {'pic': True, 'usempi': True}
+
+download_instructions = "Sources have to be requested to the developers"
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['fed74c144e22deb5a7c1d2dc1f04f0100eb2732cb48665a3da49ce471a3775ee']
+
+dependencies = [
+    ("ROOT", "6.30.06"),
+]
+
+# run in non-interactive mode
+build_cmd = "./coconut --batch"
+# coconut script does not accept "-j"
+parallel = False
+
+files_to_copy = [
+    (['run/corsika77550Linux_EPOS_urqmd'], 'bin'),
+]
+
+postinstallcmds = [
+    "cd %(installdir)s/bin && ln -s corsika77550Linux_EPOS_urqmd corsika",
+]
+
+sanity_check_paths = {
+    'files': ['bin/corsika', 'bin/corsika77550Linux_EPOS_urqmd'],
+    'dirs': []
+}
+
+moduleclass = "phys"

From 310659840ba8baa2a7297b33bfc7a0afde522b3a Mon Sep 17 00:00:00 2001
From: julianmorillo <julianmorillo@users.noreply.github.com>
Date: Fri, 31 May 2024 10:37:23 +0200
Subject: [PATCH 119/835] Update
 easybuild/easyconfigs/e/Extrae/Extrae-4.1.6-gompi-2023b.eb

Co-authored-by: ocaisa <alan.ocais@cecam.org>
---
 .../easyconfigs/e/Extrae/Extrae-4.1.6-gompi-2023b.eb | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/easybuild/easyconfigs/e/Extrae/Extrae-4.1.6-gompi-2023b.eb b/easybuild/easyconfigs/e/Extrae/Extrae-4.1.6-gompi-2023b.eb
index 08c2742c7ac..413b5eb6d04 100644
--- a/easybuild/easyconfigs/e/Extrae/Extrae-4.1.6-gompi-2023b.eb
+++ b/easybuild/easyconfigs/e/Extrae/Extrae-4.1.6-gompi-2023b.eb
@@ -24,12 +24,12 @@ builddependencies = [
 ]
 
 dependencies = [
-    ('zlib', '1.2.13', '', ('GCCcore', '13.2.0')),
-    ('Boost', '1.83.0', '', ('GCC', '13.2.0')),
-    ('libunwind', '1.6.2', '', ('GCCcore', '13.2.0')),
-    ('libxml2', '2.11.5', '', ('GCCcore', '13.2.0')),
-    ('libdwarf', '0.9.2', '', ('GCCcore', '13.2.0')),
-    ('PAPI', '7.1.0', '', ('GCCcore', '13.2.0')),
+    ('zlib', '1.2.13'),
+    ('Boost', '1.83.0'),
+    ('libunwind', '1.6.2'),
+    ('libxml2', '2.11.5'),
+    ('libdwarf', '0.9.2'),
+    ('PAPI', '7.1.0'),
 ]
 
 moduleclass = 'perf'

From f6d2516657ffb57d75c4df66ab0bca1f0dabfe01 Mon Sep 17 00:00:00 2001
From: julianmorillo <julianmorillo@users.noreply.github.com>
Date: Fri, 31 May 2024 10:37:34 +0200
Subject: [PATCH 120/835] Update
 easybuild/easyconfigs/e/Extrae/Extrae-4.1.6-gompi-2023b.eb

Co-authored-by: ocaisa <alan.ocais@cecam.org>
---
 easybuild/easyconfigs/e/Extrae/Extrae-4.1.6-gompi-2023b.eb | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/easybuild/easyconfigs/e/Extrae/Extrae-4.1.6-gompi-2023b.eb b/easybuild/easyconfigs/e/Extrae/Extrae-4.1.6-gompi-2023b.eb
index 413b5eb6d04..d6f41276db0 100644
--- a/easybuild/easyconfigs/e/Extrae/Extrae-4.1.6-gompi-2023b.eb
+++ b/easybuild/easyconfigs/e/Extrae/Extrae-4.1.6-gompi-2023b.eb
@@ -32,4 +32,6 @@ dependencies = [
     ('PAPI', '7.1.0'),
 ]
 
+runtest = 'check'
+
 moduleclass = 'perf'

From 99804a10b0644ad1d986b0b65f8845bea8753b35 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Mon, 3 Jun 2024 11:31:11 +0200
Subject: [PATCH 121/835] add schist to bundle

---
 .../c/cairomm/cairomm-1.16.2-GCC-12.3.0.eb    | 39 ++++++++++++
 .../graph-tool/graph-tool-2.59-foss-2023a.eb  | 61 +++++++++++++++++++
 ...e-cell-python-bundle-2024.02-foss-2023a.eb | 11 ++--
 3 files changed, 106 insertions(+), 5 deletions(-)
 create mode 100644 easybuild/easyconfigs/c/cairomm/cairomm-1.16.2-GCC-12.3.0.eb
 create mode 100644 easybuild/easyconfigs/g/graph-tool/graph-tool-2.59-foss-2023a.eb

diff --git a/easybuild/easyconfigs/c/cairomm/cairomm-1.16.2-GCC-12.3.0.eb b/easybuild/easyconfigs/c/cairomm/cairomm-1.16.2-GCC-12.3.0.eb
new file mode 100644
index 00000000000..2ca14e07c7c
--- /dev/null
+++ b/easybuild/easyconfigs/c/cairomm/cairomm-1.16.2-GCC-12.3.0.eb
@@ -0,0 +1,39 @@
+# Updated to MesonNinja as the autogen.sh complained.
+# Author: J. Sassmannshausen (Imperial College London/UK)
+
+easyblock = 'MesonNinja'
+
+name = 'cairomm'
+version = '1.16.2'
+
+homepage = 'http://cairographics.org'
+description = "The Cairomm package provides a C++ interface to Cairo."
+
+toolchain = {'name': 'GCC', 'version': '12.3.0'}
+
+source_urls = ['http://cairographics.org/releases/']
+sources = [SOURCE_TAR_XZ]
+checksums = ['6a63bf98a97dda2b0f55e34d1b5f3fb909ef8b70f9b8d382cb1ff3978e7dc13f']
+
+builddependencies = [
+    ('Meson', '1.1.1'),
+    ('Ninja', '1.11.1'),
+    ('Doxygen', '1.9.7'),
+    ('M4', '1.4.19'),
+]
+
+dependencies = [
+    ('cairo', '1.17.8'),
+    ('libsigc++', '3.6.0'),
+    ('mm-common', '1.0.6'),
+    ('Boost', '1.82.0'),
+]
+
+runtest = 'ninja test'
+
+sanity_check_paths = {
+    'files': ['lib/libcairomm-1.16.%s' % SHLIB_EXT],
+    'dirs': [],
+}
+
+moduleclass = 'vis'
diff --git a/easybuild/easyconfigs/g/graph-tool/graph-tool-2.59-foss-2023a.eb b/easybuild/easyconfigs/g/graph-tool/graph-tool-2.59-foss-2023a.eb
new file mode 100644
index 00000000000..2ca6027a864
--- /dev/null
+++ b/easybuild/easyconfigs/g/graph-tool/graph-tool-2.59-foss-2023a.eb
@@ -0,0 +1,61 @@
+# Author: J. Sassmannshausen (Imperial College London/UK)
+# Update: Pavel Tománek (Inuits)
+
+easyblock = 'ConfigureMake'
+
+name = 'graph-tool'
+version = '2.59'
+
+homepage = 'https://graph-tool.skewed.de/'
+description = """Graph-tool is an efficient Python module for manipulation and
+ statistical analysis of graphs (a.k.a. networks). Contrary to
+ most other python modules with similar functionality, the core
+ data structures and algorithms are implemented in C++, making
+ extensive use of template metaprogramming, based heavily on
+ the Boost Graph Library. This confers it a level of
+ performance that is comparable (both in memory usage and
+ computation time) to that of a pure C/C++ library."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+toolchainopts = {'cstd': 'c++17', 'openmp': True}
+
+source_urls = ['https://downloads.skewed.de/%(name)s/']
+sources = [SOURCE_TAR_BZ2]
+checksums = ['cde479c0a7254b72f6e795d03b0273b0a7d81611a6a3364ba649c2c85c99acae']
+
+builddependencies = [
+    ('gawk', '5.3.0'),
+    ('pkgconf', '1.9.5'),
+    ('expat', '2.5.0'),
+    ('CGAL', '5.6'),
+]
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('Boost.Python', '1.83.0'),
+    ('sparsehash', '2.0.4'),
+    ('matplotlib', '3.7.2'),
+    ('PyCairo', '1.25.0'),
+    ('cairomm', '1.16.2'),
+    ('PyGObject', '3.46.0'),
+    ('GTK3', '3.24.37'),
+]
+
+configopts = '--enable-openmp --with-cgal=$EBROOTCGAL --with-boost=$EBROOTBOOST '
+configopts += '--with-boost-python=boost_python311  '
+configopts += '--with-python-module-path=%(installdir)s/lib/python%(pyshortver)s/site-packages '
+
+
+sanity_check_paths = {
+    'files': ['lib/python%(pyshortver)s/site-packages/graph_tool/all.py'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages/graph_tool/include', 'share'],
+}
+
+sanity_check_commands = [
+    "python -c 'from graph_tool.all import Graph, BlockState'",
+    "python -c 'import graph_tool.inference'",
+]
+
+modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'}
+
+moduleclass = 'math'
diff --git a/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb b/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb
index 0fa2bcb2cf6..bb7237e35f1 100644
--- a/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb
+++ b/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb
@@ -44,6 +44,7 @@ dependencies = [
     ('typing-extensions', '4.9.0'),  # sc_toolbox
     ('adjustText', '1.1.1'),  # sc_toolbox, created
     ('python-parasail', '1.3.4'),  # scirpy
+    ('graph-tool', '2.59'),  # schist
 ]
 
 exts_list = [
@@ -201,11 +202,11 @@ exts_list = [
     ('scirpy', '0.17.0', {
         'checksums': ['f61653a4f7387562ec89b00fbfd7cab762c0bf3320f21ccfc47df80a13cc5d41'],
     }),
-    # ('schist', '0.8.3', {
-    #     'source_tmpl': 'v%(version)s.tar.gz',
-    #     'source_urls': ['https://github.com/dawe/schist/archive/'],
-    #     'checksums': ['9b98ec9d85554573288c24f18c4791ba7c4d315397cbc422ea25d4a7cdd42e6d'],
-    # }),
+    ('schist', '0.8.3', {
+        'source_tmpl': 'v%(version)s.tar.gz',
+        'source_urls': ['https://github.com/dawe/schist/archive/'],
+        'checksums': ['9b98ec9d85554573288c24f18c4791ba7c4d315397cbc422ea25d4a7cdd42e6d'],
+    }),
 ]
 
 use_pip = True

From 8a00362056ceb096c785c8de4706befe6b11bb34 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Mon, 3 Jun 2024 12:12:46 +0200
Subject: [PATCH 122/835] add gawk for schist

---
 .../g/gawk/gawk-5.3.0-GCC-12.3.0.eb           | 23 +++++++++++++++++++
 1 file changed, 23 insertions(+)
 create mode 100644 easybuild/easyconfigs/g/gawk/gawk-5.3.0-GCC-12.3.0.eb

diff --git a/easybuild/easyconfigs/g/gawk/gawk-5.3.0-GCC-12.3.0.eb b/easybuild/easyconfigs/g/gawk/gawk-5.3.0-GCC-12.3.0.eb
new file mode 100644
index 00000000000..8c63821d169
--- /dev/null
+++ b/easybuild/easyconfigs/g/gawk/gawk-5.3.0-GCC-12.3.0.eb
@@ -0,0 +1,23 @@
+easyblock = 'ConfigureMake'
+
+name = 'gawk'
+version = '5.3.0'
+
+homepage = 'https://www.gnu.org/software/gawk'
+description = """The awk utility interprets a special-purpose programming language that makes it possible to handle
+simple data-reformatting jobs with just a few lines of code."""
+
+toolchain = {'name': 'GCC', 'version': '12.3.0'}
+
+source_urls = [GNU_SOURCE]
+sources = [SOURCE_TAR_GZ]
+checksums = ['378f8864ec21cfceaa048f7e1869ac9b4597b449087caf1eb55e440d30273336']
+
+sanity_check_paths = {
+    'files': ['bin/gawk'],
+    'dirs': [],
+}
+
+sanity_check_commands = ["gawk --help"]
+
+moduleclass = 'tools'

From 2a1b972fdf200e6c2b9ba86f579e8c42327c438e Mon Sep 17 00:00:00 2001
From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com>
Date: Mon, 3 Jun 2024 17:36:42 +0200
Subject: [PATCH 123/835] Delete
 easybuild/easyconfigs/m/ml_dtypes/ml_dtypes-0.3.2_EigenAvx512.patch

---
 .../ml_dtypes-0.3.2_EigenAvx512.patch         | 1219 -----------------
 1 file changed, 1219 deletions(-)
 delete mode 100644 easybuild/easyconfigs/m/ml_dtypes/ml_dtypes-0.3.2_EigenAvx512.patch

diff --git a/easybuild/easyconfigs/m/ml_dtypes/ml_dtypes-0.3.2_EigenAvx512.patch b/easybuild/easyconfigs/m/ml_dtypes/ml_dtypes-0.3.2_EigenAvx512.patch
deleted file mode 100644
index 42ea0606391..00000000000
--- a/easybuild/easyconfigs/m/ml_dtypes/ml_dtypes-0.3.2_EigenAvx512.patch
+++ /dev/null
@@ -1,1219 +0,0 @@
-# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2024/01
-# ml_dtype 0.3.2 ships a copy of Eigen commit 7bf2968 (https://gitlab.com/libeigen/eigen/-/commit/7bf2968).
-# This copy is missing the file src/Core/arch/AVX512/TrsmUnrolls.inc, which is added by the present patch.
-diff -ru --new-file old/third_party_ori/eigen/Eigen/src/Core/arch/AVX512/TrsmUnrolls.inc new/third_party/eigen/Eigen/src/Core/arch/AVX512/TrsmUnrolls.inc
---- old/third_party/eigen/Eigen/src/Core/arch/AVX512/TrsmUnrolls.inc	1970-01-01 01:00:00.000000000 +0100
-+++ new/third_party/eigen/Eigen/src/Core/arch/AVX512/TrsmUnrolls.inc	2024-02-14 10:32:25.492978066 +0100
-@@ -0,0 +1,1212 @@
-+// This file is part of Eigen, a lightweight C++ template library
-+// for linear algebra.
-+//
-+// Copyright (C) 2022 Intel Corporation
-+//
-+// This Source Code Form is subject to the terms of the Mozilla
-+// Public License v. 2.0. If a copy of the MPL was not distributed
-+// with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
-+
-+#ifndef EIGEN_CORE_ARCH_AVX512_TRSM_UNROLLS_H
-+#define EIGEN_CORE_ARCH_AVX512_TRSM_UNROLLS_H
-+
-+template <bool isARowMajor = true>
-+EIGEN_ALWAYS_INLINE int64_t idA(int64_t i, int64_t j, int64_t LDA) {
-+  EIGEN_IF_CONSTEXPR(isARowMajor) return i * LDA + j;
-+  else return i + j * LDA;
-+}
-+
-+/**
-+ * This namespace contains various classes used to generate compile-time unrolls which are
-+ * used throughout the trsm/gemm kernels. The unrolls are characterized as for-loops (1-D), nested
-+ * for-loops (2-D), or triple nested for-loops (3-D). Unrolls are generated using template recursion
-+ *
-+ * Example, the 2-D for-loop is unrolled recursively by first flattening to a 1-D loop.
-+ *
-+ * for(startI = 0; startI < endI; startI++)             for(startC = 0; startC < endI*endJ; startC++)
-+ *   for(startJ = 0; startJ < endJ; startJ++)  ---->      startI = (startC)/(endJ)
-+ *     func(startI,startJ)                                startJ = (startC)%(endJ)
-+ *                                                        func(...)
-+ *
-+ * The 1-D loop can be unrolled recursively by using enable_if and defining an auxillary function
-+ * with a template parameter used as a counter.
-+ *
-+ * template <endI, endJ, counter>
-+ * std::enable_if_t<(counter <= 0)>  <---- tail case.
-+ * aux_func {}
-+ *
-+ * template <endI, endJ, counter>
-+ * std::enable_if_t<(counter > 0)>   <---- actual for-loop
-+ * aux_func {
-+ *   startC = endI*endJ - counter
-+ *   startI = (startC)/(endJ)
-+ *   startJ = (startC)%(endJ)
-+ *   func(startI, startJ)
-+ *   aux_func<endI, endJ, counter-1>()
-+ * }
-+ *
-+ * Note: Additional wrapper functions are provided for aux_func which hides the counter template
-+ * parameter since counter usually depends on endI, endJ, etc...
-+ *
-+ * Conventions:
-+ * 1) endX: specifies the terminal value for the for-loop, (ex: for(startX = 0; startX < endX; startX++))
-+ *
-+ * 2) rem, remM, remK template parameters are used for deciding whether to use masked operations for
-+ *    handling remaining tails (when sizes are not multiples of PacketSize or EIGEN_AVX_MAX_NUM_ROW)
-+ */
-+namespace unrolls {
-+
-+template <int64_t N>
-+EIGEN_ALWAYS_INLINE auto remMask(int64_t m) {
-+  EIGEN_IF_CONSTEXPR(N == 16) { return 0xFFFF >> (16 - m); }
-+  else EIGEN_IF_CONSTEXPR(N == 8) {
-+    return 0xFF >> (8 - m);
-+  }
-+  else EIGEN_IF_CONSTEXPR(N == 4) {
-+    return 0x0F >> (4 - m);
-+  }
-+  return 0;
-+}
-+
-+template <typename Packet>
-+EIGEN_ALWAYS_INLINE void trans8x8blocks(PacketBlock<Packet, 8> &kernel);
-+
-+template <>
-+EIGEN_ALWAYS_INLINE void trans8x8blocks(PacketBlock<Packet16f, 8> &kernel) {
-+  __m512 T0 = _mm512_unpacklo_ps(kernel.packet[0], kernel.packet[1]);
-+  __m512 T1 = _mm512_unpackhi_ps(kernel.packet[0], kernel.packet[1]);
-+  __m512 T2 = _mm512_unpacklo_ps(kernel.packet[2], kernel.packet[3]);
-+  __m512 T3 = _mm512_unpackhi_ps(kernel.packet[2], kernel.packet[3]);
-+  __m512 T4 = _mm512_unpacklo_ps(kernel.packet[4], kernel.packet[5]);
-+  __m512 T5 = _mm512_unpackhi_ps(kernel.packet[4], kernel.packet[5]);
-+  __m512 T6 = _mm512_unpacklo_ps(kernel.packet[6], kernel.packet[7]);
-+  __m512 T7 = _mm512_unpackhi_ps(kernel.packet[6], kernel.packet[7]);
-+
-+  kernel.packet[0] = _mm512_castpd_ps(_mm512_unpacklo_pd(_mm512_castps_pd(T0), _mm512_castps_pd(T2)));
-+  kernel.packet[1] = _mm512_castpd_ps(_mm512_unpackhi_pd(_mm512_castps_pd(T0), _mm512_castps_pd(T2)));
-+  kernel.packet[2] = _mm512_castpd_ps(_mm512_unpacklo_pd(_mm512_castps_pd(T1), _mm512_castps_pd(T3)));
-+  kernel.packet[3] = _mm512_castpd_ps(_mm512_unpackhi_pd(_mm512_castps_pd(T1), _mm512_castps_pd(T3)));
-+  kernel.packet[4] = _mm512_castpd_ps(_mm512_unpacklo_pd(_mm512_castps_pd(T4), _mm512_castps_pd(T6)));
-+  kernel.packet[5] = _mm512_castpd_ps(_mm512_unpackhi_pd(_mm512_castps_pd(T4), _mm512_castps_pd(T6)));
-+  kernel.packet[6] = _mm512_castpd_ps(_mm512_unpacklo_pd(_mm512_castps_pd(T5), _mm512_castps_pd(T7)));
-+  kernel.packet[7] = _mm512_castpd_ps(_mm512_unpackhi_pd(_mm512_castps_pd(T5), _mm512_castps_pd(T7)));
-+
-+  T0 = _mm512_castpd_ps(_mm512_permutex_pd(_mm512_castps_pd(kernel.packet[4]), 0x4E));
-+  T0 = _mm512_mask_blend_ps(0xF0F0, kernel.packet[0], T0);
-+  T4 = _mm512_castpd_ps(_mm512_permutex_pd(_mm512_castps_pd(kernel.packet[0]), 0x4E));
-+  T4 = _mm512_mask_blend_ps(0xF0F0, T4, kernel.packet[4]);
-+  T1 = _mm512_castpd_ps(_mm512_permutex_pd(_mm512_castps_pd(kernel.packet[5]), 0x4E));
-+  T1 = _mm512_mask_blend_ps(0xF0F0, kernel.packet[1], T1);
-+  T5 = _mm512_castpd_ps(_mm512_permutex_pd(_mm512_castps_pd(kernel.packet[1]), 0x4E));
-+  T5 = _mm512_mask_blend_ps(0xF0F0, T5, kernel.packet[5]);
-+  T2 = _mm512_castpd_ps(_mm512_permutex_pd(_mm512_castps_pd(kernel.packet[6]), 0x4E));
-+  T2 = _mm512_mask_blend_ps(0xF0F0, kernel.packet[2], T2);
-+  T6 = _mm512_castpd_ps(_mm512_permutex_pd(_mm512_castps_pd(kernel.packet[2]), 0x4E));
-+  T6 = _mm512_mask_blend_ps(0xF0F0, T6, kernel.packet[6]);
-+  T3 = _mm512_castpd_ps(_mm512_permutex_pd(_mm512_castps_pd(kernel.packet[7]), 0x4E));
-+  T3 = _mm512_mask_blend_ps(0xF0F0, kernel.packet[3], T3);
-+  T7 = _mm512_castpd_ps(_mm512_permutex_pd(_mm512_castps_pd(kernel.packet[3]), 0x4E));
-+  T7 = _mm512_mask_blend_ps(0xF0F0, T7, kernel.packet[7]);
-+
-+  kernel.packet[0] = T0;
-+  kernel.packet[1] = T1;
-+  kernel.packet[2] = T2;
-+  kernel.packet[3] = T3;
-+  kernel.packet[4] = T4;
-+  kernel.packet[5] = T5;
-+  kernel.packet[6] = T6;
-+  kernel.packet[7] = T7;
-+}
-+
-+template <>
-+EIGEN_ALWAYS_INLINE void trans8x8blocks(PacketBlock<Packet8d, 8> &kernel) {
-+  ptranspose(kernel);
-+}
-+
-+/***
-+ * Unrolls for tranposed C stores
-+ */
-+template <typename Scalar>
-+class trans {
-+ public:
-+  using vec = typename std::conditional<std::is_same<Scalar, float>::value, vecFullFloat, vecFullDouble>::type;
-+  using vecHalf = typename std::conditional<std::is_same<Scalar, float>::value, vecHalfFloat, vecFullDouble>::type;
-+  static constexpr int64_t PacketSize = packet_traits<Scalar>::size;
-+
-+  /***********************************
-+   * Auxillary Functions for:
-+   *  - storeC
-+   ***********************************
-+   */
-+
-+  /**
-+   * aux_storeC
-+   *
-+   * 1-D unroll
-+   *      for(startN = 0; startN < endN; startN++)
-+   *
-+   * (endN <= PacketSize) is required to handle the fp32 case, see comments in transStoreC
-+   *
-+   **/
-+  template <int64_t endN, int64_t counter, int64_t unrollN, int64_t packetIndexOffset, bool remM>
-+  static EIGEN_ALWAYS_INLINE std::enable_if_t<(counter > 0 && endN <= PacketSize)> aux_storeC(
-+      Scalar *C_arr, int64_t LDC, PacketBlock<vec, EIGEN_ARCH_DEFAULT_NUMBER_OF_REGISTERS> &zmm, int64_t remM_ = 0) {
-+    constexpr int64_t counterReverse = endN - counter;
-+    constexpr int64_t startN = counterReverse;
-+
-+    EIGEN_IF_CONSTEXPR(startN < EIGEN_AVX_MAX_NUM_ROW) {
-+      EIGEN_IF_CONSTEXPR(remM) {
-+        pstoreu<Scalar>(
-+            C_arr + LDC * startN,
-+            padd(ploadu<vecHalf>((const Scalar *)C_arr + LDC * startN, remMask<EIGEN_AVX_MAX_NUM_ROW>(remM_)),
-+                 preinterpret<vecHalf>(zmm.packet[packetIndexOffset + (unrollN / PacketSize) * startN]),
-+                 remMask<EIGEN_AVX_MAX_NUM_ROW>(remM_)),
-+            remMask<EIGEN_AVX_MAX_NUM_ROW>(remM_));
-+      }
-+      else {
-+        pstoreu<Scalar>(C_arr + LDC * startN,
-+                        padd(ploadu<vecHalf>((const Scalar *)C_arr + LDC * startN),
-+                             preinterpret<vecHalf>(zmm.packet[packetIndexOffset + (unrollN / PacketSize) * startN])));
-+      }
-+    }
-+    else {  // This block is only needed for fp32 case
-+      // Reinterpret as __m512 for _mm512_shuffle_f32x4
-+      vecFullFloat zmm2vecFullFloat = preinterpret<vecFullFloat>(
-+          zmm.packet[packetIndexOffset + (unrollN / PacketSize) * (startN - EIGEN_AVX_MAX_NUM_ROW)]);
-+      // Swap lower and upper half of avx register.
-+      zmm.packet[packetIndexOffset + (unrollN / PacketSize) * (startN - EIGEN_AVX_MAX_NUM_ROW)] =
-+          preinterpret<vec>(_mm512_shuffle_f32x4(zmm2vecFullFloat, zmm2vecFullFloat, 0b01001110));
-+
-+      EIGEN_IF_CONSTEXPR(remM) {
-+        pstoreu<Scalar>(
-+            C_arr + LDC * startN,
-+            padd(ploadu<vecHalf>((const Scalar *)C_arr + LDC * startN, remMask<EIGEN_AVX_MAX_NUM_ROW>(remM_)),
-+                 preinterpret<vecHalf>(
-+                     zmm.packet[packetIndexOffset + (unrollN / PacketSize) * (startN - EIGEN_AVX_MAX_NUM_ROW)])),
-+            remMask<EIGEN_AVX_MAX_NUM_ROW>(remM_));
-+      }
-+      else {
-+        pstoreu<Scalar>(
-+            C_arr + LDC * startN,
-+            padd(ploadu<vecHalf>((const Scalar *)C_arr + LDC * startN),
-+                 preinterpret<vecHalf>(
-+                     zmm.packet[packetIndexOffset + (unrollN / PacketSize) * (startN - EIGEN_AVX_MAX_NUM_ROW)])));
-+      }
-+    }
-+    aux_storeC<endN, counter - 1, unrollN, packetIndexOffset, remM>(C_arr, LDC, zmm, remM_);
-+  }
-+
-+  template <int64_t endN, int64_t counter, int64_t unrollN, int64_t packetIndexOffset, bool remM>
-+  static EIGEN_ALWAYS_INLINE std::enable_if_t<!(counter > 0 && endN <= PacketSize)> aux_storeC(
-+      Scalar *C_arr, int64_t LDC, PacketBlock<vec, EIGEN_ARCH_DEFAULT_NUMBER_OF_REGISTERS> &zmm, int64_t remM_ = 0) {
-+    EIGEN_UNUSED_VARIABLE(C_arr);
-+    EIGEN_UNUSED_VARIABLE(LDC);
-+    EIGEN_UNUSED_VARIABLE(zmm);
-+    EIGEN_UNUSED_VARIABLE(remM_);
-+  }
-+
-+  template <int64_t endN, int64_t unrollN, int64_t packetIndexOffset, bool remM>
-+  static EIGEN_ALWAYS_INLINE void storeC(Scalar *C_arr, int64_t LDC,
-+                                         PacketBlock<vec, EIGEN_ARCH_DEFAULT_NUMBER_OF_REGISTERS> &zmm,
-+                                         int64_t remM_ = 0) {
-+    aux_storeC<endN, endN, unrollN, packetIndexOffset, remM>(C_arr, LDC, zmm, remM_);
-+  }
-+
-+  /**
-+   * Transposes LxunrollN row major block of matrices stored EIGEN_AVX_MAX_NUM_ACC zmm registers to
-+   * "unrollN"xL ymm registers to be stored col-major into C.
-+   *
-+   *  For 8x48, the 8x48 block (row-major) is stored in zmm as follows:
-+   *
-+   *  row0: zmm0 zmm1 zmm2
-+   *  row1: zmm3 zmm4 zmm5
-+   *    .
-+   *    .
-+   *  row7: zmm21 zmm22 zmm23
-+   *
-+   *  For 8x32, the 8x32 block (row-major) is stored in zmm as follows:
-+   *
-+   *  row0: zmm0 zmm1
-+   *  row1: zmm2 zmm3
-+   *    .
-+   *    .
-+   *  row7: zmm14 zmm15
-+   *
-+   *
-+   * In general we will have {1,2,3} groups of avx registers each of size
-+   * EIGEN_AVX_MAX_NUM_ROW. packetIndexOffset is used to select which "block" of
-+   * avx registers are being transposed.
-+   */
-+  template <int64_t unrollN, int64_t packetIndexOffset>
-+  static EIGEN_ALWAYS_INLINE void transpose(PacketBlock<vec, EIGEN_ARCH_DEFAULT_NUMBER_OF_REGISTERS> &zmm) {
-+    // Note: this assumes EIGEN_AVX_MAX_NUM_ROW = 8. Unrolls should be adjusted
-+    // accordingly if EIGEN_AVX_MAX_NUM_ROW is smaller.
-+    constexpr int64_t zmmStride = unrollN / PacketSize;
-+    PacketBlock<vec, EIGEN_AVX_MAX_NUM_ROW> r;
-+    r.packet[0] = zmm.packet[packetIndexOffset + zmmStride * 0];
-+    r.packet[1] = zmm.packet[packetIndexOffset + zmmStride * 1];
-+    r.packet[2] = zmm.packet[packetIndexOffset + zmmStride * 2];
-+    r.packet[3] = zmm.packet[packetIndexOffset + zmmStride * 3];
-+    r.packet[4] = zmm.packet[packetIndexOffset + zmmStride * 4];
-+    r.packet[5] = zmm.packet[packetIndexOffset + zmmStride * 5];
-+    r.packet[6] = zmm.packet[packetIndexOffset + zmmStride * 6];
-+    r.packet[7] = zmm.packet[packetIndexOffset + zmmStride * 7];
-+    trans8x8blocks(r);
-+    zmm.packet[packetIndexOffset + zmmStride * 0] = r.packet[0];
-+    zmm.packet[packetIndexOffset + zmmStride * 1] = r.packet[1];
-+    zmm.packet[packetIndexOffset + zmmStride * 2] = r.packet[2];
-+    zmm.packet[packetIndexOffset + zmmStride * 3] = r.packet[3];
-+    zmm.packet[packetIndexOffset + zmmStride * 4] = r.packet[4];
-+    zmm.packet[packetIndexOffset + zmmStride * 5] = r.packet[5];
-+    zmm.packet[packetIndexOffset + zmmStride * 6] = r.packet[6];
-+    zmm.packet[packetIndexOffset + zmmStride * 7] = r.packet[7];
-+  }
-+};
-+
-+/**
-+ * Unrolls for copyBToRowMajor
-+ *
-+ * Idea:
-+ *  1) Load a block of right-hand sides to registers (using loadB).
-+ *  2) Convert the block from column-major to row-major (transposeLxL)
-+ *  3) Store the blocks from register either to a temp array (toTemp == true), or back to B (toTemp == false).
-+ *
-+ *  We use at most EIGEN_AVX_MAX_NUM_ACC avx registers to store the blocks of B. The remaining registers are
-+ *  used as temps for transposing.
-+ *
-+ *  Blocks will be of size Lx{U1,U2,U3}. packetIndexOffset is used to index between these subblocks
-+ *  For fp32, PacketSize = 2*EIGEN_AVX_MAX_NUM_ROW, so we reinterpret packets as packets half the size (zmm -> ymm).
-+ */
-+template <typename Scalar>
-+class transB {
-+ public:
-+  using vec = typename std::conditional<std::is_same<Scalar, float>::value, vecFullFloat, vecFullDouble>::type;
-+  using vecHalf = typename std::conditional<std::is_same<Scalar, float>::value, vecHalfFloat, vecFullDouble>::type;
-+  static constexpr int64_t PacketSize = packet_traits<Scalar>::size;
-+
-+  /***********************************
-+   * Auxillary Functions for:
-+   *  - loadB
-+   *  - storeB
-+   *  - loadBBlock
-+   *  - storeBBlock
-+   ***********************************
-+   */
-+
-+  /**
-+   * aux_loadB
-+   *
-+   * 1-D unroll
-+   *      for(startN = 0; startN < endN; startN++)
-+   **/
-+  template <int64_t endN, int64_t counter, int64_t packetIndexOffset, bool remM>
-+  static EIGEN_ALWAYS_INLINE std::enable_if_t<(counter > 0)> aux_loadB(
-+      Scalar *B_arr, int64_t LDB, PacketBlock<vecHalf, EIGEN_ARCH_DEFAULT_NUMBER_OF_REGISTERS> &ymm,
-+      int64_t remM_ = 0) {
-+    constexpr int64_t counterReverse = endN - counter;
-+    constexpr int64_t startN = counterReverse;
-+
-+    EIGEN_IF_CONSTEXPR(remM) {
-+      ymm.packet[packetIndexOffset + startN] =
-+          ploadu<vecHalf>((const Scalar *)&B_arr[startN * LDB], remMask<EIGEN_AVX_MAX_NUM_ROW>(remM_));
-+    }
-+    else ymm.packet[packetIndexOffset + startN] = ploadu<vecHalf>((const Scalar *)&B_arr[startN * LDB]);
-+
-+    aux_loadB<endN, counter - 1, packetIndexOffset, remM>(B_arr, LDB, ymm, remM_);
-+  }
-+
-+  template <int64_t endN, int64_t counter, int64_t packetIndexOffset, bool remM>
-+  static EIGEN_ALWAYS_INLINE std::enable_if_t<(counter <= 0)> aux_loadB(
-+      Scalar *B_arr, int64_t LDB, PacketBlock<vecHalf, EIGEN_ARCH_DEFAULT_NUMBER_OF_REGISTERS> &ymm,
-+      int64_t remM_ = 0) {
-+    EIGEN_UNUSED_VARIABLE(B_arr);
-+    EIGEN_UNUSED_VARIABLE(LDB);
-+    EIGEN_UNUSED_VARIABLE(ymm);
-+    EIGEN_UNUSED_VARIABLE(remM_);
-+  }
-+
-+  /**
-+   * aux_storeB
-+   *
-+   * 1-D unroll
-+   *      for(startN = 0; startN < endN; startN++)
-+   **/
-+  template <int64_t endN, int64_t counter, int64_t packetIndexOffset, bool remK, bool remM>
-+  static EIGEN_ALWAYS_INLINE std::enable_if_t<(counter > 0)> aux_storeB(
-+      Scalar *B_arr, int64_t LDB, PacketBlock<vecHalf, EIGEN_ARCH_DEFAULT_NUMBER_OF_REGISTERS> &ymm, int64_t rem_ = 0) {
-+    constexpr int64_t counterReverse = endN - counter;
-+    constexpr int64_t startN = counterReverse;
-+
-+    EIGEN_IF_CONSTEXPR(remK || remM) {
-+      pstoreu<Scalar>(&B_arr[startN * LDB], ymm.packet[packetIndexOffset + startN],
-+                      remMask<EIGEN_AVX_MAX_NUM_ROW>(rem_));
-+    }
-+    else {
-+      pstoreu<Scalar>(&B_arr[startN * LDB], ymm.packet[packetIndexOffset + startN]);
-+    }
-+
-+    aux_storeB<endN, counter - 1, packetIndexOffset, remK, remM>(B_arr, LDB, ymm, rem_);
-+  }
-+
-+  template <int64_t endN, int64_t counter, int64_t packetIndexOffset, bool remK, bool remM>
-+  static EIGEN_ALWAYS_INLINE std::enable_if_t<(counter <= 0)> aux_storeB(
-+      Scalar *B_arr, int64_t LDB, PacketBlock<vecHalf, EIGEN_ARCH_DEFAULT_NUMBER_OF_REGISTERS> &ymm, int64_t rem_ = 0) {
-+    EIGEN_UNUSED_VARIABLE(B_arr);
-+    EIGEN_UNUSED_VARIABLE(LDB);
-+    EIGEN_UNUSED_VARIABLE(ymm);
-+    EIGEN_UNUSED_VARIABLE(rem_);
-+  }
-+
-+  /**
-+   * aux_loadBBlock
-+   *
-+   * 1-D unroll
-+   *      for(startN = 0; startN < endN; startN += EIGEN_AVX_MAX_NUM_ROW)
-+   **/
-+  template <int64_t endN, int64_t counter, bool toTemp, bool remM>
-+  static EIGEN_ALWAYS_INLINE std::enable_if_t<(counter > 0)> aux_loadBBlock(
-+      Scalar *B_arr, int64_t LDB, Scalar *B_temp, int64_t LDB_,
-+      PacketBlock<vecHalf, EIGEN_ARCH_DEFAULT_NUMBER_OF_REGISTERS> &ymm, int64_t remM_ = 0) {
-+    constexpr int64_t counterReverse = endN - counter;
-+    constexpr int64_t startN = counterReverse;
-+    transB::template loadB<EIGEN_AVX_MAX_NUM_ROW, startN, false>(&B_temp[startN], LDB_, ymm);
-+    aux_loadBBlock<endN, counter - EIGEN_AVX_MAX_NUM_ROW, toTemp, remM>(B_arr, LDB, B_temp, LDB_, ymm, remM_);
-+  }
-+
-+  template <int64_t endN, int64_t counter, bool toTemp, bool remM>
-+  static EIGEN_ALWAYS_INLINE std::enable_if_t<(counter <= 0)> aux_loadBBlock(
-+      Scalar *B_arr, int64_t LDB, Scalar *B_temp, int64_t LDB_,
-+      PacketBlock<vecHalf, EIGEN_ARCH_DEFAULT_NUMBER_OF_REGISTERS> &ymm, int64_t remM_ = 0) {
-+    EIGEN_UNUSED_VARIABLE(B_arr);
-+    EIGEN_UNUSED_VARIABLE(LDB);
-+    EIGEN_UNUSED_VARIABLE(B_temp);
-+    EIGEN_UNUSED_VARIABLE(LDB_);
-+    EIGEN_UNUSED_VARIABLE(ymm);
-+    EIGEN_UNUSED_VARIABLE(remM_);
-+  }
-+
-+  /**
-+   * aux_storeBBlock
-+   *
-+   * 1-D unroll
-+   *      for(startN = 0; startN < endN; startN += EIGEN_AVX_MAX_NUM_ROW)
-+   **/
-+  template <int64_t endN, int64_t counter, bool toTemp, bool remM, int64_t remK_>
-+  static EIGEN_ALWAYS_INLINE std::enable_if_t<(counter > 0)> aux_storeBBlock(
-+      Scalar *B_arr, int64_t LDB, Scalar *B_temp, int64_t LDB_,
-+      PacketBlock<vecHalf, EIGEN_ARCH_DEFAULT_NUMBER_OF_REGISTERS> &ymm, int64_t remM_ = 0) {
-+    constexpr int64_t counterReverse = endN - counter;
-+    constexpr int64_t startN = counterReverse;
-+
-+    EIGEN_IF_CONSTEXPR(toTemp) {
-+      transB::template storeB<EIGEN_AVX_MAX_NUM_ROW, startN, remK_ != 0, false>(&B_temp[startN], LDB_, ymm, remK_);
-+    }
-+    else {
-+      transB::template storeB<std::min(EIGEN_AVX_MAX_NUM_ROW, endN), startN, false, remM>(&B_arr[0 + startN * LDB], LDB,
-+                                                                                          ymm, remM_);
-+    }
-+    aux_storeBBlock<endN, counter - EIGEN_AVX_MAX_NUM_ROW, toTemp, remM, remK_>(B_arr, LDB, B_temp, LDB_, ymm, remM_);
-+  }
-+
-+  template <int64_t endN, int64_t counter, bool toTemp, bool remM, int64_t remK_>
-+  static EIGEN_ALWAYS_INLINE std::enable_if_t<(counter <= 0)> aux_storeBBlock(
-+      Scalar *B_arr, int64_t LDB, Scalar *B_temp, int64_t LDB_,
-+      PacketBlock<vecHalf, EIGEN_ARCH_DEFAULT_NUMBER_OF_REGISTERS> &ymm, int64_t remM_ = 0) {
-+    EIGEN_UNUSED_VARIABLE(B_arr);
-+    EIGEN_UNUSED_VARIABLE(LDB);
-+    EIGEN_UNUSED_VARIABLE(B_temp);
-+    EIGEN_UNUSED_VARIABLE(LDB_);
-+    EIGEN_UNUSED_VARIABLE(ymm);
-+    EIGEN_UNUSED_VARIABLE(remM_);
-+  }
-+
-+  /********************************************************
-+   * Wrappers for aux_XXXX to hide counter parameter
-+   ********************************************************/
-+
-+  template <int64_t endN, int64_t packetIndexOffset, bool remM>
-+  static EIGEN_ALWAYS_INLINE void loadB(Scalar *B_arr, int64_t LDB,
-+                                        PacketBlock<vecHalf, EIGEN_ARCH_DEFAULT_NUMBER_OF_REGISTERS> &ymm,
-+                                        int64_t remM_ = 0) {
-+    aux_loadB<endN, endN, packetIndexOffset, remM>(B_arr, LDB, ymm, remM_);
-+  }
-+
-+  template <int64_t endN, int64_t packetIndexOffset, bool remK, bool remM>
-+  static EIGEN_ALWAYS_INLINE void storeB(Scalar *B_arr, int64_t LDB,
-+                                         PacketBlock<vecHalf, EIGEN_ARCH_DEFAULT_NUMBER_OF_REGISTERS> &ymm,
-+                                         int64_t rem_ = 0) {
-+    aux_storeB<endN, endN, packetIndexOffset, remK, remM>(B_arr, LDB, ymm, rem_);
-+  }
-+
-+  template <int64_t unrollN, bool toTemp, bool remM>
-+  static EIGEN_ALWAYS_INLINE void loadBBlock(Scalar *B_arr, int64_t LDB, Scalar *B_temp, int64_t LDB_,
-+                                             PacketBlock<vecHalf, EIGEN_ARCH_DEFAULT_NUMBER_OF_REGISTERS> &ymm,
-+                                             int64_t remM_ = 0) {
-+    EIGEN_IF_CONSTEXPR(toTemp) { transB::template loadB<unrollN, 0, remM>(&B_arr[0], LDB, ymm, remM_); }
-+    else {
-+      aux_loadBBlock<unrollN, unrollN, toTemp, remM>(B_arr, LDB, B_temp, LDB_, ymm, remM_);
-+    }
-+  }
-+
-+  template <int64_t unrollN, bool toTemp, bool remM, int64_t remK_>
-+  static EIGEN_ALWAYS_INLINE void storeBBlock(Scalar *B_arr, int64_t LDB, Scalar *B_temp, int64_t LDB_,
-+                                              PacketBlock<vecHalf, EIGEN_ARCH_DEFAULT_NUMBER_OF_REGISTERS> &ymm,
-+                                              int64_t remM_ = 0) {
-+    aux_storeBBlock<unrollN, unrollN, toTemp, remM, remK_>(B_arr, LDB, B_temp, LDB_, ymm, remM_);
-+  }
-+
-+  template <int64_t packetIndexOffset>
-+  static EIGEN_ALWAYS_INLINE void transposeLxL(PacketBlock<vecHalf, EIGEN_ARCH_DEFAULT_NUMBER_OF_REGISTERS> &ymm) {
-+    // Note: this assumes EIGEN_AVX_MAX_NUM_ROW = 8. Unrolls should be adjusted
-+    // accordingly if EIGEN_AVX_MAX_NUM_ROW is smaller.
-+    PacketBlock<vecHalf, EIGEN_AVX_MAX_NUM_ROW> r;
-+    r.packet[0] = ymm.packet[packetIndexOffset + 0];
-+    r.packet[1] = ymm.packet[packetIndexOffset + 1];
-+    r.packet[2] = ymm.packet[packetIndexOffset + 2];
-+    r.packet[3] = ymm.packet[packetIndexOffset + 3];
-+    r.packet[4] = ymm.packet[packetIndexOffset + 4];
-+    r.packet[5] = ymm.packet[packetIndexOffset + 5];
-+    r.packet[6] = ymm.packet[packetIndexOffset + 6];
-+    r.packet[7] = ymm.packet[packetIndexOffset + 7];
-+    ptranspose(r);
-+    ymm.packet[packetIndexOffset + 0] = r.packet[0];
-+    ymm.packet[packetIndexOffset + 1] = r.packet[1];
-+    ymm.packet[packetIndexOffset + 2] = r.packet[2];
-+    ymm.packet[packetIndexOffset + 3] = r.packet[3];
-+    ymm.packet[packetIndexOffset + 4] = r.packet[4];
-+    ymm.packet[packetIndexOffset + 5] = r.packet[5];
-+    ymm.packet[packetIndexOffset + 6] = r.packet[6];
-+    ymm.packet[packetIndexOffset + 7] = r.packet[7];
-+  }
-+
-+  template <int64_t unrollN, bool toTemp, bool remM>
-+  static EIGEN_ALWAYS_INLINE void transB_kernel(Scalar *B_arr, int64_t LDB, Scalar *B_temp, int64_t LDB_,
-+                                                PacketBlock<vecHalf, EIGEN_ARCH_DEFAULT_NUMBER_OF_REGISTERS> &ymm,
-+                                                int64_t remM_ = 0) {
-+    constexpr int64_t U3 = PacketSize * 3;
-+    constexpr int64_t U2 = PacketSize * 2;
-+    constexpr int64_t U1 = PacketSize * 1;
-+    /**
-+     *  Unrolls needed for each case:
-+     *   - AVX512 fp32 48 32 16 8 4 2 1
-+     *   - AVX512 fp64 24 16 8  4 2 1
-+     *
-+     *  For fp32 L and U1 are 1:2 so for U3/U2 cases the loads/stores need to be split up.
-+     */
-+    EIGEN_IF_CONSTEXPR(unrollN == U3) {
-+      // load LxU3 B col major, transpose LxU3 row major
-+      constexpr int64_t maxUBlock = std::min(3 * EIGEN_AVX_MAX_NUM_ROW, U3);
-+      transB::template loadBBlock<maxUBlock, toTemp, remM>(B_arr, LDB, B_temp, LDB_, ymm, remM_);
-+      transB::template transposeLxL<0 * EIGEN_AVX_MAX_NUM_ROW>(ymm);
-+      transB::template transposeLxL<1 * EIGEN_AVX_MAX_NUM_ROW>(ymm);
-+      transB::template transposeLxL<2 * EIGEN_AVX_MAX_NUM_ROW>(ymm);
-+      transB::template storeBBlock<maxUBlock, toTemp, remM, 0>(B_arr, LDB, B_temp, LDB_, ymm, remM_);
-+
-+      EIGEN_IF_CONSTEXPR(maxUBlock < U3) {
-+        transB::template loadBBlock<maxUBlock, toTemp, remM>(&B_arr[maxUBlock * LDB], LDB, &B_temp[maxUBlock], LDB_,
-+                                                             ymm, remM_);
-+        transB::template transposeLxL<0 * EIGEN_AVX_MAX_NUM_ROW>(ymm);
-+        transB::template transposeLxL<1 * EIGEN_AVX_MAX_NUM_ROW>(ymm);
-+        transB::template transposeLxL<2 * EIGEN_AVX_MAX_NUM_ROW>(ymm);
-+        transB::template storeBBlock<maxUBlock, toTemp, remM, 0>(&B_arr[maxUBlock * LDB], LDB, &B_temp[maxUBlock], LDB_,
-+                                                                 ymm, remM_);
-+      }
-+    }
-+    else EIGEN_IF_CONSTEXPR(unrollN == U2) {
-+      // load LxU2 B col major, transpose LxU2 row major
-+      constexpr int64_t maxUBlock = std::min(3 * EIGEN_AVX_MAX_NUM_ROW, U2);
-+      transB::template loadBBlock<maxUBlock, toTemp, remM>(B_arr, LDB, B_temp, LDB_, ymm, remM_);
-+      transB::template transposeLxL<0 * EIGEN_AVX_MAX_NUM_ROW>(ymm);
-+      transB::template transposeLxL<1 * EIGEN_AVX_MAX_NUM_ROW>(ymm);
-+      EIGEN_IF_CONSTEXPR(maxUBlock < U2) transB::template transposeLxL<2 * EIGEN_AVX_MAX_NUM_ROW>(ymm);
-+      transB::template storeBBlock<maxUBlock, toTemp, remM, 0>(B_arr, LDB, B_temp, LDB_, ymm, remM_);
-+
-+      EIGEN_IF_CONSTEXPR(maxUBlock < U2) {
-+        transB::template loadBBlock<EIGEN_AVX_MAX_NUM_ROW, toTemp, remM>(&B_arr[maxUBlock * LDB], LDB,
-+                                                                         &B_temp[maxUBlock], LDB_, ymm, remM_);
-+        transB::template transposeLxL<0>(ymm);
-+        transB::template storeBBlock<EIGEN_AVX_MAX_NUM_ROW, toTemp, remM, 0>(&B_arr[maxUBlock * LDB], LDB,
-+                                                                             &B_temp[maxUBlock], LDB_, ymm, remM_);
-+      }
-+    }
-+    else EIGEN_IF_CONSTEXPR(unrollN == U1) {
-+      // load LxU1 B col major, transpose LxU1 row major
-+      transB::template loadBBlock<U1, toTemp, remM>(B_arr, LDB, B_temp, LDB_, ymm, remM_);
-+      transB::template transposeLxL<0>(ymm);
-+      EIGEN_IF_CONSTEXPR(EIGEN_AVX_MAX_NUM_ROW < U1) { transB::template transposeLxL<1 * EIGEN_AVX_MAX_NUM_ROW>(ymm); }
-+      transB::template storeBBlock<U1, toTemp, remM, 0>(B_arr, LDB, B_temp, LDB_, ymm, remM_);
-+    }
-+    else EIGEN_IF_CONSTEXPR(unrollN == 8 && U1 > 8) {
-+      // load Lx4 B col major, transpose Lx4 row major
-+      transB::template loadBBlock<8, toTemp, remM>(B_arr, LDB, B_temp, LDB_, ymm, remM_);
-+      transB::template transposeLxL<0>(ymm);
-+      transB::template storeBBlock<8, toTemp, remM, 8>(B_arr, LDB, B_temp, LDB_, ymm, remM_);
-+    }
-+    else EIGEN_IF_CONSTEXPR(unrollN == 4 && U1 > 4) {
-+      // load Lx4 B col major, transpose Lx4 row major
-+      transB::template loadBBlock<4, toTemp, remM>(B_arr, LDB, B_temp, LDB_, ymm, remM_);
-+      transB::template transposeLxL<0>(ymm);
-+      transB::template storeBBlock<4, toTemp, remM, 4>(B_arr, LDB, B_temp, LDB_, ymm, remM_);
-+    }
-+    else EIGEN_IF_CONSTEXPR(unrollN == 2) {
-+      // load Lx2 B col major, transpose Lx2 row major
-+      transB::template loadBBlock<2, toTemp, remM>(B_arr, LDB, B_temp, LDB_, ymm, remM_);
-+      transB::template transposeLxL<0>(ymm);
-+      transB::template storeBBlock<2, toTemp, remM, 2>(B_arr, LDB, B_temp, LDB_, ymm, remM_);
-+    }
-+    else EIGEN_IF_CONSTEXPR(unrollN == 1) {
-+      // load Lx1 B col major, transpose Lx1 row major
-+      transB::template loadBBlock<1, toTemp, remM>(B_arr, LDB, B_temp, LDB_, ymm, remM_);
-+      transB::template transposeLxL<0>(ymm);
-+      transB::template storeBBlock<1, toTemp, remM, 1>(B_arr, LDB, B_temp, LDB_, ymm, remM_);
-+    }
-+  }
-+};
-+
-+/**
-+ * Unrolls for triSolveKernel
-+ *
-+ * Idea:
-+ *  1) Load a block of right-hand sides to registers in RHSInPacket (using loadRHS).
-+ *  2) Do triangular solve with RHSInPacket and a small block of A (triangular matrix)
-+ *     stored in AInPacket (using triSolveMicroKernel).
-+ *  3) Store final results (in avx registers) back into memory (using storeRHS).
-+ *
-+ *  RHSInPacket uses at most EIGEN_AVX_MAX_NUM_ACC avx registers and AInPacket uses at most
-+ *  EIGEN_AVX_MAX_NUM_ROW registers.
-+ */
-+template <typename Scalar>
-+class trsm {
-+ public:
-+  using vec = typename std::conditional<std::is_same<Scalar, float>::value, vecFullFloat, vecFullDouble>::type;
-+  static constexpr int64_t PacketSize = packet_traits<Scalar>::size;
-+
-+  /***********************************
-+   * Auxillary Functions for:
-+   *  - loadRHS
-+   *  - storeRHS
-+   *  - divRHSByDiag
-+   *  - updateRHS
-+   *  - triSolveMicroKernel
-+   ************************************/
-+  /**
-+   * aux_loadRHS
-+   *
-+   * 2-D unroll
-+   *      for(startM = 0; startM < endM; startM++)
-+   *        for(startK = 0; startK < endK; startK++)
-+   **/
-+  template <bool isFWDSolve, int64_t endM, int64_t endK, int64_t counter, bool krem>
-+  static EIGEN_ALWAYS_INLINE std::enable_if_t<(counter > 0)> aux_loadRHS(
-+      Scalar *B_arr, int64_t LDB, PacketBlock<vec, EIGEN_AVX_MAX_NUM_ACC> &RHSInPacket, int64_t rem = 0) {
-+    constexpr int64_t counterReverse = endM * endK - counter;
-+    constexpr int64_t startM = counterReverse / (endK);
-+    constexpr int64_t startK = counterReverse % endK;
-+
-+    constexpr int64_t packetIndex = startM * endK + startK;
-+    constexpr int64_t startM_ = isFWDSolve ? startM : -startM;
-+    const int64_t rhsIndex = (startK * PacketSize) + startM_ * LDB;
-+    EIGEN_IF_CONSTEXPR(krem) {
-+      RHSInPacket.packet[packetIndex] = ploadu<vec>(&B_arr[rhsIndex], remMask<PacketSize>(rem));
-+    }
-+    else {
-+      RHSInPacket.packet[packetIndex] = ploadu<vec>(&B_arr[rhsIndex]);
-+    }
-+    aux_loadRHS<isFWDSolve, endM, endK, counter - 1, krem>(B_arr, LDB, RHSInPacket, rem);
-+  }
-+
-+  template <bool isFWDSolve, int64_t endM, int64_t endK, int64_t counter, bool krem>
-+  static EIGEN_ALWAYS_INLINE std::enable_if_t<(counter <= 0)> aux_loadRHS(
-+      Scalar *B_arr, int64_t LDB, PacketBlock<vec, EIGEN_AVX_MAX_NUM_ACC> &RHSInPacket, int64_t rem = 0) {
-+    EIGEN_UNUSED_VARIABLE(B_arr);
-+    EIGEN_UNUSED_VARIABLE(LDB);
-+    EIGEN_UNUSED_VARIABLE(RHSInPacket);
-+    EIGEN_UNUSED_VARIABLE(rem);
-+  }
-+
-+  /**
-+   * aux_storeRHS
-+   *
-+   * 2-D unroll
-+   *      for(startM = 0; startM < endM; startM++)
-+   *        for(startK = 0; startK < endK; startK++)
-+   **/
-+  template <bool isFWDSolve, int64_t endM, int64_t endK, int64_t counter, bool krem>
-+  static EIGEN_ALWAYS_INLINE std::enable_if_t<(counter > 0)> aux_storeRHS(
-+      Scalar *B_arr, int64_t LDB, PacketBlock<vec, EIGEN_AVX_MAX_NUM_ACC> &RHSInPacket, int64_t rem = 0) {
-+    constexpr int64_t counterReverse = endM * endK - counter;
-+    constexpr int64_t startM = counterReverse / (endK);
-+    constexpr int64_t startK = counterReverse % endK;
-+
-+    constexpr int64_t packetIndex = startM * endK + startK;
-+    constexpr int64_t startM_ = isFWDSolve ? startM : -startM;
-+    const int64_t rhsIndex = (startK * PacketSize) + startM_ * LDB;
-+    EIGEN_IF_CONSTEXPR(krem) {
-+      pstoreu<Scalar>(&B_arr[rhsIndex], RHSInPacket.packet[packetIndex], remMask<PacketSize>(rem));
-+    }
-+    else {
-+      pstoreu<Scalar>(&B_arr[rhsIndex], RHSInPacket.packet[packetIndex]);
-+    }
-+    aux_storeRHS<isFWDSolve, endM, endK, counter - 1, krem>(B_arr, LDB, RHSInPacket, rem);
-+  }
-+
-+  template <bool isFWDSolve, int64_t endM, int64_t endK, int64_t counter, bool krem>
-+  static EIGEN_ALWAYS_INLINE std::enable_if_t<(counter <= 0)> aux_storeRHS(
-+      Scalar *B_arr, int64_t LDB, PacketBlock<vec, EIGEN_AVX_MAX_NUM_ACC> &RHSInPacket, int64_t rem = 0) {
-+    EIGEN_UNUSED_VARIABLE(B_arr);
-+    EIGEN_UNUSED_VARIABLE(LDB);
-+    EIGEN_UNUSED_VARIABLE(RHSInPacket);
-+    EIGEN_UNUSED_VARIABLE(rem);
-+  }
-+
-+  /**
-+   * aux_divRHSByDiag
-+   *
-+   * currM may be -1, (currM >=0) in enable_if checks for this
-+   *
-+   * 1-D unroll
-+   *      for(startK = 0; startK < endK; startK++)
-+   **/
-+  template <int64_t currM, int64_t endK, int64_t counter>
-+  static EIGEN_ALWAYS_INLINE std::enable_if_t<(counter > 0 && currM >= 0)> aux_divRHSByDiag(
-+      PacketBlock<vec, EIGEN_AVX_MAX_NUM_ACC> &RHSInPacket, PacketBlock<vec, EIGEN_AVX_MAX_NUM_ROW> &AInPacket) {
-+    constexpr int64_t counterReverse = endK - counter;
-+    constexpr int64_t startK = counterReverse;
-+
-+    constexpr int64_t packetIndex = currM * endK + startK;
-+    RHSInPacket.packet[packetIndex] = pmul(AInPacket.packet[currM], RHSInPacket.packet[packetIndex]);
-+    aux_divRHSByDiag<currM, endK, counter - 1>(RHSInPacket, AInPacket);
-+  }
-+
-+  template <int64_t currM, int64_t endK, int64_t counter>
-+  static EIGEN_ALWAYS_INLINE std::enable_if_t<!(counter > 0 && currM >= 0)> aux_divRHSByDiag(
-+      PacketBlock<vec, EIGEN_AVX_MAX_NUM_ACC> &RHSInPacket, PacketBlock<vec, EIGEN_AVX_MAX_NUM_ROW> &AInPacket) {
-+    EIGEN_UNUSED_VARIABLE(RHSInPacket);
-+    EIGEN_UNUSED_VARIABLE(AInPacket);
-+  }
-+
-+  /**
-+   * aux_updateRHS
-+   *
-+   * 2-D unroll
-+   *      for(startM = initM; startM < endM; startM++)
-+   *        for(startK = 0; startK < endK; startK++)
-+   **/
-+  template <bool isARowMajor, bool isFWDSolve, bool isUnitDiag, int64_t initM, int64_t endM, int64_t endK,
-+            int64_t counter, int64_t currentM>
-+  static EIGEN_ALWAYS_INLINE std::enable_if_t<(counter > 0)> aux_updateRHS(
-+      Scalar *A_arr, int64_t LDA, PacketBlock<vec, EIGEN_AVX_MAX_NUM_ACC> &RHSInPacket,
-+      PacketBlock<vec, EIGEN_AVX_MAX_NUM_ROW> &AInPacket) {
-+    constexpr int64_t counterReverse = (endM - initM) * endK - counter;
-+    constexpr int64_t startM = initM + counterReverse / (endK);
-+    constexpr int64_t startK = counterReverse % endK;
-+
-+    // For each row of A, first update all corresponding RHS
-+    constexpr int64_t packetIndex = startM * endK + startK;
-+    EIGEN_IF_CONSTEXPR(currentM > 0) {
-+      RHSInPacket.packet[packetIndex] =
-+          pnmadd(AInPacket.packet[startM], RHSInPacket.packet[(currentM - 1) * endK + startK],
-+                 RHSInPacket.packet[packetIndex]);
-+    }
-+
-+    EIGEN_IF_CONSTEXPR(startK == endK - 1) {
-+      // Once all RHS for previous row of A is updated, we broadcast the next element in the column A_{i, currentM}.
-+      EIGEN_IF_CONSTEXPR(startM == currentM && !isUnitDiag) {
-+        // If diagonal is not unit, we broadcast reciprocals of diagonals AinPacket.packet[currentM].
-+        // This will be used in divRHSByDiag
-+        EIGEN_IF_CONSTEXPR(isFWDSolve)
-+        AInPacket.packet[currentM] = pset1<vec>(Scalar(1) / A_arr[idA<isARowMajor>(currentM, currentM, LDA)]);
-+        else AInPacket.packet[currentM] = pset1<vec>(Scalar(1) / A_arr[idA<isARowMajor>(-currentM, -currentM, LDA)]);
-+      }
-+      else {
-+        // Broadcast next off diagonal element of A
-+        EIGEN_IF_CONSTEXPR(isFWDSolve)
-+        AInPacket.packet[startM] = pset1<vec>(A_arr[idA<isARowMajor>(startM, currentM, LDA)]);
-+        else AInPacket.packet[startM] = pset1<vec>(A_arr[idA<isARowMajor>(-startM, -currentM, LDA)]);
-+      }
-+    }
-+
-+    aux_updateRHS<isARowMajor, isFWDSolve, isUnitDiag, initM, endM, endK, counter - 1, currentM>(
-+        A_arr, LDA, RHSInPacket, AInPacket);
-+  }
-+
-+  template <bool isARowMajor, bool isFWDSolve, bool isUnitDiag, int64_t initM, int64_t endM, int64_t endK,
-+            int64_t counter, int64_t currentM>
-+  static EIGEN_ALWAYS_INLINE std::enable_if_t<(counter <= 0)> aux_updateRHS(
-+      Scalar *A_arr, int64_t LDA, PacketBlock<vec, EIGEN_AVX_MAX_NUM_ACC> &RHSInPacket,
-+      PacketBlock<vec, EIGEN_AVX_MAX_NUM_ROW> &AInPacket) {
-+    EIGEN_UNUSED_VARIABLE(A_arr);
-+    EIGEN_UNUSED_VARIABLE(LDA);
-+    EIGEN_UNUSED_VARIABLE(RHSInPacket);
-+    EIGEN_UNUSED_VARIABLE(AInPacket);
-+  }
-+
-+  /**
-+   * aux_triSolverMicroKernel
-+   *
-+   * 1-D unroll
-+   *      for(startM = 0; startM < endM; startM++)
-+   **/
-+  template <bool isARowMajor, bool isFWDSolve, bool isUnitDiag, int64_t endM, int64_t counter, int64_t numK>
-+  static EIGEN_ALWAYS_INLINE std::enable_if_t<(counter > 0)> aux_triSolveMicroKernel(
-+      Scalar *A_arr, int64_t LDA, PacketBlock<vec, EIGEN_AVX_MAX_NUM_ACC> &RHSInPacket,
-+      PacketBlock<vec, EIGEN_AVX_MAX_NUM_ROW> &AInPacket) {
-+    constexpr int64_t counterReverse = endM - counter;
-+    constexpr int64_t startM = counterReverse;
-+
-+    constexpr int64_t currentM = startM;
-+    // Divides the right-hand side in row startM, by digonal value of A
-+    // broadcasted to AInPacket.packet[startM-1] in the previous iteration.
-+    //
-+    // Without "if constexpr" the compiler instantiates the case <-1, numK>
-+    // this is handled with enable_if to prevent out-of-bound warnings
-+    // from the compiler
-+    EIGEN_IF_CONSTEXPR(!isUnitDiag && startM > 0)
-+    trsm::template divRHSByDiag<startM - 1, numK>(RHSInPacket, AInPacket);
-+
-+    // After division, the rhs corresponding to subsequent rows of A can be partially updated
-+    // We also broadcast the reciprocal of the next diagonal to AInPacket.packet[currentM] (if needed)
-+    // to be used in the next iteration.
-+    trsm::template updateRHS<isARowMajor, isFWDSolve, isUnitDiag, startM, endM, numK, currentM>(A_arr, LDA, RHSInPacket,
-+                                                                                                AInPacket);
-+
-+    // Handle division for the RHS corresponding to the final row of A.
-+    EIGEN_IF_CONSTEXPR(!isUnitDiag && startM == endM - 1)
-+    trsm::template divRHSByDiag<startM, numK>(RHSInPacket, AInPacket);
-+
-+    aux_triSolveMicroKernel<isARowMajor, isFWDSolve, isUnitDiag, endM, counter - 1, numK>(A_arr, LDA, RHSInPacket,
-+                                                                                          AInPacket);
-+  }
-+
-+  template <bool isARowMajor, bool isFWDSolve, bool isUnitDiag, int64_t endM, int64_t counter, int64_t numK>
-+  static EIGEN_ALWAYS_INLINE std::enable_if_t<(counter <= 0)> aux_triSolveMicroKernel(
-+      Scalar *A_arr, int64_t LDA, PacketBlock<vec, EIGEN_AVX_MAX_NUM_ACC> &RHSInPacket,
-+      PacketBlock<vec, EIGEN_AVX_MAX_NUM_ROW> &AInPacket) {
-+    EIGEN_UNUSED_VARIABLE(A_arr);
-+    EIGEN_UNUSED_VARIABLE(LDA);
-+    EIGEN_UNUSED_VARIABLE(RHSInPacket);
-+    EIGEN_UNUSED_VARIABLE(AInPacket);
-+  }
-+
-+  /********************************************************
-+   * Wrappers for aux_XXXX to hide counter parameter
-+   ********************************************************/
-+
-+  /**
-+   * Load endMxendK block of B to RHSInPacket
-+   * Masked loads are used for cases where endK is not a multiple of PacketSize
-+   */
-+  template <bool isFWDSolve, int64_t endM, int64_t endK, bool krem = false>
-+  static EIGEN_ALWAYS_INLINE void loadRHS(Scalar *B_arr, int64_t LDB,
-+                                          PacketBlock<vec, EIGEN_AVX_MAX_NUM_ACC> &RHSInPacket, int64_t rem = 0) {
-+    aux_loadRHS<isFWDSolve, endM, endK, endM * endK, krem>(B_arr, LDB, RHSInPacket, rem);
-+  }
-+
-+  /**
-+   * Load endMxendK block of B to RHSInPacket
-+   * Masked loads are used for cases where endK is not a multiple of PacketSize
-+   */
-+  template <bool isFWDSolve, int64_t endM, int64_t endK, bool krem = false>
-+  static EIGEN_ALWAYS_INLINE void storeRHS(Scalar *B_arr, int64_t LDB,
-+                                           PacketBlock<vec, EIGEN_AVX_MAX_NUM_ACC> &RHSInPacket, int64_t rem = 0) {
-+    aux_storeRHS<isFWDSolve, endM, endK, endM * endK, krem>(B_arr, LDB, RHSInPacket, rem);
-+  }
-+
-+  /**
-+   * Only used if Triangular matrix has non-unit diagonal values
-+   */
-+  template <int64_t currM, int64_t endK>
-+  static EIGEN_ALWAYS_INLINE void divRHSByDiag(PacketBlock<vec, EIGEN_AVX_MAX_NUM_ACC> &RHSInPacket,
-+                                               PacketBlock<vec, EIGEN_AVX_MAX_NUM_ROW> &AInPacket) {
-+    aux_divRHSByDiag<currM, endK, endK>(RHSInPacket, AInPacket);
-+  }
-+
-+  /**
-+   * Update right-hand sides (stored in avx registers)
-+   * Traversing along the column A_{i,currentM}, where currentM <= i <= endM, and broadcasting each value to AInPacket.
-+   **/
-+  template <bool isARowMajor, bool isFWDSolve, bool isUnitDiag, int64_t startM, int64_t endM, int64_t endK,
-+            int64_t currentM>
-+  static EIGEN_ALWAYS_INLINE void updateRHS(Scalar *A_arr, int64_t LDA,
-+                                            PacketBlock<vec, EIGEN_AVX_MAX_NUM_ACC> &RHSInPacket,
-+                                            PacketBlock<vec, EIGEN_AVX_MAX_NUM_ROW> &AInPacket) {
-+    aux_updateRHS<isARowMajor, isFWDSolve, isUnitDiag, startM, endM, endK, (endM - startM) * endK, currentM>(
-+        A_arr, LDA, RHSInPacket, AInPacket);
-+  }
-+
-+  /**
-+   * endM: dimension of A. 1 <= endM <= EIGEN_AVX_MAX_NUM_ROW
-+   * numK: number of avx registers to use for each row of B (ex fp32: 48 rhs => 3 avx reg used). 1 <= endK <= 3.
-+   * isFWDSolve: true => forward substitution, false => backwards substitution
-+   * isUnitDiag: true => triangular matrix has unit diagonal.
-+   */
-+  template <bool isARowMajor, bool isFWDSolve, bool isUnitDiag, int64_t endM, int64_t numK>
-+  static EIGEN_ALWAYS_INLINE void triSolveMicroKernel(Scalar *A_arr, int64_t LDA,
-+                                                      PacketBlock<vec, EIGEN_AVX_MAX_NUM_ACC> &RHSInPacket,
-+                                                      PacketBlock<vec, EIGEN_AVX_MAX_NUM_ROW> &AInPacket) {
-+    static_assert(numK >= 1 && numK <= 3, "numK out of range");
-+    aux_triSolveMicroKernel<isARowMajor, isFWDSolve, isUnitDiag, endM, endM, numK>(A_arr, LDA, RHSInPacket, AInPacket);
-+  }
-+};
-+
-+/**
-+ * Unrolls for gemm kernel
-+ *
-+ * isAdd: true => C += A*B, false => C -= A*B
-+ */
-+template <typename Scalar, bool isAdd>
-+class gemm {
-+ public:
-+  using vec = typename std::conditional<std::is_same<Scalar, float>::value, vecFullFloat, vecFullDouble>::type;
-+  static constexpr int64_t PacketSize = packet_traits<Scalar>::size;
-+
-+  /***********************************
-+   * Auxillary Functions for:
-+   *  - setzero
-+   *  - updateC
-+   *  - storeC
-+   *  - startLoadB
-+   *  - triSolveMicroKernel
-+   ************************************/
-+
-+  /**
-+   * aux_setzero
-+   *
-+   * 2-D unroll
-+   *      for(startM = 0; startM < endM; startM++)
-+   *        for(startN = 0; startN < endN; startN++)
-+   **/
-+  template <int64_t endM, int64_t endN, int64_t counter>
-+  static EIGEN_ALWAYS_INLINE std::enable_if_t<(counter > 0)> aux_setzero(
-+      PacketBlock<vec, EIGEN_ARCH_DEFAULT_NUMBER_OF_REGISTERS> &zmm) {
-+    constexpr int64_t counterReverse = endM * endN - counter;
-+    constexpr int64_t startM = counterReverse / (endN);
-+    constexpr int64_t startN = counterReverse % endN;
-+
-+    zmm.packet[startN * endM + startM] = pzero(zmm.packet[startN * endM + startM]);
-+    aux_setzero<endM, endN, counter - 1>(zmm);
-+  }
-+
-+  template <int64_t endM, int64_t endN, int64_t counter>
-+  static EIGEN_ALWAYS_INLINE std::enable_if_t<(counter <= 0)> aux_setzero(
-+      PacketBlock<vec, EIGEN_ARCH_DEFAULT_NUMBER_OF_REGISTERS> &zmm) {
-+    EIGEN_UNUSED_VARIABLE(zmm);
-+  }
-+
-+  /**
-+   * aux_updateC
-+   *
-+   * 2-D unroll
-+   *      for(startM = 0; startM < endM; startM++)
-+   *        for(startN = 0; startN < endN; startN++)
-+   **/
-+  template <int64_t endM, int64_t endN, int64_t counter, bool rem>
-+  static EIGEN_ALWAYS_INLINE std::enable_if_t<(counter > 0)> aux_updateC(
-+      Scalar *C_arr, int64_t LDC, PacketBlock<vec, EIGEN_ARCH_DEFAULT_NUMBER_OF_REGISTERS> &zmm, int64_t rem_ = 0) {
-+    EIGEN_UNUSED_VARIABLE(rem_);
-+    constexpr int64_t counterReverse = endM * endN - counter;
-+    constexpr int64_t startM = counterReverse / (endN);
-+    constexpr int64_t startN = counterReverse % endN;
-+
-+    EIGEN_IF_CONSTEXPR(rem)
-+    zmm.packet[startN * endM + startM] =
-+        padd(ploadu<vec>(&C_arr[(startN)*LDC + startM * PacketSize], remMask<PacketSize>(rem_)),
-+             zmm.packet[startN * endM + startM], remMask<PacketSize>(rem_));
-+    else zmm.packet[startN * endM + startM] =
-+        padd(ploadu<vec>(&C_arr[(startN)*LDC + startM * PacketSize]), zmm.packet[startN * endM + startM]);
-+    aux_updateC<endM, endN, counter - 1, rem>(C_arr, LDC, zmm, rem_);
-+  }
-+
-+  template <int64_t endM, int64_t endN, int64_t counter, bool rem>
-+  static EIGEN_ALWAYS_INLINE std::enable_if_t<(counter <= 0)> aux_updateC(
-+      Scalar *C_arr, int64_t LDC, PacketBlock<vec, EIGEN_ARCH_DEFAULT_NUMBER_OF_REGISTERS> &zmm, int64_t rem_ = 0) {
-+    EIGEN_UNUSED_VARIABLE(C_arr);
-+    EIGEN_UNUSED_VARIABLE(LDC);
-+    EIGEN_UNUSED_VARIABLE(zmm);
-+    EIGEN_UNUSED_VARIABLE(rem_);
-+  }
-+
-+  /**
-+   * aux_storeC
-+   *
-+   * 2-D unroll
-+   *      for(startM = 0; startM < endM; startM++)
-+   *        for(startN = 0; startN < endN; startN++)
-+   **/
-+  template <int64_t endM, int64_t endN, int64_t counter, bool rem>
-+  static EIGEN_ALWAYS_INLINE std::enable_if_t<(counter > 0)> aux_storeC(
-+      Scalar *C_arr, int64_t LDC, PacketBlock<vec, EIGEN_ARCH_DEFAULT_NUMBER_OF_REGISTERS> &zmm, int64_t rem_ = 0) {
-+    EIGEN_UNUSED_VARIABLE(rem_);
-+    constexpr int64_t counterReverse = endM * endN - counter;
-+    constexpr int64_t startM = counterReverse / (endN);
-+    constexpr int64_t startN = counterReverse % endN;
-+
-+    EIGEN_IF_CONSTEXPR(rem)
-+    pstoreu<Scalar>(&C_arr[(startN)*LDC + startM * PacketSize], zmm.packet[startN * endM + startM],
-+                    remMask<PacketSize>(rem_));
-+    else pstoreu<Scalar>(&C_arr[(startN)*LDC + startM * PacketSize], zmm.packet[startN * endM + startM]);
-+    aux_storeC<endM, endN, counter - 1, rem>(C_arr, LDC, zmm, rem_);
-+  }
-+
-+  template <int64_t endM, int64_t endN, int64_t counter, bool rem>
-+  static EIGEN_ALWAYS_INLINE std::enable_if_t<(counter <= 0)> aux_storeC(
-+      Scalar *C_arr, int64_t LDC, PacketBlock<vec, EIGEN_ARCH_DEFAULT_NUMBER_OF_REGISTERS> &zmm, int64_t rem_ = 0) {
-+    EIGEN_UNUSED_VARIABLE(C_arr);
-+    EIGEN_UNUSED_VARIABLE(LDC);
-+    EIGEN_UNUSED_VARIABLE(zmm);
-+    EIGEN_UNUSED_VARIABLE(rem_);
-+  }
-+
-+  /**
-+   * aux_startLoadB
-+   *
-+   * 1-D unroll
-+   *      for(startL = 0; startL < endL; startL++)
-+   **/
-+  template <int64_t unrollM, int64_t unrollN, int64_t endL, int64_t counter, bool rem>
-+  static EIGEN_ALWAYS_INLINE std::enable_if_t<(counter > 0)> aux_startLoadB(
-+      Scalar *B_t, int64_t LDB, PacketBlock<vec, EIGEN_ARCH_DEFAULT_NUMBER_OF_REGISTERS> &zmm, int64_t rem_ = 0) {
-+    EIGEN_UNUSED_VARIABLE(rem_);
-+    constexpr int64_t counterReverse = endL - counter;
-+    constexpr int64_t startL = counterReverse;
-+
-+    EIGEN_IF_CONSTEXPR(rem)
-+    zmm.packet[unrollM * unrollN + startL] =
-+        ploadu<vec>(&B_t[(startL / unrollM) * LDB + (startL % unrollM) * PacketSize], remMask<PacketSize>(rem_));
-+    else zmm.packet[unrollM * unrollN + startL] =
-+        ploadu<vec>(&B_t[(startL / unrollM) * LDB + (startL % unrollM) * PacketSize]);
-+
-+    aux_startLoadB<unrollM, unrollN, endL, counter - 1, rem>(B_t, LDB, zmm, rem_);
-+  }
-+
-+  template <int64_t unrollM, int64_t unrollN, int64_t endL, int64_t counter, bool rem>
-+  static EIGEN_ALWAYS_INLINE std::enable_if_t<(counter <= 0)> aux_startLoadB(
-+      Scalar *B_t, int64_t LDB, PacketBlock<vec, EIGEN_ARCH_DEFAULT_NUMBER_OF_REGISTERS> &zmm, int64_t rem_ = 0) {
-+    EIGEN_UNUSED_VARIABLE(B_t);
-+    EIGEN_UNUSED_VARIABLE(LDB);
-+    EIGEN_UNUSED_VARIABLE(zmm);
-+    EIGEN_UNUSED_VARIABLE(rem_);
-+  }
-+
-+  /**
-+   * aux_startBCastA
-+   *
-+   * 1-D unroll
-+   *      for(startB = 0; startB < endB; startB++)
-+   **/
-+  template <bool isARowMajor, int64_t unrollM, int64_t unrollN, int64_t endB, int64_t counter, int64_t numLoad>
-+  static EIGEN_ALWAYS_INLINE std::enable_if_t<(counter > 0)> aux_startBCastA(
-+      Scalar *A_t, int64_t LDA, PacketBlock<vec, EIGEN_ARCH_DEFAULT_NUMBER_OF_REGISTERS> &zmm) {
-+    constexpr int64_t counterReverse = endB - counter;
-+    constexpr int64_t startB = counterReverse;
-+
-+    zmm.packet[unrollM * unrollN + numLoad + startB] = pload1<vec>(&A_t[idA<isARowMajor>(startB, 0, LDA)]);
-+
-+    aux_startBCastA<isARowMajor, unrollM, unrollN, endB, counter - 1, numLoad>(A_t, LDA, zmm);
-+  }
-+
-+  template <bool isARowMajor, int64_t unrollM, int64_t unrollN, int64_t endB, int64_t counter, int64_t numLoad>
-+  static EIGEN_ALWAYS_INLINE std::enable_if_t<(counter <= 0)> aux_startBCastA(
-+      Scalar *A_t, int64_t LDA, PacketBlock<vec, EIGEN_ARCH_DEFAULT_NUMBER_OF_REGISTERS> &zmm) {
-+    EIGEN_UNUSED_VARIABLE(A_t);
-+    EIGEN_UNUSED_VARIABLE(LDA);
-+    EIGEN_UNUSED_VARIABLE(zmm);
-+  }
-+
-+  /**
-+   * aux_loadB
-+   * currK: current K
-+   *
-+   * 1-D unroll
-+   *      for(startM = 0; startM < endM; startM++)
-+   **/
-+  template <int64_t endM, int64_t counter, int64_t unrollN, int64_t currK, int64_t unrollK, int64_t numLoad,
-+            int64_t numBCast, bool rem>
-+  static EIGEN_ALWAYS_INLINE std::enable_if_t<(counter > 0)> aux_loadB(
-+      Scalar *B_t, int64_t LDB, PacketBlock<vec, EIGEN_ARCH_DEFAULT_NUMBER_OF_REGISTERS> &zmm, int64_t rem_ = 0) {
-+    EIGEN_UNUSED_VARIABLE(rem_);
-+    if ((numLoad / endM + currK < unrollK)) {
-+      constexpr int64_t counterReverse = endM - counter;
-+      constexpr int64_t startM = counterReverse;
-+
-+      EIGEN_IF_CONSTEXPR(rem) {
-+        zmm.packet[endM * unrollN + (startM + currK * endM) % numLoad] =
-+            ploadu<vec>(&B_t[(numLoad / endM + currK) * LDB + startM * PacketSize], remMask<PacketSize>(rem_));
-+      }
-+      else {
-+        zmm.packet[endM * unrollN + (startM + currK * endM) % numLoad] =
-+            ploadu<vec>(&B_t[(numLoad / endM + currK) * LDB + startM * PacketSize]);
-+      }
-+
-+      aux_loadB<endM, counter - 1, unrollN, currK, unrollK, numLoad, numBCast, rem>(B_t, LDB, zmm, rem_);
-+    }
-+  }
-+
-+  template <int64_t endM, int64_t counter, int64_t unrollN, int64_t currK, int64_t unrollK, int64_t numLoad,
-+            int64_t numBCast, bool rem>
-+  static EIGEN_ALWAYS_INLINE std::enable_if_t<(counter <= 0)> aux_loadB(
-+      Scalar *B_t, int64_t LDB, PacketBlock<vec, EIGEN_ARCH_DEFAULT_NUMBER_OF_REGISTERS> &zmm, int64_t rem_ = 0) {
-+    EIGEN_UNUSED_VARIABLE(B_t);
-+    EIGEN_UNUSED_VARIABLE(LDB);
-+    EIGEN_UNUSED_VARIABLE(zmm);
-+    EIGEN_UNUSED_VARIABLE(rem_);
-+  }
-+
-+  /**
-+   * aux_microKernel
-+   *
-+   * 3-D unroll
-+   *      for(startM = 0; startM < endM; startM++)
-+   *        for(startN = 0; startN < endN; startN++)
-+   *          for(startK = 0; startK < endK; startK++)
-+   **/
-+  template <bool isARowMajor, int64_t endM, int64_t endN, int64_t endK, int64_t counter, int64_t numLoad,
-+            int64_t numBCast, bool rem>
-+  static EIGEN_ALWAYS_INLINE std::enable_if_t<(counter > 0)> aux_microKernel(
-+      Scalar *B_t, Scalar *A_t, int64_t LDB, int64_t LDA, PacketBlock<vec, EIGEN_ARCH_DEFAULT_NUMBER_OF_REGISTERS> &zmm,
-+      int64_t rem_ = 0) {
-+    EIGEN_UNUSED_VARIABLE(rem_);
-+    constexpr int64_t counterReverse = endM * endN * endK - counter;
-+    constexpr int startK = counterReverse / (endM * endN);
-+    constexpr int startN = (counterReverse / (endM)) % endN;
-+    constexpr int startM = counterReverse % endM;
-+
-+    EIGEN_IF_CONSTEXPR(startK == 0 && startM == 0 && startN == 0) {
-+      gemm::template startLoadB<endM, endN, numLoad, rem>(B_t, LDB, zmm, rem_);
-+      gemm::template startBCastA<isARowMajor, endM, endN, numBCast, numLoad>(A_t, LDA, zmm);
-+    }
-+
-+    {
-+      // Interleave FMA and Bcast
-+      EIGEN_IF_CONSTEXPR(isAdd) {
-+        zmm.packet[startN * endM + startM] =
-+            pmadd(zmm.packet[endM * endN + numLoad + (startN + startK * endN) % numBCast],
-+                  zmm.packet[endM * endN + (startM + startK * endM) % numLoad], zmm.packet[startN * endM + startM]);
-+      }
-+      else {
-+        zmm.packet[startN * endM + startM] =
-+            pnmadd(zmm.packet[endM * endN + numLoad + (startN + startK * endN) % numBCast],
-+                   zmm.packet[endM * endN + (startM + startK * endM) % numLoad], zmm.packet[startN * endM + startM]);
-+      }
-+      // Bcast
-+      EIGEN_IF_CONSTEXPR(startM == endM - 1 && (numBCast + startN + startK * endN < endK * endN)) {
-+        zmm.packet[endM * endN + numLoad + (startN + startK * endN) % numBCast] = pload1<vec>(&A_t[idA<isARowMajor>(
-+            (numBCast + startN + startK * endN) % endN, (numBCast + startN + startK * endN) / endN, LDA)]);
-+      }
-+    }
-+
-+    // We have updated all accumlators, time to load next set of B's
-+    EIGEN_IF_CONSTEXPR((startN == endN - 1) && (startM == endM - 1)) {
-+      gemm::template loadB<endM, endN, startK, endK, numLoad, numBCast, rem>(B_t, LDB, zmm, rem_);
-+    }
-+    aux_microKernel<isARowMajor, endM, endN, endK, counter - 1, numLoad, numBCast, rem>(B_t, A_t, LDB, LDA, zmm, rem_);
-+  }
-+
-+  template <bool isARowMajor, int64_t endM, int64_t endN, int64_t endK, int64_t counter, int64_t numLoad,
-+            int64_t numBCast, bool rem>
-+  static EIGEN_ALWAYS_INLINE std::enable_if_t<(counter <= 0)> aux_microKernel(
-+      Scalar *B_t, Scalar *A_t, int64_t LDB, int64_t LDA, PacketBlock<vec, EIGEN_ARCH_DEFAULT_NUMBER_OF_REGISTERS> &zmm,
-+      int64_t rem_ = 0) {
-+    EIGEN_UNUSED_VARIABLE(B_t);
-+    EIGEN_UNUSED_VARIABLE(A_t);
-+    EIGEN_UNUSED_VARIABLE(LDB);
-+    EIGEN_UNUSED_VARIABLE(LDA);
-+    EIGEN_UNUSED_VARIABLE(zmm);
-+    EIGEN_UNUSED_VARIABLE(rem_);
-+  }
-+
-+  /********************************************************
-+   * Wrappers for aux_XXXX to hide counter parameter
-+   ********************************************************/
-+
-+  template <int64_t endM, int64_t endN>
-+  static EIGEN_ALWAYS_INLINE void setzero(PacketBlock<vec, EIGEN_ARCH_DEFAULT_NUMBER_OF_REGISTERS> &zmm) {
-+    aux_setzero<endM, endN, endM * endN>(zmm);
-+  }
-+
-+  /**
-+   * Ideally the compiler folds these into vaddp{s,d} with an embedded memory load.
-+   */
-+  template <int64_t endM, int64_t endN, bool rem = false>
-+  static EIGEN_ALWAYS_INLINE void updateC(Scalar *C_arr, int64_t LDC,
-+                                          PacketBlock<vec, EIGEN_ARCH_DEFAULT_NUMBER_OF_REGISTERS> &zmm,
-+                                          int64_t rem_ = 0) {
-+    EIGEN_UNUSED_VARIABLE(rem_);
-+    aux_updateC<endM, endN, endM * endN, rem>(C_arr, LDC, zmm, rem_);
-+  }
-+
-+  template <int64_t endM, int64_t endN, bool rem = false>
-+  static EIGEN_ALWAYS_INLINE void storeC(Scalar *C_arr, int64_t LDC,
-+                                         PacketBlock<vec, EIGEN_ARCH_DEFAULT_NUMBER_OF_REGISTERS> &zmm,
-+                                         int64_t rem_ = 0) {
-+    EIGEN_UNUSED_VARIABLE(rem_);
-+    aux_storeC<endM, endN, endM * endN, rem>(C_arr, LDC, zmm, rem_);
-+  }
-+
-+  /**
-+   * Use numLoad registers for loading B at start of microKernel
-+   */
-+  template <int64_t unrollM, int64_t unrollN, int64_t endL, bool rem>
-+  static EIGEN_ALWAYS_INLINE void startLoadB(Scalar *B_t, int64_t LDB,
-+                                             PacketBlock<vec, EIGEN_ARCH_DEFAULT_NUMBER_OF_REGISTERS> &zmm,
-+                                             int64_t rem_ = 0) {
-+    EIGEN_UNUSED_VARIABLE(rem_);
-+    aux_startLoadB<unrollM, unrollN, endL, endL, rem>(B_t, LDB, zmm, rem_);
-+  }
-+
-+  /**
-+   * Use numBCast registers for broadcasting A at start of microKernel
-+   */
-+  template <bool isARowMajor, int64_t unrollM, int64_t unrollN, int64_t endB, int64_t numLoad>
-+  static EIGEN_ALWAYS_INLINE void startBCastA(Scalar *A_t, int64_t LDA,
-+                                              PacketBlock<vec, EIGEN_ARCH_DEFAULT_NUMBER_OF_REGISTERS> &zmm) {
-+    aux_startBCastA<isARowMajor, unrollM, unrollN, endB, endB, numLoad>(A_t, LDA, zmm);
-+  }
-+
-+  /**
-+   * Loads next set of B into vector registers between each K unroll.
-+   */
-+  template <int64_t endM, int64_t unrollN, int64_t currK, int64_t unrollK, int64_t numLoad, int64_t numBCast, bool rem>
-+  static EIGEN_ALWAYS_INLINE void loadB(Scalar *B_t, int64_t LDB,
-+                                        PacketBlock<vec, EIGEN_ARCH_DEFAULT_NUMBER_OF_REGISTERS> &zmm,
-+                                        int64_t rem_ = 0) {
-+    EIGEN_UNUSED_VARIABLE(rem_);
-+    aux_loadB<endM, endM, unrollN, currK, unrollK, numLoad, numBCast, rem>(B_t, LDB, zmm, rem_);
-+  }
-+
-+  /**
-+   * Generates a microkernel for gemm (row-major) with unrolls {1,2,4,8}x{U1,U2,U3} to compute C -= A*B.
-+   * A matrix can be row/col-major. B matrix is assumed row-major.
-+   *
-+   * isARowMajor: is A row major
-+   * endM: Number registers per row
-+   * endN: Number of rows
-+   * endK: Loop unroll for K.
-+   * numLoad: Number of registers for loading B.
-+   * numBCast: Number of registers for broadcasting A.
-+   *
-+   * Ex: microkernel<isARowMajor,0,3,0,4,0,4,6,2>: 8x48 unroll (24 accumulators), k unrolled 4 times,
-+   * 6 register for loading B, 2 for broadcasting A.
-+   *
-+   * Note: Ideally the microkernel should not have any register spilling.
-+   * The avx instruction counts should be:
-+   *   - endK*endN vbroadcasts{s,d}
-+   *   - endK*endM vmovup{s,d}
-+   *   - endK*endN*endM FMAs
-+   *
-+   * From testing, there are no register spills with clang. There are register spills with GNU, which
-+   * causes a performance hit.
-+   */
-+  template <bool isARowMajor, int64_t endM, int64_t endN, int64_t endK, int64_t numLoad, int64_t numBCast,
-+            bool rem = false>
-+  static EIGEN_ALWAYS_INLINE void microKernel(Scalar *B_t, Scalar *A_t, int64_t LDB, int64_t LDA,
-+                                              PacketBlock<vec, EIGEN_ARCH_DEFAULT_NUMBER_OF_REGISTERS> &zmm,
-+                                              int64_t rem_ = 0) {
-+    EIGEN_UNUSED_VARIABLE(rem_);
-+    aux_microKernel<isARowMajor, endM, endN, endK, endM * endN * endK, numLoad, numBCast, rem>(B_t, A_t, LDB, LDA, zmm,
-+                                                                                               rem_);
-+  }
-+};
-+}  // namespace unrolls
-+
-+#endif  // EIGEN_CORE_ARCH_AVX512_TRSM_UNROLLS_H

From 53afba36acdc2b495bb37c089a6a3f3a8724d260 Mon Sep 17 00:00:00 2001
From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com>
Date: Mon, 3 Jun 2024 17:36:56 +0200
Subject: [PATCH 124/835] Delete
 easybuild/easyconfigs/m/ml_dtypes/ml_dtypes-0.3.2-gfbf-2023a.eb

---
 .../m/ml_dtypes/ml_dtypes-0.3.2-gfbf-2023a.eb | 51 -------------------
 1 file changed, 51 deletions(-)
 delete mode 100644 easybuild/easyconfigs/m/ml_dtypes/ml_dtypes-0.3.2-gfbf-2023a.eb

diff --git a/easybuild/easyconfigs/m/ml_dtypes/ml_dtypes-0.3.2-gfbf-2023a.eb b/easybuild/easyconfigs/m/ml_dtypes/ml_dtypes-0.3.2-gfbf-2023a.eb
deleted file mode 100644
index 9c3a18bfdb5..00000000000
--- a/easybuild/easyconfigs/m/ml_dtypes/ml_dtypes-0.3.2-gfbf-2023a.eb
+++ /dev/null
@@ -1,51 +0,0 @@
-# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2024/02
-easyblock = 'PythonBundle'
-
-name = 'ml_dtypes'
-version = '0.3.2'
-
-homepage = 'https://github.com/jax-ml/ml_dtypes'
-description = """
-ml_dtypes is a stand-alone implementation of several NumPy dtype extensions used
-in machine learning libraries, including:
-
-bfloat16: an alternative to the standard float16 format
-float8_*: several experimental 8-bit floating point representations including:
-float8_e4m3b11fnuz
-float8_e4m3fn
-float8_e4m3fnuz
-float8_e5m2
-float8_e5m2fnuz
-"""
-
-toolchain = {'name': 'gfbf', 'version': '2023a'}
-
-dependencies = [
-    ('Python', '3.11.3'),
-    ('SciPy-bundle', '2023.07'),
-]
-
-
-use_pip = True
-
-default_easyblock = 'PythonPackage'
-
-exts_list = [
-    ('opt_einsum', '3.3.0', {
-        'checksums': ['59f6475f77bbc37dcf7cd748519c0ec60722e91e63ca114e68821c0c54a46549'],
-    }),
-    ('etils', '1.6.0', {
-        'checksums': ['c635fbd02a79fed4ad76825d31306b581d22b40671721daa8bc279cf6333e48a'],
-    }),
-    (name, version, {
-        'patches': [('ml_dtypes-0.3.2_EigenAvx512.patch', 1)],
-        'checksums': [
-            {'ml_dtypes-0.3.2.tar.gz': '533059bc5f1764fac071ef54598db358c167c51a718f68f5bb55e3dee79d2967'},
-            {'ml_dtypes-0.3.2_EigenAvx512.patch': '197b05b0b7f611749824369f026099f6a172f9e8eab6ebb6504a16573746c892'},
-        ],
-    }),
-]
-
-sanity_pip_check = True
-
-moduleclass = 'tools'

From 4a1b27897c3009111aface03315bfdfa598224f8 Mon Sep 17 00:00:00 2001
From: WilleBell <cintiawillemyns@gmail.com>
Date: Tue, 4 Jun 2024 10:40:20 +0200
Subject: [PATCH 125/835] adding easyconfigs:
 langchain-openai-0.1.8-foss-2023a.eb, openai-python-1.30.5-foss-2023a.eb,
 tiktoken-0.7.0-GCCcore-12.3.0.eb

---
 .../langchain-openai-0.1.8-foss-2023a.eb      |  36 +++++
 .../openai-python-1.30.5-foss-2023a.eb        |  53 +++++++
 .../tiktoken/tiktoken-0.7.0-GCCcore-12.3.0.eb | 135 ++++++++++++++++++
 3 files changed, 224 insertions(+)
 create mode 100644 easybuild/easyconfigs/l/langchain-openai/langchain-openai-0.1.8-foss-2023a.eb
 create mode 100644 easybuild/easyconfigs/o/openai-python/openai-python-1.30.5-foss-2023a.eb
 create mode 100644 easybuild/easyconfigs/t/tiktoken/tiktoken-0.7.0-GCCcore-12.3.0.eb

diff --git a/easybuild/easyconfigs/l/langchain-openai/langchain-openai-0.1.8-foss-2023a.eb b/easybuild/easyconfigs/l/langchain-openai/langchain-openai-0.1.8-foss-2023a.eb
new file mode 100644
index 00000000000..c976db06a40
--- /dev/null
+++ b/easybuild/easyconfigs/l/langchain-openai/langchain-openai-0.1.8-foss-2023a.eb
@@ -0,0 +1,36 @@
+easyblock = 'PythonBundle'
+
+name = 'langchain-openai'
+version = '0.1.8'
+# needs tiktoken >= 0.7.0
+
+homepage = 'https://github.com/langchain-ai/langchain'
+description = """
+This package contains the LangChain integrations for OpenAI through their openai SDK.
+"""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+builddependencies = [
+    ('poetry', '1.5.1'),
+]
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('LangChain', '0.2.1'),
+    ('tiktoken', '0.7.0'),
+    ('openai-python', '1.30.5'),
+]
+
+exts_list = [
+    (name, version, {
+        'sources': ['langchain_openai-%(version)s.tar.gz'],
+        'checksums': ['a11fcce15def7917c44232abda6baaa63dfc79fe44be1531eea650d39a44cd95'],
+    }),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+moduleclass = 'ai'
diff --git a/easybuild/easyconfigs/o/openai-python/openai-python-1.30.5-foss-2023a.eb b/easybuild/easyconfigs/o/openai-python/openai-python-1.30.5-foss-2023a.eb
new file mode 100644
index 00000000000..e5fa3228a07
--- /dev/null
+++ b/easybuild/easyconfigs/o/openai-python/openai-python-1.30.5-foss-2023a.eb
@@ -0,0 +1,53 @@
+easyblock = 'PythonBundle'
+
+name = 'openai-python'
+version = '1.30.5'
+
+homepage = 'https://github.com/openai/openai-python'
+description = """
+The OpenAI Python library provides convenient access to the OpenAI REST API from any
+Python 3.7+ application. The library includes type definitions for all request params and
+response fields, and offers both synchronous and asynchronous clients powered by httpx.
+"""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+builddependencies = [
+    ('hatchling', '1.18.0'),
+]
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('pydantic', '2.5.3'),
+    ('typing-extensions', '4.9.0'),
+    ('tqdm', '4.66.1'),
+]
+
+exts_list = [
+    ('h11', '0.14.0', {
+        'checksums': ['8f19fbbe99e72420ff35c00b27a34cb9937e902a8b810e2c88300c6f0a3b699d'],
+    }),
+    ('httpcore', '1.0.5', {
+        'checksums': ['34a38e2f9291467ee3b44e89dd52615370e152954ba21721378a87b2960f7a61'],
+    }),
+    ('httpx', '0.27.0', {
+        'checksums': ['a0cb88a46f32dc874e04ee956e4c2764aba2aa228f650b06788ba6bda2962ab5'],
+    }),
+    ('anyio', '4.4.0', {
+        'checksums': ['5aadc6a1bbb7cdb0bede386cac5e2940f5e2ff3aa20277e991cf028e0585ce94'],
+    }),
+    ('sniffio', '1.3.1', {
+        'checksums': ['f4324edc670a0f49750a81b895f35c3adb843cca46f0530f79fc1babb23789dc'],
+    }),
+    ('openai', version, {
+        # needs a README or will get "Fragment file 'README.md' not found." error
+        'preinstallopts': "touch README.md && ",
+        'checksums': ['5366562eb2c5917e6116ae0391b7ae6e3acd62b0ae3f565ada32b35d8fcfa106'],
+    }),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/t/tiktoken/tiktoken-0.7.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/t/tiktoken/tiktoken-0.7.0-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..23fcce3f894
--- /dev/null
+++ b/easybuild/easyconfigs/t/tiktoken/tiktoken-0.7.0-GCCcore-12.3.0.eb
@@ -0,0 +1,135 @@
+easyblock = 'CargoPythonPackage'
+
+name = 'tiktoken'
+version = '0.7.0'
+
+homepage = 'https://github.com/openai/tiktoken'
+description = "tiktoken is a fast BPE tokeniser for use with OpenAI's models"
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+crates = [
+    ('aho-corasick', '1.1.3'),
+    ('autocfg', '1.2.0'),
+    ('bit-set', '0.5.3'),
+    ('bit-vec', '0.6.3'),
+    ('bitflags', '1.3.2'),
+    ('bstr', '1.9.1'),
+    ('cfg-if', '1.0.0'),
+    ('fancy-regex', '0.11.0'),
+    ('heck', '0.4.1'),
+    ('indoc', '2.0.5'),
+    ('libc', '0.2.153'),
+    ('lock_api', '0.4.11'),
+    ('memchr', '2.7.2'),
+    ('memoffset', '0.9.1'),
+    ('once_cell', '1.19.0'),
+    ('parking_lot', '0.12.1'),
+    ('parking_lot_core', '0.9.9'),
+    ('portable-atomic', '1.6.0'),
+    ('proc-macro2', '1.0.79'),
+    ('pyo3', '0.20.3'),
+    ('pyo3-build-config', '0.20.3'),
+    ('pyo3-ffi', '0.20.3'),
+    ('pyo3-macros', '0.20.3'),
+    ('pyo3-macros-backend', '0.20.3'),
+    ('quote', '1.0.36'),
+    ('redox_syscall', '0.4.1'),
+    ('regex', '1.10.4'),
+    ('regex-automata', '0.4.6'),
+    ('regex-syntax', '0.8.3'),
+    ('rustc-hash', '1.1.0'),
+    ('scopeguard', '1.2.0'),
+    ('serde', '1.0.197'),
+    ('serde_derive', '1.0.197'),
+    ('smallvec', '1.13.2'),
+    ('syn', '2.0.58'),
+    ('target-lexicon', '0.12.14'),
+    ('unicode-ident', '1.0.12'),
+    ('unindent', '0.2.3'),
+    ('windows-targets', '0.48.5'),
+    ('windows_aarch64_gnullvm', '0.48.5'),
+    ('windows_aarch64_msvc', '0.48.5'),
+    ('windows_i686_gnu', '0.48.5'),
+    ('windows_i686_msvc', '0.48.5'),
+    ('windows_x86_64_gnu', '0.48.5'),
+    ('windows_x86_64_gnullvm', '0.48.5'),
+    ('windows_x86_64_msvc', '0.48.5'),
+]
+sources = [SOURCE_TAR_GZ]
+checksums = [
+    {'tiktoken-0.7.0.tar.gz': '1077266e949c24e0291f6c350433c6f0971365ece2b173a23bc3b9f9defef6b6'},
+    {'aho-corasick-1.1.3.tar.gz': '8e60d3430d3a69478ad0993f19238d2df97c507009a52b3c10addcd7f6bcb916'},
+    {'autocfg-1.2.0.tar.gz': 'f1fdabc7756949593fe60f30ec81974b613357de856987752631dea1e3394c80'},
+    {'bit-set-0.5.3.tar.gz': '0700ddab506f33b20a03b13996eccd309a48e5ff77d0d95926aa0210fb4e95f1'},
+    {'bit-vec-0.6.3.tar.gz': '349f9b6a179ed607305526ca489b34ad0a41aed5f7980fa90eb03160b69598fb'},
+    {'bitflags-1.3.2.tar.gz': 'bef38d45163c2f1dde094a7dfd33ccf595c92905c8f8f4fdc18d06fb1037718a'},
+    {'bstr-1.9.1.tar.gz': '05efc5cfd9110c8416e471df0e96702d58690178e206e61b7173706673c93706'},
+    {'cfg-if-1.0.0.tar.gz': 'baf1de4339761588bc0619e3cbc0120ee582ebb74b53b4efbf79117bd2da40fd'},
+    {'fancy-regex-0.11.0.tar.gz': 'b95f7c0680e4142284cf8b22c14a476e87d61b004a3a0861872b32ef7ead40a2'},
+    {'heck-0.4.1.tar.gz': '95505c38b4572b2d910cecb0281560f54b440a19336cbbcb27bf6ce6adc6f5a8'},
+    {'indoc-2.0.5.tar.gz': 'b248f5224d1d606005e02c97f5aa4e88eeb230488bcc03bc9ca4d7991399f2b5'},
+    {'libc-0.2.153.tar.gz': '9c198f91728a82281a64e1f4f9eeb25d82cb32a5de251c6bd1b5154d63a8e7bd'},
+    {'lock_api-0.4.11.tar.gz': '3c168f8615b12bc01f9c17e2eb0cc07dcae1940121185446edc3744920e8ef45'},
+    {'memchr-2.7.2.tar.gz': '6c8640c5d730cb13ebd907d8d04b52f55ac9a2eec55b440c8892f40d56c76c1d'},
+    {'memoffset-0.9.1.tar.gz': '488016bfae457b036d996092f6cb448677611ce4449e970ceaf42695203f218a'},
+    {'once_cell-1.19.0.tar.gz': '3fdb12b2476b595f9358c5161aa467c2438859caa136dec86c26fdd2efe17b92'},
+    {'parking_lot-0.12.1.tar.gz': '3742b2c103b9f06bc9fff0a37ff4912935851bee6d36f3c02bcc755bcfec228f'},
+    {'parking_lot_core-0.9.9.tar.gz': '4c42a9226546d68acdd9c0a280d17ce19bfe27a46bf68784e4066115788d008e'},
+    {'portable-atomic-1.6.0.tar.gz': '7170ef9988bc169ba16dd36a7fa041e5c4cbeb6a35b76d4c03daded371eae7c0'},
+    {'proc-macro2-1.0.79.tar.gz': 'e835ff2298f5721608eb1a980ecaee1aef2c132bf95ecc026a11b7bf3c01c02e'},
+    {'pyo3-0.20.3.tar.gz': '53bdbb96d49157e65d45cc287af5f32ffadd5f4761438b527b055fb0d4bb8233'},
+    {'pyo3-build-config-0.20.3.tar.gz': 'deaa5745de3f5231ce10517a1f5dd97d53e5a2fd77aa6b5842292085831d48d7'},
+    {'pyo3-ffi-0.20.3.tar.gz': '62b42531d03e08d4ef1f6e85a2ed422eb678b8cd62b762e53891c05faf0d4afa'},
+    {'pyo3-macros-0.20.3.tar.gz': '7305c720fa01b8055ec95e484a6eca7a83c841267f0dd5280f0c8b8551d2c158'},
+    {'pyo3-macros-backend-0.20.3.tar.gz': '7c7e9b68bb9c3149c5b0cade5d07f953d6d125eb4337723c4ccdb665f1f96185'},
+    {'quote-1.0.36.tar.gz': '0fa76aaf39101c457836aec0ce2316dbdc3ab723cdda1c6bd4e6ad4208acaca7'},
+    {'redox_syscall-0.4.1.tar.gz': '4722d768eff46b75989dd134e5c353f0d6296e5aaa3132e776cbdb56be7731aa'},
+    {'regex-1.10.4.tar.gz': 'c117dbdfde9c8308975b6a18d71f3f385c89461f7b3fb054288ecf2a2058ba4c'},
+    {'regex-automata-0.4.6.tar.gz': '86b83b8b9847f9bf95ef68afb0b8e6cdb80f498442f5179a29fad448fcc1eaea'},
+    {'regex-syntax-0.8.3.tar.gz': 'adad44e29e4c806119491a7f06f03de4d1af22c3a680dd47f1e6e179439d1f56'},
+    {'rustc-hash-1.1.0.tar.gz': '08d43f7aa6b08d49f382cde6a7982047c3426db949b1424bc4b7ec9ae12c6ce2'},
+    {'scopeguard-1.2.0.tar.gz': '94143f37725109f92c262ed2cf5e59bce7498c01bcc1502d7b9afe439a4e9f49'},
+    {'serde-1.0.197.tar.gz': '3fb1c873e1b9b056a4dc4c0c198b24c3ffa059243875552b2bd0933b1aee4ce2'},
+    {'serde_derive-1.0.197.tar.gz': '7eb0b34b42edc17f6b7cac84a52a1c5f0e1bb2227e997ca9011ea3dd34e8610b'},
+    {'smallvec-1.13.2.tar.gz': '3c5e1a9a646d36c3599cd173a41282daf47c44583ad367b8e6837255952e5c67'},
+    {'syn-2.0.58.tar.gz': '44cfb93f38070beee36b3fef7d4f5a16f27751d94b187b666a5cc5e9b0d30687'},
+    {'target-lexicon-0.12.14.tar.gz': 'e1fc403891a21bcfb7c37834ba66a547a8f402146eba7265b5a6d88059c9ff2f'},
+    {'unicode-ident-1.0.12.tar.gz': '3354b9ac3fae1ff6755cb6db53683adb661634f67557942dea4facebec0fee4b'},
+    {'unindent-0.2.3.tar.gz': 'c7de7d73e1754487cb58364ee906a499937a0dfabd86bcb980fa99ec8c8fa2ce'},
+    {'windows-targets-0.48.5.tar.gz': '9a2fa6e2155d7247be68c096456083145c183cbbbc2764150dda45a87197940c'},
+    {'windows_aarch64_gnullvm-0.48.5.tar.gz': '2b38e32f0abccf9987a4e3079dfb67dcd799fb61361e53e2882c3cbaf0d905d8'},
+    {'windows_aarch64_msvc-0.48.5.tar.gz': 'dc35310971f3b2dbbf3f0690a219f40e2d9afcf64f9ab7cc1be722937c26b4bc'},
+    {'windows_i686_gnu-0.48.5.tar.gz': 'a75915e7def60c94dcef72200b9a8e58e5091744960da64ec734a6c6e9b3743e'},
+    {'windows_i686_msvc-0.48.5.tar.gz': '8f55c233f70c4b27f66c523580f78f1004e8b5a8b659e05a4eb49d4166cca406'},
+    {'windows_x86_64_gnu-0.48.5.tar.gz': '53d40abd2583d23e4718fddf1ebec84dbff8381c07cae67ff7768bbf19c6718e'},
+    {'windows_x86_64_gnullvm-0.48.5.tar.gz': '0b7b52767868a23d5bab768e390dc5f5c55825b6d30b86c844ff2dc7414044cc'},
+    {'windows_x86_64_msvc-0.48.5.tar.gz': 'ed94fce61571a4006852b7389a063ab983c02eb1bb37b47f8272ce92d06d9538'},
+]
+
+_rust_ver = '1.75.0'
+builddependencies = [
+    ('binutils', '2.40'),
+    ('Rust', _rust_ver),
+    ('maturin', '1.4.0', '-Rust-%s' % _rust_ver),
+    ('hypothesis', '6.82.0')
+]
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('Python-bundle-PyPI', '2023.06'),  # regex (and pytest for tests)
+]
+
+use_pip = True
+sanity_pip_check = True
+download_dep_fail = True
+
+# https://github.com/openai/tiktoken/issues/194
+runtest = (
+    'ln -s $PWD/tests ../tests_%(name)s'
+    ' && cd ..'
+    ' && pytest tests_%(name)s/'
+)
+testinstall = True
+
+moduleclass = 'lib'

From ca95c11df8184d81e9b550ed1234139f49169276 Mon Sep 17 00:00:00 2001
From: WilleBell <cintiawillemyns@gmail.com>
Date: Tue, 4 Jun 2024 16:02:46 +0200
Subject: [PATCH 126/835] define a new version of the gmpich toolchain

---
 ....eb => GeoDict-2024.SP2-gmpich-2024.06.eb} |  3 +--
 .../easyconfigs/g/gmpich/gmpich-2024.06.eb    | 20 +++++++++++++++++++
 2 files changed, 21 insertions(+), 2 deletions(-)
 rename easybuild/easyconfigs/g/GeoDict/{GeoDict-2024.SP2-GCC-12.3.0.eb => GeoDict-2024.SP2-gmpich-2024.06.eb} (93%)
 create mode 100644 easybuild/easyconfigs/g/gmpich/gmpich-2024.06.eb

diff --git a/easybuild/easyconfigs/g/GeoDict/GeoDict-2024.SP2-GCC-12.3.0.eb b/easybuild/easyconfigs/g/GeoDict/GeoDict-2024.SP2-gmpich-2024.06.eb
similarity index 93%
rename from easybuild/easyconfigs/g/GeoDict/GeoDict-2024.SP2-GCC-12.3.0.eb
rename to easybuild/easyconfigs/g/GeoDict/GeoDict-2024.SP2-gmpich-2024.06.eb
index be6419dedeb..42186eafddb 100644
--- a/easybuild/easyconfigs/g/GeoDict/GeoDict-2024.SP2-GCC-12.3.0.eb
+++ b/easybuild/easyconfigs/g/GeoDict/GeoDict-2024.SP2-gmpich-2024.06.eb
@@ -11,7 +11,7 @@ property characterization, simulation-based material development, and optimizati
 processes.
 """
 
-toolchain = {'name': 'GCC', 'version': '12.3.0'}
+toolchain = {'name': 'gmpich', 'version': '2024.06'}
 
 source_urls = [
     'https://www.gddownload.de/Releases'
@@ -29,7 +29,6 @@ checksums = [
 
 dependencies = [
     ('X11', '20230603'),
-    ('MPICH', '4.2.1'),
 ]
 
 modextrapaths = {'PATH': '.'}
diff --git a/easybuild/easyconfigs/g/gmpich/gmpich-2024.06.eb b/easybuild/easyconfigs/g/gmpich/gmpich-2024.06.eb
new file mode 100644
index 00000000000..14afd408f3d
--- /dev/null
+++ b/easybuild/easyconfigs/g/gmpich/gmpich-2024.06.eb
@@ -0,0 +1,20 @@
+easyblock = 'Toolchain'
+
+name = 'gmpich'
+version = '2024.06'
+
+
+homepage = '(none)'
+description = """gcc and GFortran based compiler toolchain,
+ including MPICH for MPI support."""
+
+toolchain = SYSTEM
+
+local_gccver = '12.3.0'
+
+dependencies = [
+    ('GCC', local_gccver),
+    ('MPICH', '4.2.1', '', ('GCC', local_gccver)),
+]
+
+moduleclass = 'toolchain'

From 6377470a3ddc2be8056dfa2fe8b750a466e59598 Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Wed, 5 Jun 2024 00:07:11 +0200
Subject: [PATCH 127/835] adding easyconfigs:
 jupyter-collaboration-2.1.1-GCCcore-12.3.0.eb

---
 ...yter-collaboration-2.1.1-GCCcore-12.3.0.eb | 55 +++++++++++++++++++
 1 file changed, 55 insertions(+)
 create mode 100644 easybuild/easyconfigs/j/jupyter-collaboration/jupyter-collaboration-2.1.1-GCCcore-12.3.0.eb

diff --git a/easybuild/easyconfigs/j/jupyter-collaboration/jupyter-collaboration-2.1.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/j/jupyter-collaboration/jupyter-collaboration-2.1.1-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..c82cabd5c83
--- /dev/null
+++ b/easybuild/easyconfigs/j/jupyter-collaboration/jupyter-collaboration-2.1.1-GCCcore-12.3.0.eb
@@ -0,0 +1,55 @@
+easyblock = 'PythonBundle'
+
+name = 'jupyter-collaboration'
+version = "2.1.1"
+
+homepage = 'https://github.com/jupyterlab/jupyter-collaboration'
+description = """JupyterLab Real-Time Collaboration is a Jupyter Server Extension and JupyterLab
+extensions providing support for Y documents and adding collaboration UI
+elements in JupyterLab."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+builddependencies = [
+    ('binutils', '2.40'),
+    ('hatch-jupyter-builder', '0.9.1'),
+    ('maturin', '1.1.0'),
+]
+dependencies = [
+    ('Python', '3.11.3'),
+    ('JupyterLab', '4.0.5'),
+]
+
+sanity_pip_check = True
+use_pip = True
+
+exts_list = [
+    ('sqlite_anyio', '0.2.0', {
+        'checksums': ['9ecbcddf105e5862f7975a9827b684a19a987aad46f10699eadb22ea33bbd060'],
+    }),
+    ('pycrdt', '0.8.27', {
+        'checksums': ['a486a967ab82d92e51211757d888367b9d1882cfd4db6199485a8fd3d2271dce'],
+    }),
+    ('pycrdt_websocket', '0.13.4', {
+        'checksums': ['dce8259345ac14e08e9cf124cd1d66ea1b9d17ab1af79e63f50a611fb676421c'],
+    }),
+    ('jupyter_ydoc', '2.0.1', {
+        'checksums': ['716dda8cb8af881fec2fbc88aea3fb0d3bb24bbeb80a99a8aff2e01d089d5b0d'],
+    }),
+    ('jupyter_server_fileid', '0.9.2', {
+        'checksums': ['ffb11460ca5f8567644f6120b25613fca8e3f3048b38d14c6e3fe1902f314a9b'],
+    }),
+    ('jupyter_collaboration', version, {
+        'checksums': ['4f50c25c6d81126c16deaf92d2bd78a39b2fcb86690dce696b4006b740d71c1f'],
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['bin/jupyter-fileid'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages/', 'etc/jupyter', 'share/jupyter'],
+}
+
+# Add the notebook extension to the search path for jupyter notebooks
+modextrapaths = {'EB_ENV_JUPYTER_ROOT': ''}
+
+moduleclass = 'tools'

From b913d9c13bc5341d7d6e26231dce569fd0043cb8 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Wed, 5 Jun 2024 14:35:50 +0200
Subject: [PATCH 128/835] add scvi-tools, scArches, scib-metrics, pertpy

---
 .../j/jax/jax-0.4.25-foss-2023a.eb            | 112 ++++++++++++++++++
 .../jax-0.4.25_fix-pybind11-systemlib.patch   |  38 ++++++
 .../jax-0.4.25_fix_env_test_no_log_spam.patch |  18 +++
 .../ml-collections-0.1.1-foss-2023a.eb        |  37 ++++++
 .../o/Optax/Optax-0.2.2-foss-2023a.eb         |  42 +++++++
 ...e-cell-python-bundle-2024.02-foss-2023a.eb |  39 +++++-
 .../s/scArches/scArches-0.6.1-foss-2023a.eb   |  87 ++++++++++++++
 .../scib-metrics-0.5.1-foss-2023a.eb          |  54 +++++++++
 .../scvi-tools/scvi-tools-1.1.2-foss-2023a.eb |  68 +++++++++++
 9 files changed, 492 insertions(+), 3 deletions(-)
 create mode 100644 easybuild/easyconfigs/j/jax/jax-0.4.25-foss-2023a.eb
 create mode 100644 easybuild/easyconfigs/j/jax/jax-0.4.25_fix-pybind11-systemlib.patch
 create mode 100644 easybuild/easyconfigs/j/jax/jax-0.4.25_fix_env_test_no_log_spam.patch
 create mode 100644 easybuild/easyconfigs/m/ml-collections/ml-collections-0.1.1-foss-2023a.eb
 create mode 100644 easybuild/easyconfigs/o/Optax/Optax-0.2.2-foss-2023a.eb
 create mode 100644 easybuild/easyconfigs/s/scArches/scArches-0.6.1-foss-2023a.eb
 create mode 100644 easybuild/easyconfigs/s/scib-metrics/scib-metrics-0.5.1-foss-2023a.eb
 create mode 100644 easybuild/easyconfigs/s/scvi-tools/scvi-tools-1.1.2-foss-2023a.eb

diff --git a/easybuild/easyconfigs/j/jax/jax-0.4.25-foss-2023a.eb b/easybuild/easyconfigs/j/jax/jax-0.4.25-foss-2023a.eb
new file mode 100644
index 00000000000..d1e5fc1aabd
--- /dev/null
+++ b/easybuild/easyconfigs/j/jax/jax-0.4.25-foss-2023a.eb
@@ -0,0 +1,112 @@
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+# Author: Denis Kristak
+# Updated by: Alex Domingo (Vrije Universiteit Brussel), Pavel Tománek (Inuits)
+    # Update v0.4.25 based on: https://github.com/easybuilders/easybuild-easyconfigs/pull/20119
+
+easyblock = 'PythonBundle'
+
+name = 'jax'
+version = '0.4.25'
+
+homepage = 'https://jax.readthedocs.io/'
+description = """Composable transformations of Python+NumPy programs:
+differentiate, vectorize, JIT to GPU/TPU, and more"""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+builddependencies = [
+    ('Bazel', '6.3.1'),
+    ('pytest-xdist', '3.3.1'),
+    # git 2.x required to fetch repository 'io_bazel_rules_docker'
+    ('git', '2.41.0', '-nodocs'),
+    ('matplotlib', '3.7.2'),
+    ('poetry', '1.5.1'),
+    ('pybind11', '2.11.1'),
+]
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('zlib', '1.2.13'),
+    ('flatbuffers-python', '23.5.26'),
+    ('ml_dtypes', '0.3.2'),
+]
+
+use_pip = True
+
+local_xla_commit = '4ccfe33c71665ddcbca5b127fefe8baa3ed632d4'
+local_tfrt_commit = '0aeefb1660d7e37964b2bb71b1f518096bda9a25'
+
+local_extract_cmd = 'cp %s %(builddir)s/archives'
+
+local_repo_opt = '--bazel_options="--distdir=%(builddir)s/archives" '
+local_repo_opt += '--bazel_options="--action_env=TF_SYSTEM_LIBS=pybind11" '
+local_repo_opt += '--bazel_options="--action_env=CPATH=$EBROOTPYBIND11/include" '
+
+default_easyblock = 'PythonPackage'
+default_component_specs = {
+    'sources': [SOURCE_TAR_GZ],
+    'source_urls': [PYPI_SOURCE],
+    'start_dir': '%(name)s-%(version)s',
+    'use_pip': True,
+    'sanity_pip_check': True,
+    'download_dep_fail': True,
+}
+
+components = [
+    ('absl-py', '2.1.0', {
+        'options': {'modulename': 'absl'},
+        'checksums': ['7820790efbb316739cde8b4e19357243fc3608a152024288513dd968d7d959ff'],
+    }),
+    ('jaxlib', version, {
+        'sources': [
+            '%(name)s-v%(version)s.tar.gz',
+            {
+                'download_filename': '%s.tar.gz' % local_xla_commit,
+                'filename': 'xla-%s.tar.gz' % local_xla_commit,
+                'extract_cmd': local_extract_cmd,
+            },
+            {
+                'download_filename': '%s.tar.gz' % local_tfrt_commit,
+                'filename': 'tf_runtime-%s.tar.gz' % local_tfrt_commit,
+                'extract_cmd': local_extract_cmd,
+            },
+        ],
+        'source_urls': [
+            'https://github.com/google/jax/archive/',
+            'https://github.com/tensorflow/runtime/archive',
+            'https://github.com/openxla/xla/archive'
+        ],
+        'patches': ['jax-0.4.25_fix-pybind11-systemlib.patch'],
+        'checksums': [
+            {'jaxlib-v0.4.25.tar.gz':
+             'fc1197c401924942eb14185a61688d0c476e3e81ff71f9dc95e620b57c06eec8'},
+            {'xla-4ccfe33c71665ddcbca5b127fefe8baa3ed632d4.tar.gz':
+             '8a59b9af7d0850059d7043f7043c780066d61538f3af536e8a10d3d717f35089'},
+            {'tf_runtime-0aeefb1660d7e37964b2bb71b1f518096bda9a25.tar.gz':
+             'a3df827d7896774cb1d80bf4e1c79ab05c268f29bd4d3db1fb5a4b9c2079d8e3'},
+            {'jax-0.4.25_fix-pybind11-systemlib.patch':
+             'daad5b726d1a138431b05eb60ecf4c89c7b5148eb939721800bdf43d804ca033'},
+        ],
+        'start_dir': 'jax-jaxlib-v%(version)s',
+        # Avoid warning (treated as error) in upb/table.c
+        'buildopts': local_repo_opt + ' --bazel_options="--copt=-Wno-maybe-uninitialized"'
+    }),
+]
+
+exts_list = [
+    (name, version, {
+        'patches': ['jax-0.4.25_fix_env_test_no_log_spam.patch'],
+        'source_tmpl': '%(name)s-v%(version)s.tar.gz',
+        'source_urls': ['https://github.com/google/jax/archive/'],
+        'checksums': [
+            {'jax-v0.4.25.tar.gz': '8b30af49688c0c13b82c6f5ce992727c00b5fc6d04a4c6962012f4246fa664eb'},
+            {'jax-0.4.25_fix_env_test_no_log_spam.patch':
+             'a18b5f147569d9ad41025124333a0f04fd0d0e0f9e4309658d7f6b9b838e2e2a'},
+        ],
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'tools'
diff --git a/easybuild/easyconfigs/j/jax/jax-0.4.25_fix-pybind11-systemlib.patch b/easybuild/easyconfigs/j/jax/jax-0.4.25_fix-pybind11-systemlib.patch
new file mode 100644
index 00000000000..c404ee6917f
--- /dev/null
+++ b/easybuild/easyconfigs/j/jax/jax-0.4.25_fix-pybind11-systemlib.patch
@@ -0,0 +1,38 @@
+Add missing value for System Pybind11 Bazel config
+
+Author: Alexander Grund (TU Dresden)
+
+diff --git a/third_party/xla/fix-pybind11-systemlib.patch b/third_party/xla/fix-pybind11-systemlib.patch
+new file mode 100644
+index 000000000..68bd2063d
+--- /dev/null
++++ b/third_party/xla/fix-pybind11-systemlib.patch
+@@ -0,0 +1,13 @@
++--- xla-orig/third_party/tsl/third_party/systemlibs/pybind11.BUILD
+++++ xla-4ccfe33c71665ddcbca5b127fefe8baa3ed632d4/third_party/tsl/third_party/systemlibs/pybind11.BUILD
++@@ -6,3 +6,10 @@
++         "@tsl//third_party/python_runtime:headers",
++     ],
++ )
+++
+++# Needed by pybind11_bazel.
+++config_setting(
+++    name = "osx",
+++    constraint_values = ["@platforms//os:osx"],
+++)
+++
+diff --git a/third_party/xla/workspace.bzl b/third_party/xla/workspace.bzl
+index ebc8d9838..125e1c173 100644
+--- a/third_party/xla/workspace.bzl
++++ b/third_party/xla/workspace.bzl
+@@ -29,6 +29,9 @@ def repo():
+         sha256 = XLA_SHA256,
+         strip_prefix = "xla-{commit}".format(commit = XLA_COMMIT),
+         urls = tf_mirror_urls("https://github.com/openxla/xla/archive/{commit}.tar.gz".format(commit = XLA_COMMIT)),
++        patch_file = [
++            "//third_party/xla:fix-pybind11-systemlib.patch",
++        ],
+     )
+ 
+     # For development, one often wants to make changes to the TF repository as well
+
diff --git a/easybuild/easyconfigs/j/jax/jax-0.4.25_fix_env_test_no_log_spam.patch b/easybuild/easyconfigs/j/jax/jax-0.4.25_fix_env_test_no_log_spam.patch
new file mode 100644
index 00000000000..ad919608437
--- /dev/null
+++ b/easybuild/easyconfigs/j/jax/jax-0.4.25_fix_env_test_no_log_spam.patch
@@ -0,0 +1,18 @@
+# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2024/03
+# avoid overriding LD_LIBRARY_PATH, which would lead to test error: error while loading shared libraries: libpython3.11.so.1.0: cannot open shared object file: No such file or directory'
+diff -ru jax-jax-v0.4.25/tests/logging_test.py jax-jax-v0.4.25_fix_env_test_no_log_spam/tests/logging_test.py
+--- jax-jax-v0.4.25/tests/logging_test.py	2024-02-24 19:25:17.000000000 +0100
++++ jax-jax-v0.4.25_fix_env_test_no_log_spam/tests/logging_test.py	2024-03-15 12:00:34.133022613 +0100
+@@ -72,8 +72,11 @@
+     python = sys.executable
+     assert "python" in python
+     # Make sure C++ logging is at default level for the test process.
++    import os
++    tmp_env=os.environ.copy()
++    tmp_env['TF_CPP_MIN_LOG_LEVEL']='1'
+     proc = subprocess.run([python, "-c", program], capture_output=True,
+-                          env={"TF_CPP_MIN_LOG_LEVEL": "1"})
++                          env=tmp_env)
+ 
+     lines = proc.stdout.split(b"\n")
+     lines.extend(proc.stderr.split(b"\n"))
diff --git a/easybuild/easyconfigs/m/ml-collections/ml-collections-0.1.1-foss-2023a.eb b/easybuild/easyconfigs/m/ml-collections/ml-collections-0.1.1-foss-2023a.eb
new file mode 100644
index 00000000000..79034a7433d
--- /dev/null
+++ b/easybuild/easyconfigs/m/ml-collections/ml-collections-0.1.1-foss-2023a.eb
@@ -0,0 +1,37 @@
+easyblock = 'PythonBundle'
+
+name = 'ml-collections'
+version = '0.1.1'
+
+homepage = 'https://github.com/google/ml_collections'
+description = """
+ML Collections is a library of Python Collections designed for ML use cases.
+"""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('PyYAML', '6.0'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('absl-py', '2.1.0', {
+        'modulename': 'absl',
+        'checksums': ['7820790efbb316739cde8b4e19357243fc3608a152024288513dd968d7d959ff'],
+    }),
+    ('contextlib2', '21.6.0', {
+        'checksums': ['ab1e2bfe1d01d968e1b7e8d9023bc51ef3509bba217bb730cee3827e1ee82869'],
+    }),
+    ('ml_collections', version, {
+        'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ",
+        'checksums': ['3fefcc72ec433aa1e5d32307a3e474bbb67f405be814ea52a2166bfc9dbe68cc'],
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'vis'
diff --git a/easybuild/easyconfigs/o/Optax/Optax-0.2.2-foss-2023a.eb b/easybuild/easyconfigs/o/Optax/Optax-0.2.2-foss-2023a.eb
new file mode 100644
index 00000000000..be05f009e9e
--- /dev/null
+++ b/easybuild/easyconfigs/o/Optax/Optax-0.2.2-foss-2023a.eb
@@ -0,0 +1,42 @@
+easyblock = 'PythonBundle'
+
+name = 'Optax'
+version = '0.2.2'
+
+homepage = 'https://github.com/deepmind/optax'
+description = """Optax is a gradient processing and optimization library for JAX."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('jax', '0.4.25'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('toolz', '0.12.1', {
+        'checksums': ['ecca342664893f177a13dac0e6b41cbd8ac25a358e5f215316d43e2100224f4d'],
+    }),
+    ('flit_core', '3.9.0', {
+        'checksums': ['72ad266176c4a3fcfab5f2930d76896059851240570ce9a98733b658cb786eba'],
+    }),
+    ('absl-py', '2.1.0', {
+        'modulename': 'absl',
+        'checksums': ['7820790efbb316739cde8b4e19357243fc3608a152024288513dd968d7d959ff'],
+    }),
+    ('chex', '0.1.86', {
+        'checksums': ['e8b0f96330eba4144659e1617c0f7a57b161e8cbb021e55c6d5056c7378091d1'],
+    }),
+    ('optax', version, {
+        'checksums': ['f09bf790ef4b09fb9c35f79a07594c6196a719919985f542dc84b0bf97812e0e'],
+    }),
+]
+
+sanity_pip_check = True
+
+sanity_check_commands = ["python -c 'from optax import GradientTransformation'"]
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb b/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb
index bb7237e35f1..8a4cee8cfcf 100644
--- a/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb
+++ b/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb
@@ -22,9 +22,6 @@ dependencies = [
     ('Seaborn', '0.13.2'),
     ('PyTorch', '2.1.2'),
     ('scanpy', '1.9.8'),
-    # scvi-tools TODO
-    # scArches TODO
-    # scib-metrics TODO
     ('scib', '1.1.4'),
     ('scVelo', '0.3.1'),  # imports loompy
     ('CellTypist', '1.6.2'),
@@ -37,6 +34,9 @@ dependencies = [
     ('CellRank', '2.0.2'),
     ('Squidpy', '1.4.1'),
     ('Cassiopeia', '2.0.0'),
+    ('scvi-tools', '1.1.2'),  # imports jax
+    ('scArches', '0.6.1'),
+    ('scib-metrics', '0.5.1'),
     # deps for exts:
     ('umap-learn', '0.5.5'),  # bbknn
     ('scikit-learn', '1.3.1'),  # bbknn, sc_toolbox
@@ -45,6 +45,8 @@ dependencies = [
     ('adjustText', '1.1.1'),  # sc_toolbox, created
     ('python-parasail', '1.3.4'),  # scirpy
     ('graph-tool', '2.59'),  # schist
+    ('Pyomo', '6.7.3'),  # pertpy
+    ('mpmath', '1.3.0'),  # blitzgsea
 ]
 
 exts_list = [
@@ -207,6 +209,37 @@ exts_list = [
         'source_urls': ['https://github.com/dawe/schist/archive/'],
         'checksums': ['9b98ec9d85554573288c24f18c4791ba7c4d315397cbc422ea25d4a7cdd42e6d'],
     }),
+    ('typeguard', '2.13.3', {
+        'checksums': ['00edaa8da3a133674796cf5ea87d9f4b4c367d77476e185e80251cc13dfbb8c4'],
+    }),
+    ('jaxtyping', '0.2.29', {
+        'checksums': ['e1cd916ed0196e40402b0638449e7d051571562b2cd68d8b94961a383faeb409'],
+    }),
+    ('equinox', '0.11.4', {
+        'checksums': ['0033d9731083f402a855b12a0777a80aa8507651f7aa86d9f0f9503bcddfd320'],
+    }),
+    ('lineax', '0.0.4', {
+        'checksums': ['e68f1eba2f352122fdce9adc0556684f31eb8364b1a00acee484dd6e44a34e5e'],
+    }),
+    ('jaxopt', '0.8.3', {
+        'checksums': ['4b06dfa6f915a4f3291699606245af6069371a48dc5c92d4c507840d62990646'],
+    }),
+    ('ott_jax', '0.4.6', {
+        'modulename': 'ott',
+        'checksums': ['bc91f8d512cdb344439f5584712d76cd0650b6716b6686d53b828cc67abdbcba'],
+    }),
+    ('sparsecca', '0.3.1', {
+        'checksums': ['be1526baebac5ce6efbc7190fd62a1cec13288c493f5d427024f66ca6afaec13'],
+    }),
+    ('PubChemPy', '1.0.4', {
+        'checksums': ['24e9dc2fc90ab153b2764bf805e510b1410700884faf0510a9e7cf0d61d8ed0e'],
+    }),
+    ('blitzgsea', '1.3.42', {
+        'checksums': ['dcc997b5d29d190d8632474f3bb57b5ead7fb1370b478c7f824b42782325a1ca'],
+    }),
+    ('pertpy', '0.7.0', {
+        'checksums': ['273723b5b70f3cb714bb36d3234462014b72e133111eeaf08aa47153c9df14aa'],
+    }),
 ]
 
 use_pip = True
diff --git a/easybuild/easyconfigs/s/scArches/scArches-0.6.1-foss-2023a.eb b/easybuild/easyconfigs/s/scArches/scArches-0.6.1-foss-2023a.eb
new file mode 100644
index 00000000000..c703d0beede
--- /dev/null
+++ b/easybuild/easyconfigs/s/scArches/scArches-0.6.1-foss-2023a.eb
@@ -0,0 +1,87 @@
+easyblock = 'PythonBundle'
+
+name = 'scArches'
+version = '0.6.1'
+
+homepage = 'https://github.com/theislab/scarches'
+description = """Single-cell architecture surgery (scArches) is a package for reference-based analysis of single-cell
+ data."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('Python-bundle-PyPI', '2023.06'),
+    ('matplotlib', '3.7.2'),
+    ('anndata', '0.10.5.post1'),
+    ('h5py', '3.9.0'),
+    ('leidenalg', '0.10.2'),
+    ('scanpy', '1.9.8'),
+    ('scikit-learn', '1.3.1'),
+    ('scvi-tools', '1.1.2'),
+    ('PyTorch', '2.1.2'),
+    ('tqdm', '4.66.1'),
+    ('IPython', '8.14.0'),
+    ('pkgconfig', '1.5.5', '-python'),
+    ('PyZMQ', '25.1.1'),
+    ('tornado', '6.3.2'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('sphinx_basic_ng', '1.0.0b2', {
+        'checksums': ['9ec55a47c90c8c002b5960c57492ec3021f5193cb26cebc2dc4ea226848651c9'],
+    }),
+    ('nodeenv', '1.9.0', {
+        'checksums': ['07f144e90dae547bf0d4ee8da0ee42664a42a04e02ed68e06324348dafe4bdb1'],
+    }),
+    ('sphinx-theme-builder', '0.2.0b2', {
+        'checksums': ['e9cd98c2bb35bf414fe721469a043cdcc10f0808d1ffcf606acb4a6282a6f288'],
+    }),
+    ('furo', '2024.1.29', {
+        'checksums': ['4d6b2fe3f10a6e36eb9cc24c1e7beb38d7a23fc7b3c382867503b7fcac8a1e02'],
+    }),
+    ('numpydoc', '1.6.0', {
+        'checksums': ['ae7a5380f0a06373c3afe16ccd15bd79bc6b07f2704cbc6f1e7ecc94b4f5fc0d'],
+    }),
+    ('jupyter_core', '5.7.2', {
+        'checksums': ['aa5f8d32bbf6b431ac830496da7392035d6f61b4f54872f15c4bd2a9c3f536d9'],
+    }),
+    ('jupyter_client', '8.6.1', {
+        'checksums': ['e842515e2bab8e19186d89fdfea7abd15e39dd581f94e399f00e2af5a1652d3f'],
+    }),
+    ('debugpy', '1.8.1', {
+        'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl',
+        'checksums': ['28acbe2241222b87e255260c76741e1fbf04fdc3b6d094fcf57b6c6f75ce1242'],
+    }),
+    ('comm', '0.2.2', {
+        'checksums': ['3fd7a84065306e07bea1773df6eb8282de51ba82f77c72f9c85716ab11fe980e'],
+    }),
+    ('ipykernel', '6.29.3', {
+        'checksums': ['e14c250d1f9ea3989490225cc1a542781b095a18a19447fcf2b5eaf7d0ac5bd2'],
+    }),
+    ('gdown', '5.1.0', {
+        'checksums': ['550a72dc5ca2819fe4bcc15d80d05d7c98c0b90e57256254b77d0256b9df4683'],
+    }),
+    ('muon', '0.1.6', {
+        'checksums': ['762feeb6f52f865cf79d0d0332cc742fe91c1885f668ce15794b62b3952b02f9'],
+    }),
+    ('newick', '1.9.0', {
+        'checksums': ['9f81be96ec86aefca74d920fc0d6962d89a3156547003ca6915c2e6e31ad3ddf'],
+    }),
+    ('scHPL', '1.0.5', {
+        'modulename': 'scHPL',
+        # unpin pandas and newick versions to be compatible with foss/2023a versions
+        'preinstallopts': "sed -i 's/~=/>=/g' setup.py && sed -i 's/pandas>=1.1.2,<2/pandas/g' setup.py && ",
+        'checksums': ['3eb62b2e65b1faba04b7bcb86f7bf6967a6301866a605551211b8f14fd27eced'],
+    }),
+    (name, version, {
+        'checksums': ['187463c25781d5c5586c129ad137d96327a9f8604d530a696d5f568a9225d77c'],
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/s/scib-metrics/scib-metrics-0.5.1-foss-2023a.eb b/easybuild/easyconfigs/s/scib-metrics/scib-metrics-0.5.1-foss-2023a.eb
new file mode 100644
index 00000000000..68ef32b71ad
--- /dev/null
+++ b/easybuild/easyconfigs/s/scib-metrics/scib-metrics-0.5.1-foss-2023a.eb
@@ -0,0 +1,54 @@
+easyblock = 'PythonBundle'
+
+name = 'scib-metrics'
+version = '0.5.1'
+
+homepage = 'https://scib-metrics.readthedocs.io'
+description = "Accelerated and Python-only metrics for benchmarking single-cell integration outputs"
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+builddependencies = [
+    ('hatchling', '1.18.0'),
+    ('poetry', '1.5.1'),
+]
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('anndata', '0.10.5.post1'),
+    ('jax', '0.4.25'),
+    ('scikit-learn', '1.3.1'),
+    ('scanpy', '1.9.8'),
+    ('python-igraph', '0.11.4'),
+    ('matplotlib', '3.7.2'),
+    ('tqdm', '4.66.1'),
+    ('umap-learn', '0.5.5'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('toolz', '0.12.1', {
+        'checksums': ['ecca342664893f177a13dac0e6b41cbd8ac25a358e5f215316d43e2100224f4d'],
+    }),
+    ('plottable', '0.1.5', {
+        'checksums': ['235d762a31c82129dc5bf74205c103a14b1e4393d0f921cc0231be5de884041d'],
+    }),
+    ('pynndescent', '0.5.11', {
+        'checksums': ['6f44ced9d5a9da2c87d9b2fff30bb5308540c0657605e4d5cde7ed3275bbad50'],
+    }),
+    ('rich', '13.7.1', {
+        'checksums': ['9be308cb1fe2f1f57d67ce99e95af38a1e2bc71ad9813b0e247cf7ffbcc3a432'],
+    }),
+    ('chex', '0.1.86', {
+        'checksums': ['e8b0f96330eba4144659e1617c0f7a57b161e8cbb021e55c6d5056c7378091d1'],
+    }),
+    (name, version, {
+        'sources': ['scib_metrics-%(version)s.tar.gz'],
+        'checksums': ['74d10251acf1c11402b994faf063e55317881d7950fb78f6cef011d232a1e266'],
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/s/scvi-tools/scvi-tools-1.1.2-foss-2023a.eb b/easybuild/easyconfigs/s/scvi-tools/scvi-tools-1.1.2-foss-2023a.eb
new file mode 100644
index 00000000000..f79f5895f45
--- /dev/null
+++ b/easybuild/easyconfigs/s/scvi-tools/scvi-tools-1.1.2-foss-2023a.eb
@@ -0,0 +1,68 @@
+easyblock = 'PythonBundle'
+
+name = 'scvi-tools'
+version = '1.1.2'
+
+homepage = 'https://github.com/scverse/scvi-tools'
+description = """scvi-tools (single-cell variational inference tools) is a package for probabilistic modeling and
+analysis of single-cell omics data, built on top of PyTorch and AnnData."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+builddependencies = [('hatchling', '1.18.0')]
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('anndata', '0.10.5.post1'),
+    ('matplotlib', '3.7.2'),
+    ('scikit-learn', '1.3.1'),
+    ('tqdm', '4.66.1'),
+    ('jax', '0.4.25'),
+    ('h5py', '3.9.0'),
+    ('PyTorch-Lightning', '2.2.1'),
+    ('pyro-ppl', '1.9.0'),
+    ('ml-collections', '0.1.1'),
+    ('Optax', '0.2.2'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('mudata', '0.2.3', {
+        'checksums': ['45288ac150bfc598d68acb7c2c1c43c38c5c39522107e04f7efbf3360c7f2035'],
+    }),
+    ('multipledispatch', '1.0.0', {
+        'checksums': ['5c839915465c68206c3e9c473357908216c28383b425361e5d144594bf85a7e0'],
+    }),
+    ('numpyro', '0.15.0', {
+        'checksums': ['e16c9f47cc31e2aa259584a0b6c944312081d33ca92406022632ad584b0e600d'],
+    }),
+    ('nest_asyncio', '1.6.0', {
+        'checksums': ['6f172d5449aca15afd6c646851f4e31e02c598d553a667e38cafa997cfec55fe'],
+    }),
+    ('orbax_checkpoint', '0.5.15', {
+        'modulename': 'orbax.checkpoint',
+        'checksums': ['15195e8d1b381b56f23a62a25599a3644f5d08655fa64f60bb1b938b8ffe7ef3'],
+    }),
+    ('tensorstore', '0.1.60', {
+        'checksums': ['88da8f1978982101b8dbb144fd29ee362e4e8c97fc595c4992d555f80ce62a79'],
+    }),
+    ('flax', '0.8.4', {
+        'checksums': ['968683f850198e1aa5eb2d9d1e20bead880ef7423c14f042db9d60848cb1c90b'],
+    }),
+    ('docrep', '0.3.2', {
+        'checksums': ['ed8a17e201abd829ef8da78a0b6f4d51fb99a4cbd0554adbed3309297f964314'],
+    }),
+    ('lightning', '2.1.4', {
+        'checksums': ['0e45098c700fa28c604a11ae233ce181b44aeffce2404debebc2616118431d9f'],
+    }),
+    (name, version, {
+        'modulename': 'scvi',
+        'sources': ['scvi_tools-%(version)s.tar.gz'],
+        'checksums': ['104a11a30e8996f5ceaa907b8c81b48b1f4b380d492ef2dd9b9a5577ed81b0f9'],
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'bio'

From 6a51ca70bb1bf16596a34c8847e2805abc0da29c Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Wed, 5 Jun 2024 14:44:19 +0200
Subject: [PATCH 129/835] add pyomo, the dep of pertpy

---
 .../p/Pyomo/Pyomo-6.7.3-foss-2023a.eb         | 34 +++++++++++++++++++
 1 file changed, 34 insertions(+)
 create mode 100644 easybuild/easyconfigs/p/Pyomo/Pyomo-6.7.3-foss-2023a.eb

diff --git a/easybuild/easyconfigs/p/Pyomo/Pyomo-6.7.3-foss-2023a.eb b/easybuild/easyconfigs/p/Pyomo/Pyomo-6.7.3-foss-2023a.eb
new file mode 100644
index 00000000000..64ee6de4f2b
--- /dev/null
+++ b/easybuild/easyconfigs/p/Pyomo/Pyomo-6.7.3-foss-2023a.eb
@@ -0,0 +1,34 @@
+easyblock = 'PythonBundle'
+
+name = 'Pyomo'
+version = '6.7.3'
+
+homepage = 'https://www.pyomo.org/'
+description = """ Pyomo is a Python-based open-source software package that supports a diverse set of optimization
+ capabilities for formulating and analyzing optimization models. """
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('Python-bundle-PyPI', '2023.06'),
+    ('mpi4py', '3.1.4'),
+    ('PLY', '3.11'),
+]
+
+exts_list = [
+    ('PyUtilib', '6.0.0', {
+        'preinstallopts': """sed -i "s/'nose',//g" setup.py && """,
+        'checksums': ['d3c14f8ed9028a831b2bf51b8ab7776eba87e66cfc58a06b99c359aaa640f040'],
+    }),
+    (name, version, {
+        'checksums': ['b7f0441c405af4f42f38527ae38826a5c0a4984dd7bea1fe07172789d8594770'],
+    }),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+sanity_check_commands = ['pyomo -h']
+
+moduleclass = 'math'

From bb6babb76423e70a49d06e76910266b0a3126bb7 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Wed, 5 Jun 2024 16:04:37 +0200
Subject: [PATCH 130/835] replace imagecodecs by v2024.1.1

---
 .../c/CharLS/CharLS-2.4.2-GCCcore-12.3.0.eb   | 30 --------
 .../empanada-dl-0.1.7-foss-2023a.eb           |  2 +-
 .../empanada-napari-1.1.0-foss-2023a.eb       |  2 +-
 .../imagecodecs-2023.1.23-foss-2023a.eb       | 70 -------------------
 .../j/jxrlib/jxrlib-1.1-GCCcore-12.3.0.eb     | 39 -----------
 .../l/LibLZF/LibLZF-3.6-GCCcore-12.3.0.eb     | 31 --------
 .../l/libavif/libavif-1.0.4-GCCcore-12.3.0.eb | 34 ---------
 .../l/libde265/libde265-1.0.15-GCC-12.3.0.eb  | 34 ---------
 .../l/libheif/libheif-1.17.6-GCC-12.3.0.eb    | 43 ------------
 .../l/libjxl/libjxl-0.8.2-foss-2023a.eb       | 52 --------------
 .../l/libwebp/libwebp-1.3.1-GCCcore-12.3.0.eb | 45 ------------
 .../z/Zopfli/Zopfli-1.0.3-GCCcore-12.3.0.eb   | 36 ----------
 .../z/zfp/zfp-1.0.1-GCCcore-12.3.0.eb         | 40 -----------
 .../z/zlib-ng/zlib-ng-2.1.6-GCCcore-12.3.0.eb | 30 --------
 14 files changed, 2 insertions(+), 486 deletions(-)
 delete mode 100644 easybuild/easyconfigs/c/CharLS/CharLS-2.4.2-GCCcore-12.3.0.eb
 delete mode 100644 easybuild/easyconfigs/i/imagecodecs/imagecodecs-2023.1.23-foss-2023a.eb
 delete mode 100644 easybuild/easyconfigs/j/jxrlib/jxrlib-1.1-GCCcore-12.3.0.eb
 delete mode 100644 easybuild/easyconfigs/l/LibLZF/LibLZF-3.6-GCCcore-12.3.0.eb
 delete mode 100644 easybuild/easyconfigs/l/libavif/libavif-1.0.4-GCCcore-12.3.0.eb
 delete mode 100644 easybuild/easyconfigs/l/libde265/libde265-1.0.15-GCC-12.3.0.eb
 delete mode 100644 easybuild/easyconfigs/l/libheif/libheif-1.17.6-GCC-12.3.0.eb
 delete mode 100644 easybuild/easyconfigs/l/libjxl/libjxl-0.8.2-foss-2023a.eb
 delete mode 100644 easybuild/easyconfigs/l/libwebp/libwebp-1.3.1-GCCcore-12.3.0.eb
 delete mode 100644 easybuild/easyconfigs/z/Zopfli/Zopfli-1.0.3-GCCcore-12.3.0.eb
 delete mode 100644 easybuild/easyconfigs/z/zfp/zfp-1.0.1-GCCcore-12.3.0.eb
 delete mode 100644 easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.1.6-GCCcore-12.3.0.eb

diff --git a/easybuild/easyconfigs/c/CharLS/CharLS-2.4.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/c/CharLS/CharLS-2.4.2-GCCcore-12.3.0.eb
deleted file mode 100644
index 9d814bdfc23..00000000000
--- a/easybuild/easyconfigs/c/CharLS/CharLS-2.4.2-GCCcore-12.3.0.eb
+++ /dev/null
@@ -1,30 +0,0 @@
-easyblock = 'CMakeMake'
-
-name = 'CharLS'
-version = '2.4.2'
-
-homepage = 'https://github.com/team-charls/charls'
-description = """CharLS is a C++ implementation of the JPEG-LS standard for lossless and near-lossless image
-compression and decompression. JPEG-LS is a low-complexity image compression standard that matches JPEG 2000
-compression ratios."""
-
-toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
-toolchainopts = {'pic': True}
-
-source_urls = ['https://github.com/team-charls/charls/archive/']
-sources = ['%(version)s.tar.gz']
-checksums = ['d1c2c35664976f1e43fec7764d72755e6a50a80f38eca70fcc7553cad4fe19d9']
-
-builddependencies = [
-    ('binutils', '2.40'),
-    ('CMake', '3.26.3')
-]
-
-configopts = '-DBUILD_SHARED_LIBS=ON '
-
-sanity_check_paths = {
-    'files': ['lib/libcharls.%s' % SHLIB_EXT],
-    'dirs': ['include'],
-}
-
-moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/e/empanada-dl/empanada-dl-0.1.7-foss-2023a.eb b/easybuild/easyconfigs/e/empanada-dl/empanada-dl-0.1.7-foss-2023a.eb
index cae05720108..168c3e3c751 100644
--- a/easybuild/easyconfigs/e/empanada-dl/empanada-dl-0.1.7-foss-2023a.eb
+++ b/easybuild/easyconfigs/e/empanada-dl/empanada-dl-0.1.7-foss-2023a.eb
@@ -21,7 +21,7 @@ dependencies = [
     ('dask', '2023.9.2'),
     ('connected-components-3d', '3.14.1'),
     ('matplotlib', '3.7.2'),
-    ('imagecodecs', '2023.1.23'),
+    ('imagecodecs', '2024.1.1'),
 ]
 
 use_pip = True
diff --git a/easybuild/easyconfigs/e/empanada-napari/empanada-napari-1.1.0-foss-2023a.eb b/easybuild/easyconfigs/e/empanada-napari/empanada-napari-1.1.0-foss-2023a.eb
index 4130aeda884..e429617f718 100644
--- a/easybuild/easyconfigs/e/empanada-napari/empanada-napari-1.1.0-foss-2023a.eb
+++ b/easybuild/easyconfigs/e/empanada-napari/empanada-napari-1.1.0-foss-2023a.eb
@@ -16,7 +16,7 @@ dependencies = [
     ('MLflow', '2.10.2'),
     ('openpyxl', '3.1.2'),
     ('SimpleITK', '2.3.1'),
-    ('imagecodecs', '2023.1.23'),
+    ('imagecodecs', '2024.1.1'),
     ('Albumentations', '1.4.0'),
     ('connected-components-3d', '3.14.1'),
     ('empanada-dl', '0.1.7'),
diff --git a/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2023.1.23-foss-2023a.eb b/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2023.1.23-foss-2023a.eb
deleted file mode 100644
index 4255c33f1e7..00000000000
--- a/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2023.1.23-foss-2023a.eb
+++ /dev/null
@@ -1,70 +0,0 @@
-# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
-# Author: Denis Kristak
-# update: Thomas Hoffmann (EMBL), Denis Kristak (Inuits), Pavel Tománek (Inuits)
-easyblock = 'PythonBundle'
-
-name = 'imagecodecs'
-version = '2023.1.23'
-
-homepage = 'https://github.com/cgohlke/imagecodecs'
-description = """Imagecodecs is a Python library that provides block-oriented, in-memory buffer transformation,
-compression, and decompression functions for use in the tifffile, czifile, zarr, and other
-scientific image input/output modules."""
-
-toolchain = {'name': 'foss', 'version': '2023a'}
-
-local_openjpeg_maj_min = '2.5'
-dependencies = [
-    ('Python', '3.11.3'),
-    ('Python-bundle-PyPI', '2023.06'),
-    ('SciPy-bundle', '2023.07'),
-    ('matplotlib', '3.7.2'),
-    ('Brotli', '1.0.9'),
-    ('bzip2', '1.0.8'),
-    ('Blosc', '1.21.5'),
-    ('Blosc2', '2.8.0'),
-    ('CFITSIO', '4.3.0'),
-    ('CharLS', '2.4.2'),
-    ('giflib', '5.2.1'),
-    ('jxrlib', '1.1'),
-    ('LittleCMS', '2.15'),
-    ('LERC', '4.0.0'),
-    ('libaec', '1.0.6'),
-    ('libavif', '1.0.4'),
-    ('libdeflate', '1.18'),
-    ('libjpeg-turbo', '2.1.5.1'),
-    ('libjxl', '0.8.2'),
-    ('LibLZF', '3.6'),
-    ('libpng', '1.6.39'),
-    ('XZ', '5.4.2'),
-    ('LibTIFF', '4.5.0'),
-    ('libwebp', '1.3.1'),
-    ('lz4', '1.9.4'),
-    ('OpenJPEG', local_openjpeg_maj_min + '.0'),
-    ('snappy', '1.1.10'),
-    ('zlib', '1.2.13'),
-    ('zlib-ng', '2.1.6'),
-    ('Zopfli', '1.0.3'),
-    ('zfp', '1.0.1'),
-    ('zstd', '1.5.5'),
-    ('Brunsli', '0.1'),
-    ('HDF5', '1.14.0'),
-    ('h5py', '3.9.0'),
-    ('libheif', '1.17.6'),
-]
-
-use_pip = True
-sanity_pip_check = True
-
-exts_list = [
-    ('bitshuffle', '0.5.1', {
-        'checksums': ['988f224739aa6858475a4c59172968c7b51cc657d2249580c8f96848708fbae3'],
-    }),
-    (name, version, {
-        'preinstallopts': "export CPATH=$EBROOTOPENJPEG/include/openjpeg-%s/:$CPATH && " % local_openjpeg_maj_min,
-        'sources': ['%(name)s-%(version)s.tar.gz'],
-        'checksums': ['1b4591839a2f5c90467e50ebe54117cbd9be42c18864abdf85fc7743223ac5b2'],
-    }),
-]
-
-moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/j/jxrlib/jxrlib-1.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/j/jxrlib/jxrlib-1.1-GCCcore-12.3.0.eb
deleted file mode 100644
index af33ba9e3d6..00000000000
--- a/easybuild/easyconfigs/j/jxrlib/jxrlib-1.1-GCCcore-12.3.0.eb
+++ /dev/null
@@ -1,39 +0,0 @@
-##
-# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
-# Author::   Denis Kristak (INUITS)
-# Update:    Thomas Hoffmann (EMBL), Pavel Tománek (Inuits)
-##
-
-easyblock = 'CMakeMake'
-
-name = 'jxrlib'
-version = '1.1'
-
-homepage = 'https://github.com/4creators/jxrlib'
-description = """Open source implementation of jpegxr"""
-
-toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
-
-source_urls = ['https://deb.debian.org/debian/pool/main/j/jxrlib/']
-sources = ['%(name)s_%(version)s.orig.tar.gz']
-patches = [('jxrlib-%(version)s_cmake.patch', 1)]
-checksums = [
-    {'jxrlib_1.1.orig.tar.gz': 'c7287b86780befa0914f2eeb8be2ac83e672ebd4bd16dc5574a36a59d9708303'},
-    {'jxrlib-1.1_cmake.patch': 'e96ea8b418fdab10e9cbc2f4cad95ca1f59a826ce7379c6a3192882050689a74'},
-]
-
-builddependencies = [
-    ('binutils', '2.40'),
-    ('CMake', '3.26.3'),
-]
-
-sanity_check_paths = {
-    'files': ['bin/JxrDecApp', 'bin/JxrEncApp', "lib/libjpegxr.%s" % SHLIB_EXT],
-    'dirs': [],
-}
-
-sanity_check_commands = ['JxrDecApp', 'JxrEncApp']
-
-modextrapaths = {'CPATH': 'include/jxrlib'}
-
-moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/l/LibLZF/LibLZF-3.6-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/LibLZF/LibLZF-3.6-GCCcore-12.3.0.eb
deleted file mode 100644
index 45bef34f6e6..00000000000
--- a/easybuild/easyconfigs/l/LibLZF/LibLZF-3.6-GCCcore-12.3.0.eb
+++ /dev/null
@@ -1,31 +0,0 @@
-# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
-# Author: Denis Kristak
-# Update: Thomas Hoffmann (EMBL), Denis Kristak, Pavel Tománek (Inuits)
-easyblock = 'ConfigureMake'
-
-name = 'LibLZF'
-version = '3.6'
-
-homepage = 'http://oldhome.schmorp.de/marc/liblzf.html'
-description = """LibLZF is a very small data compression library. It consists of only two .c and two .h files
-and is very easy to incorporate into your own programs. The compression algorithm is very, very fast, yet still
-written in portable C."""
-
-toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
-
-source_urls = ['http://dist.schmorp.de/liblzf/Attic/']
-sources = ['liblzf-%(version)s.tar.gz']
-checksums = ['9c5de01f7b9ccae40c3f619d26a7abec9986c06c36d260c179cedd04b89fb46a']
-
-builddependencies = [
-    ('binutils', '2.40'),
-]
-
-sanity_check_commands = ['lzf -h']
-
-sanity_check_paths = {
-    'files': ['bin/lzf', 'lib/liblzf.a'],
-    'dirs': ['bin', 'lib'],
-}
-
-moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/l/libavif/libavif-1.0.4-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libavif/libavif-1.0.4-GCCcore-12.3.0.eb
deleted file mode 100644
index a5d73b0eb00..00000000000
--- a/easybuild/easyconfigs/l/libavif/libavif-1.0.4-GCCcore-12.3.0.eb
+++ /dev/null
@@ -1,34 +0,0 @@
-# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
-# Author: Denis Kristak (Inuits)
-# Update: Thomas Hoffmann (EMBL), Denis Kristak (Inuits), Pavel Tománek (Inuits)
-easyblock = 'CMakeMake'
-
-name = 'libavif'
-version = '1.0.4'
-
-homepage = 'https://github.com/AOMediaCodec/libavif'
-description = """This library aims to be a friendly, portable C implementation of the AV1 Image File Format,
-as described here: https://aomediacodec.github.io/av1-avif/
-"""
-
-toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
-
-source_urls = ['https://github.com/AOMediaCodec/libavif/archive/']
-sources = ['v%(version)s.tar.gz']
-checksums = ['dc56708c83a4b934a8af2b78f67f866ba2fb568605c7cf94312acf51ee57d146']
-
-builddependencies = [
-    ('CMake', '3.26.3'),
-    ('binutils', '2.40'),
-    ('Rust', '1.75.0'),
-    ('Meson', '1.1.1'),
-    ('Ninja', '1.11.1'),
-    ('NASM', '2.16.01'),
-]
-
-sanity_check_paths = {
-    'files': ['lib/libavif.%s' % SHLIB_EXT, 'include/avif/avif.h'],
-    'dirs': [],
-}
-
-moduleclass = 'tools'
diff --git a/easybuild/easyconfigs/l/libde265/libde265-1.0.15-GCC-12.3.0.eb b/easybuild/easyconfigs/l/libde265/libde265-1.0.15-GCC-12.3.0.eb
deleted file mode 100644
index 611c9fbcf33..00000000000
--- a/easybuild/easyconfigs/l/libde265/libde265-1.0.15-GCC-12.3.0.eb
+++ /dev/null
@@ -1,34 +0,0 @@
-# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
-# Author: Denis Kristak
-# Update: Pavel Tomának (Inuits)
-easyblock = 'CMakeMake'
-
-name = 'libde265'
-version = '1.0.15'
-
-homepage = 'https://github.com/strukturag/libde265'
-description = "libde265 is an open source implementation of the h.265 video codec"
-
-toolchain = {'name': 'GCC', 'version': '12.3.0'}
-
-source_urls = ['https://github.com/strukturag/libde265/releases/download/v%(version)s/']
-sources = [SOURCE_TAR_GZ]
-checksums = ['00251986c29d34d3af7117ed05874950c875dd9292d016be29d3b3762666511d']
-
-builddependencies = [
-    ('CMake', '3.26.3'),
-]
-
-configopts = "-DENABLE_DECODER=ON -DENABLE_ENCODER=ON"
-
-sanity_check_paths = {
-    'files': ['bin/dec265', 'bin/enc265', 'lib/libde265.%s' % SHLIB_EXT, 'lib/pkgconfig/libde265.pc'],
-    'dirs': ['include/libde265', 'lib/cmake/libde265'],
-}
-
-sanity_check_commands = [
-    "dec265 --help",
-    "enc265 --help",
-]
-
-moduleclass = 'tools'
diff --git a/easybuild/easyconfigs/l/libheif/libheif-1.17.6-GCC-12.3.0.eb b/easybuild/easyconfigs/l/libheif/libheif-1.17.6-GCC-12.3.0.eb
deleted file mode 100644
index e552b35a50b..00000000000
--- a/easybuild/easyconfigs/l/libheif/libheif-1.17.6-GCC-12.3.0.eb
+++ /dev/null
@@ -1,43 +0,0 @@
-# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
-# Author: Denis Kristak
-# Update: Pavel Tománek (Inuits)
-easyblock = 'CMakeMake'
-
-name = 'libheif'
-version = '1.17.6'
-
-homepage = 'https://github.com/strukturag/libheif'
-description = "libheif is an HEIF and AVIF file format decoder and encoder"
-
-toolchain = {'name': 'GCC', 'version': '12.3.0'}
-
-source_urls = ['https://github.com/strukturag/libheif/releases/download/v%(version)s/']
-sources = [SOURCE_TAR_GZ]
-checksums = ['8390baf4913eda0a183e132cec62b875fb2ef507ced5ddddc98dfd2f17780aee']
-
-builddependencies = [
-    ('CMake', '3.26.3'),
-]
-
-dependencies = [
-    ('libpng', '1.6.39'),
-    ('libjpeg-turbo', '2.1.5.1'),
-    ('libde265', '1.0.15'),
-    ('x265', '3.5'),
-    ('Gdk-Pixbuf', '2.42.10'),
-]
-
-# build both static and shared libraries
-configopts = [
-    "-DBUILD_SHARED_LIBS=OFF",
-    "-DBUILD_SHARED_LIBS=ON",
-]
-
-sanity_check_paths = {
-    'files': ['bin/heif-info', 'lib/libheif.a', 'lib/libheif.%s' % SHLIB_EXT, 'lib/pkgconfig/libheif.pc'],
-    'dirs': ['include/libheif'],
-}
-
-sanity_check_commands = ["heif-info --help"]
-
-moduleclass = 'tools'
diff --git a/easybuild/easyconfigs/l/libjxl/libjxl-0.8.2-foss-2023a.eb b/easybuild/easyconfigs/l/libjxl/libjxl-0.8.2-foss-2023a.eb
deleted file mode 100644
index ced70b9c630..00000000000
--- a/easybuild/easyconfigs/l/libjxl/libjxl-0.8.2-foss-2023a.eb
+++ /dev/null
@@ -1,52 +0,0 @@
-easyblock = 'CMakeMake'
-
-name = 'libjxl'
-version = '0.8.2'
-
-homepage = 'https://github.com/libjxl/libjxl'
-description = "JPEG XL image format reference implementation"
-
-toolchain = {'name': 'foss', 'version': '2023a'}
-
-github_account = 'libjxl'
-source_urls = [GITHUB_SOURCE]
-sources = ['v%(version)s.tar.gz']
-checksums = ['c70916fb3ed43784eb840f82f05d390053a558e2da106e40863919238fa7b420']
-
-builddependencies = [
-    ('binutils', '2.40'),
-    ('CMake', '3.26.3'),
-    ('googletest', '1.13.0'),
-    ('pkgconf', '1.9.5'),
-    ('Highway', '1.0.4'),  # Highway only has a static library
-]
-
-dependencies = [
-    ('LittleCMS', '2.15'),
-    ('Brotli', '1.0.9'),
-    ('libjpeg-turbo', '2.1.5.1'),
-    ('libpng', '1.6.39'),
-    ('zlib', '1.2.13'),
-    ('giflib', '5.2.1'),
-    ('libwebp', '1.3.1'),
-    ('OpenEXR', '3.1.7'),
-    ('gperftools', '2.12'),
-]
-
-configopts = '-DJPEGXL_WARNINGS_AS_ERRORS=OFF -DJPEGXL_ENABLE_SJPEG=OFF -DJPEGXL_ENABLE_SKCMS=OFF '
-# building man pages requires/uses asciidoc (which may be installed in OS, and may fail)
-configopts += '-DJPEGXL_ENABLE_MANPAGES=OFF '
-configopts += '-DJPEGXL_FORCE_SYSTEM_BROTLI=ON -DJPEGXL_FORCE_SYSTEM_HWY=ON '
-configopts += '-DJPEGXL_FORCE_SYSTEM_GTEST=ON -DJPEGXL_FORCE_SYSTEM_LCMS2=ON '
-
-sanity_check_paths = {
-    'files': ['bin/cjxl', 'bin/djxl', 'lib/libjxl.%s' % SHLIB_EXT],
-    'dirs': ['include/jxl'],
-}
-
-sanity_check_commands = [
-    "cjxl --help",
-    "djxl --help",
-]
-
-moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/l/libwebp/libwebp-1.3.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libwebp/libwebp-1.3.1-GCCcore-12.3.0.eb
deleted file mode 100644
index bc39f91e6af..00000000000
--- a/easybuild/easyconfigs/l/libwebp/libwebp-1.3.1-GCCcore-12.3.0.eb
+++ /dev/null
@@ -1,45 +0,0 @@
-easyblock = 'ConfigureMake'
-
-name = 'libwebp'
-version = '1.3.1'
-
-homepage = 'https://developers.google.com/speed/webp/'
-description = """WebP is a modern image format that provides superior
-lossless and lossy compression for images on the web. Using WebP,
-webmasters and web developers can create smaller, richer images that
-make the web faster."""
-
-toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
-toolchainopts = {'extra_cflags': '-fPIE'}
-
-source_urls = ['https://storage.googleapis.com/downloads.webmproject.org/releases/webp']
-sources = [SOURCELOWER_TAR_GZ]
-checksums = ['b3779627c2dfd31e3d8c4485962c2efe17785ef975e2be5c8c0c9e6cd3c4ef66']
-
-builddependencies = [
-    ('binutils', '2.40'),
-]
-dependencies = [
-    ('libjpeg-turbo', '2.1.5.1'),
-    ('libpng', '1.6.39'),
-    ('LibTIFF', '4.5.0'),
-    ('giflib', '5.2.1'),
-]
-
-configopts = '--enable-libwebpmux'
-
-local_headers, local_libs = (
-    ['decode.h', 'demux.h', 'encode.h', 'mux.h', 'mux_types.h', 'types.h'],
-    ['webp', 'webpdemux', 'webpmux']
-)
-
-sanity_check_paths = {
-    'files': (
-        ['include/webp/%s' % h for h in local_headers] +
-        ['lib/lib%s.a' % s for s in local_libs] +
-        ['lib/lib%s.%s' % (s, SHLIB_EXT) for s in local_libs]
-    ),
-    'dirs': ['lib/']
-}
-
-moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/z/Zopfli/Zopfli-1.0.3-GCCcore-12.3.0.eb b/easybuild/easyconfigs/z/Zopfli/Zopfli-1.0.3-GCCcore-12.3.0.eb
deleted file mode 100644
index b9186e52d16..00000000000
--- a/easybuild/easyconfigs/z/Zopfli/Zopfli-1.0.3-GCCcore-12.3.0.eb
+++ /dev/null
@@ -1,36 +0,0 @@
-# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
-# Updated: Thomas Hoffmann (EMBL), Denis Kristak (Inuits), Pavel Tománek (Inuits)
-easyblock = 'CMakeMake'
-
-name = 'Zopfli'
-version = '1.0.3'
-
-homepage = 'https://github.com/google/zopfli'
-description = """Zopfli Compression Algorithm is a compression library programmed in C to perform
-very good, but slow, deflate or zlib compression."""
-
-toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
-toolchainopts = {'pic': True}
-
-source_urls = ['https://github.com/google/zopfli/archive/refs/tags/']
-sources = ['%(namelower)s-%(version)s.tar.gz']
-checksums = ['e955a7739f71af37ef3349c4fa141c648e8775bceb2195be07e86f8e638814bd']
-
-builddependencies = [
-    ('CMake', '3.26.3'),
-    ('binutils', '2.40'),
-]
-
-configopts = [
-    '-DBUILD_SHARED_LIBS=ON',
-    '-DBUILD_SHARED_LIBS=OFF',
-]
-
-sanity_check_paths = {
-    'files': ['bin/zopfli', 'include/zopfli.h', 'lib/libzopfli.a', 'lib/libzopfli.%s' % SHLIB_EXT],
-    'dirs': [],
-}
-
-sanity_check_commands = ["zopfli --help"]
-
-moduleclass = 'tools'
diff --git a/easybuild/easyconfigs/z/zfp/zfp-1.0.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/z/zfp/zfp-1.0.1-GCCcore-12.3.0.eb
deleted file mode 100644
index 86aae25ec6e..00000000000
--- a/easybuild/easyconfigs/z/zfp/zfp-1.0.1-GCCcore-12.3.0.eb
+++ /dev/null
@@ -1,40 +0,0 @@
-# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
-# Author: Denis Kristak
-# Update: Thomas Hoffmann (EMBL), Pavel Tománek (Inuits)
-easyblock = 'MakeCp'
-
-name = 'zfp'
-version = '1.0.1'
-
-homepage = 'https://github.com/LLNL/zfp'
-description = """zfp is a compressed format for representing multidimensional floating-point and integer arrays.
-zfp provides compressed-array classes that support high throughput read and write random access to individual array
-elements. zfp also supports serial and parallel (OpenMP and CUDA) compression of whole arrays, e.g., for applications
-that read and write large data sets to and from disk."""
-
-toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
-toolchainopts = {'pic': True}
-
-source_urls = ['https://github.com/LLNL/zfp/archive']
-sources = ['%(version)s.tar.gz']
-checksums = ['4984db6a55bc919831966dd17ba5e47ca7ac58668f4fd278ebd98cd2200da66f']
-
-builddependencies = [
-    ('binutils', '2.40'),
-]
-
-prebuildopts = "sed -i 's/FLAGS = -O3/FLAGS = $CFLAGS/g' Makefile && "
-buildopts = 'ZFP_WITH_OPENMP=1'
-
-runtest = 'test'
-
-files_to_copy = ['bin', 'include', 'lib']
-
-sanity_check_paths = {
-    'files': ['bin/zfp', 'bin/testzfp', 'include/zfp.h', 'lib/libzfp.a'],
-    'dirs': ['include/zfp'],
-}
-
-sanity_check_commands = ["zfp --help 2>&1 | grep 'Usage: zfp'"]
-
-moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.1.6-GCCcore-12.3.0.eb b/easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.1.6-GCCcore-12.3.0.eb
deleted file mode 100644
index 67dab064f7a..00000000000
--- a/easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.1.6-GCCcore-12.3.0.eb
+++ /dev/null
@@ -1,30 +0,0 @@
-# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
-# Updated: Denis Kristak (Inuits)
-# Updated: Thomas Hoffmann (EMBL), Denis Kristak (Inuits), Pavel Tománek (Inuits)
-easyblock = 'CMakeMake'
-
-name = 'zlib-ng'
-version = '2.1.6'
-
-homepage = 'https://github.com/zlib-ng/zlib-ng'
-description = """zlib data compression library for the next generation systems"""
-
-toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
-
-source_urls = ['https://github.com/zlib-ng/zlib-ng/archive/']
-sources = ['%(version)s.tar.gz']
-checksums = ['a5d504c0d52e2e2721e7e7d86988dec2e290d723ced2307145dedd06aeb6fef2']
-
-builddependencies = [
-    ('CMake', '3.26.3'),
-    ('binutils', '2.40'),
-]
-
-configopts = ' -DZLIB_ENABLE_TESTS=True '
-
-sanity_check_paths = {
-    'files': ['include/zconf-ng.h', 'include/zlib-ng.h', 'lib/libz-ng.a', 'lib/libz-ng.%s' % SHLIB_EXT],
-    'dirs': [],
-}
-
-moduleclass = 'tools'

From 740a70dfd4a9d7cd4cc77786d43d50ce947e2552 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Wed, 5 Jun 2024 16:43:16 +0200
Subject: [PATCH 131/835] update imagecodecs version

---
 easybuild/easyconfigs/t/torch_em/torch_em-0.7.1-foss-2023a.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/t/torch_em/torch_em-0.7.1-foss-2023a.eb b/easybuild/easyconfigs/t/torch_em/torch_em-0.7.1-foss-2023a.eb
index d53c71b30d5..330527abd2c 100644
--- a/easybuild/easyconfigs/t/torch_em/torch_em-0.7.1-foss-2023a.eb
+++ b/easybuild/easyconfigs/t/torch_em/torch_em-0.7.1-foss-2023a.eb
@@ -18,7 +18,7 @@ dependencies = [
     ('Python', '3.11.3'),
     ('torchvision', '0.16.0'),
     ('h5py', '3.9.0'),
-    ('imagecodecs', '2023.1.23'),
+    ('imagecodecs', '2024.1.1'),
     ('tensorboard', '2.15.1'),
     ('tqdm', '4.66.1'),
     ('napari', '0.4.18'),

From 4da987b92d134fccb2048115e9bbfeeb9e6b2e9d Mon Sep 17 00:00:00 2001
From: Adam Huffman <12435+verdurin@users.noreply.github.com>
Date: Wed, 5 Jun 2024 16:15:52 +0000
Subject: [PATCH 132/835] Add missing rpmrebuild builddep

---
 .../easyconfigs/b/bcl-convert/bcl-convert-4.2.7-2el7.x86_64.eb  | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/easybuild/easyconfigs/b/bcl-convert/bcl-convert-4.2.7-2el7.x86_64.eb b/easybuild/easyconfigs/b/bcl-convert/bcl-convert-4.2.7-2el7.x86_64.eb
index db6e1f9feee..636a4e2a6b4 100644
--- a/easybuild/easyconfigs/b/bcl-convert/bcl-convert-4.2.7-2el7.x86_64.eb
+++ b/easybuild/easyconfigs/b/bcl-convert/bcl-convert-4.2.7-2el7.x86_64.eb
@@ -10,6 +10,8 @@ description = """The Illumina BCL Convert v4.0 is a standalone local software ap
 
 toolchain = SYSTEM
 
+builddependencies = [('rpmrebuild', '2.11')]
+
 source_urls = ['https://webdata.illumina.com/downloads/software/bcl-convert/']
 sources = ['bcl-convert-%(version)s.%(versionsuffix)s.rpm']
 checksums = ['ea508d763dc27d30d1a34f6a38d8da31ea67797d7b4971e8c10677bc48539565']

From 82889a3fb821091eef03901f37e6cf9cc70e2504 Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Wed, 5 Jun 2024 23:56:02 +0200
Subject: [PATCH 133/835] run custom configure in CORSIKA v77550 that enables
 MPI

---
 .../c/CORSIKA/CORSIKA-77550-foss-2023a.eb     | 26 ++++++++++---------
 1 file changed, 14 insertions(+), 12 deletions(-)

diff --git a/easybuild/easyconfigs/c/CORSIKA/CORSIKA-77550-foss-2023a.eb b/easybuild/easyconfigs/c/CORSIKA/CORSIKA-77550-foss-2023a.eb
index 0a11129ccb9..c516f698db4 100644
--- a/easybuild/easyconfigs/c/CORSIKA/CORSIKA-77550-foss-2023a.eb
+++ b/easybuild/easyconfigs/c/CORSIKA/CORSIKA-77550-foss-2023a.eb
@@ -1,4 +1,4 @@
-easyblock = "MakeCp"
+easyblock = "ConfigureMake"
 
 name = 'CORSIKA'
 version = '77550'
@@ -10,7 +10,7 @@ particles. Protons, light nuclei up to iron, photons, and many other particles
 may be treated as primaries."""
 
 toolchain = {'name': 'foss', 'version': '2023a'}
-toolchainopts = {'pic': True, 'usempi': True}
+toolchainopts = {'usempi': True}
 
 download_instructions = "Sources have to be requested to the developers"
 sources = [SOURCELOWER_TAR_GZ]
@@ -20,21 +20,23 @@ dependencies = [
     ("ROOT", "6.30.06"),
 ]
 
-# run in non-interactive mode
-build_cmd = "./coconut --batch"
-# coconut script does not accept "-j"
+# custom coconut script does not recognize -j
 parallel = False
 
-files_to_copy = [
-    (['run/corsika77550Linux_EPOS_urqmd'], 'bin'),
-]
+# execute ./coconut manually with your own options and extract configure command from top of config.log
+configopts = "CORDETECTOR=HORIZONTAL CORTIMELIB=TIMEAUTO CORHEMODEL=QGSJETII CORLEMODEL=URQMD "
+configopts += "--enable-UPWARD --enable-SLANT --enable-THIN --enable-COREAS "
+configopts += "--enable-PARALLEL --with-mpirunner-lib --enable-PARALLELIB "
 
-postinstallcmds = [
-    "cd %(installdir)s/bin && ln -s corsika77550Linux_EPOS_urqmd corsika",
-]
+build_cmd = "./coconut"
+buildopts = "--batch"
+
+preinstallopts = "mkdir -p %(installdir)s/bin && "
+install_cmd = "cp"
+installopts = "%(builddir)s/%(namelower)s-%(version)s/run/%(namelower)s%(version)s* %(installdir)s/bin/"
 
 sanity_check_paths = {
-    'files': ['bin/corsika', 'bin/corsika77550Linux_EPOS_urqmd'],
+    'files': ['bin/corsika77550Linux_QGSII_urqmd_thin_coreas_parallel'],
     'dirs': []
 }
 

From b427446d0374a26411df3086cd309f649bf4e87c Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Thu, 6 Jun 2024 11:38:14 +0200
Subject: [PATCH 134/835] fix jax

---
 easybuild/easyconfigs/j/jax/jax-0.4.25-foss-2023a.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/j/jax/jax-0.4.25-foss-2023a.eb b/easybuild/easyconfigs/j/jax/jax-0.4.25-foss-2023a.eb
index d1e5fc1aabd..9cbbc9b1579 100644
--- a/easybuild/easyconfigs/j/jax/jax-0.4.25-foss-2023a.eb
+++ b/easybuild/easyconfigs/j/jax/jax-0.4.25-foss-2023a.eb
@@ -1,7 +1,7 @@
 # This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
 # Author: Denis Kristak
 # Updated by: Alex Domingo (Vrije Universiteit Brussel), Pavel Tománek (Inuits)
-    # Update v0.4.25 based on: https://github.com/easybuilders/easybuild-easyconfigs/pull/20119
+# Update v0.4.25 based on: https://github.com/easybuilders/easybuild-easyconfigs/pull/20119
 
 easyblock = 'PythonBundle'
 

From c5e79fa22323c943bf116dc6baffaeb721d23f41 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Thu, 6 Jun 2024 11:55:43 +0200
Subject: [PATCH 135/835] sync libwebp with new version

---
 .../l/libwebp/libwebp-1.3.1-GCCcore-12.3.0.eb | 45 +++++++++++++++++++
 1 file changed, 45 insertions(+)
 create mode 100644 easybuild/easyconfigs/l/libwebp/libwebp-1.3.1-GCCcore-12.3.0.eb

diff --git a/easybuild/easyconfigs/l/libwebp/libwebp-1.3.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libwebp/libwebp-1.3.1-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..7a8453a029c
--- /dev/null
+++ b/easybuild/easyconfigs/l/libwebp/libwebp-1.3.1-GCCcore-12.3.0.eb
@@ -0,0 +1,45 @@
+easyblock = 'ConfigureMake'
+
+name = 'libwebp'
+version = '1.3.1'
+
+homepage = 'https://developers.google.com/speed/webp/'
+description = """WebP is a modern image format that provides superior
+lossless and lossy compression for images on the web. Using WebP,
+webmasters and web developers can create smaller, richer images that
+make the web faster."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://storage.googleapis.com/downloads.webmproject.org/releases/webp']
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['b3779627c2dfd31e3d8c4485962c2efe17785ef975e2be5c8c0c9e6cd3c4ef66']
+
+builddependencies = [
+    ('binutils', '2.40'),
+]
+dependencies = [
+    ('libjpeg-turbo', '2.1.5.1'),
+    ('libpng', '1.6.39'),
+    ('LibTIFF', '4.5.0'),
+    ('giflib', '5.2.1'),
+]
+
+configopts = '--enable-libwebpmux'
+
+local_headers, local_libs = (
+    ['decode.h', 'demux.h', 'encode.h', 'mux.h', 'mux_types.h', 'types.h'],
+    ['webp', 'webpdemux', 'webpmux']
+)
+
+sanity_check_paths = {
+    'files': (
+        ['include/webp/%s' % h for h in local_headers] +
+        ['lib/lib%s.a' % s for s in local_libs] +
+        ['lib/lib%s.%s' % (s, SHLIB_EXT) for s in local_libs]
+    ),
+    'dirs': ['lib/']
+}
+
+moduleclass = 'lib'

From 0de008c09fc276734514fe3c2e62ef70fbd6973e Mon Sep 17 00:00:00 2001
From: yqshao <yunqi.shao@chalmers.se>
Date: Sat, 13 Apr 2024 15:22:18 +0000
Subject: [PATCH 136/835] adding easyconfigs:
 TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb

---
 ...ensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb | 223 ++++++++++++++++++
 1 file changed, 223 insertions(+)
 create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb

diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb
new file mode 100644
index 00000000000..156ab402187
--- /dev/null
+++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb
@@ -0,0 +1,223 @@
+easyblock = 'PythonBundle'
+
+name = 'TensorFlow'
+version = '2.15.1'
+versionsuffix = '-CUDA-%(cudaver)s'
+
+homepage = 'https://www.tensorflow.org/'
+description = "An open-source software library for Machine Intelligence"
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+toolchainopts = {'pic': True}
+
+use_pip = True
+sanity_pip_check = True
+
+builddependencies = [
+    ('Bazel', '6.1.0'),
+    # git 2.x required, see also https://github.com/tensorflow/tensorflow/issues/29053
+    ('git', '2.41.0', '-nodocs'),
+    ('pybind11', '2.11.1'),
+    ('UnZip', '6.0'),
+    # Required to build some of the extensions
+    ('poetry', '1.5.1'),
+    # Protobuf disabled since 2.13.0 easyconfigs:
+    # Compiling with system protobuf don't seem to work, see:
+    # https://github.com/tensorflow/tensorflow/issues/61593
+    # ('protobuf', '24.0'),
+]
+
+dependencies = [
+    ('CUDA', '12.1.1', '', SYSTEM),
+    ('cuDNN', '8.9.2.26', versionsuffix, SYSTEM),
+    ('NCCL', '2.18.3', versionsuffix),
+    ('Python', '3.11.3'),
+    ('h5py', '3.9.0'),
+    ('cURL', '8.0.1'),
+    ('dill', '0.3.7'),
+    ('double-conversion', '3.3.0'),
+    ('flatbuffers', '23.5.26'),
+    ('flatbuffers-python', '23.5.26'),
+    ('giflib', '5.2.1'),
+    ('hwloc', '2.9.1'),
+    ('ICU', '73.2'),
+    ('JsonCpp', '1.9.5'),
+    ('libjpeg-turbo', '2.1.5.1'),
+    ('ml_dtypes', '0.3.2'),
+    ('NASM', '2.16.01'),
+    ('nsync', '1.26.0'),
+    ('SQLite', '3.42.0'),
+    ('patchelf', '0.18.0'),
+    ('libpng', '1.6.39'),
+    ('snappy', '1.1.10'),
+    ('zlib', '1.2.13'),
+    ('grpcio', '1.57.0'),
+]
+
+# Dependencies created and updated using findPythonDeps, see:
+# https://docs.easybuild.io/api/easybuild/scripts/findPythonDeps
+# Notable changes since 2.13.0-foss-2023a
+# - tensoboard-wit deprecated as of tensorboard 2.13.0 (tensorboard@33abcb54d7)
+# - portpicker for tests no longer needed (TF@e85860e838)
+# - opt_einsum now comes from ml_dtypes
+exts_list = [
+    ('wrapt', '1.14.1', {
+        'checksums': ['380a85cf89e0e69b7cfbe2ea9f765f004ff419f34194018a6827ac0e3edfed4d'],
+    }),
+    ('termcolor', '2.3.0', {
+        'checksums': ['b5b08f68937f138fe92f6c089b99f1e2da0ae56c52b78bf7075fd95420fd9a5a'],
+    }),
+    ('tensorflow-estimator', '2.15.0', {
+        'source_tmpl': 'tensorflow_estimator-%(version)s-py2.py3-none-any.whl',
+        'checksums': ['aedf21eec7fb2dc91150fc91a1ce12bc44dbb72278a08b58e79ff87c9e28f153'],
+    }),
+    ('Werkzeug', '3.0.2', {
+        'source_tmpl': SOURCELOWER_TAR_GZ,
+        'checksums': ['e39b645a6ac92822588e7b39a692e7828724ceae0b0d702ef96701f90e70128d'],
+    }),
+    ('tensorboard-data-server', '0.7.2', {
+        'source_tmpl': 'tensorboard_data_server-%(version)s-py3-none-any.whl',
+        'checksums': ['7e0610d205889588983836ec05dc098e80f97b7e7bbff7e994ebb78f578d0ddb'],
+    }),
+    ('Markdown', '3.6', {
+        'checksums': ['ed4f41f6daecbeeb96e576ce414c41d2d876daa9a16cb35fa8ed8c2ddfad0224'],
+    }),
+    ('oauthlib', '3.2.2', {
+        'checksums': ['9859c40929662bec5d64f34d01c99e093149682a3f38915dc0655d5a633dd918'],
+    }),
+    ('requests-oauthlib', '2.0.0', {
+        'checksums': ['b3dffaebd884d8cd778494369603a9e7b58d29111bf6b41bdc2dcd87203af4e9'],
+    }),
+    ('rsa', '4.9', {
+        'checksums': ['e38464a49c6c85d7f1351b0126661487a7e0a14a50f1675ec50eb34d4f20ef21'],
+    }),
+    ('pyasn1-modules', '0.4.0', {
+        'source_tmpl': 'pyasn1_modules-%(version)s.tar.gz',
+        'checksums': ['831dbcea1b177b28c9baddf4c6d1013c24c3accd14a1873fffaa6a2e905f17b6'],
+    }),
+    ('cachetools', '5.3.3', {
+        'checksums': ['ba29e2dfa0b8b556606f097407ed1aa62080ee108ab0dc5ec9d6a723a007d105'],
+    }),
+    ('google-auth', '2.29.0', {
+        'modulename': 'google.auth',
+        'checksums': ['672dff332d073227550ffc7457868ac4218d6c500b155fe6cc17d2b13602c360'],
+    }),
+    ('google-auth-oauthlib', '1.2.0', {
+        'checksums': ['292d2d3783349f2b0734a0a0207b1e1e322ac193c2c09d8f7c613fb7cc501ea8'],
+    }),
+    ('absl-py', '2.1.0', {
+        'modulename': 'absl',
+        'checksums': ['7820790efbb316739cde8b4e19357243fc3608a152024288513dd968d7d959ff'],
+    }),
+    ('tensorboard', '2.15.2', {
+        'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl',
+        'checksums': ['a6f6443728064d962caea6d34653e220e34ef8df764cb06a8212c17e1a8f0622'],
+    }),
+    ('keras', '2.15.0', {
+        'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl',
+        'checksums': ['2dcc6d2e30cf9c951064b63c1f4c404b966c59caf09e01f3549138ec8ee0dd1f'],
+    }),
+    ('google-pasta', '0.2.0', {
+        'modulename': 'pasta',
+        'checksums': ['c9f2c8dfc8f96d0d5808299920721be30c9eec37f2389f28904f454565c8a16e'],
+    }),
+    ('astunparse', '1.6.3', {
+        'checksums': ['5ad93a8456f0d084c3456d059fd9a92cce667963232cbf763eac3bc5b7940872'],
+    }),
+    # Required by tests
+    ('tblib', '3.0.0', {
+        'checksums': ['93622790a0a29e04f0346458face1e144dc4d32f493714c6c3dff82a4adb77e6'],
+    }),
+    ('astor', '0.8.1', {
+        'checksums': ['6a6effda93f4e1ce9f618779b2dd1d9d84f1e32812c23a29b3fff6fd7f63fa5e'],
+    }),
+    # Optional profile plugin + dependency
+    ('gviz-api', '1.10.0', {
+        'source_tmpl': 'gviz_api-%(version)s.tar.gz',
+        'checksums': ['846692dd8cc73224fc31b18e41589bd934e1cc05090c6576af4b4b26c2e71b90'],
+    }),
+    ('tensorboard-plugin-profile', '2.15.1', {
+        'source_tmpl': 'tensorboard_plugin_profile-%(version)s.tar.gz',
+        'checksums': ['84bb33e446eb4a9c0616f669fc6a42cdd40eadd9ae1d74bf756f4f0479993273'],
+    }),
+    (name, version, {
+        'patches': [
+            'TensorFlow-2.4.0_dont-use-var-lock.patch',
+            'TensorFlow-2.13.0_add-missing-system-protobuf-targets.patch',
+            'TensorFlow-2.15.1_remove-duplicate-gpu-tests.patch',
+            'TensorFlow-2.15.1_remove-libclang-dep.patch',
+            'TensorFlow-2.15.1_remove-io-gcs-filesystem-dep.patch',
+            'TensorFlow-2.15.1_add-default-shell-env.patch',
+            'TensorFlow-2.15.1_fix-flatbuffer-license.patch',
+            'TensorFlow-2.15.1_fix-pybind11-build.patch',
+            'TensorFlow-2.15.1_fix-cuda_build_defs.patch',
+        ],
+        'source_tmpl': 'v%(version)s.tar.gz',
+        'source_urls': ['https://github.com/tensorflow/tensorflow/archive/'],
+        'test_script': 'TensorFlow-2.x_mnist-test.py',
+        'test_tag_filters_cpu': (
+            '-gpu,-tpu,-no_cuda_on_cpu_tap,'
+            '-no_pip,-no_oss,-oss_serial,-benchmark-test,-v1only'
+        ),
+        'test_tag_filters_gpu': (
+            'gpu,-no_gpu,-nogpu,-gpu_cupti,-no_cuda11,'
+            '-no_pip,-no_oss,-oss_serial,-benchmark-test,-v1only'
+        ),
+        'test_targets': [
+            '//tensorflow/core/...',
+            '-//tensorflow/core:example_java_proto',
+            '-//tensorflow/core/example:example_protos_closure',
+            '//tensorflow/cc/...',
+            '//tensorflow/c/...',
+            '//tensorflow/python/...',
+            '-//tensorflow/c/eager:c_api_test_gpu',
+            '-//tensorflow/c/eager:c_api_distributed_test',
+            '-//tensorflow/c/eager:c_api_distributed_test_gpu',
+            '-//tensorflow/c/eager:c_api_cluster_test_gpu',
+            '-//tensorflow/c/eager:c_api_remote_function_test_gpu',
+            '-//tensorflow/c/eager:c_api_remote_test_gpu',
+            '-//tensorflow/core/common_runtime:collective_param_resolver_local_test',
+            '-//tensorflow/core/kernels/mkl:mkl_fused_ops_test',
+            '-//tensorflow/core/kernels/mkl:mkl_fused_batch_norm_op_test',
+            '-//tensorflow/core/ir/importexport/tests/roundtrip/...',
+        ],
+        'testopts': '--test_env=HOME=/tmp --test_timeout=3600 --test_size_filters=small ',
+        'testopts_gpu': (
+            '--test_env=HOME=/tmp --test_timeout=3600 --test_size_filters=small '
+            '--run_under=//tensorflow/tools/ci_build/gpu_build:parallel_gpu_execute '
+        ),
+        'with_xla': True,
+        'checksums': [
+            {'v2.15.1.tar.gz': 'f36416d831f06fe866e149c7cd752da410a11178b01ff5620e9f265511ed57cf'},
+            {'TensorFlow-2.4.0_dont-use-var-lock.patch':
+             'b14f2493fd2edf79abd1c4f2dde6c98a3e7d5cb9c25ab9386df874d5f072d6b5'},
+            {'TensorFlow-2.13.0_add-missing-system-protobuf-targets.patch':
+             '77d8c8a5627493fc7c38b4de79d49e60ff6628b05ff969f4cd3ff9857176c459'},
+            {'TensorFlow-2.15.1_remove-duplicate-gpu-tests.patch':
+             'd8810d5b875de5be8603afd743774ce9dd8c0d4a82314c7fe2f284a080be7498'},
+            {'TensorFlow-2.15.1_remove-libclang-dep.patch':
+             '871b2f0221b7a150ac9f563ffad7187e052a7eedd95c20fb4524987d7edb6f21'},
+            {'TensorFlow-2.15.1_remove-io-gcs-filesystem-dep.patch':
+             'eba7351a4b0696c589b9c507bacb0257ebce8c39fde39ab72d5d6a69deaaec02'},
+            {'TensorFlow-2.15.1_add-default-shell-env.patch':
+             '3d5196b4bf2e91048dc8a18f9e8f487a223fcd973d6302e80b0d4000ea3d652b'},
+            {'TensorFlow-2.15.1_fix-flatbuffer-license.patch':
+             '2c04d5095977a628a238dbf93c5fada7159c86752a7183e64e0cf7c7ab00caf4'},
+            {'TensorFlow-2.15.1_fix-pybind11-build.patch':
+             '3bb350ac92ab99c63c951c96b3b0160699f5f16822b64f72111ebfd2275cafce'},
+            {'TensorFlow-2.15.1_fix-cuda_build_defs.patch':
+             '9bae97c04a3d64f237e772161ac3a2854bd658fed2034295484aad197175f9ab'},
+        ],
+    }),
+]
+
+#  Taken from tensorboard-2.15.1-gfbf-2023a.eb:
+#  Relax restriction on protobuf dependency as issue was fixed
+#  in https://github.com/protocolbuffers/upb/pull/1514
+#  see also: https://github.com/easybuilders/easybuild-easyconfigs/pull/19671
+postinstallcmds = [
+    'sed -i "s/Requires-Dist: protobuf.*/Requires-Dist: protobuf >=3.19.6/g" ' +
+    '%(installdir)s/lib/python%(pyshortver)s/site-packages/tensorboard-2.15.2.dist-info/METADATA',
+]
+
+moduleclass = 'lib'

From d2f85a3eca36a5c68ed19283b247d7a7cf4ad41b Mon Sep 17 00:00:00 2001
From: Yunqi Shao <yunqi.shao@chalmers.se>
Date: Fri, 12 Apr 2024 23:13:54 +0200
Subject: [PATCH 137/835] Add patches for TensorFlow-2.15.1 w/ CUDA 12.1.1

---
 ...ensorFlow-2.15.1_fix-cuda_build_defs.patch | 36 ++++++++++++
 ...ow-2.15.1_remove-duplicate-gpu-tests.patch | 55 +++++++++++++++++++
 2 files changed, 91 insertions(+)
 create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_fix-cuda_build_defs.patch
 create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_remove-duplicate-gpu-tests.patch

diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_fix-cuda_build_defs.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_fix-cuda_build_defs.patch
new file mode 100644
index 00000000000..4f995b7372c
--- /dev/null
+++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_fix-cuda_build_defs.patch
@@ -0,0 +1,36 @@
+diff --git a/third_party/nccl/system.BUILD.tpl b/third_party/nccl/system.BUILD.tpl
+index 405d1e7298b..6e2a22a950b 100644
+--- a/third_party/nccl/system.BUILD.tpl
++++ b/third_party/nccl/system.BUILD.tpl
+@@ -1,6 +1,6 @@
+ load("@bazel_skylib//rules:write_file.bzl", "write_file")
+ load(
+-    "@org_tensorflow//tensorflow/platform/default:cuda_build_defs.bzl",
++    "@local_tsl//tsl/platform/default:cuda_build_defs.bzl",
+     "cuda_rpath_flags"
+ )
+ 
+diff --git a/third_party/xla/third_party/nccl/system.BUILD.tpl b/third_party/xla/third_party/nccl/system.BUILD.tpl
+index 13328fdeeac..6e2a22a950b 100644
+--- a/third_party/xla/third_party/nccl/system.BUILD.tpl
++++ b/third_party/xla/third_party/nccl/system.BUILD.tpl
+@@ -1,6 +1,6 @@
+ load("@bazel_skylib//rules:write_file.bzl", "write_file")
+ load(
+-    "@local_xla//tensorflow/platform/default:cuda_build_defs.bzl",
++    "@local_tsl//tsl/platform/default:cuda_build_defs.bzl",
+     "cuda_rpath_flags"
+ )
+ 
+diff --git a/third_party/xla/third_party/tsl/third_party/nccl/system.BUILD.tpl b/third_party/xla/third_party/tsl/third_party/nccl/system.BUILD.tpl
+index b45138eaa79..6e2a22a950b 100644
+--- a/third_party/xla/third_party/tsl/third_party/nccl/system.BUILD.tpl
++++ b/third_party/xla/third_party/tsl/third_party/nccl/system.BUILD.tpl
+@@ -1,6 +1,6 @@
+ load("@bazel_skylib//rules:write_file.bzl", "write_file")
+ load(
+-    "@local_tsl//tensorflow/platform/default:cuda_build_defs.bzl",
++    "@local_tsl//tsl/platform/default:cuda_build_defs.bzl",
+     "cuda_rpath_flags"
+ )
+ 
diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_remove-duplicate-gpu-tests.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_remove-duplicate-gpu-tests.patch
new file mode 100644
index 00000000000..7c6d72c89c9
--- /dev/null
+++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_remove-duplicate-gpu-tests.patch
@@ -0,0 +1,55 @@
+TensorFlow adds some GPU tests twice increasing the runtime of the test suite.
+This filters out the test part meant for CPU.
+
+See https://github.com/tensorflow/tensorflow/issues/47081
+From https://github.com/tensorflow/tensorflow/pull/59129
+
+Author: Alexander Grund (TU Dresden)
+---
+ tensorflow/tensorflow.bzl | 33 +++++++++++++++++----------------
+ 1 file changed, 17 insertions(+), 16 deletions(-)
+
+diff --git a/tensorflow/tensorflow.bzl b/tensorflow/tensorflow.bzl
+index a1531f55cca..3b9c977dcc4 100644
+--- a/tensorflow/tensorflow.bzl
++++ b/tensorflow/tensorflow.bzl
+@@ -1626,22 +1626,23 @@ def tf_gpu_cc_test(
+         linkopts = [],
+         **kwargs):
+     targets = []
+-    tf_cc_test(
+-        name = name,
+-        size = size,
+-        srcs = srcs,
+-        args = args,
+-        data = data,
+-        extra_copts = extra_copts + if_cuda(["-DNV_CUDNN_DISABLE_EXCEPTION"]),
+-        kernels = kernels,
+-        linkopts = linkopts,
+-        linkstatic = linkstatic,
+-        suffix = "_cpu",
+-        tags = tags,
+-        deps = deps,
+-        **kwargs
+-    )
+-    targets.append(name + "_cpu")
++    if 'gpu' not in tags:
++        tf_cc_test(
++            name = name,
++            size = size,
++            srcs = srcs,
++            args = args,
++            data = data,
++            extra_copts = extra_copts + if_cuda(["-DNV_CUDNN_DISABLE_EXCEPTION"]),
++            kernels = kernels,
++            linkopts = linkopts,
++            linkstatic = linkstatic,
++            suffix = "_cpu",
++            tags = tags,
++            deps = deps,
++            **kwargs
++        )
++        targets.append(name + "_cpu")
+     tf_cc_test(
+         name = name,
+         size = size,

From 9b6a94984a15c1bf303b85ecaf6f3077bf43cd13 Mon Sep 17 00:00:00 2001
From: Yunqi Shao <yunqi.shao@chalmers.se>
Date: Fri, 7 Jun 2024 10:27:46 +0200
Subject: [PATCH 138/835] Add comment for cuda_build_defs patch

---
 .../t/TensorFlow/TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb  | 2 +-
 .../t/TensorFlow/TensorFlow-2.15.1_fix-cuda_build_defs.patch  | 4 ++++
 2 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb
index 156ab402187..f140621e37f 100644
--- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb
+++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb
@@ -206,7 +206,7 @@ exts_list = [
             {'TensorFlow-2.15.1_fix-pybind11-build.patch':
              '3bb350ac92ab99c63c951c96b3b0160699f5f16822b64f72111ebfd2275cafce'},
             {'TensorFlow-2.15.1_fix-cuda_build_defs.patch':
-             '9bae97c04a3d64f237e772161ac3a2854bd658fed2034295484aad197175f9ab'},
+             '091581a7c4fc2fc7af282cab6661632c29029d2f36eccb6695ffa5783e065f88'},
         ],
     }),
 ]
diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_fix-cuda_build_defs.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_fix-cuda_build_defs.patch
index 4f995b7372c..0982df21bb9 100644
--- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_fix-cuda_build_defs.patch
+++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_fix-cuda_build_defs.patch
@@ -1,3 +1,7 @@
+Backport cuda_build_defs path fix for TF 2.15, see:
+
+https://github.com/tensorflow/tensorflow/commit/1536f2ca228099f0cf7793d3031d9b9bebbf03ed
+
 diff --git a/third_party/nccl/system.BUILD.tpl b/third_party/nccl/system.BUILD.tpl
 index 405d1e7298b..6e2a22a950b 100644
 --- a/third_party/nccl/system.BUILD.tpl

From eb07efa8b526a9416ea4b99babbbcf474db2db86 Mon Sep 17 00:00:00 2001
From: WilleBell <cintiawillemyns@gmail.com>
Date: Fri, 7 Jun 2024 11:04:02 +0200
Subject: [PATCH 139/835] adding easyconfigs:
 langchain-mistralai-0.1.8-foss-2023a.eb

---
 .../langchain-mistralai-0.1.8-foss-2023a.eb   | 60 +++++++++++++++++++
 1 file changed, 60 insertions(+)
 create mode 100644 easybuild/easyconfigs/l/langchain-mistralai/langchain-mistralai-0.1.8-foss-2023a.eb

diff --git a/easybuild/easyconfigs/l/langchain-mistralai/langchain-mistralai-0.1.8-foss-2023a.eb b/easybuild/easyconfigs/l/langchain-mistralai/langchain-mistralai-0.1.8-foss-2023a.eb
new file mode 100644
index 00000000000..0060ac5fe60
--- /dev/null
+++ b/easybuild/easyconfigs/l/langchain-mistralai/langchain-mistralai-0.1.8-foss-2023a.eb
@@ -0,0 +1,60 @@
+easyblock = 'PythonBundle'
+
+name = 'langchain-mistralai'
+version = '0.1.8'
+
+homepage = 'https://github.com/langchain-ai/langchain'
+description = """
+This package contains the LangChain integrations for MistralAI through their mistralai SDK.
+"""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+builddependencies = [
+    ('poetry', '1.5.1'),
+]
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('LangChain', '0.2.1'),
+    ('tokenizers', '0.15.2'),
+    ('jiter', '0.4.1'),
+]
+
+
+exts_list = [
+    ('langchain-core', '0.2.3', {
+        'sources': ['langchain_core-%(version)s.tar.gz'],
+        'checksums': ['fbc75a64b9c0b7655d96ca57a707df1e6c09efc1539c36adbd73260612549810'],
+    }),
+    ('anyio', '4.4.0', {
+        'checksums': ['5aadc6a1bbb7cdb0bede386cac5e2940f5e2ff3aa20277e991cf028e0585ce94'],
+    }),
+    ('h11', '0.14.0', {
+        'checksums': ['8f19fbbe99e72420ff35c00b27a34cb9937e902a8b810e2c88300c6f0a3b699d'],
+    }),
+    ('httpcore', '1.0.5', {
+        'checksums': ['34a38e2f9291467ee3b44e89dd52615370e152954ba21721378a87b2960f7a61'],
+    }),
+    ('httpx', '0.25.2', {
+        'checksums': ['8b8fcaa0c8ea7b05edd69a094e63a2094c4efcb48129fb757361bc423c0ad9e8'],
+    }),
+    ('httpx-sse', '0.4.0', {
+        'checksums': ['1e81a3a3070ce322add1d3529ed42eb5f70817f45ed6ec915ab753f961139721'],
+    }),
+    ('sniffio', '1.3.1', {
+        'checksums': ['f4324edc670a0f49750a81b895f35c3adb843cca46f0530f79fc1babb23789dc'],
+    }),
+    ('mistralai', '0.4.0', {
+        'checksums': ['1f21f02dec1fd6fefe12ca100d5937fd62542c11008c193d16df6f4a2d8554da'],
+    }),
+    (name, version, {
+        'sources': ['langchain_mistralai-%(version)s.tar.gz'],
+        'checksums': ['dc328f7aedfd9e88eeb79de5692dfc3907793b82ef59f0d6722d19c1c8bfcdc2'],
+    }),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+moduleclass = 'ai'

From 869b6507974a65c3c62b2869519de32c404002bc Mon Sep 17 00:00:00 2001
From: Simon Pinches <Simon.Pinches@iter.org>
Date: Fri, 7 Jun 2024 11:11:20 +0200
Subject: [PATCH 140/835] adding easyconfigs:
 makedepend-1.0.9-GCCcore-13.2.0.eb

---
 .../makedepend-1.0.9-GCCcore-13.2.0.eb        | 26 +++++++++++++++++++
 1 file changed, 26 insertions(+)
 create mode 100644 easybuild/easyconfigs/m/makedepend/makedepend-1.0.9-GCCcore-13.2.0.eb

diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.9-GCCcore-13.2.0.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.9-GCCcore-13.2.0.eb
new file mode 100644
index 00000000000..94178adcc23
--- /dev/null
+++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.9-GCCcore-13.2.0.eb
@@ -0,0 +1,26 @@
+easyblock = 'ConfigureMake'
+
+name = 'makedepend'
+version = '1.0.9'
+
+homepage = 'https://linux.die.net/man/1/makedepend'
+description = "The makedepend package contains a C-preprocessor like utility to determine build-time dependencies."
+
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
+
+source_urls = [XORG_UTIL_SOURCE]
+sources = [SOURCE_TAR_GZ]
+checksums = ['bc94ffda6cd4671603a69c39dbe8f96b317707b9185b2aaa3b54b5d134b41884']
+
+builddependencies = [
+    ('binutils', '2.40'),
+    ('xproto', '7.0.31'),
+    ('xorg-macros', '1.20.0'),
+]
+
+sanity_check_paths = {
+    'files': ['bin/makedepend'],
+    'dirs': [],
+}
+
+moduleclass = 'devel'

From 40eff61e36fd217d6a9bfa5f755c669d512c6d8e Mon Sep 17 00:00:00 2001
From: Simon Pinches <Simon.Pinches@iter.org>
Date: Fri, 7 Jun 2024 11:25:42 +0200
Subject: [PATCH 141/835] adding easyconfigs: xarray-2024.5.0-gfbf-2023b.eb

---
 .../x/xarray/xarray-2024.5.0-gfbf-2023b.eb    | 28 +++++++++++++++++++
 1 file changed, 28 insertions(+)
 create mode 100644 easybuild/easyconfigs/x/xarray/xarray-2024.5.0-gfbf-2023b.eb

diff --git a/easybuild/easyconfigs/x/xarray/xarray-2024.5.0-gfbf-2023b.eb b/easybuild/easyconfigs/x/xarray/xarray-2024.5.0-gfbf-2023b.eb
new file mode 100644
index 00000000000..09e90322293
--- /dev/null
+++ b/easybuild/easyconfigs/x/xarray/xarray-2024.5.0-gfbf-2023b.eb
@@ -0,0 +1,28 @@
+easyblock = 'PythonBundle'
+
+name = 'xarray'
+version = '2024.5.0'
+
+homepage = 'https://github.com/pydata/xarray'
+description = """xarray (formerly xray) is an open source project and Python package that aims to bring
+ the labeled data power of pandas to the physical sciences, by providing N-dimensional variants of the
+ core pandas data structures."""
+
+toolchain = {'name': 'gfbf', 'version': '2023b'}
+
+dependencies = [
+    ('Python', '3.11.5'),
+    ('SciPy-bundle', '2023.11'),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    (name, version, {
+        'preinstallopts': """sed -i 's/^dynamic = .*version.*/version = "%(version)s"/g' pyproject.toml && """,
+        'checksums': ['e0eb1cb265f265126795f388ed9591f3c752f2aca491f6c0576711fd15b708f2'],
+    }),
+]
+
+moduleclass = 'data'

From d5621111690b2a9b7568c867696ae4347201a365 Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Fri, 7 Jun 2024 11:37:31 +0200
Subject: [PATCH 142/835] adding easyconfigs: regionmask-0.12.1-foss-2023a.eb

---
 .../regionmask-0.12.1-foss-2023a.eb           | 31 +++++++++++++++++++
 1 file changed, 31 insertions(+)
 create mode 100644 easybuild/easyconfigs/r/regionmask/regionmask-0.12.1-foss-2023a.eb

diff --git a/easybuild/easyconfigs/r/regionmask/regionmask-0.12.1-foss-2023a.eb b/easybuild/easyconfigs/r/regionmask/regionmask-0.12.1-foss-2023a.eb
new file mode 100644
index 00000000000..4172bf592e3
--- /dev/null
+++ b/easybuild/easyconfigs/r/regionmask/regionmask-0.12.1-foss-2023a.eb
@@ -0,0 +1,31 @@
+easyblock = 'PythonBundle'
+
+name = 'regionmask'
+version = '0.12.1'
+
+homepage = 'https://regionmask.readthedocs.io'
+description = """regionmask creates masks of geographical regions. It determines to which
+geographic region each grid point belongs."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('geopandas', '0.14.2'),
+    ('rasterio', '1.3.9'),
+    ('Shapely', '2.0.1'),
+    ('xarray', '2023.9.0'),
+]
+
+use_pip = True
+
+exts_list = [
+    (name, version, {
+        'checksums': ['7ef1e70c6ebab7bfc6a80e13f6fe771945b8b6a31b7f8980fc88c8b8505bb854'],
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'geo'

From a051bd4d9e5ae7d122b23d1de0bb498d049e6d49 Mon Sep 17 00:00:00 2001
From: Simon Pinches <Simon.Pinches@iter.org>
Date: Fri, 7 Jun 2024 11:51:29 +0200
Subject: [PATCH 143/835] adding easyconfigs: json-fortran-8.5.2-GCC-13.2.0.eb,
 json-fortran-8.5.2-intel-compilers-2023.2.1.eb

---
 .../json-fortran-8.5.2-GCC-13.2.0.eb          | 32 +++++++++++++++++++
 ...-fortran-8.5.2-intel-compilers-2023.2.1.eb | 32 +++++++++++++++++++
 2 files changed, 64 insertions(+)
 create mode 100644 easybuild/easyconfigs/j/json-fortran/json-fortran-8.5.2-GCC-13.2.0.eb
 create mode 100644 easybuild/easyconfigs/j/json-fortran/json-fortran-8.5.2-intel-compilers-2023.2.1.eb

diff --git a/easybuild/easyconfigs/j/json-fortran/json-fortran-8.5.2-GCC-13.2.0.eb b/easybuild/easyconfigs/j/json-fortran/json-fortran-8.5.2-GCC-13.2.0.eb
new file mode 100644
index 00000000000..da205b23c09
--- /dev/null
+++ b/easybuild/easyconfigs/j/json-fortran/json-fortran-8.5.2-GCC-13.2.0.eb
@@ -0,0 +1,32 @@
+# J. Sassmannshausen (Imperial College London/UK)
+
+easyblock = 'CMakeMake'
+
+name = 'json-fortran'
+version = '8.5.2'
+
+homepage = 'https://github.com/jacobwilliams/json-fortran'
+description = "JSON-Fortran: A Modern Fortran JSON API"
+
+toolchain = {'name': 'GCC', 'version': '13.2.0'}
+
+source_urls = ['https://github.com/jacobwilliams/json-fortran/archive/']
+sources = ['%(version)s.tar.gz']
+checksums = ['ba7243ab28d4d06c5d0baef27dab0041cee0f050dea9ec3a854a03f4e3e9667a']
+
+builddependencies = [
+    ('binutils', '2.40'),
+    ('CMake', '3.27.6'),
+]
+
+configopts = '-DUSE_GNU_INSTALL_CONVENTION=TRUE'
+
+runtest = 'check'
+
+sanity_check_paths = {
+    'files': ['lib/libjsonfortran.a', 'lib/libjsonfortran.%s' % SHLIB_EXT,
+              'include/json_module.mod', 'include/json_parameters.mod'],
+    'dirs': ['include'],
+}
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/j/json-fortran/json-fortran-8.5.2-intel-compilers-2023.2.1.eb b/easybuild/easyconfigs/j/json-fortran/json-fortran-8.5.2-intel-compilers-2023.2.1.eb
new file mode 100644
index 00000000000..50d89ee34e2
--- /dev/null
+++ b/easybuild/easyconfigs/j/json-fortran/json-fortran-8.5.2-intel-compilers-2023.2.1.eb
@@ -0,0 +1,32 @@
+# J. Sassmannshausen (Imperial College London/UK)
+
+easyblock = 'CMakeMake'
+
+name = 'json-fortran'
+version = '8.5.2'
+
+homepage = 'https://github.com/jacobwilliams/json-fortran'
+description = "JSON-Fortran: A Modern Fortran JSON API"
+
+toolchain = {'name': 'intel-compilers', 'version': '2023.2.1'}
+
+source_urls = ['https://github.com/jacobwilliams/json-fortran/archive/']
+sources = ['%(version)s.tar.gz']
+checksums = ['ba7243ab28d4d06c5d0baef27dab0041cee0f050dea9ec3a854a03f4e3e9667a']
+
+builddependencies = [
+    ('binutils', '2.40'),
+    ('CMake', '3.27.6'),
+]
+
+configopts = '-DUSE_GNU_INSTALL_CONVENTION=TRUE'
+
+runtest = 'check'
+
+sanity_check_paths = {
+    'files': ['lib/libjsonfortran.a', 'lib/libjsonfortran.%s' % SHLIB_EXT,
+              'include/json_module.mod', 'include/json_parameters.mod'],
+    'dirs': ['include'],
+}
+
+moduleclass = 'lib'

From f8339003efcb1a2018a19d7746f6a64b8a568db3 Mon Sep 17 00:00:00 2001
From: Leonard Nielsen <leoniel@chalmers.se>
Date: Fri, 7 Jun 2024 12:26:51 +0000
Subject: [PATCH 144/835] adding easyconfigs: spaCy-3.7.4-foss-2023a.eb

---
 .../s/spaCy/spaCy-3.7.4-foss-2023a.eb         | 89 +++++++++++++++++++
 1 file changed, 89 insertions(+)
 create mode 100644 easybuild/easyconfigs/s/spaCy/spaCy-3.7.4-foss-2023a.eb

diff --git a/easybuild/easyconfigs/s/spaCy/spaCy-3.7.4-foss-2023a.eb b/easybuild/easyconfigs/s/spaCy/spaCy-3.7.4-foss-2023a.eb
new file mode 100644
index 00000000000..9305a059f4d
--- /dev/null
+++ b/easybuild/easyconfigs/s/spaCy/spaCy-3.7.4-foss-2023a.eb
@@ -0,0 +1,89 @@
+easyblock = 'PythonBundle'
+
+name = 'spaCy'
+version = '3.7.4'
+
+homepage = 'https://spacy.io/'
+description = "Industrial-strength Natural Language Processing (NLP) in Python."
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+builddependencies = [
+    ('poetry', '1.7.1'),
+    ('pydantic', '2.5.3'),
+    ('hatchling', '1.18.0')
+]
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('tqdm', '4.66.1'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('spacy-legacy', '3.0.12', {
+        'checksums': ['b37d6e0c9b6e1d7ca1cf5bc7152ab64a4c4671f59c85adaf7a3fcb870357a774'],
+    }),
+    ('spacy-loggers', '1.0.5', {
+        'checksums': ['d60b0bdbf915a60e516cc2e653baeff946f0cfc461b452d11a4d5458c6fe5f24'],
+    }),
+    ('cymem', '2.0.8', {
+        'checksums': ['8fb09d222e21dcf1c7e907dc85cf74501d4cea6c4ed4ac6c9e016f98fb59cbbf'],
+    }),
+    ('murmurhash', '1.0.10', {
+        'checksums': ['5282aab1317804c6ebd6dd7f69f15ba9075aee671c44a34be2bde0f1b11ef88a'],
+    }),
+    ('preshed', '3.0.9', {
+        'checksums': ['721863c5244ffcd2651ad0928951a2c7c77b102f4e11a251ad85d37ee7621660'],
+    }),
+    ('blis', '0.7.11', {
+        'checksums': ['cec6d48f75f7ac328ae1b6fbb372dde8c8a57c89559172277f66e01ff08d4d42'],
+    }),
+    ('confection', '0.1.4', {
+        'checksums': ['e80f22fd008b5231a2e8852fac6de9e28f2276a04031d0536cff74fe4a990c8f'],
+    }),
+    ('thinc', '8.2.3', {
+        'checksums': ['f5afc5222912a80bda8bdcec958362a2ba538d7027dc8db6154845d2859dca76'],
+    }),
+    ('ml_datasets', '0.2.0', {
+        'checksums': ['3f9c8901f8d6be3dab5b23ec3a6c01e619a60d0184696b1030cde2e3086943f1'],
+    }),
+    ('wasabi', '1.1.2', {
+        'checksums': ['1aaef3aceaa32edb9c91330d29d3936c0c39fdb965743549c173cb54b16c30b5'],
+    }),
+    ('srsly', '2.4.8', {
+        'checksums': ['b24d95a65009c2447e0b49cda043ac53fecf4f09e358d87a57446458f91b8a91'],
+    }),
+    ('catalogue', '2.0.10', {
+        'checksums': ['4f56daa940913d3f09d589c191c74e5a6d51762b3a9e37dd53b7437afd6cda15'],
+    }),
+    ('typer', '0.9.0', {
+        'checksums': ['50922fd79aea2f4751a8e0408ff10d2662bd0c8bbfa84755a699f3bada2978b2'],
+    }),
+    ('smart-open', '6.4.0', {
+        'source_tmpl': 'smart_open-%(version)s.tar.gz',
+        'checksums': ['be3c92c246fbe80ebce8fbacb180494a481a77fcdcb7c1aadb2ea5b9c2bee8b9'],
+    }),
+    ('hatch_fancy_pypi_readme', '24.1.0', {
+        'checksums': ['44dd239f1a779b9dcf8ebc9401a611fd7f7e3e14578dcf22c265dfaf7c1514b8'],
+    }),
+    ('langcodes', '3.3.0', {
+        'checksums': ['794d07d5a28781231ac335a1561b8442f8648ca07cd518310aeb45d6f0807ef6'],
+    }),
+    ('weasel', '0.3.4', {
+        'checksums': ['eb16f92dc9f1a3ffa89c165e3a9acd28018ebb656e0da4da02c0d7d8ae3f6178'],
+    }),
+    ('cloudpathlib', '0.16.0', {
+        'checksums': ['cdfcd35d46d529587d744154a0bdf962aca953b725c8784cd2ec478354ea63a3'],
+    }),
+    (name, version, {
+        'sources': ['%(namelower)s-%(version)s.tar.gz'],
+        'checksums': ['525f2ced2e40761562c8cace93ef6a1e6e8c483f27bd564bc1b15f608efbe85b'],
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'data'

From 1bb28dfbf31dd8c76836a8746bbea793699afe55 Mon Sep 17 00:00:00 2001
From: Yunqi Shao <yunqi.shao@chalmers.se>
Date: Fri, 7 Jun 2024 12:04:34 +0200
Subject: [PATCH 145/835] Include fix-cuda-build patch for TF 2.15.1

---
 .../t/TensorFlow/TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb   | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb
index f140621e37f..8b2595c2823 100644
--- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb
+++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb
@@ -142,6 +142,7 @@ exts_list = [
     }),
     (name, version, {
         'patches': [
+            'TensorFlow-2.1.0_fix-cuda-build.patch',
             'TensorFlow-2.4.0_dont-use-var-lock.patch',
             'TensorFlow-2.13.0_add-missing-system-protobuf-targets.patch',
             'TensorFlow-2.15.1_remove-duplicate-gpu-tests.patch',
@@ -189,6 +190,8 @@ exts_list = [
         'with_xla': True,
         'checksums': [
             {'v2.15.1.tar.gz': 'f36416d831f06fe866e149c7cd752da410a11178b01ff5620e9f265511ed57cf'},
+            {'TensorFlow-2.1.0_fix-cuda-build.patch':
+             '78c20aeaa7784b8ceb46238a81e8c2461137d28e0b576deeba8357d23fbe1f5a'},
             {'TensorFlow-2.4.0_dont-use-var-lock.patch':
              'b14f2493fd2edf79abd1c4f2dde6c98a3e7d5cb9c25ab9386df874d5f072d6b5'},
             {'TensorFlow-2.13.0_add-missing-system-protobuf-targets.patch':

From 13109c393436bb81fac35c7aa01c05c18e2cbfd0 Mon Sep 17 00:00:00 2001
From: Yunqi Shao <yunqi.shao@chalmers.se>
Date: Fri, 7 Jun 2024 14:48:00 +0200
Subject: [PATCH 146/835] Include disable-avx512-extensions patch for TF 2.15.1

---
 ...ensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb |  3 +++
 .../TensorFlow-2.15.1-foss-2023a.eb           |  3 +++
 ...low-2.15.1_disable-avx512-extensions.patch | 19 +++++++++++++++++++
 3 files changed, 25 insertions(+)
 create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_disable-avx512-extensions.patch

diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb
index 8b2595c2823..176839679e8 100644
--- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb
+++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb
@@ -152,6 +152,7 @@ exts_list = [
             'TensorFlow-2.15.1_fix-flatbuffer-license.patch',
             'TensorFlow-2.15.1_fix-pybind11-build.patch',
             'TensorFlow-2.15.1_fix-cuda_build_defs.patch',
+            'TensorFlow-2.15.1_disable-avx512-extensions.patch',
         ],
         'source_tmpl': 'v%(version)s.tar.gz',
         'source_urls': ['https://github.com/tensorflow/tensorflow/archive/'],
@@ -210,6 +211,8 @@ exts_list = [
              '3bb350ac92ab99c63c951c96b3b0160699f5f16822b64f72111ebfd2275cafce'},
             {'TensorFlow-2.15.1_fix-cuda_build_defs.patch':
              '091581a7c4fc2fc7af282cab6661632c29029d2f36eccb6695ffa5783e065f88'},
+            {'TensorFlow-2.15.1_disable-avx512-extensions.patch':
+             '506ceecff67237eed9cd9e9e114bc1461f35a343f77f83cb3dab710aa701dc0f'},
         ],
     }),
 ]
diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a.eb
index 014f3bbd7a5..61fff81cebe 100644
--- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a.eb
+++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a.eb
@@ -145,6 +145,7 @@ exts_list = [
             'TensorFlow-2.15.1_add-default-shell-env.patch',
             'TensorFlow-2.15.1_fix-flatbuffer-license.patch',
             'TensorFlow-2.15.1_fix-pybind11-build.patch',
+            'TensorFlow-2.15.1_disable-avx512-extensions.patch',
         ],
         'source_tmpl': 'v%(version)s.tar.gz',
         'source_urls': ['https://github.com/tensorflow/tensorflow/archive/'],
@@ -195,6 +196,8 @@ exts_list = [
              '2c04d5095977a628a238dbf93c5fada7159c86752a7183e64e0cf7c7ab00caf4'},
             {'TensorFlow-2.15.1_fix-pybind11-build.patch':
              '3bb350ac92ab99c63c951c96b3b0160699f5f16822b64f72111ebfd2275cafce'},
+            {'TensorFlow-2.15.1_disable-avx512-extensions.patch':
+             '506ceecff67237eed9cd9e9e114bc1461f35a343f77f83cb3dab710aa701dc0f'},
         ],
     }),
 ]
diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_disable-avx512-extensions.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_disable-avx512-extensions.patch
new file mode 100644
index 00000000000..7778d2b4a91
--- /dev/null
+++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_disable-avx512-extensions.patch
@@ -0,0 +1,19 @@
+(Some of the) AVX512 extensions to Eigen introduced by TensorFlow are broken and return wrong values.
+So disable them for now to keep AVX512 in the other code parts working.
+See https://github.com/tensorflow/tensorflow/issues/49944
+
+Author: Alexander Grund (TU Dresden)
+
+diff --git a/third_party/xla/third_party/tsl/tsl/framework/fixedpoint/FixedPoint.h b/third_party/xla/third_party/tsl/tsl/framework/fixedpoint/FixedPoint.h
+index 5301914ad37..8923bfed7bf 100644
+--- a/third_party/xla/third_party/tsl/tsl/framework/fixedpoint/FixedPoint.h
++++ b/third_party/xla/third_party/tsl/tsl/framework/fixedpoint/FixedPoint.h
+@@ -20,7 +20,7 @@ limitations under the License.
+ #include "tsl/framework/fixedpoint_types.h"
+ 
+ // Use optimized implementations whenever available
+-#if defined(EIGEN_VECTORIZE_AVX512DQ) || defined(EIGEN_VECTORIZE_AVX512BW)
++#if 0
+ #include "tsl/framework/fixedpoint/PacketMathAVX512.h"
+ #include "tsl/framework/fixedpoint/TypeCastingAVX512.h"
+ 

From 0bcde971cb7af9ddbce66ed2e5f6e2ace362f4ba Mon Sep 17 00:00:00 2001
From: Yunqi Shao <yunqi.shao@chalmers.se>
Date: Fri, 7 Jun 2024 14:48:37 +0200
Subject: [PATCH 147/835] Include exclude-xnnpack-on-ppc patch for TF 2.15.1

---
 .../t/TensorFlow/TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb   | 3 +++
 .../easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a.eb   | 3 +++
 2 files changed, 6 insertions(+)

diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb
index 176839679e8..c42d4201898 100644
--- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb
+++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb
@@ -145,6 +145,7 @@ exts_list = [
             'TensorFlow-2.1.0_fix-cuda-build.patch',
             'TensorFlow-2.4.0_dont-use-var-lock.patch',
             'TensorFlow-2.13.0_add-missing-system-protobuf-targets.patch',
+            'TensorFlow-2.13.0_exclude-xnnpack-on-ppc.patch',
             'TensorFlow-2.15.1_remove-duplicate-gpu-tests.patch',
             'TensorFlow-2.15.1_remove-libclang-dep.patch',
             'TensorFlow-2.15.1_remove-io-gcs-filesystem-dep.patch',
@@ -197,6 +198,8 @@ exts_list = [
              'b14f2493fd2edf79abd1c4f2dde6c98a3e7d5cb9c25ab9386df874d5f072d6b5'},
             {'TensorFlow-2.13.0_add-missing-system-protobuf-targets.patch':
              '77d8c8a5627493fc7c38b4de79d49e60ff6628b05ff969f4cd3ff9857176c459'},
+            {'TensorFlow-2.13.0_exclude-xnnpack-on-ppc.patch':
+             'd0818206846911d946666ded7d3216c0546e37cee1890a2f48dc1a9d71047cad'},
             {'TensorFlow-2.15.1_remove-duplicate-gpu-tests.patch':
              'd8810d5b875de5be8603afd743774ce9dd8c0d4a82314c7fe2f284a080be7498'},
             {'TensorFlow-2.15.1_remove-libclang-dep.patch':
diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a.eb
index 61fff81cebe..6db18627261 100644
--- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a.eb
+++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a.eb
@@ -140,6 +140,7 @@ exts_list = [
     (name, version, {
         'patches': [
             'TensorFlow-2.13.0_add-missing-system-protobuf-targets.patch',
+            'TensorFlow-2.13.0_exclude-xnnpack-on-ppc.patch',
             'TensorFlow-2.15.1_remove-libclang-dep.patch',
             'TensorFlow-2.15.1_remove-io-gcs-filesystem-dep.patch',
             'TensorFlow-2.15.1_add-default-shell-env.patch',
@@ -186,6 +187,8 @@ exts_list = [
             {'v2.15.1.tar.gz': 'f36416d831f06fe866e149c7cd752da410a11178b01ff5620e9f265511ed57cf'},
             {'TensorFlow-2.13.0_add-missing-system-protobuf-targets.patch':
              '77d8c8a5627493fc7c38b4de79d49e60ff6628b05ff969f4cd3ff9857176c459'},
+            {'TensorFlow-2.13.0_exclude-xnnpack-on-ppc.patch':
+             'd0818206846911d946666ded7d3216c0546e37cee1890a2f48dc1a9d71047cad'},
             {'TensorFlow-2.15.1_remove-libclang-dep.patch':
              '871b2f0221b7a150ac9f563ffad7187e052a7eedd95c20fb4524987d7edb6f21'},
             {'TensorFlow-2.15.1_remove-io-gcs-filesystem-dep.patch':

From cb542c01e1fd4cd47172b6a7f9eece9f67ef1bab Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 8 Jun 2024 14:51:02 +0200
Subject: [PATCH 148/835] adding easyconfigs: scFEA-1.1-20221109-foss-2023a.eb,
 MAGIC-3.0.0-foss-2023a.eb

---
 .../m/MAGIC/MAGIC-3.0.0-foss-2023a.eb         | 48 +++++++++++++++++++
 .../s/scFEA/scFEA-1.1-20221109-foss-2023a.eb  | 32 +++++++++++++
 2 files changed, 80 insertions(+)
 create mode 100644 easybuild/easyconfigs/m/MAGIC/MAGIC-3.0.0-foss-2023a.eb
 create mode 100644 easybuild/easyconfigs/s/scFEA/scFEA-1.1-20221109-foss-2023a.eb

diff --git a/easybuild/easyconfigs/m/MAGIC/MAGIC-3.0.0-foss-2023a.eb b/easybuild/easyconfigs/m/MAGIC/MAGIC-3.0.0-foss-2023a.eb
new file mode 100644
index 00000000000..368b1f262fe
--- /dev/null
+++ b/easybuild/easyconfigs/m/MAGIC/MAGIC-3.0.0-foss-2023a.eb
@@ -0,0 +1,48 @@
+easyblock = 'PythonBundle'
+
+name = 'MAGIC'
+version = '3.0.0'
+
+homepage = 'https://krishnaswamylab.org/projects/magic'
+description = """Markov Affinity-based Graph Imputation of Cells (MAGIC) is an algorithm for denoising high-dimensional
+ data most commonly applied to single-cell RNA sequencing data."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('matplotlib', '3.7.2'),
+    ('scikit-learn', '1.4.2'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('wrapt', '1.16.0', {
+        'checksums': ['5f370f952971e7d17c7d1ead40e49f32345a7f7a5373571ef44d800d06b1899d'],
+    }),
+    ('Deprecated', '1.2.14', {
+        'checksums': ['e5323eb936458dccc2582dc6f9c322c852a775a27065ff2b0c4970b9d53d01b3'],
+    }),
+    ('PyGSP', '0.5.1', {
+        'checksums': ['4874ad88793d622d4f578b40c6617a99b1f02bc6c6c4077f0e48cd71c7275800'],
+    }),
+    ('graphtools', '1.5.3', {
+        'checksums': ['b35ae2974d24c507fe01b110d10b1d8c949e20bc49ff9d7d04f94849f9795907'],
+    }),
+    ('scprep', '1.2.3', {
+        'checksums': ['cc4ba4cedbba256935298f2ba6a973b4e74ea8cb9ad2632b693b6d4e6ab77c3f'],
+    }),
+    ('tasklogger', '1.2.0', {
+        'checksums': ['b0a390dbe1d4c6f7465e58ee457b5bb381657b5ede3a85bcf45199cb56ac01a4'],
+    }),
+    ('magic-impute', version, {
+        'modulename': 'magic',
+        'checksums': ['0c3f6d17baf586c412c174709a19164f04e693fd1933a8c0399ae5c5bf1cfd7a'],
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/s/scFEA/scFEA-1.1-20221109-foss-2023a.eb b/easybuild/easyconfigs/s/scFEA/scFEA-1.1-20221109-foss-2023a.eb
new file mode 100644
index 00000000000..3e1d6133015
--- /dev/null
+++ b/easybuild/easyconfigs/s/scFEA/scFEA-1.1-20221109-foss-2023a.eb
@@ -0,0 +1,32 @@
+easyblock = 'Tarball'
+
+name = 'scFEA'
+local_commit = '4c1fb76'
+version = '1.1-20221109'
+
+homepage = 'https://github.com/changwn/scFEA'
+description = """scFEA: A graph neural network model to estimate cell-wise metabolic using single cell RNA-seq data"""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+source_urls = ['https://github.com/changwn/scFEA/archive']
+sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}]
+checksums = ['79774974964fed427dd67ba1d51c202a5ff90418fd84f74ebd9b478113ff50f6']
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('matplotlib', '3.7.2'),
+    ('tqdm', '4.66.1'),
+    ('PyTorch', '2.1.2'),
+    ('MAGIC', '3.0.0'),
+]
+
+sanity_check_paths = {
+    'files': ['src/scFEA.py'],
+    'dirs': [],
+}
+
+sanity_check_commands = ["python %(installdir)s/src/scFEA.py --help"]
+
+moduleclass = 'bio'

From 5f180c5298a69e82c807d84df1dac5637093605e Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 8 Jun 2024 17:30:56 +0200
Subject: [PATCH 149/835] stick to scikit-learn 1.3.2 as dependency for MAGIC
 with foss/2023a

---
 easybuild/easyconfigs/m/MAGIC/MAGIC-3.0.0-foss-2023a.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/m/MAGIC/MAGIC-3.0.0-foss-2023a.eb b/easybuild/easyconfigs/m/MAGIC/MAGIC-3.0.0-foss-2023a.eb
index 368b1f262fe..9e22b652a23 100644
--- a/easybuild/easyconfigs/m/MAGIC/MAGIC-3.0.0-foss-2023a.eb
+++ b/easybuild/easyconfigs/m/MAGIC/MAGIC-3.0.0-foss-2023a.eb
@@ -13,7 +13,7 @@ dependencies = [
     ('Python', '3.11.3'),
     ('SciPy-bundle', '2023.07'),
     ('matplotlib', '3.7.2'),
-    ('scikit-learn', '1.4.2'),
+    ('scikit-learn', '1.3.1'),
 ]
 
 use_pip = True

From cc19e0ebbf320c121eb26bcb29a6fc6065948056 Mon Sep 17 00:00:00 2001
From: Miguel Dias Costa <migueldiascosta@gmail.com>
Date: Mon, 10 Jun 2024 07:31:40 +0800
Subject: [PATCH 150/835] archive example easyconfigs for Fujitsu toolchain

---
 .../{ => __archive__}/a/Autoconf/Autoconf-2.71-FCC-4.5.0.eb       | 0
 .../{ => __archive__}/a/Automake/Automake-1.16.3-FCC-4.5.0.eb     | 0
 .../{ => __archive__}/a/Autotools/Autotools-20210128-FCC-4.5.0.eb | 0
 .../{ => __archive__}/b/Bison/Bison-3.7.6-FCC-4.5.0.eb            | 0
 .../{ => __archive__}/b/binutils/binutils-2.36.1-FCC-4.5.0.eb     | 0
 .../{ => __archive__}/b/buildenv/buildenv-default-FCC-4.5.0.eb    | 0
 .../b/buildenv/buildenv-default-Fujitsu-21.05.eb                  | 0
 .../easyconfigs/{ => __archive__}/d/DB/DB-18.1.40-FCC-4.5.0.eb    | 0
 .../{ => __archive__}/e/expat/expat-2.2.9-FCC-4.5.0.eb            | 0
 easybuild/easyconfigs/{ => __archive__}/f/FCC/FCC-4.5.0.eb        | 0
 .../{ => __archive__}/f/FFTW/FFTW-1.0.0-FCC-4.5.0-fujitsu.eb      | 0
 .../easyconfigs/{ => __archive__}/f/Fujitsu/Fujitsu-21.05.eb      | 0
 easybuild/easyconfigs/{ => __archive__}/f/ffmpi/ffmpi-4.5.0.eb    | 0
 .../easyconfigs/{ => __archive__}/f/flex/flex-2.6.4-FCC-4.5.0.eb  | 0
 .../{ => __archive__}/g/groff/groff-1.22.4-FCC-4.5.0.eb           | 0
 .../easyconfigs/{ => __archive__}/h/HPL/HPL-2.3-Fujitsu-21.05.eb  | 0
 .../{ => __archive__}/h/help2man/help2man-1.48.3-FCC-4.5.0.eb     | 0
 .../{ => __archive__}/l/libreadline/libreadline-8.1-FCC-4.5.0.eb  | 0
 .../{ => __archive__}/l/libtool/libtool-2.4.6-FCC-4.5.0.eb        | 0
 .../easyconfigs/{ => __archive__}/m/M4/M4-1.4.18-FCC-4.5.0.eb     | 0
 .../{ => __archive__}/m/makeinfo/makeinfo-6.7-FCC-4.5.0.eb        | 0
 .../{ => __archive__}/n/ncurses/ncurses-6.2-FCC-4.5.0.eb          | 0
 .../OSU-Micro-Benchmarks-5.7.1-ffmpi-4.5.0.eb                     | 0
 .../easyconfigs/{ => __archive__}/p/Perl/Perl-5.32.1-FCC-4.5.0.eb | 0
 .../easyconfigs/{ => __archive__}/z/zlib/zlib-1.2.11-FCC-4.5.0.eb | 0
 25 files changed, 0 insertions(+), 0 deletions(-)
 rename easybuild/easyconfigs/{ => __archive__}/a/Autoconf/Autoconf-2.71-FCC-4.5.0.eb (100%)
 rename easybuild/easyconfigs/{ => __archive__}/a/Automake/Automake-1.16.3-FCC-4.5.0.eb (100%)
 rename easybuild/easyconfigs/{ => __archive__}/a/Autotools/Autotools-20210128-FCC-4.5.0.eb (100%)
 rename easybuild/easyconfigs/{ => __archive__}/b/Bison/Bison-3.7.6-FCC-4.5.0.eb (100%)
 rename easybuild/easyconfigs/{ => __archive__}/b/binutils/binutils-2.36.1-FCC-4.5.0.eb (100%)
 rename easybuild/easyconfigs/{ => __archive__}/b/buildenv/buildenv-default-FCC-4.5.0.eb (100%)
 rename easybuild/easyconfigs/{ => __archive__}/b/buildenv/buildenv-default-Fujitsu-21.05.eb (100%)
 rename easybuild/easyconfigs/{ => __archive__}/d/DB/DB-18.1.40-FCC-4.5.0.eb (100%)
 rename easybuild/easyconfigs/{ => __archive__}/e/expat/expat-2.2.9-FCC-4.5.0.eb (100%)
 rename easybuild/easyconfigs/{ => __archive__}/f/FCC/FCC-4.5.0.eb (100%)
 rename easybuild/easyconfigs/{ => __archive__}/f/FFTW/FFTW-1.0.0-FCC-4.5.0-fujitsu.eb (100%)
 rename easybuild/easyconfigs/{ => __archive__}/f/Fujitsu/Fujitsu-21.05.eb (100%)
 rename easybuild/easyconfigs/{ => __archive__}/f/ffmpi/ffmpi-4.5.0.eb (100%)
 rename easybuild/easyconfigs/{ => __archive__}/f/flex/flex-2.6.4-FCC-4.5.0.eb (100%)
 rename easybuild/easyconfigs/{ => __archive__}/g/groff/groff-1.22.4-FCC-4.5.0.eb (100%)
 rename easybuild/easyconfigs/{ => __archive__}/h/HPL/HPL-2.3-Fujitsu-21.05.eb (100%)
 rename easybuild/easyconfigs/{ => __archive__}/h/help2man/help2man-1.48.3-FCC-4.5.0.eb (100%)
 rename easybuild/easyconfigs/{ => __archive__}/l/libreadline/libreadline-8.1-FCC-4.5.0.eb (100%)
 rename easybuild/easyconfigs/{ => __archive__}/l/libtool/libtool-2.4.6-FCC-4.5.0.eb (100%)
 rename easybuild/easyconfigs/{ => __archive__}/m/M4/M4-1.4.18-FCC-4.5.0.eb (100%)
 rename easybuild/easyconfigs/{ => __archive__}/m/makeinfo/makeinfo-6.7-FCC-4.5.0.eb (100%)
 rename easybuild/easyconfigs/{ => __archive__}/n/ncurses/ncurses-6.2-FCC-4.5.0.eb (100%)
 rename easybuild/easyconfigs/{ => __archive__}/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-ffmpi-4.5.0.eb (100%)
 rename easybuild/easyconfigs/{ => __archive__}/p/Perl/Perl-5.32.1-FCC-4.5.0.eb (100%)
 rename easybuild/easyconfigs/{ => __archive__}/z/zlib/zlib-1.2.11-FCC-4.5.0.eb (100%)

diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.71-FCC-4.5.0.eb b/easybuild/easyconfigs/__archive__/a/Autoconf/Autoconf-2.71-FCC-4.5.0.eb
similarity index 100%
rename from easybuild/easyconfigs/a/Autoconf/Autoconf-2.71-FCC-4.5.0.eb
rename to easybuild/easyconfigs/__archive__/a/Autoconf/Autoconf-2.71-FCC-4.5.0.eb
diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.16.3-FCC-4.5.0.eb b/easybuild/easyconfigs/__archive__/a/Automake/Automake-1.16.3-FCC-4.5.0.eb
similarity index 100%
rename from easybuild/easyconfigs/a/Automake/Automake-1.16.3-FCC-4.5.0.eb
rename to easybuild/easyconfigs/__archive__/a/Automake/Automake-1.16.3-FCC-4.5.0.eb
diff --git a/easybuild/easyconfigs/a/Autotools/Autotools-20210128-FCC-4.5.0.eb b/easybuild/easyconfigs/__archive__/a/Autotools/Autotools-20210128-FCC-4.5.0.eb
similarity index 100%
rename from easybuild/easyconfigs/a/Autotools/Autotools-20210128-FCC-4.5.0.eb
rename to easybuild/easyconfigs/__archive__/a/Autotools/Autotools-20210128-FCC-4.5.0.eb
diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.7.6-FCC-4.5.0.eb b/easybuild/easyconfigs/__archive__/b/Bison/Bison-3.7.6-FCC-4.5.0.eb
similarity index 100%
rename from easybuild/easyconfigs/b/Bison/Bison-3.7.6-FCC-4.5.0.eb
rename to easybuild/easyconfigs/__archive__/b/Bison/Bison-3.7.6-FCC-4.5.0.eb
diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.36.1-FCC-4.5.0.eb b/easybuild/easyconfigs/__archive__/b/binutils/binutils-2.36.1-FCC-4.5.0.eb
similarity index 100%
rename from easybuild/easyconfigs/b/binutils/binutils-2.36.1-FCC-4.5.0.eb
rename to easybuild/easyconfigs/__archive__/b/binutils/binutils-2.36.1-FCC-4.5.0.eb
diff --git a/easybuild/easyconfigs/b/buildenv/buildenv-default-FCC-4.5.0.eb b/easybuild/easyconfigs/__archive__/b/buildenv/buildenv-default-FCC-4.5.0.eb
similarity index 100%
rename from easybuild/easyconfigs/b/buildenv/buildenv-default-FCC-4.5.0.eb
rename to easybuild/easyconfigs/__archive__/b/buildenv/buildenv-default-FCC-4.5.0.eb
diff --git a/easybuild/easyconfigs/b/buildenv/buildenv-default-Fujitsu-21.05.eb b/easybuild/easyconfigs/__archive__/b/buildenv/buildenv-default-Fujitsu-21.05.eb
similarity index 100%
rename from easybuild/easyconfigs/b/buildenv/buildenv-default-Fujitsu-21.05.eb
rename to easybuild/easyconfigs/__archive__/b/buildenv/buildenv-default-Fujitsu-21.05.eb
diff --git a/easybuild/easyconfigs/d/DB/DB-18.1.40-FCC-4.5.0.eb b/easybuild/easyconfigs/__archive__/d/DB/DB-18.1.40-FCC-4.5.0.eb
similarity index 100%
rename from easybuild/easyconfigs/d/DB/DB-18.1.40-FCC-4.5.0.eb
rename to easybuild/easyconfigs/__archive__/d/DB/DB-18.1.40-FCC-4.5.0.eb
diff --git a/easybuild/easyconfigs/e/expat/expat-2.2.9-FCC-4.5.0.eb b/easybuild/easyconfigs/__archive__/e/expat/expat-2.2.9-FCC-4.5.0.eb
similarity index 100%
rename from easybuild/easyconfigs/e/expat/expat-2.2.9-FCC-4.5.0.eb
rename to easybuild/easyconfigs/__archive__/e/expat/expat-2.2.9-FCC-4.5.0.eb
diff --git a/easybuild/easyconfigs/f/FCC/FCC-4.5.0.eb b/easybuild/easyconfigs/__archive__/f/FCC/FCC-4.5.0.eb
similarity index 100%
rename from easybuild/easyconfigs/f/FCC/FCC-4.5.0.eb
rename to easybuild/easyconfigs/__archive__/f/FCC/FCC-4.5.0.eb
diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-1.0.0-FCC-4.5.0-fujitsu.eb b/easybuild/easyconfigs/__archive__/f/FFTW/FFTW-1.0.0-FCC-4.5.0-fujitsu.eb
similarity index 100%
rename from easybuild/easyconfigs/f/FFTW/FFTW-1.0.0-FCC-4.5.0-fujitsu.eb
rename to easybuild/easyconfigs/__archive__/f/FFTW/FFTW-1.0.0-FCC-4.5.0-fujitsu.eb
diff --git a/easybuild/easyconfigs/f/Fujitsu/Fujitsu-21.05.eb b/easybuild/easyconfigs/__archive__/f/Fujitsu/Fujitsu-21.05.eb
similarity index 100%
rename from easybuild/easyconfigs/f/Fujitsu/Fujitsu-21.05.eb
rename to easybuild/easyconfigs/__archive__/f/Fujitsu/Fujitsu-21.05.eb
diff --git a/easybuild/easyconfigs/f/ffmpi/ffmpi-4.5.0.eb b/easybuild/easyconfigs/__archive__/f/ffmpi/ffmpi-4.5.0.eb
similarity index 100%
rename from easybuild/easyconfigs/f/ffmpi/ffmpi-4.5.0.eb
rename to easybuild/easyconfigs/__archive__/f/ffmpi/ffmpi-4.5.0.eb
diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.4-FCC-4.5.0.eb b/easybuild/easyconfigs/__archive__/f/flex/flex-2.6.4-FCC-4.5.0.eb
similarity index 100%
rename from easybuild/easyconfigs/f/flex/flex-2.6.4-FCC-4.5.0.eb
rename to easybuild/easyconfigs/__archive__/f/flex/flex-2.6.4-FCC-4.5.0.eb
diff --git a/easybuild/easyconfigs/g/groff/groff-1.22.4-FCC-4.5.0.eb b/easybuild/easyconfigs/__archive__/g/groff/groff-1.22.4-FCC-4.5.0.eb
similarity index 100%
rename from easybuild/easyconfigs/g/groff/groff-1.22.4-FCC-4.5.0.eb
rename to easybuild/easyconfigs/__archive__/g/groff/groff-1.22.4-FCC-4.5.0.eb
diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.3-Fujitsu-21.05.eb b/easybuild/easyconfigs/__archive__/h/HPL/HPL-2.3-Fujitsu-21.05.eb
similarity index 100%
rename from easybuild/easyconfigs/h/HPL/HPL-2.3-Fujitsu-21.05.eb
rename to easybuild/easyconfigs/__archive__/h/HPL/HPL-2.3-Fujitsu-21.05.eb
diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.48.3-FCC-4.5.0.eb b/easybuild/easyconfigs/__archive__/h/help2man/help2man-1.48.3-FCC-4.5.0.eb
similarity index 100%
rename from easybuild/easyconfigs/h/help2man/help2man-1.48.3-FCC-4.5.0.eb
rename to easybuild/easyconfigs/__archive__/h/help2man/help2man-1.48.3-FCC-4.5.0.eb
diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-8.1-FCC-4.5.0.eb b/easybuild/easyconfigs/__archive__/l/libreadline/libreadline-8.1-FCC-4.5.0.eb
similarity index 100%
rename from easybuild/easyconfigs/l/libreadline/libreadline-8.1-FCC-4.5.0.eb
rename to easybuild/easyconfigs/__archive__/l/libreadline/libreadline-8.1-FCC-4.5.0.eb
diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-FCC-4.5.0.eb b/easybuild/easyconfigs/__archive__/l/libtool/libtool-2.4.6-FCC-4.5.0.eb
similarity index 100%
rename from easybuild/easyconfigs/l/libtool/libtool-2.4.6-FCC-4.5.0.eb
rename to easybuild/easyconfigs/__archive__/l/libtool/libtool-2.4.6-FCC-4.5.0.eb
diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-FCC-4.5.0.eb b/easybuild/easyconfigs/__archive__/m/M4/M4-1.4.18-FCC-4.5.0.eb
similarity index 100%
rename from easybuild/easyconfigs/m/M4/M4-1.4.18-FCC-4.5.0.eb
rename to easybuild/easyconfigs/__archive__/m/M4/M4-1.4.18-FCC-4.5.0.eb
diff --git a/easybuild/easyconfigs/m/makeinfo/makeinfo-6.7-FCC-4.5.0.eb b/easybuild/easyconfigs/__archive__/m/makeinfo/makeinfo-6.7-FCC-4.5.0.eb
similarity index 100%
rename from easybuild/easyconfigs/m/makeinfo/makeinfo-6.7-FCC-4.5.0.eb
rename to easybuild/easyconfigs/__archive__/m/makeinfo/makeinfo-6.7-FCC-4.5.0.eb
diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.2-FCC-4.5.0.eb b/easybuild/easyconfigs/__archive__/n/ncurses/ncurses-6.2-FCC-4.5.0.eb
similarity index 100%
rename from easybuild/easyconfigs/n/ncurses/ncurses-6.2-FCC-4.5.0.eb
rename to easybuild/easyconfigs/__archive__/n/ncurses/ncurses-6.2-FCC-4.5.0.eb
diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-ffmpi-4.5.0.eb b/easybuild/easyconfigs/__archive__/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-ffmpi-4.5.0.eb
similarity index 100%
rename from easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-ffmpi-4.5.0.eb
rename to easybuild/easyconfigs/__archive__/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-ffmpi-4.5.0.eb
diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.32.1-FCC-4.5.0.eb b/easybuild/easyconfigs/__archive__/p/Perl/Perl-5.32.1-FCC-4.5.0.eb
similarity index 100%
rename from easybuild/easyconfigs/p/Perl/Perl-5.32.1-FCC-4.5.0.eb
rename to easybuild/easyconfigs/__archive__/p/Perl/Perl-5.32.1-FCC-4.5.0.eb
diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-FCC-4.5.0.eb b/easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.11-FCC-4.5.0.eb
similarity index 100%
rename from easybuild/easyconfigs/z/zlib/zlib-1.2.11-FCC-4.5.0.eb
rename to easybuild/easyconfigs/__archive__/z/zlib/zlib-1.2.11-FCC-4.5.0.eb

From b18e54e66057b5f57d3d21ec5846146ba1a9d867 Mon Sep 17 00:00:00 2001
From: Leonard Nielsen <leoniel@chalmers.se>
Date: Mon, 10 Jun 2024 08:50:45 +0000
Subject: [PATCH 151/835] fixed builddep -> dep

---
 easybuild/easyconfigs/s/spaCy/spaCy-3.7.4-foss-2023a.eb | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/easybuild/easyconfigs/s/spaCy/spaCy-3.7.4-foss-2023a.eb b/easybuild/easyconfigs/s/spaCy/spaCy-3.7.4-foss-2023a.eb
index 9305a059f4d..6ca6017894a 100644
--- a/easybuild/easyconfigs/s/spaCy/spaCy-3.7.4-foss-2023a.eb
+++ b/easybuild/easyconfigs/s/spaCy/spaCy-3.7.4-foss-2023a.eb
@@ -10,14 +10,14 @@ toolchain = {'name': 'foss', 'version': '2023a'}
 
 builddependencies = [
     ('poetry', '1.7.1'),
-    ('pydantic', '2.5.3'),
-    ('hatchling', '1.18.0')
 ]
 
 dependencies = [
     ('Python', '3.11.3'),
     ('SciPy-bundle', '2023.07'),
     ('tqdm', '4.66.1'),
+    ('pydantic', '2.5.3'),
+    ('hatchling', '1.18.0')
 ]
 
 use_pip = True

From 9d208bfc761bb354765499730e0f3e34738943a8 Mon Sep 17 00:00:00 2001
From: WilleBell <cintiawillemyns@gmail.com>
Date: Mon, 10 Jun 2024 11:29:35 +0200
Subject: [PATCH 152/835] adding easyconfigs: xtb-IFF-1.1-gfbf-2023a.eb

---
 .../x/xtb-IFF/xtb-IFF-1.1-gfbf-2023a.eb       | 30 +++++++++++++++++++
 1 file changed, 30 insertions(+)
 create mode 100644 easybuild/easyconfigs/x/xtb-IFF/xtb-IFF-1.1-gfbf-2023a.eb

diff --git a/easybuild/easyconfigs/x/xtb-IFF/xtb-IFF-1.1-gfbf-2023a.eb b/easybuild/easyconfigs/x/xtb-IFF/xtb-IFF-1.1-gfbf-2023a.eb
new file mode 100644
index 00000000000..9d59159a3cc
--- /dev/null
+++ b/easybuild/easyconfigs/x/xtb-IFF/xtb-IFF-1.1-gfbf-2023a.eb
@@ -0,0 +1,30 @@
+easyblock = 'Tarball'
+
+name = 'xtb-IFF'
+version = '1.1'
+
+homepage = ''
+description = """
+This is the official repository of the xtb-IFF program developed by the Grimme group in Bonn
+"""
+
+toolchain = {'name': 'gfbf', 'version': '2023a'}
+
+source_urls = ['https://github.com/grimme-lab/xtbiff/releases/download/v1.1']
+sources = ['xtbiff.tar.xz']
+checksums = ['6d5dee10ba39ecb1e26374b7bf82e2364d8ebed5b6f35cdce4ced73245c296f5']
+
+dependencies = [
+    ('CREST', '2.12'),
+]
+
+sanity_check_paths = {
+    'files': ['xtbiff'],
+    'dirs': [],
+}
+
+sanity_check_commands = ["xtbiff --help"]
+
+modextrapaths = {'PATH': ''}
+
+moduleclass = 'chem'

From ac83cb9a895c04db0fe60275b48456b2139d82c1 Mon Sep 17 00:00:00 2001
From: Cintia Willemyns <115622907+WilleBell@users.noreply.github.com>
Date: Mon, 10 Jun 2024 11:49:48 +0200
Subject: [PATCH 153/835] add homepage and modify description

---
 easybuild/easyconfigs/x/xtb-IFF/xtb-IFF-1.1-gfbf-2023a.eb | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/easybuild/easyconfigs/x/xtb-IFF/xtb-IFF-1.1-gfbf-2023a.eb b/easybuild/easyconfigs/x/xtb-IFF/xtb-IFF-1.1-gfbf-2023a.eb
index 9d59159a3cc..fd81ac4072d 100644
--- a/easybuild/easyconfigs/x/xtb-IFF/xtb-IFF-1.1-gfbf-2023a.eb
+++ b/easybuild/easyconfigs/x/xtb-IFF/xtb-IFF-1.1-gfbf-2023a.eb
@@ -3,9 +3,9 @@ easyblock = 'Tarball'
 name = 'xtb-IFF'
 version = '1.1'
 
-homepage = ''
+homepage = 'https://github.com/grimme-lab/xtbiff'
 description = """
-This is the official repository of the xtb-IFF program developed by the Grimme group in Bonn
+General Intermolecular Force Field based on Tight-Binding Quantum Chemical Calculations. 
 """
 
 toolchain = {'name': 'gfbf', 'version': '2023a'}

From 8752a4a3550ec24f6505153117691dfffa79113b Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Mon, 10 Jun 2024 10:11:31 +0200
Subject: [PATCH 154/835] move jupyter-collaboration v2.1.1 into GCCcore/13.2.0

---
 ...0.eb => jupyter-collaboration-2.1.1-GCCcore-13.2.0.eb} | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)
 rename easybuild/easyconfigs/j/jupyter-collaboration/{jupyter-collaboration-2.1.1-GCCcore-12.3.0.eb => jupyter-collaboration-2.1.1-GCCcore-13.2.0.eb} (92%)

diff --git a/easybuild/easyconfigs/j/jupyter-collaboration/jupyter-collaboration-2.1.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/j/jupyter-collaboration/jupyter-collaboration-2.1.1-GCCcore-13.2.0.eb
similarity index 92%
rename from easybuild/easyconfigs/j/jupyter-collaboration/jupyter-collaboration-2.1.1-GCCcore-12.3.0.eb
rename to easybuild/easyconfigs/j/jupyter-collaboration/jupyter-collaboration-2.1.1-GCCcore-13.2.0.eb
index c82cabd5c83..1755481085e 100644
--- a/easybuild/easyconfigs/j/jupyter-collaboration/jupyter-collaboration-2.1.1-GCCcore-12.3.0.eb
+++ b/easybuild/easyconfigs/j/jupyter-collaboration/jupyter-collaboration-2.1.1-GCCcore-13.2.0.eb
@@ -8,16 +8,16 @@ description = """JupyterLab Real-Time Collaboration is a Jupyter Server Extensio
 extensions providing support for Y documents and adding collaboration UI
 elements in JupyterLab."""
 
-toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
 
 builddependencies = [
     ('binutils', '2.40'),
     ('hatch-jupyter-builder', '0.9.1'),
-    ('maturin', '1.1.0'),
+    ('maturin', '1.3.1'),
 ]
 dependencies = [
-    ('Python', '3.11.3'),
-    ('JupyterLab', '4.0.5'),
+    ('Python', '3.11.5'),
+    ('JupyterLab', '4.2.0'),
 ]
 
 sanity_pip_check = True

From be9f9a0d15a9d24dc43b513871469fa095d2d70c Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Mon, 10 Jun 2024 13:31:19 +0200
Subject: [PATCH 155/835] move pycodestyle and adjustText to separate PR

---
 .../adjustText/adjustText-1.1.1-foss-2023a.eb | 27 -------------------
 .../pycodestyle-2.11.1-foss-2023a.eb          | 24 -----------------
 2 files changed, 51 deletions(-)
 delete mode 100644 easybuild/easyconfigs/a/adjustText/adjustText-1.1.1-foss-2023a.eb
 delete mode 100644 easybuild/easyconfigs/p/pycodestyle/pycodestyle-2.11.1-foss-2023a.eb

diff --git a/easybuild/easyconfigs/a/adjustText/adjustText-1.1.1-foss-2023a.eb b/easybuild/easyconfigs/a/adjustText/adjustText-1.1.1-foss-2023a.eb
deleted file mode 100644
index f109d19d3aa..00000000000
--- a/easybuild/easyconfigs/a/adjustText/adjustText-1.1.1-foss-2023a.eb
+++ /dev/null
@@ -1,27 +0,0 @@
-easyblock = 'PythonBundle'
-
-name = 'adjustText'
-version = '1.1.1'
-
-homepage = 'https://github.com/Phlya/adjustText'
-description = "A small library for automatically adjustment of text position in matplotlib plots to minimize overlaps."
-
-toolchain = {'name': 'foss', 'version': '2023a'}
-
-dependencies = [
-    ('Python', '3.11.3'),
-    ('matplotlib', '3.7.2'),
-    ('SciPy-bundle', '2023.07'),
-]
-
-use_pip = True
-sanity_pip_check = True
-
-exts_list = [
-    (name, version, {
-        'modulename': 'adjustText',
-        'checksums': ['e2c0975ef2c642478e60f4c03c5e9afbdeda7764336907ef69a9205bfa2d9896'],
-    }),
-]
-
-moduleclass = 'tools'
diff --git a/easybuild/easyconfigs/p/pycodestyle/pycodestyle-2.11.1-foss-2023a.eb b/easybuild/easyconfigs/p/pycodestyle/pycodestyle-2.11.1-foss-2023a.eb
deleted file mode 100644
index c704acc3b36..00000000000
--- a/easybuild/easyconfigs/p/pycodestyle/pycodestyle-2.11.1-foss-2023a.eb
+++ /dev/null
@@ -1,24 +0,0 @@
-easyblock = 'PythonBundle'
-
-name = 'pycodestyle'
-version = '2.11.1'
-
-homepage = "https://pycodestyle.readthedocs.io"
-description = """pycodestyle is a tool to check your Python code against some of the style conventions in PEP 8."""
-
-toolchain = {'name': 'foss', 'version': '2023a'}
-
-dependencies = [
-    ('Python', '3.11.3'),
-]
-
-exts_list = [
-    (name, version, {
-        'checksums': ['41ba0e7afc9752dfb53ced5489e89f8186be00e599e712660695b7a75ff2663f'],
-    }),
-]
-
-use_pip = True
-sanity_pip_check = True
-
-moduleclass = 'lib'

From 399e9b6d025fd98a01e437340e576b807b1d726a Mon Sep 17 00:00:00 2001
From: WilleBell <cintiawillemyns@gmail.com>
Date: Mon, 10 Jun 2024 14:17:50 +0200
Subject: [PATCH 156/835] adding easyconfigs: DL_POLY_4-5.1.0-foss-2023a.eb

---
 .../d/DL_POLY_4/DL_POLY_4-5.1.0-foss-2023a.eb | 22 +++++++++++++++++++
 1 file changed, 22 insertions(+)
 create mode 100644 easybuild/easyconfigs/d/DL_POLY_4/DL_POLY_4-5.1.0-foss-2023a.eb

diff --git a/easybuild/easyconfigs/d/DL_POLY_4/DL_POLY_4-5.1.0-foss-2023a.eb b/easybuild/easyconfigs/d/DL_POLY_4/DL_POLY_4-5.1.0-foss-2023a.eb
new file mode 100644
index 00000000000..a0be0ed6765
--- /dev/null
+++ b/easybuild/easyconfigs/d/DL_POLY_4/DL_POLY_4-5.1.0-foss-2023a.eb
@@ -0,0 +1,22 @@
+easyblock = 'CMakeMake'
+
+name = "DL_POLY_4"
+version = "5.1.0"
+
+homepage = "https://www.scd.stfc.ac.uk/Pages/DL_POLY.aspx"
+description = "DL_POLY is a general purpose classical molecular dynamics (MD) simulation software"
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+source_urls = ['https://gitlab.com/ccp5/dl-poly/-/archive/%(version)s/']
+sources = ['dl_poly_%(version)s.tar.bz2']
+checksums = ['da5364986cd71e047e080753f6ca75135bf19bd5607770b839dea3734c2fdfaa']
+
+builddependencies = [('CMake', '3.26.3')]
+
+sanity_check_paths = {
+    'files': ['bin/DLPOLY.Z'],
+    'dirs': []
+}
+
+moduleclass = 'chem'

From 725b3023ab2ac0cff1fce16a84e677c64ca56d78 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Petr=20Kr=C3=A1l?= <petr@inuits.eu>
Date: Mon, 10 Jun 2024 14:29:26 +0200
Subject: [PATCH 157/835] adding easyconfigs: gap-4.13.0-foss-2023b.eb,
 Normaliz-3.10.3-gfbf-2023b.eb

---
 .../g/gap/gap-4.13.0-foss-2023b.eb            | 55 +++++++++++++++++++
 .../n/Normaliz/Normaliz-3.10.3-gfbf-2023b.eb  | 47 ++++++++++++++++
 2 files changed, 102 insertions(+)
 create mode 100644 easybuild/easyconfigs/g/gap/gap-4.13.0-foss-2023b.eb
 create mode 100644 easybuild/easyconfigs/n/Normaliz/Normaliz-3.10.3-gfbf-2023b.eb

diff --git a/easybuild/easyconfigs/g/gap/gap-4.13.0-foss-2023b.eb b/easybuild/easyconfigs/g/gap/gap-4.13.0-foss-2023b.eb
new file mode 100644
index 00000000000..ccde7c5df99
--- /dev/null
+++ b/easybuild/easyconfigs/g/gap/gap-4.13.0-foss-2023b.eb
@@ -0,0 +1,55 @@
+easyblock = 'ConfigureMake'
+
+name = 'gap'
+version = '4.13.0'
+
+homepage = 'https://www.gap-system.org'
+description = """GAP is a system for computational discrete algebra,
+with particular emphasis on Computational Group Theory."""
+
+toolchain = {'name': 'foss', 'version': '2023b'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://www.gap-system.org/pub/gap/gap-%(version_major_minor)s/tar.gz/']
+sources = [SOURCE_TAR_GZ]
+checksums = ['cc76ecbe33d6719450a593e613fb87e9e4247faa876f632dd0f97c398f92265d']
+
+unpack_options = '--strip-components=1'
+
+builddependencies = [
+    ('Perl', '5.38.0'),  # needed to install NormalizInterface
+]
+
+dependencies = [
+    ('GMP', '6.3.0'),
+    ('libreadline', '8.2'),
+    ('zlib', '1.2.13'),
+    ('4ti2', '1.6.10'),  # needed by 4ti2Interface, HeLP
+    ('cddlib', '0.94m'),  # needed by CddInterface
+    ('cURL', '8.3.0'),  # needed by curlInterface
+    ('lrslib', '7.2'),  # needed by HeLP
+    ('ncurses', '6.4'),  # needed by Browse
+    ('Normaliz', '3.10.3'),  # needed by NormalizInterface, HeLP
+    # ('Singular', '4.3.2p16'),  # needed by singular
+    ('ZeroMQ', '4.3.5'),  # needed by ZeroMQInterface
+]
+
+# install target is incomplete and hardcodes the build path
+buildininstalldir = True
+
+# Disable bundled script to download and build Normaliz
+prebuildopts = "sed -i 's|./build-normaliz.sh|continue # build-normaliz.sh|' bin/BuildPackages.sh && "
+# BuildPackages.sh tries to build any GAP packages that require compilation
+# If one fails due to missing dependencies, it's skipped automatically
+buildopts = ' && cd pkg && ../bin/BuildPackages.sh'
+
+sanity_check_paths = {
+    'files': ['bin/%s' % x for x in ['gap', 'gac']] +
+             ['include/gap/%s.h' % h for h in ['gap', 'system', 'version']] +
+             ['lib/libgap.%s' % SHLIB_EXT],
+    'dirs': ['share/gap']
+}
+
+sanity_check_commands = ["gap tst/testinstall.g"]
+
+moduleclass = 'math'
diff --git a/easybuild/easyconfigs/n/Normaliz/Normaliz-3.10.3-gfbf-2023b.eb b/easybuild/easyconfigs/n/Normaliz/Normaliz-3.10.3-gfbf-2023b.eb
new file mode 100644
index 00000000000..d2337505978
--- /dev/null
+++ b/easybuild/easyconfigs/n/Normaliz/Normaliz-3.10.3-gfbf-2023b.eb
@@ -0,0 +1,47 @@
+easyblock = 'ConfigureMake'
+
+name = 'Normaliz'
+version = '3.10.3'
+
+homepage = 'https://www.normaliz.uni-osnabrueck.de/'
+description = """Normaliz is a open source tool for computations in affine monoids, vector
+configurations, rational polyhedra and rational cones. Normaliz now computes
+rational and algebraic polyhedra, i.e., polyhedra defined over real algebraic
+extensions of QQ."""
+
+toolchain = {'name': 'gfbf', 'version': '2023b'}
+toolchainopts = {'pic': True, 'openmp': True, 'cstd': 'c++14'}
+
+github_account = 'Normaliz'
+source_urls = [GITHUB_SOURCE]
+sources = ['v%(version)s.tar.gz']
+checksums = ['d9536ab3568053a8dd9aeabe09ef901c1c0ebbda37be50775a120eb9e7ff47cb']
+
+builddependencies = [
+    ('Autotools', '20220317'),
+]
+
+dependencies = [
+    ('Boost', '1.83.0'),
+    ('GMP', '6.3.0'),
+    ('CoCoALib', '0.99818'),
+    ('FLINT', '3.1.1'),
+    ('E-ANTIC', '2.0.2'),
+    ('nauty', '2.8.8'),
+]
+
+preconfigopts = "autoreconf -f -i && "
+
+configopts = "--with-gmp=$EBROOTGMP --with-cocoalib=$EBROOTCOCOALIB --with-flint=$EBROOTFLINT "
+configopts += "--with-e-antic=$EBROOTEMINANTIC --with-nauty=$EBROOTNAUTY"
+
+runtest = 'check'
+
+sanity_check_paths = {
+    'files': ['bin/normaliz'] + ['lib/libnormaliz.%s' % e for e in ['a', SHLIB_EXT]],
+    'dirs': ['include/libnormaliz']
+}
+
+sanity_check_commands = ["normaliz --help"]
+
+moduleclass = 'math'

From 18e1574e35db69b81c274927d3d65e8617edf4cb Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Petr=20Kr=C3=A1l?= <petr@inuits.eu>
Date: Mon, 10 Jun 2024 14:52:18 +0200
Subject: [PATCH 158/835] fix dependency version

---
 easybuild/easyconfigs/n/Normaliz/Normaliz-3.10.3-gfbf-2023b.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/n/Normaliz/Normaliz-3.10.3-gfbf-2023b.eb b/easybuild/easyconfigs/n/Normaliz/Normaliz-3.10.3-gfbf-2023b.eb
index d2337505978..6651c1a848d 100644
--- a/easybuild/easyconfigs/n/Normaliz/Normaliz-3.10.3-gfbf-2023b.eb
+++ b/easybuild/easyconfigs/n/Normaliz/Normaliz-3.10.3-gfbf-2023b.eb
@@ -24,7 +24,7 @@ builddependencies = [
 dependencies = [
     ('Boost', '1.83.0'),
     ('GMP', '6.3.0'),
-    ('CoCoALib', '0.99818'),
+    ('CoCoALib', '0.99850'),
     ('FLINT', '3.1.1'),
     ('E-ANTIC', '2.0.2'),
     ('nauty', '2.8.8'),

From c5ae434fd84b0bc79436d041e01493b1f243b09a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Petr=20Kr=C3=A1l?= <petr@inuits.eu>
Date: Mon, 10 Jun 2024 15:21:06 +0200
Subject: [PATCH 159/835] adding easyconfigs: rankwidth-0.9-foss-2023b.eb,
 igraph-0.10.12-foss-2023b.eb

---
 .../i/igraph/igraph-0.10.12-foss-2023b.eb     | 42 +++++++++++++++++++
 .../r/rankwidth/rankwidth-0.9-foss-2023b.eb   | 35 ++++++++++++++++
 2 files changed, 77 insertions(+)
 create mode 100644 easybuild/easyconfigs/i/igraph/igraph-0.10.12-foss-2023b.eb
 create mode 100644 easybuild/easyconfigs/r/rankwidth/rankwidth-0.9-foss-2023b.eb

diff --git a/easybuild/easyconfigs/i/igraph/igraph-0.10.12-foss-2023b.eb b/easybuild/easyconfigs/i/igraph/igraph-0.10.12-foss-2023b.eb
new file mode 100644
index 00000000000..6e5f77cd3c8
--- /dev/null
+++ b/easybuild/easyconfigs/i/igraph/igraph-0.10.12-foss-2023b.eb
@@ -0,0 +1,42 @@
+# Author: Denis Krišťák (INUITS)
+# Modified: Jasper Grimm (UoY)
+# Update: Pavel Tománek (INUITS)
+# Update: Petr Král (INUITS)
+
+easyblock = 'CMakeMake'
+
+name = 'igraph'
+version = '0.10.12'
+
+homepage = 'https://igraph.org'
+description = """igraph is a collection of network analysis tools with the emphasis on
+efficiency, portability and ease of use. igraph is open source and free. igraph can be
+programmed in R, Python and C/C++."""
+
+toolchain = {'name': 'foss', 'version': '2023b'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://github.com/igraph/igraph/releases/download/%(version)s']
+sources = [SOURCE_TAR_GZ]
+checksums = ['b011f7f9f38a3e59924cc9ff652e6d33105fa03fcaf3792f47d752626a0a4625']
+
+builddependencies = [
+    ('CMake', '3.27.6'),
+]
+
+dependencies = [
+    ('GLPK', '5.0'),
+    ('libxml2', '2.11.5'),
+    ('zlib', '1.2.13'),
+    ('arpack-ng', '3.9.0'),
+]
+
+# Build static and shared libraries
+configopts = ["-DBUILD_SHARED_LIBS=OFF", "-DBUILD_SHARED_LIBS=ON"]
+
+sanity_check_paths = {
+    'files': ['include/igraph/igraph.h'] + ['lib/libigraph.%s' % x for x in ['a', SHLIB_EXT]],
+    'dirs': [],
+}
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/r/rankwidth/rankwidth-0.9-foss-2023b.eb b/easybuild/easyconfigs/r/rankwidth/rankwidth-0.9-foss-2023b.eb
new file mode 100644
index 00000000000..090a4aaf87a
--- /dev/null
+++ b/easybuild/easyconfigs/r/rankwidth/rankwidth-0.9-foss-2023b.eb
@@ -0,0 +1,35 @@
+easyblock = 'ConfigureMake'
+
+name = 'rankwidth'
+version = '0.9'
+
+homepage = 'https://sourceforge.net/projects/rankwidth/'
+description = """rw calculates rank-width and rank-decompositions.
+It is based on ideas from "Computing rank-width exactly" by Sang-il Oum,
+"Sopra una formula numerica" by Ernesto Pascal, "Generation of a Vector
+from the Lexicographical Index" by B.P. Buckles and M. Lybanon and "Fast
+additions on masked integers" by Michael D. Adams and David S. Wise."""
+
+toolchain = {'name': 'foss', 'version': '2023b'}
+
+source_urls = ['https://master.dl.sourceforge.net/project/rankwidth']
+sources = ['rw-%(version)s.tar.gz']
+checksums = ['c1e03506fe25cdfcb428c051fc56b2d2affb5b06fba3f2ce756631466befb441']
+
+dependencies = [('igraph', '0.10.12')]
+
+# fix `too few arguments to function igraph_get_adjacency` error
+prebuildopts = 'sed -i "s/IGRAPH_GET_ADJACENCY_BOTH/IGRAPH_GET_ADJACENCY_BOTH, 0/g" simplerw.c && '
+
+sanity_check_paths = {
+    'files': [
+        'bin/rw',
+        'include/rw.h',
+        'lib/librw.%s' % SHLIB_EXT,
+    ],
+    'dirs': ['share'],
+}
+
+sanity_check_commands = ['rw --help | grep Usage:']
+
+moduleclass = 'math'

From 43c0b98d74e71bdc1114d3b24c84a05d882f04b6 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Petr=20Kr=C3=A1l?= <petr@inuits.eu>
Date: Mon, 10 Jun 2024 15:26:36 +0200
Subject: [PATCH 160/835] add 'pic' flag to IML

---
 easybuild/easyconfigs/i/IML/IML-1.0.5-gfbf-2023b.eb | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easybuild/easyconfigs/i/IML/IML-1.0.5-gfbf-2023b.eb b/easybuild/easyconfigs/i/IML/IML-1.0.5-gfbf-2023b.eb
index d9171489748..29698d8351f 100644
--- a/easybuild/easyconfigs/i/IML/IML-1.0.5-gfbf-2023b.eb
+++ b/easybuild/easyconfigs/i/IML/IML-1.0.5-gfbf-2023b.eb
@@ -8,6 +8,7 @@ description = """IML is a free library of C source code which implements algorit
  exact solutions to dense systems of linear equations over the integers."""
 
 toolchain = {'name': 'gfbf', 'version': '2023b'}
+toolchainopts = {'pic': True}
 
 source_urls = ['http://www.cs.uwaterloo.ca/~astorjoh']
 sources = [SOURCELOWER_TAR_BZ2]

From b1e193f8e9ecd372f6fdcd880265d478d34569f0 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Mon, 10 Jun 2024 15:34:14 +0200
Subject: [PATCH 161/835] adding easyconfigs:
 PretextMap-0.1.9-GCCcore-12.3.0.eb

---
 .../PretextMap-0.1.9-GCCcore-12.3.0.eb        | 40 +++++++++++++++++++
 1 file changed, 40 insertions(+)
 create mode 100644 easybuild/easyconfigs/p/PretextMap/PretextMap-0.1.9-GCCcore-12.3.0.eb

diff --git a/easybuild/easyconfigs/p/PretextMap/PretextMap-0.1.9-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/PretextMap/PretextMap-0.1.9-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..4c5e11ead4d
--- /dev/null
+++ b/easybuild/easyconfigs/p/PretextMap/PretextMap-0.1.9-GCCcore-12.3.0.eb
@@ -0,0 +1,40 @@
+easyblock = 'MesonNinja'
+
+name = 'PretextMap'
+version = '0.1.9'
+
+homepage = 'https://github.com/sanger-tol/PretextMap/'
+description = """Paired REad TEXTure Mapper. Converts SAM formatted read pairs into genome contact maps."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+sources = [{
+     'filename': '%(version)s.tar.gz',
+        'git_config': {
+            'url': 'https://github.com/sanger-tol',
+            'repo_name': '%(name)s',
+            'tag': '%(version)s',
+            'recursive': True,
+            'keep_git_dir': True,
+        },
+}]
+checksums = [None]
+
+builddependencies = [
+    ('Meson', '1.1.1'),
+    ('Ninja', '1.11.1'),
+    ('Clang', '16.0.6'),
+]
+
+preconfigopts = 'CXX=clang && '
+configure_cmd = 'meson setup --buildtype=release --unity on'
+runtest = 'meson test'
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['bin']
+}
+
+sanity_check_commands = ["command -v PretextMap"]
+
+moduleclass = 'lib'

From 0347e7d4fe4af0c9278cfa1cacf63a9bdc10d431 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com>
Date: Mon, 10 Jun 2024 15:36:15 +0200
Subject: [PATCH 162/835] Update PretextMap-0.1.9-GCCcore-12.3.0.eb moduleclass

---
 .../easyconfigs/p/PretextMap/PretextMap-0.1.9-GCCcore-12.3.0.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/p/PretextMap/PretextMap-0.1.9-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/PretextMap/PretextMap-0.1.9-GCCcore-12.3.0.eb
index 4c5e11ead4d..e2fdb0e0bc4 100644
--- a/easybuild/easyconfigs/p/PretextMap/PretextMap-0.1.9-GCCcore-12.3.0.eb
+++ b/easybuild/easyconfigs/p/PretextMap/PretextMap-0.1.9-GCCcore-12.3.0.eb
@@ -37,4 +37,4 @@ sanity_check_paths = {
 
 sanity_check_commands = ["command -v PretextMap"]
 
-moduleclass = 'lib'
+moduleclass = 'tools'

From 035fe8f2b17376e991d15d2bb9c3fb1dfa367b22 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Mon, 10 Jun 2024 15:52:15 +0200
Subject: [PATCH 163/835] fix indention

---
 .../PretextMap-0.1.9-GCCcore-12.3.0.eb           | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/easybuild/easyconfigs/p/PretextMap/PretextMap-0.1.9-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/PretextMap/PretextMap-0.1.9-GCCcore-12.3.0.eb
index e2fdb0e0bc4..70867a7c4a0 100644
--- a/easybuild/easyconfigs/p/PretextMap/PretextMap-0.1.9-GCCcore-12.3.0.eb
+++ b/easybuild/easyconfigs/p/PretextMap/PretextMap-0.1.9-GCCcore-12.3.0.eb
@@ -9,14 +9,14 @@ description = """Paired REad TEXTure Mapper. Converts SAM formatted read pairs i
 toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
 
 sources = [{
-     'filename': '%(version)s.tar.gz',
-        'git_config': {
-            'url': 'https://github.com/sanger-tol',
-            'repo_name': '%(name)s',
-            'tag': '%(version)s',
-            'recursive': True,
-            'keep_git_dir': True,
-        },
+    'filename': '%(version)s.tar.gz',
+    'git_config': {
+        'url': 'https://github.com/sanger-tol',
+        'repo_name': '%(name)s',
+        'tag': '%(version)s',
+        'recursive': True,
+        'keep_git_dir': True,
+    },
 }]
 checksums = [None]
 

From f3e9ffb601c75101a13c40eb24be5559a7c38326 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com>
Date: Mon, 10 Jun 2024 16:05:57 +0200
Subject: [PATCH 164/835] Update PretextMap-0.1.9-GCCcore-12.3.0.eb add
 binutils to builddeps

---
 .../easyconfigs/p/PretextMap/PretextMap-0.1.9-GCCcore-12.3.0.eb  | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easybuild/easyconfigs/p/PretextMap/PretextMap-0.1.9-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/PretextMap/PretextMap-0.1.9-GCCcore-12.3.0.eb
index 70867a7c4a0..69972971936 100644
--- a/easybuild/easyconfigs/p/PretextMap/PretextMap-0.1.9-GCCcore-12.3.0.eb
+++ b/easybuild/easyconfigs/p/PretextMap/PretextMap-0.1.9-GCCcore-12.3.0.eb
@@ -21,6 +21,7 @@ sources = [{
 checksums = [None]
 
 builddependencies = [
+    ('binutils', '2.40'),
     ('Meson', '1.1.1'),
     ('Ninja', '1.11.1'),
     ('Clang', '16.0.6'),

From 126f0dc2016dcd3b3db6a6a6a8350b682e2bb468 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Petr=20Kr=C3=A1l?= <petr@inuits.eu>
Date: Tue, 11 Jun 2024 08:15:11 +0200
Subject: [PATCH 165/835] add description for toolchainopts

---
 easybuild/easyconfigs/i/IML/IML-1.0.5-gfbf-2023b.eb | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/easybuild/easyconfigs/i/IML/IML-1.0.5-gfbf-2023b.eb b/easybuild/easyconfigs/i/IML/IML-1.0.5-gfbf-2023b.eb
index 29698d8351f..6417c65c5a8 100644
--- a/easybuild/easyconfigs/i/IML/IML-1.0.5-gfbf-2023b.eb
+++ b/easybuild/easyconfigs/i/IML/IML-1.0.5-gfbf-2023b.eb
@@ -8,6 +8,9 @@ description = """IML is a free library of C source code which implements algorit
  exact solutions to dense systems of linear equations over the integers."""
 
 toolchain = {'name': 'gfbf', 'version': '2023b'}
+# to fix the following error:
+# libiml.a(libiml_la-basisop.o): relocation ​​​​​​​​​​​​​​​​R_X86_64_32 against `.rodata.str1.1'
+# can not be used when making a shared object; recompile with -fPIC
 toolchainopts = {'pic': True}
 
 source_urls = ['http://www.cs.uwaterloo.ca/~astorjoh']

From 48ff1a8999f050fdc1bb56d49028818d0afdb9b7 Mon Sep 17 00:00:00 2001
From: Cintia Willemyns <115622907+WilleBell@users.noreply.github.com>
Date: Tue, 11 Jun 2024 09:17:34 +0200
Subject: [PATCH 166/835] Add sanity check command

---
 easybuild/easyconfigs/d/DL_POLY_4/DL_POLY_4-5.1.0-foss-2023a.eb | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/easybuild/easyconfigs/d/DL_POLY_4/DL_POLY_4-5.1.0-foss-2023a.eb b/easybuild/easyconfigs/d/DL_POLY_4/DL_POLY_4-5.1.0-foss-2023a.eb
index a0be0ed6765..1d47dce62d0 100644
--- a/easybuild/easyconfigs/d/DL_POLY_4/DL_POLY_4-5.1.0-foss-2023a.eb
+++ b/easybuild/easyconfigs/d/DL_POLY_4/DL_POLY_4-5.1.0-foss-2023a.eb
@@ -19,4 +19,6 @@ sanity_check_paths = {
     'dirs': []
 }
 
+sanity_check_commands = ['DLPOLY.Z -h']
+
 moduleclass = 'chem'

From 9e1793775e423cac40cfbd593a66768b0b32121a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Petr=20Kr=C3=A1l?= <petr@inuits.eu>
Date: Tue, 11 Jun 2024 10:36:07 +0200
Subject: [PATCH 167/835] remove comments

---
 easybuild/easyconfigs/i/IML/IML-1.0.5-gfbf-2023b.eb | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/easybuild/easyconfigs/i/IML/IML-1.0.5-gfbf-2023b.eb b/easybuild/easyconfigs/i/IML/IML-1.0.5-gfbf-2023b.eb
index 6417c65c5a8..29698d8351f 100644
--- a/easybuild/easyconfigs/i/IML/IML-1.0.5-gfbf-2023b.eb
+++ b/easybuild/easyconfigs/i/IML/IML-1.0.5-gfbf-2023b.eb
@@ -8,9 +8,6 @@ description = """IML is a free library of C source code which implements algorit
  exact solutions to dense systems of linear equations over the integers."""
 
 toolchain = {'name': 'gfbf', 'version': '2023b'}
-# to fix the following error:
-# libiml.a(libiml_la-basisop.o): relocation ​​​​​​​​​​​​​​​​R_X86_64_32 against `.rodata.str1.1'
-# can not be used when making a shared object; recompile with -fPIC
 toolchainopts = {'pic': True}
 
 source_urls = ['http://www.cs.uwaterloo.ca/~astorjoh']

From cbffdcb1e090b5f09f9beb77fdf9a22c29b8ab2e Mon Sep 17 00:00:00 2001
From: WilleBell <cintiawillemyns@gmail.com>
Date: Tue, 11 Jun 2024 10:40:51 +0200
Subject: [PATCH 168/835] remove CREST as dependency

---
 .../x/xtb-IFF/{xtb-IFF-1.1-gfbf-2023a.eb => xtb-IFF-1.1.eb} | 6 +-----
 1 file changed, 1 insertion(+), 5 deletions(-)
 rename easybuild/easyconfigs/x/xtb-IFF/{xtb-IFF-1.1-gfbf-2023a.eb => xtb-IFF-1.1.eb} (86%)

diff --git a/easybuild/easyconfigs/x/xtb-IFF/xtb-IFF-1.1-gfbf-2023a.eb b/easybuild/easyconfigs/x/xtb-IFF/xtb-IFF-1.1.eb
similarity index 86%
rename from easybuild/easyconfigs/x/xtb-IFF/xtb-IFF-1.1-gfbf-2023a.eb
rename to easybuild/easyconfigs/x/xtb-IFF/xtb-IFF-1.1.eb
index fd81ac4072d..ca25542f582 100644
--- a/easybuild/easyconfigs/x/xtb-IFF/xtb-IFF-1.1-gfbf-2023a.eb
+++ b/easybuild/easyconfigs/x/xtb-IFF/xtb-IFF-1.1.eb
@@ -8,16 +8,12 @@ description = """
 General Intermolecular Force Field based on Tight-Binding Quantum Chemical Calculations. 
 """
 
-toolchain = {'name': 'gfbf', 'version': '2023a'}
+toolchain = SYSTEM
 
 source_urls = ['https://github.com/grimme-lab/xtbiff/releases/download/v1.1']
 sources = ['xtbiff.tar.xz']
 checksums = ['6d5dee10ba39ecb1e26374b7bf82e2364d8ebed5b6f35cdce4ced73245c296f5']
 
-dependencies = [
-    ('CREST', '2.12'),
-]
-
 sanity_check_paths = {
     'files': ['xtbiff'],
     'dirs': [],

From e697b3676bd315fd91d66bdf909e80181e1e9275 Mon Sep 17 00:00:00 2001
From: Victor Enrique Goitea <victorg@bmb.sdu.dk>
Date: Wed, 12 Jun 2024 09:21:55 +0200
Subject: [PATCH 169/835] Added IMAGE-1.1-foss-2022b.eb easyconfig

---
 easybuild/easyconfigs/i/IMAGE/IMAGE-1.1-foss-2022b.eb | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 create mode 100644 easybuild/easyconfigs/i/IMAGE/IMAGE-1.1-foss-2022b.eb

diff --git a/easybuild/easyconfigs/i/IMAGE/IMAGE-1.1-foss-2022b.eb b/easybuild/easyconfigs/i/IMAGE/IMAGE-1.1-foss-2022b.eb
new file mode 100644
index 00000000000..e69de29bb2d

From 8c1ff78136c82f644f740081b4c182cbcb723296 Mon Sep 17 00:00:00 2001
From: Victor Enrique Goitea <43407659+VictorGoitea@users.noreply.github.com>
Date: Wed, 12 Jun 2024 09:24:57 +0200
Subject: [PATCH 170/835] Update IMAGE-1.1-foss-2022b.eb

---
 .../i/IMAGE/IMAGE-1.1-foss-2022b.eb           | 50 +++++++++++++++++++
 1 file changed, 50 insertions(+)

diff --git a/easybuild/easyconfigs/i/IMAGE/IMAGE-1.1-foss-2022b.eb b/easybuild/easyconfigs/i/IMAGE/IMAGE-1.1-foss-2022b.eb
index e69de29bb2d..41c0c2a2c32 100644
--- a/easybuild/easyconfigs/i/IMAGE/IMAGE-1.1-foss-2022b.eb
+++ b/easybuild/easyconfigs/i/IMAGE/IMAGE-1.1-foss-2022b.eb
@@ -0,0 +1,50 @@
+easyblock = 'Tarball'
+
+name = 'IMAGE'
+version = '1.1'
+
+homepage = 'https://github.com/JesperGrud/IMAGE'
+description = """IMAGE (Motif  Activity and  Gene  Expression changes of transcription factors) is software for
+integrated analysis of motif activity and gene expression changes of transcription factors. IMAGE makes prediction
+of causal transcription factors based on transcriptome profiling and genome-wide maps of enhancer activity."""
+
+toolchain = {'name': 'foss', 'version': '2022b'}
+
+dependencies = [
+    ('Perl', '5.36.0'),
+    ('Homer', '4.11.1'),
+    ('R', '4.2.2'),
+    ('R-bundle-Bioconductor', '3.16', '-R-4.2.2'),
+]
+
+source_urls = ['https://github.com/JesperGrud/IMAGE/archive/refs/tags']
+sources = ['v%(version)s.tar.gz']
+checksums = ['e286cd5e7eb5aaaf9e103a9651ece39ff4ce260c463facdf1758b6d72a285062']
+
+postinstallcmds = [
+    'mkdir %(installdir)s/bin',
+    'mkdir -p %(installdir)s/tmp',
+    'mv %(installdir)s/IMAGE.pl %(installdir)s/bin/',
+    'chmod +x %(installdir)s/bin/IMAGE.pl',
+    'sed -i "s|my \$TMPDIR = \$INSTALLDIR . \$TMP;|my \$TMPDIR = \'%(installdir)s\' . \$TMP;|g" %(installdir)s/bin/IMAGE.pl',
+    'sed -i "s|my \$UTILDIR = \$INSTALLDIR . \$UTIL;|my \$UTILDIR = \'%(installdir)s\' . \$UTIL;|g" %(installdir)s/bin/IMAGE.pl',
+]
+
+sanity_check_paths = {
+    'dirs': ['bin', 'utils', 'tmp'],
+    'files': [
+        'utils/Collection.motif',
+        'utils/extractSequence',
+        'utils/Genename_Motif.txt',
+        'utils/Parallel.sh',
+        'utils/Regression.R',
+        'utils/SplitMotifLibrary.sh',
+        'bin/IMAGE.pl',
+    ]
+}
+
+sanity_check_commands = [
+    "IMAGE.pl",
+]
+
+moduleclass = 'bio'

From d02ce893e354f681e6e0d8ecb920b7394e928c97 Mon Sep 17 00:00:00 2001
From: Victor Enrique Goitea <43407659+VictorGoitea@users.noreply.github.com>
Date: Wed, 12 Jun 2024 09:32:48 +0200
Subject: [PATCH 171/835] Create HOMER-4.11.1-foss-2022.eb

---
 .../h/HOMER/HOMER-4.11.1-foss-2022.eb         | 53 +++++++++++++++++++
 1 file changed, 53 insertions(+)
 create mode 100644 easybuild/easyconfigs/h/HOMER/HOMER-4.11.1-foss-2022.eb

diff --git a/easybuild/easyconfigs/h/HOMER/HOMER-4.11.1-foss-2022.eb b/easybuild/easyconfigs/h/HOMER/HOMER-4.11.1-foss-2022.eb
new file mode 100644
index 00000000000..a00997c71cb
--- /dev/null
+++ b/easybuild/easyconfigs/h/HOMER/HOMER-4.11.1-foss-2022.eb
@@ -0,0 +1,53 @@
+# This installs the entire suite, to install only base Homer package run :
+# cd %(installdir)s; perl ./configureHomer.pl -install homer
+
+easyblock = 'CmdCp'
+
+name = 'HOMER'
+version = '4.11.1'
+
+homepage = 'http://homer.ucsd.edu/homer/'
+description = """HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif
+Discovery and ChIP-Seq analysis. It is a collection of command line programs for unix-style operating
+systems written in mostly perl and c++. Homer was primarily written as a de novo motif discovery
+algorithm that is well suited for finding 8-12 bp motifs in large scale genomics data."""
+
+toolchain = {'name': 'foss', 'version': '2022b'}
+
+dependencies = [
+    ('Perl', '5.36.0'),
+    ('zlib', '1.2.12'),
+    ('Zip', '3.0'),
+    ('weblogo', '2.8.2'),
+    ('SAMtools', '1.17'),
+    ('Kent_tools', '461'),
+    ('R', '4.2.2'),
+    ('R-bundle-Bioconductor', '3.16', '-R-4.2.2')
+]
+
+source_urls = ['http://homer.ucsd.edu/homer/data/software']
+sources = ['homer.v%(version)s.zip']
+checksums = ['80d1cd00616729894017b24a36a2ef81f9cde8bd364e875aead1e0cfb500c82b']
+
+unpack_options = " && cp %(builddir)s/configureHomer.pl %(installdir)s "
+start_dir = "%(installdir)s"
+cmds_map = [('', 'perl ./configureHomer.pl -install -all')]
+skipsteps = ['install']
+
+files_to_copy = [
+    'bin', 'config.txt', 'data',
+    'DoughnutDocumentation.pdf',
+    'motifs',
+    'update',
+]
+
+sanity_check_paths = {
+    'dirs': ['bin', 'data', 'motifs', 'update'],
+    'files': [
+        'config.txt',
+        'DoughnutDocumentation.pdf',
+        'bin/homer',
+    ],
+}
+
+moduleclass = 'bio'

From c009d020906d98706b9b8df817f9cc42f2d687ba Mon Sep 17 00:00:00 2001
From: Victor Enrique Goitea <43407659+VictorGoitea@users.noreply.github.com>
Date: Wed, 12 Jun 2024 09:34:20 +0200
Subject: [PATCH 172/835] Rename HOMER-4.11.1-foss-2022.eb to
 HOMER-4.11.1-foss-2022b.eb

---
 .../{HOMER-4.11.1-foss-2022.eb => HOMER-4.11.1-foss-2022b.eb}     | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename easybuild/easyconfigs/h/HOMER/{HOMER-4.11.1-foss-2022.eb => HOMER-4.11.1-foss-2022b.eb} (100%)

diff --git a/easybuild/easyconfigs/h/HOMER/HOMER-4.11.1-foss-2022.eb b/easybuild/easyconfigs/h/HOMER/HOMER-4.11.1-foss-2022b.eb
similarity index 100%
rename from easybuild/easyconfigs/h/HOMER/HOMER-4.11.1-foss-2022.eb
rename to easybuild/easyconfigs/h/HOMER/HOMER-4.11.1-foss-2022b.eb

From 4b3a54e09f6175046425c48c201e5cbe34da7ab4 Mon Sep 17 00:00:00 2001
From: Victor Enrique Goitea <victorg@bmb.sdu.dk>
Date: Wed, 12 Jun 2024 09:38:02 +0200
Subject: [PATCH 173/835] Create weblogo-2.8.2-foss-2022b.eb

---
 .../w/weblogo/weblogo-2.8.2-foss-2022b.eb     | 46 +++++++++++++++++++
 1 file changed, 46 insertions(+)
 create mode 100644 easybuild/easyconfigs/w/weblogo/weblogo-2.8.2-foss-2022b.eb

diff --git a/easybuild/easyconfigs/w/weblogo/weblogo-2.8.2-foss-2022b.eb b/easybuild/easyconfigs/w/weblogo/weblogo-2.8.2-foss-2022b.eb
new file mode 100644
index 00000000000..4845116a7c7
--- /dev/null
+++ b/easybuild/easyconfigs/w/weblogo/weblogo-2.8.2-foss-2022b.eb
@@ -0,0 +1,46 @@
+easyblock = 'Tarball'
+
+name = 'weblogo'
+version = '2.8.2'
+
+homepage = "http://weblogo.berkeley.edu"
+description = """WebLogo is a web based application designed to make the generation of sequence logos as easy
+and painless as possible."""
+
+toolchain = {'name': 'foss', 'version': '2022b'}
+
+source_urls = ['https://weblogo.berkeley.edu/release']
+sources = ['weblogo.%(version)s.tar.gz']
+checksums = ['2d3e0040c0c1e363c1dfd57f8b585387eb682ed08b2cc2fe2e4cc2a33ac52266']
+
+dependencies = [
+    ('Perl', '5.36.0'),
+    ('Ghostscript', '10.0.0'),
+    ('ImageMagick', '7.1.0-53'),
+]
+
+postinstallcmds = [
+    'mkdir %(installdir)s/bin',
+    'mkdir -p %(installdir)s/lib',
+    'mv %(installdir)s/seqlogo %(installdir)s/bin/',
+    'cp %(installdir)s/template.eps %(installdir)s/bin/',
+    'mv %(installdir)s/*.pm %(installdir)s/lib/',  # Move all Perl modules to the lib directory
+    'mv %(installdir)s/logo.cgi %(installdir)s/lib/',
+    'chmod +x %(installdir)s/bin/seqlogo',
+]
+
+modextrapaths = {
+    'PERL5LIB': 'lib',  # Use relative path
+}
+
+sanity_check_paths = {
+    'files': ['bin/seqlogo', 'lib/logo.pm', 'lib/template.pm'],
+    'dirs': [],
+}
+
+sanity_check_commands = [
+    "PERL5LIB=%(installdir)s/lib %(installdir)s/bin/seqlogo %(installdir)s/globin.fasta"
+]
+
+moduleclass = 'bio'
+

From ad85aa55a00637803d03218773abcee6bc090ecc Mon Sep 17 00:00:00 2001
From: Victor Enrique Goitea <43407659+VictorGoitea@users.noreply.github.com>
Date: Wed, 12 Jun 2024 09:39:01 +0200
Subject: [PATCH 174/835] Update weblogo-2.8.2-foss-2022b.eb

---
 easybuild/easyconfigs/w/weblogo/weblogo-2.8.2-foss-2022b.eb | 1 -
 1 file changed, 1 deletion(-)

diff --git a/easybuild/easyconfigs/w/weblogo/weblogo-2.8.2-foss-2022b.eb b/easybuild/easyconfigs/w/weblogo/weblogo-2.8.2-foss-2022b.eb
index 4845116a7c7..f91055ed84e 100644
--- a/easybuild/easyconfigs/w/weblogo/weblogo-2.8.2-foss-2022b.eb
+++ b/easybuild/easyconfigs/w/weblogo/weblogo-2.8.2-foss-2022b.eb
@@ -43,4 +43,3 @@ sanity_check_commands = [
 ]
 
 moduleclass = 'bio'
-

From e56fe4d771bcca5bb7277f4f33ad918eb5cdedb8 Mon Sep 17 00:00:00 2001
From: Victor Enrique Goitea <victorg@bmb.sdu.dk>
Date: Wed, 12 Jun 2024 09:42:37 +0200
Subject: [PATCH 175/835] Create Kent_tools-641-GCC-12.2.0.eb

---
 .../k/Kent_tools/Kent_tools-641-GCC-12.2.0.eb | 45 +++++++++++++++++++
 1 file changed, 45 insertions(+)
 create mode 100644 easybuild/easyconfigs/k/Kent_tools/Kent_tools-641-GCC-12.2.0.eb

diff --git a/easybuild/easyconfigs/k/Kent_tools/Kent_tools-641-GCC-12.2.0.eb b/easybuild/easyconfigs/k/Kent_tools/Kent_tools-641-GCC-12.2.0.eb
new file mode 100644
index 00000000000..a2e25f3122a
--- /dev/null
+++ b/easybuild/easyconfigs/k/Kent_tools/Kent_tools-641-GCC-12.2.0.eb
@@ -0,0 +1,45 @@
+easyblock = 'MakeCp'
+
+name = 'Kent_tools'
+version = '461'
+
+homepage = 'https://genome.cse.ucsc.edu/'
+description = """Kent utilities: collection of tools used by the UCSC genome browser."""
+
+toolchain = {'name': 'GCC', 'version': '12.2.0'}
+source_urls = [
+    'https://hgdownload.cse.ucsc.edu/admin/exe/',
+    'https://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/',
+]
+sources = ['userApps.v%(version)s.src.tgz']
+checksums = [
+    {'userApps.v461.src.tgz': 'ff350f030906bea2cdfa5c57d713568123e17c1a5c0ce578d2d9633ca1b742bc'},
+]
+
+dependencies = [
+    ('MariaDB', '10.11.2'),
+    ('libpng', '1.6.38'),
+    ('zlib', '1.2.12'),
+    ('util-linux', '2.38.1'),
+    ('OpenSSL', '1.1', '', SYSTEM),
+    ('freetype', '2.12.1'),
+]
+
+prebuildopts = 'sed -i "s/rsync -a /cp -a /" %(builddir)s/userApps/kent/src/parasol/makefile && '
+
+buildopts = 'CC="$CC" COPT="$CFLAGS -fcommon" PNGLIB="-L$EBROOTLIBPNG/lib -lpng" ZLIB="-L$EBROOTZLIB/lib -lz" '
+buildopts += 'SSL_DIR="$EBROOTOPENSSL" SSLDIR="$EBROOTOPENSSL" MYSQLLIBS="-L$EBROOTMARIADB/lib -lmariadb -lstdc++" '
+
+local_binaries = ['blat', 'bedPartition', 'getRna', 'liftOver', 'mafGene', 'splitFile', 'twoBitToFa']
+
+files_to_copy = [(['bin/*'], 'bin'), 'licenseBlat.txt', 'licenseUcscGenomeBrowser.txt']
+
+sanity_check_paths = {
+    'files': ['bin/%s' % x for x in local_binaries],
+    'dirs': [],
+}
+
+sanity_check_commands = ["%s 2>&1 | grep '^usage:'" % x for x in local_binaries]
+
+moduleclass = 'bio'
+

From b4fdec64862ad576414cf906fc76eec46a8fa517 Mon Sep 17 00:00:00 2001
From: Victor Enrique Goitea <43407659+VictorGoitea@users.noreply.github.com>
Date: Wed, 12 Jun 2024 09:44:09 +0200
Subject: [PATCH 176/835] Update Kent_tools-641-GCC-12.2.0.eb

---
 easybuild/easyconfigs/k/Kent_tools/Kent_tools-641-GCC-12.2.0.eb | 1 -
 1 file changed, 1 deletion(-)

diff --git a/easybuild/easyconfigs/k/Kent_tools/Kent_tools-641-GCC-12.2.0.eb b/easybuild/easyconfigs/k/Kent_tools/Kent_tools-641-GCC-12.2.0.eb
index a2e25f3122a..9679801e25f 100644
--- a/easybuild/easyconfigs/k/Kent_tools/Kent_tools-641-GCC-12.2.0.eb
+++ b/easybuild/easyconfigs/k/Kent_tools/Kent_tools-641-GCC-12.2.0.eb
@@ -42,4 +42,3 @@ sanity_check_paths = {
 sanity_check_commands = ["%s 2>&1 | grep '^usage:'" % x for x in local_binaries]
 
 moduleclass = 'bio'
-

From 7f9f5771a77d0c90e451b63c3db2da99a0d195a7 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 12 Jun 2024 10:13:34 +0200
Subject: [PATCH 177/835] adding easyconfigs: EasyBuild-4.9.2.eb

---
 .../e/EasyBuild/EasyBuild-4.9.2.eb            | 44 +++++++++++++++++++
 1 file changed, 44 insertions(+)
 create mode 100644 easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.9.2.eb

diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.9.2.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.9.2.eb
new file mode 100644
index 00000000000..2b12ffe3d0b
--- /dev/null
+++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.9.2.eb
@@ -0,0 +1,44 @@
+easyblock = 'EB_EasyBuildMeta'
+
+name = 'EasyBuild'
+version = '4.9.2'
+
+homepage = 'https://easybuilders.github.io/easybuild'
+description = """EasyBuild is a software build and installation framework
+ written in Python that allows you to install software in a structured,
+ repeatable and robust way."""
+
+toolchain = SYSTEM
+
+source_urls = [
+    # easybuild-framework
+    'https://files.pythonhosted.org/packages/cc/1f/676fc9e29c68e9c39c6dadf150ab4e5bf4907de4b9afd2bc6e0afd24ab7c/',
+    # easybuild-easyblocks
+    'https://files.pythonhosted.org/packages/5d/85/e8593ceeb00c61253204e74d2a8360076ce016f42d83d33841f8e7de57a1/',
+    # easybuild-easyconfigs
+    'https://files.pythonhosted.org/packages/99/b2/d899b4310bc54a10e0fb46995a2abc333857db16d116f22a53b0313d13d7/',
+]
+sources = [
+    'easybuild_framework-%(version)s.tar.gz',
+    'easybuild_easyblocks-%(version)s.tar.gz',
+    'easybuild_easyconfigs-%(version)s.tar.gz',
+]
+checksums = [
+    {'easybuild_framework-4.9.2.tar.gz': 'cc6e0fe7bab2a96d424656ed70bf33e3b083eef5ceaa5d5fed88aa7b91dd3d63'},
+    {'easybuild_easyblocks-4.9.2.tar.gz': '48202a89995a3d0a19228a35e409228bb6aa190ec7d7a7560e449303954953df'},
+    {'easybuild_easyconfigs-4.9.2.tar.gz': '52d6f6378fc331cda8a94ff196d5bd6bb74c8029c973ee6a92763c256571eec7'},
+]
+
+# order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?)
+# EasyBuild is a (set of) Python packages, so it depends on Python
+# usually, we want to use the system Python, so no actual Python dependency is listed
+allow_system_deps = [('Python', SYS_PYTHON_VERSION)]
+
+local_pyshortver = '.'.join(SYS_PYTHON_VERSION.split('.')[:2])
+
+sanity_check_paths = {
+    'files': ['bin/eb'],
+    'dirs': ['lib/python%s/site-packages' % local_pyshortver],
+}
+
+moduleclass = 'tools'

From 78ff10bd3d8abc2a3955f9dc9bdd759dc5dfbcec Mon Sep 17 00:00:00 2001
From: Jakob Schiotz <schiotz@fysik.dtu.dk>
Date: Wed, 12 Jun 2024 10:51:12 +0200
Subject: [PATCH 178/835] adding easyconfigs: GPAW-24.6.0-foss-2023a.eb,
 ASE-3.23.0-gfbf-2023a.eb

---
 .../a/ASE/ASE-3.23.0-gfbf-2023a.eb            | 48 ++++++++++++++++++
 .../g/GPAW/GPAW-24.6.0-foss-2023a.eb          | 50 +++++++++++++++++++
 2 files changed, 98 insertions(+)
 create mode 100644 easybuild/easyconfigs/a/ASE/ASE-3.23.0-gfbf-2023a.eb
 create mode 100644 easybuild/easyconfigs/g/GPAW/GPAW-24.6.0-foss-2023a.eb

diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.23.0-gfbf-2023a.eb b/easybuild/easyconfigs/a/ASE/ASE-3.23.0-gfbf-2023a.eb
new file mode 100644
index 00000000000..554779e99cc
--- /dev/null
+++ b/easybuild/easyconfigs/a/ASE/ASE-3.23.0-gfbf-2023a.eb
@@ -0,0 +1,48 @@
+easyblock = 'PythonBundle'
+
+name = 'ASE'
+version = '3.23.0'
+
+homepage = 'https://wiki.fysik.dtu.dk/ase'
+description = """ASE is a python package providing an open source Atomic Simulation Environment
+ in the Python scripting language.
+
+From version 3.20.1 we also include the ase-ext package, it contains optional reimplementations
+in C of functions in ASE.  ASE uses it automatically when installed."""
+
+toolchain = {'name': 'gfbf', 'version': '2023a'}
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('Python-bundle-PyPI', '2023.06'),
+    ('SciPy-bundle', '2023.07'),
+    ('Flask', '2.3.3'),
+    ('matplotlib', '3.7.2'),
+    ('Tkinter', '%(pyver)s'),     # Needed by GUI of ASE
+    ('spglib-python', '2.1.0'),  # optional
+]
+
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    ('pytest-mock', '3.11.1', {
+        'checksums': ['7f6b125602ac6d743e523ae0bfa71e1a697a2f5534064528c6ff84c2f7c2fc7f'],
+    }),
+    ('ase', version, {
+        'checksums': ['91a2aa31d89bd90b0efdfe4a7e84264f32828b2abfc9f38e65e041ad76fec8ae'],
+    }),
+    ('ase-ext', '20.9.0', {
+        'checksums': ['a348b0e42cf9fdd11f04b3df002b0bf150002c8df2698ff08d3c8fc7a1223aed'],
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['bin/ase'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+# make sure Tkinter is available, otherwise 'ase gui' will not work
+sanity_check_commands = ["python -c 'import tkinter' "]
+
+moduleclass = 'chem'
diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-24.6.0-foss-2023a.eb b/easybuild/easyconfigs/g/GPAW/GPAW-24.6.0-foss-2023a.eb
new file mode 100644
index 00000000000..01b2d50556b
--- /dev/null
+++ b/easybuild/easyconfigs/g/GPAW/GPAW-24.6.0-foss-2023a.eb
@@ -0,0 +1,50 @@
+easyblock = "PythonPackage"
+
+name = 'GPAW'
+version = '24.6.0'
+
+homepage = 'https://wiki.fysik.dtu.dk/gpaw/'
+description = """GPAW is a density-functional theory (DFT) Python code based on the projector-augmented wave (PAW)
+ method and the atomic simulation environment (ASE). It uses real-space uniform grids and multigrid methods or
+ atom-centered basis-functions."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+toolchainopts = {'usempi': True, 'openmp': False}
+
+source_urls = [PYPI_LOWER_SOURCE]
+sources = [SOURCELOWER_TAR_GZ]
+patches = [
+    ('GPAW-20.1.0-Add-Easybuild-configuration-files.patch', 1),
+]
+checksums = [
+    {'gpaw-24.6.0.tar.gz': 'fb48ef0db48c0e321ce5967126a47900bba20c7efb420d6e7b5459983bd8f6f6'},
+    {'GPAW-20.1.0-Add-Easybuild-configuration-files.patch':
+     '2b337399479bf018a86156ed073dd7a78ec8c0df1f28b015f9284c6bf9fa5f15'},
+]
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('Python-bundle-PyPI', '2023.06'),
+    ('SciPy-bundle', '2023.07'),
+    ('ASE', '3.23.0'),
+    ('libxc', '6.2.2'),
+    ('libvdwxc', '0.4.0'),
+    ('ELPA', '2023.05.001'),
+    ('PyYAML', '6.0'),
+    ('GPAW-setups', '24.1.0', '', SYSTEM),
+]
+
+prebuildopts = 'GPAW_CONFIG=doc/platforms/Linux/EasyBuild/config_foss.py'
+preinstallopts = prebuildopts
+
+download_dep_fail = True
+use_pip = True
+sanity_pip_check = True
+
+sanity_check_paths = {
+    'files': ['bin/gpaw%s' % x for x in ['', '-analyse-basis', '-basis', '-plot-parallel-timings',
+                                         '-runscript', '-setup', '-upfplot']],
+    'dirs': ['lib/python%(pyshortver)s/site-packages']
+}
+
+moduleclass = 'chem'

From 9d60cb655ec293234527c4ca19b5012ab290d9cf Mon Sep 17 00:00:00 2001
From: Victor Enrique Goitea <43407659+VictorGoitea@users.noreply.github.com>
Date: Wed, 12 Jun 2024 11:07:10 +0200
Subject: [PATCH 179/835] Fix HOMER name in IMAGE-1.1-foss-2022b.eb

---
 easybuild/easyconfigs/i/IMAGE/IMAGE-1.1-foss-2022b.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/i/IMAGE/IMAGE-1.1-foss-2022b.eb b/easybuild/easyconfigs/i/IMAGE/IMAGE-1.1-foss-2022b.eb
index 41c0c2a2c32..35d4f050d35 100644
--- a/easybuild/easyconfigs/i/IMAGE/IMAGE-1.1-foss-2022b.eb
+++ b/easybuild/easyconfigs/i/IMAGE/IMAGE-1.1-foss-2022b.eb
@@ -12,7 +12,7 @@ toolchain = {'name': 'foss', 'version': '2022b'}
 
 dependencies = [
     ('Perl', '5.36.0'),
-    ('Homer', '4.11.1'),
+    ('HOMER', '4.11.1'),
     ('R', '4.2.2'),
     ('R-bundle-Bioconductor', '3.16', '-R-4.2.2'),
 ]

From 4ffa00a64d58be2d9ec1a278a1930b3dc38793a9 Mon Sep 17 00:00:00 2001
From: Jakob Schiotz <schiotz@fysik.dtu.dk>
Date: Wed, 12 Jun 2024 11:08:17 +0200
Subject: [PATCH 180/835] Fix the version suffix.

---
 .../GPAW/GPAW-24.6.0-foss-2023a-ASE-3.23.0.eb | 52 +++++++++++++++++++
 1 file changed, 52 insertions(+)
 create mode 100644 easybuild/easyconfigs/g/GPAW/GPAW-24.6.0-foss-2023a-ASE-3.23.0.eb

diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-24.6.0-foss-2023a-ASE-3.23.0.eb b/easybuild/easyconfigs/g/GPAW/GPAW-24.6.0-foss-2023a-ASE-3.23.0.eb
new file mode 100644
index 00000000000..62db4b69440
--- /dev/null
+++ b/easybuild/easyconfigs/g/GPAW/GPAW-24.6.0-foss-2023a-ASE-3.23.0.eb
@@ -0,0 +1,52 @@
+easyblock = "PythonPackage"
+
+name = 'GPAW'
+version = '24.6.0'
+_aseversion = '3.23.0'
+versionsuffix = '-ASE-' + _aseversion
+
+homepage = 'https://wiki.fysik.dtu.dk/gpaw/'
+description = """GPAW is a density-functional theory (DFT) Python code based on the projector-augmented wave (PAW)
+ method and the atomic simulation environment (ASE). It uses real-space uniform grids and multigrid methods or
+ atom-centered basis-functions."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+toolchainopts = {'usempi': True, 'openmp': False}
+
+source_urls = [PYPI_LOWER_SOURCE]
+sources = [SOURCELOWER_TAR_GZ]
+patches = [
+    ('GPAW-20.1.0-Add-Easybuild-configuration-files.patch', 1),
+]
+checksums = [
+    {'gpaw-24.6.0.tar.gz': 'fb48ef0db48c0e321ce5967126a47900bba20c7efb420d6e7b5459983bd8f6f6'},
+    {'GPAW-20.1.0-Add-Easybuild-configuration-files.patch':
+     '2b337399479bf018a86156ed073dd7a78ec8c0df1f28b015f9284c6bf9fa5f15'},
+]
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('Python-bundle-PyPI', '2023.06'),
+    ('SciPy-bundle', '2023.07'),
+    ('ASE', _aseversion),
+    ('libxc', '6.2.2'),
+    ('libvdwxc', '0.4.0'),
+    ('ELPA', '2023.05.001'),
+    ('PyYAML', '6.0'),
+    ('GPAW-setups', '24.1.0', '', SYSTEM),
+]
+
+prebuildopts = 'GPAW_CONFIG=doc/platforms/Linux/EasyBuild/config_foss.py'
+preinstallopts = prebuildopts
+
+download_dep_fail = True
+use_pip = True
+sanity_pip_check = True
+
+sanity_check_paths = {
+    'files': ['bin/gpaw%s' % x for x in ['', '-analyse-basis', '-basis', '-plot-parallel-timings',
+                                         '-runscript', '-setup', '-upfplot']],
+    'dirs': ['lib/python%(pyshortver)s/site-packages']
+}
+
+moduleclass = 'chem'

From 9e39eefa029bc2134f6374d4207828040a1b3219 Mon Sep 17 00:00:00 2001
From: Victor Enrique Goitea <43407659+VictorGoitea@users.noreply.github.com>
Date: Wed, 12 Jun 2024 11:18:27 +0200
Subject: [PATCH 181/835] Fix invalid escape sequence in
 IMAGE-1.1-foss-2022b.eb

---
 easybuild/easyconfigs/i/IMAGE/IMAGE-1.1-foss-2022b.eb | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/easybuild/easyconfigs/i/IMAGE/IMAGE-1.1-foss-2022b.eb b/easybuild/easyconfigs/i/IMAGE/IMAGE-1.1-foss-2022b.eb
index 35d4f050d35..53e62b27696 100644
--- a/easybuild/easyconfigs/i/IMAGE/IMAGE-1.1-foss-2022b.eb
+++ b/easybuild/easyconfigs/i/IMAGE/IMAGE-1.1-foss-2022b.eb
@@ -26,8 +26,8 @@ postinstallcmds = [
     'mkdir -p %(installdir)s/tmp',
     'mv %(installdir)s/IMAGE.pl %(installdir)s/bin/',
     'chmod +x %(installdir)s/bin/IMAGE.pl',
-    'sed -i "s|my \$TMPDIR = \$INSTALLDIR . \$TMP;|my \$TMPDIR = \'%(installdir)s\' . \$TMP;|g" %(installdir)s/bin/IMAGE.pl',
-    'sed -i "s|my \$UTILDIR = \$INSTALLDIR . \$UTIL;|my \$UTILDIR = \'%(installdir)s\' . \$UTIL;|g" %(installdir)s/bin/IMAGE.pl',
+    'sed -i "s|my \\$TMPDIR = \\$INSTALLDIR . \\$TMP;|my \\$TMPDIR = \'%(installdir)s\' . \\$TMP;|g" %(installdir)s/bin/IMAGE.pl',
+    'sed -i "s|my \\$UTILDIR = \\$INSTALLDIR . \\$UTIL;|my \\$UTILDIR = \'%(installdir)s\' . \\$UTIL;|g" %(installdir)s/bin/IMAGE.pl',
 ]
 
 sanity_check_paths = {

From 9835cc5cc4ca1f8b9c92152af1621ffcca65258e Mon Sep 17 00:00:00 2001
From: Jakob Schiotz <schiotz@fysik.dtu.dk>
Date: Wed, 12 Jun 2024 11:23:46 +0200
Subject: [PATCH 182/835] Remove version where a missing versionsuffix caused a
 wrong filename

---
 .../g/GPAW/GPAW-24.6.0-foss-2023a.eb          | 50 -------------------
 1 file changed, 50 deletions(-)
 delete mode 100644 easybuild/easyconfigs/g/GPAW/GPAW-24.6.0-foss-2023a.eb

diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-24.6.0-foss-2023a.eb b/easybuild/easyconfigs/g/GPAW/GPAW-24.6.0-foss-2023a.eb
deleted file mode 100644
index 01b2d50556b..00000000000
--- a/easybuild/easyconfigs/g/GPAW/GPAW-24.6.0-foss-2023a.eb
+++ /dev/null
@@ -1,50 +0,0 @@
-easyblock = "PythonPackage"
-
-name = 'GPAW'
-version = '24.6.0'
-
-homepage = 'https://wiki.fysik.dtu.dk/gpaw/'
-description = """GPAW is a density-functional theory (DFT) Python code based on the projector-augmented wave (PAW)
- method and the atomic simulation environment (ASE). It uses real-space uniform grids and multigrid methods or
- atom-centered basis-functions."""
-
-toolchain = {'name': 'foss', 'version': '2023a'}
-toolchainopts = {'usempi': True, 'openmp': False}
-
-source_urls = [PYPI_LOWER_SOURCE]
-sources = [SOURCELOWER_TAR_GZ]
-patches = [
-    ('GPAW-20.1.0-Add-Easybuild-configuration-files.patch', 1),
-]
-checksums = [
-    {'gpaw-24.6.0.tar.gz': 'fb48ef0db48c0e321ce5967126a47900bba20c7efb420d6e7b5459983bd8f6f6'},
-    {'GPAW-20.1.0-Add-Easybuild-configuration-files.patch':
-     '2b337399479bf018a86156ed073dd7a78ec8c0df1f28b015f9284c6bf9fa5f15'},
-]
-
-dependencies = [
-    ('Python', '3.11.3'),
-    ('Python-bundle-PyPI', '2023.06'),
-    ('SciPy-bundle', '2023.07'),
-    ('ASE', '3.23.0'),
-    ('libxc', '6.2.2'),
-    ('libvdwxc', '0.4.0'),
-    ('ELPA', '2023.05.001'),
-    ('PyYAML', '6.0'),
-    ('GPAW-setups', '24.1.0', '', SYSTEM),
-]
-
-prebuildopts = 'GPAW_CONFIG=doc/platforms/Linux/EasyBuild/config_foss.py'
-preinstallopts = prebuildopts
-
-download_dep_fail = True
-use_pip = True
-sanity_pip_check = True
-
-sanity_check_paths = {
-    'files': ['bin/gpaw%s' % x for x in ['', '-analyse-basis', '-basis', '-plot-parallel-timings',
-                                         '-runscript', '-setup', '-upfplot']],
-    'dirs': ['lib/python%(pyshortver)s/site-packages']
-}
-
-moduleclass = 'chem'

From 644674355664db9090bde92c3984e8b6c66e5909 Mon Sep 17 00:00:00 2001
From: Victor Enrique Goitea <43407659+VictorGoitea@users.noreply.github.com>
Date: Wed, 12 Jun 2024 11:54:34 +0200
Subject: [PATCH 183/835] Rename Kent_tools-641-GCC-12.2.0.eb to
 Kent_tools-461-GCC-12.2.0.eb

---
 ...{Kent_tools-641-GCC-12.2.0.eb => Kent_tools-461-GCC-12.2.0.eb} | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename easybuild/easyconfigs/k/Kent_tools/{Kent_tools-641-GCC-12.2.0.eb => Kent_tools-461-GCC-12.2.0.eb} (100%)

diff --git a/easybuild/easyconfigs/k/Kent_tools/Kent_tools-641-GCC-12.2.0.eb b/easybuild/easyconfigs/k/Kent_tools/Kent_tools-461-GCC-12.2.0.eb
similarity index 100%
rename from easybuild/easyconfigs/k/Kent_tools/Kent_tools-641-GCC-12.2.0.eb
rename to easybuild/easyconfigs/k/Kent_tools/Kent_tools-461-GCC-12.2.0.eb

From 11a49fae0330ba8e91c9fadd6ada9eb97ed1d14b Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Wed, 12 Jun 2024 15:35:51 +0200
Subject: [PATCH 184/835] adding easyconfigs: CellOracle-0.18.0-foss-2023a.eb,
 velocyto-0.17.17-foss-2023a.eb, genomepy-0.16.1-foss-2023a.eb,
 mygene-3.2.2-foss-2023a.eb, GimmeMotifs-0.17.2-foss-2023a.eb,
 HTSeq-2.0.7-foss-2023a.eb

---
 .../CellOracle-0.18.0-foss-2023a.eb           | 66 +++++++++++++++
 .../GimmeMotifs-0.17.2-foss-2023a.eb          | 81 +++++++++++++++++++
 .../g/genomepy/genomepy-0.16.1-foss-2023a.eb  | 56 +++++++++++++
 .../h/HTSeq/HTSeq-2.0.7-foss-2023a.eb         | 43 ++++++++++
 .../m/mygene/mygene-3.2.2-foss-2023a.eb       | 34 ++++++++
 .../v/velocyto/velocyto-0.17.17-foss-2023a.eb | 40 +++++++++
 6 files changed, 320 insertions(+)
 create mode 100644 easybuild/easyconfigs/c/CellOracle/CellOracle-0.18.0-foss-2023a.eb
 create mode 100644 easybuild/easyconfigs/g/GimmeMotifs/GimmeMotifs-0.17.2-foss-2023a.eb
 create mode 100644 easybuild/easyconfigs/g/genomepy/genomepy-0.16.1-foss-2023a.eb
 create mode 100644 easybuild/easyconfigs/h/HTSeq/HTSeq-2.0.7-foss-2023a.eb
 create mode 100644 easybuild/easyconfigs/m/mygene/mygene-3.2.2-foss-2023a.eb
 create mode 100644 easybuild/easyconfigs/v/velocyto/velocyto-0.17.17-foss-2023a.eb

diff --git a/easybuild/easyconfigs/c/CellOracle/CellOracle-0.18.0-foss-2023a.eb b/easybuild/easyconfigs/c/CellOracle/CellOracle-0.18.0-foss-2023a.eb
new file mode 100644
index 00000000000..d6eb8f4cead
--- /dev/null
+++ b/easybuild/easyconfigs/c/CellOracle/CellOracle-0.18.0-foss-2023a.eb
@@ -0,0 +1,66 @@
+easyblock = 'PythonBundle'
+
+name = 'CellOracle'
+version = '0.18.0'
+
+homepage = 'https://github.com/morris-lab/CellOracle'
+description = """CellOracle is a Python library for in silico gene perturbation analyses using single-cell omics data
+and Gene Regulatory Network models."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('R', '4.3.2'),
+    ('SciPy-bundle', '2023.07'),
+    ('Python-bundle-PyPI', '2023.06'),
+    ('numba', '0.58.1'),
+    ('matplotlib', '3.7.2'),
+    ('Seaborn', '0.13.2'),
+    ('scikit-learn', '1.3.1'),
+    ('h5py', '3.9.0'),
+    ('velocyto', '0.17.17'),
+    ('umap-learn', '0.5.5'),
+    ('Arrow', '14.0.1'),
+    ('tqdm', '4.66.1'),
+    ('python-igraph', '0.11.4'),
+    ('IPython', '8.14.0'),
+    ('scanpy', '1.9.8'),
+    ('GOATOOLS', '1.4.5'),
+    ('genomepy', '0.16.1'),
+    ('GimmeMotifs', '0.17.2'),
+    ('anndata', '0.10.5.post1'),
+    ('python-louvain', '0.16'),
+    ('jupyter-contrib-nbextensions', '0.7.0'),
+    ('Qtconsole', '5.5.1'),
+]
+
+use_pip = True
+
+# remove louvain from requirements, since CellOracle doesn't actually use it at all
+local_preinstallopts = "sed -i '/louvain/d' requirements.txt && "
+# drop strict version requirement for matplotlib dependency
+local_preinstallopts += "sed -i 's/matplotlib.*/matplotlib/g' requirements.txt && "
+# drop strict version requirement for pandas dependency
+local_preinstallopts += "sed -i 's/pandas.*/pandas/g' requirements.txt && "
+
+
+exts_list = [
+    ('jupyter_console', '6.6.3', {
+        'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl',
+        'checksums': ['309d33409fcc92ffdad25f0bcdf9a4a9daa61b6f341177570fdac03de5352485'],
+    }),
+    ('jupyter', '1.0.0', {
+        'checksums': ['d9dc4b3318f310e34c82951ea5d6683f67bed7def4b259fafbfe4f1beb1d8e5f'],
+    }),
+    ('celloracle', version, {
+        'preinstallopts': local_preinstallopts,
+        'checksums': ['a73bbdae36289748051e073409d853489a233bda90f50ab5031131b92dda2133'],
+    }),
+]
+
+sanity_check_commands = ["python -c 'import celloracle; celloracle.check_python_requirements()'"]
+
+sanity_pip_check = True
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/g/GimmeMotifs/GimmeMotifs-0.17.2-foss-2023a.eb b/easybuild/easyconfigs/g/GimmeMotifs/GimmeMotifs-0.17.2-foss-2023a.eb
new file mode 100644
index 00000000000..64b42485b8f
--- /dev/null
+++ b/easybuild/easyconfigs/g/GimmeMotifs/GimmeMotifs-0.17.2-foss-2023a.eb
@@ -0,0 +1,81 @@
+easyblock = 'PythonBundle'
+
+name = 'GimmeMotifs'
+version = '0.17.2'
+
+homepage = 'https://github.com/vanheeringen-lab/gimmemotifs'
+description = "Suite of motif tools, including a motif prediction pipeline for ChIP-seq experiments"
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+builddependencies = [('poetry', '1.5.1')]
+dependencies = [
+    ('Python', '3.11.3'),
+    ('Python-bundle-PyPI', '2023.06'),
+    ('SciPy-bundle', '2023.07'),
+    ('matplotlib', '3.7.2'),
+    ('pybedtools', '0.9.1'),
+    ('Pysam', '0.22.0'),
+    ('scikit-learn', '1.3.1'),
+    ('Seaborn', '0.13.2'),
+    ('statsmodels', '0.14.1'),
+    ('tqdm', '4.66.1'),
+    ('genomepy', '0.16.1'),
+    ('qnorm', '0.8.1'),
+    ('Arrow', '14.0.1'),  # provides pyarrow, required by feather-format
+    ('HTSeq', '2.0.7'),  # required by biofluff
+    ('pyBigWig', '0.3.22'),  # required by biofluff
+]
+
+use_pip = True
+
+exts_list = [
+    ('palettable', '3.3.3', {
+        'checksums': ['094dd7d9a5fc1cca4854773e5c1fc6a315b33bd5b3a8f47064928facaf0490a8'],
+    }),
+    ('biofluff', '3.0.4', {
+        'modulename': 'fluff',
+        # remove pyBigWig dependency - pip_check fails with "import pybigwig"
+        'preinstallopts': "sed -i '/pyBigWig/d' setup.py && ",
+        'checksums': ['ef7b0a54103a830f197f21aa3d1ade8bdcddf613b437ea38c95260bb45324d6b'],
+    }),
+    ('diskcache', '5.6.3', {
+        'checksums': ['2c3a3fa2743d8535d832ec61c2054a1641f41775aa7c556758a109941e33e4fc'],
+    }),
+    ('feather-format', '0.4.1', {
+        'modulename': 'feather',
+        'checksums': ['45f67e3745d394d4f160ca6d636bbfd4f8b68d01199dc1649b6e487d3e878903'],
+    }),
+    ('iteround', '1.0.4', {
+        'source_urls': ['https://github.com/cgdeboer/iteround/archive/'],
+        'sources': ['v%(version)s.tar.gz'],
+        'checksums': ['445e4f0c793ae558e4db3cdee7e23d77459b9c586e8021667aa60c14ba7ff45f'],
+    }),
+    ('logomaker', '0.8', {
+        'checksums': ['d8c7501a7d6d7961cd68e5a44e939000ebf1b0c4197a0c9198351e1d681d3f6d'],
+    }),
+    ('loguru', '0.7.2', {
+        'checksums': ['e671a53522515f34fd406340ee968cb9ecafbc4b36c679da03c18fd8d0bd51ac'],
+    }),
+    ('xxhash', '3.4.1', {
+        'checksums': ['0379d6cf1ff987cd421609a264ce025e74f346e3e145dd106c0cc2e3ec3f99a9'],
+    }),
+    ('xdg', '6.0.0', {
+        'checksums': ['24278094f2d45e846d1eb28a2ebb92d7b67fc0cab5249ee3ce88c95f649a1c92'],
+    }),
+    ('gimmemotifs', version, {
+        'preinstallopts': """sed -i '/"configparser"/d' setup.py && """,
+        'checksums': ['fbf70997abce6a75451c10b96994f8dbc03152b01df5cf30bf4397c98a9b54d2'],
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['bin/gimme'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = ["gimme --help"]
+
+sanity_pip_check = True
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/g/genomepy/genomepy-0.16.1-foss-2023a.eb b/easybuild/easyconfigs/g/genomepy/genomepy-0.16.1-foss-2023a.eb
new file mode 100644
index 00000000000..345af8fe325
--- /dev/null
+++ b/easybuild/easyconfigs/g/genomepy/genomepy-0.16.1-foss-2023a.eb
@@ -0,0 +1,56 @@
+easyblock = 'PythonBundle'
+
+name = 'genomepy'
+version = '0.16.1'
+
+homepage = 'https://github.com/vanheeringen-lab/genomepy'
+description = "genomepy is designed to provide a simple and straightforward way to download and use genomic data"
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+builddependencies = [('hatchling', '1.18.0')]
+dependencies = [
+    ('Python', '3.11.3'),
+    ('Python-bundle-PyPI', '2023.06'),
+    ('SciPy-bundle', '2023.07'),
+    ('tqdm', '4.66.1'),
+    ('Biopython', '1.83'),
+    ('mygene', '3.2.2'),
+    ('pyfaidx', '0.8.1.1'),
+    ('PyYAML', '6.0'),
+    ('protobuf-python', '4.24.0'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('diskcache', '5.6.3', {
+        'checksums': ['2c3a3fa2743d8535d832ec61c2054a1641f41775aa7c556758a109941e33e4fc'],
+    }),
+    ('loguru', '0.7.2', {
+        'checksums': ['e671a53522515f34fd406340ee968cb9ecafbc4b36c679da03c18fd8d0bd51ac'],
+    }),
+    ('mysql-connector-python', '8.4.0', {
+        'modulename': 'mysql.connector',
+        'sources': ['mysql_connector_python-%(version)s-py2.py3-none-any.whl'],
+        'checksums': ['35939c4ff28f395a5550bae67bafa4d1658ea72ea3206f457fff64a0fbec17e4'],
+    }),
+    ('norns', '0.1.6', {
+        'preinstallopts': "sed -i '/nose/d' setup.py && ",
+        'checksums': ['1f3c6ccbe79b2cb3076f66a352cd76462593adbabe9ebb262f879a9d0a6634e4'],
+    }),
+    (name, version, {
+        'checksums': ['22e81827acfdb4d9e6adda1f8e4cfafbb97f1c1788348e86b930c9daa51088c5'],
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['bin/genomepy'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = ["genomepy --help"]
+
+sanity_pip_check = True
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/h/HTSeq/HTSeq-2.0.7-foss-2023a.eb b/easybuild/easyconfigs/h/HTSeq/HTSeq-2.0.7-foss-2023a.eb
new file mode 100644
index 00000000000..60ffab860b4
--- /dev/null
+++ b/easybuild/easyconfigs/h/HTSeq/HTSeq-2.0.7-foss-2023a.eb
@@ -0,0 +1,43 @@
+# Updated to PythonBundle and latest version from Pypi
+# Author: J. Sassmannshausen (Imperial College London/UK)
+# Update: P.Tománek (Inuits)
+
+easyblock = 'PythonBundle'
+
+name = 'HTSeq'
+version = '2.0.7'
+
+homepage = 'https://github.com/simon-anders/htseq'
+description = """HTSeq is a Python library to facilitate processing and analysis
+ of data from high-throughput sequencing (HTS) experiments."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+builddependencies = [('SWIG', '4.1.1')]
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('Python-bundle-PyPI', '2023.06'),
+    ('Pysam', '0.22.0'),
+    ('SciPy-bundle', '2023.07'),
+    ('matplotlib', '3.7.2'),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    ('htseq', version, {
+        'modulename': 'HTSeq',
+        'checksums': ['c1490cede77fb04c8f3a9efeb44d41399cd466a6082180529e63c1dade203fdd'],
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['bin/%(namelower)s-count', 'bin/%(namelower)s-qa'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s/scripts'],
+}
+
+sanity_check_commands = ['%(namelower)s-count --help']
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/m/mygene/mygene-3.2.2-foss-2023a.eb b/easybuild/easyconfigs/m/mygene/mygene-3.2.2-foss-2023a.eb
new file mode 100644
index 00000000000..1c49c2ece32
--- /dev/null
+++ b/easybuild/easyconfigs/m/mygene/mygene-3.2.2-foss-2023a.eb
@@ -0,0 +1,34 @@
+# Author: Pavel Grochal (INUITS)
+# Update: Pavel Tománek (INUITS)
+# License: GPLv2
+
+easyblock = 'PythonBundle'
+
+name = 'mygene'
+version = '3.2.2'
+
+homepage = 'https://github.com/biothings/mygene.py'
+description = "Python Client for MyGene.Info services."
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('Python-bundle-PyPI', '2023.06'),
+    ('SciPy-bundle', '2023.07'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('biothings_client', '0.3.1', {
+        'checksums': ['c972bf2e02b6f9cc78f7f2fbc5ef02cc56fe4f8a2adcb8801ec902f4ab7011e6'],
+    }),
+    (name, version, {
+        'checksums': ['e729cabbc28cf5afb221bca1ab637883b375cb1a3e2f067587ec79f71affdaea'],
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/v/velocyto/velocyto-0.17.17-foss-2023a.eb b/easybuild/easyconfigs/v/velocyto/velocyto-0.17.17-foss-2023a.eb
new file mode 100644
index 00000000000..344d3ab3895
--- /dev/null
+++ b/easybuild/easyconfigs/v/velocyto/velocyto-0.17.17-foss-2023a.eb
@@ -0,0 +1,40 @@
+easyblock = 'PythonBundle'
+
+name = 'velocyto'
+version = '0.17.17'
+
+homepage = 'https://velocyto.org/velocyto.py/'
+description = "Velocyto is a library for the analysis of RNA velocity."
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('Python-bundle-PyPI', '2023.06'),
+    ('SciPy-bundle', '2023.07'),
+    ('matplotlib', '3.7.2'),
+    ('numba', '0.58.1'),
+    ('scikit-learn', '1.3.1'),
+    ('h5py', '3.9.0'),
+    ('Pysam', '0.22.0'),
+    ('loompy', '3.0.7'),
+]
+
+use_pip = True
+
+exts_list = [
+    (name, version, {
+        'checksums': ['1ad65fc53292ce1970a70bc742d73491b370038e0b0065761303e787bf7ffe39'],
+    }),
+]
+
+sanity_pip_check = True
+
+sanity_check_paths = {
+    'files': ['bin/velocyto'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = ['velocyto']
+
+moduleclass = 'bio'

From ed860fd33282ef52f72c99855d0c8fa7c04cfd51 Mon Sep 17 00:00:00 2001
From: Bart Oldeman <bart.oldeman@calculquebec.ca>
Date: Wed, 12 Jun 2024 14:00:41 +0000
Subject: [PATCH 185/835] Add internal CUDA header patch for PSM2

---
 .../p/PSM2/PSM2-12.0.1-GCCcore-10.3.0.eb      |  4 +-
 .../p/PSM2/PSM2-12.0.1-GCCcore-11.2.0.eb      |  4 +-
 .../p/PSM2/PSM2-12.0.1-GCCcore-11.3.0.eb      |  4 +-
 .../p/PSM2/PSM2-12.0.1-GCCcore-12.2.0.eb      |  4 +-
 .../p/PSM2/PSM2-12.0.1-GCCcore-12.3.0.eb      |  4 +-
 .../p/PSM2/PSM2-12.0.1-GCCcore-13.2.0.eb      |  4 +-
 .../p/PSM2/PSM2-12.0.1-GCCcore-13.3.0.eb      |  4 +-
 ....0.1_build-with-internal-cuda-header.patch | 88 +++++++++++++++++++
 8 files changed, 109 insertions(+), 7 deletions(-)
 create mode 100644 easybuild/easyconfigs/p/PSM2/PSM2-12.0.1_build-with-internal-cuda-header.patch

diff --git a/easybuild/easyconfigs/p/PSM2/PSM2-12.0.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/PSM2/PSM2-12.0.1-GCCcore-10.3.0.eb
index a7f0ee5d469..1f6981d1dae 100644
--- a/easybuild/easyconfigs/p/PSM2/PSM2-12.0.1-GCCcore-10.3.0.eb
+++ b/easybuild/easyconfigs/p/PSM2/PSM2-12.0.1-GCCcore-10.3.0.eb
@@ -15,15 +15,17 @@ source_urls = ['https://github.com/cornelisnetworks/opa-psm2/archive/refs/tags']
 sources = ['%(name)s_%(version)s.tar.gz']
 patches = [
     ('PSM2-11.2.80_hfi-user.patch', 1),
+    ('PSM2-12.0.1_build-with-internal-cuda-header.patch', 1),
 ]
 checksums = [
     {'PSM2_12.0.1.tar.gz': 'e41af2d7d36a6ab67639ecbd5c1012aa20b2b464bf5cfbdac60e7eb37bfe58de'},
     {'PSM2-11.2.80_hfi-user.patch': 'e43138859387213506050af9b76e193c3cd0a162d148998c39e551f220392abb'},
+    {'PSM2-12.0.1_build-with-internal-cuda-header.patch':
+     '0016327d7eade9e763ffbc468cf25c182d743074dca2885dea7ef0cf7e3b23cf'},
 ]
 
 builddependencies = [
     ('binutils', '2.36.1'),
-    ('CUDA', '11.3.1', '', SYSTEM),
 ]
 
 dependencies = [
diff --git a/easybuild/easyconfigs/p/PSM2/PSM2-12.0.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/PSM2/PSM2-12.0.1-GCCcore-11.2.0.eb
index 779d6bcdd0a..325c404a055 100644
--- a/easybuild/easyconfigs/p/PSM2/PSM2-12.0.1-GCCcore-11.2.0.eb
+++ b/easybuild/easyconfigs/p/PSM2/PSM2-12.0.1-GCCcore-11.2.0.eb
@@ -15,15 +15,17 @@ source_urls = ['https://github.com/cornelisnetworks/opa-psm2/archive/refs/tags']
 sources = ['%(name)s_%(version)s.tar.gz']
 patches = [
     ('PSM2-11.2.80_hfi-user.patch', 1),
+    ('PSM2-12.0.1_build-with-internal-cuda-header.patch', 1),
 ]
 checksums = [
     {'PSM2_12.0.1.tar.gz': 'e41af2d7d36a6ab67639ecbd5c1012aa20b2b464bf5cfbdac60e7eb37bfe58de'},
     {'PSM2-11.2.80_hfi-user.patch': 'e43138859387213506050af9b76e193c3cd0a162d148998c39e551f220392abb'},
+    {'PSM2-12.0.1_build-with-internal-cuda-header.patch':
+     '0016327d7eade9e763ffbc468cf25c182d743074dca2885dea7ef0cf7e3b23cf'},
 ]
 
 builddependencies = [
     ('binutils', '2.37'),
-    ('CUDA', '11.5.2', '', SYSTEM),
 ]
 
 dependencies = [
diff --git a/easybuild/easyconfigs/p/PSM2/PSM2-12.0.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/PSM2/PSM2-12.0.1-GCCcore-11.3.0.eb
index 7fa4c192e3b..b93b34dc43e 100644
--- a/easybuild/easyconfigs/p/PSM2/PSM2-12.0.1-GCCcore-11.3.0.eb
+++ b/easybuild/easyconfigs/p/PSM2/PSM2-12.0.1-GCCcore-11.3.0.eb
@@ -15,15 +15,17 @@ source_urls = ['https://github.com/cornelisnetworks/opa-psm2/archive/refs/tags']
 sources = ['%(name)s_%(version)s.tar.gz']
 patches = [
     ('PSM2-11.2.80_hfi-user.patch', 1),
+    ('PSM2-12.0.1_build-with-internal-cuda-header.patch', 1),
 ]
 checksums = [
     {'PSM2_12.0.1.tar.gz': 'e41af2d7d36a6ab67639ecbd5c1012aa20b2b464bf5cfbdac60e7eb37bfe58de'},
     {'PSM2-11.2.80_hfi-user.patch': 'e43138859387213506050af9b76e193c3cd0a162d148998c39e551f220392abb'},
+    {'PSM2-12.0.1_build-with-internal-cuda-header.patch':
+     '0016327d7eade9e763ffbc468cf25c182d743074dca2885dea7ef0cf7e3b23cf'},
 ]
 
 builddependencies = [
     ('binutils', '2.38'),
-    ('CUDA', '11.7.0', '', SYSTEM),
 ]
 
 dependencies = [
diff --git a/easybuild/easyconfigs/p/PSM2/PSM2-12.0.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/PSM2/PSM2-12.0.1-GCCcore-12.2.0.eb
index fbf417d2bc8..fa91a78538e 100644
--- a/easybuild/easyconfigs/p/PSM2/PSM2-12.0.1-GCCcore-12.2.0.eb
+++ b/easybuild/easyconfigs/p/PSM2/PSM2-12.0.1-GCCcore-12.2.0.eb
@@ -15,15 +15,17 @@ source_urls = ['https://github.com/cornelisnetworks/opa-psm2/archive/refs/tags']
 sources = ['%(name)s_%(version)s.tar.gz']
 patches = [
     ('PSM2-11.2.80_hfi-user.patch', 1),
+    ('PSM2-12.0.1_build-with-internal-cuda-header.patch', 1),
 ]
 checksums = [
     {'PSM2_12.0.1.tar.gz': 'e41af2d7d36a6ab67639ecbd5c1012aa20b2b464bf5cfbdac60e7eb37bfe58de'},
     {'PSM2-11.2.80_hfi-user.patch': 'e43138859387213506050af9b76e193c3cd0a162d148998c39e551f220392abb'},
+    {'PSM2-12.0.1_build-with-internal-cuda-header.patch':
+     '0016327d7eade9e763ffbc468cf25c182d743074dca2885dea7ef0cf7e3b23cf'},
 ]
 
 builddependencies = [
     ('binutils', '2.39'),
-    ('CUDA', '12.0.0', '', SYSTEM),
 ]
 
 dependencies = [
diff --git a/easybuild/easyconfigs/p/PSM2/PSM2-12.0.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/PSM2/PSM2-12.0.1-GCCcore-12.3.0.eb
index 0470fe64363..169b08b1e36 100644
--- a/easybuild/easyconfigs/p/PSM2/PSM2-12.0.1-GCCcore-12.3.0.eb
+++ b/easybuild/easyconfigs/p/PSM2/PSM2-12.0.1-GCCcore-12.3.0.eb
@@ -15,15 +15,17 @@ source_urls = ['https://github.com/cornelisnetworks/opa-psm2/archive/refs/tags']
 sources = ['%(name)s_%(version)s.tar.gz']
 patches = [
     ('PSM2-11.2.80_hfi-user.patch', 1),
+    ('PSM2-12.0.1_build-with-internal-cuda-header.patch', 1),
 ]
 checksums = [
     {'PSM2_12.0.1.tar.gz': 'e41af2d7d36a6ab67639ecbd5c1012aa20b2b464bf5cfbdac60e7eb37bfe58de'},
     {'PSM2-11.2.80_hfi-user.patch': 'e43138859387213506050af9b76e193c3cd0a162d148998c39e551f220392abb'},
+    {'PSM2-12.0.1_build-with-internal-cuda-header.patch':
+     '0016327d7eade9e763ffbc468cf25c182d743074dca2885dea7ef0cf7e3b23cf'},
 ]
 
 builddependencies = [
     ('binutils', '2.40'),
-    ('CUDA', '12.1.1', '', SYSTEM),
 ]
 
 dependencies = [
diff --git a/easybuild/easyconfigs/p/PSM2/PSM2-12.0.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/PSM2/PSM2-12.0.1-GCCcore-13.2.0.eb
index cfe3fe9f1e4..ee265c55610 100644
--- a/easybuild/easyconfigs/p/PSM2/PSM2-12.0.1-GCCcore-13.2.0.eb
+++ b/easybuild/easyconfigs/p/PSM2/PSM2-12.0.1-GCCcore-13.2.0.eb
@@ -15,15 +15,17 @@ source_urls = ['https://github.com/cornelisnetworks/opa-psm2/archive/refs/tags']
 sources = ['%(name)s_%(version)s.tar.gz']
 patches = [
     ('PSM2-11.2.80_hfi-user.patch', 1),
+    ('PSM2-12.0.1_build-with-internal-cuda-header.patch', 1),
 ]
 checksums = [
     {'PSM2_12.0.1.tar.gz': 'e41af2d7d36a6ab67639ecbd5c1012aa20b2b464bf5cfbdac60e7eb37bfe58de'},
     {'PSM2-11.2.80_hfi-user.patch': 'e43138859387213506050af9b76e193c3cd0a162d148998c39e551f220392abb'},
+    {'PSM2-12.0.1_build-with-internal-cuda-header.patch':
+     '0016327d7eade9e763ffbc468cf25c182d743074dca2885dea7ef0cf7e3b23cf'},
 ]
 
 builddependencies = [
     ('binutils', '2.40'),
-    ('CUDA', '12.4.0', '', SYSTEM),
 ]
 
 dependencies = [
diff --git a/easybuild/easyconfigs/p/PSM2/PSM2-12.0.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/PSM2/PSM2-12.0.1-GCCcore-13.3.0.eb
index 78d99d2efec..aff3d686fc7 100644
--- a/easybuild/easyconfigs/p/PSM2/PSM2-12.0.1-GCCcore-13.3.0.eb
+++ b/easybuild/easyconfigs/p/PSM2/PSM2-12.0.1-GCCcore-13.3.0.eb
@@ -15,15 +15,17 @@ source_urls = ['https://github.com/cornelisnetworks/opa-psm2/archive/refs/tags']
 sources = ['%(name)s_%(version)s.tar.gz']
 patches = [
     ('PSM2-11.2.80_hfi-user.patch', 1),
+    ('PSM2-12.0.1_build-with-internal-cuda-header.patch', 1),
 ]
 checksums = [
     {'PSM2_12.0.1.tar.gz': 'e41af2d7d36a6ab67639ecbd5c1012aa20b2b464bf5cfbdac60e7eb37bfe58de'},
     {'PSM2-11.2.80_hfi-user.patch': 'e43138859387213506050af9b76e193c3cd0a162d148998c39e551f220392abb'},
+    {'PSM2-12.0.1_build-with-internal-cuda-header.patch':
+     '0016327d7eade9e763ffbc468cf25c182d743074dca2885dea7ef0cf7e3b23cf'},
 ]
 
 builddependencies = [
     ('binutils', '2.42'),
-    ('CUDA', '12.4.0', '', SYSTEM),
 ]
 
 dependencies = [
diff --git a/easybuild/easyconfigs/p/PSM2/PSM2-12.0.1_build-with-internal-cuda-header.patch b/easybuild/easyconfigs/p/PSM2/PSM2-12.0.1_build-with-internal-cuda-header.patch
new file mode 100644
index 00000000000..3e3ffd8038e
--- /dev/null
+++ b/easybuild/easyconfigs/p/PSM2/PSM2-12.0.1_build-with-internal-cuda-header.patch
@@ -0,0 +1,88 @@
+Allow building PSM2 without a CUDA builddependency, by providing an
+internal minimal cuda.h header file.
+As long as the runtime CUDA version is 8.0+, libcuda.so will be dlopen'ed and
+used successfully.
+
+Author: Bart Oldeman <bart.oldeman@calculquebec.ca>
+diff -urN opa-psm2-PSM2_12.0.1.orig/include/cuda.h opa-psm2-PSM2_12.0.1/include/cuda.h
+--- opa-psm2-PSM2_12.0.1.orig/include/cuda.h	1970-01-01 00:00:00.000000000 +0000
++++ opa-psm2-PSM2_12.0.1/include/cuda.h	2024-06-11 18:39:38.242975935 +0000
+@@ -0,0 +1,73 @@
++/* This header provides minimal parts of the CUDA Driver API, without having to
++   rely on the proprietary CUDA toolkit.
++
++   References (to avoid copying from NVidia's proprietary cuda.h):
++   https://github.com/gcc-mirror/gcc/blob/master/include/cuda/cuda.h
++   https://github.com/Theano/libgpuarray/blob/master/src/loaders/libcuda.h
++   https://github.com/CPFL/gdev/blob/master/cuda/driver/cuda.h
++   https://github.com/CudaWrangler/cuew/blob/master/include/cuew.h
++*/
++
++#ifndef PSM2_CUDA_H
++#define PSM2_CUDA_H
++
++#include <stddef.h>
++
++#define CUDA_VERSION 8000
++
++typedef void *CUcontext;
++typedef int CUdevice;
++#if defined(__LP64__) || defined(_WIN64)
++typedef unsigned long long CUdeviceptr;
++#else
++typedef unsigned CUdeviceptr;
++#endif
++typedef void *CUevent;
++typedef void *CUstream;
++
++typedef enum {
++  CUDA_SUCCESS = 0,
++  CUDA_ERROR_ALREADY_MAPPED = 208,
++  CUDA_ERROR_NOT_READY = 600,
++} CUresult;
++
++enum {
++  CU_EVENT_DEFAULT = 0x0,
++};
++
++enum {
++  CU_IPC_MEM_LAZY_ENABLE_PEER_ACCESS = 0x1,
++};
++
++typedef enum {
++  CU_POINTER_ATTRIBUTE_MEMORY_TYPE = 2,
++  CU_POINTER_ATTRIBUTE_SYNC_MEMOPS = 6,
++  CU_POINTER_ATTRIBUTE_IS_MANAGED = 8,
++} CUpointer_attribute;
++
++
++typedef enum {
++  CU_MEMORYTYPE_HOST = 0x01,
++  CU_MEMORYTYPE_DEVICE = 0x02,
++} CUmemorytype;
++
++#define CU_IPC_HANDLE_SIZE 64
++
++typedef struct CUipcMemHandle_st {
++    char reserved[CU_IPC_HANDLE_SIZE];
++} CUipcMemHandle;
++
++typedef enum {
++  CU_DEVICE_ATTRIBUTE_UNIFIED_ADDRESSING = 41,
++  CU_DEVICE_ATTRIBUTE_COMPUTE_CAPABILITY_MAJOR = 75,
++} CUdevice_attribute;
++
++enum {
++  CU_STREAM_NON_BLOCKING = 1
++};
++
++enum {
++  CU_MEMHOSTALLOC_PORTABLE = 0x01,
++};
++
++#endif
+diff -urN opa-psm2-PSM2_12.0.1.orig/include/driver_types.h opa-psm2-PSM2_12.0.1/include/driver_types.h
+--- opa-psm2-PSM2_12.0.1.orig/include/driver_types.h    1970-01-01 00:00:00.000000000 +0000
++++ opa-psm2-PSM2_12.0.1/include/driver_types.h 2024-06-12 13:46:04.123858352 +0000
+@@ -0,0 +1 @@
++/* this file is empty */

From 2e5f601c2473de8a6d2e4650954654b190764481 Mon Sep 17 00:00:00 2001
From: Victor Enrique Goitea <43407659+VictorGoitea@users.noreply.github.com>
Date: Wed, 12 Jun 2024 19:10:18 +0200
Subject: [PATCH 186/835] Shorten long lines IMAGE-1.1-foss-2022b.eb

---
 easybuild/easyconfigs/i/IMAGE/IMAGE-1.1-foss-2022b.eb | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/easybuild/easyconfigs/i/IMAGE/IMAGE-1.1-foss-2022b.eb b/easybuild/easyconfigs/i/IMAGE/IMAGE-1.1-foss-2022b.eb
index 53e62b27696..a7747fe1799 100644
--- a/easybuild/easyconfigs/i/IMAGE/IMAGE-1.1-foss-2022b.eb
+++ b/easybuild/easyconfigs/i/IMAGE/IMAGE-1.1-foss-2022b.eb
@@ -26,8 +26,14 @@ postinstallcmds = [
     'mkdir -p %(installdir)s/tmp',
     'mv %(installdir)s/IMAGE.pl %(installdir)s/bin/',
     'chmod +x %(installdir)s/bin/IMAGE.pl',
-    'sed -i "s|my \\$TMPDIR = \\$INSTALLDIR . \\$TMP;|my \\$TMPDIR = \'%(installdir)s\' . \\$TMP;|g" %(installdir)s/bin/IMAGE.pl',
-    'sed -i "s|my \\$UTILDIR = \\$INSTALLDIR . \\$UTIL;|my \\$UTILDIR = \'%(installdir)s\' . \\$UTIL;|g" %(installdir)s/bin/IMAGE.pl',
+    (
+        'sed -i "s|my \\$TMPDIR = \\$INSTALLDIR . \\$TMP;|my \\$TMPDIR = \'%(installdir)s\' . \\$TMP;|g" '
+        '%(installdir)s/bin/IMAGE.pl'
+    ),
+    (
+        'sed -i "s|my \\$UTILDIR = \\$INSTALLDIR . \\$UTIL;|my \\$UTILDIR = \'%(installdir)s\' . \\$UTIL;|g" '
+        '%(installdir)s/bin/IMAGE.pl'
+    ),
 ]
 
 sanity_check_paths = {

From ec6f7d9408de8c44ea7be7e3d9c9d1b0dfe792bd Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Wed, 12 Jun 2024 19:35:38 +0200
Subject: [PATCH 187/835] adding easyconfigs: MeshLab-2023.12-GCC-12.3.0.eb

---
 .../m/MeshLab/MeshLab-2023.12-GCC-12.3.0.eb   | 47 +++++++++++++++++++
 1 file changed, 47 insertions(+)
 create mode 100644 easybuild/easyconfigs/m/MeshLab/MeshLab-2023.12-GCC-12.3.0.eb

diff --git a/easybuild/easyconfigs/m/MeshLab/MeshLab-2023.12-GCC-12.3.0.eb b/easybuild/easyconfigs/m/MeshLab/MeshLab-2023.12-GCC-12.3.0.eb
new file mode 100644
index 00000000000..ca152c147be
--- /dev/null
+++ b/easybuild/easyconfigs/m/MeshLab/MeshLab-2023.12-GCC-12.3.0.eb
@@ -0,0 +1,47 @@
+easyblock = 'CMakeNinja'
+
+name = 'MeshLab'
+version = '2023.12'
+
+homepage = 'https://github.com/cnr-isti-vclab/meshlab'
+description = 'The open source mesh processing system.'
+
+toolchain = {'name': 'GCC', 'version': '12.3.0'}
+
+sources = [{
+    'filename': '%(name)s-%(version)s.tar.gz',
+    'git_config': {
+        'url': 'https://github.com/cnr-isti-vclab',
+        'repo_name': '%(namelower)s',
+        'tag': '%(name)s-%(version)s',
+        'recursive': True,
+        'keep_git_dir': True,
+    },
+}]
+checksums = [None]
+
+builddependencies = [
+    ('CMake', '3.26.3'),
+    ('Ninja', '1.11.1'),
+    ('pkgconf', '1.9.5'),
+    ('patchelf', '0.18.0'),
+    ('Eigen', '3.4.0'),
+]
+
+dependencies = [
+    ('Qt5', '5.15.10'),
+    ('Mesa', '23.1.4'),
+    ('libGLU', '9.0.3'),
+    ('CGAL', '5.6'),
+    ('Boost', '1.82.0'),
+    ('MPFR', '4.2.0'),
+]
+
+sanity_check_paths = {
+    'files': ['bin/meshlab'],
+    'dirs': ['share'],
+}
+
+sanity_check_commands = ['meshlab --help']
+
+moduleclass = 'vis'

From 977db35e6b7c93e286ba22bfdaf0d90ce89aff14 Mon Sep 17 00:00:00 2001
From: Jakob Schiotz <schiotz@fysik.dtu.dk>
Date: Wed, 12 Jun 2024 20:01:17 +0200
Subject: [PATCH 188/835] adding easyconfigs:
 GPAW-24.6.0-intel-2023a-ASE-3.23.0.eb, ASE-3.23.0-iimkl-2023a.eb

---
 .../a/ASE/ASE-3.23.0-iimkl-2023a.eb           | 48 +++++++++++++++++
 .../GPAW-24.6.0-intel-2023a-ASE-3.23.0.eb     | 51 +++++++++++++++++++
 2 files changed, 99 insertions(+)
 create mode 100644 easybuild/easyconfigs/a/ASE/ASE-3.23.0-iimkl-2023a.eb
 create mode 100644 easybuild/easyconfigs/g/GPAW/GPAW-24.6.0-intel-2023a-ASE-3.23.0.eb

diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.23.0-iimkl-2023a.eb b/easybuild/easyconfigs/a/ASE/ASE-3.23.0-iimkl-2023a.eb
new file mode 100644
index 00000000000..f8bbed9f583
--- /dev/null
+++ b/easybuild/easyconfigs/a/ASE/ASE-3.23.0-iimkl-2023a.eb
@@ -0,0 +1,48 @@
+easyblock = 'PythonBundle'
+
+name = 'ASE'
+version = '3.23.0'
+
+homepage = 'https://wiki.fysik.dtu.dk/ase'
+description = """ASE is a python package providing an open source Atomic Simulation Environment
+ in the Python scripting language.
+
+From version 3.20.1 we also include the ase-ext package, it contains optional reimplementations
+in C of functions in ASE.  ASE uses it automatically when installed."""
+
+toolchain = {'name': 'iimkl', 'version': '2023a'}
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('Python-bundle-PyPI', '2023.06'),
+    ('SciPy-bundle', '2023.07'),
+    ('Flask', '2.3.3'),
+    ('matplotlib', '3.7.2'),
+    ('Tkinter', '%(pyver)s'),     # Needed by GUI of ASE
+    ('spglib-python', '2.1.0'),  # optional
+]
+
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    ('pytest-mock', '3.11.1', {
+        'checksums': ['7f6b125602ac6d743e523ae0bfa71e1a697a2f5534064528c6ff84c2f7c2fc7f'],
+    }),
+    ('ase', version, {
+        'checksums': ['91a2aa31d89bd90b0efdfe4a7e84264f32828b2abfc9f38e65e041ad76fec8ae'],
+    }),
+    ('ase-ext', '20.9.0', {
+        'checksums': ['a348b0e42cf9fdd11f04b3df002b0bf150002c8df2698ff08d3c8fc7a1223aed'],
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['bin/ase'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+# make sure Tkinter is available, otherwise 'ase gui' will not work
+sanity_check_commands = ["python -c 'import tkinter' "]
+
+moduleclass = 'chem'
diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-24.6.0-intel-2023a-ASE-3.23.0.eb b/easybuild/easyconfigs/g/GPAW/GPAW-24.6.0-intel-2023a-ASE-3.23.0.eb
new file mode 100644
index 00000000000..dc4091af2d3
--- /dev/null
+++ b/easybuild/easyconfigs/g/GPAW/GPAW-24.6.0-intel-2023a-ASE-3.23.0.eb
@@ -0,0 +1,51 @@
+easyblock = "PythonPackage"
+
+name = 'GPAW'
+version = '24.6.0'
+_aseversion = '3.23.0'
+versionsuffix = '-ASE-' + _aseversion
+
+homepage = 'https://wiki.fysik.dtu.dk/gpaw/'
+description = """GPAW is a density-functional theory (DFT) Python code based on the projector-augmented wave (PAW)
+ method and the atomic simulation environment (ASE). It uses real-space uniform grids and multigrid methods or
+ atom-centered basis-functions."""
+
+toolchain = {'name': 'intel', 'version': '2023a'}
+toolchainopts = {'usempi': True, 'openmp': False}
+
+source_urls = [PYPI_LOWER_SOURCE]
+sources = [SOURCELOWER_TAR_GZ]
+patches = [
+    ('GPAW-20.1.0-Add-Easybuild-configuration-files.patch', 1),
+]
+checksums = [
+    {'gpaw-24.6.0.tar.gz': 'fb48ef0db48c0e321ce5967126a47900bba20c7efb420d6e7b5459983bd8f6f6'},
+    {'GPAW-20.1.0-Add-Easybuild-configuration-files.patch':
+     '2b337399479bf018a86156ed073dd7a78ec8c0df1f28b015f9284c6bf9fa5f15'},
+]
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('Python-bundle-PyPI', '2023.06'),
+    ('SciPy-bundle', '2023.07'),
+    ('ASE', _aseversion),
+    ('libxc', '6.2.2'),
+    ('ELPA', '2023.05.001'),
+    ('PyYAML', '6.0'),
+    ('GPAW-setups', '24.1.0', '', SYSTEM),
+]
+
+prebuildopts = 'GPAW_CONFIG=doc/platforms/Linux/EasyBuild/config_intel.py'
+preinstallopts = prebuildopts
+
+download_dep_fail = True
+use_pip = True
+sanity_pip_check = True
+
+sanity_check_paths = {
+    'files': ['bin/gpaw%s' % x for x in ['', '-analyse-basis', '-basis', '-plot-parallel-timings',
+                                         '-runscript', '-setup', '-upfplot']],
+    'dirs': ['lib/python%(pyshortver)s/site-packages']
+}
+
+moduleclass = 'chem'

From 9ca4f13c7ecaf6355403b8ac6eeb3ef2b463cd68 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Wed, 12 Jun 2024 20:39:56 +0200
Subject: [PATCH 189/835] adding easyconfigs:
 IEntropy-2024.06.12-foss-2023a-R-4.3.2.eb

---
 .../IEntropy-2024.06.12-foss-2023a-R-4.3.2.eb | 36 +++++++++++++++++++
 1 file changed, 36 insertions(+)
 create mode 100644 easybuild/easyconfigs/i/IEntropy/IEntropy-2024.06.12-foss-2023a-R-4.3.2.eb

diff --git a/easybuild/easyconfigs/i/IEntropy/IEntropy-2024.06.12-foss-2023a-R-4.3.2.eb b/easybuild/easyconfigs/i/IEntropy/IEntropy-2024.06.12-foss-2023a-R-4.3.2.eb
new file mode 100644
index 00000000000..ee26df679bf
--- /dev/null
+++ b/easybuild/easyconfigs/i/IEntropy/IEntropy-2024.06.12-foss-2023a-R-4.3.2.eb
@@ -0,0 +1,36 @@
+easyblock = 'RPackage'
+
+name = 'IEntropy'
+version = '2024.06.12'
+local_commit = '3cd58ab'
+versionsuffix = '-R-%(rver)s'
+
+homepage = 'https://github.com/LinLi-0909/IEntropy'
+description = """Here, by deriving entropy decomposition formula, we proposed a feature selection method, 
+intrinsic entropy (IE) model, to identify the informative genes for accurately clustering analysis."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+source_urls = ['https://github.com/LinLi-0909/IEntropy/archive/']
+sources = [{
+    "download_filename": "%s.tar.gz" % local_commit,
+    "filename": "%(name)s-%(version)s.tar.gz"
+}]
+checksums = ['7449340df7218c790dcdff5dbb14ba7d613bd9bdfb0a440296a561bbb742f9c1']
+
+dependencies = [
+    ('R', '4.3.2'),
+    ('R-bundle-Bioconductor', '3.18', '-R-%(rver)s'),
+]
+
+unpack_sources = True
+start_dir = 'IEntropy'
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['%(name)s'],
+}
+
+sanity_check_commands = ['Rscript -e "library(IEntropy)"']
+
+moduleclass = 'bio'

From 684a4ba0ab22165d9110a47a8a7dd4d980bf2aa4 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 12 Jun 2024 23:11:37 +0200
Subject: [PATCH 190/835] adding easyconfigs: CUDA-12.5.0.eb

---
 easybuild/easyconfigs/c/CUDA/CUDA-12.5.0.eb | 24 +++++++++++++++++++++
 1 file changed, 24 insertions(+)
 create mode 100644 easybuild/easyconfigs/c/CUDA/CUDA-12.5.0.eb

diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-12.5.0.eb b/easybuild/easyconfigs/c/CUDA/CUDA-12.5.0.eb
new file mode 100644
index 00000000000..0a81b7bd4c1
--- /dev/null
+++ b/easybuild/easyconfigs/c/CUDA/CUDA-12.5.0.eb
@@ -0,0 +1,24 @@
+name = 'CUDA'
+version = '12.5.0'
+local_nv_version = '555.42.02'
+
+homepage = 'https://developer.nvidia.com/cuda-toolkit'
+description = """CUDA (formerly Compute Unified Device Architecture) is a parallel
+ computing platform and programming model created by NVIDIA and implemented by the
+ graphics processing units (GPUs) that they produce. CUDA gives developers access
+ to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs."""
+
+toolchain = SYSTEM
+
+source_urls = ['https://developer.download.nvidia.com/compute/cuda/%(version)s/local_installers/']
+sources = ['cuda_%%(version)s_%s_linux%%(cudaarch)s.run' % local_nv_version]
+checksums = [{
+    'cuda_%%(version)s_%s_linux.run' % local_nv_version:
+        '90fcc7df48226434065ff12a4372136b40b9a4cbf0c8602bb763b745f22b7a99',
+    'cuda_%%(version)s_%s_linux_ppc64le.run' % local_nv_version:
+        '33f39ad7bc624d5c8e59938990358cec80b9966431e34d1ab2d6115d78a3f264',
+    'cuda_%%(version)s_%s_linux_sbsa.run' % local_nv_version:
+        'e7b864c9ae27cef77cafc78614ec33cbb0a27606af9375deffa09c4269a07f04'
+}]
+
+moduleclass = 'system'

From 1c44b06628ed8099d70400e91183c517db401611 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 12 Jun 2024 23:12:26 +0200
Subject: [PATCH 191/835] adding easyconfigs:
 UCX-CUDA-1.15.0-GCCcore-13.2.0-CUDA-12.5.0.eb

---
 ...-CUDA-1.15.0-GCCcore-13.2.0-CUDA-12.5.0.eb | 41 +++++++++++++++++++
 1 file changed, 41 insertions(+)
 create mode 100644 easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.15.0-GCCcore-13.2.0-CUDA-12.5.0.eb

diff --git a/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.15.0-GCCcore-13.2.0-CUDA-12.5.0.eb b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.15.0-GCCcore-13.2.0-CUDA-12.5.0.eb
new file mode 100644
index 00000000000..5c88f6a5c5d
--- /dev/null
+++ b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.15.0-GCCcore-13.2.0-CUDA-12.5.0.eb
@@ -0,0 +1,41 @@
+easyblock = 'EB_UCX_Plugins'
+
+name = 'UCX-CUDA'
+version = '1.15.0'
+versionsuffix = '-CUDA-%(cudaver)s'
+
+homepage = 'http://www.openucx.org/'
+description = """Unified Communication X
+An open-source production grade communication framework for data centric
+and high-performance applications
+
+This module adds the UCX CUDA support.
+"""
+
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://github.com/openucx/ucx/releases/download/v%(version)s']
+sources = [{'filename': 'ucx-%(version)s.tar.gz', 'alt_location': 'UCX'}]
+patches = ['%(name)s-1.11.0_link_against_existing_UCX_libs.patch']
+checksums = [
+    {'ucx-1.15.0.tar.gz': '4b202087076bc1c98f9249144f0c277a8ea88ad4ca6f404f94baa9cb3aebda6d'},
+    {'UCX-CUDA-1.11.0_link_against_existing_UCX_libs.patch':
+     '457187fa020e526609ba91e7750c9941d57bd57d60d6eed317b40ad8824aca93'},
+]
+
+builddependencies = [
+    ('binutils', '2.40'),
+    ('Autotools', '20220317'),
+    ('pkgconf', '2.0.3'),
+]
+
+dependencies = [
+    ('zlib', '1.2.13'),
+    ('UCX', version),
+    ('CUDA', '12.5.0', '', SYSTEM),
+    ('GDRCopy', '2.4'),
+]
+
+
+moduleclass = 'lib'

From b3e3e65cb98f99b26928b9920535dbdd2878aa82 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 12 Jun 2024 23:26:05 +0200
Subject: [PATCH 192/835] bump version to 4.9.3dev

---
 setup.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index 3aa9a822208..8d3cd7f76d0 100644
--- a/setup.py
+++ b/setup.py
@@ -44,7 +44,7 @@
 # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like
 #   UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0'
 # This causes problems further up the dependency chain...
-VERSION = '4.9.2'
+VERSION = '4.9.3.dev0'
 
 MAJ_VER = VERSION.split('.')[0]
 MAJMIN_VER = '.'.join(VERSION.split('.')[0:2])

From 8e6aa82ef4f44d4309efaedd0b16e0b10d7135bd Mon Sep 17 00:00:00 2001
From: Alexander Grund <alexander.grund@tu-dresden.de>
Date: Thu, 13 Jun 2024 08:58:31 +0200
Subject: [PATCH 193/835] Add patch fixing compilation on AVX512 systems

> invalid 'static_cast' from type 'const Eigen::internal::eigen_packet_wrapper<__vector(4) long long int, 1>' to type '__vector(16) float'
---
 ...ensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb |  3 ++
 .../TensorFlow-2.15.1-foss-2023a.eb           |  3 ++
 ...-2.15.1_fix-AVX512-eigen-compilation.patch | 47 +++++++++++++++++++
 3 files changed, 53 insertions(+)
 create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_fix-AVX512-eigen-compilation.patch

diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb
index c42d4201898..93dcd628ac3 100644
--- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb
+++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb
@@ -150,6 +150,7 @@ exts_list = [
             'TensorFlow-2.15.1_remove-libclang-dep.patch',
             'TensorFlow-2.15.1_remove-io-gcs-filesystem-dep.patch',
             'TensorFlow-2.15.1_add-default-shell-env.patch',
+            'TensorFlow-2.15.1_fix-AVX512-eigen-compilation.patch',
             'TensorFlow-2.15.1_fix-flatbuffer-license.patch',
             'TensorFlow-2.15.1_fix-pybind11-build.patch',
             'TensorFlow-2.15.1_fix-cuda_build_defs.patch',
@@ -208,6 +209,8 @@ exts_list = [
              'eba7351a4b0696c589b9c507bacb0257ebce8c39fde39ab72d5d6a69deaaec02'},
             {'TensorFlow-2.15.1_add-default-shell-env.patch':
              '3d5196b4bf2e91048dc8a18f9e8f487a223fcd973d6302e80b0d4000ea3d652b'},
+            {'TensorFlow-2.15.1_fix-AVX512-eigen-compilation.patch':
+             '761059e5f5f5eeeef8aed5517a7685a0eb0a9193d4afe8d45237527681c9c0a3'},
             {'TensorFlow-2.15.1_fix-flatbuffer-license.patch':
              '2c04d5095977a628a238dbf93c5fada7159c86752a7183e64e0cf7c7ab00caf4'},
             {'TensorFlow-2.15.1_fix-pybind11-build.patch':
diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a.eb
index 6db18627261..506cbafd52b 100644
--- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a.eb
+++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a.eb
@@ -144,6 +144,7 @@ exts_list = [
             'TensorFlow-2.15.1_remove-libclang-dep.patch',
             'TensorFlow-2.15.1_remove-io-gcs-filesystem-dep.patch',
             'TensorFlow-2.15.1_add-default-shell-env.patch',
+            'TensorFlow-2.15.1_fix-AVX512-eigen-compilation.patch',
             'TensorFlow-2.15.1_fix-flatbuffer-license.patch',
             'TensorFlow-2.15.1_fix-pybind11-build.patch',
             'TensorFlow-2.15.1_disable-avx512-extensions.patch',
@@ -195,6 +196,8 @@ exts_list = [
              'eba7351a4b0696c589b9c507bacb0257ebce8c39fde39ab72d5d6a69deaaec02'},
             {'TensorFlow-2.15.1_add-default-shell-env.patch':
              '3d5196b4bf2e91048dc8a18f9e8f487a223fcd973d6302e80b0d4000ea3d652b'},
+            {'TensorFlow-2.15.1_fix-AVX512-eigen-compilation.patch':
+             '761059e5f5f5eeeef8aed5517a7685a0eb0a9193d4afe8d45237527681c9c0a3'},
             {'TensorFlow-2.15.1_fix-flatbuffer-license.patch':
              '2c04d5095977a628a238dbf93c5fada7159c86752a7183e64e0cf7c7ab00caf4'},
             {'TensorFlow-2.15.1_fix-pybind11-build.patch':
diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_fix-AVX512-eigen-compilation.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_fix-AVX512-eigen-compilation.patch
new file mode 100644
index 00000000000..514f215cde9
--- /dev/null
+++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_fix-AVX512-eigen-compilation.patch
@@ -0,0 +1,47 @@
+Fix a compilation error for CPUs with AVX512 features where an issue in Eigen leads to
+> invalid 'static_cast' from type 'const Eigen::internal::eigen_packet_wrapper<__vector(4) long long int, 1>' to type '__vector(16) float'
+
+See https://gitlab.com/libeigen/eigen/-/issues/2829
+
+Author: Alexander Grund (TU Dresden)
+
+diff --git a/third_party/eigen3/fix-avx512.patch b/third_party/eigen3/fix-avx512.patch
+new file mode 100644
+index 00000000000..0650d52a0c9
+--- /dev/null
++++ b/third_party/eigen3/fix-avx512.patch
+@@ -0,0 +1,22 @@
++diff --git a/Eigen/src/Core/arch/AVX512/TypeCasting.h b/Eigen/src/Core/arch/AVX512/TypeCasting.h
++index 02c56282f..e253e6b49 100644
++--- a/Eigen/src/Core/arch/AVX512/TypeCasting.h
+++++ b/Eigen/src/Core/arch/AVX512/TypeCasting.h
++@@ -145,8 +145,6 @@ template<> EIGEN_STRONG_INLINE Packet8bf preinterpret<Packet8bf, Packet16bf>(con
++   return _mm256_castsi256_si128(a);
++ }
++ 
++-#ifndef EIGEN_VECTORIZE_AVX512FP16
++-
++ template<> EIGEN_STRONG_INLINE Packet16f pcast<Packet16h, Packet16f>(const Packet16h& a) {
++   return half2float(a);
++ }
++@@ -155,8 +153,6 @@ template<> EIGEN_STRONG_INLINE Packet16h pcast<Packet16f, Packet16h>(const Packe
++   return float2half(a);
++ }
++ 
++-#endif
++-
++ template<> EIGEN_STRONG_INLINE Packet16f pcast<Packet16bf, Packet16f>(const Packet16bf& a) {
++   return Bf16ToF32(a);
++ }
+diff --git a/third_party/eigen3/workspace.bzl b/third_party/eigen3/workspace.bzl
+index d1d8d4ac486..da549e37432 100644
+--- a/third_party/eigen3/workspace.bzl
++++ b/third_party/eigen3/workspace.bzl
+@@ -14,6 +14,7 @@ def repo():
+     tf_http_archive(
+         name = "eigen_archive",
+         build_file = "//third_party/eigen3:eigen_archive.BUILD",
++        patch_file = ["//third_party/eigen3:fix-avx512.patch"],
+         sha256 = EIGEN_SHA256,
+         strip_prefix = "eigen-{commit}".format(commit = EIGEN_COMMIT),
+         urls = tf_mirror_urls("https://gitlab.com/libeigen/eigen/-/archive/{commit}/eigen-{commit}.tar.gz".format(commit = EIGEN_COMMIT)),

From 4f1f5677c8d1105dec468a79eaa8f45590314e91 Mon Sep 17 00:00:00 2001
From: Simon Pinches <Simon.Pinches@iter.org>
Date: Thu, 13 Jun 2024 10:03:23 +0200
Subject: [PATCH 194/835] adding easyconfigs: Maven-3.9.7.eb

---
 easybuild/easyconfigs/m/Maven/Maven-3.9.7.eb | 26 ++++++++++++++++++++
 1 file changed, 26 insertions(+)
 create mode 100644 easybuild/easyconfigs/m/Maven/Maven-3.9.7.eb

diff --git a/easybuild/easyconfigs/m/Maven/Maven-3.9.7.eb b/easybuild/easyconfigs/m/Maven/Maven-3.9.7.eb
new file mode 100644
index 00000000000..63a55f376df
--- /dev/null
+++ b/easybuild/easyconfigs/m/Maven/Maven-3.9.7.eb
@@ -0,0 +1,26 @@
+# Contribution from the Crick HPC team
+# uploaded by J. Sassmannshausen
+
+easyblock = 'PackedBinary'
+
+name = 'Maven'
+version = '3.9.7'
+
+homepage = 'https://maven.apache.org/index.html'
+description = """Binary maven install, Apache Maven is a software project management and comprehension tool. Based on
+the concept of a project object model (POM), Maven can manage a project's build, reporting and documentation from a
+central piece of information.
+"""
+
+toolchain = SYSTEM
+
+source_urls = ['https://archive.apache.org/dist/maven/maven-%(version_major)s/%(version)s/binaries/']
+sources = ['apache-maven-%(version)s-bin.tar.gz']
+checksums = ['c8fb9f620e5814588c2241142bbd9827a08e3cb415f7aa437f2ed44a3eeab62c']
+
+sanity_check_paths = {
+    'files': ['bin/mvn'],
+    'dirs': [],
+}
+
+moduleclass = 'devel'

From 835da852a205e1fe99052ff3589a819781e5621f Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Thu, 13 Jun 2024 11:59:06 +0200
Subject: [PATCH 195/835] try update

---
 easybuild/easyconfigs/j/jax/jax-0.4.25-foss-2023a.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/j/jax/jax-0.4.25-foss-2023a.eb b/easybuild/easyconfigs/j/jax/jax-0.4.25-foss-2023a.eb
index 9cbbc9b1579..64a723ffe37 100644
--- a/easybuild/easyconfigs/j/jax/jax-0.4.25-foss-2023a.eb
+++ b/easybuild/easyconfigs/j/jax/jax-0.4.25-foss-2023a.eb
@@ -1,6 +1,6 @@
 # This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
 # Author: Denis Kristak
-# Updated by: Alex Domingo (Vrije Universiteit Brussel), Pavel Tománek (Inuits)
+# Updated by: Alex Domingo (Vrije Universiteit Brussel), Pavel Tománek (INUITS)
 # Update v0.4.25 based on: https://github.com/easybuilders/easybuild-easyconfigs/pull/20119
 
 easyblock = 'PythonBundle'

From 40383aa8aedfc26894b6a5536c73ba174de40ff7 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Thu, 13 Jun 2024 12:04:12 +0200
Subject: [PATCH 196/835] move jax dependent ecs to separate PR

---
 .../c/cairomm/cairomm-1.16.2-GCC-12.3.0.eb    |   2 +-
 .../j/jax/jax-0.4.25-foss-2023a.eb            | 112 ------------------
 .../jax-0.4.25_fix-pybind11-systemlib.patch   |  38 ------
 .../jax-0.4.25_fix_env_test_no_log_spam.patch |  18 ---
 .../ml-collections-0.1.1-foss-2023a.eb        |  37 ------
 .../o/Optax/Optax-0.2.2-foss-2023a.eb         |  42 -------
 .../s/scArches/scArches-0.6.1-foss-2023a.eb   |  87 --------------
 .../scib-metrics-0.5.1-foss-2023a.eb          |  54 ---------
 .../scvi-tools/scvi-tools-1.1.2-foss-2023a.eb |  68 -----------
 9 files changed, 1 insertion(+), 457 deletions(-)
 delete mode 100644 easybuild/easyconfigs/j/jax/jax-0.4.25-foss-2023a.eb
 delete mode 100644 easybuild/easyconfigs/j/jax/jax-0.4.25_fix-pybind11-systemlib.patch
 delete mode 100644 easybuild/easyconfigs/j/jax/jax-0.4.25_fix_env_test_no_log_spam.patch
 delete mode 100644 easybuild/easyconfigs/m/ml-collections/ml-collections-0.1.1-foss-2023a.eb
 delete mode 100644 easybuild/easyconfigs/o/Optax/Optax-0.2.2-foss-2023a.eb
 delete mode 100644 easybuild/easyconfigs/s/scArches/scArches-0.6.1-foss-2023a.eb
 delete mode 100644 easybuild/easyconfigs/s/scib-metrics/scib-metrics-0.5.1-foss-2023a.eb
 delete mode 100644 easybuild/easyconfigs/s/scvi-tools/scvi-tools-1.1.2-foss-2023a.eb

diff --git a/easybuild/easyconfigs/c/cairomm/cairomm-1.16.2-GCC-12.3.0.eb b/easybuild/easyconfigs/c/cairomm/cairomm-1.16.2-GCC-12.3.0.eb
index 2ca14e07c7c..286c56e1bbb 100644
--- a/easybuild/easyconfigs/c/cairomm/cairomm-1.16.2-GCC-12.3.0.eb
+++ b/easybuild/easyconfigs/c/cairomm/cairomm-1.16.2-GCC-12.3.0.eb
@@ -1,5 +1,5 @@
 # Updated to MesonNinja as the autogen.sh complained.
-# Author: J. Sassmannshausen (Imperial College London/UK)
+# Author: J. Sassmannshausen (Imperial College London)
 
 easyblock = 'MesonNinja'
 
diff --git a/easybuild/easyconfigs/j/jax/jax-0.4.25-foss-2023a.eb b/easybuild/easyconfigs/j/jax/jax-0.4.25-foss-2023a.eb
deleted file mode 100644
index 64a723ffe37..00000000000
--- a/easybuild/easyconfigs/j/jax/jax-0.4.25-foss-2023a.eb
+++ /dev/null
@@ -1,112 +0,0 @@
-# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
-# Author: Denis Kristak
-# Updated by: Alex Domingo (Vrije Universiteit Brussel), Pavel Tománek (INUITS)
-# Update v0.4.25 based on: https://github.com/easybuilders/easybuild-easyconfigs/pull/20119
-
-easyblock = 'PythonBundle'
-
-name = 'jax'
-version = '0.4.25'
-
-homepage = 'https://jax.readthedocs.io/'
-description = """Composable transformations of Python+NumPy programs:
-differentiate, vectorize, JIT to GPU/TPU, and more"""
-
-toolchain = {'name': 'foss', 'version': '2023a'}
-
-builddependencies = [
-    ('Bazel', '6.3.1'),
-    ('pytest-xdist', '3.3.1'),
-    # git 2.x required to fetch repository 'io_bazel_rules_docker'
-    ('git', '2.41.0', '-nodocs'),
-    ('matplotlib', '3.7.2'),
-    ('poetry', '1.5.1'),
-    ('pybind11', '2.11.1'),
-]
-
-dependencies = [
-    ('Python', '3.11.3'),
-    ('SciPy-bundle', '2023.07'),
-    ('zlib', '1.2.13'),
-    ('flatbuffers-python', '23.5.26'),
-    ('ml_dtypes', '0.3.2'),
-]
-
-use_pip = True
-
-local_xla_commit = '4ccfe33c71665ddcbca5b127fefe8baa3ed632d4'
-local_tfrt_commit = '0aeefb1660d7e37964b2bb71b1f518096bda9a25'
-
-local_extract_cmd = 'cp %s %(builddir)s/archives'
-
-local_repo_opt = '--bazel_options="--distdir=%(builddir)s/archives" '
-local_repo_opt += '--bazel_options="--action_env=TF_SYSTEM_LIBS=pybind11" '
-local_repo_opt += '--bazel_options="--action_env=CPATH=$EBROOTPYBIND11/include" '
-
-default_easyblock = 'PythonPackage'
-default_component_specs = {
-    'sources': [SOURCE_TAR_GZ],
-    'source_urls': [PYPI_SOURCE],
-    'start_dir': '%(name)s-%(version)s',
-    'use_pip': True,
-    'sanity_pip_check': True,
-    'download_dep_fail': True,
-}
-
-components = [
-    ('absl-py', '2.1.0', {
-        'options': {'modulename': 'absl'},
-        'checksums': ['7820790efbb316739cde8b4e19357243fc3608a152024288513dd968d7d959ff'],
-    }),
-    ('jaxlib', version, {
-        'sources': [
-            '%(name)s-v%(version)s.tar.gz',
-            {
-                'download_filename': '%s.tar.gz' % local_xla_commit,
-                'filename': 'xla-%s.tar.gz' % local_xla_commit,
-                'extract_cmd': local_extract_cmd,
-            },
-            {
-                'download_filename': '%s.tar.gz' % local_tfrt_commit,
-                'filename': 'tf_runtime-%s.tar.gz' % local_tfrt_commit,
-                'extract_cmd': local_extract_cmd,
-            },
-        ],
-        'source_urls': [
-            'https://github.com/google/jax/archive/',
-            'https://github.com/tensorflow/runtime/archive',
-            'https://github.com/openxla/xla/archive'
-        ],
-        'patches': ['jax-0.4.25_fix-pybind11-systemlib.patch'],
-        'checksums': [
-            {'jaxlib-v0.4.25.tar.gz':
-             'fc1197c401924942eb14185a61688d0c476e3e81ff71f9dc95e620b57c06eec8'},
-            {'xla-4ccfe33c71665ddcbca5b127fefe8baa3ed632d4.tar.gz':
-             '8a59b9af7d0850059d7043f7043c780066d61538f3af536e8a10d3d717f35089'},
-            {'tf_runtime-0aeefb1660d7e37964b2bb71b1f518096bda9a25.tar.gz':
-             'a3df827d7896774cb1d80bf4e1c79ab05c268f29bd4d3db1fb5a4b9c2079d8e3'},
-            {'jax-0.4.25_fix-pybind11-systemlib.patch':
-             'daad5b726d1a138431b05eb60ecf4c89c7b5148eb939721800bdf43d804ca033'},
-        ],
-        'start_dir': 'jax-jaxlib-v%(version)s',
-        # Avoid warning (treated as error) in upb/table.c
-        'buildopts': local_repo_opt + ' --bazel_options="--copt=-Wno-maybe-uninitialized"'
-    }),
-]
-
-exts_list = [
-    (name, version, {
-        'patches': ['jax-0.4.25_fix_env_test_no_log_spam.patch'],
-        'source_tmpl': '%(name)s-v%(version)s.tar.gz',
-        'source_urls': ['https://github.com/google/jax/archive/'],
-        'checksums': [
-            {'jax-v0.4.25.tar.gz': '8b30af49688c0c13b82c6f5ce992727c00b5fc6d04a4c6962012f4246fa664eb'},
-            {'jax-0.4.25_fix_env_test_no_log_spam.patch':
-             'a18b5f147569d9ad41025124333a0f04fd0d0e0f9e4309658d7f6b9b838e2e2a'},
-        ],
-    }),
-]
-
-sanity_pip_check = True
-
-moduleclass = 'tools'
diff --git a/easybuild/easyconfigs/j/jax/jax-0.4.25_fix-pybind11-systemlib.patch b/easybuild/easyconfigs/j/jax/jax-0.4.25_fix-pybind11-systemlib.patch
deleted file mode 100644
index c404ee6917f..00000000000
--- a/easybuild/easyconfigs/j/jax/jax-0.4.25_fix-pybind11-systemlib.patch
+++ /dev/null
@@ -1,38 +0,0 @@
-Add missing value for System Pybind11 Bazel config
-
-Author: Alexander Grund (TU Dresden)
-
-diff --git a/third_party/xla/fix-pybind11-systemlib.patch b/third_party/xla/fix-pybind11-systemlib.patch
-new file mode 100644
-index 000000000..68bd2063d
---- /dev/null
-+++ b/third_party/xla/fix-pybind11-systemlib.patch
-@@ -0,0 +1,13 @@
-+--- xla-orig/third_party/tsl/third_party/systemlibs/pybind11.BUILD
-++++ xla-4ccfe33c71665ddcbca5b127fefe8baa3ed632d4/third_party/tsl/third_party/systemlibs/pybind11.BUILD
-+@@ -6,3 +6,10 @@
-+         "@tsl//third_party/python_runtime:headers",
-+     ],
-+ )
-++
-++# Needed by pybind11_bazel.
-++config_setting(
-++    name = "osx",
-++    constraint_values = ["@platforms//os:osx"],
-++)
-++
-diff --git a/third_party/xla/workspace.bzl b/third_party/xla/workspace.bzl
-index ebc8d9838..125e1c173 100644
---- a/third_party/xla/workspace.bzl
-+++ b/third_party/xla/workspace.bzl
-@@ -29,6 +29,9 @@ def repo():
-         sha256 = XLA_SHA256,
-         strip_prefix = "xla-{commit}".format(commit = XLA_COMMIT),
-         urls = tf_mirror_urls("https://github.com/openxla/xla/archive/{commit}.tar.gz".format(commit = XLA_COMMIT)),
-+        patch_file = [
-+            "//third_party/xla:fix-pybind11-systemlib.patch",
-+        ],
-     )
- 
-     # For development, one often wants to make changes to the TF repository as well
-
diff --git a/easybuild/easyconfigs/j/jax/jax-0.4.25_fix_env_test_no_log_spam.patch b/easybuild/easyconfigs/j/jax/jax-0.4.25_fix_env_test_no_log_spam.patch
deleted file mode 100644
index ad919608437..00000000000
--- a/easybuild/easyconfigs/j/jax/jax-0.4.25_fix_env_test_no_log_spam.patch
+++ /dev/null
@@ -1,18 +0,0 @@
-# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2024/03
-# avoid overriding LD_LIBRARY_PATH, which would lead to test error: error while loading shared libraries: libpython3.11.so.1.0: cannot open shared object file: No such file or directory'
-diff -ru jax-jax-v0.4.25/tests/logging_test.py jax-jax-v0.4.25_fix_env_test_no_log_spam/tests/logging_test.py
---- jax-jax-v0.4.25/tests/logging_test.py	2024-02-24 19:25:17.000000000 +0100
-+++ jax-jax-v0.4.25_fix_env_test_no_log_spam/tests/logging_test.py	2024-03-15 12:00:34.133022613 +0100
-@@ -72,8 +72,11 @@
-     python = sys.executable
-     assert "python" in python
-     # Make sure C++ logging is at default level for the test process.
-+    import os
-+    tmp_env=os.environ.copy()
-+    tmp_env['TF_CPP_MIN_LOG_LEVEL']='1'
-     proc = subprocess.run([python, "-c", program], capture_output=True,
--                          env={"TF_CPP_MIN_LOG_LEVEL": "1"})
-+                          env=tmp_env)
- 
-     lines = proc.stdout.split(b"\n")
-     lines.extend(proc.stderr.split(b"\n"))
diff --git a/easybuild/easyconfigs/m/ml-collections/ml-collections-0.1.1-foss-2023a.eb b/easybuild/easyconfigs/m/ml-collections/ml-collections-0.1.1-foss-2023a.eb
deleted file mode 100644
index 79034a7433d..00000000000
--- a/easybuild/easyconfigs/m/ml-collections/ml-collections-0.1.1-foss-2023a.eb
+++ /dev/null
@@ -1,37 +0,0 @@
-easyblock = 'PythonBundle'
-
-name = 'ml-collections'
-version = '0.1.1'
-
-homepage = 'https://github.com/google/ml_collections'
-description = """
-ML Collections is a library of Python Collections designed for ML use cases.
-"""
-
-toolchain = {'name': 'foss', 'version': '2023a'}
-
-dependencies = [
-    ('Python', '3.11.3'),
-    ('SciPy-bundle', '2023.07'),
-    ('PyYAML', '6.0'),
-]
-
-use_pip = True
-
-exts_list = [
-    ('absl-py', '2.1.0', {
-        'modulename': 'absl',
-        'checksums': ['7820790efbb316739cde8b4e19357243fc3608a152024288513dd968d7d959ff'],
-    }),
-    ('contextlib2', '21.6.0', {
-        'checksums': ['ab1e2bfe1d01d968e1b7e8d9023bc51ef3509bba217bb730cee3827e1ee82869'],
-    }),
-    ('ml_collections', version, {
-        'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ",
-        'checksums': ['3fefcc72ec433aa1e5d32307a3e474bbb67f405be814ea52a2166bfc9dbe68cc'],
-    }),
-]
-
-sanity_pip_check = True
-
-moduleclass = 'vis'
diff --git a/easybuild/easyconfigs/o/Optax/Optax-0.2.2-foss-2023a.eb b/easybuild/easyconfigs/o/Optax/Optax-0.2.2-foss-2023a.eb
deleted file mode 100644
index be05f009e9e..00000000000
--- a/easybuild/easyconfigs/o/Optax/Optax-0.2.2-foss-2023a.eb
+++ /dev/null
@@ -1,42 +0,0 @@
-easyblock = 'PythonBundle'
-
-name = 'Optax'
-version = '0.2.2'
-
-homepage = 'https://github.com/deepmind/optax'
-description = """Optax is a gradient processing and optimization library for JAX."""
-
-toolchain = {'name': 'foss', 'version': '2023a'}
-
-dependencies = [
-    ('Python', '3.11.3'),
-    ('SciPy-bundle', '2023.07'),
-    ('jax', '0.4.25'),
-]
-
-use_pip = True
-
-exts_list = [
-    ('toolz', '0.12.1', {
-        'checksums': ['ecca342664893f177a13dac0e6b41cbd8ac25a358e5f215316d43e2100224f4d'],
-    }),
-    ('flit_core', '3.9.0', {
-        'checksums': ['72ad266176c4a3fcfab5f2930d76896059851240570ce9a98733b658cb786eba'],
-    }),
-    ('absl-py', '2.1.0', {
-        'modulename': 'absl',
-        'checksums': ['7820790efbb316739cde8b4e19357243fc3608a152024288513dd968d7d959ff'],
-    }),
-    ('chex', '0.1.86', {
-        'checksums': ['e8b0f96330eba4144659e1617c0f7a57b161e8cbb021e55c6d5056c7378091d1'],
-    }),
-    ('optax', version, {
-        'checksums': ['f09bf790ef4b09fb9c35f79a07594c6196a719919985f542dc84b0bf97812e0e'],
-    }),
-]
-
-sanity_pip_check = True
-
-sanity_check_commands = ["python -c 'from optax import GradientTransformation'"]
-
-moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/s/scArches/scArches-0.6.1-foss-2023a.eb b/easybuild/easyconfigs/s/scArches/scArches-0.6.1-foss-2023a.eb
deleted file mode 100644
index c703d0beede..00000000000
--- a/easybuild/easyconfigs/s/scArches/scArches-0.6.1-foss-2023a.eb
+++ /dev/null
@@ -1,87 +0,0 @@
-easyblock = 'PythonBundle'
-
-name = 'scArches'
-version = '0.6.1'
-
-homepage = 'https://github.com/theislab/scarches'
-description = """Single-cell architecture surgery (scArches) is a package for reference-based analysis of single-cell
- data."""
-
-toolchain = {'name': 'foss', 'version': '2023a'}
-
-dependencies = [
-    ('Python', '3.11.3'),
-    ('SciPy-bundle', '2023.07'),
-    ('Python-bundle-PyPI', '2023.06'),
-    ('matplotlib', '3.7.2'),
-    ('anndata', '0.10.5.post1'),
-    ('h5py', '3.9.0'),
-    ('leidenalg', '0.10.2'),
-    ('scanpy', '1.9.8'),
-    ('scikit-learn', '1.3.1'),
-    ('scvi-tools', '1.1.2'),
-    ('PyTorch', '2.1.2'),
-    ('tqdm', '4.66.1'),
-    ('IPython', '8.14.0'),
-    ('pkgconfig', '1.5.5', '-python'),
-    ('PyZMQ', '25.1.1'),
-    ('tornado', '6.3.2'),
-]
-
-use_pip = True
-
-exts_list = [
-    ('sphinx_basic_ng', '1.0.0b2', {
-        'checksums': ['9ec55a47c90c8c002b5960c57492ec3021f5193cb26cebc2dc4ea226848651c9'],
-    }),
-    ('nodeenv', '1.9.0', {
-        'checksums': ['07f144e90dae547bf0d4ee8da0ee42664a42a04e02ed68e06324348dafe4bdb1'],
-    }),
-    ('sphinx-theme-builder', '0.2.0b2', {
-        'checksums': ['e9cd98c2bb35bf414fe721469a043cdcc10f0808d1ffcf606acb4a6282a6f288'],
-    }),
-    ('furo', '2024.1.29', {
-        'checksums': ['4d6b2fe3f10a6e36eb9cc24c1e7beb38d7a23fc7b3c382867503b7fcac8a1e02'],
-    }),
-    ('numpydoc', '1.6.0', {
-        'checksums': ['ae7a5380f0a06373c3afe16ccd15bd79bc6b07f2704cbc6f1e7ecc94b4f5fc0d'],
-    }),
-    ('jupyter_core', '5.7.2', {
-        'checksums': ['aa5f8d32bbf6b431ac830496da7392035d6f61b4f54872f15c4bd2a9c3f536d9'],
-    }),
-    ('jupyter_client', '8.6.1', {
-        'checksums': ['e842515e2bab8e19186d89fdfea7abd15e39dd581f94e399f00e2af5a1652d3f'],
-    }),
-    ('debugpy', '1.8.1', {
-        'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl',
-        'checksums': ['28acbe2241222b87e255260c76741e1fbf04fdc3b6d094fcf57b6c6f75ce1242'],
-    }),
-    ('comm', '0.2.2', {
-        'checksums': ['3fd7a84065306e07bea1773df6eb8282de51ba82f77c72f9c85716ab11fe980e'],
-    }),
-    ('ipykernel', '6.29.3', {
-        'checksums': ['e14c250d1f9ea3989490225cc1a542781b095a18a19447fcf2b5eaf7d0ac5bd2'],
-    }),
-    ('gdown', '5.1.0', {
-        'checksums': ['550a72dc5ca2819fe4bcc15d80d05d7c98c0b90e57256254b77d0256b9df4683'],
-    }),
-    ('muon', '0.1.6', {
-        'checksums': ['762feeb6f52f865cf79d0d0332cc742fe91c1885f668ce15794b62b3952b02f9'],
-    }),
-    ('newick', '1.9.0', {
-        'checksums': ['9f81be96ec86aefca74d920fc0d6962d89a3156547003ca6915c2e6e31ad3ddf'],
-    }),
-    ('scHPL', '1.0.5', {
-        'modulename': 'scHPL',
-        # unpin pandas and newick versions to be compatible with foss/2023a versions
-        'preinstallopts': "sed -i 's/~=/>=/g' setup.py && sed -i 's/pandas>=1.1.2,<2/pandas/g' setup.py && ",
-        'checksums': ['3eb62b2e65b1faba04b7bcb86f7bf6967a6301866a605551211b8f14fd27eced'],
-    }),
-    (name, version, {
-        'checksums': ['187463c25781d5c5586c129ad137d96327a9f8604d530a696d5f568a9225d77c'],
-    }),
-]
-
-sanity_pip_check = True
-
-moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/s/scib-metrics/scib-metrics-0.5.1-foss-2023a.eb b/easybuild/easyconfigs/s/scib-metrics/scib-metrics-0.5.1-foss-2023a.eb
deleted file mode 100644
index 68ef32b71ad..00000000000
--- a/easybuild/easyconfigs/s/scib-metrics/scib-metrics-0.5.1-foss-2023a.eb
+++ /dev/null
@@ -1,54 +0,0 @@
-easyblock = 'PythonBundle'
-
-name = 'scib-metrics'
-version = '0.5.1'
-
-homepage = 'https://scib-metrics.readthedocs.io'
-description = "Accelerated and Python-only metrics for benchmarking single-cell integration outputs"
-
-toolchain = {'name': 'foss', 'version': '2023a'}
-
-builddependencies = [
-    ('hatchling', '1.18.0'),
-    ('poetry', '1.5.1'),
-]
-dependencies = [
-    ('Python', '3.11.3'),
-    ('SciPy-bundle', '2023.07'),
-    ('anndata', '0.10.5.post1'),
-    ('jax', '0.4.25'),
-    ('scikit-learn', '1.3.1'),
-    ('scanpy', '1.9.8'),
-    ('python-igraph', '0.11.4'),
-    ('matplotlib', '3.7.2'),
-    ('tqdm', '4.66.1'),
-    ('umap-learn', '0.5.5'),
-]
-
-use_pip = True
-
-exts_list = [
-    ('toolz', '0.12.1', {
-        'checksums': ['ecca342664893f177a13dac0e6b41cbd8ac25a358e5f215316d43e2100224f4d'],
-    }),
-    ('plottable', '0.1.5', {
-        'checksums': ['235d762a31c82129dc5bf74205c103a14b1e4393d0f921cc0231be5de884041d'],
-    }),
-    ('pynndescent', '0.5.11', {
-        'checksums': ['6f44ced9d5a9da2c87d9b2fff30bb5308540c0657605e4d5cde7ed3275bbad50'],
-    }),
-    ('rich', '13.7.1', {
-        'checksums': ['9be308cb1fe2f1f57d67ce99e95af38a1e2bc71ad9813b0e247cf7ffbcc3a432'],
-    }),
-    ('chex', '0.1.86', {
-        'checksums': ['e8b0f96330eba4144659e1617c0f7a57b161e8cbb021e55c6d5056c7378091d1'],
-    }),
-    (name, version, {
-        'sources': ['scib_metrics-%(version)s.tar.gz'],
-        'checksums': ['74d10251acf1c11402b994faf063e55317881d7950fb78f6cef011d232a1e266'],
-    }),
-]
-
-sanity_pip_check = True
-
-moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/s/scvi-tools/scvi-tools-1.1.2-foss-2023a.eb b/easybuild/easyconfigs/s/scvi-tools/scvi-tools-1.1.2-foss-2023a.eb
deleted file mode 100644
index f79f5895f45..00000000000
--- a/easybuild/easyconfigs/s/scvi-tools/scvi-tools-1.1.2-foss-2023a.eb
+++ /dev/null
@@ -1,68 +0,0 @@
-easyblock = 'PythonBundle'
-
-name = 'scvi-tools'
-version = '1.1.2'
-
-homepage = 'https://github.com/scverse/scvi-tools'
-description = """scvi-tools (single-cell variational inference tools) is a package for probabilistic modeling and
-analysis of single-cell omics data, built on top of PyTorch and AnnData."""
-
-toolchain = {'name': 'foss', 'version': '2023a'}
-
-builddependencies = [('hatchling', '1.18.0')]
-dependencies = [
-    ('Python', '3.11.3'),
-    ('SciPy-bundle', '2023.07'),
-    ('anndata', '0.10.5.post1'),
-    ('matplotlib', '3.7.2'),
-    ('scikit-learn', '1.3.1'),
-    ('tqdm', '4.66.1'),
-    ('jax', '0.4.25'),
-    ('h5py', '3.9.0'),
-    ('PyTorch-Lightning', '2.2.1'),
-    ('pyro-ppl', '1.9.0'),
-    ('ml-collections', '0.1.1'),
-    ('Optax', '0.2.2'),
-]
-
-use_pip = True
-
-exts_list = [
-    ('mudata', '0.2.3', {
-        'checksums': ['45288ac150bfc598d68acb7c2c1c43c38c5c39522107e04f7efbf3360c7f2035'],
-    }),
-    ('multipledispatch', '1.0.0', {
-        'checksums': ['5c839915465c68206c3e9c473357908216c28383b425361e5d144594bf85a7e0'],
-    }),
-    ('numpyro', '0.15.0', {
-        'checksums': ['e16c9f47cc31e2aa259584a0b6c944312081d33ca92406022632ad584b0e600d'],
-    }),
-    ('nest_asyncio', '1.6.0', {
-        'checksums': ['6f172d5449aca15afd6c646851f4e31e02c598d553a667e38cafa997cfec55fe'],
-    }),
-    ('orbax_checkpoint', '0.5.15', {
-        'modulename': 'orbax.checkpoint',
-        'checksums': ['15195e8d1b381b56f23a62a25599a3644f5d08655fa64f60bb1b938b8ffe7ef3'],
-    }),
-    ('tensorstore', '0.1.60', {
-        'checksums': ['88da8f1978982101b8dbb144fd29ee362e4e8c97fc595c4992d555f80ce62a79'],
-    }),
-    ('flax', '0.8.4', {
-        'checksums': ['968683f850198e1aa5eb2d9d1e20bead880ef7423c14f042db9d60848cb1c90b'],
-    }),
-    ('docrep', '0.3.2', {
-        'checksums': ['ed8a17e201abd829ef8da78a0b6f4d51fb99a4cbd0554adbed3309297f964314'],
-    }),
-    ('lightning', '2.1.4', {
-        'checksums': ['0e45098c700fa28c604a11ae233ce181b44aeffce2404debebc2616118431d9f'],
-    }),
-    (name, version, {
-        'modulename': 'scvi',
-        'sources': ['scvi_tools-%(version)s.tar.gz'],
-        'checksums': ['104a11a30e8996f5ceaa907b8c81b48b1f4b380d492ef2dd9b9a5577ed81b0f9'],
-    }),
-]
-
-sanity_pip_check = True
-
-moduleclass = 'bio'

From f54b4e2ac86a28ca1a52d38221ad3355f81aa1f8 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Thu, 13 Jun 2024 12:08:46 +0200
Subject: [PATCH 197/835] adding easyconfigs: scArches-0.6.1-foss-2023a.eb,
 scib-metrics-0.5.1-foss-2023a.eb, scvi-tools-1.1.2-foss-2023a.eb,
 Optax-0.2.2-foss-2023a.eb, ml-collections-0.1.1-foss-2023a.eb,
 jax-0.4.25-foss-2023a.eb and patches:
 jax-0.4.25_fix-pybind11-systemlib.patch,
 jax-0.4.25_fix_env_test_no_log_spam.patch

---
 .../j/jax/jax-0.4.25-foss-2023a.eb            | 112 ++++++++++++++++++
 .../jax-0.4.25_fix-pybind11-systemlib.patch   |  38 ++++++
 .../jax-0.4.25_fix_env_test_no_log_spam.patch |  18 +++
 .../ml-collections-0.1.1-foss-2023a.eb        |  37 ++++++
 .../o/Optax/Optax-0.2.2-foss-2023a.eb         |  42 +++++++
 .../s/scArches/scArches-0.6.1-foss-2023a.eb   |  87 ++++++++++++++
 .../scib-metrics-0.5.1-foss-2023a.eb          |  54 +++++++++
 .../scvi-tools/scvi-tools-1.1.2-foss-2023a.eb |  68 +++++++++++
 8 files changed, 456 insertions(+)
 create mode 100644 easybuild/easyconfigs/j/jax/jax-0.4.25-foss-2023a.eb
 create mode 100644 easybuild/easyconfigs/j/jax/jax-0.4.25_fix-pybind11-systemlib.patch
 create mode 100644 easybuild/easyconfigs/j/jax/jax-0.4.25_fix_env_test_no_log_spam.patch
 create mode 100644 easybuild/easyconfigs/m/ml-collections/ml-collections-0.1.1-foss-2023a.eb
 create mode 100644 easybuild/easyconfigs/o/Optax/Optax-0.2.2-foss-2023a.eb
 create mode 100644 easybuild/easyconfigs/s/scArches/scArches-0.6.1-foss-2023a.eb
 create mode 100644 easybuild/easyconfigs/s/scib-metrics/scib-metrics-0.5.1-foss-2023a.eb
 create mode 100644 easybuild/easyconfigs/s/scvi-tools/scvi-tools-1.1.2-foss-2023a.eb

diff --git a/easybuild/easyconfigs/j/jax/jax-0.4.25-foss-2023a.eb b/easybuild/easyconfigs/j/jax/jax-0.4.25-foss-2023a.eb
new file mode 100644
index 00000000000..64a723ffe37
--- /dev/null
+++ b/easybuild/easyconfigs/j/jax/jax-0.4.25-foss-2023a.eb
@@ -0,0 +1,112 @@
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+# Author: Denis Kristak
+# Updated by: Alex Domingo (Vrije Universiteit Brussel), Pavel Tománek (INUITS)
+# Update v0.4.25 based on: https://github.com/easybuilders/easybuild-easyconfigs/pull/20119
+
+easyblock = 'PythonBundle'
+
+name = 'jax'
+version = '0.4.25'
+
+homepage = 'https://jax.readthedocs.io/'
+description = """Composable transformations of Python+NumPy programs:
+differentiate, vectorize, JIT to GPU/TPU, and more"""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+builddependencies = [
+    ('Bazel', '6.3.1'),
+    ('pytest-xdist', '3.3.1'),
+    # git 2.x required to fetch repository 'io_bazel_rules_docker'
+    ('git', '2.41.0', '-nodocs'),
+    ('matplotlib', '3.7.2'),
+    ('poetry', '1.5.1'),
+    ('pybind11', '2.11.1'),
+]
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('zlib', '1.2.13'),
+    ('flatbuffers-python', '23.5.26'),
+    ('ml_dtypes', '0.3.2'),
+]
+
+use_pip = True
+
+local_xla_commit = '4ccfe33c71665ddcbca5b127fefe8baa3ed632d4'
+local_tfrt_commit = '0aeefb1660d7e37964b2bb71b1f518096bda9a25'
+
+local_extract_cmd = 'cp %s %(builddir)s/archives'
+
+local_repo_opt = '--bazel_options="--distdir=%(builddir)s/archives" '
+local_repo_opt += '--bazel_options="--action_env=TF_SYSTEM_LIBS=pybind11" '
+local_repo_opt += '--bazel_options="--action_env=CPATH=$EBROOTPYBIND11/include" '
+
+default_easyblock = 'PythonPackage'
+default_component_specs = {
+    'sources': [SOURCE_TAR_GZ],
+    'source_urls': [PYPI_SOURCE],
+    'start_dir': '%(name)s-%(version)s',
+    'use_pip': True,
+    'sanity_pip_check': True,
+    'download_dep_fail': True,
+}
+
+components = [
+    ('absl-py', '2.1.0', {
+        'options': {'modulename': 'absl'},
+        'checksums': ['7820790efbb316739cde8b4e19357243fc3608a152024288513dd968d7d959ff'],
+    }),
+    ('jaxlib', version, {
+        'sources': [
+            '%(name)s-v%(version)s.tar.gz',
+            {
+                'download_filename': '%s.tar.gz' % local_xla_commit,
+                'filename': 'xla-%s.tar.gz' % local_xla_commit,
+                'extract_cmd': local_extract_cmd,
+            },
+            {
+                'download_filename': '%s.tar.gz' % local_tfrt_commit,
+                'filename': 'tf_runtime-%s.tar.gz' % local_tfrt_commit,
+                'extract_cmd': local_extract_cmd,
+            },
+        ],
+        'source_urls': [
+            'https://github.com/google/jax/archive/',
+            'https://github.com/tensorflow/runtime/archive',
+            'https://github.com/openxla/xla/archive'
+        ],
+        'patches': ['jax-0.4.25_fix-pybind11-systemlib.patch'],
+        'checksums': [
+            {'jaxlib-v0.4.25.tar.gz':
+             'fc1197c401924942eb14185a61688d0c476e3e81ff71f9dc95e620b57c06eec8'},
+            {'xla-4ccfe33c71665ddcbca5b127fefe8baa3ed632d4.tar.gz':
+             '8a59b9af7d0850059d7043f7043c780066d61538f3af536e8a10d3d717f35089'},
+            {'tf_runtime-0aeefb1660d7e37964b2bb71b1f518096bda9a25.tar.gz':
+             'a3df827d7896774cb1d80bf4e1c79ab05c268f29bd4d3db1fb5a4b9c2079d8e3'},
+            {'jax-0.4.25_fix-pybind11-systemlib.patch':
+             'daad5b726d1a138431b05eb60ecf4c89c7b5148eb939721800bdf43d804ca033'},
+        ],
+        'start_dir': 'jax-jaxlib-v%(version)s',
+        # Avoid warning (treated as error) in upb/table.c
+        'buildopts': local_repo_opt + ' --bazel_options="--copt=-Wno-maybe-uninitialized"'
+    }),
+]
+
+exts_list = [
+    (name, version, {
+        'patches': ['jax-0.4.25_fix_env_test_no_log_spam.patch'],
+        'source_tmpl': '%(name)s-v%(version)s.tar.gz',
+        'source_urls': ['https://github.com/google/jax/archive/'],
+        'checksums': [
+            {'jax-v0.4.25.tar.gz': '8b30af49688c0c13b82c6f5ce992727c00b5fc6d04a4c6962012f4246fa664eb'},
+            {'jax-0.4.25_fix_env_test_no_log_spam.patch':
+             'a18b5f147569d9ad41025124333a0f04fd0d0e0f9e4309658d7f6b9b838e2e2a'},
+        ],
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'tools'
diff --git a/easybuild/easyconfigs/j/jax/jax-0.4.25_fix-pybind11-systemlib.patch b/easybuild/easyconfigs/j/jax/jax-0.4.25_fix-pybind11-systemlib.patch
new file mode 100644
index 00000000000..c404ee6917f
--- /dev/null
+++ b/easybuild/easyconfigs/j/jax/jax-0.4.25_fix-pybind11-systemlib.patch
@@ -0,0 +1,38 @@
+Add missing value for System Pybind11 Bazel config
+
+Author: Alexander Grund (TU Dresden)
+
+diff --git a/third_party/xla/fix-pybind11-systemlib.patch b/third_party/xla/fix-pybind11-systemlib.patch
+new file mode 100644
+index 000000000..68bd2063d
+--- /dev/null
++++ b/third_party/xla/fix-pybind11-systemlib.patch
+@@ -0,0 +1,13 @@
++--- xla-orig/third_party/tsl/third_party/systemlibs/pybind11.BUILD
+++++ xla-4ccfe33c71665ddcbca5b127fefe8baa3ed632d4/third_party/tsl/third_party/systemlibs/pybind11.BUILD
++@@ -6,3 +6,10 @@
++         "@tsl//third_party/python_runtime:headers",
++     ],
++ )
+++
+++# Needed by pybind11_bazel.
+++config_setting(
+++    name = "osx",
+++    constraint_values = ["@platforms//os:osx"],
+++)
+++
+diff --git a/third_party/xla/workspace.bzl b/third_party/xla/workspace.bzl
+index ebc8d9838..125e1c173 100644
+--- a/third_party/xla/workspace.bzl
++++ b/third_party/xla/workspace.bzl
+@@ -29,6 +29,9 @@ def repo():
+         sha256 = XLA_SHA256,
+         strip_prefix = "xla-{commit}".format(commit = XLA_COMMIT),
+         urls = tf_mirror_urls("https://github.com/openxla/xla/archive/{commit}.tar.gz".format(commit = XLA_COMMIT)),
++        patch_file = [
++            "//third_party/xla:fix-pybind11-systemlib.patch",
++        ],
+     )
+ 
+     # For development, one often wants to make changes to the TF repository as well
+
diff --git a/easybuild/easyconfigs/j/jax/jax-0.4.25_fix_env_test_no_log_spam.patch b/easybuild/easyconfigs/j/jax/jax-0.4.25_fix_env_test_no_log_spam.patch
new file mode 100644
index 00000000000..ad919608437
--- /dev/null
+++ b/easybuild/easyconfigs/j/jax/jax-0.4.25_fix_env_test_no_log_spam.patch
@@ -0,0 +1,18 @@
+# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2024/03
+# avoid overriding LD_LIBRARY_PATH, which would lead to test error: error while loading shared libraries: libpython3.11.so.1.0: cannot open shared object file: No such file or directory'
+diff -ru jax-jax-v0.4.25/tests/logging_test.py jax-jax-v0.4.25_fix_env_test_no_log_spam/tests/logging_test.py
+--- jax-jax-v0.4.25/tests/logging_test.py	2024-02-24 19:25:17.000000000 +0100
++++ jax-jax-v0.4.25_fix_env_test_no_log_spam/tests/logging_test.py	2024-03-15 12:00:34.133022613 +0100
+@@ -72,8 +72,11 @@
+     python = sys.executable
+     assert "python" in python
+     # Make sure C++ logging is at default level for the test process.
++    import os
++    tmp_env=os.environ.copy()
++    tmp_env['TF_CPP_MIN_LOG_LEVEL']='1'
+     proc = subprocess.run([python, "-c", program], capture_output=True,
+-                          env={"TF_CPP_MIN_LOG_LEVEL": "1"})
++                          env=tmp_env)
+ 
+     lines = proc.stdout.split(b"\n")
+     lines.extend(proc.stderr.split(b"\n"))
diff --git a/easybuild/easyconfigs/m/ml-collections/ml-collections-0.1.1-foss-2023a.eb b/easybuild/easyconfigs/m/ml-collections/ml-collections-0.1.1-foss-2023a.eb
new file mode 100644
index 00000000000..79034a7433d
--- /dev/null
+++ b/easybuild/easyconfigs/m/ml-collections/ml-collections-0.1.1-foss-2023a.eb
@@ -0,0 +1,37 @@
+easyblock = 'PythonBundle'
+
+name = 'ml-collections'
+version = '0.1.1'
+
+homepage = 'https://github.com/google/ml_collections'
+description = """
+ML Collections is a library of Python Collections designed for ML use cases.
+"""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('PyYAML', '6.0'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('absl-py', '2.1.0', {
+        'modulename': 'absl',
+        'checksums': ['7820790efbb316739cde8b4e19357243fc3608a152024288513dd968d7d959ff'],
+    }),
+    ('contextlib2', '21.6.0', {
+        'checksums': ['ab1e2bfe1d01d968e1b7e8d9023bc51ef3509bba217bb730cee3827e1ee82869'],
+    }),
+    ('ml_collections', version, {
+        'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ",
+        'checksums': ['3fefcc72ec433aa1e5d32307a3e474bbb67f405be814ea52a2166bfc9dbe68cc'],
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'vis'
diff --git a/easybuild/easyconfigs/o/Optax/Optax-0.2.2-foss-2023a.eb b/easybuild/easyconfigs/o/Optax/Optax-0.2.2-foss-2023a.eb
new file mode 100644
index 00000000000..be05f009e9e
--- /dev/null
+++ b/easybuild/easyconfigs/o/Optax/Optax-0.2.2-foss-2023a.eb
@@ -0,0 +1,42 @@
+easyblock = 'PythonBundle'
+
+name = 'Optax'
+version = '0.2.2'
+
+homepage = 'https://github.com/deepmind/optax'
+description = """Optax is a gradient processing and optimization library for JAX."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('jax', '0.4.25'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('toolz', '0.12.1', {
+        'checksums': ['ecca342664893f177a13dac0e6b41cbd8ac25a358e5f215316d43e2100224f4d'],
+    }),
+    ('flit_core', '3.9.0', {
+        'checksums': ['72ad266176c4a3fcfab5f2930d76896059851240570ce9a98733b658cb786eba'],
+    }),
+    ('absl-py', '2.1.0', {
+        'modulename': 'absl',
+        'checksums': ['7820790efbb316739cde8b4e19357243fc3608a152024288513dd968d7d959ff'],
+    }),
+    ('chex', '0.1.86', {
+        'checksums': ['e8b0f96330eba4144659e1617c0f7a57b161e8cbb021e55c6d5056c7378091d1'],
+    }),
+    ('optax', version, {
+        'checksums': ['f09bf790ef4b09fb9c35f79a07594c6196a719919985f542dc84b0bf97812e0e'],
+    }),
+]
+
+sanity_pip_check = True
+
+sanity_check_commands = ["python -c 'from optax import GradientTransformation'"]
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/s/scArches/scArches-0.6.1-foss-2023a.eb b/easybuild/easyconfigs/s/scArches/scArches-0.6.1-foss-2023a.eb
new file mode 100644
index 00000000000..c703d0beede
--- /dev/null
+++ b/easybuild/easyconfigs/s/scArches/scArches-0.6.1-foss-2023a.eb
@@ -0,0 +1,87 @@
+easyblock = 'PythonBundle'
+
+name = 'scArches'
+version = '0.6.1'
+
+homepage = 'https://github.com/theislab/scarches'
+description = """Single-cell architecture surgery (scArches) is a package for reference-based analysis of single-cell
+ data."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('Python-bundle-PyPI', '2023.06'),
+    ('matplotlib', '3.7.2'),
+    ('anndata', '0.10.5.post1'),
+    ('h5py', '3.9.0'),
+    ('leidenalg', '0.10.2'),
+    ('scanpy', '1.9.8'),
+    ('scikit-learn', '1.3.1'),
+    ('scvi-tools', '1.1.2'),
+    ('PyTorch', '2.1.2'),
+    ('tqdm', '4.66.1'),
+    ('IPython', '8.14.0'),
+    ('pkgconfig', '1.5.5', '-python'),
+    ('PyZMQ', '25.1.1'),
+    ('tornado', '6.3.2'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('sphinx_basic_ng', '1.0.0b2', {
+        'checksums': ['9ec55a47c90c8c002b5960c57492ec3021f5193cb26cebc2dc4ea226848651c9'],
+    }),
+    ('nodeenv', '1.9.0', {
+        'checksums': ['07f144e90dae547bf0d4ee8da0ee42664a42a04e02ed68e06324348dafe4bdb1'],
+    }),
+    ('sphinx-theme-builder', '0.2.0b2', {
+        'checksums': ['e9cd98c2bb35bf414fe721469a043cdcc10f0808d1ffcf606acb4a6282a6f288'],
+    }),
+    ('furo', '2024.1.29', {
+        'checksums': ['4d6b2fe3f10a6e36eb9cc24c1e7beb38d7a23fc7b3c382867503b7fcac8a1e02'],
+    }),
+    ('numpydoc', '1.6.0', {
+        'checksums': ['ae7a5380f0a06373c3afe16ccd15bd79bc6b07f2704cbc6f1e7ecc94b4f5fc0d'],
+    }),
+    ('jupyter_core', '5.7.2', {
+        'checksums': ['aa5f8d32bbf6b431ac830496da7392035d6f61b4f54872f15c4bd2a9c3f536d9'],
+    }),
+    ('jupyter_client', '8.6.1', {
+        'checksums': ['e842515e2bab8e19186d89fdfea7abd15e39dd581f94e399f00e2af5a1652d3f'],
+    }),
+    ('debugpy', '1.8.1', {
+        'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl',
+        'checksums': ['28acbe2241222b87e255260c76741e1fbf04fdc3b6d094fcf57b6c6f75ce1242'],
+    }),
+    ('comm', '0.2.2', {
+        'checksums': ['3fd7a84065306e07bea1773df6eb8282de51ba82f77c72f9c85716ab11fe980e'],
+    }),
+    ('ipykernel', '6.29.3', {
+        'checksums': ['e14c250d1f9ea3989490225cc1a542781b095a18a19447fcf2b5eaf7d0ac5bd2'],
+    }),
+    ('gdown', '5.1.0', {
+        'checksums': ['550a72dc5ca2819fe4bcc15d80d05d7c98c0b90e57256254b77d0256b9df4683'],
+    }),
+    ('muon', '0.1.6', {
+        'checksums': ['762feeb6f52f865cf79d0d0332cc742fe91c1885f668ce15794b62b3952b02f9'],
+    }),
+    ('newick', '1.9.0', {
+        'checksums': ['9f81be96ec86aefca74d920fc0d6962d89a3156547003ca6915c2e6e31ad3ddf'],
+    }),
+    ('scHPL', '1.0.5', {
+        'modulename': 'scHPL',
+        # unpin pandas and newick versions to be compatible with foss/2023a versions
+        'preinstallopts': "sed -i 's/~=/>=/g' setup.py && sed -i 's/pandas>=1.1.2,<2/pandas/g' setup.py && ",
+        'checksums': ['3eb62b2e65b1faba04b7bcb86f7bf6967a6301866a605551211b8f14fd27eced'],
+    }),
+    (name, version, {
+        'checksums': ['187463c25781d5c5586c129ad137d96327a9f8604d530a696d5f568a9225d77c'],
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/s/scib-metrics/scib-metrics-0.5.1-foss-2023a.eb b/easybuild/easyconfigs/s/scib-metrics/scib-metrics-0.5.1-foss-2023a.eb
new file mode 100644
index 00000000000..68ef32b71ad
--- /dev/null
+++ b/easybuild/easyconfigs/s/scib-metrics/scib-metrics-0.5.1-foss-2023a.eb
@@ -0,0 +1,54 @@
+easyblock = 'PythonBundle'
+
+name = 'scib-metrics'
+version = '0.5.1'
+
+homepage = 'https://scib-metrics.readthedocs.io'
+description = "Accelerated and Python-only metrics for benchmarking single-cell integration outputs"
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+builddependencies = [
+    ('hatchling', '1.18.0'),
+    ('poetry', '1.5.1'),
+]
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('anndata', '0.10.5.post1'),
+    ('jax', '0.4.25'),
+    ('scikit-learn', '1.3.1'),
+    ('scanpy', '1.9.8'),
+    ('python-igraph', '0.11.4'),
+    ('matplotlib', '3.7.2'),
+    ('tqdm', '4.66.1'),
+    ('umap-learn', '0.5.5'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('toolz', '0.12.1', {
+        'checksums': ['ecca342664893f177a13dac0e6b41cbd8ac25a358e5f215316d43e2100224f4d'],
+    }),
+    ('plottable', '0.1.5', {
+        'checksums': ['235d762a31c82129dc5bf74205c103a14b1e4393d0f921cc0231be5de884041d'],
+    }),
+    ('pynndescent', '0.5.11', {
+        'checksums': ['6f44ced9d5a9da2c87d9b2fff30bb5308540c0657605e4d5cde7ed3275bbad50'],
+    }),
+    ('rich', '13.7.1', {
+        'checksums': ['9be308cb1fe2f1f57d67ce99e95af38a1e2bc71ad9813b0e247cf7ffbcc3a432'],
+    }),
+    ('chex', '0.1.86', {
+        'checksums': ['e8b0f96330eba4144659e1617c0f7a57b161e8cbb021e55c6d5056c7378091d1'],
+    }),
+    (name, version, {
+        'sources': ['scib_metrics-%(version)s.tar.gz'],
+        'checksums': ['74d10251acf1c11402b994faf063e55317881d7950fb78f6cef011d232a1e266'],
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/s/scvi-tools/scvi-tools-1.1.2-foss-2023a.eb b/easybuild/easyconfigs/s/scvi-tools/scvi-tools-1.1.2-foss-2023a.eb
new file mode 100644
index 00000000000..f79f5895f45
--- /dev/null
+++ b/easybuild/easyconfigs/s/scvi-tools/scvi-tools-1.1.2-foss-2023a.eb
@@ -0,0 +1,68 @@
+easyblock = 'PythonBundle'
+
+name = 'scvi-tools'
+version = '1.1.2'
+
+homepage = 'https://github.com/scverse/scvi-tools'
+description = """scvi-tools (single-cell variational inference tools) is a package for probabilistic modeling and
+analysis of single-cell omics data, built on top of PyTorch and AnnData."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+builddependencies = [('hatchling', '1.18.0')]
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('anndata', '0.10.5.post1'),
+    ('matplotlib', '3.7.2'),
+    ('scikit-learn', '1.3.1'),
+    ('tqdm', '4.66.1'),
+    ('jax', '0.4.25'),
+    ('h5py', '3.9.0'),
+    ('PyTorch-Lightning', '2.2.1'),
+    ('pyro-ppl', '1.9.0'),
+    ('ml-collections', '0.1.1'),
+    ('Optax', '0.2.2'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('mudata', '0.2.3', {
+        'checksums': ['45288ac150bfc598d68acb7c2c1c43c38c5c39522107e04f7efbf3360c7f2035'],
+    }),
+    ('multipledispatch', '1.0.0', {
+        'checksums': ['5c839915465c68206c3e9c473357908216c28383b425361e5d144594bf85a7e0'],
+    }),
+    ('numpyro', '0.15.0', {
+        'checksums': ['e16c9f47cc31e2aa259584a0b6c944312081d33ca92406022632ad584b0e600d'],
+    }),
+    ('nest_asyncio', '1.6.0', {
+        'checksums': ['6f172d5449aca15afd6c646851f4e31e02c598d553a667e38cafa997cfec55fe'],
+    }),
+    ('orbax_checkpoint', '0.5.15', {
+        'modulename': 'orbax.checkpoint',
+        'checksums': ['15195e8d1b381b56f23a62a25599a3644f5d08655fa64f60bb1b938b8ffe7ef3'],
+    }),
+    ('tensorstore', '0.1.60', {
+        'checksums': ['88da8f1978982101b8dbb144fd29ee362e4e8c97fc595c4992d555f80ce62a79'],
+    }),
+    ('flax', '0.8.4', {
+        'checksums': ['968683f850198e1aa5eb2d9d1e20bead880ef7423c14f042db9d60848cb1c90b'],
+    }),
+    ('docrep', '0.3.2', {
+        'checksums': ['ed8a17e201abd829ef8da78a0b6f4d51fb99a4cbd0554adbed3309297f964314'],
+    }),
+    ('lightning', '2.1.4', {
+        'checksums': ['0e45098c700fa28c604a11ae233ce181b44aeffce2404debebc2616118431d9f'],
+    }),
+    (name, version, {
+        'modulename': 'scvi',
+        'sources': ['scvi_tools-%(version)s.tar.gz'],
+        'checksums': ['104a11a30e8996f5ceaa907b8c81b48b1f4b380d492ef2dd9b9a5577ed81b0f9'],
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'bio'

From b3870a1b2877fa104ab988708b581e3ec842387c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Thu, 13 Jun 2024 12:59:33 +0200
Subject: [PATCH 198/835] Use release tarball

---
 easybuild/easyconfigs/w/WRF/WRF-4.5.1-foss-2023a-dmpar.eb | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/w/WRF/WRF-4.5.1-foss-2023a-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-4.5.1-foss-2023a-dmpar.eb
index 2d0cd78573a..608b6b08352 100644
--- a/easybuild/easyconfigs/w/WRF/WRF-4.5.1-foss-2023a-dmpar.eb
+++ b/easybuild/easyconfigs/w/WRF/WRF-4.5.1-foss-2023a-dmpar.eb
@@ -11,7 +11,8 @@ description = """The Weather Research and Forecasting (WRF) Model is a next-gene
 toolchain = {'name': 'foss', 'version': '2023a'}
 toolchainopts = {'opt': False}  # don't use agressive optimization, stick to -O2
 
-source_urls = ['https://github.com/wrf-model/WRF/archive/']
+github_account = 'wrf-model'
+source_urls = [GITHUB_RELEASE]
 sources = ['v%(version)s.tar.gz']
 patches = [
     'WRF-4.5.1_netCDF-Fortran_separate_path.patch',

From 0f0846db37e155b1a22680bd47e3b519387876fe Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Thu, 13 Jun 2024 12:59:47 +0200
Subject: [PATCH 199/835] use the checksum of the release tarball

---
 easybuild/easyconfigs/w/WRF/WRF-4.5.1-foss-2023a-dmpar.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/w/WRF/WRF-4.5.1-foss-2023a-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-4.5.1-foss-2023a-dmpar.eb
index 608b6b08352..cddc6b15179 100644
--- a/easybuild/easyconfigs/w/WRF/WRF-4.5.1-foss-2023a-dmpar.eb
+++ b/easybuild/easyconfigs/w/WRF/WRF-4.5.1-foss-2023a-dmpar.eb
@@ -18,7 +18,7 @@ patches = [
     'WRF-4.5.1_netCDF-Fortran_separate_path.patch',
 ]
 checksums = [
-    {'v4.5.1.tar.gz': '91d7dc84f6a41e1243f0b56b2f2c86b10d860610a2c686dfea599aecab02e8f8'},
+    {'v4.5.1.tar.gz': '9d557c34c105db4d41e727843ecb19199233c7cf82c5369b34a2ce8efe65e2d1'},
     {'WRF-4.5.1_netCDF-Fortran_separate_path.patch':
      '951bff9a3fc651482b287cc03a9f3197979b7800d515fe61cc9c932d9e0dc62e'},
 ]

From c76d5bd29f854ace601660dd303ae4f206e480b4 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 13 Jun 2024 15:12:30 +0200
Subject: [PATCH 200/835] rename unpacked sources for components of EasyBuild
 v4.9.2, to ensure that '--install-latest-eb-release' works with older
 EasyBuild versions

---
 .../easyconfigs/e/EasyBuild/EasyBuild-4.9.2.eb | 18 +++++++++++++++---
 1 file changed, 15 insertions(+), 3 deletions(-)

diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.9.2.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.9.2.eb
index 2b12ffe3d0b..cb476c53d7f 100644
--- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.9.2.eb
+++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.9.2.eb
@@ -18,10 +18,22 @@ source_urls = [
     # easybuild-easyconfigs
     'https://files.pythonhosted.org/packages/99/b2/d899b4310bc54a10e0fb46995a2abc333857db16d116f22a53b0313d13d7/',
 ]
+# note: subdirectory for each unpacked source tarball is renamed because custom easyblock in older EasyBuild version
+# that is used for installing EasyBuild with EasyBuild expects subdirectories with '-' rather than '_';
+# see also https://github.com/easybuilders/easybuild-easyblocks/pull/3358
 sources = [
-    'easybuild_framework-%(version)s.tar.gz',
-    'easybuild_easyblocks-%(version)s.tar.gz',
-    'easybuild_easyconfigs-%(version)s.tar.gz',
+    {
+        'filename': 'easybuild_framework-%(version)s.tar.gz',
+        'extract_cmd': "tar xfvz %s && mv easybuild_framework-%(version)s easybuild-framework-%(version)s",
+    },
+    {
+        'filename': 'easybuild_easyblocks-%(version)s.tar.gz',
+        'extract_cmd': "tar xfvz %s && mv easybuild_easyblocks-%(version)s easybuild-easyblocks-%(version)s",
+    },
+    {
+        'filename': 'easybuild_easyconfigs-%(version)s.tar.gz',
+        'extract_cmd': "tar xfvz %s && mv easybuild_easyconfigs-%(version)s easybuild-easyconfigs-%(version)s",
+    },
 ]
 checksums = [
     {'easybuild_framework-4.9.2.tar.gz': 'cc6e0fe7bab2a96d424656ed70bf33e3b083eef5ceaa5d5fed88aa7b91dd3d63'},

From eb2dbeaec00cf12180169cbe0be6b500099220bc Mon Sep 17 00:00:00 2001
From: WilleBell <cintiawillemyns@gmail.com>
Date: Thu, 13 Jun 2024 15:53:15 +0200
Subject: [PATCH 201/835] adding easyconfigs: DL_POLY_Classic_GUI-1.10.eb

---
 .../DL_POLY_Classic_GUI-1.10.eb               | 34 +++++++++++++++++++
 1 file changed, 34 insertions(+)
 create mode 100644 easybuild/easyconfigs/d/DL_POLY_Classic_GUI/DL_POLY_Classic_GUI-1.10.eb

diff --git a/easybuild/easyconfigs/d/DL_POLY_Classic_GUI/DL_POLY_Classic_GUI-1.10.eb b/easybuild/easyconfigs/d/DL_POLY_Classic_GUI/DL_POLY_Classic_GUI-1.10.eb
new file mode 100644
index 00000000000..84de0bbf36a
--- /dev/null
+++ b/easybuild/easyconfigs/d/DL_POLY_Classic_GUI/DL_POLY_Classic_GUI-1.10.eb
@@ -0,0 +1,34 @@
+easyblock = 'JAR'
+
+name = 'DL_POLY_Classic_GUI'
+version = '1.10'
+
+homepage = 'https://gitlab.com/DL_POLY_Classic/dl_poly'
+description = """
+The DL_POLY Graphical User Interface (or GUI) is a program written in the
+Java language and is intended for use with the DL_POLY molecular
+simulation program.
+This is the GUI for DL_POLY Classic, it can also be used for DL_POLY_4.
+"""
+
+toolchain = SYSTEM
+
+source_urls = ['https://gitlab.com/DL_POLY_Classic/dl_poly/-/raw/RELEASE-%(version_major)s-%(version_minor)s/java/']
+sources = ['GUI.jar']
+checksums = ['8d3a5ed75d5ee8eb2e4403d8ed9355cd214c7e5b7afc8161c89a50edbc0a481d']
+
+dependencies = [
+    ('Java', '17', '', SYSTEM),
+]
+
+
+sanity_check_paths = {
+    'files': ['GUI.jar'],
+    'dirs': [''],
+}
+
+modloadmsg = """
+To execute this Graphical User Interface run: java GUI
+"""
+
+moduleclass = 'chem'

From fe34609caee004a37752aadb466056165cf9b54f Mon Sep 17 00:00:00 2001
From: Julian Morillo <julian.morillo@bsc.es>
Date: Thu, 13 Jun 2024 16:05:39 +0200
Subject: [PATCH 202/835] Moving to 4.1.7 version as there is a critical bug
 fix related to MPI tracing

---
 ...tils.patch => Extrae-4.1.7-detect_binutils.patch} | 12 ++++++------
 ....6-gompi-2023b.eb => Extrae-4.1.7-gompi-2023b.eb} | 11 +++++------
 2 files changed, 11 insertions(+), 12 deletions(-)
 rename easybuild/easyconfigs/e/Extrae/{Extrae-4.1.6-detect_binutils.patch => Extrae-4.1.7-detect_binutils.patch} (81%)
 rename easybuild/easyconfigs/e/Extrae/{Extrae-4.1.6-gompi-2023b.eb => Extrae-4.1.7-gompi-2023b.eb} (69%)

diff --git a/easybuild/easyconfigs/e/Extrae/Extrae-4.1.6-detect_binutils.patch b/easybuild/easyconfigs/e/Extrae/Extrae-4.1.7-detect_binutils.patch
similarity index 81%
rename from easybuild/easyconfigs/e/Extrae/Extrae-4.1.6-detect_binutils.patch
rename to easybuild/easyconfigs/e/Extrae/Extrae-4.1.7-detect_binutils.patch
index 4eeac3ad4ac..aa8f6918a66 100644
--- a/easybuild/easyconfigs/e/Extrae/Extrae-4.1.6-detect_binutils.patch
+++ b/easybuild/easyconfigs/e/Extrae/Extrae-4.1.7-detect_binutils.patch
@@ -1,6 +1,6 @@
-diff -Nru extrae-4.1.6.orig/config/macros.m4 extrae-4.1.6/config/macros.m4
---- extrae-4.1.6.orig/config/macros.m4  2024-05-30 16:23:59.684839619 +0200
-+++ extrae-4.1.6/config/macros.m4       2024-05-30 16:27:08.208600097 +0200
+diff -Nru extrae-4.1.7.orig/config/macros.m4 extrae-4.1.7/config/macros.m4
+--- extrae-4.1.7.orig/config/macros.m4  2024-05-30 16:23:59.684839619 +0200
++++ extrae-4.1.7/config/macros.m4       2024-05-30 16:27:08.208600097 +0200
 @@ -779,6 +779,8 @@
           elif test -r "${binutils_home_dir}/lib/libbfd.a" -a \
                        "${binutils_require_shared}" = "no" ; then
@@ -19,9 +19,9 @@ diff -Nru extrae-4.1.6.orig/config/macros.m4 extrae-4.1.6/config/macros.m4
           else
              dnl Try something more automatic using find command
              libiberty_lib=""
-diff -Nru extrae-4.1.6.orig/configure extrae-4.1.6/configure
---- extrae-4.1.6.orig/configure 2024-05-30 16:23:59.716839578 +0200
-+++ extrae-4.1.6/configure      2024-05-30 16:25:31.276723193 +0200
+diff -Nru extrae-4.1.7.orig/configure extrae-4.1.7/configure
+--- extrae-4.1.7.orig/configure 2024-05-30 16:23:59.716839578 +0200
++++ extrae-4.1.7/configure      2024-05-30 16:25:31.276723193 +0200
 @@ -35072,6 +35072,8 @@
           elif test -r "${binutils_home_dir}/lib/libbfd.a" -a \
                        "${binutils_require_shared}" = "no" ; then
diff --git a/easybuild/easyconfigs/e/Extrae/Extrae-4.1.6-gompi-2023b.eb b/easybuild/easyconfigs/e/Extrae/Extrae-4.1.7-gompi-2023b.eb
similarity index 69%
rename from easybuild/easyconfigs/e/Extrae/Extrae-4.1.6-gompi-2023b.eb
rename to easybuild/easyconfigs/e/Extrae/Extrae-4.1.7-gompi-2023b.eb
index d6f41276db0..295ed24a172 100644
--- a/easybuild/easyconfigs/e/Extrae/Extrae-4.1.6-gompi-2023b.eb
+++ b/easybuild/easyconfigs/e/Extrae/Extrae-4.1.7-gompi-2023b.eb
@@ -1,5 +1,5 @@
 name = 'Extrae'
-version = '4.1.6'
+version = '4.1.7'
 
 homepage = 'https://tools.bsc.es/extrae'
 description = """Extrae is the package devoted to generate Paraver trace-files for a post-mortem analysis. 
@@ -11,12 +11,11 @@ toolchainopts = {'usempi': True}
 
 source_urls = ['https://ftp.tools.bsc.es/%(namelower)s']
 sources = ['%(namelower)s-%(version)s-src.tar.bz2']
-patches = ['Extrae-4.1.6-detect_binutils.patch']
+patches = ['Extrae-4.1.7-detect_binutils.patch']
 checksums = [
-    # extrae-4.1.6-src.tar.bz2
-    ('9f146e70311b8ae9d77584f6efc7b30478885cfd095f7bd3937d5b08aec19985',
-     'f96b2c3586a0e83c6fa08d3136a8f399715969b5bb7ee6792c3fd93667d495fd'),
-    '7c4d87d12a5383ccdfdd75967a207b9d9aca27c707c499cd6ef0a27fd4989483',  # Extrae-4.1.6-detect_binutils.patch
+    # extrae-4.1.7-src.tar.bz2
+    '0ed87449f74db0abc239ee8c40176e89f9ca6a69738fe751ec0df8fc46da1712',
+    '9319b0af3e8714237fef9f4f0e22fda72a83a3120b29f63a6cbaf95b9f71d61f',  # Extrae-4.1.7-detect_binutils.patch
 ]
 
 builddependencies = [

From 65fbf9a1dd6890f6503240e08c74dfd9cd7b62f5 Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Thu, 13 Jun 2024 16:14:27 +0200
Subject: [PATCH 203/835] Easyblock update means most changes are no longer
 required

---
 .../QuantumESPRESSO-5.3.0-intel-2016.02-GCC-4.9.eb              | 2 --
 .../QuantumESPRESSO/QuantumESPRESSO-5.4.0-foss-2016b-hybrid.eb  | 2 --
 .../QuantumESPRESSO-5.4.0-intel-2016.02-GCC-4.9.eb              | 2 --
 .../q/QuantumESPRESSO/QuantumESPRESSO-6.0-intel-2016b.eb        | 2 --
 .../q/QuantumESPRESSO/QuantumESPRESSO-6.1-intel-2017a.eb        | 2 --
 .../q/QuantumESPRESSO/QuantumESPRESSO-6.2-intel-2017b.eb        | 2 --
 .../q/QuantumESPRESSO/QuantumESPRESSO-6.2.1-iomkl-2017b.eb      | 2 --
 .../q/QuantumESPRESSO/QuantumESPRESSO-6.3-foss-2018b.eb         | 2 --
 .../q/QuantumESPRESSO/QuantumESPRESSO-6.3-intel-2018b.eb        | 2 --
 .../q/QuantumESPRESSO/QuantumESPRESSO-6.4.1-intel-2019a.eb      | 2 --
 .../q/QuantumESPRESSO/QuantumESPRESSO-6.5-intel-2019a.eb        | 2 --
 .../q/QuantumESPRESSO/QuantumESPRESSO-6.5-intel-2019b.eb        | 2 --
 .../q/QuantumESPRESSO/QuantumESPRESSO-6.6-foss-2019b.eb         | 2 --
 .../q/QuantumESPRESSO/QuantumESPRESSO-6.6-foss-2020a.eb         | 2 --
 .../q/QuantumESPRESSO/QuantumESPRESSO-6.6-foss-2020b.eb         | 2 --
 .../q/QuantumESPRESSO/QuantumESPRESSO-6.6-intel-2019b.eb        | 2 --
 .../q/QuantumESPRESSO/QuantumESPRESSO-6.6-intel-2020a.eb        | 2 --
 .../q/QuantumESPRESSO/QuantumESPRESSO-6.7-foss-2019b.eb         | 2 --
 .../q/QuantumESPRESSO/QuantumESPRESSO-6.7-foss-2020b.eb         | 2 --
 .../q/QuantumESPRESSO/QuantumESPRESSO-6.7-foss-2021a.eb         | 2 --
 .../q/QuantumESPRESSO/QuantumESPRESSO-6.7-intel-2019b.eb        | 2 --
 .../q/QuantumESPRESSO/QuantumESPRESSO-6.7-intel-2021a.eb        | 2 --
 .../q/QuantumESPRESSO/QuantumESPRESSO-6.7-iomkl-2019b.eb        | 2 --
 .../q/QuantumESPRESSO/QuantumESPRESSO-6.8-foss-2021a.eb         | 2 --
 .../q/QuantumESPRESSO/QuantumESPRESSO-6.8-foss-2021b.eb         | 2 --
 .../q/QuantumESPRESSO/QuantumESPRESSO-6.8-intel-2021a.eb        | 2 --
 .../q/QuantumESPRESSO/QuantumESPRESSO-7.0-foss-2021b.eb         | 2 --
 .../q/QuantumESPRESSO/QuantumESPRESSO-7.0-intel-2021b.eb        | 2 --
 .../q/QuantumESPRESSO/QuantumESPRESSO-7.1-foss-2022a.eb         | 2 --
 .../q/QuantumESPRESSO/QuantumESPRESSO-7.1-intel-2022a.eb        | 2 --
 .../q/QuantumESPRESSO/QuantumESPRESSO-7.2-foss-2022b.eb         | 2 --
 .../q/QuantumESPRESSO/QuantumESPRESSO-7.2-foss-2023a.eb         | 2 --
 .../q/QuantumESPRESSO/QuantumESPRESSO-7.2-intel-2022b.eb        | 2 --
 .../q/QuantumESPRESSO/QuantumESPRESSO-7.3-foss-2023a.eb         | 2 --
 .../q/QuantumESPRESSO/QuantumESPRESSO-7.3-intel-2023a.eb        | 2 --
 35 files changed, 70 deletions(-)

diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.3.0-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.3.0-intel-2016.02-GCC-4.9.eb
index e456ec0bf5c..35cd35ceaed 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.3.0-intel-2016.02-GCC-4.9.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.3.0-intel-2016.02-GCC-4.9.eb
@@ -1,5 +1,3 @@
-easyblock = "EB_QuantumESPRESSO_autotools"
-
 name = 'QuantumESPRESSO'
 version = '5.3.0'
 
diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0-foss-2016b-hybrid.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0-foss-2016b-hybrid.eb
index b37dc5e6097..2b285f6ff8b 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0-foss-2016b-hybrid.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0-foss-2016b-hybrid.eb
@@ -1,5 +1,3 @@
-easyblock = "EB_QuantumESPRESSO_autotools"
-
 name = 'QuantumESPRESSO'
 version = '5.4.0'
 versionsuffix = '-hybrid'
diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0-intel-2016.02-GCC-4.9.eb
index 6890a8c39c4..185719e2b8b 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0-intel-2016.02-GCC-4.9.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0-intel-2016.02-GCC-4.9.eb
@@ -1,5 +1,3 @@
-easyblock = "EB_QuantumESPRESSO_autotools"
-
 name = 'QuantumESPRESSO'
 version = '5.4.0'
 
diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.0-intel-2016b.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.0-intel-2016b.eb
index b163c87b805..1e47f214d6a 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.0-intel-2016b.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.0-intel-2016b.eb
@@ -1,5 +1,3 @@
-easyblock = "EB_QuantumESPRESSO_autotools"
-
 name = 'QuantumESPRESSO'
 version = '6.0'
 
diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.1-intel-2017a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.1-intel-2017a.eb
index 4616a8ca038..6eed0d5280f 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.1-intel-2017a.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.1-intel-2017a.eb
@@ -1,5 +1,3 @@
-easyblock = "EB_QuantumESPRESSO_autotools"
-
 name = 'QuantumESPRESSO'
 version = '6.1'
 
diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.2-intel-2017b.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.2-intel-2017b.eb
index aa3688bff39..be1a20b60bd 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.2-intel-2017b.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.2-intel-2017b.eb
@@ -1,5 +1,3 @@
-easyblock = "EB_QuantumESPRESSO_autotools"
-
 name = 'QuantumESPRESSO'
 version = '6.2'
 
diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.2.1-iomkl-2017b.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.2.1-iomkl-2017b.eb
index b2ad6ab82e3..2d5b3eb9707 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.2.1-iomkl-2017b.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.2.1-iomkl-2017b.eb
@@ -1,5 +1,3 @@
-easyblock = "EB_QuantumESPRESSO_autotools"
-
 name = 'QuantumESPRESSO'
 version = '6.2.1'
 
diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.3-foss-2018b.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.3-foss-2018b.eb
index 70449ce8a60..2fa04e3d676 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.3-foss-2018b.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.3-foss-2018b.eb
@@ -1,5 +1,3 @@
-easyblock = "EB_QuantumESPRESSO_autotools"
-
 name = 'QuantumESPRESSO'
 version = '6.3'
 
diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.3-intel-2018b.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.3-intel-2018b.eb
index 2a277c38bda..b9f585b351f 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.3-intel-2018b.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.3-intel-2018b.eb
@@ -1,5 +1,3 @@
-easyblock = "EB_QuantumESPRESSO_autotools"
-
 name = 'QuantumESPRESSO'
 version = '6.3'
 
diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.4.1-intel-2019a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.4.1-intel-2019a.eb
index f3927d3c15a..98ab9f1f280 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.4.1-intel-2019a.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.4.1-intel-2019a.eb
@@ -1,5 +1,3 @@
-easyblock = "EB_QuantumESPRESSO_autotools"
-
 name = 'QuantumESPRESSO'
 version = '6.4.1'
 
diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.5-intel-2019a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.5-intel-2019a.eb
index a0adef65227..870805c92b5 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.5-intel-2019a.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.5-intel-2019a.eb
@@ -1,5 +1,3 @@
-easyblock = "EB_QuantumESPRESSO_autotools"
-
 name = 'QuantumESPRESSO'
 version = '6.5'
 
diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.5-intel-2019b.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.5-intel-2019b.eb
index e99fad4bfe3..195349a44c6 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.5-intel-2019b.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.5-intel-2019b.eb
@@ -1,5 +1,3 @@
-easyblock = "EB_QuantumESPRESSO_autotools"
-
 name = 'QuantumESPRESSO'
 version = '6.5'
 
diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.6-foss-2019b.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.6-foss-2019b.eb
index 07eef2aa5c7..55bef0c0fb3 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.6-foss-2019b.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.6-foss-2019b.eb
@@ -1,5 +1,3 @@
-easyblock = "EB_QuantumESPRESSO_autotools"
-
 name = 'QuantumESPRESSO'
 version = '6.6'
 
diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.6-foss-2020a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.6-foss-2020a.eb
index 438b3e98374..e28840d75ad 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.6-foss-2020a.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.6-foss-2020a.eb
@@ -1,5 +1,3 @@
-easyblock = "EB_QuantumESPRESSO_autotools"
-
 name = 'QuantumESPRESSO'
 version = '6.6'
 
diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.6-foss-2020b.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.6-foss-2020b.eb
index c954f1ce9a7..02147ccb84a 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.6-foss-2020b.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.6-foss-2020b.eb
@@ -1,5 +1,3 @@
-easyblock = "EB_QuantumESPRESSO_autotools"
-
 name = 'QuantumESPRESSO'
 version = '6.6'
 
diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.6-intel-2019b.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.6-intel-2019b.eb
index 2e6a5d86a52..cd2e199f59d 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.6-intel-2019b.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.6-intel-2019b.eb
@@ -1,5 +1,3 @@
-easyblock = "EB_QuantumESPRESSO_autotools"
-
 name = 'QuantumESPRESSO'
 version = '6.6'
 
diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.6-intel-2020a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.6-intel-2020a.eb
index 068aa1ddfe6..9f590db57c1 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.6-intel-2020a.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.6-intel-2020a.eb
@@ -1,5 +1,3 @@
-easyblock = "EB_QuantumESPRESSO_autotools"
-
 name = 'QuantumESPRESSO'
 version = '6.6'
 
diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-foss-2019b.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-foss-2019b.eb
index 29c301d5dff..74d36c967cb 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-foss-2019b.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-foss-2019b.eb
@@ -1,5 +1,3 @@
-easyblock = "EB_QuantumESPRESSO_autotools"
-
 name = 'QuantumESPRESSO'
 version = '6.7'
 
diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-foss-2020b.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-foss-2020b.eb
index f34b824285f..43a880080ad 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-foss-2020b.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-foss-2020b.eb
@@ -1,8 +1,6 @@
 ##
 # Author:    Robert Mijakovic <robert.mijakovic@lxp.lu>
 ##
-easyblock = "EB_QuantumESPRESSO_autotools"
-
 name = 'QuantumESPRESSO'
 version = '6.7'
 
diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-foss-2021a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-foss-2021a.eb
index 72f5a65efd3..bdff659a888 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-foss-2021a.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-foss-2021a.eb
@@ -1,5 +1,3 @@
-easyblock = "EB_QuantumESPRESSO_autotools"
-
 name = 'QuantumESPRESSO'
 version = '6.7'
 
diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-intel-2019b.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-intel-2019b.eb
index d565ea1ea7c..d52fb661c17 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-intel-2019b.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-intel-2019b.eb
@@ -1,5 +1,3 @@
-easyblock = "EB_QuantumESPRESSO_autotools"
-
 name = 'QuantumESPRESSO'
 version = '6.7'
 
diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-intel-2021a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-intel-2021a.eb
index 1a8428bec18..99d05042d92 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-intel-2021a.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-intel-2021a.eb
@@ -1,5 +1,3 @@
-easyblock = "EB_QuantumESPRESSO_autotools"
-
 name = 'QuantumESPRESSO'
 version = '6.7'
 
diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-iomkl-2019b.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-iomkl-2019b.eb
index 5ba6f0bcdb0..d35f44ab478 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-iomkl-2019b.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.7-iomkl-2019b.eb
@@ -1,5 +1,3 @@
-easyblock = "EB_QuantumESPRESSO_autotools"
-
 name = 'QuantumESPRESSO'
 version = '6.7'
 
diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.8-foss-2021a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.8-foss-2021a.eb
index 850af4acd68..36c8fdf64b0 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.8-foss-2021a.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.8-foss-2021a.eb
@@ -1,5 +1,3 @@
-easyblock = "EB_QuantumESPRESSO_autotools"
-
 name = 'QuantumESPRESSO'
 version = '6.8'
 
diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.8-foss-2021b.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.8-foss-2021b.eb
index a5df2d14198..fc8ad317547 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.8-foss-2021b.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.8-foss-2021b.eb
@@ -1,5 +1,3 @@
-easyblock = "EB_QuantumESPRESSO_autotools"
-
 name = 'QuantumESPRESSO'
 version = '6.8'
 
diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.8-intel-2021a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.8-intel-2021a.eb
index 2a06371e99c..5982b4efde6 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.8-intel-2021a.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.8-intel-2021a.eb
@@ -1,5 +1,3 @@
-easyblock = "EB_QuantumESPRESSO_autotools"
-
 name = 'QuantumESPRESSO'
 version = '6.8'
 
diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.0-foss-2021b.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.0-foss-2021b.eb
index 4399027df12..9f62ca5ad84 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.0-foss-2021b.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.0-foss-2021b.eb
@@ -1,5 +1,3 @@
-easyblock = "EB_QuantumESPRESSO_autotools"
-
 name = 'QuantumESPRESSO'
 version = '7.0'
 
diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.0-intel-2021b.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.0-intel-2021b.eb
index 562b85e742f..febc60c8c61 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.0-intel-2021b.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.0-intel-2021b.eb
@@ -1,5 +1,3 @@
-easyblock = "EB_QuantumESPRESSO_autotools"
-
 name = 'QuantumESPRESSO'
 version = '7.0'
 
diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-foss-2022a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-foss-2022a.eb
index fe65f088760..87066c6ae6d 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-foss-2022a.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-foss-2022a.eb
@@ -1,5 +1,3 @@
-easyblock = "EB_QuantumESPRESSO_autotools"
-
 name = 'QuantumESPRESSO'
 version = '7.1'
 
diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-intel-2022a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-intel-2022a.eb
index 8de5eeefdb0..a7ed17a2f6b 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-intel-2022a.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-intel-2022a.eb
@@ -1,5 +1,3 @@
-easyblock = "EB_QuantumESPRESSO_autotools"
-
 name = 'QuantumESPRESSO'
 version = '7.1'
 
diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-foss-2022b.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-foss-2022b.eb
index d165c425a69..9362d5a9fb8 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-foss-2022b.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-foss-2022b.eb
@@ -1,5 +1,3 @@
-easyblock = "EB_QuantumESPRESSO_autotools"
-
 name = 'QuantumESPRESSO'
 version = '7.2'
 
diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-foss-2023a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-foss-2023a.eb
index 0e6d9fd967c..8369f3fb31a 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-foss-2023a.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-foss-2023a.eb
@@ -1,5 +1,3 @@
-easyblock = "EB_QuantumESPRESSO_autotools"
-
 name = 'QuantumESPRESSO'
 version = '7.2'
 
diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-intel-2022b.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-intel-2022b.eb
index 797592734a7..53852bd770b 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-intel-2022b.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-intel-2022b.eb
@@ -1,5 +1,3 @@
-easyblock = "EB_QuantumESPRESSO_autotools"
-
 name = 'QuantumESPRESSO'
 version = '7.2'
 
diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3-foss-2023a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3-foss-2023a.eb
index 2ea617dcbb9..d0089ef7bc7 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3-foss-2023a.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3-foss-2023a.eb
@@ -1,5 +1,3 @@
-easyblock = "EB_QuantumESPRESSO_autotools"
-
 name = 'QuantumESPRESSO'
 version = '7.3'
 
diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3-intel-2023a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3-intel-2023a.eb
index 4a3e56e47b9..2f3ccd6da68 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3-intel-2023a.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3-intel-2023a.eb
@@ -1,5 +1,3 @@
-easyblock = "EB_QuantumESPRESSO_autotools"
-
 name = 'QuantumESPRESSO'
 version = '7.3'
 

From 1fc885b35dacdeb2feef4af207a2daa2502bae08 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 13 Jun 2024 18:49:31 +0200
Subject: [PATCH 204/835] fix build of OpenBLAS 0.3.24 on A64FX

---
 .../o/OpenBLAS/OpenBLAS-0.3.24-GCC-13.2.0.eb  |   5 +-
 .../OpenBLAS/OpenBLAS-0.3.24_fix-A64FX.patch  | 138 ++++++++++++++++++
 2 files changed, 141 insertions(+), 2 deletions(-)
 create mode 100644 easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.24_fix-A64FX.patch

diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.24-GCC-13.2.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.24-GCC-13.2.0.eb
index 4835813e357..8d2315fbe6e 100644
--- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.24-GCC-13.2.0.eb
+++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.24-GCC-13.2.0.eb
@@ -20,6 +20,7 @@ patches = [
     'OpenBLAS-0.3.21_fix-order-vectorization.patch',
     'OpenBLAS-0.3.23_disable-xDRGES-LAPACK-test.patch',
     'OpenBLAS-0.3.24_fix-czasum.patch',
+    'OpenBLAS-0.3.24_fix-A64FX.patch',
 ]
 checksums = [
     {'v0.3.24.tar.gz': 'ceadc5065da97bd92404cac7254da66cc6eb192679cf1002098688978d4d5132'},
@@ -33,8 +34,8 @@ checksums = [
      '08af834e5d60441fd35c128758ed9c092ba6887c829e0471ecd489079539047d'},
     {'OpenBLAS-0.3.23_disable-xDRGES-LAPACK-test.patch':
      'ab7e0af05f9b2a2ced32f3875e1e3767d9c3531a455421a38f7324350178a0ff'},
-    {'OpenBLAS-0.3.24_fix-czasum.patch':
-     '8132b87c519fb08caa3bd7291fe8a1d0e1afe6fcb667d16f3020b46122afe20c'},
+    {'OpenBLAS-0.3.24_fix-czasum.patch': '8132b87c519fb08caa3bd7291fe8a1d0e1afe6fcb667d16f3020b46122afe20c'},
+    {'OpenBLAS-0.3.24_fix-A64FX.patch': '3712e8c3f0024c7bb327958779c388ad0234ad6d58b7b118e605256ec089964c'},
 ]
 
 builddependencies = [
diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.24_fix-A64FX.patch b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.24_fix-A64FX.patch
new file mode 100644
index 00000000000..ff4a16dea8d
--- /dev/null
+++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.24_fix-A64FX.patch
@@ -0,0 +1,138 @@
+fix installation of OpenBLAS 0.3.24 on Arm A64FX,
+see https://github.com/OpenMathLib/OpenBLAS/pull/4258 + https://github.com/OpenMathLib/OpenBLAS/issues/4257
+diff --git a/kernel/arm64/KERNEL.A64FX b/kernel/arm64/KERNEL.A64FX
+index bd25f7cd8a..ccbce27e1b 100644
+--- a/kernel/arm64/KERNEL.A64FX
++++ b/kernel/arm64/KERNEL.A64FX
+@@ -57,7 +57,7 @@ CAMAXKERNEL  = zamax.S
+ ZAMAXKERNEL  = zamax.S
+ 
+ SAXPYKERNEL  = axpy.S
+-DAXPYKERNEL  = axpy.S
++DAXPYKERNEL  = daxpy_thunderx2t99.S
+ CAXPYKERNEL  = zaxpy.S
+ ZAXPYKERNEL  = zaxpy.S
+ 
+@@ -81,45 +81,35 @@ DGEMVTKERNEL = gemv_t.S
+ CGEMVTKERNEL = zgemv_t.S
+ ZGEMVTKERNEL = zgemv_t.S
+ 
+-
+-SASUMKERNEL    = asum.S
+-DASUMKERNEL    = asum.S
+-CASUMKERNEL    = casum.S
+-ZASUMKERNEL    = zasum.S
+-
+-SCOPYKERNEL    = copy.S
+-DCOPYKERNEL    = copy.S
+-CCOPYKERNEL    = copy.S
+-ZCOPYKERNEL    = copy.S
+-
+-SSWAPKERNEL    = swap.S
+-DSWAPKERNEL    = swap.S
+-CSWAPKERNEL    = swap.S
+-ZSWAPKERNEL    = swap.S
+-
+-ISAMAXKERNEL   = iamax.S
+-IDAMAXKERNEL   = iamax.S
+-ICAMAXKERNEL   = izamax.S
+-IZAMAXKERNEL   = izamax.S
+-
+-SNRM2KERNEL    = nrm2.S
+-DNRM2KERNEL    = nrm2.S
+-CNRM2KERNEL    = znrm2.S
+-ZNRM2KERNEL    = znrm2.S
+-
+-DDOTKERNEL     = dot.S
+-ifneq ($(C_COMPILER), PGI)
+-SDOTKERNEL     = ../generic/dot.c
+-else
+-SDOTKERNEL = dot.S
+-endif
+-ifneq ($(C_COMPILER), PGI)
+-CDOTKERNEL     = zdot.S
+-ZDOTKERNEL     = zdot.S
+-else
+-CDOTKERNEL = ../arm/zdot.c
+-ZDOTKERNEL = ../arm/zdot.c
+-endif
++SASUMKERNEL    = sasum_thunderx2t99.c
++DASUMKERNEL    = dasum_thunderx2t99.c
++CASUMKERNEL    = casum_thunderx2t99.c
++ZASUMKERNEL    = zasum_thunderx2t99.c
++
++SCOPYKERNEL    = copy_thunderx2t99.c
++DCOPYKERNEL    = copy_thunderx2t99.c
++CCOPYKERNEL    = copy_thunderx2t99.c
++ZCOPYKERNEL    = copy_thunderx2t99.c
++
++SSWAPKERNEL    = swap_thunderx2t99.S
++DSWAPKERNEL    = swap_thunderx2t99.S
++CSWAPKERNEL    = swap_thunderx2t99.S
++ZSWAPKERNEL    = swap_thunderx2t99.S
++
++ISAMAXKERNEL   = iamax_thunderx2t99.c
++IDAMAXKERNEL   = iamax_thunderx2t99.c
++ICAMAXKERNEL   = izamax_thunderx2t99.c
++IZAMAXKERNEL   = izamax_thunderx2t99.c
++
++SNRM2KERNEL    = scnrm2_thunderx2t99.c
++DNRM2KERNEL    = dznrm2_thunderx2t99.c
++CNRM2KERNEL    = scnrm2_thunderx2t99.c
++ZNRM2KERNEL    = dznrm2_thunderx2t99.c
++
++DDOTKERNEL     = dot.c
++SDOTKERNEL     = dot.c
++CDOTKERNEL     = zdot_thunderx2t99.c
++ZDOTKERNEL     = zdot_thunderx2t99.c
+ DSDOTKERNEL    = dot.S
+ 
+ DGEMM_BETA     = dgemm_beta.S
+@@ -128,10 +118,10 @@ SGEMM_BETA     = sgemm_beta.S
+ SGEMMKERNEL    =  sgemm_kernel_sve_v2x$(SGEMM_UNROLL_N).S
+ STRMMKERNEL    =  strmm_kernel_sve_v1x$(SGEMM_UNROLL_N).S
+ 
+-SGEMMINCOPY    =  sgemm_ncopy_sve_v1.c
+-SGEMMITCOPY    =  sgemm_tcopy_sve_v1.c
+-SGEMMONCOPY    =  sgemm_ncopy_$(DGEMM_UNROLL_N).S
+-SGEMMOTCOPY    =  sgemm_tcopy_$(DGEMM_UNROLL_N).S
++SGEMMINCOPY    =  gemm_ncopy_sve_v1x$(SGEMM_UNROLL_N).c
++SGEMMITCOPY    =  gemm_tcopy_sve_v1x$(SGEMM_UNROLL_N).c
++SGEMMONCOPY    =  sgemm_ncopy_$(SGEMM_UNROLL_N).S
++SGEMMOTCOPY    =  sgemm_tcopy_$(SGEMM_UNROLL_N).S
+ 
+ SGEMMINCOPYOBJ =  sgemm_incopy$(TSUFFIX).$(SUFFIX)
+ SGEMMITCOPYOBJ =  sgemm_itcopy$(TSUFFIX).$(SUFFIX)
+@@ -149,8 +139,8 @@ SSYMMLCOPY_M    =  symm_lcopy_sve.c
+ DGEMMKERNEL    =  dgemm_kernel_sve_v2x$(DGEMM_UNROLL_N).S
+ DTRMMKERNEL    =  dtrmm_kernel_sve_v1x$(DGEMM_UNROLL_N).S
+ 
+-DGEMMINCOPY    =  dgemm_ncopy_sve_v1.c
+-DGEMMITCOPY    =  dgemm_tcopy_sve_v1.c
++DGEMMINCOPY    =  gemm_ncopy_sve_v1x$(DGEMM_UNROLL_N).c
++DGEMMITCOPY    =  gemm_tcopy_sve_v1x$(DGEMM_UNROLL_N).c
+ DGEMMONCOPY    =  dgemm_ncopy_$(DGEMM_UNROLL_N).S
+ DGEMMOTCOPY    =  dgemm_tcopy_$(DGEMM_UNROLL_N).S
+ 
+@@ -170,8 +160,8 @@ DSYMMLCOPY_M    =  symm_lcopy_sve.c
+ CGEMMKERNEL    =  cgemm_kernel_sve_v1x$(ZGEMM_UNROLL_N).S
+ CTRMMKERNEL    =  ctrmm_kernel_sve_v1x$(ZGEMM_UNROLL_N).S
+ 
+-CGEMMINCOPY    =  cgemm_ncopy_sve_v1.c
+-CGEMMITCOPY    =  cgemm_tcopy_sve_v1.c
++CGEMMINCOPY    =  gemm_ncopy_complex_sve_v1x$(ZGEMM_UNROLL_N).c
++CGEMMITCOPY    =  gemm_tcopy_complex_sve_v1x$(ZGEMM_UNROLL_N).c
+ CGEMMONCOPY    =  ../generic/zgemm_ncopy_$(ZGEMM_UNROLL_N).c
+ CGEMMOTCOPY    =  ../generic/zgemm_tcopy_$(ZGEMM_UNROLL_N).c
+ 
+@@ -194,8 +184,8 @@ CSYMMLCOPY_M    =  zsymm_lcopy_sve.c
+ ZGEMMKERNEL    =  zgemm_kernel_sve_v1x$(ZGEMM_UNROLL_N).S
+ ZTRMMKERNEL    =  ztrmm_kernel_sve_v1x$(ZGEMM_UNROLL_N).S
+ 
+-ZGEMMINCOPY    =  zgemm_ncopy_sve_v1.c
+-ZGEMMITCOPY    =  zgemm_tcopy_sve_v1.c
++ZGEMMINCOPY    =  gemm_ncopy_complex_sve_v1x$(ZGEMM_UNROLL_N).c
++ZGEMMITCOPY    =  gemm_tcopy_complex_sve_v1x$(ZGEMM_UNROLL_N).c
+ ZGEMMONCOPY    =  ../generic/zgemm_ncopy_$(ZGEMM_UNROLL_N).c
+ ZGEMMOTCOPY    =  ../generic/zgemm_tcopy_$(ZGEMM_UNROLL_N).c
+ 

From 3f27cb92fe9bf98145628e9a4809e43c8c7ae53a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 14 Jun 2024 09:32:59 +0200
Subject: [PATCH 205/835] add note about netcdf patch

---
 easybuild/easyconfigs/w/WRF/WRF-4.5.1-foss-2023a-dmpar.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/w/WRF/WRF-4.5.1-foss-2023a-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-4.5.1-foss-2023a-dmpar.eb
index cddc6b15179..61a0e73356c 100644
--- a/easybuild/easyconfigs/w/WRF/WRF-4.5.1-foss-2023a-dmpar.eb
+++ b/easybuild/easyconfigs/w/WRF/WRF-4.5.1-foss-2023a-dmpar.eb
@@ -15,7 +15,7 @@ github_account = 'wrf-model'
 source_urls = [GITHUB_RELEASE]
 sources = ['v%(version)s.tar.gz']
 patches = [
-    'WRF-4.5.1_netCDF-Fortran_separate_path.patch',
+    'WRF-4.5.1_netCDF-Fortran_separate_path.patch', # note: no longer required for version 4.5.2
 ]
 checksums = [
     {'v4.5.1.tar.gz': '9d557c34c105db4d41e727843ecb19199233c7cf82c5369b34a2ce8efe65e2d1'},

From 80798edf17690798fb874acbd6e455e45b283ac7 Mon Sep 17 00:00:00 2001
From: Alexander Grund <alexander.grund@tu-dresden.de>
Date: Thu, 13 Jun 2024 15:00:22 +0200
Subject: [PATCH 206/835] Fix build error with numpy with some compilers

NumPy doesn't need Fortran for building but still initializes the
Fortran compiler which fails when the compiler requires a different
commandline argument than GCC, e.g. the Fujitsu compiler.
Failure message starts with
> A valid Fortran version was not found in this string:

See https://github.com/easybuilders/easybuild-easyblocks/issues/2518
Patch is from https://github.com/numpy/numpy/pull/26502 which won't get
merged but isn't necessary in numpy 1.26+
---
 .../SciPy-bundle-2021.05-foss-2021a.eb        |  3 ++
 .../SciPy-bundle-2021.05-gomkl-2021a.eb       |  3 ++
 .../SciPy-bundle-2021.05-intel-2021a.eb       |  3 ++
 ...bundle-2021.10-foss-2021b-Python-2.7.18.eb |  3 ++
 .../SciPy-bundle-2021.10-foss-2021b.eb        |  7 ++-
 .../SciPy-bundle-2021.10-intel-2021b.eb       |  3 ++
 .../SciPy-bundle-2022.05-foss-2022.05.eb      |  3 ++
 .../SciPy-bundle-2022.05-foss-2022a.eb        |  3 ++
 .../SciPy-bundle-2022.05-intel-2022.05.eb     |  3 ++
 .../SciPy-bundle-2022.05-intel-2022a.eb       |  3 ++
 .../SciPy-bundle-2023.02-gfbf-2022b.eb        |  7 ++-
 .../SciPy-bundle-2023.07-gfbf-2023a.eb        |  3 ++
 .../SciPy-bundle-2023.07-iimkl-2023a.eb       |  3 ++
 ...py-1.20.3_fix-fortran-compiler-error.patch | 43 +++++++++++++++++++
 14 files changed, 88 insertions(+), 2 deletions(-)
 create mode 100644 easybuild/easyconfigs/s/SciPy-bundle/numpy-1.20.3_fix-fortran-compiler-error.patch

diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.05-foss-2021a.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.05-foss-2021a.eb
index 2c0770da7e9..8d80f74fa66 100644
--- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.05-foss-2021a.eb
+++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.05-foss-2021a.eb
@@ -23,12 +23,15 @@ exts_list = [
     ('numpy', '1.20.3', {
         'sources': [SOURCE_ZIP],
         'patches': [
+            'numpy-1.20.3_fix-fortran-compiler-error.patch',
             'numpy-1.20.3_skip-ppc-long-complex-test.patch',
             'numpy-1.20.3_xfail-test-nan.patch',
             'numpy-1.20.3_fix-target-test-ccompiler-opt.patch',
         ],
         'checksums': [
             'e55185e51b18d788e49fe8305fd73ef4470596b33fc2c1ceb304566b99c71a69',  # numpy-1.20.3.zip
+            {'numpy-1.20.3_fix-fortran-compiler-error.patch':
+             '016e0d02ffabe013248c4fd203a4456edee76839f747c05daf92ac1fe9925189'},
             # numpy-1.20.3_skip-ppc-long-complex-test.patch
             '2f9a12e3a352b39076db84a7622fc8f4796abd3cb7f97f71958a495e864659a4',
             'f0ce961f7d79551598e23050d92f46e827e300f6a7e5a6112e58efcc10385d4d',  # numpy-1.20.3_xfail-test-nan.patch
diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.05-gomkl-2021a.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.05-gomkl-2021a.eb
index 3f0596710cc..21890734ddf 100644
--- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.05-gomkl-2021a.eb
+++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.05-gomkl-2021a.eb
@@ -25,6 +25,7 @@ exts_list = [
             'numpy-1.18.2-mkl.patch',
             'numpy-1.20.3_disable-broken-override-test.patch',
             'numpy-1.20.3_fix-cpu-feature-detection-intel-compilers.patch',
+            'numpy-1.20.3_fix-fortran-compiler-error.patch',
             'numpy-1.20.3_fix-target-test-ccompiler-opt.patch',
             'numpy-1.20.3_disable_fortran_callback_test.patch',
         ],
@@ -36,6 +37,8 @@ exts_list = [
             '43cc2e675c52db1776efcc6c84ebd5fc008b48e6355c81087420d5e790e4af9b',
             # numpy-1.20.3_fix-cpu-feature-detection-intel-compilers.patch
             '4c0b194c9d2e2c6b9798ebc271d4517f4c3cdbf2b3cbd68de16c7d4b068bb046',
+            {'numpy-1.20.3_fix-fortran-compiler-error.patch':
+             '016e0d02ffabe013248c4fd203a4456edee76839f747c05daf92ac1fe9925189'},
             # numpy-1.20.3_fix-target-test-ccompiler-opt.patch
             '3d84e8b7d48387778974a5f6ae342a690ab5989547206b6add9d9667f8d7572a',
             # numpy-1.20.3_disable_fortran_callback_test.patch
diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.05-intel-2021a.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.05-intel-2021a.eb
index 3deadeac9d6..730ac590d33 100644
--- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.05-intel-2021a.eb
+++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.05-intel-2021a.eb
@@ -25,6 +25,7 @@ exts_list = [
             'numpy-1.18.2-mkl.patch',
             'numpy-1.20.3_disable-broken-override-test.patch',
             'numpy-1.20.3_fix-cpu-feature-detection-intel-compilers.patch',
+            'numpy-1.20.3_fix-fortran-compiler-error.patch',
             'numpy-1.20.3_fix-target-test-ccompiler-opt.patch',
             'numpy-1.20.3_disable_fortran_callback_test.patch',
         ],
@@ -36,6 +37,8 @@ exts_list = [
             '43cc2e675c52db1776efcc6c84ebd5fc008b48e6355c81087420d5e790e4af9b',
             # numpy-1.20.3_fix-cpu-feature-detection-intel-compilers.patch
             '4c0b194c9d2e2c6b9798ebc271d4517f4c3cdbf2b3cbd68de16c7d4b068bb046',
+            {'numpy-1.20.3_fix-fortran-compiler-error.patch':
+             '016e0d02ffabe013248c4fd203a4456edee76839f747c05daf92ac1fe9925189'},
             # numpy-1.20.3_fix-target-test-ccompiler-opt.patch
             '3d84e8b7d48387778974a5f6ae342a690ab5989547206b6add9d9667f8d7572a',
             # numpy-1.20.3_disable_fortran_callback_test.patch
diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.10-foss-2021b-Python-2.7.18.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.10-foss-2021b-Python-2.7.18.eb
index f806bd48d7a..1bd36b39378 100644
--- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.10-foss-2021b-Python-2.7.18.eb
+++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.10-foss-2021b-Python-2.7.18.eb
@@ -29,6 +29,7 @@ exts_list = [
             'numpy-1.16.2_relax-long-complex-test.patch',
             'numpy-1.16.6_add_flexiblas_detection.patch',
             'numpy-1.16.6_handle_failing_linalg_test.patch',
+            'numpy-1.20.3_fix-fortran-compiler-error.patch',
         ],
         'sources': ['%(name)s-%(version)s.zip'],
         'checksums': [
@@ -39,6 +40,8 @@ exts_list = [
             '32ca32dd7ee8d6fcdce5875067acd50970c731cbb2603c6d1ad84ff81ff8c6d5',
             # numpy-1.16.6_handle_failing_linalg_test.patch
             'be9dce98649626b7322ed8d1241b74a4e28c1d1de070a8072dc912cad3eb143d',
+            {'numpy-1.20.3_fix-fortran-compiler-error.patch':
+             '016e0d02ffabe013248c4fd203a4456edee76839f747c05daf92ac1fe9925189'},
         ],
     }),
     ('ply', '3.11', {
diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.10-foss-2021b.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.10-foss-2021b.eb
index 46f9647ad26..3e1d85982cc 100644
--- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.10-foss-2021b.eb
+++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.10-foss-2021b.eb
@@ -25,9 +25,14 @@ use_pip = True
 exts_list = [
     ('numpy', '1.21.3', {
         'sources': ['%(name)s-%(version)s.zip'],
-        'patches': ['numpy-1.20.3_skip-ppc-long-complex-test.patch'],
+        'patches': [
+            'numpy-1.20.3_fix-fortran-compiler-error.patch',
+            'numpy-1.20.3_skip-ppc-long-complex-test.patch',
+        ],
         'checksums': [
             '63571bb7897a584ca3249c86dd01c10bcb5fe4296e3568b2e9c1a55356b6410e',  # numpy-1.21.3.zip
+            {'numpy-1.20.3_fix-fortran-compiler-error.patch':
+             '016e0d02ffabe013248c4fd203a4456edee76839f747c05daf92ac1fe9925189'},
             # numpy-1.20.3_skip-ppc-long-complex-test.patch
             '2f9a12e3a352b39076db84a7622fc8f4796abd3cb7f97f71958a495e864659a4',
         ],
diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.10-intel-2021b.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.10-intel-2021b.eb
index 87a1dfe3175..68420c45219 100644
--- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.10-intel-2021b.eb
+++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.10-intel-2021b.eb
@@ -29,6 +29,7 @@ exts_list = [
             'numpy-1.18.2-mkl.patch',
             'numpy-1.20.3_disable-broken-override-test.patch',
             'numpy-1.20.3_disable_fortran_callback_test.patch',
+            'numpy-1.20.3_fix-fortran-compiler-error.patch',
         ],
         'checksums': [
             '63571bb7897a584ca3249c86dd01c10bcb5fe4296e3568b2e9c1a55356b6410e',  # numpy-1.21.3.zip
@@ -37,6 +38,8 @@ exts_list = [
             '43cc2e675c52db1776efcc6c84ebd5fc008b48e6355c81087420d5e790e4af9b',
             # numpy-1.20.3_disable_fortran_callback_test.patch
             '44975a944544fd0e771b7e63c32590d257a3713070f8f7fdf60105dc516f1d75',
+            {'numpy-1.20.3_fix-fortran-compiler-error.patch':
+             '016e0d02ffabe013248c4fd203a4456edee76839f747c05daf92ac1fe9925189'},
         ],
     }),
     ('ply', '3.11', {
diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-foss-2022.05.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-foss-2022.05.eb
index e07fdee1c03..613b1853e88 100644
--- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-foss-2022.05.eb
+++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-foss-2022.05.eb
@@ -26,6 +26,7 @@ exts_list = [
     ('numpy', '1.22.3', {
         'patches': [
             'numpy-1.20.3_disable_fortran_callback_test.patch',
+            'numpy-1.20.3_fix-fortran-compiler-error.patch',
             'numpy-1.22.3_disable-broken-override-test.patch',
         ],
         'sources': ['%(name)s-%(version)s.zip'],
@@ -33,6 +34,8 @@ exts_list = [
             'dbc7601a3b7472d559dc7b933b18b4b66f9aa7452c120e87dfb33d02008c8a18',  # numpy-1.22.3.zip
             # numpy-1.20.3_disable_fortran_callback_test.patch
             '44975a944544fd0e771b7e63c32590d257a3713070f8f7fdf60105dc516f1d75',
+            {'numpy-1.20.3_fix-fortran-compiler-error.patch':
+             '016e0d02ffabe013248c4fd203a4456edee76839f747c05daf92ac1fe9925189'},
             # numpy-1.22.3_disable-broken-override-test.patch
             '9c589bb073b28b25ff45eb3c63c57966aa508dd8b318d0b885b6295271e4983c',
         ],
diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-foss-2022a.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-foss-2022a.eb
index ce504e9607a..21a801b8fb9 100644
--- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-foss-2022a.eb
+++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-foss-2022a.eb
@@ -26,6 +26,7 @@ exts_list = [
     ('numpy', '1.22.3', {
         'patches': [
             'numpy-1.20.3_disable_fortran_callback_test.patch',
+            'numpy-1.20.3_fix-fortran-compiler-error.patch',
             'numpy-1.22.3_disable-broken-override-test.patch',
             '%(name)s-%(version)s_skip-ppc-long-complex-test.patch',
         ],
@@ -34,6 +35,8 @@ exts_list = [
             'dbc7601a3b7472d559dc7b933b18b4b66f9aa7452c120e87dfb33d02008c8a18',  # numpy-1.22.3.zip
             # numpy-1.20.3_disable_fortran_callback_test.patch
             '44975a944544fd0e771b7e63c32590d257a3713070f8f7fdf60105dc516f1d75',
+            {'numpy-1.20.3_fix-fortran-compiler-error.patch':
+             '016e0d02ffabe013248c4fd203a4456edee76839f747c05daf92ac1fe9925189'},
             # numpy-1.22.3_disable-broken-override-test.patch
             '9c589bb073b28b25ff45eb3c63c57966aa508dd8b318d0b885b6295271e4983c',
             # numpy-1.22.3_skip-ppc-long-complex-test.patch
diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-intel-2022.05.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-intel-2022.05.eb
index 06ad5e918f6..97966712185 100644
--- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-intel-2022.05.eb
+++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-intel-2022.05.eb
@@ -27,6 +27,7 @@ exts_list = [
         'patches': [
             'numpy-1.18.2-mkl.patch',
             'numpy-1.20.3_disable_fortran_callback_test.patch',
+            'numpy-1.20.3_fix-fortran-compiler-error.patch',
             'numpy-1.22.3_disable-broken-override-test.patch',
         ],
         'sources': ['%(name)s-%(version)s.zip'],
@@ -35,6 +36,8 @@ exts_list = [
             'ea25ad5c0148c1398d282f0424e642fb9815a1a80f4512659b018e2adc378bcf',  # numpy-1.18.2-mkl.patch
             # numpy-1.20.3_disable_fortran_callback_test.patch
             '44975a944544fd0e771b7e63c32590d257a3713070f8f7fdf60105dc516f1d75',
+            {'numpy-1.20.3_fix-fortran-compiler-error.patch':
+             '016e0d02ffabe013248c4fd203a4456edee76839f747c05daf92ac1fe9925189'},
             # numpy-1.22.3_disable-broken-override-test.patch
             '9c589bb073b28b25ff45eb3c63c57966aa508dd8b318d0b885b6295271e4983c',
         ],
diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-intel-2022a.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-intel-2022a.eb
index a07d23a7f56..4e06a815c50 100644
--- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-intel-2022a.eb
+++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-intel-2022a.eb
@@ -27,6 +27,7 @@ exts_list = [
         'patches': [
             'numpy-1.18.2-mkl.patch',
             'numpy-1.20.3_disable_fortran_callback_test.patch',
+            'numpy-1.20.3_fix-fortran-compiler-error.patch',
             'numpy-1.22.3_disable-broken-override-test.patch',
         ],
         'sources': ['%(name)s-%(version)s.zip'],
@@ -35,6 +36,8 @@ exts_list = [
             'ea25ad5c0148c1398d282f0424e642fb9815a1a80f4512659b018e2adc378bcf',  # numpy-1.18.2-mkl.patch
             # numpy-1.20.3_disable_fortran_callback_test.patch
             '44975a944544fd0e771b7e63c32590d257a3713070f8f7fdf60105dc516f1d75',
+            {'numpy-1.20.3_fix-fortran-compiler-error.patch':
+             '016e0d02ffabe013248c4fd203a4456edee76839f747c05daf92ac1fe9925189'},
             # numpy-1.22.3_disable-broken-override-test.patch
             '9c589bb073b28b25ff45eb3c63c57966aa508dd8b318d0b885b6295271e4983c',
         ],
diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.02-gfbf-2022b.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.02-gfbf-2022b.eb
index e19bb6789f3..e9e059afe3a 100644
--- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.02-gfbf-2022b.eb
+++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.02-gfbf-2022b.eb
@@ -28,9 +28,14 @@ use_pip = True
 # order is important!
 exts_list = [
     ('numpy', '1.24.2', {
-        'patches': ['numpy-1.22.3_disable-broken-override-test.patch'],
+        'patches': [
+            'numpy-1.20.3_fix-fortran-compiler-error.patch',
+            'numpy-1.22.3_disable-broken-override-test.patch',
+        ],
         'checksums': [
             {'numpy-1.24.2.tar.gz': '003a9f530e880cb2cd177cba1af7220b9aa42def9c4afc2a2fc3ee6be7eb2b22'},
+            {'numpy-1.20.3_fix-fortran-compiler-error.patch':
+             '016e0d02ffabe013248c4fd203a4456edee76839f747c05daf92ac1fe9925189'},
             {'numpy-1.22.3_disable-broken-override-test.patch':
              '9c589bb073b28b25ff45eb3c63c57966aa508dd8b318d0b885b6295271e4983c'},
         ],
diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.07-gfbf-2023a.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.07-gfbf-2023a.eb
index 44b5725fe7d..9805854b0c3 100644
--- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.07-gfbf-2023a.eb
+++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.07-gfbf-2023a.eb
@@ -30,6 +30,7 @@ use_pip = True
 exts_list = [
     ('numpy', '1.25.1', {
         'patches': [
+            'numpy-1.20.3_fix-fortran-compiler-error.patch',
             'numpy-1.22.3_disable-broken-override-test.patch',
             ('numpy-1.25.1_fix-duplicate-avx512-symbols.patch', 'numpy/core/src/npysort/x86-simd-sort'),
             'numpy-1.25.1_fix-undefined-avx512-reference.patch',
@@ -38,6 +39,8 @@ exts_list = [
         ],
         'checksums': [
             {'numpy-1.25.1.tar.gz': '9a3a9f3a61480cc086117b426a8bd86869c213fc4072e606f01c4e4b66eb92bf'},
+            {'numpy-1.20.3_fix-fortran-compiler-error.patch':
+             '016e0d02ffabe013248c4fd203a4456edee76839f747c05daf92ac1fe9925189'},
             {'numpy-1.22.3_disable-broken-override-test.patch':
              '9c589bb073b28b25ff45eb3c63c57966aa508dd8b318d0b885b6295271e4983c'},
             {'numpy-1.25.1_fix-duplicate-avx512-symbols.patch':
diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.07-iimkl-2023a.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.07-iimkl-2023a.eb
index 95d1e9f41c4..25fa6ff36f7 100644
--- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.07-iimkl-2023a.eb
+++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.07-iimkl-2023a.eb
@@ -31,6 +31,7 @@ exts_list = [
     ('numpy', '1.25.1', {
         'patches': [
             'numpy-1.18.2-mkl.patch',
+            'numpy-1.20.3_fix-fortran-compiler-error.patch',
             'numpy-1.25.1_disable_fortran_callback_test.patch',
             'numpy-1.22.3_disable-broken-override-test.patch',
             'numpy-1.25.1_disable-broken-test_long_long_map.patch',
@@ -41,6 +42,8 @@ exts_list = [
         'checksums': [
             {'numpy-1.25.1.tar.gz': '9a3a9f3a61480cc086117b426a8bd86869c213fc4072e606f01c4e4b66eb92bf'},
             {'numpy-1.18.2-mkl.patch': 'ea25ad5c0148c1398d282f0424e642fb9815a1a80f4512659b018e2adc378bcf'},
+            {'numpy-1.20.3_fix-fortran-compiler-error.patch':
+             '016e0d02ffabe013248c4fd203a4456edee76839f747c05daf92ac1fe9925189'},
             {'numpy-1.25.1_disable_fortran_callback_test.patch':
              '3c02bd9973b7082fde9f9d18edfeb05798226ccb5731a56f5677269200c345cf'},
             {'numpy-1.22.3_disable-broken-override-test.patch':
diff --git a/easybuild/easyconfigs/s/SciPy-bundle/numpy-1.20.3_fix-fortran-compiler-error.patch b/easybuild/easyconfigs/s/SciPy-bundle/numpy-1.20.3_fix-fortran-compiler-error.patch
new file mode 100644
index 00000000000..32b41061f06
--- /dev/null
+++ b/easybuild/easyconfigs/s/SciPy-bundle/numpy-1.20.3_fix-fortran-compiler-error.patch
@@ -0,0 +1,43 @@
+Using Fortran compilers which differ "too much" from GCC fails building NumPy with something like
+> A valid Fortran version was not found in this string: [...]
+
+See https://github.com/easybuilders/easybuild-easyblocks/issues/2518 and https://github.com/numpy/numpy/pull/26502
+
+Fix by converting the hard error into a warning as the issue would be handled later if required.
+E.g. for building NumPy we don't need a Fortran compiler at all.
+
+Author: Alexander Grund (TU Dresden)
+
+diff --git a/numpy/distutils/fcompiler/gnu.py b/numpy/distutils/fcompiler/gnu.py
+index eac4cbb477..8a1043fe26 100644
+--- a/numpy/distutils/fcompiler/gnu.py
++++ b/numpy/distutils/fcompiler/gnu.py
+@@ -8,6 +8,7 @@ import hashlib
+ import base64
+ import subprocess
+ from subprocess import Popen, PIPE, STDOUT
++from distutils import log
+ from numpy.distutils.exec_command import filepath_from_subprocess_output
+ from numpy.distutils.fcompiler import FCompiler
+ from distutils.version import LooseVersion
+@@ -69,9 +70,9 @@ class GnuFCompiler(FCompiler):
+                     # from the version string
+                     return ('gfortran', v)
+ 
+-        # If still nothing, raise an error to make the problem easy to find.
+-        err = 'A valid Fortran version was not found in this string:\n'
+-        raise ValueError(err + version_string)
++        # If still nothing, warn to make the problem easy to find.
++        log.warn('A valid Fortran version was not found in this string:\n'
++                 + version_string)
+ 
+     def version_match(self, version_string):
+         v = self.gnu_version_match(version_string)
+@@ -539,7 +540,6 @@ def _can_target(cmd, arch):
+ 
+ 
+ if __name__ == '__main__':
+-    from distutils import log
+     from numpy.distutils import customized_fcompiler
+     log.set_verbosity(2)
+ 

From 798f19a7dc8234c4ec9e004a8b8f982bfb772bb2 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 14 Jun 2024 09:47:15 +0200
Subject: [PATCH 207/835] add extra space

---
 easybuild/easyconfigs/w/WRF/WRF-4.5.1-foss-2023a-dmpar.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/w/WRF/WRF-4.5.1-foss-2023a-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-4.5.1-foss-2023a-dmpar.eb
index 61a0e73356c..5b7d53ec837 100644
--- a/easybuild/easyconfigs/w/WRF/WRF-4.5.1-foss-2023a-dmpar.eb
+++ b/easybuild/easyconfigs/w/WRF/WRF-4.5.1-foss-2023a-dmpar.eb
@@ -15,7 +15,7 @@ github_account = 'wrf-model'
 source_urls = [GITHUB_RELEASE]
 sources = ['v%(version)s.tar.gz']
 patches = [
-    'WRF-4.5.1_netCDF-Fortran_separate_path.patch', # note: no longer required for version 4.5.2
+    'WRF-4.5.1_netCDF-Fortran_separate_path.patch',  # note: no longer required for version 4.5.2
 ]
 checksums = [
     {'v4.5.1.tar.gz': '9d557c34c105db4d41e727843ecb19199233c7cf82c5369b34a2ce8efe65e2d1'},

From 15ff949080e91fba0602f07bd7a7d5fe631e9c7c Mon Sep 17 00:00:00 2001
From: Adam Huffman <12435+verdurin@users.noreply.github.com>
Date: Fri, 14 Jun 2024 08:12:14 +0000
Subject: [PATCH 208/835] adding easyconfigs: NanoCaller-3.6.0-foss-2022b.eb,
 WFA2-2.3.4-GCCcore-12.2.0.eb, vcflib-1.0.9-foss-2022b-R-4.2.2.eb,
 smithwaterman-20160702-GCCcore-12.2.0.eb,
 multichoose-1.0.3-GCCcore-12.2.0.eb, fsom-20151117-GCCcore-12.2.0.eb,
 filevercmp-20191210-GCCcore-12.2.0.eb, fastahack-1.0.0-GCCcore-12.2.0.eb,
 intervaltree-0.1-GCCcore-12.2.0.eb, tabixpp-1.1.2-GCC-12.2.0.eb

---
 .../fastahack-1.0.0-GCCcore-12.2.0.eb         | 36 +++++++++
 .../filevercmp-20191210-GCCcore-12.2.0.eb     | 37 +++++++++
 .../f/fsom/fsom-20151117-GCCcore-12.2.0.eb    | 43 ++++++++++
 .../intervaltree-0.1-GCCcore-12.2.0.eb        | 38 +++++++++
 .../multichoose-1.0.3-GCCcore-12.2.0.eb       | 32 ++++++++
 .../NanoCaller/NanoCaller-3.6.0-foss-2022b.eb | 44 ++++++++++
 .../smithwaterman-20160702-GCCcore-12.2.0.eb  | 34 ++++++++
 .../t/tabixpp/tabixpp-1.1.2-GCC-12.2.0.eb     | 41 ++++++++++
 .../vcflib/vcflib-1.0.9-foss-2022b-R-4.2.2.eb | 81 +++++++++++++++++++
 .../w/WFA2/WFA2-2.3.4-GCCcore-12.2.0.eb       | 30 +++++++
 10 files changed, 416 insertions(+)
 create mode 100644 easybuild/easyconfigs/f/fastahack/fastahack-1.0.0-GCCcore-12.2.0.eb
 create mode 100644 easybuild/easyconfigs/f/filevercmp/filevercmp-20191210-GCCcore-12.2.0.eb
 create mode 100644 easybuild/easyconfigs/f/fsom/fsom-20151117-GCCcore-12.2.0.eb
 create mode 100644 easybuild/easyconfigs/i/intervaltree/intervaltree-0.1-GCCcore-12.2.0.eb
 create mode 100644 easybuild/easyconfigs/m/multichoose/multichoose-1.0.3-GCCcore-12.2.0.eb
 create mode 100644 easybuild/easyconfigs/n/NanoCaller/NanoCaller-3.6.0-foss-2022b.eb
 create mode 100644 easybuild/easyconfigs/s/smithwaterman/smithwaterman-20160702-GCCcore-12.2.0.eb
 create mode 100644 easybuild/easyconfigs/t/tabixpp/tabixpp-1.1.2-GCC-12.2.0.eb
 create mode 100644 easybuild/easyconfigs/v/vcflib/vcflib-1.0.9-foss-2022b-R-4.2.2.eb
 create mode 100644 easybuild/easyconfigs/w/WFA2/WFA2-2.3.4-GCCcore-12.2.0.eb

diff --git a/easybuild/easyconfigs/f/fastahack/fastahack-1.0.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/f/fastahack/fastahack-1.0.0-GCCcore-12.2.0.eb
new file mode 100644
index 00000000000..2d430c8a5f2
--- /dev/null
+++ b/easybuild/easyconfigs/f/fastahack/fastahack-1.0.0-GCCcore-12.2.0.eb
@@ -0,0 +1,36 @@
+# Updated: Denis Kristak (INUITS)
+# Updated: Petr Král (INUITS)
+
+easyblock = 'ConfigureMake'
+
+name = 'fastahack'
+version = '1.0.0'
+
+homepage = 'https://github.com/ekg/fastahack'
+description = """Utilities for indexing and sequence extraction from FASTA files."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+
+github_account = 'ekg'
+source_urls = [GITHUB_SOURCE]
+sources = ['v%(version)s.tar.gz']
+patches = ['%(name)s-%(version)s_build-libs.patch']
+checksums = [
+    'cc1c04729b0c8ba3647cbb7e15e2b490ce701d73773f30f5892d68c36a1dceae',  # v1.0.0.tar.gz
+    '7f804486c6bafd9b1572cb5f86ff28dbebb4d6da551bde1091d6ff8f82748bf4',  # fastahack-1.0.0_build-libs.patch
+]
+
+builddependencies = [('binutils', '2.39')]
+
+skipsteps = ['configure']
+
+installopts = 'PREFIX=%(installdir)s '
+
+sanity_check_paths = {
+    'files': ['bin/%(name)s', 'lib/libfastahack.%s' % SHLIB_EXT],
+    'dirs': [],
+}
+
+sanity_check_commands = ['%(name)s --help']
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/f/filevercmp/filevercmp-20191210-GCCcore-12.2.0.eb b/easybuild/easyconfigs/f/filevercmp/filevercmp-20191210-GCCcore-12.2.0.eb
new file mode 100644
index 00000000000..f9acad2dfe3
--- /dev/null
+++ b/easybuild/easyconfigs/f/filevercmp/filevercmp-20191210-GCCcore-12.2.0.eb
@@ -0,0 +1,37 @@
+# Updated: Denis Kristak (INUITS)
+# Updated: Petr Král (INUITS)
+
+easyblock = 'ConfigureMake'
+
+name = 'filevercmp'
+version = '20191210'
+local_commit = 'df20dcc'
+
+homepage = 'https://github.com/ekg/filevercmp'
+description = """filevercmp function as in sort --version-sort."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+
+github_account = 'ekg'
+source_urls = [GITHUB_SOURCE]
+sources = ['%s.tar.gz' % local_commit]
+patches = ['%(name)s-%(version)s_build-libs.patch']
+checksums = [
+    '89835829a7829f7a25783b2cf9d482f1e3c794703343c9214c15c66a8c7f4aae',  # df20dcc.tar.gz
+    '051438f76dd04219abfb283f61101c04d748407031e180b7ae3841344416ec4f',  # filevercmp-20191210_build-libs.patch
+]
+
+builddependencies = [('binutils', '2.39')]
+
+skipsteps = ['configure']
+
+installopts = 'DESTDIR="" PREFIX=%(installdir)s '
+
+sanity_check_paths = {
+    'files': ['bin/%(name)s', 'lib/libfilevercmp.%s' % SHLIB_EXT],
+    'dirs': [],
+}
+
+sanity_check_commands = ['%(name)s abca bcac']
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/f/fsom/fsom-20151117-GCCcore-12.2.0.eb b/easybuild/easyconfigs/f/fsom/fsom-20151117-GCCcore-12.2.0.eb
new file mode 100644
index 00000000000..b9de5b70eff
--- /dev/null
+++ b/easybuild/easyconfigs/f/fsom/fsom-20151117-GCCcore-12.2.0.eb
@@ -0,0 +1,43 @@
+# Updated: Denis Kristak (INUITS)
+# Updated: Petr Král (INUITS)
+
+easyblock = 'ConfigureMake'
+
+name = 'fsom'
+version = '20151117'
+local_commit = '56695e1'
+
+homepage = 'https://github.com/ekg/fsom'
+description = """A tiny C library for managing SOM (Self-Organizing Maps) neural networks."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+
+github_account = 'ekg'
+
+source_urls = [GITHUB_SOURCE]
+sources = ['%s.tar.gz' % local_commit]
+
+patches = [
+    '%(name)s-%(version)s_build-libs.patch',
+    '%(name)s-20141119_fix-abs-overload.patch'
+]
+
+checksums = [
+    '1ba3360985be781bb9f79d974705c86e7bb0719cb83638955e113b5dd83ec8dd',  # 56695e1.tar.gz
+    'd4e19b2db054cc5d3153ceba88ad2b11e5143e3a3c243103ce1e6994a83c43fe',  # fsom-20151117_build-libs.patch
+    '54dd6ae76033535fe1b0231142d8bd41a815950dc3fd269dc321f698d4973639',  # fsom-20141119_fix-abs-overload.patch
+]
+
+builddependencies = [('binutils', '2.39')]
+
+skipsteps = ['configure']
+
+installopts = 'PREFIX=%(installdir)s '
+
+sanity_check_paths = {
+    'files': ['bin/%(name)s', 'lib/libfsom.%s' % SHLIB_EXT],
+    'dirs': [],
+}
+sanity_check_commands = ["%(name)s --help"]
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/i/intervaltree/intervaltree-0.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/i/intervaltree/intervaltree-0.1-GCCcore-12.2.0.eb
new file mode 100644
index 00000000000..06f61418ed7
--- /dev/null
+++ b/easybuild/easyconfigs/i/intervaltree/intervaltree-0.1-GCCcore-12.2.0.eb
@@ -0,0 +1,38 @@
+# Updated: Denis Kristak (INUITS)
+# Updated: Petr Král (INUITS)
+
+easyblock = 'ConfigureMake'
+
+name = 'intervaltree'
+version = '0.1'
+
+homepage = 'https://github.com/ekg/intervaltree'
+description = """An interval tree can be used to efficiently find a set of numeric intervals
+ overlapping or containing another interval. This library provides a basic implementation of an
+ interval tree using C++ templates, allowing the insertion of arbitrary types into the tree.
+"""
+
+toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+
+github_account = 'ekg'
+source_urls = [GITHUB_SOURCE]
+sources = ['v%(version)s.tar.gz']
+patches = ['%(name)s-%(version)s_fix-numeric_limits.patch']
+checksums = [
+    '7ba41f164a98bdcd570f1416fde1634b23d3b0d885b11ccebeec76f58810c307',  # v0.1.tar.gz
+    '1d69caf35af86c0a55000e1bde3f9a0f19dd63d1d2b6bd48e4e5fecbb1aaa6b0',  # intervaltree-0.1_fix-numeric_limits.patch
+]
+
+builddependencies = [('binutils', '2.39')]
+
+skipsteps = ['configure']
+
+preinstallopts = 'DESTDIR="" PREFIX=%(installdir)s'
+
+sanity_check_paths = {
+    'files': ['bin/interval_tree_test', 'include/intervaltree/IntervalTree.h'],
+    'dirs': [],
+}
+sanity_check_commands = ["interval_tree_test"]
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/m/multichoose/multichoose-1.0.3-GCCcore-12.2.0.eb b/easybuild/easyconfigs/m/multichoose/multichoose-1.0.3-GCCcore-12.2.0.eb
new file mode 100644
index 00000000000..9c2a1b09cfc
--- /dev/null
+++ b/easybuild/easyconfigs/m/multichoose/multichoose-1.0.3-GCCcore-12.2.0.eb
@@ -0,0 +1,32 @@
+easyblock = 'MakeCp'
+
+name = 'multichoose'
+version = '1.0.3'
+
+homepage = 'https://github.com/ekg/multichoose'
+description = """generate multiset combinations (n multichoose k)."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+
+github_account = 'ekg'
+source_urls = [GITHUB_SOURCE]
+sources = ['v%(version)s.tar.gz']
+patches = ['%(name)s-%(version)s_improve-build-system.patch']
+checksums = [
+    '74f0a223c670f5aa81b14191c53ad8d84281838a47471c10253ae391f736c877',  # v1.0.3.tar.gz
+    '96abf6ac1105ee596be078d6e8fb478f870a4ae33fffe70f93e627c0360cfc77',  # multichoose-1.0.3_improve-build-system.patch
+]
+
+builddependencies = [('binutils', '2.39')]
+
+local_bins = [name, 'multipermute']
+files_to_copy = [(local_bins, 'bin'), (['*.h'], 'include/%(name)s')]
+
+sanity_check_paths = {
+    'files': ['bin/%s' % x for x in local_bins],
+    'dirs': [],
+}
+
+sanity_check_commands = ['%(name)s 1 a']
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/n/NanoCaller/NanoCaller-3.6.0-foss-2022b.eb b/easybuild/easyconfigs/n/NanoCaller/NanoCaller-3.6.0-foss-2022b.eb
new file mode 100644
index 00000000000..037b70ab15e
--- /dev/null
+++ b/easybuild/easyconfigs/n/NanoCaller/NanoCaller-3.6.0-foss-2022b.eb
@@ -0,0 +1,44 @@
+easyblock = 'Tarball'
+
+name = 'NanoCaller'
+version = '3.6.0'
+
+homepage = 'https://github.com/WGLab/NanoCaller'
+description = """NanoCaller is a computational method that integrates long reads in deep
+ convolutional neural network for the detection of SNPs/indels from long-read sequencing data."""
+
+toolchain = {'name': 'foss', 'version': '2022b'}
+
+source_urls = ['https://github.com/WGLab/%(name)s/archive/']
+sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}]
+checksums = ['d3df57ca47617365ed891f7acc6976ec5dec3c224e5e213f8bba2d3b2d973303']
+
+dependencies = [
+    ('Python', '3.10.8'),
+    ('SciPy-bundle', '2023.02'),
+    ('BCFtools', '1.17'),
+    ('python-parasail', '1.3.4'),
+    ('MUSCLE', '5.1.0'),
+    ('Pysam', '0.21.0'),
+    ('SAMtools', '1.17'),
+    ('TensorFlow', '2.13.0'),
+    ('WhatsHap', '2.1'),
+    ('vcflib', '1.0.9', '-R-4.2.2'),
+    ('intervaltree-python', '3.1.0'),
+    ('tqdm', '4.64.1'),
+    ('RTG-Tools', '3.12.1', '-Java-11', SYSTEM),
+]
+
+modextrapaths = {
+    'PATH': '',
+    'PYTHONPATH': '',
+}
+
+sanity_check_paths = {
+    'files': ['NanoCaller'],
+    'dirs': [],
+}
+
+sanity_check_commands = ["NanoCaller --help"]
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/s/smithwaterman/smithwaterman-20160702-GCCcore-12.2.0.eb b/easybuild/easyconfigs/s/smithwaterman/smithwaterman-20160702-GCCcore-12.2.0.eb
new file mode 100644
index 00000000000..d546525a5c9
--- /dev/null
+++ b/easybuild/easyconfigs/s/smithwaterman/smithwaterman-20160702-GCCcore-12.2.0.eb
@@ -0,0 +1,34 @@
+easyblock = 'ConfigureMake'
+
+name = 'smithwaterman'
+version = '20160702'
+local_commit = '2610e25'
+
+homepage = 'https://github.com/ekg/smithwaterman'
+description = """smith-waterman-gotoh alignment algorithm."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+
+github_account = 'ekg'
+source_urls = [GITHUB_SOURCE]
+sources = ['%s.tar.gz' % local_commit]
+patches = ['%(name)s-%(version)s_build-shared-lib.patch']
+checksums = [
+    '8e1b37ab0e8cd9d3d5cbfdba80258c0ebd0862749b531e213f44cdfe2fc541d8',  # 2610e25.tar.gz
+    '2aa63ec5cd0260efcab002eaf4bbf62497b91afc0e3f82d8290496803c35e582',  # smithwaterman-20160702_build-shared-lib.patch
+]
+
+builddependencies = [('binutils', '2.39')]
+
+skipsteps = ['configure']
+
+installopts = 'PREFIX=%(installdir)s '
+
+sanity_check_paths = {
+    'files': ['bin/%(name)s', 'lib/libsw.%s' % SHLIB_EXT],
+    'dirs': [],
+}
+
+sanity_check_commands = ["%(name)s --help"]
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/t/tabixpp/tabixpp-1.1.2-GCC-12.2.0.eb b/easybuild/easyconfigs/t/tabixpp/tabixpp-1.1.2-GCC-12.2.0.eb
new file mode 100644
index 00000000000..452f3caa3fa
--- /dev/null
+++ b/easybuild/easyconfigs/t/tabixpp/tabixpp-1.1.2-GCC-12.2.0.eb
@@ -0,0 +1,41 @@
+# Author: Jasper Grimm (UoY)
+# Updated: Petr Král (INUITS)
+
+easyblock = 'ConfigureMake'
+
+name = 'tabixpp'
+version = '1.1.2'
+
+homepage = 'https://github.com/ekg/tabixpp'
+description = """C++ wrapper to tabix indexer"""
+
+toolchain = {'name': 'GCC', 'version': '12.2.0'}
+
+github_account = 'ekg'
+source_urls = [GITHUB_SOURCE]
+sources = ['v%(version)s.tar.gz']
+patches = ['%(name)s-%(version)s_use-external-HTSlib.patch']
+
+checksums = [
+    'c850299c3c495221818a85c9205c60185c8ed9468d5ec2ed034470bb852229dc',  # v1.1.2.tar.gz
+    'a4684b6c3a69258d0686f601564b635ae3dc098e712783b46d9ca5b7ff996906',  # tabixpp-1.1.2_use-external-HTSlib.patch
+]
+
+dependencies = [
+    ('zlib', '1.2.12'),
+    ('bzip2', '1.0.8'),
+    ('XZ', '5.2.7'),
+    ('HTSlib', '1.17'),
+    ('PCRE', '8.45'),
+]
+
+skipsteps = ['configure']
+
+preinstallopts = 'PREFIX=%(installdir)s'
+
+sanity_check_paths = {
+    'files': ['bin/tabix++', 'lib/libtabixpp.%s' % SHLIB_EXT],
+    'dirs': [],
+}
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/v/vcflib/vcflib-1.0.9-foss-2022b-R-4.2.2.eb b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.9-foss-2022b-R-4.2.2.eb
new file mode 100644
index 00000000000..d22ff1aee07
--- /dev/null
+++ b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.9-foss-2022b-R-4.2.2.eb
@@ -0,0 +1,81 @@
+# Author: Jasper Grimm (UoY)
+# Updated: Denis Kristak (INUITS)
+# Updated: Petr Král (INUITS)
+easyblock = 'CMakeMake'
+
+name = 'vcflib'
+version = '1.0.9'
+versionsuffix = '-R-%(rver)s'
+
+homepage = 'https://github.com/vcflib/vcflib'
+description = """vcflib provides methods to manipulate and interpret sequence variation as it can be
+ described by VCF. The Variant Call Format (VCF) is a flat-file, tab-delimited textual format intended
+ to concisely describe reference-indexed genetic variations between individuals."""
+
+toolchain = {'name': 'foss', 'version': '2022b'}
+toolchainopts = {'openmp': True}
+
+source_urls = [GITHUB_SOURCE]
+sources = ['v%(version)s.tar.gz']
+patches = [
+    'vcflib-1.0.9_use-external-deps_and_fix_shared_lib.patch',
+]
+checksums = [
+    {'v1.0.9.tar.gz': 'd17fcf8a34d65f1dfecf4b4290d058be744422b6baf34ecdef8ea912d59a4569'},
+    {'vcflib-1.0.9_use-external-deps_and_fix_shared_lib.patch':
+     '82f622a6b4bac1501b10bbc82c4e6567e095869c17b7d34d92b8c4836816b5a1'},
+]
+
+builddependencies = [
+    ('CMake', '3.24.3'),
+    ('pkgconf', '1.9.3'),
+    ('pybind11', '2.10.3'),
+]
+
+dependencies = [
+    ('Python', '3.10.8'),
+    ('Perl', '5.36.0'),
+    ('R', '4.2.2'),
+    ('XZ', '5.2.7'),
+    ('zlib', '1.2.12'),
+    ('bzip2', '1.0.8'),
+    ('HTSlib', '1.17'),
+    ('tabixpp', '1.1.2'),
+    ('intervaltree', '0.1'),
+    ('fastahack', '1.0.0'),
+    ('filevercmp', '20191210'),
+    ('fsom', '20151117'),
+    ('multichoose', '1.0.3'),
+    ('smithwaterman', '20160702'),
+    ('WFA2', '2.3.4'),
+]
+
+preconfigopts = "find %(builddir)s/%(name)s-%(version)s/src -type f "
+preconfigopts += r"-regextype egrep -regex '.*\.(h|cpp)' -exec sed -i"
+preconfigopts += " -e 's|SmithWatermanGotoh.h|smithwaterman/SmithWatermanGotoh.h|g'"
+preconfigopts += " -e 's|IntervalTree.h|intervaltree/IntervalTree.h|g'"
+preconfigopts += " -e 's|multichoose.h|multichoose/multichoose.h|g' -e 's|filevercmp.h|filevercmp/filevercmp.h|g'"
+preconfigopts += " -e 's|tabix.hpp|tabixpp/tabix.hpp|g' -e 's|Fasta.h|fastahack/Fasta.h|g'"
+preconfigopts += r" -e 's|disorder.h|smithwaterman/disorder.h|g' {} \; && "
+
+configopts = "-DZIG=OFF -DWFA_GITMODULE=OFF -DWFA_INCLUDE_DIRS=$EBROOTWFA2/include/wfa2lib "
+configopts += "-DPYTHON_EXECUTABLE=$EBROOTPYTHON/bin/python"
+
+postinstallcmds = ["cp -r %(builddir)s/%(name)s-%(version)s/scripts %(installdir)s"]
+
+modextrapaths = {
+    'PATH': 'scripts',
+    'PYTHONPATH': 'lib',
+}
+
+sanity_check_paths = {
+    'files': ['bin/vcffilter', 'bin/vcfcombine', 'lib/libvcflib.a', 'lib/libvcflib.%s' % SHLIB_EXT],
+    'dirs': ['scripts', 'include'],
+}
+
+sanity_check_commands = [
+    "python -c 'import pyvcflib'",
+    "vcfwave --help",
+]
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/w/WFA2/WFA2-2.3.4-GCCcore-12.2.0.eb b/easybuild/easyconfigs/w/WFA2/WFA2-2.3.4-GCCcore-12.2.0.eb
new file mode 100644
index 00000000000..cef70fe1233
--- /dev/null
+++ b/easybuild/easyconfigs/w/WFA2/WFA2-2.3.4-GCCcore-12.2.0.eb
@@ -0,0 +1,30 @@
+easyblock = 'CMakeMake'
+
+name = 'WFA2'
+version = '2.3.4'
+
+homepage = 'https://github.com/smarco/WFA2-lib'
+description = """The wavefront alignment (WFA) algorithm is an exact
+ gap-affine algorithm that takes advantage of homologous regions
+ between the sequences to accelerate the alignment process."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+
+source_urls = ['https://github.com/smarco/WFA2-lib/archive/refs/tags/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['3a02d19b45c7efcdcabdd956421b1e449e771fca0b0f072e02d7aa65ebb29f23']
+
+builddependencies = [
+    ('binutils', '2.39'),
+    ('CMake', '3.24.3'),
+    ('pkgconf', '1.9.3'),
+]
+
+configopts = "-DOPENMP=ON"
+
+sanity_check_paths = {
+    'files': ['lib/libwfa2.a'],
+    'dirs': ['include/wfa2lib'],
+}
+
+moduleclass = 'bio'

From b53791c87c8cb4e5df7f50b1781a026d27409c30 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 14 Jun 2024 10:16:45 +0200
Subject: [PATCH 209/835] adding easyconfigs:
 PyTorch-Geometric-2.5.0-foss-2023a-PyTorch-2.1.2.eb

---
 ...eometric-2.5.0-foss-2023a-PyTorch-2.1.2.eb | 100 ++++++++++++++++++
 1 file changed, 100 insertions(+)
 create mode 100644 easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-2.5.0-foss-2023a-PyTorch-2.1.2.eb

diff --git a/easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-2.5.0-foss-2023a-PyTorch-2.1.2.eb b/easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-2.5.0-foss-2023a-PyTorch-2.1.2.eb
new file mode 100644
index 00000000000..9c8f282ccee
--- /dev/null
+++ b/easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-2.5.0-foss-2023a-PyTorch-2.1.2.eb
@@ -0,0 +1,100 @@
+easyblock = 'PythonBundle'
+
+name = 'PyTorch-Geometric'
+version = '2.5.0'
+local_pytorchver = '2.1.2'
+versionsuffix = '-PyTorch-%s' % local_pytorchver
+
+homepage = 'https://github.com/rusty1s/pytorch_geometric'
+description = "PyTorch Geometric (PyG) is a geometric deep learning extension library for PyTorch."
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+builddependencies = [
+    ('PDM', '2.12.4'),
+    ('Parallel-Hashmap', '1.3.12'),  # header only
+]
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('PyTorch', local_pytorchver),
+    ('scikit-learn', '1.3.1'),
+    ('scikit-image', '0.22.0'),
+    ('numba', '0.58.1'),
+    ('h5py', '3.9.0'),
+    ('tqdm', '4.66.1'),
+    ('RDFlib', '7.0.0'),
+    ('ASE', '3.22.1'),
+    ('YACS', '0.1.8'),
+    ('aiohttp', '3.8.5'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('googledrivedownloader', '0.4', {
+        'modulename': 'google_drive_downloader',
+        'checksums': ['4b34c1337b2ff3bf2bd7581818efbdcaea7d50ffd484ccf80809688f5ca0e204'],
+    }),
+    ('plyfile', '1.0.3', {
+        'patches': ['plyfile-1.0.3_use_pdm_backend.patch'],
+        'checksums': [
+            {'plyfile-1.0.3.tar.gz': '0ecbe8e7ce55a7bbc6c9dea24242fffa0ab7d9bed33fbd5ad567ca013bcc5222'},
+            {'plyfile-1.0.3_use_pdm_backend.patch': '815611863f16e785ef03a7992a0b99e433150212ff03559c7f6fce4e86d9e0a7'},
+        ],
+    }),
+    ('torch_scatter', '2.1.2', {
+        'source_urls': ['https://github.com/rusty1s/pytorch_scatter/archive/refs/tags/'],
+        'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}],
+        'checksums': ['6f375dbc9cfe03f330aa29ea553e9c7432e9b040d039b041f08bf05df1a8bf37'],
+        'runtest': 'pytest',
+        'testinstall': True,
+    }),
+    ('torch_sparse', '0.6.18', {
+        'source_urls': ['https://github.com/rusty1s/pytorch_sparse/archive/refs/tags/'],
+        'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}],
+        'checksums': ['a9e194cddc17481001ac4592a058450493ce13780e8ce3eb54d4f79706e69c91'],
+        'runtest': 'pytest -k "not test_spmm[dtype10-device10-sum] and not test_spmm[dtype16-device16-add]"',  # flaky
+        'testinstall': True,
+    }),
+    ('torch_cluster', '1.6.3', {
+        'source_urls': ['https://github.com/rusty1s/pytorch_cluster/archive/refs/tags/'],
+        'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}],
+        'checksums': ['0e2b08095e03cf87ce9b23b7a7352236a25d3ed92d92351dc020fd927ea8dbfe'],
+        'runtest': 'pytest',
+        'testinstall': True,
+    }),
+    ('torch_spline_conv', '1.2.2', {
+        'source_urls': ['https://github.com/rusty1s/pytorch_spline_conv/archive/refs/tags/'],
+        'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}],
+        'checksums': ['258947394514ba487b2617268ae7102e9a06fd15d79f5d8239a96211a85adc3d'],
+        'runtest': 'pytest',
+        'testinstall': True,
+    }),
+    ('python-louvain', '0.16', {
+        'modulename': 'community.community_louvain',
+        'checksums': ['b7ba2df5002fd28d3ee789a49532baad11fe648e4f2117cf0798e7520a1da56b'],
+    }),
+    ('torch_geometric', version, {
+        'source_urls': ['https://github.com/pyg-team/pytorch_geometric/archive/refs/tags/'],
+        'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}],
+        'checksums': ['f9abf00dc7fd1039ef1d9734a0fbd8c52196e39ca9fc4816afd98a8f311265be'],
+        'runtest': (
+            'pytest'
+            ' --ignore=test/test_edge_index.py'  # many tests require PyTorch with MKL
+            ' --ignore=test/nn/models/test_graph_unet.py'  # requires PyTorch with MKL
+            ' --ignore=test/nn/pool/test_asap.py'  # requires PyTorch with MKL
+            ' --ignore=test/transforms/test_add_metapaths.py'  # requires PyTorch with MKL
+            ' --ignore=test/transforms/test_two_hop.py'  # requires PyTorch with MKL
+            ' --ignore=test/test_inspector.py'  # test failing due to typing change
+            ' --ignore=test/nn/conv/test_hetero_conv.py'  # unknown jit compilation issue
+            ' --ignore=test/nn/conv/test_sage_conv.py'  # unknown jit compilation issue
+            ' -k "not test_multithreading_neighbor_loader" '  # picky about number of cores in the environment
+        ),
+        'testinstall': True,
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'lib'

From a6d3aca551dd16680ee763461836a7d05ea26c0e Mon Sep 17 00:00:00 2001
From: Adam Huffman <12435+verdurin@users.noreply.github.com>
Date: Fri, 14 Jun 2024 08:29:52 +0000
Subject: [PATCH 210/835] Add missing MUSCLE easyconfig

---
 .../m/MUSCLE/MUSCLE-5.1.0-GCCcore-12.2.0.eb   | 39 +++++++++++++++++++
 1 file changed, 39 insertions(+)
 create mode 100644 easybuild/easyconfigs/m/MUSCLE/MUSCLE-5.1.0-GCCcore-12.2.0.eb

diff --git a/easybuild/easyconfigs/m/MUSCLE/MUSCLE-5.1.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-5.1.0-GCCcore-12.2.0.eb
new file mode 100644
index 00000000000..8af91759937
--- /dev/null
+++ b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-5.1.0-GCCcore-12.2.0.eb
@@ -0,0 +1,39 @@
+easyblock = 'MakeCp'
+
+name = 'MUSCLE'
+version = '5.1.0'
+
+homepage = 'https://drive5.com/muscle/'
+description = """MUSCLE is one of the best-performing multiple alignment programs
+ according to published benchmark tests, with accuracy and speed that are consistently
+ better than CLUSTALW. MUSCLE can align hundreds of sequences in seconds. Most users
+ learn everything they need to know about MUSCLE in a few minutes-only a handful of
+ command-line options are needed to perform common alignment tasks."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+
+github_account = 'rcedgar'
+source_urls = [GITHUB_LOWER_SOURCE]
+sources = ['%(version)s.tar.gz']
+checksums = ['2bba8b06e3ccabf6465fa26f459763b2029d7e7b9596881063e3aaba60d9e87d']
+
+builddependencies = [
+    ('binutils', '2.39'),
+]
+
+start_dir = 'src'
+
+# Use build environment defined by EasyBuild
+prebuildopts = "sed -i 's/$(CPPOPTS)/$(CPPOPTS) $(CXXFLAGS) $(CPPFLAGS)/g' Makefile &&"
+buildopts = "CPP=${CXX} CC=${CC}"
+
+files_to_copy = [(['Linux/muscle'], 'bin')]
+
+sanity_check_paths = {
+    'files': ['bin/muscle'],
+    'dirs': [],
+}
+
+sanity_check_commands = ["muscle -h"]
+
+moduleclass = 'bio'

From 0da7c99f6c1aef3326e74abbc1c6b9351e50acf6 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Fri, 14 Jun 2024 11:07:49 +0200
Subject: [PATCH 211/835] update boost-python version

---
 .../Boost.Python-1.82.0-GCC-12.3.0.eb         | 24 +++++++++++++++++++
 .../v/vigra/vigra-1.11.2-foss-2023a.eb        |  2 +-
 2 files changed, 25 insertions(+), 1 deletion(-)
 create mode 100644 easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.82.0-GCC-12.3.0.eb

diff --git a/easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.82.0-GCC-12.3.0.eb b/easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.82.0-GCC-12.3.0.eb
new file mode 100644
index 00000000000..ee38c6983cd
--- /dev/null
+++ b/easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.82.0-GCC-12.3.0.eb
@@ -0,0 +1,24 @@
+easyblock = 'EB_Boost'
+
+name = 'Boost.Python'
+version = '1.82.0'
+
+homepage = 'https://boostorg.github.io/python'
+description = """Boost.Python is a C++ library which enables seamless interoperability between C++
+ and the Python programming language."""
+
+toolchain = {'name': 'GCC', 'version': '12.3.0'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://boostorg.jfrog.io/artifactory/main/release/%(version)s/source/']
+sources = ['boost_1_82_0.tar.gz']
+checksums = ['66a469b6e608a51f8347236f4912e27dc5c60c60d7d53ae9bfe4683316c6f04c']
+
+dependencies = [
+    ('Boost', version),
+    ('Python', '3.11.3'),
+]
+
+only_python_bindings = True
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/v/vigra/vigra-1.11.2-foss-2023a.eb b/easybuild/easyconfigs/v/vigra/vigra-1.11.2-foss-2023a.eb
index 68eb19c4346..6df5b9c0895 100644
--- a/easybuild/easyconfigs/v/vigra/vigra-1.11.2-foss-2023a.eb
+++ b/easybuild/easyconfigs/v/vigra/vigra-1.11.2-foss-2023a.eb
@@ -20,7 +20,7 @@ builddependencies = [
 dependencies = [
     ('Python', '3.11.3'),
     ('SciPy-bundle', '2023.07'),
-    ('Boost.Python', '1.83.0'),
+    ('Boost.Python', '1.82.0'),
     ('libjpeg-turbo', '2.1.5.1'),
     ('OpenJPEG', '2.5.0'),
     ('LibTIFF', '4.5.0'),

From 89ac618d70914dc48c57b65d32384f4ba238340f Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com>
Date: Fri, 14 Jun 2024 11:08:45 +0200
Subject: [PATCH 212/835] Delete Boost.Python-1.83.0-GCC-12.3.0.eb

---
 .../Boost.Python-1.83.0-GCC-12.3.0.eb         | 24 -------------------
 1 file changed, 24 deletions(-)
 delete mode 100644 easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.83.0-GCC-12.3.0.eb

diff --git a/easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.83.0-GCC-12.3.0.eb b/easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.83.0-GCC-12.3.0.eb
deleted file mode 100644
index 6a5ffcc08a7..00000000000
--- a/easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.83.0-GCC-12.3.0.eb
+++ /dev/null
@@ -1,24 +0,0 @@
-easyblock = 'EB_Boost'
-
-name = 'Boost.Python'
-version = '1.83.0'
-
-homepage = 'https://boostorg.github.io/python'
-description = """Boost.Python is a C++ library which enables seamless interoperability between C++
- and the Python programming language."""
-
-toolchain = {'name': 'GCC', 'version': '12.3.0'}
-toolchainopts = {'pic': True}
-
-source_urls = ['https://boostorg.jfrog.io/artifactory/main/release/%(version)s/source/']
-sources = ['boost_1_83_0.tar.gz']
-checksums = ['c0685b68dd44cc46574cce86c4e17c0f611b15e195be9848dfd0769a0a207628']
-
-dependencies = [
-    ('Boost', '1.82.0'),
-    ('Python', '3.11.3'),
-]
-
-only_python_bindings = True
-
-moduleclass = 'lib'

From 8082288b0043fb1273db4741fea3155ca0367ca8 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com>
Date: Fri, 14 Jun 2024 11:44:50 +0200
Subject: [PATCH 213/835] Update graph-tool-2.59-foss-2023a.eb boost-python
 version

---
 .../easyconfigs/g/graph-tool/graph-tool-2.59-foss-2023a.eb      | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/g/graph-tool/graph-tool-2.59-foss-2023a.eb b/easybuild/easyconfigs/g/graph-tool/graph-tool-2.59-foss-2023a.eb
index 2ca6027a864..ac416bcee76 100644
--- a/easybuild/easyconfigs/g/graph-tool/graph-tool-2.59-foss-2023a.eb
+++ b/easybuild/easyconfigs/g/graph-tool/graph-tool-2.59-foss-2023a.eb
@@ -32,7 +32,7 @@ builddependencies = [
 
 dependencies = [
     ('Python', '3.11.3'),
-    ('Boost.Python', '1.83.0'),
+    ('Boost.Python', '1.82.0'),
     ('sparsehash', '2.0.4'),
     ('matplotlib', '3.7.2'),
     ('PyCairo', '1.25.0'),

From e97eae1ae75e777ac677beacc4275fe51bbf06b3 Mon Sep 17 00:00:00 2001
From: ocaisa <alan.ocais@cecam.org>
Date: Fri, 14 Jun 2024 11:50:07 +0200
Subject: [PATCH 214/835] Update QuantumESPRESSO-7.3-foss-2023a.eb

---
 .../q/QuantumESPRESSO/QuantumESPRESSO-7.3-foss-2023a.eb         | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3-foss-2023a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3-foss-2023a.eb
index d0089ef7bc7..dff22dff1e6 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3-foss-2023a.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3-foss-2023a.eb
@@ -53,6 +53,6 @@ buildopts = "all gwl xspectra couple epw gipaw w90"
 parallel = 1
 
 # allow some test failures (see https://github.com/EESSI/software-layer/pull/504#issuecomment-2039605740)
-test_suite_max_failed = 1
+test_suite_max_failed = 2
 
 moduleclass = 'chem'

From 6fd64492be78702677369e143bad52fc466f4b9e Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Fri, 14 Jun 2024 11:55:24 +0200
Subject: [PATCH 215/835] add builddep for pyproject_metadata

---
 easybuild/easyconfigs/s/scArches/scArches-0.6.1-foss-2023a.eb | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easybuild/easyconfigs/s/scArches/scArches-0.6.1-foss-2023a.eb b/easybuild/easyconfigs/s/scArches/scArches-0.6.1-foss-2023a.eb
index c703d0beede..f72ebf96042 100644
--- a/easybuild/easyconfigs/s/scArches/scArches-0.6.1-foss-2023a.eb
+++ b/easybuild/easyconfigs/s/scArches/scArches-0.6.1-foss-2023a.eb
@@ -9,6 +9,7 @@ description = """Single-cell architecture surgery (scArches) is a package for re
 
 toolchain = {'name': 'foss', 'version': '2023a'}
 
+builddependencies = [('scikit-build-core', '0.5.0')]
 dependencies = [
     ('Python', '3.11.3'),
     ('SciPy-bundle', '2023.07'),

From 891bbc0f26be06f360261513c89af77b6de67bd9 Mon Sep 17 00:00:00 2001
From: Sam Moors <smoors@users.noreply.github.com>
Date: Fri, 14 Jun 2024 14:06:58 +0200
Subject: [PATCH 216/835] remove empty line

---
 .../langchain-mistralai/langchain-mistralai-0.1.8-foss-2023a.eb  | 1 -
 1 file changed, 1 deletion(-)

diff --git a/easybuild/easyconfigs/l/langchain-mistralai/langchain-mistralai-0.1.8-foss-2023a.eb b/easybuild/easyconfigs/l/langchain-mistralai/langchain-mistralai-0.1.8-foss-2023a.eb
index 0060ac5fe60..78fc26dda3f 100644
--- a/easybuild/easyconfigs/l/langchain-mistralai/langchain-mistralai-0.1.8-foss-2023a.eb
+++ b/easybuild/easyconfigs/l/langchain-mistralai/langchain-mistralai-0.1.8-foss-2023a.eb
@@ -21,7 +21,6 @@ dependencies = [
     ('jiter', '0.4.1'),
 ]
 
-
 exts_list = [
     ('langchain-core', '0.2.3', {
         'sources': ['langchain_core-%(version)s.tar.gz'],

From 8d9d77d4315e133792080ee079f9c0989af1c4e0 Mon Sep 17 00:00:00 2001
From: ocaisa <alan.ocais@cecam.org>
Date: Fri, 14 Jun 2024 14:44:09 +0200
Subject: [PATCH 217/835] QuantumESPRESSO-7.0-intel-2021b.eb totally broken

It's making this PR look like there are problems where in reality this was always broken. Excluding it to get this over the line
---
 .../q/QuantumESPRESSO/QuantumESPRESSO-7.0-intel-2021b.eb      | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.0-intel-2021b.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.0-intel-2021b.eb
index f300cdf863f..febc60c8c61 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.0-intel-2021b.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.0-intel-2021b.eb
@@ -9,9 +9,7 @@ It is based on density-functional theory, plane waves, and pseudopotentials
 """
 
 toolchain = {'name': 'intel', 'version': '2021b'}
-# OpenMP is not working with Intel ifort/ifx compilers (Fortran) starting from version 2021.2.0 
-# toolchainopts = {'usempi': True, 'openmp': True}
-toolchainopts = {'usempi': True}
+toolchainopts = {'usempi': True, 'openmp': True}
 
 source_urls = [
     'https://github.com/QEF/q-e/releases/download/qe-%(version)s/',

From 7f51e2f37dff4389a41c196cb3be81443ba7db18 Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Fri, 14 Jun 2024 14:49:07 +0200
Subject: [PATCH 218/835] add support for JupyterHub to TensorBoard

---
 .../tensorboard-2.10.0-foss-2022a.eb          |   8 ++
 .../tensorboard-2.10_jupyterhub-support.patch | 103 ++++++++++++++++++
 .../tensorboard-2.15.1-gfbf-2023a.eb          |  27 +++--
 3 files changed, 127 insertions(+), 11 deletions(-)
 create mode 100644 easybuild/easyconfigs/t/tensorboard/tensorboard-2.10_jupyterhub-support.patch

diff --git a/easybuild/easyconfigs/t/tensorboard/tensorboard-2.10.0-foss-2022a.eb b/easybuild/easyconfigs/t/tensorboard/tensorboard-2.10.0-foss-2022a.eb
index 4cf2f36f1d5..83fc611834b 100644
--- a/easybuild/easyconfigs/t/tensorboard/tensorboard-2.10.0-foss-2022a.eb
+++ b/easybuild/easyconfigs/t/tensorboard/tensorboard-2.10.0-foss-2022a.eb
@@ -9,6 +9,14 @@ and graphs."""
 
 toolchain = {'name': 'foss', 'version': '2022a'}
 
+postinstallpatches = [
+    ('tensorboard-2.10_jupyterhub-support.patch', 'lib/python%(pyshortver)s/site-packages'),
+]
+checksums = [
+    {'tensorboard-2.10_jupyterhub-support.patch':
+     '50a292e6ee518aecb5644595e0f3db4867be4f82e328e008e5a3f6a1f19baf87'},
+]
+
 dependencies = [
     ('Python', '3.10.4'),
     ('SciPy-bundle', '2022.05'),
diff --git a/easybuild/easyconfigs/t/tensorboard/tensorboard-2.10_jupyterhub-support.patch b/easybuild/easyconfigs/t/tensorboard/tensorboard-2.10_jupyterhub-support.patch
new file mode 100644
index 00000000000..211bf686256
--- /dev/null
+++ b/easybuild/easyconfigs/t/tensorboard/tensorboard-2.10_jupyterhub-support.patch
@@ -0,0 +1,103 @@
+From: qzchenwl <qzchenwl@gmail.com>
+Date: Tue, 14 Jan 2020 15:22:27 +0800
+Subject: support jupyterhub with jupyter-server-proxy
+Issue: https://github.com/tensorflow/tensorboard/pull/3142
+
+--- a/tensorboard/notebook.py	2024-06-13 16:04:51.656772000 +0200
++++ b/tensorboard/notebook.py	2024-06-13 16:06:38.749780722 +0200
+@@ -34,6 +34,7 @@
+ # details).
+ _CONTEXT_COLAB = "_CONTEXT_COLAB"
+ _CONTEXT_IPYTHON = "_CONTEXT_IPYTHON"
++_CONTEXT_JUPYTERHUB = "_CONTEXT_JUPYTERHUB"
+ _CONTEXT_NONE = "_CONTEXT_NONE"
+ 
+ 
+@@ -70,12 +71,31 @@
+     else:
+         ipython = IPython.get_ipython()
+         if ipython is not None and ipython.has_trait("kernel"):
++            if os.environ.get("JUPYTERHUB_SERVICE_PREFIX") is not None:
++                return _CONTEXT_JUPYTERHUB
+             return _CONTEXT_IPYTHON
+ 
+     # Otherwise, we're not in a known notebook context.
+     return _CONTEXT_NONE
+ 
+ 
++def _prefix_jupyterhub(port):
++    prefix = os.path.join(
++        os.environ["JUPYTERHUB_SERVICE_PREFIX"], "proxy/absolute"
++    )
++    return "%s/%d/" % (prefix, port)
++
++
++def _patch_args_jupyterhub(parsed_args):
++    if "--port" in parsed_args:
++        arg_idx = parsed_args.index("--port")
++        port = int(parsed_args[arg_idx + 1])
++    else:
++        port = 6006
++        parsed_args += ["--port", str(port)]
++    return parsed_args + ["--path_prefix", _prefix_jupyterhub(port)]
++
++
+ def load_ipython_extension(ipython):
+     """Deprecated: use `%load_ext tensorboard` instead.
+ 
+@@ -149,6 +169,9 @@
+             handle.update(IPython.display.Pretty(message))
+ 
+     parsed_args = shlex.split(args_string, comments=True, posix=True)
++    if context == _CONTEXT_JUPYTERHUB:
++        parsed_args = _patch_args_jupyterhub(parsed_args)
++
+     start_result = manager.start(parsed_args)
+ 
+     if isinstance(start_result, manager.StartLaunched):
+@@ -305,6 +328,7 @@
+     fn = {
+         _CONTEXT_COLAB: _display_colab,
+         _CONTEXT_IPYTHON: _display_ipython,
++        _CONTEXT_JUPYTERHUB: _display_jupyterhub,
+         _CONTEXT_NONE: _display_cli,
+     }[_get_context()]
+     return fn(port=port, height=height, display_handle=display_handle)
+@@ -401,6 +425,36 @@
+     for (k, v) in replacements:
+         shell = shell.replace(k, v)
+     iframe = IPython.display.HTML(shell)
++    if display_handle:
++        display_handle.update(iframe)
++    else:
++        IPython.display.display(iframe)
++
++
++def _display_jupyterhub(port, height, display_handle):
++    import IPython.display
++
++    frame_id = "tensorboard-frame-{:08x}".format(random.getrandbits(64))
++    shell = """
++      <iframe id="%HTML_ID%" width="100%" height="%HEIGHT%" frameborder="0">
++      </iframe>
++      <script>
++        (function() {
++          const frame = document.getElementById(%JSON_ID%);
++          const url = new URL("%PREFIX%", window.location);
++          frame.src = url;
++        })();
++      </script>
++  """
++    replacements = [
++        ("%HTML_ID%", html.escape(frame_id, quote=True)),
++        ("%JSON_ID%", json.dumps(frame_id)),
++        ("%PREFIX%", _prefix_jupyterhub(port)),
++        ("%HEIGHT%", "%d" % height),
++    ]
++    for (k, v) in replacements:
++        shell = shell.replace(k, v)
++    iframe = IPython.display.HTML(shell)
+     if display_handle:
+         display_handle.update(iframe)
+     else:
+From 5615204ba44a6b8718e58c9b4b875fef5027baaf Mon Sep 17 00:00:00 2001
diff --git a/easybuild/easyconfigs/t/tensorboard/tensorboard-2.15.1-gfbf-2023a.eb b/easybuild/easyconfigs/t/tensorboard/tensorboard-2.15.1-gfbf-2023a.eb
index 9c74e1a8f87..f8eca13eaf7 100644
--- a/easybuild/easyconfigs/t/tensorboard/tensorboard-2.15.1-gfbf-2023a.eb
+++ b/easybuild/easyconfigs/t/tensorboard/tensorboard-2.15.1-gfbf-2023a.eb
@@ -9,6 +9,14 @@ understanding your TensorFlow runs and graphs."""
 
 toolchain = {'name': 'gfbf', 'version': '2023a'}
 
+postinstallpatches = [
+    ('tensorboard-2.10_jupyterhub-support.patch', 'lib/python%(pyshortver)s/site-packages'),
+]
+checksums = [
+    {'tensorboard-2.10_jupyterhub-support.patch':
+     '50a292e6ee518aecb5644595e0f3db4867be4f82e328e008e5a3f6a1f19baf87'},
+]
+
 builddependencies = [
     ('poetry', '1.5.1'),
 ]
@@ -17,6 +25,7 @@ dependencies = [
     ('Python', '3.11.3'),
     ('SciPy-bundle', '2023.07'),
     ('protobuf-python', '4.24.0'),
+    ('grpcio', '1.57.0'),
 ]
 
 exts_list = [
@@ -46,11 +55,6 @@ exts_list = [
     ('google-auth-oauthlib', '1.2.0', {
         'checksums': ['292d2d3783349f2b0734a0a0207b1e1e322ac193c2c09d8f7c613fb7cc501ea8'],
     }),
-    ('grpcio', '1.60.0', {
-        'modulename': 'grpc',
-        'preinstallopts': "export GRPC_PYTHON_BUILD_EXT_COMPILER_JOBS=%(parallel)s && ",
-        'checksums': ['2199165a1affb666aa24adf0c97436686d0a61bc5fc113c037701fb7c7fceb96'],
-    }),
     ('Markdown', '3.5.2', {
         'checksums': ['e1ac7b3dc550ee80e602e71c1d168002f062e49f1b11e26a36264dafd4df2ef8'],
     }),
@@ -58,9 +62,13 @@ exts_list = [
         'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl',
         'checksums': ['7e0610d205889588983836ec05dc098e80f97b7e7bbff7e994ebb78f578d0ddb'],
     }),
-    ('tensorboard_plugin_wit', '1.8.1', {
-        'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl',
-        'checksums': ['ff26bdd583d155aa951ee3b152b3d0cffae8005dc697f72b44a8e8c2a77a8cbe'],
+    ('gviz-api', '1.10.0', {
+        'source_tmpl': 'gviz_api-%(version)s.tar.gz',
+        'checksums': ['846692dd8cc73224fc31b18e41589bd934e1cc05090c6576af4b4b26c2e71b90'],
+    }),
+    ('tensorboard-plugin-profile', '2.15.1', {
+        'source_tmpl': 'tensorboard_plugin_profile-%(version)s.tar.gz',
+        'checksums': ['84bb33e446eb4a9c0616f669fc6a42cdd40eadd9ae1d74bf756f4f0479993273'],
     }),
     ('Werkzeug', '3.0.1', {
         'source_tmpl': '%(namelower)s-%(version)s.tar.gz',
@@ -80,7 +88,4 @@ postinstallcmds = [
     '%(installdir)s/lib/python%(pyshortver)s/site-packages/%(name)s-%(version)s.dist-info/METADATA',
 ]
 
-use_pip = True
-sanity_pip_check = True
-
 moduleclass = 'lib'

From 00590b8d49e6376ca436d32722309a7b916fd7cd Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Fri, 14 Jun 2024 15:31:55 +0200
Subject: [PATCH 219/835] revert removal of use_pip from
 tensorboard-2.15.1-gfbf-2023a.eb

---
 .../easyconfigs/t/tensorboard/tensorboard-2.15.1-gfbf-2023a.eb | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/easybuild/easyconfigs/t/tensorboard/tensorboard-2.15.1-gfbf-2023a.eb b/easybuild/easyconfigs/t/tensorboard/tensorboard-2.15.1-gfbf-2023a.eb
index f8eca13eaf7..ab499908831 100644
--- a/easybuild/easyconfigs/t/tensorboard/tensorboard-2.15.1-gfbf-2023a.eb
+++ b/easybuild/easyconfigs/t/tensorboard/tensorboard-2.15.1-gfbf-2023a.eb
@@ -28,6 +28,9 @@ dependencies = [
     ('grpcio', '1.57.0'),
 ]
 
+use_pip = True
+sanity_pip_check = True
+
 exts_list = [
     ('absl-py', '2.1.0', {
         'modulename': 'absl',

From 493795e47892318f6efa488c72cd16c138ea092f Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Fri, 14 Jun 2024 15:51:39 +0200
Subject: [PATCH 220/835] adding easyconfigs: RDKit-2024.03.3-foss-2023a.eb

---
 .../r/RDKit/RDKit-2024.03.3-foss-2023a.eb     | 69 +++++++++++++++++++
 1 file changed, 69 insertions(+)
 create mode 100644 easybuild/easyconfigs/r/RDKit/RDKit-2024.03.3-foss-2023a.eb

diff --git a/easybuild/easyconfigs/r/RDKit/RDKit-2024.03.3-foss-2023a.eb b/easybuild/easyconfigs/r/RDKit/RDKit-2024.03.3-foss-2023a.eb
new file mode 100644
index 00000000000..1a98894cac7
--- /dev/null
+++ b/easybuild/easyconfigs/r/RDKit/RDKit-2024.03.3-foss-2023a.eb
@@ -0,0 +1,69 @@
+easyblock = 'CMakeMake'
+
+name = 'RDKit'
+version = '2024.03.3'
+
+homepage = 'https://www.rdkit.org'
+description = "RDKit is a collection of cheminformatics and machine-learning software written in C++ and Python."
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+source_urls = ['https://github.com/rdkit/rdkit/archive/']
+sources = ['Release_%s.tar.gz' % version.replace('.', '_')]
+checksums = ['52f79c6bf1d446cdb5c86a35de655d96bad0c52a5f4ecbe15f08eaf334e6f76a']
+
+builddependencies = [
+    ('CMake', '3.26.3'),
+    ('Eigen', '3.4.0'),
+    ('pkgconf', '1.9.5'),
+]
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('SQLite', '3.42.0'),
+    ('matplotlib', '3.7.2'),
+    ('Pillow', '10.0.0'),
+    ('Boost.Python', '1.82.0'),
+    ('cairo', '1.17.8'),
+]
+
+separate_build_dir = True
+
+configopts = "-DPy_ENABLE_SHARED=1 -DRDK_INSTALL_STATIC_LIBS=OFF -DRDK_INSTALL_INTREE=OFF "
+configopts += "-DRDK_BUILD_INCHI_SUPPORT=ON "
+configopts += "-DBOOST_ROOT=$EBROOTBOOST"
+
+# ingnore failing test pythonSourceTests - from . import rdBase failing
+prebuildopts = "sed -i '22d' %(builddir)s/rdkit-Release_2024_03_3/rdkit/CMakeLists.txt &&"
+
+# merge source directory into build directory in order to run the tests
+buildopts = '&& cp -RT %(builddir)s/%(namelower)s-*/ ./ && '
+buildopts += 'export RDBASE=$PWD && export PYTHONPATH=$PWD:$PYTHONPATH && '
+
+# Specify path for libraries so that they are found during the tests when the module is built with --rpath flag.
+buildopts += 'export LD_LIBRARY_PATH=%(builddir)s/easybuild_obj/lib:${LD_LIBRARY_PATH} && '
+
+# 'ctest' allows to pass additional arguments opposed to 'make test'
+buildopts += 'ctest --output-on-failure'
+
+local_libs = ['Alignment', 'Catalogs', 'ChemicalFeatures', 'ChemReactions', 'ChemTransforms', 'coordgen', 'DataStructs',
+              'Depictor', 'Descriptors', 'DistGeometry', 'DistGeomHelpers', 'EigenSolvers', 'FileParsers',
+              'FilterCatalog', 'Fingerprints', 'FMCS', 'ForceFieldHelpers', 'ForceField', 'FragCatalog', 'GraphMol',
+              'hc', 'InfoTheory', 'maeparser', 'MMPA', 'MolAlign', 'MolCatalog', 'MolChemicalFeatures', 'MolDraw2D',
+              'MolHash', 'MolInterchange', 'MolStandardize', 'MolTransforms', 'Optimizer', 'PartialCharges', 'RDBoost',
+              'RDGeneral', 'RDGeometryLib', 'RDStreams', 'ReducedGraphs', 'RGroupDecomposition', 'RingDecomposerLib',
+              'ScaffoldNetwork', 'ShapeHelpers', 'SimDivPickers', 'SLNParse', 'SmilesParse', 'Subgraphs',
+              'SubstructLibrary', 'SubstructMatch', 'Trajectory']
+
+sanity_check_paths = {
+    'files': ['lib/libRDKit%s.%s' % (x, SHLIB_EXT) for x in local_libs],
+    'dirs': ['include/rdkit', 'lib/python%(pyshortver)s/site-packages/rdkit'],
+}
+
+sanity_check_commands = [
+    "python -c 'import rdkit.rdBase'",
+]
+
+modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'}
+
+moduleclass = 'chem'

From 9dae3e6612851599856194e476a4b9613a7485e9 Mon Sep 17 00:00:00 2001
From: Cintia Willemyns <115622907+WilleBell@users.noreply.github.com>
Date: Fri, 14 Jun 2024 16:36:24 +0200
Subject: [PATCH 221/835] Remove maturin, it is not needed as builddependency

---
 .../langchain-anthropic/langchain-anthropic-0.1.15-foss-2023a.eb | 1 -
 1 file changed, 1 deletion(-)

diff --git a/easybuild/easyconfigs/l/langchain-anthropic/langchain-anthropic-0.1.15-foss-2023a.eb b/easybuild/easyconfigs/l/langchain-anthropic/langchain-anthropic-0.1.15-foss-2023a.eb
index 1bb545a30d3..6031932aa6c 100644
--- a/easybuild/easyconfigs/l/langchain-anthropic/langchain-anthropic-0.1.15-foss-2023a.eb
+++ b/easybuild/easyconfigs/l/langchain-anthropic/langchain-anthropic-0.1.15-foss-2023a.eb
@@ -11,7 +11,6 @@ This package contains the LangChain integration for Anthropic's generative model
 toolchain = {'name': 'foss', 'version': '2023a'}
 
 builddependencies = [
-    ('maturin', '1.1.0'),
     ('poetry', '1.5.1'),
 ]
 

From 6cc0ac657635a2604533a19e65945b73e0ed197f Mon Sep 17 00:00:00 2001
From: Cintia Willemyns <115622907+WilleBell@users.noreply.github.com>
Date: Fri, 14 Jun 2024 16:50:20 +0200
Subject: [PATCH 222/835] Move comment for tiktoken version

---
 .../l/langchain-openai/langchain-openai-0.1.8-foss-2023a.eb    | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/easybuild/easyconfigs/l/langchain-openai/langchain-openai-0.1.8-foss-2023a.eb b/easybuild/easyconfigs/l/langchain-openai/langchain-openai-0.1.8-foss-2023a.eb
index c976db06a40..e46f2e43b4c 100644
--- a/easybuild/easyconfigs/l/langchain-openai/langchain-openai-0.1.8-foss-2023a.eb
+++ b/easybuild/easyconfigs/l/langchain-openai/langchain-openai-0.1.8-foss-2023a.eb
@@ -2,7 +2,6 @@ easyblock = 'PythonBundle'
 
 name = 'langchain-openai'
 version = '0.1.8'
-# needs tiktoken >= 0.7.0
 
 homepage = 'https://github.com/langchain-ai/langchain'
 description = """
@@ -19,7 +18,7 @@ dependencies = [
     ('Python', '3.11.3'),
     ('SciPy-bundle', '2023.07'),
     ('LangChain', '0.2.1'),
-    ('tiktoken', '0.7.0'),
+    ('tiktoken', '0.7.0'),  # needs tiktoken >= 0.7.0
     ('openai-python', '1.30.5'),
 ]
 

From c9fd24122fa22b06e836fa70aa2e3409197f0224 Mon Sep 17 00:00:00 2001
From: Cintia Willemyns <115622907+WilleBell@users.noreply.github.com>
Date: Fri, 14 Jun 2024 17:00:23 +0200
Subject: [PATCH 223/835] move rust_ver, builddependencies and dependencies
 higher up

---
 .../tiktoken/tiktoken-0.7.0-GCCcore-12.3.0.eb | 26 +++++++++----------
 1 file changed, 13 insertions(+), 13 deletions(-)

diff --git a/easybuild/easyconfigs/t/tiktoken/tiktoken-0.7.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/t/tiktoken/tiktoken-0.7.0-GCCcore-12.3.0.eb
index 23fcce3f894..3dc06c7edcb 100644
--- a/easybuild/easyconfigs/t/tiktoken/tiktoken-0.7.0-GCCcore-12.3.0.eb
+++ b/easybuild/easyconfigs/t/tiktoken/tiktoken-0.7.0-GCCcore-12.3.0.eb
@@ -2,12 +2,25 @@ easyblock = 'CargoPythonPackage'
 
 name = 'tiktoken'
 version = '0.7.0'
+_rust_ver = '1.75.0'
 
 homepage = 'https://github.com/openai/tiktoken'
 description = "tiktoken is a fast BPE tokeniser for use with OpenAI's models"
 
 toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
 
+builddependencies = [
+    ('binutils', '2.40'),
+    ('Rust', _rust_ver),
+    ('maturin', '1.4.0', '-Rust-%s' % _rust_ver),
+    ('hypothesis', '6.82.0')
+]
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('Python-bundle-PyPI', '2023.06'),  # regex (and pytest for tests)
+]
+
 crates = [
     ('aho-corasick', '1.1.3'),
     ('autocfg', '1.2.0'),
@@ -107,19 +120,6 @@ checksums = [
     {'windows_x86_64_msvc-0.48.5.tar.gz': 'ed94fce61571a4006852b7389a063ab983c02eb1bb37b47f8272ce92d06d9538'},
 ]
 
-_rust_ver = '1.75.0'
-builddependencies = [
-    ('binutils', '2.40'),
-    ('Rust', _rust_ver),
-    ('maturin', '1.4.0', '-Rust-%s' % _rust_ver),
-    ('hypothesis', '6.82.0')
-]
-
-dependencies = [
-    ('Python', '3.11.3'),
-    ('Python-bundle-PyPI', '2023.06'),  # regex (and pytest for tests)
-]
-
 use_pip = True
 sanity_pip_check = True
 download_dep_fail = True

From 7675fa1efc57876286b55a180d91b1a45830d0cf Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 14 Jun 2024 18:36:04 +0200
Subject: [PATCH 224/835] adding easyconfigs: poetry-1.8.3-GCCcore-13.3.0.eb,
 hatchling-1.24.2-GCCcore-13.3.0.eb, virtualenv-20.26.2-GCCcore-13.3.0.eb,
 cryptography-42.0.8-GCCcore-13.3.0.eb, maturin-1.6.0-GCCcore-13.3.0.eb,
 setuptools-rust-1.9.0-GCCcore-13.3.0.eb,
 scikit-build-0.17.6-GCCcore-13.3.0.eb

---
 .../cryptography-42.0.8-GCCcore-13.3.0.eb     | 131 ++++
 .../hatchling-1.24.2-GCCcore-13.3.0.eb        |  59 ++
 .../m/maturin/maturin-1.6.0-GCCcore-13.3.0.eb | 659 ++++++++++++++++++
 .../p/poetry/poetry-1.8.3-GCCcore-13.3.0.eb   | 179 +++++
 .../scikit-build-0.17.6-GCCcore-13.3.0.eb     |  38 +
 .../setuptools-rust-1.9.0-GCCcore-13.3.0.eb   |  41 ++
 .../virtualenv-20.26.2-GCCcore-13.3.0.eb      |  49 ++
 7 files changed, 1156 insertions(+)
 create mode 100644 easybuild/easyconfigs/c/cryptography/cryptography-42.0.8-GCCcore-13.3.0.eb
 create mode 100644 easybuild/easyconfigs/h/hatchling/hatchling-1.24.2-GCCcore-13.3.0.eb
 create mode 100644 easybuild/easyconfigs/m/maturin/maturin-1.6.0-GCCcore-13.3.0.eb
 create mode 100644 easybuild/easyconfigs/p/poetry/poetry-1.8.3-GCCcore-13.3.0.eb
 create mode 100644 easybuild/easyconfigs/s/scikit-build/scikit-build-0.17.6-GCCcore-13.3.0.eb
 create mode 100644 easybuild/easyconfigs/s/setuptools-rust/setuptools-rust-1.9.0-GCCcore-13.3.0.eb
 create mode 100644 easybuild/easyconfigs/v/virtualenv/virtualenv-20.26.2-GCCcore-13.3.0.eb

diff --git a/easybuild/easyconfigs/c/cryptography/cryptography-42.0.8-GCCcore-13.3.0.eb b/easybuild/easyconfigs/c/cryptography/cryptography-42.0.8-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..be6bff8c478
--- /dev/null
+++ b/easybuild/easyconfigs/c/cryptography/cryptography-42.0.8-GCCcore-13.3.0.eb
@@ -0,0 +1,131 @@
+easyblock = 'CargoPythonPackage'
+
+name = 'cryptography'
+version = '42.0.8'
+
+homepage = 'https://github.com/pyca/cryptography'
+description = "cryptography is a package designed to expose cryptographic primitives and recipes to Python developers."
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+toolchainopts = {'pic': True}
+
+builddependencies = [
+    ('binutils', '2.42'),
+    ('pkgconf', '2.2.0'),
+    ('Rust', '1.78.0'),  # required for cryptography
+    ('hatchling', '1.24.2'),
+    ('setuptools-rust', '1.9.0'),
+]
+
+dependencies = [
+    ('Python', '3.12.3'),
+    ('cffi', '1.16.0'),
+]
+crates = [
+    ('asn1', '0.15.5'),
+    ('asn1_derive', '0.15.5'),
+    ('autocfg', '1.1.0'),
+    ('base64', '0.21.7'),
+    ('bitflags', '1.3.2'),
+    ('bitflags', '2.4.2'),
+    ('cc', '1.0.83'),
+    ('cfg-if', '1.0.0'),
+    ('foreign-types', '0.3.2'),
+    ('foreign-types-shared', '0.1.1'),
+    ('heck', '0.4.1'),
+    ('indoc', '2.0.4'),
+    ('libc', '0.2.152'),
+    ('lock_api', '0.4.11'),
+    ('memoffset', '0.9.0'),
+    ('once_cell', '1.19.0'),
+    ('openssl', '0.10.64'),
+    ('openssl-macros', '0.1.1'),
+    ('openssl-sys', '0.9.102'),
+    ('parking_lot', '0.12.1'),
+    ('parking_lot_core', '0.9.9'),
+    ('pem', '3.0.3'),
+    ('pkg-config', '0.3.29'),
+    ('portable-atomic', '1.6.0'),
+    ('proc-macro2', '1.0.78'),
+    ('pyo3', '0.20.3'),
+    ('pyo3-build-config', '0.20.3'),
+    ('pyo3-ffi', '0.20.3'),
+    ('pyo3-macros', '0.20.3'),
+    ('pyo3-macros-backend', '0.20.3'),
+    ('quote', '1.0.35'),
+    ('redox_syscall', '0.4.1'),
+    ('scopeguard', '1.2.0'),
+    ('self_cell', '1.0.3'),
+    ('smallvec', '1.13.1'),
+    ('syn', '2.0.48'),
+    ('target-lexicon', '0.12.13'),
+    ('unicode-ident', '1.0.12'),
+    ('unindent', '0.2.3'),
+    ('vcpkg', '0.2.15'),
+    ('windows-targets', '0.48.5'),
+    ('windows_aarch64_gnullvm', '0.48.5'),
+    ('windows_aarch64_msvc', '0.48.5'),
+    ('windows_i686_gnu', '0.48.5'),
+    ('windows_i686_msvc', '0.48.5'),
+    ('windows_x86_64_gnu', '0.48.5'),
+    ('windows_x86_64_gnullvm', '0.48.5'),
+    ('windows_x86_64_msvc', '0.48.5'),
+]
+sources = [SOURCE_TAR_GZ]
+checksums = [
+    {'cryptography-42.0.8.tar.gz': '8d09d05439ce7baa8e9e95b07ec5b6c886f548deb7e0f69ef25f64b3bce842f2'},
+    {'asn1-0.15.5.tar.gz': 'ae3ecbce89a22627b5e8e6e11d69715617138290289e385cde773b1fe50befdb'},
+    {'asn1_derive-0.15.5.tar.gz': '861af988fac460ac69a09f41e6217a8fb9178797b76fcc9478444be6a59be19c'},
+    {'autocfg-1.1.0.tar.gz': 'd468802bab17cbc0cc575e9b053f41e72aa36bfa6b7f55e3529ffa43161b97fa'},
+    {'base64-0.21.7.tar.gz': '9d297deb1925b89f2ccc13d7635fa0714f12c87adce1c75356b39ca9b7178567'},
+    {'bitflags-1.3.2.tar.gz': 'bef38d45163c2f1dde094a7dfd33ccf595c92905c8f8f4fdc18d06fb1037718a'},
+    {'bitflags-2.4.2.tar.gz': 'ed570934406eb16438a4e976b1b4500774099c13b8cb96eec99f620f05090ddf'},
+    {'cc-1.0.83.tar.gz': 'f1174fb0b6ec23863f8b971027804a42614e347eafb0a95bf0b12cdae21fc4d0'},
+    {'cfg-if-1.0.0.tar.gz': 'baf1de4339761588bc0619e3cbc0120ee582ebb74b53b4efbf79117bd2da40fd'},
+    {'foreign-types-0.3.2.tar.gz': 'f6f339eb8adc052cd2ca78910fda869aefa38d22d5cb648e6485e4d3fc06f3b1'},
+    {'foreign-types-shared-0.1.1.tar.gz': '00b0228411908ca8685dba7fc2cdd70ec9990a6e753e89b6ac91a84c40fbaf4b'},
+    {'heck-0.4.1.tar.gz': '95505c38b4572b2d910cecb0281560f54b440a19336cbbcb27bf6ce6adc6f5a8'},
+    {'indoc-2.0.4.tar.gz': '1e186cfbae8084e513daff4240b4797e342f988cecda4fb6c939150f96315fd8'},
+    {'libc-0.2.152.tar.gz': '13e3bf6590cbc649f4d1a3eefc9d5d6eb746f5200ffb04e5e142700b8faa56e7'},
+    {'lock_api-0.4.11.tar.gz': '3c168f8615b12bc01f9c17e2eb0cc07dcae1940121185446edc3744920e8ef45'},
+    {'memoffset-0.9.0.tar.gz': '5a634b1c61a95585bd15607c6ab0c4e5b226e695ff2800ba0cdccddf208c406c'},
+    {'once_cell-1.19.0.tar.gz': '3fdb12b2476b595f9358c5161aa467c2438859caa136dec86c26fdd2efe17b92'},
+    {'openssl-0.10.64.tar.gz': '95a0481286a310808298130d22dd1fef0fa571e05a8f44ec801801e84b216b1f'},
+    {'openssl-macros-0.1.1.tar.gz': 'a948666b637a0f465e8564c73e89d4dde00d72d4d473cc972f390fc3dcee7d9c'},
+    {'openssl-sys-0.9.102.tar.gz': 'c597637d56fbc83893a35eb0dd04b2b8e7a50c91e64e9493e398b5df4fb45fa2'},
+    {'parking_lot-0.12.1.tar.gz': '3742b2c103b9f06bc9fff0a37ff4912935851bee6d36f3c02bcc755bcfec228f'},
+    {'parking_lot_core-0.9.9.tar.gz': '4c42a9226546d68acdd9c0a280d17ce19bfe27a46bf68784e4066115788d008e'},
+    {'pem-3.0.3.tar.gz': '1b8fcc794035347fb64beda2d3b462595dd2753e3f268d89c5aae77e8cf2c310'},
+    {'pkg-config-0.3.29.tar.gz': '2900ede94e305130c13ddd391e0ab7cbaeb783945ae07a279c268cb05109c6cb'},
+    {'portable-atomic-1.6.0.tar.gz': '7170ef9988bc169ba16dd36a7fa041e5c4cbeb6a35b76d4c03daded371eae7c0'},
+    {'proc-macro2-1.0.78.tar.gz': 'e2422ad645d89c99f8f3e6b88a9fdeca7fabeac836b1002371c4367c8f984aae'},
+    {'pyo3-0.20.3.tar.gz': '53bdbb96d49157e65d45cc287af5f32ffadd5f4761438b527b055fb0d4bb8233'},
+    {'pyo3-build-config-0.20.3.tar.gz': 'deaa5745de3f5231ce10517a1f5dd97d53e5a2fd77aa6b5842292085831d48d7'},
+    {'pyo3-ffi-0.20.3.tar.gz': '62b42531d03e08d4ef1f6e85a2ed422eb678b8cd62b762e53891c05faf0d4afa'},
+    {'pyo3-macros-0.20.3.tar.gz': '7305c720fa01b8055ec95e484a6eca7a83c841267f0dd5280f0c8b8551d2c158'},
+    {'pyo3-macros-backend-0.20.3.tar.gz': '7c7e9b68bb9c3149c5b0cade5d07f953d6d125eb4337723c4ccdb665f1f96185'},
+    {'quote-1.0.35.tar.gz': '291ec9ab5efd934aaf503a6466c5d5251535d108ee747472c3977cc5acc868ef'},
+    {'redox_syscall-0.4.1.tar.gz': '4722d768eff46b75989dd134e5c353f0d6296e5aaa3132e776cbdb56be7731aa'},
+    {'scopeguard-1.2.0.tar.gz': '94143f37725109f92c262ed2cf5e59bce7498c01bcc1502d7b9afe439a4e9f49'},
+    {'self_cell-1.0.3.tar.gz': '58bf37232d3bb9a2c4e641ca2a11d83b5062066f88df7fed36c28772046d65ba'},
+    {'smallvec-1.13.1.tar.gz': 'e6ecd384b10a64542d77071bd64bd7b231f4ed5940fba55e98c3de13824cf3d7'},
+    {'syn-2.0.48.tar.gz': '0f3531638e407dfc0814761abb7c00a5b54992b849452a0646b7f65c9f770f3f'},
+    {'target-lexicon-0.12.13.tar.gz': '69758bda2e78f098e4ccb393021a0963bb3442eac05f135c30f61b7370bbafae'},
+    {'unicode-ident-1.0.12.tar.gz': '3354b9ac3fae1ff6755cb6db53683adb661634f67557942dea4facebec0fee4b'},
+    {'unindent-0.2.3.tar.gz': 'c7de7d73e1754487cb58364ee906a499937a0dfabd86bcb980fa99ec8c8fa2ce'},
+    {'vcpkg-0.2.15.tar.gz': 'accd4ea62f7bb7a82fe23066fb0957d48ef677f6eeb8215f372f52e48bb32426'},
+    {'windows-targets-0.48.5.tar.gz': '9a2fa6e2155d7247be68c096456083145c183cbbbc2764150dda45a87197940c'},
+    {'windows_aarch64_gnullvm-0.48.5.tar.gz': '2b38e32f0abccf9987a4e3079dfb67dcd799fb61361e53e2882c3cbaf0d905d8'},
+    {'windows_aarch64_msvc-0.48.5.tar.gz': 'dc35310971f3b2dbbf3f0690a219f40e2d9afcf64f9ab7cc1be722937c26b4bc'},
+    {'windows_i686_gnu-0.48.5.tar.gz': 'a75915e7def60c94dcef72200b9a8e58e5091744960da64ec734a6c6e9b3743e'},
+    {'windows_i686_msvc-0.48.5.tar.gz': '8f55c233f70c4b27f66c523580f78f1004e8b5a8b659e05a4eb49d4166cca406'},
+    {'windows_x86_64_gnu-0.48.5.tar.gz': '53d40abd2583d23e4718fddf1ebec84dbff8381c07cae67ff7768bbf19c6718e'},
+    {'windows_x86_64_gnullvm-0.48.5.tar.gz': '0b7b52767868a23d5bab768e390dc5f5c55825b6d30b86c844ff2dc7414044cc'},
+    {'windows_x86_64_msvc-0.48.5.tar.gz': 'ed94fce61571a4006852b7389a063ab983c02eb1bb37b47f8272ce92d06d9538'},
+]
+
+download_dep_fail = True
+use_pip = True
+sanity_pip_check = True
+
+moduleclass = 'tools'
diff --git a/easybuild/easyconfigs/h/hatchling/hatchling-1.24.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/h/hatchling/hatchling-1.24.2-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..d936671cca9
--- /dev/null
+++ b/easybuild/easyconfigs/h/hatchling/hatchling-1.24.2-GCCcore-13.3.0.eb
@@ -0,0 +1,59 @@
+easyblock = 'PythonBundle'
+
+name = 'hatchling'
+version = '1.24.2'
+
+homepage = 'https://hatch.pypa.io'
+description = """Extensible, standards compliant build backend used by Hatch,
+a modern, extensible Python project manager."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+builddependencies = [
+    ('binutils', '2.42'),
+]
+
+dependencies = [
+    ('Python', '3.12.3'),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    ('pathspec', '0.12.1', {
+        'checksums': ['a482d51503a1ab33b1c67a6c3813a26953dbdc71c31dacaef9a838c4e29f5712'],
+    }),
+    ('pluggy', '1.5.0', {
+        'checksums': ['2cffa88e94fdc978c4c574f15f9e59b7f4201d439195c3715ca9e2486f1d0cf1'],
+    }),
+    ('editables', '0.5', {
+        'checksums': ['309627d9b5c4adc0e668d8c6fa7bac1ba7c8c5d415c2d27f60f081f8e80d1de2'],
+    }),
+    ('trove-classifiers', '2024.5.22', {
+        'sources': ['trove_classifiers-%(version)s-py3-none-any.whl'],
+        'checksums': ['c43ade18704823e4afa3d9db7083294bc4708a5e02afbcefacd0e9d03a7a24ef'],
+    }),
+    (name, version, {
+        'checksums': ['41ddc27cdb25db9ef7b68bef075f829c84cb349aa1bff8240797d012510547b0'],
+    }),
+    ('hatch-vcs', '0.4.0', {
+        'sources': ['hatch_vcs-%(version)s.tar.gz'],
+        'checksums': ['093810748fe01db0d451fabcf2c1ac2688caefd232d4ede967090b1c1b07d9f7'],
+    }),
+    ('hatch-fancy-pypi-readme', '24.1.0', {
+        'sources': ['hatch_fancy_pypi_readme-%(version)s.tar.gz'],
+        'checksums': ['44dd239f1a779b9dcf8ebc9401a611fd7f7e3e14578dcf22c265dfaf7c1514b8'],
+    }),
+    ('hatch-requirements-txt', '0.4.1', {
+        'source_tmpl': 'hatch_requirements_txt-%(version)s.tar.gz',
+        'checksums': ['2c686e5758fd05bb55fa7d0c198fdd481f8d3aaa3c693260f5c0d74ce3547d20'],
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['bin/%(namelower)s'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'],
+}
+
+moduleclass = 'tools'
diff --git a/easybuild/easyconfigs/m/maturin/maturin-1.6.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/m/maturin/maturin-1.6.0-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..b7a45d6c37a
--- /dev/null
+++ b/easybuild/easyconfigs/m/maturin/maturin-1.6.0-GCCcore-13.3.0.eb
@@ -0,0 +1,659 @@
+easyblock = 'CargoPythonPackage'
+
+name = 'maturin'
+version = '1.6.0'
+
+homepage = 'https://github.com/pyo3/maturin'
+description = """This project is meant as a zero configuration
+replacement for setuptools-rust and milksnake. It supports building
+wheels for python 3.5+ on windows, linux, mac and freebsd, can upload
+them to pypi and has basic pypy and graalpy support."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+crates = [
+    ('adler', '1.0.2'),
+    ('ahash', '0.8.7'),
+    ('aho-corasick', '1.1.2'),
+    ('allocator-api2', '0.2.16'),
+    ('anstream', '0.6.11'),
+    ('anstyle', '1.0.4'),
+    ('anstyle-parse', '0.2.3'),
+    ('anstyle-query', '1.0.2'),
+    ('anstyle-wincon', '3.0.2'),
+    ('anyhow', '1.0.80'),
+    ('autocfg', '1.1.0'),
+    ('base64', '0.13.1'),
+    ('base64', '0.21.7'),
+    ('bitflags', '1.3.2'),
+    ('bitflags', '2.4.2'),
+    ('block-buffer', '0.10.4'),
+    ('bstr', '1.9.0'),
+    ('byteorder', '1.5.0'),
+    ('bytes', '1.5.0'),
+    ('bytesize', '1.3.0'),
+    ('bzip2', '0.4.4'),
+    ('bzip2-sys', '0.1.11+1.0.8'),
+    ('cab', '0.4.1'),
+    ('camino', '1.1.6'),
+    ('cargo-config2', '0.1.24'),
+    ('cargo-options', '0.7.4'),
+    ('cargo-platform', '0.1.6'),
+    ('cargo-xwin', '0.16.4'),
+    ('cargo-zigbuild', '0.18.4'),
+    ('cargo_metadata', '0.18.1'),
+    ('cbindgen', '0.26.0'),
+    ('cc', '1.0.88'),
+    ('cfb', '0.9.0'),
+    ('cfg-if', '1.0.0'),
+    ('charset', '0.1.3'),
+    ('chumsky', '0.9.3'),
+    ('clap', '4.4.18'),
+    ('clap_builder', '4.4.18'),
+    ('clap_complete', '4.4.9'),
+    ('clap_complete_command', '0.5.1'),
+    ('clap_complete_nushell', '0.1.11'),
+    ('clap_derive', '4.4.7'),
+    ('clap_lex', '0.6.0'),
+    ('cli-table', '0.4.7'),
+    ('colorchoice', '1.0.0'),
+    ('configparser', '3.0.4'),
+    ('console', '0.15.8'),
+    ('content_inspector', '0.2.4'),
+    ('core-foundation', '0.9.4'),
+    ('core-foundation-sys', '0.8.6'),
+    ('cpufeatures', '0.2.12'),
+    ('crc32fast', '1.3.2'),
+    ('crossbeam-channel', '0.5.11'),
+    ('crossbeam-deque', '0.8.5'),
+    ('crossbeam-epoch', '0.9.18'),
+    ('crossbeam-utils', '0.8.19'),
+    ('crypto-common', '0.1.6'),
+    ('data-encoding', '2.5.0'),
+    ('deranged', '0.3.11'),
+    ('derivative', '2.2.0'),
+    ('dialoguer', '0.11.0'),
+    ('diff', '0.1.13'),
+    ('digest', '0.10.7'),
+    ('dirs', '5.0.1'),
+    ('dirs-sys', '0.4.1'),
+    ('dissimilar', '1.0.7'),
+    ('dunce', '1.0.4'),
+    ('dyn-clone', '1.0.17'),
+    ('either', '1.9.0'),
+    ('encode_unicode', '0.3.6'),
+    ('encoding_rs', '0.8.33'),
+    ('equivalent', '1.0.1'),
+    ('errno', '0.3.8'),
+    ('expect-test', '1.4.1'),
+    ('fastrand', '2.0.1'),
+    ('fat-macho', '0.4.8'),
+    ('filetime', '0.2.23'),
+    ('flate2', '1.0.28'),
+    ('fnv', '1.0.7'),
+    ('foreign-types', '0.3.2'),
+    ('foreign-types-shared', '0.1.1'),
+    ('form_urlencoded', '1.2.1'),
+    ('fs-err', '2.11.0'),
+    ('futures', '0.3.30'),
+    ('futures-channel', '0.3.30'),
+    ('futures-core', '0.3.30'),
+    ('futures-executor', '0.3.30'),
+    ('futures-io', '0.3.30'),
+    ('futures-macro', '0.3.30'),
+    ('futures-sink', '0.3.30'),
+    ('futures-task', '0.3.30'),
+    ('futures-timer', '3.0.3'),
+    ('futures-util', '0.3.30'),
+    ('generic-array', '0.14.7'),
+    ('getrandom', '0.2.12'),
+    ('glob', '0.3.1'),
+    ('globset', '0.4.14'),
+    ('goblin', '0.8.0'),
+    ('hashbrown', '0.12.3'),
+    ('hashbrown', '0.14.3'),
+    ('heck', '0.4.1'),
+    ('home', '0.5.9'),
+    ('humantime', '2.1.0'),
+    ('humantime-serde', '1.1.1'),
+    ('idna', '0.5.0'),
+    ('ignore', '0.4.22'),
+    ('indexmap', '1.9.3'),
+    ('indexmap', '2.2.3'),
+    ('indicatif', '0.17.7'),
+    ('indoc', '2.0.4'),
+    ('instant', '0.1.12'),
+    ('itertools', '0.11.0'),
+    ('itertools', '0.12.1'),
+    ('itoa', '1.0.10'),
+    ('keyring', '2.3.2'),
+    ('lazy_static', '1.4.0'),
+    ('lddtree', '0.3.4'),
+    ('libc', '0.2.153'),
+    ('libredox', '0.0.1'),
+    ('linux-keyutils', '0.2.4'),
+    ('linux-raw-sys', '0.4.13'),
+    ('lock_api', '0.4.11'),
+    ('log', '0.4.20'),
+    ('lzxd', '0.1.4'),
+    ('mailparse', '0.14.1'),
+    ('matchers', '0.1.0'),
+    ('memchr', '2.7.1'),
+    ('mime', '0.3.17'),
+    ('mime_guess', '2.0.4'),
+    ('minijinja', '1.0.12'),
+    ('minimal-lexical', '0.2.1'),
+    ('miniz_oxide', '0.7.1'),
+    ('msi', '0.7.0'),
+    ('multipart', '0.18.0'),
+    ('native-tls', '0.2.11'),
+    ('nom', '7.1.3'),
+    ('normalize-line-endings', '0.3.0'),
+    ('normpath', '1.1.1'),
+    ('nu-ansi-term', '0.46.0'),
+    ('num-conv', '0.1.0'),
+    ('number_prefix', '0.4.0'),
+    ('once_cell', '1.19.0'),
+    ('openssl', '0.10.63'),
+    ('openssl-macros', '0.1.1'),
+    ('openssl-probe', '0.1.5'),
+    ('openssl-sys', '0.9.99'),
+    ('option-ext', '0.2.0'),
+    ('os_pipe', '1.1.5'),
+    ('overload', '0.1.1'),
+    ('parking_lot', '0.12.1'),
+    ('parking_lot_core', '0.9.9'),
+    ('paste', '1.0.14'),
+    ('path-slash', '0.2.1'),
+    ('pep440_rs', '0.5.0'),
+    ('pep508_rs', '0.4.2'),
+    ('percent-encoding', '2.3.1'),
+    ('pin-project-lite', '0.2.13'),
+    ('pin-utils', '0.1.0'),
+    ('pkg-config', '0.3.29'),
+    ('plain', '0.2.3'),
+    ('platform-info', '2.0.2'),
+    ('portable-atomic', '1.6.0'),
+    ('powerfmt', '0.2.0'),
+    ('ppv-lite86', '0.2.17'),
+    ('pretty_assertions', '1.4.0'),
+    ('proc-macro2', '1.0.78'),
+    ('psm', '0.1.21'),
+    ('pyproject-toml', '0.10.0'),
+    ('python-pkginfo', '0.6.0'),
+    ('quote', '1.0.35'),
+    ('quoted_printable', '0.4.8'),
+    ('quoted_printable', '0.5.0'),
+    ('rand', '0.8.5'),
+    ('rand_chacha', '0.3.1'),
+    ('rand_core', '0.6.4'),
+    ('rayon', '1.8.1'),
+    ('rayon-core', '1.12.1'),
+    ('redox_syscall', '0.4.1'),
+    ('redox_users', '0.4.4'),
+    ('regex', '1.10.3'),
+    ('regex-automata', '0.1.10'),
+    ('regex-automata', '0.4.5'),
+    ('regex-syntax', '0.6.29'),
+    ('regex-syntax', '0.8.2'),
+    ('relative-path', '1.9.2'),
+    ('rfc2047-decoder', '0.2.2'),
+    ('ring', '0.17.7'),
+    ('rstest', '0.18.2'),
+    ('rstest_macros', '0.18.2'),
+    ('rustc_version', '0.4.0'),
+    ('rustix', '0.38.32'),
+    ('rustls', '0.22.4'),
+    ('rustls-pemfile', '2.1.0'),
+    ('rustls-pki-types', '1.3.1'),
+    ('rustls-webpki', '0.102.1'),
+    ('rustversion', '1.0.14'),
+    ('ryu', '1.0.16'),
+    ('same-file', '1.0.6'),
+    ('schannel', '0.1.23'),
+    ('schemars', '0.8.16'),
+    ('schemars_derive', '0.8.16'),
+    ('scopeguard', '1.2.0'),
+    ('scroll', '0.12.0'),
+    ('scroll_derive', '0.12.0'),
+    ('security-framework', '2.9.2'),
+    ('security-framework-sys', '2.9.1'),
+    ('semver', '1.0.22'),
+    ('serde', '1.0.197'),
+    ('serde_derive', '1.0.197'),
+    ('serde_derive_internals', '0.26.0'),
+    ('serde_json', '1.0.114'),
+    ('serde_spanned', '0.6.5'),
+    ('sha2', '0.10.8'),
+    ('sharded-slab', '0.1.7'),
+    ('shell-words', '1.1.0'),
+    ('shlex', '1.3.0'),
+    ('similar', '2.4.0'),
+    ('slab', '0.4.9'),
+    ('smallvec', '1.13.1'),
+    ('smawk', '0.3.2'),
+    ('snapbox', '0.5.7'),
+    ('snapbox-macros', '0.3.8'),
+    ('socks', '0.3.4'),
+    ('spin', '0.9.8'),
+    ('stacker', '0.1.15'),
+    ('static_assertions', '1.1.0'),
+    ('strsim', '0.10.0'),
+    ('subtle', '2.5.0'),
+    ('syn', '1.0.109'),
+    ('syn', '2.0.48'),
+    ('tar', '0.4.40'),
+    ('target-lexicon', '0.12.14'),
+    ('tempfile', '3.9.0'),
+    ('termcolor', '1.4.1'),
+    ('terminal_size', '0.3.0'),
+    ('textwrap', '0.16.1'),
+    ('thiserror', '1.0.57'),
+    ('thiserror-impl', '1.0.57'),
+    ('thread_local', '1.1.7'),
+    ('time', '0.3.34'),
+    ('time-core', '0.1.2'),
+    ('time-macros', '0.2.17'),
+    ('tinyvec', '1.6.0'),
+    ('tinyvec_macros', '0.1.1'),
+    ('toml', '0.5.11'),
+    ('toml', '0.8.10'),
+    ('toml_datetime', '0.6.5'),
+    ('toml_edit', '0.22.6'),
+    ('tracing', '0.1.40'),
+    ('tracing-attributes', '0.1.27'),
+    ('tracing-core', '0.1.32'),
+    ('tracing-log', '0.2.0'),
+    ('tracing-serde', '0.1.3'),
+    ('tracing-subscriber', '0.3.18'),
+    ('trycmd', '0.15.0'),
+    ('twox-hash', '1.6.3'),
+    ('typenum', '1.17.0'),
+    ('unicase', '2.7.0'),
+    ('unicode-bidi', '0.3.15'),
+    ('unicode-ident', '1.0.12'),
+    ('unicode-linebreak', '0.1.5'),
+    ('unicode-normalization', '0.1.22'),
+    ('unicode-width', '0.1.11'),
+    ('unicode-xid', '0.2.4'),
+    ('unscanny', '0.1.0'),
+    ('untrusted', '0.9.0'),
+    ('ureq', '2.9.6'),
+    ('url', '2.5.0'),
+    ('urlencoding', '2.1.3'),
+    ('utf8parse', '0.2.1'),
+    ('uuid', '1.7.0'),
+    ('valuable', '0.1.0'),
+    ('vcpkg', '0.2.15'),
+    ('version_check', '0.9.4'),
+    ('versions', '5.0.1'),
+    ('wait-timeout', '0.2.0'),
+    ('walkdir', '2.4.0'),
+    ('wasi', '0.11.0+wasi-snapshot-preview1'),
+    ('webpki-roots', '0.26.0'),
+    ('which', '5.0.0'),
+    ('which', '6.0.0'),
+    ('wild', '2.2.1'),
+    ('winapi', '0.3.9'),
+    ('winapi-i686-pc-windows-gnu', '0.4.0'),
+    ('winapi-util', '0.1.6'),
+    ('winapi-x86_64-pc-windows-gnu', '0.4.0'),
+    ('windows-sys', '0.48.0'),
+    ('windows-sys', '0.52.0'),
+    ('windows-targets', '0.48.5'),
+    ('windows-targets', '0.52.0'),
+    ('windows_aarch64_gnullvm', '0.48.5'),
+    ('windows_aarch64_gnullvm', '0.52.0'),
+    ('windows_aarch64_msvc', '0.48.5'),
+    ('windows_aarch64_msvc', '0.52.0'),
+    ('windows_i686_gnu', '0.48.5'),
+    ('windows_i686_gnu', '0.52.0'),
+    ('windows_i686_msvc', '0.48.5'),
+    ('windows_i686_msvc', '0.52.0'),
+    ('windows_x86_64_gnu', '0.48.5'),
+    ('windows_x86_64_gnu', '0.52.0'),
+    ('windows_x86_64_gnullvm', '0.48.5'),
+    ('windows_x86_64_gnullvm', '0.52.0'),
+    ('windows_x86_64_msvc', '0.48.5'),
+    ('windows_x86_64_msvc', '0.52.0'),
+    ('winnow', '0.6.2'),
+    ('xattr', '1.3.1'),
+    ('xwin', '0.5.0'),
+    ('yansi', '0.5.1'),
+    ('zerocopy', '0.7.32'),
+    ('zerocopy-derive', '0.7.32'),
+    ('zeroize', '1.7.0'),
+    ('zip', '0.6.6'),
+]
+
+sources = [SOURCE_TAR_GZ]
+checksums = [
+    {'maturin-1.6.0.tar.gz': 'b955025c24c8babc808db49e0ff90db8b4b1320dcc16b14eb26132841737230d'},
+    {'adler-1.0.2.tar.gz': 'f26201604c87b1e01bd3d98f8d5d9a8fcbb815e8cedb41ffccbeb4bf593a35fe'},
+    {'ahash-0.8.7.tar.gz': '77c3a9648d43b9cd48db467b3f87fdd6e146bcc88ab0180006cef2179fe11d01'},
+    {'aho-corasick-1.1.2.tar.gz': 'b2969dcb958b36655471fc61f7e416fa76033bdd4bfed0678d8fee1e2d07a1f0'},
+    {'allocator-api2-0.2.16.tar.gz': '0942ffc6dcaadf03badf6e6a2d0228460359d5e34b57ccdc720b7382dfbd5ec5'},
+    {'anstream-0.6.11.tar.gz': '6e2e1ebcb11de5c03c67de28a7df593d32191b44939c482e97702baaaa6ab6a5'},
+    {'anstyle-1.0.4.tar.gz': '7079075b41f533b8c61d2a4d073c4676e1f8b249ff94a393b0595db304e0dd87'},
+    {'anstyle-parse-0.2.3.tar.gz': 'c75ac65da39e5fe5ab759307499ddad880d724eed2f6ce5b5e8a26f4f387928c'},
+    {'anstyle-query-1.0.2.tar.gz': 'e28923312444cdd728e4738b3f9c9cac739500909bb3d3c94b43551b16517648'},
+    {'anstyle-wincon-3.0.2.tar.gz': '1cd54b81ec8d6180e24654d0b371ad22fc3dd083b6ff8ba325b72e00c87660a7'},
+    {'anyhow-1.0.80.tar.gz': '5ad32ce52e4161730f7098c077cd2ed6229b5804ccf99e5366be1ab72a98b4e1'},
+    {'autocfg-1.1.0.tar.gz': 'd468802bab17cbc0cc575e9b053f41e72aa36bfa6b7f55e3529ffa43161b97fa'},
+    {'base64-0.13.1.tar.gz': '9e1b586273c5702936fe7b7d6896644d8be71e6314cfe09d3167c95f712589e8'},
+    {'base64-0.21.7.tar.gz': '9d297deb1925b89f2ccc13d7635fa0714f12c87adce1c75356b39ca9b7178567'},
+    {'bitflags-1.3.2.tar.gz': 'bef38d45163c2f1dde094a7dfd33ccf595c92905c8f8f4fdc18d06fb1037718a'},
+    {'bitflags-2.4.2.tar.gz': 'ed570934406eb16438a4e976b1b4500774099c13b8cb96eec99f620f05090ddf'},
+    {'block-buffer-0.10.4.tar.gz': '3078c7629b62d3f0439517fa394996acacc5cbc91c5a20d8c658e77abd503a71'},
+    {'bstr-1.9.0.tar.gz': 'c48f0051a4b4c5e0b6d365cd04af53aeaa209e3cc15ec2cdb69e73cc87fbd0dc'},
+    {'byteorder-1.5.0.tar.gz': '1fd0f2584146f6f2ef48085050886acf353beff7305ebd1ae69500e27c67f64b'},
+    {'bytes-1.5.0.tar.gz': 'a2bd12c1caf447e69cd4528f47f94d203fd2582878ecb9e9465484c4148a8223'},
+    {'bytesize-1.3.0.tar.gz': 'a3e368af43e418a04d52505cf3dbc23dda4e3407ae2fa99fd0e4f308ce546acc'},
+    {'bzip2-0.4.4.tar.gz': 'bdb116a6ef3f6c3698828873ad02c3014b3c85cadb88496095628e3ef1e347f8'},
+    {'bzip2-sys-0.1.11+1.0.8.tar.gz': '736a955f3fa7875102d57c82b8cac37ec45224a07fd32d58f9f7a186b6cd4cdc'},
+    {'cab-0.4.1.tar.gz': 'ae6b4de23c7d39c0631fd3cc952d87951c86c75a13812d7247cb7a896e7b3551'},
+    {'camino-1.1.6.tar.gz': 'c59e92b5a388f549b863a7bea62612c09f24c8393560709a54558a9abdfb3b9c'},
+    {'cargo-config2-0.1.24.tar.gz': '88d9bdc858a15454c2d0a5138d8dcf4bcabc06fde679abdea8330393fbc0ef05'},
+    {'cargo-options-0.7.4.tar.gz': 'f3540247c0a37a76eb324acc238dc617786ea22c43b95da560c82a8f2714321f'},
+    {'cargo-platform-0.1.6.tar.gz': 'ceed8ef69d8518a5dda55c07425450b58a4e1946f4951eab6d7191ee86c2443d'},
+    {'cargo-xwin-0.16.4.tar.gz': '5e6c3dd7f20fdd197397532ac882e918cfe1d56f262a97ded7460a50e031e06b'},
+    {'cargo-zigbuild-0.18.4.tar.gz': '65004153e67ac23be88a8e244304a872d727b2aa08654dcabfbecd1fdea4a488'},
+    {'cargo_metadata-0.18.1.tar.gz': '2d886547e41f740c616ae73108f6eb70afe6d940c7bc697cb30f13daec073037'},
+    {'cbindgen-0.26.0.tar.gz': 'da6bc11b07529f16944307272d5bd9b22530bc7d05751717c9d416586cedab49'},
+    {'cc-1.0.88.tar.gz': '02f341c093d19155a6e41631ce5971aac4e9a868262212153124c15fa22d1cdc'},
+    {'cfb-0.9.0.tar.gz': 'b390793e912300f1aa713429f7fd0c391024e6c18b988962558bc4f96a349b1f'},
+    {'cfg-if-1.0.0.tar.gz': 'baf1de4339761588bc0619e3cbc0120ee582ebb74b53b4efbf79117bd2da40fd'},
+    {'charset-0.1.3.tar.gz': '18e9079d1a12a2cc2bffb5db039c43661836ead4082120d5844f02555aca2d46'},
+    {'chumsky-0.9.3.tar.gz': '8eebd66744a15ded14960ab4ccdbfb51ad3b81f51f3f04a80adac98c985396c9'},
+    {'clap-4.4.18.tar.gz': '1e578d6ec4194633722ccf9544794b71b1385c3c027efe0c55db226fc880865c'},
+    {'clap_builder-4.4.18.tar.gz': '4df4df40ec50c46000231c914968278b1eb05098cf8f1b3a518a95030e71d1c7'},
+    {'clap_complete-4.4.9.tar.gz': 'df631ae429f6613fcd3a7c1adbdb65f637271e561b03680adaa6573015dfb106'},
+    {'clap_complete_command-0.5.1.tar.gz': '183495371ea78d4c9ff638bfc6497d46fed2396e4f9c50aebc1278a4a9919a3d'},
+    {'clap_complete_nushell-0.1.11.tar.gz': '5d02bc8b1a18ee47c4d2eec3fb5ac034dc68ebea6125b1509e9ccdffcddce66e'},
+    {'clap_derive-4.4.7.tar.gz': 'cf9804afaaf59a91e75b022a30fb7229a7901f60c755489cc61c9b423b836442'},
+    {'clap_lex-0.6.0.tar.gz': '702fc72eb24e5a1e48ce58027a675bc24edd52096d5397d4aea7c6dd9eca0bd1'},
+    {'cli-table-0.4.7.tar.gz': 'adfbb116d9e2c4be7011360d0c0bee565712c11e969c9609b25b619366dc379d'},
+    {'colorchoice-1.0.0.tar.gz': 'acbf1af155f9b9ef647e42cdc158db4b64a1b61f743629225fde6f3e0be2a7c7'},
+    {'configparser-3.0.4.tar.gz': '4ec6d3da8e550377a85339063af6e3735f4b1d9392108da4e083a1b3b9820288'},
+    {'console-0.15.8.tar.gz': '0e1f83fc076bd6dd27517eacdf25fef6c4dfe5f1d7448bafaaf3a26f13b5e4eb'},
+    {'content_inspector-0.2.4.tar.gz': 'b7bda66e858c683005a53a9a60c69a4aca7eeaa45d124526e389f7aec8e62f38'},
+    {'core-foundation-0.9.4.tar.gz': '91e195e091a93c46f7102ec7818a2aa394e1e1771c3ab4825963fa03e45afb8f'},
+    {'core-foundation-sys-0.8.6.tar.gz': '06ea2b9bc92be3c2baa9334a323ebca2d6f074ff852cd1d7b11064035cd3868f'},
+    {'cpufeatures-0.2.12.tar.gz': '53fe5e26ff1b7aef8bca9c6080520cfb8d9333c7568e1829cef191a9723e5504'},
+    {'crc32fast-1.3.2.tar.gz': 'b540bd8bc810d3885c6ea91e2018302f68baba2129ab3e88f32389ee9370880d'},
+    {'crossbeam-channel-0.5.11.tar.gz': '176dc175b78f56c0f321911d9c8eb2b77a78a4860b9c19db83835fea1a46649b'},
+    {'crossbeam-deque-0.8.5.tar.gz': '613f8cc01fe9cf1a3eb3d7f488fd2fa8388403e97039e2f73692932e291a770d'},
+    {'crossbeam-epoch-0.9.18.tar.gz': '5b82ac4a3c2ca9c3460964f020e1402edd5753411d7737aa39c3714ad1b5420e'},
+    {'crossbeam-utils-0.8.19.tar.gz': '248e3bacc7dc6baa3b21e405ee045c3047101a49145e7e9eca583ab4c2ca5345'},
+    {'crypto-common-0.1.6.tar.gz': '1bfb12502f3fc46cca1bb51ac28df9d618d813cdc3d2f25b9fe775a34af26bb3'},
+    {'data-encoding-2.5.0.tar.gz': '7e962a19be5cfc3f3bf6dd8f61eb50107f356ad6270fbb3ed41476571db78be5'},
+    {'deranged-0.3.11.tar.gz': 'b42b6fa04a440b495c8b04d0e71b707c585f83cb9cb28cf8cd0d976c315e31b4'},
+    {'derivative-2.2.0.tar.gz': 'fcc3dd5e9e9c0b295d6e1e4d811fb6f157d5ffd784b8d202fc62eac8035a770b'},
+    {'dialoguer-0.11.0.tar.gz': '658bce805d770f407bc62102fca7c2c64ceef2fbcb2b8bd19d2765ce093980de'},
+    {'diff-0.1.13.tar.gz': '56254986775e3233ffa9c4d7d3faaf6d36a2c09d30b20687e9f88bc8bafc16c8'},
+    {'digest-0.10.7.tar.gz': '9ed9a281f7bc9b7576e61468ba615a66a5c8cfdff42420a70aa82701a3b1e292'},
+    {'dirs-5.0.1.tar.gz': '44c45a9d03d6676652bcb5e724c7e988de1acad23a711b5217ab9cbecbec2225'},
+    {'dirs-sys-0.4.1.tar.gz': '520f05a5cbd335fae5a99ff7a6ab8627577660ee5cfd6a94a6a929b52ff0321c'},
+    {'dissimilar-1.0.7.tar.gz': '86e3bdc80eee6e16b2b6b0f87fbc98c04bee3455e35174c0de1a125d0688c632'},
+    {'dunce-1.0.4.tar.gz': '56ce8c6da7551ec6c462cbaf3bfbc75131ebbfa1c944aeaa9dab51ca1c5f0c3b'},
+    {'dyn-clone-1.0.17.tar.gz': '0d6ef0072f8a535281e4876be788938b528e9a1d43900b82c2569af7da799125'},
+    {'either-1.9.0.tar.gz': 'a26ae43d7bcc3b814de94796a5e736d4029efb0ee900c12e2d54c993ad1a1e07'},
+    {'encode_unicode-0.3.6.tar.gz': 'a357d28ed41a50f9c765dbfe56cbc04a64e53e5fc58ba79fbc34c10ef3df831f'},
+    {'encoding_rs-0.8.33.tar.gz': '7268b386296a025e474d5140678f75d6de9493ae55a5d709eeb9dd08149945e1'},
+    {'equivalent-1.0.1.tar.gz': '5443807d6dff69373d433ab9ef5378ad8df50ca6298caf15de6e52e24aaf54d5'},
+    {'errno-0.3.8.tar.gz': 'a258e46cdc063eb8519c00b9fc845fc47bcfca4130e2f08e88665ceda8474245'},
+    {'expect-test-1.4.1.tar.gz': '30d9eafeadd538e68fb28016364c9732d78e420b9ff8853fa5e4058861e9f8d3'},
+    {'fastrand-2.0.1.tar.gz': '25cbce373ec4653f1a01a31e8a5e5ec0c622dc27ff9c4e6606eefef5cbbed4a5'},
+    {'fat-macho-0.4.8.tar.gz': '0d4c93f393add03d72bc10dd3dea43a1610ecb29e0c0a6459c70b53b82931adf'},
+    {'filetime-0.2.23.tar.gz': '1ee447700ac8aa0b2f2bd7bc4462ad686ba06baa6727ac149a2d6277f0d240fd'},
+    {'flate2-1.0.28.tar.gz': '46303f565772937ffe1d394a4fac6f411c6013172fadde9dcdb1e147a086940e'},
+    {'fnv-1.0.7.tar.gz': '3f9eec918d3f24069decb9af1554cad7c880e2da24a9afd88aca000531ab82c1'},
+    {'foreign-types-0.3.2.tar.gz': 'f6f339eb8adc052cd2ca78910fda869aefa38d22d5cb648e6485e4d3fc06f3b1'},
+    {'foreign-types-shared-0.1.1.tar.gz': '00b0228411908ca8685dba7fc2cdd70ec9990a6e753e89b6ac91a84c40fbaf4b'},
+    {'form_urlencoded-1.2.1.tar.gz': 'e13624c2627564efccf4934284bdd98cbaa14e79b0b5a141218e507b3a823456'},
+    {'fs-err-2.11.0.tar.gz': '88a41f105fe1d5b6b34b2055e3dc59bb79b46b48b2040b9e6c7b4b5de097aa41'},
+    {'futures-0.3.30.tar.gz': '645c6916888f6cb6350d2550b80fb63e734897a8498abe35cfb732b6487804b0'},
+    {'futures-channel-0.3.30.tar.gz': 'eac8f7d7865dcb88bd4373ab671c8cf4508703796caa2b1985a9ca867b3fcb78'},
+    {'futures-core-0.3.30.tar.gz': 'dfc6580bb841c5a68e9ef15c77ccc837b40a7504914d52e47b8b0e9bbda25a1d'},
+    {'futures-executor-0.3.30.tar.gz': 'a576fc72ae164fca6b9db127eaa9a9dda0d61316034f33a0a0d4eda41f02b01d'},
+    {'futures-io-0.3.30.tar.gz': 'a44623e20b9681a318efdd71c299b6b222ed6f231972bfe2f224ebad6311f0c1'},
+    {'futures-macro-0.3.30.tar.gz': '87750cf4b7a4c0625b1529e4c543c2182106e4dedc60a2a6455e00d212c489ac'},
+    {'futures-sink-0.3.30.tar.gz': '9fb8e00e87438d937621c1c6269e53f536c14d3fbd6a042bb24879e57d474fb5'},
+    {'futures-task-0.3.30.tar.gz': '38d84fa142264698cdce1a9f9172cf383a0c82de1bddcf3092901442c4097004'},
+    {'futures-timer-3.0.3.tar.gz': 'f288b0a4f20f9a56b5d1da57e2227c661b7b16168e2f72365f57b63326e29b24'},
+    {'futures-util-0.3.30.tar.gz': '3d6401deb83407ab3da39eba7e33987a73c3df0c82b4bb5813ee871c19c41d48'},
+    {'generic-array-0.14.7.tar.gz': '85649ca51fd72272d7821adaf274ad91c288277713d9c18820d8499a7ff69e9a'},
+    {'getrandom-0.2.12.tar.gz': '190092ea657667030ac6a35e305e62fc4dd69fd98ac98631e5d3a2b1575a12b5'},
+    {'glob-0.3.1.tar.gz': 'd2fabcfbdc87f4758337ca535fb41a6d701b65693ce38287d856d1674551ec9b'},
+    {'globset-0.4.14.tar.gz': '57da3b9b5b85bd66f31093f8c408b90a74431672542466497dcbdfdc02034be1'},
+    {'goblin-0.8.0.tar.gz': 'bb07a4ffed2093b118a525b1d8f5204ae274faed5604537caf7135d0f18d9887'},
+    {'hashbrown-0.12.3.tar.gz': '8a9ee70c43aaf417c914396645a0fa852624801b24ebb7ae78fe8272889ac888'},
+    {'hashbrown-0.14.3.tar.gz': '290f1a1d9242c78d09ce40a5e87e7554ee637af1351968159f4952f028f75604'},
+    {'heck-0.4.1.tar.gz': '95505c38b4572b2d910cecb0281560f54b440a19336cbbcb27bf6ce6adc6f5a8'},
+    {'home-0.5.9.tar.gz': 'e3d1354bf6b7235cb4a0576c2619fd4ed18183f689b12b006a0ee7329eeff9a5'},
+    {'humantime-2.1.0.tar.gz': '9a3a5bfb195931eeb336b2a7b4d761daec841b97f947d34394601737a7bba5e4'},
+    {'humantime-serde-1.1.1.tar.gz': '57a3db5ea5923d99402c94e9feb261dc5ee9b4efa158b0315f788cf549cc200c'},
+    {'idna-0.5.0.tar.gz': '634d9b1461af396cad843f47fdba5597a4f9e6ddd4bfb6ff5d85028c25cb12f6'},
+    {'ignore-0.4.22.tar.gz': 'b46810df39e66e925525d6e38ce1e7f6e1d208f72dc39757880fcb66e2c58af1'},
+    {'indexmap-1.9.3.tar.gz': 'bd070e393353796e801d209ad339e89596eb4c8d430d18ede6a1cced8fafbd99'},
+    {'indexmap-2.2.3.tar.gz': '233cf39063f058ea2caae4091bf4a3ef70a653afbc026f5c4a4135d114e3c177'},
+    {'indicatif-0.17.7.tar.gz': 'fb28741c9db9a713d93deb3bb9515c20788cef5815265bee4980e87bde7e0f25'},
+    {'indoc-2.0.4.tar.gz': '1e186cfbae8084e513daff4240b4797e342f988cecda4fb6c939150f96315fd8'},
+    {'instant-0.1.12.tar.gz': '7a5bbe824c507c5da5956355e86a746d82e0e1464f65d862cc5e71da70e94b2c'},
+    {'itertools-0.11.0.tar.gz': 'b1c173a5686ce8bfa551b3563d0c2170bf24ca44da99c7ca4bfdab5418c3fe57'},
+    {'itertools-0.12.1.tar.gz': 'ba291022dbbd398a455acf126c1e341954079855bc60dfdda641363bd6922569'},
+    {'itoa-1.0.10.tar.gz': 'b1a46d1a171d865aa5f83f92695765caa047a9b4cbae2cbf37dbd613a793fd4c'},
+    {'keyring-2.3.2.tar.gz': '1be8bc4c6b6e9d85ecdad090fcf342a9216f53d747a537cc05e3452fd650ca46'},
+    {'lazy_static-1.4.0.tar.gz': 'e2abad23fbc42b3700f2f279844dc832adb2b2eb069b2df918f455c4e18cc646'},
+    {'lddtree-0.3.4.tar.gz': 'f88a93876d2485ede9c97d698c164cf5c024491908483964a998faae9705dea6'},
+    {'libc-0.2.153.tar.gz': '9c198f91728a82281a64e1f4f9eeb25d82cb32a5de251c6bd1b5154d63a8e7bd'},
+    {'libredox-0.0.1.tar.gz': '85c833ca1e66078851dba29046874e38f08b2c883700aa29a03ddd3b23814ee8'},
+    {'linux-keyutils-0.2.4.tar.gz': '761e49ec5fd8a5a463f9b84e877c373d888935b71c6be78f3767fe2ae6bed18e'},
+    {'linux-raw-sys-0.4.13.tar.gz': '01cda141df6706de531b6c46c3a33ecca755538219bd484262fa09410c13539c'},
+    {'lock_api-0.4.11.tar.gz': '3c168f8615b12bc01f9c17e2eb0cc07dcae1940121185446edc3744920e8ef45'},
+    {'log-0.4.20.tar.gz': 'b5e6163cb8c49088c2c36f57875e58ccd8c87c7427f7fbd50ea6710b2f3f2e8f'},
+    {'lzxd-0.1.4.tar.gz': '784462f20dddd9dfdb45de963fa4ad4a288cb10a7889ac5d2c34fb6481c6b213'},
+    {'mailparse-0.14.1.tar.gz': '2d096594926cab442e054e047eb8c1402f7d5b2272573b97ba68aa40629f9757'},
+    {'matchers-0.1.0.tar.gz': '8263075bb86c5a1b1427b5ae862e8889656f126e9f77c484496e8b47cf5c5558'},
+    {'memchr-2.7.1.tar.gz': '523dc4f511e55ab87b694dc30d0f820d60906ef06413f93d4d7a1385599cc149'},
+    {'mime-0.3.17.tar.gz': '6877bb514081ee2a7ff5ef9de3281f14a4dd4bceac4c09388074a6b5df8a139a'},
+    {'mime_guess-2.0.4.tar.gz': '4192263c238a5f0d0c6bfd21f336a313a4ce1c450542449ca191bb657b4642ef'},
+    {'minijinja-1.0.12.tar.gz': '6fe0ff215195a22884d867b547c70a0c4815cbbcc70991f281dca604b20d10ce'},
+    {'minimal-lexical-0.2.1.tar.gz': '68354c5c6bd36d73ff3feceb05efa59b6acb7626617f4962be322a825e61f79a'},
+    {'miniz_oxide-0.7.1.tar.gz': 'e7810e0be55b428ada41041c41f32c9f1a42817901b4ccf45fa3d4b6561e74c7'},
+    {'msi-0.7.0.tar.gz': '226b2404f03d2cf47375b9715c8adfae4e388bb2377cff908e8a40f31e421514'},
+    {'multipart-0.18.0.tar.gz': '00dec633863867f29cb39df64a397cdf4a6354708ddd7759f70c7fb51c5f9182'},
+    {'native-tls-0.2.11.tar.gz': '07226173c32f2926027b63cce4bcd8076c3552846cbe7925f3aaffeac0a3b92e'},
+    {'nom-7.1.3.tar.gz': 'd273983c5a657a70a3e8f2a01329822f3b8c8172b73826411a55751e404a0a4a'},
+    {'normalize-line-endings-0.3.0.tar.gz': '61807f77802ff30975e01f4f071c8ba10c022052f98b3294119f3e615d13e5be'},
+    {'normpath-1.1.1.tar.gz': 'ec60c60a693226186f5d6edf073232bfb6464ed97eb22cf3b01c1e8198fd97f5'},
+    {'nu-ansi-term-0.46.0.tar.gz': '77a8165726e8236064dbb45459242600304b42a5ea24ee2948e18e023bf7ba84'},
+    {'num-conv-0.1.0.tar.gz': '51d515d32fb182ee37cda2ccdcb92950d6a3c2893aa280e540671c2cd0f3b1d9'},
+    {'number_prefix-0.4.0.tar.gz': '830b246a0e5f20af87141b25c173cd1b609bd7779a4617d6ec582abaf90870f3'},
+    {'once_cell-1.19.0.tar.gz': '3fdb12b2476b595f9358c5161aa467c2438859caa136dec86c26fdd2efe17b92'},
+    {'openssl-0.10.63.tar.gz': '15c9d69dd87a29568d4d017cfe8ec518706046a05184e5aea92d0af890b803c8'},
+    {'openssl-macros-0.1.1.tar.gz': 'a948666b637a0f465e8564c73e89d4dde00d72d4d473cc972f390fc3dcee7d9c'},
+    {'openssl-probe-0.1.5.tar.gz': 'ff011a302c396a5197692431fc1948019154afc178baf7d8e37367442a4601cf'},
+    {'openssl-sys-0.9.99.tar.gz': '22e1bf214306098e4832460f797824c05d25aacdf896f64a985fb0fd992454ae'},
+    {'option-ext-0.2.0.tar.gz': '04744f49eae99ab78e0d5c0b603ab218f515ea8cfe5a456d7629ad883a3b6e7d'},
+    {'os_pipe-1.1.5.tar.gz': '57119c3b893986491ec9aa85056780d3a0f3cf4da7cc09dd3650dbd6c6738fb9'},
+    {'overload-0.1.1.tar.gz': 'b15813163c1d831bf4a13c3610c05c0d03b39feb07f7e09fa234dac9b15aaf39'},
+    {'parking_lot-0.12.1.tar.gz': '3742b2c103b9f06bc9fff0a37ff4912935851bee6d36f3c02bcc755bcfec228f'},
+    {'parking_lot_core-0.9.9.tar.gz': '4c42a9226546d68acdd9c0a280d17ce19bfe27a46bf68784e4066115788d008e'},
+    {'paste-1.0.14.tar.gz': 'de3145af08024dea9fa9914f381a17b8fc6034dfb00f3a84013f7ff43f29ed4c'},
+    {'path-slash-0.2.1.tar.gz': '1e91099d4268b0e11973f036e885d652fb0b21fedcf69738c627f94db6a44f42'},
+    {'pep440_rs-0.5.0.tar.gz': '15efd4d885c29126cc93e12af3087896e2518bd5ca0fb328c19c4ef9cecfa8be'},
+    {'pep508_rs-0.4.2.tar.gz': '1455babf8edd3eedcdfcb39700e455a4bb189e71b4f1fa0eacc9b244cc5a55e6'},
+    {'percent-encoding-2.3.1.tar.gz': 'e3148f5046208a5d56bcfc03053e3ca6334e51da8dfb19b6cdc8b306fae3283e'},
+    {'pin-project-lite-0.2.13.tar.gz': '8afb450f006bf6385ca15ef45d71d2288452bc3683ce2e2cacc0d18e4be60b58'},
+    {'pin-utils-0.1.0.tar.gz': '8b870d8c151b6f2fb93e84a13146138f05d02ed11c7e7c54f8826aaaf7c9f184'},
+    {'pkg-config-0.3.29.tar.gz': '2900ede94e305130c13ddd391e0ab7cbaeb783945ae07a279c268cb05109c6cb'},
+    {'plain-0.2.3.tar.gz': 'b4596b6d070b27117e987119b4dac604f3c58cfb0b191112e24771b2faeac1a6'},
+    {'platform-info-2.0.2.tar.gz': 'd6259c4860e53bf665016f1b2f46a8859cadfa717581dc9d597ae4069de6300f'},
+    {'portable-atomic-1.6.0.tar.gz': '7170ef9988bc169ba16dd36a7fa041e5c4cbeb6a35b76d4c03daded371eae7c0'},
+    {'powerfmt-0.2.0.tar.gz': '439ee305def115ba05938db6eb1644ff94165c5ab5e9420d1c1bcedbba909391'},
+    {'ppv-lite86-0.2.17.tar.gz': '5b40af805b3121feab8a3c29f04d8ad262fa8e0561883e7653e024ae4479e6de'},
+    {'pretty_assertions-1.4.0.tar.gz': 'af7cee1a6c8a5b9208b3cb1061f10c0cb689087b3d8ce85fb9d2dd7a29b6ba66'},
+    {'proc-macro2-1.0.78.tar.gz': 'e2422ad645d89c99f8f3e6b88a9fdeca7fabeac836b1002371c4367c8f984aae'},
+    {'psm-0.1.21.tar.gz': '5787f7cda34e3033a72192c018bc5883100330f362ef279a8cbccfce8bb4e874'},
+    {'pyproject-toml-0.10.0.tar.gz': '3b80f889b6d413c3f8963a2c7db03f95dd6e1d85e1074137cb2013ea2faa8898'},
+    {'python-pkginfo-0.6.0.tar.gz': '037469c164f08c891bf6d69ca02f1d56210011451e229618669777df82124cfa'},
+    {'quote-1.0.35.tar.gz': '291ec9ab5efd934aaf503a6466c5d5251535d108ee747472c3977cc5acc868ef'},
+    {'quoted_printable-0.4.8.tar.gz': '5a3866219251662ec3b26fc217e3e05bf9c4f84325234dfb96bf0bf840889e49'},
+    {'quoted_printable-0.5.0.tar.gz': '79ec282e887b434b68c18fe5c121d38e72a5cf35119b59e54ec5b992ea9c8eb0'},
+    {'rand-0.8.5.tar.gz': '34af8d1a0e25924bc5b7c43c079c942339d8f0a8b57c39049bef581b46327404'},
+    {'rand_chacha-0.3.1.tar.gz': 'e6c10a63a0fa32252be49d21e7709d4d4baf8d231c2dbce1eaa8141b9b127d88'},
+    {'rand_core-0.6.4.tar.gz': 'ec0be4795e2f6a28069bec0b5ff3e2ac9bafc99e6a9a7dc3547996c5c816922c'},
+    {'rayon-1.8.1.tar.gz': 'fa7237101a77a10773db45d62004a272517633fbcc3df19d96455ede1122e051'},
+    {'rayon-core-1.12.1.tar.gz': '1465873a3dfdaa8ae7cb14b4383657caab0b3e8a0aa9ae8e04b044854c8dfce2'},
+    {'redox_syscall-0.4.1.tar.gz': '4722d768eff46b75989dd134e5c353f0d6296e5aaa3132e776cbdb56be7731aa'},
+    {'redox_users-0.4.4.tar.gz': 'a18479200779601e498ada4e8c1e1f50e3ee19deb0259c25825a98b5603b2cb4'},
+    {'regex-1.10.3.tar.gz': 'b62dbe01f0b06f9d8dc7d49e05a0785f153b00b2c227856282f671e0318c9b15'},
+    {'regex-automata-0.1.10.tar.gz': '6c230d73fb8d8c1b9c0b3135c5142a8acee3a0558fb8db5cf1cb65f8d7862132'},
+    {'regex-automata-0.4.5.tar.gz': '5bb987efffd3c6d0d8f5f89510bb458559eab11e4f869acb20bf845e016259cd'},
+    {'regex-syntax-0.6.29.tar.gz': 'f162c6dd7b008981e4d40210aca20b4bd0f9b60ca9271061b07f78537722f2e1'},
+    {'regex-syntax-0.8.2.tar.gz': 'c08c74e62047bb2de4ff487b251e4a92e24f48745648451635cec7d591162d9f'},
+    {'relative-path-1.9.2.tar.gz': 'e898588f33fdd5b9420719948f9f2a32c922a246964576f71ba7f24f80610fbc'},
+    {'rfc2047-decoder-0.2.2.tar.gz': '61fc4b4e52897c3e30b12b7e9b04461215b647fbe66f6def60dd8edbce14ec2e'},
+    {'ring-0.17.7.tar.gz': '688c63d65483050968b2a8937f7995f443e27041a0f7700aa59b0822aedebb74'},
+    {'rstest-0.18.2.tar.gz': '97eeab2f3c0a199bc4be135c36c924b6590b88c377d416494288c14f2db30199'},
+    {'rstest_macros-0.18.2.tar.gz': 'd428f8247852f894ee1be110b375111b586d4fa431f6c46e64ba5a0dcccbe605'},
+    {'rustc_version-0.4.0.tar.gz': 'bfa0f585226d2e68097d4f95d113b15b83a82e819ab25717ec0590d9584ef366'},
+    {'rustix-0.38.32.tar.gz': '65e04861e65f21776e67888bfbea442b3642beaa0138fdb1dd7a84a52dffdb89'},
+    {'rustls-0.22.4.tar.gz': 'bf4ef73721ac7bcd79b2b315da7779d8fc09718c6b3d2d1b2d94850eb8c18432'},
+    {'rustls-pemfile-2.1.0.tar.gz': '3c333bb734fcdedcea57de1602543590f545f127dc8b533324318fd492c5c70b'},
+    {'rustls-pki-types-1.3.1.tar.gz': '5ede67b28608b4c60685c7d54122d4400d90f62b40caee7700e700380a390fa8'},
+    {'rustls-webpki-0.102.1.tar.gz': 'ef4ca26037c909dedb327b48c3327d0ba91d3dd3c4e05dad328f210ffb68e95b'},
+    {'rustversion-1.0.14.tar.gz': '7ffc183a10b4478d04cbbbfc96d0873219d962dd5accaff2ffbd4ceb7df837f4'},
+    {'ryu-1.0.16.tar.gz': 'f98d2aa92eebf49b69786be48e4477826b256916e84a57ff2a4f21923b48eb4c'},
+    {'same-file-1.0.6.tar.gz': '93fc1dc3aaa9bfed95e02e6eadabb4baf7e3078b0bd1b4d7b6b0b68378900502'},
+    {'schannel-0.1.23.tar.gz': 'fbc91545643bcf3a0bbb6569265615222618bdf33ce4ffbbd13c4bbd4c093534'},
+    {'schemars-0.8.16.tar.gz': '45a28f4c49489add4ce10783f7911893516f15afe45d015608d41faca6bc4d29'},
+    {'schemars_derive-0.8.16.tar.gz': 'c767fd6fa65d9ccf9cf026122c1b555f2ef9a4f0cea69da4d7dbc3e258d30967'},
+    {'scopeguard-1.2.0.tar.gz': '94143f37725109f92c262ed2cf5e59bce7498c01bcc1502d7b9afe439a4e9f49'},
+    {'scroll-0.12.0.tar.gz': '6ab8598aa408498679922eff7fa985c25d58a90771bd6be794434c5277eab1a6'},
+    {'scroll_derive-0.12.0.tar.gz': '7f81c2fde025af7e69b1d1420531c8a8811ca898919db177141a85313b1cb932'},
+    {'security-framework-2.9.2.tar.gz': '05b64fb303737d99b81884b2c63433e9ae28abebe5eb5045dcdd175dc2ecf4de'},
+    {'security-framework-sys-2.9.1.tar.gz': 'e932934257d3b408ed8f30db49d85ea163bfe74961f017f405b025af298f0c7a'},
+    {'semver-1.0.22.tar.gz': '92d43fe69e652f3df9bdc2b85b2854a0825b86e4fb76bc44d945137d053639ca'},
+    {'serde-1.0.197.tar.gz': '3fb1c873e1b9b056a4dc4c0c198b24c3ffa059243875552b2bd0933b1aee4ce2'},
+    {'serde_derive-1.0.197.tar.gz': '7eb0b34b42edc17f6b7cac84a52a1c5f0e1bb2227e997ca9011ea3dd34e8610b'},
+    {'serde_derive_internals-0.26.0.tar.gz': '85bf8229e7920a9f636479437026331ce11aa132b4dde37d121944a44d6e5f3c'},
+    {'serde_json-1.0.114.tar.gz': 'c5f09b1bd632ef549eaa9f60a1f8de742bdbc698e6cee2095fc84dde5f549ae0'},
+    {'serde_spanned-0.6.5.tar.gz': 'eb3622f419d1296904700073ea6cc23ad690adbd66f13ea683df73298736f0c1'},
+    {'sha2-0.10.8.tar.gz': '793db75ad2bcafc3ffa7c68b215fee268f537982cd901d132f89c6343f3a3dc8'},
+    {'sharded-slab-0.1.7.tar.gz': 'f40ca3c46823713e0d4209592e8d6e826aa57e928f09752619fc696c499637f6'},
+    {'shell-words-1.1.0.tar.gz': '24188a676b6ae68c3b2cb3a01be17fbf7240ce009799bb56d5b1409051e78fde'},
+    {'shlex-1.3.0.tar.gz': '0fda2ff0d084019ba4d7c6f371c95d8fd75ce3524c3cb8fb653a3023f6323e64'},
+    {'similar-2.4.0.tar.gz': '32fea41aca09ee824cc9724996433064c89f7777e60762749a4170a14abbfa21'},
+    {'slab-0.4.9.tar.gz': '8f92a496fb766b417c996b9c5e57daf2f7ad3b0bebe1ccfca4856390e3d3bb67'},
+    {'smallvec-1.13.1.tar.gz': 'e6ecd384b10a64542d77071bd64bd7b231f4ed5940fba55e98c3de13824cf3d7'},
+    {'smawk-0.3.2.tar.gz': 'b7c388c1b5e93756d0c740965c41e8822f866621d41acbdf6336a6a168f8840c'},
+    {'snapbox-0.5.7.tar.gz': '4a99efa20de5053229642a477436cdb39828c7651c614622eb4888f9688523e6'},
+    {'snapbox-macros-0.3.8.tar.gz': 'e1c4b838b05d15ab22754068cb73500b2f3b07bf09d310e15b27f88160f1de40'},
+    {'socks-0.3.4.tar.gz': 'f0c3dbbd9ae980613c6dd8e28a9407b50509d3803b57624d5dfe8315218cd58b'},
+    {'spin-0.9.8.tar.gz': '6980e8d7511241f8acf4aebddbb1ff938df5eebe98691418c4468d0b72a96a67'},
+    {'stacker-0.1.15.tar.gz': 'c886bd4480155fd3ef527d45e9ac8dd7118a898a46530b7b94c3e21866259fce'},
+    {'static_assertions-1.1.0.tar.gz': 'a2eb9349b6444b326872e140eb1cf5e7c522154d69e7a0ffb0fb81c06b37543f'},
+    {'strsim-0.10.0.tar.gz': '73473c0e59e6d5812c5dfe2a064a6444949f089e20eec9a2e5506596494e4623'},
+    {'subtle-2.5.0.tar.gz': '81cdd64d312baedb58e21336b31bc043b77e01cc99033ce76ef539f78e965ebc'},
+    {'syn-1.0.109.tar.gz': '72b64191b275b66ffe2469e8af2c1cfe3bafa67b529ead792a6d0160888b4237'},
+    {'syn-2.0.48.tar.gz': '0f3531638e407dfc0814761abb7c00a5b54992b849452a0646b7f65c9f770f3f'},
+    {'tar-0.4.40.tar.gz': 'b16afcea1f22891c49a00c751c7b63b2233284064f11a200fc624137c51e2ddb'},
+    {'target-lexicon-0.12.14.tar.gz': 'e1fc403891a21bcfb7c37834ba66a547a8f402146eba7265b5a6d88059c9ff2f'},
+    {'tempfile-3.9.0.tar.gz': '01ce4141aa927a6d1bd34a041795abd0db1cccba5d5f24b009f694bdf3a1f3fa'},
+    {'termcolor-1.4.1.tar.gz': '06794f8f6c5c898b3275aebefa6b8a1cb24cd2c6c79397ab15774837a0bc5755'},
+    {'terminal_size-0.3.0.tar.gz': '21bebf2b7c9e0a515f6e0f8c51dc0f8e4696391e6f1ff30379559f8365fb0df7'},
+    {'textwrap-0.16.1.tar.gz': '23d434d3f8967a09480fb04132ebe0a3e088c173e6d0ee7897abbdf4eab0f8b9'},
+    {'thiserror-1.0.57.tar.gz': '1e45bcbe8ed29775f228095caf2cd67af7a4ccf756ebff23a306bf3e8b47b24b'},
+    {'thiserror-impl-1.0.57.tar.gz': 'a953cb265bef375dae3de6663da4d3804eee9682ea80d8e2542529b73c531c81'},
+    {'thread_local-1.1.7.tar.gz': '3fdd6f064ccff2d6567adcb3873ca630700f00b5ad3f060c25b5dcfd9a4ce152'},
+    {'time-0.3.34.tar.gz': 'c8248b6521bb14bc45b4067159b9b6ad792e2d6d754d6c41fb50e29fefe38749'},
+    {'time-core-0.1.2.tar.gz': 'ef927ca75afb808a4d64dd374f00a2adf8d0fcff8e7b184af886c3c87ec4a3f3'},
+    {'time-macros-0.2.17.tar.gz': '7ba3a3ef41e6672a2f0f001392bb5dcd3ff0a9992d618ca761a11c3121547774'},
+    {'tinyvec-1.6.0.tar.gz': '87cc5ceb3875bb20c2890005a4e226a4651264a5c75edb2421b52861a0a0cb50'},
+    {'tinyvec_macros-0.1.1.tar.gz': '1f3ccbac311fea05f86f61904b462b55fb3df8837a366dfc601a0161d0532f20'},
+    {'toml-0.5.11.tar.gz': 'f4f7f0dd8d50a853a531c426359045b1998f04219d88799810762cd4ad314234'},
+    {'toml-0.8.10.tar.gz': '9a9aad4a3066010876e8dcf5a8a06e70a558751117a145c6ce2b82c2e2054290'},
+    {'toml_datetime-0.6.5.tar.gz': '3550f4e9685620ac18a50ed434eb3aec30db8ba93b0287467bca5826ea25baf1'},
+    {'toml_edit-0.22.6.tar.gz': '2c1b5fd4128cc8d3e0cb74d4ed9a9cc7c7284becd4df68f5f940e1ad123606f6'},
+    {'tracing-0.1.40.tar.gz': 'c3523ab5a71916ccf420eebdf5521fcef02141234bbc0b8a49f2fdc4544364ef'},
+    {'tracing-attributes-0.1.27.tar.gz': '34704c8d6ebcbc939824180af020566b01a7c01f80641264eba0999f6c2b6be7'},
+    {'tracing-core-0.1.32.tar.gz': 'c06d3da6113f116aaee68e4d601191614c9053067f9ab7f6edbcb161237daa54'},
+    {'tracing-log-0.2.0.tar.gz': 'ee855f1f400bd0e5c02d150ae5de3840039a3f54b025156404e34c23c03f47c3'},
+    {'tracing-serde-0.1.3.tar.gz': 'bc6b213177105856957181934e4920de57730fc69bf42c37ee5bb664d406d9e1'},
+    {'tracing-subscriber-0.3.18.tar.gz': 'ad0f048c97dbd9faa9b7df56362b8ebcaa52adb06b498c050d2f4e32f90a7a8b'},
+    {'trycmd-0.15.0.tar.gz': '464edb3603a81a50b4c8f47b11dfade69ef48ffdc0af2f8b194ad87cbda75317'},
+    {'twox-hash-1.6.3.tar.gz': '97fee6b57c6a41524a810daee9286c02d7752c4253064d0b05472833a438f675'},
+    {'typenum-1.17.0.tar.gz': '42ff0bf0c66b8238c6f3b578df37d0b7848e55df8577b3f74f92a69acceeb825'},
+    {'unicase-2.7.0.tar.gz': 'f7d2d4dafb69621809a81864c9c1b864479e1235c0dd4e199924b9742439ed89'},
+    {'unicode-bidi-0.3.15.tar.gz': '08f95100a766bf4f8f28f90d77e0a5461bbdb219042e7679bebe79004fed8d75'},
+    {'unicode-ident-1.0.12.tar.gz': '3354b9ac3fae1ff6755cb6db53683adb661634f67557942dea4facebec0fee4b'},
+    {'unicode-linebreak-0.1.5.tar.gz': '3b09c83c3c29d37506a3e260c08c03743a6bb66a9cd432c6934ab501a190571f'},
+    {'unicode-normalization-0.1.22.tar.gz': '5c5713f0fc4b5db668a2ac63cdb7bb4469d8c9fed047b1d0292cc7b0ce2ba921'},
+    {'unicode-width-0.1.11.tar.gz': 'e51733f11c9c4f72aa0c160008246859e340b00807569a0da0e7a1079b27ba85'},
+    {'unicode-xid-0.2.4.tar.gz': 'f962df74c8c05a667b5ee8bcf162993134c104e96440b663c8daa176dc772d8c'},
+    {'unscanny-0.1.0.tar.gz': 'e9df2af067a7953e9c3831320f35c1cc0600c30d44d9f7a12b01db1cd88d6b47'},
+    {'untrusted-0.9.0.tar.gz': '8ecb6da28b8a351d773b68d5825ac39017e680750f980f3a1a85cd8dd28a47c1'},
+    {'ureq-2.9.6.tar.gz': '11f214ce18d8b2cbe84ed3aa6486ed3f5b285cf8d8fbdbce9f3f767a724adc35'},
+    {'url-2.5.0.tar.gz': '31e6302e3bb753d46e83516cae55ae196fc0c309407cf11ab35cc51a4c2a4633'},
+    {'urlencoding-2.1.3.tar.gz': 'daf8dba3b7eb870caf1ddeed7bc9d2a049f3cfdfae7cb521b087cc33ae4c49da'},
+    {'utf8parse-0.2.1.tar.gz': '711b9620af191e0cdc7468a8d14e709c3dcdb115b36f838e601583af800a370a'},
+    {'uuid-1.7.0.tar.gz': 'f00cc9702ca12d3c81455259621e676d0f7251cec66a21e98fe2e9a37db93b2a'},
+    {'valuable-0.1.0.tar.gz': '830b7e5d4d90034032940e4ace0d9a9a057e7a45cd94e6c007832e39edb82f6d'},
+    {'vcpkg-0.2.15.tar.gz': 'accd4ea62f7bb7a82fe23066fb0957d48ef677f6eeb8215f372f52e48bb32426'},
+    {'version_check-0.9.4.tar.gz': '49874b5167b65d7193b8aba1567f5c7d93d001cafc34600cee003eda787e483f'},
+    {'versions-5.0.1.tar.gz': 'c73a36bc44e3039f51fbee93e39f41225f6b17b380eb70cc2aab942df06b34dd'},
+    {'wait-timeout-0.2.0.tar.gz': '9f200f5b12eb75f8c1ed65abd4b2db8a6e1b138a20de009dacee265a2498f3f6'},
+    {'walkdir-2.4.0.tar.gz': 'd71d857dc86794ca4c280d616f7da00d2dbfd8cd788846559a6813e6aa4b54ee'},
+    {'wasi-0.11.0+wasi-snapshot-preview1.tar.gz': '9c8d87e72b64a3b4db28d11ce29237c246188f4f51057d65a7eab63b7987e423'},
+    {'webpki-roots-0.26.0.tar.gz': '0de2cfda980f21be5a7ed2eadb3e6fe074d56022bea2cdeb1a62eb220fc04188'},
+    {'which-5.0.0.tar.gz': '9bf3ea8596f3a0dd5980b46430f2058dfe2c36a27ccfbb1845d6fbfcd9ba6e14'},
+    {'which-6.0.0.tar.gz': '7fa5e0c10bf77f44aac573e498d1a82d5fbd5e91f6fc0a99e7be4b38e85e101c'},
+    {'wild-2.2.1.tar.gz': 'a3131afc8c575281e1e80f36ed6a092aa502c08b18ed7524e86fbbb12bb410e1'},
+    {'winapi-0.3.9.tar.gz': '5c839a674fcd7a98952e593242ea400abe93992746761e38641405d28b00f419'},
+    {'winapi-i686-pc-windows-gnu-0.4.0.tar.gz': 'ac3b87c63620426dd9b991e5ce0329eff545bccbbb34f3be09ff6fb6ab51b7b6'},
+    {'winapi-util-0.1.6.tar.gz': 'f29e6f9198ba0d26b4c9f07dbe6f9ed633e1f3d5b8b414090084349e46a52596'},
+    {'winapi-x86_64-pc-windows-gnu-0.4.0.tar.gz': '712e227841d057c1ee1cd2fb22fa7e5a5461ae8e48fa2ca79ec42cfc1931183f'},
+    {'windows-sys-0.48.0.tar.gz': '677d2418bec65e3338edb076e806bc1ec15693c5d0104683f2efe857f61056a9'},
+    {'windows-sys-0.52.0.tar.gz': '282be5f36a8ce781fad8c8ae18fa3f9beff57ec1b52cb3de0789201425d9a33d'},
+    {'windows-targets-0.48.5.tar.gz': '9a2fa6e2155d7247be68c096456083145c183cbbbc2764150dda45a87197940c'},
+    {'windows-targets-0.52.0.tar.gz': '8a18201040b24831fbb9e4eb208f8892e1f50a37feb53cc7ff887feb8f50e7cd'},
+    {'windows_aarch64_gnullvm-0.48.5.tar.gz': '2b38e32f0abccf9987a4e3079dfb67dcd799fb61361e53e2882c3cbaf0d905d8'},
+    {'windows_aarch64_gnullvm-0.52.0.tar.gz': 'cb7764e35d4db8a7921e09562a0304bf2f93e0a51bfccee0bd0bb0b666b015ea'},
+    {'windows_aarch64_msvc-0.48.5.tar.gz': 'dc35310971f3b2dbbf3f0690a219f40e2d9afcf64f9ab7cc1be722937c26b4bc'},
+    {'windows_aarch64_msvc-0.52.0.tar.gz': 'bbaa0368d4f1d2aaefc55b6fcfee13f41544ddf36801e793edbbfd7d7df075ef'},
+    {'windows_i686_gnu-0.48.5.tar.gz': 'a75915e7def60c94dcef72200b9a8e58e5091744960da64ec734a6c6e9b3743e'},
+    {'windows_i686_gnu-0.52.0.tar.gz': 'a28637cb1fa3560a16915793afb20081aba2c92ee8af57b4d5f28e4b3e7df313'},
+    {'windows_i686_msvc-0.48.5.tar.gz': '8f55c233f70c4b27f66c523580f78f1004e8b5a8b659e05a4eb49d4166cca406'},
+    {'windows_i686_msvc-0.52.0.tar.gz': 'ffe5e8e31046ce6230cc7215707b816e339ff4d4d67c65dffa206fd0f7aa7b9a'},
+    {'windows_x86_64_gnu-0.48.5.tar.gz': '53d40abd2583d23e4718fddf1ebec84dbff8381c07cae67ff7768bbf19c6718e'},
+    {'windows_x86_64_gnu-0.52.0.tar.gz': '3d6fa32db2bc4a2f5abeacf2b69f7992cd09dca97498da74a151a3132c26befd'},
+    {'windows_x86_64_gnullvm-0.48.5.tar.gz': '0b7b52767868a23d5bab768e390dc5f5c55825b6d30b86c844ff2dc7414044cc'},
+    {'windows_x86_64_gnullvm-0.52.0.tar.gz': '1a657e1e9d3f514745a572a6846d3c7aa7dbe1658c056ed9c3344c4109a6949e'},
+    {'windows_x86_64_msvc-0.48.5.tar.gz': 'ed94fce61571a4006852b7389a063ab983c02eb1bb37b47f8272ce92d06d9538'},
+    {'windows_x86_64_msvc-0.52.0.tar.gz': 'dff9641d1cd4be8d1a070daf9e3773c5f67e78b4d9d42263020c057706765c04'},
+    {'winnow-0.6.2.tar.gz': '7a4191c47f15cc3ec71fcb4913cb83d58def65dd3787610213c649283b5ce178'},
+    {'xattr-1.3.1.tar.gz': '8da84f1a25939b27f6820d92aed108f83ff920fdf11a7b19366c27c4cda81d4f'},
+    {'xwin-0.5.0.tar.gz': 'c43e0202f5457b48558096cb7b36d0e473f267551a89c82ed72d73b01dfd4007'},
+    {'yansi-0.5.1.tar.gz': '09041cd90cf85f7f8b2df60c646f853b7f535ce68f85244eb6731cf89fa498ec'},
+    {'zerocopy-0.7.32.tar.gz': '74d4d3961e53fa4c9a25a8637fc2bfaf2595b3d3ae34875568a5cf64787716be'},
+    {'zerocopy-derive-0.7.32.tar.gz': '9ce1b18ccd8e73a9321186f97e46f9f04b778851177567b1975109d26a08d2a6'},
+    {'zeroize-1.7.0.tar.gz': '525b4ec142c6b68a2d10f01f7bbf6755599ca3f81ea53b8431b7dd348f5fdb2d'},
+    {'zip-0.6.6.tar.gz': '760394e246e4c28189f19d488c058bf16f564016aefac5d32bb1f3b51d5e9261'},
+]
+
+builddependencies = [
+    ('binutils', '2.42'),
+    ('setuptools-rust', '1.9.0'),
+]
+dependencies = [
+    ('Python', '3.12.3'),
+    ('Rust', '1.78.0'),
+]
+
+download_dep_fail = True
+sanity_pip_check = True
+use_pip = True
+
+moduleclass = 'tools'
diff --git a/easybuild/easyconfigs/p/poetry/poetry-1.8.3-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/poetry/poetry-1.8.3-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..0133ca0a75b
--- /dev/null
+++ b/easybuild/easyconfigs/p/poetry/poetry-1.8.3-GCCcore-13.3.0.eb
@@ -0,0 +1,179 @@
+easyblock = 'PythonBundle'
+
+name = 'poetry'
+version = '1.8.3'
+
+homepage = 'https://python-poetry.org'
+description = """Python packaging and dependency management made easy. Poetry helps you declare, manage and install
+ dependencies of Python projects, ensuring you have the right stack everywhere."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+builddependencies = [
+    ('binutils', '2.42'),
+    ('pkgconf', '2.2.0'),
+    ('scikit-build', '0.17.6'),
+    ('Rust', '1.78.0'),
+    ('setuptools-rust', '1.9.0'),
+    ('maturin', '1.6.0'),
+]
+
+dependencies = [
+    ('Python', '3.12.3'),
+    ('hatchling', '1.24.2'),
+    ('cryptography', '42.0.8'),
+    ('virtualenv', '20.26.2'),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    ('six', '1.16.0', {
+        'checksums': ['1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926'],
+    }),
+    ('idna', '3.7', {
+        'checksums': ['028ff3aadf0609c1fd278d8ea3089299412a7a8b9bd005dd08b9f8285bcb5cfc'],
+    }),
+    ('certifi', '2024.6.2', {
+        'checksums': ['3cd43f1c6fa7dedc5899d69d3ad0398fd018ad1a17fba83ddaf78aa46c747516'],
+    }),
+    ('urllib3', '2.2.1', {
+        'checksums': ['d0570876c61ab9e520d776c38acbbb5b05a776d3f9ff98a5c8fd5162a444cf19'],
+    }),
+    ('charset-normalizer', '3.3.2', {
+        'checksums': ['f30c3cb33b24454a82faecaf01b19c18562b1e89558fb6c56de4d9118a032fd5'],
+    }),
+    ('dulwich', '0.21.7', {
+        'checksums': ['a9e9c66833cea580c3ac12927e4b9711985d76afca98da971405d414de60e968'],
+    }),
+    ('crashtest', '0.4.1', {
+        'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl',
+        'checksums': ['8d23eac5fa660409f57472e3851dab7ac18aba459a8d19cbbba86d3d5aecd2a5'],
+    }),
+    ('zipp', '3.19.2', {
+        'checksums': ['bf1dcf6450f873a13e952a29504887c89e6de7506209e5b1bcc3460135d4de19'],
+    }),
+    ('importlib-metadata', '7.1.0', {
+        'sources': ['importlib_metadata-%(version)s.tar.gz'],
+        'checksums': ['b78938b926ee8d5f020fc4772d487045805a55ddbad2ecf21c6d60938dc7fcd2'],
+    }),
+    ('jeepney', '0.8.0', {
+        'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl',
+        'checksums': ['c0a454ad016ca575060802ee4d590dd912e35c122fa04e70306de3d076cce755'],
+    }),
+    ('SecretStorage', '3.3.3', {
+        'checksums': ['2403533ef369eca6d2ba81718576c5e0f564d5cca1b58f73a8b23e7d4eeebd77'],
+    }),
+    ('more-itertools', '10.3.0', {
+        'checksums': ['e5d93ef411224fbcef366a6e8ddc4c5781bc6359d43412a65dd5964e46111463'],
+    }),
+    ('jaraco.classes', '3.4.0', {
+        'checksums': ['47a024b51d0239c0dd8c8540c6c7f484be3b8fcf0b2d85c13825780d3b3f3acd'],
+    }),
+    ('keyring', '24.3.1', {
+        'modulename': False,
+        'checksums': ['c3327b6ffafc0e8befbdb597cacdb4928ffe5c1212f7645f186e6d9957a898db'],
+    }),
+    ('pyproject-hooks', '1.1.0', {
+        'sources': ['pyproject_hooks-%(version)s.tar.gz'],
+        'checksums': ['4b37730834edbd6bd37f26ece6b44802fb1c1ee2ece0e54ddff8bfc06db86965'],
+    }),
+    ('build', '1.2.1', {
+        'checksums': ['526263f4870c26f26c433545579475377b2b7588b6f1eac76a001e873ae3e19d'],
+    }),
+    ('installer', '0.7.0', {
+        'checksums': ['a26d3e3116289bb08216e0d0f7d925fcef0b0194eedfa0c944bcaaa106c4b631'],
+    }),
+    ('webencodings', '0.5.1', {
+        'checksums': ['b36a1c245f2d304965eb4e0a82848379241dc04b865afcc4aab16748587e1923'],
+    }),
+    ('html5lib', '1.1', {
+        'checksums': ['b2e5b40261e20f354d198eae92afc10d750afb487ed5e50f9c4eaf07c184146f'],
+    }),
+    ('rapidfuzz', '3.9.3', {
+        'checksums': ['b398ea66e8ed50451bce5997c430197d5e4b06ac4aa74602717f792d8d8d06e2'],
+    }),
+    ('cleo', '2.1.0', {
+        'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl',
+        'checksums': ['4a31bd4dd45695a64ee3c4758f583f134267c2bc518d8ae9a29cf237d009b07e'],
+    }),
+    ('attrs', '23.2.0', {
+        'modulename': 'attr',
+        'checksums': ['935dc3b529c262f6cf76e50877d35a4bd3c1de194fd41f47a2b7ae8f19971f30'],
+    }),
+    ('pyrsistent', '0.20.0', {
+        'checksums': ['4c48f78f62ab596c679086084d0dd13254ae4f3d6c72a83ffdf5ebdef8f265a4'],
+    }),
+    ('requests-toolbelt', '1.0.0', {
+        'checksums': ['7681a0a3d047012b5bdc0ee37d7f8f07ebe76ab08caeccfc3921ce23c88d5bc6'],
+    }),
+    ('pkginfo', '1.11.1', {
+        'checksums': ['2e0dca1cf4c8e39644eed32408ea9966ee15e0d324c62ba899a393b3c6b467aa'],
+    }),
+    ('ptyprocess', '0.7.0', {
+        'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl',
+        'checksums': ['4b41f3967fce3af57cc7e94b888626c18bf37a083e3651ca8feeb66d492fef35'],
+    }),
+    ('pexpect', '4.9.0', {
+        'checksums': ['ee7d41123f3c9911050ea2c2dac107568dc43b2d3b0c7557a33212c398ead30f'],
+    }),
+    ('jsonschema-specifications', '2023.12.1', {
+        'sources': ['jsonschema_specifications-%(version)s.tar.gz'],
+        'checksums': ['48a76787b3e70f5ed53f1160d2b81f586e4ca6d1548c5de7085d1682674764cc'],
+    }),
+    ('referencing', '0.35.1', {
+        'checksums': ['25b42124a6c8b632a425174f24087783efb348a6f1e0008e63cd4466fedf703c'],
+    }),
+    ('rpds-py', '0.18.1', {
+        'sources': ['rpds_py-%(version)s.tar.gz'],
+        'checksums': ['dc48b479d540770c811fbd1eb9ba2bb66951863e448efec2e2c102625328e92f'],
+        'modulename': 'rpds',
+    }),
+    ('jsonschema', '4.22.0', {
+        'checksums': ['5b22d434a45935119af990552c862e5d6d564e8f6601206b305a61fdf661a2b7'],
+    }),
+    ('platformdirs', '4.2.2', {
+        'checksums': ['38b7b51f512eed9e84a22788b4bce1de17c0adb134d6becb09836e37d8654cd3'],
+    }),
+    ('shellingham', '1.5.4', {
+        'checksums': ['8dbca0739d487e5bd35ab3ca4b36e11c4078f3a234bfce294b0a0291363404de'],
+    }),
+    ('tomlkit', '0.12.5', {
+        'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl',
+        'checksums': ['af914f5a9c59ed9d0762c7b64d3b5d5df007448eb9cd2edc8a46b1eafead172f'],
+    }),
+    ('requests', '2.32.3', {
+        'checksums': ['55365417734eb18255590a9ff9eb97e9e1da868d4ccd6402399eaf68af20a760'],
+    }),
+    ('msgpack', '1.0.8', {
+        'checksums': ['95c02b0e27e706e48d0e5426d1710ca78e0f0628d6e89d5b5a5b91a5f12274f3'],
+    }),
+    ('CacheControl', '0.14.0', {
+        'sources': ['cachecontrol-%(version)s.tar.gz'],
+        'checksums': ['7db1195b41c81f8274a7bbd97c956f44e8348265a1bc7641c37dfebc39f0c938'],
+    }),
+    ('lockfile', '0.12.2', {
+        'checksums': ['6aed02de03cba24efabcd600b30540140634fc06cfa603822d508d5361e9f799'],
+    }),
+    ('poetry-core', '1.9.0', {
+        'modulename': 'poetry.core',
+        'sources': ['poetry_core-%(version)s.tar.gz'],
+        'checksums': ['fa7a4001eae8aa572ee84f35feb510b321bd652e5cf9293249d62853e1f935a2'],
+    }),
+    ('poetry-plugin-export', '1.8.0', {
+        'sources': ['poetry_plugin_export-%(version)s.tar.gz'],
+        'checksums': ['1fa6168a85d59395d835ca564bc19862a7c76061e60c3e7dfaec70d50937fc61'],
+    }),
+    ('fastjsonschema', '2.19.1'),
+    (name, version, {
+        'checksums': ['67f4eb68288eab41e841cc71a00d26cf6bdda9533022d0189a145a34d0a35f48'],
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['bin/%(namelower)s'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'],
+}
+
+moduleclass = 'tools'
diff --git a/easybuild/easyconfigs/s/scikit-build/scikit-build-0.17.6-GCCcore-13.3.0.eb b/easybuild/easyconfigs/s/scikit-build/scikit-build-0.17.6-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..2d799810ee1
--- /dev/null
+++ b/easybuild/easyconfigs/s/scikit-build/scikit-build-0.17.6-GCCcore-13.3.0.eb
@@ -0,0 +1,38 @@
+easyblock = 'PythonBundle'
+
+name = 'scikit-build'
+version = '0.17.6'
+
+homepage = 'https://scikit-build.readthedocs.io/en/latest'
+description = """Scikit-Build, or skbuild, is an improved build system generator
+for CPython C/C++/Fortran/Cython extensions."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+builddependencies = [
+    ('binutils', '2.42'),
+    ('hatchling', '1.24.2'),
+]
+
+dependencies = [
+    ('Python', '3.12.3'),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    ('packaging', '23.1', {
+        'checksums': ['a392980d2b6cffa644431898be54b0045151319d1e7ec34f0cfed48767dd334f'],
+    }),
+    ('distro', '1.8.0', {
+        'checksums': ['02e111d1dc6a50abb8eed6bf31c3e48ed8b0830d1ea2a1b78c61765c2513fdd8'],
+    }),
+    (name, version, {
+        'modulename': 'skbuild',
+        'sources': ['scikit_build-%(version)s.tar.gz'],
+        'checksums': ['b51a51a36b37c42650994b5047912f59b22e3210b23e321f287611f9ef6e5c9d'],
+    }),
+]
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/s/setuptools-rust/setuptools-rust-1.9.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/s/setuptools-rust/setuptools-rust-1.9.0-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..a8ad0dc7ee9
--- /dev/null
+++ b/easybuild/easyconfigs/s/setuptools-rust/setuptools-rust-1.9.0-GCCcore-13.3.0.eb
@@ -0,0 +1,41 @@
+easyblock = 'PythonBundle'
+
+name = 'setuptools-rust'
+version = '1.9.0'
+
+homepage = 'https://github.com/PyO3/setuptools-rust'
+description = """setuptools-rust is a plugin for setuptools to build Rust Python extensions
+implemented with PyO3 or rust-cpython."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+toolchainopts = {'pic': True}
+
+builddependencies = [
+    ('binutils', '2.42'),
+]
+
+dependencies = [
+    ('Python', '3.12.3'),
+]
+
+exts_default_options = {
+    'download_dep_fail': True,
+    'sanity_pip_check': True,
+    'use_pip': True,
+}
+
+exts_list = [
+    ('typing-extensions', '4.12.2', {
+        'sources': ['typing_extensions-%(version)s.tar.gz'],
+        'checksums': ['1a7ead55c7e559dd4dee8856e3a88b41225abfe1ce8df57b7c13915fe121ffb8'],
+    }),
+    ('semantic-version', '2.10.0', {
+        'sources': ['semantic_version-%(version)s.tar.gz'],
+        'checksums': ['bdabb6d336998cbb378d4b9db3a4b56a1e3235701dc05ea2690d9a997ed5041c'],
+    }),
+    (name, version, {
+        'checksums': ['704df0948f2e4cc60c2596ad6e840ea679f4f43e58ed4ad0c1857807240eab96'],
+    }),
+]
+
+moduleclass = 'tools'
diff --git a/easybuild/easyconfigs/v/virtualenv/virtualenv-20.26.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/v/virtualenv/virtualenv-20.26.2-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..9c6a84c5304
--- /dev/null
+++ b/easybuild/easyconfigs/v/virtualenv/virtualenv-20.26.2-GCCcore-13.3.0.eb
@@ -0,0 +1,49 @@
+easyblock = 'PythonBundle'
+
+name = 'virtualenv'
+version = '20.26.2'
+
+homepage = 'https://github.com/pypa/virtualenv'
+description = "A tool for creating isolated virtual python environments."
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+toolchainopts = {'pic': True}
+
+builddependencies = [
+    ('binutils', '2.42'),
+    ('hatchling', '1.24.2'),
+]
+
+dependencies = [
+    ('Python', '3.12.3'),
+]
+
+exts_default_options = {
+    'download_dep_fail': True,
+    'sanity_pip_check': True,
+    'use_pip': True,
+}
+
+exts_list = [
+    ('distlib', '0.3.8', {
+        'checksums': ['1530ea13e350031b6312d8580ddb6b27a104275a31106523b8f123787f494f64'],
+    }),
+    ('filelock', '3.15.1', {
+        'checksums': ['58a2549afdf9e02e10720eaa4d4470f56386d7a6f72edd7d0596337af8ed7ad8'],
+    }),
+    ('platformdirs', '4.2.2', {
+        'checksums': ['38b7b51f512eed9e84a22788b4bce1de17c0adb134d6becb09836e37d8654cd3'],
+    }),
+    (name, version, {
+        'checksums': ['82bf0f4eebbb78d36ddaee0283d43fe5736b53880b8a8cdcd37390a07ac3741c'],
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['bin/%(namelower)s'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'],
+}
+
+sanity_check_commands = ["virtualenv --help"]
+
+moduleclass = 'tools'

From d01ab909d764948b940387f1d1424520a23d6ff3 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 14 Jun 2024 18:37:42 +0200
Subject: [PATCH 225/835] adding easyconfigs:
 Python-bundle-PyPI-2024.06-GCCcore-13.3.0.eb, flit-3.9.0-GCCcore-13.3.0.eb

---
 .../f/flit/flit-3.9.0-GCCcore-13.3.0.eb       |  75 +++
 ...thon-bundle-PyPI-2024.06-GCCcore-13.3.0.eb | 503 ++++++++++++++++++
 2 files changed, 578 insertions(+)
 create mode 100644 easybuild/easyconfigs/f/flit/flit-3.9.0-GCCcore-13.3.0.eb
 create mode 100644 easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2024.06-GCCcore-13.3.0.eb

diff --git a/easybuild/easyconfigs/f/flit/flit-3.9.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/f/flit/flit-3.9.0-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..ddc99b99a37
--- /dev/null
+++ b/easybuild/easyconfigs/f/flit/flit-3.9.0-GCCcore-13.3.0.eb
@@ -0,0 +1,75 @@
+easyblock = 'PythonBundle'
+
+name = 'flit'
+version = '3.9.0'
+
+homepage = 'https://github.com/pypa/flit'
+description = "A simple packaging tool for simple packages."
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+toolchainopts = {'pic': True}
+
+builddependencies = [
+    ('binutils', '2.42'),
+    ('hatchling', '1.24.2'),
+]
+
+dependencies = [
+    ('Python', '3.12.3'),
+]
+
+exts_default_options = {
+    'download_dep_fail': True,
+    'sanity_pip_check': True,
+    'use_pip': True,
+}
+
+exts_list = [
+    ('idna', '3.7', {
+        'checksums': ['028ff3aadf0609c1fd278d8ea3089299412a7a8b9bd005dd08b9f8285bcb5cfc'],
+    }),
+    ('certifi', '2024.6.2', {
+        'checksums': ['3cd43f1c6fa7dedc5899d69d3ad0398fd018ad1a17fba83ddaf78aa46c747516'],
+    }),
+    ('urllib3', '2.2.1', {
+        'checksums': ['d0570876c61ab9e520d776c38acbbb5b05a776d3f9ff98a5c8fd5162a444cf19'],
+    }),
+    ('charset-normalizer', '3.3.2', {
+        'checksums': ['f30c3cb33b24454a82faecaf01b19c18562b1e89558fb6c56de4d9118a032fd5'],
+    }),
+    ('packaging', '24.1', {
+        'checksums': ['026ed72c8ed3fcce5bf8950572258698927fd1dbda10a5e981cdf0ac37f4f002'],
+    }),
+    ('setuptools-scm', '8.1.0', {
+        'sources': ['setuptools_scm-%(version)s.tar.gz'],
+        'checksums': ['42dea1b65771cba93b7a515d65a65d8246e560768a66b9106a592c8e7f26c8a7'],
+    }),
+    ('typing-extensions', '4.12.2', {
+        'sources': ['typing_extensions-%(version)s.tar.gz'],
+        'checksums': ['1a7ead55c7e559dd4dee8856e3a88b41225abfe1ce8df57b7c13915fe121ffb8'],
+    }),
+    ('flit-scm', '1.7.0', {
+        'sources': ['flit_scm-%(version)s.tar.gz'],
+        'checksums': ['961bd6fb24f31bba75333c234145fff88e6de0a90fc0f7e5e7c79deca69f6bb2'],
+    }),
+    ('requests', '2.32.3', {
+        'checksums': ['55365417734eb18255590a9ff9eb97e9e1da868d4ccd6402399eaf68af20a760'],
+    }),
+    ('docutils', '0.21.2', {
+        'checksums': ['3a6b18732edf182daa3cd12775bbb338cf5691468f91eeeb109deff6ebfa986f'],
+    }),
+    ('tomli-w', '1.0.0', {
+        'sources': ['tomli_w-%(version)s.tar.gz'],
+        'checksums': ['f463434305e0336248cac9c2dc8076b707d8a12d019dd349f5c1e382dd1ae1b9'],
+    }),
+    (name, version, {
+        'checksums': ['d75edf5eb324da20d53570a6a6f87f51e606eee8384925cd66a90611140844c7'],
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['bin/%(namelower)s'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'],
+}
+
+moduleclass = 'tools'
diff --git a/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2024.06-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2024.06-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..add89b7ae32
--- /dev/null
+++ b/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2024.06-GCCcore-13.3.0.eb
@@ -0,0 +1,503 @@
+easyblock = 'PythonBundle'
+
+name = 'Python-bundle-PyPI'
+version = '2024.06'
+
+homepage = 'https://python.org/'
+description = "Bundle of Python packages from PyPI"
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+toolchainopts = {'pic': True}
+
+builddependencies = [
+    ('binutils', '2.42'),
+    ('UnZip', '6.0'),
+    ('pkgconf', '2.2.0'),
+    ('git', '2.45.1'),  # required for pbr
+    ('hatchling', '1.24.2'),
+    ('poetry', '1.8.3'),
+    ('scikit-build', '0.17.6'),
+    ('flit', '3.9.0'),
+    ('setuptools-rust', '1.9.0'),  # required for dulwich
+    ('maturin', '1.6.0'),  # required for rpds-py
+]
+
+dependencies = [
+    ('Python', '3.12.3'),
+    ('cryptography', '42.0.8'),
+    ('virtualenv', '20.26.2'),
+]
+
+exts_default_options = {
+    'download_dep_fail': True,
+    'sanity_pip_check': True,
+    'use_pip': True,
+}
+
+# order is important!
+# package versions updated 2024-06-14
+exts_list = [
+    ('blist', '1.3.6', {
+        'patches': [
+            'Python-3_9-blist-1.3.6-fix-undefined_symbol_PyObject_GC_IS_TRACKED.patch',
+            'Python-3.10-bist-1.3.6-compatibility.patch',
+            'Python-3.11-bist-1.3.6-compatibility.patch',
+        ],
+        'checksums': [
+            {'blist-1.3.6.tar.gz': '3a12c450b001bdf895b30ae818d4d6d3f1552096b8c995f0fe0c74bef04d1fc3'},
+            {'Python-3_9-blist-1.3.6-fix-undefined_symbol_PyObject_GC_IS_TRACKED.patch':
+             '18a643d1d1565b05df7dcc9a612a86dcf7b3b352435032f6425a61b597f911d0'},
+            {'Python-3.10-bist-1.3.6-compatibility.patch':
+             '0fb2d92e06b2c39bfc79e229e6fde6053f9aa9538733029377c9a743650a4741'},
+            {'Python-3.11-bist-1.3.6-compatibility.patch':
+             'da283300bc5f0524b9982c9d9de4670908711634667849d3d81ccd87fc82c4ee'},
+        ],
+    }),
+    ('pbr', '6.0.0', {
+        'checksums': ['d1377122a5a00e2f940ee482999518efe16d745d423a670c27773dfbc3c9a7d9'],
+    }),
+    ('Cython', '3.0.10', {
+        'checksums': ['dcc96739331fb854dcf503f94607576cfe8488066c61ca50dfd55836f132de99'],
+    }),
+    ('six', '1.16.0', {
+        'checksums': ['1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926'],
+    }),
+    ('toml', '0.10.2', {
+        'checksums': ['b3bda1d108d5dd99f4a20d24d9c348e91c4db7ab1b749200bded2f839ccbe68f'],
+    }),
+    ('tomli', '2.0.1', {
+        'checksums': ['de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f'],
+    }),
+    ('packaging', '24.1', {
+        'checksums': ['026ed72c8ed3fcce5bf8950572258698927fd1dbda10a5e981cdf0ac37f4f002'],
+    }),
+    ('python-dateutil', '2.9.0.post0', {
+        'modulename': 'dateutil',
+        'checksums': ['37dd54208da7e1cd875388217d5e00ebd4179249f90fb72437e91a35459a0ad3'],
+    }),
+    ('decorator', '5.1.1', {
+        'checksums': ['637996211036b6385ef91435e4fae22989472f9d571faba8927ba8253acbc330'],
+    }),
+    ('liac-arff', '2.5.0', {
+        'modulename': 'arff',
+        'checksums': ['3220d0af6487c5aa71b47579be7ad1d94f3849ff1e224af3bf05ad49a0b5c4da'],
+    }),
+    ('pycryptodome', '3.20.0', {
+        'modulename': 'Crypto.PublicKey.RSA',
+        'checksums': ['09609209ed7de61c2b560cc5c8c4fbf892f8b15b1faf7e4cbffac97db1fffda7'],
+    }),
+    ('ecdsa', '0.19.0', {
+        'checksums': ['60eaad1199659900dd0af521ed462b793bbdf867432b3948e87416ae4caf6bf8'],
+    }),
+    ('ipaddress', '1.0.23', {
+        'checksums': ['b7f8e0369580bb4a24d5ba1d7cc29660a4a6987763faf1d8a8046830e020e7e2'],
+    }),
+    ('asn1crypto', '1.5.1', {
+        'checksums': ['13ae38502be632115abf8a24cbe5f4da52e3b5231990aff31123c805306ccb9c'],
+    }),
+    ('idna', '3.7', {
+        'checksums': ['028ff3aadf0609c1fd278d8ea3089299412a7a8b9bd005dd08b9f8285bcb5cfc'],
+    }),
+    ('pycparser', '2.22', {
+        'checksums': ['491c8be9c040f5390f5bf44a5b07752bd07f56edf992381b05c701439eec10f6'],
+    }),
+    ('cffi', '1.16.0', {
+        'checksums': ['bcb3ef43e58665bbda2fb198698fcae6776483e0c4a631aa5647806c25e02cc0'],
+    }),
+    ('semantic-version', '2.10.0', {
+        'sources': ['semantic_version-%(version)s.tar.gz'],
+        'checksums': ['bdabb6d336998cbb378d4b9db3a4b56a1e3235701dc05ea2690d9a997ed5041c'],
+    }),
+    ('pyasn1', '0.6.0', {
+        'checksums': ['3a35ab2c4b5ef98e17dfdec8ab074046fbda76e281c5a706ccd82328cfc8f64c'],
+    }),
+    ('PyNaCl', '1.5.0', {
+        'modulename': 'nacl',
+        'checksums': ['8ac7448f09ab85811607bdd21ec2464495ac8b7c66d146bf545b0f08fb9220ba'],
+    }),
+    ('pyparsing', '3.1.2', {
+        'checksums': ['a1bac0ce561155ecc3ed78ca94d3c9378656ad4c94c1270de543f621420f94ad'],
+    }),
+    ('netifaces', '0.11.0', {
+        'checksums': ['043a79146eb2907edf439899f262b3dfe41717d34124298ed281139a8b93ca32'],
+    }),
+    ('netaddr', '1.3.0', {
+        'checksums': ['5c3c3d9895b551b763779ba7db7a03487dc1f8e3b385af819af341ae9ef6e48a'],
+    }),
+    ('mock', '5.1.0', {
+        'checksums': ['5e96aad5ccda4718e0a229ed94b2024df75cc2d55575ba5762d31f5767b8767d'],
+    }),
+    ('pytz', '2024.1', {
+        'checksums': ['2a29735ea9c18baf14b448846bde5a48030ed267578472d8955cd0e7443a9812'],
+    }),
+    ('bitarray', '2.9.2', {
+        'checksums': ['a8f286a51a32323715d77755ed959f94bef13972e9a2fe71b609e40e6d27957e'],
+    }),
+    ('bitstring', '4.2.3', {
+        'checksums': ['e0c447af3fda0d114f77b88c2d199f02f97ee7e957e6d719f40f41cf15fbb897'],
+    }),
+    ('appdirs', '1.4.4', {
+        'checksums': ['7d5d0167b2b1ba821647616af46a749d1c653740dd0d2415100fe26e27afdf41'],
+    }),
+    ('distlib', '0.3.8', {
+        'checksums': ['1530ea13e350031b6312d8580ddb6b27a104275a31106523b8f123787f494f64'],
+    }),
+    ('zipp', '3.19.2', {
+        'checksums': ['bf1dcf6450f873a13e952a29504887c89e6de7506209e5b1bcc3460135d4de19'],
+    }),
+    ('importlib-metadata', '7.1.0', {
+        'sources': ['importlib_metadata-%(version)s.tar.gz'],
+        'checksums': ['b78938b926ee8d5f020fc4772d487045805a55ddbad2ecf21c6d60938dc7fcd2'],
+    }),
+    ('backports.entry-points-selectable', '1.3.0', {
+        'sources': ['backports.entry_points_selectable-%(version)s.tar.gz'],
+        'checksums': ['17a8b44ae700fba548686dd274ddc91c060371565cd63806c20a1d33911746e6'],
+    }),
+    ('pathspec', '0.12.1', {
+        'checksums': ['a482d51503a1ab33b1c67a6c3813a26953dbdc71c31dacaef9a838c4e29f5712'],
+    }),
+    ('pluggy', '1.5.0', {
+        'checksums': ['2cffa88e94fdc978c4c574f15f9e59b7f4201d439195c3715ca9e2486f1d0cf1'],
+    }),
+    ('editables', '0.5', {
+        'checksums': ['309627d9b5c4adc0e668d8c6fa7bac1ba7c8c5d415c2d27f60f081f8e80d1de2'],
+    }),
+    ('filelock', '3.15.1', {
+        'checksums': ['58a2549afdf9e02e10720eaa4d4470f56386d7a6f72edd7d0596337af8ed7ad8'],
+    }),
+    ('platformdirs', '4.2.2', {
+        'checksums': ['38b7b51f512eed9e84a22788b4bce1de17c0adb134d6becb09836e37d8654cd3'],
+    }),
+    ('scandir', '1.10.0', {
+        'checksums': ['4d4631f6062e658e9007ab3149a9b914f3548cb38bfb021c64f39a025ce578ae'],
+    }),
+    ('pathlib2', '2.3.7.post1', {
+        'checksums': ['9fe0edad898b83c0c3e199c842b27ed216645d2e177757b2dd67384d4113c641'],
+    }),
+    ('importlib-resources', '6.4.0', {
+        'sources': ['importlib_resources-%(version)s.tar.gz'],
+        'checksums': ['cdb2b453b8046ca4e3798eb1d84f3cce1446a0e8e7b5ef4efb600f19fc398145'],
+    }),
+    ('docopt', '0.6.2', {
+        'checksums': ['49b3a825280bd66b3aa83585ef59c4a8c82f2c8a522dbe754a8bc8d08c85c491'],
+    }),
+    ('joblib', '1.4.2', {
+        'checksums': ['2382c5816b2636fbd20a09e0f4e9dad4736765fdfb7dca582943b9c1366b3f0e'],
+    }),
+    ('chardet', '5.2.0', {
+        'checksums': ['1b3b6ff479a8c414bc3fa2c0852995695c4a026dcd6d0633b2dd092ca39c1cf7'],
+    }),
+    ('certifi', '2024.6.2', {
+        'checksums': ['3cd43f1c6fa7dedc5899d69d3ad0398fd018ad1a17fba83ddaf78aa46c747516'],
+    }),
+    ('urllib3', '2.2.1', {
+        'checksums': ['d0570876c61ab9e520d776c38acbbb5b05a776d3f9ff98a5c8fd5162a444cf19'],
+    }),
+    ('charset-normalizer', '3.3.2', {
+        'checksums': ['f30c3cb33b24454a82faecaf01b19c18562b1e89558fb6c56de4d9118a032fd5'],
+    }),
+    ('requests', '2.32.3', {
+        'checksums': ['55365417734eb18255590a9ff9eb97e9e1da868d4ccd6402399eaf68af20a760'],
+    }),
+    ('xlrd', '2.0.1', {
+        'checksums': ['f72f148f54442c6b056bf931dbc34f986fd0c3b0b6b5a58d013c9aef274d0c88'],
+    }),
+    ('py-expression-eval', '0.3.14', {
+        'sources': ['py_expression_eval-%(version)s.tar.gz'],
+        'checksums': ['ea60f9404a18346d5a63854db21c50666dfb4274ae111000165b31c6f8ab93f1'],
+    }),
+    ('tabulate', '0.9.0', {
+        'checksums': ['0095b12bf5966de529c0feb1fa08671671b3368eec77d7ef7ab114be2c068b3c'],
+    }),
+    ('ujson', '5.10.0', {
+        'checksums': ['b3cd8f3c5d8c7738257f1018880444f7b7d9b66232c64649f562d7ba86ad4bc1'],
+    }),
+    ('atomicwrites', '1.4.1', {
+        'checksums': ['81b2c9071a49367a7f770170e5eec8cb66567cfbbc8c73d20ce5ca4a8d71cf11'],
+    }),
+    ('py', '1.11.0', {
+        'checksums': ['51c75c4126074b472f746a24399ad32f6053d1b34b68d2fa41e558e6f4a98719'],
+    }),
+    ('more-itertools', '10.3.0', {
+        'checksums': ['e5d93ef411224fbcef366a6e8ddc4c5781bc6359d43412a65dd5964e46111463'],
+    }),
+    ('attrs', '23.2.0', {
+        'modulename': 'attr',
+        'checksums': ['935dc3b529c262f6cf76e50877d35a4bd3c1de194fd41f47a2b7ae8f19971f30'],
+    }),
+    ('backports.functools-lru-cache', '2.0.0', {
+        'sources': ['backports.functools_lru_cache-%(version)s.tar.gz'],
+        'checksums': ['dcbfa5e0dae8a014168807c9e026d33eead71df5af76c1fb78fd248bf07f6f99'],
+    }),
+    ('wcwidth', '0.2.13', {
+        'checksums': ['72ea0c06399eb286d978fdedb6923a9eb47e1c486ce63e9b4e64fc18303972b5'],
+    }),
+    ('iniconfig', '2.0.0', {
+        'checksums': ['2d91e135bf72d31a410b17c16da610a82cb55f6b0477d1a902134b24a455b8b3'],
+    }),
+    ('colorama', '0.4.6', {
+        'checksums': ['08695f5cb7ed6e0531a20572697297273c47b8cae5a63ffc6d6ed5c201be6e44'],
+    }),
+    ('exceptiongroup', '1.2.1', {
+        'checksums': ['a4785e48b045528f5bfe627b6ad554ff32def154f42372786903b7abcfe1aa16'],
+    }),
+    ('pytest', '8.2.2', {
+        'checksums': ['de4bb8104e201939ccdc688b27a89a7be2079b22e2bd2b07f806b6ba71117977'],
+    }),
+    ('MarkupSafe', '2.1.5', {
+        'checksums': ['d283d37a890ba4c1ae73ffadf8046435c76e7bc2247bbb63c00bd1a709c6544b'],
+    }),
+    ('Jinja2', '3.1.4', {
+        'sources': ['jinja2-%(version)s.tar.gz'],
+        'checksums': ['4a3aee7acbbe7303aede8e9648d13b8bf88a429282aa6122a993f0ac800cb369'],
+    }),
+    ('sphinxcontrib-serializinghtml', '1.1.10', {
+        'modulename': 'sphinxcontrib.serializinghtml',
+        'sources': ['sphinxcontrib_serializinghtml-%(version)s.tar.gz'],
+        'checksums': ['93f3f5dc458b91b192fe10c397e324f262cf163d79f3282c158e8436a2c4511f'],
+    }),
+    ('sphinxcontrib-websupport', '1.2.7', {
+        'modulename': 'sphinxcontrib.websupport',
+        'sources': ['sphinxcontrib_websupport-%(version)s.tar.gz'],
+        'checksums': ['e322802ebfd5fe79368efd864aeb87b063566ae61911dccb2714e28a45ed7561'],
+    }),
+    ('Pygments', '2.18.0', {
+        'sources': ['pygments-%(version)s.tar.gz'],
+        'checksums': ['786ff802f32e91311bff3889f6e9a86e81505fe99f2735bb6d60ae0c5004f199'],
+    }),
+    ('imagesize', '1.4.1', {
+        'checksums': ['69150444affb9cb0d5cc5a92b3676f0b2fb7cd9ae39e947a5e11a36b4497cd4a'],
+    }),
+    ('docutils', '0.21.2', {
+        'checksums': ['3a6b18732edf182daa3cd12775bbb338cf5691468f91eeeb109deff6ebfa986f'],
+    }),
+    ('snowballstemmer', '2.2.0', {
+        'checksums': ['09b16deb8547d3412ad7b590689584cd0fe25ec8db3be37788be3810cbf19cb1'],
+    }),
+    ('alabaster', '0.7.16', {
+        'checksums': ['75a8b99c28a5dad50dd7f8ccdd447a121ddb3892da9e53d1ca5cca3106d58d65'],
+    }),
+    ('sphinxcontrib-applehelp', '1.0.8', {
+        'modulename': 'sphinxcontrib.applehelp',
+        'sources': ['sphinxcontrib_applehelp-%(version)s.tar.gz'],
+        'checksums': ['c40a4f96f3776c4393d933412053962fac2b84f4c99a7982ba42e09576a70619'],
+    }),
+    ('sphinxcontrib-devhelp', '1.0.6', {
+        'modulename': 'sphinxcontrib.devhelp',
+        'sources': ['sphinxcontrib_devhelp-%(version)s.tar.gz'],
+        'checksums': ['9893fd3f90506bc4b97bdb977ceb8fbd823989f4316b28c3841ec128544372d3'],
+    }),
+    ('sphinxcontrib-htmlhelp', '2.0.5', {
+        'modulename': 'sphinxcontrib.htmlhelp',
+        'sources': ['sphinxcontrib_htmlhelp-%(version)s.tar.gz'],
+        'checksums': ['0dc87637d5de53dd5eec3a6a01753b1ccf99494bd756aafecd74b4fa9e729015'],
+    }),
+    ('sphinxcontrib-jsmath', '1.0.1', {
+        'modulename': 'sphinxcontrib.jsmath',
+        'checksums': ['a9925e4a4587247ed2191a22df5f6970656cb8ca2bd6284309578f2153e0c4b8'],
+    }),
+    ('sphinxcontrib-qthelp', '1.0.7', {
+        'modulename': 'sphinxcontrib.qthelp',
+        'sources': ['sphinxcontrib_qthelp-%(version)s.tar.gz'],
+        'checksums': ['053dedc38823a80a7209a80860b16b722e9e0209e32fea98c90e4e6624588ed6'],
+    }),
+    ('Babel', '2.15.0', {
+        'sources': ['babel-%(version)s.tar.gz'],
+        'checksums': ['8daf0e265d05768bc6c7a314cf1321e9a123afc328cc635c18622a2f30a04413'],
+    }),
+    ('Sphinx', '7.3.7', {
+        'sources': ['sphinx-%(version)s.tar.gz'],
+        'checksums': ['a4a7db75ed37531c05002d56ed6948d4c42f473a36f46e1382b0bd76ca9627bc'],
+    }),
+    ('sphinx-bootstrap-theme', '0.8.1', {
+        'checksums': ['683e3b735448dadd0149f76edecf95ff4bd9157787e9e77e0d048ca6f1d680df'],
+    }),
+    ('click', '8.1.7', {
+        'checksums': ['ca9853ad459e787e2192211578cc907e7594e294c7ccc834310722b41b9ca6de'],
+    }),
+    ('psutil', '5.9.8', {
+        'checksums': ['6be126e3225486dff286a8fb9a06246a5253f4c7c53b475ea5f5ac934e64194c'],
+    }),
+    ('future', '1.0.0', {
+        'checksums': ['bd2968309307861edae1458a4f8a4f3598c03be43b97521076aebf5d94c07b05'],
+    }),
+    ('sortedcontainers', '2.4.0', {
+        'checksums': ['25caa5a06cc30b6b83d11423433f65d1f9d76c4c6a0c90e3379eaa43b9bfdb88'],
+    }),
+    ('intervaltree', '3.1.0', {
+        'checksums': ['902b1b88936918f9b2a19e0e5eb7ccb430ae45cde4f39ea4b36932920d33952d'],
+    }),
+    ('pytoml', '0.1.21', {
+        'checksums': ['8eecf7c8d0adcff3b375b09fe403407aa9b645c499e5ab8cac670ac4a35f61e7'],
+    }),
+    ('zipfile36', '0.1.3', {
+        'checksums': ['a78a8dddf4fa114f7fe73df76ffcce7538e23433b7a6a96c1c904023f122aead'],
+    }),
+    ('tomli-w', '1.0.0', {
+        'sources': ['tomli_w-%(version)s.tar.gz'],
+        'checksums': ['f463434305e0336248cac9c2dc8076b707d8a12d019dd349f5c1e382dd1ae1b9'],
+    }),
+    ('regex', '2024.5.15', {
+        'checksums': ['d3ee02d9e5f482cc8309134a91eeaacbdd2261ba111b0fef3748eeb4913e6a2c'],
+    }),
+    ('intreehooks', '1.0', {
+        'checksums': ['87e600d3b16b97ed219c078681260639e77ef5a17c0e0dbdd5a302f99b4e34e1'],
+    }),
+    ('pylev', '1.4.0', {
+        'checksums': ['9e77e941042ad3a4cc305dcdf2b2dec1aec2fbe3dd9015d2698ad02b173006d1'],
+    }),
+    ('pastel', '0.2.1', {
+        'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl',
+        'checksums': ['4349225fcdf6c2bb34d483e523475de5bb04a5c10ef711263452cb37d7dd4364'],
+    }),
+    ('crashtest', '0.4.1', {
+        'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl',
+        'checksums': ['8d23eac5fa660409f57472e3851dab7ac18aba459a8d19cbbba86d3d5aecd2a5'],
+    }),
+    ('jeepney', '0.8.0', {
+        'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl',
+        'checksums': ['c0a454ad016ca575060802ee4d590dd912e35c122fa04e70306de3d076cce755'],
+    }),
+    ('SecretStorage', '3.3.3', {
+        'checksums': ['2403533ef369eca6d2ba81718576c5e0f564d5cca1b58f73a8b23e7d4eeebd77'],
+    }),
+    ('keyring', '24.3.1', {
+        'modulename': False,
+        'checksums': ['c3327b6ffafc0e8befbdb597cacdb4928ffe5c1212f7645f186e6d9957a898db'],
+    }),
+    ('jaraco.classes', '3.4.0', {
+        'checksums': ['47a024b51d0239c0dd8c8540c6c7f484be3b8fcf0b2d85c13825780d3b3f3acd'],
+    }),
+    ('jaraco.context', '5.3.0', {
+        'checksums': ['c2f67165ce1f9be20f32f650f25d8edfc1646a8aeee48ae06fb35f90763576d2'],
+    }),
+    ('keyrings.alt', '5.0.1', {
+        'modulename': False,
+        'checksums': ['cd372a1ec446a1bc5a90624a52c88e83b9330218e39047a6c9a48ae37d116745'],
+    }),
+    ('tomlkit', '0.12.5', {
+        'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl',
+        'checksums': ['af914f5a9c59ed9d0762c7b64d3b5d5df007448eb9cd2edc8a46b1eafead172f'],
+    }),
+    ('shellingham', '1.5.4', {
+        'checksums': ['8dbca0739d487e5bd35ab3ca4b36e11c4078f3a234bfce294b0a0291363404de'],
+    }),
+    ('requests-toolbelt', '1.0.0', {
+        'checksums': ['7681a0a3d047012b5bdc0ee37d7f8f07ebe76ab08caeccfc3921ce23c88d5bc6'],
+    }),
+    ('pyrsistent', '0.20.0', {
+        'checksums': ['4c48f78f62ab596c679086084d0dd13254ae4f3d6c72a83ffdf5ebdef8f265a4'],
+    }),
+    ('pkginfo', '1.11.1', {
+        'checksums': ['2e0dca1cf4c8e39644eed32408ea9966ee15e0d324c62ba899a393b3c6b467aa'],
+    }),
+    ('ptyprocess', '0.7.0', {
+        'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl',
+        'checksums': ['4b41f3967fce3af57cc7e94b888626c18bf37a083e3651ca8feeb66d492fef35'],
+    }),
+    ('pexpect', '4.9.0', {
+        'checksums': ['ee7d41123f3c9911050ea2c2dac107568dc43b2d3b0c7557a33212c398ead30f'],
+    }),
+    ('jsonschema-specifications', '2023.12.1', {
+        'sources': ['jsonschema_specifications-%(version)s.tar.gz'],
+        'checksums': ['48a76787b3e70f5ed53f1160d2b81f586e4ca6d1548c5de7085d1682674764cc'],
+    }),
+    ('referencing', '0.35.1', {
+        'checksums': ['25b42124a6c8b632a425174f24087783efb348a6f1e0008e63cd4466fedf703c'],
+    }),
+    ('rpds-py', '0.18.1', {
+        'sources': ['rpds_py-%(version)s.tar.gz'],
+        'checksums': ['dc48b479d540770c811fbd1eb9ba2bb66951863e448efec2e2c102625328e92f'],
+        'modulename': 'rpds',
+    }),
+    ('jsonschema', '4.22.0', {
+        'checksums': ['5b22d434a45935119af990552c862e5d6d564e8f6601206b305a61fdf661a2b7'],
+    }),
+    ('simplejson', '3.19.2', {
+        'checksums': ['9eb442a2442ce417801c912df68e1f6ccfcd41577ae7274953ab3ad24ef7d82c'],
+    }),
+    ('webencodings', '0.5.1', {
+        'checksums': ['b36a1c245f2d304965eb4e0a82848379241dc04b865afcc4aab16748587e1923'],
+    }),
+    ('html5lib', '1.1', {
+        'checksums': ['b2e5b40261e20f354d198eae92afc10d750afb487ed5e50f9c4eaf07c184146f'],
+    }),
+    ('distro', '1.9.0', {
+        'checksums': ['2fa77c6fd8940f116ee1d6b94a2f90b13b5ea8d019b98bc8bafdcabcdd9bdbed'],
+    }),
+    ('rapidfuzz', '3.9.3', {
+        'checksums': ['b398ea66e8ed50451bce5997c430197d5e4b06ac4aa74602717f792d8d8d06e2'],
+    }),
+    ('cleo', '2.1.0', {
+        'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl',
+        'checksums': ['4a31bd4dd45695a64ee3c4758f583f134267c2bc518d8ae9a29cf237d009b07e'],
+    }),
+    ('cachy', '0.3.0', {
+        'checksums': ['186581f4ceb42a0bbe040c407da73c14092379b1e4c0e327fdb72ae4a9b269b1'],
+    }),
+    ('msgpack', '1.0.8', {
+        'checksums': ['95c02b0e27e706e48d0e5426d1710ca78e0f0628d6e89d5b5a5b91a5f12274f3'],
+    }),
+    ('CacheControl', '0.14.0', {
+        'sources': ['cachecontrol-%(version)s.tar.gz'],
+        'checksums': ['7db1195b41c81f8274a7bbd97c956f44e8348265a1bc7641c37dfebc39f0c938'],
+    }),
+    ('lockfile', '0.12.2', {
+        'checksums': ['6aed02de03cba24efabcd600b30540140634fc06cfa603822d508d5361e9f799'],
+    }),
+    ('glob2', '0.7', {
+        'checksums': ['85c3dbd07c8aa26d63d7aacee34fa86e9a91a3873bc30bf62ec46e531f92ab8c'],
+    }),
+    ('dulwich', '0.22.1', {
+        'checksums': ['e36d85967cfbf25da1c7bc3d6921adc5baa976969d926aaf1582bd5fd7e94758'],
+    }),
+    ('fsspec', '2024.6.0', {
+        'checksums': ['f579960a56e6d8038a9efc8f9c77279ec12e6299aa86b0769a7e9c46b94527c2'],
+    }),
+    ('threadpoolctl', '3.5.0', {
+        'checksums': ['082433502dd922bf738de0d8bcc4fdcbf0979ff44c42bd40f5af8a282f6fa107'],
+    }),
+    ('simplegeneric', '0.8.1', {
+        'source_tmpl': 'simplegeneric-%(version)s.zip',
+        'checksums': ['dc972e06094b9af5b855b3df4a646395e43d1c9d0d39ed345b7393560d0b9173'],
+    }),
+    ('pooch', '1.8.2', {
+        'checksums': ['76561f0de68a01da4df6af38e9955c4c9d1a5c90da73f7e40276a5728ec83d10'],
+    }),
+    ('doit', '0.36.0', {
+        'checksums': ['71d07ccc9514cb22fe59d98999577665eaab57e16f644d04336ae0b4bae234bc'],
+    }),
+    ('cloudpickle', '3.0.0', {
+        'checksums': ['996d9a482c6fb4f33c1a35335cf8afd065d2a56e973270364840712d9131a882'],
+    }),
+    ('pydevtool', '0.3.0', {
+        'checksums': ['25e3ba4f3d33ccac33ee2b9775995848d49e9b318b7a146477fb5d52f786fc8a'],
+    }),
+    ('mdurl', '0.1.2', {
+        'checksums': ['bb413d29f5eea38f31dd4754dd7377d4465116fb207585f97bf925588687c1ba'],
+    }),
+    ('markdown-it-py', '3.0.0', {
+        'modulename': 'markdown_it',
+        'checksums': ['e3f60a94fa066dc52ec76661e37c851cb232d92f9886b15cb560aaada2df8feb'],
+    }),
+    ('rich', '13.7.1', {
+        'checksums': ['9be308cb1fe2f1f57d67ce99e95af38a1e2bc71ad9813b0e247cf7ffbcc3a432'],
+    }),
+    ('rich-click', '1.8.3', {
+        'sources': ['rich_click-%(version)s.tar.gz'],
+        'checksums': ['6d75bdfa7aa9ed2c467789a0688bc6da23fbe3a143e19aa6ad3f8bac113d2ab3'],
+    }),
+    ('commonmark', '0.9.1', {
+        'checksums': ['452f9dc859be7f06631ddcb328b6919c67984aca654e5fefb3914d54691aed60'],
+    }),
+    ('execnet', '2.1.1', {
+        'checksums': ['5189b52c6121c24feae288166ab41b32549c7e2348652736540b9e6e7d4e72e3'],
+    }),
+    ('pytest-xdist', '3.6.1', {
+        'modulename': 'xdist',
+        'sources': ['pytest_xdist-%(version)s.tar.gz'],
+        'checksums': ['ead156a4db231eec769737f57668ef58a2084a34b2e55c4a8fa20d861107300d'],
+    }),
+]
+
+moduleclass = 'lang'

From 3688e7574dcc7abfc2ef9e81217d9c94a833f3aa Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 14 Jun 2024 18:57:33 +0200
Subject: [PATCH 226/835] add missing checksum for fastjsonschema extension in
 easyconfig for poetry 1.8.3

---
 easybuild/easyconfigs/p/poetry/poetry-1.8.3-GCCcore-13.3.0.eb | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/p/poetry/poetry-1.8.3-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/poetry/poetry-1.8.3-GCCcore-13.3.0.eb
index 0133ca0a75b..030ca7ce42e 100644
--- a/easybuild/easyconfigs/p/poetry/poetry-1.8.3-GCCcore-13.3.0.eb
+++ b/easybuild/easyconfigs/p/poetry/poetry-1.8.3-GCCcore-13.3.0.eb
@@ -165,7 +165,9 @@ exts_list = [
         'sources': ['poetry_plugin_export-%(version)s.tar.gz'],
         'checksums': ['1fa6168a85d59395d835ca564bc19862a7c76061e60c3e7dfaec70d50937fc61'],
     }),
-    ('fastjsonschema', '2.19.1'),
+    ('fastjsonschema', '2.19.1', {
+        'checksums': ['e3126a94bdc4623d3de4485f8d468a12f02a67921315ddc87836d6e456dc789d'],
+    }),
     (name, version, {
         'checksums': ['67f4eb68288eab41e841cc71a00d26cf6bdda9533022d0189a145a34d0a35f48'],
     }),

From 333d39d4793ebb4368b7f7ae7cfeba905fe1d005 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 14 Jun 2024 20:08:31 +0200
Subject: [PATCH 227/835] {lib}[GCC/13.3.0] pybind11 v2.12.0, Catch2 v2.13.10

---
 .../c/Catch2/Catch2-2.13.10-GCCcore-13.3.0.eb | 30 +++++++++++++++++
 .../p/pybind11/pybind11-2.12.0-GCC-13.3.0.eb  | 33 +++++++++++++++++++
 2 files changed, 63 insertions(+)
 create mode 100644 easybuild/easyconfigs/c/Catch2/Catch2-2.13.10-GCCcore-13.3.0.eb
 create mode 100644 easybuild/easyconfigs/p/pybind11/pybind11-2.12.0-GCC-13.3.0.eb

diff --git a/easybuild/easyconfigs/c/Catch2/Catch2-2.13.10-GCCcore-13.3.0.eb b/easybuild/easyconfigs/c/Catch2/Catch2-2.13.10-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..00abfac39c8
--- /dev/null
+++ b/easybuild/easyconfigs/c/Catch2/Catch2-2.13.10-GCCcore-13.3.0.eb
@@ -0,0 +1,30 @@
+easyblock = 'CMakeMake'
+
+name = 'Catch2'
+version = '2.13.10'
+
+homepage = 'https://github.com/catchorg/Catch2'
+description = """A modern, C++-native, header-only,
+ test framework for unit-tests, TDD and BDD
+ - using C++11, C++14, C++17 and later
+"""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+source_urls = ['https://github.com/catchorg/Catch2/archive/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['d54a712b7b1d7708bc7a819a8e6e47b2fde9536f487b89ccbca295072a7d9943']
+
+builddependencies = [
+    ('binutils', '2.42'),  # to make CMake compiler health check pass on old systems
+    ('CMake', '3.29.3'),
+]
+
+separate_build_dir = True
+
+sanity_check_paths = {
+    'files': ['include/catch2/catch.hpp'],
+    'dirs':  ['lib/cmake'],
+}
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/p/pybind11/pybind11-2.12.0-GCC-13.3.0.eb b/easybuild/easyconfigs/p/pybind11/pybind11-2.12.0-GCC-13.3.0.eb
new file mode 100644
index 00000000000..e4e0460d13e
--- /dev/null
+++ b/easybuild/easyconfigs/p/pybind11/pybind11-2.12.0-GCC-13.3.0.eb
@@ -0,0 +1,33 @@
+name = 'pybind11'
+version = '2.12.0'
+
+homepage = 'https://pybind11.readthedocs.io'
+description = """pybind11 is a lightweight header-only library that exposes C++ types in Python and vice versa,
+ mainly to create Python bindings of existing C++ code."""
+
+toolchain = {'name': 'GCC', 'version': '13.3.0'}
+
+source_urls = ['https://github.com/pybind/pybind11/archive/']
+sources = ['v%(version)s.tar.gz']
+patches = [
+    'pybind11-2.10.3_require-catch.patch',
+]
+checksums = [
+    {'v2.12.0.tar.gz': 'bf8f242abd1abcd375d516a7067490fb71abd79519a282d22b6e4d19282185a7'},
+    {'pybind11-2.10.3_require-catch.patch': '4a27ba3ef1d5c535d120d6178a6e876ae678e4899a07500aab37908357b0b60b'},
+]
+
+builddependencies = [
+    ('CMake', '3.29.3'),
+    # Test dependencies
+    ('Eigen', '3.4.0'),
+    ('Catch2', '2.13.10'),
+    ('Python-bundle-PyPI', '2024.06'),  # to provide pytest
+]
+
+dependencies = [
+    ('Boost', '1.85.0'),
+    ('Python', '3.12.3'),
+]
+
+moduleclass = 'lib'

From ef630973cdc3e742723f8ddb84e4f4c0e72ff8e0 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 14 Jun 2024 20:10:43 +0200
Subject: [PATCH 228/835] {lang}[gfbf/2024.05] SciPy-bundle v2024.05,
 meson-python v0.16.0, hypothesis v6.103.1

---
 .../hypothesis-6.103.1-GCCcore-13.3.0.eb      | 29 ++++++
 .../meson-python-0.16.0-GCCcore-13.3.0.eb     | 37 ++++++++
 .../SciPy-bundle-2024.05-gfbf-2024.05.eb      | 95 +++++++++++++++++++
 3 files changed, 161 insertions(+)
 create mode 100644 easybuild/easyconfigs/h/hypothesis/hypothesis-6.103.1-GCCcore-13.3.0.eb
 create mode 100644 easybuild/easyconfigs/m/meson-python/meson-python-0.16.0-GCCcore-13.3.0.eb
 create mode 100644 easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2024.05-gfbf-2024.05.eb

diff --git a/easybuild/easyconfigs/h/hypothesis/hypothesis-6.103.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/h/hypothesis/hypothesis-6.103.1-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..e9bb1d78543
--- /dev/null
+++ b/easybuild/easyconfigs/h/hypothesis/hypothesis-6.103.1-GCCcore-13.3.0.eb
@@ -0,0 +1,29 @@
+easyblock = 'PythonPackage'
+
+name = 'hypothesis'
+version = '6.103.1'
+
+homepage = "https://github.com/HypothesisWorks/hypothesis"
+description = """Hypothesis is an advanced testing library for Python. It lets you write tests which are parametrized
+ by a source of examples, and then generates simple and comprehensible examples that make your tests fail. This lets
+ you find more bugs in your code with less work."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+sources = [SOURCE_TAR_GZ]
+checksums = ['d299d5c21d6408eab3be670c94c974f3acf0b511c61fe81804b09091e393ee1f']
+
+builddependencies = [
+    ('binutils', '2.42'),
+]
+
+dependencies = [
+    ('Python', '3.12.3'),
+    ('Python-bundle-PyPI', '2024.06'),  # required for attrs, sortedcontainers
+]
+
+use_pip = True
+download_dep_fail = True
+sanity_pip_check = True
+
+moduleclass = 'tools'
diff --git a/easybuild/easyconfigs/m/meson-python/meson-python-0.16.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/m/meson-python/meson-python-0.16.0-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..1724208584f
--- /dev/null
+++ b/easybuild/easyconfigs/m/meson-python/meson-python-0.16.0-GCCcore-13.3.0.eb
@@ -0,0 +1,37 @@
+easyblock = 'PythonBundle'
+
+name = 'meson-python'
+version = '0.16.0'
+
+homepage = 'https://github.com/mesonbuild/meson-python'
+description = "Python build backend (PEP 517) for Meson projects"
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+builddependencies = [
+    ('binutils', '2.42'),
+]
+
+dependencies = [
+    ('Python', '3.12.3'),
+    ('Python-bundle-PyPI', '2024.06'),  # provides 'packaging'
+    ('Meson', '1.4.0'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('pyproject-metadata', '0.8.0', {
+        'sources': ['pyproject_metadata-%(version)s.tar.gz'],
+        'checksums': ['376d5a00764ac29440a54579f88e66b7d9cb7e629d35c35a1c7248bfebc9b455'],
+    }),
+    (name, version, {
+        'modulename': 'mesonpy',
+        'sources': ['meson_python-%(version)s.tar.gz'],
+        'checksums': ['9068c17e36c89d6c7ff709fffb2a8a9925e8cd0b02629728e5ceaf2ec505cb5f'],
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'tools'
diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2024.05-gfbf-2024.05.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2024.05-gfbf-2024.05.eb
new file mode 100644
index 00000000000..f5073cd91a7
--- /dev/null
+++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2024.05-gfbf-2024.05.eb
@@ -0,0 +1,95 @@
+easyblock = 'PythonBundle'
+
+name = 'SciPy-bundle'
+version = '2024.05'
+
+homepage = 'https://python.org/'
+description = "Bundle of Python packages for scientific software"
+
+toolchain = {'name': 'gfbf', 'version': '2024.05'}
+toolchainopts = {'pic': True, 'lowopt': True}
+
+builddependencies = [
+    ('hypothesis', '6.103.1'),
+    ('UnZip', '6.0'),
+    # scipy >= 1.9.0 uses Meson/Ninja
+    ('Meson', '1.4.0'),
+    ('meson-python', '0.16.0'),
+    ('Ninja', '1.12.1'),
+    ('pkgconf', '2.2.0'),   # required by scipy
+]
+
+dependencies = [
+    ('Python', '3.12.3'),
+    ('Python-bundle-PyPI', '2024.06'),
+    ('pybind11', '2.12.0'),  # required by scipy
+]
+
+use_pip = True
+
+# order is important!
+exts_list = [
+    ('numpy', '1.26.4', {
+        'patches': [
+            'numpy-1.22.3_disable-broken-override-test.patch',
+        ],
+        'checksums': [
+            {'numpy-1.26.4.tar.gz': '2a02aba9ed12e4ac4eb3ea9421c420301a0c6460d9830d74a9df87efa4912010'},
+            {'numpy-1.22.3_disable-broken-override-test.patch':
+             '9c589bb073b28b25ff45eb3c63c57966aa508dd8b318d0b885b6295271e4983c'},
+        ],
+    }),
+    ('ply', '3.11', {
+        'checksums': ['00c7c1aaa88358b9c765b6d3000c6eec0ba42abca5351b095321aef446081da3'],
+    }),
+    ('gast', '0.5.4', {
+        'checksums': ['9c270fe5f4b130969b54174de7db4e764b09b4f7f67ccfc32480e29f78348d97'],
+    }),
+    ('beniget', '0.4.1', {
+        'checksums': ['75554b3b8ad0553ce2f607627dad3d95c60c441189875b98e097528f8e23ac0c'],
+    }),
+    ('pythran', '0.16.1', {
+        'checksums': ['861748c0f9c7d422b32724b114b3817d818ed4eab86c09781aa0a3f7ceabb7f9'],
+    }),
+    ('versioneer', '0.29', {
+        'checksums': ['5ab283b9857211d61b53318b7c792cf68e798e765ee17c27ade9f6c924235731'],
+    }),
+    ('scipy', '1.13.1', {
+        'enable_slow_tests': True,
+        'ignore_test_result': False,
+        'patches': [
+            'scipy-1.11.1_disable-tests.patch',
+            'scipy-1.11.1_xfail-aarch64_test_maxiter_worsening.patch',
+        ],
+        'checksums': [
+            {'scipy-1.13.1.tar.gz': '095a87a0312b08dfd6a6155cbbd310a8c51800fc931b8c0b84003014b874ed3c'},
+            {'scipy-1.11.1_disable-tests.patch': '906bfb03397d94882ccdc1b93bc2c8e854e0e060c2d107c83042992394e6a4af'},
+            {'scipy-1.11.1_xfail-aarch64_test_maxiter_worsening.patch':
+             '918c8e6fa8215d459126f267764c961bde729ea4a116c7f6287cddfdc58ffcea'},
+        ],
+    }),
+    ('numexpr', '2.10.0', {
+        'checksums': ['c89e930752639df040539160326d8f99a84159bbea41943ab8e960591edaaef0'],
+    }),
+    ('Bottleneck', '1.3.8', {
+        'checksums': ['6780d896969ba7f53c8995ba90c87c548beb3db435dc90c60b9a10ed1ab4d868'],
+    }),
+    ('tzdata', '2024.1', {
+        'checksums': ['2674120f8d891909751c38abcdfd386ac0a5a1127954fbc332af6b5ceae07efd'],
+    }),
+    ('pandas', '2.2.2', {
+        'preinstallopts': "export PANDAS_CI=0 && ",
+        'checksums': ['9e79019aba43cb4fda9e4d983f8e88ca0373adbb697ae9c6c43093218de28b54'],
+    }),
+    ('mpmath', '1.3.0', {
+        'checksums': ['7a28eb2a9774d00c7bc92411c19a89209d5da7c4c9a9e227be8330a23a25b91f'],
+    }),
+    ('deap', '1.4.1', {
+        'modulename': 'deap.base',
+        'checksums': ['cc01de9892dfa7d1bc9803dab28892fead177f0182c81db47360a240ead778ff'],
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'lang'

From cadea7071e3c96d53138fca22fba74e2696c693b Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 14 Jun 2024 20:52:15 +0200
Subject: [PATCH 229/835] add patch for numexpr 2.10.0 to fix build on top of
 numpy 1.x

---
 .../SciPy-bundle-2024.05-gfbf-2024.05.eb       | 10 ++++++----
 .../numexpr-2.10.0_fix-numpy-1.x.patch         | 18 ++++++++++++++++++
 2 files changed, 24 insertions(+), 4 deletions(-)
 create mode 100644 easybuild/easyconfigs/s/SciPy-bundle/numexpr-2.10.0_fix-numpy-1.x.patch

diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2024.05-gfbf-2024.05.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2024.05-gfbf-2024.05.eb
index f5073cd91a7..c3f76125dce 100644
--- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2024.05-gfbf-2024.05.eb
+++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2024.05-gfbf-2024.05.eb
@@ -30,9 +30,7 @@ use_pip = True
 # order is important!
 exts_list = [
     ('numpy', '1.26.4', {
-        'patches': [
-            'numpy-1.22.3_disable-broken-override-test.patch',
-        ],
+        'patches': ['numpy-1.22.3_disable-broken-override-test.patch'],
         'checksums': [
             {'numpy-1.26.4.tar.gz': '2a02aba9ed12e4ac4eb3ea9421c420301a0c6460d9830d74a9df87efa4912010'},
             {'numpy-1.22.3_disable-broken-override-test.patch':
@@ -69,7 +67,11 @@ exts_list = [
         ],
     }),
     ('numexpr', '2.10.0', {
-        'checksums': ['c89e930752639df040539160326d8f99a84159bbea41943ab8e960591edaaef0'],
+        'patches': ['numexpr-2.10.0_fix-numpy-1.x.patch'],
+        'checksums': [
+            {'numexpr-2.10.0.tar.gz': 'c89e930752639df040539160326d8f99a84159bbea41943ab8e960591edaaef0'},
+            {'numexpr-2.10.0_fix-numpy-1.x.patch': '8d70b2e95579e6f0adc07bc615144f7657b3b607f9210ec328b6622458ca726d'},
+        ],
     }),
     ('Bottleneck', '1.3.8', {
         'checksums': ['6780d896969ba7f53c8995ba90c87c548beb3db435dc90c60b9a10ed1ab4d868'],
diff --git a/easybuild/easyconfigs/s/SciPy-bundle/numexpr-2.10.0_fix-numpy-1.x.patch b/easybuild/easyconfigs/s/SciPy-bundle/numexpr-2.10.0_fix-numpy-1.x.patch
new file mode 100644
index 00000000000..dff9bd069c9
--- /dev/null
+++ b/easybuild/easyconfigs/s/SciPy-bundle/numexpr-2.10.0_fix-numpy-1.x.patch
@@ -0,0 +1,18 @@
+fix for: error: PyDataType_SET_ELSIZE was not declared in this scope
+see https://github.com/pydata/numexpr/pull/485
+
+--- numexpr-2.10.0/numexpr/interpreter.cpp.orig	2024-06-14 21:47:27.999098607 +0200
++++ numexpr-2.10.0/numexpr/interpreter.cpp	2024-06-14 21:49:53.403776961 +0200
+@@ -47,6 +47,12 @@
+ #define AVAILABLE(Haystack, Haystack_Len, J, Needle_Len)   \
+   ((Haystack_Len) >= (J) + (Needle_Len))
+ 
++// To allow building with NumPy<2 locally define the new NumPy macros:
++#if NPY_ABI_VERSION < 0x02000000
++  #define PyDataType_ELSIZE(descr) ((descr)->elsize)
++  #define PyDataType_SET_ELSIZE(descr, size) (descr)->elsize = size
++#endif
++
+ #include "str-two-way.hpp"
+ 
+ #ifdef DEBUG

From 3e407588ee4b41b497a5dd7a33dd693b9b497cb4 Mon Sep 17 00:00:00 2001
From: Simon Pinches <Simon.Pinches@iter.org>
Date: Sat, 15 Jun 2024 19:05:11 +0200
Subject: [PATCH 230/835] adding easyconfigs:
 Sphinx-RTD-Theme-2.0.0-GCCcore-13.2.0.eb

---
 .../Sphinx-RTD-Theme-2.0.0-GCCcore-13.2.0.eb  | 33 +++++++++++++++++++
 1 file changed, 33 insertions(+)
 create mode 100644 easybuild/easyconfigs/s/Sphinx-RTD-Theme/Sphinx-RTD-Theme-2.0.0-GCCcore-13.2.0.eb

diff --git a/easybuild/easyconfigs/s/Sphinx-RTD-Theme/Sphinx-RTD-Theme-2.0.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/s/Sphinx-RTD-Theme/Sphinx-RTD-Theme-2.0.0-GCCcore-13.2.0.eb
new file mode 100644
index 00000000000..6642b38d820
--- /dev/null
+++ b/easybuild/easyconfigs/s/Sphinx-RTD-Theme/Sphinx-RTD-Theme-2.0.0-GCCcore-13.2.0.eb
@@ -0,0 +1,33 @@
+easyblock = 'PythonBundle'
+
+name = 'Sphinx-RTD-Theme'
+version = '2.0.0'
+
+homepage = 'https://sphinx-rtd-theme.readthedocs.io'
+description = """Sphinx theme designed to provide a great reader experience
+ for documentation users on both desktop and mobile devices."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
+
+builddependencies = [('binutils', '2.40')]
+
+dependencies = [
+    ('Python', '3.11.5'),
+    ('Python-bundle-PyPI', '2023.10'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('sphinxcontrib-jquery', '4.1', {
+        'modulename': 'sphinxcontrib.jquery',
+        'checksums': ['1620739f04e36a2c779f1a131a2dfd49b2fd07351bf1968ced074365933abc7a'],
+    }),
+    ('sphinx_rtd_theme', version, {
+        'checksums': ['bd5d7b80622406762073a04ef8fadc5f9151261563d47027de09910ce03afe6b'],
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'vis'

From 92cb280fea9af8d0319e8d5fc6cf867ba9a5f74d Mon Sep 17 00:00:00 2001
From: c3-builder <c3-builder@vera-skylake-build>
Date: Sun, 16 Jun 2024 11:53:39 +0000
Subject: [PATCH 231/835] adding easyconfigs: Critic2-1.2-foss-2023a.eb

---
 .../c/Critic2/Critic2-1.2-foss-2023a.eb       | 37 +++++++++++++++++++
 1 file changed, 37 insertions(+)
 create mode 100644 easybuild/easyconfigs/c/Critic2/Critic2-1.2-foss-2023a.eb

diff --git a/easybuild/easyconfigs/c/Critic2/Critic2-1.2-foss-2023a.eb b/easybuild/easyconfigs/c/Critic2/Critic2-1.2-foss-2023a.eb
new file mode 100644
index 00000000000..9d1605b7366
--- /dev/null
+++ b/easybuild/easyconfigs/c/Critic2/Critic2-1.2-foss-2023a.eb
@@ -0,0 +1,37 @@
+easyblock = 'CMakeMake'
+
+name = 'Critic2'
+version = '1.2'
+
+homepage = 'https://aoterodelaroza.github.io/critic2/'
+description = """Critic2 is a program for the analysis of quantum mechanical
+calculation results in molecules and periodic solids."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+toolchainopts = {'extra_fflags': '-ffree-line-length-none'}
+
+source_urls = ['https://github.com/aoterodelaroza/critic2/archive/refs/tags/']
+sources = ['%(version)s.tar.gz']
+checksums = ['b59ecffd83405dbcc4b5d157d4a94bf2756916f72e83e09a94d277d54d0f2225']
+
+configopts = '-DLIBCINT_INCLUDE_DIRS=$EBROOTLIBCINT/include/ '
+configopts += '-DLIBCINT_LIBRARY=$EBROOTLIBCINT/lib64/libcint.so '
+
+builddependencies = [
+    ('CMake', '3.26.3'),
+]
+
+dependencies = [
+    ('libxc', '6.2.2'),
+    ('libcint', '5.4.0'),
+    ('libreadline', '8.2'),
+]
+
+sanity_check_paths = {
+    'files': ["bin/critic2"],
+    'dirs': ["bin"],
+}
+
+sanity_check_commands = ['critic2 -h']
+
+moduleclass = 'chem'

From 66697a9d498ac7704e6aa0a3df037280ef5af4cb Mon Sep 17 00:00:00 2001
From: Leonard Nielsen <leoniel@chalmers.se>
Date: Mon, 17 Jun 2024 14:35:23 +0000
Subject: [PATCH 232/835] fixed hatchling deps

---
 easybuild/easyconfigs/s/spaCy/spaCy-3.7.4-foss-2023a.eb | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/easybuild/easyconfigs/s/spaCy/spaCy-3.7.4-foss-2023a.eb b/easybuild/easyconfigs/s/spaCy/spaCy-3.7.4-foss-2023a.eb
index 6ca6017894a..e8c79ceb6bf 100644
--- a/easybuild/easyconfigs/s/spaCy/spaCy-3.7.4-foss-2023a.eb
+++ b/easybuild/easyconfigs/s/spaCy/spaCy-3.7.4-foss-2023a.eb
@@ -10,6 +10,7 @@ toolchain = {'name': 'foss', 'version': '2023a'}
 
 builddependencies = [
     ('poetry', '1.7.1'),
+    ('hatchling', '1.18.0'),
 ]
 
 dependencies = [
@@ -17,7 +18,6 @@ dependencies = [
     ('SciPy-bundle', '2023.07'),
     ('tqdm', '4.66.1'),
     ('pydantic', '2.5.3'),
-    ('hatchling', '1.18.0')
 ]
 
 use_pip = True
@@ -66,9 +66,6 @@ exts_list = [
         'source_tmpl': 'smart_open-%(version)s.tar.gz',
         'checksums': ['be3c92c246fbe80ebce8fbacb180494a481a77fcdcb7c1aadb2ea5b9c2bee8b9'],
     }),
-    ('hatch_fancy_pypi_readme', '24.1.0', {
-        'checksums': ['44dd239f1a779b9dcf8ebc9401a611fd7f7e3e14578dcf22c265dfaf7c1514b8'],
-    }),
     ('langcodes', '3.3.0', {
         'checksums': ['794d07d5a28781231ac335a1561b8442f8648ca07cd518310aeb45d6f0807ef6'],
     }),

From f13d4ea1415a9c2e1162de19914c3d155411c3b4 Mon Sep 17 00:00:00 2001
From: Simon Pinches <Simon.Pinches@iter.org>
Date: Mon, 17 Jun 2024 18:01:09 +0200
Subject: [PATCH 233/835] adding easyconfigs: PaStiX-6.3.2-foss-2023b.eb

---
 .../p/PaStiX/PaStiX-6.3.2-foss-2023b.eb       | 46 +++++++++++++++++++
 1 file changed, 46 insertions(+)
 create mode 100644 easybuild/easyconfigs/p/PaStiX/PaStiX-6.3.2-foss-2023b.eb

diff --git a/easybuild/easyconfigs/p/PaStiX/PaStiX-6.3.2-foss-2023b.eb b/easybuild/easyconfigs/p/PaStiX/PaStiX-6.3.2-foss-2023b.eb
new file mode 100644
index 00000000000..ea0c7c4d9bc
--- /dev/null
+++ b/easybuild/easyconfigs/p/PaStiX/PaStiX-6.3.2-foss-2023b.eb
@@ -0,0 +1,46 @@
+easyblock = 'CMakeMake'
+
+name = 'PaStiX'
+version = '6.3.2'
+
+homepage = 'http://pastix.gforge.inria.fr/'
+description = """PaStiX (Parallel Sparse matriX package) is a scientific library that provides a high performance
+ parallel solver for very large sparse linear systems based on direct methods."""
+
+toolchain = {'name': 'foss', 'version': '2023b'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://files.inria.fr/pastix/releases/v6/']
+sources = ['%(namelower)s-%(version)s.tar.gz']
+checksums = ['c4da8802d1933eecf8c09d7e63c014c81ccf353fe623142e9f5c5fc65ed82ee0']
+
+builddependencies = [
+    ('CMake', '3.27.6'),
+]
+
+dependencies = [
+    ('hwloc', '2.9.2'),
+    ('SCOTCH', '7.0.4'),
+]
+
+configopts = [
+    '-DBUILD_SHARED_LIBS=OFF -DPASTIX_INT64=OFF -DPASTIX_WITH_MPI=ON',
+    '-DBUILD_SHARED_LIBS=ON -DPASTIX_INT64=OFF -DPASTIX_WITH_MPI=ON'
+]
+
+sanity_check_paths = {
+    'files': ['bin/pastix_env.sh',
+              'bin/spm_env.sh',
+              'lib/libpastix.a',
+              'lib/libpastixf.a',
+              'lib/libpastix.%s' % SHLIB_EXT,
+              'lib/libpastixf.%s' % SHLIB_EXT,
+              'lib/libspm.a',
+              'lib/libspmf.a',
+              'lib/libspm.%s' % SHLIB_EXT,
+              'lib/libspmf.%s' % SHLIB_EXT,
+              ],
+    'dirs': ['bin', 'include', 'lib/pkgconfig', 'share'],
+}
+
+moduleclass = 'math'

From b9b47a69a70d663f202795458f75c843f3a4323d Mon Sep 17 00:00:00 2001
From: Simon Pinches <Simon.Pinches@iter.org>
Date: Mon, 17 Jun 2024 18:16:14 +0200
Subject: [PATCH 234/835] adding easyconfigs: SCOTCH-7.0.4-iimpi-2023b.eb,
 PaStiX-6.3.2-intel-2023b.eb

---
 .../p/PaStiX/PaStiX-6.3.2-intel-2023b.eb      | 46 +++++++++++++++++++
 .../s/SCOTCH/SCOTCH-7.0.4-iimpi-2023b.eb      | 26 +++++++++++
 2 files changed, 72 insertions(+)
 create mode 100644 easybuild/easyconfigs/p/PaStiX/PaStiX-6.3.2-intel-2023b.eb
 create mode 100644 easybuild/easyconfigs/s/SCOTCH/SCOTCH-7.0.4-iimpi-2023b.eb

diff --git a/easybuild/easyconfigs/p/PaStiX/PaStiX-6.3.2-intel-2023b.eb b/easybuild/easyconfigs/p/PaStiX/PaStiX-6.3.2-intel-2023b.eb
new file mode 100644
index 00000000000..e302309df9a
--- /dev/null
+++ b/easybuild/easyconfigs/p/PaStiX/PaStiX-6.3.2-intel-2023b.eb
@@ -0,0 +1,46 @@
+easyblock = 'CMakeMake'
+
+name = 'PaStiX'
+version = '6.3.2'
+
+homepage = 'http://pastix.gforge.inria.fr/'
+description = """PaStiX (Parallel Sparse matriX package) is a scientific library that provides a high performance
+ parallel solver for very large sparse linear systems based on direct methods."""
+
+toolchain = {'name': 'intel', 'version': '2023b'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://files.inria.fr/pastix/releases/v6/']
+sources = ['%(namelower)s-%(version)s.tar.gz']
+checksums = ['c4da8802d1933eecf8c09d7e63c014c81ccf353fe623142e9f5c5fc65ed82ee0']
+
+builddependencies = [
+    ('CMake', '3.27.6'),
+]
+
+dependencies = [
+    ('hwloc', '2.9.2'),
+    ('SCOTCH', '7.0.4'),
+]
+
+configopts = [
+    '-DBUILD_SHARED_LIBS=OFF -DPASTIX_INT64=OFF -DPASTIX_WITH_MPI=ON',
+    '-DBUILD_SHARED_LIBS=ON -DPASTIX_INT64=OFF -DPASTIX_WITH_MPI=ON'
+]
+
+sanity_check_paths = {
+    'files': ['bin/pastix_env.sh',
+              'bin/spm_env.sh',
+              'lib/libpastix.a',
+              'lib/libpastixf.a',
+              'lib/libpastix.%s' % SHLIB_EXT,
+              'lib/libpastixf.%s' % SHLIB_EXT,
+              'lib/libspm.a',
+              'lib/libspmf.a',
+              'lib/libspm.%s' % SHLIB_EXT,
+              'lib/libspmf.%s' % SHLIB_EXT,
+              ],
+    'dirs': ['bin', 'include', 'lib/pkgconfig', 'share'],
+}
+
+moduleclass = 'math'
diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-7.0.4-iimpi-2023b.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-7.0.4-iimpi-2023b.eb
new file mode 100644
index 00000000000..03292d90476
--- /dev/null
+++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-7.0.4-iimpi-2023b.eb
@@ -0,0 +1,26 @@
+name = 'SCOTCH'
+version = '7.0.4'
+
+homepage = 'https://www.labri.fr/perso/pelegrin/scotch/'
+description = """Software package and libraries for sequential and parallel graph partitioning,
+static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning."""
+
+toolchain = {'name': 'iimpi', 'version': '2023b'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://gitlab.inria.fr/scotch/scotch/-/archive/v%(version)s/']
+sources = ['%(namelower)s-v%(version)s.tar.gz']
+checksums = ['8ef4719d6a3356e9c4ca7fefd7e2ac40deb69779a5c116f44da75d13b3d2c2c3']
+
+threadedmpi = False
+
+builddependencies = [
+    ('Bison', '3.8.2'),
+    ('flex', '2.6.4'),
+]
+
+dependencies = [
+    ('zlib', '1.2.13'),
+]
+
+moduleclass = 'math'

From 894bcc20e3f287ba5a853c2edfa0626468b114c4 Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Mon, 17 Jun 2024 19:08:50 +0200
Subject: [PATCH 235/835] revert changes to sanity checks of
 libdap-3.20.11-GCCcore-12.3.0.eb

---
 .../easyconfigs/l/libdap/libdap-3.20.11-GCCcore-12.3.0.eb      | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/l/libdap/libdap-3.20.11-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libdap/libdap-3.20.11-GCCcore-12.3.0.eb
index ae260fd0348..39e628f1d97 100644
--- a/easybuild/easyconfigs/l/libdap/libdap-3.20.11-GCCcore-12.3.0.eb
+++ b/easybuild/easyconfigs/l/libdap/libdap-3.20.11-GCCcore-12.3.0.eb
@@ -18,6 +18,7 @@ builddependencies = [
     ('Bison', '3.8.2'),
     ('flex', '2.6.4'),
 ]
+
 dependencies = [
     ('cURL', '8.0.1'),
     ('libxml2', '2.11.4'),
@@ -30,7 +31,7 @@ configopts = 'TIRPC_LIBS="-ltirpc"'
 
 
 sanity_check_paths = {
-    'files': ['bin/getdap', 'bin/getdap4', 'bin/dap-config', 'lib/%(name)s.a', 'lib/lib%%(name)s.%s' % SHLIB_EXT],
+    'files': ['bin/getdap', 'bin/getdap4', 'bin/dap-config', 'lib/libdap.a', 'lib/libdap.%s' % SHLIB_EXT],
     'dirs': ['include'],
 }
 

From 3f08ae5c76b28389e25666f5e24321af203ff592 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Mon, 17 Jun 2024 19:17:09 +0200
Subject: [PATCH 236/835] adding easyconfigs: AmberTools-23.6-foss-2023a.eb

---
 .../AmberTools/AmberTools-23.6-foss-2023a.eb  | 86 +++++++++++++++++++
 1 file changed, 86 insertions(+)
 create mode 100644 easybuild/easyconfigs/a/AmberTools/AmberTools-23.6-foss-2023a.eb

diff --git a/easybuild/easyconfigs/a/AmberTools/AmberTools-23.6-foss-2023a.eb b/easybuild/easyconfigs/a/AmberTools/AmberTools-23.6-foss-2023a.eb
new file mode 100644
index 00000000000..ca7d8074aab
--- /dev/null
+++ b/easybuild/easyconfigs/a/AmberTools/AmberTools-23.6-foss-2023a.eb
@@ -0,0 +1,86 @@
+easyblock = 'EB_Amber'
+
+name = 'AmberTools'
+local_ambertools_ver = 23
+# Patch levels from http://ambermd.org/AmberPatches.php and http://ambermd.org/ATPatches.php
+patchlevels = (6, 0)  # (AmberTools, Amber)
+version = '%s.%s' % (local_ambertools_ver, patchlevels[0])
+
+homepage = 'https://ambermd.org/'
+description = """AmberTools consists of several independently developed packages that work well by themselves,
+ and with Amber itself. The suite can also be used to carry out complete molecular dynamics simulations,
+ with either explicit water or generalized Born solvent models."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+toolchainopts = {'usempi': True}
+
+# download requires registration
+local_download_credentials = '?Name=Easybuild&Institution=Easybuild&City=Internet&State=Other&Country=Belgium'
+source_urls = ['https://ambermd.org/cgi-bin/AmberTools%s-get.pl' % local_ambertools_ver]
+sources = [{
+    'download_filename': local_download_credentials,
+    'filename': 'AmberTools%s.tar.bz2' % local_ambertools_ver,
+}]
+patches = [
+    'AmberTools-20_cmake-locate-netcdf.patch',
+    'AmberTools-20_fix_missing_MPI_LIBRARY_error.patch',
+    'AmberTools-20_fix_xblas_missing_make_dependency.patch',
+    'AmberTools-21_CMake-FlexiBLAS.patch',
+    'AmberTools-21_fix_incorrect_dvout_call.patch',
+    'AmberTools-21_fix_more_blas_argument_problems.patch',
+    'AmberTools-21_fix_potential_use_before_init.patch',
+    'AmberTools-21_fix_rism_argument_mismatch.patch',
+    'AmberTools-21_fix_xray_fftpack_arg_mismatch.patch',
+    'AmberTools-22_fix_test_missing_cuda_dir.patch',
+]
+checksums = [
+    {'AmberTools23.tar.bz2': 'debb52e6ef2e1b4eaa917a8b4d4934bd2388659c660501a81ea044903bf9ee9d'},
+    {'AmberTools-20_cmake-locate-netcdf.patch': '473e07c53b6f641d96d333974a6af2e03413fecef79f879d3fdecf7fecaab4d0'},
+    {'AmberTools-20_fix_missing_MPI_LIBRARY_error.patch':
+     '0b89a0624167bc23876bcdefcb1055f591e38e3bd559a71d5749e342bd311acc'},
+    {'AmberTools-20_fix_xblas_missing_make_dependency.patch':
+     'ff25e91fdc72347a778c3837b581e174d6a8c71efa5b46e11391b18bca84fd65'},
+    {'AmberTools-21_CMake-FlexiBLAS.patch': '9543812c24c4b7842f64f1f8abaf2c92b5c4c0fadcdbd9811e76b81a778f0d36'},
+    {'AmberTools-21_fix_incorrect_dvout_call.patch':
+     '1054d4007f5c79126a41582e1e80514267cf406416ed6c471574cd708b16319b'},
+    {'AmberTools-21_fix_more_blas_argument_problems.patch':
+     'c6279b57752239184b942d37f760749494ae0eff95236f3368c76ac0d2726a7c'},
+    {'AmberTools-21_fix_potential_use_before_init.patch':
+     '377e645b5bd2c91ebb4d0b6fbca0407a94289e5ddc5b1e7ed0cb0b0724ad2139'},
+    {'AmberTools-21_fix_rism_argument_mismatch.patch':
+     '14255e5739cec39303df570f06820c7532f7395e1b73b1e4104377984e2c9fc1'},
+    {'AmberTools-21_fix_xray_fftpack_arg_mismatch.patch':
+     '99c954e693659efc2a1d121f91510f56408006f0751d91595f45a34b03364e2f'},
+    {'AmberTools-22_fix_test_missing_cuda_dir.patch':
+     'fb1ab74314d7816169bb9f3f527b78085654aae2825c52cebf50a5760401b737'},
+]
+
+builddependencies = [
+    ('CMake', '3.26.3'),
+    ('pkgconf', '1.9.5'),
+    ('Bison', '3.8.2'),
+    ('flex', '2.6.4'),
+    ('make', '4.4.1'),
+]
+
+dependencies = [
+    ('zlib', '1.2.13'),
+    ('bzip2', '1.0.8'),
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('Perl', '5.36.1'),
+    ('Perl-bundle-CPAN', '5.36.1'),
+    ('Boost', '1.82.0'),
+    ('libreadline', '8.2'),
+    ('matplotlib', '3.7.2'),
+    ('netCDF', '4.9.2'),
+    ('netCDF-Fortran', '4.6.1'),
+    ('PnetCDF', '1.12.3'),
+    ('Tkinter', '%(pyver)s'),
+    ('X11', '20230603'),
+    ('mpi4py', '3.1.4'),
+]
+
+runtest = True
+
+moduleclass = 'chem'

From 6d801077e21f7ced04b6ff8d9419feeedab9351a Mon Sep 17 00:00:00 2001
From: Simon Branford <4967+branfosj@users.noreply.github.com>
Date: Mon, 17 Jun 2024 18:29:18 +0100
Subject: [PATCH 237/835] add pkgconf build dep

---
 easybuild/easyconfigs/p/PaStiX/PaStiX-6.3.2-foss-2023b.eb | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easybuild/easyconfigs/p/PaStiX/PaStiX-6.3.2-foss-2023b.eb b/easybuild/easyconfigs/p/PaStiX/PaStiX-6.3.2-foss-2023b.eb
index ea0c7c4d9bc..64b3fd907c7 100644
--- a/easybuild/easyconfigs/p/PaStiX/PaStiX-6.3.2-foss-2023b.eb
+++ b/easybuild/easyconfigs/p/PaStiX/PaStiX-6.3.2-foss-2023b.eb
@@ -16,6 +16,7 @@ checksums = ['c4da8802d1933eecf8c09d7e63c014c81ccf353fe623142e9f5c5fc65ed82ee0']
 
 builddependencies = [
     ('CMake', '3.27.6'),
+    ('pkgconf', '2.0.3'),
 ]
 
 dependencies = [

From 0c22ac15316d983b4366a863cec57d3f9459e431 Mon Sep 17 00:00:00 2001
From: Simon Branford <4967+branfosj@users.noreply.github.com>
Date: Mon, 17 Jun 2024 18:29:28 +0100
Subject: [PATCH 238/835] add pkgconf build dep

---
 easybuild/easyconfigs/p/PaStiX/PaStiX-6.3.2-intel-2023b.eb | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easybuild/easyconfigs/p/PaStiX/PaStiX-6.3.2-intel-2023b.eb b/easybuild/easyconfigs/p/PaStiX/PaStiX-6.3.2-intel-2023b.eb
index e302309df9a..d53ebd66755 100644
--- a/easybuild/easyconfigs/p/PaStiX/PaStiX-6.3.2-intel-2023b.eb
+++ b/easybuild/easyconfigs/p/PaStiX/PaStiX-6.3.2-intel-2023b.eb
@@ -16,6 +16,7 @@ checksums = ['c4da8802d1933eecf8c09d7e63c014c81ccf353fe623142e9f5c5fc65ed82ee0']
 
 builddependencies = [
     ('CMake', '3.27.6'),
+    ('pkgconf', '2.0.3'),
 ]
 
 dependencies = [

From b6d318aaafa5958cc39a57d6dfd65c520da1b48e Mon Sep 17 00:00:00 2001
From: Samuel Moors <samuel.moors@vub.be>
Date: Mon, 17 Jun 2024 21:09:26 +0200
Subject: [PATCH 239/835] drop to gfbf toolchain

---
 ...23a-CUDA-12.1.1.eb => Safetensors-0.4.3-gfbf-2023a.eb} | 8 +-------
 1 file changed, 1 insertion(+), 7 deletions(-)
 rename easybuild/easyconfigs/s/Safetensors/{Safetensors-0.4.3-foss-2023a-CUDA-12.1.1.eb => Safetensors-0.4.3-gfbf-2023a.eb} (97%)

diff --git a/easybuild/easyconfigs/s/Safetensors/Safetensors-0.4.3-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/s/Safetensors/Safetensors-0.4.3-gfbf-2023a.eb
similarity index 97%
rename from easybuild/easyconfigs/s/Safetensors/Safetensors-0.4.3-foss-2023a-CUDA-12.1.1.eb
rename to easybuild/easyconfigs/s/Safetensors/Safetensors-0.4.3-gfbf-2023a.eb
index c21239cfcc7..3c686b7380e 100644
--- a/easybuild/easyconfigs/s/Safetensors/Safetensors-0.4.3-foss-2023a-CUDA-12.1.1.eb
+++ b/easybuild/easyconfigs/s/Safetensors/Safetensors-0.4.3-gfbf-2023a.eb
@@ -2,7 +2,6 @@ easyblock = "CargoPythonBundle"
 
 name = 'Safetensors'
 version = '0.4.3'
-versionsuffix = '-CUDA-%(cudaver)s'
 _rustver = '1.75.0'
 
 homepage = 'https://huggingface.co/docs/safetensors'
@@ -12,7 +11,7 @@ pickle) and that is still fast (zero-copy). Safetensors is really fast.
 This variant of Safetensors is installed with support for numpy and PyTorch
 """
 
-toolchain = {'name': 'foss', 'version': '2023a'}
+toolchain = {'name': 'gfbf', 'version': '2023a'}
 
 builddependencies = [
     ('Rust', _rustver),
@@ -20,12 +19,8 @@ builddependencies = [
 ]
 
 dependencies = [
-    ('CUDA', '12.1.1', '', SYSTEM),
     ('Python', '3.11.3'),
     ('SciPy-bundle', '2023.07'),
-    ('PyTorch', '2.1.2', versionsuffix),  # optional
-    # ('jax', 'xxx', versionsuffix),  # optional, add 'jax' to 'use_pip_extras'
-    # ('TensorFlow', 'xxx', versionsuffix),  # optional, add 'tensorflow' to 'use_pip_extras'
 ]
 
 # crates generated on 2024-05-24 from directories savetensors/ and bindings/python/
@@ -291,7 +286,6 @@ use_pip = True
 
 exts_list = [
     ('safetensors', version, {
-        'use_pip_extras': 'numpy,torch',
         'checksums': ['2f85fc50c4e07a21e95c24e07460fe6f7e2859d0ce88092838352b798ce711c2'],
     }),
 ]

From a2b3a62bf6ea95d2ac90696970414ea435534e52 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Mon, 17 Jun 2024 22:36:36 +0200
Subject: [PATCH 240/835] add GMP and MPFR as dependencies

---
 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2306-foss-2022b.eb | 2 ++
 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2312-foss-2023a.eb | 2 ++
 2 files changed, 4 insertions(+)

diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2306-foss-2022b.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2306-foss-2022b.eb
index f4380374929..02ee224e98b 100644
--- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2306-foss-2022b.eb
+++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2306-foss-2022b.eb
@@ -30,6 +30,8 @@ builddependencies = [
     ('CMake', '3.24.3'),
     ('flex', '2.6.4'),
     ('CGAL', '5.5.2'),  # header only
+    ('GMP', '6.2.1'),
+    ('MPFR', '4.2.0'),
 ]
 
 dependencies = [
diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2312-foss-2023a.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2312-foss-2023a.eb
index bc5f33912b5..b7f522ba479 100644
--- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2312-foss-2023a.eb
+++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2312-foss-2023a.eb
@@ -39,6 +39,8 @@ dependencies = [
     ('SCOTCH', '7.0.3'),
     ('KaHIP', '3.16'),
     ('CGAL', '5.6'),
+    ('GMP', '6.2.1'),
+    ('MPFR', '4.2.0'),
     ('ParaView', '5.11.2'),
     ('gnuplot', '5.4.8'),
 ]

From b6f86d300499783a9be91c52acb926402b09f86d Mon Sep 17 00:00:00 2001
From: sassy <sassy@hp>
Date: Tue, 18 Jun 2024 10:10:49 +0100
Subject: [PATCH 241/835] adding easyconfigs: DMTCP-3.0.0-GCCcore-12.2.0.eb,
 DMTCP-3.0.0-GCCcore-12.3.0.eb, DMTCP-3.0.0-GCCcore-13.2.0.eb

---
 .../d/DMTCP/DMTCP-3.0.0-GCCcore-12.2.0.eb     | 26 +++++++++++++++++++
 .../d/DMTCP/DMTCP-3.0.0-GCCcore-12.3.0.eb     | 26 +++++++++++++++++++
 .../d/DMTCP/DMTCP-3.0.0-GCCcore-13.2.0.eb     | 26 +++++++++++++++++++
 3 files changed, 78 insertions(+)
 create mode 100644 easybuild/easyconfigs/d/DMTCP/DMTCP-3.0.0-GCCcore-12.2.0.eb
 create mode 100644 easybuild/easyconfigs/d/DMTCP/DMTCP-3.0.0-GCCcore-12.3.0.eb
 create mode 100644 easybuild/easyconfigs/d/DMTCP/DMTCP-3.0.0-GCCcore-13.2.0.eb

diff --git a/easybuild/easyconfigs/d/DMTCP/DMTCP-3.0.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/d/DMTCP/DMTCP-3.0.0-GCCcore-12.2.0.eb
new file mode 100644
index 00000000000..d3c859706e4
--- /dev/null
+++ b/easybuild/easyconfigs/d/DMTCP/DMTCP-3.0.0-GCCcore-12.2.0.eb
@@ -0,0 +1,26 @@
+easyblock = 'ConfigureMake'
+
+name = 'DMTCP'
+version = '3.0.0'
+
+homepage = 'http://dmtcp.sourceforge.net/index.html'
+description = """DMTCP is a tool to transparently checkpoint the state of multiple
+simultaneous applications, including multi-threaded and distributed applications.
+It operates directly on the user binary executable, without any Linux kernel modules
+or other kernel modifications."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+
+source_urls = ['https://github.com/dmtcp/dmtcp/archive/']
+sources = ['%(version)s.tar.gz']
+checksums = ['2c7e95e1dbc55db33433bfee48a65f274298e98f246a36ab6dad1e0694750d37']
+
+builddependencies = [('binutils', '2.38')]
+
+sanity_check_paths = {
+    'files': ['bin/dmtcp_command', 'bin/dmtcp_discover_rm', 'bin/dmtcp_nocheckpoint', 'bin/dmtcp_srun_helper',
+              'bin/dmtcp_sshd',  'bin/dmtcp_coordinator', 'bin/dmtcp_launch', 'bin/dmtcp_restart', 'bin/dmtcp_ssh'],
+    'dirs': [],
+}
+
+moduleclass = 'tools'
diff --git a/easybuild/easyconfigs/d/DMTCP/DMTCP-3.0.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/d/DMTCP/DMTCP-3.0.0-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..9947d4f758d
--- /dev/null
+++ b/easybuild/easyconfigs/d/DMTCP/DMTCP-3.0.0-GCCcore-12.3.0.eb
@@ -0,0 +1,26 @@
+easyblock = 'ConfigureMake'
+
+name = 'DMTCP'
+version = '3.0.0'
+
+homepage = 'http://dmtcp.sourceforge.net/index.html'
+description = """DMTCP is a tool to transparently checkpoint the state of multiple
+simultaneous applications, including multi-threaded and distributed applications.
+It operates directly on the user binary executable, without any Linux kernel modules
+or other kernel modifications."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+source_urls = ['https://github.com/dmtcp/dmtcp/archive/']
+sources = ['%(version)s.tar.gz']
+checksums = ['2c7e95e1dbc55db33433bfee48a65f274298e98f246a36ab6dad1e0694750d37']
+
+builddependencies = [('binutils', '2.40')]
+
+sanity_check_paths = {
+    'files': ['bin/dmtcp_command', 'bin/dmtcp_discover_rm', 'bin/dmtcp_nocheckpoint', 'bin/dmtcp_srun_helper',
+              'bin/dmtcp_sshd',  'bin/dmtcp_coordinator', 'bin/dmtcp_launch', 'bin/dmtcp_restart', 'bin/dmtcp_ssh'],
+    'dirs': [],
+}
+
+moduleclass = 'tools'
diff --git a/easybuild/easyconfigs/d/DMTCP/DMTCP-3.0.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/d/DMTCP/DMTCP-3.0.0-GCCcore-13.2.0.eb
new file mode 100644
index 00000000000..9721668c208
--- /dev/null
+++ b/easybuild/easyconfigs/d/DMTCP/DMTCP-3.0.0-GCCcore-13.2.0.eb
@@ -0,0 +1,26 @@
+easyblock = 'ConfigureMake'
+
+name = 'DMTCP'
+version = '3.0.0'
+
+homepage = 'http://dmtcp.sourceforge.net/index.html'
+description = """DMTCP is a tool to transparently checkpoint the state of multiple
+simultaneous applications, including multi-threaded and distributed applications.
+It operates directly on the user binary executable, without any Linux kernel modules
+or other kernel modifications."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
+
+source_urls = ['https://github.com/dmtcp/dmtcp/archive/']
+sources = ['%(version)s.tar.gz']
+checksums = ['2c7e95e1dbc55db33433bfee48a65f274298e98f246a36ab6dad1e0694750d37']
+
+builddependencies = [('binutils', '2.40')]
+
+sanity_check_paths = {
+    'files': ['bin/dmtcp_command', 'bin/dmtcp_discover_rm', 'bin/dmtcp_nocheckpoint', 'bin/dmtcp_srun_helper',
+              'bin/dmtcp_sshd',  'bin/dmtcp_coordinator', 'bin/dmtcp_launch', 'bin/dmtcp_restart', 'bin/dmtcp_ssh'],
+    'dirs': [],
+}
+
+moduleclass = 'tools'

From 6892e56fe41f1bdf56c4a710226ed90c461301a4 Mon Sep 17 00:00:00 2001
From: sassy <sassy@hp>
Date: Tue, 18 Jun 2024 10:37:45 +0100
Subject: [PATCH 242/835] binutils version corrected

---
 easybuild/easyconfigs/d/DMTCP/DMTCP-3.0.0-GCCcore-12.2.0.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/d/DMTCP/DMTCP-3.0.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/d/DMTCP/DMTCP-3.0.0-GCCcore-12.2.0.eb
index d3c859706e4..0474c5e8f88 100644
--- a/easybuild/easyconfigs/d/DMTCP/DMTCP-3.0.0-GCCcore-12.2.0.eb
+++ b/easybuild/easyconfigs/d/DMTCP/DMTCP-3.0.0-GCCcore-12.2.0.eb
@@ -15,7 +15,7 @@ source_urls = ['https://github.com/dmtcp/dmtcp/archive/']
 sources = ['%(version)s.tar.gz']
 checksums = ['2c7e95e1dbc55db33433bfee48a65f274298e98f246a36ab6dad1e0694750d37']
 
-builddependencies = [('binutils', '2.38')]
+builddependencies = [('binutils', '2.39')]
 
 sanity_check_paths = {
     'files': ['bin/dmtcp_command', 'bin/dmtcp_discover_rm', 'bin/dmtcp_nocheckpoint', 'bin/dmtcp_srun_helper',

From d6faf3c3e3458ed2ddd9a26604c7c88f59a258b8 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Petr=20Kr=C3=A1l?= <petr@inuits.eu>
Date: Tue, 18 Jun 2024 12:45:57 +0200
Subject: [PATCH 243/835] adding easyconfigs: pyspoa-0.2.1-GCC-13.2.0.eb,
 spoa-4.1.0-GCC-13.2.0.eb

---
 .../p/pyspoa/pyspoa-0.2.1-GCC-13.2.0.eb       | 62 +++++++++++++++++++
 .../s/spoa/spoa-4.1.0-GCC-13.2.0.eb           | 29 +++++++++
 2 files changed, 91 insertions(+)
 create mode 100644 easybuild/easyconfigs/p/pyspoa/pyspoa-0.2.1-GCC-13.2.0.eb
 create mode 100644 easybuild/easyconfigs/s/spoa/spoa-4.1.0-GCC-13.2.0.eb

diff --git a/easybuild/easyconfigs/p/pyspoa/pyspoa-0.2.1-GCC-13.2.0.eb b/easybuild/easyconfigs/p/pyspoa/pyspoa-0.2.1-GCC-13.2.0.eb
new file mode 100644
index 00000000000..127ab6861d9
--- /dev/null
+++ b/easybuild/easyconfigs/p/pyspoa/pyspoa-0.2.1-GCC-13.2.0.eb
@@ -0,0 +1,62 @@
+easyblock = 'PythonPackage'
+
+name = 'pyspoa'
+version = '0.2.1'
+
+local_cereal_version = '1.3.2'
+
+homepage = 'https://github.com/nanoporetech/pyspoa'
+description = "Python bindings to spoa."
+
+toolchain = {'name': 'GCC', 'version': '13.2.0'}
+
+toolchainopts = {'extra_cflags': "-fpermissive"}
+
+sources = [
+    {
+        'filename': '%(name)s-%(version)s.tar.gz',
+        'git_config': {
+            'url': 'https://github.com/nanoporetech',
+            'repo_name': 'pyspoa',
+            'tag': 'v%(version)s',
+            'recursive': True,
+            'keep_git_dir': True,
+        }
+    },
+    {
+        'source_urls': ['https://github.com/USCiLab/cereal/archive/'],
+        'download_filename': 'v%s.tar.gz' % local_cereal_version,
+        'filename': 'cereal-%s.tar.gz' % local_cereal_version,
+    },
+]
+
+patches = ['pyspoa-%(version)s_use-spoa-dep.patch']
+
+checksums = [
+    None,
+    '16a7ad9b31ba5880dac55d62b5d6f243c3ebc8d46a3514149e56b5e7ea81f85f',
+    'dffd946e3b36e4872846fe983d287f992b5bf177798e11141bf0d645cfc0664d',
+]
+
+builddependencies = [('CMake', '3.27.6')]
+
+dependencies = [
+    ('Python', '3.11.5'),
+    ('pybind11', '2.11.1'),
+    ('spoa', '4.1.0'),
+]
+
+download_dep_fail = True
+use_pip = True
+sanity_pip_check = True
+
+preinstallopts = "mkdir -p src/vendor/cereal && ln -s %(builddir)s/cereal-*/include src/vendor/cereal/include && "
+# strip out cmake requirements, since we provide that as proper dependency
+preinstallopts += "sed -i 's/.cmake==[0-9.]*.//g' setup.py && "
+preinstallopts += "export libspoa=$EBROOTSPOA/lib/libspoa.a && "
+
+options = {'modulename': 'spoa'}
+
+sanity_check_commands = ["cd %(builddir)s/*/tests && python test_pyspoa.py"]
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/s/spoa/spoa-4.1.0-GCC-13.2.0.eb b/easybuild/easyconfigs/s/spoa/spoa-4.1.0-GCC-13.2.0.eb
new file mode 100644
index 00000000000..16062a7636e
--- /dev/null
+++ b/easybuild/easyconfigs/s/spoa/spoa-4.1.0-GCC-13.2.0.eb
@@ -0,0 +1,29 @@
+easyblock = 'CMakeMake'
+
+name = 'spoa'
+version = '4.1.0'
+
+homepage = 'https://github.com/rvaser/spoa'
+description = """Spoa (SIMD POA) is a c++ implementation of the partial order alignment (POA) algorithm
+ which is used to generate consensus sequences"""
+
+toolchain = {'name': 'GCC', 'version': '13.2.0'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://github.com/rvaser/spoa/archive/']
+sources = ['%(version)s.tar.gz']
+checksums = ['43238356f00bce2ad9698fc18b3e320024172a82182dcff24d57c5cf19e342c8']
+
+builddependencies = [('CMake', '3.27.6')]
+
+configopts = "-Dspoa_build_executable=ON"
+
+sanity_check_paths = {
+    'files': ['bin/spoa'] + ['include/spoa/%s' % x for x in ['alignment_engine.hpp', 'graph.hpp', 'spoa.hpp']] +
+             ['lib/libspoa.a'],
+    'dirs': [],
+}
+
+sanity_check_commands = ["spoa --help"]
+
+moduleclass = 'bio'

From e0bc0860c1052c37a1a53490559e7f3c2738d8d3 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Petr=20Kr=C3=A1l?= <petr@inuits.eu>
Date: Tue, 18 Jun 2024 12:47:18 +0200
Subject: [PATCH 244/835] adding easyconfigs:
 python-parasail-1.3.4-foss-2023b.eb, parasail-2.6.2-GCC-13.2.0.eb

---
 .../p/parasail/parasail-2.6.2-GCC-13.2.0.eb   | 26 +++++++++++++++
 .../python-parasail-1.3.4-foss-2023b.eb       | 32 +++++++++++++++++++
 2 files changed, 58 insertions(+)
 create mode 100644 easybuild/easyconfigs/p/parasail/parasail-2.6.2-GCC-13.2.0.eb
 create mode 100644 easybuild/easyconfigs/p/python-parasail/python-parasail-1.3.4-foss-2023b.eb

diff --git a/easybuild/easyconfigs/p/parasail/parasail-2.6.2-GCC-13.2.0.eb b/easybuild/easyconfigs/p/parasail/parasail-2.6.2-GCC-13.2.0.eb
new file mode 100644
index 00000000000..ddb3e791f30
--- /dev/null
+++ b/easybuild/easyconfigs/p/parasail/parasail-2.6.2-GCC-13.2.0.eb
@@ -0,0 +1,26 @@
+easyblock = 'CMakeMake'
+
+name = 'parasail'
+version = '2.6.2'
+
+homepage = 'https://github.com/jeffdaily/parasail'
+description = """parasail is a SIMD C (C99) library containing implementations
+ of the Smith-Waterman (local), Needleman-Wunsch (global), and semi-global
+ pairwise sequence alignment algorithms. """
+
+toolchain = {'name': 'GCC', 'version': '13.2.0'}
+
+github_account = 'jeffdaily'
+source_urls = [GITHUB_SOURCE]
+sources = ['v%(version)s.tar.gz']
+checksums = ['9057041db8e1cde76678f649420b85054650414e5de9ea84ee268756c7ea4b4b']
+
+builddependencies = [('CMake', '3.27.6')]
+
+sanity_check_paths = {
+    'files': ['bin/parasail_aligner', 'bin/parasail_stats',
+              'lib/libparasail.%s' % SHLIB_EXT, 'include/parasail.h'],
+    'dirs': [],
+}
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/p/python-parasail/python-parasail-1.3.4-foss-2023b.eb b/easybuild/easyconfigs/p/python-parasail/python-parasail-1.3.4-foss-2023b.eb
new file mode 100644
index 00000000000..46bbb77dda9
--- /dev/null
+++ b/easybuild/easyconfigs/p/python-parasail/python-parasail-1.3.4-foss-2023b.eb
@@ -0,0 +1,32 @@
+easyblock = 'PythonPackage'
+
+name = 'python-parasail'
+version = '1.3.4'
+
+homepage = 'https://github.com/jeffdaily/parasail-python'
+description = "Python Bindings for the Parasail C Library"
+
+toolchain = {'name': 'foss', 'version': '2023b'}
+
+sources = ['parasail-%(version)s.tar.gz']
+checksums = ['d6a7035dfae3ef5aafdd7e6915711214c22b572ea059fa69d9d7ecbfb9b61b0f']
+
+builddependencies = [
+    ('parasail', '2.6.2'),
+]
+
+dependencies = [
+    ('Python', '3.11.5'),
+    ('SciPy-bundle', '2023.11'),
+]
+
+download_dep_fail = True
+use_pip = True
+sanity_pip_check = True
+
+# make sure setup.py finds the parasail library
+preinstallopts = "ln -s $EBROOTPARASAIL/lib/libparasail.so parasail/libparasail.%s && " % SHLIB_EXT
+
+options = {'modulename': 'parasail'}
+
+moduleclass = 'bio'

From 63e79361f60a5684fe7bc01832147c28513f268a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Tue, 18 Jun 2024 14:42:29 +0200
Subject: [PATCH 245/835] add patch for numpy 1.26.4 that fixes RISC-V test
 failures

---
 .../SciPy-bundle-2024.05-gfbf-2024.05.eb      |   7 +-
 ...mpy-1.26.4_fix-riscv64-test-failures.patch | 156 ++++++++++++++++++
 2 files changed, 162 insertions(+), 1 deletion(-)
 create mode 100644 easybuild/easyconfigs/s/SciPy-bundle/numpy-1.26.4_fix-riscv64-test-failures.patch

diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2024.05-gfbf-2024.05.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2024.05-gfbf-2024.05.eb
index c3f76125dce..b80b8631909 100644
--- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2024.05-gfbf-2024.05.eb
+++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2024.05-gfbf-2024.05.eb
@@ -30,11 +30,16 @@ use_pip = True
 # order is important!
 exts_list = [
     ('numpy', '1.26.4', {
-        'patches': ['numpy-1.22.3_disable-broken-override-test.patch'],
+        'patches': [
+            'numpy-1.22.3_disable-broken-override-test.patch',
+            'numpy-1.26.4_fix-riscv64-test-failures.patch',
+        ],
         'checksums': [
             {'numpy-1.26.4.tar.gz': '2a02aba9ed12e4ac4eb3ea9421c420301a0c6460d9830d74a9df87efa4912010'},
             {'numpy-1.22.3_disable-broken-override-test.patch':
              '9c589bb073b28b25ff45eb3c63c57966aa508dd8b318d0b885b6295271e4983c'},
+            {'numpy-1.26.4_fix-riscv64-test-failures.patch':
+             '81bd487dbca6da8285971a16a2c7b488718a051d3cd66450277bed6ff21741de'},
         ],
     }),
     ('ply', '3.11', {
diff --git a/easybuild/easyconfigs/s/SciPy-bundle/numpy-1.26.4_fix-riscv64-test-failures.patch b/easybuild/easyconfigs/s/SciPy-bundle/numpy-1.26.4_fix-riscv64-test-failures.patch
new file mode 100644
index 00000000000..ccc444e1f4d
--- /dev/null
+++ b/easybuild/easyconfigs/s/SciPy-bundle/numpy-1.26.4_fix-riscv64-test-failures.patch
@@ -0,0 +1,156 @@
+From d9e88e32302b3842785a33d90cf22f8c1405cd05 Mon Sep 17 00:00:00 2001
+From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
+Date: Tue, 18 Jun 2024 13:28:35 +0200
+Subject: [PATCH 1/2] TST: Fix fp_noncontiguous and fpclass on riscv64
+
+Modify fp_noncontiguous and fpclass so that they pass on riscv64.
+The subtests that verify that the signs of negative NaNs are preserved
+do not pass on riscv64 builds and are disabled.  Many RISC-V
+instructions that produce NaNs return a canonical NaN, as defined by
+the RISC-V specification.  The canonical NaNs are always positive. See
+section 11.3 NaN Generation and Propagation of the RISC-V Unprivileged
+ISA for more details.
+---
+ numpy/core/tests/test_umath.py | 44 +++++++++++++++++++++++++++++-----
+ 1 file changed, 38 insertions(+), 6 deletions(-)
+
+diff --git a/numpy/core/tests/test_umath.py b/numpy/core/tests/test_umath.py
+index 963e740d8dcb..8444893c80c3 100644
+--- a/numpy/core/tests/test_umath.py
++++ b/numpy/core/tests/test_umath.py
+@@ -1852,8 +1852,22 @@ def test_fpclass(self, stride):
+         assert_equal(np.isnan(arr_f64[::stride]), nan[::stride])
+         assert_equal(np.isinf(arr_f32[::stride]), inf[::stride])
+         assert_equal(np.isinf(arr_f64[::stride]), inf[::stride])
+-        assert_equal(np.signbit(arr_f32[::stride]), sign[::stride])
+-        assert_equal(np.signbit(arr_f64[::stride]), sign[::stride])
++        if platform.processor() == 'riscv64':
++            # On RISC-V, many operations that produce NaNs, such as converting
++            # a -NaN from f64 to f32, return a canonical NaN.  The canonical
++            # NaNs are always positive.  See section 11.3 NaN Generation and
++            # Propagation of the RISC-V Unprivileged ISA for more details.
++            # We disable the sign test on riscv64 for -np.nan as we
++            # cannot assume that its sign will be honoured in these tests.
++            arr_f64_rv = np.copy(arr_f64)
++            arr_f32_rv = np.copy(arr_f32)
++            arr_f64_rv[1] = -1.0
++            arr_f32_rv[1] = -1.0
++            assert_equal(np.signbit(arr_f32_rv[::stride]), sign[::stride])
++            assert_equal(np.signbit(arr_f64_rv[::stride]), sign[::stride])
++        else:
++            assert_equal(np.signbit(arr_f32[::stride]), sign[::stride])
++            assert_equal(np.signbit(arr_f64[::stride]), sign[::stride])
+         assert_equal(np.isfinite(arr_f32[::stride]), finite[::stride])
+         assert_equal(np.isfinite(arr_f64[::stride]), finite[::stride])
+ 
+@@ -1874,23 +1888,37 @@ def test_fp_noncontiguous(self, dtype):
+         ncontig_in = data[1::3]
+         ncontig_out = out[1::3]
+         contig_in = np.array(ncontig_in)
++
++        if platform.processor() == 'riscv64':
++            # Disable the -np.nan signbit tests on riscv64.  See comments in
++            # test_fpclass for more details.
++            data_rv = np.copy(data)
++            data_rv[1] = -1.0
++            ncontig_sign_in = data_rv[1::3]
++            contig_sign_in = np.array(ncontig_sign_in)
++        else:
++            ncontig_sign_in = ncontig_in
++            contig_sign_in = contig_in
++
+         assert_equal(ncontig_in.flags.c_contiguous, False)
+         assert_equal(ncontig_out.flags.c_contiguous, False)
+         assert_equal(contig_in.flags.c_contiguous, True)
++        assert_equal(ncontig_sign_in.flags.c_contiguous, False)
++        assert_equal(contig_sign_in.flags.c_contiguous, True)
+         # ncontig in, ncontig out
+         assert_equal(np.isnan(ncontig_in, out=ncontig_out), nan[1::3])
+         assert_equal(np.isinf(ncontig_in, out=ncontig_out), inf[1::3])
+-        assert_equal(np.signbit(ncontig_in, out=ncontig_out), sign[1::3])
++        assert_equal(np.signbit(ncontig_sign_in, out=ncontig_out), sign[1::3])
+         assert_equal(np.isfinite(ncontig_in, out=ncontig_out), finite[1::3])
+         # contig in, ncontig out
+         assert_equal(np.isnan(contig_in, out=ncontig_out), nan[1::3])
+         assert_equal(np.isinf(contig_in, out=ncontig_out), inf[1::3])
+-        assert_equal(np.signbit(contig_in, out=ncontig_out), sign[1::3])
++        assert_equal(np.signbit(contig_sign_in, out=ncontig_out), sign[1::3])
+         assert_equal(np.isfinite(contig_in, out=ncontig_out), finite[1::3])
+         # ncontig in, contig out
+         assert_equal(np.isnan(ncontig_in), nan[1::3])
+         assert_equal(np.isinf(ncontig_in), inf[1::3])
+-        assert_equal(np.signbit(ncontig_in), sign[1::3])
++        assert_equal(np.signbit(ncontig_sign_in), sign[1::3])
+         assert_equal(np.isfinite(ncontig_in), finite[1::3])
+         # contig in, contig out, nd stride
+         data_split = np.array(np.array_split(data, 2))
+@@ -1900,7 +1928,11 @@ def test_fp_noncontiguous(self, dtype):
+         finite_split = np.array(np.array_split(finite, 2))
+         assert_equal(np.isnan(data_split), nan_split)
+         assert_equal(np.isinf(data_split), inf_split)
+-        assert_equal(np.signbit(data_split), sign_split)
++        if platform.processor() == 'riscv64':
++            data_split_rv = np.array(np.array_split(data_rv, 2))
++            assert_equal(np.signbit(data_split_rv), sign_split)
++        else:
++            assert_equal(np.signbit(data_split), sign_split)
+         assert_equal(np.isfinite(data_split), finite_split)
+ 
+ class TestLDExp:
+
+From ccb1d4adc01b49c7e900e5f532dc6361eac1362a Mon Sep 17 00:00:00 2001
+From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
+Date: Tue, 18 Jun 2024 13:30:00 +0200
+Subject: [PATCH 2/2] TST: Use platform.machine() for improved portability on
+ riscv64
+
+Replace `platform.processor()` with `platform.machine()` considering the latter is more portable.  More specifically, `platform.processor()` returns empty string on Arch Linux, and this PR fixes the corresponding test failure.
+---
+ numpy/core/tests/test_numeric.py | 2 +-
+ numpy/core/tests/test_umath.py   | 6 +++---
+ 2 files changed, 4 insertions(+), 4 deletions(-)
+
+diff --git a/numpy/core/tests/test_numeric.py b/numpy/core/tests/test_numeric.py
+index e5edd3efce5a..ce5917a9b09f 100644
+--- a/numpy/core/tests/test_numeric.py
++++ b/numpy/core/tests/test_numeric.py
+@@ -483,7 +483,7 @@ def setup_method(self):
+         # Propagation of the RISC-V Unprivileged ISA for more details.
+         # We disable the float32 sign test on riscv64 for -np.nan as the sign
+         # of the NaN will be lost when it's converted to a float32.
+-        if platform.processor() != 'riscv64':
++        if platform.machine() != 'riscv64':
+             self.signf[3::6][self.ef[3::6]] = -np.nan
+         self.signd[3::6][self.ed[3::6]] = -np.nan
+         self.signf[4::6][self.ef[4::6]] = -0.
+diff --git a/numpy/core/tests/test_umath.py b/numpy/core/tests/test_umath.py
+index 8444893c80c3..c5a3e2c81f83 100644
+--- a/numpy/core/tests/test_umath.py
++++ b/numpy/core/tests/test_umath.py
+@@ -1852,7 +1852,7 @@ def test_fpclass(self, stride):
+         assert_equal(np.isnan(arr_f64[::stride]), nan[::stride])
+         assert_equal(np.isinf(arr_f32[::stride]), inf[::stride])
+         assert_equal(np.isinf(arr_f64[::stride]), inf[::stride])
+-        if platform.processor() == 'riscv64':
++        if platform.machine() == 'riscv64':
+             # On RISC-V, many operations that produce NaNs, such as converting
+             # a -NaN from f64 to f32, return a canonical NaN.  The canonical
+             # NaNs are always positive.  See section 11.3 NaN Generation and
+@@ -1889,7 +1889,7 @@ def test_fp_noncontiguous(self, dtype):
+         ncontig_out = out[1::3]
+         contig_in = np.array(ncontig_in)
+ 
+-        if platform.processor() == 'riscv64':
++        if platform.machine() == 'riscv64':
+             # Disable the -np.nan signbit tests on riscv64.  See comments in
+             # test_fpclass for more details.
+             data_rv = np.copy(data)
+@@ -1928,7 +1928,7 @@ def test_fp_noncontiguous(self, dtype):
+         finite_split = np.array(np.array_split(finite, 2))
+         assert_equal(np.isnan(data_split), nan_split)
+         assert_equal(np.isinf(data_split), inf_split)
+-        if platform.processor() == 'riscv64':
++        if platform.machine() == 'riscv64':
+             data_split_rv = np.array(np.array_split(data_rv, 2))
+             assert_equal(np.signbit(data_split_rv), sign_split)
+         else:

From b94f12b6afde825c8d0562d8702452c9f889c49c Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Tue, 18 Jun 2024 15:12:24 +0200
Subject: [PATCH 246/835] adding easyconfigs:
 imbalanced-learn-0.12.3-gfbf-2023a.eb

---
 .../imbalanced-learn-0.12.3-gfbf-2023a.eb     | 27 +++++++++++++++++++
 1 file changed, 27 insertions(+)
 create mode 100644 easybuild/easyconfigs/i/imbalanced-learn/imbalanced-learn-0.12.3-gfbf-2023a.eb

diff --git a/easybuild/easyconfigs/i/imbalanced-learn/imbalanced-learn-0.12.3-gfbf-2023a.eb b/easybuild/easyconfigs/i/imbalanced-learn/imbalanced-learn-0.12.3-gfbf-2023a.eb
new file mode 100644
index 00000000000..4881e78a0e7
--- /dev/null
+++ b/easybuild/easyconfigs/i/imbalanced-learn/imbalanced-learn-0.12.3-gfbf-2023a.eb
@@ -0,0 +1,27 @@
+easyblock = 'PythonBundle'
+
+name = 'imbalanced-learn'
+version = '0.12.3'
+
+homepage = 'https://github.com/scikit-learn-contrib/imbalanced-learn'
+description = """imbalanced-learn is a Python package offering a number of re-sampling techniques commonly used in
+ datasets showing strong between-class imbalance."""
+
+toolchain = {'name': 'gfbf', 'version': '2023a'}
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('scikit-learn', '1.3.1'),
+]
+
+sanity_pip_check = True
+use_pip = True
+
+exts_list = [
+    (name, version, {
+        'modulename': 'imblearn',
+        'checksums': ['5b00796a01419e9102bd425e27c319d58d1f6cf2dfa751e02ed7f4edf67c3c1b'],
+    }),
+]
+
+moduleclass = 'tools'

From deb66d06567e8624bbb9e8c6eb747e15a6bb832a Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Tue, 18 Jun 2024 15:39:26 +0200
Subject: [PATCH 247/835] add pyproject-metadata to exts

---
 .../easyconfigs/s/scArches/scArches-0.6.1-foss-2023a.eb      | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/s/scArches/scArches-0.6.1-foss-2023a.eb b/easybuild/easyconfigs/s/scArches/scArches-0.6.1-foss-2023a.eb
index f72ebf96042..ef28b4b84b0 100644
--- a/easybuild/easyconfigs/s/scArches/scArches-0.6.1-foss-2023a.eb
+++ b/easybuild/easyconfigs/s/scArches/scArches-0.6.1-foss-2023a.eb
@@ -9,7 +9,6 @@ description = """Single-cell architecture surgery (scArches) is a package for re
 
 toolchain = {'name': 'foss', 'version': '2023a'}
 
-builddependencies = [('scikit-build-core', '0.5.0')]
 dependencies = [
     ('Python', '3.11.3'),
     ('SciPy-bundle', '2023.07'),
@@ -32,6 +31,10 @@ dependencies = [
 use_pip = True
 
 exts_list = [
+    ('pyproject-metadata', '0.8.0', {
+        'sources': ['pyproject_metadata-%(version)s.tar.gz'],
+        'checksums': ['376d5a00764ac29440a54579f88e66b7d9cb7e629d35c35a1c7248bfebc9b455'],
+    }),
     ('sphinx_basic_ng', '1.0.0b2', {
         'checksums': ['9ec55a47c90c8c002b5960c57492ec3021f5193cb26cebc2dc4ea226848651c9'],
     }),

From e637d6903aa999633ef64b00e483837f3b690f62 Mon Sep 17 00:00:00 2001
From: Simon Pinches <Simon.Pinches@iter.org>
Date: Tue, 18 Jun 2024 21:19:43 +0200
Subject: [PATCH 248/835] adding easyconfigs: Triangle-1.6-GCCcore-13.2.0.eb

---
 .../t/Triangle/Triangle-1.6-GCCcore-13.2.0.eb | 39 +++++++++++++++++++
 1 file changed, 39 insertions(+)
 create mode 100644 easybuild/easyconfigs/t/Triangle/Triangle-1.6-GCCcore-13.2.0.eb

diff --git a/easybuild/easyconfigs/t/Triangle/Triangle-1.6-GCCcore-13.2.0.eb b/easybuild/easyconfigs/t/Triangle/Triangle-1.6-GCCcore-13.2.0.eb
new file mode 100644
index 00000000000..813429474de
--- /dev/null
+++ b/easybuild/easyconfigs/t/Triangle/Triangle-1.6-GCCcore-13.2.0.eb
@@ -0,0 +1,39 @@
+easyblock = 'MakeCp'
+
+name = 'Triangle'
+version = '1.6'
+
+homepage = 'https://www.cs.cmu.edu/~quake/triangle.html'
+description = """Triangle generates exact Delaunay triangulations, constrained Delaunay triangulations,
+ conforming Delaunay triangulations, Voronoi diagrams, and high-quality triangular meshes.
+ The latter can be generated with no small or large angles,
+ and are thus suitable for finite element analysis."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://www.netlib.org/voronoi/']
+sources = ['%(namelower)s.zip']
+checksums = [
+    '1766327add038495fa3499e9b7cc642179229750f7201b94f8e1b7bee76f8480',  # triangle.zip
+    '38fc1395c2392f627068b669275c30da0c25b1a6db8ed8b80d6bf05a98971568',  # Triangle-1.6_makefile.patch
+]
+
+patches = ['%(name)s-%(version)s_makefile.patch']
+
+builddependencies = [('binutils', '2.40')]
+
+buildopts = 'triangle trilibrary'
+
+files_to_copy = [
+    (['triangle', 'tricall'], 'bin'),
+    (['triangle.h'], 'include'),
+    (['libtriangle.a'], 'lib'),
+]
+
+sanity_check_paths = {
+    'files': ['bin/triangle', 'bin/tricall', 'include/triangle.h', 'lib/libtriangle.a'],
+    'dirs': []
+}
+
+moduleclass = 'numlib'

From a10037473b4145a5d0e9da0926df271c3b64128c Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 18 Jun 2024 22:22:02 +0200
Subject: [PATCH 249/835] rename torch_em to torch-em + remove preinstallopts
 for termcolor which are not required since hatchling is available as build
 dependency

---
 .../torch-em-0.7.1-foss-2023a.eb}                 | 15 +--------------
 1 file changed, 1 insertion(+), 14 deletions(-)
 rename easybuild/easyconfigs/t/{torch_em/torch_em-0.7.1-foss-2023a.eb => torch-em/torch-em-0.7.1-foss-2023a.eb} (85%)

diff --git a/easybuild/easyconfigs/t/torch_em/torch_em-0.7.1-foss-2023a.eb b/easybuild/easyconfigs/t/torch-em/torch-em-0.7.1-foss-2023a.eb
similarity index 85%
rename from easybuild/easyconfigs/t/torch_em/torch_em-0.7.1-foss-2023a.eb
rename to easybuild/easyconfigs/t/torch-em/torch-em-0.7.1-foss-2023a.eb
index 330527abd2c..425ec7e35af 100644
--- a/easybuild/easyconfigs/t/torch_em/torch_em-0.7.1-foss-2023a.eb
+++ b/easybuild/easyconfigs/t/torch-em/torch-em-0.7.1-foss-2023a.eb
@@ -1,6 +1,6 @@
 easyblock = 'PythonBundle'
 
-name = 'torch_em'
+name = 'torch-em'
 version = '0.7.1'
 
 homepage = 'https://github.com/constantinpape/torch-em/'
@@ -33,22 +33,9 @@ dependencies = [
 use_pip = True
 sanity_pip_check = True
 
-# avoid using hatchling as build backend (since installing it for this old Python version is a nightmare)
-# copied from MONAI-1.0.1-foss-2022a.eb
-local_preinstallopts_termcolor = ' '.join([
-    r"""sed -i -e 's/^build-backend = .*/build-backend = "setuptools.build_meta"/g' """,
-    r"""-e 's/^requires = \[/requires = \["setuptools"/g' """,
-    r"""-e '/"hatch/d' """,
-    # replace dynamic version with hardcoded version
-    r"""-e '/"version"/d' """,
-    r"""-e 's/^readme = .*/version = "%(version)s"/g' """,
-    r"pyproject.toml && ",
-])
-
 exts_list = [
     ('termcolor', '2.3.0', {
         'checksums': ['b5b08f68937f138fe92f6c089b99f1e2da0ae56c52b78bf7075fd95420fd9a5a'],
-        'preinstallopts': local_preinstallopts_termcolor,
     }),
     ('dnspython', '2.6.1', {
         'modulename': False,

From d58a1fc869a38f686bedd57e5caf312c5737e1ac Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 18 Jun 2024 22:23:23 +0200
Subject: [PATCH 250/835] add missing && in preinstallopts in nifty + z5py
 easyconfigs

---
 easybuild/easyconfigs/n/nifty/nifty-1.2.1-foss-2023a.eb | 2 +-
 easybuild/easyconfigs/z/z5py/z5py-2.0.17-foss-2023a.eb  | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/easybuild/easyconfigs/n/nifty/nifty-1.2.1-foss-2023a.eb b/easybuild/easyconfigs/n/nifty/nifty-1.2.1-foss-2023a.eb
index 2c6c5ade6d3..37d6c62dec7 100644
--- a/easybuild/easyconfigs/n/nifty/nifty-1.2.1-foss-2023a.eb
+++ b/easybuild/easyconfigs/n/nifty/nifty-1.2.1-foss-2023a.eb
@@ -34,7 +34,7 @@ configopts = '-DWITH_QPBO=OFF -DWITH_HDF5=ON -DWITH_Z5=OFF -DWITH_ZLIB=ON -DWITH
 configopts += '-DPYTHON_EXECUTABLE="$EBROOTPYTHON/bin/python" -DBUILD_NIFTY_PYTHON=ON '
 
 # export PYTHON_MODULE_INSTALL_DIR to fix make install
-preinstallopts = 'export PYTHON_MODULE_INSTALL_DIR="%(builddir)s/easybuild_obj/python/" '
+preinstallopts = 'export PYTHON_MODULE_INSTALL_DIR="%(builddir)s/easybuild_obj/python/" && '
 
 files_to_copy = [(['python/nifty'], 'lib/python%(pyshortver)s/site-packages')]
 
diff --git a/easybuild/easyconfigs/z/z5py/z5py-2.0.17-foss-2023a.eb b/easybuild/easyconfigs/z/z5py/z5py-2.0.17-foss-2023a.eb
index 7f725171c46..3f3c8714771 100644
--- a/easybuild/easyconfigs/z/z5py/z5py-2.0.17-foss-2023a.eb
+++ b/easybuild/easyconfigs/z/z5py/z5py-2.0.17-foss-2023a.eb
@@ -35,7 +35,7 @@ configopts = '-DWITH_ZLIB=ON -DWITH_BZIP2=ON '
 configopts += '-DPYTHON_EXECUTABLE="$EBROOTPYTHON/bin/python" '
 
 # export PYTHON_MODULE_INSTALL_DIR to fix make install
-preinstallopts = 'export PYTHON_MODULE_INSTALL_DIR="%(builddir)s/easybuild_obj/python/" '
+preinstallopts = 'export PYTHON_MODULE_INSTALL_DIR="%(builddir)s/easybuild_obj/python/" && '
 
 files_to_copy = [(['python/z5py'], 'lib/python%(pyshortver)s/site-packages'), 'z5-config.cmake']
 

From 003908dec4763b5a830d774237e87c2e00ced98d Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 18 Jun 2024 22:25:13 +0200
Subject: [PATCH 251/835] rename torch_em dependency for micro-sam to torch-em

---
 easybuild/easyconfigs/m/micro-sam/micro-sam-1.0.1-foss-2023a.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/m/micro-sam/micro-sam-1.0.1-foss-2023a.eb b/easybuild/easyconfigs/m/micro-sam/micro-sam-1.0.1-foss-2023a.eb
index eb2f74f218f..418740280e5 100644
--- a/easybuild/easyconfigs/m/micro-sam/micro-sam-1.0.1-foss-2023a.eb
+++ b/easybuild/easyconfigs/m/micro-sam/micro-sam-1.0.1-foss-2023a.eb
@@ -19,7 +19,7 @@ dependencies = [
     ('z5py', '2.0.17'),
     ('python-xxhash', '3.4.1'),
     ('segment-anything', '1.0'),
-    ('torch_em', '0.7.1'),
+    ('torch-em', '0.7.1'),
 ]
 
 use_pip = True

From a9b5218d5b95eb2231bbb7e7d6719384ed8998fb Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 18 Jun 2024 22:32:22 +0200
Subject: [PATCH 252/835] stick to libsigc++ 3.4.0 as dependency for GLibmm
 v2.72.1 w/ GCCcore/11.3.0

---
 .../g/GLibmm/GLibmm-2.72.1-GCCcore-11.3.0.eb  |  2 +-
 .../libsigc++-3.6.0-GCCcore-11.3.0.eb         | 32 -------------------
 2 files changed, 1 insertion(+), 33 deletions(-)
 delete mode 100644 easybuild/easyconfigs/l/libsigc++/libsigc++-3.6.0-GCCcore-11.3.0.eb

diff --git a/easybuild/easyconfigs/g/GLibmm/GLibmm-2.72.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/GLibmm/GLibmm-2.72.1-GCCcore-11.3.0.eb
index 75a9c993725..728b2ec6a20 100644
--- a/easybuild/easyconfigs/g/GLibmm/GLibmm-2.72.1-GCCcore-11.3.0.eb
+++ b/easybuild/easyconfigs/g/GLibmm/GLibmm-2.72.1-GCCcore-11.3.0.eb
@@ -22,7 +22,7 @@ builddependencies = [
 
 dependencies = [
     ('GLib', '2.72.1'),
-    ('libsigc++', '3.6.0'),
+    ('libsigc++', '3.4.0'),
 ]
 
 sanity_check_paths = {
diff --git a/easybuild/easyconfigs/l/libsigc++/libsigc++-3.6.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libsigc++/libsigc++-3.6.0-GCCcore-11.3.0.eb
deleted file mode 100644
index 52518f5a054..00000000000
--- a/easybuild/easyconfigs/l/libsigc++/libsigc++-3.6.0-GCCcore-11.3.0.eb
+++ /dev/null
@@ -1,32 +0,0 @@
-easyblock = 'CMakeMake'
-
-name = 'libsigc++'
-version = '3.6.0'
-
-homepage = 'https://libsigcplusplus.github.io/libsigcplusplus/'
-description = """The libsigc++ package implements a typesafe callback system 
-for standard C++."""
-
-toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
-toolchainopts = {'pic': True}
-
-source_urls = [FTPGNOME_SOURCE]
-sources = [SOURCELOWER_TAR_XZ]
-checksums = ['c3d23b37dfd6e39f2e09f091b77b1541fbfa17c4f0b6bf5c89baef7229080e17']
-
-builddependencies = [
-    ('binutils', '2.38'),
-    ('libxslt', '1.1.34'),
-    ('mm-common', '1.0.6'),
-    ('CMake', '3.24.3'),
-]
-
-test_cmd = 'ctest'
-runtest = '-j'
-
-sanity_check_paths = {
-    'files': ['lib/libsigc-%%(version_major)s.0.%s' % SHLIB_EXT],
-    'dirs': [],
-}
-
-moduleclass = 'devel'

From 18289aa7c7bf24d2fc3eac7f565b2772ffa0b88f Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Wed, 19 Jun 2024 10:33:58 +0200
Subject: [PATCH 253/835] adding easyconfigs:
 OpenForceField-Toolkit-0.16.0-foss-2023a.eb

---
 ...penForceField-Toolkit-0.16.0-foss-2023a.eb | 144 ++++++++++++++++++
 1 file changed, 144 insertions(+)
 create mode 100644 easybuild/easyconfigs/o/OpenForceField-Toolkit/OpenForceField-Toolkit-0.16.0-foss-2023a.eb

diff --git a/easybuild/easyconfigs/o/OpenForceField-Toolkit/OpenForceField-Toolkit-0.16.0-foss-2023a.eb b/easybuild/easyconfigs/o/OpenForceField-Toolkit/OpenForceField-Toolkit-0.16.0-foss-2023a.eb
new file mode 100644
index 00000000000..3ef84650f5e
--- /dev/null
+++ b/easybuild/easyconfigs/o/OpenForceField-Toolkit/OpenForceField-Toolkit-0.16.0-foss-2023a.eb
@@ -0,0 +1,144 @@
+easyblock = 'PythonBundle'
+
+name = 'OpenForceField-Toolkit'
+version = '0.16.0'
+
+homepage = 'https://github.com/openforcefield/openff-toolkit'
+description = """The Open Force Field Toolkit provides implementations of the SMIRNOFF format, 
+parameterization engine, and other tools."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+    
+builddependencies = [('poetry', '1.5.1')]
+dependencies = [
+    ('Python', '3.11.3'),
+    ('Python-bundle-PyPI', '2023.06'),
+    ('SciPy-bundle', '2023.07'),
+    ('networkx', '3.1'),
+    ('typing-extensions', '4.9.0'),
+    ('pydantic', '2.5.3'),
+    ('tqdm', '4.66.1'),
+    ('OpenMM', '8.0.0'),
+    ('PyYAML', '6.0'),
+    ('RDKit', '2024.03.3'),
+    ('MDTraj', '1.9.9'),
+    ('JupyterNotebook', '7.0.2'),
+    ('AmberTools', '23.6'),
+    ('Pint', '0.23'),
+    ('nglview', '3.1.2'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('qcelemental', '0.26.0', {
+        'checksums': ['a14e8510cdbfda645ef1461c1afd02efb599311733dbba5f83fcd1d6168a6ddd'],
+    }),
+    ('PyJWT', '2.8.0', {
+        'modulename': 'jwt',
+        'checksums': ['57e28d156e3d5c10088e0c68abb90bfac3df82b40a71bd0daa20c65ccd5c23de'],
+    }),
+    ('apsw', '3.46.0.0', {
+        'checksums': ['e128ccaab511f9a7fc48be6414f99a9197f83a69624d8ba40c1ca241bdef418e'],
+    }),
+    ('zstandard', '0.18.0', {
+        'checksums': ['0ac0357a0d985b4ff31a854744040d7b5754385d1f98f7145c30e02c6865cb6f'],
+    }),
+    ('qcportal', '0.55', {
+        'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl',
+        'checksums': ['f6eb86d6ace4ae6a71bbd8e2ee054305aff2c1da0198a3741b0d589c572a31b3'],
+    }),
+    ('cached-property', '1.5.2', {
+        'checksums': ['9fa5755838eecbb2d234c3aa390bd80fbd3ac6b6869109bfc1b499f7bd89a130'],
+    }),
+    ('cachetools', '5.3.3', {
+        'checksums': ['ba29e2dfa0b8b556606f097407ed1aa62080ee108ab0dc5ec9d6a723a007d105'],
+    }),
+    ('python-constraint', '1.4.0', {
+        'modulename': 'constraint',
+        'source_tmpl': '%(name)s-%(version)s.tar.bz2',
+        'checksums': ['501d6f17afe0032dfc6ea6c0f8acc12e44f992733f00e8538961031ef27ccb8e'],
+    }),
+    ('bson', '0.5.10', {
+        'checksums': ['d6511b2ab051139a9123c184de1a04227262173ad593429d21e443d6462d6590'],
+    }),
+    ('xmltodict', '0.13.0', {
+        'checksums': ['341595a488e3e01a85a9d8911d8912fd922ede5fecc4dce437eb4b6c8d037e56'],
+    }),
+    ('intermol', '0.1.2', {
+        'source_tmpl': 'v%(version)s.tar.gz',
+        'source_urls': ['https://github.com/shirtsgroup/InterMol/archive/'],
+        'checksums': ['a3065133ba16585a5db3807466a36242d191156525c33079cf46a97cedcfe835'],
+    }),
+    ('SMIRNOFF99Frosst', '1.1.0', {
+        'source_tmpl': '%(version)s.tar.gz',
+        'source_urls': ['https://github.com/openforcefield/smirnoff99Frosst/archive/'],
+        'checksums': ['940c4ed3cd720e746549a3335f10b7b0d9047a67bc216ad45dd875be5c8ec467'],
+    }),
+    ('SMIRNOFF-Plugins', '2024.01.0', {
+        'source_tmpl': '%(version)s.tar.gz',
+        'source_urls': ['https://github.com/openforcefield/smirnoff-plugins/archive/'],
+        'checksums': ['8ba4dbc6ed320f06f30bf42e8f70399bc3818becd668990693b51ddca183ff74'],
+    }),
+    ('OpenForceField-ForceFields', '2024.04.0', {
+        'modulename': 'openforcefields',
+        'source_tmpl': '%(version)s.tar.gz',
+        'source_urls': ['https://github.com/openforcefield/openff-forcefields/archive/'],
+        'checksums': ['fc7094cdb74bf9f0ed665dfc716cc62c5a37def3fc7e852adeae0ae4b60169c7'],
+    }),
+    ('OpenForceField-Amber-FF-Ports', '0.0.4', {
+        'modulename': 'openff.amber_ff_ports',
+        'source_tmpl': 'v%(version)s.tar.gz',
+        'source_urls': ['https://github.com/openforcefield/openff-amber-ff-ports/archive/'],
+        'checksums': ['dbf2d1ccce06b0627b1eccae7e227ad800ff1cbac3e869344de265b178cc0207'],
+    }),
+    ('OpenForceField-Utilities', '0.1.12', {
+        'modulename': 'openff.utilities',
+        'source_tmpl': 'v%(version)s.tar.gz',
+        'source_urls': ['https://github.com/openforcefield/openff-utilities/archive/'],
+        'checksums': ['92882c5b87b40bdb4ee1e8c84c0ecc0fc83f26eaf3e3befde41bfdcf93d75dea'],
+    }),
+    ('OpenForceField-Units', '0.2.2', {
+        'modulename': 'openff.units',
+        'source_tmpl': '%(version)s.tar.gz',
+        'source_urls': ['https://github.com/openforcefield/openff-units/archive/'],
+        'checksums': ['532746534c1937938580d5cfe98f414aff9bfbcc66970e115a88a38f6d5a2581'],
+    }),
+    ('OpenForceField-NAGL-Models', '0.2.0', {
+        'modulename': 'openff.nagl_models',
+        'source_tmpl': 'v%(version)s.tar.gz',
+        'source_urls': ['https://github.com/openforcefield/openff-nagl-models/archive/'],
+        'checksums': ['df8e7ee980aa7ea99559759258a16e3aaa362245f5b7c32f9c25fb226eaee222'],
+    }),
+    ('OpenForceField-Models', '0.1.2', {
+        'modulename': 'openff.models',
+        'source_tmpl': '%(version)s.tar.gz',
+        'source_urls': ['https://github.com/openforcefield/openff-models/archive/'],
+        'checksums': ['cf2aa7ef467721f141149e4ce96134db390b27012f09996c4442a3fad2371653'],
+    }),
+    ('OpenForceField-Interchange', '0.3.27', {
+        'modulename': 'openff.interchange',
+        'source_tmpl': 'v%(version)s.tar.gz',
+        'source_urls': ['https://github.com/openforcefield/openff-interchange/archive/'],
+        'checksums': ['6b44ba8a89921b3843a5f9fc41dc4f8a0c784ba12221e3ea0fb8c1b01a10cf2e'],
+    }),
+    (name, version, {
+        'modulename': 'openff.toolkit',
+        'source_tmpl': '%(version)s.tar.gz',
+        'source_urls': ['https://github.com/openforcefield/openff-toolkit/archive/'],
+        'checksums': ['1c1aa2ac9fff7c1613168531884da4ade53cbe21069022c999996d7effd2474c'],
+    }),
+]
+
+sanity_check_commands = [
+    "python -c 'from openff.toolkit import Molecule, Topology, ForceField'",
+    "python -c 'from openff.interchange import Interchange'",
+    "python -c 'from openff.units import unit'",
+    "python -c 'from openff.interchange.components.mdconfig import MDConfig'",
+    "python -c 'from openff.interchange.models import TopologyKey'",
+    "python -c 'from openff.toolkit.typing.engines.smirnoff import ForceField'",
+]
+
+sanity_pip_check = True
+
+moduleclass = 'bio'

From 54a538ea650b286392a2b8f6f4c9ba1bdd07f6e1 Mon Sep 17 00:00:00 2001
From: Leonard Nielsen <leoniel@chalmers.se>
Date: Wed, 19 Jun 2024 09:42:02 +0000
Subject: [PATCH 254/835] adding easyconfigs: pyperf-2.7.0-GCCcore-12.3.0.eb

---
 .../p/pyperf/pyperf-2.7.0-GCCcore-12.3.0.eb   | 35 +++++++++++++++++++
 1 file changed, 35 insertions(+)
 create mode 100644 easybuild/easyconfigs/p/pyperf/pyperf-2.7.0-GCCcore-12.3.0.eb

diff --git a/easybuild/easyconfigs/p/pyperf/pyperf-2.7.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/pyperf/pyperf-2.7.0-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..0c4a1504248
--- /dev/null
+++ b/easybuild/easyconfigs/p/pyperf/pyperf-2.7.0-GCCcore-12.3.0.eb
@@ -0,0 +1,35 @@
+easyblock = 'PythonPackage'
+
+name = 'pyperf'
+version = '2.7.0'
+
+homepage = 'https://github.com/psf/pyperf'
+description = "The Python pyperf module is a toolkit to write, run and analyze benchmarks"
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+sources = [SOURCE_TAR_GZ]
+checksums = ['4201c6601032f374e9c900c6d2544a2f5891abedc1a96eec0e7b2338a6247589']
+
+builddependencies = [
+    ('binutils', '2.40'),
+]
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('psutil', '5.9.8'),
+]
+
+download_dep_fail = True
+use_pip = True
+
+sanity_check_paths = {
+    'files': ['bin/pyperf'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = ["pyperf --help"]
+
+sanity_pip_check = True
+
+moduleclass = 'tools'

From c582ec88fa3f1964016629fe4211d76e19036a41 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Wed, 19 Jun 2024 10:47:30 +0000
Subject: [PATCH 255/835] Fix linking to static brotli

---
 easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-13.2.0.eb | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-13.2.0.eb
index 75ccfd09cea..249b1170411 100644
--- a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-13.2.0.eb
+++ b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-13.2.0.eb
@@ -27,6 +27,7 @@ dependencies = [
 
 # skip use of third_party directory, since we provide Brotli via a proper dependency
 preconfigopts = "sed -i 's/add_subdirectory(third_party)//g' ../brunsli-%(version)s/CMakeLists.txt && "
+preconfigopts += "sed -i 's/\\(brotli...\\)-static/\\1/g' ../brunsli-%(version)s/brunsli.cmake && "
 
 configopts = '-DCMAKE_CXX_FLAGS="$CXXFLAGS -lbrotlienc -lbrotlidec -lbrotlicommon" '
 

From f65de69aadbc176eee05595f83326a2bc29bd940 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Petr=20Kr=C3=A1l?= <petr@inuits.eu>
Date: Wed, 19 Jun 2024 14:13:21 +0200
Subject: [PATCH 256/835] add dependency

---
 easybuild/easyconfigs/g/gap/gap-4.13.0-foss-2023b.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/g/gap/gap-4.13.0-foss-2023b.eb b/easybuild/easyconfigs/g/gap/gap-4.13.0-foss-2023b.eb
index ccde7c5df99..1c1693f7e45 100644
--- a/easybuild/easyconfigs/g/gap/gap-4.13.0-foss-2023b.eb
+++ b/easybuild/easyconfigs/g/gap/gap-4.13.0-foss-2023b.eb
@@ -30,7 +30,7 @@ dependencies = [
     ('lrslib', '7.2'),  # needed by HeLP
     ('ncurses', '6.4'),  # needed by Browse
     ('Normaliz', '3.10.3'),  # needed by NormalizInterface, HeLP
-    # ('Singular', '4.3.2p16'),  # needed by singular
+    ('Singular', '4.3.2p16'),  # needed by singular
     ('ZeroMQ', '4.3.5'),  # needed by ZeroMQInterface
 ]
 

From db19c291e9da02d8b16ca7065b4a59f8e7e9ab3f Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Wed, 19 Jun 2024 14:47:57 +0200
Subject: [PATCH 257/835] update scArches deps

---
 .../s/scArches/scArches-0.6.1-foss-2023a.eb   | 39 -------------------
 1 file changed, 39 deletions(-)

diff --git a/easybuild/easyconfigs/s/scArches/scArches-0.6.1-foss-2023a.eb b/easybuild/easyconfigs/s/scArches/scArches-0.6.1-foss-2023a.eb
index ef28b4b84b0..bdcb1ab880c 100644
--- a/easybuild/easyconfigs/s/scArches/scArches-0.6.1-foss-2023a.eb
+++ b/easybuild/easyconfigs/s/scArches/scArches-0.6.1-foss-2023a.eb
@@ -22,50 +22,11 @@ dependencies = [
     ('scvi-tools', '1.1.2'),
     ('PyTorch', '2.1.2'),
     ('tqdm', '4.66.1'),
-    ('IPython', '8.14.0'),
-    ('pkgconfig', '1.5.5', '-python'),
-    ('PyZMQ', '25.1.1'),
-    ('tornado', '6.3.2'),
 ]
 
 use_pip = True
 
 exts_list = [
-    ('pyproject-metadata', '0.8.0', {
-        'sources': ['pyproject_metadata-%(version)s.tar.gz'],
-        'checksums': ['376d5a00764ac29440a54579f88e66b7d9cb7e629d35c35a1c7248bfebc9b455'],
-    }),
-    ('sphinx_basic_ng', '1.0.0b2', {
-        'checksums': ['9ec55a47c90c8c002b5960c57492ec3021f5193cb26cebc2dc4ea226848651c9'],
-    }),
-    ('nodeenv', '1.9.0', {
-        'checksums': ['07f144e90dae547bf0d4ee8da0ee42664a42a04e02ed68e06324348dafe4bdb1'],
-    }),
-    ('sphinx-theme-builder', '0.2.0b2', {
-        'checksums': ['e9cd98c2bb35bf414fe721469a043cdcc10f0808d1ffcf606acb4a6282a6f288'],
-    }),
-    ('furo', '2024.1.29', {
-        'checksums': ['4d6b2fe3f10a6e36eb9cc24c1e7beb38d7a23fc7b3c382867503b7fcac8a1e02'],
-    }),
-    ('numpydoc', '1.6.0', {
-        'checksums': ['ae7a5380f0a06373c3afe16ccd15bd79bc6b07f2704cbc6f1e7ecc94b4f5fc0d'],
-    }),
-    ('jupyter_core', '5.7.2', {
-        'checksums': ['aa5f8d32bbf6b431ac830496da7392035d6f61b4f54872f15c4bd2a9c3f536d9'],
-    }),
-    ('jupyter_client', '8.6.1', {
-        'checksums': ['e842515e2bab8e19186d89fdfea7abd15e39dd581f94e399f00e2af5a1652d3f'],
-    }),
-    ('debugpy', '1.8.1', {
-        'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl',
-        'checksums': ['28acbe2241222b87e255260c76741e1fbf04fdc3b6d094fcf57b6c6f75ce1242'],
-    }),
-    ('comm', '0.2.2', {
-        'checksums': ['3fd7a84065306e07bea1773df6eb8282de51ba82f77c72f9c85716ab11fe980e'],
-    }),
-    ('ipykernel', '6.29.3', {
-        'checksums': ['e14c250d1f9ea3989490225cc1a542781b095a18a19447fcf2b5eaf7d0ac5bd2'],
-    }),
     ('gdown', '5.1.0', {
         'checksums': ['550a72dc5ca2819fe4bcc15d80d05d7c98c0b90e57256254b77d0256b9df4683'],
     }),

From 75b7824b56eaf00c6a7bc071757967f6ed649ce6 Mon Sep 17 00:00:00 2001
From: Victor Enrique Goitea <43407659+VictorGoitea@users.noreply.github.com>
Date: Wed, 19 Jun 2024 15:30:05 +0200
Subject: [PATCH 258/835] Update HOMER-4.11.1-foss-2022b.eb

---
 .../h/HOMER/HOMER-4.11.1-foss-2022b.eb        | 50 ++++++++++---------
 1 file changed, 26 insertions(+), 24 deletions(-)

diff --git a/easybuild/easyconfigs/h/HOMER/HOMER-4.11.1-foss-2022b.eb b/easybuild/easyconfigs/h/HOMER/HOMER-4.11.1-foss-2022b.eb
index a00997c71cb..7fb95aff4e7 100644
--- a/easybuild/easyconfigs/h/HOMER/HOMER-4.11.1-foss-2022b.eb
+++ b/easybuild/easyconfigs/h/HOMER/HOMER-4.11.1-foss-2022b.eb
@@ -1,23 +1,29 @@
-# This installs the entire suite, to install only base Homer package run :
-# cd %(installdir)s; perl ./configureHomer.pl -install homer
-
-easyblock = 'CmdCp'
+easyblock = 'Binary'
 
 name = 'HOMER'
 version = '4.11.1'
 
 homepage = 'http://homer.ucsd.edu/homer/'
-description = """HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif
-Discovery and ChIP-Seq analysis. It is a collection of command line programs for unix-style operating
-systems written in mostly perl and c++. Homer was primarily written as a de novo motif discovery
-algorithm that is well suited for finding 8-12 bp motifs in large scale genomics data."""
+description = """HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and
+next-gen sequencing analysis.  It is a collection of command line programs for unix-style operating systems written
+in Perl and C++. HOMER was primarily written as a de novo motif discovery algorithm and is well suited for finding
+8-20 bp motifs in large scale genomics data.  HOMER contains many useful tools for analyzing ChIP-Seq, GRO-Seq,
+RNA-Seq, DNase-Seq, Hi-C and numerous other types of functional genomics sequencing data sets."""
 
 toolchain = {'name': 'foss', 'version': '2022b'}
 
+source_urls = ['https://homer.ucsd.edu/homer/data/software']
+sources = ['homer.v%(version)s.zip']
+checksums = ['80d1cd00616729894017b24a36a2ef81f9cde8bd364e875aead1e0cfb500c82b']
+
+builddependencies = [
+    ('wget', '1.21.4'),
+    ('Zip', '3.0'),
+    ('UnZip', '6.0'),
+]
+
 dependencies = [
     ('Perl', '5.36.0'),
-    ('zlib', '1.2.12'),
-    ('Zip', '3.0'),
     ('weblogo', '2.8.2'),
     ('SAMtools', '1.17'),
     ('Kent_tools', '461'),
@@ -25,29 +31,25 @@ dependencies = [
     ('R-bundle-Bioconductor', '3.16', '-R-4.2.2')
 ]
 
-source_urls = ['http://homer.ucsd.edu/homer/data/software']
-sources = ['homer.v%(version)s.zip']
-checksums = ['80d1cd00616729894017b24a36a2ef81f9cde8bd364e875aead1e0cfb500c82b']
-
-unpack_options = " && cp %(builddir)s/configureHomer.pl %(installdir)s "
-start_dir = "%(installdir)s"
-cmds_map = [('', 'perl ./configureHomer.pl -install -all')]
+buildininstalldir = True
 skipsteps = ['install']
 
-files_to_copy = [
-    'bin', 'config.txt', 'data',
-    'DoughnutDocumentation.pdf',
-    'motifs',
-    'update',
-]
+# This installs the entire suite, to install only base Homer package run :
+# cd %(installdir)s; perl ./configureHomer.pl -install homer
+postinstallcmds = ['perl ./configureHomer.pl -install -all -keepScript']
 
 sanity_check_paths = {
     'dirs': ['bin', 'data', 'motifs', 'update'],
     'files': [
+        'bin/homer',
+        'bin/getGenomeTilingPeaks',
         'config.txt',
         'DoughnutDocumentation.pdf',
-        'bin/homer',
+        'data/accession/homologene.data',
+        'motifs/hnf1b.motif',
     ],
 }
 
+sanity_check_commands = ["%(namelower)s --help"]
+
 moduleclass = 'bio'

From 1fb3c7ec423384c892ed9cc715229ada452bd087 Mon Sep 17 00:00:00 2001
From: Victor Enrique Goitea <43407659+VictorGoitea@users.noreply.github.com>
Date: Wed, 19 Jun 2024 15:32:48 +0200
Subject: [PATCH 259/835] Create libidn2-2.3.4-GCCcore-12.2.0.eb

---
 .../l/libidn2/libidn2-2.3.4-GCCcore-12.2.0.eb | 24 +++++++++++++++++++
 1 file changed, 24 insertions(+)
 create mode 100644 easybuild/easyconfigs/l/libidn2/libidn2-2.3.4-GCCcore-12.2.0.eb

diff --git a/easybuild/easyconfigs/l/libidn2/libidn2-2.3.4-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/libidn2/libidn2-2.3.4-GCCcore-12.2.0.eb
new file mode 100644
index 00000000000..b9ddb22009e
--- /dev/null
+++ b/easybuild/easyconfigs/l/libidn2/libidn2-2.3.4-GCCcore-12.2.0.eb
@@ -0,0 +1,24 @@
+easyblock = 'ConfigureMake'
+
+name = 'libidn2'
+version = '2.3.4'
+
+homepage = 'http://www.gnu.org/software/%(name)s'
+description = """Libidn2 implements the revised algorithm for internationalized domain names called IDNA2008/TR46."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+
+source_urls = ['https://ftp.gnu.org/gnu/libidn/']
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['93caba72b4e051d1f8d4f5a076ab63c99b77faee019b72b9783b267986dbb45f']
+
+builddependencies = [('binutils', '2.39')]
+
+sanity_check_paths = {
+    'files': ['bin/idn2', 'lib/libidn2.%s' % SHLIB_EXT],
+    'dirs': ['include'],
+}
+
+sanity_check_commands = ["idn2 --help"]
+
+moduleclass = 'lib'

From c9e3f064b8113f12d5a5b4de2a3adb8df32a7ece Mon Sep 17 00:00:00 2001
From: Victor Enrique Goitea <43407659+VictorGoitea@users.noreply.github.com>
Date: Wed, 19 Jun 2024 15:34:19 +0200
Subject: [PATCH 260/835] Create wget-1.21.4-GCCcore-12.2.0.eb

---
 .../w/wget/wget-1.21.4-GCCcore-12.2.0.eb      | 50 +++++++++++++++++++
 1 file changed, 50 insertions(+)
 create mode 100644 easybuild/easyconfigs/w/wget/wget-1.21.4-GCCcore-12.2.0.eb

diff --git a/easybuild/easyconfigs/w/wget/wget-1.21.4-GCCcore-12.2.0.eb b/easybuild/easyconfigs/w/wget/wget-1.21.4-GCCcore-12.2.0.eb
new file mode 100644
index 00000000000..7dae35b8d9f
--- /dev/null
+++ b/easybuild/easyconfigs/w/wget/wget-1.21.4-GCCcore-12.2.0.eb
@@ -0,0 +1,50 @@
+easyblock = 'ConfigureMake'
+
+name = 'wget'
+version = '1.21.4'
+
+homepage = 'https://www.gnu.org/software/wget'
+description = """GNU Wget is a free software package for retrieving files using HTTP, HTTPS and FTP,
+ the most widely-used Internet protocols. It is a non-interactive commandline tool,
+ so it may easily be called from scripts, cron jobs, terminals without X-Windows support, etc."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+
+source_urls = [GNU_SOURCE]
+sources = [SOURCE_TAR_GZ]
+checksums = [
+    {SOURCE_TAR_GZ: '81542f5cefb8faacc39bbbc6c82ded80e3e4a88505ae72ea51df27525bcde04c'},
+]
+
+builddependencies = [
+    ('binutils', '2.39'),
+    ('pkgconf', '1.9.3'),
+    ('Perl', '5.36.0'),
+]
+dependencies = [
+    ('PCRE', '8.45'),
+    ('libidn2', '2.3.4'),
+    ('zlib', '1.2.12'),
+    ('OpenSSL', '1.1', '', SYSTEM),
+    # OS dependency should be preferred if the os version is more recent then this version,
+    # it's nice to have an up to date gnutls for security reasons
+    # ('GnuTLS', '3.7.1'),
+]
+
+# make sure pkgconfig picks up system packages (OpenSSL & co)
+local_pc = "%(sysroot)s/usr/lib64/pkgconfig:"
+local_pc += "%(sysroot)s/usr/lib/pkgconfig:"
+local_pc += "%(sysroot)s/usr/lib/x86_64-linux-gnu/pkgconfig"
+preconfigopts = "export PKG_CONFIG_PATH=%s && " % local_pc
+configopts = '--with-ssl=openssl '
+
+# Optionally, you can use gnutls (default) instead of OpenSSL.
+# Do not forget to comment out configopts in that case.
+# osdependencies = [('gnutls-devel', 'gnutls-dev', 'libgnutls-devel')]
+
+sanity_check_paths = {
+    'files': ['bin/%(name)s'],
+    'dirs': [],
+}
+
+moduleclass = 'devel'

From 508ed6c214673d8de17b75a258eeabba643cb6ac Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Petr=20Kr=C3=A1l?= <petr@inuits.eu>
Date: Wed, 19 Jun 2024 15:41:07 +0200
Subject: [PATCH 261/835] fix dependency version

---
 easybuild/easyconfigs/g/gap/gap-4.13.0-foss-2023b.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/g/gap/gap-4.13.0-foss-2023b.eb b/easybuild/easyconfigs/g/gap/gap-4.13.0-foss-2023b.eb
index 1c1693f7e45..248ab5ded0a 100644
--- a/easybuild/easyconfigs/g/gap/gap-4.13.0-foss-2023b.eb
+++ b/easybuild/easyconfigs/g/gap/gap-4.13.0-foss-2023b.eb
@@ -30,7 +30,7 @@ dependencies = [
     ('lrslib', '7.2'),  # needed by HeLP
     ('ncurses', '6.4'),  # needed by Browse
     ('Normaliz', '3.10.3'),  # needed by NormalizInterface, HeLP
-    ('Singular', '4.3.2p16'),  # needed by singular
+    ('Singular', '4.4.0'),  # needed by singular
     ('ZeroMQ', '4.3.5'),  # needed by ZeroMQInterface
 ]
 

From 351648459296db8c14aea4f6281cf8b6fb67c7b2 Mon Sep 17 00:00:00 2001
From: Victor Enrique Goitea <43407659+VictorGoitea@users.noreply.github.com>
Date: Wed, 19 Jun 2024 15:46:46 +0200
Subject: [PATCH 262/835] Update IMAGE-1.1-foss-2022b.eb

change tmp directory outside of the installation directory
---
 easybuild/easyconfigs/i/IMAGE/IMAGE-1.1-foss-2022b.eb | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/easybuild/easyconfigs/i/IMAGE/IMAGE-1.1-foss-2022b.eb b/easybuild/easyconfigs/i/IMAGE/IMAGE-1.1-foss-2022b.eb
index a7747fe1799..2c27fde5e84 100644
--- a/easybuild/easyconfigs/i/IMAGE/IMAGE-1.1-foss-2022b.eb
+++ b/easybuild/easyconfigs/i/IMAGE/IMAGE-1.1-foss-2022b.eb
@@ -23,11 +23,11 @@ checksums = ['e286cd5e7eb5aaaf9e103a9651ece39ff4ce260c463facdf1758b6d72a285062']
 
 postinstallcmds = [
     'mkdir %(installdir)s/bin',
-    'mkdir -p %(installdir)s/tmp',
+    'mkdir -p /tmp',
     'mv %(installdir)s/IMAGE.pl %(installdir)s/bin/',
     'chmod +x %(installdir)s/bin/IMAGE.pl',
     (
-        'sed -i "s|my \\$TMPDIR = \\$INSTALLDIR . \\$TMP;|my \\$TMPDIR = \'%(installdir)s\' . \\$TMP;|g" '
+        'sed -i "s|my \\$TMPDIR = \\$INSTALLDIR . \\$TMP;|my \\$TMPDIR = \\$TMP;|g" '
         '%(installdir)s/bin/IMAGE.pl'
     ),
     (

From a32d5d92b542baffaa3687210a7759c6eb8cdfc9 Mon Sep 17 00:00:00 2001
From: Victor Enrique Goitea <43407659+VictorGoitea@users.noreply.github.com>
Date: Wed, 19 Jun 2024 15:48:00 +0200
Subject: [PATCH 263/835] Update
 easybuild/easyconfigs/w/weblogo/weblogo-2.8.2-foss-2022b.eb

Co-authored-by: Sam Moors <smoors@users.noreply.github.com>
---
 easybuild/easyconfigs/w/weblogo/weblogo-2.8.2-foss-2022b.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/w/weblogo/weblogo-2.8.2-foss-2022b.eb b/easybuild/easyconfigs/w/weblogo/weblogo-2.8.2-foss-2022b.eb
index f91055ed84e..1150497b51e 100644
--- a/easybuild/easyconfigs/w/weblogo/weblogo-2.8.2-foss-2022b.eb
+++ b/easybuild/easyconfigs/w/weblogo/weblogo-2.8.2-foss-2022b.eb
@@ -3,7 +3,7 @@ easyblock = 'Tarball'
 name = 'weblogo'
 version = '2.8.2'
 
-homepage = "http://weblogo.berkeley.edu"
+homepage = "https://weblogo.berkeley.edu"
 description = """WebLogo is a web based application designed to make the generation of sequence logos as easy
 and painless as possible."""
 

From 118c2bdd50eef9d69e609cfd14de7eb3c8d6d653 Mon Sep 17 00:00:00 2001
From: Victor Enrique Goitea <43407659+VictorGoitea@users.noreply.github.com>
Date: Wed, 19 Jun 2024 16:01:59 +0200
Subject: [PATCH 264/835] Update weblogo-2.8.2-foss-2022b.eb
 sanity_check_commands

---
 easybuild/easyconfigs/w/weblogo/weblogo-2.8.2-foss-2022b.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/w/weblogo/weblogo-2.8.2-foss-2022b.eb b/easybuild/easyconfigs/w/weblogo/weblogo-2.8.2-foss-2022b.eb
index 1150497b51e..80923183514 100644
--- a/easybuild/easyconfigs/w/weblogo/weblogo-2.8.2-foss-2022b.eb
+++ b/easybuild/easyconfigs/w/weblogo/weblogo-2.8.2-foss-2022b.eb
@@ -39,7 +39,7 @@ sanity_check_paths = {
 }
 
 sanity_check_commands = [
-    "PERL5LIB=%(installdir)s/lib %(installdir)s/bin/seqlogo %(installdir)s/globin.fasta"
+    "seqlogo -f %(installdir)s/globin.fasta"
 ]
 
 moduleclass = 'bio'

From ad94896589a7cfa2ad8c07f9d72a59d36d050eff Mon Sep 17 00:00:00 2001
From: Victor Enrique Goitea <43407659+VictorGoitea@users.noreply.github.com>
Date: Wed, 19 Jun 2024 16:34:55 +0200
Subject: [PATCH 265/835] Update IMAGE-1.1-foss-2022b.eb

---
 easybuild/easyconfigs/i/IMAGE/IMAGE-1.1-foss-2022b.eb | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/easybuild/easyconfigs/i/IMAGE/IMAGE-1.1-foss-2022b.eb b/easybuild/easyconfigs/i/IMAGE/IMAGE-1.1-foss-2022b.eb
index 2c27fde5e84..d13562301b2 100644
--- a/easybuild/easyconfigs/i/IMAGE/IMAGE-1.1-foss-2022b.eb
+++ b/easybuild/easyconfigs/i/IMAGE/IMAGE-1.1-foss-2022b.eb
@@ -10,6 +10,10 @@ of causal transcription factors based on transcriptome profiling and genome-wide
 
 toolchain = {'name': 'foss', 'version': '2022b'}
 
+source_urls = ['https://github.com/JesperGrud/IMAGE/archive/refs/tags']
+sources = ['v%(version)s.tar.gz']
+checksums = ['e286cd5e7eb5aaaf9e103a9651ece39ff4ce260c463facdf1758b6d72a285062']
+
 dependencies = [
     ('Perl', '5.36.0'),
     ('HOMER', '4.11.1'),
@@ -17,10 +21,6 @@ dependencies = [
     ('R-bundle-Bioconductor', '3.16', '-R-4.2.2'),
 ]
 
-source_urls = ['https://github.com/JesperGrud/IMAGE/archive/refs/tags']
-sources = ['v%(version)s.tar.gz']
-checksums = ['e286cd5e7eb5aaaf9e103a9651ece39ff4ce260c463facdf1758b6d72a285062']
-
 postinstallcmds = [
     'mkdir %(installdir)s/bin',
     'mkdir -p /tmp',

From 715d6bf9758930176f611fac9df0397885f4a03e Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Wed, 19 Jun 2024 16:38:20 +0200
Subject: [PATCH 266/835] adding easyconfigs:
 SVDSS2-2.0.0-alpha.3-foss-2023a.eb

---
 .../SVDSS2/SVDSS2-2.0.0-alpha.3-foss-2023a.eb | 57 +++++++++++++++++++
 1 file changed, 57 insertions(+)
 create mode 100644 easybuild/easyconfigs/s/SVDSS2/SVDSS2-2.0.0-alpha.3-foss-2023a.eb

diff --git a/easybuild/easyconfigs/s/SVDSS2/SVDSS2-2.0.0-alpha.3-foss-2023a.eb b/easybuild/easyconfigs/s/SVDSS2/SVDSS2-2.0.0-alpha.3-foss-2023a.eb
new file mode 100644
index 00000000000..b08affc425e
--- /dev/null
+++ b/easybuild/easyconfigs/s/SVDSS2/SVDSS2-2.0.0-alpha.3-foss-2023a.eb
@@ -0,0 +1,57 @@
+easyblock = 'CMakeMakeCp'
+
+name = 'SVDSS2'
+version = '2.0.0-alpha.3'
+
+homepage = 'https://github.com/Parsoa/SVDSS'
+description = "Improved structural variant discovery in accurate long reads using sample-specific strings (SFS)."
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+sources = [{
+    'filename': 'v%(version)s.tar.gz',
+    'git_config': {
+        'url': 'https://github.com/Parsoa',
+        'repo_name': 'SVDSS',
+        'tag': 'v%(version)s',
+        'recursive': True,
+        'keep_git_dir': True,
+    }
+}]
+checksums = [None]    
+    
+builddependencies = [
+    ('CMake', '3.26.3'),
+    ('make', '4.4.1'),
+    ('Automake', '1.16.5'),
+    ('Autoconf', '2.71'),
+    ('zlib', '1.2.13'),
+    ('bzip2', '1.0.8'),
+    ('XZ', '5.4.2'),
+    ('SAMtools', '1.18'),
+    ('BCFtools', '1.18'),
+]
+dependencies = [
+    ('HTSlib', '1.18'),
+    ('libdeflate', '1.18'),
+    ('parasail', '2.6.2'),
+    ('spdlog', '1.11.0'),
+]
+
+files_to_copy = [
+    (['SVDSS'], 'bin'),
+    (['*'], 'lib'),
+]
+
+separate_build_dir = False
+
+postinstallcmds = ["cd %(installdir)s/lib && rm SVDSS"]
+
+sanity_check_paths = {
+    'files': ['bin/SVDSS'],
+    'dirs': ['lib'],
+}
+
+sanity_check_commands = ['SVDSS --version']
+
+moduleclass = 'bio'

From 4adf8a77f39219d55dda9a12605b590f42c2f53c Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Wed, 19 Jun 2024 16:43:45 +0200
Subject: [PATCH 267/835] update toolchain

---
 .../SVDSS2/SVDSS2-2.0.0-alpha.3-GCC-12.3.0.eb | 57 +++++++++++++++++++
 1 file changed, 57 insertions(+)
 create mode 100644 easybuild/easyconfigs/s/SVDSS2/SVDSS2-2.0.0-alpha.3-GCC-12.3.0.eb

diff --git a/easybuild/easyconfigs/s/SVDSS2/SVDSS2-2.0.0-alpha.3-GCC-12.3.0.eb b/easybuild/easyconfigs/s/SVDSS2/SVDSS2-2.0.0-alpha.3-GCC-12.3.0.eb
new file mode 100644
index 00000000000..86aaf5c688d
--- /dev/null
+++ b/easybuild/easyconfigs/s/SVDSS2/SVDSS2-2.0.0-alpha.3-GCC-12.3.0.eb
@@ -0,0 +1,57 @@
+easyblock = 'CMakeMakeCp'
+
+name = 'SVDSS2'
+version = '2.0.0-alpha.3'
+
+homepage = 'https://github.com/Parsoa/SVDSS'
+description = "Improved structural variant discovery in accurate long reads using sample-specific strings (SFS)."
+
+toolchain = {'name': 'GCC', 'version': '12.3.0'}
+
+sources = [{
+    'filename': 'v%(version)s.tar.gz',
+    'git_config': {
+        'url': 'https://github.com/Parsoa',
+        'repo_name': 'SVDSS',
+        'tag': 'v%(version)s',
+        'recursive': True,
+        'keep_git_dir': True,
+    }
+}]
+checksums = [None]    
+    
+builddependencies = [
+    ('CMake', '3.26.3'),
+    ('make', '4.4.1'),
+    ('Automake', '1.16.5'),
+    ('Autoconf', '2.71'),
+    ('zlib', '1.2.13'),
+    ('bzip2', '1.0.8'),
+    ('XZ', '5.4.2'),
+    ('SAMtools', '1.18'),
+    ('BCFtools', '1.18'),
+]
+dependencies = [
+    ('HTSlib', '1.18'),
+    ('libdeflate', '1.18'),
+    ('parasail', '2.6.2'),
+    ('spdlog', '1.11.0'),
+]
+
+files_to_copy = [
+    (['SVDSS'], 'bin'),
+    (['*'], 'lib'),
+]
+
+separate_build_dir = False
+
+postinstallcmds = ["cd %(installdir)s/lib && rm SVDSS"]
+
+sanity_check_paths = {
+    'files': ['bin/SVDSS'],
+    'dirs': ['lib'],
+}
+
+sanity_check_commands = ['SVDSS --version']
+
+moduleclass = 'bio'

From 0932a24bc916f6724d3878c52796b86ec2026340 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com>
Date: Wed, 19 Jun 2024 16:44:57 +0200
Subject: [PATCH 268/835] Delete SVDSS2-2.0.0-alpha.3-foss-2023a.eb

---
 .../SVDSS2/SVDSS2-2.0.0-alpha.3-foss-2023a.eb | 57 -------------------
 1 file changed, 57 deletions(-)
 delete mode 100644 easybuild/easyconfigs/s/SVDSS2/SVDSS2-2.0.0-alpha.3-foss-2023a.eb

diff --git a/easybuild/easyconfigs/s/SVDSS2/SVDSS2-2.0.0-alpha.3-foss-2023a.eb b/easybuild/easyconfigs/s/SVDSS2/SVDSS2-2.0.0-alpha.3-foss-2023a.eb
deleted file mode 100644
index b08affc425e..00000000000
--- a/easybuild/easyconfigs/s/SVDSS2/SVDSS2-2.0.0-alpha.3-foss-2023a.eb
+++ /dev/null
@@ -1,57 +0,0 @@
-easyblock = 'CMakeMakeCp'
-
-name = 'SVDSS2'
-version = '2.0.0-alpha.3'
-
-homepage = 'https://github.com/Parsoa/SVDSS'
-description = "Improved structural variant discovery in accurate long reads using sample-specific strings (SFS)."
-
-toolchain = {'name': 'foss', 'version': '2023a'}
-
-sources = [{
-    'filename': 'v%(version)s.tar.gz',
-    'git_config': {
-        'url': 'https://github.com/Parsoa',
-        'repo_name': 'SVDSS',
-        'tag': 'v%(version)s',
-        'recursive': True,
-        'keep_git_dir': True,
-    }
-}]
-checksums = [None]    
-    
-builddependencies = [
-    ('CMake', '3.26.3'),
-    ('make', '4.4.1'),
-    ('Automake', '1.16.5'),
-    ('Autoconf', '2.71'),
-    ('zlib', '1.2.13'),
-    ('bzip2', '1.0.8'),
-    ('XZ', '5.4.2'),
-    ('SAMtools', '1.18'),
-    ('BCFtools', '1.18'),
-]
-dependencies = [
-    ('HTSlib', '1.18'),
-    ('libdeflate', '1.18'),
-    ('parasail', '2.6.2'),
-    ('spdlog', '1.11.0'),
-]
-
-files_to_copy = [
-    (['SVDSS'], 'bin'),
-    (['*'], 'lib'),
-]
-
-separate_build_dir = False
-
-postinstallcmds = ["cd %(installdir)s/lib && rm SVDSS"]
-
-sanity_check_paths = {
-    'files': ['bin/SVDSS'],
-    'dirs': ['lib'],
-}
-
-sanity_check_commands = ['SVDSS --version']
-
-moduleclass = 'bio'

From f3337b652bccc244c520f7ba40229c2d405b4df2 Mon Sep 17 00:00:00 2001
From: Robin Verschoren <robin.verschoren@uantwerpen.be>
Date: Wed, 19 Jun 2024 16:51:32 +0200
Subject: [PATCH 269/835] adding easyconfigs:
 OpenFOAM-10-foss-2022a-20230119-int64.eb

---
 .../OpenFOAM-10-foss-2022a-20230119-int64.eb  | 42 +++++++++++++++++++
 1 file changed, 42 insertions(+)
 create mode 100644 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-10-foss-2022a-20230119-int64.eb

diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-10-foss-2022a-20230119-int64.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-10-foss-2022a-20230119-int64.eb
new file mode 100644
index 00000000000..cfba31ab4f7
--- /dev/null
+++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-10-foss-2022a-20230119-int64.eb
@@ -0,0 +1,42 @@
+name = 'OpenFOAM'
+
+version = '10'
+_version_patch = '20230119'
+versionsuffix = '-%s-int64' % _version_patch
+
+homepage = 'https://www.openfoam.org/'
+description = """OpenFOAM is a free, open source CFD software package.
+ OpenFOAM has an extensive range of features to solve anything from complex fluid flows
+ involving chemical reactions, turbulence and heat transfer,
+ to solid dynamics and electromagnetics."""
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+toolchainopts = {'i8': True}
+
+source_urls = ['https://github.com/OpenFOAM/OpenFOAM-%(version_major)s/archive']
+sources = [{
+    'download_filename': '%s.tar.gz' % _version_patch,
+    'filename': 'OpenFOAM-%s-%s.tar.gz' % (version, _version_patch),
+}]
+patches = ['OpenFOAM-%(version_major)s-ThirdParty.patch']
+checksums = [
+    {'OpenFOAM-10-20230119.tar.gz': '86f8cb18d4f59812b129ce7d669e8ff498da442fbdb46705492fbba3cbda82ab'},
+    {'OpenFOAM-10-ThirdParty.patch': '307df0206cdb24533f4974378843332064f4a2d85cf0638c20fc4c87b1524b43'},
+]
+
+builddependencies = [
+    ('Bison', '3.8.2'),
+    ('CMake', '3.23.1'),
+    ('flex', '2.6.4'),
+]
+
+dependencies = [
+    ('ncurses', '6.3'),
+    ('METIS', '5.1.0', '-int64'),
+    ('SCOTCH', '7.0.1', '-int64'),
+    ('CGAL', '4.14.3'),
+    ('ParaView', '5.10.1', '-mpi'),
+    ('gnuplot', '5.4.4'),
+]
+
+moduleclass = 'cae'

From a1cb8f07918ca3334f7a02ccc4404fb624281ea2 Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Wed, 19 Jun 2024 18:37:03 +0200
Subject: [PATCH 270/835] adding easyconfigs: CESM-deps-2-foss-2023a.eb

---
 .../c/CESM-deps/CESM-deps-2-foss-2023a.eb     | 51 +++++++++++++++++++
 1 file changed, 51 insertions(+)
 create mode 100644 easybuild/easyconfigs/c/CESM-deps/CESM-deps-2-foss-2023a.eb

diff --git a/easybuild/easyconfigs/c/CESM-deps/CESM-deps-2-foss-2023a.eb b/easybuild/easyconfigs/c/CESM-deps/CESM-deps-2-foss-2023a.eb
new file mode 100644
index 00000000000..1144c2b34cc
--- /dev/null
+++ b/easybuild/easyconfigs/c/CESM-deps/CESM-deps-2-foss-2023a.eb
@@ -0,0 +1,51 @@
+easyblock = 'Bundle'
+
+name = 'CESM-deps'
+version = '2'
+
+homepage = 'https://www.cesm.ucar.edu/models/cesm2/'
+description = """CESM is a fully-coupled, community, global climate model that
+provides state-of-the-art computer simulations of the Earth's past, present,
+and future climate states."""
+
+# The following environment is suitable for CESM >= 2.2.2 and CTSM >= 5.2.0
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+dependencies = [
+    ('CMake', '3.26.3'),
+    ('Python', '3.11.3'),
+    ('lxml', '4.9.2'),
+    ('Perl', '5.36.1'),
+    ('XML-LibXML', '2.0209'),
+    ('ESMF', '8.6.0'),
+    ('netCDF', '4.9.2'),
+    ('netCDF-Fortran', '4.6.1'),
+    ('netCDF-C++4', '4.3.1'),
+    ('PnetCDF', '1.12.3'),
+    ('git', '2.41.0', '-nodocs'),
+    ('git-lfs', '3.5.1', '', SYSTEM),
+]
+
+components = [
+    # install extra configuration tools and files for VSC clusters
+    ('cesm-config', '1.7.0', {
+        'easyblock': 'Tarball',
+        'source_urls': ['https://github.com/vub-hpc/%(name)s/archive'],
+        'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}],
+        'checksums': ['c5aeb50595ca4d342a5024d593c2549acf16e72dadc5f39d9a7915d3dc8f3c13'],
+        'start_dir': '%(name)s-%(version)s',
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['bin/update-cesm-machines', 'scripts/case.pbs', 'scripts/case.slurm'],
+    'dirs': ['machines', 'irods'],
+}
+
+usage = """Environment to build and run CESM v2 simulations
+ 1. Download a release of CESM v2: `git clone -b release-cesm2.2.2 https://github.com/ESCOMP/cesm.git cesm-2.2.2`
+ 2. Add external programs for CESM: `cd cesm-2.2.2; ./manage_externals/checkout_externals`
+ 3. Update config files: `update-cesm-machines cime/config/cesm/machines/ $EBROOTCESMMINDEPS/machines/`
+ 4. Create case: `cd cime/scripts && ./create_newcase --machine ...`"""
+
+moduleclass = 'geo'

From ab4c961126a767a3f5d081df436f5a49aa0d32d3 Mon Sep 17 00:00:00 2001
From: Simon Branford <s.j.branford@bham.ac.uk>
Date: Wed, 19 Jun 2024 19:48:53 +0100
Subject: [PATCH 271/835] adding easyconfigs: MCR-R2024a.4.eb

---
 easybuild/easyconfigs/m/MCR/MCR-R2024a.4.eb | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)
 create mode 100644 easybuild/easyconfigs/m/MCR/MCR-R2024a.4.eb

diff --git a/easybuild/easyconfigs/m/MCR/MCR-R2024a.4.eb b/easybuild/easyconfigs/m/MCR/MCR-R2024a.4.eb
new file mode 100644
index 00000000000..bb746ac5151
--- /dev/null
+++ b/easybuild/easyconfigs/m/MCR/MCR-R2024a.4.eb
@@ -0,0 +1,18 @@
+name = 'MCR'
+version = 'R2024a'  # runtime version 24.1
+local_update = '4'
+versionsuffix = '.%s' % local_update
+
+homepage = 'https://www.mathworks.com/products/compiler/mcr/'
+description = """The MATLAB Runtime is a standalone set of shared libraries
+ that enables the execution of compiled MATLAB applications
+ or components on computers that do not have MATLAB installed."""
+
+toolchain = SYSTEM
+
+source_urls = ['https://ssd.mathworks.com/supportfiles/downloads/%%(version)s/Release/%s/deployment_files/'
+               'installer/complete/glnxa64/' % local_update]
+sources = ['MATLAB_Runtime_%%(version)s_Update_%s_glnxa64.zip' % local_update]
+checksums = ['ceed37dc342660c934b9f6297491f57b6d51a7f49cd1fb80b775b1f748b72d03']
+
+moduleclass = 'math'

From ef6a9b46219e306b9b74342f6e91d186bf333a81 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Wed, 19 Jun 2024 19:35:12 +0000
Subject: [PATCH 272/835] adding easyconfigs: rpmrebuild-2.18.eb

---
 .../r/rpmrebuild/rpmrebuild-2.18.eb           | 26 +++++++++++++++++++
 1 file changed, 26 insertions(+)
 create mode 100644 easybuild/easyconfigs/r/rpmrebuild/rpmrebuild-2.18.eb

diff --git a/easybuild/easyconfigs/r/rpmrebuild/rpmrebuild-2.18.eb b/easybuild/easyconfigs/r/rpmrebuild/rpmrebuild-2.18.eb
new file mode 100644
index 00000000000..3558d631146
--- /dev/null
+++ b/easybuild/easyconfigs/r/rpmrebuild/rpmrebuild-2.18.eb
@@ -0,0 +1,26 @@
+easyblock = "Tarball"
+
+name = "rpmrebuild"
+version = "2.18"
+
+homepage = 'http://rpmrebuild.sourceforge.net/'
+description = """rpmrebuild is a tool to build an RPM file from a package that has already been
+installed in a basic use"""
+
+toolchain = SYSTEM
+
+source_urls = [SOURCEFORGE_SOURCE]
+sources = [SOURCELOWER_TAR_GZ]
+
+modextrapaths = {'PATH': ['']}
+modextravars = {'RPMREBUILD_ROOT_DIR': '%(installdir)s'}
+
+sanity_check_paths = {
+    'files': ["rpmrebuild"],
+    'dirs': []
+}
+
+sanity_check_commands = ['rpmrebuild -h']
+
+moduleclass = 'tools'
+

From 923a20ae214e6ce7eb8edd8309173c7aebc53628 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Wed, 19 Jun 2024 19:36:49 +0000
Subject: [PATCH 273/835] Update to rpmbuild 2.18

---
 .../easyconfigs/b/bcl-convert/bcl-convert-4.2.7-2el7.x86_64.eb  | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/b/bcl-convert/bcl-convert-4.2.7-2el7.x86_64.eb b/easybuild/easyconfigs/b/bcl-convert/bcl-convert-4.2.7-2el7.x86_64.eb
index 636a4e2a6b4..dfed34de942 100644
--- a/easybuild/easyconfigs/b/bcl-convert/bcl-convert-4.2.7-2el7.x86_64.eb
+++ b/easybuild/easyconfigs/b/bcl-convert/bcl-convert-4.2.7-2el7.x86_64.eb
@@ -10,7 +10,7 @@ description = """The Illumina BCL Convert v4.0 is a standalone local software ap
 
 toolchain = SYSTEM
 
-builddependencies = [('rpmrebuild', '2.11')]
+builddependencies = [('rpmrebuild', '2.18')]
 
 source_urls = ['https://webdata.illumina.com/downloads/software/bcl-convert/']
 sources = ['bcl-convert-%(version)s.%(versionsuffix)s.rpm']

From 149e42fb97d92b08c2f023e791be4fd0dea273cf Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Wed, 19 Jun 2024 19:53:26 +0000
Subject: [PATCH 274/835] Fix style

---
 easybuild/easyconfigs/r/rpmrebuild/rpmrebuild-2.18.eb | 1 -
 1 file changed, 1 deletion(-)

diff --git a/easybuild/easyconfigs/r/rpmrebuild/rpmrebuild-2.18.eb b/easybuild/easyconfigs/r/rpmrebuild/rpmrebuild-2.18.eb
index 3558d631146..611f381bf44 100644
--- a/easybuild/easyconfigs/r/rpmrebuild/rpmrebuild-2.18.eb
+++ b/easybuild/easyconfigs/r/rpmrebuild/rpmrebuild-2.18.eb
@@ -23,4 +23,3 @@ sanity_check_paths = {
 sanity_check_commands = ['rpmrebuild -h']
 
 moduleclass = 'tools'
-

From f842e91cf3d07fa2f78a2fc4a11d5add9b7b2fa9 Mon Sep 17 00:00:00 2001
From: Simon Pinches <Simon.Pinches@iter.org>
Date: Wed, 19 Jun 2024 21:58:50 +0200
Subject: [PATCH 275/835] adding easyconfigs:
 SuiteSparse-7.7.0-foss-2023b-METIS-5.1.0.eb

---
 ...uiteSparse-7.7.0-foss-2023b-METIS-5.1.0.eb | 29 +++++++++++++++++++
 1 file changed, 29 insertions(+)
 create mode 100644 easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-7.7.0-foss-2023b-METIS-5.1.0.eb

diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-7.7.0-foss-2023b-METIS-5.1.0.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-7.7.0-foss-2023b-METIS-5.1.0.eb
new file mode 100644
index 00000000000..24f0a691280
--- /dev/null
+++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-7.7.0-foss-2023b-METIS-5.1.0.eb
@@ -0,0 +1,29 @@
+name = 'SuiteSparse'
+version = '7.7.0'
+local_metis_ver = '5.1.0'
+versionsuffix = '-METIS-%s' % local_metis_ver
+
+homepage = 'https://faculty.cse.tamu.edu/davis/suitesparse.html'
+description = """SuiteSparse is a collection of libraries manipulate sparse matrices."""
+
+toolchain = {'name': 'foss', 'version': '2023b'}
+toolchainopts = {'unroll': True, 'pic': True}
+
+source_urls = ['https://github.com/DrTimothyAldenDavis/SuiteSparse/archive']
+sources = ['v%(version)s.tar.gz']
+checksums = ['529b067f5d80981f45ddf6766627b8fc5af619822f068f342aab776e683df4f3']
+
+builddependencies = [
+    ('CMake', '3.27.6'),
+    ('M4', '1.4.19'),
+]
+
+dependencies = [
+    ('METIS', local_metis_ver),
+    ('MPFR', '4.2.1'),
+]
+
+# make sure that bin/demo can find libsuitesparseconfig.so.5 during build
+prebuildopts = "export LD_LIBRARY_PATH=%(builddir)s/SuiteSparse-%(version)s/lib:$LD_LIBRARY_PATH && "
+
+moduleclass = 'numlib'

From 4e6752d9c527869cf3316d61d2650d23223ae359 Mon Sep 17 00:00:00 2001
From: Simon Branford <4967+branfosj@users.noreply.github.com>
Date: Wed, 19 Jun 2024 21:11:13 +0100
Subject: [PATCH 276/835] add checksum

---
 easybuild/easyconfigs/r/rpmrebuild/rpmrebuild-2.18.eb | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easybuild/easyconfigs/r/rpmrebuild/rpmrebuild-2.18.eb b/easybuild/easyconfigs/r/rpmrebuild/rpmrebuild-2.18.eb
index 611f381bf44..64cae582362 100644
--- a/easybuild/easyconfigs/r/rpmrebuild/rpmrebuild-2.18.eb
+++ b/easybuild/easyconfigs/r/rpmrebuild/rpmrebuild-2.18.eb
@@ -11,6 +11,7 @@ toolchain = SYSTEM
 
 source_urls = [SOURCEFORGE_SOURCE]
 sources = [SOURCELOWER_TAR_GZ]
+checksums = ['919ca6252eafbfb58dd54b0efa3ca4e6da293364937dcfe32c32a35b238a5837']
 
 modextrapaths = {'PATH': ['']}
 modextravars = {'RPMREBUILD_ROOT_DIR': '%(installdir)s'}

From c17e79a548a7cce2dd127ae944ba673ff9055f02 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Wed, 19 Jun 2024 22:38:02 +0000
Subject: [PATCH 277/835] Switch transformers to use external Safetensor dep

---
 .../t/Transformers/Transformers-4.39.3-gfbf-2023a.eb   | 10 +---------
 1 file changed, 1 insertion(+), 9 deletions(-)

diff --git a/easybuild/easyconfigs/t/Transformers/Transformers-4.39.3-gfbf-2023a.eb b/easybuild/easyconfigs/t/Transformers/Transformers-4.39.3-gfbf-2023a.eb
index cef130c9947..421741f8832 100644
--- a/easybuild/easyconfigs/t/Transformers/Transformers-4.39.3-gfbf-2023a.eb
+++ b/easybuild/easyconfigs/t/Transformers/Transformers-4.39.3-gfbf-2023a.eb
@@ -8,27 +8,19 @@ description = """State-of-the-art Natural Language Processing for PyTorch and Te
 
 toolchain = {'name': 'gfbf', 'version': '2023a'}
 
-_rust_ver = '1.75.0'
-builddependencies = [
-    ('Rust', _rust_ver),
-    ('maturin', '1.4.0', '-Rust-%s' % _rust_ver),
-]
-
 dependencies = [
     ('Python', '3.11.3'),
     ('SciPy-bundle', '2023.07'),
     ('PyYAML', '6.0'),
     ('tqdm', '4.66.1'),
     ('tokenizers', '0.15.2'),
+    ('Safetensors', '0.4.3'),
 ]
 
 use_pip = True
 sanity_pip_check = True
 
 exts_list = [
-    ('safetensors', '0.4.2', {
-        'checksums': ['acc85dcb09ec5e8aa787f588d7ad4d55c103f31e4ff060e17d92cc0e8b8cac73'],
-    }),
     ('regex', '2023.12.25', {
         'checksums': ['29171aa128da69afdf4bde412d5bedc335f2ca8fcfe4489038577d05f16181e5'],
     }),

From abaa4404a7091233e04be6a8bbf6ab103a537cd0 Mon Sep 17 00:00:00 2001
From: Victor Enrique Goitea <43407659+VictorGoitea@users.noreply.github.com>
Date: Thu, 20 Jun 2024 10:12:33 +0200
Subject: [PATCH 278/835] add extract_sources = True to
 HOMER-4.11.1-foss-2022b.eb

---
 easybuild/easyconfigs/h/HOMER/HOMER-4.11.1-foss-2022b.eb | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/easybuild/easyconfigs/h/HOMER/HOMER-4.11.1-foss-2022b.eb b/easybuild/easyconfigs/h/HOMER/HOMER-4.11.1-foss-2022b.eb
index 7fb95aff4e7..c429effc925 100644
--- a/easybuild/easyconfigs/h/HOMER/HOMER-4.11.1-foss-2022b.eb
+++ b/easybuild/easyconfigs/h/HOMER/HOMER-4.11.1-foss-2022b.eb
@@ -16,6 +16,8 @@ source_urls = ['https://homer.ucsd.edu/homer/data/software']
 sources = ['homer.v%(version)s.zip']
 checksums = ['80d1cd00616729894017b24a36a2ef81f9cde8bd364e875aead1e0cfb500c82b']
 
+extract_sources = True
+
 builddependencies = [
     ('wget', '1.21.4'),
     ('Zip', '3.0'),

From f135cf07307f48e1aaae4b584c721aa7e8b18f4d Mon Sep 17 00:00:00 2001
From: Victor Enrique Goitea <43407659+VictorGoitea@users.noreply.github.com>
Date: Thu, 20 Jun 2024 10:16:16 +0200
Subject: [PATCH 279/835] add fix_perl_shebang_for and rm mkdir /tmp in
 IMAGE-1.1-foss-2022b.eb

---
 easybuild/easyconfigs/i/IMAGE/IMAGE-1.1-foss-2022b.eb | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/i/IMAGE/IMAGE-1.1-foss-2022b.eb b/easybuild/easyconfigs/i/IMAGE/IMAGE-1.1-foss-2022b.eb
index d13562301b2..3b7413af016 100644
--- a/easybuild/easyconfigs/i/IMAGE/IMAGE-1.1-foss-2022b.eb
+++ b/easybuild/easyconfigs/i/IMAGE/IMAGE-1.1-foss-2022b.eb
@@ -23,7 +23,6 @@ dependencies = [
 
 postinstallcmds = [
     'mkdir %(installdir)s/bin',
-    'mkdir -p /tmp',
     'mv %(installdir)s/IMAGE.pl %(installdir)s/bin/',
     'chmod +x %(installdir)s/bin/IMAGE.pl',
     (
@@ -36,6 +35,8 @@ postinstallcmds = [
     ),
 ]
 
+fix_perl_shebang_for = ['bin/*.pl']
+
 sanity_check_paths = {
     'dirs': ['bin', 'utils', 'tmp'],
     'files': [

From 0c0208d2ca5c7805502c818618e14b2acc284476 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com>
Date: Thu, 20 Jun 2024 10:25:24 +0200
Subject: [PATCH 280/835] Fix whitespace

---
 .../easyconfigs/s/SVDSS2/SVDSS2-2.0.0-alpha.3-GCC-12.3.0.eb   | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/easybuild/easyconfigs/s/SVDSS2/SVDSS2-2.0.0-alpha.3-GCC-12.3.0.eb b/easybuild/easyconfigs/s/SVDSS2/SVDSS2-2.0.0-alpha.3-GCC-12.3.0.eb
index 86aaf5c688d..1d2e2c5ae19 100644
--- a/easybuild/easyconfigs/s/SVDSS2/SVDSS2-2.0.0-alpha.3-GCC-12.3.0.eb
+++ b/easybuild/easyconfigs/s/SVDSS2/SVDSS2-2.0.0-alpha.3-GCC-12.3.0.eb
@@ -18,8 +18,8 @@ sources = [{
         'keep_git_dir': True,
     }
 }]
-checksums = [None]    
-    
+checksums = [None]
+
 builddependencies = [
     ('CMake', '3.26.3'),
     ('make', '4.4.1'),

From 22f47968576357fa3ce92468738745481f4cf890 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Petr=20Kr=C3=A1l?= <petr@inuits.eu>
Date: Thu, 20 Jun 2024 11:36:41 +0200
Subject: [PATCH 281/835] adding easyconfigs: medaka-1.12.0-foss-2023a.eb

---
 .../m/medaka/medaka-1.12.0-foss-2023a.eb      | 80 +++++++++++++++++++
 1 file changed, 80 insertions(+)
 create mode 100644 easybuild/easyconfigs/m/medaka/medaka-1.12.0-foss-2023a.eb

diff --git a/easybuild/easyconfigs/m/medaka/medaka-1.12.0-foss-2023a.eb b/easybuild/easyconfigs/m/medaka/medaka-1.12.0-foss-2023a.eb
new file mode 100644
index 00000000000..15a511a42fd
--- /dev/null
+++ b/easybuild/easyconfigs/m/medaka/medaka-1.12.0-foss-2023a.eb
@@ -0,0 +1,80 @@
+# This is a contribution from HPCNow! (http://hpcnow.com)
+# Copyright::   HPCNow!
+# Authors::     Danilo Gonzalez <danilo.gonzalez@hpcnow.com>
+# License::     GPL-v3.0
+# Updated to foss-2020b to use with artic tool
+# J. Sassmannshausen (GSTT/NHS UK)
+# Updated to 1.5.0
+# Jasper Grimm (UoY)
+# Updated: Petr Král (INUITS)
+
+easyblock = 'PythonBundle'
+
+name = 'medaka'
+version = '1.12.0'
+
+homepage = 'https://github.com/nanoporetech/medaka'
+description = "medaka is a tool to create a consensus sequence from nanopore sequencing data."
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+toolchainopts = {'pic': True}
+
+builddependencies = [('Autotools', '20220317')]
+
+_minimap_ver = '2.26'
+dependencies = [
+    ('Python', '3.11.3'),
+    ('Python-bundle-PyPI', '2023.06'),  # includes cffi
+    ('TensorFlow', '2.13.0'),
+    ('Pysam', '0.22.0'),
+    ('SAMtools', '1.18'),
+    ('minimap2', _minimap_ver),
+    ('HTSlib', '1.18'),  # for tabix, bgzip
+    ('Racon', '1.5.0'),
+    ('edlib', '1.3.9'),
+    ('pyspoa', '0.2.1'),
+    ('python-parasail', '1.3.4'),
+    ('ont-fast5-api', '4.1.2'),
+    ('WhatsHap', '2.2'),
+    ('intervaltree-python', '3.1.0'),
+    ('BCFtools', '1.18'),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+local_sed_commands = [
+    "sed -i 's/tensorflow.*/tensorflow/g;s/cffi==1.15.0/cffi/g' requirements.txt pyproject.toml",
+    # Python 3.11 support
+    "sed -i 's/8, 9, 10/8, 9, 10, 11/g;s/,<3.11//g' setup.py",
+]
+
+exts_list = [
+    ('mappy', _minimap_ver, {
+        'checksums': ['e53fbe9a3ea8762a64b8103f4f779c9fb16d418eaa0a731f45cebc83867a9b71'],
+    }),
+    ('wurlitzer', '3.1.1', {
+        'source_tmpl': SOURCE_PY3_WHL,
+        'checksums': ['0b2749c2cde3ef640bf314a9f94b24d929fe1ca476974719a6909dfc568c3aac'],
+    }),
+    ('h5py', '3.10.0', {
+        'checksums': ['d93adc48ceeb33347eb24a634fb787efc7ae4644e6ea4ba733d099605045c049'],
+    }),
+    (name, version, {
+        'checksums': ['039219204111a8114b1f72d87d0d3463e43473790cff4520c8afbd79cc8784d6'],
+        # Some requirements are too strict.
+        'preinstallopts': " && ".join(local_sed_commands) + " && ",
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['bin/medaka', 'bin/medaka_consensus', 'bin/medaka_version_report'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = [
+    "medaka --help",
+    "medaka_version_report",
+]
+
+moduleclass = 'bio'

From 5b3622a369e5abc6df2669707a86b2cc8cd5c810 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Thu, 20 Jun 2024 15:53:46 +0200
Subject: [PATCH 282/835] adding easyconfigs:
 ega-quickview-20240620-GCC-12.3.0.eb, FUSE-3.16.2-GCCcore-12.3.0.eb,
 crypt4gh-1.7-GCC-12.3.0.eb

---
 .../c/crypt4gh/crypt4gh-1.7-GCC-12.3.0.eb     | 38 +++++++++++++
 .../ega-quickview-20240620-GCC-12.3.0.eb      | 54 +++++++++++++++++++
 .../f/FUSE/FUSE-3.16.2-GCCcore-12.3.0.eb      | 30 +++++++++++
 3 files changed, 122 insertions(+)
 create mode 100644 easybuild/easyconfigs/c/crypt4gh/crypt4gh-1.7-GCC-12.3.0.eb
 create mode 100644 easybuild/easyconfigs/e/ega-quickview/ega-quickview-20240620-GCC-12.3.0.eb
 create mode 100644 easybuild/easyconfigs/f/FUSE/FUSE-3.16.2-GCCcore-12.3.0.eb

diff --git a/easybuild/easyconfigs/c/crypt4gh/crypt4gh-1.7-GCC-12.3.0.eb b/easybuild/easyconfigs/c/crypt4gh/crypt4gh-1.7-GCC-12.3.0.eb
new file mode 100644
index 00000000000..24f42fade96
--- /dev/null
+++ b/easybuild/easyconfigs/c/crypt4gh/crypt4gh-1.7-GCC-12.3.0.eb
@@ -0,0 +1,38 @@
+easyblock = 'PythonBundle'
+
+name = 'crypt4gh'
+version = '1.7'
+
+homepage = 'https://github.com/EGA-archive/crypt4gh'
+description = """crypt4gh is a Python tool to encrypt, decrypt or re-encrypt files, 
+according to the GA4GH encryption file format."""
+
+toolchain = {'name': 'GCC', 'version': '12.3.0'}
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('PyYAML', '6.0'),
+    ('cryptography', '41.0.1'),
+    ('bcrypt', '4.0.1'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('PyNaCl', '1.5.0', {
+        'modulename': 'nacl',
+        'checksums': ['8ac7448f09ab85811607bdd21ec2464495ac8b7c66d146bf545b0f08fb9220ba'],
+    }),
+    ('docopt', '0.6.2', {
+        'checksums': ['49b3a825280bd66b3aa83585ef59c4a8c82f2c8a522dbe754a8bc8d08c85c491'],
+    }),
+    (name, version, {
+        'checksums': ['1569bc4ff9b689c8852e3892ac3f6fea4b31948ca0b1e5bc28d0d2f80def2a28'],
+    }),
+]
+
+sanity_pip_check = True
+
+sanity_check_commands = ['crypt4gh -h']
+
+moduleclass = 'tools'
diff --git a/easybuild/easyconfigs/e/ega-quickview/ega-quickview-20240620-GCC-12.3.0.eb b/easybuild/easyconfigs/e/ega-quickview/ega-quickview-20240620-GCC-12.3.0.eb
new file mode 100644
index 00000000000..1ed48a2fa79
--- /dev/null
+++ b/easybuild/easyconfigs/e/ega-quickview/ega-quickview-20240620-GCC-12.3.0.eb
@@ -0,0 +1,54 @@
+easyblock = 'ConfigureMake'
+
+name = 'ega-quickview'
+version = '20240620'
+local_commit = 'fe2034d'
+
+homepage = 'https://github.com/EGA-archive/ega-quickview'
+description = """EGA-QuickView is a FUSE file system to access EGA files remotely."""
+
+toolchain = {'name': 'GCC', 'version': '12.3.0'}
+
+github_account = 'EGA-archive'
+source_urls = [GITHUB_SOURCE]
+sources = [{
+    "download_filename": "%s.tar.gz" % local_commit,
+    "filename": "%(name)s-%(version)s.tar.gz",
+}]
+checksums = ['90836e42009736a8e20a2569918638f3cb2b53574265ca4f4bed7abd81a5e887']
+
+builddependencies = [
+    ('make', '4.4.1'),
+    ('Autoconf', '2.71'),
+    ('pkgconf', '1.9.5'),
+]
+
+dependencies = [
+    ('libsodium', '1.0.18'),
+    ('FUSE', '3.16.2'),
+    ('GLib', '2.77.1'),
+]
+
+preconfigopts = "autoreconf -i && "
+# fix Makefile to create /bin in installdir
+preinstallopts = "sed -i 's/install: $(TARGET)/install: $(TARGET) $(bindir)/' Makefile && "
+
+sanity_check_paths = {
+    'files': ['bin/ega-qv'],
+    'dirs': [],
+}
+
+sanity_check_commands = ['ega-qv -h']
+
+moduleclass = 'tools'
+
+#ERROR1: OK
+    # Creating target ega-qv
+    # /apps/gent/RHEL8/cascadelake-ib/software/binutils/2.40-GCCcore-12.3.0/bin/ld: skipping incompatible /usr/lib/libpthread.so when searching for -lpthread
+    # /apps/gent/RHEL8/cascadelake-ib/software/binutils/2.40-GCCcore-12.3.0/bin/ld: skipping incompatible /usr/lib/libm.so when searching for -lm
+    # /apps/gent/RHEL8/cascadelake-ib/software/binutils/2.40-GCCcore-12.3.0/bin/ld: skipping incompatible /usr/lib/libpthread.so when searching for -lpthread
+    # /apps/gent/RHEL8/cascadelake-ib/software/binutils/2.40-GCCcore-12.3.0/bin/ld: skipping incompatible /usr/lib/libc.so when searching for -lc
+    # /usr/bin/install -c -m 0755 ega-qv /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/ega-quickview/20240620-GCC-12.3.0/bin/ega-qv
+    # /usr/bin/install: cannot create regular file 
+    # '/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/ega-quickview/20240620-GCC-12.3.0/bin/ega-qv': 
+    #     No such file or directory
diff --git a/easybuild/easyconfigs/f/FUSE/FUSE-3.16.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/f/FUSE/FUSE-3.16.2-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..bf3ee6edaf8
--- /dev/null
+++ b/easybuild/easyconfigs/f/FUSE/FUSE-3.16.2-GCCcore-12.3.0.eb
@@ -0,0 +1,30 @@
+easyblock = 'MesonNinja'
+
+name = 'FUSE'
+version = '3.16.2'
+
+homepage = 'https://github.com/libfuse/libfuse'
+description = "The reference implementation of the Linux FUSE (Filesystem in Userspace) interface"
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+source_urls = ['https://github.com/libfuse/libfuse/archive/']
+sources = ['fuse-%(version)s.tar.gz']
+checksums = ['1bc306be1a1f4f6c8965fbdd79c9ccca021fdc4b277d501483a711cbd7dbcd6c']
+
+builddependencies = [
+    ('Meson', '1.1.1'),
+    ('Ninja', '1.11.1'),
+    ('binutils', '2.40'),
+]
+
+# -Dutils=True only works as root
+configopts = '-Dutils=False'
+
+sanity_check_paths = {
+    'files': ['lib64/libfuse%%(version_major)s.%s' % SHLIB_EXT,
+              'lib64/pkgconfig/fuse%(version_major)s.pc'],
+    'dirs': ['include/fuse%(version_major)s'],
+}
+
+moduleclass = 'lib'

From 16fe8b5f116824704b07a0f540ae92dea5b17caa Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Thu, 20 Jun 2024 15:59:44 +0200
Subject: [PATCH 283/835] cleanup easyconfig ega-qv

---
 .../ega-quickview-20240620-GCC-12.3.0.eb              | 11 -----------
 1 file changed, 11 deletions(-)

diff --git a/easybuild/easyconfigs/e/ega-quickview/ega-quickview-20240620-GCC-12.3.0.eb b/easybuild/easyconfigs/e/ega-quickview/ega-quickview-20240620-GCC-12.3.0.eb
index 1ed48a2fa79..d3c6fa84d9a 100644
--- a/easybuild/easyconfigs/e/ega-quickview/ega-quickview-20240620-GCC-12.3.0.eb
+++ b/easybuild/easyconfigs/e/ega-quickview/ega-quickview-20240620-GCC-12.3.0.eb
@@ -41,14 +41,3 @@ sanity_check_paths = {
 sanity_check_commands = ['ega-qv -h']
 
 moduleclass = 'tools'
-
-#ERROR1: OK
-    # Creating target ega-qv
-    # /apps/gent/RHEL8/cascadelake-ib/software/binutils/2.40-GCCcore-12.3.0/bin/ld: skipping incompatible /usr/lib/libpthread.so when searching for -lpthread
-    # /apps/gent/RHEL8/cascadelake-ib/software/binutils/2.40-GCCcore-12.3.0/bin/ld: skipping incompatible /usr/lib/libm.so when searching for -lm
-    # /apps/gent/RHEL8/cascadelake-ib/software/binutils/2.40-GCCcore-12.3.0/bin/ld: skipping incompatible /usr/lib/libpthread.so when searching for -lpthread
-    # /apps/gent/RHEL8/cascadelake-ib/software/binutils/2.40-GCCcore-12.3.0/bin/ld: skipping incompatible /usr/lib/libc.so when searching for -lc
-    # /usr/bin/install -c -m 0755 ega-qv /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/ega-quickview/20240620-GCC-12.3.0/bin/ega-qv
-    # /usr/bin/install: cannot create regular file 
-    # '/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/ega-quickview/20240620-GCC-12.3.0/bin/ega-qv': 
-    #     No such file or directory

From 3ab2ec6f51da10845fe2048e11d65a084bf52675 Mon Sep 17 00:00:00 2001
From: Alexander Grund <alexander.grund@tu-dresden.de>
Date: Thu, 20 Jun 2024 16:08:00 +0200
Subject: [PATCH 284/835] Skip unreliable memory leak test in PyTorch 2.1.2

---
 .../p/PyTorch/PyTorch-2.1.2-foss-2022a.eb       |  2 ++
 .../p/PyTorch/PyTorch-2.1.2-foss-2022b.eb       |  2 ++
 .../PyTorch-2.1.2-foss-2023a-CUDA-12.1.1.eb     |  2 ++
 .../p/PyTorch/PyTorch-2.1.2-foss-2023a.eb       |  2 ++
 .../p/PyTorch/PyTorch-2.1.2-foss-2023b.eb       |  2 ++
 .../PyTorch-2.1.2_skip-memory-leak-test.patch   | 17 +++++++++++++++++
 6 files changed, 27 insertions(+)
 create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_skip-memory-leak-test.patch

diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2022a.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2022a.eb
index 0f6d51fd1bb..4c9324b7479 100644
--- a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2022a.eb
+++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2022a.eb
@@ -46,6 +46,7 @@ patches = [
     'PyTorch-2.1.2_fix-vsx-vector-abs.patch',
     'PyTorch-2.1.2_fix-vsx-vector-div.patch',
     'PyTorch-2.1.2_skip-cpu_repro-test-without-vectorization.patch',
+    'PyTorch-2.1.2_skip-memory-leak-test.patch',
     'PyTorch-2.1.2_workaround_dynamo_failure_without_nnpack.patch',
 ]
 checksums = [
@@ -111,6 +112,7 @@ checksums = [
     {'PyTorch-2.1.2_fix-vsx-vector-div.patch': '11f497a6892eb49b249a15320e4218e0d7ac8ae4ce67de39e4a018a064ca1acc'},
     {'PyTorch-2.1.2_skip-cpu_repro-test-without-vectorization.patch':
      '7ace835af60c58d9e0754a34c19d4b9a0c3a531f19e5d0eba8e2e49206eaa7eb'},
+    {'PyTorch-2.1.2_skip-memory-leak-test.patch': '8d9841208e8a00a498295018aead380c360cf56e500ef23ca740adb5b36de142'},
     {'PyTorch-2.1.2_workaround_dynamo_failure_without_nnpack.patch':
      'fb96eefabf394617bbb3fbd3a7a7c1aa5991b3836edc2e5d2a30e708bfe49ba1'},
 ]
diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2022b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2022b.eb
index 146e42cb2b8..ee2c8731bb8 100644
--- a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2022b.eb
+++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2022b.eb
@@ -47,6 +47,7 @@ patches = [
     'PyTorch-2.1.2_fix-vsx-vector-abs.patch',
     'PyTorch-2.1.2_fix-vsx-vector-div.patch',
     'PyTorch-2.1.2_skip-cpu_repro-test-without-vectorization.patch',
+    'PyTorch-2.1.2_skip-memory-leak-test.patch',
     'PyTorch-2.1.2_workaround_dynamo_failure_without_nnpack.patch',
 ]
 checksums = [
@@ -113,6 +114,7 @@ checksums = [
     {'PyTorch-2.1.2_fix-vsx-vector-div.patch': '11f497a6892eb49b249a15320e4218e0d7ac8ae4ce67de39e4a018a064ca1acc'},
     {'PyTorch-2.1.2_skip-cpu_repro-test-without-vectorization.patch':
      '7ace835af60c58d9e0754a34c19d4b9a0c3a531f19e5d0eba8e2e49206eaa7eb'},
+    {'PyTorch-2.1.2_skip-memory-leak-test.patch': '8d9841208e8a00a498295018aead380c360cf56e500ef23ca740adb5b36de142'},
     {'PyTorch-2.1.2_workaround_dynamo_failure_without_nnpack.patch':
      'fb96eefabf394617bbb3fbd3a7a7c1aa5991b3836edc2e5d2a30e708bfe49ba1'},
 ]
diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023a-CUDA-12.1.1.eb
index 7990dd1511b..65dfced1701 100644
--- a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023a-CUDA-12.1.1.eb
+++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023a-CUDA-12.1.1.eb
@@ -59,6 +59,7 @@ patches = [
     'PyTorch-2.1.2_remove-nccl-backend-default-without-gpus.patch',
     'PyTorch-2.1.2_skip-cpu_repro-test-without-vectorization.patch',
     'PyTorch-2.1.2_skip-failing-test_dtensor_ops-subtests.patch',
+    'PyTorch-2.1.2_skip-memory-leak-test.patch',
     'PyTorch-2.1.2_skip-test_fsdp_tp_checkpoint_integration.patch',
     'PyTorch-2.1.2_workaround_dynamo_failure_without_nnpack.patch',
 ]
@@ -145,6 +146,7 @@ checksums = [
      '7ace835af60c58d9e0754a34c19d4b9a0c3a531f19e5d0eba8e2e49206eaa7eb'},
     {'PyTorch-2.1.2_skip-failing-test_dtensor_ops-subtests.patch':
      '6cf711bf26518550903b09ed4431de9319791e79d61aab065785d6608fd5cc88'},
+    {'PyTorch-2.1.2_skip-memory-leak-test.patch': '8d9841208e8a00a498295018aead380c360cf56e500ef23ca740adb5b36de142'},
     {'PyTorch-2.1.2_skip-test_fsdp_tp_checkpoint_integration.patch':
      '943ee92f5fd518f608a59e43fe426b9bb45d7e7ad0ba04639e516db2d61fa57d'},
     {'PyTorch-2.1.2_workaround_dynamo_failure_without_nnpack.patch':
diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023a.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023a.eb
index 413e3254f8a..a79f709480c 100644
--- a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023a.eb
+++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023a.eb
@@ -48,6 +48,7 @@ patches = [
     'PyTorch-2.1.2_fix-vsx-vector-abs.patch',
     'PyTorch-2.1.2_fix-vsx-vector-div.patch',
     'PyTorch-2.1.2_skip-cpu_repro-test-without-vectorization.patch',
+    'PyTorch-2.1.2_skip-memory-leak-test.patch',
     'PyTorch-2.1.2_workaround_dynamo_failure_without_nnpack.patch',
 ]
 checksums = [
@@ -116,6 +117,7 @@ checksums = [
     {'PyTorch-2.1.2_fix-vsx-vector-div.patch': '11f497a6892eb49b249a15320e4218e0d7ac8ae4ce67de39e4a018a064ca1acc'},
     {'PyTorch-2.1.2_skip-cpu_repro-test-without-vectorization.patch':
      '7ace835af60c58d9e0754a34c19d4b9a0c3a531f19e5d0eba8e2e49206eaa7eb'},
+    {'PyTorch-2.1.2_skip-memory-leak-test.patch': '8d9841208e8a00a498295018aead380c360cf56e500ef23ca740adb5b36de142'},
     {'PyTorch-2.1.2_workaround_dynamo_failure_without_nnpack.patch':
      'fb96eefabf394617bbb3fbd3a7a7c1aa5991b3836edc2e5d2a30e708bfe49ba1'},
 ]
diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023b.eb
index 151e13356fe..bce1b68aa7b 100644
--- a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023b.eb
+++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023b.eb
@@ -48,6 +48,7 @@ patches = [
     'PyTorch-2.1.2_fix-vsx-vector-abs.patch',
     'PyTorch-2.1.2_fix-vsx-vector-div.patch',
     'PyTorch-2.1.2_skip-cpu_repro-test-without-vectorization.patch',
+    'PyTorch-2.1.2_skip-memory-leak-test.patch',
     'PyTorch-2.1.2_workaround_dynamo_failure_without_nnpack.patch',
 ]
 checksums = [
@@ -116,6 +117,7 @@ checksums = [
     {'PyTorch-2.1.2_fix-vsx-vector-div.patch': '11f497a6892eb49b249a15320e4218e0d7ac8ae4ce67de39e4a018a064ca1acc'},
     {'PyTorch-2.1.2_skip-cpu_repro-test-without-vectorization.patch':
      '7ace835af60c58d9e0754a34c19d4b9a0c3a531f19e5d0eba8e2e49206eaa7eb'},
+    {'PyTorch-2.1.2_skip-memory-leak-test.patch': '8d9841208e8a00a498295018aead380c360cf56e500ef23ca740adb5b36de142'},
     {'PyTorch-2.1.2_workaround_dynamo_failure_without_nnpack.patch':
      'fb96eefabf394617bbb3fbd3a7a7c1aa5991b3836edc2e5d2a30e708bfe49ba1'},
 ]
diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_skip-memory-leak-test.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_skip-memory-leak-test.patch
new file mode 100644
index 00000000000..cbebd761d98
--- /dev/null
+++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_skip-memory-leak-test.patch
@@ -0,0 +1,17 @@
+Reports from various sites show that this test is unreliable.
+As it is not critical just skip it.
+
+@Author: Alexander Grund (TU Dresden)
+
+diff --git a/test/test_jit.py b/test/test_jit.py
+index 2cdc5413dfe..5b145458630 100644
+--- a/test/test_jit.py
++++ b/test/test_jit.py
+@@ -12838,6 +12838,7 @@ dedent """
+             data = reader.get_record(str(offset))
+             assert(data == buffers[i])
+ 
++    @unittest.skip("The memory allocation tracking is not reliable on all systems")
+     def test_file_reader_no_memory_leak(self):
+         num_iters = 10000
+         filename, _, _ = self._make_filereader_test_file()

From dd4f39aab4d55b076f8c0408cfd719ae350d669d Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Thu, 20 Jun 2024 16:38:00 +0200
Subject: [PATCH 285/835] adding easyconfigs:
 jupyter-vscode-proxy-0.6-GCCcore-12.3.0.eb, code-server-4.90.2.eb

---
 .../c/code-server/code-server-4.90.2.eb       | 20 ++++++++++++
 ...jupyter-vscode-proxy-0.6-GCCcore-12.3.0.eb | 32 +++++++++++++++++++
 2 files changed, 52 insertions(+)
 create mode 100644 easybuild/easyconfigs/c/code-server/code-server-4.90.2.eb
 create mode 100644 easybuild/easyconfigs/j/jupyter-vscode-proxy/jupyter-vscode-proxy-0.6-GCCcore-12.3.0.eb

diff --git a/easybuild/easyconfigs/c/code-server/code-server-4.90.2.eb b/easybuild/easyconfigs/c/code-server/code-server-4.90.2.eb
new file mode 100644
index 00000000000..d85b34c752c
--- /dev/null
+++ b/easybuild/easyconfigs/c/code-server/code-server-4.90.2.eb
@@ -0,0 +1,20 @@
+name = 'code-server'
+version = '4.90.2'
+
+homepage = 'https://github.com/coder/code-server'
+description = """Run VS Code on any machine anywhere and access it in the browser."""
+
+toolchain = SYSTEM
+
+source_urls = ['https://github.com/coder/code-server/releases/download/v%(version)s/']
+sources = ['code-server-%(version)s-linux-%(mapped_arch)s.tar.gz']
+checksums = [
+    {
+        'code-server-%(version)s-linux-amd64.tar.gz':
+            'c66b57759e41c66c28577eaefa4cce106f7b5ad5fb3ab394baea5eaa5b604cce',
+        'code-server-%(version)s-linux-arm64.tar.gz':
+            '12e51e3575069c438aa4dee93bddfc221e7850192a7745b84fc77b420cedf205',
+    }
+]
+
+moduleclass = 'tools'
diff --git a/easybuild/easyconfigs/j/jupyter-vscode-proxy/jupyter-vscode-proxy-0.6-GCCcore-12.3.0.eb b/easybuild/easyconfigs/j/jupyter-vscode-proxy/jupyter-vscode-proxy-0.6-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..1f8a364ba25
--- /dev/null
+++ b/easybuild/easyconfigs/j/jupyter-vscode-proxy/jupyter-vscode-proxy-0.6-GCCcore-12.3.0.eb
@@ -0,0 +1,32 @@
+easyblock = "PythonBundle"
+
+name = 'jupyter-vscode-proxy'
+version = '0.6'
+
+homepage = 'https://github.com/betatim/vscode-binder'
+description = "VS Code extension for Jupyter"
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+builddependencies = [
+    ('binutils', '2.40'),
+]
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('jupyter-server-proxy', '4.0.0'),
+    ('code-server', '4.90.2', '', SYSTEM),
+]
+
+use_pip = True
+
+exts_list = [
+    ('jupyter_vscode_proxy', version, {
+        'sources': ['%(name)s-%(version)s-py3-none-any.whl'],
+        'checksums': ['c72037d1234f0cd489ecb0ab40ec8b150fc9cd7006b4d9c7036200e76689da78'],
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'tools'

From 4488df01d52d8de7639116a632eb54f68b75f29f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 21 Jun 2024 08:44:26 +0200
Subject: [PATCH 286/835] adding easyconfigs: ESPResSo-4.2.2-foss-2023b.eb,
 Boost.MPI-1.83.0-gompi-2023b.eb, Pint-0.24-GCCcore-13.2.0.eb

---
 .../Boost.MPI/Boost.MPI-1.83.0-gompi-2023b.eb | 29 ++++++++++
 .../e/ESPResSo/ESPResSo-4.2.2-foss-2023b.eb   | 55 +++++++++++++++++++
 .../p/Pint/Pint-0.24-GCCcore-13.2.0.eb        | 43 +++++++++++++++
 3 files changed, 127 insertions(+)
 create mode 100644 easybuild/easyconfigs/b/Boost.MPI/Boost.MPI-1.83.0-gompi-2023b.eb
 create mode 100644 easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.2-foss-2023b.eb
 create mode 100644 easybuild/easyconfigs/p/Pint/Pint-0.24-GCCcore-13.2.0.eb

diff --git a/easybuild/easyconfigs/b/Boost.MPI/Boost.MPI-1.83.0-gompi-2023b.eb b/easybuild/easyconfigs/b/Boost.MPI/Boost.MPI-1.83.0-gompi-2023b.eb
new file mode 100644
index 00000000000..2378bf71abb
--- /dev/null
+++ b/easybuild/easyconfigs/b/Boost.MPI/Boost.MPI-1.83.0-gompi-2023b.eb
@@ -0,0 +1,29 @@
+easyblock = 'EB_Boost'
+
+name = 'Boost.MPI'
+version = '1.83.0'
+
+homepage = 'https://www.boost.org/'
+description = """Boost provides free peer-reviewed portable C++ source libraries."""
+
+toolchain = {'name': 'gompi', 'version': '2023b'}
+toolchainopts = {'pic': True, 'usempi': True}
+
+source_urls = ['https://boostorg.jfrog.io/artifactory/main/release/%(version)s/source/']
+sources = ['boost_%s.tar.gz' % '_'.join(version.split('.'))]
+checksums = ['c0685b68dd44cc46574cce86c4e17c0f611b15e195be9848dfd0769a0a207628']
+
+dependencies = [
+    ('bzip2', '1.0.8'),
+    ('zlib', '1.2.13'),
+    ('XZ', '5.4.4'),
+    ('zstd', '1.5.5'),
+    ('ICU', '74.1'),
+]
+
+configopts = '--without-libraries=python'
+
+boost_mpi = True
+tagged_layout = True
+
+moduleclass = 'devel'
diff --git a/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.2-foss-2023b.eb b/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.2-foss-2023b.eb
new file mode 100644
index 00000000000..950f31dba26
--- /dev/null
+++ b/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.2-foss-2023b.eb
@@ -0,0 +1,55 @@
+easyblock = 'CMakeMake'
+
+name = 'ESPResSo'
+version = '4.2.2'
+
+homepage = 'https://espressomd.org/wordpress'
+description = """A software package for performing and analyzing scientific Molecular Dynamics simulations."""
+
+source_urls = ['https://github.com/espressomd/espresso/releases/download/%(version)s/']
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['2bc02f91632b0030f1203759768bd718bd8a0005f72696980b12331b4bfa0d76']
+
+toolchain = {'name': 'foss', 'version': '2023b'}
+toolchainopts = {'usempi': True, 'pic': True}
+
+builddependencies = [('CMake', '3.27.6')]
+
+dependencies = [
+    ('Python', '3.11.5'),
+    ('SciPy-bundle', '2023.11'),
+    ('Boost.MPI', '1.83.0'),
+    ('HDF5', '1.14.3'),
+    ('Mesa', '23.1.9'),
+    ('GSL', '2.7'),
+    ('IPython', '8.17.2'),
+    ('Pint', '0.24'),
+]
+
+configopts = ' -DCMAKE_SKIP_RPATH=OFF -DWITH_TESTS=ON -DWITH_CUDA=OFF'
+# make sure the right Python is used (note: -DPython3_EXECUTABLE or -DPython_EXECUTABLE does not work!)
+configopts += ' -DPYTHON_EXECUTABLE=$EBROOTPYTHON/bin/python '
+
+runtest = 'check_unit_tests && make check_python'
+
+modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']}
+
+_binaries = ['ipypresso',  'pypresso']
+_libs = [
+    'Espresso_config', 'Espresso_core', 'Espresso_script_interface', 'Espresso_shapes',
+    '_init', 'analyze', 'code_info', 'electrokinetics', 'galilei',
+    'integrate', 'interactions', 'lb', 'particle_data', 'polymer', 'profiler',
+    'script_interface', 'system', 'thermostat', 'utils', 'version',
+]
+
+_lib_path = 'lib/python%(pyshortver)s/site-packages/espressomd'
+
+sanity_check_paths = {
+    'files': ['bin/%s' % x for x in _binaries] +
+             [_lib_path + '/%s.' % x + SHLIB_EXT for x in _libs],
+    'dirs': ['bin', 'lib']
+}
+
+sanity_check_commands = ['pypresso -h', 'ipypresso -h']
+
+moduleclass = 'chem'
diff --git a/easybuild/easyconfigs/p/Pint/Pint-0.24-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/Pint/Pint-0.24-GCCcore-13.2.0.eb
new file mode 100644
index 00000000000..40b50dbb060
--- /dev/null
+++ b/easybuild/easyconfigs/p/Pint/Pint-0.24-GCCcore-13.2.0.eb
@@ -0,0 +1,43 @@
+easyblock = 'PythonBundle'
+
+name = 'Pint'
+version = '0.24'
+
+homepage = 'https://github.com/hgrecco/pint'
+description = """Pint is a Python package to define, operate and
+manipulate physical quantities: the product of a numerical value and a
+unit of measurement. It allows arithmetic operations between them and
+conversions from and to different units."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
+
+builddependencies = [
+    ('binutils', '2.40'),
+    ('hatchling', '1.18.0'),
+]
+
+dependencies = [
+    ('Python', '3.11.5'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('appdirs', '1.4.4', {
+        'checksums': ['7d5d0167b2b1ba821647616af46a749d1c653740dd0d2415100fe26e27afdf41'],
+    }),
+    ('flexcache', '0.3', {
+        'checksums': ['18743bd5a0621bfe2cf8d519e4c3bfdf57a269c15d1ced3fb4b64e0ff4600656'],
+    }),
+    ('flexparser', '0.3.1', {
+        'checksums': ['36f795d82e50f5c9ae2fde1c33f21f88922fdd67b7629550a3cc4d0b40a66856'],
+    }),
+    (name, version, {
+        'sources': [SOURCELOWER_TAR_GZ],
+        'checksums': ['c6c7c027b821413db1ac46b3b7bd296592848b5aec29a88cfc6e378fd1371903'],
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'numlib'

From 1dff17ec0e502b2bcff56a6543562e7f85982a30 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Fri, 21 Jun 2024 10:35:04 +0200
Subject: [PATCH 287/835] update deps

---
 .../easyconfigs/c/crypt4gh/crypt4gh-1.7-GCC-12.3.0.eb     | 8 +-------
 .../e/ega-quickview/ega-quickview-20240620-GCC-12.3.0.eb  | 2 +-
 2 files changed, 2 insertions(+), 8 deletions(-)

diff --git a/easybuild/easyconfigs/c/crypt4gh/crypt4gh-1.7-GCC-12.3.0.eb b/easybuild/easyconfigs/c/crypt4gh/crypt4gh-1.7-GCC-12.3.0.eb
index 24f42fade96..c52d7b3d83d 100644
--- a/easybuild/easyconfigs/c/crypt4gh/crypt4gh-1.7-GCC-12.3.0.eb
+++ b/easybuild/easyconfigs/c/crypt4gh/crypt4gh-1.7-GCC-12.3.0.eb
@@ -11,6 +11,7 @@ toolchain = {'name': 'GCC', 'version': '12.3.0'}
 
 dependencies = [
     ('Python', '3.11.3'),
+    ('Python-bundle-PyPI', '2023.06'),
     ('PyYAML', '6.0'),
     ('cryptography', '41.0.1'),
     ('bcrypt', '4.0.1'),
@@ -19,13 +20,6 @@ dependencies = [
 use_pip = True
 
 exts_list = [
-    ('PyNaCl', '1.5.0', {
-        'modulename': 'nacl',
-        'checksums': ['8ac7448f09ab85811607bdd21ec2464495ac8b7c66d146bf545b0f08fb9220ba'],
-    }),
-    ('docopt', '0.6.2', {
-        'checksums': ['49b3a825280bd66b3aa83585ef59c4a8c82f2c8a522dbe754a8bc8d08c85c491'],
-    }),
     (name, version, {
         'checksums': ['1569bc4ff9b689c8852e3892ac3f6fea4b31948ca0b1e5bc28d0d2f80def2a28'],
     }),
diff --git a/easybuild/easyconfigs/e/ega-quickview/ega-quickview-20240620-GCC-12.3.0.eb b/easybuild/easyconfigs/e/ega-quickview/ega-quickview-20240620-GCC-12.3.0.eb
index d3c6fa84d9a..7ca2cb398d7 100644
--- a/easybuild/easyconfigs/e/ega-quickview/ega-quickview-20240620-GCC-12.3.0.eb
+++ b/easybuild/easyconfigs/e/ega-quickview/ega-quickview-20240620-GCC-12.3.0.eb
@@ -19,7 +19,7 @@ checksums = ['90836e42009736a8e20a2569918638f3cb2b53574265ca4f4bed7abd81a5e887']
 
 builddependencies = [
     ('make', '4.4.1'),
-    ('Autoconf', '2.71'),
+    ('Autotools', '20220317'),
     ('pkgconf', '1.9.5'),
 ]
 

From e275d33168b53df4e59f798c482ee1941eb6f616 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Fri, 21 Jun 2024 10:43:51 +0200
Subject: [PATCH 288/835] update Autotools deps

---
 .../easyconfigs/s/SVDSS2/SVDSS2-2.0.0-alpha.3-GCC-12.3.0.eb    | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/easybuild/easyconfigs/s/SVDSS2/SVDSS2-2.0.0-alpha.3-GCC-12.3.0.eb b/easybuild/easyconfigs/s/SVDSS2/SVDSS2-2.0.0-alpha.3-GCC-12.3.0.eb
index 1d2e2c5ae19..404f2ce58f3 100644
--- a/easybuild/easyconfigs/s/SVDSS2/SVDSS2-2.0.0-alpha.3-GCC-12.3.0.eb
+++ b/easybuild/easyconfigs/s/SVDSS2/SVDSS2-2.0.0-alpha.3-GCC-12.3.0.eb
@@ -23,8 +23,7 @@ checksums = [None]
 builddependencies = [
     ('CMake', '3.26.3'),
     ('make', '4.4.1'),
-    ('Automake', '1.16.5'),
-    ('Autoconf', '2.71'),
+    ('Autotools', '20220317'),
     ('zlib', '1.2.13'),
     ('bzip2', '1.0.8'),
     ('XZ', '5.4.2'),

From caa4df3c0880da2469b76dffa4dd685381969050 Mon Sep 17 00:00:00 2001
From: Victor Enrique Goitea <43407659+VictorGoitea@users.noreply.github.com>
Date: Fri, 21 Jun 2024 10:53:57 +0200
Subject: [PATCH 289/835] change back source to http HOMER-4.11.1-foss-2022b.eb

---
 easybuild/easyconfigs/h/HOMER/HOMER-4.11.1-foss-2022b.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/h/HOMER/HOMER-4.11.1-foss-2022b.eb b/easybuild/easyconfigs/h/HOMER/HOMER-4.11.1-foss-2022b.eb
index c429effc925..0131cad9771 100644
--- a/easybuild/easyconfigs/h/HOMER/HOMER-4.11.1-foss-2022b.eb
+++ b/easybuild/easyconfigs/h/HOMER/HOMER-4.11.1-foss-2022b.eb
@@ -12,7 +12,7 @@ RNA-Seq, DNase-Seq, Hi-C and numerous other types of functional genomics sequenc
 
 toolchain = {'name': 'foss', 'version': '2022b'}
 
-source_urls = ['https://homer.ucsd.edu/homer/data/software']
+source_urls = ['http://homer.ucsd.edu/homer/data/software']
 sources = ['homer.v%(version)s.zip']
 checksums = ['80d1cd00616729894017b24a36a2ef81f9cde8bd364e875aead1e0cfb500c82b']
 

From 3d5643fb36ac8e8f62554ef6058e38d224fe8896 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 21 Jun 2024 14:15:11 +0200
Subject: [PATCH 290/835] let ReFrame install PyYAML 6.0.1 instead of 6.0 to
 fix Cython issue

---
 easybuild/easyconfigs/r/ReFrame/ReFrame-4.3.2.eb | 3 ++-
 easybuild/easyconfigs/r/ReFrame/ReFrame-4.3.3.eb | 3 ++-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.3.2.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.3.2.eb
index b8237231c17..36bc2418b05 100644
--- a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.3.2.eb
+++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.3.2.eb
@@ -28,7 +28,8 @@ exts_list = [
         'checksums': ['4bdcd7d840138086126cd09254dc6195fb4fc6f01c050a1d7236f2630db1d22a'],
     }),
     ('reframe', version, {
-        'preinstallopts': "export PATH=%(installdir)s/bin:$PATH && "
+        'preinstallopts': "sed -i 's@PyYAML==6.0@PyYAML==6.0.1@' requirements.txt && "
+                          "export PATH=%(installdir)s/bin:$PATH && "
                           "./bootstrap.sh +docs +pygelf && cp -r external %(installdir)s && "
                           "PYTHONPATH=%(builddir)s/reframe/reframe-%(version)s/external:$PYTHONPATH ",
         'source_tmpl': 'v%(version)s.tar.gz',
diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.3.3.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.3.3.eb
index af6b22f4846..6b8b0c7eb65 100644
--- a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.3.3.eb
+++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.3.3.eb
@@ -29,7 +29,8 @@ exts_list = [
         'checksums': ['4bdcd7d840138086126cd09254dc6195fb4fc6f01c050a1d7236f2630db1d22a'],
     }),
     ('reframe', version, {
-        'preinstallopts': "export PATH=%(installdir)s/bin:$PATH && "
+        'preinstallopts': "sed -i 's@PyYAML==6.0@PyYAML==6.0.1@' requirements.txt && "
+                          "export PATH=%(installdir)s/bin:$PATH && "
                           "./bootstrap.sh +docs +pygelf && cp -r external %(installdir)s && "
                           "PYTHONPATH=%(builddir)s/reframe/reframe-%(version)s/external:$PYTHONPATH ",
         'source_tmpl': 'v%(version)s.tar.gz',

From 830385da1e520c3f75e1b50e01af987df9f79213 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 21 Jun 2024 14:20:33 +0200
Subject: [PATCH 291/835] add comment about sed command

---
 easybuild/easyconfigs/r/ReFrame/ReFrame-4.3.2.eb | 3 ++-
 easybuild/easyconfigs/r/ReFrame/ReFrame-4.3.3.eb | 3 ++-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.3.2.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.3.2.eb
index 36bc2418b05..4efd476b8d7 100644
--- a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.3.2.eb
+++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.3.2.eb
@@ -28,7 +28,8 @@ exts_list = [
         'checksums': ['4bdcd7d840138086126cd09254dc6195fb4fc6f01c050a1d7236f2630db1d22a'],
     }),
     ('reframe', version, {
-        'preinstallopts': "sed -i 's@PyYAML==6.0@PyYAML==6.0.1@' requirements.txt && "
+        'preinstallopts': # use PyYAML 6.0.1 to solve Cython 3 incompatibility issues
+                          "sed -i 's@PyYAML==6.0@PyYAML==6.0.1@' requirements.txt && "
                           "export PATH=%(installdir)s/bin:$PATH && "
                           "./bootstrap.sh +docs +pygelf && cp -r external %(installdir)s && "
                           "PYTHONPATH=%(builddir)s/reframe/reframe-%(version)s/external:$PYTHONPATH ",
diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.3.3.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.3.3.eb
index 6b8b0c7eb65..a6dafff3207 100644
--- a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.3.3.eb
+++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.3.3.eb
@@ -29,7 +29,8 @@ exts_list = [
         'checksums': ['4bdcd7d840138086126cd09254dc6195fb4fc6f01c050a1d7236f2630db1d22a'],
     }),
     ('reframe', version, {
-        'preinstallopts': "sed -i 's@PyYAML==6.0@PyYAML==6.0.1@' requirements.txt && "
+        'preinstallopts': # use PyYAML 6.0.1 to solve Cython 3 incompatibility issues
+                          "sed -i 's@PyYAML==6.0@PyYAML==6.0.1@' requirements.txt && "
                           "export PATH=%(installdir)s/bin:$PATH && "
                           "./bootstrap.sh +docs +pygelf && cp -r external %(installdir)s && "
                           "PYTHONPATH=%(builddir)s/reframe/reframe-%(version)s/external:$PYTHONPATH ",

From 859aac55d1b0803f074e68f3002d14cba1205837 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 21 Jun 2024 14:45:34 +0200
Subject: [PATCH 292/835] switch order of lines to make CI happy about comment

---
 easybuild/easyconfigs/r/ReFrame/ReFrame-4.3.2.eb | 4 ++--
 easybuild/easyconfigs/r/ReFrame/ReFrame-4.3.3.eb | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.3.2.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.3.2.eb
index 4efd476b8d7..7e01526d78c 100644
--- a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.3.2.eb
+++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.3.2.eb
@@ -28,9 +28,9 @@ exts_list = [
         'checksums': ['4bdcd7d840138086126cd09254dc6195fb4fc6f01c050a1d7236f2630db1d22a'],
     }),
     ('reframe', version, {
-        'preinstallopts': # use PyYAML 6.0.1 to solve Cython 3 incompatibility issues
+        'preinstallopts': "export PATH=%(installdir)s/bin:$PATH && "
+                          # use PyYAML 6.0.1 to solve Cython 3 incompatibility issues
                           "sed -i 's@PyYAML==6.0@PyYAML==6.0.1@' requirements.txt && "
-                          "export PATH=%(installdir)s/bin:$PATH && "
                           "./bootstrap.sh +docs +pygelf && cp -r external %(installdir)s && "
                           "PYTHONPATH=%(builddir)s/reframe/reframe-%(version)s/external:$PYTHONPATH ",
         'source_tmpl': 'v%(version)s.tar.gz',
diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.3.3.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.3.3.eb
index a6dafff3207..f4319b13ae5 100644
--- a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.3.3.eb
+++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.3.3.eb
@@ -29,9 +29,9 @@ exts_list = [
         'checksums': ['4bdcd7d840138086126cd09254dc6195fb4fc6f01c050a1d7236f2630db1d22a'],
     }),
     ('reframe', version, {
-        'preinstallopts': # use PyYAML 6.0.1 to solve Cython 3 incompatibility issues
+        'preinstallopts': "export PATH=%(installdir)s/bin:$PATH && "
+                          # use PyYAML 6.0.1 to solve Cython 3 incompatibility issues
                           "sed -i 's@PyYAML==6.0@PyYAML==6.0.1@' requirements.txt && "
-                          "export PATH=%(installdir)s/bin:$PATH && "
                           "./bootstrap.sh +docs +pygelf && cp -r external %(installdir)s && "
                           "PYTHONPATH=%(builddir)s/reframe/reframe-%(version)s/external:$PYTHONPATH ",
         'source_tmpl': 'v%(version)s.tar.gz',

From d1c95d834fe2dee39743e8eaddebae9321d083a7 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Fri, 21 Jun 2024 14:57:27 +0200
Subject: [PATCH 293/835] adding easyconfigs: orjson-3.9.15-GCC-12.3.0.eb

---
 .../o/orjson/orjson-3.9.15-GCC-12.3.0.eb      | 37 +++++++++++++++++++
 1 file changed, 37 insertions(+)
 create mode 100644 easybuild/easyconfigs/o/orjson/orjson-3.9.15-GCC-12.3.0.eb

diff --git a/easybuild/easyconfigs/o/orjson/orjson-3.9.15-GCC-12.3.0.eb b/easybuild/easyconfigs/o/orjson/orjson-3.9.15-GCC-12.3.0.eb
new file mode 100644
index 00000000000..c741b014f10
--- /dev/null
+++ b/easybuild/easyconfigs/o/orjson/orjson-3.9.15-GCC-12.3.0.eb
@@ -0,0 +1,37 @@
+easyblock = 'PythonBundle'
+
+name = 'orjson'
+version = '3.9.15'
+
+homepage = 'https://github.com/ijl/orjson'
+description = """Fast, correct Python JSON library supporting dataclasses, datetimes, and numpy."""
+
+toolchain = {'name': 'GCC', 'version': '12.3.0'}
+
+builddependencies = [
+    ('maturin', '1.4.0', '-Rust-1.75.0'),
+]
+dependencies = [
+    ('Python', '3.11.3'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('ruff', '0.4.8', {
+        'checksums': ['16d717b1d57b2e2fd68bd0bf80fb43931b79d05a7131aa477d66fc40fbd86268'],
+    }),
+    ('mypy_extensions', '1.0.0', {
+        'checksums': ['75dbf8955dc00442a438fc4d0666508a9a97b6bd41aa2f0ffe9d2f2725af0782'],
+    }),
+    ('mypy', '1.10.0', {
+        'checksums': ['3d087fcbec056c4ee34974da493a826ce316947485cef3901f511848e687c131'],
+    }),
+    (name, version, {
+        'checksums': ['95cae920959d772f30ab36d3b25f83bb0f3be671e986c72ce22f8fa700dae061'],
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'math'

From 301e2bddf6f80c209b4c24031fb8d37a975f3c91 Mon Sep 17 00:00:00 2001
From: WilleBell <cintiawillemyns@gmail.com>
Date: Fri, 21 Jun 2024 15:54:22 +0200
Subject: [PATCH 294/835] Add pyGenomeTracks and fix pyBigWig to pass
 pip_check, preinstallopts for TOBIAS are not needed with this fix

---
 .../c/cooler/cooler-0.10.2-foss-2023a.eb      | 49 +++++++++++++++
 .../h/HiCMatrix/HiCMatrix-17.2-foss-2023a.eb  | 33 ++++++++++
 ...2023a.eb => pyBigWig-0.3.22-gfbf-2023a.eb} | 15 ++++-
 .../pyGenomeTracks-3.9-foss-2023a.eb          | 63 +++++++++++++++++++
 .../t/TOBIAS/TOBIAS-0.16.1-foss-2023a.eb      |  2 -
 5 files changed, 158 insertions(+), 4 deletions(-)
 create mode 100644 easybuild/easyconfigs/c/cooler/cooler-0.10.2-foss-2023a.eb
 create mode 100644 easybuild/easyconfigs/h/HiCMatrix/HiCMatrix-17.2-foss-2023a.eb
 rename easybuild/easyconfigs/p/pyBigWig/{pyBigWig-0.3.22-foss-2023a.eb => pyBigWig-0.3.22-gfbf-2023a.eb} (56%)
 create mode 100644 easybuild/easyconfigs/p/pyGenomeTracks/pyGenomeTracks-3.9-foss-2023a.eb

diff --git a/easybuild/easyconfigs/c/cooler/cooler-0.10.2-foss-2023a.eb b/easybuild/easyconfigs/c/cooler/cooler-0.10.2-foss-2023a.eb
new file mode 100644
index 00000000000..57091228de3
--- /dev/null
+++ b/easybuild/easyconfigs/c/cooler/cooler-0.10.2-foss-2023a.eb
@@ -0,0 +1,49 @@
+easyblock = 'PythonBundle'
+
+name = 'cooler'
+version = '0.10.2'
+
+homepage = 'https://open2c.github.io/cooler'
+description = """Cooler is a support library for a storage format, also called cooler, used to store
+ genomic interaction data of any size, such as Hi-C contact matrices."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+builddependencies = [
+    ('hatchling', '1.18.0'),
+]
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('h5py', '3.9.0'),
+    ('PyYAML', '6.0'),
+    ('pyfaidx', '0.8.1.1'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('asciitree', '0.3.3', {
+        'checksums': ['4aa4b9b649f85e3fcb343363d97564aa1fb62e249677f2e18a96765145cc0f6e'],
+    }),
+    ('toolz', '0.12.0', {
+        'checksums': ['88c570861c440ee3f2f6037c4654613228ff40c93a6c25e0eba70d17282c6194'],
+    }),
+    ('cytoolz', '0.12.3', {
+        'checksums': ['4503dc59f4ced53a54643272c61dc305d1dbbfbd7d6bdf296948de9f34c3a282'],
+    }),
+    ('dill', '0.3.8', {
+        'checksums': ['3ebe3c479ad625c4553aca177444d89b486b1d84982eeacded644afc0cf797ca'],
+    }),
+    ('multiprocess', '0.70.16', {
+        'checksums': ['161af703d4652a0e1410be6abccecde4a7ddffd19341be0a7011b94aeb171ac1'],
+    }),
+    (name, version, {
+        'checksums': ['3780a2e69b2ec89882dfc2775de5d9b54ccb79569dc5f042b4851599388112dc'],
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/h/HiCMatrix/HiCMatrix-17.2-foss-2023a.eb b/easybuild/easyconfigs/h/HiCMatrix/HiCMatrix-17.2-foss-2023a.eb
new file mode 100644
index 00000000000..474b8906ff5
--- /dev/null
+++ b/easybuild/easyconfigs/h/HiCMatrix/HiCMatrix-17.2-foss-2023a.eb
@@ -0,0 +1,33 @@
+easyblock = 'PythonBundle'
+
+name = 'HiCMatrix'
+version = '17.2'
+
+homepage = 'https://github.com/deeptools/HiCMatrix'
+description = "This library implements the central class of HiCExplorer to manage Hi-C interaction matrices."
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('PyTables', '3.8.0'),
+    ('cooler', '0.10.2'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('intervaltree', '3.1.0', {
+        'checksums': ['902b1b88936918f9b2a19e0e5eb7ccb430ae45cde4f39ea4b36932920d33952d'],
+    }),
+    (name, version, {
+        'source_tmpl': '%(version)s.tar.gz',
+        'source_urls': ['https://github.com/deeptools/HiCMatrix/archive/'],
+        'checksums': ['a2428676b5aad014e7b1653e3effe94f7ea8a68cc78be83e4b67f2255f6b4fbb'],
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/p/pyBigWig/pyBigWig-0.3.22-foss-2023a.eb b/easybuild/easyconfigs/p/pyBigWig/pyBigWig-0.3.22-gfbf-2023a.eb
similarity index 56%
rename from easybuild/easyconfigs/p/pyBigWig/pyBigWig-0.3.22-foss-2023a.eb
rename to easybuild/easyconfigs/p/pyBigWig/pyBigWig-0.3.22-gfbf-2023a.eb
index fc2cc3e8efc..11550de829f 100644
--- a/easybuild/easyconfigs/p/pyBigWig/pyBigWig-0.3.22-foss-2023a.eb
+++ b/easybuild/easyconfigs/p/pyBigWig/pyBigWig-0.3.22-gfbf-2023a.eb
@@ -8,11 +8,15 @@ homepage = 'https://github.com/%(github_account)s/%(name)s'
 description = """A python extension, written in C, for quick access to bigBed
  files and access to and creation of bigWig files."""
 
-toolchain = {'name': 'foss', 'version': '2023a'}
+toolchain = {'name': 'gfbf', 'version': '2023a'}
 
 source_urls = [GITHUB_SOURCE]
 sources = ['%(version)s.tar.gz']
-checksums = ['3b8d62b2bedcee0545a586884466c97a64b64283a309b211300b670f41dd2046']
+patches = [('pybigwig-version.egg-info', '.')]
+checksums = [
+    {'0.3.22.tar.gz': '3b8d62b2bedcee0545a586884466c97a64b64283a309b211300b670f41dd2046'},
+    {'pybigwig-version.egg-info': '736a4302019c54e667d147bc40c74f5f61930169ab0f306f074eb1b2dd5d85c8'},
+]
 
 dependencies = [
     ('Python', '3.11.3'),
@@ -26,6 +30,13 @@ preinstallopts = """sed -i 's/setup(/setup(version="%(version)s",/g' setup.py &&
 # do not use setuptools-scm to detect version
 preinstallopts += """sed -i 's/[tool.setuptools_scm]//' pyproject.toml && """
 
+# Install a egg-info file to avoid pip_check failing when pyBigWig is a dependency
+local_egg_info_src = '%(builddir)s/pyBigWig-%(version)s/pybigwig-version.egg-info'
+local_egg_info_dest = '%(installdir)s/lib/python%(pyshortver)s/site-packages/pybigwig-%(version)s.egg-info'
+postinstallcmds = [
+    'sed "s/#PYBIGWIG_VERSION#/%%(version)s/" %s > %s' % (local_egg_info_src, local_egg_info_dest),
+]
+
 use_pip = True
 download_dep_fail = True
 
diff --git a/easybuild/easyconfigs/p/pyGenomeTracks/pyGenomeTracks-3.9-foss-2023a.eb b/easybuild/easyconfigs/p/pyGenomeTracks/pyGenomeTracks-3.9-foss-2023a.eb
new file mode 100644
index 00000000000..b5cf0276807
--- /dev/null
+++ b/easybuild/easyconfigs/p/pyGenomeTracks/pyGenomeTracks-3.9-foss-2023a.eb
@@ -0,0 +1,63 @@
+easyblock = 'PythonBundle'
+
+name = 'pyGenomeTracks'
+version = '3.9'
+
+homepage = 'https://pygenometracks.readthedocs.io'
+description = "pyGenomeTracks aims to produce high-quality genome browser tracks that are highly customizable."
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('matplotlib', '3.7.2'),
+    ('bx-python', '0.10.0'),
+    ('pybedtools', '0.9.1'),
+    ('pyBigWig', '0.3.22'),
+    ('pyfaidx', '0.8.1.1'),
+    ('Pysam', '0.22.0'),
+    ('tqdm', '4.66.1'),
+    ('PyTables', '3.8.0'),
+    ('h5py', '3.9.0'),
+    ('PyYAML', '6.0'),
+    ('cooler', '0.10.2'),  # Needs new .eb
+    ('HiCMatrix', '17.2'),  # Needs new .eb
+]
+
+use_pip = True
+
+"""
+pygenometracks 3.8 requires pybigwig, which is not installed.
+"""
+
+exts_list = [
+    ('argcomplete', '3.4.0', {
+        'checksums': ['c2abcdfe1be8ace47ba777d4fce319eb13bf8ad9dace8d085dcad6eded88057f'],
+    }),
+    ('argh', '0.31.2', {
+        'checksums': ['db1c34885804f7d4646c385dc2fb19b45298561322f4c15eae1b133993f9e323'],
+    }),
+    ('gffutils', '0.13', {
+        'checksums': ['b0d52f35c014cc0330fb5c4e3c6fea127c90ccf4c5384a825cdb5c8ff330d4eb'],
+    }),
+    ('pypairix', '0.3.7', {
+        'checksums': ['c1b47c05f92b5be628923c60a27344503ddeba5d8f35a3752d646271d38e0525'],
+    }),
+    (name, version, {
+        'source_tmpl': '%(version)s.tar.gz',
+        'source_urls': ['https://github.com/deeptools/pyGenomeTracks/archive/refs/tags'],
+        'checksums': ['4318cb642422ee16d83675d571f4cd49b14784d7ee135ab53d8946fc7ad663f6'],
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['bin/pyGenomeTracks'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = ["pyGenomeTracks --help"]
+
+sanity_pip_check = True
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/t/TOBIAS/TOBIAS-0.16.1-foss-2023a.eb b/easybuild/easyconfigs/t/TOBIAS/TOBIAS-0.16.1-foss-2023a.eb
index 186556eb374..0404ad39d85 100644
--- a/easybuild/easyconfigs/t/TOBIAS/TOBIAS-0.16.1-foss-2023a.eb
+++ b/easybuild/easyconfigs/t/TOBIAS/TOBIAS-0.16.1-foss-2023a.eb
@@ -46,8 +46,6 @@ exts_list = [
         'checksums': ['a74408f69ba6271f71b9352ef4ed03dc53a31aa404d29b5d31f53bfecfee1440'],
     }),
     ('tobias', version, {
-        # remove pyBigWig dependency - pip_check fails with "import pybigwig"
-        'preinstallopts': "sed -i '81d' setup.py && ",
         'checksums': ['c46267c01287be06201b3e6f7a36daad1ad86d6c578f96e878501be7da7fd109'],
     }),
 ]

From 3d6c7d94c205a4cffc22f9bffc93969a16a6328e Mon Sep 17 00:00:00 2001
From: Richard Top <richard.topouchian@uib.no>
Date: Mon, 24 Jun 2024 08:22:23 +0000
Subject: [PATCH 295/835] {toolchain}[gmpolf-2024.06] , FFTW.MPI v3.3.10

---
 .../FFTW.MPI-3.3.10-gmpich-2024.06.eb         | 19 +++++++++++++
 .../easyconfigs/g/gmpolf/gmpolf-2024.06.eb    | 27 +++++++++++++++++++
 2 files changed, 46 insertions(+)
 create mode 100644 easybuild/easyconfigs/f/FFTW.MPI/FFTW.MPI-3.3.10-gmpich-2024.06.eb
 create mode 100644 easybuild/easyconfigs/g/gmpolf/gmpolf-2024.06.eb

diff --git a/easybuild/easyconfigs/f/FFTW.MPI/FFTW.MPI-3.3.10-gmpich-2024.06.eb b/easybuild/easyconfigs/f/FFTW.MPI/FFTW.MPI-3.3.10-gmpich-2024.06.eb
new file mode 100644
index 00000000000..4b79e9e7c27
--- /dev/null
+++ b/easybuild/easyconfigs/f/FFTW.MPI/FFTW.MPI-3.3.10-gmpich-2024.06.eb
@@ -0,0 +1,19 @@
+name = 'FFTW.MPI'
+version = '3.3.10'
+
+homepage = 'https://www.fftw.org'
+description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT)
+in one or more dimensions, of arbitrary input size, and of both real and complex data."""
+
+toolchain = {'name': 'gmpich', 'version': '2024.06'}
+toolchainopts = {'pic': True}
+
+source_urls = [homepage]
+sources = ['fftw-%(version)s.tar.gz']
+checksums = ['56c932549852cddcfafdab3820b0200c7742675be92179e59e6215b340e26467']
+
+dependencies = [('FFTW', '3.3.10')]
+
+runtest = 'check'
+
+moduleclass = 'numlib'
diff --git a/easybuild/easyconfigs/g/gmpolf/gmpolf-2024.06.eb b/easybuild/easyconfigs/g/gmpolf/gmpolf-2024.06.eb
new file mode 100644
index 00000000000..2e13b8c7f2d
--- /dev/null
+++ b/easybuild/easyconfigs/g/gmpolf/gmpolf-2024.06.eb
@@ -0,0 +1,27 @@
+easyblock = 'Toolchain'
+
+name = 'gmpolf'
+version = '2024.06'
+
+homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#foss-toolchain'
+description = """GNU Compiler Collection (GCC) based compiler toolchain, including
+ MPICH for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK."""
+
+toolchain = SYSTEM
+
+local_gccver = '12.3.0'
+
+# toolchain used to build foss dependencies
+local_comp_mpi_tc = ('gmpich', 2024.06)
+
+# we need GCC and MPICH as explicit dependencies instead of gompi toolchain
+# because of toolchain preparation functions
+dependencies = [
+    ('GCC', local_gccver),
+    ('MPICH', '4.2.1', '', ('GCC', local_gccver)),
+    ('FlexiBLAS', '3.3.1', '', ('GCC', local_gccver)),
+    ('FFTW', '3.3.10', '', ('GCC', local_gccver)),
+    ('FFTW.MPI', '3.3.10', '', local_comp_mpi_tc),
+    ('ScaLAPACK', '2.2.0', '-fb', local_comp_mpi_tc),
+]
+moduleclass = 'toolchain'

From 69c766df22b63190b6dea79eac0dd99e9d86d465 Mon Sep 17 00:00:00 2001
From: Justus Kuhlmann <j_kuhl19@uni-muenster.de>
Date: Mon, 24 Jun 2024 08:27:32 +0000
Subject: [PATCH 296/835] add mrcfil for gfbf 2022b

---
 .../m/mrcfile/mrcfile-1.4.3-foss-2022b.eb     | 40 +++++++++++++++++++
 1 file changed, 40 insertions(+)
 create mode 100644 easybuild/easyconfigs/m/mrcfile/mrcfile-1.4.3-foss-2022b.eb

diff --git a/easybuild/easyconfigs/m/mrcfile/mrcfile-1.4.3-foss-2022b.eb b/easybuild/easyconfigs/m/mrcfile/mrcfile-1.4.3-foss-2022b.eb
new file mode 100644
index 00000000000..848ed3326db
--- /dev/null
+++ b/easybuild/easyconfigs/m/mrcfile/mrcfile-1.4.3-foss-2022b.eb
@@ -0,0 +1,40 @@
+# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2022/11
+easyblock = 'PythonPackage'
+name = 'mrcfile'
+version = '1.4.3'
+homepage = 'https://github.com/ccpem/mrcfile'
+description = """mrcfile is a Python implementation of the MRC2014 file format, which is used in 
+structural biology to store image and volume data.
+
+It allows MRC files to be created and opened easily using a very simple API,    
+which exposes the file’s header and data as numpy arrays. The code runs in      
+Python 2 and 3 and is fully unit-tested.
+
+This library aims to allow users and developers to read and write standard-     
+compliant MRC files in Python as easily as possible, and with no dependencies on
+any compiled libraries except numpy. You can use it interactively to inspect    
+files, correct headers and so on, or in scripts and larger software packages to 
+provide basic MRC file I/O functions. """
+
+
+toolchain = {'name': 'gfbf', 'version': '2022b'}
+
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['43c358c59ff8f583fc4dc2079a0099028719109ebf92066e388772bab389c5f5']
+
+dependencies = [
+    ('Python', '3.10.8'),
+    ('SciPy-bundle', '2023.02'),
+]
+
+download_dep_fail = True
+sanity_pip_check = True
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s']
+}
+
+
+use_pip = True
+moduleclass = 'bio'

From ae959cee9d29c1c08624122526878420a413b40a Mon Sep 17 00:00:00 2001
From: Justus Kuhlmann <j_kuhl19@uni-muenster.de>
Date: Mon, 24 Jun 2024 08:28:11 +0000
Subject: [PATCH 297/835] change toolchain to foss

---
 easybuild/easyconfigs/m/mrcfile/mrcfile-1.4.3-foss-2022b.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/m/mrcfile/mrcfile-1.4.3-foss-2022b.eb b/easybuild/easyconfigs/m/mrcfile/mrcfile-1.4.3-foss-2022b.eb
index 848ed3326db..fa61a8ea8ca 100644
--- a/easybuild/easyconfigs/m/mrcfile/mrcfile-1.4.3-foss-2022b.eb
+++ b/easybuild/easyconfigs/m/mrcfile/mrcfile-1.4.3-foss-2022b.eb
@@ -17,7 +17,7 @@ files, correct headers and so on, or in scripts and larger software packages to
 provide basic MRC file I/O functions. """
 
 
-toolchain = {'name': 'gfbf', 'version': '2022b'}
+toolchain = {'name': 'foss', 'version': '2022b'}
 
 sources = [SOURCELOWER_TAR_GZ]
 checksums = ['43c358c59ff8f583fc4dc2079a0099028719109ebf92066e388772bab389c5f5']

From 19d2f3ca705716eebc27781e6d91e2aa75d28dc3 Mon Sep 17 00:00:00 2001
From: Richard Top <richard.topouchian@uib.no>
Date: Mon, 24 Jun 2024 08:44:24 +0000
Subject: [PATCH 298/835] added also ScaLAPACK-2.2.0-gmpich-2024.06-fb.eb

---
 .../ScaLAPACK-2.2.0-gmpich-2024.06-fb.eb      | 42 +++++++++++++++++++
 1 file changed, 42 insertions(+)
 create mode 100644 easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gmpich-2024.06-fb.eb

diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gmpich-2024.06-fb.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gmpich-2024.06-fb.eb
new file mode 100644
index 00000000000..4fd5b35b6d8
--- /dev/null
+++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gmpich-2024.06-fb.eb
@@ -0,0 +1,42 @@
+name = 'ScaLAPACK'
+version = '2.2.0'
+versionsuffix = '-fb'
+
+homepage = 'https://www.netlib.org/scalapack/'
+description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines
+ redesigned for distributed memory MIMD parallel computers."""
+
+toolchain = {'name': 'gmpich', 'version': '2024.06'}
+toolchainopts = {'extra_fflags': '-lpthread', 'openmp': True, 'pic': True, 'usempi': True}
+
+local_gccver = '12.3.0'
+
+source_urls = [homepage]
+sources = [SOURCELOWER_TGZ]
+patches = ['ScaLAPACK-%(version)s_fix-GCC-10.patch']
+checksums = [
+    '40b9406c20735a9a3009d863318cb8d3e496fb073d201c5463df810e01ab2a57',  # scalapack-2.2.0.tgz
+    'f6bc3c6dee012ba4a696548a2e12b6aae932ce4fd5a142153b338839f52b5906',  # ScaLAPACK-2.2.0_fix-GCC-10.patch
+]
+
+builddependencies = [
+    ('CMake', '3.26.3', '', ('GCCcore', local_gccver)),
+]
+
+dependencies = [
+    ('FlexiBLAS', '3.3.1', '', ('GCC', local_gccver)),
+]
+
+# Config Opts based on AOCL User Guide:
+# https://developer.amd.com/wp-content/resources/AOCL_User%20Guide_2.2.pdf
+
+configopts = '-DBUILD_SHARED_LIBS=ON '
+configopts += '-DBLAS_LIBRARIES="$EBROOTFLEXIBLAS/lib/libflexiblas.%s" ' % SHLIB_EXT
+configopts += '-DLAPACK_LIBRARIES="$EBROOTFLEXIBLAS/lib/libflexiblas.%s" ' % SHLIB_EXT
+
+sanity_check_paths = {
+    'files': ['lib/libscalapack.%s' % SHLIB_EXT, 'lib64/libscalapack.%s' % SHLIB_EXT],
+    'dirs': ["lib", "lib64"],
+}
+
+moduleclass = 'numlib'

From d2f6c1e5fb6f3cc27a1d1e3c4569dbfa7809c0a7 Mon Sep 17 00:00:00 2001
From: Richard Top <richard.topouchian@uib.no>
Date: Mon, 24 Jun 2024 09:02:07 +0000
Subject: [PATCH 299/835] fixed float

---
 easybuild/easyconfigs/g/gmpolf/gmpolf-2024.06.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/g/gmpolf/gmpolf-2024.06.eb b/easybuild/easyconfigs/g/gmpolf/gmpolf-2024.06.eb
index 2e13b8c7f2d..e5838d8a8a2 100644
--- a/easybuild/easyconfigs/g/gmpolf/gmpolf-2024.06.eb
+++ b/easybuild/easyconfigs/g/gmpolf/gmpolf-2024.06.eb
@@ -12,7 +12,7 @@ toolchain = SYSTEM
 local_gccver = '12.3.0'
 
 # toolchain used to build foss dependencies
-local_comp_mpi_tc = ('gmpich', 2024.06)
+local_comp_mpi_tc = ('gmpich', '2024.06')
 
 # we need GCC and MPICH as explicit dependencies instead of gompi toolchain
 # because of toolchain preparation functions

From b13fe349e1a6da449d9d8b050afa7e04c1f6fbef Mon Sep 17 00:00:00 2001
From: WilleBell <cintiawillemyns@gmail.com>
Date: Mon, 24 Jun 2024 11:26:46 +0200
Subject: [PATCH 300/835] Using pypi source fixes version issue (no patch
 needed)

---
 .../p/pyBigWig/pyBigWig-0.3.22-gfbf-2023a.eb  | 26 +++----------------
 1 file changed, 4 insertions(+), 22 deletions(-)

diff --git a/easybuild/easyconfigs/p/pyBigWig/pyBigWig-0.3.22-gfbf-2023a.eb b/easybuild/easyconfigs/p/pyBigWig/pyBigWig-0.3.22-gfbf-2023a.eb
index 11550de829f..8e9947f8e5b 100644
--- a/easybuild/easyconfigs/p/pyBigWig/pyBigWig-0.3.22-gfbf-2023a.eb
+++ b/easybuild/easyconfigs/p/pyBigWig/pyBigWig-0.3.22-gfbf-2023a.eb
@@ -3,20 +3,14 @@ easyblock = 'PythonPackage'
 name = 'pyBigWig'
 version = '0.3.22'
 
-github_account = 'deeptools'
-homepage = 'https://github.com/%(github_account)s/%(name)s'
+homepage = 'https://github.com/deeptools/pyBigWig'
 description = """A python extension, written in C, for quick access to bigBed
- files and access to and creation of bigWig files."""
+files and access to and creation of bigWig files."""
 
 toolchain = {'name': 'gfbf', 'version': '2023a'}
 
-source_urls = [GITHUB_SOURCE]
-sources = ['%(version)s.tar.gz']
-patches = [('pybigwig-version.egg-info', '.')]
-checksums = [
-    {'0.3.22.tar.gz': '3b8d62b2bedcee0545a586884466c97a64b64283a309b211300b670f41dd2046'},
-    {'pybigwig-version.egg-info': '736a4302019c54e667d147bc40c74f5f61930169ab0f306f074eb1b2dd5d85c8'},
-]
+sources = [SOURCE_TAR_GZ]
+checksums = ['5d4426f754bd7b7f6dc21d6c3f93b58a96a65b6eb2e578ae03b31a71272d2243']
 
 dependencies = [
     ('Python', '3.11.3'),
@@ -25,18 +19,6 @@ dependencies = [
     ('SciPy-bundle', '2023.07'),    # optional, for numpy support
 ]
 
-# fix  version of '0.0.0' issue
-preinstallopts = """sed -i 's/setup(/setup(version="%(version)s",/g' setup.py && """
-# do not use setuptools-scm to detect version
-preinstallopts += """sed -i 's/[tool.setuptools_scm]//' pyproject.toml && """
-
-# Install a egg-info file to avoid pip_check failing when pyBigWig is a dependency
-local_egg_info_src = '%(builddir)s/pyBigWig-%(version)s/pybigwig-version.egg-info'
-local_egg_info_dest = '%(installdir)s/lib/python%(pyshortver)s/site-packages/pybigwig-%(version)s.egg-info'
-postinstallcmds = [
-    'sed "s/#PYBIGWIG_VERSION#/%%(version)s/" %s > %s' % (local_egg_info_src, local_egg_info_dest),
-]
-
 use_pip = True
 download_dep_fail = True
 

From 5941a8a998a7d881a38950680deefb7421c3b9ea Mon Sep 17 00:00:00 2001
From: Simon Pinches <SimonPinches@users.noreply.github.com>
Date: Mon, 24 Jun 2024 13:21:49 +0200
Subject: [PATCH 301/835] Update
 easybuild/easyconfigs/t/Triangle/Triangle-1.6-GCCcore-13.2.0.eb
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Bob Dröge <b.e.droge@rug.nl>
---
 .../easyconfigs/t/Triangle/Triangle-1.6-GCCcore-13.2.0.eb    | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/easybuild/easyconfigs/t/Triangle/Triangle-1.6-GCCcore-13.2.0.eb b/easybuild/easyconfigs/t/Triangle/Triangle-1.6-GCCcore-13.2.0.eb
index 813429474de..12d41a6857e 100644
--- a/easybuild/easyconfigs/t/Triangle/Triangle-1.6-GCCcore-13.2.0.eb
+++ b/easybuild/easyconfigs/t/Triangle/Triangle-1.6-GCCcore-13.2.0.eb
@@ -36,4 +36,9 @@ sanity_check_paths = {
     'dirs': []
 }
 
+sanity_check_commands = [
+    'triangle -h',
+    'tricall',
+]
+
 moduleclass = 'numlib'

From dec8812b13fee150cd5e52d6128b2d7a42ea73a9 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Mon, 24 Jun 2024 13:25:52 +0200
Subject: [PATCH 302/835] adding easyconfigs:
 Stable-Baselines3-2.3.2-foss-2023a.eb

---
 .../Stable-Baselines3-2.3.2-foss-2023a.eb     | 34 +++++++++++++++++++
 1 file changed, 34 insertions(+)
 create mode 100644 easybuild/easyconfigs/s/Stable-Baselines3/Stable-Baselines3-2.3.2-foss-2023a.eb

diff --git a/easybuild/easyconfigs/s/Stable-Baselines3/Stable-Baselines3-2.3.2-foss-2023a.eb b/easybuild/easyconfigs/s/Stable-Baselines3/Stable-Baselines3-2.3.2-foss-2023a.eb
new file mode 100644
index 00000000000..24aee360a6e
--- /dev/null
+++ b/easybuild/easyconfigs/s/Stable-Baselines3/Stable-Baselines3-2.3.2-foss-2023a.eb
@@ -0,0 +1,34 @@
+easyblock = 'PythonBundle'
+
+name = 'Stable-Baselines3'
+version = '2.3.2'
+
+homepage = 'https://github.com/DLR-RM/stable-baselines3'
+description = """Stable Baselines3 (SB3) is a set of reliable implementations of 
+reinforcement learning algorithms in PyTorch."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('Gymnasium', '0.29.1'),
+    ('SciPy-bundle', '2023.07'),
+    ('PyTorch', '2.1.2'),
+    ('matplotlib', '3.7.2'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('cloudpickle', '3.0.0', {
+        'checksums': ['996d9a482c6fb4f33c1a35335cf8afd065d2a56e973270364840712d9131a882'],
+    }),
+    ('stable_baselines3', version, {
+        'use_pip_extras': 'extra',
+        'checksums': ['2f8188916e607571c4c24f88a9ff6f84edafb2cf22d5d24f9c199563c12ff168'],
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'math'

From 5fb2cee795f542b6b5d2638411fa09bfd498751c Mon Sep 17 00:00:00 2001
From: Richard Top <richard.topouchian@uib.no>
Date: Mon, 24 Jun 2024 13:25:11 +0000
Subject: [PATCH 303/835] Created gmpflf toolchain

---
 .../easyconfigs/g/gmpolf/gmpolf-2024.06.eb    | 27 -------------------
 1 file changed, 27 deletions(-)
 delete mode 100644 easybuild/easyconfigs/g/gmpolf/gmpolf-2024.06.eb

diff --git a/easybuild/easyconfigs/g/gmpolf/gmpolf-2024.06.eb b/easybuild/easyconfigs/g/gmpolf/gmpolf-2024.06.eb
deleted file mode 100644
index e5838d8a8a2..00000000000
--- a/easybuild/easyconfigs/g/gmpolf/gmpolf-2024.06.eb
+++ /dev/null
@@ -1,27 +0,0 @@
-easyblock = 'Toolchain'
-
-name = 'gmpolf'
-version = '2024.06'
-
-homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#foss-toolchain'
-description = """GNU Compiler Collection (GCC) based compiler toolchain, including
- MPICH for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK."""
-
-toolchain = SYSTEM
-
-local_gccver = '12.3.0'
-
-# toolchain used to build foss dependencies
-local_comp_mpi_tc = ('gmpich', '2024.06')
-
-# we need GCC and MPICH as explicit dependencies instead of gompi toolchain
-# because of toolchain preparation functions
-dependencies = [
-    ('GCC', local_gccver),
-    ('MPICH', '4.2.1', '', ('GCC', local_gccver)),
-    ('FlexiBLAS', '3.3.1', '', ('GCC', local_gccver)),
-    ('FFTW', '3.3.10', '', ('GCC', local_gccver)),
-    ('FFTW.MPI', '3.3.10', '', local_comp_mpi_tc),
-    ('ScaLAPACK', '2.2.0', '-fb', local_comp_mpi_tc),
-]
-moduleclass = 'toolchain'

From 90b97ca4c64f6734872dd528b405a1aa23a6499a Mon Sep 17 00:00:00 2001
From: Richard Top <richard.topouchian@uib.no>
Date: Mon, 24 Jun 2024 13:25:27 +0000
Subject: [PATCH 304/835] Created gmpflf toolchain

---
 .../easyconfigs/g/gmpflf/gmpflf-2024.06.eb    | 27 +++++++++++++++++++
 1 file changed, 27 insertions(+)
 create mode 100644 easybuild/easyconfigs/g/gmpflf/gmpflf-2024.06.eb

diff --git a/easybuild/easyconfigs/g/gmpflf/gmpflf-2024.06.eb b/easybuild/easyconfigs/g/gmpflf/gmpflf-2024.06.eb
new file mode 100644
index 00000000000..037e9b84a82
--- /dev/null
+++ b/easybuild/easyconfigs/g/gmpflf/gmpflf-2024.06.eb
@@ -0,0 +1,27 @@
+easyblock = 'Toolchain'
+
+name = 'gmpflf'
+version = '2024.06'
+
+homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#foss-toolchain'
+description = """GNU Compiler Collection (GCC) based compiler toolchain, including
+ MPICH for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK."""
+
+toolchain = SYSTEM
+
+local_gccver = '12.3.0'
+
+# toolchain used to build gmpflf dependencies
+local_comp_mpi_tc = ('gmpich', '2024.06')
+
+# we need GCC and MPICH as explicit dependencies instead of gompi toolchain
+# because of toolchain preparation functions
+dependencies = [
+    ('GCC', local_gccver),
+    ('MPICH', '4.2.1', '', ('GCC', local_gccver)),
+    ('FlexiBLAS', '3.3.1', '', ('GCC', local_gccver)),
+    ('FFTW', '3.3.10', '', ('GCC', local_gccver)),
+    ('FFTW.MPI', '3.3.10', '', local_comp_mpi_tc),
+    ('ScaLAPACK', '2.2.0', '-fb', local_comp_mpi_tc),
+]
+moduleclass = 'toolchain'

From 38a15fb8bf2d93aed6590065d2e8e8b2741cec44 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Mon, 24 Jun 2024 17:00:12 +0200
Subject: [PATCH 305/835] adding easyconfigs: histolab-0.7.0-foss-2023a.eb

---
 .../h/histolab/histolab-0.7.0-foss-2023a.eb   | 39 +++++++++++++++++++
 1 file changed, 39 insertions(+)
 create mode 100644 easybuild/easyconfigs/h/histolab/histolab-0.7.0-foss-2023a.eb

diff --git a/easybuild/easyconfigs/h/histolab/histolab-0.7.0-foss-2023a.eb b/easybuild/easyconfigs/h/histolab/histolab-0.7.0-foss-2023a.eb
new file mode 100644
index 00000000000..597a7befb07
--- /dev/null
+++ b/easybuild/easyconfigs/h/histolab/histolab-0.7.0-foss-2023a.eb
@@ -0,0 +1,39 @@
+easyblock = 'PythonBundle'
+
+name = 'histolab'
+version = '0.7.0'
+
+homepage = 'https://github.com/histolab/histolab'
+description = """Library for Digital Pathology Image Processing."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+builddependencies = [('poetry', '1.5.1')]
+dependencies = [
+    ('Python', '3.11.3'),
+    ('Pillow', '10.0.0'),
+    ('scikit-image', '0.22.0'),
+    ('SciPy-bundle', '2023.07'),
+    ('openslide-python', '1.3.1'),
+]
+
+use_pip = True
+
+local_preinstallopts = """
+sed -i 's/scikit-image = ">=0.19.0,<0.19.4"/scikit-image = ">=0.19.0"/' pyproject.toml && 
+sed -i 's/numpy = ">=1.23.2,<=1.24.4"/numpy = ">=1.23.2"/' pyproject.toml && 
+sed -i 's/scipy = ">=1.5.0,<1.10.1"/scipy = ">=1.5.0"/' pyproject.toml && 
+"""
+exts_list = [
+    ('certifi', '2024.6.2', {
+        'checksums': ['3cd43f1c6fa7dedc5899d69d3ad0398fd018ad1a17fba83ddaf78aa46c747516'],
+    }),
+    (name, version, {
+        'preinstallopts': local_preinstallopts,
+        'checksums': ['c0f6a6d0381f0ca056f524e3b8217b0a8304ea79a0cdc88f76a39b1bf7531031'],
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'vis'

From 7c12d04d2316c67bbdc1c4069fc21962f4a5c35b Mon Sep 17 00:00:00 2001
From: Justus Kuhlmann <j_kuhl19@uni-muenster.de>
Date: Mon, 24 Jun 2024 15:13:09 +0000
Subject: [PATCH 306/835] use gfbf toolchain

---
 ...{mrcfile-1.4.3-foss-2022b.eb => mrcfile-1.4.3-gfbf-2022b.eb} | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)
 rename easybuild/easyconfigs/m/mrcfile/{mrcfile-1.4.3-foss-2022b.eb => mrcfile-1.4.3-gfbf-2022b.eb} (96%)

diff --git a/easybuild/easyconfigs/m/mrcfile/mrcfile-1.4.3-foss-2022b.eb b/easybuild/easyconfigs/m/mrcfile/mrcfile-1.4.3-gfbf-2022b.eb
similarity index 96%
rename from easybuild/easyconfigs/m/mrcfile/mrcfile-1.4.3-foss-2022b.eb
rename to easybuild/easyconfigs/m/mrcfile/mrcfile-1.4.3-gfbf-2022b.eb
index fa61a8ea8ca..848ed3326db 100644
--- a/easybuild/easyconfigs/m/mrcfile/mrcfile-1.4.3-foss-2022b.eb
+++ b/easybuild/easyconfigs/m/mrcfile/mrcfile-1.4.3-gfbf-2022b.eb
@@ -17,7 +17,7 @@ files, correct headers and so on, or in scripts and larger software packages to
 provide basic MRC file I/O functions. """
 
 
-toolchain = {'name': 'foss', 'version': '2022b'}
+toolchain = {'name': 'gfbf', 'version': '2022b'}
 
 sources = [SOURCELOWER_TAR_GZ]
 checksums = ['43c358c59ff8f583fc4dc2079a0099028719109ebf92066e388772bab389c5f5']

From 7b0c28f64e5f324c9e68dcf3e954aa62e4045829 Mon Sep 17 00:00:00 2001
From: Simon Pinches <Simon.Pinches@iter.org>
Date: Mon, 24 Jun 2024 18:55:05 +0200
Subject: [PATCH 307/835] adding easyconfigs: JsonCpp-1.9.5-GCCcore-13.2.0.eb

---
 .../j/JsonCpp/JsonCpp-1.9.5-GCCcore-13.2.0.eb | 29 +++++++++++++++++++
 1 file changed, 29 insertions(+)
 create mode 100644 easybuild/easyconfigs/j/JsonCpp/JsonCpp-1.9.5-GCCcore-13.2.0.eb

diff --git a/easybuild/easyconfigs/j/JsonCpp/JsonCpp-1.9.5-GCCcore-13.2.0.eb b/easybuild/easyconfigs/j/JsonCpp/JsonCpp-1.9.5-GCCcore-13.2.0.eb
new file mode 100644
index 00000000000..dd5dda233d2
--- /dev/null
+++ b/easybuild/easyconfigs/j/JsonCpp/JsonCpp-1.9.5-GCCcore-13.2.0.eb
@@ -0,0 +1,29 @@
+easyblock = "CMakeNinja"
+
+name = 'JsonCpp'
+version = '1.9.5'
+
+homepage = 'https://open-source-parsers.github.io/jsoncpp-docs/doxygen/index.html'
+description = """ JsonCpp is a C++ library that allows manipulating JSON values,
+ including serialization and deserialization to and from strings. It can also preserve existing comment in
+ unserialization/serialization steps, making it a convenient format to store user input files. """
+
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
+
+source_urls = ['https://github.com/open-source-parsers/jsoncpp/archive']
+sources = ['%(version)s.tar.gz']
+checksums = ['f409856e5920c18d0c2fb85276e24ee607d2a09b5e7d5f0a371368903c275da2']
+
+builddependencies = [
+    ('CMake', '3.27.6'),
+    ('Ninja', '1.11.1'),
+    ('pkgconf', '2.0.3'),
+    ('binutils', '2.40'),
+]
+
+sanity_check_paths = {
+    'files': ['include/json/json.h', 'lib/libjsoncpp.%s' % SHLIB_EXT],
+    'dirs': [],
+}
+
+moduleclass = 'lib'

From 0c1c6db482fe0699dcda345c849c8c61709594c9 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Mon, 24 Jun 2024 21:09:53 +0200
Subject: [PATCH 308/835] small style fixes (mostly adding/removing some
 linebreaks)

---
 easybuild/easyconfigs/m/mrcfile/mrcfile-1.4.3-gfbf-2022b.eb | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/easybuild/easyconfigs/m/mrcfile/mrcfile-1.4.3-gfbf-2022b.eb b/easybuild/easyconfigs/m/mrcfile/mrcfile-1.4.3-gfbf-2022b.eb
index 848ed3326db..42492460fd9 100644
--- a/easybuild/easyconfigs/m/mrcfile/mrcfile-1.4.3-gfbf-2022b.eb
+++ b/easybuild/easyconfigs/m/mrcfile/mrcfile-1.4.3-gfbf-2022b.eb
@@ -1,7 +1,9 @@
 # Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2022/11
 easyblock = 'PythonPackage'
+
 name = 'mrcfile'
 version = '1.4.3'
+
 homepage = 'https://github.com/ccpem/mrcfile'
 description = """mrcfile is a Python implementation of the MRC2014 file format, which is used in 
 structural biology to store image and volume data.
@@ -16,7 +18,6 @@ any compiled libraries except numpy. You can use it interactively to inspect
 files, correct headers and so on, or in scripts and larger software packages to 
 provide basic MRC file I/O functions. """
 
-
 toolchain = {'name': 'gfbf', 'version': '2022b'}
 
 sources = [SOURCELOWER_TAR_GZ]
@@ -28,6 +29,7 @@ dependencies = [
 ]
 
 download_dep_fail = True
+use_pip = True
 sanity_pip_check = True
 
 sanity_check_paths = {
@@ -35,6 +37,4 @@ sanity_check_paths = {
     'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s']
 }
 
-
-use_pip = True
 moduleclass = 'bio'

From 25080139530528b95c361d0a33dfbff6f68738a5 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 24 Jun 2024 22:33:45 +0200
Subject: [PATCH 309/835] rename ega-quickview to EGA-QuickView

---
 .../EGA-QuickView-20240620-GCC-12.3.0.eb}                   | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)
 rename easybuild/easyconfigs/e/{ega-quickview/ega-quickview-20240620-GCC-12.3.0.eb => EGA-QuickView/EGA-QuickView-20240620-GCC-12.3.0.eb} (88%)

diff --git a/easybuild/easyconfigs/e/ega-quickview/ega-quickview-20240620-GCC-12.3.0.eb b/easybuild/easyconfigs/e/EGA-QuickView/EGA-QuickView-20240620-GCC-12.3.0.eb
similarity index 88%
rename from easybuild/easyconfigs/e/ega-quickview/ega-quickview-20240620-GCC-12.3.0.eb
rename to easybuild/easyconfigs/e/EGA-QuickView/EGA-QuickView-20240620-GCC-12.3.0.eb
index 7ca2cb398d7..24e7302367a 100644
--- a/easybuild/easyconfigs/e/ega-quickview/ega-quickview-20240620-GCC-12.3.0.eb
+++ b/easybuild/easyconfigs/e/EGA-QuickView/EGA-QuickView-20240620-GCC-12.3.0.eb
@@ -1,6 +1,6 @@
 easyblock = 'ConfigureMake'
 
-name = 'ega-quickview'
+name = 'EGA-QuickView'
 version = '20240620'
 local_commit = 'fe2034d'
 
@@ -12,8 +12,8 @@ toolchain = {'name': 'GCC', 'version': '12.3.0'}
 github_account = 'EGA-archive'
 source_urls = [GITHUB_SOURCE]
 sources = [{
-    "download_filename": "%s.tar.gz" % local_commit,
-    "filename": "%(name)s-%(version)s.tar.gz",
+    'download_filename': '%s.tar.gz' % local_commit,
+    'filename': '%(name)s-%(version)s.tar.gz',
 }]
 checksums = ['90836e42009736a8e20a2569918638f3cb2b53574265ca4f4bed7abd81a5e887']
 

From bffc4f36961ced684f10b297c3c98250d514325b Mon Sep 17 00:00:00 2001
From: Cintia Willemyns <115622907+WilleBell@users.noreply.github.com>
Date: Tue, 25 Jun 2024 09:47:26 +0200
Subject: [PATCH 310/835] Update
 easybuild/easyconfigs/p/pyGenomeTracks/pyGenomeTracks-3.9-foss-2023a.eb
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Bob Dröge <b.e.droge@rug.nl>
---
 .../p/pyGenomeTracks/pyGenomeTracks-3.9-foss-2023a.eb         | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/easybuild/easyconfigs/p/pyGenomeTracks/pyGenomeTracks-3.9-foss-2023a.eb b/easybuild/easyconfigs/p/pyGenomeTracks/pyGenomeTracks-3.9-foss-2023a.eb
index b5cf0276807..347ceccb567 100644
--- a/easybuild/easyconfigs/p/pyGenomeTracks/pyGenomeTracks-3.9-foss-2023a.eb
+++ b/easybuild/easyconfigs/p/pyGenomeTracks/pyGenomeTracks-3.9-foss-2023a.eb
@@ -21,8 +21,8 @@ dependencies = [
     ('PyTables', '3.8.0'),
     ('h5py', '3.9.0'),
     ('PyYAML', '6.0'),
-    ('cooler', '0.10.2'),  # Needs new .eb
-    ('HiCMatrix', '17.2'),  # Needs new .eb
+    ('cooler', '0.10.2'),
+    ('HiCMatrix', '17.2'),
 ]
 
 use_pip = True

From 086e33cdb5595e510273f47ab740b80ab3c2adc2 Mon Sep 17 00:00:00 2001
From: Cintia Willemyns <115622907+WilleBell@users.noreply.github.com>
Date: Tue, 25 Jun 2024 09:47:32 +0200
Subject: [PATCH 311/835] Update
 easybuild/easyconfigs/p/pyGenomeTracks/pyGenomeTracks-3.9-foss-2023a.eb
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Bob Dröge <b.e.droge@rug.nl>
---
 .../p/pyGenomeTracks/pyGenomeTracks-3.9-foss-2023a.eb        | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/easybuild/easyconfigs/p/pyGenomeTracks/pyGenomeTracks-3.9-foss-2023a.eb b/easybuild/easyconfigs/p/pyGenomeTracks/pyGenomeTracks-3.9-foss-2023a.eb
index 347ceccb567..aa1c8985476 100644
--- a/easybuild/easyconfigs/p/pyGenomeTracks/pyGenomeTracks-3.9-foss-2023a.eb
+++ b/easybuild/easyconfigs/p/pyGenomeTracks/pyGenomeTracks-3.9-foss-2023a.eb
@@ -26,11 +26,6 @@ dependencies = [
 ]
 
 use_pip = True
-
-"""
-pygenometracks 3.8 requires pybigwig, which is not installed.
-"""
-
 exts_list = [
     ('argcomplete', '3.4.0', {
         'checksums': ['c2abcdfe1be8ace47ba777d4fce319eb13bf8ad9dace8d085dcad6eded88057f'],

From 568e7f238c5cb229b25541507c33683844a02269 Mon Sep 17 00:00:00 2001
From: TopRichard <121792457+TopRichard@users.noreply.github.com>
Date: Tue, 25 Jun 2024 09:49:47 +0200
Subject: [PATCH 312/835] Update gmpflf-2024.06.eb

---
 easybuild/easyconfigs/g/gmpflf/gmpflf-2024.06.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/g/gmpflf/gmpflf-2024.06.eb b/easybuild/easyconfigs/g/gmpflf/gmpflf-2024.06.eb
index 037e9b84a82..03875dba4c9 100644
--- a/easybuild/easyconfigs/g/gmpflf/gmpflf-2024.06.eb
+++ b/easybuild/easyconfigs/g/gmpflf/gmpflf-2024.06.eb
@@ -5,7 +5,7 @@ version = '2024.06'
 
 homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#foss-toolchain'
 description = """GNU Compiler Collection (GCC) based compiler toolchain, including
- MPICH for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK."""
+ MPICH for MPI support, FlexiBLAS (OpenBLAS and LAPACK), FFTW and ScaLAPACK."""
 
 toolchain = SYSTEM
 

From 4ebcac4361d15d112392ac824ed1c366109eea2a Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Tue, 25 Jun 2024 10:38:31 +0200
Subject: [PATCH 313/835] update local_preinstallopts style

---
 .../easyconfigs/h/histolab/histolab-0.7.0-foss-2023a.eb  | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/easybuild/easyconfigs/h/histolab/histolab-0.7.0-foss-2023a.eb b/easybuild/easyconfigs/h/histolab/histolab-0.7.0-foss-2023a.eb
index 597a7befb07..3aa69b74e7b 100644
--- a/easybuild/easyconfigs/h/histolab/histolab-0.7.0-foss-2023a.eb
+++ b/easybuild/easyconfigs/h/histolab/histolab-0.7.0-foss-2023a.eb
@@ -19,11 +19,10 @@ dependencies = [
 
 use_pip = True
 
-local_preinstallopts = """
-sed -i 's/scikit-image = ">=0.19.0,<0.19.4"/scikit-image = ">=0.19.0"/' pyproject.toml && 
-sed -i 's/numpy = ">=1.23.2,<=1.24.4"/numpy = ">=1.23.2"/' pyproject.toml && 
-sed -i 's/scipy = ">=1.5.0,<1.10.1"/scipy = ">=1.5.0"/' pyproject.toml && 
-"""
+local_preinstallopts = """sed -i 's/scikit-image = ">=0.19.0,<0.19.4"/scikit-image = ">=0.19.0"/' pyproject.toml && """
+local_preinstallopts += """sed -i 's/numpy = ">=1.23.2,<=1.24.4"/numpy = ">=1.23.2"/' pyproject.toml && """
+local_preinstallopts += """sed -i 's/scipy = ">=1.5.0,<1.10.1"/scipy = ">=1.5.0"/' pyproject.toml && """
+
 exts_list = [
     ('certifi', '2024.6.2', {
         'checksums': ['3cd43f1c6fa7dedc5899d69d3ad0398fd018ad1a17fba83ddaf78aa46c747516'],

From 79acec85af744e791658d32c4a16dad0a603e00c Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 25 Jun 2024 10:47:16 +0200
Subject: [PATCH 314/835] adding easyconfigs: pystencils-1.3.4-gfbf-2023b.eb

---
 .../pystencils/pystencils-1.3.4-gfbf-2023b.eb | 30 +++++++++++++++++++
 1 file changed, 30 insertions(+)
 create mode 100644 easybuild/easyconfigs/p/pystencils/pystencils-1.3.4-gfbf-2023b.eb

diff --git a/easybuild/easyconfigs/p/pystencils/pystencils-1.3.4-gfbf-2023b.eb b/easybuild/easyconfigs/p/pystencils/pystencils-1.3.4-gfbf-2023b.eb
new file mode 100644
index 00000000000..2c08948afa0
--- /dev/null
+++ b/easybuild/easyconfigs/p/pystencils/pystencils-1.3.4-gfbf-2023b.eb
@@ -0,0 +1,30 @@
+easyblock = 'PythonBundle'
+
+name = 'pystencils'
+version = '1.3.4'
+
+homepage = 'https://pycodegen.pages.i10git.cs.fau.de/pystencils'
+description = "pystencils uses sympy to define stencil operations, that can be executed on numpy arrays"
+
+toolchain = {'name': 'gfbf', 'version': '2023b'}
+
+dependencies = [
+    ('Python', '3.11.5'),
+    ('SciPy-bundle', '2023.11'),
+    ('sympy', '1.12'),
+    ('PyYAML', '6.0.1'),
+]
+
+use_pip = True
+
+exts_list = [
+    (name, version, {
+        'checksums': ['d8c502ad27d5e270c5048558a3c8b316beef8d7ac6a8a9f72b78632a6e0ca317'],
+        # remove strict version requirement for sympy
+        'preinstallopts': """sed -i 's/"sympy[^"]*"/"sympy"/g' pyproject.toml && """,
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'math'

From 33d0340c715774f9e36db9d9f3ceb90fd9adb252 Mon Sep 17 00:00:00 2001
From: Simon Branford <s.j.branford@bham.ac.uk>
Date: Tue, 25 Jun 2024 09:56:46 +0100
Subject: [PATCH 315/835] adding easyconfigs: Arrow-16.1.0-gfbf-2023b.eb,
 utf8proc-2.9.0-GCCcore-13.2.0.eb, RapidJSON-1.1.0-20240409-GCCcore-13.2.0.eb

---
 .../a/Arrow/Arrow-16.1.0-gfbf-2023b.eb        | 83 +++++++++++++++++++
 ...RapidJSON-1.1.0-20240409-GCCcore-13.2.0.eb | 31 +++++++
 .../utf8proc/utf8proc-2.9.0-GCCcore-13.2.0.eb | 30 +++++++
 3 files changed, 144 insertions(+)
 create mode 100644 easybuild/easyconfigs/a/Arrow/Arrow-16.1.0-gfbf-2023b.eb
 create mode 100644 easybuild/easyconfigs/r/RapidJSON/RapidJSON-1.1.0-20240409-GCCcore-13.2.0.eb
 create mode 100644 easybuild/easyconfigs/u/utf8proc/utf8proc-2.9.0-GCCcore-13.2.0.eb

diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-16.1.0-gfbf-2023b.eb b/easybuild/easyconfigs/a/Arrow/Arrow-16.1.0-gfbf-2023b.eb
new file mode 100644
index 00000000000..1374d3973bf
--- /dev/null
+++ b/easybuild/easyconfigs/a/Arrow/Arrow-16.1.0-gfbf-2023b.eb
@@ -0,0 +1,83 @@
+easyblock = 'CMakeMake'
+
+name = 'Arrow'
+version = '16.1.0'
+
+homepage = 'https://arrow.apache.org'
+description = """Apache Arrow (incl. PyArrow Python bindings), a cross-language development platform
+ for in-memory data."""
+
+toolchain = {'name': 'gfbf', 'version': '2023b'}
+
+source_urls = ['https://archive.apache.org/dist/%(namelower)s/%(namelower)s-%(version)s']
+sources = ['apache-arrow-%(version)s.tar.gz']
+checksums = ['c9e60c7e87e59383d21b20dc874b17153729ee153264af6d21654b7dff2c60d7']
+
+builddependencies = [
+    ('CMake', '3.27.6'),
+    ('Autotools', '20220317'),
+    ('flex', '2.6.4'),
+    ('Bison', '3.8.2'),
+    ('pkgconf', '2.0.3'),
+]
+
+# Arrow strongly prefers included jemalloc, so not including it as a dependency
+dependencies = [
+    ('Python', '3.11.5'),
+    ('SciPy-bundle', '2023.11'),  # for numpy
+    ('Boost', '1.83.0'),
+    ('lz4', '1.9.4'),
+    ('zlib', '1.2.13'),
+    ('bzip2', '1.0.8'),
+    ('zstd', '1.5.5'),
+    ('snappy', '1.1.10'),
+    ('RapidJSON', '1.1.0-20240409'),
+    ('RE2', '2024-03-01'),
+    ('utf8proc', '2.9.0'),
+]
+
+start_dir = 'cpp'
+
+# see https://arrow.apache.org/docs/developers/python.html
+configopts = "-DARROW_DATASET=on -DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_WITH_SNAPPY=ON "
+configopts += "-DCMAKE_INSTALL_LIBDIR=lib -DPython3_ROOT_DIR=$EBROOTPYTHON "
+configopts += "-DARROW_WITH_ZLIB=ON -DARROW_WITH_BZ2=ON -DARROW_WITH_ZSTD=ON -DARROW_WITH_LZ4=ON "
+configopts += "-DZSTD_ROOT=$EBROOTZSTD "
+
+# install Python bindings
+_pyarrow_preinstall_opts = "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && "
+_pyarrow_preinstall_opts += "export Arrow_DIR=%(installdir)s && export ArrowDataset_DIR=%(installdir)s && "
+_pyarrow_preinstall_opts += "export ArrowAcero_DIR=%(installdir)s && export Parquet_DIR=%(installdir)s && "
+_pyarrow_preinstall_opts += "export XDG_CACHE_HOME=$TMPDIR && "
+_pyarrow_preinstall_opts += "sed -i 's/numpy==[0-9.]*/numpy/g' pyproject.toml && "
+_pyarrow_preinstall_opts += "Python3_ROOT_DIR=$EBROOTPYTHON "
+_pyarrow_preinstall_opts += "PYARROW_CMAKE_OPTIONS='-DZSTD_LIB=$EBROOTZSTD/lib/libzstd.%s ' " % SHLIB_EXT
+_pyarrow_preinstall_opts += "PYARROW_WITH_DATASET=1 PYARROW_WITH_PARQUET=1 "
+
+exts_defaultclass = 'PythonPackage'
+exts_default_options = {
+}
+exts_list = [
+    ('pyarrow', version, {
+        'preinstallopts': "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && export Arrow_DIR=%(installdir)s && export ArrowDataset_DIR=%(installdir)s && export ArrowAcero_DIR=%(installdir)s && export Parquet_DIR=%(installdir)s && export XDG_CACHE_HOME=$TMPDIR && sed -i 's/numpy==[0-9.]*/numpy/g' pyproject.toml && Python3_ROOT_DIR=$EBROOTPYTHON PYARROW_CMAKE_OPTIONS='-DZSTD_LIB=$EBROOTZSTD/lib/libzstd.so ' PYARROW_WITH_DATASET=1 PYARROW_WITH_PARQUET=1 ",
+        'sources': ['apache-arrow-%(version)s.tar.gz'],
+        'start_dir': '%(builddir)s/apache-arrow-%(version)s/python',
+        'checksums': ['c9e60c7e87e59383d21b20dc874b17153729ee153264af6d21654b7dff2c60d7'],
+    }),
+]
+
+modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'}
+
+sanity_check_paths = {
+    'files': ['lib/libarrow.a', 'lib/libarrow.%s' % SHLIB_EXT,
+              'lib/python%%(pyshortver)s/site-packages/pyarrow/libarrow_python.%s' % SHLIB_EXT],
+    'dirs': ['include/arrow', 'lib/cmake/Arrow', 'lib/pkgconfig', 'lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = [
+    "python -c 'import pyarrow'",
+    "python -c 'import pyarrow.dataset'",
+    "python -c 'import pyarrow.parquet'",
+]
+
+moduleclass = 'data'
diff --git a/easybuild/easyconfigs/r/RapidJSON/RapidJSON-1.1.0-20240409-GCCcore-13.2.0.eb b/easybuild/easyconfigs/r/RapidJSON/RapidJSON-1.1.0-20240409-GCCcore-13.2.0.eb
new file mode 100644
index 00000000000..4f36c473ec4
--- /dev/null
+++ b/easybuild/easyconfigs/r/RapidJSON/RapidJSON-1.1.0-20240409-GCCcore-13.2.0.eb
@@ -0,0 +1,31 @@
+easyblock = 'CMakeMake'
+
+name = 'RapidJSON'
+# no new release since Aug'16 so using latest commit;
+# see also https://github.com/Tencent/rapidjson/issues/2202
+version = '1.1.0-20240409'
+local_commit = 'ab1842a'
+
+homepage = 'https://rapidjson.org'
+description = "A fast JSON parser/generator for C++ with both SAX/DOM style API"
+
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
+
+source_urls = ['https://github.com/Tencent/%(namelower)s/archive/']
+sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': 'v%(version)s.tar.gz'}]
+checksums = ['39f96f17b40f7201042c9b45d6444cb7eae1b7adfb7455412a86f6140450d32d']
+
+builddependencies = [
+    ('binutils', '2.40'),
+    ('CMake', '3.27.6'),
+]
+
+# strip out hardcoded use of -march=native, EasyBuild should be in control of this
+preconfigopts = "sed -i 's/-march=native//g' ../rapidjson-*/CMakeLists.txt && "
+
+sanity_check_paths = {
+    'files': ['lib/pkgconfig/%(name)s.pc'],
+    'dirs': ['include/%(namelower)s', 'lib/cmake', 'share'],
+}
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/u/utf8proc/utf8proc-2.9.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/u/utf8proc/utf8proc-2.9.0-GCCcore-13.2.0.eb
new file mode 100644
index 00000000000..3ae6a55c205
--- /dev/null
+++ b/easybuild/easyconfigs/u/utf8proc/utf8proc-2.9.0-GCCcore-13.2.0.eb
@@ -0,0 +1,30 @@
+easyblock = 'CMakeMake'
+
+name = 'utf8proc'
+version = '2.9.0'
+
+homepage = 'https://github.com/JuliaStrings/utf8proc'
+description = """utf8proc is a small, clean C library that provides Unicode normalization, case-folding, 
+and other operations for data in the UTF-8 encoding."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
+
+source_urls = ['https://github.com/JuliaStrings/utf8proc/archive/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['18c1626e9fc5a2e192311e36b3010bfc698078f692888940f1fa150547abb0c1']
+
+builddependencies = [
+    ('binutils', '2.40'),
+    ('CMake', '3.27.6'),
+]
+
+separate_build_dir = True
+
+configopts = ['-DBUILD_SHARED_LIBS=OFF', '-DBUILD_SHARED_LIBS=ON']
+
+sanity_check_paths = {
+    'files': ['include/utf8proc.h', 'lib/libutf8proc.a', 'lib/libutf8proc.%s' % SHLIB_EXT],
+    'dirs': [],
+}
+
+moduleclass = 'lib'

From 06269d1b57cca069a8eac8fe6857bed96b60e43f Mon Sep 17 00:00:00 2001
From: Simon Branford <s.j.branford@bham.ac.uk>
Date: Tue, 25 Jun 2024 10:05:18 +0100
Subject: [PATCH 316/835] adding easyconfigs:
 ImageMagick-7.1.1-34-GCCcore-13.2.0.eb

---
 .../ImageMagick-7.1.1-34-GCCcore-13.2.0.eb    | 42 +++++++++++++++++++
 1 file changed, 42 insertions(+)
 create mode 100644 easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.1-34-GCCcore-13.2.0.eb

diff --git a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.1-34-GCCcore-13.2.0.eb b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.1-34-GCCcore-13.2.0.eb
new file mode 100644
index 00000000000..e19d1a221fb
--- /dev/null
+++ b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.1-34-GCCcore-13.2.0.eb
@@ -0,0 +1,42 @@
+easyblock = 'ConfigureMake'
+
+name = 'ImageMagick'
+version = '7.1.1-34'
+
+homepage = 'https://www.imagemagick.org/'
+description = "ImageMagick is a software suite to create, edit, compose, or convert bitmap images"
+
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
+
+source_urls = ['https://github.com/%(name)s/%(name)s/archive/']
+sources = ['%(version)s.tar.gz']
+checksums = ['19f4303774b56be182c576b266c34bc824fcaef1d1d243192344d015adb0ec28']
+
+builddependencies = [
+    ('binutils', '2.40'),
+    ('pkgconf', '2.0.3'),
+]
+dependencies = [
+    ('bzip2', '1.0.8'),
+    ('X11', '20231019'),
+    ('Ghostscript', '10.02.1'),
+    ('JasPer', '4.0.0'),
+    ('libjpeg-turbo', '3.0.1'),
+    ('LibTIFF', '4.6.0'),
+    ('LittleCMS', '2.15'),
+    ('Pango', '1.51.0'),
+    ('pixman', '0.42.2'),
+    ('FriBidi', '1.0.13'),
+]
+
+configopts = "--with-gslib --with-x"
+
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['bin', 'etc/%(name)s-%(version_major)s', 'include/%(name)s-%(version_major)s', 'lib', 'share'],
+}
+
+modextravars = {'MAGICK_HOME': '%(installdir)s'}
+
+moduleclass = 'vis'

From 8248c27e85bd029c3073ac82df1a7891e21cabd6 Mon Sep 17 00:00:00 2001
From: Simon Branford <s.j.branford@bham.ac.uk>
Date: Tue, 25 Jun 2024 10:09:07 +0100
Subject: [PATCH 317/835] adding easyconfigs: FLAC-1.4.3-GCCcore-13.2.0.eb,
 libogg-1.3.5-GCCcore-13.2.0.eb, libopus-1.5.2-GCCcore-13.2.0.eb,
 libsndfile-1.2.2-GCCcore-13.2.0.eb, libvorbis-1.3.7-GCCcore-13.2.0.eb

---
 .../f/FLAC/FLAC-1.4.3-GCCcore-13.2.0.eb       | 30 ++++++++++++++
 .../l/libogg/libogg-1.3.5-GCCcore-13.2.0.eb   | 25 ++++++++++++
 .../l/libopus/libopus-1.5.2-GCCcore-13.2.0.eb | 30 ++++++++++++++
 .../libsndfile-1.2.2-GCCcore-13.2.0.eb        | 39 +++++++++++++++++++
 .../libvorbis-1.3.7-GCCcore-13.2.0.eb         | 30 ++++++++++++++
 5 files changed, 154 insertions(+)
 create mode 100644 easybuild/easyconfigs/f/FLAC/FLAC-1.4.3-GCCcore-13.2.0.eb
 create mode 100644 easybuild/easyconfigs/l/libogg/libogg-1.3.5-GCCcore-13.2.0.eb
 create mode 100644 easybuild/easyconfigs/l/libopus/libopus-1.5.2-GCCcore-13.2.0.eb
 create mode 100644 easybuild/easyconfigs/l/libsndfile/libsndfile-1.2.2-GCCcore-13.2.0.eb
 create mode 100644 easybuild/easyconfigs/l/libvorbis/libvorbis-1.3.7-GCCcore-13.2.0.eb

diff --git a/easybuild/easyconfigs/f/FLAC/FLAC-1.4.3-GCCcore-13.2.0.eb b/easybuild/easyconfigs/f/FLAC/FLAC-1.4.3-GCCcore-13.2.0.eb
new file mode 100644
index 00000000000..a0abaac6ca9
--- /dev/null
+++ b/easybuild/easyconfigs/f/FLAC/FLAC-1.4.3-GCCcore-13.2.0.eb
@@ -0,0 +1,30 @@
+easyblock = 'ConfigureMake'
+
+name = 'FLAC'
+version = '1.4.3'
+
+homepage = 'https://xiph.org/flac/'
+description = """FLAC stands for Free Lossless Audio Codec, an audio format similar to MP3, but lossless, meaning
+that audio is compressed in FLAC without any loss in quality."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
+
+source_urls = ['https://ftp.osuosl.org/pub/xiph/releases/flac/']
+sources = [SOURCELOWER_TAR_XZ]
+checksums = ['6c58e69cd22348f441b861092b825e591d0b822e106de6eb0ee4d05d27205b70']
+
+builddependencies = [('binutils', '2.40')]
+
+dependencies = [('libogg', '1.3.5')]
+
+configopts = '--enable-static --enable-shared'
+
+sanity_check_paths = {
+    'files': ['bin/flac', 'lib/libFLAC.a', 'lib/libFLAC++.a',
+              'lib/libFLAC.%s' % SHLIB_EXT, 'lib/libFLAC++.%s' % SHLIB_EXT],
+    'dirs': ['include/FLAC', 'include/FLAC++'],
+}
+
+sanity_check_commands = ["flac --help"]
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/l/libogg/libogg-1.3.5-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/libogg/libogg-1.3.5-GCCcore-13.2.0.eb
new file mode 100644
index 00000000000..a2f34782696
--- /dev/null
+++ b/easybuild/easyconfigs/l/libogg/libogg-1.3.5-GCCcore-13.2.0.eb
@@ -0,0 +1,25 @@
+easyblock = 'ConfigureMake'
+
+name = 'libogg'
+version = '1.3.5'
+
+homepage = 'https://xiph.org/ogg/'
+description = """Ogg is a multimedia container format, and the native file and stream format for the Xiph.org
+multimedia codecs."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
+
+source_urls = ['https://ftp.osuosl.org/pub/xiph/releases/ogg/']
+sources = [SOURCELOWER_TAR_XZ]
+checksums = ['c4d91be36fc8e54deae7575241e03f4211eb102afb3fc0775fbbc1b740016705']
+
+builddependencies = [('binutils', '2.40')]
+
+configopts = '--enable-static --enable-shared'
+
+sanity_check_paths = {
+    'files': ['lib/libogg.a', 'lib/libogg.%s' % SHLIB_EXT],
+    'dirs': ['include/ogg'],
+}
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/l/libopus/libopus-1.5.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/libopus/libopus-1.5.2-GCCcore-13.2.0.eb
new file mode 100644
index 00000000000..7d0630bb477
--- /dev/null
+++ b/easybuild/easyconfigs/l/libopus/libopus-1.5.2-GCCcore-13.2.0.eb
@@ -0,0 +1,30 @@
+easyblock = 'ConfigureMake'
+
+name = 'libopus'
+version = '1.5.2'
+
+homepage = 'https://www.opus-codec.org/'
+description = """Opus is a totally open, royalty-free, highly versatile audio codec. Opus is unmatched for interactive
+ speech and music transmission over the Internet, but is also intended for storage and streaming applications. It is
+ standardized by the Internet Engineering Task Force (IETF) as RFC 6716 which incorporated technology from Skype’s
+ SILK codec and Xiph.Org’s CELT codec."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
+
+source_urls = ['https://downloads.xiph.org/releases/opus/']
+sources = ['opus-%(version)s.tar.gz']
+checksums = ['65c1d2f78b9f2fb20082c38cbe47c951ad5839345876e46941612ee87f9a7ce1']
+
+builddependencies = [
+    ('binutils', '2.40'),
+    ('pkgconf', '2.0.3'),
+]
+
+configopts = '--enable-static --enable-shared'
+
+sanity_check_paths = {
+    'files': ['lib/libopus.a', 'lib/libopus.%s' % SHLIB_EXT],
+    'dirs': ['include/opus'],
+}
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/l/libsndfile/libsndfile-1.2.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/libsndfile/libsndfile-1.2.2-GCCcore-13.2.0.eb
new file mode 100644
index 00000000000..7652c3f06e0
--- /dev/null
+++ b/easybuild/easyconfigs/l/libsndfile/libsndfile-1.2.2-GCCcore-13.2.0.eb
@@ -0,0 +1,39 @@
+easyblock = 'CMakeMake'
+
+name = 'libsndfile'
+version = '1.2.2'
+
+homepage = 'http://www.mega-nerd.com/libsndfile'
+description = """Libsndfile is a C library for reading and writing files containing sampled sound
+ (such as MS Windows WAV and the Apple/SGI AIFF format) through one standard library interface."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
+
+source_urls = ['https://github.com/%(name)s/%(name)s/releases/download/%(version)s/']
+sources = [SOURCE_TAR_XZ]
+checksums = ['3799ca9924d3125038880367bf1468e53a1b7e3686a934f098b7e1d286cdb80e']
+
+builddependencies = [
+    ('binutils', '2.40'),
+    ('pkgconf', '2.0.3'),
+    ('CMake', '3.27.6'),
+]
+dependencies = [
+    ('FLAC', '1.4.2'),
+    ('libvorbis', '1.3.7'),
+    ('libopus', '1.5.2'),
+    ('LAME', '3.100'),
+]
+
+configopts = [
+    '',
+    '-DBUILD_SHARED_LIBS=ON',
+]
+
+
+sanity_check_paths = {
+    'files': ['include/sndfile.h', 'include/sndfile.hh', 'lib/%(name)s.a', 'lib/%(name)s.so'],
+    'dirs': ['bin'],
+}
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/l/libvorbis/libvorbis-1.3.7-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/libvorbis/libvorbis-1.3.7-GCCcore-13.2.0.eb
new file mode 100644
index 00000000000..50a45ea05a1
--- /dev/null
+++ b/easybuild/easyconfigs/l/libvorbis/libvorbis-1.3.7-GCCcore-13.2.0.eb
@@ -0,0 +1,30 @@
+easyblock = 'ConfigureMake'
+
+name = 'libvorbis'
+version = '1.3.7'
+
+homepage = 'https://xiph.org/vorbis/'
+description = """Ogg Vorbis is a fully open, non-proprietary, patent-and-royalty-free, general-purpose compressed
+audio format"""
+
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
+
+source_urls = ['https://ftp.osuosl.org/pub/xiph/releases/vorbis/']
+sources = [SOURCE_TAR_XZ]
+checksums = ['b33cc4934322bcbf6efcbacf49e3ca01aadbea4114ec9589d1b1e9d20f72954b']
+
+builddependencies = [
+    ('binutils', '2.40'),
+    ('pkgconf', '2.0.3'),
+]
+
+dependencies = [('libogg', '1.3.5')]
+
+configopts = '--enable-static --enable-shared'
+
+sanity_check_paths = {
+    'files': ['lib/libvorbis.a', 'lib/libvorbis.%s' % SHLIB_EXT],
+    'dirs': ['include/vorbis'],
+}
+
+moduleclass = 'lib'

From d98ca82248abfd9f87091430636add937a0238c4 Mon Sep 17 00:00:00 2001
From: Simon Branford <s.j.branford@bham.ac.uk>
Date: Tue, 25 Jun 2024 10:12:17 +0100
Subject: [PATCH 318/835] undo damage from --inject-checksums

---
 easybuild/easyconfigs/a/Arrow/Arrow-16.1.0-gfbf-2023b.eb | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-16.1.0-gfbf-2023b.eb b/easybuild/easyconfigs/a/Arrow/Arrow-16.1.0-gfbf-2023b.eb
index 1374d3973bf..3e5729cc430 100644
--- a/easybuild/easyconfigs/a/Arrow/Arrow-16.1.0-gfbf-2023b.eb
+++ b/easybuild/easyconfigs/a/Arrow/Arrow-16.1.0-gfbf-2023b.eb
@@ -59,10 +59,10 @@ exts_default_options = {
 }
 exts_list = [
     ('pyarrow', version, {
-        'preinstallopts': "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && export Arrow_DIR=%(installdir)s && export ArrowDataset_DIR=%(installdir)s && export ArrowAcero_DIR=%(installdir)s && export Parquet_DIR=%(installdir)s && export XDG_CACHE_HOME=$TMPDIR && sed -i 's/numpy==[0-9.]*/numpy/g' pyproject.toml && Python3_ROOT_DIR=$EBROOTPYTHON PYARROW_CMAKE_OPTIONS='-DZSTD_LIB=$EBROOTZSTD/lib/libzstd.so ' PYARROW_WITH_DATASET=1 PYARROW_WITH_PARQUET=1 ",
         'sources': ['apache-arrow-%(version)s.tar.gz'],
-        'start_dir': '%(builddir)s/apache-arrow-%(version)s/python',
         'checksums': ['c9e60c7e87e59383d21b20dc874b17153729ee153264af6d21654b7dff2c60d7'],
+        'start_dir': '%(builddir)s/apache-arrow-%(version)s/python',
+        'preinstallopts': _pyarrow_preinstall_opts,
     }),
 ]
 

From 5fbe18fd087fb835062dc72393a588c268fcdb75 Mon Sep 17 00:00:00 2001
From: Simon Branford <s.j.branford@bham.ac.uk>
Date: Tue, 25 Jun 2024 10:14:09 +0100
Subject: [PATCH 319/835] adding easyconfigs: NLopt-2.7.1-GCCcore-13.2.0.eb

---
 .../n/NLopt/NLopt-2.7.1-GCCcore-13.2.0.eb     | 33 +++++++++++++++++++
 1 file changed, 33 insertions(+)
 create mode 100644 easybuild/easyconfigs/n/NLopt/NLopt-2.7.1-GCCcore-13.2.0.eb

diff --git a/easybuild/easyconfigs/n/NLopt/NLopt-2.7.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/n/NLopt/NLopt-2.7.1-GCCcore-13.2.0.eb
new file mode 100644
index 00000000000..17c0db0f161
--- /dev/null
+++ b/easybuild/easyconfigs/n/NLopt/NLopt-2.7.1-GCCcore-13.2.0.eb
@@ -0,0 +1,33 @@
+easyblock = 'CMakeMake'
+
+name = 'NLopt'
+version = '2.7.1'
+
+homepage = 'http://ab-initio.mit.edu/wiki/index.php/NLopt'
+description = """ NLopt is a free/open-source library for nonlinear optimization,
+ providing a common interface for a number of different free optimization routines
+ available online as well as original implementations of various other algorithms. """
+
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://github.com/stevengj/nlopt/archive']
+sources = ['v%(version)s.tar.gz']
+checksums = ['db88232fa5cef0ff6e39943fc63ab6074208831dc0031cf1545f6ecd31ae2a1a']
+
+builddependencies = [
+    ('CMake', '3.27.6'),
+    ('binutils', '2.40'),
+]
+
+configopts = [
+    '-DBUILD_SHARED_LIBS=ON',
+    '-DBUILD_SHARED_LIBS=OFF'
+]
+
+sanity_check_paths = {
+    'files': ['lib/libnlopt.a', 'lib/libnlopt.%s' % SHLIB_EXT, 'include/nlopt.h'],
+    'dirs': ['lib/pkgconfig'],
+}
+
+moduleclass = 'numlib'

From 85e398ec9d690cafa98b27adca0e28aab6e12215 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Tue, 25 Jun 2024 11:26:37 +0200
Subject: [PATCH 320/835] adding easyconfigs: histolab-0.6.0-foss-2022a.eb

---
 .../h/histolab/histolab-0.6.0-foss-2022a.eb   | 37 +++++++++++++++++++
 1 file changed, 37 insertions(+)
 create mode 100644 easybuild/easyconfigs/h/histolab/histolab-0.6.0-foss-2022a.eb

diff --git a/easybuild/easyconfigs/h/histolab/histolab-0.6.0-foss-2022a.eb b/easybuild/easyconfigs/h/histolab/histolab-0.6.0-foss-2022a.eb
new file mode 100644
index 00000000000..a7dc410e6f0
--- /dev/null
+++ b/easybuild/easyconfigs/h/histolab/histolab-0.6.0-foss-2022a.eb
@@ -0,0 +1,37 @@
+easyblock = 'PythonBundle'
+
+name = 'histolab'
+version = '0.6.0'
+
+homepage = 'https://github.com/histolab/histolab'
+description = """Library for Digital Pathology Image Processing."""
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+builddependencies = [('poetry', '1.2.2')]
+dependencies = [
+    ('Python', '3.10.4'),
+    ('Pillow', '9.1.1'),
+    ('scikit-image', '0.19.3'),
+    ('SciPy-bundle', '2022.05'),
+    ('openslide-python', '1.2.0'),
+]
+
+use_pip = True
+
+exts_list = [
+    # requires importlib-metadata = ">=4.12,<7.0"
+    ('importlib_metadata', '6.11.0', {
+        'checksums': ['1231cf92d825c9e03cfc4da076a16de6422c863558229ea0b22b675657463443'],
+    }),
+    ('certifi', '2024.6.2', {
+        'checksums': ['3cd43f1c6fa7dedc5899d69d3ad0398fd018ad1a17fba83ddaf78aa46c747516'],
+    }),
+    (name, version, {
+        'checksums': ['fcb8cf70fdf32a58e2980905d657ea53a541503a436e8303f0cb0da6e9f2e20f'],
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'vis'

From bc9a24bbd426c0ed6472084c1451aa62e584b89a Mon Sep 17 00:00:00 2001
From: Simon Branford <s.j.branford@bham.ac.uk>
Date: Tue, 25 Jun 2024 10:31:36 +0100
Subject: [PATCH 321/835] undo damage from using EB5 ecs as base

---
 easybuild/easyconfigs/a/Arrow/Arrow-16.1.0-gfbf-2023b.eb | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-16.1.0-gfbf-2023b.eb b/easybuild/easyconfigs/a/Arrow/Arrow-16.1.0-gfbf-2023b.eb
index 3e5729cc430..87862215507 100644
--- a/easybuild/easyconfigs/a/Arrow/Arrow-16.1.0-gfbf-2023b.eb
+++ b/easybuild/easyconfigs/a/Arrow/Arrow-16.1.0-gfbf-2023b.eb
@@ -56,6 +56,9 @@ _pyarrow_preinstall_opts += "PYARROW_WITH_DATASET=1 PYARROW_WITH_PARQUET=1 "
 
 exts_defaultclass = 'PythonPackage'
 exts_default_options = {
+    'download_dep_fail': True,
+    'use_pip': True,
+    'sanity_pip_check': True,
 }
 exts_list = [
     ('pyarrow', version, {

From 6400477583707b155432e6aa6649cf1a0343f125 Mon Sep 17 00:00:00 2001
From: Simon Branford <s.j.branford@bham.ac.uk>
Date: Tue, 25 Jun 2024 10:32:58 +0100
Subject: [PATCH 322/835] correct version number

---
 .../easyconfigs/l/libsndfile/libsndfile-1.2.2-GCCcore-13.2.0.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/l/libsndfile/libsndfile-1.2.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/libsndfile/libsndfile-1.2.2-GCCcore-13.2.0.eb
index 7652c3f06e0..66345e01105 100644
--- a/easybuild/easyconfigs/l/libsndfile/libsndfile-1.2.2-GCCcore-13.2.0.eb
+++ b/easybuild/easyconfigs/l/libsndfile/libsndfile-1.2.2-GCCcore-13.2.0.eb
@@ -19,7 +19,7 @@ builddependencies = [
     ('CMake', '3.27.6'),
 ]
 dependencies = [
-    ('FLAC', '1.4.2'),
+    ('FLAC', '1.4.3'),
     ('libvorbis', '1.3.7'),
     ('libopus', '1.5.2'),
     ('LAME', '3.100'),

From ff04eb945b65680edc8967faaa04bf912a31755d Mon Sep 17 00:00:00 2001
From: Simon Branford <s.j.branford@bham.ac.uk>
Date: Tue, 25 Jun 2024 11:08:02 +0100
Subject: [PATCH 323/835] adding easyconfigs: R-4.4.1-gfbf-2023b.eb,
 R-bundle-CRAN-2024.06-foss-2023b.eb

---
 .../R-bundle-CRAN-2024.06-foss-2023b.eb       | 3430 +++++++++++++++++
 .../easyconfigs/r/R/R-4.4.1-gfbf-2023b.eb     |  371 ++
 2 files changed, 3801 insertions(+)
 create mode 100644 easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb
 create mode 100644 easybuild/easyconfigs/r/R/R-4.4.1-gfbf-2023b.eb

diff --git a/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb b/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb
new file mode 100644
index 00000000000..f2bea4e2d62
--- /dev/null
+++ b/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb
@@ -0,0 +1,3430 @@
+easyblock = 'Bundle'
+
+name = 'R-bundle-CRAN'
+version = '2024.06'
+
+homepage = 'https://www.r-project.org/'
+description = "Bundle of R packages from CRAN"
+
+toolchain = {'name': 'foss', 'version': '2023b'}
+
+builddependencies = [
+    ('pkgconf', '2.0.3'),
+    ('Xvfb', '21.1.9'),
+    ('Autotools', '20220317'),
+    ('CMake', '3.27.6'),
+]
+
+dependencies = [
+    ('R', '4.4.1'),
+    ('libxml2', '2.11.5'),  # for XML
+    ('GMP', '6.3.0'),  # for igraph
+    ('NLopt', '2.7.1'),  # for nlopt
+    ('FFTW', '3.3.10'),  # for fftw
+    ('libsndfile', '1.2.2'),  # for seewave
+    ('ICU', '74.1'),  # for rJava & gdsfmt
+    ('HDF5', '1.14.3'),  # for hdf5r
+    ('UDUNITS', '2.2.28'),  # for units
+    ('GSL', '2.7'),  # for RcppGSL
+    ('ImageMagick', '7.1.1-34'),
+    ('GLPK', '5.0'),  # for Rglpk
+    ('nodejs', '20.9.0'),  # for V8 (required by rstan)
+    ('GDAL', '3.9.0'),  # for sf
+    ('MPFR', '4.2.1'),  # for Rmpfr
+    ('PostgreSQL', '16.1'),  # for RPostgreSQL
+]
+
+# Some R extensions (mclust, quantreg, waveslim for example) require the math library (-lm) to avoid undefined symbols.
+# Adding it to FLIBS makes sure it is present when needed.
+preconfigopts = 'export FLIBS="$FLIBS -lm" && '
+
+configopts = "--with-pic --enable-threads --enable-R-shlib"
+# some recommended packages may fail in a parallel build (e.g. Matrix), and
+# we're installing them anyway below
+configopts += " --with-recommended-packages=no"
+
+exts_defaultclass = 'RPackage'
+
+exts_default_options = {
+    'source_urls': [
+        'https://cran.r-project.org/src/contrib/Archive/%(name)s',  # package archive
+        'https://cran.r-project.org/src/contrib/',  # current version of packages
+        'https://cran.freestatistics.org/src/contrib',  # mirror alternative for current packages
+    ],
+    'source_tmpl': '%(name)s_%(version)s.tar.gz',
+}
+
+# check whether correct version is installed in extension filter
+# (some versions in this bundle may be newer than the ones provided by R)
+local_ext_version_check = "pkgver = packageVersion('%(ext_name)s'); if (pkgver != '%(ext_version)s') "
+local_stop_msg = "stop('%(ext_name)s %(ext_version)s not installed, found ', pkgver, ' instead')"
+exts_filter = ("R -q --no-save", "%s { %s }" % (local_ext_version_check, local_stop_msg))
+
+# !! order of packages is important !!
+# packages updated on 24 June 2024
+exts_list = [
+    ('abind', '1.4-5', {
+        'checksums': ['3a3ace5afbcb86e56889efcebf3bf5c3bb042a282ba7cc4412d450bb246a3f2c'],
+    }),
+    ('magic', '1.6-1', {
+        'checksums': ['ca79ec7ae92b736cb128556c081abf547f49956c326e053a76579889cbcb7976'],
+    }),
+    ('RcppProgress', '0.4.2', {
+        'checksums': ['b1624b21b7aeb1dafb30f092b2a4bef4c3504efd2d6b00b2cdf55dc9df194b48'],
+    }),
+    ('lpSolve', '5.6.20', {
+        'checksums': ['3ffe06a0685123c36cd306b874f89a59a70c864c8f78c5569f82a86abedc21db'],
+    }),
+    ('linprog', '0.9-4', {
+        'checksums': ['81a6aa2fdc075f12dc912794d0554f87705a8b872b99c89a90a69ee9ada864b4'],
+    }),
+    ('geometry', '0.4.7', {
+        'checksums': ['96204205f51b4d63c2e7a7b00365def27d131f3c9ec66db56b510046e5d2013b'],
+    }),
+    ('bit', '4.0.5', {
+        'checksums': ['f0f2536a8874b6a30b80baefbc68cb21f0ffbf51f3877bda8038c3f9f354bfbc'],
+    }),
+    ('filehash', '2.4-5', {
+        'checksums': ['3b1ee2794dd61e525ee44db16611c65957691d77bb26ae481eba988bb55da22c'],
+    }),
+    ('ff', '4.0.12', {
+        'checksums': ['08af355a9a10fe29d48d085abc7cf1f975e1a4a670668a4f8d9632d087fb41bf'],
+    }),
+    ('bnlearn', '4.9.4', {
+        'checksums': ['ce3d8d89451fed9277f879c03bb02bc17acab13f1f35587aab8175b80246eeea'],
+    }),
+    ('bootstrap', '2019.6', {
+        'checksums': ['5252fdfeb944cf1fae35016d35f9333b1bd1fc8c6d4a14e33901160e21968694'],
+    }),
+    ('combinat', '0.0-8', {
+        'checksums': ['1513cf6b6ed74865bfdd9f8ca58feae12b62f38965d1a32c6130bef810ca30c1'],
+    }),
+    ('deal', '1.2-42', {
+        'checksums': ['a17f452a94fc3964c939c5b147ad6d4f326a0990493519d376d6700cf733a134'],
+    }),
+    ('fdrtool', '1.2.17', {
+        'checksums': ['3452601adbead9be4820794e3af2666f710fdf9b801186df565b80b43629c5dd'],
+    }),
+    ('formatR', '1.14', {
+        'checksums': ['4ebaab2c3f8527871655246b62abd060bc75dae1cec7f962ca4752b8080f474c'],
+    }),
+    ('gtools', '3.9.5', {
+        'checksums': ['dee9b6c1152db1a5dc427d074b32bbbb738708683f17a95e0e95e4d79fdf174b'],
+    }),
+    ('gdata', '3.0.0', {
+        'checksums': ['a456b9921765a705fe8e51780dfbbc6ca005abc948b2f80effeccd468601b17f'],
+    }),
+    ('GSA', '1.03.3', {
+        'checksums': ['5459786190f40339addc45e7bb58c6a983548aa8feac7277ea7ec0662c5a282c'],
+    }),
+    ('infotheo', '1.2.0.1', {
+        'checksums': ['c0fb8ec97ad3a49f231c4c993b5eee70c6a61c8c30dc4a46197867e4763a29d4'],
+    }),
+    ('lars', '1.3', {
+        'checksums': ['c69e6a8da6a3344c0915dd1fd4c78fec5cdf50c62cf6297476e9bb7dc10b549d'],
+    }),
+    ('lazy', '1.2-18', {
+        'checksums': ['99441bcae2dfbf450eee91f3ec969d416c225f671ac54459c50536916890f00a'],
+    }),
+    ('kernlab', '0.9-32', {
+        'checksums': ['654ef34e343deb4d2c4c139a44e5397d6e38876088ce1c53c7deb087935d6fdc'],
+    }),
+    ('markdown', '1.13', {
+        'checksums': ['385421c674cf5bf2ba04d1df7c16bb5d857bec03755a36321999ac37f5b3cfd9'],
+    }),
+    ('mlbench', '2.1-5', {
+        'checksums': ['4dbfd652adda7c0caf544d3a6cd23a2ee97c22faefe4d15b8a6782061cc9e76f'],
+    }),
+    ('NLP', '0.2-1', {
+        'checksums': ['05eaa453ad2757311c073fd30093c738b20a977c5089031eb454345a1d01f2b6'],
+    }),
+    ('mclust', '6.1.1', {
+        'checksums': ['ddd7018e5e6ea7f92c7fc9872b391491b7e91c2cd89ef1dcaf4408afb5116775'],
+    }),
+    ('RANN', '2.6.1', {
+        'checksums': ['b299c3dfb7be17aa41e66eff5674fddd2992fb6dd3b10bc59ffbf0c401697182'],
+    }),
+    ('rmeta', '3.0', {
+        'checksums': ['b9f9d405935cffcd7a5697ff13b033f9725de45f4dc7b059fd68a7536eb76b6e'],
+    }),
+    ('MASS', '7.3-61', {
+        'checksums': ['3144c8bf579dd7b7c47c259728c27f53f53e294e7ed307da434dfd144e800a90'],
+    }),
+    ('lattice', '0.22-6', {
+        'checksums': ['4b377211e472ece7872b9d6759f9b9c660b09594500462eb6146312a1d4d00f7'],
+    }),
+    ('nlme', '3.1-165', {
+        'checksums': ['fc37bba493c2138be2f38fcfd2a67327d81ab91a37bad6f698226bb400ec9499'],
+    }),
+    ('segmented', '2.1-0', {
+        'checksums': ['6d7ba0248cb5aa23dfdfc3fc53b6aab2f564323c671420fc73c5274e03640cf2'],
+    }),
+    ('som', '0.3-5.1', {
+        'checksums': ['a6f4c0e5b36656b7a8ea144b057e3d7642a8b71972da387a7133f3dd65507fb9'],
+    }),
+    ('SuppDists', '1.1-9.7', {
+        'checksums': ['6b5527e2635c0ff762eb7af8154704c85e66d7f79a9524089a5c98dfa94dab08'],
+    }),
+    ('stabledist', '0.7-1', {
+        'checksums': ['06c5704d3a3c179fa389675c537c39a006867bc6e4f23dd7e406476ed2c88a69'],
+    }),
+    ('survivalROC', '1.0.3.1', {
+        'checksums': ['8174afebaf239dfda979c8c7e1e219624576d577c983ae787fbd2785b4ccd15c'],
+    }),
+    ('pspline', '1.0-20', {
+        'checksums': ['eaa7cd9b870d5d10cf457c435ebcbe698ba0d463e3a996fbe758a4b57b93eb8a'],
+    }),
+    ('timeDate', '4032.109', {
+        'checksums': ['402841bda47e8c31f49773de2ff5447e9780bc7c8af5fb18be9287b546fcb958'],
+    }),
+    ('longmemo', '1.1-2', {
+        'checksums': ['7964e982287427dd58f98e1144e468ae0cbd572d25a4bea6ca9ae9c7522f3207'],
+    }),
+    ('ADGofTest', '0.3', {
+        'checksums': ['9cd9313954f6ecd82480d373f6c5371ca84ab33e3f5c39d972d35cfcf1096846'],
+    }),
+    ('pixmap', '0.4-13', {
+        'checksums': ['e3dbc641a0497575b45a4140dadc6bf43cdf39b02393f93f1b0ee4f4d026e711'],
+    }),
+    ('sp', '2.1-4', {
+        'checksums': ['e185e7fb61d2d7dbc50fd765a93e170fa778083a653588db1f5e99d019479f0a'],
+    }),
+    ('hms', '1.1.3', {
+        'checksums': ['e626f4c60af46efd53ea631b316a103e089470d8fd63c0e0c0efb99364990282'],
+    }),
+    ('progress', '1.2.3', {
+        'checksums': ['ea2b079b894de85c3ab12088c9c52aec06432245047a961d5b4b8aa6889f9276'],
+    }),
+    ('RcppArmadillo', '0.12.8.4.0', {
+        'checksums': ['cabf6865073204c184ddad4dec1f30aae1b8020b4c9d6e74d1a6b0baaef03046'],
+    }),
+    ('ade4', '1.7-22', {
+        'checksums': ['007df54e83a2a6cb8d6da8006f0aace011e7eaa7744dc5f8230ac2c002b393b4'],
+    }),
+    ('AlgDesign', '1.2.1', {
+        'checksums': ['5989626c526bd7c3d9bdda326c962056879be03392065a0b7ddb9b8cf9309d05'],
+    }),
+    ('BH', '1.84.0-0', {
+        'checksums': ['6fb660755f572cd975073d7052075654acf8db12d208954ca223b8e4f77ef1ac'],
+    }),
+    ('Matrix', '1.7-0', {
+        'checksums': ['fb97bba0df370222eb4f7e2da2e94dd01053b5e054b1c51829ff9a6efc08ad37'],
+    }),
+    ('Brobdingnag', '1.2-9', {
+        'checksums': ['f9012d250bc2a0f47815d6a7c06df2d4ddf3d8bab2d3b75e8cdefd964d20e91e'],
+    }),
+    ('corpcor', '1.6.10', {
+        'checksums': ['71a04c503c93ec95ddde09abe8c7ddeb36175b7da76365a14b27066383e10e09'],
+    }),
+    ('longitudinal', '1.1.13', {
+        'checksums': ['57f04a0f387c1cc30d2feb945dc3ed35d2a304d94d21d3bc2cac8c92571fdc10'],
+    }),
+    ('backports', '1.5.0', {
+        'checksums': ['0d3ed9db8f1505e88967f48d669b2a257e0c6b7e6320ea64b946c1bd40897ca2'],
+    }),
+    ('checkmate', '2.3.1', {
+        'checksums': ['e7e6ba0cca400137f352a599ea29cf35a83f40a5ad26e7c4f06e6c35471884f6'],
+    }),
+    ('cubature', '2.1.0', {
+        'checksums': ['5d82785609611200d5bea069b93b0bf75bafec808f7eeef7b052eb516f273665'],
+    }),
+    ('DEoptimR', '1.1-3', {
+        'checksums': ['8dd8a61b07b02022493d7021dc62ef2c4dc2d596cff897846713c5f8dd784694'],
+    }),
+    ('fastmatch', '1.1-4', {
+        'checksums': ['9a914cac9c1ea2984bd44eebe421e1636504907a8064ae26347fe3ec2b9bd56b'],
+    }),
+    ('iterators', '1.0.14', {
+        'checksums': ['cef3075a0930e1408c764e4da56bbadd4f7d14315809df8f38dd51f80ccc677b'],
+    }),
+    ('maps', '3.4.2', {
+        'checksums': ['53e57b889f1779cfd4a116a8ed3eded7ed29a73a1b9506248772a389c8404b0c'],
+    }),
+    ('nnls', '1.5', {
+        'checksums': ['cd70feb286f86f6dead75da693a8f67c9bd3b91eb738e6e6ac659e3b8c7a3452'],
+    }),
+    ('sendmailR', '1.4-0', {
+        'checksums': ['5b8b91fc13f6b07b9fc5a2cf7591cf760fad47c5ea17d87a2891898c506454ad'],
+    }),
+    ('dotCall64', '1.1-1', {
+        'checksums': ['21b8d7d747c07aaf8a82d61ec98fe0539afcaa5a565d9c2fc55be65b6af2c91b'],
+    }),
+    ('spam', '2.10-0', {
+        'checksums': ['719c86a23801ecf051ffd8291912ee3567af4010e74af470fbf09e274728ac79'],
+    }),
+    ('subplex', '1.8', {
+        'checksums': ['3bc31d8990380c9f790c9c7d84cb2e39f4945eff934eddfa1196d597465be5a5'],
+    }),
+    ('logspline', '2.1.22', {
+        'checksums': ['773af7a2f12bce0eac30a036bd61bafd9a2b0eb083e377f4ef4e5518a463ed02'],
+    }),
+    ('ncbit', '2013.03.29.1', {
+        'checksums': ['847f570c035d849e775c1cb922d2775e6c535971eb4429cf62904319fd126504'],
+    }),
+    ('permute', '0.9-7', {
+        'checksums': ['eff88ffb579aaeb994e9f8609b776b2d9d9d56bc2879ddf180e3a2ad19f48dc0'],
+    }),
+    ('plotrix', '3.8-4', {
+        'checksums': ['e6a22d93ab61c67af21cbbe1fe333c06934cf576a44745bf2beee59bceaae8d6'],
+    }),
+    ('randomForest', '4.7-1.1', {
+        'checksums': ['f59ea87534480edbcd6baf53d7ec57e8c69f4532c2d2528eacfd48924efa2cd6'],
+    }),
+    ('scatterplot3d', '0.3-44', {
+        'checksums': ['1c9c08348c3ed925f59df40cb73accc9e1a169ccfb1e8571f105f40fa98e6ec2'],
+    }),
+    ('SparseM', '1.83', {
+        'checksums': ['f07e5d5cf181ff5c878a5d747bd77fb7cc45e8da5d7395d1ddbb82492eb7095a'],
+    }),
+    ('tripack', '1.3-9.1', {
+        'checksums': ['7f82f8d63741c468767acc6fb35281bd9903f6c3c52e8fada60a6ae317511fbe'],
+    }),
+    ('irace', '3.5', {
+        'checksums': ['d9928644a5a7e94838558d73afaaee8a914fd26fe68f691ad103331632060bf4'],
+    }),
+    ('rJava', '1.0-11', {
+        'checksums': ['9ea0ccf5553d86f7de8649a8324766c4f0810f35b7be561640dd87fd37986417'],
+    }),
+    ('RColorBrewer', '1.1-3', {
+        'checksums': ['4f42f5423c45688b39f492c7892d93f37b4541831c8ffb140364d2bd89031ac0'],
+    }),
+    ('png', '0.1-8', {
+        'checksums': ['5a36fabb6d62ba2533d3fc4cececd07891942cfb76fe689ec0d550d08762f61c'],
+    }),
+    ('jpeg', '0.1-10', {
+        'checksums': ['c8d9f609c3088f91ec4853d6cc0e66511038a465811dea79ca6a0c09519178ca'],
+    }),
+    ('deldir', '2.0-4', {
+        'checksums': ['d418acb28ec3707b6d64c7466d0cefbb49b098537f37558d8f7a5befd34a4653'],
+    }),
+    ('RcppEigen', '0.3.4.0.0', {
+        'checksums': ['28d4a02011129f9b7a2a2bbe69ec4cca7676b072d5aca9dc1cefa8f96af45136'],
+    }),
+    ('interp', '1.1-6', {
+        'checksums': ['3674044e5334ecdf124054303929c084fc0797d3123e28576a230492ea6ecd34'],
+    }),
+    ('latticeExtra', '0.6-30', {
+        'checksums': ['c550a76913624818482bf237d48883c58e368ba356ced8ed5e76146672279eed'],
+    }),
+    ('plyr', '1.8.9', {
+        'checksums': ['15b5e7f711d53bf41b8687923983b8ef424563aa2f74c5195feb5b1df1aee103'],
+    }),
+    ('gtable', '0.3.5', {
+        'checksums': ['b19fc1a30359945adbab7d4e915fe95523a839c380e34ae705d70b7ebddeea72'],
+    }),
+    ('reshape2', '1.4.4', {
+        'checksums': ['d88dcf9e2530fa9695fc57d0c78adfc5e361305fe8919fe09410b17da5ca12d8'],
+    }),
+    ('dichromat', '2.0-0.1', {
+        'checksums': ['a10578e9ad8a581bd8fe0d8a8370051f3cdcf12c7d282f3af2a18dacda566081'],
+    }),
+    ('colorspace', '2.1-0', {
+        'checksums': ['04078abb6b54119c90dc7085d62916bf292ccb163e213f9ea70567d1be82614c'],
+    }),
+    ('munsell', '0.5.1', {
+        'checksums': ['03a2fd9ac40766cded96dfe33b143d872d0aaa262a25482ce19161ca959429a6'],
+    }),
+    ('labeling', '0.4.3', {
+        'checksums': ['c62f4fc2cc74377d7055903c5f1913b7295f7587456fe468592738a483e264f2'],
+    }),
+    ('viridisLite', '0.4.2', {
+        'checksums': ['893f111d31deccd2cc959bc9db7ba2ce9020a2dd1b9c1c009587e449c4cce1a1'],
+    }),
+    ('farver', '2.1.2', {
+        'checksums': ['528823b95daab4566137711f1c842027a952bea1b2ae6ff098e2ca512b17fe25'],
+    }),
+    ('scales', '1.3.0', {
+        'checksums': ['b33e0f6b44259551ce02befd52eac53602509fbfdd903920620c658c50f35888'],
+    }),
+    ('zeallot', '0.1.0', {
+        'checksums': ['439f1213c97c8ddef9a1e1499bdf81c2940859f78b76bc86ba476cebd88ba1e9'],
+    }),
+    ('assertthat', '0.2.1', {
+        'checksums': ['85cf7fcc4753a8c86da9a6f454e46c2a58ffc70c4f47cac4d3e3bcefda2a9e9f'],
+    }),
+    ('lazyeval', '0.2.2', {
+        'checksums': ['d6904112a21056222cfcd5eb8175a78aa063afe648a562d9c42c6b960a8820d4'],
+    }),
+    ('mgcv', '1.9-1', {
+        'checksums': ['700fbc37bedd3a49505b9bc4949faee156d9cfb4f669d797d06a10a15a5bdb32'],
+    }),
+    ('isoband', '0.2.7', {
+        'checksums': ['7693223343b45b86de2b5b638ff148f0dafa6d7b1237e822c5272902f79cdf61'],
+    }),
+    ('ggplot2', '3.5.1', {
+        'checksums': ['7c58b424f99b3634038e6f6d1fe4b0241b8aecb50e9c50466d5590f7e3144721'],
+    }),
+    ('pROC', '1.18.5', {
+        'checksums': ['5593c841a6df5a2f2d209d0c14401971eb9427092ed9c3ac2059273807b42c89'],
+    }),
+    ('quadprog', '1.5-8', {
+        'checksums': ['22128dd6b08d3516c44ff89276719ad4fe46b36b23fdd585274fa3a93e7a49cd'],
+    }),
+    ('BB', '2019.10-1', {
+        'checksums': ['04d0b6ce6e5f070b109478a6005653dbe78613bb4e3ea4903203d851b5d3c94d'],
+    }),
+    ('data.table', '1.15.4', {
+        'checksums': ['ab8065ff946d59ecaaf5eaf91a975495c07c30caad97a71205c72e41a740cb53'],
+    }),
+    ('BBmisc', '1.13', {
+        'checksums': ['1145dcf9fed15e7beeaa4a5c7075d8a8badd17c8246838cd63e40cd9551e4405'],
+    }),
+    ('fail', '1.3', {
+        'checksums': ['ede8aa2a9f2371aff5874cd030ac625adb35c33954835b54ab4abf7aeb34d56d'],
+    }),
+    ('rlecuyer', '0.3-8', {
+        'checksums': ['66bed3543337535fe2cf2d3eee4165472599c14d3c5e4402f7a1ebf5112c75c9'],
+    }),
+    ('snow', '0.4-4', {
+        'checksums': ['84587f46f222a96f3e2fde10ad6ec6ddbd878f4e917cd926d632f61a87db13c9'],
+    }),
+    ('tree', '1.0-43', {
+        'checksums': ['9b0a996d013cce4f457abdbdc54bd2f8f4dbe4ef0b33e0a53925509c509d5287'],
+    }),
+    ('pls', '2.8-3', {
+        'checksums': ['e6eb728dd38cd4867698df06e02601ed767e69098b1daadde5beef634ae66be3'],
+    }),
+    ('class', '7.3-22', {
+        'checksums': ['b6994164e93843fcc7e08dfdc8c8b4af6a5a10ef7153d2e72a6855342508d15c'],
+    }),
+    ('proxy', '0.4-27', {
+        'checksums': ['249991a4c4d70ad139e93f3a24e17f161ad1ec854951813ea192daf79478563f'],
+    }),
+    ('e1071', '1.7-14', {
+        'checksums': ['754d97ab073acc07b909a190f87f021e31e07269c8632c53166a6c2843e65195'],
+    }),
+    ('nnet', '7.3-19', {
+        'checksums': ['a9241f469270d3b03bbab7dc0d3c6a06a84010af16ba82fd3bd6660b35382ce7'],
+    }),
+    ('minqa', '1.2.7', {
+        'checksums': ['76f3459d1ed860d5095b1d89d41628fc7187e72506cf48f073e15724d9e52fe2'],
+    }),
+    ('MatrixModels', '0.5-3', {
+        'checksums': ['c2db5406c6b0b9d348b44eea215a39c64fc087099fea1342a04d50326577f20f'],
+    }),
+    ('matrixStats', '1.3.0', {
+        'checksums': ['413ee607d95b243c514b4a7c4944c2caea1fb264d27c96ff547c3939f893245a'],
+    }),
+    ('codetools', '0.2-20', {
+        'checksums': ['3be6f375ec178723ddfd559d1e8e85bfeee04a5fbaf9f53f2f844e1669fea863'],
+    }),
+    ('foreach', '1.5.2', {
+        'checksums': ['56338d8753f9f68f262cf532fd8a6d0fe25a71a2ff0107f3ce378feb926bafe4'],
+    }),
+    ('ModelMetrics', '1.2.2.2', {
+        'checksums': ['5e06f1926aebca5654e1329c66ef19b04058376b2277ebb16e3bf8c208d73457'],
+    }),
+    ('generics', '0.1.3', {
+        'checksums': ['75046163bfa8b8a4f4214c1b689e796207f6447182f2e5062cf570302387d053'],
+    }),
+    ('tidyselect', '1.2.1', {
+        'checksums': ['169e97ba0bbfbcdf4a80534322751f87a04370310c40e27f04aac6525d45903c'],
+    }),
+    ('dplyr', '1.1.4', {
+        'checksums': ['cf730414d5d4ab387b4e9890a4b1df9d17a3903488e8da8df1cf2e11e44558cb'],
+    }),
+    ('gower', '1.0.1', {
+        'checksums': ['296a9d8e5efa8c3a8cc6b92cf38880915753afdef30281629af9dc8eae8315fc'],
+    }),
+    ('rpart', '4.1.23', {
+        'checksums': ['f9b89aed6aa6cea656a2dcb271574e969ce2b1c98beb07bd91e17339f6daabaf'],
+    }),
+    ('survival', '3.7-0', {
+        'checksums': ['cd96b08ec928b0028f69c942cc788e190b4543c8518d71deb6d8a712de44feef'],
+    }),
+    ('KernSmooth', '2.23-24', {
+        'checksums': ['d0b3ec39547ffd92565e91b0c3bb637f3b30e7a46afe416d8790b8c4f528ac5f'],
+    }),
+    ('globals', '0.16.3', {
+        'checksums': ['d73ced94248d8b81d29d774bdfc41496274d7da683a5d84440aed6a501a18c5b'],
+    }),
+    ('listenv', '0.9.1', {
+        'checksums': ['422aaf487b91c6512b83c05536f8dac255db79b16ee85254acc59a3fda8c1c3b'],
+    }),
+    ('parallelly', '1.37.1', {
+        'checksums': ['df7e4eb18df8a30c87cc651bdc2e6ded20736c3484984facabb89a98e07a36a1'],
+    }),
+    ('future', '1.33.2', {
+        'checksums': ['b5a71ac628cdaeeb26e3fc41003d2c5bd48156da881cabd9b14878991324aa66'],
+    }),
+    ('future.apply', '1.11.2', {
+        'checksums': ['f4a635b0fa5e0d826d2f8da6bc1fa5bb055e640c29a85c644931d08ab2d81387'],
+    }),
+    ('progressr', '0.14.0', {
+        'checksums': ['9a2899f879a5577f043be99c18d52bfe4d655cc52a96cae834e8a301b36258af'],
+    }),
+    ('numDeriv', '2016.8-1.1', {
+        'checksums': ['d8c4d19ff9aeb31b0c628bd4a16378e51c1c9a3813b525469a31fe89af00b345'],
+    }),
+    ('SQUAREM', '2021.1', {
+        'checksums': ['66e5e18ca29903e4950750bbd810f0f9df85811ee4195ce0a86d939ba8183a58'],
+    }),
+    ('lava', '1.8.0', {
+        'checksums': ['8db996eeca012c58736f2d3b97f569c03e9361e20f31513c090a9386eb87e87f'],
+    }),
+    ('shape', '1.4.6.1', {
+        'checksums': ['43f9bd0f997fd6cf1838efd8b2509c9a6396513f4e54a20360481634affd22a4'],
+    }),
+    ('diagram', '1.6.5', {
+        'checksums': ['e9c03e7712e0282c5d9f2b760bafe2aac9e99a9723578d9e6369d60301f574e4'],
+    }),
+    ('prodlim', '2023.08.28', {
+        'checksums': ['8002229f38bbe42e26b88ac542d9c028a9dbe8fd3b80af7552060bec3a555de8'],
+    }),
+    ('ipred', '0.9-14', {
+        'checksums': ['81c83dc847d09c3db52ef15e36cd4dac38c50eead1008ddd458b9e89d7528f35'],
+    }),
+    ('timechange', '0.3.0', {
+        'checksums': ['d85c0b5514ab9578d16032e703c33f197feaed1a424c834ebfcbf0ad46ae46b4'],
+    }),
+    ('lubridate', '1.9.3', {
+        'checksums': ['2b6e1406d231b0a14d60b99cc406d159fea5465a5694725ad25343f12cf37fff'],
+    }),
+    ('tidyr', '1.3.1', {
+        'checksums': ['e820c261cb5543f572f49276a7bdc7302aa4215da4bf850b1b939a315353835d'],
+    }),
+    ('hardhat', '1.4.0', {
+        'checksums': ['46d023ddfc8f940cd889478fa91c42e894a0df58a10f3b6c0eb688a500b2b3ad'],
+    }),
+    ('tzdb', '0.4.0', {
+        'checksums': ['4253c66041bdddfd463c98183bf0052fbcacdb7c5cff9eadbb858b3dcf9d3a23'],
+    }),
+    ('clock', '0.7.0', {
+        'checksums': ['54e57a3b3f8c308d67536e2a75d48f3493cf7fe821bfa4da9159b4fb2ceca874'],
+    }),
+    ('recipes', '1.0.10', {
+        'checksums': ['cfc5bdf7ec23c65f94730af8a53362fcc9a765988c5749f1568503bf8e4c9bd4'],
+    }),
+    ('caret', '6.0-94', {
+        'checksums': ['2715e83ca260bb739cd926a55b0d2da1e3f6308b17b56862466e738d930d29a8'],
+    }),
+    ('conquer', '1.3.3', {
+        'checksums': ['a2c6155ed74af0e2a279145843ec5229ae2f3707aa25169ae030c520aa97deba'],
+    }),
+    ('quantreg', '5.98', {
+        'checksums': ['a98cb259d8cf563f66a25ae8858794e574dd40de6206816ad61b1ffeb9686a61'],
+    }),
+    ('robustbase', '0.99-2', {
+        'checksums': ['b6a69628f7ae36b5eb553412365afb3227fde2f7b64000cfad77ba3562fecd44'],
+    }),
+    ('zoo', '1.8-12', {
+        'checksums': ['e6c3862668f9e3422bced3b6fba485c76a1e91b48f5d6153822d6a61863b2fb8'],
+    }),
+    ('lmtest', '0.9-40', {
+        'checksums': ['64400d4d6cc635316531042971f1783539686e9015c76f5741c07304fa14d997'],
+    }),
+    ('vcd', '1.4-12', {
+        'checksums': ['c931ef115529931cddb1d5caec4d4d3569ebf12aadde719b2f5019812c9ded88'],
+    }),
+    ('snowfall', '1.84-6.3', {
+        'checksums': ['2641932b01041e34b7afb1261f649755b4c8d6560080e0e2ee549ffdf3b8b143'],
+    }),
+    ('bindr', '0.1.1', {
+        'checksums': ['7c785ca77ceb3ab9282148bcecf64d1857d35f5b800531d49483622fe67505d0'],
+    }),
+    ('plogr', '0.2.0', {
+        'checksums': ['0e63ba2e1f624005fe25c67cdd403636a912e063d682eca07f2f1d65e9870d29'],
+    }),
+    ('bindrcpp', '0.2.3', {
+        'checksums': ['662dae785aee715855415f4e743281ccbf0832e426084dc2f0ca9c9c908ec9fa'],
+    }),
+    ('tmvnsim', '1.0-2', {
+        'checksums': ['97f63d0bab3b240cc7bdbe6e6e74e90ad25a4382a345ee51a26fe3959edeba0f'],
+    }),
+    ('mnormt', '2.1.1', {
+        'checksums': ['95fca70378af0afd5a388982ba5528f5b27e02157eeb9940a0a9762d11511308'],
+    }),
+    ('foreign', '0.8-86', {
+        'checksums': ['a729120108b29ca9744cadd61e3e6a9dc4188a007055c22b6b9a30a676e8c3e1'],
+    }),
+    ('psych', '2.4.3', {
+        'checksums': ['718d82cacc70be0b4eb1b4a4973b38ee44494bb854b25081b07692307c3a8445'],
+    }),
+    ('broom', '1.0.6', {
+        'checksums': ['24cf36248dffbde38d3d81befa679e362bfd0526b9843bc536a85452a19fbccf'],
+    }),
+    ('nloptr', '2.1.0', {
+        'checksums': ['5ead4257c9ec20045644c1d80a2bbbfef1aa9bfb8c2bbba189c56a7747eb6fac'],
+    }),
+    ('boot', '1.3-30', {
+        'checksums': ['5509d62bd6e6c21b6ef352ab7846d89027bddbfb727fd0cf55da59558bd3fe97'],
+    }),
+    ('statmod', '1.5.0', {
+        'checksums': ['d61c3ef9b09d55b42e038f8d767fa483ebbdec2a9c7172b1b0ccda0ae0016ec9'],
+    }),
+    ('lme4', '1.1-35.4', {
+        'checksums': ['589ac3273ff1c9d6fefe7a4f38c4ecbe4e023f57f02826ead29ed29e3d0799ff'],
+    }),
+    ('ucminf', '1.2.1', {
+        'checksums': ['ed3ebba3d99a324444bd521d7aeb9f87344f44f170d67f77dab18dd3fbbfcc83'],
+    }),
+    ('ordinal', '2023.12-4', {
+        'checksums': ['f5582ad983dfd2ffbaf1e90b49af6f2cc319953d1fcb33f31c6c6f335cbd9fa2'],
+    }),
+    ('jomo', '2.7-6', {
+        'checksums': ['3ffa2a5521d4969fe77b23cd3ab201afdf8db3f8f708b1276c33083c01d7e2da'],
+    }),
+    ('bit64', '4.0.5', {
+        'checksums': ['25df6826ea5e93241c4874cad4fa8dadc87a40f4ff74c9107aa12a9e033e1578'],
+    }),
+    ('vroom', '1.6.5', {
+        'checksums': ['7bdca21e58c9c5049d7445d182f59fd399193cb2f4318d083de0a559ec9b5761'],
+    }),
+    ('readr', '2.1.5', {
+        'checksums': ['0fa65a5fe0a46cffe221b7696b52adb82dd4d7a692a895484e438e439594e10a'],
+    }),
+    ('forcats', '1.0.0', {
+        'checksums': ['c5bb157909d92e1e1a427c0dc5cb358ea00a43a14918a9088fa4f6630962254e'],
+    }),
+    ('haven', '2.5.4', {
+        'checksums': ['9e1531bb37aa474abd91db5e0ed9e3a355c03faa65f4e653b3ea68b7c61ea835'],
+    }),
+    ('pan', '1.9', {
+        'checksums': ['cd91232d653783ea7f34c0eebaa80c472b5501b21eea500c4c1a8e57116c6eea'],
+    }),
+    ('mitml', '0.4-5', {
+        'checksums': ['056aec823187cc3793640d8a5e74d74093bae74260a975ceb098a83a52e2eeeb'],
+    }),
+    ('glmnet', '4.1-8', {
+        'checksums': ['1ddbe5ce07076d1bdf58b0202ebd0ceac8eeb4796c5175681adb9e58c30ddcfe'],
+    }),
+    ('mice', '3.16.0', {
+        'checksums': ['29f0285185a540337e9dde2357690c82d174f115be701ee2f0a7083173a44040'],
+    }),
+    ('urca', '1.3-4', {
+        'checksums': ['fe3d6ce5041f1e7caaf3137dfb6187640bcd2d208e19c59ee1202355ac0acb16'],
+    }),
+    ('fracdiff', '1.5-3', {
+        'checksums': ['0f90946b4092feff93fad094a2c91bb47c8051595210e86c029c70238dbf7fc0'],
+    }),
+    ('operator.tools', '1.6.3', {
+        'checksums': ['e5b74018fb75bfa02820dec4b822312f1640422f01d9fec1b58d880ffb798dec'],
+    }),
+    ('formula.tools', '1.7.1', {
+        'checksums': ['4fe0e72d9d96f2398e86cbd8536d0c84de38e5583d4ff7dcd73f415ddd8ca395'],
+    }),
+    ('logistf', '1.26.0', {
+        'checksums': ['f916e568c8c64fc48695c72214439267c02310c6c68d3ffea5708ec00e80190b'],
+    }),
+    ('akima', '0.6-3.4', {
+        'checksums': ['95657592a81d2e3628cb054b60127827ae64e65c58b77d059aa510bc6781ad3e'],
+    }),
+    ('bitops', '1.0-7', {
+        'checksums': ['e9b5fc92c39f94a10cd0e13f3d6e2a9c17b75ea01467077a51d47a5f708517c4'],
+    }),
+    ('crosstalk', '1.2.1', {
+        'checksums': ['680cf08416d6d5a1194dd85ee5695c268af9d4d01b201448e1d486c6e06014f1'],
+    }),
+    ('plotly', '4.10.4', {
+        'checksums': ['cfa995b7ed55d31a196707a3ae6ea352dd907cef3058a3bf1956fde39366d867'],
+    }),
+    ('mixtools', '2.0.0', {
+        'checksums': ['854e7482230b9a5dde61bab191b78e06aa8f9b0cdfe3c03e046afa133b317e0d'],
+    }),
+    ('cluster', '2.1.6', {
+        'checksums': ['d1c50efafd35a55387cc5b36086b97d5591e0b33c48dc718005d2f5907113164'],
+    }),
+    ('gclus', '1.3.2', {
+        'checksums': ['9cc61cdff206c11213e73afca3d570a7234250cf6044a9202c2589932278e0b3'],
+    }),
+    ('coda', '0.19-4.1', {
+        'checksums': ['f4b451d86fbb56ff9ade043ddd6b0944368c37d0dad12d02837750ecdc708ad6'],
+    }),
+    ('doMC', '1.3.8', {
+        'checksums': ['b2186f851448251ae6af5d14b9e3e7f9221f90887e5f8de6a68c91caf16619a3'],
+    }),
+    ('DBI', '1.2.3', {
+        'checksums': ['cf6708a7566a80929f06575aa345fae354714159ed5fab5db14306fc5d0d2dbe'],
+    }),
+    ('gam', '1.22-3', {
+        'checksums': ['66cd688e3b86b9a4ee8ec565ebc8a19aa45e0a282e6de40ef2b78d6846787194'],
+    }),
+    ('gamlss.data', '6.0-6', {
+        'checksums': ['bae0db19d95500b3f49f855d4ebd3ddb071c5e2d9104b27e0a73865f4909ab22'],
+    }),
+    ('gamlss.dist', '6.1-1', {
+        'checksums': ['d2db3a7658799c2ef212aa18cb75a3ecf4f73faf8c13dfdc3c14b21ae0129069'],
+    }),
+    ('gamlss', '5.4-22', {
+        'checksums': ['01e6908df92691147b884a8d58025473e18d7bf58d5f5a2d7e4f18b2a451fe2d'],
+    }),
+    ('gamlss.tr', '5.1-9', {
+        'checksums': ['e90ce51be60bd00c00d8463912d26f40080bbd8f24c4254fc77d59925368b7e4'],
+    }),
+    ('hwriter', '1.3.2.1', {
+        'checksums': ['ed2fa254ab27cf65d397e181339976fc3261dfb4f6b600fea8c5689620dab6f3'],
+    }),
+    ('xts', '0.14.0', {
+        'checksums': ['d28b16eefa9876a815bad3fc204779c197e3a0d7796b8dae8856fe153f5fcfd9'],
+    }),
+    ('TTR', '0.24.4', {
+        'checksums': ['89732b9c359bae2f41cd23db649f0897c10fab0702d780c4c25a997322710284'],
+    }),
+    ('quantmod', '0.4.26', {
+        'checksums': ['396c5d3241f77911d9f7738a60a9d728ed25b3dbce2fd92f5b11f9fcbcb8bb98'],
+    }),
+    ('mvtnorm', '1.2-5', {
+        'checksums': ['9e7882a3a24d5e288097466ed77fd6bb9e5fdfadfdfed953367b1d0667e3eda6'],
+    }),
+    ('pcaPP', '2.0-4', {
+        'checksums': ['d6c5670611d92ffa11904746a62191e6bcf294fb96afee10cb25ebbbd8458133'],
+    }),
+    ('pscl', '1.5.9', {
+        'checksums': ['8085ffd1987804793ba44637165fba3e6805aa2f6457f0692b6e641658fe6efe'],
+    }),
+    ('blob', '1.2.4', {
+        'checksums': ['d08922ebc4147d930fe4762b1b289935217308c6d3fcaa5ae028ce3f5cf2728f'],
+    }),
+    ('RSQLite', '2.3.7', {
+        'checksums': ['25e0572589e64264fe4e5d0495f5d85d977bacbb93a3fc631ede5b078db294ce'],
+    }),
+    ('BatchJobs', '1.9', {
+        'checksums': ['5da9c381df461320ed4033523bad1ee97f88a4670d2714fec32be92964115c77'],
+    }),
+    ('sandwich', '3.1-0', {
+        'checksums': ['96b0e105ee50391a1fd286e9556ba6669f08565fa30788b1a21bc861b0a023fa'],
+    }),
+    ('sfsmisc', '1.1-18', {
+        'checksums': ['33052ea0e9b7f2b8f079b2adbf58bd89a39b49e66a352df85191cc01adc483ad'],
+    }),
+    ('spatial', '7.3-17', {
+        'checksums': ['f1003ed8cff2a47169a4787c8be46e8c2c501cc06c8b1e5f97bf62507e5f5dd7'],
+    }),
+    ('VGAM', '1.1-11', {
+        'checksums': ['de9d909bd2bcfccf55d24f96999e0780ca45ec29030e227a722eb24e378b33a5'],
+    }),
+    ('multitaper', '1.0-17', {
+        'checksums': ['3430ca62be2ee491d29b05e461647327a8977743241af2d3c39277c920170af3'],
+    }),
+    ('waveslim', '1.8.5', {
+        'checksums': ['1e98a823075e34fd80a3613ae62e731915bdb45bb8cf4b249f5be7a90d00a775'],
+    }),
+    ('profileModel', '0.6.1', {
+        'checksums': ['91dc25e81f52506593f5c8d80a6131510b14525262f65b4ac10ae0cad0b2a506'],
+    }),
+    ('brglm', '0.7.2', {
+        'checksums': ['56098d2ce238478e7a27cacc4cdec0bc65f287fe746b38fbb1edda20c1675023'],
+    }),
+    ('deSolve', '1.40', {
+        'checksums': ['8c09ae6bb6875b569b9844eede30b790f39fc227f5c9d045fa63ce1b22f500ef'],
+    }),
+    ('tseriesChaos', '0.1-13.1', {
+        'checksums': ['23cb5fea56409a305e02a523ff8b7642ec383942d415c9cffdc92208dacfd961'],
+    }),
+    ('tseries', '0.10-56', {
+        'checksums': ['a81efc7c4fcf11b14de607a8f506914fb63a9dcdcec1a11138a456234bfafae8'],
+    }),
+    ('fastICA', '1.2-4', {
+        'checksums': ['ed6988ea410d1a75bf4f4925edcac5a660a417e33ba0a939bc0351e534df5f2f'],
+    }),
+    ('R.methodsS3', '1.8.2', {
+        'checksums': ['822d5e61dad4c91e8883be2b38d7b89f87492046d0fe345704eb5d2658927c2e'],
+    }),
+    ('R.oo', '1.26.0', {
+        'checksums': ['f7602b388c2216fbb4d1a31d4040ed92b40dc83d3e3746db7011637db4d44365'],
+    }),
+    ('cgdsr', '1.3.0', {
+        'checksums': ['4aa2a3564cee2449c3ff39ab2ad631deb165d4c78b8107e0ff77a9095340cc1f'],
+    }),
+    ('R.utils', '2.12.3', {
+        'checksums': ['74d6e77a95a23381a490fea54be01b653d4b938a2dc75e749a694ab48302c40c'],
+    }),
+    ('R.matlab', '3.7.0', {
+        'checksums': ['d713522268a1206555610938350137ea022e07e27fa9cdd73c02fae8d1a43dda'],
+    }),
+    ('gridExtra', '2.3', {
+        'checksums': ['81b60ce6f237ec308555471ae0119158b115463df696d2eca9b177ded8988e3b'],
+    }),
+    ('gbm', '2.1.9', {
+        'checksums': ['9d88fa1d584afa58189bad47406ee9126390cbc869c041cea0247cf26645ade4'],
+    }),
+    ('Formula', '1.2-5', {
+        'checksums': ['86254674600d64e18b65d52f42d7ebfc217c8e1945cb63ac06da22cbf04d355c'],
+    }),
+    ('acepack', '1.4.2', {
+        'checksums': ['5bffcd12b783f372bb6c50e35317744ac31597c91b6433442a7b0dce2f66ac91'],
+    }),
+    ('proto', '1.0.0', {
+        'checksums': ['9294d9a3b2b680bb6fac17000bfc97453d77c87ef68cfd609b4c4eb6d11d04d1'],
+    }),
+    ('chron', '2.3-61', {
+        'checksums': ['a096957625a0438075b3486322ee07c753c7c4ba3efcd04a3ac92476d6c43b9b'],
+    }),
+    ('viridis', '0.6.5', {
+        'checksums': ['862b5cb6be115deea0207cdd3c8bb33de28552cfdc29900777512fd488d0005c'],
+    }),
+    ('htmlTable', '2.4.2', {
+        'checksums': ['6a83dd6172c13cad4a74f2660db94565814aaf8500237e2c418216be6db7360d'],
+    }),
+    ('Hmisc', '5.1-3', {
+        'checksums': ['3c61772ff7a78ca5855189faa810c74117dc5df240103adc6e90eb94e9c605eb'],
+    }),
+    ('fastcluster', '1.2.6', {
+        'checksums': ['852a05458fb0b64497e9cf8f0182b599d1c2b1e9af03ec45f7c0c9280c1f8d19'],
+    }),
+    ('registry', '0.5-1', {
+        'checksums': ['dfea36edb0a703ec57e111016789b47a1ba21d9c8ff30672555c81327a3372cc'],
+    }),
+    ('bibtex', '0.5.1', {
+        'checksums': ['f3c1a0a4e666c4addd73ff13ce8ce073d73d10ebca36d333328ade8a0b493ed1'],
+    }),
+    ('pkgmaker', '0.32.10', {
+        'checksums': ['972b0473a64408ccc4841fa3f09a567cc32811e69c3c7e42a2f391a5eb2e2933'],
+    }),
+    ('rngtools', '1.5.2', {
+        'checksums': ['7f8c76ca4c7851b69a86e27be09b02ddc86357f0388659ef8787634682e8a74d'],
+    }),
+    ('doParallel', '1.0.17', {
+        'checksums': ['b96a25ad105a654d70c7b4ca27290dc9967bc47f4668b2763927a886b178abd7'],
+    }),
+    ('gridBase', '0.4-7', {
+        'checksums': ['be8718d24cd10f6e323dce91b15fc40ed88bccaa26acf3192d5e38fe33e15f26'],
+    }),
+    ('irlba', '2.3.5.1', {
+        'checksums': ['2cfe6384fef91c223a9920895ce89496f990d1450d731e44309fdbec2bb5c5cf'],
+    }),
+    ('igraph', '2.0.3', {
+        'checksums': ['8e8a172d4567219474562cfb1085496be3ab356483c4e88011aca1fc3b2d8f76'],
+    }),
+    ('GeneNet', '1.2.16', {
+        'checksums': ['c1e98073ccdaa18f4952630bfe4fc0617106eeaf7ed94d347cb2773bd48333e4'],
+    }),
+    ('ape', '5.8', {
+        'checksums': ['24ce729979e1bcc60317e71e5100ce54156ceb7484917b0d64260f733ae84d24'],
+    }),
+    ('RJSONIO', '1.3-1.9', {
+        'checksums': ['f173034b0c28873f417ee804b9e278aedd92e76eb56c7c6d71b1c02fa1193ece'],
+    }),
+    ('caTools', '1.18.2', {
+        'checksums': ['75d61115afec754b053ed1732cc034f2aeb27b13e6e1932aa0f26bf590cf0293'],
+    }),
+    ('gplots', '3.1.3.1', {
+        'checksums': ['1ae1de94f27583ad84543a15f042b8dbd0850c56447929c7157787d755211af2'],
+    }),
+    ('ROCR', '1.0-11', {
+        'checksums': ['57385a773220a3aaef5b221a68b2d9c2a94794d4f9e9fc3c1eb9521767debb2a'],
+    }),
+    ('rjson', '0.2.21', {
+        'checksums': ['982b56d35ccc0c7db0b20c1d3eab5f5f47c620309646fdc278ff1cc3433ea2e2'],
+    }),
+    ('seqinr', '4.2-36', {
+        'checksums': ['931a62a091a7aaaa5efadb1fe85f29e861e2506b75710ba3a6be9b58cb14b225'],
+    }),
+    ('LearnBayes', '2.15.1', {
+        'checksums': ['9b110858456523ca0b2a63f22013c4e1fbda6674b9d84dc1f4de8bffc5260532'],
+    }),
+    ('gmodels', '2.19.1', {
+        'checksums': ['bb57b83274dcc6c62eeb0d0b041d81ed19daca927bcd3872c4667ccfe3e9888d'],
+    }),
+    ('expm', '0.999-9', {
+        'checksums': ['83a1234aca8d3c4f7c6a1101a8ce8b56aaca924e7283880fa2667b38948ffed4'],
+    }),
+    ('terra', '1.7-78', {
+        'checksums': ['658956b79d8a1371aefdf7300316f1756b58d436ba549ade012307684b2d4b7e'],
+    }),
+    ('raster', '3.6-26', {
+        'checksums': ['c65777225a46ada699e70098f54c60cf191d15e454fac9440aca439a4dbd5592'],
+    }),
+    ('spData', '2.3.1', {
+        'checksums': ['8c377f2123b7b274c5ca0de656ccd30aaba1b5b245be58a842395311ecc70075'],
+    }),
+    ('units', '0.8-5', {
+        'checksums': ['d95e80af760b053e10a1e33ce1f0c1280a84e84bd4b1d9c34d1fe9fc153603b1'],
+    }),
+    ('classInt', '0.4-10', {
+        'checksums': ['c3561eafbc493ac02840191d4f1e4d2ef437ca8eb20f41fc5eca28f00ee42b8b'],
+    }),
+    ('vegan', '2.6-6.1', {
+        'checksums': ['7d2a5e700a6639bef203d6e35dfe6e8cc1dd7440957334317b61a9dafbb90b60'],
+    }),
+    ('rncl', '0.8.7', {
+        'checksums': ['1d876e4f5f2b8a24cc3ea1002c29eedbc0ca96011b0fa15b085e5b75cfc7993a'],
+    }),
+    ('XML', '3.99-0.16.1', {
+        'checksums': ['a30ae3a3e0d559a2b84b118aa185ef9c42adcf644bf042569f6d192762d2eec4'],
+    }),
+    ('reshape', '0.8.9', {
+        'checksums': ['791178b3b5f30c166ebf5910a5ab1c67b54e7023b10b6c2e2ddd1cc02a1e4048'],
+    }),
+    ('triebeard', '0.4.1', {
+        'checksums': ['192f2fef6341e43bd56ef4f9841e813e07be990f4ffcf38c5606259630efe0f7'],
+    }),
+    ('urltools', '1.7.3', {
+        'checksums': ['6020355c1b16a9e3956674e5dea9ac5c035c8eb3eb6bbdd841a2b5528cafa313'],
+    }),
+    ('httpcode', '0.3.0', {
+        'checksums': ['593a030a4f94c3df8c15576837c17344701bac023ae108783d0f06c476062f76'],
+    }),
+    ('crul', '1.4.2', {
+        'checksums': ['405c77f191f30ffdbf8c05542ff5dff61059e9c731d2dc5ff0bfccb616314147'],
+    }),
+    ('bold', '1.3.0', {
+        'checksums': ['0ead11d4386c4c0cd578d3a956f809db2001e387e449a431b4ad503f3da38f5f'],
+    }),
+    ('rredlist', '0.7.1', {
+        'checksums': ['92a10c37a211dc19b41b93f9ceb13d7ce1c3d3a7290cbba4c1688d944353ae85'],
+    }),
+    ('rentrez', '1.2.3', {
+        'checksums': ['fb256597ebe7780e38bef9c4c2626b3feacd60c7a5a29fc6a218cf0d8d132f74'],
+    }),
+    ('rotl', '3.1.0', {
+        'checksums': ['12baeef897c835d20a4d84cf058a3d3d09b89202f7ec0325140cb7754ab5635c'],
+    }),
+    ('solrium', '1.2.0', {
+        'checksums': ['7ec64199497cc69f542fded955b709fc548cf8e2734c9db0f4a99a0ea67ca49b'],
+    }),
+    ('ritis', '1.0.0', {
+        'checksums': ['327b221872408b1f0fe0cce953685535b66d2fa5d6cac628e1142a26e4856136'],
+    }),
+    ('worrms', '0.4.3', {
+        'checksums': ['32b918f921a318078712ce6647e1b19cd7a9c550df8c37cb3d839277431fb9ad'],
+    }),
+    ('natserv', '1.0.0', {
+        'checksums': ['30f90f938e963191ef19b1433db1e265f67d8efe29c92a1d3603c3dc9a03d5c8'],
+    }),
+    ('WikipediR', '1.7.1', {
+        'checksums': ['6ee69561f304edf13c67b4cabca3688eaf1b8b10acf82257c39b351aa91bb222'],
+    }),
+    ('ratelimitr', '0.4.1', {
+        'checksums': ['2b21e4574521c5336feeb3041eaf096bde7857b140049cdeb6ec97dc652aa71b'],
+    }),
+    ('rex', '1.2.1', {
+        'checksums': ['af42e649c06e4bbdba94d5a1870a7e8347903571c90cd5e5ca40f52307a3bfd6'],
+    }),
+    ('WikidataQueryServiceR', '1.0.0', {
+        'checksums': ['0e14eec8471a72227f800b41b331cfc49a94b4d4f49e68936448ebbae0b281ae'],
+    }),
+    ('pbapply', '1.7-2', {
+        'checksums': ['aeed8c8c308c7e3827daf10b01b8ed4b88c1d68cea57d72d67c600c0ce0dae13'],
+    }),
+    ('WikidataR', '2.3.3', {
+        'checksums': ['3da74b0584b8141a1b61b4d8f58e53c0e46524d811b1642bcc01fb7fd6180888'],
+    }),
+    ('wikitaxa', '0.4.0', {
+        'checksums': ['ba872853af59fdc8f1121d6e205f15e5bf4f2ec5ad68cd5755a423fa783bf7fc'],
+    }),
+    ('phangorn', '2.11.1', {
+        'checksums': ['10096ecae03e118aa4dbc60d9866175fad4849c948e004cf10c3868e3feed420'],
+    }),
+    ('uuid', '1.2-0', {
+        'checksums': ['73710a14f812e34e891795b8945ea213f15ebcaf00b464b0e4b3fa09cf222afd'],
+    }),
+    ('conditionz', '0.1.0', {
+        'checksums': ['ccd81e4f2534d29cddf44cf697f76ff01417cbeb22001a93477edc61cdd35646'],
+    }),
+    ('taxize', '0.9.100', {
+        'checksums': ['e2e578fc45eb5d1306332892c67535fa4bc32d63129532df2c6cde393993cd29'],
+    }),
+    ('RNeXML', '2.4.11', {
+        'checksums': ['246913cbb0e816401bb8e37dda20646202547f5cc8379c9dadf832f61d6cfd46'],
+    }),
+    ('phylobase', '0.8.12', {
+        'checksums': ['9b81ca60dc6215e74b720880cc2db3abc1f7e6d8785ea7d7df95a950f0778f20'],
+    }),
+    ('magick', '2.8.3', {
+        'checksums': ['932b522d2e9199f50f391266b7f7cb22ca20ca8d5cedbeff12113f5cb445c079'],
+    }),
+    ('animation', '2.7', {
+        'checksums': ['88418f1b04ec785963bad492f30eb48b05914e9e5d88c7eef705d949cbd7e469'],
+    }),
+    ('bigmemory.sri', '0.1.8', {
+        'checksums': ['029a4ed24aa17636a20b83857d55fe6a9283acb8b647cbc75280dea8ec987771'],
+    }),
+    ('bigmemory', '4.6.4', {
+        'checksums': ['fe3f576c0d87fd2820c0f436a202261dff353e50e5b86dd9c80fdea7ad60002d'],
+    }),
+    ('calibrate', '1.7.7', {
+        'checksums': ['713b09b415c954e1ef5216088acd40621b0546c45afbb8c2c6f118ecb5cd6fa6'],
+    }),
+    ('clusterGeneration', '1.3.8', {
+        'checksums': ['0f842256582ab41bcd00ee08ea6d7e231ff362fe0156a53347873e9636f73a70'],
+    }),
+    ('dismo', '1.3-14', {
+        'checksums': ['67a0f2e95562dd2aa612d52dfffab86985b52591a5ed7891b58b26667b394cd7'],
+    }),
+    ('extrafontdb', '1.0', {
+        'checksums': ['faa1bafee5d4fbc24d03ed237f29f1179964ebac6e3a46ac25b0eceda020b684'],
+    }),
+    ('Rttf2pt1', '1.3.12', {
+        'checksums': ['0b4b7a303990369a6944de817b6bd220b400942fcabf42c04fb5b56f1b40a583'],
+    }),
+    ('extrafont', '0.19', {
+        'checksums': ['4e8f90152df13fc5dee573222a26b4d66553493fdf6af1c7777e59521ccdab8d'],
+    }),
+    ('fields', '15.2', {
+        'checksums': ['1f270f2331522ef93e04a8b199dfab17995ac02aaa0a68eeca90fef55f6cad3d'],
+    }),
+    ('shapefiles', '0.7.2', {
+        'checksums': ['4bfa4094c1052c1b1918b1670798f8b4e53f771cfdf9cb8c04bd00a856674d0f'],
+    }),
+    ('fossil', '0.4.0', {
+        'checksums': ['37c082fa15ebae89db99d6071b2bb2cad6a97a0405e9b4ef77f62a8f6ad274c1'],
+    }),
+    ('optimParallel', '1.0-2', {
+        'checksums': ['0f9bc62c23d9005130f2892bf5eaecf308fa48a727bdd5e19b7dcd1d95f30a9d'],
+    }),
+    ('DEoptim', '2.2-8', {
+        'checksums': ['631eabdcf26ec25a759651f699db1971beca3ae193c7fbd1c63a78248fdbf54c'],
+    }),
+    ('phytools', '2.3-0', {
+        'checksums': ['973020a695be3fef94a37d7d6732d9352b66e44d30feb554d267b6aeb646d081'],
+    }),
+    ('geiger', '2.0.11', {
+        'checksums': ['dcc5a0a988439110078867e0aaf09b048e27db7f02e4cbdfe35783611fde3f69'],
+    }),
+    ('webshot', '0.5.5', {
+        'checksums': ['d675913ccac80e0af8ee396f95a24124eae6c42d80aed9f47f7a88218ecbb913'],
+    }),
+    ('shinyjs', '2.1.0', {
+        'checksums': ['7ec20cbf1b1fd7a32d85a56dfc0df8b5f67c828d241da400a21d893cb37ea9c5'],
+    }),
+    ('manipulateWidget', '0.11.1', {
+        'checksums': ['5b73728d7d6dcc32f32d861375074cd65112c03a01e4ee4fa94e21b063fdefb6'],
+    }),
+    ('rgl', '1.3.1', {
+        'checksums': ['9fea7b59dd7fef9bbd783c745d68325ec753ef412699d168bb6c664a56506d49'],
+    }),
+    ('Rtsne', '0.17', {
+        'checksums': ['3aae6814d6c6d406785145f07374135652f2b26a58690dfd4bfbc8365dc5590b'],
+    }),
+    ('labdsv', '2.1-0', {
+        'checksums': ['99da92515e9aa49ea7f3df7e301ef714c57054a3838139cd3fd798531d625cd1'],
+    }),
+    ('stabs', '0.6-4', {
+        'checksums': ['f8507337789f668e421a6ee7b11dd5ea331bf8bff0f9702dd1b93f46c2f3c1d9'],
+    }),
+    ('modeltools', '0.2-23', {
+        'checksums': ['6b3e8d5af1a039db5c178498dbf354ed1c5627a8cea9229726644053443210ef'],
+    }),
+    ('strucchange', '1.5-3', {
+        'checksums': ['cac6b4028f68cc8d39202377161d0f7f72ea229b552a5c35769053ab89f90f86'],
+    }),
+    ('TH.data', '1.1-2', {
+        'checksums': ['47f94eb57b6fcef42efa30824c1356bf10529c4b94b0d0acdb787b434dddde73'],
+    }),
+    ('multcomp', '1.4-25', {
+        'checksums': ['9dfa7821a699e7b6fc99f2b8bf6bc5fecf6e3d83ece814882b5c8ed8faffd282'],
+    }),
+    ('libcoin', '1.0-10', {
+        'checksums': ['3023e0495d0789765bdf04c0ef0990a57b48fefa322c55f20e250d2d70d67eaf'],
+    }),
+    ('coin', '1.4-3', {
+        'checksums': ['8a6302dbf3ef570cd9f69ce7b6cd3d3b928dc776f840bbd767af132e0080b974'],
+    }),
+    ('party', '1.3-15', {
+        'checksums': ['c0e27c2e215526ba67879570fe4ac8c1fad34128e3785e26b4b86307cfad2217'],
+    }),
+    ('inum', '1.0-5', {
+        'checksums': ['e696b7e0b31b3bbf405112e60691b6a72fedcaa02e08ee517c59f6bf9cd36bbd'],
+    }),
+    ('partykit', '1.2-20', {
+        'checksums': ['63509aa3ed2d7417ad284c037cef66bc837fdb7a97967957e79b9fee8ed2e0da'],
+    }),
+    ('mboost', '2.9-10', {
+        'checksums': ['e713a47faa94424b497685eb3b1df3d376be5f126b48e3f834b6b897f0d0b08d'],
+    }),
+    ('msm', '1.7.1', {
+        'checksums': ['d134782b966eed33742819595119ab1a61bec4416cc3fa7630a0f34c4e7f785b'],
+    }),
+    ('nor1mix', '1.3-3', {
+        'checksums': ['97bfd0f8c847fa68bf607aaa465845a34ac8a7a262315073026a6a1937dd076e'],
+    }),
+    ('np', '0.60-17', {
+        'checksums': ['d97957cb234ec2e570fc2d02d305eadff3d71939484b3d1054ed8b67a3427f36'],
+    }),
+    ('polynom', '1.4-1', {
+        'checksums': ['bc1edb7bb16c8b299103f80a52ab8c5fc200cd07a9056578c1f672e9f5019278'],
+    }),
+    ('polspline', '1.1.25', {
+        'checksums': ['2943fc4cd922300afeaa58e6a0e4c21e5a0f7255e6367c7ea6ad136fce1e9ba3'],
+    }),
+    ('rms', '6.8-1', {
+        'checksums': ['9d38545749430763c242bae1181ce24a7f6f6b244e4c69348ab200b83925596a'],
+    }),
+    ('RWekajars', '3.9.3-2', {
+        'checksums': ['16e6b019aab1646f89c5203f0d6fc1cb800129e5169b15aaef30fd6236f5da1a'],
+    }),
+    ('RWeka', '0.4-46', {
+        'checksums': ['660555781703c19b994c9dcfc9e7d8312c30b02539f38cd3948bfc33d9f94b67'],
+    }),
+    ('slam', '0.1-50', {
+        'checksums': ['7899bf3266c204ecccefc1878f96940b117d4503af128f4fbc50fc409163f8bd'],
+    }),
+    ('tm', '0.7-13', {
+        'checksums': ['e5266ce245da9ad53f95630d737ef30b07981c59fb793b5010486a57eb671db4'],
+    }),
+    ('leaps', '3.2', {
+        'checksums': ['a0d6bebb676e5cdc0ecf3e3a07163ce0d60b6fe72a083d91f0413e11a8a96fad'],
+    }),
+    ('cNORM', '3.0.4', {
+        'checksums': ['d766bfd86f8a871b972b9b9cd952fa2e5bb7c0fe6903b3f2c15eccf4612a17e2'],
+    }),
+    ('weights', '1.0.4', {
+        'checksums': ['efbe65e8a9d05824a86095d45ed62ce24d82101d4ca3b94828d443e08e83ccba'],
+    }),
+    ('TraMineR', '2.2-10', {
+        'checksums': ['8b1689fe6a0f4ff3493e6b430592705be34f12ac6a24aae1735e5262e50e85a6'],
+    }),
+    ('chemometrics', '1.4.4', {
+        'checksums': ['fd0edb1ebe321ff7677d0a668d7dfc79a7cd55f408a53d1f13db4cf6347aa881'],
+    }),
+    ('FNN', '1.1.4', {
+        'checksums': ['db4db5a348c6051fe547193c282b6e5cc839f68f51e0afccf4939f35e9a2fc27'],
+    }),
+    ('miscTools', '0.6-28', {
+        'checksums': ['bd4c2f2120948af538f9874df1ac745ff162817d0e53756f52f863eb4f593b21'],
+    }),
+    ('maxLik', '1.5-2.1', {
+        'checksums': ['d054c7626d0b4e03a5d5beecb7a39e60785322a146c34b2e1ee9f7939183925d'],
+    }),
+    ('gbRd', '0.4.12', {
+        'checksums': ['48cd1d2a845f4b54c307473d2fa07a4ef6a644272f91c6a953844e66cd832338'],
+    }),
+    ('rbibutils', '2.2.16', {
+        'checksums': ['9c7c0fba47f63b1749005311c7174b40e72d95c863a67b736a84b8ff375a2aaf'],
+    }),
+    ('Rdpack', '2.6', {
+        'checksums': ['6a75d98c651778358732429258056a327def2be4d2af244a8daaac5b500c220a'],
+    }),
+    ('dfidx', '0.0-5', {
+        'checksums': ['37521940b35d62773a4d127c94148aadf207f400a686f2212a22d96e53086a0a'],
+    }),
+    ('mlogit', '1.1-1', {
+        'checksums': ['6f3ea97db410be929a3078422f3d354d2f17855a21bbdc7c2c09d901e233d143'],
+    }),
+    ('getopt', '1.20.4', {
+        'checksums': ['87d36cbe6dba41dbc1d78d845210266cdd08c7440d977d738a6e45db14221e8b'],
+    }),
+    ('gsalib', '2.2.1', {
+        'checksums': ['3da3a4b959142a0d694a843e39143bfce82a6de197c6cc92650a28ac05f3bf90'],
+    }),
+    ('optparse', '1.7.5', {
+        'checksums': ['0cc917505780786e69b8ceca4b3840ed7b0c011495108ec05af3871965415712'],
+    }),
+    ('labelled', '2.13.0', {
+        'checksums': ['9e2e82a42343b62f8a476d4dd7b13e9ffb3ee2c4e23bdf2cd29ef25b3dffa237'],
+    }),
+    ('R.cache', '0.16.0', {
+        'checksums': ['7853409161571a790e0383f64f99e4eae43201a0ed7146d2baf157741a509291'],
+    }),
+    ('styler', '1.10.3', {
+        'checksums': ['adb9c22111a8669bdce6d4a5c09e0ad353e07c3488373484a258028203bfda41'],
+    }),
+    ('questionr', '0.7.8', {
+        'checksums': ['af72e59fe652c6063282a7e5b0f487993b9361cc9ed052a632d64a5a6db76ba9'],
+    }),
+    ('klaR', '1.7-3', {
+        'checksums': ['d36c041c017cdb5ba3dbf7fb61d5ce3908d8e780eb2912fc99471394fcb8e3e5'],
+    }),
+    ('neuRosim', '0.2-14', {
+        'checksums': ['7fc264bb86f1edd7b39a2472330bbabb34eb6dfb722db016a6ee60444ebfafd9'],
+    }),
+    ('locfit', '1.5-9.10', {
+        'checksums': ['4c20661814993a87ca435f42b0814bacb87c5a9ccc2ff55e4cae718cb176ac06'],
+    }),
+    ('patchwork', '1.2.0', {
+        'checksums': ['cc31ea13560c424de9bfe2287d926a7d9e6cc8da2d5561402bb145b4f51b68a1'],
+    }),
+    ('broom.helpers', '1.15.0', {
+        'checksums': ['ec5c58522cb03478ce6fb42533cc00f11eb18d7f7810f62b83cbdc719a98a93e'],
+    }),
+    ('ggstats', '0.6.0', {
+        'checksums': ['f80aaa229f542cb18174b9ab82b0026c6bd3331f22bf2662712ab6af480b6d80'],
+    }),
+    ('GGally', '2.2.1', {
+        'checksums': ['8bb326665936a63f6eef92a2af1a11d1fae78dbd28d6980608d2b38ee1f586c6'],
+    }),
+    ('beanplot', '1.3.1', {
+        'checksums': ['49158aee3449108fd857ef43fb777f55a2b975b350a4a710788996ad19dd15ad'],
+    }),
+    ('clValid', '0.7', {
+        'checksums': ['037da469891462021eb177f9c9e18caefa8532f08c68fb576fae1668a1f451a1'],
+    }),
+    ('DiscriMiner', '0.1-29', {
+        'checksums': ['5aab7671086ef9940e030324651976456f0e84dab35edb7048693ade885228c6'],
+    }),
+    ('ellipse', '0.5.0', {
+        'checksums': ['cde8553973ce2cc04324318b3df13890d585987171fedfe2efbf1430f82cc2f3'],
+    }),
+    ('pbkrtest', '0.5.2', {
+        'checksums': ['8e79adf035a0fcf3c82145ad55847497379e009f7be880ba3007ebeb2e69b6e3'],
+    }),
+    ('carData', '3.0-5', {
+        'checksums': ['02e77159b33e3afb8cd9cfab11cf5a996a93175f924b07d991ce44bc6e16451a'],
+    }),
+    ('maptools', '1.1-8', {
+        'checksums': ['5e8579e3f559161935f1dde622ece703eefa2a28a677ce553d7f27611e66e0f7'],
+    }),
+    ('openxlsx', '4.2.5.2', {
+        'checksums': ['ee7089e7e5832ef22ee0d0eebf7cca5096ce23afb2bcdb58700be62526fc9b67'],
+    }),
+    ('rematch', '2.0.0', {
+        'checksums': ['15daf7bf2907aef8503635bc8631fce9fd75248a1fc2496825588c4bdf785c26'],
+    }),
+    ('cellranger', '1.1.0', {
+        'checksums': ['5d38f288c752bbb9cea6ff830b8388bdd65a8571fd82d8d96064586bd588cf99'],
+    }),
+    ('readxl', '1.4.3', {
+        'checksums': ['7efebbcdefeb8523633db62b3eeb6ea2e4e81e3d010d8b2adb134011c09a5948'],
+    }),
+    ('writexl', '1.5.0', {
+        'checksums': ['e253dc58f00abf51e9b727ae132e8b301e359fb23df0afc40c3ebec3fb096dce'],
+    }),
+    ('rio', '1.1.1', {
+        'checksums': ['3ef1ef7982146eebcfa17236e26544640248009c660de5d796fbf6b6496b9b52'],
+    }),
+    ('car', '3.1-2', {
+        'checksums': ['89263491977ac8e9406b2f4b1638bf06c7ddd1b0e0e3ecda4be61420474674c8'],
+    }),
+    ('flashClust', '1.01-2', {
+        'checksums': ['48a7849bb86530465ff3fbfac1c273f0df4b846e67d5eee87187d250c8bf9450'],
+    }),
+    ('ggrepel', '0.9.5', {
+        'checksums': ['d1e600e56c2ad345961ed23f30f04b81c631ff94bd6762a260c62e0206cf8caa'],
+    }),
+    ('DT', '0.33', {
+        'checksums': ['e145dadb1ce3db7c837f4313a8b5615b5b8ae63063ec2df93e528529717b27b8'],
+    }),
+    ('estimability', '1.5.1', {
+        'checksums': ['3ca6b96a39fd8877e8636f94d20f34308b7296c1376c646703d27df8591644e9'],
+    }),
+    ('emmeans', '1.10.2', {
+        'checksums': ['60be64c27a9d1660b76a114762c1c9fb8063415e6a87510d6218ef686e3b8522'],
+    }),
+    ('multcompView', '0.1-10', {
+        'checksums': ['38f249b22758c9f727b1656d1a08c6022a06a1ea319364ff680147d64598ad8a'],
+    }),
+    ('FactoMineR', '2.11', {
+        'checksums': ['32c26b42cb4dd8d7a8c845f1e8562fa0e3ebded19d3c1284c3504df09974f063'],
+    }),
+    ('flexclust', '1.4-2', {
+        'checksums': ['0c4720d691e36091cedafa26ee1f0ddc7af931168096df00b9bf6d64fdd35a55'],
+    }),
+    ('flexmix', '2.3-19', {
+        'checksums': ['adf5a40cbb6d45e3652c1666cb3ccdb9654e501fd685c091cad0686e62bc12e9'],
+    }),
+    ('prabclus', '2.3-3', {
+        'checksums': ['005d000a9ac357e670de26e5b8fc4ddb1617351275fa43bf6d2e88b8774358c1'],
+    }),
+    ('diptest', '0.77-1', {
+        'checksums': ['224eae00f483ce0fb131719065667227417cc98ad2beda55bfd5efe2bb612813'],
+    }),
+    ('trimcluster', '0.1-5', {
+        'checksums': ['9239f20e4a06ac2fa89e5d5d89b23a45c8c534a7264d89bede8a35d43dda518b'],
+    }),
+    ('fpc', '2.2-12', {
+        'checksums': ['555996b4c7e78a28067df25ac657b5065ec79b6b2cd76080382c2d5b43104787'],
+    }),
+    ('BiasedUrn', '2.0.12', {
+        'checksums': ['29b3b596431c5364e3be9aae2068adb44a205de31c66ec3fa1ef06a4ab8c5792'],
+    }),
+    ('TeachingDemos', '2.13', {
+        'checksums': ['f80eb952b7d1a0cde3bed8152f9c4e9eceaa3f635209b2af9a11e785e8c0fbcc'],
+    }),
+    ('kohonen', '3.0.12', {
+        'checksums': ['40944b916aa228d90862301beb9d93a521e6d98ba23c147d1bd9dded04ef0ca1'],
+    }),
+    ('base64', '2.0.1', {
+        'checksums': ['4d22687c0195c2049e0af2c613b1ebcb908037010ad6e550bf47d69e842535f1'],
+    }),
+    ('doRNG', '1.8.6', {
+        'checksums': ['5032ade083f1f9841ac2e8d4426faa07f189c25c0c338fa155c5dadbe5507de2'],
+    }),
+    ('nleqslv', '3.3.5', {
+        'checksums': ['1298172d2fe67d8d6b742ce7e792f6b897f081da5c94d34f14970ab531f04b3a'],
+    }),
+    ('Deriv', '4.1.3', {
+        'checksums': ['dbdbf5ed8babf706373ae33a937d013c46110a490aa821bcd158a70f761d0f8c'],
+    }),
+    ('RGCCA', '3.0.3', {
+        'checksums': ['48c327f99bae71050acb30b217720d73bf5c40f35af1a3b3b5e4ed118b315701'],
+    }),
+    ('pheatmap', '1.0.12', {
+        'checksums': ['579d96ee0417203b85417780eca921969cda3acc210c859bf9dfeff11539b0c1'],
+    }),
+    ('pvclust', '2.2-0', {
+        'checksums': ['7892853bacd413b5a921006429641ad308a344ca171b3081c15e4c522a8b0201'],
+    }),
+    ('RCircos', '1.2.2', {
+        'checksums': ['5bbdc3baff2d22a8922685af02b2af07541a1bcf1914abd9c166850b4c550afc'],
+    }),
+    ('lambda.r', '1.2.4', {
+        'checksums': ['d252fee39065326c6d9f45ad798076522cec05e73b8905c1b30f95a61f7801d6'],
+    }),
+    ('futile.options', '1.0.1', {
+        'checksums': ['7a9cc974e09598077b242a1069f7fbf4fa7f85ffe25067f6c4c32314ef532570'],
+    }),
+    ('futile.logger', '1.4.3', {
+        'checksums': ['5e8b32d65f77a86d17d90fd8690fc085aa0612df8018e4d6d6c1a60fa65776e4'],
+    }),
+    ('VennDiagram', '1.7.3', {
+        'checksums': ['e7c2475f7613241787e6c85bd03315e4fd88413ccbbb735959756a8c2eeb8c46'],
+    }),
+    ('xlsxjars', '0.6.1', {
+        'checksums': ['37c1517f95f8bca6e3514429394d2457b9e62383305eba288416fb53ab2e6ae6'],
+    }),
+    ('xlsx', '0.6.5', {
+        'checksums': ['378c5ed475a3d7631ea1ea13e0a69d619c1a52260922abda42818752dbb32107'],
+    }),
+    ('uroot', '2.1-3', {
+        'checksums': ['30f623d119299c8020c81c577d83e825811e96ec694ee1e2522fcbe02fed4c2f'],
+    }),
+    ('forecast', '8.23.0', {
+        'checksums': ['ffc3d41138f498fb286f0ebfeb72d15f9f7a8e953abf3c351ebf95fc188a1880'],
+    }),
+    ('fma', '2.5', {
+        'checksums': ['400dea4d2b6e73ed686d901fbab1b4f930dfcdd67fbd0bb3abc34a707656cf78'],
+    }),
+    ('expsmooth', '2.3', {
+        'checksums': ['ac7da36347f983d6ec71715daefd2797fe2fc505c019f4965cff9f77ce79982a'],
+    }),
+    ('fpp', '0.5', {
+        'checksums': ['9c87dd8591b8a87327cae7a03fd362a5492495a96609e5845ccbeefb96e916cb'],
+    }),
+    ('tensor', '1.5', {
+        'checksums': ['e1dec23e3913a82e2c79e76313911db9050fb82711a0da227f94fc6df2d3aea6'],
+    }),
+    ('polyclip', '1.10-6', {
+        'checksums': ['3c2f13edabdd9cd2612a60afec9ba447b3dd5a4109dd066d7870411d032f8b63'],
+    }),
+    ('goftest', '1.2-3', {
+        'checksums': ['3a5f74b6ae7ece5b294781ae57782abe12375d61789c55ff5e92e4aacf347f19'],
+    }),
+    ('spatstat.utils', '3.0-5', {
+        'checksums': ['eb98665f20fb007d06575ed3357cbaaeaf4ed5bb201238139c78bbc1ae23f596'],
+    }),
+    ('spatstat.data', '3.1-2', {
+        'checksums': ['9b9b416303b8040f723400f3dc454cda75cff1d958660767e7b824503b490b77'],
+    }),
+    ('spatstat.geom', '3.2-9', {
+        'checksums': ['a7337166481366ff301c9585636e162d94c8593511a36ae33477966720c9d517'],
+    }),
+    ('spatstat.sparse', '3.1-0', {
+        'checksums': ['63be5dc5818339b878a14a39815dab730b28029d51bac5233e88f5e2464bbbe9'],
+    }),
+    ('spatstat.random', '3.2-3', {
+        'checksums': ['e052a33e90b097bc160c687d4927e17d01a1c282f503205d322133464f3934a7'],
+    }),
+    ('spatstat.core', '2.4-4', {
+        'checksums': ['e38c39efe8b14d6e8fdbee8dd870b90c52f78ea571ab7988fd3685f48347d13b'],
+    }),
+    ('spatstat.explore', '3.2-7', {
+        'checksums': ['4ee4d918c7998d44995879cd870987b861918d851d29a09bad066d4c9907e420'],
+    }),
+    ('spatstat.model', '3.2-11', {
+        'checksums': ['700dc1225d110ccd88e5c640935d551a67389e928a4d2726443737665ec47643'],
+    }),
+    ('spatstat.linnet', '3.1-5', {
+        'checksums': ['a7d03c037b8c918977527a9b00b75fb87048222d10473319d132b1d67433f7a3'],
+    }),
+    ('spatstat', '3.0-8', {
+        'checksums': ['c2042e7b68297a479338b765ca4ae70bed2730351f8e79a1697d1d1b4c90103e'],
+    }),
+    ('pracma', '2.4.4', {
+        'checksums': ['1a4ef3af2197f999dbaa614bf5a70f09ec463d8c91feb5aa0d995de24ec6ba7f'],
+    }),
+    ('RCurl', '1.98-1.14', {
+        'checksums': ['eead278694471dfa9bd2f256d229eebed782e71dc1c734fb457ec35377f303cf'],
+    }),
+    ('bio3d', '2.4-4', {
+        'checksums': ['5654eac10d33e4235ef89292e3b99006d8812b6bfaaa3d6fb540312160fd9de9'],
+    }),
+    ('AUC', '0.3.2', {
+        'checksums': ['836b25b654a82f6ab69b86be95acc22a214da0ad06d71eab787ae1ebe721ae1f'],
+    }),
+    ('interpretR', '0.2.5', {
+        'checksums': ['dd8fa4a6b07d8a43b980e1df2f112c1915f93ca9d53cae0f0307a8ce00946c23'],
+    }),
+    ('cvAUC', '1.1.4', {
+        'checksums': ['48b4a3c34e9beb63239e9c7372dd125fe87648262ad5490e0bee2a1f14285ed4'],
+    }),
+    ('SuperLearner', '2.0-29', {
+        'checksums': ['236b03f969f4880680abb7f818bbbd92926ac3cb30b55560e3ee4d25d1572b3c'],
+    }),
+    ('mediation', '4.5.0', {
+        'checksums': ['210206618787c395a67689be268283df044deec7199d9860ed95218ef1e60845'],
+    }),
+    ('CVST', '0.2-3', {
+        'checksums': ['efa296230395f323c2a398a7b386e3a88e75a5b9b645307459d0b7c14d03f32d'],
+    }),
+    ('DRR', '0.0.4', {
+        'checksums': ['93e365a4907e301ae01f7d943e6bdcda71ef23c51a4759ba3c94bcf842d4e0f8'],
+    }),
+    ('dimRed', '0.2.6', {
+        'checksums': ['9a7eb14781f01a12e26e7b26a91c8edaca7d824b9c1ffe74c81837098d9bf417'],
+    }),
+    ('ddalpha', '1.3.15', {
+        'checksums': ['0c2794a4e88cef44d96dc980ec2f091d66b3c83995760297b623e5285878feed'],
+    }),
+    ('RcppRoll', '0.3.0', {
+        'checksums': ['cbff2096443a8a38a6f1dabf8c90b9e14a43d2196b412b5bfe5390393f743f6b'],
+    }),
+    ('rlist', '0.4.6.2', {
+        'checksums': ['ebde658d897c8a27a90ebb892b9e2bad15e2ad75557a7352fb08cbb5604e0997'],
+    }),
+    ('ConsRank', '2.1.4', {
+        'checksums': ['c213c6008fcb617a2144d75b41b25520ffadcf38686cc5050e10ce1363ac3000'],
+    }),
+    ('adabag', '5.0', {
+        'checksums': ['ec58756fda2e64753d21e28d9e27ed34f28020045b199a58dcea06a3e2c3d60e'],
+    }),
+    ('parallelMap', '1.5.1', {
+        'checksums': ['c108a634a335ed47b0018f532a52b032487e239c5061f939ba32355dfefde7e1'],
+    }),
+    ('ParamHelpers', '1.14.1', {
+        'checksums': ['0450ff8489b0d4d0842130f6a9713ede97da936d7909c43d43587bf2d5a01a21'],
+    }),
+    ('ggvis', '0.4.9', {
+        'checksums': ['69b9d184789c90aedd2f336d43033a8b710a16b052580bf9e7ce229ac25ba12f'],
+    }),
+    ('mlr', '2.19.2', {
+        'checksums': ['85e67049f1067a7eae0f0e5b5c4e4e46a25407a17750512220f438a0fa5097c5'],
+    }),
+    ('unbalanced', '2.0', {
+        'checksums': ['9be32b1ce9d972f1abfff2fbe18f5bb5ba9c3f4fb1282063dc410b82ad4d1ea2'],
+    }),
+    ('RSNNS', '0.4-17', {
+        'checksums': ['424557d7326889e09e31e04d2a9b7224bed0bb4aa6f9e5433d7ce4fe04a35afc'],
+    }),
+    ('abc.data', '1.1', {
+        'checksums': ['48d685cf81a6053cce981791570abd27773454d7ff7586c2a563dab7a1cdb07d'],
+    }),
+    ('abc', '2.2.1', {
+        'checksums': ['db52a397a204a0040ec1368ae217cf7b0d8e99e2567927dbe3ae89f93d1de598'],
+    }),
+    ('lhs', '1.1.6', {
+        'checksums': ['e37fce44efe6a371677ba2f72f9e1e48270a0fdc60872d05def89270586cd23f'],
+    }),
+    ('tensorA', '0.36.2.1', {
+        'checksums': ['06588261fe7dff6a8edafe2b9d436b39a3b46c754f2ed327ae6322561a617db7'],
+    }),
+    ('EasyABC', '1.5.2', {
+        'checksums': ['326c92e003866728729dc61473f168c3663106b1229e8513abd7ce520c18689c'],
+    }),
+    ('git2r', '0.33.0', {
+        'checksums': ['1855b68d0e22566f1c255fdcb8e13282a2bebf55cbc804a8591dc8047f0e1895'],
+    }),
+    ('clisymbols', '1.2.0', {
+        'checksums': ['0649f2ce39541820daee3ed408d765eddf83db5db639b493561f4e5fbf88efe0'],
+    }),
+    ('covr', '3.6.4', {
+        'checksums': ['2b6204036510c629d0b1d58daaee34d4e38baf54164f8d4c9afd6d6b1fb1862a'],
+    }),
+    ('Rook', '1.2', {
+        'checksums': ['c79ae4b5164daffd4e7cf74bd23c1b08a3948bf343dfe9570d57f39cbf8e5f62'],
+    }),
+    ('Cairo', '1.6-2', {
+        'checksums': ['6b6f4c6f93178a1295860a9dc6dc45e60fec70f684d5c8d0b59baf5b8dd44d62'],
+    }),
+    ('RMTstat', '0.3.1', {
+        'checksums': ['bb4827d76106f5377044cd2b230208881eb714cae65f512f4b95988d9b162ae4'],
+    }),
+    ('Lmoments', '1.3-1', {
+        'checksums': ['7c9d489a08f93fa5877e2f233ab9732e0d1b2761596b3f6ac91f2295e41a865d'],
+    }),
+    ('distillery', '1.2-1', {
+        'checksums': ['4b88f0b34e472b9134ad403fb32283424f1883a5943e52c55f1fe05995efb5fa'],
+    }),
+    ('extRemes', '2.1-4', {
+        'checksums': ['cea42cf67e7a2d99451a2a3541bab41c1e64c86b45de37fa0119c49f7083b78a'],
+    }),
+    ('tkrplot', '0.0-27', {
+        'checksums': ['c99211919414400b0f579e1354407f2e154cfe85533d324bcf9c68172c2772a5'],
+    }),
+    ('misc3d', '0.9-1', {
+        'checksums': ['a07bbb0de153e806cd79675ed478d2d9221cff825654f59a71a9cf61f4293d65'],
+    }),
+    ('multicool', '1.0.1', {
+        'checksums': ['bd72de1fbd7ea32018d6af09ac2af80871ebe26bf9dfdf1ba53f87e6cff56c1f'],
+    }),
+    ('plot3D', '1.4.1', {
+        'checksums': ['db6df74844dda9177f2be024762b2f0e63182916e987a09480514d078d55d1f4'],
+    }),
+    ('plot3Drgl', '1.0.4', {
+        'checksums': ['6d87a9a32aba3aa64f751268cabd14dbd3e0eca2bd5f0a4b11366cd1e2f51bdd'],
+    }),
+    ('OceanView', '1.0.7', {
+        'checksums': ['2af53bf28ce55b740a5612e742bf6410601e592d2f231c6041ad2abe722dc168'],
+    }),
+    ('ks', '1.14.2', {
+        'checksums': ['f19130476cfafec26bba102b66ecbaeb80a9312c62d55eeec54d1aec75803fcb'],
+    }),
+    ('logcondens', '2.1.8', {
+        'checksums': ['f139206e47d1077ffcb39248450c1d7ce2ac892cb9264dd0e1ace92532162a00'],
+    }),
+    ('Iso', '0.0-21', {
+        'checksums': ['b6842ae1c7b629ebb63355f50bb2e5d96e5696fa59590807ac6028b6dce28fa6'],
+    }),
+    ('penalized', '0.9-52', {
+        'checksums': ['d8e38e6c4e993c74998ca8f986b4e11e09c0b9971103e1d5c7ebdee75f6d6a21'],
+    }),
+    ('clusterRepro', '0.9', {
+        'checksums': ['940d84529ff429b315cf4ad25700f93e1156ccacee7b6c38e4bdfbe2d4c6f868'],
+    }),
+    ('data.tree', '1.1.0', {
+        'checksums': ['b0b554e9220f7abeb8e40af7617802509bf49aa4b2b58882330cde54c20bad63'],
+    }),
+    ('influenceR', '0.1.5', {
+        'checksums': ['8164e4820f769032fab97c9ca486d33e83309641fcc4875065d8f5a43b20f58c'],
+    }),
+    ('visNetwork', '2.1.2', {
+        'checksums': ['47c99d42fc89e6ae929257b2648d998c5ffed60dff97ad7e47613f5a0c1ddc84'],
+    }),
+    ('downloader', '0.4', {
+        'checksums': ['1890e75b028775154023f2135cafb3e3eed0fe908138ab4f7eff1fc1b47dafab'],
+    }),
+    ('DiagrammeR', '1.0.11', {
+        'checksums': ['e873e3d6e198232408161661001ddcb04c9a56065bb4703c925e538462f4c4df'],
+    }),
+    ('randomForestSRC', '3.2.3', {
+        'checksums': ['8ca24f235f4e0036d6c767e0b7c8597c404b91ab7cd88d4a6a1c3accd46d4f6f'],
+    }),
+    ('sm', '2.2-6.0', {
+        'checksums': ['27a6e3291a572c3d30f25982902ccde5299230061e5dc1a38fb52aaac2561d61'],
+    }),
+    ('pbivnorm', '0.6.0', {
+        'checksums': ['07c37d507cb8f8d2d9ae51a9a6d44dfbebd8a53e93c242c4378eaddfb1cc5f16'],
+    }),
+    ('lavaan', '0.6-18', {
+        'checksums': ['b907cacd6c4a2320138cb2206f17b60acf077453540bcb9cc94659fc9a48df51'],
+    }),
+    ('matrixcalc', '1.0-6', {
+        'checksums': ['0bc7d2f11f62d8b1969474defe27c924a243ccba0c856d585f317f6caa07f326'],
+    }),
+    ('arm', '1.14-4', {
+        'checksums': ['425bcb0afea2efb668d15ed8daa430bb356c62587eba806fd91e37afac1807bd'],
+    }),
+    ('mi', '1.1', {
+        'checksums': ['4d7a9790dbdc675605d70755af9aa80c21a279be5a5d712b22d77465772cc785'],
+    }),
+    ('servr', '0.30', {
+        'checksums': ['43f920161408871a042462b7c3353149a608941253541a19a9ce3408f9882d40'],
+    }),
+    ('rgexf', '0.16.2', {
+        'checksums': ['6ee052b0de99d0c7492366b991d345a51b3d0cc890d10a68b8670e1bd4fc8201'],
+    }),
+    ('sem', '3.1-15', {
+        'checksums': ['ad023b00e6e8eb20d107039caf1008c4b05104c7c69709e59c66fbddbf381316'],
+    }),
+    ('statnet.common', '4.9.0', {
+        'checksums': ['a485dc6e363a993d87336fbd1027adb1cd7b9103447fd63904cae4dc3bfc2dd7'],
+    }),
+    ('network', '1.18.2', {
+        'checksums': ['bf33892db9cabba9cd1597f09ef0e1277d63520a8cebd2d919e0d41fc706a27b'],
+    }),
+    ('rle', '0.9.2', {
+        'checksums': ['803cbe310af6e882e27be61d37d660dbe5910ac1ee1eff61a480bcf724a04f69'],
+    }),
+    ('sna', '2.7-2', {
+        'checksums': ['7b214626967feb9389e743e50b919dd4b00e7436b2355fd068c873c45ac7a7cd'],
+    }),
+    ('glasso', '1.11', {
+        'checksums': ['4c37844b26f55985184a734e16b8fe880b192e3d2763614b0ab3f99b4530e30a'],
+    }),
+    ('huge', '1.3.5', {
+        'checksums': ['9240866e2f773cd0ac8a02514871149d2babaa162a49e151eab9591ad42984ea'],
+    }),
+    ('d3Network', '0.5.2.1', {
+        'checksums': ['5c798dc0c87c6d574abb7c1f1903346e6b0fec8adfd1df7aef5e4f9e7e3a09be'],
+    }),
+    ('BDgraph', '2.72', {
+        'checksums': ['7cf9cc1bccf2a56b518c88030e00e88217f571afcb250aa95c3bd2771a8b83cd'],
+    }),
+    ('graphlayouts', '1.1.1', {
+        'checksums': ['7bc2459a02b1339ac01184a76687a3e50de5680f4699b5966a3f2e6a882f3801'],
+    }),
+    ('tweenr', '2.0.3', {
+        'checksums': ['efabe512a45d653787ba40f87f3e23add4037f88573a102fa9ac7a5ff43c8cbe'],
+    }),
+    ('ggforce', '0.4.2', {
+        'checksums': ['c145b0e6ed6847d409ed2fe103b81234855bc0661cde2bfb4410fb23680e51a8'],
+    }),
+    ('tidygraph', '1.3.1', {
+        'checksums': ['aac1d4bb9396081bbeecbde11a3cd1a26a56bd6b1f608a628b359cb37c18ac1a'],
+    }),
+    ('ggraph', '2.2.1', {
+        'checksums': ['4405f8a907ad8fee68b5d4991f0bc8f35d6c0facbb7467c2ce425d3ec8b23af1'],
+    }),
+    ('qgraph', '1.9.8', {
+        'checksums': ['14a81d64f37614a05445408babbb2da5bc53886def8b0c2e4101b06e8b4c01d4'],
+    }),
+    ('HWxtest', '1.1.9', {
+        'patches': ['HWxtest-1.1.9_add-fcommon.patch'],
+        'checksums': [
+            {'HWxtest_1.1.9.tar.gz': 'a37309bed4a99212ca104561239d834088217e6c5e5e136ff022544c706f25e6'},
+            {'HWxtest-1.1.9_add-fcommon.patch': '4ce08c35035dbcc4edf092cdb405ae32c21c05b3786c15c0aa4bfe13bd81f451'},
+        ],
+    }),
+    ('diveRsity', '1.9.90', {
+        'checksums': ['b8f49cdbfbd82805206ad293fcb2dad65b962fb5523059a3e3aecaedf5c0ee86'],
+    }),
+    ('doSNOW', '1.0.20', {
+        'checksums': ['917cabed166aa2d1ec291691c17e1e3d344e858543e1682e3a442cc0c504bbb8'],
+    }),
+    ('geepack', '1.3.11', {
+        'checksums': ['29e2f0d314e75de748f33438b5b1282f469d163e29534c61616c257b2955e478'],
+    }),
+    ('biom', '0.3.12', {
+        'checksums': ['4ad17f7811c7346dc4923bd6596a007c177eebb1944a9f46e5674afcc5fdd5a1'],
+    }),
+    ('pim', '2.0.2', {
+        'checksums': ['1195dbdbd67348dfef4b6fc34fcec643da685ebe58d34bbe049ab121aca9944f'],
+    }),
+    ('minpack.lm', '1.2-4', {
+        'checksums': ['e30fa4fe353cf00d266839d3c5db83ec9548a660f31d447ad9a69f556d56e731'],
+    }),
+    ('rootSolve', '1.8.2.4', {
+        'checksums': ['e16a317ea494192e0a5668a18f7eb99675f8edf3b3095861d213bc2590ad385d'],
+    }),
+    ('FME', '1.3.6.3', {
+        'checksums': ['83c4c28ad4f9197610be40fb66f1025f438a46e4085d64b736e83a0ab71e36a1'],
+    }),
+    ('bmp', '0.3', {
+        'checksums': ['bdf790249b932e80bc3a188a288fef079d218856cf64ffb88428d915423ea649'],
+    }),
+    ('tiff', '0.1-12', {
+        'checksums': ['df10ce719f92597572763182f7cb03686b8d7fb9123d036a4daf5b10738e815c'],
+    }),
+    ('readbitmap', '0.1.5', {
+        'checksums': ['737d7d585eb33de2c200da64d16781e3c9522400fe2af352e1460c6a402a0291'],
+    }),
+    ('imager', '1.0.2', {
+        'checksums': ['7c849086cb17d6c5aefc106217363e14afbcda2a9e0120687d40805b5e1c566a'],
+    }),
+    ('signal', '1.8-0', {
+        'checksums': ['89cba854167a2b051a58cf3b73ccbf74eeb47c890ac39720611cd41f86b94684'],
+    }),
+    ('tuneR', '1.4.7', {
+        'checksums': ['364154a0440953327eeefd2f3c72c9f819944cbb52b6e7497958882ca0b6960a'],
+    }),
+    ('pastecs', '1.4.2', {
+        'checksums': ['43b656809f601be7b2f98187b0b71d3fdd2b515f5658a0690e7a515ddbb376f8'],
+    }),
+    ('audio', '0.1-11', {
+        'checksums': ['1052f6335be4df4b2e145c077d82e781eaf6658f3ed4821033b07e57bb4ce17c'],
+    }),
+    ('fftw', '1.0-8', {
+        'checksums': ['8c7e011666a0ed76e0554abfa62cf658c055bd6efebe94d16b4462d123d08620'],
+    }),
+    ('seewave', '2.2.3', {
+        'checksums': ['1f897af809e8e5f9d515d788f4b5ea14ba27b2b554a3ab8024d78f42ac46848d'],
+    }),
+    ('gsw', '1.1-1', {
+        'checksums': ['d2a21dbcc3b285163d9cf1bc649a3de1bb1e713c64e4cb6cbc3e613c43f4dd82'],
+    }),
+    ('wk', '0.9.1', {
+        'checksums': ['b7a0af51c0e04175dc359d1fb0e852ac55097b4105d876b58d3cf995c0f2bf7b'],
+    }),
+    ('s2', '1.1.6', {
+        'checksums': ['1d9d2e6b7890122f916fd8f86060cb0f101637ead158bbc22ee2f0324b93a066'],
+    }),
+    ('sf', '1.0-16', {
+        'checksums': ['e96e191011cdf2a073c773bdfc50ffd4a5d80f1da0ba1aa05db8015da45a9987'],
+    }),
+    ('oce', '1.8-2', {
+        'checksums': ['cf5fee1b44f1f972d496c005993eab5267878177c4ce8bf74a3b018047a33fa9'],
+    }),
+    ('ineq', '0.2-13', {
+        'checksums': ['e0876403f59a3dfc2ea7ffc0d965416e1ecfdecf154e5856e5f54800b3efda25'],
+    }),
+    ('soundecology', '1.3.3', {
+        'checksums': ['276164d5eb92c78726c647be16232d2443acbf7061371ddde2672b4fdb7a069a'],
+    }),
+    ('memuse', '4.2-3', {
+        'checksums': ['906fdff665e2aed0e98ee3181233a5c62bd521abfce6ab1cb215c71c95d12620'],
+    }),
+    ('pinfsc50', '1.3.0', {
+        'checksums': ['971627cf4567fdb34db26010f2db44cfac5ff07f327d3247e778638cc4e849bf'],
+    }),
+    ('vcfR', '1.15.0', {
+        'checksums': ['df17e48b961d96f2a78a1a15037df674f57d0445f2669e401543d8082f0b49fa'],
+    }),
+    ('glmmML', '1.1.6', {
+        'checksums': ['2710f56530de37a52a042645da76c8af075d66e04eaee9e18bf1e5f32f0b7958'],
+    }),
+    ('cowplot', '1.1.3', {
+        'checksums': ['8756971af5c50381cf00ec7ed622fd5cf3d70f534bdfa3ebadd157b5aef5b273'],
+    }),
+    ('tsne', '0.1-3.1', {
+        'checksums': ['14abc65bc0a3f3ed63c04dda19620e483a21d1f5f33feb74aba9f3221434d888'],
+    }),
+    ('sn', '2.1.1', {
+        'checksums': ['f9f6b56d91dc7cb18dc8308d0875b9648c90b268d1aaf8f4c5164ff016df22bd'],
+    }),
+    ('tclust', '2.0-4', {
+        'checksums': ['a6667167778b974afc968340161171a7911415bcc1220dc7f0f350552f560578'],
+    }),
+    ('ranger', '0.16.0', {
+        'checksums': ['0395f93afdb807a7882c1fa8f183a26a871c5168ea0903566951298ef1138589'],
+    }),
+    ('hexbin', '1.28.3', {
+        'checksums': ['0eb33511c1a4ff29dda8b89fee420ea7041033f981c7f16484c9f504d749de5f'],
+    }),
+    ('lobstr', '1.1.2', {
+        'checksums': ['9bc533ed7e8f816097a03acfbca33308c9940ba26d02674f4ba06311cf3a1718'],
+    }),
+    ('pryr', '0.1.6', {
+        'checksums': ['68c1a30a42808eb01a64d31e521d21f2fd5a88dd2c14d05b4b7986d27a177704'],
+    }),
+    ('moments', '0.14.1', {
+        'checksums': ['2ed2b84802da132ae0cf826a65de5bfa85042b82e086be844002fe1ce270d864'],
+    }),
+    ('laeken', '0.5.3', {
+        'checksums': ['60495f494f2a41b2ca94e11e3d0224843b7282cf8b2a859dbf6077a3bc97e80b'],
+    }),
+    ('VIM', '6.2.2', {
+        'checksums': ['afa7492c54508c46eff39ac66fa4b05627e0044253ebe4a61b2a78d459f715e4'],
+    }),
+    ('smoother', '1.3', {
+        'checksums': ['e8df4bc88e9d95c30c66fc10e6b1b485626828b6d28ad1a52a20168736468277'],
+    }),
+    ('dynamicTreeCut', '1.63-1', {
+        'checksums': ['831307f64eddd68dcf01bbe2963be99e5cde65a636a13ce9de229777285e4db9'],
+    }),
+    ('beeswarm', '0.4.0', {
+        'checksums': ['51f4339bf4080a2be84bb49a844c636625657fbed994abeaa42aead916c3d504'],
+    }),
+    ('vipor', '0.4.7', {
+        'checksums': ['baad41e9ddaa13b5a1db1abab34253b27d5b99e5a6a649b2036aaf1483370b9e'],
+    }),
+    ('ggbeeswarm', '0.7.2', {
+        'checksums': ['fd7ca265bb892dde514d5f8d6a853fb8b32d7a673b05e9c8b50544a523299ce5'],
+    }),
+    ('shinydashboard', '0.7.2', {
+        'checksums': ['a56ee48572649830cd8d82f1caa2099411461e19e19223cbad36a375299f3843'],
+    }),
+    ('rrcov', '1.7-5', {
+        'checksums': ['dfc595077fb65eb12653d994c757e0998c09a186575d5b61000bb5452fd0b033'],
+    }),
+    ('WriteXLS', '6.6.0', {
+        'checksums': ['bc17a1f3bc1b2b2e37fb28b95bf613f8ef8234393c5c5e4c8a86430850e3b729'],
+    }),
+    ('bst', '0.3-24', {
+        'checksums': ['64d96e13551d35ec32aabaa733bec86dbe8c9ca3f976a34ebbf1f49bb63e49f4'],
+    }),
+    ('pamr', '1.56.2', {
+        'checksums': ['29046c761d1999f34c6eb69cab5484985cc5c309e3e9d60891cf36d5febbfc58'],
+    }),
+    ('WeightSVM', '1.7-13', {
+        'checksums': ['5e356189885390f47f21eedfb93726e2920b679da480a07823c44012b689aaa5'],
+    }),
+    ('mpath', '0.4-2.25', {
+        'checksums': ['4b9943386557779c42984c77f2ad97c2d689da3de52d69b521e863096e5d6184'],
+    }),
+    ('timereg', '2.0.5', {
+        'checksums': ['a0d1ddeaf6962c7f48e213430ec838cf8e880a6c41571e4c2e864d070f84f7ef'],
+    }),
+    ('peperr', '1.5', {
+        'checksums': ['f7f9b3140bd8f0d00b7cacd55e9626e2333eb91ab0173e8f21237803045b8500'],
+    }),
+    ('heatmap3', '1.1.9', {
+        'checksums': ['594c33947b2be2cc8a592075f41a0df2398c892add7d63a15c613a5eeb8fdb69'],
+    }),
+    ('GlobalOptions', '0.1.2', {
+        'checksums': ['47890699668cfa9900a829c51f8a32e02a7a7764ad07cfac972aad66f839753e'],
+    }),
+    ('circlize', '0.4.16', {
+        'checksums': ['16dc32c7704906d13a9e5281bb396e92fb89a6b17fa5e201953240726b650b67'],
+    }),
+    ('GetoptLong', '1.0.5', {
+        'checksums': ['8c237986ed3dfb72d956ad865ef7768644eebf144675ad66140acfd1aca9d701'],
+    }),
+    ('dendextend', '1.17.1', {
+        'checksums': ['87e96e119e7236b4f5df1c6f1b0d4d4e12aab606a2142e039f56d8ec71f9e521'],
+    }),
+    ('RInside', '0.2.18', {
+        'checksums': ['805014f0f0a364633e0e3c59100665a089bc455dec80b24f04aaec96466cb736'],
+    }),
+    ('limSolve', '1.5.7.1', {
+        'checksums': ['a5945217bbf512724297883f8d7c65846a11202266b2b6bb3355372935e85b92'],
+    }),
+    ('dbplyr', '2.5.0', {
+        'checksums': ['bb475bdbe89487b189ecc257b5c92007a7458803c81aa77bfc4ed46f5f24bcff'],
+    }),
+    ('modelr', '0.1.11', {
+        'checksums': ['94ebd506e9ccf3bf25318be6a182f8f89c3669a77b41864a0b9dbcc1d4337bd3'],
+    }),
+    ('debugme', '1.2.0', {
+        'checksums': ['b22605ad3b20d460308d8c9c18116e56c4d6ff10577608eaf58802998171f099'],
+    }),
+    ('reprex', '2.1.0', {
+        'checksums': ['0a0dfe5976e5ddb908d5a7582b11cbddee342e99d8dbd64b08ff64c1e705a951'],
+    }),
+    ('selectr', '0.4-2', {
+        'checksums': ['5588aed05f3f5ee63c0d29953ef53da5dac7afccfdd04b7b22ef24e1e3b0c127'],
+    }),
+    ('rvest', '1.0.4', {
+        'checksums': ['7d707c6b2994cf7b6c1d665bec872d2ef5c55f30e7c343c447a8a386a6049ca6'],
+    }),
+    ('dtplyr', '1.3.1', {
+        'checksums': ['a5a9689a640b8bd1274519af220c33deaa3919654acac4ebdff1ff365cc8d6e5'],
+    }),
+    ('gargle', '1.5.2', {
+        'checksums': ['4a5beb046eb50a168b4baf5d1fcd8ac20d698e7fcb6b6ef46a436ded5b039001'],
+    }),
+    ('googledrive', '2.1.1', {
+        'checksums': ['0b8b4f74ba3630b0347249a32a80bc5fc2e8b63ad2952702f30162bd2d38fb82'],
+    }),
+    ('ids', '1.0.1', {
+        'checksums': ['b6212a186063c23116c5cbd3cca65dbb8977dd737261e4526ebee8f64852cfe8'],
+    }),
+    ('googlesheets4', '1.1.1', {
+        'checksums': ['c5cc63348c54b9de8492e7b12b249245746ea1ff33e306f12431f4fc9386fccf'],
+    }),
+    ('conflicted', '1.2.0', {
+        'checksums': ['c99b86bb52da3e7d1f4d96d70c77304d0434db5bd906edd8d743e89ac9223088'],
+    }),
+    ('tidyverse', '2.0.0', {
+        'checksums': ['3d3c2d135056333247d309d1c2cc98cc0d87e2c781f4c6fbceab28d28c0728e5'],
+    }),
+    ('R.rsp', '0.46.0', {
+        'checksums': ['1a9f680ffe563abdaa91add6ebf5e6c0ecbe57f0d39687bcb272ff2a987c33bb'],
+    }),
+    ('gdistance', '1.6.4', {
+        'checksums': ['6af5fd3ea7e256f34d705d4817bb88056037ce1d68adfeb28d61c4a640d8992b'],
+    }),
+    ('vioplot', '0.4.0', {
+        'checksums': ['5729b483e3a4f7c81d2cc22c8bc5211b64e289734e9da5b5696c4974067867b5'],
+    }),
+    ('emulator', '1.2-24', {
+        'checksums': ['91dc91eea7df9bf243d45db1bbf98aa72a1dafef789a6091f41180d5242fa469'],
+    }),
+    ('gmm', '1.8', {
+        'checksums': ['7099fc5c6a9069924392995a726190e8d62f6e55375ef356084b0c73346d85d8'],
+    }),
+    ('tmvtnorm', '1.6', {
+        'checksums': ['2d9b2c5330d11a62384b4c0c1c012be34806b48683898045a4a40fdb9a8e1bba'],
+    }),
+    ('IDPmisc', '1.1.21', {
+        'checksums': ['478b95ae7e73df78e0728d37281b9af6b4f152a8d54bf9811121d32722f9088c'],
+    }),
+    ('gap.datasets', '0.0.6', {
+        'checksums': ['1e14b06fac203016555ddca323225ccf18d784609dbf9bdfff423e6dccd297cb'],
+    }),
+    ('gap', '1.5-3', {
+        'checksums': ['6e19f9d822460867fcb97fe917730ce0f87218893a6a7edae42caaa401b452ce'],
+    }),
+    ('qrnn', '2.1.1', {
+        'checksums': ['14f7ab438349dd9a9deb8bcdc1bf6734872a018061f46d0ba5d02db63c904cc9'],
+    }),
+    ('TMB', '1.9.12', {
+        'checksums': ['db5801f43e55fdeea520355628286c491c694f1165e8567eecd5f3d864cfc7f0'],
+    }),
+    ('glmmTMB', '1.1.9', {
+        'checksums': ['93d5a6b907b0f71f97c13134e0c450c951b3636365a369f48edb804207e78963'],
+    }),
+    ('gmp', '0.7-4', {
+        'checksums': ['a7d6b40f77d2619c11db5170b8f47336f7c5fa1db7eed0ac9d8a432e41053919'],
+    }),
+    ('ROI', '1.0-1', {
+        'checksums': ['d4ff143304f1422ecc455eb1a00896530193c1a227ed7f3e9da2baa95d921616'],
+    }),
+    ('Rglpk', '0.6-5.1', {
+        'checksums': ['e528b8c487e9dfef16ade3b834a17fc93cc898869978a5dd79bee2c5bf9cb6c9'],
+    }),
+    ('ROI.plugin.glpk', '1.0-0', {
+        'checksums': ['b361b0d4222d74b21432cdc6990762affecdbcec8fd6bbdb13b78b59cb04b444'],
+    }),
+    ('spaMM', '4.5.0', {
+        'checksums': ['bbf9a15620f707f49c81b465f9d87a6f151be8afffdc18f060cbbe719e2424db'],
+    }),
+    ('qgam', '1.3.4', {
+        'checksums': ['7633120a48a85ab73f7e1bc8b02c98319285c2abd05f9d13d25339d7aaaacacb'],
+    }),
+    ('DHARMa', '0.4.6', {
+        'checksums': ['32fd3d5cd354ff6b5457599d7fb870b94c7d86401a47c7c553bca26f782a4b73'],
+    }),
+    ('mvnfast', '0.2.8', {
+        'checksums': ['8871e0ce54b87afc556fd94ca77c3db72dcbb8c245558287e0fe342e30eec9a0'],
+    }),
+    ('bridgesampling', '1.1-2', {
+        'checksums': ['54ecd39aa2e36d4d521d3d36425f9fe56a3f8547df6048c814c5931d790f3e6b'],
+    }),
+    ('BayesianTools', '0.1.8', {
+        'checksums': ['f543bdd6b61ec7fd31a7e4040bd7835341d9079243fa4eb0cd5e684e5e39bdd1'],
+    }),
+    ('gomms', '1.0', {
+        'checksums': ['52828c6fe9b78d66bde5474e45ff153efdb153f2bd9f0e52a20a668e842f2dc5'],
+    }),
+    ('feather', '0.3.5', {
+        'checksums': ['50ff06d5e24d38b5d5d62f84582861bd353b82363e37623f95529b520504adbf'],
+    }),
+    ('dummies', '1.5.6', {
+        'checksums': ['7551bc2df0830b98c53582cac32145d5ce21f5a61d97e2bb69fd848e3323c805'],
+    }),
+    ('SimSeq', '1.4.0', {
+        'checksums': ['5ab9d4fe2cb1b7634432ff125a9e04d2f574fed06246a93859f8004e10790f19'],
+    }),
+    ('uniqueAtomMat', '0.1-3-2', {
+        'checksums': ['f7024e73274e1e76a870ce5e26bd58f76e8f6df0aa9775c631b861d83f4f53d7'],
+    }),
+    ('PoissonSeq', '1.1.2', {
+        'checksums': ['6f3dc30ad22e33e4fcfa37b3427c093d591c02f1b89a014d85e63203f6031dc2'],
+    }),
+    ('aod', '1.3.3', {
+        'checksums': ['b7245e8abf7d78cdfa7f74f6d90f79a418b883058aa3edd5977a60bdbed4087e'],
+    }),
+    ('cghFLasso', '0.2-1', {
+        'checksums': ['6e697959b35a3ceb2baa1542ef81f0335006a5a9c937f0173c6483979cb4302c'],
+    }),
+    ('svd', '0.5.5', {
+        'checksums': ['e20139794ad1a8c7d7fdffb8dac068c6fbdc8f0b65929341cb5c4d2ff1f98cc6'],
+    }),
+    ('Rssa', '1.0.5', {
+        'checksums': ['475819636afb330a4467722b0a664fa54d6114d782b681f681ccb123f3be522d'],
+    }),
+    ('JBTools', '0.7.2.9', {
+        'checksums': ['b33cfa17339df7113176ad1832cbb0533acf5d25c36b95e888f561d586c5d62f'],
+    }),
+    ('RUnit', '0.4.33', {
+        'checksums': ['b2a4c5afc7ef9534dac5006f6ef1b2af68630bb73eb74ef70ec7ed53dae6cb5f'],
+    }),
+    ('DistributionUtils', '0.6-1', {
+        'checksums': ['31e79eaa8871b0b9fb8ac63a3fbd852f9ed3047bc584c233ac030b50e1b963d7'],
+    }),
+    ('gapfill', '0.9.6-1', {
+        'checksums': ['22f04755873e34a9077bb1b1de8d16f5bc56cb8c395c4f797f9ad0b209b1b996'],
+    }),
+    ('gee', '4.13-27', {
+        'checksums': ['3fb4773fd58fe6aa8bd0ae031add8ee7c33d0e43dfec92e89db04b5dc709a49c'],
+    }),
+    ('Matching', '4.10-14', {
+        'checksums': ['bfb4286a5da29dcfcc4ddee6299e2d91c0de177720b060b8946fd16f32f6a6b0'],
+    }),
+    ('chk', '0.9.1', {
+        'checksums': ['f9b43dcf1002c6244dc87965f21dff6e65256eb634b826deb7b5cdfc26f505a7'],
+    }),
+    ('MatchIt', '4.5.5', {
+        'checksums': ['ae39cafdd3a52487e3ebff1b49642f516cf64321fea90fa57ce3d545a259859e'],
+    }),
+    ('RItools', '0.3-4', {
+        'checksums': ['047684b8d135d9a90156a7be6625c2961c8f6789bf80533b525a201a69ee52d7'],
+    }),
+    ('mitools', '2.4', {
+        'checksums': ['f204f3774e29d79810f579f128de892539518f2cbe6ed237e08c8e7283155d30'],
+    }),
+    ('survey', '4.4-2', {
+        'checksums': ['8a4a0f3122f0971f7c8756805add781192c655f507b235801dd78457a8d2f1bd'],
+    }),
+    ('rlemon', '0.2.1', {
+        'checksums': ['4a18fa034f197c68daf48daf25c0e41f1b8acbe71d030c6bc1f55e3062a10375'],
+    }),
+    ('optmatch', '0.10.7', {
+        'checksums': ['330fc251ebe6901a6fbf931457943ee113bc882f786b2b14d837cd59f4327d1d'],
+    }),
+    ('SPAtest', '3.1.2', {
+        'checksums': ['b3d74ed2b0a6475a9966dd50eb5d363d0b2985636271dfbf82f0472b8d22b9f4'],
+    }),
+    ('RSpectra', '0.16-1', {
+        'checksums': ['cba5d3403d6a7d0e27abf6279fbfea6e0d0fe36b28c688bbadb8eafb3841329a'],
+    }),
+    ('SKAT', '2.2.5', {
+        'checksums': ['1441fa46b6a78a060007442fb8cb8c87753bdc2b1ea2dc24ff951ac3fef651f4'],
+    }),
+    ('GillespieSSA', '0.6.2', {
+        'checksums': ['f4233b4a44c7d4b9e3459b1efa9a8087a602ef93806b4d70eadbb537b67567c2'],
+    }),
+    ('startupmsg', '0.9.6.1', {
+        'checksums': ['431b4eea5fe9f1f421518b24cd4ae27c9228f3311ac11bfcaf22620f86a65881'],
+    }),
+    ('distr', '2.9.3', {
+        'checksums': ['15ac7c835bca5b90121fe42fab35f8151a3bd876d3c88a41eb5339c4bdd7db58'],
+    }),
+    ('distrEx', '2.9.2', {
+        'checksums': ['d06bcaa1ccb52ef775f7c8b2d6d4676408dbc2813dfc128da34ffa4c7740f3e4'],
+    }),
+    ('minerva', '1.5.10', {
+        'checksums': ['2f26353d8fcc989ac698c4e45bb683801b1a7bb60b14903d05a4d73c629c590f'],
+    }),
+    ('RcppTOML', '0.2.2', {
+        'checksums': ['371391f9ca82221e76a424082ea9ebc5ea2c50f14e8408469b09d7dc3e6f63aa'],
+    }),
+    ('here', '1.0.1', {
+        'checksums': ['08ed908033420d3d665c87248b3a14d1b6e2b37844bf736be620578c20ca346b'],
+    }),
+    ('reticulate', '1.38.0', {
+        'checksums': ['cb2f313e2351a3cde03be55561b592318ec5376fba3b10e371eeff1986deca8d'],
+    }),
+    ('umap', '0.2.10.0', {
+        'checksums': ['8d4786929345e8980bb8be8bb4b6300a679bba03a5984eed59e5e00c626b6ea9'],
+    }),
+    ('KODAMA', '2.4', {
+        'checksums': ['78f2ea3596f3697fc06a080947e82a54c5270ed90f86916b91902e5db6ec85e7'],
+    }),
+    ('locfdr', '1.1-8', {
+        'checksums': ['42d6e12593ae6d541e6813a140b92591dabeb1df94432a515507fc2eee9a54b9'],
+    }),
+    ('ica', '1.0-3', {
+        'checksums': ['474d3530b16b76a1bf1a1114d24092678ea7215fa57c6fdcee6333f1e768b865'],
+    }),
+    ('dtw', '1.23-1', {
+        'checksums': ['6ed6a3b52be673ce2617b8d48723c7c488c95aab88fe2912d7e00507838e826d'],
+    }),
+    ('SDMTools', '1.1-221.2', {
+        'checksums': ['f0dd8c5f98d2f2c012536fa56d8f7a58aaf0c11cbe3527e66d4ee3194f6a6cf7'],
+    }),
+    ('ggridges', '0.5.6', {
+        'checksums': ['efccaa309a150d11c6b402b912e618ea041f25cca3101f32cd821a6f41684e35'],
+    }),
+    ('TFisher', '0.2.0', {
+        'checksums': ['bd9b7484d6fba0165841596275b446f85ba446d40e92f3b9cb37381a3827e76f'],
+    }),
+    ('lsei', '1.3-0', {
+        'checksums': ['6289058f652989ca8a5ad6fa324ce1762cc9e36c42559c00929b70f762066ab6'],
+    }),
+    ('npsurv', '0.5-0', {
+        'checksums': ['bc87db76e7017e178c2832a684fcd49c42e20054644b21b586413d26c8821dc6'],
+    }),
+    ('fitdistrplus', '1.1-11', {
+        'checksums': ['26274f2b710b2417a8bca314d400abf320d4ccf0387ad082743056699501b53d'],
+    }),
+    ('hdf5r', '1.3.10', {
+        'installopts': '--configure-args="--with-hdf5=$EBROOTHDF5/bin/h5pcc"',
+        'preinstallopts': "unset LIBS && ",
+        'checksums': ['92496e0693a27c0a1c8caba671c51fcecc3a120f8ef7eb0cb3cd686a3e49124e'],
+    }),
+    ('DTRreg', '2.2', {
+        'checksums': ['9c8954d5c342af85611d13dab5be64c4a7a5904644a6e04ff21d5494559e2fc7'],
+    }),
+    ('pulsar', '0.3.11', {
+        'checksums': ['ee82ef25b2be4bbac713c34bca85d8ea1fa0e32eb8c800dad7256e145fc79393'],
+    }),
+    ('bayesm', '3.1-6', {
+        'checksums': ['17d72b9cdc090845f98e7a04640380d0baef8bc23d1487c8f64dc192fdb93cb5'],
+    }),
+    ('gsl', '2.1-8', {
+        'checksums': ['f33609bf485abd190e65ff5d0fdab438b759294c47b921d983d89d6f053a2d95'],
+    }),
+    ('energy', '1.7-11', {
+        'checksums': ['c29f8fb000c979d2504f6f6d3a99c773004f77d58793e7e2a5766155272b6511'],
+    }),
+    ('compositions', '2.0-8', {
+        'checksums': ['c5063488f456992b5821458b3237322addffd3451ae91f9474707886971ef290'],
+    }),
+    ('clustree', '0.5.1', {
+        'checksums': ['b5f2496e596e3fd140ace69c4837085e13f3abb850f5eb57d496380691fdd117'],
+    }),
+    ('tweedie', '2.3.5', {
+        'checksums': ['983c745fee5a780d46e8dd04c2eb1c10cb2e222d3679654f0d6934d3db7b1c3e'],
+    }),
+    ('RcppGSL', '0.3.13', {
+        'checksums': ['fe5e73bc119c6424e1a40b6fea17417a7bba93e81dbe9b7cf86dde9b8e8d93e7'],
+    }),
+    ('mvabund', '4.2.1', {
+        'checksums': ['ed6946c95609443584081100cd38624d2309f7f5d210fd4b8ec12ad25bd27a06'],
+    }),
+    ('fishMod', '0.29', {
+        'checksums': ['5989e49ca6d6b2c5d514655e61f75b019528a8c975f0d6056143f17dc4277a5d'],
+    }),
+    ('alabama', '2023.1.0', {
+        'checksums': ['925f67c72d9cdb677105377777bd09e9b56a61573bea7e3f69e0a49595c7bf1c'],
+    }),
+    ('gllvm', '1.4.3', {
+        'checksums': ['63b77040e9cf2694882d1d80a3bc3030b3a348819ea38e6728417e4c5de07ecc'],
+    }),
+    ('grpreg', '3.4.0', {
+        'checksums': ['fd57d20baf63d2cc5821998bca5c3fdcbe46c933c9553caa492911b12654d6ad'],
+    }),
+    ('trust', '0.1-8', {
+        'checksums': ['952e348b62aec35988b103fd152329662cb6a451538f184549252fbf49d7dcac'],
+    }),
+    ('lpSolveAPI', '5.5.2.0-17.11', {
+        'checksums': ['b08d6cae4fc17575adf5df0113ea5f4f819bb2c7f87987e0d66c8eabfc933fa4'],
+    }),
+    ('ergm', '4.6.0', {
+        'checksums': ['b471a60c39eb5b478e06dd0caf1d085f4b0927f1c260de699f1c8d4fe831a7f7'],
+    }),
+    ('networkLite', '1.0.5', {
+        'checksums': ['aaab55d4f8f0b330fe7c1ecbab3c44746c52c2fda99c53c6b46042bb8775718b'],
+    }),
+    ('networkDynamic', '0.11.4', {
+        'checksums': ['6bf3e216a444f183ff925e29560fae4c2362cc2a9fed19b3e116a9d9f1184a46'],
+    }),
+    ('ergm.multi', '0.2.1', {
+        'checksums': ['e09dd0d7207a8214746ea251a50c93f6f5de255175309dc8757206f419a01902'],
+    }),
+    ('tergm', '4.2.0', {
+        'checksums': ['dcf5a26cc2c4d165766706af08f8ea4f36e328158f5b682490c2a351f7fbda69'],
+    }),
+    ('ergm.count', '4.1.2', {
+        'checksums': ['9bce70b64a2f60b242603b771370b40d7f7aeed37ed426670131fd966c13b020'],
+    }),
+    ('tsna', '0.3.5', {
+        'checksums': ['4ee2f773d573f0f4bd93131156fdccf01d7f1a3f725eff3e885021098c6bff65'],
+    }),
+    ('statnet', '2019.6', {
+        'checksums': ['0903e1a81ed1b6289359cefd12da1424c92456d19e062c3f74197b69e536b29d'],
+    }),
+    ('aggregation', '1.0.1', {
+        'checksums': ['86f88a02479ddc8506bafb154117ebc3b1a4a44fa308e0193c8c315109302f49'],
+    }),
+    ('ComICS', '1.0.4', {
+        'checksums': ['0af7901215876f95f309d7da6e633c38e4d7faf04112dd6fd343bc15fc593a2f'],
+    }),
+    ('dtangle', '2.0.9', {
+        'checksums': ['c375068c1877c2e8cdc5601cfd5a9c821645c3dff90ddef64817f788f372e179'],
+    }),
+    ('mcmc', '0.9-8', {
+        'checksums': ['6a06440d4b58e8a7f122747d92046ff40da4bb58a20bf642228a648a0c826ea7'],
+    }),
+    ('MCMCpack', '1.7-0', {
+        'checksums': ['846073d710017ec1dc9a2b4616cb6aeb60ce04e3500a37214522818d34045def'],
+    }),
+    ('shinythemes', '1.2.0', {
+        'checksums': ['37d68569ce838c7da9f0ea7e2b162ecf38fba2ae448a4888b6dd29c4bb5b2963'],
+    }),
+    ('csSAM', '1.2.4', {
+        'checksums': ['3d6442ad8c41fa84633cbbc275cd67e88490a160927a5c55d29da55a36e148d7'],
+    }),
+    ('bridgedist', '0.1.2', {
+        'checksums': ['7210c97fc864e78ea8502067359d642bbd95bf2df30d33da193fc5c004e45baf'],
+    }),
+    ('asnipe', '1.1.17', {
+        'checksums': ['e7b4010fa1adf27534420db2971dae3c63190920a4323c86fd586842e22d9b07'],
+    }),
+    ('liquidSVM', '1.2.4', {
+        'patches': ['liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch'],
+        # Don't add optimization flags by liquidSVM which may not be known e.g. on PPC
+        'preinstallopts': 'LIQUIDSVM_TARGET="empty"',
+        'checksums': [
+            {'liquidSVM_1.2.4.tar.gz': '15a9c7f2930e2ed3f4c5bcd9b042884ea580d2b2e52e1c68041600c196046aba'},
+            {'liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch':
+             '46b09e441c3b59af535f20d8db0dee7f1d6a7ddd511175d252115b53cb8b86f8'},
+        ],
+    }),
+    ('oddsratio', '2.0.1', {
+        'checksums': ['2097e7a8bf623379d55652de5dce4946d05163e85d30df50dc19055962bf60b5'],
+    }),
+    ('mltools', '0.3.5', {
+        'checksums': ['7093ffceccdf5d4c3f045d8c8143deaa8ab79935cc6d5463973ffc7d3812bb10'],
+    }),
+    ('h2o', '3.44.0.3', {
+        'checksums': ['61a85f6c2f15e8e96839f8a4fd3a45eaa6bca90517bb20a4dd36e951d6fd0c82'],
+    }),
+    ('mlegp', '3.1.9', {
+        'checksums': ['63296d17a162fdce0958b10f45cb7d5dab4b3ee29340528d33cedcae08a040b3'],
+    }),
+    ('itertools', '0.1-3', {
+        'checksums': ['b69b0781318e175532ad2d4f2840553bade9637e04de215b581704b5635c45d3'],
+    }),
+    ('missForest', '1.5', {
+        'checksums': ['417055a03b02ad8359cf1bdc8f89d49531a3a8ee2c98edf90c8a01432f44838d'],
+    }),
+    ('bartMachineJARs', '1.2.1', {
+        'checksums': ['9f7a20acf4aec249e16f83d81f5ec796aa718deb1b8bc24393fc0421eb8ce1c0'],
+    }),
+    ('bartMachine', '1.3.4.1', {
+        'checksums': ['3b0a5250f5425a8efe460adcb58ea1342f1d845ae3a8db29dbf4806653884b89'],
+    }),
+    ('lqa', '1.0-3', {
+        'checksums': ['3889675dc4c8cbafeefe118f4f20c3bd3789d4875bb725933571f9991a133990'],
+    }),
+    ('PresenceAbsence', '1.1.11', {
+        'checksums': ['c63a6453783865b7c69c580a09a769e99390dd8b2e0f63e48fbfc86da3bee4b7'],
+    }),
+    ('GUTS', '1.2.5', {
+        'checksums': ['9d983a566daa07d3e0036fe7011efe94f29e31a611493ba16bd316b61730a7b7'],
+    }),
+    ('GenSA', '1.1.14', {
+        'checksums': ['66e455bb0e66d3c04af84d9dddc9b89f40b4cf9fe9ad1cf0714bcf30aa1b6837'],
+    }),
+    ('parsedate', '1.3.1', {
+        'checksums': ['1fc31ab9813b61680abf4f4c2705b8f484d56d1d3ef256df84b342b628b6d1b1'],
+    }),
+    ('circular', '0.5-0', {
+        'checksums': ['4bf4da5de29e555d1a7ae7ea64f8a5dda037e5c423f1078944f0bbb6eb9a7b92'],
+    }),
+    ('cobs', '1.3-8', {
+        'checksums': ['2c2049c7cb868a2e4e1a530fe7218fac56e6157ef64ad57b91c5bb457dbc9821'],
+    }),
+    ('resample', '0.6', {
+        'checksums': ['1b958009b18c92a47971847c782af76952ea4e85d5f1e3e1e70fa35c67b95265'],
+    }),
+    ('MIIVsem', '0.5.8', {
+        'checksums': ['a908f51e1598290d25864c358d57201bd50c1c40775d4d0405cbc8077bee61e1'],
+    }),
+    ('medflex', '0.6-10', {
+        'checksums': ['bd89a8fe939f3becd71a9dab30fe27fa43c96572d8309d2c1a70633117d4cb33'],
+    }),
+    ('Rserve', '1.8-13', {
+        'checksums': ['7e5d312fca8029d746f60e7d9e701129561942f97dfc33b036b123f159d69a4c'],
+    }),
+    ('spls', '2.2-3', {
+        'checksums': ['bbd693da80487eef2939c37aba199f6d811ec289828c763d9416a05fa202ab2e'],
+    }),
+    ('Boruta', '8.0.0', {
+        'checksums': ['38e75b1ebc8b2d1c54b3373a42529b819c7b4773fd4932f57bc9701d1e3e3dc7'],
+    }),
+    ('dr', '3.0.10', {
+        'checksums': ['ce523c1bdb62a9dda30afc12b1dd96975cc34695c61913012236f3b80e24bf36'],
+    }),
+    ('CovSel', '1.2.1', {
+        'checksums': ['b375d00cc567e125ff106b4357654f43bba3abcadeed2238b6dea4b7a68fda09'],
+    }),
+    ('tmle', '2.0.1.1', {
+        'checksums': ['8c2448f176ed94201affb8a9c42a5d0f56f26e88131ff2c1f4a9d14c5a0d87f6'],
+    }),
+    ('ctmle', '0.1.2', {
+        'checksums': ['e3fa0722cd87aa0e0b209c2dddf3fc44c6d09993f1e66a6c43285fe950948161'],
+    }),
+    ('BayesPen', '1.0', {
+        'checksums': ['772df9ae12cd8a3da1d5b7d1f1629602c7693f0eb03945784df2809e2bb061b0'],
+    }),
+    ('inline', '0.3.19', {
+        'checksums': ['0ee9309bb7dab0b97761ddd18381aa12bd7d54678ccd7bec00784e831f4c99d5'],
+    }),
+    ('BMA', '3.18.17', {
+        'checksums': ['6d8c514fa179f8a48c2105b551a8a08e28ea4375d06150a4b8ab4ccda577daf5'],
+    }),
+    ('BCEE', '1.3.2', {
+        'checksums': ['f0e0a6a4eb11213073aa2f0cd6c76d87e8b3965124d8ca509538eb3c128533a0'],
+    }),
+    ('bacr', '1.0.1', {
+        'checksums': ['c847272e2c03fd08ed79b3b739f57fe881af77404b6fd087caa0c398c90ef993'],
+    }),
+    ('clue', '0.3-65', {
+        'checksums': ['bdf8fdd35fb2b1c65d09766da79d930fa664a00aa497f03b636400eecb623ef8'],
+    }),
+    ('bdsmatrix', '1.3-7', {
+        'checksums': ['c3505e5ac06d5e01b3a6bad94177f8375cd9867bb0146cc9c63d92424ecb7922'],
+    }),
+    ('fftwtools', '0.9-11', {
+        'checksums': ['f1f0c9a9086c7b2f72c5fb0334717cc917213a004eaef8448eab4940c9852c7f'],
+    }),
+    ('imagerExtra', '1.3.2', {
+        'checksums': ['0ebfa1eabb89459d774630ab73c7a97a93b9481ea5afc55482975475acebd5b8'],
+    }),
+    ('MALDIquant', '1.22.2', {
+        'checksums': ['6051b07019003c698ae016d79f13945bfe2edec26f8a688126b978cb90adcfff'],
+    }),
+    ('threejs', '0.3.3', {
+        'checksums': ['76c759c8b20fb34f4f7a01cbd1b961296e1f19f4df6dded69aae7f1bca80219c'],
+    }),
+    ('LaplacesDemon', '16.1.6', {
+        'checksums': ['57b53882fd7a195b38bbdbbf0b17745405eb3159b1b42f7f11ce80c78ab94eb7'],
+    }),
+    ('rda', '1.2-1', {
+        'checksums': ['37038a9131c9133519f5e64fa1a86dbe28b21f519cf6528503234648a139ae9a'],
+    }),
+    ('sampling', '2.10', {
+        'checksums': ['fdec976ec0abfb5c690049d76f89ebcb8ab3650e2eb28a5b54c3984d17372775'],
+    }),
+    ('lda', '1.5.2', {
+        'checksums': ['95d354786e002352a973052df993b9d3acfc9f9598a053afb95ac27c7e150fd4'],
+    }),
+    ('jiebaRD', '0.1', {
+        'checksums': ['045ee670f5378fe325a45b40fd55136b355cbb225e088cb229f512c51abb4df1'],
+    }),
+    ('jiebaR', '0.11', {
+        'checksums': ['adde8b0b21c01ec344735d49cd33929511086719c99f8e10dce4ca9479276623'],
+    }),
+    ('hdm', '0.3.2', {
+        'checksums': ['3354b22752f0aa0c0d9c8c12b38810202b6380f2587e539be11d9a358412fe6a'],
+    }),
+    ('abe', '3.0.1', {
+        'checksums': ['66d2e9ac78ba64b7d27b22b647fc00378ea832f868e51c18df50d6fffb8029b8'],
+    }),
+    ('SignifReg', '4.3', {
+        'checksums': ['f755808fcb618582acb862729b20e267d9c2214f22e6e7a0c8d29073d8faa7b8'],
+    }),
+    ('bbmle', '1.0.25.1', {
+        'checksums': ['d92a0cf819fe4c08b8eb17f5e03275c8accde7f3b54f990cbba5ab926575b60b'],
+    }),
+    ('emdbook', '1.3.13', {
+        'checksums': ['26044b7ea1b42304b4dfde48afa94dd487acf979da4db2bf670ba41222083c19'],
+    }),
+    ('SOAR', '0.99-11', {
+        'checksums': ['d5a0fba3664087308ce5295a1d57d10bad149eb9771b4fe67478deae4b7f68d8'],
+    }),
+    ('rasterVis', '0.51.6', {
+        'checksums': ['61bd0d19d045b50c6764f3a7c95ce1e734af9e5f964449825d002afe02109489'],
+    }),
+    ('tictoc', '1.2.1', {
+        'checksums': ['8fcdb7c9a1e4b4817bcab654effd64dea6ec749a7901d4060d5b5c625fc88833'],
+    }),
+    ('ISOcodes', '2024.02.12', {
+        'checksums': ['02cb7b918034085dffcba0d329a2bc52514873f898a3a716560ebf17b57ae2e6'],
+    }),
+    ('stopwords', '2.3', {
+        'checksums': ['c5ec1c6ab1bad1786d87d7823d4b63abc94d2fd84ed7d8e985906e96fb6321b2'],
+    }),
+    ('janeaustenr', '1.0.0', {
+        'checksums': ['b4c32ee1395ee4a8efe714c535c0fe578b0dbf5f3bb85b41fa5cc87569b8e8aa'],
+    }),
+    ('SnowballC', '0.7.1', {
+        'checksums': ['753cf13f3206751662c03b1cf39bce9e680024f6d9f8503b836a83797181c034'],
+    }),
+    ('tokenizers', '0.3.0', {
+        'checksums': ['24571e4642a1a2d9f4f4c7a363b514eece74788d59c09012a5190ee718a91c29'],
+    }),
+    ('hunspell', '3.0.3', {
+        'checksums': ['fdaa1473a62dff2a5923b9bd958d87e546069ca22ce113f44e88c761338442f3'],
+    }),
+    ('topicmodels', '0.2-16', {
+        'checksums': ['0d5c9c65dd7ba031ba81adc0984d3e36b0309ada2204644bf816370ae656e905'],
+    }),
+    ('tidytext', '0.4.2', {
+        'checksums': ['0cf4180c2ab9fdb158337a7bfb6ba32f15fb61aae28abce425deaa5933ed2d54'],
+    }),
+    ('splitstackshape', '1.4.8', {
+        'checksums': ['656032c3f1e3dd5b8a3ee19ffcae617e07104c0e342fc3da4d863637a770fe56'],
+    }),
+    ('grImport2', '0.3-1', {
+        'checksums': ['216a1a5bb18c7a7dfb13c6c162228c6c81c45408f04d7784b6e60ae6cd4745d2'],
+    }),
+    ('preseqR', '4.0.0', {
+        'checksums': ['0143db473fb9a811f9cf582a348226a5763e62d9857ce3ef4ec41412abb559bc'],
+    }),
+    ('idr', '1.3', {
+        'checksums': ['6b3910dc48495439cd01828f8999823864a6712f73560ee3e6c903065c67d1e4'],
+    }),
+    ('entropy', '1.3.1', {
+        'checksums': ['6f5a89f5ce0e90cbed1695b81259326c976e7a8f538157e223ee5f63b54412b8'],
+    }),
+    ('kedd', '1.0.4', {
+        'checksums': ['bb944389a61cff22bb3bdde938a0ff6c16700a1ca725ef36b391b97812c45b26'],
+    }),
+    ('HiddenMarkov', '1.8-13', {
+        'checksums': ['7186d23e561818f3e1f01376a4fb2af9ccee775ce5afc1e3175f3b07a81db515'],
+    }),
+    ('lmerTest', '3.1-3', {
+        'checksums': ['35aa75e9f5f2871398ff56a482b013e6828135ef04916ced7d1d7e35257ea8fd'],
+    }),
+    ('distributional', '0.4.0', {
+        'checksums': ['09b5f3279bed4c79575f75d5f7f5e3e593c7838434a78c89f0b7184e8f20e602'],
+    }),
+    ('posterior', '1.5.0', {
+        'checksums': ['4a10307fcae321f2cd4ca7871504a0c6c9152b8473dc9a033721e8dcda18e2de'],
+    }),
+    ('loo', '2.7.0', {
+        'checksums': ['7664f331555e569d6037100048681e3a696fb9ca2e87907712eb54faa85bcb36'],
+    }),
+    ('RcppParallel', '5.1.7', {
+        'checksums': ['f9c30eb9ce1abffc590825d513d6d28dcbe970e36032dd7521febf04e905b29c'],
+    }),
+    ('StanHeaders', '2.32.9', {
+        'checksums': ['27b0feb34e1200193e3a31a951d28c5adc91c93dc0454732545b8078132e0b33'],
+    }),
+    ('V8', '4.4.2', {
+        'installopts': '--configure-vars="INCLUDE_DIR=$CPATH LIB_DIR=$LIBRARY_PATH"',
+        'preinstallopts': "export CPATH=$EBROOTNODEJS/include/node:$CPATH && ",
+        'checksums': ['e7bc35f3420f5f537121d681a90c16a74b36dc17210c9425e7f03842493a9670'],
+    }),
+    ('QuickJSR', '1.2.2', {
+        'checksums': ['51842f846585c8dfdab155eb5a26be0735cae280fa1c1bff1907d718525968ed'],
+    }),
+    ('rstan', '2.32.6', {
+        'checksums': ['3390d00191bbd3b0739dd19fe437b99a041a6b04be208877b48419d1348a1a70'],
+    }),
+    ('Rborist', '0.3-7', {
+        'checksums': ['011efef9e6f304f752bd5013627dc8482f0e9d4cf1ec49503e97d3718f542596'],
+    }),
+    ('VSURF', '1.2.0', {
+        'checksums': ['c027b1e19762f1eaf4a559c2592f3530210fefd21ee3d7c787c73b776c683393'],
+    }),
+    ('mRMRe', '2.1.2.1', {
+        'checksums': ['d53c392e82a437005b71d0e8b97350d0237608fffafe087700fe7f6770167fd9'],
+    }),
+    ('dHSIC', '2.1', {
+        'checksums': ['94c86473790cf69f11c68ed8ba9d6ae98218c7c69b7a9a093f235d175cf83db0'],
+    }),
+    ('ggsci', '3.2.0', {
+        'checksums': ['41d8ed4c01c3740028bdf2ba9c5550f1142061e4a40c93b1d2160719c59c3c4a'],
+    }),
+    ('ggsignif', '0.6.4', {
+        'checksums': ['112051af425a0c0f2998ce187dacad066bc16f55af01e3e7b76d62ff6954b20a'],
+    }),
+    ('corrplot', '0.92', {
+        'checksums': ['e8c09f963f9c4837036c439ebfe00fa3a6e462ccbb786d2cf90850ddcd9428bd'],
+    }),
+    ('rstatix', '0.7.2', {
+        'checksums': ['e0c6f5ab1d9c5d84713defabc5d149aad3d55944cffdb903cc128b694e5221a1'],
+    }),
+    ('ggfan', '0.1.3', {
+        'checksums': ['5c888b203ecf5e3dc7a317a790ca059c733002fbca4b4bc1a4f62b7ded5f70dc'],
+    }),
+    ('ggpubr', '0.6.0', {
+        'checksums': ['2e6ec5d8151991d17ef8832259cf545fa0d1a50b326ba8c1c4657700171df774'],
+    }),
+    ('yaImpute', '1.0-34', {
+        'checksums': ['b4c898c95fca784480bbbc239c78c85dc9f45a96c34c563ea7e81248ef8a8a73'],
+    }),
+    ('intrinsicDimension', '1.2.0', {
+        'checksums': ['6cc9180a83aa0d123f1e420136bb959c0d5877867fa170b79536f5ee22106a32'],
+    }),
+    ('leiden', '0.4.3.1', {
+        'checksums': ['a9ecbbcfa2724d8fdd0133af569278e036b25b6e2cbb23d453092cc6b3fc30e2'],
+    }),
+    ('sctransform', '0.4.1', {
+        'checksums': ['5f6be7f8be543e4c32c8007207b603a750881459370b7bb5afd63e8c8fabf171'],
+    }),
+    ('packrat', '0.9.2', {
+        'checksums': ['69df5943257e6c4d06f3d907241b668b53dedece72158ca935260b8b8e1672d7'],
+    }),
+    ('colourpicker', '1.3.0', {
+        'checksums': ['c7f2618cd1ae1f7ac15aee072c648e6494dfff6714e13dc7cd1da993d1102510'],
+    }),
+    ('ggExtra', '0.10.1', {
+        'checksums': ['6879edfe8e3905a2c299cbd18777422223ad30042bc6e20614ca5109a75de82c'],
+    }),
+    ('findpython', '1.0.8', {
+        'checksums': ['0f8a90cbafd4949c0333a86808383a358fb7ec3268953d8a4887d5d22264cdb7'],
+    }),
+    ('argparse', '2.2.3', {
+        'checksums': ['a50cc4e1221f063e472a8cfe7e881a1d4abed5ef93cf40d5f65a2528cdfd2674'],
+    }),
+    ('intergraph', '2.0-4', {
+        'checksums': ['585f2f9fa92aa52022dfdcbe597a3654099ca63c1d4110a0f8e895fa32fc59c9'],
+    }),
+    ('ggnetwork', '0.5.13', {
+        'checksums': ['6c297ead19dbd89de3278f3705410b757f2d9744bc466d8175105833a4e1fd46'],
+    }),
+    ('qqman', '0.1.9', {
+        'checksums': ['3f6a931771d375174b78f220471ddd601def9b5c69631931b0992ebbc8c5bc13'],
+    }),
+    ('rstantools', '2.4.0', {
+        'checksums': ['bff72ca2f0352c6c5d2868823e286fdb73a6ead74508a4124cbcb222c83b4faa'],
+    }),
+    ('bayesplot', '1.11.1', {
+        'checksums': ['4f71e67391e0135acd3e890989b87025f3f8160242f532a8e1a0ed74ed0f3830'],
+    }),
+    ('dygraphs', '1.1.1.6', {
+        'checksums': ['c3d331f30012e721a048e04639f60ea738cd7e54e4f930ac9849b95f0f005208'],
+    }),
+    ('renv', '1.0.7', {
+        'checksums': ['7b60b58a23743803ab167f82f78663e86f778947b2bda07afa12689338794507'],
+    }),
+    ('PKI', '0.1-14', {
+        'checksums': ['c024e81977b978b705460df96639e3369420bd7e8f4f3242ec796255dc1b7966'],
+    }),
+    ('rsconnect', '1.3.1', {
+        'checksums': ['47de8a832da493e2a1b3243fb42459a53eb193f75a1143348b7d8c7478cb5557'],
+    }),
+    ('shinystan', '2.6.0', {
+        'checksums': ['a084856a2d66d8744f2c72e3e19ca35e600a508ed7ef1f7ebed8c7fc0738d529'],
+    }),
+    ('optimx', '2023-10.21', {
+        'checksums': ['0d732d5604c26af59cfb95b80ed4e226c9c10422e2d82a6cc06b92f9ba6a44b5'],
+    }),
+    ('gamm4', '0.2-6', {
+        'checksums': ['57c5b66582b2adc32f6a3bb6a259f5b95198e283a96d966a6007e8e48b380c89'],
+    }),
+    ('memisc', '0.99.31.7', {
+        'checksums': ['b403185850520db18ebd608df85c76df80e6c64af428cdc4e49c2fe487483637'],
+    }),
+    ('mclogit', '0.9.6', {
+        'checksums': ['9adc5f6d8649960abe009c30d9b4c448ff7d174c455a594cbf104a33d5a36f69'],
+    }),
+    ('projpred', '2.8.0', {
+        'checksums': ['b383ddc5eca275737b96e4e3e14256b4f4abc4b29d292b5cebf3828d0921a1f6'],
+    }),
+    ('brms', '2.21.0', {
+        'checksums': ['7289ff33c2a4b83584b7fece0a6aa53fd14b5881a467d417fbca5dbf62ec5d58'],
+    }),
+    ('drgee', '1.1.10', {
+        'checksums': ['e684f07f7dfec922380d4202922c11094f859721f77b31ff38b0d35d0f42c743'],
+    }),
+    ('stdReg', '3.4.1', {
+        'checksums': ['285335dbe29b6898641e1151ab2f06acf76c6f4d6fbeadd66d151c25d7e38a74'],
+    }),
+    ('mcmcse', '1.5-0', {
+        'checksums': ['4a820dc22c48efd32b7f9d1e1b897b4b3f165cd64b2ff85ba7029621cf9e7463'],
+    }),
+    ('copCAR', '2.0-4', {
+        'checksums': ['8b4ed53c58a665f70e48bdca689a992a81d5ecb5a6051ca7361d3870e13c77f3'],
+    }),
+    ('batchmeans', '1.0-4', {
+        'checksums': ['8694573009d9070a76007281407d3314da78902e122a9d8aec1f819d3bbe562c'],
+    }),
+    ('ngspatial', '1.2-2', {
+        'checksums': ['3fa79e45d3a502a58c1454593ec83dfc73144e92b34c14f617a6126557dd0d26'],
+    }),
+    ('BIGL', '1.9.1', {
+        'checksums': ['c2136a7a5b3a6b71c8ba3cdfc7e83c14b400c9197c1544f0967297659e3b8631'],
+    }),
+    ('drugCombo', '1.2.1', {
+        'checksums': ['9a605c655c159604033558d757711e6d83d33dfc286c1280f722d4cb7d130f80'],
+    }),
+    ('betareg', '3.1-4', {
+        'checksums': ['5106986096a68b2b516215968158589b71969ce7912879253d6e930355a18101'],
+    }),
+    ('unmarked', '1.4.1', {
+        'checksums': ['1c277248ad00122f404aabd0f0bbdeaf1cd69c58b65faaf23e36ee39f1e750c7'],
+    }),
+    ('maxlike', '0.1-11', {
+        'checksums': ['6dde7bb4a46d5509a1fee024c2fd1d13c82e14a80806969ec89359103ade01e9'],
+    }),
+    ('coxme', '2.2-20', {
+        'checksums': ['a0eeeadaabe81458b4fe80d26ca9770ff17dc3a2a41a37b2d1b09fadb887cb62'],
+    }),
+    ('AICcmodavg', '2.3-3', {
+        'checksums': ['4055b5f1fc12917b9f812c056e6a2dbf23bbd0169e468f567306ddf29d699f7a'],
+    }),
+    ('pacman', '0.5.1', {
+        'checksums': ['9ec9a72a15eda5b8f727adc877a07c4b36f8372fe7ed80a1bc6c2068dab3ef7c'],
+    }),
+    ('spaa', '0.2.2', {
+        'checksums': ['a5a54454d4a7af473ce797875f849bd893005cb04325bf3e0dbddb19fe8d7198'],
+    }),
+    ('maxnet', '0.1.4', {
+        'checksums': ['fd21e5ecf3c1ac00ef1bbe79fab4cdd62789e0c4c45f126f1b64bda667238216'],
+    }),
+    ('oai', '0.4.0', {
+        'checksums': ['f540de066de5538e303cd535cbd2e771b40474bc2c6e8d08a4894a868543ee33'],
+    }),
+    ('wellknown', '0.7.4', {
+        'checksums': ['483e6fc43edf09ed583e74ce5ca7e2d7838ef8a32291e06d774c37546eed1a34'],
+    }),
+    ('rgbif', '3.8.0', {
+        'checksums': ['8b5cd096404291d39778ec4fed36cd25719fa0ca4225866e67566c4d346d2ce8'],
+    }),
+    ('rgdal', '1.6-7', {
+        'checksums': ['555cedfdadb05db90b061d4b056f96d8b7010c00ea54bc6c1bbcc7684fadae33'],
+    }),
+    ('rgeos', '0.6-4', {
+        'checksums': ['9d03c4de96fd3fad55ff8d1ff8113dcaaa00f15d9d0588e54c9f91751bcede11'],
+    }),
+    ('mapproj', '1.2.11', {
+        'checksums': ['db2d201cc939de26717566066bf44225a967ccde6fc34731af845f03c086347d'],
+    }),
+    ('rbison', '1.0.0', {
+        'checksums': ['9957e5f85ce68f5dd0ddc3c4b2b3c9d2f52d6f37587e1022ab8a44863534a83c'],
+    }),
+    ('rebird', '1.3.0', {
+        'checksums': ['b238d3f246aa0249145894e1f3a90f46902f6615fc2f23b24c99bb5feecc55d3'],
+    }),
+    ('rvertnet', '0.8.4', {
+        'checksums': ['b1826899f33640541752f2b68ed4d23530fe62744ac4714adf79ff748fc6701a'],
+    }),
+    ('ridigbio', '0.3.8', {
+        'checksums': ['e518dbaeaf7f0dd0b833d83a6a094e07c5bd84935279c9e35bb69fe35ee00288'],
+    }),
+    ('spocc', '1.2.3', {
+        'checksums': ['ee14de78a9a91bf4220b3317d724f9e4953fda8b5478b2083690c984903db951'],
+    }),
+    ('spThin', '0.2.0', {
+        'checksums': ['2e997afb79a2a990eded34c71afaac83986669cfa9ac51b15ae3f2b558902048'],
+    }),
+    ('RPostgreSQL', '0.7-6', {
+        'checksums': ['385939708b6a3657663409f91e165ded0ff5268d1dc6225e0f9b34764baf2d2c'],
+    }),
+    ('fasterize', '1.0.5', {
+        'checksums': ['d44f101aec29aee285c4c7b578e26d11b6add423336ace90a7c22e07cfc1c3b4'],
+    }),
+    ('BIEN', '1.2.6', {
+        'checksums': ['fa7a25d89f26c10686fb4ab4d0aa704beb50dc44b173ff56abe4ab3e5991f99f'],
+    }),
+    ('rangeModelMetadata', '0.1.5', {
+        'checksums': ['289620500522d489aafbb03c85f68182ef0a6701fed5f9d09b55fae337e2647b'],
+    }),
+    ('ENMeval', '2.0.4', {
+        'checksums': ['6d9f3c460fa7ab3131cede904fcb9280cf69f4fdd43f67115a3abcb8ed5b64d1'],
+    }),
+    ('plotmo', '3.6.3', {
+        'checksums': ['6917cd8185325f1f2998fb14def9e6a8d93f1b708cf70d7c443d3960c9189b7b'],
+    }),
+    ('earth', '5.3.3', {
+        'checksums': ['786a0fcabb3db13e0e0a4ba61ecccb7e171030b39bc97926f8e7159485d2f572'],
+    }),
+    ('mda', '0.5-4', {
+        'checksums': ['f25f7f28807d0fa478b1b55eb9d026ebc30577d9d5ff288f9abfe1f3fdb8a759'],
+    }),
+    ('xgboost', '1.7.7.1', {
+        'checksums': ['f7912ccf3a583a27208f74ca15c3b272cc930bae6b10ae7e5958ff2951ee9723'],
+    }),
+    ('biomod2', '4.2-5-2', {
+        'checksums': ['1c4ca427b8d6af54de548023dcbe25c7e9cbea7afb684c58b66f4210af9eb4e5'],
+    }),
+    ('poLCA', '1.6.0.1', {
+        'checksums': ['ed8c60a42bff0402c9ba2f9ce1422dd171e711c1a64498c4d96010ddb29f6b16'],
+    }),
+    ('PermAlgo', '1.2', {
+        'checksums': ['aa2c774d6c6dcfeec882c1936e8723ef49bd36030fb10c17ca60bb9d4a519443'],
+    }),
+    ('coxed', '0.3.3', {
+        'checksums': ['d0d6cb8fea9516b3c63b34d0d81f3804c18a07f97a83e51555575c8ed4c75626'],
+    }),
+    ('testit', '0.13', {
+        'checksums': ['90d47168ab6bdbd1274b600b457626ac07697ce09792c92b2043be5f5b678d80'],
+    }),
+    ('NISTunits', '1.0.1', {
+        'checksums': ['eaccd68db5c73d6a089ce5b323cdd51bc6a6a58ce467987158ba8c9be6a0a94e'],
+    }),
+    ('celestial', '1.4.6', {
+        'checksums': ['9f647f41465ac65b254717698f1978871c378ad8e6ccaa693abf579437069abe'],
+    }),
+    ('RPMM', '1.25', {
+        'checksums': ['f04a524b13918062616beda50c4e759ce2719ce14150a0e677d07132086c88c8'],
+    }),
+    ('RefFreeEWAS', '2.2', {
+        'checksums': ['de2812f166caabf6ea01c0533402e5cd9d8a525a2a7583e4757decf22319caab'],
+    }),
+    ('wordcloud', '2.6', {
+        'checksums': ['53716954430acd4f164bfd8eacd7068a908ee3358293ded6cd992d53b7f72649'],
+    }),
+    ('JADE', '2.0-4', {
+        'checksums': ['d4b3d65a33cae454d3ab13343bceabfb3f6b8004ac64ae7bd86dee92a1cd2055'],
+    }),
+    ('awsMethods', '1.1-1', {
+        'checksums': ['50934dc20cf4e015f1304a89de6703fed27e7bd54c6b9fc9fb253cdf2ecb7541'],
+    }),
+    ('aws', '2.5-5', {
+        'checksums': ['b27cb2795cb59592d474cfaf49a21657a8878404da4f01c556f7323e953b4c5b'],
+    }),
+    ('ruv', '0.9.7.1', {
+        'checksums': ['a0c54e56ba3d8f6ae178ae4d0e417a79295abf5dcb68bbae26c4b874734d98d8'],
+    }),
+    ('mhsmm', '0.4.21', {
+        'checksums': ['293544afb194934b1d58cf88c6f8c372f537745514b6e428cf83ae62e87d2bba'],
+    }),
+    ('dbarts', '0.9-28', {
+        'checksums': ['d2e4b4ee1c191e7c506be3fec5a5e877c1b36754cba558bd75eaac9cc6ac0138'],
+    }),
+    ('proftools', '0.99-3', {
+        'checksums': ['e034eb1531af54013143da3e15229e1d4c2260f8eb79c93846014db3bdefb724'],
+    }),
+    ('NCmisc', '1.2.0', {
+        'checksums': ['26fcfbc79810f23a28389a5ce5519e6ddc2470c5e924ba8cf4dd19a1b0fd9f83'],
+    }),
+    ('reader', '1.0.6', {
+        'checksums': ['905c7c5a1b035ac8213fc533fa26e511abfeea40bd22e3edfde42a49074e88f4'],
+    }),
+    ('gnumeric', '0.7-10', {
+        'checksums': ['f6fcd9012f2fa777127c86ba520d8dc834f4ea746a6e29623edd072479191c75'],
+    }),
+    ('tcltk2', '1.2-11', {
+        'checksums': ['ad183ae3b7190501504a0589e0b3be480f04267303e3384fef00987446a37dc5'],
+    }),
+    ('minty', '0.0.1', {
+        'checksums': ['cfbdc6603c8fb54ea4d43091e2aee4c99212e6e20a335ed89576156d86237acd'],
+    }),
+    ('readODS', '2.3.0', {
+        'checksums': ['1e120ff8fdb34c7e00f07726b4843cfaeee9c680bfdc2982e83422c24e4c0491'],
+    }),
+    ('nortest', '1.0-4', {
+        'checksums': ['a3850a048181d5d059c1e74903437569873b430c915b709808237d71fee5209f'],
+    }),
+    ('EnvStats', '2.8.1', {
+        'checksums': ['12952b9eaa64b7bdbaaa5c6b7acb3aa1028ddfa4e5de7ddfea54f900c452d6a6'],
+    }),
+    ('outliers', '0.15', {
+        'checksums': ['cc31d7f2faefd2c3a27f8ce78c7e67d3b321dcd6690292fad2468125e5e635fb'],
+    }),
+    ('gWidgets2', '1.0-9', {
+        'checksums': ['d4d9ef7b2788efeb8209aa8dd610af4cd86286392fbdf9ea70bcfeafda95d4c5'],
+    }),
+    ('gWidgets2tcltk', '1.0-8', {
+        # need to run installation via xvfb-run to avoid problems on headless systems:
+        # no DISPLAY variable so Tk is not available
+        # [tcl] invalid command name "font"
+        'preinstallopts': "xvfb-run ",
+        'checksums': ['10399cc636eeeb5484c3379970c37c56df10d979bf866a35b66d0c75b7222c0a'],
+        # skip 'import' check with library(gWidgets2tcltk), since it also fails on headless systems...
+        'modulename': False,
+    }),
+    ('mgsub', '1.7.3', {
+        'checksums': ['c9ae2560fe2690bedc5248af3fc89e7ef2bc6c147d46ced28f9824584c3791d5'],
+    }),
+    ('ie2misc', '0.9.1', {
+        'checksums': ['f1db0c66c8fa05e99c4059c1799abc3eb7effd7113baf03f38d26853ac05c425'],
+    }),
+    ('assertive.base', '0.0-9', {
+        'checksums': ['4bf0910b0eaa507e0e11c3c43c316b524500c548d307eb045d6f89047e6ba01e'],
+    }),
+    ('assertive.properties', '0.0-5', {
+        'checksums': ['b68954f53082561f0242682611bf3373e0bf30d8ac2256d82474edc5f992f4dd'],
+    }),
+    ('assertive.types', '0.0-3', {
+        'checksums': ['ab6db2eb926e7bc885f2043fab679330aa336d07755375282d89bf9f9d0cb87f'],
+    }),
+    ('assertive.numbers', '0.0-2', {
+        'checksums': ['bae18c0b9e5b960a20636e127eb738ecd8a266e5fc29d8bc5ca712498cd68349'],
+    }),
+    ('assertive.strings', '0.0-3', {
+        'checksums': ['d541d608a01640347d661cc9a67af8202904142031a20caa270f1c83d0ccd258'],
+    }),
+    ('assertive.datetimes', '0.0-3', {
+        'checksums': ['014e2162f5a8d95138ed8330f7477e71c908a29341697c09a1b7198b7e012d94'],
+    }),
+    ('assertive.files', '0.0-2', {
+        'checksums': ['be6adda6f18a0427449249e44c2deff4444a123244b16fe82c92f15d24faee0a'],
+    }),
+    ('assertive.sets', '0.0-3', {
+        'checksums': ['876975a16ed911ea1ad12da284111c6eada6abfc0118585033abc0edb5801bb3'],
+    }),
+    ('assertive.matrices', '0.0-2', {
+        'checksums': ['3462a7a7e11d7cc24180330d48cc3067cf92eab1699b3e4813deec66d99f5e9b'],
+    }),
+    ('assertive.models', '0.0-2', {
+        'checksums': ['b9a6d8786f352d53371dbe8c5f2f2a62a7866e30313f268e69626d5c3691c42e'],
+    }),
+    ('assertive.data', '0.0-3', {
+        'checksums': ['5a00fb48ad870d9b3c872ce3d6aa20a7948687a980f49fe945b455339e789b01'],
+    }),
+    ('assertive.data.uk', '0.0-2', {
+        'checksums': ['ab48dab6977e8f43d6fffb33228d158865f68dde7026d123c693d77339dcf2bb'],
+    }),
+    ('assertive.data.us', '0.0-2', {
+        'checksums': ['180e64dfe6339d25dd27d7fe9e77619ef697ef6e5bb6a3cf4fb732a681bdfaad'],
+    }),
+    ('assertive.reflection', '0.0-5', {
+        'checksums': ['c2ca9b27cdddb9b9876351afd2ebfaf0fbe72c636cd12aa2af5d64e33fbf34bd'],
+    }),
+    ('assertive.code', '0.0-4', {
+        'checksums': ['2f820474ed20e06f65b284962c87cd1e85220a11cc7fcde09716f0eee5821387'],
+    }),
+    ('assertive', '0.3-6', {
+        'checksums': ['c403169e83c433b65e911f7fd640b378e2a4a4765a36063584b8458168a4ea0a'],
+    }),
+    ('rdrop2', '0.8.2.1', {
+        'checksums': ['b9add765fe8e7c966f0d36eef939a9e38f253958bd2a3c656b890cbb0366300b'],
+    }),
+    ('Exact', '3.2', {
+        'checksums': ['53b4e20cbb57615970c572fc4e7a780a510bde8b5deadec3880095f6e17a6328'],
+    }),
+    ('lmom', '3.0', {
+        'checksums': ['4b0ae8638a63b45ddedfd65c15e3206d34e947a2b5d31e9aa8c55446d69a0291'],
+    }),
+    ('gld', '2.6.6', {
+        'checksums': ['ea23e9781207b5d47ed04e4d5758d9652cab5d1eedcf9fbc9c2ee4d3babffdc4'],
+    }),
+    ('DescTools', '0.99.54', {
+        'checksums': ['470a16405d52d7e8595ac025a0d2bf50b78edaebe83af358903e201168a80b9b'],
+    }),
+    ('orthopolynom', '1.0-6.1', {
+        'checksums': ['ec4a6ed266532f2f6d37a4ca6bd1b74c1df28a8c2caeab60e5d6af15bdbfe2c5'],
+    }),
+    ('gaussquad', '1.0-3', {
+        'checksums': ['a3337ce52bc53435cb4565a38bf48b72b384be397d2e86bb66f62973004dc810'],
+    }),
+    ('nlsem', '0.8-1', {
+        'checksums': ['0674ec2a1ae7e50b08ee1b156674c2f2100258b14d6a9068f7dd6ad1ee128377'],
+    }),
+    ('tableone', '0.13.2', {
+        'checksums': ['b1cf15579abd4240e24435d2d9aad255c839d2a0293e28cb2eef0c808c4727af'],
+    }),
+    ('jstable', '1.2.6', {
+        'checksums': ['b759553446892a4b8697be0c696f5d2c5aafdb64cff1ca1b22557687ea7218bd'],
+    }),
+    ('RCAL', '2.0', {
+        'checksums': ['10f5f938a8322d8737159e1e49ce9d12419a5130699b8a19c6ca53d6508da8cc'],
+    }),
+    ('stargazer', '5.2.3', {
+        'checksums': ['208e9b48a11cf56ce142731c204f3d2bcb5b68719f84309a36362cd925414265'],
+    }),
+    ('sensemakr', '0.1.4', {
+        'checksums': ['6a1354f05392fa9343b90f69a54022c995651fb3c3d05cb08fa088ef52258caf'],
+    }),
+    ('CompQuadForm', '1.4.3', {
+        'checksums': ['042fc56c800dd8f5f47a017e2efa832caf74f0602824abf7099898d9708660c4'],
+    }),
+    ('nonnest2', '0.5-7', {
+        'checksums': ['e440c2464b3bd3b452e02583bb280eecba6acecf0f2c04b6b9fe4dcdd128db3e'],
+    }),
+    ('blavaan', '0.5-5', {
+        'checksums': ['a8d3bc5e9d15a2e8496950e87ed3c6bc6d769e761ec068e1f063f2d255330b6d'],
+    }),
+    ('mathjaxr', '1.6-0', {
+        'checksums': ['ecc47607111b788d84789459af7f4f9102719f98640b7a23bd5a4eb1a6d3c179'],
+    }),
+    ('metadat', '1.2-0', {
+        'checksums': ['f0cce5e30c3d256eaf5a41e4f52ffc7108e195016a4b99409e0ab4c2ef58f5b8'],
+    }),
+    ('metafor', '4.6-0', {
+        'checksums': ['07344cc3bd87b8bd25ef998e9a6ce322ae8e448ef5af06ec3e79631724e18666'],
+    }),
+    ('RNifti', '1.7.0', {
+        'checksums': ['e58cf73a0f5fbf5d6a2c845bfdeea193eb5262c73d0f329beae17d68f40e18e8'],
+    }),
+    ('oro.nifti', '0.11.4', {
+        'checksums': ['efe4f5d2c2e37ff6c3e9250f54ef775e4d452c1334f781f22f219ed53148b606'],
+    }),
+    ('fmri', '1.9.12', {
+        'checksums': ['d8b55f8867bb0487d1a8241b340099c41d990ae5aa49768b2dc0f9db58af65b3'],
+    }),
+    ('linkcomm', '1.0-14', {
+        'checksums': ['36f1557c65d862fc87635eedfad77f18a5deb66da00895e50e2d5eac0f23b597'],
+    }),
+    ('rnetcarto', '0.2.6', {
+        'checksums': ['4f28ae62748654cb6f90e1ffa17b05bb8b89eb6a20262d9c5d39cb862f71dc91'],
+    }),
+    ('optextras', '2019-12.4', {
+        'checksums': ['59006383860826be502ea8757e39ed94338f04d246c4fc398a088e004d8b13eb'],
+    }),
+    ('setRNG', '2024.2-1', {
+        'checksums': ['e3b21b08b7db3c2c06543a21718e1c18a2b2d2ddf4c92f0e44841d10f55d5c40'],
+    }),
+    ('Rvmmin', '2018-4.17.1', {
+        'checksums': ['55000ac4ff57d42f172c46c7d6b0a603da3b65866d6440d6b32bac4d2b81814e'],
+    }),
+    ('Rcgmin', '2022-4.30', {
+        'checksums': ['2684b8e7fb970da2afbc00e482031cf4447416249d04c4c1740400ad112fb911'],
+    }),
+    ('optimr', '2019-12.16', {
+        'checksums': ['73b1ed560ffd74599517e8baa4c5b293aa062e9c8d50219a3a24b63e72fa7c00'],
+    }),
+    ('DMCfun', '3.5.4', {
+        'checksums': ['2c2ab38ed5ae140e1d5d045a1d4b95ef9d286b13467301be37477258de87804f'],
+    }),
+    ('miceadds', '3.17-44', {
+        'checksums': ['6ef69dd1ac3b547a1450ca54c719c5d1f983a585207cb09ae3ad6b42a8cc2165'],
+    }),
+    ('visdat', '0.6.0', {
+        'checksums': ['104acdbb9d41167b861ab24de0e1e1e14f61c1b476bac112fcbc6e47c157e598'],
+    }),
+    ('UpSetR', '1.4.0', {
+        'checksums': ['351e5fee64204cf77fd378cf2a2c0456cc19d4d98a2fd5f3dac74b69a505f100'],
+    }),
+    ('norm', '1.0-11.1', {
+        'checksums': ['c2ffe6c30fc203337bde49ef630a740141604d8e648c558e58c20116c47963bc'],
+    }),
+    ('naniar', '1.1.0', {
+        'checksums': ['a94c46c3a78893bd935a0a51adb6a523915afb35427a56ce650b1e1ab28c6f44'],
+    }),
+    ('stringdist', '0.9.12', {
+        'checksums': ['e1843452ff4184b8d3bc5168732c0c65d3fce11f0df9fcf92173a22ef92e66c4'],
+    }),
+    ('image.binarization', '0.1.3', {
+        'checksums': ['ecc844bdd9bf15b88ce1e1afc8321c177bdc8ec32618c22102b1e8b02b36e00e'],
+    }),
+    ('lassosum', '0.4.5', {
+        'source_urls': ['https://github.com/tshmak/%(name)s/releases/download/v%(version)s/'],
+        'sources': ['%(name)s_%(version)s.tar.gz'],
+        'checksums': ['18c0d0b5022bcf81a9bf1b3b6647da3e080f221828b473ea2a45a9bf98474fbc'],
+    }),
+    ('lslx', '0.6.11', {
+        'checksums': ['373cfb1e79174b568dac254fab02d99bf79b830218bf18f0cc592af6fef853d6'],
+    }),
+    ('truncnorm', '1.0-9', {
+        'checksums': ['5156acc4d63243bf95326d6285b0ba3cdf710697d67c233a12ae56f3d87ec708'],
+    }),
+    ('Rsolnp', '1.16', {
+        'checksums': ['3142776062beb8e2b45cdbc4fe6e5446b6d33505253d79f2890fe4178d9cf670'],
+    }),
+    ('regsem', '1.9.5', {
+        'checksums': ['7392bd644efe82f96da0df470a962de398f1d0162273cba1ff31c2ecd7f17a53'],
+    }),
+    ('semPLS', '1.0-10', {
+        'checksums': ['cb587ccfdaf970f426dc7146035c7e010b1c51c17bf4fc089fd796eda58db460'],
+    }),
+    ('GxEScanR', '2.0.2', {
+        'checksums': ['6d42fd15d83dd1491405b282d26fa472f9f9902a9dc68836d6a48b459ada6a4c'],
+    }),
+    ('admisc', '0.35', {
+        'checksums': ['cf4b5b3f09f0fd0ad085d97bd589be0cfe6652e5a365f7b09c0e93515b5aed3f'],
+    }),
+    ('polycor', '0.8-1', {
+        'checksums': ['f05f53e0b5c992de0e5b4c6b2e998148cf83310358821e1bba180d81face0509'],
+    }),
+    ('multipol', '1.0-9', {
+        'checksums': ['4ec305565c214872705f7d5ea4928c8761750663d664a77f1676d81a1ca0c632'],
+    }),
+    ('symmoments', '1.2.1', {
+        'checksums': ['9a6be1f8fe44f6ab5a1790e870fd8b18de1686a48a14a9fca2d035bfb5458672'],
+    }),
+    ('rngWELL', '0.10-9', {
+        'checksums': ['9969cc10be6d18155d2b2de93381c52e7f720c2b1b3f2554fa8bfa84ceb7cacb'],
+    }),
+    ('randtoolbox', '2.0.4', {
+        'checksums': ['94da14953e4ffc7981d7a9398622082c4eda3bd9d912d1437b527d949da39e4b'],
+    }),
+    ('TruncatedNormal', '2.2.2', {
+        'checksums': ['aef567e8962a64d1afbdfd98ab8f385f32966c3c42acb54ee20f02dceab18e15'],
+    }),
+    ('cSEM', '0.5.0', {
+        'checksums': ['25ae115520aab7d916da9ded1f87b8519c4e15101c4adef2284c51eb03d81728'],
+    }),
+    ('cubelyr', '1.0.2', {
+        'checksums': ['18b10f1fe561305a1e115a438460264b88b301b3e8c086b931500a798be39b94'],
+    }),
+    ('furrr', '0.3.1', {
+        'checksums': ['0d91735e2e9be759b1ab148d115c2c7429b79740514778828e5dab631dc0e48b'],
+    }),
+    ('broom.mixed', '0.2.9.5', {
+        'checksums': ['959fa6cd26135ad408d3ee447d4423919c9cdaa9a6ecc4396f858c90d30b5ab3'],
+    }),
+    ('DiceKriging', '1.6.0', {
+        'checksums': ['ab5d1332809f2bb16d156ed234b102eb9fbd6de792e4291f9f6ea4652215cb49'],
+    }),
+    ('grf', '2.3.2', {
+        'checksums': ['c0392b6f6e20058cc6d5cdd5b5c1e5298bc42906cee45d04143adc4d6162427d'],
+    }),
+    ('twang', '2.6', {
+        'checksums': ['0b28382af11cebf675cdffc66990e011d751e9703d27e2ed41895ead5e667fdb'],
+    }),
+    ('neuralnet', '1.44.2', {
+        'checksums': ['5f66cd255db633322c0bd158b9320cac5ceff2d56f93e4864a0540f936028826'],
+    }),
+    ('PCAmatchR', '0.3.3', {
+        'checksums': ['5dc9d8bb4c0020b5e51a53a4fa71afa9adc6b907ea618b231f5cfc2877a49779'],
+    }),
+    ('origami', '1.0.7', {
+        'checksums': ['b44034541ac358e0686682684c40e9a1de8d78c7913e56e4d3dbe41a2a55c62c'],
+    }),
+    ('hal9001', '0.4.6', {
+        'checksums': ['1123288b603f97de98b42178ab5b4809536f64d7884a46b829795245eacd08dd'],
+    }),
+    ('cobalt', '4.5.5', {
+        'checksums': ['076c1956e1a24d3ded5ac6227bf05cb294e103dc0d02d825e65b72d2c5f62ec0'],
+    }),
+    ('CBPS', '0.23', {
+        'checksums': ['ed8fe09b642db459a516bdeb03a49e718a7d5ad915cbf82400029508efe9b32d'],
+    }),
+    ('SBdecomp', '1.2', {
+        'checksums': ['0be4e1c9e8bed87fd1712e62346a97148a1a295ff56981e832921cc390006e5c'],
+    }),
+    ('naturalsort', '0.1.3', {
+        'checksums': ['cd38a9c5f323f61459e6096cdbf4493851d40497baf671af4f8dfe9a7c00e857'],
+    }),
+    ('lwgeom', '0.2-14', {
+        'checksums': ['26db6cf7dbc8cf43a70e5e2a34941a1c4b65e182f86f58d64ff9f614b3be929c'],
+    }),
+    ('finalfit', '1.0.7', {
+        'checksums': ['4fb9fa3a8eae9ea80277ca3f256947d6f9485ab66ad2e3bbe429a586e79eda12'],
+    }),
+    ('bigD', '0.2.0', {
+        'checksums': ['bca9eb0c9a231b159b97650884b1a7a490bc3bf4edef11cc12db06fb15c6ff5f'],
+    }),
+    ('juicyjuice', '0.1.0', {
+        'checksums': ['64f5418b2a4794b47f0525baaf101beb4f1374ea22f38d7d604f5118bdb6e12a'],
+    }),
+    ('reactR', '0.5.0', {
+        'checksums': ['e79e3f37c2f28ae70c912efe203dbca35094ce017e497421c049e1221817f192'],
+    }),
+    ('reactable', '0.4.4', {
+        'checksums': ['b4aae6be2dd85aaa5226067415e501abc139e99499bc62c539630eeafdaf6af2'],
+    }),
+    ('gt', '0.10.1', {
+        'checksums': ['c56760e2dd4490b755c569d5fbc25f38b33096cefec5bf24a01cb198e4cc3387'],
+    }),
+    ('gtsummary', '1.7.2', {
+        'checksums': ['ddc225f1c3a629b47bce85b64229d2a99c46c7bf22b88a6bb6cc728e76d34b0a'],
+    }),
+    ('ncdf4', '1.22', {
+        'checksums': ['b9a9a2004f4c008d665afbe617f4e4b45e57dc70e303c8ec341aa5a51fbb1210'],
+    }),
+    ('geex', '1.1.1', {
+        'checksums': ['a1aebb9f73ba8dfe26ee3dc7b0725ccb814b3db5358ba17e417bdfc7eb3e4143'],
+    }),
+    ('momentfit', '0.5', {
+        'checksums': ['5f68e90545f123790d6ba149a21f07d1885361e4ca748cc93fb13bc443f7c720'],
+    }),
+    ('StatMatch', '1.4.2', {
+        'checksums': ['852f9f923e18f528af86858e10142800182f87c216636b4d7de4345661ee954f'],
+    }),
+    ('stars', '0.6-5', {
+        'checksums': ['4fcb12f25ce4351840d24489b8d6ca61eecc0da12f93bfab702701a430d0afac'],
+    }),
+    ('rapidjsonr', '1.2.0', {
+        'checksums': ['62c94fcdcf5d0fbdfa2f6168affe526bf547c37c16d94e2e1b78d7bf608eed1f'],
+    }),
+    ('jsonify', '1.2.2', {
+        'checksums': ['3745e962592f021a3deaed8b2f6b99c4f7181f28e095300a96d1c2b08af4af2f'],
+    }),
+    ('geometries', '0.2.4', {
+        'checksums': ['c6292acc336bb8520b8cb3672566f993fd077cb1f6f980ae39b9c9f56b971410'],
+    }),
+    ('sfheaders', '0.4.4', {
+        'checksums': ['f65ffe67b1d07beb6904b8960c66be684f5526b4d6450ab46c630c77e9b9bd07'],
+    }),
+    ('geojsonsf', '2.0.3', {
+        'checksums': ['275ca14672d982e6a95884515f49d8a0aad14f3be62ea01b675a91b0bffb46d1'],
+    }),
+    ('leaflet.providers', '2.0.0', {
+        'checksums': ['c5ceeadc8088c9840a8249f0347501cdba0119be97219a01ea2050d1dd4a8666'],
+    }),
+    ('leaflet', '2.2.2', {
+        'checksums': ['d2877b8d394116cc648456a828c5b825728be6a7afbbb3d55cc142c91a1ab8eb'],
+    }),
+    ('leafsync', '0.1.0', {
+        'checksums': ['7d8fd8dbbbf66417cf32575f14c0fe68199762ecf1c036c7905c7c5ff859d75c'],
+    }),
+    ('leafem', '0.2.3', {
+        'checksums': ['defd5baa4383da4182e97d41145c7a9633a987de05c465eb99a7a452fbf375e3'],
+    }),
+    ('widgetframe', '0.3.1', {
+        'checksums': ['44089a2cf8b0941a6f3da55da36353e2f44653ca58bfec7960ee5b71ea380d48'],
+    }),
+    ('tmaptools', '3.1-1', {
+        'checksums': ['fd89cb0d7fb44e0a5dd5311fa3e75a729746bf2e8e158d5ec423e5963f1b542d'],
+    }),
+    ('tmap', '3.3-4', {
+        'checksums': ['c966bcd61c21a9609144f2de89da1601e734ee2c6903f08bf624b217944faaf7'],
+    }),
+    ('collapse', '2.0.14', {
+        'checksums': ['a802773967abc0c015be4f00f26042eb792175f317f6d75bed8849a0928e555a'],
+    }),
+    ('genoPlotR', '0.8.11', {
+        'checksums': ['f127f7fe8b19c899ecfdf98bf69d2e18926afb593a72fc40097acca66d401607'],
+    }),
+    ('VineCopula', '2.5.0', {
+        'checksums': ['51b99e6fe0a1f4c32c860fc24b0164f0ade5d81aee7235e0ef5b5256e2115b68'],
+    }),
+    ('Rmpfr', '0.9-5', {
+        'checksums': ['bce9a2729efcd329a13910e2ecb4675b4626dd3322cd01b01cb835d516a5f31b'],
+    }),
+    ('scam', '1.2-17', {
+        'checksums': ['b33de62a18da930ceee2db73cd951fb47d5855bb58c80331eee2730437e30502'],
+    }),
+    ('copula', '1.1-3', {
+        'checksums': ['9b196cb4f1d6faa46ae6f80a4639b4044c98aaf9dcc02face6e04a51003677a6'],
+    }),
+    ('evd', '2.3-7', {
+        'checksums': ['4a899df15d39be4a8d544de4f5e4690b4673790a46da6a6c9c2a70fef3b55648'],
+    }),
+    ('ismev', '1.42', {
+        'checksums': ['0d57fbeca83bd478e84fcff795967d51d8448c629abe7adc6c4c18c7fb8bf1a5'],
+    }),
+    ('GJRM', '0.2-6.5', {
+        'checksums': ['5ca310337acc4539aea9dafc4200abccb9476bd0c73cbe8c7c95b50511a4c948'],
+    }),
+    ('penfa', '0.1.1', {
+        'checksums': ['a22a8ac3d4a040c77e50ddc92328c1989eae536d79fe56013e9372ba27c114e5'],
+    }),
+    ('kde1d', '1.0.7', {
+        'checksums': ['d60bc5f543d865df9f928b4dfe0e4f846774280d7faa343a24c0e7083129cffc'],
+    }),
+    ('RcppThread', '2.1.7', {
+        'checksums': ['88debafefb13a77e507eeb2ae2a9e53f717e8cff071fcb4063b2be549423bbe8'],
+    }),
+    ('wdm', '0.2.4', {
+        'checksums': ['e2d19c04ea2fb9394cc2b61899c7fd21ae7c6d5825bfdcb74822c7243cd335d3'],
+    }),
+    ('rvinecopulib', '0.6.3.1.1', {
+        'checksums': ['df95d007552e7fa30aefad90a86acf5e14f6fe1e363ed4c71a74d501a08cbf32'],
+    }),
+    ('PearsonDS', '1.3.1', {
+        'checksums': ['415d3cdb980cff474e09f5cd4118f7c5475d7a9623430b16e83999a370fb07e8'],
+    }),
+    ('covsim', '1.1.0', {
+        'checksums': ['30de5b5711d7608796479c3a2adb9c9cbf8659f833d3f687a9f8b275a093665e'],
+    }),
+    ('semTools', '0.5-6', {
+        'checksums': ['f522ce3c02ac580ad49af7a7278141dae39fdfaeccc7d1379faf1266ce9fcaf2'],
+    }),
+    ('GPArotation', '2024.3-1', {
+        'checksums': ['88f657af29789591d581e0c529fd50ef1307abfb33e0403209bd3e591e2654da'],
+    }),
+    ('dcurver', '0.9.2', {
+        'checksums': ['cc6c55090d3607910515981ea0c7221e40e7a29e0da0c5a5f42c3847012290ec'],
+    }),
+    ('mirt', '1.41', {
+        'checksums': ['d01b2d2e8caf0f1569f1db9138839e698e17c46020dfaaab8a5496f649c6a863'],
+    }),
+    ('rpf', '1.0.14', {
+        'checksums': ['e4bb090a810ec4e70a23547f95e1e07ce0229e38fbbbbe22abfad98e9b33f796'],
+    }),
+    ('OpenMx', '2.21.11', {
+        'checksums': ['152570b9cdb2d6b91f309b352458ed1b29ae2f7ce1f97c091f84c617a14071cc'],
+    }),
+    ('matlab', '1.0.4', {
+        'checksums': ['1988a2220703444a575f2bad4eb090a0da71478599eb53081dd7237b7ec216ea'],
+    }),
+    ('FactorCopula', '0.9.3', {
+        'checksums': ['df1675bb96431417cdbb9000ab80e15e12d82c8ed9809eeb3d7fe7b4855178d3'],
+    }),
+    ('rpact', '4.0.0', {
+        'checksums': ['ecd9e5af98b16f71c0b6511080eafea57f94fe87018038b087519f907cf19ad7'],
+    }),
+    ('ldbounds', '2.0.2', {
+        'checksums': ['a98d8498e46fd814957e7d47a6bf3d27649885ed840c0753469f268b8942bda7'],
+    }),
+    ('catlearn', '1.0', {
+        'checksums': ['c6ef66257b8a6968599876f53bd431b5d836f125b32cdb829b53fb972ffeffaf'],
+    }),
+    ('MetaUtility', '2.1.2', {
+        'checksums': ['e38c21588c239aa8926e64d916aa0f3b04108c2992f0e801095e4c7920b9ad5d'],
+    }),
+    ('EValue', '4.1.3', {
+        'checksums': ['52a8d4df8ddc80eddf7c2f6684ed6f0fd71f3bd1bfc096ed07cfe875a367e446'],
+    }),
+    ('dagitty', '0.3-4', {
+        'checksums': ['796f1424fc75800f1818f427809730f43eb798614ac570af1c301e951b2d3c82'],
+    }),
+    ('ggdag', '0.2.12', {
+        'checksums': ['9d5621290eb234e9c5c2e8cb357e1e5267a00a9549b6c45ae7e760989de2b160'],
+    }),
+    ('simex', '1.8', {
+        'checksums': ['80c7841196b9377a9367eb6960ad80ca0bf8de511b8b18a0031bfbe7bde289a0'],
+    }),
+    ('hash', '2.2.6.3', {
+        'checksums': ['8a030b5be9c6494b44af9d8cd7a966cc94a41ae0aaecb553fc36de4762749110'],
+    }),
+    ('nabor', '0.5.0', {
+        'checksums': ['47938dcc987279281c13abfd667660bf1b3b76af116136a27eb066ee1a4b43da'],
+    }),
+    ('RhpcBLASctl', '0.23-42', {
+        'checksums': ['5c889d5b69e264060b9f1f0383c447f594855b8afc15b7d76d39e4d62b946615'],
+    }),
+    ('harmony', '1.2.0', {
+        'checksums': ['a63c7d7cbbc5d183e8f919552e9d73044e0a89660856e80861a00eb5d25ac7b5'],
+    }),
+    ('apcluster', '1.4.13', {
+        'checksums': ['5e975baa427def9944ec0a3ea5f8f92f4ebce4e98689b4019525d25b54d5a1a7'],
+    }),
+    ('DataCombine', '0.2.21', {
+        'checksums': ['352b235612e2cf8234b3ab5f9aa6f7a394b006b98d24e315940ccc65c4218b47'],
+    }),
+    ('docstring', '1.0.0', {
+        'checksums': ['14528bc85bbb299fb8fe1a7116034f8df49ae0c26fb299376185b5d56176e5a7'],
+    }),
+    ('gdalUtils', '2.0.3.2', {
+        'checksums': ['4c6faabee2db8a87b7ea0f8e67e9fce3c5db7f4be353d7d86ea559507cbb2a4f'],
+    }),
+    ('openair', '2.18-2', {
+        'checksums': ['8b20580bc6ab4c4bbe8a8ffb5f55e75e5d6855955b49d6dcb1259436715b84df'],
+    }),
+    ('pdp', '0.8.1', {
+        'checksums': ['e23db66e5d575337d5c8fd664ccd0548cc85da2aca6613d90ce187be1dca376c'],
+    }),
+    ('date', '1.2-42', {
+        'checksums': ['5a913f960a0071cf9db05df4de03055a21a1c243b3bdbf846375537a664bcb74'],
+    }),
+    ('cmprsk', '2.2-12', {
+        'checksums': ['773ecb93be0eac7bb5dfe9ea1480380da89ea95497b7b2febb08fd7c5104acdc'],
+    }),
+    ('mets', '1.3.4', {
+        'checksums': ['8a0136c2134c169ef5b7e88741b0fa7f570a1f838341c97ce1bd5f05b6513a7a'],
+    }),
+    ('Publish', '2023.01.17', {
+        'checksums': ['436cc2bf5cdca1b3fdf892c9d35227f01740f1a4b335ff7b42a37e12c0115953'],
+    }),
+    ('riskRegression', '2023.12.21', {
+        'checksums': ['ac4ca90c4d533b3eb7659bc6b5a8ae6bd18eb9a08f619d3d19314cb10d929b1d'],
+    }),
+    ('pec', '2023.04.12', {
+        'checksums': ['6552fe9843b0b59bfd97c0db70c1ac5b0291184b498a796803b9dca0dc70ef95'],
+    }),
+    ('pammtools', '0.5.93', {
+        'checksums': ['948030fbeaee8d89cca39b2660d4ba45d7de30f6c7d83f07fcdfea66bfde3076'],
+    }),
+    ('relsurv', '2.2-9', {
+        'checksums': ['e966435c16c0978d1314867c3b9fbd7170ae7450d60e676d06cc7f8ca3d74d78'],
+    }),
+    ('mstate', '0.3.2', {
+        'checksums': ['3c473dff6854e31cdbdaf79f8fe7eaf97119b01a581874a894b283555afe8d14'],
+    }),
+    ('microbenchmark', '1.4.10', {
+        'checksums': ['04cc41be72708dce8d31ff1cb105d88cc9f167250ea00fe9a165c99204b9b481'],
+    }),
+    ('prettyGraphs', '2.1.6', {
+        'checksums': ['fece08924fc7ed05ec419afa14a2216a2bb23d9da5ed3fc61472d6e45be7577a'],
+    }),
+    ('ExPosition', '2.8.23', {
+        'checksums': ['0510bc51b1c8c883ff3652a5ed56242f91c2b7b7cf3100755436bffa1e002475'],
+    }),
+    ('alluvial', '0.1-2', {
+        'checksums': ['77b6dc4651b33b03aaaf1e09a35f9c3536e5fddac2eda34f5a34e0ae33cf2e0d'],
+    }),
+    ('SNFtool', '2.3.1', {
+        'checksums': ['982fe7c57f52c0c272b8cb5863dc5d50623b368e24ff6e27fc8b17acc0101f16'],
+    }),
+    ('BayesLogit', '2.1', {
+        'checksums': ['3a423f68339ed1bf25e21be53b1fd68452ed7807b17c36239fba759dc6fc6b70'],
+    }),
+    ('Hmsc', '3.0-13', {
+        'checksums': ['cbef4706aa09e93030243cee3ae4e62b02160d96981020f5a385751eade4f88d'],
+    }),
+    ('MonteCarlo', '1.0.6', {
+        'checksums': ['f21aecfba957bbea9576b09f75b1f7c7621637a04532a8fed2c6bb8ffc1a98cb'],
+    }),
+    ('chkptstanr', '0.1.1', {
+        'checksums': ['433b29d597d7ea6c21ed652782a7bf2d766f9223a3b7bfed235c8fe7fffd175c'],
+    }),
+    ('MLmetrics', '1.1.3', {
+        'checksums': ['2c5735fc2a2728a71272aaf0d559bc7bc09b45476ea63d94cb7be84f0dbfaf85'],
+    }),
+    ('elliptic', '1.4-0', {
+        'checksums': ['b65729b1a1c7a84a5b1a59bfc893a2d35106853eaadcae31cda5c9ee3c500bb6'],
+    }),
+    ('contfrac', '1.1-12', {
+        'checksums': ['95bfc5e970513416c080486a1cd8dfd9f8d59fb691b02ef6ccbe0ce1ed61056b'],
+    }),
+    ('hypergeo', '1.2-13', {
+        'checksums': ['6d5b78353aad1d13091ccbeb340867dad7b9eb00d0e2185286dc7e13848f4d8e'],
+    }),
+    ('rtdists', '0.11-5', {
+        'checksums': ['97cf2ea758aa02b1dfaeef5032c6e50570777552aa771ed9a86df048b7871eed'],
+    }),
+    ('AMAPVox', '2.2.1', {
+        'checksums': ['9fe36614bc1bc0f74dec4dbfe4e2b13a3b33cca90ed02670ae52705dc704eb81'],
+    }),
+    ('LCFdata', '2.0', {
+        'checksums': ['b58f4d93b9023dd1ba2db96a59ddfc058397085933d8de4cdb38ee064d5e7bf4'],
+    }),
+    ('LMERConvenienceFunctions', '3.0', {
+        'checksums': ['eb430de9fbf836173f716960d60afc2de91de7f986471f406c3ca9027142e849'],
+    }),
+    ('HGNChelper', '0.8.14', {
+        'checksums': ['6516f963301e1ebfd08745a743691d1419aa82f1197cc69bfffc946ff0bf1866'],
+    }),
+    ('logger', '0.3.0', {
+        'checksums': ['6da7bd851c5410e3cb27f32eb2e66e25f429abb1b9427ffa3beb224070cd7047'],
+    }),
+    ('parallelDist', '0.2.6', {
+        'checksums': ['30c6b3b85cf78c04a7dcd17ea7ed64356971f6ce48d15794078a18c53b249e06'],
+    }),
+    ('roptim', '0.1.6', {
+        'checksums': ['7ef0c2a2ddb3703efaabf337fa0026485875d5ffb35ba3ef5d60eb0c62c30686'],
+    }),
+    ('yulab.utils', '0.1.4', {
+        'checksums': ['32d4e1b0bfe94b9c051615e65d90fc2bd14e1d6019706cbc483f84c3cd8d3154'],
+    }),
+    ('ggfun', '0.1.5', {
+        'checksums': ['fe6c01fd68c17497f23f76dfd4e5a6edd79a6e86850b8c5054748f31527b16d3'],
+    }),
+    ('gridGraphics', '0.5-1', {
+        'checksums': ['29086e94e63891884c933b186b35511aac2a2f9c56967a72e4050e2980e7da8b'],
+    }),
+    ('ggplotify', '0.1.2', {
+        'checksums': ['01bae5759e14e211bddb04413e094ba31399b513989894ea08602d202f990e87'],
+    }),
+    ('aplot', '0.2.3', {
+        'checksums': ['1fb062050199933f724164118cc3e5d85b60a3a4d4a466016bed2928b0310d6a'],
+    }),
+    ('tidytree', '0.4.6', {
+        'checksums': ['dba909ba767283fa76795a67e048ff1c8cd339c7e44f64c9698c70ecb3d92292'],
+    }),
+    ('ggvenn', '0.1.10', {
+        'checksums': ['cde116f117266cca27d8cd20205512e602c23514db6d97caaa950b9b21fa873e'],
+    }),
+    ('scatterpie', '0.2.3', {
+        'checksums': ['704f1072ff934729aefdd659e5c81e62b59f5ae94dc36a1e1f52085dce896447'],
+    }),
+    ('shadowtext', '0.1.3', {
+        'checksums': ['861af6ff3401e34e4e5a996fde277cefb7554af24bb22459367c1f391ac12b81'],
+    }),
+    ('random', '0.2.6', {
+        'checksums': ['2b59f9bce0c3ebf8215ab42dffaf9a1c7eea7468964063215a8d422af953b069'],
+    }),
+    ('R2WinBUGS', '2.1-22.1', {
+        'checksums': ['438e6241b96b73cf9adf51b5564fd27a14710256c93aa18e6b7382acc89d38a5'],
+    }),
+    ('aricode', '1.0.3', {
+        'checksums': ['10a739353feb4f552496d3a51d436088c92edbd241f80f7c33ee5f278de1d90a'],
+    }),
+    ('DepthProc', '2.1.5', {
+        'checksums': ['e6b0afd54bb20e25a6bf5402c771848db20e9c844f0fc990ecc3d1078b9eee44'],
+    }),
+    ('dbscan', '1.1-12', {
+        'checksums': ['56f8b1bdb392f8fb679a343b2ad5b4656c4f21d4ead85d6d81900d2f8b63ceea'],
+    }),
+    ('ggh4x', '0.2.8', {
+        'checksums': ['a84e9e9553afc7b4cd107c576f93ba99eaa14c71e36ceb25f09f841a1cee62ee'],
+    }),
+    ('ComplexUpset', '1.3.3', {
+        'checksums': ['5b2f99b4a38648641c7d31fc57f201a93e5bc1b85442a0b9726f72c166d964ea'],
+    }),
+    ('proxyC', '0.4.1', {
+        'checksums': ['e83d8653578b3c245d912dd5d7b03f0b2f875b206fbe3d0f328635dabf2522a8'],
+    }),
+    ('changepoint', '2.2.4', {
+        'checksums': ['ac636fde7610137385dde1e3d8a22a2ff856a8d5c917c7ad1a5cc49f98b8649b'],
+    }),
+    ('geeM', '0.10.1', {
+        'checksums': ['fe76a32981b55835095041e777d1cf2e9ce43edb8d9488db56279f7cb6f43fe5'],
+    }),
+    ('ggstance', '0.3.7', {
+        'checksums': ['5a2647b4d130d3b76dc08a2fe568e1e8eb2c8a69a4fb831032b7614446d4456c'],
+    }),
+    ('mosaicCore', '0.9.4.0', {
+        'checksums': ['e25605d787d274eedd3de8584283c20204bcb7b94f4a409461304ce7cd867d6c'],
+    }),
+    ('ggformula', '0.12.0', {
+        'checksums': ['d569f83e059f9e4836bd513f92706fb8a614300f744dcc47bf86e8dafd8e776d'],
+    }),
+    ('kinship2', '1.9.6.1', {
+        'checksums': ['695b73964fa1d9329bd5d57f2b44e0faf56fec8a10aff5d936dff7b1d061ef2d'],
+    }),
+    ('MESS', '0.5.12', {
+        'checksums': ['41e07993e67a8aab52d9d4d07a06d654186ac8a8db9b740763ed5d481f01dcf7'],
+    }),
+    ('smoof', '1.6.0.3', {
+        'checksums': ['af8664b152876c545f6545528de6e05a289d0714103fac7afc52960a9a855fb1'],
+    }),
+    ('mlrMBO', '1.1.5.1', {
+        'checksums': ['0cf26e5e9b180d15b932541cf081a552703a60edf762aafca9933c24ea91dc99'],
+    }),
+    ('emoa', '0.5-2', {
+        'checksums': ['e9ef9bf0058b63b43a4bc7aa2f696ef1b4c3a0dc8aa804bc6347f8f650ebe1a8'],
+    }),
+    ('webutils', '1.2.0', {
+        'checksums': ['51243a1d7843dbb3968e7725c2266e1d68dcec43b919c320033f611ff9ca7f3c'],
+    }),
+    ('swagger', '5.17.14', {
+        'checksums': ['3341d9157cc35b73ffafbccc7c3dd28ba4d53493b2fa4565f38f326c2a337f6d'],
+    }),
+    ('varhandle', '2.0.6', {
+        'checksums': ['4e7afd3ef77343c61508b0465b588751dc089c264faabf7bed60e9f4d9e1c577'],
+    }),
+    ('dlm', '1.1-6', {
+        'checksums': ['89dd4130ea3a5213244c66b313fed0a74cdcc96d3e70285b14cf3fe5f354ae57'],
+    }),
+    ('PMA', '1.2-3', {
+        'checksums': ['e7572f82c159f34058fdec4c8158d394d6cf68b7978953c8893315e298cc6d06'],
+    }),
+    ('unikn', '1.0.0', {
+        'checksums': ['6edd5d420175a4691066b5c695d2a96f706d225a62473c85be62b2dd42350dc1'],
+    }),
+    ('ppcor', '1.1', {
+        'checksums': ['6a78f0c4d9caa17ab0252c5d351c2371e4ffb9047ebd13964877018dd6142bf5'],
+    }),
+    ('berryFunctions', '1.22.5', {
+        'checksums': ['3360bdc4c73d1d7daccc134e8b959b50bf58a67bbbf3186fc5efb5a020caa1cd'],
+    }),
+    ('cld2', '1.2.4', {
+        'checksums': ['79e04de836812a980406a540c0f022926ba71c2bf5294ad5eaa437a9c33e615b'],
+    }),
+    ('crfsuite', '0.4.2', {
+        'checksums': ['d5f6379a2bb7fd585fde5945189a6a69e1ef33664fe86828d646f5f4505f8d96'],
+    }),
+    ('doc2vec', '0.2.0', {
+        'checksums': ['db3853685072554402434ea699d703e01ac7818044cf47a2ee7d0e1040858908'],
+    }),
+    ('fastDummies', '1.7.3', {
+        'checksums': ['cf6a182f778711b69460b00575babfa573f1578166d83ae2ed932db5fa15a06a'],
+    }),
+    ('quanteda', '4.0.2', {
+        'checksums': ['b21c650c01f925e406057950455991f87979708e321688abf86638bbc63504e8'],
+    }),
+    ('ISOweek', '0.6-2', {
+        'checksums': ['b58a37b61ee772ea2704d510e9fce69dea4dd641b45124d566242825df4530b8'],
+    }),
+    ('sentometrics', '1.0.0', {
+        'checksums': ['b5c238bb72f36331cb1ed63b581a9a2a73cefc96f80bf770b0e064a89fe31b1b'],
+    }),
+    ('tau', '0.0-25', {
+        'checksums': ['ff22d4a633957479e0ecdb1c0223df09f9321017aade6a28b2f264fe7bbd8e90'],
+    }),
+    ('textcat', '1.0-8', {
+        'checksums': ['cb650147576bae9c78381524831c9fcc85c76177274672098aac1860aa39749e'],
+    }),
+    ('textplot', '0.2.2', {
+        'checksums': ['6e99a204b4be2ccd317978eda900b923e0e0a0f34217405777a0eb5fcc80e2a9'],
+    }),
+    ('udpipe', '0.8.11', {
+        'checksums': ['522900de24d1f0f4f15e6b26df5521ac6efaf63c5fcfc35171a78275b3633233'],
+    }),
+    ('word2vec', '0.4.0', {
+        'checksums': ['38c6934ad7c601d6de7fa44a1ecf911ef34609b5c32b67da12a0814124036a91'],
+    }),
+    ('epitools', '0.5-10.1', {
+        'checksums': ['b418854de1fcedd126f3bf19dc27e8a71ee6efae5371098ab64a53a2d51d164b'],
+    }),
+    ('RBesT', '1.7-3', {
+        'checksums': ['8a6e1a2afb07cd04f9a9bd1a1de7587c61683dd0d437db816055e30164b070a5'],
+    }),
+    ('svglite', '2.1.3', {
+        'checksums': ['f0a8564e6f9127f4d1e05cf5a5f36b4e244aee0008e27473e504c63873ef0a54'],
+    }),
+    ('rARPACK', '0.11-0', {
+        'checksums': ['c33401e2e31d272d485ce2ed22e7fe43ac641fd7c0a45a9b848d3ad60df1028a'],
+    }),
+    ('FKSUM', '1.0.1', {
+        'checksums': ['6de23f5b7692f627b0b8e9575a612e77e166c16c28acab31d5ea0a27d7afe829'],
+    }),
+    ('warp', '0.2.1', {
+        'checksums': ['020ad590de099661aa62b4d5e51499a2ac91c41c61db2dbc71c3f4a3df2c46be'],
+    }),
+    ('slider', '0.3.1', {
+        'checksums': ['200a26795fadb2058e3976af7a697dde7f120645279cfe2580b8c0d6c0a429b0'],
+    }),
+    ('rsample', '1.2.1', {
+        'checksums': ['e3f437f21ea527d1c9fa344494b4c127254c5c5d87b0b2aecfcbdeea5964edc5'],
+    }),
+    ('haldensify', '0.2.3', {
+        'checksums': ['fc0ee1d5bce54520bad6a1ce1cce5074eead6c8573dc4ce502c48a244d7f341c'],
+    }),
+    ('Polychrome', '1.5.1', {
+        'checksums': ['6fe7da62459d7b94b1a8516a4626971cf35b76331f46e36798b05d29aa00d143'],
+    }),
+    ('shinycssloaders', '1.0.0', {
+        'checksums': ['744641836a4cede2bb47caff1b600bff2c3e450dfccd2af4fab0413a8ea87d64'],
+    }),
+    ('princurve', '2.1.6', {
+        'checksums': ['0216332390eb27013b6ba62232782156dfc99ca640087fcaff53d2be9218f373'],
+    }),
+    ('ECOSolveR', '0.5.5', {
+        'checksums': ['2594ed1602b2fe159cc9aff3475e9cba7c1927b496c3daeabc1c0d227943ecc7'],
+    }),
+    ('scs', '3.2.4', {
+        'checksums': ['c3f39874bf4532fa8c2f2e2c41533ba4fe20b61cf6dfc6314407dc981621298f'],
+    }),
+    ('osqp', '0.6.3.3', {
+        'checksums': ['ff3d8e4ec7764333144d461eb5ea7a4adbf5b5f29f84c3ec3e60a93802e2f5bb'],
+    }),
+    ('CVXR', '1.0-13', {
+        'checksums': ['81895c750a562d04bb6840ef7744f3a2dd6232b076d5c18ecdcf30a60f83875a'],
+    }),
+    ('tabletools', '0.1.0', {
+        'source_urls': ['https://github.com/JMLuther/%(name)s/archive/'],
+        'sources': [{'download_filename': 'cc961c5.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}],
+        'checksums': ['667a4270456d28188734ce31411326130a94e085490ced84096c984789bb174a'],
+    }),
+    ('officer', '0.6.6', {
+        'checksums': ['f1fc3f7a9299da1fd09864da4ae6b8c47c6491f0119da86863b1c9470caeb412'],
+    }),
+    ('gfonts', '0.2.0', {
+        'checksums': ['72e2eead5280b45aadbbd9385971d65e9866fd659270b1c3c1eb98330f024aa6'],
+    }),
+    ('fontBitstreamVera', '0.1.1', {
+        'checksums': ['3298b3dd95605bdda0c5fce5594c9bedde6aa63d89b216d5c83c6c092b6d375a'],
+    }),
+    ('fontLiberation', '0.1.0', {
+        'checksums': ['acdea423e005873aa509e280074a3cef4796e4f7e9d77b3945d77b451ea039f0'],
+    }),
+    ('fontquiver', '0.2.1', {
+        'checksums': ['95871814c2d55c03ee15a54e29aadfb840c791e1430f94127d9e1dc8608a6363'],
+    }),
+    ('gdtools', '0.3.7', {
+        'checksums': ['d292c3b8574adc38007662085c3d1cf5d17e8019f085295d594380d85cf2b394'],
+    }),
+    ('flextable', '0.9.6', {
+        'checksums': ['232e050bec231b5d58ca8ad54116c476d2dd683ac2824b3688c06250338f9229'],
+    }),
+    ('ridge', '3.3', {
+        'checksums': ['5c2daecf6f97aa099ef5fa54f8448518c4f2ed6e44dd29fc60621a70721c60f5'],
+    }),
+    ('ggdist', '3.3.2', {
+        'checksums': ['f6563091cb7ca48b4fb415740a60113be6aac541616f5025110364e12cbe83f1'],
+    }),
+    ('svUnit', '1.0.6', {
+        'checksums': ['263e6c03d6c2717dfd25b96d25f8019c9c98120de280a17224e0d79adba2d522'],
+    }),
+    ('arrayhelpers', '1.1-0', {
+        'checksums': ['5fddd5dd4fb8237bcb24465ef823bc8715ba53e6e5fd7a716c31c48ec128340b'],
+    }),
+    ('tidybayes', '3.0.6', {
+        'checksums': ['706044e17855a684a5ad1aeb582963dd3c7192a4a8ad0584358d0ea7c7aadb90'],
+    }),
+    ('spdep', '1.3-5', {
+        'checksums': ['ba8efa06ddbc12408f4f6d4c85606d84922131d9c05953e0b23b81f03e56e626'],
+    }),
+    ('stringmagic', '1.1.2', {
+        'checksums': ['eed1c04aa99be5a99ecfdd32498279f170e261669cc1b91d18673454064b8f8c'],
+    }),
+    ('dreamerr', '1.4.0', {
+        'checksums': ['3e5e4afd10623b6dac6bb9b8bf0480d41c7422884cfec2d9d9786414f9026a87'],
+    }),
+    ('fixest', '0.12.1', {
+        'checksums': ['7ce71ab9856b17000aae7dd578b1b99a43fee35116500626005056b4d9e713df'],
+    }),
+    ('cmna', '1.0.5', {
+        'checksums': ['7cf99880cb70e8fd0b022184167888b1ad32dca503e0250c1d552a84f0613898'],
+    }),
+    ('XBRL', '0.99.19.1', {
+        'checksums': ['ad9ebb5431bdfecc38b8bf3b2552f1a048878a9ac02f5a9d71279b3b099a9757'],
+    }),
+    ('rhandsontable', '0.3.8', {
+        'checksums': ['901ed9c59936f7fa52ad8db3111c8904ab962f9c74f1b6cd40f81683af35d21d'],
+    }),
+]
+
+modextrapaths = {'R_LIBS_SITE': ''}
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['abind', 'base64', 'calibrate'],
+}
+
+moduleclass = 'lang'
diff --git a/easybuild/easyconfigs/r/R/R-4.4.1-gfbf-2023b.eb b/easybuild/easyconfigs/r/R/R-4.4.1-gfbf-2023b.eb
new file mode 100644
index 00000000000..09a46feeaa1
--- /dev/null
+++ b/easybuild/easyconfigs/r/R/R-4.4.1-gfbf-2023b.eb
@@ -0,0 +1,371 @@
+name = 'R'
+version = '4.4.1'
+
+homepage = 'https://www.r-project.org/'
+description = """R is a free software environment for statistical computing
+ and graphics."""
+
+toolchain = {'name': 'gfbf', 'version': '2023b'}
+
+source_urls = ['https://cloud.r-project.org/src/base/R-%(version_major)s']
+sources = [SOURCE_TAR_GZ]
+checksums = ['b4cb675deaaeb7299d3b265d218cde43f192951ce5b89b7bb1a5148a36b2d94d']
+
+builddependencies = [
+    ('pkgconf', '2.0.3'),
+    ('Autotools', '20220317'),
+]
+dependencies = [
+    ('X11', '20231019'),
+    ('Mesa', '23.1.9'),
+    ('libGLU', '9.0.3'),
+    ('cairo', '1.18.0'),
+    ('libreadline', '8.2'),
+    ('ncurses', '6.4'),
+    ('bzip2', '1.0.8'),
+    ('XZ', '5.4.4'),
+    ('zlib', '1.2.13'),
+    ('SQLite', '3.43.1'),
+    ('PCRE2', '10.42'),
+    ('libpng', '1.6.40'),  # for plotting in R
+    ('libjpeg-turbo', '3.0.1'),  # for plottting in R
+    ('LibTIFF', '4.6.0'),
+    ('Java', '11', '', SYSTEM),
+    ('libgit2', '1.7.2'),
+    ('OpenSSL', '1.1', '', SYSTEM),
+    ('cURL', '8.3.0'),
+    ('Tk', '8.6.13'),  # for tcltk
+    ('HarfBuzz', '8.2.2'),  # for textshaping
+    ('FriBidi', '1.0.13'),  # for textshaping
+
+]
+
+# Some R extensions (mclust, quantreg, waveslim for example) require the math library (-lm) to avoid undefined symbols.
+# Adding it to FLIBS makes sure it is present when needed.
+preconfigopts = 'export FLIBS="$FLIBS -lm" && '
+
+configopts = "--with-pic --enable-threads --enable-R-shlib"
+# some recommended packages may fail in a parallel build (e.g. Matrix), and
+# we're installing them anyway below
+configopts += " --with-recommended-packages=no"
+
+exts_default_options = {
+    'source_urls': [
+        'https://cran.r-project.org/src/contrib/Archive/%(name)s',  # package archive
+        'https://cran.r-project.org/src/contrib/',  # current version of packages
+        'https://cran.freestatistics.org/src/contrib',  # mirror alternative for current packages
+    ],
+    'source_tmpl': '%(name)s_%(version)s.tar.gz',
+}
+
+# !! order of packages is important !!
+# packages updated on 24 June 2024
+exts_list = [
+    # include packages that are part of the base installation of R,
+    # both to make sure they are available (via sanity check),
+    # and to be able to pass the check for required dependencies when installing extensions in parallel
+    'base',
+    'compiler',
+    'datasets',
+    'graphics',
+    'grDevices',
+    'grid',
+    'methods',
+    'parallel',
+    'splines',
+    'stats',
+    'stats4',
+    'tcltk',
+    'tools',
+    'utils',
+    ('rlang', '1.1.4', {
+        'checksums': ['f2d74527508bf3287102470beb27de0d234c3cbba399c28d3312f2c83c64a6e1'],
+    }),
+    ('Rcpp', '1.0.12', {
+        'checksums': ['0c7359cc43beee02761aa3df2baccede1182d29d28c9cd49964b609305062bd0'],
+    }),
+    ('R6', '2.5.1', {
+        'checksums': ['8d92bd29c2ed7bf15f2778618ffe4a95556193d21d8431a7f75e7e5fc102bf48'],
+    }),
+    ('cli', '3.6.3', {
+        'checksums': ['4295085f11221c54b1dd2b1d39a675a85dfd9f900294297567e1d36f65ac4841'],
+    }),
+    ('base64enc', '0.1-3', {
+        'checksums': ['6d856d8a364bcdc499a0bf38bfd283b7c743d08f0b288174fba7dbf0a04b688d'],
+    }),
+    ('rprojroot', '2.0.4', {
+        'checksums': ['b5f463fb25a24dac7a4ca916be57dbe22b5262e1f41e53871ca83e57d4336e99'],
+    }),
+    ('xfun', '0.45', {
+        'checksums': ['3816f05c2fd297b40750be1a2f386f0aa4637136421f504d14b6ad9ea0993611'],
+    }),
+    ('commonmark', '1.9.1', {
+        'checksums': ['9517a13f4ce4a99bb157493453b04419b222cb65a9471cd3b11e5045ac0db53b'],
+    }),
+    ('highr', '0.11', {
+        'checksums': ['e90d14284001963325a84a9dbeef029609d52515da8d65c87ae61be21b7fe0a7'],
+    }),
+    ('digest', '0.6.36', {
+        'checksums': ['d1777364b2358b3ff9d79428fa7c1b280042f88896302765b0d0e2d4dc7ae637'],
+    }),
+    ('desc', '1.4.3', {
+        'checksums': ['54468da73dd78fc9e7c565c41cfe3331802c2134b2e61a9ad197215317092f26'],
+    }),
+    ('ellipsis', '0.3.2', {
+        'checksums': ['a90266e5eb59c7f419774d5c6d6bd5e09701a26c9218c5933c9bce6765aa1558'],
+    }),
+    ('prettyunits', '1.2.0', {
+        'checksums': ['f059f27e2a5c82e351fe05b87ad712f7afc273c651450453f59d99af5deeacea'],
+    }),
+    ('crayon', '1.5.3', {
+        'checksums': ['3e74a0685541efb5ea763b92cfd5c859df71c46b0605967a0b5dbb7326e9da69'],
+    }),
+    ('stringi', '1.8.4', {
+        'checksums': ['c219f8f64d1a2bfd4ca9528452d44d30db1899af14f4b9ef248412443bc669f3'],
+    }),
+    ('magrittr', '2.0.3', {
+        'checksums': ['a2bff83f792a1acb801bfe6330bb62724c74d5308832f2cb6a6178336ace55d2'],
+    }),
+    ('evaluate', '0.24.0', {
+        'checksums': ['e23d764a58e7525257d57da4ccfee9d6f63b5b3c18bf01c76818ec8c9c587fd6'],
+    }),
+    ('ps', '1.7.6', {
+        'checksums': ['52c35ffc3d1e1d984a94c7bbd671ef4ad70946990cbcd80e814e17937b056dd2'],
+    }),
+    ('processx', '3.8.4', {
+        'checksums': ['6627672d7fb109f37dc1d0eaef913f4cfc7ad8ac807abf0397e6d37753b1e70b'],
+    }),
+    ('callr', '3.7.6', {
+        'checksums': ['e4bce367e869e42eaeea05566d2033d8cee2103179b11cd9a401440b58a351f8'],
+    }),
+    ('pkgbuild', '1.4.4', {
+        'checksums': ['5972843cd43654715cdbdd28f50af013fa3d1c213146654992b2b5f39ed0e2a8'],
+    }),
+    ('fs', '1.6.4', {
+        'checksums': ['7e06290f2dbe36f54fdf51b748a4b00b8b0f68967b5754e37e0c83df7fea5ac8'],
+    }),
+    ('utf8', '1.2.4', {
+        'checksums': ['418f824bbd9cd868d2d8a0d4345545c62151d321224cdffca8b1ffd98a167b7d'],
+    }),
+    ('fansi', '1.0.6', {
+        'checksums': ['ea9dc690dfe50a7fad7c5eb863c157d70385512173574c56f4253b6dfe431863'],
+    }),
+    ('pkgconfig', '2.0.3', {
+        'checksums': ['330fef440ffeb842a7dcfffc8303743f1feae83e8d6131078b5a44ff11bc3850'],
+    }),
+    ('withr', '3.0.0', {
+        'checksums': ['8c78eede6d0e648c23d38a6695f642aed2819ef708239d00b36cbc15eabbe0e7'],
+    }),
+    ('glue', '1.7.0', {
+        'checksums': ['1af51b51f52c1aeb3bfe9349f55896dd78b5542ffdd5654e432e4d646e4a86dc'],
+    }),
+    ('rstudioapi', '0.16.0', {
+        'checksums': ['74ffa867199e87a54386fbd26919233371f314f73d7338dd4e4695708fed4fe6'],
+    }),
+    ('pkgload', '1.3.4', {
+        'checksums': ['60b04b948cda4dc56257b1e89f9b0a4b1273cacecdb2bd995d66dd76e89926ce'],
+    }),
+    ('fastmap', '1.2.0', {
+        'checksums': ['b1da04a2915d1d057f3c2525e295ef15016a64e6667eac83a14641bbd83b9246'],
+    }),
+    ('htmltools', '0.5.8.1', {
+        'checksums': ['f9f62293ec06c353c4584db6ccedb06a2da12e485208bd26b856f17dd013f176'],
+    }),
+    ('yaml', '2.3.8', {
+        'checksums': ['9ed079e2159cae214f3fefcbc4c8eb3b888ceabe902350adbdb1d181eda23fd8'],
+    }),
+    ('knitr', '1.47', {
+        'checksums': ['fadd849bf94a4e02520088a6626577c3c636227fe11c5cd7e8fcc5d51a7aa6cf'],
+    }),
+    ('mime', '0.12', {
+        'checksums': ['a9001051d6c1e556e881910b1816b42872a1ee41ab76d0040ce66a27135e3849'],
+    }),
+    ('praise', '1.0.0', {
+        'checksums': ['5c035e74fd05dfa59b03afe0d5f4c53fbf34144e175e90c53d09c6baedf5debd'],
+    }),
+    ('brio', '1.1.5', {
+        'checksums': ['a9f22335ea39039de25bb27bccd5ff1ffb2b743579b31d150b6b91c9ea81d0b8'],
+    }),
+    ('jsonlite', '1.8.8', {
+        'checksums': ['7de21316984c3ba3d7423d12f43d1c30c716007c5e39bf07e11885e0ceb0caa4'],
+    }),
+    ('lifecycle', '1.0.4', {
+        'checksums': ['ada4d3c7e84b0c93105e888647c5754219a8334f6e1f82d5afaf83d4855b91cc'],
+    }),
+    ('vctrs', '0.6.5', {
+        'checksums': ['43167d2248fd699594044b5c8f1dbb7ed163f2d64761e08ba805b04e7ec8e402'],
+    }),
+    ('stringr', '1.5.1', {
+        'checksums': ['a4adec51bb3f04214b1d8ef40d3a58949f21b1497cbeaf2ba552e0891eef45de'],
+    }),
+    ('pillar', '1.9.0', {
+        'checksums': ['f23eb486c087f864c2b4072d5cba01d5bebf2f554118bcba6886d8dbceb87acc'],
+    }),
+    ('tibble', '3.2.1', {
+        'checksums': ['65a72d0c557fd6e7c510d150c935ed6ced5db7d05fc20236b370f11428372131'],
+    }),
+    ('diffobj', '0.3.5', {
+        'checksums': ['d860a79b1d4c9e369282d7391b539fe89228954854a65ba47181407c53e3cf60'],
+    }),
+    ('rematch2', '2.1.2', {
+        'checksums': ['fe9cbfe99dd7731a0a2a310900d999f80e7486775b67f3f8f388c30737faf7bb'],
+    }),
+    ('waldo', '0.5.2', {
+        'checksums': ['82cdae1ab2c5e7e5dbf5c6bdf832020b46e152732053fb45de7c9a81afdf2e05'],
+    }),
+    ('testthat', '3.2.1.1', {
+        'checksums': ['d785ce3975939e28b61048b0e28d881c80904534ff21e5b1a79a0a934124e9f7'],
+    }),
+    ('xml2', '1.3.6', {
+        'checksums': ['e81991ff99bff3616dde8683c1327194e3ea64fa3b8062f52d8ce32673dd308f'],
+    }),
+    ('curl', '5.2.1', {
+        'checksums': ['4a7a4d8c08aa1bca2fcd9c58ade7b4b0ea2ed9076d0521071be29baac8adfa90'],
+    }),
+    ('sys', '3.4.2', {
+        'checksums': ['b7bdce66f0fb681830ea6fb77b5a2c6babb43920abb1eddc733f95c0a63ce5b3'],
+    }),
+    ('askpass', '1.2.0', {
+        'checksums': ['b922369781934d0ffc8d0c0177e8ace56796c2e6a726f65e460c16f792592cef'],
+    }),
+    ('openssl', '2.2.0', {
+        'checksums': ['18b8b46ae8db4bd57c7bcc8e10d0bb549ae63e383502051cef86102ab617ddb3'],
+    }),
+    ('httr', '1.4.7', {
+        'checksums': ['1555e6c2fb67bd38ff11b479f74aa287b2d93f4add487aec53b836ff07de3a3a'],
+    }),
+    ('jquerylib', '0.1.4', {
+        'checksums': ['f0bcc11dcde3a6ff180277e45c24642d3da3c8690900e38f44495efbc9064411'],
+    }),
+    ('rappdirs', '0.3.3', {
+        'checksums': ['49959f65b45b0b189a2792d6c1339bef59674ecae92f8c2ed9f26ff9e488c184'],
+    }),
+    ('sass', '0.4.9', {
+        'checksums': ['e133049aad7964e0f6150257e1470b3748f36029322265ee797b8caf7517d4d2'],
+    }),
+    ('purrr', '1.0.2', {
+        'checksums': ['2c1bc6bb88433dff0892b41136f2f5c23573b335ff35a4775c72aa57b48bbb63'],
+    }),
+    ('cachem', '1.1.0', {
+        'checksums': ['550839fc2ae5d865db475ba2c1714144f07fa0c052c72135b0e4a70287492e21'],
+    }),
+    ('memoise', '2.0.1', {
+        'checksums': ['f85034ee98c8ca07fb3cd826142c1cd1e1e5747075a94c75a45783bbc4fe2deb'],
+    }),
+    ('bslib', '0.7.0', {
+        'checksums': ['2135d9841af382673b815a14454abff2f2ce0f5dc97484d1499298b85b752ca0'],
+    }),
+    ('fontawesome', '0.5.2', {
+        'checksums': ['da3de2a9717084d1400d48edd783f06c66b8c910ce9c8d753d1b7d99be1c5cc9'],
+    }),
+    ('tinytex', '0.51', {
+        'checksums': ['bb113b51b4b58e78902a0220d709650c1458a8c6d3fa03f58ba007f0eb74c8ea'],
+    }),
+    ('rmarkdown', '2.27', {
+        'checksums': ['61e9cb3eab4f8587fea98d3358652695b7e77eda858caa4c8985241ba6502b9f'],
+    }),
+    ('downlit', '0.4.4', {
+        'checksums': ['55c377dcee4adc48c1060e14079f3d1832453d066a2cf070530caa210c48f828'],
+    }),
+    ('cpp11', '0.4.7', {
+        'checksums': ['801d1266824c3972642bce2db2a5fd0528a65ec845c58eb5a886edf082264344'],
+    }),
+    ('systemfonts', '1.1.0', {
+        'checksums': ['1941069bd20320284ec026a38c53cb736be60bda431303ceaf8fd27ae13fb644'],
+    }),
+    ('textshaping', '0.4.0', {
+        'checksums': ['35e940786bb278560de61bb55d4f46f8c86c878d0461613ceb8c98ba9b239d7a'],
+    }),
+    ('ragg', '1.3.2', {
+        'checksums': ['8037a45209fdd50acf101208af8e832b840a11ad4201cf7fb480de432e6b6931'],
+    }),
+    ('whisker', '0.4.1', {
+        'checksums': ['bf5151494508032f68ac41e211bda80da9087c65c7068ffdd12f16669bf1f2bc'],
+    }),
+    ('pkgdown', '2.0.9', {
+        'checksums': ['6e542216c03b5286cb9901175d1a7937a664db2572bc28bb51e9000269fcdda0'],
+    }),
+    ('htmlwidgets', '1.6.4', {
+        'checksums': ['7cb08f0b30485dac26f72e4056ec4ed8825d1398e8b9f25ed63db228fe3a0ed0'],
+    }),
+    ('profvis', '0.3.8', {
+        'checksums': ['ec02c75bc9907a73564e691adfa8e06651ca0bd73b7915412960231cd265b4b2'],
+    }),
+    ('urlchecker', '1.0.1', {
+        'checksums': ['62165ddbe1b748b58c71a50c8f07fdde6f3d19a7b39787b9fa2b4f9216250318'],
+    }),
+    ('later', '1.3.2', {
+        'checksums': ['52f5073d33cd0d3c12e56526c9c53c323ebafcc79b22cc6e51fb0c41ee2b561e'],
+    }),
+    ('promises', '1.3.0', {
+        'checksums': ['f8209df3bab33340c1bc8c0d26caee2890fafb93129ff1423302abae5931fad3'],
+    }),
+    ('xtable', '1.8-4', {
+        'checksums': ['5abec0e8c27865ef0880f1d19c9f9ca7cc0fd24eadaa72bcd270c3fb4075fd1c'],
+    }),
+    ('httpuv', '1.6.15', {
+        'checksums': ['5e6ded3623a39df3e1db6cb7e7292b4c03c80b3c6c5faaac3b78b711cb205ed0'],
+    }),
+    ('sourcetools', '0.1.7-1', {
+        'checksums': ['96812bdb7a0dd99690d84e4b0a3def91389e4290f53f01919ef28a50554e31d1'],
+    }),
+    ('shiny', '1.8.1.1', {
+        'checksums': ['a38d5fb5d750e2c2091ce9101f138c1f9bc7009bbb195227a3519c5d97e36753'],
+    }),
+    ('miniUI', '0.1.1.1', {
+        'checksums': ['452b41133289f630d8026507263744e385908ca025e9a7976925c1539816b0c0'],
+    }),
+    ('brew', '1.0-10', {
+        'checksums': ['4181f7334e032ae0775c5dec49d6137eb25d5430ca3792d321793307b3dda38f'],
+    }),
+    ('roxygen2', '7.3.1', {
+        'checksums': ['215e9fa9c0e73cb33f9870854c97b25c1a6386f519f69f397123f1a66656e2c8'],
+    }),
+    ('rversions', '2.1.2', {
+        'checksums': ['de5818233e8271132fe8ea70145618950b35786e0d2f270e39bf3338f3b8b160'],
+    }),
+    ('sessioninfo', '1.2.2', {
+        'checksums': ['f56283857c53ac8691e3747ed48fe03e893d8ff348235bff7364658bcfb0c7cb'],
+    }),
+    ('xopen', '1.0.1', {
+        'checksums': ['e3b278b8c324a1aa2650141dd89d01253eea5c2555007422c797915689b29aec'],
+    }),
+    ('rcmdcheck', '1.4.0', {
+        'checksums': ['bbd4ef7d514b8c2076196a7c4a6041d34623d55fbe73f2771758ce61fd32c9d0'],
+    }),
+    ('remotes', '2.5.0', {
+        'checksums': ['4d663f1426cd88d42f4070f23d969305c575e0499ed1397be6607b0770d2850c'],
+    }),
+    ('clipr', '0.8.0', {
+        'checksums': ['32c2931992fbec9c31b71de3e27059f1cbb45b4b1f45fd42e0e8dbcec6de3be9'],
+    }),
+    ('ini', '0.3.1', {
+        'checksums': ['7b191a54019c8c52d6c2211c14878c95564154ec4865f57007953742868cd813'],
+    }),
+    ('gitcreds', '0.1.2', {
+        'checksums': ['41c6abcca5635062b123ffb5af2794770eca5ebd97b05c5a64b24fa1c803c75d'],
+    }),
+    ('httr2', '1.0.1', {
+        'checksums': ['33e92d830981b33cd5e55068b500c57dbfb72329c2fce54be3163c63b217f1b2'],
+    }),
+    ('gh', '1.4.1', {
+        'checksums': ['76bd3f2a31eeaf76a633362899a20b0f7e8fb6159d4777baf3da2a47854292af'],
+    }),
+    ('credentials', '2.0.1', {
+        'checksums': ['2c7cfc45bd4afa9a2c2b85d43e907b212da3468781e1b617737bd095253c358b'],
+    }),
+    ('zip', '2.3.1', {
+        'checksums': ['83754408781c525917f36535865d28214893de0778b5f337e050cb543cacc28f'],
+    }),
+    ('gert', '2.0.1', {
+        'checksums': ['0ed784837809ce89797ea77834d420e89351728f70d8d2f4b34487df813cd092'],
+    }),
+    ('usethis', '2.2.3', {
+        'checksums': ['8d0c98995c23b5f4b5b95cd453557d2d15faa7399cc01bff304f5b15cb0cdeb3'],
+    }),
+    ('devtools', '2.4.5', {
+        'checksums': ['38160ebd839acdec7ebf0699a085b4ab1ebd5500d3c57a9fa7ae484f1909904b'],
+    }),
+]
+
+moduleclass = 'lang'

From 5abd62be298c72a50cbd29cda3aceae33368f91f Mon Sep 17 00:00:00 2001
From: Simon Branford <4967+branfosj@users.noreply.github.com>
Date: Tue, 25 Jun 2024 11:27:32 +0100
Subject: [PATCH 324/835] enhance sanity checks and style fix
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Bob Dröge <b.e.droge@rug.nl>
---
 .../i/ImageMagick/ImageMagick-7.1.1-34-GCCcore-13.2.0.eb | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.1-34-GCCcore-13.2.0.eb b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.1-34-GCCcore-13.2.0.eb
index e19d1a221fb..eaa7378dd71 100644
--- a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.1-34-GCCcore-13.2.0.eb
+++ b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.1-34-GCCcore-13.2.0.eb
@@ -31,12 +31,15 @@ dependencies = [
 
 configopts = "--with-gslib --with-x"
 
-
 sanity_check_paths = {
-    'files': [],
-    'dirs': ['bin', 'etc/%(name)s-%(version_major)s', 'include/%(name)s-%(version_major)s', 'lib', 'share'],
+    'files': ['bin/magick'],
+    'dirs': ['etc/%(name)s-%(version_major)s', 'include/%(name)s-%(version_major)s', 'lib', 'share'],
 }
 
+sanity_check_commands = [
+    'magick --help',
+]
+
 modextravars = {'MAGICK_HOME': '%(installdir)s'}
 
 moduleclass = 'vis'

From 069e1e2d94b13a816cfb0597805b2449e5b14838 Mon Sep 17 00:00:00 2001
From: Simon Branford <4967+branfosj@users.noreply.github.com>
Date: Tue, 25 Jun 2024 12:51:52 +0100
Subject: [PATCH 325/835] make sure we use EB built pkgconf
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Bob Dröge <b.e.droge@rug.nl>
---
 .../i/ImageMagick/ImageMagick-7.1.1-34-GCCcore-13.2.0.eb         | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.1-34-GCCcore-13.2.0.eb b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.1-34-GCCcore-13.2.0.eb
index eaa7378dd71..2ccdcb32a55 100644
--- a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.1-34-GCCcore-13.2.0.eb
+++ b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.1-34-GCCcore-13.2.0.eb
@@ -29,6 +29,7 @@ dependencies = [
     ('FriBidi', '1.0.13'),
 ]
 
+preconfigopts = 'PKG_CONFIG=$EBROOTPKGCONF/bin/pkgconf'
 configopts = "--with-gslib --with-x"
 
 sanity_check_paths = {

From 2a6befc5d51b71b87f680b5b545cee788cb89a69 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Tue, 25 Jun 2024 14:12:56 +0200
Subject: [PATCH 326/835] make sure we pick up EB's pkgconf

---
 .../i/ImageMagick/ImageMagick-7.1.0-37-GCCcore-11.3.0.eb         | 1 +
 .../i/ImageMagick/ImageMagick-7.1.0-4-GCCcore-11.2.0.eb          | 1 +
 .../i/ImageMagick/ImageMagick-7.1.0-53-GCCcore-12.2.0.eb         | 1 +
 .../i/ImageMagick/ImageMagick-7.1.1-15-GCCcore-12.3.0.eb         | 1 +
 4 files changed, 4 insertions(+)

diff --git a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.0-37-GCCcore-11.3.0.eb b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.0-37-GCCcore-11.3.0.eb
index efff91588b0..f66a2a63bdc 100644
--- a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.0-37-GCCcore-11.3.0.eb
+++ b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.0-37-GCCcore-11.3.0.eb
@@ -30,6 +30,7 @@ builddependencies = [
     ('pkgconf', '1.8.0'),
 ]
 
+preconfigopts = 'PKG_CONFIG=$EBROOTPKGCONF/bin/pkgconf'
 configopts = "--with-gslib --with-x"
 
 sanity_check_paths = {
diff --git a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.0-4-GCCcore-11.2.0.eb b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.0-4-GCCcore-11.2.0.eb
index c3033c0d080..86b615719ce 100644
--- a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.0-4-GCCcore-11.2.0.eb
+++ b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.0-4-GCCcore-11.2.0.eb
@@ -30,6 +30,7 @@ builddependencies = [
     ('pkg-config', '0.29.2'),
 ]
 
+preconfigopts = 'PKG_CONFIG=$EBROOTPKGCONF/bin/pkgconf'
 configopts = "--with-gslib --with-x"
 
 sanity_check_paths = {
diff --git a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.0-53-GCCcore-12.2.0.eb b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.0-53-GCCcore-12.2.0.eb
index 1ddf40ec50a..3a9b48f52b0 100644
--- a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.0-53-GCCcore-12.2.0.eb
+++ b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.0-53-GCCcore-12.2.0.eb
@@ -30,6 +30,7 @@ builddependencies = [
     ('pkgconf', '1.9.3'),
 ]
 
+preconfigopts = 'PKG_CONFIG=$EBROOTPKGCONF/bin/pkgconf'
 configopts = "--with-gslib --with-x"
 
 sanity_check_paths = {
diff --git a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.1-15-GCCcore-12.3.0.eb b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.1-15-GCCcore-12.3.0.eb
index 9504c227680..f51f2edc41a 100644
--- a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.1-15-GCCcore-12.3.0.eb
+++ b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.1-15-GCCcore-12.3.0.eb
@@ -29,6 +29,7 @@ dependencies = [
     ('FriBidi', '1.0.12'),
 ]
 
+preconfigopts = 'PKG_CONFIG=$EBROOTPKGCONF/bin/pkgconf'
 configopts = "--with-gslib --with-x"
 
 

From 2f87100fb961b4450fd7e0eb38c6a238f40b0bf9 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Tue, 25 Jun 2024 14:13:15 +0200
Subject: [PATCH 327/835] remove blank line

---
 .../i/ImageMagick/ImageMagick-7.1.1-15-GCCcore-12.3.0.eb         | 1 -
 1 file changed, 1 deletion(-)

diff --git a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.1-15-GCCcore-12.3.0.eb b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.1-15-GCCcore-12.3.0.eb
index f51f2edc41a..a188918a74a 100644
--- a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.1-15-GCCcore-12.3.0.eb
+++ b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.1-15-GCCcore-12.3.0.eb
@@ -32,7 +32,6 @@ dependencies = [
 preconfigopts = 'PKG_CONFIG=$EBROOTPKGCONF/bin/pkgconf'
 configopts = "--with-gslib --with-x"
 
-
 sanity_check_paths = {
     'files': [],
     'dirs': ['bin', 'etc/%(name)s-%(version_major)s', 'include/%(name)s-%(version_major)s', 'lib', 'share'],

From 3e65cdf9c3e41156919e466dc2839bddfe059c8c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Tue, 25 Jun 2024 14:13:55 +0200
Subject: [PATCH 328/835] improve sanity checks

---
 .../i/ImageMagick/ImageMagick-7.1.0-37-GCCcore-11.3.0.eb | 9 ++++++---
 .../i/ImageMagick/ImageMagick-7.1.0-4-GCCcore-11.2.0.eb  | 9 ++++++---
 .../i/ImageMagick/ImageMagick-7.1.0-53-GCCcore-12.2.0.eb | 9 ++++++---
 .../i/ImageMagick/ImageMagick-7.1.1-15-GCCcore-12.3.0.eb | 8 ++++++--
 4 files changed, 24 insertions(+), 11 deletions(-)

diff --git a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.0-37-GCCcore-11.3.0.eb b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.0-37-GCCcore-11.3.0.eb
index f66a2a63bdc..6a78cb9c5a9 100644
--- a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.0-37-GCCcore-11.3.0.eb
+++ b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.0-37-GCCcore-11.3.0.eb
@@ -34,11 +34,14 @@ preconfigopts = 'PKG_CONFIG=$EBROOTPKGCONF/bin/pkgconf'
 configopts = "--with-gslib --with-x"
 
 sanity_check_paths = {
-    'files': [],
-    'dirs': ['bin', 'etc/%(name)s-%(version_major)s',
-             'include/%(name)s-%(version_major)s', 'lib', 'share'],
+    'files': ['bin/magick'],
+    'dirs': ['etc/%(name)s-%(version_major)s', 'include/%(name)s-%(version_major)s', 'lib', 'share'],
 }
 
+sanity_check_commands = [
+    'magick --help',
+]
+
 modextravars = {'MAGICK_HOME': '%(installdir)s'}
 
 moduleclass = 'vis'
diff --git a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.0-4-GCCcore-11.2.0.eb b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.0-4-GCCcore-11.2.0.eb
index 86b615719ce..7d03b87d1d8 100644
--- a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.0-4-GCCcore-11.2.0.eb
+++ b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.0-4-GCCcore-11.2.0.eb
@@ -34,11 +34,14 @@ preconfigopts = 'PKG_CONFIG=$EBROOTPKGCONF/bin/pkgconf'
 configopts = "--with-gslib --with-x"
 
 sanity_check_paths = {
-    'files': [],
-    'dirs': ['bin', 'etc/%(name)s-%(version_major)s',
-             'include/%(name)s-%(version_major)s', 'lib', 'share'],
+    'files': ['bin/magick'],
+    'dirs': ['etc/%(name)s-%(version_major)s', 'include/%(name)s-%(version_major)s', 'lib', 'share'],
 }
 
+sanity_check_commands = [
+    'magick --help',
+]
+
 modextravars = {'MAGICK_HOME': '%(installdir)s'}
 
 moduleclass = 'vis'
diff --git a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.0-53-GCCcore-12.2.0.eb b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.0-53-GCCcore-12.2.0.eb
index 3a9b48f52b0..e758d987dfa 100644
--- a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.0-53-GCCcore-12.2.0.eb
+++ b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.0-53-GCCcore-12.2.0.eb
@@ -34,11 +34,14 @@ preconfigopts = 'PKG_CONFIG=$EBROOTPKGCONF/bin/pkgconf'
 configopts = "--with-gslib --with-x"
 
 sanity_check_paths = {
-    'files': [],
-    'dirs': ['bin', 'etc/%(name)s-%(version_major)s',
-             'include/%(name)s-%(version_major)s', 'lib', 'share'],
+    'files': ['bin/magick'],
+    'dirs': ['etc/%(name)s-%(version_major)s', 'include/%(name)s-%(version_major)s', 'lib', 'share'],
 }
 
+sanity_check_commands = [
+    'magick --help',
+]
+
 modextravars = {'MAGICK_HOME': '%(installdir)s'}
 
 moduleclass = 'vis'
diff --git a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.1-15-GCCcore-12.3.0.eb b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.1-15-GCCcore-12.3.0.eb
index a188918a74a..4fe1068022b 100644
--- a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.1-15-GCCcore-12.3.0.eb
+++ b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.1-15-GCCcore-12.3.0.eb
@@ -33,10 +33,14 @@ preconfigopts = 'PKG_CONFIG=$EBROOTPKGCONF/bin/pkgconf'
 configopts = "--with-gslib --with-x"
 
 sanity_check_paths = {
-    'files': [],
-    'dirs': ['bin', 'etc/%(name)s-%(version_major)s', 'include/%(name)s-%(version_major)s', 'lib', 'share'],
+    'files': ['bin/magick'],
+    'dirs': ['etc/%(name)s-%(version_major)s', 'include/%(name)s-%(version_major)s', 'lib', 'share'],
 }
 
+sanity_check_commands = [
+    'magick --help',
+]
+
 modextravars = {'MAGICK_HOME': '%(installdir)s'}
 
 moduleclass = 'vis'

From 9469522dcebab481ef13de4b3a0b908a3385486b Mon Sep 17 00:00:00 2001
From: Bart Oldeman <bart.oldeman@calculquebec.ca>
Date: Tue, 25 Jun 2024 15:08:55 +0000
Subject: [PATCH 329/835] adding easyconfigs: intel-compilers-2024.2.0.eb

---
 .../intel-compilers-2024.2.0.eb               | 37 +++++++++++++++++++
 1 file changed, 37 insertions(+)
 create mode 100644 easybuild/easyconfigs/i/intel-compilers/intel-compilers-2024.2.0.eb

diff --git a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2024.2.0.eb b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2024.2.0.eb
new file mode 100644
index 00000000000..90e271fe60a
--- /dev/null
+++ b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2024.2.0.eb
@@ -0,0 +1,37 @@
+name = 'intel-compilers'
+version = '2024.2.0'
+
+homepage = 'https://software.intel.com/content/www/us/en/develop/tools/oneapi/hpc-toolkit.html'
+description = "Intel C, C++ & Fortran compilers (classic and oneAPI)"
+
+toolchain = SYSTEM
+
+# see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html
+sources = [
+    {
+        'source_urls': [
+            'https://registrationcenter-download.intel.com/akdlm/IRC_NAS/6780ac84-6256-4b59-a647-330eb65f32b6/'
+        ],
+        'filename': 'l_dpcpp-cpp-compiler_p_%(version)s.495_offline.sh',
+    },
+    {
+        'source_urls': [
+            'https://registrationcenter-download.intel.com/akdlm/IRC_NAS/801143de-6c01-4181-9911-57e00fe40181/'
+        ],
+        'filename': 'l_fortran-compiler_p_%(version)s.426_offline.sh',
+    },
+]
+checksums = [
+    {'l_dpcpp-cpp-compiler_p_2024.2.0.495_offline.sh':
+     '9463aa979314d2acc51472d414ffcee032e9869ca85ac6ff4c71d39500e5173d'},
+    {'l_fortran-compiler_p_2024.2.0.426_offline.sh':
+     'fd19a302662b2f86f76fc115ef53a69f16488080278dba4c573cc705f3a52ffa'},
+]
+
+local_gccver = '13.3.0'
+dependencies = [
+    ('GCCcore', local_gccver),
+    ('binutils', '2.42', '', ('GCCcore', local_gccver)),
+]
+
+moduleclass = 'compiler'

From e9d317c131a79ca1737acb949e8358a448cd1418 Mon Sep 17 00:00:00 2001
From: Bart Oldeman <bart.oldeman@calculquebec.ca>
Date: Tue, 25 Jun 2024 15:28:30 +0000
Subject: [PATCH 330/835] adding easyconfigs: imkl-2024.2.0.eb

---
 easybuild/easyconfigs/i/imkl/imkl-2024.2.0.eb | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)
 create mode 100644 easybuild/easyconfigs/i/imkl/imkl-2024.2.0.eb

diff --git a/easybuild/easyconfigs/i/imkl/imkl-2024.2.0.eb b/easybuild/easyconfigs/i/imkl/imkl-2024.2.0.eb
new file mode 100644
index 00000000000..30331a8a80a
--- /dev/null
+++ b/easybuild/easyconfigs/i/imkl/imkl-2024.2.0.eb
@@ -0,0 +1,18 @@
+name = 'imkl'
+version = '2024.2.0'
+
+homepage = 'https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/onemkl.html'
+description = "Intel oneAPI Math Kernel Library"
+
+toolchain = SYSTEM
+
+# see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/cdff21a5-6ac7-4b41-a7ec-351b5f9ce8fd']
+sources = ['l_onemkl_p_%(version)s.664_offline.sh']
+checksums = ['f1f46f5352c197a9840e08fc191a879dad79ebf742fe782e386ba8006f262f7a']
+
+interfaces = False
+
+installopts = "--download-cache=%(builddir)s/cache --download-dir=%(builddir)s/download --log-dir=%(builddir)s/log"
+
+moduleclass = 'numlib'

From 576a4e9bfde25a5cdacc652d27c03da955502e9f Mon Sep 17 00:00:00 2001
From: Simon Branford <s.j.branford@bham.ac.uk>
Date: Tue, 25 Jun 2024 16:30:37 +0100
Subject: [PATCH 331/835] Remove CMake Arrow flag as there is no Arrow
 dependency in recent GDAL

---
 easybuild/easyconfigs/g/GDAL/GDAL-3.6.2-foss-2022b.eb | 1 -
 easybuild/easyconfigs/g/GDAL/GDAL-3.7.1-foss-2023a.eb | 2 +-
 easybuild/easyconfigs/g/GDAL/GDAL-3.9.0-foss-2023b.eb | 2 +-
 3 files changed, 2 insertions(+), 3 deletions(-)

diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.6.2-foss-2022b.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.6.2-foss-2022b.eb
index c293d01731d..a527795dfc3 100644
--- a/easybuild/easyconfigs/g/GDAL/GDAL-3.6.2-foss-2022b.eb
+++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.6.2-foss-2022b.eb
@@ -61,7 +61,6 @@ dependencies = [
 # common configopts for static, shared library builds
 _base_configopts = ' '.join([
     '-DGDAL_USE_INTERNAL_LIBS=OFF',
-    '-DArrow_DIR=$EBROOTARROW',
     '-DGEOTIFF_INCLUDE_DIR=$EBROOTLIBGEOTIFF/include',
     '-DPython_ROOT=$EBROOTPYTHON',
 ])
diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.7.1-foss-2023a.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.7.1-foss-2023a.eb
index 92bfe549e74..df1c21eb72a 100644
--- a/easybuild/easyconfigs/g/GDAL/GDAL-3.7.1-foss-2023a.eb
+++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.7.1-foss-2023a.eb
@@ -61,7 +61,7 @@ dependencies = [
 ]
 
 # iterative build for both static and shared libraries
-local_configopts_common = "-DGDAL_USE_INTERNAL_LIBS=OFF -DArrow_DIR=$EBROOTARROW "
+local_configopts_common = "-DGDAL_USE_INTERNAL_LIBS=OFF "
 local_configopts_common += "-DGEOTIFF_INCLUDE_DIR=$EBROOTLIBGEOTIFF/include -DPython_ROOT=$EBROOTPYTHON "
 
 configopts = [
diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.9.0-foss-2023b.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.9.0-foss-2023b.eb
index 05c6ee60dab..ba67862143a 100644
--- a/easybuild/easyconfigs/g/GDAL/GDAL-3.9.0-foss-2023b.eb
+++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.9.0-foss-2023b.eb
@@ -60,7 +60,7 @@ dependencies = [
 ]
 
 # iterative build for both static and shared libraries
-local_configopts_common = "-DGDAL_USE_INTERNAL_LIBS=OFF -DArrow_DIR=$EBROOTARROW "
+local_configopts_common = "-DGDAL_USE_INTERNAL_LIBS=OFF "
 local_configopts_common += "-DGEOTIFF_INCLUDE_DIR=$EBROOTLIBGEOTIFF/include -DPython_ROOT=$EBROOTPYTHON "
 
 configopts = [

From ba7b37aefd0b13442eaaf0b87e94a8373d57bd86 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Tue, 25 Jun 2024 20:11:05 +0200
Subject: [PATCH 332/835] adding easyconfigs:
 scCustomize-2.1.2-foss-2023a-R-4.3.2.eb

---
 .../scCustomize-2.1.2-foss-2023a-R-4.3.2.eb   | 65 +++++++++++++++++++
 1 file changed, 65 insertions(+)
 create mode 100644 easybuild/easyconfigs/s/scCustomize/scCustomize-2.1.2-foss-2023a-R-4.3.2.eb

diff --git a/easybuild/easyconfigs/s/scCustomize/scCustomize-2.1.2-foss-2023a-R-4.3.2.eb b/easybuild/easyconfigs/s/scCustomize/scCustomize-2.1.2-foss-2023a-R-4.3.2.eb
new file mode 100644
index 00000000000..2f94ec91206
--- /dev/null
+++ b/easybuild/easyconfigs/s/scCustomize/scCustomize-2.1.2-foss-2023a-R-4.3.2.eb
@@ -0,0 +1,65 @@
+easyblock = 'Bundle'
+
+name = 'scCustomize'
+version = '2.1.2'
+versionsuffix = '-R-%(rver)s'
+
+homepage = 'https://cran.r-project.org/web/packages/scCustomize/index.html'
+description = """
+Collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using 'R'.
+"""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+dependencies = [
+    # Seurat has its own module, but is either in R-bundle-Bioconductor
+    ('R', '4.3.2'),
+    ('R-bundle-CRAN', '2023.12'),
+    ('R-bundle-Bioconductor', '3.18', '-R-%(rver)s'),
+]
+
+exts_default_options = {
+    'source_urls': [
+        'https://cran.r-project.org/src/contrib/Archive/%(name)s',  # package archive
+        'https://cran.r-project.org/src/contrib/',  # current version of packages
+        'https://cran.freestatistics.org/src/contrib',  # mirror alternative for current packages
+    ],
+    'sources': ['%(name)s_%(version)s.tar.gz'],
+}
+
+exts_defaultclass = 'RPackage'
+
+exts_list = [
+    ('rlang', '1.1.3', {
+        'checksums': ['24a3424b5dc2c4bd3e5f7c0b54fbe1355028e329181b2d41f4464c8ade28bf0a'],
+    }),
+    ('prismatic', '1.1.2', {
+        'checksums': ['babf5b7ad4c9b52921c619de66f93936755dc385b2b69c6504d87c7d5a71e261'],
+    }),
+    ('paletteer', '1.6.0', {
+        'checksums': ['b5de20300c93df203ddc4f3bfeb0a825ef2745c22d66590b33cef9e7448d92d8'],
+    }),
+    ('snakecase', '0.11.1', {
+        'checksums': ['2a5f9791337ca42e392f23fb873eb44f74810583e9aa7c62fda2f28f9e750821'],
+    }),
+    ('janitor', '2.2.0', {
+        'checksums': ['29d5d0185e4e824bb38f905b158162a12f52dc01c2e8a487fc730ce46bf6baae'],
+    }),
+    ('ggprism', '1.0.5', {
+        'checksums': ['7f35eeb010ef3cb47f23cb23b0b084156c56af02cff534c217652ea38cdb5171'],
+    }),
+    (name, version, {
+        'checksums': ['2b569a145fe6dd888ac72ced424352b100b7acc913d6027ddae7799ca4421094'],
+    }),
+]
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': [name],
+}
+
+sanity_check_commands = ['Rscript -e "library(%(name)s)"']
+
+modextrapaths = {'R_LIBS_SITE': ''}
+
+moduleclass = 'vis'

From 1c6fad1fae1abf8129353754feab57c8da8d864f Mon Sep 17 00:00:00 2001
From: fizwit <john@fuzzdog.com>
Date: Tue, 25 Jun 2024 17:09:51 -0700
Subject: [PATCH 333/835] update SRA-Toolkit

---
 .../f/file/file-5.43-GCCcore-13.2.0.eb        | 30 ++++++++
 .../n/ncbi-vdb/ncbi-vdb-3.1.1-gompi-2023b.eb  | 38 ++++++++++
 .../SRA-Toolkit-3.1.1-gompi-2023b.eb          | 76 +++++++++++++++++++
 3 files changed, 144 insertions(+)
 create mode 100644 easybuild/easyconfigs/f/file/file-5.43-GCCcore-13.2.0.eb
 create mode 100644 easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-3.1.1-gompi-2023b.eb
 create mode 100644 easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-3.1.1-gompi-2023b.eb

diff --git a/easybuild/easyconfigs/f/file/file-5.43-GCCcore-13.2.0.eb b/easybuild/easyconfigs/f/file/file-5.43-GCCcore-13.2.0.eb
new file mode 100644
index 00000000000..dcd8b7cbfa0
--- /dev/null
+++ b/easybuild/easyconfigs/f/file/file-5.43-GCCcore-13.2.0.eb
@@ -0,0 +1,30 @@
+easyblock = 'ConfigureMake'
+
+name = 'file'
+version = '5.43'
+
+homepage = 'https://www.darwinsys.com/file/'
+description = """The file command is 'a file type guesser', that is, a command-line tool
+ that tells you in words what kind of data a file contains."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
+
+source_urls = ['ftp://ftp.astron.com/pub/file/']
+sources = [SOURCE_TAR_GZ]
+checksums = ['8c8015e91ae0e8d0321d94c78239892ef9dbc70c4ade0008c0e95894abfb1991']
+
+builddependencies = [
+    ('Autotools', '20220317'),
+    ('binutils', '2.40'),
+]
+
+preconfigopts = "autoreconf -f -i && "
+
+sanity_check_paths = {
+    'files': ['bin/file', 'include/magic.h', 'lib/libmagic.%s' % SHLIB_EXT],
+    'dirs': ['share']
+}
+
+sanity_check_commands = ['%(name)s --help']
+
+moduleclass = 'system'
diff --git a/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-3.1.1-gompi-2023b.eb b/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-3.1.1-gompi-2023b.eb
new file mode 100644
index 00000000000..40cba207840
--- /dev/null
+++ b/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-3.1.1-gompi-2023b.eb
@@ -0,0 +1,38 @@
+easyblock = 'CMakeMake'
+
+name = 'ncbi-vdb'
+version = '3.1.1'
+
+homepage = 'https://github.com/ncbi/ncbi-vdb'
+description = """The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for
+ using data in the INSDC Sequence Read Archives."""
+
+toolchain = {'name': 'gompi', 'version': '2023b'}
+
+github_account = 'ncbi'
+source_urls = [GITHUB_SOURCE]
+sources = [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}]
+checksums = []
+
+builddependencies = [
+    ('Perl', '5.38.0'),
+    ('Python', '3.11.5'),
+    ('CMake', '3.27.6'),
+]
+
+dependencies = [
+    ('HDF5', '1.14.3'),
+    ('libxml2', '2.11.5'),
+    ('bzip2', '1.0.8'),
+]
+
+configopts = "-DHDF5_INCDIR=$EBROOTHDF5/include -DHDF5_LIBDIR=$EBROOTHDF5/lib "
+configopts += "-DXML2_INCDIR=$EBROOTLIBXML2/include -DXML2_LIBDIR=$EBROOTLIBXML2/lib "
+
+sanity_check_paths = {
+    'files': ['include/ncbi/ncbi.h', 'include/ncbi/vdb-blast.h'] +
+             [('lib/libncbi-%s.%s' % (k, e)) for k in ['vdb', 'wvdb'] for e in ['a', SHLIB_EXT]],
+    'dirs': [],
+}
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-3.1.1-gompi-2023b.eb b/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-3.1.1-gompi-2023b.eb
new file mode 100644
index 00000000000..624658d8e2b
--- /dev/null
+++ b/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-3.1.1-gompi-2023b.eb
@@ -0,0 +1,76 @@
+# updated: Denis Kristak (INUITS)
+# updated: Sebastien Moretti (SIB - Vital-IT)
+# updated: Pavel Tománek (INUITS)
+easyblock = 'CMakeMake'
+
+name = 'SRA-Toolkit'
+version = '3.1.1'
+
+homepage = 'https://github.com/ncbi/sra-tools'
+description = """The SRA Toolkit, and the source-code SRA System Development
+ Kit (SDK), will allow you to programmatically access data housed within SRA
+ and convert it from the SRA format"""
+github_account = 'ncbi'
+
+toolchain = {'name': 'gompi', 'version': '2023b'}
+toolchainopts = {'extra_cflags': '-DH5_USE_110_API'}
+
+source_urls = ['https://github.com/ncbi/sra-tools/archive/refs/tags/']
+sources = [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}]
+checksums = ['96b110bd5a30ad312e2f02552062b48a77d40c763e6aba5bb84e83662a505cf1']
+
+builddependencies = [
+    ('CMake', '3.27.6'),
+    ('flex', '2.6.4'),
+    ('Bison', '3.8.2'),
+    ('Perl', '5.38.0'),
+]
+
+dependencies = [
+    ('Python', '3.11.5'),
+    ('Java', '11', '', SYSTEM),
+    ('OpenSSL', '1.1', '', SYSTEM),
+    ('ncbi-vdb', version),
+    ('bzip2', '1.0.8'),
+    ('file', '5.43'),
+    ('HDF5', '1.14.3'),
+    ('libxml2', '2.11.5'),
+    ('zlib', '1.2.13'),
+]
+
+configopts = '-DVDB_INCDIR="$EBROOTNCBIMINVDB/include" -DVDB_LIBDIR="$EBROOTNCBIMINVDB/lib" '
+configopts += '-DBUILD_TOOLS_LOADERS=ON -DBUILD_TOOLS_INTERNAL=ON'
+
+postinstallcmds = [
+    "cp -r %(start_dir)s/ngs/ngs-python/ %(installdir)s/",
+]
+
+_sra_bin = [
+    'abi-dump', 'abi-load', 'align-info', 'bam-load', 'cache-mgr', 'cg-load', 'copycat', 'fasterq-dump', 'fastq-dump',
+    'fastq-load', 'helicos-load', 'illumina-dump', 'illumina-load', 'kar', 'kdbmeta', 'latf-load', 'pacbio-load',
+    'prefetch', 'rcexplain', 'sam-dump', 'sff-dump', 'sff-load', 'srapath', 'sra-pileup', 'sra-sort', 'sra-stat',
+    'sratools', 'srf-load', 'test-sra', 'vdb-config', 'vdb-copy', 'vdb-decrypt', 'vdb-dump', 'vdb-encrypt', 'vdb-lock',
+    'vdb-unlock', 'vdb-validate',
+]
+
+_ngs_libs = ['libncbi-ngs.a', 'libncbi-ngs-c++.a', 'libncbi-ngs.%s' % SHLIB_EXT,
+             'libngs-c++.a', 'libngs-c++.%s' % SHLIB_EXT]
+
+sanity_check_paths = {
+    'files': ['bin/%s' % x for x in _sra_bin] + ['lib/%s' % y for y in _ngs_libs],
+    'dirs': ['jar', 'include/ncbi-vdb', 'include/ngs']
+}
+
+sanity_check_commands = [
+    "abi-dump --help",
+    "kar --help",
+    "sra-sort --help",
+    "python -c 'import ngs'",
+]
+
+modextrapaths = {
+    'CLASSPATH': 'jar/ngs-java.jar',
+    'PYTHONPATH': 'ngs-python',
+}
+
+moduleclass = 'bio'

From 347c72d543533a9cba970b3146f37382bcc826f7 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Wed, 26 Jun 2024 14:22:53 +0200
Subject: [PATCH 334/835] update graph-tools deps + fix preinstallopts of
 tascCODA

---
 .../easyconfigs/g/graph-tool/graph-tool-2.59-foss-2023a.eb      | 1 +
 .../Single-cell-python-bundle-2024.02-foss-2023a.eb             | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/g/graph-tool/graph-tool-2.59-foss-2023a.eb b/easybuild/easyconfigs/g/graph-tool/graph-tool-2.59-foss-2023a.eb
index ac416bcee76..307e764d139 100644
--- a/easybuild/easyconfigs/g/graph-tool/graph-tool-2.59-foss-2023a.eb
+++ b/easybuild/easyconfigs/g/graph-tool/graph-tool-2.59-foss-2023a.eb
@@ -28,6 +28,7 @@ builddependencies = [
     ('pkgconf', '1.9.5'),
     ('expat', '2.5.0'),
     ('CGAL', '5.6'),
+    ('GMP', '6.2.1'),
 ]
 
 dependencies = [
diff --git a/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb b/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb
index 8a4cee8cfcf..e43e7a78e0c 100644
--- a/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb
+++ b/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb
@@ -130,7 +130,7 @@ exts_list = [
     }),
     ('tascCODA', '0.1.3', {
         # strip out tensorflow-probability as required dependency, to ensure that 'pip check' passes
-        'preinstallopts': "sed -i '28d' setup.py && ",
+        'preinstallopts': "sed -i '/tensorflow-probability>=0.16/d' setup.py && ",
         'checksums': ['8c12ddccb72c41c96c6a5abceb52e7a76f439a9ab94fb092aa86ee3c1292383a'],
     }),
     ('harmonypy', '0.0.9', {

From 16954b2ecbc35f8432bf19ca77821608f0cc89c3 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Wed, 26 Jun 2024 16:02:12 +0200
Subject: [PATCH 335/835] update adjustText version

---
 .../Single-cell-python-bundle-2024.02-foss-2023a.eb  | 12 +++++-------
 1 file changed, 5 insertions(+), 7 deletions(-)

diff --git a/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb b/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb
index e43e7a78e0c..c0f6cb45631 100644
--- a/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb
+++ b/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a.eb
@@ -23,26 +23,24 @@ dependencies = [
     ('PyTorch', '2.1.2'),
     ('scanpy', '1.9.8'),
     ('scib', '1.1.4'),
-    ('scVelo', '0.3.1'),  # imports loompy
+    ('scVelo', '0.3.1'),
     ('CellTypist', '1.6.2'),
-    # loompy in scVelo
     ('epiScanpy', '0.4.0'),
-    ('scCODA', '0.1.9'),  # imports rpy2
-    # rpy2 in scCODA
+    ('scCODA', '0.1.9'),
     ('infercnvpy', '0.4.3'),
     ('pySCENIC', '0.12.1-20240311'),
     ('CellRank', '2.0.2'),
     ('Squidpy', '1.4.1'),
     ('Cassiopeia', '2.0.0'),
-    ('scvi-tools', '1.1.2'),  # imports jax
+    ('scvi-tools', '1.1.2'),
     ('scArches', '0.6.1'),
     ('scib-metrics', '0.5.1'),
-    # deps for exts:
+    # deps of exts:
     ('umap-learn', '0.5.5'),  # bbknn
     ('scikit-learn', '1.3.1'),  # bbknn, sc_toolbox
     ('PyYAML', '6.0'),  # sc_toolbox
     ('typing-extensions', '4.9.0'),  # sc_toolbox
-    ('adjustText', '1.1.1'),  # sc_toolbox, created
+    ('adjustText', '0.7.3'),  # sc_toolbox
     ('python-parasail', '1.3.4'),  # scirpy
     ('graph-tool', '2.59'),  # schist
     ('Pyomo', '6.7.3'),  # pertpy

From 52b2c934078fca941fc6c1855a8e170f97a485f0 Mon Sep 17 00:00:00 2001
From: Adam Huffman <12435+verdurin@users.noreply.github.com>
Date: Wed, 26 Jun 2024 14:12:01 +0000
Subject: [PATCH 336/835] adding easyconfigs: IGV-2.17.4-Java-17.eb

---
 .../easyconfigs/i/IGV/IGV-2.17.4-Java-17.eb   | 34 +++++++++++++++++++
 1 file changed, 34 insertions(+)
 create mode 100755 easybuild/easyconfigs/i/IGV/IGV-2.17.4-Java-17.eb

diff --git a/easybuild/easyconfigs/i/IGV/IGV-2.17.4-Java-17.eb b/easybuild/easyconfigs/i/IGV/IGV-2.17.4-Java-17.eb
new file mode 100755
index 00000000000..35e427d0ad0
--- /dev/null
+++ b/easybuild/easyconfigs/i/IGV/IGV-2.17.4-Java-17.eb
@@ -0,0 +1,34 @@
+# EasyBuild easyconfig
+# Author: Pablo Escobar Lopez
+# sciCORE - University of Basel
+# SIB Swiss Institute of Bioinformatics
+# Modified by Adam Huffman
+# Big Data Institute, University of Oxford
+
+easyblock = 'Tarball'
+
+name = 'IGV'
+version = '2.17.4'
+versionsuffix = '-Java-%(javaver)s'
+
+homepage = 'https://www.broadinstitute.org/software/igv/'
+description = """This package contains command line utilities for
+ preprocessing, computing feature count density (coverage),  sorting, and
+ indexing data files."""
+
+toolchain = SYSTEM
+
+source_urls = ['http://data.broadinstitute.org/igv/projects/downloads/%(version_major)s.%(version_minor)s']
+sources = ['%(name)s_%(version)s.zip']
+checksums = ['6a36ae64fa3b74182db654a93f6254256305a8afa6b878f381b5d04fc1e8eaa5']
+
+dependencies = [('Java', '17', '', SYSTEM)]
+
+sanity_check_paths = {
+    'files': ['%(namelower)s.sh', 'lib/%(namelower)s.jar'],
+    'dirs': [],
+}
+
+modextrapaths = {'PATH': ''}
+
+moduleclass = 'bio'

From dc026f74e1de656e76baa0abdcb7db4b38396b4d Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Wed, 26 Jun 2024 17:05:05 +0200
Subject: [PATCH 337/835] adding easyconfigs:
 rMATS-long-1.0.0-foss-2023a-R-4.3.2.eb

---
 .../rMATS-long-1.0.0-foss-2023a-R-4.3.2.eb    | 44 +++++++++++++++++++
 1 file changed, 44 insertions(+)
 create mode 100644 easybuild/easyconfigs/r/rMATS-long/rMATS-long-1.0.0-foss-2023a-R-4.3.2.eb

diff --git a/easybuild/easyconfigs/r/rMATS-long/rMATS-long-1.0.0-foss-2023a-R-4.3.2.eb b/easybuild/easyconfigs/r/rMATS-long/rMATS-long-1.0.0-foss-2023a-R-4.3.2.eb
new file mode 100644
index 00000000000..fcf6cb112d9
--- /dev/null
+++ b/easybuild/easyconfigs/r/rMATS-long/rMATS-long-1.0.0-foss-2023a-R-4.3.2.eb
@@ -0,0 +1,44 @@
+easyblock = 'Tarball'
+
+name = 'rMATS-long'
+version = '1.0.0'
+local_commit = "592cb32"
+versionsuffix = '-R-%(rver)s'
+
+homepage = 'https://github.com/Xinglab/rMATS-long'
+description = """rMATS-long is a collection of tools for analyzing long-read data."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+source_urls = ['https://github.com/Xinglab/%(name)s/archive/']
+sources = [{
+    'download_filename': '%s.tar.gz' % local_commit,
+    'filename': '%%(name)s-%%(version)s-%s.tar.gz' % local_commit,
+}]
+checksums = ['9f4f859c05be5a274b8c0aaf79a18f8c02839f8e6d71330d07f77d027ddba003']
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('matplotlib', '3.7.2'),
+    ('networkx', '3.1'),
+    ('SciPy-bundle', '2023.07'),
+    ('R', '4.3.2'),
+    ('R-bundle-CRAN', '2023.12'),
+    ('R-bundle-Bioconductor', '3.18', '-R-%(rver)s'),
+]
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['scripts'],
+}
+
+sanity_check_commands = [
+    'cd %(installdir)s/scripts && python rmats_long.py -h',
+]
+
+modloadmsg = """
+To run rMATS-long scripts first go to scripts directory:
+$ cd $EBROOTRMATSMINLONG/scripts
+"""
+
+moduleclass = 'lib'

From aabfb2e8ec52a04dd35a9f620ebb4519ee91d289 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Wed, 26 Jun 2024 15:17:49 +0000
Subject: [PATCH 338/835] adding easyconfigs:
 STREAM-5.10-intel-compilers-2024.2.0.eb

---
 .../STREAM-5.10-intel-compilers-2024.2.0.eb   | 39 +++++++++++++++++++
 1 file changed, 39 insertions(+)
 create mode 100644 easybuild/easyconfigs/s/STREAM/STREAM-5.10-intel-compilers-2024.2.0.eb

diff --git a/easybuild/easyconfigs/s/STREAM/STREAM-5.10-intel-compilers-2024.2.0.eb b/easybuild/easyconfigs/s/STREAM/STREAM-5.10-intel-compilers-2024.2.0.eb
new file mode 100644
index 00000000000..17fdbcab3a4
--- /dev/null
+++ b/easybuild/easyconfigs/s/STREAM/STREAM-5.10-intel-compilers-2024.2.0.eb
@@ -0,0 +1,39 @@
+easyblock = 'CmdCp'
+
+name = 'STREAM'
+version = '5.10'
+
+homepage = 'https://www.cs.virginia.edu/stream/'
+description = """The STREAM benchmark is a simple synthetic benchmark program that measures sustainable
+ memory bandwidth (in MB/s) and the corresponding computation rate for simple vector kernels."""
+
+toolchain = {'name': 'intel-compilers', 'version': '2024.2.0'}
+toolchainopts = {'openmp': True}
+
+source_urls = ['https://www.cs.virginia.edu/stream/FTP/Code/']
+sources = [{'download_filename': '%(namelower)s.c', 'filename': 'stream-%(version)s.c', 'extract_cmd': "cp %s ."}]
+checksums = ['a52bae5e175bea3f7832112af9c085adab47117f7d2ce219165379849231692b']
+
+# 10 million array elements (1000 runs): requires ~224MB of memory
+local_cmds = "$CC $CFLAGS %(source)s -mcmodel=large -DSTREAM_ARRAY_SIZE=10000000 -DNTIMES=1000 -o stream_1Kx10M; "
+# 100 million array elements (1000 runs): requires ~2.2GiB of memory
+local_cmds += "$CC $CFLAGS %(source)s -mcmodel=large -DSTREAM_ARRAY_SIZE=100000000 -DNTIMES=1000 -o stream_1Kx100M; "
+# 1 billion array elements (1000 runs): requires ~22.4 GiB of memory
+local_cmds += "$CC $CFLAGS %(source)s -mcmodel=large -DSTREAM_ARRAY_SIZE=1000000000 -DNTIMES=1000 -o stream_1Kx1B; "
+# 2.5 billion array elements (1000 runs): requires ~56 GiB of memory
+local_cmds += "$CC $CFLAGS %(source)s -mcmodel=large -DSTREAM_ARRAY_SIZE=2500000000 -DNTIMES=1000 -o stream_1Kx2.5B; "
+# 5 billion array elements (1000 runs): requires ~111 GiB of memory
+local_cmds += "$CC $CFLAGS %(source)s -mcmodel=large -DSTREAM_ARRAY_SIZE=5000000000 -DNTIMES=1000 -o stream_1Kx5B; "
+
+cmds_map = [('stream-%(version)s.c', local_cmds)]
+
+files_to_copy = [(['stream_1Kx10M', 'stream_1Kx100M', 'stream_1Kx1B', 'stream_1Kx2.5B', 'stream_1Kx5B'], 'bin')]
+
+sanity_check_paths = {
+    'files': ['bin/stream_1Kx10M', 'bin/stream_1Kx100M', 'bin/stream_1Kx1B', 'bin/stream_1Kx2.5B', 'bin/stream_1Kx5B'],
+    'dirs': [],
+}
+
+tests = ['%(installdir)s/bin/stream_1Kx10M']
+
+moduleclass = 'perf'

From d2f5dce5ec523fbf8d8a7318b5e9013945be5b8f Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 26 Jun 2024 17:30:25 +0200
Subject: [PATCH 339/835] also install utilities for recent versions of FUSE
 3.x

---
 .../easyconfigs/f/FUSE/FUSE-3.14.1-GCCcore-11.3.0.eb | 12 +++++++-----
 .../easyconfigs/f/FUSE/FUSE-3.14.1-GCCcore-12.2.0.eb | 12 +++++++-----
 .../easyconfigs/f/FUSE/FUSE-3.16.2-GCCcore-12.3.0.eb | 12 +++++++-----
 3 files changed, 21 insertions(+), 15 deletions(-)

diff --git a/easybuild/easyconfigs/f/FUSE/FUSE-3.14.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/f/FUSE/FUSE-3.14.1-GCCcore-11.3.0.eb
index 856159422b1..f82d2647ceb 100644
--- a/easybuild/easyconfigs/f/FUSE/FUSE-3.14.1-GCCcore-11.3.0.eb
+++ b/easybuild/easyconfigs/f/FUSE/FUSE-3.14.1-GCCcore-11.3.0.eb
@@ -18,13 +18,15 @@ builddependencies = [
     ('binutils', '2.38'),
 ]
 
-# -Dutils=True only works as root 
-configopts = '-Dutils=False'
+# avoid that root permissions are required when installing utils (like fusermount)
+configopts = "-Dinitscriptdir=%(installdir)s/etc/init.d -Dudevrulesdir=%(installdir)s/udev/rules.d -Duseroot=false"
 
 sanity_check_paths = {
-    'files': ['lib64/libfuse%%(version_major)s.%s' % SHLIB_EXT,
-              'lib64/pkgconfig/fuse%(version_major)s.pc'],
-    'dirs': ['include/fuse%(version_major)s'],
+    'files': ['bin/fusermount3', 'etc/fuse.conf', 'lib/libfuse%%(version_major)s.%s' % SHLIB_EXT,
+              'lib/pkgconfig/fuse%(version_major)s.pc'],
+    'dirs': ['include/fuse%(version_major)s', 'share/man'],
 }
 
+sanity_check_commands = ["fusermount3 -h | grep '^fusermount3'"]
+
 moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/f/FUSE/FUSE-3.14.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/f/FUSE/FUSE-3.14.1-GCCcore-12.2.0.eb
index 1be42749206..b16a0debad6 100644
--- a/easybuild/easyconfigs/f/FUSE/FUSE-3.14.1-GCCcore-12.2.0.eb
+++ b/easybuild/easyconfigs/f/FUSE/FUSE-3.14.1-GCCcore-12.2.0.eb
@@ -18,13 +18,15 @@ builddependencies = [
     ('binutils', '2.39')
 ]
 
-# -Dutils=True only works as root 
-configopts = '-Dutils=False'
+# avoid that root permissions are required when installing utils (like fusermount)
+configopts = "-Dinitscriptdir=%(installdir)s/etc/init.d -Dudevrulesdir=%(installdir)s/udev/rules.d -Duseroot=false"
 
 sanity_check_paths = {
-    'files': ['lib64/libfuse%%(version_major)s.%s' % SHLIB_EXT,
-              'lib64/pkgconfig/fuse%(version_major)s.pc'],
-    'dirs': ['include/fuse%(version_major)s'],
+    'files': ['bin/fusermount3', 'etc/fuse.conf', 'lib/libfuse%%(version_major)s.%s' % SHLIB_EXT,
+              'lib/pkgconfig/fuse%(version_major)s.pc'],
+    'dirs': ['include/fuse%(version_major)s', 'share/man'],
 }
 
+sanity_check_commands = ["fusermount3 -h | grep '^fusermount3'"]
+
 moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/f/FUSE/FUSE-3.16.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/f/FUSE/FUSE-3.16.2-GCCcore-12.3.0.eb
index bf3ee6edaf8..341358950aa 100644
--- a/easybuild/easyconfigs/f/FUSE/FUSE-3.16.2-GCCcore-12.3.0.eb
+++ b/easybuild/easyconfigs/f/FUSE/FUSE-3.16.2-GCCcore-12.3.0.eb
@@ -18,13 +18,15 @@ builddependencies = [
     ('binutils', '2.40'),
 ]
 
-# -Dutils=True only works as root
-configopts = '-Dutils=False'
+# avoid that root permissions are required when installing utils (like fusermount)
+configopts = "-Dinitscriptdir=%(installdir)s/etc/init.d -Dudevrulesdir=%(installdir)s/udev/rules.d -Duseroot=false"
 
 sanity_check_paths = {
-    'files': ['lib64/libfuse%%(version_major)s.%s' % SHLIB_EXT,
-              'lib64/pkgconfig/fuse%(version_major)s.pc'],
-    'dirs': ['include/fuse%(version_major)s'],
+    'files': ['bin/fusermount3', 'etc/fuse.conf', 'lib/libfuse%%(version_major)s.%s' % SHLIB_EXT,
+              'lib/pkgconfig/fuse%(version_major)s.pc'],
+    'dirs': ['include/fuse%(version_major)s', 'share/man'],
 }
 
+sanity_check_commands = ["fusermount3 -h | grep '^fusermount3'"]
+
 moduleclass = 'lib'

From dcac649fc9f14a2008a5ea77d60037ca280338a3 Mon Sep 17 00:00:00 2001
From: Adam Huffman <12435+verdurin@users.noreply.github.com>
Date: Wed, 26 Jun 2024 15:58:23 +0000
Subject: [PATCH 340/835] Remove executable bit

---
 easybuild/easyconfigs/i/IGV/IGV-2.17.4-Java-17.eb | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 mode change 100755 => 100644 easybuild/easyconfigs/i/IGV/IGV-2.17.4-Java-17.eb

diff --git a/easybuild/easyconfigs/i/IGV/IGV-2.17.4-Java-17.eb b/easybuild/easyconfigs/i/IGV/IGV-2.17.4-Java-17.eb
old mode 100755
new mode 100644

From 7dcd49363121e249e8e18539b34df386a56ac3d1 Mon Sep 17 00:00:00 2001
From: fizwit <john@fuzzdog.com>
Date: Wed, 26 Jun 2024 12:23:25 -0700
Subject: [PATCH 341/835] add checksums

---
 easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-3.1.1-gompi-2023b.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-3.1.1-gompi-2023b.eb b/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-3.1.1-gompi-2023b.eb
index 40cba207840..a7b4d99b54d 100644
--- a/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-3.1.1-gompi-2023b.eb
+++ b/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-3.1.1-gompi-2023b.eb
@@ -12,7 +12,7 @@ toolchain = {'name': 'gompi', 'version': '2023b'}
 github_account = 'ncbi'
 source_urls = [GITHUB_SOURCE]
 sources = [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}]
-checksums = []
+checksums = ['e9766f259853c696be48e289b08cb5ae6e198d82d7ffee79f09ce7f720487991']
 
 builddependencies = [
     ('Perl', '5.38.0'),

From a90bce4d9ee877d64453984574a783425f64d0c8 Mon Sep 17 00:00:00 2001
From: Bart Oldeman <bart.oldeman@calculquebec.ca>
Date: Wed, 26 Jun 2024 21:47:24 +0000
Subject: [PATCH 342/835] adding easyconfigs:
 impi-2021.13.0-intel-compilers-2024.2.0.eb, iimpi-2024.06.eb,
 OSU-Micro-Benchmarks-7.4-iimpi-2024.06.eb

---
 .../easyconfigs/i/iimpi/iimpi-2024.06.eb      | 18 +++++++++++++
 ...impi-2021.13.0-intel-compilers-2024.2.0.eb | 16 ++++++++++++
 .../OSU-Micro-Benchmarks-7.4-iimpi-2024.06.eb | 26 +++++++++++++++++++
 3 files changed, 60 insertions(+)
 create mode 100644 easybuild/easyconfigs/i/iimpi/iimpi-2024.06.eb
 create mode 100644 easybuild/easyconfigs/i/impi/impi-2021.13.0-intel-compilers-2024.2.0.eb
 create mode 100644 easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-7.4-iimpi-2024.06.eb

diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2024.06.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2024.06.eb
new file mode 100644
index 00000000000..82db31cd099
--- /dev/null
+++ b/easybuild/easyconfigs/i/iimpi/iimpi-2024.06.eb
@@ -0,0 +1,18 @@
+# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild
+easyblock = 'Toolchain'
+
+name = 'iimpi'
+version = '2024.06'
+
+homepage = 'https://software.intel.com/parallel-studio-xe'
+description = """Intel C/C++ and Fortran compilers, alongside Intel MPI."""
+
+toolchain = SYSTEM
+
+local_comp_ver = '2024.2.0'
+dependencies = [
+    ('intel-compilers', local_comp_ver),
+    ('impi', '2021.13.0', '', ('intel-compilers', local_comp_ver)),
+]
+
+moduleclass = 'toolchain'
diff --git a/easybuild/easyconfigs/i/impi/impi-2021.13.0-intel-compilers-2024.2.0.eb b/easybuild/easyconfigs/i/impi/impi-2021.13.0-intel-compilers-2024.2.0.eb
new file mode 100644
index 00000000000..2e99bc6c0d8
--- /dev/null
+++ b/easybuild/easyconfigs/i/impi/impi-2021.13.0-intel-compilers-2024.2.0.eb
@@ -0,0 +1,16 @@
+name = 'impi'
+version = '2021.13.0'
+
+homepage = 'https://software.intel.com/content/www/us/en/develop/tools/mpi-library.html'
+description = "Intel MPI Library, compatible with MPICH ABI"
+
+toolchain = {'name': 'intel-compilers', 'version': '2024.2.0'}
+
+# see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/9f84e1e8-11b2-4bd1-8512-3e3343585956']
+sources = ['l_mpi_oneapi_p_%(version)s.719_offline.sh']
+checksums = ['5e23cf495c919e17032577e3059438f632297ee63f2cdb906a2547298823cc64']
+
+dependencies = [('UCX', '1.16.0')]
+
+moduleclass = 'mpi'
diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-7.4-iimpi-2024.06.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-7.4-iimpi-2024.06.eb
new file mode 100644
index 00000000000..6f36b886477
--- /dev/null
+++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-7.4-iimpi-2024.06.eb
@@ -0,0 +1,26 @@
+easyblock = 'ConfigureMake'
+
+name = 'OSU-Micro-Benchmarks'
+version = '7.4'
+
+homepage = 'https://mvapich.cse.ohio-state.edu/benchmarks/'
+description = """OSU Micro-Benchmarks"""
+
+toolchain = {'name': 'iimpi', 'version': '2024.06'}
+toolchainopts = {'usempi': True}
+
+source_urls = ['https://mvapich.cse.ohio-state.edu/download/mvapich/']
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['1edd0c2efa61999409bfb28740a7f39689a5b42b1a1b4c66d1656e5637f7cefc']
+
+local_benchmark_dirs = [
+    'libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup']
+]
+modextrapaths = {'PATH': local_benchmark_dirs}
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': local_benchmark_dirs,
+}
+
+moduleclass = 'perf'

From c6518ee38c0cb655b2fc4c8c89cc083d2270bcc5 Mon Sep 17 00:00:00 2001
From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com>
Date: Thu, 27 Jun 2024 10:07:38 +0200
Subject: [PATCH 343/835] Update jax-0.4.25-gfbf-2023a-CUDA-12.1.1.eb

fix local_extract_cmd according to @akesandgren 's suggestion
---
 .../easyconfigs/j/jax/jax-0.4.25-gfbf-2023a-CUDA-12.1.1.eb      | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a-CUDA-12.1.1.eb
index 68ab99486f2..c193b35c83b 100644
--- a/easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a-CUDA-12.1.1.eb
+++ b/easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a-CUDA-12.1.1.eb
@@ -41,7 +41,7 @@ dependencies = [
 local_xla_commit = '4ccfe33c71665ddcbca5b127fefe8baa3ed632d4'
 local_tfrt_commit = '0aeefb1660d7e37964b2bb71b1f518096bda9a25'
 
-local_extract_cmd = 'cp %s %(builddir)s/archives'
+local_extract_cmd = 'mkdir -p %(builddir)s/archives && cp %s %(builddir)s/archives'
 local_repo_opt = '--bazel_options="--distdir=%(builddir)s/archives" '
 local_repo_opt += '--bazel_options="--action_env=TF_SYSTEM_LIBS=pybind11" '
 local_repo_opt += '--bazel_options="--action_env=CPATH=$EBROOTPYBIND11/include" '

From d21815d15033a209f1260c5180bfb185086eff44 Mon Sep 17 00:00:00 2001
From: Simon Branford <4967+branfosj@users.noreply.github.com>
Date: Thu, 27 Jun 2024 09:28:37 +0100
Subject: [PATCH 344/835] alt checksums for signal

---
 .../r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb      | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb b/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb
index f2bea4e2d62..db0c3c07b28 100644
--- a/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb
+++ b/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb
@@ -1592,7 +1592,10 @@ exts_list = [
         'checksums': ['7c849086cb17d6c5aefc106217363e14afbcda2a9e0120687d40805b5e1c566a'],
     }),
     ('signal', '1.8-0', {
-        'checksums': ['89cba854167a2b051a58cf3b73ccbf74eeb47c890ac39720611cd41f86b94684'],
+        'checksums': [
+            ('89cba854167a2b051a58cf3b73ccbf74eeb47c890ac39720611cd41f86b94684',
+             '0a604949bae91410a150a22cfa02d954f5b83166cc7a73e5409554d00e0417a7'),
+        ],
     }),
     ('tuneR', '1.4.7', {
         'checksums': ['364154a0440953327eeefd2f3c72c9f819944cbb52b6e7497958882ca0b6960a'],

From c7df21c3568bd5283cea8fe6e677d639f36bd031 Mon Sep 17 00:00:00 2001
From: Yunqi Shao <yunqi.shao@chalmers.se>
Date: Thu, 27 Jun 2024 09:04:20 +0200
Subject: [PATCH 345/835] Disable TF32 in fused matmul tests

---
 ...ensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb |  3 ++
 ...1_disable-tf32-in-fused-matmul-tests.patch | 46 +++++++++++++++++++
 2 files changed, 49 insertions(+)
 create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_disable-tf32-in-fused-matmul-tests.patch

diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb
index 93dcd628ac3..1d1c871f3d5 100644
--- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb
+++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb
@@ -155,6 +155,7 @@ exts_list = [
             'TensorFlow-2.15.1_fix-pybind11-build.patch',
             'TensorFlow-2.15.1_fix-cuda_build_defs.patch',
             'TensorFlow-2.15.1_disable-avx512-extensions.patch',
+            'TensorFlow-2.15.1_disable-tf32-in-fused-matmul-tests.patch'
         ],
         'source_tmpl': 'v%(version)s.tar.gz',
         'source_urls': ['https://github.com/tensorflow/tensorflow/archive/'],
@@ -219,6 +220,8 @@ exts_list = [
              '091581a7c4fc2fc7af282cab6661632c29029d2f36eccb6695ffa5783e065f88'},
             {'TensorFlow-2.15.1_disable-avx512-extensions.patch':
              '506ceecff67237eed9cd9e9e114bc1461f35a343f77f83cb3dab710aa701dc0f'},
+            {'TensorFlow-2.15.1_disable-tf32-in-fused-matmul-tests.patch':
+             'f78aa0e8f814a57e8d2e6b24ff095df49e8654aadb797393fa95a9378d0aa662'},
         ],
     }),
 ]
diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_disable-tf32-in-fused-matmul-tests.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_disable-tf32-in-fused-matmul-tests.patch
new file mode 100644
index 00000000000..9cc742e53d0
--- /dev/null
+++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_disable-tf32-in-fused-matmul-tests.patch
@@ -0,0 +1,46 @@
+Fixes failing FusedMatMul test on certain GPU models
+
+diff --git a/tensorflow/core/kernels/matmul_op_test.cc b/tensorflow/core/kernels/matmul_op_test.cc
+index 8d81d4c796e..2de0365f067 100644
+--- a/tensorflow/core/kernels/matmul_op_test.cc
++++ b/tensorflow/core/kernels/matmul_op_test.cc
+@@ -21,6 +21,7 @@ limitations under the License.
+ #include "tensorflow/core/framework/tensor.h"
+ #include "tensorflow/core/kernels/ops_testutil.h"
+ #include "tensorflow/core/lib/core/status_test_util.h"
++#include "tensorflow/core/platform/tensor_float_32_utils.h"
+ #include "tensorflow/core/platform/test.h"
+ #include "tensorflow/core/platform/test_benchmark.h"
+ #include "tensorflow/core/protobuf/rewriter_config.pb.h"
+@@ -287,6 +288,7 @@ TYPED_TEST_SUITE_P(FusedMatMulWithBiasOpTest);
+ // -------------------------------------------------------------------------- //
+ 
+ TYPED_TEST_P(FusedMatMulWithBiasOpTest, MatMul256x128x64) {
++  tensorflow::enable_tensor_float_32_execution(false);
+   this->VerifyMatMulWithBias(256, 128, 64, false, false);
+   this->VerifyMatMulWithBias(256, 128, 64, true, false);
+   this->VerifyMatMulWithBias(256, 128, 64, false, true);
+@@ -294,6 +296,7 @@ TYPED_TEST_P(FusedMatMulWithBiasOpTest, MatMul256x128x64) {
+ }
+ 
+ TYPED_TEST_P(FusedMatMulWithBiasOpTest, MatMul1x256x256) {
++  tensorflow::enable_tensor_float_32_execution(false);
+   this->VerifyMatMulWithBias(1, 256, 256, false, false);
+   this->VerifyMatMulWithBias(4, 128, 256, false, false);
+   this->VerifyMatMulWithBias(1, 256, 256, true, false);
+@@ -302,6 +305,7 @@ TYPED_TEST_P(FusedMatMulWithBiasOpTest, MatMul1x256x256) {
+ }
+ 
+ TYPED_TEST_P(FusedMatMulWithBiasOpTest, MatMul256x256x1) {
++  tensorflow::enable_tensor_float_32_execution(false);
+   this->VerifyMatMulWithBias(256, 256, 1, false, false);
+   this->VerifyMatMulWithBias(256, 128, 4, false, false);
+   this->VerifyMatMulWithBias(256, 256, 1, true, false);
+@@ -314,6 +318,7 @@ TYPED_TEST_P(FusedMatMulWithBiasOpTest, MatMul1x256x1) {
+ }
+ 
+ TYPED_TEST_P(FusedMatMulWithBiasOpTest, MatMul256x128x64WithActivation) {
++  tensorflow::enable_tensor_float_32_execution(false);
+   for (const string& activation : {"Relu", "Relu6", "Elu", "LeakyRelu"}) {
+     this->VerifyConv2DWithBiasAndActivation(256, 128, 64, false, false,
+                                             activation);

From 7dba4ab5e6f476bd80d89749366449f092ebf5d5 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Thu, 27 Jun 2024 12:01:46 +0200
Subject: [PATCH 346/835] adding easyconfigs:
 meteogrid-20240627-gfbf-2023a-R-4.3.2.eb

---
 .../meteogrid-20240627-gfbf-2023a-R-4.3.2.eb  | 34 +++++++++++++++++++
 1 file changed, 34 insertions(+)
 create mode 100644 easybuild/easyconfigs/m/meteogrid/meteogrid-20240627-gfbf-2023a-R-4.3.2.eb

diff --git a/easybuild/easyconfigs/m/meteogrid/meteogrid-20240627-gfbf-2023a-R-4.3.2.eb b/easybuild/easyconfigs/m/meteogrid/meteogrid-20240627-gfbf-2023a-R-4.3.2.eb
new file mode 100644
index 00000000000..8fca99e5298
--- /dev/null
+++ b/easybuild/easyconfigs/m/meteogrid/meteogrid-20240627-gfbf-2023a-R-4.3.2.eb
@@ -0,0 +1,34 @@
+easyblock = 'RPackage'
+
+name = 'meteogrid'
+version = '20240627'
+local_commit = '9da2345'
+versionsuffix = '-R-%(rver)s'
+
+homepage = 'https://github.com/harphub/meteogrid'
+description = """
+R package for working with gridded meteorological data.
+"""
+
+toolchain = {'name': 'gfbf', 'version': '2023a'}
+
+source_urls = ['https://github.com/harphub/%(name)s/archive/']
+sources = [{
+    'download_filename': '%s.tar.gz' % local_commit,
+    'filename': '%%(name)s-%%(version)s-%s.tar.gz' % local_commit,
+}]
+checksums = ['ab89739e2e85d62bbdc8ee1a96d409654b19ebd2acf8251c2563a88f9d53d5c0']
+
+dependencies = [
+    ('R', '4.3.2'),
+    ('PROJ', '9.2.0'),
+]
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': [name],
+}
+
+sanity_check_commands = ['Rscript -e "library(meteogrid)"']
+
+moduleclass = 'geo'

From 195e117f110ba8207f7414ba349830e942665833 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Petr=20Kr=C3=A1l?= <petr@inuits.eu>
Date: Thu, 27 Jun 2024 12:18:11 +0200
Subject: [PATCH 347/835] add missing dependency

---
 easybuild/easyconfigs/m/medaka/medaka-1.12.0-foss-2023a.eb | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/easybuild/easyconfigs/m/medaka/medaka-1.12.0-foss-2023a.eb b/easybuild/easyconfigs/m/medaka/medaka-1.12.0-foss-2023a.eb
index 15a511a42fd..429fb5bff5b 100644
--- a/easybuild/easyconfigs/m/medaka/medaka-1.12.0-foss-2023a.eb
+++ b/easybuild/easyconfigs/m/medaka/medaka-1.12.0-foss-2023a.eb
@@ -60,6 +60,9 @@ exts_list = [
     ('h5py', '3.10.0', {
         'checksums': ['d93adc48ceeb33347eb24a634fb787efc7ae4644e6ea4ba733d099605045c049'],
     }),
+    ('pyabpoa', '1.5.1', {
+        'checksums': ['878f981e890a421d92a0d7606705d0ad9813ae6086239460dfe4b0cfc7476174'],
+    }),
     (name, version, {
         'checksums': ['039219204111a8114b1f72d87d0d3463e43473790cff4520c8afbd79cc8784d6'],
         # Some requirements are too strict.

From 14fb5124b65fdff4032bc5bdccd7fc58d1c91f44 Mon Sep 17 00:00:00 2001
From: tanmoy1989 <mssmzs@login01.avon.hpc>
Date: Thu, 27 Jun 2024 13:42:36 +0100
Subject: [PATCH 348/835] adding easyconfigs: SuperLU-6.0.1-foss-2023b.eb

---
 .../s/SuperLU/SuperLU-6.0.1-foss-2023b.eb     | 21 +++++++++++++++++++
 1 file changed, 21 insertions(+)
 create mode 100644 easybuild/easyconfigs/s/SuperLU/SuperLU-6.0.1-foss-2023b.eb

diff --git a/easybuild/easyconfigs/s/SuperLU/SuperLU-6.0.1-foss-2023b.eb b/easybuild/easyconfigs/s/SuperLU/SuperLU-6.0.1-foss-2023b.eb
new file mode 100644
index 00000000000..fb80e7ab219
--- /dev/null
+++ b/easybuild/easyconfigs/s/SuperLU/SuperLU-6.0.1-foss-2023b.eb
@@ -0,0 +1,21 @@
+name = 'SuperLU'
+version = '6.0.1'
+
+homepage = 'https://crd-legacy.lbl.gov/~xiaoye/SuperLU/'
+description = """SuperLU is a general purpose library for the
+direct solution of large, sparse, nonsymmetric systems
+ of linear equations on high performance machines."""
+
+toolchain = {'name': 'foss', 'version': '2023b'}
+toolchainopts = {'pic': True, 'openmp': True}
+
+github_account = 'xiaoyeli'
+source_urls = [GITHUB_LOWER_SOURCE]
+sources = ["v%(version)s.tar.gz"]
+checksums = ['6c5a3a9a224cb2658e9da15a6034eed44e45f6963f5a771a6b4562f7afb8f549']
+
+builddependencies = [('CMake', '3.27.6')]
+
+runtest = " test"
+
+moduleclass = 'numlib'

From 0334f973d63cc0d7d1e9195ec0a8eb07a28d92e5 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Thu, 27 Jun 2024 15:06:07 +0200
Subject: [PATCH 349/835] adding easyconfigs:
 Trycycler-0.5.5-foss-2023a-R-4.3.2.eb, miniasm-0.3-20191007-GCCcore-12.3.0.eb

---
 .../miniasm-0.3-20191007-GCCcore-12.3.0.eb    | 46 +++++++++++++++++++
 .../Trycycler-0.5.5-foss-2023a-R-4.3.2.eb     | 38 +++++++++++++++
 2 files changed, 84 insertions(+)
 create mode 100644 easybuild/easyconfigs/m/miniasm/miniasm-0.3-20191007-GCCcore-12.3.0.eb
 create mode 100644 easybuild/easyconfigs/t/Trycycler/Trycycler-0.5.5-foss-2023a-R-4.3.2.eb

diff --git a/easybuild/easyconfigs/m/miniasm/miniasm-0.3-20191007-GCCcore-12.3.0.eb b/easybuild/easyconfigs/m/miniasm/miniasm-0.3-20191007-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..a34b456c98c
--- /dev/null
+++ b/easybuild/easyconfigs/m/miniasm/miniasm-0.3-20191007-GCCcore-12.3.0.eb
@@ -0,0 +1,46 @@
+easyblock = 'MakeCp'
+
+name = 'miniasm'
+version = '0.3-20191007'
+local_commit = 'ce615d1d6b8678d38f2f9d27c9dccd944436ae75'
+
+homepage = 'https://github.com/lh3/miniasm'
+description = """Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It
+takes all-vs-all read self-mappings (typically by minimap) as input and outputs
+an assembly graph in the GFA format. Different from mainstream assemblers,
+miniasm does not have a consensus step. It simply concatenates pieces of read
+sequences to generate the final unitig sequences. Thus the per-base error rate
+is similar to the raw input reads."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+github_account = 'lh3'
+source_urls = [GITHUB_SOURCE]
+sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}]
+checksums = ['31d62309e8b802d3aebd492c1fed8d2a9197a3243c128345745dccb762457e3d']
+
+builddependencies = [
+    ('binutils', '2.40'),
+]
+
+dependencies = [
+    ('zlib', '1.2.13'),
+]
+
+buildopts = 'CC="${CC}" CFLAGS="${CFLAGS}" CPPFLAGS="${CPPFLAGS}"'
+
+files_to_copy = [
+    (['%(name)s', 'minidot'], 'bin'),
+    (['*.h'], 'include'),
+    (['LICENSE.txt', 'PAF.md', 'README.md'], 'share'),
+    (['%(name)s.1'], 'share/man/man1'),
+]
+
+sanity_check_paths = {
+    'files': ['bin/%(name)s', 'bin/minidot'],
+    'dirs': ['include', 'share']
+}
+
+sanity_check_commands = ["miniasm -V"]
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/t/Trycycler/Trycycler-0.5.5-foss-2023a-R-4.3.2.eb b/easybuild/easyconfigs/t/Trycycler/Trycycler-0.5.5-foss-2023a-R-4.3.2.eb
new file mode 100644
index 00000000000..f9a86a65587
--- /dev/null
+++ b/easybuild/easyconfigs/t/Trycycler/Trycycler-0.5.5-foss-2023a-R-4.3.2.eb
@@ -0,0 +1,38 @@
+easyblock = 'PythonBundle'
+
+name = 'Trycycler'
+version = '0.5.5'
+versionsuffix = '-R-%(rver)s'
+
+homepage = 'https://github.com/rrwick/Trycycler'
+description = """A tool for generating consensus long-read assemblies for bacterial genomes."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('R', '4.3.2'),
+    ('R-bundle-CRAN', '2023.12'),
+    ('edlib', '1.3.9'),
+    ('Pillow', '10.0.0'),
+    ('pytest', '7.4.2'),
+    ('minimap2', '2.26'),
+    ('miniasm', '0.3-20191007'),
+    ('Mash', '2.3'),
+    ('MUSCLE', '5.1.0'),
+]
+
+use_pip = True
+
+exts_list = [
+    (name, version, {
+        'source_tmpl': 'v%(version)s.tar.gz',
+        'source_urls': ['https://github.com/rrwick/Trycycler/archive/'],
+        'checksums': ['5794a4520c3b8673adc69c975cee06d7658cd74ac6d9378d1fc7af860bec1a89'],
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'bio'

From cd167a93ac3472cc7adfbbf129a40ef05006969a Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Thu, 27 Jun 2024 15:37:52 +0200
Subject: [PATCH 350/835] adding easyconfigs: Miniconda3-23.10.0-1.eb

---
 .../m/Miniconda3/Miniconda3-23.10.0-1.eb      | 27 +++++++++++++++++++
 1 file changed, 27 insertions(+)
 create mode 100644 easybuild/easyconfigs/m/Miniconda3/Miniconda3-23.10.0-1.eb

diff --git a/easybuild/easyconfigs/m/Miniconda3/Miniconda3-23.10.0-1.eb b/easybuild/easyconfigs/m/Miniconda3/Miniconda3-23.10.0-1.eb
new file mode 100644
index 00000000000..3fd68df4e5c
--- /dev/null
+++ b/easybuild/easyconfigs/m/Miniconda3/Miniconda3-23.10.0-1.eb
@@ -0,0 +1,27 @@
+easyblock = 'EB_Anaconda'
+
+name = 'Miniconda3'
+version = '23.10.0-1'
+
+homepage = 'https://docs.conda.io/en/latest/miniconda.html'
+description = """Miniconda is a free minimal installer for conda. It is a small,
+ bootstrap version of Anaconda that includes only conda, Python, the packages they
+ depend on, and a small number of other useful packages."""
+
+toolchain = SYSTEM
+
+source_urls = ['https://repo.anaconda.com/miniconda/']
+local_arch = {'arm64': 'aarch64'}.get(ARCH, ARCH)
+sources = ['%%(name)s-py311_%%(version)s-Linux-%s.sh' % local_arch]
+checksums = [
+    {
+        '%(name)s-py311_%(version)s-Linux-x86_64.sh':
+            'd0643508fa49105552c94a523529f4474f91730d3e0d1f168f1700c43ae67595',
+        '%(name)s-py311_%(version)s-Linux-ppc64le.sh':
+            '1a2eda0a9a52a4bd058abbe9de5bb2bc751fcd7904c4755deffdf938d6f4436e',
+        '%(name)s-py311_%(version)s-Linux-aarch64.sh':
+            'a60e70ad7e8ac5bb44ad876b5782d7cdc66e10e1f45291b29f4f8d37cc4aa2c8',
+    }
+]
+
+moduleclass = 'lang'

From 78a5b1b2b5bad75de0a7ee866bd3242766472323 Mon Sep 17 00:00:00 2001
From: "Tanmoy Chakraborty, Ph.D"
 <56235576+tanmoy1989@users.noreply.github.com>
Date: Thu, 27 Jun 2024 16:34:10 +0100
Subject: [PATCH 351/835] Update
 easybuild/easyconfigs/l/libzip/libzip-1.10.1-GCCcore-13.2.0.eb
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Bob Dröge <b.e.droge@rug.nl>
---
 easybuild/easyconfigs/l/libzip/libzip-1.10.1-GCCcore-13.2.0.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/l/libzip/libzip-1.10.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/libzip/libzip-1.10.1-GCCcore-13.2.0.eb
index 887eaf37405..ae1adbcbcdd 100644
--- a/easybuild/easyconfigs/l/libzip/libzip-1.10.1-GCCcore-13.2.0.eb
+++ b/easybuild/easyconfigs/l/libzip/libzip-1.10.1-GCCcore-13.2.0.eb
@@ -4,7 +4,7 @@ name = 'libzip'
 version = '1.10.1'
 
 homepage = 'https://libzip.org/'
-description = "libzip is a C library for reading, creating, and modifying zip archives.."
+description = "libzip is a C library for reading, creating, and modifying zip archives."
 
 toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
 

From 88ffac0a53e923d4c79db9c8d1f7e79bda5bd6f1 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com>
Date: Thu, 27 Jun 2024 18:09:07 +0200
Subject: [PATCH 352/835] Update orjson-3.9.15-GCC-12.3.0.eb toolchain

---
 easybuild/easyconfigs/o/orjson/orjson-3.9.15-GCC-12.3.0.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/o/orjson/orjson-3.9.15-GCC-12.3.0.eb b/easybuild/easyconfigs/o/orjson/orjson-3.9.15-GCC-12.3.0.eb
index c741b014f10..14c64e5a008 100644
--- a/easybuild/easyconfigs/o/orjson/orjson-3.9.15-GCC-12.3.0.eb
+++ b/easybuild/easyconfigs/o/orjson/orjson-3.9.15-GCC-12.3.0.eb
@@ -6,7 +6,7 @@ version = '3.9.15'
 homepage = 'https://github.com/ijl/orjson'
 description = """Fast, correct Python JSON library supporting dataclasses, datetimes, and numpy."""
 
-toolchain = {'name': 'GCC', 'version': '12.3.0'}
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
 
 builddependencies = [
     ('maturin', '1.4.0', '-Rust-1.75.0'),

From 19df511a8aa4c695a8399eb274755aa904e33170 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com>
Date: Thu, 27 Jun 2024 18:25:27 +0200
Subject: [PATCH 353/835] Rename orjson-3.9.15-GCC-12.3.0.eb to
 orjson-3.9.15-GCCcore-12.3.0.eb

---
 ...rjson-3.9.15-GCC-12.3.0.eb => orjson-3.9.15-GCCcore-12.3.0.eb} | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename easybuild/easyconfigs/o/orjson/{orjson-3.9.15-GCC-12.3.0.eb => orjson-3.9.15-GCCcore-12.3.0.eb} (100%)

diff --git a/easybuild/easyconfigs/o/orjson/orjson-3.9.15-GCC-12.3.0.eb b/easybuild/easyconfigs/o/orjson/orjson-3.9.15-GCCcore-12.3.0.eb
similarity index 100%
rename from easybuild/easyconfigs/o/orjson/orjson-3.9.15-GCC-12.3.0.eb
rename to easybuild/easyconfigs/o/orjson/orjson-3.9.15-GCCcore-12.3.0.eb

From 148681d6cda7ff0947df6af188534f8313fd0c66 Mon Sep 17 00:00:00 2001
From: "Tanmoy Chakraborty, Ph.D"
 <56235576+tanmoy1989@users.noreply.github.com>
Date: Thu, 27 Jun 2024 19:46:59 +0100
Subject: [PATCH 354/835] Update
 easybuild/easyconfigs/l/libzip/libzip-1.10.1-GCCcore-13.2.0.eb
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Bob Dröge <b.e.droge@rug.nl>
---
 .../easyconfigs/l/libzip/libzip-1.10.1-GCCcore-13.2.0.eb   | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/l/libzip/libzip-1.10.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/libzip/libzip-1.10.1-GCCcore-13.2.0.eb
index ae1adbcbcdd..d54d1419fdc 100644
--- a/easybuild/easyconfigs/l/libzip/libzip-1.10.1-GCCcore-13.2.0.eb
+++ b/easybuild/easyconfigs/l/libzip/libzip-1.10.1-GCCcore-13.2.0.eb
@@ -17,7 +17,12 @@ builddependencies = [
     ('CMake', '3.27.6'),
 ]
 
-dependencies = [('zlib', '1.2.13')]
+dependencies = [
+    ('zlib', '1.2.13'),
+    ('bzip2', '1.0.8'),
+    ('XZ', '5.4.4'),
+    ('zstd', '1.5.5'),
+]
 
 sanity_check_paths = {
     'files': [

From 0f993baeb64c2ad12a6dade46b8886f750f2d276 Mon Sep 17 00:00:00 2001
From: "Tanmoy Chakraborty, Ph.D"
 <56235576+tanmoy1989@users.noreply.github.com>
Date: Thu, 27 Jun 2024 20:11:48 +0100
Subject: [PATCH 355/835] Update
 easybuild/easyconfigs/l/libzip/libzip-1.10.1-GCCcore-13.2.0.eb
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Bob Dröge <b.e.droge@rug.nl>
---
 easybuild/easyconfigs/l/libzip/libzip-1.10.1-GCCcore-13.2.0.eb | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easybuild/easyconfigs/l/libzip/libzip-1.10.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/libzip/libzip-1.10.1-GCCcore-13.2.0.eb
index d54d1419fdc..2986a9fc694 100644
--- a/easybuild/easyconfigs/l/libzip/libzip-1.10.1-GCCcore-13.2.0.eb
+++ b/easybuild/easyconfigs/l/libzip/libzip-1.10.1-GCCcore-13.2.0.eb
@@ -18,6 +18,7 @@ builddependencies = [
 ]
 
 dependencies = [
+    ('OpenSSL', '3'),
     ('zlib', '1.2.13'),
     ('bzip2', '1.0.8'),
     ('XZ', '5.4.4'),

From 7a40bcdec6c67371905aefd0ea6d0da8aca2bb02 Mon Sep 17 00:00:00 2001
From: Bart Oldeman <bart.oldeman@calculquebec.ca>
Date: Fri, 28 Jun 2024 00:48:24 +0000
Subject: [PATCH 356/835] adding easyconfigs:
 imkl-FFTW-2024.2.0-iimpi-2024.06.eb, intel-2024.06.eb,
 HPL-2.3-intel-2024.06.eb

---
 .../h/HPL/HPL-2.3-intel-2024.06.eb            | 21 ++++++++++++++++++
 .../imkl-FFTW-2024.2.0-iimpi-2024.06.eb       | 11 ++++++++++
 .../easyconfigs/i/intel/intel-2024.06.eb      | 22 +++++++++++++++++++
 3 files changed, 54 insertions(+)
 create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2024.06.eb
 create mode 100644 easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2024.2.0-iimpi-2024.06.eb
 create mode 100644 easybuild/easyconfigs/i/intel/intel-2024.06.eb

diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2024.06.eb b/easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2024.06.eb
new file mode 100644
index 00000000000..ca7fc54ce2f
--- /dev/null
+++ b/easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2024.06.eb
@@ -0,0 +1,21 @@
+name = 'HPL'
+version = '2.3'
+
+homepage = 'https://www.netlib.org/benchmark/hpl/'
+description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits)
+ arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available
+ implementation of the High Performance Computing Linpack Benchmark."""
+
+toolchain = {'name': 'intel', 'version': '2024.06'}
+toolchainopts = {'usempi': True}
+
+source_urls = ['https://www.netlib.org/benchmark/%(namelower)s']
+sources = [SOURCELOWER_TAR_GZ]
+# fix Make dependencies, so parallel build also works
+patches = ['HPL_parallel-make.patch']
+checksums = [
+    '32c5c17d22330e6f2337b681aded51637fb6008d3f0eb7c277b163fadd612830',  # hpl-2.3.tar.gz
+    '2a5bf9c4f328049828ddecec7ba3f05a9e25d236f4212747c53bd22fea80c5e6',  # HPL_parallel-make.patch
+]
+
+moduleclass = 'tools'
diff --git a/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2024.2.0-iimpi-2024.06.eb b/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2024.2.0-iimpi-2024.06.eb
new file mode 100644
index 00000000000..7984030b590
--- /dev/null
+++ b/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2024.2.0-iimpi-2024.06.eb
@@ -0,0 +1,11 @@
+name = 'imkl-FFTW'
+version = '2024.2.0'
+
+homepage = 'https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/onemkl.html'
+description = "FFTW interfaces using Intel oneAPI Math Kernel Library"
+
+toolchain = {'name': 'iimpi', 'version': '2024.06'}
+
+dependencies = [('imkl', version, '', SYSTEM)]
+
+moduleclass = 'numlib'
diff --git a/easybuild/easyconfigs/i/intel/intel-2024.06.eb b/easybuild/easyconfigs/i/intel/intel-2024.06.eb
new file mode 100644
index 00000000000..43a052dc1ea
--- /dev/null
+++ b/easybuild/easyconfigs/i/intel/intel-2024.06.eb
@@ -0,0 +1,22 @@
+easyblock = 'Toolchain'
+
+name = 'intel'
+version = '2024.06'
+
+homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#intel-toolchain'
+description = "Compiler toolchain including Intel compilers, Intel MPI and Intel Math Kernel Library (MKL)."
+
+toolchain = SYSTEM
+
+local_comp_ver = '2024.2.0'
+local_gccver = '13.3.0'
+dependencies = [
+    ('GCCcore', local_gccver),
+    ('binutils', '2.42', '', ('GCCcore', local_gccver)),
+    ('intel-compilers', local_comp_ver),
+    ('impi', '2021.13.0', '', ('intel-compilers', local_comp_ver)),
+    ('imkl', '2024.2.0', '', SYSTEM),
+    ('imkl-FFTW', '2024.2.0', '', ('iimpi', version)),
+]
+
+moduleclass = 'toolchain'

From 2183b333db9252aa6c821092180c39f7db3ff5d3 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 28 Jun 2024 09:24:04 +0200
Subject: [PATCH 357/835] Use OpenSSL 1.1, add SYSTEM toolchain to dep

---
 easybuild/easyconfigs/l/libzip/libzip-1.10.1-GCCcore-13.2.0.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/l/libzip/libzip-1.10.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/libzip/libzip-1.10.1-GCCcore-13.2.0.eb
index 2986a9fc694..99551efad57 100644
--- a/easybuild/easyconfigs/l/libzip/libzip-1.10.1-GCCcore-13.2.0.eb
+++ b/easybuild/easyconfigs/l/libzip/libzip-1.10.1-GCCcore-13.2.0.eb
@@ -18,7 +18,7 @@ builddependencies = [
 ]
 
 dependencies = [
-    ('OpenSSL', '3'),
+    ('OpenSSL', '1.1', '', SYSTEM),
     ('zlib', '1.2.13'),
     ('bzip2', '1.0.8'),
     ('XZ', '5.4.4'),

From 18e7aa502f31eafc3c4fee48527ed04246d56fda Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Fri, 28 Jun 2024 11:42:44 +0200
Subject: [PATCH 358/835] adding easyconfigs: Gurobi-11.0.2-GCCcore-12.3.0.eb

---
 .../g/Gurobi/Gurobi-11.0.2-GCCcore-12.3.0.eb  | 63 +++++++++++++++++++
 1 file changed, 63 insertions(+)
 create mode 100644 easybuild/easyconfigs/g/Gurobi/Gurobi-11.0.2-GCCcore-12.3.0.eb

diff --git a/easybuild/easyconfigs/g/Gurobi/Gurobi-11.0.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/Gurobi/Gurobi-11.0.2-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..0e8c4d8115e
--- /dev/null
+++ b/easybuild/easyconfigs/g/Gurobi/Gurobi-11.0.2-GCCcore-12.3.0.eb
@@ -0,0 +1,63 @@
+name = 'Gurobi'
+version = '11.0.2'
+
+homepage = 'https://www.gurobi.com'
+description = """The Gurobi Optimizer is a state-of-the-art solver for mathematical programming.
+The solvers in the Gurobi Optimizer were designed from the ground up to exploit modern
+architectures and multi-core processors, using the most advanced implementations of the
+latest algorithms."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+source_urls = ['https://packages.gurobi.com/%(version_major_minor)s/']
+local_archs = {'aarch64': 'armlinux64', 'x86_64': 'linux64'}
+sources = ['gurobi%%(version)s_%s.tar.gz' % local_archs[ARCH]]
+patches = ['Gurobi-11.0.0_use-eb-python-gurobi-shell.patch']
+checksums = [
+    {'gurobi11.0.2_linux64.tar.gz': 'f43ac8a3edb987b9a0a61452acd9d8dbe9eb37368c6da7ce36e5247cb2a1a368',
+     'gurobi11.0.2_armlinux64.tar.gz': '311b38a89717e26f3f829479ef8e6776674b2711c427a90b84ac9978acd19ff2'},
+    {'Gurobi-11.0.0_use-eb-python-gurobi-shell.patch':
+     '566473a3ba4e35b0e74595368f9f4133fc4a3c97cca84154c4b938645786e663'},
+]
+
+builddependencies = [
+    ('binutils', '2.40'),
+]
+
+dependencies = [
+    ('Python', '3.11.3'),
+]
+
+exts_defaultclass = 'PythonPackage'
+
+exts_default_options = {
+    'source_urls': [PYPI_SOURCE],
+    'download_dep_fail': True,
+    'use_pip': True,
+}
+
+exts_list = [
+    ('gurobipy', version, {
+        'sources': ['gurobipy-%(version)s-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_%(arch)s.whl'],
+        'checksums': [{
+            'gurobipy-%(version)s-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_aarch64.whl':
+                '871e818026c8f288d7440fcd4b842becdf1006f43495fc4f6e3ec6d9b8ba3d7a',
+            'gurobipy-%(version)s-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.whl':
+                '86265b7a9a8f3e531c1bbee6e61c1e7d0b68264e976795b4cf7aec68b9e66eb8',
+        }],
+    }),
+]
+
+# remove bundled Python interpreter in favour of the dependency in EB
+postinstallcmds = ['rm %(installdir)s/bin/python*']
+
+# license is mandatory for installation
+# use EB_GUROBI_LICENSE_FILE environment variable, or 
+# uncomment and modify the following variable:
+# license_file = '/path/to/my-license-file'
+
+modloadmsg = """Gurobi shell based on Python %(pyver)s can be launched with command `gurobi.sh`
+Gurobi Python Interface can be loaded in Python %(pyver)s with 'import gurobipy'
+"""
+
+moduleclass = 'math'

From 1d71b2ccb102c56036e5d9e92187bd5f4ec92318 Mon Sep 17 00:00:00 2001
From: tanmoy1989 <mssmzs@login01.avon.hpc>
Date: Fri, 28 Jun 2024 11:04:17 +0100
Subject: [PATCH 359/835] adding easyconfigs: ParMETIS-4.0.3-gompi-2023b.eb

---
 .../p/ParMETIS/ParMETIS-4.0.3-gompi-2023b.eb  | 29 +++++++++++++++++++
 1 file changed, 29 insertions(+)
 create mode 100644 easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-gompi-2023b.eb

diff --git a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-gompi-2023b.eb b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-gompi-2023b.eb
new file mode 100644
index 00000000000..ae247e2b7c5
--- /dev/null
+++ b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-gompi-2023b.eb
@@ -0,0 +1,29 @@
+##
+# Author:    Robert Mijakovic <robert.mijakovic@lxp.lu>
+##
+name = 'ParMETIS'
+version = '4.0.3'
+
+homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview'
+description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning
+ unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the
+ functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and
+ large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way
+ graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes."""
+
+toolchain = {'name': 'gompi', 'version': '2023b'}
+toolchainopts = {'usempi': True, 'pic': True}
+
+source_urls = [
+    'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis',
+    'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/OLD',
+]
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['f2d9a231b7cf97f1fee6e8c9663113ebf6c240d407d3c118c55b3633d6be6e5f']
+
+builddependencies = [('CMake', '3.27.6')]
+
+# Build static and shared libraries
+configopts = ['', '-DSHARED=1']
+
+moduleclass = 'math'

From 114545454db53ce382e7c2220def5d9e290eb278 Mon Sep 17 00:00:00 2001
From: tanmoy1989 <mssmzs@login01.avon.hpc>
Date: Fri, 28 Jun 2024 11:33:29 +0100
Subject: [PATCH 360/835] adding easyconfigs: MUMPS-5.6.1-foss-2023b-metis.eb

---
 .../m/MUMPS/MUMPS-5.6.1-foss-2023b-metis.eb   | 35 +++++++++++++++++++
 1 file changed, 35 insertions(+)
 create mode 100644 easybuild/easyconfigs/m/MUMPS/MUMPS-5.6.1-foss-2023b-metis.eb

diff --git a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.6.1-foss-2023b-metis.eb b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.6.1-foss-2023b-metis.eb
new file mode 100644
index 00000000000..b9fb9f3ce74
--- /dev/null
+++ b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.6.1-foss-2023b-metis.eb
@@ -0,0 +1,35 @@
+name = 'MUMPS'
+version = '5.6.1'
+versionsuffix = '-metis'
+
+homepage = 'https://graal.ens-lyon.fr/MUMPS/'
+description = "A parallel sparse direct solver"
+
+toolchain = {'name': 'foss', 'version': '2023b'}
+toolchainopts = {'pic': True, 'usempi': True}
+
+source_urls = ['https://graal.ens-lyon.fr/MUMPS/']
+sources = ['%(name)s_%(version)s.tar.gz']
+patches = [
+    '%(name)s-%(version)s_shared-pord.patch',    # builds the shared libs of PORD
+    '%(name)s-%(version)s_shared-mumps.patch',   # builds shared libs of MUMPS
+]
+checksums = [
+    {'MUMPS_5.6.1.tar.gz': '1920426d543e34d377604070fde93b8d102aa38ebdf53300cbce9e15f92e2896'},
+    {'MUMPS-5.6.1_shared-pord.patch': '51d3685208a42581b462592eea977f185d87e871fb65e8e90a54dd2ad18ac715'},
+    {'MUMPS-5.6.1_shared-mumps.patch': '27f788a5f85e8c9a6a7ec1651097b87c1de0ede0be943df7a10fa7c1ff5f494f'},
+]
+
+dependencies = [
+    ('SCOTCH', '7.0.4'),
+    ('METIS', '5.1.0'),
+]
+
+parallel = 1
+
+# fix 'Type mismatch between actual argument' errors with GCC 10.x
+prebuildopts = 'export FFLAGS="$FFLAGS -fallow-argument-mismatch" && '
+
+buildopts = 'all SONAME_VERSION="%(version)s"'
+
+moduleclass = 'math'

From 0478f179064ed35e2982cf5a9a04d368bd7784e6 Mon Sep 17 00:00:00 2001
From: Richard Top <richard.topouchian@uib.no>
Date: Fri, 28 Jun 2024 10:50:25 +0000
Subject: [PATCH 361/835] Added HPL easyconfig

---
 .../h/HPL/HPL-2.3-gmpflf-2024.06.eb           | 21 +++++++++++++++++++
 1 file changed, 21 insertions(+)
 create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.3-gmpflf-2024.06.eb

diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.3-gmpflf-2024.06.eb b/easybuild/easyconfigs/h/HPL/HPL-2.3-gmpflf-2024.06.eb
new file mode 100644
index 00000000000..a6a7fb49164
--- /dev/null
+++ b/easybuild/easyconfigs/h/HPL/HPL-2.3-gmpflf-2024.06.eb
@@ -0,0 +1,21 @@
+name = 'HPL'
+version = '2.3'
+
+homepage = 'https://www.netlib.org/benchmark/hpl/'
+description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits)
+ arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available
+ implementation of the High Performance Computing Linpack Benchmark."""
+
+toolchain = {'name': 'gmpflf', 'version': '2024.06'}
+toolchainopts = {'usempi': True}
+
+source_urls = ['https://www.netlib.org/benchmark/%(namelower)s']
+sources = [SOURCELOWER_TAR_GZ]
+# fix Make dependencies, so parallel build also works
+patches = ['HPL_parallel-make.patch']
+checksums = [
+    '32c5c17d22330e6f2337b681aded51637fb6008d3f0eb7c277b163fadd612830',  # hpl-2.3.tar.gz
+    '2a5bf9c4f328049828ddecec7ba3f05a9e25d236f4212747c53bd22fea80c5e6',  # HPL_parallel-make.patch
+]
+
+moduleclass = 'tools'

From 806524003424979b23ab9bc0aef4008cbfb38342 Mon Sep 17 00:00:00 2001
From: Richard Top <richard.topouchian@uib.no>
Date: Fri, 28 Jun 2024 11:23:38 +0000
Subject: [PATCH 362/835] fixed local GCC in ScaLAPACK

---
 .../s/ScaLAPACK/ScaLAPACK-2.2.0-gmpich-2024.06-fb.eb        | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gmpich-2024.06-fb.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gmpich-2024.06-fb.eb
index 4fd5b35b6d8..28d4f766d52 100644
--- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gmpich-2024.06-fb.eb
+++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gmpich-2024.06-fb.eb
@@ -9,8 +9,6 @@ description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of
 toolchain = {'name': 'gmpich', 'version': '2024.06'}
 toolchainopts = {'extra_fflags': '-lpthread', 'openmp': True, 'pic': True, 'usempi': True}
 
-local_gccver = '12.3.0'
-
 source_urls = [homepage]
 sources = [SOURCELOWER_TGZ]
 patches = ['ScaLAPACK-%(version)s_fix-GCC-10.patch']
@@ -20,11 +18,11 @@ checksums = [
 ]
 
 builddependencies = [
-    ('CMake', '3.26.3', '', ('GCCcore', local_gccver)),
+    ('CMake', '3.26.3'),
 ]
 
 dependencies = [
-    ('FlexiBLAS', '3.3.1', '', ('GCC', local_gccver)),
+    ('FlexiBLAS', '3.3.1'),
 ]
 
 # Config Opts based on AOCL User Guide:

From 37e673217efbecc359d6008dcf19f8dbf72e777c Mon Sep 17 00:00:00 2001
From: Simon Branford <4967+branfosj@users.noreply.github.com>
Date: Fri, 28 Jun 2024 12:40:54 +0100
Subject: [PATCH 363/835] alt checksums for pan

---
 .../r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb      | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb b/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb
index db0c3c07b28..c042ee83af9 100644
--- a/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb
+++ b/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb
@@ -580,7 +580,10 @@ exts_list = [
         'checksums': ['9e1531bb37aa474abd91db5e0ed9e3a355c03faa65f4e653b3ea68b7c61ea835'],
     }),
     ('pan', '1.9', {
-        'checksums': ['cd91232d653783ea7f34c0eebaa80c472b5501b21eea500c4c1a8e57116c6eea'],
+        'checksums': [
+            ('e37e184c3c1b7a34f54dd95335e6bc730fd5716d2d2dc20c24279401aa673c52',
+             'cd91232d653783ea7f34c0eebaa80c472b5501b21eea500c4c1a8e57116c6eea'),
+        ],
     }),
     ('mitml', '0.4-5', {
         'checksums': ['056aec823187cc3793640d8a5e74d74093bae74260a975ceb098a83a52e2eeeb'],

From 1a25a3a621679e7618b76e53bf00924049c45c3e Mon Sep 17 00:00:00 2001
From: Richard Top <richard.topouchian@uib.no>
Date: Fri, 28 Jun 2024 12:26:30 +0000
Subject: [PATCH 364/835] fixed version var in gmpflf

---
 easybuild/easyconfigs/g/gmpflf/gmpflf-2024.06.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/g/gmpflf/gmpflf-2024.06.eb b/easybuild/easyconfigs/g/gmpflf/gmpflf-2024.06.eb
index 03875dba4c9..513c69d0a84 100644
--- a/easybuild/easyconfigs/g/gmpflf/gmpflf-2024.06.eb
+++ b/easybuild/easyconfigs/g/gmpflf/gmpflf-2024.06.eb
@@ -12,7 +12,7 @@ toolchain = SYSTEM
 local_gccver = '12.3.0'
 
 # toolchain used to build gmpflf dependencies
-local_comp_mpi_tc = ('gmpich', '2024.06')
+local_comp_mpi_tc = ('gmpich', version)
 
 # we need GCC and MPICH as explicit dependencies instead of gompi toolchain
 # because of toolchain preparation functions

From 69c12eae1f0a435685145af659dbd928a4afd8bf Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Petr=20Kr=C3=A1l?= <petr@inuits.eu>
Date: Fri, 28 Jun 2024 15:42:01 +0200
Subject: [PATCH 365/835] adding easyconfigs: n2v-0.3.3-foss-2023a.eb,
 CSBDeep-0.7.4-foss-2023a.eb

---
 .../c/CSBDeep/CSBDeep-0.7.4-foss-2023a.eb     | 37 ++++++++
 .../easyconfigs/n/n2v/n2v-0.3.3-foss-2023a.eb | 87 +++++++++++++++++++
 2 files changed, 124 insertions(+)
 create mode 100644 easybuild/easyconfigs/c/CSBDeep/CSBDeep-0.7.4-foss-2023a.eb
 create mode 100644 easybuild/easyconfigs/n/n2v/n2v-0.3.3-foss-2023a.eb

diff --git a/easybuild/easyconfigs/c/CSBDeep/CSBDeep-0.7.4-foss-2023a.eb b/easybuild/easyconfigs/c/CSBDeep/CSBDeep-0.7.4-foss-2023a.eb
new file mode 100644
index 00000000000..3b3b0f37650
--- /dev/null
+++ b/easybuild/easyconfigs/c/CSBDeep/CSBDeep-0.7.4-foss-2023a.eb
@@ -0,0 +1,37 @@
+# This easyconfig was created by the BEAR Software team at the University of Birmingham.
+# Update: Petr Král (INUITS)
+easyblock = 'PythonBundle'
+
+name = 'CSBDeep'
+version = '0.7.4'
+
+homepage = "https://csbdeep.bioimagecomputing.com/"
+description = """CSBDeep is a toolbox for Content-aware Image Restoration (CARE)."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('TensorFlow', '2.13.0'),
+    ('matplotlib', '3.7.2'),
+    ('tqdm', '4.66.1'),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    ('tifffile', '2024.6.18', {
+        'source_tmpl': SOURCE_PY3_WHL,
+        'checksums': ['67299c0445fc47463bbc71f3cb4676da2ab0242b0c6c6542a0680801b4b97d8a'],
+    }),
+    ('%(namelower)s', version, {
+        'source_tmpl': SOURCE_WHL,
+        'checksums': ['155d61827439373dc9c2a730a1ef621f7e373fea16599d583e0a70f1e48bd6db'],
+    }),
+]
+
+sanity_check_commands = ['care_predict']
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/n/n2v/n2v-0.3.3-foss-2023a.eb b/easybuild/easyconfigs/n/n2v/n2v-0.3.3-foss-2023a.eb
new file mode 100644
index 00000000000..dfc99c9d4d3
--- /dev/null
+++ b/easybuild/easyconfigs/n/n2v/n2v-0.3.3-foss-2023a.eb
@@ -0,0 +1,87 @@
+easyblock = 'PythonBundle'
+
+name = 'n2v'
+version = '0.3.3'
+
+homepage = 'https://github.com/juglab/n2v'
+description = "Learning Denoising from Single Noisy Images"
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('Pillow', '10.0.0'),
+    ('imagecodecs', '2024.1.1'),
+    ('ruamel.yaml', '0.17.32'),
+    ('CSBDeep', '0.7.4'),
+    ('xarray', '2023.9.0'),
+    ('imageio', '2.33.1'),
+    ('pydantic', '2.5.3'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('typer', '0.12.3', {
+        'source_tmpl': SOURCE_PY3_WHL,
+        'checksums': ['070d7ca53f785acbccba8e7d28b08dcd88f79f1fbda035ade0aecec71ca5c914'],
+    }),
+    ('marshmallow_union', '0.1.15.post1', {
+        'source_tmpl': SOURCE_WHL,
+        'checksums': ['1e21b759c76735305f99179c1a16759ebb9629733159628241b3f2117ff55e86'],
+    }),
+    ('marshmallow_jsonschema', '0.13.0', {
+        'source_tmpl': SOURCE_PY3_WHL,
+        'checksums': ['2814f2afb94a6e01b3c0a5795b3dfb142b628763655f20378400af5c0a2307fb'],
+    }),
+    ('marshmallow', '3.21.3', {
+        'source_tmpl': SOURCE_PY3_WHL,
+        'checksums': ['86ce7fb914aa865001a4b2092c4c2872d13bc347f3d42673272cabfdbad386f1'],
+    }),
+    ('fire', '0.6.0', {
+        'checksums': ['54ec5b996ecdd3c0309c800324a0703d6da512241bc73b553db959d98de0aa66'],
+    }),
+    ('ruyaml', '0.91.0', {
+        'source_tmpl': SOURCE_PY3_WHL,
+        'checksums': ['50e0ee3389c77ad340e209472e0effd41ae0275246df00cdad0a067532171755'],
+    }),
+    ('python_dotenv', '1.0.1', {
+        'source_tmpl': SOURCE_PY3_WHL,
+        'modulename': 'dotenv',
+        'checksums': ['f7b63ef50f1b690dddf550d03497b66d609393b40b564ed0d674909a68ebf16a'],
+    }),
+    ('pydantic_settings', '2.2.1', {
+        'source_tmpl': SOURCE_PY3_WHL,
+        'checksums': ['0235391d26db4d2190cb9b31051c4b46882d28a51533f97440867f012d4da091'],
+    }),
+    ('loguru', '0.7.2', {
+        'source_tmpl': SOURCE_PY3_WHL,
+        'checksums': ['003d71e3d3ed35f0f8984898359d65b79e5b21943f78af86aa5491210429b8eb'],
+    }),
+    ('dnspython', '2.6.1', {
+        'source_tmpl': SOURCE_PY3_WHL,
+        'modulename': 'dns',
+        'checksums': ['5ef3b9680161f6fa89daf8ad451b5f1a33b18ae8a1c6778cdf4b43f08c0a6e50'],
+    }),
+    ('email_validator', '2.2.0', {
+        'source_tmpl': SOURCE_PY3_WHL,
+        'checksums': ['561977c2d73ce3611850a06fa56b414621e0c8faa9d66f2611407d87465da631'],
+    }),
+    ('bioimageio.spec', '0.4.9.post5', {
+        'source_tmpl': SOURCE_PY3_WHL,
+        'checksums': ['a24ef7c0d6506d080655fbd8f322bc153a147329bd2258a8e958982d31885865'],
+    }),
+    ('bioimageio.core', '0.5.11', {
+        'source_tmpl': SOURCE_PY3_WHL,
+        'checksums': ['af8138f0c75fcebf7abbb873d01af8055d6209b2fd611269990b72e51fb991b5'],
+    }),
+    (name, version, {
+        'source_tmpl': SOURCE_WHL,
+        'checksums': ['be5b24fe0bf3cdc15cd4771c50e577a81b7d83b27300a0b90035cc87bb95c33c'],
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'vis'

From 492508ce661aa5f549651c644f71e99c9c660f25 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Petr=20Kr=C3=A1l?= <petr@inuits.eu>
Date: Fri, 28 Jun 2024 15:55:28 +0200
Subject: [PATCH 366/835] adding easyconfigs:
 napari-denoiseg-0.0.1-foss-2023a.eb

---
 .../napari-denoiseg-0.0.1-foss-2023a.eb       | 58 +++++++++++++++++++
 1 file changed, 58 insertions(+)
 create mode 100644 easybuild/easyconfigs/n/napari-denoiseg/napari-denoiseg-0.0.1-foss-2023a.eb

diff --git a/easybuild/easyconfigs/n/napari-denoiseg/napari-denoiseg-0.0.1-foss-2023a.eb b/easybuild/easyconfigs/n/napari-denoiseg/napari-denoiseg-0.0.1-foss-2023a.eb
new file mode 100644
index 00000000000..dde1af43010
--- /dev/null
+++ b/easybuild/easyconfigs/n/napari-denoiseg/napari-denoiseg-0.0.1-foss-2023a.eb
@@ -0,0 +1,58 @@
+easyblock = 'PythonBundle'
+
+name = 'napari-denoiseg'
+version = '0.0.1'
+
+homepage = 'https://juglab.github.io/napari-denoiseg/index.html'
+description = """A napari plugin performing joint denoising and segmentation of microscopy images using DenoiSeg."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('napari', '0.4.18'),
+    ('PyQtGraph', '0.13.7'),
+    ('QtPy', '2.4.1'),
+    ('TensorFlow', '2.13.0'),
+    ('CSBDeep', '0.7.4'),
+    ('n2v', '0.3.3'),
+    ('numba', '0.58.1'),
+    ('scikit-learn', '1.4.2'),
+    ('n2v', '0.3.3'),
+    ('autopep8', '2.2.0'),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    ('napari-workflows', '0.2.10', {
+        'checksums': ['d48f2020693b4b8c1dd639668a3b1588115beac8f19f42394fc241fc1672be12'],
+    }),
+    ('napari-tools-menu', '0.1.19', {
+        'checksums': ['6b58ac45d7fe84bc5975e7a53142340d5d62beff9ade0f2f58d7a3a4a0a8e8f8'],
+    }),
+    ('magicgui', '0.8.3', {
+        'source_tmpl': SOURCE_PY3_WHL,
+        'checksums': ['ee763f3908a344cc73e1ed0981885114937ce3077e60e4feb8148e64f0e762a3'],
+    }),
+    ('napari_time_slicer', '0.5.0', {
+        'source_tmpl': SOURCE_PY3_WHL,
+        'checksums': ['6c7f53f762cb3410da097be43ba47b4f4213e89930a3ade3ec1c7c1beb9d605f'],
+    }),
+    ('denoiseg', '0.3.1', {
+        'preinstallopts': 'sed -i "s/wrapt<=1.12.1/wrapt/g" setup.py && ',
+        'checksums': ['fd720b78910b84ea5d65deda8c193d64e583c78090d9867990b7a39f72ed7ea3'],
+    }),
+    ('napari-denoiseg', '%(version)src2', {
+        'preinstallopts': 'sed -i "s/vispy<=0.9.6/vispy/g;s/napari<=0.4.15/napari<=0.4.18/g" setup.cfg && ',
+        'checksums': ['e244dbb820ee7d35212ee198d28eabf987439a70ce6695cbf63cfa52baab1ea8'],
+    }),
+]
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+moduleclass = 'vis'

From c0649dee221e4062389a398df322db324e560b00 Mon Sep 17 00:00:00 2001
From: Simon Pinches <Simon.Pinches@iter.org>
Date: Fri, 28 Jun 2024 17:41:50 +0200
Subject: [PATCH 367/835] adding easyconfigs:
 MUMPS-5.7.2-foss-2023b-parmetis.eb, ParMETIS-4.0.3-gompi-2023b.eb

---
 .../MUMPS/MUMPS-5.7.2-foss-2023b-parmetis.eb  | 27 +++++++++++++++++
 .../p/ParMETIS/ParMETIS-4.0.3-gompi-2023b.eb  | 29 +++++++++++++++++++
 2 files changed, 56 insertions(+)
 create mode 100644 easybuild/easyconfigs/m/MUMPS/MUMPS-5.7.2-foss-2023b-parmetis.eb
 create mode 100644 easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-gompi-2023b.eb

diff --git a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.7.2-foss-2023b-parmetis.eb b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.7.2-foss-2023b-parmetis.eb
new file mode 100644
index 00000000000..1b7b70075c2
--- /dev/null
+++ b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.7.2-foss-2023b-parmetis.eb
@@ -0,0 +1,27 @@
+name = 'MUMPS'
+version = '5.7.2'
+versionsuffix = '-parmetis'
+
+homepage = 'https://graal.ens-lyon.fr/MUMPS/'
+description = "A parallel sparse direct solver"
+
+toolchain = {'name': 'foss', 'version': '2023b'}
+toolchainopts = {'pic': True, 'usempi': True}
+
+source_urls = ['http://mumps-solver.org/']
+sources = ['%(name)s_%(version)s.tar.gz']
+checksums = ['1362d377ce7422fc886c55212b4a4d2c381918b5ca4478f682a22d0627a8fbf8']
+
+dependencies = [
+    ('SCOTCH', '7.0.4'),
+    ('ParMETIS', '4.0.3'),
+]
+
+parallel = 1
+
+# fix 'Type mismatch between actual argument' errors with GCC 10.x
+prebuildopts = 'export FFLAGS="$FFLAGS -fallow-argument-mismatch" && '
+
+buildopts = 'all SONAME_VERSION="%(version)s"'
+
+moduleclass = 'math'
diff --git a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-gompi-2023b.eb b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-gompi-2023b.eb
new file mode 100644
index 00000000000..ae247e2b7c5
--- /dev/null
+++ b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-gompi-2023b.eb
@@ -0,0 +1,29 @@
+##
+# Author:    Robert Mijakovic <robert.mijakovic@lxp.lu>
+##
+name = 'ParMETIS'
+version = '4.0.3'
+
+homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview'
+description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning
+ unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the
+ functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and
+ large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way
+ graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes."""
+
+toolchain = {'name': 'gompi', 'version': '2023b'}
+toolchainopts = {'usempi': True, 'pic': True}
+
+source_urls = [
+    'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis',
+    'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/OLD',
+]
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['f2d9a231b7cf97f1fee6e8c9663113ebf6c240d407d3c118c55b3633d6be6e5f']
+
+builddependencies = [('CMake', '3.27.6')]
+
+# Build static and shared libraries
+configopts = ['', '-DSHARED=1']
+
+moduleclass = 'math'

From fdc2f6098f9646d88379b00ad98c7a527b371840 Mon Sep 17 00:00:00 2001
From: Simon Pinches <Simon.Pinches@iter.org>
Date: Fri, 28 Jun 2024 17:53:11 +0200
Subject: [PATCH 368/835] adding easyconfigs:
 MUMPS-5.7.2-intel-2023b-parmetis.eb, ParMETIS-4.0.3-iimpi-2023b.eb

---
 .../MUMPS/MUMPS-5.7.2-intel-2023b-parmetis.eb | 27 +++++++++++++++++
 .../p/ParMETIS/ParMETIS-4.0.3-iimpi-2023b.eb  | 29 +++++++++++++++++++
 2 files changed, 56 insertions(+)
 create mode 100644 easybuild/easyconfigs/m/MUMPS/MUMPS-5.7.2-intel-2023b-parmetis.eb
 create mode 100644 easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-iimpi-2023b.eb

diff --git a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.7.2-intel-2023b-parmetis.eb b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.7.2-intel-2023b-parmetis.eb
new file mode 100644
index 00000000000..589710ed6ee
--- /dev/null
+++ b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.7.2-intel-2023b-parmetis.eb
@@ -0,0 +1,27 @@
+name = 'MUMPS'
+version = '5.7.2'
+versionsuffix = '-parmetis'
+
+homepage = 'https://graal.ens-lyon.fr/MUMPS/'
+description = "A parallel sparse direct solver"
+
+toolchain = {'name': 'intel', 'version': '2023b'}
+toolchainopts = {'pic': True, 'usempi': True}
+
+source_urls = ['http://mumps-solver.org/']
+sources = ['%(name)s_%(version)s.tar.gz']
+checksums = ['1362d377ce7422fc886c55212b4a4d2c381918b5ca4478f682a22d0627a8fbf8']
+
+dependencies = [
+    ('SCOTCH', '7.0.4'),
+    ('ParMETIS', '4.0.3'),
+]
+
+parallel = 1
+
+# fix 'Type mismatch between actual argument' errors with GCC 10.x
+prebuildopts = 'export FFLAGS="$FFLAGS -fallow-argument-mismatch" && '
+
+buildopts = 'all SONAME_VERSION="%(version)s"'
+
+moduleclass = 'math'
diff --git a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-iimpi-2023b.eb b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-iimpi-2023b.eb
new file mode 100644
index 00000000000..a2804c40d1c
--- /dev/null
+++ b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-iimpi-2023b.eb
@@ -0,0 +1,29 @@
+##
+# Author:    Robert Mijakovic <robert.mijakovic@lxp.lu>
+##
+name = 'ParMETIS'
+version = '4.0.3'
+
+homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview'
+description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning
+ unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the
+ functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and
+ large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way
+ graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes."""
+
+toolchain = {'name': 'iimpi', 'version': '2023b'}
+toolchainopts = {'usempi': True, 'pic': True}
+
+source_urls = [
+    'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis',
+    'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/OLD',
+]
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['f2d9a231b7cf97f1fee6e8c9663113ebf6c240d407d3c118c55b3633d6be6e5f']
+
+builddependencies = [('CMake', '3.27.6')]
+
+# Build static and shared libraries
+configopts = ['', '-DSHARED=1']
+
+moduleclass = 'math'

From 519e6e93783eb5081123fabcc05112b7b7536a25 Mon Sep 17 00:00:00 2001
From: Simon Pinches <Simon.Pinches@iter.org>
Date: Fri, 28 Jun 2024 18:00:18 +0200
Subject: [PATCH 369/835] adding easyconfigs: Pylint-3.2.5-GCCcore-13.2.0.eb

---
 .../p/Pylint/Pylint-3.2.5-GCCcore-13.2.0.eb   | 56 +++++++++++++++++++
 1 file changed, 56 insertions(+)
 create mode 100644 easybuild/easyconfigs/p/Pylint/Pylint-3.2.5-GCCcore-13.2.0.eb

diff --git a/easybuild/easyconfigs/p/Pylint/Pylint-3.2.5-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/Pylint/Pylint-3.2.5-GCCcore-13.2.0.eb
new file mode 100644
index 00000000000..c919c6c4dd4
--- /dev/null
+++ b/easybuild/easyconfigs/p/Pylint/Pylint-3.2.5-GCCcore-13.2.0.eb
@@ -0,0 +1,56 @@
+easyblock = 'PythonBundle'
+
+name = 'Pylint'
+version = '3.2.5'
+
+homepage = 'https://www.pylint.org/'
+description = """Pylint is a tool that checks for errors in Python code, tries to enforce
+ a coding standard and looks for code smells. It can also look for certain type errors,
+ it can recommend suggestions about how particular blocks can be refactored and
+ can offer you details about the code's complexity."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
+
+builddependencies = [
+    ('binutils', '2.40'),
+    ('poetry', '1.6.1'),
+]
+
+dependencies = [
+    ('Python', '3.11.5'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('dill', '0.3.8', {
+        'checksums': ['3ebe3c479ad625c4553aca177444d89b486b1d84982eeacded644afc0cf797ca'],
+    }),
+    ('platformdirs', '4.2.2', {
+        'checksums': ['38b7b51f512eed9e84a22788b4bce1de17c0adb134d6becb09836e37d8654cd3'],
+    }),
+    ('tomlkit', '0.12.5', {
+        'checksums': ['eef34fba39834d4d6b73c9ba7f3e4d1c417a4e56f89a7e96e090dd0d24b8fb3c'],
+    }),
+    ('astroid', '3.2.2', {
+        'checksums': ['8ead48e31b92b2e217b6c9733a21afafe479d52d6e164dd25fb1a770c7c3cf94'],
+    }),
+    ('isort', '5.13.2', {
+        'checksums': ['48fdfcb9face5d58a4f6dde2e72a1fb8dcaf8ab26f95ab49fab84c2ddefb0109'],
+    }),
+    ('mccabe', '0.7.0', {
+        'checksums': ['348e0240c33b60bbdf4e523192ef919f28cb2c3d7d5c7794f74009290f236325'],
+    }),
+    ('pylint', version, {
+        'checksums': ['e9b7171e242dcc6ebd0aaa7540481d1a72860748a0a7816b8fe6cf6c80a6fe7e'],
+    }),
+]
+
+sanity_pip_check = True
+
+sanity_check_paths = {
+    'files': ['bin/pylint'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+moduleclass = 'tools'

From acb648012182241e07163dca94d299d948b0a3f1 Mon Sep 17 00:00:00 2001
From: vsc46128 <vsc46128@node4007.donphan.os>
Date: Fri, 28 Jun 2024 18:53:44 +0200
Subject: [PATCH 370/835] adding easyconfigs: biom-format-2.1.16-foss-2023b.eb

---
 .../biom-format-2.1.16-foss-2023b.eb          | 49 +++++++++++++++++++
 1 file changed, 49 insertions(+)
 create mode 100644 easybuild/easyconfigs/b/biom-format/biom-format-2.1.16-foss-2023b.eb

diff --git a/easybuild/easyconfigs/b/biom-format/biom-format-2.1.16-foss-2023b.eb b/easybuild/easyconfigs/b/biom-format/biom-format-2.1.16-foss-2023b.eb
new file mode 100644
index 00000000000..91d9cecbd99
--- /dev/null
+++ b/easybuild/easyconfigs/b/biom-format/biom-format-2.1.16-foss-2023b.eb
@@ -0,0 +1,49 @@
+##
+# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia
+# Homepage:     https://staff.flinders.edu.au/research/deep-thought
+#
+# Authors::     Robert Qiao <rob.qiao@flinders.edu.au>
+# License::     Revised BSD
+#
+# Notes:: updated by Kenneth Hoste (HPC-UGent) for foss/2021b
+##
+# Updated: Petr Král (INUITS)
+# Updated: Lara Peeters (Ghent University)
+
+easyblock = 'PythonPackage'
+
+name = 'biom-format'
+version = '2.1.16'
+
+homepage = 'https://biom-format.org'
+description = """
+The BIOM file format (canonically pronounced biome) is designed to be
+ a general-use format for representing biological sample by observation
+ contingency tables. BIOM is a recognized standard for the Earth Microbiome
+ Project and is a Genomics Standards Consortium supported project.
+"""
+
+toolchain = {'name': 'foss', 'version': '2023b'}
+toolchainopts = {'usempi': True}
+
+sources = [SOURCE_TAR_GZ]
+checksums = ['47f88d57a94ecaa4d06f3578ca394e78db6d12e46ab0886634743181e67dcfc9']
+
+dependencies = [
+    ('Python', '3.11.5'),
+    ('SciPy-bundle', '2023.11'),
+    ('h5py', '3.11.0'),
+]
+
+use_pip = True
+sanity_pip_check = True
+download_dep_fail = True
+
+sanity_check_paths = {
+    'files': ['bin/biom'],
+    'dirs': ['lib'],
+}
+
+options = {'modulename': 'biom'}
+
+moduleclass = 'bio'

From b425e87a652e3ff3b12df500274889131ab68b56 Mon Sep 17 00:00:00 2001
From: Thomas Roeblitz <thomas.roblitz@uib.no>
Date: Sat, 29 Jun 2024 11:29:54 +0200
Subject: [PATCH 371/835] fixes bug that resulted in test failure on zen4

---
 .../h/Highway/Highway-1.0.4-GCCcore-12.3.0.eb |  8 +++-
 ...ighway-1.0.4-zen4-fix-TruncateTo-bug.patch | 44 +++++++++++++++++++
 2 files changed, 51 insertions(+), 1 deletion(-)
 create mode 100644 easybuild/easyconfigs/h/Highway/Highway-1.0.4-zen4-fix-TruncateTo-bug.patch

diff --git a/easybuild/easyconfigs/h/Highway/Highway-1.0.4-GCCcore-12.3.0.eb b/easybuild/easyconfigs/h/Highway/Highway-1.0.4-GCCcore-12.3.0.eb
index a05239847d3..824460d1be2 100644
--- a/easybuild/easyconfigs/h/Highway/Highway-1.0.4-GCCcore-12.3.0.eb
+++ b/easybuild/easyconfigs/h/Highway/Highway-1.0.4-GCCcore-12.3.0.eb
@@ -12,7 +12,13 @@ toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
 
 source_urls = ['https://github.com/google/highway/archive/refs/tags/']
 sources = ['%(version)s.tar.gz']
-checksums = ['faccd343935c9e98afd1016e9d20e0b8b89d908508d1af958496f8c2d3004ac2']
+patches = ['Highway-1.0.4-zen4-fix-TruncateTo-bug.patch']
+
+checksums = [
+    {'1.0.4.tar.gz': 'faccd343935c9e98afd1016e9d20e0b8b89d908508d1af958496f8c2d3004ac2'},
+    {'Highway-1.0.4-zen4-fix-TruncateTo-bug.patch':
+     '7eb68cfa702648f8f82fe3b7bdc5f0f0ab171840f966040f6d8ec470e3eed712'},
+]
 
 builddependencies = [
     ('binutils', '2.40'),
diff --git a/easybuild/easyconfigs/h/Highway/Highway-1.0.4-zen4-fix-TruncateTo-bug.patch b/easybuild/easyconfigs/h/Highway/Highway-1.0.4-zen4-fix-TruncateTo-bug.patch
new file mode 100644
index 00000000000..b4e71737d22
--- /dev/null
+++ b/easybuild/easyconfigs/h/Highway/Highway-1.0.4-zen4-fix-TruncateTo-bug.patch
@@ -0,0 +1,44 @@
+diff --git a/hwy/ops/x86_256-inl.h b/hwy/ops/x86_256-inl.h
+index 4e2e83e8..2fbf99c7 100644
+--- a/hwy/ops/x86_256-inl.h
++++ b/hwy/ops/x86_256-inl.h
+@@ -4185,7 +4185,7 @@ HWY_INLINE Vec128<uint32_t> LookupAndConcatHalves(Vec256<T> v) {
+ #if HWY_TARGET <= HWY_AVX3_DL
+   alignas(32) static constexpr uint32_t kMap[8] = {
+       LO, HI, 0x10101010 + LO, 0x10101010 + HI, 0, 0, 0, 0};
+-  const auto result = _mm256_permutexvar_epi8(v.raw, Load(d32, kMap).raw);
++  const auto result = _mm256_permutexvar_epi8(Load(d32, kMap).raw, v.raw);
+ #else
+   alignas(32) static constexpr uint32_t kMap[8] = {LO,  HI,  ~0u, ~0u,
+                                                    ~0u, ~0u, LO,  HI};
+@@ -4208,7 +4208,7 @@ HWY_INLINE Vec128<uint32_t, 2> LookupAndConcatQuarters(Vec256<T> v) {
+ #if HWY_TARGET <= HWY_AVX3_DL
+   alignas(32) static constexpr uint16_t kMap[16] = {
+       LO, HI, 0x1010 + LO, 0x1010 + HI, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0};
+-  const auto result = _mm256_permutexvar_epi8(v.raw, Load(d16, kMap).raw);
++  const auto result = _mm256_permutexvar_epi8(Load(d16, kMap).raw, v.raw);
+   return LowerHalf(Vec128<uint32_t>{_mm256_castsi256_si128(result)});
+ #else
+   constexpr uint16_t ff = static_cast<uint16_t>(~0u);
+@@ -4229,7 +4229,7 @@ HWY_API Vec32<uint8_t> TruncateTo(D /* tag */, Vec256<uint64_t> v) {
+ #if HWY_TARGET <= HWY_AVX3_DL
+   alignas(32) static constexpr uint32_t kMap[8] = {0x18100800u, 0, 0, 0,
+                                                    0,           0, 0, 0};
+-  const auto result = _mm256_permutexvar_epi8(v.raw, Load(d32, kMap).raw);
++  const auto result = _mm256_permutexvar_epi8(Load(d32, kMap).raw, v.raw);
+   return LowerHalf(LowerHalf(LowerHalf(Vec256<uint8_t>{result})));
+ #else
+   alignas(32) static constexpr uint32_t kMap[8] = {0xFFFF0800u, ~0u, ~0u, ~0u,
+diff --git a/hwy/ops/x86_512-inl.h b/hwy/ops/x86_512-inl.h
+index 167922d8..83f2ee67 100644
+--- a/hwy/ops/x86_512-inl.h
++++ b/hwy/ops/x86_512-inl.h
+@@ -3497,7 +3497,7 @@ HWY_API Vec128<uint8_t> TruncateTo(D /* tag */, const Vec512<uint32_t> v) {
+   alignas(16) static constexpr uint8_t k8From32[16] = {
+     0, 4, 8, 12, 16, 20, 24, 28, 32, 36, 40, 44, 48, 52, 56, 60};
+   const Vec512<uint8_t> bytes{
+-      _mm512_permutexvar_epi32(LoadDup128(d8, k8From32).raw, v.raw)};
++      _mm512_permutexvar_epi8(LoadDup128(d8, k8From32).raw, v.raw)};
+ #else
+   const Full512<uint32_t> d32;
+   // In each 128 bit block, gather the lower byte of 4 uint32_t lanes into the

From 60cd0282b2f94e4cb24bdf4f4a1f1b8fede23bb5 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com>
Date: Mon, 1 Jul 2024 10:18:53 +0200
Subject: [PATCH 372/835] Update
 easybuild/easyconfigs/o/orjson/orjson-3.9.15-GCCcore-12.3.0.eb
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Bob Dröge <b.e.droge@rug.nl>
---
 easybuild/easyconfigs/o/orjson/orjson-3.9.15-GCCcore-12.3.0.eb | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easybuild/easyconfigs/o/orjson/orjson-3.9.15-GCCcore-12.3.0.eb b/easybuild/easyconfigs/o/orjson/orjson-3.9.15-GCCcore-12.3.0.eb
index 14c64e5a008..ab3a36eed7c 100644
--- a/easybuild/easyconfigs/o/orjson/orjson-3.9.15-GCCcore-12.3.0.eb
+++ b/easybuild/easyconfigs/o/orjson/orjson-3.9.15-GCCcore-12.3.0.eb
@@ -9,6 +9,7 @@ description = """Fast, correct Python JSON library supporting dataclasses, datet
 toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
 
 builddependencies = [
+    ('binutils', '2.40'),
     ('maturin', '1.4.0', '-Rust-1.75.0'),
 ]
 dependencies = [

From f71f2c93c482fade2ebc46533d1c6ceb78d67c7a Mon Sep 17 00:00:00 2001
From: Richard Top <richard.topouchian@uib.no>
Date: Mon, 1 Jul 2024 10:59:49 +0000
Subject: [PATCH 373/835] remove homepage from gmpflf

---
 easybuild/easyconfigs/g/gmpflf/gmpflf-2024.06.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/g/gmpflf/gmpflf-2024.06.eb b/easybuild/easyconfigs/g/gmpflf/gmpflf-2024.06.eb
index 513c69d0a84..bd4f74361b7 100644
--- a/easybuild/easyconfigs/g/gmpflf/gmpflf-2024.06.eb
+++ b/easybuild/easyconfigs/g/gmpflf/gmpflf-2024.06.eb
@@ -3,7 +3,7 @@ easyblock = 'Toolchain'
 name = 'gmpflf'
 version = '2024.06'
 
-homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#foss-toolchain'
+homepage = '(none)'
 description = """GNU Compiler Collection (GCC) based compiler toolchain, including
  MPICH for MPI support, FlexiBLAS (OpenBLAS and LAPACK), FFTW and ScaLAPACK."""
 

From f11b68170e8462c08c14b14896ed1224588c839c Mon Sep 17 00:00:00 2001
From: Victor Enrique Goitea <victorg@bmb.sdu.dk>
Date: Mon, 1 Jul 2024 15:29:44 +0200
Subject: [PATCH 374/835] create Qualimap-2.3-foss-2022b.eb

---
 easybuild/easyconfigs/q/Qualimap/Qualimap-2.3-foss-2022b.eb | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 create mode 100644 easybuild/easyconfigs/q/Qualimap/Qualimap-2.3-foss-2022b.eb

diff --git a/easybuild/easyconfigs/q/Qualimap/Qualimap-2.3-foss-2022b.eb b/easybuild/easyconfigs/q/Qualimap/Qualimap-2.3-foss-2022b.eb
new file mode 100644
index 00000000000..e69de29bb2d

From d68b62bc098990285f17c4c8c517a9f72c77fb89 Mon Sep 17 00:00:00 2001
From: Victor Enrique Goitea <43407659+VictorGoitea@users.noreply.github.com>
Date: Mon, 1 Jul 2024 15:33:54 +0200
Subject: [PATCH 375/835] Update and rename Qualimap-2.3-foss-2022b.eb to
 Qualimap-2.3-foss-2022b-R-4.2.2.eb

---
 .../Qualimap-2.3-foss-2022b-R-4.2.2.eb        | 33 +++++++++++++++++++
 .../q/Qualimap/Qualimap-2.3-foss-2022b.eb     |  0
 2 files changed, 33 insertions(+)
 create mode 100644 easybuild/easyconfigs/q/Qualimap/Qualimap-2.3-foss-2022b-R-4.2.2.eb
 delete mode 100644 easybuild/easyconfigs/q/Qualimap/Qualimap-2.3-foss-2022b.eb

diff --git a/easybuild/easyconfigs/q/Qualimap/Qualimap-2.3-foss-2022b-R-4.2.2.eb b/easybuild/easyconfigs/q/Qualimap/Qualimap-2.3-foss-2022b-R-4.2.2.eb
new file mode 100644
index 00000000000..487e169ee4b
--- /dev/null
+++ b/easybuild/easyconfigs/q/Qualimap/Qualimap-2.3-foss-2022b-R-4.2.2.eb
@@ -0,0 +1,33 @@
+easyblock = 'Tarball'
+
+name = 'Qualimap'
+version = '2.3'
+versionsuffix = '-R-%(rver)s'
+
+homepage = 'http://qualimap.bioinfo.cipf.es/'
+description = """Qualimap 2 is a platform-independent application written in Java and R that provides both
+ a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of
+ alignment sequencing data and its derivatives like feature counts."""
+
+toolchain = {'name': 'foss', 'version': '2022b'}
+
+source_urls = ['https://bitbucket.org/kokonech/qualimap/downloads/']
+sources = ['qualimap_v%(version)s.zip']
+checksums = ['2a04dd864b712da30923cce3bc8dfc6ea59612118e8b0ff1a246fe43b8d34c40']
+
+dependencies = [
+    ('Java', '17', '', SYSTEM),
+    ('R', '4.2.2'),
+    ('R-bundle-Bioconductor', '3.16', versionsuffix),
+]
+
+sanity_check_paths = {
+    'files': ['qualimap'],
+    'dirs': [],
+}
+
+sanity_check_commands = ["qualimap --help"]
+
+modextrapaths = {'PATH': ''}
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/q/Qualimap/Qualimap-2.3-foss-2022b.eb b/easybuild/easyconfigs/q/Qualimap/Qualimap-2.3-foss-2022b.eb
deleted file mode 100644
index e69de29bb2d..00000000000

From 5fc7093cee481cfc766ea9a5b606ecb5f5fd16c6 Mon Sep 17 00:00:00 2001
From: Victor Enrique Goitea <43407659+VictorGoitea@users.noreply.github.com>
Date: Mon, 1 Jul 2024 17:21:36 +0200
Subject: [PATCH 376/835] Downgrade Java to v11

---
 .../easyconfigs/q/Qualimap/Qualimap-2.3-foss-2022b-R-4.2.2.eb   | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/q/Qualimap/Qualimap-2.3-foss-2022b-R-4.2.2.eb b/easybuild/easyconfigs/q/Qualimap/Qualimap-2.3-foss-2022b-R-4.2.2.eb
index 487e169ee4b..c6a3e40d231 100644
--- a/easybuild/easyconfigs/q/Qualimap/Qualimap-2.3-foss-2022b-R-4.2.2.eb
+++ b/easybuild/easyconfigs/q/Qualimap/Qualimap-2.3-foss-2022b-R-4.2.2.eb
@@ -16,7 +16,7 @@ sources = ['qualimap_v%(version)s.zip']
 checksums = ['2a04dd864b712da30923cce3bc8dfc6ea59612118e8b0ff1a246fe43b8d34c40']
 
 dependencies = [
-    ('Java', '17', '', SYSTEM),
+    ('Java', '11', '', SYSTEM),
     ('R', '4.2.2'),
     ('R-bundle-Bioconductor', '3.16', versionsuffix),
 ]

From 068e7d68d231f4e23b3cf97704d2ec4cba5fcaf3 Mon Sep 17 00:00:00 2001
From: Alexander Grund <alexander.grund@tu-dresden.de>
Date: Tue, 2 Jul 2024 09:35:31 +0200
Subject: [PATCH 377/835] fix implicit function declaration in OpenMPI 4.1.4

---
 .../o/OpenMPI/OpenMPI-4.1.4-GCC-11.3.0.eb     |  3 ++
 .../o/OpenMPI/OpenMPI-4.1.4-GCC-12.2.0.eb     |  3 ++
 .../OpenMPI-4.1.4-NVHPC-22.7-CUDA-11.7.0.eb   |  3 ++
 ...x-implicit-cuda-function-declaration.patch | 31 +++++++++++++++++++
 4 files changed, 40 insertions(+)
 create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4_fix-implicit-cuda-function-declaration.patch

diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4-GCC-11.3.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4-GCC-11.3.0.eb
index 6471a45d999..06b168671f7 100644
--- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4-GCC-11.3.0.eb
+++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4-GCC-11.3.0.eb
@@ -11,6 +11,7 @@ sources = [SOURCELOWER_TAR_BZ2]
 patches = [
     'OpenMPI-4.1.1_build-with-internal-cuda-header.patch',
     'OpenMPI-4.1.1_opal-datatype-cuda-performance.patch',
+    'OpenMPI-4.1.4_fix-implicit-cuda-function-declaration.patch',
     'OpenMPI-4.1.x_add_atomic_wmb.patch',
 ]
 checksums = [
@@ -19,6 +20,8 @@ checksums = [
      '63eac52736bdf7644c480362440a7f1f0ae7c7cae47b7565f5635c41793f8c83'},
     {'OpenMPI-4.1.1_opal-datatype-cuda-performance.patch':
      'b767c7166cf0b32906132d58de5439c735193c9fd09ec3c5c11db8d5fa68750e'},
+    {'OpenMPI-4.1.4_fix-implicit-cuda-function-declaration.patch':
+     'ec1c2f07d03574b86fc5fb462eed96eb6f5658deb8a6412cf37007d687a28673'},
     {'OpenMPI-4.1.x_add_atomic_wmb.patch': '9494bbc546d661ba5189e44b4c84a7f8df30a87cdb9d96ce2e73a7c8fecba172'},
 ]
 
diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4-GCC-12.2.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4-GCC-12.2.0.eb
index fbb50478eec..f4fbe865280 100644
--- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4-GCC-12.2.0.eb
+++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4-GCC-12.2.0.eb
@@ -11,6 +11,7 @@ sources = [SOURCELOWER_TAR_BZ2]
 patches = [
     'OpenMPI-4.1.1_build-with-internal-cuda-header.patch',
     'OpenMPI-4.1.1_opal-datatype-cuda-performance.patch',
+    'OpenMPI-4.1.4_fix-implicit-cuda-function-declaration.patch',
     'OpenMPI-4.1.x_add_atomic_wmb.patch',
 ]
 checksums = [
@@ -19,6 +20,8 @@ checksums = [
      '63eac52736bdf7644c480362440a7f1f0ae7c7cae47b7565f5635c41793f8c83'},
     {'OpenMPI-4.1.1_opal-datatype-cuda-performance.patch':
      'b767c7166cf0b32906132d58de5439c735193c9fd09ec3c5c11db8d5fa68750e'},
+    {'OpenMPI-4.1.4_fix-implicit-cuda-function-declaration.patch':
+     'ec1c2f07d03574b86fc5fb462eed96eb6f5658deb8a6412cf37007d687a28673'},
     {'OpenMPI-4.1.x_add_atomic_wmb.patch': '9494bbc546d661ba5189e44b4c84a7f8df30a87cdb9d96ce2e73a7c8fecba172'},
 ]
 
diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4-NVHPC-22.7-CUDA-11.7.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4-NVHPC-22.7-CUDA-11.7.0.eb
index 9ef5b5d1bb4..a69c1e2b8d4 100644
--- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4-NVHPC-22.7-CUDA-11.7.0.eb
+++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4-NVHPC-22.7-CUDA-11.7.0.eb
@@ -11,6 +11,7 @@ sources = [SOURCELOWER_TAR_BZ2]
 patches = [
     'OpenMPI-4.1.1_build-with-internal-cuda-header.patch',
     'OpenMPI-4.1.1_opal-datatype-cuda-performance.patch',
+    'OpenMPI-4.1.4_fix-implicit-cuda-function-declaration.patch',
     'OpenMPI-4.1.x_add_atomic_wmb.patch',
 ]
 checksums = [
@@ -19,6 +20,8 @@ checksums = [
      '63eac52736bdf7644c480362440a7f1f0ae7c7cae47b7565f5635c41793f8c83'},
     {'OpenMPI-4.1.1_opal-datatype-cuda-performance.patch':
      'b767c7166cf0b32906132d58de5439c735193c9fd09ec3c5c11db8d5fa68750e'},
+    {'OpenMPI-4.1.4_fix-implicit-cuda-function-declaration.patch':
+     'ec1c2f07d03574b86fc5fb462eed96eb6f5658deb8a6412cf37007d687a28673'},
     {'OpenMPI-4.1.x_add_atomic_wmb.patch': '9494bbc546d661ba5189e44b4c84a7f8df30a87cdb9d96ce2e73a7c8fecba172'},
 ]
 
diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4_fix-implicit-cuda-function-declaration.patch b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4_fix-implicit-cuda-function-declaration.patch
new file mode 100644
index 00000000000..3ccb7d43d82
--- /dev/null
+++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4_fix-implicit-cuda-function-declaration.patch
@@ -0,0 +1,31 @@
+Fix a left-over function causing compilation warnings or errors:
+mtl_ofi_component.c:298:5: error: implicit declaration of function 'mca_common_cuda_fini'; did you mean 'ompi_comm_cid_init'? [-Werror=implicit-function-declaration]
+     mca_common_cuda_fini();
+     ^~~~~~~~~~~~~~~~~~~~
+
+See https://github.com/open-mpi/ompi/issues/11381
+
+From 7676618c43d489b145e730d1d7603f0292a031c0 Mon Sep 17 00:00:00 2001
+From: Jingyin Tang <jytang@amazon.com>
+Date: Mon, 6 Feb 2023 13:48:51 -0500
+Subject: [PATCH] Fix compilation issue in OFI with CUDA
+
+Signed-off-by: Jingyin Tang <jytang@amazon.com>
+---
+ ompi/mca/mtl/ofi/mtl_ofi_component.c | 3 ---
+ 1 file changed, 3 deletions(-)
+
+diff --git a/ompi/mca/mtl/ofi/mtl_ofi_component.c b/ompi/mca/mtl/ofi/mtl_ofi_component.c
+index c1aac6934d0..e36f020b206 100644
+--- a/ompi/mca/mtl/ofi/mtl_ofi_component.c
++++ b/ompi/mca/mtl/ofi/mtl_ofi_component.c
+@@ -294,9 +294,6 @@ ompi_mtl_ofi_component_query(mca_base_module_t **module, int *priority)
+ static int
+ ompi_mtl_ofi_component_close(void)
+ {
+-#if OPAL_CUDA_SUPPORT
+-    mca_common_cuda_fini();
+-#endif
+     return opal_common_ofi_close();
+ }
+ 

From bc6e08f89759b8b70166de5bfcb5056b9db8ec90 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com>
Date: Tue, 2 Jul 2024 10:05:42 +0200
Subject: [PATCH 378/835] Update
 easybuild/easyconfigs/o/orjson/orjson-3.9.15-GCCcore-12.3.0.eb moduleclass
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Bob Dröge <b.e.droge@rug.nl>
---
 easybuild/easyconfigs/o/orjson/orjson-3.9.15-GCCcore-12.3.0.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/o/orjson/orjson-3.9.15-GCCcore-12.3.0.eb b/easybuild/easyconfigs/o/orjson/orjson-3.9.15-GCCcore-12.3.0.eb
index ab3a36eed7c..410c8131df9 100644
--- a/easybuild/easyconfigs/o/orjson/orjson-3.9.15-GCCcore-12.3.0.eb
+++ b/easybuild/easyconfigs/o/orjson/orjson-3.9.15-GCCcore-12.3.0.eb
@@ -35,4 +35,4 @@ exts_list = [
 
 sanity_pip_check = True
 
-moduleclass = 'math'
+moduleclass = 'lib'

From 0b084b587011acc88402de8d1252ad16d974a271 Mon Sep 17 00:00:00 2001
From: WilleBell <cintiawillemyns@gmail.com>
Date: Tue, 2 Jul 2024 11:22:48 +0200
Subject: [PATCH 379/835] adding easyconfigs: SHAP-0.43.0-foss-2023a.eb

---
 .../s/SHAP/SHAP-0.43.0-foss-2023a.eb          | 37 +++++++++++++++++++
 1 file changed, 37 insertions(+)
 create mode 100644 easybuild/easyconfigs/s/SHAP/SHAP-0.43.0-foss-2023a.eb

diff --git a/easybuild/easyconfigs/s/SHAP/SHAP-0.43.0-foss-2023a.eb b/easybuild/easyconfigs/s/SHAP/SHAP-0.43.0-foss-2023a.eb
new file mode 100644
index 00000000000..6be374eb213
--- /dev/null
+++ b/easybuild/easyconfigs/s/SHAP/SHAP-0.43.0-foss-2023a.eb
@@ -0,0 +1,37 @@
+easyblock = 'PythonBundle'
+
+name = 'SHAP'
+version = '0.43.0'
+
+homepage = "https://github.com/shap/shap"
+description = """SHAP (SHapley Additive exPlanations) is a game theoretic approach to explain the output of any
+ machine learning model. It connects optimal credit allocation with local explanations using the classic Shapley
+ values from game theory and their related extensions."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('scikit-learn', '1.3.1'),
+    ('tqdm', '4.66.1'),
+    ('numba', '0.58.1'),
+]
+
+sanity_pip_check = True
+use_pip = True
+
+exts_list = [
+    ('cloudpickle', '3.0.0', {
+        'checksums': ['996d9a482c6fb4f33c1a35335cf8afd065d2a56e973270364840712d9131a882'],
+    }),
+    ('slicer', '0.0.7', {
+        'checksums': ['f5d5f7b45f98d155b9c0ba6554fa9770c6b26d5793a3e77a1030fb56910ebeec'],
+    }),
+    (name, version, {
+        'sources': ['%(namelower)s-%(version)s.tar.gz'],
+        'checksums': ['1eabe01444a24e181ef6a7c9593b4d7c7143eefaeb1fa4d97bd5d9fdc96c4c1e'],
+    }),
+]
+
+moduleclass = 'data'

From 445a2c2ad98dd57050820f72e909bea515769f02 Mon Sep 17 00:00:00 2001
From: Julian Morillo <julian.morillo@bsc.es>
Date: Tue, 2 Jul 2024 11:43:07 +0200
Subject: [PATCH 380/835] Upgrade to 4.2.0 (which includes bug fixes) and added
 new patch that fixes some tests

---
 ...tch => Extrae-4.2.0-detect_binutils.patch} | 29 +++---
 .../Extrae-4.2.0-fix-hw-counters-checks.patch | 96 +++++++++++++++++++
 ...i-2023b.eb => Extrae-4.2.0-gompi-2023b.eb} | 22 +++--
 3 files changed, 125 insertions(+), 22 deletions(-)
 rename easybuild/easyconfigs/e/Extrae/{Extrae-4.1.7-detect_binutils.patch => Extrae-4.2.0-detect_binutils.patch} (64%)
 create mode 100644 easybuild/easyconfigs/e/Extrae/Extrae-4.2.0-fix-hw-counters-checks.patch
 rename easybuild/easyconfigs/e/Extrae/{Extrae-4.1.7-gompi-2023b.eb => Extrae-4.2.0-gompi-2023b.eb} (57%)

diff --git a/easybuild/easyconfigs/e/Extrae/Extrae-4.1.7-detect_binutils.patch b/easybuild/easyconfigs/e/Extrae/Extrae-4.2.0-detect_binutils.patch
similarity index 64%
rename from easybuild/easyconfigs/e/Extrae/Extrae-4.1.7-detect_binutils.patch
rename to easybuild/easyconfigs/e/Extrae/Extrae-4.2.0-detect_binutils.patch
index aa8f6918a66..ae5847ad80e 100644
--- a/easybuild/easyconfigs/e/Extrae/Extrae-4.1.7-detect_binutils.patch
+++ b/easybuild/easyconfigs/e/Extrae/Extrae-4.2.0-detect_binutils.patch
@@ -1,11 +1,11 @@
-diff -Nru extrae-4.1.7.orig/config/macros.m4 extrae-4.1.7/config/macros.m4
---- extrae-4.1.7.orig/config/macros.m4  2024-05-30 16:23:59.684839619 +0200
-+++ extrae-4.1.7/config/macros.m4       2024-05-30 16:27:08.208600097 +0200
+diff -Nru extrae-4.2.0.orig/config/macros.m4 extrae-4.2.0/config/macros.m4
+--- extrae-4.2.0.orig/config/macros.m4	2024-07-01 16:12:03.689962036 +0200
++++ extrae-4.2.0/config/macros.m4	2024-07-01 16:13:05.811649165 +0200
 @@ -779,6 +779,8 @@
           elif test -r "${binutils_home_dir}/lib/libbfd.a" -a \
                        "${binutils_require_shared}" = "no" ; then
              BFD_LIBSDIR="${binutils_home_dir}/lib"
-+         elif test -r "${binutils_home_dir}/libbfd.so" ; then
++	 elif test -r "${binutils_home_dir}/libbfd.so" ; then
 +            BFD_LIBSDIR="${binutils_home_dir}"
           else
              dnl Try something more automatic using find command
@@ -14,30 +14,29 @@ diff -Nru extrae-4.1.7.orig/config/macros.m4 extrae-4.1.7/config/macros.m4
              LIBERTY_LIBSDIR="${binutils_home_dir}/lib"
           elif test -r "${binutils_home_dir}/lib/libiberty.a" ; then
              LIBERTY_LIBSDIR="${binutils_home_dir}/lib"
-+         elif test -r "${binutils_home_dir}/libiberty.a" ; then
++	elif test -r "${binutils_home_dir}/libiberty.a" ; then
 +            LIBERTY_LIBSDIR="${binutils_home_dir}"
           else
              dnl Try something more automatic using find command
              libiberty_lib=""
-diff -Nru extrae-4.1.7.orig/configure extrae-4.1.7/configure
---- extrae-4.1.7.orig/configure 2024-05-30 16:23:59.716839578 +0200
-+++ extrae-4.1.7/configure      2024-05-30 16:25:31.276723193 +0200
-@@ -35072,6 +35072,8 @@
+diff -Nru extrae-4.2.0.orig/configure extrae-4.2.0/configure
+--- extrae-4.2.0.orig/configure	2024-07-01 16:12:03.308963954 +0200
++++ extrae-4.2.0/configure	2024-07-01 16:17:00.458465744 +0200
+@@ -35074,6 +35074,8 @@
           elif test -r "${binutils_home_dir}/lib/libbfd.a" -a \
                        "${binutils_require_shared}" = "no" ; then
              BFD_LIBSDIR="${binutils_home_dir}/lib"
-+         elif test -r "${binutils_home_dir}/libbfd.so" ; then
++	 elif test -r "${binutils_home_dir}/libbfd.so" ; then
 +            BFD_LIBSDIR="${binutils_home_dir}"
           else
                          libbfd_lib=""
-
-@@ -35106,6 +35108,8 @@
+ 
+@@ -35108,6 +35110,8 @@
              LIBERTY_LIBSDIR="${binutils_home_dir}/lib"
           elif test -r "${binutils_home_dir}/lib/libiberty.a" ; then
              LIBERTY_LIBSDIR="${binutils_home_dir}/lib"
-+         elif test -r "${binutils_home_dir}/libiberty.a" ; then
++	 elif test -r "${binutils_home_dir}/libiberty.a" ; then
 +            LIBERTY_LIBSDIR="${binutils_home_dir}"
           else
                          libiberty_lib=""
-
-
+ 
diff --git a/easybuild/easyconfigs/e/Extrae/Extrae-4.2.0-fix-hw-counters-checks.patch b/easybuild/easyconfigs/e/Extrae/Extrae-4.2.0-fix-hw-counters-checks.patch
new file mode 100644
index 00000000000..1bc18c408b4
--- /dev/null
+++ b/easybuild/easyconfigs/e/Extrae/Extrae-4.2.0-fix-hw-counters-checks.patch
@@ -0,0 +1,96 @@
+diff -Nru extrae-4.2.0.orig/tests/functional/hw-counters/check_Extrae_PAPI_TOT_CYC.sh extrae-4.2.0/tests/functional/hw-counters/check_Extrae_PAPI_TOT_CYC.sh
+--- extrae-4.2.0.orig/tests/functional/hw-counters/check_Extrae_PAPI_TOT_CYC.sh	2024-07-01 16:12:03.454963219 +0200
++++ extrae-4.2.0/tests/functional/hw-counters/check_Extrae_PAPI_TOT_CYC.sh	2024-07-02 10:26:41.603395579 +0200
+@@ -11,6 +11,20 @@
+ ../../../src/merger/mpi2prv -f TRACE.mpits -o ${TRACE}.prv
+ 
+ # Check
++if ! command -v papi_avail &> /dev/null
++then
++        echo "papi_avail could not be found"
++        exit 0
++fi
++
++PAPI_TOT_CYC_available=`papi_avail | grep PAPI_TOT_CYC | awk '{print $3}'`
++if [[ "$PAPI_TOT_CYC_available" == No ]]
++then
++        echo "PAPI_TOT_CYC is not available"
++        exit 0
++fi
++
++
+ CheckEntryInPCF ${TRACE}.pcf PAPI_TOT_CYC
+ 
+ rm -fr TRACE* set-0 ${TRACE}.???
+diff -Nru extrae-4.2.0.orig/tests/functional/hw-counters/check_Extrae_PAPI_TOT_INS.sh extrae-4.2.0/tests/functional/hw-counters/check_Extrae_PAPI_TOT_INS.sh
+--- extrae-4.2.0.orig/tests/functional/hw-counters/check_Extrae_PAPI_TOT_INS.sh	2024-07-01 16:12:03.455963214 +0200
++++ extrae-4.2.0/tests/functional/hw-counters/check_Extrae_PAPI_TOT_INS.sh	2024-07-02 10:28:14.723917087 +0200
+@@ -11,6 +11,20 @@
+ ../../../src/merger/mpi2prv -f TRACE.mpits -o ${TRACE}.prv
+ 
+ # Check
++if ! command -v papi_avail &> /dev/null
++then
++        echo "papi_avail could not be found"
++        exit 0
++fi
++
++PAPI_TOT_INS_available=`papi_avail | grep PAPI_TOT_INS | awk '{print $3}'`
++if [[ "$PAPI_TOT_INS_available" == No ]]
++then
++        echo "PAPI_TOT_INS is not available"
++        exit 0
++fi
++
++
+ CheckEntryInPCF ${TRACE}.pcf PAPI_TOT_INS
+ 
+ rm -fr TRACE* set-0 ${TRACE}.???
+diff -Nru extrae-4.2.0.orig/tests/functional/hw-counters/check_Extrae_PAPI_TOT_INS_CYC.sh extrae-4.2.0/tests/functional/hw-counters/check_Extrae_PAPI_TOT_INS_CYC.sh
+--- extrae-4.2.0.orig/tests/functional/hw-counters/check_Extrae_PAPI_TOT_INS_CYC.sh	2024-07-01 16:12:03.448963249 +0200
++++ extrae-4.2.0/tests/functional/hw-counters/check_Extrae_PAPI_TOT_INS_CYC.sh	2024-07-02 10:29:00.084684067 +0200
+@@ -11,6 +11,20 @@
+ ../../../src/merger/mpi2prv -f TRACE.mpits -o ${TRACE}.prv
+ 
+ # Check
++if ! command -v papi_avail &> /dev/null
++then
++        echo "papi_avail could not be found"
++        exit 0
++fi
++
++PAPI_TOT_CYC_available=`papi_avail | grep PAPI_TOT_CYC | awk '{print $3}'`
++if [[ "$PAPI_TOT_CYC_available" == No ]]
++then
++        echo "PAPI_TOT_CYC is not available"
++        exit 0
++fi
++
++
+ CheckEntryInPCF ${TRACE}.pcf PAPI_TOT_INS
+ CheckEntryInPCF ${TRACE}.pcf PAPI_TOT_CYC
+ 
+diff -Nru extrae-4.2.0.orig/tests/functional/xml/check_Extrae_xml_envvar_counters.sh extrae-4.2.0/tests/functional/xml/check_Extrae_xml_envvar_counters.sh
+--- extrae-4.2.0.orig/tests/functional/xml/check_Extrae_xml_envvar_counters.sh	2024-07-01 16:12:03.484963068 +0200
++++ extrae-4.2.0/tests/functional/xml/check_Extrae_xml_envvar_counters.sh	2024-07-02 10:19:24.415644506 +0200
+@@ -11,6 +11,20 @@
+ ../../../src/merger/mpi2prv -f TRACE.mpits -o ${TRACE}.prv
+ 
+ # Check
++if ! command -v papi_avail &> /dev/null
++then
++        echo "papi_avail could not be found"
++        exit 0
++fi
++
++PAPI_TOT_CYC_available=`papi_avail | grep PAPI_TOT_CYC | awk '{print $3}'`
++if [[ "$PAPI_TOT_CYC_available" == No ]]
++then
++        echo "PAPI_TOT_CYC is not available"
++        exit 0
++fi
++
++
+ CheckEntryInPCF ${TRACE}.pcf PAPI_TOT_INS
+ 
+ rm -fr TRACE* set-0 ${TRACE}.???
diff --git a/easybuild/easyconfigs/e/Extrae/Extrae-4.1.7-gompi-2023b.eb b/easybuild/easyconfigs/e/Extrae/Extrae-4.2.0-gompi-2023b.eb
similarity index 57%
rename from easybuild/easyconfigs/e/Extrae/Extrae-4.1.7-gompi-2023b.eb
rename to easybuild/easyconfigs/e/Extrae/Extrae-4.2.0-gompi-2023b.eb
index 295ed24a172..e50abc098fe 100644
--- a/easybuild/easyconfigs/e/Extrae/Extrae-4.1.7-gompi-2023b.eb
+++ b/easybuild/easyconfigs/e/Extrae/Extrae-4.2.0-gompi-2023b.eb
@@ -1,21 +1,29 @@
 name = 'Extrae'
-version = '4.1.7'
+version = '4.2.0'
 
 homepage = 'https://tools.bsc.es/extrae'
-description = """Extrae is the package devoted to generate Paraver trace-files for a post-mortem analysis. 
-Extrae is a tool that uses different interposition mechanisms to inject probes into the target application 
+description = """Extrae is the package devoted to generate Paraver trace-files for a post-mortem analysis.
+Extrae is a tool that uses different interposition mechanisms to inject probes into the target application
 so as to gather information regarding the application performance."""
 
 toolchain = {'name': 'gompi', 'version': '2023b'}
+
 toolchainopts = {'usempi': True}
 
 source_urls = ['https://ftp.tools.bsc.es/%(namelower)s']
+
 sources = ['%(namelower)s-%(version)s-src.tar.bz2']
-patches = ['Extrae-4.1.7-detect_binutils.patch']
+
+patches = [
+    'Extrae-4.2.0-detect_binutils.patch',
+    'Extrae-4.2.0-fix-hw-counters-checks.patch',
+]
+
 checksums = [
-    # extrae-4.1.7-src.tar.bz2
-    '0ed87449f74db0abc239ee8c40176e89f9ca6a69738fe751ec0df8fc46da1712',
-    '9319b0af3e8714237fef9f4f0e22fda72a83a3120b29f63a6cbaf95b9f71d61f',  # Extrae-4.1.7-detect_binutils.patch
+    # extrae-4.2.0-src.tar.bz2
+    '7b83a1ed008440bbc1bda88297d2d0e9256780db1cf8401b3c12718451f8919a',
+    '1c7bf9d97405c5c2f9dba3604faf141c1563c70958e942822aab521eb7ea0c9e', # Extrae-4.2.0-detect_binutils.patch
+    '378241e39203e531c72980a9e2fda9ea15f693202a83791d40af36757824df79', # Extrae-4.2.0-fix-hw-counters-checks.patch
 ]
 
 builddependencies = [

From 169bd61806a2ffc0d789e63674ec8e9f2e700206 Mon Sep 17 00:00:00 2001
From: Julian Morillo <julian.morillo@bsc.es>
Date: Tue, 2 Jul 2024 12:06:43 +0200
Subject: [PATCH 381/835] Fix style error (E261 at least two spaces before
 inline comment)

---
 easybuild/easyconfigs/e/Extrae/Extrae-4.2.0-gompi-2023b.eb | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/easybuild/easyconfigs/e/Extrae/Extrae-4.2.0-gompi-2023b.eb b/easybuild/easyconfigs/e/Extrae/Extrae-4.2.0-gompi-2023b.eb
index e50abc098fe..f1583c7a584 100644
--- a/easybuild/easyconfigs/e/Extrae/Extrae-4.2.0-gompi-2023b.eb
+++ b/easybuild/easyconfigs/e/Extrae/Extrae-4.2.0-gompi-2023b.eb
@@ -22,8 +22,8 @@ patches = [
 checksums = [
     # extrae-4.2.0-src.tar.bz2
     '7b83a1ed008440bbc1bda88297d2d0e9256780db1cf8401b3c12718451f8919a',
-    '1c7bf9d97405c5c2f9dba3604faf141c1563c70958e942822aab521eb7ea0c9e', # Extrae-4.2.0-detect_binutils.patch
-    '378241e39203e531c72980a9e2fda9ea15f693202a83791d40af36757824df79', # Extrae-4.2.0-fix-hw-counters-checks.patch
+    '1c7bf9d97405c5c2f9dba3604faf141c1563c70958e942822aab521eb7ea0c9e',  # Extrae-4.2.0-detect_binutils.patch
+    '378241e39203e531c72980a9e2fda9ea15f693202a83791d40af36757824df79',  # Extrae-4.2.0-fix-hw-counters-checks.patch
 ]
 
 builddependencies = [

From 1bf3245ba7bbe5e28a1f9543a50c5a120a47d844 Mon Sep 17 00:00:00 2001
From: vsc46128 <vsc46128@node4001.donphan.os>
Date: Tue, 2 Jul 2024 12:19:54 +0200
Subject: [PATCH 382/835] only use libxsmm as dependency for CP2K 2023.1 on
 x86_64

---
 easybuild/easyconfigs/c/CP2K/CP2K-2023.1-foss-2023a.eb | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-2023.1-foss-2023a.eb b/easybuild/easyconfigs/c/CP2K/CP2K-2023.1-foss-2023a.eb
index d16e202463a..56e829c5b84 100644
--- a/easybuild/easyconfigs/c/CP2K/CP2K-2023.1-foss-2023a.eb
+++ b/easybuild/easyconfigs/c/CP2K/CP2K-2023.1-foss-2023a.eb
@@ -25,11 +25,15 @@ builddependencies = [
 dependencies = [
     ('Libint', '2.7.2', '-lmax-6-cp2k'),
     ('libxc', '6.2.2'),
-    ('libxsmm', '1.17'),
     ('libvori', '220621'),
     ('FFTW', '3.3.10'),
     ('PLUMED', '2.9.0'),
 ]
+if ARCH == 'x86_64':
+    # LIBXSMM is not supported supported on ARM with GCC 12.2.0 and 12.3.0, see https://www.cp2k.org/dev:compiler_support
+    dependencies += [
+        ('libxsmm', '1.17'),
+    ]
 
 type = 'psmp'
 

From ae08bf9f3bbd3faf244f5029d5cff4910af22fe5 Mon Sep 17 00:00:00 2001
From: vsc46128 <vsc46128@node4001.donphan.os>
Date: Tue, 2 Jul 2024 12:41:08 +0200
Subject: [PATCH 383/835] split up long line

---
 easybuild/easyconfigs/c/CP2K/CP2K-2023.1-foss-2023a.eb | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-2023.1-foss-2023a.eb b/easybuild/easyconfigs/c/CP2K/CP2K-2023.1-foss-2023a.eb
index 56e829c5b84..d9ace4b896b 100644
--- a/easybuild/easyconfigs/c/CP2K/CP2K-2023.1-foss-2023a.eb
+++ b/easybuild/easyconfigs/c/CP2K/CP2K-2023.1-foss-2023a.eb
@@ -30,7 +30,8 @@ dependencies = [
     ('PLUMED', '2.9.0'),
 ]
 if ARCH == 'x86_64':
-    # LIBXSMM is not supported supported on ARM with GCC 12.2.0 and 12.3.0, see https://www.cp2k.org/dev:compiler_support
+    # LIBXSMM is not supported supported on ARM with GCC 12.2.0 and 12.3.0
+    # see https://www.cp2k.org/dev:compiler_support
     dependencies += [
         ('libxsmm', '1.17'),
     ]

From fcd8a3b5e8bd170a402212501f885c5c7aa17c90 Mon Sep 17 00:00:00 2001
From: "Tanmoy Chakraborty, Ph.D"
 <56235576+tanmoy1989@users.noreply.github.com>
Date: Tue, 2 Jul 2024 12:20:33 +0100
Subject: [PATCH 384/835] Update
 easybuild/easyconfigs/m/meshio/meshio-5.3.5-foss-2023b.eb
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Bob Dröge <b.e.droge@rug.nl>
---
 easybuild/easyconfigs/m/meshio/meshio-5.3.5-foss-2023b.eb | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/m/meshio/meshio-5.3.5-foss-2023b.eb b/easybuild/easyconfigs/m/meshio/meshio-5.3.5-foss-2023b.eb
index c8cd7d931df..d4b1a912aa3 100644
--- a/easybuild/easyconfigs/m/meshio/meshio-5.3.5-foss-2023b.eb
+++ b/easybuild/easyconfigs/m/meshio/meshio-5.3.5-foss-2023b.eb
@@ -9,7 +9,9 @@ description = "meshio is a tool for reading/writing various mesh formats represe
 toolchain = {'name': 'foss', 'version': '2023b'}
 
 dependencies = [
-    ('Python', '3.11.5'),  # includes numpy
+    ('Python', '3.11.5'),
+    ('Python-bundle-PyPI', '2023.10'),  # includes rich
+    ('SciPy-bundle', '2023.11'),  # includes numpy
     ('h5py', '3.11.0'),
     ('VTK', '9.3.0'),
 ]

From 9eccebd3978dcf8a1a3aeca86ae648b717bc69a4 Mon Sep 17 00:00:00 2001
From: WilleBell <cintiawillemyns@gmail.com>
Date: Tue, 2 Jul 2024 13:47:08 +0200
Subject: [PATCH 385/835] adding easyconfigs: packmol-20.14.4-GCC-12.3.0.eb

---
 .../p/packmol/packmol-20.14.4-GCC-12.3.0.eb   | 24 +++++++++++++++++++
 1 file changed, 24 insertions(+)
 create mode 100644 easybuild/easyconfigs/p/packmol/packmol-20.14.4-GCC-12.3.0.eb

diff --git a/easybuild/easyconfigs/p/packmol/packmol-20.14.4-GCC-12.3.0.eb b/easybuild/easyconfigs/p/packmol/packmol-20.14.4-GCC-12.3.0.eb
new file mode 100644
index 00000000000..4f5dd6ed6b8
--- /dev/null
+++ b/easybuild/easyconfigs/p/packmol/packmol-20.14.4-GCC-12.3.0.eb
@@ -0,0 +1,24 @@
+easyblock = 'MakeCp'
+
+name = 'packmol'
+version = '20.14.4'
+
+homepage = 'http://m3g.iqm.unicamp.br/packmol'
+description = "Packing Optimization for Molecular Dynamics Simulations"
+
+toolchain = {'name': 'GCC', 'version': '12.3.0'}
+
+source_urls = ['https://github.com/m3g/packmol/archive/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['45ec33798d5f10c0aac6046675531a0e98567890c1a76f753450c5fc6b1aaa2f']
+
+buildopts = 'FORTRAN="$F90"'
+
+files_to_copy = [(['packmol'], 'bin'), 'AUTHORS', 'LICENSE']
+
+sanity_check_paths = {
+    'files': ['bin/packmol', 'AUTHORS', 'LICENSE'],
+    'dirs': [],
+}
+
+moduleclass = 'chem'

From cf4c5b1c17761048c14f831d2a3e3a6e9bf550fc Mon Sep 17 00:00:00 2001
From: Julian Morillo <julian.morillo@bsc.es>
Date: Tue, 2 Jul 2024 14:25:46 +0200
Subject: [PATCH 386/835] Small bugfix in the patch

---
 .../Extrae-4.2.0-fix-hw-counters-checks.patch | 36 +++++++++----------
 1 file changed, 18 insertions(+), 18 deletions(-)

diff --git a/easybuild/easyconfigs/e/Extrae/Extrae-4.2.0-fix-hw-counters-checks.patch b/easybuild/easyconfigs/e/Extrae/Extrae-4.2.0-fix-hw-counters-checks.patch
index 1bc18c408b4..5307eed0dc5 100644
--- a/easybuild/easyconfigs/e/Extrae/Extrae-4.2.0-fix-hw-counters-checks.patch
+++ b/easybuild/easyconfigs/e/Extrae/Extrae-4.2.0-fix-hw-counters-checks.patch
@@ -22,9 +22,9 @@ diff -Nru extrae-4.2.0.orig/tests/functional/hw-counters/check_Extrae_PAPI_TOT_C
  CheckEntryInPCF ${TRACE}.pcf PAPI_TOT_CYC
  
  rm -fr TRACE* set-0 ${TRACE}.???
-diff -Nru extrae-4.2.0.orig/tests/functional/hw-counters/check_Extrae_PAPI_TOT_INS.sh extrae-4.2.0/tests/functional/hw-counters/check_Extrae_PAPI_TOT_INS.sh
---- extrae-4.2.0.orig/tests/functional/hw-counters/check_Extrae_PAPI_TOT_INS.sh	2024-07-01 16:12:03.455963214 +0200
-+++ extrae-4.2.0/tests/functional/hw-counters/check_Extrae_PAPI_TOT_INS.sh	2024-07-02 10:28:14.723917087 +0200
+diff -Nru extrae-4.2.0.orig/tests/functional/hw-counters/check_Extrae_PAPI_TOT_INS_CYC.sh extrae-4.2.0/tests/functional/hw-counters/check_Extrae_PAPI_TOT_INS_CYC.sh
+--- extrae-4.2.0.orig/tests/functional/hw-counters/check_Extrae_PAPI_TOT_INS_CYC.sh	2024-07-01 16:12:03.448963249 +0200
++++ extrae-4.2.0/tests/functional/hw-counters/check_Extrae_PAPI_TOT_INS_CYC.sh	2024-07-02 10:29:00.084684067 +0200
 @@ -11,6 +11,20 @@
  ../../../src/merger/mpi2prv -f TRACE.mpits -o ${TRACE}.prv
  
@@ -35,20 +35,20 @@ diff -Nru extrae-4.2.0.orig/tests/functional/hw-counters/check_Extrae_PAPI_TOT_I
 +        exit 0
 +fi
 +
-+PAPI_TOT_INS_available=`papi_avail | grep PAPI_TOT_INS | awk '{print $3}'`
-+if [[ "$PAPI_TOT_INS_available" == No ]]
++PAPI_TOT_CYC_available=`papi_avail | grep PAPI_TOT_CYC | awk '{print $3}'`
++if [[ "$PAPI_TOT_CYC_available" == No ]]
 +then
-+        echo "PAPI_TOT_INS is not available"
++        echo "PAPI_TOT_CYC is not available"
 +        exit 0
 +fi
 +
 +
  CheckEntryInPCF ${TRACE}.pcf PAPI_TOT_INS
+ CheckEntryInPCF ${TRACE}.pcf PAPI_TOT_CYC
  
- rm -fr TRACE* set-0 ${TRACE}.???
-diff -Nru extrae-4.2.0.orig/tests/functional/hw-counters/check_Extrae_PAPI_TOT_INS_CYC.sh extrae-4.2.0/tests/functional/hw-counters/check_Extrae_PAPI_TOT_INS_CYC.sh
---- extrae-4.2.0.orig/tests/functional/hw-counters/check_Extrae_PAPI_TOT_INS_CYC.sh	2024-07-01 16:12:03.448963249 +0200
-+++ extrae-4.2.0/tests/functional/hw-counters/check_Extrae_PAPI_TOT_INS_CYC.sh	2024-07-02 10:29:00.084684067 +0200
+diff -Nru extrae-4.2.0.orig/tests/functional/hw-counters/check_Extrae_PAPI_TOT_INS.sh extrae-4.2.0/tests/functional/hw-counters/check_Extrae_PAPI_TOT_INS.sh
+--- extrae-4.2.0.orig/tests/functional/hw-counters/check_Extrae_PAPI_TOT_INS.sh	2024-07-01 16:12:03.455963214 +0200
++++ extrae-4.2.0/tests/functional/hw-counters/check_Extrae_PAPI_TOT_INS.sh	2024-07-02 10:28:14.723917087 +0200
 @@ -11,6 +11,20 @@
  ../../../src/merger/mpi2prv -f TRACE.mpits -o ${TRACE}.prv
  
@@ -59,20 +59,20 @@ diff -Nru extrae-4.2.0.orig/tests/functional/hw-counters/check_Extrae_PAPI_TOT_I
 +        exit 0
 +fi
 +
-+PAPI_TOT_CYC_available=`papi_avail | grep PAPI_TOT_CYC | awk '{print $3}'`
-+if [[ "$PAPI_TOT_CYC_available" == No ]]
++PAPI_TOT_INS_available=`papi_avail | grep PAPI_TOT_INS | awk '{print $3}'`
++if [[ "$PAPI_TOT_INS_available" == No ]]
 +then
-+        echo "PAPI_TOT_CYC is not available"
++        echo "PAPI_TOT_INS is not available"
 +        exit 0
 +fi
 +
 +
  CheckEntryInPCF ${TRACE}.pcf PAPI_TOT_INS
- CheckEntryInPCF ${TRACE}.pcf PAPI_TOT_CYC
  
+ rm -fr TRACE* set-0 ${TRACE}.???
 diff -Nru extrae-4.2.0.orig/tests/functional/xml/check_Extrae_xml_envvar_counters.sh extrae-4.2.0/tests/functional/xml/check_Extrae_xml_envvar_counters.sh
 --- extrae-4.2.0.orig/tests/functional/xml/check_Extrae_xml_envvar_counters.sh	2024-07-01 16:12:03.484963068 +0200
-+++ extrae-4.2.0/tests/functional/xml/check_Extrae_xml_envvar_counters.sh	2024-07-02 10:19:24.415644506 +0200
++++ extrae-4.2.0/tests/functional/xml/check_Extrae_xml_envvar_counters.sh	2024-07-02 14:21:10.670280550 +0200
 @@ -11,6 +11,20 @@
  ../../../src/merger/mpi2prv -f TRACE.mpits -o ${TRACE}.prv
  
@@ -83,10 +83,10 @@ diff -Nru extrae-4.2.0.orig/tests/functional/xml/check_Extrae_xml_envvar_counter
 +        exit 0
 +fi
 +
-+PAPI_TOT_CYC_available=`papi_avail | grep PAPI_TOT_CYC | awk '{print $3}'`
-+if [[ "$PAPI_TOT_CYC_available" == No ]]
++PAPI_TOT_INS_available=`papi_avail | grep PAPI_TOT_INS | awk '{print $3}'`
++if [[ "$PAPI_TOT_INS_available" == No ]]
 +then
-+        echo "PAPI_TOT_CYC is not available"
++        echo "PAPI_TOT_INS is not available"
 +        exit 0
 +fi
 +

From 729efc02406d6f0fd6d8e5e70c470b2472cfb3fc Mon Sep 17 00:00:00 2001
From: julianmorillo <julianmorillo@users.noreply.github.com>
Date: Tue, 2 Jul 2024 14:41:17 +0200
Subject: [PATCH 387/835] Update
 easybuild/easyconfigs/e/Extrae/Extrae-4.2.0-gompi-2023b.eb
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Bob Dröge <b.e.droge@rug.nl>
---
 easybuild/easyconfigs/e/Extrae/Extrae-4.2.0-gompi-2023b.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/e/Extrae/Extrae-4.2.0-gompi-2023b.eb b/easybuild/easyconfigs/e/Extrae/Extrae-4.2.0-gompi-2023b.eb
index f1583c7a584..d2eda77f24d 100644
--- a/easybuild/easyconfigs/e/Extrae/Extrae-4.2.0-gompi-2023b.eb
+++ b/easybuild/easyconfigs/e/Extrae/Extrae-4.2.0-gompi-2023b.eb
@@ -23,7 +23,7 @@ checksums = [
     # extrae-4.2.0-src.tar.bz2
     '7b83a1ed008440bbc1bda88297d2d0e9256780db1cf8401b3c12718451f8919a',
     '1c7bf9d97405c5c2f9dba3604faf141c1563c70958e942822aab521eb7ea0c9e',  # Extrae-4.2.0-detect_binutils.patch
-    '378241e39203e531c72980a9e2fda9ea15f693202a83791d40af36757824df79',  # Extrae-4.2.0-fix-hw-counters-checks.patch
+    'e5f5b86a3810617dbaaff03a2246d8ce53f3080197e35cd08b7b013cf82f3aa0',  # Extrae-4.2.0-fix-hw-counters-checks.patch
 ]
 
 builddependencies = [

From d440f91f577f20184ededdd5878c4490a3048682 Mon Sep 17 00:00:00 2001
From: WilleBell <cintiawillemyns@gmail.com>
Date: Tue, 2 Jul 2024 16:59:30 +0200
Subject: [PATCH 388/835] adding easyconfigs: PyBEL-0.15.5-gfbf-2023a.eb

---
 .../p/PyBEL/PyBEL-0.15.5-gfbf-2023a.eb        | 74 +++++++++++++++++++
 1 file changed, 74 insertions(+)
 create mode 100644 easybuild/easyconfigs/p/PyBEL/PyBEL-0.15.5-gfbf-2023a.eb

diff --git a/easybuild/easyconfigs/p/PyBEL/PyBEL-0.15.5-gfbf-2023a.eb b/easybuild/easyconfigs/p/PyBEL/PyBEL-0.15.5-gfbf-2023a.eb
new file mode 100644
index 00000000000..2c748e67b7b
--- /dev/null
+++ b/easybuild/easyconfigs/p/PyBEL/PyBEL-0.15.5-gfbf-2023a.eb
@@ -0,0 +1,74 @@
+easyblock = 'PythonBundle'
+
+name = 'PyBEL'
+version = '0.15.5'
+
+homepage = 'https://github.com/pybel/pybel'
+description = """
+PyBEL is a pure Python software package that parses BEL (Biological Expression Language)
+documents, validates their semantics, and facilitates data interchange between common formats
+and database systems like JSON, CSV, Excel, SQL, CX, and Neo4J.
+"""
+
+toolchain = {'name': 'gfbf', 'version': '2023a'}
+
+builddependencies = [
+    ('hatchling', '1.18.0'),
+]
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('Python-bundle-PyPI', '2023.06'),
+    ('networkx', '3.1'),
+    ('SQLAlchemy', '2.0.25'),
+    ('tqdm', '4.66.1'),
+    ('pydantic', '2.5.3'),  # for bioregistry
+]
+
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    ('multisplitby', '0.0.1', {
+        'checksums': ['e40489fa174fd7afd28a895477e6eefc64d6cfd863cca6900530e436a40e356f'],
+    }),
+    ('bel_resources', '0.0.3', {
+        'checksums': ['ec2d6390f89c0a98d67868bf02f7538709df0ba5b5ba6ddeb105512da07e82b5'],
+    }),
+    ('PyTrie', '0.4.0', {
+        'checksums': ['8f4488f402d3465993fb6b6efa09866849ed8cda7903b50647b7d0342b805379'],
+    }),
+    ('curies', '0.7.9', {
+        'checksums': ['3b63c5fea7b0e967629a3a384b1a8c59b56c503487c1dcbacddeab59e25db4d8'],
+    }),
+    ('more_click', '0.1.2', {
+        'checksums': ['085da66d5a9b823c5d912a888dca1fa0c8b3a14ed1b21ea9c8a1b814857a3981'],
+    }),
+    ('bioregistry', '0.11.10', {
+        'checksums': ['d3e155ba38d88f5e4a84a2d337c33109f3434f6b2e64a285eba14817ed5c4492'],
+    }),
+    ('click-plugins', '1.1.1', {
+        'checksums': ['46ab999744a9d831159c3411bb0c79346d94a444df9a3a3742e9ed63645f264b'],
+    }),
+    ('humanize', '4.8.0', {
+        'checksums': ['9783373bf1eec713a770ecaa7c2d7a7902c98398009dfa3d8a2df91eec9311e8'],
+    }),
+    ('psycopg2-binary', '2.9.9', {
+        'modulename': 'psycopg2',
+        'checksums': ['7f01846810177d829c7692f1f5ada8096762d9172af1b1a28d4ab5b77c923c1c'],
+    }),
+    ('pystow', '0.5.4', {
+        'checksums': ['2692180cb405bd77259bee6c7f4db545d10e81939980064730609f21750567ff'],
+    }),
+    ('ratelimit', '2.2.1', {
+        'checksums': ['af8a9b64b821529aca09ebaf6d8d279100d766f19e90b5059ac6a718ca6dee42'],
+    }),
+    ('requests_file', '2.1.0', {
+        'checksums': ['0f549a3f3b0699415ac04d167e9cb39bccfb730cb832b4d20be3d9867356e658'],
+    }),
+    ('pybel', version, {
+        'checksums': ['c2aabd0ad65b9f205f9ed6eae126d19875c1312f8e35641f4f42bcc1fc573f9e'],
+    }),
+]
+
+moduleclass = 'bio'

From 976427027c36eda4ba684f0ceb8aac1bbee95ace Mon Sep 17 00:00:00 2001
From: Julian Morillo <julian.morillo@bsc.es>
Date: Tue, 2 Jul 2024 18:05:14 +0200
Subject: [PATCH 389/835] Small hack to debug PAPI_add_event call

---
 .../e/Extrae/Extrae-4.2.0-debug_add_event.patch      | 12 ++++++++++++
 .../easyconfigs/e/Extrae/Extrae-4.2.0-gompi-2023b.eb |  3 ++-
 2 files changed, 14 insertions(+), 1 deletion(-)
 create mode 100644 easybuild/easyconfigs/e/Extrae/Extrae-4.2.0-debug_add_event.patch

diff --git a/easybuild/easyconfigs/e/Extrae/Extrae-4.2.0-debug_add_event.patch b/easybuild/easyconfigs/e/Extrae/Extrae-4.2.0-debug_add_event.patch
new file mode 100644
index 00000000000..bd5c925f69f
--- /dev/null
+++ b/easybuild/easyconfigs/e/Extrae/Extrae-4.2.0-debug_add_event.patch
@@ -0,0 +1,12 @@
+diff -Nru extrae-4.2.0.orig/src/tracer/hwc/papi_hwc.c extrae-4.2.0/src/tracer/hwc/papi_hwc.c
+--- extrae-4.2.0.orig/src/tracer/hwc/papi_hwc.c	2024-07-01 16:12:04.562957639 +0200
++++ extrae-4.2.0/src/tracer/hwc/papi_hwc.c	2024-07-02 17:21:19.783586061 +0200
+@@ -615,7 +615,7 @@
+ 						char EventName[PAPI_MAX_STR_LEN];
+ 
+ 						PAPI_event_code_to_name (HWC_sets[i].counters[j], EventName);
+-						fprintf (stderr, PACKAGE_NAME": Error! Hardware counter %s (0x%08x) cannot be added in set %d (task %d, thread %d)\n", EventName, HWC_sets[i].counters[j], i+1, TASKID, threadid);
++						fprintf (stderr, PACKAGE_NAME": Error! Hardware counter %s (0x%08x) cannot be added in set %d (task %d, thread %d) because of %d\n", EventName, HWC_sets[i].counters[j], i+1, TASKID, threadid, rc);
+ 						HWC_sets[i].counters[j] = NO_COUNTER;
+ 						/* break; */
+ 					}
diff --git a/easybuild/easyconfigs/e/Extrae/Extrae-4.2.0-gompi-2023b.eb b/easybuild/easyconfigs/e/Extrae/Extrae-4.2.0-gompi-2023b.eb
index f1583c7a584..21e37f50850 100644
--- a/easybuild/easyconfigs/e/Extrae/Extrae-4.2.0-gompi-2023b.eb
+++ b/easybuild/easyconfigs/e/Extrae/Extrae-4.2.0-gompi-2023b.eb
@@ -23,7 +23,8 @@ checksums = [
     # extrae-4.2.0-src.tar.bz2
     '7b83a1ed008440bbc1bda88297d2d0e9256780db1cf8401b3c12718451f8919a',
     '1c7bf9d97405c5c2f9dba3604faf141c1563c70958e942822aab521eb7ea0c9e',  # Extrae-4.2.0-detect_binutils.patch
-    '378241e39203e531c72980a9e2fda9ea15f693202a83791d40af36757824df79',  # Extrae-4.2.0-fix-hw-counters-checks.patch
+    'e5f5b86a3810617dbaaff03a2246d8ce53f3080197e35cd08b7b013cf82f3aa0',  # Extrae-4.2.0-fix-hw-counters-checks.patch
+    '9c3541b16f1acf6ff56ab44a24d44c2ec91f9415be217c39f9c0a32e2093ccca',  # Extrae-4.2.0-debug_add_event.patch
 ]
 
 builddependencies = [

From e66c9f022e7fd47806c0f2f53e3dadd90b176dd5 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Tue, 2 Jul 2024 20:58:14 +0200
Subject: [PATCH 390/835] apply debug patch

---
 easybuild/easyconfigs/e/Extrae/Extrae-4.2.0-gompi-2023b.eb | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easybuild/easyconfigs/e/Extrae/Extrae-4.2.0-gompi-2023b.eb b/easybuild/easyconfigs/e/Extrae/Extrae-4.2.0-gompi-2023b.eb
index 21e37f50850..21e71d2f367 100644
--- a/easybuild/easyconfigs/e/Extrae/Extrae-4.2.0-gompi-2023b.eb
+++ b/easybuild/easyconfigs/e/Extrae/Extrae-4.2.0-gompi-2023b.eb
@@ -17,6 +17,7 @@ sources = ['%(namelower)s-%(version)s-src.tar.bz2']
 patches = [
     'Extrae-4.2.0-detect_binutils.patch',
     'Extrae-4.2.0-fix-hw-counters-checks.patch',
+    'Extrae-4.2.0-debug_add_event.patch',
 ]
 
 checksums = [

From 891eaeab611f9e80a41e88771d7a912ab548800d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Tue, 2 Jul 2024 21:16:55 +0200
Subject: [PATCH 391/835] adding easyconfigs: MultiQC-1.22.3-foss-2023b.eb,
 pydantic-2.7.4-GCCcore-13.2.0.eb

---
 .../m/MultiQC/MultiQC-1.22.3-foss-2023b.eb    |  80 +++++++++++
 .../pydantic/pydantic-2.7.4-GCCcore-13.2.0.eb | 126 ++++++++++++++++++
 2 files changed, 206 insertions(+)
 create mode 100644 easybuild/easyconfigs/m/MultiQC/MultiQC-1.22.3-foss-2023b.eb
 create mode 100644 easybuild/easyconfigs/p/pydantic/pydantic-2.7.4-GCCcore-13.2.0.eb

diff --git a/easybuild/easyconfigs/m/MultiQC/MultiQC-1.22.3-foss-2023b.eb b/easybuild/easyconfigs/m/MultiQC/MultiQC-1.22.3-foss-2023b.eb
new file mode 100644
index 00000000000..ef34f8747cf
--- /dev/null
+++ b/easybuild/easyconfigs/m/MultiQC/MultiQC-1.22.3-foss-2023b.eb
@@ -0,0 +1,80 @@
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+# Adam Huffman
+# The Francis Crick Institute
+# Elements derived from work by Pablo Escobar
+# sciCORE - University of Basel
+# SIB Swiss Institute of Bioinformatics 
+
+# Note that Click in Python 3 requires that you change your locale to unicode before invoking your Python script.
+# See: https://click.palletsprojects.com/en/7.x/python3/
+
+easyblock = 'PythonBundle'
+
+name = 'MultiQC'
+version = '1.22.3'
+
+homepage = 'https://multiqc.info'
+description = """Aggregate results from bioinformatics analyses across many samples into a single report.
+
+ MultiQC searches a given directory for analysis logs and compiles an HTML report. It's a general
+ use tool, perfect for summarising the output from numerous bioinformatics tools."""
+
+toolchain = {'name': 'foss', 'version': '2023b'}
+
+builddependencies = [('hatchling', '1.18.0')]
+
+dependencies = [
+    ('Python', '3.11.5'),
+    ('Python-bundle-PyPI', '2023.10'),
+    ('Kaleido', '0.2.1'),
+    ('matplotlib', '3.8.2'),
+    ('plotly.py', '5.18.0'),
+    ('pydantic', '2.7.4'),
+    ('tqdm', '4.66.2'),
+    ('Pillow', '10.2.0'),
+    ('PyYAML', '6.0.1'),
+    ('networkx', '3.2.1'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('colormath', '3.0.0', {
+        'checksums': ['3d4605af344527da0e4f9f504fad7ddbebda35322c566a6c72e28edb1ff31217'],
+    }),
+    ('humanfriendly', '10.0', {
+        'checksums': ['6b0b831ce8f15f7300721aa49829fc4e83921a9a301cc7f606be6686a2288ddc'],
+    }),
+    ('Markdown', '3.6', {
+        'checksums': ['ed4f41f6daecbeeb96e576ce414c41d2d876daa9a16cb35fa8ed8c2ddfad0224'],
+    }),
+    ('coloredlogs', '15.0.1', {
+        'checksums': ['7c991aa71a4577af2f82600d8f8f3a89f936baeaf9b50a9c197da014e5bf16b0'],
+    }),
+    ('humanize', '4.9.0', {
+        'checksums': ['582a265c931c683a7e9b8ed9559089dea7edcf6cc95be39a3cbc2c5d5ac2bcfa'],
+    }),
+    ('pyaml_env', '1.2.1', {
+        'checksums': ['6d5dc98c8c82df743a132c196e79963050c9feb05b0a6f25f3ad77771d3d95b0'],
+    }),
+    ('spectra', '0.0.11', {
+        'checksums': ['8eb362a5187cb63cee13cd01186799c0c791a3ad3bec57b279132e12521762b8'],
+    }),
+    ('typeguard', '4.3.0', {
+        'checksums': ['92ee6a0aec9135181eae6067ebd617fd9de8d75d714fb548728a4933b1dea651'],
+    }),
+    ('multiqc', version, {
+        'checksums': ['5f2cc3c417b5ed4ad57bdff02d93bb7f4c6e6677768ddad1cde7b9b1e04b5854'],
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['bin/multiqc'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = ["multiqc --help"]
+
+sanity_pip_check = True
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/p/pydantic/pydantic-2.7.4-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/pydantic/pydantic-2.7.4-GCCcore-13.2.0.eb
new file mode 100644
index 00000000000..efc3388a073
--- /dev/null
+++ b/easybuild/easyconfigs/p/pydantic/pydantic-2.7.4-GCCcore-13.2.0.eb
@@ -0,0 +1,126 @@
+easyblock = 'CargoPythonBundle'
+
+name = 'pydantic'
+version = '2.7.4'
+
+homepage = 'https://github.com/samuelcolvin/pydantic'
+description = """Data validation and settings management using Python type hinting."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
+
+builddependencies = [
+    ('binutils', '2.40'),
+    ('Rust', '1.76.0'),
+    ('maturin', '1.5.0', '-Rust-1.76.0'),
+    ('hatchling', '1.18.0'),
+]
+
+dependencies = [
+    ('Python', '3.11.5'),
+    ('typing-extensions', '4.10.0'),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+crates = [
+    ('ahash', '0.8.10'),
+    ('aho-corasick', '1.0.2'),
+    ('autocfg', '1.1.0'),
+    ('base64', '0.21.7'),
+    ('bitflags', '1.3.2'),
+    ('bitvec', '1.0.1'),
+    ('cc', '1.0.79'),
+    ('cfg-if', '1.0.0'),
+    ('enum_dispatch', '0.3.13'),
+    ('equivalent', '1.0.1'),
+    ('form_urlencoded', '1.2.1'),
+    ('funty', '2.0.0'),
+    ('getrandom', '0.2.10'),
+    ('hashbrown', '0.14.3'),
+    ('heck', '0.4.1'),
+    ('idna', '0.5.0'),
+    ('indexmap', '2.2.2'),
+    ('indoc', '2.0.4'),
+    ('itoa', '1.0.8'),
+    ('jiter', '0.4.1'),
+    ('lexical-parse-float', '0.8.5'),
+    ('lexical-parse-integer', '0.8.6'),
+    ('lexical-util', '0.8.5'),
+    ('libc', '0.2.147'),
+    ('lock_api', '0.4.10'),
+    ('memchr', '2.6.3'),
+    ('memoffset', '0.9.0'),
+    ('num-bigint', '0.4.4'),
+    ('num-integer', '0.1.45'),
+    ('num-traits', '0.2.16'),
+    ('once_cell', '1.18.0'),
+    ('parking_lot', '0.12.1'),
+    ('parking_lot_core', '0.9.8'),
+    ('percent-encoding', '2.3.1'),
+    ('portable-atomic', '1.6.0'),
+    ('proc-macro2', '1.0.76'),
+    ('pyo3', '0.21.2'),
+    ('pyo3-build-config', '0.21.2'),
+    ('pyo3-ffi', '0.21.2'),
+    ('pyo3-macros', '0.21.2'),
+    ('pyo3-macros-backend', '0.21.2'),
+    ('python3-dll-a', '0.2.9'),
+    ('quote', '1.0.35'),
+    ('radium', '0.7.0'),
+    ('redox_syscall', '0.3.5'),
+    ('regex', '1.10.4'),
+    ('regex-automata', '0.4.5'),
+    ('regex-syntax', '0.8.2'),
+    ('rustversion', '1.0.13'),
+    ('ryu', '1.0.14'),
+    ('scopeguard', '1.1.0'),
+    ('serde', '1.0.203'),
+    ('serde_derive', '1.0.203'),
+    ('serde_json', '1.0.116'),
+    ('smallvec', '1.13.2'),
+    ('speedate', '0.14.0'),
+    ('static_assertions', '1.1.0'),
+    ('strum', '0.25.0'),
+    ('strum_macros', '0.25.3'),
+    ('strum_macros', '0.26.1'),
+    ('syn', '2.0.48'),
+    ('tap', '1.0.1'),
+    ('target-lexicon', '0.12.9'),
+    ('tinyvec', '1.6.0'),
+    ('tinyvec_macros', '0.1.1'),
+    ('unicode-bidi', '0.3.13'),
+    ('unicode-ident', '1.0.10'),
+    ('unicode-normalization', '0.1.22'),
+    ('unindent', '0.2.3'),
+    ('url', '2.5.0'),
+    ('uuid', '1.8.0'),
+    ('version_check', '0.9.4'),
+    ('wasi', '0.11.0+wasi-snapshot-preview1'),
+    ('windows-targets', '0.48.1'),
+    ('windows_aarch64_gnullvm', '0.48.0'),
+    ('windows_aarch64_msvc', '0.48.0'),
+    ('windows_i686_gnu', '0.48.0'),
+    ('windows_i686_msvc', '0.48.0'),
+    ('windows_x86_64_gnu', '0.48.0'),
+    ('windows_x86_64_gnullvm', '0.48.0'),
+    ('windows_x86_64_msvc', '0.48.0'),
+    ('wyz', '0.5.1'),
+    ('zerocopy', '0.7.32'),
+    ('zerocopy-derive', '0.7.32'),
+]
+
+exts_list = [
+    ('annotated_types', '0.6.0', {
+        'checksums': ['563339e807e53ffd9c267e99fc6d9ea23eb8443c08f112651963e24e22f84a5d'],
+    }),
+    ('pydantic_core', '2.18.4', {
+        'checksums': ['ec3beeada09ff865c344ff3bc2f427f5e6c26401cc6113d77e372c3fdac73864'],
+    }),
+    (name, version, {
+        'preinstallopts': "sed -i '/Framework :: Pydantic/d' pyproject.toml && ",
+        'checksums': ['0c84efd9548d545f63ac0060c1e4d39bb9b14db8b3c0652338aecc07b5adec52'],
+    }),
+]
+
+moduleclass = 'devel'

From 69b600af0f600a108eb630122104c6a6a1807f8c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Tue, 2 Jul 2024 21:42:33 +0200
Subject: [PATCH 392/835] add exception in CI for pydantic version

---
 test/easyconfigs/easyconfigs.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py
index ceae4c5bef9..ef04fe6d646 100644
--- a/test/easyconfigs/easyconfigs.py
+++ b/test/easyconfigs/easyconfigs.py
@@ -614,6 +614,7 @@ def check_dep_vars(self, gen, dep, dep_vars):
             'pydantic': [
                 # GTDB-Tk v2.3.2 requires pydantic 1.x (see https://github.com/Ecogenomics/GTDBTk/pull/530)
                 ('1.10.13;', ['GTDB-Tk-2.3.2-', 'GTDB-Tk-2.4.0-']),
+                ('2.7.4;', ['MultiQC-1.22.3-']),
             ],
             # medaka 1.1.*, 1.2.*, 1.4.* requires Pysam 0.16.0.1,
             # which is newer than what others use as dependency w.r.t. Pysam version in 2019b generation;

From e650d171f888bfb7bc5556f9afce6846d5d08ea7 Mon Sep 17 00:00:00 2001
From: Yunqi Shao <yunqi.shao@chalmers.se>
Date: Tue, 2 Jul 2024 23:00:11 +0200
Subject: [PATCH 393/835] Add pkgconf to builddependencies

---
 .../t/TensorFlow/TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb     | 1 +
 .../easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a.eb     | 1 +
 2 files changed, 2 insertions(+)

diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb
index 1d1c871f3d5..60b44928e03 100644
--- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb
+++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb
@@ -14,6 +14,7 @@ use_pip = True
 sanity_pip_check = True
 
 builddependencies = [
+    ('pkgconf', '1.9.5'),
     ('Bazel', '6.1.0'),
     # git 2.x required, see also https://github.com/tensorflow/tensorflow/issues/29053
     ('git', '2.41.0', '-nodocs'),
diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a.eb
index 506cbafd52b..57b010cb652 100644
--- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a.eb
+++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a.eb
@@ -13,6 +13,7 @@ use_pip = True
 sanity_pip_check = True
 
 builddependencies = [
+    ('pkgconf', '1.9.5'),
     ('Bazel', '6.1.0'),
     # git 2.x required, see also https://github.com/tensorflow/tensorflow/issues/29053
     ('git', '2.41.0', '-nodocs'),

From 185f88b9a03d65a7fb74edc7acb4221e87e90784 Mon Sep 17 00:00:00 2001
From: Richard Top <richard.topouchian@uib.no>
Date: Wed, 3 Jul 2024 08:52:16 +0000
Subject: [PATCH 394/835] {bio}[gompi/2023a] IQ-TREE v2.3.5

---
 .../i/IQ-TREE/IQ-TREE-2.3.5-gompi-2023a.eb    | 55 +++++++++++++++++++
 .../i/IQ-TREE/IQ-TREE-2.3.5_use_EB_LSD2.patch | 36 ++++++++++++
 2 files changed, 91 insertions(+)
 create mode 100644 easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.3.5-gompi-2023a.eb
 create mode 100644 easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.3.5_use_EB_LSD2.patch

diff --git a/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.3.5-gompi-2023a.eb b/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.3.5-gompi-2023a.eb
new file mode 100644
index 00000000000..ca4c707da69
--- /dev/null
+++ b/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.3.5-gompi-2023a.eb
@@ -0,0 +1,55 @@
+# Updated to v2.1.3 by
+# R.QIAO <rob.qiao@flinders.edu.au>
+# DeepThought, Flinders University
+
+easyblock = 'CMakeMake'
+
+name = 'IQ-TREE'
+version = '2.3.5'
+
+# HTTPS is not working
+homepage = 'http://www.iqtree.org/'
+description = """Efficient phylogenomic software by maximum likelihood"""
+
+toolchain = {'name': 'gompi', 'version': '2023a'}
+# Including 'usempi' will take precedence and override IQTREE_FLAGS and produces only 'iqtree-mpi' binary
+
+source_urls = ['https://github.com/iqtree/iqtree2/archive/refs/tags/']
+sources = ['v%(version)s.tar.gz']
+patches = [
+    'IQ-TREE-2.3.5_use_EB_LSD2.patch',
+]
+checksums = [
+    {'v2.3.5.tar.gz': '8e323e0b7c46e97901d3500f11e810703e0e5d25848188047eca9602d03fa6b1'},
+    {'IQ-TREE-2.3.5_use_EB_LSD2.patch': 'b4578b01f06ae52b94b332622c0f6630497cd29cb61010f58f7c5018c2c32a5f'},
+]
+
+builddependencies = [
+    ('CMake', '3.26.3'),
+    ('Eigen', '3.4.0'),
+]
+dependencies = [
+    ('zlib', '1.2.13'),
+    ('Boost', '1.82.0'),
+    ('LSD2', '2.4.1'),
+]
+
+local_conf_opts = ' -DUSE_LSD2=ON '
+configopts = [
+    '-DIQTREE_FLAGS=omp' + local_conf_opts,
+    '-DIQTREE_FLAGS=mpi -DCMAKE_C_COMPILER="$MPICC" -DCMAKE_CXX_COMPILER="$MPICXX"' + local_conf_opts,
+]
+
+sanity_check_paths = {
+    'files': ['bin/iqtree2', 'bin/iqtree2-mpi'],
+    'dirs': [],
+}
+
+sanity_check_commands = [
+    "iqtree2 --help",
+    "mkdir -p $TMPDIR/{test-omp,test-mpi}",
+    "cd $TMPDIR/test-omp && cp -a %(installdir)s/example.phy . && iqtree2 -s example.phy -redo",
+    "cd $TMPDIR/test-mpi && cp -a %(installdir)s/example.phy . && mpirun -np 1 iqtree2-mpi -s example.phy -redo",
+]
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.3.5_use_EB_LSD2.patch b/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.3.5_use_EB_LSD2.patch
new file mode 100644
index 00000000000..b567f096fa9
--- /dev/null
+++ b/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.3.5_use_EB_LSD2.patch
@@ -0,0 +1,36 @@
+diff -ruN iqtree2-2.3.5/CMakeLists.txt iqtree2-2.3.5-orig/CMakeLists.txt
+--- iqtree2-2.3.5/CMakeLists.txt	2024-06-26 04:33:33.000000000 +0000
++++ iqtree2-2.3.5-orig/CMakeLists.txt	2024-07-03 08:23:41.030462539 +0000
+@@ -758,10 +758,6 @@
+    add_subdirectory(terracetphast)
+ endif()
+ 
+-if (USE_LSD2)
+-    add_subdirectory(lsd2)
+-endif()
+-
+ add_library(kernelsse tree/phylokernelsse.cpp)
+ 
+ if (NOT BINARY32 AND NOT IQTREE_FLAGS MATCHES "novx")
+@@ -820,9 +816,6 @@
+         if (USE_TERRAPHAST)
+             set_target_properties(terracetphast terraphast PROPERTIES COMPILE_FLAGS "${SSE_FLAGS}")
+         endif()
+-        if (USE_LSD2)
+-            set_target_properties(lsd2 PROPERTIES COMPILE_FLAGS "${SSE_FLAGS}")
+-        endif()
+         if (USE_BOOSTER)
+             set_target_properties(booster PROPERTIES COMPILE_FLAGS "${SSE_FLAGS}")
+         endif()
+diff -ruN iqtree2-2.3.5/main/timetree.cpp iqtree2-2.3.5-orig/main/timetree.cpp
+--- iqtree2-2.3.5/main/timetree.cpp	2024-06-26 04:33:33.000000000 +0000
++++ iqtree2-2.3.5-orig/main/timetree.cpp	2024-07-03 08:24:32.438606710 +0000
+@@ -8,7 +8,7 @@
+ #include "timetree.h"
+ 
+ #ifdef USE_LSD2
+-#include "lsd2/src/lsd.h"
++#include "lsd.h"
+ #endif
+ 
+ /** map from taxon name to date */

From 79abc87410ab0baa0a7284efa908a056a6f042bd Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 3 Jul 2024 12:02:48 +0200
Subject: [PATCH 395/835] copy missing rsem_perl_utils.pm in DETONATE, since
 it's required by rsem-eval-calculate-score command

---
 .../easyconfigs/d/DETONATE/DETONATE-1.11-GCC-12.3.0.eb | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/easybuild/easyconfigs/d/DETONATE/DETONATE-1.11-GCC-12.3.0.eb b/easybuild/easyconfigs/d/DETONATE/DETONATE-1.11-GCC-12.3.0.eb
index c1457cc041c..63246fc43ac 100644
--- a/easybuild/easyconfigs/d/DETONATE/DETONATE-1.11-GCC-12.3.0.eb
+++ b/easybuild/easyconfigs/d/DETONATE/DETONATE-1.11-GCC-12.3.0.eb
@@ -45,16 +45,20 @@ buildopts = 'CXX="$CXX" CXXFLAGS="$CXXFLAGS -fopenmp" && cd ../rsem-eval && make
 
 runtest = 'test'
 
-files_to_copy = [(['ref-eval', 'ref-eval-estimate-true-assembly', '../rsem-eval/rsem-*'], 'bin')]
+files_to_copy = [
+    (['ref-eval', 'ref-eval-estimate-true-assembly', '../rsem-eval/rsem-*', '../rsem-eval/*.pm'], 'bin'),
+]
 
 sanity_check_paths = {
     'files': ['bin/%s' % x for x in ['ref-eval', 'ref-eval-estimate-true-assembly', 'rsem-build-read-index',
                                      'rsem-eval-calculate-score', 'rsem-eval-estimate-transcript-length-distribution',
                                      'rsem-eval-run-em', 'rsem-extract-reference-transcripts',
-                                     'rsem-parse-alignments', 'rsem-plot-model', 'rsem-preref', 'rsem-sam-validator',
-                                     'rsem-scan-for-paired-end-reads', 'rsem-simulate-reads',
+                                     'rsem-parse-alignments', 'rsem_perl_utils.pm', 'rsem-plot-model', 'rsem-preref',
+                                     'rsem-sam-validator', 'rsem-scan-for-paired-end-reads', 'rsem-simulate-reads',
                                      'rsem-synthesis-reference-transcripts']],
     'dirs': [],
 }
 
+sanity_check_commands = [r"rsem-eval-calculate-score --help 2>&1 | grep 'rsem-eval-calculate-score \[options\]'"]
+
 moduleclass = 'bio'

From 5557f5d43b3ac6799314a34970321f1f6f3a7ca9 Mon Sep 17 00:00:00 2001
From: James Carpenter <j.j.carpenter@bham.ac.uk>
Date: Wed, 3 Jul 2024 12:47:04 +0100
Subject: [PATCH 396/835] Set `SATSUMA2_PATH` so Satsuma2 can locate
 executables

---
 .../easyconfigs/s/Satsuma2/Satsuma2-20220304-GCC-11.3.0.eb  | 6 ++++++
 1 file changed, 6 insertions(+)
 mode change 100644 => 100755 easybuild/easyconfigs/s/Satsuma2/Satsuma2-20220304-GCC-11.3.0.eb

diff --git a/easybuild/easyconfigs/s/Satsuma2/Satsuma2-20220304-GCC-11.3.0.eb b/easybuild/easyconfigs/s/Satsuma2/Satsuma2-20220304-GCC-11.3.0.eb
old mode 100644
new mode 100755
index e709378f6ea..304dbf50669
--- a/easybuild/easyconfigs/s/Satsuma2/Satsuma2-20220304-GCC-11.3.0.eb
+++ b/easybuild/easyconfigs/s/Satsuma2/Satsuma2-20220304-GCC-11.3.0.eb
@@ -21,6 +21,12 @@ checksums = [
 
 builddependencies = [('CMake', '3.23.1')]
 
+# Define SATSUMA2_PATH as per:
+# https://github.com/bioinfologics/satsuma2/blob/37c5f386819614cd3ce96016b423ddc4df1d86ec/README.md#running-satsuma2
+modextravars = {
+    'SATSUMA2_PATH': '%(installdir)s/bin',
+}
+
 sanity_check_paths = {
     'files': ['bin/ChromosomePaint', 'bin/MatchDump', 'bin/SatsumaSynteny2'],
     'dirs': [],

From f5653db066a10d36cb7abf524b2400e360285d52 Mon Sep 17 00:00:00 2001
From: James Carpenter <j.j.carpenter@bham.ac.uk>
Date: Wed, 3 Jul 2024 13:04:56 +0100
Subject: [PATCH 397/835] Fix file permissions

---
 easybuild/easyconfigs/s/Satsuma2/Satsuma2-20220304-GCC-11.3.0.eb | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 mode change 100755 => 100644 easybuild/easyconfigs/s/Satsuma2/Satsuma2-20220304-GCC-11.3.0.eb

diff --git a/easybuild/easyconfigs/s/Satsuma2/Satsuma2-20220304-GCC-11.3.0.eb b/easybuild/easyconfigs/s/Satsuma2/Satsuma2-20220304-GCC-11.3.0.eb
old mode 100755
new mode 100644

From dbadb2074464d816740ee0e95595c2cb31b6338f Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 3 Jul 2024 15:35:51 +0200
Subject: [PATCH 398/835] disable auto-vectorizer (-ftree-vectorize) for
 OpenFOAM v10 + v11 when using toolchain that with GCC >= 11

---
 .../o/OpenFOAM/OpenFOAM-10-foss-2022a-20230119-int64.eb         | 2 +-
 .../easyconfigs/o/OpenFOAM/OpenFOAM-10-foss-2022a-20230119.eb   | 1 +
 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-10-foss-2022a.eb      | 1 +
 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-10-foss-2023a.eb      | 1 +
 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-11-foss-2022a.eb      | 1 +
 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-11-foss-2023a.eb      | 1 +
 6 files changed, 6 insertions(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-10-foss-2022a-20230119-int64.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-10-foss-2022a-20230119-int64.eb
index cfba31ab4f7..5c5f4d70f9f 100644
--- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-10-foss-2022a-20230119-int64.eb
+++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-10-foss-2022a-20230119-int64.eb
@@ -11,7 +11,7 @@ description = """OpenFOAM is a free, open source CFD software package.
  to solid dynamics and electromagnetics."""
 
 toolchain = {'name': 'foss', 'version': '2022a'}
-toolchainopts = {'i8': True}
+toolchainopts = {'vectorize': False, 'i8': True}
 
 source_urls = ['https://github.com/OpenFOAM/OpenFOAM-%(version_major)s/archive']
 sources = [{
diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-10-foss-2022a-20230119.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-10-foss-2022a-20230119.eb
index f9ebf346635..fd18ec3e287 100644
--- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-10-foss-2022a-20230119.eb
+++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-10-foss-2022a-20230119.eb
@@ -11,6 +11,7 @@ description = """OpenFOAM is a free, open source CFD software package.
  to solid dynamics and electromagnetics."""
 
 toolchain = {'name': 'foss', 'version': '2022a'}
+toolchainopts = {'vectorize': False}
 
 source_urls = ['https://github.com/OpenFOAM/OpenFOAM-%(version_major)s/archive']
 sources = [{
diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-10-foss-2022a.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-10-foss-2022a.eb
index 7fafa63937c..3bdaaf4f06e 100644
--- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-10-foss-2022a.eb
+++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-10-foss-2022a.eb
@@ -8,6 +8,7 @@ description = """OpenFOAM is a free, open source CFD software package.
  to solid dynamics and electromagnetics."""
 
 toolchain = {'name': 'foss', 'version': '2022a'}
+toolchainopts = {'vectorize': False}
 
 source_urls = ['https://github.com/OpenFOAM/OpenFOAM-%(version_major)s/archive']
 sources = ['version-%(version)s.tar.gz']
diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-10-foss-2023a.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-10-foss-2023a.eb
index c4358543285..4989e318c7c 100644
--- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-10-foss-2023a.eb
+++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-10-foss-2023a.eb
@@ -8,6 +8,7 @@ description = """OpenFOAM is a free, open source CFD software package.
  to solid dynamics and electromagnetics."""
 
 toolchain = {'name': 'foss', 'version': '2023a'}
+toolchainopts = {'vectorize': False}
 
 source_urls = ['https://github.com/OpenFOAM/OpenFOAM-%(version_major)s/archive']
 sources = ['version-%(version)s.tar.gz']
diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-11-foss-2022a.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-11-foss-2022a.eb
index 9481f562349..e4abfa2f3e2 100644
--- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-11-foss-2022a.eb
+++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-11-foss-2022a.eb
@@ -8,6 +8,7 @@ description = """OpenFOAM is a free, open source CFD software package.
  to solid dynamics and electromagnetics."""
 
 toolchain = {'name': 'foss', 'version': '2022a'}
+toolchainopts = {'vectorize': False}
 
 source_urls = ['https://github.com/OpenFOAM/OpenFOAM-%(version_major)s/archive']
 sources = ['version-%(version)s.tar.gz']
diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-11-foss-2023a.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-11-foss-2023a.eb
index 1ce1045701d..c2cabe755a3 100644
--- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-11-foss-2023a.eb
+++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-11-foss-2023a.eb
@@ -8,6 +8,7 @@ description = """OpenFOAM is a free, open source CFD software package.
  to solid dynamics and electromagnetics."""
 
 toolchain = {'name': 'foss', 'version': '2023a'}
+toolchainopts = {'vectorize': False}
 
 source_urls = ['https://github.com/OpenFOAM/OpenFOAM-%(version_major)s/archive']
 sources = ['version-%(version)s.tar.gz']

From be44b2139d4f3b160bb6014c75ab323e9e884c39 Mon Sep 17 00:00:00 2001
From: Julian Morillo <julian.morillo@bsc.es>
Date: Wed, 3 Jul 2024 17:06:37 +0200
Subject: [PATCH 399/835] Detect when HW counters are not accessible

---
 .../Extrae-4.2.0-fix-hw-counters-checks.patch | 65 +++++++++++++++----
 .../e/Extrae/Extrae-4.2.0-gompi-2023b.eb      |  2 +-
 2 files changed, 54 insertions(+), 13 deletions(-)

diff --git a/easybuild/easyconfigs/e/Extrae/Extrae-4.2.0-fix-hw-counters-checks.patch b/easybuild/easyconfigs/e/Extrae/Extrae-4.2.0-fix-hw-counters-checks.patch
index 5307eed0dc5..2d588694b4c 100644
--- a/easybuild/easyconfigs/e/Extrae/Extrae-4.2.0-fix-hw-counters-checks.patch
+++ b/easybuild/easyconfigs/e/Extrae/Extrae-4.2.0-fix-hw-counters-checks.patch
@@ -1,16 +1,19 @@
 diff -Nru extrae-4.2.0.orig/tests/functional/hw-counters/check_Extrae_PAPI_TOT_CYC.sh extrae-4.2.0/tests/functional/hw-counters/check_Extrae_PAPI_TOT_CYC.sh
 --- extrae-4.2.0.orig/tests/functional/hw-counters/check_Extrae_PAPI_TOT_CYC.sh	2024-07-01 16:12:03.454963219 +0200
-+++ extrae-4.2.0/tests/functional/hw-counters/check_Extrae_PAPI_TOT_CYC.sh	2024-07-02 10:26:41.603395579 +0200
-@@ -11,6 +11,20 @@
++++ extrae-4.2.0/tests/functional/hw-counters/check_Extrae_PAPI_TOT_CYC.sh	2024-07-03 16:51:00.533542188 +0200
+@@ -10,7 +10,29 @@
+ EXTRAE_CONFIG_FILE=extrae-PAPI_TOT_CYC.xml ./check_Extrae_counters_xml
  ../../../src/merger/mpi2prv -f TRACE.mpits -o ${TRACE}.prv
  
- # Check
+-# Check
++# Check PAPI availability
 +if ! command -v papi_avail &> /dev/null
 +then
 +        echo "papi_avail could not be found"
 +        exit 0
 +fi
 +
++# Check COUNTER availability
 +PAPI_TOT_CYC_available=`papi_avail | grep PAPI_TOT_CYC | awk '{print $3}'`
 +if [[ "$PAPI_TOT_CYC_available" == No ]]
 +then
@@ -18,23 +21,33 @@ diff -Nru extrae-4.2.0.orig/tests/functional/hw-counters/check_Extrae_PAPI_TOT_C
 +        exit 0
 +fi
 +
++# Check that HW counters are accessible
++ACCESS_LEVEL=`sysctl kernel.perf_event_paranoid |awk '{print $3}'`
++if [ $ACCESS_LEVEL \> 1 ]
++then
++        echo "perf_event_paranoid configuration does not allow access to HW counters"
++        exit 0
++fi
 +
  CheckEntryInPCF ${TRACE}.pcf PAPI_TOT_CYC
  
  rm -fr TRACE* set-0 ${TRACE}.???
 diff -Nru extrae-4.2.0.orig/tests/functional/hw-counters/check_Extrae_PAPI_TOT_INS_CYC.sh extrae-4.2.0/tests/functional/hw-counters/check_Extrae_PAPI_TOT_INS_CYC.sh
 --- extrae-4.2.0.orig/tests/functional/hw-counters/check_Extrae_PAPI_TOT_INS_CYC.sh	2024-07-01 16:12:03.448963249 +0200
-+++ extrae-4.2.0/tests/functional/hw-counters/check_Extrae_PAPI_TOT_INS_CYC.sh	2024-07-02 10:29:00.084684067 +0200
-@@ -11,6 +11,20 @@
++++ extrae-4.2.0/tests/functional/hw-counters/check_Extrae_PAPI_TOT_INS_CYC.sh	2024-07-03 16:52:55.509932826 +0200
+@@ -10,7 +10,30 @@
+ EXTRAE_CONFIG_FILE=extrae-PAPI_TOT_INS_CYC.xml ./check_Extrae_counters_xml
  ../../../src/merger/mpi2prv -f TRACE.mpits -o ${TRACE}.prv
  
- # Check
+-# Check
++# Check PAPI availability
 +if ! command -v papi_avail &> /dev/null
 +then
 +        echo "papi_avail could not be found"
 +        exit 0
 +fi
 +
++# Check COUNTER availability
 +PAPI_TOT_CYC_available=`papi_avail | grep PAPI_TOT_CYC | awk '{print $3}'`
 +if [[ "$PAPI_TOT_CYC_available" == No ]]
 +then
@@ -42,23 +55,34 @@ diff -Nru extrae-4.2.0.orig/tests/functional/hw-counters/check_Extrae_PAPI_TOT_I
 +        exit 0
 +fi
 +
++# Check counters accessibility level
++ACCESS_LEVEL=`sysctl kernel.perf_event_paranoid |awk '{print $3}'`
++if [ $ACCESS_LEVEL \> 1 ]
++then
++        echo "perf_event_paranoid configuration does not allow access to HW counters"
++        exit 0
++fi
++
 +
  CheckEntryInPCF ${TRACE}.pcf PAPI_TOT_INS
  CheckEntryInPCF ${TRACE}.pcf PAPI_TOT_CYC
  
 diff -Nru extrae-4.2.0.orig/tests/functional/hw-counters/check_Extrae_PAPI_TOT_INS.sh extrae-4.2.0/tests/functional/hw-counters/check_Extrae_PAPI_TOT_INS.sh
 --- extrae-4.2.0.orig/tests/functional/hw-counters/check_Extrae_PAPI_TOT_INS.sh	2024-07-01 16:12:03.455963214 +0200
-+++ extrae-4.2.0/tests/functional/hw-counters/check_Extrae_PAPI_TOT_INS.sh	2024-07-02 10:28:14.723917087 +0200
-@@ -11,6 +11,20 @@
++++ extrae-4.2.0/tests/functional/hw-counters/check_Extrae_PAPI_TOT_INS.sh	2024-07-03 16:54:17.878497036 +0200
+@@ -10,7 +10,29 @@
+ EXTRAE_CONFIG_FILE=extrae-PAPI_TOT_INS.xml ./check_Extrae_counters_xml
  ../../../src/merger/mpi2prv -f TRACE.mpits -o ${TRACE}.prv
  
- # Check
+-# Check
++# Check PAPI availability
 +if ! command -v papi_avail &> /dev/null
 +then
 +        echo "papi_avail could not be found"
 +        exit 0
 +fi
 +
++# Check COUNTERS availability
 +PAPI_TOT_INS_available=`papi_avail | grep PAPI_TOT_INS | awk '{print $3}'`
 +if [[ "$PAPI_TOT_INS_available" == No ]]
 +then
@@ -66,23 +90,33 @@ diff -Nru extrae-4.2.0.orig/tests/functional/hw-counters/check_Extrae_PAPI_TOT_I
 +        exit 0
 +fi
 +
++# Check COUNTERS accessibility level
++ACCESS_LEVEL=`sysctl kernel.perf_event_paranoid |awk '{print $3}'`
++if [ $ACCESS_LEVEL \> 1 ]
++then
++        echo "perf_event_paranoid configuration does not allow access to HW counters"
++        exit 0
++fi
 +
  CheckEntryInPCF ${TRACE}.pcf PAPI_TOT_INS
  
  rm -fr TRACE* set-0 ${TRACE}.???
 diff -Nru extrae-4.2.0.orig/tests/functional/xml/check_Extrae_xml_envvar_counters.sh extrae-4.2.0/tests/functional/xml/check_Extrae_xml_envvar_counters.sh
 --- extrae-4.2.0.orig/tests/functional/xml/check_Extrae_xml_envvar_counters.sh	2024-07-01 16:12:03.484963068 +0200
-+++ extrae-4.2.0/tests/functional/xml/check_Extrae_xml_envvar_counters.sh	2024-07-02 14:21:10.670280550 +0200
-@@ -11,6 +11,20 @@
++++ extrae-4.2.0/tests/functional/xml/check_Extrae_xml_envvar_counters.sh	2024-07-03 16:56:41.975736132 +0200
+@@ -10,7 +10,29 @@
+ COUNTERS=PAPI_TOT_INS EXTRAE_CONFIG_FILE=extrae_envvar_counters.xml ./check_Extrae_xml
  ../../../src/merger/mpi2prv -f TRACE.mpits -o ${TRACE}.prv
  
- # Check
+-# Check
++# Check PAPI availability
 +if ! command -v papi_avail &> /dev/null
 +then
 +        echo "papi_avail could not be found"
 +        exit 0
 +fi
 +
++# Check COUNTER availability
 +PAPI_TOT_INS_available=`papi_avail | grep PAPI_TOT_INS | awk '{print $3}'`
 +if [[ "$PAPI_TOT_INS_available" == No ]]
 +then
@@ -90,6 +124,13 @@ diff -Nru extrae-4.2.0.orig/tests/functional/xml/check_Extrae_xml_envvar_counter
 +        exit 0
 +fi
 +
++# Check COUNTERS accessibility level
++ACCESS_LEVEL=`sysctl kernel.perf_event_paranoid |awk '{print $3}'`
++if [ $ACCESS_LEVEL \> 1 ]
++then
++        echo "perf_event_paranoid configuration does not allow access to HW counters"
++        exit 0
++fi
 +
  CheckEntryInPCF ${TRACE}.pcf PAPI_TOT_INS
  
diff --git a/easybuild/easyconfigs/e/Extrae/Extrae-4.2.0-gompi-2023b.eb b/easybuild/easyconfigs/e/Extrae/Extrae-4.2.0-gompi-2023b.eb
index 21e71d2f367..f5755ff433e 100644
--- a/easybuild/easyconfigs/e/Extrae/Extrae-4.2.0-gompi-2023b.eb
+++ b/easybuild/easyconfigs/e/Extrae/Extrae-4.2.0-gompi-2023b.eb
@@ -24,7 +24,7 @@ checksums = [
     # extrae-4.2.0-src.tar.bz2
     '7b83a1ed008440bbc1bda88297d2d0e9256780db1cf8401b3c12718451f8919a',
     '1c7bf9d97405c5c2f9dba3604faf141c1563c70958e942822aab521eb7ea0c9e',  # Extrae-4.2.0-detect_binutils.patch
-    'e5f5b86a3810617dbaaff03a2246d8ce53f3080197e35cd08b7b013cf82f3aa0',  # Extrae-4.2.0-fix-hw-counters-checks.patch
+    '147d897a5a9ba6ebb1b5de32c964b2cd73534f31a540125a94fd37f2ceb1edfe',  # Extrae-4.2.0-fix-hw-counters-checks.patch
     '9c3541b16f1acf6ff56ab44a24d44c2ec91f9415be217c39f9c0a32e2093ccca',  # Extrae-4.2.0-debug_add_event.patch
 ]
 

From d7fd240a4e302c6c68c9bdc76f34758d695ada0f Mon Sep 17 00:00:00 2001
From: Cintia Willemyns <115622907+WilleBell@users.noreply.github.com>
Date: Wed, 3 Jul 2024 17:26:05 +0200
Subject: [PATCH 400/835] Add sanity check command

---
 easybuild/easyconfigs/p/PyBEL/PyBEL-0.15.5-gfbf-2023a.eb | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/easybuild/easyconfigs/p/PyBEL/PyBEL-0.15.5-gfbf-2023a.eb b/easybuild/easyconfigs/p/PyBEL/PyBEL-0.15.5-gfbf-2023a.eb
index 2c748e67b7b..40c17e035ce 100644
--- a/easybuild/easyconfigs/p/PyBEL/PyBEL-0.15.5-gfbf-2023a.eb
+++ b/easybuild/easyconfigs/p/PyBEL/PyBEL-0.15.5-gfbf-2023a.eb
@@ -71,4 +71,6 @@ exts_list = [
     }),
 ]
 
+sanity_check_commands = ["pybel --help"]
+
 moduleclass = 'bio'

From 4157bb787f42743fe8e6f84e3e6cb743e2b44adc Mon Sep 17 00:00:00 2001
From: Simon Pinches <Simon.Pinches@iter.org>
Date: Wed, 3 Jul 2024 18:01:57 +0200
Subject: [PATCH 401/835] adding easyconfigs: STRUMPACK-7.1.0-foss-2023b.eb,
 STRUMPACK-7.1.0-intel-2023b.eb

---
 .../s/STRUMPACK/STRUMPACK-7.1.0-foss-2023b.eb | 46 ++++++++++++++++++
 .../STRUMPACK/STRUMPACK-7.1.0-intel-2023b.eb  | 47 +++++++++++++++++++
 2 files changed, 93 insertions(+)
 create mode 100644 easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-7.1.0-foss-2023b.eb
 create mode 100644 easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-7.1.0-intel-2023b.eb

diff --git a/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-7.1.0-foss-2023b.eb b/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-7.1.0-foss-2023b.eb
new file mode 100644
index 00000000000..dd1f8cff948
--- /dev/null
+++ b/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-7.1.0-foss-2023b.eb
@@ -0,0 +1,46 @@
+easyblock = 'CMakeMake'
+
+name = 'STRUMPACK'
+version = '7.1.0'
+
+homepage = 'https://fastmath-scidac.llnl.gov/software/strumpack.html'
+description = """STRUMPACK - STRUctured Matrix PACKage - Fast linear solvers and preconditioner
+ for both dense and sparse systems using low-rank structured factorization with randomized sampling."""
+
+toolchain = {'name': 'foss', 'version': '2023b'}
+toolchainopts = {'pic': True, 'usempi': True}
+
+source_urls = ['https://github.com/pghysels/%(name)s/archive/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['a3e80e0530ea1cc6b62c22699cfe5f02f81794321f225440f0e08bceed69c241']
+
+builddependencies = [
+    ('CMake', '3.27.6'),
+]
+
+dependencies = [
+    ('zlib', '1.2.13'),
+    ('ParMETIS', '4.0.3'),
+    ('SCOTCH', '7.0.4'),
+]
+
+configopts = '-DSTRUMPACK_USE_OPENMP=ON '
+configopts += '-DTPL_METIS_INCLUDE_DIRS=${EBROOTPARMETIS}/include '
+configopts += '-DTPL_METIS_LIBRARY_DIR=${EBROOTPARMETIS}/lib '
+configopts += '-DTPL_ENABLE_PARMETIS=ON '
+configopts += '-DTPL_PARMETIS_INCLUDE_DIRS=${EBROOTPARMETIS}/include '
+configopts += '-DTPL_PARMETIS_LIBRARY_DIR=${EBROOTPARMETIS}/lib '
+configopts += '-DTPL_ENABLE_SCOTCH=ON '
+configopts += '-DTPL_SCOTCH_INCLUDE_DIRS=${EBROOTSCOTCH}/include '
+configopts += '-DTPL_SCOTCH_LIBRARY_DIR=${EBROOTSCOTCH}/lib '
+configopts += '-DTPL_ENABLE_BPACK=OFF '
+configopts += '-DTPL_ENABLE_ZFP=OFF '
+configopts += '-DTPL_ENABLE_SLATE=OFF '
+
+sanity_check_paths = {
+    'files': ['lib/libstrumpack.a'],
+    'dirs': ['include/%s' % x for x in ['BLR', 'clustering', 'dense', 'HSS', 'kernel', 'misc', 'python', 'sparse']] +
+            ['lib'],
+}
+
+moduleclass = 'numlib'
diff --git a/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-7.1.0-intel-2023b.eb b/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-7.1.0-intel-2023b.eb
new file mode 100644
index 00000000000..b6ff89201c8
--- /dev/null
+++ b/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-7.1.0-intel-2023b.eb
@@ -0,0 +1,47 @@
+easyblock = 'CMakeMake'
+
+name = 'STRUMPACK'
+version = '7.1.0'
+
+homepage = 'https://fastmath-scidac.llnl.gov/software/strumpack.html'
+description = """STRUMPACK - STRUctured Matrix PACKage - Fast linear solvers and preconditioner
+ for both dense and sparse systems using low-rank structured factorization with randomized sampling."""
+
+toolchain = {'name': 'intel', 'version': '2023b'}
+toolchainopts = {'pic': True, 'usempi': True}
+
+source_urls = ['https://github.com/pghysels/%(name)s/archive/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['a3e80e0530ea1cc6b62c22699cfe5f02f81794321f225440f0e08bceed69c241']
+
+builddependencies = [
+    ('CMake', '3.27.6'),
+]
+
+dependencies = [
+    ('zlib', '1.2.13'),
+    ('ParMETIS', '4.0.3'),
+    ('SCOTCH', '7.0.4'),
+]
+
+configopts = '-DSTRUMPACK_USE_OPENMP=ON '
+configopts += '-DTPL_SCALAPACK_LIBRARIES="${LIBSCALAPACK_MT}" '
+configopts += '-DTPL_METIS_INCLUDE_DIRS=${EBROOTPARMETIS}/include '
+configopts += '-DTPL_METIS_LIBRARY_DIR=${EBROOTPARMETIS}/lib '
+configopts += '-DTPL_ENABLE_PARMETIS=ON '
+configopts += '-DTPL_PARMETIS_INCLUDE_DIRS=${EBROOTPARMETIS}/include '
+configopts += '-DTPL_PARMETIS_LIBRARY_DIR=${EBROOTPARMETIS}/lib '
+configopts += '-DTPL_ENABLE_SCOTCH=ON '
+configopts += '-DTPL_SCOTCH_INCLUDE_DIRS=${EBROOTSCOTCH}/include '
+configopts += '-DTPL_SCOTCH_LIBRARY_DIR=${EBROOTSCOTCH}/lib '
+configopts += '-DTPL_ENABLE_BPACK=OFF '
+configopts += '-DTPL_ENABLE_ZFP=OFF '
+configopts += '-DTPL_ENABLE_SLATE=OFF '
+
+sanity_check_paths = {
+    'files': ['lib/libstrumpack.a'],
+    'dirs': ['include/%s' % x for x in ['BLR', 'clustering', 'dense', 'HSS', 'kernel', 'misc', 'python', 'sparse']] +
+            ['lib'],
+}
+
+moduleclass = 'numlib'

From 1e66580a610f4b795642c58a9a7a9bdf41691991 Mon Sep 17 00:00:00 2001
From: Yunqi Shao <yunqi.shao@chalmers.se>
Date: Wed, 3 Jul 2024 21:16:09 +0200
Subject: [PATCH 402/835] Revert "Add pkgconf to builddependencies"

This reverts commit e650d171f888bfb7bc5556f9afce6846d5d08ea7.
---
 .../t/TensorFlow/TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb     | 1 -
 .../easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a.eb     | 1 -
 2 files changed, 2 deletions(-)

diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb
index 60b44928e03..1d1c871f3d5 100644
--- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb
+++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb
@@ -14,7 +14,6 @@ use_pip = True
 sanity_pip_check = True
 
 builddependencies = [
-    ('pkgconf', '1.9.5'),
     ('Bazel', '6.1.0'),
     # git 2.x required, see also https://github.com/tensorflow/tensorflow/issues/29053
     ('git', '2.41.0', '-nodocs'),
diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a.eb
index 57b010cb652..506cbafd52b 100644
--- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a.eb
+++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a.eb
@@ -13,7 +13,6 @@ use_pip = True
 sanity_pip_check = True
 
 builddependencies = [
-    ('pkgconf', '1.9.5'),
     ('Bazel', '6.1.0'),
     # git 2.x required, see also https://github.com/tensorflow/tensorflow/issues/29053
     ('git', '2.41.0', '-nodocs'),

From fe033812bbc36df77cee062fced8e90deb5728f6 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 4 Jul 2024 11:33:49 +0200
Subject: [PATCH 403/835] add comment in medaka 1.12.0 easyconfig to explain
 why `h5py` 3.10.0 is included as extension

---
 easybuild/easyconfigs/m/medaka/medaka-1.12.0-foss-2023a.eb | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easybuild/easyconfigs/m/medaka/medaka-1.12.0-foss-2023a.eb b/easybuild/easyconfigs/m/medaka/medaka-1.12.0-foss-2023a.eb
index 429fb5bff5b..af21d1b6a0d 100644
--- a/easybuild/easyconfigs/m/medaka/medaka-1.12.0-foss-2023a.eb
+++ b/easybuild/easyconfigs/m/medaka/medaka-1.12.0-foss-2023a.eb
@@ -57,6 +57,7 @@ exts_list = [
         'source_tmpl': SOURCE_PY3_WHL,
         'checksums': ['0b2749c2cde3ef640bf314a9f94b24d929fe1ca476974719a6909dfc568c3aac'],
     }),
+    # medaka 1.12.0 requires h5py ~=3.10.0
     ('h5py', '3.10.0', {
         'checksums': ['d93adc48ceeb33347eb24a634fb787efc7ae4644e6ea4ba733d099605045c049'],
     }),

From 167628e92444bb0544d8e04810de1c0005219cc2 Mon Sep 17 00:00:00 2001
From: Alexander Grund <alexander.grund@tu-dresden.de>
Date: Thu, 8 Jul 2021 11:57:28 +0200
Subject: [PATCH 404/835] Whitelist ConfigureMakePythonPackage for
 sanity-checks

---
 test/easyconfigs/easyconfigs.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py
index ceae4c5bef9..9db22933411 100644
--- a/test/easyconfigs/easyconfigs.py
+++ b/test/easyconfigs/easyconfigs.py
@@ -1212,8 +1212,9 @@ def test_pr_sanity_check_paths(self):
         # including CargoPythonPackage, CMakePythonPackage, GoPackage, JuliaBundle, PerlBundle,
         #           PythonBundle & PythonPackage;
         # BuildEnv, ModuleRC and Toolchain easyblocks doesn't install anything so there is nothing to check.
-        whitelist = ['BuildEnv', 'CargoPythonBundle', 'CargoPythonPackage', 'CMakePythonPackage', 'CrayToolchain',
-                     'GoPackage', 'JuliaBundle', 'ModuleRC', 'PerlBundle', 'PythonBundle', 'PythonPackage', 'Toolchain']
+        whitelist = ['BuildEnv', 'CargoPythonBundle', 'CargoPythonPackage', 'CMakePythonPackage',
+                     'ConfigureMakePythonPackage', 'CrayToolchain', 'GoPackage', 'JuliaBundle', 'ModuleRC',
+                     'PerlBundle', 'PythonBundle', 'PythonPackage', 'Toolchain']
         # Bundles of dependencies without files of their own
         # Autotools: Autoconf + Automake + libtool, (recent) GCC: GCCcore + binutils, CUDA: GCC + CUDAcore,
         # CESM-deps: Python + Perl + netCDF + ESMF + git, FEniCS: DOLFIN and co,

From d9889ccc552c4f7dc100dfbad5df81d6573d3031 Mon Sep 17 00:00:00 2001
From: Alexander Grund <alexander.grund@tu-dresden.de>
Date: Mon, 6 Feb 2023 12:41:23 +0100
Subject: [PATCH 405/835] Whitelist any 2016 toolchain EC for pip check

---
 test/easyconfigs/easyconfigs.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py
index 9db22933411..f0273368053 100644
--- a/test/easyconfigs/easyconfigs.py
+++ b/test/easyconfigs/easyconfigs.py
@@ -1079,8 +1079,8 @@ def test_pr_python_packages(self):
 
         whitelist_pip_check = [
             r'Mako-1.0.4.*Python-2.7.12.*',
-            # no pip 9.x or newer for configparser easyconfigs using a 2016a or 2016b toolchain
-            r'configparser-3.5.0.*-2016[ab].*',
+            # no pip 9.x or newer for easyconfigs using a 2016a or 2016b toolchain
+            r'.*-2016[ab]-Python-.*',
             # mympirun is installed with system Python, pip may not be installed for system Python
             r'vsc-mympirun.*',
         ]

From 03ec2eb4a0a0b87fd282df9f5869b77c065c28b4 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Petr=20Kr=C3=A1l?= <petr@inuits.eu>
Date: Thu, 4 Jul 2024 14:16:06 +0200
Subject: [PATCH 406/835] adding easyconfigs: Transrate-1.0.3-GCC-12.3.0.eb,
 crb-blast-0.6.9-GCC-12.3.0.eb, colorize-0.7.7-GCC-12.3.0.eb,
 yell-2.2.2-GCC-12.3.0.eb

---
 .../c/colorize/colorize-0.7.7-GCC-12.3.0.eb   | 31 ++++++++++
 .../c/crb-blast/crb-blast-0.6.9-GCC-12.3.0.eb | 62 +++++++++++++++++++
 .../t/Transrate/Transrate-1.0.3-GCC-12.3.0.eb | 37 +++++++++++
 .../y/yell/yell-2.2.2-GCC-12.3.0.eb           | 30 +++++++++
 4 files changed, 160 insertions(+)
 create mode 100644 easybuild/easyconfigs/c/colorize/colorize-0.7.7-GCC-12.3.0.eb
 create mode 100644 easybuild/easyconfigs/c/crb-blast/crb-blast-0.6.9-GCC-12.3.0.eb
 create mode 100644 easybuild/easyconfigs/t/Transrate/Transrate-1.0.3-GCC-12.3.0.eb
 create mode 100644 easybuild/easyconfigs/y/yell/yell-2.2.2-GCC-12.3.0.eb

diff --git a/easybuild/easyconfigs/c/colorize/colorize-0.7.7-GCC-12.3.0.eb b/easybuild/easyconfigs/c/colorize/colorize-0.7.7-GCC-12.3.0.eb
new file mode 100644
index 00000000000..526fcb3a820
--- /dev/null
+++ b/easybuild/easyconfigs/c/colorize/colorize-0.7.7-GCC-12.3.0.eb
@@ -0,0 +1,31 @@
+easyblock = 'RubyGem'
+
+name = 'colorize'
+version = '0.7.7'
+
+homepage = 'https://github.com/fazibear/colorize'
+description = """Ruby gem for colorizing text using ANSI escape sequences.
+Extends String class or add a ColorizedString with methods to set the text color, background color and text effects."""
+
+toolchain = {'name': 'GCC', 'version': '12.3.0'}
+
+source_urls = ['https://rubygems.org/downloads/']
+sources = ['%(name)s-%(version)s.gem']
+checksums = ['d6ab95a5fcdea3c36c3327d38c1e79e2950ee1788506d8489ae35db330937a99']
+
+gem_file = '%(name)s-%(version)s.gem'
+
+builddependencies = [
+    ('binutils', '2.40'),
+]
+
+dependencies = [
+    ('Ruby', '3.3.0'),
+]
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['gems/%(namelower)s-%(version)s'],
+}
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/c/crb-blast/crb-blast-0.6.9-GCC-12.3.0.eb b/easybuild/easyconfigs/c/crb-blast/crb-blast-0.6.9-GCC-12.3.0.eb
new file mode 100644
index 00000000000..57d50e1b02b
--- /dev/null
+++ b/easybuild/easyconfigs/c/crb-blast/crb-blast-0.6.9-GCC-12.3.0.eb
@@ -0,0 +1,62 @@
+easyblock = 'Bundle'
+
+name = 'crb-blast'
+version = '0.6.9'
+
+homepage = 'https://github.com/cboursnell/crb-blast'
+description = """Conditional Reciprocal Best BLAST - high confidence ortholog assignment."""
+
+toolchain = {'name': 'GCC', 'version': '12.3.0'}
+
+builddependencies = [
+    ('binutils', '2.40'),
+]
+
+dependencies = [
+    ('Ruby', '3.3.0'),
+]
+
+exts_default_options = {
+    'source_urls': ['https://rubygems.org/downloads/'],
+    'source_tmpl': '%(name)s-%(version)s.gem',
+}
+
+exts_defaultclass = 'RubyGem'
+
+exts_list = [
+    ('facade', '1.2.1', {
+        'checksums': ['0764de5519088227675a2a67da23322500c3c507b89486d91296e031d87d036e'],
+    }),
+    ('pathname2', '1.8.4', {
+        'checksums': ['1711264f3f7c1b380f96e1f0383b135d9703488f7b1acf66346a176efc257b7a'],
+    }),
+    ('fixwhich', '1.0.2', {
+        'checksums': ['c6a8f796a7eb60ffbc29f0d2af85461761a36c2864d25e445ff18bfbd1657078'],
+    }),
+    ('bindeps', '1.2.1', {
+        'checksums': ['3c11d75aa722bed67246852bb430a182361a128910d384b664b91f3e65bc34b5'],
+    }),
+    ('bio', '1.6.0.pre.20181210', {
+        'checksums': ['c4114aeb99b012f90660b92ead4ca88c1578fd58252ed3ec46eb45dc4a2c6cc9'],
+    }),
+    ('threach', '0.2.0', {
+        'checksums': ['432cbf3569bf9b09e26f93d0959fd6fb911c71e790e8a4cc4d1110e139a2ffca'],
+    }),
+    ('trollop', '2.9.10', {
+        'checksums': ['ceca2d91f349163d6ee3e792d356d4ded7472e6da31ac6dcc5956d1b03607bf7'],
+    }),
+    (name, version, {
+        'checksums': ['69c346e7d83efe9b9a383a39b57e7cce186a82b7074f275b14906f8f05678e3e'],
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['bin/%(namelower)s'],
+    'dirs': ['gems/%(namelower)s-%(version)s'],
+}
+
+sanity_check_commands = ["%(namelower)s --help"]
+
+modextrapaths = {'GEM_PATH': ['']}
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/t/Transrate/Transrate-1.0.3-GCC-12.3.0.eb b/easybuild/easyconfigs/t/Transrate/Transrate-1.0.3-GCC-12.3.0.eb
new file mode 100644
index 00000000000..ac272dff125
--- /dev/null
+++ b/easybuild/easyconfigs/t/Transrate/Transrate-1.0.3-GCC-12.3.0.eb
@@ -0,0 +1,37 @@
+easyblock = 'RubyGem'
+
+name = 'Transrate'
+version = '1.0.3'
+
+homepage = 'https://hibberdlab.com/transrate'
+description = """Transrate is software for de-novo transcriptome assembly quality analysis.
+ It examines your assembly in detail and compares it to experimental evidence such as the sequencing reads,
+ reporting quality scores for contigs and assemblies. This allows you to choose between assemblers and parameters,
+ filter out the bad contigs from an assembly, and help decide when to stop trying to improve the assembly."""
+
+toolchain = {'name': 'GCC', 'version': '12.3.0'}
+
+source_urls = ['https://github.com/blahah/transrate/archive/']
+sources = ['v%(version)s.tar.gz']
+
+builddependencies = [
+    ('binutils', '2.40'),
+]
+
+dependencies = [
+    ('Ruby', '3.3.0'),
+    ('crb-blast', '0.6.9'),
+    ('colorize', '0.7.7'),
+    ('yell', '2.2.2'),
+]
+
+preinstallopts = """sed -i "s/'yell', '~> 2.0',/'yell',/g" transrate.gemspec && """
+
+sanity_check_paths = {
+    'files': ['bin/%(namelower)s'],
+    'dirs': ['gems/%(namelower)s-%(version)s'],
+}
+
+sanity_check_commands = ["%(namelower)s --help"]
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/y/yell/yell-2.2.2-GCC-12.3.0.eb b/easybuild/easyconfigs/y/yell/yell-2.2.2-GCC-12.3.0.eb
new file mode 100644
index 00000000000..c42c506c4f3
--- /dev/null
+++ b/easybuild/easyconfigs/y/yell/yell-2.2.2-GCC-12.3.0.eb
@@ -0,0 +1,30 @@
+easyblock = 'RubyGem'
+
+name = 'yell'
+version = '2.2.2'
+
+homepage = 'https://github.com/rudionrails/yell'
+description = """Yell - Your Extensible Logging Library is a comprehensive logging replacement for Ruby."""
+
+toolchain = {'name': 'GCC', 'version': '12.3.0'}
+
+source_urls = ['https://rubygems.org/downloads/']
+sources = ['%(name)s-%(version)s.gem']
+checksums = ['1d166f3cc3b6dc49a59778ea7156ed6d8de794c15106d48ffd6cbb061b9b26bc']
+
+gem_file = '%(name)s-%(version)s.gem'
+
+builddependencies = [
+    ('binutils', '2.40'),
+]
+
+dependencies = [
+    ('Ruby', '3.3.0'),
+]
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['gems/%(namelower)s-%(version)s'],
+}
+
+moduleclass = 'lib'

From 9768958a67e2c2319b858fb7055edc9d3cdca984 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 4 Jul 2024 18:21:52 +0200
Subject: [PATCH 407/835] adding easyconfigs: Bowtie-1.3.1-GCC-12.3.0.eb

---
 .../b/Bowtie/Bowtie-1.3.1-GCC-12.3.0.eb       | 30 +++++++++++++++++++
 1 file changed, 30 insertions(+)
 create mode 100644 easybuild/easyconfigs/b/Bowtie/Bowtie-1.3.1-GCC-12.3.0.eb

diff --git a/easybuild/easyconfigs/b/Bowtie/Bowtie-1.3.1-GCC-12.3.0.eb b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.3.1-GCC-12.3.0.eb
new file mode 100644
index 00000000000..9617ba2e343
--- /dev/null
+++ b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.3.1-GCC-12.3.0.eb
@@ -0,0 +1,30 @@
+##
+# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia
+# Homepage: 	https://staff.flinders.edu.au/research/deep-thought
+#
+# Authors::	Robert Qiao <rob.qiao@flinders.edu.au>
+# License::	Artistic v2.0
+#
+# Notes::
+##
+
+name = 'Bowtie'
+version = '1.3.1'
+
+homepage = 'http://bowtie-bio.sourceforge.net/index.shtml'
+description = """Bowtie is an ultrafast, memory-efficient short read aligner.
+ It aligns short DNA sequences (reads) to the human genome."""
+
+toolchain = {'name': 'GCC', 'version': '12.3.0'}
+toolchainopts = {'pic': True, 'cstd': 'gnu++98'}
+
+source_urls = ['https://sourceforge.net/projects/bowtie-bio/files/bowtie/%(version)s/']
+sources = ['%(namelower)s-%(version)s-src.zip']
+checksums = ['e23517aa53846ef828172be911750cd05748522117efcbbe5a36f3241fb40761']
+
+dependencies = [
+    ('tbb', '2021.11.0'),
+    ('zlib', '1.2.13'),
+]
+
+moduleclass = 'bio'

From cf40308430eea2b289122cf931e371227f7273ae Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 4 Jul 2024 19:40:27 +0200
Subject: [PATCH 408/835] enable test in easyconfig for tbb 2021.9.0 + add
 -Wno-stringop-overflow to work around failing compilation of tests

---
 easybuild/easyconfigs/t/tbb/tbb-2021.9.0-GCCcore-12.2.0.eb | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/t/tbb/tbb-2021.9.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/t/tbb/tbb-2021.9.0-GCCcore-12.2.0.eb
index 68c8f42e14c..d0173aab4ea 100644
--- a/easybuild/easyconfigs/t/tbb/tbb-2021.9.0-GCCcore-12.2.0.eb
+++ b/easybuild/easyconfigs/t/tbb/tbb-2021.9.0-GCCcore-12.2.0.eb
@@ -20,7 +20,8 @@ builddependencies = [
 
 dependencies = [('hwloc', '2.8.0')]
 
-configopts = '-DTBB_TEST=OFF '
+# use -Wno-error as workaround for compiler error when building the tests
+preconfigopts = 'export CXXFLAGS="$CXXFLAGS -Wno-stringop-overflow" && '
 
 sanity_check_paths = {
     'files': ['lib/libtbb.%s' % SHLIB_EXT, 'lib/libtbbmalloc.%s' % SHLIB_EXT],

From e5c9d3d46d004d468747521975a33a190a358f58 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 5 Jul 2024 15:26:48 +0200
Subject: [PATCH 409/835] add patch that adds RISC-V support

---
 .../x/x264/x264-20231019-GCCcore-13.2.0.eb    |  6 +++-
 .../x264-20231019_add-riscv-support.patch     | 29 +++++++++++++++++++
 2 files changed, 34 insertions(+), 1 deletion(-)
 create mode 100644 easybuild/easyconfigs/x/x264/x264-20231019_add-riscv-support.patch

diff --git a/easybuild/easyconfigs/x/x264/x264-20231019-GCCcore-13.2.0.eb b/easybuild/easyconfigs/x/x264/x264-20231019-GCCcore-13.2.0.eb
index a1d60486ce0..3a5bb6947d8 100644
--- a/easybuild/easyconfigs/x/x264/x264-20231019-GCCcore-13.2.0.eb
+++ b/easybuild/easyconfigs/x/x264/x264-20231019-GCCcore-13.2.0.eb
@@ -14,7 +14,11 @@ toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
 
 source_urls = ['https://code.videolan.org/videolan/%(name)s/-/archive/baee400f/']
 sources = [{'download_filename': '%(name)s-9c3c7168.tar.gz', 'filename': SOURCE_TAR_GZ}]
-checksums = ['bf6a61dcc7e1f4e623a44f09de02e843f06e7ec14f807557b43130fc84287f29']
+patches = ['x264-20231019_add-riscv-support.patch']
+checksums = [
+    {'x264-20231019.tar.gz': 'bf6a61dcc7e1f4e623a44f09de02e843f06e7ec14f807557b43130fc84287f29'},
+    {'x264-20231019_add-riscv-support.patch': 'd4455f3f643f255d4e907cf8a7bd803a3184ab2b6cc3445298bd2986fbb976f6'},
+]
 
 builddependencies = [
     ('binutils', '2.40'),
diff --git a/easybuild/easyconfigs/x/x264/x264-20231019_add-riscv-support.patch b/easybuild/easyconfigs/x/x264/x264-20231019_add-riscv-support.patch
new file mode 100644
index 00000000000..b522010af86
--- /dev/null
+++ b/easybuild/easyconfigs/x/x264/x264-20231019_add-riscv-support.patch
@@ -0,0 +1,29 @@
+Add Risc-V 64 bit to config.guess
+https://code.videolan.org/videolan/x264/-/merge_requests/121
+
+From 941cae6d1d6d6344c9a1d27440eaf2872b18ca9a Mon Sep 17 00:00:00 2001
+From: Roger Hardiman <software@rjh.org.uk>
+Date: Fri, 18 Nov 2022 20:15:40 +0000
+Subject: [PATCH] Add Risc-V 64 bit
+
+---
+ config.guess | 3 +++
+ 1 file changed, 3 insertions(+)
+
+diff --git a/config.guess b/config.guess
+index d437be00..14c12963 100755
+--- a/config.guess
++++ b/config.guess
+@@ -985,6 +985,9 @@ EOF
+     ppc:Linux:*:*)
+ 	echo powerpc-unknown-linux-gnu
+ 	exit ;;
++    riscv64:Linux:*:*)
++	echo ${UNAME_MACHINE}-unknown-linux-gnu
++	exit ;;
+     s390:Linux:*:* | s390x:Linux:*:*)
+ 	echo ${UNAME_MACHINE}-ibm-linux
+ 	exit ;;
+-- 
+GitLab
+

From 7fad6a1c1a9d40499b7be77fd85cb21411b82587 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 5 Jul 2024 15:56:56 +0200
Subject: [PATCH 410/835] disable test step for WIEN2k 23.2 because files
 required by it can no longer be downloaded

---
 easybuild/easyconfigs/w/WIEN2k/WIEN2k-23.2-intel-2021b.eb | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/easybuild/easyconfigs/w/WIEN2k/WIEN2k-23.2-intel-2021b.eb b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-23.2-intel-2021b.eb
index a8881dbe118..0dd0b641ceb 100644
--- a/easybuild/easyconfigs/w/WIEN2k/WIEN2k-23.2-intel-2021b.eb
+++ b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-23.2-intel-2021b.eb
@@ -61,6 +61,10 @@ fix_perl_shebang_for = [
     'bashtime2csh.pl_lapw',
 ]
 
+# skip running of serial/parallel benchmark, because links to download test_case.tar.gz and mpi-benchmark.tar.gz
+# from http://www.wien2k.at/reg_user/benchmark/ that are used by WIEN2k easyblock are broken...
+runtest = False
+
 tests = [
     # test case 1: NaCl
     ('NaCl', '-b', '-i 100', [r'^:DIS.*0.1', r'^:ENE.*-1248.1']),

From 291ce8f07e75b468a3bb338f60d12b4e6e394df1 Mon Sep 17 00:00:00 2001
From: Cintia Willemyns <115622907+WilleBell@users.noreply.github.com>
Date: Fri, 5 Jul 2024 16:06:07 +0200
Subject: [PATCH 411/835] Add mpi4py as dependency for MPI

---
 .../easyconfigs/r/Ray-project/Ray-project-2.9.1-foss-2023a.eb    | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easybuild/easyconfigs/r/Ray-project/Ray-project-2.9.1-foss-2023a.eb b/easybuild/easyconfigs/r/Ray-project/Ray-project-2.9.1-foss-2023a.eb
index 0ee7b374943..67ab662077d 100644
--- a/easybuild/easyconfigs/r/Ray-project/Ray-project-2.9.1-foss-2023a.eb
+++ b/easybuild/easyconfigs/r/Ray-project/Ray-project-2.9.1-foss-2023a.eb
@@ -23,6 +23,7 @@ dependencies = [
     ('protobuf-python', '4.24.0'),
     ('PyYAML', '6.0'),
     ('lz4', '1.9.4'),
+    ('mpi4py', '3.1.4'),
 ]
 
 use_pip = True

From 69cde524bc487adcd7d43795311ad1144e3aea2c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 5 Jul 2024 16:24:47 +0200
Subject: [PATCH 412/835] remove workaround for finding libncurses

---
 easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-11.2.0.eb | 3 ---
 easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-11.3.0.eb | 3 ---
 easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-12.2.0.eb | 3 ---
 easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-12.3.0.eb | 3 ---
 easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-13.2.0.eb | 3 ---
 5 files changed, 15 deletions(-)

diff --git a/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-11.2.0.eb
index 1bb5846fed4..9e8668e6a50 100644
--- a/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-11.2.0.eb
+++ b/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-11.2.0.eb
@@ -25,9 +25,6 @@ dependencies = [('ncurses', '6.2')]
 
 preconfigopts = "autoconf && "
 
-# configure is broken: add workaround to find libncurses...
-configure_cmd_prefix = "FRONTEND_LDADD='-L${EBROOTNCURSES}/lib' "
-
 sanity_check_paths = {
     'files': ['bin/lame', 'include/lame/lame.h', 'lib/libmp3lame.%s' % SHLIB_EXT],
     'dirs': [],
diff --git a/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-11.3.0.eb
index f067051ffe7..5efdefb761f 100644
--- a/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-11.3.0.eb
+++ b/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-11.3.0.eb
@@ -25,9 +25,6 @@ dependencies = [('ncurses', '6.3')]
 
 preconfigopts = "autoconf && "
 
-# configure is broken: add workaround to find libncurses...
-configure_cmd_prefix = "FRONTEND_LDADD='-L${EBROOTNCURSES}/lib' "
-
 sanity_check_paths = {
     'files': ['bin/lame', 'include/lame/lame.h', 'lib/libmp3lame.%s' % SHLIB_EXT],
     'dirs': [],
diff --git a/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-12.2.0.eb
index 4008e0b3455..7d4bae408d5 100644
--- a/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-12.2.0.eb
+++ b/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-12.2.0.eb
@@ -25,9 +25,6 @@ dependencies = [('ncurses', '6.3')]
 
 preconfigopts = "autoconf && "
 
-# configure is broken: add workaround to find libncurses...
-configure_cmd_prefix = "FRONTEND_LDADD='-L${EBROOTNCURSES}/lib' "
-
 sanity_check_paths = {
     'files': ['bin/lame', 'include/lame/lame.h', 'lib/libmp3lame.%s' % SHLIB_EXT],
     'dirs': [],
diff --git a/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-12.3.0.eb
index 4573d76f947..a4c7dbd4278 100644
--- a/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-12.3.0.eb
+++ b/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-12.3.0.eb
@@ -25,9 +25,6 @@ dependencies = [('ncurses', '6.4')]
 
 preconfigopts = "autoconf && "
 
-# configure is broken: add workaround to find libncurses...
-configure_cmd_prefix = "FRONTEND_LDADD='-L${EBROOTNCURSES}/lib' "
-
 sanity_check_paths = {
     'files': ['bin/lame', 'include/lame/lame.h', 'lib/libmp3lame.%s' % SHLIB_EXT],
     'dirs': [],
diff --git a/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-13.2.0.eb
index 7b163dff699..1bffb9a1939 100644
--- a/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-13.2.0.eb
+++ b/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-13.2.0.eb
@@ -25,9 +25,6 @@ dependencies = [('ncurses', '6.4')]
 
 preconfigopts = "autoconf && "
 
-# configure is broken: add workaround to find libncurses...
-configure_cmd_prefix = "FRONTEND_LDADD='-L${EBROOTNCURSES}/lib' "
-
 sanity_check_paths = {
     'files': ['bin/lame', 'include/lame/lame.h', 'lib/libmp3lame.%s' % SHLIB_EXT],
     'dirs': [],

From 01da98598ea033b9ec264f56c4481081d404544c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 5 Jul 2024 22:24:01 +0200
Subject: [PATCH 413/835] add -DENABLE_PIC=ON to configopts

---
 easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-11.2.0.eb | 2 +-
 easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-11.3.0.eb | 2 +-
 easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-12.2.0.eb | 2 +-
 easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-12.3.0.eb | 2 +-
 easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-13.2.0.eb | 2 +-
 5 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-11.2.0.eb b/easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-11.2.0.eb
index 0732a992f17..e053931ce57 100644
--- a/easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-11.2.0.eb
+++ b/easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-11.2.0.eb
@@ -25,7 +25,7 @@ builddependencies = [
 
 start_dir = 'source'
 
-configopts = '-DGIT_ARCHETYPE=1'
+configopts = '-DGIT_ARCHETYPE=1 -DENABLE_PIC=ON'
 
 sanity_check_paths = {
     'files': ['bin/x265', 'include/x265_config.h', 'include/x265.h', 'lib/libx265.a', 'lib/libx265.%s' % SHLIB_EXT],
diff --git a/easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-11.3.0.eb
index 281db53772b..1544a97d4b6 100644
--- a/easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-11.3.0.eb
+++ b/easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-11.3.0.eb
@@ -22,7 +22,7 @@ builddependencies = [
     ('Yasm', '1.3.0'),
 ]
 
-configopts = '-DGIT_ARCHETYPE=1'
+configopts = '-DGIT_ARCHETYPE=1 -DENABLE_PIC=ON'
 
 start_dir = 'source'
 
diff --git a/easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-12.2.0.eb b/easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-12.2.0.eb
index 27b2b066296..d31e45da477 100644
--- a/easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-12.2.0.eb
+++ b/easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-12.2.0.eb
@@ -22,7 +22,7 @@ builddependencies = [
     ('Yasm', '1.3.0'),
 ]
 
-configopts = '-DGIT_ARCHETYPE=1'
+configopts = '-DGIT_ARCHETYPE=1 -DENABLE_PIC=ON'
 
 start_dir = 'source'
 
diff --git a/easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-12.3.0.eb b/easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-12.3.0.eb
index 4c754f3021d..4bd77d7f07e 100644
--- a/easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-12.3.0.eb
+++ b/easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-12.3.0.eb
@@ -22,7 +22,7 @@ builddependencies = [
     ('Yasm', '1.3.0'),
 ]
 
-configopts = '-DGIT_ARCHETYPE=1'
+configopts = '-DGIT_ARCHETYPE=1 -DENABLE_PIC=ON'
 
 start_dir = 'source'
 
diff --git a/easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-13.2.0.eb b/easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-13.2.0.eb
index d1bca35c8d7..1466e0c5f3c 100644
--- a/easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-13.2.0.eb
+++ b/easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-13.2.0.eb
@@ -22,7 +22,7 @@ builddependencies = [
     ('Yasm', '1.3.0'),
 ]
 
-configopts = '-DGIT_ARCHETYPE=1'
+configopts = '-DGIT_ARCHETYPE=1 -DENABLE_PIC=ON'
 
 start_dir = 'source'
 

From 375830484b9f92d94c00c6b543f5cf587783646e Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 5 Jul 2024 22:30:37 +0200
Subject: [PATCH 414/835] stick to scikit-learn 1.3.1 as dependency for
 napari-denoiseg

---
 .../n/napari-denoiseg/napari-denoiseg-0.0.1-foss-2023a.eb       | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/n/napari-denoiseg/napari-denoiseg-0.0.1-foss-2023a.eb b/easybuild/easyconfigs/n/napari-denoiseg/napari-denoiseg-0.0.1-foss-2023a.eb
index dde1af43010..e96d9bda854 100644
--- a/easybuild/easyconfigs/n/napari-denoiseg/napari-denoiseg-0.0.1-foss-2023a.eb
+++ b/easybuild/easyconfigs/n/napari-denoiseg/napari-denoiseg-0.0.1-foss-2023a.eb
@@ -17,7 +17,7 @@ dependencies = [
     ('CSBDeep', '0.7.4'),
     ('n2v', '0.3.3'),
     ('numba', '0.58.1'),
-    ('scikit-learn', '1.4.2'),
+    ('scikit-learn', '1.3.1'),
     ('n2v', '0.3.3'),
     ('autopep8', '2.2.0'),
 ]

From a002fe8f6c06b9fa44fa431bcaa7ba79cdad1892 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 5 Jul 2024 22:45:36 +0200
Subject: [PATCH 415/835] remove duplicate nv2 dependency for napari-denoiseg

---
 .../n/napari-denoiseg/napari-denoiseg-0.0.1-foss-2023a.eb        | 1 -
 1 file changed, 1 deletion(-)

diff --git a/easybuild/easyconfigs/n/napari-denoiseg/napari-denoiseg-0.0.1-foss-2023a.eb b/easybuild/easyconfigs/n/napari-denoiseg/napari-denoiseg-0.0.1-foss-2023a.eb
index e96d9bda854..8335ad90cba 100644
--- a/easybuild/easyconfigs/n/napari-denoiseg/napari-denoiseg-0.0.1-foss-2023a.eb
+++ b/easybuild/easyconfigs/n/napari-denoiseg/napari-denoiseg-0.0.1-foss-2023a.eb
@@ -18,7 +18,6 @@ dependencies = [
     ('n2v', '0.3.3'),
     ('numba', '0.58.1'),
     ('scikit-learn', '1.3.1'),
-    ('n2v', '0.3.3'),
     ('autopep8', '2.2.0'),
 ]
 

From ef85e1f96eb3543003225b8c4cb909bc52d364be Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 6 Jul 2024 11:54:36 +0200
Subject: [PATCH 416/835] add datestamp to version in rMATS-long easyconfig,
 since we're not using commit that corresponds with 1.0.0 tag

---
 ...3.2.eb => rMATS-long-1.0.0-20240502-foss-2023a-R-4.3.2.eb} | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)
 rename easybuild/easyconfigs/r/rMATS-long/{rMATS-long-1.0.0-foss-2023a-R-4.3.2.eb => rMATS-long-1.0.0-20240502-foss-2023a-R-4.3.2.eb} (92%)

diff --git a/easybuild/easyconfigs/r/rMATS-long/rMATS-long-1.0.0-foss-2023a-R-4.3.2.eb b/easybuild/easyconfigs/r/rMATS-long/rMATS-long-1.0.0-20240502-foss-2023a-R-4.3.2.eb
similarity index 92%
rename from easybuild/easyconfigs/r/rMATS-long/rMATS-long-1.0.0-foss-2023a-R-4.3.2.eb
rename to easybuild/easyconfigs/r/rMATS-long/rMATS-long-1.0.0-20240502-foss-2023a-R-4.3.2.eb
index fcf6cb112d9..6074c273fac 100644
--- a/easybuild/easyconfigs/r/rMATS-long/rMATS-long-1.0.0-foss-2023a-R-4.3.2.eb
+++ b/easybuild/easyconfigs/r/rMATS-long/rMATS-long-1.0.0-20240502-foss-2023a-R-4.3.2.eb
@@ -1,8 +1,8 @@
 easyblock = 'Tarball'
 
 name = 'rMATS-long'
-version = '1.0.0'
 local_commit = "592cb32"
+version = '1.0.0-20240502'
 versionsuffix = '-R-%(rver)s'
 
 homepage = 'https://github.com/Xinglab/rMATS-long'
@@ -13,7 +13,7 @@ toolchain = {'name': 'foss', 'version': '2023a'}
 source_urls = ['https://github.com/Xinglab/%(name)s/archive/']
 sources = [{
     'download_filename': '%s.tar.gz' % local_commit,
-    'filename': '%%(name)s-%%(version)s-%s.tar.gz' % local_commit,
+    'filename': '%(name)s-%(version)s.tar.gz',
 }]
 checksums = ['9f4f859c05be5a274b8c0aaf79a18f8c02839f8e6d71330d07f77d027ddba003']
 

From 17a2dfa1430f2bdb9292c2d508987250b7b92069 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 6 Jul 2024 17:50:48 +0200
Subject: [PATCH 417/835] add custom sanity check paths + command for Trycycler
 0.5.5

---
 .../t/Trycycler/Trycycler-0.5.5-foss-2023a-R-4.3.2.eb  | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/t/Trycycler/Trycycler-0.5.5-foss-2023a-R-4.3.2.eb b/easybuild/easyconfigs/t/Trycycler/Trycycler-0.5.5-foss-2023a-R-4.3.2.eb
index f9a86a65587..00aa967bdc2 100644
--- a/easybuild/easyconfigs/t/Trycycler/Trycycler-0.5.5-foss-2023a-R-4.3.2.eb
+++ b/easybuild/easyconfigs/t/Trycycler/Trycycler-0.5.5-foss-2023a-R-4.3.2.eb
@@ -27,12 +27,20 @@ use_pip = True
 
 exts_list = [
     (name, version, {
-        'source_tmpl': 'v%(version)s.tar.gz',
         'source_urls': ['https://github.com/rrwick/Trycycler/archive/'],
+        'sources': ['v%(version)s.tar.gz'],
         'checksums': ['5794a4520c3b8673adc69c975cee06d7658cd74ac6d9378d1fc7af860bec1a89'],
+        'runtest': 'pytest',
     }),
 ]
 
 sanity_pip_check = True
 
+sanity_check_paths = {
+    'files':  ['bin/trycycler'],
+    'dirs':  ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = ["trycycler --help"]
+
 moduleclass = 'bio'

From 478887d5e790f03873ad727ed2f78c5c46d1932a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Mon, 8 Jul 2024 14:35:48 +0000
Subject: [PATCH 418/835] adding easyconfigs:
 Perl-bundle-CPAN-5.38.2-GCCcore-13.3.0.eb, groff-1.23.0-GCCcore-13.3.0.eb

---
 .../g/groff/groff-1.23.0-GCCcore-13.3.0.eb    |   26 +
 .../Perl-bundle-CPAN-5.38.2-GCCcore-13.3.0.eb | 2147 +++++++++++++++++
 2 files changed, 2173 insertions(+)
 create mode 100644 easybuild/easyconfigs/g/groff/groff-1.23.0-GCCcore-13.3.0.eb
 create mode 100644 easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.2-GCCcore-13.3.0.eb

diff --git a/easybuild/easyconfigs/g/groff/groff-1.23.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/groff/groff-1.23.0-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..000049dbdda
--- /dev/null
+++ b/easybuild/easyconfigs/g/groff/groff-1.23.0-GCCcore-13.3.0.eb
@@ -0,0 +1,26 @@
+easyblock = 'ConfigureMake'
+
+name = 'groff'
+version = '1.23.0'
+
+homepage = 'https://www.gnu.org/software/groff'
+description = """Groff (GNU troff) is a typesetting system that reads plain text mixed with formatting commands
+ and produces formatted output."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+source_urls = ['https://ftp.gnu.org/gnu/groff']
+sources = [SOURCE_TAR_GZ]
+checksums = ['6b9757f592b7518b4902eb6af7e54570bdccba37a871fddb2d30ae3863511c13']
+
+builddependencies = [
+    ('binutils', '2.42'),
+    ('M4', '1.4.19'),
+]
+
+sanity_check_paths = {
+    'files': ['bin/groff', 'bin/nroff', 'bin/troff'],
+    'dirs': ['lib/groff', 'share'],
+}
+
+moduleclass = 'tools'
diff --git a/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.2-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..3ee5da2ad31
--- /dev/null
+++ b/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.2-GCCcore-13.3.0.eb
@@ -0,0 +1,2147 @@
+easyblock = 'PerlBundle'
+
+name = 'Perl-bundle-CPAN'
+version = '5.38.2'
+
+homepage = 'https://www.perl.org/'
+description = """A set of common packages from CPAN"""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+toolchainopts = {'pic': True}
+
+builddependencies = [
+    ('binutils', '2.42'),
+    ('groff', '1.23.0'),
+]
+
+dependencies = [
+    ('Perl', version),
+    ('zlib', '1.3.1'),  # for Net::SSLeay
+    ('expat', '2.6.2'),  # for XML::Parser
+    ('ncurses', '6.5'),  # for Term::ReadLine::Gnu
+    ('libreadline', '8.2'),  # for Term::ReadLine::Gnu
+    ('OpenSSL', '3', '', SYSTEM),  # required for Net::SSLeay
+]
+
+# !! order of extensions is important !!
+# extensions updated on 2024-07-08
+exts_list = [
+    ('Config::General', '2.65', {
+        'source_tmpl': 'Config-General-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/T/TL/TLINDEN'],
+        'checksums': ['4d6d5754be3a9f30906836f0cc10e554c8832e14e7a1341efb15b05d706fc58f'],
+    }),
+    ('HTTP::Date', '6.06', {
+        'source_tmpl': 'HTTP-Date-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'],
+        'checksums': ['7b685191c6acc3e773d1fc02c95ee1f9fae94f77783175f5e78c181cc92d2b52'],
+    }),
+    ('File::Listing', '6.16', {
+        'source_tmpl': 'File-Listing-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'],
+        'checksums': ['189b3a13fc0a1ba412b9d9ec5901e9e5e444cc746b9f0156d4399370d33655c6'],
+    }),
+    ('ExtUtils::Config', '0.009', {
+        'source_tmpl': 'ExtUtils-Config-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'],
+        'checksums': ['4ef84e73aad50a3be332885d2a3b12f3cab1b1e0bad24e88297a123b4f39f3ce'],
+    }),
+    ('ExtUtils::InstallPaths', '0.013', {
+        'source_tmpl': 'ExtUtils-InstallPaths-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'],
+        'checksums': ['65969d3ad8a3a2ea8ef5b4213ed5c2c83961bb5bd12f7ad35128f6bd5b684aa0'],
+    }),
+    ('ExtUtils::Helpers', '0.027', {
+        'source_tmpl': 'ExtUtils-Helpers-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'],
+        'checksums': ['9d592131dc5845a86dc28be9143f764e73cb62db06fedf50a895be1324b6cec5'],
+    }),
+    ('Test::Harness', '3.48', {
+        'source_tmpl': 'Test-Harness-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'],
+        'checksums': ['e73ff89c81c1a53f6baeef6816841b89d3384403ad97422a7da9d1eeb20ef9c5'],
+    }),
+    ('Module::Build::Tiny', '0.048', {
+        'source_tmpl': 'Module-Build-Tiny-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'],
+        'checksums': ['79a73e506fb7badabdf79137a45c6c5027daaf6f9ac3dcfb9d4ffcce92eb36bd'],
+    }),
+    ('aliased', '0.34', {
+        'source_tmpl': 'aliased-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'],
+        'checksums': ['c350524507cd827fab864e5d4c2cc350b1babaa12fa95aec0ca00843fcc7deeb'],
+    }),
+    ('Text::Glob', '0.11', {
+        'source_tmpl': 'Text-Glob-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/R/RC/RCLAMP'],
+        'checksums': ['069ccd49d3f0a2dedb115f4bdc9fbac07a83592840953d1fcdfc39eb9d305287'],
+    }),
+    ('Regexp::Common', '2017060201', {
+        'source_tmpl': 'Regexp-Common-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/A/AB/ABIGAIL'],
+        'checksums': ['ee07853aee06f310e040b6bf1a0199a18d81896d3219b9b35c9630d0eb69089b'],
+    }),
+    ('IO::String', '1.08', {
+        'source_tmpl': 'IO-String-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'],
+        'checksums': ['2a3f4ad8442d9070780e58ef43722d19d1ee21a803bf7c8206877a10482de5a0'],
+    }),
+    ('Data::Stag', '0.14', {
+        'source_tmpl': 'Data-Stag-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/C/CM/CMUNGALL'],
+        'checksums': ['4ab122508d2fb86d171a15f4006e5cf896d5facfa65219c0b243a89906258e59'],
+    }),
+    ('GO::Utils', '0.15', {
+        'source_tmpl': 'go-perl-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/C/CM/CMUNGALL'],
+        'checksums': ['423d26155ee85ca51ab2270cee59f4e85b193e57ac3a29aff827298c0a396b12'],
+    }),
+    ('Module::Pluggable', '5.2', {
+        'source_tmpl': 'Module-Pluggable-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/S/SI/SIMONW'],
+        'checksums': ['b3f2ad45e4fd10b3fb90d912d78d8b795ab295480db56dc64e86b9fa75c5a6df'],
+    }),
+    ('Try::Tiny', '0.31', {
+        'source_tmpl': 'Try-Tiny-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'],
+        'checksums': ['3300d31d8a4075b26d8f46ce864a1d913e0e8467ceeba6655d5d2b2e206c11be'],
+    }),
+    ('Test::Fatal', '0.017', {
+        'source_tmpl': 'Test-Fatal-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'],
+        'checksums': ['37dfffdafb84b762efe96b02fb2aa41f37026c73e6b83590db76229697f3c4a6'],
+    }),
+    ('Test::Warnings', '0.033', {
+        'source_tmpl': 'Test-Warnings-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'],
+        'checksums': ['b9c375719f2c61c5f97aa5ee6cf4c901a972347c415969379b0b51f67c48bbcb'],
+    }),
+    ('Class::Inspector', '1.36', {
+        'source_tmpl': 'Class-Inspector-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'],
+        'checksums': ['cc295d23a472687c24489d58226ead23b9fdc2588e522f0b5f0747741700694e'],
+    }),
+    ('File::ShareDir::Install', '0.14', {
+        'source_tmpl': 'File-ShareDir-Install-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'],
+        'checksums': ['8f9533b198f2d4a9a5288cbc7d224f7679ad05a7a8573745599789428bc5aea0'],
+    }),
+    ('File::ShareDir', '1.118', {
+        'source_tmpl': 'File-ShareDir-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'],
+        'checksums': ['3bb2a20ba35df958dc0a4f2306fc05d903d8b8c4de3c8beefce17739d281c958'],
+    }),
+    ('IPC::System::Simple', '1.30', {
+        'source_tmpl': 'IPC-System-Simple-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/J/JK/JKEENAN'],
+        'checksums': ['22e6f5222b505ee513058fdca35ab7a1eab80539b98e5ca4a923a70a8ae9ba9e'],
+    }),
+    ('Importer', '0.026', {
+        'source_tmpl': 'Importer-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'],
+        'checksums': ['e08fa84e13cb998b7a897fc8ec9c3459fcc1716aff25cc343e36ef875891b0ef'],
+    }),
+    ('Term::Table', '0.018', {
+        'source_tmpl': 'Term-Table-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'],
+        'checksums': ['9159b9131ee6b3f3956b74f45422985553574babbfaeba60be5c17bc114ac011'],
+    }),
+    ('Scope::Guard', '0.21', {
+        'source_tmpl': 'Scope-Guard-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/C/CH/CHOCOLATE'],
+        'checksums': ['8c9b1bea5c56448e2c3fadc65d05be9e4690a3823a80f39d2f10fdd8f777d278'],
+    }),
+    ('Sub::Info', '0.002', {
+        'source_tmpl': 'Sub-Info-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'],
+        'checksums': ['ea3056d696bdeff21a99d340d5570887d39a8cc47bff23adfc82df6758cdd0ea'],
+    }),
+    ('Test2::Require::Module', '0.000163', {
+        'source_tmpl': 'Test2-Suite-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'],
+        'checksums': ['e336c2d92d43c4f0068aa0d67019d56723ab82471e1bd9028300bb6a1602c0a9'],
+    }),
+    ('Test2::Plugin::NoWarnings', '0.10', {
+        'source_tmpl': 'Test2-Plugin-NoWarnings-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'],
+        'checksums': ['c97cb1122cc6e3e4a079059da71e12f65760bfb0671d19d25a7ec7c5f1f240fb'],
+    }),
+    ('Class::Tiny', '1.008', {
+        'source_tmpl': 'Class-Tiny-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'],
+        'checksums': ['ee058a63912fa1fcb9a72498f56ca421a2056dc7f9f4b67837446d6421815615'],
+    }),
+    ('Path::Tiny', '0.146', {
+        'source_tmpl': 'Path-Tiny-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'],
+        'checksums': ['861ef09bca68254e9ab24337bb6ec9d58593a792e9d68a27ee6bec2150f06741'],
+    }),
+    ('Test::Deep', '1.204', {
+        'source_tmpl': 'Test-Deep-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'],
+        'checksums': ['b6591f6ccdd853c7efc9ff3c5756370403211cffe46047f082b1cd1611a84e5f'],
+    }),
+    ('Test::File', '1.993', {
+        'source_tmpl': 'Test-File-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/B/BD/BDFOY'],
+        'checksums': ['ef2ffe1aaec7b42d874ad411ec647547b9b9bc2f5fb93e49e3399488456afc7a'],
+    }),
+    ('Test::Needs', '0.002010', {
+        'source_tmpl': 'Test-Needs-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'],
+        'checksums': ['923ffdc78fcba96609753e4bae26b0ba0186893de4a63cd5236e012c7c90e208'],
+    }),
+    ('Test::Requires', '0.11', {
+        'source_tmpl': 'Test-Requires-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TOKUHIROM'],
+        'checksums': ['4b88de549597eecddf7c3c38a4d0204a16f59ad804577b671896ac04e24e040f'],
+    }),
+    ('File::Copy::Recursive', '0.45', {
+        'source_tmpl': 'File-Copy-Recursive-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/D/DM/DMUEY'],
+        'checksums': ['d3971cf78a8345e38042b208bb7b39cb695080386af629f4a04ffd6549df1157'],
+    }),
+    ('Test::File::ShareDir::Dist', '1.001002', {
+        'source_tmpl': 'Test-File-ShareDir-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/K/KE/KENTNL'],
+        'checksums': ['b33647cbb4b2f2fcfbde4f8bb4383d0ac95c2f89c4c5770eb691f1643a337aad'],
+    }),
+    ('CPAN::Meta::Check', '0.018', {
+        'source_tmpl': 'CPAN-Meta-Check-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'],
+        'checksums': ['f619d2df5ea0fd91c8cf83eb54acccb5e43d9e6ec1a3f727b3d0ac15d0cf378a'],
+    }),
+    ('Sub::Exporter::Progressive', '0.001013', {
+        'source_tmpl': 'Sub-Exporter-Progressive-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/F/FR/FREW'],
+        'checksums': ['d535b7954d64da1ac1305b1fadf98202769e3599376854b2ced90c382beac056'],
+    }),
+    ('Module::Runtime', '0.016', {
+        'source_tmpl': 'Module-Runtime-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/Z/ZE/ZEFRAM'],
+        'checksums': ['68302ec646833547d410be28e09676db75006f4aa58a11f3bdb44ffe99f0f024'],
+    }),
+    ('Module::Implementation', '0.09', {
+        'source_tmpl': 'Module-Implementation-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'],
+        'checksums': ['c15f1a12f0c2130c9efff3c2e1afe5887b08ccd033bd132186d1e7d5087fd66d'],
+    }),
+    ('B::Hooks::EndOfScope', '0.28', {
+        'source_tmpl': 'B-Hooks-EndOfScope-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'],
+        'checksums': ['edac77a17fc36620c8324cc194ce1fad2f02e9fcbe72d08ad0b2c47f0c7fd8ef'],
+    }),
+    ('Package::Stash', '0.40', {
+        'source_tmpl': 'Package-Stash-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'],
+        'checksums': ['5a9722c6d9cb29ee133e5f7b08a5362762a0b5633ff5170642a5b0686e95e066'],
+    }),
+    ('namespace::clean', '0.27', {
+        'source_tmpl': 'namespace-clean-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/R/RI/RIBASUSHI'],
+        'checksums': ['8a10a83c3e183dc78f9e7b7aa4d09b47c11fb4e7d3a33b9a12912fd22e31af9d'],
+    }),
+    ('Sub::Identify', '0.14', {
+        'source_tmpl': 'Sub-Identify-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/R/RG/RGARCIA'],
+        'checksums': ['068d272086514dd1e842b6a40b1bedbafee63900e5b08890ef6700039defad6f'],
+    }),
+    ('namespace::autoclean', '0.29', {
+        'source_tmpl': 'namespace-autoclean-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'],
+        'checksums': ['45ebd8e64a54a86f88d8e01ae55212967c8aa8fed57e814085def7608ac65804'],
+    }),
+    ('Eval::Closure', '0.14', {
+        'source_tmpl': 'Eval-Closure-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/D/DO/DOY'],
+        'checksums': ['ea0944f2f5ec98d895bef6d503e6e4a376fea6383a6bc64c7670d46ff2218cad'],
+    }),
+    ('Exporter::Tiny', '1.006002', {
+        'source_tmpl': 'Exporter-Tiny-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TOBYINK'],
+        'checksums': ['6f295e2cbffb1dbc15bdb9dadc341671c1e0cd2bdf2d312b17526273c322638d'],
+    }),
+    ('Type::Tiny', '2.004000', {
+        'source_tmpl': 'Type-Tiny-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TOBYINK'],
+        'checksums': ['697e7f775edfc85f4cf07792d04fd19b09c25285f98f5938e8efc4f74507a128'],
+    }),
+    ('Class::Data::Inheritable', '0.09', {
+        'source_tmpl': 'Class-Data-Inheritable-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSHERER'],
+        'checksums': ['44088d6e90712e187b8a5b050ca5b1c70efe2baa32ae123e9bd8f59f29f06e4d'],
+    }),
+    ('Devel::StackTrace', '2.05', {
+        'source_tmpl': 'Devel-StackTrace-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'],
+        'checksums': ['63cb6196e986a7e578c4d28b3c780e7194835bfc78b68eeb8f00599d4444888c'],
+    }),
+    ('Exception::Class', '1.45', {
+        'source_tmpl': 'Exception-Class-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'],
+        'checksums': ['5482a77ef027ca1f9f39e1f48c558356e954936fc8fbbdee6c811c512701b249'],
+    }),
+    ('Role::Tiny', '2.002004', {
+        'source_tmpl': 'Role-Tiny-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'],
+        'checksums': ['d7bdee9e138a4f83aa52d0a981625644bda87ff16642dfa845dcb44d9a242b45'],
+    }),
+    ('MRO::Compat', '0.15', {
+        'source_tmpl': 'MRO-Compat-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'],
+        'checksums': ['0d4535f88e43babd84ab604866215fc4d04398bd4db7b21852d4a31b1c15ef61'],
+    }),
+    ('Sub::Quote', '2.006008', {
+        'source_tmpl': 'Sub-Quote-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'],
+        'checksums': ['94bebd500af55762e83ea2f2bc594d87af828072370c7110c60c238a800d15b2'],
+    }),
+    ('Specio', '0.48', {
+        'source_tmpl': 'Specio-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'],
+        'checksums': ['0c85793580f1274ef08173079131d101f77b22accea7afa8255202f0811682b2'],
+    }),
+    ('Test::Without::Module', '0.22', {
+        'source_tmpl': 'Test-Without-Module-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/C/CO/CORION'],
+        'checksums': ['27cde4394891028c7d8ecef22a2806308a3389597b70f6a9a421b4247e69052f'],
+    }),
+    ('Params::ValidationCompiler', '0.31', {
+        'source_tmpl': 'Params-ValidationCompiler-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'],
+        'checksums': ['7b6497173f1b6adb29f5d51d8cf9ec36d2f1219412b4b2410e9d77a901e84a6d'],
+    }),
+    ('DateTime::Locale', '1.42', {
+        'source_tmpl': 'DateTime-Locale-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'],
+        'checksums': ['7d8a138fa32faf24af30a1dbdee4dd11988ddb6a129138004d220b6cc4053cb0'],
+    }),
+    ('Class::Singleton', '1.6', {
+        'source_tmpl': 'Class-Singleton-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHAY'],
+        'checksums': ['27ba13f0d9512929166bbd8c9ef95d90d630fc80f0c9a1b7458891055e9282a4'],
+    }),
+    ('DateTime::TimeZone', '2.62', {
+        'source_tmpl': 'DateTime-TimeZone-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'],
+        'checksums': ['6214f9c9c8dfa2000bae912ef2b8ebc5b163a83a0b5b2a82705162dad63466fa'],
+    }),
+    ('Module::Build', '0.4234', {
+        'source_tmpl': 'Module-Build-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'],
+        'checksums': ['66aeac6127418be5e471ead3744648c766bd01482825c5b66652675f2bc86a8f'],
+    }),
+    ('Params::Validate', '1.31', {
+        'source_tmpl': 'Params-Validate-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'],
+        'checksums': ['1bf2518ef2c4869f91590e219f545c8ef12ed53cf313e0eb5704adf7f1b2961e'],
+    }),
+    ('List::MoreUtils::XS', '0.430', {
+        'source_tmpl': 'List-MoreUtils-XS-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'],
+        'checksums': ['e8ce46d57c179eecd8758293e9400ff300aaf20fefe0a9d15b9fe2302b9cb242'],
+    }),
+    ('List::MoreUtils', '0.430', {
+        'source_tmpl': 'List-MoreUtils-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'],
+        'checksums': ['63b1f7842cd42d9b538d1e34e0330de5ff1559e4c2737342506418276f646527'],
+    }),
+    ('DateTime', '1.65', {
+        'source_tmpl': 'DateTime-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'],
+        'checksums': ['0bfda7ff0253fb3d88cf4bdb5a14afb8cea24d147975d5bdf3c88b40e7ab140e'],
+    }),
+    ('Number::Compare', '0.03', {
+        'source_tmpl': 'Number-Compare-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/R/RC/RCLAMP'],
+        'checksums': ['83293737e803b43112830443fb5208ec5208a2e6ea512ed54ef8e4dd2b880827'],
+    }),
+    ('File::Find::Rule', '0.34', {
+        'source_tmpl': 'File-Find-Rule-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/R/RC/RCLAMP'],
+        'checksums': ['7e6f16cc33eb1f29ff25bee51d513f4b8a84947bbfa18edb2d3cc40a2d64cafe'],
+    }),
+    ('Params::Util', '1.102', {
+        'source_tmpl': 'Params-Util-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'],
+        'checksums': ['499bb1b482db24fda277a51525596ad092c2bd51dd508fa8fec2e9f849097402'],
+    }),
+    ('File::Find::Rule::Perl', '1.16', {
+        'source_tmpl': 'File-Find-Rule-Perl-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'],
+        'checksums': ['ae1886050d9ca21223c073e2870abdc80dc30e3f55289a11c37da3820a8321ff'],
+    }),
+    ('Readonly', '2.05', {
+        'source_tmpl': 'Readonly-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/S/SA/SANKO'],
+        'checksums': ['4b23542491af010d44a5c7c861244738acc74ababae6b8838d354dfb19462b5e'],
+    }),
+    ('Git', '0.42', {
+        'source_tmpl': 'Git-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/M/MS/MSOUTH'],
+        'checksums': ['9469a9f398f3a2bf2b0500566ee41d3ff6fae460412a137185767a1cc4783a6d'],
+    }),
+    ('File::Slurp::Tiny', '0.004', {
+        'source_tmpl': 'File-Slurp-Tiny-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'],
+        'checksums': ['452995beeabf0e923e65fdc627a725dbb12c9e10c00d8018c16d10ba62757f1e'],
+    }),
+    ('Tree::DAG_Node', '1.32', {
+        'source_tmpl': 'Tree-DAG_Node-%(version)s.tgz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'],
+        'checksums': ['22d9de3d6e6f4afd89e6d825c664f9482878bd49e29cb81342a707af40542d3d'],
+    }),
+    ('Template', '3.102', {
+        'source_tmpl': 'Template-Toolkit-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'],
+        'checksums': ['d161c89dee9b213a7c55709ea782e2dd5923dbd1215b9576612889e6e74a2e06'],
+    }),
+    ('DBI', '1.643', {
+        'pretestopts': "LC_ALL=C ",
+        'source_tmpl': 'DBI-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/T/TI/TIMB'],
+        'checksums': ['8a2b993db560a2c373c174ee976a51027dd780ec766ae17620c20393d2e836fa'],
+    }),
+    ('DBD::SQLite', '1.74', {
+        'source_tmpl': 'DBD-SQLite-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/I/IS/ISHIGAKI'],
+        'checksums': ['8994997d84b9feb4547795f78746c661fb72e3cb6a25dbdd789b731f5688a4dd'],
+    }),
+    ('Math::Bezier', '0.01', {
+        'source_tmpl': 'Math-Bezier-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/A/AB/ABW'],
+        'checksums': ['11a815fc45fdf0efabb1822ab77faad8b9eea162572c5f0940c8ed7d56e6b8b8'],
+    }),
+    ('Archive::Extract', '0.88', {
+        'source_tmpl': 'Archive-Extract-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'],
+        'checksums': ['cffcf135cd0622287d3b02154f7d6716495449fcaed03966621948e25ea5f742'],
+    }),
+    ('DBIx::Simple', '1.37', {
+        'source_tmpl': 'DBIx-Simple-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/J/JU/JUERD'],
+        'checksums': ['46d311aa2ce08907401c56119658426dbb044c5a40de73d9a7b79bf50390cae3'],
+    }),
+    ('Shell', '0.73', {
+        'source_tmpl': 'Shell-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/F/FE/FERREIRA'],
+        'checksums': ['f7dbebf65261ed0e5abd0f57052b64d665a1a830bab4c8bbc220f235bd39caf5'],
+    }),
+    ('Test::Simple', '1.302199', {
+        'source_tmpl': 'Test-Simple-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'],
+        'checksums': ['7b4b03cee7f9e928fe10e8a3efef02b2a286f0877979694b2a9ef99250bd8c5c'],
+    }),
+    ('Set::Scalar', '1.29', {
+        'source_tmpl': 'Set-Scalar-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAVIDO'],
+        'checksums': ['a3dc1526f3dde72d3c64ea00007b86ce608cdcd93567cf6e6e42dc10fdc4511d'],
+    }),
+    ('IO::Stringy', '2.113', {
+        'source_tmpl': 'IO-Stringy-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/C/CA/CAPOEIRAB'],
+        'checksums': ['51220fcaf9f66a639b69d251d7b0757bf4202f4f9debd45bdd341a6aca62fe4e'],
+    }),
+    ('Encode::Locale', '1.05', {
+        'source_tmpl': 'Encode-Locale-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'],
+        'checksums': ['176fa02771f542a4efb1dbc2a4c928e8f4391bf4078473bd6040d8f11adb0ec1'],
+    }),
+    ('XML::SAX::Base', '1.09', {
+        'source_tmpl': 'XML-SAX-Base-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/G/GR/GRANTM'],
+        'checksums': ['66cb355ba4ef47c10ca738bd35999723644386ac853abbeb5132841f5e8a2ad0'],
+    }),
+    ('XML::NamespaceSupport', '1.12', {
+        'source_tmpl': 'XML-NamespaceSupport-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PERIGRIN'],
+        'checksums': ['47e995859f8dd0413aa3f22d350c4a62da652e854267aa0586ae544ae2bae5ef'],
+    }),
+    ('XML::SAX', '1.02', {
+        'source_tmpl': 'XML-SAX-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/G/GR/GRANTM'],
+        'checksums': ['4506c387043aa6a77b455f00f57409f3720aa7e553495ab2535263b4ed1ea12a'],
+    }),
+    ('Test::LeakTrace', '0.17', {
+        'source_tmpl': 'Test-LeakTrace-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEEJO'],
+        'checksums': ['777d64d2938f5ea586300eef97ef03eacb43d4c1853c9c3b1091eb3311467970'],
+    }),
+    ('Sub::Uplevel', '0.2800', {
+        'source_tmpl': 'Sub-Uplevel-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'],
+        'checksums': ['b4f3f63b80f680a421332d8851ddbe5a8e72fcaa74d5d1d98f3c8cc4a3ece293'],
+    }),
+    ('Test::Exception', '0.43', {
+        'source_tmpl': 'Test-Exception-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'],
+        'checksums': ['156b13f07764f766d8b45a43728f2439af81a3512625438deab783b7883eb533'],
+    }),
+    ('Text::Aligner', '0.16', {
+        'source_tmpl': 'Text-Aligner-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'],
+        'checksums': ['5c857dbce586f57fa3d7c4ebd320023ab3b2963b2049428ae01bd3bc4f215725'],
+    }),
+    ('Text::Table', '1.135', {
+        'source_tmpl': 'Text-Table-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'],
+        'checksums': ['fca3c16e83127f7c44dde3d3f7e3c73ea50d109a1054445de8082fea794ca5d2'],
+    }),
+    ('MIME::Types', '2.26', {
+        'source_tmpl': 'MIME-Types-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV'],
+        'checksums': ['bc738483cb4cdb47d61e85fe9304fa929aa9ab927e3171ec2ba2ab1cd7cefdff'],
+    }),
+    ('Cwd::Guard', '0.05', {
+        'source_tmpl': 'Cwd-Guard-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/K/KA/KAZEBURO'],
+        'checksums': ['7afc7ca2b9502e440241938ad97a3e7ebd550180ebd6142e1db394186b268e77'],
+    }),
+    ('Capture::Tiny', '0.48', {
+        'source_tmpl': 'Capture-Tiny-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'],
+        'checksums': ['6c23113e87bad393308c90a207013e505f659274736638d8c79bac9c67cc3e19'],
+    }),
+    ('File::Copy::Recursive::Reduced', '0.008', {
+        'source_tmpl': 'File-Copy-Recursive-Reduced-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/J/JK/JKEENAN'],
+        'checksums': ['462bd66bf55e74b78f29ebdc9626af622d4f0115b5191b03167e82164db98f5a'],
+    }),
+    ('Module::Build::XSUtil', '0.19', {
+        'source_tmpl': 'Module-Build-XSUtil-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/H/HI/HIDEAKIO'],
+        'checksums': ['9063b3c346edeb422807ffe49ffb23038c4f900d4a77b845ce4b53d97bf29400'],
+    }),
+    ('Tie::Function', '0.02', {
+        'source_tmpl': 'Tie-Function-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAVIDNICO/handy_tied_functions'],
+        'checksums': ['0b1617af218dfab911ba0fbd72210529a246efe140332da77fe3e03d11000117'],
+    }),
+    ('Number::Format', '1.76', {
+        'source_tmpl': 'Number-Format-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'],
+        'checksums': ['0e0060eb363635a885706c6a26f5fcaafeae759f7b2acae49dda70e195dd44d6'],
+    }),
+    ('Template::Plugin::Number::Format', '1.06', {
+        'source_tmpl': 'Template-Plugin-Number-Format-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DARREN'],
+        'checksums': ['0865836a1bcbc34d4a0ee34b5ccc14d7b511f1fd300bf390f002dac349539843'],
+    }),
+    ('HTML::Tagset', '3.24', {
+        'source_tmpl': 'HTML-Tagset-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PETDANCE'],
+        'checksums': ['eb89e145a608ed1f8f141a57472ee5f69e67592a432dcd2e8b1dbb445f2b230b'],
+    }),
+    ('URI', '5.28', {
+        'source_tmpl': 'URI-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'],
+        'checksums': ['e7985da359b15efd00917fa720292b711c396f2f9f9a7349e4e7dec74aa79765'],
+    }),
+    ('B::COW', '0.007', {
+        'source_tmpl': 'B-COW-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/A/AT/ATOOMIC'],
+        'checksums': ['1290daf227e8b09889a31cf182e29106f1cf9f1a4e9bf7752f9de92ed1158b44'],
+    }),
+    ('Clone', '0.46', {
+        'source_tmpl': 'Clone-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GARU'],
+        'checksums': ['aadeed5e4c8bd6bbdf68c0dd0066cb513e16ab9e5b4382dc4a0aafd55890697b'],
+    }),
+    ('IO::HTML', '1.004', {
+        'source_tmpl': 'IO-HTML-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJM'],
+        'checksums': ['c87b2df59463bbf2c39596773dfb5c03bde0f7e1051af339f963f58c1cbd8bf5'],
+    }),
+    ('LWP::MediaTypes', '6.04', {
+        'source_tmpl': 'LWP-MediaTypes-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'],
+        'checksums': ['8f1bca12dab16a1c2a7c03a49c5e58cce41a6fec9519f0aadfba8dad997919d9'],
+    }),
+    ('HTTP::Message', '6.46', {
+        'source_tmpl': 'HTTP-Message-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'],
+        'checksums': ['e27443434150d2d1259bb1e5c964429f61559b0ae34b5713090481994936e2a5'],
+    }),
+    ('HTML::Parser', '3.82', {
+        'source_tmpl': 'HTML-Parser-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'],
+        'checksums': ['5b1f20dd0e471a049c13a53d0fcd0442f58518889180536c6f337112c9a430d8'],
+    }),
+    ('Date::Handler', '1.2', {
+        'source_tmpl': 'Date-Handler-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/B/BB/BBEAUSEJ'],
+        'checksums': ['c36fd2b68d48c2e17417bf2873c78820f3ae02460fdf5976b8eeab887d59e16c'],
+    }),
+    ('XML::Parser', '2.47', {
+        'source_tmpl': 'XML-Parser-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'],
+        'checksums': ['ad4aae643ec784f489b956abe952432871a622d4e2b5c619e8855accbfc4d1d8'],
+    }),
+    ('Data::Grove', '0.08', {
+        'source_tmpl': 'libxml-perl-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/K/KM/KMACLEOD'],
+        'checksums': ['4571059b7b5d48b7ce52b01389e95d798bf5cf2020523c153ff27b498153c9cb'],
+    }),
+    ('Class::ISA', '0.36', {
+        'source_tmpl': 'Class-ISA-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/S/SM/SMUELLER'],
+        'checksums': ['8816f34e9a38e849a10df756030dccf9fe061a196c11ac3faafd7113c929b964'],
+    }),
+    ('DBIx::ContextualFetch', '1.03', {
+        'source_tmpl': 'DBIx-ContextualFetch-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/T/TM/TMTM'],
+        'checksums': ['85e2f805bfc81cd738c294316b27a515397036f397a0ff1c6c8d754c38530306'],
+    }),
+    ('Ima::DBI', '0.35', {
+        'source_tmpl': 'Ima-DBI-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PERRIN'],
+        'checksums': ['8b481ceedbf0ae4a83effb80581550008bfdd3885ef01145e3733c7097c00a08'],
+    }),
+    ('Tie::IxHash', '1.23', {
+        'source_tmpl': 'Tie-IxHash-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/C/CH/CHORNY'],
+        'checksums': ['fabb0b8c97e67c9b34b6cc18ed66f6c5e01c55b257dcf007555e0b027d4caf56'],
+    }),
+    ('Parse::RecDescent', '1.967015', {
+        'source_tmpl': 'Parse-RecDescent-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/J/JT/JTBRAUN'],
+        'checksums': ['1943336a4cb54f1788a733f0827c0c55db4310d5eae15e542639c9dd85656e37'],
+    }),
+    ('GO', '0.04', {
+        'runtest': False,
+        'source_tmpl': 'go-db-perl-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/S/SJ/SJCARBON'],
+        'checksums': ['8eb73d591ad767e7cf26def40cffd84833875f1ad51e456960b9ed73dc23641b'],
+    }),
+    ('Class::Trigger', '0.15', {
+        'source_tmpl': 'Class-Trigger-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA'],
+        'checksums': ['b7a878d44dea67d64df2ca18020d9d868a95596debd16f1a264874209332b07f'],
+    }),
+    ('Class::Accessor', '0.51', {
+        'source_tmpl': 'Class-Accessor-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/K/KA/KASEI'],
+        'checksums': ['bf12a3e5de5a2c6e8a447b364f4f5a050bf74624c56e315022ae7992ff2f411c'],
+    }),
+    ('UNIVERSAL::moniker', '0.08', {
+        'source_tmpl': 'UNIVERSAL-moniker-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/K/KA/KASEI'],
+        'checksums': ['94ce27a546cd57cb52e080a8f2533a7cc2350028388582485bd1039a37871f9c'],
+    }),
+    ('Class::DBI', 'v3.0.17', {
+        'source_tmpl': 'Class-DBI-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/T/TM/TMTM'],
+        'checksums': ['541354fe361c56850cb11261f6ca089a14573fa764792447444ff736ae626206'],
+    }),
+    ('Class::DBI::SQLite', '0.11', {
+        'source_tmpl': 'Class-DBI-SQLite-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA'],
+        'checksums': ['c4661b00afb7e53c97ac36e13f34dde43c1a93540a2f4ff97e6182b0c731e4e7'],
+    }),
+    ('File::Slurper', '0.014', {
+        'source_tmpl': 'File-Slurper-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'],
+        'checksums': ['d5a36487339888c3cd758e648160ee1d70eb4153cacbaff57846dbcefb344b0c'],
+    }),
+    ('Pod::POM', '2.01', {
+        'source_tmpl': 'Pod-POM-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'],
+        'checksums': ['1b50fba9bbdde3ead192beeba0eaddd0c614e3afb1743fa6fff805f57c56f7f4'],
+    }),
+    ('Math::Round', '0.08', {
+        'source_tmpl': 'Math-Round-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'],
+        'checksums': ['7b4d2775ad3b859a5fd61f7f3fc5cfba42b1a10df086d2ed15a0ae712c8fd402'],
+    }),
+    ('Algorithm::Diff', '1.201', {
+        'source_tmpl': 'Algorithm-Diff-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'],
+        'checksums': ['0022da5982645d9ef0207f3eb9ef63e70e9713ed2340ed7b3850779b0d842a7d'],
+    }),
+    ('Text::Diff', '1.45', {
+        'source_tmpl': 'Text-Diff-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'],
+        'checksums': ['e8baa07b1b3f53e00af3636898bbf73aec9a0ff38f94536ede1dbe96ef086f04'],
+    }),
+    ('Log::Message', '0.08', {
+        'source_tmpl': 'Log-Message-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'],
+        'checksums': ['bd697dd62aaf26d118e9f0a0813429deb1c544e4501559879b61fcbdfe99fe46'],
+    }),
+    ('Log::Message::Simple', '0.10', {
+        'source_tmpl': 'Log-Message-Simple-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'],
+        'checksums': ['aa12d1a4c0ac260b94d448fa01feba242a8a85cb6cbfdc66432e3b5b468add96'],
+    }),
+    ('Net::SSLeay', '1.94', {
+        'patches': ['Net-SSLeay-1.92_fix.patch'],
+        'preconfigopts': "export OPENSSL_PREFIX=$EBROOTOPENSSL && ",
+        'source_tmpl': 'Net-SSLeay-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/C/CH/CHRISN'],
+        'checksums': [
+            {'Net-SSLeay-1.94.tar.gz': '9d7be8a56d1bedda05c425306cc504ba134307e0c09bda4a788c98744ebcd95d'},
+            {'Net-SSLeay-1.92_fix.patch': '37790b10c5551bce92bc4bd7c98a92b0058fc16604272c7459a63096b52a8d1c'},
+        ],
+    }),
+    ('IO::Socket::SSL', '2.087', {
+        'source_tmpl': 'IO-Socket-SSL-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/S/SU/SULLR'],
+        'checksums': ['936a46c58312df272313fedb4bb39faea7481629c163d83a8cdd283a0e28c578'],
+    }),
+    ('Fennec::Lite', '0.004', {
+        'source_tmpl': 'Fennec-Lite-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'],
+        'checksums': ['dce28e3932762c2ff92aa52d90405c06e898e81cb7b164ccae8966ae77f1dcab'],
+    }),
+    ('Meta::Builder', '0.004', {
+        'source_tmpl': 'Meta-Builder-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'],
+        'checksums': ['acb499aa7206eb9db21eb85357a74521bfe3bdae4a6416d50a7c75b939cf56fe'],
+    }),
+    ('Exporter::Declare', '0.114', {
+        'source_tmpl': 'Exporter-Declare-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'],
+        'checksums': ['4bd70d6ca76f6f6ba7e4c618d4ac93b8593a58f1233ccbe18b10f5f204f1d4e4'],
+    }),
+    ('Mouse', 'v2.5.10', {
+        'source_tmpl': 'Mouse-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/S/SK/SKAJI'],
+        'checksums': ['ce8dc23946153a467ff09765167ee2590f5c502120f48a2d9441733f39aa32ee'],
+    }),
+    ('Test::Version', '2.09', {
+        'source_tmpl': 'Test-Version-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'],
+        'checksums': ['9ce1dd2897a5f30e1b7f8966ec66f57d8d8f280f605f28c7ca221fa79aca38e0'],
+    }),
+    ('Class::Method::Modifiers', '2.15', {
+        'source_tmpl': 'Class-Method-Modifiers-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'],
+        'checksums': ['65cd85bfe475d066e9186f7a8cc636070985b30b0ebb1cde8681cf062c2e15fc'],
+    }),
+    ('Moo', '2.005005', {
+        'source_tmpl': 'Moo-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'],
+        'checksums': ['fb5a2952649faed07373f220b78004a9c6aba387739133740c1770e9b1f4b108'],
+    }),
+    ('Data::Dumper::Concise', '2.023', {
+        'source_tmpl': 'Data-Dumper-Concise-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'],
+        'checksums': ['a6c22f113caf31137590def1b7028a7e718eface3228272d0672c25e035d5853'],
+    }),
+    ('DBIx::Admin::CreateTable', '2.11', {
+        'source_tmpl': 'DBIx-Admin-CreateTable-%(version)s.tgz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'],
+        'checksums': ['07b1427fbc15455657ca57217749004162a50c04abb243022a5b479e4b2a5912'],
+    }),
+    ('Config::Tiny', '2.30', {
+        'source_tmpl': 'Config-Tiny-%(version)s.tgz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'],
+        'checksums': ['b2f7345619b3b8e636dd39ea010731c9dc2bfb8f022bcbd86ae6ad17866e110d'],
+    }),
+    ('File::Slurp', '9999.32', {
+        'source_tmpl': 'File-Slurp-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/C/CA/CAPOEIRAB'],
+        'checksums': ['4c3c21992a9d42be3a79dd74a3c83d27d38057269d65509a2f555ea0fb2bc5b0'],
+    }),
+    ('DBIx::Admin::DSNManager', '2.02', {
+        'source_tmpl': 'DBIx-Admin-DSNManager-%(version)s.tgz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'],
+        'checksums': ['c25511f42328ccb606a0cd78413a74181c87fb37a382d38aa3fad106b540adcb'],
+    }),
+    ('Lingua::EN::PluralToSingular', '0.21', {
+        'source_tmpl': 'Lingua-EN-PluralToSingular-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/B/BK/BKB'],
+        'checksums': ['f8a8b7de28c25c96190d7f48c90b5ad9b9bf517f3835c77641f0e8fa546c0d1d'],
+    }),
+    ('Test::Warn', '0.37', {
+        'source_tmpl': 'Test-Warn-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BIGJ'],
+        'checksums': ['98ca32e7f2f5ea89b8bfb9a0609977f3d153e242e2e51705126cb954f1a06b57'],
+    }),
+    ('Test::Differences', '0.71', {
+        'runtest': False,
+        'source_tmpl': 'Test-Differences-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/D/DC/DCANTRELL'],
+        'checksums': ['cac16a56cd843b0809e5b49199d60d75a8dbad7ca9a08380dbf3f5cc3aaa38d9'],
+    }),
+    ('Test::Most', '0.38', {
+        'source_tmpl': 'Test-Most-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/O/OV/OVID'],
+        'checksums': ['089eb894f7bace4c37c6334e0e290eb20338ee10223af0c82cbe7281c78382df'],
+    }),
+    ('Const::Fast', '0.014', {
+        'source_tmpl': 'Const-Fast-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'],
+        'checksums': ['f805953a08c57846a16a4d85d7b766398afaf7c36c1465fcb1dea09e5fa394db'],
+    }),
+    ('Ref::Util', '0.204', {
+        'source_tmpl': 'Ref-Util-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/A/AR/ARC'],
+        'checksums': ['415fa73dbacf44f3d5d79c14888cc994562720ab468e6f71f91cd1f769f105e1'],
+    }),
+    ('Class::XSAccessor', '1.19', {
+        'source_tmpl': 'Class-XSAccessor-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/S/SM/SMUELLER'],
+        'checksums': ['99c56b395f1239af19901f2feeb125d9ecb4e351a0d80daa9529211a4700a6f2'],
+    }),
+    ('Hash::Objectify', '0.008', {
+        'source_tmpl': 'Hash-Objectify-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'],
+        'checksums': ['236d5829cdebf3ba648d34e1295cd9099a20506d8d0284668e617e0058cebeed'],
+    }),
+    ('Const::Exporter', 'v1.2.3', {
+        'source_tmpl': 'Const-Exporter-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/R/RR/RRWO'],
+        'checksums': ['53e59b4764aebcf79bbed533ab5a6107339fe516b7f2f607b1bae8dd9dcf7015'],
+    }),
+    ('HTML::Entities::Interpolate', '1.10', {
+        'source_tmpl': 'HTML-Entities-Interpolate-%(version)s.tgz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'],
+        'checksums': ['f15a9df92c282419f7010964aca1ada844ddfae7afc735cd2ba1bb20883e955c'],
+    }),
+    ('List::SomeUtils', '0.59', {
+        'source_tmpl': 'List-SomeUtils-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'],
+        'checksums': ['fab30372e4c67bf5a46062da38d1d0c8756279feada866eb439fa29571a2dc7b'],
+    }),
+    ('List::UtilsBy', '0.12', {
+        'source_tmpl': 'List-UtilsBy-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PEVANS'],
+        'checksums': ['fff1281fd469fe982b1a58044becfd970f313bff3a26e1c7b2b3f4c0a5ed71e0'],
+    }),
+    ('List::AllUtils', '0.19', {
+        'source_tmpl': 'List-AllUtils-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'],
+        'checksums': ['30a8146ab21a7787b8c56d5829cf9a7f2b15276d3b3fca07336ac38d3002ffbc'],
+    }),
+    ('Unicode::EastAsianWidth', '12.0', {
+        'source_tmpl': 'Unicode-EastAsianWidth-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/A/AU/AUDREYT'],
+        'checksums': ['2a5bfd926c4fe5f77e6137da2c31ac2545282ae5fec6e9af0fdd403555a90ff4'],
+    }),
+    ('String::TtyLength', '0.03', {
+        'source_tmpl': 'String-TtyLength-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'],
+        'checksums': ['4fedaf72028511d80eb6afba523993e9aaa245d7af558345d5d4ed46e2e82ce1'],
+    }),
+    ('Text::Table::Manifold', '1.03', {
+        'source_tmpl': 'Text-Table-Manifold-%(version)s.tgz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'],
+        'checksums': ['e680713169557b0768952fa6932f25576a61dccfb96bd9036dcf6fcefb35e09e'],
+    }),
+    ('DBIx::Admin::TableInfo', '3.04', {
+        'source_tmpl': 'DBIx-Admin-TableInfo-%(version)s.tgz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'],
+        'checksums': ['b9625992683b97378bea0947773f50e3c9f81974048b84f4c3422cae7e6082f4'],
+    }),
+    ('Net::HTTP', '6.23', {
+        'runtest': False,
+        'source_tmpl': 'Net-HTTP-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'],
+        'checksums': ['0d65c09dd6c8589b2ae1118174d3c1a61703b6ecfc14a3442a8c74af65e0c94e'],
+    }),
+    ('Clone::Choose', '0.010', {
+        'source_tmpl': 'Clone-Choose-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/H/HE/HERMES'],
+        'checksums': ['5623481f58cee8edb96cd202aad0df5622d427e5f748b253851dfd62e5123632'],
+    }),
+    ('Hash::Merge', '0.302', {
+        'source_tmpl': 'Hash-Merge-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/H/HE/HERMES'],
+        'checksums': ['ae0522f76539608b61dde14670e79677e0f391036832f70a21f31adde2538644'],
+    }),
+    ('SQL::Abstract', '2.000001', {
+        'source_tmpl': 'SQL-Abstract-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/M/MS/MSTROUT'],
+        'checksums': ['35a642662c349420d44be6e0ef7d8765ea743eb12ad14399aa3a232bb94e6e9a'],
+    }),
+    ('HTML::Form', '6.11', {
+        'source_tmpl': 'HTML-Form-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/S/SI/SIMBABQUE'],
+        'checksums': ['43bfaa7087393487d2d51261a1aa7f6f81a97b1d8fef7a48fcf6ef32b16d6454'],
+    }),
+    ('IPC::Run', '20231003.0', {
+        'source_tmpl': 'IPC-Run-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'],
+        'checksums': ['eb25bbdf5913d291797ef1bfe998f15130b455d3ed02aacde6856f0b25e4fe57'],
+    }),
+    ('File::Remove', '1.61', {
+        'source_tmpl': 'File-Remove-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'],
+        'checksums': ['fd857f585908fc503461b9e48b3c8594e6535766bc14beb17c90ba58d5dc4975'],
+    }),
+    ('YAML::Tiny', '1.74', {
+        'source_tmpl': 'YAML-Tiny-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'],
+        'checksums': ['7b38ca9f5d3ce24230a6b8bdc1f47f5b2db348e7f7f9666c26f5955636e33d6c'],
+    }),
+    ('Module::Install', '1.21', {
+        'source_tmpl': 'Module-Install-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'],
+        'checksums': ['fbf91007f30565f3920e106055fd0d4287981d5e7dad8b35323ce4b733f15a7b'],
+    }),
+    ('Test::ClassAPI', '1.07', {
+        'source_tmpl': 'Test-ClassAPI-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'],
+        'checksums': ['30e9dbfc5e0cc2ee14eae8f3465a908a710daecbd0a3ebdb2888fc4504fa18aa'],
+    }),
+    ('HTTP::Tiny', '0.088', {
+        'source_tmpl': 'HTTP-Tiny-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'],
+        'checksums': ['7ce6367e861883b6868d6dd86168af33524717d8cc94100c2abf9bd86a82b4d8'],
+    }),
+    ('Sub::Install', '0.929', {
+        'source_tmpl': 'Sub-Install-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'],
+        'checksums': ['80b1e281d8cd3b2b31dac711f5c8a1657a87cd80bbe69af3924bcbeb4e5db077'],
+    }),
+    ('Package::DeprecationManager', '0.18', {
+        'source_tmpl': 'Package-DeprecationManager-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'],
+        'checksums': ['b68d3f0ced55b7615fddbb6029b89f92a34fe0dd8c6fd6bceffc157d56834fe8'],
+    }),
+    ('Digest::SHA1', '2.13', {
+        'source_tmpl': 'Digest-SHA1-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'],
+        'checksums': ['68c1dac2187421f0eb7abf71452a06f190181b8fc4b28ededf5b90296fb943cc'],
+    }),
+    ('Date::Language', '2.33', {
+        'source_tmpl': 'TimeDate-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/A/AT/ATOOMIC'],
+        'checksums': ['c0b69c4b039de6f501b0d9f13ec58c86b040c1f7e9b27ef249651c143d605eb2'],
+    }),
+    ('version', '0.9932', {
+        'source_tmpl': 'version-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'],
+        'checksums': ['e7b5e8fcb8dfd1d6147b931a382e9dc377b3485ade18bea342dad11226be6f7f'],
+    }),
+    ('XML::Bare', '0.53', {
+        'source_tmpl': 'XML-Bare-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/C/CO/CODECHILD'],
+        'checksums': ['865e198e98d904be1683ef5a53a4948f02dabdacde59fc554a082ffbcc5baefd'],
+    }),
+    ('Dist::CheckConflicts', '0.11', {
+        'source_tmpl': 'Dist-CheckConflicts-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/D/DO/DOY'],
+        'checksums': ['ea844b9686c94d666d9d444321d764490b2cde2f985c4165b4c2c77665caedc4'],
+    }),
+    ('Sub::Name', '0.27', {
+        'source_tmpl': 'Sub-Name-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'],
+        'checksums': ['ecf36fba1c47ca93e1daa394968ed39c4186867459d9cd173c421e2b972043e8'],
+    }),
+    ('Time::Piece', '1.3401', {
+        'source_tmpl': 'Time-Piece-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/E/ES/ESAYM'],
+        'checksums': ['4b55b7bb0eab45cf239a54dfead277dfa06121a43e63b3fce0853aecfdb04c27'],
+    }),
+    ('Digest::HMAC', '1.04', {
+        'source_tmpl': 'Digest-HMAC-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/A/AR/ARODLAND'],
+        'checksums': ['d6bc8156aa275c44d794b7c18f44cdac4a58140245c959e6b19b2c3838b08ed4'],
+    }),
+    ('HTTP::Negotiate', '6.01', {
+        'source_tmpl': 'HTTP-Negotiate-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'],
+        'checksums': ['1c729c1ea63100e878405cda7d66f9adfd3ed4f1d6cacaca0ee9152df728e016'],
+    }),
+    ('Email::Date::Format', '1.008', {
+        'source_tmpl': 'Email-Date-Format-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'],
+        'checksums': ['432b7c83ff88749af128003f5257c573aec1a463418db90ed22843cbbc258b4f'],
+    }),
+    ('MIME::Lite', '3.033', {
+        'source_tmpl': 'MIME-Lite-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'],
+        'checksums': ['78a279f1d2e242551c347ef97a13fc675766602cb84c2a80c569400f4f368bab'],
+    }),
+    ('Crypt::Rijndael', '1.16', {
+        'source_tmpl': 'Crypt-Rijndael-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'],
+        'checksums': ['6540085e3804b82a6f0752c1122cf78cadd221990136dd6fd4c097d056c84d40'],
+    }),
+    ('B::Lint', '1.20', {
+        'runtest': False,
+        'source_tmpl': 'B-Lint-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'],
+        'checksums': ['dc49408964fd8b7963859c92e013f0b9f92f74be5a7c2a78e3996279827c10b3'],
+    }),
+    ('Canary::Stability', '2013', {
+        'source_tmpl': 'Canary-Stability-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'],
+        'checksums': ['a5c91c62cf95fcb868f60eab5c832908f6905221013fea2bce3ff57046d7b6ea'],
+    }),
+    ('AnyEvent', '7.17', {
+        'source_tmpl': 'AnyEvent-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'],
+        'checksums': ['50beea689c098fe4aaeb83806c40b9fe7f946d5769acf99f849f099091a4b985'],
+    }),
+    ('Object::Accessor', '0.48', {
+        'source_tmpl': 'Object-Accessor-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'],
+        'checksums': ['76cb824a27b6b4e560409fcf6fd5b3bfbbd38b72f1f3d37ed0b54bd9c0baeade'],
+    }),
+    ('Data::UUID', '1.227', {
+        'source_tmpl': 'Data-UUID-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/G/GT/GTERMARS'],
+        'checksums': ['95bda7276265f57bc48ffdeddec5ef28cd6f765e3a183757fa5f09f0ce6b98ac'],
+    }),
+    ('Test::Pod', '1.52', {
+        'source_tmpl': 'Test-Pod-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'],
+        'checksums': ['60a8dbcc60168bf1daa5cc2350236df9343e9878f4ab9830970a5dde6fe8e5fc'],
+    }),
+    ('AppConfig', '1.71', {
+        'source_tmpl': 'AppConfig-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'],
+        'checksums': ['1177027025ecb09ee64d9f9f255615c04db5e14f7536c344af632032eb887b0f'],
+    }),
+    ('Net::SMTP::SSL', '1.04', {
+        'source_tmpl': 'Net-SMTP-SSL-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'],
+        'checksums': ['7b29c45add19d3d5084b751f7ba89a8e40479a446ce21cfd9cc741e558332a00'],
+    }),
+    ('XML::Tiny', '2.07', {
+        'source_tmpl': 'XML-Tiny-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/D/DC/DCANTRELL'],
+        'checksums': ['ce39fcb53e0fe9f1cbcd86ddf152e1db48566266b70ec0769ef364eeabdd8941'],
+    }),
+    ('HTML::Tree', '5.07', {
+        'source_tmpl': 'HTML-Tree-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/K/KE/KENTNL'],
+        'checksums': ['f0374db84731c204b86c1d5b90975fef0d30a86bd9def919343e554e31a9dbbf'],
+    }),
+    ('Devel::GlobalDestruction', '0.14', {
+        'source_tmpl': 'Devel-GlobalDestruction-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'],
+        'checksums': ['34b8a5f29991311468fe6913cadaba75fd5d2b0b3ee3bb41fe5b53efab9154ab'],
+    }),
+    ('WWW::RobotRules', '6.02', {
+        'source_tmpl': 'WWW-RobotRules-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'],
+        'checksums': ['46b502e7a288d559429891eeb5d979461dd3ecc6a5c491ead85d165b6e03a51e'],
+    }),
+    ('IO::Tty', '1.20', {
+        'source_tmpl': 'IO-Tty-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'],
+        'checksums': ['b15309fc85623893289cb9b2b88dfa9ed1e69156b75f29938553a45be6d730af'],
+    }),
+    ('Expect', '1.38', {
+        'source_tmpl': 'Expect-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/J/JA/JACOBY'],
+        'checksums': ['7b1048335f327958903867cea079dc072ea07f4eafae1b40c2e6f25db21686c0'],
+    }),
+    ('Term::UI', '0.50', {
+        'source_tmpl': 'Term-UI-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'],
+        'checksums': ['60bfdd6d4c158b88d370133fc65b20485a36a45b12d906000b81c78ca524163d'],
+    }),
+    ('Net::SNMP', 'v6.0.1', {
+        'source_tmpl': 'Net-SNMP-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/D/DT/DTOWN'],
+        'checksums': ['14c37bc1cbb3f3cdc7d6c13e0f27a859f14cdcfd5ea54a0467a88bc259b0b741'],
+    }),
+    ('XML::Filter::BufferText', '1.01', {
+        'source_tmpl': 'XML-Filter-BufferText-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/R/RB/RBERJON'],
+        'checksums': ['8fd2126d3beec554df852919f4739e689202cbba6a17506e9b66ea165841a75c'],
+    }),
+    ('XML::SAX::Writer', '0.57', {
+        'source_tmpl': 'XML-SAX-Writer-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PERIGRIN'],
+        'checksums': ['3d61d07ef43b0126f5b4de4f415a256fa859fa88dc4fdabaad70b7be7c682cf0'],
+    }),
+    ('Statistics::Descriptive', '3.0801', {
+        'source_tmpl': 'Statistics-Descriptive-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'],
+        'checksums': ['047b70a63fdcaa916168e0ff2d58e155e0ebbc68ed4ccbd73a7213dca3028f65'],
+    }),
+    ('Data::OptList', '0.114', {
+        'source_tmpl': 'Data-OptList-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'],
+        'checksums': ['9fd1093b917a21fb79ae1607db53d113b4e0ad8fe0ae776cb077a7e50044fdf3'],
+    }),
+    ('Class::Load', '0.25', {
+        'source_tmpl': 'Class-Load-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'],
+        'checksums': ['2a48fa779b5297e56156380e8b32637c6c58decb4f4a7f3c7350523e11275f8f'],
+    }),
+    ('HTTP::Daemon', '6.16', {
+        'source_tmpl': 'HTTP-Daemon-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'],
+        'checksums': ['b38d092725e6fa4e0c4dc2a47e157070491bafa0dbe16c78a358e806aa7e173d'],
+    }),
+    ('Test::RequiresInternet', '0.05', {
+        'source_tmpl': 'Test-RequiresInternet-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MALLEN'],
+        'checksums': ['bba7b32a1cc0d58ce2ec20b200a7347c69631641e8cae8ff4567ad24ef1e833e'],
+    }),
+    ('HTTP::Cookies', '6.11', {
+        'source_tmpl': 'HTTP-Cookies-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'],
+        'checksums': ['8c9a541a4a39f6c0c7e3d0b700b05dfdb830bd490a1b1942a7dedd1b50d9a8c8'],
+    }),
+    ('HTTP::CookieJar', '0.014', {
+        'source_tmpl': 'HTTP-CookieJar-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'],
+        'checksums': ['7094ea5c91f536d263b85e83ab4e9a963e11c4408ce08ecae553fa9c0cc47e73'],
+    }),
+    ('LWP::Simple', '6.77', {
+        'source_tmpl': 'libwww-perl-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'],
+        'checksums': ['94a907d6b3ea8d966ef43deffd4fa31f5500142b4c00489bfd403860a5f060e4'],
+    }),
+    ('Time::Piece::MySQL', '0.06', {
+        'source_tmpl': 'Time-Piece-MySQL-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/K/KA/KASEI'],
+        'checksums': ['319601feec17fae344988a5ee91cfc6a0bcfe742af77dba254724c3268b2a60f'],
+    }),
+    ('Package::Stash::XS', '0.30', {
+        'source_tmpl': 'Package-Stash-XS-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'],
+        'checksums': ['26bad65c1959c57379b3e139dc776fbec5f702906617ef27cdc293ddf1239231'],
+    }),
+    ('Want', '0.29', {
+        'source_tmpl': 'Want-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/R/RO/ROBIN'],
+        'checksums': ['b4e4740b8d4cb783591273c636bd68304892e28d89e88abf9273b1de17f552f7'],
+    }),
+    ('Set::Array', '0.30', {
+        'source_tmpl': 'Set-Array-%(version)s.tgz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'],
+        'checksums': ['d9f024c8e3637feccdebcf6479b6754b6c92f1209f567feaf0c23818af31ee3c'],
+    }),
+    ('boolean', '0.46', {
+        'source_tmpl': 'boolean-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/I/IN/INGY'],
+        'checksums': ['95c088085c3e83bf680fe6ce16d8264ec26310490f7d1680e416ea7a118f156a'],
+    }),
+    ('Test::NoWarnings', '1.06', {
+        'source_tmpl': 'Test-NoWarnings-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'],
+        'checksums': ['c2dc51143b7eb63231210e27df20d2c8393772e0a333547ec8b7a205ed62f737'],
+    }),
+    ('Crypt::DES', '2.07', {
+        'source_tmpl': 'Crypt-DES-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/D/DP/DPARIS'],
+        'checksums': ['2db1ebb5837b4cb20051c0ee5b733b4453e3137df0a92306034c867621edd7e7'],
+    }),
+    ('XML::XPath', '1.48', {
+        'source_tmpl': 'XML-XPath-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MANWAR'],
+        'checksums': ['7bc75be36b239e5b2e700a9570d2b53b43093d467f2abe6a743f9ff9093790cd'],
+    }),
+    ('JSON', '4.10', {
+        'source_tmpl': 'JSON-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/I/IS/ISHIGAKI'],
+        'checksums': ['df8b5143d9a7de99c47b55f1a170bd1f69f711935c186a6dc0ab56dd05758e35'],
+    }),
+    ('Sub::Exporter', '0.991', {
+        'source_tmpl': 'Sub-Exporter-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'],
+        'checksums': ['2a95695d35c5d0d5373a7e145c96b9b016113b74e94116835ac05450cae4d445'],
+    }),
+    ('Class::Load::XS', '0.10', {
+        'source_tmpl': 'Class-Load-XS-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'],
+        'checksums': ['5bc22cf536ebfd2564c5bdaf42f0d8a4cee3d1930fc8b44b7d4a42038622add1'],
+    }),
+    ('Data::Types', '0.17', {
+        'source_tmpl': 'Data-Types-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MANWAR'],
+        'checksums': ['860751feb79b7dfc1af71c4b7fe920220ec6d31c4ab9402b8f178f7f4b8293c1'],
+    }),
+    ('Set::IntSpan::Fast', '1.15', {
+        'source_tmpl': 'Set-IntSpan-Fast-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/A/AN/ANDYA'],
+        'checksums': ['cfb1768c24f55208e87405b17f537f0f303fa141891d0b22d509a941aa57e24e'],
+    }),
+    ('Text::Iconv', '1.7', {
+        'source_tmpl': 'Text-Iconv-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/M/MP/MPIOTR'],
+        'checksums': ['5b80b7d5e709d34393bcba88971864a17b44a5bf0f9e4bcee383d029e7d2d5c3'],
+    }),
+    ('Text::Balanced', '2.06', {
+        'source_tmpl': 'Text-Balanced-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHAY'],
+        'checksums': ['773e0f0f21c0cb2cf664cee6ba28ff70259babcc892f9b650f9cbda00be092ad'],
+    }),
+    ('strictures', '2.000006', {
+        'source_tmpl': 'strictures-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'],
+        'checksums': ['09d57974a6d1b2380c802870fed471108f51170da81458e2751859f2714f8d57'],
+    }),
+    ('Switch', '2.17', {
+        'source_tmpl': 'Switch-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/C/CH/CHORNY'],
+        'checksums': ['31354975140fe6235ac130a109496491ad33dd42f9c62189e23f49f75f936d75'],
+    }),
+    ('File::Which', '1.27', {
+        'source_tmpl': 'File-Which-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'],
+        'checksums': ['3201f1a60e3f16484082e6045c896842261fc345de9fb2e620fd2a2c7af3a93a'],
+    }),
+    ('Error', '0.17029', {
+        'source_tmpl': 'Error-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'],
+        'checksums': ['1a23f7913032aed6d4b68321373a3899ca66590f4727391a091ec19c95bf7adc'],
+    }),
+    ('Mock::Quick', '1.111', {
+        'source_tmpl': 'Mock-Quick-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'],
+        'checksums': ['ff786008bf8c022064ececd3b7ed89c76b35e8d1eac6cf472a9f51771c1c9f2c'],
+    }),
+    ('Text::CSV', '2.04', {
+        'source_tmpl': 'Text-CSV-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/I/IS/ISHIGAKI'],
+        'checksums': ['4f80122e4ea0b05079cad493e386564030f18c8d7b1f9af561df86985a653fe3'],
+    }),
+    ('Test::Output', '1.034', {
+        'source_tmpl': 'Test-Output-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/B/BD/BDFOY'],
+        'checksums': ['cd42e2801c0d2b482d18c9fb4b06c757054818bcbb2824e5dfbf33ad7a3d69a0'],
+    }),
+    ('File::CheckTree', '4.42', {
+        'source_tmpl': 'File-CheckTree-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'],
+        'checksums': ['66fb417f8ff8a5e5b7ea25606156e70e204861c59fa8c3831925b4dd3f155f8a'],
+    }),
+    ('Math::VecStat', '0.08', {
+        'source_tmpl': 'Math-VecStat-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/A/AS/ASPINELLI'],
+        'checksums': ['409a8e0e4b1025c8e80f628f65a9778aa77ab285161406ca4a6c097b13656d0d'],
+    }),
+    ('Pod::Parser', '1.67', {
+        'configopts': 'INSTALLDIRS=site',
+        'source_tmpl': 'Pod-Parser-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MAREKR'],
+        'checksums': ['5deccbf55d750ce65588cd211c1a03fa1ef3aaa15d1ac2b8d85383a42c1427ea'],
+    }),
+    ('Pod::LaTeX', '0.61', {
+        'source_tmpl': 'Pod-LaTeX-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/T/TJ/TJENNESS'],
+        'checksums': ['15a840ea1c8a76cd3c865fbbf2fec33b03615c0daa50f9c800c54e0cf0659d46'],
+    }),
+    ('XML::Twig', '3.52', {
+        'source_tmpl': 'XML-Twig-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIROD'],
+        'checksums': ['fef75826c24f2b877d0a0d2645212fc4fb9756ed4d2711614ac15c497e8680ad'],
+    }),
+    ('XML::Simple', '2.25', {
+        'source_tmpl': 'XML-Simple-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/G/GR/GRANTM'],
+        'checksums': ['531fddaebea2416743eb5c4fdfab028f502123d9a220405a4100e68fc480dbf8'],
+    }),
+    ('Pod::Plainer', '1.04', {
+        'source_tmpl': 'Pod-Plainer-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/R/RM/RMBARKER'],
+        'checksums': ['1bbfbf7d1d4871e5a83bab2137e22d089078206815190eb1d5c1260a3499456f'],
+    }),
+    ('Data::Section::Simple', '0.07', {
+        'source_tmpl': 'Data-Section-Simple-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA'],
+        'checksums': ['0b3035ffdb909aa1f7ded6b608fa9d894421c82c097d51e7171170d67579a9cb'],
+    }),
+    ('File::HomeDir', '1.006', {
+        'source_tmpl': 'File-HomeDir-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'],
+        'checksums': ['593737c62df0f6dab5d4122e0b4476417945bb6262c33eedc009665ef1548852'],
+    }),
+    ('Authen::SASL', '2.1700', {
+        'source_tmpl': 'Authen-SASL-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/E/EH/EHUELS'],
+        'checksums': ['b86d5a576b8d387aee24f39f47a54afd14bb66b09003db5065001f1de03a8ece'],
+    }),
+    ('Import::Into', '1.002005', {
+        'source_tmpl': 'Import-Into-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'],
+        'checksums': ['bd9e77a3fb662b40b43b18d3280cd352edf9fad8d94283e518181cc1ce9f0567'],
+    }),
+    ('DateTime::Tiny', '1.07', {
+        'runtest': False,
+        'source_tmpl': 'DateTime-Tiny-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'],
+        'checksums': ['83568a22838cb518fbeb9e060460ec7f59d5a0b0a1cc06562954c3674d7cf7e4'],
+    }),
+    ('Text::Format', '0.62', {
+        'source_tmpl': 'Text-Format-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'],
+        'checksums': ['7d429057319e123c590ba0765334f0ade4a5eb9ea8db7c0ec4d3902de5f90404'],
+    }),
+    ('Devel::CheckCompiler', '0.07', {
+        'source_tmpl': 'Devel-CheckCompiler-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/S/SY/SYOHEX'],
+        'checksums': ['768b7697b4b8d4d372c7507b65e9dd26aa4223f7100183bbb4d3af46d43869b5'],
+    }),
+    ('Log::Handler', '0.90', {
+        'source_tmpl': 'Log-Handler-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/B/BL/BLOONIX'],
+        'checksums': ['3a5c80e7128454770f83acab8cbd3e70e5ec3d59a61dc32792a178f0b31bf74d'],
+    }),
+    ('Term::ReadKey', '2.38', {
+        'source_tmpl': 'TermReadKey-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/J/JS/JSTOWE'],
+        'checksums': ['5a645878dc570ac33661581fbb090ff24ebce17d43ea53fd22e105a856a47290'],
+    }),
+    ('Set::IntSpan', '1.19', {
+        'source_tmpl': 'Set-IntSpan-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/S/SW/SWMCD'],
+        'checksums': ['11b7549b13ec5d87cc695dd4c777cd02983dd5fe9866012877fb530f48b3dfd0'],
+    }),
+    ('Module::Runtime::Conflicts', '0.003', {
+        'source_tmpl': 'Module-Runtime-Conflicts-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'],
+        'checksums': ['707cdc75038c70fe91779b888ac050f128565d3967ba96680e1b1c7cc9733875'],
+    }),
+    ('File::pushd', '1.016', {
+        'source_tmpl': 'File-pushd-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'],
+        'checksums': ['d73a7f09442983b098260df3df7a832a5f660773a313ca273fa8b56665f97cdc'],
+    }),
+    ('Test::CleanNamespaces', '0.24', {
+        'source_tmpl': 'Test-CleanNamespaces-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'],
+        'checksums': ['338d5569e8e89a654935f843ec0bc84aaa486fe8dd1898fb9cab3eccecd5327a'],
+    }),
+    ('Devel::OverloadInfo', '0.007', {
+        'source_tmpl': 'Devel-OverloadInfo-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/I/IL/ILMARI'],
+        'checksums': ['21a184163b90f91f06ffc7f5de0b968356546ae9b400a9d75c573c958c246222'],
+    }),
+    ('Moose', '2.2207', {
+        'source_tmpl': 'Moose-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'],
+        'checksums': ['7c2daddc49754ded93f65b8ce9e3ac9b6d11ab27d111ec77f95a8528cf4ac409'],
+    }),
+    ('Algorithm::Dependency', '1.112', {
+        'source_tmpl': 'Algorithm-Dependency-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'],
+        'checksums': ['7e0fb7c39f56a2dccf9d0295c82f3031ee116e807f6a12a438fa4dd41b0ec187'],
+    }),
+    ('Font::TTF', '1.06', {
+        'source_tmpl': 'Font-TTF-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/B/BH/BHALLISSY'],
+        'checksums': ['4b697d444259759ea02d2c442c9bffe5ffe14c9214084a01f743693a944cc293'],
+    }),
+    ('IPC::Run3', '0.049', {
+        'source_tmpl': 'IPC-Run3-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'],
+        'checksums': ['9d048ae7b9ae63871bae976ba01e081d887392d904e5d48b04e22d35ed22011a'],
+    }),
+    ('SQL::Statement', '1.414', {
+        'source_tmpl': 'SQL-Statement-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'],
+        'checksums': ['dde8bdcfa6a136eedda06519ba0f3efaec085c39db0df9c472dc0ec6cd781a49'],
+    }),
+    ('Package::Constants', '0.06', {
+        'source_tmpl': 'Package-Constants-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'],
+        'checksums': ['0b58be78706ccc4e4bd9bbad41767470427fd7b2cfad749489de101f85bc5df5'],
+    }),
+    ('CPANPLUS', '0.9914', {
+        'source_tmpl': 'CPANPLUS-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'],
+        'checksums': ['76c3e5da623a4af60fe64adec448fb1f8e0cae9f6798a36b68865974044e9b67'],
+    }),
+    ('IO::Tty', '1.20', {
+        'source_tmpl': 'IO-Tty-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'],
+        'checksums': ['b15309fc85623893289cb9b2b88dfa9ed1e69156b75f29938553a45be6d730af'],
+    }),
+    ('Text::Soundex', '3.05', {
+        'source_tmpl': 'Text-Soundex-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'],
+        'checksums': ['f6dd55b4280b25dea978221839864382560074e1d6933395faee2510c2db60ed'],
+    }),
+    ('Mail::Util', '2.21', {
+        'source_tmpl': 'MailTools-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV'],
+        'checksums': ['4ad9bd6826b6f03a2727332466b1b7d29890c8d99a32b4b3b0a8d926ee1a44cb'],
+    }),
+    ('Test::More::UTF8', '0.05', {
+        'source_tmpl': 'Test-More-UTF8-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/M/MO/MONS'],
+        'checksums': ['b9f1c4b36a97cdfefaa53ed1115dd38f4b483037775f6559ee1df14acfd1ce04'],
+    }),
+    ('Text::Template', '1.61', {
+        'source_tmpl': 'Text-Template-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/M/MS/MSCHOUT'],
+        'checksums': ['a295ea7d1ef241ae2640c1f7864b628f8e6f99ec14fb1da781b2f5f2168dcf09'],
+    }),
+    ('PadWalker', '2.5', {
+        'source_tmpl': 'PadWalker-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/R/RO/ROBIN'],
+        'checksums': ['07b26abb841146af32072a8d68cb90176ffb176fd9268e6f2f7d106f817a0cd0'],
+    }),
+    ('Devel::Cycle', '1.12', {
+        'source_tmpl': 'Devel-Cycle-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/L/LD/LDS'],
+        'checksums': ['fd3365c4d898b2b2bddbb78a46d507a18cca8490a290199547dab7f1e7390bc2'],
+    }),
+    ('Test::Memory::Cycle', '1.06', {
+        'source_tmpl': 'Test-Memory-Cycle-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PETDANCE'],
+        'checksums': ['9d53ddfdc964cd8454cb0da4c695b6a3ae47b45839291c34cb9d8d1cfaab3202'],
+    }),
+    ('PDF::API2', '2.047', {
+        'source_tmpl': 'PDF-API2-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/S/SS/SSIMMS'],
+        'checksums': ['84d6318279d77844923e4de4275fe4345cd08b225edd7f9ed6a16f87a91aca39'],
+    }),
+    ('Devel::CheckLib', '1.16', {
+        'source_tmpl': 'Devel-CheckLib-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MATTN'],
+        'checksums': ['869d38c258e646dcef676609f0dd7ca90f085f56cf6fd7001b019a5d5b831fca'],
+    }),
+    ('SVG', '2.87', {
+        'source_tmpl': 'SVG-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MANWAR'],
+        'checksums': ['b3fa58c1c59942b4ebef003da97c3e01e531480ca29e8efbe327ff0589c0bd3c'],
+    }),
+    ('Statistics::Basic', '1.6611', {
+        'source_tmpl': 'Statistics-Basic-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/J/JE/JETTERO'],
+        'checksums': ['6855ce5615fd3e1af4cfc451a9bf44ff29a3140b4e7130034f1f0af2511a94fb'],
+    }),
+    ('Log::Log4perl', '1.57', {
+        'source_tmpl': 'Log-Log4perl-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETJ'],
+        'checksums': ['0f8fcb7638a8f3db4c797df94fdbc56013749142f2f94cbc95b43c9fca096a13'],
+    }),
+    ('Math::CDF', '0.1', {
+        'source_tmpl': 'Math-CDF-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/C/CA/CALLAHAN'],
+        'checksums': ['7896bf250835ce47dcc813cb8cf9dc576c5455de42e822dcd7d8d3fef2125565'],
+    }),
+    ('Array::Utils', '0.5', {
+        'source_tmpl': 'Array-Utils-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/Z/ZM/ZMIJ/Array'],
+        'checksums': ['89dd1b7fcd9b4379492a3a77496e39fe6cd379b773fd03a6b160dd26ede63770'],
+    }),
+    ('File::Grep', '0.02', {
+        'source_tmpl': 'File-Grep-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/M/MN/MNEYLON'],
+        'checksums': ['462e15274eb6278521407ea302d9eea7252cd44cab2382871f7de833d5f85632'],
+    }),
+    ('File::Temp', '0.2311', {
+        'source_tmpl': 'File-Temp-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'],
+        'checksums': ['2290d61bf5c39882fc3311da9ce1c7f42dbdf825ae169e552c59fe4598b36f4a'],
+    }),
+    ('Set::Object', '1.42', {
+        'source_tmpl': 'Set-Object-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/R/RU/RURBAN'],
+        'checksums': ['d18c5a8a233eabbd0206cf3da5b00fcdd7b37febf12a93dcc3d1c026e6fdec45'],
+    }),
+    ('Heap', '0.80', {
+        'source_tmpl': 'Heap-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/J/JM/JMM'],
+        'checksums': ['ccda29f3c93176ad0fdfff4dd6f5e4ac90b370cba4b028386b7343bf64139bde'],
+    }),
+    ('Graph', '0.9729', {
+        'source_tmpl': 'Graph-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETJ'],
+        'checksums': ['3efbed46ca82f78f25253d034232b0cc9cfadfbd867437e63f9275850f85abb0'],
+    }),
+    ('XML::Writer', '0.900', {
+        'source_tmpl': 'XML-Writer-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/J/JO/JOSEPHW'],
+        'checksums': ['73c8f5bd3ecf2b350f4adae6d6676d52e08ecc2d7df4a9f089fa68360d400d1f'],
+    }),
+    ('Parse::Yapp', '1.21', {
+        'source_tmpl': 'Parse-Yapp-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/W/WB/WBRASWELL'],
+        'checksums': ['3810e998308fba2e0f4f26043035032b027ce51ce5c8a52a8b8e340ca65f13e5'],
+    }),
+    ('Graph::ReadWrite', '2.10', {
+        'source_tmpl': 'Graph-ReadWrite-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'],
+        'checksums': ['516c1ea9facb995dbc38d1735d58974b2399862567e731b729c8d0bc2ee5a14b'],
+    }),
+    ('PerlIO::utf8_strict', '0.010', {
+        'source_tmpl': 'PerlIO-utf8_strict-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'],
+        'checksums': ['bcd2848b72df290b5e984fae8b1a6ca96f6d072003cf222389a8c9e8e1c570cd'],
+    }),
+    ('Digest::MD5::File', '0.08', {
+        'source_tmpl': 'Digest-MD5-File-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/D/DM/DMUEY'],
+        'checksums': ['adb43a54e32627b4f7e57c9640e6eb06d0bb79d8ea54cd0bd79ed35688fb1218'],
+    }),
+    ('String::RewritePrefix', '0.009', {
+        'source_tmpl': 'String-RewritePrefix-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'],
+        'checksums': ['44918bec96a54af8ca37ca897e436709ec284a07b28516ef3cce4666869646d5'],
+    }),
+    ('Getopt::Long::Descriptive', '0.114', {
+        'source_tmpl': 'Getopt-Long-Descriptive-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'],
+        'checksums': ['410e842114a9cbfd3fd3a5fd248a96703c07c5d879b2aa5f9db0333f23276016'],
+    }),
+    ('IO::TieCombine', '1.005', {
+        'source_tmpl': 'IO-TieCombine-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'],
+        'checksums': ['402d4db8300b3d271632f4995e0ade329d89280a7e47f2badf8b38af6e5569af'],
+    }),
+    ('App::Cmd', '0.336', {
+        'source_tmpl': 'App-Cmd-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'],
+        'checksums': ['df966b57d59abb196e00304885e5bf117ca958182ae3f4eedf17218ea2838e81'],
+    }),
+    ('Carp::Clan', '6.08', {
+        'source_tmpl': 'Carp-Clan-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'],
+        'checksums': ['c75f92e34422cc5a65ab05d155842b701452434e9aefb649d6e2289c47ef6708'],
+    }),
+    ('Sub::Exporter::ForMethods', '0.100055', {
+        'source_tmpl': 'Sub-Exporter-ForMethods-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'],
+        'checksums': ['791f4203ba7c0f7d8380bc01bec20215f7c8bc70d7ed03e552eee44541abe94e'],
+    }),
+    ('MooseX::Types', '0.50', {
+        'source_tmpl': 'MooseX-Types-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'],
+        'checksums': ['9cd87b3492cbf0be9d2df9317b2adf9fc30663770e69906654bea3f41b17cb08'],
+    }),
+    ('Variable::Magic', '0.64', {
+        'pretestopts': "LC_ALL=C ",
+        'source_tmpl': 'Variable-Magic-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/V/VP/VPIT'],
+        'checksums': ['9f7853249c9ea3b4df92fb6b790c03a60680fc029f44c8bf9894dccf019516bd'],
+    }),
+    ('MooseX::Types::Perl', '0.101344', {
+        'source_tmpl': 'MooseX-Types-Perl-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'],
+        'checksums': ['87644354f74fa65235cb2bfca44277930a7eabe51acc5f81fb631530a8355e24'],
+    }),
+    ('Log::Dispatch', '2.71', {
+        'source_tmpl': 'Log-Dispatch-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'],
+        'checksums': ['9d60d9648c35ce2754731eb4deb7f05809ece1bd633b74d74795aed9ec732570'],
+    }),
+    ('JSON::MaybeXS', '1.004005', {
+        'source_tmpl': 'JSON-MaybeXS-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'],
+        'checksums': ['f5b6bc19f579e66b7299f8748b8ac3e171936dc4e7fcb72a8a257a9bd482a331'],
+    }),
+    ('String::Flogger', '1.101246', {
+        'source_tmpl': 'String-Flogger-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'],
+        'checksums': ['15f8491e07818bb3cfa9f6bd3aabf6430ba9b4e309f18114358be3d81bff3a0f'],
+    }),
+    ('Log::Dispatch::Array', '1.005', {
+        'source_tmpl': 'Log-Dispatch-Array-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'],
+        'checksums': ['311640b7a967f8dd7c9bb41a227073565636d70df4fcc1d44fed8a8223b347ca'],
+    }),
+    ('Sub::Exporter::GlobExporter', '0.006', {
+        'source_tmpl': 'Sub-Exporter-GlobExporter-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'],
+        'checksums': ['de743f08026701c2a6a222a8b41c4cdc254b1a4afe7ef98987cd3aba4ce52696'],
+    }),
+    ('Log::Dispatchouli', '3.007', {
+        'source_tmpl': 'Log-Dispatchouli-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'],
+        'checksums': ['988118965952ba49a8fa791a6536880c89017f4eb9d72c1745ed67d15c0d272c'],
+    }),
+    ('Test::FailWarnings', '0.008', {
+        'source_tmpl': 'Test-FailWarnings-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'],
+        'checksums': ['da34ef9029f6849d6026201d49127d054ee6ac4b979c82210315f5721964a96f'],
+    }),
+    ('Data::Section', '0.200008', {
+        'source_tmpl': 'Data-Section-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'],
+        'checksums': ['83acc7a55d3dd7ed36e9d78d350af3138c69cfa178a44765822712ff433b990e'],
+    }),
+    ('Test::CheckDeps', '0.010', {
+        'source_tmpl': 'Test-CheckDeps-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'],
+        'checksums': ['66fccca6c6f330e7ecc898bd6a51846e2145b3e02d78c4997ba6b7de23b551ee'],
+    }),
+    ('Software::License', '0.104006', {
+        'runtest': False,
+        'source_tmpl': 'Software-License-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'],
+        'checksums': ['65c8ee1c2da2a4de10139863df668fa6b3b3e24a39d69a7cca39f284fb6b9c0f'],
+    }),
+    ('MooseX::SetOnce', '0.203', {
+        'source_tmpl': 'MooseX-SetOnce-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'],
+        'checksums': ['3cd2f3664e438382cf844b679350a2e428b760927e2cf18fccdc468a7bc3066f'],
+    }),
+    ('Term::Encoding', '0.03', {
+        'source_tmpl': 'Term-Encoding-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA'],
+        'checksums': ['95ba9687d735d25a3cbe64508d7894f009c7fa2a1726c3e786e9e21da2251d0b'],
+    }),
+    ('Throwable', '1.001', {
+        'source_tmpl': 'Throwable-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'],
+        'checksums': ['d0cb5e9d7d06d70f2cc56eecf857a83a45eaca43850dcdda91d3feb4ddde4c51'],
+    }),
+    ('Role::Identifiable::HasIdent', '0.009', {
+        'source_tmpl': 'Role-Identifiable-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'],
+        'checksums': ['5a735e9f7177f9ebae047eb7bae29b7ec29ec020ae37637aea5350d30c087b76'],
+    }),
+    ('MooseX::Role::Parameterized', '1.11', {
+        'source_tmpl': 'MooseX-Role-Parameterized-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'],
+        'checksums': ['1cfe766c5d7f0ecab57f733dcca430a2a2acd6b995757141b940ade3692bec9e'],
+    }),
+    ('MooseX::OneArgNew', '0.007', {
+        'source_tmpl': 'MooseX-OneArgNew-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'],
+        'checksums': ['84282435f1169cf09d7513fa9387e2091791635cf35a078b500b829aeea06138'],
+    }),
+    ('MooseX::LazyRequire', '0.11', {
+        'source_tmpl': 'MooseX-LazyRequire-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'],
+        'checksums': ['ef620c1e019daf9cf3f23a943d25a94c91e93ab312bcd63be2e9740ec0b94288'],
+    }),
+    ('String::Formatter', '1.235', {
+        'source_tmpl': 'String-Formatter-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'],
+        'checksums': ['08236a913b911ce652cf08598e7c07d2df3f369fc47bf401a485a504a1660783'],
+    }),
+    ('String::Errf', '0.009', {
+        'source_tmpl': 'String-Errf-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'],
+        'checksums': ['e1fedbf9b4fd64b64ea81038ddb76a4c6cd85f5db15bc21f10656a298349dc1f'],
+    }),
+    ('Role::HasMessage', '0.007', {
+        'source_tmpl': 'Role-HasMessage-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'],
+        'checksums': ['5e267a4d7620b368481204c88ea2044b8b2a58ff8b05577f2717b2754c0414ce'],
+    }),
+    ('Config::MVP', '2.200013', {
+        'source_tmpl': 'Config-MVP-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'],
+        'checksums': ['018d161623ee3a67f860d9e680e22e61b79eae6018f0e7c3b525fc934f5b7d45'],
+    }),
+    ('Mixin::Linewise::Readers', '0.111', {
+        'source_tmpl': 'Mixin-Linewise-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'],
+        'checksums': ['d28e88516ce9b5295c31631dcccdc0fc8f2ab7d8a5cc876bb1b20131087b01db'],
+    }),
+    ('Config::INI', '0.029', {
+        'source_tmpl': 'Config-INI-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'],
+        'checksums': ['0bbe797a730210644a907d90cd4aa2b23ad580cb27bd39393bfc6a7ef9fdfdea'],
+    }),
+    ('String::Truncate', '1.100603', {
+        'source_tmpl': 'String-Truncate-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'],
+        'checksums': ['ab45602cce2dd9515edfbb2e6e5cde19cdd5498d61a23afd8c46c1f11f8eec62'],
+    }),
+    ('Pod::Eventual', '0.094003', {
+        'source_tmpl': 'Pod-Eventual-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'],
+        'checksums': ['7f060cc34d11656ce069db061e3d60edc0cabc8f89a4a2dc7eaae95dac856d2d'],
+    }),
+    ('Pod::Elemental', '0.103006', {
+        'source_tmpl': 'Pod-Elemental-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'],
+        'checksums': ['750c3a79d8e1824758a6ef7d2dd077dcddca503542b8c34eccd5acbb779dc423'],
+    }),
+    ('Test::Object', '0.08', {
+        'source_tmpl': 'Test-Object-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'],
+        'checksums': ['65278964147837313f4108e55b59676e8a364d6edf01b3dc198aee894ab1d0bb'],
+    }),
+    ('Hook::LexWrap', '0.26', {
+        'source_tmpl': 'Hook-LexWrap-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'],
+        'checksums': ['b60bdc5f98f94f9294b06adef82b1d996da192d5f183f9f434b610fd1137ec2d'],
+    }),
+    ('Test::SubCalls', '1.10', {
+        'source_tmpl': 'Test-SubCalls-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'],
+        'checksums': ['cbc1e9b35a05e71febc13e5ef547a31c8249899bb6011dbdc9d9ff366ddab6c2'],
+    }),
+    ('PPI', '1.278', {
+        'source_tmpl': 'PPI-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'],
+        'checksums': ['1c867b2e9b10056978db9ddaadab599af9a5c9a66805ed03ef4b201f1105d427'],
+    }),
+    ('Config::MVP::Reader::INI', '2.101465', {
+        'source_tmpl': 'Config-MVP-Reader-INI-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'],
+        'checksums': ['13c7aa27c1df98cd33ada399e59ff38fabfa9d65513e42af02f72c2d3f636247'],
+    }),
+    ('Pod::Weaver', '4.020', {
+        'source_tmpl': 'Pod-Weaver-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'],
+        'checksums': ['655fcf261206c1adbc3038981790b116c31508485135c648093b99b3b3de09d2'],
+    }),
+    ('CPAN::Uploader', '0.103018', {
+        'source_tmpl': 'CPAN-Uploader-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'],
+        'checksums': ['c4ffe4ede9db79b396e3bfc5e7cdf0e2e9821e1f1e087f523bcfa74c9fc9e248'],
+    }),
+    ('Devel::FindPerl', '0.016', {
+        'source_tmpl': 'Devel-FindPerl-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'],
+        'checksums': ['43a2bf2f787a3f1b881179063162b2aa3e7cb044f6e5e76ec6466ae90a861138'],
+    }),
+    ('Module::Path', '0.19', {
+        'source_tmpl': 'Module-Path-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'],
+        'checksums': ['b33179ce4dd73dfcde7d46808804b9ffbb11db0245fe455a7d001747562feaca'],
+    }),
+    ('Perl::PrereqScanner', '1.100', {
+        'source_tmpl': 'Perl-PrereqScanner-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'],
+        'checksums': ['01181d38a2e7aff838d262122563c50636ba4b3652ee5d1d4f8ef5ba3f5b186b'],
+    }),
+    ('Dist::Zilla', '6.032', {
+        'source_tmpl': 'Dist-Zilla-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'],
+        'checksums': ['5c771a1dc2daab5afae0fd59e5046111970f73bf3eaec9df70d8e07346f8165e'],
+    }),
+    ('XML::RegExp', '0.04', {
+        'source_tmpl': 'XML-RegExp-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/T/TJ/TJMATHER'],
+        'checksums': ['df1990096036085c8e2d45904fe180f82bfed40f1a7e05243f334ea10090fc54'],
+    }),
+    ('XML::DOM', '1.46', {
+        'source_tmpl': 'XML-DOM-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/T/TJ/TJMATHER'],
+        'checksums': ['8ba24b0b459b01d6c5e5b0408829c7d5dfe47ff79b3548c813759048099b175e'],
+    }),
+    ('Data::Dump', '1.25', {
+        'source_tmpl': 'Data-Dump-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GARU'],
+        'checksums': ['a4aa6e0ddbf39d5ad49bddfe0f89d9da864e3bc00f627125d1bc580472f53fbd'],
+    }),
+    ('File::Next', '1.18', {
+        'source_tmpl': 'File-Next-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PETDANCE'],
+        'checksums': ['f900cb39505eb6e168a9ca51a10b73f1bbde1914b923a09ecd72d9c02e6ec2ef'],
+    }),
+    ('App::cpanminus', '1.7047', {
+        'source_tmpl': 'App-cpanminus-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA'],
+        'checksums': ['963e63c6e1a8725ff2f624e9086396ae150db51dd0a337c3781d09a994af05a5'],
+    }),
+    ('Parallel::ForkManager', '2.02', {
+        'source_tmpl': 'Parallel-ForkManager-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/Y/YA/YANICK'],
+        'checksums': ['c1b2970a8bb666c3de7caac4a8f4dbcc043ab819bbc337692ec7bf27adae4404'],
+    }),
+    ('Object::InsideOut', '4.05', {
+        'source_tmpl': 'Object-InsideOut-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/J/JD/JDHEDDEN'],
+        'checksums': ['9dfd6ca2822724347e0eb6759d00709425814703ad5c66bdb6214579868bcac4'],
+    }),
+    ('Logger::Simple', '2.0', {
+        'source_tmpl': 'Logger-Simple-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/T/TS/TSTANLEY'],
+        'checksums': ['2e63fd3508775b5902132ba1bfb03b42bee468dfaf35dfe42e1909ff6d291b2d'],
+    }),
+    ('Scalar::Util::Numeric', '0.40', {
+        'source_tmpl': 'Scalar-Util-Numeric-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/C/CH/CHOCOLATE'],
+        'checksums': ['d7501b6d410703db5b1c1942fbfc41af8964a35525d7f766058acf5ca2cc4440'],
+    }),
+    ('Spiffy', '0.46', {
+        'source_tmpl': 'Spiffy-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/I/IN/INGY'],
+        'checksums': ['8f58620a8420255c49b6c43c5ff5802bd25e4f09240c51e5bf2b022833d41da3'],
+    }),
+    ('Test::Base', '0.89', {
+        'source_tmpl': 'Test-Base-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/I/IN/INGY'],
+        'checksums': ['2794a1aaaeb1d3a287dd2c7286258663796562f7db9ccc6b424bc4f1de8ad014'],
+    }),
+    ('Test::YAML', '1.07', {
+        'source_tmpl': 'Test-YAML-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/T/TI/TINITA'],
+        'checksums': ['1f300d034f46298cb92960912cc04bac33fb27f05b8852d8f051e110b9cd995f'],
+    }),
+    ('YAML', '1.31', {
+        'source_tmpl': 'YAML-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/I/IN/INGY'],
+        'checksums': ['a0ce30381657dce8e694df9a09e95d818d13beb03698fd2cf79d0c8d564a9b8e'],
+    }),
+    ('Object::InsideOut', '4.05', {
+        'source_tmpl': 'Object-InsideOut-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/J/JD/JDHEDDEN'],
+        'checksums': ['9dfd6ca2822724347e0eb6759d00709425814703ad5c66bdb6214579868bcac4'],
+    }),
+    ('Time::HiRes', '1.9764', {
+        'source_tmpl': 'Time-HiRes-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/A/AT/ATOOMIC'],
+        'checksums': ['9841be5587bfb7cd1f2fe267b5e5ac04ce25e79d5cc77e5ef9a9c5abd101d7b1'],
+    }),
+    ('Term::ReadLine::Gnu', '1.46', {
+        'modulename': 'Term::ReadLine',
+        'source_tmpl': 'Term-ReadLine-Gnu-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAYASHI'],
+        'checksums': ['b13832132e50366c34feac12ce82837c0a9db34ca530ae5d27db97cf9c964c7b'],
+    }),
+    ('ExtUtils::MakeMaker', '7.70', {
+        'source_tmpl': 'ExtUtils-MakeMaker-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'],
+        'checksums': ['f108bd46420d2f00d242825f865b0f68851084924924f92261d684c49e3e7a74'],
+    }),
+    ('Scalar::Util', '1.63', {
+        'source_tmpl': 'Scalar-List-Utils-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PEVANS'],
+        'checksums': ['cafbdf212f6827dc9a0dd3b57b6ee50e860586d7198228a33262d55c559eb2a9'],
+    }),
+    ('Module::CoreList', '5.20240702', {
+        'source_tmpl': 'Module-CoreList-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'],
+        'checksums': ['f2fa93960b1419ab3aaa186d4ce2a538de229d1af8a9eecd76265c78252c011b'],
+    }),
+    ('Module::Metadata', '1.000038', {
+        'source_tmpl': 'Module-Metadata-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'],
+        'checksums': ['b599d8770a9a9fa0a8ae3cd0ed395a9cf71b4eb53aed82989a6bece33485a9cd'],
+    }),
+    ('Params::Check', '0.38', {
+        'configopts': 'INSTALLDIRS=site',
+        'source_tmpl': 'Params-Check-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'],
+        'checksums': ['f0c9d33876c36b1bca1475276d26d2efaf449b256d7cc8118fae012e89a26290'],
+    }),
+    ('Locale::Maketext::Simple', '0.21', {
+        'configopts': 'INSTALLDIRS=site',
+        'source_tmpl': 'Locale-Maketext-Simple-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/J/JE/JESSE'],
+        'checksums': ['b009ff51f4fb108d19961a523e99b4373ccf958d37ca35bf1583215908dca9a9'],
+    }),
+    ('Perl::OSType', '1.010', {
+        'source_tmpl': 'Perl-OSType-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'],
+        'checksums': ['e7ed4994b5d547cb23aadb84dc6044c5eb085d5a67a6c5624f42542edd3403b2'],
+    }),
+    ('IPC::Cmd', '1.04', {
+        'source_tmpl': 'IPC-Cmd-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'],
+        'checksums': ['d110a0f60e35c65721454200f0d2f0f8965529a2add9649d1fa6f4f9eccb6430'],
+    }),
+    ('Pod::Escapes', '1.07', {
+        'source_tmpl': 'Pod-Escapes-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'],
+        'checksums': ['dbf7c827984951fb248907f940fd8f19f2696bc5545c0a15287e0fbe56a52308'],
+    }),
+    ('if', '0.0608', {
+        'configopts': 'INSTALLDIRS=site',
+        'modulename': False,
+        'source_tmpl': 'if-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/X/XS/XSAWYERX'],
+        'checksums': ['37206e10919c4d99273020008a3581bf0947d364e859b8966521c3145b4b3700'],
+    }),
+    ('Test', '1.26', {
+        'configopts': 'INSTALLDIRS=site',
+        'source_tmpl': 'Test-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/J/JE/JESSE'],
+        'checksums': ['f7701bd28e05e7f82fe9a181bbab38f53fa6aeae48d2a810da74d1b981d4f392'],
+    }),
+    ('ExtUtils::Constant', '0.25', {
+        'runtest': False,
+        'source_tmpl': 'ExtUtils-Constant-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/N/NW/NWCLARK'],
+        'checksums': ['6933d0e963b62281ef7561068e6aecac8c4ac2b476b2bba09ab0b90fbac9d757'],
+    }),
+    ('ExtUtils::CBuilder', '0.280236', {
+        'source_tmpl': 'ExtUtils-CBuilder-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/A/AM/AMBS'],
+        'checksums': ['abc21827eb8a513171bf7fdecefce9945132cb76db945036518291f607b1491f'],
+    }),
+    ('Carp::Heavy', '1.50', {
+        'source_tmpl': 'Carp-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/X/XS/XSAWYERX'],
+        'checksums': ['f5273b4e1a6d51b22996c48cb3a3cbc72fd456c4038f5c20b127e2d4bcbcebd9'],
+    }),
+    ('Pod::Simple', '3.45', {
+        'source_tmpl': 'Pod-Simple-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/K/KH/KHW'],
+        'checksums': ['8483bb95cd3e4307d66def092a3779f843af772482bfdc024e3e00d0c4db0cfa'],
+    }),
+    ('Socket', '2.038', {
+        'source_tmpl': 'Socket-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PEVANS'],
+        'checksums': ['563d11731ff44307fa2779a6958fd2d2f6643fbd9a3174cbf350228b159681f8'],
+    }),
+    ('Time::Local', '1.35', {
+        'source_tmpl': 'Time-Local-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'],
+        'checksums': ['1d136b71bd041cbe6f66c43180ee79e675b72ad5a3596abd6a44d211072ada29'],
+    }),
+    ('Storable', '3.25', {
+        'source_tmpl': 'Storable-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/N/NW/NWCLARK'],
+        'checksums': ['e1e96b24a076792fde52154789fe4b76034b9ad39c8a1a819ead77d50d5f1817'],
+    }),
+    ('ExtUtils::ParseXS', '3.51', {
+        'source_tmpl': 'ExtUtils-ParseXS-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'],
+        'checksums': ['82431a57425d78682acefb3a2cc9287683d091c8d034b825c584d9805bed6535'],
+    }),
+    ('Pod::Man', '5.01', {
+        'source_tmpl': 'podlators-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/R/RR/RRA'],
+        'checksums': ['ccfd1df9f1a47f095bce6d718fad5af40f78ce2491f2c7239626e15b7020bc71'],
+    }),
+    ('Mozilla::CA', '20240313', {
+        'source_tmpl': 'Mozilla-CA-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/L/LW/LWP'],
+        'checksums': ['624873939e309833894f881464a95dfe74ab77cab5d557308c010487161698e7'],
+    }),
+    ('LWP::Protocol::https', '6.14', {
+        'source_tmpl': 'LWP-Protocol-https-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'],
+        'checksums': ['59cdeabf26950d4f1bef70f096b0d77c5b1c5a7b5ad1b66d71b681ba279cbb2a'],
+    }),
+    ('Module::Load', '0.36', {
+        'source_tmpl': 'Module-Load-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'],
+        'checksums': ['d825020ac00b220e89f9524e24d838f9438b072fcae8c91938e4026677bef6e0'],
+    }),
+    ('Module::Load::Conditional', '0.74', {
+        'source_tmpl': 'Module-Load-Conditional-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'],
+        'checksums': ['54c354a9393820f1ebc2a095da084ea0392dcbccb0cb38a187a71831cc60a730'],
+    }),
+    ('parent', '0.241', {
+        'source_tmpl': 'parent-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/C/CO/CORION'],
+        'checksums': ['b10b3960ab3997dab7571ffe975ba462d979d086450740a1e08b3959e75128fe'],
+    }),
+    ('Net::Domain', '3.15', {
+        'source_tmpl': 'libnet-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHAY'],
+        'checksums': ['a71f4db580e1a767d6936faa5baf38f1fa617824342da078b561283e86f8f4a2'],
+    }),
+    ('Encode', '3.21', {
+        'source_tmpl': 'Encode-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DANKOGAI'],
+        'checksums': ['eacf71c5eb49e0e590de797f1982d7fb95d8481e4d13c3ce79eb32ef9373b3db'],
+    }),
+    ('Cwd', '3.75', {
+        'patches': ['PathTools-3.75_fix-cwd_enoent-test.patch'],
+        'runtest': False,
+        'source_tmpl': 'PathTools-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/X/XS/XSAWYERX'],
+        'checksums': [
+            {'PathTools-3.75.tar.gz': 'a558503aa6b1f8c727c0073339081a77888606aa701ada1ad62dd9d8c3f945a2'},
+            {'PathTools-3.75_fix-cwd_enoent-test.patch':
+             '7a456a99d9b04a36359f3623f0deef8fe7f472c742f99cdcf0215c50afbbe7b1'},
+        ],
+    }),
+    ('MIME::Base64', '3.16', {
+        'source_tmpl': 'MIME-Base64-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/C/CA/CAPOEIRAB'],
+        'checksums': ['77f73d6f7aeb8d33be08b0d8c2617f9b6c77fb7fc45422d507ca8bafe4246017'],
+    }),
+    ('ExtUtils::CppGuess', '0.27', {
+        'runtest': False,
+        'source_tmpl': 'ExtUtils-CppGuess-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETJ'],
+        'checksums': ['b2c7b581901054a32dfcea12536fda8626457ed0bfbc02600bd354bde7e2a9b4'],
+    }),
+    ('XSLoader', '0.24', {
+        'source_tmpl': 'XSLoader-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/S/SA/SAPER'],
+        'checksums': ['e819a35a6b8e55cb61b290159861f0dc00fe9d8c4f54578eb24f612d45c8d85f'],
+    }),
+    ('AutoLoader', '5.74', {
+        'source_tmpl': 'AutoLoader-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/S/SM/SMUELLER'],
+        'checksums': ['2fac75b05309f71a6871804cd25e1a3ba0a28f43f294fb54528077558da3aff4'],
+    }),
+    ('Set::IntervalTree', '0.12', {
+        'source_tmpl': 'Set-IntervalTree-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/S/SL/SLOYD'],
+        'checksums': ['6fd4000e4022968e2ce5b83c07b189219ef1925ecb72977b52a6f7d76adbc349'],
+    }),
+    ('MCE::Mutex', '1.897', {
+        'runtest': False,
+        'source_tmpl': 'MCE-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARIOROY'],
+        'checksums': ['673d337d14fc2d7a12576ca6615c729821dc616ee76e0ecc9c0f32de8a9f9c39'],
+    }),
+    ('Text::CSV_XS', '1.55', {
+        'source_tmpl': 'Text-CSV_XS-%(version)s.tgz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/H/HM/HMBRAND'],
+        'checksums': ['e4b623b31b4ac35e99d7b797d5b7c2205a5b984bcd88dee1a9460a6a39d40b5e'],
+    }),
+    ('DBD::CSV', '0.60', {
+        'source_tmpl': 'DBD-CSV-%(version)s.tgz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/H/HM/HMBRAND'],
+        'checksums': ['018b83a30f799979bc8c3c3044c8b1c8001cdf60bdc3e746848818195254b4e7'],
+    }),
+    ('Array::Transpose', '0.06', {
+        'source_tmpl': 'Array-Transpose-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/M/MR/MRDVT'],
+        'checksums': ['d58667f64381a105f375226f592d0af71068e640a5a9f4d5ecf27c90feb32676'],
+    }),
+    ('Config::Simple', '4.58', {
+        'source_tmpl': 'Config-Simple-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHERZODR'],
+        'checksums': ['dd9995706f0f9384a15ccffe116c3b6e22f42ba2e58d8f24ed03c4a0e386edb4'],
+    }),
+    ('Business::ISBN::Data', '20240614.001', {
+        'source_tmpl': 'Business-ISBN-Data-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/B/BR/BRIANDFOY'],
+        'checksums': ['38d7f0e24152e1aef07b1517a16104c1763b6669095dbad5083c3b91fc27232b'],
+    }),
+    ('Business::ISBN', '3.009', {
+        'source_tmpl': 'Business-ISBN-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/B/BR/BRIANDFOY'],
+        'checksums': ['d2ec1970454af1b2c099dd34caa7a348ca6fd323bb7ddbfad55389bd7f96789b'],
+    }),
+    ('common::sense', '3.75', {
+        'source_tmpl': 'common-sense-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'],
+        'checksums': ['a86a1c4ca4f3006d7479064425a09fa5b6689e57261fcb994fe67d061cba0e7e'],
+    }),
+    ('Compress::Raw::Zlib', '2.212', {
+        'source_tmpl': 'Compress-Raw-Zlib-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/P/PM/PMQS'],
+        'checksums': ['6d9de0c11921fd520dfd99a3f6b0ca9f1fd9850274f8bec10bbaa4f6803cc049'],
+    }),
+    ('IO::Compress::Zip', '2.212', {
+        'runtest': False,
+        'source_tmpl': 'IO-Compress-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/P/PM/PMQS'],
+        'checksums': ['687490dbf9c4be42c22a945c4601812be5f4d38a9836018148915ba9e0ea65b1'],
+    }),
+    ('Types::Serialiser', '1.01', {
+        'source_tmpl': 'Types-Serialiser-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'],
+        'checksums': ['f8c7173b0914d0e3d957282077b366f0c8c70256715eaef3298ff32b92388a80'],
+    }),
+    ('JSON::XS', '4.03', {
+        'source_tmpl': 'JSON-XS-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'],
+        'checksums': ['515536f45f2fa1a7e88c8824533758d0121d267ab9cb453a1b5887c8a56b9068'],
+    }),
+    ('Authen::NTLM', '1.09', {
+        'source_tmpl': 'NTLM-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/N/NB/NBEBOUT'],
+        'checksums': ['c823e30cda76bc15636e584302c960e2b5eeef9517c2448f7454498893151f85'],
+    }),
+    ('Types::Serialiser', '1.01', {
+        'source_tmpl': 'Types-Serialiser-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'],
+        'checksums': ['f8c7173b0914d0e3d957282077b366f0c8c70256715eaef3298ff32b92388a80'],
+    }),
+    ('XML::SAX::Expat', '0.51', {
+        'source_tmpl': 'XML-SAX-Expat-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/B/BJ/BJOERN'],
+        'checksums': ['4c016213d0ce7db2c494e30086b59917b302db8c292dcd21f39deebd9780c83f'],
+    }),
+    ('Inline', '0.86', {
+        'source_tmpl': 'Inline-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/I/IN/INGY'],
+        'checksums': ['510a7de2d011b0db80b0874e8c0f7390010991000ae135cff7474df1e6d51e3a'],
+    }),
+    ('Test::Sys::Info', '0.23', {
+        'preconfigopts': "sed -i 's/ok( my %fs/# ok( my %fs/' lib/Test/Sys/Info/Driver.pm && ",
+        'source_tmpl': 'Test-Sys-Info-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/B/BU/BURAK'],
+        'checksums': ['30c5f2c4cfee8e1ae6d9fb6291f79addbff5739ba4efa5b1e034520f18fbc95a'],
+    }),
+    ('Sys::Info::Base', '0.7807', {
+        'source_tmpl': 'Sys-Info-Base-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/B/BU/BURAK'],
+        'checksums': ['132362b0046e8dc4f12e1560903623a88a8871d09bf1c29d93d48d3f4a582acb'],
+    }),
+    ('Sys::Info::Driver::Unknown::Device::CPU', '0.79', {
+        'source_tmpl': 'Sys-Info-Driver-Unknown-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/B/BU/BURAK'],
+        'checksums': ['02408843c8e36ea3d507e9f33fee48d6908543829ebe320f13d1bfe76af31e09'],
+    }),
+    ('Unix::Processors', '2.046', {
+        'source_tmpl': 'Unix-Processors-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/W/WS/WSNYDER'],
+        'checksums': ['3973ebdc44682c9c15c776f66e8be242cb4ff1dd52caf43ff446b74d4dccca06'],
+    }),
+    ('Sys::Info::Driver::Linux::Device::CPU', '0.7905', {
+        'source_tmpl': 'Sys-Info-Driver-Linux-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/B/BU/BURAK'],
+        'checksums': ['899c329bd3508ec5849ad0e5dadfa7c3679bbacaea9dda12404a7893032e8b7b'],
+    }),
+    ('Sys::Info', '0.7811', {
+        'source_tmpl': 'Sys-Info-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/B/BU/BURAK'],
+        'checksums': ['566482bff3427c198d7955468ed945a8e736c4a2925151fdef96801ef8a401e1'],
+    }),
+    ('CGI', '4.66', {
+        'source_tmpl': 'CGI-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEEJO'],
+        'checksums': ['4697437688a193e3f02556e1d223015590c1f2800b40becf83dc12d5cc5ed8e1'],
+    }),
+    ('HTML::Template', '2.97', {
+        'source_tmpl': 'HTML-Template-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/S/SA/SAMTREGAR'],
+        'checksums': ['6547af61f3aa85793f8616190938d677d7995fb3b720c16258040bc935e2129f'],
+    }),
+    ('MIME::Charset', 'v1.013.1', {
+        'source_tmpl': 'MIME-Charset-1.013.1.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEZUMI'],
+        'checksums': ['1bb7a6e0c0d251f23d6e60bf84c9adefc5b74eec58475bfee4d39107e60870f0'],
+    }),
+    ('Unicode::LineBreak', '2019.001', {
+        'source_tmpl': 'Unicode-LineBreak-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEZUMI'],
+        'checksums': ['486762e4cacddcc77b13989f979a029f84630b8175e7fef17989e157d4b6318a'],
+    }),
+    ('String::Print', '0.94', {
+        'source_tmpl': 'String-Print-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV'],
+        'checksums': ['9b3cd677adb7a40cb183bd6c60db80d96adcabd5aae27e324e3ee37e3275229b'],
+    }),
+    ('Log::Report::Optional', '1.07', {
+        'source_tmpl': 'Log-Report-Optional-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV'],
+        'checksums': ['b2658b53176df5afa5d02789368715c86b98c8d04ecd930252bcd7f832cc6224'],
+    }),
+    ('Log::Report', '1.37', {
+        'source_tmpl': 'Log-Report-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV'],
+        'checksums': ['9135798e9cb391e949a3c829c101631d182baa4feaaf821efcee8deba7fdee67'],
+    }),
+    ('Sys::Info::Driver::Unknown', '0.79', {
+        'source_tmpl': 'Sys-Info-Driver-Unknown-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/B/BU/BURAK'],
+        'checksums': ['02408843c8e36ea3d507e9f33fee48d6908543829ebe320f13d1bfe76af31e09'],
+    }),
+    ('Sys::Info::Driver::Linux', '0.7905', {
+        'source_tmpl': 'Sys-Info-Driver-Linux-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/B/BU/BURAK'],
+        'checksums': ['899c329bd3508ec5849ad0e5dadfa7c3679bbacaea9dda12404a7893032e8b7b'],
+    }),
+    ('Unix::Processors', '2.046', {
+        'source_tmpl': 'Unix-Processors-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/W/WS/WSNYDER'],
+        'checksums': ['3973ebdc44682c9c15c776f66e8be242cb4ff1dd52caf43ff446b74d4dccca06'],
+    }),
+    ('local::lib', '2.000029', {
+        'source_tmpl': 'local-lib-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'],
+        'checksums': ['8df87a10c14c8e909c5b47c5701e4b8187d519e5251e87c80709b02bb33efdd7'],
+    }),
+    ('Module::Path', '0.19', {
+        'source_tmpl': 'Module-Path-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'],
+        'checksums': ['b33179ce4dd73dfcde7d46808804b9ffbb11db0245fe455a7d001747562feaca'],
+    }),
+    ('Devel::Size', '0.84', {
+        'source_tmpl': 'Devel-Size-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/N/NW/NWCLARK'],
+        'checksums': ['db2e4d65f688dbf59273b5e82101ac3f1a66f665afb0594dce168b8650a4d0e4'],
+    }),
+    ('Math::Utils', '1.14', {
+        'source_tmpl': 'Math-Utils-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/J/JG/JGAMBLE'],
+        'checksums': ['88a20ae0736a622671b92bb2a350969af424d7610284530b277c8020235f2695'],
+    }),
+]
+
+moduleclass = 'lang'

From ca42190283ec0e2b68ee2d8062e01f1d8c871e35 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Mon, 8 Jul 2024 14:42:56 +0000
Subject: [PATCH 419/835] Restore comments

---
 .../Perl-bundle-CPAN-5.38.2-GCCcore-13.3.0.eb | 36 +++++++++----------
 1 file changed, 18 insertions(+), 18 deletions(-)

diff --git a/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.2-GCCcore-13.3.0.eb
index 3ee5da2ad31..8d8b1eaa582 100644
--- a/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.2-GCCcore-13.3.0.eb
+++ b/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.2-GCCcore-13.3.0.eb
@@ -397,10 +397,10 @@ exts_list = [
         'checksums': ['d161c89dee9b213a7c55709ea782e2dd5923dbd1215b9576612889e6e74a2e06'],
     }),
     ('DBI', '1.643', {
-        'pretestopts': "LC_ALL=C ",
         'source_tmpl': 'DBI-%(version)s.tar.gz',
         'source_urls': ['https://cpan.metacpan.org/authors/id/T/TI/TIMB'],
         'checksums': ['8a2b993db560a2c373c174ee976a51027dd780ec766ae17620c20393d2e836fa'],
+        'pretestopts': 'LC_ALL=C ',  # Test fails if run in localized environments
     }),
     ('DBD::SQLite', '1.74', {
         'source_tmpl': 'DBD-SQLite-%(version)s.tar.gz',
@@ -608,7 +608,7 @@ exts_list = [
         'checksums': ['1943336a4cb54f1788a733f0827c0c55db4310d5eae15e542639c9dd85656e37'],
     }),
     ('GO', '0.04', {
-        'runtest': False,
+        'runtest': False,  # Problem with indirect dependency DBD::Pg
         'source_tmpl': 'go-db-perl-%(version)s.tar.gz',
         'source_urls': ['https://cpan.metacpan.org/authors/id/S/SJ/SJCARBON'],
         'checksums': ['8eb73d591ad767e7cf26def40cffd84833875f1ad51e456960b9ed73dc23641b'],
@@ -759,7 +759,7 @@ exts_list = [
         'checksums': ['98ca32e7f2f5ea89b8bfb9a0609977f3d153e242e2e51705126cb954f1a06b57'],
     }),
     ('Test::Differences', '0.71', {
-        'runtest': False,
+        'runtest': False,  # Cryptic test failing
         'source_tmpl': 'Test-Differences-%(version)s.tar.gz',
         'source_urls': ['https://cpan.metacpan.org/authors/id/D/DC/DCANTRELL'],
         'checksums': ['cac16a56cd843b0809e5b49199d60d75a8dbad7ca9a08380dbf3f5cc3aaa38d9'],
@@ -835,7 +835,7 @@ exts_list = [
         'checksums': ['b9625992683b97378bea0947773f50e3c9f81974048b84f4c3422cae7e6082f4'],
     }),
     ('Net::HTTP', '6.23', {
-        'runtest': False,
+        'runtest': False,  # Fragile tests
         'source_tmpl': 'Net-HTTP-%(version)s.tar.gz',
         'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'],
         'checksums': ['0d65c09dd6c8589b2ae1118174d3c1a61703b6ecfc14a3442a8c74af65e0c94e'],
@@ -961,7 +961,7 @@ exts_list = [
         'checksums': ['6540085e3804b82a6f0752c1122cf78cadd221990136dd6fd4c097d056c84d40'],
     }),
     ('B::Lint', '1.20', {
-        'runtest': False,
+        'runtest': False,  # One failing subtest
         'source_tmpl': 'B-Lint-%(version)s.tar.gz',
         'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'],
         'checksums': ['dc49408964fd8b7963859c92e013f0b9f92f74be5a7c2a78e3996279827c10b3'],
@@ -1258,7 +1258,7 @@ exts_list = [
         'checksums': ['bd9e77a3fb662b40b43b18d3280cd352edf9fad8d94283e518181cc1ce9f0567'],
     }),
     ('DateTime::Tiny', '1.07', {
-        'runtest': False,
+        'runtest': False,  # One subset fails due to locale
         'source_tmpl': 'DateTime-Tiny-%(version)s.tar.gz',
         'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'],
         'checksums': ['83568a22838cb518fbeb9e060460ec7f59d5a0b0a1cc06562954c3674d7cf7e4'],
@@ -1504,10 +1504,10 @@ exts_list = [
         'checksums': ['9cd87b3492cbf0be9d2df9317b2adf9fc30663770e69906654bea3f41b17cb08'],
     }),
     ('Variable::Magic', '0.64', {
-        'pretestopts': "LC_ALL=C ",
         'source_tmpl': 'Variable-Magic-%(version)s.tar.gz',
         'source_urls': ['https://cpan.metacpan.org/authors/id/V/VP/VPIT'],
         'checksums': ['9f7853249c9ea3b4df92fb6b790c03a60680fc029f44c8bf9894dccf019516bd'],
+        'pretestopts': 'LC_ALL=C ',  # Test fails if run in localized environments
     }),
     ('MooseX::Types::Perl', '0.101344', {
         'source_tmpl': 'MooseX-Types-Perl-%(version)s.tar.gz',
@@ -1560,7 +1560,7 @@ exts_list = [
         'checksums': ['66fccca6c6f330e7ecc898bd6a51846e2145b3e02d78c4997ba6b7de23b551ee'],
     }),
     ('Software::License', '0.104006', {
-        'runtest': False,
+        'runtest': False,  # This test just suddenly started to fail
         'source_tmpl': 'Software-License-%(version)s.tar.gz',
         'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'],
         'checksums': ['65c8ee1c2da2a4de10139863df668fa6b3b3e24a39d69a7cca39f284fb6b9c0f'],
@@ -1802,13 +1802,13 @@ exts_list = [
         'checksums': ['b599d8770a9a9fa0a8ae3cd0ed395a9cf71b4eb53aed82989a6bece33485a9cd'],
     }),
     ('Params::Check', '0.38', {
-        'configopts': 'INSTALLDIRS=site',
+        'configopts': 'INSTALLDIRS=site',  # Force it to correctly use site_perl
         'source_tmpl': 'Params-Check-%(version)s.tar.gz',
         'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'],
         'checksums': ['f0c9d33876c36b1bca1475276d26d2efaf449b256d7cc8118fae012e89a26290'],
     }),
     ('Locale::Maketext::Simple', '0.21', {
-        'configopts': 'INSTALLDIRS=site',
+        'configopts': 'INSTALLDIRS=site',  # Force it to correctly use site_perl
         'source_tmpl': 'Locale-Maketext-Simple-%(version)s.tar.gz',
         'source_urls': ['https://cpan.metacpan.org/authors/id/J/JE/JESSE'],
         'checksums': ['b009ff51f4fb108d19961a523e99b4373ccf958d37ca35bf1583215908dca9a9'],
@@ -1829,20 +1829,20 @@ exts_list = [
         'checksums': ['dbf7c827984951fb248907f940fd8f19f2696bc5545c0a15287e0fbe56a52308'],
     }),
     ('if', '0.0608', {
-        'configopts': 'INSTALLDIRS=site',
+        'configopts': 'INSTALLDIRS=site',  # Force it to correctly use site_perl
         'modulename': False,
         'source_tmpl': 'if-%(version)s.tar.gz',
         'source_urls': ['https://cpan.metacpan.org/authors/id/X/XS/XSAWYERX'],
         'checksums': ['37206e10919c4d99273020008a3581bf0947d364e859b8966521c3145b4b3700'],
     }),
     ('Test', '1.26', {
-        'configopts': 'INSTALLDIRS=site',
+        'configopts': 'INSTALLDIRS=site',  # Force it to correctly use site_perl
         'source_tmpl': 'Test-%(version)s.tar.gz',
         'source_urls': ['https://cpan.metacpan.org/authors/id/J/JE/JESSE'],
         'checksums': ['f7701bd28e05e7f82fe9a181bbab38f53fa6aeae48d2a810da74d1b981d4f392'],
     }),
     ('ExtUtils::Constant', '0.25', {
-        'runtest': False,
+        'runtest': False,  # Somehow has syntax errors in tests
         'source_tmpl': 'ExtUtils-Constant-%(version)s.tar.gz',
         'source_urls': ['https://cpan.metacpan.org/authors/id/N/NW/NWCLARK'],
         'checksums': ['6933d0e963b62281ef7561068e6aecac8c4ac2b476b2bba09ab0b90fbac9d757'],
@@ -1923,10 +1923,10 @@ exts_list = [
         'checksums': ['eacf71c5eb49e0e590de797f1982d7fb95d8481e4d13c3ce79eb32ef9373b3db'],
     }),
     ('Cwd', '3.75', {
-        'patches': ['PathTools-3.75_fix-cwd_enoent-test.patch'],
-        'runtest': False,
+        'runtest': False,  # Single failure about a tainted PATH
         'source_tmpl': 'PathTools-%(version)s.tar.gz',
         'source_urls': ['https://cpan.metacpan.org/authors/id/X/XS/XSAWYERX'],
+        'patches': ['PathTools-3.75_fix-cwd_enoent-test.patch'],
         'checksums': [
             {'PathTools-3.75.tar.gz': 'a558503aa6b1f8c727c0073339081a77888606aa701ada1ad62dd9d8c3f945a2'},
             {'PathTools-3.75_fix-cwd_enoent-test.patch':
@@ -1939,7 +1939,7 @@ exts_list = [
         'checksums': ['77f73d6f7aeb8d33be08b0d8c2617f9b6c77fb7fc45422d507ca8bafe4246017'],
     }),
     ('ExtUtils::CppGuess', '0.27', {
-        'runtest': False,
+        'runtest': False,  # Poorly written test
         'source_tmpl': 'ExtUtils-CppGuess-%(version)s.tar.gz',
         'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETJ'],
         'checksums': ['b2c7b581901054a32dfcea12536fda8626457ed0bfbc02600bd354bde7e2a9b4'],
@@ -1960,7 +1960,7 @@ exts_list = [
         'checksums': ['6fd4000e4022968e2ce5b83c07b189219ef1925ecb72977b52a6f7d76adbc349'],
     }),
     ('MCE::Mutex', '1.897', {
-        'runtest': False,
+        'runtest': False,  # Single failing subtest
         'source_tmpl': 'MCE-%(version)s.tar.gz',
         'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARIOROY'],
         'checksums': ['673d337d14fc2d7a12576ca6615c729821dc616ee76e0ecc9c0f32de8a9f9c39'],
@@ -2006,7 +2006,6 @@ exts_list = [
         'checksums': ['6d9de0c11921fd520dfd99a3f6b0ca9f1fd9850274f8bec10bbaa4f6803cc049'],
     }),
     ('IO::Compress::Zip', '2.212', {
-        'runtest': False,
         'source_tmpl': 'IO-Compress-%(version)s.tar.gz',
         'source_urls': ['https://cpan.metacpan.org/authors/id/P/PM/PMQS'],
         'checksums': ['687490dbf9c4be42c22a945c4601812be5f4d38a9836018148915ba9e0ea65b1'],
@@ -2042,6 +2041,7 @@ exts_list = [
         'checksums': ['510a7de2d011b0db80b0874e8c0f7390010991000ae135cff7474df1e6d51e3a'],
     }),
     ('Test::Sys::Info', '0.23', {
+        # test fails on systems without /etc/fstab - so comment it out
         'preconfigopts': "sed -i 's/ok( my %fs/# ok( my %fs/' lib/Test/Sys/Info/Driver.pm && ",
         'source_tmpl': 'Test-Sys-Info-%(version)s.tar.gz',
         'source_urls': ['https://cpan.metacpan.org/authors/id/B/BU/BURAK'],

From bfd5675f1fb9dc2082f77685d201e5f3c802cb83 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Mon, 8 Jul 2024 15:10:34 +0000
Subject: [PATCH 420/835] Add additional dep

---
 .../Perl-bundle-CPAN-5.38.2-GCCcore-13.3.0.eb                | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.2-GCCcore-13.3.0.eb
index 8d8b1eaa582..5c51ff66c07 100644
--- a/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.2-GCCcore-13.3.0.eb
+++ b/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.2-GCCcore-13.3.0.eb
@@ -61,6 +61,11 @@ exts_list = [
         'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'],
         'checksums': ['e73ff89c81c1a53f6baeef6816841b89d3384403ad97422a7da9d1eeb20ef9c5'],
     }),
+    ('CPAN::Requirements::Dynamic', '0.001', {
+        'source_tmpl': 'CPAN-Requirements-Dynamic-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'],
+        'checksums': ['4b590e712b9aca680c3631855ee16a50b84fa0227c362e13b237a75a01489ef5'],
+    }),
     ('Module::Build::Tiny', '0.048', {
         'source_tmpl': 'Module-Build-Tiny-%(version)s.tar.gz',
         'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'],

From 3591795d91ef7cf5a7221010d46009fdcb7a4a23 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Mon, 8 Jul 2024 15:28:12 +0000
Subject: [PATCH 421/835] Add additional dep

---
 .../Perl-bundle-CPAN-5.38.2-GCCcore-13.3.0.eb                | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.2-GCCcore-13.3.0.eb
index 5c51ff66c07..d4dd0fabd78 100644
--- a/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.2-GCCcore-13.3.0.eb
+++ b/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.2-GCCcore-13.3.0.eb
@@ -61,6 +61,11 @@ exts_list = [
         'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'],
         'checksums': ['e73ff89c81c1a53f6baeef6816841b89d3384403ad97422a7da9d1eeb20ef9c5'],
     }),
+    ('CPAN::Meta::Requirements', '2.143', {
+        'source_tmpl': 'CPAN-Meta-Requirements-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS/'],
+        'checksums': ['4b590e712b9aca680c3631855ee16a50b84fa0227c362e13b237a75a01489ef5'],
+    }),
     ('CPAN::Requirements::Dynamic', '0.001', {
         'source_tmpl': 'CPAN-Requirements-Dynamic-%(version)s.tar.gz',
         'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'],

From f2737727208db50ef2bc9c27d45ac03fee803a61 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Mon, 8 Jul 2024 15:38:03 +0000
Subject: [PATCH 422/835] Fix checksum

---
 .../Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.2-GCCcore-13.3.0.eb  | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.2-GCCcore-13.3.0.eb
index d4dd0fabd78..e1afa3106e6 100644
--- a/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.2-GCCcore-13.3.0.eb
+++ b/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.2-GCCcore-13.3.0.eb
@@ -64,7 +64,7 @@ exts_list = [
     ('CPAN::Meta::Requirements', '2.143', {
         'source_tmpl': 'CPAN-Meta-Requirements-%(version)s.tar.gz',
         'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS/'],
-        'checksums': ['4b590e712b9aca680c3631855ee16a50b84fa0227c362e13b237a75a01489ef5'],
+        'checksums': ['6ec7e4697bb5a8cea0ee3c8bd5d4b20ce086168a8084778d6e7a4c37356fdf8b'],
     }),
     ('CPAN::Requirements::Dynamic', '0.001', {
         'source_tmpl': 'CPAN-Requirements-Dynamic-%(version)s.tar.gz',

From af9e876772c9455dc89ed1090e5d05bd2e5d2fb5 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Mon, 8 Jul 2024 15:56:43 +0000
Subject: [PATCH 423/835] Drop patch

---
 .../Perl-bundle-CPAN-5.38.2-GCCcore-13.3.0.eb               | 6 +-----
 1 file changed, 1 insertion(+), 5 deletions(-)

diff --git a/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.2-GCCcore-13.3.0.eb
index e1afa3106e6..02f9f0872af 100644
--- a/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.2-GCCcore-13.3.0.eb
+++ b/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.2-GCCcore-13.3.0.eb
@@ -684,14 +684,10 @@ exts_list = [
         'checksums': ['aa12d1a4c0ac260b94d448fa01feba242a8a85cb6cbfdc66432e3b5b468add96'],
     }),
     ('Net::SSLeay', '1.94', {
-        'patches': ['Net-SSLeay-1.92_fix.patch'],
         'preconfigopts': "export OPENSSL_PREFIX=$EBROOTOPENSSL && ",
         'source_tmpl': 'Net-SSLeay-%(version)s.tar.gz',
         'source_urls': ['https://cpan.metacpan.org/authors/id/C/CH/CHRISN'],
-        'checksums': [
-            {'Net-SSLeay-1.94.tar.gz': '9d7be8a56d1bedda05c425306cc504ba134307e0c09bda4a788c98744ebcd95d'},
-            {'Net-SSLeay-1.92_fix.patch': '37790b10c5551bce92bc4bd7c98a92b0058fc16604272c7459a63096b52a8d1c'},
-        ],
+        'checksums': ['9d7be8a56d1bedda05c425306cc504ba134307e0c09bda4a788c98744ebcd95d'],
     }),
     ('IO::Socket::SSL', '2.087', {
         'source_tmpl': 'IO-Socket-SSL-%(version)s.tar.gz',

From 300c6b8cf317ff8edefae6cf40a528608a4a8da8 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Mon, 8 Jul 2024 16:58:00 +0000
Subject: [PATCH 424/835] Add another required extension

---
 .../Perl-bundle-CPAN-5.38.2-GCCcore-13.3.0.eb                | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.2-GCCcore-13.3.0.eb
index 02f9f0872af..39679dc0366 100644
--- a/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.2-GCCcore-13.3.0.eb
+++ b/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.2-GCCcore-13.3.0.eb
@@ -2011,6 +2011,11 @@ exts_list = [
         'source_urls': ['https://cpan.metacpan.org/authors/id/P/PM/PMQS'],
         'checksums': ['6d9de0c11921fd520dfd99a3f6b0ca9f1fd9850274f8bec10bbaa4f6803cc049'],
     }),
+    ('Compress::Raw::Bzip2', '2.212', {
+        'source_tmpl': 'Compress-Raw-Bzip2-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/P/PM/PMQS'],
+        'checksums': ['6caeee843c428f45fa9646ea98dc675470db63dbac0ee3e2d8e9ee4eb58a856d'],
+    }),
     ('IO::Compress::Zip', '2.212', {
         'source_tmpl': 'IO-Compress-%(version)s.tar.gz',
         'source_urls': ['https://cpan.metacpan.org/authors/id/P/PM/PMQS'],

From 658fb09ad1826c317aa990e139dad04e4a74ad2b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Mon, 8 Jul 2024 17:28:48 +0000
Subject: [PATCH 425/835] adding easyconfigs: gh-2.52.0.eb

---
 easybuild/easyconfigs/g/gh/gh-2.52.0.eb | 28 +++++++++++++++++++++++++
 1 file changed, 28 insertions(+)
 create mode 100644 easybuild/easyconfigs/g/gh/gh-2.52.0.eb

diff --git a/easybuild/easyconfigs/g/gh/gh-2.52.0.eb b/easybuild/easyconfigs/g/gh/gh-2.52.0.eb
new file mode 100644
index 00000000000..53a5bb57d66
--- /dev/null
+++ b/easybuild/easyconfigs/g/gh/gh-2.52.0.eb
@@ -0,0 +1,28 @@
+easyblock = 'GoPackage'
+
+name = 'gh'
+version = '2.52.0'
+
+homepage = 'https://github.com/cli/'
+description = "GitHub’s official command line tool"
+
+toolchain = SYSTEM
+
+source_urls = ['https://github.com/cli/cli/archive']
+sources = ['v%(version)s.tar.gz']
+checksums = ['41de39d0f1bcacb454d9b8a46e5b97ff8b8e803cd26d284e553e45bf025325d9']
+
+builddependencies = [
+    ('Go', '1.22.1')
+]
+
+installopts = './cmd/%(name)s'
+
+sanity_check_paths = {
+    'files': ['bin/%(name)s'],
+    'dirs': []
+}
+
+sanity_check_commands = ['%(name)s --version']
+
+moduleclass = 'tools'

From 54266588d33a456dd98cf9926c096085b64ef5ea Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Mon, 8 Jul 2024 19:56:47 +0000
Subject: [PATCH 426/835] adding easyconfigs: X11-20231019-GCCcore-13.3.0.eb,
 intltool-0.51.0-GCCcore-13.3.0.eb

---
 .../intltool-0.51.0-GCCcore-13.3.0.eb         |  37 +++
 .../x/X11/X11-20231019-GCCcore-13.3.0.eb      | 214 ++++++++++++++++++
 2 files changed, 251 insertions(+)
 create mode 100644 easybuild/easyconfigs/i/intltool/intltool-0.51.0-GCCcore-13.3.0.eb
 create mode 100644 easybuild/easyconfigs/x/X11/X11-20231019-GCCcore-13.3.0.eb

diff --git a/easybuild/easyconfigs/i/intltool/intltool-0.51.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/i/intltool/intltool-0.51.0-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..e5797e51b02
--- /dev/null
+++ b/easybuild/easyconfigs/i/intltool/intltool-0.51.0-GCCcore-13.3.0.eb
@@ -0,0 +1,37 @@
+easyblock = 'ConfigureMake'
+
+name = 'intltool'
+version = '0.51.0'
+
+homepage = 'https://freedesktop.org/wiki/Software/intltool/'
+description = """intltool is a set of tools to centralize translation of
+ many different file formats using GNU gettext-compatible PO files."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+source_urls = ['https://launchpad.net/intltool/trunk/%(version)s/+download/']
+sources = [SOURCE_TAR_GZ]
+patches = ['intltool-%(version)s_fix-Perl-compat.patch']
+checksums = [
+    '67c74d94196b153b774ab9f89b2fa6c6ba79352407037c8c14d5aeb334e959cd',  # intltool-0.51.0.tar.gz
+    'e839f7228b2b92301831bca88ed0bc7bce5dbf862568f1644642988204903db6',  # intltool-0.51.0_fix-Perl-compat.patch
+]
+
+builddependencies = [
+    ('binutils', '2.42'),
+]
+
+dependencies = [
+    ('Perl-bundle-CPAN', '5.38.2'),
+]
+
+fix_perl_shebang_for = ['bin/intltool-*']
+
+sanity_check_paths = {
+    'files': ['bin/intltool%s' % x for x in ['-extract', '-merge', '-prepare', '-update', 'ize']],
+    'dirs': []
+}
+
+sanity_check_commands = ["intltool-merge --help"]
+
+moduleclass = 'devel'
diff --git a/easybuild/easyconfigs/x/X11/X11-20231019-GCCcore-13.3.0.eb b/easybuild/easyconfigs/x/X11/X11-20231019-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..afc2781dc63
--- /dev/null
+++ b/easybuild/easyconfigs/x/X11/X11-20231019-GCCcore-13.3.0.eb
@@ -0,0 +1,214 @@
+easyblock = 'Bundle'
+
+name = 'X11'
+version = '20231019'
+
+homepage = 'https://www.x.org'
+description = "The X Window System (X11) is a windowing system for bitmap displays"
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+builddependencies = [
+    ('binutils', '2.42'),
+    ('Autotools', '20231222'),
+    ('Bison', '3.8.2'),
+    ('gettext', '0.22.5'),
+    ('pkgconf', '2.2.0'),
+    ('intltool', '0.51.0'),
+    ('Meson', '1.4.0'),
+    ('Ninja', '1.12.1'),
+    ('Doxygen', '1.11.0'),
+]
+
+dependencies = [
+    ('bzip2', '1.0.8'),
+    ('fontconfig', '2.15.0'),
+    ('freetype', '2.13.2'),
+    ('zlib', '1.3.1'),
+    ('xorg-macros', '1.20.1'),
+    ('libpciaccess', '0.18.1'),
+]
+
+source_urls = [
+    XORG_LIB_SOURCE,
+    XORG_PROTO_SOURCE,
+    'https://xcb.freedesktop.org/dist/',
+    'https://xkbcommon.org/download/',
+    XORG_DATA_SOURCE + '/xkeyboard-config',
+    XORG_DATA_SOURCE,
+]
+
+default_easyblock = 'ConfigureMake'
+
+default_component_specs = {
+    'sources': [SOURCE_TAR_GZ],
+    'start_dir': '%(name)s-%(version)s',
+}
+
+components = [
+    ('libpthread-stubs', '0.5', {  # 2023-07-18
+        'checksums': ['593196cc746173d1e25cb54a93a87fd749952df68699aab7e02c085530e87747'],
+    }),
+    ('xorgproto', '2024.1', {  # 2024-03-26
+        'checksums': ['c791aad9b5847781175388ebe2de85cb5f024f8dabf526d5d699c4f942660cc3'],
+    }),
+    ('libXau', '1.0.11', {  # 2022-12-08
+        'checksums': ['3a321aaceb803577a4776a5efe78836eb095a9e44bbc7a465d29463e1a14f189'],
+    }),
+    ('libXdmcp', '1.1.5', {  # 2024-03-02
+        'checksums': ['55041a8ff8992ab02777478c4b19c249c0f8399f05a752cb4a1a868a9a0ccb9a'],
+    }),
+    ('xcb-proto', '1.17.0', {  # 2024-04-15
+        'checksums': ['d9c7f010b1105fc3858bf07b5169b2dd8e7493c6652b1fe45f3321d874f291d7'],
+    }),
+    ('libxcb', '1.17.0', {  # 2024-04-15
+        'checksums': ['bc0f75f84b28e6496a19a1d094d7e47def861a50cb7cce5b23b62eecdc2a4479'],
+    }),
+    ('xtrans', '1.5.0', {  # 2023-06-03
+        'checksums': ['a806f8a92f879dcd0146f3f1153fdffe845f2fc0df9b1a26c19312b7b0a29c86'],
+    }),
+    ('libxkbcommon', '1.7.0', {  # 2024-03-23
+        'easyblock': 'MesonNinja',
+        'sources': [SOURCE_TAR_XZ],
+        'checksums': ['0edc14eccdd391514458bc5f5a4b99863ed2d651e4dd761a90abf4f46ef99c2b'],
+        'preconfigopts': '',
+        'configopts': '-Denable-wayland=false -Denable-docs=false ',
+    }),
+    ('libX11', '1.8.9', {  # 2024-04-05
+        'checksums': ['793ebebf569f12c864b77401798d38814b51790fce206e01a431e5feb982e20b'],
+    }),
+    ('libXext', '1.3.6', {  # 2024-02-04
+        'checksums': ['1a3dcda154f803be0285b46c9338515804b874b5ccc7a2b769ab7fd76f1035bd'],
+    }),
+    ('libFS', '1.0.9', {  # 2022-08-26
+        'checksums': ['8bc2762f63178905228a28670539badcfa2c8793f7b6ce3f597b7741b932054a'],
+    }),
+    ('libICE', '1.1.1', {  # 2022-12-08
+        'checksums': ['04fbd34a11ba08b9df2e3cdb2055c2e3c1c51b3257f683d7fcf42dabcf8e1210'],
+    }),
+    ('libSM', '1.2.4', {  # 2022-12-20
+        'checksums': ['51464ce1abce323d5b6707ceecf8468617106e1a8a98522f8342db06fd024c15'],
+    }),
+    ('libXScrnSaver', '1.2.4', {  # 2022-12-05
+        'checksums': ['0656b2630475104d6df75d91ebb8e0153e61d14e9871ef1f403bcda4a62a838a'],
+    }),
+    ('libXt', '1.3.0', {  # 2023-05-09
+        'checksums': ['de4a80c4cc7785b9620e572de71026805f68e85a2bf16c386009ef0e50be3f77'],
+    }),
+    ('libXmu', '1.2.1', {  # 2024-04-16
+        'checksums': ['3091d711cdc1d8ea0f545a13b90d1464c3c3ab64778fd121f0d789b277a80289'],
+    }),
+    ('libXpm', '3.5.17', {  # 2023-10-03
+        'checksums': ['959466c7dfcfcaa8a65055bfc311f74d4c43d9257900f85ab042604d286df0c6'],
+    }),
+    ('libXaw', '1.0.16', {  # 2024-03-10
+        'checksums': ['ca8a613884c922985202075b3cc8ee8821bfa83a5eb066189ae3cca131e63972'],
+    }),
+    ('libXfixes', '6.0.1', {  # 2023-04-09
+        'checksums': ['e69eaa321173c748ba6e2f15c7cf8da87f911d3ea1b6af4b547974aef6366bec'],
+    }),
+    ('libXcomposite', '0.4.6', {  # 2022-12-04
+        'checksums': ['3599dfcd96cd48d45e6aeb08578aa27636fa903f480f880c863622c2b352d076'],
+    }),
+    ('libXrender', '0.9.11', {  # 2022-10-22
+        'checksums': ['6aec3ca02e4273a8cbabf811ff22106f641438eb194a12c0ae93c7e08474b667'],
+    }),
+    ('libXcursor', '1.2.2', {  # 2024-03-02
+        'checksums': ['77f96b9ad0a3c422cfa826afabaf1e02b9bfbfc8908c5fa1a45094faad074b98'],
+    }),
+    ('libXdamage', '1.1.6', {  # 2022-12-04
+        'checksums': ['2afcc139eb6eb926ffe344494b1fc023da25def42874496e6e6d3aa8acef8595'],
+    }),
+    ('libfontenc', '1.1.8', {  # 2024-03-02
+        'checksums': ['5e5f210329823f08f97bfe9fd5b4105070c789bc5aef88ce01d86d8203d4aa9f'],
+    }),
+    ('libXfont', '1.5.4', {  # 2017-11-28
+        'checksums': ['59be6eab53f7b0feb6b7933c11d67d076ae2c0fd8921229c703fc7a4e9a80d6e'],
+    }),
+    ('libXfont2', '2.0.6', {  # 2022-08-26
+        'checksums': ['a944df7b6837c8fa2067f6a5fc25d89b0acc4011cd0bc085106a03557fb502fc'],
+    }),
+    ('libXft', '2.3.8', {  # 2023-04-17
+        'checksums': ['32e48fe2d844422e64809e4e99b9d8aed26c1b541a5acf837c5037b8d9f278a8'],
+    }),
+    ('libXi', '1.8.1', {  # 2023-05-04
+        'checksums': ['3b5f47c223e4b63d7f7fe758886b8bf665b20a7edb6962c423892fd150e326ea'],
+    }),
+    ('libXinerama', '1.1.5', {  # 2022-10-29
+        'checksums': ['2efa855cb42dc620eff3b77700d8655695e09aaa318f791f201fa60afa72b95c'],
+    }),
+    ('libXrandr', '1.5.4', {  # 2023-10-04
+        'checksums': ['c72c94dc3373512ceb67f578952c5d10915b38cc9ebb0fd176a49857b8048e22'],
+    }),
+    ('libXres', '1.2.2', {  # 2022-12-05
+        'checksums': ['8abce597ced4a7ab89032aee91f6f784d9960adc772b2b59f17e515cd4127950'],
+    }),
+    ('libXtst', '1.2.4', {  # 2022-09-27
+        'checksums': ['01366506aeb033f6dffca5326af85f670746b0cabbfd092aabefb046cf48c445'],
+    }),
+    ('libXv', '1.0.12', {  # 2022-12-05
+        'checksums': ['ce706619a970a580a0e35e9b5c98bdd2af243ac6494c65f44608a89a86100126'],
+    }),
+    ('libXvMC', '1.0.14', {  # 2024-02-04
+        'checksums': ['e630b4373af8c67a7c8f07ebe626a1269a613d262d1f737b57231a06f7c34b4e'],
+    }),
+    ('libXxf86dga', '1.1.6', {  # 2022-12-05
+        'checksums': ['87c7482b1e29b4eeb415815641c4f69c00545a8138e1b73ff1f361f7d9c22ac4'],
+    }),
+    ('libXxf86vm', '1.1.5', {  # 2022-09-27
+        'checksums': ['f3f1c29fef8accb0adbd854900c03c6c42f1804f2bc1e4f3ad7b2e1f3b878128'],
+    }),
+    ('libdmx', '1.1.5', {  # 2023-06-03
+        'checksums': ['070e82cc1daa1b21ee1339aef56a909eab04cbe7d430fabfbb01ecd21b2dd9f3'],
+    }),
+    ('libxkbfile', '1.1.3', {  # 2024-02-04
+        'checksums': ['d1a7e659bc7ae1aa1fc1ecced261c734df5ad5d86af1ef7a946be0e2d841e51d'],
+    }),
+    ('libxshmfence', '1.3.2', {  # 2022-12-08
+        'checksums': ['e93a85099604beb244ee756dcaf70e18b08701c1ca84c4de0126cd71bd6c8181'],
+    }),
+    ('xcb-util', '0.4.1', {  # 2022-12-20
+        'checksums': ['21c6e720162858f15fe686cef833cf96a3e2a79875f84007d76f6d00417f593a'],
+    }),
+    ('xcb-util-image', '0.4.1', {  # 2022-10-18
+        'checksums': ['0ebd4cf809043fdeb4f980d58cdcf2b527035018924f8c14da76d1c81001293b'],
+    }),
+    ('xcb-util-keysyms', '0.4.1', {  # 2022-10-19
+        'checksums': ['1fa21c0cea3060caee7612b6577c1730da470b88cbdf846fa4e3e0ff78948e54'],
+    }),
+    ('xcb-util-renderutil', '0.3.10', {  # 2022-10-19
+        'checksums': ['e04143c48e1644c5e074243fa293d88f99005b3c50d1d54358954404e635128a'],
+    }),
+    ('xcb-util-wm', '0.4.2', {  # 2022-10-19
+        'checksums': ['dcecaaa535802fd57c84cceeff50c64efe7f2326bf752e16d2b77945649c8cd7'],
+    }),
+    ('xcb-util-cursor', '0.1.5', {  # 2023-10-19
+        'checksums': ['0e9c5446dc6f3beb8af6ebfcc9e27bcc6da6fe2860f7fc07b99144dfa568e93b'],
+    }),
+    ('xkeyboard-config', '2.42', {  # 2024-06-07
+        'easyblock': 'MesonNinja',
+        'sources': [SOURCE_TAR_XZ],
+        'checksums': ['7a3dba1bec7dc7191432da021242d17c9cf6c89690e6c57b0de048ff8c9d2ae3'],
+        # required to overrule parent preconfigopts that runs autogen.sh if configure script is missing
+        'preconfigopts': '',
+    }),
+    ('printproto', '1.0.5', {  # 2011-01-06
+        'checksums': ['e8b6f405fd865f0ea7a3a2908dfbf06622f57f2f91359ec65d13b955e49843fc'],
+    }),
+    ('libXp', '1.0.4', {  # 2022-09-12
+        'checksums': ['05e46af1ccb68f1752cca5879774a4fb9bf3b19fe088eb745034956e0c6fadba'],
+    }),
+    ('xbitmaps', '1.1.3', {  # 2023-02-23
+        'checksums': ['93b433b7ff223c4685fdba583b4bd30f2706be2413a670021084422d85b0269d'],
+    }),
+]
+
+preconfigopts = "if [ ! -f configure ]; then ./autogen.sh; fi && "
+
+sanity_check_paths = {
+    'files': ['include/X11/Xlib.h', 'include/X11/Xutil.h'],
+    'dirs': ['include/GL', 'include/X11', 'include/X11/extensions', 'lib/pkgconfig',
+             'share/pkgconfig', 'share/X11/xkb'],
+}
+
+moduleclass = 'vis'

From dc306e732fc62043356483a6449748cde64f810f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Mon, 8 Jul 2024 20:31:06 +0000
Subject: [PATCH 427/835] Fix checksums

---
 .../x/X11/X11-20231019-GCCcore-13.3.0.eb      | 28 +++++++++----------
 1 file changed, 14 insertions(+), 14 deletions(-)

diff --git a/easybuild/easyconfigs/x/X11/X11-20231019-GCCcore-13.3.0.eb b/easybuild/easyconfigs/x/X11/X11-20231019-GCCcore-13.3.0.eb
index afc2781dc63..14dc6751a9f 100644
--- a/easybuild/easyconfigs/x/X11/X11-20231019-GCCcore-13.3.0.eb
+++ b/easybuild/easyconfigs/x/X11/X11-20231019-GCCcore-13.3.0.eb
@@ -50,19 +50,19 @@ components = [
         'checksums': ['593196cc746173d1e25cb54a93a87fd749952df68699aab7e02c085530e87747'],
     }),
     ('xorgproto', '2024.1', {  # 2024-03-26
-        'checksums': ['c791aad9b5847781175388ebe2de85cb5f024f8dabf526d5d699c4f942660cc3'],
+        'checksums': ['4f6b9b4faf91e5df8265b71843a91fc73dc895be6210c84117a996545df296ce'],
     }),
     ('libXau', '1.0.11', {  # 2022-12-08
         'checksums': ['3a321aaceb803577a4776a5efe78836eb095a9e44bbc7a465d29463e1a14f189'],
     }),
     ('libXdmcp', '1.1.5', {  # 2024-03-02
-        'checksums': ['55041a8ff8992ab02777478c4b19c249c0f8399f05a752cb4a1a868a9a0ccb9a'],
+        'checksums': ['31a7abc4f129dcf6f27ae912c3eedcb94d25ad2e8f317f69df6eda0bc4e4f2f3'],
     }),
     ('xcb-proto', '1.17.0', {  # 2024-04-15
-        'checksums': ['d9c7f010b1105fc3858bf07b5169b2dd8e7493c6652b1fe45f3321d874f291d7'],
+        'checksums': ['392d3c9690f8c8202a68fdb89c16fd55159ab8d65000a6da213f4a1576e97a16'],
     }),
     ('libxcb', '1.17.0', {  # 2024-04-15
-        'checksums': ['bc0f75f84b28e6496a19a1d094d7e47def861a50cb7cce5b23b62eecdc2a4479'],
+        'checksums': ['2c69287424c9e2128cb47ffe92171e10417041ec2963bceafb65cb3fcf8f0b85'],
     }),
     ('xtrans', '1.5.0', {  # 2023-06-03
         'checksums': ['a806f8a92f879dcd0146f3f1153fdffe845f2fc0df9b1a26c19312b7b0a29c86'],
@@ -70,15 +70,15 @@ components = [
     ('libxkbcommon', '1.7.0', {  # 2024-03-23
         'easyblock': 'MesonNinja',
         'sources': [SOURCE_TAR_XZ],
-        'checksums': ['0edc14eccdd391514458bc5f5a4b99863ed2d651e4dd761a90abf4f46ef99c2b'],
+        'checksums': ['65782f0a10a4b455af9c6baab7040e2f537520caa2ec2092805cdfd36863b247'],
         'preconfigopts': '',
         'configopts': '-Denable-wayland=false -Denable-docs=false ',
     }),
     ('libX11', '1.8.9', {  # 2024-04-05
-        'checksums': ['793ebebf569f12c864b77401798d38814b51790fce206e01a431e5feb982e20b'],
+        'checksums': ['57ca5f07d263788ad661a86f4139412e8b699662e6b60c20f1f028c25a935e48'],
     }),
     ('libXext', '1.3.6', {  # 2024-02-04
-        'checksums': ['1a3dcda154f803be0285b46c9338515804b874b5ccc7a2b769ab7fd76f1035bd'],
+        'checksums': ['1a0ac5cd792a55d5d465ced8dbf403ed016c8e6d14380c0ea3646c4415496e3d'],
     }),
     ('libFS', '1.0.9', {  # 2022-08-26
         'checksums': ['8bc2762f63178905228a28670539badcfa2c8793f7b6ce3f597b7741b932054a'],
@@ -96,13 +96,13 @@ components = [
         'checksums': ['de4a80c4cc7785b9620e572de71026805f68e85a2bf16c386009ef0e50be3f77'],
     }),
     ('libXmu', '1.2.1', {  # 2024-04-16
-        'checksums': ['3091d711cdc1d8ea0f545a13b90d1464c3c3ab64778fd121f0d789b277a80289'],
+        'checksums': ['bf0902583dd1123856c11e0a5085bd3c6e9886fbbd44954464975fd7d52eb599'],
     }),
     ('libXpm', '3.5.17', {  # 2023-10-03
         'checksums': ['959466c7dfcfcaa8a65055bfc311f74d4c43d9257900f85ab042604d286df0c6'],
     }),
     ('libXaw', '1.0.16', {  # 2024-03-10
-        'checksums': ['ca8a613884c922985202075b3cc8ee8821bfa83a5eb066189ae3cca131e63972'],
+        'checksums': ['012f90adf8739f2f023d63a5fee1528949cf2aba92ef7ac1abcfc2ae9cf28798'],
     }),
     ('libXfixes', '6.0.1', {  # 2023-04-09
         'checksums': ['e69eaa321173c748ba6e2f15c7cf8da87f911d3ea1b6af4b547974aef6366bec'],
@@ -114,13 +114,13 @@ components = [
         'checksums': ['6aec3ca02e4273a8cbabf811ff22106f641438eb194a12c0ae93c7e08474b667'],
     }),
     ('libXcursor', '1.2.2', {  # 2024-03-02
-        'checksums': ['77f96b9ad0a3c422cfa826afabaf1e02b9bfbfc8908c5fa1a45094faad074b98'],
+        'checksums': ['98c3a30a3f85274c167d1ac5419d681ce41f14e27bfa5fe3003c8172cd8af104'],
     }),
     ('libXdamage', '1.1.6', {  # 2022-12-04
         'checksums': ['2afcc139eb6eb926ffe344494b1fc023da25def42874496e6e6d3aa8acef8595'],
     }),
     ('libfontenc', '1.1.8', {  # 2024-03-02
-        'checksums': ['5e5f210329823f08f97bfe9fd5b4105070c789bc5aef88ce01d86d8203d4aa9f'],
+        'checksums': ['b55039f70959a1b2f02f4ec8db071e5170528d2c9180b30575dccf7510d7fb9f'],
     }),
     ('libXfont', '1.5.4', {  # 2017-11-28
         'checksums': ['59be6eab53f7b0feb6b7933c11d67d076ae2c0fd8921229c703fc7a4e9a80d6e'],
@@ -150,7 +150,7 @@ components = [
         'checksums': ['ce706619a970a580a0e35e9b5c98bdd2af243ac6494c65f44608a89a86100126'],
     }),
     ('libXvMC', '1.0.14', {  # 2024-02-04
-        'checksums': ['e630b4373af8c67a7c8f07ebe626a1269a613d262d1f737b57231a06f7c34b4e'],
+        'checksums': ['3ad5d2b991219e2bf9b2f85d40b12c16f1afec038715e462f6058af73a9b5ef8'],
     }),
     ('libXxf86dga', '1.1.6', {  # 2022-12-05
         'checksums': ['87c7482b1e29b4eeb415815641c4f69c00545a8138e1b73ff1f361f7d9c22ac4'],
@@ -162,7 +162,7 @@ components = [
         'checksums': ['070e82cc1daa1b21ee1339aef56a909eab04cbe7d430fabfbb01ecd21b2dd9f3'],
     }),
     ('libxkbfile', '1.1.3', {  # 2024-02-04
-        'checksums': ['d1a7e659bc7ae1aa1fc1ecced261c734df5ad5d86af1ef7a946be0e2d841e51d'],
+        'checksums': ['c4c2687729d1f920f165ebb96557a1ead2ef655809ab5eaa66a1ad36dc31050d'],
     }),
     ('libxshmfence', '1.3.2', {  # 2022-12-08
         'checksums': ['e93a85099604beb244ee756dcaf70e18b08701c1ca84c4de0126cd71bd6c8181'],
@@ -188,7 +188,7 @@ components = [
     ('xkeyboard-config', '2.42', {  # 2024-06-07
         'easyblock': 'MesonNinja',
         'sources': [SOURCE_TAR_XZ],
-        'checksums': ['7a3dba1bec7dc7191432da021242d17c9cf6c89690e6c57b0de048ff8c9d2ae3'],
+        'checksums': ['a6b06ebfc1f01fc505f2f05f265f95f67cc8873a54dd247e3c2d754b8f7e0807'],
         # required to overrule parent preconfigopts that runs autogen.sh if configure script is missing
         'preconfigopts': '',
     }),

From 4ddc93e2064cab5e9bc88a300dc62c62cb711938 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Mon, 8 Jul 2024 20:42:01 +0000
Subject: [PATCH 428/835] adding easyconfigs: Wayland-1.23.0-GCCcore-13.3.0.eb

---
 .../Wayland/Wayland-1.23.0-GCCcore-13.3.0.eb  | 63 +++++++++++++++++++
 1 file changed, 63 insertions(+)
 create mode 100644 easybuild/easyconfigs/w/Wayland/Wayland-1.23.0-GCCcore-13.3.0.eb

diff --git a/easybuild/easyconfigs/w/Wayland/Wayland-1.23.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/w/Wayland/Wayland-1.23.0-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..b774886e5cb
--- /dev/null
+++ b/easybuild/easyconfigs/w/Wayland/Wayland-1.23.0-GCCcore-13.3.0.eb
@@ -0,0 +1,63 @@
+# Author: Jasper Grimm (UoY)
+# URL of Wayland download changed to GitLab due to changes upstream
+# Author: J. Sassmannshausen (Imperial College London/UK)
+easyblock = 'Bundle'
+
+name = 'Wayland'
+version = '1.23.0'
+
+homepage = 'https://wayland.freedesktop.org/'
+description = """
+Wayland is a project to define a protocol for a compositor to talk to
+ its clients as well as a library implementation of the protocol.  The
+ compositor can be a standalone display server running on Linux kernel
+ modesetting and evdev input devices, an X application, or a wayland
+ client itself.  The clients can be traditional applications, X servers
+ (rootless or fullscreen) or other display servers.
+"""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+builddependencies = [
+    ('CMake', '3.29.3'),
+    ('Meson', '1.4.0'),
+    ('Ninja', '1.12.1'),
+    ('pkgconf', '2.2.0'),
+    ('binutils', '2.42'),
+]
+
+dependencies = [
+    ('libffi', '3.4.5'),
+    ('expat', '2.6.2'),
+    ('libxml2', '2.12.7'),
+]
+
+default_easyblock = 'MesonNinja'
+default_component_specs = {
+    'start_dir': '%(namelower)s-%(version)s',
+}
+
+components = [
+    ('wayland', version, {
+        'source_urls': ['https://gitlab.freedesktop.org/wayland/%(namelower)s/-/releases/%(version)s/downloads'],
+        'checksums': ['05b3e1574d3e67626b5974f862f36b5b427c7ceeb965cb36a4e6c2d342e45ab2'],
+        'sources': [SOURCE_TAR_XZ],
+        'configopts': "-Ddocumentation=false",
+    }),
+    ('wayland-protocols', '1.36', {
+        'source_urls': ['https://gitlab.freedesktop.org/wayland/%(namelower)s/-/releases/%(version)s/downloads'],
+        'checksums': ['71fd4de05e79f9a1ca559fac30c1f8365fa10346422f9fe795f74d77b9ef7e92'],
+        'sources': [SOURCE_TAR_XZ],
+        'preconfigopts': "PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH "
+    }),
+]
+
+_libs = ['lib/libwayland-%s.%s' % (x, SHLIB_EXT) for x in ['client', 'cursor', 'egl', 'server']]
+sanity_check_paths = {
+    'files': ['bin/wayland-scanner'] + _libs,
+    'dirs': ['lib'],
+}
+
+sanity_check_commands = ["wayland-scanner --help", "wayland-scanner --version"]
+
+moduleclass = 'vis'

From 979b3bde93874fa9c4a0f4841b7e07c11322b30c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Mon, 8 Jul 2024 21:59:06 +0000
Subject: [PATCH 429/835] Fix name

---
 ...0231019-GCCcore-13.3.0.eb => X11-20240607-GCCcore-13.3.0.eb} | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)
 rename easybuild/easyconfigs/x/X11/{X11-20231019-GCCcore-13.3.0.eb => X11-20240607-GCCcore-13.3.0.eb} (99%)

diff --git a/easybuild/easyconfigs/x/X11/X11-20231019-GCCcore-13.3.0.eb b/easybuild/easyconfigs/x/X11/X11-20240607-GCCcore-13.3.0.eb
similarity index 99%
rename from easybuild/easyconfigs/x/X11/X11-20231019-GCCcore-13.3.0.eb
rename to easybuild/easyconfigs/x/X11/X11-20240607-GCCcore-13.3.0.eb
index 14dc6751a9f..64a4416b30e 100644
--- a/easybuild/easyconfigs/x/X11/X11-20231019-GCCcore-13.3.0.eb
+++ b/easybuild/easyconfigs/x/X11/X11-20240607-GCCcore-13.3.0.eb
@@ -1,7 +1,7 @@
 easyblock = 'Bundle'
 
 name = 'X11'
-version = '20231019'
+version = '20240607'
 
 homepage = 'https://www.x.org'
 description = "The X Window System (X11) is a windowing system for bitmap displays"

From d280af8d8bc19a9f0bf010a6f3336e10bba37e2b Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Tue, 9 Jul 2024 13:56:11 +0200
Subject: [PATCH 430/835] add visit and update vtk-9.3.0

---
 .../q/Qwt/Qwt-6.3.0-GCCcore-12.3.0.eb         | 39 ++++++++
 .../easyconfigs/v/VTK/VTK-9.2.6-foss-2023a.eb | 98 +++++++++++++++++++
 .../easyconfigs/v/VTK/VTK-9.3.0-foss-2023a.eb |  8 +-
 .../v/Visit/Visit-3.4.1-foss-2023a.eb         | 75 ++++++++++++++
 4 files changed, 219 insertions(+), 1 deletion(-)
 create mode 100644 easybuild/easyconfigs/q/Qwt/Qwt-6.3.0-GCCcore-12.3.0.eb
 create mode 100644 easybuild/easyconfigs/v/VTK/VTK-9.2.6-foss-2023a.eb
 create mode 100644 easybuild/easyconfigs/v/Visit/Visit-3.4.1-foss-2023a.eb

diff --git a/easybuild/easyconfigs/q/Qwt/Qwt-6.3.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/q/Qwt/Qwt-6.3.0-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..f208a034542
--- /dev/null
+++ b/easybuild/easyconfigs/q/Qwt/Qwt-6.3.0-GCCcore-12.3.0.eb
@@ -0,0 +1,39 @@
+easyblock = 'ConfigureMake'
+
+name = 'Qwt'
+version = '6.3.0'
+
+homepage = 'https://qwt.sourceforge.io/'
+description = """The Qwt library contains GUI Components and utility classes which are primarily useful for programs
+ with a technical background."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+source_urls = [SOURCEFORGE_SOURCE]
+sources = [SOURCELOWER_TAR_BZ2]
+patches = ['Qwt-6.2.0_fix-install-prefix.patch']
+checksums = [
+    {'qwt-6.3.0.tar.bz2': 'dcb085896c28aaec5518cbc08c0ee2b4e60ada7ac929d82639f6189851a6129a'},
+    {'Qwt-6.2.0_fix-install-prefix.patch': 'ac5c329c0693d565b461cdd3b36c1b96b4d09885e1e0c10929fc7a9021c03bad'},
+]
+
+builddependencies = [
+    ('binutils', '2.40'),
+    ('pkgconf', '1.9.5'),
+]
+
+dependencies = [
+    ('Qt5', '5.15.10'),
+]
+
+skipsteps = ['configure']
+
+prebuildopts = 'export QWT_PREFIX=%(installdir)s && '
+prebuildopts += "qmake qwt.pro && "
+
+sanity_check_paths = {
+    'files': ['lib/libqwt.%s' % SHLIB_EXT, 'lib/pkgconfig/Qt5Qwt6.pc'],
+    'dirs': ['doc', 'features', 'include', 'plugins'],
+}
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/v/VTK/VTK-9.2.6-foss-2023a.eb b/easybuild/easyconfigs/v/VTK/VTK-9.2.6-foss-2023a.eb
new file mode 100644
index 00000000000..5c6c6f7a122
--- /dev/null
+++ b/easybuild/easyconfigs/v/VTK/VTK-9.2.6-foss-2023a.eb
@@ -0,0 +1,98 @@
+##
+# Authors::
+# * Fotis Georgatos <fotis@cern.ch>
+# * Robert Mijakovic <robert.mijakovic@lxp.lu>
+# Update: Pavel Tománek (Inuits)
+##
+
+easyblock = 'CMakeNinja'
+
+name = 'VTK'
+version = '9.2.6'
+
+homepage = 'https://www.vtk.org'
+description = """The Visualization Toolkit (VTK) is an open-source, freely available software system for
+ 3D computer graphics, image processing and visualization. VTK consists of a C++ class library and several
+ interpreted interface layers including Tcl/Tk, Java, and Python. VTK supports a wide variety of visualization
+ algorithms including: scalar, vector, tensor, texture, and volumetric methods; and advanced modeling techniques
+ such as: implicit modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+toolchainopts = {'usempi': True}
+
+source_urls = ['https://www.vtk.org/files/release/%(version_major_minor)s']
+sources = [
+    SOURCE_TAR_GZ,
+    '%(name)sData-%(version)s.tar.gz',
+]
+patches = [('vtk-version.egg-info', '.')]
+checksums = [
+    {'VTK-9.2.6.tar.gz': '06fc8d49c4e56f498c40fcb38a563ed8d4ec31358d0101e8988f0bb4d539dd12'},
+    {'VTKData-9.2.6.tar.gz': '032c4b827173f859c898403d25360dc99409a4674559ad58f48828f23a6258b8'},
+    {'vtk-version.egg-info': '787b82415ae7a4a1f815b4db0e25f7abc809a05fc85d7d219627f3a7e5d3867b'},
+]
+
+builddependencies = [
+    ('CMake', '3.26.3'),
+    ('Ninja', '1.11.1'),
+]
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('XZ', '5.4.2'),
+    ('libGLU', '9.0.3'),
+    ('X11', '20230603'),
+    ('Qt5', '5.15.10'),
+]
+
+separate_build_dir = True
+
+# OpenGL
+configopts = "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT
+configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT
+configopts += "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include "
+# Python
+configopts += "-DVTK_WRAP_PYTHON=ON -DVTK_PYTHON_VERSION=3 -DVTK_PYTHON_OPTIONAL_LINK=OFF "
+configopts += "-DPython3_EXECUTABLE=$EBROOTPYTHON/bin/python3 "
+configopts += "-DPython3_INCLUDE_DIR=$EBROOTPYTHON/include/python%(pyshortver)s "
+configopts += "-DPython3_LIBRARY=$EBROOTPYTHON/lib/libpython%(pyshortver)s.so "
+# Other
+configopts += "-DVTK_USE_MPI=ON "
+configopts += "-DCMAKE_INSTALL_LIBDIR=lib "
+configopts += "-DVTK_QT_VERSION=5 "
+configopts += "-DQt5_DIR=$EBROOTQT5 "
+configopts += "-DVTK_MODULE_ENABLE_VTK_GuiSupportQt=YES "
+configopts += "-DVTK_MODULE_ENABLE_VTK_ViewsQt=YES"
+
+preinstallopts = "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && "
+
+# Install a egg-info file so VTK is more python friendly, required for mayavi
+local_egg_info_src = '%(builddir)s/VTK-%(version)s/vtk-version.egg-info'
+local_egg_info_dest = '%(installdir)s/lib/python%(pyshortver)s/site-packages/vtk-%(version)s.egg-info'
+postinstallcmds = [
+    'sed "s/#VTK_VERSION#/%%(version)s/" %s > %s' % (local_egg_info_src, local_egg_info_dest),
+]
+
+modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']}
+
+local_vtk_exec = ['vtk%s-%%(version_major_minor)s' % x
+                  for x in ['WrapJava', 'ParseJava', 'WrapPythonInit', 'WrapPython', 'WrapHierarchy']]
+local_vtk_exec += ['vtkpython']
+local_vtk_libs = ['CommonCore', 'IONetCDF', 'ParallelCore', 'RenderingOpenGL2']
+
+sanity_check_paths = {
+    'files': ['bin/%s' % x for x in local_vtk_exec] + ['include/vtk-%(version_major_minor)s/vtkMPI.h'] +
+             ['lib/libvtk%s-%%(version_major_minor)s.%s' % (l, SHLIB_EXT) for l in local_vtk_libs],
+    'dirs': ['lib/python%(pyshortver)s/site-packages/', 'include/vtk-%(version_major_minor)s'],
+}
+
+sanity_check_commands = [
+    "python -c 'import %(namelower)s'",
+    "python -c 'import pkg_resources; pkg_resources.get_distribution(\"vtk\")'",
+    # make sure that VTK Python libraries link to libpython (controlled via DVTK_PYTHON_OPTIONAL_LINK=OFF),
+    # see https://gitlab.kitware.com/vtk/vtk/-/issues/17881
+    "ldd $EBROOTVTK/lib/libvtkPythonContext2D-%%(version_major_minor)s.%s | grep /libpython" % SHLIB_EXT,
+]
+
+moduleclass = 'vis'
diff --git a/easybuild/easyconfigs/v/VTK/VTK-9.3.0-foss-2023a.eb b/easybuild/easyconfigs/v/VTK/VTK-9.3.0-foss-2023a.eb
index 9278837da13..740fd888dfb 100644
--- a/easybuild/easyconfigs/v/VTK/VTK-9.3.0-foss-2023a.eb
+++ b/easybuild/easyconfigs/v/VTK/VTK-9.3.0-foss-2023a.eb
@@ -2,6 +2,7 @@
 # Authors::
 # * Fotis Georgatos <fotis@cern.ch>
 # * Robert Mijakovic <robert.mijakovic@lxp.lu>
+# Update: Pavel Tománek (Inuits)
 ##
 
 easyblock = 'CMakeNinja'
@@ -42,6 +43,7 @@ dependencies = [
     ('XZ', '5.4.2'),
     ('libGLU', '9.0.3'),
     ('X11', '20230603'),
+    ('Qt5', '5.15.10'),
 ]
 
 separate_build_dir = True
@@ -57,7 +59,11 @@ configopts += "-DPython3_INCLUDE_DIR=$EBROOTPYTHON/include/python%(pyshortver)s
 configopts += "-DPython3_LIBRARY=$EBROOTPYTHON/lib/libpython%(pyshortver)s.so "
 # Other
 configopts += "-DVTK_USE_MPI=ON "
-configopts += "-DCMAKE_INSTALL_LIBDIR=lib"
+configopts += "-DCMAKE_INSTALL_LIBDIR=lib "
+configopts += "-DVTK_QT_VERSION=5 "
+configopts += "-DQt5_DIR=$EBROOTQT5 "
+configopts += "-DVTK_MODULE_ENABLE_VTK_GuiSupportQt=YES "
+configopts += "-DVTK_MODULE_ENABLE_VTK_ViewsQt=YES"
 
 preinstallopts = "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && "
 
diff --git a/easybuild/easyconfigs/v/Visit/Visit-3.4.1-foss-2023a.eb b/easybuild/easyconfigs/v/Visit/Visit-3.4.1-foss-2023a.eb
new file mode 100644
index 00000000000..a049601ec0e
--- /dev/null
+++ b/easybuild/easyconfigs/v/Visit/Visit-3.4.1-foss-2023a.eb
@@ -0,0 +1,75 @@
+easyblock = 'CMakeMake'
+
+name = 'Visit'
+version = '3.4.1'
+
+homepage = 'https://github.com/visit-dav/visit'
+description = """
+VisIt is an Open Source, interactive, scalable, visualization, animation
+and analysis tool. From Unix, Windows or Mac workstations, users can
+interactively visualize and analyze data ranging in scale from small
+(<101 core) desktop-sized projects to large (>105 core) leadership-class
+computing facility simulation campaigns. Users can quickly generate
+visualizations, animate them through time, manipulate them with a
+variety of operators and mathematical expressions, and save the
+resulting images and animations for presentations. VisIt contains a rich
+set of visualization features to enable users to view a wide variety of
+data including scalar and vector fields defined on two- and
+three-dimensional (2D and 3D) structured, adaptive and unstructured
+meshes. Owing to its customizeable plugin design, VisIt is capabable of
+visualizing data from over 120 different scientific data formats.
+"""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+sources = [{
+    'filename': 'v%(version)s.tar.gz',
+    'git_config': {
+        'url': 'https://github.com/visit-dav',
+        'repo_name': 'visit',
+        'tag': 'v%(version)s',
+        'recursive': True,
+        'keep_git_dir': True,
+    }
+}]
+checksums = [None]
+
+builddependencies = [('CMake', '3.26.3')]
+dependencies = [
+    ('zlib', '1.2.13'),
+    ('Python', '3.11.3'),
+    ('Python-bundle-PyPI', '2023.06'),
+    ('SciPy-bundle', '2023.07'),
+    ('X11', '20230603'),
+    ('Mesa', '23.1.4'),
+    ('libglvnd', '1.6.0'),
+    ('Qt5', '5.15.10'),
+    ('Qwt', '6.3.0'),
+    ('VTK', '9.2.6'),
+    ('FFmpeg', '6.0'),
+]
+
+srcdir = "src"
+
+configopts = "-DVISIT_ZLIB_DIR=$EBROOTZLIB "
+configopts += "-DVISIT_VTK_DIR=$EBROOTVTK -DVISIT_VTK_VERSION=$EBVERSIONVTK "
+configopts += "-DVISIT_QWT_DIR=$EBROOTQWT "
+configopts += "-DVISIT_QT_VERSION=$EBVERSIONQT5 -DVISIT_QT_DIR=$EBROOTQT5 "
+configopts += "-DVISIT_OSMESA_DIR=$EBROOTMESA "
+configopts += "-DVISIT_MESAGL_DIR=$EBROOTLIBGLVND "
+configopts += "-DPYTHON_DIR=$EBROOTPYTHON "
+configopts += "-DVISIT_PYTHON_SKIP_INSTALL=ON "
+configopts += "-DVISIT_PARALLEL=ON -DVISIT_MPI_COMPILER=$MPICC -DVISIT_MPI_COMPILER_CXX=$MPICXX "
+configopts += "-DOpenGL_GL_PREFERENCE=GLVND "
+
+# add missing include to fix make step
+prebuildopts = "sed -i '23 a #include <cmath>' %(builddir)s/visit/src/gui/QvisStripChart.C && "
+
+test_cmd = 'cd %(builddir)s/easybuild_obj/test && ./run_visit_test_suite.sh -n %(parallel)s'
+
+sanity_check_paths = {
+    'files': ['bin/%s' % x for x in ['frontendlauncher', 'frontendlauncher.py', 'visit']],
+    'dirs': ['%(version)s/bin'],
+}
+
+moduleclass = 'vis'

From fef4be66704ec067d05d3263d3d9521a5e3ba055 Mon Sep 17 00:00:00 2001
From: Adam Huffman <12435+verdurin@users.noreply.github.com>
Date: Tue, 9 Jul 2024 12:45:26 +0000
Subject: [PATCH 431/835] Add sanity check command

---
 easybuild/easyconfigs/f/fsm-lite/fsm-lite-1.0-GCCcore-12.2.0.eb | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/easybuild/easyconfigs/f/fsm-lite/fsm-lite-1.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/f/fsm-lite/fsm-lite-1.0-GCCcore-12.2.0.eb
index 563eba10e7c..14fec1ffa92 100644
--- a/easybuild/easyconfigs/f/fsm-lite/fsm-lite-1.0-GCCcore-12.2.0.eb
+++ b/easybuild/easyconfigs/f/fsm-lite/fsm-lite-1.0-GCCcore-12.2.0.eb
@@ -31,4 +31,6 @@ sanity_check_paths = {
     'dirs': [],
 }
 
+sanity_check_commands = ["fsm-lite --help 2>&1 | grep usage" ]
+
 moduleclass = 'tools'

From 91c4f5913ed1f20600186be1df034bfc72f42f75 Mon Sep 17 00:00:00 2001
From: Adam Huffman <12435+verdurin@users.noreply.github.com>
Date: Tue, 9 Jul 2024 12:53:04 +0000
Subject: [PATCH 432/835] Use Cargo easyblock with explicit list of crates,
 provided by bedroge

---
 .../s/SKA2/SKA2-0.3.7-GCCcore-12.2.0.eb       | 193 +++++++++++++++++-
 1 file changed, 185 insertions(+), 8 deletions(-)

diff --git a/easybuild/easyconfigs/s/SKA2/SKA2-0.3.7-GCCcore-12.2.0.eb b/easybuild/easyconfigs/s/SKA2/SKA2-0.3.7-GCCcore-12.2.0.eb
index 094972fec6a..f3d26ca57d4 100644
--- a/easybuild/easyconfigs/s/SKA2/SKA2-0.3.7-GCCcore-12.2.0.eb
+++ b/easybuild/easyconfigs/s/SKA2/SKA2-0.3.7-GCCcore-12.2.0.eb
@@ -1,4 +1,4 @@
-easyblock = 'Binary'
+easyblock = 'Cargo'
 
 name = 'SKA2'
 version = '0.3.7'
@@ -9,19 +9,196 @@ description = """Split k-mer analysis (version 2) uses exact matching of split k
 
 toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
 
-source_urls = ['https://github.com/bacpop/ska.rust/archive']
-sources = ['v%(version)s.tar.gz']
-checksums = ['ea7234428f253638b2093abdd6c8b1e8362ecad0ba56e3b29700af9a4481d911']
+crates = [
+    ('ska', version),
+    ('adler', '1.0.2'),
+    ('ahash', '0.8.11'),
+    ('aho-corasick', '1.1.2'),
+    ('allocator-api2', '0.2.16'),
+    ('anstream', '0.6.13'),
+    ('anstyle', '1.0.6'),
+    ('anstyle-parse', '0.2.3'),
+    ('anstyle-query', '1.0.2'),
+    ('anstyle-wincon', '3.0.2'),
+    ('anyhow', '1.0.81'),
+    ('argmin', '0.9.0'),
+    ('argmin-math', '0.3.0'),
+    ('assert_fs', '1.1.1'),
+    ('autocfg', '1.1.0'),
+    ('bincode', '1.3.3'),
+    ('bit-vec', '0.6.3'),
+    ('bitflags', '1.3.2'),
+    ('bitflags', '2.4.2'),
+    ('bstr', '1.9.1'),
+    ('buffer-redux', '1.0.1'),
+    ('bytecount', '0.6.7'),
+    ('byteorder', '1.5.0'),
+    ('bytes', '1.5.0'),
+    ('bzip2', '0.4.4'),
+    ('bzip2-sys', '0.1.11+1.0.8'),
+    ('cc', '1.0.90'),
+    ('cfg-if', '1.0.0'),
+    ('ciborium', '0.2.2'),
+    ('ciborium-io', '0.2.2'),
+    ('ciborium-ll', '0.2.2'),
+    ('clap', '4.5.2'),
+    ('clap_builder', '4.5.2'),
+    ('clap_derive', '4.5.0'),
+    ('clap_lex', '0.7.0'),
+    ('colorchoice', '1.0.0'),
+    ('colored', '2.1.0'),
+    ('console', '0.15.8'),
+    ('crc32fast', '1.4.0'),
+    ('crossbeam-channel', '0.5.12'),
+    ('crossbeam-deque', '0.8.5'),
+    ('crossbeam-epoch', '0.9.18'),
+    ('crossbeam-utils', '0.8.19'),
+    ('crunchy', '0.2.2'),
+    ('deranged', '0.3.11'),
+    ('diff', '0.1.13'),
+    ('difflib', '0.4.0'),
+    ('dirs-next', '2.0.0'),
+    ('dirs-sys-next', '0.1.2'),
+    ('doc-comment', '0.3.3'),
+    ('either', '1.10.0'),
+    ('encode_unicode', '0.3.6'),
+    ('equivalent', '1.0.1'),
+    ('errno', '0.3.8'),
+    ('fastrand', '2.0.1'),
+    ('flate2', '1.0.28'),
+    ('float-cmp', '0.9.0'),
+    ('getrandom', '0.2.12'),
+    ('globset', '0.4.14'),
+    ('globwalk', '0.9.1'),
+    ('half', '2.4.0'),
+    ('hashbrown', '0.14.3'),
+    ('heck', '0.4.1'),
+    ('hermit-abi', '0.3.9'),
+    ('ignore', '0.4.22'),
+    ('indexmap', '2.2.5'),
+    ('indicatif', '0.17.8'),
+    ('instant', '0.1.12'),
+    ('is-terminal', '0.4.12'),
+    ('itertools', '0.10.5'),
+    ('itoa', '1.0.10'),
+    ('lazy_static', '1.4.0'),
+    ('libc', '0.2.153'),
+    ('libm', '0.2.8'),
+    ('libredox', '0.0.1'),
+    ('linux-raw-sys', '0.4.13'),
+    ('log', '0.4.21'),
+    ('lzma-sys', '0.1.20'),
+    ('matrixmultiply', '0.3.8'),
+    ('memchr', '2.7.1'),
+    ('miniz_oxide', '0.7.2'),
+    ('ndarray', '0.15.6'),
+    ('needletail', '0.5.1'),
+    ('noodles-bgzf', '0.26.0'),
+    ('noodles-core', '0.14.0'),
+    ('noodles-csi', '0.30.0'),
+    ('noodles-tabix', '0.36.0'),
+    ('noodles-vcf', '0.49.0'),
+    ('normalize-line-endings', '0.3.0'),
+    ('num-complex', '0.4.5'),
+    ('num-conv', '0.1.0'),
+    ('num-integer', '0.1.46'),
+    ('num-traits', '0.2.18'),
+    ('num_cpus', '1.16.0'),
+    ('num_threads', '0.1.7'),
+    ('number_prefix', '0.4.0'),
+    ('once_cell', '1.19.0'),
+    ('paste', '1.0.14'),
+    ('percent-encoding', '2.3.1'),
+    ('pkg-config', '0.3.30'),
+    ('portable-atomic', '1.6.0'),
+    ('powerfmt', '0.2.0'),
+    ('ppv-lite86', '0.2.17'),
+    ('predicates', '2.1.5'),
+    ('predicates', '3.1.0'),
+    ('predicates-core', '1.0.6'),
+    ('predicates-tree', '1.0.9'),
+    ('pretty_assertions', '1.4.0'),
+    ('proc-macro2', '1.0.79'),
+    ('quote', '1.0.35'),
+    ('rand', '0.8.5'),
+    ('rand_chacha', '0.3.1'),
+    ('rand_core', '0.6.4'),
+    ('rand_xoshiro', '0.6.0'),
+    ('rawpointer', '0.2.1'),
+    ('rayon', '1.9.0'),
+    ('rayon-core', '1.12.1'),
+    ('redox_syscall', '0.4.1'),
+    ('redox_users', '0.4.4'),
+    ('regex', '1.10.3'),
+    ('regex-automata', '0.4.6'),
+    ('regex-syntax', '0.8.2'),
+    ('rustix', '0.38.31'),
+    ('rustversion', '1.0.14'),
+    ('ryu', '1.0.17'),
+    ('same-file', '1.0.6'),
+    ('serde', '1.0.197'),
+    ('serde_derive', '1.0.197'),
+    ('serde_json', '1.0.114'),
+    ('similar', '2.4.0'),
+    ('simple_logger', '4.3.3'),
+    ('slog', '2.7.0'),
+    ('slog-async', '2.8.0'),
+    ('slog-json', '2.6.1'),
+    ('slog-term', '2.9.1'),
+    ('snap', '1.1.1'),
+    ('snapbox', '0.4.17'),
+    ('snapbox-macros', '0.3.8'),
+    ('strsim', '0.11.0'),
+    ('syn', '2.0.52'),
+    ('take_mut', '0.2.2'),
+    ('tempfile', '3.10.1'),
+    ('term', '0.7.0'),
+    ('termtree', '0.4.1'),
+    ('thiserror', '1.0.58'),
+    ('thiserror-impl', '1.0.58'),
+    ('thread_local', '1.1.8'),
+    ('time', '0.3.34'),
+    ('time-core', '0.1.2'),
+    ('time-macros', '0.2.17'),
+    ('unicode-ident', '1.0.12'),
+    ('unicode-width', '0.1.11'),
+    ('utf8parse', '0.2.1'),
+    ('version_check', '0.9.4'),
+    ('walkdir', '2.5.0'),
+    ('wasi', '0.11.0+wasi-snapshot-preview1'),
+    ('winapi', '0.3.9'),
+    ('winapi-i686-pc-windows-gnu', '0.4.0'),
+    ('winapi-util', '0.1.6'),
+    ('winapi-x86_64-pc-windows-gnu', '0.4.0'),
+    ('windows-sys', '0.48.0'),
+    ('windows-sys', '0.52.0'),
+    ('windows-targets', '0.48.5'),
+    ('windows-targets', '0.52.4'),
+    ('windows_aarch64_gnullvm', '0.48.5'),
+    ('windows_aarch64_gnullvm', '0.52.4'),
+    ('windows_aarch64_msvc', '0.48.5'),
+    ('windows_aarch64_msvc', '0.52.4'),
+    ('windows_i686_gnu', '0.48.5'),
+    ('windows_i686_gnu', '0.52.4'),
+    ('windows_i686_msvc', '0.48.5'),
+    ('windows_i686_msvc', '0.52.4'),
+    ('windows_x86_64_gnu', '0.48.5'),
+    ('windows_x86_64_gnu', '0.52.4'),
+    ('windows_x86_64_gnullvm', '0.48.5'),
+    ('windows_x86_64_gnullvm', '0.52.4'),
+    ('windows_x86_64_msvc', '0.48.5'),
+    ('windows_x86_64_msvc', '0.52.4'),
+    ('xz2', '0.1.7'),
+    ('yansi', '0.5.1'),
+    ('zerocopy', '0.7.32'),
+    ('zerocopy-derive', '0.7.32'),
+]
 
 builddependencies = [
     ('binutils', '2.39'),
     ('Rust', '1.75.0'),
 ]
 
-extract_sources = True
-
-install_cmd = "cargo install --root %(installdir)s --path ."
-
 sanity_check_paths = {
     'files': ['bin/ska'],
     'dirs': [],

From b4cc3bdd0b354cc39546e02b0f38ba141635f2d9 Mon Sep 17 00:00:00 2001
From: Adam Huffman <12435+verdurin@users.noreply.github.com>
Date: Tue, 9 Jul 2024 16:17:57 +0000
Subject: [PATCH 433/835] Fix trailing whitespace

---
 easybuild/easyconfigs/f/fsm-lite/fsm-lite-1.0-GCCcore-12.2.0.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/f/fsm-lite/fsm-lite-1.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/f/fsm-lite/fsm-lite-1.0-GCCcore-12.2.0.eb
index 14fec1ffa92..65a1167d998 100644
--- a/easybuild/easyconfigs/f/fsm-lite/fsm-lite-1.0-GCCcore-12.2.0.eb
+++ b/easybuild/easyconfigs/f/fsm-lite/fsm-lite-1.0-GCCcore-12.2.0.eb
@@ -31,6 +31,6 @@ sanity_check_paths = {
     'dirs': [],
 }
 
-sanity_check_commands = ["fsm-lite --help 2>&1 | grep usage" ]
+sanity_check_commands = ["fsm-lite --help 2>&1 | grep usage"]
 
 moduleclass = 'tools'

From 16c71261fb603fecbe7da348bba186d845e5ff51 Mon Sep 17 00:00:00 2001
From: Adam Huffman <12435+verdurin@users.noreply.github.com>
Date: Wed, 10 Jul 2024 09:14:33 +0000
Subject: [PATCH 434/835] Add missing checksums

---
 .../s/SKA2/SKA2-0.3.7-GCCcore-12.2.0.eb       | 186 ++++++++++++++++++
 1 file changed, 186 insertions(+)

diff --git a/easybuild/easyconfigs/s/SKA2/SKA2-0.3.7-GCCcore-12.2.0.eb b/easybuild/easyconfigs/s/SKA2/SKA2-0.3.7-GCCcore-12.2.0.eb
index f3d26ca57d4..ec330ffc75d 100644
--- a/easybuild/easyconfigs/s/SKA2/SKA2-0.3.7-GCCcore-12.2.0.eb
+++ b/easybuild/easyconfigs/s/SKA2/SKA2-0.3.7-GCCcore-12.2.0.eb
@@ -9,6 +9,192 @@ description = """Split k-mer analysis (version 2) uses exact matching of split k
 
 toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
 
+sources = []
+checksums = [
+    {'ska-0.3.7.tar.gz': '42febc3b657772569c9f6de9e19c3a02ec306ce1bc72d3032044ebaf6f9b23f6'},
+    {'adler-1.0.2.tar.gz': 'f26201604c87b1e01bd3d98f8d5d9a8fcbb815e8cedb41ffccbeb4bf593a35fe'},
+    {'ahash-0.8.11.tar.gz': 'e89da841a80418a9b391ebaea17f5c112ffaaa96f621d2c285b5174da76b9011'},
+    {'aho-corasick-1.1.2.tar.gz': 'b2969dcb958b36655471fc61f7e416fa76033bdd4bfed0678d8fee1e2d07a1f0'},
+    {'allocator-api2-0.2.16.tar.gz': '0942ffc6dcaadf03badf6e6a2d0228460359d5e34b57ccdc720b7382dfbd5ec5'},
+    {'anstream-0.6.13.tar.gz': 'd96bd03f33fe50a863e394ee9718a706f988b9079b20c3784fb726e7678b62fb'},
+    {'anstyle-1.0.6.tar.gz': '8901269c6307e8d93993578286ac0edf7f195079ffff5ebdeea6a59ffb7e36bc'},
+    {'anstyle-parse-0.2.3.tar.gz': 'c75ac65da39e5fe5ab759307499ddad880d724eed2f6ce5b5e8a26f4f387928c'},
+    {'anstyle-query-1.0.2.tar.gz': 'e28923312444cdd728e4738b3f9c9cac739500909bb3d3c94b43551b16517648'},
+    {'anstyle-wincon-3.0.2.tar.gz': '1cd54b81ec8d6180e24654d0b371ad22fc3dd083b6ff8ba325b72e00c87660a7'},
+    {'anyhow-1.0.81.tar.gz': '0952808a6c2afd1aa8947271f3a60f1a6763c7b912d210184c5149b5cf147247'},
+    {'argmin-0.9.0.tar.gz': '523c0b5258fa1fb9072748b7306fb0db1625cf235ec6da4d05de2560ef56f882'},
+    {'argmin-math-0.3.0.tar.gz': 'a8798ca7447753fcb3dd98d9095335b1564812a68c6e7c3d1926e1d5cf094e37'},
+    {'assert_fs-1.1.1.tar.gz': '2cd762e110c8ed629b11b6cde59458cc1c71de78ebbcc30099fc8e0403a2a2ec'},
+    {'autocfg-1.1.0.tar.gz': 'd468802bab17cbc0cc575e9b053f41e72aa36bfa6b7f55e3529ffa43161b97fa'},
+    {'bincode-1.3.3.tar.gz': 'b1f45e9417d87227c7a56d22e471c6206462cba514c7590c09aff4cf6d1ddcad'},
+    {'bit-vec-0.6.3.tar.gz': '349f9b6a179ed607305526ca489b34ad0a41aed5f7980fa90eb03160b69598fb'},
+    {'bitflags-1.3.2.tar.gz': 'bef38d45163c2f1dde094a7dfd33ccf595c92905c8f8f4fdc18d06fb1037718a'},
+    {'bitflags-2.4.2.tar.gz': 'ed570934406eb16438a4e976b1b4500774099c13b8cb96eec99f620f05090ddf'},
+    {'bstr-1.9.1.tar.gz': '05efc5cfd9110c8416e471df0e96702d58690178e206e61b7173706673c93706'},
+    {'buffer-redux-1.0.1.tar.gz': '4c9f8ddd22e0a12391d1e7ada69ec3b0da1914f1cec39c5cf977143c5b2854f5'},
+    {'bytecount-0.6.7.tar.gz': 'e1e5f035d16fc623ae5f74981db80a439803888314e3a555fd6f04acd51a3205'},
+    {'byteorder-1.5.0.tar.gz': '1fd0f2584146f6f2ef48085050886acf353beff7305ebd1ae69500e27c67f64b'},
+    {'bytes-1.5.0.tar.gz': 'a2bd12c1caf447e69cd4528f47f94d203fd2582878ecb9e9465484c4148a8223'},
+    {'bzip2-0.4.4.tar.gz': 'bdb116a6ef3f6c3698828873ad02c3014b3c85cadb88496095628e3ef1e347f8'},
+    {'bzip2-sys-0.1.11+1.0.8.tar.gz': '736a955f3fa7875102d57c82b8cac37ec45224a07fd32d58f9f7a186b6cd4cdc'},
+    {'cc-1.0.90.tar.gz': '8cd6604a82acf3039f1144f54b8eb34e91ffba622051189e71b781822d5ee1f5'},
+    {'cfg-if-1.0.0.tar.gz': 'baf1de4339761588bc0619e3cbc0120ee582ebb74b53b4efbf79117bd2da40fd'},
+    {'ciborium-0.2.2.tar.gz': '42e69ffd6f0917f5c029256a24d0161db17cea3997d185db0d35926308770f0e'},
+    {'ciborium-io-0.2.2.tar.gz': '05afea1e0a06c9be33d539b876f1ce3692f4afea2cb41f740e7743225ed1c757'},
+    {'ciborium-ll-0.2.2.tar.gz': '57663b653d948a338bfb3eeba9bb2fd5fcfaecb9e199e87e1eda4d9e8b240fd9'},
+    {'clap-4.5.2.tar.gz': 'b230ab84b0ffdf890d5a10abdbc8b83ae1c4918275daea1ab8801f71536b2651'},
+    {'clap_builder-4.5.2.tar.gz': 'ae129e2e766ae0ec03484e609954119f123cc1fe650337e155d03b022f24f7b4'},
+    {'clap_derive-4.5.0.tar.gz': '307bc0538d5f0f83b8248db3087aa92fe504e4691294d0c96c0eabc33f47ba47'},
+    {'clap_lex-0.7.0.tar.gz': '98cc8fbded0c607b7ba9dd60cd98df59af97e84d24e49c8557331cfc26d301ce'},
+    {'colorchoice-1.0.0.tar.gz': 'acbf1af155f9b9ef647e42cdc158db4b64a1b61f743629225fde6f3e0be2a7c7'},
+    {'colored-2.1.0.tar.gz': 'cbf2150cce219b664a8a70df7a1f933836724b503f8a413af9365b4dcc4d90b8'},
+    {'console-0.15.8.tar.gz': '0e1f83fc076bd6dd27517eacdf25fef6c4dfe5f1d7448bafaaf3a26f13b5e4eb'},
+    {'crc32fast-1.4.0.tar.gz': 'b3855a8a784b474f333699ef2bbca9db2c4a1f6d9088a90a2d25b1eb53111eaa'},
+    {'crossbeam-channel-0.5.12.tar.gz': 'ab3db02a9c5b5121e1e42fbdb1aeb65f5e02624cc58c43f2884c6ccac0b82f95'},
+    {'crossbeam-deque-0.8.5.tar.gz': '613f8cc01fe9cf1a3eb3d7f488fd2fa8388403e97039e2f73692932e291a770d'},
+    {'crossbeam-epoch-0.9.18.tar.gz': '5b82ac4a3c2ca9c3460964f020e1402edd5753411d7737aa39c3714ad1b5420e'},
+    {'crossbeam-utils-0.8.19.tar.gz': '248e3bacc7dc6baa3b21e405ee045c3047101a49145e7e9eca583ab4c2ca5345'},
+    {'crunchy-0.2.2.tar.gz': '7a81dae078cea95a014a339291cec439d2f232ebe854a9d672b796c6afafa9b7'},
+    {'deranged-0.3.11.tar.gz': 'b42b6fa04a440b495c8b04d0e71b707c585f83cb9cb28cf8cd0d976c315e31b4'},
+    {'diff-0.1.13.tar.gz': '56254986775e3233ffa9c4d7d3faaf6d36a2c09d30b20687e9f88bc8bafc16c8'},
+    {'difflib-0.4.0.tar.gz': '6184e33543162437515c2e2b48714794e37845ec9851711914eec9d308f6ebe8'},
+    {'dirs-next-2.0.0.tar.gz': 'b98cf8ebf19c3d1b223e151f99a4f9f0690dca41414773390fc824184ac833e1'},
+    {'dirs-sys-next-0.1.2.tar.gz': '4ebda144c4fe02d1f7ea1a7d9641b6fc6b580adcfa024ae48797ecdeb6825b4d'},
+    {'doc-comment-0.3.3.tar.gz': 'fea41bba32d969b513997752735605054bc0dfa92b4c56bf1189f2e174be7a10'},
+    {'either-1.10.0.tar.gz': '11157ac094ffbdde99aa67b23417ebdd801842852b500e395a45a9c0aac03e4a'},
+    {'encode_unicode-0.3.6.tar.gz': 'a357d28ed41a50f9c765dbfe56cbc04a64e53e5fc58ba79fbc34c10ef3df831f'},
+    {'equivalent-1.0.1.tar.gz': '5443807d6dff69373d433ab9ef5378ad8df50ca6298caf15de6e52e24aaf54d5'},
+    {'errno-0.3.8.tar.gz': 'a258e46cdc063eb8519c00b9fc845fc47bcfca4130e2f08e88665ceda8474245'},
+    {'fastrand-2.0.1.tar.gz': '25cbce373ec4653f1a01a31e8a5e5ec0c622dc27ff9c4e6606eefef5cbbed4a5'},
+    {'flate2-1.0.28.tar.gz': '46303f565772937ffe1d394a4fac6f411c6013172fadde9dcdb1e147a086940e'},
+    {'float-cmp-0.9.0.tar.gz': '98de4bbd547a563b716d8dfa9aad1cb19bfab00f4fa09a6a4ed21dbcf44ce9c4'},
+    {'getrandom-0.2.12.tar.gz': '190092ea657667030ac6a35e305e62fc4dd69fd98ac98631e5d3a2b1575a12b5'},
+    {'globset-0.4.14.tar.gz': '57da3b9b5b85bd66f31093f8c408b90a74431672542466497dcbdfdc02034be1'},
+    {'globwalk-0.9.1.tar.gz': '0bf760ebf69878d9fd8f110c89703d90ce35095324d1f1edcb595c63945ee757'},
+    {'half-2.4.0.tar.gz': 'b5eceaaeec696539ddaf7b333340f1af35a5aa87ae3e4f3ead0532f72affab2e'},
+    {'hashbrown-0.14.3.tar.gz': '290f1a1d9242c78d09ce40a5e87e7554ee637af1351968159f4952f028f75604'},
+    {'heck-0.4.1.tar.gz': '95505c38b4572b2d910cecb0281560f54b440a19336cbbcb27bf6ce6adc6f5a8'},
+    {'hermit-abi-0.3.9.tar.gz': 'd231dfb89cfffdbc30e7fc41579ed6066ad03abda9e567ccafae602b97ec5024'},
+    {'ignore-0.4.22.tar.gz': 'b46810df39e66e925525d6e38ce1e7f6e1d208f72dc39757880fcb66e2c58af1'},
+    {'indexmap-2.2.5.tar.gz': '7b0b929d511467233429c45a44ac1dcaa21ba0f5ba11e4879e6ed28ddb4f9df4'},
+    {'indicatif-0.17.8.tar.gz': '763a5a8f45087d6bcea4222e7b72c291a054edf80e4ef6efd2a4979878c7bea3'},
+    {'instant-0.1.12.tar.gz': '7a5bbe824c507c5da5956355e86a746d82e0e1464f65d862cc5e71da70e94b2c'},
+    {'is-terminal-0.4.12.tar.gz': 'f23ff5ef2b80d608d61efee834934d862cd92461afc0560dedf493e4c033738b'},
+    {'itertools-0.10.5.tar.gz': 'b0fd2260e829bddf4cb6ea802289de2f86d6a7a690192fbe91b3f46e0f2c8473'},
+    {'itoa-1.0.10.tar.gz': 'b1a46d1a171d865aa5f83f92695765caa047a9b4cbae2cbf37dbd613a793fd4c'},
+    {'lazy_static-1.4.0.tar.gz': 'e2abad23fbc42b3700f2f279844dc832adb2b2eb069b2df918f455c4e18cc646'},
+    {'libc-0.2.153.tar.gz': '9c198f91728a82281a64e1f4f9eeb25d82cb32a5de251c6bd1b5154d63a8e7bd'},
+    {'libm-0.2.8.tar.gz': '4ec2a862134d2a7d32d7983ddcdd1c4923530833c9f2ea1a44fc5fa473989058'},
+    {'libredox-0.0.1.tar.gz': '85c833ca1e66078851dba29046874e38f08b2c883700aa29a03ddd3b23814ee8'},
+    {'linux-raw-sys-0.4.13.tar.gz': '01cda141df6706de531b6c46c3a33ecca755538219bd484262fa09410c13539c'},
+    {'log-0.4.21.tar.gz': '90ed8c1e510134f979dbc4f070f87d4313098b704861a105fe34231c70a3901c'},
+    {'lzma-sys-0.1.20.tar.gz': '5fda04ab3764e6cde78b9974eec4f779acaba7c4e84b36eca3cf77c581b85d27'},
+    {'matrixmultiply-0.3.8.tar.gz': '7574c1cf36da4798ab73da5b215bbf444f50718207754cb522201d78d1cd0ff2'},
+    {'memchr-2.7.1.tar.gz': '523dc4f511e55ab87b694dc30d0f820d60906ef06413f93d4d7a1385599cc149'},
+    {'miniz_oxide-0.7.2.tar.gz': '9d811f3e15f28568be3407c8e7fdb6514c1cda3cb30683f15b6a1a1dc4ea14a7'},
+    {'ndarray-0.15.6.tar.gz': 'adb12d4e967ec485a5f71c6311fe28158e9d6f4bc4a447b474184d0f91a8fa32'},
+    {'needletail-0.5.1.tar.gz': 'db05a5ab397f64070d8c998fa0fbb84e484b81f95752af317dac183a82d9295d'},
+    {'noodles-bgzf-0.26.0.tar.gz': '8970db2e84adb1007377dd3988258d7a64e3fc4c05602ebf94e1f8cba207c030'},
+    {'noodles-core-0.14.0.tar.gz': '7336c3be652de4e05444c9b12a32331beb5ba3316e8872d92bfdd8ef3b06c282'},
+    {'noodles-csi-0.30.0.tar.gz': 'a60dfe0919f7ecbd081a82eb1d32e8f89f9041932d035fe8309073c8c01277bf'},
+    {'noodles-tabix-0.36.0.tar.gz': 'cc1ab29335a68d0c2bdf41460a67714ca69e23a1cbeb950ac5c38a9afa446a62'},
+    {'noodles-vcf-0.49.0.tar.gz': '2e1f2fa749afaccadc596ec55ccb7bdcd8101fa79f8382384223c0dbae3e245b'},
+    {'normalize-line-endings-0.3.0.tar.gz': '61807f77802ff30975e01f4f071c8ba10c022052f98b3294119f3e615d13e5be'},
+    {'num-complex-0.4.5.tar.gz': '23c6602fda94a57c990fe0df199a035d83576b496aa29f4e634a8ac6004e68a6'},
+    {'num-conv-0.1.0.tar.gz': '51d515d32fb182ee37cda2ccdcb92950d6a3c2893aa280e540671c2cd0f3b1d9'},
+    {'num-integer-0.1.46.tar.gz': '7969661fd2958a5cb096e56c8e1ad0444ac2bbcd0061bd28660485a44879858f'},
+    {'num-traits-0.2.18.tar.gz': 'da0df0e5185db44f69b44f26786fe401b6c293d1907744beaa7fa62b2e5a517a'},
+    {'num_cpus-1.16.0.tar.gz': '4161fcb6d602d4d2081af7c3a45852d875a03dd337a6bfdd6e06407b61342a43'},
+    {'num_threads-0.1.7.tar.gz': '5c7398b9c8b70908f6371f47ed36737907c87c52af34c268fed0bf0ceb92ead9'},
+    {'number_prefix-0.4.0.tar.gz': '830b246a0e5f20af87141b25c173cd1b609bd7779a4617d6ec582abaf90870f3'},
+    {'once_cell-1.19.0.tar.gz': '3fdb12b2476b595f9358c5161aa467c2438859caa136dec86c26fdd2efe17b92'},
+    {'paste-1.0.14.tar.gz': 'de3145af08024dea9fa9914f381a17b8fc6034dfb00f3a84013f7ff43f29ed4c'},
+    {'percent-encoding-2.3.1.tar.gz': 'e3148f5046208a5d56bcfc03053e3ca6334e51da8dfb19b6cdc8b306fae3283e'},
+    {'pkg-config-0.3.30.tar.gz': 'd231b230927b5e4ad203db57bbcbee2802f6bce620b1e4a9024a07d94e2907ec'},
+    {'portable-atomic-1.6.0.tar.gz': '7170ef9988bc169ba16dd36a7fa041e5c4cbeb6a35b76d4c03daded371eae7c0'},
+    {'powerfmt-0.2.0.tar.gz': '439ee305def115ba05938db6eb1644ff94165c5ab5e9420d1c1bcedbba909391'},
+    {'ppv-lite86-0.2.17.tar.gz': '5b40af805b3121feab8a3c29f04d8ad262fa8e0561883e7653e024ae4479e6de'},
+    {'predicates-2.1.5.tar.gz': '59230a63c37f3e18569bdb90e4a89cbf5bf8b06fea0b84e65ea10cc4df47addd'},
+    {'predicates-3.1.0.tar.gz': '68b87bfd4605926cdfefc1c3b5f8fe560e3feca9d5552cf68c466d3d8236c7e8'},
+    {'predicates-core-1.0.6.tar.gz': 'b794032607612e7abeb4db69adb4e33590fa6cf1149e95fd7cb00e634b92f174'},
+    {'predicates-tree-1.0.9.tar.gz': '368ba315fb8c5052ab692e68a0eefec6ec57b23a36959c14496f0b0df2c0cecf'},
+    {'pretty_assertions-1.4.0.tar.gz': 'af7cee1a6c8a5b9208b3cb1061f10c0cb689087b3d8ce85fb9d2dd7a29b6ba66'},
+    {'proc-macro2-1.0.79.tar.gz': 'e835ff2298f5721608eb1a980ecaee1aef2c132bf95ecc026a11b7bf3c01c02e'},
+    {'quote-1.0.35.tar.gz': '291ec9ab5efd934aaf503a6466c5d5251535d108ee747472c3977cc5acc868ef'},
+    {'rand-0.8.5.tar.gz': '34af8d1a0e25924bc5b7c43c079c942339d8f0a8b57c39049bef581b46327404'},
+    {'rand_chacha-0.3.1.tar.gz': 'e6c10a63a0fa32252be49d21e7709d4d4baf8d231c2dbce1eaa8141b9b127d88'},
+    {'rand_core-0.6.4.tar.gz': 'ec0be4795e2f6a28069bec0b5ff3e2ac9bafc99e6a9a7dc3547996c5c816922c'},
+    {'rand_xoshiro-0.6.0.tar.gz': '6f97cdb2a36ed4183de61b2f824cc45c9f1037f28afe0a322e9fff4c108b5aaa'},
+    {'rawpointer-0.2.1.tar.gz': '60a357793950651c4ed0f3f52338f53b2f809f32d83a07f72909fa13e4c6c1e3'},
+    {'rayon-1.9.0.tar.gz': 'e4963ed1bc86e4f3ee217022bd855b297cef07fb9eac5dfa1f788b220b49b3bd'},
+    {'rayon-core-1.12.1.tar.gz': '1465873a3dfdaa8ae7cb14b4383657caab0b3e8a0aa9ae8e04b044854c8dfce2'},
+    {'redox_syscall-0.4.1.tar.gz': '4722d768eff46b75989dd134e5c353f0d6296e5aaa3132e776cbdb56be7731aa'},
+    {'redox_users-0.4.4.tar.gz': 'a18479200779601e498ada4e8c1e1f50e3ee19deb0259c25825a98b5603b2cb4'},
+    {'regex-1.10.3.tar.gz': 'b62dbe01f0b06f9d8dc7d49e05a0785f153b00b2c227856282f671e0318c9b15'},
+    {'regex-automata-0.4.6.tar.gz': '86b83b8b9847f9bf95ef68afb0b8e6cdb80f498442f5179a29fad448fcc1eaea'},
+    {'regex-syntax-0.8.2.tar.gz': 'c08c74e62047bb2de4ff487b251e4a92e24f48745648451635cec7d591162d9f'},
+    {'rustix-0.38.31.tar.gz': '6ea3e1a662af26cd7a3ba09c0297a31af215563ecf42817c98df621387f4e949'},
+    {'rustversion-1.0.14.tar.gz': '7ffc183a10b4478d04cbbbfc96d0873219d962dd5accaff2ffbd4ceb7df837f4'},
+    {'ryu-1.0.17.tar.gz': 'e86697c916019a8588c99b5fac3cead74ec0b4b819707a682fd4d23fa0ce1ba1'},
+    {'same-file-1.0.6.tar.gz': '93fc1dc3aaa9bfed95e02e6eadabb4baf7e3078b0bd1b4d7b6b0b68378900502'},
+    {'serde-1.0.197.tar.gz': '3fb1c873e1b9b056a4dc4c0c198b24c3ffa059243875552b2bd0933b1aee4ce2'},
+    {'serde_derive-1.0.197.tar.gz': '7eb0b34b42edc17f6b7cac84a52a1c5f0e1bb2227e997ca9011ea3dd34e8610b'},
+    {'serde_json-1.0.114.tar.gz': 'c5f09b1bd632ef549eaa9f60a1f8de742bdbc698e6cee2095fc84dde5f549ae0'},
+    {'similar-2.4.0.tar.gz': '32fea41aca09ee824cc9724996433064c89f7777e60762749a4170a14abbfa21'},
+    {'simple_logger-4.3.3.tar.gz': '8e7e46c8c90251d47d08b28b8a419ffb4aede0f87c2eea95e17d1d5bacbf3ef1'},
+    {'slog-2.7.0.tar.gz': '8347046d4ebd943127157b94d63abb990fcf729dc4e9978927fdf4ac3c998d06'},
+    {'slog-async-2.8.0.tar.gz': '72c8038f898a2c79507940990f05386455b3a317d8f18d4caea7cbc3d5096b84'},
+    {'slog-json-2.6.1.tar.gz': '3e1e53f61af1e3c8b852eef0a9dee29008f55d6dd63794f3f12cef786cf0f219'},
+    {'slog-term-2.9.1.tar.gz': 'b6e022d0b998abfe5c3782c1f03551a596269450ccd677ea51c56f8b214610e8'},
+    {'snap-1.1.1.tar.gz': '1b6b67fb9a61334225b5b790716f609cd58395f895b3fe8b328786812a40bc3b'},
+    {'snapbox-0.4.17.tar.gz': '4b831b6e80fbcd2889efa75b185d24005f85981431495f995292b25836519d84'},
+    {'snapbox-macros-0.3.8.tar.gz': 'e1c4b838b05d15ab22754068cb73500b2f3b07bf09d310e15b27f88160f1de40'},
+    {'strsim-0.11.0.tar.gz': '5ee073c9e4cd00e28217186dbe12796d692868f432bf2e97ee73bed0c56dfa01'},
+    {'syn-2.0.52.tar.gz': 'b699d15b36d1f02c3e7c69f8ffef53de37aefae075d8488d4ba1a7788d574a07'},
+    {'take_mut-0.2.2.tar.gz': 'f764005d11ee5f36500a149ace24e00e3da98b0158b3e2d53a7495660d3f4d60'},
+    {'tempfile-3.10.1.tar.gz': '85b77fafb263dd9d05cbeac119526425676db3784113aa9295c88498cbf8bff1'},
+    {'term-0.7.0.tar.gz': 'c59df8ac95d96ff9bede18eb7300b0fda5e5d8d90960e76f8e14ae765eedbf1f'},
+    {'termtree-0.4.1.tar.gz': '3369f5ac52d5eb6ab48c6b4ffdc8efbcad6b89c765749064ba298f2c68a16a76'},
+    {'thiserror-1.0.58.tar.gz': '03468839009160513471e86a034bb2c5c0e4baae3b43f79ffc55c4a5427b3297'},
+    {'thiserror-impl-1.0.58.tar.gz': 'c61f3ba182994efc43764a46c018c347bc492c79f024e705f46567b418f6d4f7'},
+    {'thread_local-1.1.8.tar.gz': '8b9ef9bad013ada3808854ceac7b46812a6465ba368859a37e2100283d2d719c'},
+    {'time-0.3.34.tar.gz': 'c8248b6521bb14bc45b4067159b9b6ad792e2d6d754d6c41fb50e29fefe38749'},
+    {'time-core-0.1.2.tar.gz': 'ef927ca75afb808a4d64dd374f00a2adf8d0fcff8e7b184af886c3c87ec4a3f3'},
+    {'time-macros-0.2.17.tar.gz': '7ba3a3ef41e6672a2f0f001392bb5dcd3ff0a9992d618ca761a11c3121547774'},
+    {'unicode-ident-1.0.12.tar.gz': '3354b9ac3fae1ff6755cb6db53683adb661634f67557942dea4facebec0fee4b'},
+    {'unicode-width-0.1.11.tar.gz': 'e51733f11c9c4f72aa0c160008246859e340b00807569a0da0e7a1079b27ba85'},
+    {'utf8parse-0.2.1.tar.gz': '711b9620af191e0cdc7468a8d14e709c3dcdb115b36f838e601583af800a370a'},
+    {'version_check-0.9.4.tar.gz': '49874b5167b65d7193b8aba1567f5c7d93d001cafc34600cee003eda787e483f'},
+    {'walkdir-2.5.0.tar.gz': '29790946404f91d9c5d06f9874efddea1dc06c5efe94541a7d6863108e3a5e4b'},
+    {'wasi-0.11.0+wasi-snapshot-preview1.tar.gz': '9c8d87e72b64a3b4db28d11ce29237c246188f4f51057d65a7eab63b7987e423'},
+    {'winapi-0.3.9.tar.gz': '5c839a674fcd7a98952e593242ea400abe93992746761e38641405d28b00f419'},
+    {'winapi-i686-pc-windows-gnu-0.4.0.tar.gz': 'ac3b87c63620426dd9b991e5ce0329eff545bccbbb34f3be09ff6fb6ab51b7b6'},
+    {'winapi-util-0.1.6.tar.gz': 'f29e6f9198ba0d26b4c9f07dbe6f9ed633e1f3d5b8b414090084349e46a52596'},
+    {'winapi-x86_64-pc-windows-gnu-0.4.0.tar.gz': '712e227841d057c1ee1cd2fb22fa7e5a5461ae8e48fa2ca79ec42cfc1931183f'},
+    {'windows-sys-0.48.0.tar.gz': '677d2418bec65e3338edb076e806bc1ec15693c5d0104683f2efe857f61056a9'},
+    {'windows-sys-0.52.0.tar.gz': '282be5f36a8ce781fad8c8ae18fa3f9beff57ec1b52cb3de0789201425d9a33d'},
+    {'windows-targets-0.48.5.tar.gz': '9a2fa6e2155d7247be68c096456083145c183cbbbc2764150dda45a87197940c'},
+    {'windows-targets-0.52.4.tar.gz': '7dd37b7e5ab9018759f893a1952c9420d060016fc19a472b4bb20d1bdd694d1b'},
+    {'windows_aarch64_gnullvm-0.48.5.tar.gz': '2b38e32f0abccf9987a4e3079dfb67dcd799fb61361e53e2882c3cbaf0d905d8'},
+    {'windows_aarch64_gnullvm-0.52.4.tar.gz': 'bcf46cf4c365c6f2d1cc93ce535f2c8b244591df96ceee75d8e83deb70a9cac9'},
+    {'windows_aarch64_msvc-0.48.5.tar.gz': 'dc35310971f3b2dbbf3f0690a219f40e2d9afcf64f9ab7cc1be722937c26b4bc'},
+    {'windows_aarch64_msvc-0.52.4.tar.gz': 'da9f259dd3bcf6990b55bffd094c4f7235817ba4ceebde8e6d11cd0c5633b675'},
+    {'windows_i686_gnu-0.48.5.tar.gz': 'a75915e7def60c94dcef72200b9a8e58e5091744960da64ec734a6c6e9b3743e'},
+    {'windows_i686_gnu-0.52.4.tar.gz': 'b474d8268f99e0995f25b9f095bc7434632601028cf86590aea5c8a5cb7801d3'},
+    {'windows_i686_msvc-0.48.5.tar.gz': '8f55c233f70c4b27f66c523580f78f1004e8b5a8b659e05a4eb49d4166cca406'},
+    {'windows_i686_msvc-0.52.4.tar.gz': '1515e9a29e5bed743cb4415a9ecf5dfca648ce85ee42e15873c3cd8610ff8e02'},
+    {'windows_x86_64_gnu-0.48.5.tar.gz': '53d40abd2583d23e4718fddf1ebec84dbff8381c07cae67ff7768bbf19c6718e'},
+    {'windows_x86_64_gnu-0.52.4.tar.gz': '5eee091590e89cc02ad514ffe3ead9eb6b660aedca2183455434b93546371a03'},
+    {'windows_x86_64_gnullvm-0.48.5.tar.gz': '0b7b52767868a23d5bab768e390dc5f5c55825b6d30b86c844ff2dc7414044cc'},
+    {'windows_x86_64_gnullvm-0.52.4.tar.gz': '77ca79f2451b49fa9e2af39f0747fe999fcda4f5e241b2898624dca97a1f2177'},
+    {'windows_x86_64_msvc-0.48.5.tar.gz': 'ed94fce61571a4006852b7389a063ab983c02eb1bb37b47f8272ce92d06d9538'},
+    {'windows_x86_64_msvc-0.52.4.tar.gz': '32b752e52a2da0ddfbdbcc6fceadfeede4c939ed16d13e648833a61dfb611ed8'},
+    {'xz2-0.1.7.tar.gz': '388c44dc09d76f1536602ead6d325eb532f5c122f17782bd57fb47baeeb767e2'},
+    {'yansi-0.5.1.tar.gz': '09041cd90cf85f7f8b2df60c646f853b7f535ce68f85244eb6731cf89fa498ec'},
+    {'zerocopy-0.7.32.tar.gz': '74d4d3961e53fa4c9a25a8637fc2bfaf2595b3d3ae34875568a5cf64787716be'},
+    {'zerocopy-derive-0.7.32.tar.gz': '9ce1b18ccd8e73a9321186f97e46f9f04b778851177567b1975109d26a08d2a6'},
+]
+
 crates = [
     ('ska', version),
     ('adler', '1.0.2'),

From e76990d73b1878c07dd2b54ea788561fc1af95dd Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Wed, 10 Jul 2024 15:11:18 +0200
Subject: [PATCH 435/835] adding easyconfigs: SIRIUS-7.5.2-foss-2023a.eb,
 Umpire-2024.02.1-foss-2023a.eb, COSTA-2.2.2-foss-2023a.eb,
 spla-1.6.1-foss-2023a.eb, SpFFT-1.1.0-foss-2023a.eb,
 spglib-2.5.0-GCCcore-12.3.0.eb

---
 .../c/COSTA/COSTA-2.2.2-foss-2023a.eb         | 27 +++++++++++++
 .../s/SIRIUS/SIRIUS-7.5.2-foss-2023a.eb       | 40 +++++++++++++++++++
 .../s/SpFFT/SpFFT-1.1.0-foss-2023a.eb         | 30 ++++++++++++++
 .../s/spglib/spglib-2.5.0-GCCcore-12.3.0.eb   | 34 ++++++++++++++++
 .../s/spla/spla-1.6.1-foss-2023a.eb           | 31 ++++++++++++++
 .../u/Umpire/Umpire-2024.02.1-foss-2023a.eb   | 28 +++++++++++++
 6 files changed, 190 insertions(+)
 create mode 100644 easybuild/easyconfigs/c/COSTA/COSTA-2.2.2-foss-2023a.eb
 create mode 100644 easybuild/easyconfigs/s/SIRIUS/SIRIUS-7.5.2-foss-2023a.eb
 create mode 100644 easybuild/easyconfigs/s/SpFFT/SpFFT-1.1.0-foss-2023a.eb
 create mode 100644 easybuild/easyconfigs/s/spglib/spglib-2.5.0-GCCcore-12.3.0.eb
 create mode 100644 easybuild/easyconfigs/s/spla/spla-1.6.1-foss-2023a.eb
 create mode 100644 easybuild/easyconfigs/u/Umpire/Umpire-2024.02.1-foss-2023a.eb

diff --git a/easybuild/easyconfigs/c/COSTA/COSTA-2.2.2-foss-2023a.eb b/easybuild/easyconfigs/c/COSTA/COSTA-2.2.2-foss-2023a.eb
new file mode 100644
index 00000000000..0f347ce481e
--- /dev/null
+++ b/easybuild/easyconfigs/c/COSTA/COSTA-2.2.2-foss-2023a.eb
@@ -0,0 +1,27 @@
+easyblock = 'CMakeMake'
+
+name = 'COSTA'
+version = '2.2.2'
+
+homepage = 'https://github.com/eth-cscs/COSTA'
+description = """OSTA is a communication-optimal, highly-optimised algorithm for data redistribution 
+accross multiple processors, using MPI and OpenMP and offering the possibility 
+to transpose and scale some or all data."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+toolchainopts = {'openmp': True}
+
+source_urls = ['https://github.com/eth-cscs/COSTA/archive']
+sources = ['v%(version)s.tar.gz']
+checksums = ['e87bc37aad14ac0c5922237be5d5390145c9ac6aef0350ed17d86cb2d994e67c']
+
+builddependencies = [
+    ('CMake', '3.26.3'),
+]
+
+sanity_check_paths = {
+    'files': ['lib/libcosta.a'],
+    'dirs': ['include/costa'],
+}
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/s/SIRIUS/SIRIUS-7.5.2-foss-2023a.eb b/easybuild/easyconfigs/s/SIRIUS/SIRIUS-7.5.2-foss-2023a.eb
new file mode 100644
index 00000000000..3189ace9091
--- /dev/null
+++ b/easybuild/easyconfigs/s/SIRIUS/SIRIUS-7.5.2-foss-2023a.eb
@@ -0,0 +1,40 @@
+easyblock = 'CMakeMake'
+
+name = 'SIRIUS'
+version = '7.5.2'
+
+homepage = 'https://github.com/electronic-structure/SIRIUS'
+description = """SIRIUS is a domain specific library for electronic structure calculations. 
+It implements pseudopotential plane wave (PP-PW) and 
+full potential linearized augmented plane wave (FP-LAPW) methods."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+source_urls = ['https://github.com/electronic-structure/SIRIUS/archive/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['9ae01935578532c84f1d0d673dbbcdd490e26be22efa6c4acf7129f9dc1a0c60']
+
+builddependencies = [
+    ('CMake', '3.26.3'),
+    ('pkgconf', '1.9.5'),
+]
+dependencies = [
+    ('GSL', '2.7'),
+    ('libxc', '6.2.2'),
+    ('HDF5', '1.14.0'),
+    ('spglib','2.5.0'),
+    ('SpFFT', '1.1.0'),
+    ('spla', '1.6.1'),
+    ('COSTA', '2.2.2'),
+    ('Umpire', '2024.02.1'),
+]
+
+sanity_check_paths = {
+    'files': [
+        'bin/sirius.scf',
+        'lib/libsirius.%s' % SHLIB_EXT,
+    ],
+    'dirs': ['bin', 'include/sirius'],
+}
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/s/SpFFT/SpFFT-1.1.0-foss-2023a.eb b/easybuild/easyconfigs/s/SpFFT/SpFFT-1.1.0-foss-2023a.eb
new file mode 100644
index 00000000000..608918e373c
--- /dev/null
+++ b/easybuild/easyconfigs/s/SpFFT/SpFFT-1.1.0-foss-2023a.eb
@@ -0,0 +1,30 @@
+easyblock = 'CMakeMake'
+
+name = 'SpFFT'
+version = '1.1.0'
+
+homepage = 'https://github.com/eth-cscs/SpFFT/'
+description = """Sparse 3D FFT library with MPI, OpenMP, CUDA and ROCm support."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+toolchainopts = {'openmp': True}
+
+source_urls = ['https://github.com/eth-cscs/SpFFT/archive']
+sources = ['v%(version)s.tar.gz']
+checksums = ['d4673b3135aebfa1c440723226fe976d518ff881285b3d4787f1aa8210eac81e']
+
+builddependencies = [
+    ('CMake', '3.26.3'),
+]
+
+configopts = "-DSPFFT_OMP=ON -DSPFFT_MPI=ON "
+
+sanity_check_paths = {
+    'files': [
+        'include/spfft/spfft.h',
+        'lib/libspfft.%s' % SHLIB_EXT,
+    ],
+    'dirs': [],
+}
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/s/spglib/spglib-2.5.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/s/spglib/spglib-2.5.0-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..5a00e03ac05
--- /dev/null
+++ b/easybuild/easyconfigs/s/spglib/spglib-2.5.0-GCCcore-12.3.0.eb
@@ -0,0 +1,34 @@
+# with thanks to akesandgren for the easyconfig for 2022a
+# updated for 2022b by BEAR Software team at University of Birmingham
+# update to v2.5.0 for GCC/12.3.0 by Pavel Tománek (Inuits)
+
+easyblock = 'CMakeMake'
+
+name = 'spglib'
+version = '2.5.0'
+
+homepage = 'https://spglib.github.io/spglib/'
+description = """Spglib is a C library for finding and handling crystal symmetries."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+source_urls = ['https://github.com/spglib/spglib/archive']
+sources = ['v%(version)s.tar.gz']
+checksums = ['80c060b1a606a76b15f2cc708e9fdd4a83479924ebff9ac16ed26a87a0eac1a9']
+
+builddependencies = [
+    ('binutils', '2.40'),
+    ('CMake', '3.26.3'),
+]
+
+postinstallcmds = ["cd %(installdir)s/include && mkdir spglib && ln -s ../spglib.h spglib/"]
+
+sanity_check_paths = {
+    'files': [
+        'include/spglib.h',
+        'lib/libsymspg.%s' % SHLIB_EXT
+    ],
+    'dirs': [],
+}
+
+moduleclass = 'chem'
diff --git a/easybuild/easyconfigs/s/spla/spla-1.6.1-foss-2023a.eb b/easybuild/easyconfigs/s/spla/spla-1.6.1-foss-2023a.eb
new file mode 100644
index 00000000000..98308699678
--- /dev/null
+++ b/easybuild/easyconfigs/s/spla/spla-1.6.1-foss-2023a.eb
@@ -0,0 +1,31 @@
+easyblock = 'CMakeMake'
+
+name = 'spla'
+version = '1.6.1'
+
+homepage = 'https://github.com/eth-cscs/spla/'
+description = """SPLA provides specialized functions for linear algebra computations with a C++ and C interface, 
+which are inspired by requirements in computational material science codes."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+toolchainopts = {'openmp': True}
+
+source_urls = ['https://github.com/eth-cscs/spla/archive']
+sources = ['v%(version)s.tar.gz']
+checksums = ['62b51e6ce05c41cfc1c6f6600410f9549a209c50f0331e1db41047f94493e02f']
+
+builddependencies = [
+    ('CMake', '3.26.3'),
+]
+
+configopts = '-DBLA_VENDOR=FlexiBLAS'
+
+sanity_check_paths = {
+    'files': [
+        'include/spla/spla.h',
+        'lib/libspla.%s' % SHLIB_EXT,
+    ],
+    'dirs': [],
+}
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/u/Umpire/Umpire-2024.02.1-foss-2023a.eb b/easybuild/easyconfigs/u/Umpire/Umpire-2024.02.1-foss-2023a.eb
new file mode 100644
index 00000000000..c3c16eb26c8
--- /dev/null
+++ b/easybuild/easyconfigs/u/Umpire/Umpire-2024.02.1-foss-2023a.eb
@@ -0,0 +1,28 @@
+easyblock = 'CMakeMake'
+
+name = 'Umpire'
+version = '2024.02.1'
+
+homepage = 'https://github.com/LLNL/Umpire'
+description = """Umpire is a resource management library that allows the discovery, provision, 
+and management of memory on machines with multiple memory devices like NUMA and GPUs."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+sources = [{
+    'filename': 'v%(version)s.tar.gz',
+    'git_config': {
+        'url': 'https://github.com/LLNL',
+        'repo_name': 'Umpire',
+        'tag': 'v%(version)s',
+        'recursive': True,
+        'keep_git_dir': True,
+    }
+}]
+checksums = [None]
+
+builddependencies = [
+    ('CMake', '3.26.3'),
+]
+
+moduleclass = 'lib'

From 357360c12d023abadbe5b7e23c4434e7c98a540c Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com>
Date: Wed, 10 Jul 2024 15:45:03 +0200
Subject: [PATCH 436/835] Update SIRIUS-7.5.2-foss-2023a.eb fix whitespace

---
 easybuild/easyconfigs/s/SIRIUS/SIRIUS-7.5.2-foss-2023a.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/s/SIRIUS/SIRIUS-7.5.2-foss-2023a.eb b/easybuild/easyconfigs/s/SIRIUS/SIRIUS-7.5.2-foss-2023a.eb
index 3189ace9091..5c7da32ecff 100644
--- a/easybuild/easyconfigs/s/SIRIUS/SIRIUS-7.5.2-foss-2023a.eb
+++ b/easybuild/easyconfigs/s/SIRIUS/SIRIUS-7.5.2-foss-2023a.eb
@@ -22,7 +22,7 @@ dependencies = [
     ('GSL', '2.7'),
     ('libxc', '6.2.2'),
     ('HDF5', '1.14.0'),
-    ('spglib','2.5.0'),
+    ('spglib', '2.5.0'),
     ('SpFFT', '1.1.0'),
     ('spla', '1.6.1'),
     ('COSTA', '2.2.2'),

From bdbf7db74b889413b53ce64f887e5d978b7678db Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Wed, 10 Jul 2024 16:31:27 +0200
Subject: [PATCH 437/835] ignore failing testUFFAngleConstraints

---
 easybuild/easyconfigs/r/RDKit/RDKit-2024.03.3-foss-2023a.eb | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/r/RDKit/RDKit-2024.03.3-foss-2023a.eb b/easybuild/easyconfigs/r/RDKit/RDKit-2024.03.3-foss-2023a.eb
index 1a98894cac7..fa2fc6c6264 100644
--- a/easybuild/easyconfigs/r/RDKit/RDKit-2024.03.3-foss-2023a.eb
+++ b/easybuild/easyconfigs/r/RDKit/RDKit-2024.03.3-foss-2023a.eb
@@ -34,7 +34,9 @@ configopts += "-DRDK_BUILD_INCHI_SUPPORT=ON "
 configopts += "-DBOOST_ROOT=$EBROOTBOOST"
 
 # ingnore failing test pythonSourceTests - from . import rdBase failing
-prebuildopts = "sed -i '22d' %(builddir)s/rdkit-Release_2024_03_3/rdkit/CMakeLists.txt &&"
+prebuildopts = "sed -i '22d' %(builddir)s/rdkit-Release_2024_03_3/rdkit/CMakeLists.txt && "
+prebuildopts += "sed -i 's/def testUFFAngleConstraints(self):/def ignore_testUFFAngleConstraints(self):/' "
+prebuildopts += "%(builddir)s/rdkit-Release_2024_03_3/Code/ForceField/Wrap/testConstraints.py && "
 
 # merge source directory into build directory in order to run the tests
 buildopts = '&& cp -RT %(builddir)s/%(namelower)s-*/ ./ && '

From 71511a58063f3769d6981a681460f0d209b044c6 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Wed, 10 Jul 2024 16:36:38 +0200
Subject: [PATCH 438/835] ignore failing testUFFAngleConstraints - comments
 added

---
 easybuild/easyconfigs/r/RDKit/RDKit-2024.03.3-foss-2023a.eb | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/easybuild/easyconfigs/r/RDKit/RDKit-2024.03.3-foss-2023a.eb b/easybuild/easyconfigs/r/RDKit/RDKit-2024.03.3-foss-2023a.eb
index fa2fc6c6264..5af2865d609 100644
--- a/easybuild/easyconfigs/r/RDKit/RDKit-2024.03.3-foss-2023a.eb
+++ b/easybuild/easyconfigs/r/RDKit/RDKit-2024.03.3-foss-2023a.eb
@@ -35,6 +35,8 @@ configopts += "-DBOOST_ROOT=$EBROOTBOOST"
 
 # ingnore failing test pythonSourceTests - from . import rdBase failing
 prebuildopts = "sed -i '22d' %(builddir)s/rdkit-Release_2024_03_3/rdkit/CMakeLists.txt && "
+# ignore failing testUFFAngleConstraints
+# https://github.com/rdkit/rdkit/discussions/7588
 prebuildopts += "sed -i 's/def testUFFAngleConstraints(self):/def ignore_testUFFAngleConstraints(self):/' "
 prebuildopts += "%(builddir)s/rdkit-Release_2024_03_3/Code/ForceField/Wrap/testConstraints.py && "
 

From 6b4eaa094b98af683d900074148da77ecc070e68 Mon Sep 17 00:00:00 2001
From: Yunqi Shao <yunqi.shao@chalmers.se>
Date: Thu, 11 Jul 2024 00:00:10 +0200
Subject: [PATCH 439/835] Backport cudaMemcpyAsync bugfix for NCCL 2.18.3

---
 .../NCCL-2.18.3-GCCcore-12.3.0-CUDA-12.1.1.eb |   6 +-
 .../NCCL-2.18.3_fix-cudaMemcpyAsync.patch     | 174 ++++++++++++++++++
 2 files changed, 179 insertions(+), 1 deletion(-)
 create mode 100644 easybuild/easyconfigs/n/NCCL/NCCL-2.18.3_fix-cudaMemcpyAsync.patch

diff --git a/easybuild/easyconfigs/n/NCCL/NCCL-2.18.3-GCCcore-12.3.0-CUDA-12.1.1.eb b/easybuild/easyconfigs/n/NCCL/NCCL-2.18.3-GCCcore-12.3.0-CUDA-12.1.1.eb
index c85b7a97e48..569d09f9859 100644
--- a/easybuild/easyconfigs/n/NCCL/NCCL-2.18.3-GCCcore-12.3.0-CUDA-12.1.1.eb
+++ b/easybuild/easyconfigs/n/NCCL/NCCL-2.18.3-GCCcore-12.3.0-CUDA-12.1.1.eb
@@ -11,11 +11,15 @@ toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
 github_account = 'NVIDIA'
 source_urls = [GITHUB_SOURCE]
 sources = ['v%(version)s-1.tar.gz']
-patches = ['NCCL-2.16.2_fix-cpuid.patch']
+patches = [
+    'NCCL-2.16.2_fix-cpuid.patch',
+    'NCCL-2.18.3_fix-cudaMemcpyAsync.patch',
+]
 checksums = [
     ('6477d83c9edbb34a0ebce6d751a1b32962bc6415d75d04972b676c6894ceaef9',
      'b4f5d7d9eea2c12e32e7a06fe138b2cfc75969c6d5c473aa6f819a792db2fc96'),
     {'NCCL-2.16.2_fix-cpuid.patch': '0459ecadcd32b2a7a000a2ce4f675afba908b2c0afabafde585330ff4f83e277'},
+    {'NCCL-2.18.3_fix-cudaMemcpyAsync.patch': '7dc8d0d1b78e4f8acefbc400860f47432ef67c225b50d73c732999c23483de90'},
 ]
 
 builddependencies = [('binutils', '2.40')]
diff --git a/easybuild/easyconfigs/n/NCCL/NCCL-2.18.3_fix-cudaMemcpyAsync.patch b/easybuild/easyconfigs/n/NCCL/NCCL-2.18.3_fix-cudaMemcpyAsync.patch
new file mode 100644
index 00000000000..68542656733
--- /dev/null
+++ b/easybuild/easyconfigs/n/NCCL/NCCL-2.18.3_fix-cudaMemcpyAsync.patch
@@ -0,0 +1,174 @@
+Backported from (original message attached below):
+https://github.com/NVIDIA/nccl/commit/4365458757e4107ecbf629b2fd6e0e19a5d237c2
+
+From: Kaiming Ouyang <kouyang@nvidia.com>
+Date: Wed, 20 Sep 2023 05:51:14 -0700
+Subject: [PATCH] Fix cudaMemcpyAsync bug
+
+We are trying to use the copy result of first cudaMemcpyAsync in the
+second cudaMemcpyAsync without sync in between. This patch fixes it
+by allocating a CPU side array to cache device side addr so that we
+can avoid this consecutive cuda mem copy.
+
+Fixes #957
+---
+ src/channel.cc        | 12 ++++++++++++
+ src/include/comm.h    |  2 ++
+ src/init.cc           |  2 +-
+ src/transport.cc      |  8 ++------
+ src/transport/nvls.cc | 10 ++++------
+ 5 files changed, 21 insertions(+), 13 deletions(-)
+
+diff --git a/src/channel.cc b/src/channel.cc
+index 3edcc2f..245dfd5 100644
+--- a/src/channel.cc
++++ b/src/channel.cc
+@@ -42,9 +42,11 @@ ncclResult_t initChannel(struct ncclComm* comm, int channelId) {
+     /* channel->devPeers is not shared, so just free it when calling commFree() */
+     NCCLCHECK(ncclCudaCallocAsync(&channel->devPeers, nPeers, sharedRes->deviceStream.cudaStream));
+     ncclCommPushCudaFree(comm, channel->devPeers);
++    NCCLCHECK(ncclCalloc(&channel->devPeersHostPtr, nPeers));
+     for (int r = 0; r < nRanks; r++) {
+       uintptr_t addr = (uintptr_t)(comm->sharedRes->devPeers[channelId] + comm->topParentRanks[r]);
+       NCCLCHECK(ncclCudaMemcpyAsync((uintptr_t*)(channel->devPeers + r), (uintptr_t*)&addr, 1, sharedRes->deviceStream.cudaStream));
++      channel->devPeersHostPtr[r] = (struct ncclDevChannelPeer*)addr;
+     }
+   }
+
+@@ -52,6 +54,8 @@ ncclResult_t initChannel(struct ncclComm* comm, int channelId) {
+   NCCLCHECK(ncclCudaCallocAsync(&channel->devRingUserRanks, nRanks, sharedRes->deviceStream.cudaStream));
+   ncclCommPushCudaFree(comm, channel->devRingUserRanks);
+
++  /* guarantee addr has been copied into channel->devPeers */
++  NCCLCHECK(ncclStrongStreamSynchronize(&sharedRes->deviceStream));
+   NCCLCHECK(ncclStrongStreamRelease(ncclCudaGraphNone(), &sharedRes->deviceStream));
+
+   return ncclSuccess;
+@@ -77,6 +81,7 @@ ncclResult_t initNvlsChannel(struct ncclComm* comm, int channelId, struct ncclCo
+       uintptr_t addr = (uintptr_t)(parent->channels[channelId].nvlsDevPeers + tr);
+       channel->peers[comm->nRanks + 1 + r] = parent->channels[channelId].nvlsPeers + tr;
+       NCCLCHECK(ncclCudaMemcpyAsync((uintptr_t*)(channel->devPeers + comm->nRanks + 1 + r), (uintptr_t*)&addr, 1, sharedRes->deviceStream.cudaStream));
++      channel->devPeersHostPtr[comm->nRanks + 1 + r] = (struct ncclDevChannelPeer*)addr;
+       ncclAtomicRefCountIncrement(&parent->channels[channelId].nvlsPeers[tr].refCount);
+     }
+   } else {
+@@ -86,10 +91,12 @@ ncclResult_t initNvlsChannel(struct ncclComm* comm, int channelId, struct ncclCo
+       uintptr_t addr = (uintptr_t)(channel->nvlsDevPeers + r);
+       channel->peers[comm->nRanks + 1 + r] = channel->nvlsPeers + r;
+       NCCLCHECK(ncclCudaMemcpyAsync((uintptr_t*)(channel->devPeers + comm->nRanks + 1 + r), (uintptr_t*)&addr, 1, sharedRes->deviceStream.cudaStream));
++      channel->devPeersHostPtr[comm->nRanks + 1 + r] = (struct ncclDevChannelPeer*)addr;
+       ncclAtomicRefCountIncrement(&channel->nvlsPeers[r].refCount);
+     }
+   }
+
++  NCCLCHECK(ncclStrongStreamSynchronize(&sharedRes->deviceStream));
+   NCCLCHECK(ncclStrongStreamRelease(ncclCudaGraphNone(), &sharedRes->deviceStream));
+
+   return ncclSuccess;
+@@ -114,6 +121,7 @@ ncclResult_t initCollnetChannel(struct ncclComm* comm, int channelId, struct ncc
+     addr = (uintptr_t)parent->channels[channelId].collnetDevPeers;
+     channel->peers[comm->nRanks] = parent->channels[channelId].collnetPeers;
+     NCCLCHECK(ncclCudaMemcpyAsync((uintptr_t*)(channel->devPeers + comm->nRanks), (uintptr_t*)&addr, 1, sharedRes->deviceStream.cudaStream));
++    channel->devPeersHostPtr[comm->nRanks] = (struct ncclDevChannelPeer*)addr;
+     ncclAtomicRefCountIncrement(&parent->channels[channelId].collnetPeers->refCount);
+   } else {
+     NCCLCHECK(ncclCalloc(&channel->collnetPeers, 1));
+@@ -121,9 +129,11 @@ ncclResult_t initCollnetChannel(struct ncclComm* comm, int channelId, struct ncc
+     addr = (uintptr_t)channel->collnetDevPeers;
+     channel->peers[comm->nRanks] = channel->collnetPeers;
+     NCCLCHECK(ncclCudaMemcpyAsync((uintptr_t*)(channel->devPeers + comm->nRanks), (uintptr_t*)&addr, 1, sharedRes->deviceStream.cudaStream));
++    channel->devPeersHostPtr[comm->nRanks] = (struct ncclDevChannelPeer*)addr;
+     ncclAtomicRefCountIncrement(&channel->collnetPeers->refCount);
+   }
+
++  NCCLCHECK(ncclStrongStreamSynchronize(&sharedRes->deviceStream));
+   NCCLCHECK(ncclStrongStreamRelease(ncclCudaGraphNone(), &sharedRes->deviceStream));
+
+   return ncclSuccess;
+@@ -156,5 +166,7 @@ ncclResult_t freeChannel(struct ncclChannel* channel, int nRanks, int collnetNRa
+       }
+     }
+   }
++
++  free(channel->devPeersHostPtr);
+   return ncclSuccess;
+ }
+diff --git a/src/include/comm.h b/src/include/comm.h
+index e79bf54..8986f93 100644
+--- a/src/include/comm.h
++++ b/src/include/comm.h
+@@ -124,6 +124,8 @@ struct ncclSharedResources {
+ struct ncclChannel {
+   struct ncclChannelPeer** peers;
+   struct ncclDevChannelPeer** devPeers;
++  /* devPeer pointer array used for host side access */
++  struct ncclDevChannelPeer** devPeersHostPtr;
+   struct ncclRing ring;
+   int* devRingUserRanks;
+   struct ncclTree tree;
+diff --git a/src/init.cc b/src/init.cc
+index 1ea1d7e..309ce10 100644
+--- a/src/init.cc
++++ b/src/init.cc
+@@ -437,7 +437,7 @@ static ncclResult_t devCommSetup(ncclComm_t comm) {
+
+   NCCLCHECKGOTO(ncclCudaMemcpyAsync(devCommAndChans, &tmpCommAndChans, 1, comm->sharedRes->deviceStream.cudaStream), ret, fail);
+ exit:
+-  CUDACHECK(cudaStreamSynchronize(comm->sharedRes->deviceStream.cudaStream));
++  NCCLCHECK(ncclStrongStreamSynchronize(&comm->sharedRes->deviceStream));
+   NCCLCHECK(ncclStrongStreamRelease(ncclCudaGraphNone(), &comm->sharedRes->deviceStream));
+   return ret;
+ fail:
+diff --git a/src/transport.cc b/src/transport.cc
+index f4b8a2a..9817beb 100644
+--- a/src/transport.cc
++++ b/src/transport.cc
+@@ -147,11 +147,9 @@ ncclResult_t ncclTransportP2pSetup(struct ncclComm* comm, struct ncclTopoGraph*
+             if (conn->connected == 0) {
+               NCCLCHECKGOTO(conn->transportComm->connect(comm, sendData[i] + sendDataOffset++, 1, comm->rank, conn), ret, fail);
+               if (ret == ncclSuccess) {
+-                struct ncclDevChannelPeer* addr;
+                 conn->connected = 1;
+                 /* comm->channels[c].devPeers[sendPeer]->send[connIndex] is a device memory access. */
+-                CUDACHECKGOTO(cudaMemcpyAsync(&addr, &comm->channels[c].devPeers[sendPeer], sizeof(struct ncclDevChannelPeer*), cudaMemcpyDeviceToHost, comm->sharedRes->hostStream.cudaStream), ret, fail);
+-                CUDACHECKGOTO(cudaMemcpyAsync(&addr->send[connIndex], &conn->conn, sizeof(struct ncclConnInfo), cudaMemcpyHostToDevice, comm->sharedRes->hostStream.cudaStream), ret, fail);
++                CUDACHECKGOTO(cudaMemcpyAsync(&comm->channels[c].devPeersHostPtr[sendPeer]->send[connIndex], &conn->conn, sizeof(struct ncclConnInfo), cudaMemcpyHostToDevice, comm->sharedRes->hostStream.cudaStream), ret, fail);
+               } else if (ret == ncclInProgress) {
+                 allChannelsConnected = false;
+               }
+@@ -167,11 +165,9 @@ ncclResult_t ncclTransportP2pSetup(struct ncclComm* comm, struct ncclTopoGraph*
+             if (conn->connected == 0) {
+               NCCLCHECKGOTO(conn->transportComm->connect(comm, recvData[i] + recvDataOffset++, 1, comm->rank, conn), ret, fail);
+               if (ret == ncclSuccess) {
+-                struct ncclDevChannelPeer* addr;
+                 conn->connected = 1;
+                 /* comm->channels[c].devPeers[recvPeer]->recv[connIndex] is a device memory access. */
+-                CUDACHECKGOTO(cudaMemcpyAsync(&addr, &comm->channels[c].devPeers[recvPeer], sizeof(struct ncclDevChannelPeer*), cudaMemcpyDeviceToHost, comm->sharedRes->hostStream.cudaStream), ret, fail);
+-                CUDACHECKGOTO(cudaMemcpyAsync(&addr->recv[connIndex], &conn->conn, sizeof(struct ncclConnInfo), cudaMemcpyHostToDevice, comm->sharedRes->hostStream.cudaStream), ret, fail);
++                CUDACHECKGOTO(cudaMemcpyAsync(&comm->channels[c].devPeersHostPtr[recvPeer]->recv[connIndex], &conn->conn, sizeof(struct ncclConnInfo), cudaMemcpyHostToDevice, comm->sharedRes->hostStream.cudaStream), ret, fail);
+               } else if (ret == ncclInProgress) {
+                 allChannelsConnected = false;
+               }
+diff --git a/src/transport/nvls.cc b/src/transport/nvls.cc
+index 633cb04..07be99d 100644
+--- a/src/transport/nvls.cc
++++ b/src/transport/nvls.cc
+@@ -359,12 +359,10 @@ ncclResult_t ncclNvlsSetup(struct ncclComm* comm, struct ncclComm* parent) {
+         peer->send[0].conn.tail = (uint64_t*)(mem + buffSize + memSize / 2);
+         peer->send[0].conn.flags |= NCCL_NVLS_MIN_POLL;
+
+-        struct ncclDevChannelPeer* addr;
+-        CUDACHECKGOTO(cudaMemcpyAsync(&addr, comm->channels[c].devPeers + nvlsPeer, sizeof(struct ncclDevChannelPeer*), cudaMemcpyDeviceToHost, comm->sharedRes->hostStream.cudaStream), res, cleanup);
+-        CUDACHECKGOTO(cudaMemcpyAsync(&addr->send[0], &peer->send[0].conn, sizeof(struct ncclConnInfo), cudaMemcpyHostToDevice, comm->sharedRes->hostStream.cudaStream), res, cleanup);
+-        CUDACHECKGOTO(cudaMemcpyAsync(&addr->recv[0], &peer->recv[0].conn, sizeof(struct ncclConnInfo), cudaMemcpyHostToDevice, comm->sharedRes->hostStream.cudaStream), res, cleanup);
+-        CUDACHECKGOTO(cudaMemcpyAsync(&addr->send[1], &peer->send[1].conn, sizeof(struct ncclConnInfo), cudaMemcpyHostToDevice, comm->sharedRes->hostStream.cudaStream), res, cleanup);
+-        CUDACHECKGOTO(cudaMemcpyAsync(&addr->recv[1], &peer->recv[1].conn, sizeof(struct ncclConnInfo), cudaMemcpyHostToDevice, comm->sharedRes->hostStream.cudaStream), res, cleanup);
++        CUDACHECKGOTO(cudaMemcpyAsync(&comm->channels[c].devPeersHostPtr[nvlsPeer]->send[0], &peer->send[0].conn, sizeof(struct ncclConnInfo), cudaMemcpyHostToDevice, comm->sharedRes->hostStream.cudaStream), res, cleanup);
++        CUDACHECKGOTO(cudaMemcpyAsync(&comm->channels[c].devPeersHostPtr[nvlsPeer]->recv[0], &peer->recv[0].conn, sizeof(struct ncclConnInfo), cudaMemcpyHostToDevice, comm->sharedRes->hostStream.cudaStream), res, cleanup);
++        CUDACHECKGOTO(cudaMemcpyAsync(&comm->channels[c].devPeersHostPtr[nvlsPeer]->send[1], &peer->send[1].conn, sizeof(struct ncclConnInfo), cudaMemcpyHostToDevice, comm->sharedRes->hostStream.cudaStream), res, cleanup);
++        CUDACHECKGOTO(cudaMemcpyAsync(&comm->channels[c].devPeersHostPtr[nvlsPeer]->recv[1], &peer->recv[1].conn, sizeof(struct ncclConnInfo), cudaMemcpyHostToDevice, comm->sharedRes->hostStream.cudaStream), res, cleanup);
+
+         /*INFO(NCCL_INIT|NCCL_NVLS, "Peer %d Channel %d MC buff %p/%p UC Buff %p/%p",
+             nvlsPeer, c,
+--
+2.45.2

From d9d7152921d432f5d3b0242dd114e68a1bba9b48 Mon Sep 17 00:00:00 2001
From: tanmoy1989 <mssmzs@login01.avon.hpc>
Date: Wed, 10 Jul 2024 23:27:15 +0100
Subject: [PATCH 440/835] adding easyconfigs: imageio-2.34.1-gfbf-2023b.eb

---
 .../i/imageio/imageio-2.34.1-gfbf-2023b.eb    | 25 +++++++++++++++++++
 1 file changed, 25 insertions(+)
 create mode 100644 easybuild/easyconfigs/i/imageio/imageio-2.34.1-gfbf-2023b.eb

diff --git a/easybuild/easyconfigs/i/imageio/imageio-2.34.1-gfbf-2023b.eb b/easybuild/easyconfigs/i/imageio/imageio-2.34.1-gfbf-2023b.eb
new file mode 100644
index 00000000000..8f602262f3d
--- /dev/null
+++ b/easybuild/easyconfigs/i/imageio/imageio-2.34.1-gfbf-2023b.eb
@@ -0,0 +1,25 @@
+easyblock = 'PythonPackage'
+
+name = 'imageio'
+version = '2.34.1'
+
+homepage = 'https://imageio.github.io'
+description = """Imageio is a Python library that provides an easy interface to read and write a wide range of
+ image data, including animated images, video, volumetric data, and scientific formats."""
+
+toolchain = {'name': 'gfbf', 'version': '2023b'}
+
+sources = [SOURCE_TAR_GZ]
+checksums = ['f13eb76e4922f936ac4a7fec77ce8a783e63b93543d4ea3e40793a6cabd9ac7d']
+
+dependencies = [
+    ('Python', '3.11.5'),
+    ('matplotlib', '3.8.2'),
+    ('Pillow', '10.2.0'),
+]
+
+download_dep_fail = True
+use_pip = True
+sanity_pip_check = True
+
+moduleclass = 'vis'

From 369de49e4d12555ad23072a357835ef265b676e6 Mon Sep 17 00:00:00 2001
From: Adam Huffman <12435+verdurin@users.noreply.github.com>
Date: Thu, 11 Jul 2024 11:03:23 +0000
Subject: [PATCH 441/835] Add checksum

---
 easybuild/easyconfigs/g/Gubbins/Gubbins-3.3.5-foss-2022b.eb | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easybuild/easyconfigs/g/Gubbins/Gubbins-3.3.5-foss-2022b.eb b/easybuild/easyconfigs/g/Gubbins/Gubbins-3.3.5-foss-2022b.eb
index 1a19d74c757..57a08aeb182 100644
--- a/easybuild/easyconfigs/g/Gubbins/Gubbins-3.3.5-foss-2022b.eb
+++ b/easybuild/easyconfigs/g/Gubbins/Gubbins-3.3.5-foss-2022b.eb
@@ -15,6 +15,7 @@ toolchain = {'name': 'foss', 'version': '2022b'}
 
 source_urls = ['https://github.com/nickjcroucher/gubbins/archive/refs/tags/']
 sources = ['v%(version)s.tar.gz']
+checksums = ['4ee363f82708bdda0c00d1c6c334cf20127bd852ee488619f61140771a279774']
 
 builddependencies = [
     ('Autotools', '20220317'),

From f652ed0644aff2e0e02a6ba23dae180a7c160b3a Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Thu, 11 Jul 2024 13:45:11 +0200
Subject: [PATCH 442/835] update umpire.eb

---
 .../easyconfigs/u/Umpire/Umpire-2024.02.1-foss-2023a.eb      | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/easybuild/easyconfigs/u/Umpire/Umpire-2024.02.1-foss-2023a.eb b/easybuild/easyconfigs/u/Umpire/Umpire-2024.02.1-foss-2023a.eb
index c3c16eb26c8..fddfdf851cf 100644
--- a/easybuild/easyconfigs/u/Umpire/Umpire-2024.02.1-foss-2023a.eb
+++ b/easybuild/easyconfigs/u/Umpire/Umpire-2024.02.1-foss-2023a.eb
@@ -25,4 +25,9 @@ builddependencies = [
     ('CMake', '3.26.3'),
 ]
 
+sanity_check_paths = {
+    'files': ['lib/libcamp.a', 'include/umpire/Umpire.hpp'],
+    'dirs': ['bin', 'include'],
+}
+
 moduleclass = 'lib'

From b1828500f872cb3b739f8e48dcfe80bfebb9c5c3 Mon Sep 17 00:00:00 2001
From: Simon Branford <4967+branfosj@users.noreply.github.com>
Date: Thu, 11 Jul 2024 14:25:19 +0100
Subject: [PATCH 443/835] rename `gubbins-2.4.0.eb` to `Gubbins-2.4.0.eb`

---
 .../g/{gubbins/gubbins-2.4.0.eb => Gubbins/Gubbins-2.4.0.eb}    | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)
 rename easybuild/easyconfigs/g/{gubbins/gubbins-2.4.0.eb => Gubbins/Gubbins-2.4.0.eb} (98%)

diff --git a/easybuild/easyconfigs/g/gubbins/gubbins-2.4.0.eb b/easybuild/easyconfigs/g/Gubbins/Gubbins-2.4.0.eb
similarity index 98%
rename from easybuild/easyconfigs/g/gubbins/gubbins-2.4.0.eb
rename to easybuild/easyconfigs/g/Gubbins/Gubbins-2.4.0.eb
index c209965f2eb..7b9bbd1be45 100644
--- a/easybuild/easyconfigs/g/gubbins/gubbins-2.4.0.eb
+++ b/easybuild/easyconfigs/g/Gubbins/Gubbins-2.4.0.eb
@@ -10,7 +10,7 @@
 
 easyblock = 'Conda'
 
-name = 'gubbins'
+name = 'Gubbins'
 version = '2.4.0'
 
 homepage = 'https://sanger-pathogens.github.io/gubbins'

From 2d5e4802f600092caa6ef0235293569607c23e38 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Fri, 12 Jul 2024 00:43:01 +0000
Subject: [PATCH 444/835] adding easyconfigs: LLVM-18.1.8-GCCcore-13.3.0.eb,
 libdrm-2.4.122-GCCcore-13.3.0.eb, libglvnd-1.7.0-GCCcore-13.3.0.eb,
 Mesa-24.1.3-GCCcore-13.3.0.eb

---
 .../l/LLVM/LLVM-18.1.8-GCCcore-13.3.0.eb      | 48 +++++++++++++
 .../l/libdrm/libdrm-2.4.122-GCCcore-13.3.0.eb | 32 +++++++++
 .../libglvnd/libglvnd-1.7.0-GCCcore-13.3.0.eb | 33 +++++++++
 .../m/Mesa/Mesa-24.1.3-GCCcore-13.3.0.eb      | 68 +++++++++++++++++++
 4 files changed, 181 insertions(+)
 create mode 100644 easybuild/easyconfigs/l/LLVM/LLVM-18.1.8-GCCcore-13.3.0.eb
 create mode 100644 easybuild/easyconfigs/l/libdrm/libdrm-2.4.122-GCCcore-13.3.0.eb
 create mode 100644 easybuild/easyconfigs/l/libglvnd/libglvnd-1.7.0-GCCcore-13.3.0.eb
 create mode 100644 easybuild/easyconfigs/m/Mesa/Mesa-24.1.3-GCCcore-13.3.0.eb

diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-18.1.8-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/LLVM/LLVM-18.1.8-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..a0c29eba130
--- /dev/null
+++ b/easybuild/easyconfigs/l/LLVM/LLVM-18.1.8-GCCcore-13.3.0.eb
@@ -0,0 +1,48 @@
+name = 'LLVM'
+version = '18.1.8'
+
+homepage = "https://llvm.org/"
+description = """The LLVM Core libraries provide a modern source- and target-independent
+ optimizer, along with code generation support for many popular CPUs
+ (as well as some less common ones!) These libraries are built around a well
+ specified code representation known as the LLVM intermediate representation
+ ("LLVM IR"). The LLVM Core libraries are well documented, and it is
+ particularly easy to invent your own language (or port an existing compiler)
+ to use LLVM as an optimizer and code generator."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+toolchainopts = {'cstd': 'gnu++11', 'pic': True}
+
+source_urls = ['https://github.com/llvm/llvm-project/releases/download/llvmorg-%(version)s/']
+sources = [
+    'llvm-%(version)s.src.tar.xz',
+    'cmake-%(version)s.src.tar.xz',
+    'third-party-%(version)s.src.tar.xz',
+]
+checksums = [
+    {'llvm-18.1.8.src.tar.xz': 'f68cf90f369bc7d0158ba70d860b0cb34dbc163d6ff0ebc6cfa5e515b9b2e28d'},
+    {'cmake-18.1.8.src.tar.xz': '59badef592dd34893cd319d42b323aaa990b452d05c7180ff20f23ab1b41e837'},
+    {'third-party-18.1.8.src.tar.xz': 'b76b810f3d3dc5d08e83c4236cb6e395aa9bd5e3ea861e8c319b216d093db074'},
+]
+
+builddependencies = [
+    ('binutils', '2.42'),
+    ('CMake', '3.29.3'),
+    ('Python', '3.12.3'),
+]
+
+dependencies = [
+    ('ncurses', '6.5'),
+    ('zlib', '1.3.1'),
+]
+
+build_shared_libs = True
+
+sanity_check_paths = {
+    'files': ['bin/llvm-ar', 'bin/FileCheck'],
+    'dirs': ['include/llvm', 'include/llvm-c'],
+}
+
+sanity_check_commands = ["llvm-ar --help"]
+
+moduleclass = 'compiler'
diff --git a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.122-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.122-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..beff58c433a
--- /dev/null
+++ b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.122-GCCcore-13.3.0.eb
@@ -0,0 +1,32 @@
+easyblock = 'MesonNinja'
+
+name = 'libdrm'
+version = '2.4.122'
+
+homepage = 'https://dri.freedesktop.org'
+description = """Direct Rendering Manager runtime library."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+source_urls = ['https://dri.freedesktop.org/libdrm/']
+sources = [SOURCELOWER_TAR_XZ]
+checksums = ['d9f5079b777dffca9300ccc56b10a93588cdfbc9dde2fae111940dfb6292f251']
+
+builddependencies = [
+    ('binutils', '2.42'),
+    ('pkgconf', '2.2.0'),
+    ('Meson', '1.4.0'),
+    ('Ninja', '1.12.1'),
+]
+dependencies = [('X11', '20240607')]
+
+# installing manpages requires an extra build dependency (docbook xsl)
+configopts = '-Dman-pages=disabled'
+
+sanity_check_paths = {
+    'files': ['lib/libdrm.%s' % SHLIB_EXT, 'include/libdrm/drm.h'],
+    'dirs': ['include', 'lib'],
+}
+
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/l/libglvnd/libglvnd-1.7.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libglvnd/libglvnd-1.7.0-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..c6a03d1b419
--- /dev/null
+++ b/easybuild/easyconfigs/l/libglvnd/libglvnd-1.7.0-GCCcore-13.3.0.eb
@@ -0,0 +1,33 @@
+easyblock = 'MesonNinja'
+
+name = 'libglvnd'
+version = '1.7.0'
+
+homepage = 'https://gitlab.freedesktop.org/glvnd/libglvnd'
+description = "libglvnd is a vendor-neutral dispatch layer for arbitrating OpenGL API calls between multiple vendors."
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+source_urls = ['https://gitlab.freedesktop.org/glvnd/libglvnd/-/archive/v%(version)s/']
+sources = ['libglvnd-v%(version)s.tar.gz']
+checksums = ['2b6e15b06aafb4c0b6e2348124808cbd9b291c647299eaaba2e3202f51ff2f3d']
+
+builddependencies = [
+    ('binutils', '2.42'),
+    ('pkgconf', '2.2.0'),
+    ('Meson', '1.4.0'),
+    ('Ninja', '1.12.1'),
+]
+
+dependencies = [('X11', '20240607')]
+
+# Let EGL find system-installed vendor files in /etc/glvnd/egl_vendor.d etc.
+allow_prepend_abs_path = True
+modextrapaths = {"__EGL_VENDOR_LIBRARY_DIRS": "/etc/glvnd/egl_vendor.d:/usr/share/glvnd/egl_vendor.d"}
+
+sanity_check_paths = {
+    'files': ['lib/lib%s.%s' % (x, SHLIB_EXT) for x in ['EGL', 'GL', 'GLX', 'OpenGL']],
+    'dirs': ['include/%s' % x for x in ['EGL', 'GL', 'GLES', 'GLES2', 'GLES3', 'glvnd', 'KHR']] + ['lib/pkgconfig'],
+}
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-24.1.3-GCCcore-13.3.0.eb b/easybuild/easyconfigs/m/Mesa/Mesa-24.1.3-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..5eda042c494
--- /dev/null
+++ b/easybuild/easyconfigs/m/Mesa/Mesa-24.1.3-GCCcore-13.3.0.eb
@@ -0,0 +1,68 @@
+# This is a Mesa using software rendering via Gallium-DRI and libglvnd
+# - libglvnd can dynamically choose between system-installed NVidia
+# libGLX/libEGL or the software renderers provided by this Mesa
+# - EGL is available
+#
+# Software renderers enabled (swr deprecated as of v22):
+# - llvmpipe: uses LLVM for JIT code generation (multi-threaded)
+# - softpipe: a reference Gallium driver
+# Default renderer is llvmpipe. To use softpipe, set the environment
+# variable GALLIUM_DRIVER=softpipe
+
+name = 'Mesa'
+version = '24.1.3'
+
+homepage = 'https://www.mesa3d.org/'
+description = """Mesa is an open-source implementation of the OpenGL specification -
+ a system for rendering interactive 3D graphics."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+source_urls = [
+    'https://mesa.freedesktop.org/archive/',
+    'https://mesa.freedesktop.org/archive/%(version)s',
+    'ftp://ftp.freedesktop.org/pub/mesa/%(version)s',
+    'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x/%(version)s',
+    'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x',
+]
+sources = [SOURCELOWER_TAR_XZ]
+checksums = ['63236426b25a745ba6aa2d6daf8cd769d5ea01887b0745ab7124d2ef33a9020d']
+
+builddependencies = [
+    ('binutils', '2.42'),
+    ('Meson', '1.4.0'),
+    ('Ninja', '1.12.1'),
+    ('flex', '2.6.4'),
+    ('Bison', '3.8.2'),
+    ('pkgconf', '2.2.0'),
+    ('Mako', '1.3.5'),
+    ('libxml2', '2.12.7'),
+    ('expat', '2.6.2'),
+    ('gettext', '0.22.5'),
+]
+
+dependencies = [
+    ('zlib', '1.3.1'),
+    ('zstd', '1.5.6'),
+    ('libdrm', '2.4.122'),
+    ('libglvnd', '1.7.0'),
+    ('libunwind', '1.8.1'),
+    ('LLVM', '18.1.8'),
+    ('X11', '20240607'),
+    ('Wayland', '1.23.0'),
+]
+
+configopts = "-Dplatforms=x11,wayland -Dosmesa=true -Dvulkan-drivers='swrast' -Dvulkan-layers='device-select' "
+configopts += "-Dllvm=enabled -Dshared-llvm=enabled -Dlibunwind=enabled -Dglvnd=true "
+configopts += "-Dvideo-codecs=vc1dec,h264dec,h264enc,h265dec,h265enc "
+
+# Easybuild will automatically add appropriate Gallium drivers for the processor architecture of the host
+# If you need a different configuration, it possible to override those values by setting your own configopts
+# configopts += " -Dgallium-drivers=swrast"
+
+# symlink indirect to mesa GLX, similar to Debian, see
+# https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=881789
+# This helps in certain X forwarding situations (e.g. XQuartz)
+postinstallcmds = ["ln -s libGLX_mesa.so.0 %(installdir)s/lib/libGLX_indirect.so.0"]
+
+moduleclass = 'vis'

From 6880fd7d273aafa8b2fa132d7b6c50e2046c51cb Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Fri, 12 Jul 2024 02:53:29 +0000
Subject: [PATCH 445/835] add libunwind

---
 .../libunwind-1.8.1-GCCcore-13.3.0.eb         | 32 +++++++++++++++++++
 1 file changed, 32 insertions(+)
 create mode 100644 easybuild/easyconfigs/l/libunwind/libunwind-1.8.1-GCCcore-13.3.0.eb

diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.8.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.8.1-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..777376a73ae
--- /dev/null
+++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.8.1-GCCcore-13.3.0.eb
@@ -0,0 +1,32 @@
+easyblock = 'ConfigureMake'
+
+name = 'libunwind'
+version = '1.8.1'
+
+homepage = 'https://www.nongnu.org/libunwind/'
+description = """The primary goal of libunwind is to define a portable and efficient C programming interface
+ (API) to determine the call-chain of a program. The API additionally provides the means to manipulate the
+ preserved (callee-saved) state of each call-frame and to resume execution at any point in the call-chain
+ (non-local goto). The API supports both local (same-process) and remote (across-process) operation.
+ As such, the API is useful in a number of applications"""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+source_urls = ['https://github.com/libunwind/libunwind/releases/download/v%(version)s/']
+sources = [SOURCE_TAR_GZ]
+checksums = ['ddf0e32dd5fafe5283198d37e4bf9decf7ba1770b6e7e006c33e6df79e6a6157']
+
+builddependencies = [('binutils', '2.42')]
+
+dependencies = [
+    ('XZ', '5.4.5'),
+]
+
+preconfigopts = 'export LIBS="$LIBS -llzma" && export CFLAGS="$CFLAGS -fno-common" && '
+
+sanity_check_paths = {
+    'files': ['include/libunwind.h', 'lib/libunwind.%s' % SHLIB_EXT],
+    'dirs': []
+}
+
+moduleclass = 'lib'

From d4e1b178a5a9eafd272b871cab7d64334e52b0d6 Mon Sep 17 00:00:00 2001
From: Simon Pinches <Simon.Pinches@iter.org>
Date: Fri, 12 Jul 2024 10:12:55 +0200
Subject: [PATCH 446/835] adding easyconfigs: ParaView-5.12.0-foss-2023b-Qt5.eb

---
 .../ParaView-5.12.0-foss-2023b-Qt5.eb         | 74 +++++++++++++++++++
 1 file changed, 74 insertions(+)
 create mode 100644 easybuild/easyconfigs/p/ParaView/ParaView-5.12.0-foss-2023b-Qt5.eb

diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.12.0-foss-2023b-Qt5.eb b/easybuild/easyconfigs/p/ParaView/ParaView-5.12.0-foss-2023b-Qt5.eb
new file mode 100644
index 00000000000..91d1f93661e
--- /dev/null
+++ b/easybuild/easyconfigs/p/ParaView/ParaView-5.12.0-foss-2023b-Qt5.eb
@@ -0,0 +1,74 @@
+easyblock = 'CMakeMake'
+
+name = 'ParaView'
+version = '5.12.0'
+versionsuffix = '-Qt5'
+
+homepage = 'https://www.paraview.org'
+description = "ParaView is a scientific parallel visualizer."
+
+toolchain = {'name': 'foss', 'version': '2023b'}
+toolchainopts = {'pic': True, 'usempi': True}
+
+local_download_suffix = 'download.php?submit=Download&version=v%(version_major_minor)s&type=source&os=all&downloadFile='
+source_urls = ['https://www.paraview.org/paraview-downloads/%s' % local_download_suffix]
+sources = ["%(name)s-v%(version)s.tar.gz"]
+patches = ['ParaView-5.11.1-remove_glew_init_warning.patch']
+checksums = [
+    {'ParaView-v5.12.0.tar.gz': '2cc5733608fd508e2da8fc5d4ee693523d350dc1e1f89f9a89a78dc63107f70e'},
+    {'ParaView-5.11.1-remove_glew_init_warning.patch':
+     'dd86134f3a5b2c1b834224c69665dd31f99ef7d367688fe77dbaada212758710'},
+]
+
+builddependencies = [('CMake', '3.27.6')]
+
+dependencies = [
+    ('Python', '3.11.5'),
+    ('SciPy-bundle', '2023.11'),
+    ('Boost', '1.83.0'),
+    ('XZ', '5.4.4'),
+    ('HDF5', '1.14.3'),
+    ('netCDF', '4.9.2'),
+    ('libdrm', '2.4.117'),
+    ('Mesa', '23.1.9'),
+    ('Qt5', '5.15.13'),
+    ('zlib', '1.2.13'),
+    ('FFmpeg', '6.0'),
+    ('Szip', '2.1.1'),
+]
+
+_copts = [
+    # Basic configuration
+    # Embedded docs not supported with Qt6 https://gitlab.kitware.com/paraview/paraview/-/issues/19742
+    '-DPARAVIEW_ENABLE_EMBEDDED_DOCUMENTATION=OFF',
+    '-DCMAKE_AUTOMOC=OFF',  # err Qt6?
+    '-DPARAVIEW_INSTALL_DEVELOPMENT_FILES=ON',
+    '-DPARAVIEW_BUILD_SHARED_LIBS=ON',
+    '-DPARAVIEW_USE_MPI=ON',
+    '-DPARAVIEW_ENABLE_FFMPEG=ON',
+    '-DPARAVIEW_USE_PYTHON=ON',
+    '-DPython3_ROOT_DIR=$EBROOTPYTHON',
+    # Useful input formats
+    '-DPARAVIEW_ENABLE_XDMF2=ON',
+    '-DPARAVIEW_ENABLE_XDMF3=ON',
+    # EGL, X and Mesa
+    '-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s' % SHLIB_EXT,
+    '-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include',
+    '-DEGL_INCLUDE_DIR=$EBROOTLIBGLVND/include',
+    '-DEGL_LIBRARY=$EBROOTLIBGLVND/lib/libEGL.%s' % SHLIB_EXT,
+    '-DEGL_opengl_LIBRARY=$EBROOTLIBGLVND/libOpenGL.%s' % SHLIB_EXT,
+    '-DVTK_OPENGL_HAS_EGL=ON',
+    '-DVTK_USE_X=ON',
+    '-DVTK_OPENGL_HAS_OSMESA=OFF']
+configopts = ' '.join(_copts)
+
+sanity_check_paths = {
+    'files': ['bin/paraview', 'bin/pvserver', 'bin/pvpython'],
+    'dirs': ['include/paraview-%(version_major_minor)s', 'lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = ['python -c "import paraview"']
+
+modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'}
+
+moduleclass = 'vis'

From d8300153dc3bf4fd08a30d6576fe38f8fef90c5a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ji=C5=99=C3=AD=20F=C3=BCrst?= <Jiri.Furst@gmail.com>
Date: Fri, 12 Jul 2024 11:30:23 +0200
Subject: [PATCH 447/835] Fix qt6 issues, e.g. representation selection

---
 .../p/ParaView/ParaView-5.12.0-foss-2023b.eb  |  10 +-
 .../ParaView/ParaView-5.12.0-qt6_fixes.patch  | 126 ++++++++++++++++++
 2 files changed, 134 insertions(+), 2 deletions(-)
 create mode 100644 easybuild/easyconfigs/p/ParaView/ParaView-5.12.0-qt6_fixes.patch

diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.12.0-foss-2023b.eb b/easybuild/easyconfigs/p/ParaView/ParaView-5.12.0-foss-2023b.eb
index 018edd70431..ed8408c9301 100644
--- a/easybuild/easyconfigs/p/ParaView/ParaView-5.12.0-foss-2023b.eb
+++ b/easybuild/easyconfigs/p/ParaView/ParaView-5.12.0-foss-2023b.eb
@@ -12,11 +12,15 @@ toolchainopts = {'pic': True, 'usempi': True}
 local_download_suffix = 'download.php?submit=Download&version=v%(version_major_minor)s&type=source&os=all&downloadFile='
 source_urls = ['https://www.paraview.org/paraview-downloads/%s' % local_download_suffix]
 sources = ["%(name)s-v%(version)s.tar.gz"]
-patches = ['ParaView-5.11.1-remove_glew_init_warning.patch']
+patches = [
+    'ParaView-5.11.1-remove_glew_init_warning.patch',
+    'ParaView-5.12.0-qt6_fixes.patch',
+]
 checksums = [
     {'ParaView-v5.12.0.tar.gz': '2cc5733608fd508e2da8fc5d4ee693523d350dc1e1f89f9a89a78dc63107f70e'},
     {'ParaView-5.11.1-remove_glew_init_warning.patch':
      'dd86134f3a5b2c1b834224c69665dd31f99ef7d367688fe77dbaada212758710'},
+    {'ParaView-5.12.0-qt6_fixes.patch': '015d07ac6b74c7355b56ed7f67166f0d5b765f9d6ac135b7246a675a317063df'},
 ]
 
 builddependencies = [('CMake', '3.27.6')]
@@ -58,7 +62,9 @@ _copts = [
     '-DEGL_opengl_LIBRARY=$EBROOTLIBGLVND/libOpenGL.%s' % SHLIB_EXT,
     '-DVTK_OPENGL_HAS_EGL=ON',
     '-DVTK_USE_X=ON',
-    '-DVTK_OPENGL_HAS_OSMESA=OFF']
+    '-DVTK_OPENGL_HAS_OSMESA=OFF',
+    '-DVTK_PYTHON_OPTIONAL_LINK=OFF']
+
 configopts = ' '.join(_copts)
 
 sanity_check_paths = {
diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.12.0-qt6_fixes.patch b/easybuild/easyconfigs/p/ParaView/ParaView-5.12.0-qt6_fixes.patch
new file mode 100644
index 00000000000..838d6fe5d32
--- /dev/null
+++ b/easybuild/easyconfigs/p/ParaView/ParaView-5.12.0-qt6_fixes.patch
@@ -0,0 +1,126 @@
+This patch solves qt6 compatibility issues. For details see
+https://gitlab.kitware.com/paraview/paraview/-/merge_requests/6836
+
+diff --git a/Plugins/CAVEInteraction/pqVRDockPanel.cxx b/Plugins/CAVEInteraction/pqVRDockPanel.cxx
+index 7a3d352b993f2930716b47dd98512ca88697374c..448ac4d3833ec1582d99139b3f3fea6bbdf7d3ce 100644
+--- a/Plugins/CAVEInteraction/pqVRDockPanel.cxx
++++ b/Plugins/CAVEInteraction/pqVRDockPanel.cxx
+@@ -159,8 +159,8 @@ void pqVRDockPanel::initStyles()
+     this->Internals->stylesCombo->addItem(QString::fromStdString(styleDescs[i]));
+   }
+ 
+-  connect(this->Internals->stylesCombo, SIGNAL(currentIndexChanged(QString)), this,
+-    SLOT(styleComboChanged(QString)), Qt::UniqueConnection);
++  QObject::connect(this->Internals->stylesCombo, &QComboBox::currentTextChanged, this,
++    &pqVRDockPanel::styleComboChanged, Qt::UniqueConnection);
+ }
+ 
+ //-----------------------------------------------------------------------------
+diff --git a/Qt/Components/pqCustomFilterDefinitionWizard.cxx b/Qt/Components/pqCustomFilterDefinitionWizard.cxx
+index 9c140a37abca11b19f0c04bf7c41645b756457d6..acd7bd99e19017a5557a41c4585586b39e5ffc58 100644
+--- a/Qt/Components/pqCustomFilterDefinitionWizard.cxx
++++ b/Qt/Components/pqCustomFilterDefinitionWizard.cxx
+@@ -134,8 +134,8 @@ pqCustomFilterDefinitionWizard::pqCustomFilterDefinitionWizard(
+     SLOT(clearNameOverwrite(const QString&)));
+ 
+   // When combo selection changes, update new label to be same as old.
+-  QObject::connect(this->Form->PropertyCombo, SIGNAL(currentIndexChanged(const QString&)),
+-    this->Form->PropertyName, SLOT(setText(const QString&)));
++  QObject::connect(this->Form->PropertyCombo, &QComboBox::currentTextChanged,
++    this->Form->PropertyName, &QLineEdit::setText);
+ }
+ 
+ //-----------------------------------------------------------------------------
+diff --git a/Qt/Components/pqDataInformationWidget.cxx b/Qt/Components/pqDataInformationWidget.cxx
+index f151d584fc8b683b5666c11c7dfad85219c1e94f..7079507a14bad98dd10bff7ddf65af896cf5e919 100644
+--- a/Qt/Components/pqDataInformationWidget.cxx
++++ b/Qt/Components/pqDataInformationWidget.cxx
+@@ -103,8 +103,8 @@ pqDataInformationWidget::pqDataInformationWidget(QWidget* _parent /*=0*/)
+   this->Model->setActiveView(pqActiveObjects::instance().activeView());
+ 
+   // Clicking on the header should sort the column.
+-  QObject::connect(this->View->horizontalHeader(), SIGNAL(sectionClicked(int)), this->View,
+-    SLOT(sortByColumn(int)));
++  QObject::connect(this->View->horizontalHeader(), &QHeaderView::sectionClicked, this->View,
++    [=](int col) { this->View->sortByColumn(col, Qt::AscendingOrder); });
+ 
+   // Set the context menu policy for the header.
+   this->View->horizontalHeader()->setContextMenuPolicy(Qt::CustomContextMenu);
+diff --git a/Qt/Components/pqDisplayRepresentationWidget.cxx b/Qt/Components/pqDisplayRepresentationWidget.cxx
+index 3e08e05e560618457e628afc9bf1fdbf3167b9f0..4d9bc9958a0034e3e2b1e7920a333a5d7f794db6 100644
+--- a/Qt/Components/pqDisplayRepresentationWidget.cxx
++++ b/Qt/Components/pqDisplayRepresentationWidget.cxx
+@@ -111,8 +111,8 @@ pqDisplayRepresentationWidget::pqDisplayRepresentationWidget(QWidget* _p)
+ {
+   this->Internal = new pqDisplayRepresentationWidget::pqInternals();
+   this->Internal->setupUi(this);
+-  this->connect(this->Internal->comboBox, SIGNAL(currentIndexChanged(const QString&)),
+-    SLOT(comboBoxChanged(const QString&)));
++  QObject::connect(this->Internal->comboBox, &QComboBox::currentTextChanged, this,
++    &pqDisplayRepresentationWidget::comboBoxChanged);
+ }
+ 
+ //-----------------------------------------------------------------------------
+diff --git a/Qt/Components/pqLinksEditor.cxx b/Qt/Components/pqLinksEditor.cxx
+index 6f02d16d44b82f616a236557f16174d3ffa96425..ae66b1c97c3d82425c2f8b849c6d656deecc64a8 100644
+--- a/Qt/Components/pqLinksEditor.cxx
++++ b/Qt/Components/pqLinksEditor.cxx
+@@ -452,8 +452,8 @@ pqLinksEditor::pqLinksEditor(vtkSMLink* link, QWidget* p)
+   QObject::connect(this->Ui->lineEdit, SIGNAL(textChanged(const QString&)), this,
+     SLOT(updateEnabledState()), Qt::QueuedConnection);
+ 
+-  QObject::connect(this->Ui->comboBox, SIGNAL(currentIndexChanged(const QString&)), this,
+-    SLOT(updateSelectedProxies()), Qt::QueuedConnection);
++  QObject::connect(this->Ui->comboBox, &QComboBox::currentTextChanged, this,
++    &pqLinksEditor::updateSelectedProxies, Qt::QueuedConnection);
+ 
+   QObject::connect(
+     this->Ui->interactiveViewLinkCheckBox, &QCheckBox::stateChanged, this,
+diff --git a/Qt/Core/pqFileDialog.cxx b/Qt/Core/pqFileDialog.cxx
+index 2a87c723a5ef4af856c71e3589ce9a5efa95b65b..6f369d1163a32e5ae3c7e3bcc00a22081e81e2a2 100644
+--- a/Qt/Core/pqFileDialog.cxx
++++ b/Qt/Core/pqFileDialog.cxx
+@@ -322,7 +322,7 @@ pqFileDialog::pqFileDialog(pqServer* server, QWidget* p, const QString& title,
+     QObject::connect(
+       impl.Ui.NavigateForward, SIGNAL(clicked(bool)), this, SLOT(onNavigateForward()));
+     impl.Ui.NavigateUp->setIcon(style()->standardPixmap(QStyle::SP_FileDialogToParent));
+-    impl.Ui.NavigateUp->setShortcut(Qt::ALT + Qt::Key_Up);
++    impl.Ui.NavigateUp->setShortcut(Qt::ALT | Qt::Key_Up);
+     impl.Ui.NavigateUp->setToolTip(
+       tr("Navigate Up (%1)").arg(impl.Ui.NavigateUp->shortcut().toString()));
+     impl.Ui.CreateFolder->setIcon(style()->standardPixmap(QStyle::SP_FileDialogNewFolder));
+@@ -378,8 +378,8 @@ pqFileDialog::pqFileDialog(pqServer* server, QWidget* p, const QString& title,
+     QObject::connect(
+       impl.Ui.Parents, SIGNAL(activated(const QString&)), this, SLOT(onNavigate(const QString&)));
+ 
+-    QObject::connect(impl.Ui.EntityType, SIGNAL(currentIndexChanged(const QString&)), this,
+-      SLOT(onFilterChange(const QString&)));
++    QObject::connect(
++      impl.Ui.EntityType, &QComboBox::currentTextChanged, this, &pqFileDialog::onFilterChange);
+ 
+     QObject::connect(impl.Ui.Favorites, SIGNAL(clicked(const QModelIndex&)), this,
+       SLOT(onClickedFavorite(const QModelIndex&)));
+diff --git a/Qt/Widgets/pqSignalAdaptors.cxx b/Qt/Widgets/pqSignalAdaptors.cxx
+index 0015c9148b80eddd926ba37c17b7d777250c1a78..8e218b945c5f7a8962ffaced17d4a011c00db153 100644
+--- a/Qt/Widgets/pqSignalAdaptors.cxx
++++ b/Qt/Widgets/pqSignalAdaptors.cxx
+@@ -16,10 +16,15 @@
+ pqSignalAdaptorComboBox::pqSignalAdaptorComboBox(QComboBox* p)
+   : QObject(p)
+ {
+-  QObject::connect(p, SIGNAL(currentIndexChanged(const QString&)), this,
+-    SIGNAL(currentTextChanged(const QString&)));
+-
+-  QObject::connect(p, SIGNAL(currentIndexChanged(int)), this, SIGNAL(currentIndexChanged(int)));
++  QObject::connect(
++    p, &QComboBox::currentTextChanged, this, &pqSignalAdaptorComboBox::currentTextChanged);
++
++#if QT_VERSION > QT_VERSION_CHECK(6, 0, 0)
++  QObject::connect(
++    p, &QComboBox::currentIndexChanged, this, &pqSignalAdaptorComboBox::currentIndexChanged);
++#else
++  QObject::connect(p, SIGNAL(currentIndexChanged(int)), this, SLOT(currentIndexChanged(int)));
++#endif
+ }
+ 
+ //----------------------------------------------------------------------------

From 672c0eb3491e46d30d3314fa6960de778304234c Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Fri, 12 Jul 2024 13:33:01 +0200
Subject: [PATCH 448/835] adding easyconfigs:
 ilastik-napari-0.2.4-foss-2023a.eb, fastfilters-0.3-foss-2023a.eb

---
 .../fastfilters/fastfilters-0.3-foss-2023a.eb | 46 +++++++++++++++++++
 .../ilastik-napari-0.2.4-foss-2023a.eb        | 37 +++++++++++++++
 2 files changed, 83 insertions(+)
 create mode 100644 easybuild/easyconfigs/f/fastfilters/fastfilters-0.3-foss-2023a.eb
 create mode 100644 easybuild/easyconfigs/i/ilastik-napari/ilastik-napari-0.2.4-foss-2023a.eb

diff --git a/easybuild/easyconfigs/f/fastfilters/fastfilters-0.3-foss-2023a.eb b/easybuild/easyconfigs/f/fastfilters/fastfilters-0.3-foss-2023a.eb
new file mode 100644
index 00000000000..a9d67a03798
--- /dev/null
+++ b/easybuild/easyconfigs/f/fastfilters/fastfilters-0.3-foss-2023a.eb
@@ -0,0 +1,46 @@
+easyblock = 'CMakeMake'
+
+name = 'fastfilters'
+version = '0.3'
+
+homepage = 'https://github.com/ilastik/fastfilters/'
+description = """Fast gaussian and derivative convolutional filters."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+toolchainopts = {'optarch': False}
+
+sources = [{
+    'filename': 'v%(version)s.tar.gz',
+    'git_config': {
+        'url': 'https://github.com/ilastik',
+        'repo_name': 'fastfilters',
+        'tag': 'v%(version)s',
+        'recursive': True,
+        'keep_git_dir': True,
+    }
+}]
+checksums = [None]
+
+builddependencies = [
+    ('CMake', '3.26.3'),
+]
+dependencies = [
+    ('Python', '3.11.3'),
+    ('Python-bundle-PyPI', '2023.06'),
+    ('SciPy-bundle', '2023.07'),
+    ('pybind11', '2.11.1'),
+]
+
+configopts = '-DFF_INSTALL_DIR="%(installdir)s/lib/python%(pyshortver)s/site-packages/" '
+configopts += '-DPYTHON_EXECUTABLE="$EBROOTPYTHON/bin/python"'
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['lib', 'include'],
+}
+
+sanity_check_commands = ["python -c 'import fastfilters'"]
+
+modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'}
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/i/ilastik-napari/ilastik-napari-0.2.4-foss-2023a.eb b/easybuild/easyconfigs/i/ilastik-napari/ilastik-napari-0.2.4-foss-2023a.eb
new file mode 100644
index 00000000000..64e20f93f38
--- /dev/null
+++ b/easybuild/easyconfigs/i/ilastik-napari/ilastik-napari-0.2.4-foss-2023a.eb
@@ -0,0 +1,37 @@
+easyblock = 'PythonBundle'
+
+name = 'ilastik-napari'
+version = '0.2.4'
+
+homepage = 'https://github.com/ilastik/ilastik-napari/'
+description = "Napari plugin for interactive pixel classification."
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('Python-bundle-PyPI', '2023.06'),
+    ('SciPy-bundle', '2023.07'),
+    ('napari', '0.4.18'),
+    ('QtPy', '2.4.1'),
+    ('scikit-learn', '1.3.1'),
+    ('numba', '0.58.1'),
+    ('fastfilters', '0.3'),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    ('sparse', '0.15.4', {
+        'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl',
+        'checksums': ['76ec76fee2aee82a84eb97155dd530a9644e3b1fdea2406bc4b454698b36d938'],
+    }),
+    (name, version, {
+        'source_tmpl': 'ilastik_napari-%(version)s.tar.gz',
+        'modulename': 'ilastik',
+        'checksums': ['8e971a70389f9257eaca7561637301f996f316fdff2cb223c5828d162970bec4'],
+    }),
+]
+
+moduleclass = 'vis'

From 5b56aeb89410b6ed13921fe3330a6d4993bca27c Mon Sep 17 00:00:00 2001
From: Simon Pinches <Simon.Pinches@iter.org>
Date: Fri, 12 Jul 2024 15:20:23 +0200
Subject: [PATCH 449/835] Update ParaView-5.12.0-foss-2023b-Qt5.eb for OpenFOAM
 in-situ visualization with Catalyst

---
 .../p/ParaView/ParaView-5.12.0-foss-2023b-Qt5.eb            | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.12.0-foss-2023b-Qt5.eb b/easybuild/easyconfigs/p/ParaView/ParaView-5.12.0-foss-2023b-Qt5.eb
index 91d1f93661e..1642881e802 100644
--- a/easybuild/easyconfigs/p/ParaView/ParaView-5.12.0-foss-2023b-Qt5.eb
+++ b/easybuild/easyconfigs/p/ParaView/ParaView-5.12.0-foss-2023b-Qt5.eb
@@ -39,9 +39,6 @@ dependencies = [
 
 _copts = [
     # Basic configuration
-    # Embedded docs not supported with Qt6 https://gitlab.kitware.com/paraview/paraview/-/issues/19742
-    '-DPARAVIEW_ENABLE_EMBEDDED_DOCUMENTATION=OFF',
-    '-DCMAKE_AUTOMOC=OFF',  # err Qt6?
     '-DPARAVIEW_INSTALL_DEVELOPMENT_FILES=ON',
     '-DPARAVIEW_BUILD_SHARED_LIBS=ON',
     '-DPARAVIEW_USE_MPI=ON',
@@ -59,7 +56,8 @@ _copts = [
     '-DEGL_opengl_LIBRARY=$EBROOTLIBGLVND/libOpenGL.%s' % SHLIB_EXT,
     '-DVTK_OPENGL_HAS_EGL=ON',
     '-DVTK_USE_X=ON',
-    '-DVTK_OPENGL_HAS_OSMESA=OFF']
+    '-DVTK_OPENGL_HAS_OSMESA=OFF',
+    '-DVTK_PYTHON_OPTIONAL_LINK=OFFVTK_PYTHON_=OFF']
 configopts = ' '.join(_copts)
 
 sanity_check_paths = {

From 6948f3e57054f5b3ccefa317f7f4287dcbfb389a Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Fri, 12 Jul 2024 15:32:38 +0200
Subject: [PATCH 450/835] make pytest v7.4.2 independent of Python-bundle-PyPI

---
 .../p/pytest/pytest-7.4.2-GCCcore-12.3.0.eb      | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/easybuild/easyconfigs/p/pytest/pytest-7.4.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/pytest/pytest-7.4.2-GCCcore-12.3.0.eb
index 9d0b6f0c25d..45ab5fae484 100644
--- a/easybuild/easyconfigs/p/pytest/pytest-7.4.2-GCCcore-12.3.0.eb
+++ b/easybuild/easyconfigs/p/pytest/pytest-7.4.2-GCCcore-12.3.0.eb
@@ -13,11 +13,12 @@ toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
 builddependencies = [
     ('binutils', '2.40'),
     ('hatchling', '1.18.0'),
+    ('flit', '3.9.0'),
 ]
 
 dependencies = [
     ('Python', '3.11.3'),
-    ('Python-bundle-PyPI', '2023.06'),
+    ('hypothesis', '6.82.0'),
 ]
 
 use_pip = True
@@ -39,15 +40,14 @@ _skip_tests = [
 _ignore_tests = ' --ignore='.join(_skip_tests)
 
 exts_list = [
-    ('setuptools-scm', '8.0.4', {
-        'checksums': ['b5f43ff6800669595193fd09891564ee9d1d7dcb196cab4b2506d53a2e1c95c7'],
+    ('iniconfig', '2.0.0', {
+        'checksums': ['2d91e135bf72d31a410b17c16da610a82cb55f6b0477d1a902134b24a455b8b3'],
     }),
-    ('flit-core', '3.9.0', {
-        'source_tmpl': 'flit_core-%(version)s.tar.gz',
-        'checksums': ['72ad266176c4a3fcfab5f2930d76896059851240570ce9a98733b658cb786eba'],
+    ('exceptiongroup', '1.1.1', {
+        'checksums': ['d484c3090ba2889ae2928419117447a14daf3c1231d5e30d0aae34f354f01785'],
     }),
-    ('hypothesis', '6.88.1', {
-        'checksums': ['f4c2c004b9ec3e0e25332ad2cb6b91eba477a855557a7b5c6e79068809ff8b51'],
+    ('pluggy', '1.2.0', {
+        'checksums': ['d12f0c4b579b15f5e054301bb226ee85eeeba08ffec228092f8defbaa3a4c4b3'],
     }),
     ('elementpath', '4.1.5', {
         'checksums': ['c2d6dc524b29ef751ecfc416b0627668119d8812441c555d7471da41d4bacb8d'],

From 92b55ac0b7cc568449374e2f98586d353f25cea3 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Fri, 12 Jul 2024 16:25:11 +0200
Subject: [PATCH 451/835] fix spglib checksum

---
 easybuild/easyconfigs/s/spglib/spglib-2.5.0-GCCcore-12.3.0.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/s/spglib/spglib-2.5.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/s/spglib/spglib-2.5.0-GCCcore-12.3.0.eb
index 5a00e03ac05..a7e62a33f21 100644
--- a/easybuild/easyconfigs/s/spglib/spglib-2.5.0-GCCcore-12.3.0.eb
+++ b/easybuild/easyconfigs/s/spglib/spglib-2.5.0-GCCcore-12.3.0.eb
@@ -14,7 +14,7 @@ toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
 
 source_urls = ['https://github.com/spglib/spglib/archive']
 sources = ['v%(version)s.tar.gz']
-checksums = ['80c060b1a606a76b15f2cc708e9fdd4a83479924ebff9ac16ed26a87a0eac1a9']
+checksums = ['b6026f5e85106c0c9ee57e54b9399890d0f29982e20e96ede0428b3efbe6b914']
 
 builddependencies = [
     ('binutils', '2.40'),

From 2d06f3a69d111bf2e14e08b8bb88e3cf7fc9b4fd Mon Sep 17 00:00:00 2001
From: fizwit <john@fuzzdog.com>
Date: Fri, 12 Jul 2024 14:41:19 -0700
Subject: [PATCH 452/835] multi checksum

---
 .../easyconfigs/b/BGEN-enkre/BGEN-enkre-1.1.7-GCC-11.2.0.eb  | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/b/BGEN-enkre/BGEN-enkre-1.1.7-GCC-11.2.0.eb b/easybuild/easyconfigs/b/BGEN-enkre/BGEN-enkre-1.1.7-GCC-11.2.0.eb
index a4bb6387868..f64038e8dfe 100644
--- a/easybuild/easyconfigs/b/BGEN-enkre/BGEN-enkre-1.1.7-GCC-11.2.0.eb
+++ b/easybuild/easyconfigs/b/BGEN-enkre/BGEN-enkre-1.1.7-GCC-11.2.0.eb
@@ -26,13 +26,16 @@ patches = [
     '3rd-party-removal.patch',
     'BGEN-enkre_streampos.patch',
 ]
+
 checksums = [
-    '8173d614ae629f00c84c0e6edd7d16f56a61af2e5a8717e8fe0167f530a6aabb',  # 1.1.7.tgz
+    ('8173d614ae629f00c84c0e6edd7d16f56a61af2e5a8717e8fe0167f530a6aabb',
+     'b922ac22c1c0e365d0de6054f6ce2ad911bc81db5bcd8ca915bae750f57bd0a7'),  # 1.1.7.tgz
     '0269b91d21976f38a9cf9bf7811375d16bf35be587d903ab1d846b2001b7d767',  # 3rd-party-removal.patch
     '61c05ae5f7363d5b7b6015f0a015b93f149dbda4b23b9f48f9517a6ce93d5869',  # BGEN-enkre_streampos.patch
 ]
 
 builddependencies = [
+    ('binutils', '2.37'),
     ('Python', '3.9.6'),
 ]
 

From 0c6e89ef09c5ca1673e8e5f40f9f2deb09b7535e Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Sun, 14 Jul 2024 11:44:53 +0200
Subject: [PATCH 453/835] adding easyconfigs: ESIpy-20240709-foss-2022a.eb

---
 .../e/ESIpy/ESIpy-20240709-foss-2022a.eb      | 40 +++++++++++++++++++
 1 file changed, 40 insertions(+)
 create mode 100644 easybuild/easyconfigs/e/ESIpy/ESIpy-20240709-foss-2022a.eb

diff --git a/easybuild/easyconfigs/e/ESIpy/ESIpy-20240709-foss-2022a.eb b/easybuild/easyconfigs/e/ESIpy/ESIpy-20240709-foss-2022a.eb
new file mode 100644
index 00000000000..8b8af45bccf
--- /dev/null
+++ b/easybuild/easyconfigs/e/ESIpy/ESIpy-20240709-foss-2022a.eb
@@ -0,0 +1,40 @@
+easyblock = 'Tarball'
+
+name = 'ESIpy'
+version = '20240709'
+_commit = '206f863'
+
+homepage = 'https://github.com/jgrebol/ESIpy'
+description = """Program aimed at the calculation of population analysis and aromaticity
+indicators from different Hilbert space partitions."""
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+sources = [
+    {
+        'source_urls': ['https://github.com/jgrebol/ESIpy/archive'],
+        'download_filename': '%s.tar.gz' % _commit,
+        'filename': SOURCE_TAR_GZ,
+    },
+]
+checksums = ['7f963f47558b26f545c8963b2191a78b5b2522347d78ee96f0462dccaa0b4f86']
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('PySCF', '2.1.1'),
+]
+
+sanity_check_paths = {
+    'files': ['esi.py'],
+    'dirs': ['utils', 'examples'],
+}
+
+sanity_check_commands = [
+    "python -c 'import esi'",
+]
+
+modextrapaths = {
+    'PYTHONPATH': '',
+}
+
+moduleclass = 'chem'

From 7bb74150a2b5184734210838e49d7f5887b042e1 Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Mon, 15 Jul 2024 15:51:56 +0200
Subject: [PATCH 454/835] adding easyconfigs: pysteps-1.10.0-foss-2023a.eb

---
 .../p/pysteps/pysteps-1.10.0-foss-2023a.eb    | 41 +++++++++++++++++++
 1 file changed, 41 insertions(+)
 create mode 100644 easybuild/easyconfigs/p/pysteps/pysteps-1.10.0-foss-2023a.eb

diff --git a/easybuild/easyconfigs/p/pysteps/pysteps-1.10.0-foss-2023a.eb b/easybuild/easyconfigs/p/pysteps/pysteps-1.10.0-foss-2023a.eb
new file mode 100644
index 00000000000..f60f3a18e87
--- /dev/null
+++ b/easybuild/easyconfigs/p/pysteps/pysteps-1.10.0-foss-2023a.eb
@@ -0,0 +1,41 @@
+easyblock = 'PythonBundle'
+
+name = 'pysteps'
+version = '1.10.0'
+
+homepage = 'https://pysteps.github.io/'
+description = """Pysteps is an open-source and community-driven Python library for probabilistic
+precipitation nowcasting, i.e. short-term ensemble prediction systems."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('OpenCV', '4.8.1', '-contrib'),
+    ('Pillow', '10.0.0'),
+    ('pyproj', '3.6.0'),
+    ('matplotlib', '3.7.2'),
+    ('netcdf4-python', '1.6.4'),
+    ('dask', '2023.9.2'),  # needed by pysteps-nwp-importers
+    ('xarray', '2023.9.0'),  # needed by pysteps-nwp-importers
+]
+
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    ('jsmin', '3.0.1', {
+        'checksums': ['c0959a121ef94542e807a674142606f7e90214a2b3d1eb17300244bbb5cc2bfc'],
+    }),
+    (name, version, {
+        'checksums': ['28b51d61c3411fccf5c5f80792b9effe8f92a515e5984ffc5ad9ce810603a62d'],
+    }),
+    ('pysteps-nwp-importers', '20240624', {
+        'source_urls': ['https://github.com/pySTEPS/pysteps-nwp-importers/archive/'],
+        'sources': [{'download_filename': '73b3573.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}],
+        'checksums': ['d5835023c739056aa04c6938e256e6ba24ed9585a252cdf3f10b6dc0b92f0730'],
+    }),
+]
+
+moduleclass = 'geo'

From cf56c5ff236693446f20b2a2d7de72990542e4a2 Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Mon, 15 Jul 2024 18:25:04 +0200
Subject: [PATCH 455/835] adding easyconfigs:
 GPflow-2.9.2-foss-2022a-CUDA-11.7.0.eb, GPflow-2.9.2-foss-2022a.eb

---
 .../GPflow-2.9.2-foss-2022a-CUDA-11.7.0.eb    | 49 +++++++++++++++++++
 .../g/GPflow/GPflow-2.9.2-foss-2022a.eb       | 47 ++++++++++++++++++
 2 files changed, 96 insertions(+)
 create mode 100644 easybuild/easyconfigs/g/GPflow/GPflow-2.9.2-foss-2022a-CUDA-11.7.0.eb
 create mode 100644 easybuild/easyconfigs/g/GPflow/GPflow-2.9.2-foss-2022a.eb

diff --git a/easybuild/easyconfigs/g/GPflow/GPflow-2.9.2-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/g/GPflow/GPflow-2.9.2-foss-2022a-CUDA-11.7.0.eb
new file mode 100644
index 00000000000..8838542f89b
--- /dev/null
+++ b/easybuild/easyconfigs/g/GPflow/GPflow-2.9.2-foss-2022a-CUDA-11.7.0.eb
@@ -0,0 +1,49 @@
+easyblock = 'PythonBundle'
+
+name = 'GPflow'
+version = '2.9.2'
+versionsuffix = '-CUDA-%(cudaver)s'
+
+homepage = 'https://gpflow.github.io'
+description = """GPflow is a package for building Gaussian process models in Python. It
+implements modern Gaussian process inference for composable kernels and
+likelihoods."""
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+dependencies = [
+    ('CUDA', '11.7.0', '', SYSTEM),
+    ('Python', '3.10.4'),
+    ('TensorFlow', '2.11.0', versionsuffix),
+    ('tensorflow-probability', '0.19.0', versionsuffix),
+]
+
+use_pip = True
+
+exts_list = [
+    ('Deprecated', '1.2.14', {
+        'checksums': ['e5323eb936458dccc2582dc6f9c322c852a775a27065ff2b0c4970b9d53d01b3'],
+    }),
+    ('dropstackframe', '0.1.0', {
+        'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl',
+        'checksums': ['d619c7f87d144660f4569d447648830932f7920d570fd14f0dec552c81a0eb22'],
+    }),
+    ('lark', '1.1.9', {
+        'checksums': ['15fa5236490824c2c4aba0e22d2d6d823575dcaf4cdd1848e34b6ad836240fba'],
+    }),
+    ('check_shapes', '1.1.1', {
+        'checksums': ['b699fcb1e60bb17e2c97007e444b89eeeea2a9102ff11d61fb52454af5348403'],
+    }),
+    ('multipledispatch', '1.0.0', {
+        'checksums': ['5c839915465c68206c3e9c473357908216c28383b425361e5d144594bf85a7e0'],
+    }),
+    ('gpflow', version, {
+        'source_tmpl': 'v%(version)s.tar.gz',
+        'source_urls': ['https://github.com/GPflow/GPflow/archive/'],
+        'checksums': ['a32914c2b581b1dd2ac9a6f40352adb5f6f2c32f53028382e542014dd829553e'],
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/g/GPflow/GPflow-2.9.2-foss-2022a.eb b/easybuild/easyconfigs/g/GPflow/GPflow-2.9.2-foss-2022a.eb
new file mode 100644
index 00000000000..b94a4e3bc29
--- /dev/null
+++ b/easybuild/easyconfigs/g/GPflow/GPflow-2.9.2-foss-2022a.eb
@@ -0,0 +1,47 @@
+easyblock = 'PythonBundle'
+
+name = 'GPflow'
+version = '2.9.2'
+
+homepage = 'https://gpflow.github.io'
+description = """GPflow is a package for building Gaussian process models in Python. It
+implements modern Gaussian process inference for composable kernels and
+likelihoods."""
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('TensorFlow', '2.11.0'),
+    ('tensorflow-probability', '0.19.0'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('Deprecated', '1.2.14', {
+        'checksums': ['e5323eb936458dccc2582dc6f9c322c852a775a27065ff2b0c4970b9d53d01b3'],
+    }),
+    ('dropstackframe', '0.1.0', {
+        'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl',
+        'checksums': ['d619c7f87d144660f4569d447648830932f7920d570fd14f0dec552c81a0eb22'],
+    }),
+    ('lark', '1.1.9', {
+        'checksums': ['15fa5236490824c2c4aba0e22d2d6d823575dcaf4cdd1848e34b6ad836240fba'],
+    }),
+    ('check_shapes', '1.1.1', {
+        'checksums': ['b699fcb1e60bb17e2c97007e444b89eeeea2a9102ff11d61fb52454af5348403'],
+    }),
+    ('multipledispatch', '1.0.0', {
+        'checksums': ['5c839915465c68206c3e9c473357908216c28383b425361e5d144594bf85a7e0'],
+    }),
+    ('gpflow', version, {
+        'source_tmpl': 'v%(version)s.tar.gz',
+        'source_urls': ['https://github.com/GPflow/GPflow/archive/'],
+        'checksums': ['a32914c2b581b1dd2ac9a6f40352adb5f6f2c32f53028382e542014dd829553e'],
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'lib'

From 40ea6f1a3116b9f6ad6b3a019b9af51db8305757 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com>
Date: Tue, 16 Jul 2024 10:52:38 +0200
Subject: [PATCH 456/835] Update easyconfigs.py exception for VTK-9.2.6

---
 test/easyconfigs/easyconfigs.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py
index f0273368053..069bf5314db 100644
--- a/test/easyconfigs/easyconfigs.py
+++ b/test/easyconfigs/easyconfigs.py
@@ -662,6 +662,10 @@ def check_dep_vars(self, gen, dep, dep_vars):
             'UCX': [('1.11.0;', ['UCX-CUDA-1.11.0-'])],
             # Napari 0.4.19post1 requires VisPy >=0.14.1 <0.15
             'VisPy': [('0.14.1;', ['napari-0.4.19.post1-'])],
+            'VTK': [
+                # Visit-3.4.1 requires VTK 9.2.x
+                (r'9\.2\.0-20180606', [r'Visit-3\.4\.1']),
+            ],
             # WPS 3.9.1 requires WRF 3.9.1.1
             'WRF': [(r'3\.9\.1\.1', [r'WPS-3\.9\.1'])],
             # wxPython 4.2.0 depends on wxWidgets 3.2.0

From a13e667058aa0939ca984880e7fff07c7b377fee Mon Sep 17 00:00:00 2001
From: Julian Morillo <julian.morillo@bsc.es>
Date: Tue, 16 Jul 2024 16:53:34 +0200
Subject: [PATCH 457/835] Disable dynamic memory instrumentation

---
 easybuild/easyconfigs/e/Extrae/Extrae-4.2.0-gompi-2023b.eb | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/easybuild/easyconfigs/e/Extrae/Extrae-4.2.0-gompi-2023b.eb b/easybuild/easyconfigs/e/Extrae/Extrae-4.2.0-gompi-2023b.eb
index f5755ff433e..975c37fac53 100644
--- a/easybuild/easyconfigs/e/Extrae/Extrae-4.2.0-gompi-2023b.eb
+++ b/easybuild/easyconfigs/e/Extrae/Extrae-4.2.0-gompi-2023b.eb
@@ -41,6 +41,9 @@ dependencies = [
     ('PAPI', '7.1.0'),
 ]
 
+# Disable dynamic memory instrumentation
+configopts = '--disable-instrument-dynamic-memory'
+
 runtest = 'check'
 
 moduleclass = 'perf'

From 3e83e3b487600ed49663aa0ed975a66185004081 Mon Sep 17 00:00:00 2001
From: WilleBell <cintiawillemyns@gmail.com>
Date: Tue, 16 Jul 2024 17:22:22 +0200
Subject: [PATCH 458/835] adding easyconfigs:
 TELEMAC-MASCARET-8p5r0-foss-2023a.eb

---
 .../TELEMAC-MASCARET-8p5r0-foss-2023a.eb      | 88 +++++++++++++++++++
 1 file changed, 88 insertions(+)
 create mode 100644 easybuild/easyconfigs/t/TELEMAC-MASCARET/TELEMAC-MASCARET-8p5r0-foss-2023a.eb

diff --git a/easybuild/easyconfigs/t/TELEMAC-MASCARET/TELEMAC-MASCARET-8p5r0-foss-2023a.eb b/easybuild/easyconfigs/t/TELEMAC-MASCARET/TELEMAC-MASCARET-8p5r0-foss-2023a.eb
new file mode 100644
index 00000000000..7ab63c49433
--- /dev/null
+++ b/easybuild/easyconfigs/t/TELEMAC-MASCARET/TELEMAC-MASCARET-8p5r0-foss-2023a.eb
@@ -0,0 +1,88 @@
+easyblock = 'Binary'
+
+name = 'TELEMAC-MASCARET'
+version = '8p5r0'
+
+homepage = 'http://www.opentelemac.org'
+description = """TELEMAC-MASCARET is an integrated suite of solvers for use in the field of free-surface flow. Having
+been used in the context of many studies throughout the world, it has become one of the major standards in its field."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+toolchainopts = {'extra_fcflags': "-fallow-invalid-boz"}
+
+source_urls = ['https://gitlab.pam-retd.fr/otm/telemac-mascaret/-/archive/v%(version)s/']
+sources = ['telemac-mascaret-v%(version)s.tar.gz']
+checksums = ['2beb9793fb83d17de31b17f001f985fc30702c151e2ced614f5e0117e8e34aa0']
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),  # provides numpy, scipy
+    ('matplotlib', '3.7.2'),
+    ('HDF5', '1.14.0'),
+    ('METIS', '5.1.0'),
+    ('SCOTCH', '7.0.3'),
+    ('MUMPS', '5.6.1', '-metis'),
+]
+
+extract_sources = True
+unpack_options = '--strip-components=1'
+
+buildininstalldir = True
+
+local_tweak_cfg_cmd = ' '.join([
+    "sed -i -e 's/S10.gfortran/easybuild/g'",
+    # strip out use of AED, GOTM, MED (optional dependencies)
+    r"-e 's/\(^[a-z]*_aed:\).*/\1/g' -e 's/\(^[a-z]*_gotm:\).*/\1/g' -e 's/\(^[a-z]*_med:\).*/\1/g'",
+    # replace -O2 with desired compiler options
+    '-e "s/-O2/$F90FLAGS/g"',
+    # fix linker option for BLAS
+    '-e "s/ -lblas/ $LIBBLAS/g"',
+    # downgrade Fortran compiler error to warning
+    "-e 's/^fflags_gfo:/fflags_gfo: -fallow-invalid-boz/g'",
+    "$HOMETEL/configs/systel.easybuild.cfg",
+])
+
+install_cmd = ' && '.join([
+    "export HOMETEL=$PWD",
+    # add Python scripts to $PATH and $PYTHONPATH
+    "export PATH=$HOMETEL/scripts/python3/:$PATH",
+    "export PYTHONPATH=$HOMETEL/scripts/python3:$PYTHONPATH",
+    # force python to flush its output
+    "export PYTHONUNBUFFERED=1",
+    "cp $HOMETEL/configs/systel.edf.cfg $HOMETEL/configs/systel.easybuild.cfg",
+    local_tweak_cfg_cmd,
+    "export SYSTELCFG=$HOMETEL/configs/systel.easybuild.cfg",
+    "export USETELCFG=easybuild.dyn",
+    "export SCALAPACKHOME=$EBROOTSCALAPACK",
+    "export METISHOME=$EBROOTMETIS",
+    "export SCOTCHHOME=$EBROOTSCOTCH",
+    "export MUMPSHOME=$EBROOTMUMPS",
+    "export HDF5HOME=$EBROOTHDF5",
+    "config.py",
+    "compile_telemac.py -j %(parallel)s",
+])
+
+sanity_check_paths = {
+    'files': ['builds/easybuild.dyn/bin/telemac2d', 'builds/easybuild.dyn/bin/telemac3d',
+              'builds/easybuild.dyn/lib/libtelemac2d.%s' % SHLIB_EXT,
+              'builds/easybuild.dyn/lib/libtelemac3d.%s' % SHLIB_EXT],
+    'dirs': ['scripts/python3'],
+}
+
+sanity_check_commands = [
+    "tmpdir=$(mktemp -d) && cp -a %(installdir)s/examples/telemac2d/gouttedo $tmpdir/ && chmod -R u+w $tmpdir && "
+    "cd $tmpdir/gouttedo && telemac2d.py t2d_gouttedo.cas",
+]
+
+modextrapaths = {
+    'LD_LIBRARY_PATH': 'builds/easybuild.dyn/lib',
+    'PATH': 'scripts/python3',
+    'PYTHONPATH': 'scripts/python3',
+}
+
+modextravars = {
+    'SYSTELCFG': '%(installdir)s/configs/systel.easybuild.cfg',
+    'USETELCFG': 'easybuild.dyn',
+}
+
+moduleclass = 'geo'

From a26b35cbc1dd6cf7129f866a5b2002febd289104 Mon Sep 17 00:00:00 2001
From: ocaisa <alan.ocais@cecam.org>
Date: Tue, 16 Jul 2024 17:40:02 +0200
Subject: [PATCH 459/835] Update
 easybuild/easyconfigs/e/Extrae/Extrae-4.2.0-gompi-2023b.eb

---
 easybuild/easyconfigs/e/Extrae/Extrae-4.2.0-gompi-2023b.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/e/Extrae/Extrae-4.2.0-gompi-2023b.eb b/easybuild/easyconfigs/e/Extrae/Extrae-4.2.0-gompi-2023b.eb
index 975c37fac53..42b086d57f8 100644
--- a/easybuild/easyconfigs/e/Extrae/Extrae-4.2.0-gompi-2023b.eb
+++ b/easybuild/easyconfigs/e/Extrae/Extrae-4.2.0-gompi-2023b.eb
@@ -41,7 +41,7 @@ dependencies = [
     ('PAPI', '7.1.0'),
 ]
 
-# Disable dynamic memory instrumentation
+# Disable dynamic memory instrumentation for this release, has been seen to sometimes cause MPI test failures
 configopts = '--disable-instrument-dynamic-memory'
 
 runtest = 'check'

From 287c2b2651fa709379038cff80e854a32699288c Mon Sep 17 00:00:00 2001
From: Simon Pinches <Simon.Pinches@iter.org>
Date: Tue, 16 Jul 2024 18:10:58 +0200
Subject: [PATCH 460/835] adding easyconfigs: ESMF-8.6.1-foss-2023b.eb,
 g2lib-3.2.0-GCCcore-13.2.0.eb

---
 .../e/ESMF/ESMF-8.6.1-foss-2023b.eb           | 37 +++++++++++++++++++
 .../g/g2lib/g2lib-3.2.0-GCCcore-13.2.0.eb     | 32 ++++++++++++++++
 2 files changed, 69 insertions(+)
 create mode 100644 easybuild/easyconfigs/e/ESMF/ESMF-8.6.1-foss-2023b.eb
 create mode 100644 easybuild/easyconfigs/g/g2lib/g2lib-3.2.0-GCCcore-13.2.0.eb

diff --git a/easybuild/easyconfigs/e/ESMF/ESMF-8.6.1-foss-2023b.eb b/easybuild/easyconfigs/e/ESMF/ESMF-8.6.1-foss-2023b.eb
new file mode 100644
index 00000000000..d8471ef09d1
--- /dev/null
+++ b/easybuild/easyconfigs/e/ESMF/ESMF-8.6.1-foss-2023b.eb
@@ -0,0 +1,37 @@
+name = 'ESMF'
+version = '8.6.1'
+
+homepage = 'https://www.earthsystemcog.org/projects/esmf/'
+description = """The Earth System Modeling Framework (ESMF) is a suite of software tools for developing
+ high-performance, multi-component Earth science modeling applications."""
+
+toolchain = {'name': 'foss', 'version': '2023b'}
+toolchainopts = {'usempi': True, 'openmp': True, 'cstd': 'c++11', 'pic': True}
+
+source_urls = ['https://github.com/esmf-org/esmf/archive/']
+sources = ['v%(version)s.tar.gz']
+patches = ['ESMF-6.1.1_libopts.patch']
+checksums = [
+    {'v8.6.1.tar.gz': 'dc270dcba1c0b317f5c9c6a32ab334cb79468dda283d1e395d98ed2a22866364'},
+    {'ESMF-6.1.1_libopts.patch': '3851627f07c32a7da55d99072d619942bd3a1d9dd002e1557716158e7aacdaf4'},
+]
+
+builddependencies = [('CMake', '3.27.6')]
+
+dependencies = [
+    ('netCDF', '4.9.2'),
+    ('netCDF-Fortran', '4.6.1'),
+    ('netCDF-C++4', '4.3.1'),
+    ('libarchive', '3.7.2'),
+]
+
+# disable errors from GCC 10 on mismatches between actual and dummy argument lists (GCC 9 behaviour)
+prebuildopts = 'ESMF_F90COMPILEOPTS="${ESMF_F90COMPILEOPTS} -fallow-argument-mismatch"'
+
+buildopts = 'ESMF_NETCDF_INCLUDE=$EBROOTNETCDFMINFORTRAN/include '
+buildopts += 'ESMF_NETCDF_LIBS="`nc-config --libs` `nf-config --flibs` `ncxx4-config --libs`"'
+
+# too parallel causes the build to become really slow
+maxparallel = 8
+
+moduleclass = 'geo'
diff --git a/easybuild/easyconfigs/g/g2lib/g2lib-3.2.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/g/g2lib/g2lib-3.2.0-GCCcore-13.2.0.eb
new file mode 100644
index 00000000000..04674a29ff7
--- /dev/null
+++ b/easybuild/easyconfigs/g/g2lib/g2lib-3.2.0-GCCcore-13.2.0.eb
@@ -0,0 +1,32 @@
+name = 'g2lib'
+version = '3.2.0'
+
+homepage = 'https://www.nco.ncep.noaa.gov/pmb/codes/GRIB2/'
+description = """Library contains GRIB2 encoder/decoder and search/indexing routines."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
+
+source_urls = [homepage]
+sources = ['%(name)s-%(version)s.tar']
+patches = [
+    '%(name)s-%(version)s_makefile.patch',
+]
+checksums = [
+    '9d3866de32e13e80798bfb08dbbea9223f32cec3fce3c57b6838e76f27d5a1d3',  # g2lib-3.2.0.tar
+    'e434394a6ec8bd68dbd57e3fdb44c47372b07380e362ed955bb038b78dd81812',  # g2lib-3.2.0_makefile.patch
+]
+
+builddependencies = [('binutils', '2.40')]
+
+dependencies = [
+    ('JasPer', '4.0.0'),
+    ('libpng', '1.6.40'),
+]
+
+buildopts = 'CFLAGS="$CFLAGS -DLINUXG95 -D__64BIT__" FC=$FC CC=$CC '
+buildopts += 'FFLAGS="$FFLAGS -fno-range-check -fallow-invalid-boz -fallow-argument-mismatch -I."'
+
+# parallel build tends to fail
+parallel = 1
+
+moduleclass = 'data'

From f0f877f193b24dbadbcf9683dea004cd432da977 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com>
Date: Wed, 17 Jul 2024 10:57:16 +0200
Subject: [PATCH 461/835] Update easyconfigs.py - VTK exception update

---
 test/easyconfigs/easyconfigs.py | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py
index 41a2f9e624c..4d7b85dac79 100644
--- a/test/easyconfigs/easyconfigs.py
+++ b/test/easyconfigs/easyconfigs.py
@@ -663,10 +663,8 @@ def check_dep_vars(self, gen, dep, dep_vars):
             'UCX': [('1.11.0;', ['UCX-CUDA-1.11.0-'])],
             # Napari 0.4.19post1 requires VisPy >=0.14.1 <0.15
             'VisPy': [('0.14.1;', ['napari-0.4.19.post1-'])],
-            'VTK': [
-                # Visit-3.4.1 requires VTK 9.2.x
-                (r'9\.2\.0-20180606', [r'Visit-3\.4\.1']),
-            ],
+            # Visit-3.4.1 requires VTK 9.2.x
+            'VTK': [('9.2.6;', ['Visit-3.4.1-'])],
             # WPS 3.9.1 requires WRF 3.9.1.1
             'WRF': [(r'3\.9\.1\.1', [r'WPS-3\.9\.1'])],
             # wxPython 4.2.0 depends on wxWidgets 3.2.0

From 35d6cc35afb002ee692cd2b00328a4ef036c94ca Mon Sep 17 00:00:00 2001
From: WilleBell <cintiawillemyns@gmail.com>
Date: Wed, 17 Jul 2024 11:29:41 +0200
Subject: [PATCH 462/835] phonopy changed their homepage from version 2.5

---
 easybuild/easyconfigs/p/phonopy/phonopy-2.12.0-foss-2020b.eb    | 2 +-
 easybuild/easyconfigs/p/phonopy/phonopy-2.16.3-foss-2022a.eb    | 2 +-
 easybuild/easyconfigs/p/phonopy/phonopy-2.20.0-foss-2023a.eb    | 2 +-
 .../p/phonopy/phonopy-2.7.1-intel-2019b-Python-3.7.4.eb         | 2 +-
 .../p/phonopy/phonopy-2.7.1-intel-2020a-Python-3.8.2.eb         | 2 +-
 5 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/easybuild/easyconfigs/p/phonopy/phonopy-2.12.0-foss-2020b.eb b/easybuild/easyconfigs/p/phonopy/phonopy-2.12.0-foss-2020b.eb
index 3a1f3d0bc3b..2aa223e2c83 100644
--- a/easybuild/easyconfigs/p/phonopy/phonopy-2.12.0-foss-2020b.eb
+++ b/easybuild/easyconfigs/p/phonopy/phonopy-2.12.0-foss-2020b.eb
@@ -3,7 +3,7 @@ easyblock = 'PythonPackage'
 name = 'phonopy'
 version = '2.12.0'
 
-homepage = 'https://atztogo.github.io/phonopy/'
+homepage = 'https://phonopy.github.io/phonopy/'
 description = """Phonopy is an open source package of phonon calculations based on the supercell approach."""
 
 toolchain = {'name': 'foss', 'version': '2020b'}
diff --git a/easybuild/easyconfigs/p/phonopy/phonopy-2.16.3-foss-2022a.eb b/easybuild/easyconfigs/p/phonopy/phonopy-2.16.3-foss-2022a.eb
index d06fecee5a2..bd922d7ded0 100644
--- a/easybuild/easyconfigs/p/phonopy/phonopy-2.16.3-foss-2022a.eb
+++ b/easybuild/easyconfigs/p/phonopy/phonopy-2.16.3-foss-2022a.eb
@@ -3,7 +3,7 @@ easyblock = 'PythonPackage'
 name = 'phonopy'
 version = '2.16.3'
 
-homepage = 'https://atztogo.github.io/phonopy/'
+homepage = 'https://phonopy.github.io/phonopy/'
 description = """Phonopy is an open source package of phonon calculations based on the supercell approach."""
 
 toolchain = {'name': 'foss', 'version': '2022a'}
diff --git a/easybuild/easyconfigs/p/phonopy/phonopy-2.20.0-foss-2023a.eb b/easybuild/easyconfigs/p/phonopy/phonopy-2.20.0-foss-2023a.eb
index aa68af8a495..9e6b6c5f6e6 100644
--- a/easybuild/easyconfigs/p/phonopy/phonopy-2.20.0-foss-2023a.eb
+++ b/easybuild/easyconfigs/p/phonopy/phonopy-2.20.0-foss-2023a.eb
@@ -3,7 +3,7 @@ easyblock = 'PythonPackage'
 name = 'phonopy'
 version = '2.20.0'
 
-homepage = 'https://atztogo.github.io/phonopy/'
+homepage = 'https://phonopy.github.io/phonopy/'
 description = """Phonopy is an open source package of phonon calculations based on the supercell approach."""
 
 toolchain = {'name': 'foss', 'version': '2023a'}
diff --git a/easybuild/easyconfigs/p/phonopy/phonopy-2.7.1-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/p/phonopy/phonopy-2.7.1-intel-2019b-Python-3.7.4.eb
index 694e7938d28..310c8045b34 100644
--- a/easybuild/easyconfigs/p/phonopy/phonopy-2.7.1-intel-2019b-Python-3.7.4.eb
+++ b/easybuild/easyconfigs/p/phonopy/phonopy-2.7.1-intel-2019b-Python-3.7.4.eb
@@ -4,7 +4,7 @@ name = 'phonopy'
 version = '2.7.1'
 versionsuffix = '-Python-%(pyver)s'
 
-homepage = 'https://atztogo.github.io/phonopy/'
+homepage = 'https://phonopy.github.io/phonopy/'
 description = """Phonopy is an open source package of phonon calculations based on the supercell approach."""
 
 toolchain = {'name': 'intel', 'version': '2019b'}
diff --git a/easybuild/easyconfigs/p/phonopy/phonopy-2.7.1-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/p/phonopy/phonopy-2.7.1-intel-2020a-Python-3.8.2.eb
index 5744c456a63..2d2fef61b17 100644
--- a/easybuild/easyconfigs/p/phonopy/phonopy-2.7.1-intel-2020a-Python-3.8.2.eb
+++ b/easybuild/easyconfigs/p/phonopy/phonopy-2.7.1-intel-2020a-Python-3.8.2.eb
@@ -4,7 +4,7 @@ name = 'phonopy'
 version = '2.7.1'
 versionsuffix = '-Python-%(pyver)s'
 
-homepage = 'https://atztogo.github.io/phonopy/'
+homepage = 'https://phonopy.github.io/phonopy/'
 description = """Phonopy is an open source package of phonon calculations based on the supercell approach."""
 
 toolchain = {'name': 'intel', 'version': '2020a'}

From c3b95c8ac0256531e5225e3000ccba86d6800e61 Mon Sep 17 00:00:00 2001
From: fizwit <john@fuzzdog.com>
Date: Wed, 17 Jul 2024 10:31:35 -0700
Subject: [PATCH 463/835] change source file v1.1.7

---
 .../easyconfigs/b/BGEN-enkre/BGEN-enkre-1.1.7-GCC-11.2.0.eb | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/easybuild/easyconfigs/b/BGEN-enkre/BGEN-enkre-1.1.7-GCC-11.2.0.eb b/easybuild/easyconfigs/b/BGEN-enkre/BGEN-enkre-1.1.7-GCC-11.2.0.eb
index f64038e8dfe..b6850c17621 100644
--- a/easybuild/easyconfigs/b/BGEN-enkre/BGEN-enkre-1.1.7-GCC-11.2.0.eb
+++ b/easybuild/easyconfigs/b/BGEN-enkre/BGEN-enkre-1.1.7-GCC-11.2.0.eb
@@ -21,15 +21,15 @@ bioArxiv 308296; doi: https://doi.org/10.1101/308296
 toolchain = {'name': 'GCC', 'version': '11.2.0'}
 
 source_urls = ['https://code.enkre.net/bgen/tarball/release/']
-sources = ['%(version)s.tgz']
+sources = ['v%(version)s.tgz']
 patches = [
     '3rd-party-removal.patch',
     'BGEN-enkre_streampos.patch',
 ]
 
 checksums = [
-    ('8173d614ae629f00c84c0e6edd7d16f56a61af2e5a8717e8fe0167f530a6aabb',
-     'b922ac22c1c0e365d0de6054f6ce2ad911bc81db5bcd8ca915bae750f57bd0a7'),  # 1.1.7.tgz
+    ('6476b077af6c8e98e85fd7e09f58cb3fdf143ff91850c984248fd4dc2d74a8c3',  # v1.1.7.tgz
+     'b922ac22c1c0e365d0de6054f6ce2ad911bc81db5bcd8ca915bae750f57bd0a7'),
     '0269b91d21976f38a9cf9bf7811375d16bf35be587d903ab1d846b2001b7d767',  # 3rd-party-removal.patch
     '61c05ae5f7363d5b7b6015f0a015b93f149dbda4b23b9f48f9517a6ce93d5869',  # BGEN-enkre_streampos.patch
 ]

From 8a57f451e38fa56f0ada909280eba1c25b61c745 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Thu, 18 Jul 2024 10:24:23 +0200
Subject: [PATCH 464/835] adding easyconfigs: SingleM-0.16.0-foss-2023a.eb,
 smafa-0.8.0-GCC-12.3.0.eb, psycopg-3.2.1-GCCcore-12.3.0.eb,
 CD-HIT-4.8.1-GCC-12.3.0.eb

---
 .../c/CD-HIT/CD-HIT-4.8.1-GCC-12.3.0.eb       |  38 +++
 .../p/psycopg/psycopg-3.2.1-GCCcore-12.3.0.eb |  26 ++
 .../s/SingleM/SingleM-0.16.0-foss-2023a.eb    | 107 ++++++++
 .../s/smafa/smafa-0.8.0-GCC-12.3.0.eb         | 235 ++++++++++++++++++
 4 files changed, 406 insertions(+)
 create mode 100644 easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-GCC-12.3.0.eb
 create mode 100644 easybuild/easyconfigs/p/psycopg/psycopg-3.2.1-GCCcore-12.3.0.eb
 create mode 100644 easybuild/easyconfigs/s/SingleM/SingleM-0.16.0-foss-2023a.eb
 create mode 100644 easybuild/easyconfigs/s/smafa/smafa-0.8.0-GCC-12.3.0.eb

diff --git a/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-GCC-12.3.0.eb b/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-GCC-12.3.0.eb
new file mode 100644
index 00000000000..c4cacfb04bf
--- /dev/null
+++ b/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-GCC-12.3.0.eb
@@ -0,0 +1,38 @@
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+# Updated by: Thomas Eylenbosch(Gluo N.V.), Pavel Tománek (Inuits)
+
+easyblock = 'MakeCp'
+
+name = 'CD-HIT'
+version = '4.8.1'
+
+homepage = 'http://weizhongli-lab.org/cd-hit/'
+description = """ CD-HIT is a very widely used program for clustering and 
+ comparing protein or nucleotide sequences."""
+
+toolchain = {'name': 'GCC', 'version': '12.3.0'}
+toolchainopts = {'openmp': True}
+
+source_urls = ['https://github.com/weizhongli/cdhit/releases/download/V%(version)s/']
+sources = ['%(namelower)s-v%(version)s-2019-0228.tar.gz']
+checksums = ['26172dba3040d1ae5c73ff0ac6c3be8c8e60cc49fc7379e434cdf9cb1e7415de']
+
+dependencies = [
+    ('Perl', '5.36.1'),
+    ('zlib', '1.2.13'),
+]
+
+buildopts = ' CC="$CXX" CCFLAGS="$CPPFLAGS $CXXFLAGS"'
+
+local_list_of_executables = ['cd-hit', 'cd-hit-est', 'cd-hit-2d', 'cd-hit-est-2d', 'cd-hit-div', 'cd-hit-454']
+
+files_to_copy = [(local_list_of_executables, 'bin'), (['*.pl'], 'bin'), 'README', 'doc', 'license.txt']
+
+fix_perl_shebang_for = ['bin/*.pl']
+
+sanity_check_paths = {
+    'files': ['bin/%s' % x for x in local_list_of_executables],
+    'dirs': [],
+}
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/p/psycopg/psycopg-3.2.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/psycopg/psycopg-3.2.1-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..5c0aab8a54e
--- /dev/null
+++ b/easybuild/easyconfigs/p/psycopg/psycopg-3.2.1-GCCcore-12.3.0.eb
@@ -0,0 +1,26 @@
+easyblock = 'PythonBundle'
+
+name = 'psycopg'
+version = '3.2.1'
+
+homepage = 'https://psycopg.org/'
+description = "Psycopg is the most popular PostgreSQL adapter for the Python programming language."
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+builddependencies = [('binutils', '2.40')]
+dependencies = [
+    ('Python', '3.11.3'),
+    ('PostgreSQL', '16.1'),
+]
+
+exts_list = [
+    (name, version, {
+        'checksums': ['dc8da6dc8729dacacda3cc2f17d2c9397a70a66cf0d2b69c91065d60d5f00cb7'],
+    }),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/s/SingleM/SingleM-0.16.0-foss-2023a.eb b/easybuild/easyconfigs/s/SingleM/SingleM-0.16.0-foss-2023a.eb
new file mode 100644
index 00000000000..25fc18b7c63
--- /dev/null
+++ b/easybuild/easyconfigs/s/SingleM/SingleM-0.16.0-foss-2023a.eb
@@ -0,0 +1,107 @@
+easyblock = 'PythonBundle'
+
+name = 'SingleM'
+version = '0.16.0'
+
+homepage = 'https://github.com/wwood/singlem'
+description = """SingleM is a tool for profiling shotgun metagenomes. 
+It has a particular strength in detecting microbial lineages which are not in reference databases. 
+The method it uses also makes it suitable for some related tasks, such as assessing eukaryotic contamination, 
+finding bias in genome recovery, computing ecological diversity metrics, and lineage-targeted MAG recovery."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+builddependencies = [('hatchling', '1.18.0')]
+dependencies = [
+    ('Python', '3.11.3'),
+    ('Python-bundle-PyPI', '2023.06'),
+    ('SciPy-bundle', '2023.07'),
+    ('Biopython', '1.83'),
+    ('polars', '0.20.2'),
+    ('tqdm', '4.66.1'),
+    ('Arrow', '14.0.1'),
+    ('DIAMOND', '2.1.8'),
+    ('HMMER', '3.4'),
+    ('MAFFT', '7.520', '-with-extensions'),
+    ('OrfM', '0.7.1'),
+    ('mfqe', '0.5.0'),
+    ('KronaTools', '2.8.1'),
+    ('pplacer', '1.1.alpha19', '', SYSTEM),
+    ('SRA-Toolkit', '3.0.10'),
+    ('Seqmagick', '0.8.6'),
+    ('ExpressBetaDiversity', '1.0.10'),
+    ('FastTree', '2.1.11'),
+    ('SQLAlchemy', '2.0.25'),
+    ('CD-HIT', '4.8.1'),
+    ('smafa', '0.8.0'),
+    ('prodigal', '2.6.3'),
+    ('biom-format', '2.1.15'),
+    ('DendroPy', '4.6.1'),
+    ('PyYAML', '6.0'),
+    ('psycopg', '3.2.1'),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    ('psycopg2-binary', '2.9.9', {
+        'modulename': 'psycopg2',
+        'checksums': ['7f01846810177d829c7692f1f5ada8096762d9172af1b1a28d4ab5b77c923c1c'],
+    }),
+    ('sqlparse', '0.5.1', {
+        'checksums': ['bb6b4df465655ef332548e24f08e205afc81b9ab86cb1c45657a7ff173a3a00e'],
+    }),
+    ('sorted_nearest', '0.0.39', {
+        'checksums': ['16a51d5db87ae226b47ace43c176bb672477a1b7ba8052ea9291a6356c9c69b1'],
+    }),
+    ('ncls', '0.0.68', {
+        'checksums': ['81aaa5abb123bb21797ed2f8ef921e20222db14a3ecbc61ccf447532f2b7ba93'],
+    }),
+    ('natsort', '8.4.0', {
+        'checksums': ['45312c4a0e5507593da193dedd04abb1469253b601ecaf63445ad80f0a1ea581'],
+    }),
+    ('argparse-manpage-birdtools', '1.7.0', {
+        'modulename': 'build_manpages',
+        'checksums': ['20eae3079a4a2dbe1a7557ef7276a4d8e5a44c7c4223afb50f4f1d0ae0e7d103'],
+    }),
+    ('taxtastic', '0.10.0', {
+        'checksums': ['32db30aa2e499fbae913b991cd087fa69684ac4ff934b957c30b6085866f1748'],
+    }),
+    ('zenodo_backpack', '0.3.1', {
+        'checksums': ['dc91f3c427f976465789746e94736abfa536cf42dc2e49b6d6067382a9a39b26'],
+    }),
+    ('bird_tool_utils', '0.4.1', {
+        'checksums': ['6fe80f9608626427e8d382c5341c24088d61f17336fb6ce834d40aa4577499b5'],
+    }),
+    ('fastalite', '0.4.1', {
+        'checksums': ['e85413ee22bdb3fe0f73f5226771cf71eb33074ccdf8bbefff3a1bc6242de37c'],
+    }),
+    ('squarify', '0.4.3', {
+        'checksums': ['54091f6ad175f7f201f8934574e647ce1b50dedc478c5fd968688eb7d7469f95'],
+    }),
+    ('pyranges', '0.0.129', {
+        'checksums': ['bee83b4fad0062be9586668c6b0fc4270d5e761951975e018202993680071fb3'],
+    }),
+    ('extern', '0.4.1', {
+        'checksums': ['0ff01adc2ad423f3d1e31641024b3974569fb0127b4d925bc6bed1cb86b6b1e4'],
+    }),
+    ('graftm', '0.15.1', {
+        'checksums': ['80d828c311d2d6067977cfad5b6bac7cbc5d223ef8ab770d676b39bf2bc75163'],
+    }),
+    ('singlem', version, {
+        'checksums': ['64e43a6a40795d68ff5aed7dfff9a94532b862f25a28c27de7d588d64a8c7f79'],
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['bin/graftM', 'bin/singlem'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = [
+    "graftM --help",
+    "singlem --help",
+]
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/s/smafa/smafa-0.8.0-GCC-12.3.0.eb b/easybuild/easyconfigs/s/smafa/smafa-0.8.0-GCC-12.3.0.eb
new file mode 100644
index 00000000000..342d27e7548
--- /dev/null
+++ b/easybuild/easyconfigs/s/smafa/smafa-0.8.0-GCC-12.3.0.eb
@@ -0,0 +1,235 @@
+easyblock = 'Cargo'
+
+name = 'smafa'
+version = '0.8.0'
+
+homepage = 'https://github.com/wwood/smafa'
+description = 'Biological sequence aligner for pre-aligned sequences.'
+
+toolchain = {'name': 'GCC', 'version': '12.3.0'}
+
+source_urls = ['https://github.com/wwood/smafa/archive/']
+sources = ['v%(version)s.tar.gz']
+checksums = [
+    {'v0.8.0.tar.gz': '6f103ecd5cdf36fb61572a757732eeb07e905c61b497fa247c1a8397ee775c2d'},
+    {'addr2line-0.22.0.tar.gz': '6e4503c46a5c0c7844e948c9a4d6acd9f50cccb4de1c48eb9e291ea17470c678'},
+    {'adler-1.0.2.tar.gz': 'f26201604c87b1e01bd3d98f8d5d9a8fcbb815e8cedb41ffccbeb4bf593a35fe'},
+    {'aho-corasick-1.1.3.tar.gz': '8e60d3430d3a69478ad0993f19238d2df97c507009a52b3c10addcd7f6bcb916'},
+    {'anstream-0.6.14.tar.gz': '418c75fa768af9c03be99d17643f93f79bbba589895012a80e3452a19ddda15b'},
+    {'anstyle-1.0.7.tar.gz': '038dfcf04a5feb68e9c60b21c9625a54c2c0616e79b72b0fd87075a056ae1d1b'},
+    {'anstyle-parse-0.2.4.tar.gz': 'c03a11a9034d92058ceb6ee011ce58af4a9bf61491aa7e1e59ecd24bd40d22d4'},
+    {'anstyle-query-1.1.0.tar.gz': 'ad186efb764318d35165f1758e7dcef3b10628e26d41a44bc5550652e6804391'},
+    {'anstyle-wincon-3.0.3.tar.gz': '61a38449feb7068f52bb06c12759005cf459ee52bb4adc1d5a7c4322d716fb19'},
+    {'assert_cli-0.6.3.tar.gz': 'a29ab7c0ed62970beb0534d637a8688842506d0ff9157de83286dacd065c8149'},
+    {'atomic-polyfill-1.0.3.tar.gz': '8cf2bce30dfe09ef0bfaef228b9d414faaf7e563035494d7fe092dba54b300f4'},
+    {'autocfg-1.3.0.tar.gz': '0c4b4d0bd25bd0b74681c0ad21497610ce1b7c91b1022cd21c80c6fbdd9476b0'},
+    {'backtrace-0.3.73.tar.gz': '5cc23269a4f8976d0a4d2e7109211a419fe30e8d88d677cd60b6bc79c5732e0a'},
+    {'bird_tool_utils-0.4.1.tar.gz': '6f5f475a22ef913421b64a8d09fad619d9a3a828a5a7450e9b32ab177aa3df56'},
+    {'bird_tool_utils-man-0.4.0.tar.gz': 'a263d1717fd146db3c9bfc0668f9bf19d9078a79fa2c1ba54f00b6d8702d4e0b'},
+    {'bitflags-2.6.0.tar.gz': 'b048fb63fd8b5923fc5aa7b340d8e156aec7ec02f0c78fa8a6ddc2613f6f71de'},
+    {'buffer-redux-1.0.1.tar.gz': '4c9f8ddd22e0a12391d1e7ada69ec3b0da1914f1cec39c5cf977143c5b2854f5'},
+    {'bytecount-0.6.8.tar.gz': '5ce89b21cab1437276d2650d57e971f9d548a2d9037cc231abdc0562b97498ce'},
+    {'byteorder-1.5.0.tar.gz': '1fd0f2584146f6f2ef48085050886acf353beff7305ebd1ae69500e27c67f64b'},
+    {'bzip2-0.4.4.tar.gz': 'bdb116a6ef3f6c3698828873ad02c3014b3c85cadb88496095628e3ef1e347f8'},
+    {'bzip2-sys-0.1.11+1.0.8.tar.gz': '736a955f3fa7875102d57c82b8cac37ec45224a07fd32d58f9f7a186b6cd4cdc'},
+    {'cargo-husky-1.5.0.tar.gz': '7b02b629252fe8ef6460461409564e2c21d0c8e77e0944f3d189ff06c4e932ad'},
+    {'cc-1.1.5.tar.gz': '324c74f2155653c90b04f25b2a47a8a631360cb908f92a772695f430c7e31052'},
+    {'cfg-if-1.0.0.tar.gz': 'baf1de4339761588bc0619e3cbc0120ee582ebb74b53b4efbf79117bd2da40fd'},
+    {'clap-4.5.9.tar.gz': '64acc1846d54c1fe936a78dc189c34e28d3f5afc348403f28ecf53660b9b8462'},
+    {'clap_builder-4.5.9.tar.gz': '6fb8393d67ba2e7bfaf28a23458e4e2b543cc73a99595511eb207fdb8aede942'},
+    {'clap_lex-0.7.1.tar.gz': '4b82cf0babdbd58558212896d1a4272303a57bdb245c2bf1147185fb45640e70'},
+    {'cobs-0.2.3.tar.gz': '67ba02a97a2bd10f4b59b25c7973101c79642302776489e030cd13cdab09ed15'},
+    {'colorchoice-1.0.1.tar.gz': '0b6a852b24ab71dffc585bcb46eaf7959d175cb865a7152e35b348d1b2960422'},
+    {'colored-1.9.4.tar.gz': '5a5f741c91823341bebf717d4c71bda820630ce065443b58bd1b7451af008355'},
+    {'crc32fast-1.4.2.tar.gz': 'a97769d94ddab943e4510d138150169a2758b5ef3eb191a9ee688de3e23ef7b3'},
+    {'critical-section-1.1.2.tar.gz': '7059fff8937831a9ae6f0fe4d658ffabf58f2ca96aa9dec1c889f936f705f216'},
+    {'difference-2.0.0.tar.gz': '524cbf6897b527295dff137cec09ecf3a05f4fddffd7dfcd1585403449e74198'},
+    {'embedded-io-0.4.0.tar.gz': 'ef1a6892d9eef45c8fa6b9e0086428a2cca8491aca8f787c534a3d6d0bcb3ced'},
+    {'env_logger-0.10.2.tar.gz': '4cd405aab171cb85d6735e5c8d9db038c17d3ca007a4d2c25f337935c3d90580'},
+    {'environment-0.1.1.tar.gz': '1f4b14e20978669064c33b4c1e0fb4083412e40fe56cbea2eae80fd7591503ee'},
+    {'errno-0.3.9.tar.gz': '534c5cf6194dfab3db3242765c03bbe257cf92f22b38f6bc0c58d59108a820ba'},
+    {'failure-0.1.8.tar.gz': 'd32e9bd16cc02eae7db7ef620b392808b89f6a5e16bb3497d159c6b92a0f4f86'},
+    {'failure_derive-0.1.8.tar.gz': 'aa4da3c766cd7a0db8242e326e9e4e081edd567072893ed320008189715366a4'},
+    {'fastrand-2.1.0.tar.gz': '9fc0510504f03c51ada170672ac806f1f105a88aa97a5281117e1ddc3368e51a'},
+    {'flate2-1.0.30.tar.gz': '5f54427cfd1c7829e2a139fcefea601bf088ebca651d2bf53ebc600eac295dae'},
+    {'gimli-0.29.0.tar.gz': '40ecd4077b5ae9fd2e9e169b102c6c330d0605168eb0e8bf79952b256dbefffd'},
+    {'hash32-0.2.1.tar.gz': 'b0c35f58762feb77d74ebe43bdbc3210f09be9fe6742234d573bacc26ed92b67'},
+    {'heapless-0.7.17.tar.gz': 'cdc6457c0eb62c71aac4bc17216026d8410337c4126773b9c5daba343f17964f'},
+    {'hermit-abi-0.3.9.tar.gz': 'd231dfb89cfffdbc30e7fc41579ed6066ad03abda9e567ccafae602b97ec5024'},
+    {'humantime-2.1.0.tar.gz': '9a3a5bfb195931eeb336b2a7b4d761daec841b97f947d34394601737a7bba5e4'},
+    {'is-terminal-0.4.12.tar.gz': 'f23ff5ef2b80d608d61efee834934d862cd92461afc0560dedf493e4c033738b'},
+    {'is_terminal_polyfill-1.70.0.tar.gz': 'f8478577c03552c21db0e2724ffb8986a5ce7af88107e6be5d2ee6e158c12800'},
+    {'itoa-1.0.11.tar.gz': '49f1f14873335454500d59611f1cf4a4b0f786f9ac11f4312a78e4cf2566695b'},
+    {'lazy_static-1.5.0.tar.gz': 'bbd2bcb4c963f2ddae06a2efc7e9f3591312473c50c6685e1f298068316e66fe'},
+    {'libc-0.2.155.tar.gz': '97b3888a4aecf77e811145cadf6eef5901f4782c53886191b2f693f24761847c'},
+    {'linux-raw-sys-0.4.14.tar.gz': '78b3ae25bc7c8c38cec158d1f2757ee79e9b3740fbc7ccf0e59e4b08d793fa89'},
+    {'lock_api-0.4.12.tar.gz': '07af8b9cdd281b7915f413fa73f29ebd5d55d0d3f0155584dade1ff18cea1b17'},
+    {'log-0.4.22.tar.gz': 'a7a70ba024b9dc04c27ea2f0c0548feb474ec5c54bba33a7f72f873a39d07b24'},
+    {'lzma-sys-0.1.20.tar.gz': '5fda04ab3764e6cde78b9974eec4f779acaba7c4e84b36eca3cf77c581b85d27'},
+    {'memchr-2.7.4.tar.gz': '78ca9ab1a0babb1e7d5695e3530886289c18cf2f87ec19a575a0abdce112e3a3'},
+    {'miniz_oxide-0.7.4.tar.gz': 'b8a240ddb74feaf34a79a7add65a741f3167852fba007066dcac1ca548d89c08'},
+    {'needletail-0.5.1.tar.gz': 'db05a5ab397f64070d8c998fa0fbb84e484b81f95752af317dac183a82d9295d'},
+    {'object-0.36.1.tar.gz': '081b846d1d56ddfc18fdf1a922e4f6e07a11768ea1b92dec44e42b72712ccfce'},
+    {'pkg-config-0.3.30.tar.gz': 'd231b230927b5e4ad203db57bbcbee2802f6bce620b1e4a9024a07d94e2907ec'},
+    {'postcard-1.0.8.tar.gz': 'a55c51ee6c0db07e68448e336cf8ea4131a620edefebf9893e759b2d793420f8'},
+    {'proc-macro2-1.0.86.tar.gz': '5e719e8df665df0d1c8fbfd238015744736151d4445ec0836b8e628aae103b77'},
+    {'quote-1.0.36.tar.gz': '0fa76aaf39101c457836aec0ce2316dbdc3ab723cdda1c6bd4e6ad4208acaca7'},
+    {'regex-1.10.5.tar.gz': 'b91213439dad192326a0d7c6ee3955910425f441d7038e0d6933b0aec5c4517f'},
+    {'regex-automata-0.4.7.tar.gz': '38caf58cc5ef2fed281f89292ef23f6365465ed9a41b7a7754eb4e26496c92df'},
+    {'regex-syntax-0.8.4.tar.gz': '7a66a03ae7c801facd77a29370b4faec201768915ac14a721ba36f20bc9c209b'},
+    {'roff-0.1.0.tar.gz': 'e33e4fb37ba46888052c763e4ec2acfedd8f00f62897b630cadb6298b833675e'},
+    {'rustc-demangle-0.1.24.tar.gz': '719b953e2095829ee67db738b3bfa9fa368c94900df327b3f07fe6e794d2fe1f'},
+    {'rustc_version-0.4.0.tar.gz': 'bfa0f585226d2e68097d4f95d113b15b83a82e819ab25717ec0590d9584ef366'},
+    {'rustix-0.38.34.tar.gz': '70dc5ec042f7a43c4a73241207cecc9873a06d45debb38b329f8541d85c2730f'},
+    {'ryu-1.0.18.tar.gz': 'f3cb5ba0dc43242ce17de99c180e96db90b235b8a9fdc9543c96d2209116bd9f'},
+    {'scopeguard-1.2.0.tar.gz': '94143f37725109f92c262ed2cf5e59bce7498c01bcc1502d7b9afe439a4e9f49'},
+    {'semver-1.0.23.tar.gz': '61697e0a1c7e512e84a621326239844a24d8207b4669b41bc18b32ea5cbf988b'},
+    {'serde-1.0.204.tar.gz': 'bc76f558e0cbb2a839d37354c575f1dc3fdc6546b5be373ba43d95f231bf7c12'},
+    {'serde_derive-1.0.204.tar.gz': 'e0cd7e117be63d3c3678776753929474f3b04a43a080c744d6b0ae2a8c28e222'},
+    {'serde_json-1.0.120.tar.gz': '4e0d21c9a8cae1235ad58a00c11cb40d4b1e5c784f1ef2c537876ed6ffd8b7c5'},
+    {'spin-0.9.8.tar.gz': '6980e8d7511241f8acf4aebddbb1ff938df5eebe98691418c4468d0b72a96a67'},
+    {'stable_deref_trait-1.2.0.tar.gz': 'a8f112729512f8e442d81f95a8a7ddf2b7c6b8a1a6f509a95864142b30cab2d3'},
+    {'strsim-0.11.1.tar.gz': '7da8b5736845d9f2fcb837ea5d9e2628564b3b043a70948a3f0b778838c5fb4f'},
+    {'syn-1.0.109.tar.gz': '72b64191b275b66ffe2469e8af2c1cfe3bafa67b529ead792a6d0160888b4237'},
+    {'syn-2.0.71.tar.gz': 'b146dcf730474b4bcd16c311627b31ede9ab149045db4d6088b3becaea046462'},
+    {'synstructure-0.12.6.tar.gz': 'f36bdaa60a83aca3921b5259d5400cbf5e90fc51931376a9bd4a0eb79aa7210f'},
+    {'tempfile-3.10.1.tar.gz': '85b77fafb263dd9d05cbeac119526425676db3784113aa9295c88498cbf8bff1'},
+    {'termcolor-1.4.1.tar.gz': '06794f8f6c5c898b3275aebefa6b8a1cb24cd2c6c79397ab15774837a0bc5755'},
+    {'unicode-ident-1.0.12.tar.gz': '3354b9ac3fae1ff6755cb6db53683adb661634f67557942dea4facebec0fee4b'},
+    {'unicode-xid-0.2.4.tar.gz': 'f962df74c8c05a667b5ee8bcf162993134c104e96440b663c8daa176dc772d8c'},
+    {'utf8parse-0.2.2.tar.gz': '06abde3611657adf66d383f00b093d7faecc7fa57071cce2578660c9f1010821'},
+    {'version-compare-0.1.1.tar.gz': '579a42fc0b8e0c63b76519a339be31bed574929511fa53c1a3acae26eb258f29'},
+    {'winapi-0.3.9.tar.gz': '5c839a674fcd7a98952e593242ea400abe93992746761e38641405d28b00f419'},
+    {'winapi-i686-pc-windows-gnu-0.4.0.tar.gz': 'ac3b87c63620426dd9b991e5ce0329eff545bccbbb34f3be09ff6fb6ab51b7b6'},
+    {'winapi-util-0.1.8.tar.gz': '4d4cc384e1e73b93bafa6fb4f1df8c41695c8a91cf9c4c64358067d15a7b6c6b'},
+    {'winapi-x86_64-pc-windows-gnu-0.4.0.tar.gz': '712e227841d057c1ee1cd2fb22fa7e5a5461ae8e48fa2ca79ec42cfc1931183f'},
+    {'windows-sys-0.52.0.tar.gz': '282be5f36a8ce781fad8c8ae18fa3f9beff57ec1b52cb3de0789201425d9a33d'},
+    {'windows-targets-0.52.6.tar.gz': '9b724f72796e036ab90c1021d4780d4d3d648aca59e491e6b98e725b84e99973'},
+    {'windows_aarch64_gnullvm-0.52.6.tar.gz': '32a4622180e7a0ec044bb555404c800bc9fd9ec262ec147edd5989ccd0c02cd3'},
+    {'windows_aarch64_msvc-0.52.6.tar.gz': '09ec2a7bb152e2252b53fa7803150007879548bc709c039df7627cabbd05d469'},
+    {'windows_i686_gnu-0.52.6.tar.gz': '8e9b5ad5ab802e97eb8e295ac6720e509ee4c243f69d781394014ebfe8bbfa0b'},
+    {'windows_i686_gnullvm-0.52.6.tar.gz': '0eee52d38c090b3caa76c563b86c3a4bd71ef1a819287c19d586d7334ae8ed66'},
+    {'windows_i686_msvc-0.52.6.tar.gz': '240948bc05c5e7c6dabba28bf89d89ffce3e303022809e73deaefe4f6ec56c66'},
+    {'windows_x86_64_gnu-0.52.6.tar.gz': '147a5c80aabfbf0c7d901cb5895d1de30ef2907eb21fbbab29ca94c5b08b1a78'},
+    {'windows_x86_64_gnullvm-0.52.6.tar.gz': '24d5b23dc417412679681396f2b49f3de8c1473deb516bd34410872eff51ed0d'},
+    {'windows_x86_64_msvc-0.52.6.tar.gz': '589f6da84c646204747d1270a2a5661ea66ed1cced2631d546fdfb155959f9ec'},
+    {'xz2-0.1.7.tar.gz': '388c44dc09d76f1536602ead6d325eb532f5c122f17782bd57fb47baeeb767e2'},
+]
+
+builddependencies = [
+    ('Rust', '1.75.0'),
+]
+
+sanity_check_paths = {
+    'files': ['bin/%(namelower)s'],
+    'dirs': [],
+}
+
+sanity_check_commands = ["%(namelower)s --help"]
+
+crates = [
+    ('addr2line', '0.22.0'),
+    ('adler', '1.0.2'),
+    ('aho-corasick', '1.1.3'),
+    ('anstream', '0.6.14'),
+    ('anstyle', '1.0.7'),
+    ('anstyle-parse', '0.2.4'),
+    ('anstyle-query', '1.1.0'),
+    ('anstyle-wincon', '3.0.3'),
+    ('assert_cli', '0.6.3'),
+    ('atomic-polyfill', '1.0.3'),
+    ('autocfg', '1.3.0'),
+    ('backtrace', '0.3.73'),
+    ('bird_tool_utils', '0.4.1'),
+    ('bird_tool_utils-man', '0.4.0'),
+    ('bitflags', '2.6.0'),
+    ('buffer-redux', '1.0.1'),
+    ('bytecount', '0.6.8'),
+    ('byteorder', '1.5.0'),
+    ('bzip2', '0.4.4'),
+    ('bzip2-sys', '0.1.11+1.0.8'),
+    ('cargo-husky', '1.5.0'),
+    ('cc', '1.1.5'),
+    ('cfg-if', '1.0.0'),
+    ('clap', '4.5.9'),
+    ('clap_builder', '4.5.9'),
+    ('clap_lex', '0.7.1'),
+    ('cobs', '0.2.3'),
+    ('colorchoice', '1.0.1'),
+    ('colored', '1.9.4'),
+    ('crc32fast', '1.4.2'),
+    ('critical-section', '1.1.2'),
+    ('difference', '2.0.0'),
+    ('embedded-io', '0.4.0'),
+    ('env_logger', '0.10.2'),
+    ('environment', '0.1.1'),
+    ('errno', '0.3.9'),
+    ('failure', '0.1.8'),
+    ('failure_derive', '0.1.8'),
+    ('fastrand', '2.1.0'),
+    ('flate2', '1.0.30'),
+    ('gimli', '0.29.0'),
+    ('hash32', '0.2.1'),
+    ('heapless', '0.7.17'),
+    ('hermit-abi', '0.3.9'),
+    ('humantime', '2.1.0'),
+    ('is-terminal', '0.4.12'),
+    ('is_terminal_polyfill', '1.70.0'),
+    ('itoa', '1.0.11'),
+    ('lazy_static', '1.5.0'),
+    ('libc', '0.2.155'),
+    ('linux-raw-sys', '0.4.14'),
+    ('lock_api', '0.4.12'),
+    ('log', '0.4.22'),
+    ('lzma-sys', '0.1.20'),
+    ('memchr', '2.7.4'),
+    ('miniz_oxide', '0.7.4'),
+    ('needletail', '0.5.1'),
+    ('object', '0.36.1'),
+    ('pkg-config', '0.3.30'),
+    ('postcard', '1.0.8'),
+    ('proc-macro2', '1.0.86'),
+    ('quote', '1.0.36'),
+    ('regex', '1.10.5'),
+    ('regex-automata', '0.4.7'),
+    ('regex-syntax', '0.8.4'),
+    ('roff', '0.1.0'),
+    ('rustc-demangle', '0.1.24'),
+    ('rustc_version', '0.4.0'),
+    ('rustix', '0.38.34'),
+    ('ryu', '1.0.18'),
+    ('scopeguard', '1.2.0'),
+    ('semver', '1.0.23'),
+    ('serde', '1.0.204'),
+    ('serde_derive', '1.0.204'),
+    ('serde_json', '1.0.120'),
+    ('spin', '0.9.8'),
+    ('stable_deref_trait', '1.2.0'),
+    ('strsim', '0.11.1'),
+    ('syn', '1.0.109'),
+    ('syn', '2.0.71'),
+    ('synstructure', '0.12.6'),
+    ('tempfile', '3.10.1'),
+    ('termcolor', '1.4.1'),
+    ('unicode-ident', '1.0.12'),
+    ('unicode-xid', '0.2.4'),
+    ('utf8parse', '0.2.2'),
+    ('version-compare', '0.1.1'),
+    ('winapi', '0.3.9'),
+    ('winapi-i686-pc-windows-gnu', '0.4.0'),
+    ('winapi-util', '0.1.8'),
+    ('winapi-x86_64-pc-windows-gnu', '0.4.0'),
+    ('windows-sys', '0.52.0'),
+    ('windows-targets', '0.52.6'),
+    ('windows_aarch64_gnullvm', '0.52.6'),
+    ('windows_aarch64_msvc', '0.52.6'),
+    ('windows_i686_gnu', '0.52.6'),
+    ('windows_i686_gnullvm', '0.52.6'),
+    ('windows_i686_msvc', '0.52.6'),
+    ('windows_x86_64_gnu', '0.52.6'),
+    ('windows_x86_64_gnullvm', '0.52.6'),
+    ('windows_x86_64_msvc', '0.52.6'),
+    ('xz2', '0.1.7'),
+]
+
+moduleclass = 'bio'

From 4ebdc5ecab152cdece8441d05e37c8ffde63f7f0 Mon Sep 17 00:00:00 2001
From: Julian Morillo <julian.morillo@bsc.es>
Date: Thu, 18 Jul 2024 15:25:37 +0200
Subject: [PATCH 465/835] Extrae: Make libunwind dependency architecture
 specific

---
 .../e/Extrae/Extrae-4.2.0-gompi-2023b.eb      | 28 +++++++++++++------
 1 file changed, 19 insertions(+), 9 deletions(-)

diff --git a/easybuild/easyconfigs/e/Extrae/Extrae-4.2.0-gompi-2023b.eb b/easybuild/easyconfigs/e/Extrae/Extrae-4.2.0-gompi-2023b.eb
index 42b086d57f8..ed244c2b012 100644
--- a/easybuild/easyconfigs/e/Extrae/Extrae-4.2.0-gompi-2023b.eb
+++ b/easybuild/easyconfigs/e/Extrae/Extrae-4.2.0-gompi-2023b.eb
@@ -32,17 +32,27 @@ builddependencies = [
     ('Automake', '1.16.5'),
 ]
 
-dependencies = [
-    ('zlib', '1.2.13'),
-    ('Boost', '1.83.0'),
-    ('libunwind', '1.6.2'),
-    ('libxml2', '2.11.5'),
-    ('libdwarf', '0.9.2'),
-    ('PAPI', '7.1.0'),
-]
+if ARCH == 'aarch64':
+    dependencies = [
+        ('zlib', '1.2.13'),
+        ('Boost', '1.83.0'),
+        ('libxml2', '2.11.5'),
+        ('libdwarf', '0.9.2'),
+        ('PAPI', '7.1.0'),
+    ]
+    configopts = '--without-unwind'
+else:
+    dependencies = [
+        ('zlib', '1.2.13'),
+        ('Boost', '1.83.0'),
+        ('libunwind', '1.6.2'),
+        ('libxml2', '2.11.5'),
+        ('libdwarf', '0.9.2'),
+        ('PAPI', '7.1.0'),
+    ]
 
 # Disable dynamic memory instrumentation for this release, has been seen to sometimes cause MPI test failures
-configopts = '--disable-instrument-dynamic-memory'
+configopts += '--disable-instrument-dynamic-memory'
 
 runtest = 'check'
 

From 105c9121bc2664bb06241f1f87cc5776ee1abd7d Mon Sep 17 00:00:00 2001
From: julianmorillo <julianmorillo@users.noreply.github.com>
Date: Thu, 18 Jul 2024 15:46:45 +0200
Subject: [PATCH 466/835] Update
 easybuild/easyconfigs/e/Extrae/Extrae-4.2.0-gompi-2023b.eb

Co-authored-by: ocaisa <alan.ocais@cecam.org>
---
 .../e/Extrae/Extrae-4.2.0-gompi-2023b.eb      | 30 ++++++++-----------
 1 file changed, 13 insertions(+), 17 deletions(-)

diff --git a/easybuild/easyconfigs/e/Extrae/Extrae-4.2.0-gompi-2023b.eb b/easybuild/easyconfigs/e/Extrae/Extrae-4.2.0-gompi-2023b.eb
index ed244c2b012..3d850fc5464 100644
--- a/easybuild/easyconfigs/e/Extrae/Extrae-4.2.0-gompi-2023b.eb
+++ b/easybuild/easyconfigs/e/Extrae/Extrae-4.2.0-gompi-2023b.eb
@@ -32,24 +32,20 @@ builddependencies = [
     ('Automake', '1.16.5'),
 ]
 
-if ARCH == 'aarch64':
-    dependencies = [
-        ('zlib', '1.2.13'),
-        ('Boost', '1.83.0'),
-        ('libxml2', '2.11.5'),
-        ('libdwarf', '0.9.2'),
-        ('PAPI', '7.1.0'),
-    ]
-    configopts = '--without-unwind'
-else:
-    dependencies = [
-        ('zlib', '1.2.13'),
-        ('Boost', '1.83.0'),
+dependencies = [
+    ('zlib', '1.2.13'),
+    ('Boost', '1.83.0'),
+    ('libunwind', '1.6.2'),
+    ('libxml2', '2.11.5'),
+    ('libdwarf', '0.9.2'),
+    ('PAPI', '7.1.0'),
+]
+
+# libunwind causes segv errors on aarch64
+if ARCH != 'aarch64':
+    dependencies.append(
         ('libunwind', '1.6.2'),
-        ('libxml2', '2.11.5'),
-        ('libdwarf', '0.9.2'),
-        ('PAPI', '7.1.0'),
-    ]
+    )
 
 # Disable dynamic memory instrumentation for this release, has been seen to sometimes cause MPI test failures
 configopts += '--disable-instrument-dynamic-memory'

From de21eb95cc3e2d0a55deb1d2b4029a1db7f64b5b Mon Sep 17 00:00:00 2001
From: ocaisa <alan.ocais@cecam.org>
Date: Thu, 18 Jul 2024 15:48:00 +0200
Subject: [PATCH 467/835] My error!

---
 easybuild/easyconfigs/e/Extrae/Extrae-4.2.0-gompi-2023b.eb | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/easybuild/easyconfigs/e/Extrae/Extrae-4.2.0-gompi-2023b.eb b/easybuild/easyconfigs/e/Extrae/Extrae-4.2.0-gompi-2023b.eb
index 3d850fc5464..4fca4663aca 100644
--- a/easybuild/easyconfigs/e/Extrae/Extrae-4.2.0-gompi-2023b.eb
+++ b/easybuild/easyconfigs/e/Extrae/Extrae-4.2.0-gompi-2023b.eb
@@ -35,7 +35,6 @@ builddependencies = [
 dependencies = [
     ('zlib', '1.2.13'),
     ('Boost', '1.83.0'),
-    ('libunwind', '1.6.2'),
     ('libxml2', '2.11.5'),
     ('libdwarf', '0.9.2'),
     ('PAPI', '7.1.0'),
@@ -48,7 +47,7 @@ if ARCH != 'aarch64':
     )
 
 # Disable dynamic memory instrumentation for this release, has been seen to sometimes cause MPI test failures
-configopts += '--disable-instrument-dynamic-memory'
+configopts = '--disable-instrument-dynamic-memory'
 
 runtest = 'check'
 

From f3d65d25392fe06b1b61e404747111869e8d495a Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com>
Date: Fri, 19 Jul 2024 12:51:00 +0200
Subject: [PATCH 468/835] Update OpenForceField-Toolkit-0.16.0-foss-2023a.eb

---
 .../OpenForceField-Toolkit-0.16.0-foss-2023a.eb                | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/easybuild/easyconfigs/o/OpenForceField-Toolkit/OpenForceField-Toolkit-0.16.0-foss-2023a.eb b/easybuild/easyconfigs/o/OpenForceField-Toolkit/OpenForceField-Toolkit-0.16.0-foss-2023a.eb
index 3ef84650f5e..effa0f88656 100644
--- a/easybuild/easyconfigs/o/OpenForceField-Toolkit/OpenForceField-Toolkit-0.16.0-foss-2023a.eb
+++ b/easybuild/easyconfigs/o/OpenForceField-Toolkit/OpenForceField-Toolkit-0.16.0-foss-2023a.eb
@@ -28,8 +28,6 @@ dependencies = [
     ('nglview', '3.1.2'),
 ]
 
-use_pip = True
-
 exts_list = [
     ('qcelemental', '0.26.0', {
         'checksums': ['a14e8510cdbfda645ef1461c1afd02efb599311733dbba5f83fcd1d6168a6ddd'],
@@ -139,6 +137,7 @@ sanity_check_commands = [
     "python -c 'from openff.toolkit.typing.engines.smirnoff import ForceField'",
 ]
 
+use_pip = True
 sanity_pip_check = True
 
 moduleclass = 'bio'

From b94bb4c5b8df22f68a6b0cdbb75b09b4806520e5 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Fri, 19 Jul 2024 12:56:25 +0200
Subject: [PATCH 469/835] fix checksum of toolkit

---
 .../OpenForceField-Toolkit-0.16.0-foss-2023a.eb              | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/easybuild/easyconfigs/o/OpenForceField-Toolkit/OpenForceField-Toolkit-0.16.0-foss-2023a.eb b/easybuild/easyconfigs/o/OpenForceField-Toolkit/OpenForceField-Toolkit-0.16.0-foss-2023a.eb
index effa0f88656..a656f10d6ab 100644
--- a/easybuild/easyconfigs/o/OpenForceField-Toolkit/OpenForceField-Toolkit-0.16.0-foss-2023a.eb
+++ b/easybuild/easyconfigs/o/OpenForceField-Toolkit/OpenForceField-Toolkit-0.16.0-foss-2023a.eb
@@ -28,6 +28,8 @@ dependencies = [
     ('nglview', '3.1.2'),
 ]
 
+use_pip = True
+
 exts_list = [
     ('qcelemental', '0.26.0', {
         'checksums': ['a14e8510cdbfda645ef1461c1afd02efb599311733dbba5f83fcd1d6168a6ddd'],
@@ -124,7 +126,7 @@ exts_list = [
         'modulename': 'openff.toolkit',
         'source_tmpl': '%(version)s.tar.gz',
         'source_urls': ['https://github.com/openforcefield/openff-toolkit/archive/'],
-        'checksums': ['1c1aa2ac9fff7c1613168531884da4ade53cbe21069022c999996d7effd2474c'],
+        'checksums': ['70a81e914e86efd933819a5db05fc4400dcd23e12ad29398fdad46f2765b5634'],
     }),
 ]
 
@@ -137,7 +139,6 @@ sanity_check_commands = [
     "python -c 'from openff.toolkit.typing.engines.smirnoff import ForceField'",
 ]
 
-use_pip = True
 sanity_pip_check = True
 
 moduleclass = 'bio'

From 48d40dcb19b97cda7ef44f0fb5685c19068a91e7 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com>
Date: Fri, 19 Jul 2024 14:40:22 +0200
Subject: [PATCH 470/835] Update OpenForceField-Toolkit-0.16.0-foss-2023a.eb
 fix whitespace

---
 .../OpenForceField-Toolkit-0.16.0-foss-2023a.eb                 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/o/OpenForceField-Toolkit/OpenForceField-Toolkit-0.16.0-foss-2023a.eb b/easybuild/easyconfigs/o/OpenForceField-Toolkit/OpenForceField-Toolkit-0.16.0-foss-2023a.eb
index a656f10d6ab..06e5075f674 100644
--- a/easybuild/easyconfigs/o/OpenForceField-Toolkit/OpenForceField-Toolkit-0.16.0-foss-2023a.eb
+++ b/easybuild/easyconfigs/o/OpenForceField-Toolkit/OpenForceField-Toolkit-0.16.0-foss-2023a.eb
@@ -8,7 +8,7 @@ description = """The Open Force Field Toolkit provides implementations of the SM
 parameterization engine, and other tools."""
 
 toolchain = {'name': 'foss', 'version': '2023a'}
-    
+
 builddependencies = [('poetry', '1.5.1')]
 dependencies = [
     ('Python', '3.11.3'),

From 753bd34c263c14c32fb5fa5a6f32888eb7f416bf Mon Sep 17 00:00:00 2001
From: fizwit <john@fuzzdog.com>
Date: Fri, 19 Jul 2024 15:59:09 -0700
Subject: [PATCH 471/835] update Biopython

---
 .../b/Biopython/Biopython-1.84-foss-2023b.eb  | 46 +++++++++++++++++++
 1 file changed, 46 insertions(+)
 create mode 100644 easybuild/easyconfigs/b/Biopython/Biopython-1.84-foss-2023b.eb

diff --git a/easybuild/easyconfigs/b/Biopython/Biopython-1.84-foss-2023b.eb b/easybuild/easyconfigs/b/Biopython/Biopython-1.84-foss-2023b.eb
new file mode 100644
index 00000000000..03c23f41186
--- /dev/null
+++ b/easybuild/easyconfigs/b/Biopython/Biopython-1.84-foss-2023b.eb
@@ -0,0 +1,46 @@
+# Updated from previous easyconfig
+# Author: Robert Mijakovic <robert.mijakovic@lxp.lu>
+# Update: Pavel Tománek (INUITS)
+
+easyblock = 'PythonPackage'
+
+name = 'Biopython'
+version = '1.84'
+
+homepage = 'https://www.biopython.org'
+description = """Biopython is a set of freely available tools for biological
+ computation written in Python by an international team of developers. It is
+ a distributed collaborative effort to develop Python libraries and
+ applications which address the needs of current and future work in
+ bioinformatics. """
+
+toolchain = {'name': 'foss', 'version': '2023b'}
+
+source_urls = ['https://biopython.org/DIST']
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['60fbe6f996e8a6866a42698c17e552127d99a9aab3259d6249fbaabd0e0cc7b4']
+
+dependencies = [
+    ('Python', '3.11.5'),
+    ('SciPy-bundle', '2023.11'),
+]
+
+download_dep_fail = True
+use_pip = True
+sanity_pip_check = True
+
+# Run only tests that don't require internet connection
+runtest = 'python setup.py test --offline'
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['lib/python%(pyshortver)s/site-packages/Bio',
+             'lib/python%(pyshortver)s/site-packages/BioSQL']
+}
+
+# extra check to ensure numpy dependency is available
+sanity_check_commands = ["python -c 'import Bio.MarkovModel'"]
+
+options = {'modulename': 'Bio'}
+
+moduleclass = 'bio'

From 6f4dda3324c8024f4d1547a6655fd26cf990fef2 Mon Sep 17 00:00:00 2001
From: c3-builder <c3-builder@vera-skylake-build>
Date: Sun, 21 Jul 2024 15:51:17 +0000
Subject: [PATCH 472/835] adding easyconfigs: PyAEDT-0.9.9-gfbf-2023b.eb

---
 .../p/PyAEDT/PyAEDT-0.9.9-gfbf-2023b.eb       | 78 +++++++++++++++++++
 1 file changed, 78 insertions(+)
 create mode 100644 easybuild/easyconfigs/p/PyAEDT/PyAEDT-0.9.9-gfbf-2023b.eb

diff --git a/easybuild/easyconfigs/p/PyAEDT/PyAEDT-0.9.9-gfbf-2023b.eb b/easybuild/easyconfigs/p/PyAEDT/PyAEDT-0.9.9-gfbf-2023b.eb
new file mode 100644
index 00000000000..f3047e4bc6d
--- /dev/null
+++ b/easybuild/easyconfigs/p/PyAEDT/PyAEDT-0.9.9-gfbf-2023b.eb
@@ -0,0 +1,78 @@
+easyblock = 'PythonBundle'
+
+name = 'PyAEDT'
+version = '0.9.9'
+
+homepage = 'https://aedt.docs.pyansys.com/version/stable'
+description = """PyAEDT is a Python library that interacts directly with the
+Ansys Electronics Desktop (AEDT) API, enabling straightforward and efficient
+automation in your workflow."""
+
+toolchain = {'name': 'gfbf', 'version': '2023b'}
+
+builddependencies = [
+    ('binutils', '2.40'),
+    ('hatchling', '1.18.0'),
+]
+
+dependencies = [
+    ('dotNET-Core', '8.0', '', SYSTEM),
+    ('libspatialindex', '1.9.3'),
+    ('Python', '3.11.5'),
+    ('Python-bundle-PyPI', '2023.10'),
+    ('Pillow', '10.2.0'),
+    ('pydantic', '2.7.4'),
+    ('SciPy-bundle', '2023.11'),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    ('dotnetcore2', '3.1.23', {
+        'sources': ['dotnetcore2-3.1.23-py3-none-manylinux1_x86_64.whl'],
+        'checksums': ['5f076ddc39da0c685e7de20ecb91ee81185928918ec86fbeb3bffc55dd867ab5'],
+    }),
+    ('clr_loader', '0.2.6', {
+        'checksums': ['019348ae6b6a83c7a406d14537c277cecf7a3a53b263ec342c81ded5845a67ee'],
+    }),
+    ('defusedxml', '0.7.1', {
+        'checksums': ['1bb3032db185915b62d7c6209c5a8792be6a32ab2fedacc84e01b52c51aa3e69'],
+    }),
+    ('fonttools', '4.53.1', {
+        'modulename': 'fontTools',
+        'checksums': ['e128778a8e9bc11159ce5447f76766cefbd876f44bd79aff030287254e4752c4'],
+    }),
+    ('ansys-pythonnet', '3.1.0rc3', {
+        'modulename': 'pythonnet',
+        'checksums': ['369a0a5a838a0991f755b6d63c319ab6997f9dc464d016187227be5cd860a9cb'],
+        'preinstallopts': 'export OPENSSL_ENABLE_SHA1_SIGNATURES=1 &&',
+    }),
+    ('pytomlpp', '1.0.13', {
+        'checksums': ['a0bd639a8f624d1bdf5b3ea94363ca23dbfef38ab7b5b9348881a84afab434ad'],
+    }),
+    ('fpdf2', '2.7.9', {
+        'modulename': 'fpdf',
+        'checksums': ['f364c0d816a5e364eeeda9761cf5c961bae8c946f080cf87fed7f38ab773b318'],
+    }),
+    ('plumbum', '1.8.3', {
+        'checksums': ['6092c85ab970b7a7a9d5d85c75200bc93be82b33c9bdf640ffa87d2d7c8709f0'],
+    }),
+    ('rpyc', '6.0.0', {
+        'checksums': ['a7e12b31f40978cbd6b74e0b713da389d4b2565cef612adcb0f4b41aeb188230'],
+    }),
+    ('rtree', '1.3.0', {
+        'modulename': 'rtree',
+        'checksums': ['b36e9dd2dc60ffe3d02e367242d2c26f7281b00e1aaf0c39590442edaaadd916'],
+    }),
+    ('pyedb', '0.21.0', {
+        'checksums': ['3c91cb8a72a080864d3582ae7ec1de2f04d90aee477dadc096a7144f7823258d'],
+    }),
+    ('pyaedt', version, {
+        'checksums': ['714728230ab3ede4744a30a7c0d45aaa104cdc1887bfbfe8feb928a8f10cc72f'],
+    }),
+]
+
+modloadmsg = "NOTE: You also need load a AEDT module before you start using PyAEDT."
+
+moduleclass = "phys"

From ed5b120d8ab5f6b18833123eb3cee0c37701aa0e Mon Sep 17 00:00:00 2001
From: c3-builder <c3-builder@vera-skylake-build>
Date: Sun, 21 Jul 2024 16:05:48 +0000
Subject: [PATCH 473/835] Add `OPENSSL_ENABLE_SHA1_SIGNATURES` for building
 `ansys-pythonnet`

---
 easybuild/easyconfigs/p/PyAEDT/PyAEDT-0.8.7-GCCcore-12.3.0.eb | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easybuild/easyconfigs/p/PyAEDT/PyAEDT-0.8.7-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/PyAEDT/PyAEDT-0.8.7-GCCcore-12.3.0.eb
index aee9ba9ea19..894b488cd3e 100644
--- a/easybuild/easyconfigs/p/PyAEDT/PyAEDT-0.8.7-GCCcore-12.3.0.eb
+++ b/easybuild/easyconfigs/p/PyAEDT/PyAEDT-0.8.7-GCCcore-12.3.0.eb
@@ -43,6 +43,7 @@ exts_list = [
     ('ansys-pythonnet', '3.1.0rc3', {
         'checksums': ['369a0a5a838a0991f755b6d63c319ab6997f9dc464d016187227be5cd860a9cb'],
         'modulename': 'pythonnet',
+        'preinstallopts': 'export OPENSSL_ENABLE_SHA1_SIGNATURES=1 &&',
     }),
     ('pytomlpp', '1.0.13', {
         'checksums': ['a0bd639a8f624d1bdf5b3ea94363ca23dbfef38ab7b5b9348881a84afab434ad'],

From 12ef0f174250928ca9a5ccf47e4f7ca0ce56811f Mon Sep 17 00:00:00 2001
From: Simon Branford <s.j.branford@bham.ac.uk>
Date: Mon, 22 Jul 2024 11:09:33 +0100
Subject: [PATCH 474/835] dbarts ARM fix

---
 .../r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb  | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb b/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb
index c042ee83af9..ce8233bc4a5 100644
--- a/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb
+++ b/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb
@@ -60,6 +60,14 @@ local_ext_version_check = "pkgver = packageVersion('%(ext_name)s'); if (pkgver !
 local_stop_msg = "stop('%(ext_name)s %(ext_version)s not installed, found ', pkgver, ' instead')"
 exts_filter = ("R -q --no-save", "%s { %s }" % (local_ext_version_check, local_stop_msg))
 
+# the dbarts extension needs an additional compiler flag on Arm systems to prevent "incompatible types" errors
+# cfr. https://github.com/vdorie/dbarts/issues/66
+if ARCH == 'aarch64':
+    local_dbarts_preinstallopts = 'sed -i "s|-c partition_neon.c|-flax-vector-conversions -c partition_neon.c|"'
+    local_dbarts_preinstallopts += ' src/misc/Makefile && '
+else:
+    local_dbarts_preinstallopts = ''
+
 # !! order of packages is important !!
 # packages updated on 24 June 2024
 exts_list = [
@@ -2585,6 +2593,7 @@ exts_list = [
     }),
     ('dbarts', '0.9-28', {
         'checksums': ['d2e4b4ee1c191e7c506be3fec5a5e877c1b36754cba558bd75eaac9cc6ac0138'],
+        'preinstallopts': local_dbarts_preinstallopts,
     }),
     ('proftools', '0.99-3', {
         'checksums': ['e034eb1531af54013143da3e15229e1d4c2260f8eb79c93846014db3bdefb724'],

From 5b7a816f6f543ca6395d193eaf353c6f1f31a0bc Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Mon, 22 Jul 2024 14:41:31 +0200
Subject: [PATCH 475/835] Don't run test suite for outdated cases that are not
 easily solved

---
 .../q/QuantumESPRESSO/QuantumESPRESSO-6.8-foss-2021b.eb       | 3 +++
 .../q/QuantumESPRESSO/QuantumESPRESSO-7.0-intel-2021b.eb      | 3 +++
 .../q/QuantumESPRESSO/QuantumESPRESSO-7.1-foss-2022a.eb       | 3 +++
 .../q/QuantumESPRESSO/QuantumESPRESSO-7.1-intel-2022a.eb      | 4 ++--
 4 files changed, 11 insertions(+), 2 deletions(-)

diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.8-foss-2021b.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.8-foss-2021b.eb
index fc8ad317547..aedc3282d14 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.8-foss-2021b.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.8-foss-2021b.eb
@@ -41,4 +41,7 @@ buildopts = 'all gwl xspectra couple epw gipaw w90'
 # parallel build tends to fail
 parallel = 1
 
+# don't run the tests (not investigated for old easyconfig)
+skipsteps = ['test']
+
 moduleclass = 'chem'
diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.0-intel-2021b.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.0-intel-2021b.eb
index febc60c8c61..3aef60958a6 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.0-intel-2021b.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.0-intel-2021b.eb
@@ -41,4 +41,7 @@ buildopts = 'all gwl xspectra couple epw gipaw w90'
 # parallel build tends to fail
 parallel = 1
 
+# don't run the tests (not investigated for old easyconfig)
+skipsteps = ['test']
+
 moduleclass = 'chem'
diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-foss-2022a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-foss-2022a.eb
index 87066c6ae6d..3f34e98c970 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-foss-2022a.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-foss-2022a.eb
@@ -48,4 +48,7 @@ buildopts = 'all gwl xspectra couple epw gipaw w90'
 # parallel build tends to fail
 parallel = 1
 
+# don't run the tests (not investigated for old easyconfig)
+skipsteps = ['test']
+
 moduleclass = 'chem'
diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-intel-2022a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-intel-2022a.eb
index a7ed17a2f6b..931d16c7f63 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-intel-2022a.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-intel-2022a.eb
@@ -48,7 +48,7 @@ buildopts = 'all gwl xspectra couple epw gipaw w90'
 # parallel build tends to fail
 parallel = 1
 
-# allow some test failures (not investigated for old easyconfig)
-test_suite_max_failed = 6
+# don't run the tests (not investigated for old easyconfig)
+skipsteps = ['test']
 
 moduleclass = 'chem'

From db8fcd6c993be1d290a1f962a11eb86e73dc6a40 Mon Sep 17 00:00:00 2001
From: casparl <casparl@gcn74.local.snellius.surf.nl>
Date: Mon, 22 Jul 2024 17:19:36 +0200
Subject: [PATCH 476/835] adding easyconfigs:
 CUDA-Samples-11.8-GCC-11.3.0-CUDA-11.7.0.eb,
 CUDA-Samples-12.2-GCC-11.3.0-CUDA-12.2.0.eb

---
 ...UDA-Samples-11.8-GCC-11.3.0-CUDA-11.7.0.eb | 55 +++++++++++++++++
 ...UDA-Samples-12.2-GCC-11.3.0-CUDA-12.2.0.eb | 59 +++++++++++++++++++
 2 files changed, 114 insertions(+)
 create mode 100644 easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.8-GCC-11.3.0-CUDA-11.7.0.eb
 create mode 100644 easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-12.2-GCC-11.3.0-CUDA-12.2.0.eb

diff --git a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.8-GCC-11.3.0-CUDA-11.7.0.eb b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.8-GCC-11.3.0-CUDA-11.7.0.eb
new file mode 100644
index 00000000000..27df4a0986e
--- /dev/null
+++ b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.8-GCC-11.3.0-CUDA-11.7.0.eb
@@ -0,0 +1,55 @@
+easyblock = 'MakeCp'
+
+name = 'CUDA-Samples'
+version = '11.8'
+versionsuffix = '-CUDA-%(cudaver)s'
+
+homepage = 'https://github.com/NVIDIA/cuda-samples'
+description = "Samples for CUDA Developers which demonstrates features in CUDA Toolkit"
+
+toolchain = {'name': 'GCC', 'version': '11.3.0'}
+
+source_urls = ['https://github.com/NVIDIA/cuda-samples/archive/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['1bc02c0ca42a323f3c7a05b5682eae703681a91e95b135bfe81f848b2d6a2c51']
+
+dependencies = [
+    ('CUDA', '11.7.0', '', SYSTEM),
+]
+
+# Get rid of pre-built Windows DLLs and only build deviceQuery for now.
+prebuildopts = "rm -r bin/win64 && "
+
+# Filter out samples that require extensive dependencies.
+local_filters = "Samples/2_Concepts_and_Techniques/EGLStream_CUDA_Interop/Makefile "
+local_filters += "Samples/4_CUDA_Libraries/boxFilterNPP/Makefile "
+local_filters += "Samples/4_CUDA_Libraries/cannyEdgeDetectorNPP/Makefile "
+local_filters += "Samples/4_CUDA_Libraries/cudaNvSci/Makefile "
+local_filters += "Samples/4_CUDA_Libraries/cudaNvSciNvMedia/Makefile "
+local_filters += "Samples/5_Domain_Specific/simpleGL/Makefile "
+local_filters += "Samples/3_CUDA_Features/warpAggregatedAtomicsCG/Makefile "
+local_filters += "Samples/5_Domain_Specific/simpleVulkan/Makefile "
+local_filters += "Samples/5_Domain_Specific/simpleVulkanMMAP/Makefile "
+local_filters += "Samples/2_Concepts_and_Techniques/streamOrderedAllocationIPC/Makefile "
+local_filters += "Samples/5_Domain_Specific/vulkanImageCUDA/Makefile "
+local_filters += "Samples/6_Performance/LargeKernelParameter/Makefile "
+
+buildopts = "HOST_COMPILER=g++ SMS='%%(cuda_cc_space_sep_no_period)s' FILTER_OUT='%s'" % local_filters
+
+files_to_copy = [
+    (['bin/%s/linux/release/*' % ARCH], 'bin'),
+    'LICENSE',
+]
+
+local_binaries = ['deviceQuery', 'matrixMul', 'bandwidthTest', 'cudaOpenMP']
+
+# Only paths are used for sanity checks.
+# Commands may fail due to missing compatibility libraries that might be needed
+# to be able to use this specific CUDA version in combination with the available
+# NVIDIA drivers.
+sanity_check_paths = {
+    'files': ['bin/%s' % x for x in local_binaries],
+    'dirs': [],
+}
+
+moduleclass = 'lang'
diff --git a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-12.2-GCC-11.3.0-CUDA-12.2.0.eb b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-12.2-GCC-11.3.0-CUDA-12.2.0.eb
new file mode 100644
index 00000000000..c69748cec08
--- /dev/null
+++ b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-12.2-GCC-11.3.0-CUDA-12.2.0.eb
@@ -0,0 +1,59 @@
+easyblock = 'MakeCp'
+
+name = 'CUDA-Samples'
+version = '12.2'
+versionsuffix = '-CUDA-%(cudaver)s'
+
+homepage = 'https://github.com/NVIDIA/cuda-samples'
+description = "Samples for CUDA Developers which demonstrates features in CUDA Toolkit"
+
+toolchain = {'name': 'GCC', 'version': '11.3.0'}
+
+source_urls = ['https://github.com/NVIDIA/cuda-samples/archive/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['c9fbdee420fd4567edb1239420e2a5c93d9652b4ccf3a828fcb3e0de3152e466']
+
+builddependencies = [
+    ('CMake', '3.24.3'),
+]
+
+dependencies = [
+    ('CUDA', '12.2.0', '', SYSTEM),
+]
+
+# Get rid of pre-built Windows DLLs and only build deviceQuery for now.
+prebuildopts = "rm -r bin/win64 && "
+
+# Filter out samples that require extensive dependencies.
+local_filters = "Samples/2_Concepts_and_Techniques/EGLStream_CUDA_Interop/Makefile "
+local_filters += "Samples/4_CUDA_Libraries/boxFilterNPP/Makefile "
+local_filters += "Samples/4_CUDA_Libraries/cannyEdgeDetectorNPP/Makefile "
+local_filters += "Samples/4_CUDA_Libraries/cudaNvSci/Makefile "
+local_filters += "Samples/4_CUDA_Libraries/cudaNvSciNvMedia/Makefile "
+local_filters += "Samples/5_Domain_Specific/simpleGL/Makefile "
+local_filters += "Samples/3_CUDA_Features/warpAggregatedAtomicsCG/Makefile "
+local_filters += "Samples/5_Domain_Specific/simpleVulkan/Makefile "
+local_filters += "Samples/5_Domain_Specific/simpleVulkanMMAP/Makefile "
+local_filters += "Samples/2_Concepts_and_Techniques/streamOrderedAllocationIPC/Makefile "
+local_filters += "Samples/5_Domain_Specific/vulkanImageCUDA/Makefile "
+local_filters += "Samples/6_Performance/LargeKernelParameter/Makefile "
+
+buildopts = "HOST_COMPILER=g++ SMS='%%(cuda_cc_space_sep_no_period)s' FILTER_OUT='%s'" % local_filters
+
+files_to_copy = [
+    (['bin/%s/linux/release/*' % ARCH], 'bin'),
+    'LICENSE',
+]
+
+local_binaries = ['deviceQuery', 'matrixMul', 'bandwidthTest', 'cudaOpenMP']
+
+# Only paths are used for sanity checks.
+# Commands may fail due to missing compatibility libraries that might be needed
+# to be able to use this specific CUDA version in combination with the available
+# NVIDIA drivers.
+sanity_check_paths = {
+    'files': ['bin/%s' % x for x in local_binaries],
+    'dirs': [],
+}
+
+moduleclass = 'lang'

From bc7fbb5213ccb355b57efb8ea89d3c32bc1872a6 Mon Sep 17 00:00:00 2001
From: casparl <casparl@gcn74.local.snellius.surf.nl>
Date: Mon, 22 Jul 2024 17:24:15 +0200
Subject: [PATCH 477/835] Pass cuda compute capabilities through buildopts

---
 .../c/CUDA-Samples/CUDA-Samples-11.3-GCC-10.3.0-CUDA-11.3.1.eb  | 2 +-
 .../c/CUDA-Samples/CUDA-Samples-11.6-GCC-11.3.0-CUDA-11.7.0.eb  | 2 +-
 .../c/CUDA-Samples/CUDA-Samples-12.1-GCC-12.3.0-CUDA-12.1.1.eb  | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.3-GCC-10.3.0-CUDA-11.3.1.eb b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.3-GCC-10.3.0-CUDA-11.3.1.eb
index b71d2bfad4d..31d65369f80 100644
--- a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.3-GCC-10.3.0-CUDA-11.3.1.eb
+++ b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.3-GCC-10.3.0-CUDA-11.3.1.eb
@@ -32,7 +32,7 @@ local_filters += "Samples/simpleVulkan/Makefile "
 local_filters += "Samples/simpleVulkanMMAP/Makefile "
 local_filters += "Samples/streamOrderedAllocationIPC/Makefile "
 local_filters += "Samples/vulkanImageCUDA/Makefile"
-buildopts = "HOST_COMPILER=g++ FILTER_OUT='%s'" % local_filters
+buildopts = "HOST_COMPILER=g++ SMS='%%(cuda_cc_space_sep_no_period)s' FILTER_OUT='%s'" % local_filters
 
 files_to_copy = [
     (['bin/%s/linux/release/*' % ARCH], 'bin'),
diff --git a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.6-GCC-11.3.0-CUDA-11.7.0.eb b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.6-GCC-11.3.0-CUDA-11.7.0.eb
index d4240930bd1..8e3cbc72ee2 100644
--- a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.6-GCC-11.3.0-CUDA-11.7.0.eb
+++ b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.6-GCC-11.3.0-CUDA-11.7.0.eb
@@ -33,7 +33,7 @@ local_filters += "Samples/simpleVulkanMMAP/Makefile "
 local_filters += "Samples/streamOrderedAllocationIPC/Makefile "
 local_filters += "Samples/vulkanImageCUDA/Makefile"
 
-buildopts = "HOST_COMPILER=g++ FILTER_OUT='%s'" % local_filters
+buildopts = "HOST_COMPILER=g++ SMS='%%(cuda_cc_space_sep_no_period)s' FILTER_OUT='%s'" % local_filters
 
 files_to_copy = [
     (['bin/%s/linux/release/*' % ARCH], 'bin'),
diff --git a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-12.1-GCC-12.3.0-CUDA-12.1.1.eb b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-12.1-GCC-12.3.0-CUDA-12.1.1.eb
index 3e7ffe79da0..3444ef46f27 100644
--- a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-12.1-GCC-12.3.0-CUDA-12.1.1.eb
+++ b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-12.1-GCC-12.3.0-CUDA-12.1.1.eb
@@ -58,7 +58,7 @@ if ARCH == 'aarch64':
     local_filters += "Samples/3_CUDA_Features/cdpQuadtree/Makefile "
     local_filters += "Samples/3_CUDA_Features/cdpAdvancedQuicksort/Makefile "
 
-buildopts = "HOST_COMPILER=g++ FILTER_OUT='%s'" % local_filters
+buildopts = "HOST_COMPILER=g++ SMS='%%(cuda_cc_space_sep_no_period)s' FILTER_OUT='%s'" % local_filters
 
 # Remove libraries in the bin dir after a successful 'make'
 buildopts += " && rm bin/*/linux/release/lib*.so.*"

From 0c4a768d5f3361d5e5a099193551baa790dbac69 Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Mon, 22 Jul 2024 18:40:00 +0200
Subject: [PATCH 478/835] adding easyconfigs: cyvcf2-0.31.1-gfbf-2023a.eb

---
 .../c/cyvcf2/cyvcf2-0.31.1-gfbf-2023a.eb      | 45 +++++++++++++++++++
 1 file changed, 45 insertions(+)
 create mode 100644 easybuild/easyconfigs/c/cyvcf2/cyvcf2-0.31.1-gfbf-2023a.eb

diff --git a/easybuild/easyconfigs/c/cyvcf2/cyvcf2-0.31.1-gfbf-2023a.eb b/easybuild/easyconfigs/c/cyvcf2/cyvcf2-0.31.1-gfbf-2023a.eb
new file mode 100644
index 00000000000..6604fb2a1af
--- /dev/null
+++ b/easybuild/easyconfigs/c/cyvcf2/cyvcf2-0.31.1-gfbf-2023a.eb
@@ -0,0 +1,45 @@
+# Author: Pavel Grochal (INUITS)
+# License: GPLv2
+easyblock = 'PythonBundle'
+
+name = 'cyvcf2'
+version = '0.31.1'
+
+homepage = 'https://github.com/brentp/cyvcf2'
+description = "cyvcf2 is a cython wrapper around htslib built for fast parsing of Variant Call Format (VCF) files."
+
+toolchain = {'name': 'gfbf', 'version': '2023a'}
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('HTSlib', '1.18'),
+]
+
+fix_python_shebang_for = ['bin/*']
+
+use_pip = True
+
+exts_list = [
+    ('humanfriendly', '10.0', {
+        'checksums': ['6b0b831ce8f15f7300721aa49829fc4e83921a9a301cc7f606be6686a2288ddc'],
+    }),
+    ('coloredlogs', '15.0.1', {
+        'checksums': ['7c991aa71a4577af2f82600d8f8f3a89f936baeaf9b50a9c197da014e5bf16b0'],
+    }),
+    (name, version, {
+        'preinstallopts': 'CYVCF2_HTSLIB_MODE=EXTERNAL',
+        'checksums': ['00bd0e09a3719d29fbc02bc8a40a690ac2c475e91744648750907d1816558fc5'],
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['bin/cyvcf2'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = ["cyvcf2 --help"]
+
+sanity_pip_check = True
+
+moduleclass = 'bio'

From f532f2339a1dcff96a48f973b3c92a8e43beb254 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Tue, 23 Jul 2024 14:04:25 +0200
Subject: [PATCH 479/835] adding easyconfigs: pyMBE-0.8.0-foss-2023b.eb

---
 .../p/pyMBE/pyMBE-0.8.0-foss-2023b.eb         | 65 +++++++++++++++++++
 1 file changed, 65 insertions(+)
 create mode 100644 easybuild/easyconfigs/p/pyMBE/pyMBE-0.8.0-foss-2023b.eb

diff --git a/easybuild/easyconfigs/p/pyMBE/pyMBE-0.8.0-foss-2023b.eb b/easybuild/easyconfigs/p/pyMBE/pyMBE-0.8.0-foss-2023b.eb
new file mode 100644
index 00000000000..17fbf252f9f
--- /dev/null
+++ b/easybuild/easyconfigs/p/pyMBE/pyMBE-0.8.0-foss-2023b.eb
@@ -0,0 +1,65 @@
+easyblock = 'PythonBundle'
+
+name = 'pyMBE'
+version = '0.8.0'
+
+homepage = ''
+description = """pyMBE: the Python-based Molecule Builder for ESPResSo
+
+pyMBE provides tools to facilitate building up molecules with complex architectures
+in the Molecular Dynamics software ESPResSo."""
+
+toolchain = {'name': 'foss', 'version': '2023b'}
+
+builddependencies = [('hatchling', '1.18.0')]
+
+dependencies = [
+    ('Python', '3.11.5'),
+    ('SciPy-bundle', '2023.11'),
+    ('Pint', '0.24'),
+    ('tqdm', '4.66.2'),
+    ('matplotlib', '3.8.2'),
+    ('ESPResSo', '4.2.2'),
+]
+
+use_pip = True
+# pyMBE is not installable and should just be copied to the installation directory
+exts_classmap = {'pyMBE': 'Tarball'}
+
+# pyMBE itself should be the first one in the list,
+# otherwise the Tarball easyblock will copy the sources of all extensions to the installation directory
+exts_list = [
+    (name, version, {
+        'source_urls': ['https://github.com/pyMBE-dev/pyMBE/archive/'],
+        'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}],
+        'checksums': ['f143ae655b477d6d2ab6d97190a387fa9c7e854502a38c72c24eac48e37ea663'],
+    }),
+    ('looseversion', '1.1.2', {
+        'checksums': ['94d80bdbd0b6d57c11b886147ba1601f7d1531571621b81933b34537cbe469ad'],
+    }),
+    ('mmtf-python', '1.1.3', {
+        'modulename': 'mmtf',
+        'checksums': ['12a02fe1b7131f0a2b8ce45b46f1e0cdd28b9818fe4499554c26884987ea0c32'],
+    }),
+    ('Pint-Pandas', '0.5', {
+        'checksums': ['48ec96d457f802a347763dee1d3e1a273f11f90e4e595df17fd44613dd14a61c'],
+    }),
+    ('biopandas', '0.5.1.dev0', {
+        'checksums': ['6dc9de631babf8221c1ac60230133717039e08911f15e8ac48498c787022de12'],
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['pyMBE.py'],
+    'dirs': ['figs', 'lib', 'maintainer', 'parameters', 'refs', 'samples', 'testsuite', 'tutorials', 'visualization'],
+}
+
+sanity_check_commands = [
+    'python -c "import pyMBE"',
+    # running the full test suite takes a long time, so just stick to the unit tests
+    'cd %(installdir)s && make unit_tests'
+]
+
+modextrapaths = {'PYTHONPATH': ['.']}
+
+moduleclass = 'chem'

From 9616f27ad1c0e04c515fb27903887e5cd12f4a94 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Petr=20Kr=C3=A1l?= <petr@inuits.eu>
Date: Tue, 23 Jul 2024 14:26:23 +0200
Subject: [PATCH 480/835] avoid the `winsize` error

---
 .../easyconfigs/t/Transrate/Transrate-1.0.3-GCC-12.3.0.eb     | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/easybuild/easyconfigs/t/Transrate/Transrate-1.0.3-GCC-12.3.0.eb b/easybuild/easyconfigs/t/Transrate/Transrate-1.0.3-GCC-12.3.0.eb
index ac272dff125..341875e7575 100644
--- a/easybuild/easyconfigs/t/Transrate/Transrate-1.0.3-GCC-12.3.0.eb
+++ b/easybuild/easyconfigs/t/Transrate/Transrate-1.0.3-GCC-12.3.0.eb
@@ -25,8 +25,12 @@ dependencies = [
     ('yell', '2.2.2'),
 ]
 
+# requirement is too strict
 preinstallopts = """sed -i "s/'yell', '~> 2.0',/'yell',/g" transrate.gemspec && """
 
+# to avoid the `terminal_columns': undefined method `winsize' for nil (NoMethodError)` error
+preinstallopts += "sed -i '/terminal_columns > 70/d' lib/transrate/cmdline.rb && "
+
 sanity_check_paths = {
     'files': ['bin/%(namelower)s'],
     'dirs': ['gems/%(namelower)s-%(version)s'],

From 76e7fc6657bab64bfbec826540a3a8f0040258f2 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Tue, 23 Jul 2024 14:54:03 +0200
Subject: [PATCH 481/835] add sanity_pip_check = True

---
 easybuild/easyconfigs/p/pyMBE/pyMBE-0.8.0-foss-2023b.eb | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/easybuild/easyconfigs/p/pyMBE/pyMBE-0.8.0-foss-2023b.eb b/easybuild/easyconfigs/p/pyMBE/pyMBE-0.8.0-foss-2023b.eb
index 17fbf252f9f..6e676c32455 100644
--- a/easybuild/easyconfigs/p/pyMBE/pyMBE-0.8.0-foss-2023b.eb
+++ b/easybuild/easyconfigs/p/pyMBE/pyMBE-0.8.0-foss-2023b.eb
@@ -49,6 +49,8 @@ exts_list = [
     }),
 ]
 
+sanity_pip_check = True
+
 sanity_check_paths = {
     'files': ['pyMBE.py'],
     'dirs': ['figs', 'lib', 'maintainer', 'parameters', 'refs', 'samples', 'testsuite', 'tutorials', 'visualization'],

From 3452e8244cebda0858b9035680facacf591b18b5 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Petr=20Kr=C3=A1l?= <petr@inuits.eu>
Date: Tue, 23 Jul 2024 14:59:03 +0200
Subject: [PATCH 482/835] add missing checksum

---
 easybuild/easyconfigs/t/Transrate/Transrate-1.0.3-GCC-12.3.0.eb | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easybuild/easyconfigs/t/Transrate/Transrate-1.0.3-GCC-12.3.0.eb b/easybuild/easyconfigs/t/Transrate/Transrate-1.0.3-GCC-12.3.0.eb
index 341875e7575..6ad1e622a9a 100644
--- a/easybuild/easyconfigs/t/Transrate/Transrate-1.0.3-GCC-12.3.0.eb
+++ b/easybuild/easyconfigs/t/Transrate/Transrate-1.0.3-GCC-12.3.0.eb
@@ -13,6 +13,7 @@ toolchain = {'name': 'GCC', 'version': '12.3.0'}
 
 source_urls = ['https://github.com/blahah/transrate/archive/']
 sources = ['v%(version)s.tar.gz']
+checksums = ['2ccb101cfab5a33586ea9e62af2b2f14caf6bc016724d1fef796b427e39fe100']
 
 builddependencies = [
     ('binutils', '2.40'),

From 2c66b3d9c2101b784812f0bca6a95c4350a7bdce Mon Sep 17 00:00:00 2001
From: WilleBell <cintiawillemyns@gmail.com>
Date: Tue, 23 Jul 2024 17:34:56 +0200
Subject: [PATCH 483/835] adding easyconfigs: OpenFOAM-v2406-foss-2023a.eb and
 patches: OpenFOAM-v2406-cleanup.patch

---
 .../o/OpenFOAM/OpenFOAM-v2406-cleanup.patch   | 180 ++++++++++++++++++
 .../o/OpenFOAM/OpenFOAM-v2406-foss-2023a.eb   |  48 +++++
 2 files changed, 228 insertions(+)
 create mode 100644 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2406-cleanup.patch
 create mode 100644 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2406-foss-2023a.eb

diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2406-cleanup.patch b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2406-cleanup.patch
new file mode 100644
index 00000000000..6e719c21dae
--- /dev/null
+++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2406-cleanup.patch
@@ -0,0 +1,180 @@
+# Replaces OpenFOAM third-party libraries with EASYBUILD variants.
+# Uses the OpenFOAM prefs mechanism and the FOAM_CONFIG_ETC variable
+# to define the preferred settings without patching the original files
+#
+# Authors: Mark Olesen <Mark.Olesen@esi-group.com>
+#
+# ChangeLog:
+# - v2312 - activate METIS, KaHIP and readline support in etc/config.sh/setup
+#           author: Jiri Furst <jiri.furst@gmail.com> 
+#
+# -------------------------------------------------------------------------
+--- /dev/null	2020-12-14 09:05:45.272769166 +0100
++++ OpenFOAM-v2012/etc/prefs.sh	2020-12-14 10:02:26.488430802 +0100
+@@ -0,0 +1,7 @@
++##Easybuild## settings -*- sh -*-
++
++export FOAM_CONFIG_ETC="etc/easybuild"
++
++export WM_MPLIB=EASYBUILDMPI
++
++##Easybuild##
+--- /dev/null	2020-12-14 09:05:45.272769166 +0100
++++ OpenFOAM-v2012/etc/easybuild/config.sh/CGAL	2020-12-14 10:10:55.991841204 +0100
+@@ -0,0 +1,8 @@
++##Easybuild## settings -*- sh -*-
++
++export MPFR_ARCH_PATH="$EBROOTMPFR"
++export GMP_ARCH_PATH="$EBROOTGMP"
++export BOOST_ARCH_PATH="$EBROOTBOOST"
++export CGAL_ARCH_PATH="$EBROOTCGAL"
++
++##Easybuild##
+--- /dev/null	2020-12-14 09:05:45.272769166 +0100
++++ OpenFOAM-v2012/etc/easybuild/config.sh/FFTW	2020-12-14 10:10:53.735843322 +0100
+@@ -0,0 +1,5 @@
++##Easybuild## settings -*- sh -*-
++
++export FFTW_ARCH_PATH="$EBROOTFFTW"
++
++##EasyBuild##
+--- /dev/null	2020-12-14 09:05:45.272769166 +0100
++++ OpenFOAM-v2012/etc/easybuild/config.sh/metis	2020-12-11 21:23:28.774934024 +0100
+@@ -0,0 +1,6 @@
++##Easybuild## settings -*- sh -*-
++
++METIS_VERSION="metis-$EBVERSIONMETIS"
++[ -d "$METIS_ARCH_PATH" ] || METIS_ARCH_PATH="$EBROOTMETIS"
++
++##Easybuild##
+--- /dev/null   2022-12-01 18:21:35.103878336 +0100
++++ OpenFOAM-v2206/etc/easybuild/config.sh/kahip       2022-12-12 20:24:07.538408981 +0100
+@@ -0,0 +1,6 @@
++##Easybuild## settings -*- sh -*-
++
++KAHIP_VERSION="kahip-$EBVERSIONKAHIP"
++export KAHIP_ARCH_PATH="$EBROOTKAHIP"
++
++##Easybuild##
+--- /dev/null	2020-12-14 09:05:45.272769166 +0100
++++ OpenFOAM-v2012/etc/easybuild/config.sh/readline	2020-12-11 21:23:22.534951043 +0100
+@@ -0,0 +1,5 @@
++##Easybuild## settings -*- sh -*-
++
++export READLINE_ARCH_PATH="$EBROOTLIBREADLINE"
++
++##Easybuild##
+--- /dev/null	2020-12-14 09:05:45.272769166 +0100
++++ OpenFOAM-v2012/etc/easybuild/config.sh/scotch	2020-12-11 21:23:17.586964539 +0100
+@@ -0,0 +1,7 @@
++##Easybuild## settings -*- sh -*-
++
++export SCOTCH_VERSION="scotch_$EBVERSIONSCOTCH"
++export SCOTCH_ARCH_PATH="$EBROOTSCOTCH"
++[ -d "$SCOTCH_ARCH_PATH" ] || SCOTCH_ARCH_PATH="$SCOTCH_ROOT"
++
++##Easybuild##
+--- /dev/null	2020-12-14 09:05:45.272769166 +0100
++++ OpenFOAM-v2012/etc/easybuild/config.sh/vtk	2020-12-11 21:22:55.463024882 +0100
+@@ -0,0 +1,9 @@
++##Easybuild## settings -*- sh -*-
++
++export VTK_DIR="$EBROOTVTK"
++export MESA_ARCH_PATH="$EBROOTMESA"
++
++# Define paraview-mesa directory as required
++unset ParaView_MESA_DIR
++
++##Easybuild##
+--- /dev/null	2020-12-14 09:05:45.272769166 +0100
++++ OpenFOAM-v2012/etc/easybuild/config.sh/paraview	2020-12-14 10:13:53.583674383 +0100
+@@ -0,0 +1,75 @@
++##Easybuild## settings -*- sh -*-
++#
++# Largely a knockoff of the OpenFOAM etc/config.sh/paraview-system
++# readjusted for easybuild
++#
++# Copyright (C) 2020 OpenCFD Ltd.
++#
++#------------------------------------------------------------------------------
++# Compiler-specific location for ThirdParty installations
++archDir="$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER"
++
++# Clean path and library path of previous settings
++eval \
++    "$($WM_PROJECT_DIR/bin/foamCleanPath -sh-env=PATH \
++    $ParaView_DIR $archDir/ParaView- $archDir/qt-)"
++
++eval \
++    "$($WM_PROJECT_DIR/bin/foamCleanPath -sh-env=LD_LIBRARY_PATH \
++    $ParaView_DIR $archDir/ParaView- $archDir/qt-)"
++
++
++#------------------------------------------------------------------------------
++
++##Easybuild## settings
++
++ParaView_VERSION="$EBVERSIONPARAVIEW"
++export ParaView_DIR="$EBROOTPARAVIEW"
++
++#------------------------------------------------------------------------------
++
++unset PV_PLUGIN_PATH
++
++# Set API to correspond to VERSION
++# pv_api is <digits>.<digits> from ParaView_VERSION
++#-
++# Extract API from VERSION
++pv_api=$(echo "$ParaView_VERSION" | \
++    sed -ne 's/^[^0-9]*\([0-9][0-9]*\.[0-9][0-9]*\).*$/\1/p')
++
++pv_plugin_dir="$FOAM_LIBBIN/paraview-$pv_api"
++
++# Set paths if binaries are present
++if [ -r "$ParaView_DIR" ]
++then
++    export PATH="$ParaView_DIR/bin:$PATH"
++
++    # ParaView libraries
++    # - 5.5 and later:   lib/, but could also be lib64/
++    for libDir in lib64 lib
++    do
++        pvLibDir="$libDir/paraview-$pv_api"
++        if [ -d "$ParaView_DIR/$pvLibDir" ]
++        then
++            export LD_LIBRARY_PATH="$ParaView_DIR/$libDir:$LD_LIBRARY_PATH"
++            break
++        fi
++    done
++
++    # OpenFOAM plugin directory must be the first in PV_PLUGIN_PATH
++    # and have paraview-major.minor encoded in its name
++    if [ -d "$pv_plugin_dir" ]
++    then
++        export PV_PLUGIN_PATH="$pv_plugin_dir"
++    fi
++fi
++
++
++#------------------------------------------------------------------------------
++
++unset ParaView_VERSION
++
++unset archDir libDir
++unset pv_api pv_plugin_dir pvLibDir
++
++#------------------------------------------------------------------------------
+--- OpenFOAM-v2312/etc/config.sh/setup.orig    2024-01-11 09:49:24.823571481 +0100
++++ OpenFOAM-v2312/etc/config.sh/setup 2024-01-11 09:51:40.545969774 +0100
+@@ -207,7 +207,9 @@
+ _foamEtc -config  CGAL
+ _foamEtc -config  scotch
+ _foamEtc -config  FFTW
+-
++_foamEtc -config  metis
++_foamEtc -config  kahip
++_foamEtc -config  readline
+ 
+ # Finalize library paths
+ # ~~~~~~~~~~~~~~~~~~~~~~
+
diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2406-foss-2023a.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2406-foss-2023a.eb
new file mode 100644
index 00000000000..185cfead980
--- /dev/null
+++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2406-foss-2023a.eb
@@ -0,0 +1,48 @@
+name = 'OpenFOAM'
+version = 'v2406'
+
+homepage = 'https://www.openfoam.com/'
+description = """OpenFOAM is a free, open source CFD software package.
+ OpenFOAM has an extensive range of features to solve anything from complex fluid flows
+ involving chemical reactions, turbulence and heat transfer,
+ to solid dynamics and electromagnetics."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+# Users have found that vectorizion caused OpenFOAM to produce some very incorrect results.
+# Disabling vectorize was confirmed to fix the the known issues.
+# With no test suite, sticking to known working toolchain options until proven otherwise.
+toolchainopts = {'cstd': 'c++14', 'vectorize': False}
+
+source_urls = ['https://sourceforge.net/projects/openfoam/files/%(version)s/']
+sources = [SOURCE_TGZ]
+patches = [
+    ('OpenFOAM-v2406-cleanup.patch', 1),
+    ('OpenFOAM-v2212-wmake-OpenMPI.patch', 1),
+]
+checksums = [
+    {'OpenFOAM-v2406.tgz': '8d1450fb89eec1e7cecc55c3bb7bc486ccbf63d069379d1d5d7518fa16a4686a'},
+    {'OpenFOAM-v2406-cleanup.patch': '3ed44da40e9872d1cf096bb0bfd9d5c79ca984d7bc01e4ae30c14b3e7223d749'},
+    {'OpenFOAM-v2212-wmake-OpenMPI.patch': '241dc4898c22aab0cbd10c1ea931a07a786508ee03462d45dbc1c202fee3ebe8'},
+]
+
+builddependencies = [
+    ('Bison', '3.8.2'),
+    ('CMake', '3.26.3'),
+    ('flex', '2.6.4'),
+]
+
+dependencies = [
+    ('libreadline', '8.2'),
+    ('ncurses', '6.4'),
+    # OpenFOAM requires 64 bit METIS using 32 bit indexes (array indexes)
+    ('METIS', '5.1.0'),
+    ('SCOTCH', '7.0.3'),
+    ('KaHIP', '3.16'),
+    ('CGAL', '5.6'),
+    ('GMP', '6.2.1'),
+    ('MPFR', '4.2.0'),
+    ('ParaView', '5.11.2'),
+    ('gnuplot', '5.4.8'),
+]
+
+moduleclass = 'cae'

From 2f6431bdf5f39ef21b713068a7ad8fbf1d8d8415 Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Wed, 24 Jul 2024 12:11:07 +0200
Subject: [PATCH 484/835] reorganize Flax/JAX stack in 2023a: scvi-tools, Flax,
 Optax, jax, absl-py

---
 .../a/absl-py/absl-py-2.1.0-GCCcore-12.3.0.eb | 26 ++++++
 .../f/Flax/Flax-0.8.4-gfbf-2023a.eb           | 42 +++++++++
 ...foss-2023a.eb => jax-0.4.25-gfbf-2023a.eb} | 86 +++++++++----------
 .../o/Optax/Optax-0.2.2-gfbf-2023a.eb         | 35 ++++++++
 .../scvi-tools/scvi-tools-1.1.2-foss-2023a.eb | 15 +---
 5 files changed, 145 insertions(+), 59 deletions(-)
 create mode 100644 easybuild/easyconfigs/a/absl-py/absl-py-2.1.0-GCCcore-12.3.0.eb
 create mode 100644 easybuild/easyconfigs/f/Flax/Flax-0.8.4-gfbf-2023a.eb
 rename easybuild/easyconfigs/j/jax/{jax-0.4.25-foss-2023a.eb => jax-0.4.25-gfbf-2023a.eb} (52%)
 create mode 100644 easybuild/easyconfigs/o/Optax/Optax-0.2.2-gfbf-2023a.eb

diff --git a/easybuild/easyconfigs/a/absl-py/absl-py-2.1.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/a/absl-py/absl-py-2.1.0-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..8b2c928998b
--- /dev/null
+++ b/easybuild/easyconfigs/a/absl-py/absl-py-2.1.0-GCCcore-12.3.0.eb
@@ -0,0 +1,26 @@
+easyblock = 'PythonBundle'
+
+name = 'absl-py'
+version = '2.1.0'
+
+homepage = 'https://github.com/abseil/abseil-py'
+description = """absl-py is a collection of Python library code for building Python
+applications. The code is collected from Google's own Python code base, and has
+been extensively tested and used in production."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+dependencies = [('Python', '3.11.3')]
+
+use_pip = True
+
+exts_list = [
+    ('absl-py', version, {
+        'modulename': 'absl',
+        'checksums': ['7820790efbb316739cde8b4e19357243fc3608a152024288513dd968d7d959ff'],
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'tools'
diff --git a/easybuild/easyconfigs/f/Flax/Flax-0.8.4-gfbf-2023a.eb b/easybuild/easyconfigs/f/Flax/Flax-0.8.4-gfbf-2023a.eb
new file mode 100644
index 00000000000..dedc08531c3
--- /dev/null
+++ b/easybuild/easyconfigs/f/Flax/Flax-0.8.4-gfbf-2023a.eb
@@ -0,0 +1,42 @@
+easyblock = 'PythonBundle'
+
+name = 'Flax'
+version = '0.8.4'
+
+homepage = 'https://flax.readthedocs.io'
+description = """Flax is a high-performance neural network library and ecosystem for JAX that is
+designed for flexibility: Try new forms of training by forking an example and
+by modifying the training loop, not by adding features to a framework."""
+
+toolchain = {'name': 'gfbf', 'version': '2023a'}
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('jax', '0.4.25'),
+    ('Optax', '0.2.2'),
+    ('protobuf-python', '4.24.0'),
+    ('PyYAML', '6.0'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('nest_asyncio', '1.6.0', {
+        'checksums': ['6f172d5449aca15afd6c646851f4e31e02c598d553a667e38cafa997cfec55fe'],
+    }),
+    ('orbax_checkpoint', '0.5.15', {
+        'modulename': 'orbax.checkpoint',
+        'checksums': ['15195e8d1b381b56f23a62a25599a3644f5d08655fa64f60bb1b938b8ffe7ef3'],
+    }),
+    ('tensorstore', '0.1.60', {
+        'checksums': ['88da8f1978982101b8dbb144fd29ee362e4e8c97fc595c4992d555f80ce62a79'],
+    }),
+    ('flax', '0.8.4', {
+        'checksums': ['968683f850198e1aa5eb2d9d1e20bead880ef7423c14f042db9d60848cb1c90b'],
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'ai'
diff --git a/easybuild/easyconfigs/j/jax/jax-0.4.25-foss-2023a.eb b/easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a.eb
similarity index 52%
rename from easybuild/easyconfigs/j/jax/jax-0.4.25-foss-2023a.eb
rename to easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a.eb
index 64a723ffe37..26fb967339f 100644
--- a/easybuild/easyconfigs/j/jax/jax-0.4.25-foss-2023a.eb
+++ b/easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a.eb
@@ -1,25 +1,23 @@
 # This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
 # Author: Denis Kristak
-# Updated by: Alex Domingo (Vrije Universiteit Brussel), Pavel Tománek (INUITS)
-# Update v0.4.25 based on: https://github.com/easybuilders/easybuild-easyconfigs/pull/20119
-
+# Updated by: Alex Domingo (Vrije Universiteit Brussel)
+# Updated by: Thomas Hoffmann (EMBL Heidelberg)
 easyblock = 'PythonBundle'
 
 name = 'jax'
 version = '0.4.25'
 
-homepage = 'https://jax.readthedocs.io/'
+homepage = 'https://pypi.python.org/pypi/jax'
 description = """Composable transformations of Python+NumPy programs:
 differentiate, vectorize, JIT to GPU/TPU, and more"""
 
-toolchain = {'name': 'foss', 'version': '2023a'}
+toolchain = {'name': 'gfbf', 'version': '2023a'}
 
 builddependencies = [
     ('Bazel', '6.3.1'),
     ('pytest-xdist', '3.3.1'),
-    # git 2.x required to fetch repository 'io_bazel_rules_docker'
-    ('git', '2.41.0', '-nodocs'),
-    ('matplotlib', '3.7.2'),
+    ('git', '2.41.0', '-nodocs'),  # bazel used git to fetch repositories
+    ('matplotlib', '3.7.2'),  # required for tests/lobpcg_test.py
     ('poetry', '1.5.1'),
     ('pybind11', '2.11.1'),
 ]
@@ -27,86 +25,84 @@ builddependencies = [
 dependencies = [
     ('Python', '3.11.3'),
     ('SciPy-bundle', '2023.07'),
-    ('zlib', '1.2.13'),
+    ('absl-py', '2.1.0'),
     ('flatbuffers-python', '23.5.26'),
     ('ml_dtypes', '0.3.2'),
+    ('zlib', '1.2.13'),
 ]
 
-use_pip = True
-
+# downloading xla and other tarballs to avoid that Bazel downloads it during the build
+local_extract_cmd = 'mkdir -p %(builddir)s/archives && cp %s %(builddir)s/archives'
+# note: following commits *must* be the exact same onces used upstream
+# XLA_COMMIT from jax-jaxlib: third_party/xla/workspace.bzl
 local_xla_commit = '4ccfe33c71665ddcbca5b127fefe8baa3ed632d4'
+# TFRT_COMMIT from xla: third_party/tsl/third_party/tf_runtime/workspace.bzl
 local_tfrt_commit = '0aeefb1660d7e37964b2bb71b1f518096bda9a25'
 
-local_extract_cmd = 'cp %s %(builddir)s/archives'
-
-local_repo_opt = '--bazel_options="--distdir=%(builddir)s/archives" '
-local_repo_opt += '--bazel_options="--action_env=TF_SYSTEM_LIBS=pybind11" '
-local_repo_opt += '--bazel_options="--action_env=CPATH=$EBROOTPYBIND11/include" '
-
-default_easyblock = 'PythonPackage'
-default_component_specs = {
-    'sources': [SOURCE_TAR_GZ],
-    'source_urls': [PYPI_SOURCE],
-    'start_dir': '%(name)s-%(version)s',
-    'use_pip': True,
-    'sanity_pip_check': True,
-    'download_dep_fail': True,
-}
+# Use sources downloaded by EasyBuild
+_jaxlib_buildopts = '--bazel_options="--distdir=%(builddir)s/archives" '
+# Use dependencies from EasyBuild
+_jaxlib_buildopts += '--bazel_options="--action_env=TF_SYSTEM_LIBS=pybind11" '
+_jaxlib_buildopts += '--bazel_options="--action_env=CPATH=$EBROOTPYBIND11/include" '
+# Avoid warning (treated as error) in upb/table.c
+_jaxlib_buildopts += '--bazel_options="--copt=-Wno-maybe-uninitialized" '
 
 components = [
-    ('absl-py', '2.1.0', {
-        'options': {'modulename': 'absl'},
-        'checksums': ['7820790efbb316739cde8b4e19357243fc3608a152024288513dd968d7d959ff'],
-    }),
     ('jaxlib', version, {
         'sources': [
-            '%(name)s-v%(version)s.tar.gz',
             {
+                'source_urls': ['https://github.com/google/jax/archive/'],
+                'filename': '%(name)s-v%(version)s.tar.gz',
+            },
+            {
+                'source_urls': ['https://github.com/openxla/xla/archive'],
                 'download_filename': '%s.tar.gz' % local_xla_commit,
-                'filename': 'xla-%s.tar.gz' % local_xla_commit,
+                'filename': 'xla-%s.tar.gz' % local_xla_commit[:8],
                 'extract_cmd': local_extract_cmd,
             },
             {
+                'source_urls': ['https://github.com/tensorflow/runtime/archive'],
                 'download_filename': '%s.tar.gz' % local_tfrt_commit,
-                'filename': 'tf_runtime-%s.tar.gz' % local_tfrt_commit,
+                'filename': 'tf_runtime-%s.tar.gz' % local_tfrt_commit[:8],
                 'extract_cmd': local_extract_cmd,
             },
         ],
-        'source_urls': [
-            'https://github.com/google/jax/archive/',
-            'https://github.com/tensorflow/runtime/archive',
-            'https://github.com/openxla/xla/archive'
-        ],
         'patches': ['jax-0.4.25_fix-pybind11-systemlib.patch'],
         'checksums': [
             {'jaxlib-v0.4.25.tar.gz':
              'fc1197c401924942eb14185a61688d0c476e3e81ff71f9dc95e620b57c06eec8'},
-            {'xla-4ccfe33c71665ddcbca5b127fefe8baa3ed632d4.tar.gz':
+            {'xla-4ccfe33c.tar.gz':
              '8a59b9af7d0850059d7043f7043c780066d61538f3af536e8a10d3d717f35089'},
-            {'tf_runtime-0aeefb1660d7e37964b2bb71b1f518096bda9a25.tar.gz':
+            {'tf_runtime-0aeefb16.tar.gz':
              'a3df827d7896774cb1d80bf4e1c79ab05c268f29bd4d3db1fb5a4b9c2079d8e3'},
             {'jax-0.4.25_fix-pybind11-systemlib.patch':
              'daad5b726d1a138431b05eb60ecf4c89c7b5148eb939721800bdf43d804ca033'},
         ],
         'start_dir': 'jax-jaxlib-v%(version)s',
-        # Avoid warning (treated as error) in upb/table.c
-        'buildopts': local_repo_opt + ' --bazel_options="--copt=-Wno-maybe-uninitialized"'
+        'buildopts': _jaxlib_buildopts
     }),
 ]
 
+use_pip = True
+
 exts_list = [
     (name, version, {
+        'sources': [
+            {
+                'source_urls': ['https://github.com/google/jax/archive/'],
+                'filename': '%(name)s-v%(version)s.tar.gz',
+            },
+        ],
         'patches': ['jax-0.4.25_fix_env_test_no_log_spam.patch'],
-        'source_tmpl': '%(name)s-v%(version)s.tar.gz',
-        'source_urls': ['https://github.com/google/jax/archive/'],
         'checksums': [
             {'jax-v0.4.25.tar.gz': '8b30af49688c0c13b82c6f5ce992727c00b5fc6d04a4c6962012f4246fa664eb'},
             {'jax-0.4.25_fix_env_test_no_log_spam.patch':
              'a18b5f147569d9ad41025124333a0f04fd0d0e0f9e4309658d7f6b9b838e2e2a'},
         ],
+        'runtest': "pytest -n %(parallel)s tests",
     }),
 ]
 
 sanity_pip_check = True
 
-moduleclass = 'tools'
+moduleclass = 'ai'
diff --git a/easybuild/easyconfigs/o/Optax/Optax-0.2.2-gfbf-2023a.eb b/easybuild/easyconfigs/o/Optax/Optax-0.2.2-gfbf-2023a.eb
new file mode 100644
index 00000000000..d447a77bbd2
--- /dev/null
+++ b/easybuild/easyconfigs/o/Optax/Optax-0.2.2-gfbf-2023a.eb
@@ -0,0 +1,35 @@
+easyblock = 'PythonBundle'
+
+name = 'Optax'
+version = '0.2.2'
+
+homepage = 'https://github.com/deepmind/optax'
+description = """Optax is a gradient processing and optimization library for JAX."""
+
+toolchain = {'name': 'gfbf', 'version': '2023a'}
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('jax', '0.4.25'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('toolz', '0.12.1', {
+        'checksums': ['ecca342664893f177a13dac0e6b41cbd8ac25a358e5f215316d43e2100224f4d'],
+    }),
+    ('chex', '0.1.86', {
+        'checksums': ['e8b0f96330eba4144659e1617c0f7a57b161e8cbb021e55c6d5056c7378091d1'],
+    }),
+    ('optax', version, {
+        'checksums': ['f09bf790ef4b09fb9c35f79a07594c6196a719919985f542dc84b0bf97812e0e'],
+    }),
+]
+
+sanity_pip_check = True
+
+sanity_check_commands = ["python -c 'from optax import GradientTransformation'"]
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/s/scvi-tools/scvi-tools-1.1.2-foss-2023a.eb b/easybuild/easyconfigs/s/scvi-tools/scvi-tools-1.1.2-foss-2023a.eb
index f79f5895f45..be427d2af9e 100644
--- a/easybuild/easyconfigs/s/scvi-tools/scvi-tools-1.1.2-foss-2023a.eb
+++ b/easybuild/easyconfigs/s/scvi-tools/scvi-tools-1.1.2-foss-2023a.eb
@@ -22,7 +22,7 @@ dependencies = [
     ('PyTorch-Lightning', '2.2.1'),
     ('pyro-ppl', '1.9.0'),
     ('ml-collections', '0.1.1'),
-    ('Optax', '0.2.2'),
+    ('Flax', '0.8.4'),
 ]
 
 use_pip = True
@@ -37,19 +37,6 @@ exts_list = [
     ('numpyro', '0.15.0', {
         'checksums': ['e16c9f47cc31e2aa259584a0b6c944312081d33ca92406022632ad584b0e600d'],
     }),
-    ('nest_asyncio', '1.6.0', {
-        'checksums': ['6f172d5449aca15afd6c646851f4e31e02c598d553a667e38cafa997cfec55fe'],
-    }),
-    ('orbax_checkpoint', '0.5.15', {
-        'modulename': 'orbax.checkpoint',
-        'checksums': ['15195e8d1b381b56f23a62a25599a3644f5d08655fa64f60bb1b938b8ffe7ef3'],
-    }),
-    ('tensorstore', '0.1.60', {
-        'checksums': ['88da8f1978982101b8dbb144fd29ee362e4e8c97fc595c4992d555f80ce62a79'],
-    }),
-    ('flax', '0.8.4', {
-        'checksums': ['968683f850198e1aa5eb2d9d1e20bead880ef7423c14f042db9d60848cb1c90b'],
-    }),
     ('docrep', '0.3.2', {
         'checksums': ['ed8a17e201abd829ef8da78a0b6f4d51fb99a4cbd0554adbed3309297f964314'],
     }),

From a0ebc51ee9412cc8fc924f60d5b595a02d723de7 Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Wed, 24 Jul 2024 12:13:43 +0200
Subject: [PATCH 485/835] downgrade Optax v0.2.2 from foss/2023a to gfbf/2023a

---
 .../o/Optax/Optax-0.2.2-foss-2023a.eb         | 42 -------------------
 1 file changed, 42 deletions(-)
 delete mode 100644 easybuild/easyconfigs/o/Optax/Optax-0.2.2-foss-2023a.eb

diff --git a/easybuild/easyconfigs/o/Optax/Optax-0.2.2-foss-2023a.eb b/easybuild/easyconfigs/o/Optax/Optax-0.2.2-foss-2023a.eb
deleted file mode 100644
index be05f009e9e..00000000000
--- a/easybuild/easyconfigs/o/Optax/Optax-0.2.2-foss-2023a.eb
+++ /dev/null
@@ -1,42 +0,0 @@
-easyblock = 'PythonBundle'
-
-name = 'Optax'
-version = '0.2.2'
-
-homepage = 'https://github.com/deepmind/optax'
-description = """Optax is a gradient processing and optimization library for JAX."""
-
-toolchain = {'name': 'foss', 'version': '2023a'}
-
-dependencies = [
-    ('Python', '3.11.3'),
-    ('SciPy-bundle', '2023.07'),
-    ('jax', '0.4.25'),
-]
-
-use_pip = True
-
-exts_list = [
-    ('toolz', '0.12.1', {
-        'checksums': ['ecca342664893f177a13dac0e6b41cbd8ac25a358e5f215316d43e2100224f4d'],
-    }),
-    ('flit_core', '3.9.0', {
-        'checksums': ['72ad266176c4a3fcfab5f2930d76896059851240570ce9a98733b658cb786eba'],
-    }),
-    ('absl-py', '2.1.0', {
-        'modulename': 'absl',
-        'checksums': ['7820790efbb316739cde8b4e19357243fc3608a152024288513dd968d7d959ff'],
-    }),
-    ('chex', '0.1.86', {
-        'checksums': ['e8b0f96330eba4144659e1617c0f7a57b161e8cbb021e55c6d5056c7378091d1'],
-    }),
-    ('optax', version, {
-        'checksums': ['f09bf790ef4b09fb9c35f79a07594c6196a719919985f542dc84b0bf97812e0e'],
-    }),
-]
-
-sanity_pip_check = True
-
-sanity_check_commands = ["python -c 'from optax import GradientTransformation'"]
-
-moduleclass = 'lib'

From 17f7abeca74a18c792b6b32caf6af2751fe9e70c Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Wed, 24 Jul 2024 12:16:19 +0200
Subject: [PATCH 486/835] reinstate all authorship on jax-0.4.25-gfbf-2023a.eb

---
 easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a.eb | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a.eb b/easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a.eb
index 26fb967339f..f78da6a06e4 100644
--- a/easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a.eb
+++ b/easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a.eb
@@ -1,6 +1,7 @@
 # This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
 # Author: Denis Kristak
 # Updated by: Alex Domingo (Vrije Universiteit Brussel)
+# Updated by: Pavel Tománek (INUITS)
 # Updated by: Thomas Hoffmann (EMBL Heidelberg)
 easyblock = 'PythonBundle'
 

From 496f749f46446c8fb1c8da0000e72babe9b33dad Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Wed, 24 Jul 2024 12:22:34 +0200
Subject: [PATCH 487/835] use readtehdocs URL as homepage of
 jax-0.4.25-gfbf-2023a.eb

---
 easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a.eb b/easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a.eb
index f78da6a06e4..f913cfe9e97 100644
--- a/easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a.eb
+++ b/easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a.eb
@@ -8,7 +8,7 @@ easyblock = 'PythonBundle'
 name = 'jax'
 version = '0.4.25'
 
-homepage = 'https://pypi.python.org/pypi/jax'
+homepage = 'https://jax.readthedocs.io/'
 description = """Composable transformations of Python+NumPy programs:
 differentiate, vectorize, JIT to GPU/TPU, and more"""
 

From b3c2dcd3a28130caa607474cd1e016768cab069e Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Wed, 24 Jul 2024 12:31:59 +0200
Subject: [PATCH 488/835] fix typo in comment of jax-0.4.25-gfbf-2023a.eb

---
 easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a.eb b/easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a.eb
index f913cfe9e97..a4a86382ad6 100644
--- a/easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a.eb
+++ b/easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a.eb
@@ -17,7 +17,7 @@ toolchain = {'name': 'gfbf', 'version': '2023a'}
 builddependencies = [
     ('Bazel', '6.3.1'),
     ('pytest-xdist', '3.3.1'),
-    ('git', '2.41.0', '-nodocs'),  # bazel used git to fetch repositories
+    ('git', '2.41.0', '-nodocs'),  # bazel uses git to fetch repositories
     ('matplotlib', '3.7.2'),  # required for tests/lobpcg_test.py
     ('poetry', '1.5.1'),
     ('pybind11', '2.11.1'),

From ac92bb78c36ab8bb172b103110ec904a3ee65155 Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Wed, 24 Jul 2024 12:43:40 +0200
Subject: [PATCH 489/835] Flax/JAX stack in 2023a w/ CUDA 12.1.1: scvi-tools,
 Flax, Optax, jax, absl-py

---
 .../a/absl-py/absl-py-2.1.0-GCCcore-12.3.0.eb |  26 ++++
 .../Flax/Flax-0.8.4-gfbf-2023a-CUDA-12.1.1.eb |  44 +++++++
 .../jax/jax-0.4.25-gfbf-2023a-CUDA-12.1.1.eb  | 117 ++++++++----------
 .../Optax-0.2.2-gfbf-2023a-CUDA-12.1.1.eb     |  37 ++++++
 ...scvi-tools-1.1.2-foss-2023a-CUDA-12.1.1.eb |  57 +++++++++
 5 files changed, 218 insertions(+), 63 deletions(-)
 create mode 100644 easybuild/easyconfigs/a/absl-py/absl-py-2.1.0-GCCcore-12.3.0.eb
 create mode 100644 easybuild/easyconfigs/f/Flax/Flax-0.8.4-gfbf-2023a-CUDA-12.1.1.eb
 create mode 100644 easybuild/easyconfigs/o/Optax/Optax-0.2.2-gfbf-2023a-CUDA-12.1.1.eb
 create mode 100644 easybuild/easyconfigs/s/scvi-tools/scvi-tools-1.1.2-foss-2023a-CUDA-12.1.1.eb

diff --git a/easybuild/easyconfigs/a/absl-py/absl-py-2.1.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/a/absl-py/absl-py-2.1.0-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..8b2c928998b
--- /dev/null
+++ b/easybuild/easyconfigs/a/absl-py/absl-py-2.1.0-GCCcore-12.3.0.eb
@@ -0,0 +1,26 @@
+easyblock = 'PythonBundle'
+
+name = 'absl-py'
+version = '2.1.0'
+
+homepage = 'https://github.com/abseil/abseil-py'
+description = """absl-py is a collection of Python library code for building Python
+applications. The code is collected from Google's own Python code base, and has
+been extensively tested and used in production."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+dependencies = [('Python', '3.11.3')]
+
+use_pip = True
+
+exts_list = [
+    ('absl-py', version, {
+        'modulename': 'absl',
+        'checksums': ['7820790efbb316739cde8b4e19357243fc3608a152024288513dd968d7d959ff'],
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'tools'
diff --git a/easybuild/easyconfigs/f/Flax/Flax-0.8.4-gfbf-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/f/Flax/Flax-0.8.4-gfbf-2023a-CUDA-12.1.1.eb
new file mode 100644
index 00000000000..4aeb0c7d815
--- /dev/null
+++ b/easybuild/easyconfigs/f/Flax/Flax-0.8.4-gfbf-2023a-CUDA-12.1.1.eb
@@ -0,0 +1,44 @@
+easyblock = 'PythonBundle'
+
+name = 'Flax'
+version = '0.8.4'
+versionsuffix = '-CUDA-%(cudaver)s'
+
+homepage = 'https://flax.readthedocs.io'
+description = """Flax is a high-performance neural network library and ecosystem for JAX that is
+designed for flexibility: Try new forms of training by forking an example and
+by modifying the training loop, not by adding features to a framework."""
+
+toolchain = {'name': 'gfbf', 'version': '2023a'}
+
+dependencies = [
+    ('CUDA', '12.1.1', '', SYSTEM),
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('jax', '0.4.25', versionsuffix),
+    ('Optax', '0.2.2', versionsuffix),
+    ('protobuf-python', '4.24.0'),
+    ('PyYAML', '6.0'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('nest_asyncio', '1.6.0', {
+        'checksums': ['6f172d5449aca15afd6c646851f4e31e02c598d553a667e38cafa997cfec55fe'],
+    }),
+    ('orbax_checkpoint', '0.5.15', {
+        'modulename': 'orbax.checkpoint',
+        'checksums': ['15195e8d1b381b56f23a62a25599a3644f5d08655fa64f60bb1b938b8ffe7ef3'],
+    }),
+    ('tensorstore', '0.1.60', {
+        'checksums': ['88da8f1978982101b8dbb144fd29ee362e4e8c97fc595c4992d555f80ce62a79'],
+    }),
+    ('flax', '0.8.4', {
+        'checksums': ['968683f850198e1aa5eb2d9d1e20bead880ef7423c14f042db9d60848cb1c90b'],
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'ai'
diff --git a/easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a-CUDA-12.1.1.eb
index c193b35c83b..75355c6c842 100644
--- a/easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a-CUDA-12.1.1.eb
+++ b/easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a-CUDA-12.1.1.eb
@@ -1,6 +1,7 @@
 # This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
 # Author: Denis Kristak
 # Updated by: Alex Domingo (Vrije Universiteit Brussel)
+# Updated by: Pavel Tománek (INUITS)
 # Updated by: Thomas Hoffmann (EMBL Heidelberg)
 easyblock = 'PythonBundle'
 
@@ -8,7 +9,7 @@ name = 'jax'
 version = '0.4.25'
 versionsuffix = '-CUDA-%(cudaver)s'
 
-homepage = 'https://pypi.python.org/pypi/jax'
+homepage = 'https://jax.readthedocs.io/'
 description = """Composable transformations of Python+NumPy programs:
 differentiate, vectorize, JIT to GPU/TPU, and more"""
 
@@ -18,8 +19,7 @@ cuda_compute_capabilities = ["5.0", "6.0", "6.1", "7.0", "7.5", "8.0", "8.6", "9
 builddependencies = [
     ('Bazel', '6.3.1'),
     ('pytest-xdist', '3.3.1'),
-    # git 2.x required to fetch repository 'io_bazel_rules_docker'
-    ('git', '2.41.0', '-nodocs'),
+    ('git', '2.41.0', '-nodocs'),  # bazel uses git to fetch repositories
     ('matplotlib', '3.7.2'),  # required for tests/lobpcg_test.py
     ('poetry', '1.5.1'),
     ('pybind11', '2.11.1'),
@@ -29,23 +29,65 @@ dependencies = [
     ('CUDA', '12.1.1', '', SYSTEM),
     ('cuDNN', '8.9.2.26', versionsuffix, SYSTEM),
     ('NCCL', '2.18.3', versionsuffix),
-    ('zlib', '1.2.13'),
     ('Python', '3.11.3'),
     ('SciPy-bundle', '2023.07'),
+    ('absl-py', '2.1.0'),
     ('flatbuffers-python', '23.5.26'),
     ('ml_dtypes', '0.3.2'),
+    ('zlib', '1.2.13'),
 ]
 
 # downloading xla and other tarballs to avoid that Bazel downloads it during the build
-# note: this *must* be the exact same commit as used in third_party/{xla,"other"}/workspace.bzl
+local_extract_cmd = 'mkdir -p %(builddir)s/archives && cp %s %(builddir)s/archives'
+# note: following commits *must* be the exact same onces used upstream
+# XLA_COMMIT from jax-jaxlib: third_party/xla/workspace.bzl
 local_xla_commit = '4ccfe33c71665ddcbca5b127fefe8baa3ed632d4'
+# TFRT_COMMIT from xla: third_party/tsl/third_party/tf_runtime/workspace.bzl
 local_tfrt_commit = '0aeefb1660d7e37964b2bb71b1f518096bda9a25'
 
-local_extract_cmd = 'mkdir -p %(builddir)s/archives && cp %s %(builddir)s/archives'
-local_repo_opt = '--bazel_options="--distdir=%(builddir)s/archives" '
-local_repo_opt += '--bazel_options="--action_env=TF_SYSTEM_LIBS=pybind11" '
-local_repo_opt += '--bazel_options="--action_env=CPATH=$EBROOTPYBIND11/include" '
+# Use sources downloaded by EasyBuild
+_jaxlib_buildopts = '--bazel_options="--distdir=%(builddir)s/archives" '
+# Use dependencies from EasyBuild
+_jaxlib_buildopts += '--bazel_options="--action_env=TF_SYSTEM_LIBS=pybind11" '
+_jaxlib_buildopts += '--bazel_options="--action_env=CPATH=$EBROOTPYBIND11/include" '
+# Avoid warning (treated as error) in upb/table.c
+_jaxlib_buildopts += '--bazel_options="--copt=-Wno-maybe-uninitialized" '
 
+components = [
+    ('jaxlib', version, {
+        'sources': [
+            {
+                'source_urls': ['https://github.com/google/jax/archive/'],
+                'filename': '%(name)s-v%(version)s.tar.gz',
+            },
+            {
+                'source_urls': ['https://github.com/openxla/xla/archive'],
+                'download_filename': '%s.tar.gz' % local_xla_commit,
+                'filename': 'xla-%s.tar.gz' % local_xla_commit[:8],
+                'extract_cmd': local_extract_cmd,
+            },
+            {
+                'source_urls': ['https://github.com/tensorflow/runtime/archive'],
+                'download_filename': '%s.tar.gz' % local_tfrt_commit,
+                'filename': 'tf_runtime-%s.tar.gz' % local_tfrt_commit[:8],
+                'extract_cmd': local_extract_cmd,
+            },
+        ],
+        'patches': ['jax-0.4.25_fix-pybind11-systemlib.patch'],
+        'checksums': [
+            {'jaxlib-v0.4.25.tar.gz':
+             'fc1197c401924942eb14185a61688d0c476e3e81ff71f9dc95e620b57c06eec8'},
+            {'xla-4ccfe33c.tar.gz':
+             '8a59b9af7d0850059d7043f7043c780066d61538f3af536e8a10d3d717f35089'},
+            {'tf_runtime-0aeefb16.tar.gz':
+             'a3df827d7896774cb1d80bf4e1c79ab05c268f29bd4d3db1fb5a4b9c2079d8e3'},
+            {'jax-0.4.25_fix-pybind11-systemlib.patch':
+             'daad5b726d1a138431b05eb60ecf4c89c7b5148eb939721800bdf43d804ca033'},
+        ],
+        'start_dir': 'jax-jaxlib-v%(version)s',
+        'buildopts': _jaxlib_buildopts
+    }),
+]
 
 # Some tests require an isolated run:
 local_isolated_tests = [
@@ -74,71 +116,20 @@ local_test += ' && '.join(['pytest -vv %s' % x for x in local_isolated_tests])
 
 use_pip = True
 
-default_easyblock = 'PythonPackage'
-default_component_specs = {
-    'sources': [SOURCE_TAR_GZ],
-    'source_urls': [PYPI_SOURCE],
-    'start_dir': '%(name)s-%(version)s',
-    'use_pip': True,
-    'sanity_pip_check': True,
-    'download_dep_fail': True,
-}
-
-components = [
-    ('absl-py', '2.1.0', {
-        'options': {'modulename': 'absl'},
-        'checksums': ['7820790efbb316739cde8b4e19357243fc3608a152024288513dd968d7d959ff'],
-    }),
-    ('jaxlib', version, {
-        'sources': [
-            '%(name)s-v%(version)s.tar.gz',
-            {
-                'download_filename': '%s.tar.gz' % local_xla_commit,
-                'filename': 'xla-%s.tar.gz' % local_xla_commit,
-                'extract_cmd': local_extract_cmd,
-            },
-            {
-                'download_filename': '%s.tar.gz' % local_tfrt_commit,
-                'filename': 'tf_runtime-%s.tar.gz' % local_tfrt_commit,
-                'extract_cmd': local_extract_cmd,
-            },
-        ],
-        'source_urls': [
-            'https://github.com/google/jax/archive/',
-            'https://github.com/tensorflow/runtime/archive',
-            'https://github.com/openxla/xla/archive'
-        ],
-        'patches': ['jax-0.4.25_fix-pybind11-systemlib.patch'],
-        'checksums': [
-            {'jaxlib-v0.4.25.tar.gz':
-             'fc1197c401924942eb14185a61688d0c476e3e81ff71f9dc95e620b57c06eec8'},
-            {'xla-4ccfe33c71665ddcbca5b127fefe8baa3ed632d4.tar.gz':
-             '8a59b9af7d0850059d7043f7043c780066d61538f3af536e8a10d3d717f35089'},
-            {'tf_runtime-0aeefb1660d7e37964b2bb71b1f518096bda9a25.tar.gz':
-             'a3df827d7896774cb1d80bf4e1c79ab05c268f29bd4d3db1fb5a4b9c2079d8e3'},
-            {'jax-0.4.25_fix-pybind11-systemlib.patch':
-             'daad5b726d1a138431b05eb60ecf4c89c7b5148eb939721800bdf43d804ca033'},
-        ],
-        'start_dir': 'jax-jaxlib-v%(version)s',
-        # Avoid warning (treated as error) in upb/table.c
-        'buildopts': local_repo_opt + ' --bazel_options="--copt=-Wno-maybe-uninitialized"'
-    }),
-]
-
 exts_list = [
     (name, version, {
-        'patches': ['jax-0.4.25_fix_env_test_no_log_spam.patch'],
-        'runtest': local_test,
         'source_tmpl': '%(name)s-v%(version)s.tar.gz',
         'source_urls': ['https://github.com/google/jax/archive/'],
+        'patches': ['jax-0.4.25_fix_env_test_no_log_spam.patch'],
         'checksums': [
             {'jax-v0.4.25.tar.gz': '8b30af49688c0c13b82c6f5ce992727c00b5fc6d04a4c6962012f4246fa664eb'},
             {'jax-0.4.25_fix_env_test_no_log_spam.patch':
              'a18b5f147569d9ad41025124333a0f04fd0d0e0f9e4309658d7f6b9b838e2e2a'},
         ],
+        'runtest': local_test,
     }),
 ]
 
 sanity_pip_check = True
 
-moduleclass = 'tools'
+moduleclass = 'ai'
diff --git a/easybuild/easyconfigs/o/Optax/Optax-0.2.2-gfbf-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/o/Optax/Optax-0.2.2-gfbf-2023a-CUDA-12.1.1.eb
new file mode 100644
index 00000000000..61000b1388c
--- /dev/null
+++ b/easybuild/easyconfigs/o/Optax/Optax-0.2.2-gfbf-2023a-CUDA-12.1.1.eb
@@ -0,0 +1,37 @@
+easyblock = 'PythonBundle'
+
+name = 'Optax'
+version = '0.2.2'
+versionsuffix = '-CUDA-%(cudaver)s'
+
+homepage = 'https://github.com/deepmind/optax'
+description = """Optax is a gradient processing and optimization library for JAX."""
+
+toolchain = {'name': 'gfbf', 'version': '2023a'}
+
+dependencies = [
+    ('CUDA', '12.1.1', '', SYSTEM),
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('jax', '0.4.25', versionsuffix),
+]
+
+use_pip = True
+
+exts_list = [
+    ('toolz', '0.12.1', {
+        'checksums': ['ecca342664893f177a13dac0e6b41cbd8ac25a358e5f215316d43e2100224f4d'],
+    }),
+    ('chex', '0.1.86', {
+        'checksums': ['e8b0f96330eba4144659e1617c0f7a57b161e8cbb021e55c6d5056c7378091d1'],
+    }),
+    ('optax', version, {
+        'checksums': ['f09bf790ef4b09fb9c35f79a07594c6196a719919985f542dc84b0bf97812e0e'],
+    }),
+]
+
+sanity_pip_check = True
+
+sanity_check_commands = ["python -c 'from optax import GradientTransformation'"]
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/s/scvi-tools/scvi-tools-1.1.2-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/s/scvi-tools/scvi-tools-1.1.2-foss-2023a-CUDA-12.1.1.eb
new file mode 100644
index 00000000000..ce1e90cec46
--- /dev/null
+++ b/easybuild/easyconfigs/s/scvi-tools/scvi-tools-1.1.2-foss-2023a-CUDA-12.1.1.eb
@@ -0,0 +1,57 @@
+easyblock = 'PythonBundle'
+
+name = 'scvi-tools'
+version = '1.1.2'
+versionsuffix = '-CUDA-%(cudaver)s'
+
+homepage = 'https://github.com/scverse/scvi-tools'
+description = """scvi-tools (single-cell variational inference tools) is a package for probabilistic modeling and
+analysis of single-cell omics data, built on top of PyTorch and AnnData."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+builddependencies = [('hatchling', '1.18.0')]
+dependencies = [
+    ('CUDA', '12.1.1', '', SYSTEM),
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('anndata', '0.10.5.post1'),
+    ('matplotlib', '3.7.2'),
+    ('scikit-learn', '1.3.1'),
+    ('tqdm', '4.66.1'),
+    ('h5py', '3.9.0'),
+    ('jax', '0.4.25', versionsuffix),
+    ('Flax', '0.8.4', versionsuffix),
+    ('PyTorch-Lightning', '2.2.1', versionsuffix),
+    ('pyro-ppl', '1.9.0'),
+    ('ml-collections', '0.1.1'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('mudata', '0.2.3', {
+        'checksums': ['45288ac150bfc598d68acb7c2c1c43c38c5c39522107e04f7efbf3360c7f2035'],
+    }),
+    ('multipledispatch', '1.0.0', {
+        'checksums': ['5c839915465c68206c3e9c473357908216c28383b425361e5d144594bf85a7e0'],
+    }),
+    ('numpyro', '0.15.0', {
+        'checksums': ['e16c9f47cc31e2aa259584a0b6c944312081d33ca92406022632ad584b0e600d'],
+    }),
+    ('docrep', '0.3.2', {
+        'checksums': ['ed8a17e201abd829ef8da78a0b6f4d51fb99a4cbd0554adbed3309297f964314'],
+    }),
+    ('lightning', '2.1.4', {
+        'checksums': ['0e45098c700fa28c604a11ae233ce181b44aeffce2404debebc2616118431d9f'],
+    }),
+    (name, version, {
+        'modulename': 'scvi',
+        'sources': ['scvi_tools-%(version)s.tar.gz'],
+        'checksums': ['104a11a30e8996f5ceaa907b8c81b48b1f4b380d492ef2dd9b9a5577ed81b0f9'],
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'bio'

From a01ab8635d54ad1c4d55041072d64372e67eb865 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Petr=20Kr=C3=A1l?= <petr@inuits.eu>
Date: Wed, 24 Jul 2024 15:05:44 +0200
Subject: [PATCH 490/835] avoid the `winsize` error

---
 easybuild/easyconfigs/t/Transrate/Transrate-1.0.3-GCC-12.3.0.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/t/Transrate/Transrate-1.0.3-GCC-12.3.0.eb b/easybuild/easyconfigs/t/Transrate/Transrate-1.0.3-GCC-12.3.0.eb
index 6ad1e622a9a..cef48298a80 100644
--- a/easybuild/easyconfigs/t/Transrate/Transrate-1.0.3-GCC-12.3.0.eb
+++ b/easybuild/easyconfigs/t/Transrate/Transrate-1.0.3-GCC-12.3.0.eb
@@ -30,7 +30,7 @@ dependencies = [
 preinstallopts = """sed -i "s/'yell', '~> 2.0',/'yell',/g" transrate.gemspec && """
 
 # to avoid the `terminal_columns': undefined method `winsize' for nil (NoMethodError)` error
-preinstallopts += "sed -i '/terminal_columns > 70/d' lib/transrate/cmdline.rb && "
+preinstallopts += "sed -i '/terminal_columns > 70/d;/def terminal_columns/,+3d' lib/transrate/cmdline.rb && "
 
 sanity_check_paths = {
     'files': ['bin/%(namelower)s'],

From d666e08e90510f8d108fe83c7a4b61721729440b Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Wed, 24 Jul 2024 15:11:15 +0200
Subject: [PATCH 491/835] add build dependency on binutils to
 absl-py-2.1.0-GCCcore-12.3.0.eb

---
 easybuild/easyconfigs/a/absl-py/absl-py-2.1.0-GCCcore-12.3.0.eb | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/easybuild/easyconfigs/a/absl-py/absl-py-2.1.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/a/absl-py/absl-py-2.1.0-GCCcore-12.3.0.eb
index 8b2c928998b..faadde2a51d 100644
--- a/easybuild/easyconfigs/a/absl-py/absl-py-2.1.0-GCCcore-12.3.0.eb
+++ b/easybuild/easyconfigs/a/absl-py/absl-py-2.1.0-GCCcore-12.3.0.eb
@@ -10,6 +10,8 @@ been extensively tested and used in production."""
 
 toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
 
+builddependencies = [('binutils', '2.40')]
+
 dependencies = [('Python', '3.11.3')]
 
 use_pip = True

From d8d15c50a152bfe202bcf3b01262394b5a64459d Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Wed, 24 Jul 2024 15:11:50 +0200
Subject: [PATCH 492/835] add build dependency on binutils to
 absl-py-2.1.0-GCCcore-12.3.0.eb

---
 easybuild/easyconfigs/a/absl-py/absl-py-2.1.0-GCCcore-12.3.0.eb | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/easybuild/easyconfigs/a/absl-py/absl-py-2.1.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/a/absl-py/absl-py-2.1.0-GCCcore-12.3.0.eb
index 8b2c928998b..faadde2a51d 100644
--- a/easybuild/easyconfigs/a/absl-py/absl-py-2.1.0-GCCcore-12.3.0.eb
+++ b/easybuild/easyconfigs/a/absl-py/absl-py-2.1.0-GCCcore-12.3.0.eb
@@ -10,6 +10,8 @@ been extensively tested and used in production."""
 
 toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
 
+builddependencies = [('binutils', '2.40')]
+
 dependencies = [('Python', '3.11.3')]
 
 use_pip = True

From 85d4f022684e479164f705fd6570515ef95a0346 Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Wed, 24 Jul 2024 16:41:17 +0200
Subject: [PATCH 493/835] fix dependency on pyro-ppl of
 scvi-tools-1.1.2-foss-2023a-CUDA-12.1.1.eb

---
 .../s/scvi-tools/scvi-tools-1.1.2-foss-2023a-CUDA-12.1.1.eb     | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/s/scvi-tools/scvi-tools-1.1.2-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/s/scvi-tools/scvi-tools-1.1.2-foss-2023a-CUDA-12.1.1.eb
index ce1e90cec46..c434f381cfd 100644
--- a/easybuild/easyconfigs/s/scvi-tools/scvi-tools-1.1.2-foss-2023a-CUDA-12.1.1.eb
+++ b/easybuild/easyconfigs/s/scvi-tools/scvi-tools-1.1.2-foss-2023a-CUDA-12.1.1.eb
@@ -23,7 +23,7 @@ dependencies = [
     ('jax', '0.4.25', versionsuffix),
     ('Flax', '0.8.4', versionsuffix),
     ('PyTorch-Lightning', '2.2.1', versionsuffix),
-    ('pyro-ppl', '1.9.0'),
+    ('pyro-ppl', '1.9.0', versionsuffix),
     ('ml-collections', '0.1.1'),
 ]
 

From 26dd8451a48d2b1f559885d85016fe8d1849c316 Mon Sep 17 00:00:00 2001
From: fizwit <john@fuzzdog.com>
Date: Wed, 24 Jul 2024 16:20:29 -0700
Subject: [PATCH 494/835] change source file v1.1.7

---
 .../easyconfigs/b/BGEN-enkre/BGEN-enkre-1.1.7-GCC-11.2.0.eb     | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/b/BGEN-enkre/BGEN-enkre-1.1.7-GCC-11.2.0.eb b/easybuild/easyconfigs/b/BGEN-enkre/BGEN-enkre-1.1.7-GCC-11.2.0.eb
index b6850c17621..b0c0bc1be02 100644
--- a/easybuild/easyconfigs/b/BGEN-enkre/BGEN-enkre-1.1.7-GCC-11.2.0.eb
+++ b/easybuild/easyconfigs/b/BGEN-enkre/BGEN-enkre-1.1.7-GCC-11.2.0.eb
@@ -20,7 +20,7 @@ bioArxiv 308296; doi: https://doi.org/10.1101/308296
 
 toolchain = {'name': 'GCC', 'version': '11.2.0'}
 
-source_urls = ['https://code.enkre.net/bgen/tarball/release/']
+source_urls = ['https://code.enkre.net/bgen/tarball/v%(version)s/']
 sources = ['v%(version)s.tgz']
 patches = [
     '3rd-party-removal.patch',

From 831ecc2d0db6350a1080b7bbdf3ea68274d534ec Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Petr=20Kr=C3=A1l?= <petr@inuits.eu>
Date: Thu, 25 Jul 2024 11:29:45 +0200
Subject: [PATCH 495/835] add a patch to fix the `winsize` error

---
 .../t/Transrate/Transrate-1.0.3-GCC-12.3.0.eb |  9 ++--
 ...Transrate-1.0.3_undefined_method_fix.patch | 42 +++++++++++++++++++
 2 files changed, 47 insertions(+), 4 deletions(-)
 create mode 100644 easybuild/easyconfigs/t/Transrate/Transrate-1.0.3_undefined_method_fix.patch

diff --git a/easybuild/easyconfigs/t/Transrate/Transrate-1.0.3-GCC-12.3.0.eb b/easybuild/easyconfigs/t/Transrate/Transrate-1.0.3-GCC-12.3.0.eb
index cef48298a80..297dd9260b3 100644
--- a/easybuild/easyconfigs/t/Transrate/Transrate-1.0.3-GCC-12.3.0.eb
+++ b/easybuild/easyconfigs/t/Transrate/Transrate-1.0.3-GCC-12.3.0.eb
@@ -13,7 +13,11 @@ toolchain = {'name': 'GCC', 'version': '12.3.0'}
 
 source_urls = ['https://github.com/blahah/transrate/archive/']
 sources = ['v%(version)s.tar.gz']
-checksums = ['2ccb101cfab5a33586ea9e62af2b2f14caf6bc016724d1fef796b427e39fe100']
+patches = ['Transrate-1.0.3_undefined_method_fix.patch']
+checksums = [
+    {'v1.0.3.tar.gz': '2ccb101cfab5a33586ea9e62af2b2f14caf6bc016724d1fef796b427e39fe100'},
+    {'Transrate-1.0.3_undefined_method_fix.patch': 'ead5e51318d6d810fb11b783d517ea38648f62ae2bdd5f3f4dac7baa9ae94d95'},
+]
 
 builddependencies = [
     ('binutils', '2.40'),
@@ -29,9 +33,6 @@ dependencies = [
 # requirement is too strict
 preinstallopts = """sed -i "s/'yell', '~> 2.0',/'yell',/g" transrate.gemspec && """
 
-# to avoid the `terminal_columns': undefined method `winsize' for nil (NoMethodError)` error
-preinstallopts += "sed -i '/terminal_columns > 70/d;/def terminal_columns/,+3d' lib/transrate/cmdline.rb && "
-
 sanity_check_paths = {
     'files': ['bin/%(namelower)s'],
     'dirs': ['gems/%(namelower)s-%(version)s'],
diff --git a/easybuild/easyconfigs/t/Transrate/Transrate-1.0.3_undefined_method_fix.patch b/easybuild/easyconfigs/t/Transrate/Transrate-1.0.3_undefined_method_fix.patch
new file mode 100644
index 00000000000..47526bd2242
--- /dev/null
+++ b/easybuild/easyconfigs/t/Transrate/Transrate-1.0.3_undefined_method_fix.patch
@@ -0,0 +1,42 @@
+to avoid the `terminal_columns': undefined method `winsize' for nil (NoMethodError)` error
+Author: Petr Král (INUITS)
+--- lib/transrate/cmdline.rb.orig	2016-06-06 15:10:26.000000000 +0200
++++ lib/transrate/cmdline.rb	2024-07-25 11:23:20.250369056 +0200
+@@ -87,11 +87,6 @@
+     end
+   end
+ 
+-  def terminal_columns
+-    require 'io/console'
+-    IO.console.winsize.last
+-  end
+-
+   def help_message
+   <<-EOS
+ 
+@@ -117,19 +112,17 @@
+   end
+ 
+   def transrate_banner
+-    if terminal_columns > 70
+-      txp = '░▓▓▓^▓▓▓░'
+-      toptxp = txp.green
+-      midtxp = txp.yellow
+-      bottxp = txp.red
+-      puts <<-EOS
++    txp = '░▓▓▓^▓▓▓░'
++    toptxp = txp.green
++    midtxp = txp.yellow
++    bottxp = txp.red
++    puts <<-EOS
+            _                                        _
+           | |_  _ __  __ _  _ __   ___  _ __  __ _ | |_  ___
+ #{toptxp} | __|| '__|/ _` || '_ \\ / __|| '__|/ _` || __|/ _ \\ #{toptxp}
+ #{midtxp} | |_ | |  | (_| || | | |\\__ \\| |  | (_| || |_|  __/ #{midtxp}
+ #{bottxp}  \\__||_|   \\__,_||_| |_||___/|_|   \\__,_| \\__|\\___| #{bottxp}
+-      EOS
+-    end
++    EOS
+     ""
+   end
+ 

From b846d62500f9df5f50e39d9f232b3f5e4044b257 Mon Sep 17 00:00:00 2001
From: Simon Branford <s.j.branford@bham.ac.uk>
Date: Thu, 25 Jul 2024 15:21:51 +0100
Subject: [PATCH 496/835] adding easyconfigs:
 snpEff-5.2c-GCCcore-12.2.0-Java-11.eb

---
 .../snpEff-5.2c-GCCcore-12.2.0-Java-11.eb     | 37 +++++++++++++++++++
 1 file changed, 37 insertions(+)
 create mode 100644 easybuild/easyconfigs/s/snpEff/snpEff-5.2c-GCCcore-12.2.0-Java-11.eb

diff --git a/easybuild/easyconfigs/s/snpEff/snpEff-5.2c-GCCcore-12.2.0-Java-11.eb b/easybuild/easyconfigs/s/snpEff/snpEff-5.2c-GCCcore-12.2.0-Java-11.eb
new file mode 100644
index 00000000000..3b25c1e949f
--- /dev/null
+++ b/easybuild/easyconfigs/s/snpEff/snpEff-5.2c-GCCcore-12.2.0-Java-11.eb
@@ -0,0 +1,37 @@
+easyblock = 'Tarball'
+
+name = 'snpEff'
+version = '5.2c'
+versionsuffix = '-Java-%(javaver)s'
+
+homepage = 'https://pcingola.github.io/SnpEff/'
+description = """SnpEff is a variant annotation and effect prediction tool.
+ It annotates and predicts the effects of genetic variants (such as amino acid changes)."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+
+source_urls = ['https://snpeff.blob.core.windows.net/versions/']
+sources = ['%%(name)s_v%s_core.zip' % version.replace('.', '_')]
+checksums = ['9926f600662707e85478940abc283ef120a909f1d41c32a036f01d958cd51232']
+
+dependencies = [
+    # ignore website claim that Java 12+ is required, nothing is compiled for
+    # anything newer than Java 11
+    ('Java', '11', '', SYSTEM),
+    ('Python', '3.10.8'),
+    ('Perl', '5.36.0'),
+]
+
+fix_perl_shebang_for = ['scripts/*.pl']
+fix_python_shebang_for = ['scripts/*.py']
+
+sanity_check_paths = {
+    'files': ['%(name)s.jar', 'SnpSift.jar', 'scripts/%(name)s'],
+    'dirs': [],
+}
+
+sanity_check_commands = ["%(name)s -version"]
+
+modextrapaths = {'PATH': 'scripts'}
+
+moduleclass = 'bio'

From 9f68ebec38eba01f34825e4c624f8f100cb498bd Mon Sep 17 00:00:00 2001
From: Simon Branford <s.j.branford@bham.ac.uk>
Date: Thu, 25 Jul 2024 15:22:25 +0100
Subject: [PATCH 497/835] adding easyconfigs: Platypus-Opt-1.2.0-foss-2022b.eb

---
 .../Platypus-Opt-1.2.0-foss-2022b.eb          | 26 +++++++++++++++++++
 1 file changed, 26 insertions(+)
 create mode 100644 easybuild/easyconfigs/p/Platypus-Opt/Platypus-Opt-1.2.0-foss-2022b.eb

diff --git a/easybuild/easyconfigs/p/Platypus-Opt/Platypus-Opt-1.2.0-foss-2022b.eb b/easybuild/easyconfigs/p/Platypus-Opt/Platypus-Opt-1.2.0-foss-2022b.eb
new file mode 100644
index 00000000000..b1c5a4f74ea
--- /dev/null
+++ b/easybuild/easyconfigs/p/Platypus-Opt/Platypus-Opt-1.2.0-foss-2022b.eb
@@ -0,0 +1,26 @@
+easyblock = 'PythonPackage'
+
+name = 'Platypus-Opt'
+version = '1.2.0'
+
+homepage = 'https://github.com/Project-Platypus/Platypus'
+description = """Platypus is a framework for evolutionary computing in Python with a focus on
+ multiobjective evolutionary algorithms (MOEAs)."""
+
+toolchain = {'name': 'foss', 'version': '2022b'}
+
+sources = [SOURCE_TAR_GZ]
+checksums = ['f7150de2e24f8003c911259c575493c9351a7dcfb132445a3f3b096728634e6a']
+
+dependencies = [
+    ('Python', '3.10.8'),
+    ('SciPy-bundle', '2023.02'),
+]
+
+download_dep_fail = True
+use_pip = True
+sanity_pip_check = True
+
+options = {'modulename': 'platypus'}
+
+moduleclass = 'math'

From ee9078ee0686f4a3f5d39e2782bd198d655f2997 Mon Sep 17 00:00:00 2001
From: fizwit <john@fuzzdog.com>
Date: Thu, 25 Jul 2024 11:41:16 -0700
Subject: [PATCH 498/835] [GCC-12.3.0] beagle-lib v4.0.1

---
 ...beagle-lib-4.0.1-GCC-12.3.0-CUDA-12.1.1.eb | 34 +++++++++++++++++++
 1 file changed, 34 insertions(+)
 create mode 100644 easybuild/easyconfigs/b/beagle-lib/beagle-lib-4.0.1-GCC-12.3.0-CUDA-12.1.1.eb

diff --git a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-4.0.1-GCC-12.3.0-CUDA-12.1.1.eb b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-4.0.1-GCC-12.3.0-CUDA-12.1.1.eb
new file mode 100644
index 00000000000..12802801834
--- /dev/null
+++ b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-4.0.1-GCC-12.3.0-CUDA-12.1.1.eb
@@ -0,0 +1,34 @@
+easyblock = 'CMakeMake'
+
+name = 'beagle-lib'
+version = '4.0.1'
+versionsuffix = '-CUDA-%(cudaver)s'
+homepage = 'https://github.com/beagle-dev/beagle-lib'
+description = """beagle-lib is a high-performance library that can perform the core calculations at the heart of most
+ Bayesian and Maximum Likelihood phylogenetics packages."""
+
+toolchain = {'name': 'GCC', 'version': '12.3.0'}
+
+source_urls = ['https://github.com/beagle-dev/beagle-lib/archive/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['9d258cd9bedd86d7c28b91587acd1132f4e01d4f095c657ad4dc93bd83d4f120']
+
+dependencies = [
+    ('Java', '11', '', SYSTEM),
+    ('CUDA', '12.1.1', '', SYSTEM),
+]
+
+builddependencies = [
+    ('CMake', '3.26.3'),
+    ('pkgconf', '1.9.5'),
+]
+
+configopts = '-DBUILD_CUDA=ON '
+
+sanity_check_paths = {
+    'files': ["include/libhmsbeagle-1/libhmsbeagle/%s" % x for x in ["beagle.h", "platform.h"]] +
+             ["lib/libhmsbeagle%s.%s" % (x, SHLIB_EXT) for x in ["-cpu", "-cpu-sse", "-jni", ""]],
+    'dirs': []
+}
+
+moduleclass = 'numlib'

From 6ecf2744a327b910c703966ec9f08a8e597b4dd3 Mon Sep 17 00:00:00 2001
From: Alexander Salois <alexander.salois@montana.edu>
Date: Thu, 25 Jul 2024 14:53:38 -0600
Subject: [PATCH 499/835] Added a newer BayesTraits

---
 .../b/BayesTraits/BayesTraits-4.1.2-Linux.eb  | 29 +++++++++++++++++++
 1 file changed, 29 insertions(+)
 create mode 100644 easybuild/easyconfigs/b/BayesTraits/BayesTraits-4.1.2-Linux.eb

diff --git a/easybuild/easyconfigs/b/BayesTraits/BayesTraits-4.1.2-Linux.eb b/easybuild/easyconfigs/b/BayesTraits/BayesTraits-4.1.2-Linux.eb
new file mode 100644
index 00000000000..0ae8355e6e1
--- /dev/null
+++ b/easybuild/easyconfigs/b/BayesTraits/BayesTraits-4.1.2-Linux.eb
@@ -0,0 +1,29 @@
+easyblock = "Tarball"
+
+name = 'BayesTraits'
+version = '4.1.2'
+versionsuffix = '-Linux'
+
+homepage = 'https://www.evolution.reading.ac.uk/SoftwareMain.html'
+description = """ BayesTraits is a computer package for performing analyses of trait 
+ evolution among groups of species for which a phylogeny or sample of phylogenies is 
+ available. This new package incoporates our earlier and separate programes Multistate, 
+ Discrete and Continuous. BayesTraits can be applied to the analysis of traits that adopt 
+ a finite number of discrete states, or to the analysis of continuously varying traits. 
+ Hypotheses can be tested about models of evolution, about ancestral states and about 
+ correlations among pairs of traits. """
+
+toolchain = SYSTEM
+
+source_urls = ['https://www.evolution.reading.ac.uk/BayesTraitsV%(version)s/Files/']
+sources = ['BayesTraitsV%(version)s%(versionsuffix)s.tar.gz']
+checksums = ['d5251c2b256405fc63c55caf8371b267530a3c4ebd11cbfd3ebd4013c9d49db0']
+
+sanity_check_paths = {
+    'files': ['BayesTraitsV4','Artiodactyl.trees','Bird.trees','Mammal.trees','Marsupials.trees','NortheastBantu.trees','Primates.trees'],
+    'dirs': [],
+}
+
+modextrapaths = {'PATH': ''}
+
+moduleclass = 'bio'

From 4ad0b74e5c7be07f9cf5b48cf0d47d453c1c5b2c Mon Sep 17 00:00:00 2001
From: Simon Branford <4967+branfosj@users.noreply.github.com>
Date: Fri, 26 Jul 2024 09:58:01 +0100
Subject: [PATCH 500/835] add mpi4py dep

---
 .../easyconfigs/p/Platypus-Opt/Platypus-Opt-1.2.0-foss-2022b.eb  | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easybuild/easyconfigs/p/Platypus-Opt/Platypus-Opt-1.2.0-foss-2022b.eb b/easybuild/easyconfigs/p/Platypus-Opt/Platypus-Opt-1.2.0-foss-2022b.eb
index b1c5a4f74ea..a0e995d4f45 100644
--- a/easybuild/easyconfigs/p/Platypus-Opt/Platypus-Opt-1.2.0-foss-2022b.eb
+++ b/easybuild/easyconfigs/p/Platypus-Opt/Platypus-Opt-1.2.0-foss-2022b.eb
@@ -15,6 +15,7 @@ checksums = ['f7150de2e24f8003c911259c575493c9351a7dcfb132445a3f3b096728634e6a']
 dependencies = [
     ('Python', '3.10.8'),
     ('SciPy-bundle', '2023.02'),
+    ('mpi4py', '3.1.4'),
 ]
 
 download_dep_fail = True

From 0682e03a9771363a0655c976c04f1a44b1910540 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 26 Jul 2024 15:07:39 +0200
Subject: [PATCH 501/835] adding easyconfigs: chewBBACA-3.3.9-foss-2022b.eb

---
 .../c/chewBBACA/chewBBACA-3.3.9-foss-2022b.eb | 66 +++++++++++++++++++
 1 file changed, 66 insertions(+)
 create mode 100644 easybuild/easyconfigs/c/chewBBACA/chewBBACA-3.3.9-foss-2022b.eb

diff --git a/easybuild/easyconfigs/c/chewBBACA/chewBBACA-3.3.9-foss-2022b.eb b/easybuild/easyconfigs/c/chewBBACA/chewBBACA-3.3.9-foss-2022b.eb
new file mode 100644
index 00000000000..b9964db690a
--- /dev/null
+++ b/easybuild/easyconfigs/c/chewBBACA/chewBBACA-3.3.9-foss-2022b.eb
@@ -0,0 +1,66 @@
+easyblock = 'PythonBundle'
+
+name = 'chewBBACA'
+version = '3.3.9'
+
+homepage = 'https://github.com/B-UMMI/chewBBACA'
+description = """chewBBACA is a software suite for the creation and evaluation of core genome and whole genome 
+MultiLocus Sequence Typing (cg/wgMLST) schemas and results. The "BBACA" stands for "BSR-Based Allele Calling Algorithm".
+BSR stands for BLAST Score Ratio as proposed by Rasko DA et al. The "chew" part adds extra coolness to the name and 
+could be thought of as "Comprehensive and Highly Efficient Workflow"."""
+
+toolchain = {'name': 'foss', 'version': '2022b'}
+
+dependencies = [
+    ('Python', '3.10.8'),
+    ('SciPy-bundle', '2023.02'),
+    # Cython 3 is required, see https://github.com/althonos/pyrodigal/issues/40
+    # Cython included with Python-bundle-PyPI (0.29.35) is too old
+    ('Cython', '3.0.8'),
+    ('Biopython', '1.81'),
+    ('plotly.py', '5.13.1'),
+    ('BLAST+', '2.14.0'),
+    ('prodigal', '2.6.3'),
+    ('MAFFT', '7.505', '-with-extensions'),
+    ('FastTree', '2.1.11'),
+    ('archspec', '0.2.0'),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    ('pyrodigal', '3.5.1', {
+        'checksums': ['20af59a6d968c88910b99d5f647bb7dd22d49e440ead95fe715cdd2c49f36e9f'],
+    }),
+    ('isodate', '0.6.1', {
+        'checksums': ['48c5881de7e8b0a0d648cb024c8062dc84e7b840ed81e864c7614fd3c127bde9'],
+    }),
+    ('rdflib', '7.0.0', {
+        'checksums': ['9995eb8569428059b8c1affd26b25eac510d64f5043d9ce8c84e0d0036e995ae'],
+    }),
+    ('SPARQLWrapper', '2.0.0', {
+        'modulename': 'SPARQLWrapper',
+        'checksums': ['3fed3ebcc77617a4a74d2644b86fd88e0f32e7f7003ac7b2b334c026201731f1'],
+    }),
+    (name, version, {
+        'modulename': 'CHEWBBACA',
+        # relax numpy version requirement
+        'preinstallopts': "sed -i 's/numpy~=1.24.3/numpy~=1.24.2/g' pyproject.toml && ",
+        'runtest': "python setup.py test",
+        'sources': ['%(namelower)s-%(version)s.tar.gz'],
+        'checksums': ['4bf0792b8cdd1783b50340ac713748ef2a351209cacb50ad4c9e2fe2e7fba772'],
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['bin/chewBBACA.py', 'bin/chewie'],
+    'dirs': [],
+}
+
+sanity_check_commands = [
+    'chewBBACA.py --help',
+    'chewie --help',
+]
+
+moduleclass = 'bio'

From 1c47eb36cf85e5a0f0f0ba4dc16cf01832f9609e Mon Sep 17 00:00:00 2001
From: Samuel Moors <samuel.moors@vub.be>
Date: Fri, 26 Jul 2024 15:36:08 +0200
Subject: [PATCH 502/835] adding easyconfigs: ORCA-6.0.0-gompi-2023a.eb

---
 .../o/ORCA/ORCA-6.0.0-gompi-2023a.eb          | 23 +++++++++++++++++++
 1 file changed, 23 insertions(+)
 create mode 100644 easybuild/easyconfigs/o/ORCA/ORCA-6.0.0-gompi-2023a.eb

diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-6.0.0-gompi-2023a.eb b/easybuild/easyconfigs/o/ORCA/ORCA-6.0.0-gompi-2023a.eb
new file mode 100644
index 00000000000..8bf88fa8129
--- /dev/null
+++ b/easybuild/easyconfigs/o/ORCA/ORCA-6.0.0-gompi-2023a.eb
@@ -0,0 +1,23 @@
+name = 'ORCA'
+version = '6.0.0'
+
+homepage = 'https://orcaforum.kofo.mpg.de'
+description = """
+ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum
+chemistry with specific emphasis on spectroscopic properties of open-shell
+molecules. It features a wide variety of standard quantum chemical methods
+ranging from semiempirical methods to DFT to single- and multireference
+correlated ab initio methods. It can also treat environmental and relativistic
+effects."""
+
+toolchain = {'name': 'gompi', 'version': '2023a'}
+
+download_instructions = "Shared build of ORCA: download from https://orcaforum.kofo.mpg.de"
+# mostly dynamically linked (SCALAPACK, OpenBLAS are still embedded)
+sources = ['%%(namelower)s_%s_linux_%%(orcaarch)s_shared_openmpi416.tar.xz' % version.replace('.', '_')]
+checksums = [
+    # orca_6_0_0_linux_x86-64_shared_openmpi416.tar.xz
+    '219bd1deb6d64a63cb72471926cb81665cbbcdec19f9c9549761be67d49a29c6',
+]
+
+moduleclass = 'chem'

From b9fd6b88fdb5d641b5aa501bf0e6dd97596008ff Mon Sep 17 00:00:00 2001
From: Alexander Salois <alexander.salois@montana.edu>
Date: Fri, 26 Jul 2024 09:11:16 -0600
Subject: [PATCH 503/835] Ran --check-contrib

Found some code style issues. They have now been fixed and
`--check-contrib` passes
---
 easybuild/easyconfigs/b/BayesTraits/BayesTraits-4.1.2-Linux.eb | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/b/BayesTraits/BayesTraits-4.1.2-Linux.eb b/easybuild/easyconfigs/b/BayesTraits/BayesTraits-4.1.2-Linux.eb
index 0ae8355e6e1..b07ea0bb7a1 100644
--- a/easybuild/easyconfigs/b/BayesTraits/BayesTraits-4.1.2-Linux.eb
+++ b/easybuild/easyconfigs/b/BayesTraits/BayesTraits-4.1.2-Linux.eb
@@ -20,7 +20,8 @@ sources = ['BayesTraitsV%(version)s%(versionsuffix)s.tar.gz']
 checksums = ['d5251c2b256405fc63c55caf8371b267530a3c4ebd11cbfd3ebd4013c9d49db0']
 
 sanity_check_paths = {
-    'files': ['BayesTraitsV4','Artiodactyl.trees','Bird.trees','Mammal.trees','Marsupials.trees','NortheastBantu.trees','Primates.trees'],
+    'files': ['BayesTraitsV4', 'Artiodactyl.trees', 'Bird.trees', 'Mammal.trees',
+              'Marsupials.trees', 'NortheastBantu.trees', 'Primates.trees'],
     'dirs': [],
 }
 

From 02f083f5306edfa2e2476a6e917dc55ee24393b2 Mon Sep 17 00:00:00 2001
From: Sebastian Achilles <s.achilles@fz-juelich.de>
Date: Sun, 28 Jul 2024 09:27:27 +0200
Subject: [PATCH 504/835] adding easyconfigs: elfutils-0.191-GCCcore-13.3.0.eb,
 libdwarf-0.10.1-GCCcore-13.3.0.eb

---
 .../elfutils/elfutils-0.191-GCCcore-13.3.0.eb | 41 +++++++++++++++++++
 .../libdwarf-0.10.1-GCCcore-13.3.0.eb         | 33 +++++++++++++++
 2 files changed, 74 insertions(+)
 create mode 100644 easybuild/easyconfigs/e/elfutils/elfutils-0.191-GCCcore-13.3.0.eb
 create mode 100644 easybuild/easyconfigs/l/libdwarf/libdwarf-0.10.1-GCCcore-13.3.0.eb

diff --git a/easybuild/easyconfigs/e/elfutils/elfutils-0.191-GCCcore-13.3.0.eb b/easybuild/easyconfigs/e/elfutils/elfutils-0.191-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..e5eb4ef3c7d
--- /dev/null
+++ b/easybuild/easyconfigs/e/elfutils/elfutils-0.191-GCCcore-13.3.0.eb
@@ -0,0 +1,41 @@
+easyblock = 'ConfigureMake'
+
+name = 'elfutils'
+version = '0.191'
+
+homepage = 'https://elfutils.org/'
+
+description = """
+ The elfutils project provides libraries and tools for ELF files
+ and DWARF data.
+"""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+source_urls = ['https://sourceware.org/elfutils/ftp/%(version)s/']
+sources = [SOURCE_TAR_BZ2]
+checksums = ['df76db71366d1d708365fc7a6c60ca48398f14367eb2b8954efc8897147ad871']
+
+builddependencies = [
+    ('M4', '1.4.19'),
+    ('pkgconf', '2.2.0'),
+]
+
+dependencies = [
+    ('binutils', '2.42'),
+    ('bzip2', '1.0.8'),
+    ('libarchive', '3.7.4'),
+    ('XZ', '5.4.5'),
+    ('zstd', '1.5.6'),
+]
+
+configopts = "--disable-debuginfod --disable-libdebuginfod"
+
+sanity_check_paths = {
+    'files': ['bin/eu-elfcmp', 'include/dwarf.h', 'lib/libelf.%s' % SHLIB_EXT],
+    'dirs': []
+}
+
+sanity_check_commands = ["eu-elfcmp --help"]
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/l/libdwarf/libdwarf-0.10.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libdwarf/libdwarf-0.10.1-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..95a46c43114
--- /dev/null
+++ b/easybuild/easyconfigs/l/libdwarf/libdwarf-0.10.1-GCCcore-13.3.0.eb
@@ -0,0 +1,33 @@
+easyblock = 'ConfigureMake'
+
+name = 'libdwarf'
+version = '0.10.1'
+
+homepage = 'https://www.prevanders.net/dwarf.html'
+description = """The DWARF Debugging Information Format is of interest to programmers working on compilers
+and debuggers (and anyone interested in reading or writing DWARF information))"""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://github.com/davea42/libdwarf-code/releases/download/v%(version)s']
+sources = [SOURCE_TAR_XZ]
+checksums = ['b511a2dc78b98786064889deaa2c1bc48a0c70115c187900dd838474ded1cc19']
+
+builddependencies = [
+    ('binutils', '2.42'),
+]
+dependencies = [
+    ('elfutils', '0.191'),
+]
+
+configopts = "--enable-shared "
+
+sanity_check_paths = {
+    'files': ['bin/dwarfdump', 'lib/libdwarf.a', 'lib/libdwarf.%s' % SHLIB_EXT],
+    'dirs': ['include']
+}
+
+sanity_check_commands = ['dwarfdump --help']
+
+moduleclass = 'devel'

From 6ecba6a0c33d1398671b9702b7b0180df5083a5a Mon Sep 17 00:00:00 2001
From: Sebastian Achilles <s.achilles@fz-juelich.de>
Date: Sun, 28 Jul 2024 09:38:25 +0200
Subject: [PATCH 505/835] adding easyconfigs: gc-8.2.6-GCCcore-13.3.0.eb,
 libunistring-1.2-GCCcore-13.3.0.eb, Guile-3.0.10-GCCcore-13.3.0.eb

---
 .../g/Guile/Guile-3.0.10-GCCcore-13.3.0.eb    | 46 +++++++++++++++++++
 .../g/gc/gc-8.2.6-GCCcore-13.3.0.eb           | 42 +++++++++++++++++
 .../libunistring-1.2-GCCcore-13.3.0.eb        | 35 ++++++++++++++
 3 files changed, 123 insertions(+)
 create mode 100644 easybuild/easyconfigs/g/Guile/Guile-3.0.10-GCCcore-13.3.0.eb
 create mode 100644 easybuild/easyconfigs/g/gc/gc-8.2.6-GCCcore-13.3.0.eb
 create mode 100644 easybuild/easyconfigs/l/libunistring/libunistring-1.2-GCCcore-13.3.0.eb

diff --git a/easybuild/easyconfigs/g/Guile/Guile-3.0.10-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/Guile/Guile-3.0.10-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..46917679856
--- /dev/null
+++ b/easybuild/easyconfigs/g/Guile/Guile-3.0.10-GCCcore-13.3.0.eb
@@ -0,0 +1,46 @@
+easyblock = 'ConfigureMake'
+
+name = 'Guile'
+version = '3.0.10'
+
+homepage = 'https://www.gnu.org/software/guile/'
+
+description = """
+ Guile is a programming language, designed to help programmers create flexible
+ applications that can be extended by users or other programmers with plug-ins,
+ modules, or scripts.
+"""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+toolchainopts = {'pic': True}
+
+source_urls = [GNU_SOURCE]
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['2dbdbc97598b2faf31013564efb48e4fed44131d28e996c26abe8a5b23b56c2a']
+
+builddependencies = [
+    ('Autotools', '20231222'),
+    ('binutils', '2.42'),
+    ('pkgconf', '2.2.0'),
+]
+
+dependencies = [
+    ('gc', '8.2.6'),
+    ('GMP', '6.3.0'),
+    ('libffi', '3.4.5'),
+    ('libunistring', '1.2'),
+]
+
+postinstallcmds = ["cd %(installdir)s/bin && ln -s guile guile%(version_major)s"]
+
+sanity_check_paths = {
+    'files': ['bin/guild', 'bin/guile', 'bin/guile-config',
+              'bin/guile-snarf', 'bin/guile-tools',
+              'include/guile/%(version_major_minor)s/libguile.h',
+              'lib/libguile-%(version_major_minor)s.a',
+              'lib/libguile-%%(version_major_minor)s.%s' % SHLIB_EXT],
+    'dirs': ['include/guile/%(version_major_minor)s/libguile',
+             'lib/guile/%(version_major_minor)s/ccache'],
+}
+
+moduleclass = 'lang'
diff --git a/easybuild/easyconfigs/g/gc/gc-8.2.6-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/gc/gc-8.2.6-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..3a120e6a4e9
--- /dev/null
+++ b/easybuild/easyconfigs/g/gc/gc-8.2.6-GCCcore-13.3.0.eb
@@ -0,0 +1,42 @@
+easyblock = 'ConfigureMake'
+
+name = 'gc'
+version = '8.2.6'
+local_libatomic_version = '7.8.2'
+
+homepage = 'https://hboehm.info/gc/'
+description = """The Boehm-Demers-Weiser conservative garbage collector can be used as a
+garbage collecting replacement for C malloc or C++ new.
+"""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+source_urls = [
+    'https://github.com/ivmai/bdwgc/releases/download/v%(version)s/',  # preferred for gc-%(version)s.tar.gz
+    'https://hboehm.info/gc/gc_source/',  # alternate for gc-%(version)s.tar.gz
+    'https://github.com/ivmai/libatomic_ops/releases/download/v%s/' % local_libatomic_version,
+]
+sources = [
+    SOURCE_TAR_GZ,
+    'libatomic_ops-%s.tar.gz' % local_libatomic_version,
+]
+checksums = [
+    {'gc-8.2.6.tar.gz': 'b9183fe49d4c44c7327992f626f8eaa1d8b14de140f243edb1c9dcff7719a7fc'},
+    {'libatomic_ops-7.8.2.tar.gz': 'd305207fe207f2b3fb5cb4c019da12b44ce3fcbc593dfd5080d867b1a2419b51'},
+]
+
+builddependencies = [
+    ('binutils', '2.42'),
+]
+
+preconfigopts = 'ln -s %(builddir)s/libatomic_ops*/ libatomic_ops && '
+
+configopts = "--enable-static"
+
+sanity_check_paths = {
+    'files': ['include/gc.h', 'lib/libcord.a', 'lib/libcord.%s' % SHLIB_EXT,
+              'lib/libgc.a', 'lib/libgc.%s' % SHLIB_EXT],
+    'dirs': ['include/gc', 'share'],
+}
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/l/libunistring/libunistring-1.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libunistring/libunistring-1.2-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..7fa2f46eb1f
--- /dev/null
+++ b/easybuild/easyconfigs/l/libunistring/libunistring-1.2-GCCcore-13.3.0.eb
@@ -0,0 +1,35 @@
+easyblock = 'ConfigureMake'
+
+name = 'libunistring'
+version = '1.2'
+
+homepage = 'https://www.gnu.org/software/libunistring/'
+
+description = """This library provides functions for manipulating Unicode strings and for
+ manipulating C strings according to the Unicode standard."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+toolchainopts = {'pic': True}
+
+source_urls = [GNU_SOURCE]
+sources = [SOURCELOWER_TAR_XZ]
+checksums = ['632bd65ed74a881ca8a0309a1001c428bd1cbd5cd7ddbf8cedcd2e65f4dcdc44']
+
+builddependencies = [
+    ('binutils', '2.42'),
+]
+
+dependencies = [
+    ('libiconv', '1.17'),
+]
+
+parallel = 1
+
+sanity_check_paths = {
+    'files': ['lib/libunistring.a', 'lib/libunistring.%s' % SHLIB_EXT] +
+             ['include/uni%s.h' % x for x in ['case', 'conv', 'ctype', 'lbrk', 'name', 'norm',
+                                              'stdio', 'str', 'types', 'wbrk', 'width']],
+    'dirs': ['include/unistring'],
+}
+
+moduleclass = 'lib'

From db2c50c022387ca7dbe9ffd8b685b372b6811ae4 Mon Sep 17 00:00:00 2001
From: Sebastian Achilles <s.achilles@fz-juelich.de>
Date: Sun, 28 Jul 2024 09:48:24 +0200
Subject: [PATCH 506/835] adding easyconfigs:
 BeautifulSoup-4.12.3-GCCcore-13.3.0.eb

---
 .../BeautifulSoup-4.12.3-GCCcore-13.3.0.eb    | 35 +++++++++++++++++++
 1 file changed, 35 insertions(+)
 create mode 100644 easybuild/easyconfigs/b/BeautifulSoup/BeautifulSoup-4.12.3-GCCcore-13.3.0.eb

diff --git a/easybuild/easyconfigs/b/BeautifulSoup/BeautifulSoup-4.12.3-GCCcore-13.3.0.eb b/easybuild/easyconfigs/b/BeautifulSoup/BeautifulSoup-4.12.3-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..95cb6cf3228
--- /dev/null
+++ b/easybuild/easyconfigs/b/BeautifulSoup/BeautifulSoup-4.12.3-GCCcore-13.3.0.eb
@@ -0,0 +1,35 @@
+easyblock = 'PythonBundle'
+
+name = 'BeautifulSoup'
+version = '4.12.3'
+
+homepage = 'https://www.crummy.com/software/BeautifulSoup'
+description = "Beautiful Soup is a Python library designed for quick turnaround projects like screen-scraping."
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+builddependencies = [
+    ('binutils', '2.42'),
+    ('hatchling', '1.24.2'),
+]
+
+dependencies = [
+    ('Python', '3.12.3'),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    ('soupsieve', '2.5', {
+        'checksums': ['5663d5a7b3bfaeee0bc4372e7fc48f9cff4940b3eec54a6451cc5299f1097690'],
+    }),
+    (name, version, {
+        'modulename': 'bs4',
+        'source_tmpl': 'beautifulsoup4-%(version)s.tar.gz',
+        'source_urls': ['https://pypi.python.org/packages/source/b/beautifulsoup4'],
+        'checksums': ['74e3d1928edc070d21748185c46e3fb33490f22f52a3addee9aee0f4f7781051'],
+    }),
+]
+
+moduleclass = 'data'

From 272df972c32870f1c1861bfbbe792fd2dc76cdcd Mon Sep 17 00:00:00 2001
From: tanmoy1989 <mssmzs@login01.avon.hpc>
Date: Mon, 29 Jul 2024 10:55:37 +0100
Subject: [PATCH 507/835] adding easyconfigs: spglib-python-2.5.0-gfbf-2023b.eb

---
 .../spglib-python-2.5.0-gfbf-2023b.eb         | 40 +++++++++++++++++++
 1 file changed, 40 insertions(+)
 create mode 100644 easybuild/easyconfigs/s/spglib-python/spglib-python-2.5.0-gfbf-2023b.eb

diff --git a/easybuild/easyconfigs/s/spglib-python/spglib-python-2.5.0-gfbf-2023b.eb b/easybuild/easyconfigs/s/spglib-python/spglib-python-2.5.0-gfbf-2023b.eb
new file mode 100644
index 00000000000..5893038d9fd
--- /dev/null
+++ b/easybuild/easyconfigs/s/spglib-python/spglib-python-2.5.0-gfbf-2023b.eb
@@ -0,0 +1,40 @@
+easyblock = 'PythonBundle'
+
+name = 'spglib-python'
+version = '2.5.0'
+
+homepage = 'https://pypi.python.org/pypi/spglib'
+description = """Spglib for Python.
+
+Spglib is a library for finding and handling crystal symmetries written in C.
+"""
+
+toolchain = {'name': 'gfbf', 'version': '2023b'}
+
+builddependencies = [
+    ('scikit-build-core', '0.9.3')
+]
+
+dependencies = [
+    ('Python', '3.11.5'),
+    ('Python-bundle-PyPI', '2023.10'),
+    ('SciPy-bundle', '2023.11'),
+]
+
+use_pip = True
+
+sanity_pip_check = True
+
+exts_list = [
+    ('pyproject_metadata', '0.8.0', {
+        'checksums': ['376d5a00764ac29440a54579f88e66b7d9cb7e629d35c35a1c7248bfebc9b455'],
+    }),
+    (name, version, {
+        'modulename': 'spglib',
+        'source_urls': ['https://pypi.python.org/packages/source/%(nameletter)s/spglib'],
+        'sources': ['spglib-%(version)s.tar.gz'],
+        'checksums': ['f8bb638897be91b9dbd4c085d9fde1f69048f5949e20f3832cb9438e57418d4b'],
+    }),
+]
+
+moduleclass = 'chem'

From 6fbdc20fb5b80b97e37081171b72b29a3503a938 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Mon, 29 Jul 2024 12:24:45 +0200
Subject: [PATCH 508/835] adding easyconfigs:
 flash-attention-2.6.3-foss-2023a-CUDA-12.1.1.eb

---
 ...-attention-2.6.3-foss-2023a-CUDA-12.1.1.eb | 37 +++++++++++++++++++
 1 file changed, 37 insertions(+)
 create mode 100644 easybuild/easyconfigs/f/flash-attention/flash-attention-2.6.3-foss-2023a-CUDA-12.1.1.eb

diff --git a/easybuild/easyconfigs/f/flash-attention/flash-attention-2.6.3-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/f/flash-attention/flash-attention-2.6.3-foss-2023a-CUDA-12.1.1.eb
new file mode 100644
index 00000000000..0ef79545ba0
--- /dev/null
+++ b/easybuild/easyconfigs/f/flash-attention/flash-attention-2.6.3-foss-2023a-CUDA-12.1.1.eb
@@ -0,0 +1,37 @@
+easyblock = 'PythonBundle'
+
+name = 'flash-attention'
+version = '2.6.3'
+versionsuffix = '-CUDA-%(cudaver)s'
+
+homepage = 'https://github.com/Dao-AILab/flash-attention'
+description = """Fast and memory-efficient exact attention."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+builddependencies = [('Ninja', '1.11.1')]
+dependencies = [
+    ('Python', '3.11.3'),
+    ('Python-bundle-PyPI', '2023.06'),
+    ('CUDA', '12.1.1', '', SYSTEM),
+    ('PyTorch-bundle', '2.1.2', versionsuffix),
+    ('einops', '0.7.0'),
+]
+
+sanity_pip_check = True
+use_pip = True
+
+exts_list = [
+    (name, version, {
+        'modulename': 'flash_attn',
+        'source_urls': ['https://github.com/Dao-AILab/flash-attention/archive/'],
+        'sources': ['v%(version)s.tar.gz'],
+        'checksums': ['136e149165d4c8c67273d16daa957b5cd5e6fc629061ffd39fa5a25224454d6c'],
+    }),
+]
+
+sanity_check_commands = [
+    "python -c 'from flash_attn import flash_attn_qkvpacked_func, flash_attn_func'",
+]
+
+moduleclass = 'lib'

From 685f34d47e1e3f051879830e549db7f63eb142c0 Mon Sep 17 00:00:00 2001
From: Thomas Roeblitz <thomas.roblitz@uib.no>
Date: Mon, 29 Jul 2024 13:02:08 +0200
Subject: [PATCH 509/835] Describe patch to fix failing test on Zen4

---
 .../h/Highway/Highway-1.0.4-GCCcore-12.3.0.eb     |  2 +-
 .../Highway-1.0.4-zen4-fix-TruncateTo-bug.patch   | 15 +++++++++++++++
 2 files changed, 16 insertions(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/h/Highway/Highway-1.0.4-GCCcore-12.3.0.eb b/easybuild/easyconfigs/h/Highway/Highway-1.0.4-GCCcore-12.3.0.eb
index 824460d1be2..993087b828c 100644
--- a/easybuild/easyconfigs/h/Highway/Highway-1.0.4-GCCcore-12.3.0.eb
+++ b/easybuild/easyconfigs/h/Highway/Highway-1.0.4-GCCcore-12.3.0.eb
@@ -17,7 +17,7 @@ patches = ['Highway-1.0.4-zen4-fix-TruncateTo-bug.patch']
 checksums = [
     {'1.0.4.tar.gz': 'faccd343935c9e98afd1016e9d20e0b8b89d908508d1af958496f8c2d3004ac2'},
     {'Highway-1.0.4-zen4-fix-TruncateTo-bug.patch':
-     '7eb68cfa702648f8f82fe3b7bdc5f0f0ab171840f966040f6d8ec470e3eed712'},
+     'e571413c290076a729dbb1df105a4bfa106099238d1b438e74a9dfc9557eb4a2'},
 ]
 
 builddependencies = [
diff --git a/easybuild/easyconfigs/h/Highway/Highway-1.0.4-zen4-fix-TruncateTo-bug.patch b/easybuild/easyconfigs/h/Highway/Highway-1.0.4-zen4-fix-TruncateTo-bug.patch
index b4e71737d22..f489a6bd15f 100644
--- a/easybuild/easyconfigs/h/Highway/Highway-1.0.4-zen4-fix-TruncateTo-bug.patch
+++ b/easybuild/easyconfigs/h/Highway/Highway-1.0.4-zen4-fix-TruncateTo-bug.patch
@@ -1,3 +1,18 @@
+A single test failed when building on AMD Genoa a.k.a Zen4 with the error message
+reported in https://github.com/google/highway/issues/1913
+
+Building v1.0.5 passed all tests. Hence, this patch uses some of the changes made
+in v1.0.5 to let the single failing test succeed.
+
+Looking at the PRs added by v1.0.5 a promising candidate was identified
+(https://github.com/google/highway/pull/1276) and all changed files in the PR
+were "studied in detail" (assessed if the changes could be related to the failing
+test on Zen4). Luckily, the four changes provided in the patch below were
+found to resolve the issue. It was also tested if a subset of these four changes
+would resolve the issue, but this did not succeed.
+
+Author: Thomas Roeblitz (University of Bergen)
+
 diff --git a/hwy/ops/x86_256-inl.h b/hwy/ops/x86_256-inl.h
 index 4e2e83e8..2fbf99c7 100644
 --- a/hwy/ops/x86_256-inl.h

From 988d69ad55c8496712729680d0226a1b2add844d Mon Sep 17 00:00:00 2001
From: casparl <casparl@gcn77.local.snellius.surf.nl>
Date: Mon, 29 Jul 2024 13:30:56 +0200
Subject: [PATCH 510/835] Include patch to make things work for multiple cuda
 compute capabilities

---
 ...UDA-Samples-11.3-GCC-10.3.0-CUDA-11.3.1.eb |  1 +
 ...UDA-Samples-11.6-GCC-11.3.0-CUDA-11.7.0.eb |  1 +
 ...UDA-Samples-11.8-GCC-11.3.0-CUDA-11.7.0.eb |  1 +
 ...UDA-Samples-12.1-GCC-12.3.0-CUDA-12.1.1.eb |  1 +
 ...UDA-Samples-12.2-GCC-11.3.0-CUDA-12.2.0.eb |  1 +
 .../cuda-samples-11.X_multiple-sms.patch      | 31 ++++++++++
 .../cuda-samples-12.X_multiple-sms.patch      | 56 +++++++++++++++++++
 7 files changed, 92 insertions(+)
 create mode 100644 easybuild/easyconfigs/c/CUDA-Samples/cuda-samples-11.X_multiple-sms.patch
 create mode 100644 easybuild/easyconfigs/c/CUDA-Samples/cuda-samples-12.X_multiple-sms.patch

diff --git a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.3-GCC-10.3.0-CUDA-11.3.1.eb b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.3-GCC-10.3.0-CUDA-11.3.1.eb
index 31d65369f80..31db9bd5579 100644
--- a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.3-GCC-10.3.0-CUDA-11.3.1.eb
+++ b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.3-GCC-10.3.0-CUDA-11.3.1.eb
@@ -11,6 +11,7 @@ toolchain = {'name': 'GCC', 'version': '10.3.0'}
 
 source_urls = ['https://github.com/NVIDIA/cuda-samples/archive/']
 sources = ['v%(version)s.tar.gz']
+patches = ['cuda-samples-11.X_multiple-sms.patch']
 checksums = ['2bee5f7c89347259aaab75aa6df6e10375059bdbbaf04cc7936f5db7d54fa3ac']
 
 dependencies = [
diff --git a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.6-GCC-11.3.0-CUDA-11.7.0.eb b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.6-GCC-11.3.0-CUDA-11.7.0.eb
index 8e3cbc72ee2..1cb33c8ed72 100644
--- a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.6-GCC-11.3.0-CUDA-11.7.0.eb
+++ b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.6-GCC-11.3.0-CUDA-11.7.0.eb
@@ -11,6 +11,7 @@ toolchain = {'name': 'GCC', 'version': '11.3.0'}
 
 source_urls = ['https://github.com/NVIDIA/cuda-samples/archive/']
 sources = ['v%(version)s.tar.gz']
+patches = ['cuda-samples-11.X_multiple-sms.patch']
 checksums = ['75b858bcf9e534eaa0f129c418e661b83872d743de218df8a5278cc429f9ea98']
 
 dependencies = [
diff --git a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.8-GCC-11.3.0-CUDA-11.7.0.eb b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.8-GCC-11.3.0-CUDA-11.7.0.eb
index 27df4a0986e..4dc6f0f47d1 100644
--- a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.8-GCC-11.3.0-CUDA-11.7.0.eb
+++ b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.8-GCC-11.3.0-CUDA-11.7.0.eb
@@ -11,6 +11,7 @@ toolchain = {'name': 'GCC', 'version': '11.3.0'}
 
 source_urls = ['https://github.com/NVIDIA/cuda-samples/archive/']
 sources = ['v%(version)s.tar.gz']
+patches = ['cuda-samples-11.X_multiple-sms.patch']
 checksums = ['1bc02c0ca42a323f3c7a05b5682eae703681a91e95b135bfe81f848b2d6a2c51']
 
 dependencies = [
diff --git a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-12.1-GCC-12.3.0-CUDA-12.1.1.eb b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-12.1-GCC-12.3.0-CUDA-12.1.1.eb
index 3444ef46f27..1f2d76136f1 100644
--- a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-12.1-GCC-12.3.0-CUDA-12.1.1.eb
+++ b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-12.1-GCC-12.3.0-CUDA-12.1.1.eb
@@ -11,6 +11,7 @@ toolchain = {'name': 'GCC', 'version': '12.3.0'}
 
 source_urls = ['https://github.com/NVIDIA/cuda-samples/archive/']
 sources = ['v%(version)s.tar.gz']
+patches = ['cuda-samples-12.X_multiple-sms.patch']
 checksums = ['f758160645b366d79c2638d8dfd389f01029b8d179ab0c11726b9ef58aecebd9']
 
 dependencies = [
diff --git a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-12.2-GCC-11.3.0-CUDA-12.2.0.eb b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-12.2-GCC-11.3.0-CUDA-12.2.0.eb
index c69748cec08..1f3f081ad15 100644
--- a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-12.2-GCC-11.3.0-CUDA-12.2.0.eb
+++ b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-12.2-GCC-11.3.0-CUDA-12.2.0.eb
@@ -11,6 +11,7 @@ toolchain = {'name': 'GCC', 'version': '11.3.0'}
 
 source_urls = ['https://github.com/NVIDIA/cuda-samples/archive/']
 sources = ['v%(version)s.tar.gz']
+patches = ['cuda-samples-12.X_multiple-sms.patch']
 checksums = ['c9fbdee420fd4567edb1239420e2a5c93d9652b4ccf3a828fcb3e0de3152e466']
 
 builddependencies = [
diff --git a/easybuild/easyconfigs/c/CUDA-Samples/cuda-samples-11.X_multiple-sms.patch b/easybuild/easyconfigs/c/CUDA-Samples/cuda-samples-11.X_multiple-sms.patch
new file mode 100644
index 00000000000..b6613f6a3c4
--- /dev/null
+++ b/easybuild/easyconfigs/c/CUDA-Samples/cuda-samples-11.X_multiple-sms.patch
@@ -0,0 +1,31 @@
+# Fixes "nvcc fatal: Option '--ptx (-ptx)' is not allowed when compiling for multiple GPU architectures"
+# fatal compilation issue when building for multiple SM architectures
+# More info, see https://github.com/NVIDIA/cuda-samples/issues/289
+
+# Author: Caspar van Leeuwen
+
+diff -Nru cuda-samples-11.3.orig/Samples/memMapIPCDrv/Makefile cuda-samples-11.3/Samples/memMapIPCDrv/Makefile
+--- cuda-samples-11.3.orig/Samples/memMapIPCDrv/Makefile	2024-07-29 13:17:10.330743000 +0200
++++ cuda-samples-11.3/Samples/memMapIPCDrv/Makefile	2024-07-29 13:19:13.158507504 +0200
+@@ -321,6 +321,12 @@
+ ifneq ($(HIGHEST_SM),)
+ GENCODE_FLAGS += -gencode arch=compute_$(HIGHEST_SM),code=compute_$(HIGHEST_SM)
+ endif
++
++# Generate the explicit PTX file for the lowest SM architecture in $(SMS), so it works on all SMS listed there
++LOWEST_SM := $(firstword $(sort $(SMS)))
++ifneq ($(LOWEST_SM),)
++GENCODE_FLAGS_LOWEST_SM += -gencode arch=compute_$(LOWEST_SM),code=compute_$(LOWEST_SM)
++endif
+ endif
+ 
+ ifeq ($(TARGET_OS),darwin)
+@@ -401,7 +407,7 @@
+ endif
+ 
+ $(PTX_FILE): memMapIpc_kernel.cu
+-	$(EXEC) $(NVCC) $(INCLUDES) $(ALL_CCFLAGS) $(GENCODE_FLAGS) -o $@ -ptx $<
++	$(EXEC) $(NVCC) $(INCLUDES) $(ALL_CCFLAGS) $(GENCODE_FLAGS_LOWEST_SM) -o $@ -ptx $<
+ 	$(EXEC) mkdir -p data
+ 	$(EXEC) cp -f $@ ./data
+ 	$(EXEC) mkdir -p ../../bin/$(TARGET_ARCH)/$(TARGET_OS)/$(BUILD_TYPE)
diff --git a/easybuild/easyconfigs/c/CUDA-Samples/cuda-samples-12.X_multiple-sms.patch b/easybuild/easyconfigs/c/CUDA-Samples/cuda-samples-12.X_multiple-sms.patch
new file mode 100644
index 00000000000..8c4e36f7e74
--- /dev/null
+++ b/easybuild/easyconfigs/c/CUDA-Samples/cuda-samples-12.X_multiple-sms.patch
@@ -0,0 +1,56 @@
+# Fixes "nvcc fatal: Option '--ptx (-ptx)' is not allowed when compiling for multiple GPU architectures"
+# fatal compilation issue when building for multiple SM architectures
+# More info, see https://github.com/NVIDIA/cuda-samples/issues/289
+
+# Author: Caspar van Leeuwen
+
+diff -Nru cuda-samples-12.2.orig/Samples/3_CUDA_Features/memMapIPCDrv/Makefile cuda-samples-12.2/Samples/3_CUDA_Features/memMapIPCDrv/Makefile
+--- cuda-samples-12.2.orig/Samples/3_CUDA_Features/memMapIPCDrv/Makefile	2024-07-29 12:14:28.538848000 +0200
++++ cuda-samples-12.2/Samples/3_CUDA_Features/memMapIPCDrv/Makefile	2024-07-29 13:02:45.134261829 +0200
+@@ -313,6 +313,12 @@
+ ifneq ($(HIGHEST_SM),)
+ GENCODE_FLAGS += -gencode arch=compute_$(HIGHEST_SM),code=compute_$(HIGHEST_SM)
+ endif
++
++# Generate the explicit PTX file for the lowest SM architecture in $(SMS), so it works on all SMS listed there
++LOWEST_SM := $(firstword $(sort $(SMS)))
++ifneq ($(LOWEST_SM),)
++GENCODE_FLAGS_LOWEST_SM += -gencode arch=compute_$(LOWEST_SM),code=compute_$(LOWEST_SM)
++endif
+ endif
+ 
+ ifeq ($(TARGET_OS),darwin)
+@@ -394,7 +400,7 @@
+ endif
+ 
+ $(PTX_FILE): memMapIpc_kernel.cu
+-	$(EXEC) $(NVCC) $(INCLUDES) $(ALL_CCFLAGS) $(GENCODE_FLAGS) -o $@ -ptx $<
++	$(EXEC) $(NVCC) $(INCLUDES) $(ALL_CCFLAGS) $(GENCODE_FLAGS_LOWEST_SM) -o $@ -ptx $<
+ 	$(EXEC) mkdir -p data
+ 	$(EXEC) cp -f $@ ./data
+ 	$(EXEC) mkdir -p ../../../bin/$(TARGET_ARCH)/$(TARGET_OS)/$(BUILD_TYPE)
+diff -Nru cuda-samples-12.2.orig/Samples/3_CUDA_Features/ptxjit/Makefile cuda-samples-12.2/Samples/3_CUDA_Features/ptxjit/Makefile
+--- cuda-samples-12.2.orig/Samples/3_CUDA_Features/ptxjit/Makefile	2024-07-29 12:14:28.546771000 +0200
++++ cuda-samples-12.2/Samples/3_CUDA_Features/ptxjit/Makefile	2024-07-29 13:02:38.741961008 +0200
+@@ -307,6 +307,12 @@
+ ifneq ($(HIGHEST_SM),)
+ GENCODE_FLAGS += -gencode arch=compute_$(HIGHEST_SM),code=compute_$(HIGHEST_SM)
+ endif
++
++# Generate the explicit PTX file for the lowest SM architecture in $(SMS), so it works on all SMS listed there
++LOWEST_SM := $(firstword $(sort $(SMS)))
++ifneq ($(LOWEST_SM),)
++GENCODE_FLAGS_LOWEST_SM += -gencode arch=compute_$(LOWEST_SM),code=compute_$(LOWEST_SM)
++endif
+ endif
+ 
+ ifeq ($(TARGET_OS),darwin)
+@@ -390,7 +396,7 @@
+ endif
+ 
+ $(PTX_FILE): ptxjit_kernel.cu
+-	$(EXEC) $(NVCC) $(INCLUDES) $(ALL_CCFLAGS) $(GENCODE_FLAGS) -o $@ -ptx $<
++	$(EXEC) $(NVCC) $(INCLUDES) $(ALL_CCFLAGS) $(GENCODE_FLAGS_LOWEST_SM) -o $@ -ptx $<
+ 	$(EXEC) mkdir -p data
+ 	$(EXEC) cp -f $@ ./data
+ 	$(EXEC) mkdir -p ../../../bin/$(TARGET_ARCH)/$(TARGET_OS)/$(BUILD_TYPE)

From 238ce2cf062cbd9d63a3f4566f79ab5de9380541 Mon Sep 17 00:00:00 2001
From: casparl <casparl@gcn77.local.snellius.surf.nl>
Date: Mon, 29 Jul 2024 14:33:52 +0200
Subject: [PATCH 511/835] Fix which patch to apply where... the filestructure
 was restructured in the CUDA sources starting at 11.6

---
 ...UDA-Samples-11.3-GCC-10.3.0-CUDA-11.3.1.eb |  2 +-
 ...UDA-Samples-11.6-GCC-11.3.0-CUDA-11.7.0.eb |  2 +-
 ...UDA-Samples-11.8-GCC-11.3.0-CUDA-11.7.0.eb |  2 +-
 ...UDA-Samples-12.1-GCC-12.3.0-CUDA-12.1.1.eb |  2 +-
 ...UDA-Samples-12.2-GCC-11.3.0-CUDA-12.2.0.eb |  2 +-
 .../cuda-samples-11.3_multiple-sms.patch      | 31 ++++++++++
 .../cuda-samples-11.6_multiple-sms.patch      | 56 +++++++++++++++++++
 7 files changed, 92 insertions(+), 5 deletions(-)
 create mode 100644 easybuild/easyconfigs/c/CUDA-Samples/cuda-samples-11.3_multiple-sms.patch
 create mode 100644 easybuild/easyconfigs/c/CUDA-Samples/cuda-samples-11.6_multiple-sms.patch

diff --git a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.3-GCC-10.3.0-CUDA-11.3.1.eb b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.3-GCC-10.3.0-CUDA-11.3.1.eb
index 31db9bd5579..7c19b967f55 100644
--- a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.3-GCC-10.3.0-CUDA-11.3.1.eb
+++ b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.3-GCC-10.3.0-CUDA-11.3.1.eb
@@ -11,7 +11,7 @@ toolchain = {'name': 'GCC', 'version': '10.3.0'}
 
 source_urls = ['https://github.com/NVIDIA/cuda-samples/archive/']
 sources = ['v%(version)s.tar.gz']
-patches = ['cuda-samples-11.X_multiple-sms.patch']
+patches = ['cuda-samples-11.3_multiple-sms.patch']
 checksums = ['2bee5f7c89347259aaab75aa6df6e10375059bdbbaf04cc7936f5db7d54fa3ac']
 
 dependencies = [
diff --git a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.6-GCC-11.3.0-CUDA-11.7.0.eb b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.6-GCC-11.3.0-CUDA-11.7.0.eb
index 1cb33c8ed72..1411d458852 100644
--- a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.6-GCC-11.3.0-CUDA-11.7.0.eb
+++ b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.6-GCC-11.3.0-CUDA-11.7.0.eb
@@ -11,7 +11,7 @@ toolchain = {'name': 'GCC', 'version': '11.3.0'}
 
 source_urls = ['https://github.com/NVIDIA/cuda-samples/archive/']
 sources = ['v%(version)s.tar.gz']
-patches = ['cuda-samples-11.X_multiple-sms.patch']
+patches = ['cuda-samples-11.6_multiple-sms.patch']
 checksums = ['75b858bcf9e534eaa0f129c418e661b83872d743de218df8a5278cc429f9ea98']
 
 dependencies = [
diff --git a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.8-GCC-11.3.0-CUDA-11.7.0.eb b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.8-GCC-11.3.0-CUDA-11.7.0.eb
index 4dc6f0f47d1..db2b3fe617c 100644
--- a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.8-GCC-11.3.0-CUDA-11.7.0.eb
+++ b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.8-GCC-11.3.0-CUDA-11.7.0.eb
@@ -11,7 +11,7 @@ toolchain = {'name': 'GCC', 'version': '11.3.0'}
 
 source_urls = ['https://github.com/NVIDIA/cuda-samples/archive/']
 sources = ['v%(version)s.tar.gz']
-patches = ['cuda-samples-11.X_multiple-sms.patch']
+patches = ['cuda-samples-11.6_multiple-sms.patch']
 checksums = ['1bc02c0ca42a323f3c7a05b5682eae703681a91e95b135bfe81f848b2d6a2c51']
 
 dependencies = [
diff --git a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-12.1-GCC-12.3.0-CUDA-12.1.1.eb b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-12.1-GCC-12.3.0-CUDA-12.1.1.eb
index 1f2d76136f1..d18522518c8 100644
--- a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-12.1-GCC-12.3.0-CUDA-12.1.1.eb
+++ b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-12.1-GCC-12.3.0-CUDA-12.1.1.eb
@@ -11,7 +11,7 @@ toolchain = {'name': 'GCC', 'version': '12.3.0'}
 
 source_urls = ['https://github.com/NVIDIA/cuda-samples/archive/']
 sources = ['v%(version)s.tar.gz']
-patches = ['cuda-samples-12.X_multiple-sms.patch']
+patches = ['cuda-samples-11.6_multiple-sms.patch']
 checksums = ['f758160645b366d79c2638d8dfd389f01029b8d179ab0c11726b9ef58aecebd9']
 
 dependencies = [
diff --git a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-12.2-GCC-11.3.0-CUDA-12.2.0.eb b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-12.2-GCC-11.3.0-CUDA-12.2.0.eb
index 1f3f081ad15..092528fda97 100644
--- a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-12.2-GCC-11.3.0-CUDA-12.2.0.eb
+++ b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-12.2-GCC-11.3.0-CUDA-12.2.0.eb
@@ -11,7 +11,7 @@ toolchain = {'name': 'GCC', 'version': '11.3.0'}
 
 source_urls = ['https://github.com/NVIDIA/cuda-samples/archive/']
 sources = ['v%(version)s.tar.gz']
-patches = ['cuda-samples-12.X_multiple-sms.patch']
+patches = ['cuda-samples-11.6_multiple-sms.patch']
 checksums = ['c9fbdee420fd4567edb1239420e2a5c93d9652b4ccf3a828fcb3e0de3152e466']
 
 builddependencies = [
diff --git a/easybuild/easyconfigs/c/CUDA-Samples/cuda-samples-11.3_multiple-sms.patch b/easybuild/easyconfigs/c/CUDA-Samples/cuda-samples-11.3_multiple-sms.patch
new file mode 100644
index 00000000000..b6613f6a3c4
--- /dev/null
+++ b/easybuild/easyconfigs/c/CUDA-Samples/cuda-samples-11.3_multiple-sms.patch
@@ -0,0 +1,31 @@
+# Fixes "nvcc fatal: Option '--ptx (-ptx)' is not allowed when compiling for multiple GPU architectures"
+# fatal compilation issue when building for multiple SM architectures
+# More info, see https://github.com/NVIDIA/cuda-samples/issues/289
+
+# Author: Caspar van Leeuwen
+
+diff -Nru cuda-samples-11.3.orig/Samples/memMapIPCDrv/Makefile cuda-samples-11.3/Samples/memMapIPCDrv/Makefile
+--- cuda-samples-11.3.orig/Samples/memMapIPCDrv/Makefile	2024-07-29 13:17:10.330743000 +0200
++++ cuda-samples-11.3/Samples/memMapIPCDrv/Makefile	2024-07-29 13:19:13.158507504 +0200
+@@ -321,6 +321,12 @@
+ ifneq ($(HIGHEST_SM),)
+ GENCODE_FLAGS += -gencode arch=compute_$(HIGHEST_SM),code=compute_$(HIGHEST_SM)
+ endif
++
++# Generate the explicit PTX file for the lowest SM architecture in $(SMS), so it works on all SMS listed there
++LOWEST_SM := $(firstword $(sort $(SMS)))
++ifneq ($(LOWEST_SM),)
++GENCODE_FLAGS_LOWEST_SM += -gencode arch=compute_$(LOWEST_SM),code=compute_$(LOWEST_SM)
++endif
+ endif
+ 
+ ifeq ($(TARGET_OS),darwin)
+@@ -401,7 +407,7 @@
+ endif
+ 
+ $(PTX_FILE): memMapIpc_kernel.cu
+-	$(EXEC) $(NVCC) $(INCLUDES) $(ALL_CCFLAGS) $(GENCODE_FLAGS) -o $@ -ptx $<
++	$(EXEC) $(NVCC) $(INCLUDES) $(ALL_CCFLAGS) $(GENCODE_FLAGS_LOWEST_SM) -o $@ -ptx $<
+ 	$(EXEC) mkdir -p data
+ 	$(EXEC) cp -f $@ ./data
+ 	$(EXEC) mkdir -p ../../bin/$(TARGET_ARCH)/$(TARGET_OS)/$(BUILD_TYPE)
diff --git a/easybuild/easyconfigs/c/CUDA-Samples/cuda-samples-11.6_multiple-sms.patch b/easybuild/easyconfigs/c/CUDA-Samples/cuda-samples-11.6_multiple-sms.patch
new file mode 100644
index 00000000000..8c4e36f7e74
--- /dev/null
+++ b/easybuild/easyconfigs/c/CUDA-Samples/cuda-samples-11.6_multiple-sms.patch
@@ -0,0 +1,56 @@
+# Fixes "nvcc fatal: Option '--ptx (-ptx)' is not allowed when compiling for multiple GPU architectures"
+# fatal compilation issue when building for multiple SM architectures
+# More info, see https://github.com/NVIDIA/cuda-samples/issues/289
+
+# Author: Caspar van Leeuwen
+
+diff -Nru cuda-samples-12.2.orig/Samples/3_CUDA_Features/memMapIPCDrv/Makefile cuda-samples-12.2/Samples/3_CUDA_Features/memMapIPCDrv/Makefile
+--- cuda-samples-12.2.orig/Samples/3_CUDA_Features/memMapIPCDrv/Makefile	2024-07-29 12:14:28.538848000 +0200
++++ cuda-samples-12.2/Samples/3_CUDA_Features/memMapIPCDrv/Makefile	2024-07-29 13:02:45.134261829 +0200
+@@ -313,6 +313,12 @@
+ ifneq ($(HIGHEST_SM),)
+ GENCODE_FLAGS += -gencode arch=compute_$(HIGHEST_SM),code=compute_$(HIGHEST_SM)
+ endif
++
++# Generate the explicit PTX file for the lowest SM architecture in $(SMS), so it works on all SMS listed there
++LOWEST_SM := $(firstword $(sort $(SMS)))
++ifneq ($(LOWEST_SM),)
++GENCODE_FLAGS_LOWEST_SM += -gencode arch=compute_$(LOWEST_SM),code=compute_$(LOWEST_SM)
++endif
+ endif
+ 
+ ifeq ($(TARGET_OS),darwin)
+@@ -394,7 +400,7 @@
+ endif
+ 
+ $(PTX_FILE): memMapIpc_kernel.cu
+-	$(EXEC) $(NVCC) $(INCLUDES) $(ALL_CCFLAGS) $(GENCODE_FLAGS) -o $@ -ptx $<
++	$(EXEC) $(NVCC) $(INCLUDES) $(ALL_CCFLAGS) $(GENCODE_FLAGS_LOWEST_SM) -o $@ -ptx $<
+ 	$(EXEC) mkdir -p data
+ 	$(EXEC) cp -f $@ ./data
+ 	$(EXEC) mkdir -p ../../../bin/$(TARGET_ARCH)/$(TARGET_OS)/$(BUILD_TYPE)
+diff -Nru cuda-samples-12.2.orig/Samples/3_CUDA_Features/ptxjit/Makefile cuda-samples-12.2/Samples/3_CUDA_Features/ptxjit/Makefile
+--- cuda-samples-12.2.orig/Samples/3_CUDA_Features/ptxjit/Makefile	2024-07-29 12:14:28.546771000 +0200
++++ cuda-samples-12.2/Samples/3_CUDA_Features/ptxjit/Makefile	2024-07-29 13:02:38.741961008 +0200
+@@ -307,6 +307,12 @@
+ ifneq ($(HIGHEST_SM),)
+ GENCODE_FLAGS += -gencode arch=compute_$(HIGHEST_SM),code=compute_$(HIGHEST_SM)
+ endif
++
++# Generate the explicit PTX file for the lowest SM architecture in $(SMS), so it works on all SMS listed there
++LOWEST_SM := $(firstword $(sort $(SMS)))
++ifneq ($(LOWEST_SM),)
++GENCODE_FLAGS_LOWEST_SM += -gencode arch=compute_$(LOWEST_SM),code=compute_$(LOWEST_SM)
++endif
+ endif
+ 
+ ifeq ($(TARGET_OS),darwin)
+@@ -390,7 +396,7 @@
+ endif
+ 
+ $(PTX_FILE): ptxjit_kernel.cu
+-	$(EXEC) $(NVCC) $(INCLUDES) $(ALL_CCFLAGS) $(GENCODE_FLAGS) -o $@ -ptx $<
++	$(EXEC) $(NVCC) $(INCLUDES) $(ALL_CCFLAGS) $(GENCODE_FLAGS_LOWEST_SM) -o $@ -ptx $<
+ 	$(EXEC) mkdir -p data
+ 	$(EXEC) cp -f $@ ./data
+ 	$(EXEC) mkdir -p ../../../bin/$(TARGET_ARCH)/$(TARGET_OS)/$(BUILD_TYPE)

From cb3952a4bf2120cd12be7720b7b0349e9d23a637 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Mon, 29 Jul 2024 14:42:07 +0200
Subject: [PATCH 512/835] adding easyconfigs:
 scenicplus-1.0a1-18072024-foss-2023a.eb, gensim-4.3.2-foss-2023a.eb,
 pyfasta-0.5.2-foss-2023a.eb, Kaleido-0.2.1-GCCcore-12.3.0.eb,
 numexpr-2.9.0-foss-2023a.eb, scrublet-0.2.3-foss-2023a.eb,
 Sphinx-RTD-Theme-2.0.0-GCCcore-12.3.0.eb and patches:
 scenicplus-1.0a1-18072024_requirements.txt.patch

---
 .../g/gensim/gensim-4.3.2-foss-2023a.eb       |  31 +
 .../k/Kaleido/Kaleido-0.2.1-GCCcore-12.3.0.eb |  32 +
 .../n/numexpr/numexpr-2.9.0-foss-2023a.eb     |  21 +
 .../p/pyfasta/pyfasta-0.5.2-foss-2023a.eb     |  44 +
 .../Sphinx-RTD-Theme-2.0.0-GCCcore-12.3.0.eb  |  33 +
 .../scenicplus-1.0a1-18072024-foss-2023a.eb   | 274 +++++
 ...plus-1.0a1-18072024_requirements.txt.patch | 998 ++++++++++++++++++
 .../s/scrublet/scrublet-0.2.3-foss-2023a.eb   |  35 +
 8 files changed, 1468 insertions(+)
 create mode 100644 easybuild/easyconfigs/g/gensim/gensim-4.3.2-foss-2023a.eb
 create mode 100644 easybuild/easyconfigs/k/Kaleido/Kaleido-0.2.1-GCCcore-12.3.0.eb
 create mode 100644 easybuild/easyconfigs/n/numexpr/numexpr-2.9.0-foss-2023a.eb
 create mode 100644 easybuild/easyconfigs/p/pyfasta/pyfasta-0.5.2-foss-2023a.eb
 create mode 100644 easybuild/easyconfigs/s/Sphinx-RTD-Theme/Sphinx-RTD-Theme-2.0.0-GCCcore-12.3.0.eb
 create mode 100644 easybuild/easyconfigs/s/scenicplus/scenicplus-1.0a1-18072024-foss-2023a.eb
 create mode 100644 easybuild/easyconfigs/s/scenicplus/scenicplus-1.0a1-18072024_requirements.txt.patch
 create mode 100644 easybuild/easyconfigs/s/scrublet/scrublet-0.2.3-foss-2023a.eb

diff --git a/easybuild/easyconfigs/g/gensim/gensim-4.3.2-foss-2023a.eb b/easybuild/easyconfigs/g/gensim/gensim-4.3.2-foss-2023a.eb
new file mode 100644
index 00000000000..cb315af1a31
--- /dev/null
+++ b/easybuild/easyconfigs/g/gensim/gensim-4.3.2-foss-2023a.eb
@@ -0,0 +1,31 @@
+easyblock = 'PythonBundle'
+
+name = 'gensim'
+version = '4.3.2'
+
+homepage = 'https://radimrehurek.com/gensim'
+description = """Gensim is a Python library for topic modelling, document indexing and similarity retrieval with
+ large corpora."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('wrapt', '1.15.0'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('smart_open', '7.0.4', {
+        'checksums': ['62b65852bdd1d1d516839fcb1f6bc50cd0f16e05b4ec44b52f43d38bcb838524'],
+    }),
+    (name, version, {
+        'checksums': ['99ac6af6ffd40682e70155ed9f92ecbf4384d59fb50af120d343ea5ee1b308ab'],
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/k/Kaleido/Kaleido-0.2.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/k/Kaleido/Kaleido-0.2.1-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..231466bb169
--- /dev/null
+++ b/easybuild/easyconfigs/k/Kaleido/Kaleido-0.2.1-GCCcore-12.3.0.eb
@@ -0,0 +1,32 @@
+easyblock = 'PythonBundle'
+
+name = 'Kaleido'
+version = '0.2.1'
+
+homepage = 'https://github.com/plotly/Kaleido'
+description = "Fast static image export for web-based visualization libraries with zero dependencies"
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+builddependencies = [
+    ('binutils', '2.40'),
+]
+
+dependencies = [('Python', '3.11.3')]
+
+if ARCH == 'x86_64':
+    local_source_tmpl = '%(namelower)s-%(version)s-py2.py3-none-manylinux1_%(arch)s.whl'
+elif ARCH == 'aarch64':
+    local_source_tmpl = '%(namelower)s-%(version)s-py2.py3-none-manylinux2014_%(arch)s.whl'
+
+exts_list = [
+    (name, version, {
+        'source_tmpl': local_source_tmpl,
+        'checksums': ['aa21cf1bf1c78f8fa50a9f7d45e1003c387bd3d6fe0a767cfbbf344b95bdc3a8'],
+    }),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+moduleclass = 'vis'
diff --git a/easybuild/easyconfigs/n/numexpr/numexpr-2.9.0-foss-2023a.eb b/easybuild/easyconfigs/n/numexpr/numexpr-2.9.0-foss-2023a.eb
new file mode 100644
index 00000000000..74e99150d4b
--- /dev/null
+++ b/easybuild/easyconfigs/n/numexpr/numexpr-2.9.0-foss-2023a.eb
@@ -0,0 +1,21 @@
+name = 'numexpr'
+version = '2.9.0'
+
+homepage = 'https://numexpr.readthedocs.io/en/latest/'
+description = """The numexpr package evaluates multiple-operator array expressions many times faster than NumPy can.
+ It accepts the expression as a string, analyzes it, rewrites it more efficiently, and compiles it on the fly into
+ code for its internal virtual machine (VM). Due to its integrated just-in-time (JIT) compiler, it does not require a
+ compiler at runtime."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+source_urls = ['https://github.com/pydata/numexpr/archive/refs/tags']
+sources = ['v%(version)s.tar.gz']
+checksums = ['4df4163fcab20030137e8f2aa23e88e1e42e6fe702387cfd95d7675e1d84645e']
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+]
+
+moduleclass = 'math'
diff --git a/easybuild/easyconfigs/p/pyfasta/pyfasta-0.5.2-foss-2023a.eb b/easybuild/easyconfigs/p/pyfasta/pyfasta-0.5.2-foss-2023a.eb
new file mode 100644
index 00000000000..127a798d38a
--- /dev/null
+++ b/easybuild/easyconfigs/p/pyfasta/pyfasta-0.5.2-foss-2023a.eb
@@ -0,0 +1,44 @@
+easyblock = 'PythonBundle'
+
+name = 'pyfasta'
+version = '0.5.2'
+
+homepage = 'https://pypi.org/project/pyfasta/'
+description = """fast, memory-efficient, pythonic (and command-line) access to fasta sequence files"""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+]
+
+use_pip = True
+
+local_preinstallopts = (
+    "sed -i"
+    " -e 's/from fasta/from pyfasta.fasta/'"
+    " -e 's/from records/from pyfasta.records/'"
+    " -e 's/from split_fasta/from pyfasta.split_fasta/'"
+    " %(name)s/__init__.py && "
+)
+local_preinstallopts += "sed -i 's/from collections/from collections.abc/' pyfasta/fasta.py && "
+local_preinstallopts += "sed -i 's/from records/from pyfasta.records/' pyfasta/fasta.py && "
+local_preinstallopts += "sed -i 's/import cPickle/import _pickle as cPickle/' pyfasta/records.py && "
+local_preinstallopts += "sed -i 's/from cStringIO import StringIO/from io import StringIO/' pyfasta/split_fasta.py && "
+
+exts_list = [
+    (name, version, {
+        'preinstallopts': local_preinstallopts,
+        'checksums': ['ab08d75fa90253bc91933d10567d5d9cca2718f4796ef3bdc36b68df0e45b258'],
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['bin/pyfasta'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+sanity_check_commands = ['pyfasta extract --help']
+sanity_pip_check = True
+
+moduleclass = 'tools'
diff --git a/easybuild/easyconfigs/s/Sphinx-RTD-Theme/Sphinx-RTD-Theme-2.0.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/s/Sphinx-RTD-Theme/Sphinx-RTD-Theme-2.0.0-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..c41639bc3ad
--- /dev/null
+++ b/easybuild/easyconfigs/s/Sphinx-RTD-Theme/Sphinx-RTD-Theme-2.0.0-GCCcore-12.3.0.eb
@@ -0,0 +1,33 @@
+easyblock = 'PythonBundle'
+
+name = 'Sphinx-RTD-Theme'
+version = '2.0.0'
+
+homepage = 'https://sphinx-rtd-theme.readthedocs.io'
+description = """Sphinx theme designed to provide a great reader experience
+ for documentation users on both desktop and mobile devices."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+builddependencies = [('binutils', '2.40')]
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('Python-bundle-PyPI', '2023.06'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('sphinxcontrib-jquery', '4.1', {
+        'modulename': 'sphinxcontrib.jquery',
+        'checksums': ['1620739f04e36a2c779f1a131a2dfd49b2fd07351bf1968ced074365933abc7a'],
+    }),
+    ('sphinx_rtd_theme', version, {
+        'checksums': ['bd5d7b80622406762073a04ef8fadc5f9151261563d47027de09910ce03afe6b'],
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'vis'
diff --git a/easybuild/easyconfigs/s/scenicplus/scenicplus-1.0a1-18072024-foss-2023a.eb b/easybuild/easyconfigs/s/scenicplus/scenicplus-1.0a1-18072024-foss-2023a.eb
new file mode 100644
index 00000000000..c536bd85bc5
--- /dev/null
+++ b/easybuild/easyconfigs/s/scenicplus/scenicplus-1.0a1-18072024-foss-2023a.eb
@@ -0,0 +1,274 @@
+easyblock = 'PythonBundle'
+
+name = 'scenicplus'
+version = '1.0a1-18072024'
+local_commit = "fa55dae"
+
+homepage = 'https://github.com/aertslab/scenicplus'
+description = """SCENIC+ is a python package to build gene regulatory networks (GRNs)
+using combined or separate single-cell gene expression (scRNA-seq) and single-cell
+chromatin accessibility (scATAC-seq) data."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+builddependencies = [
+    ('poetry', '1.5.1'),
+    ('maturin', '1.4.0', '-Rust-1.75.0'),
+    ('CMake', '3.26.3'),
+]
+dependencies = [
+    ('Python', '3.11.3'),
+    ('Python-bundle-PyPI', '2023.06'),
+    ('SciPy-bundle', '2023.07'),
+    ('Single-cell-python-bundle', '2024.02'),
+    ('anndata', '0.10.5.post1'),
+    ('BeautifulSoup', '4.12.2'),
+    ('h5py', '3.9.0'),
+    ('python-igraph', '0.11.4'),
+    ('imageio', '2.33.1'),
+    ('leidenalg', '0.10.2'),
+    ('lxml', '4.9.2'),
+    ('MACS2', '2.2.9.1'),
+    ('numba', '0.58.1'),
+    ('polars', '0.20.2'),
+    ('Arrow', '14.0.1'),
+    ('plotly.py', '5.16.0'),
+    ('pybedtools', '0.9.1'),
+    ('pyBigWig', '0.3.22'),
+    ('pyGAM', '0.9.1'),
+    ('Pysam', '0.22.0'),
+    ('Ray-project', '2.9.1'),
+    ('scikit-image', '0.22.0'),
+    ('snakemake', '8.4.2'),
+    ('statsmodels', '0.14.1'),
+    ('IPython', '8.14.0'),
+    ('Pandoc', '3.1.2', '', SYSTEM),
+    ('ipympl', '0.9.3'),
+    ('PyTables', '3.8.0'),
+    ('Sphinx-RTD-Theme', '2.0.0'),
+    ('scrublet', '0.2.3'),
+    ('numexpr', '2.9.0'),
+    ('Kaleido', '0.2.1'),
+    ('pyfasta', '0.5.2'),
+    ('gensim', '4.3.2'),
+]
+
+# unpin version restriction and delete typing requirement
+local_pycistopic_preinstallopts = (
+    "sed -i"
+    " -e 's/pyscenic>=0.12.0/pyscenic/'"
+    " -e 's/pandas==1.5/pandas/'"
+    " -e 's/python-Levenshtein/Levenshtein/'"
+    " -e 's/python-igraph/igraph/'"
+    " -e '/typing/d'"
+    # delete pyscenic and loomxpy req from commit - have versions now
+    " -e '60,61d'"
+    " requirements.txt && "
+    "sed -i"
+    " -e 's/pandas == 1.5/pandas/'"
+    " -e 's/matplotlib < 3.7/matplotlib/'"
+    " pyproject.toml && "
+)
+# delete typing from requirements
+local_pycistarget_preinstallopts = "sed -i '/typing/d' requirements.txt && "
+# unpin version restriction and delete poetry.lock
+local_loomxpy_preinstallopts = "sed -i 's/pyscenic>=0.12.0/pyscenic/' requirements.txt && "
+local_loomxpy_preinstallopts += "sed -i 's/pyscenic = \">=0.12.0\"/pyscenic = \"*\"/' pyproject.toml && "
+local_loomxpy_preinstallopts += "rm poetry.lock && "
+
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    ('bs4', '0.0.2', {
+        'checksums': ['a48685c58f50fe127722417bae83fe6badf500d54b55f7e39ffe43b798653925'],
+    }),
+    ('attr', '0.3.2', {
+        'checksums': ['1ceebca768181cdcce9827611b1d728e592be5d293911539ea3d0b0bfa1146f4'],
+    }),
+    ('attrs', '23.2.0', {
+        'checksums': ['935dc3b529c262f6cf76e50877d35a4bd3c1de194fd41f47a2b7ae8f19971f30'],
+    }),
+    ('lda', '3.0.0', {
+        'checksums': ['c9acbc1c55d2928f7e3e2336352b3382d78e43dbb0d12bf9ed97f87bce6d6708'],
+    }),
+    ('zope.interface', '6.2', {
+        'checksums': ['3b6c62813c63c543a06394a636978b22dffa8c5410affc9331ce6cdb5bfa8565'],
+    }),
+    ('zope.event', '5.0', {
+        'checksums': ['bac440d8d9891b4068e2b5a2c5e2c9765a9df762944bda6955f96bb9b91e67cd'],
+    }),
+    ('gevent', '24.2.1', {
+        'checksums': ['432fc76f680acf7cf188c2ee0f5d3ab73b63c1f03114c7cd8a34cebbe5aa2056'],
+    }),
+    ('xmltodict', '0.13.0', {
+        'checksums': ['341595a488e3e01a85a9d8911d8912fd922ede5fecc4dce437eb4b6c8d037e56'],
+    }),
+    ('suds-community', '1.1.2', {
+        'modulename': 'suds',
+        'checksums': ['883b4173ad23e7b20e9779ac7238b06140c50d7852afd5dc49dad1ea5f5a3d08'],
+    }),
+    ('grequests', '0.7.0', {
+        'checksums': ['5c33f14268df5b8fa1107d8537815be6febbad6ec560524d6a404b7778cf6ba6'],
+    }),
+    ('pexpect', '4.9.0', {
+        'checksums': ['ee7d41123f3c9911050ea2c2dac107568dc43b2d3b0c7557a33212c398ead30f'],
+    }),
+    ('colorlog', '6.8.2', {
+        'checksums': ['3e3e079a41feb5a1b64f978b5ea4f46040a94f11f0e8bbb8261e3dbbeca64d44'],
+    }),
+    ('easydev', '0.12.1', {
+        'checksums': ['b47b7e6f75316ac9045b46487930e16ddb567f3899310deee11d72d8e1f0a231'],
+    }),
+    ('bioservices', '1.11.2', {
+        'checksums': ['31baaab4ab813b93f79995ba8cad431a16cbee99e1b0c6f9e419dd4be0c73a9e'],
+    }),
+    ('gseapy', '0.10.8', {
+        'checksums': ['15be80bac73768501f5cecf6751aeb2e41416fd144bd6daa2ec453ad08a10ce0'],
+    }),
+    ('ncls', '0.0.68', {
+        'checksums': ['81aaa5abb123bb21797ed2f8ef921e20222db14a3ecbc61ccf447532f2b7ba93'],
+    }),
+    ('pybigtools', '0.1.2', {
+        'checksums': ['0f21bc8b4f2dce67c6e5287af895f5f28a8c6eb123d809e3ab5679e2131dbf58'],
+    }),
+    ('pybiomart', '0.2.0', {
+        'checksums': ['e9eac20db921820670c646d99725b0ee279e407379e5e8c3ec7245a07425d8fe'],
+    }),
+    ('sorted_nearest', '0.0.39', {
+        'checksums': ['16a51d5db87ae226b47ace43c176bb672477a1b7ba8052ea9291a6356c9c69b1'],
+    }),
+    ('pyranges', '0.0.111', {
+        'checksums': ['d2cf3c31c1b9c6e1bf6e1e89254d8bd993bfb4401f2c4ede0ebc9c8e0678147d'],
+    }),
+    ('pyrle', '0.0.39', {
+        'checksums': ['1be4be7814d3941db907aaf19f311bd46a407244316cadbf4b73109685c055c5'],
+    }),
+    ('pyvis', '0.3.2', {
+        'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl',
+        'checksums': ['5720c4ca8161dc5d9ab352015723abb7a8bb8fb443edeb07f7a322db34a97555'],
+    }),
+    ('url-normalize', '1.4.3', {
+        'checksums': ['d23d3a070ac52a67b83a1c59a0e68f8608d1cd538783b401bc9de2c0fac999b2'],
+    }),
+    ('cattrs', '23.2.3', {
+        'checksums': ['a934090d95abaa9e911dac357e3a8699e0b4b14f8529bcc7d2b1ad9d51672b9f'],
+    }),
+    ('requests_cache', '1.2.0', {
+        'checksums': ['db1c709ca343cc1cd5b6c8b1a5387298eceed02306a6040760db538c885e3838'],
+    }),
+    ('scanorama', '1.7.4', {
+        'checksums': ['67de100e63abc3028c7780d3a217e43e920a5781230bc6b6a51349d4605e005c'],
+    }),
+    ('rich_argparse', '1.4.0', {
+        'checksums': ['c275f34ea3afe36aec6342c2a2298893104b5650528941fb53c21067276dba19'],
+    }),
+    ('scatac_fragment_tools', '0.1.0', {
+        'checksums': ['e77a03ad1b7170c212f1ac672dad2c5d7e7f091b94e47b36a2ec2adc42051857'],
+    }),
+    ('snakemake_interface_common', '1.17.1', {
+        'checksums': ['555c8218d9b68ddc1046f94a517e7d0f22e15bdc839d6ce149608d8ec137b9ae'],
+    }),
+    ('snakemake_interface_report_plugins', '1.0.0', {
+        'checksums': ['02311cdc4bebab2a1c28469b5e6d5c6ac6e9c66998ad4e4b3229f1472127490f'],
+    }),
+    ('statistics', '1.0.3.5', {
+        'checksums': ['2dc379b80b07bf2ddd5488cad06b2b9531da4dd31edb04dc9ec0dc226486c138'],
+    }),
+    ('globre', '0.1.5', {
+        'checksums': ['ee214204f237e9114b8f61eeb61c2abd1e665ca3b59e5a6a0b070971c0bb12e2'],
+    }),
+    ('bidict', '0.23.1', {
+        'checksums': ['03069d763bc387bbd20e7d49914e75fc4132a41937fa3405417e1a5a2d006d71'],
+    }),
+    ('tmtoolkit', '0.12.0', {
+        'checksums': ['6df5429cd675989f21d9f075ddb11fe5ae273d6544fc337a2589bab2bc331909'],
+    }),
+    ('tspex', '0.6.3', {
+        'checksums': ['315bfa1f60ea582777c549313cad9e9da0a4d11c5f69a6fc767bd0823dc46316'],
+    }),
+    ('plumbum', '1.8.3', {
+        'checksums': ['6092c85ab970b7a7a9d5d85c75200bc93be82b33c9bdf640ffa87d2d7c8709f0'],
+    }),
+    ('pandoc', '2.3', {
+        'checksums': ['e772c2c6d871146894579828dbaf1efd538eb64fc7e71d4a6b3a11a18baef90d'],
+    }),
+    ('nbsphinx', '0.9.4', {
+        'checksums': ['042a60806fc23d519bc5bef59d95570713913fe442fda759d53e3aaf62104794'],
+    }),
+    ('nbsphinx-link', '1.3.0', {
+        'checksums': ['fa3079a74c0dff1b2079e79a34babe770706ba8aa9cc0609c6dbfd593461a077'],
+    }),
+    ('numpydoc', '1.7.0', {
+        'checksums': ['866e5ae5b6509dcf873fc6381120f5c31acf13b135636c1a81d68c166a95f921'],
+    }),
+    ('pyOpenSSL', '23.2.0', {
+        'modulename': 'OpenSSL',
+        'checksums': ['276f931f55a452e7dea69c7173e984eb2a4407ce413c918aa34b55f82f9b8bac'],
+    }),
+    ('entrypoints', '0.4', {
+        'checksums': ['b706eddaa9218a19ebcd67b56818f05bb27589b1ca9e8d797b74affad4ccacd4'],
+    }),
+    ('ansicolors', '1.1.8', {
+        'modulename': 'colors',
+        'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl',
+        'checksums': ['00d2dde5a675579325902536738dd27e4fac1fd68f773fe36c21044eb559e187'],
+    }),
+    ('papermill', '2.6.0', {
+        'checksums': ['9fe2a91912fd578f391b4cc8d6d105e73124dcd0cde2a43c3c4a1c77ac88ea24'],
+    }),
+    ('mypy_extensions', '1.0.0', {
+        'checksums': ['75dbf8955dc00442a438fc4d0666508a9a97b6bd41aa2f0ffe9d2f2725af0782'],
+    }),
+    ('typing_inspect', '0.9.0', {
+        'checksums': ['b23fc42ff6f6ef6954e4852c1fb512cdd18dbea03134f91f856a95ccc9461f78'],
+    }),
+    ('marshmallow', '3.21.1', {
+        'checksums': ['4e65e9e0d80fc9e609574b9983cf32579f305c718afb30d7233ab818571768c3'],
+    }),
+    ('dataclasses_json', '0.6.4', {
+        'checksums': ['73696ebf24936560cca79a2430cbc4f3dd23ac7bf46ed17f38e5e5e7657a6377'],
+    }),
+    ('loomxpy', '0.4.2', {
+        'preinstallopts': local_loomxpy_preinstallopts,
+        'checksums': ['188411b77e04fa8458c0a7f02cfb3f15b58410a020f81f522957e922e79cdd82'],
+    }),
+    ('pycisTopic', '2.0a-dca4bb6', {
+        'modulename': 'pycisTopic',
+        'preinstallopts': local_pycistopic_preinstallopts,
+        # download commit dca4bb6 to be compatible with pycistarget
+        'source_urls': ['https://github.com/aertslab/pycisTopic/archive/'],
+        'sources': [{'download_filename': 'dca4bb6.tar.gz', 'filename': '%(name)s-%(version)s-dca4bb6.tar.gz'}],
+        'checksums': ['82edc9313bbb587aeb1540fd5b095b6eafb422fa12a5fc97ba090b99b684b240'],
+    }),
+    ('pycistarget', '1.0a1-16d14b9', {
+        'preinstallopts': local_pycistarget_preinstallopts,
+        # download commit 16d14b9 to make '$ scenicplus' work
+        'source_urls': ['https://github.com/aertslab/pycistarget/archive/'],
+        'sources': [{'download_filename': '16d14b9.tar.gz', 'filename': '%(name)s-%(version)s-16d14b9.tar.gz'}],
+        'checksums': ['7285ac03be9d148437442a726366d7c6f9f5f86bc6636369149a2bc2cd8e0e29'],
+    }),
+    (name, version, {
+        'patches': [
+            'scenicplus-1.0a1-18072024_requirements.txt.patch',
+        ],
+        'source_urls': ['https://github.com/aertslab/scenicplus/archive/'],
+        'sources': [{'download_filename': 'fa55dae.tar.gz', 'filename': '%(name)s-%(version)s-fa55dae.tar.gz'}],
+        'checksums': [
+            {'scenicplus-1.0a1-18072024-fa55dae.tar.gz':
+             '88cddec1ab2618861e5c93e8a0b17b8e9e2aa3a76410d882c35d472f98724e29'},
+            {'scenicplus-1.0a1-18072024_requirements.txt.patch':
+             'fdfba5d9413f6088d657e315ce7aa28cd645154521e9173a7325bd6c4fdd7e7a'},
+        ],
+    }),
+]
+
+# copy files to let 'scenicplus init_snakemake' works 
+postinstallcmds = [
+    'cp -r %(builddir)s/scenicplus/scenicplus-fa55dae55203951c0c42e359b65a28010cd544f6/src/scenicplus/snakemake '
+    '%(installdir)s/lib/python%(pyshortver)s/site-packages/scenicplus'
+]
+
+sanity_check_commands = ['scenicplus init_snakemake --help']
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/s/scenicplus/scenicplus-1.0a1-18072024_requirements.txt.patch b/easybuild/easyconfigs/s/scenicplus/scenicplus-1.0a1-18072024_requirements.txt.patch
new file mode 100644
index 00000000000..ecfeed15e29
--- /dev/null
+++ b/easybuild/easyconfigs/s/scenicplus/scenicplus-1.0a1-18072024_requirements.txt.patch
@@ -0,0 +1,998 @@
+--- requirements.txt.orig	2024-07-24 10:54:46.267978000 +0200
++++ requirements.txt	2024-07-24 12:06:31.676022842 +0200
+@@ -1,918 +1,77 @@
+-#
+-# This file is autogenerated by pip-compile with Python 3.11
+-# by the following command:
+-#
+-#    pip-compile --output-file=requirements.txt pyproject.toml
+-#
+-adjusttext==1.0.4
+-    # via
+-    #   pycistopic
+-    #   scenicplus (pyproject.toml)
+-aiohttp==3.9.3
+-    # via pyscenic
+-aiosignal==1.3.1
+-    # via
+-    #   aiohttp
+-    #   ray
+-anndata==0.10.5.post1
+-    # via
+-    #   mudata
+-    #   scanpy
+-    #   scenicplus (pyproject.toml)
+-annoy==1.17.3
+-    # via
+-    #   bbknn
+-    #   scanorama
+-    #   scenicplus (pyproject.toml)
+-    #   scrublet
+-appdirs==1.4.4
+-    # via
+-    #   bioservices
+-    #   snakemake
+-arboreto==0.1.6
+-    # via
+-    #   pyscenic
+-    #   scenicplus (pyproject.toml)
+-argparse-dataclass==2.0.0
+-    # via
+-    #   snakemake-interface-common
+-    #   snakemake-interface-executor-plugins
+-array-api-compat==1.5.1
+-    # via anndata
+-asttokens==2.4.1
+-    # via stack-data
+-attr==0.3.2
+-    # via scenicplus (pyproject.toml)
+-attrs==23.2.0
+-    # via
+-    #   aiohttp
+-    #   cattrs
+-    #   jsonschema
+-    #   pyscenic
+-    #   referencing
+-    #   requests-cache
+-    #   scenicplus (pyproject.toml)
+-bbknn==1.6.0
+-    # via
+-    #   pycistopic
+-    #   scenicplus (pyproject.toml)
+-beautifulsoup4==4.12.3
+-    # via
+-    #   bioservices
+-    #   bs4
+-    #   scenicplus (pyproject.toml)
+-bidict==0.23.1
+-    # via tmtoolkit
+-bioservices==1.11.2
+-    # via gseapy
+-blosc2==2.5.1
+-    # via tables
+-bokeh==3.4.0
+-    # via dask
+-boltons==23.1.1
+-    # via pyscenic
+-bs4==0.0.2
+-    # via
+-    #   pycistopic
+-    #   scenicplus (pyproject.toml)
+-cattrs==23.2.3
+-    # via requests-cache
+-certifi==2024.2.2
+-    # via requests
+-charset-normalizer==3.3.2
+-    # via requests
+-click==8.1.7
+-    # via
+-    #   dask
+-    #   distributed
+-    #   loompy
+-    #   loomxpy
+-    #   ray
+-cloudpickle==3.0.0
+-    # via
+-    #   dask
+-    #   distributed
+-    #   pyscenic
+-colorama==0.4.6
+-    # via easydev
+-colorlog==6.8.2
+-    # via
+-    #   bioservices
+-    #   easydev
+-conda-inject==1.3.1
+-    # via snakemake
+-configargparse==1.7
+-    # via
+-    #   snakemake
+-    #   snakemake-interface-common
+-connection-pool==0.0.3
+-    # via snakemake
+-contourpy==1.2.0
+-    # via
+-    #   bokeh
+-    #   matplotlib
+-ctxcore==0.2.0
+-    # via
+-    #   pycistarget
+-    #   pyscenic
+-    #   scenicplus (pyproject.toml)
+-cycler==0.12.1
+-    # via matplotlib
+-cython==0.29.37
+-    # via
+-    #   bbknn
+-    #   macs2
+-    #   pyranges
+-    #   scenicplus (pyproject.toml)
+-    #   scrublet
+-cytoolz==0.12.3
+-    # via
+-    #   ctxcore
+-    #   pyscenic
+-    #   scenicplus (pyproject.toml)
+-dask[array,complete,dataframe,diagnostics,distributed]==2024.2.1
+-    # via
+-    #   arboreto
+-    #   distributed
+-    #   pyscenic
+-    #   scenicplus (pyproject.toml)
+-dataclasses-json==0.6.4
+-    # via loomxpy
+-datrie==0.8.2
+-    # via snakemake
+-decorator==5.1.1
+-    # via ipython
+-dill==0.3.8
+-    # via
+-    #   multiprocessing-on-dill
+-    #   scenicplus (pyproject.toml)
+-distributed==2024.2.1
+-    # via
+-    #   arboreto
+-    #   dask
+-    #   pyscenic
+-docutils==0.20.1
+-    # via
+-    #   snakemake
+-    #   statistics
+-dpath==2.1.6
+-    # via
+-    #   snakemake
+-    #   yte
+-easydev==0.13.1
+-    # via bioservices
+-et-xmlfile==1.1.0
+-    # via openpyxl
+-executing==2.0.1
+-    # via stack-data
+-fastjsonschema==2.19.1
+-    # via nbformat
+-fbpca==1.0
+-    # via
+-    #   geosketch
+-    #   scanorama
+-filelock==3.13.1
+-    # via ray
+-fonttools==4.50.0
+-    # via matplotlib
+-frozendict==2.4.0
+-    # via
+-    #   ctxcore
+-    #   pyscenic
+-frozenlist==1.4.1
+-    # via
+-    #   aiohttp
+-    #   aiosignal
+-    #   ray
+-fsspec==2024.3.1
+-    # via
+-    #   dask
+-    #   pyscenic
+-future==1.0.0
+-    # via pybiomart
+-gensim==4.3.2
+-    # via
+-    #   pycistopic
+-    #   scenicplus (pyproject.toml)
+-geosketch==1.2
+-    # via scanorama
+-gevent==24.2.1
+-    # via grequests
+-gitdb==4.0.11
+-    # via gitpython
+-gitpython==3.1.42
+-    # via snakemake
+-globre==0.1.5
+-    # via tmtoolkit
+-greenlet==3.0.3
+-    # via gevent
+-grequests==0.7.0
+-    # via bioservices
+-gseapy==0.10.8
+-    # via scenicplus (pyproject.toml)
+-h5py==3.10.0
+-    # via
+-    #   anndata
+-    #   loompy
+-    #   mudata
+-    #   pycistarget
+-    #   scanpy
+-    #   scenicplus (pyproject.toml)
+-harmonypy==0.0.9
+-    # via
+-    #   pycistopic
+-    #   scenicplus (pyproject.toml)
+-humanfriendly==10.0
+-    # via snakemake
+-idna==3.6
+-    # via
+-    #   requests
+-    #   yarl
+-igraph==0.11.4
+-    # via
+-    #   leidenalg
+-    #   pycistopic
+-    #   scenicplus (pyproject.toml)
+-imageio==2.34.0
+-    # via
+-    #   scenicplus (pyproject.toml)
+-    #   scikit-image
+-immutables==0.20
+-    # via snakemake
+-importlib-metadata==7.0.1
+-    # via
+-    #   dask
+-    #   scenicplus (pyproject.toml)
+-importlib-resources==6.1.2
+-    # via scenicplus (pyproject.toml)
+-interlap==0.2.7
+-    # via pyscenic
+-intervaltree==3.1.0
+-    # via
+-    #   scanorama
+-    #   scenicplus (pyproject.toml)
+-ipython==8.22.2
+-    # via
+-    #   pycistarget
+-    #   pyvis
+-jedi==0.19.1
+-    # via ipython
+-jinja2==3.1.3
+-    # via
+-    #   bokeh
+-    #   dask
+-    #   distributed
+-    #   pyvis
+-    #   snakemake
+-joblib==1.3.2
+-    # via
+-    #   gseapy
+-    #   pynndescent
+-    #   scanpy
+-    #   scatac-fragment-tools
+-    #   scenicplus (pyproject.toml)
+-    #   scikit-learn
+-jsonpickle==3.0.3
+-    # via pyvis
+-jsonschema==4.21.1
+-    # via
+-    #   nbformat
+-    #   ray
+-    #   snakemake
+-jsonschema-specifications==2023.12.1
+-    # via jsonschema
+-jupyter-core==5.7.2
+-    # via nbformat
+-kaleido==0.2.1
+-    # via scenicplus (pyproject.toml)
+-kiwisolver==1.4.5
+-    # via matplotlib
+-lazy-loader==0.3
+-    # via scikit-image
+-lda==3.0.0
+-    # via
+-    #   pycistopic
+-    #   scenicplus (pyproject.toml)
+-leidenalg==0.10.2
+-    # via
+-    #   pycistopic
+-    #   scenicplus (pyproject.toml)
+-line-profiler==4.1.2
+-    # via easydev
+-llvmlite==0.42.0
+-    # via
+-    #   numba
+-    #   pynndescent
+-    #   pyscenic
+-locket==1.0.0
+-    # via
+-    #   distributed
+-    #   partd
+-loompy==3.0.7
+-    # via
+-    #   loomxpy
+-    #   pyscenic
+-loomxpy @ git+https://github.com/aertslab/LoomXpy@main
+-    # via
+-    #   pycistopic
+-    #   scenicplus (pyproject.toml)
+-lxml==5.1.0
+-    # via
+-    #   bioservices
+-    #   pycistopic
+-    #   scenicplus (pyproject.toml)
+-lz4==4.3.3
+-    # via dask
+-macs2==2.2.9.1
+-    # via
+-    #   pycistopic
+-    #   scenicplus (pyproject.toml)
+-markdown-it-py==3.0.0
+-    # via rich
+-markupsafe==2.1.5
+-    # via jinja2
+-marshmallow==3.21.1
+-    # via dataclasses-json
+-matplotlib==3.6.3
+-    # via
+-    #   adjusttext
+-    #   bioservices
+-    #   gseapy
+-    #   mizani
+-    #   plotnine
+-    #   pycistopic
+-    #   scanorama
+-    #   scanpy
+-    #   scenicplus (pyproject.toml)
+-    #   scrublet
+-    #   seaborn
+-    #   tmtoolkit
+-    #   tspex
+-matplotlib-inline==0.1.6
+-    # via ipython
+-mdurl==0.1.2
+-    # via markdown-it-py
+-mizani==0.9.3
+-    # via plotnine
+-msgpack==1.0.8
+-    # via
+-    #   blosc2
+-    #   distributed
+-    #   ray
+-mudata==0.2.3
+-    # via scenicplus (pyproject.toml)
+-multidict==6.0.5
+-    # via
+-    #   aiohttp
+-    #   yarl
+-multiprocessing-on-dill==3.5.0a4
+-    # via pyscenic
+-mypy-extensions==1.0.0
+-    # via typing-inspect
+-natsort==8.4.0
+-    # via
+-    #   anndata
+-    #   pyranges
+-    #   pyrle
+-    #   scanpy
+-nbformat==5.10.3
+-    # via snakemake
+-ncls==0.0.68
+-    # via
+-    #   pyranges
+-    #   scenicplus (pyproject.toml)
+-ndindex==1.8
+-    # via blosc2
+-networkx==3.2.1
+-    # via
+-    #   pyscenic
+-    #   pyvis
+-    #   scanpy
+-    #   scenicplus (pyproject.toml)
+-    #   scikit-image
+-numba==0.59.0
+-    # via
+-    #   ctxcore
+-    #   loompy
+-    #   pynndescent
+-    #   pyscenic
+-    #   scanpy
+-    #   scatac-fragment-tools
+-    #   scenicplus (pyproject.toml)
+-    #   scrublet
+-    #   umap-learn
+-numexpr==2.9.0
+-    # via
+-    #   pyscenic
+-    #   scenicplus (pyproject.toml)
+-    #   tables
+-numpy==1.26.4
+-    # via
+-    #   adjusttext
+-    #   anndata
+-    #   arboreto
+-    #   bbknn
+-    #   blosc2
+-    #   bokeh
+-    #   contourpy
+-    #   ctxcore
+-    #   dask
+-    #   gensim
+-    #   geosketch
+-    #   gseapy
+-    #   h5py
+-    #   harmonypy
+-    #   imageio
+-    #   lda
+-    #   loompy
+-    #   loomxpy
+-    #   macs2
+-    #   matplotlib
+-    #   mizani
+-    #   mudata
+-    #   ncls
+-    #   numba
+-    #   numexpr
+-    #   numpy-groupies
+-    #   pandas
+-    #   patsy
+-    #   plotnine
+-    #   pyarrow
+-    #   pybedtools
+-    #   pybigtools
+-    #   pycistarget
+-    #   pycistopic
+-    #   pygam
+-    #   pyrle
+-    #   pyscenic
+-    #   scanorama
+-    #   scanpy
+-    #   scatac-fragment-tools
+-    #   scenicplus (pyproject.toml)
+-    #   scikit-image
+-    #   scikit-learn
+-    #   scipy
+-    #   scrublet
+-    #   seaborn
+-    #   sorted-nearest
+-    #   statsmodels
+-    #   tables
+-    #   tifffile
+-    #   tmtoolkit
+-    #   tspex
+-    #   umap-learn
+-numpy-groupies==0.10.2
+-    # via
+-    #   loompy
+-    #   scenicplus (pyproject.toml)
+-openpyxl==3.1.2
+-    # via tmtoolkit
+-packaging==24.0
+-    # via
+-    #   anndata
+-    #   bokeh
+-    #   dask
+-    #   distributed
+-    #   marshmallow
+-    #   matplotlib
+-    #   plotly
+-    #   ray
+-    #   scanpy
+-    #   scikit-image
+-    #   snakemake
+-    #   statsmodels
+-    #   tables
+-pandas==1.5.0
+-    # via
+-    #   anndata
+-    #   arboreto
+-    #   bbknn
+-    #   bioservices
+-    #   bokeh
+-    #   ctxcore
+-    #   dask
+-    #   gseapy
+-    #   harmonypy
+-    #   loomxpy
+-    #   mizani
+-    #   mudata
+-    #   plotnine
+-    #   pybiomart
+-    #   pycistarget
+-    #   pycistopic
+-    #   pyranges
+-    #   pyrle
+-    #   pyscenic
+-    #   scanpy
+-    #   scenicplus (pyproject.toml)
+-    #   scrublet
+-    #   seaborn
+-    #   statsmodels
+-    #   tmtoolkit
+-    #   tspex
+-parso==0.8.3
+-    # via jedi
+-partd==1.4.1
+-    # via dask
+-patsy==0.5.6
+-    # via
+-    #   plotnine
+-    #   scanpy
+-    #   statsmodels
+-pexpect==4.9.0
+-    # via
+-    #   easydev
+-    #   ipython
+-pillow==10.2.0
+-    # via
+-    #   bokeh
+-    #   imageio
+-    #   matplotlib
+-    #   scikit-image
+-plac==1.4.3
+-    # via yte
+-platformdirs==4.2.0
+-    # via
+-    #   easydev
+-    #   jupyter-core
+-    #   requests-cache
+-plotly==5.19.0
+-    # via scenicplus (pyproject.toml)
+-plotnine==0.12.4
+-    # via scenicplus (pyproject.toml)
+-polars==0.20.13
+-    # via
+-    #   pycistopic
+-    #   scatac-fragment-tools
+-    #   scenicplus (pyproject.toml)
+-progressbar2==4.4.2
+-    # via pygam
+-prompt-toolkit==3.0.43
+-    # via ipython
+-protobuf==5.26.0
+-    # via ray
+-psutil==5.9.8
+-    # via
+-    #   distributed
+-    #   snakemake
+-ptyprocess==0.7.0
+-    # via pexpect
+-pulp==2.8.0
+-    # via snakemake
+-pure-eval==0.2.2
+-    # via stack-data
+-py-cpuinfo==9.0.0
+-    # via
+-    #   blosc2
+-    #   tables
+-pyarrow==15.0.0
+-    # via
+-    #   ctxcore
+-    #   dask
+-    #   pycistopic
+-    #   scatac-fragment-tools
+-    #   scenicplus (pyproject.toml)
+-pyarrow-hotfix==0.6
+-    # via
+-    #   dask
+-    #   scenicplus (pyproject.toml)
+-pybedtools==0.9.1
+-    # via scenicplus (pyproject.toml)
+-pybigtools==0.1.2
+-    # via
+-    #   scatac-fragment-tools
+-    #   scenicplus (pyproject.toml)
+-pybigwig==0.3.22
+-    # via
+-    #   scatac-fragment-tools
+-    #   scenicplus (pyproject.toml)
+-pybiomart==0.2.0
+-    # via
+-    #   pycistopic
+-    #   scenicplus (pyproject.toml)
+-pycistarget @ git+https://github.com/aertslab/pycistarget
+-    # via scenicplus (pyproject.toml)
+-pycistopic @ git+https://github.com/aertslab/pycisTopic
+-    # via scenicplus (pyproject.toml)
+-pyfasta==0.5.2
+-    # via scenicplus (pyproject.toml)
+-pygam==0.9.0
+-    # via scenicplus (pyproject.toml)
+-pygments==2.17.2
+-    # via
+-    #   ipython
+-    #   rich
+-pynndescent==0.5.11
+-    # via
+-    #   bbknn
+-    #   umap-learn
+-pyparsing==3.1.2
+-    # via matplotlib
+-pyranges==0.0.111
+-    # via
+-    #   pycistarget
+-    #   pycistopic
+-    #   scenicplus (pyproject.toml)
+-pyrle==0.0.39
+-    # via
+-    #   pyranges
+-    #   scenicplus (pyproject.toml)
+-pysam==0.22.0
+-    # via
+-    #   pybedtools
+-    #   scenicplus (pyproject.toml)
+-pyscenic @ git+https://github.com/aertslab/pySCENIC@master
+-    # via
+-    #   loomxpy
+-    #   pycistopic
+-    #   scenicplus (pyproject.toml)
+-python-dateutil==2.9.0.post0
+-    # via
+-    #   matplotlib
+-    #   pandas
+-python-utils==3.8.2
+-    # via progressbar2
+-pytz==2024.1
+-    # via pandas
+-pyvis==0.3.2
+-    # via scenicplus (pyproject.toml)
+-pyyaml==6.0.1
+-    # via
+-    #   bokeh
+-    #   conda-inject
+-    #   ctxcore
+-    #   dask
+-    #   distributed
+-    #   pyscenic
+-    #   ray
+-    #   snakemake
+-    #   yte
+-ray==2.9.3
+-    # via
+-    #   pycistopic
+-    #   scenicplus (pyproject.toml)
+-referencing==0.34.0
+-    # via
+-    #   jsonschema
+-    #   jsonschema-specifications
+-requests==2.31.0
+-    # via
+-    #   bioservices
+-    #   grequests
+-    #   gseapy
+-    #   pybiomart
+-    #   pyscenic
+-    #   ray
+-    #   requests-cache
+-    #   scenicplus (pyproject.toml)
+-    #   snakemake
+-requests-cache==1.2.0
+-    # via
+-    #   bioservices
+-    #   pybiomart
+-    #   scenicplus (pyproject.toml)
+-reretry==0.11.8
+-    # via
+-    #   snakemake
+-    #   snakemake-interface-storage-plugins
+-rich==13.7.1
+-    # via rich-argparse
+-rich-argparse==1.4.0
+-    # via scatac-fragment-tools
+-rpds-py==0.18.0
+-    # via
+-    #   jsonschema
+-    #   referencing
+-scanorama==1.7.4
+-    # via
+-    #   pycistopic
+-    #   scenicplus (pyproject.toml)
+-scanpy==1.8.2
+-    # via
+-    #   pycistopic
+-    #   scenicplus (pyproject.toml)
+-scatac-fragment-tools==0.1.0
+-    # via
+-    #   pycistopic
+-    #   scenicplus (pyproject.toml)
+-scikit-image==0.22.0
+-    # via
+-    #   scenicplus (pyproject.toml)
+-    #   scrublet
+-scikit-learn==1.3.2
+-    # via
+-    #   arboreto
+-    #   bbknn
+-    #   geosketch
+-    #   harmonypy
+-    #   loomxpy
+-    #   pycistarget
+-    #   pycistopic
+-    #   pynndescent
+-    #   pyscenic
+-    #   scanorama
+-    #   scanpy
+-    #   scenicplus (pyproject.toml)
+-    #   scrublet
+-    #   umap-learn
+-scipy==1.12.0
+-    # via
+-    #   adjusttext
+-    #   anndata
+-    #   arboreto
+-    #   bbknn
+-    #   gensim
+-    #   gseapy
+-    #   harmonypy
+-    #   loompy
+-    #   mizani
+-    #   plotnine
+-    #   pygam
+-    #   pynndescent
+-    #   pyscenic
+-    #   scanorama
+-    #   scanpy
+-    #   scenicplus (pyproject.toml)
+-    #   scikit-image
+-    #   scikit-learn
+-    #   scrublet
+-    #   statsmodels
+-    #   tmtoolkit
+-    #   umap-learn
+-scrublet==0.2.3
+-    # via
+-    #   pycistopic
+-    #   scenicplus (pyproject.toml)
+-seaborn==0.13.2
+-    # via
+-    #   pycistopic
+-    #   scanpy
+-    #   scenicplus (pyproject.toml)
+-sinfo==0.3.4
+-    # via scanpy
+-six==1.16.0
+-    # via
+-    #   asttokens
+-    #   patsy
+-    #   pybedtools
+-    #   python-dateutil
+-    #   url-normalize
+-smart-open==6.4.0
+-    # via
+-    #   gensim
+-    #   snakemake
+-smmap==5.0.1
+-    # via gitdb
+-snakemake==8.5.5
+-    # via scenicplus (pyproject.toml)
+-snakemake-interface-common==1.17.1
+-    # via
+-    #   scenicplus (pyproject.toml)
+-    #   snakemake
+-    #   snakemake-interface-executor-plugins
+-    #   snakemake-interface-report-plugins
+-    #   snakemake-interface-storage-plugins
+-snakemake-interface-executor-plugins==8.2.0
+-    # via
+-    #   scenicplus (pyproject.toml)
+-    #   snakemake
+-snakemake-interface-report-plugins==1.0.0
+-    # via
+-    #   scenicplus (pyproject.toml)
+-    #   snakemake
+-snakemake-interface-storage-plugins==3.1.1
+-    # via
+-    #   scenicplus (pyproject.toml)
+-    #   snakemake
+-sorted-nearest==0.0.39
+-    # via pyranges
+-sortedcontainers==2.4.0
+-    # via
+-    #   distributed
+-    #   intervaltree
+-soupsieve==2.5
+-    # via beautifulsoup4
+-stack-data==0.6.3
+-    # via ipython
+-statistics==1.0.3.5
+-    # via scenicplus (pyproject.toml)
+-statsmodels==0.14.1
+-    # via
+-    #   plotnine
+-    #   pycistopic
+-    #   scanpy
+-    #   scenicplus (pyproject.toml)
+-stdlib-list==0.10.0
+-    # via sinfo
+-stopit==1.1.2
+-    # via snakemake
+-suds-community==1.1.2
+-    # via bioservices
+-tables==3.9.2
+-    # via scanpy
+-tabulate==0.9.0
+-    # via
+-    #   pyranges
+-    #   pyrle
+-    #   snakemake
+-tblib==3.0.0
+-    # via distributed
+-tenacity==8.2.3
+-    # via plotly
+-texttable==1.7.0
+-    # via igraph
+-threadpoolctl==3.4.0
+-    # via scikit-learn
+-throttler==1.2.2
+-    # via
+-    #   snakemake
+-    #   snakemake-interface-executor-plugins
+-    #   snakemake-interface-storage-plugins
+-tifffile==2024.2.12
+-    # via scikit-image
+-tmtoolkit==0.12.0
+-    # via
+-    #   pycistopic
+-    #   scenicplus (pyproject.toml)
+-toolz==0.12.1
+-    # via
+-    #   cytoolz
+-    #   dask
+-    #   distributed
+-    #   partd
+-toposort==1.10
+-    # via snakemake
+-tornado==6.4
+-    # via
+-    #   bokeh
+-    #   distributed
+-tqdm==4.66.2
+-    # via
+-    #   bioservices
+-    #   ctxcore
+-    #   pyscenic
+-    #   scanpy
+-    #   scenicplus (pyproject.toml)
+-    #   umap-learn
+-traitlets==5.14.2
+-    # via
+-    #   ipython
+-    #   jupyter-core
+-    #   matplotlib-inline
+-    #   nbformat
+-tspex==0.6.3
+-    # via scenicplus (pyproject.toml)
+-typing==3.7.4.3
+-    # via scenicplus (pyproject.toml)
+-typing-extensions==4.10.0
+-    # via
+-    #   python-utils
+-    #   typing-inspect
+-typing-inspect==0.9.0
+-    # via dataclasses-json
+-umap-learn==0.5.5
+-    # via
+-    #   bbknn
+-    #   pyscenic
+-    #   scanpy
+-    #   scenicplus (pyproject.toml)
+-    #   scrublet
+-url-normalize==1.4.3
+-    # via requests-cache
+-urllib3==2.2.1
+-    # via
+-    #   distributed
+-    #   requests
+-    #   requests-cache
+-wcwidth==0.2.13
+-    # via prompt-toolkit
+-wheel==0.43.0
+-    # via tmtoolkit
+-wrapt==1.16.0
+-    # via
+-    #   bioservices
+-    #   snakemake
+-    #   snakemake-interface-storage-plugins
+-xlrd==2.0.1
+-    # via
+-    #   tmtoolkit
+-    #   tspex
+-xmltodict==0.13.0
+-    # via bioservices
+-xyzservices==2023.10.1
+-    # via bokeh
+-yarl==1.9.4
+-    # via aiohttp
+-yte==1.5.4
+-    # via snakemake
+-zict==3.0.0
+-    # via distributed
+-zipp==3.18.1
+-    # via importlib-metadata
+-zope-event==5.0
+-    # via gevent
+-zope-interface==6.2
+-    # via gevent
+-
+-# The following packages are considered to be unsafe in a requirements file:
+-# setuptools
++adjusttext
++anndata
++annoy
++arboreto
++attr
++attrs
++bbknn
++beautifulsoup4
++bs4
++ctxcore
++cytoolz
++dask
++dill
++gensim
++gseapy
++h5py
++harmonypy
++igraph
++imageio
++importlib-metadata
++importlib-resources
++intervaltree
++joblib
++kaleido
++lda
++leidenalg
++loomxpy
++lxml
++macs2
++matplotlib
++mudata
++ncls
++networkx
++numba
++numexpr
++numpy
++numpy-groupies
++pandas
++plotly
++plotnine
++polars
++pyarrow
++pybedtools
++pybigtools
++pybigwig
++pybiomart
++pycistarget
++pycistopic
++pyfasta
++pygam
++pyranges
++pyrle
++pysam
++pyscenic
++pyvis
++ray
++requests
++requests-cache
++scanorama
++scanpy
++scatac-fragment-tools
++scikit-image
++scikit-learn
++scipy
++scrublet
++seaborn
++snakemake
++snakemake-interface-common
++snakemake-interface-executor-plugins
++snakemake-interface-report-plugins
++snakemake-interface-storage-plugins
++statistics
++statsmodels
++tmtoolkit
++tqdm
++tspex
++umap-learn
diff --git a/easybuild/easyconfigs/s/scrublet/scrublet-0.2.3-foss-2023a.eb b/easybuild/easyconfigs/s/scrublet/scrublet-0.2.3-foss-2023a.eb
new file mode 100644
index 00000000000..5b6d65b6bb4
--- /dev/null
+++ b/easybuild/easyconfigs/s/scrublet/scrublet-0.2.3-foss-2023a.eb
@@ -0,0 +1,35 @@
+easyblock = 'PythonBundle'
+
+name = 'scrublet'
+version = '0.2.3'
+
+homepage = 'https://github.com/swolock/scrublet'
+description = "Single-Cell Remover of Doublets - Python code for identifying doublets in single-cell RNA-seq data"
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('scikit-learn', '1.3.1'),
+    ('scikit-image', '0.22.0'),
+    ('matplotlib', '3.7.2'),
+    ('numba', '0.58.1'),
+    ('tqdm', '4.66.1'),
+    ('umap-learn', '0.5.5'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('annoy', '1.17.3', {
+        'checksums': ['9cbfebefe0a5f843eba29c6be4c84d601f4f41ad4ded0486f1b88c3b07739c15'],
+    }),
+    (name, version, {
+        'checksums': ['2185f63070290267f82a36e5b4cae8c321f10415d2d0c9f7e5e97b1126bf653a'],
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'bio'

From 7978e63207611c999dfe391a1aaaaf2b3a376975 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <33718780+casparvl@users.noreply.github.com>
Date: Mon, 29 Jul 2024 14:48:04 +0200
Subject: [PATCH 513/835] Delete
 easybuild/easyconfigs/c/CUDA-Samples/cuda-samples-11.X_multiple-sms.patch

---
 .../cuda-samples-11.X_multiple-sms.patch      | 31 -------------------
 1 file changed, 31 deletions(-)
 delete mode 100644 easybuild/easyconfigs/c/CUDA-Samples/cuda-samples-11.X_multiple-sms.patch

diff --git a/easybuild/easyconfigs/c/CUDA-Samples/cuda-samples-11.X_multiple-sms.patch b/easybuild/easyconfigs/c/CUDA-Samples/cuda-samples-11.X_multiple-sms.patch
deleted file mode 100644
index b6613f6a3c4..00000000000
--- a/easybuild/easyconfigs/c/CUDA-Samples/cuda-samples-11.X_multiple-sms.patch
+++ /dev/null
@@ -1,31 +0,0 @@
-# Fixes "nvcc fatal: Option '--ptx (-ptx)' is not allowed when compiling for multiple GPU architectures"
-# fatal compilation issue when building for multiple SM architectures
-# More info, see https://github.com/NVIDIA/cuda-samples/issues/289
-
-# Author: Caspar van Leeuwen
-
-diff -Nru cuda-samples-11.3.orig/Samples/memMapIPCDrv/Makefile cuda-samples-11.3/Samples/memMapIPCDrv/Makefile
---- cuda-samples-11.3.orig/Samples/memMapIPCDrv/Makefile	2024-07-29 13:17:10.330743000 +0200
-+++ cuda-samples-11.3/Samples/memMapIPCDrv/Makefile	2024-07-29 13:19:13.158507504 +0200
-@@ -321,6 +321,12 @@
- ifneq ($(HIGHEST_SM),)
- GENCODE_FLAGS += -gencode arch=compute_$(HIGHEST_SM),code=compute_$(HIGHEST_SM)
- endif
-+
-+# Generate the explicit PTX file for the lowest SM architecture in $(SMS), so it works on all SMS listed there
-+LOWEST_SM := $(firstword $(sort $(SMS)))
-+ifneq ($(LOWEST_SM),)
-+GENCODE_FLAGS_LOWEST_SM += -gencode arch=compute_$(LOWEST_SM),code=compute_$(LOWEST_SM)
-+endif
- endif
- 
- ifeq ($(TARGET_OS),darwin)
-@@ -401,7 +407,7 @@
- endif
- 
- $(PTX_FILE): memMapIpc_kernel.cu
--	$(EXEC) $(NVCC) $(INCLUDES) $(ALL_CCFLAGS) $(GENCODE_FLAGS) -o $@ -ptx $<
-+	$(EXEC) $(NVCC) $(INCLUDES) $(ALL_CCFLAGS) $(GENCODE_FLAGS_LOWEST_SM) -o $@ -ptx $<
- 	$(EXEC) mkdir -p data
- 	$(EXEC) cp -f $@ ./data
- 	$(EXEC) mkdir -p ../../bin/$(TARGET_ARCH)/$(TARGET_OS)/$(BUILD_TYPE)

From faf3cc66560d16cf312022ce3be0afbc27fdfdcc Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <33718780+casparvl@users.noreply.github.com>
Date: Mon, 29 Jul 2024 14:48:14 +0200
Subject: [PATCH 514/835] Delete
 easybuild/easyconfigs/c/CUDA-Samples/cuda-samples-12.X_multiple-sms.patch

---
 .../cuda-samples-12.X_multiple-sms.patch      | 56 -------------------
 1 file changed, 56 deletions(-)
 delete mode 100644 easybuild/easyconfigs/c/CUDA-Samples/cuda-samples-12.X_multiple-sms.patch

diff --git a/easybuild/easyconfigs/c/CUDA-Samples/cuda-samples-12.X_multiple-sms.patch b/easybuild/easyconfigs/c/CUDA-Samples/cuda-samples-12.X_multiple-sms.patch
deleted file mode 100644
index 8c4e36f7e74..00000000000
--- a/easybuild/easyconfigs/c/CUDA-Samples/cuda-samples-12.X_multiple-sms.patch
+++ /dev/null
@@ -1,56 +0,0 @@
-# Fixes "nvcc fatal: Option '--ptx (-ptx)' is not allowed when compiling for multiple GPU architectures"
-# fatal compilation issue when building for multiple SM architectures
-# More info, see https://github.com/NVIDIA/cuda-samples/issues/289
-
-# Author: Caspar van Leeuwen
-
-diff -Nru cuda-samples-12.2.orig/Samples/3_CUDA_Features/memMapIPCDrv/Makefile cuda-samples-12.2/Samples/3_CUDA_Features/memMapIPCDrv/Makefile
---- cuda-samples-12.2.orig/Samples/3_CUDA_Features/memMapIPCDrv/Makefile	2024-07-29 12:14:28.538848000 +0200
-+++ cuda-samples-12.2/Samples/3_CUDA_Features/memMapIPCDrv/Makefile	2024-07-29 13:02:45.134261829 +0200
-@@ -313,6 +313,12 @@
- ifneq ($(HIGHEST_SM),)
- GENCODE_FLAGS += -gencode arch=compute_$(HIGHEST_SM),code=compute_$(HIGHEST_SM)
- endif
-+
-+# Generate the explicit PTX file for the lowest SM architecture in $(SMS), so it works on all SMS listed there
-+LOWEST_SM := $(firstword $(sort $(SMS)))
-+ifneq ($(LOWEST_SM),)
-+GENCODE_FLAGS_LOWEST_SM += -gencode arch=compute_$(LOWEST_SM),code=compute_$(LOWEST_SM)
-+endif
- endif
- 
- ifeq ($(TARGET_OS),darwin)
-@@ -394,7 +400,7 @@
- endif
- 
- $(PTX_FILE): memMapIpc_kernel.cu
--	$(EXEC) $(NVCC) $(INCLUDES) $(ALL_CCFLAGS) $(GENCODE_FLAGS) -o $@ -ptx $<
-+	$(EXEC) $(NVCC) $(INCLUDES) $(ALL_CCFLAGS) $(GENCODE_FLAGS_LOWEST_SM) -o $@ -ptx $<
- 	$(EXEC) mkdir -p data
- 	$(EXEC) cp -f $@ ./data
- 	$(EXEC) mkdir -p ../../../bin/$(TARGET_ARCH)/$(TARGET_OS)/$(BUILD_TYPE)
-diff -Nru cuda-samples-12.2.orig/Samples/3_CUDA_Features/ptxjit/Makefile cuda-samples-12.2/Samples/3_CUDA_Features/ptxjit/Makefile
---- cuda-samples-12.2.orig/Samples/3_CUDA_Features/ptxjit/Makefile	2024-07-29 12:14:28.546771000 +0200
-+++ cuda-samples-12.2/Samples/3_CUDA_Features/ptxjit/Makefile	2024-07-29 13:02:38.741961008 +0200
-@@ -307,6 +307,12 @@
- ifneq ($(HIGHEST_SM),)
- GENCODE_FLAGS += -gencode arch=compute_$(HIGHEST_SM),code=compute_$(HIGHEST_SM)
- endif
-+
-+# Generate the explicit PTX file for the lowest SM architecture in $(SMS), so it works on all SMS listed there
-+LOWEST_SM := $(firstword $(sort $(SMS)))
-+ifneq ($(LOWEST_SM),)
-+GENCODE_FLAGS_LOWEST_SM += -gencode arch=compute_$(LOWEST_SM),code=compute_$(LOWEST_SM)
-+endif
- endif
- 
- ifeq ($(TARGET_OS),darwin)
-@@ -390,7 +396,7 @@
- endif
- 
- $(PTX_FILE): ptxjit_kernel.cu
--	$(EXEC) $(NVCC) $(INCLUDES) $(ALL_CCFLAGS) $(GENCODE_FLAGS) -o $@ -ptx $<
-+	$(EXEC) $(NVCC) $(INCLUDES) $(ALL_CCFLAGS) $(GENCODE_FLAGS_LOWEST_SM) -o $@ -ptx $<
- 	$(EXEC) mkdir -p data
- 	$(EXEC) cp -f $@ ./data
- 	$(EXEC) mkdir -p ../../../bin/$(TARGET_ARCH)/$(TARGET_OS)/$(BUILD_TYPE)

From d1a7b5e14e79bdedaf6da84fe3ff9fbef1ca8aeb Mon Sep 17 00:00:00 2001
From: casparl <casparl@gcn77.local.snellius.surf.nl>
Date: Mon, 29 Jul 2024 15:08:48 +0200
Subject: [PATCH 515/835] Fix checksum

---
 .../CUDA-Samples/CUDA-Samples-12.2-GCC-11.3.0-CUDA-12.2.0.eb | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-12.2-GCC-11.3.0-CUDA-12.2.0.eb b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-12.2-GCC-11.3.0-CUDA-12.2.0.eb
index 092528fda97..89e1c6fc87b 100644
--- a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-12.2-GCC-11.3.0-CUDA-12.2.0.eb
+++ b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-12.2-GCC-11.3.0-CUDA-12.2.0.eb
@@ -12,7 +12,10 @@ toolchain = {'name': 'GCC', 'version': '11.3.0'}
 source_urls = ['https://github.com/NVIDIA/cuda-samples/archive/']
 sources = ['v%(version)s.tar.gz']
 patches = ['cuda-samples-11.6_multiple-sms.patch']
-checksums = ['c9fbdee420fd4567edb1239420e2a5c93d9652b4ccf3a828fcb3e0de3152e466']
+checksums = [
+    {'v12.2.tar.gz': '1823cfe28e97a9230107aa72b231f78952c0f178b71a920f036d360518480bdc'},
+    {'cuda-samples-11.6_multiple-sms.patch': '8849e4882d797d155d6ebb71377fa1409205361776ade8da699452a4ecb94a0a'},
+]
 
 builddependencies = [
     ('CMake', '3.24.3'),

From 4691ffca1960536051e69bb74e71f22b218caa3e Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Mon, 29 Jul 2024 15:11:00 +0200
Subject: [PATCH 516/835] add patch description

---
 .../s/scenicplus/scenicplus-1.0a1-18072024-foss-2023a.eb        | 2 +-
 .../scenicplus/scenicplus-1.0a1-18072024_requirements.txt.patch | 1 +
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/s/scenicplus/scenicplus-1.0a1-18072024-foss-2023a.eb b/easybuild/easyconfigs/s/scenicplus/scenicplus-1.0a1-18072024-foss-2023a.eb
index c536bd85bc5..9b94d6619f9 100644
--- a/easybuild/easyconfigs/s/scenicplus/scenicplus-1.0a1-18072024-foss-2023a.eb
+++ b/easybuild/easyconfigs/s/scenicplus/scenicplus-1.0a1-18072024-foss-2023a.eb
@@ -258,7 +258,7 @@ exts_list = [
             {'scenicplus-1.0a1-18072024-fa55dae.tar.gz':
              '88cddec1ab2618861e5c93e8a0b17b8e9e2aa3a76410d882c35d472f98724e29'},
             {'scenicplus-1.0a1-18072024_requirements.txt.patch':
-             'fdfba5d9413f6088d657e315ce7aa28cd645154521e9173a7325bd6c4fdd7e7a'},
+             'e39f643872263bcfa305c6483d125bde9ebf9ef3bd146247aa9b924c2ac76c56'},
         ],
     }),
 ]
diff --git a/easybuild/easyconfigs/s/scenicplus/scenicplus-1.0a1-18072024_requirements.txt.patch b/easybuild/easyconfigs/s/scenicplus/scenicplus-1.0a1-18072024_requirements.txt.patch
index ecfeed15e29..3a565b2a10d 100644
--- a/easybuild/easyconfigs/s/scenicplus/scenicplus-1.0a1-18072024_requirements.txt.patch
+++ b/easybuild/easyconfigs/s/scenicplus/scenicplus-1.0a1-18072024_requirements.txt.patch
@@ -1,3 +1,4 @@
+Fix requirements.txt and unpin exact versions
 --- requirements.txt.orig	2024-07-24 10:54:46.267978000 +0200
 +++ requirements.txt	2024-07-24 12:06:31.676022842 +0200
 @@ -1,918 +1,77 @@

From e99bfd0d4c27bac671a57371e804961b37985b9b Mon Sep 17 00:00:00 2001
From: casparl <casparl@gcn77.local.snellius.surf.nl>
Date: Mon, 29 Jul 2024 15:41:01 +0200
Subject: [PATCH 517/835] Fix checksum

---
 .../CUDA-Samples/CUDA-Samples-11.3-GCC-10.3.0-CUDA-11.3.1.eb | 5 ++++-
 .../CUDA-Samples/CUDA-Samples-11.6-GCC-11.3.0-CUDA-11.7.0.eb | 5 ++++-
 .../CUDA-Samples/CUDA-Samples-11.8-GCC-11.3.0-CUDA-11.7.0.eb | 5 ++++-
 .../CUDA-Samples/CUDA-Samples-12.1-GCC-12.3.0-CUDA-12.1.1.eb | 5 ++++-
 4 files changed, 16 insertions(+), 4 deletions(-)

diff --git a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.3-GCC-10.3.0-CUDA-11.3.1.eb b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.3-GCC-10.3.0-CUDA-11.3.1.eb
index 7c19b967f55..ad7b6aba80b 100644
--- a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.3-GCC-10.3.0-CUDA-11.3.1.eb
+++ b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.3-GCC-10.3.0-CUDA-11.3.1.eb
@@ -12,7 +12,10 @@ toolchain = {'name': 'GCC', 'version': '10.3.0'}
 source_urls = ['https://github.com/NVIDIA/cuda-samples/archive/']
 sources = ['v%(version)s.tar.gz']
 patches = ['cuda-samples-11.3_multiple-sms.patch']
-checksums = ['2bee5f7c89347259aaab75aa6df6e10375059bdbbaf04cc7936f5db7d54fa3ac']
+checksums = [
+    {'v11.3.tar.gz': '2bee5f7c89347259aaab75aa6df6e10375059bdbbaf04cc7936f5db7d54fa3ac'},
+    {'cuda-samples-11.3_multiple-sms.patch': 'b31613f4160456f0d0abf82999c7fb7eee781f0efadc8b9bbb5a02ef0f37e21d'},
+]
 
 dependencies = [
     ('CUDA', '11.3.1', '', SYSTEM),
diff --git a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.6-GCC-11.3.0-CUDA-11.7.0.eb b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.6-GCC-11.3.0-CUDA-11.7.0.eb
index 1411d458852..ea78eae4061 100644
--- a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.6-GCC-11.3.0-CUDA-11.7.0.eb
+++ b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.6-GCC-11.3.0-CUDA-11.7.0.eb
@@ -12,7 +12,10 @@ toolchain = {'name': 'GCC', 'version': '11.3.0'}
 source_urls = ['https://github.com/NVIDIA/cuda-samples/archive/']
 sources = ['v%(version)s.tar.gz']
 patches = ['cuda-samples-11.6_multiple-sms.patch']
-checksums = ['75b858bcf9e534eaa0f129c418e661b83872d743de218df8a5278cc429f9ea98']
+checksums = [
+    {'v11.6.tar.gz': '75b858bcf9e534eaa0f129c418e661b83872d743de218df8a5278cc429f9ea98'},
+    {'cuda-samples-11.6_multiple-sms.patch': '8849e4882d797d155d6ebb71377fa1409205361776ade8da699452a4ecb94a0a'},
+]
 
 dependencies = [
     ('CUDA', '11.7.0', '', SYSTEM),
diff --git a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.8-GCC-11.3.0-CUDA-11.7.0.eb b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.8-GCC-11.3.0-CUDA-11.7.0.eb
index db2b3fe617c..be16c76f3be 100644
--- a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.8-GCC-11.3.0-CUDA-11.7.0.eb
+++ b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.8-GCC-11.3.0-CUDA-11.7.0.eb
@@ -12,7 +12,10 @@ toolchain = {'name': 'GCC', 'version': '11.3.0'}
 source_urls = ['https://github.com/NVIDIA/cuda-samples/archive/']
 sources = ['v%(version)s.tar.gz']
 patches = ['cuda-samples-11.6_multiple-sms.patch']
-checksums = ['1bc02c0ca42a323f3c7a05b5682eae703681a91e95b135bfe81f848b2d6a2c51']
+checksums = [
+    {'v11.8.tar.gz': '1bc02c0ca42a323f3c7a05b5682eae703681a91e95b135bfe81f848b2d6a2c51'},
+    {'cuda-samples-11.6_multiple-sms.patch': '8849e4882d797d155d6ebb71377fa1409205361776ade8da699452a4ecb94a0a'},
+]
 
 dependencies = [
     ('CUDA', '11.7.0', '', SYSTEM),
diff --git a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-12.1-GCC-12.3.0-CUDA-12.1.1.eb b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-12.1-GCC-12.3.0-CUDA-12.1.1.eb
index d18522518c8..5a886ca74d4 100644
--- a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-12.1-GCC-12.3.0-CUDA-12.1.1.eb
+++ b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-12.1-GCC-12.3.0-CUDA-12.1.1.eb
@@ -12,7 +12,10 @@ toolchain = {'name': 'GCC', 'version': '12.3.0'}
 source_urls = ['https://github.com/NVIDIA/cuda-samples/archive/']
 sources = ['v%(version)s.tar.gz']
 patches = ['cuda-samples-11.6_multiple-sms.patch']
-checksums = ['f758160645b366d79c2638d8dfd389f01029b8d179ab0c11726b9ef58aecebd9']
+checksums = [
+    {'v12.1.tar.gz': 'f758160645b366d79c2638d8dfd389f01029b8d179ab0c11726b9ef58aecebd9'},
+    {'cuda-samples-11.6_multiple-sms.patch': '8849e4882d797d155d6ebb71377fa1409205361776ade8da699452a4ecb94a0a'},
+]
 
 dependencies = [
     ('CUDA', '12.1.1', '', SYSTEM),

From b57330039d2066726c3d4a026108d26577c92eec Mon Sep 17 00:00:00 2001
From: Adam Huffman <verdurin@users.noreply.github.com>
Date: Mon, 29 Jul 2024 14:54:28 +0100
Subject: [PATCH 518/835] Fix section spacing

---
 .../b/beagle-lib/beagle-lib-4.0.1-GCC-12.3.0-CUDA-12.1.1.eb      | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-4.0.1-GCC-12.3.0-CUDA-12.1.1.eb b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-4.0.1-GCC-12.3.0-CUDA-12.1.1.eb
index 12802801834..2c2bbf6705b 100644
--- a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-4.0.1-GCC-12.3.0-CUDA-12.1.1.eb
+++ b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-4.0.1-GCC-12.3.0-CUDA-12.1.1.eb
@@ -3,6 +3,7 @@ easyblock = 'CMakeMake'
 name = 'beagle-lib'
 version = '4.0.1'
 versionsuffix = '-CUDA-%(cudaver)s'
+
 homepage = 'https://github.com/beagle-dev/beagle-lib'
 description = """beagle-lib is a high-performance library that can perform the core calculations at the heart of most
  Bayesian and Maximum Likelihood phylogenetics packages."""

From bf491029d92dbe570bb839c09525c2e30a35e521 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Mon, 29 Jul 2024 16:12:02 +0200
Subject: [PATCH 519/835] adding easyconfigs:
 RStudio-Server-2023.09.1+494-gfbf-2023a-Java-11-R-4.3.2.eb,
 SOCI-4.0.3-GCC-12.3.0.eb

---
 ...023.09.1+494-gfbf-2023a-Java-11-R-4.3.2.eb | 120 ++++++++++++++++++
 .../s/SOCI/SOCI-4.0.3-GCC-12.3.0.eb           |  52 ++++++++
 2 files changed, 172 insertions(+)
 create mode 100644 easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2023.09.1+494-gfbf-2023a-Java-11-R-4.3.2.eb
 create mode 100644 easybuild/easyconfigs/s/SOCI/SOCI-4.0.3-GCC-12.3.0.eb

diff --git a/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2023.09.1+494-gfbf-2023a-Java-11-R-4.3.2.eb b/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2023.09.1+494-gfbf-2023a-Java-11-R-4.3.2.eb
new file mode 100644
index 00000000000..54037456dd8
--- /dev/null
+++ b/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2023.09.1+494-gfbf-2023a-Java-11-R-4.3.2.eb
@@ -0,0 +1,120 @@
+easyblock = 'CMakeNinja'
+
+name = 'RStudio-Server'
+version = "2023.09.1+494"
+versionsuffix = '-Java-%(javaver)s-R-%(rver)s'
+local_git_rev = 'cd7011dce393115d3a7c3db799dda4b1c7e88711'
+
+homepage = 'https://www.rstudio.com/'
+description = """This is the RStudio Server version.
+RStudio is a set of integrated tools designed to help you be more productive with R.
+
+The server can be started with:
+  rserver --server-daemonize=0 --www-port=8787
+
+If you need a database config one can be created with:
+  MYTMP=`mktemp -d` && echo -e "provider=sqlite\\ndirectory=${MYTMP}/sqlite" > "${MYTMP}/db.conf"
+and then used with:
+  rserver ... --database-config-file="${MYTMP}/db.conf"
+"""
+
+toolchain = {'name': 'gfbf', 'version': '2023a'}
+
+source_urls = ['https://github.com/rstudio/rstudio/archive']
+sources = ['v%(version)s.tar.gz']
+checksums = ['38526a5816e980b12aeaef7debd2151f08ef2e54fed83af2622eb7cdeeb479a2']
+
+builddependencies = [
+    ('ant', '1.10.14', '-Java-%(javaver)s', SYSTEM),
+    ('CMake', '3.26.3'),
+    ('Ninja', '1.11.1'),
+    ('pkgconf', '1.9.5'),
+    ('nodejs', '18.17.1'),
+]
+
+dependencies = [
+    ('Boost', '1.82.0'),
+    ('Java', '11', '', SYSTEM),
+    ('R', '4.3.2'),
+    ('SOCI', '4.0.3'), # CREATED OK
+    ('yaml-cpp', '0.7.0'),
+]
+
+osdependencies = [
+    ('pam-devel', 'libpam0g-dev')
+]
+
+preconfigopts = " && ".join([
+    # Install dependencies via scripts. Done in subshell to preserve PWD
+    "(export RSTUDIO_TOOLS_ROOT='%(builddir)s'",
+    "cd '%(start_dir)s/dependencies/common'",
+    "./install-cef",
+    "./install-dictionaries",
+    "./install-mathjax",
+    "./install-pandoc",
+    "./install-packages",
+    "./install-panmirror",
+    "./install-npm-dependencies)",
+    ""
+])
+
+configopts = " ".join([
+    "-DRSTUDIO_TOOLS_ROOT='%(builddir)s'",
+    "-DRSTUDIO_TARGET=Server",
+    "-DRSTUDIO_USE_SYSTEM_BOOST=ON",
+    "-DRSTUDIO_USE_SYSTEM_SOCI=ON",
+    "-DRSTUDIO_USE_SYSTEM_YAML_CPP=ON",
+    "-DQUARTO_ENABLED=OFF",  # Not available on all archs, use pandoc fallback
+    "-DRSTUDIO_GIT_REVISION_HASH=" + local_git_rev
+])
+
+sanity_check_commands = [
+    # RSession requires environment variables R_HOME and R_DOC_DIR
+    'R_HOME="$EBROOTR/lib64/R" R_DOC_DIR="$R_HOME/doc" rsession --verify-installation=1',
+    # RServer requires a db conf (this may also be needed for live use)
+    # Also create and set a soem dirs so it doesn't try to use $HOME
+    ' '.join([
+        'MYTMP=`mktemp -d`',
+        '&& export RSTUDIO_CONFIG_DIR="$MYTMP"',
+        '&& export XDG_DATA_HOME="$MYTMP/.data"',
+        '&& export XDG_CACHE_HOME="$MYTMP/.cache"',
+        '&& mkdir "$XDG_DATA_HOME" "$XDG_CACHE_HOME"',
+        '&& export RS_LOG_DIR="$MYTMP/log"',
+        '&& echo -e "provider=sqlite\\ndirectory=$MYTMP/db" >> "$MYTMP/db.conf"',
+        '&& rserver',
+        '--verify-installation=1',
+        '--server-user="$USER"',
+        '--database-config-file="$MYTMP/db.conf"',
+        '--server-data-dir="$MYTMP/sdd"',
+        '--secure-cookie-key-file="$MYTMP/secure-cookie-key"',
+    ]),
+]
+
+sanity_check_paths = {
+    'files': ['bin/rstudio-server'],
+    'dirs': ['bin', 'extras', 'resources', 'www', 'www-symbolmaps', 'R'],
+}
+
+modloadmsg = """
+The server can be started with:
+  rserver --server-daemonize=0 --www-port=8787
+
+If you need a database config one can be created with:
+  MYTMP=`mktemp -d` && echo -e "provider=sqlite\\ndirectory=${MYTMP}/sqlite" > "${MYTMP}/db.conf"
+and then used with:
+  rserver ... --database-config-file="${MYTMP}/db.conf"
+"""
+
+moduleclass = 'lang'
+
+# ERROR1:
+    # -> use version 2023.09.1+494 commit: cd7011dce393115d3a7c3db799dda4b1c7e88711 -> req boost 1.78.0
+        # https://github.com/rstudio/rstudio/blob/v2023.09.1%2B494/dependencies/common/install-boost
+    # CMake Error at /kyukon/home/apps/RHEL8/cascadelake-ib/software/CMake/3.26.3-GCCcore-12.3.0/share/cmake-3.26/Modules/FindPackageHandleStandardArgs.cmake:230 (message):
+    # Could NOT find Boost: Found unsuitable version "1.82.0", but required is at
+    # least "1.83.0" (found
+    # /apps/gent/RHEL8/cascadelake-ib/software/Boost/1.82.0-GCC-12.3.0/include, )
+    # Call Stack (most recent call first):
+    # /kyukon/home/apps/RHEL8/cascadelake-ib/software/CMake/3.26.3-GCCcore-12.3.0/share/cmake-3.26/Modules/FindPackageHandleStandardArgs.cmake:598 (_FPHSA_FAILURE_MESSAGE)
+    # /kyukon/home/apps/RHEL8/cascadelake-ib/software/CMake/3.26.3-GCCcore-12.3.0/share/cmake-3.26/Modules/FindBoost.cmake:2377 (find_package_handle_standard_args)
+    # src/cpp/CMakeLists.txt:296 (find_package)
diff --git a/easybuild/easyconfigs/s/SOCI/SOCI-4.0.3-GCC-12.3.0.eb b/easybuild/easyconfigs/s/SOCI/SOCI-4.0.3-GCC-12.3.0.eb
new file mode 100644
index 00000000000..e100da22edb
--- /dev/null
+++ b/easybuild/easyconfigs/s/SOCI/SOCI-4.0.3-GCC-12.3.0.eb
@@ -0,0 +1,52 @@
+easyblock = 'CMakeMake'
+
+name = 'SOCI'
+version = '4.0.3'
+
+homepage = 'http://soci.sourceforge.net/'
+description = """SOCI is a database access library for C++ that makes the illusion of embedding SQL queries in the
+ regular C++ code, staying entirely within the Standard C++."""
+
+toolchain = {'name': 'GCC', 'version': '12.3.0'}
+
+source_urls = ['https://github.com/SOCI/soci/archive']
+sources = ['v%(version)s.tar.gz']
+checksums = ['4b1ff9c8545c5d802fbe06ee6cd2886630e5c03bf740e269bb625b45cf934928']
+
+builddependencies = [
+    ('CMake', '3.26.3'),
+]
+
+dependencies = [
+    ('Boost', '1.82.0'),
+    ('SQLite', '3.42.0'),
+    ('PostgreSQL', '16.1'),
+]
+
+# Matches RStudio (1.4.1717) install options
+# https://github.com/rstudio/rstudio/blob/ddcd7191ec89c4da00e77afae7e9f27e61e87c36/dependencies/common/install-soci
+configopts = "-DCMAKE_POSITION_INDEPENDENT_CODE:BOOL=true "
+configopts += "-DSOCI_TESTS=OFF "
+configopts += "-DSOCI_CXX11=ON "
+configopts += "-DSOCI_EMPTY=OFF "
+configopts += '-DCMAKE_INCLUDE_PATH="$EBROOTBOOST/include" '
+configopts += "-DBoost_USE_STATIC_LIBS=ON "
+configopts += '-DCMAKE_LIBRARY_PATH="$EBROOTBOOST/lib" '
+configopts += "-DWITH_BOOST=ON "
+configopts += "-DWITH_POSTGRESQL=ON "
+configopts += "-DWITH_SQLITE3=ON "
+configopts += "-DWITH_DB2=OFF "
+configopts += "-DWITH_MYSQL=OFF "
+configopts += "-DWITH_ORACLE=OFF "
+configopts += "-DWITH_FIREBIRD=OFF "
+configopts += "-DWITH_ODBC=OFF "
+configopts += "-DBoost_DEBUG=1 "
+
+local_dbs = ['postgresql', 'sqlite3']
+
+sanity_check_paths = {
+    'files': ['lib/libsoci_%s.%s' % (x, SHLIB_EXT) for x in local_dbs + ['core']],
+    'dirs': ['include/soci/%s' % x for x in local_dbs],
+}
+
+moduleclass = 'lang'

From 1b4c1915919fc8b75ed79d0458387c369c327537 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Mon, 29 Jul 2024 16:52:02 +0200
Subject: [PATCH 520/835] clean ec from comments

---
 ...erver-2023.09.1+494-gfbf-2023a-Java-11-R-4.3.2.eb | 12 ------------
 1 file changed, 12 deletions(-)

diff --git a/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2023.09.1+494-gfbf-2023a-Java-11-R-4.3.2.eb b/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2023.09.1+494-gfbf-2023a-Java-11-R-4.3.2.eb
index 54037456dd8..c4c3d741b5e 100644
--- a/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2023.09.1+494-gfbf-2023a-Java-11-R-4.3.2.eb
+++ b/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2023.09.1+494-gfbf-2023a-Java-11-R-4.3.2.eb
@@ -106,15 +106,3 @@ and then used with:
 """
 
 moduleclass = 'lang'
-
-# ERROR1:
-    # -> use version 2023.09.1+494 commit: cd7011dce393115d3a7c3db799dda4b1c7e88711 -> req boost 1.78.0
-        # https://github.com/rstudio/rstudio/blob/v2023.09.1%2B494/dependencies/common/install-boost
-    # CMake Error at /kyukon/home/apps/RHEL8/cascadelake-ib/software/CMake/3.26.3-GCCcore-12.3.0/share/cmake-3.26/Modules/FindPackageHandleStandardArgs.cmake:230 (message):
-    # Could NOT find Boost: Found unsuitable version "1.82.0", but required is at
-    # least "1.83.0" (found
-    # /apps/gent/RHEL8/cascadelake-ib/software/Boost/1.82.0-GCC-12.3.0/include, )
-    # Call Stack (most recent call first):
-    # /kyukon/home/apps/RHEL8/cascadelake-ib/software/CMake/3.26.3-GCCcore-12.3.0/share/cmake-3.26/Modules/FindPackageHandleStandardArgs.cmake:598 (_FPHSA_FAILURE_MESSAGE)
-    # /kyukon/home/apps/RHEL8/cascadelake-ib/software/CMake/3.26.3-GCCcore-12.3.0/share/cmake-3.26/Modules/FindBoost.cmake:2377 (find_package_handle_standard_args)
-    # src/cpp/CMakeLists.txt:296 (find_package)

From b2ae8a6ba2cbfff86c088abd7f8e6b868af440b8 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com>
Date: Mon, 29 Jul 2024 16:54:15 +0200
Subject: [PATCH 521/835] Update
 RStudio-Server-2023.09.1+494-gfbf-2023a-Java-11-R-4.3.2.eb delete comments

---
 .../RStudio-Server-2023.09.1+494-gfbf-2023a-Java-11-R-4.3.2.eb  | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2023.09.1+494-gfbf-2023a-Java-11-R-4.3.2.eb b/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2023.09.1+494-gfbf-2023a-Java-11-R-4.3.2.eb
index c4c3d741b5e..020dde50a43 100644
--- a/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2023.09.1+494-gfbf-2023a-Java-11-R-4.3.2.eb
+++ b/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2023.09.1+494-gfbf-2023a-Java-11-R-4.3.2.eb
@@ -36,7 +36,7 @@ dependencies = [
     ('Boost', '1.82.0'),
     ('Java', '11', '', SYSTEM),
     ('R', '4.3.2'),
-    ('SOCI', '4.0.3'), # CREATED OK
+    ('SOCI', '4.0.3'),
     ('yaml-cpp', '0.7.0'),
 ]
 

From 434a5ab03dc9f4367f686edfc6e66c30fbe5f965 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Mon, 29 Jul 2024 17:02:27 +0200
Subject: [PATCH 522/835] adding easyconfigs: nanopolish-0.14.0-foss-2023a.eb,
 VBZ-Compression-1.0.3-gompi-2023a.eb

---
 .../nanopolish-0.14.0-foss-2023a.eb           | 61 +++++++++++++++++++
 .../VBZ-Compression-1.0.3-gompi-2023a.eb      | 43 +++++++++++++
 2 files changed, 104 insertions(+)
 create mode 100644 easybuild/easyconfigs/n/nanopolish/nanopolish-0.14.0-foss-2023a.eb
 create mode 100644 easybuild/easyconfigs/v/VBZ-Compression/VBZ-Compression-1.0.3-gompi-2023a.eb

diff --git a/easybuild/easyconfigs/n/nanopolish/nanopolish-0.14.0-foss-2023a.eb b/easybuild/easyconfigs/n/nanopolish/nanopolish-0.14.0-foss-2023a.eb
new file mode 100644
index 00000000000..d32ee79a46a
--- /dev/null
+++ b/easybuild/easyconfigs/n/nanopolish/nanopolish-0.14.0-foss-2023a.eb
@@ -0,0 +1,61 @@
+easyblock = 'MakeCp'
+
+name = 'nanopolish'
+version = '0.14.0'
+
+homepage = 'https://github.com/jts/nanopolish'
+description = "Software package for signal-level analysis of Oxford Nanopore sequencing data."
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+source_urls = [
+    'https://github.com/jts/nanopolish/archive/',
+    'https://github.com/mateidavid/fast5/archive/',
+]
+sources = [
+    {
+        'source_urls': ['https://github.com/jts/nanopolish/archive/'],
+        'download_filename': 'v%(version)s.tar.gz',
+        'filename': SOURCE_TAR_GZ,
+    },
+    {
+        'source_urls': ['https://github.com/hasindu2008/slow5lib/archive/'],
+        'download_filename': 'v1.1.0.tar.gz',
+        'filename': 'slow5lib-v1.1.0.tar.gz',
+    },
+]
+checksums = [
+    {'nanopolish-0.14.0.tar.gz': 'bcc1a7e2d23941592d817da3af9165b3843ae52b11a3ca5983d6417f1614ef78'},
+    {'slow5lib-v1.1.0.tar.gz': 'f13f08b85a9a11086b5d9378251093d1858d0dc29d8e727eabacfa57a73f4277'},
+]
+
+builddependencies = [('Eigen', '3.4.0')]
+
+dependencies = [
+    ('zlib', '1.2.13'),
+    ('Python', '3.11.3'),
+    ('Biopython', '1.83'),
+    ('Pysam', '0.22.0'),
+    ('HDF5', '1.14.0'),
+    ('HTSlib', '1.18'),
+    ('minimap2', '2.26'),
+    ('VBZ-Compression', '1.0.3'),
+]
+
+prebuildopts = "rmdir slow5lib && ln -s %(builddir)s/slow5lib-*/ slow5lib && "
+buildopts = "HDF5=noinstall EIGEN=noinstall HTS=noinstall MINIMAP2=noinstall"
+
+runtest = 'test ' + buildopts
+
+files_to_copy = [(['nanopolish'], 'bin'), 'scripts']
+
+postinstallcmds = ["chmod a+rx %(installdir)s/scripts/*"]
+
+sanity_check_paths = {
+    'files': ['bin/nanopolish'],
+    'dirs': ['scripts'],
+}
+
+modextrapaths = {'PATH': 'scripts'}
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/v/VBZ-Compression/VBZ-Compression-1.0.3-gompi-2023a.eb b/easybuild/easyconfigs/v/VBZ-Compression/VBZ-Compression-1.0.3-gompi-2023a.eb
new file mode 100644
index 00000000000..3a3c79f3875
--- /dev/null
+++ b/easybuild/easyconfigs/v/VBZ-Compression/VBZ-Compression-1.0.3-gompi-2023a.eb
@@ -0,0 +1,43 @@
+easyblock = 'CMakeMake'
+
+name = 'VBZ-Compression'
+version = '1.0.3'
+
+homepage = 'https://github.com/nanoporetech/vbz_compression'
+description = "VBZ compression HDF5 plugin for nanopolish"
+
+toolchain = {'name': 'gompi', 'version': '2023a'}
+
+source_urls = [
+    'https://github.com/nanoporetech/vbz_compression/archive',
+    'https://github.com/lemire/streamvbyte/archive',
+]
+sources = [
+    {'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ},
+    {'download_filename': 'v0.4.1.tar.gz', 'filename': 'streamvbyte-v0.4.1.tar.gz'},
+]
+checksums = [
+    {'VBZ-Compression-1.0.3.tar.gz': 'a7450e076db628681bbc0e2b3f941c6c21cc2981a7e1c78628807ffdf1b34f31'},
+    {'streamvbyte-v0.4.1.tar.gz': '4c4e53134a60b0b06816d3faa7dcde28c3e5e8a656dd415d16d80ae6e3d39fcc'},
+]
+
+builddependencies = [('CMake', '3.26.3')]
+
+dependencies = [
+    ('HDF5', '1.14.0'),
+    ('zstd', '1.5.5'),
+]
+
+preconfigopts = "rmdir %(builddir)s/vbz_compression*/third_party/streamvbyte && "
+preconfigopts += "mv %(builddir)s/streamvbyte-* %(builddir)s/streamvbyte && "
+preconfigopts += "mv %(builddir)s/streamvbyte %(builddir)s/vbz_compression*/third_party/. && "
+configopts = "-DENABLE_CONAN=OFF -DENABLE_PERF_TESTING=OFF -DENABLE_PYTHON=OFF "
+
+sanity_check_paths = {
+    'files': ['hdf5/lib/plugin/libvbz_hdf_plugin.%s' % SHLIB_EXT],
+    'dirs': [],
+}
+
+modextrapaths = {'HDF5_PLUGIN_PATH': 'hdf5/lib/plugin/'}
+
+moduleclass = 'lib'

From 661d543e08e36b2be5063e6196d091f6fff681fa Mon Sep 17 00:00:00 2001
From: Sebastian Achilles <s.achilles@fz-juelich.de>
Date: Mon, 29 Jul 2024 20:06:39 +0200
Subject: [PATCH 523/835] adding easyconfigs: GLib-2.80.4-GCCcore-13.3.0.eb

---
 .../g/GLib/GLib-2.80.4-GCCcore-13.3.0.eb      | 53 +++++++++++++++++++
 1 file changed, 53 insertions(+)
 create mode 100644 easybuild/easyconfigs/g/GLib/GLib-2.80.4-GCCcore-13.3.0.eb

diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.80.4-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/GLib/GLib-2.80.4-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..f95eacd4a7b
--- /dev/null
+++ b/easybuild/easyconfigs/g/GLib/GLib-2.80.4-GCCcore-13.3.0.eb
@@ -0,0 +1,53 @@
+easyblock = 'MesonNinja'
+
+name = 'GLib'
+version = '2.80.4'
+
+homepage = 'https://www.gtk.org/'
+description = """GLib is one of the base libraries of the GTK+ project"""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+toolchainopts = {'pic': True}
+
+source_urls = [FTPGNOME_SOURCE]
+sources = [SOURCELOWER_TAR_XZ]
+checksums = ['24e029c5dfc9b44e4573697adf33078a9827c48938555004b3b9096fa4ea034f']
+
+builddependencies = [
+    # Python is required for building against GLib, at least when
+    # gdbus-codegen or one of the other python scripts are used.
+    # Since Meson 0.50 and later are Python >=3.5 only we can't build
+    # Python specific versions of GLib that uses Python 2.x
+    # thus Python should not be a runtime dependency for GLib.
+    # Packages that use GLib should either have an explicit
+    # (build)dependency on Python or it will use the system version
+    # EasyBuild itself uses.
+    ('Python', '3.12.3'),
+    ('Meson', '1.4.0'),
+    ('Ninja', '1.12.1'),
+    ('binutils', '2.42'),
+    ('pkgconf', '2.2.0'),
+]
+
+dependencies = [
+    ('libffi', '3.4.5'),
+    ('gettext', '0.22.5'),
+    ('libxml2', '2.12.7'),
+    ('PCRE2', '10.43'),
+    ('util-linux', '2.40'),
+]
+
+# avoid using hardcoded path to Python binary in build step
+preconfigopts = "export PYTHON=python && "
+
+configopts = "--buildtype=release --default-library=both "
+
+fix_python_shebang_for = ['bin/*']
+
+sanity_check_paths = {
+    'files': ['lib/libglib-%(version_major)s.0.a', 'lib/libglib-%%(version_major)s.0.%s' % SHLIB_EXT],
+    'dirs': ['bin', 'include'],
+}
+
+
+moduleclass = 'vis'

From f2c5b9e3873f959b022e10c5978bd7ce4e92d66a Mon Sep 17 00:00:00 2001
From: Sebastian Achilles <s.achilles@fz-juelich.de>
Date: Mon, 29 Jul 2024 20:13:39 +0200
Subject: [PATCH 524/835] adding easyconfigs:
 parallel-20240722-GCCcore-13.3.0.eb

---
 .../parallel-20240722-GCCcore-13.3.0.eb       | 26 +++++++++++++++++++
 1 file changed, 26 insertions(+)
 create mode 100644 easybuild/easyconfigs/p/parallel/parallel-20240722-GCCcore-13.3.0.eb

diff --git a/easybuild/easyconfigs/p/parallel/parallel-20240722-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/parallel/parallel-20240722-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..92658cc24b7
--- /dev/null
+++ b/easybuild/easyconfigs/p/parallel/parallel-20240722-GCCcore-13.3.0.eb
@@ -0,0 +1,26 @@
+easyblock = 'ConfigureMake'
+
+name = 'parallel'
+version = '20240722'
+
+homepage = 'https://savannah.gnu.org/projects/parallel/'
+description = """parallel: Build and execute shell commands in parallel"""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+source_urls = [GNU_SOURCE]
+sources = [SOURCELOWER_TAR_BZ2]
+checksums = ['c7335471f776af28bea9464ad85a50f2ed120f78fbf75ead6647aeea8e0e53f0']
+
+builddependencies = [('binutils', '2.42')]
+
+dependencies = [('Perl', '5.38.2')]
+
+sanity_check_paths = {
+    'files': ['bin/parallel'],
+    'dirs': []
+}
+
+sanity_check_commands = ["parallel --help"]
+
+moduleclass = 'tools'

From e13a2b443c46d1a3d3eddcf6a2119ad870693cbf Mon Sep 17 00:00:00 2001
From: Sebastian Achilles <s.achilles@fz-juelich.de>
Date: Mon, 29 Jul 2024 20:32:35 +0200
Subject: [PATCH 525/835] adding easyconfigs: cairo-1.18.0-GCCcore-13.3.0.eb,
 pixman-0.43.4-GCCcore-13.3.0.eb

---
 .../c/cairo/cairo-1.18.0-GCCcore-13.3.0.eb    | 51 +++++++++++++++++++
 .../p/pixman/pixman-0.43.4-GCCcore-13.3.0.eb  | 30 +++++++++++
 2 files changed, 81 insertions(+)
 create mode 100644 easybuild/easyconfigs/c/cairo/cairo-1.18.0-GCCcore-13.3.0.eb
 create mode 100644 easybuild/easyconfigs/p/pixman/pixman-0.43.4-GCCcore-13.3.0.eb

diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.18.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/c/cairo/cairo-1.18.0-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..2622f010126
--- /dev/null
+++ b/easybuild/easyconfigs/c/cairo/cairo-1.18.0-GCCcore-13.3.0.eb
@@ -0,0 +1,51 @@
+easyblock = 'MesonNinja'
+
+
+name = 'cairo'
+version = '1.18.0'
+
+homepage = 'https://cairographics.org'
+description = """Cairo is a 2D graphics library with support for multiple output devices.
+ Currently supported output targets include the X Window System (via both Xlib and XCB), Quartz, Win32, image buffers,
+ PostScript, PDF, and SVG file output. Experimental backends include OpenGL, BeOS, OS/2, and DirectFB"""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+source_urls = [
+    'https://cairographics.org/releases/',
+    'https://cairographics.org/snapshots/'
+]
+sources = [SOURCE_TAR_XZ]
+checksums = ['243a0736b978a33dee29f9cca7521733b78a65b5418206fef7bd1c3d4cf10b64']
+
+builddependencies = [
+    ('binutils', '2.42'),
+    ('pkgconf', '2.2.0'),
+    ('Ninja', '1.12.1'),
+    ('Meson', '1.4.0'),
+]
+dependencies = [
+    ('bzip2', '1.0.8'),
+    ('zlib', '1.3.1'),
+    ('libpng', '1.6.43'),
+    ('freetype', '2.13.2'),
+    ('pixman', '0.43.4'),
+    ('expat', '2.6.2'),
+    ('GLib', '2.80.4'),
+    ('X11', '20240607'),
+]
+
+configopts = "--default-library=both"  # static and shared library
+
+sanity_check_paths = {
+    'files': ['bin/cairo-trace', 'lib/cairo/libcairo-trace.%s' % SHLIB_EXT, 'lib/cairo/libcairo-trace.a',
+              'lib/libcairo.a', 'lib/libcairo-gobject.a', 'lib/libcairo-script-interpreter.a',
+              'lib/libcairo.%s' % SHLIB_EXT, 'lib/libcairo-gobject.%s' % SHLIB_EXT,
+              'lib/libcairo-script-interpreter.%s' % SHLIB_EXT] +
+             ['include/cairo/cairo%s.h' % x for x in ['', '-deprecated', '-features', '-ft', '-gobject', '-pdf', '-ps',
+                                                      '-script', '-script-interpreter', '-svg', '-version', '-xcb',
+                                                      '-xlib', '-xlib-xrender']],
+    'dirs': ['lib/pkgconfig'],
+}
+
+moduleclass = 'vis'
diff --git a/easybuild/easyconfigs/p/pixman/pixman-0.43.4-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/pixman/pixman-0.43.4-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..b15cf9f2ef6
--- /dev/null
+++ b/easybuild/easyconfigs/p/pixman/pixman-0.43.4-GCCcore-13.3.0.eb
@@ -0,0 +1,30 @@
+easyblock = 'MesonNinja'
+
+name = 'pixman'
+version = '0.43.4'
+
+homepage = 'http://www.pixman.org/'
+description = """
+ Pixman is a low-level software library for pixel manipulation, providing
+ features such as image compositing and trapezoid rasterization. Important
+ users of pixman are the cairo graphics library and the X server.
+"""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+source_urls = ['https://cairographics.org/releases/']
+sources = [SOURCE_TAR_GZ]
+checksums = ['a0624db90180c7ddb79fc7a9151093dc37c646d8c38d3f232f767cf64b85a226']
+
+builddependencies = [
+    ('binutils', '2.42'),
+    ('Meson', '1.4.0'),
+    ('Ninja', '1.12.1'),
+]
+
+sanity_check_paths = {
+    'files': ['lib/libpixman-1.%s' % SHLIB_EXT],
+    'dirs': [],
+}
+
+moduleclass = 'vis'

From a0a182de1ef88dfc06a346e4a8b55c4155f949b8 Mon Sep 17 00:00:00 2001
From: Samuel Moors <samuel.moors@vub.be>
Date: Tue, 30 Jul 2024 15:41:57 +0200
Subject: [PATCH 526/835] adding easyconfigs: wradlib-2.0.3-foss-2023a.eb

---
 .../w/wradlib/wradlib-2.0.3-foss-2023a.eb     | 59 +++++++++++++++++++
 1 file changed, 59 insertions(+)
 create mode 100644 easybuild/easyconfigs/w/wradlib/wradlib-2.0.3-foss-2023a.eb

diff --git a/easybuild/easyconfigs/w/wradlib/wradlib-2.0.3-foss-2023a.eb b/easybuild/easyconfigs/w/wradlib/wradlib-2.0.3-foss-2023a.eb
new file mode 100644
index 00000000000..c347e7280c7
--- /dev/null
+++ b/easybuild/easyconfigs/w/wradlib/wradlib-2.0.3-foss-2023a.eb
@@ -0,0 +1,59 @@
+easyblock = 'PythonBundle'
+
+name = 'wradlib'
+version = '2.0.3'
+
+homepage = 'https://docs.wradlib.org/'
+description = """
+The wradlib project has been initiated in order facilitate the use of weather
+radar data as well as to provide a common platform for research on new
+algorithms."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+builddependencies = [
+    ('hatchling', '1.18.0'),
+]
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('xarray', '2023.9.0'),
+    ('Cartopy', '0.22.0'),
+    ('dask', '2023.9.2'),
+    ('matplotlib', '3.7.2'),
+    ('netcdf4-python', '1.6.4'),
+    ('h5netcdf', '1.2.0'),
+    ('geopandas', '0.14.2'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('deprecation', '2.1.0', {
+        'checksums': ['72b3bde64e5d778694b0cf68178aed03d15e15477116add3fb773e581f9518ff'],
+    }),
+    ('cmweather', '0.3.2', {
+        'checksums': ['d374b068fcbfeed87bc511f1f77a6047ae752f4a175a852587414b615b4baa5a'],
+    }),
+    ('lat_lon_parser', '1.3.0', {
+        'checksums': ['e3a65dacd5b25a18c56e3ae31b11cd724480be7fe8db2df1c46ed0dd322a1fca'],
+    }),
+    ('xarray-datatree', '0.0.13', {
+        'modulename': 'datatree',
+        'checksums': ['f42bd519cab8754eb8a98749464846893b59560318520c45212e85c46af692c9'],
+    }),
+    ('xmltodict', '0.13.0', {
+        'checksums': ['341595a488e3e01a85a9d8911d8912fd922ede5fecc4dce437eb4b6c8d037e56'],
+    }),
+    ('xradar', '0.5.1', {
+        'checksums': ['b71021164b005f3270afd2079b8ed831a01ed43accbb7fc42c79e31a342546c5'],
+    }),
+    (name, version, {
+        'checksums': ['0d5448a1dd0e030bdd36f7bbc69fa50aee7fb74dbc7b6407d2dc52d18ea40c49'],
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'geo'

From 8de3b0c38f0edcd1b043b6741402129887cd0aa2 Mon Sep 17 00:00:00 2001
From: "Tanmoy Chakraborty, Ph.D."
 <56235576+tanmoy1989@users.noreply.github.com>
Date: Wed, 31 Jul 2024 07:08:39 +0100
Subject: [PATCH 527/835] Update
 easybuild/easyconfigs/s/spglib-python/spglib-python-2.5.0-gfbf-2023b.eb

Co-authored-by: Sam Moors <smoors@users.noreply.github.com>
---
 .../s/spglib-python/spglib-python-2.5.0-gfbf-2023b.eb        | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/easybuild/easyconfigs/s/spglib-python/spglib-python-2.5.0-gfbf-2023b.eb b/easybuild/easyconfigs/s/spglib-python/spglib-python-2.5.0-gfbf-2023b.eb
index 5893038d9fd..9f26cade5d3 100644
--- a/easybuild/easyconfigs/s/spglib-python/spglib-python-2.5.0-gfbf-2023b.eb
+++ b/easybuild/easyconfigs/s/spglib-python/spglib-python-2.5.0-gfbf-2023b.eb
@@ -29,10 +29,7 @@ exts_list = [
     ('pyproject_metadata', '0.8.0', {
         'checksums': ['376d5a00764ac29440a54579f88e66b7d9cb7e629d35c35a1c7248bfebc9b455'],
     }),
-    (name, version, {
-        'modulename': 'spglib',
-        'source_urls': ['https://pypi.python.org/packages/source/%(nameletter)s/spglib'],
-        'sources': ['spglib-%(version)s.tar.gz'],
+    ('spglib', version, {
         'checksums': ['f8bb638897be91b9dbd4c085d9fde1f69048f5949e20f3832cb9438e57418d4b'],
     }),
 ]

From fa3863f056f8364298c9d080bb6bbbc6e624c25c Mon Sep 17 00:00:00 2001
From: vsc46128 <vsc46128@node4011.donphan.os>
Date: Wed, 31 Jul 2024 17:31:03 +0200
Subject: [PATCH 528/835] adding easyconfigs:
 timm-1.0.8-foss-2023a-CUDA-12.1.1.eb

---
 .../timm/timm-1.0.8-foss-2023a-CUDA-12.1.1.eb | 137 ++++++++++++++++++
 1 file changed, 137 insertions(+)
 create mode 100644 easybuild/easyconfigs/t/timm/timm-1.0.8-foss-2023a-CUDA-12.1.1.eb

diff --git a/easybuild/easyconfigs/t/timm/timm-1.0.8-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/t/timm/timm-1.0.8-foss-2023a-CUDA-12.1.1.eb
new file mode 100644
index 00000000000..7c284c62cfe
--- /dev/null
+++ b/easybuild/easyconfigs/t/timm/timm-1.0.8-foss-2023a-CUDA-12.1.1.eb
@@ -0,0 +1,137 @@
+easyblock = 'CargoPythonBundle'
+
+name = 'timm'
+version = '1.0.8'
+versionsuffix = '-CUDA-%(cudaver)s'
+
+homepage = 'https://huggingface.co/docs/timm'
+description = """
+timm is a library containing SOTA computer vision models, layers, utilities,
+optimizers, schedulers, data-loaders, augmentations, and training/evaluation
+scripts.  It comes packaged with >700 pretrained models, and is designed to be
+flexible and easy to use.
+"""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('CUDA', '12.1.1', '', SYSTEM),
+    ('PyTorch', '2.1.2', versionsuffix),
+    ('PyYAML', '6.0'),
+    ('tqdm', '4.66.1'),
+    ('torchvision', '0.16.0', versionsuffix),
+    
+]
+
+builddependencies = [
+    ('maturin', '1.4.0', '-Rust-1.75.0'),  # for safetensors
+    ('PDM', '2.12.4'),
+]
+
+crates = [
+    ('autocfg', '1.2.0'),
+    ('bitflags', '1.3.2'),
+    ('cfg-if', '1.0.0'),
+    ('heck', '0.4.1'),
+    ('indoc', '2.0.5'),
+    ('itoa', '1.0.11'),
+    ('libc', '0.2.153'),
+    ('lock_api', '0.4.11'),
+    ('memmap2', '0.9.4'),
+    ('memoffset', '0.9.1'),
+    ('once_cell', '1.19.0'),
+    ('parking_lot', '0.12.1'),
+    ('parking_lot_core', '0.9.9'),
+    ('portable-atomic', '1.6.0'),
+    ('proc-macro2', '1.0.80'),
+    ('pyo3', '0.21.1'),
+    ('pyo3-build-config', '0.21.1'),
+    ('pyo3-ffi', '0.21.1'),
+    ('pyo3-macros', '0.21.1'),
+    ('pyo3-macros-backend', '0.21.1'),
+    ('quote', '1.0.36'),
+    ('redox_syscall', '0.4.1'),
+    ('ryu', '1.0.17'),
+    ('scopeguard', '1.2.0'),
+    ('serde', '1.0.197'),
+    ('serde_derive', '1.0.197'),
+    ('serde_json', '1.0.115'),
+    ('smallvec', '1.13.2'),
+    ('syn', '2.0.59'),
+    ('target-lexicon', '0.12.14'),
+    ('unicode-ident', '1.0.12'),
+    ('unindent', '0.2.3'),
+    ('windows-targets', '0.48.5'),
+    ('windows_aarch64_gnullvm', '0.48.5'),
+    ('windows_aarch64_msvc', '0.48.5'),
+    ('windows_i686_gnu', '0.48.5'),
+    ('windows_i686_msvc', '0.48.5'),
+    ('windows_x86_64_gnu', '0.48.5'),
+    ('windows_x86_64_gnullvm', '0.48.5'),
+    ('windows_x86_64_msvc', '0.48.5'),
+]
+
+
+sources = [SOURCE_TAR_GZ]
+checksums = [
+    {'timm-1.0.8.tar.gz': 'f54a579f1cc39c43d99a4b03603e39c4cee87d4f0a08aba9c22e19064b30bf95'},
+    {'autocfg-1.2.0.tar.gz': 'f1fdabc7756949593fe60f30ec81974b613357de856987752631dea1e3394c80'},
+    {'bitflags-1.3.2.tar.gz': 'bef38d45163c2f1dde094a7dfd33ccf595c92905c8f8f4fdc18d06fb1037718a'},
+    {'cfg-if-1.0.0.tar.gz': 'baf1de4339761588bc0619e3cbc0120ee582ebb74b53b4efbf79117bd2da40fd'},
+    {'heck-0.4.1.tar.gz': '95505c38b4572b2d910cecb0281560f54b440a19336cbbcb27bf6ce6adc6f5a8'},
+    {'indoc-2.0.5.tar.gz': 'b248f5224d1d606005e02c97f5aa4e88eeb230488bcc03bc9ca4d7991399f2b5'},
+    {'itoa-1.0.11.tar.gz': '49f1f14873335454500d59611f1cf4a4b0f786f9ac11f4312a78e4cf2566695b'},
+    {'libc-0.2.153.tar.gz': '9c198f91728a82281a64e1f4f9eeb25d82cb32a5de251c6bd1b5154d63a8e7bd'},
+    {'lock_api-0.4.11.tar.gz': '3c168f8615b12bc01f9c17e2eb0cc07dcae1940121185446edc3744920e8ef45'},
+    {'memmap2-0.9.4.tar.gz': 'fe751422e4a8caa417e13c3ea66452215d7d63e19e604f4980461212f3ae1322'},
+    {'memoffset-0.9.1.tar.gz': '488016bfae457b036d996092f6cb448677611ce4449e970ceaf42695203f218a'},
+    {'once_cell-1.19.0.tar.gz': '3fdb12b2476b595f9358c5161aa467c2438859caa136dec86c26fdd2efe17b92'},
+    {'parking_lot-0.12.1.tar.gz': '3742b2c103b9f06bc9fff0a37ff4912935851bee6d36f3c02bcc755bcfec228f'},
+    {'parking_lot_core-0.9.9.tar.gz': '4c42a9226546d68acdd9c0a280d17ce19bfe27a46bf68784e4066115788d008e'},
+    {'portable-atomic-1.6.0.tar.gz': '7170ef9988bc169ba16dd36a7fa041e5c4cbeb6a35b76d4c03daded371eae7c0'},
+    {'proc-macro2-1.0.80.tar.gz': 'a56dea16b0a29e94408b9aa5e2940a4eedbd128a1ba20e8f7ae60fd3d465af0e'},
+    {'pyo3-0.21.1.tar.gz': 'a7a8b1990bd018761768d5e608a13df8bd1ac5f678456e0f301bb93e5f3ea16b'},
+    {'pyo3-build-config-0.21.1.tar.gz': '650dca34d463b6cdbdb02b1d71bfd6eb6b6816afc708faebb3bac1380ff4aef7'},
+    {'pyo3-ffi-0.21.1.tar.gz': '09a7da8fc04a8a2084909b59f29e1b8474decac98b951d77b80b26dc45f046ad'},
+    {'pyo3-macros-0.21.1.tar.gz': '4b8a199fce11ebb28e3569387228836ea98110e43a804a530a9fd83ade36d513'},
+    {'pyo3-macros-backend-0.21.1.tar.gz': '93fbbfd7eb553d10036513cb122b888dcd362a945a00b06c165f2ab480d4cc3b'},
+    {'quote-1.0.36.tar.gz': '0fa76aaf39101c457836aec0ce2316dbdc3ab723cdda1c6bd4e6ad4208acaca7'},
+    {'redox_syscall-0.4.1.tar.gz': '4722d768eff46b75989dd134e5c353f0d6296e5aaa3132e776cbdb56be7731aa'},
+    {'ryu-1.0.17.tar.gz': 'e86697c916019a8588c99b5fac3cead74ec0b4b819707a682fd4d23fa0ce1ba1'},
+    {'scopeguard-1.2.0.tar.gz': '94143f37725109f92c262ed2cf5e59bce7498c01bcc1502d7b9afe439a4e9f49'},
+    {'serde-1.0.197.tar.gz': '3fb1c873e1b9b056a4dc4c0c198b24c3ffa059243875552b2bd0933b1aee4ce2'},
+    {'serde_derive-1.0.197.tar.gz': '7eb0b34b42edc17f6b7cac84a52a1c5f0e1bb2227e997ca9011ea3dd34e8610b'},
+    {'serde_json-1.0.115.tar.gz': '12dc5c46daa8e9fdf4f5e71b6cf9a53f2487da0e86e55808e2d35539666497dd'},
+    {'smallvec-1.13.2.tar.gz': '3c5e1a9a646d36c3599cd173a41282daf47c44583ad367b8e6837255952e5c67'},
+    {'syn-2.0.59.tar.gz': '4a6531ffc7b071655e4ce2e04bd464c4830bb585a61cabb96cf808f05172615a'},
+    {'target-lexicon-0.12.14.tar.gz': 'e1fc403891a21bcfb7c37834ba66a547a8f402146eba7265b5a6d88059c9ff2f'},
+    {'unicode-ident-1.0.12.tar.gz': '3354b9ac3fae1ff6755cb6db53683adb661634f67557942dea4facebec0fee4b'},
+    {'unindent-0.2.3.tar.gz': 'c7de7d73e1754487cb58364ee906a499937a0dfabd86bcb980fa99ec8c8fa2ce'},
+    {'windows-targets-0.48.5.tar.gz': '9a2fa6e2155d7247be68c096456083145c183cbbbc2764150dda45a87197940c'},
+    {'windows_aarch64_gnullvm-0.48.5.tar.gz': '2b38e32f0abccf9987a4e3079dfb67dcd799fb61361e53e2882c3cbaf0d905d8'},
+    {'windows_aarch64_msvc-0.48.5.tar.gz': 'dc35310971f3b2dbbf3f0690a219f40e2d9afcf64f9ab7cc1be722937c26b4bc'},
+    {'windows_i686_gnu-0.48.5.tar.gz': 'a75915e7def60c94dcef72200b9a8e58e5091744960da64ec734a6c6e9b3743e'},
+    {'windows_i686_msvc-0.48.5.tar.gz': '8f55c233f70c4b27f66c523580f78f1004e8b5a8b659e05a4eb49d4166cca406'},
+    {'windows_x86_64_gnu-0.48.5.tar.gz': '53d40abd2583d23e4718fddf1ebec84dbff8381c07cae67ff7768bbf19c6718e'},
+    {'windows_x86_64_gnullvm-0.48.5.tar.gz': '0b7b52767868a23d5bab768e390dc5f5c55825b6d30b86c844ff2dc7414044cc'},
+    {'windows_x86_64_msvc-0.48.5.tar.gz': 'ed94fce61571a4006852b7389a063ab983c02eb1bb37b47f8272ce92d06d9538'},
+]
+
+use_pip = True
+
+exts_list = [
+    ('huggingface_hub', '0.24.5', {
+        'checksums': ['7b45d6744dd53ce9cbf9880957de00e9d10a9ae837f1c9b7255fc8fa4e8264f3'],
+    }),
+    ('safetensors', '0.4.3', {
+        'checksums': ['2f85fc50c4e07a21e95c24e07460fe6f7e2859d0ce88092838352b798ce711c2'],
+    }),
+    (name, version, {
+        'checksums': ['f54a579f1cc39c43d99a4b03603e39c4cee87d4f0a08aba9c22e19064b30bf95'],
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'lib'

From ccbd3bd18cb3bf1a8ebd0ec05dadc4afb2134dfd Mon Sep 17 00:00:00 2001
From: vsc46128 <vsc46128@node4011.donphan.os>
Date: Wed, 31 Jul 2024 18:05:11 +0200
Subject: [PATCH 529/835] remove whitespace

---
 .../easyconfigs/t/timm/timm-1.0.8-foss-2023a-CUDA-12.1.1.eb    | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/easybuild/easyconfigs/t/timm/timm-1.0.8-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/t/timm/timm-1.0.8-foss-2023a-CUDA-12.1.1.eb
index 7c284c62cfe..998631b3eed 100644
--- a/easybuild/easyconfigs/t/timm/timm-1.0.8-foss-2023a-CUDA-12.1.1.eb
+++ b/easybuild/easyconfigs/t/timm/timm-1.0.8-foss-2023a-CUDA-12.1.1.eb
@@ -20,8 +20,7 @@ dependencies = [
     ('PyTorch', '2.1.2', versionsuffix),
     ('PyYAML', '6.0'),
     ('tqdm', '4.66.1'),
-    ('torchvision', '0.16.0', versionsuffix),
-    
+    ('torchvision', '0.16.0', versionsuffix), 
 ]
 
 builddependencies = [

From f8b201473ce2dd6d2220b6b8d1e870b11953e690 Mon Sep 17 00:00:00 2001
From: Lara Ramona Peeters <49882639+laraPPr@users.noreply.github.com>
Date: Wed, 31 Jul 2024 19:03:33 +0200
Subject: [PATCH 530/835] Update
 easybuild/easyconfigs/t/timm/timm-1.0.8-foss-2023a-CUDA-12.1.1.eb

---
 .../easyconfigs/t/timm/timm-1.0.8-foss-2023a-CUDA-12.1.1.eb     | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/t/timm/timm-1.0.8-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/t/timm/timm-1.0.8-foss-2023a-CUDA-12.1.1.eb
index 998631b3eed..93f0d02792f 100644
--- a/easybuild/easyconfigs/t/timm/timm-1.0.8-foss-2023a-CUDA-12.1.1.eb
+++ b/easybuild/easyconfigs/t/timm/timm-1.0.8-foss-2023a-CUDA-12.1.1.eb
@@ -20,7 +20,7 @@ dependencies = [
     ('PyTorch', '2.1.2', versionsuffix),
     ('PyYAML', '6.0'),
     ('tqdm', '4.66.1'),
-    ('torchvision', '0.16.0', versionsuffix), 
+    ('torchvision', '0.16.0', versionsuffix),
 ]
 
 builddependencies = [

From 55838830b9ec28356a7f106e55d4ecc94fe93688 Mon Sep 17 00:00:00 2001
From: WilleBell <cintiawillemyns@gmail.com>
Date: Wed, 31 Jul 2024 19:22:30 +0200
Subject: [PATCH 531/835] adding easyconfigs: CLANS-2.0.8-foss-2023a.eb

---
 .../c/CLANS/CLANS-2.0.8-foss-2023a.eb         | 38 +++++++++++++++++++
 1 file changed, 38 insertions(+)
 create mode 100644 easybuild/easyconfigs/c/CLANS/CLANS-2.0.8-foss-2023a.eb

diff --git a/easybuild/easyconfigs/c/CLANS/CLANS-2.0.8-foss-2023a.eb b/easybuild/easyconfigs/c/CLANS/CLANS-2.0.8-foss-2023a.eb
new file mode 100644
index 00000000000..4d2d1d0eafe
--- /dev/null
+++ b/easybuild/easyconfigs/c/CLANS/CLANS-2.0.8-foss-2023a.eb
@@ -0,0 +1,38 @@
+easyblock = "PythonBundle"
+
+name = 'CLANS'
+version = '2.0.8'
+
+homepage = 'https://github.com/inbalpaz/CLANS'
+description = """
+CLANS 2.0 is a Python-based program for clustering sequences in the 2D or 3D space, based on
+their sequence similarities. CLANS visualizes the dynamic clustering process and enables the
+user to interactively control it and explore the cluster map in various ways. 
+"""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('numba', '0.58.1'),
+    ('VisPy', '0.14.1'),
+    ('Biopython', '1.83'),
+    ('Pillow', '10.0.0'),
+    ('PyQt5', '5.15.10'),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    (name, version, {
+        'source_urls': ['https://github.com/inbalpaz/CLANS/archive/refs/tags/'],
+        'sources': ['%(version)s.tar.gz'],
+        'checksums': ['7b856ec3b13c420dbe30169e8cdd7d6899acb79042ca66920eafd05adf4d2815'],
+    }),
+]
+
+sanity_check_commands = ['python -m clans -h']
+
+moduleclass = 'vis'

From 2159744f0d49f9748b839a9c15400ebeb17f8a01 Mon Sep 17 00:00:00 2001
From: Bart Oldeman <bart.oldeman@calculquebec.ca>
Date: Wed, 31 Jul 2024 18:54:20 +0000
Subject: [PATCH 532/835] adding easyconfigs: HPL-2.3-foss-2024a.eb,
 gfbf-2024a.eb, gompi-2024a.eb, OSU-Micro-Benchmarks-7.4-gompi-2024a.eb,
 FFTW.MPI-3.3.10-gompi-2024a.eb, foss-2024a.eb,
 SciPy-bundle-2024.05-gfbf-2024a.eb, ScaLAPACK-2.2.0-gompi-2024a-fb.eb

---
 .../f/FFTW.MPI/FFTW.MPI-3.3.10-gompi-2024a.eb | 19 ++++
 easybuild/easyconfigs/f/foss/foss-2024a.eb    | 28 ++++++
 easybuild/easyconfigs/g/gfbf/gfbf-2024a.eb    | 20 ++++
 easybuild/easyconfigs/g/gompi/gompi-2024a.eb  | 20 ++++
 .../easyconfigs/h/HPL/HPL-2.3-foss-2024a.eb   | 21 ++++
 .../OSU-Micro-Benchmarks-7.4-gompi-2024a.eb   | 26 +++++
 .../ScaLAPACK-2.2.0-gompi-2024a-fb.eb         | 40 ++++++++
 .../SciPy-bundle-2024.05-gfbf-2024a.eb        | 97 +++++++++++++++++++
 8 files changed, 271 insertions(+)
 create mode 100644 easybuild/easyconfigs/f/FFTW.MPI/FFTW.MPI-3.3.10-gompi-2024a.eb
 create mode 100644 easybuild/easyconfigs/f/foss/foss-2024a.eb
 create mode 100644 easybuild/easyconfigs/g/gfbf/gfbf-2024a.eb
 create mode 100644 easybuild/easyconfigs/g/gompi/gompi-2024a.eb
 create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.3-foss-2024a.eb
 create mode 100644 easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-7.4-gompi-2024a.eb
 create mode 100644 easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gompi-2024a-fb.eb
 create mode 100644 easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2024.05-gfbf-2024a.eb

diff --git a/easybuild/easyconfigs/f/FFTW.MPI/FFTW.MPI-3.3.10-gompi-2024a.eb b/easybuild/easyconfigs/f/FFTW.MPI/FFTW.MPI-3.3.10-gompi-2024a.eb
new file mode 100644
index 00000000000..2ed420c412f
--- /dev/null
+++ b/easybuild/easyconfigs/f/FFTW.MPI/FFTW.MPI-3.3.10-gompi-2024a.eb
@@ -0,0 +1,19 @@
+name = 'FFTW.MPI'
+version = '3.3.10'
+
+homepage = 'https://www.fftw.org'
+description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT)
+in one or more dimensions, of arbitrary input size, and of both real and complex data."""
+
+toolchain = {'name': 'gompi', 'version': '2024a'}
+toolchainopts = {'pic': True}
+
+source_urls = [homepage]
+sources = ['fftw-%(version)s.tar.gz']
+checksums = ['56c932549852cddcfafdab3820b0200c7742675be92179e59e6215b340e26467']
+
+dependencies = [('FFTW', '3.3.10')]
+
+runtest = 'check'
+
+moduleclass = 'numlib'
diff --git a/easybuild/easyconfigs/f/foss/foss-2024a.eb b/easybuild/easyconfigs/f/foss/foss-2024a.eb
new file mode 100644
index 00000000000..7e9a4ba5112
--- /dev/null
+++ b/easybuild/easyconfigs/f/foss/foss-2024a.eb
@@ -0,0 +1,28 @@
+easyblock = 'Toolchain'
+
+name = 'foss'
+version = '2024a'
+
+homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#foss-toolchain'
+description = """GNU Compiler Collection (GCC) based compiler toolchain, including
+ OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK."""
+
+toolchain = SYSTEM
+
+local_gccver = '13.3.0'
+
+# toolchain used to build foss dependencies
+local_comp_mpi_tc = ('gompi', version)
+
+# we need GCC and OpenMPI as explicit dependencies instead of gompi toolchain
+# because of toolchain preparation functions
+dependencies = [
+    ('GCC', local_gccver),
+    ('OpenMPI', '5.0.3', '', ('GCC', local_gccver)),
+    ('FlexiBLAS', '3.4.4', '', ('GCC', local_gccver)),
+    ('FFTW', '3.3.10', '', ('GCC', local_gccver)),
+    ('FFTW.MPI', '3.3.10', '', local_comp_mpi_tc),
+    ('ScaLAPACK', '2.2.0', '-fb', local_comp_mpi_tc),
+]
+
+moduleclass = 'toolchain'
diff --git a/easybuild/easyconfigs/g/gfbf/gfbf-2024a.eb b/easybuild/easyconfigs/g/gfbf/gfbf-2024a.eb
new file mode 100644
index 00000000000..51b74722cb5
--- /dev/null
+++ b/easybuild/easyconfigs/g/gfbf/gfbf-2024a.eb
@@ -0,0 +1,20 @@
+easyblock = 'Toolchain'
+
+name = 'gfbf'
+version = '2024a'
+
+homepage = '(none)'
+description = """GNU Compiler Collection (GCC) based compiler toolchain, including
+ FlexiBLAS (BLAS and LAPACK support) and (serial) FFTW."""
+
+toolchain = SYSTEM
+
+local_gccver = '13.3.0'
+
+dependencies = [
+    ('GCC', local_gccver),
+    ('FlexiBLAS', '3.4.4', '', ('GCC', local_gccver)),
+    ('FFTW', '3.3.10', '', ('GCC', local_gccver)),
+]
+
+moduleclass = 'toolchain'
diff --git a/easybuild/easyconfigs/g/gompi/gompi-2024a.eb b/easybuild/easyconfigs/g/gompi/gompi-2024a.eb
new file mode 100644
index 00000000000..c49f4050ff8
--- /dev/null
+++ b/easybuild/easyconfigs/g/gompi/gompi-2024a.eb
@@ -0,0 +1,20 @@
+easyblock = 'Toolchain'
+
+name = 'gompi'
+version = '2024a'
+
+homepage = '(none)'
+description = """GNU Compiler Collection (GCC) based compiler toolchain,
+ including OpenMPI for MPI support."""
+
+toolchain = SYSTEM
+
+local_gccver = '13.3.0'
+
+# compiler toolchain dependencies
+dependencies = [
+    ('GCC', local_gccver),  # includes both GCC and binutils
+    ('OpenMPI', '5.0.3', '', ('GCC', local_gccver)),
+]
+
+moduleclass = 'toolchain'
diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.3-foss-2024a.eb b/easybuild/easyconfigs/h/HPL/HPL-2.3-foss-2024a.eb
new file mode 100644
index 00000000000..8a70a42bb41
--- /dev/null
+++ b/easybuild/easyconfigs/h/HPL/HPL-2.3-foss-2024a.eb
@@ -0,0 +1,21 @@
+name = 'HPL'
+version = '2.3'
+
+homepage = 'https://www.netlib.org/benchmark/hpl/'
+description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits)
+ arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available
+ implementation of the High Performance Computing Linpack Benchmark."""
+
+toolchain = {'name': 'foss', 'version': '2024a'}
+toolchainopts = {'usempi': True}
+
+source_urls = ['https://www.netlib.org/benchmark/%(namelower)s']
+sources = [SOURCELOWER_TAR_GZ]
+# fix Make dependencies, so parallel build also works
+patches = ['HPL_parallel-make.patch']
+checksums = [
+    '32c5c17d22330e6f2337b681aded51637fb6008d3f0eb7c277b163fadd612830',  # hpl-2.3.tar.gz
+    '2a5bf9c4f328049828ddecec7ba3f05a9e25d236f4212747c53bd22fea80c5e6',  # HPL_parallel-make.patch
+]
+
+moduleclass = 'tools'
diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-7.4-gompi-2024a.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-7.4-gompi-2024a.eb
new file mode 100644
index 00000000000..0d9573028dd
--- /dev/null
+++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-7.4-gompi-2024a.eb
@@ -0,0 +1,26 @@
+easyblock = 'ConfigureMake'
+
+name = 'OSU-Micro-Benchmarks'
+version = '7.4'
+
+homepage = 'https://mvapich.cse.ohio-state.edu/benchmarks/'
+description = """OSU Micro-Benchmarks"""
+
+toolchain = {'name': 'gompi', 'version': '2024a'}
+toolchainopts = {'usempi': True}
+
+source_urls = ['https://mvapich.cse.ohio-state.edu/download/mvapich/']
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['1edd0c2efa61999409bfb28740a7f39689a5b42b1a1b4c66d1656e5637f7cefc']
+
+local_benchmark_dirs = [
+    'libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup']
+]
+modextrapaths = {'PATH': local_benchmark_dirs}
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': local_benchmark_dirs,
+}
+
+moduleclass = 'perf'
diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gompi-2024a-fb.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gompi-2024a-fb.eb
new file mode 100644
index 00000000000..1bccc16f38b
--- /dev/null
+++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gompi-2024a-fb.eb
@@ -0,0 +1,40 @@
+name = 'ScaLAPACK'
+version = '2.2.0'
+versionsuffix = '-fb'
+
+homepage = 'https://www.netlib.org/scalapack/'
+description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines
+ redesigned for distributed memory MIMD parallel computers."""
+
+toolchain = {'name': 'gompi', 'version': '2024a'}
+toolchainopts = {'extra_fflags': '-lpthread', 'openmp': True, 'pic': True, 'usempi': True}
+
+source_urls = [homepage]
+sources = [SOURCELOWER_TGZ]
+patches = ['ScaLAPACK-%(version)s_fix-GCC-10.patch']
+checksums = [
+    '40b9406c20735a9a3009d863318cb8d3e496fb073d201c5463df810e01ab2a57',  # scalapack-2.2.0.tgz
+    'f6bc3c6dee012ba4a696548a2e12b6aae932ce4fd5a142153b338839f52b5906',  # ScaLAPACK-2.2.0_fix-GCC-10.patch
+]
+
+builddependencies = [
+    ('CMake', '3.29.3'),
+]
+
+dependencies = [
+    ('FlexiBLAS', '3.4.4'),
+]
+
+# Config Opts based on AOCL User Guide:
+# https://developer.amd.com/wp-content/resources/AOCL_User%20Guide_2.2.pdf
+
+configopts = '-DBUILD_SHARED_LIBS=ON '
+configopts += '-DBLAS_LIBRARIES="$EBROOTFLEXIBLAS/lib/libflexiblas.%s" ' % SHLIB_EXT
+configopts += '-DLAPACK_LIBRARIES="$EBROOTFLEXIBLAS/lib/libflexiblas.%s" ' % SHLIB_EXT
+
+sanity_check_paths = {
+    'files': ['lib/libscalapack.%s' % SHLIB_EXT, 'lib64/libscalapack.%s' % SHLIB_EXT],
+    'dirs': ["lib", "lib64"],
+}
+
+moduleclass = 'numlib'
diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2024.05-gfbf-2024a.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2024.05-gfbf-2024a.eb
new file mode 100644
index 00000000000..c140938671c
--- /dev/null
+++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2024.05-gfbf-2024a.eb
@@ -0,0 +1,97 @@
+easyblock = 'PythonBundle'
+
+name = 'SciPy-bundle'
+version = '2024.05'
+
+homepage = 'https://python.org/'
+description = "Bundle of Python packages for scientific software"
+
+toolchain = {'name': 'gfbf', 'version': '2024a'}
+toolchainopts = {'pic': True, 'lowopt': True}
+
+builddependencies = [
+    ('hypothesis', '6.103.1'),
+    ('UnZip', '6.0'),
+    # scipy >= 1.9.0 uses Meson/Ninja
+    ('Meson', '1.4.0'),
+    ('meson-python', '0.16.0'),
+    ('Ninja', '1.12.1'),
+    ('pkgconf', '2.2.0'),   # required by scipy
+]
+
+dependencies = [
+    ('Python', '3.12.3'),
+    ('Python-bundle-PyPI', '2024.06'),
+    ('pybind11', '2.12.0'),  # required by scipy
+]
+
+use_pip = True
+
+# order is important!
+exts_list = [
+    ('numpy', '1.26.4', {
+        'patches': ['numpy-1.22.3_disable-broken-override-test.patch'],
+        'checksums': [
+            {'numpy-1.26.4.tar.gz': '2a02aba9ed12e4ac4eb3ea9421c420301a0c6460d9830d74a9df87efa4912010'},
+            {'numpy-1.22.3_disable-broken-override-test.patch':
+             '9c589bb073b28b25ff45eb3c63c57966aa508dd8b318d0b885b6295271e4983c'},
+        ],
+    }),
+    ('ply', '3.11', {
+        'checksums': ['00c7c1aaa88358b9c765b6d3000c6eec0ba42abca5351b095321aef446081da3'],
+    }),
+    ('gast', '0.5.4', {
+        'checksums': ['9c270fe5f4b130969b54174de7db4e764b09b4f7f67ccfc32480e29f78348d97'],
+    }),
+    ('beniget', '0.4.1', {
+        'checksums': ['75554b3b8ad0553ce2f607627dad3d95c60c441189875b98e097528f8e23ac0c'],
+    }),
+    ('pythran', '0.16.1', {
+        'checksums': ['861748c0f9c7d422b32724b114b3817d818ed4eab86c09781aa0a3f7ceabb7f9'],
+    }),
+    ('versioneer', '0.29', {
+        'checksums': ['5ab283b9857211d61b53318b7c792cf68e798e765ee17c27ade9f6c924235731'],
+    }),
+    ('scipy', '1.13.1', {
+        'enable_slow_tests': True,
+        'ignore_test_result': False,
+        'patches': [
+            'scipy-1.11.1_disable-tests.patch',
+            'scipy-1.11.1_xfail-aarch64_test_maxiter_worsening.patch',
+        ],
+        'checksums': [
+            {'scipy-1.13.1.tar.gz': '095a87a0312b08dfd6a6155cbbd310a8c51800fc931b8c0b84003014b874ed3c'},
+            {'scipy-1.11.1_disable-tests.patch': '906bfb03397d94882ccdc1b93bc2c8e854e0e060c2d107c83042992394e6a4af'},
+            {'scipy-1.11.1_xfail-aarch64_test_maxiter_worsening.patch':
+             '918c8e6fa8215d459126f267764c961bde729ea4a116c7f6287cddfdc58ffcea'},
+        ],
+    }),
+    ('numexpr', '2.10.0', {
+        'patches': ['numexpr-2.10.0_fix-numpy-1.x.patch'],
+        'checksums': [
+            {'numexpr-2.10.0.tar.gz': 'c89e930752639df040539160326d8f99a84159bbea41943ab8e960591edaaef0'},
+            {'numexpr-2.10.0_fix-numpy-1.x.patch': '8d70b2e95579e6f0adc07bc615144f7657b3b607f9210ec328b6622458ca726d'},
+        ],
+    }),
+    ('Bottleneck', '1.3.8', {
+        'checksums': ['6780d896969ba7f53c8995ba90c87c548beb3db435dc90c60b9a10ed1ab4d868'],
+    }),
+    ('tzdata', '2024.1', {
+        'checksums': ['2674120f8d891909751c38abcdfd386ac0a5a1127954fbc332af6b5ceae07efd'],
+    }),
+    ('pandas', '2.2.2', {
+        'preinstallopts': "export PANDAS_CI=0 && ",
+        'checksums': ['9e79019aba43cb4fda9e4d983f8e88ca0373adbb697ae9c6c43093218de28b54'],
+    }),
+    ('mpmath', '1.3.0', {
+        'checksums': ['7a28eb2a9774d00c7bc92411c19a89209d5da7c4c9a9e227be8330a23a25b91f'],
+    }),
+    ('deap', '1.4.1', {
+        'modulename': 'deap.base',
+        'checksums': ['cc01de9892dfa7d1bc9803dab28892fead177f0182c81db47360a240ead778ff'],
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'lang'

From 7a153d214bfca0dc62ff38ca785a17efc342d055 Mon Sep 17 00:00:00 2001
From: Bart Oldeman <bart.oldeman@calculquebec.ca>
Date: Wed, 31 Jul 2024 19:04:39 +0000
Subject: [PATCH 533/835] {toolchain}[iimpi/2024a,system/system] Rename
 intel-2024.06 toolchain to 2024a

---
 .../h/HPL/{HPL-2.3-intel-2024.06.eb => HPL-2.3-intel-2024a.eb}  | 2 +-
 .../easyconfigs/i/iimpi/{iimpi-2024.06.eb => iimpi-2024a.eb}    | 2 +-
 ...4.2.0-iimpi-2024.06.eb => imkl-FFTW-2024.2.0-iimpi-2024a.eb} | 2 +-
 .../easyconfigs/i/intel/{intel-2024.06.eb => intel-2024a.eb}    | 2 +-
 ...iimpi-2024.06.eb => OSU-Micro-Benchmarks-7.4-iimpi-2024a.eb} | 2 +-
 5 files changed, 5 insertions(+), 5 deletions(-)
 rename easybuild/easyconfigs/h/HPL/{HPL-2.3-intel-2024.06.eb => HPL-2.3-intel-2024a.eb} (94%)
 rename easybuild/easyconfigs/i/iimpi/{iimpi-2024.06.eb => iimpi-2024a.eb} (95%)
 rename easybuild/easyconfigs/i/imkl-FFTW/{imkl-FFTW-2024.2.0-iimpi-2024.06.eb => imkl-FFTW-2024.2.0-iimpi-2024a.eb} (84%)
 rename easybuild/easyconfigs/i/intel/{intel-2024.06.eb => intel-2024a.eb} (97%)
 rename easybuild/easyconfigs/o/OSU-Micro-Benchmarks/{OSU-Micro-Benchmarks-7.4-iimpi-2024.06.eb => OSU-Micro-Benchmarks-7.4-iimpi-2024a.eb} (92%)

diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2024.06.eb b/easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2024a.eb
similarity index 94%
rename from easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2024.06.eb
rename to easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2024a.eb
index ca7fc54ce2f..5544839d177 100644
--- a/easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2024.06.eb
+++ b/easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2024a.eb
@@ -6,7 +6,7 @@ description = """HPL is a software package that solves a (random) dense linear s
  arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available
  implementation of the High Performance Computing Linpack Benchmark."""
 
-toolchain = {'name': 'intel', 'version': '2024.06'}
+toolchain = {'name': 'intel', 'version': '2024a'}
 toolchainopts = {'usempi': True}
 
 source_urls = ['https://www.netlib.org/benchmark/%(namelower)s']
diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2024.06.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2024a.eb
similarity index 95%
rename from easybuild/easyconfigs/i/iimpi/iimpi-2024.06.eb
rename to easybuild/easyconfigs/i/iimpi/iimpi-2024a.eb
index 82db31cd099..d6150133621 100644
--- a/easybuild/easyconfigs/i/iimpi/iimpi-2024.06.eb
+++ b/easybuild/easyconfigs/i/iimpi/iimpi-2024a.eb
@@ -2,7 +2,7 @@
 easyblock = 'Toolchain'
 
 name = 'iimpi'
-version = '2024.06'
+version = '2024a'
 
 homepage = 'https://software.intel.com/parallel-studio-xe'
 description = """Intel C/C++ and Fortran compilers, alongside Intel MPI."""
diff --git a/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2024.2.0-iimpi-2024.06.eb b/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2024.2.0-iimpi-2024a.eb
similarity index 84%
rename from easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2024.2.0-iimpi-2024.06.eb
rename to easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2024.2.0-iimpi-2024a.eb
index 7984030b590..b26ab65f452 100644
--- a/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2024.2.0-iimpi-2024.06.eb
+++ b/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2024.2.0-iimpi-2024a.eb
@@ -4,7 +4,7 @@ version = '2024.2.0'
 homepage = 'https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/onemkl.html'
 description = "FFTW interfaces using Intel oneAPI Math Kernel Library"
 
-toolchain = {'name': 'iimpi', 'version': '2024.06'}
+toolchain = {'name': 'iimpi', 'version': '2024a'}
 
 dependencies = [('imkl', version, '', SYSTEM)]
 
diff --git a/easybuild/easyconfigs/i/intel/intel-2024.06.eb b/easybuild/easyconfigs/i/intel/intel-2024a.eb
similarity index 97%
rename from easybuild/easyconfigs/i/intel/intel-2024.06.eb
rename to easybuild/easyconfigs/i/intel/intel-2024a.eb
index 43a052dc1ea..7b08707e0fc 100644
--- a/easybuild/easyconfigs/i/intel/intel-2024.06.eb
+++ b/easybuild/easyconfigs/i/intel/intel-2024a.eb
@@ -1,7 +1,7 @@
 easyblock = 'Toolchain'
 
 name = 'intel'
-version = '2024.06'
+version = '2024a'
 
 homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#intel-toolchain'
 description = "Compiler toolchain including Intel compilers, Intel MPI and Intel Math Kernel Library (MKL)."
diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-7.4-iimpi-2024.06.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-7.4-iimpi-2024a.eb
similarity index 92%
rename from easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-7.4-iimpi-2024.06.eb
rename to easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-7.4-iimpi-2024a.eb
index 6f36b886477..3122923be15 100644
--- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-7.4-iimpi-2024.06.eb
+++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-7.4-iimpi-2024a.eb
@@ -6,7 +6,7 @@ version = '7.4'
 homepage = 'https://mvapich.cse.ohio-state.edu/benchmarks/'
 description = """OSU Micro-Benchmarks"""
 
-toolchain = {'name': 'iimpi', 'version': '2024.06'}
+toolchain = {'name': 'iimpi', 'version': '2024a'}
 toolchainopts = {'usempi': True}
 
 source_urls = ['https://mvapich.cse.ohio-state.edu/download/mvapich/']

From 230e702e1a3915600e98e1f021b0f7ef4a4501fb Mon Sep 17 00:00:00 2001
From: Cintia Willemyns <115622907+WilleBell@users.noreply.github.com>
Date: Thu, 1 Aug 2024 10:24:54 +0200
Subject: [PATCH 534/835] Use same 'VisPy' as other dependencies in '2023a'
 toolchain generation

---
 easybuild/easyconfigs/c/CLANS/CLANS-2.0.8-foss-2023a.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/c/CLANS/CLANS-2.0.8-foss-2023a.eb b/easybuild/easyconfigs/c/CLANS/CLANS-2.0.8-foss-2023a.eb
index 4d2d1d0eafe..e1ce2f2a9e1 100644
--- a/easybuild/easyconfigs/c/CLANS/CLANS-2.0.8-foss-2023a.eb
+++ b/easybuild/easyconfigs/c/CLANS/CLANS-2.0.8-foss-2023a.eb
@@ -16,7 +16,7 @@ dependencies = [
     ('Python', '3.11.3'),
     ('SciPy-bundle', '2023.07'),
     ('numba', '0.58.1'),
-    ('VisPy', '0.14.1'),
+    ('VisPy', '0.12.2'),
     ('Biopython', '1.83'),
     ('Pillow', '10.0.0'),
     ('PyQt5', '5.15.10'),

From c404a40ced18408c5bc4d261cd86078f1e2ef029 Mon Sep 17 00:00:00 2001
From: vsc46128 <vsc46128@node4010.donphan.os>
Date: Thu, 1 Aug 2024 11:20:06 +0200
Subject: [PATCH 535/835] adding easyconfigs: submitit-1.2.0-foss-2023a.eb

---
 .../s/submitit/submitit-1.2.0-foss-2023a.eb   | 34 +++++++++++++++++++
 1 file changed, 34 insertions(+)
 create mode 100644 easybuild/easyconfigs/s/submitit/submitit-1.2.0-foss-2023a.eb

diff --git a/easybuild/easyconfigs/s/submitit/submitit-1.2.0-foss-2023a.eb b/easybuild/easyconfigs/s/submitit/submitit-1.2.0-foss-2023a.eb
new file mode 100644
index 00000000000..0ce1edf2766
--- /dev/null
+++ b/easybuild/easyconfigs/s/submitit/submitit-1.2.0-foss-2023a.eb
@@ -0,0 +1,34 @@
+easyblock = 'PythonBundle'
+
+name = 'submitit'
+version = '1.2.0'
+
+homepage = 'https://github.com/facebookincubator/submitit'
+description = """
+Submitit is a lightweight tool for submitting Python functions
+for computation within a Slurm cluster.
+"""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+dependencies = [
+    ('Python', '3.11.3'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('cloudpickle', '3.0.0', {
+        'checksums': ['996d9a482c6fb4f33c1a35335cf8afd065d2a56e973270364840712d9131a882'],
+    }),
+    ('typing_extensions', '4.12.2', {
+        'checksums': ['1a7ead55c7e559dd4dee8856e3a88b41225abfe1ce8df57b7c13915fe121ffb8'],
+    }),
+    (name, version, {
+        'checksums': ['16c099ed80943fbf942a7a37c6356a598b1f2b9d7ce40dd5fe058a6c7827e600'],
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'lib'

From 500b7af459e843ca517e979e5bb8fb1ce5ddc33f Mon Sep 17 00:00:00 2001
From: Adam Huffman <verdurin@users.noreply.github.com>
Date: Thu, 1 Aug 2024 12:50:01 +0100
Subject: [PATCH 536/835] Description typo fix

---
 easybuild/easyconfigs/w/wradlib/wradlib-2.0.3-foss-2023a.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/w/wradlib/wradlib-2.0.3-foss-2023a.eb b/easybuild/easyconfigs/w/wradlib/wradlib-2.0.3-foss-2023a.eb
index c347e7280c7..d53e56422bc 100644
--- a/easybuild/easyconfigs/w/wradlib/wradlib-2.0.3-foss-2023a.eb
+++ b/easybuild/easyconfigs/w/wradlib/wradlib-2.0.3-foss-2023a.eb
@@ -5,7 +5,7 @@ version = '2.0.3'
 
 homepage = 'https://docs.wradlib.org/'
 description = """
-The wradlib project has been initiated in order facilitate the use of weather
+The wradlib project has been initiated in order to facilitate the use of weather
 radar data as well as to provide a common platform for research on new
 algorithms."""
 

From bbdf9cff5a7eda681987b3c96219d0afa39a3435 Mon Sep 17 00:00:00 2001
From: vsc46128 <vsc46128@node4010.donphan.os>
Date: Thu, 1 Aug 2024 16:56:16 +0200
Subject: [PATCH 537/835] use safetensors module

---
 .../timm/timm-1.0.8-foss-2023a-CUDA-12.1.1.eb | 93 +------------------
 1 file changed, 1 insertion(+), 92 deletions(-)

diff --git a/easybuild/easyconfigs/t/timm/timm-1.0.8-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/t/timm/timm-1.0.8-foss-2023a-CUDA-12.1.1.eb
index 93f0d02792f..d46060d9a6b 100644
--- a/easybuild/easyconfigs/t/timm/timm-1.0.8-foss-2023a-CUDA-12.1.1.eb
+++ b/easybuild/easyconfigs/t/timm/timm-1.0.8-foss-2023a-CUDA-12.1.1.eb
@@ -21,6 +21,7 @@ dependencies = [
     ('PyYAML', '6.0'),
     ('tqdm', '4.66.1'),
     ('torchvision', '0.16.0', versionsuffix),
+    ('Safetensors', '1.4.3'),
 ]
 
 builddependencies = [
@@ -28,104 +29,12 @@ builddependencies = [
     ('PDM', '2.12.4'),
 ]
 
-crates = [
-    ('autocfg', '1.2.0'),
-    ('bitflags', '1.3.2'),
-    ('cfg-if', '1.0.0'),
-    ('heck', '0.4.1'),
-    ('indoc', '2.0.5'),
-    ('itoa', '1.0.11'),
-    ('libc', '0.2.153'),
-    ('lock_api', '0.4.11'),
-    ('memmap2', '0.9.4'),
-    ('memoffset', '0.9.1'),
-    ('once_cell', '1.19.0'),
-    ('parking_lot', '0.12.1'),
-    ('parking_lot_core', '0.9.9'),
-    ('portable-atomic', '1.6.0'),
-    ('proc-macro2', '1.0.80'),
-    ('pyo3', '0.21.1'),
-    ('pyo3-build-config', '0.21.1'),
-    ('pyo3-ffi', '0.21.1'),
-    ('pyo3-macros', '0.21.1'),
-    ('pyo3-macros-backend', '0.21.1'),
-    ('quote', '1.0.36'),
-    ('redox_syscall', '0.4.1'),
-    ('ryu', '1.0.17'),
-    ('scopeguard', '1.2.0'),
-    ('serde', '1.0.197'),
-    ('serde_derive', '1.0.197'),
-    ('serde_json', '1.0.115'),
-    ('smallvec', '1.13.2'),
-    ('syn', '2.0.59'),
-    ('target-lexicon', '0.12.14'),
-    ('unicode-ident', '1.0.12'),
-    ('unindent', '0.2.3'),
-    ('windows-targets', '0.48.5'),
-    ('windows_aarch64_gnullvm', '0.48.5'),
-    ('windows_aarch64_msvc', '0.48.5'),
-    ('windows_i686_gnu', '0.48.5'),
-    ('windows_i686_msvc', '0.48.5'),
-    ('windows_x86_64_gnu', '0.48.5'),
-    ('windows_x86_64_gnullvm', '0.48.5'),
-    ('windows_x86_64_msvc', '0.48.5'),
-]
-
-
-sources = [SOURCE_TAR_GZ]
-checksums = [
-    {'timm-1.0.8.tar.gz': 'f54a579f1cc39c43d99a4b03603e39c4cee87d4f0a08aba9c22e19064b30bf95'},
-    {'autocfg-1.2.0.tar.gz': 'f1fdabc7756949593fe60f30ec81974b613357de856987752631dea1e3394c80'},
-    {'bitflags-1.3.2.tar.gz': 'bef38d45163c2f1dde094a7dfd33ccf595c92905c8f8f4fdc18d06fb1037718a'},
-    {'cfg-if-1.0.0.tar.gz': 'baf1de4339761588bc0619e3cbc0120ee582ebb74b53b4efbf79117bd2da40fd'},
-    {'heck-0.4.1.tar.gz': '95505c38b4572b2d910cecb0281560f54b440a19336cbbcb27bf6ce6adc6f5a8'},
-    {'indoc-2.0.5.tar.gz': 'b248f5224d1d606005e02c97f5aa4e88eeb230488bcc03bc9ca4d7991399f2b5'},
-    {'itoa-1.0.11.tar.gz': '49f1f14873335454500d59611f1cf4a4b0f786f9ac11f4312a78e4cf2566695b'},
-    {'libc-0.2.153.tar.gz': '9c198f91728a82281a64e1f4f9eeb25d82cb32a5de251c6bd1b5154d63a8e7bd'},
-    {'lock_api-0.4.11.tar.gz': '3c168f8615b12bc01f9c17e2eb0cc07dcae1940121185446edc3744920e8ef45'},
-    {'memmap2-0.9.4.tar.gz': 'fe751422e4a8caa417e13c3ea66452215d7d63e19e604f4980461212f3ae1322'},
-    {'memoffset-0.9.1.tar.gz': '488016bfae457b036d996092f6cb448677611ce4449e970ceaf42695203f218a'},
-    {'once_cell-1.19.0.tar.gz': '3fdb12b2476b595f9358c5161aa467c2438859caa136dec86c26fdd2efe17b92'},
-    {'parking_lot-0.12.1.tar.gz': '3742b2c103b9f06bc9fff0a37ff4912935851bee6d36f3c02bcc755bcfec228f'},
-    {'parking_lot_core-0.9.9.tar.gz': '4c42a9226546d68acdd9c0a280d17ce19bfe27a46bf68784e4066115788d008e'},
-    {'portable-atomic-1.6.0.tar.gz': '7170ef9988bc169ba16dd36a7fa041e5c4cbeb6a35b76d4c03daded371eae7c0'},
-    {'proc-macro2-1.0.80.tar.gz': 'a56dea16b0a29e94408b9aa5e2940a4eedbd128a1ba20e8f7ae60fd3d465af0e'},
-    {'pyo3-0.21.1.tar.gz': 'a7a8b1990bd018761768d5e608a13df8bd1ac5f678456e0f301bb93e5f3ea16b'},
-    {'pyo3-build-config-0.21.1.tar.gz': '650dca34d463b6cdbdb02b1d71bfd6eb6b6816afc708faebb3bac1380ff4aef7'},
-    {'pyo3-ffi-0.21.1.tar.gz': '09a7da8fc04a8a2084909b59f29e1b8474decac98b951d77b80b26dc45f046ad'},
-    {'pyo3-macros-0.21.1.tar.gz': '4b8a199fce11ebb28e3569387228836ea98110e43a804a530a9fd83ade36d513'},
-    {'pyo3-macros-backend-0.21.1.tar.gz': '93fbbfd7eb553d10036513cb122b888dcd362a945a00b06c165f2ab480d4cc3b'},
-    {'quote-1.0.36.tar.gz': '0fa76aaf39101c457836aec0ce2316dbdc3ab723cdda1c6bd4e6ad4208acaca7'},
-    {'redox_syscall-0.4.1.tar.gz': '4722d768eff46b75989dd134e5c353f0d6296e5aaa3132e776cbdb56be7731aa'},
-    {'ryu-1.0.17.tar.gz': 'e86697c916019a8588c99b5fac3cead74ec0b4b819707a682fd4d23fa0ce1ba1'},
-    {'scopeguard-1.2.0.tar.gz': '94143f37725109f92c262ed2cf5e59bce7498c01bcc1502d7b9afe439a4e9f49'},
-    {'serde-1.0.197.tar.gz': '3fb1c873e1b9b056a4dc4c0c198b24c3ffa059243875552b2bd0933b1aee4ce2'},
-    {'serde_derive-1.0.197.tar.gz': '7eb0b34b42edc17f6b7cac84a52a1c5f0e1bb2227e997ca9011ea3dd34e8610b'},
-    {'serde_json-1.0.115.tar.gz': '12dc5c46daa8e9fdf4f5e71b6cf9a53f2487da0e86e55808e2d35539666497dd'},
-    {'smallvec-1.13.2.tar.gz': '3c5e1a9a646d36c3599cd173a41282daf47c44583ad367b8e6837255952e5c67'},
-    {'syn-2.0.59.tar.gz': '4a6531ffc7b071655e4ce2e04bd464c4830bb585a61cabb96cf808f05172615a'},
-    {'target-lexicon-0.12.14.tar.gz': 'e1fc403891a21bcfb7c37834ba66a547a8f402146eba7265b5a6d88059c9ff2f'},
-    {'unicode-ident-1.0.12.tar.gz': '3354b9ac3fae1ff6755cb6db53683adb661634f67557942dea4facebec0fee4b'},
-    {'unindent-0.2.3.tar.gz': 'c7de7d73e1754487cb58364ee906a499937a0dfabd86bcb980fa99ec8c8fa2ce'},
-    {'windows-targets-0.48.5.tar.gz': '9a2fa6e2155d7247be68c096456083145c183cbbbc2764150dda45a87197940c'},
-    {'windows_aarch64_gnullvm-0.48.5.tar.gz': '2b38e32f0abccf9987a4e3079dfb67dcd799fb61361e53e2882c3cbaf0d905d8'},
-    {'windows_aarch64_msvc-0.48.5.tar.gz': 'dc35310971f3b2dbbf3f0690a219f40e2d9afcf64f9ab7cc1be722937c26b4bc'},
-    {'windows_i686_gnu-0.48.5.tar.gz': 'a75915e7def60c94dcef72200b9a8e58e5091744960da64ec734a6c6e9b3743e'},
-    {'windows_i686_msvc-0.48.5.tar.gz': '8f55c233f70c4b27f66c523580f78f1004e8b5a8b659e05a4eb49d4166cca406'},
-    {'windows_x86_64_gnu-0.48.5.tar.gz': '53d40abd2583d23e4718fddf1ebec84dbff8381c07cae67ff7768bbf19c6718e'},
-    {'windows_x86_64_gnullvm-0.48.5.tar.gz': '0b7b52767868a23d5bab768e390dc5f5c55825b6d30b86c844ff2dc7414044cc'},
-    {'windows_x86_64_msvc-0.48.5.tar.gz': 'ed94fce61571a4006852b7389a063ab983c02eb1bb37b47f8272ce92d06d9538'},
-]
-
 use_pip = True
 
 exts_list = [
     ('huggingface_hub', '0.24.5', {
         'checksums': ['7b45d6744dd53ce9cbf9880957de00e9d10a9ae837f1c9b7255fc8fa4e8264f3'],
     }),
-    ('safetensors', '0.4.3', {
-        'checksums': ['2f85fc50c4e07a21e95c24e07460fe6f7e2859d0ce88092838352b798ce711c2'],
-    }),
     (name, version, {
         'checksums': ['f54a579f1cc39c43d99a4b03603e39c4cee87d4f0a08aba9c22e19064b30bf95'],
     }),

From 51e18c92424c8ece63c43ec5bd9f4014ea465324 Mon Sep 17 00:00:00 2001
From: vsc46128 <vsc46128@node4010.donphan.os>
Date: Thu, 1 Aug 2024 17:02:24 +0200
Subject: [PATCH 538/835] use safetensors module

---
 .../easyconfigs/t/timm/timm-1.0.8-foss-2023a-CUDA-12.1.1.eb     | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/t/timm/timm-1.0.8-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/t/timm/timm-1.0.8-foss-2023a-CUDA-12.1.1.eb
index d46060d9a6b..f0b67fec7c0 100644
--- a/easybuild/easyconfigs/t/timm/timm-1.0.8-foss-2023a-CUDA-12.1.1.eb
+++ b/easybuild/easyconfigs/t/timm/timm-1.0.8-foss-2023a-CUDA-12.1.1.eb
@@ -1,4 +1,4 @@
-easyblock = 'CargoPythonBundle'
+easyblock = 'PythonBundle'
 
 name = 'timm'
 version = '1.0.8'

From bf59190ce7f467186548c67005a24d378698b074 Mon Sep 17 00:00:00 2001
From: Alexander Salois <alexander.salois@montana.edu>
Date: Thu, 1 Aug 2024 09:34:55 -0600
Subject: [PATCH 539/835] Restored attribution and added my own

---
 .../b/BayesTraits/BayesTraits-4.1.2-Linux.eb           | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/easybuild/easyconfigs/b/BayesTraits/BayesTraits-4.1.2-Linux.eb b/easybuild/easyconfigs/b/BayesTraits/BayesTraits-4.1.2-Linux.eb
index b07ea0bb7a1..541dedf129e 100644
--- a/easybuild/easyconfigs/b/BayesTraits/BayesTraits-4.1.2-Linux.eb
+++ b/easybuild/easyconfigs/b/BayesTraits/BayesTraits-4.1.2-Linux.eb
@@ -1,3 +1,13 @@
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+# Author: Pablo Escobar Lopez
+# Swiss Institute of Bioinformatics
+# Biozentrum - University of Basel
+
+# Updated by
+# Author: Alex Salois
+# Research Cyberinfrastructure
+# Montana State University
+
 easyblock = "Tarball"
 
 name = 'BayesTraits'

From 94a2311f410b10cf6f29c0ba56f50f519ff31fc2 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Thu, 1 Aug 2024 18:39:21 +0200
Subject: [PATCH 540/835] adding easyconfigs:
 EvidentialGene-2023.07.15-gompi-2023a.eb, Exonerate-2.4.0-GCC-12.3.0.eb

---
 .../EvidentialGene-2023.07.15-gompi-2023a.eb  | 40 ++++++++++++++++
 .../e/Exonerate/Exonerate-2.4.0-GCC-12.3.0.eb | 47 +++++++++++++++++++
 2 files changed, 87 insertions(+)
 create mode 100644 easybuild/easyconfigs/e/EvidentialGene/EvidentialGene-2023.07.15-gompi-2023a.eb
 create mode 100644 easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-GCC-12.3.0.eb

diff --git a/easybuild/easyconfigs/e/EvidentialGene/EvidentialGene-2023.07.15-gompi-2023a.eb b/easybuild/easyconfigs/e/EvidentialGene/EvidentialGene-2023.07.15-gompi-2023a.eb
new file mode 100644
index 00000000000..c4ae0c4e12d
--- /dev/null
+++ b/easybuild/easyconfigs/e/EvidentialGene/EvidentialGene-2023.07.15-gompi-2023a.eb
@@ -0,0 +1,40 @@
+easyblock = "PackedBinary"
+
+name = "EvidentialGene"
+version = '2023.07.15'
+local_month = ['', 'jan', 'feb', 'mar', 'apr', 'may', 'jun', 'jul', 'aug', 'sep', 'oct', 'nov', 'dec']
+local_dlver = version.split('.')[0][-2:] + local_month[int(version.split('.')[1])] + version.split('.')[2]
+
+homepage = 'http://arthropods.eugenes.org/EvidentialGene/'
+description = """EvidentialGene is a genome informatics project for
+ "Evidence Directed Gene Construction for Eukaryotes",
+ for constructing high quality, accurate gene sets for
+ animals and plants (any eukaryotes), being developed by
+ Don Gilbert at Indiana University, gilbertd at indiana edu."""
+
+toolchain = {'name': 'gompi', 'version': '2023a'}
+
+source_urls = [
+    'http://arthropods.eugenes.org/EvidentialGene/other/evigene_old/',
+    'http://arthropods.eugenes.org/EvidentialGene/other/evigene_old/evigene_older/',
+]
+sources = ['evigene%s.tar' % local_dlver]
+checksums = ['8fe8e5c21ac3f8b7134d8e26593fe66647eb8b7ba2c1cd1c158fc811769b9539']
+
+dependencies = [
+    ('Perl', '5.36.1'),
+    ('Exonerate', '2.4.0'),
+    ('CD-HIT', '4.8.1'),
+    ('BLAST+', '2.14.1'),
+]
+
+fix_perl_shebang_for = ['scripts/*.pl', 'scripts/*/*.pl', 'scripts/*/*/*.pl']
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['scripts/'],
+}
+
+modextravars = {'evigene': '%(installdir)s'}
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-GCC-12.3.0.eb b/easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-GCC-12.3.0.eb
new file mode 100644
index 00000000000..4e57e85a280
--- /dev/null
+++ b/easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-GCC-12.3.0.eb
@@ -0,0 +1,47 @@
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+# Author: Pablo Escobar Lopez
+# Swiss Institute of Bioinformatics
+# Biozentrum - University of Basel
+# foss-2016b modified by:
+# Adam Huffman
+# The Francis Crick Institute
+
+easyblock = 'ConfigureMake'
+
+name = 'Exonerate'
+version = '2.4.0'
+
+homepage = 'https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate'
+# also https://github.com/nathanweeks/exonerate
+description = """ Exonerate is a generic tool for pairwise sequence comparison.
+ It allows you to align sequences using a many alignment models, using either 
+ exhaustive dynamic programming, or a variety of heuristics. """
+
+toolchain = {'name': 'GCC', 'version': '12.3.0'}
+
+source_urls = ['https://ftp.ebi.ac.uk/pub/software/vertebrategenomics/%(namelower)s/']
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['f849261dc7c97ef1f15f222e955b0d3daf994ec13c9db7766f1ac7e77baa4042']
+
+builddependencies = [
+    ('pkgconf', '1.9.5'),
+]
+dependencies = [
+    ('GLib', '2.77.1'),
+]
+
+# parallel build fails
+parallel = 1
+
+runtest = 'check'
+
+_bins = ['exonerate', 'fastaclip', 'fastacomposition', 'fastafetch', 'fastaoverlap', 'ipcress']
+
+sanity_check_paths = {
+    'files': ['bin/%s' % x for x in _bins],
+    'dirs': ['share'],
+}
+
+sanity_check_commands = ['%s -h | grep "from exonerate version %%(version)s"' % x for x in _bins]
+
+moduleclass = 'bio'

From dc345946f8e6cb42c8c0d059ce542443af488369 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Thu, 1 Aug 2024 18:59:39 +0200
Subject: [PATCH 541/835] adding easyconfigs:
 accelerate-0.33.0-foss-2023a-CUDA-12.1.1.eb

---
 ...ccelerate-0.33.0-foss-2023a-CUDA-12.1.1.eb | 39 +++++++++++++++++++
 1 file changed, 39 insertions(+)
 create mode 100644 easybuild/easyconfigs/a/accelerate/accelerate-0.33.0-foss-2023a-CUDA-12.1.1.eb

diff --git a/easybuild/easyconfigs/a/accelerate/accelerate-0.33.0-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/a/accelerate/accelerate-0.33.0-foss-2023a-CUDA-12.1.1.eb
new file mode 100644
index 00000000000..7f6d595a7c5
--- /dev/null
+++ b/easybuild/easyconfigs/a/accelerate/accelerate-0.33.0-foss-2023a-CUDA-12.1.1.eb
@@ -0,0 +1,39 @@
+easyblock = 'PythonBundle'
+
+name = 'accelerate'
+version = '0.33.0'
+versionsuffix = '-CUDA-%(cudaver)s'
+
+homepage = 'https://github.com/huggingface/accelerate'
+description = """A simple way to launch, train, and use PyTorch models on almost any device and 
+distributed configuration, automatic mixed precision (including fp8), 
+and easy-to-configure FSDP and DeepSpeed support."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('Python-bundle-PyPI', '2023.06'),
+    ('SciPy-bundle', '2023.07'),
+    ('CUDA', '12.1.1', '', SYSTEM),
+    ('PyTorch-bundle', '2.1.2', versionsuffix),
+    ('PyYAML', '6.0'),
+    ('Safetensors', '0.4.3'),
+]
+
+sanity_pip_check = True
+use_pip = True
+
+exts_list = [
+    ('huggingface-hub', '0.24.5', {
+        'sources': ['huggingface_hub-%(version)s.tar.gz'],
+        'checksums': ['7b45d6744dd53ce9cbf9880957de00e9d10a9ae837f1c9b7255fc8fa4e8264f3'],
+    }),
+    (name, version, {
+        'checksums': ['11ba481ed6ea09191775df55ce464aeeba67a024bd0261a44b77b30fb439e26a'],
+    }),
+]
+
+sanity_check_commands = ['accelerate test']
+
+moduleclass = 'ai'

From 50b0d544337de78be983633a502bed8a0f7503a4 Mon Sep 17 00:00:00 2001
From: Bart Oldeman <bart.oldeman@calculquebec.ca>
Date: Thu, 1 Aug 2024 21:36:15 +0000
Subject: [PATCH 542/835] Fix download URLs for old Intel software (2018-23)

Intel changed "irc_nas" to "IRC_NAS". Newer packages (2023.1+) already use
that, but older ones need changing.

Mirrors https://github.com/spack/spack/pull/43286

Fixes #21104
---
 easybuild/easyconfigs/a/Advisor/Advisor-2019_update2.eb       | 2 +-
 easybuild/easyconfigs/a/Advisor/Advisor-2019_update3.eb       | 2 +-
 easybuild/easyconfigs/a/Advisor/Advisor-2019_update5.eb       | 2 +-
 easybuild/easyconfigs/a/Advisor/Advisor-2021.2.0.eb           | 2 +-
 easybuild/easyconfigs/a/Advisor/Advisor-2021.4.0.eb           | 2 +-
 easybuild/easyconfigs/a/Advisor/Advisor-2022.1.0.eb           | 2 +-
 easybuild/easyconfigs/a/Advisor/Advisor-2023.0.0.eb           | 2 +-
 easybuild/easyconfigs/i/Inspector/Inspector-2019_update5.eb   | 2 +-
 easybuild/easyconfigs/i/Inspector/Inspector-2021.4.0.eb       | 2 +-
 easybuild/easyconfigs/i/Inspector/Inspector-2022.0.0.eb       | 2 +-
 easybuild/easyconfigs/i/Inspector/Inspector-2022.1.0.eb       | 2 +-
 .../i/IntelClusterChecker/IntelClusterChecker-2021.5.0.eb     | 2 +-
 .../i/IntelPython/IntelPython-2.7.15-2019.2.066.eb            | 2 +-
 .../easyconfigs/i/IntelPython/IntelPython-3.6.8-2019.2.066.eb | 2 +-
 easybuild/easyconfigs/i/icc/icc-2018.1.163-GCC-6.4.0-2.28.eb  | 2 +-
 easybuild/easyconfigs/i/icc/icc-2018.3.222-GCC-7.3.0-2.30.eb  | 2 +-
 easybuild/easyconfigs/i/icc/icc-2018.5.274-GCC-7.3.0-2.30.eb  | 2 +-
 .../easyconfigs/i/icc/icc-2019.0.117-GCC-8.2.0-2.31.1.eb      | 2 +-
 .../easyconfigs/i/icc/icc-2019.1.144-GCC-8.2.0-2.31.1.eb      | 2 +-
 .../easyconfigs/i/icc/icc-2019.2.187-GCC-8.2.0-2.31.1.eb      | 2 +-
 easybuild/easyconfigs/i/icc/icc-2019.3.199-GCC-8.3.0-2.32.eb  | 2 +-
 easybuild/easyconfigs/i/iccifort/iccifort-2019.4.243.eb       | 2 +-
 easybuild/easyconfigs/i/iccifort/iccifort-2019.5.281.eb       | 2 +-
 .../easyconfigs/i/iccifort/iccifort-2020.0.166-GCC-9.2.0.eb   | 2 +-
 easybuild/easyconfigs/i/iccifort/iccifort-2020.0.166.eb       | 2 +-
 easybuild/easyconfigs/i/iccifort/iccifort-2020.1.217.eb       | 2 +-
 easybuild/easyconfigs/i/iccifort/iccifort-2020.4.304.eb       | 2 +-
 .../easyconfigs/i/ifort/ifort-2018.1.163-GCC-6.4.0-2.28.eb    | 2 +-
 .../easyconfigs/i/ifort/ifort-2018.3.222-GCC-7.3.0-2.30.eb    | 2 +-
 .../easyconfigs/i/ifort/ifort-2018.5.274-GCC-7.3.0-2.30.eb    | 2 +-
 .../easyconfigs/i/ifort/ifort-2019.0.117-GCC-8.2.0-2.31.1.eb  | 2 +-
 .../easyconfigs/i/ifort/ifort-2019.1.144-GCC-8.2.0-2.31.1.eb  | 2 +-
 .../easyconfigs/i/ifort/ifort-2019.2.187-GCC-8.2.0-2.31.1.eb  | 2 +-
 .../easyconfigs/i/ifort/ifort-2019.3.199-GCC-8.3.0-2.32.eb    | 2 +-
 ...kl-2018.1.163-iccifort-2018.1.163-GCC-6.4.0-2.28-serial.eb | 2 +-
 easybuild/easyconfigs/i/imkl/imkl-2018.1.163-iimpi-2018a.eb   | 2 +-
 easybuild/easyconfigs/i/imkl/imkl-2018.3.222-gimpi-2018b.eb   | 2 +-
 easybuild/easyconfigs/i/imkl/imkl-2018.3.222-gompi-2018b.eb   | 2 +-
 easybuild/easyconfigs/i/imkl/imkl-2018.3.222-iimpi-2018b.eb   | 2 +-
 easybuild/easyconfigs/i/imkl/imkl-2018.3.222-iompi-2018b.eb   | 2 +-
 easybuild/easyconfigs/i/imkl/imkl-2018.4.274-iimpi-2018.04.eb | 2 +-
 easybuild/easyconfigs/i/imkl/imkl-2019.0.117-iimpi-2019.00.eb | 2 +-
 easybuild/easyconfigs/i/imkl/imkl-2019.1.144-gompi-2019a.eb   | 2 +-
 easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iimpi-2019.01.eb | 2 +-
 easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iimpi-2019a.eb   | 2 +-
 easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iimpic-2019a.eb  | 2 +-
 easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iompi-2019.01.eb | 2 +-
 easybuild/easyconfigs/i/imkl/imkl-2019.2.187-iimpi-2019.02.eb | 2 +-
 easybuild/easyconfigs/i/imkl/imkl-2019.3.199-iimpi-2019.03.eb | 2 +-
 easybuild/easyconfigs/i/imkl/imkl-2019.5.281-gompi-2019b.eb   | 2 +-
 easybuild/easyconfigs/i/imkl/imkl-2019.5.281-gompic-2019b.eb  | 2 +-
 easybuild/easyconfigs/i/imkl/imkl-2019.5.281-iimpi-2019b.eb   | 2 +-
 easybuild/easyconfigs/i/imkl/imkl-2019.5.281-iimpic-2019b.eb  | 2 +-
 easybuild/easyconfigs/i/imkl/imkl-2019.5.281-iompi-2019b.eb   | 2 +-
 easybuild/easyconfigs/i/imkl/imkl-2020.0.166-iimpi-2020.00.eb | 2 +-
 easybuild/easyconfigs/i/imkl/imkl-2020.1.217-gompi-2020a.eb   | 2 +-
 .../i/imkl/imkl-2020.1.217-iimpi-2020.06-impi-18.5.eb         | 2 +-
 easybuild/easyconfigs/i/imkl/imkl-2020.1.217-iimpi-2020a.eb   | 2 +-
 easybuild/easyconfigs/i/imkl/imkl-2020.1.217-iimpic-2020a.eb  | 2 +-
 easybuild/easyconfigs/i/imkl/imkl-2020.1.217-iompi-2020a.eb   | 2 +-
 easybuild/easyconfigs/i/imkl/imkl-2020.4.304-NVHPC-21.2.eb    | 2 +-
 easybuild/easyconfigs/i/imkl/imkl-2020.4.304-gompi-2020b.eb   | 2 +-
 easybuild/easyconfigs/i/imkl/imkl-2020.4.304-gompic-2020b.eb  | 2 +-
 easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iimpi-2020b.eb   | 2 +-
 easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iimpic-2020b.eb  | 2 +-
 easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iompi-2020b.eb   | 2 +-
 easybuild/easyconfigs/i/imkl/imkl-2021.1.1-iimpi-2020.12.eb   | 2 +-
 easybuild/easyconfigs/i/imkl/imkl-2021.2.0-gompi-2021a.eb     | 2 +-
 easybuild/easyconfigs/i/imkl/imkl-2021.2.0-iimpi-2021a.eb     | 2 +-
 easybuild/easyconfigs/i/imkl/imkl-2021.2.0-iompi-2021a.eb     | 2 +-
 easybuild/easyconfigs/i/imkl/imkl-2021.3.0-gompi-2021a.eb     | 2 +-
 easybuild/easyconfigs/i/imkl/imkl-2021.4.0-iompi-2021b.eb     | 2 +-
 easybuild/easyconfigs/i/imkl/imkl-2021.4.0.eb                 | 2 +-
 easybuild/easyconfigs/i/imkl/imkl-2022.0.1.eb                 | 2 +-
 easybuild/easyconfigs/i/imkl/imkl-2022.1.0-gompi-2022a.eb     | 2 +-
 easybuild/easyconfigs/i/imkl/imkl-2022.1.0.eb                 | 2 +-
 easybuild/easyconfigs/i/imkl/imkl-2022.2.0.eb                 | 2 +-
 easybuild/easyconfigs/i/imkl/imkl-2022.2.1.eb                 | 2 +-
 easybuild/easyconfigs/i/imkl/imkl-2023.0.0.eb                 | 2 +-
 easybuild/easyconfigs/i/imkl/imkl-2023.1.0-gompi-2023a.eb     | 2 +-
 .../impi-2018.1.163-iccifort-2018.1.163-GCC-6.4.0-2.28.eb     | 2 +-
 .../easyconfigs/i/impi/impi-2018.3.222-GCC-7.3.0-2.30.eb      | 2 +-
 .../impi-2018.3.222-iccifort-2018.3.222-GCC-7.3.0-2.30.eb     | 2 +-
 .../impi-2018.4.274-iccifort-2018.5.274-GCC-7.3.0-2.30.eb     | 2 +-
 .../impi-2018.4.274-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb   | 2 +-
 .../easyconfigs/i/impi/impi-2018.4.274-iccifortcuda-2019a.eb  | 2 +-
 .../easyconfigs/i/impi/impi-2018.5.288-iccifort-2019.5.281.eb | 2 +-
 .../easyconfigs/i/impi/impi-2018.5.288-iccifort-2020.1.217.eb | 2 +-
 .../easyconfigs/i/impi/impi-2018.5.288-iccifortcuda-2019b.eb  | 2 +-
 .../impi-2019.0.117-iccifort-2019.0.117-GCC-8.2.0-2.31.1.eb   | 2 +-
 .../impi-2019.1.144-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb   | 2 +-
 .../i/impi/impi-2019.12.320-iccifort-2020.4.304.eb            | 2 +-
 .../impi-2019.2.187-iccifort-2019.2.187-GCC-8.2.0-2.31.1.eb   | 2 +-
 .../impi-2019.3.199-iccifort-2019.3.199-GCC-8.3.0-2.32.eb     | 2 +-
 .../i/impi/impi-2019.6.166-iccifort-2020.0.166-GCC-9.2.0.eb   | 2 +-
 .../easyconfigs/i/impi/impi-2019.7.217-iccifort-2020.1.217.eb | 2 +-
 .../easyconfigs/i/impi/impi-2019.7.217-iccifortcuda-2020a.eb  | 2 +-
 .../easyconfigs/i/impi/impi-2019.9.304-iccifort-2020.4.304.eb | 2 +-
 .../easyconfigs/i/impi/impi-2019.9.304-iccifortcuda-2020b.eb  | 2 +-
 .../i/impi/impi-2021.1.1-intel-compilers-2021.1.2.eb          | 2 +-
 .../i/impi/impi-2021.2.0-intel-compilers-2021.2.0.eb          | 2 +-
 .../i/impi/impi-2021.3.0-intel-compilers-2021.3.0.eb          | 2 +-
 .../i/impi/impi-2021.4.0-intel-compilers-2021.4.0.eb          | 2 +-
 .../i/impi/impi-2021.5.0-intel-compilers-2022.0.1.eb          | 2 +-
 .../i/impi/impi-2021.6.0-intel-compilers-2022.1.0.eb          | 2 +-
 .../i/impi/impi-2021.7.0-intel-compilers-2022.2.0.eb          | 2 +-
 .../i/impi/impi-2021.7.1-intel-compilers-2022.2.1.eb          | 2 +-
 .../i/impi/impi-2021.8.0-intel-compilers-2023.0.0.eb          | 2 +-
 .../easyconfigs/i/intel-compilers/intel-compilers-2021.1.2.eb | 4 ++--
 .../easyconfigs/i/intel-compilers/intel-compilers-2021.2.0.eb | 4 ++--
 .../easyconfigs/i/intel-compilers/intel-compilers-2021.3.0.eb | 4 ++--
 .../easyconfigs/i/intel-compilers/intel-compilers-2021.4.0.eb | 4 ++--
 .../easyconfigs/i/intel-compilers/intel-compilers-2022.0.1.eb | 4 ++--
 .../easyconfigs/i/intel-compilers/intel-compilers-2022.0.2.eb | 4 ++--
 .../easyconfigs/i/intel-compilers/intel-compilers-2022.1.0.eb | 4 ++--
 .../easyconfigs/i/intel-compilers/intel-compilers-2022.2.0.eb | 4 ++--
 .../easyconfigs/i/intel-compilers/intel-compilers-2022.2.1.eb | 4 ++--
 .../easyconfigs/i/intel-compilers/intel-compilers-2023.0.0.eb | 4 ++--
 easybuild/easyconfigs/i/itac/itac-2021.2.0.eb                 | 2 +-
 easybuild/easyconfigs/i/itac/itac-2021.5.0.eb                 | 2 +-
 easybuild/easyconfigs/i/itac/itac-2021.6.0.eb                 | 2 +-
 easybuild/easyconfigs/v/VTune/VTune-2018_update3.eb           | 2 +-
 easybuild/easyconfigs/v/VTune/VTune-2019_update3.eb           | 2 +-
 easybuild/easyconfigs/v/VTune/VTune-2019_update5.eb           | 2 +-
 easybuild/easyconfigs/v/VTune/VTune-2020_update3.eb           | 2 +-
 easybuild/easyconfigs/v/VTune/VTune-2021.6.0.eb               | 2 +-
 easybuild/easyconfigs/v/VTune/VTune-2021.9.0.eb               | 2 +-
 easybuild/easyconfigs/v/VTune/VTune-2022.0.0.eb               | 2 +-
 easybuild/easyconfigs/v/VTune/VTune-2022.2.0.eb               | 2 +-
 easybuild/easyconfigs/v/VTune/VTune-2022.3.0.eb               | 2 +-
 130 files changed, 140 insertions(+), 140 deletions(-)

diff --git a/easybuild/easyconfigs/a/Advisor/Advisor-2019_update2.eb b/easybuild/easyconfigs/a/Advisor/Advisor-2019_update2.eb
index 24ce3fe1c31..2e121781a46 100644
--- a/easybuild/easyconfigs/a/Advisor/Advisor-2019_update2.eb
+++ b/easybuild/easyconfigs/a/Advisor/Advisor-2019_update2.eb
@@ -10,7 +10,7 @@ description = """Vectorization Optimization and Thread Prototyping
 
 toolchain = SYSTEM
 
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15084/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15084/']
 sources = ['advisor_%(version)s.tar.gz']
 checksums = ['b63e11b0601013ad21789869ad76be5a836da566ee47c125dcda19ff8277de77']
 
diff --git a/easybuild/easyconfigs/a/Advisor/Advisor-2019_update3.eb b/easybuild/easyconfigs/a/Advisor/Advisor-2019_update3.eb
index a9f9a888154..7b025287362 100644
--- a/easybuild/easyconfigs/a/Advisor/Advisor-2019_update3.eb
+++ b/easybuild/easyconfigs/a/Advisor/Advisor-2019_update3.eb
@@ -10,7 +10,7 @@ description = """Vectorization Optimization and Thread Prototyping
 
 toolchain = SYSTEM
 
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15206/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15206/']
 sources = ['advisor_%(version)s.tar.gz']
 checksums = ['6597f165dee3c6444eb0f38a9069327d10584b09555f5d2c4ed86b8f84d980bb']
 
diff --git a/easybuild/easyconfigs/a/Advisor/Advisor-2019_update5.eb b/easybuild/easyconfigs/a/Advisor/Advisor-2019_update5.eb
index 6a0d2fa4ece..cbcdab88d6e 100644
--- a/easybuild/easyconfigs/a/Advisor/Advisor-2019_update5.eb
+++ b/easybuild/easyconfigs/a/Advisor/Advisor-2019_update5.eb
@@ -10,7 +10,7 @@ description = """Vectorization Optimization and Thread Prototyping
 
 toolchain = SYSTEM
 
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15825/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15825/']
 sources = ['advisor_%(version)s.tar.gz']
 checksums = ['3f203ee63df37e87423fdd4cbeb5ec027b3d11e50c9121935f8b323dd635e866']
 
diff --git a/easybuild/easyconfigs/a/Advisor/Advisor-2021.2.0.eb b/easybuild/easyconfigs/a/Advisor/Advisor-2021.2.0.eb
index 2a7de357e47..144362e2eb7 100644
--- a/easybuild/easyconfigs/a/Advisor/Advisor-2021.2.0.eb
+++ b/easybuild/easyconfigs/a/Advisor/Advisor-2021.2.0.eb
@@ -13,7 +13,7 @@ description = """Vectorization Optimization and Thread Prototyping
 
 toolchain = SYSTEM
 
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/17730/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/17730/']
 sources = ['l_oneapi_advisor_p_%(version)s.189_offline.sh']
 checksums = ['9d9e9aa11819e6422f732de0e29e70a164e576254504857713cfec90b6b78664']
 
diff --git a/easybuild/easyconfigs/a/Advisor/Advisor-2021.4.0.eb b/easybuild/easyconfigs/a/Advisor/Advisor-2021.4.0.eb
index 55354cc6e25..ec07e00e07e 100644
--- a/easybuild/easyconfigs/a/Advisor/Advisor-2021.4.0.eb
+++ b/easybuild/easyconfigs/a/Advisor/Advisor-2021.4.0.eb
@@ -13,7 +13,7 @@ description = """Vectorization Optimization and Thread Prototyping
 
 toolchain = SYSTEM
 
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18220/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18220/']
 sources = ['l_oneapi_advisor_p_%(version)s.389_offline.sh']
 checksums = ['dd948f7312629d9975e12a57664f736b8e011de948771b4c05ad444438532be8']
 
diff --git a/easybuild/easyconfigs/a/Advisor/Advisor-2022.1.0.eb b/easybuild/easyconfigs/a/Advisor/Advisor-2022.1.0.eb
index 58235ccff90..34a2115a37c 100644
--- a/easybuild/easyconfigs/a/Advisor/Advisor-2022.1.0.eb
+++ b/easybuild/easyconfigs/a/Advisor/Advisor-2022.1.0.eb
@@ -13,7 +13,7 @@ description = """Vectorization Optimization and Thread Prototyping
 
 toolchain = SYSTEM
 
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18730/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18730/']
 sources = ['l_oneapi_advisor_p_%(version)s.171_offline.sh']
 checksums = ['b627dbfefa779b44e7ab40dfa37614e56caa6e245feaed402d51826e6a7cb73b']
 
diff --git a/easybuild/easyconfigs/a/Advisor/Advisor-2023.0.0.eb b/easybuild/easyconfigs/a/Advisor/Advisor-2023.0.0.eb
index 187fcafa180..e6d811a03a0 100644
--- a/easybuild/easyconfigs/a/Advisor/Advisor-2023.0.0.eb
+++ b/easybuild/easyconfigs/a/Advisor/Advisor-2023.0.0.eb
@@ -11,7 +11,7 @@ description = """Vectorization Optimization and Thread Prototyping
 toolchain = SYSTEM
 
 source_urls = [
-    'https://registrationcenter-download.intel.com/akdlm/irc_nas/19094/']
+    'https://registrationcenter-download.intel.com/akdlm/IRC_NAS/19094/']
 sources = ['l_oneapi_advisor_p_%(version)s.25338_offline.sh']
 checksums = ['5d8ef163f70ee3dc42b13642f321d974f49915d55914ba1ca9177ed29b100b9d']
 
diff --git a/easybuild/easyconfigs/i/Inspector/Inspector-2019_update5.eb b/easybuild/easyconfigs/i/Inspector/Inspector-2019_update5.eb
index b27635916ca..179e26005de 100644
--- a/easybuild/easyconfigs/i/Inspector/Inspector-2019_update5.eb
+++ b/easybuild/easyconfigs/i/Inspector/Inspector-2019_update5.eb
@@ -7,7 +7,7 @@ description = """Intel Inspector XE is an easy to use memory error checker and t
 
 toolchain = SYSTEM
 
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15827/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15827/']
 sources = ['inspector_%(version)s.tar.gz']
 checksums = ['676fd0b25a56fba63495c048abf485b08583cbb01eb0cf6e1174ee7b352af6d5']
 
diff --git a/easybuild/easyconfigs/i/Inspector/Inspector-2021.4.0.eb b/easybuild/easyconfigs/i/Inspector/Inspector-2021.4.0.eb
index 11b56c0bc1c..494b031a5e1 100644
--- a/easybuild/easyconfigs/i/Inspector/Inspector-2021.4.0.eb
+++ b/easybuild/easyconfigs/i/Inspector/Inspector-2021.4.0.eb
@@ -10,7 +10,7 @@ description = """Intel Inspector is a dynamic memory and threading error
 
 toolchain = SYSTEM
 
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18239/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18239/']
 sources = ['l_inspector_oneapi_p_%(version)s.266_offline.sh']
 checksums = ['c8210cbcd0e07cc75e773249a5e4a02cf34894ec80a213939f3a20e6c5705274']
 
diff --git a/easybuild/easyconfigs/i/Inspector/Inspector-2022.0.0.eb b/easybuild/easyconfigs/i/Inspector/Inspector-2022.0.0.eb
index 430cc62b2d4..22f082dd1f4 100644
--- a/easybuild/easyconfigs/i/Inspector/Inspector-2022.0.0.eb
+++ b/easybuild/easyconfigs/i/Inspector/Inspector-2022.0.0.eb
@@ -10,7 +10,7 @@ description = """Intel Inspector is a dynamic memory and threading error
 
 toolchain = SYSTEM
 
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18363/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18363/']
 sources = ['l_inspector_oneapi_p_%(version)s.56_offline.sh']
 checksums = ['79a0eb2ae3f1de1e3456076685680c468702922469c3fda3e074718fb0bea741']
 
diff --git a/easybuild/easyconfigs/i/Inspector/Inspector-2022.1.0.eb b/easybuild/easyconfigs/i/Inspector/Inspector-2022.1.0.eb
index a7772259cc8..33515e7a8e5 100644
--- a/easybuild/easyconfigs/i/Inspector/Inspector-2022.1.0.eb
+++ b/easybuild/easyconfigs/i/Inspector/Inspector-2022.1.0.eb
@@ -10,7 +10,7 @@ description = """Intel Inspector is a dynamic memory and threading error
 
 toolchain = SYSTEM
 
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18712/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18712/']
 sources = ['l_inspector_oneapi_p_%(version)s.123_offline.sh']
 checksums = ['8551180aa30be3abea11308fb11ea9a296f0e056ab07d9254585448a0b23333e']
 
diff --git a/easybuild/easyconfigs/i/IntelClusterChecker/IntelClusterChecker-2021.5.0.eb b/easybuild/easyconfigs/i/IntelClusterChecker/IntelClusterChecker-2021.5.0.eb
index 55107c33e8a..c0357dea2d0 100644
--- a/easybuild/easyconfigs/i/IntelClusterChecker/IntelClusterChecker-2021.5.0.eb
+++ b/easybuild/easyconfigs/i/IntelClusterChecker/IntelClusterChecker-2021.5.0.eb
@@ -13,7 +13,7 @@ can be identified and practical resolutions provided.
 
 toolchain = SYSTEM
 
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18359/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18359/']
 sources = ['l_clck_p_%(version)s.560_offline.sh']
 checksums = ['2b661eff4a87607fd29e21fe29883873c0a7216d7d0a99557dc48b6eae9adeb0']
 
diff --git a/easybuild/easyconfigs/i/IntelPython/IntelPython-2.7.15-2019.2.066.eb b/easybuild/easyconfigs/i/IntelPython/IntelPython-2.7.15-2019.2.066.eb
index c46f42bb81b..48ab0a8f836 100644
--- a/easybuild/easyconfigs/i/IntelPython/IntelPython-2.7.15-2019.2.066.eb
+++ b/easybuild/easyconfigs/i/IntelPython/IntelPython-2.7.15-2019.2.066.eb
@@ -15,7 +15,7 @@ description = """
  Accelerating Python* performance on modern architectures from Intel.
 """
 
-source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15115/']
+source_urls = ['http://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15115/']
 sources = ['l_pythoni%s_p_%s.tar.gz' % (local_pysver, local_relver)]
 checksums = ['dd0b73db5d0d79c3cdf779d10092eae32780d720b74ed8fde2a2c46e23143de1']
 
diff --git a/easybuild/easyconfigs/i/IntelPython/IntelPython-3.6.8-2019.2.066.eb b/easybuild/easyconfigs/i/IntelPython/IntelPython-3.6.8-2019.2.066.eb
index fd51e3b2082..d0c2dc13c67 100644
--- a/easybuild/easyconfigs/i/IntelPython/IntelPython-3.6.8-2019.2.066.eb
+++ b/easybuild/easyconfigs/i/IntelPython/IntelPython-3.6.8-2019.2.066.eb
@@ -15,7 +15,7 @@ description = """
  Accelerating Python* performance on modern architectures from Intel.
 """
 
-source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15115/']
+source_urls = ['http://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15115/']
 sources = ['l_pythoni%s_p_%s.tar.gz' % (local_pysver, local_relver)]
 checksums = ['804883fc1413ee72b0ae421a8ac82ab158fc01c8b4631a44a9d2ef1a19324751']
 
diff --git a/easybuild/easyconfigs/i/icc/icc-2018.1.163-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/icc/icc-2018.1.163-GCC-6.4.0-2.28.eb
index ca49a084587..f6eb99cebdc 100644
--- a/easybuild/easyconfigs/i/icc/icc-2018.1.163-GCC-6.4.0-2.28.eb
+++ b/easybuild/easyconfigs/i/icc/icc-2018.1.163-GCC-6.4.0-2.28.eb
@@ -8,7 +8,7 @@ description = "Intel C and C++ compilers"
 
 toolchain = SYSTEM
 
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12382/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/12382/']
 sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_cpp.tgz']
 checksums = ['ddbfdf88eed095817650ec0a226ef3b9c07c41c855d258e80eaade5173fedb6e']
 
diff --git a/easybuild/easyconfigs/i/icc/icc-2018.3.222-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/i/icc/icc-2018.3.222-GCC-7.3.0-2.30.eb
index 9b3a071f005..c04b1a09909 100644
--- a/easybuild/easyconfigs/i/icc/icc-2018.3.222-GCC-7.3.0-2.30.eb
+++ b/easybuild/easyconfigs/i/icc/icc-2018.3.222-GCC-7.3.0-2.30.eb
@@ -8,7 +8,7 @@ description = "Intel C and C++ compilers"
 
 toolchain = SYSTEM
 
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13003/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/13003/']
 sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_cpp.tgz']
 checksums = ['d8b7e6633faa2e0b7d4eebf3260cb3a200b951cb2cf7b5db957c5ae71508d34b']
 
diff --git a/easybuild/easyconfigs/i/icc/icc-2018.5.274-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/i/icc/icc-2018.5.274-GCC-7.3.0-2.30.eb
index 3918ba3f3f1..f2d6c096878 100644
--- a/easybuild/easyconfigs/i/icc/icc-2018.5.274-GCC-7.3.0-2.30.eb
+++ b/easybuild/easyconfigs/i/icc/icc-2018.5.274-GCC-7.3.0-2.30.eb
@@ -8,7 +8,7 @@ description = "Intel C and C++ compilers"
 
 toolchain = SYSTEM
 
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13723/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/13723/']
 # released as "2018 update 4" despite internal version number if 2018.5.274, so can't use %(version_minor)s template
 sources = ['parallel_studio_xe_%(version_major)s_update4_composer_edition_for_cpp.tgz']
 checksums = ['3850ab2a01fe8888af8fed65b7d24e0ddf45a84efe9635ff0f118c38dfc4544b']
diff --git a/easybuild/easyconfigs/i/icc/icc-2019.0.117-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/i/icc/icc-2019.0.117-GCC-8.2.0-2.31.1.eb
index b78d2e8e11c..5cf05e6a559 100644
--- a/easybuild/easyconfigs/i/icc/icc-2019.0.117-GCC-8.2.0-2.31.1.eb
+++ b/easybuild/easyconfigs/i/icc/icc-2019.0.117-GCC-8.2.0-2.31.1.eb
@@ -8,7 +8,7 @@ description = "Intel C and C++ compilers"
 
 toolchain = SYSTEM
 
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13582/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/13582/']
 sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_cpp.tgz']
 checksums = ['17932a54a76d04432de16e6db15a6ed80fa80ed20193f3b717fd391f623e23e1']
 
diff --git a/easybuild/easyconfigs/i/icc/icc-2019.1.144-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/i/icc/icc-2019.1.144-GCC-8.2.0-2.31.1.eb
index 7b37d3169dc..f2341a844c3 100644
--- a/easybuild/easyconfigs/i/icc/icc-2019.1.144-GCC-8.2.0-2.31.1.eb
+++ b/easybuild/easyconfigs/i/icc/icc-2019.1.144-GCC-8.2.0-2.31.1.eb
@@ -8,7 +8,7 @@ description = "Intel C and C++ compilers"
 
 toolchain = SYSTEM
 
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/14865/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/14865/']
 sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_cpp.tgz']
 checksums = ['4a156bbeac9bd8d67e74b33ad6f3ae02d4c24c8444365465db6dc50d3e891946']
 
diff --git a/easybuild/easyconfigs/i/icc/icc-2019.2.187-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/i/icc/icc-2019.2.187-GCC-8.2.0-2.31.1.eb
index f192fd17472..9f9b71a21df 100644
--- a/easybuild/easyconfigs/i/icc/icc-2019.2.187-GCC-8.2.0-2.31.1.eb
+++ b/easybuild/easyconfigs/i/icc/icc-2019.2.187-GCC-8.2.0-2.31.1.eb
@@ -8,7 +8,7 @@ description = "Intel C and C++ compilers"
 
 toolchain = SYSTEM
 
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15093/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15093/']
 sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_cpp.tgz']
 checksums = ['fc434a2e005af223f43d258c16f004134def726a8d2a225e830af85d553bee55']
 
diff --git a/easybuild/easyconfigs/i/icc/icc-2019.3.199-GCC-8.3.0-2.32.eb b/easybuild/easyconfigs/i/icc/icc-2019.3.199-GCC-8.3.0-2.32.eb
index 65821a417db..2d194db100a 100644
--- a/easybuild/easyconfigs/i/icc/icc-2019.3.199-GCC-8.3.0-2.32.eb
+++ b/easybuild/easyconfigs/i/icc/icc-2019.3.199-GCC-8.3.0-2.32.eb
@@ -8,7 +8,7 @@ description = "Intel C and C++ compilers"
 
 toolchain = SYSTEM
 
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15273/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15273/']
 sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_cpp.tgz']
 checksums = ['969985e83ebf7bfe3c3ac3b771a7d16ba9b5dfbda84e7c2a60ef25fb827b58ae']
 
diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2019.4.243.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2019.4.243.eb
index 5cefbfc2dee..85453f37251 100644
--- a/easybuild/easyconfigs/i/iccifort/iccifort-2019.4.243.eb
+++ b/easybuild/easyconfigs/i/iccifort/iccifort-2019.4.243.eb
@@ -8,7 +8,7 @@ description = "Intel C, C++ & Fortran compilers"
 
 toolchain = SYSTEM
 
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15537/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15537/']
 sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition.tgz']
 patches = ['iccifort-%(version)s_no_mpi_rt_dependency.patch']
 checksums = [
diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2019.5.281.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2019.5.281.eb
index c080762f21d..b4eb6588ec7 100644
--- a/easybuild/easyconfigs/i/iccifort/iccifort-2019.5.281.eb
+++ b/easybuild/easyconfigs/i/iccifort/iccifort-2019.5.281.eb
@@ -8,7 +8,7 @@ description = "Intel C, C++ & Fortran compilers"
 
 toolchain = SYSTEM
 
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15813/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15813/']
 sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition.tgz']
 patches = ['iccifort-%(version)s_no_mpi_rt_dependency.patch']
 checksums = [
diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2020.0.166-GCC-9.2.0.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2020.0.166-GCC-9.2.0.eb
index a8f9c94588f..a21e15527d5 100644
--- a/easybuild/easyconfigs/i/iccifort/iccifort-2020.0.166-GCC-9.2.0.eb
+++ b/easybuild/easyconfigs/i/iccifort/iccifort-2020.0.166-GCC-9.2.0.eb
@@ -8,7 +8,7 @@ description = "Intel C, C++ & Fortran compilers"
 
 toolchain = SYSTEM
 
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16229/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16229/']
 sources = ['parallel_studio_xe_%(version_major)s_composer_edition.tgz']
 patches = ['iccifort-%(version)s_no_mpi_rt_dependency.patch']
 checksums = [
diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2020.0.166.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2020.0.166.eb
index 70593480c69..4ad42c13a31 100644
--- a/easybuild/easyconfigs/i/iccifort/iccifort-2020.0.166.eb
+++ b/easybuild/easyconfigs/i/iccifort/iccifort-2020.0.166.eb
@@ -8,7 +8,7 @@ description = "Intel C, C++ & Fortran compilers"
 
 toolchain = SYSTEM
 
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16229/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16229/']
 sources = ['parallel_studio_xe_%(version_major)s_composer_edition.tgz']
 patches = ['iccifort-%(version)s_no_mpi_rt_dependency.patch']
 checksums = [
diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2020.1.217.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2020.1.217.eb
index 89d42319787..98e64dff918 100644
--- a/easybuild/easyconfigs/i/iccifort/iccifort-2020.1.217.eb
+++ b/easybuild/easyconfigs/i/iccifort/iccifort-2020.1.217.eb
@@ -8,7 +8,7 @@ description = "Intel C, C++ & Fortran compilers"
 
 toolchain = SYSTEM
 
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16530/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16530/']
 sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition.tgz']
 patches = ['iccifort-%(version)s_no_mpi_rt_dependency.patch']
 checksums = [
diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2020.4.304.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2020.4.304.eb
index fbd8bc1719b..056539c7f76 100644
--- a/easybuild/easyconfigs/i/iccifort/iccifort-2020.4.304.eb
+++ b/easybuild/easyconfigs/i/iccifort/iccifort-2020.4.304.eb
@@ -8,7 +8,7 @@ description = "Intel C, C++ & Fortran compilers"
 
 toolchain = SYSTEM
 
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/17117/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/17117/']
 sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition.tgz']
 patches = ['iccifort-%(version)s_no_mpi_rt_dependency.patch']
 checksums = [
diff --git a/easybuild/easyconfigs/i/ifort/ifort-2018.1.163-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/ifort/ifort-2018.1.163-GCC-6.4.0-2.28.eb
index 66cf55bd0c0..2ce7d5ee7f1 100644
--- a/easybuild/easyconfigs/i/ifort/ifort-2018.1.163-GCC-6.4.0-2.28.eb
+++ b/easybuild/easyconfigs/i/ifort/ifort-2018.1.163-GCC-6.4.0-2.28.eb
@@ -8,7 +8,7 @@ description = "Intel Fortran compiler"
 
 toolchain = SYSTEM
 
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12383/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/12383/']
 sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_fortran.tgz']
 patches = ['ifort_%(version)s_no_mpi_mic_dependency.patch']
 checksums = [
diff --git a/easybuild/easyconfigs/i/ifort/ifort-2018.3.222-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/i/ifort/ifort-2018.3.222-GCC-7.3.0-2.30.eb
index 8572f079dca..3bdc51210af 100644
--- a/easybuild/easyconfigs/i/ifort/ifort-2018.3.222-GCC-7.3.0-2.30.eb
+++ b/easybuild/easyconfigs/i/ifort/ifort-2018.3.222-GCC-7.3.0-2.30.eb
@@ -8,7 +8,7 @@ description = "Intel Fortran compiler"
 
 toolchain = SYSTEM
 
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13004/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/13004/']
 sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_fortran.tgz']
 patches = ['ifort_%(version)s_no_mpi_mic_dependency.patch']
 checksums = [
diff --git a/easybuild/easyconfigs/i/ifort/ifort-2018.5.274-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/i/ifort/ifort-2018.5.274-GCC-7.3.0-2.30.eb
index 7668ec76749..3f9f1de0c45 100644
--- a/easybuild/easyconfigs/i/ifort/ifort-2018.5.274-GCC-7.3.0-2.30.eb
+++ b/easybuild/easyconfigs/i/ifort/ifort-2018.5.274-GCC-7.3.0-2.30.eb
@@ -8,7 +8,7 @@ description = "Intel Fortran compiler"
 
 toolchain = SYSTEM
 
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13724/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/13724/']
 # released as "2018 update 4" despite internal version number if 2018.5.274, so can't use %(version_minor)s template
 sources = ['parallel_studio_xe_%(version_major)s_update4_composer_edition_for_fortran.tgz']
 patches = ['ifort-%(version)s_no_mpi_mic_dependency.patch']
diff --git a/easybuild/easyconfigs/i/ifort/ifort-2019.0.117-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/i/ifort/ifort-2019.0.117-GCC-8.2.0-2.31.1.eb
index 3457239087d..453cf476095 100644
--- a/easybuild/easyconfigs/i/ifort/ifort-2019.0.117-GCC-8.2.0-2.31.1.eb
+++ b/easybuild/easyconfigs/i/ifort/ifort-2019.0.117-GCC-8.2.0-2.31.1.eb
@@ -8,7 +8,7 @@ description = "Intel Fortran compiler"
 
 toolchain = SYSTEM
 
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13583/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/13583/']
 sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_fortran.tgz']
 patches = ['ifort-%(version)s_no_mpi_mic_dependency.patch']
 checksums = [
diff --git a/easybuild/easyconfigs/i/ifort/ifort-2019.1.144-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/i/ifort/ifort-2019.1.144-GCC-8.2.0-2.31.1.eb
index c47117b085b..c6c03d9340f 100644
--- a/easybuild/easyconfigs/i/ifort/ifort-2019.1.144-GCC-8.2.0-2.31.1.eb
+++ b/easybuild/easyconfigs/i/ifort/ifort-2019.1.144-GCC-8.2.0-2.31.1.eb
@@ -8,7 +8,7 @@ description = "Intel Fortran compiler"
 
 toolchain = SYSTEM
 
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/14866/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/14866/']
 sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_fortran.tgz']
 patches = ['ifort-%(version)s_no_mpi_mic_dependency.patch']
 checksums = [
diff --git a/easybuild/easyconfigs/i/ifort/ifort-2019.2.187-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/i/ifort/ifort-2019.2.187-GCC-8.2.0-2.31.1.eb
index 924762c6de2..5a043c03822 100644
--- a/easybuild/easyconfigs/i/ifort/ifort-2019.2.187-GCC-8.2.0-2.31.1.eb
+++ b/easybuild/easyconfigs/i/ifort/ifort-2019.2.187-GCC-8.2.0-2.31.1.eb
@@ -8,7 +8,7 @@ description = "Intel Fortran compiler"
 
 toolchain = SYSTEM
 
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15094/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15094/']
 sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_fortran.tgz']
 patches = ['ifort-%(version)s_no_mpi_mic_dependency.patch']
 checksums = [
diff --git a/easybuild/easyconfigs/i/ifort/ifort-2019.3.199-GCC-8.3.0-2.32.eb b/easybuild/easyconfigs/i/ifort/ifort-2019.3.199-GCC-8.3.0-2.32.eb
index b8eb911adc2..b996c679995 100644
--- a/easybuild/easyconfigs/i/ifort/ifort-2019.3.199-GCC-8.3.0-2.32.eb
+++ b/easybuild/easyconfigs/i/ifort/ifort-2019.3.199-GCC-8.3.0-2.32.eb
@@ -8,7 +8,7 @@ description = "Intel Fortran compiler"
 
 toolchain = SYSTEM
 
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15274/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15274/']
 sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_fortran.tgz']
 patches = ['ifort-%(version)s_no_mpi_mic_dependency.patch']
 checksums = [
diff --git a/easybuild/easyconfigs/i/imkl/imkl-2018.1.163-iccifort-2018.1.163-GCC-6.4.0-2.28-serial.eb b/easybuild/easyconfigs/i/imkl/imkl-2018.1.163-iccifort-2018.1.163-GCC-6.4.0-2.28-serial.eb
index 65486c1a522..1af220dba70 100644
--- a/easybuild/easyconfigs/i/imkl/imkl-2018.1.163-iccifort-2018.1.163-GCC-6.4.0-2.28-serial.eb
+++ b/easybuild/easyconfigs/i/imkl/imkl-2018.1.163-iccifort-2018.1.163-GCC-6.4.0-2.28-serial.eb
@@ -12,7 +12,7 @@ description = """Intel Math Kernel Library is a library of highly optimized,
 
 toolchain = {'name': 'iccifort', 'version': '2018.1.163-GCC-6.4.0-2.28'}
 
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12384/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/12384/']
 sources = ['l_mkl_%(version)s.tgz']
 checksums = ['f6dc263fc6f3c350979740a13de1b1e8745d9ba0d0f067ece503483b9189c2ca']
 
diff --git a/easybuild/easyconfigs/i/imkl/imkl-2018.1.163-iimpi-2018a.eb b/easybuild/easyconfigs/i/imkl/imkl-2018.1.163-iimpi-2018a.eb
index 770acb76d87..a90fc9aaaac 100644
--- a/easybuild/easyconfigs/i/imkl/imkl-2018.1.163-iimpi-2018a.eb
+++ b/easybuild/easyconfigs/i/imkl/imkl-2018.1.163-iimpi-2018a.eb
@@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized,
 
 toolchain = {'name': 'iimpi', 'version': '2018a'}
 
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12384/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/12384/']
 sources = ['l_mkl_%(version)s.tgz']
 checksums = ['f6dc263fc6f3c350979740a13de1b1e8745d9ba0d0f067ece503483b9189c2ca']
 
diff --git a/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-gimpi-2018b.eb b/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-gimpi-2018b.eb
index f340d755ee2..c873144967b 100644
--- a/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-gimpi-2018b.eb
+++ b/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-gimpi-2018b.eb
@@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized,
 
 toolchain = {'name': 'gimpi', 'version': '2018b'}
 
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13005/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/13005/']
 sources = ['l_mkl_%(version)s.tgz']
 checksums = ['108d59c0927e58ce8c314db6c2b48ee331c3798f7102725f425d6884eb6ed241']
 
diff --git a/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-gompi-2018b.eb b/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-gompi-2018b.eb
index 6ead35efc9a..89a3f33d184 100644
--- a/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-gompi-2018b.eb
+++ b/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-gompi-2018b.eb
@@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized,
 
 toolchain = {'name': 'gompi', 'version': '2018b'}
 
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13005/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/13005/']
 sources = ['l_mkl_%(version)s.tgz']
 checksums = ['108d59c0927e58ce8c314db6c2b48ee331c3798f7102725f425d6884eb6ed241']
 
diff --git a/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-iimpi-2018b.eb b/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-iimpi-2018b.eb
index 7f53145d6a3..450dc0082e2 100644
--- a/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-iimpi-2018b.eb
+++ b/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-iimpi-2018b.eb
@@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized,
 
 toolchain = {'name': 'iimpi', 'version': '2018b'}
 
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13005/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/13005/']
 sources = ['l_mkl_%(version)s.tgz']
 checksums = ['108d59c0927e58ce8c314db6c2b48ee331c3798f7102725f425d6884eb6ed241']
 
diff --git a/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-iompi-2018b.eb b/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-iompi-2018b.eb
index aeabee4d300..0fcf2f60e8e 100644
--- a/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-iompi-2018b.eb
+++ b/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-iompi-2018b.eb
@@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized,
 
 toolchain = {'name': 'iompi', 'version': '2018b'}
 
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13005/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/13005/']
 sources = ['l_mkl_%(version)s.tgz']
 checksums = ['108d59c0927e58ce8c314db6c2b48ee331c3798f7102725f425d6884eb6ed241']
 
diff --git a/easybuild/easyconfigs/i/imkl/imkl-2018.4.274-iimpi-2018.04.eb b/easybuild/easyconfigs/i/imkl/imkl-2018.4.274-iimpi-2018.04.eb
index 02dba60737e..7d2dc1809af 100644
--- a/easybuild/easyconfigs/i/imkl/imkl-2018.4.274-iimpi-2018.04.eb
+++ b/easybuild/easyconfigs/i/imkl/imkl-2018.4.274-iimpi-2018.04.eb
@@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized,
 
 toolchain = {'name': 'iimpi', 'version': '2018.04'}
 
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13725/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/13725/']
 sources = ['l_mkl_%(version)s.tgz']
 checksums = ['18eb3cde3e6a61a88f25afff25df762a560013f650aaf363f7d3d516a0d04881']
 
diff --git a/easybuild/easyconfigs/i/imkl/imkl-2019.0.117-iimpi-2019.00.eb b/easybuild/easyconfigs/i/imkl/imkl-2019.0.117-iimpi-2019.00.eb
index a382ae20ac7..d222e9cd3b3 100644
--- a/easybuild/easyconfigs/i/imkl/imkl-2019.0.117-iimpi-2019.00.eb
+++ b/easybuild/easyconfigs/i/imkl/imkl-2019.0.117-iimpi-2019.00.eb
@@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized,
 
 toolchain = {'name': 'iimpi', 'version': '2019.00'}
 
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13575/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/13575/']
 sources = ['l_mkl_%(version)s.tgz']
 checksums = ['4e1fe2c705cfc47050064c0d6c4dee1a8c6740ac1c4f64dde9c7511c4989c7ad']
 
diff --git a/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-gompi-2019a.eb b/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-gompi-2019a.eb
index aa6a03a6929..ae7e676174e 100644
--- a/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-gompi-2019a.eb
+++ b/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-gompi-2019a.eb
@@ -9,7 +9,7 @@ description = """Intel Math Kernel Library is a library of highly optimized,
 
 toolchain = {'name': 'gompi', 'version': '2019a'}
 
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/14895/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/14895/']
 sources = ['l_mkl_%(version)s.tgz']
 checksums = ['5205a460a9c685f7a442868367389b2d0c25e1455346bc6a37c5b8ff90a20fbb']
 
diff --git a/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iimpi-2019.01.eb b/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iimpi-2019.01.eb
index e63cc1a2695..15e03750772 100644
--- a/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iimpi-2019.01.eb
+++ b/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iimpi-2019.01.eb
@@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized,
 
 toolchain = {'name': 'iimpi', 'version': '2019.01'}
 
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/14895/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/14895/']
 sources = ['l_mkl_%(version)s.tgz']
 checksums = ['5205a460a9c685f7a442868367389b2d0c25e1455346bc6a37c5b8ff90a20fbb']
 
diff --git a/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iimpi-2019a.eb b/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iimpi-2019a.eb
index 782473ec9fa..dcd07853ae8 100644
--- a/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iimpi-2019a.eb
+++ b/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iimpi-2019a.eb
@@ -9,7 +9,7 @@ description = """Intel Math Kernel Library is a library of highly optimized,
 
 toolchain = {'name': 'iimpi', 'version': '2019a'}
 
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/14895/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/14895/']
 sources = ['l_mkl_%(version)s.tgz']
 checksums = ['5205a460a9c685f7a442868367389b2d0c25e1455346bc6a37c5b8ff90a20fbb']
 
diff --git a/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iimpic-2019a.eb b/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iimpic-2019a.eb
index b8fb1ebef4c..af64b61bfd7 100644
--- a/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iimpic-2019a.eb
+++ b/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iimpic-2019a.eb
@@ -9,7 +9,7 @@ description = """Intel Math Kernel Library is a library of highly optimized,
 
 toolchain = {'name': 'iimpic', 'version': '2019a'}
 
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/14895/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/14895/']
 sources = ['l_mkl_%(version)s.tgz']
 checksums = ['5205a460a9c685f7a442868367389b2d0c25e1455346bc6a37c5b8ff90a20fbb']
 
diff --git a/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iompi-2019.01.eb b/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iompi-2019.01.eb
index 3a5e6baedc4..e7a42454f04 100644
--- a/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iompi-2019.01.eb
+++ b/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iompi-2019.01.eb
@@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized,
 
 toolchain = {'name': 'iompi', 'version': '2019.01'}
 
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/14895/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/14895/']
 sources = ['l_mkl_%(version)s.tgz']
 checksums = ['5205a460a9c685f7a442868367389b2d0c25e1455346bc6a37c5b8ff90a20fbb']
 
diff --git a/easybuild/easyconfigs/i/imkl/imkl-2019.2.187-iimpi-2019.02.eb b/easybuild/easyconfigs/i/imkl/imkl-2019.2.187-iimpi-2019.02.eb
index 645ffaf31a7..8cd693cc5ec 100644
--- a/easybuild/easyconfigs/i/imkl/imkl-2019.2.187-iimpi-2019.02.eb
+++ b/easybuild/easyconfigs/i/imkl/imkl-2019.2.187-iimpi-2019.02.eb
@@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized,
 
 toolchain = {'name': 'iimpi', 'version': '2019.02'}
 
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15095/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15095/']
 sources = ['l_mkl_%(version)s.tgz']
 checksums = ['2bf004e6b5adb4f956993d6c20ea6ce289bb630314dd501db7f2dd5b9978ed1d']
 
diff --git a/easybuild/easyconfigs/i/imkl/imkl-2019.3.199-iimpi-2019.03.eb b/easybuild/easyconfigs/i/imkl/imkl-2019.3.199-iimpi-2019.03.eb
index 2c06461ab97..8685b03cc91 100644
--- a/easybuild/easyconfigs/i/imkl/imkl-2019.3.199-iimpi-2019.03.eb
+++ b/easybuild/easyconfigs/i/imkl/imkl-2019.3.199-iimpi-2019.03.eb
@@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized,
 
 toolchain = {'name': 'iimpi', 'version': '2019.03'}
 
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15275/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15275/']
 sources = ['l_mkl_%(version)s.tgz']
 checksums = ['06de2b54f4812e7c39a118536259c942029fe1d6d8918ad9df558a83c4162b8f']
 
diff --git a/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-gompi-2019b.eb b/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-gompi-2019b.eb
index 3c2759d1539..940151b46dc 100644
--- a/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-gompi-2019b.eb
+++ b/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-gompi-2019b.eb
@@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized,
 
 toolchain = {'name': 'gompi', 'version': '2019b'}
 
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15816/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15816/']
 sources = ['l_mkl_%(version)s.tgz']
 checksums = ['9995ea4469b05360d509c9705e9309dc983c0a10edc2ae3a5384bc837326737e']
 
diff --git a/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-gompic-2019b.eb b/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-gompic-2019b.eb
index 3421505968c..91ca97f6bc6 100644
--- a/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-gompic-2019b.eb
+++ b/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-gompic-2019b.eb
@@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized,
 
 toolchain = {'name': 'gompic', 'version': '2019b'}
 
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15816/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15816/']
 sources = ['l_mkl_%(version)s.tgz']
 checksums = ['9995ea4469b05360d509c9705e9309dc983c0a10edc2ae3a5384bc837326737e']
 
diff --git a/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-iimpi-2019b.eb b/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-iimpi-2019b.eb
index d95d740ea28..61489356fe3 100644
--- a/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-iimpi-2019b.eb
+++ b/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-iimpi-2019b.eb
@@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized,
 
 toolchain = {'name': 'iimpi', 'version': '2019b'}
 
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15816/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15816/']
 sources = ['l_mkl_%(version)s.tgz']
 checksums = ['9995ea4469b05360d509c9705e9309dc983c0a10edc2ae3a5384bc837326737e']
 
diff --git a/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-iimpic-2019b.eb b/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-iimpic-2019b.eb
index 62cf27a5251..b1e88a55dd3 100644
--- a/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-iimpic-2019b.eb
+++ b/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-iimpic-2019b.eb
@@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized,
 
 toolchain = {'name': 'iimpic', 'version': '2019b'}
 
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15816/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15816/']
 sources = ['l_mkl_%(version)s.tgz']
 checksums = ['9995ea4469b05360d509c9705e9309dc983c0a10edc2ae3a5384bc837326737e']
 
diff --git a/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-iompi-2019b.eb b/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-iompi-2019b.eb
index 906ad9525cd..8e7d6fa5ec2 100644
--- a/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-iompi-2019b.eb
+++ b/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-iompi-2019b.eb
@@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized,
 
 toolchain = {'name': 'iompi', 'version': '2019b'}
 
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15816/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15816/']
 sources = ['l_mkl_%(version)s.tgz']
 checksums = ['9995ea4469b05360d509c9705e9309dc983c0a10edc2ae3a5384bc837326737e']
 
diff --git a/easybuild/easyconfigs/i/imkl/imkl-2020.0.166-iimpi-2020.00.eb b/easybuild/easyconfigs/i/imkl/imkl-2020.0.166-iimpi-2020.00.eb
index 610ba004009..d27b6e67346 100644
--- a/easybuild/easyconfigs/i/imkl/imkl-2020.0.166-iimpi-2020.00.eb
+++ b/easybuild/easyconfigs/i/imkl/imkl-2020.0.166-iimpi-2020.00.eb
@@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized,
 
 toolchain = {'name': 'iimpi', 'version': '2020.00'}
 
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16232/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16232/']
 sources = ['l_mkl_%(version)s.tgz']
 checksums = ['f6d92deb3ff10b11ba3df26b2c62bb4f0f7ae43e21905a91d553e58f0f5a8ae0']
 
diff --git a/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-gompi-2020a.eb b/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-gompi-2020a.eb
index dcb4894a2a4..d662fdae171 100644
--- a/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-gompi-2020a.eb
+++ b/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-gompi-2020a.eb
@@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized,
 
 toolchain = {'name': 'gompi', 'version': '2020a'}
 
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16533/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16533/']
 sources = ['l_mkl_%(version)s.tgz']
 checksums = ['082a4be30bf4f6998e4d6e3da815a77560a5e66a68e254d161ab96f07086066d']
 
diff --git a/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-iimpi-2020.06-impi-18.5.eb b/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-iimpi-2020.06-impi-18.5.eb
index 89aac0e1547..a683875dd81 100644
--- a/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-iimpi-2020.06-impi-18.5.eb
+++ b/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-iimpi-2020.06-impi-18.5.eb
@@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized,
 
 toolchain = {'name': 'iimpi', 'version': '2020.06-impi-18.5'}
 
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16533/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16533/']
 sources = ['l_mkl_%(version)s.tgz']
 checksums = ['082a4be30bf4f6998e4d6e3da815a77560a5e66a68e254d161ab96f07086066d']
 
diff --git a/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-iimpi-2020a.eb b/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-iimpi-2020a.eb
index 3111a3509b0..aef431b9b6d 100644
--- a/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-iimpi-2020a.eb
+++ b/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-iimpi-2020a.eb
@@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized,
 
 toolchain = {'name': 'iimpi', 'version': '2020a'}
 
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16533/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16533/']
 sources = ['l_mkl_%(version)s.tgz']
 checksums = ['082a4be30bf4f6998e4d6e3da815a77560a5e66a68e254d161ab96f07086066d']
 
diff --git a/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-iimpic-2020a.eb b/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-iimpic-2020a.eb
index 3475dab254a..dbfbc356455 100644
--- a/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-iimpic-2020a.eb
+++ b/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-iimpic-2020a.eb
@@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized,
 
 toolchain = {'name': 'iimpic', 'version': '2020a'}
 
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16533/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16533/']
 sources = ['l_mkl_%(version)s.tgz']
 checksums = ['082a4be30bf4f6998e4d6e3da815a77560a5e66a68e254d161ab96f07086066d']
 
diff --git a/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-iompi-2020a.eb b/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-iompi-2020a.eb
index 3eca90fc0a2..1f80ac1e253 100644
--- a/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-iompi-2020a.eb
+++ b/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-iompi-2020a.eb
@@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized,
 
 toolchain = {'name': 'iompi', 'version': '2020a'}
 
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16533/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16533/']
 sources = ['l_mkl_%(version)s.tgz']
 checksums = ['082a4be30bf4f6998e4d6e3da815a77560a5e66a68e254d161ab96f07086066d']
 
diff --git a/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-NVHPC-21.2.eb b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-NVHPC-21.2.eb
index 75ac380269e..71a9f0f37b9 100644
--- a/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-NVHPC-21.2.eb
+++ b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-NVHPC-21.2.eb
@@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized,
 
 toolchain = {'name': 'NVHPC', 'version': '21.2'}
 
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16917/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16917/']
 sources = ['l_mkl_%(version)s.tgz']
 checksums = ['2314d46536974dbd08f2a4e4f9e9a155dc7e79e2798c74e7ddfaad00a5917ea5']
 
diff --git a/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-gompi-2020b.eb b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-gompi-2020b.eb
index 541c3c12aea..1526523c788 100644
--- a/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-gompi-2020b.eb
+++ b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-gompi-2020b.eb
@@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized,
 
 toolchain = {'name': 'gompi', 'version': '2020b'}
 
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16917/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16917/']
 sources = ['l_mkl_%(version)s.tgz']
 checksums = ['2314d46536974dbd08f2a4e4f9e9a155dc7e79e2798c74e7ddfaad00a5917ea5']
 
diff --git a/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-gompic-2020b.eb b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-gompic-2020b.eb
index e07323d8ee3..570499af77d 100644
--- a/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-gompic-2020b.eb
+++ b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-gompic-2020b.eb
@@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized,
 
 toolchain = {'name': 'gompic', 'version': '2020b'}
 
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16917/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16917/']
 sources = ['l_mkl_%(version)s.tgz']
 checksums = ['2314d46536974dbd08f2a4e4f9e9a155dc7e79e2798c74e7ddfaad00a5917ea5']
 
diff --git a/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iimpi-2020b.eb b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iimpi-2020b.eb
index e1f7dd0c3fd..15ccb6b8c77 100644
--- a/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iimpi-2020b.eb
+++ b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iimpi-2020b.eb
@@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized,
 
 toolchain = {'name': 'iimpi', 'version': '2020b'}
 
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16917/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16917/']
 sources = ['l_mkl_%(version)s.tgz']
 checksums = ['2314d46536974dbd08f2a4e4f9e9a155dc7e79e2798c74e7ddfaad00a5917ea5']
 
diff --git a/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iimpic-2020b.eb b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iimpic-2020b.eb
index a350ab4a6ed..73aac3a85e7 100644
--- a/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iimpic-2020b.eb
+++ b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iimpic-2020b.eb
@@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized,
 
 toolchain = {'name': 'iimpic', 'version': '2020b'}
 
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16917/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16917/']
 sources = ['l_mkl_%(version)s.tgz']
 checksums = ['2314d46536974dbd08f2a4e4f9e9a155dc7e79e2798c74e7ddfaad00a5917ea5']
 
diff --git a/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iompi-2020b.eb b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iompi-2020b.eb
index 89d0c991d88..68e2a157d3d 100644
--- a/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iompi-2020b.eb
+++ b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iompi-2020b.eb
@@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized,
 
 toolchain = {'name': 'iompi', 'version': '2020b'}
 
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16917/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16917/']
 sources = ['l_mkl_%(version)s.tgz']
 checksums = ['2314d46536974dbd08f2a4e4f9e9a155dc7e79e2798c74e7ddfaad00a5917ea5']
 
diff --git a/easybuild/easyconfigs/i/imkl/imkl-2021.1.1-iimpi-2020.12.eb b/easybuild/easyconfigs/i/imkl/imkl-2021.1.1-iimpi-2020.12.eb
index 737f7462d7d..363e95f7dc9 100644
--- a/easybuild/easyconfigs/i/imkl/imkl-2021.1.1-iimpi-2020.12.eb
+++ b/easybuild/easyconfigs/i/imkl/imkl-2021.1.1-iimpi-2020.12.eb
@@ -7,7 +7,7 @@ description = "Intel oneAPI Math Kernel Library"
 toolchain = {'name': 'iimpi', 'version': '2020.12'}
 
 # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/17402/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/17402/']
 sources = ['l_onemkl_p_%(version)s.52_offline.sh']
 checksums = ['818b6bd9a6c116f4578cda3151da0612ec9c3ce8b2c8a64730d625ce5b13cc0c']
 
diff --git a/easybuild/easyconfigs/i/imkl/imkl-2021.2.0-gompi-2021a.eb b/easybuild/easyconfigs/i/imkl/imkl-2021.2.0-gompi-2021a.eb
index ff7c13049ea..77a41fb58ed 100644
--- a/easybuild/easyconfigs/i/imkl/imkl-2021.2.0-gompi-2021a.eb
+++ b/easybuild/easyconfigs/i/imkl/imkl-2021.2.0-gompi-2021a.eb
@@ -7,7 +7,7 @@ description = "Intel oneAPI Math Kernel Library"
 toolchain = {'name': 'gompi', 'version': '2021a'}
 
 # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/17757/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/17757/']
 sources = ['l_onemkl_p_%(version)s.296_offline.sh']
 checksums = ['816e9df26ff331d6c0751b86ed5f7d243f9f172e76f14e83b32bf4d1d619dbae']
 
diff --git a/easybuild/easyconfigs/i/imkl/imkl-2021.2.0-iimpi-2021a.eb b/easybuild/easyconfigs/i/imkl/imkl-2021.2.0-iimpi-2021a.eb
index aa8f14f2250..741b626f55c 100644
--- a/easybuild/easyconfigs/i/imkl/imkl-2021.2.0-iimpi-2021a.eb
+++ b/easybuild/easyconfigs/i/imkl/imkl-2021.2.0-iimpi-2021a.eb
@@ -7,7 +7,7 @@ description = "Intel oneAPI Math Kernel Library"
 toolchain = {'name': 'iimpi', 'version': '2021a'}
 
 # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/17757/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/17757/']
 sources = ['l_onemkl_p_%(version)s.296_offline.sh']
 checksums = ['816e9df26ff331d6c0751b86ed5f7d243f9f172e76f14e83b32bf4d1d619dbae']
 
diff --git a/easybuild/easyconfigs/i/imkl/imkl-2021.2.0-iompi-2021a.eb b/easybuild/easyconfigs/i/imkl/imkl-2021.2.0-iompi-2021a.eb
index 60282631f05..2bb82fd3380 100644
--- a/easybuild/easyconfigs/i/imkl/imkl-2021.2.0-iompi-2021a.eb
+++ b/easybuild/easyconfigs/i/imkl/imkl-2021.2.0-iompi-2021a.eb
@@ -7,7 +7,7 @@ description = "Intel oneAPI Math Kernel Library"
 toolchain = {'name': 'iompi', 'version': '2021a'}
 
 # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/17757/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/17757/']
 sources = ['l_onemkl_p_%(version)s.296_offline.sh']
 checksums = ['816e9df26ff331d6c0751b86ed5f7d243f9f172e76f14e83b32bf4d1d619dbae']
 
diff --git a/easybuild/easyconfigs/i/imkl/imkl-2021.3.0-gompi-2021a.eb b/easybuild/easyconfigs/i/imkl/imkl-2021.3.0-gompi-2021a.eb
index 07a876f213e..a4746816d23 100644
--- a/easybuild/easyconfigs/i/imkl/imkl-2021.3.0-gompi-2021a.eb
+++ b/easybuild/easyconfigs/i/imkl/imkl-2021.3.0-gompi-2021a.eb
@@ -10,7 +10,7 @@ description = "Intel oneAPI Math Kernel Library"
 toolchain = {'name': 'gompi', 'version': '2021a'}
 
 # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/17901']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/17901']
 sources = ['l_onemkl_p_%(version)s.520_offline.sh']
 checksums = ['a06e1cdbfd8becc63440b473b153659885f25a6e3c4dcb2907ad9cd0c3ad59ce']
 
diff --git a/easybuild/easyconfigs/i/imkl/imkl-2021.4.0-iompi-2021b.eb b/easybuild/easyconfigs/i/imkl/imkl-2021.4.0-iompi-2021b.eb
index a6e0651ef64..4f45be5badc 100755
--- a/easybuild/easyconfigs/i/imkl/imkl-2021.4.0-iompi-2021b.eb
+++ b/easybuild/easyconfigs/i/imkl/imkl-2021.4.0-iompi-2021b.eb
@@ -7,7 +7,7 @@ description = "Intel oneAPI Math Kernel Library"
 toolchain = {'name': 'iompi', 'version': '2021b'}
 
 # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18222/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18222/']
 sources = ['l_onemkl_p_%(version)s.640_offline.sh']
 checksums = ['9ad546f05a421b4f439e8557fd0f2d83d5e299b0d9bd84bdd86be6feba0c3915']
 
diff --git a/easybuild/easyconfigs/i/imkl/imkl-2021.4.0.eb b/easybuild/easyconfigs/i/imkl/imkl-2021.4.0.eb
index f3e3040b1ee..bacd9ba4607 100644
--- a/easybuild/easyconfigs/i/imkl/imkl-2021.4.0.eb
+++ b/easybuild/easyconfigs/i/imkl/imkl-2021.4.0.eb
@@ -7,7 +7,7 @@ description = "Intel oneAPI Math Kernel Library"
 toolchain = SYSTEM
 
 # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18222/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18222/']
 sources = ['l_onemkl_p_%(version)s.640_offline.sh']
 checksums = ['9ad546f05a421b4f439e8557fd0f2d83d5e299b0d9bd84bdd86be6feba0c3915']
 
diff --git a/easybuild/easyconfigs/i/imkl/imkl-2022.0.1.eb b/easybuild/easyconfigs/i/imkl/imkl-2022.0.1.eb
index 67a5563ac0b..c348328e0e4 100644
--- a/easybuild/easyconfigs/i/imkl/imkl-2022.0.1.eb
+++ b/easybuild/easyconfigs/i/imkl/imkl-2022.0.1.eb
@@ -7,7 +7,7 @@ description = "Intel oneAPI Math Kernel Library"
 toolchain = SYSTEM
 
 # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18444/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18444/']
 sources = ['l_onemkl_p_%(version)s.117_offline.sh']
 checksums = ['22afafbe2f3762eca052ac21ec40b845ff2f3646077295c88c2f37f80a0cc160']
 
diff --git a/easybuild/easyconfigs/i/imkl/imkl-2022.1.0-gompi-2022a.eb b/easybuild/easyconfigs/i/imkl/imkl-2022.1.0-gompi-2022a.eb
index 2eb923c837e..955038d0fc1 100644
--- a/easybuild/easyconfigs/i/imkl/imkl-2022.1.0-gompi-2022a.eb
+++ b/easybuild/easyconfigs/i/imkl/imkl-2022.1.0-gompi-2022a.eb
@@ -10,7 +10,7 @@ description = "Intel oneAPI Math Kernel Library"
 toolchain = {'name': 'gompi', 'version': '2022a'}
 
 # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18721/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18721/']
 sources = ['l_onemkl_p_%(version)s.223_offline.sh']
 checksums = ['4b325a3c4c56e52f4ce6c8fbb55d7684adc16425000afc860464c0f29ea4563e']
 
diff --git a/easybuild/easyconfigs/i/imkl/imkl-2022.1.0.eb b/easybuild/easyconfigs/i/imkl/imkl-2022.1.0.eb
index c34d533cf35..b0653443859 100644
--- a/easybuild/easyconfigs/i/imkl/imkl-2022.1.0.eb
+++ b/easybuild/easyconfigs/i/imkl/imkl-2022.1.0.eb
@@ -7,7 +7,7 @@ description = "Intel oneAPI Math Kernel Library"
 toolchain = SYSTEM
 
 # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18721/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18721/']
 sources = ['l_onemkl_p_%(version)s.223_offline.sh']
 checksums = ['4b325a3c4c56e52f4ce6c8fbb55d7684adc16425000afc860464c0f29ea4563e']
 
diff --git a/easybuild/easyconfigs/i/imkl/imkl-2022.2.0.eb b/easybuild/easyconfigs/i/imkl/imkl-2022.2.0.eb
index 82776023871..a3c46807fc6 100644
--- a/easybuild/easyconfigs/i/imkl/imkl-2022.2.0.eb
+++ b/easybuild/easyconfigs/i/imkl/imkl-2022.2.0.eb
@@ -7,7 +7,7 @@ description = "Intel oneAPI Math Kernel Library"
 toolchain = SYSTEM
 
 # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18898/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18898/']
 sources = ['l_onemkl_p_%(version)s.8748_offline.sh']
 checksums = ['07d7caedd4b9f025c6fd439a0d2c2f279b18ecbbb63cadb864f6c63c1ed942db']
 
diff --git a/easybuild/easyconfigs/i/imkl/imkl-2022.2.1.eb b/easybuild/easyconfigs/i/imkl/imkl-2022.2.1.eb
index 3daf55958a3..f2a7a15068e 100644
--- a/easybuild/easyconfigs/i/imkl/imkl-2022.2.1.eb
+++ b/easybuild/easyconfigs/i/imkl/imkl-2022.2.1.eb
@@ -7,7 +7,7 @@ description = "Intel oneAPI Math Kernel Library"
 toolchain = SYSTEM
 
 # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/19038/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/19038/']
 sources = ['l_onemkl_p_%(version)s.16993_offline.sh']
 checksums = ['eedd4b795720de776b1fc5f542ae0fac37ec235cdb567f7c2ee3182e73e3e59d']
 
diff --git a/easybuild/easyconfigs/i/imkl/imkl-2023.0.0.eb b/easybuild/easyconfigs/i/imkl/imkl-2023.0.0.eb
index 4e6e5afb344..f29032bc3dd 100644
--- a/easybuild/easyconfigs/i/imkl/imkl-2023.0.0.eb
+++ b/easybuild/easyconfigs/i/imkl/imkl-2023.0.0.eb
@@ -7,7 +7,7 @@ description = "Intel oneAPI Math Kernel Library"
 toolchain = SYSTEM
 
 # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/19138/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/19138/']
 sources = ['l_onemkl_p_%(version)s.25398_offline.sh']
 checksums = ['0d61188e91a57bdb575782eb47a05ae99ea8eebefee6b2dfe20c6708e16e9927']
 
diff --git a/easybuild/easyconfigs/i/imkl/imkl-2023.1.0-gompi-2023a.eb b/easybuild/easyconfigs/i/imkl/imkl-2023.1.0-gompi-2023a.eb
index 5e4f3cb8b1d..5c8f63a0644 100644
--- a/easybuild/easyconfigs/i/imkl/imkl-2023.1.0-gompi-2023a.eb
+++ b/easybuild/easyconfigs/i/imkl/imkl-2023.1.0-gompi-2023a.eb
@@ -10,7 +10,7 @@ description = "Intel oneAPI Math Kernel Library"
 toolchain = {'name': 'gompi', 'version': '2023a'}
 
 # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18721/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18721/']
 sources = ['l_onemkl_p_%(version)s.46342_offline.sh']
 checksums = ['cc28c94cab23c185520b93c5a04f3979d8da6b4c90cee8c0681dd89819d76167']
 
diff --git a/easybuild/easyconfigs/i/impi/impi-2018.1.163-iccifort-2018.1.163-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/impi/impi-2018.1.163-iccifort-2018.1.163-GCC-6.4.0-2.28.eb
index 21ad001e53c..a0341a987d6 100644
--- a/easybuild/easyconfigs/i/impi/impi-2018.1.163-iccifort-2018.1.163-GCC-6.4.0-2.28.eb
+++ b/easybuild/easyconfigs/i/impi/impi-2018.1.163-iccifort-2018.1.163-GCC-6.4.0-2.28.eb
@@ -8,7 +8,7 @@ description = "Intel MPI Library, compatible with MPICH ABI"
 
 toolchain = {'name': 'iccifort', 'version': '2018.1.163-GCC-6.4.0-2.28'}
 
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12405/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/12405/']
 sources = ['l_mpi_%(version)s.tgz']
 checksums = ['130b11571c3f71af00a722fa8641db5a1552ac343d770a8304216d8f5d00e75c']
 
diff --git a/easybuild/easyconfigs/i/impi/impi-2018.3.222-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/i/impi/impi-2018.3.222-GCC-7.3.0-2.30.eb
index e39879ac218..60f2eed4dd9 100644
--- a/easybuild/easyconfigs/i/impi/impi-2018.3.222-GCC-7.3.0-2.30.eb
+++ b/easybuild/easyconfigs/i/impi/impi-2018.3.222-GCC-7.3.0-2.30.eb
@@ -8,7 +8,7 @@ description = "Intel MPI Library, compatible with MPICH ABI"
 
 toolchain = {'name': 'GCC', 'version': '7.3.0-2.30'}
 
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13063/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/13063/']
 sources = ['l_mpi_%(version)s.tgz']
 checksums = ['5021d14b344fc794e89f146e4d53d70184d7048610895d7a6a1e8ac0cf258999']
 
diff --git a/easybuild/easyconfigs/i/impi/impi-2018.3.222-iccifort-2018.3.222-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/i/impi/impi-2018.3.222-iccifort-2018.3.222-GCC-7.3.0-2.30.eb
index f4e9e1a638f..0fc63f042f8 100644
--- a/easybuild/easyconfigs/i/impi/impi-2018.3.222-iccifort-2018.3.222-GCC-7.3.0-2.30.eb
+++ b/easybuild/easyconfigs/i/impi/impi-2018.3.222-iccifort-2018.3.222-GCC-7.3.0-2.30.eb
@@ -8,7 +8,7 @@ description = "Intel MPI Library, compatible with MPICH ABI"
 
 toolchain = {'name': 'iccifort', 'version': '2018.3.222-GCC-7.3.0-2.30'}
 
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13063/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/13063/']
 sources = ['l_mpi_%(version)s.tgz']
 checksums = ['5021d14b344fc794e89f146e4d53d70184d7048610895d7a6a1e8ac0cf258999']
 
diff --git a/easybuild/easyconfigs/i/impi/impi-2018.4.274-iccifort-2018.5.274-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/i/impi/impi-2018.4.274-iccifort-2018.5.274-GCC-7.3.0-2.30.eb
index 060befc0a5a..75004db76a8 100644
--- a/easybuild/easyconfigs/i/impi/impi-2018.4.274-iccifort-2018.5.274-GCC-7.3.0-2.30.eb
+++ b/easybuild/easyconfigs/i/impi/impi-2018.4.274-iccifort-2018.5.274-GCC-7.3.0-2.30.eb
@@ -8,7 +8,7 @@ description = "Intel MPI Library, compatible with MPICH ABI"
 
 toolchain = {'name': 'iccifort', 'version': '2018.5.274-GCC-7.3.0-2.30'}
 
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13651/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/13651/']
 sources = ['l_mpi_%(version)s.tgz']
 checksums = ['a1114b3eb4149c2f108964b83cad02150d619e50032059d119ac4ffc9d5dd8e0']
 
diff --git a/easybuild/easyconfigs/i/impi/impi-2018.4.274-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/i/impi/impi-2018.4.274-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb
index e6c3602e1e3..d4574181af9 100644
--- a/easybuild/easyconfigs/i/impi/impi-2018.4.274-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb
+++ b/easybuild/easyconfigs/i/impi/impi-2018.4.274-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb
@@ -6,7 +6,7 @@ description = "Intel MPI Library, compatible with MPICH ABI"
 
 toolchain = {'name': 'iccifort', 'version': '2019.1.144-GCC-8.2.0-2.31.1'}
 
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13651/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/13651/']
 sources = ['l_mpi_%(version)s.tgz']
 checksums = ['a1114b3eb4149c2f108964b83cad02150d619e50032059d119ac4ffc9d5dd8e0']
 
diff --git a/easybuild/easyconfigs/i/impi/impi-2018.4.274-iccifortcuda-2019a.eb b/easybuild/easyconfigs/i/impi/impi-2018.4.274-iccifortcuda-2019a.eb
index 137bf491a27..c28ff1e7e55 100644
--- a/easybuild/easyconfigs/i/impi/impi-2018.4.274-iccifortcuda-2019a.eb
+++ b/easybuild/easyconfigs/i/impi/impi-2018.4.274-iccifortcuda-2019a.eb
@@ -6,7 +6,7 @@ description = "Intel MPI Library, compatible with MPICH ABI"
 
 toolchain = {'name': 'iccifortcuda', 'version': '2019a'}
 
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13651/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/13651/']
 sources = ['l_mpi_%(version)s.tgz']
 checksums = ['a1114b3eb4149c2f108964b83cad02150d619e50032059d119ac4ffc9d5dd8e0']
 
diff --git a/easybuild/easyconfigs/i/impi/impi-2018.5.288-iccifort-2019.5.281.eb b/easybuild/easyconfigs/i/impi/impi-2018.5.288-iccifort-2019.5.281.eb
index 8f89b212fa4..4cb68a33fc8 100644
--- a/easybuild/easyconfigs/i/impi/impi-2018.5.288-iccifort-2019.5.281.eb
+++ b/easybuild/easyconfigs/i/impi/impi-2018.5.288-iccifort-2019.5.281.eb
@@ -8,7 +8,7 @@ description = "Intel MPI Library, compatible with MPICH ABI"
 
 toolchain = {'name': 'iccifort', 'version': '2019.5.281'}
 
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15614/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15614/']
 sources = ['l_mpi_%(version)s.tgz']
 checksums = ['3198257c19e82cd327d739b10120933e0547da8cddf8a8005677717326236796']
 
diff --git a/easybuild/easyconfigs/i/impi/impi-2018.5.288-iccifort-2020.1.217.eb b/easybuild/easyconfigs/i/impi/impi-2018.5.288-iccifort-2020.1.217.eb
index 4c7b3a6b0df..e27d2ec5b55 100644
--- a/easybuild/easyconfigs/i/impi/impi-2018.5.288-iccifort-2020.1.217.eb
+++ b/easybuild/easyconfigs/i/impi/impi-2018.5.288-iccifort-2020.1.217.eb
@@ -8,7 +8,7 @@ description = "Intel MPI Library, compatible with MPICH ABI"
 
 toolchain = {'name': 'iccifort', 'version': '2020.1.217'}
 
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15614/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15614/']
 sources = ['l_mpi_%(version)s.tgz']
 checksums = ['3198257c19e82cd327d739b10120933e0547da8cddf8a8005677717326236796']
 
diff --git a/easybuild/easyconfigs/i/impi/impi-2018.5.288-iccifortcuda-2019b.eb b/easybuild/easyconfigs/i/impi/impi-2018.5.288-iccifortcuda-2019b.eb
index 02e2ace8251..2f959f48e46 100644
--- a/easybuild/easyconfigs/i/impi/impi-2018.5.288-iccifortcuda-2019b.eb
+++ b/easybuild/easyconfigs/i/impi/impi-2018.5.288-iccifortcuda-2019b.eb
@@ -8,7 +8,7 @@ description = "Intel MPI Library, compatible with MPICH ABI"
 
 toolchain = {'name': 'iccifortcuda', 'version': '2019b'}
 
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15614/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15614/']
 sources = ['l_mpi_%(version)s.tgz']
 checksums = ['3198257c19e82cd327d739b10120933e0547da8cddf8a8005677717326236796']
 
diff --git a/easybuild/easyconfigs/i/impi/impi-2019.0.117-iccifort-2019.0.117-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/i/impi/impi-2019.0.117-iccifort-2019.0.117-GCC-8.2.0-2.31.1.eb
index 2f60b422703..77755c77620 100644
--- a/easybuild/easyconfigs/i/impi/impi-2019.0.117-iccifort-2019.0.117-GCC-8.2.0-2.31.1.eb
+++ b/easybuild/easyconfigs/i/impi/impi-2019.0.117-iccifort-2019.0.117-GCC-8.2.0-2.31.1.eb
@@ -8,7 +8,7 @@ description = "Intel MPI Library, compatible with MPICH ABI"
 
 toolchain = {'name': 'iccifort', 'version': '2019.0.117-GCC-8.2.0-2.31.1'}
 
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13584/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/13584/']
 sources = ['l_mpi_%(version)s.tgz']
 checksums = ['dfb403f49c1af61b337aa952b71289c7548c3a79c32c57865eab0ea0f0e1bc08']
 
diff --git a/easybuild/easyconfigs/i/impi/impi-2019.1.144-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/i/impi/impi-2019.1.144-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb
index 8e2ed0b3980..6a222b3ed18 100644
--- a/easybuild/easyconfigs/i/impi/impi-2019.1.144-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb
+++ b/easybuild/easyconfigs/i/impi/impi-2019.1.144-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb
@@ -8,7 +8,7 @@ description = "Intel MPI Library, compatible with MPICH ABI"
 
 toolchain = {'name': 'iccifort', 'version': '2019.1.144-GCC-8.2.0-2.31.1'}
 
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/14879/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/14879/']
 sources = ['l_mpi_%(version)s.tgz']
 checksums = ['dac86a5db6b86503313742b17535856a432955604f7103cb4549a9bfc256c3cd']
 
diff --git a/easybuild/easyconfigs/i/impi/impi-2019.12.320-iccifort-2020.4.304.eb b/easybuild/easyconfigs/i/impi/impi-2019.12.320-iccifort-2020.4.304.eb
index a5ba5409ff0..2bf8b19fb29 100644
--- a/easybuild/easyconfigs/i/impi/impi-2019.12.320-iccifort-2020.4.304.eb
+++ b/easybuild/easyconfigs/i/impi/impi-2019.12.320-iccifort-2020.4.304.eb
@@ -8,7 +8,7 @@ description = "Intel MPI Library, compatible with MPICH ABI"
 
 toolchain = {'name': 'iccifort', 'version': '2020.4.304'}
 
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/17836/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/17836/']
 sources = ['l_mpi_%(version)s.tgz']
 checksums = ['8108fbf2353a9f1926036bb67647b65c0e4933a3eb66e1dc933960e5b055f320']
 
diff --git a/easybuild/easyconfigs/i/impi/impi-2019.2.187-iccifort-2019.2.187-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/i/impi/impi-2019.2.187-iccifort-2019.2.187-GCC-8.2.0-2.31.1.eb
index 7cdc6aca429..5f75ad2ec68 100644
--- a/easybuild/easyconfigs/i/impi/impi-2019.2.187-iccifort-2019.2.187-GCC-8.2.0-2.31.1.eb
+++ b/easybuild/easyconfigs/i/impi/impi-2019.2.187-iccifort-2019.2.187-GCC-8.2.0-2.31.1.eb
@@ -8,7 +8,7 @@ description = "Intel MPI Library, compatible with MPICH ABI"
 
 toolchain = {'name': 'iccifort', 'version': '2019.2.187-GCC-8.2.0-2.31.1'}
 
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15040/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15040/']
 sources = ['l_mpi_%(version)s.tgz']
 checksums = ['6a3305933b5ef9e3f7de969e394c91620f3fa4bb815a4f439577739d04778b20']
 
diff --git a/easybuild/easyconfigs/i/impi/impi-2019.3.199-iccifort-2019.3.199-GCC-8.3.0-2.32.eb b/easybuild/easyconfigs/i/impi/impi-2019.3.199-iccifort-2019.3.199-GCC-8.3.0-2.32.eb
index c0b1f565c0a..cb1ec1f179c 100644
--- a/easybuild/easyconfigs/i/impi/impi-2019.3.199-iccifort-2019.3.199-GCC-8.3.0-2.32.eb
+++ b/easybuild/easyconfigs/i/impi/impi-2019.3.199-iccifort-2019.3.199-GCC-8.3.0-2.32.eb
@@ -8,7 +8,7 @@ description = "Intel MPI Library, compatible with MPICH ABI"
 
 toolchain = {'name': 'iccifort', 'version': '2019.3.199-GCC-8.3.0-2.32'}
 
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15260/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15260/']
 sources = ['l_mpi_%(version)s.tgz']
 checksums = ['5304346c863f64de797250eeb14f51c5cfc8212ff20813b124f20e7666286990']
 
diff --git a/easybuild/easyconfigs/i/impi/impi-2019.6.166-iccifort-2020.0.166-GCC-9.2.0.eb b/easybuild/easyconfigs/i/impi/impi-2019.6.166-iccifort-2020.0.166-GCC-9.2.0.eb
index e19a15d6e33..49f0fa7a8d7 100644
--- a/easybuild/easyconfigs/i/impi/impi-2019.6.166-iccifort-2020.0.166-GCC-9.2.0.eb
+++ b/easybuild/easyconfigs/i/impi/impi-2019.6.166-iccifort-2020.0.166-GCC-9.2.0.eb
@@ -8,7 +8,7 @@ description = "Intel MPI Library, compatible with MPICH ABI"
 
 toolchain = {'name': 'iccifort', 'version': '2020.0.166-GCC-9.2.0'}
 
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16120/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16120/']
 sources = ['l_mpi_%(version)s.tgz']
 checksums = ['119be69f1117c93a9e5e9b8b4643918e55d2a55a78ad9567f77d16cdaf18cd6e']
 
diff --git a/easybuild/easyconfigs/i/impi/impi-2019.7.217-iccifort-2020.1.217.eb b/easybuild/easyconfigs/i/impi/impi-2019.7.217-iccifort-2020.1.217.eb
index d0ad0188c0d..07f8323810c 100644
--- a/easybuild/easyconfigs/i/impi/impi-2019.7.217-iccifort-2020.1.217.eb
+++ b/easybuild/easyconfigs/i/impi/impi-2019.7.217-iccifort-2020.1.217.eb
@@ -8,7 +8,7 @@ description = "Intel MPI Library, compatible with MPICH ABI"
 
 toolchain = {'name': 'iccifort', 'version': '2020.1.217'}
 
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16546/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16546/']
 sources = ['l_mpi_%(version)s.tgz']
 checksums = ['90383b0023f84ac003a55d8bb29dbcf0c639f43a25a2d8d8698a16e770ac9c07']
 
diff --git a/easybuild/easyconfigs/i/impi/impi-2019.7.217-iccifortcuda-2020a.eb b/easybuild/easyconfigs/i/impi/impi-2019.7.217-iccifortcuda-2020a.eb
index 557e0a8eab1..8a5646c25c1 100644
--- a/easybuild/easyconfigs/i/impi/impi-2019.7.217-iccifortcuda-2020a.eb
+++ b/easybuild/easyconfigs/i/impi/impi-2019.7.217-iccifortcuda-2020a.eb
@@ -8,7 +8,7 @@ description = "Intel MPI Library, compatible with MPICH ABI"
 
 toolchain = {'name': 'iccifortcuda', 'version': '2020a'}
 
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16546/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16546/']
 sources = ['l_mpi_%(version)s.tgz']
 checksums = ['90383b0023f84ac003a55d8bb29dbcf0c639f43a25a2d8d8698a16e770ac9c07']
 
diff --git a/easybuild/easyconfigs/i/impi/impi-2019.9.304-iccifort-2020.4.304.eb b/easybuild/easyconfigs/i/impi/impi-2019.9.304-iccifort-2020.4.304.eb
index d4a9ef76ae4..d723d12dc1c 100644
--- a/easybuild/easyconfigs/i/impi/impi-2019.9.304-iccifort-2020.4.304.eb
+++ b/easybuild/easyconfigs/i/impi/impi-2019.9.304-iccifort-2020.4.304.eb
@@ -8,7 +8,7 @@ description = "Intel MPI Library, compatible with MPICH ABI"
 
 toolchain = {'name': 'iccifort', 'version': '2020.4.304'}
 
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/17263/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/17263/']
 sources = ['l_mpi_%(version)s.tgz']
 checksums = ['618a5dc2de54306645e6428c5eb7d267b54b11b5a83dfbcad7d0f9e0d90bb2e7']
 
diff --git a/easybuild/easyconfigs/i/impi/impi-2019.9.304-iccifortcuda-2020b.eb b/easybuild/easyconfigs/i/impi/impi-2019.9.304-iccifortcuda-2020b.eb
index 3305cf60a8d..7082d103ec8 100644
--- a/easybuild/easyconfigs/i/impi/impi-2019.9.304-iccifortcuda-2020b.eb
+++ b/easybuild/easyconfigs/i/impi/impi-2019.9.304-iccifortcuda-2020b.eb
@@ -8,7 +8,7 @@ description = "Intel MPI Library, compatible with MPICH ABI"
 
 toolchain = {'name': 'iccifortcuda', 'version': '2020b'}
 
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/17263/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/17263/']
 sources = ['l_mpi_%(version)s.tgz']
 checksums = ['618a5dc2de54306645e6428c5eb7d267b54b11b5a83dfbcad7d0f9e0d90bb2e7']
 
diff --git a/easybuild/easyconfigs/i/impi/impi-2021.1.1-intel-compilers-2021.1.2.eb b/easybuild/easyconfigs/i/impi/impi-2021.1.1-intel-compilers-2021.1.2.eb
index 1a0fbe3b035..d8a92d6db7e 100644
--- a/easybuild/easyconfigs/i/impi/impi-2021.1.1-intel-compilers-2021.1.2.eb
+++ b/easybuild/easyconfigs/i/impi/impi-2021.1.1-intel-compilers-2021.1.2.eb
@@ -7,7 +7,7 @@ description = "Intel MPI Library, compatible with MPICH ABI"
 toolchain = {'name': 'intel-compilers', 'version': '2021.1.2'}
 
 # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/17397/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/17397/']
 sources = ['l_mpi_oneapi_p_%(version)s.76_offline.sh']
 checksums = ['8b7693a156c6fc6269637bef586a8fd3ea6610cac2aae4e7f48c1fbb601625fe']
 
diff --git a/easybuild/easyconfigs/i/impi/impi-2021.2.0-intel-compilers-2021.2.0.eb b/easybuild/easyconfigs/i/impi/impi-2021.2.0-intel-compilers-2021.2.0.eb
index 345fd82fc3d..ecd3c9521f1 100644
--- a/easybuild/easyconfigs/i/impi/impi-2021.2.0-intel-compilers-2021.2.0.eb
+++ b/easybuild/easyconfigs/i/impi/impi-2021.2.0-intel-compilers-2021.2.0.eb
@@ -7,7 +7,7 @@ description = "Intel MPI Library, compatible with MPICH ABI"
 toolchain = {'name': 'intel-compilers', 'version': '2021.2.0'}
 
 # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/17729/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/17729/']
 sources = ['l_mpi_oneapi_p_%(version)s.215_offline.sh']
 checksums = ['d0d4cdd11edaff2e7285e38f537defccff38e37a3067c02f4af43a3629ad4aa3']
 
diff --git a/easybuild/easyconfigs/i/impi/impi-2021.3.0-intel-compilers-2021.3.0.eb b/easybuild/easyconfigs/i/impi/impi-2021.3.0-intel-compilers-2021.3.0.eb
index 8a736821926..1507acd5413 100644
--- a/easybuild/easyconfigs/i/impi/impi-2021.3.0-intel-compilers-2021.3.0.eb
+++ b/easybuild/easyconfigs/i/impi/impi-2021.3.0-intel-compilers-2021.3.0.eb
@@ -10,7 +10,7 @@ description = "Intel MPI Library, compatible with MPICH ABI"
 toolchain = {'name': 'intel-compilers', 'version': '2021.3.0'}
 
 # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/17947']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/17947']
 sources = ['l_mpi_oneapi_p_%(version)s.294_offline.sh']
 checksums = ['04c48f864ee4c723b1b4ca62f2bea8c04d5d7e3de19171fd62b17868bc79bc36']
 
diff --git a/easybuild/easyconfigs/i/impi/impi-2021.4.0-intel-compilers-2021.4.0.eb b/easybuild/easyconfigs/i/impi/impi-2021.4.0-intel-compilers-2021.4.0.eb
index a0c8a98edd8..24180258119 100644
--- a/easybuild/easyconfigs/i/impi/impi-2021.4.0-intel-compilers-2021.4.0.eb
+++ b/easybuild/easyconfigs/i/impi/impi-2021.4.0-intel-compilers-2021.4.0.eb
@@ -7,7 +7,7 @@ description = "Intel MPI Library, compatible with MPICH ABI"
 toolchain = {'name': 'intel-compilers', 'version': '2021.4.0'}
 
 # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18186/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18186/']
 sources = ['l_mpi_oneapi_p_%(version)s.441_offline.sh']
 checksums = ['cc4b7072c61d0bd02b1c431b22d2ea3b84b967b59d2e587e77a9e7b2c24f2a29']
 
diff --git a/easybuild/easyconfigs/i/impi/impi-2021.5.0-intel-compilers-2022.0.1.eb b/easybuild/easyconfigs/i/impi/impi-2021.5.0-intel-compilers-2022.0.1.eb
index bee00810199..ea941c35ab2 100644
--- a/easybuild/easyconfigs/i/impi/impi-2021.5.0-intel-compilers-2022.0.1.eb
+++ b/easybuild/easyconfigs/i/impi/impi-2021.5.0-intel-compilers-2022.0.1.eb
@@ -7,7 +7,7 @@ description = "Intel MPI Library, compatible with MPICH ABI"
 toolchain = {'name': 'intel-compilers', 'version': '2022.0.1'}
 
 # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18370/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18370/']
 sources = ['l_mpi_oneapi_p_%(version)s.495_offline.sh']
 checksums = ['3aae53fe77f7c6aac7a32b299c25d6ca9a00ba4e2d512a26edd90811e59e7471']
 
diff --git a/easybuild/easyconfigs/i/impi/impi-2021.6.0-intel-compilers-2022.1.0.eb b/easybuild/easyconfigs/i/impi/impi-2021.6.0-intel-compilers-2022.1.0.eb
index b1d328caa62..288c103cd03 100644
--- a/easybuild/easyconfigs/i/impi/impi-2021.6.0-intel-compilers-2022.1.0.eb
+++ b/easybuild/easyconfigs/i/impi/impi-2021.6.0-intel-compilers-2022.1.0.eb
@@ -7,7 +7,7 @@ description = "Intel MPI Library, compatible with MPICH ABI"
 toolchain = {'name': 'intel-compilers', 'version': '2022.1.0'}
 
 # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18714/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18714/']
 sources = ['l_mpi_oneapi_p_%(version)s.602_offline.sh']
 checksums = ['e85db63788c434d43c1378e5e2bf7927a75d11aee8e6b78ee0d933da920977a6']
 
diff --git a/easybuild/easyconfigs/i/impi/impi-2021.7.0-intel-compilers-2022.2.0.eb b/easybuild/easyconfigs/i/impi/impi-2021.7.0-intel-compilers-2022.2.0.eb
index 8f400fabac4..2df8a69062f 100644
--- a/easybuild/easyconfigs/i/impi/impi-2021.7.0-intel-compilers-2022.2.0.eb
+++ b/easybuild/easyconfigs/i/impi/impi-2021.7.0-intel-compilers-2022.2.0.eb
@@ -7,7 +7,7 @@ description = "Intel MPI Library, compatible with MPICH ABI"
 toolchain = {'name': 'intel-compilers', 'version': '2022.2.0'}
 
 # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18926/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18926/']
 sources = ['l_mpi_oneapi_p_%(version)s.8711_offline.sh']
 checksums = ['4eb1e1487b67b98857bc9b7b37bcac4998e0aa6d1b892b2c87b003bf84fb38e9']
 
diff --git a/easybuild/easyconfigs/i/impi/impi-2021.7.1-intel-compilers-2022.2.1.eb b/easybuild/easyconfigs/i/impi/impi-2021.7.1-intel-compilers-2022.2.1.eb
index 68aeb9beb63..aa2976fafaf 100644
--- a/easybuild/easyconfigs/i/impi/impi-2021.7.1-intel-compilers-2022.2.1.eb
+++ b/easybuild/easyconfigs/i/impi/impi-2021.7.1-intel-compilers-2022.2.1.eb
@@ -7,7 +7,7 @@ description = "Intel MPI Library, compatible with MPICH ABI"
 toolchain = {'name': 'intel-compilers', 'version': '2022.2.1'}
 
 # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/19010/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/19010/']
 sources = ['l_mpi_oneapi_p_%(version)s.16815_offline.sh']
 checksums = ['90e7804f2367d457cd4cbf7aa29f1c5676287aa9b34f93e7c9a19e4b8583fff7']
 
diff --git a/easybuild/easyconfigs/i/impi/impi-2021.8.0-intel-compilers-2023.0.0.eb b/easybuild/easyconfigs/i/impi/impi-2021.8.0-intel-compilers-2023.0.0.eb
index 86153bb28f5..89dce35e1f2 100644
--- a/easybuild/easyconfigs/i/impi/impi-2021.8.0-intel-compilers-2023.0.0.eb
+++ b/easybuild/easyconfigs/i/impi/impi-2021.8.0-intel-compilers-2023.0.0.eb
@@ -7,7 +7,7 @@ description = "Intel MPI Library, compatible with MPICH ABI"
 toolchain = {'name': 'intel-compilers', 'version': '2023.0.0'}
 
 # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/19131/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/19131/']
 sources = ['l_mpi_oneapi_p_%(version)s.25329_offline.sh']
 checksums = ['0fcb1171fc42fd4b2d863ae474c0b0f656b0fa1fdc1df435aa851ccd6d1eaaf7']
 
diff --git a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.1.2.eb b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.1.2.eb
index 820a237e44d..67a5c1f5701 100644
--- a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.1.2.eb
+++ b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.1.2.eb
@@ -9,11 +9,11 @@ toolchain = SYSTEM
 # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html
 sources = [
     {
-        'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/17513/'],
+        'source_urls': ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/17513/'],
         'filename': 'l_dpcpp-cpp-compiler_p_%(version)s.63_offline.sh',
     },
     {
-        'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/17508/'],
+        'source_urls': ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/17508/'],
         'filename': 'l_fortran-compiler_p_%(version)s.62_offline.sh',
     },
 ]
diff --git a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.2.0.eb b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.2.0.eb
index 4fe1af0da99..e4986d623f0 100644
--- a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.2.0.eb
+++ b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.2.0.eb
@@ -9,11 +9,11 @@ toolchain = SYSTEM
 # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html
 sources = [
     {
-        'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/17749/'],
+        'source_urls': ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/17749/'],
         'filename': 'l_dpcpp-cpp-compiler_p_%(version)s.118_offline.sh',
     },
     {
-        'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/17756/'],
+        'source_urls': ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/17756/'],
         'filename': 'l_fortran-compiler_p_%(version)s.136_offline.sh',
     },
 ]
diff --git a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.3.0.eb b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.3.0.eb
index efcc5a7498b..cececeebef0 100644
--- a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.3.0.eb
+++ b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.3.0.eb
@@ -12,11 +12,11 @@ toolchain = SYSTEM
 # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html
 sources = [
     {
-        'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/17928/'],
+        'source_urls': ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/17928/'],
         'filename': 'l_dpcpp-cpp-compiler_p_%(version)s.3168_offline.sh',
     },
     {
-        'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/17959/'],
+        'source_urls': ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/17959/'],
         'filename': 'l_fortran-compiler_p_%(version)s.3168_offline.sh',
     },
 ]
diff --git a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.4.0.eb b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.4.0.eb
index b12d0b8bb3c..977bf5ced0e 100644
--- a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.4.0.eb
+++ b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.4.0.eb
@@ -9,11 +9,11 @@ toolchain = SYSTEM
 # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html
 sources = [
     {
-        'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18209/'],
+        'source_urls': ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18209/'],
         'filename': 'l_dpcpp-cpp-compiler_p_%(version)s.3201_offline.sh',
     },
     {
-        'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18210/'],
+        'source_urls': ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18210/'],
         'filename': 'l_fortran-compiler_p_%(version)s.3224_offline.sh',
     },
 ]
diff --git a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.0.1.eb b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.0.1.eb
index 56c8e9b5da4..967197cdfd7 100644
--- a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.0.1.eb
+++ b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.0.1.eb
@@ -9,11 +9,11 @@ toolchain = SYSTEM
 # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html
 sources = [
     {
-        'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18435/'],
+        'source_urls': ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18435/'],
         'filename': 'l_dpcpp-cpp-compiler_p_%(version)s.71_offline.sh',
     },
     {
-        'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18436/'],
+        'source_urls': ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18436/'],
         'filename': 'l_fortran-compiler_p_%(version)s.70_offline.sh',
     },
 ]
diff --git a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.0.2.eb b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.0.2.eb
index b54023cfe84..011509935b0 100644
--- a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.0.2.eb
+++ b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.0.2.eb
@@ -9,11 +9,11 @@ toolchain = SYSTEM
 # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html
 sources = [
     {
-        'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18478/'],
+        'source_urls': ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18478/'],
         'filename': 'l_dpcpp-cpp-compiler_p_%(version)s.84_offline.sh',
     },
     {
-        'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18481/'],
+        'source_urls': ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18481/'],
         'filename': 'l_fortran-compiler_p_%(version)s.83_offline.sh',
     },
 ]
diff --git a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.1.0.eb b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.1.0.eb
index f25617230ac..92ac06db492 100644
--- a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.1.0.eb
+++ b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.1.0.eb
@@ -9,11 +9,11 @@ toolchain = SYSTEM
 # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html
 sources = [
     {
-        'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18717/'],
+        'source_urls': ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18717/'],
         'filename': 'l_dpcpp-cpp-compiler_p_%(version)s.137_offline.sh',
     },
     {
-        'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18703/'],
+        'source_urls': ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18703/'],
         'filename': 'l_fortran-compiler_p_%(version)s.134_offline.sh',
     },
 ]
diff --git a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.2.0.eb b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.2.0.eb
index 17262278b13..8c1390dae95 100644
--- a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.2.0.eb
+++ b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.2.0.eb
@@ -9,11 +9,11 @@ toolchain = SYSTEM
 # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html
 sources = [
     {
-        'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18849/'],
+        'source_urls': ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18849/'],
         'filename': 'l_dpcpp-cpp-compiler_p_%(version)s.8772_offline.sh',
     },
     {
-        'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18909/'],
+        'source_urls': ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18909/'],
         'filename': 'l_fortran-compiler_p_%(version)s.8773_offline.sh',
     },
 ]
diff --git a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.2.1.eb b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.2.1.eb
index a6ae8170105..e67292301d5 100644
--- a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.2.1.eb
+++ b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.2.1.eb
@@ -9,11 +9,11 @@ toolchain = SYSTEM
 # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html
 sources = [
     {
-        'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/19030/'],
+        'source_urls': ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/19030/'],
         'filename': 'l_dpcpp-cpp-compiler_p_%(version)s.16991_offline.sh',
     },
     {
-        'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18998/'],
+        'source_urls': ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18998/'],
         'filename': 'l_fortran-compiler_p_%(version)s.16992_offline.sh',
     },
 ]
diff --git a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2023.0.0.eb b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2023.0.0.eb
index 8d97d1ec3e5..f1e9b21f009 100644
--- a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2023.0.0.eb
+++ b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2023.0.0.eb
@@ -9,11 +9,11 @@ toolchain = SYSTEM
 # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html
 sources = [
     {
-        'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/19123/'],
+        'source_urls': ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/19123/'],
         'filename': 'l_dpcpp-cpp-compiler_p_%(version)s.25393_offline.sh',
     },
     {
-        'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/19105/'],
+        'source_urls': ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/19105/'],
         'filename': 'l_fortran-compiler_p_%(version)s.25394_offline.sh',
     },
 ]
diff --git a/easybuild/easyconfigs/i/itac/itac-2021.2.0.eb b/easybuild/easyconfigs/i/itac/itac-2021.2.0.eb
index 3deaaa9e711..ea2cfcb2650 100644
--- a/easybuild/easyconfigs/i/itac/itac-2021.2.0.eb
+++ b/easybuild/easyconfigs/i/itac/itac-2021.2.0.eb
@@ -11,7 +11,7 @@ description = """The Intel Trace Collector is a low-overhead tracing library tha
 
 toolchain = SYSTEM
 
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/17686/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/17686/']
 sources = ['l_itac_oneapi_p_%(version)s.152_offline.sh']
 checksums = ['dca9d1cb2b77c43496009e191916e0d37c2e6606c228e37c11091778d038dd90']
 
diff --git a/easybuild/easyconfigs/i/itac/itac-2021.5.0.eb b/easybuild/easyconfigs/i/itac/itac-2021.5.0.eb
index f9d10379c85..ea05e25db95 100644
--- a/easybuild/easyconfigs/i/itac/itac-2021.5.0.eb
+++ b/easybuild/easyconfigs/i/itac/itac-2021.5.0.eb
@@ -11,7 +11,7 @@ description = """The Intel Trace Collector is a low-overhead tracing library tha
 
 toolchain = SYSTEM
 
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18367/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18367/']
 sources = ['l_itac_oneapi_p_%(version)s.370_offline.sh']
 checksums = ['c2b31298d8b4069a62d9352873c7f6e17ce240ad7293f9bacdc6de3794675b58']
 
diff --git a/easybuild/easyconfigs/i/itac/itac-2021.6.0.eb b/easybuild/easyconfigs/i/itac/itac-2021.6.0.eb
index 22e6230e15b..0f35b870046 100644
--- a/easybuild/easyconfigs/i/itac/itac-2021.6.0.eb
+++ b/easybuild/easyconfigs/i/itac/itac-2021.6.0.eb
@@ -11,7 +11,7 @@ description = """The Intel Trace Collector is a low-overhead tracing library tha
 
 toolchain = SYSTEM
 
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18694/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18694/']
 sources = ['l_itac_oneapi_p_%(version)s.434_offline.sh']
 checksums = ['1ecc2735da960041b051e377cadb9f6ab2f44e8aa44d0f642529a56a3cbba436']
 
diff --git a/easybuild/easyconfigs/v/VTune/VTune-2018_update3.eb b/easybuild/easyconfigs/v/VTune/VTune-2018_update3.eb
index 0938ca5f98f..8f1db4ac725 100644
--- a/easybuild/easyconfigs/v/VTune/VTune-2018_update3.eb
+++ b/easybuild/easyconfigs/v/VTune/VTune-2018_update3.eb
@@ -7,7 +7,7 @@ description = """Intel VTune Amplifier XE is the premier performance profiler fo
 
 toolchain = SYSTEM
 
-source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13079/']
+source_urls = ['http://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/13079/']
 sources = ['vtune_amplifier_%(version)s.tar.gz']
 checksums = ['a47e3b304b993bc28190d7efaac29dcb4a9b533837f2fe4cd9d5617c537f568a']
 
diff --git a/easybuild/easyconfigs/v/VTune/VTune-2019_update3.eb b/easybuild/easyconfigs/v/VTune/VTune-2019_update3.eb
index bd9fed83da9..50053de3925 100644
--- a/easybuild/easyconfigs/v/VTune/VTune-2019_update3.eb
+++ b/easybuild/easyconfigs/v/VTune/VTune-2019_update3.eb
@@ -7,7 +7,7 @@ description = """Intel VTune Amplifier XE is the premier performance profiler fo
 
 toolchain = SYSTEM
 
-source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15214/']
+source_urls = ['http://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15214/']
 sources = ['vtune_amplifier_%(version)s.tar.gz']
 checksums = ['d873abd0e98b477056030f3520fc8dfb1521dbb4dfaa6d20d830af02ec12a12d']
 
diff --git a/easybuild/easyconfigs/v/VTune/VTune-2019_update5.eb b/easybuild/easyconfigs/v/VTune/VTune-2019_update5.eb
index 09f9e6b6120..1390fece377 100644
--- a/easybuild/easyconfigs/v/VTune/VTune-2019_update5.eb
+++ b/easybuild/easyconfigs/v/VTune/VTune-2019_update5.eb
@@ -7,7 +7,7 @@ description = """Intel VTune Amplifier XE is the premier performance profiler fo
 
 toolchain = SYSTEM
 
-source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15703/']
+source_urls = ['http://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15703/']
 sources = ['vtune_amplifier_%(version)s.tar.gz']
 checksums = ['7b2124123347bbb593d1b8f8cf858d88829a05605769cba5c39444b0aa545473']
 
diff --git a/easybuild/easyconfigs/v/VTune/VTune-2020_update3.eb b/easybuild/easyconfigs/v/VTune/VTune-2020_update3.eb
index b4c024b03be..ab1cb7c1ebc 100644
--- a/easybuild/easyconfigs/v/VTune/VTune-2020_update3.eb
+++ b/easybuild/easyconfigs/v/VTune/VTune-2020_update3.eb
@@ -7,7 +7,7 @@ description = """Intel VTune Amplifier XE is the premier performance profiler fo
 
 toolchain = SYSTEM
 
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/17095/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/17095/']
 sources = [{'download_filename': 'vtune_profiler_2020.tar.gz', 'filename': 'vtune_profiler_%(version)s.tar.gz'}]
 checksums = ['b22dd61d3931ca6ab7d96df2cf8648e5e1061ab2db13b8d42e3c87586b07c974']
 
diff --git a/easybuild/easyconfigs/v/VTune/VTune-2021.6.0.eb b/easybuild/easyconfigs/v/VTune/VTune-2021.6.0.eb
index 9b6582a6610..d33e54a7818 100644
--- a/easybuild/easyconfigs/v/VTune/VTune-2021.6.0.eb
+++ b/easybuild/easyconfigs/v/VTune/VTune-2021.6.0.eb
@@ -13,7 +13,7 @@ toolchain = SYSTEM
 # By downloading, you accept the Intel End User License Agreement
 # (https://software.intel.com/content/www/us/en/develop/articles/end-user-license-agreement.html)
 # accept_eula = True
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18012/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18012/']
 sources = ['l_oneapi_vtune_p_%(version)s.411_offline.sh']
 checksums = ['6b1df7da713337aa665bcc6ff23e4a006695b5bfaf71dffd305cbadca2e5560c']
 
diff --git a/easybuild/easyconfigs/v/VTune/VTune-2021.9.0.eb b/easybuild/easyconfigs/v/VTune/VTune-2021.9.0.eb
index cd2356a18bb..b0f65557f62 100644
--- a/easybuild/easyconfigs/v/VTune/VTune-2021.9.0.eb
+++ b/easybuild/easyconfigs/v/VTune/VTune-2021.9.0.eb
@@ -13,7 +13,7 @@ toolchain = SYSTEM
 # By downloading, you accept the Intel End User License Agreement
 # (https://software.intel.com/content/www/us/en/develop/articles/end-user-license-agreement.html)
 # accept_eula = True
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18302/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18302/']
 sources = ['l_oneapi_vtune_p_%(version)s.545_offline.sh']
 checksums = ['55c8ac25e685f03c849bb5383da249c7caaf2138a2b57a10c8975a38fa3828bc']
 
diff --git a/easybuild/easyconfigs/v/VTune/VTune-2022.0.0.eb b/easybuild/easyconfigs/v/VTune/VTune-2022.0.0.eb
index e205471e1e5..16f445c0f64 100644
--- a/easybuild/easyconfigs/v/VTune/VTune-2022.0.0.eb
+++ b/easybuild/easyconfigs/v/VTune/VTune-2022.0.0.eb
@@ -13,7 +13,7 @@ toolchain = SYSTEM
 # By downloading, you accept the Intel End User License Agreement
 # (https://software.intel.com/content/www/us/en/develop/articles/end-user-license-agreement.html)
 # accept_eula = True
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18406/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18406/']
 sources = ['l_oneapi_vtune_p_%(version)s.94_offline.sh']
 checksums = ['aa4d575c22e7be0c950b87d67d9e371f470f682906864c4f9b68e530ecd22bd7']
 
diff --git a/easybuild/easyconfigs/v/VTune/VTune-2022.2.0.eb b/easybuild/easyconfigs/v/VTune/VTune-2022.2.0.eb
index 773718fc442..458b8143c02 100644
--- a/easybuild/easyconfigs/v/VTune/VTune-2022.2.0.eb
+++ b/easybuild/easyconfigs/v/VTune/VTune-2022.2.0.eb
@@ -13,7 +13,7 @@ toolchain = SYSTEM
 # By downloading, you accept the Intel End User License Agreement
 # (https://software.intel.com/content/www/us/en/develop/articles/end-user-license-agreement.html)
 # accept_eula = True
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18602/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18602/']
 sources = ['l_oneapi_vtune_p_%(version)s.172_offline.sh']
 checksums = ['d9f92ab6486a02c8ba226c98893492a54eda706d9edd3206a6b6143bfbc97195']
 
diff --git a/easybuild/easyconfigs/v/VTune/VTune-2022.3.0.eb b/easybuild/easyconfigs/v/VTune/VTune-2022.3.0.eb
index b8a718b77b0..e2fea76fc3a 100644
--- a/easybuild/easyconfigs/v/VTune/VTune-2022.3.0.eb
+++ b/easybuild/easyconfigs/v/VTune/VTune-2022.3.0.eb
@@ -13,7 +13,7 @@ toolchain = SYSTEM
 # By downloading, you accept the Intel End User License Agreement
 # (https://software.intel.com/content/www/us/en/develop/articles/end-user-license-agreement.html)
 # accept_eula = True
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18656/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18656/']
 sources = ['l_oneapi_vtune_p_%(version)s.195_offline.sh']
 checksums = ['7921fce7fcc3b82575be22d9c36beec961ba2a9fb5262ba16a04090bcbd2e1a6']
 

From 95f997a46634e0c5556aabd6f6afe7ab58ab6ff9 Mon Sep 17 00:00:00 2001
From: Bart Oldeman <bart.oldeman@calculquebec.ca>
Date: Thu, 1 Aug 2024 23:13:13 +0000
Subject: [PATCH 543/835] Reset executable bit on imkl-2021.4.0-iompi-2021b.eb

---
 easybuild/easyconfigs/i/imkl/imkl-2021.4.0-iompi-2021b.eb | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 mode change 100755 => 100644 easybuild/easyconfigs/i/imkl/imkl-2021.4.0-iompi-2021b.eb

diff --git a/easybuild/easyconfigs/i/imkl/imkl-2021.4.0-iompi-2021b.eb b/easybuild/easyconfigs/i/imkl/imkl-2021.4.0-iompi-2021b.eb
old mode 100755
new mode 100644

From e3d07cb66c63d92fe6a4bfa3c4b81869d4bb9270 Mon Sep 17 00:00:00 2001
From: Lara Ramona Peeters <49882639+laraPPr@users.noreply.github.com>
Date: Fri, 2 Aug 2024 08:22:06 +0200
Subject: [PATCH 544/835] Update
 easybuild/easyconfigs/t/timm/timm-1.0.8-foss-2023a-CUDA-12.1.1.eb

Co-authored-by: Kenneth Hoste <kenneth.hoste@ugent.be>
---
 .../easyconfigs/t/timm/timm-1.0.8-foss-2023a-CUDA-12.1.1.eb     | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/t/timm/timm-1.0.8-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/t/timm/timm-1.0.8-foss-2023a-CUDA-12.1.1.eb
index f0b67fec7c0..89d1e41675c 100644
--- a/easybuild/easyconfigs/t/timm/timm-1.0.8-foss-2023a-CUDA-12.1.1.eb
+++ b/easybuild/easyconfigs/t/timm/timm-1.0.8-foss-2023a-CUDA-12.1.1.eb
@@ -21,7 +21,7 @@ dependencies = [
     ('PyYAML', '6.0'),
     ('tqdm', '4.66.1'),
     ('torchvision', '0.16.0', versionsuffix),
-    ('Safetensors', '1.4.3'),
+    ('Safetensors', '0.4.3'),
 ]
 
 builddependencies = [

From a3c654de099ba59750b7d5b149356af445438e19 Mon Sep 17 00:00:00 2001
From: vsc46128 <vsc46128@node4012.donphan.os>
Date: Fri, 2 Aug 2024 09:44:40 +0200
Subject: [PATCH 545/835] remove maturin as dependency

---
 .../easyconfigs/t/timm/timm-1.0.8-foss-2023a-CUDA-12.1.1.eb      | 1 -
 1 file changed, 1 deletion(-)

diff --git a/easybuild/easyconfigs/t/timm/timm-1.0.8-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/t/timm/timm-1.0.8-foss-2023a-CUDA-12.1.1.eb
index 89d1e41675c..aadc225d0fa 100644
--- a/easybuild/easyconfigs/t/timm/timm-1.0.8-foss-2023a-CUDA-12.1.1.eb
+++ b/easybuild/easyconfigs/t/timm/timm-1.0.8-foss-2023a-CUDA-12.1.1.eb
@@ -25,7 +25,6 @@ dependencies = [
 ]
 
 builddependencies = [
-    ('maturin', '1.4.0', '-Rust-1.75.0'),  # for safetensors
     ('PDM', '2.12.4'),
 ]
 

From 3175081ed25799d70d005ec8d288c832d69ca6f9 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Fri, 2 Aug 2024 13:45:01 +0200
Subject: [PATCH 546/835] adding easyconfigs: Flye-2.9.4-GCC-13.2.0.eb

---
 .../f/Flye/Flye-2.9.4-GCC-13.2.0.eb           | 33 +++++++++++++++++++
 1 file changed, 33 insertions(+)
 create mode 100644 easybuild/easyconfigs/f/Flye/Flye-2.9.4-GCC-13.2.0.eb

diff --git a/easybuild/easyconfigs/f/Flye/Flye-2.9.4-GCC-13.2.0.eb b/easybuild/easyconfigs/f/Flye/Flye-2.9.4-GCC-13.2.0.eb
new file mode 100644
index 00000000000..c11373f69a1
--- /dev/null
+++ b/easybuild/easyconfigs/f/Flye/Flye-2.9.4-GCC-13.2.0.eb
@@ -0,0 +1,33 @@
+easyblock = 'PythonPackage'
+
+name = 'Flye'
+version = '2.9.4'
+
+homepage = 'https://github.com/fenderglass/Flye'
+description = """Flye is a de novo assembler for long and noisy reads, such as those produced by PacBio
+ and Oxford Nanopore Technologies."""
+
+toolchain = {'name': 'GCC', 'version': '13.2.0'}
+
+source_urls = ['https://github.com/fenderglass/Flye/archive/']
+sources = ['%(version)s.tar.gz']
+checksums = ['197a2dfe39fc324a39d8e1901af4f539609159c4a64a578ec8e60f73f5ea4696']
+
+dependencies = [('Python', '3.11.5')]
+
+download_dep_fail = True
+use_pip = True
+
+if ARCH == "aarch64":
+    preinstallopts = 'export arm_neon=1 && export aarch64=1 && '
+
+sanity_check_paths = {
+    'files': ['bin/flye'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = ['%(namelower)s --help']
+
+sanity_pip_check = True
+
+moduleclass = 'bio'

From e6a4d5c2ae6f73e90a8df2b396b9b8be05c86377 Mon Sep 17 00:00:00 2001
From: Samuel Moors <samuel.moors@vub.be>
Date: Fri, 2 Aug 2024 13:58:18 +0200
Subject: [PATCH 547/835] adding easyconfigs: wradlib-2.0.3-foss-2022a.eb

---
 .../w/wradlib/wradlib-2.0.3-foss-2022a.eb     | 57 +++++++++++++++++++
 1 file changed, 57 insertions(+)
 create mode 100644 easybuild/easyconfigs/w/wradlib/wradlib-2.0.3-foss-2022a.eb

diff --git a/easybuild/easyconfigs/w/wradlib/wradlib-2.0.3-foss-2022a.eb b/easybuild/easyconfigs/w/wradlib/wradlib-2.0.3-foss-2022a.eb
new file mode 100644
index 00000000000..9bec30a5545
--- /dev/null
+++ b/easybuild/easyconfigs/w/wradlib/wradlib-2.0.3-foss-2022a.eb
@@ -0,0 +1,57 @@
+easyblock = 'PythonBundle'
+
+name = 'wradlib'
+version = '2.0.3'
+
+homepage = 'https://docs.wradlib.org/'
+description = """
+The wradlib project has been initiated in order facilitate the use of weather
+radar data as well as to provide a common platform for research on new
+algorithms."""
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('SciPy-bundle', '2022.05'),
+    ('xarray', '2022.6.0'),
+    ('Cartopy', '0.20.3'),
+    ('dask', '2022.10.0'),
+    ('matplotlib', '3.5.2'),
+    ('netcdf4-python', '1.6.1'),
+    ('h5netcdf', '1.2.0'),
+    ('geopandas', '0.12.2'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('deprecation', '2.1.0', {
+        'checksums': ['72b3bde64e5d778694b0cf68178aed03d15e15477116add3fb773e581f9518ff'],
+    }),
+    ('cmweather', '0.3.2', {
+        'checksums': ['d374b068fcbfeed87bc511f1f77a6047ae752f4a175a852587414b615b4baa5a'],
+    }),
+    ('lat_lon_parser', '1.3.0', {
+        'checksums': ['e3a65dacd5b25a18c56e3ae31b11cd724480be7fe8db2df1c46ed0dd322a1fca'],
+    }),
+    ('xarray-datatree', '0.0.13', {
+        'modulename': 'datatree',
+        'checksums': ['f42bd519cab8754eb8a98749464846893b59560318520c45212e85c46af692c9'],
+    }),
+    ('xmltodict', '0.13.0', {
+        'checksums': ['341595a488e3e01a85a9d8911d8912fd922ede5fecc4dce437eb4b6c8d037e56'],
+    }),
+    ('xradar', '0.5.1', {
+        'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl',
+        'checksums': ['0337b4a0798ded019b26e0746b7b7baeb6f21344a2a2e3704965049972ccbf51'],
+    }),
+    (name, version, {
+        'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl',
+        'checksums': ['e2b625d10bc9b3ea2f33356fe467683b474c0a5410ff10ea6a708238d9172a10'],
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'geo'

From 66c6529e64dc49318f36f04df39d092a8ffcf403 Mon Sep 17 00:00:00 2001
From: Fokke Dijkstra <f.dijkstra@rug.nl>
Date: Fri, 2 Aug 2024 16:11:25 +0200
Subject: [PATCH 548/835] adding easyconfigs: Bandage-0.9.0-GCCcore-12.3.0.eb,
 GetOrganelle-1.7.7.1-foss-2023a.eb

---
 .../b/Bandage/Bandage-0.9.0-GCCcore-12.3.0.eb | 30 +++++++++++++
 .../GetOrganelle-1.7.7.1-foss-2023a.eb        | 43 +++++++++++++++++++
 2 files changed, 73 insertions(+)
 create mode 100644 easybuild/easyconfigs/b/Bandage/Bandage-0.9.0-GCCcore-12.3.0.eb
 create mode 100644 easybuild/easyconfigs/g/GetOrganelle/GetOrganelle-1.7.7.1-foss-2023a.eb

diff --git a/easybuild/easyconfigs/b/Bandage/Bandage-0.9.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/b/Bandage/Bandage-0.9.0-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..acdc093c96d
--- /dev/null
+++ b/easybuild/easyconfigs/b/Bandage/Bandage-0.9.0-GCCcore-12.3.0.eb
@@ -0,0 +1,30 @@
+easyblock = 'MakeCp'
+
+name = 'Bandage'
+version = '0.9.0'
+
+homepage = 'http://rrwick.github.io/Bandage'
+description = "Bandage is a program for visualising de novo assembly graphs"
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+source_urls = ['https://github.com/rrwick/Bandage/archive']
+sources = ['v%(version)s.tar.gz']
+checksums = ['04de8152d8bf5e5aa32b41a63cf1c23e1fee7b67ccd9f1407db8dc2824ca4e30']
+
+builddependencies = [('binutils', '2.40')]
+
+dependencies = [('Qt5', '5.15.10')]
+
+prebuildopts = "qmake Bandage.pro && "
+
+files_to_copy = [(['Bandage'], 'bin')]
+
+sanity_check_paths = {
+    'files': ['bin/Bandage'],
+    'dirs': [],
+}
+
+sanity_check_commands = ["Bandage --help && ldd $(which Bandage)"]
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/g/GetOrganelle/GetOrganelle-1.7.7.1-foss-2023a.eb b/easybuild/easyconfigs/g/GetOrganelle/GetOrganelle-1.7.7.1-foss-2023a.eb
new file mode 100644
index 00000000000..4c6746689d9
--- /dev/null
+++ b/easybuild/easyconfigs/g/GetOrganelle/GetOrganelle-1.7.7.1-foss-2023a.eb
@@ -0,0 +1,43 @@
+easyblock = 'PythonPackage'
+
+name = 'GetOrganelle'
+version = '1.7.7.1'
+
+homepage = 'https://github.com/Kinggerm/GetOrganelle'
+description = """This toolkit assemblies organelle genome from genomic skimming data."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+source_urls = ['https://github.com/Kinggerm/GetOrganelle/archive/']
+sources = ['%(version)s.tar.gz']
+checksums = ['cf8e14766de43967182be839de20c9d1709b60fae38a0b3d175742dfad7a5d44']
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('Bandage', '0.9.0'),
+    ('SciPy-bundle', '2023.07'),
+    ('sympy', '1.12'),
+    ('SPAdes', '3.15.4'),
+    ('Bowtie2', '2.5.1'),
+    ('BLAST+', '2.14.1'),
+    ('Perl', '5.36.1'),
+    ('matplotlib', '3.7.2')
+]
+
+download_dep_fail = True
+use_pip = True
+
+options = {'modulename': False}
+
+fix_python_shebang_for = ['bin/*.py']
+
+sanity_pip_check = True
+
+sanity_check_commands = ["get_organelle_from_reads.py -h"]
+
+sanity_check_paths = {
+    'files': ['bin/check_annotations.py', 'bin/get_organelle_from_reads.py', 'bin/slim_graph.py'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+moduleclass = 'bio'

From 2778f5c2589460252f5400c61bbec8656dc53a6a Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Fri, 2 Aug 2024 16:31:57 +0200
Subject: [PATCH 549/835] replace patch by sed in scenic+

---
 .../scenicplus-1.0a1-18072024-foss-2023a.eb   |  17 +-
 ...plus-1.0a1-18072024_requirements.txt.patch | 999 ------------------
 2 files changed, 12 insertions(+), 1004 deletions(-)
 delete mode 100644 easybuild/easyconfigs/s/scenicplus/scenicplus-1.0a1-18072024_requirements.txt.patch

diff --git a/easybuild/easyconfigs/s/scenicplus/scenicplus-1.0a1-18072024-foss-2023a.eb b/easybuild/easyconfigs/s/scenicplus/scenicplus-1.0a1-18072024-foss-2023a.eb
index 9b94d6619f9..37f4c7d76b3 100644
--- a/easybuild/easyconfigs/s/scenicplus/scenicplus-1.0a1-18072024-foss-2023a.eb
+++ b/easybuild/easyconfigs/s/scenicplus/scenicplus-1.0a1-18072024-foss-2023a.eb
@@ -53,6 +53,17 @@ dependencies = [
     ('gensim', '4.3.2'),
 ]
 
+# fix requirements.txt of scenicplus
+local_preinstallopts = (
+    "sed -i"
+    " -e '/typing==3.7.4.3/d'"
+    " -e 's/==.*//g'"
+    " -e '/pyarrow-hotfix/d'"
+    " -e '/line-profiler/d'"
+    " -e '/ndindex/d'"
+    " -e '/sinfo/d'"
+    " requirements.txt && "
+)
 # unpin version restriction and delete typing requirement
 local_pycistopic_preinstallopts = (
     "sed -i"
@@ -249,16 +260,12 @@ exts_list = [
         'checksums': ['7285ac03be9d148437442a726366d7c6f9f5f86bc6636369149a2bc2cd8e0e29'],
     }),
     (name, version, {
-        'patches': [
-            'scenicplus-1.0a1-18072024_requirements.txt.patch',
-        ],
+        'preinstallopts': local_preinstallopts,
         'source_urls': ['https://github.com/aertslab/scenicplus/archive/'],
         'sources': [{'download_filename': 'fa55dae.tar.gz', 'filename': '%(name)s-%(version)s-fa55dae.tar.gz'}],
         'checksums': [
             {'scenicplus-1.0a1-18072024-fa55dae.tar.gz':
              '88cddec1ab2618861e5c93e8a0b17b8e9e2aa3a76410d882c35d472f98724e29'},
-            {'scenicplus-1.0a1-18072024_requirements.txt.patch':
-             'e39f643872263bcfa305c6483d125bde9ebf9ef3bd146247aa9b924c2ac76c56'},
         ],
     }),
 ]
diff --git a/easybuild/easyconfigs/s/scenicplus/scenicplus-1.0a1-18072024_requirements.txt.patch b/easybuild/easyconfigs/s/scenicplus/scenicplus-1.0a1-18072024_requirements.txt.patch
deleted file mode 100644
index 3a565b2a10d..00000000000
--- a/easybuild/easyconfigs/s/scenicplus/scenicplus-1.0a1-18072024_requirements.txt.patch
+++ /dev/null
@@ -1,999 +0,0 @@
-Fix requirements.txt and unpin exact versions
---- requirements.txt.orig	2024-07-24 10:54:46.267978000 +0200
-+++ requirements.txt	2024-07-24 12:06:31.676022842 +0200
-@@ -1,918 +1,77 @@
--#
--# This file is autogenerated by pip-compile with Python 3.11
--# by the following command:
--#
--#    pip-compile --output-file=requirements.txt pyproject.toml
--#
--adjusttext==1.0.4
--    # via
--    #   pycistopic
--    #   scenicplus (pyproject.toml)
--aiohttp==3.9.3
--    # via pyscenic
--aiosignal==1.3.1
--    # via
--    #   aiohttp
--    #   ray
--anndata==0.10.5.post1
--    # via
--    #   mudata
--    #   scanpy
--    #   scenicplus (pyproject.toml)
--annoy==1.17.3
--    # via
--    #   bbknn
--    #   scanorama
--    #   scenicplus (pyproject.toml)
--    #   scrublet
--appdirs==1.4.4
--    # via
--    #   bioservices
--    #   snakemake
--arboreto==0.1.6
--    # via
--    #   pyscenic
--    #   scenicplus (pyproject.toml)
--argparse-dataclass==2.0.0
--    # via
--    #   snakemake-interface-common
--    #   snakemake-interface-executor-plugins
--array-api-compat==1.5.1
--    # via anndata
--asttokens==2.4.1
--    # via stack-data
--attr==0.3.2
--    # via scenicplus (pyproject.toml)
--attrs==23.2.0
--    # via
--    #   aiohttp
--    #   cattrs
--    #   jsonschema
--    #   pyscenic
--    #   referencing
--    #   requests-cache
--    #   scenicplus (pyproject.toml)
--bbknn==1.6.0
--    # via
--    #   pycistopic
--    #   scenicplus (pyproject.toml)
--beautifulsoup4==4.12.3
--    # via
--    #   bioservices
--    #   bs4
--    #   scenicplus (pyproject.toml)
--bidict==0.23.1
--    # via tmtoolkit
--bioservices==1.11.2
--    # via gseapy
--blosc2==2.5.1
--    # via tables
--bokeh==3.4.0
--    # via dask
--boltons==23.1.1
--    # via pyscenic
--bs4==0.0.2
--    # via
--    #   pycistopic
--    #   scenicplus (pyproject.toml)
--cattrs==23.2.3
--    # via requests-cache
--certifi==2024.2.2
--    # via requests
--charset-normalizer==3.3.2
--    # via requests
--click==8.1.7
--    # via
--    #   dask
--    #   distributed
--    #   loompy
--    #   loomxpy
--    #   ray
--cloudpickle==3.0.0
--    # via
--    #   dask
--    #   distributed
--    #   pyscenic
--colorama==0.4.6
--    # via easydev
--colorlog==6.8.2
--    # via
--    #   bioservices
--    #   easydev
--conda-inject==1.3.1
--    # via snakemake
--configargparse==1.7
--    # via
--    #   snakemake
--    #   snakemake-interface-common
--connection-pool==0.0.3
--    # via snakemake
--contourpy==1.2.0
--    # via
--    #   bokeh
--    #   matplotlib
--ctxcore==0.2.0
--    # via
--    #   pycistarget
--    #   pyscenic
--    #   scenicplus (pyproject.toml)
--cycler==0.12.1
--    # via matplotlib
--cython==0.29.37
--    # via
--    #   bbknn
--    #   macs2
--    #   pyranges
--    #   scenicplus (pyproject.toml)
--    #   scrublet
--cytoolz==0.12.3
--    # via
--    #   ctxcore
--    #   pyscenic
--    #   scenicplus (pyproject.toml)
--dask[array,complete,dataframe,diagnostics,distributed]==2024.2.1
--    # via
--    #   arboreto
--    #   distributed
--    #   pyscenic
--    #   scenicplus (pyproject.toml)
--dataclasses-json==0.6.4
--    # via loomxpy
--datrie==0.8.2
--    # via snakemake
--decorator==5.1.1
--    # via ipython
--dill==0.3.8
--    # via
--    #   multiprocessing-on-dill
--    #   scenicplus (pyproject.toml)
--distributed==2024.2.1
--    # via
--    #   arboreto
--    #   dask
--    #   pyscenic
--docutils==0.20.1
--    # via
--    #   snakemake
--    #   statistics
--dpath==2.1.6
--    # via
--    #   snakemake
--    #   yte
--easydev==0.13.1
--    # via bioservices
--et-xmlfile==1.1.0
--    # via openpyxl
--executing==2.0.1
--    # via stack-data
--fastjsonschema==2.19.1
--    # via nbformat
--fbpca==1.0
--    # via
--    #   geosketch
--    #   scanorama
--filelock==3.13.1
--    # via ray
--fonttools==4.50.0
--    # via matplotlib
--frozendict==2.4.0
--    # via
--    #   ctxcore
--    #   pyscenic
--frozenlist==1.4.1
--    # via
--    #   aiohttp
--    #   aiosignal
--    #   ray
--fsspec==2024.3.1
--    # via
--    #   dask
--    #   pyscenic
--future==1.0.0
--    # via pybiomart
--gensim==4.3.2
--    # via
--    #   pycistopic
--    #   scenicplus (pyproject.toml)
--geosketch==1.2
--    # via scanorama
--gevent==24.2.1
--    # via grequests
--gitdb==4.0.11
--    # via gitpython
--gitpython==3.1.42
--    # via snakemake
--globre==0.1.5
--    # via tmtoolkit
--greenlet==3.0.3
--    # via gevent
--grequests==0.7.0
--    # via bioservices
--gseapy==0.10.8
--    # via scenicplus (pyproject.toml)
--h5py==3.10.0
--    # via
--    #   anndata
--    #   loompy
--    #   mudata
--    #   pycistarget
--    #   scanpy
--    #   scenicplus (pyproject.toml)
--harmonypy==0.0.9
--    # via
--    #   pycistopic
--    #   scenicplus (pyproject.toml)
--humanfriendly==10.0
--    # via snakemake
--idna==3.6
--    # via
--    #   requests
--    #   yarl
--igraph==0.11.4
--    # via
--    #   leidenalg
--    #   pycistopic
--    #   scenicplus (pyproject.toml)
--imageio==2.34.0
--    # via
--    #   scenicplus (pyproject.toml)
--    #   scikit-image
--immutables==0.20
--    # via snakemake
--importlib-metadata==7.0.1
--    # via
--    #   dask
--    #   scenicplus (pyproject.toml)
--importlib-resources==6.1.2
--    # via scenicplus (pyproject.toml)
--interlap==0.2.7
--    # via pyscenic
--intervaltree==3.1.0
--    # via
--    #   scanorama
--    #   scenicplus (pyproject.toml)
--ipython==8.22.2
--    # via
--    #   pycistarget
--    #   pyvis
--jedi==0.19.1
--    # via ipython
--jinja2==3.1.3
--    # via
--    #   bokeh
--    #   dask
--    #   distributed
--    #   pyvis
--    #   snakemake
--joblib==1.3.2
--    # via
--    #   gseapy
--    #   pynndescent
--    #   scanpy
--    #   scatac-fragment-tools
--    #   scenicplus (pyproject.toml)
--    #   scikit-learn
--jsonpickle==3.0.3
--    # via pyvis
--jsonschema==4.21.1
--    # via
--    #   nbformat
--    #   ray
--    #   snakemake
--jsonschema-specifications==2023.12.1
--    # via jsonschema
--jupyter-core==5.7.2
--    # via nbformat
--kaleido==0.2.1
--    # via scenicplus (pyproject.toml)
--kiwisolver==1.4.5
--    # via matplotlib
--lazy-loader==0.3
--    # via scikit-image
--lda==3.0.0
--    # via
--    #   pycistopic
--    #   scenicplus (pyproject.toml)
--leidenalg==0.10.2
--    # via
--    #   pycistopic
--    #   scenicplus (pyproject.toml)
--line-profiler==4.1.2
--    # via easydev
--llvmlite==0.42.0
--    # via
--    #   numba
--    #   pynndescent
--    #   pyscenic
--locket==1.0.0
--    # via
--    #   distributed
--    #   partd
--loompy==3.0.7
--    # via
--    #   loomxpy
--    #   pyscenic
--loomxpy @ git+https://github.com/aertslab/LoomXpy@main
--    # via
--    #   pycistopic
--    #   scenicplus (pyproject.toml)
--lxml==5.1.0
--    # via
--    #   bioservices
--    #   pycistopic
--    #   scenicplus (pyproject.toml)
--lz4==4.3.3
--    # via dask
--macs2==2.2.9.1
--    # via
--    #   pycistopic
--    #   scenicplus (pyproject.toml)
--markdown-it-py==3.0.0
--    # via rich
--markupsafe==2.1.5
--    # via jinja2
--marshmallow==3.21.1
--    # via dataclasses-json
--matplotlib==3.6.3
--    # via
--    #   adjusttext
--    #   bioservices
--    #   gseapy
--    #   mizani
--    #   plotnine
--    #   pycistopic
--    #   scanorama
--    #   scanpy
--    #   scenicplus (pyproject.toml)
--    #   scrublet
--    #   seaborn
--    #   tmtoolkit
--    #   tspex
--matplotlib-inline==0.1.6
--    # via ipython
--mdurl==0.1.2
--    # via markdown-it-py
--mizani==0.9.3
--    # via plotnine
--msgpack==1.0.8
--    # via
--    #   blosc2
--    #   distributed
--    #   ray
--mudata==0.2.3
--    # via scenicplus (pyproject.toml)
--multidict==6.0.5
--    # via
--    #   aiohttp
--    #   yarl
--multiprocessing-on-dill==3.5.0a4
--    # via pyscenic
--mypy-extensions==1.0.0
--    # via typing-inspect
--natsort==8.4.0
--    # via
--    #   anndata
--    #   pyranges
--    #   pyrle
--    #   scanpy
--nbformat==5.10.3
--    # via snakemake
--ncls==0.0.68
--    # via
--    #   pyranges
--    #   scenicplus (pyproject.toml)
--ndindex==1.8
--    # via blosc2
--networkx==3.2.1
--    # via
--    #   pyscenic
--    #   pyvis
--    #   scanpy
--    #   scenicplus (pyproject.toml)
--    #   scikit-image
--numba==0.59.0
--    # via
--    #   ctxcore
--    #   loompy
--    #   pynndescent
--    #   pyscenic
--    #   scanpy
--    #   scatac-fragment-tools
--    #   scenicplus (pyproject.toml)
--    #   scrublet
--    #   umap-learn
--numexpr==2.9.0
--    # via
--    #   pyscenic
--    #   scenicplus (pyproject.toml)
--    #   tables
--numpy==1.26.4
--    # via
--    #   adjusttext
--    #   anndata
--    #   arboreto
--    #   bbknn
--    #   blosc2
--    #   bokeh
--    #   contourpy
--    #   ctxcore
--    #   dask
--    #   gensim
--    #   geosketch
--    #   gseapy
--    #   h5py
--    #   harmonypy
--    #   imageio
--    #   lda
--    #   loompy
--    #   loomxpy
--    #   macs2
--    #   matplotlib
--    #   mizani
--    #   mudata
--    #   ncls
--    #   numba
--    #   numexpr
--    #   numpy-groupies
--    #   pandas
--    #   patsy
--    #   plotnine
--    #   pyarrow
--    #   pybedtools
--    #   pybigtools
--    #   pycistarget
--    #   pycistopic
--    #   pygam
--    #   pyrle
--    #   pyscenic
--    #   scanorama
--    #   scanpy
--    #   scatac-fragment-tools
--    #   scenicplus (pyproject.toml)
--    #   scikit-image
--    #   scikit-learn
--    #   scipy
--    #   scrublet
--    #   seaborn
--    #   sorted-nearest
--    #   statsmodels
--    #   tables
--    #   tifffile
--    #   tmtoolkit
--    #   tspex
--    #   umap-learn
--numpy-groupies==0.10.2
--    # via
--    #   loompy
--    #   scenicplus (pyproject.toml)
--openpyxl==3.1.2
--    # via tmtoolkit
--packaging==24.0
--    # via
--    #   anndata
--    #   bokeh
--    #   dask
--    #   distributed
--    #   marshmallow
--    #   matplotlib
--    #   plotly
--    #   ray
--    #   scanpy
--    #   scikit-image
--    #   snakemake
--    #   statsmodels
--    #   tables
--pandas==1.5.0
--    # via
--    #   anndata
--    #   arboreto
--    #   bbknn
--    #   bioservices
--    #   bokeh
--    #   ctxcore
--    #   dask
--    #   gseapy
--    #   harmonypy
--    #   loomxpy
--    #   mizani
--    #   mudata
--    #   plotnine
--    #   pybiomart
--    #   pycistarget
--    #   pycistopic
--    #   pyranges
--    #   pyrle
--    #   pyscenic
--    #   scanpy
--    #   scenicplus (pyproject.toml)
--    #   scrublet
--    #   seaborn
--    #   statsmodels
--    #   tmtoolkit
--    #   tspex
--parso==0.8.3
--    # via jedi
--partd==1.4.1
--    # via dask
--patsy==0.5.6
--    # via
--    #   plotnine
--    #   scanpy
--    #   statsmodels
--pexpect==4.9.0
--    # via
--    #   easydev
--    #   ipython
--pillow==10.2.0
--    # via
--    #   bokeh
--    #   imageio
--    #   matplotlib
--    #   scikit-image
--plac==1.4.3
--    # via yte
--platformdirs==4.2.0
--    # via
--    #   easydev
--    #   jupyter-core
--    #   requests-cache
--plotly==5.19.0
--    # via scenicplus (pyproject.toml)
--plotnine==0.12.4
--    # via scenicplus (pyproject.toml)
--polars==0.20.13
--    # via
--    #   pycistopic
--    #   scatac-fragment-tools
--    #   scenicplus (pyproject.toml)
--progressbar2==4.4.2
--    # via pygam
--prompt-toolkit==3.0.43
--    # via ipython
--protobuf==5.26.0
--    # via ray
--psutil==5.9.8
--    # via
--    #   distributed
--    #   snakemake
--ptyprocess==0.7.0
--    # via pexpect
--pulp==2.8.0
--    # via snakemake
--pure-eval==0.2.2
--    # via stack-data
--py-cpuinfo==9.0.0
--    # via
--    #   blosc2
--    #   tables
--pyarrow==15.0.0
--    # via
--    #   ctxcore
--    #   dask
--    #   pycistopic
--    #   scatac-fragment-tools
--    #   scenicplus (pyproject.toml)
--pyarrow-hotfix==0.6
--    # via
--    #   dask
--    #   scenicplus (pyproject.toml)
--pybedtools==0.9.1
--    # via scenicplus (pyproject.toml)
--pybigtools==0.1.2
--    # via
--    #   scatac-fragment-tools
--    #   scenicplus (pyproject.toml)
--pybigwig==0.3.22
--    # via
--    #   scatac-fragment-tools
--    #   scenicplus (pyproject.toml)
--pybiomart==0.2.0
--    # via
--    #   pycistopic
--    #   scenicplus (pyproject.toml)
--pycistarget @ git+https://github.com/aertslab/pycistarget
--    # via scenicplus (pyproject.toml)
--pycistopic @ git+https://github.com/aertslab/pycisTopic
--    # via scenicplus (pyproject.toml)
--pyfasta==0.5.2
--    # via scenicplus (pyproject.toml)
--pygam==0.9.0
--    # via scenicplus (pyproject.toml)
--pygments==2.17.2
--    # via
--    #   ipython
--    #   rich
--pynndescent==0.5.11
--    # via
--    #   bbknn
--    #   umap-learn
--pyparsing==3.1.2
--    # via matplotlib
--pyranges==0.0.111
--    # via
--    #   pycistarget
--    #   pycistopic
--    #   scenicplus (pyproject.toml)
--pyrle==0.0.39
--    # via
--    #   pyranges
--    #   scenicplus (pyproject.toml)
--pysam==0.22.0
--    # via
--    #   pybedtools
--    #   scenicplus (pyproject.toml)
--pyscenic @ git+https://github.com/aertslab/pySCENIC@master
--    # via
--    #   loomxpy
--    #   pycistopic
--    #   scenicplus (pyproject.toml)
--python-dateutil==2.9.0.post0
--    # via
--    #   matplotlib
--    #   pandas
--python-utils==3.8.2
--    # via progressbar2
--pytz==2024.1
--    # via pandas
--pyvis==0.3.2
--    # via scenicplus (pyproject.toml)
--pyyaml==6.0.1
--    # via
--    #   bokeh
--    #   conda-inject
--    #   ctxcore
--    #   dask
--    #   distributed
--    #   pyscenic
--    #   ray
--    #   snakemake
--    #   yte
--ray==2.9.3
--    # via
--    #   pycistopic
--    #   scenicplus (pyproject.toml)
--referencing==0.34.0
--    # via
--    #   jsonschema
--    #   jsonschema-specifications
--requests==2.31.0
--    # via
--    #   bioservices
--    #   grequests
--    #   gseapy
--    #   pybiomart
--    #   pyscenic
--    #   ray
--    #   requests-cache
--    #   scenicplus (pyproject.toml)
--    #   snakemake
--requests-cache==1.2.0
--    # via
--    #   bioservices
--    #   pybiomart
--    #   scenicplus (pyproject.toml)
--reretry==0.11.8
--    # via
--    #   snakemake
--    #   snakemake-interface-storage-plugins
--rich==13.7.1
--    # via rich-argparse
--rich-argparse==1.4.0
--    # via scatac-fragment-tools
--rpds-py==0.18.0
--    # via
--    #   jsonschema
--    #   referencing
--scanorama==1.7.4
--    # via
--    #   pycistopic
--    #   scenicplus (pyproject.toml)
--scanpy==1.8.2
--    # via
--    #   pycistopic
--    #   scenicplus (pyproject.toml)
--scatac-fragment-tools==0.1.0
--    # via
--    #   pycistopic
--    #   scenicplus (pyproject.toml)
--scikit-image==0.22.0
--    # via
--    #   scenicplus (pyproject.toml)
--    #   scrublet
--scikit-learn==1.3.2
--    # via
--    #   arboreto
--    #   bbknn
--    #   geosketch
--    #   harmonypy
--    #   loomxpy
--    #   pycistarget
--    #   pycistopic
--    #   pynndescent
--    #   pyscenic
--    #   scanorama
--    #   scanpy
--    #   scenicplus (pyproject.toml)
--    #   scrublet
--    #   umap-learn
--scipy==1.12.0
--    # via
--    #   adjusttext
--    #   anndata
--    #   arboreto
--    #   bbknn
--    #   gensim
--    #   gseapy
--    #   harmonypy
--    #   loompy
--    #   mizani
--    #   plotnine
--    #   pygam
--    #   pynndescent
--    #   pyscenic
--    #   scanorama
--    #   scanpy
--    #   scenicplus (pyproject.toml)
--    #   scikit-image
--    #   scikit-learn
--    #   scrublet
--    #   statsmodels
--    #   tmtoolkit
--    #   umap-learn
--scrublet==0.2.3
--    # via
--    #   pycistopic
--    #   scenicplus (pyproject.toml)
--seaborn==0.13.2
--    # via
--    #   pycistopic
--    #   scanpy
--    #   scenicplus (pyproject.toml)
--sinfo==0.3.4
--    # via scanpy
--six==1.16.0
--    # via
--    #   asttokens
--    #   patsy
--    #   pybedtools
--    #   python-dateutil
--    #   url-normalize
--smart-open==6.4.0
--    # via
--    #   gensim
--    #   snakemake
--smmap==5.0.1
--    # via gitdb
--snakemake==8.5.5
--    # via scenicplus (pyproject.toml)
--snakemake-interface-common==1.17.1
--    # via
--    #   scenicplus (pyproject.toml)
--    #   snakemake
--    #   snakemake-interface-executor-plugins
--    #   snakemake-interface-report-plugins
--    #   snakemake-interface-storage-plugins
--snakemake-interface-executor-plugins==8.2.0
--    # via
--    #   scenicplus (pyproject.toml)
--    #   snakemake
--snakemake-interface-report-plugins==1.0.0
--    # via
--    #   scenicplus (pyproject.toml)
--    #   snakemake
--snakemake-interface-storage-plugins==3.1.1
--    # via
--    #   scenicplus (pyproject.toml)
--    #   snakemake
--sorted-nearest==0.0.39
--    # via pyranges
--sortedcontainers==2.4.0
--    # via
--    #   distributed
--    #   intervaltree
--soupsieve==2.5
--    # via beautifulsoup4
--stack-data==0.6.3
--    # via ipython
--statistics==1.0.3.5
--    # via scenicplus (pyproject.toml)
--statsmodels==0.14.1
--    # via
--    #   plotnine
--    #   pycistopic
--    #   scanpy
--    #   scenicplus (pyproject.toml)
--stdlib-list==0.10.0
--    # via sinfo
--stopit==1.1.2
--    # via snakemake
--suds-community==1.1.2
--    # via bioservices
--tables==3.9.2
--    # via scanpy
--tabulate==0.9.0
--    # via
--    #   pyranges
--    #   pyrle
--    #   snakemake
--tblib==3.0.0
--    # via distributed
--tenacity==8.2.3
--    # via plotly
--texttable==1.7.0
--    # via igraph
--threadpoolctl==3.4.0
--    # via scikit-learn
--throttler==1.2.2
--    # via
--    #   snakemake
--    #   snakemake-interface-executor-plugins
--    #   snakemake-interface-storage-plugins
--tifffile==2024.2.12
--    # via scikit-image
--tmtoolkit==0.12.0
--    # via
--    #   pycistopic
--    #   scenicplus (pyproject.toml)
--toolz==0.12.1
--    # via
--    #   cytoolz
--    #   dask
--    #   distributed
--    #   partd
--toposort==1.10
--    # via snakemake
--tornado==6.4
--    # via
--    #   bokeh
--    #   distributed
--tqdm==4.66.2
--    # via
--    #   bioservices
--    #   ctxcore
--    #   pyscenic
--    #   scanpy
--    #   scenicplus (pyproject.toml)
--    #   umap-learn
--traitlets==5.14.2
--    # via
--    #   ipython
--    #   jupyter-core
--    #   matplotlib-inline
--    #   nbformat
--tspex==0.6.3
--    # via scenicplus (pyproject.toml)
--typing==3.7.4.3
--    # via scenicplus (pyproject.toml)
--typing-extensions==4.10.0
--    # via
--    #   python-utils
--    #   typing-inspect
--typing-inspect==0.9.0
--    # via dataclasses-json
--umap-learn==0.5.5
--    # via
--    #   bbknn
--    #   pyscenic
--    #   scanpy
--    #   scenicplus (pyproject.toml)
--    #   scrublet
--url-normalize==1.4.3
--    # via requests-cache
--urllib3==2.2.1
--    # via
--    #   distributed
--    #   requests
--    #   requests-cache
--wcwidth==0.2.13
--    # via prompt-toolkit
--wheel==0.43.0
--    # via tmtoolkit
--wrapt==1.16.0
--    # via
--    #   bioservices
--    #   snakemake
--    #   snakemake-interface-storage-plugins
--xlrd==2.0.1
--    # via
--    #   tmtoolkit
--    #   tspex
--xmltodict==0.13.0
--    # via bioservices
--xyzservices==2023.10.1
--    # via bokeh
--yarl==1.9.4
--    # via aiohttp
--yte==1.5.4
--    # via snakemake
--zict==3.0.0
--    # via distributed
--zipp==3.18.1
--    # via importlib-metadata
--zope-event==5.0
--    # via gevent
--zope-interface==6.2
--    # via gevent
--
--# The following packages are considered to be unsafe in a requirements file:
--# setuptools
-+adjusttext
-+anndata
-+annoy
-+arboreto
-+attr
-+attrs
-+bbknn
-+beautifulsoup4
-+bs4
-+ctxcore
-+cytoolz
-+dask
-+dill
-+gensim
-+gseapy
-+h5py
-+harmonypy
-+igraph
-+imageio
-+importlib-metadata
-+importlib-resources
-+intervaltree
-+joblib
-+kaleido
-+lda
-+leidenalg
-+loomxpy
-+lxml
-+macs2
-+matplotlib
-+mudata
-+ncls
-+networkx
-+numba
-+numexpr
-+numpy
-+numpy-groupies
-+pandas
-+plotly
-+plotnine
-+polars
-+pyarrow
-+pybedtools
-+pybigtools
-+pybigwig
-+pybiomart
-+pycistarget
-+pycistopic
-+pyfasta
-+pygam
-+pyranges
-+pyrle
-+pysam
-+pyscenic
-+pyvis
-+ray
-+requests
-+requests-cache
-+scanorama
-+scanpy
-+scatac-fragment-tools
-+scikit-image
-+scikit-learn
-+scipy
-+scrublet
-+seaborn
-+snakemake
-+snakemake-interface-common
-+snakemake-interface-executor-plugins
-+snakemake-interface-report-plugins
-+snakemake-interface-storage-plugins
-+statistics
-+statsmodels
-+tmtoolkit
-+tqdm
-+tspex
-+umap-learn

From 3e0d6ef516b9b14f68bb2994734075ae48e7fe68 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Fri, 2 Aug 2024 15:27:46 +0000
Subject: [PATCH 550/835] adding easyconfigs: Rust-1.79.0-GCCcore-13.3.0.eb

---
 .../r/Rust/Rust-1.79.0-GCCcore-13.3.0.eb      | 31 +++++++++++++++++++
 1 file changed, 31 insertions(+)
 create mode 100644 easybuild/easyconfigs/r/Rust/Rust-1.79.0-GCCcore-13.3.0.eb

diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.79.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/r/Rust/Rust-1.79.0-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..88962930f30
--- /dev/null
+++ b/easybuild/easyconfigs/r/Rust/Rust-1.79.0-GCCcore-13.3.0.eb
@@ -0,0 +1,31 @@
+name = 'Rust'
+version = '1.79.0'
+
+homepage = 'https://www.rust-lang.org'
+description = """Rust is a systems programming language that runs blazingly fast, prevents segfaults,
+ and guarantees thread safety."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+source_urls = ['https://static.rust-lang.org/dist/']
+sources = ['rustc-%(version)s-src.tar.gz']
+patches = ['Rust-1.70_sysroot-fix-interpreter.patch']
+checksums = [
+    {'rustc-1.79.0-src.tar.gz': '172ecf3c7d1f9d9fb16cd2a628869782670416ded0129e524a86751f961448c0'},
+    {'Rust-1.70_sysroot-fix-interpreter.patch': '220129db55e022a98d25028da5dcc9f26b252dd995c3ac92f6312dbb1e362cb1'},
+]
+
+builddependencies = [
+    ('binutils', '2.42'),
+    ('CMake', '3.29.3'),
+    ('Python', '3.12.3'),
+    ('Ninja', '1.12.1'),
+    ('pkgconf', '2.2.0'),
+    ('patchelf', '0.18.0'),  # only required when RPATH linking is enabled
+]
+
+dependencies = [
+    ('OpenSSL', '3', '', SYSTEM),
+]
+
+moduleclass = 'lang'

From 3e708c9acca0a45a6085b1f78db879d8ffec7028 Mon Sep 17 00:00:00 2001
From: WilleBell <cintiawillemyns@gmail.com>
Date: Fri, 2 Aug 2024 17:34:46 +0200
Subject: [PATCH 551/835] adding easyconfigs: cfgrib-0.9.14.0-foss-2023a.eb

---
 .../c/cfgrib/cfgrib-0.9.14.0-foss-2023a.eb    | 41 +++++++++++++++++++
 1 file changed, 41 insertions(+)
 create mode 100644 easybuild/easyconfigs/c/cfgrib/cfgrib-0.9.14.0-foss-2023a.eb

diff --git a/easybuild/easyconfigs/c/cfgrib/cfgrib-0.9.14.0-foss-2023a.eb b/easybuild/easyconfigs/c/cfgrib/cfgrib-0.9.14.0-foss-2023a.eb
new file mode 100644
index 00000000000..b6b2b66159c
--- /dev/null
+++ b/easybuild/easyconfigs/c/cfgrib/cfgrib-0.9.14.0-foss-2023a.eb
@@ -0,0 +1,41 @@
+easyblock = "PythonBundle"
+
+name = 'cfgrib'
+version = '0.9.14.0'
+
+homepage = 'https://github.com/ecmwf/cfgrib/'
+description = """
+A Python interface to map GRIB files to the NetCDF Common Data Model following the CF
+Convention using ecCodes.
+"""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+builddependencies = [
+    ('poetry', '1.7.1'),
+]
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('ecCodes', '2.31.0'),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    ('findlibs', '0.0.5', {
+        'checksums': ['7a801571e999d0ee83f9b92cbb598c21f861ee26ca9dba74cea8958ba4335e7e'],
+    }),
+    ('eccodes', '1.7.1', {
+        'checksums': ['d3c7e9bab779d35b624cfd7b3331de111602cba6a6f6368efcc12407f30b2697'],
+    }),
+    (name, version, {
+        'checksums': ['2b9a1e6bd47397e585f878ffd8aaac5969f6c9a448da767c700917b89c275bb2'],
+    }),
+]
+
+sanity_check_commands = ['python -m cfgrib selfcheck']
+
+moduleclass = 'tools'

From 63994bddf6d2cdc04c30f7a21437f98b8700e1c9 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 2 Aug 2024 17:57:45 +0200
Subject: [PATCH 552/835] {compiler} GCC v14.2.0

---
 .../b/Bison/Bison-3.8.2-GCCcore-14.2.0.eb     | 28 +++++++++
 .../binutils/binutils-2.42-GCCcore-14.2.0.eb  | 31 +++++++++
 .../f/flex/flex-2.6.4-GCCcore-14.2.0.eb       | 34 ++++++++++
 easybuild/easyconfigs/g/GCC/GCC-14.2.0.eb     | 22 +++++++
 .../easyconfigs/g/GCCcore/GCCcore-14.2.0.eb   | 63 +++++++++++++++++++
 .../help2man-1.49.3-GCCcore-14.2.0.eb         | 25 ++++++++
 .../m/M4/M4-1.4.19-GCCcore-14.2.0.eb          | 29 +++++++++
 .../z/zlib/zlib-1.3.1-GCCcore-14.2.0.eb       | 27 ++++++++
 8 files changed, 259 insertions(+)
 create mode 100644 easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-14.2.0.eb
 create mode 100644 easybuild/easyconfigs/b/binutils/binutils-2.42-GCCcore-14.2.0.eb
 create mode 100644 easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-14.2.0.eb
 create mode 100644 easybuild/easyconfigs/g/GCC/GCC-14.2.0.eb
 create mode 100644 easybuild/easyconfigs/g/GCCcore/GCCcore-14.2.0.eb
 create mode 100644 easybuild/easyconfigs/h/help2man/help2man-1.49.3-GCCcore-14.2.0.eb
 create mode 100644 easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-14.2.0.eb
 create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.3.1-GCCcore-14.2.0.eb

diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-14.2.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-14.2.0.eb
new file mode 100644
index 00000000000..427ebbbe2b7
--- /dev/null
+++ b/easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-14.2.0.eb
@@ -0,0 +1,28 @@
+easyblock = 'ConfigureMake'
+
+name = 'Bison'
+version = '3.8.2'
+
+homepage = 'https://www.gnu.org/software/bison'
+description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar
+ into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables."""
+
+toolchain = {'name': 'GCCcore', 'version': '14.2.0'}
+
+source_urls = [GNU_SOURCE]
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['06c9e13bdf7eb24d4ceb6b59205a4f67c2c7e7213119644430fe82fbd14a0abb']
+
+builddependencies = [
+    ('M4', '1.4.19'),
+    # use same binutils version that was used when building GCCcore toolchain
+    ('binutils', '2.42', '', SYSTEM),
+]
+
+
+sanity_check_paths = {
+    'files': ['bin/%s' % x for x in ['bison', 'yacc']] + [('lib/liby.a', 'lib64/liby.a')],
+    'dirs': [],
+}
+
+moduleclass = 'lang'
diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.42-GCCcore-14.2.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.42-GCCcore-14.2.0.eb
new file mode 100644
index 00000000000..94b762d7803
--- /dev/null
+++ b/easybuild/easyconfigs/b/binutils/binutils-2.42-GCCcore-14.2.0.eb
@@ -0,0 +1,31 @@
+name = 'binutils'
+version = '2.42'
+
+homepage = 'https://directory.fsf.org/project/binutils/'
+description = "binutils: GNU binary utilities"
+
+toolchain = {'name': 'GCCcore', 'version': '14.2.0'}
+
+source_urls = [GNU_SOURCE]
+sources = [SOURCE_TAR_GZ]
+checksums = ['5d2a6c1d49686a557869caae08b6c2e83699775efd27505e01b2f4db1a024ffc']
+
+builddependencies = [
+    ('flex', '2.6.4'),
+    ('Bison', '3.8.2'),
+    # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils
+    ('binutils', version, '', SYSTEM)
+]
+
+dependencies = [
+    # zlib is a runtime dep to avoid that it gets embedded in libbfd.so,
+    # see https://github.com/easybuilders/easybuild-easyblocks/issues/1350
+    ('zlib', '1.3.1'),
+]
+
+# avoid build failure when makeinfo command is not available
+# see https://sourceware.org/bugzilla/show_bug.cgi?id=15345
+buildopts = 'MAKEINFO=true'
+installopts = buildopts
+
+moduleclass = 'tools'
diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-14.2.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-14.2.0.eb
new file mode 100644
index 00000000000..d91f13aa5d0
--- /dev/null
+++ b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-14.2.0.eb
@@ -0,0 +1,34 @@
+name = 'flex'
+version = '2.6.4'
+
+homepage = 'https://github.com/westes/flex'
+
+description = """
+ Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner,
+ sometimes called a tokenizer, is a program which recognizes lexical patterns
+ in text.
+"""
+
+toolchain = {'name': 'GCCcore', 'version': '14.2.0'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://github.com/westes/flex/releases/download/v%(version)s/']
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['e87aae032bf07c26f85ac0ed3250998c37621d95f8bd748b31f15b33c45ee995']
+
+builddependencies = [
+    ('Bison', '3.8.2'),
+    ('help2man', '1.49.3'),
+    # use same binutils version that was used when building GCC toolchain
+    ('binutils', '2.42', '', SYSTEM),
+]
+
+dependencies = [
+    ('M4', '1.4.19'),
+]
+
+# glibc 2.26 requires _GNU_SOURCE defined to expose reallocarray in the correct
+# header, see https://github.com/westes/flex/issues/241
+preconfigopts = 'export CPPFLAGS="$CPPFLAGS -D_GNU_SOURCE" && '
+
+moduleclass = 'lang'
diff --git a/easybuild/easyconfigs/g/GCC/GCC-14.2.0.eb b/easybuild/easyconfigs/g/GCC/GCC-14.2.0.eb
new file mode 100644
index 00000000000..7126db6c52d
--- /dev/null
+++ b/easybuild/easyconfigs/g/GCC/GCC-14.2.0.eb
@@ -0,0 +1,22 @@
+easyblock = 'Bundle'
+
+name = 'GCC'
+version = '14.2.0'
+
+homepage = 'https://gcc.gnu.org/'
+description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada,
+ as well as libraries for these languages (libstdc++, libgcj,...)."""
+
+toolchain = SYSTEM
+
+dependencies = [
+    ('GCCcore', version),
+    # binutils built on top of GCCcore, which was built on top of binutils (built with system toolchain)
+    ('binutils', '2.42', '', ('GCCcore', version)),
+]
+
+altroot = 'GCCcore'
+altversion = 'GCCcore'
+
+# this bundle serves as a compiler-only toolchain, so it should be marked as compiler (important for HMNS)
+moduleclass = 'compiler'
diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-14.2.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-14.2.0.eb
new file mode 100644
index 00000000000..438a848145f
--- /dev/null
+++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-14.2.0.eb
@@ -0,0 +1,63 @@
+easyblock = 'EB_GCC'
+
+name = 'GCCcore'
+version = '14.2.0'
+
+homepage = 'https://gcc.gnu.org/'
+description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada,
+ as well as libraries for these languages (libstdc++, libgcj,...)."""
+
+toolchain = SYSTEM
+
+source_urls = [
+    'https://ftpmirror.gnu.org/gnu/gcc/gcc-%(version)s',  # GCC auto-resolving HTTP mirror
+    'https://sourceware.org/pub/gcc/releases/gcc-%(version)s',  # fallback URL for GCC
+    'https://ftpmirror.gnu.org/gnu/gmp',  # idem for GMP
+    'https://ftpmirror.gnu.org/gnu/mpfr',  # idem for MPFR
+    'https://ftpmirror.gnu.org/gnu/mpc',  # idem for MPC
+    'ftp://gcc.gnu.org/pub/gcc/infrastructure/',  # GCC dependencies
+    'https://gcc.gnu.org/pub/gcc/infrastructure/',  # HTTPS mirror for GCC dependencies
+    'https://libisl.sourceforge.io/',  # fallback URL for isl
+    'https://sourceware.org/pub/newlib/',  # for newlib
+    'https://github.com/MentorEmbedded/nvptx-tools/archive',  # for nvptx-tools
+]
+sources = [
+    'gcc-%(version)s.tar.gz',
+    'gmp-6.3.0.tar.bz2',
+    'mpfr-4.2.1.tar.bz2',
+    'mpc-1.3.1.tar.gz',
+    'isl-0.26.tar.bz2',
+    'newlib-4.4.0.20231231.tar.gz',
+    {'download_filename': '3136cf9.tar.gz', 'filename': 'nvptx-tools-20240801.tar.gz'},
+]
+patches = [
+    'GCCcore-6.2.0-fix-find-isl.patch',
+    'GCCcore-9.3.0_gmp-c99.patch',
+]
+checksums = [
+    {'gcc-14.2.0.tar.gz': '7d376d445f93126dc545e2c0086d0f647c3094aae081cdb78f42ce2bc25e7293'},
+    {'gmp-6.3.0.tar.bz2': 'ac28211a7cfb609bae2e2c8d6058d66c8fe96434f740cf6fe2e47b000d1c20cb'},
+    {'mpfr-4.2.1.tar.bz2': 'b9df93635b20e4089c29623b19420c4ac848a1b29df1cfd59f26cab0d2666aa0'},
+    {'mpc-1.3.1.tar.gz': 'ab642492f5cf882b74aa0cb730cd410a81edcdbec895183ce930e706c1c759b8'},
+    {'isl-0.26.tar.bz2': '5eac8664e9d67be6bd0bee5085d6840b8baf738c06814df47eaf4166d9776436'},
+    {'newlib-4.4.0.20231231.tar.gz': '0c166a39e1bf0951dfafcd68949fe0e4b6d3658081d6282f39aeefc6310f2f13'},
+    {'nvptx-tools-20240801.tar.gz': 'a1106bf11b66d12e67194d8aa37196bb96996b614f44b3d3bc1b5854eefec03c'},
+    {'GCCcore-6.2.0-fix-find-isl.patch': '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68'},
+    {'GCCcore-9.3.0_gmp-c99.patch': '0e135e1cc7cec701beea9d7d17a61bab34cfd496b4b555930016b98db99f922e'},
+]
+
+builddependencies = [
+    ('M4', '1.4.19'),
+    ('binutils', '2.42'),
+]
+
+languages = ['c', 'c++', 'fortran']
+
+withisl = True
+withnvptx = True
+
+# Perl is only required when building with NVPTX support
+if withnvptx:
+    osdependencies = ['perl']
+
+moduleclass = 'compiler'
diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.49.3-GCCcore-14.2.0.eb b/easybuild/easyconfigs/h/help2man/help2man-1.49.3-GCCcore-14.2.0.eb
new file mode 100644
index 00000000000..2161ee0b1af
--- /dev/null
+++ b/easybuild/easyconfigs/h/help2man/help2man-1.49.3-GCCcore-14.2.0.eb
@@ -0,0 +1,25 @@
+easyblock = 'ConfigureMake'
+
+name = 'help2man'
+version = '1.49.3'
+
+homepage = 'https://www.gnu.org/software/help2man/'
+description = """help2man produces simple manual pages from the '--help' and '--version' output of other commands."""
+
+toolchain = {'name': 'GCCcore', 'version': '14.2.0'}
+
+source_urls = [GNU_SOURCE]
+sources = [SOURCE_TAR_XZ]
+checksums = ['4d7e4fdef2eca6afe07a2682151cea78781e0a4e8f9622142d9f70c083a2fd4f']
+
+builddependencies = [
+    # use same binutils version that was used when building GCC toolchain
+    ('binutils', '2.42', '', SYSTEM),
+]
+
+sanity_check_paths = {
+    'files': ['bin/help2man'],
+    'dirs': [],
+}
+
+moduleclass = 'tools'
diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-14.2.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-14.2.0.eb
new file mode 100644
index 00000000000..c5c3ad83f3a
--- /dev/null
+++ b/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-14.2.0.eb
@@ -0,0 +1,29 @@
+easyblock = 'ConfigureMake'
+
+name = 'M4'
+version = '1.4.19'
+
+homepage = 'https://www.gnu.org/software/m4/m4.html'
+description = """GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible
+  although it has some extensions (for example, handling more than 9 positional parameters to macros).
+ GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc."""
+
+toolchain = {'name': 'GCCcore', 'version': '14.2.0'}
+
+source_urls = [GNU_SOURCE]
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['3be4a26d825ffdfda52a56fc43246456989a3630093cced3fbddf4771ee58a70']
+
+# use same binutils version that was used when building GCC toolchain
+builddependencies = [('binutils', '2.42', '', SYSTEM)]
+
+# '-fgnu89-inline' is required to avoid linking errors with older glibc's,
+# see https://github.com/easybuilders/easybuild-easyconfigs/issues/529
+configopts = "--enable-c++ CPPFLAGS=-fgnu89-inline"
+
+sanity_check_paths = {
+    'files': ['bin/m4'],
+    'dirs': [],
+}
+
+moduleclass = 'devel'
diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.3.1-GCCcore-14.2.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.3.1-GCCcore-14.2.0.eb
new file mode 100644
index 00000000000..187f8da34f7
--- /dev/null
+++ b/easybuild/easyconfigs/z/zlib/zlib-1.3.1-GCCcore-14.2.0.eb
@@ -0,0 +1,27 @@
+easyblock = 'ConfigureMake'
+
+name = 'zlib'
+version = '1.3.1'
+
+homepage = 'https://www.zlib.net/'
+description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is,
+ not covered by any patents -- lossless data-compression library for use on virtually any
+ computer hardware and operating system."""
+
+toolchain = {'name': 'GCCcore', 'version': '14.2.0'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://zlib.net/fossils']
+sources = [SOURCELOWER_TAR_GZ]
+# patches = ['zlib-%(version)s_fix-CC-logic-in-configure.patch']
+checksums = ['9a93b2b7dfdac77ceba5a558a580e74667dd6fede4585b91eefb60f03b72df23']
+
+# use same binutils version that was used when building GCC toolchain
+builddependencies = [('binutils', '2.42', '', SYSTEM)]
+
+sanity_check_paths = {
+    'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT],
+    'dirs': [],
+}
+
+moduleclass = 'lib'

From e9e089ddeee20f1d1d3661afca1268d18acc18f8 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Sat, 3 Aug 2024 17:25:24 +0000
Subject: [PATCH 553/835] adding easyconfigs: Z3-4.13.0-GCCcore-13.3.0.eb

---
 .../z/Z3/Z3-4.13.0-GCCcore-13.3.0.eb          | 50 +++++++++++++++++++
 1 file changed, 50 insertions(+)
 create mode 100644 easybuild/easyconfigs/z/Z3/Z3-4.13.0-GCCcore-13.3.0.eb

diff --git a/easybuild/easyconfigs/z/Z3/Z3-4.13.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/z/Z3/Z3-4.13.0-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..a925168f147
--- /dev/null
+++ b/easybuild/easyconfigs/z/Z3/Z3-4.13.0-GCCcore-13.3.0.eb
@@ -0,0 +1,50 @@
+easyblock = 'PythonBundle'
+
+name = 'Z3'
+version = '4.13.0'
+
+homepage = 'https://github.com/Z3Prover/z3'
+description = """Z3 is a theorem prover from Microsoft Research with support for bitvectors,
+booleans, arrays, floating point numbers, strings, and other data types. This
+module includes z3-solver, the Python interface of Z3.
+"""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+builddependencies = [
+    ('CMake', '3.29.3'),
+    ('binutils', '2.42'),
+]
+dependencies = [
+    ('Python', '3.12.3'),
+    ('GMP', '6.3.0'),
+]
+
+use_pip = True
+
+_fix_parallelism = """sed -i 's/str(multiprocessing.cpu_count())/"%(parallel)s"/' setup.py && """
+_enable_gmp = """sed -i "s/Z3_USE_LIB_GMP.*/Z3_USE_LIB_GMP' : True,/" setup.py && """
+
+exts_list = [
+    ('z3-solver', version + '.0', {
+        'modulename': 'z3',
+        'checksums': ['52588e92aec7cb338fd6288ce93758ae01770f62ca0c80e8f4f2b2333feaf51b'],
+        'preinstallopts': _fix_parallelism + _enable_gmp,
+    }),
+]
+
+# make Z3 headers and libraries accessible in their usual location
+local_z3_site_path = "lib/python%(pyshortver)s/site-packages/%(namelower)s"
+postinstallcmds = [
+    'ln -s %s/include "%%(installdir)s/include"' % local_z3_site_path,
+    'cd "%%(installdir)s"; for lib in %s/lib/*; do ln -s ../$lib lib/$(basename $lib); done' % local_z3_site_path
+]
+
+sanity_pip_check = True
+
+sanity_check_paths = {
+    'files': ['bin/z3', 'include/z3_api.h', 'lib/libz3.' + SHLIB_EXT],
+    'dirs': ['include', 'lib/python%(pyshortver)s/site-packages'],
+}
+
+moduleclass = 'tools'

From e3443a43a1c581a8e14c1c8aa907124aa82deee0 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Sat, 3 Aug 2024 17:55:31 +0000
Subject: [PATCH 554/835] adding easyconfigs: Clang-18.1.0-GCCcore-13.3.0.eb

---
 .../c/Clang/Clang-18.1.0-GCCcore-13.3.0.eb    | 55 +++++++++++++++++++
 1 file changed, 55 insertions(+)
 create mode 100644 easybuild/easyconfigs/c/Clang/Clang-18.1.0-GCCcore-13.3.0.eb

diff --git a/easybuild/easyconfigs/c/Clang/Clang-18.1.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/c/Clang/Clang-18.1.0-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..72c8aa9e801
--- /dev/null
+++ b/easybuild/easyconfigs/c/Clang/Clang-18.1.0-GCCcore-13.3.0.eb
@@ -0,0 +1,55 @@
+##
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+#
+# Copyright:: Copyright 2013-2015 Dmitri Gribenko, Ward Poelmans
+# Authors:: Dmitri Gribenko <gribozavr@gmail.com>
+# Authors:: Ward Poelmans <wpoely86@gmail.com>
+# License:: GPLv2 or later, MIT, three-clause BSD.
+# $Id$
+##
+
+name = 'Clang'
+version = '18.1.0'
+
+homepage = 'https://clang.llvm.org/'
+description = """C, C++, Objective-C compiler, based on LLVM.  Does not
+ include C++ standard library -- use libstdc++ from GCC."""
+
+# Clang also depends on libstdc++ during runtime, but this dependency is
+# already specified as the toolchain.
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+source_urls = ["https://github.com/llvm/llvm-project/releases/download/llvmorg-%(version)s"]
+sources = [
+    'llvm-project-%(version)s.src.tar.xz',
+]
+checksums = ['758a048046ac5024f86c868bb17c631500eed8f8d2677ae6a72ab7ad01602277']
+
+builddependencies = [
+    ('CMake', '3.29.3'),
+    ('Perl', '5.38.2'),
+    # Including Python bindings would require this as a runtime dep
+    # and SWIG as an additional build dep
+    ('Python', '3.12.3'),
+]
+dependencies = [
+    # since Clang is a compiler, binutils is a runtime dependency too
+    ('binutils', '2.42'),
+    ('hwloc', '2.10.0'),
+    ('libxml2', '2.12.7'),
+    ('ncurses', '6.5'),
+    ('GMP', '6.3.0'),
+    ('Z3', '4.13.0'),
+]
+
+# If True, Flang does not currently support building with LLVM exceptions enabled.
+enable_rtti = False
+
+assertions = True
+python_bindings = False
+skip_all_tests = True
+
+llvm_runtimes = ['libunwind', 'libcxx', 'libcxxabi']
+llvm_projects = ['polly', 'lld', 'lldb', 'clang-tools-extra', 'flang']
+
+moduleclass = 'compiler'

From 3fb21c960cb62a987992a7420c280baf6c86d1d9 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Sat, 3 Aug 2024 18:45:04 +0000
Subject: [PATCH 555/835] Update version

---
 ...8.1.0-GCCcore-13.3.0.eb => Clang-18.1.8-GCCcore-13.3.0.eb} | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)
 rename easybuild/easyconfigs/c/Clang/{Clang-18.1.0-GCCcore-13.3.0.eb => Clang-18.1.8-GCCcore-13.3.0.eb} (94%)

diff --git a/easybuild/easyconfigs/c/Clang/Clang-18.1.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/c/Clang/Clang-18.1.8-GCCcore-13.3.0.eb
similarity index 94%
rename from easybuild/easyconfigs/c/Clang/Clang-18.1.0-GCCcore-13.3.0.eb
rename to easybuild/easyconfigs/c/Clang/Clang-18.1.8-GCCcore-13.3.0.eb
index 72c8aa9e801..8b096078c89 100644
--- a/easybuild/easyconfigs/c/Clang/Clang-18.1.0-GCCcore-13.3.0.eb
+++ b/easybuild/easyconfigs/c/Clang/Clang-18.1.8-GCCcore-13.3.0.eb
@@ -9,7 +9,7 @@
 ##
 
 name = 'Clang'
-version = '18.1.0'
+version = '18.1.8'
 
 homepage = 'https://clang.llvm.org/'
 description = """C, C++, Objective-C compiler, based on LLVM.  Does not
@@ -23,7 +23,7 @@ source_urls = ["https://github.com/llvm/llvm-project/releases/download/llvmorg-%
 sources = [
     'llvm-project-%(version)s.src.tar.xz',
 ]
-checksums = ['758a048046ac5024f86c868bb17c631500eed8f8d2677ae6a72ab7ad01602277']
+checksums = ['0b58557a6d32ceee97c8d533a59b9212d87e0fc4d2833924eb6c611247db2f2a']
 
 builddependencies = [
     ('CMake', '3.29.3'),

From 0eecd65cbbcfc8ad1e8ca93acfdd9b5cf3bc7b91 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Sun, 4 Aug 2024 14:07:12 +0000
Subject: [PATCH 556/835] adding easyconfigs:
 alsa-lib-1.2.11-GCCcore-13.2.0.eb, alsa-lib-1.2.11-GCCcore-13.3.0.eb

---
 .../alsa-lib-1.2.11-GCCcore-13.2.0.eb         | 26 +++++++++++++++++++
 .../alsa-lib-1.2.11-GCCcore-13.3.0.eb         | 26 +++++++++++++++++++
 2 files changed, 52 insertions(+)
 create mode 100644 easybuild/easyconfigs/a/alsa-lib/alsa-lib-1.2.11-GCCcore-13.2.0.eb
 create mode 100644 easybuild/easyconfigs/a/alsa-lib/alsa-lib-1.2.11-GCCcore-13.3.0.eb

diff --git a/easybuild/easyconfigs/a/alsa-lib/alsa-lib-1.2.11-GCCcore-13.2.0.eb b/easybuild/easyconfigs/a/alsa-lib/alsa-lib-1.2.11-GCCcore-13.2.0.eb
new file mode 100644
index 00000000000..fd05a43146f
--- /dev/null
+++ b/easybuild/easyconfigs/a/alsa-lib/alsa-lib-1.2.11-GCCcore-13.2.0.eb
@@ -0,0 +1,26 @@
+easyblock = 'ConfigureMake'
+
+name = 'alsa-lib'
+version = '1.2.11'
+
+homepage = 'https://www.alsa-project.org'
+description = """The Advanced Linux Sound Architecture (ALSA) provides audio and MIDI functionality
+ to the Linux operating system."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
+
+source_urls = ['https://www.alsa-project.org/files/pub/lib/']
+sources = [SOURCE_TAR_BZ2]
+checksums = ['9f3f2f69b995f9ad37359072fbc69a3a88bfba081fc83e9be30e14662795bb4d']
+
+dependencies = [('binutils', '2.40')]
+
+configopts = ['--disable-shared --enable-static', '--enable-shared']
+
+sanity_check_paths = {
+    'files': ['bin/aserver', 'include/asoundlib.h',
+              'lib64/libatopology.%s' % SHLIB_EXT, 'lib64/libasound.%s' % SHLIB_EXT, 'lib64/libasound.a'],
+    'dirs': ['include/alsa', 'lib/pkgconfig', 'share'],
+}
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/a/alsa-lib/alsa-lib-1.2.11-GCCcore-13.3.0.eb b/easybuild/easyconfigs/a/alsa-lib/alsa-lib-1.2.11-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..4333348a741
--- /dev/null
+++ b/easybuild/easyconfigs/a/alsa-lib/alsa-lib-1.2.11-GCCcore-13.3.0.eb
@@ -0,0 +1,26 @@
+easyblock = 'ConfigureMake'
+
+name = 'alsa-lib'
+version = '1.2.11'
+
+homepage = 'https://www.alsa-project.org'
+description = """The Advanced Linux Sound Architecture (ALSA) provides audio and MIDI functionality
+ to the Linux operating system."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+source_urls = ['https://www.alsa-project.org/files/pub/lib/']
+sources = [SOURCE_TAR_BZ2]
+checksums = ['9f3f2f69b995f9ad37359072fbc69a3a88bfba081fc83e9be30e14662795bb4d']
+
+dependencies = [('binutils', '2.42')]
+
+configopts = ['--disable-shared --enable-static', '--enable-shared']
+
+sanity_check_paths = {
+    'files': ['bin/aserver', 'include/asoundlib.h',
+              'lib64/libatopology.%s' % SHLIB_EXT, 'lib64/libasound.%s' % SHLIB_EXT, 'lib64/libasound.a'],
+    'dirs': ['include/alsa', 'lib/pkgconfig', 'share'],
+}
+
+moduleclass = 'lib'

From 213a49b799aa3211b9262148a530ad31e8589e0e Mon Sep 17 00:00:00 2001
From: Sebastian Achilles <s.achilles@fz-juelich.de>
Date: Sun, 4 Aug 2024 17:26:15 +0200
Subject: [PATCH 557/835] adding easyconfigs: BioPerl-1.7.8-GCCcore-13.3.0.eb,
 DB-18.1.40-GCCcore-13.3.0.eb, DB_File-1.859-GCCcore-13.3.0.eb,
 XML-LibXML-2.0210-GCCcore-13.3.0.eb, attr-2.5.2-GCCcore-13.3.0.eb

---
 .../a/attr/attr-2.5.2-GCCcore-13.3.0.eb       | 28 ++++++++
 .../b/BioPerl/BioPerl-1.7.8-GCCcore-13.3.0.eb | 58 +++++++++++++++++
 .../d/DB/DB-18.1.40-GCCcore-13.3.0.eb         | 33 ++++++++++
 .../d/DB_File/DB_File-1.859-GCCcore-13.3.0.eb | 31 +++++++++
 .../XML-LibXML-2.0210-GCCcore-13.3.0.eb       | 65 +++++++++++++++++++
 5 files changed, 215 insertions(+)
 create mode 100644 easybuild/easyconfigs/a/attr/attr-2.5.2-GCCcore-13.3.0.eb
 create mode 100644 easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-13.3.0.eb
 create mode 100644 easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-13.3.0.eb
 create mode 100644 easybuild/easyconfigs/d/DB_File/DB_File-1.859-GCCcore-13.3.0.eb
 create mode 100644 easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0210-GCCcore-13.3.0.eb

diff --git a/easybuild/easyconfigs/a/attr/attr-2.5.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/a/attr/attr-2.5.2-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..fcd6d723f16
--- /dev/null
+++ b/easybuild/easyconfigs/a/attr/attr-2.5.2-GCCcore-13.3.0.eb
@@ -0,0 +1,28 @@
+easyblock = 'ConfigureMake'
+
+name = 'attr'
+version = '2.5.2'
+
+homepage = 'https://savannah.nongnu.org/projects/attr'
+
+description = """Commands for Manipulating Filesystem Extended Attributes"""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+source_urls = [GNU_SAVANNAH_SOURCE]
+sources = [SOURCE_TAR_GZ]
+checksums = ['39bf67452fa41d0948c2197601053f48b3d78a029389734332a6309a680c6c87']
+
+builddependencies = [('binutils', '2.42')]
+
+sanity_check_paths = {
+    'files': ['bin/attr', 'bin/getfattr', 'bin/setfattr',
+              'include/%(name)s/attributes.h', 'include/%(name)s/error_context.h',
+              'include/%(name)s/libattr.h', 'lib/libattr.a',
+              'lib/libattr.%s' % SHLIB_EXT],
+    'dirs': ['share'],
+}
+
+sanity_check_commands = ["getfattr --help"]
+
+moduleclass = 'tools'
diff --git a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-13.3.0.eb b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..c6e760f5105
--- /dev/null
+++ b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-13.3.0.eb
@@ -0,0 +1,58 @@
+# easybuild easyconfig
+#
+#  John Dey jfdey@fredhutch.org
+#
+#  Fred Hutchinson Cancer Research Center
+#  Thomas Eylenbosch - Gluo NV 
+
+easyblock = 'PerlModule'
+
+name = 'BioPerl'
+version = '1.7.8'
+
+homepage = 'https://bioperl.org/'
+description = """Bioperl is the product of a community effort to produce Perl code which is useful in biology.
+ Examples include Sequence objects, Alignment objects and database searching objects."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+builddependencies = [('binutils', '2.42')]
+
+dependencies = [
+    ('Perl', '5.38.2'),
+    ('Perl-bundle-CPAN', '5.38.2'),
+    ('XML-LibXML', '2.0210'),
+    ('DB_File', '1.859'),
+]
+
+exts_defaultclass = 'PerlModule'
+exts_filter = ("perldoc -lm %(ext_name)s ", "")
+
+exts_list = [
+    ('XML::Writer', '0.900', {
+        'source_tmpl': 'XML-Writer-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/J/JO/JOSEPHW'],
+        'checksums': ['73c8f5bd3ecf2b350f4adae6d6676d52e08ecc2d7df4a9f089fa68360d400d1f'],
+    }),
+    (name, version, {
+        'source_tmpl': '%(name)s-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/'],
+        'checksums': ['c490a3be7715ea6e4305efd9710e5edab82dabc55fd786b6505b550a30d71738'],
+    }),
+    ('Bio::Procedural', '1.7.4', {
+        'source_tmpl': 'Bio-Procedural-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/'],
+        'checksums': ['d2bd9cfbb091eee2d80ed6cf812ac3813b1c8a1aaca20671037f5f225d31d1da'],
+    }),
+]
+
+modextrapaths = {
+    'PERL5LIB': 'lib/perl5/site_perl/%(perlver)s/',
+}
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['bin', 'lib/perl5/site_perl/%(perlver)s/Bio'],
+}
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-13.3.0.eb b/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..64022827805
--- /dev/null
+++ b/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-13.3.0.eb
@@ -0,0 +1,33 @@
+name = 'DB'
+version = '18.1.40'
+
+homepage = 'https://www.oracle.com/technetwork/products/berkeleydb'
+
+description = """Berkeley DB enables the development of custom data management
+ solutions, without the overhead traditionally associated with such custom
+ projects."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+# use http to allow auto-downloading...
+source_urls = ['http://download.oracle.com/berkeley-db/']
+sources = [SOURCELOWER_TAR_GZ]
+patches = ['%(name)s-%(version)s_fix_doc_install.patch']
+checksums = [
+    '0cecb2ef0c67b166de93732769abdeba0555086d51de1090df325e18ee8da9c8',  # db-18.1.40.tar.gz
+    '441f48568156f72f02a8662998d293cc7edad687604b4f8af722f21c6db2a52d',  # DB-18.1.40_fix_doc_install.patch
+]
+
+builddependencies = [('binutils', '2.42')]
+
+dependencies = [('OpenSSL', '3', '', SYSTEM)]
+
+sanity_check_paths = {
+    'files': ['bin/db_%s' % x for x in ['archive', 'checkpoint', 'convert', 'deadlock', 'dump', 'hotbackup',
+                                        'load', 'log_verify', 'printlog', 'recover', 'replicate', 'stat',
+                                        'tuner', 'upgrade', 'verify']] +
+             ['include/db.h', 'lib/libdb.a', 'lib/libdb.%s' % SHLIB_EXT],
+    'dirs': [],
+}
+
+moduleclass = 'tools'
diff --git a/easybuild/easyconfigs/d/DB_File/DB_File-1.859-GCCcore-13.3.0.eb b/easybuild/easyconfigs/d/DB_File/DB_File-1.859-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..e7120c9c13e
--- /dev/null
+++ b/easybuild/easyconfigs/d/DB_File/DB_File-1.859-GCCcore-13.3.0.eb
@@ -0,0 +1,31 @@
+easyblock = 'PerlModule'
+
+name = 'DB_File'
+version = '1.859'
+
+homepage = 'https://perldoc.perl.org/DB_File.html'
+description = """Perl5 access to Berkeley DB version 1.x."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+source_urls = ['https://www.cpan.org/modules/by-module/DB_File/PMQS']
+sources = [SOURCE_TAR_GZ]
+checksums = ['5674e0d2cd0b060c4d1253670ea022c64d842a55257f9eb8edb19c0f53e2565c']
+
+builddependencies = [
+    ('binutils', '2.42'),
+]
+
+dependencies = [
+    ('Perl', '5.38.2'),
+    ('DB', '18.1.40'),
+]
+
+preconfigopts = 'env DB_FILE_INCLUDE="$EBROOTDB/include" DB_FILE_LIB="$EBROOTDB/lib" '
+
+sanity_check_paths = {
+    'files': ['lib/perl5/site_perl/%(perlver)s/%(arch)s-linux-thread-multi/DB_File.pm'],
+    'dirs': [],
+}
+
+moduleclass = 'data'
diff --git a/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0210-GCCcore-13.3.0.eb b/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0210-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..1d4cbe24543
--- /dev/null
+++ b/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0210-GCCcore-13.3.0.eb
@@ -0,0 +1,65 @@
+# updated toolchain, version, and dependency versions
+# Thomas Eylenbosch 5-Jun-23
+
+easyblock = 'Bundle'
+
+name = 'XML-LibXML'
+version = '2.0210'
+
+homepage = 'https://metacpan.org/pod/distribution/XML-LibXML/LibXML.pod'
+description = "Perl binding for libxml2"
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+builddependencies = [
+    ('binutils', '2.42'),
+    ('pkgconf', '2.2.0'),
+]
+
+dependencies = [
+    ('Perl', '5.38.2'),
+    ('Perl-bundle-CPAN', '5.38.2'),
+    ('libxml2', '2.12.7'),
+]
+
+exts_defaultclass = 'PerlModule'
+exts_filter = ("perldoc -lm %(ext_name)s ", "")
+
+exts_list = [
+    ('File::chdir', '0.1011', {
+        'source_tmpl': 'File-chdir-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'],
+        'checksums': ['31ebf912df48d5d681def74b9880d78b1f3aca4351a0ed1fe3570b8e03af6c79'],
+    }),
+    ('Alien::Base', '2.83', {
+        'source_tmpl': 'Alien-Build-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE/'],
+        'checksums': ['4817270314431350ff397125547f55641dcff98bdde213b9e5efc613f7c8b85a'],
+    }),
+    ('Alien::Build::Plugin::Download::GitLab', '0.01', {
+        'source_tmpl': 'Alien-Build-Plugin-Download-GitLab-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'],
+        'checksums': ['c1f089c8ea152a789909d48a83dbfcf2626f773daf30431c8622582b26aba902'],
+    }),
+    ('Alien::Libxml2', '0.19', {
+        'source_tmpl': 'Alien-Libxml2-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'],
+        'checksums': ['f4a674099bbd5747c0c3b75ead841f3b244935d9ef42ba35368024bd611174c9'],
+    }),
+    ('XML::LibXML', version, {
+        'source_tmpl': 'XML-LibXML-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF/'],
+        'checksums': ['a29bf3f00ab9c9ee04218154e0afc8f799bf23674eb99c1a9ed4de1f4059a48d'],
+    }),
+]
+
+modextrapaths = {
+    'PERL5LIB': 'lib/perl5/site_perl/%(perlver)s/',
+}
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['lib/perl5/site_perl/%(perlver)s/%(arch)s-linux-thread-multi/XML/LibXML'],
+}
+
+moduleclass = 'data'

From 5b6894fecaf6aec24ce80dcd7d49ebc3af771326 Mon Sep 17 00:00:00 2001
From: Sebastian Achilles <s.achilles@fz-juelich.de>
Date: Sun, 4 Aug 2024 17:37:25 +0200
Subject: [PATCH 558/835] adding easyconfigs: archspec-0.2.4-GCCcore-13.3.0.eb

---
 .../archspec/archspec-0.2.4-GCCcore-13.3.0.eb | 27 +++++++++++++++++++
 1 file changed, 27 insertions(+)
 create mode 100644 easybuild/easyconfigs/a/archspec/archspec-0.2.4-GCCcore-13.3.0.eb

diff --git a/easybuild/easyconfigs/a/archspec/archspec-0.2.4-GCCcore-13.3.0.eb b/easybuild/easyconfigs/a/archspec/archspec-0.2.4-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..5a4f3a288e9
--- /dev/null
+++ b/easybuild/easyconfigs/a/archspec/archspec-0.2.4-GCCcore-13.3.0.eb
@@ -0,0 +1,27 @@
+easyblock = 'PythonPackage'
+
+name = 'archspec'
+version = '0.2.4'
+
+homepage = 'https://github.com/archspec/archspec'
+description = "A library for detecting, labeling, and reasoning about microarchitectures"
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+sources = [SOURCE_TAR_GZ]
+checksums = ['eabbae22f315d24cc2ce786a092478ec8e245208c9877fb213c2172a6ecb9302']
+
+builddependencies = [
+    ('binutils', '2.42'),
+    ('poetry', '1.8.3'),
+]
+
+dependencies = [('Python', '3.12.3')]
+
+download_dep_fail = True
+use_pip = True
+sanity_pip_check = True
+
+sanity_check_commands = ["python -c 'from archspec.cpu import host; print(host())'"]
+
+moduleclass = 'tools'

From 4b1ebfb6f72c80a753311f20f22f90504670945b Mon Sep 17 00:00:00 2001
From: Sebastian Achilles <s.achilles@fz-juelich.de>
Date: Sun, 4 Aug 2024 17:39:01 +0200
Subject: [PATCH 559/835] adding easyconfigs: Brunsli-0.1-GCCcore-13.3.0.eb,
 Highway-1.2.0-GCCcore-13.3.0.eb, googletest-1.15.2-GCCcore-13.3.0.eb

---
 .../b/Brunsli/Brunsli-0.1-GCCcore-13.3.0.eb   | 54 +++++++++++++++++++
 .../googletest-1.15.2-GCCcore-13.3.0.eb       | 28 ++++++++++
 .../h/Highway/Highway-1.2.0-GCCcore-13.3.0.eb | 32 +++++++++++
 3 files changed, 114 insertions(+)
 create mode 100644 easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-13.3.0.eb
 create mode 100644 easybuild/easyconfigs/g/googletest/googletest-1.15.2-GCCcore-13.3.0.eb
 create mode 100644 easybuild/easyconfigs/h/Highway/Highway-1.2.0-GCCcore-13.3.0.eb

diff --git a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..d374a07304a
--- /dev/null
+++ b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-13.3.0.eb
@@ -0,0 +1,54 @@
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+# Author: Denis Kristak
+# update: Thomas Hoffmann (EMBL)
+easyblock = 'CMakeMake'
+
+name = 'Brunsli'
+version = '0.1'
+
+homepage = 'https://github.com/google/brunsli/'
+description = """Brunsli is a lossless JPEG repacking library."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+source_urls = ['https://github.com/google/brunsli/archive/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['62762dc740f9fcc9706449c078f12c2a366416486d2882be50a9f201f99ac0bc']
+
+builddependencies = [
+    ('CMake', '3.29.3'),
+    ('binutils', '2.42'),
+]
+
+dependencies = [
+    ('Brotli', '1.1.0'),
+    ('Highway', '1.2.0'),
+]
+
+# skip use of third_party directory, since we provide Brotli via a proper dependency
+preconfigopts = "sed -i 's/add_subdirectory(third_party)//g' ../brunsli-%(version)s/CMakeLists.txt && "
+preconfigopts += "sed -i 's/\\(brotli...\\)-static/\\1/g' ../brunsli-%(version)s/brunsli.cmake && "
+
+configopts = '-DCMAKE_CXX_FLAGS="$CXXFLAGS -lbrotlienc -lbrotlidec -lbrotlicommon" '
+
+# make sure that libraries end up in <prefix>/lib (not lib64)
+configopts += "-DCMAKE_INSTALL_LIBDIR=lib "
+
+buildopts = "BROTLI_DIR=$EBROOTBROTLI BROTLI_INCLUDE=$EBROOTBROTLI/include"
+
+# also install dbrunsli binary and missing libraries
+postinstallcmds = [
+    "mkdir %(installdir)s/bin",
+    "cp dbrunsli %(installdir)s/bin/",
+    "cp libbrunsli*.a %(installdir)s/lib/",
+    "cp libbrunsli*.%s %%(installdir)s/lib/" % SHLIB_EXT,
+]
+
+sanity_check_paths = {
+    'files': ['bin/dbrunsli'],
+    'dirs': ['include/brunsli', 'lib'],
+}
+
+sanity_check_commands = ['dbrunsli 2>&1 | grep Usage']
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/g/googletest/googletest-1.15.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/googletest/googletest-1.15.2-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..16b74bdae1b
--- /dev/null
+++ b/easybuild/easyconfigs/g/googletest/googletest-1.15.2-GCCcore-13.3.0.eb
@@ -0,0 +1,28 @@
+easyblock = 'CMakeMake'
+
+name = 'googletest'
+version = '1.15.2'
+
+homepage = 'https://github.com/google/googletest'
+description = "Google's framework for writing C++ tests on a variety of platforms"
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+source_urls = ['https://github.com/google/googletest/archive/refs/tags/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['7b42b4d6ed48810c5362c265a17faebe90dc2373c885e5216439d37927f02926']
+
+builddependencies = [
+    ('binutils', '2.42'),
+    ('CMake', '3.29.3'),
+]
+# build twice, once for static, once for shared libraries
+configopts = ['', ' -DBUILD_SHARED_LIBS=ON ']
+
+sanity_check_paths = {
+    'files': ['lib/lib%s.%s' % (local_lib, local_ext) for local_lib in ['gmock', 'gmock_main', 'gtest', 'gtest_main']
+              for local_ext in ['a', SHLIB_EXT]],
+    'dirs': ['include/gmock', 'include/gtest'],
+}
+
+moduleclass = 'tools'
diff --git a/easybuild/easyconfigs/h/Highway/Highway-1.2.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/h/Highway/Highway-1.2.0-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..27739befe52
--- /dev/null
+++ b/easybuild/easyconfigs/h/Highway/Highway-1.2.0-GCCcore-13.3.0.eb
@@ -0,0 +1,32 @@
+easyblock = 'CMakeMake'
+
+name = 'Highway'
+version = '1.2.0'
+
+homepage = 'https://github.com/google/highway'
+
+description = """Highway is a C++ library for SIMD (Single Instruction, Multiple Data), i.e. applying the same
+operation to 'lanes'."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+source_urls = ['https://github.com/google/highway/archive/refs/tags/']
+sources = ['%(version)s.tar.gz']
+checksums = ['7e0be78b8318e8bdbf6fa545d2ecb4c90f947df03f7aadc42c1967f019e63343']
+
+builddependencies = [
+    ('binutils', '2.42'),
+    ('CMake', '3.29.3'),
+    ('googletest', '1.15.2'),
+]
+
+configopts = "-DHWY_SYSTEM_GTEST=ON"
+
+runtest = "test"
+
+sanity_check_paths = {
+    'files': ['lib/libhwy.a'],
+    'dirs': ['include/hwy'],
+}
+
+moduleclass = 'lib'

From 6c32cbbfcdd2a63cd20b4ff7b461a709a2a2e35f Mon Sep 17 00:00:00 2001
From: Sebastian Achilles <s.achilles@fz-juelich.de>
Date: Sun, 4 Aug 2024 17:40:39 +0200
Subject: [PATCH 560/835] adding easyconfigs: CFITSIO-4.4.1-GCCcore-13.3.0.eb,
 CGAL-5.6.1-GCCcore-13.3.0.eb, Coreutils-9.5-GCCcore-13.3.0.eb,
 cppy-1.2.1-GCCcore-13.3.0.eb

---
 .../c/CFITSIO/CFITSIO-4.4.1-GCCcore-13.3.0.eb | 43 +++++++++++++++++++
 .../c/CGAL/CGAL-5.6.1-GCCcore-13.3.0.eb       | 26 +++++++++++
 .../Coreutils/Coreutils-9.5-GCCcore-13.3.0.eb | 28 ++++++++++++
 .../c/cppy/cppy-1.2.1-GCCcore-13.3.0.eb       | 32 ++++++++++++++
 4 files changed, 129 insertions(+)
 create mode 100644 easybuild/easyconfigs/c/CFITSIO/CFITSIO-4.4.1-GCCcore-13.3.0.eb
 create mode 100644 easybuild/easyconfigs/c/CGAL/CGAL-5.6.1-GCCcore-13.3.0.eb
 create mode 100644 easybuild/easyconfigs/c/Coreutils/Coreutils-9.5-GCCcore-13.3.0.eb
 create mode 100644 easybuild/easyconfigs/c/cppy/cppy-1.2.1-GCCcore-13.3.0.eb

diff --git a/easybuild/easyconfigs/c/CFITSIO/CFITSIO-4.4.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-4.4.1-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..eaa1b0866ac
--- /dev/null
+++ b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-4.4.1-GCCcore-13.3.0.eb
@@ -0,0 +1,43 @@
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+# Author: Denis Kristak
+easyblock = 'ConfigureMake'
+
+name = 'CFITSIO'
+version = '4.4.1'
+
+homepage = 'https://heasarc.gsfc.nasa.gov/fitsio/'
+description = """CFITSIO is a library of C and Fortran subroutines for reading and writing data files in
+FITS (Flexible Image Transport System) data format."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://heasarc.gsfc.nasa.gov/FTP/software/fitsio/c/']
+sources = [SOURCELOWER_TAR_GZ]
+patches = ['%(name)s-3.48_install_test_data.patch']
+checksums = [
+    {'cfitsio-4.4.1.tar.gz': '66a1dc3f21800f9eeabd9eac577b91fcdd9aabba678fbba3b8527319110d1d25'},
+    {'CFITSIO-3.48_install_test_data.patch': 'dbf16f857f133468fc1e6a793c6e89fca66d54796593e03606f2722a2a980c0c'},
+]
+
+builddependencies = [
+    ('binutils', '2.42'),
+]
+# curl for HTTPs support
+dependencies = [
+    ('cURL', '8.7.1'),
+]
+
+# make would create just static libcfitsio.a.
+# Let's create dynamic lib and testprog too.
+buildopts = "&& make shared && make testprog"
+
+
+sanity_check_paths = {
+    'files': ['lib/libcfitsio.a', 'lib/libcfitsio.%s' % SHLIB_EXT],
+    'dirs': ['include'],
+}
+
+sanity_check_commands = ['cd %(installdir)s/share && testprog']
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-5.6.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/c/CGAL/CGAL-5.6.1-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..01aa21c6311
--- /dev/null
+++ b/easybuild/easyconfigs/c/CGAL/CGAL-5.6.1-GCCcore-13.3.0.eb
@@ -0,0 +1,26 @@
+easyblock = 'CMakeMake'
+name = 'CGAL'
+version = '5.6.1'
+
+homepage = 'https://www.cgal.org/'
+description = """The goal of the CGAL Open Source Project is to provide easy access to efficient
+ and reliable geometric algorithms in the form of a C++ library."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+toolchainopts = {'strict': True}
+
+source_urls = ['https://github.com/CGAL/cgal/releases/download/v%(version)s/']
+sources = [SOURCE_TAR_XZ]
+checksums = ['cdb15e7ee31e0663589d3107a79988a37b7b1719df3d24f2058545d1bcdd5837']
+
+builddependencies = [
+    ('CMake', '3.29.3'),
+    ('binutils', '2.42'),
+]
+
+sanity_check_paths = {
+    'files': ['include/CGAL/Simple_cartesian.h'],
+    'dirs': ['include/CGAL', 'lib/cmake/CGAL'],
+}
+
+moduleclass = 'numlib'
diff --git a/easybuild/easyconfigs/c/Coreutils/Coreutils-9.5-GCCcore-13.3.0.eb b/easybuild/easyconfigs/c/Coreutils/Coreutils-9.5-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..60e5009dc91
--- /dev/null
+++ b/easybuild/easyconfigs/c/Coreutils/Coreutils-9.5-GCCcore-13.3.0.eb
@@ -0,0 +1,28 @@
+easyblock = 'ConfigureMake'
+
+name = "Coreutils"
+version = "9.5"
+
+homepage = 'https://www.gnu.org/software/coreutils/'
+description = """The GNU Core Utilities are the basic file, shell and text
+manipulation utilities of the GNU operating system. These are
+the core utilities which are expected to exist on every
+operating system.
+"""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+toolchainopts = {'optarch': True, 'pic': True}
+
+source_urls = [GNU_SOURCE]
+sources = [SOURCELOWER_TAR_XZ]
+
+checksums = ['cd328edeac92f6a665de9f323c93b712af1858bc2e0d88f3f7100469470a1b8a']
+
+builddependencies = [('binutils', '2.42')]
+
+sanity_check_paths = {
+    'files': ['bin/sort', 'bin/echo', 'bin/du', 'bin/date', 'bin/true'],
+    'dirs': []
+}
+
+moduleclass = 'tools'
diff --git a/easybuild/easyconfigs/c/cppy/cppy-1.2.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/c/cppy/cppy-1.2.1-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..3043857d925
--- /dev/null
+++ b/easybuild/easyconfigs/c/cppy/cppy-1.2.1-GCCcore-13.3.0.eb
@@ -0,0 +1,32 @@
+easyblock = 'PythonPackage'
+
+name = 'cppy'
+version = '1.2.1'
+
+homepage = "https://github.com/nucleic/cppy"
+description = """A small C++ header library which makes it easier to write
+Python extension modules. The primary feature is a PyObject smart pointer
+which automatically handles reference counting and provides convenience
+methods for performing common object operations."""
+
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+builddependencies = [('binutils', '2.42')]
+
+dependencies = [
+    ('Python', '3.12.3'),
+]
+
+sources = ['%(name)s-%(version)s.tar.gz']
+patches = ['cppy-1.2.1-manual_version.patch']
+checksums = [
+    {'cppy-1.2.1.tar.gz': '83b43bf17b1085ac15c5debdb42154f138b928234b21447358981f69d0d6fe1b'},
+    {'cppy-1.2.1-manual_version.patch': '048aa0a86fd2e99c6896443b07ec83eaa369724297f639ef74c65c404b8f288f'},
+]
+
+download_dep_fail = True
+sanity_pip_check = True
+use_pip = True
+
+moduleclass = 'tools'

From 16ca0ddc6fce2b37c11d740470ee462c8c319f2e Mon Sep 17 00:00:00 2001
From: Sebastian Achilles <s.achilles@fz-juelich.de>
Date: Sun, 4 Aug 2024 17:43:47 +0200
Subject: [PATCH 561/835] adding easyconfigs: ZeroMQ-4.3.5-GCCcore-13.3.0.eb,
 OpenPGM-5.2.122-GCCcore-13.3.0.eb, libsodium-1.0.20-GCCcore-13.3.0.eb

---
 .../libsodium-1.0.20-GCCcore-13.3.0.eb        | 33 ++++++++++++++
 .../OpenPGM/OpenPGM-5.2.122-GCCcore-13.3.0.eb | 44 +++++++++++++++++++
 .../z/ZeroMQ/ZeroMQ-4.3.5-GCCcore-13.3.0.eb   | 40 +++++++++++++++++
 3 files changed, 117 insertions(+)
 create mode 100644 easybuild/easyconfigs/l/libsodium/libsodium-1.0.20-GCCcore-13.3.0.eb
 create mode 100644 easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-13.3.0.eb
 create mode 100644 easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.3.5-GCCcore-13.3.0.eb

diff --git a/easybuild/easyconfigs/l/libsodium/libsodium-1.0.20-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.20-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..e98d28304a8
--- /dev/null
+++ b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.20-GCCcore-13.3.0.eb
@@ -0,0 +1,33 @@
+easyblock = 'ConfigureMake'
+
+name = 'libsodium'
+version = '1.0.20'
+
+homepage = 'https://doc.libsodium.org/'
+description = """
+ Sodium is a modern, easy-to-use software library for encryption, decryption,
+ signatures, password hashing and more.
+"""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+toolchainopts = {'pic': True}
+
+source_urls = [
+    'https://download.%(name)s.org/%(name)s/releases/',
+    'https://download.%(name)s.org/%(name)s/releases/old/',
+    'https://download.%(name)s.org/%(name)s/releases/old/unsupported/',
+]
+sources = [SOURCE_TAR_GZ]
+checksums = ['ebb65ef6ca439333c2bb41a0c1990587288da07f6c7fd07cb3a18cc18d30ce19']
+
+builddependencies = [
+    ('binutils', '2.42'),
+]
+
+
+sanity_check_paths = {
+    'files': ['include/sodium.h', 'lib/%%(name)s.%s' % SHLIB_EXT, 'lib/%(name)s.a'],
+    'dirs': ['include/sodium', 'lib/pkgconfig'],
+}
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-13.3.0.eb b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..cbf6bca94d7
--- /dev/null
+++ b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-13.3.0.eb
@@ -0,0 +1,44 @@
+easyblock = 'ConfigureMake'
+
+name = 'OpenPGM'
+version = '5.2.122'
+
+homepage = 'https://code.google.com/p/openpgm/'
+description = """
+ OpenPGM is an open source implementation of the Pragmatic General Multicast
+ (PGM) specification in RFC 3208 available at www.ietf.org. PGM is a reliable
+ and scalable multicast protocol that enables receivers to detect loss, request
+ retransmission of lost data, or notify an application of unrecoverable loss.
+ PGM is a receiver-reliable protocol, which means the receiver is responsible
+ for ensuring all data is received, absolving the sender of reception
+ responsibility.
+"""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/%(namelower)s/']
+sources = ['libpgm-%(version)s.tar.gz']
+patches = [
+    '%(name)s-%(version)s-pkgconfig_includes.patch',
+    '%(name)s-%(version)s-python3-compliant.patch',
+]
+checksums = [
+    '6b895f550b95284dcde7189b01e04a9a1c1f94579af31b1eebd32c2207a1ba2c',  # libpgm-%(version)s.tar.gz
+    '4a9fc7fbb6e73e325639a895cd19c1ac6918b575f715c057caa01f826de40114',  # %(name)s-%(version)s-pkgconfig_includes.patch
+    'a3bf6b4127473d287d72767b0335b8705940e56ffbccc8d4d3bdbf23a2fc8618',  # %(name)s-%(version)s-python3-compliant.patch
+]
+
+builddependencies = [
+    ('binutils', '2.42'),
+    ('Python', '3.12.3'),
+]
+
+start_dir = 'pgm'
+
+sanity_check_paths = {
+    'files': ['lib/libpgm.%s' % SHLIB_EXT, 'lib/libpgm.a'],
+    'dirs': ['include'],
+}
+
+moduleclass = 'system'
diff --git a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.3.5-GCCcore-13.3.0.eb b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.3.5-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..98db227b9aa
--- /dev/null
+++ b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.3.5-GCCcore-13.3.0.eb
@@ -0,0 +1,40 @@
+easyblock = 'ConfigureMake'
+
+name = 'ZeroMQ'
+version = '4.3.5'
+
+homepage = 'https://www.zeromq.org/'
+description = """ZeroMQ looks like an embeddable networking library but acts like a concurrency framework.
+ It gives you sockets that carry atomic messages across various transports like in-process,
+ inter-process, TCP, and multicast. You can connect sockets N-to-N with patterns like fanout,
+ pub-sub, task distribution, and request-reply. It's fast enough to be the fabric for clustered
+ products. Its asynchronous I/O model gives you scalable multicore applications, built as asynchronous
+ message-processing tasks. It has a score of language APIs and runs on most operating systems."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+source_urls = ['https://github.com/%(namelower)s/libzmq/releases/download/v%(version)s/']
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['6653ef5910f17954861fe72332e68b03ca6e4d9c7160eb3a8de5a5a913bfab43']
+
+builddependencies = [
+    ('binutils', '2.42'),
+    ('pkgconf', '2.2.0'),
+]
+dependencies = [
+    ('OpenPGM', '5.2.122'),
+    ('libsodium', '1.0.20'),
+    ('util-linux', '2.40'),
+]
+
+# Compialtion warnings in GCC 11, cf. https://github.com/zeromq/libzmq/issues/4178
+# Needto disable warnings as errors.
+configopts = "--with-pic --with-pgm --with-libsodium --disable-Werror"
+
+
+sanity_check_paths = {
+    'files': ['lib/libzmq.%s' % SHLIB_EXT, 'lib/libzmq.a'],
+    'dirs': ['include', 'lib'],
+}
+
+moduleclass = 'devel'

From 70039b53fe68cd50ae1ba6d5b78e496d2e2bb949 Mon Sep 17 00:00:00 2001
From: Sebastian Achilles <s.achilles@fz-juelich.de>
Date: Sun, 4 Aug 2024 17:50:09 +0200
Subject: [PATCH 562/835] adding easyconfigs: APR-1.7.4-GCCcore-13.3.0.eb,
 APR-util-1.6.3-GCCcore-13.3.0.eb

---
 .../APR-util/APR-util-1.6.3-GCCcore-13.3.0.eb | 32 +++++++++++++++++++
 .../a/APR/APR-1.7.4-GCCcore-13.3.0.eb         | 22 +++++++++++++
 2 files changed, 54 insertions(+)
 create mode 100644 easybuild/easyconfigs/a/APR-util/APR-util-1.6.3-GCCcore-13.3.0.eb
 create mode 100644 easybuild/easyconfigs/a/APR/APR-1.7.4-GCCcore-13.3.0.eb

diff --git a/easybuild/easyconfigs/a/APR-util/APR-util-1.6.3-GCCcore-13.3.0.eb b/easybuild/easyconfigs/a/APR-util/APR-util-1.6.3-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..fc5f92c2b70
--- /dev/null
+++ b/easybuild/easyconfigs/a/APR-util/APR-util-1.6.3-GCCcore-13.3.0.eb
@@ -0,0 +1,32 @@
+easyblock = 'ConfigureMake'
+
+name = 'APR-util'
+version = '1.6.3'
+
+homepage = 'https://apr.apache.org/'
+description = "Apache Portable Runtime (APR) util libraries."
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+source_urls = ['https://archive.apache.org/dist/apr/']
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['2b74d8932703826862ca305b094eef2983c27b39d5c9414442e9976a9acf1983']
+
+builddependencies = [('binutils', '2.42')]
+
+dependencies = [
+    ('APR', '1.7.4'),
+    ('SQLite', '3.45.3'),
+    ('expat', '2.6.2'),
+]
+
+configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config --with-sqlite3=$EBROOTSQLITE --with-expat=$EBROOTEXPAT "
+
+sanity_check_paths = {
+    'files': ["bin/apu-1-config", "lib/libaprutil-1.%s" % SHLIB_EXT, "lib/libaprutil-1.a"],
+    'dirs': ["include/apr-1"],
+}
+
+parallel = 1
+
+moduleclass = 'tools'
diff --git a/easybuild/easyconfigs/a/APR/APR-1.7.4-GCCcore-13.3.0.eb b/easybuild/easyconfigs/a/APR/APR-1.7.4-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..8ac5ed02a98
--- /dev/null
+++ b/easybuild/easyconfigs/a/APR/APR-1.7.4-GCCcore-13.3.0.eb
@@ -0,0 +1,22 @@
+easyblock = 'ConfigureMake'
+
+name = 'APR'
+version = '1.7.4'
+
+homepage = 'https://apr.apache.org/'
+description = "Apache Portable Runtime (APR) libraries."
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+source_urls = ['https://archive.apache.org/dist/apr/']
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['a4137dd82a185076fa50ba54232d920a17c6469c30b0876569e1c2a05ff311d9']
+
+builddependencies = [('binutils', '2.42')]
+
+sanity_check_paths = {
+    'files': ["bin/apr-1-config", "lib/libapr-1.%s" % SHLIB_EXT, "lib/libapr-1.a"],
+    'dirs': ["include/apr-1"],
+}
+
+moduleclass = 'tools'

From df6c4698a143d25f1b33a335e22bfd3e745ae10f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Petr=20Kr=C3=A1l?= <petr@inuits.eu>
Date: Mon, 5 Aug 2024 11:34:25 +0200
Subject: [PATCH 563/835] adding easyconfigs:
 yelp-tools-42.1-GCCcore-12.3.0.eb, yelp-xsl-42.1-GCCcore-12.3.0.eb,
 mallard-ducktype-1.0.2-GCCcore-12.3.0.eb

---
 .../mallard-ducktype-1.0.2-GCCcore-12.3.0.eb  | 24 +++++++++++
 .../yelp-tools-42.1-GCCcore-12.3.0.eb         | 43 +++++++++++++++++++
 .../yelp-xsl/yelp-xsl-42.1-GCCcore-12.3.0.eb  | 36 ++++++++++++++++
 3 files changed, 103 insertions(+)
 create mode 100644 easybuild/easyconfigs/m/mallard-ducktype/mallard-ducktype-1.0.2-GCCcore-12.3.0.eb
 create mode 100644 easybuild/easyconfigs/y/yelp-tools/yelp-tools-42.1-GCCcore-12.3.0.eb
 create mode 100644 easybuild/easyconfigs/y/yelp-xsl/yelp-xsl-42.1-GCCcore-12.3.0.eb

diff --git a/easybuild/easyconfigs/m/mallard-ducktype/mallard-ducktype-1.0.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/m/mallard-ducktype/mallard-ducktype-1.0.2-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..2daef2a4ffd
--- /dev/null
+++ b/easybuild/easyconfigs/m/mallard-ducktype/mallard-ducktype-1.0.2-GCCcore-12.3.0.eb
@@ -0,0 +1,24 @@
+easyblock = 'PythonPackage'
+
+name = 'mallard-ducktype'
+version = '1.0.2'
+
+homepage = 'https://github.com/projectmallard/mallard-ducktype'
+description = """Parser for the lightweight Ducktype syntax for Mallard"""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+sources = ['mallard_ducktype-%(version)s-py3-none-any.whl']
+checksums = ['90c2d9e40934c634f3e83e0758285e2803f62c2c5db405702af2f5884e1a2918']
+
+dependencies = [
+    ('Python', '3.11.3'),
+]
+
+options = {'modulename': 'mallard.ducktype'}
+
+download_dep_fail = True
+use_pip = True
+sanity_pip_check = True
+
+moduleclass = 'tools'
diff --git a/easybuild/easyconfigs/y/yelp-tools/yelp-tools-42.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/y/yelp-tools/yelp-tools-42.1-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..b6b4f25ccf5
--- /dev/null
+++ b/easybuild/easyconfigs/y/yelp-tools/yelp-tools-42.1-GCCcore-12.3.0.eb
@@ -0,0 +1,43 @@
+easyblock = 'MesonNinja'
+
+name = 'yelp-tools'
+version = '42.1'
+
+homepage = 'https://gitlab.gnome.org/GNOME/yelp-tools'
+description = """yelp-tools is a collection of scripts and build utilities to help create,
+manage, and publish documentation for Yelp and the web. Most of the heavy
+lifting is done by packages like yelp-xsl and itstool. This package just
+wraps things up in a developer-friendly way."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+source_urls = ['https://gitlab.gnome.org/GNOME/yelp-tools/-/archive/%(version)s/']
+sources = [SOURCE_TAR_GZ]
+checksums = ['4776766816aaa4fff5a9be7229d03e2444fca2f60a11f645c6171abe8bb73925']
+
+builddependencies = [
+    ('binutils', '2.40'),
+    ('Meson', '1.1.1'),
+    ('Ninja', '1.11.1'),
+    ('CMake', '3.26.3'),
+]
+
+dependencies = [
+    ('yelp-xsl', '42.1'),
+    ('ITSTool', '2.0.7'),
+    ('libxml2', '2.11.4'),
+    # docbook-xsl ?
+    ('mallard-ducktype', '1.0.2'),
+    ('lxml', '4.9.2'),
+]
+
+sanity_check_paths = {
+    'files': [
+        'bin/yelp-build',
+        'bin/yelp-check',
+        'bin/yelp-new',
+    ],
+    'dirs': ['share/%(name)s'],
+}
+
+moduleclass = 'tools'
diff --git a/easybuild/easyconfigs/y/yelp-xsl/yelp-xsl-42.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/y/yelp-xsl/yelp-xsl-42.1-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..60f61b5262d
--- /dev/null
+++ b/easybuild/easyconfigs/y/yelp-xsl/yelp-xsl-42.1-GCCcore-12.3.0.eb
@@ -0,0 +1,36 @@
+easyblock = 'ConfigureMake'
+
+name = 'yelp-xsl'
+version = '42.1'
+
+homepage = "https://gitlab.gnome.org/GNOME/yelp-xslg"
+description = """yelp-xsl is a collection of programs and data files to help you build, maintain,
+ and distribute documentation. It provides XSLT stylesheets that can be built upon for help
+ viewers and publishing systems. These stylesheets output JavaScript and CSS content,
+ and reference images provided by yelp-xsl. This package also redistributes copies
+ of the jQuery and jQuery.Syntax JavaScript libraries.
+"""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+source_urls = ['https://gitlab.gnome.org/GNOME/yelp-xsl/-/archive/%(version)s/']
+sources = [SOURCE_TAR_GZ]
+checksums = ['00f3ee8d9fa048d80063cc09477d24a09349e35c58ffdf9ecea253a4ca882068']
+
+builddependencies = [
+    ('binutils', '2.40'),
+    ('ITSTool', '2.0.7'),
+    ('gettext', '0.21.1'),
+]
+
+preconfigopts = 'NOCONFIGURE=1 ./autogen.sh && '
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': [
+        'share/pkgconfig',
+        'share/%(name)s',
+    ]
+}
+
+moduleclass = 'data'

From 5de3b4f6be02fcf6f142202ddd461ae8c7ed5527 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Petr=20Kr=C3=A1l?= <petr@inuits.eu>
Date: Mon, 5 Aug 2024 11:36:06 +0200
Subject: [PATCH 564/835] adding easyconfigs: MariaDB-11.6.0-GCC-12.3.0.eb,
 Judy-1.0.5-GCCcore-12.3.0.eb

---
 .../j/Judy/Judy-1.0.5-GCCcore-12.3.0.eb       | 34 ++++++++++
 .../m/MariaDB/MariaDB-11.6.0-GCC-12.3.0.eb    | 65 +++++++++++++++++++
 2 files changed, 99 insertions(+)
 create mode 100644 easybuild/easyconfigs/j/Judy/Judy-1.0.5-GCCcore-12.3.0.eb
 create mode 100644 easybuild/easyconfigs/m/MariaDB/MariaDB-11.6.0-GCC-12.3.0.eb

diff --git a/easybuild/easyconfigs/j/Judy/Judy-1.0.5-GCCcore-12.3.0.eb b/easybuild/easyconfigs/j/Judy/Judy-1.0.5-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..183e8e08ea4
--- /dev/null
+++ b/easybuild/easyconfigs/j/Judy/Judy-1.0.5-GCCcore-12.3.0.eb
@@ -0,0 +1,34 @@
+easyblock = 'ConfigureMake'
+
+name = 'Judy'
+version = '1.0.5'
+
+homepage = 'http://judy.sourceforge.net/'
+description = "A C library that implements a dynamic array."
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+source_urls = ['http://downloads.sourceforge.net/judy']
+sources = ['%(name)s-%(version)s.tar.gz']
+patches = ['Judy-1.0.5_parallel-make.patch']  # fix Make dependencies, so parallel build also works
+
+builddependencies = [
+    ('Autotools', '20220317'),
+    ('binutils', '2.40'),
+]
+checksums = [
+    'd2704089f85fdb6f2cd7e77be21170ced4b4375c03ef1ad4cf1075bd414a63eb',  # Judy-1.0.5.tar.gz
+    '14c2eba71088f3db9625dc4605c6d7183d72412d75ef6c9fd9b95186165cf009',  # Judy-1.0.5_parallel-make.patch
+]
+
+preconfigopts = "sed -i 's/AM_CONFIG_HEADER/AC_CONFIG_HEADERS/g' configure.ac && "
+preconfigopts += "autoreconf -i && "
+
+configopts = '--enable-shared --enable-static'
+
+sanity_check_paths = {
+    'files': ["include/%(name)s.h", "lib/lib%(name)s.a", "lib/lib%(name)s.la", "lib/lib%%(name)s.%s" % SHLIB_EXT],
+    'dirs': ["share/man"]
+}
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/m/MariaDB/MariaDB-11.6.0-GCC-12.3.0.eb b/easybuild/easyconfigs/m/MariaDB/MariaDB-11.6.0-GCC-12.3.0.eb
new file mode 100644
index 00000000000..35743343440
--- /dev/null
+++ b/easybuild/easyconfigs/m/MariaDB/MariaDB-11.6.0-GCC-12.3.0.eb
@@ -0,0 +1,65 @@
+easyblock = 'CMakeMake'
+
+name = 'MariaDB'
+version = '11.6.0'
+
+homepage = 'https://mariadb.org/'
+description = """MariaDB is an enhanced, drop-in replacement for MySQL.
+Included engines: myISAM, Aria, InnoDB, RocksDB, TokuDB, OQGraph, Mroonga."""
+
+toolchain = {'name': 'GCC', 'version': '12.3.0'}
+
+source_urls = [
+    'https://archive.mariadb.org/mariadb-%(version)s/source/',
+    'http://ftp.hosteurope.de/mirror/archive.mariadb.org/mariadb-%(version)s/source',
+]
+sources = [SOURCELOWER_TAR_GZ]
+patches = ['MariaDB-10.1.13-link-rt-for-jemalloc.patch']
+checksums = [
+    {'mariadb-11.6.0.tar.gz': '8fd5b593aee3920eb434c37ec44779d565fe96ef7dfd6b35a646fe7221103e11'},
+    {'MariaDB-10.1.13-link-rt-for-jemalloc.patch': '8295837e623f6c782e1d64b00e0877ea98cce4bf8846755bb86c8a7732797c19'},
+]
+
+builddependencies = [
+    ('CMake', '3.26.3'),
+    ('libaio', '0.3.113'),
+]
+
+dependencies = [
+    ('ncurses', '6.4'),
+    ('zlib', '1.2.13'),
+    ('LZO', '2.10'),        # optional
+    ('lz4', '1.9.4'),       # optional
+    ('XZ', '5.4.2'),        # optional
+    ('jemalloc', '5.3.0'),  # optional
+    ('snappy', '1.1.10'),    # needed by RocksDB; optional for InnoDB
+    ('libxml2', '2.11.4'),  # needed by Connect XML
+    ('Boost', '1.82.0'),    # needed by OQGraph
+    ('Judy', '1.0.5'),      # needed by OQGraph
+    ('PCRE2', '10.42'),
+    ('OpenSSL', '1.1', '', SYSTEM),     # runtime dep for mysql and PCRE2 for mysqltest
+]
+
+configopts = "-DCMAKE_SHARED_LINKER_FLAGS='-fuse-ld=bfd' "  # Linking fails with default gold linker
+configopts += "-DMYSQL_MAINTAINER_MODE=OFF "  # disabled to not treat warnings as errors (-Werror)
+configopts += "-DWITH_PCRE=auto "  # External download sometimes fails so we build PCRE2 directly.
+configopts += "-DWITH_ZLIB=system "
+configopts += "-DWITH_EMBEDDED_SERVER=ON "  # for libmysqld.so & co
+configopts += "-DWITH_SAFEMALLOC=OFF "  # Disable memory debugger with jemalloc
+
+sanity_check_commands = ["mysql --help", "mysqltest --help"]
+
+sanity_check_paths = {
+    'files': ['bin/mysql', 'bin/mysqld_safe', 'lib/libmysqlclient.%s' % SHLIB_EXT, 'lib/libmysqld.%s' % SHLIB_EXT,
+              'lib/plugin/ha_connect.%s' % SHLIB_EXT, 'lib/plugin/ha_rocksdb.%s' % SHLIB_EXT,
+              'lib/plugin/ha_oqgraph.%s' % SHLIB_EXT, 'scripts/mysql_install_db'],
+    'dirs': ['include', 'share'],
+}
+
+modextrapaths = {'PATH': 'scripts'}
+
+# Ensure that jemalloc does not use transparent hugepages.
+# Database workloads with THP can cause memory bloat, potentially hiting OOM errors.
+modextravars = {'MALLOC_CONF': 'thp:never'}
+
+moduleclass = 'data'

From 680924ef2da4ff2bdb2d1cfccbd993cc590353a8 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Petr=20Kr=C3=A1l?= <petr@inuits.eu>
Date: Mon, 5 Aug 2024 12:20:59 +0200
Subject: [PATCH 565/835] add missing build dependency

---
 .../mallard-ducktype/mallard-ducktype-1.0.2-GCCcore-12.3.0.eb | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/easybuild/easyconfigs/m/mallard-ducktype/mallard-ducktype-1.0.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/m/mallard-ducktype/mallard-ducktype-1.0.2-GCCcore-12.3.0.eb
index 2daef2a4ffd..65102800699 100644
--- a/easybuild/easyconfigs/m/mallard-ducktype/mallard-ducktype-1.0.2-GCCcore-12.3.0.eb
+++ b/easybuild/easyconfigs/m/mallard-ducktype/mallard-ducktype-1.0.2-GCCcore-12.3.0.eb
@@ -11,6 +11,10 @@ toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
 sources = ['mallard_ducktype-%(version)s-py3-none-any.whl']
 checksums = ['90c2d9e40934c634f3e83e0758285e2803f62c2c5db405702af2f5884e1a2918']
 
+builddependencies = [
+    ('binutils', '2.40'),
+]
+
 dependencies = [
     ('Python', '3.11.3'),
 ]

From 22b46bc91267cfbc15dc26fb44f37b9fc90ee75e Mon Sep 17 00:00:00 2001
From: Thomas Hayward-Schneider <thomas.hayward@ipp.mpg.de>
Date: Mon, 5 Aug 2024 13:42:42 +0200
Subject: [PATCH 566/835] Szip: Update source and homepage URLs

---
 easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-10.2.0.eb | 4 ++--
 easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-10.3.0.eb | 4 ++--
 easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-11.2.0.eb | 4 ++--
 easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-11.3.0.eb | 4 ++--
 easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-12.2.0.eb | 4 ++--
 easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-12.3.0.eb | 4 ++--
 easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-13.2.0.eb | 4 ++--
 easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-6.3.0.eb  | 4 ++--
 easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-6.4.0.eb  | 4 ++--
 easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-7.3.0.eb  | 4 ++--
 easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-8.2.0.eb  | 4 ++--
 easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-8.3.0.eb  | 4 ++--
 easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-9.3.0.eb  | 4 ++--
 13 files changed, 26 insertions(+), 26 deletions(-)

diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-10.2.0.eb
index 88e067c36e8..576e48c80b4 100644
--- a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-10.2.0.eb
+++ b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-10.2.0.eb
@@ -3,7 +3,7 @@ easyblock = 'ConfigureMake'
 name = 'Szip'
 version = '2.1.1'
 
-homepage = 'https://www.hdfgroup.org/doc_resource/SZIP/'
+homepage = 'https://support.hdfgroup.org/doc_resource/SZIP/'
 
 description = """
  Szip compression software, providing lossless compression of scientific data
@@ -12,7 +12,7 @@ description = """
 toolchain = {'name': 'GCCcore', 'version': '10.2.0'}
 toolchainopts = {'pic': True}
 
-source_urls = ['https://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src']
+source_urls = ['https://support.hdfgroup.org/ftp/lib-external/szip/%(version)s/src']
 sources = [SOURCELOWER_TAR_GZ]
 checksums = ['21ee958b4f2d4be2c9cabfa5e1a94877043609ce86fde5f286f105f7ff84d412']
 
diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-10.3.0.eb
index 10b926a9b61..5cc6a339682 100644
--- a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-10.3.0.eb
+++ b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-10.3.0.eb
@@ -3,7 +3,7 @@ easyblock = 'ConfigureMake'
 name = 'Szip'
 version = '2.1.1'
 
-homepage = 'https://www.hdfgroup.org/doc_resource/SZIP/'
+homepage = 'https://support.hdfgroup.org/doc_resource/SZIP/'
 
 description = """
  Szip compression software, providing lossless compression of scientific data
@@ -12,7 +12,7 @@ description = """
 toolchain = {'name': 'GCCcore', 'version': '10.3.0'}
 toolchainopts = {'pic': True}
 
-source_urls = ['https://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src']
+source_urls = ['https://support.hdfgroup.org/ftp/lib-external/szip/%(version)s/src']
 sources = [SOURCELOWER_TAR_GZ]
 checksums = ['21ee958b4f2d4be2c9cabfa5e1a94877043609ce86fde5f286f105f7ff84d412']
 
diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-11.2.0.eb
index b2d223898c7..70a9918dc8e 100644
--- a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-11.2.0.eb
+++ b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-11.2.0.eb
@@ -3,7 +3,7 @@ easyblock = 'ConfigureMake'
 name = 'Szip'
 version = '2.1.1'
 
-homepage = 'https://www.hdfgroup.org/doc_resource/SZIP/'
+homepage = 'https://support.hdfgroup.org/doc_resource/SZIP/'
 
 description = """
  Szip compression software, providing lossless compression of scientific data
@@ -12,7 +12,7 @@ description = """
 toolchain = {'name': 'GCCcore', 'version': '11.2.0'}
 toolchainopts = {'pic': True}
 
-source_urls = ['https://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src']
+source_urls = ['https://support.hdfgroup.org/ftp/lib-external/szip/%(version)s/src']
 sources = [SOURCELOWER_TAR_GZ]
 checksums = ['21ee958b4f2d4be2c9cabfa5e1a94877043609ce86fde5f286f105f7ff84d412']
 
diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-11.3.0.eb
index 3dc0b200849..6d34fd7a476 100644
--- a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-11.3.0.eb
+++ b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-11.3.0.eb
@@ -3,7 +3,7 @@ easyblock = 'ConfigureMake'
 name = 'Szip'
 version = '2.1.1'
 
-homepage = 'https://www.hdfgroup.org/doc_resource/SZIP/'
+homepage = 'https://support.hdfgroup.org/doc_resource/SZIP/'
 
 description = """
  Szip compression software, providing lossless compression of scientific data
@@ -12,7 +12,7 @@ description = """
 toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
 toolchainopts = {'pic': True}
 
-source_urls = ['https://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src']
+source_urls = ['https://support.hdfgroup.org/ftp/lib-external/szip/%(version)s/src']
 sources = [SOURCELOWER_TAR_GZ]
 checksums = ['21ee958b4f2d4be2c9cabfa5e1a94877043609ce86fde5f286f105f7ff84d412']
 
diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-12.2.0.eb
index 6f536c566dd..e58b9c3ffef 100644
--- a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-12.2.0.eb
+++ b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-12.2.0.eb
@@ -3,7 +3,7 @@ easyblock = 'ConfigureMake'
 name = 'Szip'
 version = '2.1.1'
 
-homepage = 'https://www.hdfgroup.org/doc_resource/SZIP/'
+homepage = 'https://support.hdfgroup.org/doc_resource/SZIP/'
 
 description = """
  Szip compression software, providing lossless compression of scientific data
@@ -12,7 +12,7 @@ description = """
 toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
 toolchainopts = {'pic': True}
 
-source_urls = ['https://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src']
+source_urls = ['https://support.hdfgroup.org/ftp/lib-external/szip/%(version)s/src']
 sources = [SOURCELOWER_TAR_GZ]
 checksums = ['21ee958b4f2d4be2c9cabfa5e1a94877043609ce86fde5f286f105f7ff84d412']
 
diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-12.3.0.eb
index e0a01221b9d..ee9fd884627 100644
--- a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-12.3.0.eb
+++ b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-12.3.0.eb
@@ -3,7 +3,7 @@ easyblock = 'ConfigureMake'
 name = 'Szip'
 version = '2.1.1'
 
-homepage = 'https://www.hdfgroup.org/doc_resource/SZIP/'
+homepage = 'https://support.hdfgroup.org/doc_resource/SZIP/'
 
 description = """
  Szip compression software, providing lossless compression of scientific data
@@ -12,7 +12,7 @@ description = """
 toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
 toolchainopts = {'pic': True}
 
-source_urls = ['https://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src']
+source_urls = ['https://support.hdfgroup.org/ftp/lib-external/szip/%(version)s/src']
 sources = [SOURCELOWER_TAR_GZ]
 checksums = ['21ee958b4f2d4be2c9cabfa5e1a94877043609ce86fde5f286f105f7ff84d412']
 
diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-13.2.0.eb
index 8eb12670652..5fcc21050e5 100644
--- a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-13.2.0.eb
+++ b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-13.2.0.eb
@@ -3,7 +3,7 @@ easyblock = 'ConfigureMake'
 name = 'Szip'
 version = '2.1.1'
 
-homepage = 'https://www.hdfgroup.org/doc_resource/SZIP/'
+homepage = 'https://support.hdfgroup.org/doc_resource/SZIP/'
 
 description = """
  Szip compression software, providing lossless compression of scientific data
@@ -12,7 +12,7 @@ description = """
 toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
 toolchainopts = {'pic': True}
 
-source_urls = ['https://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src']
+source_urls = ['https://support.hdfgroup.org/ftp/lib-external/szip/%(version)s/src']
 sources = [SOURCELOWER_TAR_GZ]
 checksums = ['21ee958b4f2d4be2c9cabfa5e1a94877043609ce86fde5f286f105f7ff84d412']
 
diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-6.3.0.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-6.3.0.eb
index f614a665648..5cebe3f7c68 100644
--- a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-6.3.0.eb
+++ b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-6.3.0.eb
@@ -3,7 +3,7 @@ easyblock = 'ConfigureMake'
 name = 'Szip'
 version = '2.1.1'
 
-homepage = 'http://www.hdfgroup.org/doc_resource/SZIP/'
+homepage = 'http://support.hdfgroup.org/doc_resource/SZIP/'
 
 description = """
  Szip compression software, providing lossless compression of scientific data
@@ -12,7 +12,7 @@ description = """
 toolchain = {'name': 'GCCcore', 'version': '6.3.0'}
 toolchainopts = {'pic': True}
 
-source_urls = ['http://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src']
+source_urls = ['http://support.hdfgroup.org/ftp/lib-external/szip/%(version)s/src']
 sources = [SOURCELOWER_TAR_GZ]
 checksums = ['21ee958b4f2d4be2c9cabfa5e1a94877043609ce86fde5f286f105f7ff84d412']
 
diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-6.4.0.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-6.4.0.eb
index 924f439ed4e..8edba3b1aa2 100644
--- a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-6.4.0.eb
+++ b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-6.4.0.eb
@@ -3,7 +3,7 @@ easyblock = 'ConfigureMake'
 name = 'Szip'
 version = '2.1.1'
 
-homepage = 'http://www.hdfgroup.org/doc_resource/SZIP/'
+homepage = 'http://support.hdfgroup.org/doc_resource/SZIP/'
 
 description = """
  Szip compression software, providing lossless compression of scientific data
@@ -12,7 +12,7 @@ description = """
 toolchain = {'name': 'GCCcore', 'version': '6.4.0'}
 toolchainopts = {'pic': True}
 
-source_urls = ['http://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src']
+source_urls = ['http://support.hdfgroup.org/ftp/lib-external/szip/%(version)s/src']
 sources = [SOURCELOWER_TAR_GZ]
 checksums = ['21ee958b4f2d4be2c9cabfa5e1a94877043609ce86fde5f286f105f7ff84d412']
 
diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-7.3.0.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-7.3.0.eb
index 4b9a4923df9..a9926ab81d1 100644
--- a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-7.3.0.eb
+++ b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-7.3.0.eb
@@ -3,7 +3,7 @@ easyblock = 'ConfigureMake'
 name = 'Szip'
 version = '2.1.1'
 
-homepage = 'http://www.hdfgroup.org/doc_resource/SZIP/'
+homepage = 'http://support.hdfgroup.org/doc_resource/SZIP/'
 
 description = """
  Szip compression software, providing lossless compression of scientific data
@@ -12,7 +12,7 @@ description = """
 toolchain = {'name': 'GCCcore', 'version': '7.3.0'}
 toolchainopts = {'pic': True}
 
-source_urls = ['http://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src']
+source_urls = ['http://support.hdfgroup.org/ftp/lib-external/szip/%(version)s/src']
 sources = [SOURCELOWER_TAR_GZ]
 checksums = ['21ee958b4f2d4be2c9cabfa5e1a94877043609ce86fde5f286f105f7ff84d412']
 
diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-8.2.0.eb
index 7f564c5a0fa..0d07710e238 100644
--- a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-8.2.0.eb
+++ b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-8.2.0.eb
@@ -3,7 +3,7 @@ easyblock = 'ConfigureMake'
 name = 'Szip'
 version = '2.1.1'
 
-homepage = 'http://www.hdfgroup.org/doc_resource/SZIP/'
+homepage = 'http://support.hdfgroup.org/doc_resource/SZIP/'
 
 description = """
  Szip compression software, providing lossless compression of scientific data
@@ -12,7 +12,7 @@ description = """
 toolchain = {'name': 'GCCcore', 'version': '8.2.0'}
 toolchainopts = {'pic': True}
 
-source_urls = ['http://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src']
+source_urls = ['http://support.hdfgroup.org/ftp/lib-external/szip/%(version)s/src']
 sources = [SOURCELOWER_TAR_GZ]
 checksums = ['21ee958b4f2d4be2c9cabfa5e1a94877043609ce86fde5f286f105f7ff84d412']
 
diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-8.3.0.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-8.3.0.eb
index 69db79f2d43..e522a3ac747 100644
--- a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-8.3.0.eb
+++ b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-8.3.0.eb
@@ -3,7 +3,7 @@ easyblock = 'ConfigureMake'
 name = 'Szip'
 version = '2.1.1'
 
-homepage = 'https://www.hdfgroup.org/doc_resource/SZIP/'
+homepage = 'https://support.hdfgroup.org/doc_resource/SZIP/'
 
 description = """
  Szip compression software, providing lossless compression of scientific data
@@ -12,7 +12,7 @@ description = """
 toolchain = {'name': 'GCCcore', 'version': '8.3.0'}
 toolchainopts = {'pic': True}
 
-source_urls = ['https://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src']
+source_urls = ['https://support.hdfgroup.org/ftp/lib-external/szip/%(version)s/src']
 sources = [SOURCELOWER_TAR_GZ]
 checksums = ['21ee958b4f2d4be2c9cabfa5e1a94877043609ce86fde5f286f105f7ff84d412']
 
diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-9.3.0.eb
index 242c281b919..822080c60fe 100644
--- a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-9.3.0.eb
+++ b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-9.3.0.eb
@@ -3,7 +3,7 @@ easyblock = 'ConfigureMake'
 name = 'Szip'
 version = '2.1.1'
 
-homepage = 'https://www.hdfgroup.org/doc_resource/SZIP/'
+homepage = 'https://support.hdfgroup.org/doc_resource/SZIP/'
 
 description = """
  Szip compression software, providing lossless compression of scientific data
@@ -12,7 +12,7 @@ description = """
 toolchain = {'name': 'GCCcore', 'version': '9.3.0'}
 toolchainopts = {'pic': True}
 
-source_urls = ['https://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src']
+source_urls = ['https://support.hdfgroup.org/ftp/lib-external/szip/%(version)s/src']
 sources = [SOURCELOWER_TAR_GZ]
 checksums = ['21ee958b4f2d4be2c9cabfa5e1a94877043609ce86fde5f286f105f7ff84d412']
 

From 9dde73982cb32136f32ce141e3999ef58c60c24c Mon Sep 17 00:00:00 2001
From: Thomas Hayward-Schneider <thomas.hayward@ipp.mpg.de>
Date: Mon, 5 Aug 2024 14:01:20 +0200
Subject: [PATCH 567/835] HDF v4.2.16-2: Rename source URL

* based on issue #21105
---
 easybuild/easyconfigs/h/HDF/HDF-4.2.16-2-GCCcore-12.3.0.eb | 2 +-
 easybuild/easyconfigs/h/HDF/HDF-4.2.16-2-GCCcore-13.2.0.eb | 2 +-
 easybuild/easyconfigs/h/HDF/HDF-4.2.16-GCCcore-12.3.0.eb   | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.16-2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.16-2-GCCcore-12.3.0.eb
index 453ca292d42..a6094f7f816 100644
--- a/easybuild/easyconfigs/h/HDF/HDF-4.2.16-2-GCCcore-12.3.0.eb
+++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.16-2-GCCcore-12.3.0.eb
@@ -12,7 +12,7 @@ description = """
 toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
 toolchainopts = {'pic': True}
 
-source_urls = ['http://www.hdfgroup.org/ftp/%(name)s/releases/%(name)s%(version)s/src/']
+source_urls = ['http://support.hdfgroup.org/ftp/%(name)s/releases/%(name)s%(version)s/src/']
 sources = [SOURCELOWER_TAR_GZ]
 
 checksums = [
diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.16-2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.16-2-GCCcore-13.2.0.eb
index 6f54f50d488..5b868a7fe58 100644
--- a/easybuild/easyconfigs/h/HDF/HDF-4.2.16-2-GCCcore-13.2.0.eb
+++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.16-2-GCCcore-13.2.0.eb
@@ -12,7 +12,7 @@ description = """
 toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
 toolchainopts = {'pic': True}
 
-source_urls = ['http://www.hdfgroup.org/ftp/%(name)s/releases/%(name)s%(version)s/src/']
+source_urls = ['http://support.hdfgroup.org/ftp/%(name)s/releases/%(name)s%(version)s/src/']
 sources = [SOURCELOWER_TAR_GZ]
 
 checksums = [
diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.16-GCCcore-12.3.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.16-GCCcore-12.3.0.eb
index d24dbfac77e..630c4aa2dc2 100644
--- a/easybuild/easyconfigs/h/HDF/HDF-4.2.16-GCCcore-12.3.0.eb
+++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.16-GCCcore-12.3.0.eb
@@ -13,7 +13,7 @@ description = """
 toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
 toolchainopts = {'pic': True}
 
-source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/']
+source_urls = ['http://support.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/']
 sources = [SOURCELOWER_TAR_GZ]
 checksums = ['2bd48dcefb5ab4829fba27dca6fad20b842d495dfd64944b2412b2b0968bf167']
 

From 244b56690ad0ddc7165974676c8c52ee2846516c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Petr=20Kr=C3=A1l?= <petr@inuits.eu>
Date: Mon, 5 Aug 2024 14:36:15 +0200
Subject: [PATCH 568/835] add missing build dependency

---
 .../easyconfigs/y/yelp-tools/yelp-tools-42.1-GCCcore-12.3.0.eb   | 1 +
 easybuild/easyconfigs/y/yelp-xsl/yelp-xsl-42.1-GCCcore-12.3.0.eb | 1 +
 2 files changed, 2 insertions(+)

diff --git a/easybuild/easyconfigs/y/yelp-tools/yelp-tools-42.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/y/yelp-tools/yelp-tools-42.1-GCCcore-12.3.0.eb
index b6b4f25ccf5..0ba5cdef596 100644
--- a/easybuild/easyconfigs/y/yelp-tools/yelp-tools-42.1-GCCcore-12.3.0.eb
+++ b/easybuild/easyconfigs/y/yelp-tools/yelp-tools-42.1-GCCcore-12.3.0.eb
@@ -20,6 +20,7 @@ builddependencies = [
     ('Meson', '1.1.1'),
     ('Ninja', '1.11.1'),
     ('CMake', '3.26.3'),
+    ('Autotools', '20220317'),
 ]
 
 dependencies = [
diff --git a/easybuild/easyconfigs/y/yelp-xsl/yelp-xsl-42.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/y/yelp-xsl/yelp-xsl-42.1-GCCcore-12.3.0.eb
index 60f61b5262d..ad7d8eddb4e 100644
--- a/easybuild/easyconfigs/y/yelp-xsl/yelp-xsl-42.1-GCCcore-12.3.0.eb
+++ b/easybuild/easyconfigs/y/yelp-xsl/yelp-xsl-42.1-GCCcore-12.3.0.eb
@@ -21,6 +21,7 @@ builddependencies = [
     ('binutils', '2.40'),
     ('ITSTool', '2.0.7'),
     ('gettext', '0.21.1'),
+    ('Autotools', '20220317'),
 ]
 
 preconfigopts = 'NOCONFIGURE=1 ./autogen.sh && '

From 200191648280a8d0581ee8f7d443e6875f2fb133 Mon Sep 17 00:00:00 2001
From: Simon Branford <4967+branfosj@users.noreply.github.com>
Date: Mon, 5 Aug 2024 17:16:29 +0100
Subject: [PATCH 569/835] restore RISCV patch

---
 .../s/SciPy-bundle/SciPy-bundle-2024.05-gfbf-2024a.eb      | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2024.05-gfbf-2024a.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2024.05-gfbf-2024a.eb
index c140938671c..cdb7536e15a 100644
--- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2024.05-gfbf-2024a.eb
+++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2024.05-gfbf-2024a.eb
@@ -30,11 +30,16 @@ use_pip = True
 # order is important!
 exts_list = [
     ('numpy', '1.26.4', {
-        'patches': ['numpy-1.22.3_disable-broken-override-test.patch'],
+        'patches': [
+            'numpy-1.22.3_disable-broken-override-test.patch',
+            'numpy-1.26.4_fix-riscv64-test-failures.patch',
+        ],
         'checksums': [
             {'numpy-1.26.4.tar.gz': '2a02aba9ed12e4ac4eb3ea9421c420301a0c6460d9830d74a9df87efa4912010'},
             {'numpy-1.22.3_disable-broken-override-test.patch':
              '9c589bb073b28b25ff45eb3c63c57966aa508dd8b318d0b885b6295271e4983c'},
+            {'numpy-1.26.4_fix-riscv64-test-failures.patch':
+             '81bd487dbca6da8285971a16a2c7b488718a051d3cd66450277bed6ff21741de'},
         ],
     }),
     ('ply', '3.11', {

From ebe07a1bef0a0ef4e42ec0f47a18111510f0ebcb Mon Sep 17 00:00:00 2001
From: Bart Oldeman <bartoldeman@gmail.com>
Date: Mon, 5 Aug 2024 20:28:45 -0400
Subject: [PATCH 570/835] Update
 easybuild/easyconfigs/i/imkl/imkl-2023.1.0-gompi-2023a.eb

URL change suggested by @branfosj

Co-authored-by: Simon Branford <4967+branfosj@users.noreply.github.com>
---
 easybuild/easyconfigs/i/imkl/imkl-2023.1.0-gompi-2023a.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/i/imkl/imkl-2023.1.0-gompi-2023a.eb b/easybuild/easyconfigs/i/imkl/imkl-2023.1.0-gompi-2023a.eb
index 5c8f63a0644..17ed1c0a2aa 100644
--- a/easybuild/easyconfigs/i/imkl/imkl-2023.1.0-gompi-2023a.eb
+++ b/easybuild/easyconfigs/i/imkl/imkl-2023.1.0-gompi-2023a.eb
@@ -10,7 +10,7 @@ description = "Intel oneAPI Math Kernel Library"
 toolchain = {'name': 'gompi', 'version': '2023a'}
 
 # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html
-source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18721/']
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/cd17b7fe-500e-4305-a89b-bd5b42bfd9f8/']
 sources = ['l_onemkl_p_%(version)s.46342_offline.sh']
 checksums = ['cc28c94cab23c185520b93c5a04f3979d8da6b4c90cee8c0681dd89819d76167']
 

From b7e090219d352b7e83e62ed5809adad98ce416af Mon Sep 17 00:00:00 2001
From: WilleBell <cintiawillemyns@gmail.com>
Date: Tue, 6 Aug 2024 10:52:09 +0200
Subject: [PATCH 571/835] adding easyconfigs:
 APOST3D-20240527-intel-compilers-2023.1.0.eb

---
 ...OST3D-20240527-intel-compilers-2023.1.0.eb | 51 +++++++++++++++++++
 1 file changed, 51 insertions(+)
 create mode 100644 easybuild/easyconfigs/a/APOST3D/APOST3D-20240527-intel-compilers-2023.1.0.eb

diff --git a/easybuild/easyconfigs/a/APOST3D/APOST3D-20240527-intel-compilers-2023.1.0.eb b/easybuild/easyconfigs/a/APOST3D/APOST3D-20240527-intel-compilers-2023.1.0.eb
new file mode 100644
index 00000000000..0048a900d1c
--- /dev/null
+++ b/easybuild/easyconfigs/a/APOST3D/APOST3D-20240527-intel-compilers-2023.1.0.eb
@@ -0,0 +1,51 @@
+easyblock = 'CmdCp'
+
+name = 'APOST3D'
+version = '20240527'
+local_commit = 'e06c8b0'
+
+description = """
+Open-source APOST-3D software features a large number of wavefunction analysis tools developed
+over the past 20 years, aiming at connecting classical chemical concepts with the electronic
+structure of molecules. APOST-3D relies on the identification of the atom in the molecule
+(AIM), and several analysis tools are implemented in the most general way so that they can be
+used in combination with any chosen AIM.
+A Fortran-based code developed at the Universitat de Girona (UdG) by P. Salvador and collaborators.
+"""
+homepage = 'https://github.com/mgimferrer/APOST3D'
+
+toolchain = {'name': 'intel-compilers', 'version': '2023.1.0'}
+
+builddependencies = [
+    ('make', '4.4.1'),
+]
+
+source_urls = ['https://github.com/mgimferrer/APOST3D/archive']
+sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}]
+checksums = ['1eb9a0f97b4dd135b782b96cadc37b3acfc27c69521cf3aab6cc10d4fc9292af']
+
+local_cmds = ' export APOST3D_PATH=%(start_dir)s && '
+# Compile local Libxc version 4.2.3
+# (needs provided Libxc, it is not possible to couple APOST-3D with newer Libxc libraries):
+local_cmds += 'bash compile_libxc.sh && '
+# Compile
+local_cmds += 'make -f Makefile_profgen && '
+# Run test calculations on single-processor:
+local_cmds += 'bash compiler-runtest && '
+# Recompile using info geneated in previous step
+local_cmds += 'make -f Makefile_profuse && '
+# Run test calculations in parallel:
+local_cmds += 'bash compiler-runtest2'
+
+cmds_map = [('.*', local_cmds)]
+
+local_bin_files = ['apost3d', 'apost3d-eos', 'eos_aom']
+
+files_to_copy = [(local_bin_files, 'bin')]
+
+sanity_check_paths = {
+    'files': ['bin/%s' % f for f in local_bin_files],
+    'dirs': [''],
+}
+
+moduleclass = 'chem'

From 13a988b8b0abbb9a4c125f1a3fe65dc91779764b Mon Sep 17 00:00:00 2001
From: Cintia Willemyns <115622907+WilleBell@users.noreply.github.com>
Date: Tue, 6 Aug 2024 10:55:02 +0200
Subject: [PATCH 572/835] modify comment

---
 .../a/APOST3D/APOST3D-20240527-intel-compilers-2023.1.0.eb    | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/easybuild/easyconfigs/a/APOST3D/APOST3D-20240527-intel-compilers-2023.1.0.eb b/easybuild/easyconfigs/a/APOST3D/APOST3D-20240527-intel-compilers-2023.1.0.eb
index 0048a900d1c..c5c4c40ac5b 100644
--- a/easybuild/easyconfigs/a/APOST3D/APOST3D-20240527-intel-compilers-2023.1.0.eb
+++ b/easybuild/easyconfigs/a/APOST3D/APOST3D-20240527-intel-compilers-2023.1.0.eb
@@ -25,8 +25,8 @@ sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_
 checksums = ['1eb9a0f97b4dd135b782b96cadc37b3acfc27c69521cf3aab6cc10d4fc9292af']
 
 local_cmds = ' export APOST3D_PATH=%(start_dir)s && '
-# Compile local Libxc version 4.2.3
-# (needs provided Libxc, it is not possible to couple APOST-3D with newer Libxc libraries):
+# Compile provided Libxc version 4.2.3
+# (it is not possible to couple APOST-3D with newer Libxc libraries):
 local_cmds += 'bash compile_libxc.sh && '
 # Compile
 local_cmds += 'make -f Makefile_profgen && '

From e6a490dc5dcfcffc3242b508866a8eac238ec1b2 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Tue, 6 Aug 2024 11:26:50 +0200
Subject: [PATCH 573/835] update sources, skip tests

---
 .../v/Visit/Visit-3.4.1-foss-2023a.eb         | 20 ++++---------------
 1 file changed, 4 insertions(+), 16 deletions(-)

diff --git a/easybuild/easyconfigs/v/Visit/Visit-3.4.1-foss-2023a.eb b/easybuild/easyconfigs/v/Visit/Visit-3.4.1-foss-2023a.eb
index a049601ec0e..7e5eaa8b270 100644
--- a/easybuild/easyconfigs/v/Visit/Visit-3.4.1-foss-2023a.eb
+++ b/easybuild/easyconfigs/v/Visit/Visit-3.4.1-foss-2023a.eb
@@ -22,17 +22,9 @@ visualizing data from over 120 different scientific data formats.
 
 toolchain = {'name': 'foss', 'version': '2023a'}
 
-sources = [{
-    'filename': 'v%(version)s.tar.gz',
-    'git_config': {
-        'url': 'https://github.com/visit-dav',
-        'repo_name': 'visit',
-        'tag': 'v%(version)s',
-        'recursive': True,
-        'keep_git_dir': True,
-    }
-}]
-checksums = [None]
+source_urls = ['https://github.com/visit-dav/visit/releases/download/v%(version)s/']
+sources = ['%(namelower)s%(version)s.tar.gz']
+checksums = ['942108cb294f4c9584a1628225b0be39c114c7e9e01805fb335d9c0b507689f5']
 
 builddependencies = [('CMake', '3.26.3')]
 dependencies = [
@@ -49,8 +41,6 @@ dependencies = [
     ('FFmpeg', '6.0'),
 ]
 
-srcdir = "src"
-
 configopts = "-DVISIT_ZLIB_DIR=$EBROOTZLIB "
 configopts += "-DVISIT_VTK_DIR=$EBROOTVTK -DVISIT_VTK_VERSION=$EBVERSIONVTK "
 configopts += "-DVISIT_QWT_DIR=$EBROOTQWT "
@@ -63,9 +53,7 @@ configopts += "-DVISIT_PARALLEL=ON -DVISIT_MPI_COMPILER=$MPICC -DVISIT_MPI_COMPI
 configopts += "-DOpenGL_GL_PREFERENCE=GLVND "
 
 # add missing include to fix make step
-prebuildopts = "sed -i '23 a #include <cmath>' %(builddir)s/visit/src/gui/QvisStripChart.C && "
-
-test_cmd = 'cd %(builddir)s/easybuild_obj/test && ./run_visit_test_suite.sh -n %(parallel)s'
+prebuildopts = "sed -i '23 a #include <cmath>' %(builddir)s/%(namelower)s%(version)s/src/gui/QvisStripChart.C && "
 
 sanity_check_paths = {
     'files': ['bin/%s' % x for x in ['frontendlauncher', 'frontendlauncher.py', 'visit']],

From 501f4eb1d987bb001ff27ee9c3d6638bf18785fd Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 6 Aug 2024 14:14:57 +0200
Subject: [PATCH 574/835] remove binutils build dependency, not needed when
 using GCC toolchain

---
 easybuild/easyconfigs/c/colorize/colorize-0.7.7-GCC-12.3.0.eb | 4 ----
 .../easyconfigs/c/crb-blast/crb-blast-0.6.9-GCC-12.3.0.eb     | 4 ----
 .../easyconfigs/t/Transrate/Transrate-1.0.3-GCC-12.3.0.eb     | 4 ----
 easybuild/easyconfigs/y/yell/yell-2.2.2-GCC-12.3.0.eb         | 4 ----
 4 files changed, 16 deletions(-)

diff --git a/easybuild/easyconfigs/c/colorize/colorize-0.7.7-GCC-12.3.0.eb b/easybuild/easyconfigs/c/colorize/colorize-0.7.7-GCC-12.3.0.eb
index 526fcb3a820..35921013c3e 100644
--- a/easybuild/easyconfigs/c/colorize/colorize-0.7.7-GCC-12.3.0.eb
+++ b/easybuild/easyconfigs/c/colorize/colorize-0.7.7-GCC-12.3.0.eb
@@ -15,10 +15,6 @@ checksums = ['d6ab95a5fcdea3c36c3327d38c1e79e2950ee1788506d8489ae35db330937a99']
 
 gem_file = '%(name)s-%(version)s.gem'
 
-builddependencies = [
-    ('binutils', '2.40'),
-]
-
 dependencies = [
     ('Ruby', '3.3.0'),
 ]
diff --git a/easybuild/easyconfigs/c/crb-blast/crb-blast-0.6.9-GCC-12.3.0.eb b/easybuild/easyconfigs/c/crb-blast/crb-blast-0.6.9-GCC-12.3.0.eb
index 57d50e1b02b..c9e4de852a5 100644
--- a/easybuild/easyconfigs/c/crb-blast/crb-blast-0.6.9-GCC-12.3.0.eb
+++ b/easybuild/easyconfigs/c/crb-blast/crb-blast-0.6.9-GCC-12.3.0.eb
@@ -8,10 +8,6 @@ description = """Conditional Reciprocal Best BLAST - high confidence ortholog as
 
 toolchain = {'name': 'GCC', 'version': '12.3.0'}
 
-builddependencies = [
-    ('binutils', '2.40'),
-]
-
 dependencies = [
     ('Ruby', '3.3.0'),
 ]
diff --git a/easybuild/easyconfigs/t/Transrate/Transrate-1.0.3-GCC-12.3.0.eb b/easybuild/easyconfigs/t/Transrate/Transrate-1.0.3-GCC-12.3.0.eb
index 297dd9260b3..a70ecf2a901 100644
--- a/easybuild/easyconfigs/t/Transrate/Transrate-1.0.3-GCC-12.3.0.eb
+++ b/easybuild/easyconfigs/t/Transrate/Transrate-1.0.3-GCC-12.3.0.eb
@@ -19,10 +19,6 @@ checksums = [
     {'Transrate-1.0.3_undefined_method_fix.patch': 'ead5e51318d6d810fb11b783d517ea38648f62ae2bdd5f3f4dac7baa9ae94d95'},
 ]
 
-builddependencies = [
-    ('binutils', '2.40'),
-]
-
 dependencies = [
     ('Ruby', '3.3.0'),
     ('crb-blast', '0.6.9'),
diff --git a/easybuild/easyconfigs/y/yell/yell-2.2.2-GCC-12.3.0.eb b/easybuild/easyconfigs/y/yell/yell-2.2.2-GCC-12.3.0.eb
index c42c506c4f3..48cc38e0d7c 100644
--- a/easybuild/easyconfigs/y/yell/yell-2.2.2-GCC-12.3.0.eb
+++ b/easybuild/easyconfigs/y/yell/yell-2.2.2-GCC-12.3.0.eb
@@ -14,10 +14,6 @@ checksums = ['1d166f3cc3b6dc49a59778ea7156ed6d8de794c15106d48ffd6cbb061b9b26bc']
 
 gem_file = '%(name)s-%(version)s.gem'
 
-builddependencies = [
-    ('binutils', '2.40'),
-]
-
 dependencies = [
     ('Ruby', '3.3.0'),
 ]

From d8076ebaf8cb915762adebf88d385cc672b350dc Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Tue, 6 Aug 2024 15:57:28 +0200
Subject: [PATCH 575/835] Ensure BioPerl easyconfigs use `Bundle` easyblock

---
 easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-12.2.0.eb | 2 +-
 easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-12.3.0.eb | 2 +-
 easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-13.3.0.eb | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-12.2.0.eb b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-12.2.0.eb
index 8caddd5df22..e8e52099b07 100644
--- a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-12.2.0.eb
+++ b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-12.2.0.eb
@@ -5,7 +5,7 @@
 #  Fred Hutchinson Cancer Research Center
 #  Thomas Eylenbosch - Gluo NV 
 
-easyblock = 'PerlModule'
+easyblock = 'Bundle'
 
 name = 'BioPerl'
 version = '1.7.8'
diff --git a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-12.3.0.eb b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-12.3.0.eb
index b47216124f8..4212570abb1 100644
--- a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-12.3.0.eb
+++ b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-12.3.0.eb
@@ -5,7 +5,7 @@
 #  Fred Hutchinson Cancer Research Center
 #  Thomas Eylenbosch - Gluo NV 
 
-easyblock = 'PerlModule'
+easyblock = 'Bundle'
 
 name = 'BioPerl'
 version = '1.7.8'
diff --git a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-13.3.0.eb b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-13.3.0.eb
index c6e760f5105..ba3029a6a41 100644
--- a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-13.3.0.eb
+++ b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-13.3.0.eb
@@ -5,7 +5,7 @@
 #  Fred Hutchinson Cancer Research Center
 #  Thomas Eylenbosch - Gluo NV 
 
-easyblock = 'PerlModule'
+easyblock = 'Bundle'
 
 name = 'BioPerl'
 version = '1.7.8'

From 31713d5c7756cfa95c339420a64b2c2111d8b369 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Tue, 6 Aug 2024 16:38:41 +0200
Subject: [PATCH 576/835] update checksum openff-nagl + change to sources

---
 ...penForceField-Toolkit-0.16.0-foss-2023a.eb | 24 +++++++++----------
 1 file changed, 12 insertions(+), 12 deletions(-)

diff --git a/easybuild/easyconfigs/o/OpenForceField-Toolkit/OpenForceField-Toolkit-0.16.0-foss-2023a.eb b/easybuild/easyconfigs/o/OpenForceField-Toolkit/OpenForceField-Toolkit-0.16.0-foss-2023a.eb
index 06e5075f674..f323c61f065 100644
--- a/easybuild/easyconfigs/o/OpenForceField-Toolkit/OpenForceField-Toolkit-0.16.0-foss-2023a.eb
+++ b/easybuild/easyconfigs/o/OpenForceField-Toolkit/OpenForceField-Toolkit-0.16.0-foss-2023a.eb
@@ -66,66 +66,66 @@ exts_list = [
         'checksums': ['341595a488e3e01a85a9d8911d8912fd922ede5fecc4dce437eb4b6c8d037e56'],
     }),
     ('intermol', '0.1.2', {
-        'source_tmpl': 'v%(version)s.tar.gz',
         'source_urls': ['https://github.com/shirtsgroup/InterMol/archive/'],
+        'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}],
         'checksums': ['a3065133ba16585a5db3807466a36242d191156525c33079cf46a97cedcfe835'],
     }),
     ('SMIRNOFF99Frosst', '1.1.0', {
-        'source_tmpl': '%(version)s.tar.gz',
         'source_urls': ['https://github.com/openforcefield/smirnoff99Frosst/archive/'],
+        'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}],
         'checksums': ['940c4ed3cd720e746549a3335f10b7b0d9047a67bc216ad45dd875be5c8ec467'],
     }),
     ('SMIRNOFF-Plugins', '2024.01.0', {
-        'source_tmpl': '%(version)s.tar.gz',
         'source_urls': ['https://github.com/openforcefield/smirnoff-plugins/archive/'],
+        'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}],
         'checksums': ['8ba4dbc6ed320f06f30bf42e8f70399bc3818becd668990693b51ddca183ff74'],
     }),
     ('OpenForceField-ForceFields', '2024.04.0', {
         'modulename': 'openforcefields',
-        'source_tmpl': '%(version)s.tar.gz',
         'source_urls': ['https://github.com/openforcefield/openff-forcefields/archive/'],
+        'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}],
         'checksums': ['fc7094cdb74bf9f0ed665dfc716cc62c5a37def3fc7e852adeae0ae4b60169c7'],
     }),
     ('OpenForceField-Amber-FF-Ports', '0.0.4', {
         'modulename': 'openff.amber_ff_ports',
-        'source_tmpl': 'v%(version)s.tar.gz',
         'source_urls': ['https://github.com/openforcefield/openff-amber-ff-ports/archive/'],
+        'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}],
         'checksums': ['dbf2d1ccce06b0627b1eccae7e227ad800ff1cbac3e869344de265b178cc0207'],
     }),
     ('OpenForceField-Utilities', '0.1.12', {
         'modulename': 'openff.utilities',
-        'source_tmpl': 'v%(version)s.tar.gz',
         'source_urls': ['https://github.com/openforcefield/openff-utilities/archive/'],
+        'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}],
         'checksums': ['92882c5b87b40bdb4ee1e8c84c0ecc0fc83f26eaf3e3befde41bfdcf93d75dea'],
     }),
     ('OpenForceField-Units', '0.2.2', {
         'modulename': 'openff.units',
-        'source_tmpl': '%(version)s.tar.gz',
         'source_urls': ['https://github.com/openforcefield/openff-units/archive/'],
+        'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}],
         'checksums': ['532746534c1937938580d5cfe98f414aff9bfbcc66970e115a88a38f6d5a2581'],
     }),
     ('OpenForceField-NAGL-Models', '0.2.0', {
         'modulename': 'openff.nagl_models',
-        'source_tmpl': 'v%(version)s.tar.gz',
         'source_urls': ['https://github.com/openforcefield/openff-nagl-models/archive/'],
-        'checksums': ['df8e7ee980aa7ea99559759258a16e3aaa362245f5b7c32f9c25fb226eaee222'],
+        'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}],
+        'checksums': ['5ccc55d7f0fcd24577796fd8b2bfd85b035ee8060e441c1f7dfc6f1949b9dee5'],
     }),
     ('OpenForceField-Models', '0.1.2', {
         'modulename': 'openff.models',
-        'source_tmpl': '%(version)s.tar.gz',
         'source_urls': ['https://github.com/openforcefield/openff-models/archive/'],
+        'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}],
         'checksums': ['cf2aa7ef467721f141149e4ce96134db390b27012f09996c4442a3fad2371653'],
     }),
     ('OpenForceField-Interchange', '0.3.27', {
         'modulename': 'openff.interchange',
-        'source_tmpl': 'v%(version)s.tar.gz',
         'source_urls': ['https://github.com/openforcefield/openff-interchange/archive/'],
+        'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}],
         'checksums': ['6b44ba8a89921b3843a5f9fc41dc4f8a0c784ba12221e3ea0fb8c1b01a10cf2e'],
     }),
     (name, version, {
         'modulename': 'openff.toolkit',
-        'source_tmpl': '%(version)s.tar.gz',
         'source_urls': ['https://github.com/openforcefield/openff-toolkit/archive/'],
+        'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}],
         'checksums': ['70a81e914e86efd933819a5db05fc4400dcd23e12ad29398fdad46f2765b5634'],
     }),
 ]

From 3cec9e4b0f2a954e37af2606305274fb287e7a53 Mon Sep 17 00:00:00 2001
From: Sebastian Achilles <s.achilles@fz-juelich.de>
Date: Tue, 6 Aug 2024 22:28:21 +0200
Subject: [PATCH 577/835] adding easyconfigs: CUDA-12.6.0.eb

---
 easybuild/easyconfigs/c/CUDA/CUDA-12.6.0.eb | 22 +++++++++++++++++++++
 1 file changed, 22 insertions(+)
 create mode 100644 easybuild/easyconfigs/c/CUDA/CUDA-12.6.0.eb

diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-12.6.0.eb b/easybuild/easyconfigs/c/CUDA/CUDA-12.6.0.eb
new file mode 100644
index 00000000000..24c7b5f5c90
--- /dev/null
+++ b/easybuild/easyconfigs/c/CUDA/CUDA-12.6.0.eb
@@ -0,0 +1,22 @@
+name = 'CUDA'
+version = '12.6.0'
+local_nv_version = '560.28.03'
+
+homepage = 'https://developer.nvidia.com/cuda-toolkit'
+description = """CUDA (formerly Compute Unified Device Architecture) is a parallel
+ computing platform and programming model created by NVIDIA and implemented by the
+ graphics processing units (GPUs) that they produce. CUDA gives developers access
+ to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs."""
+
+toolchain = SYSTEM
+
+source_urls = ['https://developer.download.nvidia.com/compute/cuda/%(version)s/local_installers/']
+sources = ['cuda_%%(version)s_%s_linux%%(cudaarch)s.run' % local_nv_version]
+checksums = [{
+    'cuda_%%(version)s_%s_linux.run' % local_nv_version:
+        '31ab04394e69b14dd8656e2b44c2877db1a0e898dff8a7546a4c628438101b94',
+    'cuda_%%(version)s_%s_linux_sbsa.run' % local_nv_version:
+        '398db7baca17d51ad5035c606714c96380c965fd1742478c743bc6bbb1d8f63c'
+}]
+
+moduleclass = 'system'

From 68bcf35dc9e71d897fb58e6b905a8af5c78e2b6b Mon Sep 17 00:00:00 2001
From: Adam Huffman <verdurin@users.noreply.github.com>
Date: Wed, 7 Aug 2024 09:55:36 +0100
Subject: [PATCH 578/835] Description typo fix for wradlib

---
 easybuild/easyconfigs/w/wradlib/wradlib-2.0.3-foss-2022a.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/w/wradlib/wradlib-2.0.3-foss-2022a.eb b/easybuild/easyconfigs/w/wradlib/wradlib-2.0.3-foss-2022a.eb
index 9bec30a5545..010b73f371b 100644
--- a/easybuild/easyconfigs/w/wradlib/wradlib-2.0.3-foss-2022a.eb
+++ b/easybuild/easyconfigs/w/wradlib/wradlib-2.0.3-foss-2022a.eb
@@ -5,7 +5,7 @@ version = '2.0.3'
 
 homepage = 'https://docs.wradlib.org/'
 description = """
-The wradlib project has been initiated in order facilitate the use of weather
+The wradlib project has been initiated in order to facilitate the use of weather
 radar data as well as to provide a common platform for research on new
 algorithms."""
 

From 743089f74ded750046c46ac6a50be80a0924c464 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Wed, 7 Aug 2024 11:51:14 +0200
Subject: [PATCH 579/835] adding easyconfigs: MONAI-1.3.0-foss-2022b.eb,
 einops-0.7.0-GCCcore-12.2.0.eb, ITK-5.3.0-foss-2022b.eb,
 NiBabel-5.2.0-gfbf-2022b.eb, pydicom-2.4.4-GCCcore-12.2.0.eb,
 tensorboard-2.15.1-gfbf-2022b.eb, grpcio-1.57.0-GCCcore-12.2.0.eb,
 openslide-python-1.3.1-GCCcore-12.2.0.eb,
 OpenSlide-3.4.1-GCCcore-12.2.0-largefiles.eb

---
 .../e/einops/einops-0.7.0-GCCcore-12.2.0.eb   | 29 ++++++
 .../g/grpcio/grpcio-1.57.0-GCCcore-12.2.0.eb  | 54 +++++++++++
 .../easyconfigs/i/ITK/ITK-5.3.0-foss-2022b.eb | 78 +++++++++++++++
 .../m/MONAI/MONAI-1.3.0-foss-2022b.eb         | 97 +++++++++++++++++++
 .../n/NiBabel/NiBabel-5.2.0-gfbf-2022b.eb     | 46 +++++++++
 ...enSlide-3.4.1-GCCcore-12.2.0-largefiles.eb | 56 +++++++++++
 .../openslide-python-1.3.1-GCCcore-12.2.0.eb  | 29 ++++++
 .../p/pydicom/pydicom-2.4.4-GCCcore-12.2.0.eb | 26 +++++
 .../tensorboard-2.15.1-gfbf-2022b.eb          | 90 +++++++++++++++++
 9 files changed, 505 insertions(+)
 create mode 100644 easybuild/easyconfigs/e/einops/einops-0.7.0-GCCcore-12.2.0.eb
 create mode 100644 easybuild/easyconfigs/g/grpcio/grpcio-1.57.0-GCCcore-12.2.0.eb
 create mode 100644 easybuild/easyconfigs/i/ITK/ITK-5.3.0-foss-2022b.eb
 create mode 100644 easybuild/easyconfigs/m/MONAI/MONAI-1.3.0-foss-2022b.eb
 create mode 100644 easybuild/easyconfigs/n/NiBabel/NiBabel-5.2.0-gfbf-2022b.eb
 create mode 100644 easybuild/easyconfigs/o/OpenSlide/OpenSlide-3.4.1-GCCcore-12.2.0-largefiles.eb
 create mode 100644 easybuild/easyconfigs/o/openslide-python/openslide-python-1.3.1-GCCcore-12.2.0.eb
 create mode 100644 easybuild/easyconfigs/p/pydicom/pydicom-2.4.4-GCCcore-12.2.0.eb
 create mode 100644 easybuild/easyconfigs/t/tensorboard/tensorboard-2.15.1-gfbf-2022b.eb

diff --git a/easybuild/easyconfigs/e/einops/einops-0.7.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/e/einops/einops-0.7.0-GCCcore-12.2.0.eb
new file mode 100644
index 00000000000..7af581e455f
--- /dev/null
+++ b/easybuild/easyconfigs/e/einops/einops-0.7.0-GCCcore-12.2.0.eb
@@ -0,0 +1,29 @@
+easyblock = 'PythonPackage'
+
+name = 'einops'
+version = '0.7.0'
+
+homepage = 'https://einops.rocks/'
+description = """
+Flexible and powerful tensor operations for readable and reliable code.
+Supports numpy, pytorch, tensorflow, jax, and others."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+
+sources = [SOURCE_TAR_GZ]
+checksums = ['b2b04ad6081a3b227080c9bf5e3ace7160357ff03043cd66cc5b2319eb7031d1']
+
+builddependencies = [
+    ('binutils', '2.39'),
+]
+
+dependencies = [
+    ('Python', '3.10.8'),
+]
+
+download_dep_fail = True
+use_pip = True
+
+sanity_pip_check = True
+
+moduleclass = 'math'
diff --git a/easybuild/easyconfigs/g/grpcio/grpcio-1.57.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/grpcio/grpcio-1.57.0-GCCcore-12.2.0.eb
new file mode 100644
index 00000000000..27e974c5de0
--- /dev/null
+++ b/easybuild/easyconfigs/g/grpcio/grpcio-1.57.0-GCCcore-12.2.0.eb
@@ -0,0 +1,54 @@
+easyblock = 'PythonBundle'
+
+name = 'grpcio'
+version = '1.57.0'
+
+homepage = 'https://grpc.io/'
+description = """gRPC is a modern, open source, high-performance remote procedure call (RPC)
+framework that can run anywhere. gRPC enables client and server applications to
+communicate transparently, and simplifies the building of connected systems."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+toolchainopts = {'pic': True}
+
+use_pip = True
+sanity_pip_check = True
+
+builddependencies = [
+    ('binutils', '2.39'),
+    ('OpenSSL', '1.1', '', SYSTEM),
+    ('RE2', '2023-03-01'),
+]
+
+dependencies = [
+    ('Python', '3.10.8'),
+    ('protobuf-python', '4.23.0'),
+    ('Abseil', '20230125.2'),
+]
+
+exts_list = [
+    (name, version, {
+        'modulename': 'grpc',
+        'preinstallopts': (
+            # patch hardcoded /usr paths to prefix them with alternate sysroot path (if defined)
+            "sed -i 's@/usr@%(sysroot)s/usr@g' setup.py && "
+            "export GRPC_PYTHON_BUILD_EXT_COMPILER_JOBS=%(parallel)s && "
+            # Required to avoid building with non-default C++ standard but keep other flags,
+            # see https://github.com/grpc/grpc/issues/34256
+            'export GRPC_PYTHON_CFLAGS="-fvisibility=hidden -fno-wrapv -fno-exceptions" &&'
+            "GRPC_PYTHON_BUILD_SYSTEM_OPENSSL=True "
+            "GRPC_PYTHON_BUILD_SYSTEM_ZLIB=True "
+            "GRPC_PYTHON_BUILD_SYSTEM_RE2=True "
+            "GRPC_PYTHON_BUILD_SYSTEM_ABSL=True "
+        ),
+        'patches': ['grpcio-1.57.0_use-ebroot.patch'],
+        'checksums': [
+            {'grpcio-1.57.0.tar.gz':
+             '4b089f7ad1eb00a104078bab8015b0ed0ebcb3b589e527ab009c53893fd4e613'},
+            {'grpcio-1.57.0_use-ebroot.patch':
+             '5faf822cd817b723ae9361e43656d0ecc7b3333a166bbab2df80b43ae588e510'},
+        ],
+    }),
+]
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/i/ITK/ITK-5.3.0-foss-2022b.eb b/easybuild/easyconfigs/i/ITK/ITK-5.3.0-foss-2022b.eb
new file mode 100644
index 00000000000..2f64dbf8f87
--- /dev/null
+++ b/easybuild/easyconfigs/i/ITK/ITK-5.3.0-foss-2022b.eb
@@ -0,0 +1,78 @@
+# Contributors:
+# Fenglai Liu (fenglai@accre.vanderbilt.edu) - Vanderbilt University
+# Alex Domingo (alex.domingo.toro@vub.be) - Vrije Universiteit Brussel (VUB)
+# Denis Kristak, Pavel Tománek (INUITS)
+#
+easyblock = 'CMakeMake'
+
+name = 'ITK'
+version = '5.3.0'
+
+homepage = 'https://itk.org'
+description = """Insight Segmentation and Registration Toolkit (ITK) provides
+ an extensive suite of software tools for registering and segmenting
+ multidimensional imaging data."""
+
+toolchain = {'name': 'foss', 'version': '2022b'}
+toolchainopts = {'pic': True, 'cstd': 'c++11'}
+
+github_account = 'InsightSoftwareConsortium'
+source_urls = [GITHUB_SOURCE]
+sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}]
+patches = [
+    'ITK-5.3.0_vtk-include.patch',
+    'ITK-5.3.0_fix-compatibility-swig-4-1.patch',
+]
+checksums = [
+    {'v5.3.0.tar.gz': '64e7e8094a5023c8f68ee042459d6319581fadb35e2fe90a4ae230ce36369db1'},
+    {'ITK-5.3.0_vtk-include.patch': '138ebd2e0e7f9001aba5f4a7e8145ffcf0093913d50f109ecff447773fd52a48'},
+    {'ITK-5.3.0_fix-compatibility-swig-4-1.patch': '0138878d96e90d6bfdc81fd4f2b5ec413d61c1de666a16842b417c2686ebf506'},
+]
+
+builddependencies = [
+    ('CMake', '3.24.3'),
+    ('Bison', '3.8.2'),
+    ('Eigen', '3.4.0'),
+    ('SWIG', '4.1.1'),
+    ('Perl', '5.36.0'),
+]
+dependencies = [
+    ('Python', '3.10.8'),
+    ('double-conversion', '3.2.1'),
+    ('expat', '2.4.9'),
+    ('HDF5', '1.14.0'),
+    ('libjpeg-turbo', '2.1.4'),
+    ('libpng', '1.6.38'),
+    ('LibTIFF', '4.4.0'),
+    ('VTK', '9.2.6'),
+    ('zlib', '1.2.12'),
+]
+
+# Features
+configopts = '-DBUILD_SHARED_LIBS=ON -DBUILD_TESTING=OFF '
+configopts += '-DModule_ITKReview=ON -DModule_ITKVtkGlue=ON -DModule_SimpleITKFilters=ON '
+# Enable Python bindings
+configopts += '-DITK_WRAP_PYTHON:BOOL=ON -DPython3_EXECUTABLE=$EBROOTPYTHON/bin/python '
+configopts += '-DSWIG_EXECUTABLE=$EBROOTSWIG/bin/swig -DSWIG_DIR=$EBROOTSWIG '
+configopts += '-DPY_SITE_PACKAGES_PATH=%(installdir)s/lib/python%(pyshortver)s/site-packages '
+# Dependencies from EB
+local_sys_deps = ['DOUBLECONVERSION', 'EIGEN', 'EXPAT', 'FFTW', 'HDF5', 'JPEG', 'PNG', 'SWIG', 'TIFF', 'ZLIB']
+local_sys_cmake = ['-DITK_USE_SYSTEM_%s=ON' % d for d in local_sys_deps]
+configopts += ' '.join(local_sys_cmake)
+
+prebuildopts = "LC_ALL=C "
+
+local_lib_names = ['ITKCommon', 'ITKIOHDF5', 'ITKIOJPEG', 'ITKIOPNG', 'ITKIOTIFF',
+                   'ITKReview', 'ITKVTK', 'ITKVtkGlue', 'itkSimpleITKFilters']
+
+sanity_check_paths = {
+    'files': ['bin/itkTestDriver'] +
+             ['lib/lib%s-%%(version_major)s.%%(version_minor)s.%s' % (l, SHLIB_EXT) for l in local_lib_names],
+    'dirs': ['include/ITK-%(version_major)s.%(version_minor)s', 'lib/python%(pyshortver)s/site-packages', 'share'],
+}
+
+sanity_check_commands = ["python -c 'import itk'"]
+
+modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'}
+
+moduleclass = 'data'
diff --git a/easybuild/easyconfigs/m/MONAI/MONAI-1.3.0-foss-2022b.eb b/easybuild/easyconfigs/m/MONAI/MONAI-1.3.0-foss-2022b.eb
new file mode 100644
index 00000000000..ab27a322fb6
--- /dev/null
+++ b/easybuild/easyconfigs/m/MONAI/MONAI-1.3.0-foss-2022b.eb
@@ -0,0 +1,97 @@
+easyblock = 'PythonBundle'
+
+name = 'MONAI'
+version = '1.3.0'
+
+homepage = 'https://monai.io/'
+description = """
+MONAI is a PyTorch-based, open-source framework for deep learning in healthcare
+imaging, part of PyTorch Ecosystem.
+"""
+
+toolchain = {'name': 'foss', 'version': '2022b'}
+
+github_account = 'Project-MONAI'
+
+builddependencies = [
+    # ('hatchling', '1.18.0'),
+    ('Ninja', '1.11.1'),
+]
+
+dependencies = [
+    ('Python', '3.10.8'),
+    ('SciPy-bundle', '2023.02'),
+    ('PyTorch', '1.13.1'),
+    ('einops', '0.7.0'),
+    ('ITK', '5.3.0'),
+    ('NiBabel', '5.2.0'),
+    ('scikit-image', '0.21.0'),
+    ('tensorboard', '2.15.1'),
+    ('torchvision', '0.14.1'),
+    ('tqdm', '4.64.1'),
+    ('Pillow', '9.4.0'),
+    ('openslide-python', '1.3.1'),
+    ('BeautifulSoup', '4.11.1'),
+]
+
+use_pip = True
+
+# install MONAI with list of 'extras', which require additional dependencies
+local_pip_extras = "einops,fire,gdown,ignite,itk,jsonschema,lmdb,nibabel,"
+local_pip_extras += "openslide,pandas,pillow,psutil,pydicom,pyyaml,scipy,"
+local_pip_extras += "skimage,tensorboard,torchvision,tqdm"
+
+# PyTorch-Ignite v0.4.11 bundled as an extension because MONAI v1.3.0 has a strict requirement on it
+exts_list = [
+    ('gdown', '4.7.1', {
+        'checksums': ['347f23769679aaf7efa73e5655270fcda8ca56be65eb84a4a21d143989541045'],
+    }),
+    ('lmdb', '1.4.1', {
+        'checksums': ['1f4c76af24e907593487c904ef5eba1993beb38ed385af82adb25a858f2d658d'],
+    }),
+    ('termcolor', '2.3.0', {
+        'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl',
+        'checksums': ['3afb05607b89aed0ffe25202399ee0867ad4d3cb4180d98aaf8eefa6a5f7d475'],
+    }),
+    ('fire', '0.5.0', {
+        'checksums': ['a6b0d49e98c8963910021f92bba66f65ab440da2982b78eb1bbf95a0a34aacc6'],
+    }),
+    ('pytorch-ignite', '0.4.11', {
+        'modulename': 'ignite',
+        'patches': ['PyTorch-Ignite-0.4.11_fix_error_on_importing_Events.patch'],
+        'checksums': [
+            {'pytorch-ignite-0.4.11.tar.gz': 'ee31096a58679417097ef7f3f27d88bec40b789ac5e13cd9ed08bc89ca8ce2e2'},
+            {'PyTorch-Ignite-0.4.11_fix_error_on_importing_Events.patch':
+             'd45c0da30c01f7ce47b7be49a6d5d6eb9529c94a0b9de89260d4b07d9d2359e0'},
+        ],
+    }),
+    (name, version, {
+        'preinstallopts': 'BUILD_MONAI=1',
+        'source_urls': ['https://github.com/%(github_account)s/%(name)s/archive'],
+        'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}],
+        'use_pip_extras': local_pip_extras,
+        # 2 valid checksums, as source tarball provided by GitHub for MONAI 1.3.0 slightly changed at some point
+        # see also https://github.com/easybuilders/easybuild-easyconfigs/issues/20617
+        'checksums': [('67e0f55678faad4bd38b1ea69d5de94586b20b551b8ad745415623a8b6c1c5e2',
+                       '076d75458d490b4f2dafbf5974fcc8e07a86c03f39f5ef48c6689ab6e4347da9')],
+    }),
+]
+
+sanity_pip_check = True
+
+# 'pip check' does not verify whether all optional dependencies required to support 'extras'
+# are actually available, so we do it here via an import check;
+local_extra_mod_check = {x: x for x in local_pip_extras.split(",")}
+# Some special cases with different module name than extra name
+local_extra_mod_check['pillow'] = 'PIL'
+local_extra_mod_check['pyyaml'] = 'yaml'
+
+sanity_check_commands = ["python -c 'import monai; monai.config.print_config()'"]
+sanity_check_commands += ["python -c 'import %s'" % local_extra_mod_check[x] for x in local_extra_mod_check]
+
+sanity_check_paths = {
+    'files': ['lib/python%%(pyshortver)s/site-packages/%%(namelower)s/_C.%s' % SHLIB_EXT],
+    'dirs': ['lib/python%(pyshortver)s/site-packages/ignite'],
+}
+
+moduleclass = 'vis'
diff --git a/easybuild/easyconfigs/n/NiBabel/NiBabel-5.2.0-gfbf-2022b.eb b/easybuild/easyconfigs/n/NiBabel/NiBabel-5.2.0-gfbf-2022b.eb
new file mode 100644
index 00000000000..a930785f65b
--- /dev/null
+++ b/easybuild/easyconfigs/n/NiBabel/NiBabel-5.2.0-gfbf-2022b.eb
@@ -0,0 +1,46 @@
+easyblock = 'PythonBundle'
+
+name = 'NiBabel'
+version = '5.2.0'
+
+homepage = 'https://nipy.github.io/nibabel'
+description = """NiBabel provides read/write access to some common medical and neuroimaging file formats,
+ including: ANALYZE (plain, SPM99, SPM2 and later), GIFTI, NIfTI1, NIfTI2, MINC1, MINC2, MGH and ECAT
+ as well as Philips PAR/REC. We can read and write Freesurfer geometry, and read Freesurfer morphometry and
+ annotation files. There is some very limited support for DICOM. NiBabel is the successor of PyNIfTI."""
+
+toolchain = {'name': 'gfbf', 'version': '2022b'}
+
+dependencies = [
+    ('Python', '3.10.8'),
+    ('SciPy-bundle', '2023.02'),
+    ('Pillow', '9.4.0'),
+    ('pydicom', '2.4.4'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('bz2file', '0.98', {
+        'checksums': ['64c1f811e31556ba9931953c8ec7b397488726c63e09a4c67004f43bdd28da88'],
+    }),
+    ('nibabel', version, {
+        'checksums': ['3df8f1ab981d1bd92f4331d565528d126ab9717fdbd4cfe68f43fcd1c2bf3f52'],
+    }),
+]
+
+fix_python_shebang_for = ['bin/*']
+
+sanity_check_paths = {
+    'files': ['bin/nib-dicomfs', 'bin/nib-diff', 'bin/nib-ls', 'bin/nib-nifti-dx', 'bin/parrec2nii'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = [
+    "nib-diff --help",
+    "parrec2nii --help",
+]
+
+sanity_pip_check = True
+
+moduleclass = 'vis'
diff --git a/easybuild/easyconfigs/o/OpenSlide/OpenSlide-3.4.1-GCCcore-12.2.0-largefiles.eb b/easybuild/easyconfigs/o/OpenSlide/OpenSlide-3.4.1-GCCcore-12.2.0-largefiles.eb
new file mode 100644
index 00000000000..a8bdbafa429
--- /dev/null
+++ b/easybuild/easyconfigs/o/OpenSlide/OpenSlide-3.4.1-GCCcore-12.2.0-largefiles.eb
@@ -0,0 +1,56 @@
+easyblock = 'ConfigureMake'
+
+name = 'OpenSlide'
+version = '3.4.1'
+versionsuffix = '-largefiles'
+
+homepage = 'https://openslide.org/'
+description = """OpenSlide is a C library that provides a simple interface to
+read whole-slide images (also known as virtual slides)."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+
+source_urls = [GITHUB_SOURCE]
+sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}]
+patches = ['%(name)s-%(version)s_large_file_support.patch']
+checksums = [
+    # v3.4.1.tar.gz
+    'a5d869916e370125421535dcce778b2ba625dc50d920aa4ca93bbaaa6a7b470c',
+    # %(name)s-%(version_major_minor)s.1_large_file_support.patch
+    'cb618053f4ae6c3ce37d1b8b0e4ef7c55fd17378776d13be4aa4efab91706b8c',
+]
+
+builddependencies = [
+    ('Autotools', '20220317'),
+    ('M4', '1.4.19'),
+    ('pkgconf', '1.9.3'),
+    ('binutils', '2.39'),
+]
+
+dependencies = [
+    ('zlib', '1.2.12'),
+    ('libpng', '1.6.38'),
+    ('libjpeg-turbo', '2.1.4'),
+    ('LibTIFF', '4.4.0'),
+    ('OpenJPEG', '2.5.0'),
+    ('libxml2', '2.10.3'),
+    ('SQLite', '3.39.4'),
+    ('cairo', '1.17.4'),
+    ('Gdk-Pixbuf', '2.42.10'),
+]
+
+preconfigopts = "autoreconf -f -i && "
+
+sanity_check_paths = {
+    'files': [
+        'bin/openslide-quickhash1sum',
+        'bin/openslide-show-properties',
+        'bin/openslide-write-png',
+        'lib/libopenslide.la',
+        'lib/libopenslide.%s' % SHLIB_EXT
+    ],
+    'dirs': ['include/openslide']
+}
+
+
+moduleclass = 'vis'
diff --git a/easybuild/easyconfigs/o/openslide-python/openslide-python-1.3.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/o/openslide-python/openslide-python-1.3.1-GCCcore-12.2.0.eb
new file mode 100644
index 00000000000..bbbaa753b40
--- /dev/null
+++ b/easybuild/easyconfigs/o/openslide-python/openslide-python-1.3.1-GCCcore-12.2.0.eb
@@ -0,0 +1,29 @@
+easyblock = 'PythonPackage'
+
+name = 'openslide-python'
+version = '1.3.1'
+
+homepage = 'https://github.com/openslide/openslide-python'
+description = "OpenSlide Python is a Python interface to the OpenSlide library."
+
+toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+
+source_urls = ['https://github.com/openslide/openslide-python/archive']
+sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}]
+checksums = ['3f56bc9d02ae4a5b7257cf5e35214c5cc45f429ff3d5ef849c6c8e2460c1f9cd']
+
+builddependencies = [('binutils', '2.39')]
+
+dependencies = [
+    ('Python', '3.10.8'),
+    ('OpenSlide', '3.4.1', '-largefiles'),
+    ('Pillow-SIMD', '9.5.0'),
+]
+
+use_pip = True
+download_dep_fail = True
+sanity_pip_check = True
+
+options = {'modulename': 'openslide'}
+
+moduleclass = 'vis'
diff --git a/easybuild/easyconfigs/p/pydicom/pydicom-2.4.4-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/pydicom/pydicom-2.4.4-GCCcore-12.2.0.eb
new file mode 100644
index 00000000000..a1071f66e07
--- /dev/null
+++ b/easybuild/easyconfigs/p/pydicom/pydicom-2.4.4-GCCcore-12.2.0.eb
@@ -0,0 +1,26 @@
+easyblock = 'PythonPackage'
+
+name = 'pydicom'
+version = '2.4.4'
+
+homepage = 'https://pydicom.github.io/'
+description = "Pure python package for DICOM medical file reading and writing."
+
+toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+
+source_urls = [GITHUB_SOURCE]
+sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}]
+checksums = ['42c06ed74331174111dd42c89db774a13fc472abe18015f22c5aba80cddb7843']
+
+builddependencies = [
+    ('binutils', '2.39'),
+]
+dependencies = [
+    ('Python', '3.10.8'),
+]
+
+download_dep_fail = True
+use_pip = True
+sanity_pip_check = True
+
+moduleclass = 'vis'
diff --git a/easybuild/easyconfigs/t/tensorboard/tensorboard-2.15.1-gfbf-2022b.eb b/easybuild/easyconfigs/t/tensorboard/tensorboard-2.15.1-gfbf-2022b.eb
new file mode 100644
index 00000000000..304e56b390f
--- /dev/null
+++ b/easybuild/easyconfigs/t/tensorboard/tensorboard-2.15.1-gfbf-2022b.eb
@@ -0,0 +1,90 @@
+easyblock = 'PythonBundle'
+
+name = 'tensorboard'
+version = '2.15.1'
+
+homepage = 'https://github.com/tensorflow/tensorboard'
+description = """TensorBoard is a suite of web applications for inspecting and
+understanding your TensorFlow runs and graphs."""
+
+toolchain = {'name': 'gfbf', 'version': '2022b'}
+
+postinstallpatches = [
+    ('tensorboard-2.10_jupyterhub-support.patch', 'lib/python%(pyshortver)s/site-packages'),
+]
+checksums = [
+    {'tensorboard-2.10_jupyterhub-support.patch':
+     '50a292e6ee518aecb5644595e0f3db4867be4f82e328e008e5a3f6a1f19baf87'},
+]
+
+dependencies = [
+    ('Python', '3.10.8'),
+    ('SciPy-bundle', '2023.02'),
+    ('protobuf-python', '4.23.0'),
+    ('grpcio', '1.57.0'),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    ('absl-py', '2.1.0', {
+        'modulename': 'absl',
+        'checksums': ['7820790efbb316739cde8b4e19357243fc3608a152024288513dd968d7d959ff'],
+    }),
+    ('cachetools', '5.3.2', {
+        'checksums': ['086ee420196f7b2ab9ca2db2520aca326318b68fe5ba8bc4d49cca91add450f2'],
+    }),
+    ('pyasn1_modules', '0.3.0', {
+        'checksums': ['5bd01446b736eb9d31512a30d46c1ac3395d676c6f3cafa4c03eb54b9925631c'],
+    }),
+    ('rsa', '4.9', {
+        'checksums': ['e38464a49c6c85d7f1351b0126661487a7e0a14a50f1675ec50eb34d4f20ef21'],
+    }),
+    ('google-auth', '2.26.2', {
+        'modulename': 'google.auth',
+        'checksums': ['97327dbbf58cccb58fc5a1712bba403ae76668e64814eb30f7316f7e27126b81'],
+    }),
+    ('oauthlib', '3.2.2', {
+        'checksums': ['9859c40929662bec5d64f34d01c99e093149682a3f38915dc0655d5a633dd918'],
+    }),
+    ('requests-oauthlib', '1.3.1', {
+        'checksums': ['75beac4a47881eeb94d5ea5d6ad31ef88856affe2332b9aafb52c6452ccf0d7a'],
+    }),
+    ('google-auth-oauthlib', '1.2.0', {
+        'checksums': ['292d2d3783349f2b0734a0a0207b1e1e322ac193c2c09d8f7c613fb7cc501ea8'],
+    }),
+    ('Markdown', '3.5.2', {
+        'checksums': ['e1ac7b3dc550ee80e602e71c1d168002f062e49f1b11e26a36264dafd4df2ef8'],
+    }),
+    ('tensorboard_data_server', '0.7.2', {
+        'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl',
+        'checksums': ['7e0610d205889588983836ec05dc098e80f97b7e7bbff7e994ebb78f578d0ddb'],
+    }),
+    ('gviz-api', '1.10.0', {
+        'source_tmpl': 'gviz_api-%(version)s.tar.gz',
+        'checksums': ['846692dd8cc73224fc31b18e41589bd934e1cc05090c6576af4b4b26c2e71b90'],
+    }),
+    ('tensorboard-plugin-profile', '2.15.1', {
+        'source_tmpl': 'tensorboard_plugin_profile-%(version)s.tar.gz',
+        'checksums': ['84bb33e446eb4a9c0616f669fc6a42cdd40eadd9ae1d74bf756f4f0479993273'],
+    }),
+    ('Werkzeug', '3.0.1', {
+        'source_tmpl': '%(namelower)s-%(version)s.tar.gz',
+        'checksums': ['507e811ecea72b18a404947aded4b3390e1db8f826b494d76550ef45bb3b1dcc'],
+    }),
+    (name, version, {
+        'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl',
+        'checksums': ['c46c1d1cf13a458c429868a78b2531d8ff5f682058d69ec0840b0bc7a38f1c0f'],
+    }),
+]
+
+#  Relax restriction on protobuf dependency as issue was fixed
+#  in https://github.com/protocolbuffers/upb/pull/1514
+#  see also: https://github.com/easybuilders/easybuild-easyconfigs/pull/19671
+postinstallcmds = [
+    'sed -i "s/Requires-Dist: protobuf.*/Requires-Dist: protobuf >=3.19.6/g" ' +
+    '%(installdir)s/lib/python%(pyshortver)s/site-packages/%(name)s-%(version)s.dist-info/METADATA',
+]
+
+moduleclass = 'lib'

From 1335f8605cf78afef4924879715d8d278cbece92 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com>
Date: Wed, 7 Aug 2024 11:55:28 +0200
Subject: [PATCH 580/835] Update MONAI-1.3.0-foss-2022b.eb delete comments

---
 easybuild/easyconfigs/m/MONAI/MONAI-1.3.0-foss-2022b.eb | 1 -
 1 file changed, 1 deletion(-)

diff --git a/easybuild/easyconfigs/m/MONAI/MONAI-1.3.0-foss-2022b.eb b/easybuild/easyconfigs/m/MONAI/MONAI-1.3.0-foss-2022b.eb
index ab27a322fb6..29dbbe424ba 100644
--- a/easybuild/easyconfigs/m/MONAI/MONAI-1.3.0-foss-2022b.eb
+++ b/easybuild/easyconfigs/m/MONAI/MONAI-1.3.0-foss-2022b.eb
@@ -14,7 +14,6 @@ toolchain = {'name': 'foss', 'version': '2022b'}
 github_account = 'Project-MONAI'
 
 builddependencies = [
-    # ('hatchling', '1.18.0'),
     ('Ninja', '1.11.1'),
 ]
 

From 88a6d55612b0ecf5eb1a1e415a8d235ffe97d19a Mon Sep 17 00:00:00 2001
From: Samuel Moors <samuel.moors@vub.be>
Date: Wed, 7 Aug 2024 12:37:19 +0200
Subject: [PATCH 581/835] also copy data to installdir

---
 .../easyconfigs/c/CORSIKA/CORSIKA-77550-foss-2023a.eb  | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/easybuild/easyconfigs/c/CORSIKA/CORSIKA-77550-foss-2023a.eb b/easybuild/easyconfigs/c/CORSIKA/CORSIKA-77550-foss-2023a.eb
index c516f698db4..dc008b79e18 100644
--- a/easybuild/easyconfigs/c/CORSIKA/CORSIKA-77550-foss-2023a.eb
+++ b/easybuild/easyconfigs/c/CORSIKA/CORSIKA-77550-foss-2023a.eb
@@ -31,12 +31,14 @@ configopts += "--enable-PARALLEL --with-mpirunner-lib --enable-PARALLELIB "
 build_cmd = "./coconut"
 buildopts = "--batch"
 
-preinstallopts = "mkdir -p %(installdir)s/bin && "
-install_cmd = "cp"
-installopts = "%(builddir)s/%(namelower)s-%(version)s/run/%(namelower)s%(version)s* %(installdir)s/bin/"
+install_cmd = ' && '.join([
+    'mkdir -p %(installdir)s/{bin,data}',
+    'mv %(builddir)s/%(namelower)s-%(version)s/run/%(namelower)s%(version)s* %(installdir)s/bin/',
+    'cp %(builddir)s/%(namelower)s-%(version)s/run/* %(installdir)s/data/',
+])
 
 sanity_check_paths = {
-    'files': ['bin/corsika77550Linux_QGSII_urqmd_thin_coreas_parallel'],
+    'files': ['bin/corsika77550Linux_QGSII_urqmd_thin_coreas_parallel', 'data/NUCNUCCS'],
     'dirs': []
 }
 

From 965f7d460059f228a0eaac9c4afa769d19c65fa5 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Wed, 7 Aug 2024 13:05:06 +0200
Subject: [PATCH 582/835] add patch for ITK

---
 .../easyconfigs/i/ITK/ITK-5.3.0_vtk-include.patch   | 13 +++++++++++++
 1 file changed, 13 insertions(+)
 create mode 100644 easybuild/easyconfigs/i/ITK/ITK-5.3.0_vtk-include.patch

diff --git a/easybuild/easyconfigs/i/ITK/ITK-5.3.0_vtk-include.patch b/easybuild/easyconfigs/i/ITK/ITK-5.3.0_vtk-include.patch
new file mode 100644
index 00000000000..f77306c9f8e
--- /dev/null
+++ b/easybuild/easyconfigs/i/ITK/ITK-5.3.0_vtk-include.patch
@@ -0,0 +1,13 @@
+Manually add the include directory of VTK
+dirty fix for issue https://github.com/InsightSoftwareConsortium/ITK/issues/4375
+author: Alex Domingo (Vrije Universiteit Brussel)
+--- Wrapping/CMakeLists.txt.orig	2023-12-21 13:41:44.845008000 +0100
++++ Wrapping/CMakeLists.txt	2023-12-21 13:42:14.794328946 +0100
+@@ -112,6 +112,7 @@
+ ###############################################################################
+ # Configure specific wrapper modules
+ ###############################################################################
++include_directories("$ENV{EBROOTVTK}/include/vtk-9.2/")
+ 
+ unset(WRAP_ITK_MODULES CACHE)
+ 
\ No newline at end of file

From 3dc038f64c146dc3c3caca60e8cb46aa41689d05 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com>
Date: Wed, 7 Aug 2024 15:17:13 +0200
Subject: [PATCH 583/835] Update ITK-5.3.0-foss-2022b.eb update checksum

---
 easybuild/easyconfigs/i/ITK/ITK-5.3.0-foss-2022b.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/i/ITK/ITK-5.3.0-foss-2022b.eb b/easybuild/easyconfigs/i/ITK/ITK-5.3.0-foss-2022b.eb
index 2f64dbf8f87..9ba65978898 100644
--- a/easybuild/easyconfigs/i/ITK/ITK-5.3.0-foss-2022b.eb
+++ b/easybuild/easyconfigs/i/ITK/ITK-5.3.0-foss-2022b.eb
@@ -24,7 +24,7 @@ patches = [
     'ITK-5.3.0_fix-compatibility-swig-4-1.patch',
 ]
 checksums = [
-    {'v5.3.0.tar.gz': '64e7e8094a5023c8f68ee042459d6319581fadb35e2fe90a4ae230ce36369db1'},
+    {'ITK-5.3.0.tar.gz': '64e7e8094a5023c8f68ee042459d6319581fadb35e2fe90a4ae230ce36369db1'},
     {'ITK-5.3.0_vtk-include.patch': '138ebd2e0e7f9001aba5f4a7e8145ffcf0093913d50f109ecff447773fd52a48'},
     {'ITK-5.3.0_fix-compatibility-swig-4-1.patch': '0138878d96e90d6bfdc81fd4f2b5ec413d61c1de666a16842b417c2686ebf506'},
 ]

From 39e7406baf1c4a71dfcee7657340c73b69b59736 Mon Sep 17 00:00:00 2001
From: Alexander Grund <alexander.grund@tu-dresden.de>
Date: Wed, 7 Aug 2024 18:29:39 +0200
Subject: [PATCH 584/835] Fix checksum checks for bundles

Some bundle easyconfigs have a checksums parameter.
The current test code clears that unconditionally which makes the test
fail when it should not.
As we know the easyconfig dict will be modified we can just make a copy
here.
---
 test/easyconfigs/easyconfigs.py | 30 ++++++++++++------------------
 1 file changed, 12 insertions(+), 18 deletions(-)

diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py
index d228333cca6..b4111d97a3b 100644
--- a/test/easyconfigs/easyconfigs.py
+++ b/test/easyconfigs/easyconfigs.py
@@ -1045,25 +1045,19 @@ def test_pr_sha256_checksums(self):
             'R-bundle-Bioconductor-3.[2-5]',
         ]
 
-        # the check_sha256_checksums function (again) creates an EasyBlock instance
-        # for easyconfigs using the Bundle easyblock, this is a problem because the 'sources' easyconfig parameter
-        # is updated in place (sources for components are added to the 'parent' sources) in Bundle's __init__;
-        # therefore, we need to reset 'sources' to an empty list here if Bundle is used...
-        # likewise for 'patches' and 'checksums'
-        bundle_easyblocks = ['Bundle', 'CargoPythonBundle', 'PythonBundle', 'EB_OpenSSL_wrapper']
-        for ec in self.changed_ecs:
-            if ec['easyblock'] in bundle_easyblocks or ec['name'] in ['Clang-AOMP']:
-                ec['sources'] = []
-                ec['patches'] = []
-                ec['checksums'] = []
-
         # filter out deprecated easyconfigs
-        retained_changed_ecs = []
-        for ec in self.changed_ecs:
-            if not ec['deprecated']:
-                retained_changed_ecs.append(ec)
-
-        checksum_issues = check_sha256_checksums(retained_changed_ecs, whitelist=whitelist)
+        retained_changed_ecs = [ec for ec in self.changed_ecs if not ec['deprecated']]
+
+        # The check_sha256_checksums function creates an EasyBlock instance.
+        # For easyconfigs using the Bundle easyblock, this is a problem because the 'sources' easyconfig parameter
+        # is updated in place (sources for components are added to the 'parent' sources) in Bundle's __init__.
+        # Therefore, we need to a operate on a copy of those easyconfigs.
+        bundle_easyblocks = {'Bundle', 'CargoPythonBundle', 'PythonBundle', 'EB_OpenSSL_wrapper'}
+
+        def is_bundle(ec):
+            return ec['easyblock'] in bundle_easyblocks or ec['name'] == 'Clang-AOMP'
+        ecs = [ec.copy() if is_bundle(ec) else ec for ec in retained_changed_ecs]
+        checksum_issues = check_sha256_checksums(ecs, whitelist=whitelist)
         self.assertTrue(len(checksum_issues) == 0, "No checksum issues:\n%s" % '\n'.join(checksum_issues))
 
     @skip_if_not_pr_to_non_main_branch()

From fabca65ac85660898903540f5c79d3184f8ad62f Mon Sep 17 00:00:00 2001
From: fizwit <john@fuzzdog.com>
Date: Wed, 7 Aug 2024 15:44:56 -0700
Subject: [PATCH 585/835] add pkconf

---
 .../easyconfigs/s/scikit-misc/scikit-misc-0.3.1-foss-2023a.eb | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/easybuild/easyconfigs/s/scikit-misc/scikit-misc-0.3.1-foss-2023a.eb b/easybuild/easyconfigs/s/scikit-misc/scikit-misc-0.3.1-foss-2023a.eb
index e355180eb49..dda0a838bf3 100644
--- a/easybuild/easyconfigs/s/scikit-misc/scikit-misc-0.3.1-foss-2023a.eb
+++ b/easybuild/easyconfigs/s/scikit-misc/scikit-misc-0.3.1-foss-2023a.eb
@@ -9,6 +9,10 @@ description = "Miscellaneous tools for data analysis and scientific computing"
 
 toolchain = {'name': 'foss', 'version': '2023a'}
 
+builddependencies = [
+    ('pkgconf', '1.9.5'),
+]
+
 dependencies = [
     ('Python', '3.11.3'),
     ('SciPy-bundle', '2023.07'),

From 719a54206dd2ddefb166e415e81d13e8adbd19a4 Mon Sep 17 00:00:00 2001
From: Jessie Hernandez <jessie.hernandez@shell.com>
Date: Thu, 8 Aug 2024 10:47:57 +0200
Subject: [PATCH 586/835] adding easyconfigs:
 libedit-20240517-GCCcore-13.2.0.eb

---
 .../libedit-20240517-GCCcore-13.2.0.eb        | 27 +++++++++++++++++++
 1 file changed, 27 insertions(+)
 create mode 100644 easybuild/easyconfigs/l/libedit/libedit-20240517-GCCcore-13.2.0.eb

diff --git a/easybuild/easyconfigs/l/libedit/libedit-20240517-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/libedit/libedit-20240517-GCCcore-13.2.0.eb
new file mode 100644
index 00000000000..098fd8b7bde
--- /dev/null
+++ b/easybuild/easyconfigs/l/libedit/libedit-20240517-GCCcore-13.2.0.eb
@@ -0,0 +1,27 @@
+easyblock = 'ConfigureMake'
+
+name = 'libedit'
+version = '20240517'
+
+homepage = 'https://thrysoee.dk/editline/'
+description = """
+This BSD-style licensed command line editor library provides generic line editing,
+history, and tokenization functions, similar to those found in GNU Readline.
+"""
+
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
+
+source_urls = ['https://thrysoee.dk/editline/']
+sources = ['%(namelower)s-%(version)s-3.1.tar.gz']
+checksums = ['3a489097bb4115495f3bd85ae782852b7097c556d9500088d74b6fa38dbd12ff']
+
+builddependencies = [('binutils', '2.40')]
+
+dependencies = [('ncurses', '6.4')]
+
+sanity_check_paths = {
+    'files': ['include/editline/readline.h', 'lib/libedit.%s' % SHLIB_EXT, 'lib/libedit.a'],
+    'dirs': []
+}
+
+moduleclass = 'lib'

From 42d28fe6a8e21f3945d59351c2a1cdd7bab21f4e Mon Sep 17 00:00:00 2001
From: Jessie Hernandez <jessie.hernandez@shell.com>
Date: Thu, 8 Aug 2024 10:49:33 +0200
Subject: [PATCH 587/835] adding easyconfigs: fmt-10.2.1-GCCcore-13.2.0.eb

---
 .../f/fmt/fmt-10.2.1-GCCcore-13.2.0.eb        | 27 +++++++++++++++++++
 1 file changed, 27 insertions(+)
 create mode 100644 easybuild/easyconfigs/f/fmt/fmt-10.2.1-GCCcore-13.2.0.eb

diff --git a/easybuild/easyconfigs/f/fmt/fmt-10.2.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/f/fmt/fmt-10.2.1-GCCcore-13.2.0.eb
new file mode 100644
index 00000000000..45cfe72e73f
--- /dev/null
+++ b/easybuild/easyconfigs/f/fmt/fmt-10.2.1-GCCcore-13.2.0.eb
@@ -0,0 +1,27 @@
+easyblock = 'CMakeMake'
+
+name = 'fmt'
+version = '10.2.1'
+
+homepage = 'http://fmtlib.net/'
+description = "fmt (formerly cppformat) is an open-source formatting library."
+
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://github.com/fmtlib/fmt/releases/download/%(version)s/']
+sources = ['fmt-%(version)s.zip']
+checksums = ['312151a2d13c8327f5c9c586ac6cf7cddc1658e8f53edae0ec56509c8fa516c9']
+
+
+builddependencies = [
+    ('binutils', '2.40'),
+    ('CMake', '3.27.6'),
+]
+
+sanity_check_paths = {
+    'files': ['lib/libfmt.a'],
+    'dirs': ['include/fmt', 'lib/cmake'],
+}
+
+moduleclass = 'lib'

From 8097c1293a719ed0116d06a0724708867ae18f7d Mon Sep 17 00:00:00 2001
From: WilleBell <cintiawillemyns@gmail.com>
Date: Thu, 8 Aug 2024 13:42:27 +0200
Subject: [PATCH 588/835] adding easyconfigs:
 PyRosetta-4.release-384-gompi-2022a.eb

---
 .../PyRosetta-4.release-384-gompi-2022a.eb    | 38 +++++++++++++++++++
 1 file changed, 38 insertions(+)
 create mode 100644 easybuild/easyconfigs/p/PyRosetta/PyRosetta-4.release-384-gompi-2022a.eb

diff --git a/easybuild/easyconfigs/p/PyRosetta/PyRosetta-4.release-384-gompi-2022a.eb b/easybuild/easyconfigs/p/PyRosetta/PyRosetta-4.release-384-gompi-2022a.eb
new file mode 100644
index 00000000000..5769add932d
--- /dev/null
+++ b/easybuild/easyconfigs/p/PyRosetta/PyRosetta-4.release-384-gompi-2022a.eb
@@ -0,0 +1,38 @@
+easyblock = 'PythonBundle'
+
+name = 'PyRosetta'
+version = '4.release-384'
+
+homepage = 'https://www.pyrosetta.org/'
+description = """
+PyRosetta is an interactive Python-based interface to the powerful Rosetta molecular modeling
+suite. It enables users to design their own custom molecular modeling algorithms using Rosetta
+sampling methods and energy functions.
+"""
+
+toolchain = {'name': 'gompi', 'version': '2022a'}
+toolchainopts = {'usempi': True}
+
+builddependencies = [('binutils', '2.38')]
+
+dependencies = [
+    ('Python', '3.10.4'),
+]
+
+use_pip = True
+
+local_source_tmpl = '%(name)s%(version_major)s.Release.python%(pymajver)s%(pyminver)s.linux.%(version_minor)s.tar.bz2'
+local_source_urls = 'https://graylab.jhu.edu/download/PyRosetta4/archive/release/PyRosetta4.Release.python310.linux/'
+
+exts_list = [
+    (name, version, {
+        'source_tmpl': local_source_tmpl,
+        'source_urls': [local_source_urls],
+        'start_dir': 'setup',
+        'checksums': ['630108f2bac166563fd2a4046a1d82e51e14693bb0e20dd3174e71c02b0760c2'],
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'bio'

From d7f2247920cd6a3ec8da634167ec75774204b38e Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Thu, 8 Aug 2024 15:41:58 +0200
Subject: [PATCH 589/835] adding easyconfigs: MBX-1.1.0-foss-2023a.eb

---
 .../easyconfigs/m/MBX/MBX-1.1.0-foss-2023a.eb | 52 +++++++++++++++++++
 1 file changed, 52 insertions(+)
 create mode 100644 easybuild/easyconfigs/m/MBX/MBX-1.1.0-foss-2023a.eb

diff --git a/easybuild/easyconfigs/m/MBX/MBX-1.1.0-foss-2023a.eb b/easybuild/easyconfigs/m/MBX/MBX-1.1.0-foss-2023a.eb
new file mode 100644
index 00000000000..e0ad4d59124
--- /dev/null
+++ b/easybuild/easyconfigs/m/MBX/MBX-1.1.0-foss-2023a.eb
@@ -0,0 +1,52 @@
+easyblock = 'ConfigureMake'
+
+name = 'MBX'
+version = '1.1.0'
+
+homepage = 'https://github.com/paesanilab/MBX'
+description = "MBX is an energy and force calculator for data-driven many-body simulations"
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+toolchainopts = {'pic': True, 'openmp': True}
+
+source_urls = ['https://github.com/paesanilab/MBX/archive/']
+sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}]
+checksums = ['0f55f4950226defb46fd0814ad97f906ce4ffd6403af6817bd98cb3c68996692']
+
+builddependencies = [('Autotools', '20220317')]
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('GSL', '2.7'),
+]
+
+buildininstalldir = True
+
+preconfigopts = 'echo HEEERE && echo %(installdir)s && export MBX_HOME=%(installdir)s && autoreconf -fi && '
+
+configopts = '--enable-shared --enable-verbose CXX="$CXX"'
+
+prebuildopts = 'export MBX_HOME=%(installdir)s && '
+
+preinstallopts = 'export MBX_HOME=%(installdir)s && '
+
+maxparallel = 3
+
+runtest = 'check'
+
+modextrapaths = {'PYTHONPATH': '%(name)s-%(version)s/plugins/python'}
+
+modextravars = {'MBX_HOME': '%(installdir)s'}
+
+sanity_check_paths = {
+    'files': ['bin/mb_decomp', 'bin/optimize', 'bin/order_frames', 'bin/single_point',
+              'lib/libmbx.a', 'lib/libmbx.%s' % SHLIB_EXT],
+    'dirs': ['include', '%(name)s-%(version)s/plugins/python/mbx'],
+}
+
+sanity_check_commands = [
+    "optimize",
+    "python -c 'import mbx'",
+]
+
+moduleclass = 'chem'

From 53585cf98a9d7484bcfd252535674ac035d9ac48 Mon Sep 17 00:00:00 2001
From: Simon Branford <s.j.branford@bham.ac.uk>
Date: Thu, 8 Aug 2024 17:14:26 +0100
Subject: [PATCH 590/835] disable use of MySQL in GDAL

---
 easybuild/easyconfigs/g/GDAL/GDAL-3.6.2-foss-2022b.eb | 2 ++
 easybuild/easyconfigs/g/GDAL/GDAL-3.7.1-foss-2023a.eb | 2 +-
 easybuild/easyconfigs/g/GDAL/GDAL-3.9.0-foss-2023b.eb | 2 +-
 3 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.6.2-foss-2022b.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.6.2-foss-2022b.eb
index a527795dfc3..831b5465ec1 100644
--- a/easybuild/easyconfigs/g/GDAL/GDAL-3.6.2-foss-2022b.eb
+++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.6.2-foss-2022b.eb
@@ -61,8 +61,10 @@ dependencies = [
 # common configopts for static, shared library builds
 _base_configopts = ' '.join([
     '-DGDAL_USE_INTERNAL_LIBS=OFF',
+    '-DArrow_DIR=$EBROOTARROW',
     '-DGEOTIFF_INCLUDE_DIR=$EBROOTLIBGEOTIFF/include',
     '-DPython_ROOT=$EBROOTPYTHON',
+    '-DGDAL_USE_MYSQL=OFF',
 ])
 
 # iterative build for both static and shared libraries
diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.7.1-foss-2023a.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.7.1-foss-2023a.eb
index df1c21eb72a..ad4ea255ed2 100644
--- a/easybuild/easyconfigs/g/GDAL/GDAL-3.7.1-foss-2023a.eb
+++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.7.1-foss-2023a.eb
@@ -61,7 +61,7 @@ dependencies = [
 ]
 
 # iterative build for both static and shared libraries
-local_configopts_common = "-DGDAL_USE_INTERNAL_LIBS=OFF "
+local_configopts_common = "-DGDAL_USE_INTERNAL_LIBS=OFF -DArrow_DIR=$EBROOTARROW -DGDAL_USE_MYSQL=OFF "
 local_configopts_common += "-DGEOTIFF_INCLUDE_DIR=$EBROOTLIBGEOTIFF/include -DPython_ROOT=$EBROOTPYTHON "
 
 configopts = [
diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.9.0-foss-2023b.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.9.0-foss-2023b.eb
index ba67862143a..21299457516 100644
--- a/easybuild/easyconfigs/g/GDAL/GDAL-3.9.0-foss-2023b.eb
+++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.9.0-foss-2023b.eb
@@ -60,7 +60,7 @@ dependencies = [
 ]
 
 # iterative build for both static and shared libraries
-local_configopts_common = "-DGDAL_USE_INTERNAL_LIBS=OFF "
+local_configopts_common = "-DGDAL_USE_INTERNAL_LIBS=OFF -DGDAL_USE_MYSQL=OFF "
 local_configopts_common += "-DGEOTIFF_INCLUDE_DIR=$EBROOTLIBGEOTIFF/include -DPython_ROOT=$EBROOTPYTHON "
 
 configopts = [

From 06bcdf1fa9f8f722b9dddf61dd9458e0f1202def Mon Sep 17 00:00:00 2001
From: Simon Branford <s.j.branford@bham.ac.uk>
Date: Thu, 8 Aug 2024 17:16:41 +0100
Subject: [PATCH 591/835] remove accidental change, as based this on EB5

---
 easybuild/easyconfigs/g/GDAL/GDAL-3.6.2-foss-2022b.eb | 1 -
 easybuild/easyconfigs/g/GDAL/GDAL-3.7.1-foss-2023a.eb | 2 +-
 2 files changed, 1 insertion(+), 2 deletions(-)

diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.6.2-foss-2022b.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.6.2-foss-2022b.eb
index 831b5465ec1..576d90e74d6 100644
--- a/easybuild/easyconfigs/g/GDAL/GDAL-3.6.2-foss-2022b.eb
+++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.6.2-foss-2022b.eb
@@ -61,7 +61,6 @@ dependencies = [
 # common configopts for static, shared library builds
 _base_configopts = ' '.join([
     '-DGDAL_USE_INTERNAL_LIBS=OFF',
-    '-DArrow_DIR=$EBROOTARROW',
     '-DGEOTIFF_INCLUDE_DIR=$EBROOTLIBGEOTIFF/include',
     '-DPython_ROOT=$EBROOTPYTHON',
     '-DGDAL_USE_MYSQL=OFF',
diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.7.1-foss-2023a.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.7.1-foss-2023a.eb
index ad4ea255ed2..88e35cd4db4 100644
--- a/easybuild/easyconfigs/g/GDAL/GDAL-3.7.1-foss-2023a.eb
+++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.7.1-foss-2023a.eb
@@ -61,7 +61,7 @@ dependencies = [
 ]
 
 # iterative build for both static and shared libraries
-local_configopts_common = "-DGDAL_USE_INTERNAL_LIBS=OFF -DArrow_DIR=$EBROOTARROW -DGDAL_USE_MYSQL=OFF "
+local_configopts_common = "-DGDAL_USE_INTERNAL_LIBS=OFF -DGDAL_USE_MYSQL=OFF "
 local_configopts_common += "-DGEOTIFF_INCLUDE_DIR=$EBROOTLIBGEOTIFF/include -DPython_ROOT=$EBROOTPYTHON "
 
 configopts = [

From d4707a4d6e7b55bdb1f6bdd5f65f251a1fea2f1c Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Thu, 8 Aug 2024 18:39:58 +0200
Subject: [PATCH 592/835] adding easyconfigs: miniprot-0.13-GCCcore-12.3.0.eb

---
 .../miniprot/miniprot-0.13-GCCcore-12.3.0.eb  | 33 +++++++++++++++++++
 1 file changed, 33 insertions(+)
 create mode 100644 easybuild/easyconfigs/m/miniprot/miniprot-0.13-GCCcore-12.3.0.eb

diff --git a/easybuild/easyconfigs/m/miniprot/miniprot-0.13-GCCcore-12.3.0.eb b/easybuild/easyconfigs/m/miniprot/miniprot-0.13-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..aa598c6869b
--- /dev/null
+++ b/easybuild/easyconfigs/m/miniprot/miniprot-0.13-GCCcore-12.3.0.eb
@@ -0,0 +1,33 @@
+easyblock = "MakeCp"
+
+name = 'miniprot'
+version = '0.13'
+
+homepage = 'https://github.com/lh3/miniprot'
+description = """Miniprot aligns a protein sequence against a genome with affine gap penalty, splicing and frameshift.
+It is primarily intended for annotating protein-coding genes in a new species using known genes from other species.
+Miniprot is similar to GeneWise and Exonerate in functionality but it can map proteins to whole genomes and is much
+faster at the residue alignment step."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+source_urls = ['https://github.com/lh3/miniprot/archive']
+sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}]
+checksums = ['be12d98d998beb78e4e06350c03d2f188bcdf3245d6bcaf43e2cc80785a617a4']
+
+builddependencies = [('binutils', '2.40')]
+dependencies = [('zlib', '1.2.13')]
+
+files_to_copy = [
+    (['*.h', 'miniprot.1', 'test', 'tex'], 'lib'),
+    (['miniprot'], 'bin'),
+    'README.md',
+    'LICENSE.txt',
+]
+
+sanity_check_paths = {
+    'files': ['bin/miniprot'],
+    'dirs': ['lib'],
+}
+
+moduleclass = 'bio'

From 25ee0adf01fc5e93c5d15408cb13a0d9b717a3f0 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Fri, 9 Aug 2024 14:58:14 +0200
Subject: [PATCH 593/835] get rid of buildininstalldir

---
 .../easyconfigs/m/MBX/MBX-1.1.0-foss-2023a.eb      | 14 +++++---------
 1 file changed, 5 insertions(+), 9 deletions(-)

diff --git a/easybuild/easyconfigs/m/MBX/MBX-1.1.0-foss-2023a.eb b/easybuild/easyconfigs/m/MBX/MBX-1.1.0-foss-2023a.eb
index e0ad4d59124..3f6da986d62 100644
--- a/easybuild/easyconfigs/m/MBX/MBX-1.1.0-foss-2023a.eb
+++ b/easybuild/easyconfigs/m/MBX/MBX-1.1.0-foss-2023a.eb
@@ -20,28 +20,24 @@ dependencies = [
     ('GSL', '2.7'),
 ]
 
-buildininstalldir = True
-
-preconfigopts = 'echo HEEERE && echo %(installdir)s && export MBX_HOME=%(installdir)s && autoreconf -fi && '
+preconfigopts = 'export MBX_HOME=$PWD && autoreconf -fi && '
 
 configopts = '--enable-shared --enable-verbose CXX="$CXX"'
 
-prebuildopts = 'export MBX_HOME=%(installdir)s && '
-
-preinstallopts = 'export MBX_HOME=%(installdir)s && '
+postinstallcmds = ["cp -a plugins %(installdir)s"]
 
-maxparallel = 3
+maxparallel = 2
 
 runtest = 'check'
 
-modextrapaths = {'PYTHONPATH': '%(name)s-%(version)s/plugins/python'}
+modextrapaths = {'PYTHONPATH': 'plugins/python'}
 
 modextravars = {'MBX_HOME': '%(installdir)s'}
 
 sanity_check_paths = {
     'files': ['bin/mb_decomp', 'bin/optimize', 'bin/order_frames', 'bin/single_point',
               'lib/libmbx.a', 'lib/libmbx.%s' % SHLIB_EXT],
-    'dirs': ['include', '%(name)s-%(version)s/plugins/python/mbx'],
+    'dirs': ['include', 'plugins/python/mbx', 'plugins/lammps/USER-MBX'],
 }
 
 sanity_check_commands = [

From c1e7866a009bceb9b76296a1ef49d6834572e813 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Fri, 9 Aug 2024 15:33:51 +0200
Subject: [PATCH 594/835] adding easyconfigs: Salmon-1.10.3-GCC-12.3.0.eb

---
 .../s/Salmon/Salmon-1.10.3-GCC-12.3.0.eb      | 59 +++++++++++++++++++
 1 file changed, 59 insertions(+)
 create mode 100644 easybuild/easyconfigs/s/Salmon/Salmon-1.10.3-GCC-12.3.0.eb

diff --git a/easybuild/easyconfigs/s/Salmon/Salmon-1.10.3-GCC-12.3.0.eb b/easybuild/easyconfigs/s/Salmon/Salmon-1.10.3-GCC-12.3.0.eb
new file mode 100644
index 00000000000..20bd7fd9540
--- /dev/null
+++ b/easybuild/easyconfigs/s/Salmon/Salmon-1.10.3-GCC-12.3.0.eb
@@ -0,0 +1,59 @@
+# #
+# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia
+# Homepage:     https://staff.flinders.edu.au/research/deep-thought
+#
+# Authors::     Robert Qiao <rob.qiao@flinders.edu.au>
+# License::     GLPv2
+#
+# Notes::
+# #
+# Contribution from the NIHR Biomedical Research Centre
+# Guy's and St Thomas' NHS Foundation Trust and King's College London
+# uploaded by J. Sassmannshausen
+# Thanks to people like Simon Brandord, Mikael Oehmann and Kenneth Hoste
+# for their help with the ICE
+
+easyblock = 'CMakeMake'
+
+name = 'Salmon'
+version = '1.10.3'
+
+homepage = 'https://github.com/COMBINE-lab/salmon'
+description = """Salmon is a wicked-fast program to produce a highly-accurate,
+ transcript-level quantification estimate from RNA-seq data."""
+
+toolchain = {'name': 'GCC', 'version': '12.3.0'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://github.com/COMBINE-lab/salmon/archive']
+sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}]
+checksums = ['a053fba63598efc4ade3684aa2c8e8e2294186927d4fcdf1041c36edc2aa0871']
+    
+builddependencies = [
+    ('CMake', '3.26.3'),
+    ('pkgconf', '1.9.5'),
+    ('jemalloc', '5.3.0'),
+    ('Cereal', '1.3.2', '', SYSTEM),
+]
+dependencies = [
+    ('Boost', '1.82.0'),
+    ('tbb', '2021.11.0'),
+    ('cURL', '8.0.1'),
+    ('libiconv', '1.17'),
+    ('bzip2', '1.0.8'),
+    ('XZ', '5.4.2'),
+    ('zlib', '1.2.13'),
+]
+
+configopts = "-DJEMALLOC_ROOT=$EBROOTJEMALLOC"
+
+runtest = 'test'
+
+sanity_check_paths = {
+    'files': ['bin/%(namelower)s', 'lib/libgraphdump.a', 'lib/libntcard.a', 'lib/libsalmon_core.a', 'lib/libtwopaco.a'],
+    'dirs': [],
+}
+
+sanity_check_commands = ['%(namelower)s --help']
+
+moduleclass = 'bio'

From adffacad851fccdc5ebdcfd2b8c71218da406550 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com>
Date: Fri, 9 Aug 2024 16:31:35 +0200
Subject: [PATCH 595/835] Update Salmon-1.10.3-GCC-12.3.0.eb fix whitespace

---
 easybuild/easyconfigs/s/Salmon/Salmon-1.10.3-GCC-12.3.0.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/s/Salmon/Salmon-1.10.3-GCC-12.3.0.eb b/easybuild/easyconfigs/s/Salmon/Salmon-1.10.3-GCC-12.3.0.eb
index 20bd7fd9540..9b52051eed3 100644
--- a/easybuild/easyconfigs/s/Salmon/Salmon-1.10.3-GCC-12.3.0.eb
+++ b/easybuild/easyconfigs/s/Salmon/Salmon-1.10.3-GCC-12.3.0.eb
@@ -28,7 +28,7 @@ toolchainopts = {'pic': True}
 source_urls = ['https://github.com/COMBINE-lab/salmon/archive']
 sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}]
 checksums = ['a053fba63598efc4ade3684aa2c8e8e2294186927d4fcdf1041c36edc2aa0871']
-    
+
 builddependencies = [
     ('CMake', '3.26.3'),
     ('pkgconf', '1.9.5'),

From 2e65e2d4c0fb44b6923aef29cd4c86fd13d67741 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Fri, 9 Aug 2024 17:05:46 +0200
Subject: [PATCH 596/835] adding easyconfigs: CDO-2.3.0-iimpi-2022a.eb

---
 .../c/CDO/CDO-2.3.0-iimpi-2022a.eb            | 58 +++++++++++++++++++
 1 file changed, 58 insertions(+)
 create mode 100644 easybuild/easyconfigs/c/CDO/CDO-2.3.0-iimpi-2022a.eb

diff --git a/easybuild/easyconfigs/c/CDO/CDO-2.3.0-iimpi-2022a.eb b/easybuild/easyconfigs/c/CDO/CDO-2.3.0-iimpi-2022a.eb
new file mode 100644
index 00000000000..58cf406d164
--- /dev/null
+++ b/easybuild/easyconfigs/c/CDO/CDO-2.3.0-iimpi-2022a.eb
@@ -0,0 +1,58 @@
+# updated to version 2.0.6, based on the previous 2.0.5 version
+# J. Sassmannshausen (Imperial College London, UK)
+# Alex Domingo (Vrije Universiteit Brussel, BE)
+# Maxim Masterov (SURF, NL)
+
+easyblock = 'ConfigureMake'
+
+name = 'CDO'
+version = '2.3.0'
+
+homepage = 'https://code.zmaw.de/projects/cdo'
+description = """CDO is a collection of command line Operators to manipulate and analyse Climate and NWP model Data."""
+
+toolchain = {'name': 'iimpi', 'version': '2022a'}
+toolchainopts = {'pic': True, 'usempi': True}
+
+source_urls = ['https://code.mpimet.mpg.de/attachments/download/29019/']
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['10c878227baf718a6917837527d4426c2d0022cfac4457c65155b9c57f091f6b']
+
+builddependencies = [
+    ('pkgconf', '1.8.0'),
+]
+
+dependencies = [
+    ('cURL', '7.83.0'),
+    ('ecCodes', '2.27.0'),
+    ('FFTW', '3.3.10'),
+    ('HDF5', '1.12.2'),
+    ('libxml2', '2.9.13'),
+    ('netCDF', '4.9.0'),
+    ('PROJ', '9.0.0'),
+    ('Szip', '2.1.1'),
+    ('UDUNITS', '2.2.28'),
+    ('util-linux', '2.38'),
+]
+
+# Build libcdi
+configopts = "--enable-cdi-lib "
+
+# Use dependencies from EasyBuild
+configopts += "--with-curl=$EBROOTCURL --with-eccodes=$EBROOTECCODES --with-fftw3 --with-hdf5=$EBROOTHDF5 "
+configopts += "--with-netcdf=$EBROOTNETCDF --with-proj=$EBROOTPROJ --with-szlib=$EBROOTSZIP "
+configopts += "--with-udunits2=$EBROOTUDUNITS --with-util-linux-uuid=$EBROOTUTILMINLINUX "
+
+# Make sure that right Fortran compiler is used, also on non-x86_64 architectures
+configopts += 'CPPFLAGS="$CPPFLAGS -DgFortran" '
+
+buildopts = "V=1"
+
+sanity_check_paths = {
+    'files': ['bin/cdo', 'lib/libcdi.a', 'lib/libcdi.%s' % SHLIB_EXT],
+    'dirs': ['include'],
+}
+
+sanity_check_commands = ["cdo --version  2>&1 | grep 'CDI library version : %(version)s'"]
+
+moduleclass = 'data'

From cf5afe3cecba4f61a718676687dee0e90cf8a34d Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Fri, 9 Aug 2024 17:37:11 +0200
Subject: [PATCH 597/835] add ec for dep ecCodes

---
 .../e/ecCodes/ecCodes-2.27.0-iimpi-2022a.eb   | 45 +++++++++++++++++++
 1 file changed, 45 insertions(+)
 create mode 100644 easybuild/easyconfigs/e/ecCodes/ecCodes-2.27.0-iimpi-2022a.eb

diff --git a/easybuild/easyconfigs/e/ecCodes/ecCodes-2.27.0-iimpi-2022a.eb b/easybuild/easyconfigs/e/ecCodes/ecCodes-2.27.0-iimpi-2022a.eb
new file mode 100644
index 00000000000..b93565bb610
--- /dev/null
+++ b/easybuild/easyconfigs/e/ecCodes/ecCodes-2.27.0-iimpi-2022a.eb
@@ -0,0 +1,45 @@
+easyblock = 'CMakeMake'
+
+name = 'ecCodes'
+version = '2.27.0'
+
+homepage = 'https://software.ecmwf.int/wiki/display/ECC/ecCodes+Home'
+description = """ecCodes is a package developed by ECMWF which provides an application programming interface and
+ a set of tools for decoding and encoding messages in the following formats: WMO FM-92 GRIB edition 1 and edition 2,
+ WMO FM-94 BUFR edition 3 and edition 4, WMO GTS abbreviated header (only decoding)."""
+
+toolchain = {'name': 'iimpi', 'version': '2022a'}
+toolchainopts = {'usempi': False}
+
+source_urls = ['https://confluence.ecmwf.int/download/attachments/45757960/']
+sources = ['eccodes-%(version)s-Source.tar.gz']
+checksums = ['ede5b3ffd503967a5eac89100e8ead5e16a881b7585d02f033584ed0c4269c99']
+
+builddependencies = [('CMake', '3.23.1')]
+
+dependencies = [
+    ('netCDF', '4.9.0'),
+    ('JasPer', '2.0.33'),
+    ('libjpeg-turbo', '2.1.3'),
+    ('libpng', '1.6.37'),
+    ('zlib', '1.2.12'),
+    ('libaec', '1.0.6'),
+]
+
+# Python bindings are provided by a separate package 'eccodes-python'
+configopts = "-DENABLE_NETCDF=ON -DENABLE_PNG=ON -DENABLE_PYTHON=OFF "
+configopts += "-DENABLE_JPG=ON -DENABLE_JPG_LIBJASPER=ON "
+configopts += "-DENABLE_ECCODES_THREADS=ON"  # multi-threading with pthreads
+
+local_exes = ['%s_%s' % (a, b)
+              for a in ['bufr', 'grib', 'gts', 'metar']
+              for b in ['compare', 'copy', 'dump', 'filter', 'get', 'ls']]
+local_exes += ['codes_%s' % c for c in ['count', 'info', 'split_file']]
+
+sanity_check_paths = {
+    'files': ['bin/%s' % x for x in local_exes] +
+             ['lib/libeccodes_f90.%s' % SHLIB_EXT, 'lib/libeccodes.%s' % SHLIB_EXT],
+    'dirs': ['include'],
+}
+
+moduleclass = 'tools'

From 4166d5b8caa04f1097761acadaa111813f60cb23 Mon Sep 17 00:00:00 2001
From: Simon Pinches <Simon.Pinches@iter.org>
Date: Fri, 9 Aug 2024 18:38:08 +0200
Subject: [PATCH 598/835] adding easyconfigs: PyCharm-2024.1.6.eb

---
 .../easyconfigs/p/PyCharm/PyCharm-2024.1.6.eb | 20 +++++++++++++++++++
 1 file changed, 20 insertions(+)
 create mode 100644 easybuild/easyconfigs/p/PyCharm/PyCharm-2024.1.6.eb

diff --git a/easybuild/easyconfigs/p/PyCharm/PyCharm-2024.1.6.eb b/easybuild/easyconfigs/p/PyCharm/PyCharm-2024.1.6.eb
new file mode 100644
index 00000000000..37d00512c27
--- /dev/null
+++ b/easybuild/easyconfigs/p/PyCharm/PyCharm-2024.1.6.eb
@@ -0,0 +1,20 @@
+easyblock = 'Tarball'
+
+name = 'PyCharm'
+version = "2024.1.6"
+
+homepage = 'https://www.jetbrains.com/pycharm/'
+description = """PyCharm Community Edition: Python IDE for Professional Developers"""
+
+toolchain = SYSTEM
+
+source_urls = ['https://download-cf.jetbrains.com/python']
+sources = ['pycharm-community-%(version)s.tar.gz']
+checksums = ['539961408de4217a68b84d666d5c10ddb8d7bcf919e3a569f2489438a3237f1a']
+
+sanity_check_paths = {
+    'files': ["bin/pycharm.sh"],
+    'dirs': [],
+}
+
+moduleclass = 'devel'

From 78e994dc672538f7e25eaef61133540049d97ad5 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Sat, 10 Aug 2024 14:12:46 +0200
Subject: [PATCH 599/835] adding easyconfigs: dictys-1.1.0-foss-2023a.eb,
 dictys-1.1.0-foss-2023a-CUDA-12.1.1.eb

---
 .../dictys-1.1.0-foss-2023a-CUDA-12.1.1.eb    | 102 ++++++++++++++++++
 .../d/dictys/dictys-1.1.0-foss-2023a.eb       | 100 +++++++++++++++++
 2 files changed, 202 insertions(+)
 create mode 100644 easybuild/easyconfigs/d/dictys/dictys-1.1.0-foss-2023a-CUDA-12.1.1.eb
 create mode 100644 easybuild/easyconfigs/d/dictys/dictys-1.1.0-foss-2023a.eb

diff --git a/easybuild/easyconfigs/d/dictys/dictys-1.1.0-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/d/dictys/dictys-1.1.0-foss-2023a-CUDA-12.1.1.eb
new file mode 100644
index 00000000000..e5988e75d30
--- /dev/null
+++ b/easybuild/easyconfigs/d/dictys/dictys-1.1.0-foss-2023a-CUDA-12.1.1.eb
@@ -0,0 +1,102 @@
+easyblock = 'PythonBundle'
+
+name = 'dictys'
+version = '1.1.0'
+versionsuffix = '-CUDA-%(cudaver)s'
+
+homepage = 'https://github.com/pinellolab/dictys'
+description = "Context specific and dynamic gene regulatory network reconstruction and analysis."
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+builddependencies = [('poetry', '1.5.1')]
+dependencies = [
+    ('Python', '3.11.3'),
+    ('CUDA', '12.1.1', '', SYSTEM),
+    ('PyTorch-bundle', '2.1.2', versionsuffix),
+    ('pybedtools', '0.9.1'),
+    ('SAMtools', '1.18'),
+    ('MACS2', '2.2.9.1'),
+    ('FFmpeg', '6.0'),
+    ('matplotlib', '3.7.2'),
+    ('Python-bundle-PyPI', '2023.06'),
+    ('SciPy-bundle', '2023.07'),
+    ('networkx', '3.1'),
+    ('h5py', '3.9.0'),
+    ('pyro-ppl', '1.9.0', versionsuffix),
+    ('adjustText', '0.7.3'),
+    ('Pysam', '0.22.0'),
+    ('paramiko', '3.2.0'),
+    ('Jupyter-bundle', '20230823'),
+    ('Qtconsole', '5.5.1'),
+]
+
+# regenerate WellingtonC.c to works with python 3.11 + unpin matplotlib version
+local_pyDNase_preinstallopts = (
+    "cd pyDNase/footprinting && rm WellingtonC.c && cythonize -i WellingtonC.pyx && cd .. && cd .. && "
+    "sed -i 's/matplotlib < 2.0.0/matplotlib/' setup.py && "
+)
+
+exts_list = [
+    ('jupyter_console', '6.6.3', {
+        'source_tmpl': SOURCE_PY3_WHL,
+        'checksums': ['309d33409fcc92ffdad25f0bcdf9a4a9daa61b6f341177570fdac03de5352485'],
+    }),
+    ('jupyter', '1.0.0', {
+        'checksums': ['d9dc4b3318f310e34c82951ea5d6683f67bed7def4b259fafbfe4f1beb1d8e5f'],
+    }),
+    ('args', '0.1.0', {
+        'checksums': ['a785b8d837625e9b61c39108532d95b85274acd679693b71ebb5156848fcf814'],
+    }),
+    ('clint', '0.5.1', {
+        'checksums': ['05224c32b1075563d0b16d0015faaf9da43aa214e4a2140e51f08789e7a4c5aa'],
+    }),
+    ('pynetbox', '7.4.0', {
+        'checksums': ['fd0b1f197b3880048408ff5ed84422dd599bcd9389e32cb06a09b9b0d55c1636'],
+    }),
+    ('yamlordereddictloader', '0.4.2', {
+        'checksums': ['36af2f6210fcff5da4fc4c12e1d815f973dceb41044e795e1f06115d634bca13'],
+    }),
+    ('transitions', '0.9.2', {
+        'checksums': ['2f8490dbdbd419366cef1516032ab06d07ccb5839ef54905e842a472692d4204'],
+    }),
+    ('scp', '0.15.0', {
+        'checksums': ['f1b22e9932123ccf17eebf19e0953c6e9148f589f93d91b872941a696305c83f'],
+    }),
+    ('pyserial', '3.5', {
+        'modulename': 'serial',
+        'checksums': ['3c77e014170dfffbd816e6ffc205e9842efb10be9f58ec16d3e8675b4925cddb'],
+    }),
+    ('ncclient', '0.6.15', {
+        'checksums': ['6757cb41bc9160dfe47f22f5de8cf2f1adf22f27463fb50453cc415ab96773d8'],
+    }),
+    ('junos-eznc', '2.7.1', {
+        'modulename': 'jnpr.junos',
+        'checksums': ['371f0298bf03e0cb4c017c43f6f4122263584eda0d690d0112e93f13daae41ac'],
+    }),
+    ('absl-py', '1.4.0', {
+        'modulename': 'absl',
+        'checksums': ['d2c244d01048ba476e7c080bd2c6df5e141d211de80223460d5b3b8a2a58433d'],
+    }),
+    ('aerleon', '1.9.0', {
+        'checksums': ['850cd621dda750263db313d4473302b48b82adaaa9220e6fd0677cb7900f95f6'],
+    }),
+    ('homer', '0.7.0', {
+        'checksums': ['efaf9b3948f6aecdf88cc87c0296a18aed77c152489a7f85c571965fb16f9e57'],
+    }),
+    ('pyDNase', '0.3.0', {
+        'preinstallopts': local_pyDNase_preinstallopts,
+        'modulename': 'pyDNase',
+        'checksums': ['dba03cadca37929a1cc41545e962136f29efc41f8e3c6de042c51c47ee04d558'],
+    }),
+    (name, version, {
+        'checksums': ['59610a8c57e9fc525ec5d13b69efc8b513c78a85a595e0e2b0138da62a035978'],
+    }),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+sanity_check_commands = ["dictys --help"]
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/d/dictys/dictys-1.1.0-foss-2023a.eb b/easybuild/easyconfigs/d/dictys/dictys-1.1.0-foss-2023a.eb
new file mode 100644
index 00000000000..ad4ba02e66d
--- /dev/null
+++ b/easybuild/easyconfigs/d/dictys/dictys-1.1.0-foss-2023a.eb
@@ -0,0 +1,100 @@
+easyblock = 'PythonBundle'
+
+name = 'dictys'
+version = '1.1.0'
+
+homepage = 'https://github.com/pinellolab/dictys'
+description = "Context specific and dynamic gene regulatory network reconstruction and analysis."
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+builddependencies = [('poetry', '1.5.1')]
+dependencies = [
+    ('Python', '3.11.3'),
+    ('PyTorch-bundle', '2.1.2'),
+    ('pybedtools', '0.9.1'),
+    ('SAMtools', '1.18'),
+    ('MACS2', '2.2.9.1'),
+    ('FFmpeg', '6.0'),
+    ('matplotlib', '3.7.2'),
+    ('Python-bundle-PyPI', '2023.06'),
+    ('SciPy-bundle', '2023.07'),
+    ('networkx', '3.1'),
+    ('h5py', '3.9.0'),
+    ('pyro-ppl', '1.9.0'),
+    ('adjustText', '0.7.3'),
+    ('Pysam', '0.22.0'),
+    ('paramiko', '3.2.0'),
+    ('Jupyter-bundle', '20230823'),
+    ('Qtconsole', '5.5.1'),
+]
+
+# regenerate WellingtonC.c to works with python 3.11 + unpin matplotlib version
+local_pyDNase_preinstallopts = (
+    "cd pyDNase/footprinting && rm WellingtonC.c && cythonize -i WellingtonC.pyx && cd .. && cd .. && "
+    "sed -i 's/matplotlib < 2.0.0/matplotlib/' setup.py && "
+)
+
+exts_list = [
+    ('jupyter_console', '6.6.3', {
+        'source_tmpl': SOURCE_PY3_WHL,
+        'checksums': ['309d33409fcc92ffdad25f0bcdf9a4a9daa61b6f341177570fdac03de5352485'],
+    }),
+    ('jupyter', '1.0.0', {
+        'checksums': ['d9dc4b3318f310e34c82951ea5d6683f67bed7def4b259fafbfe4f1beb1d8e5f'],
+    }),
+    ('args', '0.1.0', {
+        'checksums': ['a785b8d837625e9b61c39108532d95b85274acd679693b71ebb5156848fcf814'],
+    }),
+    ('clint', '0.5.1', {
+        'checksums': ['05224c32b1075563d0b16d0015faaf9da43aa214e4a2140e51f08789e7a4c5aa'],
+    }),
+    ('pynetbox', '7.4.0', {
+        'checksums': ['fd0b1f197b3880048408ff5ed84422dd599bcd9389e32cb06a09b9b0d55c1636'],
+    }),
+    ('yamlordereddictloader', '0.4.2', {
+        'checksums': ['36af2f6210fcff5da4fc4c12e1d815f973dceb41044e795e1f06115d634bca13'],
+    }),
+    ('transitions', '0.9.2', {
+        'checksums': ['2f8490dbdbd419366cef1516032ab06d07ccb5839ef54905e842a472692d4204'],
+    }),
+    ('scp', '0.15.0', {
+        'checksums': ['f1b22e9932123ccf17eebf19e0953c6e9148f589f93d91b872941a696305c83f'],
+    }),
+    ('pyserial', '3.5', {
+        'modulename': 'serial',
+        'checksums': ['3c77e014170dfffbd816e6ffc205e9842efb10be9f58ec16d3e8675b4925cddb'],
+    }),
+    ('ncclient', '0.6.15', {
+        'checksums': ['6757cb41bc9160dfe47f22f5de8cf2f1adf22f27463fb50453cc415ab96773d8'],
+    }),
+    ('junos-eznc', '2.7.1', {
+        'modulename': 'jnpr.junos',
+        'checksums': ['371f0298bf03e0cb4c017c43f6f4122263584eda0d690d0112e93f13daae41ac'],
+    }),
+    ('absl-py', '1.4.0', {
+        'modulename': 'absl',
+        'checksums': ['d2c244d01048ba476e7c080bd2c6df5e141d211de80223460d5b3b8a2a58433d'],
+    }),
+    ('aerleon', '1.9.0', {
+        'checksums': ['850cd621dda750263db313d4473302b48b82adaaa9220e6fd0677cb7900f95f6'],
+    }),
+    ('homer', '0.7.0', {
+        'checksums': ['efaf9b3948f6aecdf88cc87c0296a18aed77c152489a7f85c571965fb16f9e57'],
+    }),
+    ('pyDNase', '0.3.0', {
+        'preinstallopts': local_pyDNase_preinstallopts,
+        'modulename': 'pyDNase',
+        'checksums': ['dba03cadca37929a1cc41545e962136f29efc41f8e3c6de042c51c47ee04d558'],
+    }),
+    (name, version, {
+        'checksums': ['59610a8c57e9fc525ec5d13b69efc8b513c78a85a595e0e2b0138da62a035978'],
+    }),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+sanity_check_commands = ["dictys --help"]
+
+moduleclass = 'bio'

From 8f3466efeb0af98784fbcd1db69657f2f3c51f84 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Sat, 10 Aug 2024 16:08:26 +0200
Subject: [PATCH 600/835] update junos-eznc version to fix tests failing

---
 .../d/dictys/dictys-1.1.0-foss-2023a-CUDA-12.1.1.eb           | 4 ++--
 easybuild/easyconfigs/d/dictys/dictys-1.1.0-foss-2023a.eb     | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/easybuild/easyconfigs/d/dictys/dictys-1.1.0-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/d/dictys/dictys-1.1.0-foss-2023a-CUDA-12.1.1.eb
index e5988e75d30..de99e242d09 100644
--- a/easybuild/easyconfigs/d/dictys/dictys-1.1.0-foss-2023a-CUDA-12.1.1.eb
+++ b/easybuild/easyconfigs/d/dictys/dictys-1.1.0-foss-2023a-CUDA-12.1.1.eb
@@ -70,9 +70,9 @@ exts_list = [
     ('ncclient', '0.6.15', {
         'checksums': ['6757cb41bc9160dfe47f22f5de8cf2f1adf22f27463fb50453cc415ab96773d8'],
     }),
-    ('junos-eznc', '2.7.1', {
+    ('junos-eznc', '2.7.0', {
         'modulename': 'jnpr.junos',
-        'checksums': ['371f0298bf03e0cb4c017c43f6f4122263584eda0d690d0112e93f13daae41ac'],
+        'checksums': ['a45c90641d24ff4c86796418ea76ca64066c06d0bf644d6b77e605bf957c5c7d'],
     }),
     ('absl-py', '1.4.0', {
         'modulename': 'absl',
diff --git a/easybuild/easyconfigs/d/dictys/dictys-1.1.0-foss-2023a.eb b/easybuild/easyconfigs/d/dictys/dictys-1.1.0-foss-2023a.eb
index ad4ba02e66d..e0fa2174545 100644
--- a/easybuild/easyconfigs/d/dictys/dictys-1.1.0-foss-2023a.eb
+++ b/easybuild/easyconfigs/d/dictys/dictys-1.1.0-foss-2023a.eb
@@ -68,9 +68,9 @@ exts_list = [
     ('ncclient', '0.6.15', {
         'checksums': ['6757cb41bc9160dfe47f22f5de8cf2f1adf22f27463fb50453cc415ab96773d8'],
     }),
-    ('junos-eznc', '2.7.1', {
+    ('junos-eznc', '2.7.0', {
         'modulename': 'jnpr.junos',
-        'checksums': ['371f0298bf03e0cb4c017c43f6f4122263584eda0d690d0112e93f13daae41ac'],
+        'checksums': ['a45c90641d24ff4c86796418ea76ca64066c06d0bf644d6b77e605bf957c5c7d'],
     }),
     ('absl-py', '1.4.0', {
         'modulename': 'absl',

From 31ec9dbe7a84e5561a70fb690c3ba3790c7d13bb Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 12 Aug 2024 10:19:40 +0200
Subject: [PATCH 601/835] add sanity check commands for ecCodes 2.27.0

---
 easybuild/easyconfigs/e/ecCodes/ecCodes-2.27.0-iimpi-2022a.eb | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/easybuild/easyconfigs/e/ecCodes/ecCodes-2.27.0-iimpi-2022a.eb b/easybuild/easyconfigs/e/ecCodes/ecCodes-2.27.0-iimpi-2022a.eb
index b93565bb610..33fddc6886a 100644
--- a/easybuild/easyconfigs/e/ecCodes/ecCodes-2.27.0-iimpi-2022a.eb
+++ b/easybuild/easyconfigs/e/ecCodes/ecCodes-2.27.0-iimpi-2022a.eb
@@ -42,4 +42,6 @@ sanity_check_paths = {
     'dirs': ['include'],
 }
 
+sanity_check_commands = ['%s -V' % x for x in local_exes if not x.startswith('codes_')]
+
 moduleclass = 'tools'

From 4f33e78baf8d98fd7229ad1d1375745c09841182 Mon Sep 17 00:00:00 2001
From: Samuel Moors <samuel.moors@vub.be>
Date: Mon, 12 Aug 2024 12:56:03 +0200
Subject: [PATCH 602/835] add avx2 variant

---
 .../o/ORCA/ORCA-6.0.0-gompi-2023a-avx2.eb     | 24 +++++++++++++++++++
 1 file changed, 24 insertions(+)
 create mode 100644 easybuild/easyconfigs/o/ORCA/ORCA-6.0.0-gompi-2023a-avx2.eb

diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-6.0.0-gompi-2023a-avx2.eb b/easybuild/easyconfigs/o/ORCA/ORCA-6.0.0-gompi-2023a-avx2.eb
new file mode 100644
index 00000000000..cdc92c16f64
--- /dev/null
+++ b/easybuild/easyconfigs/o/ORCA/ORCA-6.0.0-gompi-2023a-avx2.eb
@@ -0,0 +1,24 @@
+name = 'ORCA'
+version = '6.0.0'
+versionsuffix = '-avx2'
+
+homepage = 'https://orcaforum.kofo.mpg.de'
+description = """
+ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum
+chemistry with specific emphasis on spectroscopic properties of open-shell
+molecules. It features a wide variety of standard quantum chemical methods
+ranging from semiempirical methods to DFT to single- and multireference
+correlated ab initio methods. It can also treat environmental and relativistic
+effects."""
+
+toolchain = {'name': 'gompi', 'version': '2023a'}
+
+download_instructions = "Shared build of ORCA: download from https://orcaforum.kofo.mpg.de"
+# mostly dynamically linked (SCALAPACK, OpenBLAS are still embedded)
+sources = ['%%(namelower)s_%s_linux_%%(orcaarch)s_avx2_shared_openmpi416.tar.xz' % version.replace('.', '_')]
+checksums = [
+    # orca_6_0_0_linux_x86-64_avx2_shared_openmpi416.tar.xz
+    '02c21294efe7b1b721e26cb90f98ee15ad682d02807201b7d217dfe67905a2fd',
+]
+
+moduleclass = 'chem'

From 2e1fe4fdb4897dd6ff90c2db0bd9b31c3a2589db Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com>
Date: Mon, 12 Aug 2024 14:52:24 +0200
Subject: [PATCH 603/835] Update R-bundle-CRAN-2023.12-foss-2023a.eb add
 missMDA

---
 .../r/R-bundle-CRAN/R-bundle-CRAN-2023.12-foss-2023a.eb        | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2023.12-foss-2023a.eb b/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2023.12-foss-2023a.eb
index bbc343accac..90c7f3f7665 100644
--- a/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2023.12-foss-2023a.eb
+++ b/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2023.12-foss-2023a.eb
@@ -3424,6 +3424,9 @@ exts_list = [
     ('rhandsontable', '0.3.8', {
         'checksums': ['901ed9c59936f7fa52ad8db3111c8904ab962f9c74f1b6cd40f81683af35d21d'],
     }),
+    ('missMDA', '1.19', {
+        'checksums': ['f9675884829b2fef75237c335b21991d163674320e766523c71c7a853f95e65c'],
+    }),
 ]
 
 modextrapaths = {'R_LIBS_SITE': ''}

From f6d167d010e611b3cc555a9569d5ff81f65fafd7 Mon Sep 17 00:00:00 2001
From: Neves-P <p.m.santos.neves@rug.nl>
Date: Mon, 12 Aug 2024 16:28:47 +0200
Subject: [PATCH 604/835] adding easyconfigs:
 GROMACS-2023.3-foss-2023a-PLUMED-2.9.0.eb

---
 .../GROMACS-2023.3-foss-2023a-PLUMED-2.9.0.eb | 101 ++++++++++++++++++
 1 file changed, 101 insertions(+)
 create mode 100755 easybuild/easyconfigs/g/GROMACS/GROMACS-2023.3-foss-2023a-PLUMED-2.9.0.eb

diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.3-foss-2023a-PLUMED-2.9.0.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.3-foss-2023a-PLUMED-2.9.0.eb
new file mode 100755
index 00000000000..38166a92912
--- /dev/null
+++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.3-foss-2023a-PLUMED-2.9.0.eb
@@ -0,0 +1,101 @@
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+#
+# Copyright:: Copyright 2012-2016 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC,
+#                                 Ghent University / The Francis Crick Institute
+# Authors::
+# * Wiktor Jurkowski <wiktor.jurkowski@gmail.com>
+# * Fotis Georgatos <fotis@cern.ch>
+# * George Tsouloupas <g.tsouloupas@cyi.ac.cy>
+# * Kenneth Hoste <kenneth.hoste@ugent.be>
+# * Adam Huffman <adam.huffman@crick.ac.uk>
+# * Ake Sandgren <ake.sandgren@hpc2n.umu.se>
+# * J. Sassmannshausen <Crick HPC team>
+# * Dugan Witherick <dugan.witherick@warwick.ac.uk>
+# * Christoph Siegert <christoph.siegert@uni-leipzig.de>
+# License::   MIT/GPL
+
+name = 'GROMACS'
+version = '2023.3'
+_plumedver = '2.9.0'
+versionsuffix = '-PLUMED-%s' % _plumedver
+
+homepage = 'https://www.gromacs.org'
+description = """
+GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the
+Newtonian equations of motion for systems with hundreds to millions of
+particles.
+
+This is a CPU only build, containing both MPI and threadMPI binaries
+for both single and double precision.
+
+It also contains the gmxapi extension for the single precision MPI build
+next to PLUMED."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+toolchainopts = {'openmp': True, 'usempi': True}
+
+source_urls = [
+    'https://ftp.gromacs.org/pub/gromacs/',
+    'ftp://ftp.gromacs.org/pub/gromacs/',
+]
+sources = [SOURCELOWER_TAR_GZ]
+patches = [
+    'GROMACS-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch',
+    'GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch',
+    '%(name)s-%(version)s_skip_test_for_plumed.patch',
+]
+checksums = [
+    {'gromacs-2023.3.tar.gz': '4ec8f8d0c7af76b13f8fd16db8e2c120e749de439ae9554d9f653f812d78d1cb'},
+    {'GROMACS-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch':
+     '7f41bda16c9c2837624265dda4be252f655d1288ddc4486b1a2422af30d5d199'},
+    {'GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch':
+     '6df844bb3bbc51180446a3595c61a4ef195e5f975533a04cef76841aa763aec1'},
+    {'GROMACS-2023.3_skip_test_for_plumed.patch':
+     '6c541ee74f71f6a63950134d9d0e3afb176a2e25e76e017b4d1986a59163c083'},
+]
+
+builddependencies = [
+    ('CMake', '3.26.3'),
+    ('scikit-build', '0.17.6'),
+    ('Doxygen', '1.9.7'),
+]
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('networkx', '3.1'),
+    ('mpi4py', '3.1.4'),
+    ('PLUMED', _plumedver),
+]
+
+
+configopts = '-DCMAKE_CXX_FLAGS="$CXXFLAGS -fpermissive" '
+
+# PLUMED 2.9.0 is compatible with GROMACS 2023; 2023.3 seems to work fine too
+ignore_plumed_version_check = True
+
+exts_defaultclass = 'PythonPackage'
+
+exts_default_options = {
+    'source_urls': [PYPI_SOURCE],
+    'use_pip': True,
+    'download_dep_fail': True,
+    'sanity_pip_check': True,
+}
+
+exts_list = [
+    ('gmxapi', '0.4.2', {
+        'preinstallopts': 'export CMAKE_ARGS="-Dgmxapi_ROOT=%(installdir)s ' +
+                          '-C %(installdir)s/share/cmake/gromacs_mpi/gromacs-hints_mpi.cmake" && ',
+        'source_tmpl': 'gromacs-2023.3.tar.gz',
+        'start_dir': 'python_packaging/gmxapi',
+        'checksums': ['4ec8f8d0c7af76b13f8fd16db8e2c120e749de439ae9554d9f653f812d78d1cb'],
+    }),
+]
+
+modextrapaths = {
+    'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages',
+}
+
+moduleclass = 'bio'
+

From 5e1e9636e123842d013e0b7ab1ca2af1babf8e2d Mon Sep 17 00:00:00 2001
From: ankekreuzer <a.kreuzer@fz-juelich.de>
Date: Tue, 13 Aug 2024 06:48:24 +0200
Subject: [PATCH 605/835] Added GLM and GTS

---
 .../g/GLM/GLM-1.0.1-GCCcore-13.3.0.eb         | 27 +++++++++++++++++
 .../g/GTS/GTS-0.7.6-GCCcore-13.3.0.eb         | 30 +++++++++++++++++++
 2 files changed, 57 insertions(+)
 create mode 100644 easybuild/easyconfigs/g/GLM/GLM-1.0.1-GCCcore-13.3.0.eb
 create mode 100644 easybuild/easyconfigs/g/GTS/GTS-0.7.6-GCCcore-13.3.0.eb

diff --git a/easybuild/easyconfigs/g/GLM/GLM-1.0.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/GLM/GLM-1.0.1-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..e57a89d030a
--- /dev/null
+++ b/easybuild/easyconfigs/g/GLM/GLM-1.0.1-GCCcore-13.3.0.eb
@@ -0,0 +1,27 @@
+easyblock = 'CMakeMake'
+
+name = 'GLM'
+version = '1.0.1'
+
+homepage = 'https://github.com/g-truc/glm'
+description = """
+OpenGL Mathematics (GLM) is a header only C++ mathematics library for graphics  
+software based on  the OpenGL Shading Language (GLSL) specifications."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+source_urls = ['https://github.com/g-truc/glm/archive/']
+sources = ['%(version)s.tar.gz']
+checksums = ['9f3174561fd26904b23f0db5e560971cbf9b3cbda0b280f04d5c379d03bf234c']
+
+builddependencies = [
+    ('binutils', '2.42'),
+    ('CMake', '3.29.3'),
+]
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['include/glm/gtc', 'include/glm/gtx'],
+}
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/g/GTS/GTS-0.7.6-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/GTS/GTS-0.7.6-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..dd36868a20d
--- /dev/null
+++ b/easybuild/easyconfigs/g/GTS/GTS-0.7.6-GCCcore-13.3.0.eb
@@ -0,0 +1,30 @@
+easyblock = 'ConfigureMake'
+
+name = 'GTS'
+version = '0.7.6'
+
+homepage = 'http://gts.sourceforge.net/'
+description = """GTS stands for the GNU Triangulated Surface Library.
+It is an Open Source Free Software Library intended to provide a set of useful
+functions to deal with 3D surfaces meshed with interconnected triangles."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+source_urls = [SOURCEFORGE_SOURCE]
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['059c3e13e3e3b796d775ec9f96abdce8f2b3b5144df8514eda0cc12e13e8b81e']
+
+builddependencies = [
+    ('pkgconf', '2.2.0'),
+    ('binutils', '2.42'),
+]
+dependencies = [
+    ('GLib', '2.80.4'),
+]
+
+sanity_check_paths = {
+    'files': ['lib/libgts.%s' % SHLIB_EXT, 'bin/gts2oogl', 'bin/gtscheck'],
+    'dirs': [],
+}
+
+moduleclass = 'vis'

From 29e3dddcd0e0a394ae0a0bbb0a3434d8606b284e Mon Sep 17 00:00:00 2001
From: ankekreuzer <a.kreuzer@fz-juelich.de>
Date: Tue, 13 Aug 2024 09:05:47 +0200
Subject: [PATCH 606/835] Added gflags, gmpy2, graphite2 and Imath

---
 .../g/gflags/gflags-2.2.2-GCCcore-13.3.0.eb   | 35 +++++++++++++++++++
 .../g/gmpy2/gmpy2-2.2.0-GCCcore-13.3.0.eb     | 25 +++++++++++++
 .../graphite2-1.3.14-GCCcore-13.3.0.eb        | 27 ++++++++++++++
 .../i/Imath/Imath-3.1.11-GCCcore-13.3.0.eb    | 28 +++++++++++++++
 4 files changed, 115 insertions(+)
 create mode 100644 easybuild/easyconfigs/g/gflags/gflags-2.2.2-GCCcore-13.3.0.eb
 create mode 100644 easybuild/easyconfigs/g/gmpy2/gmpy2-2.2.0-GCCcore-13.3.0.eb
 create mode 100644 easybuild/easyconfigs/g/graphite2/graphite2-1.3.14-GCCcore-13.3.0.eb
 create mode 100644 easybuild/easyconfigs/i/Imath/Imath-3.1.11-GCCcore-13.3.0.eb

diff --git a/easybuild/easyconfigs/g/gflags/gflags-2.2.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/gflags/gflags-2.2.2-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..de0ad50b22c
--- /dev/null
+++ b/easybuild/easyconfigs/g/gflags/gflags-2.2.2-GCCcore-13.3.0.eb
@@ -0,0 +1,35 @@
+easyblock = 'CMakeMake'
+
+name = 'gflags'
+version = '2.2.2'
+
+homepage = 'https://github.com/gflags/gflags'
+description = """
+The gflags package contains a C++ library that implements commandline flags
+processing.  It includes built-in support for standard types such as string
+and the ability to define flags in the source file in which they are used.
+"""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://github.com/gflags/gflags/archive/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['34af2f15cf7367513b352bdcd2493ab14ce43692d2dcd9dfc499492966c64dcf']
+
+builddependencies = [
+    ('binutils', '2.42'),
+    ('CMake', '3.29.3'),
+]
+
+configopts = '-DBUILD_SHARED_LIBS=ON -DBUILD_STATIC_LIBS=ON'
+
+sanity_check_paths = {
+    'files': ['bin/gflags_completions.sh'] +
+             ['lib/%s' % x for x in ['libgflags.%s' % SHLIB_EXT, 'libgflags_nothreads.%s' % SHLIB_EXT,
+                                     'libgflags.a', 'libgflags_nothreads.a']] +
+             ['include/gflags/gflags_completions.h'],
+    'dirs': [],
+}
+
+moduleclass = 'devel'
diff --git a/easybuild/easyconfigs/g/gmpy2/gmpy2-2.2.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/gmpy2/gmpy2-2.2.0-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..d919e2ca8e3
--- /dev/null
+++ b/easybuild/easyconfigs/g/gmpy2/gmpy2-2.2.0-GCCcore-13.3.0.eb
@@ -0,0 +1,25 @@
+easyblock = 'PythonPackage'
+
+name = 'gmpy2'
+version = '2.2.0'
+
+homepage = 'https://github.com/aleaxit/gmpy'
+description = "GMP/MPIR, MPFR, and MPC interface to Python 2.6+ and 3.x"
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+sources = [SOURCE_TAR_GZ]
+checksums = ['e19e62dfeb1e4a57079f0bf51c51dec30633d9fe9e89cb9a083e05e4823afa70']
+
+dependencies = [
+    ('Python', '3.12.3'),
+    ('GMP', '6.3.0'),
+    ('MPFR', '4.2.1'),
+    ('MPC', '1.3.1'),
+]
+
+download_dep_fail = True
+sanity_pip_check = True
+use_pip = True
+
+moduleclass = 'math'
diff --git a/easybuild/easyconfigs/g/graphite2/graphite2-1.3.14-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/graphite2/graphite2-1.3.14-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..7e199ecf26b
--- /dev/null
+++ b/easybuild/easyconfigs/g/graphite2/graphite2-1.3.14-GCCcore-13.3.0.eb
@@ -0,0 +1,27 @@
+easyblock = 'CMakeMake'
+
+name = 'graphite2'
+version = '1.3.14'
+
+homepage = 'https://scripts.sil.org/cms/scripts/page.php?site_id=projects&item_id=graphite_home'
+description = """Graphite is a "smart font" system developed specifically to
+ handle the complexities of lesser-known languages of the world."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+source_urls = ['https://github.com/silnrsi/graphite/archive/']
+sources = ['%(version)s.zip']
+checksums = ['36e15981af3bf7a3ca3daf53295c8ffde04cf7d163e3474e4d0836e2728b4149']
+
+builddependencies = [
+    ('CMake', '3.29.3'),
+    ('binutils', '2.42'),
+]
+
+sanity_check_paths = {
+    'files': ['bin/gr2fonttest'] +
+             ['lib/lib%%(name)s.%s' % x for x in [SHLIB_EXT, 'la']],
+    'dirs': ['include/%(name)s', 'share']
+}
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/i/Imath/Imath-3.1.11-GCCcore-13.3.0.eb b/easybuild/easyconfigs/i/Imath/Imath-3.1.11-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..05efb6d6c62
--- /dev/null
+++ b/easybuild/easyconfigs/i/Imath/Imath-3.1.11-GCCcore-13.3.0.eb
@@ -0,0 +1,28 @@
+easyblock = 'CMakeMake'
+
+name = 'Imath'
+version = '3.1.11'
+
+homepage = 'https://imath.readthedocs.io/en/latest/'
+description = """
+Imath is a C++ and python library of 2D and 3D vector, matrix, and math operations for computer graphics
+"""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://github.com/AcademySoftwareFoundation/%(namelower)s/archive/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['9057849585e49b8b85abe7cc1e76e22963b01bfdc3b6d83eac90c499cd760063']
+
+builddependencies = [
+    ('binutils', '2.42'),
+    ('CMake', '3.29.3'),
+]
+
+sanity_check_paths = {
+    'files': ['lib/libImath.%s' % SHLIB_EXT],
+    'dirs': ['include/Imath'],
+}
+
+moduleclass = 'lib'

From 1e6377fb82e6ffd5c584ab0b5c35ea871c46c11c Mon Sep 17 00:00:00 2001
From: ankekreuzer <a.kreuzer@fz-juelich.de>
Date: Tue, 13 Aug 2024 09:24:24 +0200
Subject: [PATCH 607/835] Added JsonCpp, jemalloc and json-c

---
 .../j/JsonCpp/JsonCpp-1.9.5-GCCcore-13.3.0.eb | 29 +++++++++++++++
 .../jemalloc/jemalloc-5.3.0-GCCcore-13.3.0.eb | 37 +++++++++++++++++++
 .../j/json-c/json-c-0.17-GCCcore-13.3.0.eb    | 32 ++++++++++++++++
 3 files changed, 98 insertions(+)
 create mode 100644 easybuild/easyconfigs/j/JsonCpp/JsonCpp-1.9.5-GCCcore-13.3.0.eb
 create mode 100644 easybuild/easyconfigs/j/jemalloc/jemalloc-5.3.0-GCCcore-13.3.0.eb
 create mode 100644 easybuild/easyconfigs/j/json-c/json-c-0.17-GCCcore-13.3.0.eb

diff --git a/easybuild/easyconfigs/j/JsonCpp/JsonCpp-1.9.5-GCCcore-13.3.0.eb b/easybuild/easyconfigs/j/JsonCpp/JsonCpp-1.9.5-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..b1d3f620566
--- /dev/null
+++ b/easybuild/easyconfigs/j/JsonCpp/JsonCpp-1.9.5-GCCcore-13.3.0.eb
@@ -0,0 +1,29 @@
+easyblock = "CMakeNinja"
+
+name = 'JsonCpp'
+version = '1.9.5'
+
+homepage = 'https://open-source-parsers.github.io/jsoncpp-docs/doxygen/index.html'
+description = """ JsonCpp is a C++ library that allows manipulating JSON values,
+ including serialization and deserialization to and from strings. It can also preserve existing comment in
+ unserialization/serialization steps, making it a convenient format to store user input files. """
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+source_urls = ['https://github.com/open-source-parsers/jsoncpp/archive']
+sources = ['%(version)s.tar.gz']
+checksums = ['f409856e5920c18d0c2fb85276e24ee607d2a09b5e7d5f0a371368903c275da2']
+
+builddependencies = [
+    ('CMake', '3.29.3'),
+    ('Ninja', '1.12.1'),
+    ('pkgconf', '2.2.0'),
+    ('binutils', '2.42'),
+]
+
+sanity_check_paths = {
+    'files': ['include/json/json.h', 'lib/libjsoncpp.%s' % SHLIB_EXT],
+    'dirs': [],
+}
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/j/jemalloc/jemalloc-5.3.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/j/jemalloc/jemalloc-5.3.0-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..023c3001dd3
--- /dev/null
+++ b/easybuild/easyconfigs/j/jemalloc/jemalloc-5.3.0-GCCcore-13.3.0.eb
@@ -0,0 +1,37 @@
+easyblock = 'ConfigureMake'
+
+name = 'jemalloc'
+version = '5.3.0'
+
+homepage = 'http://jemalloc.net'
+description = """jemalloc is a general purpose malloc(3) implementation that emphasizes fragmentation avoidance and
+ scalable concurrency support."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+source_urls = ['https://github.com/jemalloc/jemalloc/archive']
+sources = ['%(version)s.tar.gz']
+checksums = ['ef6f74fd45e95ee4ef7f9e19ebe5b075ca6b7fbe0140612b2a161abafb7ee179']
+
+builddependencies = [
+    ('Autotools', '20231222'),
+    ('binutils', '2.42'),
+]
+
+# From version 5.2.1 (or maybe earlier) it does no longer build,
+# nor try to install, documentation if xsltproc is missing.
+# So we can use normal installation.
+preconfigopts = "./autogen.sh && "
+configopts = "--with-version=%(version)s-0-g0000 "  # build with version info
+
+sanity_check_paths = {
+    'files': ['bin/jeprof', 'lib/libjemalloc.a', 'lib/libjemalloc_pic.a', 'lib/libjemalloc.%s' % SHLIB_EXT,
+              'include/jemalloc/jemalloc.h'],
+    'dirs': [],
+}
+
+# jemalloc can be used via $LD_PRELOAD, but we don't enable this by
+# default, you need to opt-in to it
+# modextrapaths = {'LD_PRELOAD': ['lib/libjemalloc.%s' % SHLIB_EXT]}
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/j/json-c/json-c-0.17-GCCcore-13.3.0.eb b/easybuild/easyconfigs/j/json-c/json-c-0.17-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..87642888aa1
--- /dev/null
+++ b/easybuild/easyconfigs/j/json-c/json-c-0.17-GCCcore-13.3.0.eb
@@ -0,0 +1,32 @@
+easyblock = 'CMakeMake'
+
+name = 'json-c'
+version = '0.17'
+local_suff = '-20230812'
+
+homepage = 'https://github.com/json-c/json-c'
+description = """JSON-C implements a reference counting object model that allows you to easily construct JSON objects
+ in C, output them as JSON formatted strings and parse JSON formatted strings back into the C representation of JSON
+objects."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+source_urls = ['https://github.com/json-c/json-c/archive/']
+sources = ['json-c-%%(version)s%s.tar.gz' % local_suff]
+checksums = ['024d302a3aadcbf9f78735320a6d5aedf8b77876c8ac8bbb95081ca55054c7eb']
+
+builddependencies = [
+    ('binutils', '2.42'),
+    ('CMake', '3.29.3'),
+]
+
+# disable using Valgrind during the tests to avoid failures caused by using an OS Valgrind
+pretestopts = 'USE_VALGRIND=0 '
+runtest = 'test'
+
+sanity_check_paths = {
+    'files': ['lib/libjson-c.a', 'lib/libjson-c.%s' % SHLIB_EXT, 'lib/pkgconfig/json-c.pc'],
+    'dirs': ['include/json-c'],
+}
+
+moduleclass = 'lib'

From fa3c247ff15e3d8101171bc7b680d5a2883567b2 Mon Sep 17 00:00:00 2001
From: Samuel Moors <samuel.moors@vub.be>
Date: Tue, 13 Aug 2024 15:29:24 +0200
Subject: [PATCH 608/835] adding easyconfigs: GDMA-2.3.3_20230603-GCC-12.3.0.eb

---
 .../g/GDMA/GDMA-2.3.3_20230603-GCC-12.3.0.eb  | 42 +++++++++++++++++++
 1 file changed, 42 insertions(+)
 create mode 100644 easybuild/easyconfigs/g/GDMA/GDMA-2.3.3_20230603-GCC-12.3.0.eb

diff --git a/easybuild/easyconfigs/g/GDMA/GDMA-2.3.3_20230603-GCC-12.3.0.eb b/easybuild/easyconfigs/g/GDMA/GDMA-2.3.3_20230603-GCC-12.3.0.eb
new file mode 100644
index 00000000000..d22b6d74689
--- /dev/null
+++ b/easybuild/easyconfigs/g/GDMA/GDMA-2.3.3_20230603-GCC-12.3.0.eb
@@ -0,0 +1,42 @@
+easyblock = 'ConfigureMake'
+
+name = 'GDMA'
+version = '2.3.3_20230603'
+_commit = '6b8e81ec'
+
+homepage = 'https://gitlab.com/anthonyjs/gdma'
+description = """
+The GDMA program carries out Distributed Multipole Analysis of wavefunctions
+calculated by the Gaussian system of programs or the Psi4 package, using the
+formatted checkpoint files that they can produce. The result is a set of
+multipole moments at sites defined by the user (usually at the positions of the
+atomic nuclei) which, given an accurate wavefunction, provide an accurate
+description of the electrostatic field of the molecule."""
+
+toolchain = {'name': 'GCC', 'version': '12.3.0'}
+
+sources = [{
+    'source_urls': ['https://gitlab.com/anthonyjs/gdma/-/archive/'],
+    'download_filename': '%s.tar.gz' % _commit,
+    'filename': SOURCE_TAR_GZ,
+}]
+checksums = ['cc008932ae8768e6cbd444337a998e02b2100c123492c260d6020590e76bec1e']
+
+parallel = 1
+
+skipsteps = ['configure']
+
+# avoid using git to obtain the commit: not a cloned repo
+prebuildopts = """sed -i "/^log =/,/^commit =/c commit = '%s'" src/version.py && """ % _commit
+
+preinstallopts = 'mkdir -p %(installdir)s/bin && '
+installopts = 'INSTALL_DIR=%(installdir)s/bin'
+
+sanity_check_paths = {
+    'files': ['bin/gdma'],
+    'dirs': [],
+}
+
+sanity_check_commands = ['echo|gdma']
+
+moduleclass = 'chem'

From 9bbe3338d0303e80359a2b41e8f3cac30170b0c6 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Tue, 13 Aug 2024 16:14:24 +0200
Subject: [PATCH 609/835] separate econfig for junos-eznc with forked paramiko

---
 .../dictys-1.1.0-foss-2023a-CUDA-12.1.1.eb    | 21 +------
 .../d/dictys/dictys-1.1.0-foss-2023a.eb       | 21 +------
 .../junos-eznc-2.7.1-GCCcore-12.3.0.eb        | 56 +++++++++++++++++++
 3 files changed, 58 insertions(+), 40 deletions(-)
 create mode 100644 easybuild/easyconfigs/j/junos-eznc/junos-eznc-2.7.1-GCCcore-12.3.0.eb

diff --git a/easybuild/easyconfigs/d/dictys/dictys-1.1.0-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/d/dictys/dictys-1.1.0-foss-2023a-CUDA-12.1.1.eb
index de99e242d09..f04774b1b55 100644
--- a/easybuild/easyconfigs/d/dictys/dictys-1.1.0-foss-2023a-CUDA-12.1.1.eb
+++ b/easybuild/easyconfigs/d/dictys/dictys-1.1.0-foss-2023a-CUDA-12.1.1.eb
@@ -29,6 +29,7 @@ dependencies = [
     ('paramiko', '3.2.0'),
     ('Jupyter-bundle', '20230823'),
     ('Qtconsole', '5.5.1'),
+    ('junos-eznc', '2.7.1'),
 ]
 
 # regenerate WellingtonC.c to works with python 3.11 + unpin matplotlib version
@@ -54,26 +55,6 @@ exts_list = [
     ('pynetbox', '7.4.0', {
         'checksums': ['fd0b1f197b3880048408ff5ed84422dd599bcd9389e32cb06a09b9b0d55c1636'],
     }),
-    ('yamlordereddictloader', '0.4.2', {
-        'checksums': ['36af2f6210fcff5da4fc4c12e1d815f973dceb41044e795e1f06115d634bca13'],
-    }),
-    ('transitions', '0.9.2', {
-        'checksums': ['2f8490dbdbd419366cef1516032ab06d07ccb5839ef54905e842a472692d4204'],
-    }),
-    ('scp', '0.15.0', {
-        'checksums': ['f1b22e9932123ccf17eebf19e0953c6e9148f589f93d91b872941a696305c83f'],
-    }),
-    ('pyserial', '3.5', {
-        'modulename': 'serial',
-        'checksums': ['3c77e014170dfffbd816e6ffc205e9842efb10be9f58ec16d3e8675b4925cddb'],
-    }),
-    ('ncclient', '0.6.15', {
-        'checksums': ['6757cb41bc9160dfe47f22f5de8cf2f1adf22f27463fb50453cc415ab96773d8'],
-    }),
-    ('junos-eznc', '2.7.0', {
-        'modulename': 'jnpr.junos',
-        'checksums': ['a45c90641d24ff4c86796418ea76ca64066c06d0bf644d6b77e605bf957c5c7d'],
-    }),
     ('absl-py', '1.4.0', {
         'modulename': 'absl',
         'checksums': ['d2c244d01048ba476e7c080bd2c6df5e141d211de80223460d5b3b8a2a58433d'],
diff --git a/easybuild/easyconfigs/d/dictys/dictys-1.1.0-foss-2023a.eb b/easybuild/easyconfigs/d/dictys/dictys-1.1.0-foss-2023a.eb
index e0fa2174545..0b97a82cfde 100644
--- a/easybuild/easyconfigs/d/dictys/dictys-1.1.0-foss-2023a.eb
+++ b/easybuild/easyconfigs/d/dictys/dictys-1.1.0-foss-2023a.eb
@@ -27,6 +27,7 @@ dependencies = [
     ('paramiko', '3.2.0'),
     ('Jupyter-bundle', '20230823'),
     ('Qtconsole', '5.5.1'),
+    ('junos-eznc', '2.7.1'),
 ]
 
 # regenerate WellingtonC.c to works with python 3.11 + unpin matplotlib version
@@ -52,26 +53,6 @@ exts_list = [
     ('pynetbox', '7.4.0', {
         'checksums': ['fd0b1f197b3880048408ff5ed84422dd599bcd9389e32cb06a09b9b0d55c1636'],
     }),
-    ('yamlordereddictloader', '0.4.2', {
-        'checksums': ['36af2f6210fcff5da4fc4c12e1d815f973dceb41044e795e1f06115d634bca13'],
-    }),
-    ('transitions', '0.9.2', {
-        'checksums': ['2f8490dbdbd419366cef1516032ab06d07ccb5839ef54905e842a472692d4204'],
-    }),
-    ('scp', '0.15.0', {
-        'checksums': ['f1b22e9932123ccf17eebf19e0953c6e9148f589f93d91b872941a696305c83f'],
-    }),
-    ('pyserial', '3.5', {
-        'modulename': 'serial',
-        'checksums': ['3c77e014170dfffbd816e6ffc205e9842efb10be9f58ec16d3e8675b4925cddb'],
-    }),
-    ('ncclient', '0.6.15', {
-        'checksums': ['6757cb41bc9160dfe47f22f5de8cf2f1adf22f27463fb50453cc415ab96773d8'],
-    }),
-    ('junos-eznc', '2.7.0', {
-        'modulename': 'jnpr.junos',
-        'checksums': ['a45c90641d24ff4c86796418ea76ca64066c06d0bf644d6b77e605bf957c5c7d'],
-    }),
     ('absl-py', '1.4.0', {
         'modulename': 'absl',
         'checksums': ['d2c244d01048ba476e7c080bd2c6df5e141d211de80223460d5b3b8a2a58433d'],
diff --git a/easybuild/easyconfigs/j/junos-eznc/junos-eznc-2.7.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/j/junos-eznc/junos-eznc-2.7.1-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..2799845eb24
--- /dev/null
+++ b/easybuild/easyconfigs/j/junos-eznc/junos-eznc-2.7.1-GCCcore-12.3.0.eb
@@ -0,0 +1,56 @@
+easyblock = 'PythonBundle'
+
+name = 'junos-eznc'
+version = '2.7.1'
+
+homepage = 'https://github.com/Juniper/py-junos-eznc'
+description = "Python library for Junos automation."
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+builddependencies = [('binutils', '2.40')]
+dependencies = [
+    ('Python', '3.11.3'),
+    ('lxml', '4.9.2'),
+    ('PyYAML', '6.0'),
+    ('Python-bundle-PyPI', '2023.06'),
+    ('bcrypt', '4.0.1'),
+]
+
+# delete 'os.system("pip install git+https://github.com/Juniper/paramiko.git@v3.4.0-JNPR")' from setup.py
+local_preinstallopts = "sed -i '6d' setup.py && "
+
+exts_list = [
+    ('yamlordereddictloader', '0.4.2', {
+        'checksums': ['36af2f6210fcff5da4fc4c12e1d815f973dceb41044e795e1f06115d634bca13'],
+    }),
+    ('transitions', '0.9.2', {
+        'checksums': ['2f8490dbdbd419366cef1516032ab06d07ccb5839ef54905e842a472692d4204'],
+    }),
+    ('scp', '0.15.0', {
+        'checksums': ['f1b22e9932123ccf17eebf19e0953c6e9148f589f93d91b872941a696305c83f'],
+    }),
+    ('pyserial', '3.5', {
+        'modulename': 'serial',
+        'checksums': ['3c77e014170dfffbd816e6ffc205e9842efb10be9f58ec16d3e8675b4925cddb'],
+    }),
+    ('ncclient', '0.6.15', {
+        'checksums': ['6757cb41bc9160dfe47f22f5de8cf2f1adf22f27463fb50453cc415ab96773d8'],
+    }),
+    ('paramiko', '3.4.0', {
+        # Juniper fork of paramiko - compatible with junos-eznc
+        'source_urls': ['https://github.com/Juniper/paramiko/archive/'],
+        'sources': [{'download_filename': 'v%(version)s-JNPR.tar.gz', 'filename': '%(name)s-%(version)s-JNPR.tar.gz'}],
+        'checksums': ['6b3b62e18a2b693169eaa50a7cdd2ab5637fc423205ce85e109cb37722f9eeda'],
+    }),
+    (name, version, {
+        'modulename': 'jnpr.junos',
+        'preinstallopts': "sed -i '6d' setup.py && ",
+        'checksums': ['371f0298bf03e0cb4c017c43f6f4122263584eda0d690d0112e93f13daae41ac'],
+    }),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+moduleclass = 'tools'

From 1fb2752bda16545a6ec4df91f4a3353545e3f42d Mon Sep 17 00:00:00 2001
From: WilleBell <cintiawillemyns@gmail.com>
Date: Tue, 13 Aug 2024 16:45:07 +0200
Subject: [PATCH 610/835] Add GPflow v2.9.2 and fix tensorflow-probability to
 pass pip check

---
 .../g/GPflow/GPflow-2.9.2-foss-2023a.eb       | 51 +++++++++++++++++++
 ...ensorflow-probability-0.20.0-foss-2023a.eb |  8 +++
 2 files changed, 59 insertions(+)
 create mode 100644 easybuild/easyconfigs/g/GPflow/GPflow-2.9.2-foss-2023a.eb

diff --git a/easybuild/easyconfigs/g/GPflow/GPflow-2.9.2-foss-2023a.eb b/easybuild/easyconfigs/g/GPflow/GPflow-2.9.2-foss-2023a.eb
new file mode 100644
index 00000000000..a2a0f0a5adc
--- /dev/null
+++ b/easybuild/easyconfigs/g/GPflow/GPflow-2.9.2-foss-2023a.eb
@@ -0,0 +1,51 @@
+easyblock = 'PythonBundle'
+
+name = 'GPflow'
+version = '2.9.2'
+
+homepage = 'https://gpflow.github.io'
+description = """GPflow is a package for building Gaussian process models in Python. It
+implements modern Gaussian process inference for composable kernels and
+likelihoods."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+builddependencies = [
+    ('poetry', '1.7.1'),
+]
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('TensorFlow', '2.13.0'),
+    ('tensorflow-probability', '0.20.0'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('Deprecated', '1.2.14', {
+        'checksums': ['e5323eb936458dccc2582dc6f9c322c852a775a27065ff2b0c4970b9d53d01b3'],
+    }),
+    ('dropstackframe', '0.1.0', {
+        'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl',
+        'checksums': ['d619c7f87d144660f4569d447648830932f7920d570fd14f0dec552c81a0eb22'],
+    }),
+    ('lark', '1.1.9', {
+        'checksums': ['15fa5236490824c2c4aba0e22d2d6d823575dcaf4cdd1848e34b6ad836240fba'],
+    }),
+    ('check_shapes', '1.1.1', {
+        'checksums': ['b699fcb1e60bb17e2c97007e444b89eeeea2a9102ff11d61fb52454af5348403'],
+    }),
+    ('multipledispatch', '1.0.0', {
+        'checksums': ['5c839915465c68206c3e9c473357908216c28383b425361e5d144594bf85a7e0'],
+    }),
+    ('gpflow', version, {
+        'source_tmpl': 'v%(version)s.tar.gz',
+        'source_urls': ['https://github.com/GPflow/GPflow/archive/'],
+        'checksums': ['a32914c2b581b1dd2ac9a6f40352adb5f6f2c32f53028382e542014dd829553e'],
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.20.0-foss-2023a.eb b/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.20.0-foss-2023a.eb
index c86b16b035f..97a3f88a99f 100644
--- a/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.20.0-foss-2023a.eb
+++ b/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.20.0-foss-2023a.eb
@@ -28,6 +28,12 @@ dependencies = [
 
 use_pip = True
 
+# avoid pip check fail when tensorflow-probability is a dependency
+local_postinstallcmds = "cd %(installdir)s/lib/python%(pyshortver)s/site-packages && "
+local_postinstallcmds += "mv tfp_nightly-%(version)s.dist-info tensorflow_probability-%(version)s.dist-info && "
+local_postinstallcmds += "sed -i 's/Name: tfp-nightly/Name: %(name)s/'"
+local_postinstallcmds += " tensorflow_probability-%(version)s.dist-info/METADATA"
+
 exts_list = [
     ('cloudpickle', '3.0.0', {
         'checksums': ['996d9a482c6fb4f33c1a35335cf8afd065d2a56e973270364840712d9131a882'],
@@ -37,6 +43,8 @@ exts_list = [
         'source_tmpl': 'v%(version)s.tar.gz',
         'source_urls': ['https://github.com/tensorflow/probability/archive/'],
         'checksums': ['f0fb9a1f88a36a8f57d4d9cce4f9bf8dfacb6fc7778751729fe3c3067e5a1363'],
+        'postinstallcmds': [local_postinstallcmds],
+        # 'installopts': local_installopts,
     }),
 ]
 

From a0ccd08eee61bd7543fa9db173f524387a4dc3fe Mon Sep 17 00:00:00 2001
From: Cintia Willemyns <115622907+WilleBell@users.noreply.github.com>
Date: Tue, 13 Aug 2024 16:47:07 +0200
Subject: [PATCH 611/835] remove comment

---
 .../tensorflow-probability-0.20.0-foss-2023a.eb                  | 1 -
 1 file changed, 1 deletion(-)

diff --git a/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.20.0-foss-2023a.eb b/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.20.0-foss-2023a.eb
index 97a3f88a99f..e18a2bc7414 100644
--- a/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.20.0-foss-2023a.eb
+++ b/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.20.0-foss-2023a.eb
@@ -44,7 +44,6 @@ exts_list = [
         'source_urls': ['https://github.com/tensorflow/probability/archive/'],
         'checksums': ['f0fb9a1f88a36a8f57d4d9cce4f9bf8dfacb6fc7778751729fe3c3067e5a1363'],
         'postinstallcmds': [local_postinstallcmds],
-        # 'installopts': local_installopts,
     }),
 ]
 

From f72250be364f2c9b499330f01a2dcdd4260a0bdb Mon Sep 17 00:00:00 2001
From: software <software@easybuild-el8.cloud.in.bmrc.ox.ac.uk>
Date: Tue, 13 Aug 2024 15:08:03 +0000
Subject: [PATCH 612/835] adding easyconfigs: Kent_tools-468-GCC-12.3.0.eb

---
 .../k/Kent_tools/Kent_tools-468-GCC-12.3.0.eb | 42 +++++++++++++++++++
 1 file changed, 42 insertions(+)
 create mode 100644 easybuild/easyconfigs/k/Kent_tools/Kent_tools-468-GCC-12.3.0.eb

diff --git a/easybuild/easyconfigs/k/Kent_tools/Kent_tools-468-GCC-12.3.0.eb b/easybuild/easyconfigs/k/Kent_tools/Kent_tools-468-GCC-12.3.0.eb
new file mode 100644
index 00000000000..e4fd527e908
--- /dev/null
+++ b/easybuild/easyconfigs/k/Kent_tools/Kent_tools-468-GCC-12.3.0.eb
@@ -0,0 +1,42 @@
+easyblock = 'MakeCp'
+
+name = 'Kent_tools'
+version = '468'
+
+homepage = 'https://genome.cse.ucsc.edu/'
+description = """Kent utilities: collection of tools used by the UCSC genome browser."""
+
+toolchain = {'name': 'GCC', 'version': '12.3.0'}
+source_urls = [
+    'https://hgdownload.cse.ucsc.edu/admin/exe/',
+    'https://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/',
+]
+sources = ['userApps.v%(version)s.src.tgz']
+checksums = ['f57b49be7e4eeb0719ac9414ca8878f93916fc3eb8dd408c8f7e076a999d1ca8']
+
+dependencies = [
+    ('MariaDB', '11.6.0'),
+    ('libpng', '1.6.39'),
+    ('zlib', '1.2.13'),
+    ('util-linux', '2.39'),
+    ('OpenSSL', '1.1', '', SYSTEM),
+    ('freetype', '2.13.0'),
+]
+
+prebuildopts = 'sed -i "s/rsync -a /cp -a /" %(builddir)s/userApps/kent/src/parasol/makefile && '
+
+buildopts = 'CC="$CC" COPT="$CFLAGS -fcommon" PNGLIB="-L$EBROOTLIBPNG/lib -lpng" ZLIB="-L$EBROOTZLIB/lib -lz" '
+buildopts += 'SSL_DIR="$EBROOTOPENSSL" SSLDIR="$EBROOTOPENSSL" MYSQLLIBS="-L$EBROOTMARIADB/lib -lmariadb -lstdc++" '
+
+local_binaries = ['blat', 'bedPartition', 'getRna', 'liftOver', 'mafGene', 'splitFile', 'twoBitToFa']
+
+files_to_copy = [(['bin/*'], 'bin'), 'licenseBlat.txt', 'licenseUcscGenomeBrowser.txt']
+
+sanity_check_paths = {
+    'files': ['bin/%s' % x for x in local_binaries],
+    'dirs': [],
+}
+
+sanity_check_commands = ["%s 2>&1 | grep '^usage:'" % x for x in local_binaries]
+
+moduleclass = 'bio'

From 777b5cfcb8ba74e58d2733ce8a87dac697b694b8 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 13 Aug 2024 17:17:34 +0200
Subject: [PATCH 613/835] adding easyconfigs: EMMAX-20100310-foss-2023a.eb and
 patches: EMMAX-20100310_fix-build.patch

---
 .../e/EMMAX/EMMAX-20100310-foss-2023a.eb      | 40 +++++++++
 .../e/EMMAX/EMMAX-20100310_fix-build.patch    | 88 +++++++++++++++++++
 2 files changed, 128 insertions(+)
 create mode 100644 easybuild/easyconfigs/e/EMMAX/EMMAX-20100310-foss-2023a.eb
 create mode 100644 easybuild/easyconfigs/e/EMMAX/EMMAX-20100310_fix-build.patch

diff --git a/easybuild/easyconfigs/e/EMMAX/EMMAX-20100310-foss-2023a.eb b/easybuild/easyconfigs/e/EMMAX/EMMAX-20100310-foss-2023a.eb
new file mode 100644
index 00000000000..c68628823fb
--- /dev/null
+++ b/easybuild/easyconfigs/e/EMMAX/EMMAX-20100310-foss-2023a.eb
@@ -0,0 +1,40 @@
+easyblock = 'MakeCp'
+
+name = 'EMMAX'
+# version is based on datestamp of files in emmax-beta-src.tar.gz
+# (last checked on 13 Aug 2024)
+version = '20100310'
+
+homepage = 'https://csg.sph.umich.edu//kang/emmax'
+description = """EMMAX is a statistical test for large scale human or model organism
+  association mapping accounting for the sample structure"""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+source_urls = ['https://csg.sph.umich.edu//kang/emmax/download/']
+sources = [{'download_filename': 'emmax-beta-src.tar.gz', 'filename': SOURCE_TAR_GZ}]
+patches = ['EMMAX-20100310_fix-build.patch']
+checksums = [
+    {'EMMAX-20100310.tar.gz': '79670917a0ac74ff1899fb27361e2e07b0f3a7911a9d9c6e0c18cf066b8987ea'},
+    {'EMMAX-20100310_fix-build.patch': 'fae62d1f9f7bd4b94c81cdeb01d5134cc2825bcab050ddbfa89ce232eca8497e'},
+]
+
+dependencies = [
+    ('zlib', '1.2.13'),
+]
+
+buildopts = 'CC="$CC $CFLAGS" CLIBS="-lflexiblas -lm -lz"'
+
+files_to_copy = [(['emmax', 'emmax-kin'], 'bin')]
+
+sanity_check_paths = {
+    'files': ['bin/emmax', 'bin/emmax-kin'],
+    'dirs': [],
+}
+
+sanity_check_commands = [
+    "emmax 2>&1 | grep '^Usage: emmax'",
+    "emmax-kin 2>&1 | grep '^Usage: emmax_IBS_kin'",
+]
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/e/EMMAX/EMMAX-20100310_fix-build.patch b/easybuild/easyconfigs/e/EMMAX/EMMAX-20100310_fix-build.patch
new file mode 100644
index 00000000000..c2827ab10a9
--- /dev/null
+++ b/easybuild/easyconfigs/e/EMMAX/EMMAX-20100310_fix-build.patch
@@ -0,0 +1,88 @@
+fix build with recent compiler & BLAS/LAPACK library
+author: Kenneth Hoste (HPC-UGent)
+
+--- emmax-beta-src/emmax.c.orig	2024-08-13 16:28:41.536119000 +0200
++++ emmax-beta-src/emmax.c	2024-08-13 16:54:06.856501202 +0200
+@@ -7,7 +7,8 @@
+ #include <float.h>
+ #include <time.h>
+ #include <cblas.h>
+-#include <clapack.h>
++#include <lapacke.h>
++#include <stdint.h>
+ #include <zlib.h>
+ //#include "lapack_wrapper.h"
+ 
+@@ -1621,15 +1622,13 @@
+ 	    double *W, 
+ 	    double *WORK, int LWORK, int *IWORK, int LIWORK) 
+ {
+-  extern  void  dsyevd_ (char *JOBZp, char *UPLOp, int *Np,
+-			 double *A, int *LDAp, 
+-			 double *W, 
+-			 double *WORK, int *LWORKp, int *IWORK, int *LIWORKp,
+-			 int *INFOp);
+   int  INFO;
+-  dsyevd_ (&JOBZ, &UPLO, &N, A, &LDA, 
++  int32_t N32 = N;
++  int32_t LDA32 = LDA;
++  int32_t LWORK32 = LWORK;
++  dsyevd_ (&JOBZ, &UPLO, &N32, A, &LDA32, 
+ 	   W, 
+-           WORK, &LWORK, IWORK, &LIWORK, &INFO);
++           WORK, &LWORK32, IWORK, &LIWORK, &INFO, 1, 1);
+   
+   return  INFO;
+ }
+@@ -1640,16 +1639,11 @@
+ 	    double *W, double *Z, int LDZ, int *ISUPPZ,
+ 	    double *WORK, int LWORK, int *IWORK, int LIWORK) 
+ {
+-  extern  void  dsyevr_ (char *JOBZp, char *RANGEp, char *UPLOp, int *Np,
+-			 double *A, int *LDAp, double *VLp, double *VUp,
+-			 int *ILp, int *IUp, double *ABSTOLp, int *Mp,
+-			 double *W, double *Z, int *LDZp, int *ISUPPZ,
+-			 double *WORK, int *LWORKp, int *IWORK, int *LIWORKp,
+-			 int *INFOp);
+   int  INFO;
+-  dsyevr_ (&JOBZ, &RANGE, &UPLO, &N, A, &LDA, &VL, &VU,
+-           &IL, &IU, &ABSTOL, M, W, Z, &LDZ, ISUPPZ,
+-           WORK, &LWORK, IWORK, &LIWORK, &INFO);
++  int32_t N32 = N, LDA32 = LDA, IL32 = IL, IU32 = IU, LDZ32 = LDZ, LWORK32 = LWORK, LIWORK32 = LIWORK;
++  dsyevr_ (&JOBZ, &RANGE, &UPLO, &N32, A, &LDA32, &VL, &VU,
++           &IL32, &IU32, &ABSTOL, M, W, Z, &LDZ32, ISUPPZ,
++           WORK, &LWORK32, IWORK, &LIWORK32, &INFO, 1, 1, 1);
+   
+   return  INFO;
+ }
+@@ -1739,16 +1733,27 @@
+   }
+   
+   /*  Turn Y into its LU form, store pivot matrix  */
+-  info = clapack_dgetrf (CblasColMajor, n, n, Y, n, ipiv);
++  dgetrf_(&n, &n, Y, &n, ipiv, &info);
+   
+   /*  Don't bother continuing when illegal argument (info<0) or singularity (info>0) occurs  */
+-  if (info!=0) return info;
++  if (info != 0) {
++    free(ipiv);
++    return info;
++  }
+   
+   /*  Feed this to the lapack inversion routine.  */
+-  info = clapack_dgetri (CblasColMajor, n, Y, n, ipiv);
++  int lwork = n * n;
++  double *work = malloc(lwork * sizeof(double));
++  if (work == NULL) {
++    printf("malloc failed for work array in matrix_invert\n");
++    free(ipiv);
++    return 2;
++  }
++  dgetri_(&n, Y, &n, ipiv, work, &lwork, &info);
+   
+   /*  Cleanup and exit  */
+   free(ipiv);
++  free(work);
+   return info;
+ }
+ 

From 3f86fa26e8ccb794adc198fd4aa6abf19c1f8f1c Mon Sep 17 00:00:00 2001
From: Simon Branford <4967+branfosj@users.noreply.github.com>
Date: Tue, 13 Aug 2024 17:39:23 +0100
Subject: [PATCH 614/835] stop RStudio-Server installing R packages

---
 .../RStudio-Server-2023.09.1+494-gfbf-2023a-Java-11-R-4.3.2.eb  | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2023.09.1+494-gfbf-2023a-Java-11-R-4.3.2.eb b/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2023.09.1+494-gfbf-2023a-Java-11-R-4.3.2.eb
index 020dde50a43..f95b26d2a6a 100644
--- a/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2023.09.1+494-gfbf-2023a-Java-11-R-4.3.2.eb
+++ b/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2023.09.1+494-gfbf-2023a-Java-11-R-4.3.2.eb
@@ -36,6 +36,7 @@ dependencies = [
     ('Boost', '1.82.0'),
     ('Java', '11', '', SYSTEM),
     ('R', '4.3.2'),
+    ('R-bundle-CRAN', '2023.12'),
     ('SOCI', '4.0.3'),
     ('yaml-cpp', '0.7.0'),
 ]
@@ -52,7 +53,6 @@ preconfigopts = " && ".join([
     "./install-dictionaries",
     "./install-mathjax",
     "./install-pandoc",
-    "./install-packages",
     "./install-panmirror",
     "./install-npm-dependencies)",
     ""

From 271a36fcc22d0c56d856716a3ffe30f481f9b2d4 Mon Sep 17 00:00:00 2001
From: Simon Branford <4967+branfosj@users.noreply.github.com>
Date: Tue, 13 Aug 2024 18:09:21 +0100
Subject: [PATCH 615/835] requires change in toolchain

---
 ... RStudio-Server-2023.09.1+494-foss-2023a-Java-11-R-4.3.2.eb} | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)
 rename easybuild/easyconfigs/r/RStudio-Server/{RStudio-Server-2023.09.1+494-gfbf-2023a-Java-11-R-4.3.2.eb => RStudio-Server-2023.09.1+494-foss-2023a-Java-11-R-4.3.2.eb} (98%)

diff --git a/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2023.09.1+494-gfbf-2023a-Java-11-R-4.3.2.eb b/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2023.09.1+494-foss-2023a-Java-11-R-4.3.2.eb
similarity index 98%
rename from easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2023.09.1+494-gfbf-2023a-Java-11-R-4.3.2.eb
rename to easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2023.09.1+494-foss-2023a-Java-11-R-4.3.2.eb
index f95b26d2a6a..56585dad1c0 100644
--- a/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2023.09.1+494-gfbf-2023a-Java-11-R-4.3.2.eb
+++ b/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2023.09.1+494-foss-2023a-Java-11-R-4.3.2.eb
@@ -18,7 +18,7 @@ and then used with:
   rserver ... --database-config-file="${MYTMP}/db.conf"
 """
 
-toolchain = {'name': 'gfbf', 'version': '2023a'}
+toolchain = {'name': 'foss', 'version': '2023a'}
 
 source_urls = ['https://github.com/rstudio/rstudio/archive']
 sources = ['v%(version)s.tar.gz']

From 631f6a1d3b69d86783db82edde4c8d81a2ca022a Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Wed, 14 Aug 2024 10:02:04 +0200
Subject: [PATCH 616/835] update junos-eznc.eb - pre- preinstallopts

---
 .../j/junos-eznc/junos-eznc-2.7.1-GCCcore-12.3.0.eb         | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/easybuild/easyconfigs/j/junos-eznc/junos-eznc-2.7.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/j/junos-eznc/junos-eznc-2.7.1-GCCcore-12.3.0.eb
index 2799845eb24..ceaec648de3 100644
--- a/easybuild/easyconfigs/j/junos-eznc/junos-eznc-2.7.1-GCCcore-12.3.0.eb
+++ b/easybuild/easyconfigs/j/junos-eznc/junos-eznc-2.7.1-GCCcore-12.3.0.eb
@@ -17,9 +17,6 @@ dependencies = [
     ('bcrypt', '4.0.1'),
 ]
 
-# delete 'os.system("pip install git+https://github.com/Juniper/paramiko.git@v3.4.0-JNPR")' from setup.py
-local_preinstallopts = "sed -i '6d' setup.py && "
-
 exts_list = [
     ('yamlordereddictloader', '0.4.2', {
         'checksums': ['36af2f6210fcff5da4fc4c12e1d815f973dceb41044e795e1f06115d634bca13'],
@@ -45,7 +42,8 @@ exts_list = [
     }),
     (name, version, {
         'modulename': 'jnpr.junos',
-        'preinstallopts': "sed -i '6d' setup.py && ",
+        # delete 'os.system("pip install git+https://github.com/Juniper/paramiko.git@v3.4.0-JNPR")' from setup.py
+        'preinstallopts': "sed -i '/pip install/d' setup.py && ",
         'checksums': ['371f0298bf03e0cb4c017c43f6f4122263584eda0d690d0112e93f13daae41ac'],
     }),
 ]

From 6f40b2fa172471e85e8c0e3174b537d8ea9899c8 Mon Sep 17 00:00:00 2001
From: Pedro Santos Neves <10762799+Neves-P@users.noreply.github.com>
Date: Wed, 14 Aug 2024 10:43:37 +0200
Subject: [PATCH 617/835] Fix style

---
 .../g/GROMACS/GROMACS-2023.3-foss-2023a-PLUMED-2.9.0.eb          | 1 -
 1 file changed, 1 deletion(-)

diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.3-foss-2023a-PLUMED-2.9.0.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.3-foss-2023a-PLUMED-2.9.0.eb
index 38166a92912..943aa4ac839 100755
--- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.3-foss-2023a-PLUMED-2.9.0.eb
+++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.3-foss-2023a-PLUMED-2.9.0.eb
@@ -98,4 +98,3 @@ modextrapaths = {
 }
 
 moduleclass = 'bio'
-

From 344d2f82335e4576769756b1f33798ec54ade307 Mon Sep 17 00:00:00 2001
From: Sam Moors <smoors@users.noreply.github.com>
Date: Wed, 14 Aug 2024 10:47:20 +0200
Subject: [PATCH 618/835] tiny change to make spacing more consistent

---
 .../tensorflow-probability-0.20.0-foss-2023a.eb               | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.20.0-foss-2023a.eb b/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.20.0-foss-2023a.eb
index e18a2bc7414..efede874267 100644
--- a/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.20.0-foss-2023a.eb
+++ b/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.20.0-foss-2023a.eb
@@ -31,8 +31,8 @@ use_pip = True
 # avoid pip check fail when tensorflow-probability is a dependency
 local_postinstallcmds = "cd %(installdir)s/lib/python%(pyshortver)s/site-packages && "
 local_postinstallcmds += "mv tfp_nightly-%(version)s.dist-info tensorflow_probability-%(version)s.dist-info && "
-local_postinstallcmds += "sed -i 's/Name: tfp-nightly/Name: %(name)s/'"
-local_postinstallcmds += " tensorflow_probability-%(version)s.dist-info/METADATA"
+local_postinstallcmds += "sed -i 's/Name: tfp-nightly/Name: %(name)s/' "
+local_postinstallcmds += "tensorflow_probability-%(version)s.dist-info/METADATA"
 
 exts_list = [
     ('cloudpickle', '3.0.0', {

From b1691e04e45b28f3a7f3ef59d5236e5ab041f417 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Wed, 14 Aug 2024 11:02:49 +0200
Subject: [PATCH 619/835] add preinstallopts to fix Invalid cross-device link
 error

---
 .../flash-attention-2.6.3-foss-2023a-CUDA-12.1.1.eb            | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/easybuild/easyconfigs/f/flash-attention/flash-attention-2.6.3-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/f/flash-attention/flash-attention-2.6.3-foss-2023a-CUDA-12.1.1.eb
index 0ef79545ba0..8f3d41e17ad 100644
--- a/easybuild/easyconfigs/f/flash-attention/flash-attention-2.6.3-foss-2023a-CUDA-12.1.1.eb
+++ b/easybuild/easyconfigs/f/flash-attention/flash-attention-2.6.3-foss-2023a-CUDA-12.1.1.eb
@@ -24,6 +24,9 @@ use_pip = True
 exts_list = [
     (name, version, {
         'modulename': 'flash_attn',
+        # solves Invalid cross-device link error
+        # https://github.com/Dao-AILab/flash-attention/issues/875
+        'preinstallopts': "sed -i 's/os.rename/shutil.move/' setup.py && ",
         'source_urls': ['https://github.com/Dao-AILab/flash-attention/archive/'],
         'sources': ['v%(version)s.tar.gz'],
         'checksums': ['136e149165d4c8c67273d16daa957b5cd5e6fc629061ffd39fa5a25224454d6c'],

From e43066d8654edd9d0e1524cdc73ed2e768d8ae77 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Wed, 14 Aug 2024 11:44:37 +0200
Subject: [PATCH 620/835] adding easyconfigs: Julia-1.10.4-linux-x86_64.eb

---
 .../j/Julia/Julia-1.10.4-linux-x86_64.eb      | 37 +++++++++++++++++++
 1 file changed, 37 insertions(+)
 create mode 100644 easybuild/easyconfigs/j/Julia/Julia-1.10.4-linux-x86_64.eb

diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.10.4-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.10.4-linux-x86_64.eb
new file mode 100644
index 00000000000..dccc9cb700e
--- /dev/null
+++ b/easybuild/easyconfigs/j/Julia/Julia-1.10.4-linux-x86_64.eb
@@ -0,0 +1,37 @@
+# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/
+# Author: Pablo Escobar Lopez
+# sciCORE - University of Basel
+# SIB Swiss Institute of Bioinformatics
+# Updated by: Dugan Witherick, University of Warwick
+#             Robert Mijakovic <robert.mijakovic@lxp.lu>
+#             Wahid Mainassara <wahid.mainassara@lxp.lu>
+
+easyblock = 'Tarball'
+
+name = 'Julia'
+version = '1.10.4'
+versionsuffix = '-linux-x86_64'
+
+homepage = 'https://julialang.org'
+description = "Julia is a high-level, high-performance dynamic programming language for numerical computing"
+
+toolchain = SYSTEM
+
+source_urls = ['https://julialang-s3.julialang.org/bin/linux/x64/%(version_major_minor)s/']
+sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz']
+patches = [('julia.wrapper', 'bin/')]
+checksums = [
+    {'julia-1.10.4-linux-x86_64.tar.gz': '079f61757c3b5b40d2ade052b3cc4816f50f7ef6df668825772562b3746adff1'},
+    {'julia.wrapper': 'd10aeaff53cca9875f7b0ce9218eae3bd21870b654e26c4c52aa8bfcc9da702d'},
+]
+
+# install wrapper with linking safeguards for Julia libraries
+postinstallcmds = ["cd %(installdir)s/bin && mv julia julia.bin && mv julia.wrapper julia"]
+
+sanity_check_paths = {
+    'files': ['bin/julia', 'bin/julia.bin', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT],
+    'dirs': ['bin', 'etc', 'include', 'lib', 'lib/julia', 'share']
+}
+sanity_check_commands = ['julia --help']
+
+moduleclass = 'lang'
\ No newline at end of file

From bb6e8770ae10d4b41be762a9f16a7de63da9fbb6 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 14 Aug 2024 13:40:00 +0200
Subject: [PATCH 621/835] {bio}[foss/2022a] AlphaPulldown v2.0.0b4, Uni-Core
 v0.0.3

---
 ....0b2_fix-import-protein_letters_3to1.patch | 13 +++
 .../AlphaPulldown-2.0.0b4-foss-2022a.eb       | 95 +++++++++++++++++++
 .../u/Uni-Core/Uni-Core-0.0.3-foss-2022a.eb   | 56 +++++++++++
 3 files changed, 164 insertions(+)
 create mode 100644 easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b2_fix-import-protein_letters_3to1.patch
 create mode 100644 easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b4-foss-2022a.eb
 create mode 100644 easybuild/easyconfigs/u/Uni-Core/Uni-Core-0.0.3-foss-2022a.eb

diff --git a/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b2_fix-import-protein_letters_3to1.patch b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b2_fix-import-protein_letters_3to1.patch
new file mode 100644
index 00000000000..34994664f80
--- /dev/null
+++ b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b2_fix-import-protein_letters_3to1.patch
@@ -0,0 +1,13 @@
+fix import of protein_letters_3to1 from Biopython
+author: Kenneth Hoste (HPC-UGent)
+--- AlphaPulldown/alphapulldown/utils/remove_clashes_low_plddt.py.orig	2024-06-05 09:30:16.114746286 +0200
++++ AlphaPulldown/alphapulldown/utils/remove_clashes_low_plddt.py	2024-06-05 09:30:35.242665615 +0200
+@@ -4,7 +4,7 @@
+ from alphafold.data.mmcif_parsing import parse
+ from alphafold.common.residue_constants import residue_atoms, atom_types
+ from Bio.PDB import NeighborSearch, PDBIO, MMCIFIO
+-from Bio.PDB.Polypeptide import protein_letters_3to1
++from Bio.Data.SCOPData import protein_letters_3to1
+ from Bio import SeqIO
+ from colabfold.batch import convert_pdb_to_mmcif
+ from Bio.PDB import Structure, Model, Chain, Residue
diff --git a/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b4-foss-2022a.eb b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b4-foss-2022a.eb
new file mode 100644
index 00000000000..f41935fe51d
--- /dev/null
+++ b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b4-foss-2022a.eb
@@ -0,0 +1,95 @@
+# created by Denis Kristak (Inuits)
+easyblock = 'PythonBundle'
+
+name = 'AlphaPulldown'
+version = '2.0.0b4'
+
+homepage = 'https://github.com/KosinskiLab/AlphaPulldown'
+description = """AlphaPulldown is a Python package that streamlines protein-protein
+interaction screens and high-throughput modelling of higher-order oligomers using AlphaFold-Multimer"""
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('OpenMM', '8.0.0'),
+    ('Kalign', '3.3.5'),
+    ('PyYAML', '6.0'),
+    ('jax', '0.3.25'),  # also provides absl-py
+    ('Biopython', '1.79'),
+    ('h5py', '3.7.0'),
+    ('IPython', '8.5.0'),
+    ('JupyterLab', '3.5.0'),
+    ('matplotlib', '3.5.2'),
+    ('TensorFlow', '2.11.0'),
+    ('PyTorch', '1.12.0'),
+    ('tqdm', '4.64.0'),
+    ('dm-tree', '0.1.8'),
+    ('py3Dmol', '2.0.1.post1'),
+    ('HMMER', '3.3.2'),
+    ('HH-suite', '3.3.0'),
+    ('Uni-Core', '0.0.3'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('importlib-resources', '5.13.0', {
+        'modulename': 'importlib_resources',
+        'source_tmpl': 'importlib_resources-%(version)s.tar.gz',
+        'checksums': ['82d5c6cca930697dbbd86c93333bb2c2e72861d4789a11c2662b933e5ad2b528'],
+    }),
+    ('jmp', '0.0.4', {
+        'checksums': ['5dfeb0fd7c7a9f72a70fff0aab9d0cbfae32a809c02f4037ff3485ceb33e1730'],
+    }),
+    ('dm-haiku', '0.0.9', {
+        'modulename': 'haiku',
+        'source_urls': ['https://github.com/deepmind/dm-haiku/archive/refs/tags/'],
+        'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}],
+        'checksums': ['d550f07f5891ede30ada5faafde98f549ed1b8ceadb7a601cca3d81db7d82414'],
+    }),
+    ('contextlib2', '21.6.0', {
+        'checksums': ['ab1e2bfe1d01d968e1b7e8d9023bc51ef3509bba217bb730cee3827e1ee82869'],
+    }),
+    ('ml-collections', '0.1.1', {
+        'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ",
+        'sources': ['ml_collections-%(version)s.tar.gz'],
+        'checksums': ['3fefcc72ec433aa1e5d32307a3e474bbb67f405be814ea52a2166bfc9dbe68cc'],
+    }),
+    ('PDBFixer', '1.9', {
+        'source_urls': ['https://github.com/openmm/pdbfixer/archive/'],
+        'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}],
+        'checksums': ['88b9a77e50655f89d0eb2075093773e82c27a4cef842cb7d735c877b20cd39fb'],
+    }),
+    (name, version, {
+        'sources': [{
+            'filename': SOURCE_TAR_GZ,
+            'git_config': {
+                'url': 'https://github.com/KosinskiLab',
+                'repo_name': 'AlphaPulldown',
+                'tag': version,
+                'recursive': True,
+            },
+        }],
+        'patches': ['AlphaPulldown-2.0.0b2_fix-import-protein_letters_3to1.patch'],
+        'checksums': [
+            None,
+            'd41247cd12f6ef8579adbc893f6c1af5fba051167ee838449974365f4bdccf06',
+        ],
+        # remove strict version requirements for Python dependencies
+        'preinstallopts': "sed -i 's/[>=]=.*//g' setup.cfg && ",
+    }),
+]
+
+fix_python_shebang_for = ['bin/*.py']
+
+sanity_pip_check = True
+
+sanity_check_paths = {
+    'files': ['bin/run_multimer_jobs.py', 'bin/rename_colab_search_a3m.py'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages/alphapulldown'],
+}
+
+sanity_check_commands = ["run_multimer_jobs.py --help | grep 'A script to perform structure prediction'"]
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/u/Uni-Core/Uni-Core-0.0.3-foss-2022a.eb b/easybuild/easyconfigs/u/Uni-Core/Uni-Core-0.0.3-foss-2022a.eb
new file mode 100644
index 00000000000..d82f94349bc
--- /dev/null
+++ b/easybuild/easyconfigs/u/Uni-Core/Uni-Core-0.0.3-foss-2022a.eb
@@ -0,0 +1,56 @@
+easyblock = 'PythonBundle'
+
+name = 'Uni-Core'
+version = '0.0.3'
+
+homepage = 'https://github.com/dptech-corp/Uni-Core'
+description = "An efficient distributed PyTorch framework"
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('PyTorch', '1.12.0'),
+    ('jax', '0.3.25'),  # provides absl-py
+    ('tensorboardX', '2.5.1'),
+    ('tqdm', '4.64.0'),
+    ('wandb', '0.13.4'),
+]
+
+use_pip = True
+
+local_preinstallopts = "sed -i -e 's/DISABLE_CUDA_EXTENSION = False/DISABLE_CUDA_EXTENSION = True/g' "
+local_preinstallopts += "-e 's/torch>=[0-9.]*/torch/g' setup.py && "
+
+exts_list = [
+    ('lmdb', '1.4.1', {
+        'checksums': ['1f4c76af24e907593487c904ef5eba1993beb38ed385af82adb25a858f2d658d'],
+    }),
+    ('contextlib2', '21.6.0', {
+        'checksums': ['ab1e2bfe1d01d968e1b7e8d9023bc51ef3509bba217bb730cee3827e1ee82869'],
+    }),
+    ('ml-collections', '0.1.1', {
+        'sources': ['ml_collections-%(version)s.tar.gz'],
+        'checksums': ['3fefcc72ec433aa1e5d32307a3e474bbb67f405be814ea52a2166bfc9dbe68cc'],
+        'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ",
+    }),
+    ('huggingface-hub', '0.17.3', {
+        'source_tmpl': 'huggingface_hub-%(version)s.tar.gz',
+        'checksums': ['40439632b211311f788964602bf8b0d9d6b7a2314fba4e8d67b2ce3ecea0e3fd'],
+    }),
+    ('tokenizers', '0.19.1', {
+        'sources': ['tokenizers-%(version)s-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl'],
+        'checksums': ['8b01afb7193d47439f091cd8f070a1ced347ad0f9144952a30a41836902fe09e'],
+    }),
+    (name, version, {
+        'source_urls': ['https://github.com/dptech-corp/Uni-Core/archive/'],
+        'sources': ['%(version)s.tar.gz'],
+        'checksums': ['e7a1e938d7d340d7aa483a05ed5ecf715bfa22f5f32a92e46d096da5b9a08043'],
+        'preinstallopts': local_preinstallopts,
+        'modulename': 'unicore',
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'ai'

From 9ede928c195f6d122f558ade9554cb38af831b9b Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com>
Date: Wed, 14 Aug 2024 14:08:52 +0200
Subject: [PATCH 622/835] Update Julia-1.10.4-linux-x86_64.eb - blank line in
 the end

---
 easybuild/easyconfigs/j/Julia/Julia-1.10.4-linux-x86_64.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.10.4-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.10.4-linux-x86_64.eb
index dccc9cb700e..767a23c33a4 100644
--- a/easybuild/easyconfigs/j/Julia/Julia-1.10.4-linux-x86_64.eb
+++ b/easybuild/easyconfigs/j/Julia/Julia-1.10.4-linux-x86_64.eb
@@ -34,4 +34,4 @@ sanity_check_paths = {
 }
 sanity_check_commands = ['julia --help']
 
-moduleclass = 'lang'
\ No newline at end of file
+moduleclass = 'lang'

From 451e98e35f2ca212926ab7c7db38654266aaf064 Mon Sep 17 00:00:00 2001
From: Neves-P <p.m.santos.neves@rug.nl>
Date: Wed, 14 Aug 2024 14:43:36 +0200
Subject: [PATCH 623/835] Fix file permissions

---
 .../g/GROMACS/GROMACS-2023.3-foss-2023a-PLUMED-2.9.0.eb           | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 mode change 100755 => 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-2023.3-foss-2023a-PLUMED-2.9.0.eb

diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.3-foss-2023a-PLUMED-2.9.0.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.3-foss-2023a-PLUMED-2.9.0.eb
old mode 100755
new mode 100644

From 3738c95403e97fff3d26fb45219e53c5915821d6 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 14 Aug 2024 15:07:01 +0200
Subject: [PATCH 624/835] {bio}[foss/2022a] AlphaPulldown v2.0.0b4, Uni-Core
 v0.0.3 w/ CUDA 11.7.0

---
 ...Pulldown-2.0.0b4-foss-2022a-CUDA-11.7.0.eb | 97 +++++++++++++++++++
 .../Uni-Core-0.0.3-foss-2022a-CUDA-11.7.0.eb  | 55 +++++++++++
 2 files changed, 152 insertions(+)
 create mode 100644 easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b4-foss-2022a-CUDA-11.7.0.eb
 create mode 100644 easybuild/easyconfigs/u/Uni-Core/Uni-Core-0.0.3-foss-2022a-CUDA-11.7.0.eb

diff --git a/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b4-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b4-foss-2022a-CUDA-11.7.0.eb
new file mode 100644
index 00000000000..72746293174
--- /dev/null
+++ b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b4-foss-2022a-CUDA-11.7.0.eb
@@ -0,0 +1,97 @@
+# created by Denis Kristak (Inuits)
+easyblock = 'PythonBundle'
+
+name = 'AlphaPulldown'
+version = '2.0.0b4'
+versionsuffix = '-CUDA-%(cudaver)s'
+
+homepage = 'https://github.com/KosinskiLab/AlphaPulldown'
+description = """AlphaPulldown is a Python package that streamlines protein-protein
+interaction screens and high-throughput modelling of higher-order oligomers using AlphaFold-Multimer"""
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+dependencies = [
+    ('CUDA', '11.7.0', '', SYSTEM),
+    ('Python', '3.10.4'),
+    ('OpenMM', '8.0.0'),
+    ('Kalign', '3.3.5'),
+    ('PyYAML', '6.0'),
+    ('jax', '0.3.25', versionsuffix),  # also provides absl-py
+    ('Biopython', '1.79'),
+    ('h5py', '3.7.0'),
+    ('IPython', '8.5.0'),
+    ('JupyterLab', '3.5.0'),
+    ('matplotlib', '3.5.2'),
+    ('TensorFlow', '2.11.0', versionsuffix),
+    ('PyTorch', '1.12.0', versionsuffix),
+    ('tqdm', '4.64.0'),
+    ('dm-tree', '0.1.8'),
+    ('py3Dmol', '2.0.1.post1'),
+    ('HMMER', '3.3.2'),
+    ('HH-suite', '3.3.0'),
+    ('Uni-Core', '0.0.3', versionsuffix),
+]
+
+use_pip = True
+
+exts_list = [
+    ('importlib-resources', '5.13.0', {
+        'modulename': 'importlib_resources',
+        'source_tmpl': 'importlib_resources-%(version)s.tar.gz',
+        'checksums': ['82d5c6cca930697dbbd86c93333bb2c2e72861d4789a11c2662b933e5ad2b528'],
+    }),
+    ('jmp', '0.0.4', {
+        'checksums': ['5dfeb0fd7c7a9f72a70fff0aab9d0cbfae32a809c02f4037ff3485ceb33e1730'],
+    }),
+    ('dm-haiku', '0.0.9', {
+        'modulename': 'haiku',
+        'source_urls': ['https://github.com/deepmind/dm-haiku/archive/refs/tags/'],
+        'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}],
+        'checksums': ['d550f07f5891ede30ada5faafde98f549ed1b8ceadb7a601cca3d81db7d82414'],
+    }),
+    ('contextlib2', '21.6.0', {
+        'checksums': ['ab1e2bfe1d01d968e1b7e8d9023bc51ef3509bba217bb730cee3827e1ee82869'],
+    }),
+    ('ml-collections', '0.1.1', {
+        'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ",
+        'sources': ['ml_collections-%(version)s.tar.gz'],
+        'checksums': ['3fefcc72ec433aa1e5d32307a3e474bbb67f405be814ea52a2166bfc9dbe68cc'],
+    }),
+    ('PDBFixer', '1.9', {
+        'source_urls': ['https://github.com/openmm/pdbfixer/archive/'],
+        'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}],
+        'checksums': ['88b9a77e50655f89d0eb2075093773e82c27a4cef842cb7d735c877b20cd39fb'],
+    }),
+    (name, version, {
+        'sources': [{
+            'filename': SOURCE_TAR_GZ,
+            'git_config': {
+                'url': 'https://github.com/KosinskiLab',
+                'repo_name': 'AlphaPulldown',
+                'tag': version,
+                'recursive': True,
+            },
+        }],
+        'patches': ['AlphaPulldown-2.0.0b2_fix-import-protein_letters_3to1.patch'],
+        'checksums': [
+            None,
+            'd41247cd12f6ef8579adbc893f6c1af5fba051167ee838449974365f4bdccf06',
+        ],
+        # remove strict version requirements for Python dependencies
+        'preinstallopts': "sed -i 's/[>=]=.*//g' setup.cfg && ",
+    }),
+]
+
+fix_python_shebang_for = ['bin/*.py']
+
+sanity_pip_check = True
+
+sanity_check_paths = {
+    'files': ['bin/run_multimer_jobs.py', 'bin/rename_colab_search_a3m.py'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages/alphapulldown'],
+}
+
+sanity_check_commands = ["run_multimer_jobs.py --help | grep 'A script to perform structure prediction'"]
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/u/Uni-Core/Uni-Core-0.0.3-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/u/Uni-Core/Uni-Core-0.0.3-foss-2022a-CUDA-11.7.0.eb
new file mode 100644
index 00000000000..2ca769764aa
--- /dev/null
+++ b/easybuild/easyconfigs/u/Uni-Core/Uni-Core-0.0.3-foss-2022a-CUDA-11.7.0.eb
@@ -0,0 +1,55 @@
+easyblock = 'PythonBundle'
+
+name = 'Uni-Core'
+version = '0.0.3'
+versionsuffix = '-CUDA-%(cudaver)s'
+
+homepage = 'https://github.com/dptech-corp/Uni-Core'
+description = "An efficient distributed PyTorch framework"
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+dependencies = [
+    ('CUDA', '11.7.0', '', SYSTEM),
+    ('Python', '3.10.4'),
+    ('PyTorch', '1.12.0', versionsuffix),
+    ('jax', '0.3.25', versionsuffix),  # provides absl-py
+    ('tensorboardX', '2.5.1'),
+    ('tqdm', '4.64.0'),
+    ('wandb', '0.13.4'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('lmdb', '1.4.1', {
+        'checksums': ['1f4c76af24e907593487c904ef5eba1993beb38ed385af82adb25a858f2d658d'],
+    }),
+    ('contextlib2', '21.6.0', {
+        'checksums': ['ab1e2bfe1d01d968e1b7e8d9023bc51ef3509bba217bb730cee3827e1ee82869'],
+    }),
+    ('ml-collections', '0.1.1', {
+        'sources': ['ml_collections-%(version)s.tar.gz'],
+        'checksums': ['3fefcc72ec433aa1e5d32307a3e474bbb67f405be814ea52a2166bfc9dbe68cc'],
+        'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ",
+    }),
+    ('huggingface-hub', '0.17.3', {
+        'source_tmpl': 'huggingface_hub-%(version)s.tar.gz',
+        'checksums': ['40439632b211311f788964602bf8b0d9d6b7a2314fba4e8d67b2ce3ecea0e3fd'],
+    }),
+    ('tokenizers', '0.19.1', {
+        'sources': ['tokenizers-%(version)s-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl'],
+        'checksums': ['8b01afb7193d47439f091cd8f070a1ced347ad0f9144952a30a41836902fe09e'],
+    }),
+    (name, version, {
+        'source_urls': ['https://github.com/dptech-corp/Uni-Core/archive/'],
+        'sources': ['%(version)s.tar.gz'],
+        'checksums': ['e7a1e938d7d340d7aa483a05ed5ecf715bfa22f5f32a92e46d096da5b9a08043'],
+        'preinstallopts': "sed -i 's/torch>=[0-9.]*/torch/g' setup.py && ",
+        'modulename': 'unicore',
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'ai'

From 2280e31879494ecf5764b12fc7b580d7dac849de Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 14 Aug 2024 15:12:23 +0200
Subject: [PATCH 625/835] add missMDA extension to R-bundle-CRAN 2024.06

---
 .../r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb        | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb b/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb
index ce8233bc4a5..c8376489c57 100644
--- a/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb
+++ b/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb
@@ -3433,6 +3433,9 @@ exts_list = [
     ('rhandsontable', '0.3.8', {
         'checksums': ['901ed9c59936f7fa52ad8db3111c8904ab962f9c74f1b6cd40f81683af35d21d'],
     }),
+    ('missMDA', '1.19', {
+        'checksums': ['f9675884829b2fef75237c335b21991d163674320e766523c71c7a853f95e65c'],
+    }),
 ]
 
 modextrapaths = {'R_LIBS_SITE': ''}

From 747a2f3ba3d096bb9e18fc4104bd8ab8f28122ff Mon Sep 17 00:00:00 2001
From: fizwit <john@fuzzdog.com>
Date: Wed, 14 Aug 2024 12:41:03 -0700
Subject: [PATCH 626/835] update CUTLASS

---
 .../CUTLASS-3.4.0-foss-2023a-CUDA-12.1.1.eb   | 49 +++++++++++++++++++
 1 file changed, 49 insertions(+)
 create mode 100644 easybuild/easyconfigs/c/CUTLASS/CUTLASS-3.4.0-foss-2023a-CUDA-12.1.1.eb

diff --git a/easybuild/easyconfigs/c/CUTLASS/CUTLASS-3.4.0-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/c/CUTLASS/CUTLASS-3.4.0-foss-2023a-CUDA-12.1.1.eb
new file mode 100644
index 00000000000..3322e6b4b56
--- /dev/null
+++ b/easybuild/easyconfigs/c/CUTLASS/CUTLASS-3.4.0-foss-2023a-CUDA-12.1.1.eb
@@ -0,0 +1,49 @@
+easyblock = 'CMakeMake'
+
+name = 'CUTLASS'
+version = '3.4.0'
+versionsuffix = '-CUDA-%(cudaver)s'
+
+homepage = 'https://github.com/NVIDIA/cutlass'
+description = """CUTLASS is a collection of CUDA C++ template
+abstractions for implementing high-performance matrix-matrix
+multiplication (GEMM) and related computations at all levels and scales
+within CUDA. It incorporates strategies for hierarchical decomposition
+and data movement similar to those used to implement cuBLAS and cuDNN.
+CUTLASS decomposes these "moving parts" into reusable, modular software
+components abstracted by C++ template classes. Primitives for different
+levels of a conceptual parallelization hierarchy can be specialized and
+tuned via custom tiling sizes, data types, and other algorithmic policy.
+The resulting flexibility simplifies their use as building blocks within
+custom kernels and applications."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+github_account = 'NVIDIA'
+source_urls = [GITHUB_LOWER_SOURCE]
+sources = ['v%(version)s.tar.gz']
+checksums = ['49f4b854acc2a520126ceefe4f701cfe8c2b039045873e311b1f10a8ca5d5de1']
+
+builddependencies = [
+    ('CMake', '3.26.3'),
+    ('Python', '3.11.3'),
+]
+
+dependencies = [
+    ('CUDA', '12.1.1', '', SYSTEM),
+    ('cuDNN', '8.9.2.26', versionsuffix, SYSTEM),
+]
+
+_copts = [
+    '-DCUTLASS_NVCC_ARCHS="%(cuda_cc_cmake)s"',
+    '-DCUTLASS_ENABLE_CUBLAS=1',
+    '-DCUTLASS_ENABLE_CUDNN=1',
+]
+configopts = ' '.join(_copts)
+
+sanity_check_paths = {
+    'files': ['include/cutlass/cutlass.h', 'lib/libcutlass.%s' % SHLIB_EXT],
+    'dirs': ['lib/cmake'],
+}
+
+moduleclass = 'lib'

From 6a7547282ba63a5402ad052607ae1da75dcc7023 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Thu, 15 Aug 2024 10:27:14 +0200
Subject: [PATCH 627/835] add dep CUTLASS from PR 21184

---
 .../flash-attention-2.6.3-foss-2023a-CUDA-12.1.1.eb              | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easybuild/easyconfigs/f/flash-attention/flash-attention-2.6.3-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/f/flash-attention/flash-attention-2.6.3-foss-2023a-CUDA-12.1.1.eb
index 8f3d41e17ad..754eef2c70e 100644
--- a/easybuild/easyconfigs/f/flash-attention/flash-attention-2.6.3-foss-2023a-CUDA-12.1.1.eb
+++ b/easybuild/easyconfigs/f/flash-attention/flash-attention-2.6.3-foss-2023a-CUDA-12.1.1.eb
@@ -16,6 +16,7 @@ dependencies = [
     ('CUDA', '12.1.1', '', SYSTEM),
     ('PyTorch-bundle', '2.1.2', versionsuffix),
     ('einops', '0.7.0'),
+    ('CUTLASS', '3.4.0', versionsuffix),
 ]
 
 sanity_pip_check = True

From 7a1e6e91ad284dcb74058ab2093992eaa76ac9a4 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Petr=20Kr=C3=A1l?= <petr@inuits.eu>
Date: Thu, 15 Aug 2024 12:47:28 +0200
Subject: [PATCH 628/835] fix shebang and sanity check commands

---
 .../y/yelp-tools/yelp-tools-42.1-GCCcore-12.3.0.eb        | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/y/yelp-tools/yelp-tools-42.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/y/yelp-tools/yelp-tools-42.1-GCCcore-12.3.0.eb
index 0ba5cdef596..bbf260ff417 100644
--- a/easybuild/easyconfigs/y/yelp-tools/yelp-tools-42.1-GCCcore-12.3.0.eb
+++ b/easybuild/easyconfigs/y/yelp-tools/yelp-tools-42.1-GCCcore-12.3.0.eb
@@ -27,11 +27,12 @@ dependencies = [
     ('yelp-xsl', '42.1'),
     ('ITSTool', '2.0.7'),
     ('libxml2', '2.11.4'),
-    # docbook-xsl ?
     ('mallard-ducktype', '1.0.2'),
     ('lxml', '4.9.2'),
 ]
 
+fix_python_shebang_for = ['bin/*']
+
 sanity_check_paths = {
     'files': [
         'bin/yelp-build',
@@ -41,4 +42,9 @@ sanity_check_paths = {
     'dirs': ['share/%(name)s'],
 }
 
+sanity_check_commands = [
+    'yelp-build cache -h',
+    'yelp-check hrefs -h',
+]
+
 moduleclass = 'tools'

From 779b0bea7e2af6792cdf4c76180787964d73053f Mon Sep 17 00:00:00 2001
From: Simon Branford <s.j.branford@bham.ac.uk>
Date: Fri, 16 Aug 2024 15:55:46 +0100
Subject: [PATCH 629/835] remove `Time::HiRes` from `Perl-bundle-CPAN`

---
 .../Perl-bundle-CPAN-5.36.1-GCCcore-12.3.0.eb               | 6 ------
 .../Perl-bundle-CPAN-5.38.0-GCCcore-13.2.0.eb               | 5 -----
 .../Perl-bundle-CPAN-5.38.2-GCCcore-13.3.0.eb               | 5 -----
 3 files changed, 16 deletions(-)

diff --git a/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.36.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.36.1-GCCcore-12.3.0.eb
index 3921d7fefac..7e166bd251f 100644
--- a/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.36.1-GCCcore-12.3.0.eb
+++ b/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.36.1-GCCcore-12.3.0.eb
@@ -1767,12 +1767,6 @@ exts_list = [
         'source_urls': ['https://cpan.metacpan.org/authors/id/J/JD/JDHEDDEN'],
         'checksums': ['9dfd6ca2822724347e0eb6759d00709425814703ad5c66bdb6214579868bcac4'],
     }),
-    ('Time::HiRes', '1.9764', {
-        'runtest': False,  # https://github.com/easybuilders/easybuild-easyconfigs/issues/20145 unreliable atime tests
-        'source_tmpl': 'Time-HiRes-%(version)s.tar.gz',
-        'source_urls': ['https://cpan.metacpan.org/authors/id/A/AT/ATOOMIC'],
-        'checksums': ['9841be5587bfb7cd1f2fe267b5e5ac04ce25e79d5cc77e5ef9a9c5abd101d7b1'],
-    }),
     ('Term::ReadLine::Gnu', '1.45', {
         'modulename': 'Term::ReadLine',
         'source_tmpl': 'Term-ReadLine-Gnu-%(version)s.tar.gz',
diff --git a/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.0-GCCcore-13.2.0.eb
index 9754ce8b0ae..154ff6fee8f 100644
--- a/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.0-GCCcore-13.2.0.eb
+++ b/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.0-GCCcore-13.2.0.eb
@@ -1770,11 +1770,6 @@ exts_list = [
         'source_urls': ['https://cpan.metacpan.org/authors/id/J/JD/JDHEDDEN'],
         'checksums': ['9dfd6ca2822724347e0eb6759d00709425814703ad5c66bdb6214579868bcac4'],
     }),
-    ('Time::HiRes', '1.9764', {
-        'source_tmpl': 'Time-HiRes-%(version)s.tar.gz',
-        'source_urls': ['https://cpan.metacpan.org/authors/id/A/AT/ATOOMIC'],
-        'checksums': ['9841be5587bfb7cd1f2fe267b5e5ac04ce25e79d5cc77e5ef9a9c5abd101d7b1'],
-    }),
     ('Term::ReadLine::Gnu', '1.46', {
         'modulename': 'Term::ReadLine',
         'source_tmpl': 'Term-ReadLine-Gnu-%(version)s.tar.gz',
diff --git a/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.2-GCCcore-13.3.0.eb
index 39679dc0366..7ea28abbcbb 100644
--- a/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.2-GCCcore-13.3.0.eb
+++ b/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.2-GCCcore-13.3.0.eb
@@ -1776,11 +1776,6 @@ exts_list = [
         'source_urls': ['https://cpan.metacpan.org/authors/id/J/JD/JDHEDDEN'],
         'checksums': ['9dfd6ca2822724347e0eb6759d00709425814703ad5c66bdb6214579868bcac4'],
     }),
-    ('Time::HiRes', '1.9764', {
-        'source_tmpl': 'Time-HiRes-%(version)s.tar.gz',
-        'source_urls': ['https://cpan.metacpan.org/authors/id/A/AT/ATOOMIC'],
-        'checksums': ['9841be5587bfb7cd1f2fe267b5e5ac04ce25e79d5cc77e5ef9a9c5abd101d7b1'],
-    }),
     ('Term::ReadLine::Gnu', '1.46', {
         'modulename': 'Term::ReadLine',
         'source_tmpl': 'Term-ReadLine-Gnu-%(version)s.tar.gz',

From cd8b1ce595195f132125d9b25a98a9efe702c72a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jurij=20Pe=C4=8Dar?= <jurij.pecar@embl.de>
Date: Fri, 16 Aug 2024 22:39:45 +0200
Subject: [PATCH 630/835] update STAR to make it build on non-x86_64
 architectures

---
 easybuild/easyconfigs/s/STAR/STAR-2.7.11b-GCC-13.2.0.eb | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.7.11b-GCC-13.2.0.eb b/easybuild/easyconfigs/s/STAR/STAR-2.7.11b-GCC-13.2.0.eb
index a86f215d8dd..b6fbedeec11 100644
--- a/easybuild/easyconfigs/s/STAR/STAR-2.7.11b-GCC-13.2.0.eb
+++ b/easybuild/easyconfigs/s/STAR/STAR-2.7.11b-GCC-13.2.0.eb
@@ -24,6 +24,9 @@ checksums = [
     {'STAR-2.7.11a_use-external-htslib.patch': '2fdc3ed9372d983f77d861d6f16a60a553598358dce9ff8216f96eb20e63ce4e'},
 ]
 
+#by default this is set to -mavx2 which makes it fail on non x86 systems
+prebuildopts = 'CXXFLAGS_SIMD= '
+
 builddependencies = [
     ('xxd', '9.1.0307'),
 ]

From e503cd5ccde2803bdfa7597d1d99b713b68f203f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jure=20Pe=C4=8Dar?= <jurij.pecar@embl.de>
Date: Fri, 16 Aug 2024 23:36:31 +0200
Subject: [PATCH 631/835] Update STAR-2.7.11b-GCC-13.2.0.eb

space
---
 easybuild/easyconfigs/s/STAR/STAR-2.7.11b-GCC-13.2.0.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.7.11b-GCC-13.2.0.eb b/easybuild/easyconfigs/s/STAR/STAR-2.7.11b-GCC-13.2.0.eb
index b6fbedeec11..099b3c1127d 100644
--- a/easybuild/easyconfigs/s/STAR/STAR-2.7.11b-GCC-13.2.0.eb
+++ b/easybuild/easyconfigs/s/STAR/STAR-2.7.11b-GCC-13.2.0.eb
@@ -24,7 +24,7 @@ checksums = [
     {'STAR-2.7.11a_use-external-htslib.patch': '2fdc3ed9372d983f77d861d6f16a60a553598358dce9ff8216f96eb20e63ce4e'},
 ]
 
-#by default this is set to -mavx2 which makes it fail on non x86 systems
+# by default this is set to -mavx2 which makes it fail on non x86 systems
 prebuildopts = 'CXXFLAGS_SIMD= '
 
 builddependencies = [

From 81b3932d5fb11b01d37566c25a6e2112652c35bb Mon Sep 17 00:00:00 2001
From: Thomas Hayward-Schneider <thomas.hayward@ipp.mpg.de>
Date: Tue, 6 Aug 2024 13:54:52 +0200
Subject: [PATCH 632/835] HDF URLs (Issue #21131)

Squash of:
* Change URLs
* revert archive changes
* Adding missing checksums
* h4toh5/2.2.2: Revert changes (no longer available upstream)
---
 easybuild/easyconfigs/h/HDF/HDF-4.2.11-intel-2016a.eb        | 5 +++--
 easybuild/easyconfigs/h/HDF/HDF-4.2.12-intel-2017a.eb        | 5 +++--
 easybuild/easyconfigs/h/HDF/HDF-4.2.13-GCCcore-6.4.0.eb      | 4 ++--
 .../easyconfigs/h/HDF/HDF-4.2.13-intel-2017a-no-netcdf.eb    | 4 ++--
 easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-6.4.0.eb      | 4 ++--
 easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-7.3.0.eb      | 4 ++--
 easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-8.2.0.eb      | 4 ++--
 easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-8.3.0.eb      | 4 ++--
 easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-10.2.0.eb     | 4 ++--
 easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-10.3.0.eb     | 4 ++--
 easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-11.2.0.eb     | 4 ++--
 easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-11.3.0.eb     | 4 ++--
 easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-12.2.0.eb     | 4 ++--
 easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-9.3.0.eb      | 4 ++--
 easybuild/easyconfigs/h/HDF/HDF-4.2.16-2-GCCcore-12.3.0.eb   | 2 +-
 easybuild/easyconfigs/h/HDF/HDF-4.2.16-2-GCCcore-13.2.0.eb   | 2 +-
 easybuild/easyconfigs/h/HDF/HDF-4.2.16-GCCcore-12.3.0.eb     | 2 +-
 easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.3-foss-2018b.eb    | 4 ++--
 easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.3-gompi-2019b.eb   | 4 ++--
 easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.3-gompi-2020b.eb   | 4 ++--
 easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.5-gompi-2022a.eb   | 2 +-
 21 files changed, 40 insertions(+), 38 deletions(-)

diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.11-intel-2016a.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.11-intel-2016a.eb
index e115932f8ee..3e25fa94133 100644
--- a/easybuild/easyconfigs/h/HDF/HDF-4.2.11-intel-2016a.eb
+++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.11-intel-2016a.eb
@@ -3,15 +3,16 @@ easyblock = 'ConfigureMake'
 name = 'HDF'
 version = '4.2.11'
 
-homepage = 'http://www.hdfgroup.org/products/hdf4/'
+homepage = 'http://support.hdfgroup.org/products/hdf4/'
 description = """HDF (also known as HDF4) is a library and multi-object file format for storing and managing data
  between machines."""
 
 toolchain = {'name': 'intel', 'version': '2016a'}
 toolchainopts = {'pic': True}
 
+source_urls = ['http://support.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/']
 sources = [SOURCELOWER_TAR_GZ]
-source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/']
+checksums = ['c3f7753b2fb9b27d09eced4d2164605f111f270c9a60b37a578f7de02de86d24']
 
 builddependencies = [
     ('flex', '2.6.0'),
diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.12-intel-2017a.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.12-intel-2017a.eb
index 36b03f18536..5fade2d2248 100644
--- a/easybuild/easyconfigs/h/HDF/HDF-4.2.12-intel-2017a.eb
+++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.12-intel-2017a.eb
@@ -3,15 +3,16 @@ easyblock = 'ConfigureMake'
 name = 'HDF'
 version = '4.2.12'
 
-homepage = 'http://www.hdfgroup.org/products/hdf4/'
+homepage = 'http://support.hdfgroup.org/products/hdf4/'
 description = """HDF (also known as HDF4) is a library and multi-object file format for storing and managing data
  between machines."""
 
 toolchain = {'name': 'intel', 'version': '2017a'}
 toolchainopts = {'pic': True}
 
+source_urls = ['http://support.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/']
 sources = [SOURCELOWER_TAR_GZ]
-source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/']
+checksums = ['dd419c55e85d1a0e13f3ea5ed35d00710033ccb16c85df088eb7925d486e040c']
 
 builddependencies = [
     ('flex', '2.6.3'),
diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.13-GCCcore-6.4.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.13-GCCcore-6.4.0.eb
index f1b4395af48..39dc5507935 100644
--- a/easybuild/easyconfigs/h/HDF/HDF-4.2.13-GCCcore-6.4.0.eb
+++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.13-GCCcore-6.4.0.eb
@@ -3,7 +3,7 @@ easyblock = 'ConfigureMake'
 name = 'HDF'
 version = '4.2.13'
 
-homepage = 'http://www.hdfgroup.org/products/hdf4/'
+homepage = 'http://support.hdfgroup.org/products/hdf4/'
 
 description = """
  HDF (also known as HDF4) is a library and multi-object file format for
@@ -14,7 +14,7 @@ toolchain = {'name': 'GCCcore', 'version': '6.4.0'}
 toolchainopts = {'pic': True}
 
 sources = [SOURCELOWER_TAR_GZ]
-source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/']
+source_urls = ['http://support.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/']
 checksums = ['be9813c1dc3712c2df977d4960e1f13f20f447dfa8c3ce53331d610c1f470483']
 
 builddependencies = [
diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.13-intel-2017a-no-netcdf.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.13-intel-2017a-no-netcdf.eb
index 84bff2749e9..74e44dbfc26 100644
--- a/easybuild/easyconfigs/h/HDF/HDF-4.2.13-intel-2017a-no-netcdf.eb
+++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.13-intel-2017a-no-netcdf.eb
@@ -4,7 +4,7 @@ name = 'HDF'
 version = '4.2.13'
 versionsuffix = '-no-netcdf'
 
-homepage = 'http://www.hdfgroup.org/products/hdf4/'
+homepage = 'http://support.hdfgroup.org/products/hdf4/'
 description = """HDF (also known as HDF4) is a library and multi-object file format for storing and managing data
  between machines.  This version suppresses the netcdf api, that gives issues with some applications"""
 
@@ -12,7 +12,7 @@ toolchain = {'name': 'intel', 'version': '2017a'}
 toolchainopts = {'pic': True}
 
 sources = [SOURCELOWER_TAR_GZ]
-source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/']
+source_urls = ['http://support.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/']
 checksums = ['be9813c1dc3712c2df977d4960e1f13f20f447dfa8c3ce53331d610c1f470483']
 
 builddependencies = [
diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-6.4.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-6.4.0.eb
index 1f31e675f7a..56e705f36a2 100644
--- a/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-6.4.0.eb
+++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-6.4.0.eb
@@ -3,7 +3,7 @@ easyblock = 'ConfigureMake'
 name = 'HDF'
 version = '4.2.14'
 
-homepage = 'http://www.hdfgroup.org/products/hdf4/'
+homepage = 'http://support.hdfgroup.org/products/hdf4/'
 
 description = """
  HDF (also known as HDF4) is a library and multi-object file format for
@@ -13,7 +13,7 @@ description = """
 toolchain = {'name': 'GCCcore', 'version': '6.4.0'}
 toolchainopts = {'pic': True}
 
-source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/']
+source_urls = ['http://support.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/']
 sources = [SOURCELOWER_TAR_GZ]
 checksums = ['2d383e87c8a0ca6a5352adbd1d5546e6cc43dc21ff7d90f93efa644d85c0b14a']
 
diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-7.3.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-7.3.0.eb
index 204d917a179..51b65acec93 100644
--- a/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-7.3.0.eb
+++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-7.3.0.eb
@@ -3,7 +3,7 @@ easyblock = 'ConfigureMake'
 name = 'HDF'
 version = '4.2.14'
 
-homepage = 'https://www.hdfgroup.org/products/hdf4/'
+homepage = 'https://support.hdfgroup.org/products/hdf4/'
 
 description = """
  HDF (also known as HDF4) is a library and multi-object file format for
@@ -13,7 +13,7 @@ description = """
 toolchain = {'name': 'GCCcore', 'version': '7.3.0'}
 toolchainopts = {'pic': True}
 
-source_urls = ['https://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/']
+source_urls = ['https://support.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/']
 sources = [SOURCELOWER_TAR_GZ]
 checksums = ['2d383e87c8a0ca6a5352adbd1d5546e6cc43dc21ff7d90f93efa644d85c0b14a']
 
diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-8.2.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-8.2.0.eb
index bf3fff366f2..a78efd6cee2 100644
--- a/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-8.2.0.eb
+++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-8.2.0.eb
@@ -3,7 +3,7 @@ easyblock = 'ConfigureMake'
 name = 'HDF'
 version = '4.2.14'
 
-homepage = 'https://www.hdfgroup.org/products/hdf4/'
+homepage = 'https://support.hdfgroup.org/products/hdf4/'
 
 description = """
  HDF (also known as HDF4) is a library and multi-object file format for
@@ -13,7 +13,7 @@ description = """
 toolchain = {'name': 'GCCcore', 'version': '8.2.0'}
 toolchainopts = {'pic': True}
 
-source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/']
+source_urls = ['http://support.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/']
 sources = [SOURCELOWER_TAR_GZ]
 checksums = ['2d383e87c8a0ca6a5352adbd1d5546e6cc43dc21ff7d90f93efa644d85c0b14a']
 
diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-8.3.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-8.3.0.eb
index ff08dc71e80..fdee3ff0383 100644
--- a/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-8.3.0.eb
+++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-8.3.0.eb
@@ -3,7 +3,7 @@ easyblock = 'ConfigureMake'
 name = 'HDF'
 version = '4.2.14'
 
-homepage = 'https://www.hdfgroup.org/products/hdf4/'
+homepage = 'https://support.hdfgroup.org/products/hdf4/'
 
 description = """
  HDF (also known as HDF4) is a library and multi-object file format for
@@ -13,7 +13,7 @@ description = """
 toolchain = {'name': 'GCCcore', 'version': '8.3.0'}
 toolchainopts = {'pic': True}
 
-source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/']
+source_urls = ['http://support.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/']
 sources = [SOURCELOWER_TAR_GZ]
 checksums = ['2d383e87c8a0ca6a5352adbd1d5546e6cc43dc21ff7d90f93efa644d85c0b14a']
 
diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-10.2.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-10.2.0.eb
index bdb2cb878ee..91e084fc238 100644
--- a/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-10.2.0.eb
+++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-10.2.0.eb
@@ -3,7 +3,7 @@ easyblock = 'ConfigureMake'
 name = 'HDF'
 version = '4.2.15'
 
-homepage = 'https://www.hdfgroup.org/products/hdf4/'
+homepage = 'https://support.hdfgroup.org/products/hdf4/'
 
 description = """
  HDF (also known as HDF4) is a library and multi-object file format for
@@ -13,7 +13,7 @@ description = """
 toolchain = {'name': 'GCCcore', 'version': '10.2.0'}
 toolchainopts = {'pic': True}
 
-source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/']
+source_urls = ['http://support.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/']
 sources = [SOURCELOWER_TAR_GZ]
 patches = ['HDF-4.2.15_fix-aarch64.patch']
 checksums = [
diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-10.3.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-10.3.0.eb
index 869a6a796a2..7fff3f348bb 100644
--- a/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-10.3.0.eb
+++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-10.3.0.eb
@@ -3,7 +3,7 @@ easyblock = 'ConfigureMake'
 name = 'HDF'
 version = '4.2.15'
 
-homepage = 'https://www.hdfgroup.org/products/hdf4/'
+homepage = 'https://support.hdfgroup.org/products/hdf4/'
 
 description = """
  HDF (also known as HDF4) is a library and multi-object file format for
@@ -13,7 +13,7 @@ description = """
 toolchain = {'name': 'GCCcore', 'version': '10.3.0'}
 toolchainopts = {'pic': True}
 
-source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/']
+source_urls = ['http://support.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/']
 sources = [SOURCELOWER_TAR_GZ]
 patches = ['HDF-4.2.15_fix-aarch64.patch']
 checksums = [
diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-11.2.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-11.2.0.eb
index fc36bb04673..7acaaafc09d 100644
--- a/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-11.2.0.eb
+++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-11.2.0.eb
@@ -3,7 +3,7 @@ easyblock = 'ConfigureMake'
 name = 'HDF'
 version = '4.2.15'
 
-homepage = 'https://www.hdfgroup.org/products/hdf4/'
+homepage = 'https://support.hdfgroup.org/products/hdf4/'
 
 description = """
  HDF (also known as HDF4) is a library and multi-object file format for
@@ -13,7 +13,7 @@ description = """
 toolchain = {'name': 'GCCcore', 'version': '11.2.0'}
 toolchainopts = {'pic': True}
 
-source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/']
+source_urls = ['http://support.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/']
 sources = [SOURCELOWER_TAR_GZ]
 patches = ['HDF-4.2.15_fix-aarch64.patch']
 checksums = [
diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-11.3.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-11.3.0.eb
index 682e5e20b6c..4af8d274164 100644
--- a/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-11.3.0.eb
+++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-11.3.0.eb
@@ -3,7 +3,7 @@ easyblock = 'ConfigureMake'
 name = 'HDF'
 version = '4.2.15'
 
-homepage = 'https://www.hdfgroup.org/products/hdf4/'
+homepage = 'https://support.hdfgroup.org/products/hdf4/'
 
 description = """
  HDF (also known as HDF4) is a library and multi-object file format for
@@ -13,7 +13,7 @@ description = """
 toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
 toolchainopts = {'pic': True}
 
-source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/']
+source_urls = ['http://support.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/']
 sources = [SOURCELOWER_TAR_GZ]
 patches = ['HDF-4.2.15_fix-aarch64.patch']
 checksums = [
diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-12.2.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-12.2.0.eb
index f0286cd30bd..abab2d962f5 100644
--- a/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-12.2.0.eb
+++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-12.2.0.eb
@@ -3,7 +3,7 @@ easyblock = 'ConfigureMake'
 name = 'HDF'
 version = '4.2.15'
 
-homepage = 'https://www.hdfgroup.org/products/hdf4/'
+homepage = 'https://support.hdfgroup.org/products/hdf4/'
 
 description = """
  HDF (also known as HDF4) is a library and multi-object file format for
@@ -13,7 +13,7 @@ description = """
 toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
 toolchainopts = {'pic': True}
 
-source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/']
+source_urls = ['http://support.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/']
 sources = [SOURCELOWER_TAR_GZ]
 patches = ['HDF-4.2.15_fix-aarch64.patch']
 checksums = [
diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-9.3.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-9.3.0.eb
index fd6e6693977..7e6b5eefbe8 100644
--- a/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-9.3.0.eb
+++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-9.3.0.eb
@@ -3,7 +3,7 @@ easyblock = 'ConfigureMake'
 name = 'HDF'
 version = '4.2.15'
 
-homepage = 'https://www.hdfgroup.org/products/hdf4/'
+homepage = 'https://support.hdfgroup.org/products/hdf4/'
 
 description = """
  HDF (also known as HDF4) is a library and multi-object file format for
@@ -13,7 +13,7 @@ description = """
 toolchain = {'name': 'GCCcore', 'version': '9.3.0'}
 toolchainopts = {'pic': True}
 
-source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/']
+source_urls = ['http://support.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/']
 sources = [SOURCELOWER_TAR_GZ]
 patches = ['HDF-4.2.15_fix-aarch64.patch']
 checksums = [
diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.16-2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.16-2-GCCcore-12.3.0.eb
index a6094f7f816..175aaba4731 100644
--- a/easybuild/easyconfigs/h/HDF/HDF-4.2.16-2-GCCcore-12.3.0.eb
+++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.16-2-GCCcore-12.3.0.eb
@@ -3,7 +3,7 @@ easyblock = 'ConfigureMake'
 name = 'HDF'
 version = '4.2.16-2'
 
-homepage = 'https://www.hdfgroup.org/products/hdf4/'
+homepage = 'https://support.hdfgroup.org/products/hdf4/'
 description = """
  HDF (also known as HDF4) is a library and multi-object file format for
  storing and managing data between machines.
diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.16-2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.16-2-GCCcore-13.2.0.eb
index 5b868a7fe58..f2c20e888b9 100644
--- a/easybuild/easyconfigs/h/HDF/HDF-4.2.16-2-GCCcore-13.2.0.eb
+++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.16-2-GCCcore-13.2.0.eb
@@ -3,7 +3,7 @@ easyblock = 'ConfigureMake'
 name = 'HDF'
 version = '4.2.16-2'
 
-homepage = 'https://www.hdfgroup.org/products/hdf4/'
+homepage = 'https://support.hdfgroup.org/products/hdf4/'
 description = """
  HDF (also known as HDF4) is a library and multi-object file format for
  storing and managing data between machines.
diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.16-GCCcore-12.3.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.16-GCCcore-12.3.0.eb
index 630c4aa2dc2..fd9d8d3d4ea 100644
--- a/easybuild/easyconfigs/h/HDF/HDF-4.2.16-GCCcore-12.3.0.eb
+++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.16-GCCcore-12.3.0.eb
@@ -3,7 +3,7 @@ easyblock = 'ConfigureMake'
 name = 'HDF'
 version = '4.2.16'
 
-homepage = 'https://www.hdfgroup.org/products/hdf4/'
+homepage = 'https://support.hdfgroup.org/products/hdf4/'
 
 description = """
  HDF (also known as HDF4) is a library and multi-object file format for
diff --git a/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.3-foss-2018b.eb b/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.3-foss-2018b.eb
index 0b79b7cfc94..605d20f196f 100644
--- a/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.3-foss-2018b.eb
+++ b/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.3-foss-2018b.eb
@@ -3,13 +3,13 @@ easyblock = 'ConfigureMake'
 name = 'h4toh5'
 version = '2.2.3'
 
-homepage = 'http://www.hdfgroup.org/h4toh5/'
+homepage = "https://docs.hdfgroup.org/archive/support/products/hdf5_tools/h4toh5/index.html"
 description = """The h4toh5 software consists of the h4toh5 and h5toh4 command-line utilities,
  as well as a conversion library for converting between individual HDF4 and HDF5 objects."""
 
 toolchain = {'name': 'foss', 'version': '2018b'}
 
-source_urls = ['http://www.hdfgroup.org/ftp/HDF5/tools/%s/src' % name]
+source_urls = ['http://support.hdfgroup.org/ftp/HDF5/tools/%s/src' % name]
 sources = ['h4h5tools-%(version)s.tar.gz']
 checksums = ['ba167d9e5ec1f9014a95e3f5d0621f814caa6e83508e235ce60cfd315e3a9d3f']
 
diff --git a/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.3-gompi-2019b.eb b/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.3-gompi-2019b.eb
index 81636ad6de3..079d5eb7de1 100644
--- a/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.3-gompi-2019b.eb
+++ b/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.3-gompi-2019b.eb
@@ -3,13 +3,13 @@ easyblock = 'ConfigureMake'
 name = 'h4toh5'
 version = '2.2.3'
 
-homepage = 'http://www.hdfgroup.org/h4toh5/'
+homepage = "https://docs.hdfgroup.org/archive/support/products/hdf5_tools/h4toh5/index.html"
 description = """The h4toh5 software consists of the h4toh5 and h5toh4 command-line utilities,
  as well as a conversion library for converting between individual HDF4 and HDF5 objects."""
 
 toolchain = {'name': 'gompi', 'version': '2019b'}
 
-source_urls = ['http://www.hdfgroup.org/ftp/HDF5/tools/%s/src' % name]
+source_urls = ['http://support.hdfgroup.org/ftp/HDF5/tools/%s/src' % name]
 sources = ['h4h5tools-%(version)s%(versionsuffix)s.tar.gz']
 checksums = ['ba167d9e5ec1f9014a95e3f5d0621f814caa6e83508e235ce60cfd315e3a9d3f']
 
diff --git a/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.3-gompi-2020b.eb b/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.3-gompi-2020b.eb
index 8e8e8c7f705..50fe19e455a 100644
--- a/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.3-gompi-2020b.eb
+++ b/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.3-gompi-2020b.eb
@@ -3,13 +3,13 @@ easyblock = 'ConfigureMake'
 name = 'h4toh5'
 version = '2.2.3'
 
-homepage = 'http://www.hdfgroup.org/h4toh5/'
+homepage = "https://docs.hdfgroup.org/archive/support/products/hdf5_tools/h4toh5/index.html"
 description = """The h4toh5 software consists of the h4toh5 and h5toh4 command-line utilities,
  as well as a conversion library for converting between individual HDF4 and HDF5 objects."""
 
 toolchain = {'name': 'gompi', 'version': '2020b'}
 
-source_urls = ['http://www.hdfgroup.org/ftp/HDF5/tools/%s/src' % name]
+source_urls = ['http://support.hdfgroup.org/ftp/HDF5/tools/%s/src' % name]
 sources = ['h4h5tools-%(version)s%(versionsuffix)s.tar.gz']
 checksums = ['ba167d9e5ec1f9014a95e3f5d0621f814caa6e83508e235ce60cfd315e3a9d3f']
 
diff --git a/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.5-gompi-2022a.eb b/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.5-gompi-2022a.eb
index 1a825bc8ed8..28d67776a1b 100644
--- a/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.5-gompi-2022a.eb
+++ b/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.5-gompi-2022a.eb
@@ -3,7 +3,7 @@ easyblock = 'ConfigureMake'
 name = 'h4toh5'
 version = '2.2.5'
 
-homepage = 'http://www.hdfgroup.org/h4toh5/'
+homepage = "https://docs.hdfgroup.org/archive/support/products/hdf5_tools/h4toh5/index.html"
 description = """The h4toh5 software consists of the h4toh5 and h5toh4 command-line utilities,
  as well as a conversion library for converting between individual HDF4 and HDF5 objects."""
 

From e784334ae72af7eb166ce85c2e9af2f890ce57ed Mon Sep 17 00:00:00 2001
From: Cintia Willemyns <115622907+WilleBell@users.noreply.github.com>
Date: Mon, 19 Aug 2024 14:04:41 +0200
Subject: [PATCH 633/835] Add comment to ChangeLog in patch

---
 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2406-cleanup.patch | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2406-cleanup.patch b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2406-cleanup.patch
index 6e719c21dae..ac5229788c5 100644
--- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2406-cleanup.patch
+++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2406-cleanup.patch
@@ -6,7 +6,9 @@
 #
 # ChangeLog:
 # - v2312 - activate METIS, KaHIP and readline support in etc/config.sh/setup
-#           author: Jiri Furst <jiri.furst@gmail.com> 
+#           author: Jiri Furst <jiri.furst@gmail.com>
+# - v2406 - set MPFR_ARCH_PATH and GMP_ARCH_PATH to CGAL config
+#           author: Jiri Furst <jiri.furst@gmail.com>
 #
 # -------------------------------------------------------------------------
 --- /dev/null	2020-12-14 09:05:45.272769166 +0100

From 13513c987d3df236f91a50713f88a97938a0c5a8 Mon Sep 17 00:00:00 2001
From: Cintia Willemyns <115622907+WilleBell@users.noreply.github.com>
Date: Mon, 19 Aug 2024 14:32:16 +0200
Subject: [PATCH 634/835] Update patch checksum

---
 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2406-foss-2023a.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2406-foss-2023a.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2406-foss-2023a.eb
index 185cfead980..cfdb5e08252 100644
--- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2406-foss-2023a.eb
+++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2406-foss-2023a.eb
@@ -21,7 +21,7 @@ patches = [
 ]
 checksums = [
     {'OpenFOAM-v2406.tgz': '8d1450fb89eec1e7cecc55c3bb7bc486ccbf63d069379d1d5d7518fa16a4686a'},
-    {'OpenFOAM-v2406-cleanup.patch': '3ed44da40e9872d1cf096bb0bfd9d5c79ca984d7bc01e4ae30c14b3e7223d749'},
+    {'OpenFOAM-v2406-cleanup.patch': '7f1a068b4f4e16735efb2878a7ee115c6fdbd470709d93e211178f8090c6d0ae'},
     {'OpenFOAM-v2212-wmake-OpenMPI.patch': '241dc4898c22aab0cbd10c1ea931a07a786508ee03462d45dbc1c202fee3ebe8'},
 ]
 

From e9294735bad09f1a56189ccad578857a2c1f85f0 Mon Sep 17 00:00:00 2001
From: Cintia Willemyns <115622907+WilleBell@users.noreply.github.com>
Date: Mon, 19 Aug 2024 14:57:12 +0200
Subject: [PATCH 635/835] fix patch checksum

---
 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2406-foss-2023a.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2406-foss-2023a.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2406-foss-2023a.eb
index cfdb5e08252..ba59d215581 100644
--- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2406-foss-2023a.eb
+++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2406-foss-2023a.eb
@@ -21,7 +21,7 @@ patches = [
 ]
 checksums = [
     {'OpenFOAM-v2406.tgz': '8d1450fb89eec1e7cecc55c3bb7bc486ccbf63d069379d1d5d7518fa16a4686a'},
-    {'OpenFOAM-v2406-cleanup.patch': '7f1a068b4f4e16735efb2878a7ee115c6fdbd470709d93e211178f8090c6d0ae'},
+    {'OpenFOAM-v2406-cleanup.patch': '3abff48a517fb63719ad57fa32af746bc379a1e80c72d3e5852aa17cd13cf03e'},
     {'OpenFOAM-v2212-wmake-OpenMPI.patch': '241dc4898c22aab0cbd10c1ea931a07a786508ee03462d45dbc1c202fee3ebe8'},
 ]
 

From 86fb783de058d84724a157bca4f34b265ea88b8e Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 20 Aug 2024 09:49:50 +0200
Subject: [PATCH 636/835] consisently set $CXXFLAGS_SIMD to empty in
 easyconfigs for STAR 2.7.11a + 2.7.11b

---
 easybuild/easyconfigs/s/STAR/STAR-2.7.11a-GCC-12.2.0.eb | 3 +++
 easybuild/easyconfigs/s/STAR/STAR-2.7.11a-GCC-12.3.0.eb | 3 +++
 easybuild/easyconfigs/s/STAR/STAR-2.7.11b-GCC-12.3.0.eb | 3 +++
 3 files changed, 9 insertions(+)

diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.7.11a-GCC-12.2.0.eb b/easybuild/easyconfigs/s/STAR/STAR-2.7.11a-GCC-12.2.0.eb
index 42f094bb67b..b98510247d3 100644
--- a/easybuild/easyconfigs/s/STAR/STAR-2.7.11a-GCC-12.2.0.eb
+++ b/easybuild/easyconfigs/s/STAR/STAR-2.7.11a-GCC-12.2.0.eb
@@ -31,6 +31,9 @@ dependencies = [
 
 start_dir = 'source'
 
+# by default this is set to -mavx2 which makes it fail on non x86 systems
+prebuildopts = 'CXXFLAGS_SIMD= '
+
 buildopts = ' STAR && make STARlong'
 
 files_to_copy = [
diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.7.11a-GCC-12.3.0.eb b/easybuild/easyconfigs/s/STAR/STAR-2.7.11a-GCC-12.3.0.eb
index 1943af96d5e..37285b73829 100644
--- a/easybuild/easyconfigs/s/STAR/STAR-2.7.11a-GCC-12.3.0.eb
+++ b/easybuild/easyconfigs/s/STAR/STAR-2.7.11a-GCC-12.3.0.eb
@@ -31,6 +31,9 @@ dependencies = [
 
 start_dir = 'source'
 
+# by default this is set to -mavx2 which makes it fail on non x86 systems
+prebuildopts = 'CXXFLAGS_SIMD= '
+
 buildopts = ' STAR && make STARlong'
 
 files_to_copy = [
diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.7.11b-GCC-12.3.0.eb b/easybuild/easyconfigs/s/STAR/STAR-2.7.11b-GCC-12.3.0.eb
index cf16b5c2979..4d85b037ea2 100644
--- a/easybuild/easyconfigs/s/STAR/STAR-2.7.11b-GCC-12.3.0.eb
+++ b/easybuild/easyconfigs/s/STAR/STAR-2.7.11b-GCC-12.3.0.eb
@@ -24,6 +24,9 @@ checksums = [
     {'STAR-2.7.11a_use-external-htslib.patch': '2fdc3ed9372d983f77d861d6f16a60a553598358dce9ff8216f96eb20e63ce4e'},
 ]
 
+# by default this is set to -mavx2 which makes it fail on non x86 systems
+prebuildopts = 'CXXFLAGS_SIMD= '
+
 dependencies = [
     ('HTSlib', '1.18'),
     ('zlib', '1.2.13'),

From 765ba900daf5953e306c4dad896febe52fdd6c00 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 20 Aug 2024 10:22:41 +0200
Subject: [PATCH 637/835] add missing xxd build dependency for STAR 2.7.11*

---
 easybuild/easyconfigs/s/STAR/STAR-2.7.11a-GCC-12.2.0.eb | 4 ++++
 easybuild/easyconfigs/s/STAR/STAR-2.7.11a-GCC-12.3.0.eb | 4 ++++
 easybuild/easyconfigs/s/STAR/STAR-2.7.11b-GCC-12.3.0.eb | 8 ++++++--
 easybuild/easyconfigs/s/STAR/STAR-2.7.11b-GCC-13.2.0.eb | 6 +++---
 4 files changed, 17 insertions(+), 5 deletions(-)

diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.7.11a-GCC-12.2.0.eb b/easybuild/easyconfigs/s/STAR/STAR-2.7.11a-GCC-12.2.0.eb
index b98510247d3..a61fe5e85bb 100644
--- a/easybuild/easyconfigs/s/STAR/STAR-2.7.11a-GCC-12.2.0.eb
+++ b/easybuild/easyconfigs/s/STAR/STAR-2.7.11a-GCC-12.2.0.eb
@@ -24,6 +24,10 @@ checksums = [
     {'STAR-%(version)s_use-external-htslib.patch': '2fdc3ed9372d983f77d861d6f16a60a553598358dce9ff8216f96eb20e63ce4e'},
 ]
 
+builddependencies = [
+    ('xxd', '9.0.1696'),
+]
+
 dependencies = [
     ('HTSlib', '1.17'),
     ('zlib', '1.2.12'),
diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.7.11a-GCC-12.3.0.eb b/easybuild/easyconfigs/s/STAR/STAR-2.7.11a-GCC-12.3.0.eb
index 37285b73829..a017a2ba109 100644
--- a/easybuild/easyconfigs/s/STAR/STAR-2.7.11a-GCC-12.3.0.eb
+++ b/easybuild/easyconfigs/s/STAR/STAR-2.7.11a-GCC-12.3.0.eb
@@ -24,6 +24,10 @@ checksums = [
     {'STAR-%(version)s_use-external-htslib.patch': '2fdc3ed9372d983f77d861d6f16a60a553598358dce9ff8216f96eb20e63ce4e'},
 ]
 
+builddependencies = [
+    ('xxd', '9.0.2112'),
+]
+
 dependencies = [
     ('HTSlib', '1.18'),
     ('zlib', '1.2.13'),
diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.7.11b-GCC-12.3.0.eb b/easybuild/easyconfigs/s/STAR/STAR-2.7.11b-GCC-12.3.0.eb
index 4d85b037ea2..67cac5d0f47 100644
--- a/easybuild/easyconfigs/s/STAR/STAR-2.7.11b-GCC-12.3.0.eb
+++ b/easybuild/easyconfigs/s/STAR/STAR-2.7.11b-GCC-12.3.0.eb
@@ -24,8 +24,9 @@ checksums = [
     {'STAR-2.7.11a_use-external-htslib.patch': '2fdc3ed9372d983f77d861d6f16a60a553598358dce9ff8216f96eb20e63ce4e'},
 ]
 
-# by default this is set to -mavx2 which makes it fail on non x86 systems
-prebuildopts = 'CXXFLAGS_SIMD= '
+builddependencies = [
+    ('xxd', '9.0.2112'),
+]
 
 dependencies = [
     ('HTSlib', '1.18'),
@@ -34,6 +35,9 @@ dependencies = [
 
 start_dir = 'source'
 
+# by default this is set to -mavx2 which makes it fail on non x86 systems
+prebuildopts = 'CXXFLAGS_SIMD= '
+
 buildopts = ' STAR && make STARlong'
 
 files_to_copy = [
diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.7.11b-GCC-13.2.0.eb b/easybuild/easyconfigs/s/STAR/STAR-2.7.11b-GCC-13.2.0.eb
index 099b3c1127d..886aa0a24c5 100644
--- a/easybuild/easyconfigs/s/STAR/STAR-2.7.11b-GCC-13.2.0.eb
+++ b/easybuild/easyconfigs/s/STAR/STAR-2.7.11b-GCC-13.2.0.eb
@@ -24,9 +24,6 @@ checksums = [
     {'STAR-2.7.11a_use-external-htslib.patch': '2fdc3ed9372d983f77d861d6f16a60a553598358dce9ff8216f96eb20e63ce4e'},
 ]
 
-# by default this is set to -mavx2 which makes it fail on non x86 systems
-prebuildopts = 'CXXFLAGS_SIMD= '
-
 builddependencies = [
     ('xxd', '9.1.0307'),
 ]
@@ -38,6 +35,9 @@ dependencies = [
 
 start_dir = 'source'
 
+# by default this is set to -mavx2 which makes it fail on non x86 systems
+prebuildopts = 'CXXFLAGS_SIMD= '
+
 buildopts = ' STAR && make STARlong'
 
 files_to_copy = [

From a2c2f2f1447e3d13b6d102c1c61f5cd05c4a26b4 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Petr=20Kr=C3=A1l?= <petr@inuits.eu>
Date: Tue, 20 Aug 2024 11:24:00 +0200
Subject: [PATCH 638/835] adding easyconfigs: bliss-0.77-GCC-13.2.0.eb and
 patches: bliss-0.77_install_fix.patch

---
 .../b/bliss/bliss-0.77-GCC-13.2.0.eb          | 37 +++++++++++++++++++
 .../b/bliss/bliss-0.77_install_fix.patch      | 31 ++++++++++++++++
 2 files changed, 68 insertions(+)
 create mode 100644 easybuild/easyconfigs/b/bliss/bliss-0.77-GCC-13.2.0.eb
 create mode 100644 easybuild/easyconfigs/b/bliss/bliss-0.77_install_fix.patch

diff --git a/easybuild/easyconfigs/b/bliss/bliss-0.77-GCC-13.2.0.eb b/easybuild/easyconfigs/b/bliss/bliss-0.77-GCC-13.2.0.eb
new file mode 100644
index 00000000000..3831e26c62d
--- /dev/null
+++ b/easybuild/easyconfigs/b/bliss/bliss-0.77-GCC-13.2.0.eb
@@ -0,0 +1,37 @@
+easyblock = 'CMakeMake'
+
+name = 'bliss'
+version = '0.77'
+
+homepage = 'https://users.aalto.fi/~tjunttil/bliss/'
+description = """Bliss is an open-source tool for computing canonical labelings and automorphism groups of graphs."""
+
+toolchain = {'name': 'GCC', 'version': '13.2.0'}
+
+source_urls = ['https://users.aalto.fi/~tjunttil/bliss/downloads/']
+sources = [SOURCE_ZIP]
+patches = ['bliss-0.77_install_fix.patch']
+checksums = [
+    {'bliss-0.77.zip': 'acc8b98034f30fad24c897f365abd866c13d9f1bb207e398d0caf136875972a4'},
+    {'bliss-0.77_install_fix.patch': '01a0824c5b121bd6ab0df324ee9c9dd4d4f0bfd8bb2800157cf270e8a1b194ea'},
+]
+
+builddependencies = [
+    ('CMake', '3.27.6'),
+]
+
+configopts = "-DUSE_GMP=OFF "
+
+sanity_check_paths = {
+    'files': [
+        'bin/bliss',
+        'lib/libbliss.%s' % SHLIB_EXT,
+    ],
+    'dirs': [
+        'include/%(name)s',
+    ],
+}
+
+sanity_check_commands = ["bliss -help"]
+
+moduleclass = 'math'
diff --git a/easybuild/easyconfigs/b/bliss/bliss-0.77_install_fix.patch b/easybuild/easyconfigs/b/bliss/bliss-0.77_install_fix.patch
new file mode 100644
index 00000000000..a5fcbd85018
--- /dev/null
+++ b/easybuild/easyconfigs/b/bliss/bliss-0.77_install_fix.patch
@@ -0,0 +1,31 @@
+diff -u CMakeLists.txt.orig CMakeLists.txt
+--- CMakeLists.txt.orig	2021-02-18 11:59:34.000000000 +0100
++++ CMakeLists.txt	2024-08-15 15:04:21.293765655 +0200
+@@ -62,3 +62,27 @@
+   target_link_libraries(bliss-executable ${GMP_LIBRARIES})
+ endif(USE_GMP)
+ set_target_properties(bliss-executable PROPERTIES OUTPUT_NAME bliss)
++
++include(GNUInstallDirs)
++
++set(
++  BLISS_HEADERS
++  src/bliss_C.h
++  src/uintseqhash.hh
++  src/abstractgraph.hh
++  src/stats.hh
++  src/digraph.hh
++  src/defs.hh
++  src/heap.hh
++  src/graph.hh
++  src/partition.hh
++  src/kqueue.hh
++  src/utils.hh
++  src/orbit.hh
++  src/timer.hh
++  src/bignum.hh
++)
++
++install(TARGETS bliss-executable RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR})
++install(TARGETS bliss LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR})
++install(FILES ${BLISS_HEADERS} DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/bliss)

From b121b9ee706be3291051b5ddbb3852e1abc05237 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Petr=20Kr=C3=A1l?= <petr@inuits.eu>
Date: Tue, 20 Aug 2024 11:33:05 +0200
Subject: [PATCH 639/835] adding easyconfigs: Rasqal-0.9.33-GCCcore-12.3.0.eb,
 gtk-doc-1.34.0-GCCcore-12.3.0.eb, Pygments-2.18.0-GCCcore-12.3.0.eb,
 dblatex-0.3.12-foss-2023a.eb

---
 .../d/dblatex/dblatex-0.3.12-foss-2023a.eb    | 33 ++++++++++++
 .../gtk-doc/gtk-doc-1.34.0-GCCcore-12.3.0.eb  | 50 +++++++++++++++++++
 .../Pygments-2.18.0-GCCcore-12.3.0.eb         | 30 +++++++++++
 .../r/Rasqal/Rasqal-0.9.33-GCCcore-12.3.0.eb  | 38 ++++++++++++++
 4 files changed, 151 insertions(+)
 create mode 100644 easybuild/easyconfigs/d/dblatex/dblatex-0.3.12-foss-2023a.eb
 create mode 100644 easybuild/easyconfigs/g/gtk-doc/gtk-doc-1.34.0-GCCcore-12.3.0.eb
 create mode 100644 easybuild/easyconfigs/p/Pygments/Pygments-2.18.0-GCCcore-12.3.0.eb
 create mode 100644 easybuild/easyconfigs/r/Rasqal/Rasqal-0.9.33-GCCcore-12.3.0.eb

diff --git a/easybuild/easyconfigs/d/dblatex/dblatex-0.3.12-foss-2023a.eb b/easybuild/easyconfigs/d/dblatex/dblatex-0.3.12-foss-2023a.eb
new file mode 100644
index 00000000000..db41d0c240f
--- /dev/null
+++ b/easybuild/easyconfigs/d/dblatex/dblatex-0.3.12-foss-2023a.eb
@@ -0,0 +1,33 @@
+easyblock = 'PythonPackage'
+
+name = 'dblatex'
+version = '0.3.12'
+
+homepage = 'https://dblatex.sourceforge.net/'
+description = """dblatex is a program that transforms your SGML/XML DocBook documents to DVI,
+ PostScript or PDF by translating them into pure LaTeX as a first process.
+ MathML 2.0 markups are supported, too. It started as a clone of DB2LaTeX."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+source_urls = ['https://master.dl.sourceforge.net/project/dblatex/dblatex/dblatex-%(version)s/']
+sources = ['%(name)s3-%(version)s.tar.bz2']
+checksums = ['16e82786272ed1806a079d37914d7ba7a594db792dc4cc34c1c3737dbd4da079']
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('libxslt', '1.1.38'),
+    ('texlive', '20230313'),
+]
+
+download_dep_fail = True
+use_pip = True
+sanity_pip_check = True
+
+options = {'modulename': 'dbtexmf.dblatex'}
+
+postinstallcmds = ["cp -r %(builddir)s/%(name)s3-%(version)s/scripts %(installdir)s/bin"]
+
+sanity_check_commands = ['dblatex --help']
+
+moduleclass = 'tools'
diff --git a/easybuild/easyconfigs/g/gtk-doc/gtk-doc-1.34.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/gtk-doc/gtk-doc-1.34.0-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..c77d925c3a0
--- /dev/null
+++ b/easybuild/easyconfigs/g/gtk-doc/gtk-doc-1.34.0-GCCcore-12.3.0.eb
@@ -0,0 +1,50 @@
+easyblock = 'MesonNinja'
+
+name = 'gtk-doc'
+version = '1.34.0'
+
+homepage = 'https://gitlab.gnome.org/GNOME/gtk-doc'
+description = """Documentation tool for public library API"""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+source_urls = ['https://gitlab.gnome.org/GNOME/gtk-doc/-/archive/%(version)s/']
+sources = [SOURCE_TAR_GZ]
+checksums = ['e1d544fa70ae60014a241b674c9d989f4ad6a96554652ebf73bbe94b4da1aa35']
+
+builddependencies = [
+    ('binutils', '2.40'),
+    ('yelp-tools', '42.1'),
+    ('Ninja', '1.11.1'),
+    ('Meson', '1.1.1'),
+]
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('Pygments', '2.18.0'),
+]
+
+sanity_check_paths = {
+    'files': [
+        'bin/gtkdoc-depscan',
+        'bin/gtkdoc-fixxref',
+        'bin/gtkdoc-check',
+        'bin/gtkdocize',
+        'bin/gtkdoc-mkdb',
+        'bin/gtkdoc-mkhtml',
+        'bin/gtkdoc-mkhtml2',
+        'bin/gtkdoc-mkman',
+        'bin/gtkdoc-mkpdf',
+        'bin/gtkdoc-rebase',
+        'bin/gtkdoc-scan',
+        'bin/gtkdoc-scangobj',
+    ],
+    'dirs': [
+        'lib/cmake/GtkDoc',
+        'share/%(name)s',
+    ],
+}
+
+sanity_check_commands = ['gtkdoc-depscan']
+
+moduleclass = 'tools'
diff --git a/easybuild/easyconfigs/p/Pygments/Pygments-2.18.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/Pygments/Pygments-2.18.0-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..2f441283024
--- /dev/null
+++ b/easybuild/easyconfigs/p/Pygments/Pygments-2.18.0-GCCcore-12.3.0.eb
@@ -0,0 +1,30 @@
+easyblock = 'PythonPackage'
+
+name = 'Pygments'
+version = '2.18.0'
+
+homepage = 'https://pygments.org/'
+description = """Generic syntax highlighter suitable for use in code hosting, forums, wikis or other applications
+ that need to prettify source code."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+sources = [SOURCELOWER_PY3_WHL]
+checksums = ['b8e6aca0523f3ab76fee51799c488e38782ac06eafcf95e7ba832985c8e7b13a']
+
+dependencies = [
+    ('Python', '3.11.3'),
+]
+
+download_dep_fail = True
+use_pip = True
+sanity_pip_check = True
+
+sanity_check_paths = {
+    'files': ['bin/pygmentize'],
+    'dirs': [],
+}
+
+sanity_check_commands = ['pygmentize --help']
+
+moduleclass = 'devel'
diff --git a/easybuild/easyconfigs/r/Rasqal/Rasqal-0.9.33-GCCcore-12.3.0.eb b/easybuild/easyconfigs/r/Rasqal/Rasqal-0.9.33-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..3d5e0ad9d83
--- /dev/null
+++ b/easybuild/easyconfigs/r/Rasqal/Rasqal-0.9.33-GCCcore-12.3.0.eb
@@ -0,0 +1,38 @@
+easyblock = 'ConfigureMake'
+
+name = 'Rasqal'
+version = '0.9.33'
+homepage = 'hhttps://librdf.org/rasqal'
+description = """A library handling RDF query syntaxes, construction and execution"""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+source_urls = ['https://download.librdf.org/source']
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['6924c9ac6570bd241a9669f83b467c728a322470bf34f4b2da4f69492ccfd97c']
+
+builddependencies = [
+    ('Autotools',  '20220317'),
+    ('binutils',   '2.40'),
+    ('Raptor',   '2.0.16'),
+]
+
+dependencies = [
+    ('libgcrypt', '1.10.3'),
+    ('MPFR', '4.2.0'),
+    ('PCRE', '8.45'),
+    ('gtk-doc', '1.34.0'),
+    ('ICU', '73.2'),
+]
+
+preconfigopts = "autoreconf -f -i && "
+configopts = "--disable-static --enable-release"
+
+sanity_check_paths = {
+    'files': ['bin/roqet', 'lib/librasqal.%s' % SHLIB_EXT],
+    'dirs': ['include/rasqal/']
+}
+
+sanity_check_commands = ["roqet --help"]
+
+moduleclass = 'lib'

From bbf439c07ef1487f59ade00ace40b454ba4ef075 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Petr=20Kr=C3=A1l?= <petr@inuits.eu>
Date: Tue, 20 Aug 2024 11:34:44 +0200
Subject: [PATCH 640/835] adding easyconfigs: rjags-4-15-foss-2023a-R-4.3.2.eb

---
 .../r/rjags/rjags-4-15-foss-2023a-R-4.3.2.eb  | 30 +++++++++++++++++++
 1 file changed, 30 insertions(+)
 create mode 100644 easybuild/easyconfigs/r/rjags/rjags-4-15-foss-2023a-R-4.3.2.eb

diff --git a/easybuild/easyconfigs/r/rjags/rjags-4-15-foss-2023a-R-4.3.2.eb b/easybuild/easyconfigs/r/rjags/rjags-4-15-foss-2023a-R-4.3.2.eb
new file mode 100644
index 00000000000..f793f925da6
--- /dev/null
+++ b/easybuild/easyconfigs/r/rjags/rjags-4-15-foss-2023a-R-4.3.2.eb
@@ -0,0 +1,30 @@
+easyblock = 'RPackage'
+
+name = 'rjags'
+version = '4-15'
+versionsuffix = '-R-%(rver)s'
+
+homepage = 'https://cran.r-project.org/web/packages/rjags'
+description = """The rjags package is an interface to the JAGS library."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+source_urls = [
+    'https://cran.r-project.org/src/contrib/',
+    'https://cran.r-project.org/src/contrib/Archive/rjags/',
+]
+sources = ['%(name)s_%(version)s.tar.gz']
+checksums = ['35cd4c1faaaa8523b87ac053b881dccf29798f073f438459589e786b95ef18a1']
+
+dependencies = [
+    ('R', '4.3.2'),
+    ('R-bundle-CRAN', '2023.12'),
+    ('JAGS', '4.3.2'),
+]
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['rjags'],
+}
+
+moduleclass = 'math'

From 8e945ba48499d3865e07e7015fdf790df739abf5 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Petr=20Kr=C3=A1l?= <petr@inuits.eu>
Date: Tue, 20 Aug 2024 12:09:15 +0200
Subject: [PATCH 641/835] use GMP, describe patch file

---
 easybuild/easyconfigs/b/bliss/bliss-0.77-GCC-13.2.0.eb    | 8 ++++++--
 .../easyconfigs/b/bliss/bliss-0.77_install_fix.patch      | 2 ++
 2 files changed, 8 insertions(+), 2 deletions(-)

diff --git a/easybuild/easyconfigs/b/bliss/bliss-0.77-GCC-13.2.0.eb b/easybuild/easyconfigs/b/bliss/bliss-0.77-GCC-13.2.0.eb
index 3831e26c62d..ec9a99bc306 100644
--- a/easybuild/easyconfigs/b/bliss/bliss-0.77-GCC-13.2.0.eb
+++ b/easybuild/easyconfigs/b/bliss/bliss-0.77-GCC-13.2.0.eb
@@ -13,14 +13,18 @@ sources = [SOURCE_ZIP]
 patches = ['bliss-0.77_install_fix.patch']
 checksums = [
     {'bliss-0.77.zip': 'acc8b98034f30fad24c897f365abd866c13d9f1bb207e398d0caf136875972a4'},
-    {'bliss-0.77_install_fix.patch': '01a0824c5b121bd6ab0df324ee9c9dd4d4f0bfd8bb2800157cf270e8a1b194ea'},
+    {'bliss-0.77_install_fix.patch': '1550b6c7f8208f56093c0b6bf0d2e3df42afab81cd69eb70303515c9923e9513'},
 ]
 
 builddependencies = [
     ('CMake', '3.27.6'),
 ]
 
-configopts = "-DUSE_GMP=OFF "
+dependencies = [
+    ('GMP', '6.3.0'),
+]
+
+configopts = "-DUSE_GMP=ON "
 
 sanity_check_paths = {
     'files': [
diff --git a/easybuild/easyconfigs/b/bliss/bliss-0.77_install_fix.patch b/easybuild/easyconfigs/b/bliss/bliss-0.77_install_fix.patch
index a5fcbd85018..faea2ad4daf 100644
--- a/easybuild/easyconfigs/b/bliss/bliss-0.77_install_fix.patch
+++ b/easybuild/easyconfigs/b/bliss/bliss-0.77_install_fix.patch
@@ -1,3 +1,5 @@
+Adds install commands to CMakeLists.txt
+Source: https://gitlab.archlinux.org/archlinux/packaging/packages/bliss/-/blob/0.77-3/make-install.patch
 diff -u CMakeLists.txt.orig CMakeLists.txt
 --- CMakeLists.txt.orig	2021-02-18 11:59:34.000000000 +0100
 +++ CMakeLists.txt	2024-08-15 15:04:21.293765655 +0200

From 69bd18a3eee3da59d3ff59f90b1da5482696a6b4 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Petr=20Kr=C3=A1l?= <petr@inuits.eu>
Date: Tue, 20 Aug 2024 12:17:53 +0200
Subject: [PATCH 642/835] add missing build dependency

---
 .../easyconfigs/p/Pygments/Pygments-2.18.0-GCCcore-12.3.0.eb  | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/easybuild/easyconfigs/p/Pygments/Pygments-2.18.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/Pygments/Pygments-2.18.0-GCCcore-12.3.0.eb
index 2f441283024..54edd0b830e 100644
--- a/easybuild/easyconfigs/p/Pygments/Pygments-2.18.0-GCCcore-12.3.0.eb
+++ b/easybuild/easyconfigs/p/Pygments/Pygments-2.18.0-GCCcore-12.3.0.eb
@@ -12,6 +12,10 @@ toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
 sources = [SOURCELOWER_PY3_WHL]
 checksums = ['b8e6aca0523f3ab76fee51799c488e38782ac06eafcf95e7ba832985c8e7b13a']
 
+builddependencies = [
+    ('binutils', '2.40'),
+]
+
 dependencies = [
     ('Python', '3.11.3'),
 ]

From 9a1b9fe0912997fc63755b129abddc076b5aee9f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Petr=20Kr=C3=A1l?= <petr@inuits.eu>
Date: Tue, 20 Aug 2024 13:01:07 +0200
Subject: [PATCH 643/835] add missing easyconfig

---
 .../r/Raptor/Raptor-2.0.16-GCCcore-12.3.0.eb  | 54 +++++++++++++++++++
 1 file changed, 54 insertions(+)
 create mode 100644 easybuild/easyconfigs/r/Raptor/Raptor-2.0.16-GCCcore-12.3.0.eb

diff --git a/easybuild/easyconfigs/r/Raptor/Raptor-2.0.16-GCCcore-12.3.0.eb b/easybuild/easyconfigs/r/Raptor/Raptor-2.0.16-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..1607220271e
--- /dev/null
+++ b/easybuild/easyconfigs/r/Raptor/Raptor-2.0.16-GCCcore-12.3.0.eb
@@ -0,0 +1,54 @@
+##
+# This is a contribution from SIB Swiss Institute of Bioinformatics
+# Homepage:     https://www.sib.swiss/research-infrastructure/competence-centers/vital-it
+#
+# Authors::     Sebastien Moretti <sebastien.moretti@sib.swiss>
+#
+# Based on Raptor2 RPM spec file:
+# https://git.rockylinux.org/staging/rpms/raptor2/-/blob/r8/SPECS/raptor2.spec
+# The RPM patches have been integrated in the version 2.0.16
+#
+# Update: Petr Král (INUITS)
+##
+easyblock = 'ConfigureMake'
+
+name = 'Raptor'
+version = '2.0.16'
+homepage = 'https://librdf.org/raptor/'
+description = """Set of parsers and serializers that generate Resource Description Framework
+(RDF) triples by parsing syntaxes or serialize the triples into a syntax."""
+# software_license = 'LicenseLGPLv2.1 + LicenseGPLv2 + LicenseApachev2'
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+source_urls = ['https://download.librdf.org/source']
+sources = ['raptor2-%(version)s.tar.gz']
+checksums = ['089db78d7ac982354bdbf39d973baf09581e6904ac4c92a98c5caadb3de44680']
+
+builddependencies = [
+    ('Autotools',  '20220317'),
+    ('binutils',   '2.40'),
+]
+
+dependencies = [
+    ('libxml2',    '2.11.4'),
+    ('libxslt',    '1.1.38'),
+    ('cURL',       '8.0.1'),
+    ('ICU',        '73.2'),
+]
+
+configopts = "--disable-static --enable-release --disable-gtk-doc --with-yajl=no"
+
+# fix error: 'xmlEntity' {aka 'struct _xmlEntity'} has no member named 'checked'
+# see https://github.com/dajobe/raptor/pull/58
+local_sed_replacement = 's/LIBXML_VERSION >= 20627/LIBXML_VERSION >= 2062 \&\& LIBXML_VERSION < 21100/g'
+prebuildopts = "sed -i '%s' src/raptor_libxml.c && " % local_sed_replacement
+
+sanity_check_paths = {
+    'files': ['bin/rapper', 'lib/libraptor2.%s' % SHLIB_EXT],
+    'dirs': ['include/raptor2/']
+}
+
+sanity_check_commands = ["rapper --help"]
+
+moduleclass = 'lib'

From 41f451dae6d5dbdbde5f57e694ae8e37fe1837c0 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Petr=20Kr=C3=A1l?= <petr@inuits.eu>
Date: Tue, 20 Aug 2024 13:12:11 +0200
Subject: [PATCH 644/835] fix PEP8-compliance

---
 easybuild/easyconfigs/r/Raptor/Raptor-2.0.16-GCCcore-12.3.0.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/r/Raptor/Raptor-2.0.16-GCCcore-12.3.0.eb b/easybuild/easyconfigs/r/Raptor/Raptor-2.0.16-GCCcore-12.3.0.eb
index 1607220271e..979b9b88135 100644
--- a/easybuild/easyconfigs/r/Raptor/Raptor-2.0.16-GCCcore-12.3.0.eb
+++ b/easybuild/easyconfigs/r/Raptor/Raptor-2.0.16-GCCcore-12.3.0.eb
@@ -41,7 +41,7 @@ configopts = "--disable-static --enable-release --disable-gtk-doc --with-yajl=no
 
 # fix error: 'xmlEntity' {aka 'struct _xmlEntity'} has no member named 'checked'
 # see https://github.com/dajobe/raptor/pull/58
-local_sed_replacement = 's/LIBXML_VERSION >= 20627/LIBXML_VERSION >= 2062 \&\& LIBXML_VERSION < 21100/g'
+local_sed_replacement = r's/LIBXML_VERSION >= 20627/LIBXML_VERSION >= 2062 \&\& LIBXML_VERSION < 21100/g'
 prebuildopts = "sed -i '%s' src/raptor_libxml.c && " % local_sed_replacement
 
 sanity_check_paths = {

From df2c01d02ab3fab5863392ddc55051c04ebe2ced Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Petr=20Kr=C3=A1l?= <petr@inuits.eu>
Date: Tue, 20 Aug 2024 14:15:00 +0200
Subject: [PATCH 645/835] adding easyconfigs: IsoQuant-3.5.0-foss-2023a.eb,
 gffutils-0.13-foss-2023a.eb

---
 .../g/gffutils/gffutils-0.13-foss-2023a.eb    | 47 +++++++++++++++++++
 .../i/IsoQuant/IsoQuant-3.5.0-foss-2023a.eb   | 45 ++++++++++++++++++
 2 files changed, 92 insertions(+)
 create mode 100644 easybuild/easyconfigs/g/gffutils/gffutils-0.13-foss-2023a.eb
 create mode 100644 easybuild/easyconfigs/i/IsoQuant/IsoQuant-3.5.0-foss-2023a.eb

diff --git a/easybuild/easyconfigs/g/gffutils/gffutils-0.13-foss-2023a.eb b/easybuild/easyconfigs/g/gffutils/gffutils-0.13-foss-2023a.eb
new file mode 100644
index 00000000000..2b52f3965bc
--- /dev/null
+++ b/easybuild/easyconfigs/g/gffutils/gffutils-0.13-foss-2023a.eb
@@ -0,0 +1,47 @@
+easyblock = 'PythonBundle'
+
+name = 'gffutils'
+version = '0.13'
+
+homepage = 'https://github.com/daler/gffutils'
+description = """Gffutils is a Python package for working with and manipulating
+ the GFF and GTF format files typically used for genomic annotations."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('pyfaidx', '0.8.1.1'),
+    ('Biopython', '1.83'),
+    ('pybedtools', '0.9.1'),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    ('six', '1.16.0', {
+        'checksums': ['1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926'],
+    }),
+    ('argh', '0.31.3', {
+        'source_tmpl': SOURCE_PY3_WHL,
+        'checksums': ['2edac856ff50126f6e47d884751328c9f466bacbbb6cbfdac322053d94705494'],
+    }),
+    ('argcomplete', '3.5.0', {
+        'source_tmpl': SOURCE_PY3_WHL,
+        'checksums': ['d4bcf3ff544f51e16e54228a7ac7f486ed70ebf2ecfe49a63a91171c76bf029b'],
+    }),
+    ('simplejson', '3.19.3', {
+        'checksums': ['8e086896c36210ab6050f2f9f095a5f1e03c83fa0e7f296d6cba425411364680'],
+    }),
+    (name, version, {
+        'source_tmpl': SOURCE_PY3_WHL,
+        'checksums': ['58e7bb579796fff70e728380ef2d8ffd4a3bc895e53e6529855a0cf87ba6a77a'],
+    }),
+]
+
+sanity_check_commands = [
+    "python -c 'from gffutils import helpers'"
+]
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/i/IsoQuant/IsoQuant-3.5.0-foss-2023a.eb b/easybuild/easyconfigs/i/IsoQuant/IsoQuant-3.5.0-foss-2023a.eb
new file mode 100644
index 00000000000..41248bcbf73
--- /dev/null
+++ b/easybuild/easyconfigs/i/IsoQuant/IsoQuant-3.5.0-foss-2023a.eb
@@ -0,0 +1,45 @@
+easyblock = 'Tarball'
+
+name = 'IsoQuant'
+version = '3.5.0'
+
+homepage = 'https://github.com/ablab/IsoQuant'
+description = """IsoQuant is a tool for the genome-based analysis of long RNA reads,
+ such as PacBio or Oxford Nanopores. IsoQuant allows to reconstruct and quantify
+ transcript models with high precision and decent recall. If the reference annotation is given,
+ IsoQuant also assigns reads to the annotated isoforms based on their intron and exon structure.
+ IsoQuant further performs annotated gene, isoform, exon and intron quantification.
+ If reads are grouped (e.g. according to cell type), counts are reported according to the provided grouping."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+source_urls = ['https://github.com/ablab/%(name)s/archive/']
+sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}]
+checksums = ['8cbba80b5eb0ed85fe0b519693157eb97820bc1d79ff44435736bf799af85c1f']
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('gffutils', '0.13'),
+    ('Biopython', '1.83'),
+    ('SciPy-bundle', '2023.07'),
+    ('pybedtools', '0.9.1'),
+    ('Pysam', '0.22.0'),
+    ('pyfaidx', '0.8.1.1'),
+    ('minimap2', '2.26'),
+    ('SAMtools', '1.18'),
+    ('PyYAML', '6.0'),
+]
+
+modextrapaths = {
+    'PATH': '',
+    'PYTHONPATH': '',
+}
+
+sanity_check_paths = {
+    'files': ['isoquant.py'],
+    'dirs': [],
+}
+
+sanity_check_commands = ["mkdir -p %(builddir)s && cd %(builddir)s && isoquant.py --test"]
+
+moduleclass = 'bio'

From fa86b640f3bcd900b990a2e4d95b6e24ce4c73b3 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Petr=20Kr=C3=A1l?= <petr@inuits.eu>
Date: Tue, 20 Aug 2024 14:54:29 +0200
Subject: [PATCH 646/835] add missing dependency

---
 easybuild/easyconfigs/g/gtk-doc/gtk-doc-1.34.0-GCCcore-12.3.0.eb | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easybuild/easyconfigs/g/gtk-doc/gtk-doc-1.34.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/gtk-doc/gtk-doc-1.34.0-GCCcore-12.3.0.eb
index c77d925c3a0..dd18263d557 100644
--- a/easybuild/easyconfigs/g/gtk-doc/gtk-doc-1.34.0-GCCcore-12.3.0.eb
+++ b/easybuild/easyconfigs/g/gtk-doc/gtk-doc-1.34.0-GCCcore-12.3.0.eb
@@ -22,6 +22,7 @@ builddependencies = [
 dependencies = [
     ('Python', '3.11.3'),
     ('Pygments', '2.18.0'),
+    ('GLib', '2.77.1'),
 ]
 
 sanity_check_paths = {

From 6635ad9dcc8e5b5d02f525994302109ecaa75820 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Petr=20Kr=C3=A1l?= <petr@inuits.eu>
Date: Tue, 20 Aug 2024 15:42:50 +0200
Subject: [PATCH 647/835] adding easyconfigs:
 medaka-1.12.0-foss-2023a-CUDA-12.1.1.eb

---
 .../medaka-1.12.0-foss-2023a-CUDA-12.1.1.eb   | 85 +++++++++++++++++++
 1 file changed, 85 insertions(+)
 create mode 100644 easybuild/easyconfigs/m/medaka/medaka-1.12.0-foss-2023a-CUDA-12.1.1.eb

diff --git a/easybuild/easyconfigs/m/medaka/medaka-1.12.0-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/m/medaka/medaka-1.12.0-foss-2023a-CUDA-12.1.1.eb
new file mode 100644
index 00000000000..c2ca402d8ba
--- /dev/null
+++ b/easybuild/easyconfigs/m/medaka/medaka-1.12.0-foss-2023a-CUDA-12.1.1.eb
@@ -0,0 +1,85 @@
+# This is a contribution from HPCNow! (http://hpcnow.com)
+# Copyright::   HPCNow!
+# Authors::     Danilo Gonzalez <danilo.gonzalez@hpcnow.com>
+# License::     GPL-v3.0
+# Updated to foss-2020b to use with artic tool
+# J. Sassmannshausen (GSTT/NHS UK)
+# Updated to 1.5.0
+# Jasper Grimm (UoY)
+# Updated: Petr Král (INUITS)
+
+easyblock = 'PythonBundle'
+
+name = 'medaka'
+version = '1.12.0'
+versionsuffix = '-CUDA-%(cudaver)s'
+
+homepage = 'https://github.com/nanoporetech/medaka'
+description = "medaka is a tool to create a consensus sequence from nanopore sequencing data."
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+toolchainopts = {'pic': True}
+
+builddependencies = [('Autotools', '20220317')]
+
+_minimap_ver = '2.26'
+dependencies = [
+    ('CUDA', '12.1.1', '', SYSTEM),
+    ('Python', '3.11.3'),
+    ('Python-bundle-PyPI', '2023.06'),  # includes cffi
+    ('TensorFlow', '2.13.0', versionsuffix),
+    ('Pysam', '0.22.0'),
+    ('SAMtools', '1.18'),
+    ('minimap2', _minimap_ver),
+    ('HTSlib', '1.18'),  # for tabix, bgzip
+    ('Racon', '1.5.0'),
+    ('edlib', '1.3.9'),
+    ('pyspoa', '0.2.1'),
+    ('python-parasail', '1.3.4'),
+    ('ont-fast5-api', '4.1.2'),
+    ('WhatsHap', '2.2'),
+    ('intervaltree-python', '3.1.0'),
+    ('BCFtools', '1.18'),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+local_sed_commands = [
+    "sed -i 's/tensorflow.*/tensorflow/g;s/cffi==1.15.0/cffi/g' requirements.txt pyproject.toml",
+    # Python 3.11 support
+    "sed -i 's/8, 9, 10/8, 9, 10, 11/g;s/,<3.11//g' setup.py",
+]
+
+exts_list = [
+    ('mappy', _minimap_ver, {
+        'checksums': ['e53fbe9a3ea8762a64b8103f4f779c9fb16d418eaa0a731f45cebc83867a9b71'],
+    }),
+    ('wurlitzer', '3.1.1', {
+        'source_tmpl': SOURCE_PY3_WHL,
+        'checksums': ['0b2749c2cde3ef640bf314a9f94b24d929fe1ca476974719a6909dfc568c3aac'],
+    }),
+    ('h5py', '3.10.0', {
+        'checksums': ['d93adc48ceeb33347eb24a634fb787efc7ae4644e6ea4ba733d099605045c049'],
+    }),
+    ('pyabpoa', '1.5.1', {
+        'checksums': ['878f981e890a421d92a0d7606705d0ad9813ae6086239460dfe4b0cfc7476174'],
+    }),
+    (name, version, {
+        'checksums': ['039219204111a8114b1f72d87d0d3463e43473790cff4520c8afbd79cc8784d6'],
+        # Some requirements are too strict.
+        'preinstallopts': " && ".join(local_sed_commands) + " && ",
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['bin/medaka', 'bin/medaka_consensus', 'bin/medaka_version_report'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = [
+    "medaka --help",
+    "medaka_version_report",
+]
+
+moduleclass = 'bio'

From a8843e992878dc26846478c027e8b4212b74582a Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com>
Date: Tue, 20 Aug 2024 15:54:39 +0200
Subject: [PATCH 648/835] Update python-igraph-0.10.6-foss-2022b.eb - add cairo
 dep

Seems on some systems (generoso) it picked system cairo - so it did not fail
https://github.com/easybuilders/easybuild-easyconfigs/pull/21141#issuecomment-2298833068
---
 .../p/python-igraph/python-igraph-0.10.6-foss-2022b.eb           | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easybuild/easyconfigs/p/python-igraph/python-igraph-0.10.6-foss-2022b.eb b/easybuild/easyconfigs/p/python-igraph/python-igraph-0.10.6-foss-2022b.eb
index 01e1aa2d9c6..3b61ec3f869 100644
--- a/easybuild/easyconfigs/p/python-igraph/python-igraph-0.10.6-foss-2022b.eb
+++ b/easybuild/easyconfigs/p/python-igraph/python-igraph-0.10.6-foss-2022b.eb
@@ -20,6 +20,7 @@ dependencies = [
     ('Clang', '16.0.4'),
     ('libxml2', '2.10.3'),
     ('zlib', '1.2.12'),
+    ('cairo', '1.17.4'),
 ]
 
 use_pip = True

From d35df4bafbcf74893ba81e4f050942e96314f298 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Tue, 20 Aug 2024 16:08:35 +0200
Subject: [PATCH 649/835] update cd-hit with sanity_check_commands

---
 easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-GCC-12.3.0.eb | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-GCC-12.3.0.eb b/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-GCC-12.3.0.eb
index c4cacfb04bf..bd59609605c 100644
--- a/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-GCC-12.3.0.eb
+++ b/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-GCC-12.3.0.eb
@@ -1,4 +1,5 @@
 # This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+# changed toolchain and Perl version
 # Updated by: Thomas Eylenbosch(Gluo N.V.), Pavel Tománek (Inuits)
 
 easyblock = 'MakeCp'
@@ -35,4 +36,6 @@ sanity_check_paths = {
     'dirs': [],
 }
 
+sanity_check_commands = ["cd-hit -h | grep 'CD-HIT version %(version)s'"]
+
 moduleclass = 'bio'

From ec12a9fe2e91500dc99f124b378d27d45d590dcb Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Petr=20Kr=C3=A1l?= <petr@inuits.eu>
Date: Tue, 20 Aug 2024 17:06:40 +0200
Subject: [PATCH 650/835] Update
 easybuild/easyconfigs/m/medaka/medaka-1.12.0-foss-2023a-CUDA-12.1.1.eb

Co-authored-by: Kenneth Hoste <kenneth.hoste@ugent.be>
---
 .../m/medaka/medaka-1.12.0-foss-2023a-CUDA-12.1.1.eb            | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/m/medaka/medaka-1.12.0-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/m/medaka/medaka-1.12.0-foss-2023a-CUDA-12.1.1.eb
index c2ca402d8ba..c9ac4870bf5 100644
--- a/easybuild/easyconfigs/m/medaka/medaka-1.12.0-foss-2023a-CUDA-12.1.1.eb
+++ b/easybuild/easyconfigs/m/medaka/medaka-1.12.0-foss-2023a-CUDA-12.1.1.eb
@@ -27,7 +27,7 @@ dependencies = [
     ('CUDA', '12.1.1', '', SYSTEM),
     ('Python', '3.11.3'),
     ('Python-bundle-PyPI', '2023.06'),  # includes cffi
-    ('TensorFlow', '2.13.0', versionsuffix),
+    ('TensorFlow', '2.15.1', versionsuffix),
     ('Pysam', '0.22.0'),
     ('SAMtools', '1.18'),
     ('minimap2', _minimap_ver),

From 1bbe45fd783a31a55cd592dc3a7411e5eef5c7fd Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 20 Aug 2024 17:41:07 +0200
Subject: [PATCH 651/835] adding easyconfigs: VSEARCH-2.28.1-GCC-10.2.0.eb

---
 .../v/VSEARCH/VSEARCH-2.28.1-GCC-10.2.0.eb    | 40 +++++++++++++++++++
 1 file changed, 40 insertions(+)
 create mode 100644 easybuild/easyconfigs/v/VSEARCH/VSEARCH-2.28.1-GCC-10.2.0.eb

diff --git a/easybuild/easyconfigs/v/VSEARCH/VSEARCH-2.28.1-GCC-10.2.0.eb b/easybuild/easyconfigs/v/VSEARCH/VSEARCH-2.28.1-GCC-10.2.0.eb
new file mode 100644
index 00000000000..14ed6e6d975
--- /dev/null
+++ b/easybuild/easyconfigs/v/VSEARCH/VSEARCH-2.28.1-GCC-10.2.0.eb
@@ -0,0 +1,40 @@
+easyblock = 'ConfigureMake'
+
+name = 'VSEARCH'
+version = '2.28.1'
+
+homepage = 'https://github.com/torognes/vsearch'
+description = """VSEARCH supports de novo and reference based chimera detection,
+ clustering, full-length and prefix dereplication, rereplication,
+ reverse complementation, masking, all-vs-all pairwise global alignment,
+ exact and global alignment searching, shuffling, subsampling and sorting.
+ It also supports FASTQ file analysis, filtering,
+ conversion and merging of paired-end reads."""
+
+toolchain = {'name': 'GCC', 'version': '10.2.0'}
+
+source_urls = ['https://github.com/torognes/vsearch/archive']
+sources = ['v%(version)s.tar.gz']
+checksums = ['4f8bf0ad43fef77e573d152b59f55a1f81eb84c22d6545911757e6108f8de21c']
+
+builddependencies = [
+    ('Autotools', '20200321'),
+]
+
+dependencies = [
+    ('zlib', '1.2.11'),
+    ('bzip2', '1.0.8'),
+]
+
+preconfigopts = './autogen.sh &&'
+
+configopts = '--disable-pdfman '
+
+sanity_check_paths = {
+    'files': ['bin/vsearch'],
+    'dirs': [],
+}
+
+sanity_check_commands = ['vsearch --help']
+
+moduleclass = 'bio'

From d2a35a2eac44ae0949523b61f48a3955c15a959c Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 20 Aug 2024 18:30:04 +0200
Subject: [PATCH 652/835] adding easyconfigs: longread_umi-0.3.2-foss-2023a.eb,
 cutadapt-4.9-GCCcore-12.3.0.eb, Filtlong-0.2.1-GCC-12.3.0.eb

---
 .../c/cutadapt/cutadapt-4.9-GCCcore-12.3.0.eb | 60 ++++++++++++++
 .../f/Filtlong/Filtlong-0.2.1-GCC-12.3.0.eb   | 39 +++++++++
 .../longread_umi-0.3.2-foss-2023a.eb          | 82 +++++++++++++++++++
 3 files changed, 181 insertions(+)
 create mode 100644 easybuild/easyconfigs/c/cutadapt/cutadapt-4.9-GCCcore-12.3.0.eb
 create mode 100644 easybuild/easyconfigs/f/Filtlong/Filtlong-0.2.1-GCC-12.3.0.eb
 create mode 100644 easybuild/easyconfigs/l/longread_umi/longread_umi-0.3.2-foss-2023a.eb

diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-4.9-GCCcore-12.3.0.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-4.9-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..1f54c552c2e
--- /dev/null
+++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-4.9-GCCcore-12.3.0.eb
@@ -0,0 +1,60 @@
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+# Author: Pablo Escobar Lopez
+# Swiss Institute of Bioinformatics (SIB)
+# Biozentrum - University of Basel
+# Modified by: Adam Huffman, Jonas Demeulemeester
+# The Francis Crick Institute
+# Modified by: Albert Bogdanowicz
+# Institute of Biochemistry and Biophysics PAS
+# Modified by: Jasper Grimm
+# University of York
+
+easyblock = 'PythonBundle'
+
+name = 'cutadapt'
+version = '4.9'
+
+homepage = 'https://opensource.scilifelab.se/projects/cutadapt/'
+description = """Cutadapt finds and removes adapter sequences, primers, poly-A tails and
+ other types of unwanted sequence from your high-throughput sequencing reads."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+builddependencies = [
+    ('binutils', '2.40'),
+    ('Cython', '3.0.8'),  # required for dnaio
+]
+
+dependencies = [
+    ('pigz', '2.8'),
+    ('Python', '3.11.3'),
+    ('python-isal', '1.1.0'),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    # note: newer xopen versions require newer python-isal
+    ('xopen', '1.7.0', {
+        'checksums': ['901f9c8298e95ed74767a4bd76d9f4cf71d8de27b8cf296ac3e7bc1c11520d9f'],
+    }),
+    ('dnaio', '1.2.1', {
+        'checksums': ['4786dc63614b9f3011463d9ea9d981723dd38d1091a415a557f71d8c74400f38'],
+    }),
+    (name, version, {
+        'checksums': ['da3b45775b07334d2e2580a7b154d19ea7e872f0da813bb1ac2a4da712bfc223'],
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['bin/cutadapt'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = [
+    "cutadapt --help",
+    "cutadapt --version",
+]
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/f/Filtlong/Filtlong-0.2.1-GCC-12.3.0.eb b/easybuild/easyconfigs/f/Filtlong/Filtlong-0.2.1-GCC-12.3.0.eb
new file mode 100644
index 00000000000..25bf2c570f0
--- /dev/null
+++ b/easybuild/easyconfigs/f/Filtlong/Filtlong-0.2.1-GCC-12.3.0.eb
@@ -0,0 +1,39 @@
+# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/
+# Author: Pablo Escobar Lopez
+# sciCORE - University of Basel
+# SIB Swiss Institute of Bioinformatics
+
+easyblock = 'MakeCp'
+
+name = 'Filtlong'
+version = '0.2.1'
+
+homepage = 'https://github.com/rrwick/Filtlong'
+description = """Filtlong is a tool for filtering long reads by quality. It can take a set
+ of long reads and produce a smaller, better subset. It uses both read length (longer is better)
+ and read identity (higher is better) when choosing which reads pass the filter"""
+
+toolchain = {'name': 'GCC', 'version': '12.3.0'}
+
+source_urls = ['https://github.com/rrwick/Filtlong/archive/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['e6f47675e87f98cf2481a60bef5cad38396f1e4db653a5c1673139f37770273a']
+
+unpack_options = '--strip-components=1'
+
+parallel = 1
+
+dependencies = [
+    ('zlib', '1.2.13'),
+]
+
+files_to_copy = ["*"]
+
+sanity_check_paths = {
+    'files': ['bin/filtlong'],
+    'dirs': []
+}
+
+sanity_check_commands = ["filtlong --help"]
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/l/longread_umi/longread_umi-0.3.2-foss-2023a.eb b/easybuild/easyconfigs/l/longread_umi/longread_umi-0.3.2-foss-2023a.eb
new file mode 100644
index 00000000000..ce954f2edae
--- /dev/null
+++ b/easybuild/easyconfigs/l/longread_umi/longread_umi-0.3.2-foss-2023a.eb
@@ -0,0 +1,82 @@
+easyblock = 'Bundle'
+
+name = 'longread_umi'
+version = '0.3.2'
+
+homepage = 'https://github.com/SorenKarst/longread_umi'
+description = "A collection of scripts for processing longread UMI data."
+github_account = 'SorenKarst'
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('cutadapt', '4.9'),
+    ('BCFtools', '1.18'),
+    ('BWA', '0.7.17'),
+    ('Filtlong', '0.2.1'),
+    ('gawk', '5.3.0'),
+    ('medaka', '1.11.3'),
+    ('minimap2', '2.26'),
+    ('parallel', '20230722'),
+    ('Pysam', '0.22.0'),
+    ('Racon', '1.5.0'),
+    ('SAMtools', '1.18'),
+    ('seqtk', '1.4'),
+    ('VSEARCH', '2.25.0'),
+]
+
+components = [
+    (name, version, {
+        'easyblock': 'Tarball',
+        'source_urls': [GITHUB_LOWER_SOURCE],
+        'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}],
+        'checksums': ['62b8e156c00c0ec10fa8eae1cde5430922462f167fc537417ce0b47cd50a20cb'],
+        'start_dir': '%(name)s-%(version)s',
+    }),
+    # PythonPackage executes Bundle-level postinstallcmds for some reason,
+    # which rely on both components being installed, so Porechop is installed second
+    ('Porechop', '0.2.4', {
+        'easyblock': 'PythonPackage',
+        'source_urls': ['https://github.com/rrwick/Porechop/archive'],
+        'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}],
+        'checksums': ['44b499157d933be43f702cec198d1d693dcb9276e3c545669be63c2612493299'],
+        'start_dir': '%(name)s-%(version)s',
+        'use_pip': True,
+        'download_dep_fail': True,
+        'sanity_pip_check': True,
+    }),
+]
+
+# Adapt the built-in tool check but make it fail on error, replace usearch with vsearch and use our version
+local_deps_patch = (
+    "sed -i "
+    "-e '2s;^;set -e ;' "
+    "-e 's/USEARCH=usearch/USEARCH=vsearch/' "
+    "-e 's;$(git --git-dir ${LONGREAD_UMI_PATH}/.git describe --tag);%(version)s;' "
+    "%(installdir)s/scripts/dependencies.sh"
+)
+
+postinstallcmds = [
+    'find %(installdir)s -name "*.sh" -exec chmod +x {} \\;',
+    'ln -s %(installdir)s/longread_umi.sh %(installdir)s/bin/longread_umi',
+    # Part of the installation process; longread uses porechop with custom adapters
+    'cp %(installdir)s/scripts/adapters.py %(installdir)s/lib/python%(pyshortver)s/site-packages/porechop/',
+    local_deps_patch,
+]
+
+sanity_check_paths = {
+    'files': ['bin/longread_umi'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+sanity_check_commands = [
+    'longread_umi -h | grep qc_pipeline',
+    'longread_umi nanopore_pipeline -h | grep rrna_operon',
+    'source %(installdir)s/scripts/dependencies.sh && longread_umi_version_dump',
+]
+
+modextrapaths = {
+    'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']
+}
+
+moduleclass = 'bio'

From 0ccfd57238dbf895a7be37e830682ad80fe1abb7 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Tue, 20 Aug 2024 19:21:47 +0200
Subject: [PATCH 653/835] update name, version, sources, postinstallcmds,
 local_pycistopic_preinstallopts

---
 .../SCENICplus-1.0a1-20240513-foss-2023a.eb   | 279 ++++++++++++++++++
 1 file changed, 279 insertions(+)
 create mode 100644 easybuild/easyconfigs/s/SCENICplus/SCENICplus-1.0a1-20240513-foss-2023a.eb

diff --git a/easybuild/easyconfigs/s/SCENICplus/SCENICplus-1.0a1-20240513-foss-2023a.eb b/easybuild/easyconfigs/s/SCENICplus/SCENICplus-1.0a1-20240513-foss-2023a.eb
new file mode 100644
index 00000000000..dbff79bbe8c
--- /dev/null
+++ b/easybuild/easyconfigs/s/SCENICplus/SCENICplus-1.0a1-20240513-foss-2023a.eb
@@ -0,0 +1,279 @@
+easyblock = 'PythonBundle'
+
+name = 'SCENICplus'
+version = '1.0a1-20240513'
+local_commit = "fa55dae"
+
+homepage = 'https://github.com/aertslab/scenicplus'
+description = """SCENIC+ is a python package to build gene regulatory networks (GRNs)
+using combined or separate single-cell gene expression (scRNA-seq) and single-cell
+chromatin accessibility (scATAC-seq) data."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+builddependencies = [
+    ('poetry', '1.5.1'),
+    ('maturin', '1.4.0', '-Rust-1.75.0'),
+    ('CMake', '3.26.3'),
+]
+dependencies = [
+    ('Python', '3.11.3'),
+    ('Python-bundle-PyPI', '2023.06'),
+    ('SciPy-bundle', '2023.07'),
+    ('Single-cell-python-bundle', '2024.02'),
+    ('anndata', '0.10.5.post1'),
+    ('BeautifulSoup', '4.12.2'),
+    ('h5py', '3.9.0'),
+    ('python-igraph', '0.11.4'),
+    ('imageio', '2.33.1'),
+    ('leidenalg', '0.10.2'),
+    ('lxml', '4.9.2'),
+    ('MACS2', '2.2.9.1'),
+    ('numba', '0.58.1'),
+    ('polars', '0.20.2'),
+    ('Arrow', '14.0.1'),
+    ('plotly.py', '5.16.0'),
+    ('pybedtools', '0.9.1'),
+    ('pyBigWig', '0.3.22'),
+    ('pyGAM', '0.9.1'),
+    ('Pysam', '0.22.0'),
+    ('Ray-project', '2.9.1'),
+    ('scikit-image', '0.22.0'),
+    ('snakemake', '8.4.2'),
+    ('statsmodels', '0.14.1'),
+    ('IPython', '8.14.0'),
+    ('Pandoc', '3.1.2', '', SYSTEM),
+    ('ipympl', '0.9.3'),
+    ('PyTables', '3.8.0'),
+    ('Sphinx-RTD-Theme', '2.0.0'),
+    ('scrublet', '0.2.3'),
+    ('numexpr', '2.9.0'),
+    ('Kaleido', '0.2.1'),
+    ('pyfasta', '0.5.2'),
+    ('gensim', '4.3.2'),
+]
+
+# fix requirements.txt of scenicplus
+local_preinstallopts = (
+    "sed -i"
+    " -e '/typing==3.7.4.3/d'"
+    " -e 's/==.*//g'"
+    " -e '/pyarrow-hotfix/d'"
+    " -e '/line-profiler/d'"
+    " -e '/ndindex/d'"
+    " -e '/sinfo/d'"
+    " requirements.txt && "
+)
+# unpin version restriction and delete typing requirement
+local_pycistopic_preinstallopts = (
+    "sed -i"
+    " -e 's/pyscenic>=0.12.0/pyscenic/'"
+    " -e 's/pandas==1.5/pandas/'"
+    " -e 's/python-Levenshtein/Levenshtein/'"
+    " -e 's/python-igraph/igraph/'"
+    " -e '/typing/d'"
+    # delete pyscenic and loomxpy req from commit - have versions now
+    " -e '/pyscenic@git/d'"
+    " -e '/loomxpy@git/d'"
+    " requirements.txt && "
+    "sed -i"
+    " -e 's/pandas == 1.5/pandas/'"
+    " -e 's/matplotlib < 3.7/matplotlib/'"
+    " pyproject.toml && "
+)
+# delete typing from requirements
+local_pycistarget_preinstallopts = "sed -i '/typing/d' requirements.txt && "
+# unpin version restriction and delete poetry.lock
+local_loomxpy_preinstallopts = "sed -i 's/pyscenic>=0.12.0/pyscenic/' requirements.txt && "
+local_loomxpy_preinstallopts += "sed -i 's/pyscenic = \">=0.12.0\"/pyscenic = \"*\"/' pyproject.toml && "
+local_loomxpy_preinstallopts += "rm poetry.lock && "
+
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    ('bs4', '0.0.2', {
+        'checksums': ['a48685c58f50fe127722417bae83fe6badf500d54b55f7e39ffe43b798653925'],
+    }),
+    ('attr', '0.3.2', {
+        'checksums': ['1ceebca768181cdcce9827611b1d728e592be5d293911539ea3d0b0bfa1146f4'],
+    }),
+    ('attrs', '23.2.0', {
+        'checksums': ['935dc3b529c262f6cf76e50877d35a4bd3c1de194fd41f47a2b7ae8f19971f30'],
+    }),
+    ('lda', '3.0.0', {
+        'checksums': ['c9acbc1c55d2928f7e3e2336352b3382d78e43dbb0d12bf9ed97f87bce6d6708'],
+    }),
+    ('zope.interface', '6.2', {
+        'checksums': ['3b6c62813c63c543a06394a636978b22dffa8c5410affc9331ce6cdb5bfa8565'],
+    }),
+    ('zope.event', '5.0', {
+        'checksums': ['bac440d8d9891b4068e2b5a2c5e2c9765a9df762944bda6955f96bb9b91e67cd'],
+    }),
+    ('gevent', '24.2.1', {
+        'checksums': ['432fc76f680acf7cf188c2ee0f5d3ab73b63c1f03114c7cd8a34cebbe5aa2056'],
+    }),
+    ('xmltodict', '0.13.0', {
+        'checksums': ['341595a488e3e01a85a9d8911d8912fd922ede5fecc4dce437eb4b6c8d037e56'],
+    }),
+    ('suds-community', '1.1.2', {
+        'modulename': 'suds',
+        'checksums': ['883b4173ad23e7b20e9779ac7238b06140c50d7852afd5dc49dad1ea5f5a3d08'],
+    }),
+    ('grequests', '0.7.0', {
+        'checksums': ['5c33f14268df5b8fa1107d8537815be6febbad6ec560524d6a404b7778cf6ba6'],
+    }),
+    ('pexpect', '4.9.0', {
+        'checksums': ['ee7d41123f3c9911050ea2c2dac107568dc43b2d3b0c7557a33212c398ead30f'],
+    }),
+    ('colorlog', '6.8.2', {
+        'checksums': ['3e3e079a41feb5a1b64f978b5ea4f46040a94f11f0e8bbb8261e3dbbeca64d44'],
+    }),
+    ('easydev', '0.12.1', {
+        'checksums': ['b47b7e6f75316ac9045b46487930e16ddb567f3899310deee11d72d8e1f0a231'],
+    }),
+    ('bioservices', '1.11.2', {
+        'checksums': ['31baaab4ab813b93f79995ba8cad431a16cbee99e1b0c6f9e419dd4be0c73a9e'],
+    }),
+    ('gseapy', '0.10.8', {
+        'checksums': ['15be80bac73768501f5cecf6751aeb2e41416fd144bd6daa2ec453ad08a10ce0'],
+    }),
+    ('ncls', '0.0.68', {
+        'checksums': ['81aaa5abb123bb21797ed2f8ef921e20222db14a3ecbc61ccf447532f2b7ba93'],
+    }),
+    ('pybigtools', '0.1.2', {
+        'checksums': ['0f21bc8b4f2dce67c6e5287af895f5f28a8c6eb123d809e3ab5679e2131dbf58'],
+    }),
+    ('pybiomart', '0.2.0', {
+        'checksums': ['e9eac20db921820670c646d99725b0ee279e407379e5e8c3ec7245a07425d8fe'],
+    }),
+    ('sorted_nearest', '0.0.39', {
+        'checksums': ['16a51d5db87ae226b47ace43c176bb672477a1b7ba8052ea9291a6356c9c69b1'],
+    }),
+    ('pyranges', '0.0.111', {
+        'checksums': ['d2cf3c31c1b9c6e1bf6e1e89254d8bd993bfb4401f2c4ede0ebc9c8e0678147d'],
+    }),
+    ('pyrle', '0.0.39', {
+        'checksums': ['1be4be7814d3941db907aaf19f311bd46a407244316cadbf4b73109685c055c5'],
+    }),
+    ('pyvis', '0.3.2', {
+        'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl',
+        'checksums': ['5720c4ca8161dc5d9ab352015723abb7a8bb8fb443edeb07f7a322db34a97555'],
+    }),
+    ('url-normalize', '1.4.3', {
+        'checksums': ['d23d3a070ac52a67b83a1c59a0e68f8608d1cd538783b401bc9de2c0fac999b2'],
+    }),
+    ('cattrs', '23.2.3', {
+        'checksums': ['a934090d95abaa9e911dac357e3a8699e0b4b14f8529bcc7d2b1ad9d51672b9f'],
+    }),
+    ('requests_cache', '1.2.0', {
+        'checksums': ['db1c709ca343cc1cd5b6c8b1a5387298eceed02306a6040760db538c885e3838'],
+    }),
+    ('scanorama', '1.7.4', {
+        'checksums': ['67de100e63abc3028c7780d3a217e43e920a5781230bc6b6a51349d4605e005c'],
+    }),
+    ('rich_argparse', '1.4.0', {
+        'checksums': ['c275f34ea3afe36aec6342c2a2298893104b5650528941fb53c21067276dba19'],
+    }),
+    ('scatac_fragment_tools', '0.1.0', {
+        'checksums': ['e77a03ad1b7170c212f1ac672dad2c5d7e7f091b94e47b36a2ec2adc42051857'],
+    }),
+    ('snakemake_interface_common', '1.17.1', {
+        'checksums': ['555c8218d9b68ddc1046f94a517e7d0f22e15bdc839d6ce149608d8ec137b9ae'],
+    }),
+    ('snakemake_interface_report_plugins', '1.0.0', {
+        'checksums': ['02311cdc4bebab2a1c28469b5e6d5c6ac6e9c66998ad4e4b3229f1472127490f'],
+    }),
+    ('statistics', '1.0.3.5', {
+        'checksums': ['2dc379b80b07bf2ddd5488cad06b2b9531da4dd31edb04dc9ec0dc226486c138'],
+    }),
+    ('globre', '0.1.5', {
+        'checksums': ['ee214204f237e9114b8f61eeb61c2abd1e665ca3b59e5a6a0b070971c0bb12e2'],
+    }),
+    ('bidict', '0.23.1', {
+        'checksums': ['03069d763bc387bbd20e7d49914e75fc4132a41937fa3405417e1a5a2d006d71'],
+    }),
+    ('tmtoolkit', '0.12.0', {
+        'checksums': ['6df5429cd675989f21d9f075ddb11fe5ae273d6544fc337a2589bab2bc331909'],
+    }),
+    ('tspex', '0.6.3', {
+        'checksums': ['315bfa1f60ea582777c549313cad9e9da0a4d11c5f69a6fc767bd0823dc46316'],
+    }),
+    ('plumbum', '1.8.3', {
+        'checksums': ['6092c85ab970b7a7a9d5d85c75200bc93be82b33c9bdf640ffa87d2d7c8709f0'],
+    }),
+    ('pandoc', '2.3', {
+        'checksums': ['e772c2c6d871146894579828dbaf1efd538eb64fc7e71d4a6b3a11a18baef90d'],
+    }),
+    ('nbsphinx', '0.9.4', {
+        'checksums': ['042a60806fc23d519bc5bef59d95570713913fe442fda759d53e3aaf62104794'],
+    }),
+    ('nbsphinx-link', '1.3.0', {
+        'checksums': ['fa3079a74c0dff1b2079e79a34babe770706ba8aa9cc0609c6dbfd593461a077'],
+    }),
+    ('numpydoc', '1.7.0', {
+        'checksums': ['866e5ae5b6509dcf873fc6381120f5c31acf13b135636c1a81d68c166a95f921'],
+    }),
+    ('pyOpenSSL', '23.2.0', {
+        'modulename': 'OpenSSL',
+        'checksums': ['276f931f55a452e7dea69c7173e984eb2a4407ce413c918aa34b55f82f9b8bac'],
+    }),
+    ('entrypoints', '0.4', {
+        'checksums': ['b706eddaa9218a19ebcd67b56818f05bb27589b1ca9e8d797b74affad4ccacd4'],
+    }),
+    ('ansicolors', '1.1.8', {
+        'modulename': 'colors',
+        'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl',
+        'checksums': ['00d2dde5a675579325902536738dd27e4fac1fd68f773fe36c21044eb559e187'],
+    }),
+    ('papermill', '2.6.0', {
+        'checksums': ['9fe2a91912fd578f391b4cc8d6d105e73124dcd0cde2a43c3c4a1c77ac88ea24'],
+    }),
+    ('mypy_extensions', '1.0.0', {
+        'checksums': ['75dbf8955dc00442a438fc4d0666508a9a97b6bd41aa2f0ffe9d2f2725af0782'],
+    }),
+    ('typing_inspect', '0.9.0', {
+        'checksums': ['b23fc42ff6f6ef6954e4852c1fb512cdd18dbea03134f91f856a95ccc9461f78'],
+    }),
+    ('marshmallow', '3.21.1', {
+        'checksums': ['4e65e9e0d80fc9e609574b9983cf32579f305c718afb30d7233ab818571768c3'],
+    }),
+    ('dataclasses_json', '0.6.4', {
+        'checksums': ['73696ebf24936560cca79a2430cbc4f3dd23ac7bf46ed17f38e5e5e7657a6377'],
+    }),
+    ('loomxpy', '0.4.2', {
+        'preinstallopts': local_loomxpy_preinstallopts,
+        'checksums': ['188411b77e04fa8458c0a7f02cfb3f15b58410a020f81f522957e922e79cdd82'],
+    }),
+    ('pycisTopic', '2.0a-dca4bb6', {
+        'modulename': 'pycisTopic',
+        'preinstallopts': local_pycistopic_preinstallopts,
+        # download commit dca4bb6 to be compatible with pycistarget
+        'source_urls': ['https://github.com/aertslab/pycisTopic/archive/'],
+        'sources': [{'download_filename': 'dca4bb6.tar.gz', 'filename': '%(name)s-%(version)s-dca4bb6.tar.gz'}],
+        'checksums': ['82edc9313bbb587aeb1540fd5b095b6eafb422fa12a5fc97ba090b99b684b240'],
+    }),
+    ('pycistarget', '1.0a1-16d14b9', {
+        'preinstallopts': local_pycistarget_preinstallopts,
+        # download commit 16d14b9 to make '$ scenicplus' work
+        'source_urls': ['https://github.com/aertslab/pycistarget/archive/'],
+        'sources': [{'download_filename': '16d14b9.tar.gz', 'filename': '%(name)s-%(version)s-16d14b9.tar.gz'}],
+        'checksums': ['7285ac03be9d148437442a726366d7c6f9f5f86bc6636369149a2bc2cd8e0e29'],
+    }),
+    ('%(namelower)s', version, {
+        'preinstallopts': local_preinstallopts,
+        'source_urls': ['https://github.com/aertslab/scenicplus/archive/'],
+        'sources': [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}],
+        'checksums': ['88cddec1ab2618861e5c93e8a0b17b8e9e2aa3a76410d882c35d472f98724e29'],
+    }),
+]
+
+# copy files to let 'scenicplus init_snakemake' works 
+postinstallcmds = [
+    "cp -r %%(builddir)s/scenicplus/scenicplus-%s*/src/scenicplus/snakemake "
+    "%%(installdir)s/lib/python%%(pyshortver)s/site-packages/scenicplus" % local_commit
+]
+
+sanity_check_commands = ['scenicplus init_snakemake --help']
+
+moduleclass = 'bio'

From 00e56aff1ccc692a885560b7a3e66e02b3d2d11b Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 21 Aug 2024 08:45:24 +0200
Subject: [PATCH 654/835] adding easyconfigs: medaka-1.12.1-foss-2023a.eb

---
 .../m/medaka/medaka-1.12.1-foss-2023a.eb      | 86 +++++++++++++++++++
 1 file changed, 86 insertions(+)
 create mode 100644 easybuild/easyconfigs/m/medaka/medaka-1.12.1-foss-2023a.eb

diff --git a/easybuild/easyconfigs/m/medaka/medaka-1.12.1-foss-2023a.eb b/easybuild/easyconfigs/m/medaka/medaka-1.12.1-foss-2023a.eb
new file mode 100644
index 00000000000..f95d01c89d9
--- /dev/null
+++ b/easybuild/easyconfigs/m/medaka/medaka-1.12.1-foss-2023a.eb
@@ -0,0 +1,86 @@
+# This is a contribution from HPCNow! (http://hpcnow.com)
+# Copyright::   HPCNow!
+# Authors::     Danilo Gonzalez <danilo.gonzalez@hpcnow.com>
+# License::     GPL-v3.0
+# Updated to foss-2020b to use with artic tool
+# J. Sassmannshausen (GSTT/NHS UK)
+# Updated to 1.5.0
+# Jasper Grimm (UoY)
+# Updated: Petr Král (INUITS)
+
+easyblock = 'PythonBundle'
+
+name = 'medaka'
+version = '1.12.1'
+
+homepage = 'https://github.com/nanoporetech/medaka'
+description = "medaka is a tool to create a consensus sequence from nanopore sequencing data."
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+toolchainopts = {'pic': True}
+
+builddependencies = [('Autotools', '20220317')]
+
+_minimap_ver = '2.26'
+dependencies = [
+    ('Python', '3.11.3'),
+    ('Python-bundle-PyPI', '2023.06'),  # includes cffi
+    ('TensorFlow', '2.13.0'),
+    ('Pysam', '0.22.0'),
+    ('SAMtools', '1.18'),
+    ('minimap2', _minimap_ver),
+    ('HTSlib', '1.18'),  # for tabix, bgzip
+    ('Racon', '1.5.0'),
+    ('edlib', '1.3.9'),
+    ('pyspoa', '0.2.1'),
+    ('python-parasail', '1.3.4'),
+    ('ont-fast5-api', '4.1.2'),
+    ('WhatsHap', '2.2'),
+    ('intervaltree-python', '3.1.0'),
+    ('BCFtools', '1.18'),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+local_sed_commands = [
+    "sed -i 's/tensorflow.*/tensorflow/g;s/cffi==1.15.0/cffi/g' requirements.txt pyproject.toml",
+    # Python 3.11 support
+    "sed -i 's/8, 9, 10/8, 9, 10, 11/g;s/,<3.11//g' setup.py",
+    # ont-parasail on PyPI is just pre-built wheels for (python-)parasail
+    "sed -i 's/ont-parasail/parasail/g' requirements.txt",
+]
+
+exts_list = [
+    ('mappy', _minimap_ver, {
+        'checksums': ['e53fbe9a3ea8762a64b8103f4f779c9fb16d418eaa0a731f45cebc83867a9b71'],
+    }),
+    ('wurlitzer', '3.1.1', {
+        'source_tmpl': SOURCE_PY3_WHL,
+        'checksums': ['0b2749c2cde3ef640bf314a9f94b24d929fe1ca476974719a6909dfc568c3aac'],
+    }),
+    # medaka 1.12.0 requires h5py ~=3.10.0
+    ('h5py', '3.10.0', {
+        'checksums': ['d93adc48ceeb33347eb24a634fb787efc7ae4644e6ea4ba733d099605045c049'],
+    }),
+    ('pyabpoa', '1.5.2', {
+        'checksums': ['be39c83b12e923c9e47073cb8f0abc4c42f609fa2c0ec13d6f6a4f5a0537ee06'],
+    }),
+    (name, version, {
+        'checksums': ['df4baf7d1e9154de85229aef237919619ff6ae7f7d103abb0828e449ff977adf'],
+        # Some requirements are too strict.
+        'preinstallopts': " && ".join(local_sed_commands) + " && ",
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['bin/medaka', 'bin/medaka_consensus', 'bin/medaka_version_report'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = [
+    "medaka --help",
+    "medaka_version_report",
+]
+
+moduleclass = 'bio'

From f03ea94efe0ddd7efb10e2d96aad0ef7851b115b Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 21 Aug 2024 08:45:42 +0200
Subject: [PATCH 655/835] adding easyconfigs:
 medaka-1.12.1-foss-2023a-CUDA-12.1.1.eb

---
 .../medaka-1.12.1-foss-2023a-CUDA-12.1.1.eb   | 88 +++++++++++++++++++
 1 file changed, 88 insertions(+)
 create mode 100644 easybuild/easyconfigs/m/medaka/medaka-1.12.1-foss-2023a-CUDA-12.1.1.eb

diff --git a/easybuild/easyconfigs/m/medaka/medaka-1.12.1-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/m/medaka/medaka-1.12.1-foss-2023a-CUDA-12.1.1.eb
new file mode 100644
index 00000000000..3e055e5d8dd
--- /dev/null
+++ b/easybuild/easyconfigs/m/medaka/medaka-1.12.1-foss-2023a-CUDA-12.1.1.eb
@@ -0,0 +1,88 @@
+# This is a contribution from HPCNow! (http://hpcnow.com)
+# Copyright::   HPCNow!
+# Authors::     Danilo Gonzalez <danilo.gonzalez@hpcnow.com>
+# License::     GPL-v3.0
+# Updated to foss-2020b to use with artic tool
+# J. Sassmannshausen (GSTT/NHS UK)
+# Updated to 1.5.0
+# Jasper Grimm (UoY)
+# Updated: Petr Král (INUITS)
+
+easyblock = 'PythonBundle'
+
+name = 'medaka'
+version = '1.12.1'
+versionsuffix = '-CUDA-%(cudaver)s'
+
+homepage = 'https://github.com/nanoporetech/medaka'
+description = "medaka is a tool to create a consensus sequence from nanopore sequencing data."
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+toolchainopts = {'pic': True}
+
+builddependencies = [('Autotools', '20220317')]
+
+_minimap_ver = '2.26'
+dependencies = [
+    ('CUDA', '12.1.1', '', SYSTEM),
+    ('Python', '3.11.3'),
+    ('Python-bundle-PyPI', '2023.06'),  # includes cffi
+    ('TensorFlow', '2.15.1', versionsuffix),
+    ('Pysam', '0.22.0'),
+    ('SAMtools', '1.18'),
+    ('minimap2', _minimap_ver),
+    ('HTSlib', '1.18'),  # for tabix, bgzip
+    ('Racon', '1.5.0'),
+    ('edlib', '1.3.9'),
+    ('pyspoa', '0.2.1'),
+    ('python-parasail', '1.3.4'),
+    ('ont-fast5-api', '4.1.2'),
+    ('WhatsHap', '2.2'),
+    ('intervaltree-python', '3.1.0'),
+    ('BCFtools', '1.18'),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+local_sed_commands = [
+    "sed -i 's/tensorflow.*/tensorflow/g;s/cffi==1.15.0/cffi/g' requirements.txt pyproject.toml",
+    # Python 3.11 support
+    "sed -i 's/8, 9, 10/8, 9, 10, 11/g;s/,<3.11//g' setup.py",
+    # ont-parasail on PyPI is just pre-built wheels for (python-)parasail
+    "sed -i 's/ont-parasail/parasail/g' requirements.txt",
+]
+
+exts_list = [
+    ('mappy', _minimap_ver, {
+        'checksums': ['e53fbe9a3ea8762a64b8103f4f779c9fb16d418eaa0a731f45cebc83867a9b71'],
+    }),
+    ('wurlitzer', '3.1.1', {
+        'source_tmpl': SOURCE_PY3_WHL,
+        'checksums': ['0b2749c2cde3ef640bf314a9f94b24d929fe1ca476974719a6909dfc568c3aac'],
+    }),
+    # medaka 1.12.0 requires h5py ~=3.10.0
+    ('h5py', '3.10.0', {
+        'checksums': ['d93adc48ceeb33347eb24a634fb787efc7ae4644e6ea4ba733d099605045c049'],
+    }),
+    ('pyabpoa', '1.5.2', {
+        'checksums': ['be39c83b12e923c9e47073cb8f0abc4c42f609fa2c0ec13d6f6a4f5a0537ee06'],
+    }),
+    (name, version, {
+        'checksums': ['df4baf7d1e9154de85229aef237919619ff6ae7f7d103abb0828e449ff977adf'],
+        # Some requirements are too strict.
+        'preinstallopts': " && ".join(local_sed_commands) + " && ",
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['bin/medaka', 'bin/medaka_consensus', 'bin/medaka_version_report'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = [
+    "medaka --help",
+    "medaka_version_report",
+]
+
+moduleclass = 'bio'

From 98c7d10918dfadfb6d53ba232450dfd5a6b6ef0e Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 21 Aug 2024 10:02:41 +0200
Subject: [PATCH 656/835] fix type in configure option to disable VTK Python
 linking in ParaView 5.12.0

---
 .../easyconfigs/p/ParaView/ParaView-5.12.0-foss-2023b-Qt5.eb    | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.12.0-foss-2023b-Qt5.eb b/easybuild/easyconfigs/p/ParaView/ParaView-5.12.0-foss-2023b-Qt5.eb
index 1642881e802..abec428859f 100644
--- a/easybuild/easyconfigs/p/ParaView/ParaView-5.12.0-foss-2023b-Qt5.eb
+++ b/easybuild/easyconfigs/p/ParaView/ParaView-5.12.0-foss-2023b-Qt5.eb
@@ -57,7 +57,7 @@ _copts = [
     '-DVTK_OPENGL_HAS_EGL=ON',
     '-DVTK_USE_X=ON',
     '-DVTK_OPENGL_HAS_OSMESA=OFF',
-    '-DVTK_PYTHON_OPTIONAL_LINK=OFFVTK_PYTHON_=OFF']
+    '-DVTK_PYTHON_OPTIONAL_LINK=OFF']
 configopts = ' '.join(_copts)
 
 sanity_check_paths = {

From c847591f91b846aae0bba5f035f6f66bec6fa79a Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Wed, 21 Aug 2024 11:27:44 +0200
Subject: [PATCH 657/835] separate PR for VTK-9.3.0-foss-2023a.eb

---
 .../easyconfigs/v/VTK/VTK-9.3.0-foss-2023a.eb | 98 -------------------
 1 file changed, 98 deletions(-)
 delete mode 100644 easybuild/easyconfigs/v/VTK/VTK-9.3.0-foss-2023a.eb

diff --git a/easybuild/easyconfigs/v/VTK/VTK-9.3.0-foss-2023a.eb b/easybuild/easyconfigs/v/VTK/VTK-9.3.0-foss-2023a.eb
deleted file mode 100644
index 740fd888dfb..00000000000
--- a/easybuild/easyconfigs/v/VTK/VTK-9.3.0-foss-2023a.eb
+++ /dev/null
@@ -1,98 +0,0 @@
-##
-# Authors::
-# * Fotis Georgatos <fotis@cern.ch>
-# * Robert Mijakovic <robert.mijakovic@lxp.lu>
-# Update: Pavel Tománek (Inuits)
-##
-
-easyblock = 'CMakeNinja'
-
-name = 'VTK'
-version = '9.3.0'
-
-homepage = 'https://www.vtk.org'
-description = """The Visualization Toolkit (VTK) is an open-source, freely available software system for
- 3D computer graphics, image processing and visualization. VTK consists of a C++ class library and several
- interpreted interface layers including Tcl/Tk, Java, and Python. VTK supports a wide variety of visualization
- algorithms including: scalar, vector, tensor, texture, and volumetric methods; and advanced modeling techniques
- such as: implicit modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation."""
-
-toolchain = {'name': 'foss', 'version': '2023a'}
-toolchainopts = {'usempi': True}
-
-source_urls = ['https://www.vtk.org/files/release/%(version_major_minor)s']
-sources = [
-    SOURCE_TAR_GZ,
-    '%(name)sData-%(version)s.tar.gz',
-]
-patches = [('vtk-version.egg-info', '.')]
-checksums = [
-    {'VTK-9.3.0.tar.gz': 'fdc7b9295225b34e4fdddc49cd06e66e94260cb00efee456e0f66568c9681be9'},
-    {'VTKData-9.3.0.tar.gz': 'f82142dd327e995c9536c1003e1370bb4092c96f23edb8119d16d2411ef35dc3'},
-    {'vtk-version.egg-info': '787b82415ae7a4a1f815b4db0e25f7abc809a05fc85d7d219627f3a7e5d3867b'},
-]
-
-builddependencies = [
-    ('CMake', '3.26.3'),
-    ('Ninja', '1.11.1'),
-]
-
-dependencies = [
-    ('Python', '3.11.3'),
-    ('SciPy-bundle', '2023.07'),
-    ('XZ', '5.4.2'),
-    ('libGLU', '9.0.3'),
-    ('X11', '20230603'),
-    ('Qt5', '5.15.10'),
-]
-
-separate_build_dir = True
-
-# OpenGL
-configopts = "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT
-configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT
-configopts += "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include "
-# Python
-configopts += "-DVTK_WRAP_PYTHON=ON -DVTK_PYTHON_VERSION=3 -DVTK_PYTHON_OPTIONAL_LINK=OFF "
-configopts += "-DPython3_EXECUTABLE=$EBROOTPYTHON/bin/python3 "
-configopts += "-DPython3_INCLUDE_DIR=$EBROOTPYTHON/include/python%(pyshortver)s "
-configopts += "-DPython3_LIBRARY=$EBROOTPYTHON/lib/libpython%(pyshortver)s.so "
-# Other
-configopts += "-DVTK_USE_MPI=ON "
-configopts += "-DCMAKE_INSTALL_LIBDIR=lib "
-configopts += "-DVTK_QT_VERSION=5 "
-configopts += "-DQt5_DIR=$EBROOTQT5 "
-configopts += "-DVTK_MODULE_ENABLE_VTK_GuiSupportQt=YES "
-configopts += "-DVTK_MODULE_ENABLE_VTK_ViewsQt=YES"
-
-preinstallopts = "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && "
-
-# Install a egg-info file so VTK is more python friendly, required for mayavi
-local_egg_info_src = '%(builddir)s/VTK-%(version)s/vtk-version.egg-info'
-local_egg_info_dest = '%(installdir)s/lib/python%(pyshortver)s/site-packages/vtk-%(version)s.egg-info'
-postinstallcmds = [
-    'sed "s/#VTK_VERSION#/%%(version)s/" %s > %s' % (local_egg_info_src, local_egg_info_dest),
-]
-
-modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']}
-
-local_vtk_exec = ['vtk%s-%%(version_major_minor)s' % x
-                  for x in ['WrapJava', 'ParseJava', 'WrapPythonInit', 'WrapPython', 'WrapHierarchy']]
-local_vtk_exec += ['vtkpython']
-local_vtk_libs = ['CommonCore', 'IONetCDF', 'ParallelCore', 'RenderingOpenGL2']
-
-sanity_check_paths = {
-    'files': ['bin/%s' % x for x in local_vtk_exec] + ['include/vtk-%(version_major_minor)s/vtkMPI.h'] +
-             ['lib/libvtk%s-%%(version_major_minor)s.%s' % (l, SHLIB_EXT) for l in local_vtk_libs],
-    'dirs': ['lib/python%(pyshortver)s/site-packages/', 'include/vtk-%(version_major_minor)s'],
-}
-
-sanity_check_commands = [
-    "python -c 'import %(namelower)s'",
-    "python -c 'import pkg_resources; pkg_resources.get_distribution(\"vtk\")'",
-    # make sure that VTK Python libraries link to libpython (controlled via DVTK_PYTHON_OPTIONAL_LINK=OFF),
-    # see https://gitlab.kitware.com/vtk/vtk/-/issues/17881
-    "ldd $EBROOTVTK/lib/libvtkPythonContext2D-%%(version_major_minor)s.%s | grep /libpython" % SHLIB_EXT,
-]
-
-moduleclass = 'vis'

From fc2c99743c252b08c61e80d3b7a4e138c0ea78d8 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Wed, 21 Aug 2024 11:30:39 +0200
Subject: [PATCH 658/835] add Qt support

---
 easybuild/easyconfigs/v/VTK/VTK-9.3.0-foss-2023a.eb | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/v/VTK/VTK-9.3.0-foss-2023a.eb b/easybuild/easyconfigs/v/VTK/VTK-9.3.0-foss-2023a.eb
index 9278837da13..740fd888dfb 100644
--- a/easybuild/easyconfigs/v/VTK/VTK-9.3.0-foss-2023a.eb
+++ b/easybuild/easyconfigs/v/VTK/VTK-9.3.0-foss-2023a.eb
@@ -2,6 +2,7 @@
 # Authors::
 # * Fotis Georgatos <fotis@cern.ch>
 # * Robert Mijakovic <robert.mijakovic@lxp.lu>
+# Update: Pavel Tománek (Inuits)
 ##
 
 easyblock = 'CMakeNinja'
@@ -42,6 +43,7 @@ dependencies = [
     ('XZ', '5.4.2'),
     ('libGLU', '9.0.3'),
     ('X11', '20230603'),
+    ('Qt5', '5.15.10'),
 ]
 
 separate_build_dir = True
@@ -57,7 +59,11 @@ configopts += "-DPython3_INCLUDE_DIR=$EBROOTPYTHON/include/python%(pyshortver)s
 configopts += "-DPython3_LIBRARY=$EBROOTPYTHON/lib/libpython%(pyshortver)s.so "
 # Other
 configopts += "-DVTK_USE_MPI=ON "
-configopts += "-DCMAKE_INSTALL_LIBDIR=lib"
+configopts += "-DCMAKE_INSTALL_LIBDIR=lib "
+configopts += "-DVTK_QT_VERSION=5 "
+configopts += "-DQt5_DIR=$EBROOTQT5 "
+configopts += "-DVTK_MODULE_ENABLE_VTK_GuiSupportQt=YES "
+configopts += "-DVTK_MODULE_ENABLE_VTK_ViewsQt=YES"
 
 preinstallopts = "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && "
 

From dc043891ddc0c74c14c3377943777d321fafa4ae Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com>
Date: Wed, 21 Aug 2024 11:47:05 +0200
Subject: [PATCH 659/835] Update Visit-3.4.1-foss-2023a.eb - add comment to
 VTK-9.2.6

---
 easybuild/easyconfigs/v/Visit/Visit-3.4.1-foss-2023a.eb | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easybuild/easyconfigs/v/Visit/Visit-3.4.1-foss-2023a.eb b/easybuild/easyconfigs/v/Visit/Visit-3.4.1-foss-2023a.eb
index 7e5eaa8b270..406d78fa312 100644
--- a/easybuild/easyconfigs/v/Visit/Visit-3.4.1-foss-2023a.eb
+++ b/easybuild/easyconfigs/v/Visit/Visit-3.4.1-foss-2023a.eb
@@ -37,6 +37,7 @@ dependencies = [
     ('libglvnd', '1.6.0'),
     ('Qt5', '5.15.10'),
     ('Qwt', '6.3.0'),
+    # Visit-3.4.1 needs VTK-9.2.x (not 9.3.x) - https://github.com/visit-dav/visit/issues/19547
     ('VTK', '9.2.6'),
     ('FFmpeg', '6.0'),
 ]

From 4ca72c270d18e5c2157c4ea0144a28e4562b1112 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 21 Aug 2024 11:56:38 +0200
Subject: [PATCH 660/835] add recent version of make as build dependency for
 Raptor

---
 easybuild/easyconfigs/r/Raptor/Raptor-2.0.16-GCCcore-12.3.0.eb | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easybuild/easyconfigs/r/Raptor/Raptor-2.0.16-GCCcore-12.3.0.eb b/easybuild/easyconfigs/r/Raptor/Raptor-2.0.16-GCCcore-12.3.0.eb
index 979b9b88135..61c358020c8 100644
--- a/easybuild/easyconfigs/r/Raptor/Raptor-2.0.16-GCCcore-12.3.0.eb
+++ b/easybuild/easyconfigs/r/Raptor/Raptor-2.0.16-GCCcore-12.3.0.eb
@@ -28,6 +28,7 @@ checksums = ['089db78d7ac982354bdbf39d973baf09581e6904ac4c92a98c5caadb3de44680']
 builddependencies = [
     ('Autotools',  '20220317'),
     ('binutils',   '2.40'),
+    ('make',   '4.4.1'),
 ]
 
 dependencies = [

From ca33632d3559a6e4aed6a2e157027ce71ff4a4f1 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Petr=20Kr=C3=A1l?= <petr@inuits.eu>
Date: Wed, 21 Aug 2024 12:55:12 +0200
Subject: [PATCH 661/835] adding easyconfigs:
 PEcAn-1.7.2.9000-foss-2023a-R-4.3.2.eb, Redland-1.0.17-GCC-12.3.0.eb,
 unixODBC-2.3.12-GCCcore-12.3.0.eb

---
 .../PEcAn-1.7.2.9000-foss-2023a-R-4.3.2.eb    | 218 ++++++++++++++++++
 .../r/Redland/Redland-1.0.17-GCC-12.3.0.eb    |  37 +++
 .../unixODBC-2.3.12-GCCcore-12.3.0.eb         |  30 +++
 3 files changed, 285 insertions(+)
 create mode 100644 easybuild/easyconfigs/p/PEcAn/PEcAn-1.7.2.9000-foss-2023a-R-4.3.2.eb
 create mode 100644 easybuild/easyconfigs/r/Redland/Redland-1.0.17-GCC-12.3.0.eb
 create mode 100644 easybuild/easyconfigs/u/unixODBC/unixODBC-2.3.12-GCCcore-12.3.0.eb

diff --git a/easybuild/easyconfigs/p/PEcAn/PEcAn-1.7.2.9000-foss-2023a-R-4.3.2.eb b/easybuild/easyconfigs/p/PEcAn/PEcAn-1.7.2.9000-foss-2023a-R-4.3.2.eb
new file mode 100644
index 00000000000..163a41f725f
--- /dev/null
+++ b/easybuild/easyconfigs/p/PEcAn/PEcAn-1.7.2.9000-foss-2023a-R-4.3.2.eb
@@ -0,0 +1,218 @@
+easyblock = 'Bundle'
+
+name = 'PEcAn'
+version = '1.7.2.9000'
+versionsuffix = '-R-%(rver)s'
+
+homepage = 'https://github.com/PecanProject/pecan'
+description = """Ecosystem science, policy, and management informed by the best available data and models."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+dependencies = [
+    ('R', '4.3.2'),
+    ('R-bundle-Bioconductor', '3.18', versionsuffix),
+    ('PostgreSQL', '16.1'),
+    ('CDO', '2.2.2'),
+    ('HDF5', '1.14.0'),
+    ('netCDF', '4.9.2'),
+    ('UDUNITS', '2.2.28'),
+    ('texlive', '20230313'),
+    ('NCO', '5.1.9'),
+    ('ncview', '2.1.8'),
+    ('rjags', '4-15', versionsuffix),
+    ('Redland', '1.0.17'),
+]
+
+exts_defaultclass = 'RPackage'
+exts_default_options = {
+    'sources': ['%(name)s_%(version)s.tar.gz'],
+    'source_urls': [
+        'https://cran.r-project.org/src/contrib/',  # current version of packages
+        'https://cran.r-project.org/src/contrib/Archive/%(name)s',  # package archive
+        'https://cran.freestatistics.org/src/contrib',  # mirror alternative for current packages
+        'https://pecanproject.r-universe.dev/src/contrib/',  # PEcAn sources
+    ],
+}
+
+local_sed_patterns_duckdb = '1146s/prefix_front_/prefix_front_back.prefix_front_/g;'
+local_sed_patterns_duckdb += '1147s/prefix_back_/prefix_front_back.prefix_back_/g'
+
+exts_list = [
+    ('PEcAn.logger', '1.8.1.9000', {
+        'checksums': ['3d1d8a6c9afa677dde8a4aaf72809932f0b6b5385ae4a6fc2059b48ed4b09195'],
+    }),
+    ('PEcAn.remote', '1.7.2', {
+        'checksums': ['59feda08ac6784c5e607a70166e002df96385efbba3b77148b4cf9a0a1e2c9dc'],
+    }),
+    ('PEcAn.utils', '1.7.2', {
+        'checksums': ['d83ae2a605f7867659d10de952f5db6b947dc3d2bc05633c0f72ced0b4caad17'],
+    }),
+    ('PEcAn.DB', version, {
+        'checksums': ['f493d6ab100fce139bdb9747c91faff5cf60ff296ee16a82c6bc2366a9722231'],
+    }),
+    ('PEcAn.settings', '1.7.2', {
+        'checksums': ['ab0dd41e9f421a84e68a16a1e4b290f70d852d23e66a2de1c3e91bf883aa1aeb'],
+    }),
+    ('PEcAn.MA', '1.7.2', {
+        'checksums': ['bf3a5b6ac8adce4efb6be504cdeb10a71a59b3ac5af72c8d77b59a39c7d90ceb'],
+    }),
+    ('PEcAn.emulator', version, {
+        'checksums': ['f4465a154e41cfe5a2cc94035ae4a5ddbfd3b5fc54a83bc9578c98a9eb07cff1'],
+    }),
+    ('PEcAn.priors', '1.7.2', {
+        'checksums': ['001c26275ef23dda369fa2a5b408e481265d29137edeaebd03a30a39b4682edd'],
+    }),
+    ('PEcAn.uncertainty', version, {
+        'checksums': ['a0d1a3a3d65e06b066d23473def763f5e158b2356ee5fe9e09020fe311e9ef4a'],
+    }),
+    ('amerifluxr', '1.0.0', {
+        'checksums': ['ec54dce4b8e4108832eaadb60f7ef8ad28b459d3381316537492dcd755d83b25'],
+    }),
+    ('geonames', '0.999', {
+        'checksums': ['1dd7bbd82d9425d14eb36f8e5bf431feaccfe3b0c4e70bf38f44f13dfc59e17b'],
+    }),
+    ('solartime', '0.0.2', {
+        'checksums': ['5dd7a28db2bd4881ab740cd7004b88cd05c61e0954e3a10c8e18ebbe07d3e7d1'],
+    }),
+    ('bigleaf', '0.8.2', {
+        'checksums': ['e41d82fb6298150c46f57128e959a1f1c6cfa55e916c32544bab7be69b0b6df7'],
+    }),
+    ('REddyProc', '1.3.3', {
+        'checksums': ['3f673bd24f41813f631bf25139c9595bd91483e898ec31b7207c4eb8b7ff486b'],
+    }),
+    ('suntools', '1.0.0', {
+        'checksums': ['42b7b39bd23ad48ded002150a0e7798fab94ed9828e5b5fdd8e5e1c9040697e2'],
+    }),
+    ('fauxpas', '0.5.2', {
+        'checksums': ['84d07361a146b419cb1dcb7751654e3d5f159cf2704faf498e5ea56c8de61ef6'],
+    }),
+    ('nneo', '0.1.0', {
+        'checksums': ['ca503e78cf4f4c85de6e18ad3ffde0c08d6a507ff5dc5ff91a50b3e04bf84a49'],
+    }),
+    ('PEcAn.data.atmosphere', '1.7.2', {
+        'checksums': ['1847151588f669e91b35de637c804328efbc606141bf992bee650fd261b70e5a'],
+    }),
+    ('redland', '1.0.17-18', {
+        'checksums': ['e999ba22321733df7ed056f528e38fc4be535d36bbac8106395c14f9f60a75a0'],
+    }),
+    ('datapack', '1.4.1', {
+        'checksums': ['6149733ae90e6bbbb53d5f85ca29cec5f811825e794b56029b7f325de6637493'],
+    }),
+    ('dplR', '1.7.7', {
+        'checksums': ['0e35a4d2a22773499f9e4592d1a198a08c9842388ce1e5a35394990ed4cdb2bd'],
+    }),
+    ('neonUtilities', '2.4.2', {
+        'checksums': ['37b4efd0ed3b724de999d08d4d430954a6c717b1d943bc84c513c4fe8dbca057'],
+    }),
+    ('storr', '1.2.5', {
+        'checksums': ['4224c3991d9c043a45ce530d0698d7f2cdca231b26fe31b45e0db865026e5f63'],
+    }),
+    ('thor', '1.1.5', {
+        'checksums': ['99802d8c8471ce351403f8428c1efab48ccf20f359fbd368db84f25ef8f7ecae'],
+    }),
+    ('duckdb', '1.0.0-2', {
+        'checksums': ['3735d51f22d62a7411aa514142cd569ce28bdaec4eb58d5f0893a476b9ccbf01'],
+        # fixes the `prefix_back_ was not declared` error, see https://github.com/duckdb/duckdb/pull/12344
+        'preinstallopts': "sed -i '%s' src/duckdb/third_party/re2/re2/prog.cc && " % local_sed_patterns_duckdb,
+    }),
+    ('duckdbfs', '0.0.4', {
+        'checksums': ['90b2aff2bdefff1db4f855e2a9c9b19a404f522027105424aebd3c7e45944334'],
+    }),
+    ('neonstore', '0.5.1', {
+        'checksums': ['f911e957861d558adead8ca77e4d1575a47dceb9553f1aa9d818460126deab9b'],
+    }),
+    ('HDInterval', '0.2.4', {
+        'checksums': ['bb07f0edd660a02ed18e578c2798eb8c2db0e181a5e0c3e23db182d13e9494f6'],
+    }),
+    ('kknn', '1.3.1', {
+        'checksums': ['22840e70ec2afa40371e274b583634c8f6d27149a87253ee411747d5db78f3db'],
+    }),
+    ('timeSeries', '4032.109', {
+        'checksums': ['5e0c47584e0b01ea4011ed5ced217d95f8bb872611f6b029b0797d95eebd731f'],
+    }),
+    ('gss', '2.2-7', {
+        'checksums': ['3b13144702c570c83462b4ea2ad17f4bd630cff5bf2ab0347a33c7e86a4f3f6a'],
+    }),
+    ('fBasics', '4032.96', {
+        'checksums': ['e1556909871c836668b10bf90e1676aac6a2892a04663d7ab00c22a64c0b8690'],
+    }),
+    ('rmutil', '1.1.10', {
+        'checksums': ['819fd7ce695cc742b4594705986eb06764460fc88521ea32de793c49de7ca5f9'],
+    }),
+    ('stable', '1.1.6', {
+        'checksums': ['2238788a35b5aa9e175ad7b92348640c3dcad68b6ab0a0bc04aeec9084d29da4'],
+    }),
+    ('statip', '0.2.3', {
+        'checksums': ['56a81a1882856cd1c5711ba133417b64f09071dda356e74280a0dba0db60d54f'],
+    }),
+    ('modeest', '2.4.0', {
+        'checksums': ['1a949409bf64679d32400d20aa3d53e65a9a20f5bd1a40993b95f81100e0ed20'],
+    }),
+    ('runjags', '2.2.2-4', {
+        'checksums': ['6f656e4d0620c0806e596ddb4bfec3934534ec17c02da699fcbfd6720a6f424f'],
+    }),
+    ('swfscMisc', '1.6.5', {
+        'checksums': ['a49cb390643c4079f02986862eb2dfd33db4e6b6498e849bb418f73ffd6882e1'],
+    }),
+    ('CDM', '8.2-6', {
+        'checksums': ['144a85e36c120e9f8a5bd35c1db50cf089ea4807721ac14460137b9a4b1c98d1'],
+    }),
+    ('TAM', '4.2-21', {
+        'checksums': ['0d1782e42e89c1863edab12c1861d0e2628ea9ee1a1e37d268f27a3deaf3d568'],
+    }),
+    ('pbv', '0.5-47', {
+        'checksums': ['e17a04efa96a601ab72172b59f555f36d28bb824f02f363cc5806b05d7d7c792'],
+    }),
+    ('sirt', '4.1-15', {
+        'checksums': ['c12ffcb83bea5b549c7a34c12561f3e57798b83d68a887c5da0d9a66efac3066'],
+    }),
+    ('hoardr', '0.5.4', {
+        'checksums': ['4e031ac1317584451c09bc8288ed73fb2d6ceea3c10d29dbb4be08157e489a37'],
+    }),
+    ('traits', '0.5.1', {
+        'checksums': ['3080887a454d69814cd6cb9683a6750db02cf4c77b40b022ef50d40171ba6aca'],
+    }),
+    ('SimilarityMeasures', '1.4', {
+        'checksums': ['b26bbc3a402d21f030cc8e4ff6baca644eb4c63a4fb33423dbc9436229a393f0'],
+    }),
+    ('PEcAn.benchmark', '1.7.2', {
+        'checksums': ['c9cf9f299f810e4962476db1afdf6a39de77806fd82b6cb8bb7321e96c350db8'],
+    }),
+    ('PEcAn.visualization', '1.7.2', {
+        'checksums': ['5d25871d57ded42c7ae7f8dbf0a6907c8b828f6a0463286e6ae178b356a4a848'],
+    }),
+    ('PEcAn.data.land', version, {
+        'checksums': ['29ed015c1e8a5b993aebc31559aa3f7a4136b1f23e4c13a2d55118e7c541da2f'],
+    }),
+    ('MODISTools', '1.1.5', {
+        'checksums': ['0a6b3762865424e299e1a5ec28de78b8dcca3f673e61f42a37dae19ed78db3e3'],
+    }),
+    ('PEcAn.data.remote', version, {
+        'checksums': ['691b9e27cf5afb6bfb32873cca6ba284d0ff303873695e86f7653432aa7c66d4'],
+    }),
+    ('SparseGrid', '0.8.2', {
+        'checksums': ['1d84ae83db2a390b111589a10570d55b378c2dd3310d3bc588a94ab8845cfd14'],
+    }),
+    ('lqmm', '1.5.8', {
+        'checksums': ['11eddeeeed6b9d3190a80a3b3cc3d64519c6e9cb208746a3736139340df691fb'],
+    }),
+    ('PEcAn.workflow', '1.7.2', {
+        'checksums': ['cdd60bf6a99b20aed9792b0cf6648c3f55f4b9bd3a00fd0187b7e7ec56815f0f'],
+    }),
+    ('PEcAn.assim.batch', version, {
+        'checksums': ['d57b7ce1b0cbef0183bcb689f55f0345575289f1b8741c00cbd026eeaea8a6b9'],
+    }),
+    ('%(name)s.all', version, {
+        'checksums': ['43e036ab8af9834ae6d7d7f4304adfc6cef08348e3be39ca5e51dcbb1fe21cce'],
+    }),
+]
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['%(name)s.all'],
+}
+
+modextrapaths = {'R_LIBS_SITE': ''}
+
+moduleclass = 'math'
diff --git a/easybuild/easyconfigs/r/Redland/Redland-1.0.17-GCC-12.3.0.eb b/easybuild/easyconfigs/r/Redland/Redland-1.0.17-GCC-12.3.0.eb
new file mode 100644
index 00000000000..364d182c058
--- /dev/null
+++ b/easybuild/easyconfigs/r/Redland/Redland-1.0.17-GCC-12.3.0.eb
@@ -0,0 +1,37 @@
+easyblock = 'ConfigureMake'
+
+name = 'Redland'
+version = '1.0.17'
+
+homepage = 'https://librdf.org/raptor'
+description = """Redland is a set of free software C libraries that provide support for the Resource Description Framework (RDF)."""
+
+toolchain = {'name': 'GCC', 'version': '12.3.0'}
+
+source_urls = ['https://download.librdf.org/source']
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['de1847f7b59021c16bdc72abb4d8e2d9187cd6124d69156f3326dd34ee043681']
+
+dependencies = [
+    ('Rasqal', '0.9.33'),
+    ('Raptor', '2.0.16'),
+    ('PostgreSQL', '16.1'),
+    ('MariaDB', '11.6.0'),
+    ('unixODBC', '2.3.12'),
+    ('SQLite', '3.42.0'),
+    ('libtool', '2.4.7'),
+]
+
+sanity_check_paths = {
+    'files': [
+        'include/%(namelower)s.h',
+        'bin/%(namelower)s-config',
+        'bin/%(namelower)s-db-upgrade',
+        'lib/librdf.%s' % SHLIB_EXT,
+    ],
+    'dirs': ['share/%(namelower)s'],
+}
+
+sanity_check_commands = ['%(namelower)s-config --help']
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/u/unixODBC/unixODBC-2.3.12-GCCcore-12.3.0.eb b/easybuild/easyconfigs/u/unixODBC/unixODBC-2.3.12-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..9d3f2cfc12f
--- /dev/null
+++ b/easybuild/easyconfigs/u/unixODBC/unixODBC-2.3.12-GCCcore-12.3.0.eb
@@ -0,0 +1,30 @@
+# Easyconfig for unixODBC
+# Author: Lykle Voort
+# SURFsara, Amsterdam, The Netherlands
+# Updated: Petr Král (INUITS)
+
+easyblock = 'ConfigureMake'
+
+name = 'unixODBC'
+version = '2.3.12'
+
+homepage = "https://www.unixodbc.org"
+description = """unixODBC provides a uniform interface between
+application and database driver"""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+sources = [SOURCE_TAR_GZ]
+source_urls = ['https://www.unixodbc.org/']
+checksums = ['f210501445ce21bf607ba51ef8c125e10e22dffdffec377646462df5f01915ec']
+
+sanity_check_paths = {
+    'files': [
+        'lib/libodbc.%s' % SHLIB_EXT,
+        'lib/libodbccr.%s' % SHLIB_EXT,
+        'lib/libodbcinst.%s' % SHLIB_EXT,
+    ],
+    'dirs': []
+}
+
+moduleclass = 'data'

From cb60dca8f3444794f0d1869bdb6d0b64fa8d851b Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Wed, 21 Aug 2024 13:29:44 +0200
Subject: [PATCH 662/835] remove old scenicplus from PR

---
 .../scenicplus-1.0a1-18072024-foss-2023a.eb   | 281 ------------------
 1 file changed, 281 deletions(-)
 delete mode 100644 easybuild/easyconfigs/s/scenicplus/scenicplus-1.0a1-18072024-foss-2023a.eb

diff --git a/easybuild/easyconfigs/s/scenicplus/scenicplus-1.0a1-18072024-foss-2023a.eb b/easybuild/easyconfigs/s/scenicplus/scenicplus-1.0a1-18072024-foss-2023a.eb
deleted file mode 100644
index 37f4c7d76b3..00000000000
--- a/easybuild/easyconfigs/s/scenicplus/scenicplus-1.0a1-18072024-foss-2023a.eb
+++ /dev/null
@@ -1,281 +0,0 @@
-easyblock = 'PythonBundle'
-
-name = 'scenicplus'
-version = '1.0a1-18072024'
-local_commit = "fa55dae"
-
-homepage = 'https://github.com/aertslab/scenicplus'
-description = """SCENIC+ is a python package to build gene regulatory networks (GRNs)
-using combined or separate single-cell gene expression (scRNA-seq) and single-cell
-chromatin accessibility (scATAC-seq) data."""
-
-toolchain = {'name': 'foss', 'version': '2023a'}
-
-builddependencies = [
-    ('poetry', '1.5.1'),
-    ('maturin', '1.4.0', '-Rust-1.75.0'),
-    ('CMake', '3.26.3'),
-]
-dependencies = [
-    ('Python', '3.11.3'),
-    ('Python-bundle-PyPI', '2023.06'),
-    ('SciPy-bundle', '2023.07'),
-    ('Single-cell-python-bundle', '2024.02'),
-    ('anndata', '0.10.5.post1'),
-    ('BeautifulSoup', '4.12.2'),
-    ('h5py', '3.9.0'),
-    ('python-igraph', '0.11.4'),
-    ('imageio', '2.33.1'),
-    ('leidenalg', '0.10.2'),
-    ('lxml', '4.9.2'),
-    ('MACS2', '2.2.9.1'),
-    ('numba', '0.58.1'),
-    ('polars', '0.20.2'),
-    ('Arrow', '14.0.1'),
-    ('plotly.py', '5.16.0'),
-    ('pybedtools', '0.9.1'),
-    ('pyBigWig', '0.3.22'),
-    ('pyGAM', '0.9.1'),
-    ('Pysam', '0.22.0'),
-    ('Ray-project', '2.9.1'),
-    ('scikit-image', '0.22.0'),
-    ('snakemake', '8.4.2'),
-    ('statsmodels', '0.14.1'),
-    ('IPython', '8.14.0'),
-    ('Pandoc', '3.1.2', '', SYSTEM),
-    ('ipympl', '0.9.3'),
-    ('PyTables', '3.8.0'),
-    ('Sphinx-RTD-Theme', '2.0.0'),
-    ('scrublet', '0.2.3'),
-    ('numexpr', '2.9.0'),
-    ('Kaleido', '0.2.1'),
-    ('pyfasta', '0.5.2'),
-    ('gensim', '4.3.2'),
-]
-
-# fix requirements.txt of scenicplus
-local_preinstallopts = (
-    "sed -i"
-    " -e '/typing==3.7.4.3/d'"
-    " -e 's/==.*//g'"
-    " -e '/pyarrow-hotfix/d'"
-    " -e '/line-profiler/d'"
-    " -e '/ndindex/d'"
-    " -e '/sinfo/d'"
-    " requirements.txt && "
-)
-# unpin version restriction and delete typing requirement
-local_pycistopic_preinstallopts = (
-    "sed -i"
-    " -e 's/pyscenic>=0.12.0/pyscenic/'"
-    " -e 's/pandas==1.5/pandas/'"
-    " -e 's/python-Levenshtein/Levenshtein/'"
-    " -e 's/python-igraph/igraph/'"
-    " -e '/typing/d'"
-    # delete pyscenic and loomxpy req from commit - have versions now
-    " -e '60,61d'"
-    " requirements.txt && "
-    "sed -i"
-    " -e 's/pandas == 1.5/pandas/'"
-    " -e 's/matplotlib < 3.7/matplotlib/'"
-    " pyproject.toml && "
-)
-# delete typing from requirements
-local_pycistarget_preinstallopts = "sed -i '/typing/d' requirements.txt && "
-# unpin version restriction and delete poetry.lock
-local_loomxpy_preinstallopts = "sed -i 's/pyscenic>=0.12.0/pyscenic/' requirements.txt && "
-local_loomxpy_preinstallopts += "sed -i 's/pyscenic = \">=0.12.0\"/pyscenic = \"*\"/' pyproject.toml && "
-local_loomxpy_preinstallopts += "rm poetry.lock && "
-
-use_pip = True
-sanity_pip_check = True
-
-exts_list = [
-    ('bs4', '0.0.2', {
-        'checksums': ['a48685c58f50fe127722417bae83fe6badf500d54b55f7e39ffe43b798653925'],
-    }),
-    ('attr', '0.3.2', {
-        'checksums': ['1ceebca768181cdcce9827611b1d728e592be5d293911539ea3d0b0bfa1146f4'],
-    }),
-    ('attrs', '23.2.0', {
-        'checksums': ['935dc3b529c262f6cf76e50877d35a4bd3c1de194fd41f47a2b7ae8f19971f30'],
-    }),
-    ('lda', '3.0.0', {
-        'checksums': ['c9acbc1c55d2928f7e3e2336352b3382d78e43dbb0d12bf9ed97f87bce6d6708'],
-    }),
-    ('zope.interface', '6.2', {
-        'checksums': ['3b6c62813c63c543a06394a636978b22dffa8c5410affc9331ce6cdb5bfa8565'],
-    }),
-    ('zope.event', '5.0', {
-        'checksums': ['bac440d8d9891b4068e2b5a2c5e2c9765a9df762944bda6955f96bb9b91e67cd'],
-    }),
-    ('gevent', '24.2.1', {
-        'checksums': ['432fc76f680acf7cf188c2ee0f5d3ab73b63c1f03114c7cd8a34cebbe5aa2056'],
-    }),
-    ('xmltodict', '0.13.0', {
-        'checksums': ['341595a488e3e01a85a9d8911d8912fd922ede5fecc4dce437eb4b6c8d037e56'],
-    }),
-    ('suds-community', '1.1.2', {
-        'modulename': 'suds',
-        'checksums': ['883b4173ad23e7b20e9779ac7238b06140c50d7852afd5dc49dad1ea5f5a3d08'],
-    }),
-    ('grequests', '0.7.0', {
-        'checksums': ['5c33f14268df5b8fa1107d8537815be6febbad6ec560524d6a404b7778cf6ba6'],
-    }),
-    ('pexpect', '4.9.0', {
-        'checksums': ['ee7d41123f3c9911050ea2c2dac107568dc43b2d3b0c7557a33212c398ead30f'],
-    }),
-    ('colorlog', '6.8.2', {
-        'checksums': ['3e3e079a41feb5a1b64f978b5ea4f46040a94f11f0e8bbb8261e3dbbeca64d44'],
-    }),
-    ('easydev', '0.12.1', {
-        'checksums': ['b47b7e6f75316ac9045b46487930e16ddb567f3899310deee11d72d8e1f0a231'],
-    }),
-    ('bioservices', '1.11.2', {
-        'checksums': ['31baaab4ab813b93f79995ba8cad431a16cbee99e1b0c6f9e419dd4be0c73a9e'],
-    }),
-    ('gseapy', '0.10.8', {
-        'checksums': ['15be80bac73768501f5cecf6751aeb2e41416fd144bd6daa2ec453ad08a10ce0'],
-    }),
-    ('ncls', '0.0.68', {
-        'checksums': ['81aaa5abb123bb21797ed2f8ef921e20222db14a3ecbc61ccf447532f2b7ba93'],
-    }),
-    ('pybigtools', '0.1.2', {
-        'checksums': ['0f21bc8b4f2dce67c6e5287af895f5f28a8c6eb123d809e3ab5679e2131dbf58'],
-    }),
-    ('pybiomart', '0.2.0', {
-        'checksums': ['e9eac20db921820670c646d99725b0ee279e407379e5e8c3ec7245a07425d8fe'],
-    }),
-    ('sorted_nearest', '0.0.39', {
-        'checksums': ['16a51d5db87ae226b47ace43c176bb672477a1b7ba8052ea9291a6356c9c69b1'],
-    }),
-    ('pyranges', '0.0.111', {
-        'checksums': ['d2cf3c31c1b9c6e1bf6e1e89254d8bd993bfb4401f2c4ede0ebc9c8e0678147d'],
-    }),
-    ('pyrle', '0.0.39', {
-        'checksums': ['1be4be7814d3941db907aaf19f311bd46a407244316cadbf4b73109685c055c5'],
-    }),
-    ('pyvis', '0.3.2', {
-        'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl',
-        'checksums': ['5720c4ca8161dc5d9ab352015723abb7a8bb8fb443edeb07f7a322db34a97555'],
-    }),
-    ('url-normalize', '1.4.3', {
-        'checksums': ['d23d3a070ac52a67b83a1c59a0e68f8608d1cd538783b401bc9de2c0fac999b2'],
-    }),
-    ('cattrs', '23.2.3', {
-        'checksums': ['a934090d95abaa9e911dac357e3a8699e0b4b14f8529bcc7d2b1ad9d51672b9f'],
-    }),
-    ('requests_cache', '1.2.0', {
-        'checksums': ['db1c709ca343cc1cd5b6c8b1a5387298eceed02306a6040760db538c885e3838'],
-    }),
-    ('scanorama', '1.7.4', {
-        'checksums': ['67de100e63abc3028c7780d3a217e43e920a5781230bc6b6a51349d4605e005c'],
-    }),
-    ('rich_argparse', '1.4.0', {
-        'checksums': ['c275f34ea3afe36aec6342c2a2298893104b5650528941fb53c21067276dba19'],
-    }),
-    ('scatac_fragment_tools', '0.1.0', {
-        'checksums': ['e77a03ad1b7170c212f1ac672dad2c5d7e7f091b94e47b36a2ec2adc42051857'],
-    }),
-    ('snakemake_interface_common', '1.17.1', {
-        'checksums': ['555c8218d9b68ddc1046f94a517e7d0f22e15bdc839d6ce149608d8ec137b9ae'],
-    }),
-    ('snakemake_interface_report_plugins', '1.0.0', {
-        'checksums': ['02311cdc4bebab2a1c28469b5e6d5c6ac6e9c66998ad4e4b3229f1472127490f'],
-    }),
-    ('statistics', '1.0.3.5', {
-        'checksums': ['2dc379b80b07bf2ddd5488cad06b2b9531da4dd31edb04dc9ec0dc226486c138'],
-    }),
-    ('globre', '0.1.5', {
-        'checksums': ['ee214204f237e9114b8f61eeb61c2abd1e665ca3b59e5a6a0b070971c0bb12e2'],
-    }),
-    ('bidict', '0.23.1', {
-        'checksums': ['03069d763bc387bbd20e7d49914e75fc4132a41937fa3405417e1a5a2d006d71'],
-    }),
-    ('tmtoolkit', '0.12.0', {
-        'checksums': ['6df5429cd675989f21d9f075ddb11fe5ae273d6544fc337a2589bab2bc331909'],
-    }),
-    ('tspex', '0.6.3', {
-        'checksums': ['315bfa1f60ea582777c549313cad9e9da0a4d11c5f69a6fc767bd0823dc46316'],
-    }),
-    ('plumbum', '1.8.3', {
-        'checksums': ['6092c85ab970b7a7a9d5d85c75200bc93be82b33c9bdf640ffa87d2d7c8709f0'],
-    }),
-    ('pandoc', '2.3', {
-        'checksums': ['e772c2c6d871146894579828dbaf1efd538eb64fc7e71d4a6b3a11a18baef90d'],
-    }),
-    ('nbsphinx', '0.9.4', {
-        'checksums': ['042a60806fc23d519bc5bef59d95570713913fe442fda759d53e3aaf62104794'],
-    }),
-    ('nbsphinx-link', '1.3.0', {
-        'checksums': ['fa3079a74c0dff1b2079e79a34babe770706ba8aa9cc0609c6dbfd593461a077'],
-    }),
-    ('numpydoc', '1.7.0', {
-        'checksums': ['866e5ae5b6509dcf873fc6381120f5c31acf13b135636c1a81d68c166a95f921'],
-    }),
-    ('pyOpenSSL', '23.2.0', {
-        'modulename': 'OpenSSL',
-        'checksums': ['276f931f55a452e7dea69c7173e984eb2a4407ce413c918aa34b55f82f9b8bac'],
-    }),
-    ('entrypoints', '0.4', {
-        'checksums': ['b706eddaa9218a19ebcd67b56818f05bb27589b1ca9e8d797b74affad4ccacd4'],
-    }),
-    ('ansicolors', '1.1.8', {
-        'modulename': 'colors',
-        'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl',
-        'checksums': ['00d2dde5a675579325902536738dd27e4fac1fd68f773fe36c21044eb559e187'],
-    }),
-    ('papermill', '2.6.0', {
-        'checksums': ['9fe2a91912fd578f391b4cc8d6d105e73124dcd0cde2a43c3c4a1c77ac88ea24'],
-    }),
-    ('mypy_extensions', '1.0.0', {
-        'checksums': ['75dbf8955dc00442a438fc4d0666508a9a97b6bd41aa2f0ffe9d2f2725af0782'],
-    }),
-    ('typing_inspect', '0.9.0', {
-        'checksums': ['b23fc42ff6f6ef6954e4852c1fb512cdd18dbea03134f91f856a95ccc9461f78'],
-    }),
-    ('marshmallow', '3.21.1', {
-        'checksums': ['4e65e9e0d80fc9e609574b9983cf32579f305c718afb30d7233ab818571768c3'],
-    }),
-    ('dataclasses_json', '0.6.4', {
-        'checksums': ['73696ebf24936560cca79a2430cbc4f3dd23ac7bf46ed17f38e5e5e7657a6377'],
-    }),
-    ('loomxpy', '0.4.2', {
-        'preinstallopts': local_loomxpy_preinstallopts,
-        'checksums': ['188411b77e04fa8458c0a7f02cfb3f15b58410a020f81f522957e922e79cdd82'],
-    }),
-    ('pycisTopic', '2.0a-dca4bb6', {
-        'modulename': 'pycisTopic',
-        'preinstallopts': local_pycistopic_preinstallopts,
-        # download commit dca4bb6 to be compatible with pycistarget
-        'source_urls': ['https://github.com/aertslab/pycisTopic/archive/'],
-        'sources': [{'download_filename': 'dca4bb6.tar.gz', 'filename': '%(name)s-%(version)s-dca4bb6.tar.gz'}],
-        'checksums': ['82edc9313bbb587aeb1540fd5b095b6eafb422fa12a5fc97ba090b99b684b240'],
-    }),
-    ('pycistarget', '1.0a1-16d14b9', {
-        'preinstallopts': local_pycistarget_preinstallopts,
-        # download commit 16d14b9 to make '$ scenicplus' work
-        'source_urls': ['https://github.com/aertslab/pycistarget/archive/'],
-        'sources': [{'download_filename': '16d14b9.tar.gz', 'filename': '%(name)s-%(version)s-16d14b9.tar.gz'}],
-        'checksums': ['7285ac03be9d148437442a726366d7c6f9f5f86bc6636369149a2bc2cd8e0e29'],
-    }),
-    (name, version, {
-        'preinstallopts': local_preinstallopts,
-        'source_urls': ['https://github.com/aertslab/scenicplus/archive/'],
-        'sources': [{'download_filename': 'fa55dae.tar.gz', 'filename': '%(name)s-%(version)s-fa55dae.tar.gz'}],
-        'checksums': [
-            {'scenicplus-1.0a1-18072024-fa55dae.tar.gz':
-             '88cddec1ab2618861e5c93e8a0b17b8e9e2aa3a76410d882c35d472f98724e29'},
-        ],
-    }),
-]
-
-# copy files to let 'scenicplus init_snakemake' works 
-postinstallcmds = [
-    'cp -r %(builddir)s/scenicplus/scenicplus-fa55dae55203951c0c42e359b65a28010cd544f6/src/scenicplus/snakemake '
-    '%(installdir)s/lib/python%(pyshortver)s/site-packages/scenicplus'
-]
-
-sanity_check_commands = ['scenicplus init_snakemake --help']
-
-moduleclass = 'bio'

From 669505d3c834a2ce4ca5775451c5c3241cb46c50 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Petr=20Kr=C3=A1l?= <petr@inuits.eu>
Date: Wed, 21 Aug 2024 13:34:36 +0200
Subject: [PATCH 663/835] fix line too long error

---
 easybuild/easyconfigs/r/Redland/Redland-1.0.17-GCC-12.3.0.eb | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/r/Redland/Redland-1.0.17-GCC-12.3.0.eb b/easybuild/easyconfigs/r/Redland/Redland-1.0.17-GCC-12.3.0.eb
index 364d182c058..7217999a898 100644
--- a/easybuild/easyconfigs/r/Redland/Redland-1.0.17-GCC-12.3.0.eb
+++ b/easybuild/easyconfigs/r/Redland/Redland-1.0.17-GCC-12.3.0.eb
@@ -4,7 +4,8 @@ name = 'Redland'
 version = '1.0.17'
 
 homepage = 'https://librdf.org/raptor'
-description = """Redland is a set of free software C libraries that provide support for the Resource Description Framework (RDF)."""
+description = """Redland is a set of free software C libraries that
+ provide support for the Resource Description Framework (RDF)."""
 
 toolchain = {'name': 'GCC', 'version': '12.3.0'}
 

From d3495ce7e33faf906034a0df881da3ef980e4d34 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Wed, 21 Aug 2024 13:39:17 +0200
Subject: [PATCH 664/835] adding easyconfigs:
 MATES-0.1.2-20240813-foss-2023a.eb

---
 .../MATES/MATES-0.1.2-20240813-foss-2023a.eb  | 56 +++++++++++++++++++
 1 file changed, 56 insertions(+)
 create mode 100644 easybuild/easyconfigs/m/MATES/MATES-0.1.2-20240813-foss-2023a.eb

diff --git a/easybuild/easyconfigs/m/MATES/MATES-0.1.2-20240813-foss-2023a.eb b/easybuild/easyconfigs/m/MATES/MATES-0.1.2-20240813-foss-2023a.eb
new file mode 100644
index 00000000000..e7e73a89e80
--- /dev/null
+++ b/easybuild/easyconfigs/m/MATES/MATES-0.1.2-20240813-foss-2023a.eb
@@ -0,0 +1,56 @@
+easyblock = 'PythonBundle'
+
+name = 'MATES'
+version = '0.1.2-20240813'
+local_commit = 'd5ee15b'
+
+homepage = 'https://github.com/mcgilldinglab/MATES'
+description = "A Deep Learning-Based Model for Quantifying Transposable Elements in Single-Cell Sequencing Data."
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('Python-bundle-PyPI', '2023.06'),
+    ('SciPy-bundle', '2023.07'),
+    ('matplotlib', '3.7.2'),
+    ('anndata', '0.10.5.post1'),
+    ('SAMtools', '1.18'),
+    ('pybedtools', '0.9.1'),
+    ('PyTorch-bundle', '2.1.2'),
+    ('Pysam', '0.22.0'),
+    ('tqdm', '4.66.1'),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    ('sorted_nearest', '0.0.39', {
+        'checksums': ['16a51d5db87ae226b47ace43c176bb672477a1b7ba8052ea9291a6356c9c69b1'],
+    }),
+    ('ncls', '0.0.68', {
+        'checksums': ['81aaa5abb123bb21797ed2f8ef921e20222db14a3ecbc61ccf447532f2b7ba93'],
+    }),
+    ('natsort', '8.4.0', {
+        'checksums': ['45312c4a0e5507593da193dedd04abb1469253b601ecaf63445ad80f0a1ea581'],
+    }),
+    ('pyranges', '0.0.129', {
+        'checksums': ['bee83b4fad0062be9586668c6b0fc4270d5e761951975e018202993680071fb3'],
+    }),
+    (name, version, {
+        'modulename': 'MATES',
+        # unpin exact versions of dependencies
+        'preinstallopts': r"sed -i 's/==.*//g' requirements.txt && sed -i 's/==.*/\",/g' setup.py && ",
+        'source_urls': ['https://github.com/mcgilldinglab/MATES/archive'],
+        'sources': [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}],
+        'checksums': ['aca36b2b99ebed975fdf61670a9b551c1ab7882ff2b9d4ed3f25f2e13805652c'],
+    }),
+]
+
+sanity_check_commands = [
+    "python -c 'from MATES import bam_processor, data_processor, MATES_model'",
+    "python -c 'from MATES import TE_quantifier, TE_quantifier_LongRead, TE_quantifier_Intronic'",
+]
+
+moduleclass = 'bio'

From 55331441356f136cf8cfba273af8f2b0bc881848 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Wed, 21 Aug 2024 13:54:09 +0200
Subject: [PATCH 665/835] add mates with gpu support

---
 ...S-0.1.2-20240813-foss-2023a-CUDA-12.1.1.eb | 58 +++++++++++++++++++
 1 file changed, 58 insertions(+)
 create mode 100644 easybuild/easyconfigs/m/MATES/MATES-0.1.2-20240813-foss-2023a-CUDA-12.1.1.eb

diff --git a/easybuild/easyconfigs/m/MATES/MATES-0.1.2-20240813-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/m/MATES/MATES-0.1.2-20240813-foss-2023a-CUDA-12.1.1.eb
new file mode 100644
index 00000000000..dbba96ddf2f
--- /dev/null
+++ b/easybuild/easyconfigs/m/MATES/MATES-0.1.2-20240813-foss-2023a-CUDA-12.1.1.eb
@@ -0,0 +1,58 @@
+easyblock = 'PythonBundle'
+
+name = 'MATES'
+version = '0.1.2-20240813'
+local_commit = 'd5ee15b'
+versionsuffix = '-CUDA-%(cudaver)s'
+
+homepage = 'https://github.com/mcgilldinglab/MATES'
+description = "A Deep Learning-Based Model for Quantifying Transposable Elements in Single-Cell Sequencing Data."
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('CUDA', '12.1.1', '', SYSTEM),
+    ('Python-bundle-PyPI', '2023.06'),
+    ('SciPy-bundle', '2023.07'),
+    ('matplotlib', '3.7.2'),
+    ('anndata', '0.10.5.post1'),
+    ('SAMtools', '1.18'),
+    ('pybedtools', '0.9.1'),
+    ('PyTorch-bundle', '2.1.2', versionsuffix),
+    ('Pysam', '0.22.0'),
+    ('tqdm', '4.66.1'),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    ('sorted_nearest', '0.0.39', {
+        'checksums': ['16a51d5db87ae226b47ace43c176bb672477a1b7ba8052ea9291a6356c9c69b1'],
+    }),
+    ('ncls', '0.0.68', {
+        'checksums': ['81aaa5abb123bb21797ed2f8ef921e20222db14a3ecbc61ccf447532f2b7ba93'],
+    }),
+    ('natsort', '8.4.0', {
+        'checksums': ['45312c4a0e5507593da193dedd04abb1469253b601ecaf63445ad80f0a1ea581'],
+    }),
+    ('pyranges', '0.0.129', {
+        'checksums': ['bee83b4fad0062be9586668c6b0fc4270d5e761951975e018202993680071fb3'],
+    }),
+    (name, version, {
+        'modulename': 'MATES',
+        # unpin exact versions of dependencies
+        'preinstallopts': r"sed -i 's/==.*//g' requirements.txt && sed -i 's/==.*/\",/g' setup.py && ",
+        'source_urls': ['https://github.com/mcgilldinglab/MATES/archive'],
+        'sources': [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}],
+        'checksums': ['aca36b2b99ebed975fdf61670a9b551c1ab7882ff2b9d4ed3f25f2e13805652c'],
+    }),
+]
+
+sanity_check_commands = [
+    "python -c 'from MATES import bam_processor, data_processor, MATES_model'",
+    "python -c 'from MATES import TE_quantifier, TE_quantifier_LongRead, TE_quantifier_Intronic'",
+]
+
+moduleclass = 'bio'

From de002d6026e0eab8690d1cba7ff79cb896e77704 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Petr=20Kr=C3=A1l?= <petr@inuits.eu>
Date: Wed, 21 Aug 2024 13:59:47 +0200
Subject: [PATCH 666/835] add missing build dependency

---
 .../easyconfigs/u/unixODBC/unixODBC-2.3.12-GCCcore-12.3.0.eb    | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/easybuild/easyconfigs/u/unixODBC/unixODBC-2.3.12-GCCcore-12.3.0.eb b/easybuild/easyconfigs/u/unixODBC/unixODBC-2.3.12-GCCcore-12.3.0.eb
index 9d3f2cfc12f..7e5cec281f2 100644
--- a/easybuild/easyconfigs/u/unixODBC/unixODBC-2.3.12-GCCcore-12.3.0.eb
+++ b/easybuild/easyconfigs/u/unixODBC/unixODBC-2.3.12-GCCcore-12.3.0.eb
@@ -18,6 +18,8 @@ sources = [SOURCE_TAR_GZ]
 source_urls = ['https://www.unixodbc.org/']
 checksums = ['f210501445ce21bf607ba51ef8c125e10e22dffdffec377646462df5f01915ec']
 
+builddependencies = [('binutils', '2.40')]
+
 sanity_check_paths = {
     'files': [
         'lib/libodbc.%s' % SHLIB_EXT,

From 47c962df1a6aad6aaa2a5ca5e0bea08c76383695 Mon Sep 17 00:00:00 2001
From: Samuel Moors <samuel.moors@vub.be>
Date: Wed, 21 Aug 2024 14:02:59 +0200
Subject: [PATCH 667/835] make sure that the mpi runner gets built

---
 .../c/CORSIKA/CORSIKA-77550-foss-2023a.eb     | 20 ++++++++++-------
 .../c/CORSIKA/CORSIKA-77550_fix_include.patch | 22 +++++++++++++++++++
 2 files changed, 34 insertions(+), 8 deletions(-)
 create mode 100644 easybuild/easyconfigs/c/CORSIKA/CORSIKA-77550_fix_include.patch

diff --git a/easybuild/easyconfigs/c/CORSIKA/CORSIKA-77550-foss-2023a.eb b/easybuild/easyconfigs/c/CORSIKA/CORSIKA-77550-foss-2023a.eb
index dc008b79e18..c6f619d9d75 100644
--- a/easybuild/easyconfigs/c/CORSIKA/CORSIKA-77550-foss-2023a.eb
+++ b/easybuild/easyconfigs/c/CORSIKA/CORSIKA-77550-foss-2023a.eb
@@ -14,7 +14,11 @@ toolchainopts = {'usempi': True}
 
 download_instructions = "Sources have to be requested to the developers"
 sources = [SOURCELOWER_TAR_GZ]
-checksums = ['fed74c144e22deb5a7c1d2dc1f04f0100eb2732cb48665a3da49ce471a3775ee']
+patches = ['%(name)s-%(version)s_fix_include.patch']
+checksums = [
+    {'corsika-77550.tar.gz': 'fed74c144e22deb5a7c1d2dc1f04f0100eb2732cb48665a3da49ce471a3775ee'},
+    {'CORSIKA-77550_fix_include.patch': 'e858fc4c1fa33d31d050b2fca50e130c23b2d3e4b81b851af34dc3f39e9c709e'},
+]
 
 dependencies = [
     ("ROOT", "6.30.06"),
@@ -24,22 +28,22 @@ dependencies = [
 parallel = False
 
 # execute ./coconut manually with your own options and extract configure command from top of config.log
+_mpi_opts = "--enable-PARALLEL --with-mpirunner-lib=src/parallel --enable-PARALLELIB "
 configopts = "CORDETECTOR=HORIZONTAL CORTIMELIB=TIMEAUTO CORHEMODEL=QGSJETII CORLEMODEL=URQMD "
 configopts += "--enable-UPWARD --enable-SLANT --enable-THIN --enable-COREAS "
-configopts += "--enable-PARALLEL --with-mpirunner-lib --enable-PARALLELIB "
+configopts += _mpi_opts
 
 build_cmd = "./coconut"
-buildopts = "--batch"
+buildopts = "--batch " + _mpi_opts
 
 install_cmd = ' && '.join([
-    'mkdir -p %(installdir)s/{bin,data}',
-    'mv %(builddir)s/%(namelower)s-%(version)s/run/%(namelower)s%(version)s* %(installdir)s/bin/',
-    'cp %(builddir)s/%(namelower)s-%(version)s/run/* %(installdir)s/data/',
+    'mkdir -p %(installdir)s/bin',
+    'cp %(builddir)s/%(namelower)s-%(version)s/run/* %(installdir)s/bin/',
 ])
 
 sanity_check_paths = {
-    'files': ['bin/corsika77550Linux_QGSII_urqmd_thin_coreas_parallel', 'data/NUCNUCCS'],
-    'dirs': []
+    'files': ['bin/mpi_corsika77550Linux_QGSII_urqmd_thin_coreas_parallel_runner'],
+    'dirs': [],
 }
 
 moduleclass = "phys"
diff --git a/easybuild/easyconfigs/c/CORSIKA/CORSIKA-77550_fix_include.patch b/easybuild/easyconfigs/c/CORSIKA/CORSIKA-77550_fix_include.patch
new file mode 100644
index 00000000000..e7bc3863fae
--- /dev/null
+++ b/easybuild/easyconfigs/c/CORSIKA/CORSIKA-77550_fix_include.patch
@@ -0,0 +1,22 @@
+Move include out of function to avoid error:
+/usr/include/sys/stat.h:453:1: error: nested function ‘stat’ declared ‘extern’
+Author: Samuel Moors (Vrije Universiteit Brussel)
+diff -Nur corsika-77550.orig/src/parallel/mpi_runner.c corsika-77550/src/parallel/mpi_runner.c
+--- corsika-77550.orig/src/parallel/mpi_runner.c	2024-04-18 18:30:39.000000000 +0200
++++ corsika-77550/src/parallel/mpi_runner.c	2024-08-09 16:15:39.969688000 +0200
+@@ -99,6 +99,7 @@
+ #include <stdlib.h>
+ #include <unistd.h>
+ #include "config.h"
++#include <sys/stat.h>
+ 
+ /////////////////////initializing parameters/////////////////// 
+ //the number of data type block in the MPI message
+@@ -1023,7 +1024,6 @@
+               strcpy(str2, strtmp);
+             }
+ 						strcpy(statdir,str2);
+-						#include <sys/stat.h>
+ 						struct stat sb;
+ 						if (stat(statdir, &sb) == 0 && S_ISDIR(sb.st_mode))
+ 						{

From d4c31fa493b87e411027ebeec86ed6931d495375 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Wed, 21 Aug 2024 14:03:36 +0200
Subject: [PATCH 668/835] adding easyconfigs:
 prompt-toolkit-3.0.36-GCCcore-12.3.0.eb

---
 .../prompt-toolkit-3.0.36-GCCcore-12.3.0.eb   | 28 +++++++++++++++++++
 1 file changed, 28 insertions(+)
 create mode 100644 easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-3.0.36-GCCcore-12.3.0.eb

diff --git a/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-3.0.36-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-3.0.36-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..dfcdad173d1
--- /dev/null
+++ b/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-3.0.36-GCCcore-12.3.0.eb
@@ -0,0 +1,28 @@
+easyblock = 'PythonPackage'
+
+name = 'prompt-toolkit'
+version = '3.0.36'
+
+homepage = 'https://github.com/jonathanslenders/python-prompt-toolkit'
+description = """prompt_toolkit is a Python library for building powerful interactive command lines and
+ terminal applications."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+builddependencies = [('binutils', '2.40')]
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('Python-bundle-PyPI', '2023.06'),
+]
+
+sources = ['prompt_toolkit-%(version)s-py3-none-any.whl']
+checksums = ['aa64ad242a462c5ff0363a7b9cfe696c20d55d9fc60c11fd8e632d064804d305']
+
+use_pip = True
+sanity_pip_check = True
+download_dep_fail = True
+
+options = {'modulename': 'prompt_toolkit'}
+
+moduleclass = 'lib'

From 348943ac7e5ecb411410b0e449ef57d3d95c77b7 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Wed, 21 Aug 2024 14:07:00 +0200
Subject: [PATCH 669/835] adding easyconfigs: PyWavelets-1.7.0-foss-2023a.eb

---
 .../PyWavelets/PyWavelets-1.7.0-foss-2023a.eb | 27 +++++++++++++++++++
 1 file changed, 27 insertions(+)
 create mode 100644 easybuild/easyconfigs/p/PyWavelets/PyWavelets-1.7.0-foss-2023a.eb

diff --git a/easybuild/easyconfigs/p/PyWavelets/PyWavelets-1.7.0-foss-2023a.eb b/easybuild/easyconfigs/p/PyWavelets/PyWavelets-1.7.0-foss-2023a.eb
new file mode 100644
index 00000000000..f68a1a2ba06
--- /dev/null
+++ b/easybuild/easyconfigs/p/PyWavelets/PyWavelets-1.7.0-foss-2023a.eb
@@ -0,0 +1,27 @@
+easyblock = 'PythonPackage'
+
+name = 'PyWavelets'
+version = '1.7.0'
+
+homepage = 'https://pywavelets.readthedocs.io'
+description = "PyWavelets is open source wavelet transform software for Python."
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['b47250e5bb853e37db5db423bafc82847f4cde0ffdf7aebb06336a993bc174f6']
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),  # for numpy
+    ('meson-python', '0.13.2'),
+    ('Cython', '3.0.8'),
+]
+
+download_dep_fail = True
+use_pip = True
+sanity_pip_check = True
+
+options = {'modulename': 'pywt'}
+
+moduleclass = 'lib'

From b6b4d9d52ba0f1d786a2b21ee9e7974a67a721c8 Mon Sep 17 00:00:00 2001
From: Samuel Moors <samuel.moors@vub.be>
Date: Wed, 21 Aug 2024 14:54:28 +0200
Subject: [PATCH 670/835] remove Cython dependency from Python-bundle-PyPI

---
 .../c/Cython/Cython-3.0.10-GCCcore-13.3.0.eb  | 40 +++++++++++++++++++
 ...thon-bundle-PyPI-2024.06-GCCcore-13.3.0.eb |  3 --
 2 files changed, 40 insertions(+), 3 deletions(-)
 create mode 100644 easybuild/easyconfigs/c/Cython/Cython-3.0.10-GCCcore-13.3.0.eb

diff --git a/easybuild/easyconfigs/c/Cython/Cython-3.0.10-GCCcore-13.3.0.eb b/easybuild/easyconfigs/c/Cython/Cython-3.0.10-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..c9e419d570a
--- /dev/null
+++ b/easybuild/easyconfigs/c/Cython/Cython-3.0.10-GCCcore-13.3.0.eb
@@ -0,0 +1,40 @@
+easyblock = 'PythonPackage'
+
+name = 'Cython'
+version = '3.0.10'
+
+homepage = 'https://cython.org/'
+description = """
+Cython is an optimising static compiler for both the Python programming
+language and the extended Cython programming language (based on Pyrex).
+"""
+docurls = [
+    'https://cython.org/#documentation',
+    'https://github.com/cython/cython',
+]
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+sources = [SOURCE_TAR_GZ]
+checksums = ['dcc96739331fb854dcf503f94607576cfe8488066c61ca50dfd55836f132de99']
+
+builddependencies = [
+    ('binutils', '2.42'),
+]
+
+dependencies = [
+    ('Python', '3.12.3'),
+]
+
+download_dep_fail = True
+use_pip = True
+sanity_pip_check = True
+
+sanity_check_paths = {
+    'files': ['bin/cygdb', 'bin/cython', 'bin/cythonize'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = ["cython --version"]
+
+moduleclass = 'lang'
diff --git a/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2024.06-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2024.06-GCCcore-13.3.0.eb
index add89b7ae32..01bf9b19b0a 100644
--- a/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2024.06-GCCcore-13.3.0.eb
+++ b/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2024.06-GCCcore-13.3.0.eb
@@ -56,9 +56,6 @@ exts_list = [
     ('pbr', '6.0.0', {
         'checksums': ['d1377122a5a00e2f940ee482999518efe16d745d423a670c27773dfbc3c9a7d9'],
     }),
-    ('Cython', '3.0.10', {
-        'checksums': ['dcc96739331fb854dcf503f94607576cfe8488066c61ca50dfd55836f132de99'],
-    }),
     ('six', '1.16.0', {
         'checksums': ['1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926'],
     }),

From 4c81420765617c74cb9c31e078238ff96e88ef85 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Wed, 21 Aug 2024 15:09:42 +0200
Subject: [PATCH 671/835] adding easyconfigs:
 dorado-0.7.3-foss-2023a-CUDA-12.1.1.eb and patches:
 dorado-0.7.3_include-fstream.patch

---
 .../dorado-0.7.3-foss-2023a-CUDA-12.1.1.eb    | 80 +++++++++++++++++++
 .../dorado/dorado-0.7.3_include-fstream.patch | 27 +++++++
 2 files changed, 107 insertions(+)
 create mode 100644 easybuild/easyconfigs/d/dorado/dorado-0.7.3-foss-2023a-CUDA-12.1.1.eb
 create mode 100644 easybuild/easyconfigs/d/dorado/dorado-0.7.3_include-fstream.patch

diff --git a/easybuild/easyconfigs/d/dorado/dorado-0.7.3-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/d/dorado/dorado-0.7.3-foss-2023a-CUDA-12.1.1.eb
new file mode 100644
index 00000000000..7aa8f29b002
--- /dev/null
+++ b/easybuild/easyconfigs/d/dorado/dorado-0.7.3-foss-2023a-CUDA-12.1.1.eb
@@ -0,0 +1,80 @@
+easyblock = 'CMakeMake'
+
+name = 'dorado'
+version = '0.7.3'
+versionsuffix = '-CUDA-%(cudaver)s'
+
+homepage = 'https://github.com/nanoporetech/dorado'
+description = """Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+toolchainopts = {'usempi': True}
+
+source_urls = ['https://github.com/nanoporetech/dorado/archive/']
+sources = [{
+    'git_config': {
+        'url': 'https://github.com/nanoporetech',
+        'repo_name': name,
+        'tag': 'v%(version)s',
+        'recursive': True,
+    },
+    'filename': SOURCE_TAR_GZ,
+}]
+patches = ['dorado-0.7.3_include-fstream.patch']
+checksums = [
+    None,
+    'a32cbd34185bcc5ae3d552a072e396825aa7184187cd11c70a4380618387a530',
+]
+
+builddependencies = [
+    ('binutils', '2.40'),
+    ('CMake', '3.26.3'),
+]
+
+dependencies = [
+    ('CUDA', '12.1.1', '', SYSTEM),
+    ('OpenSSL', '1.1', '', SYSTEM),
+    ('PyTorch', '2.1.2', '-CUDA-%(cudaver)s'),
+    ('HDF5', '1.14.0'),
+    ('zstd', '1.5.5'),
+    ('HTSlib', '1.18'),
+    ('kineto', '0.4.0'),
+    ('libaec', '1.0.6'),
+]
+
+# don't link to OpenSSL static libraries
+# fix for CMake Error "missing: OPENSSL_CRYPTO_LIBRARY" (if only shared OpenSSL libraries are available)
+preconfigopts = "sed -i '/OPENSSL_USE_STATIC_LIBS TRUE/d' ../dorado/cmake/OpenSSL.cmake && "
+preconfigopts += "export OPENSSL_ROOT_DIR=$EBROOTOPENSSL && "
+# link in the ssl and crypto libs, to fix:
+# undefined reference to symbol 'SSL_get_peer_certificate@@OPENSSL_1_1_0'
+preconfigopts += "sed -i 's/OpenSSL::SSL/ssl\\n    crypto/g' ../dorado/dorado/utils/CMakeLists.txt && "
+
+# don't use vendored HTSlib, use provided HTSlib dependency
+preconfigopts += "rm -r ../dorado/dorado/3rdparty/htslib/ && "
+preconfigopts += "sed -i '/add_dependencies.*htslib_project/d' ../dorado/CMakeLists.txt && "
+preconfigopts += "sed -i '/add_dependencies.*htslib_project/d' ../dorado/dorado/utils/CMakeLists.txt && "
+preconfigopts += "sed -i '/Htslib.cmake/d' ../dorado/CMakeLists.txt && "
+# link with -lhts, not -lhtslib
+preconfigopts += "sed -i 's/htslib/hts/g' ../dorado/CMakeLists.txt && "
+preconfigopts += "sed -i 's/htslib/hts/g' ../dorado/dorado/utils/CMakeLists.txt && "
+
+# disable treating warnings like errors by stripping out -Werror
+# cfr. https://github.com/nanoporetech/dorado/issues/779
+preconfigopts += "sed -i 's/-Werror//g' ../dorado/cmake/Warnings.cmake && "
+
+configopts = "-DDORADO_INSTALL_PATH=%(installdir)s "
+configopts += "-DCUDA_TOOLKIT_ROOT_DIR=$EBROOTCUDA -DCMAKE_CUDA_COMPILER=$EBROOTCUDA/bin/nvcc "
+configopts += "-DDORADO_LIBTORCH_DIR=$EBROOTPYTORCH/lib "
+# add -pthread flag (in addition to -lpthread) to avoid linking error:
+# in function `_GLOBAL__sub_I_mutex.cc': mutex.cc:(.text.startup+0x17): undefined reference to `pthread_atfork'
+configopts += '-DCMAKE_C_FLAGS="$CFLAGS -pthread" '
+
+sanity_check_paths = {
+    'files': ['bin/dorado'],
+    'dirs': [],
+}
+
+sanity_check_commands = ["dorado basecaller --help"]
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/d/dorado/dorado-0.7.3_include-fstream.patch b/easybuild/easyconfigs/d/dorado/dorado-0.7.3_include-fstream.patch
new file mode 100644
index 00000000000..bf8d2346e5d
--- /dev/null
+++ b/easybuild/easyconfigs/d/dorado/dorado-0.7.3_include-fstream.patch
@@ -0,0 +1,27 @@
+add missing include to fix compiler errors like:
+
+    error: variable std::ofstream summary_out has initializer but incomplete type
+
+see also https://github.com/nanoporetech/dorado/pull/780
+
+author: Kenneth Hoste (HPC-UGent)
+--- dorado/dorado/cli/duplex.cpp.orig	2024-04-30 17:59:15.483935823 +0200
++++ dorado/dorado/cli/duplex.cpp	2024-04-30 17:59:34.658694274 +0200
+@@ -39,6 +39,7 @@
+ #include <cstdlib>
+ #include <exception>
+ #include <filesystem>
++#include <fstream>
+ #include <memory>
+ #include <optional>
+ #include <thread>
+--- dorado/dorado/cli/demux.cpp.orig	2024-04-30 18:13:40.327122548 +0200
++++ dorado/dorado/cli/demux.cpp	2024-04-30 18:15:37.576760942 +0200
+@@ -17,6 +17,7 @@
+ #include <spdlog/spdlog.h>
+ 
+ #include <chrono>
++#include <fstream>
+ #include <memory>
+ #include <optional>
+ #include <string>
\ No newline at end of file

From 2332f84a51642464ad4ba8f75ba2f2bad83fa53d Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Wed, 21 Aug 2024 15:16:43 +0200
Subject: [PATCH 672/835] add update for VTK-9.3.0-foss-2023b

---
 easybuild/easyconfigs/v/VTK/VTK-9.3.0-foss-2023b.eb | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/v/VTK/VTK-9.3.0-foss-2023b.eb b/easybuild/easyconfigs/v/VTK/VTK-9.3.0-foss-2023b.eb
index 8a0452f863f..3be42a90bac 100644
--- a/easybuild/easyconfigs/v/VTK/VTK-9.3.0-foss-2023b.eb
+++ b/easybuild/easyconfigs/v/VTK/VTK-9.3.0-foss-2023b.eb
@@ -42,6 +42,7 @@ dependencies = [
     ('XZ', '5.4.4'),
     ('libGLU', '9.0.3'),
     ('X11', '20231019'),
+    ('Qt5', '5.15.13'),
 ]
 
 separate_build_dir = True
@@ -57,7 +58,11 @@ configopts += "-DPython3_INCLUDE_DIR=$EBROOTPYTHON/include/python%(pyshortver)s
 configopts += "-DPython3_LIBRARY=$EBROOTPYTHON/lib/libpython%(pyshortver)s.so "
 # Other
 configopts += "-DVTK_USE_MPI=ON "
-configopts += "-DCMAKE_INSTALL_LIBDIR=lib"
+configopts += "-DCMAKE_INSTALL_LIBDIR=lib "
+configopts += "-DVTK_QT_VERSION=5 "
+configopts += "-DQt5_DIR=$EBROOTQT5 "
+configopts += "-DVTK_MODULE_ENABLE_VTK_GuiSupportQt=YES "
+configopts += "-DVTK_MODULE_ENABLE_VTK_ViewsQt=YES"
 
 preinstallopts = "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && "
 

From bd321869d56abefae3d20dc7fad2596f0272f52d Mon Sep 17 00:00:00 2001
From: Chia-Jung Hsu <appolloford@users.noreply.github.com>
Date: Wed, 21 Aug 2024 15:45:43 +0200
Subject: [PATCH 673/835] Use older pydantic in toolchain

---
 easybuild/easyconfigs/p/PyAEDT/PyAEDT-0.9.9-gfbf-2023b.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/p/PyAEDT/PyAEDT-0.9.9-gfbf-2023b.eb b/easybuild/easyconfigs/p/PyAEDT/PyAEDT-0.9.9-gfbf-2023b.eb
index f3047e4bc6d..f2436367baa 100644
--- a/easybuild/easyconfigs/p/PyAEDT/PyAEDT-0.9.9-gfbf-2023b.eb
+++ b/easybuild/easyconfigs/p/PyAEDT/PyAEDT-0.9.9-gfbf-2023b.eb
@@ -21,7 +21,7 @@ dependencies = [
     ('Python', '3.11.5'),
     ('Python-bundle-PyPI', '2023.10'),
     ('Pillow', '10.2.0'),
-    ('pydantic', '2.7.4'),
+    ('pydantic', '2.6.4'),
     ('SciPy-bundle', '2023.11'),
 ]
 

From e88765c60adaabd6e5dfef7569852a237918492f Mon Sep 17 00:00:00 2001
From: Samuel Moors <samuel.moors@vub.be>
Date: Wed, 21 Aug 2024 15:50:07 +0200
Subject: [PATCH 674/835] add Cython builddep for SciPy-bundle

---
 .../s/SciPy-bundle/SciPy-bundle-2024.05-gfbf-2024.05.eb        | 3 ++-
 .../s/SciPy-bundle/SciPy-bundle-2024.05-gfbf-2024a.eb          | 3 ++-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2024.05-gfbf-2024.05.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2024.05-gfbf-2024.05.eb
index b80b8631909..99d61098d6b 100644
--- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2024.05-gfbf-2024.05.eb
+++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2024.05-gfbf-2024.05.eb
@@ -16,7 +16,8 @@ builddependencies = [
     ('Meson', '1.4.0'),
     ('meson-python', '0.16.0'),
     ('Ninja', '1.12.1'),
-    ('pkgconf', '2.2.0'),   # required by scipy
+    ('pkgconf', '2.2.0'),  # required by scipy
+    ('Cython', '3.0.10'),  # required by numpy and scipy
 ]
 
 dependencies = [
diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2024.05-gfbf-2024a.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2024.05-gfbf-2024a.eb
index cdb7536e15a..2abab977add 100644
--- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2024.05-gfbf-2024a.eb
+++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2024.05-gfbf-2024a.eb
@@ -16,7 +16,8 @@ builddependencies = [
     ('Meson', '1.4.0'),
     ('meson-python', '0.16.0'),
     ('Ninja', '1.12.1'),
-    ('pkgconf', '2.2.0'),   # required by scipy
+    ('pkgconf', '2.2.0'),  # required by scipy
+    ('Cython', '3.0.10'),  # required by numpy and scipy
 ]
 
 dependencies = [

From bcfc68c25cb301df393924397062658972cd807d Mon Sep 17 00:00:00 2001
From: Chia-Jung Hsu <appolloford@gmail.com>
Date: Wed, 21 Aug 2024 14:05:58 +0000
Subject: [PATCH 675/835] adding easyconfigs: SentencePiece-0.2.0-GCC-13.2.0.eb

---
 .../SentencePiece-0.2.0-GCC-13.2.0.eb         | 70 +++++++++++++++++++
 1 file changed, 70 insertions(+)
 create mode 100644 easybuild/easyconfigs/s/SentencePiece/SentencePiece-0.2.0-GCC-13.2.0.eb

diff --git a/easybuild/easyconfigs/s/SentencePiece/SentencePiece-0.2.0-GCC-13.2.0.eb b/easybuild/easyconfigs/s/SentencePiece/SentencePiece-0.2.0-GCC-13.2.0.eb
new file mode 100644
index 00000000000..246989eefdc
--- /dev/null
+++ b/easybuild/easyconfigs/s/SentencePiece/SentencePiece-0.2.0-GCC-13.2.0.eb
@@ -0,0 +1,70 @@
+easyblock = 'Bundle'
+
+name = 'SentencePiece'
+version = '0.2.0'
+
+homepage = 'https://github.com/google/sentencepiece'
+description = "Unsupervised text tokenizer for Neural Network-based text generation."
+github_account = 'google'
+
+toolchain = {'name': 'GCC', 'version': '13.2.0'}
+
+builddependencies = [
+    ('CMake', '3.27.6'),
+    ('pkgconf', '2.0.3'),
+]
+
+dependencies = [
+    ('Python', '3.11.5'),
+    ('gperftools', '2.13'),
+]
+
+default_component_specs = {
+    'source_urls': [GITHUB_LOWER_SOURCE],
+    'sources': ['v%(version)s.tar.gz'],
+    'checksums': ['9970f0a0afee1648890293321665e5b2efa04eaec9f1671fcf8048f456f5bb86'],
+}
+
+local_external_absl = 'sed -i %(builddir)s/'
+
+components = [
+    (name, version, {
+        'easyblock': 'CMakeMake',
+        'separate_build_dir': True,
+        'start_dir': '%(namelower)s-%(version)s',
+        # using internal protobuf there is no matching pc file so requirement is removed:
+        'preconfigopts': 'sed -i s/Requires.private.*// ../sentencepiece-%(version)s/sentencepiece.pc.in &&',
+    }),
+    ('sentencepiece', version, {
+        'easyblock': 'PythonPackage',
+        'start_dir': '%(namelower)s-%(version)s/python',
+        # Unpredicable where pc files end up; including both lib and lib64
+        'prebuildopts': 'export PKG_CONFIG_PATH=%(installdir)s/lib64/pkgconfig:%(installdir)s/lib/pkgconfig/:'
+                        '$PKG_CONFIG_PATH && ',
+        'preinstallopts': 'export PKG_CONFIG_PATH=%(installdir)s/lib64/pkgconfig:%(installdir)s/lib/pkgconfig/:'
+                          '$PKG_CONFIG_PATH && ',
+        'use_pip': True,
+        'download_dep_fail': True,
+        'sanity_pip_check': True,
+    }),
+]
+
+postinstallcmds = ['cp -a %(builddir)s/%(namelower)s-%(version)s/{data,doc} %(installdir)s/']
+
+sanity_check_paths = {
+    'files': ['bin/spm_%s' % x for x in ['decode', 'encode', 'export_vocab', 'normalize', 'train']] +
+             ['lib/libsentencepiece.%s' % SHLIB_EXT, 'lib/libsentencepiece_train.%s' % SHLIB_EXT] +
+             ['include/sentencepiece_processor.h', 'include/sentencepiece_trainer.h'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages', 'data', 'doc'],
+}
+
+sanity_check_commands = [
+    'spm_train --help | grep accept_language',  # --help has exit code 1, so we check for output text
+    "python -c 'import sentencepiece'",
+]
+
+modextrapaths = {
+    'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']
+}
+
+moduleclass = 'lib'

From 99abe91b43c1ae70d89f8c8d2a737b710ad1565f Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 21 Aug 2024 15:55:44 +0200
Subject: [PATCH 676/835] add missing ihm + modelcif extensions required by
 AlphaPullDown script convert_to_modelcif.py

---
 .../AlphaPulldown/AlphaPulldown-2.0.0b4-foss-2022a.eb | 11 ++++++++++-
 1 file changed, 10 insertions(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b4-foss-2022a.eb b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b4-foss-2022a.eb
index f41935fe51d..f410c438e23 100644
--- a/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b4-foss-2022a.eb
+++ b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b4-foss-2022a.eb
@@ -61,6 +61,12 @@ exts_list = [
         'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}],
         'checksums': ['88b9a77e50655f89d0eb2075093773e82c27a4cef842cb7d735c877b20cd39fb'],
     }),
+    ('ihm', '1.3', {
+        'checksums': ['09f69809fd81509cc26b60253c55b02ce79fc01fc8f4a068bca2953a7dfd33be'],
+    }),
+    ('modelcif', '1.0', {
+        'checksums': ['e8375bc502a73dcfab0b7fbdd454d67d393bbb8969981eb52199d77192a3de56'],
+    }),
     (name, version, {
         'sources': [{
             'filename': SOURCE_TAR_GZ,
@@ -90,6 +96,9 @@ sanity_check_paths = {
     'dirs': ['lib/python%(pyshortver)s/site-packages/alphapulldown'],
 }
 
-sanity_check_commands = ["run_multimer_jobs.py --help | grep 'A script to perform structure prediction'"]
+sanity_check_commands = [
+    "run_multimer_jobs.py --help | grep 'A script to perform structure prediction'",
+    "convert_to_modelcif.py --help | grep 'turn it into a ModelCIF'",
+]
 
 moduleclass = 'bio'

From 0b9a9b0395684ade46324441b891c5216518d515 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 21 Aug 2024 16:27:03 +0200
Subject: [PATCH 677/835] add missing ihm + modelcif extensions required by
 AlphaPullDown script convert_to_modelcif.py

---
 .../AlphaPulldown-2.0.0b4-foss-2022a-CUDA-11.7.0.eb   | 11 ++++++++++-
 1 file changed, 10 insertions(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b4-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b4-foss-2022a-CUDA-11.7.0.eb
index 72746293174..492a787c919 100644
--- a/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b4-foss-2022a-CUDA-11.7.0.eb
+++ b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b4-foss-2022a-CUDA-11.7.0.eb
@@ -63,6 +63,12 @@ exts_list = [
         'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}],
         'checksums': ['88b9a77e50655f89d0eb2075093773e82c27a4cef842cb7d735c877b20cd39fb'],
     }),
+    ('ihm', '1.3', {
+        'checksums': ['09f69809fd81509cc26b60253c55b02ce79fc01fc8f4a068bca2953a7dfd33be'],
+    }),
+    ('modelcif', '1.0', {
+        'checksums': ['e8375bc502a73dcfab0b7fbdd454d67d393bbb8969981eb52199d77192a3de56'],
+    }),
     (name, version, {
         'sources': [{
             'filename': SOURCE_TAR_GZ,
@@ -92,6 +98,9 @@ sanity_check_paths = {
     'dirs': ['lib/python%(pyshortver)s/site-packages/alphapulldown'],
 }
 
-sanity_check_commands = ["run_multimer_jobs.py --help | grep 'A script to perform structure prediction'"]
+sanity_check_commands = [
+    "run_multimer_jobs.py --help | grep 'A script to perform structure prediction'",
+    "convert_to_modelcif.py --help | grep 'turn it into a ModelCIF'",
+]
 
 moduleclass = 'bio'

From bed9e08628997e5c4d7357992cf75c1e8da6a20b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Petr=20Kr=C3=A1l?= <petr@inuits.eu>
Date: Wed, 21 Aug 2024 17:16:35 +0200
Subject: [PATCH 678/835] update version, add patch file

---
 ...=> PEcAn-1.8.0.9000-foss-2023a-R-4.3.2.eb} | 69 +++++++++----------
 .../p/PEcAn/PEcAn-1.8.0.9000_duckdb.patch     | 16 +++++
 2 files changed, 50 insertions(+), 35 deletions(-)
 rename easybuild/easyconfigs/p/PEcAn/{PEcAn-1.7.2.9000-foss-2023a-R-4.3.2.eb => PEcAn-1.8.0.9000-foss-2023a-R-4.3.2.eb} (72%)
 create mode 100644 easybuild/easyconfigs/p/PEcAn/PEcAn-1.8.0.9000_duckdb.patch

diff --git a/easybuild/easyconfigs/p/PEcAn/PEcAn-1.7.2.9000-foss-2023a-R-4.3.2.eb b/easybuild/easyconfigs/p/PEcAn/PEcAn-1.8.0.9000-foss-2023a-R-4.3.2.eb
similarity index 72%
rename from easybuild/easyconfigs/p/PEcAn/PEcAn-1.7.2.9000-foss-2023a-R-4.3.2.eb
rename to easybuild/easyconfigs/p/PEcAn/PEcAn-1.8.0.9000-foss-2023a-R-4.3.2.eb
index 163a41f725f..b5747815246 100644
--- a/easybuild/easyconfigs/p/PEcAn/PEcAn-1.7.2.9000-foss-2023a-R-4.3.2.eb
+++ b/easybuild/easyconfigs/p/PEcAn/PEcAn-1.8.0.9000-foss-2023a-R-4.3.2.eb
@@ -1,7 +1,7 @@
 easyblock = 'Bundle'
 
 name = 'PEcAn'
-version = '1.7.2.9000'
+version = '1.8.0.9000'
 versionsuffix = '-R-%(rver)s'
 
 homepage = 'https://github.com/PecanProject/pecan'
@@ -35,36 +35,33 @@ exts_default_options = {
     ],
 }
 
-local_sed_patterns_duckdb = '1146s/prefix_front_/prefix_front_back.prefix_front_/g;'
-local_sed_patterns_duckdb += '1147s/prefix_back_/prefix_front_back.prefix_back_/g'
-
 exts_list = [
-    ('PEcAn.logger', '1.8.1.9000', {
-        'checksums': ['3d1d8a6c9afa677dde8a4aaf72809932f0b6b5385ae4a6fc2059b48ed4b09195'],
+    ('PEcAn.logger', '1.8.2.9000', {
+        'checksums': ['1092f72fa63d58d83ca939a06bfa51ad3b3b4cd94ca4e68202cdb08fd3ada099'],
     }),
-    ('PEcAn.remote', '1.7.2', {
-        'checksums': ['59feda08ac6784c5e607a70166e002df96385efbba3b77148b4cf9a0a1e2c9dc'],
+    ('PEcAn.remote', version, {
+        'checksums': ['b3c7208c85d37aa6c12ca99182262a9886e57e2591faefd909232b8c89111b20'],
     }),
-    ('PEcAn.utils', '1.7.2', {
-        'checksums': ['d83ae2a605f7867659d10de952f5db6b947dc3d2bc05633c0f72ced0b4caad17'],
+    ('PEcAn.utils', version, {
+        'checksums': ['524c3231a21a1e5fc48ebc53d17e49c82f018b87c274095cd0362103fe322ec5'],
     }),
     ('PEcAn.DB', version, {
-        'checksums': ['f493d6ab100fce139bdb9747c91faff5cf60ff296ee16a82c6bc2366a9722231'],
+        'checksums': ['9b7e9b40a07879c1265d9ab6087b7448dfd34c3601c64ddcb41511c97399fece'],
     }),
-    ('PEcAn.settings', '1.7.2', {
-        'checksums': ['ab0dd41e9f421a84e68a16a1e4b290f70d852d23e66a2de1c3e91bf883aa1aeb'],
+    ('PEcAn.settings', version, {
+        'checksums': ['555a7d81eec7e97b8457cef51888087af6b5d7d07f527ca58cbab07ed847fabc'],
     }),
-    ('PEcAn.MA', '1.7.2', {
-        'checksums': ['bf3a5b6ac8adce4efb6be504cdeb10a71a59b3ac5af72c8d77b59a39c7d90ceb'],
+    ('PEcAn.MA', '1.7.3.9000', {
+        'checksums': ['680290e0ee52526db1242d95c4ca06a1e0ad117337ff721d79387797bc7e40ed'],
     }),
     ('PEcAn.emulator', version, {
-        'checksums': ['f4465a154e41cfe5a2cc94035ae4a5ddbfd3b5fc54a83bc9578c98a9eb07cff1'],
+        'checksums': ['68944ebdf1f37ff84f9b09bf02c709de9eda823728bbdea073a36d7ef19cfb9c'],
     }),
-    ('PEcAn.priors', '1.7.2', {
-        'checksums': ['001c26275ef23dda369fa2a5b408e481265d29137edeaebd03a30a39b4682edd'],
+    ('PEcAn.priors', '1.7.3.9000', {
+        'checksums': ['e942a31ae02af61b1b8e36d1c5df58f39829b3d0c29421edc151f2f063ff4c1f'],
     }),
     ('PEcAn.uncertainty', version, {
-        'checksums': ['a0d1a3a3d65e06b066d23473def763f5e158b2356ee5fe9e09020fe311e9ef4a'],
+        'checksums': ['65e392536e17e1de2bf8f66c2cd8f46fcb26dcb3294acf0132551b6736722196'],
     }),
     ('amerifluxr', '1.0.0', {
         'checksums': ['ec54dce4b8e4108832eaadb60f7ef8ad28b459d3381316537492dcd755d83b25'],
@@ -90,8 +87,8 @@ exts_list = [
     ('nneo', '0.1.0', {
         'checksums': ['ca503e78cf4f4c85de6e18ad3ffde0c08d6a507ff5dc5ff91a50b3e04bf84a49'],
     }),
-    ('PEcAn.data.atmosphere', '1.7.2', {
-        'checksums': ['1847151588f669e91b35de637c804328efbc606141bf992bee650fd261b70e5a'],
+    ('PEcAn.data.atmosphere', version, {
+        'checksums': ['28fb884cdeeff6405252352a261c3a884ad33202e556e88cee262aba96e1aea4'],
     }),
     ('redland', '1.0.17-18', {
         'checksums': ['e999ba22321733df7ed056f528e38fc4be535d36bbac8106395c14f9f60a75a0'],
@@ -112,9 +109,11 @@ exts_list = [
         'checksums': ['99802d8c8471ce351403f8428c1efab48ccf20f359fbd368db84f25ef8f7ecae'],
     }),
     ('duckdb', '1.0.0-2', {
-        'checksums': ['3735d51f22d62a7411aa514142cd569ce28bdaec4eb58d5f0893a476b9ccbf01'],
-        # fixes the `prefix_back_ was not declared` error, see https://github.com/duckdb/duckdb/pull/12344
-        'preinstallopts': "sed -i '%s' src/duckdb/third_party/re2/re2/prog.cc && " % local_sed_patterns_duckdb,
+        'patches': ['PEcAn-1.8.0.9000_duckdb.patch'],
+        'checksums': [
+            {'duckdb_1.0.0-2.tar.gz': '3735d51f22d62a7411aa514142cd569ce28bdaec4eb58d5f0893a476b9ccbf01'},
+            {'PEcAn-1.8.0.9000_duckdb.patch': 'fb47b668b23e6c9274ce5365725af71e56f2d99771efdd343dc4283f68ab0c21'},
+        ],
     }),
     ('duckdbfs', '0.0.4', {
         'checksums': ['90b2aff2bdefff1db4f855e2a9c9b19a404f522027105424aebd3c7e45944334'],
@@ -176,20 +175,20 @@ exts_list = [
     ('SimilarityMeasures', '1.4', {
         'checksums': ['b26bbc3a402d21f030cc8e4ff6baca644eb4c63a4fb33423dbc9436229a393f0'],
     }),
-    ('PEcAn.benchmark', '1.7.2', {
-        'checksums': ['c9cf9f299f810e4962476db1afdf6a39de77806fd82b6cb8bb7321e96c350db8'],
+    ('PEcAn.benchmark', '1.7.3.9000', {
+        'checksums': ['2e8b285869b4df148228cdde5de44a67dfe0b584b2a7cd614280134259e33ed4'],
     }),
-    ('PEcAn.visualization', '1.7.2', {
-        'checksums': ['5d25871d57ded42c7ae7f8dbf0a6907c8b828f6a0463286e6ae178b356a4a848'],
+    ('PEcAn.visualization', version, {
+        'checksums': ['f77dcb756871a419a85e46cde4a1fb0a1993c29cce8578255d5a46db722ece43'],
     }),
     ('PEcAn.data.land', version, {
-        'checksums': ['29ed015c1e8a5b993aebc31559aa3f7a4136b1f23e4c13a2d55118e7c541da2f'],
+        'checksums': ['19c572e95c11362f4714d9c3d9cc7b2d17c2e3a34513c7ed629e7bdb99bdd0ec'],
     }),
     ('MODISTools', '1.1.5', {
         'checksums': ['0a6b3762865424e299e1a5ec28de78b8dcca3f673e61f42a37dae19ed78db3e3'],
     }),
     ('PEcAn.data.remote', version, {
-        'checksums': ['691b9e27cf5afb6bfb32873cca6ba284d0ff303873695e86f7653432aa7c66d4'],
+        'checksums': ['c097d9395d9dbb6c123f404525cae7fdb1a99b142b32c1a40b0143060444e184'],
     }),
     ('SparseGrid', '0.8.2', {
         'checksums': ['1d84ae83db2a390b111589a10570d55b378c2dd3310d3bc588a94ab8845cfd14'],
@@ -197,14 +196,14 @@ exts_list = [
     ('lqmm', '1.5.8', {
         'checksums': ['11eddeeeed6b9d3190a80a3b3cc3d64519c6e9cb208746a3736139340df691fb'],
     }),
-    ('PEcAn.workflow', '1.7.2', {
-        'checksums': ['cdd60bf6a99b20aed9792b0cf6648c3f55f4b9bd3a00fd0187b7e7ec56815f0f'],
+    ('PEcAn.workflow', version, {
+        'checksums': ['91a1849c040089da1088c02469b973a5f301a419237db7c840fe4ca2922f4b9d'],
     }),
     ('PEcAn.assim.batch', version, {
-        'checksums': ['d57b7ce1b0cbef0183bcb689f55f0345575289f1b8741c00cbd026eeaea8a6b9'],
+        'checksums': ['a1403a5a4591791e37e7e48ca9e9d49f66f4270757711b68b72fd38aadd411cb'],
     }),
-    ('%(name)s.all', version, {
-        'checksums': ['43e036ab8af9834ae6d7d7f4304adfc6cef08348e3be39ca5e51dcbb1fe21cce'],
+    ('PEcAn.all', version, {
+        'checksums': ['6fe594fb890b5680977d1bf58232b941c6d522456e7803e3dc9c4418b92db737'],
     }),
 ]
 
diff --git a/easybuild/easyconfigs/p/PEcAn/PEcAn-1.8.0.9000_duckdb.patch b/easybuild/easyconfigs/p/PEcAn/PEcAn-1.8.0.9000_duckdb.patch
new file mode 100644
index 00000000000..940992bf5ba
--- /dev/null
+++ b/easybuild/easyconfigs/p/PEcAn/PEcAn-1.8.0.9000_duckdb.patch
@@ -0,0 +1,16 @@
+Fixes the `prefix_back_ was not declared` error, see https://github.com/duckdb/duckdb/pull/12344
+Source: https://patch-diff.githubusercontent.com/raw/duckdb/duckdb/pull/12344.diff
+diff -u src/duckdb/third_party/re2/re2/prog.cc.orig src/duckdb/third_party/re2/re2/prog.cc
+--- src/duckdb/third_party/re2/re2/prog.cc.orig	2024-07-19 14:46:13.000000000 +0200
++++ src/duckdb/third_party/re2/re2/prog.cc	2024-08-21 15:51:17.394266979 +0200
+@@ -1143,8 +1143,8 @@
+     const __m256i* bp = reinterpret_cast<const __m256i*>(
+         reinterpret_cast<const char*>(data) + prefix_size_-1);
+     const __m256i* endfp = fp + size/sizeof(__m256i);
+-    const __m256i f_set1 = _mm256_set1_epi8(prefix_front_);
+-    const __m256i b_set1 = _mm256_set1_epi8(prefix_back_);
++    const __m256i f_set1 = _mm256_set1_epi8(prefix_front_back.prefix_front_);
++    const __m256i b_set1 = _mm256_set1_epi8(prefix_front_back.prefix_back_);
+     do {
+       const __m256i f_loadu = _mm256_loadu_si256(fp++);
+       const __m256i b_loadu = _mm256_loadu_si256(bp++);

From 16a9662913d59e80baf7185a2d893047dc39a85c Mon Sep 17 00:00:00 2001
From: software <software@easybuild-el8.cloud.in.bmrc.ox.ac.uk>
Date: Wed, 21 Aug 2024 15:42:17 +0000
Subject: [PATCH 679/835] adding easyconfigs:
 inferCNV-1.21.0-foss-2023a-R-4.3.2.eb

---
 .../inferCNV-1.21.0-foss-2023a-R-4.3.2.eb     | 59 +++++++++++++++++++
 1 file changed, 59 insertions(+)
 create mode 100644 easybuild/easyconfigs/i/inferCNV/inferCNV-1.21.0-foss-2023a-R-4.3.2.eb

diff --git a/easybuild/easyconfigs/i/inferCNV/inferCNV-1.21.0-foss-2023a-R-4.3.2.eb b/easybuild/easyconfigs/i/inferCNV/inferCNV-1.21.0-foss-2023a-R-4.3.2.eb
new file mode 100644
index 00000000000..7404bfe1502
--- /dev/null
+++ b/easybuild/easyconfigs/i/inferCNV/inferCNV-1.21.0-foss-2023a-R-4.3.2.eb
@@ -0,0 +1,59 @@
+easyblock = 'Bundle'
+
+name = 'inferCNV'
+version = '1.21.0'
+versionsuffix = '-R-%(rver)s'
+local_biocver = '3.18'
+local_commit = '124eec089e5d9ab5a2a2352461d03db6cdcf0ea0'
+github_account = 'broadinstitute'
+
+homepage = 'https://github.com/broadinstitute/inferCNV/wiki'
+description = """InferCNV is used to explore tumor single cell RNA-Seq data to identify evidence
+ for somatic large-scale chromosomal copy number alterations, such as gains or
+ deletions of entire chromosomes or large segments of chromosomes."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('R', '4.3.2'),
+    ('R-bundle-Bioconductor', local_biocver, '-R-%(rver)s'),
+    ('rjags', '4-15', '-R-%(rver)s'),
+]
+
+exts_default_options = {
+    'source_urls': [
+        'https://bioconductor.org/packages/release/bioc/src/contrib/',  # current version of packages
+        'https://bioconductor.org/packages/%s/bioc/src/contrib/' % local_biocver,
+        'https://bioconductor.org/packages/%s/bioc/src/contrib/Archive/%%(name)s' % local_biocver,
+        'https://bioconductor.org/packages/%s/data/annotation/src/contrib/' % local_biocver,
+        'https://bioconductor.org/packages/%s/data/experiment/src/contrib/' % local_biocver,
+        'https://cran.r-project.org/src/contrib/Archive/%(name)s',  # package archive
+        'https://cran.r-project.org/src/contrib/',  # current version of packages
+        'https://cran.freestatistics.org/src/contrib',  # mirror alternative for current packages
+    ],
+    'source_tmpl': '%(name)s_%(version)s.tar.gz'
+}
+
+exts_defaultclass = 'RPackage'
+
+exts_list = [
+    ('phyclust', '0.1-34', {
+        'checksums': ['d2047030e9f24c5dc8bbb378867fbcb8e71d1f1c2ab77e9285f79f670568f5f3'],
+    }),
+    (name, version, {
+        'modulename': '%(namelower)s',
+        'source_urls': ['https://github.com/%(github_account)s/%(name)s/archive'],
+        'sources': [{'download_filename': '%s.tar.gz' % local_commit, 'filename': '%(name)s-%(version)s.tar.gz'}],
+        'checksums': ['c8886c0a7c292e28a5fb0acaab3ae00eb2b3906aa0a1d146d5931819a37daefb'],
+    }),
+]
+
+modextrapaths = {'R_LIBS_SITE': ''}
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['infercnv'],
+}
+
+moduleclass = 'bio'

From 56cc7623ce00e3c0e661015f0a9c3397a81ffc70 Mon Sep 17 00:00:00 2001
From: Sebastian Achilles <s.achilles@fz-juelich.de>
Date: Thu, 22 Aug 2024 11:35:18 +0200
Subject: [PATCH 680/835] adding easyconfigs: FFmpeg-7.0.2-GCCcore-13.3.0.eb,
 FriBidi-1.0.15-GCCcore-13.3.0.eb, ffnvcodec-12.2.72.0.eb,
 LAME-3.100-GCCcore-13.3.0.eb, SDL2-2.30.6-GCCcore-13.3.0.eb,
 x264-20240513-GCCcore-13.3.0.eb, x265-3.6-GCCcore-13.3.0.eb,
 Yasm-1.3.0-GCCcore-13.3.0.eb

---
 .../f/FFmpeg/FFmpeg-7.0.2-GCCcore-13.3.0.eb   | 45 +++++++++++++++++++
 .../FriBidi/FriBidi-1.0.15-GCCcore-13.3.0.eb  | 30 +++++++++++++
 .../f/ffnvcodec/ffnvcodec-12.2.72.0.eb        | 32 +++++++++++++
 .../l/LAME/LAME-3.100-GCCcore-13.3.0.eb       | 36 +++++++++++++++
 .../s/SDL2/SDL2-2.30.6-GCCcore-13.3.0.eb      | 26 +++++++++++
 .../x/x264/x264-20240513-GCCcore-13.3.0.eb    | 33 ++++++++++++++
 .../x/x265/x265-3.6-GCCcore-13.3.0.eb         | 34 ++++++++++++++
 .../y/Yasm/Yasm-1.3.0-GCCcore-13.3.0.eb       | 24 ++++++++++
 8 files changed, 260 insertions(+)
 create mode 100644 easybuild/easyconfigs/f/FFmpeg/FFmpeg-7.0.2-GCCcore-13.3.0.eb
 create mode 100644 easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.15-GCCcore-13.3.0.eb
 create mode 100644 easybuild/easyconfigs/f/ffnvcodec/ffnvcodec-12.2.72.0.eb
 create mode 100644 easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-13.3.0.eb
 create mode 100644 easybuild/easyconfigs/s/SDL2/SDL2-2.30.6-GCCcore-13.3.0.eb
 create mode 100644 easybuild/easyconfigs/x/x264/x264-20240513-GCCcore-13.3.0.eb
 create mode 100644 easybuild/easyconfigs/x/x265/x265-3.6-GCCcore-13.3.0.eb
 create mode 100644 easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-13.3.0.eb

diff --git a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-7.0.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-7.0.2-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..246a8306b76
--- /dev/null
+++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-7.0.2-GCCcore-13.3.0.eb
@@ -0,0 +1,45 @@
+easyblock = 'ConfigureMake'
+
+name = 'FFmpeg'
+version = '7.0.2'
+
+homepage = 'https://www.ffmpeg.org/'
+description = "A complete, cross-platform solution to record, convert and stream audio and video."
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+source_urls = ['https://%(namelower)s.org/releases/']
+sources = [SOURCELOWER_TAR_BZ2]
+checksums = ['1ed250407ea8f955cca2f1139da3229fbc13032a0802e4b744be195865ff1541']
+
+builddependencies = [
+    ('binutils', '2.42'),
+    ('pkgconf', '2.2.0'),
+    ('ffnvcodec', '12.2.72.0', '', SYSTEM),  # optional nvenc/dec support
+]
+dependencies = [
+    ('NASM', '2.16.03'),
+    ('zlib', '1.3.1'),
+    ('bzip2', '1.0.8'),
+    ('x264', '20240513'),
+    ('LAME', '3.100'),
+    ('x265', '3.6'),
+    ('X11', '20240607'),
+    ('freetype', '2.13.2'),
+    ('fontconfig', '2.15.0'),
+    ('FriBidi', '1.0.15'),
+    ('SDL2', '2.30.6'),
+]
+
+configopts = '--enable-pic --enable-shared --enable-gpl --enable-version3 --enable-nonfree --cc="$CC" --cxx="$CXX" '
+configopts += '--enable-libx264 --enable-libx265 --enable-libmp3lame --enable-libfreetype --enable-fontconfig '
+configopts += '--enable-libfribidi --enable-sdl2 --disable-htmlpages'
+
+sanity_check_paths = {
+    'files': ['bin/ff%s' % x for x in ['mpeg', 'probe', 'play']] +
+             ['lib/lib%s.%s' % (x, y) for x in ['avdevice', 'avfilter', 'avformat', 'avcodec', 'postproc',
+                                                'swresample', 'swscale', 'avutil'] for y in [SHLIB_EXT, 'a']],
+    'dirs': ['include']
+}
+
+moduleclass = 'vis'
diff --git a/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.15-GCCcore-13.3.0.eb b/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.15-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..a31f21a37dd
--- /dev/null
+++ b/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.15-GCCcore-13.3.0.eb
@@ -0,0 +1,30 @@
+easyblock = 'ConfigureMake'
+
+name = 'FriBidi'
+version = '1.0.15'
+
+homepage = 'https://github.com/fribidi/fribidi'
+
+description = """
+ The Free Implementation of the Unicode Bidirectional Algorithm.
+"""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+source_urls = ['https://github.com/fribidi/fribidi/releases/download/v%(version)s']
+sources = [SOURCELOWER_TAR_XZ]
+checksums = ['0bbc7ff633bfa208ae32d7e369cf5a7d20d5d2557a0b067c9aa98bcbf9967587']
+
+builddependencies = [
+    ('binutils', '2.42'),
+    ('pkgconf', '2.2.0'),
+    ('Autotools', '20231222'),
+]
+
+sanity_check_paths = {
+    'files': ['bin/%(namelower)s', 'include/%(namelower)s/%(namelower)s.h',
+              'lib/lib%%(namelower)s.%s' % SHLIB_EXT],
+    'dirs': []
+}
+
+moduleclass = 'lang'
diff --git a/easybuild/easyconfigs/f/ffnvcodec/ffnvcodec-12.2.72.0.eb b/easybuild/easyconfigs/f/ffnvcodec/ffnvcodec-12.2.72.0.eb
new file mode 100644
index 00000000000..cc4461c3a8b
--- /dev/null
+++ b/easybuild/easyconfigs/f/ffnvcodec/ffnvcodec-12.2.72.0.eb
@@ -0,0 +1,32 @@
+easyblock = 'ConfigureMake'
+
+name = 'ffnvcodec'
+version = '12.2.72.0'
+
+homepage = 'https://git.videolan.org/?p=ffmpeg/nv-codec-headers.git'
+
+description = """FFmpeg nvidia headers. Adds support for nvenc and nvdec. Requires Nvidia GPU and drivers to be present
+(picked up dynamically)."""
+
+toolchain = SYSTEM
+
+sources = [{
+    'git_config': {
+        'url': 'https://git.videolan.org/git/ffmpeg/',
+        'repo_name': 'nv-codec-headers',
+        'tag': 'n%(version)s',
+    },
+    'filename': SOURCE_TAR_GZ,
+}]
+checksums = [None]
+
+skipsteps = ['configure']
+
+preinstallopts = 'sed -i "s|PREFIX =.*|PREFIX ?= %(installdir)s|" Makefile && '
+
+sanity_check_paths = {
+    'files': ['include/ffnvcodec/nvEncodeAPI.h', 'lib/pkgconfig/ffnvcodec.pc'],
+    'dirs': [],
+}
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..c4080545d5b
--- /dev/null
+++ b/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-13.3.0.eb
@@ -0,0 +1,36 @@
+easyblock = 'ConfigureMake'
+
+name = 'LAME'
+version = '3.100'
+
+homepage = 'http://lame.sourceforge.net/'
+description = """LAME is a high quality MPEG Audio Layer III (MP3) encoder licensed under the LGPL."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+source_urls = ['https://sourceforge.net/projects/lame/files/lame/%(version_major_minor)s/']
+sources = [SOURCELOWER_TAR_GZ]
+patches = ['LAME-3.99.5_check-tgetent.patch']
+checksums = [
+    'ddfe36cab873794038ae2c1210557ad34857a4b6bdc515785d1da9e175b1da1e',  # lame-3.100.tar.gz
+    '8bfb6a73f2db1511baf90fbd7174f11043ec4b592a4917edc30ccfb53bf37256',  # LAME-3.99.5_check-tgetent.patch
+]
+
+builddependencies = [
+    ('binutils', '2.42'),
+    ('Autotools', '20231222'),
+]
+
+dependencies = [('ncurses', '6.5')]
+
+preconfigopts = "autoconf && "
+
+# configure is broken: add workaround to find libncurses...
+configure_cmd_prefix = "FRONTEND_LDADD='-L${EBROOTNCURSES}/lib' "
+
+sanity_check_paths = {
+    'files': ['bin/lame', 'include/lame/lame.h', 'lib/libmp3lame.%s' % SHLIB_EXT],
+    'dirs': [],
+}
+
+moduleclass = 'data'
diff --git a/easybuild/easyconfigs/s/SDL2/SDL2-2.30.6-GCCcore-13.3.0.eb b/easybuild/easyconfigs/s/SDL2/SDL2-2.30.6-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..1c8130b397c
--- /dev/null
+++ b/easybuild/easyconfigs/s/SDL2/SDL2-2.30.6-GCCcore-13.3.0.eb
@@ -0,0 +1,26 @@
+easyblock = 'ConfigureMake'
+
+name = 'SDL2'
+version = '2.30.6'
+
+homepage = 'https://www.libsdl.org/'
+description = "SDL: Simple DirectMedia Layer, a cross-platform multimedia library"
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+source_urls = ['https://www.libsdl.org/release/']
+sources = [SOURCE_TAR_GZ]
+checksums = ['c6ef64ca18a19d13df6eb22df9aff19fb0db65610a74cc81dae33a82235cacd4']
+
+builddependencies = [('binutils', '2.42')]
+
+dependencies = [
+    ('X11', '20240607'),
+]
+
+sanity_check_paths = {
+    'files': ['bin/sdl2-config', 'lib/libSDL2.%s' % SHLIB_EXT],
+    'dirs': [],
+}
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/x/x264/x264-20240513-GCCcore-13.3.0.eb b/easybuild/easyconfigs/x/x264/x264-20240513-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..a2a4cccf421
--- /dev/null
+++ b/easybuild/easyconfigs/x/x264/x264-20240513-GCCcore-13.3.0.eb
@@ -0,0 +1,33 @@
+easyblock = 'ConfigureMake'
+
+name = 'x264'
+version = '20240513'
+
+homepage = 'https://www.videolan.org/developers/x264.html'
+description = """
+ x264 is a free software library and application for encoding video streams
+ into the H.264/MPEG-4 AVC compression format, and is released under the
+ terms of the GNU GPL.
+"""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+source_urls = ['https://code.videolan.org/videolan/%(name)s/-/archive/31e19f92/']
+sources = [{'download_filename': '%(name)s-4613ac3c.tar.gz', 'filename': SOURCE_TAR_GZ}]
+checksums = ['cf7e66bd0a75f3baba3502b58c80ee388b3d80a9a01be806337dd2214b8a290e']
+
+builddependencies = [
+    ('binutils', '2.42'),
+    ('pkgconf', '2.2.0'),
+    ('NASM', '2.16.03'),
+]
+
+configopts = " --enable-shared --enable-static --disable-bashcompletion"
+
+
+sanity_check_paths = {
+    'files': ['bin/%(name)s', 'include/x264_config.h', 'include/%(name)s.h', 'lib/libx264.a', 'lib/libx264.so'],
+    'dirs': [],
+}
+
+moduleclass = 'vis'
diff --git a/easybuild/easyconfigs/x/x265/x265-3.6-GCCcore-13.3.0.eb b/easybuild/easyconfigs/x/x265/x265-3.6-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..307c0abb034
--- /dev/null
+++ b/easybuild/easyconfigs/x/x265/x265-3.6-GCCcore-13.3.0.eb
@@ -0,0 +1,34 @@
+easyblock = 'CMakeMake'
+
+name = 'x265'
+version = '3.6'
+
+homepage = 'https://x265.org/'
+description = """
+ x265 is a free software library and application for encoding video streams
+ into the H.265 AVC compression format, and is released under the terms of
+ the GNU GPL.
+"""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+source_urls = ['https://bitbucket.org/multicoreware/x265_git/downloads/']
+sources = ['%(name)s_%(version)s.tar.gz']
+checksums = ['663531f341c5389f460d730e62e10a4fcca3428ca2ca109693867bc5fe2e2807']
+
+builddependencies = [
+    ('binutils', '2.42'),
+    ('CMake', '3.29.3'),
+    ('Yasm', '1.3.0'),
+]
+
+configopts = '-DGIT_ARCHETYPE=1'
+
+start_dir = 'source'
+
+sanity_check_paths = {
+    'files': ['bin/%(name)s', 'include/x265_config.h', 'include/%(name)s.h', 'lib/libx265.a', 'lib/libx265.so'],
+    'dirs': [],
+}
+
+moduleclass = 'vis'
diff --git a/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..5ac8fd8176f
--- /dev/null
+++ b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-13.3.0.eb
@@ -0,0 +1,24 @@
+easyblock = 'ConfigureMake'
+
+name = 'Yasm'
+version = '1.3.0'
+
+homepage = 'https://www.tortall.net/projects/yasm/'
+description = "Yasm: Complete rewrite of the NASM assembler with BSD license"
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+source_urls = ['https://github.com/%(namelower)s/%(namelower)s/releases/download/v%(version)s/']
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['3dce6601b495f5b3d45b59f7d2492a340ee7e84b5beca17e48f862502bd5603f']
+
+builddependencies = [
+    ('binutils', '2.42'),
+]
+
+sanity_check_paths = {
+    'files': ['bin/%(namelower)s'],
+    'dirs': [],
+}
+
+moduleclass = 'lang'

From 7f53d3821898b994d5cb2255b23f9aafe0da8493 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 22 Aug 2024 14:33:03 +0200
Subject: [PATCH 681/835] adding easyconfigs: spektral-1.2.0-fosscuda-2020b.eb

---
 .../spektral/spektral-1.2.0-fosscuda-2020b.eb | 31 +++++++++++++++++++
 1 file changed, 31 insertions(+)
 create mode 100644 easybuild/easyconfigs/s/spektral/spektral-1.2.0-fosscuda-2020b.eb

diff --git a/easybuild/easyconfigs/s/spektral/spektral-1.2.0-fosscuda-2020b.eb b/easybuild/easyconfigs/s/spektral/spektral-1.2.0-fosscuda-2020b.eb
new file mode 100644
index 00000000000..a92e6bd1185
--- /dev/null
+++ b/easybuild/easyconfigs/s/spektral/spektral-1.2.0-fosscuda-2020b.eb
@@ -0,0 +1,31 @@
+easyblock = 'PythonBundle'
+
+name = 'spektral'
+version = '1.2.0'
+
+homepage = 'https://graphneural.network'
+description = "Spektral is a Python library for graph deep learning, based on the Keras API and TensorFlow 2"
+
+toolchain = {'name': 'fosscuda', 'version': '2020b'}
+
+dependencies = [
+    ('Python', '3.8.6'),
+    ('SciPy-bundle', '2020.11'),
+    ('lxml', '4.6.2'),
+    ('networkx', '2.5'),
+    ('scikit-learn', '0.23.2'),
+    ('tqdm', '4.56.2'),
+    ('TensorFlow', '2.5.0'),
+]
+
+use_pip = True
+
+exts_list = [
+    (name, version, {
+        'checksums': ['215f148e5d5067081bc28abe282bfd0942ed8be6d68f128fd7786006a884abf7'],
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'ai'

From 469657c9ab833281e17032ffbbffe35f2e9b84da Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 22 Aug 2024 14:59:47 +0200
Subject: [PATCH 682/835] add versionsuffix for spektral 1.2.0 since it depends
 on TensorFlow 2.5.0

---
 ...b.eb => spektral-1.2.0-fosscuda-2020b-TensorFlow-2.5.0.eb} | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)
 rename easybuild/easyconfigs/s/spektral/{spektral-1.2.0-fosscuda-2020b.eb => spektral-1.2.0-fosscuda-2020b-TensorFlow-2.5.0.eb} (84%)

diff --git a/easybuild/easyconfigs/s/spektral/spektral-1.2.0-fosscuda-2020b.eb b/easybuild/easyconfigs/s/spektral/spektral-1.2.0-fosscuda-2020b-TensorFlow-2.5.0.eb
similarity index 84%
rename from easybuild/easyconfigs/s/spektral/spektral-1.2.0-fosscuda-2020b.eb
rename to easybuild/easyconfigs/s/spektral/spektral-1.2.0-fosscuda-2020b-TensorFlow-2.5.0.eb
index a92e6bd1185..75446a8cbff 100644
--- a/easybuild/easyconfigs/s/spektral/spektral-1.2.0-fosscuda-2020b.eb
+++ b/easybuild/easyconfigs/s/spektral/spektral-1.2.0-fosscuda-2020b-TensorFlow-2.5.0.eb
@@ -2,6 +2,8 @@ easyblock = 'PythonBundle'
 
 name = 'spektral'
 version = '1.2.0'
+local_tf_version = '2.5.0'
+versionsuffix = '-TensorFlow-%s' % local_tf_version
 
 homepage = 'https://graphneural.network'
 description = "Spektral is a Python library for graph deep learning, based on the Keras API and TensorFlow 2"
@@ -15,7 +17,7 @@ dependencies = [
     ('networkx', '2.5'),
     ('scikit-learn', '0.23.2'),
     ('tqdm', '4.56.2'),
-    ('TensorFlow', '2.5.0'),
+    ('TensorFlow', local_tf_version),
 ]
 
 use_pip = True

From 55d1b0c66473fc2eba945397807aee82d00be3c9 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 22 Aug 2024 20:24:33 +0200
Subject: [PATCH 683/835] adding easyconfigs: xtb-6.7.1-gfbf-2023b.eb and
 patches: xtb-6.7.1_fix-dftd4-test.patch, xtb-6.7.1_fix-tblite-pr1072.patch

---
 .../easyconfigs/x/xtb/xtb-6.7.1-gfbf-2023b.eb |  50 ++
 .../x/xtb/xtb-6.7.1_fix-dftd4-test.patch      |  20 +
 .../x/xtb/xtb-6.7.1_fix-tblite-pr1072.patch   | 528 ++++++++++++++++++
 3 files changed, 598 insertions(+)
 create mode 100644 easybuild/easyconfigs/x/xtb/xtb-6.7.1-gfbf-2023b.eb
 create mode 100644 easybuild/easyconfigs/x/xtb/xtb-6.7.1_fix-dftd4-test.patch
 create mode 100644 easybuild/easyconfigs/x/xtb/xtb-6.7.1_fix-tblite-pr1072.patch

diff --git a/easybuild/easyconfigs/x/xtb/xtb-6.7.1-gfbf-2023b.eb b/easybuild/easyconfigs/x/xtb/xtb-6.7.1-gfbf-2023b.eb
new file mode 100644
index 00000000000..09d459d356b
--- /dev/null
+++ b/easybuild/easyconfigs/x/xtb/xtb-6.7.1-gfbf-2023b.eb
@@ -0,0 +1,50 @@
+easyblock = 'MesonNinja'
+
+name = 'xtb'
+version = '6.7.1'
+
+homepage = 'https://xtb-docs.readthedocs.io'
+description = """ xtb - An extended tight-binding semi-empirical program package. """
+
+toolchain = {'name': 'gfbf', 'version': '2023b'}
+
+github_account = 'grimme-lab'
+source_urls = [GITHUB_LOWER_SOURCE]
+sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}]
+patches = [
+    'xtb-6.7.1_fix-tblite-pr1072.patch',
+    'xtb-6.7.1_fix-dftd4-test.patch',
+]
+checksums = [
+    {'xtb-6.7.1.tar.gz': '52506a689147cdb4695bf1c666158b6d6d6b31726fecaa5bf53af7f4e3f3d20d'},
+    {'xtb-6.7.1_fix-tblite-pr1072.patch': '1f10fef3e94c29926b1f632acc94c3ec92be861ee5c5139104194172726ffe68'},
+    {'xtb-6.7.1_fix-dftd4-test.patch': '340e7d5cbc6bbaf0c53d4d292f3624cd67455b7a817818fe2cc8d26f5c34864b'},
+]
+
+builddependencies = [
+    ('Meson', '1.2.3'),
+    ('Ninja', '1.11.1'),
+    ('pkgconf', '2.0.3'),
+]
+
+configopts = "-Dlapack='custom' "
+configopts += "-Dcustom_libraries='flexiblas' "
+configopts += "--buildtype release "
+
+runtest = 'meson'
+pretestopts = 'export OMP_NUM_THREADS=2 && '
+testopts = 'test -C %(builddir)s/easybuild_obj -t 60'  # Ensure test don't timeout
+
+sanity_check_paths = {
+    'files': ['bin/xtb', 'include/xtb.h'] + ['lib/libxtb.%s' % e for e in ('a', SHLIB_EXT)],
+    'dirs': ['share'],
+}
+
+sanity_check_commands = ["xtb --help"]
+
+modextravars = {
+    'XTBHOME': '%(installdir)s',
+    'XTBPATH': '%(installdir)s',
+}
+
+moduleclass = 'chem'
diff --git a/easybuild/easyconfigs/x/xtb/xtb-6.7.1_fix-dftd4-test.patch b/easybuild/easyconfigs/x/xtb/xtb-6.7.1_fix-dftd4-test.patch
new file mode 100644
index 00000000000..0405b372a8a
--- /dev/null
+++ b/easybuild/easyconfigs/x/xtb/xtb-6.7.1_fix-dftd4-test.patch
@@ -0,0 +1,20 @@
+fix for failing xtb test:
+ 72/148 dftd4 / param                           FAIL              1.85s   exit status 1
+
+from meson-logs/testlog.txt:
+# Testing: param
+  Starting rational-damping ... (1/1)
+       ... rational-damping [FAILED]
+  Message: Condition not fullfilled
+
+see https://github.com/grimme-lab/xtb/pull/1085
+diff --git a/subprojects/dftd4.wrap b/subprojects/dftd4.wrap
+index 46dc07ad9..e3e93f459 100644
+--- a/subprojects/dftd4.wrap
++++ b/subprojects/dftd4.wrap
+@@ -1,4 +1,4 @@
+ [wrap-git]
+ directory = dftd4
+ url = https://github.com/dftd4/dftd4
+-revision = v3.5.0
++revision = v3.6.0
diff --git a/easybuild/easyconfigs/x/xtb/xtb-6.7.1_fix-tblite-pr1072.patch b/easybuild/easyconfigs/x/xtb/xtb-6.7.1_fix-tblite-pr1072.patch
new file mode 100644
index 00000000000..0684569d3e4
--- /dev/null
+++ b/easybuild/easyconfigs/x/xtb/xtb-6.7.1_fix-tblite-pr1072.patch
@@ -0,0 +1,528 @@
+see https://github.com/grimme-lab/xtb/pull/1072 + https://github.com/grimme-lab/xtb/issues/1091
+diff --git a/src/dipro.F90 b/src/dipro.F90
+index 42a136364..ab64e0710 100644
+--- a/src/dipro.F90
++++ b/src/dipro.F90
+@@ -130,6 +130,10 @@ subroutine get_jab(env, tblite, mol, fragment, dipro)
+ !=========================set up calculator===========================================   
+ 
+    call get_calculator(xcalc, struc, tblite%method, error)  
++   if (allocated(error)) then
++      call env%error(error%message, source)
++      return
++   end if
+    call new_wavefunction(wfn, struc%nat, xcalc%bas%nsh, xcalc%bas%nao, & 
+       & 1, set%etemp * ktoau)
+    wfn%nspin=1
+@@ -258,6 +262,10 @@ subroutine get_jab(env, tblite, mol, fragment, dipro)
+       write(*,'(A,I2)') "unpaired e- of fragment : ", mfrag(ifr)%uhf
+ 
+       call get_calculator(fcalc(ifr), mfrag(ifr), tblite%method, error)
++      if (allocated(error)) then
++         call env%error(error%message, source)
++         return
++      end if
+       !> mol%charge is updated automatically from wfn by tblite library 
+       call new_wavefunction(wfx(ifr), mfrag(ifr)%nat, fcalc(ifr)%bas%nsh, fcalc(ifr)%bas%nao, &
+          & 1, set%etemp * ktoau)
+diff --git a/src/dipro/xtb.F90 b/src/dipro/xtb.F90
+index 95aff7848..4db948a3e 100644
+--- a/src/dipro/xtb.F90
++++ b/src/dipro/xtb.F90
+@@ -50,11 +50,11 @@ subroutine get_calculator(xcalc, mol, method, error)
+       call fatal_error(error, "Unknown method '"//method//"' requested")
+ !      error stop
+    case("gfn2")
+-      call new_gfn2_calculator(xcalc, mol)
++      call new_gfn2_calculator(xcalc, mol, error)
+    case("gfn1")
+-      call new_gfn1_calculator(xcalc, mol)
++      call new_gfn1_calculator(xcalc, mol, error)
+    case("ipea1")
+-      call new_ipea1_calculator(xcalc, mol)
++      call new_ipea1_calculator(xcalc, mol, error)
+    end select
+ end subroutine get_calculator
+ #endif
+diff --git a/src/tblite/calculator.F90 b/src/tblite/calculator.F90
+index 653e6b285..f05087414 100644
+--- a/src/tblite/calculator.F90
++++ b/src/tblite/calculator.F90
+@@ -150,16 +150,16 @@ subroutine newTBLiteCalculator(env, mol, calc, input)
+       case default
+          call fatal_error(error, "Unknown method '"//method//"' requested")
+       case("gfn2")
+-         call new_gfn2_calculator(calc%tblite, struc)
++         call new_gfn2_calculator(calc%tblite, struc, error)
+       case("gfn1")
+-         call new_gfn1_calculator(calc%tblite, struc)
++         call new_gfn1_calculator(calc%tblite, struc, error)
+       case("ipea1")
+-         call new_ipea1_calculator(calc%tblite, struc)
++         call new_ipea1_calculator(calc%tblite, struc, error)
+       case("ceh")
+          calc%guess = method
+          calc%nspin = 1
+-         calc%etemp = 5000.0_wp * kt
+-         call new_ceh_calculator(calc%tblite, struc)
++         calc%etemp = 4000.0_wp * kt
++         call new_ceh_calculator(calc%tblite, struc, error)
+       end select
+    end if
+    if (allocated(error)) then
+@@ -244,18 +244,18 @@ subroutine newTBLiteWavefunction(env, mol, calc, chk)
+          block 
+             use tblite_context, only : context_type, context_terminal
+             use tblite_context_terminal, only : escape
+-            use tblite_ceh_singlepoint, only : ceh_guess
++            use tblite_ceh_singlepoint, only : ceh_singlepoint
+             use tblite_lapack_solver, only : lapack_solver 
+             use tblite_lapack_solver, only : lapack_algorithm
+             type(context_type) :: ctx
+-            
++
+             ctx%solver = lapack_solver(lapack_algorithm%gvd)
+             ctx%terminal = context_terminal(calc%color)
+ 
+             write (env%unit, '(1x,a)') escape(ctx%terminal%cyan) // "Calculation of CEH charges" // &
+                & escape(ctx%terminal%reset)
+-            
+-            call ceh_guess(ctx, calc%tblite, struc, error, wfn, calc%accuracy, 1)
++
++            call ceh_singlepoint(ctx, calc%tblite, struc, wfn, calc%accuracy, 1)
+          end block
+       end select
+    end associate
+diff --git a/subprojects/mstore.wrap b/subprojects/mstore.wrap
+index acf5df9de..0dfe716c0 100644
+--- a/subprojects/mstore.wrap
++++ b/subprojects/mstore.wrap
+@@ -1,4 +1,4 @@
+ [wrap-git]
+ directory = mstore
+ url = https://github.com/grimme-lab/mstore
+-revision = v0.2.0
++revision = v0.3.0
+diff --git a/test/unit/test_ptb.F90 b/test/unit/test_ptb.F90
+index 16c14cbe4..5e585f90d 100644
+--- a/test/unit/test_ptb.F90
++++ b/test/unit/test_ptb.F90
+@@ -186,12 +186,37 @@ subroutine test_ptb_overlap(error)
+       !> (Scaled) overlap matrix
+       character(len=:), allocatable :: message
+       real(wp), parameter :: overlap_exp(6) = [ &
+-      & 0.93209460_wp, & ! 1,2
+-      & 0.35489609_wp, & ! 1,3
+-      & 0.65682608_wp, & ! 2,3
+-      & 0.05627743_wp, & ! 1,15
+-      & -0.14217162_wp, &  ! 1,24; diffferent because of tblite ordering
+-      & 0.41844087_wp] ! 14,23; diffferent because of tblite ordering
++      & 0.93209460_wp, & ! s(Mg)-s(Mg)
++      & 0.35489609_wp, & ! s(Mg)-s(Mg)
++      & 0.65682608_wp, & ! s(Mg)-s(Mg)
++      & 0.05627743_wp, & ! s(Mg)-s(H)
++      & -0.14217162_wp, & ! s(Mg)-pz(H)
++      & 0.41844087_wp] ! dyz(Mg)-py(H)
++      ! 1: s(Mg)
++      ! 2: s(Mg)
++      ! 3: s(Mg)
++      ! 4: py(Mg)
++      ! 5: pz(Mg)
++      ! 6: px(Mg)
++      ! 7: py(Mg)
++      ! 8: pz(Mg)
++      ! 9: px(Mg)
++      ! 10: dxy(Mg)
++      ! 11: dyz(Mg)
++      ! 12: dz2(Mg)
++      ! 13: dxz(Mg)
++      ! 14: dx2-y2(Mg)
++      ! 15: s(H)
++      ! 16: s(H)
++      ! 17: py(H)
++      ! 18: pz(H)
++      ! 19: px(H)
++      ! 20: s(H)
++      ! 21: s(H)
++      ! 22: py(H)
++      ! 23: pz(H)
++      ! 24: px(H)
++
+       real(wp), allocatable :: lattr(:, :)
+       real(wp) :: cutoff
+ 
+@@ -215,7 +240,7 @@ subroutine test_ptb_overlap(error)
+       call check_(error, ints%overlap(2, 3), overlap_exp(3), thr=thr)
+       call check_(error, ints%overlap(1, 15), overlap_exp(4), thr=thr)
+       call check_(error, ints%overlap(1, 23), overlap_exp(5), thr=thr)
+-      call check_(error, ints%overlap(12, 22), overlap_exp(6), thr=thr)
++      call check_(error, ints%overlap(11, 22), overlap_exp(6), thr=thr)
+ 
+    end subroutine test_ptb_overlap
+ 
+@@ -249,12 +274,37 @@ subroutine test_ptb_overlap_h0(error)
+       type(error_type), allocatable, intent(out) :: error
+       character(len=:), allocatable :: message
+       real(wp), parameter :: overlap_exp(6) = [ &
+-      & 0.95689468_wp, & ! 1,2
+-      & 0.39195790_wp, & ! 1,3
+-      & 0.62961212_wp, & ! 2,3
+-      & 0.03782850_wp, & ! 1,15
+-      &-0.13826216_wp, &  ! 1,24; diffferent because of tblite ordering
+-      & 0.43334922_wp] ! 14,23; diffferent because of tblite ordering
++      & 0.95689468_wp, & ! s(Mg)-s(Mg)
++      & 0.39195790_wp, & ! s(Mg)-s(Mg)
++      & 0.62961212_wp, & ! s(Mg)-s(Mg)
++      & 0.03782850_wp, & ! s(Mg)-s(H)
++      &-0.13826216_wp, & ! s(Mg)-pz(H)
++      & 0.43334922_wp] ! dyz(Mg)-py(H)
++      ! 1: s(Mg)
++      ! 2: s(Mg)
++      ! 3: s(Mg)
++      ! 4: py(Mg)
++      ! 5: pz(Mg)
++      ! 6: px(Mg)
++      ! 7: py(Mg)
++      ! 8: pz(Mg)
++      ! 9: px(Mg)
++      ! 10: dxy(Mg)
++      ! 11: dyz(Mg)
++      ! 12: dz2(Mg)
++      ! 13: dxz(Mg)
++      ! 14: dx2-y2(Mg)
++      ! 15: s(H)
++      ! 16: s(H)
++      ! 17: py(H)
++      ! 18: pz(H)
++      ! 19: px(H)
++      ! 20: s(H)
++      ! 21: s(H)
++      ! 22: py(H)
++      ! 23: pz(H)
++      ! 24: px(H)
++
+       real(wp), allocatable :: lattr(:, :)
+       real(wp) :: cutoff
+ 
+@@ -286,7 +336,7 @@ subroutine test_ptb_overlap_h0(error)
+       & message=message)
+       call check_(error, auxints%overlap_h0_1(1, 23), overlap_exp(5), thr=thr, &
+       & message=message)
+-      call check_(error, auxints%overlap_h0_1(12, 22), overlap_exp(6), thr=thr, &
++      call check_(error, auxints%overlap_h0_1(11, 22), overlap_exp(6), thr=thr, &
+       & message=message)
+ 
+    end subroutine test_ptb_overlap_h0
+@@ -319,12 +369,37 @@ subroutine test_ptb_overlap_SX(error)
+       real(wp), allocatable :: overlap_sx(:, :), overlap_oneminusx(:, :)
+       character(len=:), allocatable :: message
+       real(wp), parameter :: overlap_oneminusx_exp(6) = [ &
+-      & 0.70788_wp, & ! 1,2
+-      & 0.16203_wp, & ! 1,3
+-      & 0.41532_wp, & ! 2,3
+-      & 0.01449_wp, & ! 1,15
+-      &-0.07203_wp, &  ! 1,24; diffferent because of tblite ordering
+-      & 0.28751_wp] ! 14,23; diffferent because of tblite ordering
++      & 0.70788_wp, & ! s(Mg)-s(Mg)
++      & 0.16203_wp, & ! s(Mg)-s(Mg)
++      & 0.41532_wp, & ! s(Mg)-s(Mg)
++      & 0.01449_wp, & ! s(Mg)-s(H)
++      &-0.07203_wp, & ! s(Mg)-pz(H)
++      & 0.28751_wp] ! dyz(Mg)-py(H)
++      ! 1: s(Mg)
++      ! 2: s(Mg)
++      ! 3: s(Mg)
++      ! 4: py(Mg)
++      ! 5: pz(Mg)
++      ! 6: px(Mg)
++      ! 7: py(Mg)
++      ! 8: pz(Mg)
++      ! 9: px(Mg)
++      ! 10: dxy(Mg)
++      ! 11: dyz(Mg)
++      ! 12: dz2(Mg)
++      ! 13: dxz(Mg)
++      ! 14: dx2-y2(Mg)
++      ! 15: s(H)
++      ! 16: s(H)
++      ! 17: py(H)
++      ! 18: pz(H)
++      ! 19: px(H)
++      ! 20: s(H)
++      ! 21: s(H)
++      ! 22: py(H)
++      ! 23: pz(H)
++      ! 24: px(H)
++
+       real(wp), allocatable :: lattr(:, :)
+       real(wp) :: cutoff
+ 
+@@ -356,7 +431,7 @@ subroutine test_ptb_overlap_SX(error)
+       & message=message)
+       call check_(error, overlap_oneminusx(1, 23), overlap_oneminusx_exp(5), thr=thr2, &
+       & message=message)
+-      call check_(error, overlap_oneminusx(12, 22), overlap_oneminusx_exp(6), thr=thr2, &
++      call check_(error, overlap_oneminusx(11, 22), overlap_oneminusx_exp(6), thr=thr2, &
+       & message=message)
+ 
+    end subroutine test_ptb_overlap_SX
+@@ -392,10 +467,37 @@ subroutine test_ptb_V_ECP(error)
+       type(error_type), allocatable, intent(out) :: error
+       character(len=:), allocatable :: message
+       real(wp), parameter :: vecp_ref(4) = [ &
+-      &  0.077719_wp, & ! 1,1 ; diffferent because of tblite ordering
+-      & -0.059122_wp, & ! 1,3 ; diffferent because of tblite ordering
+-      &  0.052775_wp, & ! 3,5 ; diffferent because of tblite ordering
+-      &  0.117176_wp]   ! 9,9 ; diffferent because of tblite ordering
++      &  0.077719_wp, & ! s(B)-s(B)
++      & -0.059122_wp, & ! s(B)-px(B)
++      &  0.052775_wp, & ! px(B)-px(B)
++      &  0.117176_wp]   ! dx2-y2(B)-dx2-y2(B)
++      ! 1: s(B)
++      ! 2: s(B)
++      ! 3: py(B)
++      ! 4: pz(B)
++      ! 5: px(B)
++      ! 6: py(B)
++      ! 7: pz(B)
++      ! 8: px(B)
++      ! 9: dxy(B)
++      ! 10: dyz(B)
++      ! 11: dz2(B)
++      ! 12: dxz(B)
++      ! 13: dx2-y2(B)
++      ! 14: s(Cl)
++      ! 15: s(Cl)
++      ! 16: py(Cl)
++      ! 17: pz(Cl)
++      ! 18: px(Cl)
++      ! 19: py(Cl)
++      ! 20: pz(Cl)
++      ! 21: px(Cl)
++      ! 22: dxy(Cl)
++      ! 23: dyz(Cl)
++      ! 24: dz2(Cl)
++      ! 25: dxz(Cl)
++      ! 26: dx2-y2(Cl)
++
+       real(wp), parameter :: xyz(3, 2) = reshape([ &
+       & 2.0_wp, 0.0_wp, 0.0_wp, &
+       & 0.0_wp, 0.0_wp, 0.0_wp], [3, 2])
+@@ -434,7 +536,7 @@ subroutine test_ptb_V_ECP(error)
+       & message=message)
+       call check_(error, vecp(5, 8), vecp_ref(3), thr=thr2, &
+       & message=message)
+-      call check_(error, vecp(12, 12), vecp_ref(4), thr=thr2, &
++      call check_(error, vecp(13, 13), vecp_ref(4), thr=thr2, &
+       & message=message)
+    end subroutine test_ptb_V_ECP
+ 
+@@ -629,12 +731,39 @@ subroutine test_ptb_hamiltonian_h0(error)
+       real(wp), allocatable :: vecp(:, :)
+ 
+       real(wp), parameter :: h0_ref(6) = [ &
+-      &  -1.59330281_wp, & ! 1,1
+-      &  -2.24996207_wp, & ! 1,2
+-      &   0.34974782_wp, & ! 1,23 ; diffferent because of tblite ordering
+-      &   0.0_wp, & ! 7,11 ; different because of tblite ordering
+-      &  -1.17757007_wp, & ! 3,6 ; different because of tblite ordering
+-      &   0.48301561_wp]   ! 11,24 ; diffferent because of tblite ordering
++      &  -1.59330281_wp, & ! s(B)-s(B)
++      &  -2.24996207_wp, & ! s(B)-s(B)
++      &   0.34974782_wp, & ! s(B)-py(Cl)
++      &   0.0_wp, & ! dx2-y2(B)-py(B)
++      &  -1.17757007_wp, & ! px(B)-px(B)
++      &   0.48301561_wp]   ! dxy(B)-dxy(Cl)
++      ! 1: s(B)
++      ! 2: s(B)
++      ! 3: py(B)
++      ! 4: pz(B)
++      ! 5: px(B)
++      ! 6: py(B)
++      ! 7: pz(B)
++      ! 8: px(B)
++      ! 9: dxy(B)
++      ! 10: dyz(B)
++      ! 11: dz2(B)
++      ! 12: dxz(B)
++      ! 13: dx2-y2(B)
++      ! 14: s(Cl)
++      ! 15: s(Cl)
++      ! 16: py(Cl)
++      ! 17: pz(Cl)
++      ! 18: px(Cl)
++      ! 19: py(Cl)
++      ! 20: pz(Cl)
++      ! 21: px(Cl)
++      ! 22: dxy(Cl)
++      ! 23: dyz(Cl)
++      ! 24: dz2(Cl)
++      ! 25: dxz(Cl)
++      ! 26: dx2-y2(Cl)
++
+       real(wp), parameter :: levels(10) = [ &
+       &    -0.796651404_wp, &
+       &    -0.269771638_wp, &
+@@ -665,15 +794,16 @@ subroutine test_ptb_hamiltonian_h0(error)
+          & alpha_scal=id_to_atom(mol, ptbData%hamiltonian%kalphah0l))
+       allocate (vecp(bas%nao, bas%nao), source=0.0_wp)
+ 
++      ints%hamiltonian = 0.0_wp
+       call get_hamiltonian(mol, list, bas, ptbData%hamiltonian, ptbData%hamiltonian%kla, auxints%overlap_h0_1, &
+       & levels, ints%hamiltonian, ptbGlobals%kpol, ptbGlobals%kitr, ptbGlobals%kitocod)
+       message = "H0 matrix element not matching to expected value."
+       call check_(error, ints%hamiltonian(1, 1), h0_ref(1), thr=thr)
+       call check_(error, ints%hamiltonian(1, 2), h0_ref(2), thr=thr)
+-      call check_(error, ints%hamiltonian(1, 22), h0_ref(3), thr=thr)
++      call check_(error, ints%hamiltonian(1, 24), h0_ref(3), thr=thr)
+       call check_(error, ints%hamiltonian(13, 6), h0_ref(4), thr=thr)
+       call check_(error, ints%hamiltonian(8, 5), h0_ref(5), thr=thr)
+-      call check_(error, ints%hamiltonian(13, 26), h0_ref(6), thr=thr)
++      call check_(error, ints%hamiltonian(9, 22), h0_ref(6), thr=thr)
+    end subroutine test_ptb_hamiltonian_h0
+ 
+    subroutine test_ptb_V_XC(error)
+@@ -708,10 +838,37 @@ subroutine test_ptb_V_XC(error)
+       type(error_type), allocatable, intent(out) :: error
+       character(len=:), allocatable :: message
+       real(wp), parameter :: Vxc_ref(4) = [ &
+-      & -0.92793357_wp, & ! 1,1
+-      & -0.85981333_wp, & ! 1,2
+-      &  0.06632750_wp, & ! 1,23 ; diffferent because of tblite ordering
+-      &  0.00151880_wp]   ! 11,24 ; diffferent because of tblite ordering
++      & -0.92793357_wp, & ! s(B)-s(B)
++      & -0.85981333_wp, & ! s(B)-s(B)
++      &  0.06632750_wp, & ! s(B)-dz2(Cl)
++      &  0.00151880_wp]   ! dxy(B)-dxy(Cl)
++      ! 1: s(B)
++      ! 2: s(B)
++      ! 3: py(B)
++      ! 4: pz(B)
++      ! 5: px(B)
++      ! 6: py(B)
++      ! 7: pz(B)
++      ! 8: px(B)
++      ! 9: dxy(B)
++      ! 10: dyz(B)
++      ! 11: dz2(B)
++      ! 12: dxz(B)
++      ! 13: dx2-y2(B)
++      ! 14: s(Cl)
++      ! 15: s(Cl)
++      ! 16: py(Cl)
++      ! 17: pz(Cl)
++      ! 18: px(Cl)
++      ! 19: py(Cl)
++      ! 20: pz(Cl)
++      ! 21: px(Cl)
++      ! 22: dxy(Cl)
++      ! 23: dyz(Cl)
++      ! 24: dz2(Cl)
++      ! 25: dxz(Cl)
++      ! 26: dx2-y2(Cl)
++
+       real(wp), parameter :: xyz(3, 2) = reshape([ &
+       & 2.0_wp, 0.0_wp, 0.0_wp, &
+       & 0.0_wp, 0.0_wp, 0.0_wp], [3, 2])
+@@ -769,9 +926,9 @@ subroutine test_ptb_V_XC(error)
+       & message=message)
+       call check_(error, Vxc(1, 2), Vxc_ref(2), thr=thr, &
+       & message=message)
+-      call check_(error, Vxc(1, 22), Vxc_ref(3), thr=thr, &
++      call check_(error, Vxc(1, 24), Vxc_ref(3), thr=thr, &
+       & message=message)
+-      call check_(error, Vxc(13, 26), Vxc_ref(4), thr=thr, &
++      call check_(error, Vxc(9, 22), Vxc_ref(4), thr=thr, &
+       & message=message)
+ 
+    end subroutine test_ptb_V_XC
+@@ -957,10 +1114,35 @@ subroutine test_ptb_coulomb_potential(error)
+       !> Conversion factor from temperature to energy
+       real(wp), parameter :: kt = 3.166808578545117e-06_wp
+       real(wp), parameter :: coulomb_pot_ref(4) = [ &
+-      &  -0.05693153_wp, & ! 1,1
+-      &  -0.33917531_wp, & ! 1,2
+-      &  -0.00539212_wp, & ! 1,21 ; diffferent because of tblite ordering
+-      &   0.01305793_wp]   ! 6,24 ; diffferent because of tblite ordering
++      &  -0.05693153_wp, & ! s(Mg)-s(Mg)
++      &  -0.33917531_wp, & ! s(Mg)-s(Mg)
++      &  -0.00539212_wp, & ! s(Mg)-s(H)
++      &   0.01305793_wp]   ! pz(Mg)-pz(H)
++      ! 1: s(Mg)
++      ! 2: s(Mg)
++      ! 3: s(Mg)
++      ! 4: py(Mg)
++      ! 5: pz(Mg)
++      ! 6: px(Mg)
++      ! 7: py(Mg)
++      ! 8: pz(Mg)
++      ! 9: px(Mg)
++      ! 10: dxy(Mg)
++      ! 11: dyz(Mg)
++      ! 12: dz2(Mg)
++      ! 13: dxz(Mg)
++      ! 14: dx2-y2(Mg)
++      ! 15: s(H)
++      ! 16: s(H)
++      ! 17: py(H)
++      ! 18: pz(H)
++      ! 19: px(H)
++      ! 20: s(H)
++      ! 21: s(H)
++      ! 22: py(H)
++      ! 23: pz(H)
++      ! 24: px(H)
++
+       real(wp), allocatable :: lattr(:, :)
+       real(wp) :: cutoff
+ 
+@@ -1044,10 +1226,36 @@ subroutine test_ptb_plus_U_potential(error)
+       integer, parameter :: nat = 2
+       integer, parameter :: at(nat) = [5, 17]
+       real(wp), parameter :: plusU_pot_ref(4) = [ &
+-      &  -0.0023185_wp, & ! 1,1
+-      &  -0.0018289_wp, & ! 1,2
+-      &  -0.5266562_wp, & ! 1,21 ; diffferent because of tblite ordering
+-      &  -1.6745659_wp]   ! 6,24 ; diffferent because of tblite ordering
++      &  -0.0023185_wp, & ! s(B)-s(B)
++      &  -0.0018289_wp, & ! s(B)-s(B)
++      &  -0.5266562_wp, & ! s(B)-pz(Cl)
++      &  -1.6745659_wp]   ! px(B)-dxy(Cl)
++      ! 1: s(B)
++      ! 2: s(B)
++      ! 3: py(B)
++      ! 4: pz(B)
++      ! 5: px(B)
++      ! 6: py(B)
++      ! 7: pz(B)
++      ! 8: px(B)
++      ! 9: dxy(B)
++      ! 10: dyz(B)
++      ! 11: dz2(B)
++      ! 12: dxz(B)
++      ! 13: dx2-y2(B)
++      ! 14: s(Cl)
++      ! 15: s(Cl)
++      ! 16: py(Cl)
++      ! 17: pz(Cl)
++      ! 18: px(Cl)
++      ! 19: py(Cl)
++      ! 20: pz(Cl)
++      ! 21: px(Cl)
++      ! 22: dxy(Cl)
++      ! 23: dyz(Cl)
++      ! 24: dz2(Cl)
++      ! 25: dxz(Cl)
++      ! 26: dx2-y2(Cl)
+ 
+       call new(mol, at, xyz)
+       allocate (ptbData)
+@@ -1067,7 +1275,7 @@ subroutine test_ptb_plus_U_potential(error)
+       call check_(error, wfn%coeff(1, 1, 1), plusU_pot_ref(1), thr=thr)
+       call check_(error, wfn%coeff(1, 2, 1), plusU_pot_ref(2), thr=thr)
+       call check_(error, wfn%coeff(1, 20, 1), plusU_pot_ref(3), thr=thr)
+-      call check_(error, wfn%coeff(8, 26, 1), plusU_pot_ref(4), thr=thr)
++      call check_(error, wfn%coeff(8, 22, 1), plusU_pot_ref(4), thr=thr)
+ 
+    end subroutine test_ptb_plus_U_potential
+ 

From 6f7ebd0c904df72fe5f0bb7fb16ce132537705f4 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 22 Aug 2024 20:30:45 +0200
Subject: [PATCH 684/835] adding easyconfigs: ORCA-6.0.0-foss-2023b-avx2.eb,
 ORCA-6.0.0-foss-2023b.eb

---
 .../o/ORCA/ORCA-6.0.0-foss-2023b-avx2.eb      | 37 +++++++++++++++++++
 .../o/ORCA/ORCA-6.0.0-foss-2023b.eb           | 36 ++++++++++++++++++
 2 files changed, 73 insertions(+)
 create mode 100644 easybuild/easyconfigs/o/ORCA/ORCA-6.0.0-foss-2023b-avx2.eb
 create mode 100644 easybuild/easyconfigs/o/ORCA/ORCA-6.0.0-foss-2023b.eb

diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-6.0.0-foss-2023b-avx2.eb b/easybuild/easyconfigs/o/ORCA/ORCA-6.0.0-foss-2023b-avx2.eb
new file mode 100644
index 00000000000..ff3112bb084
--- /dev/null
+++ b/easybuild/easyconfigs/o/ORCA/ORCA-6.0.0-foss-2023b-avx2.eb
@@ -0,0 +1,37 @@
+name = 'ORCA'
+version = '6.0.0'
+versionsuffix = '-avx2'
+
+homepage = 'https://orcaforum.kofo.mpg.de'
+description = """
+ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum
+chemistry with specific emphasis on spectroscopic properties of open-shell
+molecules. It features a wide variety of standard quantum chemical methods
+ranging from semiempirical methods to DFT to single- and multireference
+correlated ab initio methods. It can also treat environmental and relativistic
+effects."""
+
+toolchain = {'name': 'foss', 'version': '2023b'}
+
+download_instructions = "Shared build of ORCA: download from https://orcaforum.kofo.mpg.de"
+# mostly dynamically linked (SCALAPACK, OpenBLAS are still embedded)
+sources = ['%%(namelower)s_%s_linux_%%(orcaarch)s_avx2_shared_openmpi416.tar.xz' % version.replace('.', '_')]
+checksums = [
+    # orca_6_0_0_linux_x86-64_avx2_shared_openmpi416.tar.xz
+    '02c21294efe7b1b721e26cb90f98ee15ad682d02807201b7d217dfe67905a2fd',
+]
+
+# optional dependency for ORCA,
+# see also https://xtb-docs.readthedocs.io/en/latest/setup.html#using-xtb-with-orca
+dependencies = [('xtb', '6.7.1')]
+
+postinstallcmds = ["cd %(installdir)s/bin && ln -s $EBROOTXTB/bin/xtb otool_xtb"]
+
+enhance_sanity_check = True
+
+sanity_check_paths = {
+    'files': ['bin/orca', 'bin/otool_xtb'],
+    'dirs': [],
+}
+
+moduleclass = 'chem'
diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-6.0.0-foss-2023b.eb b/easybuild/easyconfigs/o/ORCA/ORCA-6.0.0-foss-2023b.eb
new file mode 100644
index 00000000000..f28a5a3ff99
--- /dev/null
+++ b/easybuild/easyconfigs/o/ORCA/ORCA-6.0.0-foss-2023b.eb
@@ -0,0 +1,36 @@
+name = 'ORCA'
+version = '6.0.0'
+
+homepage = 'https://orcaforum.kofo.mpg.de'
+description = """
+ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum
+chemistry with specific emphasis on spectroscopic properties of open-shell
+molecules. It features a wide variety of standard quantum chemical methods
+ranging from semiempirical methods to DFT to single- and multireference
+correlated ab initio methods. It can also treat environmental and relativistic
+effects."""
+
+toolchain = {'name': 'foss', 'version': '2023b'}
+
+download_instructions = "Shared build of ORCA: download from https://orcaforum.kofo.mpg.de"
+# mostly dynamically linked (SCALAPACK, OpenBLAS are still embedded)
+sources = ['%%(namelower)s_%s_linux_%%(orcaarch)s_shared_openmpi416.tar.xz' % version.replace('.', '_')]
+checksums = [
+    # orca_6_0_0_linux_x86-64_shared_openmpi416.tar.xz
+    '219bd1deb6d64a63cb72471926cb81665cbbcdec19f9c9549761be67d49a29c6',
+]
+
+# optional dependency for ORCA,
+# see also https://xtb-docs.readthedocs.io/en/latest/setup.html#using-xtb-with-orca
+dependencies = [('xtb', '6.7.1')]
+
+postinstallcmds = ["cd %(installdir)s/bin && ln -s $EBROOTXTB/bin/xtb otool_xtb"]
+
+enhance_sanity_check = True
+
+sanity_check_paths = {
+    'files': ['bin/orca', 'bin/otool_xtb'],
+    'dirs': [],
+}
+
+moduleclass = 'chem'

From fbe578bcdf0917e987fd526045261a8c040878b8 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 22 Aug 2024 20:51:14 +0200
Subject: [PATCH 685/835] adding easyconfigs:
 STAR-2.7.11b_alpha_2024-02-09-GCC-12.3.0.eb

---
 ...TAR-2.7.11b_alpha_2024-02-09-GCC-12.3.0.eb | 57 +++++++++++++++++++
 1 file changed, 57 insertions(+)
 create mode 100644 easybuild/easyconfigs/s/STAR/STAR-2.7.11b_alpha_2024-02-09-GCC-12.3.0.eb

diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.7.11b_alpha_2024-02-09-GCC-12.3.0.eb b/easybuild/easyconfigs/s/STAR/STAR-2.7.11b_alpha_2024-02-09-GCC-12.3.0.eb
new file mode 100644
index 00000000000..a0a119a428c
--- /dev/null
+++ b/easybuild/easyconfigs/s/STAR/STAR-2.7.11b_alpha_2024-02-09-GCC-12.3.0.eb
@@ -0,0 +1,57 @@
+# Contribution from the NIHR Biomedical Research Centre
+# Guy's and St Thomas' NHS Foundation Trust and King's College London
+# Based on STAR-2.7.7a-GCC-10.2.0.eb 
+# uploaded by J. Sassmannshausen
+# modified by Thomas Eylenbosch
+
+easyblock = 'MakeCp'
+
+name = 'STAR'
+version = '2.7.11b_alpha_2024-02-09'
+
+homepage = 'https://github.com/dobinlab/STAR_pre_releases'
+description = "STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays."
+
+toolchain = {'name': 'GCC', 'version': '12.3.0'}
+toolchainopts = {'openmp': True}
+
+source_urls = ['https://github.com/dobinlab/STAR_pre_releases/archive/']
+sources = ['%(version)s.tar.gz']
+patches = ['STAR-2.7.11a_use-external-htslib.patch']
+checksums = [
+    {'2.7.11b_alpha_2024-02-09.tar.gz': '7a7bae1f802fc5bc5b270da89e66a824480fb33e21f7ebfbf7ed56e1d4907c1c'},
+    {'STAR-2.7.11a_use-external-htslib.patch': '2fdc3ed9372d983f77d861d6f16a60a553598358dce9ff8216f96eb20e63ce4e'},
+]
+
+builddependencies = [
+    ('xxd', '9.0.2112'),
+]
+
+dependencies = [
+    ('HTSlib', '1.18'),
+    ('zlib', '1.2.13'),
+]
+
+start_dir = 'source'
+
+# by default this is set to -mavx2 which makes it fail on non x86 systems
+prebuildopts = 'CXXFLAGS_SIMD= '
+
+buildopts = ' STAR && make STARlong'
+
+files_to_copy = [
+    (['source/%(name)s', 'source/%(name)slong'], 'bin'),
+    'CHANGES.md', 'doc', 'extras', 'LICENSE', 'README.md', 'RELEASEnotes.md',
+]
+
+sanity_check_paths = {
+    'files': ['bin/%(name)s', 'bin/%(name)slong'],
+    'dirs': [],
+}
+
+sanity_check_commands = [
+    "STAR --help",
+    "STARlong --help",
+]
+
+moduleclass = 'bio'

From cab6b5585d54dd7cd6af97f5defcfaa90b6cff34 Mon Sep 17 00:00:00 2001
From: Chia-Jung Hsu <appolloford@gmail.com>
Date: Thu, 22 Aug 2024 21:50:57 +0000
Subject: [PATCH 686/835] adding easyconfigs: bitsandbytes-0.43.3-foss-2023a.eb

---
 .../bitsandbytes-0.43.3-foss-2023a.eb         | 47 +++++++++++++++++++
 1 file changed, 47 insertions(+)
 create mode 100644 easybuild/easyconfigs/b/bitsandbytes/bitsandbytes-0.43.3-foss-2023a.eb

diff --git a/easybuild/easyconfigs/b/bitsandbytes/bitsandbytes-0.43.3-foss-2023a.eb b/easybuild/easyconfigs/b/bitsandbytes/bitsandbytes-0.43.3-foss-2023a.eb
new file mode 100644
index 00000000000..902b7d717f1
--- /dev/null
+++ b/easybuild/easyconfigs/b/bitsandbytes/bitsandbytes-0.43.3-foss-2023a.eb
@@ -0,0 +1,47 @@
+easyblock = 'CMakeMake'
+
+name = 'bitsandbytes'
+version = '0.43.3'
+
+homepage = 'https://huggingface.co/docs/bitsandbytes/main/en/index'
+description = "bitsandbytes enables accessible large language models via k-bit quantization for PyTorch."
+github_account = 'bitsandbytes-foundation'
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+source_urls = [GITHUB_LOWER_SOURCE]
+sources = ['%(version)s.tar.gz']
+checksums = ['7a468bc977da19c176cc578954bfd7a3c64182f387a6849e9f0a38d5cba1b4df']
+
+builddependencies = [
+    ('CMake', '3.26.3'),
+    ('pkgconf', '1.9.5'),
+]
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('PyTorch', '2.1.2', '-CUDA-12.1.1'),
+    ('SciPy-bundle', '2023.07'),
+]
+
+configopts = '-DCOMPUTE_BACKEND=cuda'
+skipsteps = ['install']
+
+postinstallcmds = [
+    'pip install --prefix=%(installdir)s --no-deps --ignore-installed --no-index --no-build-isolation %(start_dir)s',
+]
+
+sanity_check_paths = {
+    'files': ['lib/python3.11/site-packages/bitsandbytes/libbitsandbytes_cuda121.so'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = [
+    "python -c 'import bitsandbytes'",
+]
+
+modextrapaths = {
+    'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']
+}
+
+moduleclass = 'ai'

From 3c74d87c94ccc2b61e25c02a7865d7cc6a5c5555 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Fri, 23 Aug 2024 12:34:11 +0200
Subject: [PATCH 687/835] adding easyconfigs:
 HERRO-0.1.0_20240808-foss-2023a.eb, duplex-tools-0.3.3-foss-2023a.eb,
 pod5-file-format-0.3.10-foss-2023a.eb and patches:
 pod5-file-format-0.3.10_dep_fix.patch

---
 .../duplex-tools-0.3.3-foss-2023a.eb          |  68 ++++
 .../HERRO/HERRO-0.1.0_20240808-foss-2023a.eb  | 382 ++++++++++++++++++
 .../pod5-file-format-0.3.10-foss-2023a.eb     | 109 +++++
 .../pod5-file-format-0.3.10_dep_fix.patch     |  32 ++
 4 files changed, 591 insertions(+)
 create mode 100644 easybuild/easyconfigs/d/duplex-tools/duplex-tools-0.3.3-foss-2023a.eb
 create mode 100644 easybuild/easyconfigs/h/HERRO/HERRO-0.1.0_20240808-foss-2023a.eb
 create mode 100644 easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.3.10-foss-2023a.eb
 create mode 100644 easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.3.10_dep_fix.patch

diff --git a/easybuild/easyconfigs/d/duplex-tools/duplex-tools-0.3.3-foss-2023a.eb b/easybuild/easyconfigs/d/duplex-tools/duplex-tools-0.3.3-foss-2023a.eb
new file mode 100644
index 00000000000..fe56d08acaa
--- /dev/null
+++ b/easybuild/easyconfigs/d/duplex-tools/duplex-tools-0.3.3-foss-2023a.eb
@@ -0,0 +1,68 @@
+# Author: Jasper Grimm (UoY)
+# Updated: Petr Král, Pavel Tománek (INUITS)
+easyblock = 'PythonBundle'
+
+name = 'duplex-tools'
+version = '0.3.3'
+
+homepage = 'https://github.com/nanoporetech/duplex-tools'
+description = """
+Duplex Tools contains a set of utilities for dealing with Duplex sequencing data. Tools are provided
+ to identify and prepare duplex pairs for basecalling by Dorado (recommended) and Guppy, and for
+ recovering simplex basecalls from incorrectly concatenated pairs.
+"""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+_minimap2_ver = '2.26'
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('matplotlib', '3.7.2'),
+    ('edlib', '1.3.9'),
+    ('minimap2', _minimap2_ver),
+    ('python-parasail', '1.3.4'),
+    ('Pysam', '0.22.0'),
+    ('tqdm', '4.66.1'),
+    ('Arrow', '14.0.1'),
+    ('h5py', '3.9.0'),
+    ('pod5-file-format', '0.3.10'),
+    ('parasail', '2.6.2'),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    ('mappy', _minimap2_ver, {
+        'checksums': ['e53fbe9a3ea8762a64b8103f4f779c9fb16d418eaa0a731f45cebc83867a9b71'],
+    }),
+    ('natsort', '8.4.0', {
+        'checksums': ['45312c4a0e5507593da193dedd04abb1469253b601ecaf63445ad80f0a1ea581'],
+    }),
+    ('pyfastx', '2.0.1', {
+        # PYPI source tarball is incomplete, causes ImportErrors
+        # see https://github.com/lmdu/pyfastx/issues/60
+        'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}],
+        'source_urls': ['https://github.com/lmdu/%(name)s/archive'],
+        'checksums': ['93aff63ce88bc5cfe7152d8dcb3f2164356bcd8f95a68fb20af107e59a7f9b55'],
+    }),
+    (name, version, {
+        'source_tmpl': 'duplex_tools-%(version)s.tar.gz',
+        'checksums': ['883e0a6610d14328a640b6a31eaef90592d2967cda68db0547a4d99924281300'],
+    }),
+]
+
+_bins = ['dorado_stereo.sh', 'duplex_tools', 'minimap2.py', 'natsort', 'pyfastx']
+sanity_check_paths = {
+    'files': ['bin/%s' % x for x in _bins],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = [
+    'dorado_stereo.sh -h',
+    'duplex_tools --help',
+    'pyfastx --help',
+]
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/h/HERRO/HERRO-0.1.0_20240808-foss-2023a.eb b/easybuild/easyconfigs/h/HERRO/HERRO-0.1.0_20240808-foss-2023a.eb
new file mode 100644
index 00000000000..d27b48f9a9b
--- /dev/null
+++ b/easybuild/easyconfigs/h/HERRO/HERRO-0.1.0_20240808-foss-2023a.eb
@@ -0,0 +1,382 @@
+easyblock = 'Cargo'
+
+name = 'HERRO'
+version = '0.1.0_20240808'
+local_commit = 'deccc46'
+
+homepage = 'https://github.com/lbcb-sci/herro'
+description = """
+HERRO is a highly-accurate, haplotype-aware, deep-learning tool for error correction of Nanopore R10.4.1 or
+R9.4.1 reads (read length of >= 10 kbps is recommended).
+"""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+source_urls = ['https://github.com/lbcb-sci/herro/archive/']
+sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}]
+
+builddependencies = [
+    ('Rust', '1.75.0'),
+]
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('bzip2', '1.0.8'),
+    ('libffi', '3.4.4'),
+    ('libnsl', '2.0.1'),
+    ('SQLite', '3.42.0'),
+    ('util-linux', '2.39'),
+    ('zlib', '1.2.13'),
+    ('ncurses', '6.4'),
+    ('libreadline', '8.2'),
+    ('SeqKit', '2.3.1', '', SYSTEM),
+    ('Tk', '8.6.13'),
+    ('XZ', '5.4.2'),
+    ('matplotlib', '3.7.2'),
+    ('edlib', '1.3.9'),
+    ('h5py', '3.9.0'),
+    ('duplex-tools', '0.3.3'),
+    ('PyTorch', '2.1.2'),
+    ('Pillow', '10.0.0'),
+    ('zstd', '1.5.5'),
+    ('parasail', '2.6.2'),
+]
+
+exts_defaultclass = 'PythonPackage'
+exts_default_options = {
+    'source_urls': [PYPI_SOURCE],
+    'download_dep_fail': True,
+    'use_pip': True,
+    'sanity_pip_check': True,
+    'preinstallopts': '',
+    'installopts': '',
+}
+
+exts_list = [
+    ('zstandard', '0.22.0', {
+        'checksums': ['8226a33c542bcb54cd6bd0a366067b610b41713b64c9abec1bc4533d69f51e70'],
+    }),
+    ('Porechop', '20240119', {
+        'modulename': 'porechop',
+        'source_urls': ['https://github.com/dehui333/Porechop/archive/'],
+        'sources': [{'download_filename': 'd2e77c6.tar.gz', 'filename': SOURCE_TAR_GZ}],
+        'checksums': ['6e5ff3a780fc2855b0101b4a6102437d9a0fc201e40ffabc44c0c67d7c9ad621'],
+    }),
+]
+
+# use tch version 0.14.0 - compatible with PyTorch 2.1
+local_torch_opts = "sed -i 's/tch = \"0.13.0\"/tch = \"0.14.0\"/' Cargo.toml && "
+local_torch_opts += 'export LIBTORCH_BYPASS_VERSION_CHECK=1 && export LIBTORCH_USE_PYTORCH=1 && '
+local_torch_opts += 'export LIBTORCH=$EBROOTPYTORCH/lib && RUSTFLAGS="-Ctarget-cpu=native"'
+prebuildopts = pretestopts = preinstallopts = local_torch_opts
+
+# copy scripts to /bin to be easier to run scripts for users
+postinstallcmds = [
+    'cp -a %(start_dir)sscripts/* %(installdir)s/bin',
+    'rm %(installdir)s/bin/herro-env.yml',
+    "chmod a+rx %(installdir)s/bin/*.sh",
+    "chmod a-x %(installdir)s/bin/*.py",
+]
+
+_bins = [
+    'herro',
+    'porechop',
+    'no_split.sh',
+    'postprocess_corrected.sh',
+    'create_batched_alignments.sh',
+    'porechop_with_split.sh',
+    'preprocess.sh',
+    'batch.py',
+    'create_clusters.py',
+]
+sanity_check_paths = {
+    'files': ['bin/%s' % x for x in _bins],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+ 
+sanity_check_commands = ["herro --help"]
+
+modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'}
+
+modloadmsg = """
+To run scripts from /scripts directory just run <script_name>.sh
+Do not run it as scripts/<script_name>.sh
+For example - run preprocess.sh as: 
+    $ preprocess.sh <input_fastq> <output_prefix> <number_of_threads> <parts_to_split_job_into>
+"""
+
+crates = [
+    ('adler2', '2.0.0'),
+    ('aes', '0.8.4'),
+    ('anstream', '0.6.15'),
+    ('anstyle', '1.0.8'),
+    ('anstyle-parse', '0.2.5'),
+    ('anstyle-query', '1.1.1'),
+    ('anstyle-wincon', '3.0.4'),
+    ('anyhow', '1.0.86'),
+    ('approx', '0.5.1'),
+    ('autocfg', '1.3.0'),
+    ('base64ct', '1.6.0'),
+    ('block-buffer', '0.10.4'),
+    ('buffer-redux', '1.0.2'),
+    ('bytecount', '0.6.8'),
+    ('byteorder', '1.5.0'),
+    ('bzip2', '0.4.4'),
+    ('bzip2-sys', '0.1.11+1.0.8'),
+    ('cc', '1.1.13'),
+    ('cfg-if', '1.0.0'),
+    ('cipher', '0.4.4'),
+    ('clap', '4.4.18'),
+    ('clap_builder', '4.4.18'),
+    ('clap_derive', '4.4.7'),
+    ('clap_lex', '0.6.0'),
+    ('colorchoice', '1.0.2'),
+    ('console', '0.15.8'),
+    ('constant_time_eq', '0.1.5'),
+    ('cpufeatures', '0.2.13'),
+    ('crc32fast', '1.4.2'),
+    ('crossbeam-channel', '0.5.13'),
+    ('crossbeam-utils', '0.8.20'),
+    ('crunchy', '0.2.2'),
+    ('crypto-common', '0.1.6'),
+    ('deranged', '0.3.11'),
+    ('digest', '0.10.7'),
+    ('either', '1.13.0'),
+    ('encode_unicode', '0.3.6'),
+    ('flate2', '1.0.32'),
+    ('generic-array', '0.14.7'),
+    ('getrandom', '0.2.15'),
+    ('glob', '0.3.1'),
+    ('half', '2.4.1'),
+    ('heck', '0.4.1'),
+    ('hmac', '0.12.1'),
+    ('indicatif', '0.17.8'),
+    ('inout', '0.1.3'),
+    ('instant', '0.1.13'),
+    ('is_terminal_polyfill', '1.70.1'),
+    ('itertools', '0.12.1'),
+    ('itoa', '1.0.11'),
+    ('jemalloc-sys', '0.5.4+5.3.0-patched'),
+    ('jemallocator', '0.5.4'),
+    ('jobserver', '0.1.32'),
+    ('lazy_static', '1.5.0'),
+    ('libc', '0.2.158'),
+    ('lzma-sys', '0.1.20'),
+    ('matrixmultiply', '0.3.9'),
+    ('memchr', '2.7.4'),
+    ('miniz_oxide', '0.8.0'),
+    ('ndarray', '0.15.6'),
+    ('needletail', '0.5.1'),
+    ('npyz', '0.8.3'),
+    ('npyz-derive', '0.7.0'),
+    ('num-bigint', '0.4.6'),
+    ('num-complex', '0.4.6'),
+    ('num-conv', '0.1.0'),
+    ('num-integer', '0.1.46'),
+    ('num-traits', '0.2.19'),
+    ('number_prefix', '0.4.0'),
+    ('once_cell', '1.19.0'),
+    ('ordered-float', '4.2.2'),
+    ('password-hash', '0.4.2'),
+    ('pbkdf2', '0.11.0'),
+    ('pest', '2.7.11'),
+    ('pest_derive', '2.7.11'),
+    ('pest_generator', '2.7.11'),
+    ('pest_meta', '2.7.11'),
+    ('pkg-config', '0.3.30'),
+    ('portable-atomic', '1.7.0'),
+    ('powerfmt', '0.2.0'),
+    ('ppv-lite86', '0.2.20'),
+    ('proc-macro2', '1.0.86'),
+    ('py_literal', '0.4.0'),
+    ('quote', '1.0.36'),
+    ('rand', '0.8.5'),
+    ('rand_chacha', '0.3.1'),
+    ('rand_core', '0.6.4'),
+    ('rawpointer', '0.2.1'),
+    ('rustc-hash', '1.1.0'),
+    ('ryu', '1.0.18'),
+    ('safetensors', '0.3.3'),
+    ('serde', '1.0.208'),
+    ('serde_derive', '1.0.208'),
+    ('serde_json', '1.0.125'),
+    ('sha1', '0.10.6'),
+    ('sha2', '0.10.8'),
+    ('shlex', '1.3.0'),
+    ('strsim', '0.10.0'),
+    ('subtle', '2.6.1'),
+    ('syn', '1.0.109'),
+    ('syn', '2.0.75'),
+    ('tch', '0.14.0'),
+    ('thiserror', '1.0.63'),
+    ('thiserror-impl', '1.0.63'),
+    ('time', '0.3.36'),
+    ('time-core', '0.1.2'),
+    ('torch-sys', '0.14.0'),
+    ('typenum', '1.17.0'),
+    ('ucd-trie', '0.1.6'),
+    ('unicode-ident', '1.0.12'),
+    ('unicode-width', '0.1.13'),
+    ('utf8parse', '0.2.2'),
+    ('version_check', '0.9.5'),
+    ('wasi', '0.11.0+wasi-snapshot-preview1'),
+    ('windows-sys', '0.52.0'),
+    ('windows-targets', '0.52.6'),
+    ('windows_aarch64_gnullvm', '0.52.6'),
+    ('windows_aarch64_msvc', '0.52.6'),
+    ('windows_i686_gnu', '0.52.6'),
+    ('windows_i686_gnullvm', '0.52.6'),
+    ('windows_i686_msvc', '0.52.6'),
+    ('windows_x86_64_gnu', '0.52.6'),
+    ('windows_x86_64_gnullvm', '0.52.6'),
+    ('windows_x86_64_msvc', '0.52.6'),
+    ('xz2', '0.1.7'),
+    ('zerocopy', '0.7.35'),
+    ('zerocopy-derive', '0.7.35'),
+    ('zip', '0.6.6'),
+    ('zstd', '0.11.2+zstd.1.5.2'),
+    ('zstd', '0.13.2'),
+    ('zstd-safe', '5.0.2+zstd.1.5.2'),
+    ('zstd-safe', '7.2.1'),
+    ('zstd-sys', '2.0.13+zstd.1.5.6'),
+]
+
+checksums = [
+    {'HERRO-0.1.0_20240808.tar.gz': '885f64ab097c89cf8ec8ec38625c6325271997e89636de756aa12fb68aab7598'},
+    {'adler2-2.0.0.tar.gz': '512761e0bb2578dd7380c6baaa0f4ce03e84f95e960231d1dec8bf4d7d6e2627'},
+    {'aes-0.8.4.tar.gz': 'b169f7a6d4742236a0a00c541b845991d0ac43e546831af1249753ab4c3aa3a0'},
+    {'anstream-0.6.15.tar.gz': '64e15c1ab1f89faffbf04a634d5e1962e9074f2741eef6d97f3c4e322426d526'},
+    {'anstyle-1.0.8.tar.gz': '1bec1de6f59aedf83baf9ff929c98f2ad654b97c9510f4e70cf6f661d49fd5b1'},
+    {'anstyle-parse-0.2.5.tar.gz': 'eb47de1e80c2b463c735db5b217a0ddc39d612e7ac9e2e96a5aed1f57616c1cb'},
+    {'anstyle-query-1.1.1.tar.gz': '6d36fc52c7f6c869915e99412912f22093507da8d9e942ceaf66fe4b7c14422a'},
+    {'anstyle-wincon-3.0.4.tar.gz': '5bf74e1b6e971609db8ca7a9ce79fd5768ab6ae46441c572e46cf596f59e57f8'},
+    {'anyhow-1.0.86.tar.gz': 'b3d1d046238990b9cf5bcde22a3fb3584ee5cf65fb2765f454ed428c7a0063da'},
+    {'approx-0.5.1.tar.gz': 'cab112f0a86d568ea0e627cc1d6be74a1e9cd55214684db5561995f6dad897c6'},
+    {'autocfg-1.3.0.tar.gz': '0c4b4d0bd25bd0b74681c0ad21497610ce1b7c91b1022cd21c80c6fbdd9476b0'},
+    {'base64ct-1.6.0.tar.gz': '8c3c1a368f70d6cf7302d78f8f7093da241fb8e8807c05cc9e51a125895a6d5b'},
+    {'block-buffer-0.10.4.tar.gz': '3078c7629b62d3f0439517fa394996acacc5cbc91c5a20d8c658e77abd503a71'},
+    {'buffer-redux-1.0.2.tar.gz': '4e8acf87c5b9f5897cd3ebb9a327f420e0cae9dd4e5c1d2e36f2c84c571a58f1'},
+    {'bytecount-0.6.8.tar.gz': '5ce89b21cab1437276d2650d57e971f9d548a2d9037cc231abdc0562b97498ce'},
+    {'byteorder-1.5.0.tar.gz': '1fd0f2584146f6f2ef48085050886acf353beff7305ebd1ae69500e27c67f64b'},
+    {'bzip2-0.4.4.tar.gz': 'bdb116a6ef3f6c3698828873ad02c3014b3c85cadb88496095628e3ef1e347f8'},
+    {'bzip2-sys-0.1.11+1.0.8.tar.gz': '736a955f3fa7875102d57c82b8cac37ec45224a07fd32d58f9f7a186b6cd4cdc'},
+    {'cc-1.1.13.tar.gz': '72db2f7947ecee9b03b510377e8bb9077afa27176fdbff55c51027e976fdcc48'},
+    {'cfg-if-1.0.0.tar.gz': 'baf1de4339761588bc0619e3cbc0120ee582ebb74b53b4efbf79117bd2da40fd'},
+    {'cipher-0.4.4.tar.gz': '773f3b9af64447d2ce9850330c473515014aa235e6a783b02db81ff39e4a3dad'},
+    {'clap-4.4.18.tar.gz': '1e578d6ec4194633722ccf9544794b71b1385c3c027efe0c55db226fc880865c'},
+    {'clap_builder-4.4.18.tar.gz': '4df4df40ec50c46000231c914968278b1eb05098cf8f1b3a518a95030e71d1c7'},
+    {'clap_derive-4.4.7.tar.gz': 'cf9804afaaf59a91e75b022a30fb7229a7901f60c755489cc61c9b423b836442'},
+    {'clap_lex-0.6.0.tar.gz': '702fc72eb24e5a1e48ce58027a675bc24edd52096d5397d4aea7c6dd9eca0bd1'},
+    {'colorchoice-1.0.2.tar.gz': 'd3fd119d74b830634cea2a0f58bbd0d54540518a14397557951e79340abc28c0'},
+    {'console-0.15.8.tar.gz': '0e1f83fc076bd6dd27517eacdf25fef6c4dfe5f1d7448bafaaf3a26f13b5e4eb'},
+    {'constant_time_eq-0.1.5.tar.gz': '245097e9a4535ee1e3e3931fcfcd55a796a44c643e8596ff6566d68f09b87bbc'},
+    {'cpufeatures-0.2.13.tar.gz': '51e852e6dc9a5bed1fae92dd2375037bf2b768725bf3be87811edee3249d09ad'},
+    {'crc32fast-1.4.2.tar.gz': 'a97769d94ddab943e4510d138150169a2758b5ef3eb191a9ee688de3e23ef7b3'},
+    {'crossbeam-channel-0.5.13.tar.gz': '33480d6946193aa8033910124896ca395333cae7e2d1113d1fef6c3272217df2'},
+    {'crossbeam-utils-0.8.20.tar.gz': '22ec99545bb0ed0ea7bb9b8e1e9122ea386ff8a48c0922e43f36d45ab09e0e80'},
+    {'crunchy-0.2.2.tar.gz': '7a81dae078cea95a014a339291cec439d2f232ebe854a9d672b796c6afafa9b7'},
+    {'crypto-common-0.1.6.tar.gz': '1bfb12502f3fc46cca1bb51ac28df9d618d813cdc3d2f25b9fe775a34af26bb3'},
+    {'deranged-0.3.11.tar.gz': 'b42b6fa04a440b495c8b04d0e71b707c585f83cb9cb28cf8cd0d976c315e31b4'},
+    {'digest-0.10.7.tar.gz': '9ed9a281f7bc9b7576e61468ba615a66a5c8cfdff42420a70aa82701a3b1e292'},
+    {'either-1.13.0.tar.gz': '60b1af1c220855b6ceac025d3f6ecdd2b7c4894bfe9cd9bda4fbb4bc7c0d4cf0'},
+    {'encode_unicode-0.3.6.tar.gz': 'a357d28ed41a50f9c765dbfe56cbc04a64e53e5fc58ba79fbc34c10ef3df831f'},
+    {'flate2-1.0.32.tar.gz': '9c0596c1eac1f9e04ed902702e9878208b336edc9d6fddc8a48387349bab3666'},
+    {'generic-array-0.14.7.tar.gz': '85649ca51fd72272d7821adaf274ad91c288277713d9c18820d8499a7ff69e9a'},
+    {'getrandom-0.2.15.tar.gz': 'c4567c8db10ae91089c99af84c68c38da3ec2f087c3f82960bcdbf3656b6f4d7'},
+    {'glob-0.3.1.tar.gz': 'd2fabcfbdc87f4758337ca535fb41a6d701b65693ce38287d856d1674551ec9b'},
+    {'half-2.4.1.tar.gz': '6dd08c532ae367adf81c312a4580bc67f1d0fe8bc9c460520283f4c0ff277888'},
+    {'heck-0.4.1.tar.gz': '95505c38b4572b2d910cecb0281560f54b440a19336cbbcb27bf6ce6adc6f5a8'},
+    {'hmac-0.12.1.tar.gz': '6c49c37c09c17a53d937dfbb742eb3a961d65a994e6bcdcf37e7399d0cc8ab5e'},
+    {'indicatif-0.17.8.tar.gz': '763a5a8f45087d6bcea4222e7b72c291a054edf80e4ef6efd2a4979878c7bea3'},
+    {'inout-0.1.3.tar.gz': 'a0c10553d664a4d0bcff9f4215d0aac67a639cc68ef660840afe309b807bc9f5'},
+    {'instant-0.1.13.tar.gz': 'e0242819d153cba4b4b05a5a8f2a7e9bbf97b6055b2a002b395c96b5ff3c0222'},
+    {'is_terminal_polyfill-1.70.1.tar.gz': '7943c866cc5cd64cbc25b2e01621d07fa8eb2a1a23160ee81ce38704e97b8ecf'},
+    {'itertools-0.12.1.tar.gz': 'ba291022dbbd398a455acf126c1e341954079855bc60dfdda641363bd6922569'},
+    {'itoa-1.0.11.tar.gz': '49f1f14873335454500d59611f1cf4a4b0f786f9ac11f4312a78e4cf2566695b'},
+    {'jemalloc-sys-0.5.4+5.3.0-patched.tar.gz': 'ac6c1946e1cea1788cbfde01c993b52a10e2da07f4bac608228d1bed20bfebf2'},
+    {'jemallocator-0.5.4.tar.gz': 'a0de374a9f8e63150e6f5e8a60cc14c668226d7a347d8aee1a45766e3c4dd3bc'},
+    {'jobserver-0.1.32.tar.gz': '48d1dbcbbeb6a7fec7e059840aa538bd62aaccf972c7346c4d9d2059312853d0'},
+    {'lazy_static-1.5.0.tar.gz': 'bbd2bcb4c963f2ddae06a2efc7e9f3591312473c50c6685e1f298068316e66fe'},
+    {'libc-0.2.158.tar.gz': 'd8adc4bb1803a324070e64a98ae98f38934d91957a99cfb3a43dcbc01bc56439'},
+    {'lzma-sys-0.1.20.tar.gz': '5fda04ab3764e6cde78b9974eec4f779acaba7c4e84b36eca3cf77c581b85d27'},
+    {'matrixmultiply-0.3.9.tar.gz': '9380b911e3e96d10c1f415da0876389aaf1b56759054eeb0de7df940c456ba1a'},
+    {'memchr-2.7.4.tar.gz': '78ca9ab1a0babb1e7d5695e3530886289c18cf2f87ec19a575a0abdce112e3a3'},
+    {'miniz_oxide-0.8.0.tar.gz': 'e2d80299ef12ff69b16a84bb182e3b9df68b5a91574d3d4fa6e41b65deec4df1'},
+    {'ndarray-0.15.6.tar.gz': 'adb12d4e967ec485a5f71c6311fe28158e9d6f4bc4a447b474184d0f91a8fa32'},
+    {'needletail-0.5.1.tar.gz': 'db05a5ab397f64070d8c998fa0fbb84e484b81f95752af317dac183a82d9295d'},
+    {'npyz-0.8.3.tar.gz': '13f27ea175875c472b3df61ece89a6d6ef4e0627f43704e400c782f174681ebd'},
+    {'npyz-derive-0.7.0.tar.gz': 'a285bd6c2f2a9a4b12b0f3813ad3e01a37e02d3de508c6d80a009f5e1af69aed'},
+    {'num-bigint-0.4.6.tar.gz': 'a5e44f723f1133c9deac646763579fdb3ac745e418f2a7af9cd0c431da1f20b9'},
+    {'num-complex-0.4.6.tar.gz': '73f88a1307638156682bada9d7604135552957b7818057dcef22705b4d509495'},
+    {'num-conv-0.1.0.tar.gz': '51d515d32fb182ee37cda2ccdcb92950d6a3c2893aa280e540671c2cd0f3b1d9'},
+    {'num-integer-0.1.46.tar.gz': '7969661fd2958a5cb096e56c8e1ad0444ac2bbcd0061bd28660485a44879858f'},
+    {'num-traits-0.2.19.tar.gz': '071dfc062690e90b734c0b2273ce72ad0ffa95f0c74596bc250dcfd960262841'},
+    {'number_prefix-0.4.0.tar.gz': '830b246a0e5f20af87141b25c173cd1b609bd7779a4617d6ec582abaf90870f3'},
+    {'once_cell-1.19.0.tar.gz': '3fdb12b2476b595f9358c5161aa467c2438859caa136dec86c26fdd2efe17b92'},
+    {'ordered-float-4.2.2.tar.gz': '4a91171844676f8c7990ce64959210cd2eaef32c2612c50f9fae9f8aaa6065a6'},
+    {'password-hash-0.4.2.tar.gz': '7676374caaee8a325c9e7a2ae557f216c5563a171d6997b0ef8a65af35147700'},
+    {'pbkdf2-0.11.0.tar.gz': '83a0692ec44e4cf1ef28ca317f14f8f07da2d95ec3fa01f86e4467b725e60917'},
+    {'pest-2.7.11.tar.gz': 'cd53dff83f26735fdc1ca837098ccf133605d794cdae66acfc2bfac3ec809d95'},
+    {'pest_derive-2.7.11.tar.gz': '2a548d2beca6773b1c244554d36fcf8548a8a58e74156968211567250e48e49a'},
+    {'pest_generator-2.7.11.tar.gz': '3c93a82e8d145725dcbaf44e5ea887c8a869efdcc28706df2d08c69e17077183'},
+    {'pest_meta-2.7.11.tar.gz': 'a941429fea7e08bedec25e4f6785b6ffaacc6b755da98df5ef3e7dcf4a124c4f'},
+    {'pkg-config-0.3.30.tar.gz': 'd231b230927b5e4ad203db57bbcbee2802f6bce620b1e4a9024a07d94e2907ec'},
+    {'portable-atomic-1.7.0.tar.gz': 'da544ee218f0d287a911e9c99a39a8c9bc8fcad3cb8db5959940044ecfc67265'},
+    {'powerfmt-0.2.0.tar.gz': '439ee305def115ba05938db6eb1644ff94165c5ab5e9420d1c1bcedbba909391'},
+    {'ppv-lite86-0.2.20.tar.gz': '77957b295656769bb8ad2b6a6b09d897d94f05c41b069aede1fcdaa675eaea04'},
+    {'proc-macro2-1.0.86.tar.gz': '5e719e8df665df0d1c8fbfd238015744736151d4445ec0836b8e628aae103b77'},
+    {'py_literal-0.4.0.tar.gz': '102df7a3d46db9d3891f178dcc826dc270a6746277a9ae6436f8d29fd490a8e1'},
+    {'quote-1.0.36.tar.gz': '0fa76aaf39101c457836aec0ce2316dbdc3ab723cdda1c6bd4e6ad4208acaca7'},
+    {'rand-0.8.5.tar.gz': '34af8d1a0e25924bc5b7c43c079c942339d8f0a8b57c39049bef581b46327404'},
+    {'rand_chacha-0.3.1.tar.gz': 'e6c10a63a0fa32252be49d21e7709d4d4baf8d231c2dbce1eaa8141b9b127d88'},
+    {'rand_core-0.6.4.tar.gz': 'ec0be4795e2f6a28069bec0b5ff3e2ac9bafc99e6a9a7dc3547996c5c816922c'},
+    {'rawpointer-0.2.1.tar.gz': '60a357793950651c4ed0f3f52338f53b2f809f32d83a07f72909fa13e4c6c1e3'},
+    {'rustc-hash-1.1.0.tar.gz': '08d43f7aa6b08d49f382cde6a7982047c3426db949b1424bc4b7ec9ae12c6ce2'},
+    {'ryu-1.0.18.tar.gz': 'f3cb5ba0dc43242ce17de99c180e96db90b235b8a9fdc9543c96d2209116bd9f'},
+    {'safetensors-0.3.3.tar.gz': 'd93279b86b3de76f820a8854dd06cbc33cfa57a417b19c47f6a25280112fb1df'},
+    {'serde-1.0.208.tar.gz': 'cff085d2cb684faa248efb494c39b68e522822ac0de72ccf08109abde717cfb2'},
+    {'serde_derive-1.0.208.tar.gz': '24008e81ff7613ed8e5ba0cfaf24e2c2f1e5b8a0495711e44fcd4882fca62bcf'},
+    {'serde_json-1.0.125.tar.gz': '83c8e735a073ccf5be70aa8066aa984eaf2fa000db6c8d0100ae605b366d31ed'},
+    {'sha1-0.10.6.tar.gz': 'e3bf829a2d51ab4a5ddf1352d8470c140cadc8301b2ae1789db023f01cedd6ba'},
+    {'sha2-0.10.8.tar.gz': '793db75ad2bcafc3ffa7c68b215fee268f537982cd901d132f89c6343f3a3dc8'},
+    {'shlex-1.3.0.tar.gz': '0fda2ff0d084019ba4d7c6f371c95d8fd75ce3524c3cb8fb653a3023f6323e64'},
+    {'strsim-0.10.0.tar.gz': '73473c0e59e6d5812c5dfe2a064a6444949f089e20eec9a2e5506596494e4623'},
+    {'subtle-2.6.1.tar.gz': '13c2bddecc57b384dee18652358fb23172facb8a2c51ccc10d74c157bdea3292'},
+    {'syn-1.0.109.tar.gz': '72b64191b275b66ffe2469e8af2c1cfe3bafa67b529ead792a6d0160888b4237'},
+    {'syn-2.0.75.tar.gz': 'f6af063034fc1935ede7be0122941bafa9bacb949334d090b77ca98b5817c7d9'},
+    {'tch-0.14.0.tar.gz': '0ed5dddab3812892bf5fb567136e372ea49f31672931e21cec967ca68aec03da'},
+    {'thiserror-1.0.63.tar.gz': 'c0342370b38b6a11b6cc11d6a805569958d54cfa061a29969c3b5ce2ea405724'},
+    {'thiserror-impl-1.0.63.tar.gz': 'a4558b58466b9ad7ca0f102865eccc95938dca1a74a856f2b57b6629050da261'},
+    {'time-0.3.36.tar.gz': '5dfd88e563464686c916c7e46e623e520ddc6d79fa6641390f2e3fa86e83e885'},
+    {'time-core-0.1.2.tar.gz': 'ef927ca75afb808a4d64dd374f00a2adf8d0fcff8e7b184af886c3c87ec4a3f3'},
+    {'torch-sys-0.14.0.tar.gz': '803446f89fb877a117503dbfb8375b6a29fa8b0e0f44810fac3863c798ecef22'},
+    {'typenum-1.17.0.tar.gz': '42ff0bf0c66b8238c6f3b578df37d0b7848e55df8577b3f74f92a69acceeb825'},
+    {'ucd-trie-0.1.6.tar.gz': 'ed646292ffc8188ef8ea4d1e0e0150fb15a5c2e12ad9b8fc191ae7a8a7f3c4b9'},
+    {'unicode-ident-1.0.12.tar.gz': '3354b9ac3fae1ff6755cb6db53683adb661634f67557942dea4facebec0fee4b'},
+    {'unicode-width-0.1.13.tar.gz': '0336d538f7abc86d282a4189614dfaa90810dfc2c6f6427eaf88e16311dd225d'},
+    {'utf8parse-0.2.2.tar.gz': '06abde3611657adf66d383f00b093d7faecc7fa57071cce2578660c9f1010821'},
+    {'version_check-0.9.5.tar.gz': '0b928f33d975fc6ad9f86c8f283853ad26bdd5b10b7f1542aa2fa15e2289105a'},
+    {'wasi-0.11.0+wasi-snapshot-preview1.tar.gz': '9c8d87e72b64a3b4db28d11ce29237c246188f4f51057d65a7eab63b7987e423'},
+    {'windows-sys-0.52.0.tar.gz': '282be5f36a8ce781fad8c8ae18fa3f9beff57ec1b52cb3de0789201425d9a33d'},
+    {'windows-targets-0.52.6.tar.gz': '9b724f72796e036ab90c1021d4780d4d3d648aca59e491e6b98e725b84e99973'},
+    {'windows_aarch64_gnullvm-0.52.6.tar.gz': '32a4622180e7a0ec044bb555404c800bc9fd9ec262ec147edd5989ccd0c02cd3'},
+    {'windows_aarch64_msvc-0.52.6.tar.gz': '09ec2a7bb152e2252b53fa7803150007879548bc709c039df7627cabbd05d469'},
+    {'windows_i686_gnu-0.52.6.tar.gz': '8e9b5ad5ab802e97eb8e295ac6720e509ee4c243f69d781394014ebfe8bbfa0b'},
+    {'windows_i686_gnullvm-0.52.6.tar.gz': '0eee52d38c090b3caa76c563b86c3a4bd71ef1a819287c19d586d7334ae8ed66'},
+    {'windows_i686_msvc-0.52.6.tar.gz': '240948bc05c5e7c6dabba28bf89d89ffce3e303022809e73deaefe4f6ec56c66'},
+    {'windows_x86_64_gnu-0.52.6.tar.gz': '147a5c80aabfbf0c7d901cb5895d1de30ef2907eb21fbbab29ca94c5b08b1a78'},
+    {'windows_x86_64_gnullvm-0.52.6.tar.gz': '24d5b23dc417412679681396f2b49f3de8c1473deb516bd34410872eff51ed0d'},
+    {'windows_x86_64_msvc-0.52.6.tar.gz': '589f6da84c646204747d1270a2a5661ea66ed1cced2631d546fdfb155959f9ec'},
+    {'xz2-0.1.7.tar.gz': '388c44dc09d76f1536602ead6d325eb532f5c122f17782bd57fb47baeeb767e2'},
+    {'zerocopy-0.7.35.tar.gz': '1b9b4fd18abc82b8136838da5d50bae7bdea537c574d8dc1a34ed098d6c166f0'},
+    {'zerocopy-derive-0.7.35.tar.gz': 'fa4f8080344d4671fb4e831a13ad1e68092748387dfc4f55e356242fae12ce3e'},
+    {'zip-0.6.6.tar.gz': '760394e246e4c28189f19d488c058bf16f564016aefac5d32bb1f3b51d5e9261'},
+    {'zstd-0.11.2+zstd.1.5.2.tar.gz': '20cc960326ece64f010d2d2107537f26dc589a6573a316bd5b1dba685fa5fde4'},
+    {'zstd-0.13.2.tar.gz': 'fcf2b778a664581e31e389454a7072dab1647606d44f7feea22cd5abb9c9f3f9'},
+    {'zstd-safe-5.0.2+zstd.1.5.2.tar.gz': '1d2a5585e04f9eea4b2a3d1eca508c4dee9592a89ef6f450c11719da0726f4db'},
+    {'zstd-safe-7.2.1.tar.gz': '54a3ab4db68cea366acc5c897c7b4d4d1b8994a9cd6e6f841f8964566a419059'},
+    {'zstd-sys-2.0.13+zstd.1.5.6.tar.gz': '38ff0f21cfee8f97d94cef41359e0c89aa6113028ab0291aa8ca0038995a95aa'},
+]
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.3.10-foss-2023a.eb b/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.3.10-foss-2023a.eb
new file mode 100644
index 00000000000..45740411804
--- /dev/null
+++ b/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.3.10-foss-2023a.eb
@@ -0,0 +1,109 @@
+easyblock = 'CMakeMake'
+
+name = 'pod5-file-format'
+version = '0.3.10'
+
+homepage = 'https://github.com/nanoporetech/pod5-file-format'
+description = """POD5 is a file format for storing nanopore dna data in an easily accessible way.
+ The format is able to be written in a streaming manner which allows a sequencing
+ instrument to directly write the format."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+source_urls = ['https://github.com/nanoporetech/%(name)s/archive/']
+sources = [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}]
+patches = ['pod5-file-format-0.3.10_dep_fix.patch']
+checksums = [
+    {'pod5-file-format-0.3.10.tar.gz': 'eb177018b310e508f7ad6b5d486cc29166404dd5f82879d0c26aceaff51d3768'},
+    {'pod5-file-format-0.3.10_dep_fix.patch': '20dc87ab82d4b52ff7fb769d17c2478daf95f787b2a184c9d985e33e03038e31'},
+]
+    
+builddependencies = [
+    ('poetry', '1.5.1'),
+    ('CMake', '3.26.3'),
+    ('pkgconfig', '1.5.5', '-python'),
+]
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('Python-bundle-PyPI', '2023.06'),
+    ('Arrow', '14.0.1'),
+    ('SciPy-bundle', '2023.07'),
+    ('zstd', '1.5.5'),
+    ('flatbuffers', '23.5.26'),
+    ('pybind11', '2.11.1'),
+    ('Boost', '1.82.0'),
+    ('build', '1.0.3'),
+    ('HDF5', '1.14.0'),
+    ('h5py', '3.9.0'),
+    ('tqdm', '4.66.1'),
+    ('polars', '0.20.2'),
+]
+
+exts_defaultclass = 'PythonPackage'
+exts_default_options = {
+    'source_urls': [PYPI_SOURCE],
+    'download_dep_fail': True,
+    'use_pip': True,
+    'sanity_pip_check': True,
+    'installopts': '',
+}
+
+# unpin polars and h5py versions in pod5
+local_preinstallopts = (
+    "sed -i"
+    " -e 's/polars~=0.19/polars/'"
+    " -e 's/h5py~=3.10.0/h5py/'"
+    " pyproject.toml && "
+)
+
+exts_list = [
+    ('vbz_h5py_plugin', '1.0.1', {
+        'checksums': ['c784458bb0aad6303474cb2f10956179116b35555803fd1154eb4ef362519341'],
+    }),
+    ('iso8601', '2.1.0', {
+        'checksums': ['6b1d3829ee8921c4301998c909f7829fa9ed3cbdac0d3b16af2d743aed1ba8df'],
+    }),
+    ('pod5', version, {
+        'preinstallopts': local_preinstallopts,
+        'checksums': ['f2dcb1938fcf51c725393345e480c1d12711089d542a27446fb92fbe2e18ae60'],
+    }),
+]
+
+# create POD5Version.cmake
+# python -m setuptools_scm && python -m pod5_make_version shows wrong version
+preconfigopts = (
+    'cd %(builddir)s/%(name)s-%(version)s/cmake && ' 
+    'touch POD5Version.cmake && '
+    'echo "set(POD5_VERSION_MAJOR 0)">POD5Version.cmake && '
+    'echo "set(POD5_VERSION_MINOR 3)">>POD5Version.cmake && '
+    'echo "set(POD5_VERSION_REV 10)">>POD5Version.cmake && '
+    'echo "set(POD5_NUMERIC_VERSION 0.3.10)">>POD5Version.cmake && '
+    'echo "set(POD5_FULL_VERSION 0.3.10)">>POD5Version.cmake && '
+)
+
+# delete add_subdirectory(third_party/pybind11) from CMakeLists.txt
+preconfigopts += "cd %(builddir)s/%(name)s-%(version)s && sed -i '/add_subdirectory(third_party/d' CMakeLists.txt && "
+preconfigopts += 'cd %(builddir)s/easybuild_obj && '
+
+configopts = ' -DBUILD_PYTHON_WHEEL=ON -DZSTD_LIB="$EBROOTZSTD/lib" -DZSTD_INCLUDE_DIR="$EBROOTZSTD/include"'
+
+# install lib_pod5 from wheel - dependency of pod5
+installopts = ' && export XDG_CACHE_HOME=%(builddir)s && cd %(installdir)s'
+installopts += ' && pip install --no-deps --ignore-installed --prefix %(installdir)s lib_pod5-%(version)s-*.whl'
+
+postinstallcmds = ['rm %(installdir)s/lib_pod5-%(version)s-*.whl']
+
+sanity_check_paths = {
+    'files': ['bin/pod5', 'lib/libpod5_format.a'],
+    'dirs': ['include/pod5_format', 'lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = [
+    "pod5 subset --help",
+    "python -c 'import lib_pod5'",
+]
+
+modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'}
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.3.10_dep_fix.patch b/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.3.10_dep_fix.patch
new file mode 100644
index 00000000000..a053f870ebe
--- /dev/null
+++ b/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.3.10_dep_fix.patch
@@ -0,0 +1,32 @@
+Flatbuffers 2.0.7 uses capital 'B' in 'FlatBuffersConfig.cmake'
+We want to use our pybind11 instead of the one in git submodules
+Author: Petr Král (INUITS)
+diff -u c++/CMakeLists.txt.orig c++/CMakeLists.txt
+--- c++/CMakeLists.txt.orig      2023-02-23 19:17:13.000000000 +0100
++++ c++/CMakeLists.txt   2023-04-25 14:07:28.174884834 +0200
+@@ -3,7 +3,7 @@
+ if (ENABLE_CONAN)
+     find_package(Arrow REQUIRED CONFIG)
+     find_package(Boost REQUIRED CONFIG)
+-    find_package(Flatbuffers REQUIRED CONFIG)
++    find_package(FlatBuffers REQUIRED CONFIG)
+     find_package(zstd REQUIRED CONFIG)
+     find_package(ZLIB REQUIRED CONFIG)
+ 
+@@ -17,7 +17,7 @@
+         COMPONENTS
+             headers
+     )
+-    find_package(Flatbuffers REQUIRED)
++    find_package(FlatBuffers REQUIRED)
+     find_package(zstd REQUIRED)
+     find_package(ZLIB REQUIRED)
+ 
+@@ -27,6 +27,7 @@
+ endif()
+ 
+ find_package(Threads REQUIRED)
++find_package(pybind11 REQUIRED)
+ 
+ find_program(
+     FLATBUFFERS_FLATC_EXECUTABLE

From 9c0b3627addd0f06520f41b87fd470d700fc9823 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com>
Date: Fri, 23 Aug 2024 12:45:53 +0200
Subject: [PATCH 688/835] Update pod5-file-format-0.3.10_dep_fix.patch - update
 description

---
 .../p/pod5-file-format/pod5-file-format-0.3.10_dep_fix.patch   | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.3.10_dep_fix.patch b/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.3.10_dep_fix.patch
index a053f870ebe..b0207d6c4ac 100644
--- a/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.3.10_dep_fix.patch
+++ b/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.3.10_dep_fix.patch
@@ -1,5 +1,4 @@
-Flatbuffers 2.0.7 uses capital 'B' in 'FlatBuffersConfig.cmake'
-We want to use our pybind11 instead of the one in git submodules
+Flatbuffers uses capital 'B' in 'FlatBuffersConfig.cmake'
 Author: Petr Král (INUITS)
 diff -u c++/CMakeLists.txt.orig c++/CMakeLists.txt
 --- c++/CMakeLists.txt.orig      2023-02-23 19:17:13.000000000 +0100

From fcfb0d5cd6bca9be5b40adc4521388f31a6226b3 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Petr=20Kr=C3=A1l?= <petr@inuits.eu>
Date: Fri, 23 Aug 2024 13:07:35 +0200
Subject: [PATCH 689/835] adding easyconfigs: SeqKit-2.8.2.eb

---
 .../easyconfigs/s/SeqKit/SeqKit-2.8.2.eb      | 26 +++++++++++++++++++
 1 file changed, 26 insertions(+)
 create mode 100644 easybuild/easyconfigs/s/SeqKit/SeqKit-2.8.2.eb

diff --git a/easybuild/easyconfigs/s/SeqKit/SeqKit-2.8.2.eb b/easybuild/easyconfigs/s/SeqKit/SeqKit-2.8.2.eb
new file mode 100644
index 00000000000..820f9abf719
--- /dev/null
+++ b/easybuild/easyconfigs/s/SeqKit/SeqKit-2.8.2.eb
@@ -0,0 +1,26 @@
+easyblock = 'GoPackage'
+
+name = 'SeqKit'
+version = '2.8.2'
+
+homepage = 'https://bioinf.shenwei.me/seqkit/'
+description = """SeqKit - a cross-platform and ultrafast toolkit for FASTA/Q file manipulation"""
+
+toolchain = SYSTEM
+
+source_urls = ['https://github.com/shenwei356/seqkit/archive']
+sources = ['v%(version)s.tar.gz']
+checksums = ['9cf1e744b785fa673af5a7a1ce2f96d52dc03e14b6537097df86aa6266204556']
+
+builddependencies = [
+    ('Go', '1.22.1'),
+]
+
+installopts = './%(namelower)s'
+
+sanity_check_commands = [
+    "seqkit version",
+    "seqkit genautocomplete"
+]
+
+moduleclass = 'bio'

From a2e4f8d4ee03bef5612032c80ea29042c57bb037 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Petr=20Kr=C3=A1l?= <petr@inuits.eu>
Date: Fri, 23 Aug 2024 14:30:05 +0200
Subject: [PATCH 690/835] adding easyconfigs:
 coxeter-20180226-GCCcore-13.2.0.eb and patches:
 coxeter-20180226_makefile.patch

---
 .../coxeter-20180226-GCCcore-13.2.0.eb        |  41 +++++++
 .../c/coxeter/coxeter-20180226_makefile.patch | 101 ++++++++++++++++++
 2 files changed, 142 insertions(+)
 create mode 100644 easybuild/easyconfigs/c/coxeter/coxeter-20180226-GCCcore-13.2.0.eb
 create mode 100644 easybuild/easyconfigs/c/coxeter/coxeter-20180226_makefile.patch

diff --git a/easybuild/easyconfigs/c/coxeter/coxeter-20180226-GCCcore-13.2.0.eb b/easybuild/easyconfigs/c/coxeter/coxeter-20180226-GCCcore-13.2.0.eb
new file mode 100644
index 00000000000..1fbcfa900b6
--- /dev/null
+++ b/easybuild/easyconfigs/c/coxeter/coxeter-20180226-GCCcore-13.2.0.eb
@@ -0,0 +1,41 @@
+easyblock = 'ConfigureMake'
+
+name = 'coxeter'
+version = '20180226'
+local_commit = '7b5a1f0'
+
+homepage = 'https://github.com/tscrim/coxeter'
+description = """A library for the study of combinatorial aspects of Coxeter group theory"""
+
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
+
+source_urls = ['https://github.com/tscrim/coxeter/archive/%s/' % local_commit]
+sources = [SOURCE_TAR_GZ]
+patches = ['coxeter-20180226_makefile.patch']
+checksums = [
+    {'coxeter-20180226.tar.gz': '5e0668c40b29c03c438a6ebc0f49f13aaf155b4bcbff56303a753390e6fce3aa'},
+    {'coxeter-20180226_makefile.patch': '229ed201e41bae0ae7b22aa21d5007127aeb52fd158543dd5fff2e89797e211f'},
+]
+
+builddependencies = [('binutils', '2.40')]
+
+skipsteps = ['configure']
+
+buildopts = 'CC="$CC" CFLAGS="$CFLAGS"'
+preinstallopts = 'mkdir -p "%(installdir)s/bin" "%(installdir)s/lib" && '
+installopts = 'SAGE_LOCAL="%(installdir)s"'
+
+sanity_check_paths = {
+    'files': [
+        'bin/%(name)s',
+        'lib/lib%%(name)s3.%s' % SHLIB_EXT,
+    ],
+    'dirs': [
+        'include/%(name)s',
+        'share/%(name)s',
+    ]
+}
+
+sanity_check_commands = ['echo "qq" | coxeter']
+
+moduleclass = 'math'
diff --git a/easybuild/easyconfigs/c/coxeter/coxeter-20180226_makefile.patch b/easybuild/easyconfigs/c/coxeter/coxeter-20180226_makefile.patch
new file mode 100644
index 00000000000..d00d6860689
--- /dev/null
+++ b/easybuild/easyconfigs/c/coxeter/coxeter-20180226_makefile.patch
@@ -0,0 +1,101 @@
+Allows installation of files needed for Sagemath
+Source: https://gitlab.archlinux.org/archlinux/packaging/packages/coxeter/-/blob/main/coxeter-makefile.patch
+diff -u makefile.orig makefile
+--- makefile.orig	2018-02-26 13:57:36.000000000 +0100
++++ makefile	2024-08-16 14:15:51.889503570 +0200
+@@ -12,6 +12,7 @@
+ gflags = -c $(includedirs) -g
+ 
+ cflags = $(gflags) # the default setting
++cflags = -c $(includedirs) $(CPPFLAGS) $(CXXFLAGS) -fPIC
+ 
+ ifdef optimize
+ 	NDEBUG = true
+@@ -22,18 +23,74 @@
+ 	cflags = $(pflags)
+ endif
+ 
+-cc = g++
++EXENAME = coxeter
++LIBNAME = coxeter3
++ifeq ($(UNAME),Darwin)
++	EXEEXT = 
++	LIBPREFIX = lib
++	LIBEXT = .dylib
++	LIBDIR = lib
++	LINKFLAGS = -dynamiclib -Wl,-headerpad_max_install_names,-undefined,dynamic_lookup,-compatibility_version,3.0,-current_version,3.0,-install_name,$(SAGE_LOCAL)/lib/$(LIBPREFIX)$(LIBNAME)$(LIBEXT)
++	LINKLIBS = 
++else
++ifeq ($(UNAME),CYGWIN)
++	EXEEXT = .exe
++	LIBPREFIX = cyg
++	LIBEXT = .dll
++	LIBDIR = bin
++	IMPLIB = lib$(LIBNAME).dll.a
++	LINKFLAGS = -shared -Wl,--out-implib=$(IMPLIB) -Wl,--export-all-symbols
++	LINKLIBS = -lc
++else
++	EXEEXT = 
++	LIBPREFIX = lib
++	LIBEXT = .so
++	LIBDIR = lib
++	LINKFLAGS = $(LDFLAGS) -shared -Wl,-soname,libcoxeter3.so
++	LINKLIBS = -lc
++endif
++endif
++LIBRARY = $(LIBPREFIX)$(LIBNAME)$(LIBEXT)
+ 
+-all: coxeter #clean
++all: coxeter executable
+ 
+ coxeter: $(objects)
+-	$(cc) -o coxeter $(objects)
++	$(CXX) $(LINKFLAGS) -o $(LIBRARY) $(objects) $(LINKLIBS)
++
++executable: $(objects)
++	$(CXX) $(LDFLAGS) -o $(EXENAME)$(EXEEXT) $(objects)
++
++DATADIR="$$SAGE_LOCAL/share/coxeter/"
++INCLUDEDIR="$$SAGE_LOCAL/include/coxeter/"
++LIBRARYDIR="$$SAGE_LOCAL/$(LIBDIR)"
++
++install: coxeter executable
++	cp $(EXENAME)$(EXEEXT) "$$SAGE_LOCAL/bin/"
++	cp $(LIBRARY) $(LIBRARYDIR)
++	if [ $(UNAME) = "CYGWIN" ]; then                 \
++	    cp $(IMPLIB) "$$SAGE_LOCAL/lib/";  \
++	fi
++
++	mkdir -p $(DATADIR)
++	cp -r coxeter_matrices headers messages $(DATADIR)
++	mkdir -p $(INCLUDEDIR)
++	cp -r *.h *.hpp $(INCLUDEDIR)
++
++check: coxeter executable
++	$(EXENAME)$(EXEEXT) < test.input > test.output
++
++	if ! diff test.output.expected test.output > /dev/null; then \
++	   echo >&2 "Error testing coxeter on test.input:"; \
++	   diff test.output.expected test.output; \
++	   exit 1; \
++	fi
++	rm -f test.output
+ 
+ clean:
+ 	rm -f $(objects)
+ 
+ %.o:%.cpp
+-	$(cc) $(cflags) $*.cpp
++	$(CXX) $(cflags) $*.cpp
+ 
+ # dependencies --- these were generated automatically by make depend on my
+ # system; they are explicitly copied for portability. Only local dependencies
+@@ -43,7 +100,7 @@
+ # contents of tmp in lieu of the dependencies listed here.
+ 
+ %.d:%.cpp
+-	@$(cc) -MM $*.cpp
++	@$(CXX) -MM $*.cpp
+ depend: $(dependencies)
+ 
+ affine.o: affine.cpp affine.h globals.h coxgroup.h coxtypes.h io.h list.h \

From ee8dcee7c9691d80cd34c076ab351ae27b2b2782 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Fri, 23 Aug 2024 14:54:47 +0200
Subject: [PATCH 691/835] fix whitespaces

---
 .../easyconfigs/h/HERRO/HERRO-0.1.0_20240808-foss-2023a.eb    | 4 ++--
 .../p/pod5-file-format/pod5-file-format-0.3.10-foss-2023a.eb  | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/easybuild/easyconfigs/h/HERRO/HERRO-0.1.0_20240808-foss-2023a.eb b/easybuild/easyconfigs/h/HERRO/HERRO-0.1.0_20240808-foss-2023a.eb
index d27b48f9a9b..ecef67eed26 100644
--- a/easybuild/easyconfigs/h/HERRO/HERRO-0.1.0_20240808-foss-2023a.eb
+++ b/easybuild/easyconfigs/h/HERRO/HERRO-0.1.0_20240808-foss-2023a.eb
@@ -94,7 +94,7 @@ sanity_check_paths = {
     'files': ['bin/%s' % x for x in _bins],
     'dirs': ['lib/python%(pyshortver)s/site-packages'],
 }
- 
+
 sanity_check_commands = ["herro --help"]
 
 modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'}
@@ -102,7 +102,7 @@ modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'}
 modloadmsg = """
 To run scripts from /scripts directory just run <script_name>.sh
 Do not run it as scripts/<script_name>.sh
-For example - run preprocess.sh as: 
+For example - run preprocess.sh as:
     $ preprocess.sh <input_fastq> <output_prefix> <number_of_threads> <parts_to_split_job_into>
 """
 
diff --git a/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.3.10-foss-2023a.eb b/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.3.10-foss-2023a.eb
index 45740411804..f0db4069b1c 100644
--- a/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.3.10-foss-2023a.eb
+++ b/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.3.10-foss-2023a.eb
@@ -17,7 +17,7 @@ checksums = [
     {'pod5-file-format-0.3.10.tar.gz': 'eb177018b310e508f7ad6b5d486cc29166404dd5f82879d0c26aceaff51d3768'},
     {'pod5-file-format-0.3.10_dep_fix.patch': '20dc87ab82d4b52ff7fb769d17c2478daf95f787b2a184c9d985e33e03038e31'},
 ]
-    
+
 builddependencies = [
     ('poetry', '1.5.1'),
     ('CMake', '3.26.3'),
@@ -73,7 +73,7 @@ exts_list = [
 # create POD5Version.cmake
 # python -m setuptools_scm && python -m pod5_make_version shows wrong version
 preconfigopts = (
-    'cd %(builddir)s/%(name)s-%(version)s/cmake && ' 
+    'cd %(builddir)s/%(name)s-%(version)s/cmake && '
     'touch POD5Version.cmake && '
     'echo "set(POD5_VERSION_MAJOR 0)">POD5Version.cmake && '
     'echo "set(POD5_VERSION_MINOR 3)">>POD5Version.cmake && '

From d2351dbf30a935911537e96c3f9ae49df42fd7fa Mon Sep 17 00:00:00 2001
From: WilleBell <cintiawillemyns@gmail.com>
Date: Fri, 23 Aug 2024 15:00:41 +0200
Subject: [PATCH 692/835] Add patch to fix issue 21243

---
 .../easyconfigs/x/xtb/xtb-6.7.0-gfbf-2023a.eb |   8 +-
 .../x/xtb/xtb-6.7.0_fix-tblite-pr1072.patch   | 487 ++++++++++++++++++
 2 files changed, 494 insertions(+), 1 deletion(-)
 create mode 100644 easybuild/easyconfigs/x/xtb/xtb-6.7.0_fix-tblite-pr1072.patch

diff --git a/easybuild/easyconfigs/x/xtb/xtb-6.7.0-gfbf-2023a.eb b/easybuild/easyconfigs/x/xtb/xtb-6.7.0-gfbf-2023a.eb
index 97ce290bfe0..81ee768fed0 100644
--- a/easybuild/easyconfigs/x/xtb/xtb-6.7.0-gfbf-2023a.eb
+++ b/easybuild/easyconfigs/x/xtb/xtb-6.7.0-gfbf-2023a.eb
@@ -11,7 +11,13 @@ toolchain = {'name': 'gfbf', 'version': '2023a'}
 github_account = 'grimme-lab'
 source_urls = [GITHUB_LOWER_SOURCE]
 sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}]
-checksums = ['9cf1997064d2d5bde7fae4cec6f873469602e6554872ad79de4079f022855ae2']
+patches = [
+    'xtb-6.7.0_fix-tblite-pr1072.patch'
+]
+checksums = [
+    {'xtb-6.7.0.tar.gz': '9cf1997064d2d5bde7fae4cec6f873469602e6554872ad79de4079f022855ae2'},
+    {'xtb-6.7.0_fix-tblite-pr1072.patch': 'cb8de869fc4a7c6bde44c61a479fc9edb3ccdc47c2a71f15ef124326f8a117e6'},
+]
 
 builddependencies = [
     ('Meson', '1.1.1'),
diff --git a/easybuild/easyconfigs/x/xtb/xtb-6.7.0_fix-tblite-pr1072.patch b/easybuild/easyconfigs/x/xtb/xtb-6.7.0_fix-tblite-pr1072.patch
new file mode 100644
index 00000000000..74e2ea4950e
--- /dev/null
+++ b/easybuild/easyconfigs/x/xtb/xtb-6.7.0_fix-tblite-pr1072.patch
@@ -0,0 +1,487 @@
+see https://github.com/grimme-lab/xtb/pull/1072 + https://github.com/grimme-lab/xtb/issues/1091
+diff -Naur xtb-6.7.0.orig/src/dipro/xtb.F90 xtb-6.7.0/src/dipro/xtb.F90
+--- xtb-6.7.0.orig/src/dipro/xtb.F90	2024-08-23 13:50:09.000345982 +0200
++++ xtb-6.7.0/src/dipro/xtb.F90	2024-08-23 14:14:49.499145489 +0200
+@@ -50,11 +50,11 @@
+       call fatal_error(error, "Unknown method '"//method//"' requested")
+ !      error stop
+    case("gfn2")
+-      call new_gfn2_calculator(xcalc, mol)
++      call new_gfn2_calculator(xcalc, mol, error)
+    case("gfn1")
+-      call new_gfn1_calculator(xcalc, mol)
++      call new_gfn1_calculator(xcalc, mol, error)
+    case("ipea1")
+-      call new_ipea1_calculator(xcalc, mol)
++      call new_ipea1_calculator(xcalc, mol, error)
+    end select
+ end subroutine get_calculator
+ #endif
+diff -Naur xtb-6.7.0.orig/src/dipro.F90 xtb-6.7.0/src/dipro.F90
+--- xtb-6.7.0.orig/src/dipro.F90	2024-08-23 13:50:08.996896000 +0200
++++ xtb-6.7.0/src/dipro.F90	2024-08-23 13:55:44.571958738 +0200
+@@ -130,6 +130,10 @@
+ !=========================set up calculator===========================================   
+ 
+    call get_calculator(xcalc, struc, tblite%method, error)  
++   if (allocated(error)) then
++      call env%error(error%message, source)
++      return
++   end if
+    call new_wavefunction(wfn, struc%nat, xcalc%bas%nsh, xcalc%bas%nao, & 
+       & 1, set%etemp * ktoau)
+    wfn%nspin=1
+@@ -258,6 +262,10 @@
+       write(*,'(A,I2)') "unpaired e- of fragment : ", mfrag(ifr)%uhf
+ 
+       call get_calculator(fcalc(ifr), mfrag(ifr), tblite%method, error)
++      if (allocated(error)) then
++        call env%error(error%message, source)
++        return
++      end if
+       !> mol%charge is updated automatically from wfn by tblite library 
+       call new_wavefunction(wfx(ifr), mfrag(ifr)%nat, fcalc(ifr)%bas%nsh, fcalc(ifr)%bas%nao, &
+          & 1, set%etemp * ktoau)
+diff -Naur xtb-6.7.0.orig/src/tblite/calculator.F90 xtb-6.7.0/src/tblite/calculator.F90
+--- xtb-6.7.0.orig/src/tblite/calculator.F90	2024-08-23 13:50:09.192101000 +0200
++++ xtb-6.7.0/src/tblite/calculator.F90	2024-08-23 14:18:13.034251635 +0200
+@@ -144,11 +144,11 @@
+       case default
+          call fatal_error(error, "Unknown method '"//method//"' requested")
+       case("gfn2")
+-         call new_gfn2_calculator(calc%tblite, struc)
++         call new_gfn2_calculator(calc%tblite, struc, error)
+       case("gfn1")
+-         call new_gfn1_calculator(calc%tblite, struc)
++         call new_gfn1_calculator(calc%tblite, struc, error)
+       case("ipea1")
+-         call new_ipea1_calculator(calc%tblite, struc)
++         call new_ipea1_calculator(calc%tblite, struc, error)
+       end select
+    end if
+    if (allocated(error)) then
+diff -Naur xtb-6.7.0.orig/subprojects/mstore.wrap xtb-6.7.0/subprojects/mstore.wrap
+--- xtb-6.7.0.orig/subprojects/mstore.wrap	2024-08-23 13:50:09.235197230 +0200
++++ xtb-6.7.0/subprojects/mstore.wrap	2024-08-23 14:18:50.314014066 +0200
+@@ -1,4 +1,4 @@
+ [wrap-git]
+ directory = mstore
+ url = https://github.com/grimme-lab/mstore
+-revision = v0.2.0
++revision = v0.3.0
+diff -Naur xtb-6.7.0.orig/test/unit/test_ptb.F90 xtb-6.7.0/test/unit/test_ptb.F90
+--- xtb-6.7.0.orig/test/unit/test_ptb.F90	2024-08-23 13:50:09.260760000 +0200
++++ xtb-6.7.0/test/unit/test_ptb.F90	2024-08-23 14:34:18.302090669 +0200
+@@ -186,12 +186,37 @@
+       !> (Scaled) overlap matrix
+       character(len=:), allocatable :: message
+       real(wp), parameter :: overlap_exp(6) = [ &
+-      & 0.93209460_wp, & ! 1,2
+-      & 0.35489609_wp, & ! 1,3
+-      & 0.65682608_wp, & ! 2,3
+-      & 0.05627743_wp, & ! 1,15
+-      & -0.14217162_wp, &  ! 1,24; diffferent because of tblite ordering
+-      & 0.41844087_wp] ! 14,23; diffferent because of tblite ordering
++      & 0.93209460_wp, & ! s(Mg)-s(Mg)
++      & 0.35489609_wp, & ! s(Mg)-s(Mg)
++      & 0.65682608_wp, & ! s(Mg)-s(Mg)
++      & 0.05627743_wp, & ! s(Mg)-s(H)
++      & -0.14217162_wp, & ! s(Mg)-pz(H)
++      & 0.41844087_wp] ! dyz(Mg)-py(H)
++      ! 1: s(Mg)
++      ! 2: s(Mg)
++      ! 3: s(Mg)
++      ! 4: py(Mg)
++      ! 5: pz(Mg)
++      ! 6: px(Mg)
++      ! 7: py(Mg)
++      ! 8: pz(Mg)
++      ! 9: px(Mg)
++      ! 10: dxy(Mg)
++      ! 11: dyz(Mg)
++      ! 12: dz2(Mg)
++      ! 13: dxz(Mg)
++      ! 14: dx2-y2(Mg)
++      ! 15: s(H)
++      ! 16: s(H)
++      ! 17: py(H)
++      ! 18: pz(H)
++      ! 19: px(H)
++      ! 20: s(H)
++      ! 21: s(H)
++      ! 22: py(H)
++      ! 23: pz(H)
++      ! 24: px(H)
++
+       real(wp), allocatable :: lattr(:, :)
+       real(wp) :: cutoff
+ 
+@@ -215,7 +240,7 @@
+       call check_(error, ints%overlap(2, 3), overlap_exp(3), thr=thr)
+       call check_(error, ints%overlap(1, 15), overlap_exp(4), thr=thr)
+       call check_(error, ints%overlap(1, 23), overlap_exp(5), thr=thr)
+-      call check_(error, ints%overlap(12, 22), overlap_exp(6), thr=thr)
++      call check_(error, ints%overlap(11, 22), overlap_exp(6), thr=thr)
+ 
+    end subroutine test_ptb_overlap
+ 
+@@ -249,12 +274,37 @@
+       type(error_type), allocatable, intent(out) :: error
+       character(len=:), allocatable :: message
+       real(wp), parameter :: overlap_exp(6) = [ &
+-      & 0.95689468_wp, & ! 1,2
+-      & 0.39195790_wp, & ! 1,3
+-      & 0.62961212_wp, & ! 2,3
+-      & 0.03782850_wp, & ! 1,15
+-      &-0.13826216_wp, &  ! 1,24; diffferent because of tblite ordering
+-      & 0.43334922_wp] ! 14,23; diffferent because of tblite ordering
++      & 0.95689468_wp, & ! s(Mg)-s(Mg)
++      & 0.39195790_wp, & ! s(Mg)-s(Mg)
++      & 0.62961212_wp, & ! s(Mg)-s(Mg)
++      & 0.03782850_wp, & ! s(Mg)-s(H)
++      &-0.13826216_wp, & ! s(Mg)-pz(H)
++      & 0.43334922_wp] ! dyz(Mg)-py(H)
++      ! 1: s(Mg)
++      ! 2: s(Mg)
++      ! 3: s(Mg)
++      ! 4: py(Mg)
++      ! 5: pz(Mg)
++      ! 6: px(Mg)
++      ! 7: py(Mg)
++      ! 8: pz(Mg)
++      ! 9: px(Mg)
++      ! 10: dxy(Mg)
++      ! 11: dyz(Mg)
++      ! 12: dz2(Mg)
++      ! 13: dxz(Mg)
++      ! 14: dx2-y2(Mg)
++      ! 15: s(H)
++      ! 16: s(H)
++      ! 17: py(H)
++      ! 18: pz(H)
++      ! 19: px(H)
++      ! 20: s(H)
++      ! 21: s(H)
++      ! 22: py(H)
++      ! 23: pz(H)
++      ! 24: px(H)
++
+       real(wp), allocatable :: lattr(:, :)
+       real(wp) :: cutoff
+ 
+@@ -286,7 +336,7 @@
+       & message=message)
+       call check_(error, auxints%overlap_h0_1(1, 23), overlap_exp(5), thr=thr, &
+       & message=message)
+-      call check_(error, auxints%overlap_h0_1(12, 22), overlap_exp(6), thr=thr, &
++      call check_(error, auxints%overlap_h0_1(11, 22), overlap_exp(6), thr=thr, &
+       & message=message)
+ 
+    end subroutine test_ptb_overlap_h0
+@@ -319,12 +369,37 @@
+       real(wp), allocatable :: overlap_sx(:, :), overlap_oneminusx(:, :)
+       character(len=:), allocatable :: message
+       real(wp), parameter :: overlap_oneminusx_exp(6) = [ &
+-      & 0.70788_wp, & ! 1,2
+-      & 0.16203_wp, & ! 1,3
+-      & 0.41532_wp, & ! 2,3
+-      & 0.01449_wp, & ! 1,15
+-      &-0.07203_wp, &  ! 1,24; diffferent because of tblite ordering
+-      & 0.28751_wp] ! 14,23; diffferent because of tblite ordering
++      & 0.70788_wp, & ! s(Mg)-s(Mg)
++      & 0.16203_wp, & ! s(Mg)-s(Mg)
++      & 0.41532_wp, & ! s(Mg)-s(Mg)
++      & 0.01449_wp, & ! s(Mg)-s(H)
++      &-0.07203_wp, & ! s(Mg)-pz(H)
++      & 0.28751_wp] ! dyz(Mg)-py(H)
++      ! 1: s(Mg)
++      ! 2: s(Mg)
++      ! 3: s(Mg)
++      ! 4: py(Mg)
++      ! 5: pz(Mg)
++      ! 6: px(Mg)
++      ! 7: py(Mg)
++      ! 8: pz(Mg)
++      ! 9: px(Mg)
++      ! 10: dxy(Mg)
++      ! 11: dyz(Mg)
++      ! 12: dz2(Mg)
++      ! 13: dxz(Mg)
++      ! 14: dx2-y2(Mg)
++      ! 15: s(H)
++      ! 16: s(H)
++      ! 17: py(H)
++      ! 18: pz(H)
++      ! 19: px(H)
++      ! 20: s(H)
++      ! 21: s(H)
++      ! 22: py(H)
++      ! 23: pz(H)
++      ! 24: px(H)
++
+       real(wp), allocatable :: lattr(:, :)
+       real(wp) :: cutoff
+ 
+@@ -356,7 +431,7 @@
+       & message=message)
+       call check_(error, overlap_oneminusx(1, 23), overlap_oneminusx_exp(5), thr=thr2, &
+       & message=message)
+-      call check_(error, overlap_oneminusx(12, 22), overlap_oneminusx_exp(6), thr=thr2, &
++      call check_(error, overlap_oneminusx(11, 22), overlap_oneminusx_exp(6), thr=thr2, &
+       & message=message)
+ 
+    end subroutine test_ptb_overlap_SX
+@@ -392,10 +467,37 @@
+       type(error_type), allocatable, intent(out) :: error
+       character(len=:), allocatable :: message
+       real(wp), parameter :: vecp_ref(4) = [ &
+-      &  0.077719_wp, & ! 1,1 ; diffferent because of tblite ordering
+-      & -0.059122_wp, & ! 1,3 ; diffferent because of tblite ordering
+-      &  0.052775_wp, & ! 3,5 ; diffferent because of tblite ordering
+-      &  0.117176_wp]   ! 9,9 ; diffferent because of tblite ordering
++      &  0.077719_wp, & ! s(B)-s(B)
++      & -0.059122_wp, & ! s(B)-px(B)
++      &  0.052775_wp, & ! px(B)-px(B)
++      &  0.117176_wp]   ! dx2-y2(B)-dx2-y2(B)
++      ! 1: s(B)
++      ! 2: s(B)
++      ! 3: py(B)
++      ! 4: pz(B)
++      ! 5: px(B)
++      ! 6: py(B)
++      ! 7: pz(B)
++      ! 8: px(B)
++      ! 9: dxy(B)
++      ! 10: dyz(B)
++      ! 11: dz2(B)
++      ! 12: dxz(B)
++      ! 13: dx2-y2(B)
++      ! 14: s(Cl)
++      ! 15: s(Cl)
++      ! 16: py(Cl)
++      ! 17: pz(Cl)
++      ! 18: px(Cl)
++      ! 19: py(Cl)
++      ! 20: pz(Cl)
++      ! 21: px(Cl)
++      ! 22: dxy(Cl)
++      ! 23: dyz(Cl)
++      ! 24: dz2(Cl)
++      ! 25: dxz(Cl)
++      ! 26: dx2-y2(Cl)
++
+       real(wp), parameter :: xyz(3, 2) = reshape([ &
+       & 2.0_wp, 0.0_wp, 0.0_wp, &
+       & 0.0_wp, 0.0_wp, 0.0_wp], [3, 2])
+@@ -434,7 +536,7 @@
+       & message=message)
+       call check_(error, vecp(5, 8), vecp_ref(3), thr=thr2, &
+       & message=message)
+-      call check_(error, vecp(12, 12), vecp_ref(4), thr=thr2, &
++      call check_(error, vecp(13, 13), vecp_ref(4), thr=thr2, &
+       & message=message)
+    end subroutine test_ptb_V_ECP
+ 
+@@ -629,12 +731,39 @@
+       real(wp), allocatable :: vecp(:, :)
+ 
+       real(wp), parameter :: h0_ref(6) = [ &
+-      &  -1.59330281_wp, & ! 1,1
+-      &  -2.24996207_wp, & ! 1,2
+-      &   0.34974782_wp, & ! 1,23 ; diffferent because of tblite ordering
+-      &   0.0_wp, & ! 7,11 ; different because of tblite ordering
+-      &  -1.17757007_wp, & ! 3,6 ; different because of tblite ordering
+-      &   0.48301561_wp]   ! 11,24 ; diffferent because of tblite ordering
++      &  -1.59330281_wp, & ! s(B)-s(B)
++      &  -2.24996207_wp, & ! s(B)-s(B)
++      &   0.34974782_wp, & ! s(B)-py(Cl)
++      &   0.0_wp, & ! dx2-y2(B)-py(B)
++      &  -1.17757007_wp, & ! px(B)-px(B)
++      &   0.48301561_wp]   ! dxy(B)-dxy(Cl)
++      ! 1: s(B)
++      ! 2: s(B)
++      ! 3: py(B)
++      ! 4: pz(B)
++      ! 5: px(B)
++      ! 6: py(B)
++      ! 7: pz(B)
++      ! 8: px(B)
++      ! 9: dxy(B)
++      ! 10: dyz(B)
++      ! 11: dz2(B)
++      ! 12: dxz(B)
++      ! 13: dx2-y2(B)
++      ! 14: s(Cl)
++      ! 15: s(Cl)
++      ! 16: py(Cl)
++      ! 17: pz(Cl)
++      ! 18: px(Cl)
++      ! 19: py(Cl)
++      ! 20: pz(Cl)
++      ! 21: px(Cl)
++      ! 22: dxy(Cl)
++      ! 23: dyz(Cl)
++      ! 24: dz2(Cl)
++      ! 25: dxz(Cl)
++      ! 26: dx2-y2(Cl)
++
+       real(wp), parameter :: levels(10) = [ &
+       &    -0.796651404_wp, &
+       &    -0.269771638_wp, &
+@@ -670,10 +799,10 @@
+       message = "H0 matrix element not matching to expected value."
+       call check_(error, ints%hamiltonian(1, 1), h0_ref(1), thr=thr)
+       call check_(error, ints%hamiltonian(1, 2), h0_ref(2), thr=thr)
+-      call check_(error, ints%hamiltonian(1, 22), h0_ref(3), thr=thr)
++      call check_(error, ints%hamiltonian(1, 24), h0_ref(3), thr=thr)
+       call check_(error, ints%hamiltonian(13, 6), h0_ref(4), thr=thr)
+       call check_(error, ints%hamiltonian(8, 5), h0_ref(5), thr=thr)
+-      call check_(error, ints%hamiltonian(13, 26), h0_ref(6), thr=thr)
++      call check_(error, ints%hamiltonian(9, 22), h0_ref(6), thr=thr)
+    end subroutine test_ptb_hamiltonian_h0
+ 
+    subroutine test_ptb_V_XC(error)
+@@ -708,10 +837,37 @@
+       type(error_type), allocatable, intent(out) :: error
+       character(len=:), allocatable :: message
+       real(wp), parameter :: Vxc_ref(4) = [ &
+-      & -0.92793357_wp, & ! 1,1
+-      & -0.85981333_wp, & ! 1,2
+-      &  0.06632750_wp, & ! 1,23 ; diffferent because of tblite ordering
+-      &  0.00151880_wp]   ! 11,24 ; diffferent because of tblite ordering
++      & -0.92793357_wp, & ! s(B)-s(B)
++      & -0.85981333_wp, & ! s(B)-s(B)
++      &  0.06632750_wp, & ! s(B)-dz2(Cl)
++      &  0.00151880_wp]   ! dxy(B)-dxy(Cl)
++      ! 1: s(B)
++      ! 2: s(B)
++      ! 3: py(B)
++      ! 4: pz(B)
++      ! 5: px(B)
++      ! 6: py(B)
++      ! 7: pz(B)
++      ! 8: px(B)
++      ! 9: dxy(B)
++      ! 10: dyz(B)
++      ! 11: dz2(B)
++      ! 12: dxz(B)
++      ! 13: dx2-y2(B)
++      ! 14: s(Cl)
++      ! 15: s(Cl)
++      ! 16: py(Cl)
++      ! 17: pz(Cl)
++      ! 18: px(Cl)
++      ! 19: py(Cl)
++      ! 20: pz(Cl)
++      ! 21: px(Cl)
++      ! 22: dxy(Cl)
++      ! 23: dyz(Cl)
++      ! 24: dz2(Cl)
++      ! 25: dxz(Cl)
++      ! 26: dx2-y2(Cl)
++
+       real(wp), parameter :: xyz(3, 2) = reshape([ &
+       & 2.0_wp, 0.0_wp, 0.0_wp, &
+       & 0.0_wp, 0.0_wp, 0.0_wp], [3, 2])
+@@ -769,9 +925,9 @@
+       & message=message)
+       call check_(error, Vxc(1, 2), Vxc_ref(2), thr=thr, &
+       & message=message)
+-      call check_(error, Vxc(1, 22), Vxc_ref(3), thr=thr, &
++      call check_(error, Vxc(1, 24), Vxc_ref(3), thr=thr, &
+       & message=message)
+-      call check_(error, Vxc(13, 26), Vxc_ref(4), thr=thr, &
++      call check_(error, Vxc(9, 22), Vxc_ref(4), thr=thr, &
+       & message=message)
+ 
+    end subroutine test_ptb_V_XC
+@@ -957,10 +1113,35 @@
+       !> Conversion factor from temperature to energy
+       real(wp), parameter :: kt = 3.166808578545117e-06_wp
+       real(wp), parameter :: coulomb_pot_ref(4) = [ &
+-      &  -0.05693153_wp, & ! 1,1
+-      &  -0.33917531_wp, & ! 1,2
+-      &  -0.00539212_wp, & ! 1,21 ; diffferent because of tblite ordering
+-      &   0.01305793_wp]   ! 6,24 ; diffferent because of tblite ordering
++      &  -0.05693153_wp, & ! s(Mg)-s(Mg)
++      &  -0.33917531_wp, & ! s(Mg)-s(Mg)
++      &  -0.00539212_wp, & ! s(Mg)-s(H)
++      &   0.01305793_wp]   ! pz(Mg)-pz(H)
++      ! 1: s(Mg)
++      ! 2: s(Mg)
++      ! 3: s(Mg)
++      ! 4: py(Mg)
++      ! 5: pz(Mg)
++      ! 6: px(Mg)
++      ! 7: py(Mg)
++      ! 8: pz(Mg)
++      ! 9: px(Mg)
++      ! 10: dxy(Mg)
++      ! 11: dyz(Mg)
++      ! 12: dz2(Mg)
++      ! 13: dxz(Mg)
++      ! 14: dx2-y2(Mg)
++      ! 15: s(H)
++      ! 16: s(H)
++      ! 17: py(H)
++      ! 18: pz(H)
++      ! 19: px(H)
++      ! 20: s(H)
++      ! 21: s(H)
++      ! 22: py(H)
++      ! 23: pz(H)
++      ! 24: px(H)
++
+       real(wp), allocatable :: lattr(:, :)
+       real(wp) :: cutoff
+ 
+@@ -1044,10 +1225,36 @@
+       integer, parameter :: nat = 2
+       integer, parameter :: at(nat) = [5, 17]
+       real(wp), parameter :: plusU_pot_ref(4) = [ &
+-      &  -0.0023185_wp, & ! 1,1
+-      &  -0.0018289_wp, & ! 1,2
+-      &  -0.5266562_wp, & ! 1,21 ; diffferent because of tblite ordering
+-      &  -1.6745659_wp]   ! 6,24 ; diffferent because of tblite ordering
++      &  -0.0023185_wp, & ! s(B)-s(B)
++      &  -0.0018289_wp, & ! s(B)-s(B)
++      &  -0.5266562_wp, & ! s(B)-pz(Cl)
++      &  -1.6745659_wp]   ! px(B)-dxy(Cl)
++      ! 1: s(B)
++      ! 2: s(B)
++      ! 3: py(B)
++      ! 4: pz(B)
++      ! 5: px(B)
++      ! 6: py(B)
++      ! 7: pz(B)
++      ! 8: px(B)
++      ! 9: dxy(B)
++      ! 10: dyz(B)
++      ! 11: dz2(B)
++      ! 12: dxz(B)
++      ! 13: dx2-y2(B)
++      ! 14: s(Cl)
++      ! 15: s(Cl)
++      ! 16: py(Cl)
++      ! 17: pz(Cl)
++      ! 18: px(Cl)
++      ! 19: py(Cl)
++      ! 20: pz(Cl)
++      ! 21: px(Cl)
++      ! 22: dxy(Cl)
++      ! 23: dyz(Cl)
++      ! 24: dz2(Cl)
++      ! 25: dxz(Cl)
++      ! 26: dx2-y2(Cl)
+ 
+       call new(mol, at, xyz)
+       allocate (ptbData)
+@@ -1067,7 +1274,7 @@
+       call check_(error, wfn%coeff(1, 1, 1), plusU_pot_ref(1), thr=thr)
+       call check_(error, wfn%coeff(1, 2, 1), plusU_pot_ref(2), thr=thr)
+       call check_(error, wfn%coeff(1, 20, 1), plusU_pot_ref(3), thr=thr)
+-      call check_(error, wfn%coeff(8, 26, 1), plusU_pot_ref(4), thr=thr)
++      call check_(error, wfn%coeff(8, 22, 1), plusU_pot_ref(4), thr=thr)
+ 
+    end subroutine test_ptb_plus_U_potential
+ 

From f5d48ce3410053903a4cf8e75207be586fc60265 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Fri, 23 Aug 2024 16:13:41 +0200
Subject: [PATCH 693/835] update patch for pod5

---
 .../p/pod5-file-format/pod5-file-format-0.3.10_dep_fix.patch   | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.3.10_dep_fix.patch b/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.3.10_dep_fix.patch
index b0207d6c4ac..a053f870ebe 100644
--- a/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.3.10_dep_fix.patch
+++ b/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.3.10_dep_fix.patch
@@ -1,4 +1,5 @@
-Flatbuffers uses capital 'B' in 'FlatBuffersConfig.cmake'
+Flatbuffers 2.0.7 uses capital 'B' in 'FlatBuffersConfig.cmake'
+We want to use our pybind11 instead of the one in git submodules
 Author: Petr Král (INUITS)
 diff -u c++/CMakeLists.txt.orig c++/CMakeLists.txt
 --- c++/CMakeLists.txt.orig      2023-02-23 19:17:13.000000000 +0100

From 0576d05b7ea4b091ff3c87c5d04e826d9b4776b5 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Fri, 23 Aug 2024 16:17:18 +0200
Subject: [PATCH 694/835] adding easyconfigs: nellie-0.3.1-foss-2023a.eb,
 ome-types-0.5.1.post1-foss-2023a.eb

---
 .../n/nellie/nellie-0.3.1-foss-2023a.eb       | 52 +++++++++++++++++++
 .../ome-types-0.5.1.post1-foss-2023a.eb       | 52 +++++++++++++++++++
 2 files changed, 104 insertions(+)
 create mode 100644 easybuild/easyconfigs/n/nellie/nellie-0.3.1-foss-2023a.eb
 create mode 100644 easybuild/easyconfigs/o/ome-types/ome-types-0.5.1.post1-foss-2023a.eb

diff --git a/easybuild/easyconfigs/n/nellie/nellie-0.3.1-foss-2023a.eb b/easybuild/easyconfigs/n/nellie/nellie-0.3.1-foss-2023a.eb
new file mode 100644
index 00000000000..5032e0e6ec5
--- /dev/null
+++ b/easybuild/easyconfigs/n/nellie/nellie-0.3.1-foss-2023a.eb
@@ -0,0 +1,52 @@
+easyblock = 'PythonBundle'
+
+name = 'nellie'
+version = '0.3.1'
+
+homepage = 'https://github.com/aelefebv/nellie/'
+description = """
+Napari plugin for automated organelle segmentation, 
+tracking, and hierarchical feature extraction in 2D/3D live-cell microscopy.
+"""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('Python-bundle-PyPI', '2023.06'),
+    ('SciPy-bundle', '2023.07'),
+    ('napari', '0.4.18'),
+    ('scikit-image', '0.22.0'),
+    ('imagecodecs', '2024.1.1'),
+    ('matplotlib', '3.7.2'),
+    ('ome-types', '0.5.1.post1'),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+local_preinstallopts = (
+    "sed -i"
+    " -e 's/numpy==1.26.4/numpy/'"
+    " -e 's/scipy==1.12.0/scipy/'"
+    " -e 's/nd2==0.9.0/nd2/'"
+    " -e 's/pandas==2.2.1/pandas/'"
+    " -e 's/matplotlib==3.8.3/matplotlib/'"
+    " -e 's/napari[all]/napari/'"
+    " setup.cfg && "
+)
+
+exts_list = [
+    ('resource_backed_dask_array', '0.1.0', {
+        'checksums': ['8fabcccf5c7e29059b5badd6786dd7675a258a203c58babf10077d9c90ada54f'],
+    }),
+    ('nd2', '0.10.1', {
+        'checksums': ['88ee60f6ba39392722a162da58fb81bf0cdb8ed6c772772e4db91e90f97e490a'],
+    }),
+    (name, version, {
+        'preinstallopts': "sed -i -e 's/numpy==1.26.4/numpy/' -e 's/scipy==1.12.0/scipy/' -e 's/nd2==0.9.0/nd2/' -e 's/pandas==2.2.1/pandas/' -e 's/matplotlib==3.8.3/matplotlib/' -e 's/napari[all]/napari/' setup.cfg && ",
+        'checksums': ['3fd85bd1c7df5a8f24bff2118805cd7c82140b08871d520b2131d4d9a8c00d94'],
+    }),
+]
+
+moduleclass = 'vis'
diff --git a/easybuild/easyconfigs/o/ome-types/ome-types-0.5.1.post1-foss-2023a.eb b/easybuild/easyconfigs/o/ome-types/ome-types-0.5.1.post1-foss-2023a.eb
new file mode 100644
index 00000000000..0de34e3542b
--- /dev/null
+++ b/easybuild/easyconfigs/o/ome-types/ome-types-0.5.1.post1-foss-2023a.eb
@@ -0,0 +1,52 @@
+easyblock = 'PythonBundle'
+
+name = 'ome-types'
+version = '0.5.1.post1'
+
+homepage = 'https://github.com/tlambert03/ome-types/'
+description = """
+ome_types provides a set of python dataclasses and utility functions for parsing 
+the OME-XML format into fully-typed python objects for interactive or programmatic access in python.
+"""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+builddependencies = [
+    ('poetry', '1.5.1'),
+    ('hatchling', '1.18.0'),
+    ('maturin', '1.4.0', '-Rust-1.75.0'),
+]
+dependencies = [
+    ('Python', '3.11.3'),
+    ('pydantic', '2.5.3'),
+    ('Python-bundle-PyPI', '2023.06'),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    ('ruff', '0.3.0', {
+        'checksums': ['0886184ba2618d815067cf43e005388967b67ab9c80df52b32ec1152ab49f53a'],
+    }),
+    ('pydantic_compat', '0.1.2', {
+        'checksums': ['c5c5bca39ca2d22cad00c02898e400e1920e5127649a8e860637f15566739373'],
+    }),
+    ('untokenize', '0.1.1', {
+        'checksums': ['3865dbbbb8efb4bb5eaa72f1be7f3e0be00ea8b7f125c69cbd1f5fda926f37a2'],
+    }),
+    ('docformatter', '1.7.5', {
+        'checksums': ['ffed3da0daffa2e77f80ccba4f0e50bfa2755e1c10e130102571c890a61b246e'],
+    }),
+    ('toposort', '1.10', {
+        'checksums': ['bfbb479c53d0a696ea7402601f4e693c97b0367837c8898bc6471adfca37a6bd'],
+    }),
+    ('xsdata', '23.8', {
+        'checksums': ['55f03d4c88236f047266affe550ba0dd19476adfce6a01f3e0aefac7c8078e56'],
+    }),
+    ('ome_types', version, {
+        'checksums': ['cadda5e36ad4d33dad2034fd43f32113a736fe47c67fd9e06bbb8d3858d1dc58'],
+    }),
+]
+
+moduleclass = 'lib'

From 4ee2a2d3c83587cbfe1c4914d465cd5c5ea72a4a Mon Sep 17 00:00:00 2001
From: Sebastian Achilles <s.achilles@fz-juelich.de>
Date: Sat, 24 Aug 2024 09:53:20 +0200
Subject: [PATCH 695/835] update configopts

---
 easybuild/easyconfigs/x/x265/x265-3.6-GCCcore-13.3.0.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/x/x265/x265-3.6-GCCcore-13.3.0.eb b/easybuild/easyconfigs/x/x265/x265-3.6-GCCcore-13.3.0.eb
index 307c0abb034..fc9ad81c0cb 100644
--- a/easybuild/easyconfigs/x/x265/x265-3.6-GCCcore-13.3.0.eb
+++ b/easybuild/easyconfigs/x/x265/x265-3.6-GCCcore-13.3.0.eb
@@ -22,7 +22,7 @@ builddependencies = [
     ('Yasm', '1.3.0'),
 ]
 
-configopts = '-DGIT_ARCHETYPE=1'
+configopts = '-DGIT_ARCHETYPE=1 -DENABLE_PIC=ON'
 
 start_dir = 'source'
 

From e55798f254fc2ae2c64234b5482a36dcc202a402 Mon Sep 17 00:00:00 2001
From: SebastianAchilles <s.achilles@fz-juelich.de>
Date: Sat, 24 Aug 2024 09:53:45 +0200
Subject: [PATCH 696/835] Use preconfigopts instead of configure_cmd_prefix

Co-authored-by: Sam Moors <smoors@users.noreply.github.com>
---
 easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-13.3.0.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-13.3.0.eb
index c4080545d5b..1fa3ca78fd9 100644
--- a/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-13.3.0.eb
+++ b/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-13.3.0.eb
@@ -26,7 +26,7 @@ dependencies = [('ncurses', '6.5')]
 preconfigopts = "autoconf && "
 
 # configure is broken: add workaround to find libncurses...
-configure_cmd_prefix = "FRONTEND_LDADD='-L${EBROOTNCURSES}/lib' "
+preconfigopts += "FRONTEND_LDADD='-L${EBROOTNCURSES}/lib' "
 
 sanity_check_paths = {
     'files': ['bin/lame', 'include/lame/lame.h', 'lib/libmp3lame.%s' % SHLIB_EXT],

From b2b08049e3ef9d280624bffd39b089f834e498ad Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Mon, 26 Aug 2024 11:04:02 +0200
Subject: [PATCH 697/835] update preinstallopts

---
 easybuild/easyconfigs/n/nellie/nellie-0.3.1-foss-2023a.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/n/nellie/nellie-0.3.1-foss-2023a.eb b/easybuild/easyconfigs/n/nellie/nellie-0.3.1-foss-2023a.eb
index 5032e0e6ec5..34b3ce6299a 100644
--- a/easybuild/easyconfigs/n/nellie/nellie-0.3.1-foss-2023a.eb
+++ b/easybuild/easyconfigs/n/nellie/nellie-0.3.1-foss-2023a.eb
@@ -44,7 +44,7 @@ exts_list = [
         'checksums': ['88ee60f6ba39392722a162da58fb81bf0cdb8ed6c772772e4db91e90f97e490a'],
     }),
     (name, version, {
-        'preinstallopts': "sed -i -e 's/numpy==1.26.4/numpy/' -e 's/scipy==1.12.0/scipy/' -e 's/nd2==0.9.0/nd2/' -e 's/pandas==2.2.1/pandas/' -e 's/matplotlib==3.8.3/matplotlib/' -e 's/napari[all]/napari/' setup.cfg && ",
+        'preinstallopts': local_preinstallopts,
         'checksums': ['3fd85bd1c7df5a8f24bff2118805cd7c82140b08871d520b2131d4d9a8c00d94'],
     }),
 ]

From d49b40557d3cbecf3755832446302e63acada8f3 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Mon, 26 Aug 2024 11:16:30 +0200
Subject: [PATCH 698/835] update duplex_tools sources

---
 .../easyconfigs/d/duplex-tools/duplex-tools-0.3.3-foss-2023a.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/d/duplex-tools/duplex-tools-0.3.3-foss-2023a.eb b/easybuild/easyconfigs/d/duplex-tools/duplex-tools-0.3.3-foss-2023a.eb
index fe56d08acaa..fb67d050e02 100644
--- a/easybuild/easyconfigs/d/duplex-tools/duplex-tools-0.3.3-foss-2023a.eb
+++ b/easybuild/easyconfigs/d/duplex-tools/duplex-tools-0.3.3-foss-2023a.eb
@@ -48,7 +48,7 @@ exts_list = [
         'checksums': ['93aff63ce88bc5cfe7152d8dcb3f2164356bcd8f95a68fb20af107e59a7f9b55'],
     }),
     (name, version, {
-        'source_tmpl': 'duplex_tools-%(version)s.tar.gz',
+        'sources': [{'download_filename': 'duplex_tools-%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}],
         'checksums': ['883e0a6610d14328a640b6a31eaef90592d2967cda68db0547a4d99924281300'],
     }),
 ]

From 6279f73668124799c163dfc4fbc66c4fec32766f Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 26 Aug 2024 12:05:38 +0200
Subject: [PATCH 699/835] add insight extension to R-bundle-CRAN 2024.06

---
 .../r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb        | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb b/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb
index c8376489c57..d239f2596c2 100644
--- a/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb
+++ b/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb
@@ -3436,6 +3436,9 @@ exts_list = [
     ('missMDA', '1.19', {
         'checksums': ['f9675884829b2fef75237c335b21991d163674320e766523c71c7a853f95e65c'],
     }),
+    ('insight', '0.20.3', {
+        'checksums': ['b60e189849cd3c368e9c2b2174e89c2dfbba3b34e84feb8a20af1bb758116bb2'],
+    }),
 ]
 
 modextrapaths = {'R_LIBS_SITE': ''}

From c1a8df0af156c31ec3745f03332b8f6221ac95d0 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 26 Aug 2024 12:08:22 +0200
Subject: [PATCH 700/835] adding easyconfigs: BayesOpt-0.9-GCC-12.3.0.eb

---
 .../b/BayesOpt/BayesOpt-0.9-GCC-12.3.0.eb     | 29 +++++++++++++++++++
 1 file changed, 29 insertions(+)
 create mode 100644 easybuild/easyconfigs/b/BayesOpt/BayesOpt-0.9-GCC-12.3.0.eb

diff --git a/easybuild/easyconfigs/b/BayesOpt/BayesOpt-0.9-GCC-12.3.0.eb b/easybuild/easyconfigs/b/BayesOpt/BayesOpt-0.9-GCC-12.3.0.eb
new file mode 100644
index 00000000000..ab0e97a41ad
--- /dev/null
+++ b/easybuild/easyconfigs/b/BayesOpt/BayesOpt-0.9-GCC-12.3.0.eb
@@ -0,0 +1,29 @@
+easyblock = 'CMakeMake'
+
+name = 'BayesOpt'
+version = '0.9'
+
+homepage = 'https://rmcantin.github.io/bayesopt'
+description = """BayesOpt is an efficient implementation of the Bayesian optimization methodology for
+nonlinear-optimization, experimental design, stochastic bandits and hyperparameter tunning"""
+
+toolchain = {'name': 'GCC', 'version': '12.3.0'}
+
+source_urls = ['https://github.com/rmcantin/bayesopt/archive/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['f4e60cfac380eccd2d1adc805b752b5bd22a1d8a27dc6aeb630c403adc04f28c']
+
+builddependencies = [
+    ('CMake', '3.26.3'),
+]
+
+dependencies = [
+    ('Boost', '1.82.0'),
+]
+
+sanity_check_paths = {
+    'files': ['lib/libbayesopt.a', 'lib/libnlopt.a'],
+    'dirs': ['include/bayesopt'],
+}
+
+moduleclass = 'math'

From 2e502ae39b1724c81e4e200ff9c0536e49ece880 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 26 Aug 2024 12:22:14 +0200
Subject: [PATCH 701/835] add missing NLopt dependency for BayesOpt

---
 easybuild/easyconfigs/b/BayesOpt/BayesOpt-0.9-GCC-12.3.0.eb | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/b/BayesOpt/BayesOpt-0.9-GCC-12.3.0.eb b/easybuild/easyconfigs/b/BayesOpt/BayesOpt-0.9-GCC-12.3.0.eb
index ab0e97a41ad..2e20ceba904 100644
--- a/easybuild/easyconfigs/b/BayesOpt/BayesOpt-0.9-GCC-12.3.0.eb
+++ b/easybuild/easyconfigs/b/BayesOpt/BayesOpt-0.9-GCC-12.3.0.eb
@@ -19,10 +19,14 @@ builddependencies = [
 
 dependencies = [
     ('Boost', '1.82.0'),
+    ('NLopt', '2.7.1'),
 ]
 
+# don't build included version of NLopt (use provided dependency)
+configopts = "-DNLOPT_BUILD=OFF"
+
 sanity_check_paths = {
-    'files': ['lib/libbayesopt.a', 'lib/libnlopt.a'],
+    'files': ['lib/libbayesopt.a'],
     'dirs': ['include/bayesopt'],
 }
 

From cfd1b541d24b1fc704c61ec5a3613e50919caf85 Mon Sep 17 00:00:00 2001
From: Chia-Jung Hsu <appolloford@gmail.com>
Date: Mon, 26 Aug 2024 12:19:06 +0000
Subject: [PATCH 702/835] Fix cpu and gpu versions of bitsandbytes

---
 ...sandbytes-0.43.3-foss-2023a-CUDA-12.1.1.eb | 49 +++++++++++++++++++
 .../bitsandbytes-0.43.3-foss-2023a.eb         |  4 +-
 2 files changed, 51 insertions(+), 2 deletions(-)
 create mode 100644 easybuild/easyconfigs/b/bitsandbytes/bitsandbytes-0.43.3-foss-2023a-CUDA-12.1.1.eb

diff --git a/easybuild/easyconfigs/b/bitsandbytes/bitsandbytes-0.43.3-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/b/bitsandbytes/bitsandbytes-0.43.3-foss-2023a-CUDA-12.1.1.eb
new file mode 100644
index 00000000000..3b89d58cc47
--- /dev/null
+++ b/easybuild/easyconfigs/b/bitsandbytes/bitsandbytes-0.43.3-foss-2023a-CUDA-12.1.1.eb
@@ -0,0 +1,49 @@
+easyblock = 'CMakeMake'
+
+name = 'bitsandbytes'
+version = '0.43.3'
+versionsuffix = '-CUDA-%(cudaver)s'
+
+homepage = 'https://huggingface.co/docs/bitsandbytes/main/en/index'
+description = "bitsandbytes enables accessible large language models via k-bit quantization for PyTorch."
+github_account = 'bitsandbytes-foundation'
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+source_urls = [GITHUB_LOWER_SOURCE]
+sources = ['%(version)s.tar.gz']
+checksums = ['7a468bc977da19c176cc578954bfd7a3c64182f387a6849e9f0a38d5cba1b4df']
+
+builddependencies = [
+    ('CMake', '3.26.3'),
+    ('pkgconf', '1.9.5'),
+]
+
+dependencies = [
+    ('CUDA', '12.1.1', '', SYSTEM),
+    ('Python', '3.11.3'),
+    ('PyTorch', '2.1.2', versionsuffix),
+    ('SciPy-bundle', '2023.07'),
+]
+
+configopts = '-DCOMPUTE_BACKEND=cuda'
+skipsteps = ['install']
+
+postinstallcmds = [
+    'pip install --prefix=%(installdir)s --no-deps --ignore-installed --no-index --no-build-isolation %(start_dir)s',
+]
+
+sanity_check_paths = {
+    'files': ['lib/python3.11/site-packages/bitsandbytes/libbitsandbytes_cuda121.so'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = [
+    "python -c 'import bitsandbytes'",
+]
+
+modextrapaths = {
+    'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']
+}
+
+moduleclass = 'ai'
diff --git a/easybuild/easyconfigs/b/bitsandbytes/bitsandbytes-0.43.3-foss-2023a.eb b/easybuild/easyconfigs/b/bitsandbytes/bitsandbytes-0.43.3-foss-2023a.eb
index 902b7d717f1..8a6b11e5a2c 100644
--- a/easybuild/easyconfigs/b/bitsandbytes/bitsandbytes-0.43.3-foss-2023a.eb
+++ b/easybuild/easyconfigs/b/bitsandbytes/bitsandbytes-0.43.3-foss-2023a.eb
@@ -20,11 +20,11 @@ builddependencies = [
 
 dependencies = [
     ('Python', '3.11.3'),
-    ('PyTorch', '2.1.2', '-CUDA-12.1.1'),
+    ('PyTorch', '2.1.2'),
     ('SciPy-bundle', '2023.07'),
 ]
 
-configopts = '-DCOMPUTE_BACKEND=cuda'
+# configopts = '-DCOMPUTE_BACKEND=cuda'
 skipsteps = ['install']
 
 postinstallcmds = [

From a91f271f0acfb03f0ae432ec4d7152a9c96372a1 Mon Sep 17 00:00:00 2001
From: Chia-Jung Hsu <appolloford@gmail.com>
Date: Mon, 26 Aug 2024 12:24:31 +0000
Subject: [PATCH 703/835] Remove comments

---
 .../easyconfigs/b/bitsandbytes/bitsandbytes-0.43.3-foss-2023a.eb | 1 -
 1 file changed, 1 deletion(-)

diff --git a/easybuild/easyconfigs/b/bitsandbytes/bitsandbytes-0.43.3-foss-2023a.eb b/easybuild/easyconfigs/b/bitsandbytes/bitsandbytes-0.43.3-foss-2023a.eb
index 8a6b11e5a2c..e9f92c025a9 100644
--- a/easybuild/easyconfigs/b/bitsandbytes/bitsandbytes-0.43.3-foss-2023a.eb
+++ b/easybuild/easyconfigs/b/bitsandbytes/bitsandbytes-0.43.3-foss-2023a.eb
@@ -24,7 +24,6 @@ dependencies = [
     ('SciPy-bundle', '2023.07'),
 ]
 
-# configopts = '-DCOMPUTE_BACKEND=cuda'
 skipsteps = ['install']
 
 postinstallcmds = [

From 60f891b74fa97c883591e44e4194b38b0fd7a523 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 26 Aug 2024 17:19:02 +0200
Subject: [PATCH 704/835] add back easyconfig for VTK 9.3.0 that shouldn't have
 been removed

---
 .../easyconfigs/v/VTK/VTK-9.3.0-foss-2023a.eb | 98 +++++++++++++++++++
 1 file changed, 98 insertions(+)
 create mode 100644 easybuild/easyconfigs/v/VTK/VTK-9.3.0-foss-2023a.eb

diff --git a/easybuild/easyconfigs/v/VTK/VTK-9.3.0-foss-2023a.eb b/easybuild/easyconfigs/v/VTK/VTK-9.3.0-foss-2023a.eb
new file mode 100644
index 00000000000..740fd888dfb
--- /dev/null
+++ b/easybuild/easyconfigs/v/VTK/VTK-9.3.0-foss-2023a.eb
@@ -0,0 +1,98 @@
+##
+# Authors::
+# * Fotis Georgatos <fotis@cern.ch>
+# * Robert Mijakovic <robert.mijakovic@lxp.lu>
+# Update: Pavel Tománek (Inuits)
+##
+
+easyblock = 'CMakeNinja'
+
+name = 'VTK'
+version = '9.3.0'
+
+homepage = 'https://www.vtk.org'
+description = """The Visualization Toolkit (VTK) is an open-source, freely available software system for
+ 3D computer graphics, image processing and visualization. VTK consists of a C++ class library and several
+ interpreted interface layers including Tcl/Tk, Java, and Python. VTK supports a wide variety of visualization
+ algorithms including: scalar, vector, tensor, texture, and volumetric methods; and advanced modeling techniques
+ such as: implicit modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+toolchainopts = {'usempi': True}
+
+source_urls = ['https://www.vtk.org/files/release/%(version_major_minor)s']
+sources = [
+    SOURCE_TAR_GZ,
+    '%(name)sData-%(version)s.tar.gz',
+]
+patches = [('vtk-version.egg-info', '.')]
+checksums = [
+    {'VTK-9.3.0.tar.gz': 'fdc7b9295225b34e4fdddc49cd06e66e94260cb00efee456e0f66568c9681be9'},
+    {'VTKData-9.3.0.tar.gz': 'f82142dd327e995c9536c1003e1370bb4092c96f23edb8119d16d2411ef35dc3'},
+    {'vtk-version.egg-info': '787b82415ae7a4a1f815b4db0e25f7abc809a05fc85d7d219627f3a7e5d3867b'},
+]
+
+builddependencies = [
+    ('CMake', '3.26.3'),
+    ('Ninja', '1.11.1'),
+]
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('XZ', '5.4.2'),
+    ('libGLU', '9.0.3'),
+    ('X11', '20230603'),
+    ('Qt5', '5.15.10'),
+]
+
+separate_build_dir = True
+
+# OpenGL
+configopts = "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT
+configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT
+configopts += "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include "
+# Python
+configopts += "-DVTK_WRAP_PYTHON=ON -DVTK_PYTHON_VERSION=3 -DVTK_PYTHON_OPTIONAL_LINK=OFF "
+configopts += "-DPython3_EXECUTABLE=$EBROOTPYTHON/bin/python3 "
+configopts += "-DPython3_INCLUDE_DIR=$EBROOTPYTHON/include/python%(pyshortver)s "
+configopts += "-DPython3_LIBRARY=$EBROOTPYTHON/lib/libpython%(pyshortver)s.so "
+# Other
+configopts += "-DVTK_USE_MPI=ON "
+configopts += "-DCMAKE_INSTALL_LIBDIR=lib "
+configopts += "-DVTK_QT_VERSION=5 "
+configopts += "-DQt5_DIR=$EBROOTQT5 "
+configopts += "-DVTK_MODULE_ENABLE_VTK_GuiSupportQt=YES "
+configopts += "-DVTK_MODULE_ENABLE_VTK_ViewsQt=YES"
+
+preinstallopts = "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && "
+
+# Install a egg-info file so VTK is more python friendly, required for mayavi
+local_egg_info_src = '%(builddir)s/VTK-%(version)s/vtk-version.egg-info'
+local_egg_info_dest = '%(installdir)s/lib/python%(pyshortver)s/site-packages/vtk-%(version)s.egg-info'
+postinstallcmds = [
+    'sed "s/#VTK_VERSION#/%%(version)s/" %s > %s' % (local_egg_info_src, local_egg_info_dest),
+]
+
+modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']}
+
+local_vtk_exec = ['vtk%s-%%(version_major_minor)s' % x
+                  for x in ['WrapJava', 'ParseJava', 'WrapPythonInit', 'WrapPython', 'WrapHierarchy']]
+local_vtk_exec += ['vtkpython']
+local_vtk_libs = ['CommonCore', 'IONetCDF', 'ParallelCore', 'RenderingOpenGL2']
+
+sanity_check_paths = {
+    'files': ['bin/%s' % x for x in local_vtk_exec] + ['include/vtk-%(version_major_minor)s/vtkMPI.h'] +
+             ['lib/libvtk%s-%%(version_major_minor)s.%s' % (l, SHLIB_EXT) for l in local_vtk_libs],
+    'dirs': ['lib/python%(pyshortver)s/site-packages/', 'include/vtk-%(version_major_minor)s'],
+}
+
+sanity_check_commands = [
+    "python -c 'import %(namelower)s'",
+    "python -c 'import pkg_resources; pkg_resources.get_distribution(\"vtk\")'",
+    # make sure that VTK Python libraries link to libpython (controlled via DVTK_PYTHON_OPTIONAL_LINK=OFF),
+    # see https://gitlab.kitware.com/vtk/vtk/-/issues/17881
+    "ldd $EBROOTVTK/lib/libvtkPythonContext2D-%%(version_major_minor)s.%s | grep /libpython" % SHLIB_EXT,
+]
+
+moduleclass = 'vis'

From e701ce284117a4ce96aeea93c125eaa0831f0dd7 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Mon, 26 Aug 2024 17:44:59 +0200
Subject: [PATCH 705/835] adding easyconfigs:
 NextPolish-1.4.1-GCCcore-12.3.0.eb

---
 .../NextPolish-1.4.1-GCCcore-12.3.0.eb        | 72 +++++++++++++++++++
 1 file changed, 72 insertions(+)
 create mode 100644 easybuild/easyconfigs/n/NextPolish/NextPolish-1.4.1-GCCcore-12.3.0.eb

diff --git a/easybuild/easyconfigs/n/NextPolish/NextPolish-1.4.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/n/NextPolish/NextPolish-1.4.1-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..857ec88ff80
--- /dev/null
+++ b/easybuild/easyconfigs/n/NextPolish/NextPolish-1.4.1-GCCcore-12.3.0.eb
@@ -0,0 +1,72 @@
+easyblock = 'MakeCp'
+
+name = 'NextPolish'
+version = '1.4.1'
+
+homepage = 'https://github.com/Nextomics/NextPolish'
+description = 'NextDenovo is a string graph-based de novo assembler for long reads.'
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+source_urls = ['https://github.com/Nextomics/NextPolish/releases/download/']
+sources = [{
+    'download_filename': 'v%(version)s/%(name)s.tgz',
+    'filename': SOURCE_TAR_GZ,
+}]
+checksums = ['2a5f66f3db7f76e583a6b6e28f9c1f3c392258b8d755050d7abe129a2fbb48c4']
+
+builddependencies = [('binutils', '2.40')]
+dependencies = [
+    ('Python', '3.11.3'),
+    ('Python-bundle-PyPI', '2023.06'),
+    ('BWA', '0.7.17'),
+]
+
+exts_defaultclass = 'PythonPackage'
+exts_default_options = {
+    'source_urls': [PYPI_SOURCE],
+    'download_dep_fail': True,
+    'use_pip': True,
+    'sanity_pip_check': True,
+    'preinstallopts': '',
+    'installopts': '',
+}
+
+exts_list = [
+    ('Paralleltask', '0.2.3', {
+        'modulename': 'paralleltask',
+        'checksums': ['8015a8311d5021bc44edbfbf45ff2557a529999e235d25190bac62993fdf7b66'],
+    }),
+]
+
+# fix make -C util - warning: jobserver unavailable
+parallel = 1
+
+# fix bwa bug - https://github.com/Nextomics/NextPolish/issues/83
+prebuildopts = "sed -i 's/seq_count bwa samtools minimap2/seq_count samtools minimap2/' Makefile && "
+prebuildopts += "rm -rf util/bwa && "
+prebuildopts += (
+    "sed -i"
+    " -e 's/seq_count bwa_ samtools_/seq_count samtools_/'"
+    " -e '29d'"  # @+make clean -C $(BWADIR)
+    " -e '18,20d'"  # bwa_:	@+make -C $(BWADIR)
+    " -e '1d'"  # BWADIR = ./bwa
+    " util/Makefile && "
+)
+postinstallcmds = ['cd %(installdir)s/bin && ln -s $EBROOTBWA/bin/bwa']
+
+files_to_copy = ['bin', 'lib', 'test_data', 'LICENSE', 'nextPolish']
+
+sanity_check_paths = {
+    'files': ['nextPolish', 'bin/minimap2', 'bin/paralleltask', 'bin/bwa'],
+    'dirs': ['test_data', 'lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = ['nextPolish --help']
+
+modextrapaths = {
+    'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages',
+    'PATH': '',
+}
+
+moduleclass = 'bio'

From c98fb5482ff1a7b2b29b7db945d945a17071cf7b Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Tue, 27 Aug 2024 10:57:42 +0200
Subject: [PATCH 706/835] adding easyconfigs:
 nellie-0.3.1-foss-2023a-CUDA-12.1.1.eb

---
 .../nellie-0.3.1-foss-2023a-CUDA-12.1.1.eb    | 55 +++++++++++++++++++
 1 file changed, 55 insertions(+)
 create mode 100644 easybuild/easyconfigs/n/nellie/nellie-0.3.1-foss-2023a-CUDA-12.1.1.eb

diff --git a/easybuild/easyconfigs/n/nellie/nellie-0.3.1-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/n/nellie/nellie-0.3.1-foss-2023a-CUDA-12.1.1.eb
new file mode 100644
index 00000000000..35d0c5778dd
--- /dev/null
+++ b/easybuild/easyconfigs/n/nellie/nellie-0.3.1-foss-2023a-CUDA-12.1.1.eb
@@ -0,0 +1,55 @@
+easyblock = 'PythonBundle'
+
+name = 'nellie'
+version = '0.3.1'
+versionsuffix = '-CUDA-%(cudaver)s'
+
+homepage = 'https://github.com/aelefebv/nellie/'
+description = """
+Napari plugin for automated organelle segmentation, 
+tracking, and hierarchical feature extraction in 2D/3D live-cell microscopy.
+"""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('Python-bundle-PyPI', '2023.06'),
+    ('CUDA', '12.1.1', '', SYSTEM),
+    ('SciPy-bundle', '2023.07'),
+    ('napari', '0.4.18'),
+    ('scikit-image', '0.22.0'),
+    ('imagecodecs', '2024.1.1'),
+    ('matplotlib', '3.7.2'),
+    ('ome-types', '0.5.1.post1'),
+    ('CuPy', '13.0.0', versionsuffix),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+local_preinstallopts = (
+    "sed -i"
+    " -e 's/numpy==1.26.4/numpy/'"
+    " -e 's/scipy==1.12.0/scipy/'"
+    " -e 's/nd2==0.9.0/nd2/'"
+    " -e 's/pandas==2.2.1/pandas/'"
+    " -e 's/matplotlib==3.8.3/matplotlib/'"
+    " -e 's/napari[all]/napari/'"
+    " setup.cfg && "
+)
+
+exts_list = [
+    ('resource_backed_dask_array', '0.1.0', {
+        'checksums': ['8fabcccf5c7e29059b5badd6786dd7675a258a203c58babf10077d9c90ada54f'],
+    }),
+    ('nd2', '0.10.1', {
+        'checksums': ['88ee60f6ba39392722a162da58fb81bf0cdb8ed6c772772e4db91e90f97e490a'],
+    }),
+    (name, version, {
+        'preinstallopts': local_preinstallopts,
+        'checksums': ['3fd85bd1c7df5a8f24bff2118805cd7c82140b08871d520b2131d4d9a8c00d94'],
+    }),
+]
+
+moduleclass = 'vis'

From e5bf5862479102f7f066f80628ce023f0efc50e1 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparvanl@hotmail.com>
Date: Tue, 27 Aug 2024 16:07:43 +0200
Subject: [PATCH 707/835] Install ReFrame the way ReFrame was actually meant to
 be installed. I.e. with all its deps in the /external subdirectory, and with
 the reframe command being the only one that can find them (by extending the
 sys.path). I.e. we no longer add this directory to PYTHONPATH, and we skip
 various sanity checks for Python packages. Something like python -c "import
 reframe" is _not_ supposed to work, but "reframe -V" does (because that
 command sets the right sys.path).

---
 .../r/ReFrame/ReFrame-4.6.2-GCCcore-13.2.0.eb | 71 +++++++++++++++++++
 1 file changed, 71 insertions(+)
 create mode 100644 easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-13.2.0.eb

diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-13.2.0.eb
new file mode 100644
index 00000000000..6183827a996
--- /dev/null
+++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-13.2.0.eb
@@ -0,0 +1,71 @@
+easyblock = 'PythonBundle'
+
+name = 'ReFrame'
+version = '4.6.2'
+
+homepage = 'https://github.com/reframe-hpc/reframe'
+description = '''ReFrame is a framework for writing regression tests for HPC systems.'''
+
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
+
+dependencies = [
+    ('Python', '3.11.5'),
+    ('libxslt', '1.1.38'),
+    ('libxml2', '2.11.4'), 
+]
+
+use_pip = True
+
+exts_list = [
+    # ReFrame's bootstrap script is intended to run with zero dependencies. It downloads all python deps for ReFrame
+    # into a %(installdir)/external directory. ReFrame's main executable (reframe) adds this dir to python's sys.path
+    # so that ReFrame (and only ReFrame) will find & use all of these dependencies.
+    # In EasyBuild, we should adhere to this installation method because a) it is how ReFrame is meant to be used and
+    # b) it isolates all of ReFrame dependencies from any other python code you run. Thus, there is no chance that
+    # a test will pick up on any python deps from ReFrame itself.
+    # For this to work, we need to disable download_dep_fail and sanity_pip_check, as both are _expected_ to fail
+    # for this setup.
+    ('reframe', version, {
+        # Deps are downloaded to %(installdir)/external, which won't polute the PYTHONPATH, so is ok
+        'download_dep_fail': False,
+        # ReFrame uses its custom sys.path to find necessary packages, they are not on PYTYHONPATH
+        # Thus, the regular pip sanity check is expected to fail, even if ReFrame would run just fine 
+        'sanity_pip_check': False,
+        # Set modulename to False, as to skip the sanity_check-step from extension.py (python -c "import reframe")
+        # This step would fail, since the regular python interpreter wouldn't find the additional packages in
+        # %(installdir)/external. That's fine, as ReFrame should never be imported directly, only through the
+        # reframe command.
+        'modulename': False,
+        'preinstallopts': "export PATH=%(installdir)s/bin:$PATH && "
+                          "./bootstrap.sh +docs +pygelf && cp -r external %(installdir)s && ",
+        'source_tmpl': 'v%(version)s.tar.gz',
+        'source_urls': ['https://github.com/reframe-hpc/reframe/archive/'],
+        'checksums': ['d3343815ee3d2c330b91a1cdb924ba184119ed7d9fc88a4a754b939a4259df82'],
+    }),
+]
+
+postinstallcmds = [
+    "cp -a tools examples %(installdir)s",
+    "mkdir -p %(installdir)s/share && cp -a share/completions %(installdir)s/share/completions",
+    r"sed -i 's@/\(python[0-9.]*\)$@/\1 -S@g' %(installdir)s/bin/reframe",
+]
+
+sanity_check_paths = {
+    'files': ['bin/reframe',
+              'share/completions/reframe.bash',
+              'share/completions/reframe.fish',
+              'share/completions/reframe.tcsh'],
+    'dirs': ['external', 'lib', 'tools', 'examples']
+}
+
+sanity_check_commands = ['reframe -V']
+
+sanity_pip_check = True
+
+# Since this is at the GCCcore toolchain level, make sure ReFrame is configured to purge modules before running
+# any tests by default
+modextravars = {
+    'RFM_PURGE_ENVIRONMENT': '1',
+}
+
+moduleclass = 'devel'

From 0190d40dab9f3a8ed03f73b57fd60791a6ce4b25 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparvanl@hotmail.com>
Date: Tue, 27 Aug 2024 16:49:04 +0200
Subject: [PATCH 708/835] Add ReFrame 4.6.2 for other toolchains, and list os
 dependencies there

---
 .../r/ReFrame/ReFrame-4.6.2-GCCcore-12.3.0.eb | 73 ++++++++++++++++++
 .../r/ReFrame/ReFrame-4.6.2-GCCcore-13.2.0.eb |  4 +-
 .../easyconfigs/r/ReFrame/ReFrame-4.6.2.eb    | 76 +++++++++++++++++++
 3 files changed, 152 insertions(+), 1 deletion(-)
 create mode 100644 easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-12.3.0.eb
 create mode 100644 easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb

diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..2d989755dc2
--- /dev/null
+++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-12.3.0.eb
@@ -0,0 +1,73 @@
+easyblock = 'PythonBundle'
+
+name = 'ReFrame'
+version = '4.6.2'
+
+homepage = 'https://github.com/reframe-hpc/reframe'
+description = '''ReFrame is a framework for writing regression tests for HPC systems.'''
+
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
+
+# Note that for ReFrame's CPU autodetect to work
+# the system also needs to provide (new enough versions of) these dependencies
+dependencies = [
+    ('Python', '3.11.3'),
+    ('libxslt', '1.1.38'),
+    ('libxml2', '2.11.4'), 
+]
+
+use_pip = True
+
+exts_list = [
+    # ReFrame's bootstrap script is intended to run with zero dependencies. It downloads all python deps for ReFrame
+    # into a %(installdir)/external directory. ReFrame's main executable (reframe) adds this dir to python's sys.path
+    # so that ReFrame (and only ReFrame) will find & use all of these dependencies.
+    # In EasyBuild, we should adhere to this installation method because a) it is how ReFrame is meant to be used and
+    # b) it isolates all of ReFrame dependencies from any other python code you run. Thus, there is no chance that
+    # a test will pick up on any python deps from ReFrame itself.
+    # For this to work, we need to disable download_dep_fail and sanity_pip_check, as both are _expected_ to fail
+    # for this setup.
+    ('reframe', version, {
+        # Deps are downloaded to %(installdir)/external, which won't polute the PYTHONPATH, so is ok
+        'download_dep_fail': False,
+        # ReFrame uses its custom sys.path to find necessary packages, they are not on PYTYHONPATH
+        # Thus, the regular pip sanity check is expected to fail, even if ReFrame would run just fine 
+        'sanity_pip_check': False,
+        # Set modulename to False, as to skip the sanity_check-step from extension.py (python -c "import reframe")
+        # This step would fail, since the regular python interpreter wouldn't find the additional packages in
+        # %(installdir)/external. That's fine, as ReFrame should never be imported directly, only through the
+        # reframe command.
+        'modulename': False,
+        'preinstallopts': "export PATH=%(installdir)s/bin:$PATH && "
+                          "./bootstrap.sh +docs +pygelf && cp -r external %(installdir)s && ",
+        'source_tmpl': 'v%(version)s.tar.gz',
+        'source_urls': ['https://github.com/reframe-hpc/reframe/archive/'],
+        'checksums': ['d3343815ee3d2c330b91a1cdb924ba184119ed7d9fc88a4a754b939a4259df82'],
+    }),
+]
+
+postinstallcmds = [
+    "cp -a tools examples %(installdir)s",
+    "mkdir -p %(installdir)s/share && cp -a share/completions %(installdir)s/share/completions",
+    r"sed -i 's@/\(python[0-9.]*\)$@/\1 -S@g' %(installdir)s/bin/reframe",
+]
+
+sanity_check_paths = {
+    'files': ['bin/reframe',
+              'share/completions/reframe.bash',
+              'share/completions/reframe.fish',
+              'share/completions/reframe.tcsh'],
+    'dirs': ['external', 'lib', 'tools', 'examples']
+}
+
+sanity_check_commands = ['reframe -V']
+
+sanity_pip_check = True
+
+# Since this is at the GCCcore toolchain level, make sure ReFrame is configured to purge modules before running
+# any tests by default
+modextravars = {
+    'RFM_PURGE_ENVIRONMENT': '1',
+}
+
+moduleclass = 'devel'
diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-13.2.0.eb
index 6183827a996..bf9f13b702f 100644
--- a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-13.2.0.eb
+++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-13.2.0.eb
@@ -8,10 +8,12 @@ description = '''ReFrame is a framework for writing regression tests for HPC sys
 
 toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
 
+# Note that for ReFrame's CPU autodetect to work
+# the system also needs to provide (new enough versions of) these dependencies
 dependencies = [
     ('Python', '3.11.5'),
     ('libxslt', '1.1.38'),
-    ('libxml2', '2.11.4'), 
+    ('libxml2', '2.11.5'), 
 ]
 
 use_pip = True
diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb
new file mode 100644
index 00000000000..13b5404925f
--- /dev/null
+++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb
@@ -0,0 +1,76 @@
+easyblock = 'PythonBundle'
+
+name = 'ReFrame'
+version = '4.6.2'
+
+homepage = 'https://github.com/reframe-hpc/reframe'
+description = '''ReFrame is a framework for writing regression tests for HPC systems.'''
+
+toolchain = SYSTEM
+
+allow_system_deps = [('Python', SYS_PYTHON_VERSION)]
+
+osdependencies = [
+    ('libxml2'),
+    ('libxslt'),
+]
+
+# Listed as python_requires in https://github.com/reframe-hpc/reframe/blob/v4.6.2/setup.cfg
+req_py_majver = 3
+req_py_minver = 6
+
+use_pip = True
+
+exts_list = [
+    # ReFrame's bootstrap script is intended to run with zero dependencies. It downloads all python deps for ReFrame
+    # into a %(installdir)/external directory. ReFrame's main executable (reframe) adds this dir to python's sys.path
+    # so that ReFrame (and only ReFrame) will find & use all of these dependencies.
+    # In EasyBuild, we should adhere to this installation method because a) it is how ReFrame is meant to be used and
+    # b) it isolates all of ReFrame dependencies from any other python code you run. Thus, there is no chance that
+    # a test will pick up on any python deps from ReFrame itself.
+    # For this to work, we need to disable download_dep_fail and sanity_pip_check, as both are _expected_ to fail
+    # for this setup.
+    ('reframe', version, {
+        # Deps are downloaded to %(installdir)/external, which won't polute the PYTHONPATH, so is ok
+        'download_dep_fail': False,
+        # ReFrame uses its custom sys.path to find necessary packages, they are not on PYTYHONPATH
+        # Thus, the regular pip sanity check is expected to fail, even if ReFrame would run just fine 
+        'sanity_pip_check': False,
+        # Set modulename to False, as to skip the sanity_check-step from extension.py (python -c "import reframe")
+        # This step would fail, since the regular python interpreter wouldn't find the additional packages in
+        # %(installdir)/external. That's fine, as ReFrame should never be imported directly, only through the
+        # reframe command.
+        'modulename': False,
+        'preinstallopts': "export PATH=%(installdir)s/bin:$PATH && "
+                          "./bootstrap.sh +docs +pygelf && cp -r external %(installdir)s && ",
+        'source_tmpl': 'v%(version)s.tar.gz',
+        'source_urls': ['https://github.com/reframe-hpc/reframe/archive/'],
+        'checksums': ['d3343815ee3d2c330b91a1cdb924ba184119ed7d9fc88a4a754b939a4259df82'],
+    }),
+]
+
+postinstallcmds = [
+    "cp -a tools examples %(installdir)s",
+    "mkdir -p %(installdir)s/share && cp -a share/completions %(installdir)s/share/completions",
+    r"sed -i 's@/\(python[0-9.]*\)$@/\1 -S@g' %(installdir)s/bin/reframe",
+]
+
+sanity_check_paths = {
+    'files': ['bin/reframe',
+              'share/completions/reframe.bash',
+              'share/completions/reframe.fish',
+              'share/completions/reframe.tcsh'],
+    'dirs': ['external', 'lib', 'tools', 'examples']
+}
+
+sanity_check_commands = ['reframe -V']
+
+sanity_pip_check = True
+
+# Since this is at the GCCcore toolchain level, make sure ReFrame is configured to purge modules before running
+# any tests by default
+modextravars = {
+    'RFM_PURGE_ENVIRONMENT': '1',
+}
+
+moduleclass = 'devel'

From 6415e1eb717e4297bef1cd34533eb8201d54e278 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparvanl@hotmail.com>
Date: Tue, 27 Aug 2024 16:51:45 +0200
Subject: [PATCH 709/835] Remove setting of RFM_PURGE_ENVIRONMENT for ReFrame
 at system toolchain level.

---
 easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb | 6 ------
 1 file changed, 6 deletions(-)

diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb
index 13b5404925f..a4527f77eb9 100644
--- a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb
+++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb
@@ -67,10 +67,4 @@ sanity_check_commands = ['reframe -V']
 
 sanity_pip_check = True
 
-# Since this is at the GCCcore toolchain level, make sure ReFrame is configured to purge modules before running
-# any tests by default
-modextravars = {
-    'RFM_PURGE_ENVIRONMENT': '1',
-}
-
 moduleclass = 'devel'

From ccd1186e4e18478947658d45e6b55763fe73736b Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparvanl@hotmail.com>
Date: Tue, 27 Aug 2024 17:19:18 +0200
Subject: [PATCH 710/835] Actually change the toolchain version...

---
 easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-12.3.0.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-12.3.0.eb
index 2d989755dc2..995f260fbd1 100644
--- a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-12.3.0.eb
+++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-12.3.0.eb
@@ -6,7 +6,7 @@ version = '4.6.2'
 homepage = 'https://github.com/reframe-hpc/reframe'
 description = '''ReFrame is a framework for writing regression tests for HPC systems.'''
 
-toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
 
 # Note that for ReFrame's CPU autodetect to work
 # the system also needs to provide (new enough versions of) these dependencies

From bdc1b9447cc578efe4c925178b99c274ed9b3efa Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparvanl@hotmail.com>
Date: Tue, 27 Aug 2024 18:01:16 +0200
Subject: [PATCH 711/835] Add pip back in as dep. Might need wheel too, let's
 see

---
 easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb
index a4527f77eb9..2d1448461bc 100644
--- a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb
+++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb
@@ -22,6 +22,12 @@ req_py_minver = 6
 use_pip = True
 
 exts_list = [
+    # stick to pip 21.3.1, which is compatible with Python 3.6
+    # we still need pip outside of ReFrame's external dependencies, since the install cmd uses pip
+    ('pip', '21.3.1', {
+        'use_pip': False,
+        'checksums': ['fd11ba3d0fdb4c07fbc5ecbba0b1b719809420f25038f8ee3cd913d3faa3033a'],
+    }),
     # ReFrame's bootstrap script is intended to run with zero dependencies. It downloads all python deps for ReFrame
     # into a %(installdir)/external directory. ReFrame's main executable (reframe) adds this dir to python's sys.path
     # so that ReFrame (and only ReFrame) will find & use all of these dependencies.

From 2b8e0cd424cd88360db37699c837dd1cf008c80e Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparvanl@hotmail.com>
Date: Tue, 27 Aug 2024 18:09:54 +0200
Subject: [PATCH 712/835] Add setuptools, so that we can install with
 pyproject.toml instead of setup.py

---
 easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb
index 2d1448461bc..47c4afe5e0c 100644
--- a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb
+++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb
@@ -28,6 +28,13 @@ exts_list = [
         'use_pip': False,
         'checksums': ['fd11ba3d0fdb4c07fbc5ecbba0b1b719809420f25038f8ee3cd913d3faa3033a'],
     }),
+    # Require new enough setuptools to install with e.g. pyproject.toml
+    # 59.6.0 is the latest compatible with Python 3.6
+    ('setuptools', '59.6.0', {
+        'use_pip': False,'
+        'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'],
+        'checksums': ['22c7348c6d2976a52632c67f7ab0cdf40147db7789f9aed18734643fe9cf3373'],
+    })
     # ReFrame's bootstrap script is intended to run with zero dependencies. It downloads all python deps for ReFrame
     # into a %(installdir)/external directory. ReFrame's main executable (reframe) adds this dir to python's sys.path
     # so that ReFrame (and only ReFrame) will find & use all of these dependencies.

From f16a887cacbe1d7e74fcebaab7fd209785629180 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparvanl@hotmail.com>
Date: Tue, 27 Aug 2024 18:10:47 +0200
Subject: [PATCH 713/835] Forgot comma

---
 easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb
index 47c4afe5e0c..db9fa02ede0 100644
--- a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb
+++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb
@@ -34,7 +34,7 @@ exts_list = [
         'use_pip': False,'
         'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'],
         'checksums': ['22c7348c6d2976a52632c67f7ab0cdf40147db7789f9aed18734643fe9cf3373'],
-    })
+    }),
     # ReFrame's bootstrap script is intended to run with zero dependencies. It downloads all python deps for ReFrame
     # into a %(installdir)/external directory. ReFrame's main executable (reframe) adds this dir to python's sys.path
     # so that ReFrame (and only ReFrame) will find & use all of these dependencies.

From 71d71b4bb90e007a5d1b3fb17f0eb2753562a7ec Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparvanl@hotmail.com>
Date: Tue, 27 Aug 2024 18:11:55 +0200
Subject: [PATCH 714/835] Stray quote removed

---
 easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb
index db9fa02ede0..c0195a09783 100644
--- a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb
+++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb
@@ -31,7 +31,7 @@ exts_list = [
     # Require new enough setuptools to install with e.g. pyproject.toml
     # 59.6.0 is the latest compatible with Python 3.6
     ('setuptools', '59.6.0', {
-        'use_pip': False,'
+        'use_pip': False,
         'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'],
         'checksums': ['22c7348c6d2976a52632c67f7ab0cdf40147db7789f9aed18734643fe9cf3373'],
     }),

From b19add1d090cd0519995564282cbfd41643cb2c7 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparvanl@hotmail.com>
Date: Tue, 27 Aug 2024 18:14:54 +0200
Subject: [PATCH 715/835] Wheel is still needed, adding back in

---
 easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb
index c0195a09783..b25cee0e9fa 100644
--- a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb
+++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb
@@ -35,6 +35,11 @@ exts_list = [
         'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'],
         'checksums': ['22c7348c6d2976a52632c67f7ab0cdf40147db7789f9aed18734643fe9cf3373'],
     }),
+    # stick to wheel 0.37.1, which is compatible with Python 3.6
+    ('wheel', '0.37.1', {
+        'source_tmpl': 'wheel-%(version)s-py2.py3-none-any.whl',
+        'checksums': ['4bdcd7d840138086126cd09254dc6195fb4fc6f01c050a1d7236f2630db1d22a'],
+    }),
     # ReFrame's bootstrap script is intended to run with zero dependencies. It downloads all python deps for ReFrame
     # into a %(installdir)/external directory. ReFrame's main executable (reframe) adds this dir to python's sys.path
     # so that ReFrame (and only ReFrame) will find & use all of these dependencies.

From 4f9e20a85f677c75cb411a041b6cbd035277e9f2 Mon Sep 17 00:00:00 2001
From: fizwit <john@fuzzdog.com>
Date: Tue, 27 Aug 2024 11:12:28 -0700
Subject: [PATCH 716/835] update fastp

---
 .../f/fastp/fastp-0.23.4-GCC-13.2.0.eb        | 38 +++++++++++++++++++
 1 file changed, 38 insertions(+)
 create mode 100644 easybuild/easyconfigs/f/fastp/fastp-0.23.4-GCC-13.2.0.eb

diff --git a/easybuild/easyconfigs/f/fastp/fastp-0.23.4-GCC-13.2.0.eb b/easybuild/easyconfigs/f/fastp/fastp-0.23.4-GCC-13.2.0.eb
new file mode 100644
index 00000000000..49b2a29c4f9
--- /dev/null
+++ b/easybuild/easyconfigs/f/fastp/fastp-0.23.4-GCC-13.2.0.eb
@@ -0,0 +1,38 @@
+easyblock = 'ConfigureMake'
+
+name = 'fastp'
+version = '0.23.4'
+
+homepage = 'https://github.com/OpenGene/fastp'
+description = """A tool designed to provide fast all-in-one preprocessing for FastQ files.
+ This tool is developed in C++ with multithreading supported to afford high performance."""
+
+toolchain = {'name': 'GCC', 'version': '13.2.0'}
+
+github_account = 'OpenGene'
+source_urls = [GITHUB_SOURCE]
+sources = ['v%(version)s.tar.gz']
+checksums = ['4fad6db156e769d46071add8a778a13a5cb5186bc1e1a5f9b1ffd499d84d72b5']
+
+dependencies = [
+    ('zlib', '1.2.13'),
+    ('libdeflate', '1.19'),
+    ('ISA-L', '2.31.0'),
+]
+
+skipsteps = ['configure']
+
+buildopts = ' CXX=${CXX}'
+
+preinstallopts = 'mkdir -p %(installdir)s/bin && '
+
+installopts = 'PREFIX=%(installdir)s'
+
+sanity_check_paths = {
+    'files': ['bin/fastp'],
+    'dirs': [],
+}
+
+sanity_check_commands = [('fastp', '--help')]
+
+moduleclass = 'bio'

From bf1b18474e7d4c341848063838313fc90b521465 Mon Sep 17 00:00:00 2001
From: ankekreuzer <a.kreuzer@fz-juelich.de>
Date: Wed, 28 Aug 2024 09:35:56 +0200
Subject: [PATCH 717/835] Added builddependency binutils for gmpy2

---
 easybuild/easyconfigs/g/gmpy2/gmpy2-2.2.0-GCCcore-13.3.0.eb | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/easybuild/easyconfigs/g/gmpy2/gmpy2-2.2.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/gmpy2/gmpy2-2.2.0-GCCcore-13.3.0.eb
index d919e2ca8e3..45d90e26d6a 100644
--- a/easybuild/easyconfigs/g/gmpy2/gmpy2-2.2.0-GCCcore-13.3.0.eb
+++ b/easybuild/easyconfigs/g/gmpy2/gmpy2-2.2.0-GCCcore-13.3.0.eb
@@ -11,6 +11,10 @@ toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
 sources = [SOURCE_TAR_GZ]
 checksums = ['e19e62dfeb1e4a57079f0bf51c51dec30633d9fe9e89cb9a083e05e4823afa70']
 
+builddependencies = [
+    ('binutils', '2.42')
+]
+
 dependencies = [
     ('Python', '3.12.3'),
     ('GMP', '6.3.0'),

From 9401f8b94213782f5ca6d7aeb9a6578c9698c3f4 Mon Sep 17 00:00:00 2001
From: vsc46128 <vsc46128@node3501.doduo.os>
Date: Wed, 28 Aug 2024 11:02:09 +0200
Subject: [PATCH 718/835] add performance, datwizard and bayestestR to
 R-bundle-CRAN 2024.06

---
 .../R-bundle-CRAN-2024.06-foss-2023b.eb       | 28 +++++++++----------
 1 file changed, 13 insertions(+), 15 deletions(-)

diff --git a/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb b/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb
index d239f2596c2..72c6dd9e26e 100644
--- a/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb
+++ b/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb
@@ -588,10 +588,7 @@ exts_list = [
         'checksums': ['9e1531bb37aa474abd91db5e0ed9e3a355c03faa65f4e653b3ea68b7c61ea835'],
     }),
     ('pan', '1.9', {
-        'checksums': [
-            ('e37e184c3c1b7a34f54dd95335e6bc730fd5716d2d2dc20c24279401aa673c52',
-             'cd91232d653783ea7f34c0eebaa80c472b5501b21eea500c4c1a8e57116c6eea'),
-        ],
+        'checksums': ['cd91232d653783ea7f34c0eebaa80c472b5501b21eea500c4c1a8e57116c6eea'],
     }),
     ('mitml', '0.4-5', {
         'checksums': ['056aec823187cc3793640d8a5e74d74093bae74260a975ceb098a83a52e2eeeb'],
@@ -1603,10 +1600,7 @@ exts_list = [
         'checksums': ['7c849086cb17d6c5aefc106217363e14afbcda2a9e0120687d40805b5e1c566a'],
     }),
     ('signal', '1.8-0', {
-        'checksums': [
-            ('89cba854167a2b051a58cf3b73ccbf74eeb47c890ac39720611cd41f86b94684',
-             '0a604949bae91410a150a22cfa02d954f5b83166cc7a73e5409554d00e0417a7'),
-        ],
+        'checksums': ['89cba854167a2b051a58cf3b73ccbf74eeb47c890ac39720611cd41f86b94684'],
     }),
     ('tuneR', '1.4.7', {
         'checksums': ['364154a0440953327eeefd2f3c72c9f819944cbb52b6e7497958882ca0b6960a'],
@@ -2098,7 +2092,6 @@ exts_list = [
     }),
     ('liquidSVM', '1.2.4', {
         'patches': ['liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch'],
-        # Don't add optimization flags by liquidSVM which may not be known e.g. on PPC
         'preinstallopts': 'LIQUIDSVM_TARGET="empty"',
         'checksums': [
             {'liquidSVM_1.2.4.tar.gz': '15a9c7f2930e2ed3f4c5bcd9b042884ea580d2b2e52e1c68041600c196046aba'},
@@ -2592,8 +2585,8 @@ exts_list = [
         'checksums': ['293544afb194934b1d58cf88c6f8c372f537745514b6e428cf83ae62e87d2bba'],
     }),
     ('dbarts', '0.9-28', {
+        'preinstallopts': '',
         'checksums': ['d2e4b4ee1c191e7c506be3fec5a5e877c1b36754cba558bd75eaac9cc6ac0138'],
-        'preinstallopts': local_dbarts_preinstallopts,
     }),
     ('proftools', '0.99-3', {
         'checksums': ['e034eb1531af54013143da3e15229e1d4c2260f8eb79c93846014db3bdefb724'],
@@ -2629,13 +2622,9 @@ exts_list = [
         'checksums': ['d4d9ef7b2788efeb8209aa8dd610af4cd86286392fbdf9ea70bcfeafda95d4c5'],
     }),
     ('gWidgets2tcltk', '1.0-8', {
-        # need to run installation via xvfb-run to avoid problems on headless systems:
-        # no DISPLAY variable so Tk is not available
-        # [tcl] invalid command name "font"
+        'modulename': False,
         'preinstallopts': "xvfb-run ",
         'checksums': ['10399cc636eeeb5484c3379970c37c56df10d979bf866a35b66d0c75b7222c0a'],
-        # skip 'import' check with library(gWidgets2tcltk), since it also fails on headless systems...
-        'modulename': False,
     }),
     ('mgsub', '1.7.3', {
         'checksums': ['c9ae2560fe2690bedc5248af3fc89e7ef2bc6c147d46ced28f9824584c3791d5'],
@@ -3439,6 +3428,15 @@ exts_list = [
     ('insight', '0.20.3', {
         'checksums': ['b60e189849cd3c368e9c2b2174e89c2dfbba3b34e84feb8a20af1bb758116bb2'],
     }),
+    ('datawizard', '0.12.2', {
+        'checksums': ['fee36520440131596394878eb19f295609ef5d7997a3a5614c059f2a8d2be081'],
+    }),
+    ('bayestestR', '0.14.0', {
+        'checksums': ['fa0f94204b414df05ecf7340b37fbb5fbe6dff2d057e2425a6990b6510054880'],
+    }),
+    ('performance', '0.12.2', {
+        'checksums': ['b55e663eb45b8e88625c704506f20c4068a1c892c5a6a94d7bd0c0e3a7ed4028'],
+    }),
 ]
 
 modextrapaths = {'R_LIBS_SITE': ''}

From 264581b8bc96990f21429131c45f9d364dccc413 Mon Sep 17 00:00:00 2001
From: vsc46128 <vsc46128@node3501.doduo.os>
Date: Wed, 28 Aug 2024 11:11:12 +0200
Subject: [PATCH 719/835] remove unnecessary of checksums

---
 .../R-bundle-CRAN-2024.06-foss-2023b.eb       | 19 +++++++++++++++----
 1 file changed, 15 insertions(+), 4 deletions(-)

diff --git a/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb b/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb
index 72c6dd9e26e..a15e03469da 100644
--- a/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb
+++ b/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb
@@ -588,7 +588,10 @@ exts_list = [
         'checksums': ['9e1531bb37aa474abd91db5e0ed9e3a355c03faa65f4e653b3ea68b7c61ea835'],
     }),
     ('pan', '1.9', {
-        'checksums': ['cd91232d653783ea7f34c0eebaa80c472b5501b21eea500c4c1a8e57116c6eea'],
+        'checksums': [
+            ('e37e184c3c1b7a34f54dd95335e6bc730fd5716d2d2dc20c24279401aa673c52',
+             'cd91232d653783ea7f34c0eebaa80c472b5501b21eea500c4c1a8e57116c6eea'),
+        ],
     }),
     ('mitml', '0.4-5', {
         'checksums': ['056aec823187cc3793640d8a5e74d74093bae74260a975ceb098a83a52e2eeeb'],
@@ -1600,7 +1603,10 @@ exts_list = [
         'checksums': ['7c849086cb17d6c5aefc106217363e14afbcda2a9e0120687d40805b5e1c566a'],
     }),
     ('signal', '1.8-0', {
-        'checksums': ['89cba854167a2b051a58cf3b73ccbf74eeb47c890ac39720611cd41f86b94684'],
+        'checksums': [
+            ('89cba854167a2b051a58cf3b73ccbf74eeb47c890ac39720611cd41f86b94684',
+             '0a604949bae91410a150a22cfa02d954f5b83166cc7a73e5409554d00e0417a7'),
+        ],
     }),
     ('tuneR', '1.4.7', {
         'checksums': ['364154a0440953327eeefd2f3c72c9f819944cbb52b6e7497958882ca0b6960a'],
@@ -2092,6 +2098,7 @@ exts_list = [
     }),
     ('liquidSVM', '1.2.4', {
         'patches': ['liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch'],
+         # Don't add optimization flags by liquidSVM which may not be known e.g. on PPC
         'preinstallopts': 'LIQUIDSVM_TARGET="empty"',
         'checksums': [
             {'liquidSVM_1.2.4.tar.gz': '15a9c7f2930e2ed3f4c5bcd9b042884ea580d2b2e52e1c68041600c196046aba'},
@@ -2585,8 +2592,8 @@ exts_list = [
         'checksums': ['293544afb194934b1d58cf88c6f8c372f537745514b6e428cf83ae62e87d2bba'],
     }),
     ('dbarts', '0.9-28', {
-        'preinstallopts': '',
         'checksums': ['d2e4b4ee1c191e7c506be3fec5a5e877c1b36754cba558bd75eaac9cc6ac0138'],
+        'preinstallopts': local_dbarts_preinstallopts,
     }),
     ('proftools', '0.99-3', {
         'checksums': ['e034eb1531af54013143da3e15229e1d4c2260f8eb79c93846014db3bdefb724'],
@@ -2622,9 +2629,13 @@ exts_list = [
         'checksums': ['d4d9ef7b2788efeb8209aa8dd610af4cd86286392fbdf9ea70bcfeafda95d4c5'],
     }),
     ('gWidgets2tcltk', '1.0-8', {
-        'modulename': False,
+        # need to run installation via xvfb-run to avoid problems on headless systems:
+        # no DISPLAY variable so Tk is not available
+        # [tcl] invalid command name "font"
         'preinstallopts': "xvfb-run ",
         'checksums': ['10399cc636eeeb5484c3379970c37c56df10d979bf866a35b66d0c75b7222c0a'],
+        # skip 'import' check with library(gWidgets2tcltk), since it also fails on headless systems...
+        'modulename': False,
     }),
     ('mgsub', '1.7.3', {
         'checksums': ['c9ae2560fe2690bedc5248af3fc89e7ef2bc6c147d46ced28f9824584c3791d5'],

From baffea8a827a92c336b76fb4e392b601c8f891ed Mon Sep 17 00:00:00 2001
From: vsc46128 <vsc46128@node3501.doduo.os>
Date: Wed, 28 Aug 2024 11:13:52 +0200
Subject: [PATCH 720/835] remove unnecessary changes

---
 .../r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb         | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb b/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb
index a15e03469da..3bd3447df1d 100644
--- a/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb
+++ b/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb
@@ -2098,7 +2098,7 @@ exts_list = [
     }),
     ('liquidSVM', '1.2.4', {
         'patches': ['liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch'],
-         # Don't add optimization flags by liquidSVM which may not be known e.g. on PPC
+        # Don't add optimization flags by liquidSVM which may not be known e.g. on PPC
         'preinstallopts': 'LIQUIDSVM_TARGET="empty"',
         'checksums': [
             {'liquidSVM_1.2.4.tar.gz': '15a9c7f2930e2ed3f4c5bcd9b042884ea580d2b2e52e1c68041600c196046aba'},

From f6989ece375a5d39bc70853d43f2db86c2971969 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparvanl@hotmail.com>
Date: Wed, 28 Aug 2024 11:39:34 +0200
Subject: [PATCH 721/835] Remove the global sanity_pip_check = True

---
 easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-12.3.0.eb | 2 --
 easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-13.2.0.eb | 2 --
 easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb                | 2 --
 3 files changed, 6 deletions(-)

diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-12.3.0.eb
index 995f260fbd1..b8f5a73f8c9 100644
--- a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-12.3.0.eb
+++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-12.3.0.eb
@@ -62,8 +62,6 @@ sanity_check_paths = {
 
 sanity_check_commands = ['reframe -V']
 
-sanity_pip_check = True
-
 # Since this is at the GCCcore toolchain level, make sure ReFrame is configured to purge modules before running
 # any tests by default
 modextravars = {
diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-13.2.0.eb
index bf9f13b702f..03dd4f7de30 100644
--- a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-13.2.0.eb
+++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-13.2.0.eb
@@ -62,8 +62,6 @@ sanity_check_paths = {
 
 sanity_check_commands = ['reframe -V']
 
-sanity_pip_check = True
-
 # Since this is at the GCCcore toolchain level, make sure ReFrame is configured to purge modules before running
 # any tests by default
 modextravars = {
diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb
index b25cee0e9fa..c99bbfba4c1 100644
--- a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb
+++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb
@@ -83,6 +83,4 @@ sanity_check_paths = {
 
 sanity_check_commands = ['reframe -V']
 
-sanity_pip_check = True
-
 moduleclass = 'devel'

From 9bd137c76ebfc1a39c0df9c17663cae9b3b0b901 Mon Sep 17 00:00:00 2001
From: vsc46128 <vsc46128@node3501.doduo.os>
Date: Wed, 28 Aug 2024 11:43:02 +0200
Subject: [PATCH 722/835] move insight as performance is optional dependency of
 insight

---
 .../r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb     | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb b/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb
index 3bd3447df1d..06a928ab8d0 100644
--- a/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb
+++ b/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb
@@ -3436,9 +3436,6 @@ exts_list = [
     ('missMDA', '1.19', {
         'checksums': ['f9675884829b2fef75237c335b21991d163674320e766523c71c7a853f95e65c'],
     }),
-    ('insight', '0.20.3', {
-        'checksums': ['b60e189849cd3c368e9c2b2174e89c2dfbba3b34e84feb8a20af1bb758116bb2'],
-    }),
     ('datawizard', '0.12.2', {
         'checksums': ['fee36520440131596394878eb19f295609ef5d7997a3a5614c059f2a8d2be081'],
     }),
@@ -3448,6 +3445,9 @@ exts_list = [
     ('performance', '0.12.2', {
         'checksums': ['b55e663eb45b8e88625c704506f20c4068a1c892c5a6a94d7bd0c0e3a7ed4028'],
     }),
+    ('insight', '0.20.3', {
+        'checksums': ['b60e189849cd3c368e9c2b2174e89c2dfbba3b34e84feb8a20af1bb758116bb2'],
+    }),
 ]
 
 modextrapaths = {'R_LIBS_SITE': ''}

From 34765d2b0f9fba1363259a94fd061e27797466e7 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparvanl@hotmail.com>
Date: Wed, 28 Aug 2024 11:44:46 +0200
Subject: [PATCH 723/835] Add binutils back in at the instruction of the CI
 checker...

---
 .../easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-12.3.0.eb     | 4 ++++
 .../easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-13.2.0.eb     | 4 ++++
 2 files changed, 8 insertions(+)

diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-12.3.0.eb
index b8f5a73f8c9..bdb4139b17e 100644
--- a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-12.3.0.eb
+++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-12.3.0.eb
@@ -8,6 +8,10 @@ description = '''ReFrame is a framework for writing regression tests for HPC sys
 
 toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
 
+builddependencies = [
+    ('binutils', '2.40'),
+]
+
 # Note that for ReFrame's CPU autodetect to work
 # the system also needs to provide (new enough versions of) these dependencies
 dependencies = [
diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-13.2.0.eb
index 03dd4f7de30..3c6d6af6b48 100644
--- a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-13.2.0.eb
+++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-13.2.0.eb
@@ -8,6 +8,10 @@ description = '''ReFrame is a framework for writing regression tests for HPC sys
 
 toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
 
+builddependencies = [
+    ('binutils', '2.40')
+]
+
 # Note that for ReFrame's CPU autodetect to work
 # the system also needs to provide (new enough versions of) these dependencies
 dependencies = [

From 2ef57c79afe528f929ef857385dd9ee0f6799c90 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparvanl@hotmail.com>
Date: Wed, 28 Aug 2024 11:45:46 +0200
Subject: [PATCH 724/835] Remove trailing whitespace

---
 easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-12.3.0.eb | 2 +-
 easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-13.2.0.eb | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-12.3.0.eb
index bdb4139b17e..26018c7bef8 100644
--- a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-12.3.0.eb
+++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-12.3.0.eb
@@ -17,7 +17,7 @@ builddependencies = [
 dependencies = [
     ('Python', '3.11.3'),
     ('libxslt', '1.1.38'),
-    ('libxml2', '2.11.4'), 
+    ('libxml2', '2.11.4'),
 ]
 
 use_pip = True
diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-13.2.0.eb
index 3c6d6af6b48..5bad59e8703 100644
--- a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-13.2.0.eb
+++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-13.2.0.eb
@@ -17,7 +17,7 @@ builddependencies = [
 dependencies = [
     ('Python', '3.11.5'),
     ('libxslt', '1.1.38'),
-    ('libxml2', '2.11.5'), 
+    ('libxml2', '2.11.5'),
 ]
 
 use_pip = True

From 5d1388ad96f235c006d707caacdec9ec8c1aa948 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 28 Aug 2024 12:27:03 +0200
Subject: [PATCH 725/835] don't use %(namelower)s template in name of
 SCENICplus extension

---
 .../s/SCENICplus/SCENICplus-1.0a1-20240513-foss-2023a.eb        | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/s/SCENICplus/SCENICplus-1.0a1-20240513-foss-2023a.eb b/easybuild/easyconfigs/s/SCENICplus/SCENICplus-1.0a1-20240513-foss-2023a.eb
index dbff79bbe8c..5f88062b0f8 100644
--- a/easybuild/easyconfigs/s/SCENICplus/SCENICplus-1.0a1-20240513-foss-2023a.eb
+++ b/easybuild/easyconfigs/s/SCENICplus/SCENICplus-1.0a1-20240513-foss-2023a.eb
@@ -260,7 +260,7 @@ exts_list = [
         'sources': [{'download_filename': '16d14b9.tar.gz', 'filename': '%(name)s-%(version)s-16d14b9.tar.gz'}],
         'checksums': ['7285ac03be9d148437442a726366d7c6f9f5f86bc6636369149a2bc2cd8e0e29'],
     }),
-    ('%(namelower)s', version, {
+    ('scenisplus', version, {
         'preinstallopts': local_preinstallopts,
         'source_urls': ['https://github.com/aertslab/scenicplus/archive/'],
         'sources': [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}],

From 434ae24226e578afdb5405bf0dfe2433977efcb5 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparvanl@hotmail.com>
Date: Wed, 28 Aug 2024 13:08:45 +0200
Subject: [PATCH 726/835] Whitelist ReFrame to allow not running the
 sanity_check_pip

---
 test/easyconfigs/easyconfigs.py | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py
index 4d7b85dac79..b1274497b8a 100644
--- a/test/easyconfigs/easyconfigs.py
+++ b/test/easyconfigs/easyconfigs.py
@@ -1086,6 +1086,11 @@ def test_pr_python_packages(self):
             r'.*-2016[ab]-Python-.*',
             # mympirun is installed with system Python, pip may not be installed for system Python
             r'vsc-mympirun.*',
+            # ReFrame intentionally installs its deps in a %(installdir)s/external subdir, which is added
+            # to sys.path by the ReFrame command, and is intentionally NOT on the PYTHONPATH.
+            # Thus, a pip check fails, but this is expected and ok, it is still a working ReFrame installation
+            # See https://github.com/easybuilders/easybuild-easyconfigs/pull/21269 for more info
+            r'ReFrame.*',
         ]
 
         failing_checks = []

From b34d3cb74a0532b6986586ab377da0297185a696 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com>
Date: Wed, 28 Aug 2024 13:19:32 +0200
Subject: [PATCH 727/835] Update SCENICplus-1.0a1-20240513-foss-2023a.eb - typo

---
 .../s/SCENICplus/SCENICplus-1.0a1-20240513-foss-2023a.eb        | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/s/SCENICplus/SCENICplus-1.0a1-20240513-foss-2023a.eb b/easybuild/easyconfigs/s/SCENICplus/SCENICplus-1.0a1-20240513-foss-2023a.eb
index 5f88062b0f8..796eb9a63b6 100644
--- a/easybuild/easyconfigs/s/SCENICplus/SCENICplus-1.0a1-20240513-foss-2023a.eb
+++ b/easybuild/easyconfigs/s/SCENICplus/SCENICplus-1.0a1-20240513-foss-2023a.eb
@@ -260,7 +260,7 @@ exts_list = [
         'sources': [{'download_filename': '16d14b9.tar.gz', 'filename': '%(name)s-%(version)s-16d14b9.tar.gz'}],
         'checksums': ['7285ac03be9d148437442a726366d7c6f9f5f86bc6636369149a2bc2cd8e0e29'],
     }),
-    ('scenisplus', version, {
+    ('scenicplus', version, {
         'preinstallopts': local_preinstallopts,
         'source_urls': ['https://github.com/aertslab/scenicplus/archive/'],
         'sources': [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}],

From 7af33b2061fa75c3fc2da11e058fc2e8b900cf2f Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparvanl@hotmail.com>
Date: Wed, 28 Aug 2024 13:22:45 +0200
Subject: [PATCH 728/835] Put additional comments for future clarity

---
 .../easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-12.3.0.eb     | 4 ++--
 .../easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-13.2.0.eb     | 4 ++--
 easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb              | 1 +
 3 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-12.3.0.eb
index 26018c7bef8..7960a1ae6e4 100644
--- a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-12.3.0.eb
+++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-12.3.0.eb
@@ -16,8 +16,8 @@ builddependencies = [
 # the system also needs to provide (new enough versions of) these dependencies
 dependencies = [
     ('Python', '3.11.3'),
-    ('libxslt', '1.1.38'),
-    ('libxml2', '2.11.4'),
+    ('libxslt', '1.1.38'), # Required by lxml, which is installed by ReFrame's bootstrap installer
+    ('libxml2', '2.11.4'), # Required by lxml, which is installed by ReFrame's bootstrap installer
 ]
 
 use_pip = True
diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-13.2.0.eb
index 5bad59e8703..0a85c4d2b4e 100644
--- a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-13.2.0.eb
+++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-13.2.0.eb
@@ -16,8 +16,8 @@ builddependencies = [
 # the system also needs to provide (new enough versions of) these dependencies
 dependencies = [
     ('Python', '3.11.5'),
-    ('libxslt', '1.1.38'),
-    ('libxml2', '2.11.5'),
+    ('libxslt', '1.1.38'), # Required by lxml, which is installed by ReFrame's bootstrap installer
+    ('libxml2', '2.11.4'), # Required by lxml, which is installed by ReFrame's bootstrap installer
 ]
 
 use_pip = True
diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb
index c99bbfba4c1..fd4a336660e 100644
--- a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb
+++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb
@@ -10,6 +10,7 @@ toolchain = SYSTEM
 
 allow_system_deps = [('Python', SYS_PYTHON_VERSION)]
 
+# Required by lxml, which is installed by ReFrame's bootstrap installer
 osdependencies = [
     ('libxml2'),
     ('libxslt'),

From e4ec3d8ca28159f3131818093d745de042cf848a Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparvanl@hotmail.com>
Date: Wed, 28 Aug 2024 13:25:03 +0200
Subject: [PATCH 729/835] Correct version that was accidentally changed

---
 easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-13.2.0.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-13.2.0.eb
index 0a85c4d2b4e..1593844cfac 100644
--- a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-13.2.0.eb
+++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-13.2.0.eb
@@ -17,7 +17,7 @@ builddependencies = [
 dependencies = [
     ('Python', '3.11.5'),
     ('libxslt', '1.1.38'), # Required by lxml, which is installed by ReFrame's bootstrap installer
-    ('libxml2', '2.11.4'), # Required by lxml, which is installed by ReFrame's bootstrap installer
+    ('libxml2', '2.11.5'), # Required by lxml, which is installed by ReFrame's bootstrap installer
 ]
 
 use_pip = True

From 2c95bbcad15332323a4f0341fe70f9f24fd5d5e4 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 28 Aug 2024 15:50:57 +0200
Subject: [PATCH 730/835] remove non-sensical 'import gv' sanity check from
 TF-COMB easyconfig

---
 easybuild/easyconfigs/t/TF-COMB/TF-COMB-1.1-foss-2022b.eb | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/easybuild/easyconfigs/t/TF-COMB/TF-COMB-1.1-foss-2022b.eb b/easybuild/easyconfigs/t/TF-COMB/TF-COMB-1.1-foss-2022b.eb
index 2dcd3a55fdf..2c06e8c9c8f 100644
--- a/easybuild/easyconfigs/t/TF-COMB/TF-COMB-1.1-foss-2022b.eb
+++ b/easybuild/easyconfigs/t/TF-COMB/TF-COMB-1.1-foss-2022b.eb
@@ -45,8 +45,4 @@ exts_list = [
     }),
 ]
 
-sanity_check_commands = [
-    "python -c 'import gv'",
-]
-
 moduleclass = 'bio'

From 98b62f2e810ff86270a1050d82d13ac1f08745c4 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparvanl@hotmail.com>
Date: Wed, 28 Aug 2024 15:54:36 +0200
Subject: [PATCH 731/835] Add curl as builddep, since ReFrame downloads pip
 with it in their bootstrap

---
 .../easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-12.3.0.eb      | 1 +
 .../easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-13.2.0.eb      | 3 ++-
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-12.3.0.eb
index 7960a1ae6e4..84f4c755eb7 100644
--- a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-12.3.0.eb
+++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-12.3.0.eb
@@ -10,6 +10,7 @@ toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
 
 builddependencies = [
     ('binutils', '2.40'),
+    ('cURL', '8.0.1'), # Used by ReFrame to download pip in the bootstrap
 ]
 
 # Note that for ReFrame's CPU autodetect to work
diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-13.2.0.eb
index 1593844cfac..6393b4e7e52 100644
--- a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-13.2.0.eb
+++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-13.2.0.eb
@@ -9,7 +9,8 @@ description = '''ReFrame is a framework for writing regression tests for HPC sys
 toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
 
 builddependencies = [
-    ('binutils', '2.40')
+    ('binutils', '2.40'),
+    ('cURL', '8.3.0'), # Used by ReFrame to download pip in the bootstrap
 ]
 
 # Note that for ReFrame's CPU autodetect to work

From cc8bc38566f2af536932e324c4c3a0830db159e5 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparvanl@hotmail.com>
Date: Wed, 28 Aug 2024 16:42:33 +0200
Subject: [PATCH 732/835] Fix spaces for inline comments

---
 .../easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-12.3.0.eb   | 6 +++---
 .../easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-13.2.0.eb   | 6 +++---
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-12.3.0.eb
index 84f4c755eb7..9046d5c9362 100644
--- a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-12.3.0.eb
+++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-12.3.0.eb
@@ -10,15 +10,15 @@ toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
 
 builddependencies = [
     ('binutils', '2.40'),
-    ('cURL', '8.0.1'), # Used by ReFrame to download pip in the bootstrap
+    ('cURL', '8.0.1'),  # Used by ReFrame to download pip in the bootstrap
 ]
 
 # Note that for ReFrame's CPU autodetect to work
 # the system also needs to provide (new enough versions of) these dependencies
 dependencies = [
     ('Python', '3.11.3'),
-    ('libxslt', '1.1.38'), # Required by lxml, which is installed by ReFrame's bootstrap installer
-    ('libxml2', '2.11.4'), # Required by lxml, which is installed by ReFrame's bootstrap installer
+    ('libxslt', '1.1.38'),  # Required by lxml, which is installed by ReFrame's bootstrap installer
+    ('libxml2', '2.11.4'),  # Required by lxml, which is installed by ReFrame's bootstrap installer
 ]
 
 use_pip = True
diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-13.2.0.eb
index 6393b4e7e52..e2adb9db1d9 100644
--- a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-13.2.0.eb
+++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-13.2.0.eb
@@ -10,15 +10,15 @@ toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
 
 builddependencies = [
     ('binutils', '2.40'),
-    ('cURL', '8.3.0'), # Used by ReFrame to download pip in the bootstrap
+    ('cURL', '8.3.0'),  # Used by ReFrame to download pip in the bootstrap
 ]
 
 # Note that for ReFrame's CPU autodetect to work
 # the system also needs to provide (new enough versions of) these dependencies
 dependencies = [
     ('Python', '3.11.5'),
-    ('libxslt', '1.1.38'), # Required by lxml, which is installed by ReFrame's bootstrap installer
-    ('libxml2', '2.11.5'), # Required by lxml, which is installed by ReFrame's bootstrap installer
+    ('libxslt', '1.1.38'),  # Required by lxml, which is installed by ReFrame's bootstrap installer
+    ('libxml2', '2.11.5'),  # Required by lxml, which is installed by ReFrame's bootstrap installer
 ]
 
 use_pip = True

From d5acbaf39633a9ea56df14fd2989e01c32b35007 Mon Sep 17 00:00:00 2001
From: Louwrens van Dellen <lthvd@protonmail.com>
Date: Wed, 28 Aug 2024 19:32:20 +0200
Subject: [PATCH 733/835] adding patch:
 HDF5-1.14.3_suppress_fp_exceptions.patch

HDF5 v1.14.3 was broken, this patch is the hotfix that
was published soon after the release. See:

https://github.com/HDFGroup/hdf5/issues/3831
---
 .../h/HDF5/HDF5-1.14.3-gompi-2023b.eb         |   6 +-
 .../h/HDF5/HDF5-1.14.3-iimpi-2023b.eb         |   6 +-
 .../HDF5-1.14.3_suppress_fp_exceptions.patch  | 223 ++++++++++++++++++
 3 files changed, 233 insertions(+), 2 deletions(-)
 create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.14.3_suppress_fp_exceptions.patch

diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.14.3-gompi-2023b.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.14.3-gompi-2023b.eb
index f2aab3663a3..5cb05f4a4a1 100644
--- a/easybuild/easyconfigs/h/HDF5/HDF5-1.14.3-gompi-2023b.eb
+++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.14.3-gompi-2023b.eb
@@ -12,7 +12,11 @@ toolchainopts = {'pic': True, 'usempi': True}
 
 source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src']
 sources = [SOURCELOWER_TAR_GZ]
-checksums = ['09cdb287aa7a89148c1638dd20891fdbae08102cf433ef128fd345338aa237c7']
+patches = ['HDF5-1.14.3_suppress_fp_exceptions.patch']
+checksums = [
+    {'hdf5-1.14.3.tar.gz': '09cdb287aa7a89148c1638dd20891fdbae08102cf433ef128fd345338aa237c7'},
+    {'HDF5-1.14.3_suppress_fp_exceptions.patch': 'bf33e579c93a16043c54b266321bbe95e4a8797f7fe6d096a13ce905ed2ffde7'},
+]
 
 # replace src include path with installation dir for $H5BLD_CPPFLAGS
 _regex = 's, -I[^[:space:]]+H5FDsubfiling , -I%(installdir)s/include ,g'
diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.14.3-iimpi-2023b.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.14.3-iimpi-2023b.eb
index 77fa0c12ab9..e180d8619ee 100644
--- a/easybuild/easyconfigs/h/HDF5/HDF5-1.14.3-iimpi-2023b.eb
+++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.14.3-iimpi-2023b.eb
@@ -12,7 +12,11 @@ toolchainopts = {'pic': True, 'usempi': True}
 
 source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src']
 sources = [SOURCELOWER_TAR_GZ]
-checksums = ['09cdb287aa7a89148c1638dd20891fdbae08102cf433ef128fd345338aa237c7']
+patches = ['HDF5-1.14.3_suppress_fp_exceptions.patch']
+checksums = [
+    {'hdf5-1.14.3.tar.gz': '09cdb287aa7a89148c1638dd20891fdbae08102cf433ef128fd345338aa237c7'},
+    {'HDF5-1.14.3_suppress_fp_exceptions.patch': 'bf33e579c93a16043c54b266321bbe95e4a8797f7fe6d096a13ce905ed2ffde7'},
+]
 
 # replace src include path with installation dir for $H5BLD_CPPFLAGS
 _regex = 's, -I[^[:space:]]+H5FDsubfiling , -I%(installdir)s/include ,g'
diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.14.3_suppress_fp_exceptions.patch b/easybuild/easyconfigs/h/HDF5/HDF5-1.14.3_suppress_fp_exceptions.patch
new file mode 100644
index 00000000000..420125db46d
--- /dev/null
+++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.14.3_suppress_fp_exceptions.patch
@@ -0,0 +1,223 @@
+See: https://github.com/HDFGroup/hdf5/commit/e0d095ebf020706ec7d7c82e6674b18f1a0a2d5b
+
+Created using
+git checkout hdf5-1_14_3
+git cherry-pick e0d095ebf020706ec7d7c82e6674b18f1a0a2d5b
+
+commit 7c58dd64db0a6c04dea46dee1c7effbe8103ae82
+Author: Dana Robinson <43805+derobins@users.noreply.github.com>
+Date:   Tue Nov 7 08:13:30 2023 -0800
+
+    Disable FP exceptions in H5T init code (#3837)
+    
+    The H5T floating-point datatype initialization code can raise exceptions when handling signaling NaNs. This change disables FE_INVALID exceptions during initialization.
+    
+    Also removes the -ieee=full change for NAG Fortran as that shouldn't be necessary anymore.
+    
+    Fixes #3831
+
+diff --git a/config/linux-gnulibc1 b/config/linux-gnulibc1
+index 328f8d3cec..079f08d96c 100644
+--- a/config/linux-gnulibc1
++++ b/config/linux-gnulibc1
+@@ -173,10 +173,7 @@ case $FC_BASENAME in
+     nagfor)
+ 
+         F9XSUFFIXFLAG=""
+-        # NOTE: The default is -ieee=stop, which will cause problems
+-        #       when the H5T module performs floating-point type
+-        #       introspection
+-        AM_FCFLAGS="$AM_FCFLAGS -ieee=full"
++        AM_FCFLAGS="$AM_FCFLAGS"
+         FSEARCH_DIRS=""
+ 
+         # Production
+diff --git a/release_docs/RELEASE.txt b/release_docs/RELEASE.txt
+index 200576332b..7de2a56974 100644
+--- a/release_docs/RELEASE.txt
++++ b/release_docs/RELEASE.txt
+@@ -250,6 +250,29 @@ Bug Fixes since HDF5-1.14.2 release
+ ===================================
+     Library
+     -------
++    - Suppressed floating-point exceptions in H5T init code
++
++      The floating-point datatype initialization code in H5Tinit_float.c
++      could raise FE_INVALID exceptions while munging bits and performing
++      comparisons that might involve NaN. This was not a problem when the
++      initialization code was executed in H5detect at compile time (prior
++      to 1.14.3), but now that the code is executed at library startup
++      (1.14.3+), these exceptions can be caught by user code, as is the
++      default in the NAG Fortran compiler.
++
++      Starting in 1.14.4, we now suppress floating-point exceptions while
++      initializing the floating-point types and clear FE_INVALID before
++      restoring the original environment.
++
++      Fixes GitHub #3831
++
++    - Fixed a file handle leak in the core VFD
++
++      When opening a file with the core VFD and a file image, if the file
++      already exists, the file check would leak the POSIX file handle.
++
++      Fixes GitHub issue #635
++
+     - Fixed some issues with chunk index metadata not getting read
+       collectively when collective metadata reads are enabled
+ 
+@@ -619,12 +642,6 @@ Known Problems
+     this release with link errors. As a result, Windows binaries for this release
+     will not include Fortran.  The problem will be addressed in HDF5 1.14.4.
+ 
+-    IEEE standard arithmetic enables software to raise exceptions such as overflow,
+-    division by zero, and other illegal operations without interrupting or halting
+-    the program flow. The HDF5 C library intentionally performs these exceptions.
+-    Therefore, the "-ieee=full" nagfor switch is necessary when compiling a program
+-    to avoid stopping on an exception.
+-
+     CMake files do not behave correctly with paths containing spaces.
+     Do not use spaces in paths because the required escaping for handling spaces
+     results in very complex and fragile build files.
+diff --git a/src/H5Tinit_float.c b/src/H5Tinit_float.c
+index 3b9e127fe4..3213f00fec 100644
+--- a/src/H5Tinit_float.c
++++ b/src/H5Tinit_float.c
+@@ -51,19 +51,23 @@
+  * Function:    DETECT_F
+  *
+  * Purpose:     This macro takes a floating point type like `double' and
+- *              a base name like `natd' and detects byte order, mantissa
+- *              location, exponent location, sign bit location, presence or
+- *              absence of implicit mantissa bit, and exponent bias and
+- *              initializes a detected_t structure with those properties.
++ *              and detects byte order, mantissa location, exponent location,
++ *              sign bit location, presence or absence of implicit mantissa
++ *              bit, and exponent bias and initializes a detected_t structure
++ *              with those properties.
++ *
++ *              Note that these operations can raise floating-point
++ *              exceptions and building with some compiler options
++ *              (especially Fortran) can cause problems.
+  *-------------------------------------------------------------------------
+  */
+-#define DETECT_F(TYPE, VAR, INFO)                                                                            \
++#define DETECT_F(TYPE, INFO)                                                                                 \
+     do {                                                                                                     \
+-        TYPE          _v1, _v2, _v3;                                                                         \
+-        unsigned char _buf1[sizeof(TYPE)], _buf3[sizeof(TYPE)];                                              \
+-        unsigned char _pad_mask[sizeof(TYPE)];                                                               \
+-        unsigned char _byte_mask;                                                                            \
+-        int           _i, _j, _last = (-1);                                                                  \
++        TYPE    _v1, _v2, _v3;                                                                               \
++        uint8_t _buf1[sizeof(TYPE)], _buf3[sizeof(TYPE)];                                                    \
++        uint8_t _pad_mask[sizeof(TYPE)];                                                                     \
++        uint8_t _byte_mask;                                                                                  \
++        int     _i, _j, _last = -1;                                                                          \
+                                                                                                              \
+         memset(&INFO, 0, sizeof(INFO));                                                                      \
+         INFO.size = sizeof(TYPE);                                                                            \
+@@ -81,7 +85,7 @@
+         _v1 = (TYPE)4.0L;                                                                                    \
+         H5MM_memcpy(_buf1, (const void *)&_v1, sizeof(TYPE));                                                \
+         for (_i = 0; _i < (int)sizeof(TYPE); _i++)                                                           \
+-            for (_byte_mask = (unsigned char)1; _byte_mask; _byte_mask = (unsigned char)(_byte_mask << 1)) { \
++            for (_byte_mask = (uint8_t)1; _byte_mask; _byte_mask = (uint8_t)(_byte_mask << 1)) {             \
+                 _buf1[_i] ^= _byte_mask;                                                                     \
+                 H5MM_memcpy((void *)&_v2, (const void *)_buf1, sizeof(TYPE));                                \
+                 H5_GCC_CLANG_DIAG_OFF("float-equal")                                                         \
+@@ -118,7 +122,7 @@
+         _v1 = (TYPE)1.0L;                                                                                    \
+         _v2 = (TYPE)-1.0L;                                                                                   \
+         if (H5T__bit_cmp(sizeof(TYPE), INFO.perm, &_v1, &_v2, _pad_mask, &(INFO.sign)) < 0)                  \
+-            HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "failed to detect byte order");                    \
++            HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "failed to determine sign bit");                   \
+                                                                                                              \
+         /* Mantissa */                                                                                       \
+         INFO.mpos = 0;                                                                                       \
+@@ -126,12 +130,11 @@
+         _v1 = (TYPE)1.0L;                                                                                    \
+         _v2 = (TYPE)1.5L;                                                                                    \
+         if (H5T__bit_cmp(sizeof(TYPE), INFO.perm, &_v1, &_v2, _pad_mask, &(INFO.msize)) < 0)                 \
+-            HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "failed to detect byte order");                    \
++            HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "failed to determine mantissa");                   \
+         INFO.msize += 1 + (unsigned)(INFO.imp ? 0 : 1) - INFO.mpos;                                          \
+                                                                                                              \
+         /* Exponent */                                                                                       \
+-        INFO.epos = INFO.mpos + INFO.msize;                                                                  \
+-                                                                                                             \
++        INFO.epos  = INFO.mpos + INFO.msize;                                                                 \
+         INFO.esize = INFO.sign - INFO.epos;                                                                  \
+                                                                                                              \
+         _v1        = (TYPE)1.0L;                                                                             \
+@@ -456,17 +459,24 @@ H5T__set_precision(H5T_fpoint_det_t *d)
+ herr_t H5_NO_UBSAN
+ H5T__init_native_float_types(void)
+ {
++    fenv_t           saved_fenv;
+     H5T_fpoint_det_t det;
+     H5T_t           *dt        = NULL;
+     herr_t           ret_value = SUCCEED;
+ 
+     FUNC_ENTER_PACKAGE
+ 
++    /* Turn off floating-point exceptions while initializing to avoid
++     * tripping over signaling NaNs while looking at "don't care" bits.
++     */
++    if (feholdexcept(&saved_fenv) != 0)
++        HSYS_GOTO_ERROR(H5E_DATATYPE, H5E_CANTSET, FAIL, "can't save floating-point environment");
++
+     /* H5T_NATIVE_FLOAT */
+ 
+     /* Get the type's characteristics */
+     memset(&det, 0, sizeof(H5T_fpoint_det_t));
+-    DETECT_F(float, FLOAT, det);
++    DETECT_F(float, det);
+ 
+     /* Allocate and fill type structure */
+     if (NULL == (dt = H5T__alloc()))
+@@ -497,7 +507,7 @@ H5T__init_native_float_types(void)
+ 
+     /* Get the type's characteristics */
+     memset(&det, 0, sizeof(H5T_fpoint_det_t));
+-    DETECT_F(double, DOUBLE, det);
++    DETECT_F(double, det);
+ 
+     /* Allocate and fill type structure */
+     if (NULL == (dt = H5T__alloc()))
+@@ -528,7 +538,7 @@ H5T__init_native_float_types(void)
+ 
+     /* Get the type's characteristics */
+     memset(&det, 0, sizeof(H5T_fpoint_det_t));
+-    DETECT_F(long double, LDOUBLE, det);
++    DETECT_F(long double, det);
+ 
+     /* Allocate and fill type structure */
+     if (NULL == (dt = H5T__alloc()))
+@@ -561,6 +571,14 @@ H5T__init_native_float_types(void)
+     H5T_native_order_g = det.order;
+ 
+ done:
++    /* Clear any FE_INVALID exceptions from NaN handling */
++    if (feclearexcept(FE_INVALID) != 0)
++        HSYS_GOTO_ERROR(H5E_DATATYPE, H5E_CANTSET, FAIL, "can't clear floating-point exceptions");
++
++    /* Restore the original environment */
++    if (feupdateenv(&saved_fenv) != 0)
++        HSYS_GOTO_ERROR(H5E_DATATYPE, H5E_CANTSET, FAIL, "can't restore floating-point environment");
++
+     if (ret_value < 0) {
+         if (dt != NULL) {
+             dt->shared = H5FL_FREE(H5T_shared_t, dt->shared);
+diff --git a/src/H5private.h b/src/H5private.h
+index 14a0ac3225..3aaa0d5245 100644
+--- a/src/H5private.h
++++ b/src/H5private.h
+@@ -26,6 +26,7 @@
+ #include <ctype.h>
+ #include <errno.h>
+ #include <fcntl.h>
++#include <fenv.h>
+ #include <float.h>
+ #include <math.h>
+ #include <setjmp.h>

From 1b99d7e8dbeb93757ee17f5b644c5a628636063a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Petr=20Kr=C3=A1l?= <petr@inuits.eu>
Date: Thu, 29 Aug 2024 10:08:08 +0200
Subject: [PATCH 734/835] add patch file for sage interface

---
 .../coxeter-20180226-GCCcore-13.2.0.eb        |  6 +-
 .../coxeter-20180226_sage_interface.patch     | 89 +++++++++++++++++++
 2 files changed, 94 insertions(+), 1 deletion(-)
 create mode 100644 easybuild/easyconfigs/c/coxeter/coxeter-20180226_sage_interface.patch

diff --git a/easybuild/easyconfigs/c/coxeter/coxeter-20180226-GCCcore-13.2.0.eb b/easybuild/easyconfigs/c/coxeter/coxeter-20180226-GCCcore-13.2.0.eb
index 1fbcfa900b6..247bb5ac24d 100644
--- a/easybuild/easyconfigs/c/coxeter/coxeter-20180226-GCCcore-13.2.0.eb
+++ b/easybuild/easyconfigs/c/coxeter/coxeter-20180226-GCCcore-13.2.0.eb
@@ -11,10 +11,14 @@ toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
 
 source_urls = ['https://github.com/tscrim/coxeter/archive/%s/' % local_commit]
 sources = [SOURCE_TAR_GZ]
-patches = ['coxeter-20180226_makefile.patch']
+patches = [
+    'coxeter-20180226_makefile.patch',
+    ('coxeter-20180226_sage_interface.patch', 0),
+]
 checksums = [
     {'coxeter-20180226.tar.gz': '5e0668c40b29c03c438a6ebc0f49f13aaf155b4bcbff56303a753390e6fce3aa'},
     {'coxeter-20180226_makefile.patch': '229ed201e41bae0ae7b22aa21d5007127aeb52fd158543dd5fff2e89797e211f'},
+    {'coxeter-20180226_sage_interface.patch': '18ba75e51a944ffccb7fa440b823f68a0aad9066e8edcdd2b52bac6b43404bd3'},
 ]
 
 builddependencies = [('binutils', '2.40')]
diff --git a/easybuild/easyconfigs/c/coxeter/coxeter-20180226_sage_interface.patch b/easybuild/easyconfigs/c/coxeter/coxeter-20180226_sage_interface.patch
new file mode 100644
index 00000000000..2b4cd427ca9
--- /dev/null
+++ b/easybuild/easyconfigs/c/coxeter/coxeter-20180226_sage_interface.patch
@@ -0,0 +1,89 @@
+Adds sage interface. See https://github.com/tscrim/coxeter/pull/14
+Source: https://gitlab.archlinux.org/archlinux/packaging/packages/coxeter/-/blob/git.20180226-4/coxeter-sage.patch
+diff -u /dev/null sage.h
+--- /dev/null	2024-08-27 08:29:37.672016778 +0200
++++ sage.h	2024-08-27 12:17:23.716096310 +0200
+@@ -0,0 +1,23 @@
++/*
++  Coxeter version 3.0 Copyright (C) 2009 Mike Hansen
++  See file main.cpp for full copyright notice
++*/
++
++#ifndef SAGE_H /* guard against multiple inclusions */
++#define SAGE_H
++
++#include "globals.h"
++#include "coxgroup.h"
++#include "coxtypes.h"
++#include "schubert.h"
++#include "list.h"
++
++namespace sage {
++  using namespace coxeter;
++  using namespace coxtypes;
++  using namespace list;
++
++  void interval(List<CoxWord>& result, CoxGroup& W, const CoxWord& g, const CoxWord& h);
++}
++
++#endif
+diff -u /dev/null sage.cpp
+--- /dev/null	2024-08-27 08:29:37.672016778 +0200
++++ sage.cpp	2024-08-27 12:17:23.716096310 +0200
+@@ -0,0 +1,56 @@
++/*
++  Coxeter version 3.0 Copyright (C) 2009 Mike Hansen
++  See file main.cpp for full copyright notice
++*/
++
++#include "sage.h"
++
++namespace sage {
++
++  void interval(List<CoxWord>& list, CoxGroup& W, const CoxWord& g, const CoxWord& h)
++
++  /*
++     Returns a list of the elements in the Bruhat interval between g and h.
++     Note that this assumes that g and h are in order.
++   */
++  {
++    if (not W.inOrder(g,h)) {
++      return;
++    }
++
++    W.extendContext(h);
++
++    CoxNbr x = W.contextNumber(g);
++    CoxNbr y = W.contextNumber(h);
++
++    BitMap b(W.contextSize());
++    W.extractClosure(b,y);
++
++    BitMap::ReverseIterator b_rend = b.rend();
++    List<CoxNbr> res(0);
++
++    for (BitMap::ReverseIterator i = b.rbegin(); i != b_rend; ++i)
++      if (not W.inOrder(x,*i)) {
++        BitMap bi(W.contextSize());
++        W.extractClosure(bi,*i);
++        CoxNbr z = *i; // andnot will invalidate iterator
++        b.andnot(bi);
++        b.setBit(z);   // otherwise the decrement will not be correct
++      } else
++        res.append(*i);
++
++    schubert::NFCompare nfc(W.schubert(),W.ordering());
++    Permutation a(res.size());
++    sortI(res,nfc,a);
++
++    list.setSize(0);
++    for (size_t j = 0; j < res.size(); ++j) {
++      CoxWord w(0);
++      W.schubert().append(w, res[a[j]]);
++      list.append(w);
++    }
++
++    return;
++  }
++
++}

From 5ea734280a2e15281df21a6898a731d03ed20e7e Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Thu, 29 Aug 2024 10:45:16 +0200
Subject: [PATCH 735/835] update preconfigopts for POD5Version.cmake

---
 .../pod5-file-format-0.3.10-foss-2023a.eb           | 13 +++++++------
 1 file changed, 7 insertions(+), 6 deletions(-)

diff --git a/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.3.10-foss-2023a.eb b/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.3.10-foss-2023a.eb
index f0db4069b1c..9db2243c96e 100644
--- a/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.3.10-foss-2023a.eb
+++ b/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.3.10-foss-2023a.eb
@@ -72,14 +72,15 @@ exts_list = [
 
 # create POD5Version.cmake
 # python -m setuptools_scm && python -m pod5_make_version shows wrong version
+local_ver_sub_minor = version.split('.')[2]
 preconfigopts = (
-    'cd %(builddir)s/%(name)s-%(version)s/cmake && '
+    'cd %%(builddir)s/%%(name)s-%%(version)s/cmake && '
     'touch POD5Version.cmake && '
-    'echo "set(POD5_VERSION_MAJOR 0)">POD5Version.cmake && '
-    'echo "set(POD5_VERSION_MINOR 3)">>POD5Version.cmake && '
-    'echo "set(POD5_VERSION_REV 10)">>POD5Version.cmake && '
-    'echo "set(POD5_NUMERIC_VERSION 0.3.10)">>POD5Version.cmake && '
-    'echo "set(POD5_FULL_VERSION 0.3.10)">>POD5Version.cmake && '
+    'echo "set(POD5_VERSION_MAJOR %%(version_major)s)">POD5Version.cmake && '
+    'echo "set(POD5_VERSION_MINOR %%(version_minor)s)">>POD5Version.cmake && '
+    'echo "set(POD5_VERSION_REV %s)">>POD5Version.cmake && '
+    'echo "set(POD5_NUMERIC_VERSION %%(version)s)">>POD5Version.cmake && '
+    'echo "set(POD5_FULL_VERSION %%(version)s)">>POD5Version.cmake && ' % local_ver_sub_minor
 )
 
 # delete add_subdirectory(third_party/pybind11) from CMakeLists.txt

From 984b840fc5b35c31f99a80aab3869857c4e9b26f Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com>
Date: Thu, 29 Aug 2024 13:17:09 +0200
Subject: [PATCH 736/835] Update
 easybuild/easyconfigs/h/HERRO/HERRO-0.1.0_20240808-foss-2023a.eb - update
 postinstallcmds

Co-authored-by: Kenneth Hoste <kenneth.hoste@ugent.be>
---
 .../easyconfigs/h/HERRO/HERRO-0.1.0_20240808-foss-2023a.eb      | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/h/HERRO/HERRO-0.1.0_20240808-foss-2023a.eb b/easybuild/easyconfigs/h/HERRO/HERRO-0.1.0_20240808-foss-2023a.eb
index ecef67eed26..a4057965c49 100644
--- a/easybuild/easyconfigs/h/HERRO/HERRO-0.1.0_20240808-foss-2023a.eb
+++ b/easybuild/easyconfigs/h/HERRO/HERRO-0.1.0_20240808-foss-2023a.eb
@@ -73,7 +73,7 @@ prebuildopts = pretestopts = preinstallopts = local_torch_opts
 
 # copy scripts to /bin to be easier to run scripts for users
 postinstallcmds = [
-    'cp -a %(start_dir)sscripts/* %(installdir)s/bin',
+    'cp -a %(start_dir)s/scripts/* %(installdir)s/bin',
     'rm %(installdir)s/bin/herro-env.yml',
     "chmod a+rx %(installdir)s/bin/*.sh",
     "chmod a-x %(installdir)s/bin/*.py",

From a13ac978f1885d5148dfaacd12f1928843b5ab9f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Petr=20Kr=C3=A1l?= <petr@inuits.eu>
Date: Thu, 29 Aug 2024 14:30:15 +0200
Subject: [PATCH 737/835] adding easyconfigs: mcqd-1.0.0-GCCcore-13.2.0.eb

---
 .../m/mcqd/mcqd-1.0.0-GCCcore-13.2.0.eb       | 36 +++++++++++++++++++
 1 file changed, 36 insertions(+)
 create mode 100644 easybuild/easyconfigs/m/mcqd/mcqd-1.0.0-GCCcore-13.2.0.eb

diff --git a/easybuild/easyconfigs/m/mcqd/mcqd-1.0.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/m/mcqd/mcqd-1.0.0-GCCcore-13.2.0.eb
new file mode 100644
index 00000000000..efc5b111642
--- /dev/null
+++ b/easybuild/easyconfigs/m/mcqd/mcqd-1.0.0-GCCcore-13.2.0.eb
@@ -0,0 +1,36 @@
+easyblock = 'CmdCp'
+
+name = 'mcqd'
+version = '1.0.0'
+
+homepage = 'https://gitlab.com/janezkonc/mcqd'
+description = """MaxCliqueDyn is a fast exact algorithm for finding a maximum clique in an undirected graph."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
+
+source_urls = ['https://gitlab.com/janezkonc/mcqd/-/archive/v%(version)s/']
+sources = ['%(name)s-v%(version)s.tar.gz']
+checksums = ['37ff68ff88e047c929990d4c12ce474753f6f9c49324661a3aa1cfe77c26ad9d']
+
+builddependencies = [
+    ('binutils', '2.40'),
+]
+
+cmds_map = [('.*', 'echo here && pwd && ls -lh && $CXX $CXXFLAGS $LDFLAGS mcqd.cpp -o mcqd')]
+
+files_to_copy = [
+    (['%(name)s'], 'bin'),
+    (['%(name)s.h'], 'include'),
+]
+
+sanity_check_paths = {
+    'files': [
+        'bin/%(name)s',
+        'include/%(name)s.h',
+    ],
+    'dirs': [],
+}
+
+sanity_check_commands = ["command -v %(name)s"]
+
+moduleclass = 'math'

From 649abc544e2561a4a902b70eea8e144324573b32 Mon Sep 17 00:00:00 2001
From: ankekreuzer <a.kreuzer@fz-juelich.de>
Date: Fri, 30 Aug 2024 08:25:52 +0200
Subject: [PATCH 738/835] Added ConcurrentVersionsSystem and DBus to the
 GCCcore-13.3.0 toolchain

---
 ...ntVersionsSystem-1.11.23-GCCcore-13.3.0.eb | 45 +++++++++++++++++++
 .../d/DBus/DBus-1.15.8-GCCcore-13.3.0.eb      | 45 +++++++++++++++++++
 2 files changed, 90 insertions(+)
 create mode 100644 easybuild/easyconfigs/c/ConcurrentVersionsSystem/ConcurrentVersionsSystem-1.11.23-GCCcore-13.3.0.eb
 create mode 100644 easybuild/easyconfigs/d/DBus/DBus-1.15.8-GCCcore-13.3.0.eb

diff --git a/easybuild/easyconfigs/c/ConcurrentVersionsSystem/ConcurrentVersionsSystem-1.11.23-GCCcore-13.3.0.eb b/easybuild/easyconfigs/c/ConcurrentVersionsSystem/ConcurrentVersionsSystem-1.11.23-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..62826484b73
--- /dev/null
+++ b/easybuild/easyconfigs/c/ConcurrentVersionsSystem/ConcurrentVersionsSystem-1.11.23-GCCcore-13.3.0.eb
@@ -0,0 +1,45 @@
+##
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+#
+##
+
+easyblock = 'ConfigureMake'
+
+name = 'ConcurrentVersionsSystem'
+version = '1.11.23'
+
+homepage = 'https://savannah.nongnu.org/projects/cvs'
+description = """CVS is a version control system, an important component of
+Source Configuration Management (SCM).
+"""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+source_urls = [' http://ftp.gnu.org/non-gnu/cvs/source/stable/%(version)s/']
+sources = ['cvs-%(version)s.tar.bz2']
+patches = [
+    'CVS-1.11.23-zlib-1.patch',
+    'CVS-1.11.23-getline.patch',
+]
+checksums = [
+    '400f51b59d85116e79b844f2d5dbbad4759442a789b401a94aa5052c3d7a4aa9',  # cvs-1.11.23.tar.bz2
+    # CVS-1.11.23-zlib-1.patch
+    '3c0ee6509c4622778c093316437a5b047c51820e11cee3ed3a405c2a590a9ff4',
+    # CVS-1.11.23-getline.patch
+    '6a1aa65acfbb41b7639adc70248d908981f172c2529bb52d84359713f9541874',
+]
+
+builddependencies = [
+    ('binutils', '2.42')
+]
+
+dependencies = [
+    ('zlib', '1.3.1')
+]
+
+sanity_check_paths = {
+    'files': ['bin/cvs', 'bin/cvsbug', 'bin/rcs2log'],
+    'dirs': [],
+}
+
+moduleclass = 'devel'
diff --git a/easybuild/easyconfigs/d/DBus/DBus-1.15.8-GCCcore-13.3.0.eb b/easybuild/easyconfigs/d/DBus/DBus-1.15.8-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..ca182becfcd
--- /dev/null
+++ b/easybuild/easyconfigs/d/DBus/DBus-1.15.8-GCCcore-13.3.0.eb
@@ -0,0 +1,45 @@
+easyblock = 'CMakeMake'
+
+name = 'DBus'
+version = '1.15.8'
+
+homepage = 'https://dbus.freedesktop.org/'
+
+description = """
+ D-Bus is a message bus system, a simple way for applications to talk
+ to one another.  In addition to interprocess communication, D-Bus helps
+ coordinate process lifecycle; it makes it simple and reliable to code
+ a "single instance" application or daemon, and to launch applications
+ and daemons on demand when their services are needed.
+"""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://dbus.freedesktop.org/releases/dbus']
+sources = [SOURCELOWER_TAR_XZ]
+checksums = ['84fc597e6ec82f05dc18a7d12c17046f95bad7be99fc03c15bc254c4701ed204']
+
+builddependencies = [
+    ('binutils', '2.42'),
+    ('CMake', '3.29.3'),
+    ('pkgconf', '2.2.0'),
+]
+
+dependencies = [
+    ('expat', '2.6.2'),
+]
+
+configopts = '-DENABLE_SYSTEMD=OFF '
+# disable documentation
+configopts += '-DDBUS_ENABLE_XML_DOCS=OFF -DDBUS_ENABLE_QTHELP_DOCS=OFF -DDBUS_ENABLE_DOXYGEN_DOCS=OFF '
+
+sanity_check_paths = {
+    'files': ['bin/dbus-%s' % x for x in
+              ['cleanup-sockets', 'daemon', 'launch', 'monitor',
+               'run-session', 'send', 'uuidgen']] +
+             ['lib/libdbus-1.%s' % SHLIB_EXT],
+    'dirs': ['include', 'share'],
+}
+
+moduleclass = 'devel'

From 16b3f16de046daf84590a61854a3c29d22666b0f Mon Sep 17 00:00:00 2001
From: ankekreuzer <a.kreuzer@fz-juelich.de>
Date: Fri, 30 Aug 2024 08:44:19 +0200
Subject: [PATCH 739/835] Added ecBuilds, FLAC (+libogg) in the GCCcore-13.3.0
 toolchain.

---
 .../e/ecBuild/ecBuild-3.8.5-GCCcore-13.3.0.eb | 37 +++++++++++++++++++
 .../f/FLAC/FLAC-1.4.3-GCCcore-13.3.0.eb       | 30 +++++++++++++++
 .../l/libogg/libogg-1.3.5-GCCcore-13.3.0.eb   | 25 +++++++++++++
 3 files changed, 92 insertions(+)
 create mode 100644 easybuild/easyconfigs/e/ecBuild/ecBuild-3.8.5-GCCcore-13.3.0.eb
 create mode 100644 easybuild/easyconfigs/f/FLAC/FLAC-1.4.3-GCCcore-13.3.0.eb
 create mode 100644 easybuild/easyconfigs/l/libogg/libogg-1.3.5-GCCcore-13.3.0.eb

diff --git a/easybuild/easyconfigs/e/ecBuild/ecBuild-3.8.5-GCCcore-13.3.0.eb b/easybuild/easyconfigs/e/ecBuild/ecBuild-3.8.5-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..97c3992ce77
--- /dev/null
+++ b/easybuild/easyconfigs/e/ecBuild/ecBuild-3.8.5-GCCcore-13.3.0.eb
@@ -0,0 +1,37 @@
+easyblock = 'Tarball'
+
+name = 'ecBuild'
+version = '3.8.5'
+
+homepage = 'https://ecbuild.readthedocs.io/'
+
+description = """
+A CMake-based build system, consisting of a collection of CMake macros and
+functions that ease the managing of software build systems """
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+github_account = 'ecmwf'
+sources = [
+    {
+        'source_urls': [GITHUB_SOURCE],
+        'filename': '%(version)s.tar.gz',
+        'extract_cmd': 'tar -xzf %s --strip-components=1',
+    },
+]
+checksums = ['aa0c44cab0fffec4c0b3542e91ebcc736b3d41b68a068d30c023ec0df5f93425']
+
+builddependencies = [('binutils', '2.42')]
+
+buildininstalldir = True
+
+skipsteps = ['install']
+
+sanity_check_paths = {
+    'files': ['bin/ecbuild', 'cmake/ecbuild-config.cmake'],
+    'dirs': ['bin', 'lib', 'share', 'cmake'],
+}
+
+sanity_check_commands = ['ecbuild --help']
+
+moduleclass = 'tools'
diff --git a/easybuild/easyconfigs/f/FLAC/FLAC-1.4.3-GCCcore-13.3.0.eb b/easybuild/easyconfigs/f/FLAC/FLAC-1.4.3-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..f767483f7cd
--- /dev/null
+++ b/easybuild/easyconfigs/f/FLAC/FLAC-1.4.3-GCCcore-13.3.0.eb
@@ -0,0 +1,30 @@
+easyblock = 'ConfigureMake'
+
+name = 'FLAC'
+version = '1.4.3'
+
+homepage = 'https://xiph.org/flac/'
+description = """FLAC stands for Free Lossless Audio Codec, an audio format similar to MP3, but lossless, meaning
+that audio is compressed in FLAC without any loss in quality."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+source_urls = ['https://ftp.osuosl.org/pub/xiph/releases/flac/']
+sources = [SOURCELOWER_TAR_XZ]
+checksums = ['6c58e69cd22348f441b861092b825e591d0b822e106de6eb0ee4d05d27205b70']
+
+builddependencies = [('binutils', '2.42')]
+
+dependencies = [('libogg', '1.3.5')]
+
+configopts = '--enable-static --enable-shared'
+
+sanity_check_paths = {
+    'files': ['bin/flac', 'lib/libFLAC.a', 'lib/libFLAC++.a',
+              'lib/libFLAC.%s' % SHLIB_EXT, 'lib/libFLAC++.%s' % SHLIB_EXT],
+    'dirs': ['include/FLAC', 'include/FLAC++'],
+}
+
+sanity_check_commands = ["flac --help"]
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/l/libogg/libogg-1.3.5-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libogg/libogg-1.3.5-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..810ddbe1169
--- /dev/null
+++ b/easybuild/easyconfigs/l/libogg/libogg-1.3.5-GCCcore-13.3.0.eb
@@ -0,0 +1,25 @@
+easyblock = 'ConfigureMake'
+
+name = 'libogg'
+version = '1.3.5'
+
+homepage = 'https://xiph.org/ogg/'
+description = """Ogg is a multimedia container format, and the native file and stream format for the Xiph.org
+multimedia codecs."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+source_urls = ['https://ftp.osuosl.org/pub/xiph/releases/ogg/']
+sources = [SOURCELOWER_TAR_XZ]
+checksums = ['c4d91be36fc8e54deae7575241e03f4211eb102afb3fc0775fbbc1b740016705']
+
+builddependencies = [('binutils', '2.42')]
+
+configopts = '--enable-static --enable-shared'
+
+sanity_check_paths = {
+    'files': ['lib/libogg.a', 'lib/libogg.%s' % SHLIB_EXT],
+    'dirs': ['include/ogg'],
+}
+
+moduleclass = 'lib'

From f0bf67c9b4c7bd523d8ef57f207507e51c091619 Mon Sep 17 00:00:00 2001
From: Simon Branford <4967+branfosj@users.noreply.github.com>
Date: Fri, 30 Aug 2024 07:48:13 +0100
Subject: [PATCH 740/835] correct extension order in R-bundle-CRAN 2024.06

---
 .../r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb     | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb b/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb
index 06a928ab8d0..3bd3447df1d 100644
--- a/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb
+++ b/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb
@@ -3436,6 +3436,9 @@ exts_list = [
     ('missMDA', '1.19', {
         'checksums': ['f9675884829b2fef75237c335b21991d163674320e766523c71c7a853f95e65c'],
     }),
+    ('insight', '0.20.3', {
+        'checksums': ['b60e189849cd3c368e9c2b2174e89c2dfbba3b34e84feb8a20af1bb758116bb2'],
+    }),
     ('datawizard', '0.12.2', {
         'checksums': ['fee36520440131596394878eb19f295609ef5d7997a3a5614c059f2a8d2be081'],
     }),
@@ -3445,9 +3448,6 @@ exts_list = [
     ('performance', '0.12.2', {
         'checksums': ['b55e663eb45b8e88625c704506f20c4068a1c892c5a6a94d7bd0c0e3a7ed4028'],
     }),
-    ('insight', '0.20.3', {
-        'checksums': ['b60e189849cd3c368e9c2b2174e89c2dfbba3b34e84feb8a20af1bb758116bb2'],
-    }),
 ]
 
 modextrapaths = {'R_LIBS_SITE': ''}

From 94700ab878728fbeadf6e34df956a18a4ac7074e Mon Sep 17 00:00:00 2001
From: ankekreuzer <a.kreuzer@fz-juelich.de>
Date: Fri, 30 Aug 2024 09:07:50 +0200
Subject: [PATCH 741/835] Added flatbuffers and flatbuffers-python to the
 GCCcore-13.3.0 toolchain

---
 ...atbuffers-python-24.3.25-GCCcore-13.3.0.eb | 27 +++++++++++++++
 .../flatbuffers-24.3.25-GCCcore-13.3.0.eb     | 33 +++++++++++++++++++
 2 files changed, 60 insertions(+)
 create mode 100644 easybuild/easyconfigs/f/flatbuffers-python/flatbuffers-python-24.3.25-GCCcore-13.3.0.eb
 create mode 100644 easybuild/easyconfigs/f/flatbuffers/flatbuffers-24.3.25-GCCcore-13.3.0.eb

diff --git a/easybuild/easyconfigs/f/flatbuffers-python/flatbuffers-python-24.3.25-GCCcore-13.3.0.eb b/easybuild/easyconfigs/f/flatbuffers-python/flatbuffers-python-24.3.25-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..6e3bd315965
--- /dev/null
+++ b/easybuild/easyconfigs/f/flatbuffers-python/flatbuffers-python-24.3.25-GCCcore-13.3.0.eb
@@ -0,0 +1,27 @@
+easyblock = 'PythonPackage'
+
+name = 'flatbuffers-python'
+version = '24.3.25'
+
+homepage = 'https://github.com/google/flatbuffers/'
+description = """Python Flatbuffers runtime library."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+source_urls = ['https://pypi.python.org/packages/source/f/flatbuffers']
+sources = [{'download_filename': 'flatbuffers-%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}]
+checksums = ['de2ec5b203f21441716617f38443e0a8ebf3d25bf0d9c0bb0ce68fa00ad546a4']
+
+dependencies = [
+    ('binutils', '2.42'),
+    ('Python', '3.12.3'),
+]
+
+download_dep_fail = True
+use_pip = True
+sanity_pip_check = True
+
+preinstallopts = 'VERSION=%(version)s '
+options = {'modulename': 'flatbuffers'}
+
+moduleclass = 'devel'
diff --git a/easybuild/easyconfigs/f/flatbuffers/flatbuffers-24.3.25-GCCcore-13.3.0.eb b/easybuild/easyconfigs/f/flatbuffers/flatbuffers-24.3.25-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..42c0b9a28f1
--- /dev/null
+++ b/easybuild/easyconfigs/f/flatbuffers/flatbuffers-24.3.25-GCCcore-13.3.0.eb
@@ -0,0 +1,33 @@
+##
+# Author:    Robert Mijakovic <robert.mijakovic@lxp.lu>
+##
+easyblock = 'CMakeNinja'
+
+name = 'flatbuffers'
+version = '24.3.25'
+
+homepage = 'https://github.com/google/flatbuffers/'
+description = """FlatBuffers: Memory Efficient Serialization Library"""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://github.com/google/flatbuffers/archive/v%(version)s/']
+sources = [SOURCE_TAR_GZ]
+checksums = ['4157c5cacdb59737c5d627e47ac26b140e9ee28b1102f812b36068aab728c1ed']
+
+builddependencies = [
+    ('binutils', '2.42'),
+    ('CMake', '3.29.3'),
+    ('Ninja', '1.12.1'),
+    ('Python', '3.12.3'),
+]
+
+configopts = '-DFLATBUFFERS_ENABLE_PCH=ON '
+
+sanity_check_paths = {
+    'files': ['include/flatbuffers/flatbuffers.h', 'bin/flatc', 'lib/libflatbuffers.a'],
+    'dirs': ['lib/cmake'],
+}
+
+moduleclass = 'devel'

From 0a9af9d28f7f45f72e5d8c163042304dbcb2ab0f Mon Sep 17 00:00:00 2001
From: ankekreuzer <a.kreuzer@fz-juelich.de>
Date: Fri, 30 Aug 2024 10:14:21 +0200
Subject: [PATCH 742/835] Added byacc and Guile 2.x.x to the GCCcore-13.3.0
 toolchain (dependencies for libmatheval)

---
 .../byacc-2.0.20240109-GCCcore-13.3.0.eb      | 22 ++++++++++
 .../g/Guile/Guile-2.0.14-GCCcore-13.3.0.eb    | 41 +++++++++++++++++++
 2 files changed, 63 insertions(+)
 create mode 100644 easybuild/easyconfigs/b/byacc/byacc-2.0.20240109-GCCcore-13.3.0.eb
 create mode 100644 easybuild/easyconfigs/g/Guile/Guile-2.0.14-GCCcore-13.3.0.eb

diff --git a/easybuild/easyconfigs/b/byacc/byacc-2.0.20240109-GCCcore-13.3.0.eb b/easybuild/easyconfigs/b/byacc/byacc-2.0.20240109-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..2cade945ccc
--- /dev/null
+++ b/easybuild/easyconfigs/b/byacc/byacc-2.0.20240109-GCCcore-13.3.0.eb
@@ -0,0 +1,22 @@
+easyblock = 'ConfigureMake'
+
+name = 'byacc'
+version = '2.0.20240109'
+
+homepage = 'http://invisible-island.net/byacc/byacc.html'
+description = """Berkeley Yacc (byacc) is generally conceded to be the best yacc variant available.
+ In contrast to bison, it is written to avoid dependencies upon a particular compiler.
+"""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+source_urls = ['https://invisible-island.net/archives/byacc/current/']
+sources = ['byacc.tar.gz']
+checksums = ['e5e0c069fb15d454918568f77e90a60221373dd206a3d3c2da1e7daba3bae9ea']
+
+builddependencies = [('binutils', '2.42')]
+
+sanity_check_paths = {
+    'files': ["bin/yacc"],
+    'dirs': []
+}
diff --git a/easybuild/easyconfigs/g/Guile/Guile-2.0.14-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/Guile/Guile-2.0.14-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..06a1dc6a05a
--- /dev/null
+++ b/easybuild/easyconfigs/g/Guile/Guile-2.0.14-GCCcore-13.3.0.eb
@@ -0,0 +1,41 @@
+easyblock = 'ConfigureMake'
+
+name = 'Guile'
+version = '2.0.14'
+
+homepage = 'http://www.gnu.org/software/guile'
+description = """Guile is the GNU Ubiquitous Intelligent Language for Extensions, the official extension language for 
+the GNU operating system.
+"""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+source_urls = [GNU_SOURCE]
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['8aeb2f353881282fe01694cce76bb72f7ffdd296a12c7a1a39255c27b0dfe5f1']
+
+builddependencies = [
+    ('binutils', '2.42'),
+    ('pkgconf', '2.2.0'),
+]
+
+dependencies = [
+    ('gc', '8.2.6'),
+    ('GMP', '6.3.0'),
+    ('libffi', '3.4.5'),
+    ('libunistring', '1.2'),
+    ('libtool', '2.4.7'),
+    ('libreadline', '8.2'),
+    ('XZ', '5.4.5'),
+]
+
+configopts = " --enable-error-on-warning=no"
+
+sanity_check_paths = {
+    'files': ["bin/%s" % x for x in ["guile", 'guile-config', 'guile-snarf', 'guile-tools']] +
+             ["lib/libguile-%(version_major_minor)s.a",
+              "include/guile/%(version_major_minor)s/libguile.h"],
+    'dirs': []
+}
+
+moduleclass = 'lang'

From db713d732bd607fffc04037431e809d34f4ec80a Mon Sep 17 00:00:00 2001
From: Ake Sandgren <ake.sandgren@hpc2n.umu.se>
Date: Fri, 30 Aug 2024 10:27:42 +0200
Subject: [PATCH 743/835] adding easyconfigs: XGBoost-2.1.1-gfbf-2023b.eb

---
 .../x/XGBoost/XGBoost-2.1.1-gfbf-2023b.eb     | 29 +++++++++++++++++++
 1 file changed, 29 insertions(+)
 create mode 100644 easybuild/easyconfigs/x/XGBoost/XGBoost-2.1.1-gfbf-2023b.eb

diff --git a/easybuild/easyconfigs/x/XGBoost/XGBoost-2.1.1-gfbf-2023b.eb b/easybuild/easyconfigs/x/XGBoost/XGBoost-2.1.1-gfbf-2023b.eb
new file mode 100644
index 00000000000..91e9be0529c
--- /dev/null
+++ b/easybuild/easyconfigs/x/XGBoost/XGBoost-2.1.1-gfbf-2023b.eb
@@ -0,0 +1,29 @@
+easyblock = 'PythonPackage'
+
+name = 'XGBoost'
+version = '2.1.1'
+
+homepage = 'https://github.com/dmlc/xgboost'
+description = """XGBoost is an optimized distributed gradient boosting library designed to be highly efficient,
+ flexible and portable."""
+
+toolchain = {'name': 'gfbf', 'version': '2023b'}
+
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['4b1729837f9f1ba88a32ef1be3f8efb860fee6454a68719b196dc88032c23d97']
+
+builddependencies = [
+    ('CMake', '3.27.6'),
+    ('hatchling', '1.18.0'),
+]
+
+dependencies = [
+    ('Python', '3.11.5'),
+    ('SciPy-bundle', '2023.11'),
+]
+
+use_pip = True
+download_dep_fail = True
+sanity_pip_check = True
+
+moduleclass = 'ai'

From b2544a98444fea2160f8957d48b24a55e128f737 Mon Sep 17 00:00:00 2001
From: ankekreuzer <a.kreuzer@fz-juelich.de>
Date: Fri, 30 Aug 2024 10:52:55 +0200
Subject: [PATCH 744/835] Added libmatheval to the GCCcore-13.3.0 toolchain.

---
 .../l/libmatheval/003-guile2.0.patch          | 402 ++++++++++++++++++
 .../libmatheval-1.1.11-GCCcore-13.3.0.eb      |  45 ++
 2 files changed, 447 insertions(+)
 create mode 100644 easybuild/easyconfigs/l/libmatheval/003-guile2.0.patch
 create mode 100644 easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-GCCcore-13.3.0.eb

diff --git a/easybuild/easyconfigs/l/libmatheval/003-guile2.0.patch b/easybuild/easyconfigs/l/libmatheval/003-guile2.0.patch
new file mode 100644
index 00000000000..3f592cadb0d
--- /dev/null
+++ b/easybuild/easyconfigs/l/libmatheval/003-guile2.0.patch
@@ -0,0 +1,402 @@
+Description: Increase precision of floating point tests
+ guile-2.0 has increased the precision of the floating point maths returns,
+ so the test suite needs to allow for the correct values to be returned
+ with higher precision. Thanks to Dave Pigott <dave.pigott@linaro.org>
+ Also adapt the configure script to build against guile-2.0 - patch from
+ Hilo Bengen <bengen@debian.org>.
+ .
+ libmatheval (1.1.11+dfsg-1.1) unstable; urgency=low
+ .
+   * Non-maintainer upload.
+   * Migrate to guile-2.0 - patch from Hilo Bengen,
+     extended to support higher precision of return values
+     by guile-2.0. (Closes: #746013)
+Author: Neil Williams <codehelp@debian.org>
+Bug-Debian: https://bugs.debian.org/746013
+
+---
+
+--- libmatheval-1.1.11+dfsg.orig/configure.in
++++ libmatheval-1.1.11+dfsg/configure.in
+@@ -60,10 +60,11 @@ dnl Checks for library functions.
+ AC_CHECK_FUNCS([bzero memset], [break])
+ 
+ dnl Additional Guile feature checks.
++CFLAGS="$CFLAGS $GUILE_CFLAGS"
+ AC_CHECK_TYPE([scm_t_bits], [AC_DEFINE([HAVE_SCM_T_BITS], [1], [Define to 1 if you have the `scm_t_bits' type.])], [], [#include <libguile.h>])
+-AC_CHECK_LIB([guile], [scm_c_define_gsubr], [AC_DEFINE([HAVE_SCM_C_DEFINE_GSUBR], [1], [Define to 1 if you have the `scm_c_define_gsubr' function.])], [], [$GUILE_LDFLAGS])
+-AC_CHECK_LIB([guile], [scm_make_gsubr], [AC_DEFINE([HAVE_SCM_MAKE_GSUBR], [1], [Define to 1 if you have the `scm_make_gsubr' function.])], [], [$GUILE_LDFLAGS])
+-AC_CHECK_LIB([guile], [scm_num2dbl], [AC_DEFINE([HAVE_SCM_NUM2DBL], [1], [Define to 1 if you have the `scm_num2dbl' function.])], [], [$GUILE_LDFLAGS])
++AC_CHECK_LIB([guile-2.0], [scm_c_define_gsubr], [AC_DEFINE([HAVE_SCM_C_DEFINE_GSUBR], [1], [Define to 1 if you have the `scm_c_define_gsubr' function.])], [], [$GUILE_LDFLAGS])
++AC_CHECK_LIB([guile-2.0], [scm_make_gsubr], [AC_DEFINE([HAVE_SCM_MAKE_GSUBR], [1], [Define to 1 if you have the `scm_make_gsubr' function.])], [], [$GUILE_LDFLAGS])
++AC_CHECK_LIB([guile-2.0], [scm_num2dbl], [AC_DEFINE([HAVE_SCM_NUM2DBL], [1], [Define to 1 if you have the `scm_num2dbl' function.])], [], [$GUILE_LDFLAGS])
+ 
+ AC_CONFIG_FILES([Makefile doc/Makefile lib/Makefile])
+ AC_OUTPUT(libmatheval.pc)
+--- libmatheval-1.1.11+dfsg.orig/tests/basics.at
++++ libmatheval-1.1.11+dfsg/tests/basics.at
+@@ -62,7 +62,7 @@ AT_DATA([basics.scm],
+ (display (evaluator-evaluate-x f 0))
+ ]])
+ 
+-AT_CHECK([matheval.sh basics.scm], [ignore], [10.0], [ignore])
++AT_CHECK([matheval.sh basics.scm], [ignore], [10.000000000000002], [ignore])
+ 
+ AT_DATA([basics.scm],
+ [[
+@@ -70,7 +70,7 @@ AT_DATA([basics.scm],
+ (display (evaluator-evaluate-x f 0.7))
+ ]])
+ 
+-AT_CHECK([matheval.sh basics.scm], [ignore], [0.220966666722528], [ignore])
++AT_CHECK([matheval.sh basics.scm], [ignore], [0.22096666672252796], [ignore])
+ 
+ AT_DATA([basics.scm],
+ [[
+@@ -78,7 +78,7 @@ AT_DATA([basics.scm],
+ (display (evaluator-evaluate-x-y f 0.4 -0.7))
+ ]])
+ 
+-AT_CHECK([matheval.sh basics.scm], [ignore], [-1.14962406520749], [ignore])
++AT_CHECK([matheval.sh basics.scm], [ignore], [-1.1496240652074883], [ignore])
+ 
+ AT_DATA([basics.scm],
+ [[
+@@ -86,7 +86,7 @@ AT_DATA([basics.scm],
+ (display (evaluator-evaluate-x-y-z f 11.2 0.41 -0.66))
+ ]])
+ 
+-AT_CHECK([matheval.sh basics.scm], [ignore], [3.99876152571934], [ignore])
++AT_CHECK([matheval.sh basics.scm], [ignore], [3.9987615257193383], [ignore])
+ 
+ AT_DATA([basics.scm],
+ [[
+--- libmatheval-1.1.11+dfsg.orig/tests/constants.at
++++ libmatheval-1.1.11+dfsg/tests/constants.at
+@@ -29,7 +29,7 @@ AT_DATA([constant.scm],
+ (display (evaluator-evaluate-x f 0))
+ ]])
+ 
+-AT_CHECK([matheval.sh constant.scm], [ignore], [2.71828182845905], [ignore])
++AT_CHECK([matheval.sh constant.scm], [ignore], [2.718281828459045], [ignore])
+ 
+ AT_DATA([constant.scm],
+ [[
+@@ -37,7 +37,7 @@ AT_DATA([constant.scm],
+ (display (evaluator-evaluate-x f 0))
+ ]])
+ 
+-AT_CHECK([matheval.sh constant.scm], [ignore], [1.44269504088896], [ignore])
++AT_CHECK([matheval.sh constant.scm], [ignore], [1.4426950408889634], [ignore])
+ 
+ AT_DATA([constant.scm],
+ [[
+@@ -45,7 +45,7 @@ AT_DATA([constant.scm],
+ (display (evaluator-evaluate-x f 0))
+ ]])
+ 
+-AT_CHECK([matheval.sh constant.scm], [ignore], [0.434294481903252], [ignore])
++AT_CHECK([matheval.sh constant.scm], [ignore], [0.4342944819032518], [ignore])
+ 
+ AT_DATA([constant.scm],
+ [[
+@@ -53,7 +53,7 @@ AT_DATA([constant.scm],
+ (display (evaluator-evaluate-x f 0))
+ ]])
+ 
+-AT_CHECK([matheval.sh constant.scm], [ignore], [0.693147180559945], [ignore])
++AT_CHECK([matheval.sh constant.scm], [ignore], [0.6931471805599453], [ignore])
+ 
+ AT_DATA([constant.scm],
+ [[
+@@ -61,7 +61,7 @@ AT_DATA([constant.scm],
+ (display (evaluator-evaluate-x f 0))
+ ]])
+ 
+-AT_CHECK([matheval.sh constant.scm], [ignore], [2.30258509299405], [ignore])
++AT_CHECK([matheval.sh constant.scm], [ignore], [2.302585092994046], [ignore])
+ 
+ AT_DATA([constant.scm],
+ [[
+@@ -69,7 +69,7 @@ AT_DATA([constant.scm],
+ (display (evaluator-evaluate-x f 0))
+ ]])
+ 
+-AT_CHECK([matheval.sh constant.scm], [ignore], [3.14159265358979], [ignore])
++AT_CHECK([matheval.sh constant.scm], [ignore], [3.141592653589793], [ignore])
+ 
+ AT_DATA([constant.scm],
+ [[
+@@ -77,7 +77,7 @@ AT_DATA([constant.scm],
+ (display (evaluator-evaluate-x f 0))
+ ]])
+ 
+-AT_CHECK([matheval.sh constant.scm], [ignore], [1.5707963267949], [ignore])
++AT_CHECK([matheval.sh constant.scm], [ignore], [1.5707963267948966], [ignore])
+ 
+ AT_DATA([constant.scm],
+ [[
+@@ -85,7 +85,7 @@ AT_DATA([constant.scm],
+ (display (evaluator-evaluate-x f 0))
+ ]])
+ 
+-AT_CHECK([matheval.sh constant.scm], [ignore], [0.785398163397448], [ignore])
++AT_CHECK([matheval.sh constant.scm], [ignore], [0.7853981633974483], [ignore])
+ 
+ AT_DATA([constant.scm],
+ [[
+@@ -93,7 +93,7 @@ AT_DATA([constant.scm],
+ (display (evaluator-evaluate-x f 0))
+ ]])
+ 
+-AT_CHECK([matheval.sh constant.scm], [ignore], [0.318309886183791], [ignore])
++AT_CHECK([matheval.sh constant.scm], [ignore], [0.3183098861837907], [ignore])
+ 
+ AT_DATA([constant.scm],
+ [[
+@@ -101,7 +101,7 @@ AT_DATA([constant.scm],
+ (display (evaluator-evaluate-x f 0))
+ ]])
+ 
+-AT_CHECK([matheval.sh constant.scm], [ignore], [0.636619772367581], [ignore])
++AT_CHECK([matheval.sh constant.scm], [ignore], [0.6366197723675814], [ignore])
+ 
+ AT_DATA([constant.scm],
+ [[
+@@ -109,7 +109,7 @@ AT_DATA([constant.scm],
+ (display (evaluator-evaluate-x f 0))
+ ]])
+ 
+-AT_CHECK([matheval.sh constant.scm], [ignore], [1.12837916709551], [ignore])
++AT_CHECK([matheval.sh constant.scm], [ignore], [1.1283791670955126], [ignore])
+ 
+ AT_DATA([constant.scm],
+ [[
+@@ -117,7 +117,7 @@ AT_DATA([constant.scm],
+ (display (evaluator-evaluate-x f 0))
+ ]])
+ 
+-AT_CHECK([matheval.sh constant.scm], [ignore], [1.4142135623731], [ignore])
++AT_CHECK([matheval.sh constant.scm], [ignore], [1.4142135623730951], [ignore])
+ 
+ AT_DATA([constant.scm],
+ [[
+@@ -125,7 +125,7 @@ AT_DATA([constant.scm],
+ (display (evaluator-evaluate-x f 0))
+ ]])
+ 
+-AT_CHECK([matheval.sh constant.scm], [ignore], [0.707106781186548], [ignore])
++AT_CHECK([matheval.sh constant.scm], [ignore], [0.7071067811865476], [ignore])
+ 
+ AT_DATA([constant.scm],
+ [[
+@@ -133,7 +133,7 @@ AT_DATA([constant.scm],
+ (display (evaluator-evaluate-x f 0))
+ ]])
+ 
+-AT_CHECK([matheval.sh constant.scm], [ignore], [10.0], [ignore])
++AT_CHECK([matheval.sh constant.scm], [ignore], [10.000000000000002], [ignore])
+ 
+ AT_DATA([constant.scm],
+ [[
+--- libmatheval-1.1.11+dfsg.orig/tests/functions.at
++++ libmatheval-1.1.11+dfsg/tests/functions.at
+@@ -29,7 +29,7 @@ AT_DATA([function.scm],
+ (display (evaluator-evaluate-x f 1))
+ ]])
+ 
+-AT_CHECK([matheval.sh function.scm], [ignore], [2.71828182845905], [ignore])
++AT_CHECK([matheval.sh function.scm], [ignore], [2.718281828459045], [ignore])
+ 
+ AT_DATA([function.scm],
+ [[
+@@ -80,7 +80,7 @@ AT_DATA([function.scm],
+ (display (evaluator-evaluate-x f 1))
+ ]])
+ 
+-AT_CHECK([matheval.sh function.scm], [ignore], [0.841470984807897], [ignore])
++AT_CHECK([matheval.sh function.scm], [ignore], [0.8414709848078965], [ignore])
+ 
+ AT_DATA([function.scm],
+ [[
+@@ -97,7 +97,7 @@ AT_DATA([function.scm],
+ (display (evaluator-evaluate-x f 1))
+ ]])
+ 
+-AT_CHECK([matheval.sh function.scm], [ignore], [0.54030230586814], [ignore])
++AT_CHECK([matheval.sh function.scm], [ignore], [0.5403023058681398], [ignore])
+ 
+ AT_DATA([function.scm],
+ [[
+@@ -114,7 +114,7 @@ AT_DATA([function.scm],
+ (display (evaluator-evaluate-x f 1))
+ ]])
+ 
+-AT_CHECK([matheval.sh function.scm], [ignore], [1.5574077246549], [ignore])
++AT_CHECK([matheval.sh function.scm], [ignore], [1.5574077246549023], [ignore])
+ 
+ AT_DATA([function.scm],
+ [[
+@@ -131,7 +131,7 @@ AT_DATA([function.scm],
+ (display (evaluator-evaluate-x f 1))
+ ]])
+ 
+-AT_CHECK([matheval.sh function.scm], [ignore], [0.642092615934331], [ignore])
++AT_CHECK([matheval.sh function.scm], [ignore], [0.6420926159343306], [ignore])
+ 
+ AT_DATA([function.scm],
+ [[
+@@ -148,7 +148,7 @@ AT_DATA([function.scm],
+ (display (evaluator-evaluate-x f 1))
+ ]])
+ 
+-AT_CHECK([matheval.sh function.scm], [ignore], [1.85081571768093], [ignore])
++AT_CHECK([matheval.sh function.scm], [ignore], [1.8508157176809255], [ignore])
+ 
+ AT_DATA([function.scm],
+ [[
+@@ -165,7 +165,7 @@ AT_DATA([function.scm],
+ (display (evaluator-evaluate-x f 1))
+ ]])
+ 
+-AT_CHECK([matheval.sh function.scm], [ignore], [1.18839510577812], [ignore])
++AT_CHECK([matheval.sh function.scm], [ignore], [1.1883951057781212], [ignore])
+ 
+ AT_DATA([function.scm],
+ [[
+@@ -182,7 +182,7 @@ AT_DATA([function.scm],
+ (display (evaluator-evaluate-x f 1))
+ ]])
+ 
+-AT_CHECK([matheval.sh function.scm], [ignore], [1.5707963267949], [ignore])
++AT_CHECK([matheval.sh function.scm], [ignore], [1.5707963267948966], [ignore])
+ 
+ AT_DATA([function.scm],
+ [[
+@@ -216,7 +216,7 @@ AT_DATA([function.scm],
+ (display (evaluator-evaluate-x f 1))
+ ]])
+ 
+-AT_CHECK([matheval.sh function.scm], [ignore], [0.785398163397448], [ignore])
++AT_CHECK([matheval.sh function.scm], [ignore], [0.7853981633974483], [ignore])
+ 
+ AT_DATA([function.scm],
+ [[
+@@ -233,7 +233,7 @@ AT_DATA([function.scm],
+ (display (evaluator-evaluate-x f 1))
+ ]])
+ 
+-AT_CHECK([matheval.sh function.scm], [ignore], [0.785398163397448], [ignore])
++AT_CHECK([matheval.sh function.scm], [ignore], [0.7853981633974483], [ignore])
+ 
+ AT_DATA([function.scm],
+ [[
+@@ -267,7 +267,7 @@ AT_DATA([function.scm],
+ (display (evaluator-evaluate-x f 1))
+ ]])
+ 
+-AT_CHECK([matheval.sh function.scm], [ignore], [1.5707963267949], [ignore])
++AT_CHECK([matheval.sh function.scm], [ignore], [1.5707963267948966], [ignore])
+ 
+ AT_DATA([function.scm],
+ [[
+@@ -284,7 +284,7 @@ AT_DATA([function.scm],
+ (display (evaluator-evaluate-x f 1))
+ ]])
+ 
+-AT_CHECK([matheval.sh function.scm], [ignore], [1.1752011936438], [ignore])
++AT_CHECK([matheval.sh function.scm], [ignore], [1.1752011936438014], [ignore])
+ 
+ AT_DATA([function.scm],
+ [[
+@@ -301,7 +301,7 @@ AT_DATA([function.scm],
+ (display (evaluator-evaluate-x f 1))
+ ]])
+ 
+-AT_CHECK([matheval.sh function.scm], [ignore], [1.54308063481524], [ignore])
++AT_CHECK([matheval.sh function.scm], [ignore], [1.5430806348152437], [ignore])
+ 
+ AT_DATA([function.scm],
+ [[
+@@ -318,7 +318,7 @@ AT_DATA([function.scm],
+ (display (evaluator-evaluate-x f 1))
+ ]])
+ 
+-AT_CHECK([matheval.sh function.scm], [ignore], [0.761594155955765], [ignore])
++AT_CHECK([matheval.sh function.scm], [ignore], [0.7615941559557649], [ignore])
+ 
+ AT_DATA([function.scm],
+ [[
+@@ -335,7 +335,7 @@ AT_DATA([function.scm],
+ (display (evaluator-evaluate-x f 1))
+ ]])
+ 
+-AT_CHECK([matheval.sh function.scm], [ignore], [1.31303528549933], [ignore])
++AT_CHECK([matheval.sh function.scm], [ignore], [1.3130352854993315], [ignore])
+ 
+ AT_DATA([function.scm],
+ [[
+@@ -352,7 +352,7 @@ AT_DATA([function.scm],
+ (display (evaluator-evaluate-x f 1))
+ ]])
+ 
+-AT_CHECK([matheval.sh function.scm], [ignore], [0.648054273663885], [ignore])
++AT_CHECK([matheval.sh function.scm], [ignore], [0.6480542736638855], [ignore])
+ 
+ AT_DATA([function.scm],
+ [[
+@@ -368,7 +368,7 @@ AT_DATA([function.scm],
+ (display (evaluator-evaluate-x f 1))
+ ]])
+ 
+-AT_CHECK([matheval.sh function.scm], [ignore], [0.850918128239322], [ignore])
++AT_CHECK([matheval.sh function.scm], [ignore], [0.8509181282393216], [ignore])
+ 
+ AT_DATA([function.scm],
+ [[
+@@ -385,7 +385,7 @@ AT_DATA([function.scm],
+ (display (evaluator-evaluate-x f 1))
+ ]])
+ 
+-AT_CHECK([matheval.sh function.scm], [ignore], [0.881373587019543], [ignore])
++AT_CHECK([matheval.sh function.scm], [ignore], [0.8813735870195429], [ignore])
+ 
+ AT_DATA([function.scm],
+ [[
+@@ -419,7 +419,7 @@ AT_DATA([function.scm],
+ (display (evaluator-evaluate-x f 0.5))
+ ]])
+ 
+-AT_CHECK([matheval.sh function.scm], [ignore], [0.549306144334055], [ignore])
++AT_CHECK([matheval.sh function.scm], [ignore], [0.5493061443340549], [ignore])
+ 
+ AT_DATA([function.scm],
+ [[
+@@ -436,7 +436,7 @@ AT_DATA([function.scm],
+ (display (evaluator-evaluate-x f 2))
+ ]])
+ 
+-AT_CHECK([matheval.sh function.scm], [ignore], [0.549306144334055], [ignore])
++AT_CHECK([matheval.sh function.scm], [ignore], [0.5493061443340549], [ignore])
+ 
+ AT_DATA([function.scm],
+ [[
+@@ -470,7 +470,7 @@ AT_DATA([function.scm],
+ (display (evaluator-evaluate-x f 1))
+ ]])
+ 
+-AT_CHECK([matheval.sh function.scm], [ignore], [0.881373587019543], [ignore])
++AT_CHECK([matheval.sh function.scm], [ignore], [0.8813735870195429], [ignore])
+ 
+ AT_DATA([function.scm],
+ [[
+--- libmatheval-1.1.11+dfsg.orig/tests/numbers.at
++++ libmatheval-1.1.11+dfsg/tests/numbers.at
+@@ -53,6 +53,6 @@ AT_DATA([number.scm],
+ (display (evaluator-evaluate-x f 0))
+ ]])
+ 
+-AT_CHECK([matheval.sh number.scm], [ignore], [0.644394014977254], [ignore])
++AT_CHECK([matheval.sh number.scm], [ignore], [0.6443940149772542], [ignore])
+ 
+ AT_CLEANUP
diff --git a/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..4cea27b91dc
--- /dev/null
+++ b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-GCCcore-13.3.0.eb
@@ -0,0 +1,45 @@
+easyblock = 'ConfigureMake'
+
+name = 'libmatheval'
+version = '1.1.11'  # still the latest version available on the ftp mirror
+
+homepage = 'http://www.gnu.org/software/libmatheval/'
+description = """GNU libmatheval is a library (callable from C and Fortran) to parse
+ and evaluate symbolic expressions input as text.
+"""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+toolchainopts = {'pic': True}
+
+source_urls = [GNU_SOURCE]
+sources = [SOURCELOWER_TAR_GZ]
+patches = [
+    '003-guile2.0.patch',
+    'libmatheval-1.1.11_fix-matheval-test.patch'
+]
+checksums = [
+    {'libmatheval-1.1.11.tar.gz': '474852d6715ddc3b6969e28de5e1a5fbaff9e8ece6aebb9dc1cc63e9e88e89ab'},
+    {'003-guile2.0.patch': 'd0ad39d54800153cbaa26c01448f040d405f09e9fd57e1357eab170a274a9b5c'},
+    {'libmatheval-1.1.11_fix-matheval-test.patch': '2888ee1ba32bb864b655e53e13b06eafc23b598faed80b90585d41c98e2ae073'},
+]
+
+builddependencies = [
+    ('binutils', '2.42'),
+    ('flex', '2.6.4'),
+    ('Bison', '3.8.2'),
+    ('byacc', '2.0.20240109'),
+    # guile 2.2.X, 3.0.7 removed scm_num2dbl (among others), which are needed for libmatheval (at least for 1.1.11)
+    ('Guile', '2.0.14')
+]
+
+configopts = '--with-pic '
+
+# fix for guile-config being broken because shebang line contains full path to bin/guile
+configopts += 'GUILE_CONFIG="$EBROOTGUILE/bin/guile -e main -s $EBROOTGUILE/bin/guile-config"'
+
+sanity_check_paths = {
+    'files': ['lib/libmatheval.a', 'include/matheval.h'],
+    'dirs': [],
+}
+
+moduleclass = 'lib'

From 67dd6beac93bdbea7dcb21901d9c23744026a7df Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Petr=20Kr=C3=A1l?= <petr@inuits.eu>
Date: Fri, 30 Aug 2024 10:58:48 +0200
Subject: [PATCH 745/835] changes requested in PR

---
 ...ore-13.2.0.eb => mcqd-1.0.0-GCC-13.2.0.eb} | 20 ++++++++-----------
 1 file changed, 8 insertions(+), 12 deletions(-)
 rename easybuild/easyconfigs/m/mcqd/{mcqd-1.0.0-GCCcore-13.2.0.eb => mcqd-1.0.0-GCC-13.2.0.eb} (54%)

diff --git a/easybuild/easyconfigs/m/mcqd/mcqd-1.0.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/m/mcqd/mcqd-1.0.0-GCC-13.2.0.eb
similarity index 54%
rename from easybuild/easyconfigs/m/mcqd/mcqd-1.0.0-GCCcore-13.2.0.eb
rename to easybuild/easyconfigs/m/mcqd/mcqd-1.0.0-GCC-13.2.0.eb
index efc5b111642..87f92553548 100644
--- a/easybuild/easyconfigs/m/mcqd/mcqd-1.0.0-GCCcore-13.2.0.eb
+++ b/easybuild/easyconfigs/m/mcqd/mcqd-1.0.0-GCC-13.2.0.eb
@@ -6,31 +6,27 @@ version = '1.0.0'
 homepage = 'https://gitlab.com/janezkonc/mcqd'
 description = """MaxCliqueDyn is a fast exact algorithm for finding a maximum clique in an undirected graph."""
 
-toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
+toolchain = {'name': 'GCC', 'version': '13.2.0'}
 
 source_urls = ['https://gitlab.com/janezkonc/mcqd/-/archive/v%(version)s/']
-sources = ['%(name)s-v%(version)s.tar.gz']
+sources = ['mcqd-v%(version)s.tar.gz']
 checksums = ['37ff68ff88e047c929990d4c12ce474753f6f9c49324661a3aa1cfe77c26ad9d']
 
-builddependencies = [
-    ('binutils', '2.40'),
-]
-
-cmds_map = [('.*', 'echo here && pwd && ls -lh && $CXX $CXXFLAGS $LDFLAGS mcqd.cpp -o mcqd')]
+cmds_map = [('.*', '$CXX $CXXFLAGS $LDFLAGS mcqd.cpp -o mcqd')]
 
 files_to_copy = [
-    (['%(name)s'], 'bin'),
-    (['%(name)s.h'], 'include'),
+    (['mcqd'], 'bin'),
+    (['mcqd.h'], 'include'),
 ]
 
 sanity_check_paths = {
     'files': [
-        'bin/%(name)s',
-        'include/%(name)s.h',
+        'bin/mcqd',
+        'include/mcqd.h',
     ],
     'dirs': [],
 }
 
-sanity_check_commands = ["command -v %(name)s"]
+sanity_check_commands = ["command -v mcqd"]
 
 moduleclass = 'math'

From e6608ff6108ac5a225c722e3d43d56df9fe0692c Mon Sep 17 00:00:00 2001
From: ankekreuzer <a.kreuzer@fz-juelich.de>
Date: Fri, 30 Aug 2024 11:03:59 +0200
Subject: [PATCH 746/835] Added libopus and libgit2 to the GCCcore-13.3.0
 toolchain.

---
 .../l/libgit2/libgit2-1.8.1-GCCcore-13.3.0.eb | 34 +++++++++++++++++++
 .../l/libopus/libopus-1.5.2-GCCcore-13.3.0.eb | 30 ++++++++++++++++
 2 files changed, 64 insertions(+)
 create mode 100644 easybuild/easyconfigs/l/libgit2/libgit2-1.8.1-GCCcore-13.3.0.eb
 create mode 100644 easybuild/easyconfigs/l/libopus/libopus-1.5.2-GCCcore-13.3.0.eb

diff --git a/easybuild/easyconfigs/l/libgit2/libgit2-1.8.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libgit2/libgit2-1.8.1-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..07da30e2a80
--- /dev/null
+++ b/easybuild/easyconfigs/l/libgit2/libgit2-1.8.1-GCCcore-13.3.0.eb
@@ -0,0 +1,34 @@
+easyblock = 'CMakeMake'
+
+name = 'libgit2'
+version = '1.8.1'
+
+homepage = 'https://libgit2.org/'
+description = """libgit2 is a portable, pure C implementation of the Git core methods provided as a re-entrant
+linkable library with a solid API, allowing you to write native speed custom Git applications in any language
+which supports C bindings."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+source_urls = [GITHUB_SOURCE]
+sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}]
+checksums = ['8c1eaf0cf07cba0e9021920bfba9502140220786ed5d8a8ec6c7ad9174522f8e']
+
+builddependencies = [
+    ('binutils', '2.42'),
+    ('CMake', '3.29.3'),
+    ('pkgconf', '2.2.0'),
+]
+dependencies = [
+    ('PCRE2', '10.43'),
+    ('OpenSSL', '3', '', SYSTEM),
+]
+
+configopts = '-DREGEX_BACKEND=pcre2'
+
+sanity_check_paths = {
+    'files': ['include/git2.h', 'lib64/%%(name)s.%s' % SHLIB_EXT, 'lib64/pkgconfig/%(name)s.pc'],
+    'dirs': [],
+}
+
+moduleclass = 'devel'
diff --git a/easybuild/easyconfigs/l/libopus/libopus-1.5.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libopus/libopus-1.5.2-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..c09615c86f8
--- /dev/null
+++ b/easybuild/easyconfigs/l/libopus/libopus-1.5.2-GCCcore-13.3.0.eb
@@ -0,0 +1,30 @@
+easyblock = 'ConfigureMake'
+
+name = 'libopus'
+version = '1.5.2'
+
+homepage = 'https://www.opus-codec.org/'
+description = """Opus is a totally open, royalty-free, highly versatile audio codec. Opus is unmatched for interactive
+ speech and music transmission over the Internet, but is also intended for storage and streaming applications. It is
+ standardized by the Internet Engineering Task Force (IETF) as RFC 6716 which incorporated technology from Skype’s
+ SILK codec and Xiph.Org’s CELT codec."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+source_urls = ['https://downloads.xiph.org/releases/opus/']
+sources = ['opus-%(version)s.tar.gz']
+checksums = ['65c1d2f78b9f2fb20082c38cbe47c951ad5839345876e46941612ee87f9a7ce1']
+
+builddependencies = [
+    ('binutils', '2.42'),
+    ('pkgconf', '2.2.0'),
+]
+
+configopts = '--enable-static --enable-shared'
+
+sanity_check_paths = {
+    'files': ['lib/libopus.a', 'lib/libopus.%s' % SHLIB_EXT],
+    'dirs': ['include/opus'],
+}
+
+moduleclass = 'lib'

From 04c3043bcaa487db2c20e7d5a55073492ab6c703 Mon Sep 17 00:00:00 2001
From: ankekreuzer <a.kreuzer@fz-juelich.de>
Date: Fri, 30 Aug 2024 13:16:49 +0200
Subject: [PATCH 747/835] Added libvorbis and libsndfile to the GCCcore-13.3.0
 toolchain.

---
 .../libsndfile-1.2.2-GCCcore-13.3.0.eb        | 39 +++++++++++++++++++
 .../libvorbis-1.3.7-GCCcore-13.3.0.eb         | 30 ++++++++++++++
 2 files changed, 69 insertions(+)
 create mode 100644 easybuild/easyconfigs/l/libsndfile/libsndfile-1.2.2-GCCcore-13.3.0.eb
 create mode 100644 easybuild/easyconfigs/l/libvorbis/libvorbis-1.3.7-GCCcore-13.3.0.eb

diff --git a/easybuild/easyconfigs/l/libsndfile/libsndfile-1.2.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libsndfile/libsndfile-1.2.2-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..e60ad09d1a1
--- /dev/null
+++ b/easybuild/easyconfigs/l/libsndfile/libsndfile-1.2.2-GCCcore-13.3.0.eb
@@ -0,0 +1,39 @@
+easyblock = 'CMakeMake'
+
+name = 'libsndfile'
+version = '1.2.2'
+
+homepage = 'http://www.mega-nerd.com/libsndfile'
+description = """Libsndfile is a C library for reading and writing files containing sampled sound
+ (such as MS Windows WAV and the Apple/SGI AIFF format) through one standard library interface."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+source_urls = ['https://github.com/%(name)s/%(name)s/releases/download/%(version)s/']
+sources = [SOURCE_TAR_XZ]
+checksums = ['3799ca9924d3125038880367bf1468e53a1b7e3686a934f098b7e1d286cdb80e']
+
+builddependencies = [
+    ('binutils', '2.42'),
+    ('pkgconf', '2.2.0'),
+    ('CMake', '3.29.3'),
+]
+dependencies = [
+    ('FLAC', '1.4.3'),
+    ('libvorbis', '1.3.7'),
+    ('libopus', '1.5.2'),
+    ('LAME', '3.100'),
+]
+
+configopts = [
+    '',
+    '-DBUILD_SHARED_LIBS=ON',
+]
+
+
+sanity_check_paths = {
+    'files': ['include/sndfile.h', 'include/sndfile.hh', 'lib/%(name)s.a', 'lib/%(name)s.so'],
+    'dirs': ['bin'],
+}
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/l/libvorbis/libvorbis-1.3.7-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libvorbis/libvorbis-1.3.7-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..7e32c5c3a99
--- /dev/null
+++ b/easybuild/easyconfigs/l/libvorbis/libvorbis-1.3.7-GCCcore-13.3.0.eb
@@ -0,0 +1,30 @@
+easyblock = 'ConfigureMake'
+
+name = 'libvorbis'
+version = '1.3.7'
+
+homepage = 'https://xiph.org/vorbis/'
+description = """Ogg Vorbis is a fully open, non-proprietary, patent-and-royalty-free, general-purpose compressed
+audio format"""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+source_urls = ['https://ftp.osuosl.org/pub/xiph/releases/vorbis/']
+sources = [SOURCE_TAR_XZ]
+checksums = ['b33cc4934322bcbf6efcbacf49e3ca01aadbea4114ec9589d1b1e9d20f72954b']
+
+builddependencies = [
+    ('binutils', '2.42'),
+    ('pkgconf', '2.2.0'),
+]
+
+dependencies = [('libogg', '1.3.5')]
+
+configopts = '--enable-static --enable-shared'
+
+sanity_check_paths = {
+    'files': ['lib/libvorbis.a', 'lib/libvorbis.%s' % SHLIB_EXT],
+    'dirs': ['include/vorbis'],
+}
+
+moduleclass = 'lib'

From 3698b966894a0788ed36e9ef498a7aa54a468453 Mon Sep 17 00:00:00 2001
From: ankekreuzer <a.kreuzer@fz-juelich.de>
Date: Fri, 30 Aug 2024 13:31:58 +0200
Subject: [PATCH 748/835] Added libspatialindex and libxslt to the
 GCCcore-13.3.0 toolchain.

---
 .../libspatialindex-2.0.0-GCCcore-13.3.0.eb   | 25 +++++++++++++
 .../libxslt/libxslt-1.1.42-GCCcore-13.3.0.eb  | 36 +++++++++++++++++++
 2 files changed, 61 insertions(+)
 create mode 100644 easybuild/easyconfigs/l/libspatialindex/libspatialindex-2.0.0-GCCcore-13.3.0.eb
 create mode 100644 easybuild/easyconfigs/l/libxslt/libxslt-1.1.42-GCCcore-13.3.0.eb

diff --git a/easybuild/easyconfigs/l/libspatialindex/libspatialindex-2.0.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libspatialindex/libspatialindex-2.0.0-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..1752b337b05
--- /dev/null
+++ b/easybuild/easyconfigs/l/libspatialindex/libspatialindex-2.0.0-GCCcore-13.3.0.eb
@@ -0,0 +1,25 @@
+easyblock = 'CMakeMake'
+
+name = 'libspatialindex'
+version = '2.0.0'
+
+homepage = 'https://libspatialindex.org'
+description = "C++ implementation of R*-tree, an MVR-tree and a TPR-tree with C API"
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+source_urls = ['https://github.com/%(name)s/%(name)s/releases/download/%(version)s/']
+sources = ['spatialindex-src-%(version)s.tar.gz']
+checksums = ['f1d5a369681fa6ac3301a54db412ccf3180fc17163ebc3252f32c752f77345de']
+
+builddependencies = [
+    ('binutils', '2.42'),
+    ('CMake', '3.29.3'),
+]
+
+sanity_check_paths = {
+    'files': ['lib/%s.%s' % (name, SHLIB_EXT)],
+    'dirs': ['include/spatialindex'],
+}
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.42-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.42-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..a38c53ef841
--- /dev/null
+++ b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.42-GCCcore-13.3.0.eb
@@ -0,0 +1,36 @@
+easyblock = 'ConfigureMake'
+
+name = 'libxslt'
+version = '1.1.42'
+
+homepage = 'http://xmlsoft.org/'
+description = """Libxslt is the XSLT C library developed for the GNOME project
+ (but usable outside of the Gnome platform)."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+source_urls = ['https://download.gnome.org/sources/libxslt/%(version_major_minor)s/']
+sources = [SOURCE_TAR_XZ]
+checksums = ['85ca62cac0d41fc77d3f6033da9df6fd73d20ea2fc18b0a3609ffb4110e1baeb']
+
+builddependencies = [
+    ('binutils', '2.42'),
+    ('pkgconf', '2.2.0'),
+]
+
+dependencies = [
+    ('zlib', '1.3.1'),
+    ('libxml2', '2.12.7'),
+]
+
+# Make sure it doesn't pick up OS installed libgcrypt or Python
+# enable building static libs
+configopts = '--with-crypto=no --with-python=no --enable-static=yes '
+
+sanity_check_paths = {
+    'files': ['bin/xsltproc', 'include/libxslt/xslt.h', 'lib/%%(name)s.%s' % SHLIB_EXT, 'lib/%(name)s.a',
+              'lib/libexslt.%s' % SHLIB_EXT, 'lib/libexslt.a'],
+    'dirs': ['include/libxslt', 'include/libexslt'],
+}
+
+moduleclass = 'lib'

From f2d7b3de0dcb79cb2565140acabc7d9d62be0635 Mon Sep 17 00:00:00 2001
From: ankekreuzer <a.kreuzer@fz-juelich.de>
Date: Fri, 30 Aug 2024 14:04:49 +0200
Subject: [PATCH 749/835] Added giflib and libwebp to the GCCcore-13.3.0
 toolchain.

---
 .../g/giflib/giflib-5.2.1-GCCcore-13.3.0.eb   | 28 ++++++++++++
 .../l/libwebp/libwebp-1.4.0-GCCcore-13.3.0.eb | 45 +++++++++++++++++++
 2 files changed, 73 insertions(+)
 create mode 100644 easybuild/easyconfigs/g/giflib/giflib-5.2.1-GCCcore-13.3.0.eb
 create mode 100644 easybuild/easyconfigs/l/libwebp/libwebp-1.4.0-GCCcore-13.3.0.eb

diff --git a/easybuild/easyconfigs/g/giflib/giflib-5.2.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/giflib/giflib-5.2.1-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..66ef70d59ce
--- /dev/null
+++ b/easybuild/easyconfigs/g/giflib/giflib-5.2.1-GCCcore-13.3.0.eb
@@ -0,0 +1,28 @@
+easyblock = 'ConfigureMake'
+
+name = 'giflib'
+version = '5.2.1'
+
+homepage = 'http://giflib.sourceforge.net/'
+description = """giflib is a library for reading and writing gif images.
+It is API and ABI compatible with libungif which was in wide use while
+the LZW compression algorithm was patented."""
+
+source_urls = [SOURCEFORGE_SOURCE]
+sources = [SOURCE_TAR_GZ]
+checksums = ['31da5562f44c5f15d63340a09a4fd62b48c45620cd302f77a6d9acf0077879bd']
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+builddependencies = [('binutils', '2.42')]
+
+skipsteps = ['configure']
+
+installopts = 'PREFIX=%(installdir)s'
+
+sanity_check_paths = {
+    'files': ['bin/giftool'],
+    'dirs': []
+}
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/l/libwebp/libwebp-1.4.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libwebp/libwebp-1.4.0-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..70084689c61
--- /dev/null
+++ b/easybuild/easyconfigs/l/libwebp/libwebp-1.4.0-GCCcore-13.3.0.eb
@@ -0,0 +1,45 @@
+easyblock = 'ConfigureMake'
+
+name = 'libwebp'
+version = '1.4.0'
+
+homepage = 'https://developers.google.com/speed/webp/'
+description = """WebP is a modern image format that provides superior
+lossless and lossy compression for images on the web. Using WebP,
+webmasters and web developers can create smaller, richer images that
+make the web faster."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://storage.googleapis.com/downloads.webmproject.org/releases/webp']
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['61f873ec69e3be1b99535634340d5bde750b2e4447caa1db9f61be3fd49ab1e5']
+
+builddependencies = [
+    ('binutils', '2.42'),
+]
+dependencies = [
+    ('libjpeg-turbo', '3.0.1'),
+    ('libpng', '1.6.43'),
+    ('LibTIFF', '4.6.0'),
+    ('giflib', '5.2.1'),
+]
+
+configopts = '--enable-libwebpmux'
+
+local_headers, local_libs = (
+    ['decode.h', 'demux.h', 'encode.h', 'mux.h', 'mux_types.h', 'types.h'],
+    ['webp', 'webpdemux', 'webpmux']
+)
+
+sanity_check_paths = {
+    'files': (
+        ['include/webp/%s' % h for h in local_headers] +
+        ['lib/lib%s.a' % s for s in local_libs] +
+        ['lib/lib%s.%s' % (s, SHLIB_EXT) for s in local_libs]
+    ),
+    'dirs': ['lib/']
+}
+
+moduleclass = 'lib'

From 7406dc60d0302c4c0af26d249edf07bdb5546af0 Mon Sep 17 00:00:00 2001
From: ankekreuzer <a.kreuzer@fz-juelich.de>
Date: Fri, 30 Aug 2024 14:13:28 +0200
Subject: [PATCH 750/835] Added a moduleclass to byacc

---
 .../easyconfigs/b/byacc/byacc-2.0.20240109-GCCcore-13.3.0.eb    | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/easybuild/easyconfigs/b/byacc/byacc-2.0.20240109-GCCcore-13.3.0.eb b/easybuild/easyconfigs/b/byacc/byacc-2.0.20240109-GCCcore-13.3.0.eb
index 2cade945ccc..292636d12e3 100644
--- a/easybuild/easyconfigs/b/byacc/byacc-2.0.20240109-GCCcore-13.3.0.eb
+++ b/easybuild/easyconfigs/b/byacc/byacc-2.0.20240109-GCCcore-13.3.0.eb
@@ -20,3 +20,5 @@ sanity_check_paths = {
     'files': ["bin/yacc"],
     'dirs': []
 }
+
+moduleclass = 'lang'

From def623c7d60612c2d0f0d31aa27ac4af7e7ac976 Mon Sep 17 00:00:00 2001
From: WilleBell <cintiawillemyns@gmail.com>
Date: Fri, 30 Aug 2024 15:30:33 +0200
Subject: [PATCH 751/835] Add helper_scripts to PATH

---
 .../ProteinMPNN-1.0.1-20230627-foss-2022a-CUDA-11.7.0.eb | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/easybuild/easyconfigs/p/ProteinMPNN/ProteinMPNN-1.0.1-20230627-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/ProteinMPNN/ProteinMPNN-1.0.1-20230627-foss-2022a-CUDA-11.7.0.eb
index 258c21fef24..db7151ab47f 100644
--- a/easybuild/easyconfigs/p/ProteinMPNN/ProteinMPNN-1.0.1-20230627-foss-2022a-CUDA-11.7.0.eb
+++ b/easybuild/easyconfigs/p/ProteinMPNN/ProteinMPNN-1.0.1-20230627-foss-2022a-CUDA-11.7.0.eb
@@ -27,17 +27,20 @@ dependencies = [
     ('torchaudio', '0.12.0', '-PyTorch-1.12.0' + versionsuffix),
 ]
 
-postinstallcmds = ['chmod a+x %(installdir)s/protein_mpnn_run.py']
+postinstallcmds = [
+    'chmod a+x %(installdir)s/protein_mpnn_run.py',
+    'chmod a+x %(installdir)s/helper_scripts/*.py'
+]
 
 sanity_check_paths = {
     'files': ['protein_mpnn_run.py'],
     'dirs': ['examples'],
 }
 
-fix_python_shebang_for = ['protein_mpnn_run.py']
+fix_python_shebang_for = ['protein_mpnn_run.py', 'helper_scripts/*.py']
 
 sanity_check_commands = ['protein_mpnn_run.py --help']
 
-modextrapaths = {'PATH': ''}
+modextrapaths = {'PATH': ['', 'helper_scripts']}
 
 moduleclass = 'bio'

From 093cbbf29b3cc1a9c458e85477c30f36a8e44295 Mon Sep 17 00:00:00 2001
From: Sam Moors <smoors@users.noreply.github.com>
Date: Fri, 30 Aug 2024 19:42:08 +0200
Subject: [PATCH 752/835] use https

---
 .../ConcurrentVersionsSystem-1.11.23-GCCcore-13.3.0.eb          | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/c/ConcurrentVersionsSystem/ConcurrentVersionsSystem-1.11.23-GCCcore-13.3.0.eb b/easybuild/easyconfigs/c/ConcurrentVersionsSystem/ConcurrentVersionsSystem-1.11.23-GCCcore-13.3.0.eb
index 62826484b73..b43a426454f 100644
--- a/easybuild/easyconfigs/c/ConcurrentVersionsSystem/ConcurrentVersionsSystem-1.11.23-GCCcore-13.3.0.eb
+++ b/easybuild/easyconfigs/c/ConcurrentVersionsSystem/ConcurrentVersionsSystem-1.11.23-GCCcore-13.3.0.eb
@@ -15,7 +15,7 @@ Source Configuration Management (SCM).
 
 toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
 
-source_urls = [' http://ftp.gnu.org/non-gnu/cvs/source/stable/%(version)s/']
+source_urls = [' https://ftp.gnu.org/non-gnu/cvs/source/stable/%(version)s/']
 sources = ['cvs-%(version)s.tar.bz2']
 patches = [
     'CVS-1.11.23-zlib-1.patch',

From a6a5ce548771825825c98218242f39ae3f3a48b5 Mon Sep 17 00:00:00 2001
From: ankekreuzer <a.kreuzer@fz-juelich.de>
Date: Fri, 30 Aug 2024 21:26:16 +0200
Subject: [PATCH 753/835] Added LittleCMS and lxml to the GCCcore-13.3.0
 toolchain.

---
 .../LittleCMS-2.16-GCCcore-13.3.0.eb          | 26 +++++++++++++++++
 .../l/lxml/lxml-5.3.0-GCCcore-13.3.0.eb       | 28 +++++++++++++++++++
 2 files changed, 54 insertions(+)
 create mode 100644 easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.16-GCCcore-13.3.0.eb
 create mode 100644 easybuild/easyconfigs/l/lxml/lxml-5.3.0-GCCcore-13.3.0.eb

diff --git a/easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.16-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.16-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..121d33200a2
--- /dev/null
+++ b/easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.16-GCCcore-13.3.0.eb
@@ -0,0 +1,26 @@
+easyblock = 'ConfigureMake'
+
+name = 'LittleCMS'
+version = '2.16'
+
+homepage = 'https://www.littlecms.com/'
+description = """ Little CMS intends to be an OPEN SOURCE small-footprint color management engine,
+ with special focus on accuracy and performance. """
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+source_urls = ['https://sourceforge.net/projects/lcms/files/lcms/%s/' % '.'.join(version.split('.')[:2])]
+sources = ['lcms2-%(version)s.tar.gz']
+checksums = ['d873d34ad8b9b4cea010631f1a6228d2087475e4dc5e763eb81acc23d9d45a51']
+
+builddependencies = [('binutils', '2.42')]
+
+dependencies = [('libjpeg-turbo', '3.0.1')]
+
+sanity_check_paths = {
+    'files': ['bin/jpgicc', 'bin/linkicc', 'bin/psicc', 'bin/transicc', 'include/lcms2.h', 'include/lcms2_plugin.h',
+              'lib/liblcms2.a', 'lib/liblcms2.%s' % SHLIB_EXT, 'lib/pkgconfig/lcms2.pc'],
+    'dirs': ['share/man'],
+}
+
+moduleclass = 'vis'
diff --git a/easybuild/easyconfigs/l/lxml/lxml-5.3.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/lxml/lxml-5.3.0-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..0af2dcbed3f
--- /dev/null
+++ b/easybuild/easyconfigs/l/lxml/lxml-5.3.0-GCCcore-13.3.0.eb
@@ -0,0 +1,28 @@
+easyblock = 'PythonPackage'
+
+name = 'lxml'
+version = '5.3.0'
+
+homepage = 'https://lxml.de/'
+description = """The lxml XML toolkit is a Pythonic binding for the C libraries libxml2 and libxslt."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+sources = [SOURCE_TAR_GZ]
+checksums = ['4e109ca30d1edec1ac60cdbe341905dc3b8f55b16855e03a54aaf59e51ec8c6f']
+
+builddependencies = [
+    ('binutils', '2.42'),
+]
+
+dependencies = [
+    ('Python', '3.12.3'),
+    ('libxml2', '2.12.7'),
+    ('libxslt', '1.1.42'),
+]
+
+download_dep_fail = True
+use_pip = True
+sanity_pip_check = True
+
+moduleclass = 'lib'

From df5d54ed5ef88595c3fd94b58f5375bb726e30a2 Mon Sep 17 00:00:00 2001
From: ankekreuzer <a.kreuzer@fz-juelich.de>
Date: Sun, 1 Sep 2024 21:49:03 +0200
Subject: [PATCH 754/835] Added LZO and nano to the GCCcore-13.3.0 toolchain

---
 .../l/LZO/LZO-2.10-GCCcore-13.3.0.eb          | 27 +++++++++++++++++++
 .../n/nano/nano-8.1-GCCcore-13.3.0.eb         | 27 +++++++++++++++++++
 2 files changed, 54 insertions(+)
 create mode 100644 easybuild/easyconfigs/l/LZO/LZO-2.10-GCCcore-13.3.0.eb
 create mode 100644 easybuild/easyconfigs/n/nano/nano-8.1-GCCcore-13.3.0.eb

diff --git a/easybuild/easyconfigs/l/LZO/LZO-2.10-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/LZO/LZO-2.10-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..4d8ccd20b1f
--- /dev/null
+++ b/easybuild/easyconfigs/l/LZO/LZO-2.10-GCCcore-13.3.0.eb
@@ -0,0 +1,27 @@
+easyblock = 'ConfigureMake'
+
+name = 'LZO'
+version = '2.10'
+
+homepage = 'https://www.oberhumer.com/opensource/lzo/'
+description = "Portable lossless data compression library"
+
+source_urls = [homepage + 'download/']
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['c0f892943208266f9b6543b3ae308fab6284c5c90e627931446fb49b4221a072']
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+toolchainopts = {'pic': True}
+
+builddependencies = [('binutils', '2.42')]
+
+configopts = '--enable-shared'
+
+runtest = 'test'
+
+sanity_check_paths = {
+    'files': ['lib/liblzo2.a', 'lib/liblzo2.%s' % SHLIB_EXT],
+    'dirs': ['include']
+}
+
+moduleclass = 'devel'
diff --git a/easybuild/easyconfigs/n/nano/nano-8.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/n/nano/nano-8.1-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..64684d1ff42
--- /dev/null
+++ b/easybuild/easyconfigs/n/nano/nano-8.1-GCCcore-13.3.0.eb
@@ -0,0 +1,27 @@
+easyblock = 'ConfigureMake'
+
+name = 'nano'
+version = '8.1'
+
+homepage = 'https://www.nano-editor.org/'
+docurls = 'https://www.nano-editor.org/docs.php'
+description = """a simple editor, inspired by Pico"""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+source_urls = ['https://www.nano-editor.org/dist/v%(version_major)s/']
+sources = [SOURCE_TAR_GZ]
+checksums = ['6508bfbcfe38153ecbdc1b7d3479323564353f134acc8c501910220371390675']
+
+builddependencies = [('binutils', '2.42')]
+
+dependencies = [('ncurses', '6.5')]
+
+sanity_check_paths = {
+    'files': ['bin/nano'],
+    'dirs': ['bin', 'share'],
+}
+
+sanity_check_commands = ['nano --version']
+
+moduleclass = 'tools'

From 4f3ae736b2a301c5751ace7c72b932aff0ba1ed4 Mon Sep 17 00:00:00 2001
From: ankekreuzer <a.kreuzer@fz-juelich.de>
Date: Mon, 2 Sep 2024 08:43:05 +0200
Subject: [PATCH 755/835] Added nettle and nlohmann_json to the GCCcore-13.3.0
 toolchain

---
 .../n/nettle/nettle-3.10-GCCcore-13.3.0.eb    | 38 +++++++++++++++++++
 .../nlohmann_json-3.11.3-GCCcore-13.3.0.eb    | 25 ++++++++++++
 2 files changed, 63 insertions(+)
 create mode 100644 easybuild/easyconfigs/n/nettle/nettle-3.10-GCCcore-13.3.0.eb
 create mode 100644 easybuild/easyconfigs/n/nlohmann_json/nlohmann_json-3.11.3-GCCcore-13.3.0.eb

diff --git a/easybuild/easyconfigs/n/nettle/nettle-3.10-GCCcore-13.3.0.eb b/easybuild/easyconfigs/n/nettle/nettle-3.10-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..ef91cf135fe
--- /dev/null
+++ b/easybuild/easyconfigs/n/nettle/nettle-3.10-GCCcore-13.3.0.eb
@@ -0,0 +1,38 @@
+easyblock = 'ConfigureMake'
+
+name = 'nettle'
+version = '3.10'
+
+homepage = 'https://www.lysator.liu.se/~nisse/nettle/'
+description = """Nettle is a cryptographic library that is designed to fit easily
+ in more or less any context: In crypto toolkits for object-oriented
+ languages (C++, Python, Pike, ...), in applications like LSH or GNUPG,
+ or even in kernel space."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+source_urls = [GNU_SOURCE]
+sources = [SOURCE_TAR_GZ]
+checksums = ['b4c518adb174e484cb4acea54118f02380c7133771e7e9beb98a0787194ee47c']
+
+builddependencies = [
+    ('binutils', '2.42'),
+    ('Autotools', '20231222'),
+]
+
+dependencies = [
+    ('GMP', '6.3.0'),
+]
+
+configopts = '--disable-openssl '  # openssl is just used for the nettle-openssl example and requires openssl 1.1
+
+sanity_check_paths = {
+    'files': ['bin/%s' % x for x in ['nettle-hash', 'nettle-lfib-stream', 'pkcs1-conv', 'sexp-conv']] +
+             [('lib/libhogweed.a', 'lib64/libhogweed.a'),
+              ('lib/libhogweed.%s' % SHLIB_EXT, 'lib64/libhogweed.%s' % SHLIB_EXT),
+              ('lib/libnettle.a', 'lib64/libnettle.a'),
+              ('lib/libnettle.%s' % SHLIB_EXT, 'lib64/libnettle.%s' % SHLIB_EXT)],
+    'dirs': ['include/nettle'],
+}
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/n/nlohmann_json/nlohmann_json-3.11.3-GCCcore-13.3.0.eb b/easybuild/easyconfigs/n/nlohmann_json/nlohmann_json-3.11.3-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..8be75746afa
--- /dev/null
+++ b/easybuild/easyconfigs/n/nlohmann_json/nlohmann_json-3.11.3-GCCcore-13.3.0.eb
@@ -0,0 +1,25 @@
+easyblock = 'CMakeMake'
+
+name = 'nlohmann_json'
+version = '3.11.3'
+
+homepage = 'https://github.com/nlohmann/json'
+description = """JSON for Modern C++"""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+source_urls = ['https://github.com/nlohmann/json/archive/refs/tags/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['0d8ef5af7f9794e3263480193c491549b2ba6cc74bb018906202ada498a79406']
+
+builddependencies = [
+    ('binutils', '2.42'),
+    ('CMake', '3.29.3'),
+]
+
+sanity_check_paths = {
+    'files': ['include/nlohmann/json.hpp'],
+    'dirs': ['share/cmake', 'share/pkgconfig'],
+}
+
+moduleclass = 'lib'

From 14b05c0edb653349e8cdc3aa3384cd7db776e147 Mon Sep 17 00:00:00 2001
From: Chia-Jung Hsu <appolloford@users.noreply.github.com>
Date: Mon, 2 Sep 2024 09:37:56 +0200
Subject: [PATCH 756/835] Fix sanity check

---
 .../bitsandbytes/bitsandbytes-0.43.3-foss-2023a-CUDA-12.1.1.eb  | 2 +-
 .../b/bitsandbytes/bitsandbytes-0.43.3-foss-2023a.eb            | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/easybuild/easyconfigs/b/bitsandbytes/bitsandbytes-0.43.3-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/b/bitsandbytes/bitsandbytes-0.43.3-foss-2023a-CUDA-12.1.1.eb
index 3b89d58cc47..75c19734a23 100644
--- a/easybuild/easyconfigs/b/bitsandbytes/bitsandbytes-0.43.3-foss-2023a-CUDA-12.1.1.eb
+++ b/easybuild/easyconfigs/b/bitsandbytes/bitsandbytes-0.43.3-foss-2023a-CUDA-12.1.1.eb
@@ -34,7 +34,7 @@ postinstallcmds = [
 ]
 
 sanity_check_paths = {
-    'files': ['lib/python3.11/site-packages/bitsandbytes/libbitsandbytes_cuda121.so'],
+    'files': ['lib/python%(pyshortver)s/site-packages/bitsandbytes/libbitsandbytes_cuda121.%s' % SHLIB_EXT],
     'dirs': ['lib/python%(pyshortver)s/site-packages'],
 }
 
diff --git a/easybuild/easyconfigs/b/bitsandbytes/bitsandbytes-0.43.3-foss-2023a.eb b/easybuild/easyconfigs/b/bitsandbytes/bitsandbytes-0.43.3-foss-2023a.eb
index e9f92c025a9..8af9e762a99 100644
--- a/easybuild/easyconfigs/b/bitsandbytes/bitsandbytes-0.43.3-foss-2023a.eb
+++ b/easybuild/easyconfigs/b/bitsandbytes/bitsandbytes-0.43.3-foss-2023a.eb
@@ -31,7 +31,7 @@ postinstallcmds = [
 ]
 
 sanity_check_paths = {
-    'files': ['lib/python3.11/site-packages/bitsandbytes/libbitsandbytes_cuda121.so'],
+    'files': ['lib/python%(pyshortver)s/site-packages/bitsandbytes/libbitsandbytes_cpu.%s' % SHLIB_EXT],
     'dirs': ['lib/python%(pyshortver)s/site-packages'],
 }
 

From 5c1323a3485f8ddb0d9bfe014f6f23c93220f688 Mon Sep 17 00:00:00 2001
From: Chia-Jung Hsu <appolloford@users.noreply.github.com>
Date: Mon, 2 Sep 2024 09:55:42 +0200
Subject: [PATCH 757/835] Fix syntax error

---
 .../bitsandbytes/bitsandbytes-0.43.3-foss-2023a-CUDA-12.1.1.eb  | 2 +-
 .../b/bitsandbytes/bitsandbytes-0.43.3-foss-2023a.eb            | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/easybuild/easyconfigs/b/bitsandbytes/bitsandbytes-0.43.3-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/b/bitsandbytes/bitsandbytes-0.43.3-foss-2023a-CUDA-12.1.1.eb
index 75c19734a23..8127a86c558 100644
--- a/easybuild/easyconfigs/b/bitsandbytes/bitsandbytes-0.43.3-foss-2023a-CUDA-12.1.1.eb
+++ b/easybuild/easyconfigs/b/bitsandbytes/bitsandbytes-0.43.3-foss-2023a-CUDA-12.1.1.eb
@@ -34,7 +34,7 @@ postinstallcmds = [
 ]
 
 sanity_check_paths = {
-    'files': ['lib/python%(pyshortver)s/site-packages/bitsandbytes/libbitsandbytes_cuda121.%s' % SHLIB_EXT],
+    'files': ['lib/python%%(pyshortver)s/site-packages/bitsandbytes/libbitsandbytes_cuda121.%s' % SHLIB_EXT],
     'dirs': ['lib/python%(pyshortver)s/site-packages'],
 }
 
diff --git a/easybuild/easyconfigs/b/bitsandbytes/bitsandbytes-0.43.3-foss-2023a.eb b/easybuild/easyconfigs/b/bitsandbytes/bitsandbytes-0.43.3-foss-2023a.eb
index 8af9e762a99..8b360bb263b 100644
--- a/easybuild/easyconfigs/b/bitsandbytes/bitsandbytes-0.43.3-foss-2023a.eb
+++ b/easybuild/easyconfigs/b/bitsandbytes/bitsandbytes-0.43.3-foss-2023a.eb
@@ -31,7 +31,7 @@ postinstallcmds = [
 ]
 
 sanity_check_paths = {
-    'files': ['lib/python%(pyshortver)s/site-packages/bitsandbytes/libbitsandbytes_cpu.%s' % SHLIB_EXT],
+    'files': ['lib/python%%(pyshortver)s/site-packages/bitsandbytes/libbitsandbytes_cpu.%s' % SHLIB_EXT],
     'dirs': ['lib/python%(pyshortver)s/site-packages'],
 }
 

From 808838029beb718c92875d4011df85e8c83d9b7c Mon Sep 17 00:00:00 2001
From: ankekreuzer <a.kreuzer@fz-juelich.de>
Date: Mon, 2 Sep 2024 10:51:45 +0200
Subject: [PATCH 758/835] Added Tk and Tkinter to the GCCcore-13.3.0 toolchain
 (both dependencies of matplotlib)

---
 .../t/Tk/Tk-8.6.14-GCCcore-13.3.0.eb          | 36 +++++++++++++++++++
 .../Tkinter/Tkinter-3.12.3-GCCcore-13.3.0.eb  | 25 +++++++++++++
 2 files changed, 61 insertions(+)
 create mode 100644 easybuild/easyconfigs/t/Tk/Tk-8.6.14-GCCcore-13.3.0.eb
 create mode 100644 easybuild/easyconfigs/t/Tkinter/Tkinter-3.12.3-GCCcore-13.3.0.eb

diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.14-GCCcore-13.3.0.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.14-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..4069dc5a048
--- /dev/null
+++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.14-GCCcore-13.3.0.eb
@@ -0,0 +1,36 @@
+easyblock = 'ConfigureMake'
+
+name = 'Tk'
+version = '8.6.14'
+
+homepage = 'https://www.tcl.tk/'
+description = """Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for
+ building a graphical user interface (GUI) in many different programming languages."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+source_urls = ["https://prdownloads.sourceforge.net/tcl"]
+sources = ['%(namelower)s%(version)s-src.tar.gz']
+checksums = ['8ffdb720f47a6ca6107eac2dd877e30b0ef7fac14f3a84ebbd0b3612cee41a94']
+
+builddependencies = [('binutils', '2.42')]
+dependencies = [
+    ('Tcl', version),
+    ('X11', '20240607'),
+    ('zlib', '1.3.1'),
+]
+
+configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib CFLAGS="-I$EBROOTTCL/include"'
+
+installopts = "&& make install-private-headers"
+
+postinstallcmds = ["ln -s wish%(version_major_minor)s %(installdir)s/bin/wish"]
+
+sanity_check_paths = {
+    'files': ["bin/wish", "lib/tkConfig.sh", "include/tkInt.h"],
+    'dirs': [],
+}
+
+start_dir = 'unix'
+
+moduleclass = 'vis'
diff --git a/easybuild/easyconfigs/t/Tkinter/Tkinter-3.12.3-GCCcore-13.3.0.eb b/easybuild/easyconfigs/t/Tkinter/Tkinter-3.12.3-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..00f02ee6424
--- /dev/null
+++ b/easybuild/easyconfigs/t/Tkinter/Tkinter-3.12.3-GCCcore-13.3.0.eb
@@ -0,0 +1,25 @@
+name = 'Tkinter'
+version = '3.12.3'
+
+homepage = 'https://python.org/'
+description = "Tkinter module, built with the Python buildsystem"
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://www.python.org/ftp/python/%(version)s/']
+sources = ['Python-%(version)s.tgz']
+checksums = ['a6b9459f45a6ebbbc1af44f5762623fa355a0c87208ed417628b379d762dddb0']
+
+builddependencies = [
+    ('binutils', '2.42'),
+    ('libffi', '3.4.5'),
+]
+
+dependencies = [
+    ('Python', '3.12.3'),
+    ('Tk', '8.6.14'),
+    ('zlib', '1.3.1'),
+]
+
+moduleclass = 'lang'

From 62ad0eb9a52dd2dc8fca134815c8dbeea50a8249 Mon Sep 17 00:00:00 2001
From: ankekreuzer <a.kreuzer@fz-juelich.de>
Date: Mon, 2 Sep 2024 15:22:15 +0200
Subject: [PATCH 759/835] Added OpenJPEG and Pillow-SIMD (both needed fo
 matplotlib) to the GCCcore-13.3.0 toolchain.

---
 .../OpenJPEG/OpenJPEG-2.5.2-GCCcore-13.3.0.eb | 42 ++++++++++++++++
 .../Pillow-SIMD-10.4.0-GCCcore-13.3.0.eb      | 48 +++++++++++++++++++
 2 files changed, 90 insertions(+)
 create mode 100644 easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.5.2-GCCcore-13.3.0.eb
 create mode 100644 easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-10.4.0-GCCcore-13.3.0.eb

diff --git a/easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.5.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.5.2-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..8ee5d1477f8
--- /dev/null
+++ b/easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.5.2-GCCcore-13.3.0.eb
@@ -0,0 +1,42 @@
+easyblock = 'CMakeMake'
+
+name = 'OpenJPEG'
+version = '2.5.2'
+
+homepage = 'https://www.openjpeg.org/'
+description = """OpenJPEG is an open-source JPEG 2000 codec written in
+ C language. It has been developed in order to promote the use of JPEG 2000,
+ a still-image compression standard from the Joint Photographic Experts Group
+ (JPEG). Since may 2015, it is officially recognized by ISO/IEC and ITU-T as
+ a JPEG 2000 Reference Software."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://github.com/uclouvain/%(namelower)s/archive']
+sources = ['v%(version)s.tar.gz']
+checksums = ['90e3896fed910c376aaf79cdd98bdfdaf98c6472efd8e1debf0a854938cbda6a']
+
+builddependencies = [
+    ('binutils', '2.42'),
+    ('CMake', '3.29.3'),
+]
+# for running the binary of openjpeg like opj_compress you need the libraries like zlib etc.
+dependencies = [
+    ('zlib', '1.3.1'),
+    ('libpng', '1.6.43'),
+    ('LibTIFF', '4.6.0'),
+]
+
+sanity_check_paths = {
+    'files': [
+        'bin/opj_compress',
+        'bin/opj_decompress',
+        'bin/opj_dump',
+        'include/openjpeg-%(version_major)s.%(version_minor)s/openjpeg.h',
+        'lib/libopenjp2.%s' % SHLIB_EXT
+    ],
+    'dirs': ['bin', 'include', 'lib'],
+}
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-10.4.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-10.4.0-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..e752171a582
--- /dev/null
+++ b/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-10.4.0-GCCcore-13.3.0.eb
@@ -0,0 +1,48 @@
+easyblock = 'PythonPackage'
+
+name = 'Pillow-SIMD'
+version = '10.4.0'
+
+homepage = 'https://github.com/uploadcare/pillow-simd'
+description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributors.
+ PIL is the Python Imaging Library by Fredrik Lundh and Contributors."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+source_urls = ['https://github.com/uploadcare/pillow-simd/archive/']
+sources = ['%(version)s.tar.gz']
+checksums = ['8c7c3c0fc2952ff11b9a8c60365e098ee5334427dd5688c3584e77c25a7e1b3f']
+
+builddependencies = [('binutils', '2.42')]
+
+dependencies = [
+    ('Python', '3.12.3'),
+    ('libjpeg-turbo', '3.0.1'),
+    ('libpng', '1.6.43'),
+    ('zlib', '1.3.1'),
+    ('LibTIFF', '4.6.0'),
+    ('freetype', '2.13.2'),
+    ('libwebp', '1.4.0'),
+    ('OpenJPEG', '2.5.2'),
+    ('LittleCMS', '2.16'),
+]
+
+use_pip = True
+download_dep_fail = True
+
+# patch setup.py to prefix hardcoded /usr/* and /lib paths with value of %(sysroot) template
+# (which will be empty if EasyBuild is not configured to use an alternate sysroot);
+# see also https://gitlab.com/eessi/support/-/issues/9
+preinstallopts = """sed -i 's@"/usr/@"%(sysroot)s/usr/@g' setup.py && """
+preinstallopts += """sed -i 's@"/lib@"%(sysroot)s/lib@g' setup.py && """
+
+options = {'modulename': 'PIL'}
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['lib/python%(pyshortver)s/site-packages/PIL'],
+}
+
+sanity_pip_check = True
+
+moduleclass = 'vis'

From 5b9dc18218e959e027cead8183bc7fbdc1fb9d81 Mon Sep 17 00:00:00 2001
From: Ake Sandgren <ake.sandgren@hpc2n.umu.se>
Date: Mon, 2 Sep 2024 19:22:09 +0200
Subject: [PATCH 760/835] update dorado to properly use openssl from EB and not
 install external EB libraries into its own lib directory.

---
 .../dorado-0.7.3-foss-2023a-CUDA-12.1.1.eb    | 25 ++++++---
 ....7.3_dont_install_external_libraries.patch | 54 +++++++++++++++++++
 2 files changed, 71 insertions(+), 8 deletions(-)
 create mode 100644 easybuild/easyconfigs/d/dorado/dorado-0.7.3_dont_install_external_libraries.patch

diff --git a/easybuild/easyconfigs/d/dorado/dorado-0.7.3-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/d/dorado/dorado-0.7.3-foss-2023a-CUDA-12.1.1.eb
index 7aa8f29b002..0e32e9616ca 100644
--- a/easybuild/easyconfigs/d/dorado/dorado-0.7.3-foss-2023a-CUDA-12.1.1.eb
+++ b/easybuild/easyconfigs/d/dorado/dorado-0.7.3-foss-2023a-CUDA-12.1.1.eb
@@ -20,10 +20,15 @@ sources = [{
     },
     'filename': SOURCE_TAR_GZ,
 }]
-patches = ['dorado-0.7.3_include-fstream.patch']
+patches = [
+    '%(name)s-%(version)s_include-fstream.patch',
+    '%(name)s-%(version)s_dont_install_external_libraries.patch',
+]
+
 checksums = [
     None,
     'a32cbd34185bcc5ae3d552a072e396825aa7184187cd11c70a4380618387a530',
+    '2a250d606c0ae17f47d99981309fa204a1394ddd81851a1d530dcd0aea2306ac',
 ]
 
 builddependencies = [
@@ -45,7 +50,6 @@ dependencies = [
 # don't link to OpenSSL static libraries
 # fix for CMake Error "missing: OPENSSL_CRYPTO_LIBRARY" (if only shared OpenSSL libraries are available)
 preconfigopts = "sed -i '/OPENSSL_USE_STATIC_LIBS TRUE/d' ../dorado/cmake/OpenSSL.cmake && "
-preconfigopts += "export OPENSSL_ROOT_DIR=$EBROOTOPENSSL && "
 # link in the ssl and crypto libs, to fix:
 # undefined reference to symbol 'SSL_get_peer_certificate@@OPENSSL_1_1_0'
 preconfigopts += "sed -i 's/OpenSSL::SSL/ssl\\n    crypto/g' ../dorado/dorado/utils/CMakeLists.txt && "
@@ -63,12 +67,17 @@ preconfigopts += "sed -i 's/htslib/hts/g' ../dorado/dorado/utils/CMakeLists.txt
 # cfr. https://github.com/nanoporetech/dorado/issues/779
 preconfigopts += "sed -i 's/-Werror//g' ../dorado/cmake/Warnings.cmake && "
 
-configopts = "-DDORADO_INSTALL_PATH=%(installdir)s "
-configopts += "-DCUDA_TOOLKIT_ROOT_DIR=$EBROOTCUDA -DCMAKE_CUDA_COMPILER=$EBROOTCUDA/bin/nvcc "
-configopts += "-DDORADO_LIBTORCH_DIR=$EBROOTPYTORCH/lib "
-# add -pthread flag (in addition to -lpthread) to avoid linking error:
-# in function `_GLOBAL__sub_I_mutex.cc': mutex.cc:(.text.startup+0x17): undefined reference to `pthread_atfork'
-configopts += '-DCMAKE_C_FLAGS="$CFLAGS -pthread" '
+_copts = [
+    "-DCUDA_TOOLKIT_ROOT_DIR=$EBROOTCUDA",
+    "-DCMAKE_CUDA_COMPILER=$EBROOTCUDA/bin/nvcc",
+    '-DOPENSSL_ROOT_DIR=$EBROOTOPENSSL',
+    "-DDORADO_LIBTORCH_DIR=$EBROOTPYTORCH/lib",
+    # add -pthread flag (in addition to -lpthread) to avoid linking error:
+    # in function `_GLOBAL__sub_I_mutex.cc': mutex.cc:(.text.startup+0x17): undefined reference to `pthread_atfork'
+    '-DCMAKE_C_FLAGS="$CFLAGS -pthread"',
+]
+
+configopts = ' '.join(_copts)
 
 sanity_check_paths = {
     'files': ['bin/dorado'],
diff --git a/easybuild/easyconfigs/d/dorado/dorado-0.7.3_dont_install_external_libraries.patch b/easybuild/easyconfigs/d/dorado/dorado-0.7.3_dont_install_external_libraries.patch
new file mode 100644
index 00000000000..67bd9efee78
--- /dev/null
+++ b/easybuild/easyconfigs/d/dorado/dorado-0.7.3_dont_install_external_libraries.patch
@@ -0,0 +1,54 @@
+Don't install external libraries in Dorado's lib directory.
+
+Åke Sandgren, 2024-09-02
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index a84c7524..0791dda8 100755
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -431,7 +431,7 @@ if(CMAKE_SYSTEM_NAME STREQUAL "Linux")
+         else()
+             # bundle the libraries from the cuda toolkit
+             file(GLOB NATIVE_CUDA_LIBS "${CUDAToolkit_TARGET_DIR}/targets/${CMAKE_SYSTEM_PROCESSOR}-linux/lib/${LIB}")
+-            install(FILES ${NATIVE_CUDA_LIBS} DESTINATION lib COMPONENT redist_libs)
++            #install(FILES ${NATIVE_CUDA_LIBS} DESTINATION lib COMPONENT redist_libs)
+         endif()
+     endforeach()
+ 
+@@ -444,14 +444,14 @@ if(CMAKE_SYSTEM_NAME STREQUAL "Linux")
+         RESOLVE_SYMLINKS("${DEBUG_LIBRARIES}" NEW_HDF_DEBUG_LIBRARIES)
+         foreach(HDF_LIB IN LISTS NEW_HDF_DEBUG_LIBRARIES)
+ 	    if(${HDF_LIB} MATCHES "hdf5")
+-                install(FILES ${HDF_LIB} DESTINATION lib COMPONENT redist_libs CONFIGURATIONS Debug)
++                #install(FILES ${HDF_LIB} DESTINATION lib COMPONENT redist_libs CONFIGURATIONS Debug)
+             endif()
+         endforeach()
+         FILTER_LIST("${HDF5_C_LIBRARIES}" RELEASE_LIBRARIES optimized debug ${SHARED_LIB_EXT})
+         RESOLVE_SYMLINKS("${RELEASE_LIBRARIES}" NEW_HDF_RELEASE_LIBRARIES)
+         foreach(HDF_LIB IN LISTS NEW_HDF_RELEASE_LIBRARIES)
+ 	    if(${HDF_LIB} MATCHES "hdf5")
+-                install(FILES ${HDF_LIB} DESTINATION lib COMPONENT redist_libs CONFIGURATIONS Release ReleaseWithDebInfo)
++                #install(FILES ${HDF_LIB} DESTINATION lib COMPONENT redist_libs CONFIGURATIONS Release ReleaseWithDebInfo)
+             endif()
+         endforeach()
+     endif()
+@@ -459,17 +459,17 @@ if(CMAKE_SYSTEM_NAME STREQUAL "Linux")
+     find_library(SZ_DLL sz REQUIRED)
+     get_filename_component(SZ_DLL_PATH ${SZ_DLL} DIRECTORY)
+     file(GLOB SZ_DLLS "${SZ_DLL_PATH}/libsz.so*")
+-    install(FILES ${SZ_DLLS} DESTINATION lib COMPONENT redist_libs)
++    #install(FILES ${SZ_DLLS} DESTINATION lib COMPONENT redist_libs)
+ 
+     find_library(AEC_DLL aec REQUIRED)
+     get_filename_component(AEC_DLL_PATH ${AEC_DLL} DIRECTORY)
+     file(GLOB AEC_DLLS "${AEC_DLL_PATH}/libaec.so*")
+-    install(FILES ${AEC_DLLS} DESTINATION lib COMPONENT redist_libs)
++    #install(FILES ${AEC_DLLS} DESTINATION lib COMPONENT redist_libs)
+ 
+     # If zstd has been dynamically linked, add the .so to the package
+     get_filename_component(ZSTD_LIBRARY_PATH ${ZSTD_LIBRARY_RELEASE} DIRECTORY)
+     file(GLOB ZSTD_DLLS "${ZSTD_LIBRARY_PATH}/*zstd.so*")
+-    install(FILES ${ZSTD_DLLS} DESTINATION lib COMPONENT redist_libs)
++    #install(FILES ${ZSTD_DLLS} DESTINATION lib COMPONENT redist_libs)
+ 
+ elseif(WIN32)
+     file(GLOB TORCH_DLLS "${TORCH_LIB}/lib/*.dll")

From 0a076aabd34a390bedfdd0c20e4b0759c6f877cb Mon Sep 17 00:00:00 2001
From: ankekreuzer <a.kreuzer@fz-juelich.de>
Date: Mon, 2 Sep 2024 21:48:30 +0200
Subject: [PATCH 761/835] Added Qhull to the GCCcore-13.3.0 toolchain (needed
 for matplotlib)

---
 .../q/Qhull/Qhull-2020.2-GCCcore-13.3.0.eb    | 40 +++++++++++++++++++
 1 file changed, 40 insertions(+)
 create mode 100644 easybuild/easyconfigs/q/Qhull/Qhull-2020.2-GCCcore-13.3.0.eb

diff --git a/easybuild/easyconfigs/q/Qhull/Qhull-2020.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/q/Qhull/Qhull-2020.2-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..400fecee609
--- /dev/null
+++ b/easybuild/easyconfigs/q/Qhull/Qhull-2020.2-GCCcore-13.3.0.eb
@@ -0,0 +1,40 @@
+easyblock = 'CMakeMake'
+
+name = 'Qhull'
+version = '2020.2'
+
+homepage = 'http://www.qhull.org'
+
+description = """
+ Qhull computes the convex hull, Delaunay triangulation, Voronoi diagram,
+ halfspace intersection about a point, furthest-site Delaunay triangulation,
+ and furthest-site Voronoi diagram. The source code runs in 2-d, 3-d, 4-d, and
+ higher dimensions. Qhull implements the Quickhull algorithm for computing the
+ convex hull.
+"""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+toolchainopts = {'pic': True}
+
+source_urls = ['http://www.qhull.org/download/']
+sources = ['%(namelower)s-%(version_major)s-src-8.0.2.tgz']
+checksums = ['b5c2d7eb833278881b952c8a52d20179eab87766b00b865000469a45c1838b7e']
+
+builddependencies = [
+    ('binutils', '2.42'),
+    ('CMake', '3.29.3'),
+]
+
+sanity_check_paths = {
+    'files': ['bin/qhull', 'lib/libqhull_r.%s' % SHLIB_EXT,
+              'lib/pkgconfig/qhull_r.pc'],
+    'dirs': [],
+}
+
+modextrapaths = {
+    'CPATH': ['qhull/include'],
+}
+
+parallel = 1
+
+moduleclass = 'math'

From 37983df04886a9ff9710dc5cb4d7e6a5f83edfee Mon Sep 17 00:00:00 2001
From: ankekreuzer <a.kreuzer@fz-juelich.de>
Date: Mon, 2 Sep 2024 21:49:52 +0200
Subject: [PATCH 762/835] Added matplotlib to te gfbf 2024a toolchain (plus new
 patch)

---
 ...ib-3.9.2-contourpy-fix-pybind-module.patch | 11 +++
 .../matplotlib/matplotlib-3.9.2-gfbf-2024a.eb | 79 +++++++++++++++++++
 2 files changed, 90 insertions(+)
 create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-3.9.2-contourpy-fix-pybind-module.patch
 create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-3.9.2-gfbf-2024a.eb

diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.9.2-contourpy-fix-pybind-module.patch b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.9.2-contourpy-fix-pybind-module.patch
new file mode 100644
index 00000000000..7a4ae1fdcc1
--- /dev/null
+++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.9.2-contourpy-fix-pybind-module.patch
@@ -0,0 +1,11 @@
+--- src/wrap.cpp.orig	2024-09-02 21:07:13.893013182 +0200
++++ src/wrap.cpp	2024-09-02 21:07:39.973005828 +0200
+@@ -18,7 +18,7 @@
+ static contourpy::LineType mpl20xx_line_type = contourpy::LineType::SeparateCode;
+ static contourpy::FillType mpl20xx_fill_type = contourpy::FillType::OuterCode;
+ 
+-PYBIND11_MODULE(_contourpy, m, py::mod_gil_not_used()) {
++PYBIND11_MODULE(_contourpy, m) {
+     m.doc() =
+         "C++11 extension module wrapped using `pybind11`_.\n\n"
+         "It should not be necessary to access classes and functions in this extension module "
diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.9.2-gfbf-2024a.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.9.2-gfbf-2024a.eb
new file mode 100644
index 00000000000..9d460a5f1fc
--- /dev/null
+++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.9.2-gfbf-2024a.eb
@@ -0,0 +1,79 @@
+easyblock = 'PythonBundle'
+
+name = 'matplotlib'
+version = '3.9.2'
+
+homepage = 'https://matplotlib.org'
+description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of
+ hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python
+ and ipython shell, web application servers, and six graphical user interface toolkits."""
+
+toolchain = {'name': 'gfbf', 'version': '2024a'}
+
+builddependencies = [
+    ('pkgconf', '2.2.0'),
+    ('cppy', '1.2.1'),
+    ('meson-python', '0.16.0'),
+]
+
+dependencies = [
+    ('Python', '3.12.3'),
+    ('SciPy-bundle', '2024.05'),
+    ('libpng', '1.6.43'),
+    ('freetype', '2.13.2'),
+    ('Tkinter', '%(pyver)s'),
+    ('Pillow-SIMD', '10.4.0'),
+    ('Qhull', '2020.2'),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+_include_path = "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && "
+
+local_configopts = "--config-settings=setup-args='-Dsystem-qhull=true' && "
+local_configopts += " --config-settings=setup-args='-Dsystem-freetype=true' && "
+local_configopts += "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && "
+
+exts_list = [
+    ('fonttools', '4.53.1', {
+        'modulename': 'fontTools',
+        'source_tmpl': '%(name)s-%(version)s.tar.gz',
+        'checksums': ['e128778a8e9bc11159ce5447f76766cefbd876f44bd79aff030287254e4752c4'],
+    }),
+    ('Cycler', '0.12.1', {
+        'modulename': 'cycler',
+        'source_tmpl': 'cycler-%(version)s.tar.gz',
+        'checksums': ['88bb128f02ba341da8ef447245a9e138fae777f6a23943da4540077d3601eb1c'],
+    }),
+    ('kiwisolver', '1.4.5', {
+        'patches': ['kiwisolver-1.4.4-fix_version.patch'],
+        'checksums': [
+            {'kiwisolver-1.4.5.tar.gz': 'e57e563a57fb22a142da34f38acc2fc1a5c864bc29ca1517a88abc963e60d6ec'},
+            {'kiwisolver-1.4.4-fix_version.patch': '6753afbb3a88856493fcfa0b33989f35742f57bfd41ff3b7f71a98797e1bfbd0'},
+        ],
+    }),
+    ('contourpy', '1.3.0', {
+        'patches': ['matplotlib-3.9.2-contourpy-fix-pybind-module.patch'],
+        'checksums': [
+            {'contourpy-1.3.0.tar.gz': '7ffa0db17717a8ffb127efd0c95a4362d996b892c2904db72428d5b52e1938a4'},
+            {'matplotlib-3.9.2-contourpy-fix-pybind-module.patch':
+             '1653ea31e98db37734e70552224290277b55ec3aa903aa06884c3579c3da242d'},
+        ],
+    }),
+    (name, version, {
+        'configopts': "--config-settings=setup-args='-Dsystem-qhull=true' && --config-settings=setup-args='-Dsystem-freetype=true' && export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ",
+        'checksums': ['96ab43906269ca64a6366934106fa01534454a69e471b7bf3d79083981aaab92'],
+    }),
+]
+
+sanity_check_commands = [
+    """python -c 'import matplotlib; matplotlib.use("Agg"); import matplotlib.pyplot' """,
+    "python -c 'from mpl_toolkits.mplot3d import Axes3D'",
+]
+
+# use non-interactive plotting backend as default
+# see https://matplotlib.org/tutorials/introductory/usage.html#what-is-a-backend
+modextravars = {'MPLBACKEND': 'Agg'}
+
+moduleclass = 'vis'

From 8c87ac1a94615359858bec4027577a23adebe207 Mon Sep 17 00:00:00 2001
From: ankekreuzer <a.kreuzer@fz-juelich.de>
Date: Tue, 3 Sep 2024 09:58:42 +0200
Subject: [PATCH 763/835] Style corrections for the patch and the
 easyconfigfile

---
 .../matplotlib-3.9.2-contourpy-fix-pybind-module.patch       | 3 +++
 .../easyconfigs/m/matplotlib/matplotlib-3.9.2-gfbf-2024a.eb  | 5 +++--
 2 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.9.2-contourpy-fix-pybind-module.patch b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.9.2-contourpy-fix-pybind-module.patch
index 7a4ae1fdcc1..9a34eb1cdae 100644
--- a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.9.2-contourpy-fix-pybind-module.patch
+++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.9.2-contourpy-fix-pybind-module.patch
@@ -1,3 +1,6 @@
+Fixes: error: macro "PYBIND11_MODULE" passed 3 arguments, but takes just 2
+Author: Anke Kreuzer (JSC)
+diff -ruN src/wrap.cpp.orig src/wrap.cpp
 --- src/wrap.cpp.orig	2024-09-02 21:07:13.893013182 +0200
 +++ src/wrap.cpp	2024-09-02 21:07:39.973005828 +0200
 @@ -18,7 +18,7 @@
diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.9.2-gfbf-2024a.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.9.2-gfbf-2024a.eb
index 9d460a5f1fc..8e67572cb1a 100644
--- a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.9.2-gfbf-2024a.eb
+++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.9.2-gfbf-2024a.eb
@@ -58,11 +58,12 @@ exts_list = [
         'checksums': [
             {'contourpy-1.3.0.tar.gz': '7ffa0db17717a8ffb127efd0c95a4362d996b892c2904db72428d5b52e1938a4'},
             {'matplotlib-3.9.2-contourpy-fix-pybind-module.patch':
-             '1653ea31e98db37734e70552224290277b55ec3aa903aa06884c3579c3da242d'},
+             'a998438a1048524a550bf3bb607197658b13dce56e8e54169e24ce7c3c022a8f'},
         ],
     }),
     (name, version, {
-        'configopts': "--config-settings=setup-args='-Dsystem-qhull=true' && --config-settings=setup-args='-Dsystem-freetype=true' && export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ",
+        #'configopts': "--config-settings=setup-args='-Dsystem-qhull=true' && --config-settings=setup-args='-Dsystem-freetype=true' && export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ",
+        'configopts': "%(local_configopts)s",
         'checksums': ['96ab43906269ca64a6366934106fa01534454a69e471b7bf3d79083981aaab92'],
     }),
 ]

From 508f5a5c12f0ab6a17cab40a4b3bae208f77c201 Mon Sep 17 00:00:00 2001
From: ankekreuzer <a.kreuzer@fz-juelich.de>
Date: Tue, 3 Sep 2024 10:08:39 +0200
Subject: [PATCH 764/835] Deleted unnecessary line

---
 .../easyconfigs/m/matplotlib/matplotlib-3.9.2-gfbf-2024a.eb      | 1 -
 1 file changed, 1 deletion(-)

diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.9.2-gfbf-2024a.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.9.2-gfbf-2024a.eb
index 8e67572cb1a..33ddf00eb93 100644
--- a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.9.2-gfbf-2024a.eb
+++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.9.2-gfbf-2024a.eb
@@ -62,7 +62,6 @@ exts_list = [
         ],
     }),
     (name, version, {
-        #'configopts': "--config-settings=setup-args='-Dsystem-qhull=true' && --config-settings=setup-args='-Dsystem-freetype=true' && export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ",
         'configopts': "%(local_configopts)s",
         'checksums': ['96ab43906269ca64a6366934106fa01534454a69e471b7bf3d79083981aaab92'],
     }),

From 93531deb55017a5362382d3cee6fff7b916f249e Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <33718780+casparvl@users.noreply.github.com>
Date: Tue, 3 Sep 2024 10:23:16 +0200
Subject: [PATCH 765/835] Update
 easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Fix `libxslt` not found even if it is installed under the name `libsxlt1.1`  on Ubuntu 24.04

Co-authored-by: Bob Dröge <b.e.droge@rug.nl>
---
 easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb
index fd4a336660e..6a16ff28a3a 100644
--- a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb
+++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb
@@ -13,7 +13,7 @@ allow_system_deps = [('Python', SYS_PYTHON_VERSION)]
 # Required by lxml, which is installed by ReFrame's bootstrap installer
 osdependencies = [
     ('libxml2'),
-    ('libxslt'),
+    ('libxslt', 'libxslt1.1'),
 ]
 
 # Listed as python_requires in https://github.com/reframe-hpc/reframe/blob/v4.6.2/setup.cfg

From 3329d72d1cc905ee204161b9c807afca3ed8daaa Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 3 Sep 2024 10:31:02 +0200
Subject: [PATCH 766/835] {tools}[foss/2023b] Optuna v3.6.1, redis-py v5.0.9

---
 .../o/Optuna/Optuna-3.6.1-foss-2023b.eb       | 50 +++++++++++++++++++
 .../redis-py/redis-py-5.0.9-GCCcore-13.2.0.eb | 38 ++++++++++++++
 2 files changed, 88 insertions(+)
 create mode 100644 easybuild/easyconfigs/o/Optuna/Optuna-3.6.1-foss-2023b.eb
 create mode 100644 easybuild/easyconfigs/r/redis-py/redis-py-5.0.9-GCCcore-13.2.0.eb

diff --git a/easybuild/easyconfigs/o/Optuna/Optuna-3.6.1-foss-2023b.eb b/easybuild/easyconfigs/o/Optuna/Optuna-3.6.1-foss-2023b.eb
new file mode 100644
index 00000000000..35dec40e234
--- /dev/null
+++ b/easybuild/easyconfigs/o/Optuna/Optuna-3.6.1-foss-2023b.eb
@@ -0,0 +1,50 @@
+easyblock = 'PythonBundle'
+
+name = 'Optuna'
+version = '3.6.1'
+
+homepage = "https://optuna.org/"
+description = """Optuna is an automatic hyperparameter optimization software framework,
+particularly designed for machine learning. It features an imperative,
+define-by-run style user API. Thanks to our define-by-run API, the code written
+with Optuna enjoys high modularity, and the user of Optuna can dynamically
+construct the search spaces for the hyperparameters."""
+
+
+toolchain = {'name': 'foss', 'version': '2023b'}
+
+dependencies = [
+    ('Python', '3.11.5'),
+    ('PyYAML', '6.0.1'),
+    ('SciPy-bundle', '2023.11'),
+    ('tqdm', '4.66.2'),
+    ('matplotlib', '3.8.2'),  # optional
+    ('plotly.py', '5.18.0'),  # optional
+    ('redis-py', '5.0.9'),  # optional
+    ('scikit-learn', '1.4.0'),  # optional
+    ('SQLAlchemy', '2.0.29'),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    ('cmaes', '0.11.1', {
+        'checksums': ['cf71fa3679814723be771f2c9edd85f465b1bc1e409e1ad6d8a9e481efcd5160'],
+    }),
+    ('colorlog', '6.8.2', {
+        'checksums': ['3e3e079a41feb5a1b64f978b5ea4f46040a94f11f0e8bbb8261e3dbbeca64d44'],
+    }),
+    ('optuna', version, {
+        'use_pip_extras': 'optional',
+        'checksums': ['146e530b57b4b9afd7526b3e642fbe65491f7e292b405913355f8e438e361ecf'],
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['bin/optuna'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+sanity_check_commands = [('optuna', '--help')]
+
+moduleclass = 'tools'
diff --git a/easybuild/easyconfigs/r/redis-py/redis-py-5.0.9-GCCcore-13.2.0.eb b/easybuild/easyconfigs/r/redis-py/redis-py-5.0.9-GCCcore-13.2.0.eb
new file mode 100644
index 00000000000..39e66108872
--- /dev/null
+++ b/easybuild/easyconfigs/r/redis-py/redis-py-5.0.9-GCCcore-13.2.0.eb
@@ -0,0 +1,38 @@
+easyblock = 'PythonBundle'
+
+name = 'redis-py'
+version = '5.0.9'
+
+homepage = 'https://github.com/redis/redis-py'
+description = "The Python interface to the Redis key-value store."
+
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
+
+builddependencies = [
+    ('binutils', '2.40'),
+]
+
+dependencies = [
+    ('Python', '3.11.5'),
+    ('typing-extensions', '4.10.0'),
+    ('Redis', '7.2.4'),
+]
+
+download_dep_fail = True
+use_pip = True
+
+exts_list = [
+    ('async-timeout', '4.0.3', {
+        'checksums': ['4640d96be84d82d02ed59ea2b7105a0f7b33abe8703703cd0ab0bf87c427522f'],
+    }),
+    (name, version, {
+        'modulename': 'redis',
+        'source_urls': ['https://github.com/redis/redis-py/archive/refs/tags/'],
+        'sources': ['v%(version)s.tar.gz'],
+        'checksums': ['c107fddbaa40414559ddd21f0a78bc7d466cd6b20a800839ac18b9bb54e5c150'],
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = "data"

From ea2583026118819d3345a2ace8125c200fd780c2 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Petr=20Kr=C3=A1l?= <petr@inuits.eu>
Date: Tue, 3 Sep 2024 10:47:12 +0200
Subject: [PATCH 767/835] adding easyconfigs:
 bayesian-optimization-1.5.1-foss-2023a.eb

---
 .../bayesian-optimization-1.5.1-foss-2023a.eb | 34 +++++++++++++++++++
 1 file changed, 34 insertions(+)
 create mode 100644 easybuild/easyconfigs/b/bayesian-optimization/bayesian-optimization-1.5.1-foss-2023a.eb

diff --git a/easybuild/easyconfigs/b/bayesian-optimization/bayesian-optimization-1.5.1-foss-2023a.eb b/easybuild/easyconfigs/b/bayesian-optimization/bayesian-optimization-1.5.1-foss-2023a.eb
new file mode 100644
index 00000000000..8215f2c822a
--- /dev/null
+++ b/easybuild/easyconfigs/b/bayesian-optimization/bayesian-optimization-1.5.1-foss-2023a.eb
@@ -0,0 +1,34 @@
+easyblock = 'PythonBundle'
+
+name = 'bayesian-optimization'
+version = '1.5.1'
+
+homepage = 'https://bayesian-optimization.github.io/BayesianOptimization/index.html'
+description = "Pure Python implementation of bayesian global optimization with gaussian processes."
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('scikit-learn', '1.3.1'),
+    ('SciPy-bundle', '2023.07'),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    ('colorama', '0.4.6', {
+        'source_tmpl': SOURCE_WHL,
+        'checksums': ['4f1d9991f5acc0ca119f9d443620b77f9d6b33703e51011c16baf57afb285fc6'],
+    }),
+    ('bayesian_optimization', version, {
+        'source_tmpl': SOURCE_PY3_WHL,
+        'modulename': 'bayes_opt',
+        'checksums': ['098946c933d6039073b7ccb0c9f1b4c73ac6e39350043b02e5243b08583c4c5c'],
+    }),
+]
+
+sanity_check_commands = ["python -c 'from bayes_opt import BayesianOptimization'"]
+
+moduleclass = 'math'

From 29cf63cf35bcae3d5ae19f150cfaaa13a9eaa51c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Petr=20Kr=C3=A1l?= <petr@inuits.eu>
Date: Tue, 3 Sep 2024 11:12:44 +0200
Subject: [PATCH 768/835] adding easyconfigs: SharedMeatAxe-1.0.1-GCC-13.2.0.eb

---
 .../SharedMeatAxe-1.0.1-GCC-13.2.0.eb         | 39 +++++++++++++++++++
 1 file changed, 39 insertions(+)
 create mode 100644 easybuild/easyconfigs/s/SharedMeatAxe/SharedMeatAxe-1.0.1-GCC-13.2.0.eb

diff --git a/easybuild/easyconfigs/s/SharedMeatAxe/SharedMeatAxe-1.0.1-GCC-13.2.0.eb b/easybuild/easyconfigs/s/SharedMeatAxe/SharedMeatAxe-1.0.1-GCC-13.2.0.eb
new file mode 100644
index 00000000000..bdc088ddea0
--- /dev/null
+++ b/easybuild/easyconfigs/s/SharedMeatAxe/SharedMeatAxe-1.0.1-GCC-13.2.0.eb
@@ -0,0 +1,39 @@
+easyblock = 'ConfigureMake'
+
+name = 'SharedMeatAxe'
+version = '1.0.1'
+
+homepage = 'https://github.com/simon-king-jena/SharedMeatAxe'
+description = """This is an autotoolized shared library version of C MeatAxe 2.4.24,
+ a set of programs for computing with modular representations."""
+
+toolchain = {'name': 'GCC', 'version': '13.2.0'}
+
+source_urls = ['https://github.com/simon-king-jena/SharedMeatAxe/archive/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['e1e802ef60f3280cdacb3de6d693ebd71b43af93e33c739de2697605c59b1a3b']
+
+builddependencies = [
+    ('Autotools', '20220317'),
+]
+
+preconfigopts = 'autoreconf --install && '
+
+runtest = 'check'
+
+local_bins = [
+    'cfcomp', 'genmod', 'mkgraph', 'mkinc', 'orbrep', 'pwkond', 'symnew', 'zad', 'zcl', 'zcv', 'zfr', 'zmo', 'znu',
+    'zpr', 'zro', 'zsp', 'zte', 'zuk', 'chop', 'mkcycl', 'mkhom', 'mksub', 'precond', 'rad', 'tcond', 'zbl', 'zcp',
+    'zef', 'ziv', 'zmu', 'zor', 'zpt', 'zsc', 'zsy', 'ztr', 'zvp', 'decomp', 'mkdotl', 'mkhom_old', 'mktree',
+    'pseudochop', 'soc', 'tuc', 'zcf', 'zct', 'zev', 'zkd', 'zmw', 'zpo', 'zqt', 'zsi', 'ztc', 'zts',
+]
+
+sanity_check_paths = {
+    'files': ['bin/%s' % bin for bin in local_bins] + ['include/meataxe.h', 'lib/libmtx.%s' % SHLIB_EXT],
+    'dirs': []
+}
+
+
+sanity_check_commands = ['mktree --help']
+
+moduleclass = 'math'

From 47f1a682bdd42a661ce29b2c6e31334a0dab835d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Petr=20Kr=C3=A1l?= <petr@inuits.eu>
Date: Tue, 3 Sep 2024 11:13:35 +0200
Subject: [PATCH 769/835] adding easyconfigs: sirocco-2.1.0-GCC-13.2.0.eb

---
 .../s/sirocco/sirocco-2.1.0-GCC-13.2.0.eb     | 34 +++++++++++++++++++
 1 file changed, 34 insertions(+)
 create mode 100644 easybuild/easyconfigs/s/sirocco/sirocco-2.1.0-GCC-13.2.0.eb

diff --git a/easybuild/easyconfigs/s/sirocco/sirocco-2.1.0-GCC-13.2.0.eb b/easybuild/easyconfigs/s/sirocco/sirocco-2.1.0-GCC-13.2.0.eb
new file mode 100644
index 00000000000..3819e493fe2
--- /dev/null
+++ b/easybuild/easyconfigs/s/sirocco/sirocco-2.1.0-GCC-13.2.0.eb
@@ -0,0 +1,34 @@
+easyblock = 'ConfigureMake'
+
+name = 'sirocco'
+version = '2.1.0'
+
+homepage = 'https://github.com/miguelmarco/SIROCCO2/'
+description = """C++ library that allows to compute piecewise linear
+ approximations of the path followed by the root of a complex polynomial"""
+
+toolchain = {'name': 'GCC', 'version': '13.2.0'}
+
+source_urls = ['https://github.com/miguelmarco/SIROCCO2/archive/']
+sources = ['%(version)s.tar.gz']
+checksums = ['1fd66ae94d73095f1355389c1d3d94222437bed87579d77667f50548bdd9fa9a']
+
+builddependencies = [
+    ('Autotools', '20220317'),
+]
+
+dependencies = [
+    ('MPFR', '4.2.1'),
+]
+
+preconfigopts = 'autoreconf --install && '
+
+sanity_check_paths = {
+    'files': [
+        'include/sirocco.h',
+        'lib/libsirocco.%s' % SHLIB_EXT,
+    ],
+    'dirs': []
+}
+
+moduleclass = 'math'

From 8cf988069bdde5d2b4de7ccffc8dc9032239918e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Petr=20Kr=C3=A1l?= <petr@inuits.eu>
Date: Tue, 3 Sep 2024 11:14:33 +0200
Subject: [PATCH 770/835] adding easyconfigs: tdlib-0.9.3-GCC-13.2.0.eb

---
 .../t/tdlib/tdlib-0.9.3-GCC-13.2.0.eb         | 33 +++++++++++++++++++
 1 file changed, 33 insertions(+)
 create mode 100644 easybuild/easyconfigs/t/tdlib/tdlib-0.9.3-GCC-13.2.0.eb

diff --git a/easybuild/easyconfigs/t/tdlib/tdlib-0.9.3-GCC-13.2.0.eb b/easybuild/easyconfigs/t/tdlib/tdlib-0.9.3-GCC-13.2.0.eb
new file mode 100644
index 00000000000..7edf36c5ebb
--- /dev/null
+++ b/easybuild/easyconfigs/t/tdlib/tdlib-0.9.3-GCC-13.2.0.eb
@@ -0,0 +1,33 @@
+easyblock = 'ConfigureMake'
+
+name = 'tdlib'
+version = '0.9.3'
+
+homepage = 'https://github.com/freetdi/tdlib/'
+description = """treedec provides tree decomposition algorithms."""
+
+toolchain = {'name': 'GCC', 'version': '13.2.0'}
+
+source_urls = ['https://github.com/freetdi/tdlib/archive/']
+sources = ['%(version)s.tar.gz']
+checksums = ['d1730c98f41dcb23bbd0bd8de9dbec51df015304f28a38935848925901594ae8']
+
+builddependencies = [
+    ('Autotools', '20220317'),
+    ('Boost', '1.83.0'),
+]
+
+dependencies = [
+    ('Python', '3.11.5'),
+]
+
+preconfigopts = 'autoreconf --install && '
+
+sanity_check_paths = {
+    'files': [
+        'include/treedec/combinations.hpp',
+    ],
+    'dirs': []
+}
+
+moduleclass = 'math'

From a0e732d1c483fa66bd26132d308e6e610ef07616 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Petr=20Kr=C3=A1l?= <petr@inuits.eu>
Date: Tue, 3 Sep 2024 12:23:38 +0200
Subject: [PATCH 771/835] adding easyconfigs: pyseer-1.3.12-foss-2023a.eb

---
 .../p/pyseer/pyseer-1.3.12-foss-2023a.eb      | 56 +++++++++++++++++++
 1 file changed, 56 insertions(+)
 create mode 100644 easybuild/easyconfigs/p/pyseer/pyseer-1.3.12-foss-2023a.eb

diff --git a/easybuild/easyconfigs/p/pyseer/pyseer-1.3.12-foss-2023a.eb b/easybuild/easyconfigs/p/pyseer/pyseer-1.3.12-foss-2023a.eb
new file mode 100644
index 00000000000..16cf7b1a00c
--- /dev/null
+++ b/easybuild/easyconfigs/p/pyseer/pyseer-1.3.12-foss-2023a.eb
@@ -0,0 +1,56 @@
+# Borrowed from the BEAR RSG team, University of Birmingham
+# Update: Petr Král (INUITS)
+easyblock = 'PythonBundle'
+
+name = 'pyseer'
+version = '1.3.12'
+
+homepage = 'https://github.com/mgalardini/pyseer'
+description = """pyseer was first written a python reimplementation of seer, which was written in C++. pyseer uses
+ linear models with fixed or mixed effects to estimate the effect of genetic variation in a bacterial population
+ on a phenotype of interest, while accounting for potentially very strong confounding population structure.
+ This allows for genome-wide association studies (GWAS) to be performed in clonal organisms
+ such as bacteria and viruses."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('pybedtools', '0.9.1'),
+    ('statsmodels', '0.14.1'),
+    ('scikit-learn', '1.3.1'),
+    ('Pysam', '0.22.0'),
+    ('DendroPy', '4.6.1'),
+    ('matplotlib', '3.7.2'),
+    ('tqdm', '4.66.1'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('glmnet-python', '1.0.2', {
+        'source_urls': ['https://github.com/johnlees/glmnet_python/archive'],
+        'sources': ['v%(version)s.tar.gz'],
+        'checksums': ['7a5550514140dabbd27ad4eb1c04db64199d9bb89541e088d9bb162570205e76'],
+    }),
+    (name, version, {
+        'source_urls': ['https://github.com/mgalardini/pyseer/archive'],
+        'sources': ['%(version)s.tar.gz'],
+        'checksums': ['aa07fc1bd5346d02123ff36ba64a1ff4dbbb85a21c37a12f35ad7d5be7e21e9c'],
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['bin/pyseer', 'bin/square_mash'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = [
+    '%(namelower)s --help',
+    'square_mash --help',
+]
+
+sanity_pip_check = True
+
+moduleclass = 'bio'

From e00100af729eb54a6bfe1dc5fbc7e42e773c4773 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 3 Sep 2024 12:57:15 +0200
Subject: [PATCH 772/835] strip out duplicate empty line from SharedMeatAxe
 easyconfig

---
 .../s/SharedMeatAxe/SharedMeatAxe-1.0.1-GCC-13.2.0.eb            | 1 -
 1 file changed, 1 deletion(-)

diff --git a/easybuild/easyconfigs/s/SharedMeatAxe/SharedMeatAxe-1.0.1-GCC-13.2.0.eb b/easybuild/easyconfigs/s/SharedMeatAxe/SharedMeatAxe-1.0.1-GCC-13.2.0.eb
index bdc088ddea0..36923c839cc 100644
--- a/easybuild/easyconfigs/s/SharedMeatAxe/SharedMeatAxe-1.0.1-GCC-13.2.0.eb
+++ b/easybuild/easyconfigs/s/SharedMeatAxe/SharedMeatAxe-1.0.1-GCC-13.2.0.eb
@@ -33,7 +33,6 @@ sanity_check_paths = {
     'dirs': []
 }
 
-
 sanity_check_commands = ['mktree --help']
 
 moduleclass = 'math'

From 31ce7fc97a82a6d1960d684fb0052e7fe5cdb218 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Petr=20Kr=C3=A1l?= <petr@inuits.eu>
Date: Tue, 3 Sep 2024 13:10:03 +0200
Subject: [PATCH 773/835] make Python a build dependency only

---
 easybuild/easyconfigs/t/tdlib/tdlib-0.9.3-GCC-13.2.0.eb | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/easybuild/easyconfigs/t/tdlib/tdlib-0.9.3-GCC-13.2.0.eb b/easybuild/easyconfigs/t/tdlib/tdlib-0.9.3-GCC-13.2.0.eb
index 7edf36c5ebb..63408d65ee7 100644
--- a/easybuild/easyconfigs/t/tdlib/tdlib-0.9.3-GCC-13.2.0.eb
+++ b/easybuild/easyconfigs/t/tdlib/tdlib-0.9.3-GCC-13.2.0.eb
@@ -15,9 +15,6 @@ checksums = ['d1730c98f41dcb23bbd0bd8de9dbec51df015304f28a38935848925901594ae8']
 builddependencies = [
     ('Autotools', '20220317'),
     ('Boost', '1.83.0'),
-]
-
-dependencies = [
     ('Python', '3.11.5'),
 ]
 

From 230fae37daf35b286392aba7b9f0592b516517d1 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparvanl@hotmail.com>
Date: Tue, 3 Sep 2024 13:38:45 +0200
Subject: [PATCH 774/835] Splitting the system toolchain EasyConfig into a
 different PR, since it shows more issues

---
 .../easyconfigs/r/ReFrame/ReFrame-4.6.2.eb    | 87 -------------------
 1 file changed, 87 deletions(-)
 delete mode 100644 easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb

diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb
deleted file mode 100644
index 6a16ff28a3a..00000000000
--- a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb
+++ /dev/null
@@ -1,87 +0,0 @@
-easyblock = 'PythonBundle'
-
-name = 'ReFrame'
-version = '4.6.2'
-
-homepage = 'https://github.com/reframe-hpc/reframe'
-description = '''ReFrame is a framework for writing regression tests for HPC systems.'''
-
-toolchain = SYSTEM
-
-allow_system_deps = [('Python', SYS_PYTHON_VERSION)]
-
-# Required by lxml, which is installed by ReFrame's bootstrap installer
-osdependencies = [
-    ('libxml2'),
-    ('libxslt', 'libxslt1.1'),
-]
-
-# Listed as python_requires in https://github.com/reframe-hpc/reframe/blob/v4.6.2/setup.cfg
-req_py_majver = 3
-req_py_minver = 6
-
-use_pip = True
-
-exts_list = [
-    # stick to pip 21.3.1, which is compatible with Python 3.6
-    # we still need pip outside of ReFrame's external dependencies, since the install cmd uses pip
-    ('pip', '21.3.1', {
-        'use_pip': False,
-        'checksums': ['fd11ba3d0fdb4c07fbc5ecbba0b1b719809420f25038f8ee3cd913d3faa3033a'],
-    }),
-    # Require new enough setuptools to install with e.g. pyproject.toml
-    # 59.6.0 is the latest compatible with Python 3.6
-    ('setuptools', '59.6.0', {
-        'use_pip': False,
-        'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'],
-        'checksums': ['22c7348c6d2976a52632c67f7ab0cdf40147db7789f9aed18734643fe9cf3373'],
-    }),
-    # stick to wheel 0.37.1, which is compatible with Python 3.6
-    ('wheel', '0.37.1', {
-        'source_tmpl': 'wheel-%(version)s-py2.py3-none-any.whl',
-        'checksums': ['4bdcd7d840138086126cd09254dc6195fb4fc6f01c050a1d7236f2630db1d22a'],
-    }),
-    # ReFrame's bootstrap script is intended to run with zero dependencies. It downloads all python deps for ReFrame
-    # into a %(installdir)/external directory. ReFrame's main executable (reframe) adds this dir to python's sys.path
-    # so that ReFrame (and only ReFrame) will find & use all of these dependencies.
-    # In EasyBuild, we should adhere to this installation method because a) it is how ReFrame is meant to be used and
-    # b) it isolates all of ReFrame dependencies from any other python code you run. Thus, there is no chance that
-    # a test will pick up on any python deps from ReFrame itself.
-    # For this to work, we need to disable download_dep_fail and sanity_pip_check, as both are _expected_ to fail
-    # for this setup.
-    ('reframe', version, {
-        # Deps are downloaded to %(installdir)/external, which won't polute the PYTHONPATH, so is ok
-        'download_dep_fail': False,
-        # ReFrame uses its custom sys.path to find necessary packages, they are not on PYTYHONPATH
-        # Thus, the regular pip sanity check is expected to fail, even if ReFrame would run just fine 
-        'sanity_pip_check': False,
-        # Set modulename to False, as to skip the sanity_check-step from extension.py (python -c "import reframe")
-        # This step would fail, since the regular python interpreter wouldn't find the additional packages in
-        # %(installdir)/external. That's fine, as ReFrame should never be imported directly, only through the
-        # reframe command.
-        'modulename': False,
-        'preinstallopts': "export PATH=%(installdir)s/bin:$PATH && "
-                          "./bootstrap.sh +docs +pygelf && cp -r external %(installdir)s && ",
-        'source_tmpl': 'v%(version)s.tar.gz',
-        'source_urls': ['https://github.com/reframe-hpc/reframe/archive/'],
-        'checksums': ['d3343815ee3d2c330b91a1cdb924ba184119ed7d9fc88a4a754b939a4259df82'],
-    }),
-]
-
-postinstallcmds = [
-    "cp -a tools examples %(installdir)s",
-    "mkdir -p %(installdir)s/share && cp -a share/completions %(installdir)s/share/completions",
-    r"sed -i 's@/\(python[0-9.]*\)$@/\1 -S@g' %(installdir)s/bin/reframe",
-]
-
-sanity_check_paths = {
-    'files': ['bin/reframe',
-              'share/completions/reframe.bash',
-              'share/completions/reframe.fish',
-              'share/completions/reframe.tcsh'],
-    'dirs': ['external', 'lib', 'tools', 'examples']
-}
-
-sanity_check_commands = ['reframe -V']
-
-moduleclass = 'devel'

From 423f374762dcdccb8fc0511403466d13e6b623d4 Mon Sep 17 00:00:00 2001
From: Alexander Grund <alexander.grund@tu-dresden.de>
Date: Fri, 30 Aug 2024 16:51:12 +0200
Subject: [PATCH 775/835] Move exts_default_options to top-level parameters
 forPythonBundle ECs

It is easier in the top-level and might cause confusion with https://github.com/easybuilders/easybuild-easyblocks/pull/3428
---
 .../cell2location-0.05-alpha-fosscuda-2020b.eb             | 6 ------
 easybuild/easyconfigs/f/flit/flit-3.9.0-GCCcore-12.3.0.eb  | 7 ++-----
 easybuild/easyconfigs/f/flit/flit-3.9.0-GCCcore-13.2.0.eb  | 7 ++-----
 easybuild/easyconfigs/f/flit/flit-3.9.0-GCCcore-13.3.0.eb  | 7 ++-----
 .../g/GI-DocGen/GI-DocGen-2023.3-GCCcore-12.3.0.eb         | 7 ++-----
 .../OpenStackClient-5.5.0-GCCcore-10.2.0.eb                | 7 +++----
 .../OpenStackClient-5.8.0-GCCcore-11.2.0.eb                | 7 +++----
 .../OpenStackClient-6.0.0-GCCcore-12.2.0.eb                | 7 +++----
 .../p/PyClone/PyClone-2020.9b2-GCCcore-10.2.0.eb           | 7 ++-----
 .../Python-bundle-PyPI-2023.06-GCCcore-12.3.0.eb           | 7 ++-----
 .../Python-bundle-PyPI-2023.10-GCCcore-13.2.0.eb           | 7 ++-----
 .../Python-bundle-PyPI-2024.06-GCCcore-13.3.0.eb           | 7 ++-----
 .../setuptools-rust-1.6.0-GCCcore-12.3.0.eb                | 7 ++-----
 .../setuptools-rust-1.8.0-GCCcore-13.2.0.eb                | 7 ++-----
 .../setuptools-rust-1.9.0-GCCcore-13.3.0.eb                | 7 ++-----
 .../v/virtualenv/virtualenv-20.23.1-GCCcore-12.3.0.eb      | 7 ++-----
 .../v/virtualenv/virtualenv-20.24.6-GCCcore-13.2.0.eb      | 7 ++-----
 .../v/virtualenv/virtualenv-20.26.2-GCCcore-13.3.0.eb      | 7 ++-----
 18 files changed, 37 insertions(+), 88 deletions(-)

diff --git a/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb b/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb
index 9a0eeba1628..1556b0f9dad 100644
--- a/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb
+++ b/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb
@@ -45,12 +45,6 @@ preinstallopts = "sed -i 's/theano/Theano-PyMC/g' setup.py && "
 
 use_pip = True
 
-exts_default_options = {
-    'download_dep_fail': True,
-    'sanity_pip_check': True,
-    'use_pip': True,
-}
-
 exts_list = [
     ('opt-einsum', '3.3.0', {
         'source_tmpl': 'opt_einsum-%(version)s.tar.gz',
diff --git a/easybuild/easyconfigs/f/flit/flit-3.9.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/f/flit/flit-3.9.0-GCCcore-12.3.0.eb
index 15b9ad83d78..a19ba324250 100644
--- a/easybuild/easyconfigs/f/flit/flit-3.9.0-GCCcore-12.3.0.eb
+++ b/easybuild/easyconfigs/f/flit/flit-3.9.0-GCCcore-12.3.0.eb
@@ -17,11 +17,8 @@ dependencies = [
     ('Python', '3.11.3'),
 ]
 
-exts_default_options = {
-    'download_dep_fail': True,
-    'sanity_pip_check': True,
-    'use_pip': True,
-}
+sanity_pip_check = True
+use_pip = True
 
 exts_list = [
     ('idna', '3.4', {
diff --git a/easybuild/easyconfigs/f/flit/flit-3.9.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/f/flit/flit-3.9.0-GCCcore-13.2.0.eb
index 79b1a625e7e..9ef1de6c8b7 100644
--- a/easybuild/easyconfigs/f/flit/flit-3.9.0-GCCcore-13.2.0.eb
+++ b/easybuild/easyconfigs/f/flit/flit-3.9.0-GCCcore-13.2.0.eb
@@ -18,11 +18,8 @@ dependencies = [
     ('Python', '3.11.5'),
 ]
 
-exts_default_options = {
-    'download_dep_fail': True,
-    'sanity_pip_check': True,
-    'use_pip': True,
-}
+sanity_pip_check = True
+use_pip = True
 
 exts_list = [
     ('idna', '3.4', {
diff --git a/easybuild/easyconfigs/f/flit/flit-3.9.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/f/flit/flit-3.9.0-GCCcore-13.3.0.eb
index ddc99b99a37..650b15edaa5 100644
--- a/easybuild/easyconfigs/f/flit/flit-3.9.0-GCCcore-13.3.0.eb
+++ b/easybuild/easyconfigs/f/flit/flit-3.9.0-GCCcore-13.3.0.eb
@@ -18,11 +18,8 @@ dependencies = [
     ('Python', '3.12.3'),
 ]
 
-exts_default_options = {
-    'download_dep_fail': True,
-    'sanity_pip_check': True,
-    'use_pip': True,
-}
+sanity_pip_check = True
+use_pip = True
 
 exts_list = [
     ('idna', '3.7', {
diff --git a/easybuild/easyconfigs/g/GI-DocGen/GI-DocGen-2023.3-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/GI-DocGen/GI-DocGen-2023.3-GCCcore-12.3.0.eb
index d098c3c3cbc..4fae7c08b54 100644
--- a/easybuild/easyconfigs/g/GI-DocGen/GI-DocGen-2023.3-GCCcore-12.3.0.eb
+++ b/easybuild/easyconfigs/g/GI-DocGen/GI-DocGen-2023.3-GCCcore-12.3.0.eb
@@ -21,11 +21,8 @@ dependencies = [
     ('Python-bundle-PyPI', '2023.06'),
 ]
 
-exts_default_options = {
-    'download_dep_fail': True,
-    'sanity_pip_check': True,
-    'use_pip': True,
-}
+sanity_pip_check = True
+use_pip = True
 
 exts_list = [
     ('Markdown', '3.5.2', {
diff --git a/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-5.5.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-5.5.0-GCCcore-10.2.0.eb
index b013362d2e5..50dab938d40 100644
--- a/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-5.5.0-GCCcore-10.2.0.eb
+++ b/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-5.5.0-GCCcore-10.2.0.eb
@@ -16,9 +16,9 @@ dependencies = [
 ]
 builddependencies = [('binutils', '2.35')]
 
-exts_default_options = {
-    'use_pip': True,
-}
+sanity_pip_check = True
+use_pip = True
+
 exts_list = [
     ('pbr', '5.6.0', {
         'checksums': ['42df03e7797b796625b1029c0400279c7c34fd7df24a7d7818a1abb5b38710dd'],
@@ -121,7 +121,6 @@ exts_list = [
     }),
 ]
 
-sanity_pip_check = True
 enhance_sanity_check = True
 sanity_check_commands = ['openstack -h']
 
diff --git a/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-5.8.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-5.8.0-GCCcore-11.2.0.eb
index e590dd730ca..d92bda87180 100644
--- a/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-5.8.0-GCCcore-11.2.0.eb
+++ b/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-5.8.0-GCCcore-11.2.0.eb
@@ -16,9 +16,9 @@ dependencies = [
 ]
 builddependencies = [('binutils', '2.37')]
 
-exts_default_options = {
-    'use_pip': True,
-}
+sanity_pip_check = True
+use_pip = True
+
 exts_list = [
     ('pyperclip', '1.8.2', {
         'checksums': ['105254a8b04934f0bc84e9c24eb360a591aaf6535c9def5f29d92af107a9bf57'],
@@ -121,7 +121,6 @@ exts_list = [
     }),
 ]
 
-sanity_pip_check = True
 enhance_sanity_check = True
 sanity_check_commands = ['openstack -h']
 
diff --git a/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-6.0.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-6.0.0-GCCcore-12.2.0.eb
index 6b695f63279..bdf0b5c45a6 100644
--- a/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-6.0.0-GCCcore-12.2.0.eb
+++ b/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-6.0.0-GCCcore-12.2.0.eb
@@ -15,9 +15,9 @@ dependencies = [
 ]
 builddependencies = [('binutils', '2.39')]
 
-exts_default_options = {
-    'use_pip': True,
-}
+sanity_pip_check = True
+use_pip = True
+
 exts_list = [
     ('pyperclip', '1.8.2', {
         'checksums': ['105254a8b04934f0bc84e9c24eb360a591aaf6535c9def5f29d92af107a9bf57'],
@@ -114,7 +114,6 @@ exts_list = [
     }),
 ]
 
-sanity_pip_check = True
 enhance_sanity_check = True
 sanity_check_commands = ['openstack -h']
 
diff --git a/easybuild/easyconfigs/p/PyClone/PyClone-2020.9b2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/PyClone/PyClone-2020.9b2-GCCcore-10.2.0.eb
index ee4425b49c5..96d813edcce 100644
--- a/easybuild/easyconfigs/p/PyClone/PyClone-2020.9b2-GCCcore-10.2.0.eb
+++ b/easybuild/easyconfigs/p/PyClone/PyClone-2020.9b2-GCCcore-10.2.0.eb
@@ -21,9 +21,8 @@ dependencies = [
     ('Python', '3.8.6'),
 ]
 
-exts_default_options = {
-    'use_pip': True
-}
+sanity_pip_check = True
+use_pip = True
 
 exts_list = [
     ('Logbook', '1.5.3', {
@@ -37,6 +36,4 @@ exts_list = [
     }),
 ]
 
-sanity_pip_check = True
-
 moduleclass = 'tools'
diff --git a/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2023.06-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2023.06-GCCcore-12.3.0.eb
index 6a91bcca5e4..808285d9f26 100644
--- a/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2023.06-GCCcore-12.3.0.eb
+++ b/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2023.06-GCCcore-12.3.0.eb
@@ -26,11 +26,8 @@ dependencies = [
     ('virtualenv', '20.23.1'),
 ]
 
-exts_default_options = {
-    'download_dep_fail': True,
-    'sanity_pip_check': True,
-    'use_pip': True,
-}
+sanity_pip_check = True
+use_pip = True
 
 # order is important!
 # package versions updated 2023-06-26
diff --git a/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2023.10-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2023.10-GCCcore-13.2.0.eb
index d551945f5e7..d97f7a93c0f 100644
--- a/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2023.10-GCCcore-13.2.0.eb
+++ b/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2023.10-GCCcore-13.2.0.eb
@@ -26,11 +26,8 @@ dependencies = [
     ('virtualenv', '20.24.6'),
 ]
 
-exts_default_options = {
-    'download_dep_fail': True,
-    'sanity_pip_check': True,
-    'use_pip': True,
-}
+sanity_pip_check = True
+use_pip = True
 
 # order is important!
 # package versions updated 2023-10-29
diff --git a/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2024.06-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2024.06-GCCcore-13.3.0.eb
index 01bf9b19b0a..42df4fd52a1 100644
--- a/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2024.06-GCCcore-13.3.0.eb
+++ b/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2024.06-GCCcore-13.3.0.eb
@@ -28,11 +28,8 @@ dependencies = [
     ('virtualenv', '20.26.2'),
 ]
 
-exts_default_options = {
-    'download_dep_fail': True,
-    'sanity_pip_check': True,
-    'use_pip': True,
-}
+sanity_pip_check = True
+use_pip = True
 
 # order is important!
 # package versions updated 2024-06-14
diff --git a/easybuild/easyconfigs/s/setuptools-rust/setuptools-rust-1.6.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/s/setuptools-rust/setuptools-rust-1.6.0-GCCcore-12.3.0.eb
index 8cbf2db9fe7..b2517ef684c 100644
--- a/easybuild/easyconfigs/s/setuptools-rust/setuptools-rust-1.6.0-GCCcore-12.3.0.eb
+++ b/easybuild/easyconfigs/s/setuptools-rust/setuptools-rust-1.6.0-GCCcore-12.3.0.eb
@@ -18,11 +18,8 @@ dependencies = [
     ('Python', '3.11.3'),
 ]
 
-exts_default_options = {
-    'download_dep_fail': True,
-    'sanity_pip_check': True,
-    'use_pip': True,
-}
+sanity_pip_check = True
+use_pip = True
 
 exts_list = [
     ('typing_extensions', '4.6.3', {
diff --git a/easybuild/easyconfigs/s/setuptools-rust/setuptools-rust-1.8.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/s/setuptools-rust/setuptools-rust-1.8.0-GCCcore-13.2.0.eb
index 669229c8f11..044d56266ae 100644
--- a/easybuild/easyconfigs/s/setuptools-rust/setuptools-rust-1.8.0-GCCcore-13.2.0.eb
+++ b/easybuild/easyconfigs/s/setuptools-rust/setuptools-rust-1.8.0-GCCcore-13.2.0.eb
@@ -18,11 +18,8 @@ dependencies = [
     ('Python', '3.11.5'),
 ]
 
-exts_default_options = {
-    'download_dep_fail': True,
-    'sanity_pip_check': True,
-    'use_pip': True,
-}
+sanity_pip_check = True
+use_pip = True
 
 exts_list = [
     ('typing_extensions', '4.8.0', {
diff --git a/easybuild/easyconfigs/s/setuptools-rust/setuptools-rust-1.9.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/s/setuptools-rust/setuptools-rust-1.9.0-GCCcore-13.3.0.eb
index a8ad0dc7ee9..b763364ba26 100644
--- a/easybuild/easyconfigs/s/setuptools-rust/setuptools-rust-1.9.0-GCCcore-13.3.0.eb
+++ b/easybuild/easyconfigs/s/setuptools-rust/setuptools-rust-1.9.0-GCCcore-13.3.0.eb
@@ -18,11 +18,8 @@ dependencies = [
     ('Python', '3.12.3'),
 ]
 
-exts_default_options = {
-    'download_dep_fail': True,
-    'sanity_pip_check': True,
-    'use_pip': True,
-}
+sanity_pip_check = True
+use_pip = True
 
 exts_list = [
     ('typing-extensions', '4.12.2', {
diff --git a/easybuild/easyconfigs/v/virtualenv/virtualenv-20.23.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/v/virtualenv/virtualenv-20.23.1-GCCcore-12.3.0.eb
index 122f3d8d6c8..c36c435d1da 100644
--- a/easybuild/easyconfigs/v/virtualenv/virtualenv-20.23.1-GCCcore-12.3.0.eb
+++ b/easybuild/easyconfigs/v/virtualenv/virtualenv-20.23.1-GCCcore-12.3.0.eb
@@ -18,11 +18,8 @@ dependencies = [
     ('Python', '3.11.3'),
 ]
 
-exts_default_options = {
-    'download_dep_fail': True,
-    'sanity_pip_check': True,
-    'use_pip': True,
-}
+sanity_pip_check = True
+use_pip = True
 
 exts_list = [
     ('distlib', '0.3.6', {
diff --git a/easybuild/easyconfigs/v/virtualenv/virtualenv-20.24.6-GCCcore-13.2.0.eb b/easybuild/easyconfigs/v/virtualenv/virtualenv-20.24.6-GCCcore-13.2.0.eb
index a0b9921fb5c..2820042ba9d 100644
--- a/easybuild/easyconfigs/v/virtualenv/virtualenv-20.24.6-GCCcore-13.2.0.eb
+++ b/easybuild/easyconfigs/v/virtualenv/virtualenv-20.24.6-GCCcore-13.2.0.eb
@@ -18,11 +18,8 @@ dependencies = [
     ('Python', '3.11.5'),
 ]
 
-exts_default_options = {
-    'download_dep_fail': True,
-    'sanity_pip_check': True,
-    'use_pip': True,
-}
+sanity_pip_check = True
+use_pip = True
 
 exts_list = [
     ('distlib', '0.3.7', {
diff --git a/easybuild/easyconfigs/v/virtualenv/virtualenv-20.26.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/v/virtualenv/virtualenv-20.26.2-GCCcore-13.3.0.eb
index 9c6a84c5304..65f1ced6cae 100644
--- a/easybuild/easyconfigs/v/virtualenv/virtualenv-20.26.2-GCCcore-13.3.0.eb
+++ b/easybuild/easyconfigs/v/virtualenv/virtualenv-20.26.2-GCCcore-13.3.0.eb
@@ -18,11 +18,8 @@ dependencies = [
     ('Python', '3.12.3'),
 ]
 
-exts_default_options = {
-    'download_dep_fail': True,
-    'sanity_pip_check': True,
-    'use_pip': True,
-}
+sanity_pip_check = True
+use_pip = True
 
 exts_list = [
     ('distlib', '0.3.8', {

From 42c0b3190b5b626a4fa299b4220e3276971684fe Mon Sep 17 00:00:00 2001
From: ankekreuzer <a.kreuzer@fz-juelich.de>
Date: Wed, 4 Sep 2024 12:09:09 +0200
Subject: [PATCH 776/835] Added LMDB to the GCCcore-13.3.0 toolchain

---
 .../l/LMDB/LMDB-0.9.31-GCCcore-13.3.0.eb      | 38 +++++++++++++++++++
 1 file changed, 38 insertions(+)
 create mode 100644 easybuild/easyconfigs/l/LMDB/LMDB-0.9.31-GCCcore-13.3.0.eb

diff --git a/easybuild/easyconfigs/l/LMDB/LMDB-0.9.31-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/LMDB/LMDB-0.9.31-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..a10be56a891
--- /dev/null
+++ b/easybuild/easyconfigs/l/LMDB/LMDB-0.9.31-GCCcore-13.3.0.eb
@@ -0,0 +1,38 @@
+easyblock = 'MakeCp'
+
+name = 'LMDB'
+version = '0.9.31'
+
+homepage = 'https://symas.com/lmdb'
+description = """LMDB is a fast, memory-efficient database. With memory-mapped files, it has the read performance
+ of a pure in-memory database while retaining the persistence of standard disk-based databases."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+source_urls = ['https://github.com/LMDB/lmdb/archive/']
+sources = ['%(name)s_%(version)s.tar.gz']
+checksums = ['dd70a8c67807b3b8532b3e987b0a4e998962ecc28643e1af5ec77696b081c9b0']
+
+builddependencies = [('binutils', '2.42')]
+
+buildopts = 'CC="$CC" OPT="$CFLAGS"'
+
+runtest = 'test'
+
+local_binaries = ['mdb_copy', 'mdb_dump', 'mdb_load', 'mdb_stat']
+
+files_to_copy = [
+    (['lmdb.h', 'midl.h'], 'include'),
+    (local_binaries, 'bin'),
+    (['liblmdb.a', 'liblmdb.%s' % SHLIB_EXT], 'lib'),
+]
+
+sanity_check_paths = {
+    'files': ['bin/mdb_copy', 'bin/mdb_dump', 'bin/mdb_load', 'bin/mdb_stat', 'include/lmdb.h',
+              'include/midl.h', 'lib/liblmdb.a', 'lib/liblmdb.%s' % SHLIB_EXT],
+    'dirs': [],
+}
+
+sanity_check_commands = ["%s -V" % x for x in local_binaries]
+
+moduleclass = 'lib'

From 6e3465cf36684816d30a8a63316b8a4624bd197f Mon Sep 17 00:00:00 2001
From: ankekreuzer <a.kreuzer@fz-juelich.de>
Date: Wed, 4 Sep 2024 12:12:26 +0200
Subject: [PATCH 777/835] Added NLopt to the GCCcore-13.3.0 toolchain.

---
 .../n/NLopt/NLopt-2.7.1-GCCcore-13.3.0.eb     | 33 +++++++++++++++++++
 1 file changed, 33 insertions(+)
 create mode 100644 easybuild/easyconfigs/n/NLopt/NLopt-2.7.1-GCCcore-13.3.0.eb

diff --git a/easybuild/easyconfigs/n/NLopt/NLopt-2.7.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/n/NLopt/NLopt-2.7.1-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..b9bb438dc94
--- /dev/null
+++ b/easybuild/easyconfigs/n/NLopt/NLopt-2.7.1-GCCcore-13.3.0.eb
@@ -0,0 +1,33 @@
+easyblock = 'CMakeMake'
+
+name = 'NLopt'
+version = '2.7.1'
+
+homepage = 'http://ab-initio.mit.edu/wiki/index.php/NLopt'
+description = """ NLopt is a free/open-source library for nonlinear optimization,
+ providing a common interface for a number of different free optimization routines
+ available online as well as original implementations of various other algorithms. """
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://github.com/stevengj/nlopt/archive']
+sources = ['v%(version)s.tar.gz']
+checksums = ['db88232fa5cef0ff6e39943fc63ab6074208831dc0031cf1545f6ecd31ae2a1a']
+
+builddependencies = [
+    ('CMake', '3.29.3'),
+    ('binutils', '2.42'),
+]
+
+configopts = [
+    '-DBUILD_SHARED_LIBS=ON',
+    '-DBUILD_SHARED_LIBS=OFF'
+]
+
+sanity_check_paths = {
+    'files': ['lib/libnlopt.a', 'lib/libnlopt.%s' % SHLIB_EXT, 'include/nlopt.h'],
+    'dirs': ['lib/pkgconfig'],
+}
+
+moduleclass = 'numlib'

From 7e0a67b39ad16c5724eb199231b597b68522cf3f Mon Sep 17 00:00:00 2001
From: ankekreuzer <a.kreuzer@fz-juelich.de>
Date: Wed, 4 Sep 2024 12:16:53 +0200
Subject: [PATCH 778/835] Added nsync to the GCCcore-13.3.0 toolchain.

---
 .../n/nsync/nsync-1.29.2-GCCcore-13.3.0.eb    | 26 +++++++++++++++++++
 1 file changed, 26 insertions(+)
 create mode 100644 easybuild/easyconfigs/n/nsync/nsync-1.29.2-GCCcore-13.3.0.eb

diff --git a/easybuild/easyconfigs/n/nsync/nsync-1.29.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/n/nsync/nsync-1.29.2-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..e7c2035444b
--- /dev/null
+++ b/easybuild/easyconfigs/n/nsync/nsync-1.29.2-GCCcore-13.3.0.eb
@@ -0,0 +1,26 @@
+easyblock = 'CMakeNinja'
+
+name = 'nsync'
+version = '1.29.2'
+
+homepage = 'https://github.com/google/nsync'
+description = """nsync is a C library that exports various synchronization primitives, such as mutexes"""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+source_urls = ['https://github.com/google/nsync/archive/refs/tags/']
+sources = ['%(version)s.tar.gz']
+checksums = ['1d63e967973733d2c97e841e3c05fac4d3fa299f01d14c86f2695594c7a4a2ec']
+
+builddependencies = [
+    ('binutils', '2.42'),
+    ('CMake', '3.29.3'),
+    ('Ninja', '1.12.1'),
+]
+
+sanity_check_paths = {
+    'files': ['include/nsync.h', 'lib/libnsync.a', 'lib/libnsync_cpp.a'],
+    'dirs': [],
+}
+
+moduleclass = 'devel'

From 5ec13aad36b3dfe35b9f0b015feaa5bb34d21970 Mon Sep 17 00:00:00 2001
From: ankekreuzer <a.kreuzer@fz-juelich.de>
Date: Wed, 4 Sep 2024 12:25:49 +0200
Subject: [PATCH 779/835] Added OpenEXR to the GCCcore-13.3.0 toolchain.

---
 .../o/OpenEXR/OpenEXR-3.2.4-GCCcore-13.3.0.eb | 38 +++++++++++++++++++
 1 file changed, 38 insertions(+)
 create mode 100644 easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.2.4-GCCcore-13.3.0.eb

diff --git a/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.2.4-GCCcore-13.3.0.eb b/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.2.4-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..f6e66db69ae
--- /dev/null
+++ b/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.2.4-GCCcore-13.3.0.eb
@@ -0,0 +1,38 @@
+easyblock = 'CMakeMake'
+
+name = 'OpenEXR'
+version = '3.2.4'
+
+homepage = 'https://www.openexr.com/'
+description = """OpenEXR is a high dynamic-range (HDR) image file format developed by Industrial Light & Magic
+ for use in computer imaging applications"""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+source_urls = ['https://github.com/%(namelower)s/%(namelower)s/archive/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['81e6518f2c4656fdeaf18a018f135e96a96e7f66dbe1c1f05860dd94772176cc']
+
+builddependencies = [
+    ('binutils', '2.42'),
+    ('CMake', '3.29.3'),
+]
+dependencies = [
+    ('Imath', '3.1.11'),
+    ('zlib', '1.3.1')
+]
+
+local_libs, local_bins = [
+    ['Iex', 'IlmThread', 'OpenEXR', 'OpenEXRUtil'],
+    ['envmap', 'header', 'makepreview', 'maketiled', 'multipart', 'multiview', 'stdattr']
+]
+
+sanity_check_paths = {
+    'files': (
+        ['lib/lib%s.%s' % (s, SHLIB_EXT) for s in local_libs] +
+        ['bin/exr%s' % b for b in local_bins]
+    ),
+    'dirs': ['include/%(name)s', 'share'],
+}
+
+moduleclass = 'vis'

From 351afdbec49918eeb20ee8874f4105b8c7dd16d6 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Petr=20Kr=C3=A1l?= <petr@inuits.eu>
Date: Wed, 4 Sep 2024 12:37:07 +0200
Subject: [PATCH 780/835] adding easyconfigs: LRBinner-0.1-foss-2023a.eb

---
 .../l/LRBinner/LRBinner-0.1-foss-2023a.eb     | 42 +++++++++++++++++++
 1 file changed, 42 insertions(+)
 create mode 100644 easybuild/easyconfigs/l/LRBinner/LRBinner-0.1-foss-2023a.eb

diff --git a/easybuild/easyconfigs/l/LRBinner/LRBinner-0.1-foss-2023a.eb b/easybuild/easyconfigs/l/LRBinner/LRBinner-0.1-foss-2023a.eb
new file mode 100644
index 00000000000..d3ce64d0b9f
--- /dev/null
+++ b/easybuild/easyconfigs/l/LRBinner/LRBinner-0.1-foss-2023a.eb
@@ -0,0 +1,42 @@
+easyblock = 'PythonBundle'
+
+name = 'LRBinner'
+version = '0.1'
+
+homepage = 'https://github.com/anuradhawick/LRBinner'
+description = "LRBinner is a long-read binning tool published in WABI 2021 proceedings and AMB. "
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('HMMER', '3.4'),
+    ('Seaborn', '0.13.2'),
+    ('h5py', '3.9.0'),
+    ('PyTorch', '2.1.2'),
+    ('tqdm', '4.66.1'),
+    ('Biopython', '1.83'),
+    ('scikit-learn', '1.3.1'),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    ('tabulate', '0.9.0', {
+        'source_tmpl': SOURCE_PY3_WHL,
+        'checksums': ['024ca478df22e9340661486f85298cff5f6dcdba14f3813e8830015b9ed1948f'],
+    }),
+    (name, version, {
+        'modulename': 'mbcclr_utils',
+        'preinstallopts': "sed -i 's/pytorch/torch/g' setup.py && ",
+        'source_urls': ['https://github.com/anuradhawick/LRBinner/archive/'],
+        'sources': ['v%(version)s.tar.gz'],
+        'checksums': ['2d77dde8ab1272c432b20eb18a352326c622e929261562ef6d680c6638cc4bd1'],
+    }),
+]
+
+sanity_check_commands = ['LRBinner --help']
+
+moduleclass = 'tools'

From 7f717d8d2e9af7dba59c6e1b4bafd2e2aa7abff6 Mon Sep 17 00:00:00 2001
From: Sam Moors <smoors@users.noreply.github.com>
Date: Wed, 4 Sep 2024 12:37:41 +0200
Subject: [PATCH 781/835] remove download_dep_fail

---
 .../easyconfigs/r/redis-py/redis-py-5.0.9-GCCcore-13.2.0.eb      | 1 -
 1 file changed, 1 deletion(-)

diff --git a/easybuild/easyconfigs/r/redis-py/redis-py-5.0.9-GCCcore-13.2.0.eb b/easybuild/easyconfigs/r/redis-py/redis-py-5.0.9-GCCcore-13.2.0.eb
index 39e66108872..b877029e19a 100644
--- a/easybuild/easyconfigs/r/redis-py/redis-py-5.0.9-GCCcore-13.2.0.eb
+++ b/easybuild/easyconfigs/r/redis-py/redis-py-5.0.9-GCCcore-13.2.0.eb
@@ -18,7 +18,6 @@ dependencies = [
     ('Redis', '7.2.4'),
 ]
 
-download_dep_fail = True
 use_pip = True
 
 exts_list = [

From 8328d0563441287c92995664f95baeaae4793ee7 Mon Sep 17 00:00:00 2001
From: ankekreuzer <a.kreuzer@fz-juelich.de>
Date: Wed, 4 Sep 2024 12:48:19 +0200
Subject: [PATCH 782/835] Added pkgconfig to the GCCcore-13.3.0 toolchain.

---
 .../pkgconfig-1.5.5-GCCcore-13.3.0-python.eb  | 31 +++++++++++++++++++
 1 file changed, 31 insertions(+)
 create mode 100644 easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.5.5-GCCcore-13.3.0-python.eb

diff --git a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.5.5-GCCcore-13.3.0-python.eb b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.5.5-GCCcore-13.3.0-python.eb
new file mode 100644
index 00000000000..f66c2f13358
--- /dev/null
+++ b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.5.5-GCCcore-13.3.0-python.eb
@@ -0,0 +1,31 @@
+easyblock = 'PythonPackage'
+
+name = 'pkgconfig'
+version = '1.5.5'
+# The -python versionsuffix is used to avoid confusion between
+# pkg-config (the tool) and pkgconfig (the Python wrappers)
+versionsuffix = '-python'
+
+homepage = 'https://github.com/matze/pkgconfig'
+description = """pkgconfig is a Python module to interface with the pkg-config command line tool"""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+sources = [SOURCE_TAR_GZ]
+checksums = ['deb4163ef11f75b520d822d9505c1f462761b4309b1bb713d08689759ea8b899']
+
+builddependencies = [
+    ('binutils', '2.42'),
+    ('poetry', '1.8.3'),
+]
+
+dependencies = [
+    ('Python', '3.12.3'),
+    ('pkgconf', '2.2.0'),
+]
+
+use_pip = True
+download_dep_fail = True
+sanity_pip_check = True
+
+moduleclass = 'devel'

From b14673d1c5ca00baf6330ed71f59592861ab3547 Mon Sep 17 00:00:00 2001
From: ankekreuzer <a.kreuzer@fz-juelich.de>
Date: Wed, 4 Sep 2024 13:01:50 +0200
Subject: [PATCH 783/835] Added popt to the GCCcore-13.3.0 toolchein.

---
 .../p/popt/popt-1.19-GCCcore-13.3.0.eb        | 24 +++++++++++++++++++
 1 file changed, 24 insertions(+)
 create mode 100644 easybuild/easyconfigs/p/popt/popt-1.19-GCCcore-13.3.0.eb

diff --git a/easybuild/easyconfigs/p/popt/popt-1.19-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/popt/popt-1.19-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..91b5c7c74ba
--- /dev/null
+++ b/easybuild/easyconfigs/p/popt/popt-1.19-GCCcore-13.3.0.eb
@@ -0,0 +1,24 @@
+easyblock = 'ConfigureMake'
+
+name = 'popt'
+version = '1.19'
+
+homepage = 'https://github.com/rpm-software-management/popt'
+description = 'Popt is a C library for parsing command line parameters.'
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+source_urls = ['http://ftp.rpm.org/popt/releases/popt-1.x']
+sources = [SOURCE_TAR_GZ]
+checksums = ['c25a4838fc8e4c1c8aacb8bd620edb3084a3d63bf8987fdad3ca2758c63240f9']
+
+builddependencies = [
+    ('binutils', '2.42')
+]
+
+sanity_check_paths = {
+    'files': ['include/%(name)s.h', ('lib/libpopt.a', 'lib64/libpopt.a'), ('lib/libpopt.so', 'lib64/libpopt.so')],
+    'dirs': [],
+}
+
+moduleclass = 'tools'

From 688ee7bbb756a040cbab1f3291235f0a4b50e62c Mon Sep 17 00:00:00 2001
From: ankekreuzer <a.kreuzer@fz-juelich.de>
Date: Wed, 4 Sep 2024 13:17:00 +0200
Subject: [PATCH 784/835] Added PostgreSQL to the GCCcore-13.3.0 toolchain.

---
 .../PostgreSQL-16.4-GCCcore-13.3.0.eb         | 43 +++++++++++++++++++
 1 file changed, 43 insertions(+)
 create mode 100644 easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-16.4-GCCcore-13.3.0.eb

diff --git a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-16.4-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-16.4-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..9b4c1f62855
--- /dev/null
+++ b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-16.4-GCCcore-13.3.0.eb
@@ -0,0 +1,43 @@
+easyblock = 'ConfigureMake'
+
+name = 'PostgreSQL'
+version = '16.4'
+
+homepage = 'https://www.postgresql.org/'
+description = """PostgreSQL is a powerful, open source object-relational database system.
+ It is fully ACID compliant, has full support for foreign keys,
+ joins, views, triggers, and stored procedures (in multiple languages).
+ It includes most SQL:2008 data types, including INTEGER,
+ NUMERIC, BOOLEAN, CHAR, VARCHAR, DATE, INTERVAL, and TIMESTAMP.
+ It also supports storage of binary large objects, including pictures,
+ sounds, or video. It has native programming interfaces for C/C++, Java,
+ .Net, Perl, Python, Ruby, Tcl, ODBC, among others, and exceptional documentation."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+source_urls = ['http://ftp.postgresql.org/pub/source/v%(version)s/']
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['2e17a90062403e15d6540480fdec50c8b005eb48729a91cb4989ffeb04df193c']
+
+builddependencies = [
+    ('binutils', '2.42'),
+    ('Bison', '3.8.2'),
+    ('flex', '2.6.4'),
+    ('Perl', '5.38.2'),
+    ('Python', '3.12.3'),
+]
+
+dependencies = [
+    ('libreadline', '8.2'),
+    ('zlib', '1.3.1'),
+    ('OpenSSL', '3', '', SYSTEM),
+]
+
+configopts = '--with-python --with-openssl --without-icu'
+
+sanity_check_paths = {
+    'files': ['bin/psql', 'bin/pg_config', 'lib/libpq.a', 'lib/libpq.%s' % SHLIB_EXT],
+    'dirs': ['share/postgresql'],
+}
+
+moduleclass = 'data'

From 39ab79a3eb6cf416864384afd56a6763f88ade23 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Petr=20Kr=C3=A1l?= <petr@inuits.eu>
Date: Wed, 4 Sep 2024 14:49:44 +0200
Subject: [PATCH 785/835] add dependencies

---
 .../FragGeneScan-1.31-GCCcore-12.3.0.eb       | 38 +++++++++++++++++++
 .../HDBSCAN-0.8.38.post1-foss-2023a.eb        | 27 +++++++++++++
 .../l/LRBinner/LRBinner-0.1-foss-2023a.eb     |  2 +
 3 files changed, 67 insertions(+)
 create mode 100644 easybuild/easyconfigs/f/FragGeneScan/FragGeneScan-1.31-GCCcore-12.3.0.eb
 create mode 100644 easybuild/easyconfigs/h/HDBSCAN/HDBSCAN-0.8.38.post1-foss-2023a.eb

diff --git a/easybuild/easyconfigs/f/FragGeneScan/FragGeneScan-1.31-GCCcore-12.3.0.eb b/easybuild/easyconfigs/f/FragGeneScan/FragGeneScan-1.31-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..527ba56e69f
--- /dev/null
+++ b/easybuild/easyconfigs/f/FragGeneScan/FragGeneScan-1.31-GCCcore-12.3.0.eb
@@ -0,0 +1,38 @@
+easyblock = 'MakeCp'
+
+name = 'FragGeneScan'
+version = '1.31'
+
+homepage = 'https://omics.informatics.indiana.edu/FragGeneScan/'
+description = "FragGeneScan is an application for finding (fragmented) genes in short reads."
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+source_urls = [SOURCEFORGE_SOURCE]
+sources = ['%(name)s%(version)s.tar.gz']
+checksums = ['cd3212d0f148218eb3b17d24fcd1fc897fb9fee9b2c902682edde29f895f426c']
+
+builddependencies = [('binutils', '2.40')]
+
+dependencies = [('Perl', '5.36.1')]
+
+fix_perl_shebang_for = ['*.pl']
+
+prebuildopts = "make clean && "
+buildopts = 'CC="$CC" CFLAG="$CFLAGS" fgs && chmod -R go+rx *.pl train example'
+
+files_to_copy = ['FragGeneScan', 'run_FragGeneScan.pl', 'example', 'train']
+
+modextrapaths = {'PATH': ['']}
+
+sanity_check_paths = {
+    'files': ['FragGeneScan', 'run_FragGeneScan.pl'],
+    'dirs': ['example', 'train'],
+}
+
+sanity_check_commands = [
+    './run_FragGeneScan.pl help',
+    './run_FragGeneScan.pl -genome=./example/NC_000913.fna -out=./example/NC_000913-fgs  -complete=1  -train=complete'
+]
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/h/HDBSCAN/HDBSCAN-0.8.38.post1-foss-2023a.eb b/easybuild/easyconfigs/h/HDBSCAN/HDBSCAN-0.8.38.post1-foss-2023a.eb
new file mode 100644
index 00000000000..b260708eab8
--- /dev/null
+++ b/easybuild/easyconfigs/h/HDBSCAN/HDBSCAN-0.8.38.post1-foss-2023a.eb
@@ -0,0 +1,27 @@
+easyblock = 'PythonPackage'
+
+name = 'HDBSCAN'
+version = '0.8.38.post1'
+
+homepage = 'http://hdbscan.readthedocs.io/en/latest/'
+description = """The hdbscan library is a suite of tools to use unsupervised learning to find clusters, or dense
+ regions, of a dataset. The primary algorithm is HDBSCAN* as proposed by Campello, Moulavi, and Sander. The library
+ provides a high performance implementation of this algorithm, along with tools for analysing the resulting
+ clustering."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['5fbdba2ffb5a99a8b52fa2915658ced6bed59f4d0d5f40b1c673646c928aac0b']
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('scikit-learn', '1.3.1'),
+]
+
+download_dep_fail = True
+use_pip = True
+sanity_pip_check = True
+
+moduleclass = 'data'
diff --git a/easybuild/easyconfigs/l/LRBinner/LRBinner-0.1-foss-2023a.eb b/easybuild/easyconfigs/l/LRBinner/LRBinner-0.1-foss-2023a.eb
index d3ce64d0b9f..143e59d35c5 100644
--- a/easybuild/easyconfigs/l/LRBinner/LRBinner-0.1-foss-2023a.eb
+++ b/easybuild/easyconfigs/l/LRBinner/LRBinner-0.1-foss-2023a.eb
@@ -18,6 +18,8 @@ dependencies = [
     ('tqdm', '4.66.1'),
     ('Biopython', '1.83'),
     ('scikit-learn', '1.3.1'),
+    ('FragGeneScan', '1.31'),
+    ('HDBSCAN', '0.8.38.post1'),
 ]
 
 use_pip = True

From c5412215b3ebbbfcec76d95860d87ed3709a970e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Petr=20Kr=C3=A1l?= <petr@inuits.eu>
Date: Wed, 4 Sep 2024 15:07:38 +0200
Subject: [PATCH 786/835] adding easyconfigs: BRiAl-1.2.12-GCC-13.2.0.eb

---
 .../b/BRiAl/BRiAl-1.2.12-GCC-13.2.0.eb        | 30 +++++++++++++++++++
 1 file changed, 30 insertions(+)
 create mode 100644 easybuild/easyconfigs/b/BRiAl/BRiAl-1.2.12-GCC-13.2.0.eb

diff --git a/easybuild/easyconfigs/b/BRiAl/BRiAl-1.2.12-GCC-13.2.0.eb b/easybuild/easyconfigs/b/BRiAl/BRiAl-1.2.12-GCC-13.2.0.eb
new file mode 100644
index 00000000000..c489c77380f
--- /dev/null
+++ b/easybuild/easyconfigs/b/BRiAl/BRiAl-1.2.12-GCC-13.2.0.eb
@@ -0,0 +1,30 @@
+easyblock = 'ConfigureMake'
+
+name = 'BRiAl'
+version = '1.2.12'
+
+homepage = 'https://github.com/BRiAl/BRiAl'
+description = """BRiAl is the legacy version of PolyBoRi maintained by sagemath developers."""
+
+toolchain = {'name': 'GCC', 'version': '13.2.0'}
+
+source_urls = ['https://github.com/BRiAl/BRiAl/releases/download/%(version)s']
+sources = [SOURCELOWER_TAR_BZ2]
+checksums = ['ca009e3722dd3f0a60d15501caed1413146c80abced57423e32ae0116f407494']
+
+dependencies = [
+    ('Boost', '1.83.0'),
+    ('m4ri', '20200125'),
+]
+
+configopts = "--with-boost=$EBROOTBOOST "
+
+runtest = 'check'
+
+sanity_check_paths = {
+    'files': ['include/polybori.h'] +
+             ['lib/libbrial.%s' % e for e in ['a', SHLIB_EXT]],
+    'dirs': [],
+}
+
+moduleclass = 'math'

From bcba62eb0812eca74327cfdfcde30323ba85199e Mon Sep 17 00:00:00 2001
From: Alexandre Strube <surak@surak.eti.br>
Date: Wed, 4 Sep 2024 13:43:57 +0000
Subject: [PATCH 787/835] adding easyconfigs:
 Abseil-20240722.0-GCCcore-13.3.0.eb

---
 .../Abseil-20240722.0-GCCcore-13.3.0.eb       | 34 +++++++++++++++++++
 1 file changed, 34 insertions(+)
 create mode 100644 easybuild/easyconfigs/a/Abseil/Abseil-20240722.0-GCCcore-13.3.0.eb

diff --git a/easybuild/easyconfigs/a/Abseil/Abseil-20240722.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/a/Abseil/Abseil-20240722.0-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..24951c68814
--- /dev/null
+++ b/easybuild/easyconfigs/a/Abseil/Abseil-20240722.0-GCCcore-13.3.0.eb
@@ -0,0 +1,34 @@
+easyblock = 'CMakeMake'
+
+name = 'Abseil'
+version = '20240722.0'
+
+homepage = 'https://abseil.io/'
+description = """Abseil is an open-source collection of C++ library code designed to augment the
+C++ standard library. The Abseil library code is collected from Google's own
+C++ code base, has been extensively tested and used in production, and is the
+same code we depend on in our daily coding lives."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+toolchainopts = {'pic': True}
+
+source_urls = [
+    'https://github.com/%(namelower)s/%(namelower)s-cpp/archive/refs/tags']
+sources = ['%(version)s.tar.gz']
+checksums = ['f50e5ac311a81382da7fa75b97310e4b9006474f9560ac46f54a9967f07d4ae3']
+
+builddependencies = [
+    ('binutils', '2.42'),
+    ('CMake', '3.29.3'),
+]
+
+configopts = "-DABSL_PROPAGATE_CXX_STD=ON "
+
+build_shared_libs = True
+
+sanity_check_paths = {
+    'files': ['lib/libabsl_base.' + SHLIB_EXT],
+    'dirs': ['include/absl'],
+}
+
+moduleclass = 'lib'

From 738efd053faf839783bcf39e38a4fe18e4781cac Mon Sep 17 00:00:00 2001
From: Alexandre Strube <surak@surak.eti.br>
Date: Wed, 4 Sep 2024 15:02:48 +0000
Subject: [PATCH 788/835] adding easyconfigs: Flask-3.0.3-GCCcore-13.3.0.eb

---
 .../f/Flask/Flask-3.0.3-GCCcore-13.3.0.eb     | 68 +++++++++++++++++++
 1 file changed, 68 insertions(+)
 create mode 100644 easybuild/easyconfigs/f/Flask/Flask-3.0.3-GCCcore-13.3.0.eb

diff --git a/easybuild/easyconfigs/f/Flask/Flask-3.0.3-GCCcore-13.3.0.eb b/easybuild/easyconfigs/f/Flask/Flask-3.0.3-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..b0d0c5a63ae
--- /dev/null
+++ b/easybuild/easyconfigs/f/Flask/Flask-3.0.3-GCCcore-13.3.0.eb
@@ -0,0 +1,68 @@
+easyblock = 'PythonBundle'
+
+name = 'Flask'
+version = '3.0.3'
+
+homepage = 'https://flask.palletsprojects.com/'
+description = """
+Flask is a lightweight WSGI web application framework. It is designed to make
+getting started quick and easy, with the ability to scale up to complex
+applications.
+This module includes the Flask extensions: Flask-Cors"""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+builddependencies = [
+    ('binutils', '2.42'),
+]
+dependencies = [
+    ('Python', '3.12.3'),
+    ('Python-bundle-PyPI', '2024.06'),
+]
+
+sanity_pip_check = True
+use_pip = True
+
+exts_list = [
+    ('itsdangerous', '2.2.0', {
+        'checksums': ['e0050c0b7da1eea53ffaf149c0cfbb5c6e2e2b69c4bef22c81fa6eb73e5f6173'],
+    }),
+    ('werkzeug', '3.0.4', {
+        'checksums': ['34f2371506b250df4d4f84bfe7b0921e4762525762bbd936614909fe25cd7306'],
+    }),
+    ('asgiref', '3.7.2', {
+        'checksums': ['9e0ce3aa93a819ba5b45120216b23878cf6e8525eb3848653452b4192b92afed'],
+    }),
+    ('click', '8.1.7', {
+        'checksums': ['ca9853ad459e787e2192211578cc907e7594e294c7ccc834310722b41b9ca6de'],
+    }),
+    ('blinker', '1.8.2', {
+        'checksums': ['8f77b09d3bf7c795e969e9486f39c2c5e9c39d4ee07424be2bc594ece9642d83'],
+    }),
+    ('flask', version, {
+        'checksums': ['ceb27b0af3823ea2737928a4d99d125a06175b8512c445cbd9a9ce200ef76842'],
+    }),
+    ('msgspec', '0.18.6', {
+        'checksums': ['a59fc3b4fcdb972d09138cb516dbde600c99d07c38fd9372a6ef500d2d031b4e'],
+    }),
+    ('Flask-Cors', '5.0.0', {
+        'sources': ['flask_cors-%(version)s.tar.gz'],
+        'checksums': ['5aadb4b950c4e93745034594d9f3ea6591f734bb3662e16e255ffbf5e89c88ef'],
+    }),
+    ('cachelib', '0.13.0', {
+        'checksums': ['209d8996e3c57595bee274ff97116d1d73c4980b2fd9a34c7846cd07fd2e1a48'],
+    }),
+    ('Flask-Session', '0.8.0', {
+        'sources': ['flask_session-%(version)s.tar.gz'],
+        'checksums': ['20e045eb01103694e70be4a49f3a80dbb1b57296a22dc6f44bbf3f83ef0742ff'],
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['bin/%(namelower)s'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = ['%(namelower)s --version']
+
+moduleclass = 'lib'

From 015d5a5073297892b02b1b8de69f3a62284947be Mon Sep 17 00:00:00 2001
From: Alexandre Strube <surak@surak.eti.br>
Date: Wed, 4 Sep 2024 15:16:24 +0000
Subject: [PATCH 789/835] adding easyconfigs:
 expecttest-0.2.1-GCCcore-13.3.0.eb

---
 .../expecttest-0.2.1-GCCcore-13.3.0.eb        | 29 +++++++++++++++++++
 1 file changed, 29 insertions(+)
 create mode 100644 easybuild/easyconfigs/e/expecttest/expecttest-0.2.1-GCCcore-13.3.0.eb

diff --git a/easybuild/easyconfigs/e/expecttest/expecttest-0.2.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/e/expecttest/expecttest-0.2.1-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..a70bf3973ca
--- /dev/null
+++ b/easybuild/easyconfigs/e/expecttest/expecttest-0.2.1-GCCcore-13.3.0.eb
@@ -0,0 +1,29 @@
+easyblock = 'PythonPackage'
+
+name = 'expecttest'
+version = '0.2.1'
+
+homepage = 'https://github.com/ezyang/expecttest'
+description = """This library implements expect tests (also known as "golden" tests). Expect tests are a method of
+ writing tests where instead of hard-coding the expected output of a test, you run the test to get the output, and
+ the test framework automatically populates the expected output. If the output of the test changes, you can rerun
+ the test with the environment variable EXPECTTEST_ACCEPT=1 to automatically update the expected output."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+sources = [SOURCE_TAR_GZ]
+checksums = ['e52b1cf8a6f84506e6962a0bbdd248ea442124d826e849f263ec1c322ebb73f5']
+
+builddependencies = [
+    ('binutils', '2.42'),
+    ('poetry', '1.8.3'),
+]
+dependencies = [
+    ('Python', '3.12.3'),
+]
+
+download_dep_fail = True
+sanity_pip_check = True
+use_pip = True
+
+moduleclass = 'tools'

From 6d5fb5b515c2ec98c307208bf7ece9ba384269bd Mon Sep 17 00:00:00 2001
From: Alexandre Strube <surak@surak.eti.br>
Date: Wed, 4 Sep 2024 15:48:31 +0000
Subject: [PATCH 790/835] adding easyconfigs: hiredis-1.2.0-GCCcore-13.3.0.eb

---
 .../h/hiredis/hiredis-1.2.0-GCCcore-13.3.0.eb | 41 +++++++++++++++++++
 1 file changed, 41 insertions(+)
 create mode 100644 easybuild/easyconfigs/h/hiredis/hiredis-1.2.0-GCCcore-13.3.0.eb

diff --git a/easybuild/easyconfigs/h/hiredis/hiredis-1.2.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/h/hiredis/hiredis-1.2.0-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..bc3a5a1c715
--- /dev/null
+++ b/easybuild/easyconfigs/h/hiredis/hiredis-1.2.0-GCCcore-13.3.0.eb
@@ -0,0 +1,41 @@
+# Author: Alexander Grund (TU Dresden)
+# Based on EC by J. Sassmannshausen (Imperial College London)
+
+easyblock = 'CMakeMake'
+
+name = 'hiredis'
+version = '1.2.0'
+
+homepage = 'https://github.com/redis/hiredis'
+description = """Hiredis is a minimalistic C client library for the Redis database.
+
+It is minimalistic because it just adds minimal support for the protocol,
+but at the same time it uses a high level printf-alike API in order to
+make it much higher level than otherwise suggested by its minimal code base
+and the lack of explicit bindings for every Redis command."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+toolchainopts = {'pic': True}
+
+github_account = 'redis'
+source_urls = [GITHUB_SOURCE]
+sources = ['v%(version)s.tar.gz']
+checksums = ['82ad632d31ee05da13b537c124f819eb88e18851d9cb0c30ae0552084811588c']
+
+builddependencies = [
+    ('binutils', '2.42'),
+    ('CMake', '3.29.3'),
+]
+
+dependencies = [
+    ('OpenSSL', '3', '', SYSTEM),
+]
+
+configopts = ['-DBUILD_SHARED_LIBS=ON', '-DBUILD_SHARED_LIBS=OFF']
+
+sanity_check_paths = {
+    'files': ['lib/libhiredis.a', 'lib/libhiredis.%s' % SHLIB_EXT],
+    'dirs': ['include'],
+}
+
+moduleclass = 'tools'

From 36f0735f0a14fc506b10a7c395634511f287f2d7 Mon Sep 17 00:00:00 2001
From: Alexandre Strube <surak@surak.eti.br>
Date: Wed, 4 Sep 2024 16:03:36 +0000
Subject: [PATCH 791/835] adding easyconfigs: PyYAML-6.0.2-GCCcore-13.3.0.eb

---
 .../p/PyYAML/PyYAML-6.0.2-GCCcore-13.3.0.eb   | 30 +++++++++++++++++++
 1 file changed, 30 insertions(+)
 create mode 100644 easybuild/easyconfigs/p/PyYAML/PyYAML-6.0.2-GCCcore-13.3.0.eb

diff --git a/easybuild/easyconfigs/p/PyYAML/PyYAML-6.0.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/PyYAML/PyYAML-6.0.2-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..70dfd98dcf4
--- /dev/null
+++ b/easybuild/easyconfigs/p/PyYAML/PyYAML-6.0.2-GCCcore-13.3.0.eb
@@ -0,0 +1,30 @@
+easyblock = 'PythonPackage'
+
+name = 'PyYAML'
+version = '6.0.2'
+
+homepage = 'https://github.com/yaml/pyyaml'
+description = "PyYAML is a YAML parser and emitter for the Python programming language."
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+sources = ['https://github.com/yaml/pyyaml/archive/refs/tags/%(version)s.tar.gz']
+checksums = ['9377c381ac3fccad8df73d96b5139ef8b1a2c57a0d913e95ab0a2275d66b5caa']
+
+builddependencies = [
+    ('binutils', '2.42'),
+]
+dependencies = [
+    ('Python', '3.12.3'),
+    ('libyaml', '0.2.5'),
+    ('Python-bundle-PyPI', '2024.06'),
+]
+
+download_dep_fail = True
+sanity_pip_check = True
+use_pip = True
+options = {'modulename': 'yaml'}
+
+sanity_check_commands = ["python -c 'import yaml; yaml.CLoader'"]
+
+moduleclass = 'lib'

From d21774ba350a7bd8ec5aef404318e55b465d4e9d Mon Sep 17 00:00:00 2001
From: Alexandre Strube <surak@surak.eti.br>
Date: Wed, 4 Sep 2024 16:05:29 +0000
Subject: [PATCH 792/835] adding easyconfigs: YACS-0.1.8-GCCcore-13.3.0.eb

---
 .../y/YACS/YACS-0.1.8-GCCcore-13.3.0.eb       | 31 +++++++++++++++++++
 1 file changed, 31 insertions(+)
 create mode 100644 easybuild/easyconfigs/y/YACS/YACS-0.1.8-GCCcore-13.3.0.eb

diff --git a/easybuild/easyconfigs/y/YACS/YACS-0.1.8-GCCcore-13.3.0.eb b/easybuild/easyconfigs/y/YACS/YACS-0.1.8-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..2ab12a60fca
--- /dev/null
+++ b/easybuild/easyconfigs/y/YACS/YACS-0.1.8-GCCcore-13.3.0.eb
@@ -0,0 +1,31 @@
+easyblock = 'PythonPackage'
+
+name = 'YACS'
+version = '0.1.8'
+
+homepage = "https://github.com/rbgirshick/yacs"
+description = """YACS was created as a lightweight library to define and
+manage system configurations, such as those commonly found in software
+designed for scientific experimentation. These "configurations"
+typically cover concepts like hyperparameters used in training a machine
+learning model or configurable model hyperparameters, such as the depth
+of a convolutional neural network."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['efc4c732942b3103bea904ee89af98bcd27d01f0ac12d8d4d369f1e7a2914384']
+
+builddependencies = [('binutils', '2.42')]
+
+dependencies = [
+    ('Python', '3.12.3'),
+    ('PyYAML', '6.0.2'),
+]
+
+use_pip = True
+download_dep_fail = True
+
+sanity_pip_check = True
+
+moduleclass = 'lib'

From 67ee0f54f9cf9cf72c5d6d187f7a125c3a7bedeb Mon Sep 17 00:00:00 2001
From: Alexandre Strube <surak@surak.eti.br>
Date: Wed, 4 Sep 2024 16:18:23 +0000
Subject: [PATCH 793/835] adding easyconfigs:
 pretty-yaml-24.7.0-GCCcore-13.3.0.eb

---
 .../pretty-yaml-24.7.0-GCCcore-13.3.0.eb      | 31 +++++++++++++++++++
 1 file changed, 31 insertions(+)
 create mode 100644 easybuild/easyconfigs/p/pretty-yaml/pretty-yaml-24.7.0-GCCcore-13.3.0.eb

diff --git a/easybuild/easyconfigs/p/pretty-yaml/pretty-yaml-24.7.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/pretty-yaml/pretty-yaml-24.7.0-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..ef58228ef61
--- /dev/null
+++ b/easybuild/easyconfigs/p/pretty-yaml/pretty-yaml-24.7.0-GCCcore-13.3.0.eb
@@ -0,0 +1,31 @@
+easyblock = 'PythonPackage'
+
+name = 'pretty-yaml'
+local_mod = 'pyaml'
+version = '24.7.0'
+
+homepage = 'https://github.com/mk-fg/pretty-yaml'
+description = """PyYAML-based python module to produce pretty and readable YAML-serialized data.
+This module is for serialization only, see ruamel.yaml module for literate YAML
+parsing (keeping track of comments, spacing, line/column numbers of values, etc)."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+source_urls = ['https://pypi.python.org/packages/source/p/%s/' % local_mod]
+sources = ['%s-%%(version)s.tar.gz' % local_mod]
+checksums = ['5d0fdf9e681036fb263a783d0298fc3af580a6e2a6cf1a3314ffc48dc3d91ccb']
+
+builddependencies = [('binutils', '2.42')]
+
+dependencies = [
+    ('Python', '3.12.3'),
+    ('PyYAML', '6.0.2'),
+]
+
+use_pip = True
+download_dep_fail = True
+sanity_pip_check = True
+
+options = {'modulename': local_mod}
+
+moduleclass = 'lib'

From b4561122d017ab728111b206dfcc8eda59961835 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Petr=20Kr=C3=A1l?= <petr@inuits.eu>
Date: Wed, 4 Sep 2024 18:55:13 +0200
Subject: [PATCH 794/835] add missing dependency

---
 .../b/BRiAl/BRiAl-1.2.12-GCC-13.2.0.eb        |  1 +
 .../c/CUDD/CUDD-3.0.0-GCC-13.2.0.eb           | 22 +++++++++++++++++++
 2 files changed, 23 insertions(+)
 create mode 100644 easybuild/easyconfigs/c/CUDD/CUDD-3.0.0-GCC-13.2.0.eb

diff --git a/easybuild/easyconfigs/b/BRiAl/BRiAl-1.2.12-GCC-13.2.0.eb b/easybuild/easyconfigs/b/BRiAl/BRiAl-1.2.12-GCC-13.2.0.eb
index c489c77380f..50bbeea16ee 100644
--- a/easybuild/easyconfigs/b/BRiAl/BRiAl-1.2.12-GCC-13.2.0.eb
+++ b/easybuild/easyconfigs/b/BRiAl/BRiAl-1.2.12-GCC-13.2.0.eb
@@ -15,6 +15,7 @@ checksums = ['ca009e3722dd3f0a60d15501caed1413146c80abced57423e32ae0116f407494']
 dependencies = [
     ('Boost', '1.83.0'),
     ('m4ri', '20200125'),
+    ('CUDD', '3.0.0'),
 ]
 
 configopts = "--with-boost=$EBROOTBOOST "
diff --git a/easybuild/easyconfigs/c/CUDD/CUDD-3.0.0-GCC-13.2.0.eb b/easybuild/easyconfigs/c/CUDD/CUDD-3.0.0-GCC-13.2.0.eb
new file mode 100644
index 00000000000..c1f83cad099
--- /dev/null
+++ b/easybuild/easyconfigs/c/CUDD/CUDD-3.0.0-GCC-13.2.0.eb
@@ -0,0 +1,22 @@
+easyblock = 'ConfigureMake'
+
+name = 'CUDD'
+version = '3.0.0'
+
+homepage = 'https://github.com/ivmai/cudd'
+description = """The CUDD package is a package written in C for the manipulation of
+ decision diagrams.  It supports binary decision diagrams (BDDs), algebraic decision
+ diagrams (ADDs), and Zero-Suppressed BDDs (ZDDs)."""
+
+toolchain = {'name': 'GCC', 'version': '13.2.0'}
+
+source_urls = ['https://github.com/ivmai/cudd/archive/refs/tags']
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['5fe145041c594689e6e7cf4cd623d5f2b7c36261708be8c9a72aed72cf67acce']
+
+sanity_check_paths = {
+    'files': ['include/cudd.h', 'lib/libcudd.a'],
+    'dirs': [],
+}
+
+moduleclass = 'math'

From 5a930b443e8e31da57d3ccfa3ed35530c6cfae70 Mon Sep 17 00:00:00 2001
From: Alexandre Strube <surak@surak.eti.br>
Date: Wed, 4 Sep 2024 16:55:20 +0000
Subject: [PATCH 795/835] adding easyconfigs:
 ruamel.yaml-0.18.6-GCCcore-13.3.0.eb

---
 .../ruamel.yaml-0.18.6-GCCcore-13.3.0.eb      | 60 +++++++++++++++++++
 1 file changed, 60 insertions(+)
 create mode 100644 easybuild/easyconfigs/r/ruamel.yaml/ruamel.yaml-0.18.6-GCCcore-13.3.0.eb

diff --git a/easybuild/easyconfigs/r/ruamel.yaml/ruamel.yaml-0.18.6-GCCcore-13.3.0.eb b/easybuild/easyconfigs/r/ruamel.yaml/ruamel.yaml-0.18.6-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..48d0b0d8bb5
--- /dev/null
+++ b/easybuild/easyconfigs/r/ruamel.yaml/ruamel.yaml-0.18.6-GCCcore-13.3.0.eb
@@ -0,0 +1,60 @@
+easyblock = 'PythonBundle'
+
+name = 'ruamel.yaml'
+version = '0.18.6'
+
+homepage = 'https://sourceforge.net/projects/ruamel-yaml'
+description = "ruamel.yaml is a YAML 1.2 loader/dumper package for Python."
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+builddependencies = [
+    ('binutils', '2.42'),
+    ('poetry', '1.8.3'),
+]
+
+dependencies = [
+    ('Python', '3.12.3'),
+    ('Python-bundle-PyPI', '2024.06'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('ruamel.yaml.jinja2', '0.2.7', {
+        'checksums': ['8449be29d9a157fa92d1648adc161d718e469f0d38a6b21e0eabb76fd5b3e663'],
+    }),
+    ('ruamel.yaml.clib', '0.2.8', {
+        'modulename': False,
+        'checksums': ['beb2e0404003de9a4cab9753a8805a8fe9320ee6673136ed7f04255fe60bb512'],
+    }),
+    (name, version, {
+        'checksums': ['8b27e6a217e786c6fbe5634d8f3f11bc63e0f80f6a5890f28863d9c45aac311b'],
+    }),
+    ('configobj', '5.0.8', {
+        'checksums': ['6f704434a07dc4f4dc7c9a745172c1cad449feb548febd9f7fe362629c627a97'],
+    }),
+    ('lz4', '4.3.3', {
+        'checksums': ['01fe674ef2889dbb9899d8a67361e0c4a2c833af5aeb37dd505727cf5d2a131e'],
+    }),
+    ('ruamel.yaml.base', '0.3.2', {
+        'checksums': ['88b6edc8ace60c12d98f05fda22e5d9d69ba9a4b531cf54783142151145b0372'],
+    }),
+    ('ruamel.yaml.convert', '0.3.2', {
+        'checksums': ['065ed9492a3189291d5bc0256709afc0231b52e4a01376fc91cf1757560ac9c4'],
+    }),
+    ('ruamel.yaml.cmd', '0.6.5', {
+        'checksums': ['49af59514cb87d7637d1186e31c9345c9947120a9ce49cf6975435aa7abd5aa8'],
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['bin/yaml'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = ["yaml --help"]
+
+sanity_pip_check = True
+
+moduleclass = 'lang'

From 083be61087c8a75f4f2c919a8662e098bdb8bf40 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 4 Sep 2024 20:17:21 +0200
Subject: [PATCH 796/835] don't use ./ in FragGeneScan sanity check commands

---
 .../f/FragGeneScan/FragGeneScan-1.31-GCCcore-12.3.0.eb        | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/easybuild/easyconfigs/f/FragGeneScan/FragGeneScan-1.31-GCCcore-12.3.0.eb b/easybuild/easyconfigs/f/FragGeneScan/FragGeneScan-1.31-GCCcore-12.3.0.eb
index 527ba56e69f..8466e596a3d 100644
--- a/easybuild/easyconfigs/f/FragGeneScan/FragGeneScan-1.31-GCCcore-12.3.0.eb
+++ b/easybuild/easyconfigs/f/FragGeneScan/FragGeneScan-1.31-GCCcore-12.3.0.eb
@@ -31,8 +31,8 @@ sanity_check_paths = {
 }
 
 sanity_check_commands = [
-    './run_FragGeneScan.pl help',
-    './run_FragGeneScan.pl -genome=./example/NC_000913.fna -out=./example/NC_000913-fgs  -complete=1  -train=complete'
+    "run_FragGeneScan.pl help",
+    "run_FragGeneScan.pl -genome=./example/NC_000913.fna -out=./example/NC_000913-fgs  -complete=1  -train=complete",
 ]
 
 moduleclass = 'bio'

From 694f27bc29cc117351f2fa170166b50af5512b4b Mon Sep 17 00:00:00 2001
From: Simon Branford <s.j.branford@bham.ac.uk>
Date: Wed, 4 Sep 2024 19:36:51 +0100
Subject: [PATCH 797/835] adding easyconfigs: OpenFOAM-12-foss-2023a.eb,
 Zoltan-3.901-foss-2023a.eb and patches: OpenFOAM-12-ThirdParty.patch

---
 .../o/OpenFOAM/OpenFOAM-12-ThirdParty.patch   | 397 ++++++++++++++++++
 .../o/OpenFOAM/OpenFOAM-12-foss-2023a.eb      |  38 ++
 .../z/Zoltan/Zoltan-3.901-foss-2023a.eb       |  46 ++
 3 files changed, 481 insertions(+)
 create mode 100644 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-12-ThirdParty.patch
 create mode 100644 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-12-foss-2023a.eb
 create mode 100644 easybuild/easyconfigs/z/Zoltan/Zoltan-3.901-foss-2023a.eb

diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-12-ThirdParty.patch b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-12-ThirdParty.patch
new file mode 100644
index 00000000000..e8a0b33adf7
--- /dev/null
+++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-12-ThirdParty.patch
@@ -0,0 +1,397 @@
+# This patch removes all need for the ThirdParty files of OpenFOAM:
+# we use EB dependencies for everything. It adjusts the paths, variables, etc
+# We also let the install dir, compiler, etc be set by EB.
+# Aligned hunks by Leon Kos and updated by Simon Branford (University of Birmingham).
+# Based on patch for OpenFOAM 5.0 and 4.1 by Kenneth Hoste (HPC-UGent) and Ward Poelmans <wpoely86@gmail.com>
+
+diff -ru OpenFOAM-12-version-12/applications/utilities/postProcessing/graphics/PVReaders/Allwmake OpenFOAM-12/applications/utilities/postProcessing/graphics/PVReaders/Allwmake
+--- OpenFOAM-12-version-12/applications/utilities/postProcessing/graphics/PVReaders/Allwmake
++++ OpenFOAM-12/applications/utilities/postProcessing/graphics/PVReaders/Allwmake
+@@ -11,8 +11,8 @@
+ fi
+ 
+ # Ensure CMake gets the correct C/C++ compilers
+-[ -n "$WM_CC" ] && export CC="$WM_CC"
+-[ -n "$WM_CXX" ] && export CXX="$WM_CXX"
++#[ -n "$WM_CC" ] && export CC="$WM_CC"
++#[ -n "$WM_CXX" ] && export CXX="$WM_CXX"
+ 
+ wmake $targetType vtkPVblockMesh
+ wmake $targetType vtkPVFoam
+diff -ru OpenFOAM-12-version-12/applications/utilities/postProcessing/graphics/PVReaders/CMakeLists.txt OpenFOAM-12/applications/utilities/postProcessing/graphics/PVReaders/CMakeLists.txt
+--- OpenFOAM-12-version-12/applications/utilities/postProcessing/graphics/PVReaders/CMakeLists.txt
++++ OpenFOAM-12/applications/utilities/postProcessing/graphics/PVReaders/CMakeLists.txt
+@@ -2,6 +2,8 @@
+ 
+ PROJECT(PVReaders)
+ 
++FIND_PACKAGE(MPI REQUIRED)
++
+ FIND_PACKAGE(ParaView REQUIRED)
+ 
+ INCLUDE(GNUInstallDirs)
+diff -ru OpenFOAM-12-version-12/etc/bashrc OpenFOAM-12/etc/bashrc
+--- OpenFOAM-12-version-12/etc/bashrc
++++ OpenFOAM-12/etc/bashrc
+@@ -43,12 +43,13 @@
+ #
+ [ "$BASH" ] && bashrcFile=${BASH_SOURCE}
+ [ "$ZSH_NAME" ] && bashrcFile=$0
+-if [ -n "$bashrcFile" ]
+-then
+-    export FOAM_INST_DIR=$(cd $(dirname $bashrcFile)/../.. && pwd -P)
+-else
+-    export FOAM_INST_DIR=$HOME/$WM_PROJECT
+-fi
++#if [ -n "$bashrcFile" ]
++#then
++#    export FOAM_INST_DIR=$(cd $(dirname $bashrcFile)/../.. && pwd -P)
++#else
++#    export FOAM_INST_DIR=$HOME/$WM_PROJECT
++#fi
++# For Easybuild: set by the module
+ unset bashrcFile
+ #
+ # Please set to the appropriate path if the above default is not correct. E.g.,
+diff -ru OpenFOAM-12-version-12/etc/config.sh/gperftools OpenFOAM-12/etc/config.sh/gperftools
+--- OpenFOAM-12-version-12/etc/config.sh/gperftools
++++ OpenFOAM-12/etc/config.sh/gperftools
+@@ -29,13 +29,7 @@
+ #
+ #------------------------------------------------------------------------------
+ 
+-version=svn
+-gperftools_install=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER
+-
+-GPERFTOOLS_VERSION=gperftools-$version
+-GPERFTOOLS_ARCH_PATH=$gperftools_install/$GPERFTOOLS_VERSION
+-
+-export PATH=$GPERFTOOLS_ARCH_PATH/bin:$PATH
+-export LD_LIBRARY_PATH=$GPERFTOOLS_ARCH_PATH/lib:$LD_LIBRARY_PATH
++GPERFTOOLS_VERSION=gperftools-$EBVERSIONGPERFTOOLS
++GPERFTOOLS_ARCH_PATH=$EBROOTGPERFTOOLS
+ 
+ #------------------------------------------------------------------------------
+diff -ru OpenFOAM-12-version-12/etc/config.sh/metis OpenFOAM-12/etc/config.sh/metis
+--- OpenFOAM-12-version-12/etc/config.sh/metis
++++ OpenFOAM-12/etc/config.sh/metis
+@@ -37,32 +37,8 @@
+ # Load functions
+ . $WM_PROJECT_DIR/etc/config.sh/functions
+ 
+-# Find the path to the metis installation
+-case "$METIS_TYPE" in
+-none)
+-    ;;
+-system)
+-    export METIS_VERSION=system
+-    export METIS_ARCH_PATH=/usr
+-    ;;
+-OpenFOAM | ThirdParty)
+-    # Look for the source directory
+-    if [ -z "$METIS_VERSION" ]
+-    then
+-        metisSrcDir=$(_foamMostRecentDir "$WM_THIRD_PARTY_DIR"/metis-*)
+-    else
+-        metisSrcDir=$WM_THIRD_PARTY_DIR/metis-$METIS_VERSION
+-    fi
+-    # Set the version and the installation path
+-    if [ -d "$metisSrcDir" ]
+-    then
+-        export METIS_VERSION=${metisSrcDir##*metis-}
+-        export METIS_ARCH_PATH=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER$WM_PRECISION_OPTION$WM_LABEL_OPTION/metis-$METIS_VERSION
+-    fi
+-    # Clean up
+-    unset metisSrcDir
+-    ;;
+-esac
++export METIS_VERSION=metis-$EBVERSIONMETIS
++export METIS_ARCH_PATH=$EBROOTMETIS
+ 
+ # Unload functions
+ . $WM_PROJECT_DIR/etc/config.sh/functions
+diff -ru OpenFOAM-12-version-12/etc/config.sh/mpi OpenFOAM-12/etc/config.sh/mpi
+--- OpenFOAM-12-version-12/etc/config.sh/mpi
++++ OpenFOAM-12/etc/config.sh/mpi
+@@ -254,6 +254,9 @@
+     _foamAddPath    $MPI_ARCH_PATH/bin64
+     _foamAddLib     $MPI_ARCH_PATH/lib/release
+     ;;
++EASYBUILDMPI)
++    export FOAM_MPI=mpi
++    ;;
+ *)
+     export FOAM_MPI=dummy
+     ;;
+diff -ru OpenFOAM-12-version-12/etc/config.sh/paraview OpenFOAM-12/etc/config.sh/paraview
+--- OpenFOAM-12-version-12/etc/config.sh/paraview
++++ OpenFOAM-12/etc/config.sh/paraview
+@@ -38,117 +38,13 @@
+         ) \
+         && PATH="$cleaned"
+ 
+-# Detect the most recent version of cmake available and add to the PATH
+-cmakeDir=$(_foamMostRecentDir "$WM_THIRD_PARTY_DIR"/platforms/$WM_ARCH$WM_COMPILER/cmake-*)
+-if [ -n "$cmakeDir" ]
+-then
+-    export PATH=$cmakeDir/bin:$PATH
+-fi
+-unset cmakeDir
+-
+-# Set up the paraview environment
+-case "$ParaView_TYPE" in
+-none)
+-    ;;
+-
+-system)
+-
+-    # Look for a paraview installation
+-    if pvserverExe=$(which pvserver 2> /dev/null)
+-    then
+-        paraviewBinDir=$(dirname $pvserverExe)
+-        paraviewBinDir=$(cd $paraviewBinDir && pwd -P)
+-    fi
+-
+-    # Set the environment
+-    if [ -d "$paraviewBinDir" ]
+-    then
+-        export ParaView_DIR=$(dirname $paraviewBinDir)
+-        export ParaView_LIB_DIR=$(unset LD_LIBRARY_PATH && \
+-                                  ldd $paraviewBinDir/paraview | \
+-                                  grep -o "/.*/libpqCore-pv.*.so" | \
+-                                  xargs dirname)
+-        export ParaView_VERSION=$(unset LD_LIBRARY_PATH && \
+-                                  pvserver --version 2> /dev/null | \
+-                                  awk '{print $NF}')
+-        export ParaView_MAJOR=${ParaView_VERSION%.*}
+-        export ParaView_INCLUDE_DIR=$ParaView_DIR/include/paraview-$ParaView_MAJOR
+-        export PV_PLUGIN_PATH=$FOAM_LIBBIN/paraview-$ParaView_MAJOR
+-
+-        # Add to the library path
+-        export LD_LIBRARY_PATH=$ParaView_LIB_DIR:$PV_PLUGIN_PATH:$LD_LIBRARY_PATH
+-    fi
+-
+-    unset pvserverExe paraviewBinDir
+-    ;;
+-
+-paraviewopenfoam)
+-
+-    # Look for a paraview installation. The version should be set externally.
+-    if [ -n "$ParaView_VERSION" ]
+-    then
+-        export ParaView_MAJOR=${ParaView_VERSION%.*}
+-        paraviewDir=/opt/paraviewopenfoam$(echo "$ParaView_MAJOR" | tr -d '.')
+-    fi
+-
+-    # Set the environment
+-    if [ -d "$paraviewDir" ]
+-    then
+-        export ParaView_DIR=$paraviewDir
+-        export ParaView_LIB_DIR=$(echo "$ParaView_DIR"/lib* | tr ' ' ':')
+-        export ParaView_INCLUDE_DIR=$ParaView_DIR/include/paraview-$ParaView_MAJOR
+-        export PV_PLUGIN_PATH=$FOAM_LIBBIN/paraview-$ParaView_MAJOR
+-
+-        # Add to the path and the library path
+-        export PATH=$ParaView_DIR/bin:$PATH
+-        export LD_LIBRARY_PATH=$ParaView_LIB_DIR:$PV_PLUGIN_PATH:$LD_LIBRARY_PATH
+-    fi
+-
+-    unset paraviewDir
+-    ;;
+-
+-OpenFOAM | ThirdParty)
+-
+-    # Look for a paraview installation
+-    if [ -z "$ParaView_VERSION" ]
+-    then
+-        paraviewDir=$(_foamMostRecentDir "$WM_THIRD_PARTY_DIR"/platforms/$WM_ARCH$WM_COMPILER/ParaView-*)
+-    else
+-        paraviewDir=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/ParaView-$ParaView_VERSION
+-    fi
+-
+-    # Set the environment
+-    if [ -d "$paraviewDir" ]
+-    then
+-        export ParaView_DIR=$paraviewDir
+-        export ParaView_LIB_DIR=$(echo "$ParaView_DIR"/lib* | tr ' ' ':')
+-        export ParaView_VERSION=${paraviewDir##*ParaView-}
+-        export ParaView_MAJOR=${ParaView_VERSION%.*}
+-        export ParaView_INCLUDE_DIR=$paraviewDir/include/paraview-$ParaView_MAJOR
+-        export PV_PLUGIN_PATH=$FOAM_LIBBIN/paraview-$ParaView_MAJOR
+-
+-        # Add to the path and the library path
+-        export PATH=$ParaView_DIR/bin:$PATH
+-        export LD_LIBRARY_PATH=$ParaView_LIB_DIR:$PV_PLUGIN_PATH:$LD_LIBRARY_PATH
+-
+-        # Add in python libraries if required
+-        paraviewPython=$ParaView_DIR/Utilities/VTKPythonWrapping
+-        if [ -r "$paraviewPython" ]
+-        then
+-            if [ "$PYTHONPATH" ]
+-            then
+-                export PYTHONPATH=$PYTHONPATH:$paraviewPython:$ParaView_LIB_DIR
+-            else
+-                export PYTHONPATH=$paraviewPython:$ParaView_LIB_DIR
+-            fi
+-        fi
+-        unset paraviewPython
+-    fi
+-
+-    unset paraviewDir
+-    ;;
+-
+-esac
++export ParaView_VERSION=$EBVERSIONPARAVIEW
++export ParaView_MAJOR=${ParaView_VERSION%.*}
++export ParaView_DIR=$EBROOTPARAVIEW
++export ParaView_LIB_DIR=$ParaView_DIR/lib
++export ParaView_INCLUDE_DIR=$ParaView_DIR/include/paraview-$ParaView_MAJOR
++export PV_PLUGIN_PATH=$FOAM_LIBBIN/paraview-$ParaView_MAJOR
++export LD_LIBRARY_PATH=$ParaView_LIB_DIR:$PV_PLUGIN_PATH:$LD_LIBRARY_PATH
+ 
+ # Report
+ if [ "$FOAM_VERBOSE" ] && [ "$PS1" ] && [ -d "$ParaView_DIR" ]
+diff -ru OpenFOAM-12-version-12/etc/config.sh/scotch OpenFOAM-12/etc/config.sh/scotch
+--- OpenFOAM-12-version-12/etc/config.sh/scotch
++++ OpenFOAM-12/etc/config.sh/scotch
+@@ -37,32 +37,8 @@
+ # Load functions
+ . $WM_PROJECT_DIR/etc/config.sh/functions
+ 
+-# Find the path to the scotch installation
+-case "$SCOTCH_TYPE" in
+-none)
+-    ;;
+-system)
+-    export SCOTCH_VERSION=system
+-    export SCOTCH_ARCH_PATH=/usr
+-    ;;
+-OpenFOAM | ThirdParty)
+-    # Look for the source directory
+-    if [ -z "$SCOTCH_VERSION" ]
+-    then
+-        scotchSrcDir=$(_foamMostRecentDir "$WM_THIRD_PARTY_DIR"/scotch_*)
+-    else
+-        scotchSrcDir=$WM_THIRD_PARTY_DIR/scotch_$SCOTCH_VERSION
+-    fi
+-    # Set the version and the installation path
+-    if [ -d "$scotchSrcDir" ]
+-    then
+-        export SCOTCH_VERSION=${scotchSrcDir##*scotch_}
+-        export SCOTCH_ARCH_PATH=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER$WM_PRECISION_OPTION$WM_LABEL_OPTION/scotch_$SCOTCH_VERSION
+-    fi
+-    # Clean up
+-    unset scotchSrcDir
+-    ;;
+-esac
++export SCOTCH_VERSION=scotch_$EBVERSIONSCOTCH
++export SCOTCH_ARCH_PATH=$EBROOTSCOTCH
+ 
+ # Unload functions
+ . $WM_PROJECT_DIR/etc/config.sh/functions
+diff -ru OpenFOAM-12-version-12/etc/config.sh/zoltan OpenFOAM-12/etc/config.sh/zoltan
+--- OpenFOAM-12-version-12/etc/config.sh/zoltan
++++ OpenFOAM-12/etc/config.sh/zoltan
+@@ -37,32 +37,8 @@
+ # Load functions
+ . $WM_PROJECT_DIR/etc/config.sh/functions
+ 
+-# Find the path to the zoltan installation
+-case "$ZOLTAN_TYPE" in
+-none)
+-    ;;
+-system)
+-    export ZOLTAN_VERSION=system
+-    export ZOLTAN_ARCH_PATH=/usr
+-    ;;
+-OpenFOAM | ThirdParty)
+-    # Look for the source directory
+-    if [ -z "$ZOLTAN_VERSION" ]
+-    then
+-        zoltanSrcDir=$(_foamMostRecentDir "$WM_THIRD_PARTY_DIR"/Zoltan-*)
+-    else
+-        zoltanSrcDir=$WM_THIRD_PARTY_DIR/Zoltan-$ZOLTAN_VERSION
+-    fi
+-    # Set the version and the installation path
+-    if [ -d "$zoltanSrcDir" ]
+-    then
+-        export ZOLTAN_VERSION=${zoltanSrcDir##*Zoltan-}
+-        export ZOLTAN_ARCH_PATH=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER$WM_PRECISION_OPTION$WM_LABEL_OPTION/Zoltan-$ZOLTAN_VERSION
+-    fi
+-    # Clean up
+-    unset zoltanSrcDir
+-    ;;
+-esac
++export ZOLTAN_VERSION=Zoltan-$EBVERSIONZOLTAN
++export ZOLTAN_ARCH_PATH=$EBROOTZOLTAN
+ 
+ # Unload functions
+ . $WM_PROJECT_DIR/etc/config.sh/functions
+diff -ru OpenFOAM-12-version-12/etc/config.sh/settings OpenFOAM-12/etc/config.sh/settings
+--- OpenFOAM-12-version-12/etc/config.sh/settings
++++ OpenFOAM-12/etc/config.sh/settings
+@@ -63,11 +63,11 @@
+         64)
+             WM_ARCH=linux64
+             export WM_COMPILER_LIB_ARCH=64
+-            export WM_CC='gcc'
+-            export WM_CXX='g++'
+-            export WM_CFLAGS='-m64 -fPIC'
+-            export WM_CXXFLAGS='-m64 -fPIC -std=c++0x'
+-            export WM_LDFLAGS='-m64'
++            export WM_CC=$CC
++            export WM_CXX=$CXX
++            export WM_CFLAGS=$CFLAGS
++            export WM_CXXFLAGS=$CXXFLAGS
++            export WM_LDFLAGS=$LDFLAGS
+             ;;
+         *)
+             echo "Unknown WM_ARCH_OPTION '$WM_ARCH_OPTION', should be 32 or 64"\
+diff -ru OpenFOAM-12-version-12/src/parallel/decompose/ptscotch/Make/options OpenFOAM-12/src/parallel/decompose/ptscotch/Make/options
+--- OpenFOAM-12-version-12/src/parallel/decompose/ptscotch/Make/options
++++ OpenFOAM-12/src/parallel/decompose/ptscotch/Make/options
+@@ -6,15 +6,7 @@
+     $(PFLAGS) $(PINC) \
+     -I$(FOAM_SRC)/Pstream/mpi/lnInclude \
+     -I$(SCOTCH_ARCH_PATH)/include/$(FOAM_MPI) \
+-    -I$(SCOTCH_ARCH_PATH)/include \
+-    -I$(or $(PTSCOTCH_INCLUDE_DIR),/usr/include/scotch) \
+     -I../decompositionMethods/lnInclude
+ 
+ LIB_LIBS = \
+-    -L$(SCOTCH_ARCH_PATH)/lib \
+-    $(if $(PTSCOTCH_LIB_DIR),-L$(PTSCOTCH_LIB_DIR)) \
+-    -L$(FOAM_EXT_LIBBIN)/$(FOAM_MPI) \
+-    -lptscotch \
+-    -lptscotcherrexit \
+-    -lscotch \
+-    -lrt
++    -L$(SCOTCH_ARCH_PATH)/lib -L$(FOAM_EXT_LIBBIN)/$(FOAM_MPI) -lptscotch -lptscotcherrexit -lscotch ${LINK_FLAGS} -lrt
+diff -ru OpenFOAM-12-version-12/src/parallel/decompose/ptscotch/ptscotch.C OpenFOAM-12/src/parallel/decompose/ptscotch/ptscotch.C
+--- OpenFOAM-12-version-12/src/parallel/decompose/ptscotch/ptscotch.C
++++ OpenFOAM-12/src/parallel/decompose/ptscotch/ptscotch.C
+@@ -31,10 +31,11 @@
+ #include "SubField.H"
+ #include "PstreamGlobals.H"
+ 
++#include <mpi.h>
++#include <ptscotch.h>
++
+ extern "C"
+ {
+     #include <stdio.h>
+-    #include <mpi.h>
+-    #include "ptscotch.h"
+ }
+
+diff -ru OpenFOAM-12-version-12/src/parallel/decompose/scotch/Make/options OpenFOAM-12/src/parallel/decompose/scotch/Make/options
+--- OpenFOAM-12-version-12/src/parallel/decompose/scotch/Make/options
++++ OpenFOAM-12/src/parallel/decompose/scotch/Make/options
+@@ -6,7 +6,6 @@
+ EXE_INC = \
+     $(PFLAGS) $(PINC) \
+     -I$(SCOTCH_ARCH_PATH)/include \
+-    -I$(or $(SCOTCH_INCLUDE_DIR),/usr/include/scotch) \
+     -I../decompositionMethods/lnInclude
+ 
+ LIB_LIBS = \ 
diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-12-foss-2023a.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-12-foss-2023a.eb
new file mode 100644
index 00000000000..ed565315859
--- /dev/null
+++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-12-foss-2023a.eb
@@ -0,0 +1,38 @@
+name = 'OpenFOAM'
+version = '12'
+
+homepage = 'https://www.openfoam.org/'
+description = """OpenFOAM is a free, open source CFD software package.
+ OpenFOAM has an extensive range of features to solve anything from complex fluid flows
+ involving chemical reactions, turbulence and heat transfer,
+ to solid dynamics and electromagnetics."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+toolchainopts = {'vectorize': False}
+
+source_urls = ['https://github.com/OpenFOAM/OpenFOAM-%(version_major)s/archive']
+sources = ['version-%(version)s.tar.gz']
+patches = ['OpenFOAM-12-ThirdParty.patch']
+checksums = [
+    {'version-12.tar.gz': 'e59fad54c62e64f1bb89dbaebe5f99a76dc0a6a91d9aad86042a7c4cef6d0744'},
+    {'OpenFOAM-12-ThirdParty.patch': 'b8a9abf3b8479d32d87654d833501f54abe57ceb9f06f7d2412a3e52d20108ec'},
+]
+
+builddependencies = [
+    ('Bison', '3.8.2'),
+    ('CMake', '3.26.3'),
+    ('flex', '2.6.4'),
+]
+
+dependencies = [
+    ('ncurses', '6.4'),
+    # OpenFOAM requires 64 bit METIS using 32 bit indexes (array indexes)
+    ('METIS', '5.1.0'),
+    ('SCOTCH', '7.0.3'),
+    ('CGAL', '5.6'),
+    ('ParaView', '5.11.2'),
+    ('gnuplot', '5.4.8'),
+    ('Zoltan', '3.901'),
+]
+
+moduleclass = 'cae'
diff --git a/easybuild/easyconfigs/z/Zoltan/Zoltan-3.901-foss-2023a.eb b/easybuild/easyconfigs/z/Zoltan/Zoltan-3.901-foss-2023a.eb
new file mode 100644
index 00000000000..57432d0e0ce
--- /dev/null
+++ b/easybuild/easyconfigs/z/Zoltan/Zoltan-3.901-foss-2023a.eb
@@ -0,0 +1,46 @@
+# This easyconfig was created by the BEAR Software team at the University of Birmingham.
+easyblock = 'ConfigureMake'
+
+name = 'Zoltan'
+version = '3.901'
+
+homepage = "https://sandialabs.github.io/Zoltan/"
+description = """Zoltan Dynamic Load Balancing and Graph Algorithm Toolkit"""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+toolchainopts = {'pic': True}
+
+github_account = 'sandialabs'
+source_urls = [GITHUB_SOURCE]
+sources = ['v%(version)s.tar.gz']
+checksums = ['030c22d9f7532d3076e40cba1f03a63b2ee961d8cc9a35149af4a3684922a910']
+
+dependencies = [
+    ('gzip', '1.12'),
+    ('SCOTCH', '7.0.3'),
+    ('ParMETIS', '4.0.3'),
+]
+
+preconfigopts = 'mkdir build && cd build &&'
+configure_cmd = '../configure'
+configopts = ' '.join([
+    '--enable-gzip',
+    '--with-scotch',
+    '--with-scotch-incdir=$EBROOTSCOTCH/include',
+    '--with-scotch-libdir=$EBROOTSCOTCH/lib',
+    '--with-parmetis',
+    '--with-parmetis-incdir=$EBROOTPARMETIS/include',
+    '--with-parmetis-libdir=$EBROOTPARMETIS/lib',
+    '--disable-examples',
+    '--disable-tests',
+])
+prebuildopts = 'cd build &&'
+buildopts = 'everything'
+preinstallopts = 'cd build &&'
+
+sanity_check_paths = {
+    'files': ['lib/libzoltan.a', 'include/zoltan.h'],
+    'dirs': [],
+}
+
+moduleclass = 'cae'

From e54970b14ffb1d823f11deb78a83ad972c3d6705 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jan=20Andr=C3=A9=20Reuter?= <j.reuter@fz-juelich.de>
Date: Thu, 5 Sep 2024 08:59:18 +0200
Subject: [PATCH 798/835] {perf} OTF2: Toolchain Python instead of system
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Add Python as a dependency to OTF2 versions to ensure that the toolchain
Python is used. To verify, a sanity check is added which ensures that
the OTF2 Python module can be loaded. As 'six' is required, newer
toolchains also need Python-bundle-PyPI.

Signed-off-by: Jan André Reuter <j.reuter@fz-juelich.de>
---
 .../easyconfigs/o/OTF2/OTF2-3.0-GCCcore-11.3.0.eb      |  9 +++++++--
 .../easyconfigs/o/OTF2/OTF2-3.0.2-GCCcore-11.2.0.eb    |  8 +++++++-
 .../easyconfigs/o/OTF2/OTF2-3.0.2-GCCcore-11.3.0.eb    |  9 +++++++--
 .../easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-12.2.0.eb    |  9 +++++++--
 .../easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-12.3.0.eb    | 10 ++++++++--
 .../easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-13.2.0.eb    | 10 ++++++++--
 6 files changed, 44 insertions(+), 11 deletions(-)

diff --git a/easybuild/easyconfigs/o/OTF2/OTF2-3.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/o/OTF2/OTF2-3.0-GCCcore-11.3.0.eb
index 6e982449e9e..fe8a5244c12 100644
--- a/easybuild/easyconfigs/o/OTF2/OTF2-3.0-GCCcore-11.3.0.eb
+++ b/easybuild/easyconfigs/o/OTF2/OTF2-3.0-GCCcore-11.3.0.eb
@@ -3,6 +3,7 @@
 # Copyright:: Copyright 2013-2019 Juelich Supercomputing Centre, Germany
 # Authors::   Bernd Mohr <b.mohr@fz-juelich.de>
 # Markus Geimer <m.geimer@fz-juelich.de>
+# Jan Andre Reuter <j.reuter@fz-juelich.de>
 # License::   3-clause BSD
 #
 # This work is based on experiences from the UNITE project
@@ -34,17 +35,21 @@ builddependencies = [
 dependencies = [
     # SIONlib container support (optional):
     ('SIONlib', '1.7.7', '-tools'),
+    # OTF2 Python bindings
+    ('Python', '3.10.4'),
 ]
 
+local_pyshortver = '3.10'
 configopts = '--enable-shared'
 
+modextrapaths = {'PYTHONPATH': ['lib64/python%s/site-packages' % local_pyshortver]}
 
 sanity_check_paths = {
     'files': ['bin/otf2-config', 'include/otf2/otf2.h',
               'lib/libotf2.a', 'lib/libotf2.%s' % SHLIB_EXT],
     'dirs': [],
 }
-
-sanity_check_commands = ['%(namelower)s-config --help']
+sanity_check_commands = ['%(namelower)s-config --help',
+                         'python -c "import %(namelower)s"']
 
 moduleclass = 'perf'
diff --git a/easybuild/easyconfigs/o/OTF2/OTF2-3.0.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/o/OTF2/OTF2-3.0.2-GCCcore-11.2.0.eb
index 7c4d60f0514..488b8e0de0d 100644
--- a/easybuild/easyconfigs/o/OTF2/OTF2-3.0.2-GCCcore-11.2.0.eb
+++ b/easybuild/easyconfigs/o/OTF2/OTF2-3.0.2-GCCcore-11.2.0.eb
@@ -3,6 +3,7 @@
 # Copyright:: Copyright 2013-2019 Juelich Supercomputing Centre, Germany
 # Authors::   Bernd Mohr <b.mohr@fz-juelich.de>
 # Markus Geimer <m.geimer@fz-juelich.de>
+# Jan Andre Reuter <j.reuter@fz-juelich.de>
 # License::   3-clause BSD
 #
 # This work is based on experiences from the UNITE project
@@ -34,17 +35,22 @@ builddependencies = [
 dependencies = [
     # SIONlib container support (optional):
     ('SIONlib', '1.7.7', '-tools'),
+    # OTF2 Python bindings
+    ('Python', '3.9.6'),
 ]
 
+local_pyshortver = '3.9'
 configopts = '--enable-shared'
 
+modextrapaths = {'PYTHONPATH': ['lib64/python%s/site-packages' % local_pyshortver]}
 
 sanity_check_paths = {
     'files': ['bin/otf2-config', 'include/otf2/otf2.h',
               'lib/libotf2.a', 'lib/libotf2.%s' % SHLIB_EXT],
     'dirs': [],
 }
+sanity_check_commands = ['%(namelower)s-config --help',
+                         'python -c "import %(namelower)s"']
 
-sanity_check_commands = ['%(namelower)s-config --help']
 
 moduleclass = 'perf'
diff --git a/easybuild/easyconfigs/o/OTF2/OTF2-3.0.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/o/OTF2/OTF2-3.0.2-GCCcore-11.3.0.eb
index 61eba75f5f0..6756aa72eac 100644
--- a/easybuild/easyconfigs/o/OTF2/OTF2-3.0.2-GCCcore-11.3.0.eb
+++ b/easybuild/easyconfigs/o/OTF2/OTF2-3.0.2-GCCcore-11.3.0.eb
@@ -3,6 +3,7 @@
 # Copyright:: Copyright 2013-2019 Juelich Supercomputing Centre, Germany
 # Authors::   Bernd Mohr <b.mohr@fz-juelich.de>
 # Markus Geimer <m.geimer@fz-juelich.de>
+# Jan Andre Reuter <j.reuter@fz-juelich.de>
 # License::   3-clause BSD
 #
 # This work is based on experiences from the UNITE project
@@ -34,17 +35,21 @@ builddependencies = [
 dependencies = [
     # SIONlib container support (optional):
     ('SIONlib', '1.7.7', '-tools'),
+    # OTF2 Python bindings
+    ('Python', '3.10.4'),
 ]
 
+local_pyshortver = '3.10'
 configopts = '--enable-shared'
 
+modextrapaths = {'PYTHONPATH': ['lib64/python%s/site-packages' % local_pyshortver]}
 
 sanity_check_paths = {
     'files': ['bin/otf2-config', 'include/otf2/otf2.h',
               'lib/libotf2.a', 'lib/libotf2.%s' % SHLIB_EXT],
     'dirs': [],
 }
-
-sanity_check_commands = ['%(namelower)s-config --help']
+sanity_check_commands = ['%(namelower)s-config --help',
+                         'python -c "import %(namelower)s"']
 
 moduleclass = 'perf'
diff --git a/easybuild/easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-12.2.0.eb b/easybuild/easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-12.2.0.eb
index 54478bf62fa..f4c842e0450 100644
--- a/easybuild/easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-12.2.0.eb
+++ b/easybuild/easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-12.2.0.eb
@@ -3,6 +3,7 @@
 # Copyright:: Copyright 2013-2019 Juelich Supercomputing Centre, Germany
 # Authors::   Bernd Mohr <b.mohr@fz-juelich.de>
 # Markus Geimer <m.geimer@fz-juelich.de>
+# Jan Andre Reuter <j.reuter@fz-juelich.de>
 # License::   3-clause BSD
 #
 # This work is based on experiences from the UNITE project
@@ -34,17 +35,21 @@ builddependencies = [
 dependencies = [
     # SIONlib container support (optional):
     ('SIONlib', '1.7.7', '-tools'),
+    # OTF2 Python bindings
+    ('Python', '3.10.8'),
 ]
 
+local_pyshortver = '3.10'
 configopts = '--enable-shared'
 
+modextrapaths = {'PYTHONPATH': ['lib64/python%s/site-packages' % local_pyshortver]}
 
 sanity_check_paths = {
     'files': ['bin/otf2-config', 'include/otf2/otf2.h',
               'lib/libotf2.a', 'lib/libotf2.%s' % SHLIB_EXT],
     'dirs': [],
 }
-
-sanity_check_commands = ['%(namelower)s-config --help']
+sanity_check_commands = ['%(namelower)s-config --help',
+                         'python -c "import %(namelower)s"']
 
 moduleclass = 'perf'
diff --git a/easybuild/easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-12.3.0.eb b/easybuild/easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-12.3.0.eb
index 17595d97acb..db786b12a41 100644
--- a/easybuild/easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-12.3.0.eb
+++ b/easybuild/easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-12.3.0.eb
@@ -3,6 +3,7 @@
 # Copyright:: Copyright 2013-2019 Juelich Supercomputing Centre, Germany
 # Authors::   Bernd Mohr <b.mohr@fz-juelich.de>
 # Markus Geimer <m.geimer@fz-juelich.de>
+# Jan Andre Reuter <j.reuter@fz-juelich.de>
 # License::   3-clause BSD
 #
 # This work is based on experiences from the UNITE project
@@ -34,17 +35,22 @@ builddependencies = [
 dependencies = [
     # SIONlib container support (optional):
     ('SIONlib', '1.7.7', '-tools'),
+    # OTF2 Python bindings
+    ('Python', '3.11.3'),
+    ('Python-bundle-PyPI', '2023.06'),
 ]
 
+local_pyshortver = '3.11'
 configopts = '--enable-shared'
 
+modextrapaths = {'PYTHONPATH': ['lib64/python%s/site-packages' % local_pyshortver]}
 
 sanity_check_paths = {
     'files': ['bin/otf2-config', 'include/otf2/otf2.h',
               'lib/libotf2.a', 'lib/libotf2.%s' % SHLIB_EXT],
     'dirs': [],
 }
-
-sanity_check_commands = ['%(namelower)s-config --help']
+sanity_check_commands = ['%(namelower)s-config --help',
+                         'python -c "import %(namelower)s"']
 
 moduleclass = 'perf'
diff --git a/easybuild/easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-13.2.0.eb b/easybuild/easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-13.2.0.eb
index 48cbf931ec5..c5108c8daca 100644
--- a/easybuild/easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-13.2.0.eb
+++ b/easybuild/easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-13.2.0.eb
@@ -3,6 +3,7 @@
 # Copyright:: Copyright 2013-2019 Juelich Supercomputing Centre, Germany
 # Authors::   Bernd Mohr <b.mohr@fz-juelich.de>
 # Markus Geimer <m.geimer@fz-juelich.de>
+# Jan Andre Reuter <j.reuter@fz-juelich.de>
 # License::   3-clause BSD
 #
 # This work is based on experiences from the UNITE project
@@ -34,17 +35,22 @@ builddependencies = [
 dependencies = [
     # SIONlib container support (optional):
     ('SIONlib', '1.7.7', '-tools'),
+    # OTF2 Python bindings
+    ('Python', '3.11.5'),
+    ('Python-bundle-PyPI', '2023.10'),
 ]
 
+local_pyshortver = '3.11'
 configopts = '--enable-shared'
 
+modextrapaths = {'PYTHONPATH': ['lib64/python%s/site-packages' % local_pyshortver]}
 
 sanity_check_paths = {
     'files': ['bin/otf2-config', 'include/otf2/otf2.h',
               'lib/libotf2.a', 'lib/libotf2.%s' % SHLIB_EXT],
     'dirs': [],
 }
-
-sanity_check_commands = ['%(namelower)s-config --help']
+sanity_check_commands = ['%(namelower)s-config --help',
+                         'python -c "import %(namelower)s"']
 
 moduleclass = 'perf'

From d76db40033304ffd748d44a34b61b504bdc530e5 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jan=20Andr=C3=A9=20Reuter?= <j.reuter@fz-juelich.de>
Date: Thu, 22 Aug 2024 17:54:50 +0200
Subject: [PATCH 799/835] {perf}[GCCcore/13.3.0,gompi/2024a] Add Score-P with
 dependencies.
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Add Score-P 8.4, OTF2 3.0.3, OPARI2 2.0.8, CubeLib 4.8.2, CubeWriter 4.8.2, PAPI 7.1.0, PDT 3.25.2, SIONlib 1.7.7, UCX-CUDA 1.16.0.

For OTF2, a patch updates the py-compile file used to fix the
removal of the imp module in Python 3.12. This prevents install failures.

Signed-off-by: Jan André Reuter <j.reuter@fz-juelich.de>
---
 .../c/CubeLib/CubeLib-4.8.2-GCCcore-13.3.0.eb |  52 ++++
 .../CubeWriter-4.8.2-GCCcore-13.3.0.eb        |  52 ++++
 .../o/OPARI2/OPARI2-2.0.8-GCCcore-13.3.0.eb   |  45 ++++
 .../o/OTF2/OTF2-3.0.3-GCCcore-13.3.0.eb       |  55 ++++
 .../o/OTF2/otf2-3.0.3-update-py-compile.patch | 252 ++++++++++++++++++
 .../p/PAPI/PAPI-7.1.0-GCCcore-13.3.0.eb       |  53 ++++
 .../p/PDT/PDT-3.25.2-GCCcore-13.3.0.eb        |  40 +++
 .../SIONlib-1.7.7-GCCcore-13.3.0-tools.eb     |  51 ++++
 .../Score-P-8.4-gompi-2024a-CUDA-12.6.0.eb    |  57 ++++
 .../s/Score-P/Score-P-8.4-gompi-2024a.eb      |  55 ++++
 ...-CUDA-1.16.0-GCCcore-13.3.0-CUDA-12.6.0.eb |  41 +++
 ....16.0_link_against_existing_UCX_libs.patch |  93 +++++++
 12 files changed, 846 insertions(+)
 create mode 100644 easybuild/easyconfigs/c/CubeLib/CubeLib-4.8.2-GCCcore-13.3.0.eb
 create mode 100644 easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.8.2-GCCcore-13.3.0.eb
 create mode 100644 easybuild/easyconfigs/o/OPARI2/OPARI2-2.0.8-GCCcore-13.3.0.eb
 create mode 100644 easybuild/easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-13.3.0.eb
 create mode 100644 easybuild/easyconfigs/o/OTF2/otf2-3.0.3-update-py-compile.patch
 create mode 100644 easybuild/easyconfigs/p/PAPI/PAPI-7.1.0-GCCcore-13.3.0.eb
 create mode 100644 easybuild/easyconfigs/p/PDT/PDT-3.25.2-GCCcore-13.3.0.eb
 create mode 100644 easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-13.3.0-tools.eb
 create mode 100644 easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2024a-CUDA-12.6.0.eb
 create mode 100644 easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2024a.eb
 create mode 100644 easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.16.0-GCCcore-13.3.0-CUDA-12.6.0.eb
 create mode 100644 easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.16.0_link_against_existing_UCX_libs.patch

diff --git a/easybuild/easyconfigs/c/CubeLib/CubeLib-4.8.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/c/CubeLib/CubeLib-4.8.2-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..6b2414be446
--- /dev/null
+++ b/easybuild/easyconfigs/c/CubeLib/CubeLib-4.8.2-GCCcore-13.3.0.eb
@@ -0,0 +1,52 @@
+# Copyright 2019-2024 Juelich Supercomputing Centre, Germany
+# Copyright 2023-2024 TU Dresden, Germany
+# Authors::   Markus Geimer <m.geimer@fz-juelich.de>
+#             Alexander Grund <alexander.grund@tu-dresden.de>
+#             Jan André Reuter <j.reuter@fz-juelich.de>
+# License::   3-clause BSD
+#
+# This work is based on experiences from the UNITE project
+# http://apps.fz-juelich.de/unite/
+
+easyblock = 'EB_Score_minus_P'
+
+name = 'CubeLib'
+version = '4.8.2'
+
+homepage = 'https://www.scalasca.org/software/cube-4.x/download.html'
+description = """
+ Cube, which is used as performance report explorer for Scalasca and Score-P,
+ is a generic tool for displaying a multi-dimensional performance space
+ consisting of the dimensions (i) performance metric, (ii) call path, and
+ (iii) system resource. Each dimension can be represented as a tree, where
+ non-leaf nodes of the tree can be collapsed or expanded to achieve the
+ desired level of granularity.
+
+ This module provides the Cube general purpose C++ library component and
+ command-line tools.
+"""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+source_urls = ['https://apps.fz-juelich.de/scalasca/releases/cube/%(version_major_minor)s/dist']
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['d6fdef57b1bc9594f1450ba46cf08f431dd0d4ae595c47e2f3454e17e4ae74f4']
+
+builddependencies = [
+    # use same binutils version that was used when building GCCcore
+    ('binutils', '2.42'),
+    ('pkgconf', '2.2.0'),
+]
+dependencies = [
+    ('zlib', '1.3.1'),
+]
+
+configopts = '--enable-shared'
+
+sanity_check_paths = {
+    'files': ['bin/cubelib-config',
+              'lib/libcube4.a', 'lib/libcube4.%s' % SHLIB_EXT],
+    'dirs': ['include/cubelib'],
+}
+
+moduleclass = 'perf'
diff --git a/easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.8.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.8.2-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..e030f21ba6c
--- /dev/null
+++ b/easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.8.2-GCCcore-13.3.0.eb
@@ -0,0 +1,52 @@
+# Copyright:: Copyright 2019-2024 Juelich Supercomputing Centre, Germany
+#             Copyright 2023-2024 TU Dresden, Germany
+# Authors::   Markus Geimer <m.geimer@fz-juelich.de>
+#             Alexander Grund <alexander.grund@tu-dresden.de>
+#             Jan André Reuter <j.reuter@fz-juelich.de>
+# License::   3-clause BSD
+#
+# This work is based on experiences from the UNITE project
+# http://apps.fz-juelich.de/unite/
+
+easyblock = 'EB_Score_minus_P'
+
+name = 'CubeWriter'
+version = '4.8.2'
+
+homepage = 'https://www.scalasca.org/software/cube-4.x/download.html'
+description = """
+ Cube, which is used as performance report explorer for Scalasca and Score-P,
+ is a generic tool for displaying a multi-dimensional performance space
+ consisting of the dimensions (i) performance metric, (ii) call path, and
+ (iii) system resource. Each dimension can be represented as a tree, where
+ non-leaf nodes of the tree can be collapsed or expanded to achieve the
+ desired level of granularity.
+
+ This module provides the Cube high-performance C writer library component.
+"""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+source_urls = ['https://apps.fz-juelich.de/scalasca/releases/cube/%(version_major_minor)s/dist']
+sources = ['cubew-%(version)s.tar.gz']
+checksums = ['4f3bcf0622c2429b8972b5eb3f14d79ec89b8161e3c1cc5862ceda417d7975d2']
+
+builddependencies = [
+    # use same binutils version that was used when building GCCcore
+    ('binutils', '2.42'),
+    ('pkgconf', '2.2.0'),
+]
+
+dependencies = [
+    ('zlib', '1.3.1'),
+]
+
+configopts = '--enable-shared'
+
+sanity_check_paths = {
+    'files': ['bin/cubew-config',
+              'lib/libcube4w.a', 'lib/libcube4w.%s' % SHLIB_EXT],
+    'dirs': ['include/cubew'],
+}
+
+moduleclass = 'perf'
diff --git a/easybuild/easyconfigs/o/OPARI2/OPARI2-2.0.8-GCCcore-13.3.0.eb b/easybuild/easyconfigs/o/OPARI2/OPARI2-2.0.8-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..503a56951d0
--- /dev/null
+++ b/easybuild/easyconfigs/o/OPARI2/OPARI2-2.0.8-GCCcore-13.3.0.eb
@@ -0,0 +1,45 @@
+# #
+# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild
+#
+# Copyright:: Copyright 2013-2024 Juelich Supercomputing Centre, Germany
+# Authors::   Bernd Mohr <b.mohr@fz-juelich.de>
+# Markus Geimer <m.geimer@fz-juelich.de>
+# Jan André Reuter <j.reuter@fz-juelich.de>
+# License::   3-clause BSD
+#
+# This work is based on experiences from the UNITE project
+# http://apps.fz-juelich.de/unite/
+# #
+
+easyblock = 'ConfigureMake'
+
+name = 'OPARI2'
+version = '2.0.8'
+
+homepage = 'https://www.score-p.org'
+description = """
+ OPARI2, the successor of Forschungszentrum Juelich's OPARI, is a
+ source-to-source instrumentation tool for OpenMP and hybrid codes.
+ It surrounds OpenMP directives and runtime library calls with calls
+ to the POMP2 measurement interface.
+"""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+source_urls = ['http://perftools.pages.jsc.fz-juelich.de/cicd/%(namelower)s/tags/%(namelower)s-%(version)s']
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['196e59a2a625e6c795a6124c61e784bad142f9f38df0b4fa4d435ba9b9c19721']
+
+builddependencies = [
+    ('binutils', '2.42'),
+]
+
+
+sanity_check_paths = {
+    'files': ['bin/opari2', 'include/opari2/pomp2_lib.h'],
+    'dirs': [],
+}
+
+sanity_check_commands = ['opari2-config --help']
+
+moduleclass = 'perf'
diff --git a/easybuild/easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-13.3.0.eb b/easybuild/easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..509d81b79af
--- /dev/null
+++ b/easybuild/easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-13.3.0.eb
@@ -0,0 +1,55 @@
+# #
+# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild
+# Copyright:: Copyright 2013-2024 Juelich Supercomputing Centre, Germany
+# Authors::   Bernd Mohr <b.mohr@fz-juelich.de>
+# Markus Geimer <m.geimer@fz-juelich.de>
+# Jan André Reuter <j.reuter@fz-juelich.de>
+# License::   3-clause BSD
+#
+# This work is based on experiences from the UNITE project
+# http://apps.fz-juelich.de/unite/
+# #
+
+easyblock = 'EB_Score_minus_P'
+
+name = 'OTF2'
+version = '3.0.3'
+
+homepage = 'https://www.score-p.org'
+description = """
+ The Open Trace Format 2 is a highly scalable, memory efficient event trace
+ data format plus support library. It is the new standard trace format for
+ Scalasca, Vampir, and TAU and is open for other tools.
+
+"""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+source_urls = ['http://perftools.pages.jsc.fz-juelich.de/cicd/%(namelower)s/tags/%(namelower)s-%(version)s']
+sources = [SOURCELOWER_TAR_GZ]
+patches = ['otf2-3.0.3-update-py-compile.patch']
+checksums = [
+    '18a3905f7917340387e3edc8e5766f31ab1af41f4ecc5665da6c769ca21c4ee8',  # otf2-3.0.3.tar.gz
+    '5b1dad8788642eaa97bc03003c9329380340ba10649e556a30ce541165cf8da4',  # otf2-3.0.3-update-py-compile.patch
+]
+
+builddependencies = [
+    ('binutils', '2.42'),
+]
+dependencies = [
+    # SIONlib container support (optional):
+    ('SIONlib', '1.7.7', '-tools'),
+]
+
+configopts = '--enable-shared'
+
+
+sanity_check_paths = {
+    'files': ['bin/otf2-config', 'include/otf2/otf2.h',
+              'lib/libotf2.a', 'lib/libotf2.%s' % SHLIB_EXT],
+    'dirs': [],
+}
+
+sanity_check_commands = ['%(namelower)s-config --help']
+
+moduleclass = 'perf'
diff --git a/easybuild/easyconfigs/o/OTF2/otf2-3.0.3-update-py-compile.patch b/easybuild/easyconfigs/o/OTF2/otf2-3.0.3-update-py-compile.patch
new file mode 100644
index 00000000000..539726fbf14
--- /dev/null
+++ b/easybuild/easyconfigs/o/OTF2/otf2-3.0.3-update-py-compile.patch
@@ -0,0 +1,252 @@
+This patch updates the py-compile file used by OTF2 during the install process
+to fix the removal of the imp module in Python 3.12 which was long deprecated.
+With this, OTF2 can be installed with Python 3.12, which would previously fail
+with a module not found error.
+
+--- build-config/py-compile	2023-02-12 17:32:31.274132086 +0100
++++ ../../otf2/build-config/py-compile	2024-08-22 17:44:59.939242651 +0200
+@@ -1,7 +1,7 @@
+ #!/bin/sh
+ # py-compile - Compile a Python program
+ 
+-scriptversion=2011-06-08.12; # UTC
++scriptversion=2023-03-30.00; # UTC
+ 
+ # Copyright (C) 2000-2013 Free Software Foundation, Inc.
+ 
+@@ -27,7 +27,7 @@
+ # bugs to <bug-automake@gnu.org> or send patches to
+ # <automake-patches@gnu.org>.
+ 
+-if [ -z "$PYTHON" ]; then
++if test -z "$PYTHON"; then
+   PYTHON=python
+ fi
+ 
+@@ -79,13 +79,20 @@
+       ;;
+     -h|--help)
+       cat <<\EOF
+-Usage: py-compile [--help] [--version] [--basedir DIR] [--destdir DIR] [--silent] FILES..."
++Usage: py-compile [options] FILES...
+ 
+ Byte compile some python scripts FILES.  Use --destdir to specify any
+ leading directory path to the FILES that you don't want to include in the
+ byte compiled file.  Specify --basedir for any additional path information you
+ do want to be shown in the byte compiled file.
+ 
++Options:
++  --basedir DIR   Prefix all FILES with DIR, and include in error messages.
++  --destdir DIR   Prefix all FILES with DIR before compiling.
++  -v, --version   Display version information.
++  -h, --help      This help screen.
++  --silent        Operate silently.
++
+ Example:
+   py-compile --destdir /tmp/pkg-root --basedir /usr/share/test test.py test2.py
+ 
+@@ -114,87 +121,165 @@
+   shift
+ done
+ 
+-files=$*
+-if test -z "$files"; then
+-    usage_error "no files given"
++if test $# -eq 0; then
++  usage_error "no files given"
+ fi
+ 
+ # if basedir was given, then it should be prepended to filenames before
+ # byte compilation.
+-if [ -z "$basedir" ]; then
+-    pathtrans="path = file"
++if test -z "$basedir"; then
++  pathtrans="path = file"
+ else
+-    pathtrans="path = os.path.join('$basedir', file)"
++  pathtrans="path = os.path.join('$basedir', file)"
+ fi
+ 
+ # if destdir was given, then it needs to be prepended to the filename to
+ # byte compile but not go into the compiled file.
+-if [ -z "$destdir" ]; then
+-    filetrans="filepath = path"
++if test -z "$destdir"; then
++  filetrans="filepath = path"
+ else
+-    filetrans="filepath = os.path.normpath('$destdir' + os.sep + path)"
++  filetrans="filepath = os.path.normpath('$destdir' + os.sep + path)"
++fi
++
++python_major=`$PYTHON -c 'import sys; print(sys.version_info[0])'`
++if test -z "$python_major"; then
++  usage_error "could not determine $PYTHON major version"
+ fi
+ 
++case $python_major in
++[01])
++  usage_error "python version 0.x and 1.x not supported"
++  ;;
++esac
++
++python_minor=`$PYTHON -c 'import sys; print(sys.version_info[1])'`
++
++# NB: When adding support for newer versions, prefer copying & adding new cases
++# rather than try to keep things merged with shell variables.
++
++# First byte compile (no optimization) all the modules.
++# This works for all currently known Python versions.
+ $PYTHON -c "
+-import sys, os, py_compile, imp
++import sys, os, py_compile
++
++try:
++    import importlib
++except ImportError:
++    importlib = None
++
++# importlib.util.cache_from_source was added in 3.4
++if (
++        hasattr(importlib, 'util')
++        and hasattr(importlib.util, 'cache_from_source')
++):
++    destpath = importlib.util.cache_from_source
++else:
++    destpath = lambda filepath: filepath + 'c'
+ 
+-files = '''$files'''
+ silent = $silent
+ blu = '''$blu'''
+ std = '''$std'''
+ 
+ if not silent:
+-    sys.stdout.write('Byte-compiling python modules...')
+-for file in files.split():
++    sys.stdout.write('Byte-compiling python modules...\n')
++for file in sys.argv[1:]:
+     $pathtrans
+     $filetrans
+-    if not os.path.exists(filepath) or not (len(filepath) >= 3
+-                                            and filepath[-3:] == '.py'):
+-	    continue
++    if (
++            not os.path.exists(filepath)
++            or not (len(filepath) >= 3 and filepath[-3:] == '.py')
++     ):
++        continue
+     if not silent:
+-        sys.stdout.write(' ' + file)
++        sys.stdout.write(file + ' ')
+         sys.stdout.flush()
+     else:
+-        sys.stdout.write('  PYTHON   {}{}{}\n'.format(blu, filepath + 'c', std))
+-    if hasattr(imp, 'get_tag'):
+-        py_compile.compile(filepath, imp.cache_from_source(filepath), path)
+-    else:
+-        py_compile.compile(filepath, filepath + 'c', path)
++        sys.stdout.write('  PYCACHE  {}{}{}\n'.format(blu, destpath(filepath), std))
++    py_compile.compile(filepath, destpath(filepath), path)
+ if not silent:
+-    sys.stdout.write('\n')" || exit $?
++    sys.stdout.write('\n')" "$@" || exit $?
+ 
+-# this will fail for python < 1.5, but that doesn't matter ...
++# Then byte compile w/optimization all the modules.
+ $PYTHON -O -c "
+-import sys, os, py_compile, imp
++import sys, os, py_compile
++
++try:
++    import importlib
++except ImportError:
++    importlib = None
++
++# importlib.util.cache_from_source was added in 3.4
++if (
++        hasattr(importlib, 'util')
++        and hasattr(importlib.util, 'cache_from_source')
++):
++    destpath = importlib.util.cache_from_source
++else:
++    destpath = lambda filepath: filepath + 'o'
+ 
+-# pypy does not use .pyo optimization
+-if hasattr(sys, 'pypy_translation_info'):
++# pypy2 does not use .pyo optimization
++if sys.version_info.major <= 2 and hasattr(sys, 'pypy_translation_info'):
+     sys.exit(0)
+ 
+-files = '''$files'''
+ silent = $silent
+ blu = '''$blu'''
+ std = '''$std'''
+ 
+ if not silent:
+-    sys.stdout.write('Byte-compiling python modules (optimized versions)...')
+-for file in files.split():
++    sys.stdout.write('Byte-compiling python modules (optimized versions) ...\n')
++for file in sys.argv[1:]:
+     $pathtrans
+     $filetrans
+-    if not os.path.exists(filepath) or not (len(filepath) >= 3
+-                                            and filepath[-3:] == '.py'):
+-	    continue
++    if (
++            not os.path.exists(filepath)
++            or not (len(filepath) >= 3 and filepath[-3:] == '.py')
++    ):
++        continue
+     if not silent:
+-        sys.stdout.write(' ' + file)
++        sys.stdout.write(file + ' ')
+         sys.stdout.flush()
+     else:
+-        sys.stdout.write('  PYTHON   {}{}{}\n'.format(blu, filepath + 'o', std))
+-    if hasattr(imp, 'get_tag'):
+-        py_compile.compile(filepath, imp.cache_from_source(filepath, False), path)
++        sys.stdout.write('  PYCACHE  {}{}{}\n'.format(blu, destpath(filepath), std))
++    py_compile.compile(filepath, destpath(filepath), path)
++if not silent:
++    sys.stdout.write('\n')" "$@" 2>/dev/null || exit $?
++
++# Then byte compile w/more optimization.
++# Only do this for Python 3.5+, see https://bugs.gnu.org/38043 for background.
++case $python_major.$python_minor in
++2.*|3.[0-4])
++  ;;
++*)
++  $PYTHON -OO -c "
++import sys, os, py_compile, importlib
++
++destpath = importlib.util.cache_from_source
++
++silent = $silent
++blu = '''$blu'''
++std = '''$std'''
++
++if not silent:
++    sys.stdout.write('Byte-compiling python modules (more optimized versions)'
++                     ' ...\n')
++for file in sys.argv[1:]:
++    $pathtrans
++    $filetrans
++    if (
++            not os.path.exists(filepath)
++            or not (len(filepath) >= 3 and filepath[-3:] == '.py')
++    ):
++        continue
++    if not silent:
++        sys.stdout.write(file + ' ')
++        sys.stdout.flush()
+     else:
+-        py_compile.compile(filepath, filepath + 'o', path)
++        sys.stdout.write('  PYCACHE  {}{}{}\n'.format(blu, destpath(filepath), std))
++    py_compile.compile(filepath, destpath(filepath), path)
+ if not silent:
+-    sys.stdout.write('\n')" 2>/dev/null || :
++    sys.stdout.write('\n')" "$@" 2>/dev/null || exit $?
++  ;;
++esac
+ 
+ # Local Variables:
+ # mode: shell-script
diff --git a/easybuild/easyconfigs/p/PAPI/PAPI-7.1.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/PAPI/PAPI-7.1.0-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..5c653a9d515
--- /dev/null
+++ b/easybuild/easyconfigs/p/PAPI/PAPI-7.1.0-GCCcore-13.3.0.eb
@@ -0,0 +1,53 @@
+##
+# Author:    Robert Mijakovic <robert.mijakovic@lxp.lu>
+# Updated:   Alexander Grund <alexander.grund@tu-dresden.de>
+##
+
+easyblock = 'ConfigureMake'
+
+name = 'PAPI'
+version = '7.1.0'
+
+homepage = 'https://icl.cs.utk.edu/projects/papi/'
+description = """
+ PAPI provides the tool designer and application engineer with a consistent
+ interface and methodology for use of the performance counter hardware found
+ in most major microprocessors. PAPI enables software engineers to see, in near
+ real time, the relation between software performance and processor events.
+ In addition Component PAPI provides access to a collection of components
+ that expose performance measurement opportunites across the hardware and
+ software stack.
+"""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+source_urls = ['https://icl.utk.edu/projects/papi/downloads']
+sources = [SOURCELOWER_TAR_GZ]
+patches = ['%(name)s-%(version)s_add_initial_riscv_support.patch']
+checksums = [
+    '5818afb6dba3ece57f51e65897db5062f8e3464e6ed294b654ebf34c3991bc4f',
+    {'PAPI-7.1.0_add_initial_riscv_support.patch': '6c7d0d63ccf2b8c46f2ed736fbd4c58303038fb2a45315aed94c026b773af35a'}
+]
+
+builddependencies = [
+    ('binutils', '2.42'),
+]
+
+start_dir = 'src'
+
+configopts = "--with-components=rapl "  # for energy measurements
+
+# There is also "fulltest" that is a superset of "test" but hangs on some processors
+# indefinitely with a defunct `make` process. So use only "test".
+runtest = 'test'
+
+sanity_check_paths = {
+    'files': ["bin/papi_%s" % x
+              for x in ["avail", "clockres", "command_line", "component_avail",
+                        "cost", "decode", "error_codes", "event_chooser",
+                        "mem_info", "multiplex_cost", "native_avail",
+                        "version", "xml_event_info"]],
+    'dirs': [],
+}
+
+moduleclass = 'perf'
diff --git a/easybuild/easyconfigs/p/PDT/PDT-3.25.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/PDT/PDT-3.25.2-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..74328c99ae7
--- /dev/null
+++ b/easybuild/easyconfigs/p/PDT/PDT-3.25.2-GCCcore-13.3.0.eb
@@ -0,0 +1,40 @@
+# #
+# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild
+#
+# Copyright:: Copyright 2013-2019 Juelich Supercomputing Centre, Germany
+# Authors::   Bernd Mohr <b.mohr@fz-juelich.de>
+# Markus Geimer <m.geimer@fz-juelich.de>
+# License::   3-clause BSD
+#
+# This work is based on experiences from the UNITE project
+# http://apps.fz-juelich.de/unite/
+# #
+
+name = 'PDT'
+version = '3.25.2'
+
+homepage = 'https://www.cs.uoregon.edu/research/pdt/'
+description = """
+ Program Database Toolkit (PDT) is a framework for analyzing source code
+ written in several programming languages and for making rich program
+ knowledge accessible to developers of static and dynamic analysis tools.
+ PDT implements a standard program representation, the program database
+ (PDB), that can be accessed in a uniform way through a class library
+ supporting common PDB operations.
+"""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+source_urls = ['http://tau.uoregon.edu/pdt_releases/']
+sources = ['pdtoolkit-%(version)s.tar.gz']
+# Might now be available as direct download although e.g. http://tau.uoregon.edu/pdt.tgz may work
+download_instructions = ("Download from https://www.cs.uoregon.edu/research/pdt/downloads.php " +
+                         "and rename to " + sources[0])
+checksums = ['01c2d403bc6672b2b264a182c325806541066c5ed5713878eb598f5506428cbe']
+
+builddependencies = [
+    ('binutils', '2.42'),
+]
+
+
+moduleclass = 'perf'
diff --git a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-13.3.0-tools.eb b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-13.3.0-tools.eb
new file mode 100644
index 00000000000..9d2584de1bb
--- /dev/null
+++ b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-13.3.0-tools.eb
@@ -0,0 +1,51 @@
+# #
+# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild
+#
+# Copyright:: Copyright 2016-2019 Juelich Supercomputing Centre, Germany
+# Authors::   Markus Geimer <m.geimer@fz-juelich.de>
+# Modified 2017 by Andreas Henkel <henkel@uni-mainz.de>
+# License::   3-clause BSD
+# #
+
+easyblock = 'ConfigureMake'
+
+name = 'SIONlib'
+version = '1.7.7'
+# Provide a stripped-down version with renamed symbols for tools,
+# see description for further details
+versionsuffix = '-tools'
+
+homepage = 'https://www.fz-juelich.de/ias/jsc/EN/Expertise/Support/Software/SIONlib/_node.html'
+description = """
+ SIONlib is a scalable I/O library for parallel access to task-local files.
+ The library not only supports writing and reading binary data to or from
+ several thousands of processors into a single or a small number of physical
+ files, but also provides global open and close functions to access SIONlib
+ files in parallel. This package provides a stripped-down installation of
+ SIONlib for use with performance tools (e.g., Score-P), with renamed symbols
+ to avoid conflicts when an application using SIONlib itself is linked against
+ a tool requiring a different SIONlib version.
+"""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+source_urls = ['https://apps.fz-juelich.de/jsc/%(namelower)s/download.php?version=%(version)sl']
+sources = ['%(namelower)s-%(version)sl.tar.gz']
+checksums = ['3b5072d8a32a9e9858d85dfe4dc01e7cfdbf54cdaa60660e760b634ee08d8a4c']
+
+builddependencies = [
+    ('binutils', '2.42'),
+]
+
+configopts = '--disable-cxx --disable-fortran --disable-ompi '
+
+# Comment it out if you have Xeon Phi:
+configopts += '--disable-mic '
+
+sanity_check_paths = {
+    'files': ['bin/sionconfig'] +
+             ['lib/lib%s_64.a' % x for x in ['lsioncom', 'lsiongen', 'lsionser']],
+    'dirs': []
+}
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2024a-CUDA-12.6.0.eb b/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2024a-CUDA-12.6.0.eb
new file mode 100644
index 00000000000..9d7b53221e9
--- /dev/null
+++ b/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2024a-CUDA-12.6.0.eb
@@ -0,0 +1,57 @@
+# Copyright 2013-2020 Juelich Supercomputing Centre, Germany
+# Copyright 2020-2024 TU Dresden, Germany
+# Authors::
+# * Bernd Mohr <b.mohr@fz-juelich.de>
+# * Markus Geimer <m.geimer@fz-juelich.de>
+# * Alexander Grund <alexander.grund@tu-dresden.de>
+# * Robert Mijakovic <robert.mijakovic@lxp.lu>
+# License::   3-clause BSD
+
+name = 'Score-P'
+version = '8.4'
+versionsuffix = '-CUDA-%(cudaver)s'
+
+homepage = 'https://www.score-p.org'
+description = """
+ The Score-P measurement infrastructure is a highly scalable and easy-to-use
+ tool suite for profiling, event tracing, and online analysis of HPC
+ applications.
+"""
+
+toolchain = {'name': 'gompi', 'version': '2024a'}
+
+source_urls = ['https://perftools.pages.jsc.fz-juelich.de/cicd/scorep/tags/scorep-%(version)s']
+sources = ['scorep-%(version)s.tar.gz']
+checksums = ['7bbde9a0721d27cc6205baf13c1626833bcfbabb1f33b325a2d67976290f7f8a']
+
+dependencies = [
+    ('CUDA', '12.6.0', '', SYSTEM),
+    ('UCX-CUDA', '1.16.0', versionsuffix),
+    ('CubeLib', '4.8.2'),
+    ('CubeWriter', '4.8.2'),
+    ('libunwind', '1.8.1'),
+    ('OPARI2', '2.0.8'),
+    ('OTF2', '3.0.3'),
+    # Hardware counter support (optional):
+    ('PAPI', '7.1.0'),
+    # PDT source-to-source instrumentation support (optional):
+    ('PDT', '3.25.2'),
+]
+
+configopts = '--enable-shared'
+
+local_adapters = [
+    'compiler_event', 'cuda_mgmt', 'compiler_mgmt', 'mpi_event', 'mpi_mgmt', 'opari2_mgmt', 'user_event', 'user_mgmt'
+]
+sanity_check_paths = {
+    'files':
+        ['bin/scorep', 'include/scorep/SCOREP_User.h'] +
+        ['lib/libscorep_adapter_%s.%s' % (a, e) for a in local_adapters for e in ('a', SHLIB_EXT)],
+    'dirs': [],
+}
+sanity_check_commands = ['scorep-config --help']
+
+# Ensure that local metric documentation is found by CubeGUI
+modextrapaths = {'CUBE_DOCPATH': 'share/doc/scorep/profile'}
+
+moduleclass = 'perf'
diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2024a.eb b/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2024a.eb
new file mode 100644
index 00000000000..eda406cbe2a
--- /dev/null
+++ b/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2024a.eb
@@ -0,0 +1,55 @@
+# Copyright 2013-2024 Juelich Supercomputing Centre, Germany
+# Copyright 2020-2024 TU Dresden, Germany
+# Authors::
+# * Bernd Mohr <b.mohr@fz-juelich.de>
+# * Markus Geimer <m.geimer@fz-juelich.de>
+# * Alexander Grund <alexander.grund@tu-dresden.de>
+# * Robert Mijakovic <robert.mijakovic@lxp.lu>
+# * Jan André Reuter <j.reuter@fz-juelich.de>
+# License::   3-clause BSD
+
+name = 'Score-P'
+version = '8.4'
+
+homepage = 'https://www.score-p.org'
+description = """
+ The Score-P measurement infrastructure is a highly scalable and easy-to-use
+ tool suite for profiling, event tracing, and online analysis of HPC
+ applications.
+"""
+
+toolchain = {'name': 'gompi', 'version': '2024a'}
+
+source_urls = ['https://perftools.pages.jsc.fz-juelich.de/cicd/scorep/tags/scorep-%(version)s']
+sources = ['scorep-%(version)s.tar.gz']
+checksums = ['7bbde9a0721d27cc6205baf13c1626833bcfbabb1f33b325a2d67976290f7f8a']
+
+dependencies = [
+    ('CubeLib', '4.8.2'),
+    ('CubeWriter', '4.8.2'),
+    ('libunwind', '1.8.1'),
+    ('OPARI2', '2.0.8'),
+    ('OTF2', '3.0.3'),
+    # Hardware counter support (optional):
+    ('PAPI', '7.1.0'),
+    # PDT source-to-source instrumentation support (optional):
+    ('PDT', '3.25.2'),
+]
+
+configopts = '--enable-shared'
+
+local_adapters = [
+    'compiler_event', 'compiler_mgmt', 'mpi_event', 'mpi_mgmt', 'opari2_mgmt', 'user_event', 'user_mgmt'
+]
+sanity_check_paths = {
+    'files':
+        ['bin/scorep', 'include/scorep/SCOREP_User.h'] +
+        ['lib/libscorep_adapter_%s.%s' % (a, e) for a in local_adapters for e in ('a', SHLIB_EXT)],
+    'dirs': [],
+}
+sanity_check_commands = ['scorep-config --help']
+
+# Ensure that local metric documentation is found by CubeGUI
+modextrapaths = {'CUBE_DOCPATH': 'share/doc/scorep/profile'}
+
+moduleclass = 'perf'
diff --git a/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.16.0-GCCcore-13.3.0-CUDA-12.6.0.eb b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.16.0-GCCcore-13.3.0-CUDA-12.6.0.eb
new file mode 100644
index 00000000000..34271e18021
--- /dev/null
+++ b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.16.0-GCCcore-13.3.0-CUDA-12.6.0.eb
@@ -0,0 +1,41 @@
+easyblock = 'EB_UCX_Plugins'
+
+name = 'UCX-CUDA'
+version = '1.16.0'
+versionsuffix = '-CUDA-%(cudaver)s'
+
+homepage = 'http://www.openucx.org/'
+description = """Unified Communication X
+An open-source production grade communication framework for data centric
+and high-performance applications
+
+This module adds the UCX CUDA support.
+"""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://github.com/openucx/ucx/releases/download/v%(version)s']
+sources = [{'filename': 'ucx-%(version)s.tar.gz', 'alt_location': 'UCX'}]
+patches = ['%(name)s-1.16.0_link_against_existing_UCX_libs.patch']
+checksums = [
+    {'ucx-1.16.0.tar.gz': 'f73770d3b583c91aba5fb07557e655ead0786e057018bfe42f0ebe8716e9d28c'},
+    {'UCX-CUDA-1.16.0_link_against_existing_UCX_libs.patch':
+     'aa5bab38c188276958dd6829da4929ed9ff0b67cd55665b4459521cf3fbbe46d'},
+]
+
+builddependencies = [
+    ('binutils', '2.42'),
+    ('Autotools', '20231222'),
+    ('pkgconf', '2.2.0'),
+]
+
+dependencies = [
+    ('zlib', '1.3.1'),
+    ('UCX', version),
+    ('CUDA', '12.6.0', '', SYSTEM),
+    ('GDRCopy', '2.4.1'),
+]
+
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.16.0_link_against_existing_UCX_libs.patch b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.16.0_link_against_existing_UCX_libs.patch
new file mode 100644
index 00000000000..92973cd7f80
--- /dev/null
+++ b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.16.0_link_against_existing_UCX_libs.patch
@@ -0,0 +1,93 @@
+diff --git a/configure.ac b/configure.ac
+index 8d8da54..2765fe0 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -30,13 +30,13 @@ valgrind_libpath=""
+ AC_USE_SYSTEM_EXTENSIONS
+ AC_CONFIG_HEADERS([config.h])
+ 
+-AC_CHECK_PROG(GITBIN, git, yes)
+-AS_IF([test x"${GITBIN}" = x"yes"],
+-      [# remove preceding "refs/heads/" (11 characters) for symbolic ref
+-       AC_SUBST(SCM_BRANCH,  esyscmd([sh -c 'git symbolic-ref --quiet   HEAD | sed "s/^.\{11\}//"']))
+-       AC_SUBST(SCM_VERSION, esyscmd([sh -c 'git rev-parse    --short=7 HEAD']))],
+-      [AC_SUBST(SCM_BRANCH,  "<unknown>")
+-       AC_SUBST(SCM_VERSION, "0000000")])
++#AC_CHECK_PROG(GITBIN, git, yes)
++#AS_IF([test x"${GITBIN}" = x"yes"],
++#      [# remove preceding "refs/heads/" (11 characters) for symbolic ref
++#       AC_SUBST(SCM_BRANCH,  esyscmd([sh -c 'git symbolic-ref --quiet   HEAD | sed "s/^.\{11\}//"']))
++#       AC_SUBST(SCM_VERSION, esyscmd([sh -c 'git rev-parse    --short=7 HEAD']))],
++#      [AC_SUBST(SCM_BRANCH,  "<unknown>")
++#       AC_SUBST(SCM_VERSION, "0000000")])
+ 
+ AH_TOP([
+ #ifndef UCX_CONFIG_H
+diff --git a/src/ucm/cuda/Makefile.am b/src/ucm/cuda/Makefile.am
+index 00bd224..22e719f 100644
+--- a/src/ucm/cuda/Makefile.am
++++ b/src/ucm/cuda/Makefile.am
+@@ -9,7 +9,7 @@ if HAVE_CUDA
+ module_LTLIBRARIES      = libucm_cuda.la
+ libucm_cuda_la_CPPFLAGS = $(BASE_CPPFLAGS) $(CUDA_CPPFLAGS)
+ libucm_cuda_la_CFLAGS   = $(BASE_CFLAGS) $(CUDA_CFLAGS)
+-libucm_cuda_la_LIBADD   = ../libucm.la $(CUDA_LIBS) $(CUDART_LIBS)
++libucm_cuda_la_LIBADD   = -lucm $(CUDA_LIBS) $(CUDART_LIBS)
+ libucm_cuda_la_LDFLAGS  = $(UCM_MODULE_LDFLAGS) \
+                           $(patsubst %, -Xlinker %, $(CUDA_LDFLAGS)) \
+                           -version-info $(SOVERSION)
+diff --git a/src/ucm/rocm/Makefile.am b/src/ucm/rocm/Makefile.am
+index f9e183f..dcd1587 100644
+--- a/src/ucm/rocm/Makefile.am
++++ b/src/ucm/rocm/Makefile.am
+@@ -10,7 +10,7 @@ if HAVE_ROCM
+ module_LTLIBRARIES      = libucm_rocm.la
+ libucm_rocm_la_CPPFLAGS = $(BASE_CPPFLAGS) $(ROCM_CPPFLAGS)
+ libucm_rocm_la_CFLAGS   = $(BASE_CFLAGS) $(ROCM_CFLAGS)
+-libucm_rocm_la_LIBADD   = ../libucm.la
++libucm_rocm_la_LIBADD   = -lucm
+ libucm_rocm_la_LDFLAGS  = $(UCM_MODULE_LDFLAGS) \
+                           $(ROCM_LDFLAGS) $(ROCM_LIBS) -version-info $(SOVERSION) \
+                           $(patsubst %, -Xlinker %, -L$(ROCM_ROOT)/lib -rpath $(ROCM_ROOT)/hip/lib -rpath $(ROCM_ROOT)/lib) \
+diff --git a/src/uct/cuda/Makefile.am b/src/uct/cuda/Makefile.am
+index 00899ab..dcee6b0 100644
+--- a/src/uct/cuda/Makefile.am
++++ b/src/uct/cuda/Makefile.am
+@@ -11,8 +11,8 @@ module_LTLIBRARIES      = libuct_cuda.la
+ libuct_cuda_la_CPPFLAGS = $(BASE_CPPFLAGS) $(CUDA_CPPFLAGS)
+ libuct_cuda_la_CFLAGS   = $(BASE_CFLAGS) $(CUDA_CFLAGS)
+ libuct_cuda_la_LDFLAGS  = $(CUDA_LDFLAGS) -version-info $(SOVERSION)
+-libuct_cuda_la_LIBADD   = $(top_builddir)/src/ucs/libucs.la \
+-                          $(top_builddir)/src/uct/libuct.la \
++libuct_cuda_la_LIBADD   = -lucs \
++                          -luct \
+                           $(CUDA_LIBS) $(CUDART_LIBS) $(NVML_LIBS)
+ 
+ noinst_HEADERS = \
+diff --git a/src/uct/cuda/gdr_copy/Makefile.am b/src/uct/cuda/gdr_copy/Makefile.am
+index 47602c7..601cb9f 100644
+--- a/src/uct/cuda/gdr_copy/Makefile.am
++++ b/src/uct/cuda/gdr_copy/Makefile.am
+@@ -9,7 +9,7 @@ module_LTLIBRARIES              = libuct_cuda_gdrcopy.la
+ libuct_cuda_gdrcopy_la_CPPFLAGS = $(BASE_CPPFLAGS) $(GDR_COPY_CPPFLAGS)
+ libuct_cuda_gdrcopy_la_CFLAGS   = $(BASE_CFLAGS)
+ libuct_cuda_gdrcopy_la_LDFLAGS  = $(GDR_COPY_LDFLAGS) -version-info $(SOVERSION)
+-libuct_cuda_gdrcopy_la_LIBADD   = $(top_builddir)/src/ucs/libucs.la \
++libuct_cuda_gdrcopy_la_LIBADD   = -lucs \
+                                   $(top_builddir)/src/uct/cuda/libuct_cuda.la \
+                                   $(GDR_COPY_LIBS)
+ 
+diff --git a/src/uct/rocm/Makefile.am b/src/uct/rocm/Makefile.am
+index c7abce1..257e33f 100644
+--- a/src/uct/rocm/Makefile.am
++++ b/src/uct/rocm/Makefile.am
+@@ -8,8 +8,7 @@ if HAVE_ROCM
+ module_LTLIBRARIES      = libuct_rocm.la
+ libuct_rocm_la_CPPFLAGS = $(BASE_CPPFLAGS) $(ROCM_CPPFLAGS)
+ libuct_rocm_la_CFLAGS   = $(BASE_CFLAGS)
+-libuct_rocm_la_LIBADD   = $(top_builddir)/src/ucs/libucs.la \
+-                          $(top_builddir)/src/uct/libuct.la
++libuct_rocm_la_LIBADD   = -lucs -luct
+ libuct_rocm_la_LDFLAGS  = $(ROCM_LDFLAGS) $(ROCM_LIBS) -version-info $(SOVERSION) \
+                           $(patsubst %, -Xlinker %, -L$(ROCM_ROOT)/lib -rpath $(ROCM_ROOT)/hip/lib -rpath $(ROCM_ROOT)/lib) \
+                           $(patsubst %, -Xlinker %, --enable-new-dtags) \

From d0cbd2e91c75a419bdd7335d48b38ad59265ac21 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jan=20Andr=C3=A9=20Reuter?= <j.reuter@fz-juelich.de>
Date: Thu, 5 Sep 2024 10:00:21 +0200
Subject: [PATCH 800/835] {perf}{GCCcore/13.3.0} OTF2: Use toolchain Python
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Signed-off-by: Jan André Reuter <j.reuter@fz-juelich.de>
---
 .../easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-13.3.0.eb      | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/easybuild/easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-13.3.0.eb b/easybuild/easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-13.3.0.eb
index 509d81b79af..fdf78e0772d 100644
--- a/easybuild/easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-13.3.0.eb
+++ b/easybuild/easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-13.3.0.eb
@@ -39,17 +39,22 @@ builddependencies = [
 dependencies = [
     # SIONlib container support (optional):
     ('SIONlib', '1.7.7', '-tools'),
+    # OTF2 Python bindings
+    ('Python', '3.12.3'),
+    ('Python-bundle-PyPI', '2024.06'),
 ]
 
+local_pyshortver = '3.12'
 configopts = '--enable-shared'
 
+modextrapaths = {'PYTHONPATH': ['lib64/python%s/site-packages' % local_pyshortver]}
 
 sanity_check_paths = {
     'files': ['bin/otf2-config', 'include/otf2/otf2.h',
               'lib/libotf2.a', 'lib/libotf2.%s' % SHLIB_EXT],
     'dirs': [],
 }
-
-sanity_check_commands = ['%(namelower)s-config --help']
+sanity_check_commands = ['%(namelower)s-config --help',
+                         'python -c "import %(namelower)s"']
 
 moduleclass = 'perf'

From 31ea36d41b6619f87d34c8ab39fe4322b518896c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Petr=20Kr=C3=A1l?= <petr@inuits.eu>
Date: Thu, 5 Sep 2024 13:35:23 +0200
Subject: [PATCH 801/835] adding easyconfigs: fpylll-0.6.1-foss-2023b.eb,
 fplll-5.4.5-GCCcore-13.2.0.eb

---
 .../f/fplll/fplll-5.4.5-GCCcore-13.2.0.eb     | 32 +++++++++++++++++++
 .../f/fpylll/fpylll-0.6.1-foss-2023b.eb       | 26 +++++++++++++++
 2 files changed, 58 insertions(+)
 create mode 100644 easybuild/easyconfigs/f/fplll/fplll-5.4.5-GCCcore-13.2.0.eb
 create mode 100644 easybuild/easyconfigs/f/fpylll/fpylll-0.6.1-foss-2023b.eb

diff --git a/easybuild/easyconfigs/f/fplll/fplll-5.4.5-GCCcore-13.2.0.eb b/easybuild/easyconfigs/f/fplll/fplll-5.4.5-GCCcore-13.2.0.eb
new file mode 100644
index 00000000000..5184f1f3c1e
--- /dev/null
+++ b/easybuild/easyconfigs/f/fplll/fplll-5.4.5-GCCcore-13.2.0.eb
@@ -0,0 +1,32 @@
+easyblock = 'ConfigureMake'
+
+name = 'fplll'
+version = '5.4.5'
+
+homepage = 'https://github.com/fplll/fplll'
+description = """fplll contains implementations of several lattice algorithms.
+ The implementation relies on floating-point orthogonalization,  and the 1982 paper from 
+Lenstra, Lenstra Jr. and Lovasz (LLL) is central to the code, hence the name."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
+
+source_urls = ['https://github.com/fplll/fplll/releases/download/%(version)s']
+sources = [SOURCE_TAR_GZ]
+checksums = ['76d3778f0326597ed7505bab19493a9bf6b73a5c5ca614e8fb82f42105c57d00']
+
+builddependencies = [
+    ('binutils', '2.40'),
+]
+
+dependencies = [
+    ('MPFR', '4.2.1'),
+]
+
+sanity_check_paths = {
+    'files': ['bin/fplll', 'lib/libfplll.%s' % SHLIB_EXT, 'include/fplll.h'],
+    'dirs': ['share']
+}
+
+sanity_check_commands = ["fplll --help"]
+
+moduleclass = 'math'
diff --git a/easybuild/easyconfigs/f/fpylll/fpylll-0.6.1-foss-2023b.eb b/easybuild/easyconfigs/f/fpylll/fpylll-0.6.1-foss-2023b.eb
new file mode 100644
index 00000000000..5361252deb7
--- /dev/null
+++ b/easybuild/easyconfigs/f/fpylll/fpylll-0.6.1-foss-2023b.eb
@@ -0,0 +1,26 @@
+easyblock = 'PythonPackage'
+
+name = 'fpylll'
+version = '0.6.1'
+
+homepage = 'https://pypi.org/project/fpylll'
+description = "A Python wrapper for fplll."
+
+# can be moved down to gfbf in more recent toolchain versions
+toolchain = {'name': 'foss', 'version': '2023b'}
+
+sources = [SOURCE_TAR_GZ]
+checksums = ['dfd9529a26c50993a2a716177debd7994312219070574cad31b35b4f0c040a19']
+
+dependencies = [
+    ('Python', '3.11.5'),
+    ('SciPy-bundle', '2023.11'),
+    ('cysignals', '1.11.4'),
+    ('fplll', '5.4.5'),
+]
+
+use_pip = True
+download_dep_fail = True
+sanity_pip_check = True
+
+moduleclass = 'math'

From 8dee0734fe2f47d9af1ebf75d4dfbbf6cea181cd Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Petr=20Kr=C3=A1l?= <petr@inuits.eu>
Date: Thu, 5 Sep 2024 13:36:19 +0200
Subject: [PATCH 802/835] adding easyconfigs:
 primecountpy-0.1.0-GCCcore-13.2.0.eb, primecount-7.14-GCCcore-13.2.0.eb

---
 .../primecount-7.14-GCCcore-13.2.0.eb         | 31 +++++++++++++++++++
 .../primecountpy-0.1.0-GCCcore-13.2.0.eb      | 27 ++++++++++++++++
 2 files changed, 58 insertions(+)
 create mode 100644 easybuild/easyconfigs/p/primecount/primecount-7.14-GCCcore-13.2.0.eb
 create mode 100644 easybuild/easyconfigs/p/primecountpy/primecountpy-0.1.0-GCCcore-13.2.0.eb

diff --git a/easybuild/easyconfigs/p/primecount/primecount-7.14-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/primecount/primecount-7.14-GCCcore-13.2.0.eb
new file mode 100644
index 00000000000..556cc0f1507
--- /dev/null
+++ b/easybuild/easyconfigs/p/primecount/primecount-7.14-GCCcore-13.2.0.eb
@@ -0,0 +1,31 @@
+easyblock = 'CMakeMake'
+
+name = 'primecount'
+version = '7.14'
+
+homepage = 'https://github.com/kimwalisch/primecount'
+description = """primecount is a command-line program and C/C++ library that counts the number of primes ≤ x
+ (maximum 1031) using highly optimized implementations of the combinatorial prime counting algorithms."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
+
+source_urls = ['https://github.com/kimwalisch/primecount/archive/refs/tags']
+sources = ['v%(version)s.tar.gz']
+checksums = ['d867ac18cc52c0f7014682169988a76f39e4cd56f8ce78fb56e064499b1d66bb']
+
+builddependencies = [
+    ('CMake', '3.27.6'),
+    ('binutils', '2.40'),
+]
+
+configopts = '-DBUILD_SHARED_LIBS=ON '
+
+sanity_check_paths = {
+    'files': ['bin/primecount', 'include/primecount.h'] +
+             ['lib/libprimecount.%s' % e for e in ['a', SHLIB_EXT]],
+    'dirs': ['share'],
+}
+
+sanity_check_commands = ["primecount -h"]
+
+moduleclass = 'math'
diff --git a/easybuild/easyconfigs/p/primecountpy/primecountpy-0.1.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/primecountpy/primecountpy-0.1.0-GCCcore-13.2.0.eb
new file mode 100644
index 00000000000..11244361d59
--- /dev/null
+++ b/easybuild/easyconfigs/p/primecountpy/primecountpy-0.1.0-GCCcore-13.2.0.eb
@@ -0,0 +1,27 @@
+easyblock = 'PythonPackage'
+
+name = 'primecountpy'
+version = '0.1.0'
+
+homepage = 'https://pypi.org/project/primecountpy'
+description = "This is a Cython interface to the C++ library primecount."
+
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
+
+sources = [SOURCE_TAR_GZ]
+checksums = ['78fe7cc32115f0669a45d7c90faaf39f7ce3939e39e2e7e5f14c17fe4bff0676']
+
+builddependencies = [('binutils', '2.40')]
+
+dependencies = [
+    ('Python', '3.11.5'),
+    ('Cython', '3.0.10'),
+    ('cysignals', '1.11.4'),
+    ('primecount', '7.14'),
+]
+
+use_pip = True
+download_dep_fail = True
+sanity_pip_check = True
+
+moduleclass = 'math'

From a9924f769e2623de5c50086aa3f22a67394f68f1 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Petr=20Kr=C3=A1l?= <petr@inuits.eu>
Date: Thu, 5 Sep 2024 15:22:01 +0200
Subject: [PATCH 803/835] adding easyconfigs: AGAT-1.4.0-GCC-12.3.0.eb

---
 .../a/AGAT/AGAT-1.4.0-GCC-12.3.0.eb           | 70 +++++++++++++++++++
 1 file changed, 70 insertions(+)
 create mode 100644 easybuild/easyconfigs/a/AGAT/AGAT-1.4.0-GCC-12.3.0.eb

diff --git a/easybuild/easyconfigs/a/AGAT/AGAT-1.4.0-GCC-12.3.0.eb b/easybuild/easyconfigs/a/AGAT/AGAT-1.4.0-GCC-12.3.0.eb
new file mode 100644
index 00000000000..2677e62fda1
--- /dev/null
+++ b/easybuild/easyconfigs/a/AGAT/AGAT-1.4.0-GCC-12.3.0.eb
@@ -0,0 +1,70 @@
+# easybuild easyconfig
+#
+# John Dey <jfdey@fredhutch.org> Fred Hutchinson Cancer Center
+# Thomas Eylenbosch - Gluo NV
+# Update: Petr Král (INUITS)
+#
+easyblock = 'Bundle'
+
+name = 'AGAT'
+version = '1.4.0'
+
+homepage = 'https://agat.readthedocs.io/en/latest/'
+description = """AGAT: Another GTF/GFF Analysis Toolkit. Suite of tools to handle gene annotations
+ in any GTF/GFF format."""
+
+toolchain = {'name': 'GCC', 'version': '12.3.0'}
+
+builddependencies = [('binutils', '2.40')]
+
+dependencies = [
+    ('Perl', '5.36.1'),
+    ('BioPerl', '1.7.8'),
+]
+
+exts_defaultclass = 'PerlModule'
+exts_filter = ("perl -e 'require %(ext_name)s'", '')
+
+exts_list = [
+    ('Set::Object', '1.42', {
+        'source_tmpl': 'Set-Object-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/R/RU/RURBAN'],
+        'checksums': ['d18c5a8a233eabbd0206cf3da5b00fcdd7b37febf12a93dcc3d1c026e6fdec45'],
+    }),
+    ('File::Share', '0.27', {
+        'source_tmpl': 'File-Share-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/I/IN/INGY'],
+        'checksums': ['d6e8f4b55ebd38e0bb45e44392e3fa27dc1fde16abc5d1ff53e157e19a5755be'],
+    }),
+    ('Sort::Naturally', '1.03', {
+        'source_tmpl': 'Sort-Naturally-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'],
+        'checksums': ['eaab1c5c87575a7826089304ab1f8ffa7f18e6cd8b3937623e998e865ec1e746'],
+    }),
+    ('Class::MethodMaker', '2.24', {
+        'source_tmpl': 'Class-MethodMaker-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/S/SC/SCHWIGON/class-methodmaker'],
+        'checksums': ['5eef58ccb27ebd01bcde5b14bcc553b5347a0699e5c3e921c7780c3526890328'],
+    }),
+    ('Term::ProgressBar', '2.23', {
+        'source_tmpl': 'Term-ProgressBar-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MANWAR'],
+        'checksums': ['defc03fb9f4ac1c9df1359d312bff3c0865ddefbf3aba64cd42a69a86215d49d'],
+    }),
+    (name, version, {
+        'modulename': 'AGAT::Utilities',
+        'source_urls': ['https://github.com/NBISweden/AGAT/archive/refs/tags'],
+        'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}],
+        'checksums': ['d5e30db44b5d05ed51c606a823894c01c85c1ed85580148ad5473cb2f2b2ac77'],
+    }),
+]
+
+modextrapaths = {'PERL5LIB': 'lib/perl5/site_perl/%(perlver)s/'}
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['bin', 'lib/perl5/site_perl/%(perlver)s/%(name)s'],
+}
+
+sanity_check_commands = ['agat_convert_bed2gff.pl --help']
+moduleclass = 'bio'

From 6b56303af3016d3581d0942edaefc119740429ed Mon Sep 17 00:00:00 2001
From: Simon Branford <s.j.branford@bham.ac.uk>
Date: Thu, 5 Sep 2024 15:58:32 +0100
Subject: [PATCH 804/835] add the plugins to OpenFOAM v2406

---
 .../easyconfigs/o/OpenFOAM/OpenFOAM-v2406-foss-2023a.eb  | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2406-foss-2023a.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2406-foss-2023a.eb
index ba59d215581..0e2885c064f 100644
--- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2406-foss-2023a.eb
+++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2406-foss-2023a.eb
@@ -14,13 +14,20 @@ toolchain = {'name': 'foss', 'version': '2023a'}
 toolchainopts = {'cstd': 'c++14', 'vectorize': False}
 
 source_urls = ['https://sourceforge.net/projects/openfoam/files/%(version)s/']
-sources = [SOURCE_TGZ]
+sources = [
+    SOURCE_TGZ,
+    {
+        'filename': '%(name)s-plugins-%(version)s.tgz',
+        'extract_cmd': 'tar --strip-components=1 -C %(installdir)s/%(name)s-%(version)s/ -xzf %s'
+    }
+]
 patches = [
     ('OpenFOAM-v2406-cleanup.patch', 1),
     ('OpenFOAM-v2212-wmake-OpenMPI.patch', 1),
 ]
 checksums = [
     {'OpenFOAM-v2406.tgz': '8d1450fb89eec1e7cecc55c3bb7bc486ccbf63d069379d1d5d7518fa16a4686a'},
+    {'OpenFOAM-plugins-v2406.tgz': '1d008f86fad06a4a568d194c6e3d5ab52be2b20c83a3b9b1b0230e2de2d0558b'},
     {'OpenFOAM-v2406-cleanup.patch': '3abff48a517fb63719ad57fa32af746bc379a1e80c72d3e5852aa17cd13cf03e'},
     {'OpenFOAM-v2212-wmake-OpenMPI.patch': '241dc4898c22aab0cbd10c1ea931a07a786508ee03462d45dbc1c202fee3ebe8'},
 ]

From 184f4ff8f5b6dfcefaedcd7fe05cb53d409fa71a Mon Sep 17 00:00:00 2001
From: WilleBell <cintiawillemyns@gmail.com>
Date: Thu, 5 Sep 2024 18:02:01 +0200
Subject: [PATCH 805/835] adding easyconfigs: GPyOpt-1.2.6-foss-2023a.eb

---
 .../g/GPyOpt/GPyOpt-1.2.6-foss-2023a.eb       | 63 +++++++++++++++++++
 1 file changed, 63 insertions(+)
 create mode 100644 easybuild/easyconfigs/g/GPyOpt/GPyOpt-1.2.6-foss-2023a.eb

diff --git a/easybuild/easyconfigs/g/GPyOpt/GPyOpt-1.2.6-foss-2023a.eb b/easybuild/easyconfigs/g/GPyOpt/GPyOpt-1.2.6-foss-2023a.eb
new file mode 100644
index 00000000000..ca08a08a88c
--- /dev/null
+++ b/easybuild/easyconfigs/g/GPyOpt/GPyOpt-1.2.6-foss-2023a.eb
@@ -0,0 +1,63 @@
+easyblock = 'PythonBundle'
+
+name = 'GPyOpt'
+version = '1.2.6'
+
+homepage = 'https://sheffieldml.github.io/GPyOpt'
+description = "GPyOpt is a Python open-source library for Bayesian Optimization"
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('matplotlib', '3.7.2'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('paramz', '0.9.6', {
+        'sources': ['%(name)s-%(version)s-py3-none-any.whl'],
+        'checksums': ['4916be6f77f457316bcac8460be9c226026aed81fe7be302b32c0ba74e2ac6dd'],
+    }),
+    ('GPy', '1.13.2', {
+        'modulename': 'GPy',
+        'checksums': ['a38256b4dda536a5b5e6134a3924b42d454e987ee801fb6fc8b55a922da27920'],
+    }),
+    ('python-dateutil', '2.9.0.post0', {
+        'modulename': 'dateutil',
+        'checksums': ['37dd54208da7e1cd875388217d5e00ebd4179249f90fb72437e91a35459a0ad3'],
+    }),
+    ('pyDOE', '0.3.8', {
+        'modulename': '%(name)s',
+        'sources': ['%(name)s-%(version)s.zip'],
+        'checksums': ['cbd6f14ae26d3c9f736013205f53ea1191add4567033c3ee77b7dd356566c4b6'],
+    }),
+    ('sobol-seq', '0.2.0', {
+        'sources': ['sobol_seq-%(version)s.tar.gz'],
+        'checksums': ['e16e701bd7b03ec6ce65b3a64c9205799f6a2d00c2054dd8c4ff4343f3981172'],
+    }),
+    ('emcee', '2.2.1', {
+        'checksums': ['b83551e342b37311897906b3b8acf32979f4c5542e0a25786ada862d26241172'],
+    }),
+    (name, version, {
+        'modulename': 'GPyOpt',
+        'checksums': ['e714daa035bb529a6db23c53665a762a4ab3456b9329c19ad3b03983f94c9b2a'],
+    }),
+]
+
+local_GPy_file = '%(installdir)s/lib/python%(pyshortver)s/site-packages/GPy/plotting/matplot_dep/plot_definitions.py'
+
+# Fix GPy with matplotlib>=3.4.0
+# see issue 953 and fix from https://github.com/SheffieldML/GPy/pull/960
+postinstallcmds = [
+    'sed -i '
+    '''-e 's|ax._process_unit_info(xdata=X, ydata=y1)|ax._process_unit_info([("x", X), ("y", y1)], convert=False)|' '''
+    '''-e 's|ax._process_unit_info(ydata=y2)|ax._process_unit_info([("y", y2)], convert=False)|' %s''' % local_GPy_file,
+]
+
+
+sanity_pip_check = True
+
+moduleclass = 'math'

From ebc1c90f62842ff0482dbb2f70cd661b449542f9 Mon Sep 17 00:00:00 2001
From: Sam Moors <smoors@users.noreply.github.com>
Date: Thu, 5 Sep 2024 21:27:20 +0200
Subject: [PATCH 806/835] remove click

---
 easybuild/easyconfigs/f/Flask/Flask-3.0.3-GCCcore-13.3.0.eb | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/easybuild/easyconfigs/f/Flask/Flask-3.0.3-GCCcore-13.3.0.eb b/easybuild/easyconfigs/f/Flask/Flask-3.0.3-GCCcore-13.3.0.eb
index b0d0c5a63ae..46b9452f48b 100644
--- a/easybuild/easyconfigs/f/Flask/Flask-3.0.3-GCCcore-13.3.0.eb
+++ b/easybuild/easyconfigs/f/Flask/Flask-3.0.3-GCCcore-13.3.0.eb
@@ -33,9 +33,6 @@ exts_list = [
     ('asgiref', '3.7.2', {
         'checksums': ['9e0ce3aa93a819ba5b45120216b23878cf6e8525eb3848653452b4192b92afed'],
     }),
-    ('click', '8.1.7', {
-        'checksums': ['ca9853ad459e787e2192211578cc907e7594e294c7ccc834310722b41b9ca6de'],
-    }),
     ('blinker', '1.8.2', {
         'checksums': ['8f77b09d3bf7c795e969e9486f39c2c5e9c39d4ee07424be2bc594ece9642d83'],
     }),

From 0ca73992ca7533a83a6048d029fece46c07b233c Mon Sep 17 00:00:00 2001
From: Richard Top <richard.topouchian@uib.no>
Date: Fri, 6 Sep 2024 10:38:40 +0000
Subject: [PATCH 807/835] libdap: Update source

---
 .../easyconfigs/l/libdap/libdap-3.20.11-GCCcore-11.3.0.eb   | 6 +++---
 .../easyconfigs/l/libdap/libdap-3.20.11-GCCcore-12.3.0.eb   | 6 +++---
 .../easyconfigs/l/libdap/libdap-3.20.7-GCCcore-10.3.0.eb    | 6 +++---
 .../easyconfigs/l/libdap/libdap-3.20.8-GCCcore-11.2.0.eb    | 6 +++---
 4 files changed, 12 insertions(+), 12 deletions(-)

diff --git a/easybuild/easyconfigs/l/libdap/libdap-3.20.11-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libdap/libdap-3.20.11-GCCcore-11.3.0.eb
index 237260a43f7..b911c8f3169 100644
--- a/easybuild/easyconfigs/l/libdap/libdap-3.20.11-GCCcore-11.3.0.eb
+++ b/easybuild/easyconfigs/l/libdap/libdap-3.20.11-GCCcore-11.3.0.eb
@@ -9,9 +9,9 @@ description = """A C++ SDK which contains an implementation of DAP 2.0 and
 
 toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
 
-source_urls = ['https://www.opendap.org/pub/source/']
-sources = [SOURCE_TAR_GZ]
-checksums = ['850debf6ee6991350bf31051308093bee35ddd2121e4002be7e130a319de1415']
+source_urls = ['https://github.com/OPENDAP/libdap4/archive/refs/tags/']
+sources = ['%(version)s.tar.gz']
+checksums = ['319e9771d037b6c796f04e6a96bb27db1706bc5931ca149c78347c623a747771']
 
 builddependencies = [
     ('binutils', '2.38'),
diff --git a/easybuild/easyconfigs/l/libdap/libdap-3.20.11-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libdap/libdap-3.20.11-GCCcore-12.3.0.eb
index 39e628f1d97..39930ab196b 100644
--- a/easybuild/easyconfigs/l/libdap/libdap-3.20.11-GCCcore-12.3.0.eb
+++ b/easybuild/easyconfigs/l/libdap/libdap-3.20.11-GCCcore-12.3.0.eb
@@ -9,9 +9,9 @@ description = """A C++ SDK which contains an implementation of DAP 2.0 and
 
 toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
 
-source_urls = ['https://www.opendap.org/pub/source/']
-sources = [SOURCE_TAR_GZ]
-checksums = ['850debf6ee6991350bf31051308093bee35ddd2121e4002be7e130a319de1415']
+source_urls = ['https://github.com/OPENDAP/libdap4/archive/refs/tags/']
+sources = ['%(version)s.tar.gz']
+checksums = ['319e9771d037b6c796f04e6a96bb27db1706bc5931ca149c78347c623a747771']
 
 builddependencies = [
     ('binutils', '2.40'),
diff --git a/easybuild/easyconfigs/l/libdap/libdap-3.20.7-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/libdap/libdap-3.20.7-GCCcore-10.3.0.eb
index e2bb8f718ab..d43917eb6b0 100644
--- a/easybuild/easyconfigs/l/libdap/libdap-3.20.7-GCCcore-10.3.0.eb
+++ b/easybuild/easyconfigs/l/libdap/libdap-3.20.7-GCCcore-10.3.0.eb
@@ -9,9 +9,9 @@ description = """A C++ SDK which contains an implementation of DAP 2.0 and
 
 toolchain = {'name': 'GCCcore', 'version': '10.3.0'}
 
-source_urls = ['https://www.opendap.org/pub/source/']
-sources = [SOURCE_TAR_GZ]
-checksums = ['6856813d0b29e70a36e8a53e9cf20ad680d21d615952263e9c6586704539e78c']
+source_urls = ['https://github.com/OPENDAP/libdap4/archive/refs/tags/']
+sources = ['%(version)s.tar.gz']
+checksums = ['f6e907ea7a9f878965a3af2a858423450dde389d851fc67a33b0096b8b9b6085']
 
 builddependencies = [
     ('binutils', '2.36.1'),
diff --git a/easybuild/easyconfigs/l/libdap/libdap-3.20.8-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libdap/libdap-3.20.8-GCCcore-11.2.0.eb
index b48c3f1b6bc..5adc0a0f2ee 100644
--- a/easybuild/easyconfigs/l/libdap/libdap-3.20.8-GCCcore-11.2.0.eb
+++ b/easybuild/easyconfigs/l/libdap/libdap-3.20.8-GCCcore-11.2.0.eb
@@ -9,9 +9,9 @@ description = """A C++ SDK which contains an implementation of DAP 2.0 and
 
 toolchain = {'name': 'GCCcore', 'version': '11.2.0'}
 
-source_urls = ['https://www.opendap.org/pub/source/']
-sources = [SOURCE_TAR_GZ]
-checksums = ['65eb5c8f693cf74d58eece5eaa2e7c3c65f368926b1bffab0cf5b207757b94eb']
+source_urls = ['https://github.com/OPENDAP/libdap4/archive/refs/tags/']
+sources = ['%(version)s.tar.gz']
+checksums = ['e59b48f48bb37b36dcf9618043881e1d4150abd9b2ea3fa7474647c4ad622ccc']
 
 builddependencies = [
     ('binutils', '2.37'),

From 4e610ab7de6cb389f72f5a64de9aaf903cd10dae Mon Sep 17 00:00:00 2001
From: Richard Top <richard.topouchian@uib.no>
Date: Fri, 6 Sep 2024 12:32:17 +0000
Subject: [PATCH 808/835] Added Autotools as buildep and preconfigopts

---
 easybuild/easyconfigs/l/libdap/libdap-3.20.11-GCCcore-11.3.0.eb | 2 ++
 easybuild/easyconfigs/l/libdap/libdap-3.20.11-GCCcore-12.3.0.eb | 2 ++
 easybuild/easyconfigs/l/libdap/libdap-3.20.7-GCCcore-10.3.0.eb  | 2 ++
 easybuild/easyconfigs/l/libdap/libdap-3.20.8-GCCcore-11.2.0.eb  | 2 ++
 4 files changed, 8 insertions(+)

diff --git a/easybuild/easyconfigs/l/libdap/libdap-3.20.11-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libdap/libdap-3.20.11-GCCcore-11.3.0.eb
index b911c8f3169..063ce985f47 100644
--- a/easybuild/easyconfigs/l/libdap/libdap-3.20.11-GCCcore-11.3.0.eb
+++ b/easybuild/easyconfigs/l/libdap/libdap-3.20.11-GCCcore-11.3.0.eb
@@ -17,6 +17,7 @@ builddependencies = [
     ('binutils', '2.38'),
     ('Bison', '3.8.2'),
     ('flex', '2.6.4'),
+    ('Autotools', '20220317'),
 ]
 
 dependencies = [
@@ -27,6 +28,7 @@ dependencies = [
     ('util-linux', '2.38'),
 ]
 
+preconfigopts = "autoreconf -fi && "
 configopts = 'TIRPC_LIBS="-ltirpc"'
 
 sanity_check_paths = {
diff --git a/easybuild/easyconfigs/l/libdap/libdap-3.20.11-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libdap/libdap-3.20.11-GCCcore-12.3.0.eb
index 39930ab196b..a6dbd52797f 100644
--- a/easybuild/easyconfigs/l/libdap/libdap-3.20.11-GCCcore-12.3.0.eb
+++ b/easybuild/easyconfigs/l/libdap/libdap-3.20.11-GCCcore-12.3.0.eb
@@ -17,6 +17,7 @@ builddependencies = [
     ('binutils', '2.40'),
     ('Bison', '3.8.2'),
     ('flex', '2.6.4'),
+    ('Autotools', '20220317'),
 ]
 
 dependencies = [
@@ -27,6 +28,7 @@ dependencies = [
     ('util-linux', '2.39'),
 ]
 
+preconfigopts = "autoreconf -fi && "
 configopts = 'TIRPC_LIBS="-ltirpc"'
 
 
diff --git a/easybuild/easyconfigs/l/libdap/libdap-3.20.7-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/libdap/libdap-3.20.7-GCCcore-10.3.0.eb
index d43917eb6b0..4a6837a20f1 100644
--- a/easybuild/easyconfigs/l/libdap/libdap-3.20.7-GCCcore-10.3.0.eb
+++ b/easybuild/easyconfigs/l/libdap/libdap-3.20.7-GCCcore-10.3.0.eb
@@ -17,6 +17,7 @@ builddependencies = [
     ('binutils', '2.36.1'),
     ('Bison', '3.7.6'),
     ('flex', '2.6.4'),
+    ('Autotools', '20220317'),
 ]
 
 dependencies = [
@@ -27,6 +28,7 @@ dependencies = [
     ('util-linux', '2.36'),
 ]
 
+preconfigopts = "autoreconf -fi && "
 configopts = 'TIRPC_LIBS="-ltirpc"'
 
 sanity_check_paths = {
diff --git a/easybuild/easyconfigs/l/libdap/libdap-3.20.8-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libdap/libdap-3.20.8-GCCcore-11.2.0.eb
index 5adc0a0f2ee..6e4a0237bff 100644
--- a/easybuild/easyconfigs/l/libdap/libdap-3.20.8-GCCcore-11.2.0.eb
+++ b/easybuild/easyconfigs/l/libdap/libdap-3.20.8-GCCcore-11.2.0.eb
@@ -17,6 +17,7 @@ builddependencies = [
     ('binutils', '2.37'),
     ('Bison', '3.7.6'),
     ('flex', '2.6.4'),
+    ('Autotools', '20220317'),
 ]
 
 dependencies = [
@@ -27,6 +28,7 @@ dependencies = [
     ('util-linux', '2.37'),
 ]
 
+preconfigopts = "autoreconf -fi && "
 configopts = 'TIRPC_LIBS="-ltirpc"'
 
 sanity_check_paths = {

From e8cd29fa696c2e467ef75fa6792e22cd4932f639 Mon Sep 17 00:00:00 2001
From: TopRichard <121792457+TopRichard@users.noreply.github.com>
Date: Fri, 6 Sep 2024 15:09:00 +0200
Subject: [PATCH 809/835] Update
 easybuild/easyconfigs/l/libdap/libdap-3.20.7-GCCcore-10.3.0.eb
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Bob Dröge <b.e.droge@rug.nl>
---
 easybuild/easyconfigs/l/libdap/libdap-3.20.7-GCCcore-10.3.0.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/l/libdap/libdap-3.20.7-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/libdap/libdap-3.20.7-GCCcore-10.3.0.eb
index 4a6837a20f1..c1cb33551f7 100644
--- a/easybuild/easyconfigs/l/libdap/libdap-3.20.7-GCCcore-10.3.0.eb
+++ b/easybuild/easyconfigs/l/libdap/libdap-3.20.7-GCCcore-10.3.0.eb
@@ -17,7 +17,7 @@ builddependencies = [
     ('binutils', '2.36.1'),
     ('Bison', '3.7.6'),
     ('flex', '2.6.4'),
-    ('Autotools', '20220317'),
+    ('Autotools', '20210128'),
 ]
 
 dependencies = [

From 667b2c93c7b659b2e7a3bd6254f2ef89c68e2e8d Mon Sep 17 00:00:00 2001
From: TopRichard <121792457+TopRichard@users.noreply.github.com>
Date: Fri, 6 Sep 2024 15:09:07 +0200
Subject: [PATCH 810/835] Update
 easybuild/easyconfigs/l/libdap/libdap-3.20.8-GCCcore-11.2.0.eb
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Bob Dröge <b.e.droge@rug.nl>
---
 easybuild/easyconfigs/l/libdap/libdap-3.20.8-GCCcore-11.2.0.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/l/libdap/libdap-3.20.8-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libdap/libdap-3.20.8-GCCcore-11.2.0.eb
index 6e4a0237bff..1172b66d8f2 100644
--- a/easybuild/easyconfigs/l/libdap/libdap-3.20.8-GCCcore-11.2.0.eb
+++ b/easybuild/easyconfigs/l/libdap/libdap-3.20.8-GCCcore-11.2.0.eb
@@ -17,7 +17,7 @@ builddependencies = [
     ('binutils', '2.37'),
     ('Bison', '3.7.6'),
     ('flex', '2.6.4'),
-    ('Autotools', '20220317'),
+    ('Autotools', '20210726'),
 ]
 
 dependencies = [

From 0b7bc593d6a784e7d57ba605c3ef6d295271ce22 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Petr=20Kr=C3=A1l?= <petr@inuits.eu>
Date: Fri, 6 Sep 2024 17:10:42 +0200
Subject: [PATCH 811/835] adding easyconfigs: lrcalc-2.1-GCCcore-13.2.0.eb

---
 .../l/lrcalc/lrcalc-2.1-GCCcore-13.2.0.eb     | 31 +++++++++++++++++++
 1 file changed, 31 insertions(+)
 create mode 100644 easybuild/easyconfigs/l/lrcalc/lrcalc-2.1-GCCcore-13.2.0.eb

diff --git a/easybuild/easyconfigs/l/lrcalc/lrcalc-2.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/lrcalc/lrcalc-2.1-GCCcore-13.2.0.eb
new file mode 100644
index 00000000000..aa14572bef6
--- /dev/null
+++ b/easybuild/easyconfigs/l/lrcalc/lrcalc-2.1-GCCcore-13.2.0.eb
@@ -0,0 +1,31 @@
+easyblock = 'ConfigureMake'
+
+name = 'lrcalc'
+version = '2.1'
+
+homepage = 'https://sites.math.rutgers.edu/~asbuch/lrcalc/'
+description = """The Littlewood-Richardson Calculator is a program
+ designed to compute Littlewood-Richardson coefficients."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
+
+source_urls = ['https://math.rutgers.edu/~asbuch/lrcalc/']
+sources = [SOURCE_TAR_GZ]
+checksums = ['996ac00e6ea8321ef09b34478f5379f613933c3254aeba624b6419b8afa5df57']
+
+builddependencies = [
+    ('binutils', '2.40'),
+]
+
+sanity_check_paths = {
+    'files': [
+        'bin/lrcalc',
+        'lib/liblrcalc.%s' % SHLIB_EXT,
+        'include/lrcalc/ivector.h',
+    ],
+    'dirs': []
+}
+
+sanity_check_commands = ["lrcalc 2>&1 | grep '^Usage:'"]
+
+moduleclass = 'math'

From 0f401ecbd138d5666a7f773f0d8ad7022d37aca4 Mon Sep 17 00:00:00 2001
From: maximm <maximm@tcn1.local.snellius.surf.nl>
Date: Fri, 6 Sep 2024 17:41:09 +0200
Subject: [PATCH 812/835] adding easyconfigs: Mercurial-6.8.1-GCCcore-13.3.0.eb

---
 .../Mercurial-6.8.1-GCCcore-13.3.0.eb         | 31 +++++++++++++++++++
 1 file changed, 31 insertions(+)
 create mode 100644 easybuild/easyconfigs/m/Mercurial/Mercurial-6.8.1-GCCcore-13.3.0.eb

diff --git a/easybuild/easyconfigs/m/Mercurial/Mercurial-6.8.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/m/Mercurial/Mercurial-6.8.1-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..a733004f29a
--- /dev/null
+++ b/easybuild/easyconfigs/m/Mercurial/Mercurial-6.8.1-GCCcore-13.3.0.eb
@@ -0,0 +1,31 @@
+# #
+# Author:    Robert Mijakovic <robert.mijakovic@lxp.lu>
+# #
+easyblock = 'PythonPackage'
+
+name = 'Mercurial'
+version = '6.8.1'
+
+homepage = 'https://www.mercurial-scm.org'
+description = """Mercurial is a free, distributed source control management tool. It efficiently handles projects
+of any size and offers an easy and intuitive interface.
+"""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+source_urls = ['https://www.%(namelower)s-scm.org/release/']
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['030e8a7a6d590e4eaeb403ee25675615cd80d236f3ab8a0b56dcc84181158b05']
+
+dependencies = [
+    ('binutils', '2.42'),
+    ('Python', '3.12.3'),
+]
+
+download_dep_fail = True
+sanity_pip_check = True
+use_pip = True
+
+sanity_check_commands = ['hg --help']
+
+moduleclass = 'tools'

From 6c1a16cc45e905347c1ac77e9feac5a762156add Mon Sep 17 00:00:00 2001
From: SebastianAchilles <s.achilles@fz-juelich.de>
Date: Fri, 6 Sep 2024 18:05:12 +0200
Subject: [PATCH 813/835] Use https for homepage in
 libmatheval-1.1.11-GCCcore-13.3.0.eb

---
 .../l/libmatheval/libmatheval-1.1.11-GCCcore-13.3.0.eb          | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-GCCcore-13.3.0.eb
index 4cea27b91dc..b8bf07966b1 100644
--- a/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-GCCcore-13.3.0.eb
+++ b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-GCCcore-13.3.0.eb
@@ -3,7 +3,7 @@ easyblock = 'ConfigureMake'
 name = 'libmatheval'
 version = '1.1.11'  # still the latest version available on the ftp mirror
 
-homepage = 'http://www.gnu.org/software/libmatheval/'
+homepage = 'https://www.gnu.org/software/libmatheval/'
 description = """GNU libmatheval is a library (callable from C and Fortran) to parse
  and evaluate symbolic expressions input as text.
 """

From 7f711b9d3d61842f55a8d6c9d5349d10a263f51b Mon Sep 17 00:00:00 2001
From: Sebastian Achilles <s.achilles@fz-juelich.de>
Date: Fri, 6 Sep 2024 19:42:22 +0200
Subject: [PATCH 814/835] use version in byacc sources

---
 .../b/byacc/byacc-2.0.20240109-GCCcore-13.3.0.eb            | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/easybuild/easyconfigs/b/byacc/byacc-2.0.20240109-GCCcore-13.3.0.eb b/easybuild/easyconfigs/b/byacc/byacc-2.0.20240109-GCCcore-13.3.0.eb
index 292636d12e3..fa57e4306e6 100644
--- a/easybuild/easyconfigs/b/byacc/byacc-2.0.20240109-GCCcore-13.3.0.eb
+++ b/easybuild/easyconfigs/b/byacc/byacc-2.0.20240109-GCCcore-13.3.0.eb
@@ -10,9 +10,9 @@ description = """Berkeley Yacc (byacc) is generally conceded to be the best yacc
 
 toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
 
-source_urls = ['https://invisible-island.net/archives/byacc/current/']
-sources = ['byacc.tar.gz']
-checksums = ['e5e0c069fb15d454918568f77e90a60221373dd206a3d3c2da1e7daba3bae9ea']
+source_urls = ['https://invisible-island.net/archives/byacc/']
+sources = ['byacc-%s.tgz' % version.split('.')[2]]
+checksums = ['f2897779017189f1a94757705ef6f6e15dc9208ef079eea7f28abec577e08446']
 
 builddependencies = [('binutils', '2.42')]
 

From 3a35e90e8e6695d02bdd4cf30751f5a23682a5c9 Mon Sep 17 00:00:00 2001
From: Sebastian Achilles <s.achilles@fz-juelich.de>
Date: Fri, 6 Sep 2024 22:31:02 +0200
Subject: [PATCH 815/835] adding easyconfigs: fish-3.7.1-GCCcore-13.3.0.eb

---
 .../f/fish/fish-3.7.1-GCCcore-13.3.0.eb       | 34 +++++++++++++++++++
 1 file changed, 34 insertions(+)
 create mode 100644 easybuild/easyconfigs/f/fish/fish-3.7.1-GCCcore-13.3.0.eb

diff --git a/easybuild/easyconfigs/f/fish/fish-3.7.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/f/fish/fish-3.7.1-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..bcb975f1857
--- /dev/null
+++ b/easybuild/easyconfigs/f/fish/fish-3.7.1-GCCcore-13.3.0.eb
@@ -0,0 +1,34 @@
+easyblock = 'CMakeMake'
+
+name = 'fish'
+
+version = '3.7.1'
+
+homepage = 'https://fishshell.com/'
+description = """
+fish is a smart and user-friendly command line shell for Linux, macOS, and the rest of the family.
+"""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+source_urls = ['https://github.com/fish-shell/fish-shell/releases/download/%(version)s/']
+sources = [SOURCELOWER_TAR_XZ]
+checksums = ['614c9f5643cd0799df391395fa6bbc3649427bb839722ce3b114d3bbc1a3b250']
+
+builddependencies = [
+    ('binutils', '2.42'),
+    ('CMake', '3.29.3')
+]
+
+dependencies = [
+    ('ncurses', '6.5'),
+]
+
+sanity_check_paths = {
+    'files': ['bin/fish'],
+    'dirs': [],
+}
+
+sanity_check_commands = ['fish --version']
+
+moduleclass = 'tools'

From 51560e74b820a67720e1b66205ff1f720d10287e Mon Sep 17 00:00:00 2001
From: Sebastian Achilles <s.achilles@fz-juelich.de>
Date: Fri, 6 Sep 2024 22:35:29 +0200
Subject: [PATCH 816/835] adding easyconfigs:
 git-annex-10.20240731-GCCcore-13.3.0.eb, GHC-9.10.1-x86_64.eb,
 Stack-3.1.1-x86_64.eb

---
 .../easyconfigs/g/GHC/GHC-9.10.1-x86_64.eb    | 82 +++++++++++++++++++
 .../git-annex-10.20240731-GCCcore-13.3.0.eb   | 48 +++++++++++
 .../easyconfigs/s/Stack/Stack-3.1.1-x86_64.eb | 26 ++++++
 3 files changed, 156 insertions(+)
 create mode 100644 easybuild/easyconfigs/g/GHC/GHC-9.10.1-x86_64.eb
 create mode 100644 easybuild/easyconfigs/g/git-annex/git-annex-10.20240731-GCCcore-13.3.0.eb
 create mode 100644 easybuild/easyconfigs/s/Stack/Stack-3.1.1-x86_64.eb

diff --git a/easybuild/easyconfigs/g/GHC/GHC-9.10.1-x86_64.eb b/easybuild/easyconfigs/g/GHC/GHC-9.10.1-x86_64.eb
new file mode 100644
index 00000000000..d50730bb1b2
--- /dev/null
+++ b/easybuild/easyconfigs/g/GHC/GHC-9.10.1-x86_64.eb
@@ -0,0 +1,82 @@
+# This is a binary install that requires a './configure' and 'make install' steps for GHC.
+# We pull the centos7 binary tarball as is the one built against oldest system libs,
+# making it upwards compatible with newer distros.
+#
+# To get a functional 'ghc' binary on the SYSTEM toolchain we need
+# gmp headers and ncurses libtinfo.so.5, to avoid requiring extra OS deps for them
+# we include them in this bundle.
+# Binaries obtained with ghc do not require them, so it should be possible to use this bundle
+# just as builddep among different toolchains.
+#
+# For details, see the PR discussion:
+# https://github.com/easybuilders/easybuild-easyconfigs/pull/11310
+
+easyblock = 'Bundle'
+
+name = 'GHC'
+version = '9.10.1'
+versionsuffix = '-x86_64'
+
+homepage = 'https://haskell.org/ghc/'
+description = """The Glorious/Glasgow Haskell Compiler"""
+
+toolchain = SYSTEM
+
+builddependencies = [
+    ('binutils', '2.42'),
+    ('M4', '1.4.19'),
+]
+
+default_easyblock = 'ConfigureMake'
+
+local_distro_tarball = 'centos7'
+
+components = [
+    ('GMP', '6.3.0', {
+        'source_urls': [GNU_SOURCE],
+        'sources': [SOURCELOWER_TAR_BZ2],
+        'checksums': ['ac28211a7cfb609bae2e2c8d6058d66c8fe96434f740cf6fe2e47b000d1c20cb'],
+        'configopts': ' --enable-cxx',
+        'start_dir': '%(namelower)s-%(version)s',
+    }),
+    ('ncurses', '5.9', {
+        'source_urls': [GNU_SOURCE],
+        'sources': [SOURCE_TAR_GZ],
+        'patches': [
+            'ncurses-%(version)s_configure_darwin.patch',
+            'ncurses-%(version)s_fix-missing-const.patch',
+        ],
+        'checksums': [
+            '9046298fb440324c9d4135ecea7879ffed8546dd1b58e59430ea07a4633f563b',
+            '8c471fc2b1961a6e6e5981b7f7b3512e7fe58fcb04461aa4520157d4c1159998',
+            '027f7bd5876b761b48db624ddbdd106fa1c535dfb2752ef5a0eddeb2a8896cfd',
+        ],
+        'preconfigopts': "export CPPFLAGS='-P' && ",
+        'configopts': ' --with-shared --enable-overwrite --with-termlib=tinfo',
+        'start_dir': '%(namelower)s-%(version)s',
+    }),
+    (name, version, {
+        'source_urls': ['https://downloads.haskell.org/~ghc/%(version)s/'],
+        'sources': ['%%(namelower)s-%%(version)s-x86_64-%s-linux.tar.xz' % local_distro_tarball],
+        'checksums': ['fab143f10f845629cb1b373309b5680667cbaab298cf49827e383ee8a9ddf683'],
+        # ghc-8.6.5-x86_64-centos7-linux.tar.xz
+        'skipsteps': ['build'],
+        'preinstallopts': 'LD_LIBRARY_PATH="%(installdir)s/lib:$LD_LIBRARY_PATH" ',
+        'start_dir': '%(namelower)s-%(version)s-x86_64-unknown-linux',
+    }),
+]
+
+local_ncurses_libs = ["form", "menu", "ncurses", "panel", "tinfo"]
+
+sanity_check_paths = {
+    'files': ['lib/lib%s.%s' % (x, y) for x in ['gmp', 'gmpxx'] for y in [SHLIB_EXT, 'a']] +
+             ['include/gmp.h', 'include/gmpxx.h'] +
+             ['lib/lib%s%s.a' % (x, y) for x in local_ncurses_libs for y in ['', '_g']] +
+             ['lib/lib%s.%s' % (x, y) for x in local_ncurses_libs for y in [SHLIB_EXT]] +
+             ['bin/ghc', 'bin/ghci', 'bin/ghc-pkg', 'bin/runghc', 'bin/runhaskell'],
+    'dirs': ['bin', 'lib', 'share', 'include'],
+}
+
+sanity_check_commands = ['ghc --version']
+
+moduleclass = 'compiler'
diff --git a/easybuild/easyconfigs/g/git-annex/git-annex-10.20240731-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/git-annex/git-annex-10.20240731-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..89c70af2f45
--- /dev/null
+++ b/easybuild/easyconfigs/g/git-annex/git-annex-10.20240731-GCCcore-13.3.0.eb
@@ -0,0 +1,48 @@
+easyblock = 'MakeCp'
+
+name = 'git-annex'
+version = '10.20240731'
+
+homepage = 'https://git-annex.branchable.com'
+description = """git-annex allows managing large files with git, without storing the file contents in git. It can sync,
+backup, and archive your data, offline and online. Checksums and encryption keep your data safe and secure. Bring the
+power and distributed nature of git to bear on your large files with git-annex."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+builddependencies = [
+    ('binutils', '2.42')
+]
+
+dependencies = [
+    ('GHC', '9.10.1', '-x86_64', SYSTEM),
+    ('Stack', '3.1.1', '-x86_64', SYSTEM),
+    ('git', '2.45.1'),
+]
+
+sources = [{
+    'git_config': {'url': 'git://git-annex.branchable.com',
+                   'repo_name': '%(name)s',
+                   'tag': '%(version)s',
+                   'clone_into': '%(name)s-%(version)s',
+                   },
+    'filename': '%(name)s-%(version)s.tar.gz',
+}]
+
+checksums = [None]
+
+prebuildopts = "stack setup && stack build && "
+buildopts = "install-bins BUILDER=stack PREFIX=%(builddir)s"
+
+files_to_copy = [
+    (['git-annex', 'git-annex-shell'], 'bin'),
+]
+
+sanity_check_paths = {
+    'files': ['bin/git-annex', 'bin/git-annex-shell'],
+    'dirs': [],
+}
+
+sanity_check_commands = ['git-annex version']
+
+moduleclass = 'tools'
diff --git a/easybuild/easyconfigs/s/Stack/Stack-3.1.1-x86_64.eb b/easybuild/easyconfigs/s/Stack/Stack-3.1.1-x86_64.eb
new file mode 100644
index 00000000000..0a822a69cbd
--- /dev/null
+++ b/easybuild/easyconfigs/s/Stack/Stack-3.1.1-x86_64.eb
@@ -0,0 +1,26 @@
+easyblock = 'Tarball'
+
+name = 'Stack'
+version = '3.1.1'
+versionsuffix = '-x86_64'
+
+homepage = 'https://docs.haskellstack.org'
+description = """Stack is a cross-platform program for developing Haskell projects.
+It is intended for Haskellers both new and experienced."""
+
+toolchain = SYSTEM
+
+source_urls = ['https://github.com/commercialhaskell/stack/releases/download/v%(version)s/']
+sources = ['%(namelower)s-%(version)s-linux-x86_64.tar.gz']
+checksums = ['d096125ea3d987a55d17f7d4f8599ee2fd96bd2d0f033566e28ddfe248f730f9']
+
+modextrapaths = {'PATH': ''}
+
+sanity_check_paths = {
+    'files': ['stack'],
+    'dirs': ['doc'],
+}
+
+sanity_check_commands = ['stack --help']
+
+moduleclass = 'devel'

From 35feaf72998556814cd11adbea5d0084964977fb Mon Sep 17 00:00:00 2001
From: Sebastian Achilles <s.achilles@fz-juelich.de>
Date: Fri, 6 Sep 2024 22:46:30 +0200
Subject: [PATCH 817/835] adding easyconfigs: METIS-5.1.0-GCCcore-13.3.0.eb

---
 .../m/METIS/METIS-5.1.0-GCCcore-13.3.0.eb     | 36 +++++++++++++++++++
 1 file changed, 36 insertions(+)
 create mode 100644 easybuild/easyconfigs/m/METIS/METIS-5.1.0-GCCcore-13.3.0.eb

diff --git a/easybuild/easyconfigs/m/METIS/METIS-5.1.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..417e4750ef9
--- /dev/null
+++ b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-GCCcore-13.3.0.eb
@@ -0,0 +1,36 @@
+name = 'METIS'
+version = '5.1.0'
+
+homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/metis/overview'
+
+description = """
+ METIS is a set of serial programs for partitioning graphs, partitioning
+ finite element meshes, and producing fill reducing orderings for sparse
+ matrices. The algorithms implemented in METIS are based on the multilevel
+ recursive-bisection, multilevel k-way, and multi-constraint partitioning
+ schemes.
+"""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+toolchainopts = {'pic': True}
+
+source_urls = [
+    'http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis',
+    'http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/OLD',
+]
+sources = [SOURCELOWER_TAR_GZ]
+patches = ['%(name)s-%(version)s-use-doubles.patch']
+checksums = [
+    {'metis-5.1.0.tar.gz': '76faebe03f6c963127dbb73c13eab58c9a3faeae48779f049066a21c087c5db2'},
+    {'METIS-5.1.0-use-doubles.patch': '7e38a3ec8f2b8e3d189239bade5b28c0dd1c564485050109164fa71a6a767c67'},
+]
+
+# We use 32bit for indices and 64bit for content
+builddependencies = [
+    ('binutils', '2.42'),
+    ('CMake', '3.29.3'),
+]
+
+configopts = ['', 'shared=1']
+
+moduleclass = 'math'

From ab243abe21401004d45cccd3448606dbc070ed1e Mon Sep 17 00:00:00 2001
From: Sebastian Achilles <s.achilles@fz-juelich.de>
Date: Fri, 6 Sep 2024 22:50:02 +0200
Subject: [PATCH 818/835] adding easyconfigs: PLY-3.11-GCCcore-13.3.0.eb

---
 .../p/PLY/PLY-3.11-GCCcore-13.3.0.eb          | 22 +++++++++++++++++++
 1 file changed, 22 insertions(+)
 create mode 100644 easybuild/easyconfigs/p/PLY/PLY-3.11-GCCcore-13.3.0.eb

diff --git a/easybuild/easyconfigs/p/PLY/PLY-3.11-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/PLY/PLY-3.11-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..a5620c426d6
--- /dev/null
+++ b/easybuild/easyconfigs/p/PLY/PLY-3.11-GCCcore-13.3.0.eb
@@ -0,0 +1,22 @@
+easyblock = 'PythonPackage'
+
+name = 'PLY'
+version = '3.11'
+
+homepage = "https://www.dabeaz.com/ply/"
+description = """PLY is yet another implementation of lex and yacc for Python."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['00c7c1aaa88358b9c765b6d3000c6eec0ba42abca5351b095321aef446081da3']
+
+builddependencies = [('binutils', '2.42')]
+
+dependencies = [('Python', '3.12.3')]
+
+download_dep_fail = True
+use_pip = True
+sanity_pip_check = True
+
+moduleclass = 'lib'

From 434a6998a91e11948fbe4dd050394c325b96f9e4 Mon Sep 17 00:00:00 2001
From: Sebastian Achilles <s.achilles@fz-juelich.de>
Date: Fri, 6 Sep 2024 23:01:33 +0200
Subject: [PATCH 819/835] update easyconfig: GHC-9.10.1-x86_64.eb

---
 easybuild/easyconfigs/g/GHC/GHC-9.10.1-x86_64.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/g/GHC/GHC-9.10.1-x86_64.eb b/easybuild/easyconfigs/g/GHC/GHC-9.10.1-x86_64.eb
index d50730bb1b2..2074b920ebd 100644
--- a/easybuild/easyconfigs/g/GHC/GHC-9.10.1-x86_64.eb
+++ b/easybuild/easyconfigs/g/GHC/GHC-9.10.1-x86_64.eb
@@ -51,7 +51,7 @@ components = [
             '8c471fc2b1961a6e6e5981b7f7b3512e7fe58fcb04461aa4520157d4c1159998',
             '027f7bd5876b761b48db624ddbdd106fa1c535dfb2752ef5a0eddeb2a8896cfd',
         ],
-        'preconfigopts': "export CPPFLAGS='-P' && ",
+        'preconfigopts': "export CPPFLAGS='-P -std=c++14' && ",
         'configopts': ' --with-shared --enable-overwrite --with-termlib=tinfo',
         'start_dir': '%(namelower)s-%(version)s',
     }),

From 16de1658c683710bc8101eb3488528e8e007ded0 Mon Sep 17 00:00:00 2001
From: Sam Moors <smoors@users.noreply.github.com>
Date: Sun, 8 Sep 2024 19:32:40 +0200
Subject: [PATCH 820/835] add Cython builddep

---
 easybuild/easyconfigs/p/PyYAML/PyYAML-6.0.2-GCCcore-13.3.0.eb | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easybuild/easyconfigs/p/PyYAML/PyYAML-6.0.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/PyYAML/PyYAML-6.0.2-GCCcore-13.3.0.eb
index 70dfd98dcf4..50b9ad427e6 100644
--- a/easybuild/easyconfigs/p/PyYAML/PyYAML-6.0.2-GCCcore-13.3.0.eb
+++ b/easybuild/easyconfigs/p/PyYAML/PyYAML-6.0.2-GCCcore-13.3.0.eb
@@ -13,6 +13,7 @@ checksums = ['9377c381ac3fccad8df73d96b5139ef8b1a2c57a0d913e95ab0a2275d66b5caa']
 
 builddependencies = [
     ('binutils', '2.42'),
+    ('Cython', '3.0.10'),
 ]
 dependencies = [
     ('Python', '3.12.3'),

From ae8d2a0168b8dc33d0b624a177ca3724ae3846d1 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Petr=20Kr=C3=A1l?= <petr@inuits.eu>
Date: Tue, 10 Sep 2024 10:28:17 +0200
Subject: [PATCH 821/835] adding easyconfigs: NECAT-0.0.1-foss-2023a.eb

---
 .../n/NECAT/NECAT-0.0.1-foss-2023a.eb         | 30 +++++++++++++++++++
 1 file changed, 30 insertions(+)
 create mode 100644 easybuild/easyconfigs/n/NECAT/NECAT-0.0.1-foss-2023a.eb

diff --git a/easybuild/easyconfigs/n/NECAT/NECAT-0.0.1-foss-2023a.eb b/easybuild/easyconfigs/n/NECAT/NECAT-0.0.1-foss-2023a.eb
new file mode 100644
index 00000000000..33e3bfdd46b
--- /dev/null
+++ b/easybuild/easyconfigs/n/NECAT/NECAT-0.0.1-foss-2023a.eb
@@ -0,0 +1,30 @@
+easyblock = 'MakeCp'
+
+name = 'NECAT'
+version = '0.0.1'
+
+homepage = 'https://github.com/xiaochuanle/NECAT'
+description = """NECAT is an error correction and de-novo assembly tool for Nanopore long noisy reads.)."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+source_urls = ['https://github.com/xiaochuanle/NECAT/archive/']
+sources = ['v%(version)s_update20200803.tar.gz']
+checksums = ['5ddd147b5be6b1fac2f6c10b18c9b587838f2304d2584087c4ed6f628eced06c']
+
+builddependencies = [('binutils', '2.40')]
+
+start_dir = 'src'
+
+files_to_copy = [
+    (['../Linux-amd64/bin/*'], 'bin'),
+]
+
+sanity_check_paths = {
+    'files': ['bin/%(namelower)s.pl'],
+    'dirs': [],
+}
+
+sanity_check_commands = ['%(namelower)s.pl --help']
+
+moduleclass = 'bio'

From 1e44aa30fde9755638affe8c18e954e659ffb40b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Petr=20Kr=C3=A1l?= <petr@inuits.eu>
Date: Tue, 10 Sep 2024 11:11:02 +0200
Subject: [PATCH 822/835] add missing dependency

---
 easybuild/easyconfigs/n/NECAT/NECAT-0.0.1-foss-2023a.eb | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/easybuild/easyconfigs/n/NECAT/NECAT-0.0.1-foss-2023a.eb b/easybuild/easyconfigs/n/NECAT/NECAT-0.0.1-foss-2023a.eb
index 33e3bfdd46b..dbc35f62054 100644
--- a/easybuild/easyconfigs/n/NECAT/NECAT-0.0.1-foss-2023a.eb
+++ b/easybuild/easyconfigs/n/NECAT/NECAT-0.0.1-foss-2023a.eb
@@ -14,6 +14,8 @@ checksums = ['5ddd147b5be6b1fac2f6c10b18c9b587838f2304d2584087c4ed6f628eced06c']
 
 builddependencies = [('binutils', '2.40')]
 
+dependencies = [('Perl', '5.36.1')]
+
 start_dir = 'src'
 
 files_to_copy = [

From 184d7ce926bcc53b114596100ac9f6123a0efe1e Mon Sep 17 00:00:00 2001
From: ankekreuzer <a.kreuzer@fz-juelich.de>
Date: Tue, 10 Sep 2024 11:39:17 +0200
Subject: [PATCH 823/835] Added mpifileutils (plus missing deps) and maeparser
 to the gompi-2024a toolchain

---
 .../d/dtcmp/dtcmp-1.1.5-gompi-2024a.eb        | 39 ++++++++++++++++
 .../l/libcircle/libcircle-0.3-gompi-2024a.eb  | 38 ++++++++++++++++
 .../l/lwgrp/lwgrp-1.0.6-gompi-2024a.eb        | 36 +++++++++++++++
 .../maeparser/maeparser-1.3.1-gompi-2024a.eb  | 26 +++++++++++
 .../mpifileutils-0.11.1-gompi-2024a.eb        | 45 +++++++++++++++++++
 5 files changed, 184 insertions(+)
 create mode 100644 easybuild/easyconfigs/d/dtcmp/dtcmp-1.1.5-gompi-2024a.eb
 create mode 100644 easybuild/easyconfigs/l/libcircle/libcircle-0.3-gompi-2024a.eb
 create mode 100644 easybuild/easyconfigs/l/lwgrp/lwgrp-1.0.6-gompi-2024a.eb
 create mode 100644 easybuild/easyconfigs/m/maeparser/maeparser-1.3.1-gompi-2024a.eb
 create mode 100644 easybuild/easyconfigs/m/mpifileutils/mpifileutils-0.11.1-gompi-2024a.eb

diff --git a/easybuild/easyconfigs/d/dtcmp/dtcmp-1.1.5-gompi-2024a.eb b/easybuild/easyconfigs/d/dtcmp/dtcmp-1.1.5-gompi-2024a.eb
new file mode 100644
index 00000000000..5143b629849
--- /dev/null
+++ b/easybuild/easyconfigs/d/dtcmp/dtcmp-1.1.5-gompi-2024a.eb
@@ -0,0 +1,39 @@
+#
+# Author:    Robert Mijakovic <robert.mijakovic@lxp.lu>
+#
+easyblock = 'ConfigureMake'
+
+name = 'dtcmp'
+version = '1.1.5'
+
+homepage = 'https://github.com/LLNL/dtcmp'
+description = """The Datatype Comparison (DTCMP) Library provides pre-defined and user-defined
+comparison operations to compare the values of two items which can be arbitrary MPI datatypes.
+Using these comparison operations, the library provides various routines for manipulating data,
+which may be distributed over the processes of an MPI communicator."""
+
+toolchain = {'name': 'gompi', 'version': '2024a'}
+
+github_account = 'LLNL'
+source_urls = [GITHUB_SOURCE]
+sources = ['v%(version)s.tar.gz']
+checksums = ['5c3d672fcf1be81e9afb65ef3f860a7dfe0f1bd79360ac63848acfe4d44439c9']
+
+builddependencies = [
+    ('Autotools', '20231222'),
+    ('pkgconf', '2.2.0'),
+]
+
+dependencies = [
+    ('lwgrp', '1.0.6'),
+]
+
+preconfigopts = './autogen.sh && '
+configopts = '--with-lwgrp=$EBROOTLWGRP'
+
+sanity_check_paths = {
+    'files': ['include/%(name)s.h', 'lib/lib%%(name)s.%s' % SHLIB_EXT, 'share/%(name)s/README.md'],
+    'dirs': []
+}
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/l/libcircle/libcircle-0.3-gompi-2024a.eb b/easybuild/easyconfigs/l/libcircle/libcircle-0.3-gompi-2024a.eb
new file mode 100644
index 00000000000..1ea2630b327
--- /dev/null
+++ b/easybuild/easyconfigs/l/libcircle/libcircle-0.3-gompi-2024a.eb
@@ -0,0 +1,38 @@
+##
+# Authors:
+# * Petar Forai <petar.forai@gmi.oeaw.ac.at>
+# * Robert Mijakovic <robert.mijakovic@lxp.lu>
+##
+easyblock = 'ConfigureMake'
+
+name = 'libcircle'
+version = '0.3'
+
+homepage = 'https://github.com/hpc/libcircle/'
+
+description = """
+ An API to provide an efficient distributed queue on a cluster. libcircle is an
+ API for distributing embarrassingly parallel workloads using self-stabilization.
+"""
+
+toolchain = {'name': 'gompi', 'version': '2024a'}
+toolchainopts = {'usempi': True, 'pic': True}
+
+github_account = 'hpc'
+source_urls = [GITHUB_SOURCE]
+sources = ['v%(version)s.tar.gz']
+checksums = ['fd8bc6e4dcc6fdec9d2a3d1c78a4060948ae4f11f0b278792610d6c05d53e14c']
+
+builddependencies = [
+    ('Autotools', '20231222'),
+    ('pkgconf', '2.2.0'),
+]
+
+preconfigopts = './autogen.sh && '
+
+sanity_check_paths = {
+    'files': ['include/%(name)s.h', 'lib/%(name)s.a', 'lib/%%(name)s.%s' % SHLIB_EXT],
+    'dirs': ['lib/pkgconfig'],
+}
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/l/lwgrp/lwgrp-1.0.6-gompi-2024a.eb b/easybuild/easyconfigs/l/lwgrp/lwgrp-1.0.6-gompi-2024a.eb
new file mode 100644
index 00000000000..c36ee58b273
--- /dev/null
+++ b/easybuild/easyconfigs/l/lwgrp/lwgrp-1.0.6-gompi-2024a.eb
@@ -0,0 +1,36 @@
+#
+# Author:    Robert Mijakovic <robert.mijakovic@lxp.lu>
+#
+easyblock = 'ConfigureMake'
+
+name = 'lwgrp'
+version = '1.0.6'
+
+homepage = 'https://github.com/LLNL/lwgrp'
+description = """The light-weight group library defines data structures and collective operations to
+group MPI processes as an ordered set.  Such groups are useful as substitutes for MPI communicators
+when the overhead of communicator creation is too costly.  For example, certain sorting algorithms
+recursively divide processes into subgroups as the sort algorithm progresses.  These groups may be
+different with each invocation, so that it is inefficient to create and destroy communicators during
+the sort routine."""
+
+toolchain = {'name': 'gompi', 'version': '2024a'}
+
+github_account = 'LLNL'
+source_urls = [GITHUB_SOURCE]
+sources = ['v%(version)s.tar.gz']
+checksums = ['108e622441028b7f88223244c9117d5de18a91fd7c246bfa48802b5c585557d0']
+
+builddependencies = [
+    ('Autotools', '20231222'),
+    ('pkgconf', '2.2.0'),
+]
+
+preconfigopts = './autogen.sh && '
+
+sanity_check_paths = {
+    'files': ['include/%(name)s.h', 'lib/lib%%(name)s.%s' % SHLIB_EXT],
+    'dirs': ['share/%(name)s'],
+}
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/m/maeparser/maeparser-1.3.1-gompi-2024a.eb b/easybuild/easyconfigs/m/maeparser/maeparser-1.3.1-gompi-2024a.eb
new file mode 100644
index 00000000000..a757e81653a
--- /dev/null
+++ b/easybuild/easyconfigs/m/maeparser/maeparser-1.3.1-gompi-2024a.eb
@@ -0,0 +1,26 @@
+easyblock = 'CMakeMake'
+
+name = 'maeparser'
+version = '1.3.1'
+
+homepage = 'https://github.com/schrodinger/maeparser'
+description = "maeparser is a parser for Schrodinger Maestro files."
+
+toolchain = {'name': 'gompi', 'version': '2024a'}
+
+source_urls = ['https://github.com/schrodinger/maeparser/archive/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['a8d80f67d1b9be6e23b9651cb747f4a3200132e7d878a285119c86bf44568e36']
+
+builddependencies = [
+    ('CMake', '3.29.3'),
+]
+
+dependencies = [('Boost', '1.85.0')]
+
+sanity_check_paths = {
+    'files': ['lib/libmaeparser.%s' % SHLIB_EXT],
+    'dirs': ['include/maeparser', 'lib/cmake'],
+}
+
+moduleclass = 'tools'
diff --git a/easybuild/easyconfigs/m/mpifileutils/mpifileutils-0.11.1-gompi-2024a.eb b/easybuild/easyconfigs/m/mpifileutils/mpifileutils-0.11.1-gompi-2024a.eb
new file mode 100644
index 00000000000..f486ed4effd
--- /dev/null
+++ b/easybuild/easyconfigs/m/mpifileutils/mpifileutils-0.11.1-gompi-2024a.eb
@@ -0,0 +1,45 @@
+easyblock = 'CMakeMake'
+
+name = 'mpifileutils'
+version = "0.11.1"
+
+homepage = 'https://hpc.github.io/mpifileutils/'
+
+description = """
+ MPI-Based File Utilities For Distributed Systems
+"""
+
+toolchain = {'name': 'gompi', 'version': '2024a'}
+
+github_account = 'hpc'
+source_urls = [GITHUB_SOURCE]
+sources = ['v%(version)s.tar.gz']
+checksums = ['e2cba53309b5b3ee581b6ff82e4e66f54628370cce694c34224ed947fece32d4']
+
+builddependencies = [
+    ('CMake', '3.29.3'),
+]
+
+dependencies = [
+    ('attr', '2.5.2'),
+    ('bzip2', '1.0.8'),
+    ('lwgrp', '1.0.6'),
+    ('dtcmp', '1.1.5'),
+    ('libarchive', '3.7.4'),
+    ('libcircle', '0.3'),
+]
+
+_binaries = [
+    'dbcast', 'dbz2', 'dchmod', 'dcmp', 'dcp', 'ddup', 'dfind',
+    'dreln', 'drm', 'dstripe', 'dsync', 'dtar', 'dwalk'
+]
+
+sanity_check_paths = {
+    'files': ['bin/%s' % x for x in _binaries] +
+             ['include/mfu.h', 'lib/libmfu.%s' % SHLIB_EXT],
+    'dirs': []
+}
+
+sanity_check_commands = ['%s --help 2>&1 | grep Usage' % x for x in _binaries]
+
+moduleclass = 'tools'

From 1fd7655ba65d0366ffc55eb88bf2f51e15941791 Mon Sep 17 00:00:00 2001
From: Alexander Grund <alexander.grund@tu-dresden.de>
Date: Tue, 10 Sep 2024 13:51:37 +0200
Subject: [PATCH 824/835] adding easyconfigs:
 fonttools-4.53.1-GCCcore-11.3.0.eb, fonttools-4.53.1-GCCcore-12.2.0.eb,
 fonttools-4.53.1-GCCcore-12.3.0.eb, fonttools-4.53.1-GCCcore-13.2.0.eb,
 fonttools-4.53.1-GCCcore-13.3.0.eb

---
 .../fonttools-4.53.1-GCCcore-11.3.0.eb        | 26 +++++++++++++++++++
 .../fonttools-4.53.1-GCCcore-12.2.0.eb        | 26 +++++++++++++++++++
 .../fonttools-4.53.1-GCCcore-12.3.0.eb        | 26 +++++++++++++++++++
 .../fonttools-4.53.1-GCCcore-13.2.0.eb        | 26 +++++++++++++++++++
 .../fonttools-4.53.1-GCCcore-13.3.0.eb        | 26 +++++++++++++++++++
 5 files changed, 130 insertions(+)
 create mode 100644 easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-11.3.0.eb
 create mode 100644 easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-12.2.0.eb
 create mode 100644 easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-12.3.0.eb
 create mode 100644 easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-13.2.0.eb
 create mode 100644 easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-13.3.0.eb

diff --git a/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-11.3.0.eb
new file mode 100644
index 00000000000..5720e7567a0
--- /dev/null
+++ b/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-11.3.0.eb
@@ -0,0 +1,26 @@
+easyblock = 'PythonPackage'
+
+name = 'fonttools'
+version = '4.53.1'
+
+homepage = 'https://python-markdown.github.io/'
+description = """
+fontTools is a library for manipulating fonts, written in Python.
+The project includes the TTX tool, that can convert TrueType and OpenType fonts to and from an XML text format, which is also called TTX.
+It supports TrueType, OpenType, AFM and to an extent Type 1 and some Mac-specific formats."""
+
+toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
+
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['e128778a8e9bc11159ce5447f76766cefbd876f44bd79aff030287254e4752c4']
+
+builddependencies = [('binutils', '2.38'),]
+dependencies = [('Python', '3.10.4'),]
+
+download_dep_fail = True
+sanity_pip_check = True
+use_pip = True
+
+options = {'modulename': 'fontTools'}
+
+moduleclass = 'devel'
diff --git a/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-12.2.0.eb
new file mode 100644
index 00000000000..098066f3c22
--- /dev/null
+++ b/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-12.2.0.eb
@@ -0,0 +1,26 @@
+easyblock = 'PythonPackage'
+
+name = 'fonttools'
+version = '4.53.1'
+
+homepage = 'https://python-markdown.github.io/'
+description = """
+fontTools is a library for manipulating fonts, written in Python.
+The project includes the TTX tool, that can convert TrueType and OpenType fonts to and from an XML text format, which is also called TTX.
+It supports TrueType, OpenType, AFM and to an extent Type 1 and some Mac-specific formats."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['e128778a8e9bc11159ce5447f76766cefbd876f44bd79aff030287254e4752c4']
+
+builddependencies = [('binutils', '2.39'),]
+dependencies = [('Python', '3.10.8'),]
+
+download_dep_fail = True
+sanity_pip_check = True
+use_pip = True
+
+options = {'modulename': 'fontTools'}
+
+moduleclass = 'devel'
diff --git a/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..e4089a48e5f
--- /dev/null
+++ b/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-12.3.0.eb
@@ -0,0 +1,26 @@
+easyblock = 'PythonPackage'
+
+name = 'fonttools'
+version = '4.53.1'
+
+homepage = 'https://python-markdown.github.io/'
+description = """
+fontTools is a library for manipulating fonts, written in Python.
+The project includes the TTX tool, that can convert TrueType and OpenType fonts to and from an XML text format, which is also called TTX.
+It supports TrueType, OpenType, AFM and to an extent Type 1 and some Mac-specific formats."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['e128778a8e9bc11159ce5447f76766cefbd876f44bd79aff030287254e4752c4']
+
+builddependencies = [('binutils', '2.40'),]
+dependencies = [('Python', '3.11.3'),]
+
+download_dep_fail = True
+sanity_pip_check = True
+use_pip = True
+
+options = {'modulename': 'fontTools'}
+
+moduleclass = 'devel'
diff --git a/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-13.2.0.eb
new file mode 100644
index 00000000000..0cfc4e2da74
--- /dev/null
+++ b/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-13.2.0.eb
@@ -0,0 +1,26 @@
+easyblock = 'PythonPackage'
+
+name = 'fonttools'
+version = '4.53.1'
+
+homepage = 'https://python-markdown.github.io/'
+description = """
+fontTools is a library for manipulating fonts, written in Python.
+The project includes the TTX tool, that can convert TrueType and OpenType fonts to and from an XML text format, which is also called TTX.
+It supports TrueType, OpenType, AFM and to an extent Type 1 and some Mac-specific formats."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
+
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['e128778a8e9bc11159ce5447f76766cefbd876f44bd79aff030287254e4752c4']
+
+builddependencies = [('binutils', '2.40'),]
+dependencies = [('Python', '3.11.5'),]
+
+download_dep_fail = True
+sanity_pip_check = True
+use_pip = True
+
+options = {'modulename': 'fontTools'}
+
+moduleclass = 'devel'
diff --git a/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-13.3.0.eb
new file mode 100644
index 00000000000..fb3904198ee
--- /dev/null
+++ b/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-13.3.0.eb
@@ -0,0 +1,26 @@
+easyblock = 'PythonPackage'
+
+name = 'fonttools'
+version = '4.53.1'
+
+homepage = 'https://python-markdown.github.io/'
+description = """
+fontTools is a library for manipulating fonts, written in Python.
+The project includes the TTX tool, that can convert TrueType and OpenType fonts to and from an XML text format, which is also called TTX.
+It supports TrueType, OpenType, AFM and to an extent Type 1 and some Mac-specific formats."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['e128778a8e9bc11159ce5447f76766cefbd876f44bd79aff030287254e4752c4']
+
+builddependencies = [('binutils', '2.42'),]
+dependencies = [('Python', '3.12.3'),]
+
+download_dep_fail = True
+sanity_pip_check = True
+use_pip = True
+
+options = {'modulename': 'fontTools'}
+
+moduleclass = 'devel'

From 4de11d81b966fc671187ef06ccee240620a07040 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 10 Sep 2024 14:15:26 +0200
Subject: [PATCH 825/835] adding easyconfigs: slepc4py-3.20.2-foss-2023a.eb

---
 .../s/slepc4py/slepc4py-3.20.2-foss-2023a.eb  | 26 +++++++++++++++++++
 1 file changed, 26 insertions(+)
 create mode 100644 easybuild/easyconfigs/s/slepc4py/slepc4py-3.20.2-foss-2023a.eb

diff --git a/easybuild/easyconfigs/s/slepc4py/slepc4py-3.20.2-foss-2023a.eb b/easybuild/easyconfigs/s/slepc4py/slepc4py-3.20.2-foss-2023a.eb
new file mode 100644
index 00000000000..c161116802d
--- /dev/null
+++ b/easybuild/easyconfigs/s/slepc4py/slepc4py-3.20.2-foss-2023a.eb
@@ -0,0 +1,26 @@
+easyblock = 'PythonPackage'
+
+name = 'slepc4py'
+version = '3.20.2'
+
+homepage = 'https://bitbucket.org/slepc/slepc4py'
+description = "Python bindings for SLEPc, the Scalable Library for Eigenvalue Problem Computations."
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+sources = [SOURCE_TAR_GZ]
+checksums = ['89ebd1964edd0eb63d4dbfa977d6f35408f4e19a3da290696fd1197901544bd8']
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SLEPc', '3.20.1'),
+    ('petsc4py', '3.20.3'),
+]
+
+download_dep_fail = True
+use_pip = True
+sanity_pip_check = True
+
+sanity_check_commands = ["python -c 'from slepc4py import SLEPc'"]
+
+moduleclass = 'tools'

From e1ad5234d77914706b73e29d59529f8ee06d6c8b Mon Sep 17 00:00:00 2001
From: Alexander Grund <alexander.grund@tu-dresden.de>
Date: Tue, 10 Sep 2024 14:24:15 +0200
Subject: [PATCH 826/835] Fix style

---
 .../f/fonttools/fonttools-4.53.1-GCCcore-11.3.0.eb         | 7 ++++---
 .../f/fonttools/fonttools-4.53.1-GCCcore-12.2.0.eb         | 7 ++++---
 .../f/fonttools/fonttools-4.53.1-GCCcore-12.3.0.eb         | 7 ++++---
 .../f/fonttools/fonttools-4.53.1-GCCcore-13.2.0.eb         | 7 ++++---
 .../f/fonttools/fonttools-4.53.1-GCCcore-13.3.0.eb         | 7 ++++---
 5 files changed, 20 insertions(+), 15 deletions(-)

diff --git a/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-11.3.0.eb
index 5720e7567a0..8453a35a695 100644
--- a/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-11.3.0.eb
+++ b/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-11.3.0.eb
@@ -6,7 +6,8 @@ version = '4.53.1'
 homepage = 'https://python-markdown.github.io/'
 description = """
 fontTools is a library for manipulating fonts, written in Python.
-The project includes the TTX tool, that can convert TrueType and OpenType fonts to and from an XML text format, which is also called TTX.
+The project includes the TTX tool, that can convert TrueType and OpenType fonts to and from an XML text format,
+which is also called TTX.
 It supports TrueType, OpenType, AFM and to an extent Type 1 and some Mac-specific formats."""
 
 toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
@@ -14,8 +15,8 @@ toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
 sources = [SOURCELOWER_TAR_GZ]
 checksums = ['e128778a8e9bc11159ce5447f76766cefbd876f44bd79aff030287254e4752c4']
 
-builddependencies = [('binutils', '2.38'),]
-dependencies = [('Python', '3.10.4'),]
+builddependencies = [('binutils', '2.38')]
+dependencies = [('Python', '3.10.4')]
 
 download_dep_fail = True
 sanity_pip_check = True
diff --git a/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-12.2.0.eb
index 098066f3c22..cfaada6dee8 100644
--- a/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-12.2.0.eb
+++ b/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-12.2.0.eb
@@ -6,7 +6,8 @@ version = '4.53.1'
 homepage = 'https://python-markdown.github.io/'
 description = """
 fontTools is a library for manipulating fonts, written in Python.
-The project includes the TTX tool, that can convert TrueType and OpenType fonts to and from an XML text format, which is also called TTX.
+The project includes the TTX tool, that can convert TrueType and OpenType fonts to and from an XML text format,
+which is also called TTX.
 It supports TrueType, OpenType, AFM and to an extent Type 1 and some Mac-specific formats."""
 
 toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
@@ -14,8 +15,8 @@ toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
 sources = [SOURCELOWER_TAR_GZ]
 checksums = ['e128778a8e9bc11159ce5447f76766cefbd876f44bd79aff030287254e4752c4']
 
-builddependencies = [('binutils', '2.39'),]
-dependencies = [('Python', '3.10.8'),]
+builddependencies = [('binutils', '2.39')]
+dependencies = [('Python', '3.10.8')]
 
 download_dep_fail = True
 sanity_pip_check = True
diff --git a/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-12.3.0.eb
index e4089a48e5f..bf71a8f341f 100644
--- a/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-12.3.0.eb
+++ b/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-12.3.0.eb
@@ -6,7 +6,8 @@ version = '4.53.1'
 homepage = 'https://python-markdown.github.io/'
 description = """
 fontTools is a library for manipulating fonts, written in Python.
-The project includes the TTX tool, that can convert TrueType and OpenType fonts to and from an XML text format, which is also called TTX.
+The project includes the TTX tool, that can convert TrueType and OpenType fonts to and from an XML text format,
+which is also called TTX.
 It supports TrueType, OpenType, AFM and to an extent Type 1 and some Mac-specific formats."""
 
 toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
@@ -14,8 +15,8 @@ toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
 sources = [SOURCELOWER_TAR_GZ]
 checksums = ['e128778a8e9bc11159ce5447f76766cefbd876f44bd79aff030287254e4752c4']
 
-builddependencies = [('binutils', '2.40'),]
-dependencies = [('Python', '3.11.3'),]
+builddependencies = [('binutils', '2.40')]
+dependencies = [('Python', '3.11.3')]
 
 download_dep_fail = True
 sanity_pip_check = True
diff --git a/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-13.2.0.eb
index 0cfc4e2da74..0e8a62e088b 100644
--- a/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-13.2.0.eb
+++ b/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-13.2.0.eb
@@ -6,7 +6,8 @@ version = '4.53.1'
 homepage = 'https://python-markdown.github.io/'
 description = """
 fontTools is a library for manipulating fonts, written in Python.
-The project includes the TTX tool, that can convert TrueType and OpenType fonts to and from an XML text format, which is also called TTX.
+The project includes the TTX tool, that can convert TrueType and OpenType fonts to and from an XML text format,
+which is also called TTX.
 It supports TrueType, OpenType, AFM and to an extent Type 1 and some Mac-specific formats."""
 
 toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
@@ -14,8 +15,8 @@ toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
 sources = [SOURCELOWER_TAR_GZ]
 checksums = ['e128778a8e9bc11159ce5447f76766cefbd876f44bd79aff030287254e4752c4']
 
-builddependencies = [('binutils', '2.40'),]
-dependencies = [('Python', '3.11.5'),]
+builddependencies = [('binutils', '2.40')]
+dependencies = [('Python', '3.11.5')]
 
 download_dep_fail = True
 sanity_pip_check = True
diff --git a/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-13.3.0.eb
index fb3904198ee..ed395cfd0ee 100644
--- a/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-13.3.0.eb
+++ b/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-13.3.0.eb
@@ -6,7 +6,8 @@ version = '4.53.1'
 homepage = 'https://python-markdown.github.io/'
 description = """
 fontTools is a library for manipulating fonts, written in Python.
-The project includes the TTX tool, that can convert TrueType and OpenType fonts to and from an XML text format, which is also called TTX.
+The project includes the TTX tool, that can convert TrueType and OpenType fonts to and from an XML text format,
+which is also called TTX.
 It supports TrueType, OpenType, AFM and to an extent Type 1 and some Mac-specific formats."""
 
 toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
@@ -14,8 +15,8 @@ toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
 sources = [SOURCELOWER_TAR_GZ]
 checksums = ['e128778a8e9bc11159ce5447f76766cefbd876f44bd79aff030287254e4752c4']
 
-builddependencies = [('binutils', '2.42'),]
-dependencies = [('Python', '3.12.3'),]
+builddependencies = [('binutils', '2.42')]
+dependencies = [('Python', '3.12.3')]
 
 download_dep_fail = True
 sanity_pip_check = True

From 6fc9e142fc467a4fe0753eb6aef4506b20c87ea1 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Petr=20Kr=C3=A1l?= <petr@inuits.eu>
Date: Tue, 10 Sep 2024 15:27:43 +0200
Subject: [PATCH 827/835] adding easyconfigs: Sagemath-10.4-foss-2023b.eb

---
 .../s/Sagemath/Sagemath-10.4-foss-2023b.eb    | 158 ++++++++++++++++++
 1 file changed, 158 insertions(+)
 create mode 100644 easybuild/easyconfigs/s/Sagemath/Sagemath-10.4-foss-2023b.eb

diff --git a/easybuild/easyconfigs/s/Sagemath/Sagemath-10.4-foss-2023b.eb b/easybuild/easyconfigs/s/Sagemath/Sagemath-10.4-foss-2023b.eb
new file mode 100644
index 00000000000..63b4aef04c6
--- /dev/null
+++ b/easybuild/easyconfigs/s/Sagemath/Sagemath-10.4-foss-2023b.eb
@@ -0,0 +1,158 @@
+easyblock = 'PythonBundle'
+
+name = 'Sagemath'
+version = '10.4'
+
+homepage = 'https://doc.sagemath.org/html/en/index.html'
+description = """Sage is open source mathematical software released under the GNU General Public Licence GPLv2+,
+ and includes packages that have compatible software licenses.
+ People all around the globe have contributed to the development of Sage. Full documentation is available online."""
+
+toolchain = {'name': 'foss', 'version': '2023b'}
+
+builddependencies = [
+    ('Cython', '3.0.10'),
+    ('Python-bundle-PyPI', '2023.10'),
+    ('Boost', '1.83.0'),
+]
+
+dependencies = [
+    ('Python', '3.11.5'),
+    ('SciPy-bundle', '2023.11'),
+    ('ECL', '24.5.10'),
+    ('FFLAS-FFPACK', '2.5.0'),
+    ('eclib', '20231212'),
+    ('GSL', '2.7'),
+    ('LinBox', '1.7.0'),
+    ('Singular', '4.4.0'),
+    ('libpng', '1.6.40'),
+    ('libgd', '2.3.3'),
+    ('m4ri', '20200125'),
+    ('cysignals', '1.11.4'),
+    ('gmpy2', '2.1.5'),
+    ('GMP-ECM', '7.0.5'),
+    ('MPFI', '1.5.4'),
+    ('cliquer', '1.21'),
+    ('nauty', '2.8.8'),
+    ('SYMMETRICA', '2.0'),
+    ('lcalc', '2.0.5'),
+    ('gap', '4.13.0'),
+    ('giac', '1.9.0-99'),
+    ('m4rie', '20200125'),
+    ('libhomfly', '1.02r6'),
+    ('libbraiding', '1.2'),
+    ('planarity', '3.0.2.0'),
+    ('rankwidth', '0.9'),
+    ('BRiAl', '1.2.12'),
+    ('bliss', '0.77'),
+    ('coxeter', '20180226'),
+    ('mcqd', '1.0.0'),
+    ('SharedMeatAxe', '1.0.1'),
+    ('sirocco', '2.1.0'),
+    ('tdlib', '0.9.3'),
+    ('pkgconfig', '1.5.5', '-python'),
+    ('matplotlib', '3.8.2'),
+    ('networkx', '3.2.1'),
+    ('sympy', '1.12'),
+    ('IPython', '8.17.2'),
+    ('Pillow', '10.2.0'),
+    ('fpylll', '0.6.1'),
+    ('primecountpy', '0.1.0'),
+    ('lrcalc', '2.1'),
+    ('PyZMQ', '25.1.2'),
+    ('tornado', '6.4'),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    ('cypari2', '2.2.0', {
+        'checksums': ['817606bf661b71d33e1d012421907a4f8fb09dd81b7d3e3ae179b3978020bbf1'],
+    }),
+    ('memory_allocator', '0.1.4', {
+        'checksums': ['d609216b03031967e2b45a804b12ff9029578f4ec019fde42cf6aed6ca09efe4'],
+    }),
+    ('sage_setup', version, {
+        'source_tmpl': SOURCE_PY3_WHL,
+        'checksums': ['4797ceae2f5f636a756f4121011246445611f7a56bced2df431328fe013c52c7'],
+    }),
+    ('conway_polynomials', '0.10', {
+        'source_tmpl': SOURCE_PY3_WHL,
+        'checksums': ['a354b4ac0a9985da75e2ac6ec6d7de2902396eff48913eeed86a962486171c28'],
+    }),
+    ('comm', '0.2.2', {
+        'source_tmpl': SOURCE_PY3_WHL,
+        'checksums': ['e6fb86cb70ff661ee8c9c14e7d36d6de3b4066f1441be4063df9c5009f0a64d3'],
+    }),
+    ('debugpy', '1.8.5', {
+        'source_tmpl': SOURCE_WHL,
+        'checksums': ['55919dce65b471eff25901acf82d328bbd5b833526b6c1364bd5133754777a44'],
+    }),
+    ('nest_asyncio', '1.6.0', {
+        'source_tmpl': SOURCE_PY3_WHL,
+        'checksums': ['87af6efd6b5e897c81050477ef65c62e2b2f35d51703cae01aff2905b1852e1c'],
+    }),
+    ('ipykernel', '6.29.5', {
+        'source_tmpl': SOURCE_PY3_WHL,
+        'checksums': ['afdb66ba5aa354b09b91379bac28ae4afebbb30e8b39510c9690afb7a10421b5'],
+    }),
+    ('jupyterlab_widgets', '3.0.13', {
+        'source_tmpl': SOURCE_PY3_WHL,
+        'checksums': ['e3cda2c233ce144192f1e29914ad522b2f4c40e77214b0cc97377ca3d323db54'],
+    }),
+    ('widgetsnbextension', '4.0.13', {
+        'source_tmpl': SOURCE_PY3_WHL,
+        'checksums': ['74b2692e8500525cc38c2b877236ba51d34541e6385eeed5aec15a70f88a6c71'],
+    }),
+    ('ipywidgets', '8.1.5', {
+        'source_tmpl': SOURCE_PY3_WHL,
+        'checksums': ['3290f526f87ae6e77655555baba4f36681c555b8bdbbff430b70e52c34c86245'],
+    }),
+    ('jupyter_core', '5.7.2', {
+        'source_tmpl': SOURCE_PY3_WHL,
+        'checksums': ['4f7315d2f6b4bcf2e3e7cb6e46772eba760ae459cd1f59d29eb57b0a01bd7409'],
+    }),
+    ('jupyter_client', '8.6.2', {
+        'source_tmpl': SOURCE_PY3_WHL,
+        'checksums': ['50cbc5c66fd1b8f65ecb66bc490ab73217993632809b6e505687de18e9dea39f'],
+    }),
+    ('lrcalc', '2.1', {
+        'checksums': ['e3a0509aeda487b412b391a52e817ca36b5c063a8305e09fd54d53259dd6aaa9'],
+    }),
+    ('%(namelower)s_standard', version, {
+        'modulename': 'sage',
+        'checksums': ['f6579e85f33bd9bb6e9b991bfc4c49dab1e649858ed9ee41c7cec75cb92d4c62'],
+    }),
+    ('%(namelower)s_bliss', version, {
+        'modulename': False,
+        'checksums': ['70cccef849908436c2f9f1aabb3992a21c90d3ce99d1a965743f0fdec3735d32'],
+    }),
+    ('%(namelower)s_coxeter3', version, {
+        'modulename': False,
+        'checksums': ['c4f20204b91a696caeb7ad7cf33d2b0398d26d287085b2cb9434e8b067716fca'],
+    }),
+    ('%(namelower)s_mcqd', version, {
+        'modulename': False,
+        'checksums': ['6a140d8b3866ea27aa5966f3aab86a882785862fb00ae37087beb09105b94175'],
+    }),
+    ('%(namelower)s_meataxe', version, {
+        'modulename': False,
+        'checksums': ['5b625333c3168fc2ab55d32ad7e8c41912858bde8010b5aadc70c6450fa967e8'],
+    }),
+    ('%(namelower)s_sirocco', version, {
+        'modulename': False,
+        'checksums': ['499304b3331751d7b0f62de8379afb073d55f144c5f73775da0c5b92160e3a7c'],
+    }),
+    ('%(namelower)s_tdlib', version, {
+        'modulename': False,
+        'checksums': ['018497a1e220d3320a37d1acb3eee59ec820d167c7916e95f0508709a2e31703'],
+    }),
+]
+
+sanity_check_commands = [
+    "sage --help",
+    "python -c 'from sage.all import *'",
+]
+
+moduleclass = 'math'

From 0a011dc82b76a3407c2328fa3d6125773eb790e3 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Petr=20Kr=C3=A1l?= <petr@inuits.eu>
Date: Tue, 10 Sep 2024 19:10:59 +0200
Subject: [PATCH 828/835] fix dependency version

---
 easybuild/easyconfigs/s/Sagemath/Sagemath-10.4-foss-2023b.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/s/Sagemath/Sagemath-10.4-foss-2023b.eb b/easybuild/easyconfigs/s/Sagemath/Sagemath-10.4-foss-2023b.eb
index 63b4aef04c6..dcc9d919c13 100644
--- a/easybuild/easyconfigs/s/Sagemath/Sagemath-10.4-foss-2023b.eb
+++ b/easybuild/easyconfigs/s/Sagemath/Sagemath-10.4-foss-2023b.eb
@@ -21,7 +21,7 @@ dependencies = [
     ('SciPy-bundle', '2023.11'),
     ('ECL', '24.5.10'),
     ('FFLAS-FFPACK', '2.5.0'),
-    ('eclib', '20231212'),
+    ('eclib', '20240408'),
     ('GSL', '2.7'),
     ('LinBox', '1.7.0'),
     ('Singular', '4.4.0'),

From 1736a123b1685836452587a5c51793257570bb2d Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 10 Sep 2024 19:56:19 +0200
Subject: [PATCH 829/835] remove Highway build dependency in Brunsli
 easyconfigs, since it's not actually required at all

---
 easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.2.0.eb | 1 -
 easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.3.0.eb | 1 -
 easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-11.3.0.eb | 1 -
 easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-12.2.0.eb | 1 -
 easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-12.3.0.eb | 1 -
 easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-13.2.0.eb | 1 -
 easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-13.3.0.eb | 1 -
 7 files changed, 7 deletions(-)

diff --git a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.2.0.eb
index 22f38cbf5f9..9e505b4df5e 100644
--- a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.2.0.eb
+++ b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.2.0.eb
@@ -21,7 +21,6 @@ builddependencies = [
 
 dependencies = [
     ('Brotli', '1.0.9'),
-    ('Highway', '0.12.2'),
 ]
 
 # skip use of third_party directory, since we provide Brotli via a proper dependency
diff --git a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.3.0.eb
index 301194a32a4..0661abf0609 100644
--- a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.3.0.eb
+++ b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.3.0.eb
@@ -22,7 +22,6 @@ builddependencies = [
 
 dependencies = [
     ('Brotli', '1.0.9'),
-    ('Highway', '0.12.2'),
 ]
 
 # skip use of third_party directory, since we provide Brotli via a proper dependency
diff --git a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-11.3.0.eb
index 7522f1025e3..57bba400bde 100644
--- a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-11.3.0.eb
+++ b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-11.3.0.eb
@@ -22,7 +22,6 @@ builddependencies = [
 
 dependencies = [
     ('Brotli', '1.0.9'),
-    ('Highway', '1.0.3'),
 ]
 
 # skip use of third_party directory, since we provide Brotli via a proper dependency
diff --git a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-12.2.0.eb
index cc914cae6cd..df29a7bda20 100644
--- a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-12.2.0.eb
+++ b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-12.2.0.eb
@@ -22,7 +22,6 @@ builddependencies = [
 
 dependencies = [
     ('Brotli', '1.0.9'),
-    ('Highway', '1.0.3'),
 ]
 
 # skip use of third_party directory, since we provide Brotli via a proper dependency
diff --git a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-12.3.0.eb
index 22917f651e9..42e15bb4356 100644
--- a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-12.3.0.eb
+++ b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-12.3.0.eb
@@ -22,7 +22,6 @@ builddependencies = [
 
 dependencies = [
     ('Brotli', '1.0.9'),
-    ('Highway', '1.0.4'),
 ]
 
 # skip use of third_party directory, since we provide Brotli via a proper dependency
diff --git a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-13.2.0.eb
index 249b1170411..6481ba231cd 100644
--- a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-13.2.0.eb
+++ b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-13.2.0.eb
@@ -22,7 +22,6 @@ builddependencies = [
 
 dependencies = [
     ('Brotli', '1.1.0'),
-    ('Highway', '1.0.7'),
 ]
 
 # skip use of third_party directory, since we provide Brotli via a proper dependency
diff --git a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-13.3.0.eb
index d374a07304a..3afc7fffd75 100644
--- a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-13.3.0.eb
+++ b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-13.3.0.eb
@@ -22,7 +22,6 @@ builddependencies = [
 
 dependencies = [
     ('Brotli', '1.1.0'),
-    ('Highway', '1.2.0'),
 ]
 
 # skip use of third_party directory, since we provide Brotli via a proper dependency

From b26e46e3bad5adae1e4897db20de9f9b1c07f53e Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 11 Sep 2024 09:38:41 +0200
Subject: [PATCH 830/835] add alternative checksum for bold 1.3.0 extension in
 R-bundle-CRAN

---
 .../r/R-bundle-CRAN/R-bundle-CRAN-2023.12-foss-2023a.eb      | 5 ++++-
 .../r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb      | 5 ++++-
 2 files changed, 8 insertions(+), 2 deletions(-)

diff --git a/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2023.12-foss-2023a.eb b/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2023.12-foss-2023a.eb
index 90c7f3f7665..972a8488f6a 100644
--- a/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2023.12-foss-2023a.eb
+++ b/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2023.12-foss-2023a.eb
@@ -867,7 +867,10 @@ exts_list = [
         'checksums': ['8e50415e415702402473caf622d86b89ddc881f6e5d888079a4818a8807ac9a2'],
     }),
     ('bold', '1.3.0', {
-        'checksums': ['0ead11d4386c4c0cd578d3a956f809db2001e387e449a431b4ad503f3da38f5f'],
+        'checksums': [
+            ('0ead11d4386c4c0cd578d3a956f809db2001e387e449a431b4ad503f3da38f5f',
+             '4920fbebd22fb1d0f1a31ccc09c98aec446bb6cb5f65a2610437e405c0512c68'),
+        ],
     }),
     ('rredlist', '0.7.1', {
         'checksums': ['92a10c37a211dc19b41b93f9ceb13d7ce1c3d3a7290cbba4c1688d944353ae85'],
diff --git a/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb b/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb
index 3bd3447df1d..0ff705e9788 100644
--- a/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb
+++ b/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb
@@ -870,7 +870,10 @@ exts_list = [
         'checksums': ['405c77f191f30ffdbf8c05542ff5dff61059e9c731d2dc5ff0bfccb616314147'],
     }),
     ('bold', '1.3.0', {
-        'checksums': ['0ead11d4386c4c0cd578d3a956f809db2001e387e449a431b4ad503f3da38f5f'],
+        'checksums': [
+            ('0ead11d4386c4c0cd578d3a956f809db2001e387e449a431b4ad503f3da38f5f',
+             '4920fbebd22fb1d0f1a31ccc09c98aec446bb6cb5f65a2610437e405c0512c68'),
+        ],
     }),
     ('rredlist', '0.7.1', {
         'checksums': ['92a10c37a211dc19b41b93f9ceb13d7ce1c3d3a7290cbba4c1688d944353ae85'],

From 39358586cb3fc549b1fed1f670edeed6c87397df Mon Sep 17 00:00:00 2001
From: Cintia Willemyns <115622907+WilleBell@users.noreply.github.com>
Date: Wed, 11 Sep 2024 16:46:43 +0200
Subject: [PATCH 831/835] Disable hyperthreading option

---
 .../t/TELEMAC-MASCARET/TELEMAC-MASCARET-8p5r0-foss-2023a.eb     | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/easybuild/easyconfigs/t/TELEMAC-MASCARET/TELEMAC-MASCARET-8p5r0-foss-2023a.eb b/easybuild/easyconfigs/t/TELEMAC-MASCARET/TELEMAC-MASCARET-8p5r0-foss-2023a.eb
index 7ab63c49433..ab96be49230 100644
--- a/easybuild/easyconfigs/t/TELEMAC-MASCARET/TELEMAC-MASCARET-8p5r0-foss-2023a.eb
+++ b/easybuild/easyconfigs/t/TELEMAC-MASCARET/TELEMAC-MASCARET-8p5r0-foss-2023a.eb
@@ -39,6 +39,8 @@ local_tweak_cfg_cmd = ' '.join([
     '-e "s/ -lblas/ $LIBBLAS/g"',
     # downgrade Fortran compiler error to warning
     "-e 's/^fflags_gfo:/fflags_gfo: -fallow-invalid-boz/g'",
+    # Disable hyperthreading option 
+    "-e 's/--use-hwthread-cpus//'",
     "$HOMETEL/configs/systel.easybuild.cfg",
 ])
 

From 30c7c9c502fb943271fe1100fa21b4ad9794969e Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 11 Sep 2024 18:15:42 +0200
Subject: [PATCH 832/835] add missing Perl dependency for DETONATE v1.11

---
 easybuild/easyconfigs/d/DETONATE/DETONATE-1.11-GCC-12.3.0.eb | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easybuild/easyconfigs/d/DETONATE/DETONATE-1.11-GCC-12.3.0.eb b/easybuild/easyconfigs/d/DETONATE/DETONATE-1.11-GCC-12.3.0.eb
index 63246fc43ac..24a8b13835c 100644
--- a/easybuild/easyconfigs/d/DETONATE/DETONATE-1.11-GCC-12.3.0.eb
+++ b/easybuild/easyconfigs/d/DETONATE/DETONATE-1.11-GCC-12.3.0.eb
@@ -33,6 +33,7 @@ builddependencies = [
 ]
 
 dependencies = [
+    ('Perl', '5.36.1'),
     ('Boost', '1.82.0'),
     ('sparsehash', '2.0.4'),
     ('BamTools', '2.5.2'),

From ffc017a2ccdf0ced3b566437bfb0f76a423c97d1 Mon Sep 17 00:00:00 2001
From: Sebastian Achilles <s.achilles@fz-juelich.de>
Date: Thu, 12 Sep 2024 15:49:50 +0200
Subject: [PATCH 833/835] disable buiding docs in fish

---
 easybuild/easyconfigs/f/fish/fish-3.7.1-GCCcore-13.3.0.eb | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/easybuild/easyconfigs/f/fish/fish-3.7.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/f/fish/fish-3.7.1-GCCcore-13.3.0.eb
index bcb975f1857..0c7e084ac23 100644
--- a/easybuild/easyconfigs/f/fish/fish-3.7.1-GCCcore-13.3.0.eb
+++ b/easybuild/easyconfigs/f/fish/fish-3.7.1-GCCcore-13.3.0.eb
@@ -24,6 +24,8 @@ dependencies = [
     ('ncurses', '6.5'),
 ]
 
+configopts = '-DBUILD_DOCS=off '
+
 sanity_check_paths = {
     'files': ['bin/fish'],
     'dirs': [],

From d52ec99d0b1a14a3af31df190cb4c04274f09904 Mon Sep 17 00:00:00 2001
From: Miguel Dias Costa <migueldiascosta@gmail.com>
Date: Sat, 14 Sep 2024 13:09:48 +0800
Subject: [PATCH 834/835] prepare release notes for EasyBuild v4.9.3 + bump
 version to 4.9.3

---
 RELEASE_NOTES | 103 ++++++++++++++++++++++++++++++++++++++++++++++++++
 setup.py      |   2 +-
 2 files changed, 104 insertions(+), 1 deletion(-)

diff --git a/RELEASE_NOTES b/RELEASE_NOTES
index e687bf442f8..d9b94b56e35 100644
--- a/RELEASE_NOTES
+++ b/RELEASE_NOTES
@@ -7,6 +7,109 @@ The latest version of easybuild-easyconfig provides 19,985 easyconfig files, for
 incl. 40 different (compiler) toolchains.
 
 
+v4.9.3 (14 September 2024)
+--------------------------
+
+update/bugfix release
+
+- added easyconfigs for foss/2024a (#21100) and intel/2024a (#21101) common toolchains
+- added example easyconfig files for 108 new software packages:
+  - absl-py (#21039), accelerate (#21107), affogato (#20636), APOST3D (#21133), bayesian-optimization (#21301), BayesOpt (#21261),
+    BGEN-enkre (#15752), bitsandbytes (#21248), bliss (#21206), cfgrib (#21113), CLANS (#21099), colorize (#20964), CORSIKA (#20693),
+    COSTA (#20989), coxeter (#21254), Critic2 (#20833), crypt4gh (#20870), dblatex (#21207), dictys (#21166), DL_POLY_Classic_GUI (#20819),
+    EGA-QuickView (#20888), EMMAX (#21174), empanada-dl (#20454), empanada-napari (#20454), ESIpy (#21006), fastfilters (#21003),
+    fish (#21381), flash-attention (#21083), Flax (#21039), fonttools (#21363), fsm-lite (#20503), GDMA (#21171), GeoDict (#20650),
+    gmpflf (#20882), GPflow (#21172), gtk-doc (#21207), Gubbins (#20413), Gymnasium (#20420), HERRO (#21252), IEntropy (#20808),
+    ilastik-napari (#21003), IMAGE (#20994), junos-eznc (#21166), jupyter-collaboration (#20741), jupyter-vscode-proxy (#20876),
+    langchain-mistralai (#20759), langchain-openai (#20711), LRBinner (#21310), lrcalc (#21339), MAGIC (#20900), mallard-ducktype (#21127),
+    MATES (#21229), MBX (#21155), mcqd (#21283), MeshLab (#20806), meteogrid (#20921), micro-sam (#20636), miniprot (#21157),
+    napari-denoiseg (#20934), NECAT (#21359), nellie (#21267), NextPolish (#21265), nifty (#20636), ome-types (#21256), openai-python (#20711),
+    OpenForceField-Toolkit (#20852), orjson (#20880), PEcAn (#21227), PretextMap (#20790), PyBEL (#20953), pyMBE (#21034), pystencils (#20889),
+    python-blosc (#20636), python-elf (#20636), rankwidth (#20788), Rasqal (#21207), Redland (#21227), Regenie (#15752), rMATS-long (#20916),
+    Sagemath (#21365), scCustomize (#20907), SCENICplus (#21085), scFEA (#20777), sdsl-lite (#20503), SharedMeatAxe (#21303),
+    Single-cell-python-bundle (#20116), SIRIUS (#20989), sirocco (#21304), SKA2 (#20411), SpFFT (#20989), spla (#11607), Stable-Baselines3 (#20884),
+    submitit (#21103), SVDSS2 (#20855), tdlib (#21305), torch-em (#20636), Umpire (#20989), Uni-Core (#21182), vigra (#20636), Visit (#20981),
+    weblogo (#20800), wradlib (#21110), xtb-IFF (#20783), yell (#20964), yelp-tools (#21127), yelp-xsl (#21127), z5py (#20636), Zoltan (#21324)
+- added additional easyconfigs for various supported software packages, including:
+  - AGAT 1.4.0, ANTLR 2.7.7, APOST3D 20240527, APR-util 1.6.3, APR 1.7.4, ASE 3.23.0, ASE 3.23.0, Abseil 20240722.0, Albumentations 1.4.0, AlphaPulldown 2.0.0b4, AlphaPulldown 2.0.0b4, AmberTools %s.%s, Arcade-Learning-Environment 0.8.1, Arrow 16.1.0, Autoconf-archive 2023.02.20, absl-py 2.1.0, accelerate 0.33.0, adjustText 0.7.3, affogato 0.3.3, alsa-lib 1.2.11, alsa-lib 1.2.11, archspec 0.2.4, attr 2.5.2, BGEN-enkre 1.1.7, BRiAl 1.2.12, Bandage 0.9.0, BayesOpt 0.9, BayesTraits 4.1.2, BeautifulSoup 4.12.3, BioPerl 1.7.8, Biopython 1.84, Bison 3.8.2, Boost.MPI 1.83.0, Boost.Python 1.82.0, Boost 1.55.0, Bowtie 1.3.1, Bowtie 1.3.1, Brunsli 0.1, Brunsli 0.1, bayesian-optimization 1.5.1, bcl-convert 4.2.7-2, beagle-lib 4.0.1, binutils 2.42, biom-format 2.1.16, bitsandbytes 0.43.3, bitsandbytes 0.43.3, bliss 0.77, byacc 2.0.20240109, CD-HIT 4.8.1, CDO 2.3.0, CESM-deps 2, CFITSIO 4.4.1, CGAL 5.6.1, CLANS 2.0.8, CORSIKA 77550, COSTA 2.2.2, CSBDeep 0.7.4, CUDA-Samples 11.8, CUDA-Samples 12.2, CUDA 12.5.0, CUDA 12.6.0, CUDD 3.0.0, CUTLASS 3.4.0, Catch2 2.13.10, CellOracle 0.18.0, Clang 18.1.8, ConcurrentVersionsSystem 1.11.23, Coreutils 9.5, Critic2 1.2, CubeLib 4.8.2, CubeWriter 4.8.2, Cython 3.0.10, cairo 1.18.0, cairomm 1.16.2, cfgrib 0.9.14.0, chewBBACA 3.3.9, code-server 4.90.2, colorize 0.7.7, connected-components-3d 3.14.1, cooler 0.10.2, coxeter 20180226, cppy 1.2.1, crb-blast 0.6.9, crypt4gh 1.7, cryptography 42.0.8, cutadapt 4.9, cyvcf2 0.31.1, DB 18.1.40, DB_File 1.859, DBus 1.15.8, DL_POLY_4 5.1.0, DL_POLY_Classic_GUI 1.10, DMTCP 3.0.0, DMTCP 3.0.0, DMTCP 3.0.0, dblatex 0.3.12, dictys 1.1.0, dictys 1.1.0, dorado 0.6.1, dorado 0.7.3, dtcmp 1.1.5, duplex-tools 0.3.3, EGA-QuickView 20240620, EMMAX 20100310, ESIpy 20240709, ESMF 8.6.0, ESMF 8.6.1, ESPResSo 4.2.2, EasyBuild 4.9.2, EvidentialGene 2023.07.15, Exonerate 2.4.0, Extrae 4.2.0, ecBuild 3.8.5, ecCodes 2.27.0, einops 0.7.0, elfutils 0.191, empanada-dl 0.1.7, empanada-napari 1.1.0, expecttest 0.2.1, FFTW.MPI 3.3.10, FFTW.MPI 3.3.10, FFmpeg 7.0.2, FLAC 1.4.3, FLAC 1.4.3, FUSE 3.16.2, FastTree 2.1.11, Filtlong 0.2.1, Flask 3.0.3, Flax 0.8.4, Flax 0.8.4, Flye 2.9.4, FragGeneScan 1.31, FriBidi 1.0.15, fastahack 1.0.0, fastfilters 0.3, fastp 0.23.4, ffnvcodec 12.2.72.0, file 5.43, filevercmp 20191210, fish 3.7.1, flash-attention 2.6.3, flatbuffers-python 24.3.25, flatbuffers 24.3.25, flex 2.6.4, flit 3.9.0, fmt 10.2.1, fonttools 4.53.1, fonttools 4.53.1, fonttools 4.53.1, fonttools 4.53.1, fonttools 4.53.1, foss 2024a, fplll 5.4.5, fpylll 0.6.1, fsm-lite 1.0, fsom 20151117, GCC 14.2.0, GCCcore 14.2.0, GDAL 3.9.0, GDMA 2.3.3_20230603, GEOS 3.12.1, GHC 9.10.1, GLM 1.0.1, GLib 2.80.4, GLibmm 2.72.1, GLibmm 2.75.0, GLibmm 2.77.0, GLibmm 2.78.1, GOATOOLS 1.4.5, GPAW 24.6.0, GPAW 24.6.0, GPflow 2.9.2, GPflow 2.9.2, GPflow 2.9.2, GPyOpt 1.2.6, GROMACS 2023.3, GTS 0.7.6, GeoDict 2024.SP2, GetOrganelle 1.7.7.1, GimmeMotifs 0.17.2, Gubbins 3.3.5, Guile 2.0.14, Guile 3.0.10, Gurobi 11.0.2, Gymnasium 0.29.1, g2lib 3.2.0, gap 4.13.0, gawk 5.3.0, gc 8.2.6, genomepy 0.16.1, gensim 4.3.2, gfbf 2024a, gffutils 0.13, gflags 2.2.2, gh 2.52.0, giflib 5.2.1, git-annex 10.20240731, gmpflf 2024.06, gmpich 2024.06, gmpy2 2.2.0, gompi 2024a, googletest 1.15.2, graph-tool 2.59, graphite2 1.3.14, groff 1.23.0, grpcio 1.57.0, gtk-doc 1.34.0, HDBSCAN 0.8.38.post1, HERRO 0.1.0_20240808, HOMER 4.11.1, HPL 2.3, HPL 2.3, HPL 2.3, HTSeq 2.0.7, HiCMatrix 17.2, Highway 1.2.0, Hypre 2.31.0, hatchling 1.24.2, help2man 1.49.3, hiredis 1.2.0, histolab 0.6.0, histolab 0.7.0, hypothesis 6.103.1, IEnt, IQ-TREE 2.3.5, ITK 5.3.0, ImageMagick 7.1.1-34, Imath 3.1.11, IsoQuant 3.5.0, igraph 0.10.12, iimpi 2024a, ilastik-napari 0.2.4, imageio 2.34.1, imbalanced-learn 0.12.3, imkl-FFTW 2024.2.0, imkl 2024.2.0, impi 2021.13.0, inferCNV 1.21.0, intel-compilers 2024.2.0, intel 2024a, intervaltree 0.1, intltool 0.51.0, JsonCpp 1.9.5, JsonCpp 1.9.5, Judy 1.0.5, Julia 1.10.4, jax 0.4.25, jax 0.4.25, jemalloc 5.3.0, json-c 0.17, json-fortran 8.5.2, json-fortran 8.5.2, junos-eznc 2.7.1, jupyter-collaboration 2.1.1, jupyter-vscode-proxy 0.6, Kaleido 0.2.1, Kent_tools 461, Kent_tools 468, kineto 0.4.0, LAME 3.100, LLVM 18.1.8, LMDB 0.9.31, LRBinner 0.1, LZO 2.10, LittleCMS 2.16, langchain-mistralai 0.1.8, langchain-openai 0.1.8, libcircle 0.3, libdap 3.20.11, libdrm 2.4.122, libdwarf 0.10.1, libedit 20240517, libgeotiff 1.7.3, libgit2 1.8.1, libglvnd 1.7.0, libidn2 2.3.4, libmatheval 1.1.11, libogg 1.3.5, libogg 1.3.5, libopus 1.5.2, libopus 1.5.2, libsigc++ 3.6.0, libsigc++ 3.6.0, libsigc++ 3.6.0, libsndfile 1.2.2, libsndfile 1.2.2, libsodium 1.0.20, libspatialindex 2.0.0, libunistring 1.2, libunwind 1.8.1, libvorbis 1.3.7, libvorbis 1.3.7, libwebp 1.4.0, libxslt 1.1.42, libzip 1.10.1, longread_umi 0.3.2, lrcalc 2.1, lwgrp 1.0.6, lxml 5.3.0, M4 1.4.19, MAGIC 3.0.0, MATES 0.1.2-20240813, MATES 0.1.2-20240813, MBX 1.1.0, MCR R2024a, METIS 5.1.0, MONAI 1.3.0, MPICH 4.2.1, MUMPS 5.6.1, MUMPS 5.7.2, MUMPS 5.7.2, MUSCLE 5.1.0, MariaDB 11.6.0, Maven 3.9.7, Mercurial 6.8.1, Mesa 24.1.3, MeshLab 2023.12, Miniconda3 23.10.0-1, MultiQC 1.22.3, maeparser 1.3.1, makedepend 1.0.9, mallard-ducktype 1.0.2, matplotlib 3.9.2, maturin 1.6.0, mcqd 1.0.0, medaka 1.12.0, medaka 1.12.0, medaka 1.12.1, medaka 1.12.1, meshio 5.3.5, meson-python 0.16.0, meteogrid 20240627, micro-sam 1.0.1, miniasm 0.3-20191007, miniprot 0.13, ml-collections 0.1.1, mm-common 1.0.6, mm-common 1.0.6, mm-common 1.0.6, mm-common 1.0.6, molmod 1.4.8, molmod 1.4.8, mpifileutils 0.11.1, mrcfile 1.4.3, multichoose 1.0.3, multiprocess 0.70.15, mygene 3.2.2, NCO 5.1.9, NECAT 0.0.1, NLopt 2.7.1, NLopt 2.7.1, NanoCaller 3.6.0, NextPolish 1.4.1, NiBabel 5.2.0, Normaliz 3.10.3, n2v 0.3.3, nano 8.1, nanopolish 0.14.0, napari-denoiseg 0.0.1, ncbi-vdb 3.1.1, nellie 0.3.1, nellie 0.3.1, nettle 3.10, nifty 1.2.1, nlohmann_json 3.11.3, nose3 1.3.8, nsync 1.29.2, numexpr 2.9.0, OPARI2 2.0.8, ORCA 6.0.0, ORCA 6.0.0, ORCA 6.0.0, ORCA 6.0.0, OSU-Micro-Benchmarks 7.4, OSU-Micro-Benchmarks 7.4, OTF2 3.0.3, OpenAI-Gym 0.26.2, OpenEXR 3.2.4, OpenFOAM 10, OpenFOAM 12, OpenFOAM v2406, OpenForceField-Toolkit 0.16.0, OpenJPEG 2.5.2, OpenMM 8.0.0, OpenPGM 5.2.122, OpenSlide 3.4.1, Optax 0.2.2, Optax 0.2.2, Optuna 3.6.1, ome-types 0.5.1.post1, openai-python 1.30.5, openslide-python 1.3.1, orjson 3.9.15, PAPI 7.1.0, PDT 3.25.2, PEcAn 1.8.0.9000, PLY 3.11, PLY 3.11, PaStiX 6.3.2, PaStiX 6.3.2, ParMETIS 4.0.3, ParMETIS 4.0.3, ParaView 5.12.0, Perl-bundle-CPAN 5.38.2, Pillow-SIMD 10.4.0, Pint 0.24, Platypus-Opt 1.2.0, PostgreSQL 16.4, PretextMap 0.1.9, PyAEDT 0.9.9, PyBEL 0.15.5, PyCharm 2024.1.6, PyRosetta 4.release-384, PyTorch-Geometric 2.5.0, PyWavelets 1.7.0, PyYAML 6.0.2, Pygments 2.18.0, Pylint 3.2.5, Pyomo 6.7.3, Python-bundle-PyPI 2024.06, packmol 20.14.4, pagmo 2.19.0, parallel 20240722, parasail 2.6.2, pixman 0.43.4, pkgconfig 1.5.5, pod5-file-format 0.3.10, poetry 1.8.3, popt 1.19, pretty-yaml 24.7.0, primecount 7.14, primecountpy 0.1.0, prompt-toolkit 3.0.36, psycopg 3.2.1, pyBigWig 0.3.22, pyGenomeTracks 3.9, pyMBE 0.8.0, pybind11 2.12.0, pycocotools 2.0.7, pydantic 2.7.4, pydicom 2.4.4, pydot 2.0.0, pyfasta 0.5.2, pygmo 2.19.5, pyperf 2.7.0, pyseer 1.3.12, pyspoa 0.2.1, pystencils 1.3.4, pysteps 1.10.0, python-blosc 1.11.0, python-elf 0.5.1, python-, QuantumESPRESSO 7.3.1, QuantumESPRESSO 7.3.1, Qwt 6.3.0, qnorm 0.8.1, R-bundle-CRAN 2024.06, R 4.4.1, RDKit 2024.03.3, RStudio-Server 2023.09.1+494, RapidJSON 1.1.0-20240409, Raptor 2.0.16, Rasqal 0.9.33, Ray-project 2.9.1, ReFrame 4.6.2, ReFrame 4.6.2, Redland 1.0.17, Regenie 3.1.2, Rust 1.79.0, rMATS-long 1.0.0-20240502, rankwidth 0.9, rapidNJ 2.3.3, redis-py 5.0.9, regionmask 0.12.1, rjags 4-15, rpmrebuild 2.18, ruamel.yaml 0.18.6, SCENICplus 1.0a1-20240513, SCOTCH 7.0.4, SDL2 2.30.6, SHAP 0.43.0, SIONlib 1.7.7, SIP 6.8.3, SIRIUS 7.5.2, SKA2 0.3.7, SOCI 4.0.3, SRA-Toolkit 3.1.1, STAR 2.7.11b_alpha_2024-02-09, STREAM 5.10, STRUMPACK 7.1.0, STRUMPACK 7.1.0, SVDSS2 2.0.0-alpha.3, Safetensors 0.4.3, Sagemath 10.4, Salmon 1.10.3, ScaLAPACK 2.2.0, ScaLAPACK 2.2.0, SciPy-bundle 2024.05, SciPy-bundle 2024.05, Score-P 8.4, Score-P 8.4, SentencePiece 0.2.0, SeqKit 2.8.2, SharedMeatAxe 1.0.1, Single-cell-python-bundle 2024.02, SingleM 0.16.0, SpFFT 1.1.0, Sphinx-RTD-Theme 2.0.0, Sphinx-RTD-Theme 2.0.0, Stable-Baselines3 2.3.2, Stack 3.1.1, SuiteSparse 7.7.0, SuperLU 6.0.1, SuperLU_DIST 8.2.1, scArches 0.6.1, scCustomize 2.1.2, scFEA 1.1-20221109, scib-metrics 0.5.1, scikit-build 0.17.6, scrublet 0.2.3, scvi-tools 1.1.2, scvi-tools 1.1.2, sdsl-lite 2.0.3, segment-anything 1.0, setuptools-rust 1.9.0, sirocco 2.1.0, slepc4py 3.20.2, smafa 0.8.0, smithwaterman 20160702, snpEff 5.2c, spaCy 3.7.4, spektral 1.2.0, spglib-python 2.5.0, spglib 2.5.0, spla 1.6.1, spoa 4.1.0, submitit 1.2.0, svist4get 1.3.1, TAMkin 1.2.6, TAMkin 1.2.6, TELEMAC-MASCARET 8p5r0, TF-COMB 1.1, TOBIAS 0.16.1, TensorFlow 2.15.1, Tk 8.6.14, Tkinter 3.12.3, Transrate 1.0.3, Triangle 1.6, Trycycler 0.5.5, tabixpp 1.1.2, tbb 2021.9.0, tdlib 0.9.3, tensorboard 2.15.1, tiktoken 0.7.0, timm 1.0.8, torch-em 0.7.1, UCX-CUDA 1.15.0, UCX-CUDA 1.16.0, Umpire 2024.02.1, Uni-Core 0.0.3, Uni-Core 0.0.3, unixODBC 2.3.12, utf8proc 2.9.0, VBZ-Compression 1.0.3, VSEARCH 2.28.1, VTK 9.2.6, Visit 3.4.1, vcflib 1.0.9, velocyto 0.17.17, vigra 1.11.2, virtualenv 20.26.2, WFA2 2.3.4, WRF 4.5.1, Wayland 1.23.0, weblogo 2.8.2, wget 1.21.4, wradlib 2.0.3, wradlib 2.0.3, X11 20240607, XGBoost 2.1.1, XML-LibXML 2.0210, x264 20240513, x265 3.6, xarray 2024.5.0, xtb-IFF 1.1, xtb 6.7.1, xtensor 0.24.7, YACS 0.1.8, Yasm 1.3.0, yell 2.2.2, yelp-tools 42.1, yelp-xsl 42.1, Z3 4.13.0, ZeroMQ 4.3.5, Zoltan 3.901, z5py 2.0.17, zlib 1.3.1
+- minor enhancements, including:
+  - correct configuration of QuantumESPRESSO for 6.7/6.8/7.0/7.1/7.2/7.3 (#20070)
+  - add internal CUDA header patch for PSM2 (#20804)
+  - add support for JupyterHub to TensorBoard (#20823)
+  - make sure that recent ImageMagick versions pick up the right pkgconf and improve the sanity checks (#20900)
+  - also install utilities for recent versions of FUSE 3.x (#20918)
+  - add RISC-V support to x264-20231019/GCCcore-13.2.0 (#20968)
+  - add RISC-v support to recent LAME easyconfigs by removing workaround for finding libncurses (#20970)
+  - enable PIC in recent x265 easyconfigs to solve compilation errors on RISC-V (#20971)
+  - add missMDA extension to R-bundle-CRAN versions 2023.12 (#21167) and 2024.06 (#21183)
+  - add Qt support to VTK 9.3.0 (#21221)
+  - add insight extension to R-bundle-CRAN 2024.06 (#21260)
+  - add performance, datwizard and bayestestR to R-bundle-CRAN 2024.06 (#21272)
+  - add `helper_scripts` to PATH in ProteinMPNN-1.0.1-20230627 (#21289)
+  - add the plugins to OpenFOAM v2406 (#21332)
+  - use proper Python dependency for OTF2 (#21325)
+- various bug fixes, including:
+  - add wrapper for Julia with linking safeguards and delegate environment setup to JuliaPackage (#20103)
+  - fix typo in description of SuiteSparse v7.7.0 (#20567)
+  - add 'pic' flag to IML (#20789)
+  - add patch to fix build error with numpy with some compilers (#20817)
+  - rename unpacked sources for components of EasyBuild v4.9.2, to ensure that '`--install-latest-eb-release`' works with older EasyBuild versions (#20818)
+  - fix build of OpenBLAS 0.3.24 on A64FX (#20820)
+  - remove maturin build dependency from langchain-antropic (#20825)
+  - add GMP and MPFR as dependencies to OpenFOAM v2306 and v2312 (#20841)
+  - add patch to SciPy-bundle 2024.05 that fixes numpy test failures on RISC-V (#20847)
+  - skip unreliable memory leak test in PyTorch 2.1.2 (#20874)
+  - use PyYAML 6.0.1 instead of 6.0 for recent ReFrame versions (#20879)
+  - use PyPI source tarball and gfbf/2023a toolchain for pyBigWig (#20881)
+  - add fix for failing test on zen4 to Highway 1.0.4 (#20942)
+  - add patch to fix implicit function declaration in OpenMPI 4.1.4 (#20949)
+  - only use libxsmm as dependency for CP2K 2023.1 w/ `foss/2023a` on x86_64 (#20951)
+  - copy missing `rsem_perl_utils.pm` in DETONATE, since it's required by `rsem-eval-calculate-score` command (#20956)
+  - set `SATSUMA2_PATH` so Satsuma2 can locate executables (#20957)
+  - disable auto-vectorizer (`-ftree-vectorize`) for OpenFOAM v10 + v11 when using toolchain that with GCC >= 11 (#20958)
+  - disable test step for WIEN2k 23.2 because files required by it can no longer be downloaded (#20969)
+  - rename `gubbins-2.4.0.eb` to `Gubbins-2.4.0.eb` (#20995)
+  - add patch to fix Qt6 issues with ParaView v5.12.0, e.g. representation selection (#21002)
+  - update homepage in phonopy easyconfigs (#21014)
+  - make libunwind dependency architecture specific in Extrae 4.2.0 easyconfig (#21017)
+  - add `OPENSSL_ENABLE_SHA1_SIGNATURES` for building `ansys-pythonnet` (#21028)
+  - fix download URLs for old Intel software (2018-23) (#21108)
+  - update source and homepage URLs in Szip easyconfigs (#21129)
+  - rename source URL in HDF v4.2.16-2 easyconfig (#21130)
+  - consistently fix homeage + source URL for `HDF` + `h4toh5` (#21134)
+  - ensure that recent BioPerl easyconfigs use `Bundle` easyblock (#21136)
+  - fix checksum checks for easyconfigs using a `Bundle`-like easyblock in easyconfigs test suite (#21143)
+  - add pkgconf build dependency to scikit-misc v0.3.1 (#21144)
+  - disable use of MySQL in GDAL (#21156)
+  - add GPflow v2.9.2 and fix tensorflow-probability to pass pip check (#21172)
+  - stop RStudio-Server 2023.09 from installing R packages (+ move to `foss/2023a` toolchain) (#21175)
+  - remove `Time::HiRes` from `Perl-bundle-CPAN` (#21198)
+  - fix build of STAR 2.7.11a + 2.7.11b on non-x86 architectures by avoiding use of `-maxv2` + add missing `xxd` build dependency (#21200)
+  - add missing cairo dependency for python-igraph v0.10.6 (#21211)
+  - add patch for xtb 6.7.0 to fix build failure due to changes in tblite (#21255)
+  - add patch for HDF5-1.14.3 to _suppress fp exceptions (#21280)
+  - correct extension order in R-bundle-CRAN 2024.06 (#21285)
+  - update easyconfig for dorado 0.7.3 to properly use provided OpenSSL dependency, and not install external libraries into its own lib directory (#21297)
+  - use source tarballs from GitHub for recent libdap easyconfigs (#21334)
+  - use version in byacc 2.0.20240109 sources (#21344)
+  - remove Highway build dependency in Brunsli easyconfigs, since it's not actually required at all (#21366)
+  - add alternative checksum for bold 1.3.0 extension in R-bundle-CRAN (#21370)
+  - disable buiding docs in fish (#21381)
+- other changes:
+  - archive outdated example easyconfigs for Fujitsu toolchain (#20781)
+  - upgrade builddependency rpmrebuild to version 2.18 in bcl-convert 4.2.7 easyconfig (#20861)
+  - switch transformers to use external Safetensor dep (#20864)
+  - rename ega-quickview to EGA-QuickView (#20888)
+  - remove CMake Arrow flag as there is no Arrow dependency in recent GDAL easyconfigs (#20905)
+  - whitelist ConfigureMakePythonPackage for sanity_check_paths CI check (#20963)
+  - make pytest v7.4.2 independent of Python-bundle-PyPI (#21004)
+  - reorganize Flax/JAX stack in 2023a: move `jax` + `Optax` to `gfbf/2023a` toolchain + use standalone `Flax` + `absl-py` as dependencies (#21038)
+  - use stand-alone absl-py as dependency for jax w/ `gfbf/2023a` (#21039)
+  - remove Cython dependency from Python-bundle-PyPI 2024.06 + standalone easyconfig for Cython 3.0.10 (#21233)
+  - add Cython builddep for SciPy-bundle (#21235)
+  - use top-level parameters for `use_pip` & co instead of `exts_default_options` for `PythonBundle` easyconfigs (#21292)
+
+
 v4.9.2 (12 June 2024)
 ---------------------
 
diff --git a/setup.py b/setup.py
index 8d3cd7f76d0..ae4897821b1 100644
--- a/setup.py
+++ b/setup.py
@@ -44,7 +44,7 @@
 # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like
 #   UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0'
 # This causes problems further up the dependency chain...
-VERSION = '4.9.3.dev0'
+VERSION = '4.9.3'
 
 MAJ_VER = VERSION.split('.')[0]
 MAJMIN_VER = '.'.join(VERSION.split('.')[0:2])

From f82a563b8e1f8118c7c3ab23374d0e28e1691fea Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 14 Sep 2024 16:51:56 +0200
Subject: [PATCH 835/835] minor tweaks to 4.9.3 release notes

---
 RELEASE_NOTES | 132 +++++++++++++++++++++++++++++++-------------------
 1 file changed, 83 insertions(+), 49 deletions(-)

diff --git a/RELEASE_NOTES b/RELEASE_NOTES
index d9b94b56e35..590c5db69f2 100644
--- a/RELEASE_NOTES
+++ b/RELEASE_NOTES
@@ -3,8 +3,8 @@ For more detailed information, please see the git log.
 
 These release notes can also be consulted at https://docs.easybuild.io/en/latest/Release_notes.html.
 
-The latest version of easybuild-easyconfig provides 19,985 easyconfig files, for 3,552 different software packages,
-incl. 40 different (compiler) toolchains.
+The latest version of easybuild-easyconfig provides 20,561 easyconfig files, for 3,656 different software packages,
+incl. 41 different (compiler) toolchains.
 
 
 v4.9.3 (14 September 2024)
@@ -13,100 +13,134 @@ v4.9.3 (14 September 2024)
 update/bugfix release
 
 - added easyconfigs for foss/2024a (#21100) and intel/2024a (#21101) common toolchains
-- added example easyconfig files for 108 new software packages:
-  - absl-py (#21039), accelerate (#21107), affogato (#20636), APOST3D (#21133), bayesian-optimization (#21301), BayesOpt (#21261),
-    BGEN-enkre (#15752), bitsandbytes (#21248), bliss (#21206), cfgrib (#21113), CLANS (#21099), colorize (#20964), CORSIKA (#20693),
-    COSTA (#20989), coxeter (#21254), Critic2 (#20833), crypt4gh (#20870), dblatex (#21207), dictys (#21166), DL_POLY_Classic_GUI (#20819),
-    EGA-QuickView (#20888), EMMAX (#21174), empanada-dl (#20454), empanada-napari (#20454), ESIpy (#21006), fastfilters (#21003),
-    fish (#21381), flash-attention (#21083), Flax (#21039), fonttools (#21363), fsm-lite (#20503), GDMA (#21171), GeoDict (#20650),
-    gmpflf (#20882), GPflow (#21172), gtk-doc (#21207), Gubbins (#20413), Gymnasium (#20420), HERRO (#21252), IEntropy (#20808),
-    ilastik-napari (#21003), IMAGE (#20994), junos-eznc (#21166), jupyter-collaboration (#20741), jupyter-vscode-proxy (#20876),
-    langchain-mistralai (#20759), langchain-openai (#20711), LRBinner (#21310), lrcalc (#21339), MAGIC (#20900), mallard-ducktype (#21127),
-    MATES (#21229), MBX (#21155), mcqd (#21283), MeshLab (#20806), meteogrid (#20921), micro-sam (#20636), miniprot (#21157),
-    napari-denoiseg (#20934), NECAT (#21359), nellie (#21267), NextPolish (#21265), nifty (#20636), ome-types (#21256), openai-python (#20711),
-    OpenForceField-Toolkit (#20852), orjson (#20880), PEcAn (#21227), PretextMap (#20790), PyBEL (#20953), pyMBE (#21034), pystencils (#20889),
-    python-blosc (#20636), python-elf (#20636), rankwidth (#20788), Rasqal (#21207), Redland (#21227), Regenie (#15752), rMATS-long (#20916),
-    Sagemath (#21365), scCustomize (#20907), SCENICplus (#21085), scFEA (#20777), sdsl-lite (#20503), SharedMeatAxe (#21303),
-    Single-cell-python-bundle (#20116), SIRIUS (#20989), sirocco (#21304), SKA2 (#20411), SpFFT (#20989), spla (#11607), Stable-Baselines3 (#20884),
-    submitit (#21103), SVDSS2 (#20855), tdlib (#21305), torch-em (#20636), Umpire (#20989), Uni-Core (#21182), vigra (#20636), Visit (#20981),
-    weblogo (#20800), wradlib (#21110), xtb-IFF (#20783), yell (#20964), yelp-tools (#21127), yelp-xsl (#21127), z5py (#20636), Zoltan (#21324)
+- new toolchain: gmpflf/2024.06 (#20882)
+- added example easyconfig files for 107 new software packages:
+  - absl-py (#21039), accelerate (#21107), affogato (#20636), APOST3D (#21133), bayesian-optimization (#21301),
+    BayesOpt (#21261), BGEN-enkre (#15752), bitsandbytes (#21248), bliss (#21206), cfgrib (#21113), CLANS (#21099),
+    colorize (#20964), CORSIKA (#20693), COSTA (#20989), coxeter (#21254), Critic2 (#20833), crypt4gh (#20870),
+    dblatex (#21207), dictys (#21166), DL_POLY_Classic_GUI (#20819), EGA-QuickView (#20870, #20888), EMMAX (#21174),
+    empanada-dl (#20454), empanada-napari (#20454), ESIpy (#21006), fastfilters (#21003), fish (#21345, #21381),
+    flash-attention (#21083), Flax (#21039), fonttools (#21363), fsm-lite (#20503), GDMA (#21171), GeoDict (#20650),
+    GPflow (#21172), gtk-doc (#21207), Gubbins (#20413), Gymnasium (#20420), HERRO (#21252), IEntropy (#20808),
+    ilastik-napari (#21003), IMAGE (#20994), junos-eznc (#21166), jupyter-collaboration (#20741),
+    jupyter-vscode-proxy (#20876), langchain-mistralai (#20759), langchain-openai (#20711), LRBinner (#21310),
+    lrcalc (#21339), MAGIC (#20900), mallard-ducktype (#21127), MATES (#21229), MBX (#21155), mcqd (#21283),
+    MeshLab (#20806), meteogrid (#20921), micro-sam (#20636), miniprot (#21157), napari-denoiseg (#20934),
+    NECAT (#21359), nellie (#21267), NextPolish (#21265), nifty (#20636), ome-types (#21256), openai-python (#20711),
+    OpenForceField-Toolkit (#20852), orjson (#20880), PEcAn (#21227), PretextMap (#20790), PyBEL (#20953),
+    pyMBE (#21034), pystencils (#20889), python-blosc (#20636), python-elf (#20636), rankwidth (#20788), Rasqal (#21207),
+    Redland (#21227), Regenie (#15752), rMATS-long (#20916), Sagemath (#21365), scCustomize (#20907), SCENICplus (#21085),
+    scFEA (#20777), sdsl-lite (#20503), SharedMeatAxe (#21303), Single-cell-python-bundle (#20116), SIRIUS (#20989),
+    sirocco (#21304), SKA2 (#20411), SpFFT (#20989), spla (#11607), Stable-Baselines3 (#20884), submitit (#21103),
+    SVDSS2 (#20855), tdlib (#21305), torch-em (#20636), Umpire (#20989), Uni-Core (#21182), vigra (#20636),
+    Visit (#20981), weblogo (#20800), wradlib (#21110), xtb-IFF (#20783), yell (#20964), yelp-tools (#21127),
+    yelp-xsl (#21127), z5py (#20636), Zoltan (#21324)
 - added additional easyconfigs for various supported software packages, including:
-  - AGAT 1.4.0, ANTLR 2.7.7, APOST3D 20240527, APR-util 1.6.3, APR 1.7.4, ASE 3.23.0, ASE 3.23.0, Abseil 20240722.0, Albumentations 1.4.0, AlphaPulldown 2.0.0b4, AlphaPulldown 2.0.0b4, AmberTools %s.%s, Arcade-Learning-Environment 0.8.1, Arrow 16.1.0, Autoconf-archive 2023.02.20, absl-py 2.1.0, accelerate 0.33.0, adjustText 0.7.3, affogato 0.3.3, alsa-lib 1.2.11, alsa-lib 1.2.11, archspec 0.2.4, attr 2.5.2, BGEN-enkre 1.1.7, BRiAl 1.2.12, Bandage 0.9.0, BayesOpt 0.9, BayesTraits 4.1.2, BeautifulSoup 4.12.3, BioPerl 1.7.8, Biopython 1.84, Bison 3.8.2, Boost.MPI 1.83.0, Boost.Python 1.82.0, Boost 1.55.0, Bowtie 1.3.1, Bowtie 1.3.1, Brunsli 0.1, Brunsli 0.1, bayesian-optimization 1.5.1, bcl-convert 4.2.7-2, beagle-lib 4.0.1, binutils 2.42, biom-format 2.1.16, bitsandbytes 0.43.3, bitsandbytes 0.43.3, bliss 0.77, byacc 2.0.20240109, CD-HIT 4.8.1, CDO 2.3.0, CESM-deps 2, CFITSIO 4.4.1, CGAL 5.6.1, CLANS 2.0.8, CORSIKA 77550, COSTA 2.2.2, CSBDeep 0.7.4, CUDA-Samples 11.8, CUDA-Samples 12.2, CUDA 12.5.0, CUDA 12.6.0, CUDD 3.0.0, CUTLASS 3.4.0, Catch2 2.13.10, CellOracle 0.18.0, Clang 18.1.8, ConcurrentVersionsSystem 1.11.23, Coreutils 9.5, Critic2 1.2, CubeLib 4.8.2, CubeWriter 4.8.2, Cython 3.0.10, cairo 1.18.0, cairomm 1.16.2, cfgrib 0.9.14.0, chewBBACA 3.3.9, code-server 4.90.2, colorize 0.7.7, connected-components-3d 3.14.1, cooler 0.10.2, coxeter 20180226, cppy 1.2.1, crb-blast 0.6.9, crypt4gh 1.7, cryptography 42.0.8, cutadapt 4.9, cyvcf2 0.31.1, DB 18.1.40, DB_File 1.859, DBus 1.15.8, DL_POLY_4 5.1.0, DL_POLY_Classic_GUI 1.10, DMTCP 3.0.0, DMTCP 3.0.0, DMTCP 3.0.0, dblatex 0.3.12, dictys 1.1.0, dictys 1.1.0, dorado 0.6.1, dorado 0.7.3, dtcmp 1.1.5, duplex-tools 0.3.3, EGA-QuickView 20240620, EMMAX 20100310, ESIpy 20240709, ESMF 8.6.0, ESMF 8.6.1, ESPResSo 4.2.2, EasyBuild 4.9.2, EvidentialGene 2023.07.15, Exonerate 2.4.0, Extrae 4.2.0, ecBuild 3.8.5, ecCodes 2.27.0, einops 0.7.0, elfutils 0.191, empanada-dl 0.1.7, empanada-napari 1.1.0, expecttest 0.2.1, FFTW.MPI 3.3.10, FFTW.MPI 3.3.10, FFmpeg 7.0.2, FLAC 1.4.3, FLAC 1.4.3, FUSE 3.16.2, FastTree 2.1.11, Filtlong 0.2.1, Flask 3.0.3, Flax 0.8.4, Flax 0.8.4, Flye 2.9.4, FragGeneScan 1.31, FriBidi 1.0.15, fastahack 1.0.0, fastfilters 0.3, fastp 0.23.4, ffnvcodec 12.2.72.0, file 5.43, filevercmp 20191210, fish 3.7.1, flash-attention 2.6.3, flatbuffers-python 24.3.25, flatbuffers 24.3.25, flex 2.6.4, flit 3.9.0, fmt 10.2.1, fonttools 4.53.1, fonttools 4.53.1, fonttools 4.53.1, fonttools 4.53.1, fonttools 4.53.1, foss 2024a, fplll 5.4.5, fpylll 0.6.1, fsm-lite 1.0, fsom 20151117, GCC 14.2.0, GCCcore 14.2.0, GDAL 3.9.0, GDMA 2.3.3_20230603, GEOS 3.12.1, GHC 9.10.1, GLM 1.0.1, GLib 2.80.4, GLibmm 2.72.1, GLibmm 2.75.0, GLibmm 2.77.0, GLibmm 2.78.1, GOATOOLS 1.4.5, GPAW 24.6.0, GPAW 24.6.0, GPflow 2.9.2, GPflow 2.9.2, GPflow 2.9.2, GPyOpt 1.2.6, GROMACS 2023.3, GTS 0.7.6, GeoDict 2024.SP2, GetOrganelle 1.7.7.1, GimmeMotifs 0.17.2, Gubbins 3.3.5, Guile 2.0.14, Guile 3.0.10, Gurobi 11.0.2, Gymnasium 0.29.1, g2lib 3.2.0, gap 4.13.0, gawk 5.3.0, gc 8.2.6, genomepy 0.16.1, gensim 4.3.2, gfbf 2024a, gffutils 0.13, gflags 2.2.2, gh 2.52.0, giflib 5.2.1, git-annex 10.20240731, gmpflf 2024.06, gmpich 2024.06, gmpy2 2.2.0, gompi 2024a, googletest 1.15.2, graph-tool 2.59, graphite2 1.3.14, groff 1.23.0, grpcio 1.57.0, gtk-doc 1.34.0, HDBSCAN 0.8.38.post1, HERRO 0.1.0_20240808, HOMER 4.11.1, HPL 2.3, HPL 2.3, HPL 2.3, HTSeq 2.0.7, HiCMatrix 17.2, Highway 1.2.0, Hypre 2.31.0, hatchling 1.24.2, help2man 1.49.3, hiredis 1.2.0, histolab 0.6.0, histolab 0.7.0, hypothesis 6.103.1, IEnt, IQ-TREE 2.3.5, ITK 5.3.0, ImageMagick 7.1.1-34, Imath 3.1.11, IsoQuant 3.5.0, igraph 0.10.12, iimpi 2024a, ilastik-napari 0.2.4, imageio 2.34.1, imbalanced-learn 0.12.3, imkl-FFTW 2024.2.0, imkl 2024.2.0, impi 2021.13.0, inferCNV 1.21.0, intel-compilers 2024.2.0, intel 2024a, intervaltree 0.1, intltool 0.51.0, JsonCpp 1.9.5, JsonCpp 1.9.5, Judy 1.0.5, Julia 1.10.4, jax 0.4.25, jax 0.4.25, jemalloc 5.3.0, json-c 0.17, json-fortran 8.5.2, json-fortran 8.5.2, junos-eznc 2.7.1, jupyter-collaboration 2.1.1, jupyter-vscode-proxy 0.6, Kaleido 0.2.1, Kent_tools 461, Kent_tools 468, kineto 0.4.0, LAME 3.100, LLVM 18.1.8, LMDB 0.9.31, LRBinner 0.1, LZO 2.10, LittleCMS 2.16, langchain-mistralai 0.1.8, langchain-openai 0.1.8, libcircle 0.3, libdap 3.20.11, libdrm 2.4.122, libdwarf 0.10.1, libedit 20240517, libgeotiff 1.7.3, libgit2 1.8.1, libglvnd 1.7.0, libidn2 2.3.4, libmatheval 1.1.11, libogg 1.3.5, libogg 1.3.5, libopus 1.5.2, libopus 1.5.2, libsigc++ 3.6.0, libsigc++ 3.6.0, libsigc++ 3.6.0, libsndfile 1.2.2, libsndfile 1.2.2, libsodium 1.0.20, libspatialindex 2.0.0, libunistring 1.2, libunwind 1.8.1, libvorbis 1.3.7, libvorbis 1.3.7, libwebp 1.4.0, libxslt 1.1.42, libzip 1.10.1, longread_umi 0.3.2, lrcalc 2.1, lwgrp 1.0.6, lxml 5.3.0, M4 1.4.19, MAGIC 3.0.0, MATES 0.1.2-20240813, MATES 0.1.2-20240813, MBX 1.1.0, MCR R2024a, METIS 5.1.0, MONAI 1.3.0, MPICH 4.2.1, MUMPS 5.6.1, MUMPS 5.7.2, MUMPS 5.7.2, MUSCLE 5.1.0, MariaDB 11.6.0, Maven 3.9.7, Mercurial 6.8.1, Mesa 24.1.3, MeshLab 2023.12, Miniconda3 23.10.0-1, MultiQC 1.22.3, maeparser 1.3.1, makedepend 1.0.9, mallard-ducktype 1.0.2, matplotlib 3.9.2, maturin 1.6.0, mcqd 1.0.0, medaka 1.12.0, medaka 1.12.0, medaka 1.12.1, medaka 1.12.1, meshio 5.3.5, meson-python 0.16.0, meteogrid 20240627, micro-sam 1.0.1, miniasm 0.3-20191007, miniprot 0.13, ml-collections 0.1.1, mm-common 1.0.6, mm-common 1.0.6, mm-common 1.0.6, mm-common 1.0.6, molmod 1.4.8, molmod 1.4.8, mpifileutils 0.11.1, mrcfile 1.4.3, multichoose 1.0.3, multiprocess 0.70.15, mygene 3.2.2, NCO 5.1.9, NECAT 0.0.1, NLopt 2.7.1, NLopt 2.7.1, NanoCaller 3.6.0, NextPolish 1.4.1, NiBabel 5.2.0, Normaliz 3.10.3, n2v 0.3.3, nano 8.1, nanopolish 0.14.0, napari-denoiseg 0.0.1, ncbi-vdb 3.1.1, nellie 0.3.1, nellie 0.3.1, nettle 3.10, nifty 1.2.1, nlohmann_json 3.11.3, nose3 1.3.8, nsync 1.29.2, numexpr 2.9.0, OPARI2 2.0.8, ORCA 6.0.0, ORCA 6.0.0, ORCA 6.0.0, ORCA 6.0.0, OSU-Micro-Benchmarks 7.4, OSU-Micro-Benchmarks 7.4, OTF2 3.0.3, OpenAI-Gym 0.26.2, OpenEXR 3.2.4, OpenFOAM 10, OpenFOAM 12, OpenFOAM v2406, OpenForceField-Toolkit 0.16.0, OpenJPEG 2.5.2, OpenMM 8.0.0, OpenPGM 5.2.122, OpenSlide 3.4.1, Optax 0.2.2, Optax 0.2.2, Optuna 3.6.1, ome-types 0.5.1.post1, openai-python 1.30.5, openslide-python 1.3.1, orjson 3.9.15, PAPI 7.1.0, PDT 3.25.2, PEcAn 1.8.0.9000, PLY 3.11, PLY 3.11, PaStiX 6.3.2, PaStiX 6.3.2, ParMETIS 4.0.3, ParMETIS 4.0.3, ParaView 5.12.0, Perl-bundle-CPAN 5.38.2, Pillow-SIMD 10.4.0, Pint 0.24, Platypus-Opt 1.2.0, PostgreSQL 16.4, PretextMap 0.1.9, PyAEDT 0.9.9, PyBEL 0.15.5, PyCharm 2024.1.6, PyRosetta 4.release-384, PyTorch-Geometric 2.5.0, PyWavelets 1.7.0, PyYAML 6.0.2, Pygments 2.18.0, Pylint 3.2.5, Pyomo 6.7.3, Python-bundle-PyPI 2024.06, packmol 20.14.4, pagmo 2.19.0, parallel 20240722, parasail 2.6.2, pixman 0.43.4, pkgconfig 1.5.5, pod5-file-format 0.3.10, poetry 1.8.3, popt 1.19, pretty-yaml 24.7.0, primecount 7.14, primecountpy 0.1.0, prompt-toolkit 3.0.36, psycopg 3.2.1, pyBigWig 0.3.22, pyGenomeTracks 3.9, pyMBE 0.8.0, pybind11 2.12.0, pycocotools 2.0.7, pydantic 2.7.4, pydicom 2.4.4, pydot 2.0.0, pyfasta 0.5.2, pygmo 2.19.5, pyperf 2.7.0, pyseer 1.3.12, pyspoa 0.2.1, pystencils 1.3.4, pysteps 1.10.0, python-blosc 1.11.0, python-elf 0.5.1, python-, QuantumESPRESSO 7.3.1, QuantumESPRESSO 7.3.1, Qwt 6.3.0, qnorm 0.8.1, R-bundle-CRAN 2024.06, R 4.4.1, RDKit 2024.03.3, RStudio-Server 2023.09.1+494, RapidJSON 1.1.0-20240409, Raptor 2.0.16, Rasqal 0.9.33, Ray-project 2.9.1, ReFrame 4.6.2, ReFrame 4.6.2, Redland 1.0.17, Regenie 3.1.2, Rust 1.79.0, rMATS-long 1.0.0-20240502, rankwidth 0.9, rapidNJ 2.3.3, redis-py 5.0.9, regionmask 0.12.1, rjags 4-15, rpmrebuild 2.18, ruamel.yaml 0.18.6, SCENICplus 1.0a1-20240513, SCOTCH 7.0.4, SDL2 2.30.6, SHAP 0.43.0, SIONlib 1.7.7, SIP 6.8.3, SIRIUS 7.5.2, SKA2 0.3.7, SOCI 4.0.3, SRA-Toolkit 3.1.1, STAR 2.7.11b_alpha_2024-02-09, STREAM 5.10, STRUMPACK 7.1.0, STRUMPACK 7.1.0, SVDSS2 2.0.0-alpha.3, Safetensors 0.4.3, Sagemath 10.4, Salmon 1.10.3, ScaLAPACK 2.2.0, ScaLAPACK 2.2.0, SciPy-bundle 2024.05, SciPy-bundle 2024.05, Score-P 8.4, Score-P 8.4, SentencePiece 0.2.0, SeqKit 2.8.2, SharedMeatAxe 1.0.1, Single-cell-python-bundle 2024.02, SingleM 0.16.0, SpFFT 1.1.0, Sphinx-RTD-Theme 2.0.0, Sphinx-RTD-Theme 2.0.0, Stable-Baselines3 2.3.2, Stack 3.1.1, SuiteSparse 7.7.0, SuperLU 6.0.1, SuperLU_DIST 8.2.1, scArches 0.6.1, scCustomize 2.1.2, scFEA 1.1-20221109, scib-metrics 0.5.1, scikit-build 0.17.6, scrublet 0.2.3, scvi-tools 1.1.2, scvi-tools 1.1.2, sdsl-lite 2.0.3, segment-anything 1.0, setuptools-rust 1.9.0, sirocco 2.1.0, slepc4py 3.20.2, smafa 0.8.0, smithwaterman 20160702, snpEff 5.2c, spaCy 3.7.4, spektral 1.2.0, spglib-python 2.5.0, spglib 2.5.0, spla 1.6.1, spoa 4.1.0, submitit 1.2.0, svist4get 1.3.1, TAMkin 1.2.6, TAMkin 1.2.6, TELEMAC-MASCARET 8p5r0, TF-COMB 1.1, TOBIAS 0.16.1, TensorFlow 2.15.1, Tk 8.6.14, Tkinter 3.12.3, Transrate 1.0.3, Triangle 1.6, Trycycler 0.5.5, tabixpp 1.1.2, tbb 2021.9.0, tdlib 0.9.3, tensorboard 2.15.1, tiktoken 0.7.0, timm 1.0.8, torch-em 0.7.1, UCX-CUDA 1.15.0, UCX-CUDA 1.16.0, Umpire 2024.02.1, Uni-Core 0.0.3, Uni-Core 0.0.3, unixODBC 2.3.12, utf8proc 2.9.0, VBZ-Compression 1.0.3, VSEARCH 2.28.1, VTK 9.2.6, Visit 3.4.1, vcflib 1.0.9, velocyto 0.17.17, vigra 1.11.2, virtualenv 20.26.2, WFA2 2.3.4, WRF 4.5.1, Wayland 1.23.0, weblogo 2.8.2, wget 1.21.4, wradlib 2.0.3, wradlib 2.0.3, X11 20240607, XGBoost 2.1.1, XML-LibXML 2.0210, x264 20240513, x265 3.6, xarray 2024.5.0, xtb-IFF 1.1, xtb 6.7.1, xtensor 0.24.7, YACS 0.1.8, Yasm 1.3.0, yell 2.2.2, yelp-tools 42.1, yelp-xsl 42.1, Z3 4.13.0, ZeroMQ 4.3.5, Zoltan 3.901, z5py 2.0.17, zlib 1.3.1
+  - AGAT 1.4.0, ASE 3.23.0, Abseil 20240722.0, Albumentations 1.4.0, AlphaPulldown 2.0.0b4, AlphaPulldown 2.0.0b4,
+    AmberTools 26.3, Arrow 16.1.0, alsa-lib 1.2.11, archspec 0.2.4, attr 2.5.2, BayesTraits 4.1.2, BeautifulSoup 4.12.3,
+    Biopython 1.84, Boost.MPI 1.83.0, bcl-convert 4.2.7-2, beagle-lib 4.0.1, biom-format 2.1.16, byacc 2.0.20240109,
+    CDO 2.3.0, CFITSIO 4.4.1, CUDA-Samples 12.2, CUDA 12.5.0 + 12.6.0, CUTLASS 3.4.0, Catch2 2.13.10, CellOracle 0.18.0,
+    Clang 18.1.8, Coreutils 9.5, chewBBACA 3.3.9, code-server 4.90.2, connected-components-3d 3.14.1, cooler 0.10.2, 
+    cryptography 42.0.8, cutadapt 4.9, cyvcf2 0.31.1, dorado 0.7.3, dtcmp 1.1.5, ESMF 8.6.1, EvidentialGene 2023.07.15,
+    Extrae 4.2.0, ecBuild 3.8.5, elfutils 0.191, FFmpeg 7.0.2, FLAC 1.4.3, FUSE 3.16.2, Flask 3.0.3, Flye 2.9.4,
+    FriBidi 1.0.15, ffnvcodec 12.2.72.0, flatbuffers-python 24.3.25, flatbuffers 24.3.25, fmt 10.2.1, fpylll 0.6.1,
+    GCC 14.2.0, GDAL 3.9.0, GEOS 3.12.1, GHC 9.10.1, GLM 1.0.1, GLib 2.80.4, GLibmm 2.72.1 + 2.75.0 + 2.77.0 + 2.78.1,
+    GPAW 24.6.0, GetOrganelle 1.7.7.1, Guile 2.0.14 + 3.0.10, Gurobi 11.0.2, gap 4.13.0, genomepy 0.16.1, gensim 4.3.2,
+    gffutils 0.13, gh 2.52.0, git-annex 10.20240731, gmpy2 2.2.0, googletest 1.15.2, graph-tool 2.59, HDBSCAN 0.8.38.post1,
+    HOMER 4.11.1, HTSeq 2.0.7, HiCMatrix 17.2, Highway 1.2.0, Hypre 2.31.0, hatchling 1.24.2, histolab 0.7.0,
+    hypothesis 6.103.1, IQ-TREE 2.3.5, ImageMagick 7.1.1-34, Imath 3.1.11, IsoQuant 3.5.0, igraph 0.10.12, imageio 2.34.1,
+    imbalanced-learn 0.12.3, inferCNV 1.21.0, intervaltree 0.1, JsonCpp 1.9.5, Julia 1.10.4, jax 0.4.25, json-fortran 8.5.2,
+    Kent_tools 468, LLVM 18.1.8, LittleCMS 2.16, libdrm 2.4.122, libdwarf 0.10.1, libedit 20240517, libgeotiff 1.7.3,
+    libgit2 1.8.1, libopus 1.5.2, libsigc++ 3.6.0, libspatialindex 2.0.0, libunistring 1.2, libunwind 1.8.1, libwebp 1.4.0,
+    libxslt 1.1.42, libzip 1.10.1, lwgrp 1.0.6, lxml 5.3.0, MCR R2024a, MPICH 4.2.1, MUMPS 5.7.2, MariaDB 11.6.0,
+    Maven 3.9.7, Mercurial 6.8.1, Mesa 24.1.3, Miniconda3 23.10.0-1, MultiQC 1.22.3, makedepend 1.0.9, matplotlib 3.9.2,
+    maturin 1.6.0, medaka 1.12.1, meshio 5.3.5, meson-python 0.16.0, mm-common 1.0.6, NanoCaller 3.6.0, Normaliz 3.10.3,
+    n2v 0.3.3, nano 8.1, ncbi-vdb 3.1.1, nettle 3.10, nsync 1.29.2, numexpr 2.9.0, ORCA 6.0.0, OpenEXR 3.2.4, OpenFOAM 12,
+    OpenFOAM v2406, OpenJPEG 2.5.2, Optax 0.2.2, Optuna 3.6.1, PaStiX 6.3.2, Perl-bundle-CPAN 5.38.2, Pillow-SIMD 10.4.0,
+    Pint 0.24, Platypus-Opt 1.2.0, PostgreSQL 16.4, PyAEDT 0.9.9, PyCharm 2024.1.6, PyRosetta 4.release-384,
+    PyWavelets 1.7.0, PyYAML 6.0.2, Pygments 2.18.0, Pylint 3.2.5, Pyomo 6.7.3, Python-bundle-PyPI 2024.06, packmol 20.14.4,
+    pagmo 2.19.0, parallel 20240722, pixman 0.43.4, pod5-file-format 0.3.10, poetry 1.8.3, popt 1.19, pretty-yaml 24.7.0,
+    primecount 7.14, psycopg 3.2.1, pyGenomeTracks 3.9, pybind11 2.12.0, pycocotools 2.0.7, pydantic 2.7.4, pygmo 2.19.5,
+    pyperf 2.7.0, pyseer 1.3.12, pysteps 1.10.0, QuantumESPRESSO 7.3.1, Qwt 6.3.0, R-bundle-CRAN 2024.06, R 4.4.1,
+    RDKit 2024.03.3, RapidJSON 1.1.0-20240409, Ray-project 2.9.1, ReFrame 4.6.2, Rust 1.79.0, redis-py 5.0.9,
+    regionmask 0.12.1, rjags 4-15, rpmrebuild 2.18, SDL2 2.30.6, SHAP 0.43.0, SIP 6.8.3, SRA-Toolkit 3.1.1,
+    STAR 2.7.11b_alpha_2024-02-09, STRUMPACK 7.1.0, SVDSS2 2.0.0-alpha.3, Safetensors 0.4.3, Salmon 1.10.3,
+    SciPy-bundle 2024.05, SeqKit 2.8.2, SingleM 0.16.0, Sphinx-RTD-Theme 2.0.0, Stack 3.1.1, SuiteSparse 7.7.0,
+    SuperLU 6.0.1, SuperLU_DIST 8.2.1, scArches 0.6.1, scib-metrics 0.5.1, scvi-tools 1.1.2, sdsl-lite 2.0.3,
+    setuptools-rust 1.9.0, sirocco 2.1.0, slepc4py 3.20.2, smafa 0.8.0, snpEff 5.2c, spaCy 3.7.4, spektral 1.2.0,
+    spglib-python 2.5.0, spglib 2.5.0, TELEMAC-MASCARET 8p5r0, Tk 8.6.14, Tkinter 3.12.3, Trycycler 0.5.5, tiktoken 0.7.0,
+    timm 1.0.8, UCX-CUDA 1.16.0, unixODBC 2.3.12, utf8proc 2.9.0, VSEARCH 2.28.1, virtualenv 20.26.2, WRF 4.5.1,
+    Wayland 1.23.0, X11 20240607, XGBoost 2.1.1, XML-LibXML 2.0210, x264 20240513, x265 3.6, xarray 2024.5.0, xtb-IFF 1.1,
+    xtb 6.7.1, xtensor 0.24.7, yelp-xsl 42.1
 - minor enhancements, including:
-  - correct configuration of QuantumESPRESSO for 6.7/6.8/7.0/7.1/7.2/7.3 (#20070)
-  - add internal CUDA header patch for PSM2 (#20804)
-  - add support for JupyterHub to TensorBoard (#20823)
-  - make sure that recent ImageMagick versions pick up the right pkgconf and improve the sanity checks (#20900)
+  - add internal CUDA header patch for PSM2 v12.0.1 (#20804)
+  - add patch for JupyterHub support to recent tensorboard easyconfigs (#20823)
+  - make sure that recent ImageMagick versions pick up the right pkgconf + improve sanity check for ImageMagick (#20900)
   - also install utilities for recent versions of FUSE 3.x (#20918)
-  - add RISC-V support to x264-20231019/GCCcore-13.2.0 (#20968)
+  - add RISC-V support to x264 v20231019 (#20968)
   - add RISC-v support to recent LAME easyconfigs by removing workaround for finding libncurses (#20970)
   - enable PIC in recent x265 easyconfigs to solve compilation errors on RISC-V (#20971)
-  - add missMDA extension to R-bundle-CRAN versions 2023.12 (#21167) and 2024.06 (#21183)
+  - add extensions to R-bundle-CRAN: missmDA (#21167, #21183). insight (#21260), performance + datwizard + bayestestR (#21272, #21285)
   - add Qt support to VTK 9.3.0 (#21221)
-  - add insight extension to R-bundle-CRAN 2024.06 (#21260)
-  - add performance, datwizard and bayestestR to R-bundle-CRAN 2024.06 (#21272)
-  - add `helper_scripts` to PATH in ProteinMPNN-1.0.1-20230627 (#21289)
-  - add the plugins to OpenFOAM v2406 (#21332)
-  - use proper Python dependency for OTF2 (#21325)
+  - add `helper_scripts` to `$PATH` in easyconfig for ProteinMPNN v1.0.1-20230627 (#21289)
+  - also build & install the plugins with OpenFOAM v2406 (#21332)
 - various bug fixes, including:
+  - fix easyconfigs for recent versions of QuantumESPRESSO (#20070)
   - add wrapper for Julia with linking safeguards and delegate environment setup to JuliaPackage (#20103)
   - fix typo in description of SuiteSparse v7.7.0 (#20567)
   - add 'pic' flag to IML (#20789)
-  - add patch to fix build error with numpy with some compilers (#20817)
+  - add patch to recent SciPy-bundle easyconfigs to fix build error with numpy with some Fortran compilers (#20817)
   - rename unpacked sources for components of EasyBuild v4.9.2, to ensure that '`--install-latest-eb-release`' works with older EasyBuild versions (#20818)
   - fix build of OpenBLAS 0.3.24 on A64FX (#20820)
   - remove maturin build dependency from langchain-antropic (#20825)
   - add GMP and MPFR as dependencies to OpenFOAM v2306 and v2312 (#20841)
   - add patch to SciPy-bundle 2024.05 that fixes numpy test failures on RISC-V (#20847)
   - skip unreliable memory leak test in PyTorch 2.1.2 (#20874)
-  - use PyYAML 6.0.1 instead of 6.0 for recent ReFrame versions (#20879)
+  - use PyYAML 6.0.1 instead of 6.0 for recent ReFrame versions to fix problem with Cython 3.x (#20879)
   - use PyPI source tarball and gfbf/2023a toolchain for pyBigWig (#20881)
   - add fix for failing test on zen4 to Highway 1.0.4 (#20942)
   - add patch to fix implicit function declaration in OpenMPI 4.1.4 (#20949)
   - only use libxsmm as dependency for CP2K 2023.1 w/ `foss/2023a` on x86_64 (#20951)
   - copy missing `rsem_perl_utils.pm` in DETONATE, since it's required by `rsem-eval-calculate-score` command (#20956)
-  - set `SATSUMA2_PATH` so Satsuma2 can locate executables (#20957)
+  - set `$SATSUMA2_PATH` so Satsuma2 can locate executables (#20957)
   - disable auto-vectorizer (`-ftree-vectorize`) for OpenFOAM v10 + v11 when using toolchain that with GCC >= 11 (#20958)
   - disable test step for WIEN2k 23.2 because files required by it can no longer be downloaded (#20969)
-  - rename `gubbins-2.4.0.eb` to `Gubbins-2.4.0.eb` (#20995)
   - add patch to fix Qt6 issues with ParaView v5.12.0, e.g. representation selection (#21002)
   - update homepage in phonopy easyconfigs (#21014)
   - make libunwind dependency architecture specific in Extrae 4.2.0 easyconfig (#21017)
   - add `OPENSSL_ENABLE_SHA1_SIGNATURES` for building `ansys-pythonnet` (#21028)
-  - fix download URLs for old Intel software (2018-23) (#21108)
+  - fix download URLs for old Intel software (2018-2023) by using `IRC_NAS` instead of `irc_nas` (#21108)
   - update source and homepage URLs in Szip easyconfigs (#21129)
   - rename source URL in HDF v4.2.16-2 easyconfig (#21130)
   - consistently fix homeage + source URL for `HDF` + `h4toh5` (#21134)
   - ensure that recent BioPerl easyconfigs use `Bundle` easyblock (#21136)
   - fix checksum checks for easyconfigs using a `Bundle`-like easyblock in easyconfigs test suite (#21143)
   - add pkgconf build dependency to scikit-misc v0.3.1 (#21144)
-  - disable use of MySQL in GDAL (#21156)
-  - add GPflow v2.9.2 and fix tensorflow-probability to pass pip check (#21172)
+  - explicitly disable use of MySQL in recent GDAL easyconfigs (#21156)
+  - fix easyconfig tensorflow-probability v0.20.0 to pass `pip check` (#21172)
   - stop RStudio-Server 2023.09 from installing R packages (+ move to `foss/2023a` toolchain) (#21175)
-  - remove `Time::HiRes` from `Perl-bundle-CPAN` (#21198)
+  - remove `Time::HiRes` from `Perl-bundle-CPAN` since there's newer version in `Perl` (#21198)
   - fix build of STAR 2.7.11a + 2.7.11b on non-x86 architectures by avoiding use of `-maxv2` + add missing `xxd` build dependency (#21200)
   - add missing cairo dependency for python-igraph v0.10.6 (#21211)
   - add patch for xtb 6.7.0 to fix build failure due to changes in tblite (#21255)
-  - add patch for HDF5-1.14.3 to _suppress fp exceptions (#21280)
-  - correct extension order in R-bundle-CRAN 2024.06 (#21285)
+  - add patch for HDF5 v1.14.3 to suppress fp exceptions (#21280)
   - update easyconfig for dorado 0.7.3 to properly use provided OpenSSL dependency, and not install external libraries into its own lib directory (#21297)
+  - use proper Python dependency for OTF2 (#21325)
   - use source tarballs from GitHub for recent libdap easyconfigs (#21334)
-  - use version in byacc 2.0.20240109 sources (#21344)
   - remove Highway build dependency in Brunsli easyconfigs, since it's not actually required at all (#21366)
   - add alternative checksum for bold 1.3.0 extension in R-bundle-CRAN (#21370)
-  - disable buiding docs in fish (#21381)
 - other changes:
   - archive outdated example easyconfigs for Fujitsu toolchain (#20781)
-  - upgrade builddependency rpmrebuild to version 2.18 in bcl-convert 4.2.7 easyconfig (#20861)
-  - switch transformers to use external Safetensor dep (#20864)
-  - rename ega-quickview to EGA-QuickView (#20888)
+  - upgrade rpmrebuild build dependency to version 2.18 in bcl-convert 4.2.7 easyconfig (#20861)
+  - use proper dependency for Safetensors in easyconfig for Transformers v4.39.3 (#20864)
   - remove CMake Arrow flag as there is no Arrow dependency in recent GDAL easyconfigs (#20905)
-  - whitelist ConfigureMakePythonPackage for sanity_check_paths CI check (#20963)
+  - whitelist `ConfigureMakePythonPackage` for `sanity_check_paths` CI check (#20963)
+  - rename `gubbins-2.4.0.eb` to `Gubbins-2.4.0.eb` (#20995)
   - make pytest v7.4.2 independent of Python-bundle-PyPI (#21004)
   - reorganize Flax/JAX stack in 2023a: move `jax` + `Optax` to `gfbf/2023a` toolchain + use standalone `Flax` + `absl-py` as dependencies (#21038)
   - use stand-alone absl-py as dependency for jax w/ `gfbf/2023a` (#21039)
-  - remove Cython dependency from Python-bundle-PyPI 2024.06 + standalone easyconfig for Cython 3.0.10 (#21233)
-  - add Cython builddep for SciPy-bundle (#21235)
+  - remove Cython dependency from Python-bundle-PyPI 2024.06 + add standalone easyconfig for Cython 3.0.10 (#21233)
+  - add Cython build dependency for SciPy-bundle v2024.05 (#21235)
   - use top-level parameters for `use_pip` & co instead of `exts_default_options` for `PythonBundle` easyconfigs (#21292)