From 1f04f884f404c1bcf26a82fdafac8fdc1b97ace4 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 25 Jan 2022 13:51:26 +0100 Subject: [PATCH 001/599] adding easyconfigs: BeautifulSoup-4.10.0-GCCcore-10.3.0.eb, FACE-1.1.1-GCCcore-10.3.0.eb, FORD-6.1.6-GCCcore-10.3.0.eb, FoBiS-3.0.5-GCCcore-10.3.0.eb, forbear-1.2.0-GCCcore-10.3.0.eb, libaed2-1.3.0-GCC-10.3.0.eb, Simstrat-3.01-GCC-10.3.0.eb and patches: FACE-1.1.1_fix_fobos_src_filename.patch, forbear-1.2.0_use_external_FACE.patch, Simstrat-3.01_use_external_forbear_and_aed2.patch --- .../BeautifulSoup-4.10.0-GCCcore-10.3.0.eb | 34 ++++++ .../f/FACE/FACE-1.1.1-GCCcore-10.3.0.eb | 37 ++++++ .../FACE-1.1.1_fix_fobos_src_filename.patch | 49 ++++++++ .../f/FORD/FORD-6.1.6-GCCcore-10.3.0.eb | 52 +++++++++ .../f/FoBiS/FoBiS-3.0.5-GCCcore-10.3.0.eb | 38 +++++++ .../f/forbear/forbear-1.2.0-GCCcore-10.3.0.eb | 40 +++++++ .../forbear-1.2.0_use_external_FACE.patch | 105 ++++++++++++++++++ .../l/libaed2/libaed2-1.3.0-GCC-10.3.0.eb | 31 ++++++ .../s/Simstrat/Simstrat-3.01-GCC-10.3.0.eb | 44 ++++++++ ...t-3.01_use_external_forbear_and_aed2.patch | 99 +++++++++++++++++ 10 files changed, 529 insertions(+) create mode 100644 easybuild/easyconfigs/b/BeautifulSoup/BeautifulSoup-4.10.0-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/f/FACE/FACE-1.1.1-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/f/FACE/FACE-1.1.1_fix_fobos_src_filename.patch create mode 100644 easybuild/easyconfigs/f/FORD/FORD-6.1.6-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/f/FoBiS/FoBiS-3.0.5-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/f/forbear/forbear-1.2.0-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/f/forbear/forbear-1.2.0_use_external_FACE.patch create mode 100644 easybuild/easyconfigs/l/libaed2/libaed2-1.3.0-GCC-10.3.0.eb create mode 100644 easybuild/easyconfigs/s/Simstrat/Simstrat-3.01-GCC-10.3.0.eb create mode 100644 easybuild/easyconfigs/s/Simstrat/Simstrat-3.01_use_external_forbear_and_aed2.patch diff --git a/easybuild/easyconfigs/b/BeautifulSoup/BeautifulSoup-4.10.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/b/BeautifulSoup/BeautifulSoup-4.10.0-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..3c7c67ff170 --- /dev/null +++ b/easybuild/easyconfigs/b/BeautifulSoup/BeautifulSoup-4.10.0-GCCcore-10.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonBundle' + +name = 'BeautifulSoup' +version = '4.10.0' + +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': '10.3.0'} + +builddependencies = [ + ('binutils', '2.36.1') +] + +dependencies = [ + ('Python', '3.9.5'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('soupsieve', '2.3.1', { + 'checksums': ['b8d49b1cd4f037c7082a9683dfa1801aa2597fb11c3a1155b7a5b94829b4f1f9'], + }), + (name, version, { + 'modulename': 'bs4', + 'source_tmpl': 'beautifulsoup4-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/b/beautifulsoup4'], + 'checksums': ['c23ad23c521d818955a4151a67d81580319d4bf548d3d49f4223ae041ff98891'], + }), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/f/FACE/FACE-1.1.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/f/FACE/FACE-1.1.1-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..3b23657d0ed --- /dev/null +++ b/easybuild/easyconfigs/f/FACE/FACE-1.1.1-GCCcore-10.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'MakeCp' + +name = 'FACE' +version = '1.1.1' + +homepage = 'https://github.com/szaghi/FACE' +description = """A Fortran Ansi Colors (and Styles) Environment. +A KISS pure Fortran Library for easy colorize (and stylize) strings.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://github.com/szaghi/FACE/releases/download/v%(version)s'] +sources = ['%(name)s-v%(version)s.tar.gz'] +patches = [ + 'FACE-1.1.1_fix_fobos_src_filename.patch', +] +checksums = [ + 'cdc75cad2b7f443ee18e4a9ea4d264bc63b069e93cda6aa3f6a15a515b1f3721', # FACE-v1.1.1.tar.gz + '9c51e758716db8a63be393a56fc3be22b3f4f4bf90f659844fe6a07bcfe16eb8', # FACE-1.1.1_fix_fobos_src_filename.patch +] + +builddependencies = [ + ('binutils', '2.36.1'), + ('FoBiS', '3.0.5'), +] + +build_cmd = 'FoBiS.py build' +buildopts = '-mode face-shared-gnu' + +files_to_copy = [(['lib/mod/*.mod'], 'include'), (['lib/libface.%s' % SHLIB_EXT], 'lib')] + +sanity_check_paths = { + 'files': ['include/face.mod', 'lib/libface.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/f/FACE/FACE-1.1.1_fix_fobos_src_filename.patch b/easybuild/easyconfigs/f/FACE/FACE-1.1.1_fix_fobos_src_filename.patch new file mode 100644 index 00000000000..92933aee308 --- /dev/null +++ b/easybuild/easyconfigs/f/FACE/FACE-1.1.1_fix_fobos_src_filename.patch @@ -0,0 +1,49 @@ +Pull in upstream fix for file name + +Åke Sandgren, 2022-01-24 + +commit 918c19faefabc7a8b35475474daa9dc98474d505 +Author: neok-m4700 +Date: Sun Jan 14 15:39:37 2018 +0100 + + consistency with source file naming + + `FoBiS.py build -tb -mode face-shared-gnu` fails without the changes proposed by this PR (no output lib nor module) + +diff --git a/fobos b/fobos +index 0ca7a8c..3f02f4b 100644 +--- a/fobos ++++ b/fobos +@@ -35,28 +35,28 @@ build_dir = exe + [face-static-gnu] + template = template-static-gnu + build_dir = lib +-target = face.f90 ++target = face.F90 + output = libface.a + mklib = static + + [face-shared-gnu] + template = template-shared-gnu + build_dir = lib +-target = face.f90 ++target = face.F90 + output = libface.so + mklib = shared + + [face-static-intel] + template = template-static-intel + build_dir = lib +-target = face.f90 ++target = face.F90 + output = libface.a + mklib = static + + [face-shared-intel] + template = template-shared-intel + build_dir = lib +-target = face.f90 ++target = face.F90 + output = libface.so + mklib = shared + diff --git a/easybuild/easyconfigs/f/FORD/FORD-6.1.6-GCCcore-10.3.0.eb b/easybuild/easyconfigs/f/FORD/FORD-6.1.6-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..f85c40e8755 --- /dev/null +++ b/easybuild/easyconfigs/f/FORD/FORD-6.1.6-GCCcore-10.3.0.eb @@ -0,0 +1,52 @@ +easyblock = 'PythonBundle' + +name = 'FORD' +version = '6.1.6' + +homepage = 'https://github.com/Fortran-FOSS-Programmers/ford/wiki' +description = 'FORD is an automatic documentation generator for modern Fortran programs' + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +builddependencies = [ + ('binutils', '2.36.1'), +] + +dependencies = [ + ('Python', '3.9.5'), + ('Graphviz', '2.47.2',), + ('BeautifulSoup', '4.10.0'), + ('tqdm', '4.61.2'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('graphviz', '0.19.1', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'checksums': ['09ed0cde452d015fe77c4845a210eb642f28d245f5bc250d4b97808cb8f49078'], + }), + ('Markdown', '3.3.4', { + 'checksums': ['31b5b491868dcc87d6c24b7e3d19a0d730d59d3e46f4eea6430a321bed387a49'], + }), + ('markdown-include', '0.6.0', { + 'checksums': ['6f5d680e36f7780c7f0f61dca53ca581bd50d1b56137ddcd6353efafa0c3e4a2'], + }), + ('md-environ', '0.1.0', { + 'checksums': ['fe3c2a255af523d6f522831c699336cd71f9d543714067d93206ed35836f1793'], + }), + ('toposort', '1.7', { + 'checksums': ['ddc2182c42912a440511bd7ff5d3e6a1cabc3accbc674a3258c8c41cbfbb2125'], + }), + (name, version, { + 'checksums': ['c286206e6ce8c12f2e00f6c73e3b76dae830dce7b5b6f52a54512585fcfae12a'], + }), +] + +sanity_check_paths = { + 'files': ['bin/ford'], + 'dirs': ['bin', 'lib'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/f/FoBiS/FoBiS-3.0.5-GCCcore-10.3.0.eb b/easybuild/easyconfigs/f/FoBiS/FoBiS-3.0.5-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..06c9257d5bf --- /dev/null +++ b/easybuild/easyconfigs/f/FoBiS/FoBiS-3.0.5-GCCcore-10.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonBundle' + +name = 'FoBiS' +version = '3.0.5' + +homepage = 'https://github.com/szaghi/FoBiS' +description = "A Fortran Building System for automatic building modern Fortran projects" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +dependencies = [ + ('binutils', '2.36.1'), + ('Python', '3.9.5'), + ('BeautifulSoup', '4.10.0'), + ('FORD', '6.1.6'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('argparse', '1.4.0', { + 'checksums': ['62b089a55be1d8949cd2bc7e0df0bddb9e028faefc8c32038cc84862aefdd6e4'], + }), + ('PreForM.py', '1.1.3', { + 'modulename': 'PreForM', + 'checksums': ['420457c236801e8803f4e8b8c7e44a7b65a5becc11d5d75404da537b1e09f3a8'], + }), + ('configparser', '5.2.0', { + 'checksums': ['1b35798fdf1713f1c3139016cfcbc461f09edbf099d1fb658d4b7479fcaa3daa'], + }), + ('FoBiS.py', version, { + 'modulename': 'fobis', + 'checksums': ['ef23fde4199277abc693d539a81e0728571c349174da6b7476579f82482ab96c'], + }), +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/f/forbear/forbear-1.2.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/f/forbear/forbear-1.2.0-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..ef6ec74a694 --- /dev/null +++ b/easybuild/easyconfigs/f/forbear/forbear-1.2.0-GCCcore-10.3.0.eb @@ -0,0 +1,40 @@ +easyblock = 'MakeCp' + +name = 'forbear' +version = '1.2.0' + +homepage = 'https://github.com/szaghi/forbear' +description = "A Fortran Library for building and running fancy progress bar" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://github.com/szaghi/forbear/releases/download/v%(version)s'] +sources = ['%(name)s-v%(version)s.tar.gz'] +patches = [ + 'forbear-1.2.0_use_external_FACE.patch', +] +checksums = [ + '72b399526ea291e4d5bed121f8a812aadfe7cea59a1553eb0adf0f3bf5ce1554', # forbear-v1.2.0.tar.gz + '26a586affade31cb83fa23d86a889b28de4b3c30ca6d63946740da0320ba818d', # forbear-1.2.0_use_external_FACE.patch +] + +builddependencies = [ + ('binutils', '2.36.1'), + ('FoBiS', '3.0.5'), +] + +dependencies = [ + ('FACE', '1.1.1'), +] + +build_cmd = 'FoBiS.py build' +buildopts = '-mode shared-gnu ' + +files_to_copy = [(['shared/mod/*.mod'], 'include'), (['shared/libforbear.%s' % SHLIB_EXT], 'lib')] + +sanity_check_paths = { + 'files': ['include/forbear.mod', 'lib/libforbear.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/f/forbear/forbear-1.2.0_use_external_FACE.patch b/easybuild/easyconfigs/f/forbear/forbear-1.2.0_use_external_FACE.patch new file mode 100644 index 00000000000..fdf2967731e --- /dev/null +++ b/easybuild/easyconfigs/f/forbear/forbear-1.2.0_use_external_FACE.patch @@ -0,0 +1,105 @@ +Use external FACE build + +Åke Sandgren, 2022-01-25 +diff -ru forbear.orig/fobos forbear/fobos +--- forbear.orig/fobos 2017-06-11 14:56:47.000000000 +0200 ++++ forbear/fobos 2022-01-25 09:16:13.737587610 +0100 +@@ -17,7 +17,7 @@ + $DEBUG_PGI = -C -g -gopt -Mchkfpstk -Mchkptr -Mchkstk -Mcoff -traceback + $OPTIMIZE = -O3 + $EXDIRS = PENF/src/tests/ +- FACE/src/tests/ FACE/src/third_party/ ++# FACE/src/tests/ FACE/src/third_party/ + + # main modes + # GNU +@@ -117,6 +117,8 @@ + quiet = False + log = True + jobs = 2 ++ext_libs = face ++include = $EBROOTFACE/include + + [template-static-gnu] + compiler = gnu +@@ -130,6 +132,8 @@ + quiet = False + log = True + jobs = 2 ++ext_libs = face ++include = $EBROOTFACE/include + + [template-shared-gnu-debug] + compiler = gnu +@@ -144,6 +148,8 @@ + quiet = False + log = True + jobs = 2 ++ext_libs = face ++include = $EBROOTFACE/include + + [template-static-gnu-debug] + compiler = gnu +@@ -158,6 +164,8 @@ + quiet = False + log = True + jobs = 2 ++ext_libs = face ++include = $EBROOTFACE/include + + [template-shared-intel] + compiler = intel +@@ -171,6 +179,8 @@ + quiet = False + log = True + jobs = 2 ++ext_libs = face ++include = $EBROOTFACE/include + + [template-static-intel] + compiler = intel +@@ -184,6 +194,8 @@ + quiet = False + log = True + jobs = 2 ++ext_libs = face ++include = $EBROOTFACE/include + + [template-shared-intel-debug] + compiler = intel +@@ -198,6 +210,8 @@ + quiet = False + log = True + jobs = 2 ++ext_libs = face ++include = $EBROOTFACE/include + + [template-static-intel-debug] + compiler = intel +@@ -212,6 +226,8 @@ + quiet = False + log = True + jobs = 2 ++ext_libs = face ++include = $EBROOTFACE/include + + [template-static-pgi] + compiler = pgi +@@ -225,6 +241,8 @@ + quiet = False + log = True + jobs = 2 ++ext_libs = face ++include = $EBROOTFACE/include + + [template-static-pgi-debug] + compiler = pgi +@@ -239,6 +257,8 @@ + quiet = False + log = True + jobs = 2 ++ext_libs = face ++include = $EBROOTFACE/include + + # rules + [rule-makedoc] diff --git a/easybuild/easyconfigs/l/libaed2/libaed2-1.3.0-GCC-10.3.0.eb b/easybuild/easyconfigs/l/libaed2/libaed2-1.3.0-GCC-10.3.0.eb new file mode 100644 index 00000000000..f2f9d923062 --- /dev/null +++ b/easybuild/easyconfigs/l/libaed2/libaed2-1.3.0-GCC-10.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'MakeCp' + +name = 'libaed2' +version = '1.3.0' + +homepage = 'https://aquatic.science.uwa.edu.au/research/models/AED' +description = """libaed2 is a library of modules and algorithms for +simulation of "aquatic ecodynamics" - water quality, aquatic +biogeochemsitry, biotic habitat and aquatic ecosystem dynamics.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/AquaticEcoDynamics/libaed2/archive'] +sources = ['v%(version)s.tar.gz'] + +buildopts = 'OPT_FFLAGS="$FFLAGS" ' + +files_to_copy = [ + (['mod/*', 'include/*.h'], 'include'), + 'lib', +] + +maxparallel = 1 + +sanity_check_paths = { + 'files': ['lib/%(name)s.a'], + 'dirs': ['include'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/Simstrat/Simstrat-3.01-GCC-10.3.0.eb b/easybuild/easyconfigs/s/Simstrat/Simstrat-3.01-GCC-10.3.0.eb new file mode 100644 index 00000000000..bc14c143be9 --- /dev/null +++ b/easybuild/easyconfigs/s/Simstrat/Simstrat-3.01-GCC-10.3.0.eb @@ -0,0 +1,44 @@ +easyblock = 'MakeCp' + +name = 'Simstrat' +version = '3.01' + +homepage = 'http://www.eawag.ch/en/department/surf/projects/simstrat/' +description = """Simstrat is a one-dimensional physical lake model for +the simulation of stratification and mixing in deep stratified lakes.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = ['https://github.com/Eawag-AppliedSystemAnalysis/Simstrat/archive'] +sources = ['%(version)s.tar.gz'] +patches = [ + 'Simstrat-3.01_use_external_forbear_and_aed2.patch', +] +checksums = [ + 'ed504e65e11e7064d3c27643ca41785eaf1f6a8fd7a96dda5b96966ba3665c2e', # 3.01.tar.gz + # Simstrat-3.01_use_external_forbear_and_aed2.patch + 'c37ad82393c2790222bc4018831a29e0c4ddc240a3e37f7c9c613e3b944d6634', +] + +builddependencies = [ + ('FoBiS', '3.0.5'), +] + +dependencies = [ + ('forbear', '1.2.0'), + ('libaed2', '1.3.0'), +] + +prebuildopts = 'cd build && ' + +build_cmd = 'FoBiS.py build' +buildopts = '-mode release-gnu-dynamic ' + +files_to_copy = [(['build/simstrat'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/simstrat'], + 'dirs': [], +} + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/s/Simstrat/Simstrat-3.01_use_external_forbear_and_aed2.patch b/easybuild/easyconfigs/s/Simstrat/Simstrat-3.01_use_external_forbear_and_aed2.patch new file mode 100644 index 00000000000..465d0a3c380 --- /dev/null +++ b/easybuild/easyconfigs/s/Simstrat/Simstrat-3.01_use_external_forbear_and_aed2.patch @@ -0,0 +1,99 @@ +Use external forbear and aed2 libraries. + +Åke Sandgren, 2022-01-25 +diff -ru Simstrat-3.01.orig/build/fobos Simstrat-3.01/build/fobos +--- Simstrat-3.01.orig/build/fobos 2021-04-23 15:35:32.000000000 +0200 ++++ Simstrat-3.01/build/fobos 2022-01-25 09:54:07.726977196 +0100 +@@ -7,35 +7,14 @@ + lflags=-static-libgcc -static-libgfortran -static + build_dir=. + src=../src/ +-libs = ../lib/libaed2/obj/aed2_bio_utils.o +- ../lib/libaed2/obj/aed2_carbon.o +- ../lib/libaed2/obj/aed2_chlorophylla.o +- ../lib/libaed2/obj/aed2_common.o +- ../lib/libaed2/obj/aed2_core.o +- ../lib/libaed2/obj/aed2_csv_reader.o +- ../lib/libaed2/obj/aed2_dummy.o +- ../lib/libaed2/obj/aed2_nitrogen.o +- ../lib/libaed2/obj/aed2_noncohesive.o +- ../lib/libaed2/obj/aed2_organic_matter.o +- ../lib/libaed2/obj/aed2_oxygen.o +- ../lib/libaed2/obj/aed2_phosphorus.o +- ../lib/libaed2/obj/aed2_phytoplankton.o +- ../lib/libaed2/obj/aed2_sedflux.o +- ../lib/libaed2/obj/aed2_silica.o +- ../lib/libaed2/obj/aed2_totals.o +- ../lib/libaed2/obj/aed2_tracer.o +- ../lib/libaed2/obj/aed2_util.o +- ../lib/libaed2/obj/aed2_zoop_utils.o +- ../lib/libaed2/obj/aed2_zooplankton.o +- ../lib/libaed2/obj/ufz_oxygen.o +-include = ../lib/libaed2/mod/ ++include = $EBROOTLIBAED2/include $EBROOTFORBEAR/include ++ext_libs = aed2 forbear + colors=False + quiet=False + target=simstrat.f90 + output=simstrat + dependon=../lib/csv_fortran/fobos:release-gnu((direct)) + ../lib/json_fortran/fobos:release-gnu((direct)) +- ../lib/forbear/fobos:static-gnu((direct)) + log=True + + [release-gnu-dynamic] +@@ -44,12 +23,13 @@ + lflags=-dynamic-libgcc -dynamic-libgfortran -dynamic + build_dir=. + src=../src/ ++include = $EBROOTLIBAED2/include $EBROOTFORBEAR/include ++ext_libs = aed2 forbear + colors=False + quiet=False + target=simstrat.f90 + dependon=../lib/csv_fortran/fobos:release-gnu((direct)) + ../lib/json_fortran/fobos:release-gnu((direct)) +- ../lib/forbear/fobos:static-gnu((direct)) + log=True + + [release-intel] +@@ -58,6 +38,8 @@ + modsw=-module= + build_dir=. + src=../src/ ++include = $EBROOTLIBAED2/include $EBROOTFORBEAR/include ++ext_libs = aed2 forbear + colors=False + quiet=False + target=simstrat.f90 +@@ -72,13 +54,14 @@ + lflags=-static-libgcc -static-libgfortran -static + build_dir=. + src=../src/ ++include = $EBROOTLIBAED2/include $EBROOTFORBEAR/include ++ext_libs = aed2 forbear + colors=False + quiet=False + target=simstrat.f90 + output=simstrat + dependon=../lib/csv_fortran/fobos:release-gnu((direct)) + ../lib/json_fortran/fobos:release-gnu((direct)) +- ../lib/forbear/fobos:static-gnu((direct)) + log=True + + [debug-gnu-dynamic] +@@ -87,12 +70,13 @@ + lflags=-dynamic-libgcc -dynamic-libgfortran -dynamic + build_dir=. + src=../src/ ++include = $EBROOTLIBAED2/include $EBROOTFORBEAR/include ++ext_libs = aed2 forbear + colors=False + quiet=False + target=simstrat.f90 + dependon=../lib/csv_fortran/fobos:release-gnu((direct)) + ../lib/json_fortran/fobos:release-gnu((direct)) +- ../lib/forbear/fobos:static-gnu((direct)) + log=True + + [rule-makedoc] From 85fdc576f64c91987ab2d10cc1fba9f74813ba00 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 25 Jan 2022 14:22:17 +0100 Subject: [PATCH 002/599] Add missing checksum and remove trailing space. --- easybuild/easyconfigs/l/libaed2/libaed2-1.3.0-GCC-10.3.0.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libaed2/libaed2-1.3.0-GCC-10.3.0.eb b/easybuild/easyconfigs/l/libaed2/libaed2-1.3.0-GCC-10.3.0.eb index f2f9d923062..9274a05f2cd 100644 --- a/easybuild/easyconfigs/l/libaed2/libaed2-1.3.0-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/l/libaed2/libaed2-1.3.0-GCC-10.3.0.eb @@ -13,12 +13,13 @@ toolchainopts = {'pic': True} source_urls = ['https://github.com/AquaticEcoDynamics/libaed2/archive'] sources = ['v%(version)s.tar.gz'] +checksums = ['9152c2a5ac6da4162f73dc37c4a98e1cbd19a106195441b3d27a6df1911242f5'] buildopts = 'OPT_FFLAGS="$FFLAGS" ' files_to_copy = [ (['mod/*', 'include/*.h'], 'include'), - 'lib', + 'lib', ] maxparallel = 1 From d2be15c7ae2da59b3ef2c0d30c4d12f6501115a9 Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 21 Sep 2022 16:34:20 +0100 Subject: [PATCH 003/599] adding easyconfigs: DeepLabCut-2.2.0.6-foss-2021a.eb --- .../DeepLabCut-2.2.0.6-foss-2021a.eb | 65 +++++++++++++++++++ 1 file changed, 65 insertions(+) create mode 100644 easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a.eb diff --git a/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a.eb b/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a.eb new file mode 100644 index 00000000000..e1d4d8dd05a --- /dev/null +++ b/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a.eb @@ -0,0 +1,65 @@ +# Loosely based on PR #7680 +# J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'PythonBundle' + +name = 'DeepLabCut' +version = '2.2.0.6' +local_version = '%(versionsuffix)s-contrib' + +homepage = 'http://www.mousemotorlab.org/deeplabcut' +description = "Markerless tracking of user-defined features with deep learning" + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'pic': True} + +dependencies = [ + ('Python', '3.9.5'), + ('h5py', '3.2.1'), + ('IPython', '7.25.0'), + ('scikit-learn', '0.24.2'), + ('scikit-image', '0.18.3'), + ('TensorFlow', '2.6.0'), + ('PyYAML', '5.4.1'), + ('PyTables', '3.6.1'), + ('wxPython', '4.1.1'), + ('OpenCV', '4.5.3', '-contrib'), + ('numba', '0.53.1'), + ('libyaml', '0.2.5'), + ('imgaug', '0.4.0'), + ('tqdm', '4.61.2'), + ('ruamel.yaml', '0.17.21'), + ('PyYAML', '5.4.1'), + ('statsmodels', '0.12.2'), + ('PyTorch', '1.10.0'), +] + +use_pip = True + +exts_list = [ + ('filterpy', '1.4.5', { + 'sources': ['%(name)s-%(version)s.zip'], + 'checksums': ['4f2a4d39e4ea601b9ab42b2db08b5918a9538c168cff1c6895ae26646f3d73b1'], + }), + ('pandas', '1.3.3', { + 'checksums': ['272c8cb14aa9793eada6b1ebe81994616e647b5892a370c7135efb2924b701df'], + }), + ('tensorpack', '0.11', { + 'checksums': ['022b610e416e62e3575424cd08e60af27808a5fb6914294615391caf582cbd4f'], + }), + ('tf_slim', '1.1.0', { + 'source_urls': ['https://github.com/google-research/tf-slim/archive'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['964cde4b7728a408dcd5c841ab6b93d95137ab4b60db28b10400f86286bfeb8b'], + }), + ('msgpack-numpy', '0.4.8', { + 'checksums': ['c667d3180513422f9c7545be5eec5d296dcbb357e06f72ed39cc683797556e69'], + 'sources': ['msgpack-numpy-0.4.8.tar.gz'], + }), + (name, version, { + 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + 'checksums': ['4aa6694201e2aa56b9bd3e97ab27b0bc54f1364303167216174d2376d8ae0f84'], + }), +] + +moduleclass = 'lib' From 8d58eee940e79d90e948e193be979d15c03041ae Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Thu, 13 Oct 2022 15:31:32 +0200 Subject: [PATCH 004/599] adding easyconfigs: motif-2.3.8-GCCcore-11.3.0.eb, motif-2.3.8-GCCcore-10.2.0.eb --- .../m/motif/motif-2.3.8-GCCcore-10.2.0.eb | 40 ++++++++++++++++++ .../m/motif/motif-2.3.8-GCCcore-11.3.0.eb | 41 +++++++++++++++++++ 2 files changed, 81 insertions(+) create mode 100644 easybuild/easyconfigs/m/motif/motif-2.3.8-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/m/motif/motif-2.3.8-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/m/motif/motif-2.3.8-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/motif/motif-2.3.8-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..63dcdcf5ab5 --- /dev/null +++ b/easybuild/easyconfigs/m/motif/motif-2.3.8-GCCcore-10.2.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'motif' +version = '2.3.8' + +homepage = 'https://motif.ics.com/' +description = """Motif refers to both a graphical user interface (GUI) specification and the widget toolkit for building + applications that follow that specification under the X Window System on Unix and other POSIX-compliant systems. + It was the standard toolkit for the Common Desktop Environment and thus for Unix.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(name)s-%(version)s.tar.gz'] +checksums = ['859b723666eeac7df018209d66045c9853b50b4218cecadb794e2359619ebce7'] + +builddependencies = [ + ('Autotools', '20200321'), + ('flex', '2.6.4'), + ('Bison', '3.7.1'), + ('util-linux', '2.36'), +] + +dependencies = [ + ('X11', '20201008'), + ('libpng', '1.6.37'), + ('freetype', '2.10.3'), + ('libjpeg-turbo', '2.0.5'), + ('bzip2', '1.0.8'), +] + +# makefile is not parallel safe +parallel = 1 + +sanity_check_paths = { + 'files': ['lib/libMrm.a', 'lib/libUil.a', 'lib/libXm.a', 'bin/mwm', 'bin/uil', 'bin/xmbind'], + 'dirs': ['include/Mrm', 'include/uil', 'include/X11', 'include/Xm'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/motif/motif-2.3.8-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/motif/motif-2.3.8-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..8f4a300dbef --- /dev/null +++ b/easybuild/easyconfigs/m/motif/motif-2.3.8-GCCcore-11.3.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'motif' +version = '2.3.8' + +homepage = 'https://motif.ics.com/' +description = """Motif refers to both a graphical user interface (GUI) specification and the widget toolkit for building + applications that follow that specification under the X Window System on Unix and other POSIX-compliant systems. + It was the standard toolkit for the Common Desktop Environment and thus for Unix.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(name)s-%(version)s.tar.gz'] +checksums = ['859b723666eeac7df018209d66045c9853b50b4218cecadb794e2359619ebce7'] + +builddependencies = [ + ('Autotools', '20220317'), + ('flex', '2.6.4'), + ('Bison', '3.8.2'), + ('binutils', '2.38'), + ('util-linux', '2.38'), +] + +dependencies = [ + ('X11', '20220504'), + ('libpng', '1.6.37'), + ('freetype', '2.12.1'), + ('libjpeg-turbo', '2.1.3'), + ('bzip2', '1.0.8'), +] + +# makefile is not parallel safe +parallel = 1 + +sanity_check_paths = { + 'files': ['lib/libMrm.a', 'lib/libUil.a', 'lib/libXm.a', 'bin/mwm', 'bin/uil', 'bin/xmbind'], + 'dirs': ['include/Mrm', 'include/uil', 'include/X11', 'include/Xm'], +} + +moduleclass = 'vis' From 162a08790eb6dfdeb33d5fafaa1ccadb12e23613 Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 17 Oct 2022 10:24:18 +0100 Subject: [PATCH 005/599] Duplicated PyYAML and pandas removed --- .../easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a.eb | 4 ---- 1 file changed, 4 deletions(-) diff --git a/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a.eb b/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a.eb index e1d4d8dd05a..41ace2269ef 100644 --- a/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a.eb +++ b/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a.eb @@ -29,7 +29,6 @@ dependencies = [ ('imgaug', '0.4.0'), ('tqdm', '4.61.2'), ('ruamel.yaml', '0.17.21'), - ('PyYAML', '5.4.1'), ('statsmodels', '0.12.2'), ('PyTorch', '1.10.0'), ] @@ -41,9 +40,6 @@ exts_list = [ 'sources': ['%(name)s-%(version)s.zip'], 'checksums': ['4f2a4d39e4ea601b9ab42b2db08b5918a9538c168cff1c6895ae26646f3d73b1'], }), - ('pandas', '1.3.3', { - 'checksums': ['272c8cb14aa9793eada6b1ebe81994616e647b5892a370c7135efb2924b701df'], - }), ('tensorpack', '0.11', { 'checksums': ['022b610e416e62e3575424cd08e60af27808a5fb6914294615391caf582cbd4f'], }), From 5bb40ac4e28cb836ede916e1c4f070bab24211d3 Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 17 Oct 2022 11:13:04 +0100 Subject: [PATCH 006/599] pip_sanity_check added --- .../easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a.eb b/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a.eb index 41ace2269ef..d18669a6863 100644 --- a/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a.eb +++ b/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a.eb @@ -33,6 +33,8 @@ dependencies = [ ('PyTorch', '1.10.0'), ] +download_dep_fail = True +sanity_pip_check = True use_pip = True exts_list = [ From 3ffe48ee0b3ee63e48116d5270c11f48868ec72f Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 17 Oct 2022 11:42:19 +0100 Subject: [PATCH 007/599] download_dep removed as PythonBundle being used --- .../easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a.eb b/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a.eb index d18669a6863..e1b28de60f0 100644 --- a/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a.eb +++ b/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a.eb @@ -33,7 +33,6 @@ dependencies = [ ('PyTorch', '1.10.0'), ] -download_dep_fail = True sanity_pip_check = True use_pip = True From 5fbc3d70eb522ff05453c781536f45a371335d16 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 21 Oct 2022 10:54:44 +0200 Subject: [PATCH 008/599] adding easyconfigs: Coreutils-9.1-GCCcore-11.3.0.eb, Coreutils-9.1-GCCcore-12.2.0.eb --- .../Coreutils/Coreutils-9.1-GCCcore-11.3.0.eb | 27 +++++++++++++++++++ .../Coreutils/Coreutils-9.1-GCCcore-12.2.0.eb | 27 +++++++++++++++++++ 2 files changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/c/Coreutils/Coreutils-9.1-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/c/Coreutils/Coreutils-9.1-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/c/Coreutils/Coreutils-9.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/Coreutils/Coreutils-9.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..c17a9e2fafd --- /dev/null +++ b/easybuild/easyconfigs/c/Coreutils/Coreutils-9.1-GCCcore-11.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = "Coreutils" +version = "9.1" + +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': '11.3.0'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['61a1f410d78ba7e7f37a5a4f50e6d1320aca33375484a3255eddf17a38580423'] + +builddependencies = [('binutils', '2.38')] + +sanity_check_paths = { + 'files': ['bin/sort', 'bin/echo', 'bin/du', 'bin/date', 'bin/true'], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/Coreutils/Coreutils-9.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/c/Coreutils/Coreutils-9.1-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..d180e31a737 --- /dev/null +++ b/easybuild/easyconfigs/c/Coreutils/Coreutils-9.1-GCCcore-12.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = "Coreutils" +version = "9.1" + +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': '12.2.0'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['61a1f410d78ba7e7f37a5a4f50e6d1320aca33375484a3255eddf17a38580423'] + +builddependencies = [('binutils', '2.39')] + +sanity_check_paths = { + 'files': ['bin/sort', 'bin/echo', 'bin/du', 'bin/date', 'bin/true'], + 'dirs': [] +} + +moduleclass = 'tools' From d3643f8f9cd6569726f06ed0ebc3e0e51fac46ad Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 24 Oct 2022 12:24:18 +0100 Subject: [PATCH 009/599] MoviePi added, scikit-image downgraded --- .../DeepLabCut-2.2.0.6-foss-2021a.eb | 30 ++++++++++++++++++- 1 file changed, 29 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a.eb b/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a.eb index e1b28de60f0..37f47381608 100644 --- a/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a.eb +++ b/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a.eb @@ -1,4 +1,6 @@ # Loosely based on PR #7680 +# Scikit-image is added as an extension to avoid problems with imageio, +# which comes in from MoviePy # J. Sassmannshausen (Imperial College London/UK) easyblock = 'PythonBundle' @@ -18,7 +20,6 @@ dependencies = [ ('h5py', '3.2.1'), ('IPython', '7.25.0'), ('scikit-learn', '0.24.2'), - ('scikit-image', '0.18.3'), ('TensorFlow', '2.6.0'), ('PyYAML', '5.4.1'), ('PyTables', '3.6.1'), @@ -31,6 +32,7 @@ dependencies = [ ('ruamel.yaml', '0.17.21'), ('statsmodels', '0.12.2'), ('PyTorch', '1.10.0'), + ('MoviePy', '1.0.3'), ] sanity_pip_check = True @@ -53,6 +55,32 @@ exts_list = [ 'checksums': ['c667d3180513422f9c7545be5eec5d296dcbb357e06f72ed39cc683797556e69'], 'sources': ['msgpack-numpy-0.4.8.tar.gz'], }), + + # this is for scikit-image + ('PyWavelets', '1.1.1', { + 'modulename': 'pywt', + 'checksums': ['1a64b40f6acb4ffbaccce0545d7fc641744f95351f62e4c6aaa40549326008c9'], + }), + ('imread', '0.7.4', { + 'checksums': ['0487adef11a22168700968c1727020361a72f6132b6ced2b8826b02d8cbf744f'], + }), + ('pooch', '1.5.2', { + 'checksums': ['5969b2f1defbdc405df932767e05e0b536e2771c27f1f95d7f260bc99bf13581'], + }), + ('tifffile', '2021.10.12', { + 'checksums': ['0a78268a2d844af94929512d28b39bd1ea6fe46de4124103840b5fe4e1c555cd'], + }), + ('scikit-image', '0.18.1', { + 'modulename': 'skimage', + 'patches': ['scikit-image-0.18.1_fix-README-cache-perms.patch'], + 'checksums': [ + 'fbb618ca911867bce45574c1639618cdfb5d94e207432b19bc19563d80d2f171', # scikit-image-0.18.1.tar.gz + # scikit-image-0.18.1_fix-README-cache-perms.patch + '3a941401231403808963d488aaf498a712c428c3b19a1752652be9972d82b7b8', + ], + }), + # end of scikit-image + (name, version, { 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', 'checksums': ['4aa6694201e2aa56b9bd3e97ab27b0bc54f1364303167216174d2376d8ae0f84'], From 6bd55cd6ab70a9e9dbac3955a8111719cfbf3ade Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 24 Oct 2022 14:40:56 +0100 Subject: [PATCH 010/599] scikit-image readded and setup.py patched to newer version of scikit-image --- .../DeepLabCut-2.2.0.6-foss-2021a.eb | 33 +++---------------- .../deeplabcut-2.2.0.6-setup.py.patch | 15 +++++++++ 2 files changed, 20 insertions(+), 28 deletions(-) create mode 100644 easybuild/easyconfigs/d/DeepLabCut/deeplabcut-2.2.0.6-setup.py.patch diff --git a/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a.eb b/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a.eb index 37f47381608..39f304ae009 100644 --- a/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a.eb +++ b/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a.eb @@ -1,6 +1,4 @@ # Loosely based on PR #7680 -# Scikit-image is added as an extension to avoid problems with imageio, -# which comes in from MoviePy # J. Sassmannshausen (Imperial College London/UK) easyblock = 'PythonBundle' @@ -20,6 +18,7 @@ dependencies = [ ('h5py', '3.2.1'), ('IPython', '7.25.0'), ('scikit-learn', '0.24.2'), + ('scikit-image', '0.18.3'), ('TensorFlow', '2.6.0'), ('PyYAML', '5.4.1'), ('PyTables', '3.6.1'), @@ -56,34 +55,12 @@ exts_list = [ 'sources': ['msgpack-numpy-0.4.8.tar.gz'], }), - # this is for scikit-image - ('PyWavelets', '1.1.1', { - 'modulename': 'pywt', - 'checksums': ['1a64b40f6acb4ffbaccce0545d7fc641744f95351f62e4c6aaa40549326008c9'], - }), - ('imread', '0.7.4', { - 'checksums': ['0487adef11a22168700968c1727020361a72f6132b6ced2b8826b02d8cbf744f'], - }), - ('pooch', '1.5.2', { - 'checksums': ['5969b2f1defbdc405df932767e05e0b536e2771c27f1f95d7f260bc99bf13581'], - }), - ('tifffile', '2021.10.12', { - 'checksums': ['0a78268a2d844af94929512d28b39bd1ea6fe46de4124103840b5fe4e1c555cd'], - }), - ('scikit-image', '0.18.1', { - 'modulename': 'skimage', - 'patches': ['scikit-image-0.18.1_fix-README-cache-perms.patch'], - 'checksums': [ - 'fbb618ca911867bce45574c1639618cdfb5d94e207432b19bc19563d80d2f171', # scikit-image-0.18.1.tar.gz - # scikit-image-0.18.1_fix-README-cache-perms.patch - '3a941401231403808963d488aaf498a712c428c3b19a1752652be9972d82b7b8', - ], - }), - # end of scikit-image - (name, version, { 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', - 'checksums': ['4aa6694201e2aa56b9bd3e97ab27b0bc54f1364303167216174d2376d8ae0f84'], + 'patches': ['deeplabcut-2.2.0.6-setup.py.patch'], + 'checksums': ['4aa6694201e2aa56b9bd3e97ab27b0bc54f1364303167216174d2376d8ae0f84', + # deeplabcut-2.2.0.6-setup.py.patch: + '1dbef23575b105a6b2fa39f28d67bf926701d4c0b4f48bed7a6b179b7e5df2b0'], }), ] diff --git a/easybuild/easyconfigs/d/DeepLabCut/deeplabcut-2.2.0.6-setup.py.patch b/easybuild/easyconfigs/d/DeepLabCut/deeplabcut-2.2.0.6-setup.py.patch new file mode 100644 index 00000000000..9bef2d46b0c --- /dev/null +++ b/easybuild/easyconfigs/d/DeepLabCut/deeplabcut-2.2.0.6-setup.py.patch @@ -0,0 +1,15 @@ +scikit-imiage version bumped to 0.18.3 to use the one in EasyBuild +Author: J. Sassmannshausen (Imperial College London/UK) +diff --git a/deeplabcut-2.2.0.6.orig/setup.py b/deeplabcut-2.2.0.6/setup.py +index 3bff4f2..2e0926b 100644 +--- a/deeplabcut-2.2.0.6.orig/setup.py ++++ b/deeplabcut-2.2.0.6/setup.py +@@ -33,7 +33,7 @@ setuptools.setup( + "networkx", + "numpy", + "pandas>=1.0.1", +- "scikit-image>=0.17,<=0.18.1", ++ "scikit-image>=0.17,<=0.18.3", + "scikit-learn", + "scipy>=1.4", + "statsmodels>=0.11", From 09f76145da119c55329d42a55794316010aa2e31 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Fri, 18 Nov 2022 18:39:40 +0100 Subject: [PATCH 011/599] Update easybuild/easyconfigs/m/motif/motif-2.3.8-GCCcore-10.2.0.eb Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- easybuild/easyconfigs/m/motif/motif-2.3.8-GCCcore-10.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/m/motif/motif-2.3.8-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/motif/motif-2.3.8-GCCcore-10.2.0.eb index 63dcdcf5ab5..29f68f317f9 100644 --- a/easybuild/easyconfigs/m/motif/motif-2.3.8-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/m/motif/motif-2.3.8-GCCcore-10.2.0.eb @@ -18,6 +18,7 @@ builddependencies = [ ('Autotools', '20200321'), ('flex', '2.6.4'), ('Bison', '3.7.1'), + ('binutils', '2.35'), ('util-linux', '2.36'), ] From d8dea68a53dfdf34c3962dcf65652e60fa9d0d6b Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 25 Nov 2022 09:05:23 +0100 Subject: [PATCH 012/599] update Coreutils: add patch for older glibc version --- .../Coreutils/Coreutils-9.1-GCCcore-11.3.0.eb | 6 ++- .../Coreutils/Coreutils-9.1-GCCcore-12.2.0.eb | 6 ++- ...tils-9.1_avoid-syntax-error-on-glibc.patch | 43 +++++++++++++++++++ 3 files changed, 53 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/c/Coreutils/Coreutils-9.1_avoid-syntax-error-on-glibc.patch diff --git a/easybuild/easyconfigs/c/Coreutils/Coreutils-9.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/Coreutils/Coreutils-9.1-GCCcore-11.3.0.eb index c17a9e2fafd..bf09e2c9248 100644 --- a/easybuild/easyconfigs/c/Coreutils/Coreutils-9.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/c/Coreutils/Coreutils-9.1-GCCcore-11.3.0.eb @@ -15,7 +15,11 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_XZ] -checksums = ['61a1f410d78ba7e7f37a5a4f50e6d1320aca33375484a3255eddf17a38580423'] +patches = ['Coreutils-9.1_avoid-syntax-error-on-glibc.patch'] +checksums = [ + {'coreutils-9.1.tar.xz': '61a1f410d78ba7e7f37a5a4f50e6d1320aca33375484a3255eddf17a38580423'}, + {'Coreutils-9.1_avoid-syntax-error-on-glibc.patch': '57d081aaef10c65f34798475821e75352e57cc2248384a7f82e0960234a6b9d6'}, +] builddependencies = [('binutils', '2.38')] diff --git a/easybuild/easyconfigs/c/Coreutils/Coreutils-9.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/c/Coreutils/Coreutils-9.1-GCCcore-12.2.0.eb index d180e31a737..020674819a0 100644 --- a/easybuild/easyconfigs/c/Coreutils/Coreutils-9.1-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/c/Coreutils/Coreutils-9.1-GCCcore-12.2.0.eb @@ -15,7 +15,11 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_XZ] -checksums = ['61a1f410d78ba7e7f37a5a4f50e6d1320aca33375484a3255eddf17a38580423'] +patches = ['Coreutils-9.1_avoid-syntax-error-on-glibc.patch'] +checksums = [ + {'coreutils-9.1.tar.xz': '61a1f410d78ba7e7f37a5a4f50e6d1320aca33375484a3255eddf17a38580423'}, + {'Coreutils-9.1_avoid-syntax-error-on-glibc.patch': '57d081aaef10c65f34798475821e75352e57cc2248384a7f82e0960234a6b9d6'}, +] builddependencies = [('binutils', '2.39')] diff --git a/easybuild/easyconfigs/c/Coreutils/Coreutils-9.1_avoid-syntax-error-on-glibc.patch b/easybuild/easyconfigs/c/Coreutils/Coreutils-9.1_avoid-syntax-error-on-glibc.patch new file mode 100644 index 00000000000..9a0cf753d29 --- /dev/null +++ b/easybuild/easyconfigs/c/Coreutils/Coreutils-9.1_avoid-syntax-error-on-glibc.patch @@ -0,0 +1,43 @@ +From 84863a1c4dc8cca8fb0f6f670f67779cdd2d543b Mon Sep 17 00:00:00 2001 +From: Bruno Haible +Date: Sat, 30 Apr 2022 14:09:00 +0200 +Subject: string: Avoid syntax error on glibc systems with GCC 11. + +Reported by Tom Tromey in + +and by Satadru Pramanik in +. + +* lib/string.in.h (strndup): Don't rededeclare strndup if it is defined +as a macro. +--- + ChangeLog | 10 ++++++++++ + lib/string.in.h | 4 ++-- + 2 files changed, 12 insertions(+), 2 deletions(-) + + stdlib: Fix error in C++ mode on glibc systems (regr. 2022-04-13). +diff --git a/lib/string.in.h b/lib/string.in.h +index b6840fa..33160b2 100644 +--- a/lib/string.in.h ++++ b/lib/string.in.h +@@ -583,7 +583,7 @@ _GL_FUNCDECL_RPL (strndup, char *, + _GL_ATTRIBUTE_MALLOC _GL_ATTRIBUTE_DEALLOC_FREE); + _GL_CXXALIAS_RPL (strndup, char *, (char const *__s, size_t __n)); + # else +-# if !@HAVE_DECL_STRNDUP@ || __GNUC__ >= 11 ++# if !@HAVE_DECL_STRNDUP@ || (__GNUC__ >= 11 && !defined strndup) + _GL_FUNCDECL_SYS (strndup, char *, + (char const *__s, size_t __n) + _GL_ARG_NONNULL ((1)) +@@ -593,7 +593,7 @@ _GL_CXXALIAS_SYS (strndup, char *, (char const *__s, size_t __n)); + # endif + _GL_CXXALIASWARN (strndup); + #else +-# if __GNUC__ >= 11 ++# if __GNUC__ >= 11 && !defined strndup + /* For -Wmismatched-dealloc: Associate strndup with free or rpl_free. */ + _GL_FUNCDECL_SYS (strndup, char *, + (char const *__s, size_t __n) +-- +cgit v1.1 + From e34acae5bf6f2fa7a62fd76ea91ff4c4b3fa337c Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 25 Nov 2022 09:44:57 +0100 Subject: [PATCH 013/599] update Coreutils: fix E501 line too long --- .../easyconfigs/c/Coreutils/Coreutils-9.1-GCCcore-11.3.0.eb | 3 ++- .../easyconfigs/c/Coreutils/Coreutils-9.1-GCCcore-12.2.0.eb | 3 ++- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/Coreutils/Coreutils-9.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/Coreutils/Coreutils-9.1-GCCcore-11.3.0.eb index bf09e2c9248..7279f966bb8 100644 --- a/easybuild/easyconfigs/c/Coreutils/Coreutils-9.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/c/Coreutils/Coreutils-9.1-GCCcore-11.3.0.eb @@ -18,7 +18,8 @@ sources = [SOURCELOWER_TAR_XZ] patches = ['Coreutils-9.1_avoid-syntax-error-on-glibc.patch'] checksums = [ {'coreutils-9.1.tar.xz': '61a1f410d78ba7e7f37a5a4f50e6d1320aca33375484a3255eddf17a38580423'}, - {'Coreutils-9.1_avoid-syntax-error-on-glibc.patch': '57d081aaef10c65f34798475821e75352e57cc2248384a7f82e0960234a6b9d6'}, + {'Coreutils-9.1_avoid-syntax-error-on-glibc.patch': + '57d081aaef10c65f34798475821e75352e57cc2248384a7f82e0960234a6b9d6'}, ] builddependencies = [('binutils', '2.38')] diff --git a/easybuild/easyconfigs/c/Coreutils/Coreutils-9.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/c/Coreutils/Coreutils-9.1-GCCcore-12.2.0.eb index 020674819a0..52a1be553ba 100644 --- a/easybuild/easyconfigs/c/Coreutils/Coreutils-9.1-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/c/Coreutils/Coreutils-9.1-GCCcore-12.2.0.eb @@ -18,7 +18,8 @@ sources = [SOURCELOWER_TAR_XZ] patches = ['Coreutils-9.1_avoid-syntax-error-on-glibc.patch'] checksums = [ {'coreutils-9.1.tar.xz': '61a1f410d78ba7e7f37a5a4f50e6d1320aca33375484a3255eddf17a38580423'}, - {'Coreutils-9.1_avoid-syntax-error-on-glibc.patch': '57d081aaef10c65f34798475821e75352e57cc2248384a7f82e0960234a6b9d6'}, + {'Coreutils-9.1_avoid-syntax-error-on-glibc.patch': + '57d081aaef10c65f34798475821e75352e57cc2248384a7f82e0960234a6b9d6'}, ] builddependencies = [('binutils', '2.39')] From 1ec56861ffeabe53bc35e15e75d70766a710ef23 Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 22 Feb 2023 11:55:47 +0000 Subject: [PATCH 014/599] adding easyconfigs: cairomm-1.14.4-GCC-11.3.0-cairo-1.17.4.eb, cairomm-1.16.2-GCC-11.3.0-cairo-1.17.4.eb --- .../cairomm-1.14.4-GCC-11.3.0-cairo-1.17.4.eb | 39 +++++++++++++++++++ .../cairomm-1.16.2-GCC-11.3.0-cairo-1.17.4.eb | 39 +++++++++++++++++++ 2 files changed, 78 insertions(+) create mode 100644 easybuild/easyconfigs/c/cairomm/cairomm-1.14.4-GCC-11.3.0-cairo-1.17.4.eb create mode 100644 easybuild/easyconfigs/c/cairomm/cairomm-1.16.2-GCC-11.3.0-cairo-1.17.4.eb diff --git a/easybuild/easyconfigs/c/cairomm/cairomm-1.14.4-GCC-11.3.0-cairo-1.17.4.eb b/easybuild/easyconfigs/c/cairomm/cairomm-1.14.4-GCC-11.3.0-cairo-1.17.4.eb new file mode 100644 index 00000000000..a5a73baad0a --- /dev/null +++ b/easybuild/easyconfigs/c/cairomm/cairomm-1.14.4-GCC-11.3.0-cairo-1.17.4.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 = '1.14.4' +versionsuffix = '-cairo-1.17.4' + +homepage = 'http://cairographics.org' +description = "The Cairomm package provides a C++ interface to Cairo." + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['http://cairographics.org/releases/'] +sources = [SOURCE_TAR_XZ] +checksums = ['4749d25a2b2ef67cc0c014caaf5c87fa46792fc4b3ede186fb0fc932d2055158'] + +builddependencies = [ + ('CMake', '3.24.3'), + ('Meson', '0.62.1'), + ('Ninja', '1.10.2'), +] + +dependencies = [ + ('cairo', '1.17.4'), + ('libsigc++', '2.12.0'), + ('mm-common', '1.0.5'), + ('Boost', '1.79.0'), +] + +runtest = 'ninja test' + +sanity_check_paths = { + 'files': ['lib/libcairomm-1.0.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/c/cairomm/cairomm-1.16.2-GCC-11.3.0-cairo-1.17.4.eb b/easybuild/easyconfigs/c/cairomm/cairomm-1.16.2-GCC-11.3.0-cairo-1.17.4.eb new file mode 100644 index 00000000000..ffe8ff54a20 --- /dev/null +++ b/easybuild/easyconfigs/c/cairomm/cairomm-1.16.2-GCC-11.3.0-cairo-1.17.4.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' +versionsuffix = '-cairo-1.17.4' + +homepage = 'http://cairographics.org' +description = "The Cairomm package provides a C++ interface to Cairo." + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['http://cairographics.org/releases/'] +sources = [SOURCE_TAR_XZ] +checksums = ['6a63bf98a97dda2b0f55e34d1b5f3fb909ef8b70f9b8d382cb1ff3978e7dc13f'] + +builddependencies = [ + ('CMake', '3.24.3'), + ('Meson', '0.62.1'), + ('Ninja', '1.10.2'), +] + +dependencies = [ + ('cairo', '1.17.4'), + ('libsigc++', '3.4.0'), + ('mm-common', '1.0.5'), + ('Boost', '1.79.0'), +] + +runtest = 'ninja test' + +sanity_check_paths = { + 'files': ['lib/libcairomm-1.16.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' From a95f50fcc0a2f85055f22cb203696ee7bbd6b0cc Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 28 Feb 2023 10:26:22 +0000 Subject: [PATCH 015/599] cmake removed, versionsuffix of cairo removed --- ...-GCC-11.3.0-cairo-1.17.4.eb => cairomm-1.14.4-GCC-11.3.0.eb} | 2 -- ...-GCC-11.3.0-cairo-1.17.4.eb => cairomm-1.16.2-GCC-11.3.0.eb} | 2 -- 2 files changed, 4 deletions(-) rename easybuild/easyconfigs/c/cairomm/{cairomm-1.14.4-GCC-11.3.0-cairo-1.17.4.eb => cairomm-1.14.4-GCC-11.3.0.eb} (93%) rename easybuild/easyconfigs/c/cairomm/{cairomm-1.16.2-GCC-11.3.0-cairo-1.17.4.eb => cairomm-1.16.2-GCC-11.3.0.eb} (93%) diff --git a/easybuild/easyconfigs/c/cairomm/cairomm-1.14.4-GCC-11.3.0-cairo-1.17.4.eb b/easybuild/easyconfigs/c/cairomm/cairomm-1.14.4-GCC-11.3.0.eb similarity index 93% rename from easybuild/easyconfigs/c/cairomm/cairomm-1.14.4-GCC-11.3.0-cairo-1.17.4.eb rename to easybuild/easyconfigs/c/cairomm/cairomm-1.14.4-GCC-11.3.0.eb index a5a73baad0a..4bbae3a730b 100644 --- a/easybuild/easyconfigs/c/cairomm/cairomm-1.14.4-GCC-11.3.0-cairo-1.17.4.eb +++ b/easybuild/easyconfigs/c/cairomm/cairomm-1.14.4-GCC-11.3.0.eb @@ -5,7 +5,6 @@ easyblock = 'MesonNinja' name = 'cairomm' version = '1.14.4' -versionsuffix = '-cairo-1.17.4' homepage = 'http://cairographics.org' description = "The Cairomm package provides a C++ interface to Cairo." @@ -17,7 +16,6 @@ sources = [SOURCE_TAR_XZ] checksums = ['4749d25a2b2ef67cc0c014caaf5c87fa46792fc4b3ede186fb0fc932d2055158'] builddependencies = [ - ('CMake', '3.24.3'), ('Meson', '0.62.1'), ('Ninja', '1.10.2'), ] diff --git a/easybuild/easyconfigs/c/cairomm/cairomm-1.16.2-GCC-11.3.0-cairo-1.17.4.eb b/easybuild/easyconfigs/c/cairomm/cairomm-1.16.2-GCC-11.3.0.eb similarity index 93% rename from easybuild/easyconfigs/c/cairomm/cairomm-1.16.2-GCC-11.3.0-cairo-1.17.4.eb rename to easybuild/easyconfigs/c/cairomm/cairomm-1.16.2-GCC-11.3.0.eb index ffe8ff54a20..4d3b9b1d798 100644 --- a/easybuild/easyconfigs/c/cairomm/cairomm-1.16.2-GCC-11.3.0-cairo-1.17.4.eb +++ b/easybuild/easyconfigs/c/cairomm/cairomm-1.16.2-GCC-11.3.0.eb @@ -5,7 +5,6 @@ easyblock = 'MesonNinja' name = 'cairomm' version = '1.16.2' -versionsuffix = '-cairo-1.17.4' homepage = 'http://cairographics.org' description = "The Cairomm package provides a C++ interface to Cairo." @@ -17,7 +16,6 @@ sources = [SOURCE_TAR_XZ] checksums = ['6a63bf98a97dda2b0f55e34d1b5f3fb909ef8b70f9b8d382cb1ff3978e7dc13f'] builddependencies = [ - ('CMake', '3.24.3'), ('Meson', '0.62.1'), ('Ninja', '1.10.2'), ] From 21d7f6f7dc4678362ceb93a03d26261daf23a02f Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 28 Feb 2023 11:21:48 +0000 Subject: [PATCH 016/599] libsig updated to 3.4.0 --- easybuild/easyconfigs/c/cairomm/cairomm-1.14.4-GCC-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/cairomm/cairomm-1.14.4-GCC-11.3.0.eb b/easybuild/easyconfigs/c/cairomm/cairomm-1.14.4-GCC-11.3.0.eb index 4bbae3a730b..ed89cbbcb2d 100644 --- a/easybuild/easyconfigs/c/cairomm/cairomm-1.14.4-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/c/cairomm/cairomm-1.14.4-GCC-11.3.0.eb @@ -22,7 +22,7 @@ builddependencies = [ dependencies = [ ('cairo', '1.17.4'), - ('libsigc++', '2.12.0'), + ('libsigc++', '3.4.0'), ('mm-common', '1.0.5'), ('Boost', '1.79.0'), ] From 61da4a3f8433fce4eaec708e234a7cf9ab37b1bc Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 30 May 2023 14:08:50 +0200 Subject: [PATCH 017/599] adding easyconfigs: Demystify-0.0.17-foss-2020b.eb --- .../Demystify/Demystify-0.0.17-foss-2020b.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/d/Demystify/Demystify-0.0.17-foss-2020b.eb diff --git a/easybuild/easyconfigs/d/Demystify/Demystify-0.0.17-foss-2020b.eb b/easybuild/easyconfigs/d/Demystify/Demystify-0.0.17-foss-2020b.eb new file mode 100644 index 00000000000..7e1167c2acd --- /dev/null +++ b/easybuild/easyconfigs/d/Demystify/Demystify-0.0.17-foss-2020b.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'Demystify' +version = '0.0.17' + +homepage = 'https://github.com/stacs-cp/demystify' +description = """ +Demystify is a tool which allows puzzles to be expressed in a high-level +constraint programming language and uses MUSes to automatically produce +descriptions of steps in the puzzle solving.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['93779a131aa78f7de0dffdbe8e89124836b5eb6d0e9b4bc385821845a4628f52'] + +dependencies = [ + ('Python', '3.8.6'), + ('PySAT', '0.1.7.dev1'), + ('SciPy-bundle', '2020.11'), + ('Z3', '4.8.10', '-Python-%(pyver)s'), +] + +use_pip = True +sanity_pip_check = True + +moduleclass = 'math' From 06af1c76fb94fe4b38d12398642c431e32fd0f0f Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Wed, 31 May 2023 11:07:57 +0200 Subject: [PATCH 018/599] adding easyconfigs: json-fortran-8.3.0-GCCcore-10.2.0.eb, json-fortran-8.3.0-GCCcore-12.2.0.eb --- .../json-fortran-8.3.0-GCCcore-10.2.0.eb | 33 +++++++++++++++++++ .../json-fortran-8.3.0-GCCcore-12.2.0.eb | 33 +++++++++++++++++++ 2 files changed, 66 insertions(+) create mode 100644 easybuild/easyconfigs/j/json-fortran/json-fortran-8.3.0-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/j/json-fortran/json-fortran-8.3.0-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/j/json-fortran/json-fortran-8.3.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/j/json-fortran/json-fortran-8.3.0-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..30199cec525 --- /dev/null +++ b/easybuild/easyconfigs/j/json-fortran/json-fortran-8.3.0-GCCcore-10.2.0.eb @@ -0,0 +1,33 @@ +# J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'CMakeMake' + +name = 'json-fortran' +version = '8.3.0' + +homepage = 'https://github.com/jacobwilliams/json-fortran' +description = "JSON-Fortran: A Modern Fortran JSON API" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/jacobwilliams/json-fortran/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['5fe9ad709a726416cec986886503e0526419742e288c4e43f63c1c22026d1e8a'] + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.20.1'), +] + +configopts = [ + '-DUSE_GNU_INSTALL_CONVENTION=TRUE', +] + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libjsonfortran.a', 'lib/libjsonfortran.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/j/json-fortran/json-fortran-8.3.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/j/json-fortran/json-fortran-8.3.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..c2755034346 --- /dev/null +++ b/easybuild/easyconfigs/j/json-fortran/json-fortran-8.3.0-GCCcore-12.2.0.eb @@ -0,0 +1,33 @@ +# J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'CMakeMake' + +name = 'json-fortran' +version = '8.3.0' + +homepage = 'https://github.com/jacobwilliams/json-fortran' +description = "JSON-Fortran: A Modern Fortran JSON API" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/jacobwilliams/json-fortran/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['5fe9ad709a726416cec986886503e0526419742e288c4e43f63c1c22026d1e8a'] + +builddependencies = [ + ('binutils', '2.39'), + ('CMake', '3.24.3'), +] + +configopts = [ + '-DUSE_GNU_INSTALL_CONVENTION=TRUE', +] + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libjsonfortran.a', 'lib/libjsonfortran.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'lib' From eedc385de499ca4a71d81f341161ce4bd39ce9d1 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Sun, 4 Jun 2023 15:43:07 +0200 Subject: [PATCH 019/599] Update json-fortran toolchains to reflect creation of fortran modules --- ....0.eb => json-fortran-8.3.0-GCC-10.2.0.eb} | 5 +-- ....0.eb => json-fortran-8.3.0-GCC-12.2.0.eb} | 5 +-- .../json-fortran-8.3.0-iccifort-2020.4.304.eb | 34 +++++++++++++++++++ ...-fortran-8.3.0-intel-compilers-2022.2.1.eb | 34 +++++++++++++++++++ 4 files changed, 74 insertions(+), 4 deletions(-) rename easybuild/easyconfigs/j/json-fortran/{json-fortran-8.3.0-GCCcore-10.2.0.eb => json-fortran-8.3.0-GCC-10.2.0.eb} (84%) rename easybuild/easyconfigs/j/json-fortran/{json-fortran-8.3.0-GCCcore-12.2.0.eb => json-fortran-8.3.0-GCC-12.2.0.eb} (84%) create mode 100644 easybuild/easyconfigs/j/json-fortran/json-fortran-8.3.0-iccifort-2020.4.304.eb create mode 100644 easybuild/easyconfigs/j/json-fortran/json-fortran-8.3.0-intel-compilers-2022.2.1.eb diff --git a/easybuild/easyconfigs/j/json-fortran/json-fortran-8.3.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/j/json-fortran/json-fortran-8.3.0-GCC-10.2.0.eb similarity index 84% rename from easybuild/easyconfigs/j/json-fortran/json-fortran-8.3.0-GCCcore-10.2.0.eb rename to easybuild/easyconfigs/j/json-fortran/json-fortran-8.3.0-GCC-10.2.0.eb index 30199cec525..fdd554d13d3 100644 --- a/easybuild/easyconfigs/j/json-fortran/json-fortran-8.3.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/j/json-fortran/json-fortran-8.3.0-GCC-10.2.0.eb @@ -8,7 +8,7 @@ version = '8.3.0' homepage = 'https://github.com/jacobwilliams/json-fortran' description = "JSON-Fortran: A Modern Fortran JSON API" -toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchain = {'name': 'GCC', 'version': '10.2.0'} source_urls = ['https://github.com/jacobwilliams/json-fortran/archive/'] sources = ['%(version)s.tar.gz'] @@ -26,7 +26,8 @@ configopts = [ runtest = 'check' sanity_check_paths = { - 'files': ['lib/libjsonfortran.a', 'lib/libjsonfortran.%s' % SHLIB_EXT], + 'files': ['lib/libjsonfortran.a', 'lib/libjsonfortran.%s' % SHLIB_EXT, + 'include/json_module.mod', 'include/json_parameters.mod'], 'dirs': ['include'], } diff --git a/easybuild/easyconfigs/j/json-fortran/json-fortran-8.3.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/j/json-fortran/json-fortran-8.3.0-GCC-12.2.0.eb similarity index 84% rename from easybuild/easyconfigs/j/json-fortran/json-fortran-8.3.0-GCCcore-12.2.0.eb rename to easybuild/easyconfigs/j/json-fortran/json-fortran-8.3.0-GCC-12.2.0.eb index c2755034346..6ce6846cfe3 100644 --- a/easybuild/easyconfigs/j/json-fortran/json-fortran-8.3.0-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/j/json-fortran/json-fortran-8.3.0-GCC-12.2.0.eb @@ -8,7 +8,7 @@ version = '8.3.0' homepage = 'https://github.com/jacobwilliams/json-fortran' description = "JSON-Fortran: A Modern Fortran JSON API" -toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchain = {'name': 'GCC', 'version': '12.2.0'} source_urls = ['https://github.com/jacobwilliams/json-fortran/archive/'] sources = ['%(version)s.tar.gz'] @@ -26,7 +26,8 @@ configopts = [ runtest = 'check' sanity_check_paths = { - 'files': ['lib/libjsonfortran.a', 'lib/libjsonfortran.%s' % SHLIB_EXT], + 'files': ['lib/libjsonfortran.a', 'lib/libjsonfortran.%s' % SHLIB_EXT, + 'include/json_module.mod', 'include/json_parameters.mod'], 'dirs': ['include'], } diff --git a/easybuild/easyconfigs/j/json-fortran/json-fortran-8.3.0-iccifort-2020.4.304.eb b/easybuild/easyconfigs/j/json-fortran/json-fortran-8.3.0-iccifort-2020.4.304.eb new file mode 100644 index 00000000000..074e64ca5ca --- /dev/null +++ b/easybuild/easyconfigs/j/json-fortran/json-fortran-8.3.0-iccifort-2020.4.304.eb @@ -0,0 +1,34 @@ +# J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'CMakeMake' + +name = 'json-fortran' +version = '8.3.0' + +homepage = 'https://github.com/jacobwilliams/json-fortran' +description = "JSON-Fortran: A Modern Fortran JSON API" + +toolchain = {'name': 'iccifort', 'version': '2020.4.304'} + +source_urls = ['https://github.com/jacobwilliams/json-fortran/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['5fe9ad709a726416cec986886503e0526419742e288c4e43f63c1c22026d1e8a'] + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.20.1'), +] + +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-8.3.0-intel-compilers-2022.2.1.eb b/easybuild/easyconfigs/j/json-fortran/json-fortran-8.3.0-intel-compilers-2022.2.1.eb new file mode 100644 index 00000000000..36775cb2724 --- /dev/null +++ b/easybuild/easyconfigs/j/json-fortran/json-fortran-8.3.0-intel-compilers-2022.2.1.eb @@ -0,0 +1,34 @@ +# J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'CMakeMake' + +name = 'json-fortran' +version = '8.3.0' + +homepage = 'https://github.com/jacobwilliams/json-fortran' +description = "JSON-Fortran: A Modern Fortran JSON API" + +toolchain = {'name': 'intel-compilers', 'version': '2022.2.1'} + +source_urls = ['https://github.com/jacobwilliams/json-fortran/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['5fe9ad709a726416cec986886503e0526419742e288c4e43f63c1c22026d1e8a'] + +builddependencies = [ + ('binutils', '2.39'), + ('CMake', '3.24.3'), +] + +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 b7f92d85ea82cdf1c76c705716699b19ad470b42 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 19 Jun 2023 11:48:40 +0200 Subject: [PATCH 020/599] fix version string of Z3 in Demystify v0.0.17 --- .../easyconfigs/d/Demystify/Demystify-0.0.17-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/Demystify/Demystify-0.0.17-foss-2020b.eb b/easybuild/easyconfigs/d/Demystify/Demystify-0.0.17-foss-2020b.eb index 7e1167c2acd..ee305c91e29 100644 --- a/easybuild/easyconfigs/d/Demystify/Demystify-0.0.17-foss-2020b.eb +++ b/easybuild/easyconfigs/d/Demystify/Demystify-0.0.17-foss-2020b.eb @@ -19,7 +19,7 @@ dependencies = [ ('Python', '3.8.6'), ('PySAT', '0.1.7.dev1'), ('SciPy-bundle', '2020.11'), - ('Z3', '4.8.10', '-Python-%(pyver)s'), + ('Z3', '4.8.10'), ] use_pip = True From 076a39e19c67475177c5cd3ae0b441df2c574c4a Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 19 Jun 2023 11:49:29 +0200 Subject: [PATCH 021/599] set download_dep_fail in Demystify v0.0.17 --- easybuild/easyconfigs/d/Demystify/Demystify-0.0.17-foss-2020b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/d/Demystify/Demystify-0.0.17-foss-2020b.eb b/easybuild/easyconfigs/d/Demystify/Demystify-0.0.17-foss-2020b.eb index ee305c91e29..356c7a33d87 100644 --- a/easybuild/easyconfigs/d/Demystify/Demystify-0.0.17-foss-2020b.eb +++ b/easybuild/easyconfigs/d/Demystify/Demystify-0.0.17-foss-2020b.eb @@ -23,6 +23,7 @@ dependencies = [ ] use_pip = True +download_dep_fail = True sanity_pip_check = True moduleclass = 'math' From 6246a09fae232263d8bc7f27a61920f14b844342 Mon Sep 17 00:00:00 2001 From: Lev Lafayette Date: Tue, 27 Jun 2023 16:45:15 +1000 Subject: [PATCH 022/599] Create RASPA2-2.0.47-foss-2022a.eb New minor version, new toolchain --- .../r/RASPA2/RASPA2-2.0.47-foss-2022a.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/r/RASPA2/RASPA2-2.0.47-foss-2022a.eb diff --git a/easybuild/easyconfigs/r/RASPA2/RASPA2-2.0.47-foss-2022a.eb b/easybuild/easyconfigs/r/RASPA2/RASPA2-2.0.47-foss-2022a.eb new file mode 100644 index 00000000000..feb01d4ea06 --- /dev/null +++ b/easybuild/easyconfigs/r/RASPA2/RASPA2-2.0.47-foss-2022a.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'RASPA2' +version = '2.0.47' + +homepage = 'https://iraspa.org/raspa/' +description = """RASPA is a software package for simulating adsorption and diffusion of +molecules in flexible nanoporous materials.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://github.com/iRASPA/RASPA2/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['1a14524f95ab86e7a2910b53641262ec98ec23f794f1c3665982c32efc1997ed'] + +builddependencies = [ + ('Autotools', '20220317') +] + +preconfigopts = 'rm -rf autom4te.cache && ' +preconfigopts += 'mkdir m4 && ' +preconfigopts += 'aclocal && ' +preconfigopts += 'autoreconf -i && ' +preconfigopts += 'automake --add-missing && ' +preconfigopts += 'autoconf && ' + +sanity_check_paths = { + 'files': ['bin/simulate'], + 'dirs': [] +} + +sanity_check_commands = ['simulate -h'] + +moduleclass = 'phys' From 08b30e97dd25c6eac2ca56665d6713a24aa82f74 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 28 Jun 2023 16:16:30 +0000 Subject: [PATCH 023/599] adding easyconfigs: R-4.3.1-gfbf-2022b.eb --- .../easyconfigs/r/R/R-4.3.1-gfbf-2022b.eb | 374 ++++++++++++++++++ 1 file changed, 374 insertions(+) create mode 100644 easybuild/easyconfigs/r/R/R-4.3.1-gfbf-2022b.eb diff --git a/easybuild/easyconfigs/r/R/R-4.3.1-gfbf-2022b.eb b/easybuild/easyconfigs/r/R/R-4.3.1-gfbf-2022b.eb new file mode 100644 index 00000000000..772ec5bf8b3 --- /dev/null +++ b/easybuild/easyconfigs/r/R/R-4.3.1-gfbf-2022b.eb @@ -0,0 +1,374 @@ +name = 'R' +version = '4.3.1' + +homepage = 'https://www.r-project.org/' +description = """R is a free software environment for statistical computing + and graphics.""" + +toolchain = {'name': 'gfbf', 'version': '2022b'} + +source_urls = ['https://cloud.r-project.org/src/base/R-%(version_major)s'] +sources = [SOURCE_TAR_GZ] +checksums = ['8dd0bf24f1023c6f618c3b317383d291b4a494f40d73b983ac22ffea99e4ba99'] + +builddependencies = [ + ('pkgconf', '1.9.3'), + ('Xvfb', '21.1.6'), + ('Autotools', '20220317'), +] +dependencies = [ + ('X11', '20221110'), + ('Mesa', '22.2.4'), + ('libGLU', '9.0.2'), + ('cairo', '1.17.4'), + ('libreadline', '8.2'), + ('ncurses', '6.3'), + ('bzip2', '1.0.8'), + ('XZ', '5.2.7'), + ('zlib', '1.2.12'), + ('SQLite', '3.39.4'), + ('PCRE2', '10.40'), + ('libpng', '1.6.38'), # for plotting in R + ('libjpeg-turbo', '2.1.4'), # for plottting in R + ('LibTIFF', '4.4.0'), + ('Java', '11', '', SYSTEM), + ('libgit2', '1.5.0'), + ('OpenSSL', '1.1', '', SYSTEM), + ('cURL', '7.86.0'), + ('Tk', '8.6.12'), # for tcltk + ('libxml2', '2.10.3'), # for XML + ('HarfBuzz', '5.3.1'), # for textshaping + ('FriBidi', '1.0.12'), # 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" + +# specify that at least EasyBuild v3.5.0 is required, +# since we rely on the updated easyblock for R to configure correctly w.r.t. BLAS/LAPACK +easybuild_version = '3.5.0' + +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 22nd June 2023 +exts_list = [ + 'base', + 'compiler', + 'datasets', + 'graphics', + 'grDevices', + 'grid', + 'methods', + 'parallel', + 'splines', + 'stats', + 'stats4', + 'tcltk', + 'tools', + 'utils', + ('rlang', '1.1.1', { + 'checksums': ['5e5ec9a7796977216c39d94b1e342e08f0681746657067ba30de11b8fa8ada99'], + }), + ('Rcpp', '1.0.10', { + 'checksums': ['1e65e24a9981251ab5fc4f9fd65fe4eab4ba0255be3400a8c5abe20b62b5d546'], + }), + ('R6', '2.5.1', { + 'checksums': ['8d92bd29c2ed7bf15f2778618ffe4a95556193d21d8431a7f75e7e5fc102bf48'], + }), + ('cli', '3.6.1', { + 'checksums': ['be3006cec7e67f9ae25e21b4658c4bec680038c2ef7467df5f14da3311a05e36'], + }), + ('vctrs', '0.6.3', { + 'checksums': ['93dc220dcde8b440586b2260460ef354e827a17dfec1ea6a9815585a10cfa5c2'], + }), + ('base64enc', '0.1-3', { + 'checksums': ['6d856d8a364bcdc499a0bf38bfd283b7c743d08f0b288174fba7dbf0a04b688d'], + }), + ('rprojroot', '2.0.3', { + 'checksums': ['50604247470e910cecfe9b76df754bf96a0d701f81b732f7aa9c90a20d30f897'], + }), + ('xfun', '0.39', { + 'checksums': ['d0ecaabb243dd3496da6029932fcdd4772914843de7ffd0b78a172efde1356c9'], + }), + ('commonmark', '1.9.0', { + 'checksums': ['6dd01a5a26c8d436486abf69c2f6ad0f8dd1c811f575c31983aeb4dbd376548f'], + }), + ('highr', '0.10', { + 'checksums': ['ec55bc1ff66390ed66806dc2a7b6c17dbfd089b3d73fe2e369017f8cb4bc347b'], + }), + ('digest', '0.6.31', { + 'checksums': ['5a284f490eaca6750f695f00a584cfca3f180ca1046ac1107202141149d431b9'], + }), + ('desc', '1.4.2', { + 'checksums': ['758acf14be478c09ba7e84ade3a7ce512becf35d44e5e6a997b932065f2a227c'], + }), + ('ellipsis', '0.3.2', { + 'checksums': ['a90266e5eb59c7f419774d5c6d6bd5e09701a26c9218c5933c9bce6765aa1558'], + }), + ('prettyunits', '1.1.1', { + 'checksums': ['9a199aa80c6d5e50fa977bc724d6e39dae1fc597a96413053609156ee7fb75c5'], + }), + ('crayon', '1.5.2', { + 'checksums': ['70a9a505b5b3c0ee6682ad8b965e28b7e24d9f942160d0a2bad18eec22b45a7a'], + }), + ('stringi', '1.7.12', { + 'checksums': ['efe8ac2900001f986a75db5641fbb24587a6d23de274a6a85c39dfa58921e009'], + }), + ('magrittr', '2.0.3', { + 'checksums': ['a2bff83f792a1acb801bfe6330bb62724c74d5308832f2cb6a6178336ace55d2'], + }), + ('stringr', '1.5.0', { + 'checksums': ['52b159d7700a139111b4caf939e7c9c6ab3e01185181400d70a74c552826633a'], + }), + ('evaluate', '0.21', { + 'checksums': ['3178c99cee8917d7d128806d064d4fecce7845ed07f42e759dcc0adda89c22b9'], + }), + ('ps', '1.7.5', { + 'checksums': ['1abc3ae3c55797b994973f7e43bf5c7bbb4da649a0dcfad36675e196dba4cb4e'], + }), + ('processx', '3.8.1', { + 'checksums': ['e008472b81d4ca1a37a4ba7dd58e5e944f96ab2e44c8ccc8840d43e9fe99e93c'], + }), + ('callr', '3.7.3', { + 'checksums': ['567bfedf073a1d4c5785f0553341608a214938110567b9a6495ff20ebb2fd04e'], + }), + ('pkgbuild', '1.4.1', { + 'checksums': ['cdb0ace14444f362be9725bd84e9752dab92f4771296504b63b9b8084f5e8a6b'], + }), + ('fs', '1.6.2', { + 'checksums': ['548b7c0ed5ab26dc4fbd88707ae12987bcaef834dbc6de4e17d453846dc436b2'], + }), + ('utf8', '1.2.3', { + 'checksums': ['c0a88686591f4ad43b52917d0964e9df4c62d8858fe25135a1bf357dfcbd6347'], + }), + ('fansi', '1.0.4', { + 'checksums': ['3163214e6c40922bbb495229259ed8ce1bebd98b77098a6936d234e43da9c49f'], + }), + ('pillar', '1.9.0', { + 'checksums': ['f23eb486c087f864c2b4072d5cba01d5bebf2f554118bcba6886d8dbceb87acc'], + }), + ('pkgconfig', '2.0.3', { + 'checksums': ['330fef440ffeb842a7dcfffc8303743f1feae83e8d6131078b5a44ff11bc3850'], + }), + ('tibble', '3.2.1', { + 'checksums': ['65a72d0c557fd6e7c510d150c935ed6ced5db7d05fc20236b370f11428372131'], + }), + ('withr', '2.5.0', { + 'checksums': ['37317b3ed790a08407072993a05ab255f6305f95a12a16e0e28aa6aa80fc8bc0'], + }), + ('glue', '1.6.2', { + 'checksums': ['9da518f12be584c90e75fe8e07f711ee3f6fc0d03d817f72c25dc0f66499fdbf'], + }), + ('rstudioapi', '0.14', { + 'checksums': ['469d0987b1ad728a96c363a422fba712a5cebc8b11a5f7e953b4a671044dafc4'], + }), + ('pkgload', '1.3.2', { + 'checksums': ['35d19a032bfeeefcab92d76a768b4a420c2ede0920badaf48cca878592b46b2f'], + }), + ('htmltools', '0.5.5', { + 'checksums': ['c8b23fab855a89c6ed0f6d6c7cad0ff9c5ae329c0bdb479940443ee752f26659'], + }), + ('yaml', '2.3.7', { + 'checksums': ['d20cb219e0f9c48aba02f132f81cfa9ecda5e22c925e36726840218ed56680ab'], + }), + ('knitr', '1.43', { + 'checksums': ['3d29baea8c349aaa9310879ceb9a9d51bcaec39827ad46d422c3793c8a4ed53c'], + }), + ('mime', '0.12', { + 'checksums': ['a9001051d6c1e556e881910b1816b42872a1ee41ab76d0040ce66a27135e3849'], + }), + ('praise', '1.0.0', { + 'checksums': ['5c035e74fd05dfa59b03afe0d5f4c53fbf34144e175e90c53d09c6baedf5debd'], + }), + ('brio', '1.1.3', { + 'checksums': ['eaa89041856189bee545bf1c42c7920a0bb0f1f70bb477487c467ee3e8fedcc6'], + }), + ('jsonlite', '1.8.5', { + 'checksums': ['dc3cca4bdca1b6d6836c412760ea9656140683126c54cb89c3e42219dec4a3ad'], + }), + ('lifecycle', '1.0.3', { + 'checksums': ['6459fdc3211585c0cdf120427579c12149b02161efe273a64b825c05e9aa69c2'], + }), + ('diffobj', '0.3.5', { + 'checksums': ['d860a79b1d4c9e369282d7391b539fe89228954854a65ba47181407c53e3cf60'], + }), + ('rematch2', '2.1.2', { + 'checksums': ['fe9cbfe99dd7731a0a2a310900d999f80e7486775b67f3f8f388c30737faf7bb'], + }), + ('waldo', '0.5.1', { + 'checksums': ['45bf076cff449e3c506c95857734bb73fdf30040333709b8845d09a12c6fdf46'], + }), + ('testthat', '3.1.9', { + 'checksums': ['4da1f992549c9b8db211f205059ec4c5d91a45d5971d60ebae21058268448375'], + }), + ('xml2', '1.3.4', { + 'checksums': ['340bb1a18e643a5008c0b4e92d71c3b0abacb44f1742e3a77d0cb33cb73b3030'], + }), + ('curl', '5.0.1', { + 'checksums': ['b7058f9cc7fa8f649505583584b61383fc08dccf746faa5381ba3d0b8bdf93a6'], + }), + ('sys', '3.4.2', { + 'checksums': ['b7bdce66f0fb681830ea6fb77b5a2c6babb43920abb1eddc733f95c0a63ce5b3'], + }), + ('askpass', '1.1', { + 'checksums': ['db40827d1bdbb90c0aa2846a2961d3bf9d76ad1b392302f9dd84cc2fd18c001f'], + }), + ('openssl', '2.0.6', { + 'checksums': ['77f3032a16270f0d1734f269b8d348eedc75b277812854386091143082c1b3f3'], + }), + ('httr', '1.4.6', { + 'checksums': ['8d6d86cbef23738d2b4390490f7486d8cf7674f0a59c19f515f61cad35ec37b2'], + }), + ('jquerylib', '0.1.4', { + 'checksums': ['f0bcc11dcde3a6ff180277e45c24642d3da3c8690900e38f44495efbc9064411'], + }), + ('rappdirs', '0.3.3', { + 'checksums': ['49959f65b45b0b189a2792d6c1339bef59674ecae92f8c2ed9f26ff9e488c184'], + }), + ('sass', '0.4.6', { + 'checksums': ['2ee82ce709b7fdee78f7e2364d04f369f58fc2cda4bb5a235bd53c49d311c019'], + }), + ('purrr', '1.0.1', { + 'checksums': ['0a7911be3539355a4c40d136f2602befcaaad5a3f7222078500bfb969a6f2ba2'], + }), + ('fastmap', '1.1.1', { + 'checksums': ['3623809dd016ae8abd235200ba7834effc4b916915a059deb76044137c5c7173'], + }), + ('cachem', '1.0.8', { + 'checksums': ['ea9ca919fe615dce8770758ecc2fc88ac99074f66ff1cde3a0b95d40007f45c2'], + }), + ('memoise', '2.0.1', { + 'checksums': ['f85034ee98c8ca07fb3cd826142c1cd1e1e5747075a94c75a45783bbc4fe2deb'], + }), + ('bslib', '0.5.0', { + 'checksums': ['a2c6fbc62242806e10bb58c5d1ba04a6d3bf4e546bc53d7acf1b8eb1160bd115'], + }), + ('fontawesome', '0.5.0', { + 'checksums': ['4117b417a33e82d626881d7059eb54e7534cba202e75dae7e27021cb3796e90b'], + }), + ('tinytex', '0.45', { + 'checksums': ['0c2fbbd09e80af80ca6b685bf0653f070da97b85413d39af966aba28f376e92c'], + }), + ('rmarkdown', '2.22', { + 'checksums': ['c6635519503e0fcdd518696d3ac96d8d28d9d4ecd9db0532c53426002f6387b8'], + }), + ('downlit', '0.4.2', { + 'checksums': ['33dff66909104d1a5ba8e57b1288986e82b61fd5e91dce0cd358d53724b37e3c'], + }), + ('cpp11', '0.4.3', { + 'checksums': ['f1a60e4971a86dbbcf6a16bbd739b59bb66d9c45d93cfd8dedc2a87e302598f1'], + }), + ('systemfonts', '1.0.4', { + 'checksums': ['ef766c75b942f147d382664a00d6a4930f1bfe0cce9d88943f571682a85a84c0'], + }), + ('textshaping', '0.3.6', { + 'checksums': ['80e2c087962f55ce2811fbc798b09f5638c06c6b28c10cd3cb3827005b902ada'], + }), + ('ragg', '1.2.5', { + 'checksums': ['936f4d75e0e01cdeefb9f57d121cdd7812d0de5a9e1a3a8315f92ce1c84da8f9'], + }), + ('whisker', '0.4.1', { + 'checksums': ['bf5151494508032f68ac41e211bda80da9087c65c7068ffdd12f16669bf1f2bc'], + }), + ('pkgdown', '2.0.7', { + 'checksums': ['f33872869dfa8319182d87e90eab3245ff69293b3b791471bf9538afb81b356a'], + }), + ('htmlwidgets', '1.6.2', { + 'checksums': ['7fda1672a4c0fbc203c790677b6ee7c40d2c2d72be4f6772f75288fc712b10bc'], + }), + ('profvis', '0.3.8', { + 'checksums': ['ec02c75bc9907a73564e691adfa8e06651ca0bd73b7915412960231cd265b4b2'], + }), + ('urlchecker', '1.0.1', { + 'checksums': ['62165ddbe1b748b58c71a50c8f07fdde6f3d19a7b39787b9fa2b4f9216250318'], + }), + ('later', '1.3.1', { + 'checksums': ['23eed681f0b9eacebbc3c6a5ba14ee0b676a4bf6e69af194c5a36edfe11464ac'], + }), + ('promises', '1.2.0.1', { + 'checksums': ['8d3a8217909e91f4c2a2eebba5ac8fc902a9ac1a9e9d8a30815c9dc0f162c4b7'], + }), + ('xtable', '1.8-4', { + 'checksums': ['5abec0e8c27865ef0880f1d19c9f9ca7cc0fd24eadaa72bcd270c3fb4075fd1c'], + }), + ('httpuv', '1.6.11', { + 'checksums': ['8ba79e0a8351274daf2dc566c71f88e891127cdedca62ad77a4b27a8103eeef5'], + }), + ('sourcetools', '0.1.7-1', { + 'checksums': ['96812bdb7a0dd99690d84e4b0a3def91389e4290f53f01919ef28a50554e31d1'], + }), + ('shiny', '1.7.4', { + 'checksums': ['bbfcdd7375013b8f59248b3f3f4e752acd445feb25179f3f7f65cd69614da4b5'], + }), + ('miniUI', '0.1.1.1', { + 'checksums': ['452b41133289f630d8026507263744e385908ca025e9a7976925c1539816b0c0'], + }), + ('brew', '1.0-8', { + 'checksums': ['11652d5a7042d645cc5be5f9f97ff4d46083cea7d3ad2dd6ad1570b52c097826'], + }), + ('roxygen2', '7.2.3', { + 'checksums': ['d844fab977d2575ab942fa1309ac7ff67f35f099a75d8b41c79efe6ea10416da'], + }), + ('rversions', '2.1.2', { + 'checksums': ['de5818233e8271132fe8ea70145618950b35786e0d2f270e39bf3338f3b8b160'], + }), + ('sessioninfo', '1.2.2', { + 'checksums': ['f56283857c53ac8691e3747ed48fe03e893d8ff348235bff7364658bcfb0c7cb'], + }), + ('xopen', '1.0.0', { + 'checksums': ['e207603844d69c226142be95281ba2f4a056b9d8cbfae7791ba60535637b3bef'], + }), + ('rcmdcheck', '1.4.0', { + 'checksums': ['bbd4ef7d514b8c2076196a7c4a6041d34623d55fbe73f2771758ce61fd32c9d0'], + }), + ('remotes', '2.4.2', { + 'checksums': ['f2ef875f24a485bf4f55a8c830f87cdd5db868f9a8cdb624dc452d0bf66ba516'], + }), + ('clipr', '0.8.0', { + 'checksums': ['32c2931992fbec9c31b71de3e27059f1cbb45b4b1f45fd42e0e8dbcec6de3be9'], + }), + ('ini', '0.3.1', { + 'checksums': ['7b191a54019c8c52d6c2211c14878c95564154ec4865f57007953742868cd813'], + }), + ('gitcreds', '0.1.2', { + 'checksums': ['41c6abcca5635062b123ffb5af2794770eca5ebd97b05c5a64b24fa1c803c75d'], + }), + ('httr2', '0.2.3', { + 'checksums': ['352032029512f28f6f440ace0078e859ad3945d6b20841963b372523b6974b3d'], + }), + ('gh', '1.4.0', { + 'checksums': ['68c69fcd18429b378e639a09652465a4e92b7b5b5704804d0c5b1ca2b9b58b71'], + }), + ('credentials', '1.3.2', { + 'checksums': ['2ffa7c11bedbfa034adf553d0a2f2e4f6a496b858af753a09a89219cff9028b8'], + }), + ('zip', '2.3.0', { + 'checksums': ['33eba844922af9981732ee6ec1582d46cf04c562344f09a0f0f14a22c6f74543'], + }), + ('gert', '1.9.2', { + 'checksums': ['42ca1b4bcafb1fdbbc7f54df0ee4476ecd19e9e7d563b53fe7064e0086ab665e'], + }), + ('usethis', '2.2.0', { + 'checksums': ['2ccebe690aadebff96451cc9c226dc1a1e9ca5ac6ec83310e12a1312cb163b4f'], + }), + ('devtools', '2.4.5', { + 'checksums': ['38160ebd839acdec7ebf0699a085b4ab1ebd5500d3c57a9fa7ae484f1909904b'], + }), +] + +moduleclass = 'lang' From e25a4cb661ead0406dc485d5c371c643ac44e78b Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Thu, 29 Jun 2023 08:16:17 +0000 Subject: [PATCH 024/599] Fix comment formatting --- easybuild/easyconfigs/r/R/R-4.3.1-gfbf-2022b.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-4.3.1-gfbf-2022b.eb b/easybuild/easyconfigs/r/R/R-4.3.1-gfbf-2022b.eb index 772ec5bf8b3..1109fa7bb52 100644 --- a/easybuild/easyconfigs/r/R/R-4.3.1-gfbf-2022b.eb +++ b/easybuild/easyconfigs/r/R/R-4.3.1-gfbf-2022b.eb @@ -37,8 +37,8 @@ dependencies = [ ('cURL', '7.86.0'), ('Tk', '8.6.12'), # for tcltk ('libxml2', '2.10.3'), # for XML - ('HarfBuzz', '5.3.1'), # for textshaping - ('FriBidi', '1.0.12'), # for textshaping + ('HarfBuzz', '5.3.1'), # for textshaping + ('FriBidi', '1.0.12'), # for textshaping ] From ae01739d0551330ef949d2cb39b4bfac5d393ca6 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Thu, 29 Jun 2023 10:20:58 +0000 Subject: [PATCH 025/599] Fix dependency ordering for vctrs --- easybuild/easyconfigs/r/R/R-4.3.1-gfbf-2022b.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-4.3.1-gfbf-2022b.eb b/easybuild/easyconfigs/r/R/R-4.3.1-gfbf-2022b.eb index 1109fa7bb52..57028db3fbd 100644 --- a/easybuild/easyconfigs/r/R/R-4.3.1-gfbf-2022b.eb +++ b/easybuild/easyconfigs/r/R/R-4.3.1-gfbf-2022b.eb @@ -93,9 +93,6 @@ exts_list = [ ('cli', '3.6.1', { 'checksums': ['be3006cec7e67f9ae25e21b4658c4bec680038c2ef7467df5f14da3311a05e36'], }), - ('vctrs', '0.6.3', { - 'checksums': ['93dc220dcde8b440586b2260460ef354e827a17dfec1ea6a9815585a10cfa5c2'], - }), ('base64enc', '0.1-3', { 'checksums': ['6d856d8a364bcdc499a0bf38bfd283b7c743d08f0b288174fba7dbf0a04b688d'], }), @@ -204,6 +201,9 @@ exts_list = [ ('lifecycle', '1.0.3', { 'checksums': ['6459fdc3211585c0cdf120427579c12149b02161efe273a64b825c05e9aa69c2'], }), + ('vctrs', '0.6.3', { + 'checksums': ['93dc220dcde8b440586b2260460ef354e827a17dfec1ea6a9815585a10cfa5c2'], + }), ('diffobj', '0.3.5', { 'checksums': ['d860a79b1d4c9e369282d7391b539fe89228954854a65ba47181407c53e3cf60'], }), From 6336345ed2793836dd252e126e04f4edd61f16b4 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Thu, 29 Jun 2023 12:02:36 +0000 Subject: [PATCH 026/599] More dep order fixes --- .../easyconfigs/r/R/R-4.3.1-gfbf-2022b.eb | 24 +++++++++---------- 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-4.3.1-gfbf-2022b.eb b/easybuild/easyconfigs/r/R/R-4.3.1-gfbf-2022b.eb index 57028db3fbd..4d71b6f0525 100644 --- a/easybuild/easyconfigs/r/R/R-4.3.1-gfbf-2022b.eb +++ b/easybuild/easyconfigs/r/R/R-4.3.1-gfbf-2022b.eb @@ -129,9 +129,6 @@ exts_list = [ ('magrittr', '2.0.3', { 'checksums': ['a2bff83f792a1acb801bfe6330bb62724c74d5308832f2cb6a6178336ace55d2'], }), - ('stringr', '1.5.0', { - 'checksums': ['52b159d7700a139111b4caf939e7c9c6ab3e01185181400d70a74c552826633a'], - }), ('evaluate', '0.21', { 'checksums': ['3178c99cee8917d7d128806d064d4fecce7845ed07f42e759dcc0adda89c22b9'], }), @@ -156,15 +153,9 @@ exts_list = [ ('fansi', '1.0.4', { 'checksums': ['3163214e6c40922bbb495229259ed8ce1bebd98b77098a6936d234e43da9c49f'], }), - ('pillar', '1.9.0', { - 'checksums': ['f23eb486c087f864c2b4072d5cba01d5bebf2f554118bcba6886d8dbceb87acc'], - }), ('pkgconfig', '2.0.3', { 'checksums': ['330fef440ffeb842a7dcfffc8303743f1feae83e8d6131078b5a44ff11bc3850'], }), - ('tibble', '3.2.1', { - 'checksums': ['65a72d0c557fd6e7c510d150c935ed6ced5db7d05fc20236b370f11428372131'], - }), ('withr', '2.5.0', { 'checksums': ['37317b3ed790a08407072993a05ab255f6305f95a12a16e0e28aa6aa80fc8bc0'], }), @@ -177,6 +168,9 @@ exts_list = [ ('pkgload', '1.3.2', { 'checksums': ['35d19a032bfeeefcab92d76a768b4a420c2ede0920badaf48cca878592b46b2f'], }), + ('fastmap', '1.1.1', { + 'checksums': ['3623809dd016ae8abd235200ba7834effc4b916915a059deb76044137c5c7173'], + }), ('htmltools', '0.5.5', { 'checksums': ['c8b23fab855a89c6ed0f6d6c7cad0ff9c5ae329c0bdb479940443ee752f26659'], }), @@ -204,6 +198,15 @@ exts_list = [ ('vctrs', '0.6.3', { 'checksums': ['93dc220dcde8b440586b2260460ef354e827a17dfec1ea6a9815585a10cfa5c2'], }), + ('stringr', '1.5.0', { + 'checksums': ['52b159d7700a139111b4caf939e7c9c6ab3e01185181400d70a74c552826633a'], + }), + ('pillar', '1.9.0', { + 'checksums': ['f23eb486c087f864c2b4072d5cba01d5bebf2f554118bcba6886d8dbceb87acc'], + }), + ('tibble', '3.2.1', { + 'checksums': ['65a72d0c557fd6e7c510d150c935ed6ced5db7d05fc20236b370f11428372131'], + }), ('diffobj', '0.3.5', { 'checksums': ['d860a79b1d4c9e369282d7391b539fe89228954854a65ba47181407c53e3cf60'], }), @@ -246,9 +249,6 @@ exts_list = [ ('purrr', '1.0.1', { 'checksums': ['0a7911be3539355a4c40d136f2602befcaaad5a3f7222078500bfb969a6f2ba2'], }), - ('fastmap', '1.1.1', { - 'checksums': ['3623809dd016ae8abd235200ba7834effc4b916915a059deb76044137c5c7173'], - }), ('cachem', '1.0.8', { 'checksums': ['ea9ca919fe615dce8770758ecc2fc88ac99074f66ff1cde3a0b95d40007f45c2'], }), From 3a5e76333a32bb97e89e0f92c049a0afcdeb34bf Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 11 Jul 2023 17:19:15 +0200 Subject: [PATCH 027/599] use Z3 with Python bindings in Demystify v0.0.17 --- .../easyconfigs/d/Demystify/Demystify-0.0.17-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/Demystify/Demystify-0.0.17-foss-2020b.eb b/easybuild/easyconfigs/d/Demystify/Demystify-0.0.17-foss-2020b.eb index 356c7a33d87..3a7d86ba8dc 100644 --- a/easybuild/easyconfigs/d/Demystify/Demystify-0.0.17-foss-2020b.eb +++ b/easybuild/easyconfigs/d/Demystify/Demystify-0.0.17-foss-2020b.eb @@ -19,7 +19,7 @@ dependencies = [ ('Python', '3.8.6'), ('PySAT', '0.1.7.dev1'), ('SciPy-bundle', '2020.11'), - ('Z3', '4.8.10'), + ('Z3', '4.8.10', '-Python-%(pyver)s'), ] use_pip = True From 6ba5425293501d803c85fc8b27786de8e13afece Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 19 Jul 2023 13:04:28 +0200 Subject: [PATCH 028/599] Use CargoPythonBundle for timm --- .../timm-0.6.13-foss-2022a-CUDA-11.7.0.eb | 44 ++++++++++++++++++- 1 file changed, 43 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/timm/timm-0.6.13-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/t/timm/timm-0.6.13-foss-2022a-CUDA-11.7.0.eb index 7cc34b4454a..736f977f3d7 100644 --- a/easybuild/easyconfigs/t/timm/timm-0.6.13-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/t/timm/timm-0.6.13-foss-2022a-CUDA-11.7.0.eb @@ -1,4 +1,4 @@ -easyblock = 'PythonBundle' +easyblock = 'CargoPythonBundle' name = 'timm' version = '0.6.13' @@ -27,6 +27,48 @@ builddependencies = [ ('Rust', '1.65.0'), # for safetensors ] +crates = [ + ('autocfg', '1.1.0'), + ('bitflags', '1.3.2'), + ('cfg-if', '1.0.0'), + ('indoc', '1.0.9'), + ('itoa', '1.0.9'), + ('libc', '0.2.147'), + ('lock_api', '0.4.10'), + ('memmap2', '0.5.10'), + ('memoffset', '0.8.0'), + ('once_cell', '1.18.0'), + ('parking_lot', '0.12.1'), + ('parking_lot_core', '0.9.8'), + ('proc-macro2', '1.0.66'), + ('pyo3', '0.18.3'), + ('pyo3-build-config', '0.18.3'), + ('pyo3-ffi', '0.18.3'), + ('pyo3-macros', '0.18.3'), + ('pyo3-macros-backend', '0.18.3'), + ('quote', '1.0.31'), + ('redox_syscall', '0.3.5'), + ('ryu', '1.0.15'), + ('scopeguard', '1.2.0'), + ('serde', '1.0.171'), + ('serde_derive', '1.0.171'), + ('serde_json', '1.0.103'), + ('smallvec', '1.11.0'), + ('syn', '1.0.109'), + ('syn', '2.0.26'), + ('target-lexicon', '0.12.10'), + ('unicode-ident', '1.0.11'), + ('unindent', '0.1.11'), + ('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'), +] + use_pip = True exts_list = [ From 5d73ec78f0aba6871347320411d95213df37b2f5 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Fri, 11 Aug 2023 15:56:40 +0000 Subject: [PATCH 029/599] Change to gfbf/2023a and add missing deps --- .../l/libGLU/libGLU-9.0.3-GCCcore-12.3.0.eb | 27 ++ .../l/libgit2/libgit2-1.7.0-GCCcore-12.3.0.eb | 34 ++ .../easyconfigs/r/R/R-4.3.1-gfbf-2023a.eb | 374 ++++++++++++++++++ 3 files changed, 435 insertions(+) create mode 100644 easybuild/easyconfigs/l/libGLU/libGLU-9.0.3-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/l/libgit2/libgit2-1.7.0-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/r/R/R-4.3.1-gfbf-2023a.eb diff --git a/easybuild/easyconfigs/l/libGLU/libGLU-9.0.3-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.3-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..29f37b7fefc --- /dev/null +++ b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.3-GCCcore-12.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libGLU' +version = '9.0.3' + +homepage = 'https://mesa.freedesktop.org/archive/glu/' +description = """The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL. """ + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://mesa.freedesktop.org/archive/glu/'] +sources = ['glu-%(version)s.tar.xz'] +checksums = ['bd43fe12f374b1192eb15fe20e45ff456b9bc26ab57f0eee919f96ca0f8a330f'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('Mesa', '23.1.4'), +] + +sanity_check_paths = { + 'files': ['lib/libGLU.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libgit2/libgit2-1.7.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libgit2/libgit2-1.7.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..df14e87ef74 --- /dev/null +++ b/easybuild/easyconfigs/l/libgit2/libgit2-1.7.0-GCCcore-12.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'CMakeMake' + +name = 'libgit2' +version = '1.7.0' + +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': '12.3.0'} + +github_account = 'libgit2' +source_urls = [GITHUB_SOURCE] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['d9d0f84a86bf98b73e68997f5c1543cc5067d0ca9c7a5acaba3e8d117ecefef3'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), + ('pkgconf', '1.9.5'), +] + +dependencies = [ + ('PCRE', '8.45'), + ('OpenSSL', '1.1', '', SYSTEM), +] + +sanity_check_paths = { + 'files': ['include/git2.h', 'lib64/libgit2.%s' % SHLIB_EXT, 'lib64/pkgconfig/libgit2.pc'], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/r/R/R-4.3.1-gfbf-2023a.eb b/easybuild/easyconfigs/r/R/R-4.3.1-gfbf-2023a.eb new file mode 100644 index 00000000000..24764c1cd82 --- /dev/null +++ b/easybuild/easyconfigs/r/R/R-4.3.1-gfbf-2023a.eb @@ -0,0 +1,374 @@ +name = 'R' +version = '4.3.1' + +homepage = 'https://www.r-project.org/' +description = """R is a free software environment for statistical computing + and graphics.""" + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +source_urls = ['https://cloud.r-project.org/src/base/R-%(version_major)s'] +sources = [SOURCE_TAR_GZ] +checksums = ['8dd0bf24f1023c6f618c3b317383d291b4a494f40d73b983ac22ffea99e4ba99'] + +builddependencies = [ + ('pkgconf', '1.9.5'), + #('Xvfb', '21.1.6'), + ('Autotools', '20220317'), +] +dependencies = [ + ('X11', '20230603'), + ('Mesa', '23.1.4'), + ('libGLU', '9.0.3'), + ('cairo', '1.17.8'), + ('libreadline', '8.2'), + ('ncurses', '6.4'), + ('bzip2', '1.0.8'), + ('XZ', '5.4.2'), + ('zlib', '1.2.13'), + ('SQLite', '3.42.0'), + ('PCRE2', '10.42'), + ('libpng', '1.6.39'), # for plotting in R + ('libjpeg-turbo', '2.1.5.1'), # for plottting in R + ('LibTIFF', '4.5.0'), + ('Java', '11', '', SYSTEM), + ('libgit2', '1.7.0'), + ('OpenSSL', '1.1', '', SYSTEM), + ('cURL', '8.0.1'), + #('Tk', '8.6.12'), # for tcltk + #('libxml2', '2.10.3'), # for XML + #('HarfBuzz', '5.3.1'), # for textshaping + #('FriBidi', '1.0.12'), # 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" + +# specify that at least EasyBuild v3.5.0 is required, +# since we rely on the updated easyblock for R to configure correctly w.r.t. BLAS/LAPACK +easybuild_version = '3.5.0' + +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 22nd June 2023 +exts_list = [ + 'base', + 'compiler', + 'datasets', + 'graphics', + 'grDevices', + 'grid', + 'methods', + 'parallel', + 'splines', + 'stats', + 'stats4', + 'tcltk', + 'tools', + 'utils', + ('rlang', '1.1.1', { + 'checksums': ['5e5ec9a7796977216c39d94b1e342e08f0681746657067ba30de11b8fa8ada99'], + }), + ('Rcpp', '1.0.10', { + 'checksums': ['1e65e24a9981251ab5fc4f9fd65fe4eab4ba0255be3400a8c5abe20b62b5d546'], + }), + ('R6', '2.5.1', { + 'checksums': ['8d92bd29c2ed7bf15f2778618ffe4a95556193d21d8431a7f75e7e5fc102bf48'], + }), + ('cli', '3.6.1', { + 'checksums': ['be3006cec7e67f9ae25e21b4658c4bec680038c2ef7467df5f14da3311a05e36'], + }), + ('base64enc', '0.1-3', { + 'checksums': ['6d856d8a364bcdc499a0bf38bfd283b7c743d08f0b288174fba7dbf0a04b688d'], + }), + ('rprojroot', '2.0.3', { + 'checksums': ['50604247470e910cecfe9b76df754bf96a0d701f81b732f7aa9c90a20d30f897'], + }), + ('xfun', '0.39', { + 'checksums': ['d0ecaabb243dd3496da6029932fcdd4772914843de7ffd0b78a172efde1356c9'], + }), + ('commonmark', '1.9.0', { + 'checksums': ['6dd01a5a26c8d436486abf69c2f6ad0f8dd1c811f575c31983aeb4dbd376548f'], + }), + ('highr', '0.10', { + 'checksums': ['ec55bc1ff66390ed66806dc2a7b6c17dbfd089b3d73fe2e369017f8cb4bc347b'], + }), + ('digest', '0.6.31', { + 'checksums': ['5a284f490eaca6750f695f00a584cfca3f180ca1046ac1107202141149d431b9'], + }), + ('desc', '1.4.2', { + 'checksums': ['758acf14be478c09ba7e84ade3a7ce512becf35d44e5e6a997b932065f2a227c'], + }), + ('ellipsis', '0.3.2', { + 'checksums': ['a90266e5eb59c7f419774d5c6d6bd5e09701a26c9218c5933c9bce6765aa1558'], + }), + ('prettyunits', '1.1.1', { + 'checksums': ['9a199aa80c6d5e50fa977bc724d6e39dae1fc597a96413053609156ee7fb75c5'], + }), + ('crayon', '1.5.2', { + 'checksums': ['70a9a505b5b3c0ee6682ad8b965e28b7e24d9f942160d0a2bad18eec22b45a7a'], + }), + ('stringi', '1.7.12', { + 'checksums': ['efe8ac2900001f986a75db5641fbb24587a6d23de274a6a85c39dfa58921e009'], + }), + ('magrittr', '2.0.3', { + 'checksums': ['a2bff83f792a1acb801bfe6330bb62724c74d5308832f2cb6a6178336ace55d2'], + }), + ('evaluate', '0.21', { + 'checksums': ['3178c99cee8917d7d128806d064d4fecce7845ed07f42e759dcc0adda89c22b9'], + }), + ('ps', '1.7.5', { + 'checksums': ['1abc3ae3c55797b994973f7e43bf5c7bbb4da649a0dcfad36675e196dba4cb4e'], + }), + ('processx', '3.8.1', { + 'checksums': ['e008472b81d4ca1a37a4ba7dd58e5e944f96ab2e44c8ccc8840d43e9fe99e93c'], + }), + ('callr', '3.7.3', { + 'checksums': ['567bfedf073a1d4c5785f0553341608a214938110567b9a6495ff20ebb2fd04e'], + }), + ('pkgbuild', '1.4.1', { + 'checksums': ['cdb0ace14444f362be9725bd84e9752dab92f4771296504b63b9b8084f5e8a6b'], + }), + ('fs', '1.6.2', { + 'checksums': ['548b7c0ed5ab26dc4fbd88707ae12987bcaef834dbc6de4e17d453846dc436b2'], + }), + ('utf8', '1.2.3', { + 'checksums': ['c0a88686591f4ad43b52917d0964e9df4c62d8858fe25135a1bf357dfcbd6347'], + }), + ('fansi', '1.0.4', { + 'checksums': ['3163214e6c40922bbb495229259ed8ce1bebd98b77098a6936d234e43da9c49f'], + }), + ('pkgconfig', '2.0.3', { + 'checksums': ['330fef440ffeb842a7dcfffc8303743f1feae83e8d6131078b5a44ff11bc3850'], + }), + ('withr', '2.5.0', { + 'checksums': ['37317b3ed790a08407072993a05ab255f6305f95a12a16e0e28aa6aa80fc8bc0'], + }), + ('glue', '1.6.2', { + 'checksums': ['9da518f12be584c90e75fe8e07f711ee3f6fc0d03d817f72c25dc0f66499fdbf'], + }), + ('rstudioapi', '0.14', { + 'checksums': ['469d0987b1ad728a96c363a422fba712a5cebc8b11a5f7e953b4a671044dafc4'], + }), + ('pkgload', '1.3.2', { + 'checksums': ['35d19a032bfeeefcab92d76a768b4a420c2ede0920badaf48cca878592b46b2f'], + }), + ('fastmap', '1.1.1', { + 'checksums': ['3623809dd016ae8abd235200ba7834effc4b916915a059deb76044137c5c7173'], + }), + ('htmltools', '0.5.5', { + 'checksums': ['c8b23fab855a89c6ed0f6d6c7cad0ff9c5ae329c0bdb479940443ee752f26659'], + }), + ('yaml', '2.3.7', { + 'checksums': ['d20cb219e0f9c48aba02f132f81cfa9ecda5e22c925e36726840218ed56680ab'], + }), + ('knitr', '1.43', { + 'checksums': ['3d29baea8c349aaa9310879ceb9a9d51bcaec39827ad46d422c3793c8a4ed53c'], + }), + ('mime', '0.12', { + 'checksums': ['a9001051d6c1e556e881910b1816b42872a1ee41ab76d0040ce66a27135e3849'], + }), + ('praise', '1.0.0', { + 'checksums': ['5c035e74fd05dfa59b03afe0d5f4c53fbf34144e175e90c53d09c6baedf5debd'], + }), + ('brio', '1.1.3', { + 'checksums': ['eaa89041856189bee545bf1c42c7920a0bb0f1f70bb477487c467ee3e8fedcc6'], + }), + ('jsonlite', '1.8.5', { + 'checksums': ['dc3cca4bdca1b6d6836c412760ea9656140683126c54cb89c3e42219dec4a3ad'], + }), + ('lifecycle', '1.0.3', { + 'checksums': ['6459fdc3211585c0cdf120427579c12149b02161efe273a64b825c05e9aa69c2'], + }), + ('vctrs', '0.6.3', { + 'checksums': ['93dc220dcde8b440586b2260460ef354e827a17dfec1ea6a9815585a10cfa5c2'], + }), + ('stringr', '1.5.0', { + 'checksums': ['52b159d7700a139111b4caf939e7c9c6ab3e01185181400d70a74c552826633a'], + }), + ('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', '0.5.1', { + 'checksums': ['45bf076cff449e3c506c95857734bb73fdf30040333709b8845d09a12c6fdf46'], + }), + ('testthat', '3.1.9', { + 'checksums': ['4da1f992549c9b8db211f205059ec4c5d91a45d5971d60ebae21058268448375'], + }), + ('xml2', '1.3.4', { + 'checksums': ['340bb1a18e643a5008c0b4e92d71c3b0abacb44f1742e3a77d0cb33cb73b3030'], + }), + ('curl', '5.0.1', { + 'checksums': ['b7058f9cc7fa8f649505583584b61383fc08dccf746faa5381ba3d0b8bdf93a6'], + }), + ('sys', '3.4.2', { + 'checksums': ['b7bdce66f0fb681830ea6fb77b5a2c6babb43920abb1eddc733f95c0a63ce5b3'], + }), + ('askpass', '1.1', { + 'checksums': ['db40827d1bdbb90c0aa2846a2961d3bf9d76ad1b392302f9dd84cc2fd18c001f'], + }), + ('openssl', '2.0.6', { + 'checksums': ['77f3032a16270f0d1734f269b8d348eedc75b277812854386091143082c1b3f3'], + }), + ('httr', '1.4.6', { + 'checksums': ['8d6d86cbef23738d2b4390490f7486d8cf7674f0a59c19f515f61cad35ec37b2'], + }), + ('jquerylib', '0.1.4', { + 'checksums': ['f0bcc11dcde3a6ff180277e45c24642d3da3c8690900e38f44495efbc9064411'], + }), + ('rappdirs', '0.3.3', { + 'checksums': ['49959f65b45b0b189a2792d6c1339bef59674ecae92f8c2ed9f26ff9e488c184'], + }), + ('sass', '0.4.6', { + 'checksums': ['2ee82ce709b7fdee78f7e2364d04f369f58fc2cda4bb5a235bd53c49d311c019'], + }), + ('purrr', '1.0.1', { + 'checksums': ['0a7911be3539355a4c40d136f2602befcaaad5a3f7222078500bfb969a6f2ba2'], + }), + ('cachem', '1.0.8', { + 'checksums': ['ea9ca919fe615dce8770758ecc2fc88ac99074f66ff1cde3a0b95d40007f45c2'], + }), + ('memoise', '2.0.1', { + 'checksums': ['f85034ee98c8ca07fb3cd826142c1cd1e1e5747075a94c75a45783bbc4fe2deb'], + }), + ('bslib', '0.5.0', { + 'checksums': ['a2c6fbc62242806e10bb58c5d1ba04a6d3bf4e546bc53d7acf1b8eb1160bd115'], + }), + ('fontawesome', '0.5.0', { + 'checksums': ['4117b417a33e82d626881d7059eb54e7534cba202e75dae7e27021cb3796e90b'], + }), + ('tinytex', '0.45', { + 'checksums': ['0c2fbbd09e80af80ca6b685bf0653f070da97b85413d39af966aba28f376e92c'], + }), + ('rmarkdown', '2.22', { + 'checksums': ['c6635519503e0fcdd518696d3ac96d8d28d9d4ecd9db0532c53426002f6387b8'], + }), + ('downlit', '0.4.2', { + 'checksums': ['33dff66909104d1a5ba8e57b1288986e82b61fd5e91dce0cd358d53724b37e3c'], + }), + ('cpp11', '0.4.3', { + 'checksums': ['f1a60e4971a86dbbcf6a16bbd739b59bb66d9c45d93cfd8dedc2a87e302598f1'], + }), + ('systemfonts', '1.0.4', { + 'checksums': ['ef766c75b942f147d382664a00d6a4930f1bfe0cce9d88943f571682a85a84c0'], + }), + ('textshaping', '0.3.6', { + 'checksums': ['80e2c087962f55ce2811fbc798b09f5638c06c6b28c10cd3cb3827005b902ada'], + }), + ('ragg', '1.2.5', { + 'checksums': ['936f4d75e0e01cdeefb9f57d121cdd7812d0de5a9e1a3a8315f92ce1c84da8f9'], + }), + ('whisker', '0.4.1', { + 'checksums': ['bf5151494508032f68ac41e211bda80da9087c65c7068ffdd12f16669bf1f2bc'], + }), + ('pkgdown', '2.0.7', { + 'checksums': ['f33872869dfa8319182d87e90eab3245ff69293b3b791471bf9538afb81b356a'], + }), + ('htmlwidgets', '1.6.2', { + 'checksums': ['7fda1672a4c0fbc203c790677b6ee7c40d2c2d72be4f6772f75288fc712b10bc'], + }), + ('profvis', '0.3.8', { + 'checksums': ['ec02c75bc9907a73564e691adfa8e06651ca0bd73b7915412960231cd265b4b2'], + }), + ('urlchecker', '1.0.1', { + 'checksums': ['62165ddbe1b748b58c71a50c8f07fdde6f3d19a7b39787b9fa2b4f9216250318'], + }), + ('later', '1.3.1', { + 'checksums': ['23eed681f0b9eacebbc3c6a5ba14ee0b676a4bf6e69af194c5a36edfe11464ac'], + }), + ('promises', '1.2.0.1', { + 'checksums': ['8d3a8217909e91f4c2a2eebba5ac8fc902a9ac1a9e9d8a30815c9dc0f162c4b7'], + }), + ('xtable', '1.8-4', { + 'checksums': ['5abec0e8c27865ef0880f1d19c9f9ca7cc0fd24eadaa72bcd270c3fb4075fd1c'], + }), + ('httpuv', '1.6.11', { + 'checksums': ['8ba79e0a8351274daf2dc566c71f88e891127cdedca62ad77a4b27a8103eeef5'], + }), + ('sourcetools', '0.1.7-1', { + 'checksums': ['96812bdb7a0dd99690d84e4b0a3def91389e4290f53f01919ef28a50554e31d1'], + }), + ('shiny', '1.7.4', { + 'checksums': ['bbfcdd7375013b8f59248b3f3f4e752acd445feb25179f3f7f65cd69614da4b5'], + }), + ('miniUI', '0.1.1.1', { + 'checksums': ['452b41133289f630d8026507263744e385908ca025e9a7976925c1539816b0c0'], + }), + ('brew', '1.0-8', { + 'checksums': ['11652d5a7042d645cc5be5f9f97ff4d46083cea7d3ad2dd6ad1570b52c097826'], + }), + ('roxygen2', '7.2.3', { + 'checksums': ['d844fab977d2575ab942fa1309ac7ff67f35f099a75d8b41c79efe6ea10416da'], + }), + ('rversions', '2.1.2', { + 'checksums': ['de5818233e8271132fe8ea70145618950b35786e0d2f270e39bf3338f3b8b160'], + }), + ('sessioninfo', '1.2.2', { + 'checksums': ['f56283857c53ac8691e3747ed48fe03e893d8ff348235bff7364658bcfb0c7cb'], + }), + ('xopen', '1.0.0', { + 'checksums': ['e207603844d69c226142be95281ba2f4a056b9d8cbfae7791ba60535637b3bef'], + }), + ('rcmdcheck', '1.4.0', { + 'checksums': ['bbd4ef7d514b8c2076196a7c4a6041d34623d55fbe73f2771758ce61fd32c9d0'], + }), + ('remotes', '2.4.2', { + 'checksums': ['f2ef875f24a485bf4f55a8c830f87cdd5db868f9a8cdb624dc452d0bf66ba516'], + }), + ('clipr', '0.8.0', { + 'checksums': ['32c2931992fbec9c31b71de3e27059f1cbb45b4b1f45fd42e0e8dbcec6de3be9'], + }), + ('ini', '0.3.1', { + 'checksums': ['7b191a54019c8c52d6c2211c14878c95564154ec4865f57007953742868cd813'], + }), + ('gitcreds', '0.1.2', { + 'checksums': ['41c6abcca5635062b123ffb5af2794770eca5ebd97b05c5a64b24fa1c803c75d'], + }), + ('httr2', '0.2.3', { + 'checksums': ['352032029512f28f6f440ace0078e859ad3945d6b20841963b372523b6974b3d'], + }), + ('gh', '1.4.0', { + 'checksums': ['68c69fcd18429b378e639a09652465a4e92b7b5b5704804d0c5b1ca2b9b58b71'], + }), + ('credentials', '1.3.2', { + 'checksums': ['2ffa7c11bedbfa034adf553d0a2f2e4f6a496b858af753a09a89219cff9028b8'], + }), + ('zip', '2.3.0', { + 'checksums': ['33eba844922af9981732ee6ec1582d46cf04c562344f09a0f0f14a22c6f74543'], + }), + ('gert', '1.9.2', { + 'checksums': ['42ca1b4bcafb1fdbbc7f54df0ee4476ecd19e9e7d563b53fe7064e0086ab665e'], + }), + ('usethis', '2.2.0', { + 'checksums': ['2ccebe690aadebff96451cc9c226dc1a1e9ca5ac6ec83310e12a1312cb163b4f'], + }), + ('devtools', '2.4.5', { + 'checksums': ['38160ebd839acdec7ebf0699a085b4ab1ebd5500d3c57a9fa7ae484f1909904b'], + }), +] + +moduleclass = 'lang' From 1110b11611267d088e3381169bbd56d44c419229 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Fri, 11 Aug 2023 16:57:22 +0100 Subject: [PATCH 030/599] Delete R-4.3.1-gfbf-2022b.eb --- .../easyconfigs/r/R/R-4.3.1-gfbf-2022b.eb | 374 ------------------ 1 file changed, 374 deletions(-) delete mode 100644 easybuild/easyconfigs/r/R/R-4.3.1-gfbf-2022b.eb diff --git a/easybuild/easyconfigs/r/R/R-4.3.1-gfbf-2022b.eb b/easybuild/easyconfigs/r/R/R-4.3.1-gfbf-2022b.eb deleted file mode 100644 index 4d71b6f0525..00000000000 --- a/easybuild/easyconfigs/r/R/R-4.3.1-gfbf-2022b.eb +++ /dev/null @@ -1,374 +0,0 @@ -name = 'R' -version = '4.3.1' - -homepage = 'https://www.r-project.org/' -description = """R is a free software environment for statistical computing - and graphics.""" - -toolchain = {'name': 'gfbf', 'version': '2022b'} - -source_urls = ['https://cloud.r-project.org/src/base/R-%(version_major)s'] -sources = [SOURCE_TAR_GZ] -checksums = ['8dd0bf24f1023c6f618c3b317383d291b4a494f40d73b983ac22ffea99e4ba99'] - -builddependencies = [ - ('pkgconf', '1.9.3'), - ('Xvfb', '21.1.6'), - ('Autotools', '20220317'), -] -dependencies = [ - ('X11', '20221110'), - ('Mesa', '22.2.4'), - ('libGLU', '9.0.2'), - ('cairo', '1.17.4'), - ('libreadline', '8.2'), - ('ncurses', '6.3'), - ('bzip2', '1.0.8'), - ('XZ', '5.2.7'), - ('zlib', '1.2.12'), - ('SQLite', '3.39.4'), - ('PCRE2', '10.40'), - ('libpng', '1.6.38'), # for plotting in R - ('libjpeg-turbo', '2.1.4'), # for plottting in R - ('LibTIFF', '4.4.0'), - ('Java', '11', '', SYSTEM), - ('libgit2', '1.5.0'), - ('OpenSSL', '1.1', '', SYSTEM), - ('cURL', '7.86.0'), - ('Tk', '8.6.12'), # for tcltk - ('libxml2', '2.10.3'), # for XML - ('HarfBuzz', '5.3.1'), # for textshaping - ('FriBidi', '1.0.12'), # 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" - -# specify that at least EasyBuild v3.5.0 is required, -# since we rely on the updated easyblock for R to configure correctly w.r.t. BLAS/LAPACK -easybuild_version = '3.5.0' - -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 22nd June 2023 -exts_list = [ - 'base', - 'compiler', - 'datasets', - 'graphics', - 'grDevices', - 'grid', - 'methods', - 'parallel', - 'splines', - 'stats', - 'stats4', - 'tcltk', - 'tools', - 'utils', - ('rlang', '1.1.1', { - 'checksums': ['5e5ec9a7796977216c39d94b1e342e08f0681746657067ba30de11b8fa8ada99'], - }), - ('Rcpp', '1.0.10', { - 'checksums': ['1e65e24a9981251ab5fc4f9fd65fe4eab4ba0255be3400a8c5abe20b62b5d546'], - }), - ('R6', '2.5.1', { - 'checksums': ['8d92bd29c2ed7bf15f2778618ffe4a95556193d21d8431a7f75e7e5fc102bf48'], - }), - ('cli', '3.6.1', { - 'checksums': ['be3006cec7e67f9ae25e21b4658c4bec680038c2ef7467df5f14da3311a05e36'], - }), - ('base64enc', '0.1-3', { - 'checksums': ['6d856d8a364bcdc499a0bf38bfd283b7c743d08f0b288174fba7dbf0a04b688d'], - }), - ('rprojroot', '2.0.3', { - 'checksums': ['50604247470e910cecfe9b76df754bf96a0d701f81b732f7aa9c90a20d30f897'], - }), - ('xfun', '0.39', { - 'checksums': ['d0ecaabb243dd3496da6029932fcdd4772914843de7ffd0b78a172efde1356c9'], - }), - ('commonmark', '1.9.0', { - 'checksums': ['6dd01a5a26c8d436486abf69c2f6ad0f8dd1c811f575c31983aeb4dbd376548f'], - }), - ('highr', '0.10', { - 'checksums': ['ec55bc1ff66390ed66806dc2a7b6c17dbfd089b3d73fe2e369017f8cb4bc347b'], - }), - ('digest', '0.6.31', { - 'checksums': ['5a284f490eaca6750f695f00a584cfca3f180ca1046ac1107202141149d431b9'], - }), - ('desc', '1.4.2', { - 'checksums': ['758acf14be478c09ba7e84ade3a7ce512becf35d44e5e6a997b932065f2a227c'], - }), - ('ellipsis', '0.3.2', { - 'checksums': ['a90266e5eb59c7f419774d5c6d6bd5e09701a26c9218c5933c9bce6765aa1558'], - }), - ('prettyunits', '1.1.1', { - 'checksums': ['9a199aa80c6d5e50fa977bc724d6e39dae1fc597a96413053609156ee7fb75c5'], - }), - ('crayon', '1.5.2', { - 'checksums': ['70a9a505b5b3c0ee6682ad8b965e28b7e24d9f942160d0a2bad18eec22b45a7a'], - }), - ('stringi', '1.7.12', { - 'checksums': ['efe8ac2900001f986a75db5641fbb24587a6d23de274a6a85c39dfa58921e009'], - }), - ('magrittr', '2.0.3', { - 'checksums': ['a2bff83f792a1acb801bfe6330bb62724c74d5308832f2cb6a6178336ace55d2'], - }), - ('evaluate', '0.21', { - 'checksums': ['3178c99cee8917d7d128806d064d4fecce7845ed07f42e759dcc0adda89c22b9'], - }), - ('ps', '1.7.5', { - 'checksums': ['1abc3ae3c55797b994973f7e43bf5c7bbb4da649a0dcfad36675e196dba4cb4e'], - }), - ('processx', '3.8.1', { - 'checksums': ['e008472b81d4ca1a37a4ba7dd58e5e944f96ab2e44c8ccc8840d43e9fe99e93c'], - }), - ('callr', '3.7.3', { - 'checksums': ['567bfedf073a1d4c5785f0553341608a214938110567b9a6495ff20ebb2fd04e'], - }), - ('pkgbuild', '1.4.1', { - 'checksums': ['cdb0ace14444f362be9725bd84e9752dab92f4771296504b63b9b8084f5e8a6b'], - }), - ('fs', '1.6.2', { - 'checksums': ['548b7c0ed5ab26dc4fbd88707ae12987bcaef834dbc6de4e17d453846dc436b2'], - }), - ('utf8', '1.2.3', { - 'checksums': ['c0a88686591f4ad43b52917d0964e9df4c62d8858fe25135a1bf357dfcbd6347'], - }), - ('fansi', '1.0.4', { - 'checksums': ['3163214e6c40922bbb495229259ed8ce1bebd98b77098a6936d234e43da9c49f'], - }), - ('pkgconfig', '2.0.3', { - 'checksums': ['330fef440ffeb842a7dcfffc8303743f1feae83e8d6131078b5a44ff11bc3850'], - }), - ('withr', '2.5.0', { - 'checksums': ['37317b3ed790a08407072993a05ab255f6305f95a12a16e0e28aa6aa80fc8bc0'], - }), - ('glue', '1.6.2', { - 'checksums': ['9da518f12be584c90e75fe8e07f711ee3f6fc0d03d817f72c25dc0f66499fdbf'], - }), - ('rstudioapi', '0.14', { - 'checksums': ['469d0987b1ad728a96c363a422fba712a5cebc8b11a5f7e953b4a671044dafc4'], - }), - ('pkgload', '1.3.2', { - 'checksums': ['35d19a032bfeeefcab92d76a768b4a420c2ede0920badaf48cca878592b46b2f'], - }), - ('fastmap', '1.1.1', { - 'checksums': ['3623809dd016ae8abd235200ba7834effc4b916915a059deb76044137c5c7173'], - }), - ('htmltools', '0.5.5', { - 'checksums': ['c8b23fab855a89c6ed0f6d6c7cad0ff9c5ae329c0bdb479940443ee752f26659'], - }), - ('yaml', '2.3.7', { - 'checksums': ['d20cb219e0f9c48aba02f132f81cfa9ecda5e22c925e36726840218ed56680ab'], - }), - ('knitr', '1.43', { - 'checksums': ['3d29baea8c349aaa9310879ceb9a9d51bcaec39827ad46d422c3793c8a4ed53c'], - }), - ('mime', '0.12', { - 'checksums': ['a9001051d6c1e556e881910b1816b42872a1ee41ab76d0040ce66a27135e3849'], - }), - ('praise', '1.0.0', { - 'checksums': ['5c035e74fd05dfa59b03afe0d5f4c53fbf34144e175e90c53d09c6baedf5debd'], - }), - ('brio', '1.1.3', { - 'checksums': ['eaa89041856189bee545bf1c42c7920a0bb0f1f70bb477487c467ee3e8fedcc6'], - }), - ('jsonlite', '1.8.5', { - 'checksums': ['dc3cca4bdca1b6d6836c412760ea9656140683126c54cb89c3e42219dec4a3ad'], - }), - ('lifecycle', '1.0.3', { - 'checksums': ['6459fdc3211585c0cdf120427579c12149b02161efe273a64b825c05e9aa69c2'], - }), - ('vctrs', '0.6.3', { - 'checksums': ['93dc220dcde8b440586b2260460ef354e827a17dfec1ea6a9815585a10cfa5c2'], - }), - ('stringr', '1.5.0', { - 'checksums': ['52b159d7700a139111b4caf939e7c9c6ab3e01185181400d70a74c552826633a'], - }), - ('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', '0.5.1', { - 'checksums': ['45bf076cff449e3c506c95857734bb73fdf30040333709b8845d09a12c6fdf46'], - }), - ('testthat', '3.1.9', { - 'checksums': ['4da1f992549c9b8db211f205059ec4c5d91a45d5971d60ebae21058268448375'], - }), - ('xml2', '1.3.4', { - 'checksums': ['340bb1a18e643a5008c0b4e92d71c3b0abacb44f1742e3a77d0cb33cb73b3030'], - }), - ('curl', '5.0.1', { - 'checksums': ['b7058f9cc7fa8f649505583584b61383fc08dccf746faa5381ba3d0b8bdf93a6'], - }), - ('sys', '3.4.2', { - 'checksums': ['b7bdce66f0fb681830ea6fb77b5a2c6babb43920abb1eddc733f95c0a63ce5b3'], - }), - ('askpass', '1.1', { - 'checksums': ['db40827d1bdbb90c0aa2846a2961d3bf9d76ad1b392302f9dd84cc2fd18c001f'], - }), - ('openssl', '2.0.6', { - 'checksums': ['77f3032a16270f0d1734f269b8d348eedc75b277812854386091143082c1b3f3'], - }), - ('httr', '1.4.6', { - 'checksums': ['8d6d86cbef23738d2b4390490f7486d8cf7674f0a59c19f515f61cad35ec37b2'], - }), - ('jquerylib', '0.1.4', { - 'checksums': ['f0bcc11dcde3a6ff180277e45c24642d3da3c8690900e38f44495efbc9064411'], - }), - ('rappdirs', '0.3.3', { - 'checksums': ['49959f65b45b0b189a2792d6c1339bef59674ecae92f8c2ed9f26ff9e488c184'], - }), - ('sass', '0.4.6', { - 'checksums': ['2ee82ce709b7fdee78f7e2364d04f369f58fc2cda4bb5a235bd53c49d311c019'], - }), - ('purrr', '1.0.1', { - 'checksums': ['0a7911be3539355a4c40d136f2602befcaaad5a3f7222078500bfb969a6f2ba2'], - }), - ('cachem', '1.0.8', { - 'checksums': ['ea9ca919fe615dce8770758ecc2fc88ac99074f66ff1cde3a0b95d40007f45c2'], - }), - ('memoise', '2.0.1', { - 'checksums': ['f85034ee98c8ca07fb3cd826142c1cd1e1e5747075a94c75a45783bbc4fe2deb'], - }), - ('bslib', '0.5.0', { - 'checksums': ['a2c6fbc62242806e10bb58c5d1ba04a6d3bf4e546bc53d7acf1b8eb1160bd115'], - }), - ('fontawesome', '0.5.0', { - 'checksums': ['4117b417a33e82d626881d7059eb54e7534cba202e75dae7e27021cb3796e90b'], - }), - ('tinytex', '0.45', { - 'checksums': ['0c2fbbd09e80af80ca6b685bf0653f070da97b85413d39af966aba28f376e92c'], - }), - ('rmarkdown', '2.22', { - 'checksums': ['c6635519503e0fcdd518696d3ac96d8d28d9d4ecd9db0532c53426002f6387b8'], - }), - ('downlit', '0.4.2', { - 'checksums': ['33dff66909104d1a5ba8e57b1288986e82b61fd5e91dce0cd358d53724b37e3c'], - }), - ('cpp11', '0.4.3', { - 'checksums': ['f1a60e4971a86dbbcf6a16bbd739b59bb66d9c45d93cfd8dedc2a87e302598f1'], - }), - ('systemfonts', '1.0.4', { - 'checksums': ['ef766c75b942f147d382664a00d6a4930f1bfe0cce9d88943f571682a85a84c0'], - }), - ('textshaping', '0.3.6', { - 'checksums': ['80e2c087962f55ce2811fbc798b09f5638c06c6b28c10cd3cb3827005b902ada'], - }), - ('ragg', '1.2.5', { - 'checksums': ['936f4d75e0e01cdeefb9f57d121cdd7812d0de5a9e1a3a8315f92ce1c84da8f9'], - }), - ('whisker', '0.4.1', { - 'checksums': ['bf5151494508032f68ac41e211bda80da9087c65c7068ffdd12f16669bf1f2bc'], - }), - ('pkgdown', '2.0.7', { - 'checksums': ['f33872869dfa8319182d87e90eab3245ff69293b3b791471bf9538afb81b356a'], - }), - ('htmlwidgets', '1.6.2', { - 'checksums': ['7fda1672a4c0fbc203c790677b6ee7c40d2c2d72be4f6772f75288fc712b10bc'], - }), - ('profvis', '0.3.8', { - 'checksums': ['ec02c75bc9907a73564e691adfa8e06651ca0bd73b7915412960231cd265b4b2'], - }), - ('urlchecker', '1.0.1', { - 'checksums': ['62165ddbe1b748b58c71a50c8f07fdde6f3d19a7b39787b9fa2b4f9216250318'], - }), - ('later', '1.3.1', { - 'checksums': ['23eed681f0b9eacebbc3c6a5ba14ee0b676a4bf6e69af194c5a36edfe11464ac'], - }), - ('promises', '1.2.0.1', { - 'checksums': ['8d3a8217909e91f4c2a2eebba5ac8fc902a9ac1a9e9d8a30815c9dc0f162c4b7'], - }), - ('xtable', '1.8-4', { - 'checksums': ['5abec0e8c27865ef0880f1d19c9f9ca7cc0fd24eadaa72bcd270c3fb4075fd1c'], - }), - ('httpuv', '1.6.11', { - 'checksums': ['8ba79e0a8351274daf2dc566c71f88e891127cdedca62ad77a4b27a8103eeef5'], - }), - ('sourcetools', '0.1.7-1', { - 'checksums': ['96812bdb7a0dd99690d84e4b0a3def91389e4290f53f01919ef28a50554e31d1'], - }), - ('shiny', '1.7.4', { - 'checksums': ['bbfcdd7375013b8f59248b3f3f4e752acd445feb25179f3f7f65cd69614da4b5'], - }), - ('miniUI', '0.1.1.1', { - 'checksums': ['452b41133289f630d8026507263744e385908ca025e9a7976925c1539816b0c0'], - }), - ('brew', '1.0-8', { - 'checksums': ['11652d5a7042d645cc5be5f9f97ff4d46083cea7d3ad2dd6ad1570b52c097826'], - }), - ('roxygen2', '7.2.3', { - 'checksums': ['d844fab977d2575ab942fa1309ac7ff67f35f099a75d8b41c79efe6ea10416da'], - }), - ('rversions', '2.1.2', { - 'checksums': ['de5818233e8271132fe8ea70145618950b35786e0d2f270e39bf3338f3b8b160'], - }), - ('sessioninfo', '1.2.2', { - 'checksums': ['f56283857c53ac8691e3747ed48fe03e893d8ff348235bff7364658bcfb0c7cb'], - }), - ('xopen', '1.0.0', { - 'checksums': ['e207603844d69c226142be95281ba2f4a056b9d8cbfae7791ba60535637b3bef'], - }), - ('rcmdcheck', '1.4.0', { - 'checksums': ['bbd4ef7d514b8c2076196a7c4a6041d34623d55fbe73f2771758ce61fd32c9d0'], - }), - ('remotes', '2.4.2', { - 'checksums': ['f2ef875f24a485bf4f55a8c830f87cdd5db868f9a8cdb624dc452d0bf66ba516'], - }), - ('clipr', '0.8.0', { - 'checksums': ['32c2931992fbec9c31b71de3e27059f1cbb45b4b1f45fd42e0e8dbcec6de3be9'], - }), - ('ini', '0.3.1', { - 'checksums': ['7b191a54019c8c52d6c2211c14878c95564154ec4865f57007953742868cd813'], - }), - ('gitcreds', '0.1.2', { - 'checksums': ['41c6abcca5635062b123ffb5af2794770eca5ebd97b05c5a64b24fa1c803c75d'], - }), - ('httr2', '0.2.3', { - 'checksums': ['352032029512f28f6f440ace0078e859ad3945d6b20841963b372523b6974b3d'], - }), - ('gh', '1.4.0', { - 'checksums': ['68c69fcd18429b378e639a09652465a4e92b7b5b5704804d0c5b1ca2b9b58b71'], - }), - ('credentials', '1.3.2', { - 'checksums': ['2ffa7c11bedbfa034adf553d0a2f2e4f6a496b858af753a09a89219cff9028b8'], - }), - ('zip', '2.3.0', { - 'checksums': ['33eba844922af9981732ee6ec1582d46cf04c562344f09a0f0f14a22c6f74543'], - }), - ('gert', '1.9.2', { - 'checksums': ['42ca1b4bcafb1fdbbc7f54df0ee4476ecd19e9e7d563b53fe7064e0086ab665e'], - }), - ('usethis', '2.2.0', { - 'checksums': ['2ccebe690aadebff96451cc9c226dc1a1e9ca5ac6ec83310e12a1312cb163b4f'], - }), - ('devtools', '2.4.5', { - 'checksums': ['38160ebd839acdec7ebf0699a085b4ab1ebd5500d3c57a9fa7ae484f1909904b'], - }), -] - -moduleclass = 'lang' From e2a106985824b0e2fd6a811f0d6caf44027fb617 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Fri, 11 Aug 2023 17:07:29 +0100 Subject: [PATCH 031/599] libGLU was merged after I triggered the build test... --- .../l/libGLU/libGLU-9.0.3-GCCcore-12.3.0.eb | 27 ------------------- 1 file changed, 27 deletions(-) delete mode 100644 easybuild/easyconfigs/l/libGLU/libGLU-9.0.3-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/l/libGLU/libGLU-9.0.3-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.3-GCCcore-12.3.0.eb deleted file mode 100644 index 29f37b7fefc..00000000000 --- a/easybuild/easyconfigs/l/libGLU/libGLU-9.0.3-GCCcore-12.3.0.eb +++ /dev/null @@ -1,27 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libGLU' -version = '9.0.3' - -homepage = 'https://mesa.freedesktop.org/archive/glu/' -description = """The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL. """ - -toolchain = {'name': 'GCCcore', 'version': '12.3.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://mesa.freedesktop.org/archive/glu/'] -sources = ['glu-%(version)s.tar.xz'] -checksums = ['bd43fe12f374b1192eb15fe20e45ff456b9bc26ab57f0eee919f96ca0f8a330f'] - -builddependencies = [('binutils', '2.40')] - -dependencies = [ - ('Mesa', '23.1.4'), -] - -sanity_check_paths = { - 'files': ['lib/libGLU.%s' % SHLIB_EXT], - 'dirs': [], -} - -moduleclass = 'vis' From c40a81bbaea97cd88dd00ed8c5d387507be76d1e Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann Date: Tue, 29 Aug 2023 09:37:51 +0200 Subject: [PATCH 032/599] adding easyconfigs: datalad-0.18.4-GCCcore-12.2.0.eb --- .../datalad/datalad-0.18.4-GCCcore-12.2.0.eb | 67 +++++++++++++++++++ 1 file changed, 67 insertions(+) create mode 100644 easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb b/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..a18c2093734 --- /dev/null +++ b/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb @@ -0,0 +1,67 @@ +easyblock = 'PythonBundle' + +name = 'datalad' +version = "0.18.4" + +homepage = 'https://www.datalad.org/' +description = "DataLad is a free and open source distributed data management system that keeps track of your data, creates structure, ensures reproducibility, supports collaboration, and integrates with widely used data infrastructure." + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +dependencies = [ + ('git-annex', '10.20230802'), + ('Python', '3.10.8'), + ('tqdm', '4.64.1'), + ('PLY', '3.11', '-Python-3.10.8'), + ('Rust', '1.65.0'), + ('scikit-build', '0.17.2'), +] + +use_pip = True + +exts_list = [ + ('humanize', '3.13.1', { + 'checksums': ['12f113f2e369dac7f35d3823f49262934f4a22a53a6d3d4c86b736f50db88c7b'], + }), + ('fasteners', '0.18', { + 'checksums': ['cb7c13ef91e0c7e4fe4af38ecaf6b904ec3f5ce0dda06d34924b6b74b869d953'], + }), + ('patoolib', '1.12', { + 'source_tmpl': 'patool-%(version)s.tar.gz', + 'checksums': ['e3180cf8bfe13bedbcf6f5628452fca0c2c84a3b5ae8c2d3f55720ea04cb1097'], + }), + ('annexremote', '1.6.0', { + 'checksums': ['779a43e5b1b4afd294761c6587dee8ac68f453a5a8cc40f419e9ca777573ae84'], + }), + ('looseversion', '1.2.0', { + 'checksums': ['c64e71c0b29030683b4ea75aee431db2d25c4e6e533590e52129f1d9e51de204'], + }), + ('boto', '2.49.0', { + 'checksums': ['ea0d3b40a2d852767be77ca343b58a9e3a4b00d9db440efb8da74b4e58025e5a'], + }), + ('gitlab', '3.10.0', { + 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + 'checksums': ['14930a16fdd7f36f67b9373e7d4d4720e8e374800028380289db3306e9f74614'], + }), + ('iso8601', '1.0.2', { + 'checksums': ['27f503220e6845d9db954fb212b95b0362d8b7e6c1b2326a87061c3de93594b1'], + }), + (name, version, { + 'checksums': ['d832f3d70b79b7b66519ca30315791a6a265bdf8a86ddac5846489b75385cb09'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/datalad'], + 'dirs': [], +} + +sanity_check_commands = [ + "datalad --help", + "datalad --version", +] + +moduleclass = 'tools' From c246cd39470bc41bedcd6b15b17bbfa743fb8d88 Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann Date: Fri, 1 Sep 2023 12:45:22 +0000 Subject: [PATCH 033/599] remove python extention as in #18674 --- .../easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb b/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb index a18c2093734..812f649c339 100644 --- a/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb @@ -13,7 +13,7 @@ dependencies = [ ('git-annex', '10.20230802'), ('Python', '3.10.8'), ('tqdm', '4.64.1'), - ('PLY', '3.11', '-Python-3.10.8'), + ('PLY', '3.11'), ('Rust', '1.65.0'), ('scikit-build', '0.17.2'), ] From 6fb54e2da57e4b3151126365eb05c41ad05410a2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 5 Sep 2023 18:04:10 +0200 Subject: [PATCH 034/599] adding easyconfigs: SEACells-20230731-foss-2021a.eb --- .../SEACells/SEACells-20230731-foss-2021a.eb | 76 +++++++++++++++++++ 1 file changed, 76 insertions(+) create mode 100644 easybuild/easyconfigs/s/SEACells/SEACells-20230731-foss-2021a.eb diff --git a/easybuild/easyconfigs/s/SEACells/SEACells-20230731-foss-2021a.eb b/easybuild/easyconfigs/s/SEACells/SEACells-20230731-foss-2021a.eb new file mode 100644 index 00000000000..7cf0a01cbbc --- /dev/null +++ b/easybuild/easyconfigs/s/SEACells/SEACells-20230731-foss-2021a.eb @@ -0,0 +1,76 @@ +easyblock = 'PythonBundle' + +name = 'SEACells' +local_commit = 'a3486ca' +version = '20230731' + +homepage = 'https://github.com/dpeerlab/SEACells' +description = """SEACells algorithm for Inference of transcriptional and epigenomic cellular states + from single-cell genomics data""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +builddependencies = [ + ('CMake', '3.20.1'), +] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('numba', '0.53.1'), + ('scanpy', '1.8.1'), +] + +use_pip = True + +exts_list = [ + ('fcsparser', '0.2.3', { + 'checksums': ['c370f05d42898ce220cb8ea0f89988d18eaaeced063c4118cc3dcb99cbd8c17e'], + }), + ('PhenoGraph', '1.5.7', { + 'checksums': ['46b28f9e043a00deba53bb5f35dd84793669ab2bd4ce78900bf7f15f1321515a'], + }), + ('typing-extensions', '4.7.1', { + 'sources': ['typing_extensions-%(version)s.tar.gz'], + }), + ('python-utils', '3.7.0', { + 'checksums': ['1970468fff1c0adbd60b9a751e6a786223a9f0373c954571912d9cf4be49b552'], + }), + ('progressbar2', '4.2.0', { + 'checksums': ['1393922fcb64598944ad457569fbeb4b3ac189ef50b5adb9cef3284e87e394ce'], + 'modulename': 'progressbar', + }), + ('pygam', '0.8.0', { + 'checksums': ['5cae01aea8b2fede72a6da0aba1490213af54b3476745666af26bbe700479166'], + }), + ('tzlocal', '5.0.1', { + 'checksums': ['46eb99ad4bdb71f3f72b7d24f4267753e240944ecfc16f25d2719ba89827a803'], + }), + ('palantir', '1.2', { + 'preinstallopts': "sed -i '/cmake/d' setup.py && ", + 'checksums': ['2213ba7a99be62922086e30417994874c165bce1356752bbf0b4cc887b1a069e'], + }), + ('ncls', '0.0.67', { + 'checksums': ['fa3e673d60e97bb021a516287d74bb959870cf9d910ec82403b99c443d8f447e'], + }), + ('sorted-nearest', '0.0.32', { + 'sources': ['sorted_nearest-%(version)s.tar.gz'], + 'checksums': ['7ae0d8a4e10a29787e61831bac25af5c22b0bf7edb8a5efd0ab206afbb0238b4'], + }), + ('pyrle', '0.0.33', { + 'checksums': ['4c24a2e096f8dbfa4451d57ce769057e2ed6c369ee75f5dce3c4d6fa47f71a6e'], + }), + ('pyranges', '0.0.110', { + 'checksums': ['5996d22c07c490e3ad15863c63d27a225896e08700a0bcbc6e0272d071dafa5a'], + }), + (name, version, { + 'source_urls': ['https://github.com/dpeerlab/SEACells/archive/'], + 'sources': [{'download_filename': 'a3486ca.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['2e7317d975d0a0b618cbeaca95ceb61fc6abc5c8da4a7095bca763493983749e'], + 'modulename': name, + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' From 75f0d71f7c3dce0bf5bcf25644c70749ec42fadb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 5 Sep 2023 18:33:57 +0200 Subject: [PATCH 035/599] add missing checksum for typing-extensions in SEACells easyconfig --- easybuild/easyconfigs/s/SEACells/SEACells-20230731-foss-2021a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/s/SEACells/SEACells-20230731-foss-2021a.eb b/easybuild/easyconfigs/s/SEACells/SEACells-20230731-foss-2021a.eb index 7cf0a01cbbc..5d184b0d518 100644 --- a/easybuild/easyconfigs/s/SEACells/SEACells-20230731-foss-2021a.eb +++ b/easybuild/easyconfigs/s/SEACells/SEACells-20230731-foss-2021a.eb @@ -32,6 +32,7 @@ exts_list = [ }), ('typing-extensions', '4.7.1', { 'sources': ['typing_extensions-%(version)s.tar.gz'], + 'checksums': ['b75ddc264f0ba5615db7ba217daeb99701ad295353c45f9e95963337ceeeffb2'], }), ('python-utils', '3.7.0', { 'checksums': ['1970468fff1c0adbd60b9a751e6a786223a9f0373c954571912d9cf4be49b552'], From e6c3b69a06743b7a9e6519b339ecc78513061b69 Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann Date: Wed, 6 Sep 2023 10:34:45 +0000 Subject: [PATCH 036/599] flake8 compliance --- .../easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb b/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb index 812f649c339..5efbe2fe9e6 100644 --- a/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb @@ -4,7 +4,9 @@ name = 'datalad' version = "0.18.4" homepage = 'https://www.datalad.org/' -description = "DataLad is a free and open source distributed data management system that keeps track of your data, creates structure, ensures reproducibility, supports collaboration, and integrates with widely used data infrastructure." +description = "DataLad is a free and open source distributed data management system that keeps track of your data, \ +creates structure, ensures reproducibility, supports collaboration, \ +and integrates with widely used data infrastructure." toolchain = {'name': 'GCCcore', 'version': '12.2.0'} toolchainopts = {'pic': True} @@ -42,7 +44,7 @@ exts_list = [ }), ('gitlab', '3.10.0', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'checksums': ['14930a16fdd7f36f67b9373e7d4d4720e8e374800028380289db3306e9f74614'], + 'checksums': ['14930a16fdd7f36f67b9373e7d4d4720e8e374800028380289db3306e9f74614'], }), ('iso8601', '1.0.2', { 'checksums': ['27f503220e6845d9db954fb212b95b0362d8b7e6c1b2326a87061c3de93594b1'], From 3cbae9c70f123420a948da9693695346a0a01c00 Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Fri, 15 Sep 2023 10:20:14 +0000 Subject: [PATCH 037/599] adding easyconfigs: magma-2.7.2-foss-2023a-CUDA-12.1.1.eb and patches: magma-2.7.2_allow-all-sms.patch --- .../magma-2.7.2-foss-2023a-CUDA-12.1.1.eb | 43 ++++ .../m/magma/magma-2.7.2_allow-all-sms.patch | 209 ++++++++++++++++++ 2 files changed, 252 insertions(+) create mode 100644 easybuild/easyconfigs/m/magma/magma-2.7.2-foss-2023a-CUDA-12.1.1.eb create mode 100644 easybuild/easyconfigs/m/magma/magma-2.7.2_allow-all-sms.patch diff --git a/easybuild/easyconfigs/m/magma/magma-2.7.2-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/m/magma/magma-2.7.2-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..3a690766598 --- /dev/null +++ b/easybuild/easyconfigs/m/magma/magma-2.7.2-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,43 @@ +easyblock = 'CMakeMake' + +name = 'magma' +version = '2.7.2' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://icl.cs.utk.edu/magma/' +description = """The MAGMA project aims to develop a dense linear algebra library similar to + LAPACK but for heterogeneous/hybrid architectures, starting with current Multicore+GPU systems.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'pic': True, 'openmp': True} + +source_urls = ['https://icl.cs.utk.edu/projectsfiles/%(name)s/downloads/'] +sources = [SOURCE_TAR_GZ] +checksums = ['729bc1a70e518a7422fe7a3a54537a4741035a77be3349f66eac5c362576d560'] + +patches = ['%(name)s-2.7.2_allow-all-sms.patch'] + +builddependencies = [ + ('CMake', '3.26.3'), +] +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('UCX-CUDA', '1.14.1', versionsuffix), +] + +# default CUDA compute capabilities to use (override via --cuda-compute-capabilities) +cuda_compute_capabilities = ['5.0', '6.0', '7.0', '7.5', '8.0', '8.6', '9.0'] + +# make sure both static and shared libs are built +configopts = [ + '-DMKL_ILP64=ON \ + -DBUILD_SHARED_LIBS=%s \ + -DGPU_TARGET="%%(cuda_sm_space_sep)s" ' % local_shared for local_shared in ('ON', 'OFF') +] + +sanity_check_paths = { + 'files': ['lib/libmagma.%s' % SHLIB_EXT, 'lib/libmagma.a'], + 'dirs': ['include'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/magma/magma-2.7.2_allow-all-sms.patch b/easybuild/easyconfigs/m/magma/magma-2.7.2_allow-all-sms.patch new file mode 100644 index 00000000000..2adb8d87ffb --- /dev/null +++ b/easybuild/easyconfigs/m/magma/magma-2.7.2_allow-all-sms.patch @@ -0,0 +1,209 @@ +--- CMakeLists.txt.orig 2023-09-15 09:54:41.000000000 +0000 ++++ CMakeLists.txt 2023-09-15 10:01:07.000000000 +0000 +@@ -140,161 +140,14 @@ + + include_directories( ${CUDAToolkit_INCLUDE_DIRS} ) + +- if (GPU_TARGET MATCHES Fermi) +- set( GPU_TARGET "${GPU_TARGET} sm_20" ) +- endif() +- +- if (GPU_TARGET MATCHES Kepler) +- set( GPU_TARGET "${GPU_TARGET} sm_30 sm_35 sm_37" ) +- endif() +- +- if (GPU_TARGET MATCHES Maxwell) +- set( GPU_TARGET "${GPU_TARGET} sm_50" ) +- endif() +- +- if (GPU_TARGET MATCHES Pascal) +- set( GPU_TARGET "${GPU_TARGET} sm_60" ) +- endif() +- +- if (GPU_TARGET MATCHES Volta) +- set( GPU_TARGET "${GPU_TARGET} sm_70" ) +- endif() +- +- if (GPU_TARGET MATCHES Turing) +- set( GPU_TARGET "${GPU_TARGET} sm_75" ) +- endif() +- +- if (GPU_TARGET MATCHES Ampere) +- set( GPU_TARGET "${GPU_TARGET} sm_80" ) +- endif() +- +- if (GPU_TARGET MATCHES Hopper) +- set( GPU_TARGET "${GPU_TARGET} sm_90" ) +- endif() +- +- if (GPU_TARGET MATCHES sm_20) +- if (NOT MIN_ARCH) +- set( MIN_ARCH 200 ) +- endif() +- list(APPEND __cuda_architectures 20) +- message( STATUS " compile for CUDA arch 2.0 (Fermi)" ) +- endif() +- +- if (GPU_TARGET MATCHES sm_30) +- if (NOT MIN_ARCH) +- set( MIN_ARCH 300 ) +- endif() +- list(APPEND __cuda_architectures 30) +- message( STATUS " compile for CUDA arch 3.0 (Kepler)" ) +- endif() +- +- if (GPU_TARGET MATCHES sm_35) +- if (NOT MIN_ARCH) +- set( MIN_ARCH 300 ) +- endif() +- list(APPEND __cuda_architectures 35) +- message( STATUS " compile for CUDA arch 3.5 (Kepler)" ) +- endif() +- +- if (GPU_TARGET MATCHES sm_37) +- if (NOT MIN_ARCH) +- set( MIN_ARCH 300 ) +- endif() +- list(APPEND __cuda_architectures 37) +- message( STATUS " compile for CUDA arch 3.7 (Kepler)" ) +- endif() +- +- if (GPU_TARGET MATCHES sm_50) +- if (NOT MIN_ARCH) +- set( MIN_ARCH 500 ) +- endif() +- list(APPEND __cuda_architectures 50) +- message( STATUS " compile for CUDA arch 5.0 (Maxwell)" ) +- endif() +- +- if (GPU_TARGET MATCHES sm_52) +- if (NOT MIN_ARCH) +- set( MIN_ARCH 520 ) +- endif() +- list(APPEND __cuda_architectures 52) +- message( STATUS " compile for CUDA arch 5.2 (Maxwell)" ) +- endif() +- +- if (GPU_TARGET MATCHES sm_53) +- if (NOT MIN_ARCH) +- set( MIN_ARCH 530 ) +- endif() +- list(APPEND __cuda_architectures 53) +- message( STATUS " compile for CUDA arch 5.3 (Maxwell)" ) +- endif() +- +- if (GPU_TARGET MATCHES sm_60) +- if (NOT MIN_ARCH) +- set( MIN_ARCH 600 ) +- endif() +- list(APPEND __cuda_architectures 60) +- message( STATUS " compile for CUDA arch 6.0 (Pascal)" ) +- endif() +- +- if (GPU_TARGET MATCHES sm_61) +- if (NOT MIN_ARCH) +- set( MIN_ARCH 610 ) +- endif() +- list(APPEND __cuda_architectures 61) +- message( STATUS " compile for CUDA arch 6.1 (Pascal)" ) +- endif() +- +- if (GPU_TARGET MATCHES sm_62) +- if (NOT MIN_ARCH) +- set( MIN_ARCH 620 ) +- endif() +- list(APPEND __cuda_architectures 62) +- message( STATUS " compile for CUDA arch 6.2 (Pascal)" ) +- endif() +- +- if (GPU_TARGET MATCHES sm_70) +- if (NOT MIN_ARCH) +- set( MIN_ARCH 700 ) +- endif() +- list(APPEND __cuda_architectures 70) +- message( STATUS " compile for CUDA arch 7.0 (Volta)" ) +- endif() +- +- if (GPU_TARGET MATCHES sm_71) +- if (NOT MIN_ARCH) +- set( MIN_ARCH 710 ) +- endif() +- list(APPEND __cuda_architectures 71) +- message( STATUS " compile for CUDA arch 7.1 (Volta)" ) +- endif() +- +- if (GPU_TARGET MATCHES sm_75) +- if (NOT MIN_ARCH) +- set( MIN_ARCH 750 ) +- endif() +- list(APPEND __cuda_architectures 75) +- message( STATUS " compile for CUDA arch 7.5 (Turing)" ) +- endif() +- +- if (GPU_TARGET MATCHES sm_80) +- if (NOT MIN_ARCH) +- set( MIN_ARCH 800 ) +- endif() +- list(APPEND __cuda_architectures 80) +- message( STATUS " compile for CUDA arch 8.0 (Ampere)" ) +- endif() +- +- if (GPU_TARGET MATCHES sm_90) +- if (NOT MIN_ARCH) +- set( MIN_ARCH 900 ) +- endif() +- list(APPEND __cuda_architectures 90) +- message( STATUS " compile for CUDA arch 9.0 (Hopper)" ) +- endif() +- +- if (NOT MIN_ARCH) +- message( FATAL_ERROR "GPU_TARGET must contain one or more of Fermi, Kepler, Maxwell, Pascal, Volta, Turing, Ampere, or valid sm_[0-9][0-9]" ) +- endif() ++ # NVCC options for the different cards ++ # sm_xx is binary, compute_xx is PTX for forward compatability ++ # MIN_SM/MAX_SM is lowest/highest requested version ++ # NV_SM accumulates sm_xx for all requested versions ++ # NV_COMP is compute_xx for highest requested version ++ set( MIN_SM 99 ) ++ set( MAX_SM 0 ) ++ set( NV_SM "" ) + + set(CUDA_ARCHITECTURES "${__cuda_architectures}") + +@@ -312,8 +312,34 @@ + ) + endif(COMPILER_SUPPORTS_FPIC) + +- set(MAGMA_HAVE_CUDA "1") +- set(MAGMA_CUDA_ARCH_MIN "${MIN_ARCH}") ++ string( REGEX MATCHALL "sm_[0-9][0-9]" sms "${GPU_TARGET}" ) ++ list( SORT sms ) # To make output easier to reason about ++ foreach (sm IN LISTS sms) ++ string( REPLACE "sm_" "" sm "${sm}") # Remove sm_ prefix ++ if (sm LESS MIN_SM) ++ set( MIN_SM "${sm}" ) ++ endif() ++ if (sm GREATER MAX_SM) ++ set( MAX_SM "${sm}" ) ++ endif() ++ list( APPEND NV_SM -gencode arch=compute_${sm},code=sm_${sm} ) ++ string( REGEX REPLACE "([0-9])([0-9])" "\\1.\\2" cuda_arch "${sm}" ) ++ message( STATUS " compile for CUDA arch ${cuda_arch}" ) ++ endforeach() ++ ++ if (NOT NV_SM) ++ message( FATAL_ERROR ++ "GPU_TARGET must contain one or more of " ++ "Fermi, Kepler, Maxwell, Pascal, Volta, Turing, Ampere, or valid sm_[0-9][0-9]" ++ "Was: ${GPU_TARGET}" ) ++ endif() ++ ++ set( MIN_ARCH ${MIN_SM}0 ) ++ set( NV_COMP -gencode arch=compute_${MAX_SM},code=compute_${MAX_SM} ) ++ ++ list( APPEND CUDA_NVCC_FLAGS -Xcompiler -fPIC ${NV_SM} ${NV_COMP} ${FORTRAN_CONVENTION} ) ++ add_definitions( -DMAGMA_HAVE_CUDA=1 ) ++ add_definitions( -DMAGMA_CUDA_ARCH_MIN=${MIN_ARCH} ) + message( STATUS "Define -DMAGMA_HAVE_CUDA -DMAGMA_CUDA_ARCH_MIN=${MIN_ARCH}" ) + else() + message( STATUS "Could not find CUDA" ) From ba9cd3af8f833a7f25f803ba420b7957c5dd3999 Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Fri, 15 Sep 2023 12:24:45 +0200 Subject: [PATCH 038/599] Add checksum for patch --- .../m/magma/magma-2.7.2-foss-2023a-CUDA-12.1.1.eb | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/magma/magma-2.7.2-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/m/magma/magma-2.7.2-foss-2023a-CUDA-12.1.1.eb index 3a690766598..a6de0adabfc 100644 --- a/easybuild/easyconfigs/m/magma/magma-2.7.2-foss-2023a-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/m/magma/magma-2.7.2-foss-2023a-CUDA-12.1.1.eb @@ -13,9 +13,11 @@ toolchainopts = {'pic': True, 'openmp': True} source_urls = ['https://icl.cs.utk.edu/projectsfiles/%(name)s/downloads/'] sources = [SOURCE_TAR_GZ] -checksums = ['729bc1a70e518a7422fe7a3a54537a4741035a77be3349f66eac5c362576d560'] - patches = ['%(name)s-2.7.2_allow-all-sms.patch'] +checksums = [ + {'magma-2.7.2.tar.gz': '729bc1a70e518a7422fe7a3a54537a4741035a77be3349f66eac5c362576d560'}, + {'magma-2.7.2_allow-all-sms.patch': '1fe721092d0193cad7c669bd8ffaa7c093a2547967232123ffb03460742f7b98'}, +] builddependencies = [ ('CMake', '3.26.3'), From 62ac57ba816706f713403edc8f89990f7db5d8ca Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 19 Sep 2023 16:12:01 +0100 Subject: [PATCH 039/599] adding easyconfigs: FLINT-2.9.0-gfbf-2022b.eb and patches: FLINT-2.9.0-gcc-12.patch --- .../f/FLINT/FLINT-2.9.0-gcc-12.patch | 18 +++++++ .../f/FLINT/FLINT-2.9.0-gfbf-2022b.eb | 48 +++++++++++++++++++ 2 files changed, 66 insertions(+) create mode 100644 easybuild/easyconfigs/f/FLINT/FLINT-2.9.0-gcc-12.patch create mode 100644 easybuild/easyconfigs/f/FLINT/FLINT-2.9.0-gfbf-2022b.eb diff --git a/easybuild/easyconfigs/f/FLINT/FLINT-2.9.0-gcc-12.patch b/easybuild/easyconfigs/f/FLINT/FLINT-2.9.0-gcc-12.patch new file mode 100644 index 00000000000..53b39cf316d --- /dev/null +++ b/easybuild/easyconfigs/f/FLINT/FLINT-2.9.0-gcc-12.patch @@ -0,0 +1,18 @@ +Patch to run t-sdiv_qrnnd.c test with gcc-12.x compilers +See here: +https://github.com/flintlib/flint2/commit/fb8ddbcc06afa2a8f25637032fbb8211f6c6c122 +https://github.com/flintlib/flint2/issues/1175 +Author: J. Sassmannshausen (University College London/UK) +diff --git a/flint-2.9.0.orig/test/t-sdiv_qrnnd.c b/flint-2.9.0/test/t-sdiv_qrnnd.c +index 2e9822e..e2d65cd 100644 +--- a/flint-2.9.0.orig/test/t-sdiv_qrnnd.c ++++ b/flint-2.9.0/test/t-sdiv_qrnnd.c +@@ -33,7 +33,7 @@ int main(void) + { + d = n_randtest_not_zero(state); + nh = n_randtest(state); +- } while ((FLINT_ABS(nh) >= FLINT_ABS(d)/2) || (nh == WORD_MIN)); ++ } while ((nh == WORD_MIN) || (FLINT_ABS(nh) >= FLINT_ABS(d)/2)); + + nl = n_randtest(state); + diff --git a/easybuild/easyconfigs/f/FLINT/FLINT-2.9.0-gfbf-2022b.eb b/easybuild/easyconfigs/f/FLINT/FLINT-2.9.0-gfbf-2022b.eb new file mode 100644 index 00000000000..b07b543281d --- /dev/null +++ b/easybuild/easyconfigs/f/FLINT/FLINT-2.9.0-gfbf-2022b.eb @@ -0,0 +1,48 @@ +easyblock = 'CMakeMake' + +name = 'FLINT' +version = '2.9.0' + +homepage = 'https://www.flintlib.org/' + +description = """FLINT (Fast Library for Number Theory) is a C library in support of computations + in number theory. Operations that can be performed include conversions, arithmetic, computing GCDs, + factoring, solving linear systems, and evaluating special functions. In addition, FLINT provides + various low-level routines for fast arithmetic. FLINT is extensively documented and tested.""" + +toolchain = {'name': 'gfbf', 'version': '2022b'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.flintlib.org'] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + '%(name)s-2.8.4_find_flexiblas.patch', + '%(name)s-%(version)s-gcc-12.patch', +] +checksums = [ + {'flint-2.9.0.tar.gz': '2fc090d51033c93208e6c10d406397a53c983ae5343b958eb25f72a57a4ce76a'}, + {'FLINT-2.8.4_find_flexiblas.patch': '35a3db14646daf584449f2b9c6880b66e7b082a665eba56234230610bab77c6e'}, + {'FLINT-2.9.0-gcc-12.patch': 'c253f0353eea129fab70e055b0fdee0d23ec391df03d1689503540c97d5432fb'}, +] + +builddependencies = [ + ('CMake', '3.24.3'), + ('Python', '3.10.8'), +] + +dependencies = [ + ('GMP', '6.2.1'), + ('MPFR', '4.2.0'), + ('NTL', '11.5.1'), +] + +configopts = '-DWITH_NTL=on -DBUILD_TESTING=yes' + +runtest = 'test' + +sanity_check_paths = { + 'files': ['lib/lib%%(namelower)s.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'math' From 24b0be4f4a574dbdb4f66ea40ff89ff124a08af4 Mon Sep 17 00:00:00 2001 From: SebastianAchilles Date: Wed, 20 Sep 2023 22:44:37 +0200 Subject: [PATCH 040/599] Add description to magma-2.7.2_allow-all-sms.patch --- .../easyconfigs/m/magma/magma-2.7.2_allow-all-sms.patch | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/easybuild/easyconfigs/m/magma/magma-2.7.2_allow-all-sms.patch b/easybuild/easyconfigs/m/magma/magma-2.7.2_allow-all-sms.patch index 2adb8d87ffb..5b78a3f229e 100644 --- a/easybuild/easyconfigs/m/magma/magma-2.7.2_allow-all-sms.patch +++ b/easybuild/easyconfigs/m/magma/magma-2.7.2_allow-all-sms.patch @@ -1,3 +1,11 @@ +This allows to process any sm_xx passed to GPU_TARGET. Previously some were silently ignored +See https://bitbucket.org/icl/magma/issues/32/list-of-whitelisted-sm_-values-for-cuda-is +and https://bitbucket.org/icl/magma/pull-requests/5 + +Author: Alexander Grund (TU Dresden) +Updated to 2.6.1: micketeer@gmail.com +Updated to 2.7.2: Alexandre Strube (JSC) + --- CMakeLists.txt.orig 2023-09-15 09:54:41.000000000 +0000 +++ CMakeLists.txt 2023-09-15 10:01:07.000000000 +0000 @@ -140,161 +140,14 @@ From 1364b19a985b11a919f19c98bf005647585213b3 Mon Sep 17 00:00:00 2001 From: SebastianAchilles Date: Wed, 20 Sep 2023 22:48:03 +0200 Subject: [PATCH 041/599] Update checksum in magma-2.7.2-foss-2023a-CUDA-12.1.1.eb --- .../easyconfigs/m/magma/magma-2.7.2-foss-2023a-CUDA-12.1.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/magma/magma-2.7.2-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/m/magma/magma-2.7.2-foss-2023a-CUDA-12.1.1.eb index a6de0adabfc..19a155367dd 100644 --- a/easybuild/easyconfigs/m/magma/magma-2.7.2-foss-2023a-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/m/magma/magma-2.7.2-foss-2023a-CUDA-12.1.1.eb @@ -16,7 +16,7 @@ sources = [SOURCE_TAR_GZ] patches = ['%(name)s-2.7.2_allow-all-sms.patch'] checksums = [ {'magma-2.7.2.tar.gz': '729bc1a70e518a7422fe7a3a54537a4741035a77be3349f66eac5c362576d560'}, - {'magma-2.7.2_allow-all-sms.patch': '1fe721092d0193cad7c669bd8ffaa7c093a2547967232123ffb03460742f7b98'}, + {'magma-2.7.2_allow-all-sms.patch': '2996485844d7e199ea57eaebf59903d3514a03536f82b655ce30de480e28b828'}, ] builddependencies = [ From adeb24cee8cadce60deb77707870870ed067274f Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann Date: Thu, 21 Sep 2023 12:18:18 +0000 Subject: [PATCH 042/599] slightly better formatting --- .../easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb b/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb index 5efbe2fe9e6..352d18ee6e2 100644 --- a/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb @@ -43,14 +43,14 @@ exts_list = [ 'checksums': ['ea0d3b40a2d852767be77ca343b58a9e3a4b00d9db440efb8da74b4e58025e5a'], }), ('gitlab', '3.10.0', { - 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'checksums': ['14930a16fdd7f36f67b9373e7d4d4720e8e374800028380289db3306e9f74614'], + 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + 'checksums': ['14930a16fdd7f36f67b9373e7d4d4720e8e374800028380289db3306e9f74614'], }), ('iso8601', '1.0.2', { 'checksums': ['27f503220e6845d9db954fb212b95b0362d8b7e6c1b2326a87061c3de93594b1'], }), (name, version, { - 'checksums': ['d832f3d70b79b7b66519ca30315791a6a265bdf8a86ddac5846489b75385cb09'], + 'checksums': ['d832f3d70b79b7b66519ca30315791a6a265bdf8a86ddac5846489b75385cb09'], }), ] From b760928eb9d8b11aab9e6e0a10944d5630b10f77 Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann Date: Thu, 21 Sep 2023 12:40:40 +0000 Subject: [PATCH 043/599] flake8 too much indent --- .../datalad/datalad-0.18.4-GCCcore-12.2.0.eb | 22 +++++++++---------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb b/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb index 352d18ee6e2..600999ca8c5 100644 --- a/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb @@ -24,33 +24,33 @@ use_pip = True exts_list = [ ('humanize', '3.13.1', { - 'checksums': ['12f113f2e369dac7f35d3823f49262934f4a22a53a6d3d4c86b736f50db88c7b'], + 'checksums': ['12f113f2e369dac7f35d3823f49262934f4a22a53a6d3d4c86b736f50db88c7b'], }), ('fasteners', '0.18', { - 'checksums': ['cb7c13ef91e0c7e4fe4af38ecaf6b904ec3f5ce0dda06d34924b6b74b869d953'], + 'checksums': ['cb7c13ef91e0c7e4fe4af38ecaf6b904ec3f5ce0dda06d34924b6b74b869d953'], }), ('patoolib', '1.12', { - 'source_tmpl': 'patool-%(version)s.tar.gz', - 'checksums': ['e3180cf8bfe13bedbcf6f5628452fca0c2c84a3b5ae8c2d3f55720ea04cb1097'], + 'source_tmpl': 'patool-%(version)s.tar.gz', + 'checksums': ['e3180cf8bfe13bedbcf6f5628452fca0c2c84a3b5ae8c2d3f55720ea04cb1097'], }), ('annexremote', '1.6.0', { - 'checksums': ['779a43e5b1b4afd294761c6587dee8ac68f453a5a8cc40f419e9ca777573ae84'], + 'checksums': ['779a43e5b1b4afd294761c6587dee8ac68f453a5a8cc40f419e9ca777573ae84'], }), ('looseversion', '1.2.0', { - 'checksums': ['c64e71c0b29030683b4ea75aee431db2d25c4e6e533590e52129f1d9e51de204'], + 'checksums': ['c64e71c0b29030683b4ea75aee431db2d25c4e6e533590e52129f1d9e51de204'], }), ('boto', '2.49.0', { - 'checksums': ['ea0d3b40a2d852767be77ca343b58a9e3a4b00d9db440efb8da74b4e58025e5a'], + 'checksums': ['ea0d3b40a2d852767be77ca343b58a9e3a4b00d9db440efb8da74b4e58025e5a'], }), ('gitlab', '3.10.0', { - 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'checksums': ['14930a16fdd7f36f67b9373e7d4d4720e8e374800028380289db3306e9f74614'], + 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + 'checksums': ['14930a16fdd7f36f67b9373e7d4d4720e8e374800028380289db3306e9f74614'], }), ('iso8601', '1.0.2', { - 'checksums': ['27f503220e6845d9db954fb212b95b0362d8b7e6c1b2326a87061c3de93594b1'], + 'checksums': ['27f503220e6845d9db954fb212b95b0362d8b7e6c1b2326a87061c3de93594b1'], }), (name, version, { - 'checksums': ['d832f3d70b79b7b66519ca30315791a6a265bdf8a86ddac5846489b75385cb09'], + 'checksums': ['d832f3d70b79b7b66519ca30315791a6a265bdf8a86ddac5846489b75385cb09'], }), ] From 204feddba284309440d7e6074443cdab33bab290 Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann Date: Thu, 21 Sep 2023 17:00:22 +0000 Subject: [PATCH 044/599] add binutils as build dep --- .../easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb b/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb index 600999ca8c5..ac18265b966 100644 --- a/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb @@ -11,6 +11,10 @@ and integrates with widely used data infrastructure." toolchain = {'name': 'GCCcore', 'version': '12.2.0'} toolchainopts = {'pic': True} +build_dependecies = [ + ('binutils', '2.39') +] + dependencies = [ ('git-annex', '10.20230802'), ('Python', '3.10.8'), From c4942cdd92c825deadf586b7b1973dae215ff4ff Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann <82444481+jkuhl-uni@users.noreply.github.com> Date: Thu, 21 Sep 2023 19:12:59 +0200 Subject: [PATCH 045/599] small typo --- .../easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb b/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb index ac18265b966..d9888971561 100644 --- a/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb @@ -11,7 +11,7 @@ and integrates with widely used data infrastructure." toolchain = {'name': 'GCCcore', 'version': '12.2.0'} toolchainopts = {'pic': True} -build_dependecies = [ +builddependecies = [ ('binutils', '2.39') ] From a3ab0c97be2c868b1ce0aae9653b041a0b7fbae2 Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann Date: Thu, 21 Sep 2023 17:33:51 +0000 Subject: [PATCH 046/599] other small tapo --- .../easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb b/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb index d9888971561..8f48ebf11cb 100644 --- a/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb @@ -11,7 +11,7 @@ and integrates with widely used data infrastructure." toolchain = {'name': 'GCCcore', 'version': '12.2.0'} toolchainopts = {'pic': True} -builddependecies = [ +builddependencies = [ ('binutils', '2.39') ] From b53d9ce3db364d771d8d4c17731eca8d69713719 Mon Sep 17 00:00:00 2001 From: c3-builder Date: Mon, 25 Sep 2023 10:29:24 +0200 Subject: [PATCH 047/599] adding easyconfigs: SuiteSparse-7.1.0-foss-2023a.eb --- .../SuiteSparse-7.1.0-foss-2023a.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-7.1.0-foss-2023a.eb diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-7.1.0-foss-2023a.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-7.1.0-foss-2023a.eb new file mode 100644 index 00000000000..8eea586e45f --- /dev/null +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-7.1.0-foss-2023a.eb @@ -0,0 +1,25 @@ +name = 'SuiteSparse' +version = '7.1.0' + +homepage = 'https://faculty.cse.tamu.edu/davis/suitesparse.html' +description = """SuiteSparse is a collection of libraries to manipulate sparse matrices.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'unroll': True, 'pic': True} + +source_urls = ['https://github.com/DrTimothyAldenDavis/SuiteSparse/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['4cd3d161f9aa4f98ec5fa725ee5dc27bca960a3714a707a7d12b3d0abb504679'] + +builddependencies = [ + ('CMake', '3.26.3'), + # ('M4', '1.4.19'), +] + +dependencies = [ + ('MPFR', '4.2.0'), +] + +prebuildopts = 'CMAKE_OPTIONS="-DCMAKE_INSTALL_PREFIX=%(installdir)s -DBLA_VENDOR=FlexiBLAS"' + +moduleclass = 'numlib' From 2640e1af0a85ff68381dffd6306a7b969ee38c5b Mon Sep 17 00:00:00 2001 From: xina Date: Tue, 26 Sep 2023 21:05:33 +0200 Subject: [PATCH 048/599] adding easyconfigs: Molden-7.3-GCCcore-12.3.0.eb and patches: Molden-7.3_fix_arg_handling.patch, Molden-7.3_fix_makefile_for_easybuild.patch --- .../m/Molden/Molden-7.3-GCCcore-12.3.0.eb | 48 ++++++++++++ .../Molden/Molden-7.3_fix_arg_handling.patch | 22 ++++++ ...olden-7.3_fix_makefile_for_easybuild.patch | 78 +++++++++++++++++++ 3 files changed, 148 insertions(+) create mode 100644 easybuild/easyconfigs/m/Molden/Molden-7.3-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/m/Molden/Molden-7.3_fix_arg_handling.patch create mode 100644 easybuild/easyconfigs/m/Molden/Molden-7.3_fix_makefile_for_easybuild.patch diff --git a/easybuild/easyconfigs/m/Molden/Molden-7.3-GCCcore-12.3.0.eb b/easybuild/easyconfigs/m/Molden/Molden-7.3-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..f5a1c0e9c91 --- /dev/null +++ b/easybuild/easyconfigs/m/Molden/Molden-7.3-GCCcore-12.3.0.eb @@ -0,0 +1,48 @@ +easyblock = 'MakeCp' + +name = 'Molden' +version = '7.3' + +homepage = 'https://www.theochem.ru.nl/molden/' +description = """Molden is a package for displaying Molecular Density from the + Ab Initio packages GAMESS-UK, GAMESS-US and GAUSSIAN and the Semi-Empirical + packages Mopac/Ampac""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://ftp.science.ru.nl/Molden/'] +sources = ['%(namelower)s%(version)s.tar.gz'] +patches = [ + 'Molden-7.3_fix_makefile_for_easybuild.patch', + 'Molden-7.3_fix_arg_handling.patch', +] +checksums = [ + {'molden7.3.tar.gz': '870f4fa6635229791bb09bbbd07f51456b2c90101d73564dc47ed7769b8c07a1'}, + {'Molden-7.3_fix_makefile_for_easybuild.patch': '303dcd308dfb618088d014ea2956ec627d9f09b6547d547ac4b432be4e5b9d7c'}, + {'Molden-7.3_fix_arg_handling.patch': '869eb33ea4cdd022402251b59386c146e7ceaf85f838f2a002fb4c393db4c1c2'}, +] + +builddependencies = [ + ('binutils', '2.40'), + ('makedepend', '1.0.7'), +] + +dependencies = [ + ('X11', '20230603'), + ('libglvnd', '1.6.0'), + ('libGLU', '9.0.3'), +] + +buildopts = 'CC="$CC" FC="$F90" FFLAGS="$FFLAGS -fallow-argument-mismatch" all' + +parallel = 1 + +files_to_copy = [(['bin/%s' % x for x in ['ambfor', 'ambmd', 'gmolden', 'molden', 'surf']], 'bin'), + 'CopyRight', 'README', 'REGISTER'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['ambfor', 'ambmd', 'gmolden', 'molden', 'surf']] + ['README', 'REGISTER'], + 'dirs': [], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/m/Molden/Molden-7.3_fix_arg_handling.patch b/easybuild/easyconfigs/m/Molden/Molden-7.3_fix_arg_handling.patch new file mode 100644 index 00000000000..1b0d21594ec --- /dev/null +++ b/easybuild/easyconfigs/m/Molden/Molden-7.3_fix_arg_handling.patch @@ -0,0 +1,22 @@ +diff -ruN molden7.3.orig/src/molden.f molden7.3/src/molden.f +--- molden7.3.orig/src/molden.f 2023-08-09 15:22:58.503993000 +0200 ++++ molden7.3/src/molden.f 2023-09-26 20:13:01.426339279 +0200 +@@ -3814,15 +3814,15 @@ + endif + + iredir = 0 +- nargs = iargc() +- call getarg(0,liris) ++ nargs = COMMAND_ARGUMENT_COUNT() ++ call GET_COMMAND_ARGUMENT(0,liris) + call parsfn(liris,linlen(liris),20) + + ntargs = 0 + n = 0 + if (nargs.gt.0) then + 2013 n = n + 1 +- call getarg(n,liris) ++ call GET_COMMAND_ARGUMENT(n,liris) + if (liris(1:1).eq.'-') then + if (liris(1:2).eq.'-5') ido5d = 1 + if (liris(1:2).eq.'-7') ido7f = 1 diff --git a/easybuild/easyconfigs/m/Molden/Molden-7.3_fix_makefile_for_easybuild.patch b/easybuild/easyconfigs/m/Molden/Molden-7.3_fix_makefile_for_easybuild.patch new file mode 100644 index 00000000000..595dfb9a0e0 --- /dev/null +++ b/easybuild/easyconfigs/m/Molden/Molden-7.3_fix_makefile_for_easybuild.patch @@ -0,0 +1,78 @@ +diff -ruN molden7.3.orig/makefile molden7.3/makefile +--- molden7.3.orig/makefile 2023-08-09 15:22:58.725188000 +0200 ++++ molden7.3/makefile 2023-09-26 20:29:25.276603201 +0200 +@@ -13,10 +13,10 @@ + # Disregard compiler warnings on rdmolf.f + # + # +-CC = cc ++#CC = cc + LIBS = -lX11 -lm + LDR = ${FC} +-LIBSG = -L/usr/X11R6/lib -lGLU -lGL -lXmu -lX11 -lm ++LIBSG = -lGLU -lGL -lXmu -lX11 -lm + ARCH := $(shell getconf LONG_BIT) + AFLAG= -m$(ARCH) + EXTEN= +@@ -29,19 +29,6 @@ + uname := $(shell uname -s) + os := + +-ifeq ($(uname), Linux) +- os := $(shell head -n 1 /etc/issue | cut -d" " -f1) +- ifeq ($(os), Ubuntu) +- EXTEN = exten +- EXTENZ = exten2 +- LIBSG = -L/usr/X11R6/lib -lGLU -lGL -lX11 -lm +- endif +- ifeq ($(os), Debian) +- LIBSG = -L/usr/lib/X11 -lGLU -lGL -lX11 -lm +- endif +- +- choosefc := 'yes' +-endif + + ifneq (,$(findstring CYGWIN,$(uname))) + uname := Linux +@@ -53,17 +40,6 @@ + endif + + +-ifneq ($(choosefc), $(empty)) +- comg77 := $(shell which g77 | grep -i g77) +- comgfort := $(shell which gfortran | grep -i gfortran) +- ifneq ($(comg77), $(empty)) +- FC = g77 +- endif +- ifneq ($(comgfort), $(empty)) +- FC = gfortran +- endif +-endif +- + print-% : ; @echo $* = $($*) + # + # Linux version +@@ -109,17 +85,17 @@ + endif + #FFLAGS = -g ${AFLAG} + FFLAGS += -g ${AFLAG} +-LIBS = -L/usr/X11R6/lib -lX11 -lm ++LIBS = -lX11 -lm + ifeq ($(AFLAG),"-m64") +-LIBS = -L/usr/X11R6/lib64 -lX11 -lm ++LIBS = -lX11 -lm + endif + LDR = ${FC} -g ${AFLAG} +-CFLAGS = ${AFLAG} ${EXTRAZ} -c -g -I/usr/X11R6/include -DDOBACK -DHASTIMER -DCOLOR_OFFSET=0.0 ++CFLAGS = ${AFLAG} ${EXTRAZ} -c -g -DDOBACK -DHASTIMER -DCOLOR_OFFSET=0.0 + ifeq ($(os), Debian) +- CFLAGS = ${AFLAG} ${EXTRAZ} -c -I/usr/include/X11 -DDOBACK -DHASTIMER -DCOLOR_OFFSET=0.0 +- LIBS = -L/usr/lib/X11 -lX11 -lm ++ CFLAGS = ${AFLAG} ${EXTRAZ} -c -DDOBACK -DHASTIMER -DCOLOR_OFFSET=0.0 ++ LIBS = -lX11 -lm + ifeq ($(AFLAG),"-m64") +- LIBS = -L/usr/X11R6/lib64 -lX11 -lm ++ LIBS = -lX11 -lm + endif + endif + ifeq ($(os), FreeBSD) From 88ddaa5e15112aa1ad12d1426375c4a38866fc23 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 29 Sep 2023 15:46:31 +0200 Subject: [PATCH 049/599] adding easyconfigs: HPCC-1.5.0-foss-2022a.eb and patches: HPCC-1.5.0_fix_recent_mpi.patch --- .../h/HPCC/HPCC-1.5.0-foss-2022a.eb | 24 +++++++++ .../h/HPCC/HPCC-1.5.0_fix_recent_mpi.patch | 51 +++++++++++++++++++ 2 files changed, 75 insertions(+) create mode 100644 easybuild/easyconfigs/h/HPCC/HPCC-1.5.0-foss-2022a.eb create mode 100644 easybuild/easyconfigs/h/HPCC/HPCC-1.5.0_fix_recent_mpi.patch diff --git a/easybuild/easyconfigs/h/HPCC/HPCC-1.5.0-foss-2022a.eb b/easybuild/easyconfigs/h/HPCC/HPCC-1.5.0-foss-2022a.eb new file mode 100644 index 00000000000..ed86b442b73 --- /dev/null +++ b/easybuild/easyconfigs/h/HPCC/HPCC-1.5.0-foss-2022a.eb @@ -0,0 +1,24 @@ +name = 'HPCC' +version = '1.5.0' + +homepage = 'https://hpcchallenge.org/' +description = """ +HPC Challenge is a benchmark suite that measures a range memory access +patterns. The HPC Challenge benchmark consists of basically 7 tests: HPL, +DGEMM, STREAM, PTRANS, RandomAccess, FFT, Communication bandwidth and latency +""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://hpcchallenge.org/projectsfiles/hpcc/download/'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['%(name)s-%(version)s_fix_recent_mpi.patch'] +checksums = [ + {'hpcc-1.5.0.tar.gz': '0a6fef7ab9f3347e549fed65ebb98234feea9ee18aea0c8f59baefbe3cf7ffb8'}, + {'HPCC-1.5.0_fix_recent_mpi.patch': '56f1e48af423dea3b78f5614fe102586a1da7c951d6959c26e359ca1e6ad8066'}, +] + +parallel = 1 + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/HPCC/HPCC-1.5.0_fix_recent_mpi.patch b/easybuild/easyconfigs/h/HPCC/HPCC-1.5.0_fix_recent_mpi.patch new file mode 100644 index 00000000000..8f73d442794 --- /dev/null +++ b/easybuild/easyconfigs/h/HPCC/HPCC-1.5.0_fix_recent_mpi.patch @@ -0,0 +1,51 @@ +Fix build error with recent MPI version +https://github.com/icl-utk-edu/hpcc/commit/d2b9a19b4498fdced2860f3394c03f27714b6160 +From d71a04d69c727b9baf0a78bb445db3ffc4ab4c91 Mon Sep 17 00:00:00 2001 +From: Francois Mazen +Date: Sat, 15 May 2021 14:49:14 +0200 +Subject: [PATCH] Apply debian patch. + +--- + hpl/src/comm/HPL_packL.c | 8 ++++---- + 1 file changed, 4 insertions(+), 4 deletions(-) + +diff --git a/hpl/src/comm/HPL_packL.c b/hpl/src/comm/HPL_packL.c +index ddfa230..948c08d 100644 +--- a/hpl/src/comm/HPL_packL.c ++++ b/hpl/src/comm/HPL_packL.c +@@ -169,7 +169,7 @@ int HPL_packL + type[nbufs] = MPI_DOUBLE; + blen[nbufs] = m1; + if( ierr == MPI_SUCCESS ) +- ierr = MPI_Address( bufs[nbufs], &disp[nbufs] ); ++ ierr = MPI_Get_address( bufs[nbufs], &disp[nbufs] ); + + nbufs++; len -= m1; j1++; ibuf += m1; + /* +@@ -183,7 +183,7 @@ int HPL_packL + type[nbufs] = MPI_DOUBLE; + blen[nbufs] = m1; + if( ierr == MPI_SUCCESS ) +- ierr = MPI_Address( bufs[nbufs], &disp[nbufs] ); ++ ierr = MPI_Get_address( bufs[nbufs], &disp[nbufs] ); + + nbufs++; len -= m1; j1++; ibuf += m1; + } +@@ -197,7 +197,7 @@ int HPL_packL + type[nbufs] = MPI_DOUBLE; + blen[nbufs] = len; + if( ierr == MPI_SUCCESS ) +- ierr = MPI_Address( bufs[nbufs], &disp[nbufs] ); ++ ierr = MPI_Get_address( bufs[nbufs], &disp[nbufs] ); + nbufs++; + } + +@@ -208,7 +208,7 @@ int HPL_packL + * construct the struct type + */ + if( ierr == MPI_SUCCESS ) +- ierr = MPI_Type_struct( nbufs, blen, disp, type, ++ ierr = MPI_Type_create_struct( nbufs, blen, disp, type, + &PANEL->dtypes[IBUF] ); + /* + * release temporaries From 23f1e17a5df21c51140243b4c8de1a962e17b785 Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann Date: Mon, 2 Oct 2023 09:01:52 +0000 Subject: [PATCH 050/599] Made Rust a build dependency --- .../easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb b/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb index 8f48ebf11cb..7e268e45acb 100644 --- a/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb @@ -12,7 +12,8 @@ toolchain = {'name': 'GCCcore', 'version': '12.2.0'} toolchainopts = {'pic': True} builddependencies = [ - ('binutils', '2.39') + ('binutils', '2.39'), + ('Rust', '1.65.0'), ] dependencies = [ @@ -20,7 +21,6 @@ dependencies = [ ('Python', '3.10.8'), ('tqdm', '4.64.1'), ('PLY', '3.11'), - ('Rust', '1.65.0'), ('scikit-build', '0.17.2'), ] From 7938783d5c5259dd9b9a1e32ba52fa41f72ed1ff Mon Sep 17 00:00:00 2001 From: Xin An <34663977+xinan1911@users.noreply.github.com> Date: Tue, 3 Oct 2023 10:56:34 +0200 Subject: [PATCH 051/599] Update Molden-7.3_fix_arg_handling.patch description --- .../easyconfigs/m/Molden/Molden-7.3_fix_arg_handling.patch | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/m/Molden/Molden-7.3_fix_arg_handling.patch b/easybuild/easyconfigs/m/Molden/Molden-7.3_fix_arg_handling.patch index 1b0d21594ec..1893f4a7798 100644 --- a/easybuild/easyconfigs/m/Molden/Molden-7.3_fix_arg_handling.patch +++ b/easybuild/easyconfigs/m/Molden/Molden-7.3_fix_arg_handling.patch @@ -1,3 +1,5 @@ +# Use F2003 functions for argument handling. +# Author: xinan1911 (SURF) diff -ruN molden7.3.orig/src/molden.f molden7.3/src/molden.f --- molden7.3.orig/src/molden.f 2023-08-09 15:22:58.503993000 +0200 +++ molden7.3/src/molden.f 2023-09-26 20:13:01.426339279 +0200 From d5247e411177bfc200b3ef48124c03074f2be1da Mon Sep 17 00:00:00 2001 From: Xin An <34663977+xinan1911@users.noreply.github.com> Date: Tue, 3 Oct 2023 10:58:37 +0200 Subject: [PATCH 052/599] Update Molden-7.3_fix_makefile_for_easybuild.patch description --- .../m/Molden/Molden-7.3_fix_makefile_for_easybuild.patch | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/m/Molden/Molden-7.3_fix_makefile_for_easybuild.patch b/easybuild/easyconfigs/m/Molden/Molden-7.3_fix_makefile_for_easybuild.patch index 595dfb9a0e0..96b975e97a5 100644 --- a/easybuild/easyconfigs/m/Molden/Molden-7.3_fix_makefile_for_easybuild.patch +++ b/easybuild/easyconfigs/m/Molden/Molden-7.3_fix_makefile_for_easybuild.patch @@ -1,3 +1,5 @@ +# Make makefile EasyBuild friendly. +# Author: xinan1911 (SURF) diff -ruN molden7.3.orig/makefile molden7.3/makefile --- molden7.3.orig/makefile 2023-08-09 15:22:58.725188000 +0200 +++ molden7.3/makefile 2023-09-26 20:29:25.276603201 +0200 From 1a15501ad2fb51456b97e6187d831d94799bb43c Mon Sep 17 00:00:00 2001 From: Xin An <34663977+xinan1911@users.noreply.github.com> Date: Tue, 3 Oct 2023 11:33:38 +0200 Subject: [PATCH 053/599] Update checksums and sanity check commands Molden-7.3-GCCcore-12.3.0.eb checksums are updated via --inject-checksums locally after changing the patch file description. Sanity check command is added after testing locally. --- .../easyconfigs/m/Molden/Molden-7.3-GCCcore-12.3.0.eb | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/Molden/Molden-7.3-GCCcore-12.3.0.eb b/easybuild/easyconfigs/m/Molden/Molden-7.3-GCCcore-12.3.0.eb index f5a1c0e9c91..7d73969a3f7 100644 --- a/easybuild/easyconfigs/m/Molden/Molden-7.3-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/m/Molden/Molden-7.3-GCCcore-12.3.0.eb @@ -18,8 +18,8 @@ patches = [ ] checksums = [ {'molden7.3.tar.gz': '870f4fa6635229791bb09bbbd07f51456b2c90101d73564dc47ed7769b8c07a1'}, - {'Molden-7.3_fix_makefile_for_easybuild.patch': '303dcd308dfb618088d014ea2956ec627d9f09b6547d547ac4b432be4e5b9d7c'}, - {'Molden-7.3_fix_arg_handling.patch': '869eb33ea4cdd022402251b59386c146e7ceaf85f838f2a002fb4c393db4c1c2'}, + {'Molden-7.3_fix_makefile_for_easybuild.patch': 'b97d794cf92978d151d70485250367eebf719885c6a909ca3404a800903e3f7a'}, + {'Molden-7.3_fix_arg_handling.patch': 'e7d0654a7c7a0b069ff4a904d3334ea19f6b0147003bc460745db8b8d5f931cf'}, ] builddependencies = [ @@ -45,4 +45,8 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = [ +"molden -h" +] + moduleclass = 'chem' From 21bac8cbaf13f4baf4ecf5508f4435cea53d2f25 Mon Sep 17 00:00:00 2001 From: xina Date: Fri, 6 Oct 2023 10:55:24 +0200 Subject: [PATCH 054/599] adding easyconfigs: waLBerla-6.1-foss-2021a.eb --- .../w/waLBerla/waLBerla-6.1-foss-2021a.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb diff --git a/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb b/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb new file mode 100644 index 00000000000..94771f62def --- /dev/null +++ b/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb @@ -0,0 +1,39 @@ +# easyconfig file for waLBerla v6.1 + +easyblock = 'CMakeMake' + + +name = 'waLBerla' +version = '6.1' + +homepage = "https://walberla.net/index.html" +description = '''Widely applicable Lattics-Boltzmann from Erlangen is a +block-structured high-performance framework for multiphysics simulations''' + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = ['https://i10git.cs.fau.de/walberla/walberla/-/archive/v6.1'] +sources = ['%(name)s-v%(version)s.tar.gz'] +checksums = ['f0acdd9ad6543bc9306c8aae953dd5065986271d4398916ae0469db8b21c007a'] + +builddependencies = [('CMake', '3.20.1')] + +dependencies = [ + ('pybind11', '2.6.2'), + ('Python', '3.9.5') +] + +parallel = 1 + +configopts = "-WALBERLA_BUILD_WITH_PYTHON=ON -WALBERLA_BUILD_SHOWCASES=OFF -WALBERLA_BUILD_DOC=OFF" + + +sanity_check_paths = { + 'files': ['walberla/waLBerlaDefinitions.h'], + 'dirs': [''], +} + +moduleclass = 'chem' + + From c9faffbfcedf63d874c6c6ebeddd2e8024e034d4 Mon Sep 17 00:00:00 2001 From: Xin An <34663977+xinan1911@users.noreply.github.com> Date: Fri, 6 Oct 2023 11:24:53 +0200 Subject: [PATCH 055/599] Update waLBerla-6.1-foss-2021a.eb delete empty space and adjust indentation --- .../easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb b/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb index 94771f62def..063f5569218 100644 --- a/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb +++ b/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb @@ -20,8 +20,8 @@ checksums = ['f0acdd9ad6543bc9306c8aae953dd5065986271d4398916ae0469db8b21c007a'] builddependencies = [('CMake', '3.20.1')] dependencies = [ - ('pybind11', '2.6.2'), - ('Python', '3.9.5') + ('pybind11', '2.6.2'), + ('Python', '3.9.5'), ] parallel = 1 @@ -30,10 +30,8 @@ configopts = "-WALBERLA_BUILD_WITH_PYTHON=ON -WALBERLA_BUILD_SHOWCASES=OFF -WALB sanity_check_paths = { - 'files': ['walberla/waLBerlaDefinitions.h'], - 'dirs': [''], + 'files': ['walberla/waLBerlaDefinitions.h'], + 'dirs': [''], } moduleclass = 'chem' - - From 83377364e0c47c0acd964ca5a1127eedac2f0b13 Mon Sep 17 00:00:00 2001 From: Xin An <34663977+xinan1911@users.noreply.github.com> Date: Fri, 6 Oct 2023 11:53:16 +0200 Subject: [PATCH 056/599] Update waLBerla-6.1-foss-2021a.eb try to fix test error --- easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb b/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb index 063f5569218..c7bf9300968 100644 --- a/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb +++ b/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb @@ -1,8 +1,6 @@ # easyconfig file for waLBerla v6.1 - easyblock = 'CMakeMake' - name = 'waLBerla' version = '6.1' @@ -28,7 +26,6 @@ parallel = 1 configopts = "-WALBERLA_BUILD_WITH_PYTHON=ON -WALBERLA_BUILD_SHOWCASES=OFF -WALBERLA_BUILD_DOC=OFF" - sanity_check_paths = { 'files': ['walberla/waLBerlaDefinitions.h'], 'dirs': [''], From eb196705dd561c76e118100fbb49ab5db539da22 Mon Sep 17 00:00:00 2001 From: Xin An <34663977+xinan1911@users.noreply.github.com> Date: Fri, 6 Oct 2023 15:33:31 +0200 Subject: [PATCH 057/599] Update easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb Co-authored-by: Simon Branford <4967+branfosj@users.noreply.github.com> --- easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb b/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb index c7bf9300968..de18588bccc 100644 --- a/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb +++ b/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb @@ -5,8 +5,8 @@ name = 'waLBerla' version = '6.1' homepage = "https://walberla.net/index.html" -description = '''Widely applicable Lattics-Boltzmann from Erlangen is a -block-structured high-performance framework for multiphysics simulations''' +description = """Widely applicable Lattics-Boltzmann from Erlangen is a +block-structured high-performance framework for multiphysics simulations""" toolchain = {'name': 'foss', 'version': '2021a'} toolchainopts = {'usempi': True, 'pic': True} From 4f9f88c2c199bee3a0dd5a4dbc8c8f522f2e3f20 Mon Sep 17 00:00:00 2001 From: Xin An <34663977+xinan1911@users.noreply.github.com> Date: Fri, 6 Oct 2023 15:40:31 +0200 Subject: [PATCH 058/599] Update waLBerla-6.1-foss-2021a.eb update python path and cmake configuration --- easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb b/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb index de18588bccc..6a5cdbc14e3 100644 --- a/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb +++ b/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb @@ -24,7 +24,10 @@ dependencies = [ parallel = 1 -configopts = "-WALBERLA_BUILD_WITH_PYTHON=ON -WALBERLA_BUILD_SHOWCASES=OFF -WALBERLA_BUILD_DOC=OFF" +configopts = "-DWALBERLA_BUILD_WITH_PYTHON=ON " +configopts += "-DWALBERLA_BUILD_SHOWCASES=OFF " +configopts += "-DWALBERLA_BUILD_DOC=OFF " +configopts += "-DPython_ROOT_DIR=$EBROOTPYTHON " sanity_check_paths = { 'files': ['walberla/waLBerlaDefinitions.h'], From 317c78dd2f3e23e414e2b812bb29bc87bc63c10f Mon Sep 17 00:00:00 2001 From: Xin An <34663977+xinan1911@users.noreply.github.com> Date: Mon, 9 Oct 2023 11:24:51 +0200 Subject: [PATCH 059/599] Update waLBerla-6.1-foss-2021a.eb add Boost.MPI dependency --- easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb b/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb index 6a5cdbc14e3..44b93328579 100644 --- a/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb +++ b/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb @@ -20,6 +20,7 @@ builddependencies = [('CMake', '3.20.1')] dependencies = [ ('pybind11', '2.6.2'), ('Python', '3.9.5'), + ('Boost.MPI', '1.76.0'), ] parallel = 1 From 790b4246ded9a6d88dad599cb504fb0378cf24fb Mon Sep 17 00:00:00 2001 From: Xin An <34663977+xinan1911@users.noreply.github.com> Date: Tue, 17 Oct 2023 13:04:20 +0200 Subject: [PATCH 060/599] Update Molden-7.3-GCCcore-12.3.0.eb fix indentation --- easybuild/easyconfigs/m/Molden/Molden-7.3-GCCcore-12.3.0.eb | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/m/Molden/Molden-7.3-GCCcore-12.3.0.eb b/easybuild/easyconfigs/m/Molden/Molden-7.3-GCCcore-12.3.0.eb index 7d73969a3f7..f7c651b05eb 100644 --- a/easybuild/easyconfigs/m/Molden/Molden-7.3-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/m/Molden/Molden-7.3-GCCcore-12.3.0.eb @@ -45,8 +45,6 @@ sanity_check_paths = { 'dirs': [], } -sanity_check_commands = [ -"molden -h" -] +sanity_check_commands = ["molden -h"] moduleclass = 'chem' From cc7b583d35bb3bb1a499c90358aebf6d16e42a25 Mon Sep 17 00:00:00 2001 From: Xin An <34663977+xinan1911@users.noreply.github.com> Date: Wed, 18 Oct 2023 15:45:39 +0200 Subject: [PATCH 061/599] Update waLBerla-6.1-foss-2021a.eb add patch and sanity check --- .../w/waLBerla/waLBerla-6.1-foss-2021a.eb | 12 +++++++++--- 1 file changed, 9 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb b/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb index 44b93328579..e67edd92949 100644 --- a/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb +++ b/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb @@ -13,7 +13,13 @@ toolchainopts = {'usempi': True, 'pic': True} source_urls = ['https://i10git.cs.fau.de/walberla/walberla/-/archive/v6.1'] sources = ['%(name)s-v%(version)s.tar.gz'] -checksums = ['f0acdd9ad6543bc9306c8aae953dd5065986271d4398916ae0469db8b21c007a'] +patches = ['waLBerla-6.1_fix_cmakelist_for_easybuild.patch'] +checksums = [ + {'waLBerla-v6.1.tar.gz': 'f0acdd9ad6543bc9306c8aae953dd5065986271d4398916ae0469db8b21c007a'}, + {'waLBerla-6.1_fix_cmakelist_for_easybuild.patch': + '13393d523d8f2e1856ae6acffc04bc74d35b5b6a7c800cfad75fb8e3678e4dad'}, +] + builddependencies = [('CMake', '3.20.1')] @@ -31,8 +37,8 @@ configopts += "-DWALBERLA_BUILD_DOC=OFF " configopts += "-DPython_ROOT_DIR=$EBROOTPYTHON " sanity_check_paths = { - 'files': ['walberla/waLBerlaDefinitions.h'], - 'dirs': [''], + 'files': ['walberla/waLBerlaDefinitions.h', 'walberla/pythonmodule/walberla_cpp.cpython-39-x86_64-linux-gnu.so'], + 'dirs': ['walberla/pythonmodule/'] } moduleclass = 'chem' From 1a4685910a9579748f200a29477329549c29d4a7 Mon Sep 17 00:00:00 2001 From: xina Date: Wed, 18 Oct 2023 15:54:06 +0200 Subject: [PATCH 062/599] add cmake patch file --- .../waLBerla-6.1_fix_cmakelist_for_easybuild.patch | 12 ++++++++++++ 1 file changed, 12 insertions(+) create mode 100644 easybuild/easyconfigs/w/waLBerla/waLBerla-6.1_fix_cmakelist_for_easybuild.patch diff --git a/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1_fix_cmakelist_for_easybuild.patch b/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1_fix_cmakelist_for_easybuild.patch new file mode 100644 index 00000000000..62c8fad3044 --- /dev/null +++ b/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1_fix_cmakelist_for_easybuild.patch @@ -0,0 +1,12 @@ +diff -ruN walberla-v6.1.orig/CMakeLists.txt walberla-v6.1/CMakeLists.txt +--- walberla-v6.1.orig/CMakeLists.txt 2023-10-17 13:06:02.619565000 +0200 ++++ walberla-v6.1/CMakeLists.txt 2023-10-18 14:47:35.047985995 +0200 +@@ -1314,7 +1314,7 @@ + src/waLBerlaDefinitions.h ) + + install( FILES ${walberla_BINARY_DIR}/src/waLBerlaDefinitions.h DESTINATION walberla/ ) +- ++install( DIRECTORY ${walberla_BINARY_DIR}/apps/ DESTINATION walberla/ ) + + # test + if ( WALBERLA_BUILD_TESTS ) From e28901d867a7df20e07de1191a49fc2fe2917b60 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 19 Oct 2023 00:07:55 +0200 Subject: [PATCH 063/599] Drop MKL_ILP64 --- .../easyconfigs/m/magma/magma-2.7.2-foss-2023a-CUDA-12.1.1.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/magma/magma-2.7.2-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/m/magma/magma-2.7.2-foss-2023a-CUDA-12.1.1.eb index 19a155367dd..6f1484e887f 100644 --- a/easybuild/easyconfigs/m/magma/magma-2.7.2-foss-2023a-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/m/magma/magma-2.7.2-foss-2023a-CUDA-12.1.1.eb @@ -32,8 +32,7 @@ cuda_compute_capabilities = ['5.0', '6.0', '7.0', '7.5', '8.0', '8.6', '9.0'] # make sure both static and shared libs are built configopts = [ - '-DMKL_ILP64=ON \ - -DBUILD_SHARED_LIBS=%s \ + '-DBUILD_SHARED_LIBS=%s \ -DGPU_TARGET="%%(cuda_sm_space_sep)s" ' % local_shared for local_shared in ('ON', 'OFF') ] From 5fba734d82eaa0d9f0100f1e63ff6cd1f2695618 Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 23 Oct 2023 15:16:06 +0100 Subject: [PATCH 064/599] Doxygen added --- easybuild/easyconfigs/c/cairomm/cairomm-1.14.4-GCC-11.3.0.eb | 1 + easybuild/easyconfigs/c/cairomm/cairomm-1.16.2-GCC-11.3.0.eb | 1 + 2 files changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/c/cairomm/cairomm-1.14.4-GCC-11.3.0.eb b/easybuild/easyconfigs/c/cairomm/cairomm-1.14.4-GCC-11.3.0.eb index ed89cbbcb2d..74075795c30 100644 --- a/easybuild/easyconfigs/c/cairomm/cairomm-1.14.4-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/c/cairomm/cairomm-1.14.4-GCC-11.3.0.eb @@ -18,6 +18,7 @@ checksums = ['4749d25a2b2ef67cc0c014caaf5c87fa46792fc4b3ede186fb0fc932d2055158'] builddependencies = [ ('Meson', '0.62.1'), ('Ninja', '1.10.2'), + ('Doxygen', '1.9.4'), ] dependencies = [ diff --git a/easybuild/easyconfigs/c/cairomm/cairomm-1.16.2-GCC-11.3.0.eb b/easybuild/easyconfigs/c/cairomm/cairomm-1.16.2-GCC-11.3.0.eb index 4d3b9b1d798..1e37a907b91 100644 --- a/easybuild/easyconfigs/c/cairomm/cairomm-1.16.2-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/c/cairomm/cairomm-1.16.2-GCC-11.3.0.eb @@ -18,6 +18,7 @@ checksums = ['6a63bf98a97dda2b0f55e34d1b5f3fb909ef8b70f9b8d382cb1ff3978e7dc13f'] builddependencies = [ ('Meson', '0.62.1'), ('Ninja', '1.10.2'), + ('Doxygen', '1.9.4'), ] dependencies = [ From 372e1134db6de5a903499593eaab92a22977fc15 Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 23 Oct 2023 16:16:47 +0100 Subject: [PATCH 065/599] M4 added --- easybuild/easyconfigs/c/cairomm/cairomm-1.14.4-GCC-11.3.0.eb | 1 + easybuild/easyconfigs/c/cairomm/cairomm-1.16.2-GCC-11.3.0.eb | 1 + 2 files changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/c/cairomm/cairomm-1.14.4-GCC-11.3.0.eb b/easybuild/easyconfigs/c/cairomm/cairomm-1.14.4-GCC-11.3.0.eb index 74075795c30..5d792e5a489 100644 --- a/easybuild/easyconfigs/c/cairomm/cairomm-1.14.4-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/c/cairomm/cairomm-1.14.4-GCC-11.3.0.eb @@ -19,6 +19,7 @@ builddependencies = [ ('Meson', '0.62.1'), ('Ninja', '1.10.2'), ('Doxygen', '1.9.4'), + ('M4', '1.4.19'), ] dependencies = [ diff --git a/easybuild/easyconfigs/c/cairomm/cairomm-1.16.2-GCC-11.3.0.eb b/easybuild/easyconfigs/c/cairomm/cairomm-1.16.2-GCC-11.3.0.eb index 1e37a907b91..972787a1a18 100644 --- a/easybuild/easyconfigs/c/cairomm/cairomm-1.16.2-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/c/cairomm/cairomm-1.16.2-GCC-11.3.0.eb @@ -19,6 +19,7 @@ builddependencies = [ ('Meson', '0.62.1'), ('Ninja', '1.10.2'), ('Doxygen', '1.9.4'), + ('M4', '1.4.19'), ] dependencies = [ From e885f81f708ba9f876ef709d6460d086e95c75cb Mon Sep 17 00:00:00 2001 From: WilleBell Date: Mon, 23 Oct 2023 17:33:37 +0200 Subject: [PATCH 066/599] adding easyconfigs: scikit-lego-0.6.16-foss-2022a.eb --- .../scikit-lego-0.6.16-foss-2022a.eb | 55 +++++++++++++++++++ 1 file changed, 55 insertions(+) create mode 100644 easybuild/easyconfigs/s/scikit-lego/scikit-lego-0.6.16-foss-2022a.eb diff --git a/easybuild/easyconfigs/s/scikit-lego/scikit-lego-0.6.16-foss-2022a.eb b/easybuild/easyconfigs/s/scikit-lego/scikit-lego-0.6.16-foss-2022a.eb new file mode 100644 index 00000000000..af838bb40d3 --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-lego/scikit-lego-0.6.16-foss-2022a.eb @@ -0,0 +1,55 @@ +easyblock = 'PythonBundle' + +name = 'scikit-lego' +version = '0.6.16' + +homepage = 'https://github.com/koaning/scikit-lego' +description = """ +We love scikit learn but very often we find ourselves writing custom transformers, metrics and +models. The goal of this project is to attempt to consolidate these into a package that offers +code quality/testing. +""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +github_account = 'koaning' + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('scikit-learn', '1.1.2'), + ('matplotlib', '3.5.2'), + ('umap-learn', '0.5.3'), +] + +download_dep_fail = True +use_pip = True + +exts_list = [ + ('autograd', '1.6.2', { + 'checksums': ['8731e08a0c4e389d8695a40072ada4512641c113b6cace8f4cfbe8eb7e9aedeb'], + }), + ('Deprecated', '1.2.14', { + 'checksums': ['e5323eb936458dccc2582dc6f9c322c852a775a27065ff2b0c4970b9d53d01b3'], + }), + ('patsy', '0.5.3', { + 'checksums': ['bdc18001875e319bc91c812c1eb6a10be4bb13cb81eb763f466179dca3b67277'], + }), + ('wrapt', '1.14.1', { + 'checksums': ['380a85cf89e0e69b7cfbe2ea9f765f004ff419f34194018a6827ac0e3edfed4d'], + }), + (name, version, { + 'modulename': 'sklego', + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/%(github_account)s/%(name)s/archive'], + 'checksums': ['bf58f66518e9e8dca54cac634d7642b1e1a6c9984e17af6f1f71e0312dbe4a69'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' From 1cde8376536c0b3fb8287731f4f665d368a31ebe Mon Sep 17 00:00:00 2001 From: WilleBell Date: Mon, 23 Oct 2023 17:59:30 +0200 Subject: [PATCH 067/599] remove download_dep_fail --- .../easyconfigs/s/scikit-lego/scikit-lego-0.6.16-foss-2022a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/s/scikit-lego/scikit-lego-0.6.16-foss-2022a.eb b/easybuild/easyconfigs/s/scikit-lego/scikit-lego-0.6.16-foss-2022a.eb index af838bb40d3..b469cc61b1e 100644 --- a/easybuild/easyconfigs/s/scikit-lego/scikit-lego-0.6.16-foss-2022a.eb +++ b/easybuild/easyconfigs/s/scikit-lego/scikit-lego-0.6.16-foss-2022a.eb @@ -26,7 +26,6 @@ dependencies = [ ('umap-learn', '0.5.3'), ] -download_dep_fail = True use_pip = True exts_list = [ From 14d6af2299da0e7fba69a5501f35e72eb65ff8c3 Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 23 Oct 2023 22:02:06 +0100 Subject: [PATCH 068/599] Graphviz-5.0.0 added to cairomm-1.14.4 --- easybuild/easyconfigs/c/cairomm/cairomm-1.14.4-GCC-11.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/c/cairomm/cairomm-1.14.4-GCC-11.3.0.eb b/easybuild/easyconfigs/c/cairomm/cairomm-1.14.4-GCC-11.3.0.eb index 5d792e5a489..c2a98051b78 100644 --- a/easybuild/easyconfigs/c/cairomm/cairomm-1.14.4-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/c/cairomm/cairomm-1.14.4-GCC-11.3.0.eb @@ -27,6 +27,7 @@ dependencies = [ ('libsigc++', '3.4.0'), ('mm-common', '1.0.5'), ('Boost', '1.79.0'), + ('Graphviz', '5.0.0'), ] runtest = 'ninja test' From 3d50b1f614e939baaa3c247292b8e0ae11456a8b Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 23 Oct 2023 22:50:35 +0100 Subject: [PATCH 069/599] libxslt added --- easybuild/easyconfigs/c/cairomm/cairomm-1.14.4-GCC-11.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/c/cairomm/cairomm-1.14.4-GCC-11.3.0.eb b/easybuild/easyconfigs/c/cairomm/cairomm-1.14.4-GCC-11.3.0.eb index c2a98051b78..a1c2a1d16e5 100644 --- a/easybuild/easyconfigs/c/cairomm/cairomm-1.14.4-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/c/cairomm/cairomm-1.14.4-GCC-11.3.0.eb @@ -28,6 +28,7 @@ dependencies = [ ('mm-common', '1.0.5'), ('Boost', '1.79.0'), ('Graphviz', '5.0.0'), + ('libxslt', '1.1.34'), ] runtest = 'ninja test' From 506bcb2cc1e838a98e6d59c7eca02d24139ec166 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 24 Oct 2023 00:29:02 +0100 Subject: [PATCH 070/599] libsigc++ 2.12.1 used instead of not-working 3.x one --- .../easyconfigs/c/cairomm/cairomm-1.14.4-GCC-11.3.0.eb | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/c/cairomm/cairomm-1.14.4-GCC-11.3.0.eb b/easybuild/easyconfigs/c/cairomm/cairomm-1.14.4-GCC-11.3.0.eb index a1c2a1d16e5..fae81fd8e8b 100644 --- a/easybuild/easyconfigs/c/cairomm/cairomm-1.14.4-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/c/cairomm/cairomm-1.14.4-GCC-11.3.0.eb @@ -18,17 +18,16 @@ checksums = ['4749d25a2b2ef67cc0c014caaf5c87fa46792fc4b3ede186fb0fc932d2055158'] builddependencies = [ ('Meson', '0.62.1'), ('Ninja', '1.10.2'), - ('Doxygen', '1.9.4'), - ('M4', '1.4.19'), + ('pkgconf', '1.8.0'), ] dependencies = [ ('cairo', '1.17.4'), - ('libsigc++', '3.4.0'), - ('mm-common', '1.0.5'), - ('Boost', '1.79.0'), + ('libsigc++', '2.12.1'), ('Graphviz', '5.0.0'), ('libxslt', '1.1.34'), + ('mm-common', '1.0.5'), + ('Boost', '1.79.0'), ] runtest = 'ninja test' From 5e8fd96e3151c44c5a8aa398969a1c4534ce542c Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 24 Oct 2023 10:11:33 +0200 Subject: [PATCH 071/599] adding easyconfigs: PyTorch-2.0.1-foss-2022b.eb and patches: PyTorch-2.0.1_add-missing-vsx-vector-shift-functions.patch, PyTorch-2.0.1_avoid-test_quantization-failures.patch, PyTorch-2.0.1_disable-test-sharding.patch, PyTorch-2.0.1_fix-numpy-compat.patch, PyTorch-2.0.1_fix-shift-ops.patch, PyTorch-2.0.1_fix-skip-decorators.patch, PyTorch-2.0.1_fix-test_memory_profiler.patch, PyTorch-2.0.1_fix-test-ops-conf.patch, PyTorch-2.0.1_fix-torch.compile-on-ppc.patch, PyTorch-2.0.1_fix-ub-in-inductor-codegen.patch, PyTorch-2.0.1_fix-vsx-loadu.patch, PyTorch-2.0.1_no-cuda-stubs-rpath.patch, PyTorch-2.0.1_remove-test-requiring-online-access.patch, PyTorch-2.0.1_skip-diff-test-on-ppc.patch, PyTorch-2.0.1_skip-failing-gradtest.patch, PyTorch-2.0.1_skip-test_shuffle_reproducibility.patch, PyTorch-2.0.1_skip-tests-skipped-in-subprocess.patch --- .../p/PyTorch/PyTorch-2.0.1-foss-2022b.eb | 144 ++++++++++ ...d-missing-vsx-vector-shift-functions.patch | 103 +++++++ ...0.1_avoid-test_quantization-failures.patch | 19 ++ .../PyTorch-2.0.1_disable-test-sharding.patch | 18 ++ .../PyTorch-2.0.1_fix-numpy-compat.patch | 237 ++++++++++++++++ .../PyTorch/PyTorch-2.0.1_fix-shift-ops.patch | 253 ++++++++++++++++++ .../PyTorch-2.0.1_fix-skip-decorators.patch | 122 +++++++++ .../PyTorch-2.0.1_fix-test-ops-conf.patch | 26 ++ ...Torch-2.0.1_fix-test_memory_profiler.patch | 19 ++ ...Torch-2.0.1_fix-torch.compile-on-ppc.patch | 39 +++ ...rch-2.0.1_fix-ub-in-inductor-codegen.patch | 34 +++ .../PyTorch/PyTorch-2.0.1_fix-vsx-loadu.patch | 31 +++ .../PyTorch-2.0.1_no-cuda-stubs-rpath.patch | 186 +++++++++++++ ..._remove-test-requiring-online-access.patch | 30 +++ .../PyTorch-2.0.1_skip-diff-test-on-ppc.patch | 26 ++ .../PyTorch-2.0.1_skip-failing-gradtest.patch | 16 ++ ....1_skip-test_shuffle_reproducibility.patch | 20 ++ ...0.1_skip-tests-skipped-in-subprocess.patch | 34 +++ 18 files changed, 1357 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1-foss-2022b.eb create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_add-missing-vsx-vector-shift-functions.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_avoid-test_quantization-failures.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_disable-test-sharding.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_fix-numpy-compat.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_fix-shift-ops.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_fix-skip-decorators.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_fix-test-ops-conf.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_fix-test_memory_profiler.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_fix-torch.compile-on-ppc.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_fix-ub-in-inductor-codegen.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_fix-vsx-loadu.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_no-cuda-stubs-rpath.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_remove-test-requiring-online-access.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_skip-diff-test-on-ppc.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_skip-failing-gradtest.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_skip-test_shuffle_reproducibility.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_skip-tests-skipped-in-subprocess.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1-foss-2022b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1-foss-2022b.eb new file mode 100644 index 00000000000..59f471b813e --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1-foss-2022b.eb @@ -0,0 +1,144 @@ +name = 'PyTorch' +version = '2.0.1' + +homepage = 'https://pytorch.org/' +description = """Tensors and Dynamic neural networks in Python with strong GPU acceleration. +PyTorch is a deep learning framework that puts Python first.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +source_urls = [GITHUB_RELEASE] +sources = ['%(namelower)s-v%(version)s.tar.gz'] +patches = [ + 'PyTorch-1.7.0_disable-dev-shm-test.patch', + 'PyTorch-1.11.1_skip-test_init_from_local_shards.patch', + 'PyTorch-1.12.1_add-hypothesis-suppression.patch', + 'PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch', + 'PyTorch-1.12.1_fix-TestTorch.test_to.patch', + 'PyTorch-1.12.1_skip-test_round_robin.patch', + 'PyTorch-1.13.1_fix-gcc-12-warning-in-fbgemm.patch', + 'PyTorch-1.13.1_fix-protobuf-dependency.patch', + 'PyTorch-1.13.1_fix-warning-in-test-cpp-api.patch', + 'PyTorch-1.13.1_skip-failing-singular-grad-test.patch', + 'PyTorch-1.13.1_skip-tests-without-fbgemm.patch', + 'PyTorch-2.0.1_add-missing-vsx-vector-shift-functions.patch', + 'PyTorch-2.0.1_avoid-test_quantization-failures.patch', + 'PyTorch-2.0.1_disable-test-sharding.patch', + 'PyTorch-2.0.1_fix-numpy-compat.patch', + 'PyTorch-2.0.1_fix-shift-ops.patch', + 'PyTorch-2.0.1_fix-skip-decorators.patch', + 'PyTorch-2.0.1_fix-test_memory_profiler.patch', + 'PyTorch-2.0.1_fix-test-ops-conf.patch', + 'PyTorch-2.0.1_fix-torch.compile-on-ppc.patch', + 'PyTorch-2.0.1_fix-ub-in-inductor-codegen.patch', + 'PyTorch-2.0.1_fix-vsx-loadu.patch', + 'PyTorch-2.0.1_no-cuda-stubs-rpath.patch', + 'PyTorch-2.0.1_remove-test-requiring-online-access.patch', + 'PyTorch-2.0.1_skip-diff-test-on-ppc.patch', + 'PyTorch-2.0.1_skip-failing-gradtest.patch', + 'PyTorch-2.0.1_skip-test_shuffle_reproducibility.patch', + 'PyTorch-2.0.1_skip-tests-skipped-in-subprocess.patch', +] +checksums = [ + {'pytorch-v2.0.1.tar.gz': '9c564ca440265c69400ef5fdd48bf15e28af5aa4bed84c95efaad960a6699998'}, + {'PyTorch-1.7.0_disable-dev-shm-test.patch': '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a'}, + {'PyTorch-1.11.1_skip-test_init_from_local_shards.patch': + '4aeb1b0bc863d4801b0095cbce69f8794066748f0df27c6aaaf729c5ecba04b7'}, + {'PyTorch-1.12.1_add-hypothesis-suppression.patch': + 'e71ffb94ebe69f580fa70e0de84017058325fdff944866d6bd03463626edc32c'}, + {'PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch': + '1efc9850c431d702e9117d4766277d3f88c5c8b3870997c9974971bce7f2ab83'}, + {'PyTorch-1.12.1_fix-TestTorch.test_to.patch': '75f27987c3f25c501e719bd2b1c70a029ae0ee28514a97fe447516aee02b1535'}, + {'PyTorch-1.12.1_skip-test_round_robin.patch': '63d4849b78605aa088fdff695637d9473ea60dee603a3ff7f788690d70c55349'}, + {'PyTorch-1.13.1_fix-gcc-12-warning-in-fbgemm.patch': + '5c7be91a6096083a0b1315efe0001537499c600f1f569953c6a2c7f4cc1d0910'}, + {'PyTorch-1.13.1_fix-protobuf-dependency.patch': + '8bd755a0cab7233a243bc65ca57c9630dfccdc9bf8c9792f0de4e07a644fcb00'}, + {'PyTorch-1.13.1_fix-warning-in-test-cpp-api.patch': + 'bdde0f2105215c95a54de64ec4b1a4520528510663174fef6d5b900eb1db3937'}, + {'PyTorch-1.13.1_skip-failing-singular-grad-test.patch': + '72688a57b2bb617665ad1a1d5e362c5111ae912c10936bb38a089c0204729f48'}, + {'PyTorch-1.13.1_skip-tests-without-fbgemm.patch': + '481e595f673baf8ae58b41697a6792b83048b0264aa79b422f48cd8c22948bb7'}, + {'PyTorch-2.0.1_add-missing-vsx-vector-shift-functions.patch': + '245ee7f479f6f809b6ea52460113b2c49bbc2a550201f82bdfa0651c72b02ea8'}, + {'PyTorch-2.0.1_avoid-test_quantization-failures.patch': + '02e3f47e4ed1d7d6077e26f1ae50073dc2b20426269930b505f4aefe5d2f33cd'}, + {'PyTorch-2.0.1_disable-test-sharding.patch': 'a1ed7f21c9a269ea039a07a3d6574f885787b30ca5687143c96e096d31066cca'}, + {'PyTorch-2.0.1_fix-numpy-compat.patch': 'f3e5798193e0909a415d824f13772973200965db84476c1737824f2735f2db94'}, + {'PyTorch-2.0.1_fix-shift-ops.patch': '5ee655d5dba56d801d5618543b6ca299fa874939a3471f7b5449bfcb7f3f18c7'}, + {'PyTorch-2.0.1_fix-skip-decorators.patch': '2039012cef45446065e1a2097839fe20bb29fe3c1dcc926c3695ebf29832e920'}, + {'PyTorch-2.0.1_fix-test_memory_profiler.patch': + 'fd03117c46f59c1c62227d31c410c4cdd98fd35410976758cb9e7ec947582ddb'}, + {'PyTorch-2.0.1_fix-test-ops-conf.patch': '0f995e4f89baf3cbeb8666cbfe694666a2ef2bc53d97d6301f768b3ff9001fa4'}, + {'PyTorch-2.0.1_fix-torch.compile-on-ppc.patch': + '20f9172ae696da0c5c7b3bae6f0bf1221192cb1cbac3a44526a415087834bee7'}, + {'PyTorch-2.0.1_fix-ub-in-inductor-codegen.patch': + '1b37194f55ae678f3657b8728dfb896c18ffe8babe90987ce468c4fa9274f357'}, + {'PyTorch-2.0.1_fix-vsx-loadu.patch': 'a0ffa61da2d47c6acd09aaf6d4791e527d8919a6f4f1aa7ed38454cdcadb1f72'}, + {'PyTorch-2.0.1_no-cuda-stubs-rpath.patch': '8902e58a762240f24cdbf0182e99ccdfc2a93492869352fcb4ca0ec7e407f83a'}, + {'PyTorch-2.0.1_remove-test-requiring-online-access.patch': + '721ab0d35ed0ff8a46cb84ced5a98c0fb8ce6143cf6cea80b1360d3d7f64f584'}, + {'PyTorch-2.0.1_skip-diff-test-on-ppc.patch': 'f6e39cd774e5663df25507a73d37ad598157c2eadb2f47ca20a537dbe4b3e14f'}, + {'PyTorch-2.0.1_skip-failing-gradtest.patch': '8030bdec6ba49b057ab232d19a7f1a5e542e47e2ec340653a246ec9ed59f8bc1'}, + {'PyTorch-2.0.1_skip-test_shuffle_reproducibility.patch': + '7047862abc1abaff62954da59700f36d4f39fcf83167a638183b1b7f8fec78ae'}, + {'PyTorch-2.0.1_skip-tests-skipped-in-subprocess.patch': + '166c134573a95230e39b9ea09ece3ad8072f39d370c9a88fb2a1e24f6aaac2b5'}, +] + +osdependencies = [OS_PKG_IBVERBS_DEV] + +builddependencies = [ + ('CMake', '3.24.3'), + ('hypothesis', '6.68.2'), + # For tests + ('pytest-rerunfailures', '12.0'), + ('pytest-shard', '0.1.2'), +] + +dependencies = [ + ('Ninja', '1.11.1'), # Required for JIT compilation of C++ extensions + ('Python', '3.10.8'), + ('protobuf', '23.0'), + ('protobuf-python', '4.23.0'), + ('pybind11', '2.10.3'), + ('SciPy-bundle', '2023.02'), + ('PyYAML', '6.0'), + ('MPFR', '4.2.0'), + ('GMP', '6.2.1'), + ('numactl', '2.0.16'), + ('FFmpeg', '5.1.2'), + ('Pillow', '9.4.0'), + ('expecttest', '0.1.3'), + ('networkx', '3.0'), + ('sympy', '1.12'), +] + +excluded_tests = { + '': [ + # This test seems to take too long on NVIDIA Ampere at least. + 'distributed/test_distributed_spawn', + # Broken on CUDA 11.6/11.7: https://github.com/pytorch/pytorch/issues/75375 + 'distributions/test_constraints', + # no xdoctest + 'doctests', + # failing on broadwell + # See https://github.com/easybuilders/easybuild-easyconfigs/issues/17712 + 'test_native_mha', + # intermittent failures on various systems + # See https://github.com/easybuilders/easybuild-easyconfigs/issues/17712 + 'distributed/rpc/test_tensorpipe_agent', + ] +} + +runtest = 'cd test && PYTHONUNBUFFERED=1 %(python)s run_test.py --continue-through-error --verbose %(excluded_tests)s' + +# Especially test_quantization has a few corner cases that are triggered by the random input values, +# those cannot be easily avoided, see https://github.com/pytorch/pytorch/issues/107030 +# So allow a low number of tests to fail as the tests "usually" succeed +max_failed_tests = 2 + +tests = ['PyTorch-check-cpp-extension.py'] + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_add-missing-vsx-vector-shift-functions.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_add-missing-vsx-vector-shift-functions.patch new file mode 100644 index 00000000000..57e334c908f --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_add-missing-vsx-vector-shift-functions.patch @@ -0,0 +1,103 @@ +diff --git a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_int16_vsx.h b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_int16_vsx.h +index 7c300c8087c..84c84286740 100644 +--- a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_int16_vsx.h ++++ b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_int16_vsx.h +@@ -348,6 +348,7 @@ Vectorized inline minimum( + return a.minimum(b); + } + ++DEFINE_SHIFT_FUNCS(int16_t) + + } // namespace + } // namespace vec +diff --git a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_int32_vsx.h b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_int32_vsx.h +index c98ab6215e6..e1e86d3b53a 100644 +--- a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_int32_vsx.h ++++ b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_int32_vsx.h +@@ -279,6 +279,8 @@ Vectorized inline minimum( + return a.minimum(b); + } + ++DEFINE_SHIFT_FUNCS(int32_t) ++ + } // namespace + } // namespace vec + } // namespace at +diff --git a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_int64_vsx.h b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_int64_vsx.h +index a4171026a2b..70613d90443 100644 +--- a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_int64_vsx.h ++++ b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_int64_vsx.h +@@ -231,6 +231,8 @@ Vectorized inline minimum( + return a.minimum(b); + } + ++DEFINE_SHIFT_FUNCS(int64_t) ++ + } // namespace + } // namespace vec + } // namespace at +diff --git a/aten/src/ATen/cpu/vec/vec256/vsx/vsx_helpers.h b/aten/src/ATen/cpu/vec/vec256/vsx/vsx_helpers.h +index dab38458184..52032cdd817 100644 +--- a/aten/src/ATen/cpu/vec/vec256/vsx/vsx_helpers.h ++++ b/aten/src/ATen/cpu/vec/vec256/vsx/vsx_helpers.h +@@ -2,6 +2,7 @@ + #include + #include + #include ++#include + + using vbool8 = __attribute__((altivec(vector__))) __attribute__((altivec(bool__))) char; + using vbool16 = __attribute__((altivec(vector__))) __attribute__((altivec(bool__))) short; +@@ -18,6 +19,11 @@ using vuint64 = __attribute__((altivec(vector__))) unsigned long long; + using vfloat32 = __attribute__((altivec(vector__))) float; + using vfloat64 = __attribute__((altivec(vector__))) double; + ++inline auto make_vuint(vint8 v){ return reinterpret_cast(v); } ++inline auto make_vuint(vint16 v){ return reinterpret_cast(v); } ++inline auto make_vuint(vint32 v){ return reinterpret_cast(v); } ++inline auto make_vuint(vint64 v){ return reinterpret_cast(v); } ++ + #if !defined(vec_float) + C10_ALWAYS_INLINE vfloat32 vec_float(const vint32& vec_in) { + vfloat32 vec_out; +@@ -448,6 +454,40 @@ const vfloat64 vd_imag_half = vfloat64{0.0, 0.5}; + const vfloat64 vd_sqrt2_2 = vfloat64{0.70710678118654757, 0.70710678118654757}; + const vfloat64 vd_pi_2 = vfloat64{M_PI / 2.0, 0.0}; + ++template ++Vectorized VsxShiftRightArith(const Vectorized& a, const Vectorized& b) { ++ const Vectorized max_shift(sizeof(T) * CHAR_BIT - std::is_signed_v); ++ const auto mask = (b < Vectorized(0)) | (b >= max_shift); ++ const auto shift = Vectorized::blendv(b, max_shift, mask); ++ return Vectorized{ ++ vec_sra(a.vec0(), make_vuint(shift.vec0())), ++ vec_sra(a.vec1(), make_vuint(shift.vec1()))}; ++} ++ ++template ++Vectorized VsxShiftLeftArith(const Vectorized& a, const Vectorized& b) { ++ const Vectorized max_shift(sizeof(T) * CHAR_BIT); ++ const auto mask = (b < Vectorized(0)) | (b >= max_shift); ++ Vectorized ret( ++ vec_sl(a.vec0(), make_vuint(b.vec0())), ++ vec_sl(a.vec1(), make_vuint(b.vec1()))); ++ return Vectorized::blendv(ret, Vectorized(0), mask); ++} ++ ++#define DEFINE_SHIFT_FUNCS(operand_type) \ ++ template <> \ ++ Vectorized C10_ALWAYS_INLINE operator>>( \ ++ const Vectorized& a, \ ++ const Vectorized& b) { \ ++ return VsxShiftRightArith(a, b); \ ++ } \ ++ template <> \ ++ Vectorized C10_ALWAYS_INLINE operator<<( \ ++ const Vectorized& a, \ ++ const Vectorized& b) { \ ++ return VsxShiftLeftArith(a, b); \ ++ } \ ++ + } // namespace + } // namespace vec + } // namespace at diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_avoid-test_quantization-failures.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_avoid-test_quantization-failures.patch new file mode 100644 index 00000000000..01a7e098c41 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_avoid-test_quantization-failures.patch @@ -0,0 +1,19 @@ +The quantized values returned by hypothesis as test inputs might still cause overflows. +Hence reduce their maximum value by a factor that should fix most such cases. +See e.g. https://github.com/pytorch/pytorch/issues/111471 + +Author: Alexander Grund (TU Dresden) + +diff --git a/torch/testing/_internal/hypothesis_utils.py b/torch/testing/_internal/hypothesis_utils.py +index 15e7b4512a4..67df4d74e9d 100644 +--- a/torch/testing/_internal/hypothesis_utils.py ++++ b/torch/testing/_internal/hypothesis_utils.py +@@ -36,6 +36,8 @@ _ENFORCED_ZERO_POINT = defaultdict(lambda: None, { + def _get_valid_min_max(qparams): + scale, zero_point, quantized_type = qparams + adjustment = 1 + torch.finfo(torch.float).eps ++ # provide some leeway for scaling values without overflowing long ++ adjustment *= 1e4 + _long_type_info = torch.iinfo(torch.long) + long_min, long_max = _long_type_info.min / adjustment, _long_type_info.max / adjustment + # make sure intermediate results are within the range of long diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_disable-test-sharding.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_disable-test-sharding.patch new file mode 100644 index 00000000000..525d9fda1dc --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_disable-test-sharding.patch @@ -0,0 +1,18 @@ +Our error checking doesn't work well with the parallel/sharded pytorch test. +As the overall gain is low, disable it and always run the full test suite in a single process. + +Author: Alexander Grund (TU Dresden) + +diff --git a/test/run_test.py b/test/run_test.py +index 9619cb2626e..ddfb200148f 100755 +--- a/test/run_test.py ++++ b/test/run_test.py +@@ -815,7 +815,7 @@ def run_test_ops(test_module, test_directory, options): + ] + default_unittest_args.extend(rerun_options) + +- if 'slow-gradcheck' in os.getenv("BUILD_ENVIRONMENT", ""): ++ if True: + extra_unittest_args = default_unittest_args.copy() + # there are a lot of tests that take up a lot of space in slowgrad check, so don't bother parallelizing + # it's also on periodic so we don't care about TTS as much diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_fix-numpy-compat.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_fix-numpy-compat.patch new file mode 100644 index 00000000000..99b3cc6b770 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_fix-numpy-compat.patch @@ -0,0 +1,237 @@ +From ae1ed277563a1ac887faef4370ad9933c883ab9e Mon Sep 17 00:00:00 2001 +From: Omkar Salpekar +Date: Wed, 21 Jun 2023 18:16:40 +0000 +Subject: [PATCH] [codemod][numpy] replace np.str with str (#103931) + +Summary: +`np.str` is removed from numpy 1.20.0. It was an alias to builtin `str` and it's safe to do the replacement. + +The whole changes is mechanical, generated using the following onliner: +``` +fbgr -sl 'np\.str\b' | xargs perl -pi -e 's,\bnp\.str\b,str,g' +``` + +Test Plan: sandcastle + +Differential Revision: D46586144 + +Pull Request resolved: https://github.com/pytorch/pytorch/pull/103931 +Approved by: https://github.com/huydhn +--- + caffe2/python/core.py | 2 +- + caffe2/python/hypothesis_test.py | 4 ++-- + caffe2/python/layer_model_helper.py | 2 +- + caffe2/python/operator_test/adagrad_test_helper.py | 2 +- + caffe2/python/operator_test/cast_op_test.py | 2 +- + caffe2/python/operator_test/detectron_keypoints.py | 4 ++-- + caffe2/python/operator_test/tile_op_test.py | 6 +++--- + caffe2/python/schema.py | 2 +- + caffe2/python/schema_test.py | 4 ++-- + caffe2/python/utils.py | 6 +++--- + .../examples/maml_omniglot/support/omniglot_loaders.py | 4 ++-- + test/quantization/core/test_quantized_op.py | 4 ++-- + 12 files changed, 21 insertions(+), 21 deletions(-) + +diff --git a/caffe2/python/core.py b/caffe2/python/core.py +index d9f97b6121fdd2..e69af5c0a482b1 100644 +--- a/caffe2/python/core.py ++++ b/caffe2/python/core.py +@@ -1636,7 +1636,7 @@ def do_set(operator): + return do_set(self.GivenTensorIntFill) + elif array.dtype == np.int64: + return do_set(self.GivenTensorInt64Fill) +- elif array.dtype == np.str: ++ elif array.dtype == str: + return do_set(self.GivenTensorStringFill) + elif array.dtype == np.bool: + return do_set(self.GivenTensorBoolFill) +diff --git a/caffe2/python/hypothesis_test.py b/caffe2/python/hypothesis_test.py +index 02200f8cf74f18..cb5d00064b6eda 100644 +--- a/caffe2/python/hypothesis_test.py ++++ b/caffe2/python/hypothesis_test.py +@@ -1629,8 +1629,8 @@ def test_tt_sls_layer(self, gc, dc): + c0 = np.ones([10, 1, 2, 16]).astype(np.float32) + c1 = np.ones([10, 16, 2, 16]).astype(np.float32) + c2 = np.ones([10, 16, 2, 1]).astype(np.float32) +- # index = np.array([0, 1, 2, 1, 4], dtype=np.int) +- # lengths = np.array([3, 2], dtype=np.int) ++ # index = np.array([0, 1, 2, 1, 4], dtype=int) ++ # lengths = np.array([3, 2], dtype=int) + index = np.array([0, 1, 2, 1, 4], np.int64) + lengths = np.array([3, 2], np.int32) + +diff --git a/caffe2/python/layer_model_helper.py b/caffe2/python/layer_model_helper.py +index 9a8e237e302143..f21b47e57c653a 100644 +--- a/caffe2/python/layer_model_helper.py ++++ b/caffe2/python/layer_model_helper.py +@@ -148,7 +148,7 @@ def _get_global_constant_initializer_op( + op_name = 'GivenTensorIntFill' + elif array.dtype == np.int64: + op_name = 'GivenTensorInt64Fill' +- elif array.dtype == np.str: ++ elif array.dtype == str: + op_name = 'GivenTensorStringFill' + elif array.dtype == np.bool: + op_name = 'GivenTensorBoolFill' +diff --git a/caffe2/python/operator_test/adagrad_test_helper.py b/caffe2/python/operator_test/adagrad_test_helper.py +index 08caf22b266178..1fd017c4d2ac5c 100644 +--- a/caffe2/python/operator_test/adagrad_test_helper.py ++++ b/caffe2/python/operator_test/adagrad_test_helper.py +@@ -98,7 +98,7 @@ def adagrad_sparse_test_helper( + # Create an indexing array containing values that are lists of indices, + # which index into grad + if grad.size == 0: +- indices = np.empty(shape=(0,), dtype=np.int) ++ indices = np.empty(shape=(0,), dtype=int) + else: + indices = np.random.choice( + np.arange(grad.shape[0]), +diff --git a/caffe2/python/operator_test/cast_op_test.py b/caffe2/python/operator_test/cast_op_test.py +index bf2a210086e691..95540a6121bcac 100644 +--- a/caffe2/python/operator_test/cast_op_test.py ++++ b/caffe2/python/operator_test/cast_op_test.py +@@ -37,7 +37,7 @@ def test_cast_int_to_string(self, data, gc, dc): + 'Cast', 'data', 'data_cast', to=core.DataType.STRING) + + def ref(data): +- ret = data.astype(dtype=np.str) ++ ret = data.astype(dtype=str) + # the string blob will be fetched as object, we feed and re-fetch + # to mimic this. + with hu.temp_workspace('tmp_ref_int_to_string'): +diff --git a/caffe2/python/operator_test/detectron_keypoints.py b/caffe2/python/operator_test/detectron_keypoints.py +index 1abff0675993ff..319e8b5bbffd5e 100644 +--- a/caffe2/python/operator_test/detectron_keypoints.py ++++ b/caffe2/python/operator_test/detectron_keypoints.py +@@ -32,8 +32,8 @@ def heatmaps_to_keypoints(maps, rois): + heights = rois[:, 3] - rois[:, 1] + widths = np.maximum(widths, 1) + heights = np.maximum(heights, 1) +- widths_ceil = np.ceil(widths).astype(np.int) +- heights_ceil = np.ceil(heights).astype(np.int) ++ widths_ceil = np.ceil(widths).astype(int) ++ heights_ceil = np.ceil(heights).astype(int) + + num_keypoints = np.maximum(maps.shape[1], _NUM_KEYPOINTS) + +diff --git a/caffe2/python/operator_test/tile_op_test.py b/caffe2/python/operator_test/tile_op_test.py +index d39dfeee0ad72a..fbb424fe058ccb 100644 +--- a/caffe2/python/operator_test/tile_op_test.py ++++ b/caffe2/python/operator_test/tile_op_test.py +@@ -32,7 +32,7 @@ def test_tile(self, M, K, N, tiles, axis, gc, dc): + ) + + def tile_ref(X, tiles, axis): +- dims = np.asarray([1, 1, 1], dtype=np.int) ++ dims = np.asarray([1, 1, 1], dtype=int) + dims[axis] = tiles + tiled_data = np.tile(X, dims) + return (tiled_data,) +@@ -61,7 +61,7 @@ def test_tile_grad(self, M, N, tiles, gc, dc): + ) + + def tile_ref(X, tiles, axis): +- dims = np.asarray([1, 1], dtype=np.int) ++ dims = np.asarray([1, 1], dtype=int) + dims[axis] = tiles + tiled_data = np.tile(X, dims) + return (tiled_data,) +@@ -99,7 +99,7 @@ def test_tilewinput(self, M, K, N, tiles, axis, gc, dc): + ) + + def tile_ref(X, tiles, axis): +- dims = np.asarray([1, 1, 1], dtype=np.int) ++ dims = np.asarray([1, 1, 1], dtype=int) + dims[axis] = tiles + tiled_data = np.tile(X, dims) + return (tiled_data,) +diff --git a/caffe2/python/schema.py b/caffe2/python/schema.py +index ab6ec29372e2ff..ecbcb2287dddea 100644 +--- a/caffe2/python/schema.py ++++ b/caffe2/python/schema.py +@@ -1252,7 +1252,7 @@ def InitEmptyRecord(net, schema_or_record, enforce_types=False): + + + _DATA_TYPE_FOR_DTYPE = [ +- (np.str, core.DataType.STRING), ++ (str, core.DataType.STRING), + (np.float16, core.DataType.FLOAT16), + (np.float32, core.DataType.FLOAT), + (np.float64, core.DataType.DOUBLE), +diff --git a/caffe2/python/schema_test.py b/caffe2/python/schema_test.py +index 8f3ed4415fd4f5..2f3eaf38dc138d 100644 +--- a/caffe2/python/schema_test.py ++++ b/caffe2/python/schema_test.py +@@ -94,12 +94,12 @@ def testTuple(self): + s = schema.Tuple(np.int32, str, np.float32) + s2 = schema.Struct( + ('field_0', schema.Scalar(dtype=np.int32)), +- ('field_1', schema.Scalar(dtype=np.str)), ++ ('field_1', schema.Scalar(dtype=str)), + ('field_2', schema.Scalar(dtype=np.float32)) + ) + self.assertEqual(s, s2) + self.assertEqual(s[0], schema.Scalar(dtype=np.int32)) +- self.assertEqual(s[1], schema.Scalar(dtype=np.str)) ++ self.assertEqual(s[1], schema.Scalar(dtype=str)) + self.assertEqual(s[2], schema.Scalar(dtype=np.float32)) + self.assertEqual( + s[2, 0], +diff --git a/caffe2/python/utils.py b/caffe2/python/utils.py +index 02a77e74681a93..8c82faee33a4c3 100644 +--- a/caffe2/python/utils.py ++++ b/caffe2/python/utils.py +@@ -67,7 +67,7 @@ def Caffe2TensorToNumpyArray(tensor): + tensor.int64_data, dtype=np.int64).reshape(tensor.dims) + elif tensor.data_type == caffe2_pb2.TensorProto.INT32: + return np.asarray( +- tensor.int32_data, dtype=np.int).reshape(tensor.dims) # pb.INT32=>np.int use int32_data ++ tensor.int32_data, dtype=int).reshape(tensor.dims) # pb.INT32=>int use int32_data + elif tensor.data_type == caffe2_pb2.TensorProto.INT16: + return np.asarray( + tensor.int32_data, dtype=np.int16).reshape(tensor.dims) # pb.INT16=>np.int16 use int32_data +@@ -100,9 +100,9 @@ def NumpyArrayToCaffe2Tensor(arr, name=None): + elif arr.dtype == np.int64: + tensor.data_type = caffe2_pb2.TensorProto.INT64 + tensor.int64_data.extend(list(arr.flatten().astype(np.int64))) +- elif arr.dtype == np.int or arr.dtype == np.int32: ++ elif arr.dtype == int or arr.dtype == np.int32: + tensor.data_type = caffe2_pb2.TensorProto.INT32 +- tensor.int32_data.extend(arr.flatten().astype(np.int).tolist()) ++ tensor.int32_data.extend(arr.flatten().astype(int).tolist()) + elif arr.dtype == np.int16: + tensor.data_type = caffe2_pb2.TensorProto.INT16 + tensor.int32_data.extend(list(arr.flatten().astype(np.int16))) # np.int16=>pb.INT16 use int32_data +diff --git a/functorch/examples/maml_omniglot/support/omniglot_loaders.py b/functorch/examples/maml_omniglot/support/omniglot_loaders.py +index cac99b2dfbb2aa..ce636ecca0b1b2 100644 +--- a/functorch/examples/maml_omniglot/support/omniglot_loaders.py ++++ b/functorch/examples/maml_omniglot/support/omniglot_loaders.py +@@ -271,10 +271,10 @@ def load_data_cache(self, data_pack): + + # [b, setsz, 1, 84, 84] + x_spts = np.array(x_spts).astype(np.float32).reshape(self.batchsz, setsz, 1, self.resize, self.resize) +- y_spts = np.array(y_spts).astype(np.int).reshape(self.batchsz, setsz) ++ y_spts = np.array(y_spts).astype(int).reshape(self.batchsz, setsz) + # [b, qrysz, 1, 84, 84] + x_qrys = np.array(x_qrys).astype(np.float32).reshape(self.batchsz, querysz, 1, self.resize, self.resize) +- y_qrys = np.array(y_qrys).astype(np.int).reshape(self.batchsz, querysz) ++ y_qrys = np.array(y_qrys).astype(int).reshape(self.batchsz, querysz) + + x_spts, y_spts, x_qrys, y_qrys = [ + torch.from_numpy(z).to(self.device) for z in +diff --git a/test/quantization/core/test_quantized_op.py b/test/quantization/core/test_quantized_op.py +index 252d7b92f77ebb..232150a0ba34a6 100644 +--- a/test/quantization/core/test_quantized_op.py ++++ b/test/quantization/core/test_quantized_op.py +@@ -3840,9 +3840,9 @@ def test_qlinear_with_input_q_dq_qweight_dq_output_fp32( + # xnnpack forces W_zp to 0 when using symmetric quantization + # ONEDNN only supports symmetric quantization of weight + if dtype == torch.qint8 or qengine_is_onednn(): +- W_zps = np.zeros(output_channels).astype(np.int) ++ W_zps = np.zeros(output_channels).astype(int) + else: +- W_zps = np.round(np.random.rand(output_channels) * 100 - 50).astype(np.int) ++ W_zps = np.round(np.random.rand(output_channels) * 100 - 50).astype(int) + # when using symmetric quantization + # special restriction for xnnpack fully connected op weight + # [-127, 127] instead of [-128, 127] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_fix-shift-ops.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_fix-shift-ops.patch new file mode 100644 index 00000000000..f63f3cf4c5f --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_fix-shift-ops.patch @@ -0,0 +1,253 @@ +From d64fb24ee4a71d8cfe175cafc73c5f90fb26c9ac Mon Sep 17 00:00:00 2001 +From: BJ Hargrave +Date: Tue, 14 Mar 2023 15:30:41 -0400 +Subject: [PATCH 1/2] Fix operator>> for int64 vector in vec256 + +There is no vector instruction for shift right arithmetic for int64. +The operator>> implementation emulates this through other vector +instructions. It has been fixed to properly handle out-of-limit +shift values so that shift values <0 and >64 are set to 64 which +results in a value of -1 for negative inputs and 0 for non-negative +inputs (sign preserving). + +Fixes https://github.com/pytorch/pytorch/issues/70904 + +Signed-off-by: BJ Hargrave +--- + aten/src/ATen/cpu/vec/vec256/vec256_int.h | 16 +++++++++++----- + 1 file changed, 11 insertions(+), 5 deletions(-) + +diff --git a/aten/src/ATen/cpu/vec/vec256/vec256_int.h b/aten/src/ATen/cpu/vec/vec256/vec256_int.h +index 81e9d687d10a7b..784514f49e1d48 100644 +--- a/aten/src/ATen/cpu/vec/vec256/vec256_int.h ++++ b/aten/src/ATen/cpu/vec/vec256/vec256_int.h +@@ -1481,16 +1481,22 @@ Vectorized inline operator<<(const Vectorized& a, const Vector + + template <> + Vectorized inline operator>>(const Vectorized& a, const Vectorized& b) { +- // No vector instruction for right shifting int64_t, so emulating it ++ // No vector instruction for right arithmetic shifting int64_t, so emulating it + // instead. + ++ // Clamp the shift values such that shift values < 0 and > 64 are changed to 64 ++ // which results in -1 for negative input and 0 for non-negative input. ++ __m256i zero = _mm256_set1_epi64x(0); ++ __m256i max_shift = _mm256_set1_epi64x(64); ++ __m256i mask = _mm256_or_si256(_mm256_cmpgt_epi64(zero, b), _mm256_cmpgt_epi64(b, max_shift)); ++ __m256i shift = _mm256_blendv_epi8(b, max_shift, mask); + // Shift the number logically to the right, thus filling the most + // significant bits with 0s. Then, replace these bits with the sign + // bit. +- __m256i sign_bits = _mm256_cmpgt_epi64(_mm256_set1_epi64x(0), a); +- __m256i b_inv_mod_64 = _mm256_sub_epi64(_mm256_set1_epi64x(64), b); +- __m256i sign_ext = _mm256_sllv_epi64(sign_bits, b_inv_mod_64); +- __m256i c = _mm256_srlv_epi64(a, b); ++ __m256i sign_bits = _mm256_cmpgt_epi64(zero, a); ++ __m256i sign_shift = _mm256_sub_epi64(max_shift, shift); ++ __m256i sign_ext = _mm256_sllv_epi64(sign_bits, sign_shift); ++ __m256i c = _mm256_srlv_epi64(a, shift); + c = _mm256_or_si256(c, sign_ext); + + return c; + +From 734e2cea43ee782d756f04bc21c625b8fdd36d31 Mon Sep 17 00:00:00 2001 +From: BJ Hargrave +Date: Mon, 13 Mar 2023 10:56:00 -0400 +Subject: [PATCH 2/2] Fix CPU bitwise shifts for out-of-limit shift values + +Negative shift values and positive shift values greater than the +bit size of the dtype (limit 0..bits) now yield expected results +which are consistent with numpy. + +Left shift with an out-of-limit shift value result in a value of 0. +Right shift with an out-of-limit shift value results in a value of -1 +for negative inputs and 0 for non-negative inputs (sign preserving). + +Fixes https://github.com/pytorch/pytorch/issues/70904 + +Signed-off-by: BJ Hargrave +--- + aten/src/ATen/cpu/vec/vec_base.h | 18 ++++++++-- + aten/src/ATen/native/cpu/BinaryOpsKernel.cpp | 9 +++++ + test/functorch/test_vmap.py | 12 ------- + test/test_binary_ufuncs.py | 37 ++++++++++++++++++++ + 4 files changed, 62 insertions(+), 14 deletions(-) + +diff --git a/aten/src/ATen/cpu/vec/vec_base.h b/aten/src/ATen/cpu/vec/vec_base.h +index cb0e37054b4d32..8f006ae0f6634f 100644 +--- a/aten/src/ATen/cpu/vec/vec_base.h ++++ b/aten/src/ATen/cpu/vec/vec_base.h +@@ -20,6 +20,7 @@ + #include + #include + #include ++#include + + #include + #include +@@ -803,17 +804,30 @@ inline Vectorized operator~(const Vectorized& a) { + } + + template Vectorized inline operator<<(const Vectorized &a, const Vectorized &b) { ++ constexpr T max_shift = sizeof(T) * CHAR_BIT; + Vectorized c; + for (int i = 0; i != Vectorized::size(); i++) { +- c[i] = a[i] << b[i]; ++ T shift = b[i]; ++ if ((static_cast>(shift) < 0) || (shift >= max_shift)) { ++ c[i] = 0; ++ } else { ++ c[i] = static_cast>(a[i]) << shift; ++ } + } + return c; + } + + template Vectorized inline operator>>(const Vectorized &a, const Vectorized &b) { ++ // right shift value to retain sign bit for signed and no bits for unsigned ++ constexpr T max_shift = sizeof(T) * CHAR_BIT - std::is_signed_v; + Vectorized c; + for (int i = 0; i != Vectorized::size(); i++) { +- c[i] = a[i] >> b[i]; ++ T shift = b[i]; ++ if ((static_cast>(shift) < 0) || (shift >= max_shift)) { ++ c[i] = a[i] >> max_shift; ++ } else { ++ c[i] = a[i] >> shift; ++ } + } + return c; + } +diff --git a/aten/src/ATen/native/cpu/BinaryOpsKernel.cpp b/aten/src/ATen/native/cpu/BinaryOpsKernel.cpp +index d0393aaf18bf8b..d2d0892d8ea956 100644 +--- a/aten/src/ATen/native/cpu/BinaryOpsKernel.cpp ++++ b/aten/src/ATen/native/cpu/BinaryOpsKernel.cpp +@@ -316,6 +316,10 @@ void lshift_kernel(TensorIteratorBase& iter) { + AT_DISPATCH_INTEGRAL_TYPES(iter.dtype(), "lshift_cpu", [&]() { + cpu_kernel_vec(iter, + [](scalar_t a, scalar_t b) -> scalar_t { ++ constexpr scalar_t max_shift = sizeof(scalar_t) * CHAR_BIT; ++ if ((static_cast>(b) < 0) || (b >= max_shift)) { ++ return 0; ++ } + return static_cast>(a) << b; + }, + [](Vectorized a, Vectorized b) { +@@ -385,6 +389,11 @@ void rshift_kernel(TensorIteratorBase& iter) { + AT_DISPATCH_INTEGRAL_TYPES(iter.dtype(), "rshift_cpu", [&]() { + cpu_kernel_vec(iter, + [](scalar_t a, scalar_t b) -> scalar_t { ++ // right shift value to retain sign bit for signed and no bits for unsigned ++ constexpr scalar_t max_shift = sizeof(scalar_t) * CHAR_BIT - std::is_signed_v; ++ if ((static_cast>(b) < 0) || (b >= max_shift)) { ++ return a >> max_shift; ++ } + return a >> b; + }, + [](Vectorized a, Vectorized b) { +diff --git a/test/functorch/test_vmap.py b/test/functorch/test_vmap.py +index a5fb144f881880..5c352cf8fdf6f0 100644 +--- a/test/functorch/test_vmap.py ++++ b/test/functorch/test_vmap.py +@@ -27,8 +27,6 @@ + instantiate_parametrized_tests, + subtest, + TEST_WITH_UBSAN, +- IS_MACOS, +- IS_X86 + ) + from torch.testing._internal.common_device_type import \ + toleranceOverride, tol +@@ -46,7 +44,6 @@ + compute_quantities_for_vmap_test, + is_valid_inplace_sample_input, + decorate, +- expectedFailureIf + ) + import types + from collections import namedtuple +@@ -3572,10 +3569,6 @@ def test(): + xfail('addcdiv'), + xfail('addcmul'), + xfail('clamp'), +- # AssertionError: Tensor-likes are not equal! +- xfail('bitwise_left_shift', device_type='cpu'), +- decorate('bitwise_right_shift', device_type='cpu', +- decorator=expectedFailureIf(not (IS_MACOS and IS_X86))), + + # UBSAN: runtime error: shift exponent -1 is negative + decorate('bitwise_left_shift', decorator=unittest.skipIf(TEST_WITH_UBSAN, "Fails with above error")), +@@ -3734,11 +3727,6 @@ def test_vmap_exhaustive(self, device, dtype, op): + xfail('linalg.lu', ''), + skip('linalg.ldl_solve', ''), + skip('_softmax_backward_data'), +- # AssertionError: Tensor-likes are not equal! +- # Issue: https://github.com/pytorch/pytorch/issues/70904 +- xfail('bitwise_left_shift', device_type='cpu'), +- decorate('bitwise_right_shift', device_type='cpu', +- decorator=expectedFailureIf(not (IS_MACOS and IS_X86))), + # UBSAN: runtime error: shift exponent -1 is negative + decorate('bitwise_left_shift', decorator=unittest.skipIf(TEST_WITH_UBSAN, "Fails with above error")), + decorate('bitwise_right_shift', decorator=unittest.skipIf(TEST_WITH_UBSAN, "Fails with above error")), +diff --git a/test/test_binary_ufuncs.py b/test/test_binary_ufuncs.py +index 52d7c7a4ffcb00..bf3e4d43494932 100644 +--- a/test/test_binary_ufuncs.py ++++ b/test/test_binary_ufuncs.py +@@ -4,6 +4,7 @@ + import numpy as np + + import itertools ++from itertools import chain + from itertools import product + import math + import random +@@ -53,6 +54,7 @@ + floating_types_and, + floating_and_complex_types, + get_all_math_dtypes, ++ get_all_int_dtypes, + ) + from torch.testing._internal.common_methods_invocations import ( + binary_ufuncs, +@@ -3139,6 +3141,41 @@ def test_signed_shift(self, device, dtype): + self.assertEqual(a >> 1, expected_r) + self.compare_with_numpy(lambda x: x >> 1, lambda x: np.right_shift(x, 1), a) + ++ @onlyCPU ++ @dtypes(*get_all_int_dtypes()) ++ def test_shift_limits(self, device, dtype): ++ "Ensure that CPU integer bit shifting works as expected with out-of-limits shift values." ++ # Issue #70904 ++ iinfo = torch.iinfo(dtype) ++ bits = iinfo.bits ++ low = iinfo.min ++ high = iinfo.max ++ exact_dtype = dtype != torch.uint8 # numpy changes dtype from uint8 to int16 for some out-of-limits shift values ++ for input in ( ++ torch.tensor([-1, 0, 1], device=device, dtype=dtype), # small for non-vectorized operation ++ torch.tensor([low, high], device=device, dtype=dtype), # small for non-vectorized operation ++ make_tensor((64, 64, 64), low=low, high=high, device=device, dtype=dtype), # large for vectorized operation ++ ): ++ shift_left_expected = torch.zeros_like(input) ++ shift_right_expected = torch.clamp(input, -1, 0) ++ for shift in chain(range(-100, -1), range(bits, 100)): ++ shift_left = input << shift ++ self.assertEqual(shift_left, shift_left_expected, msg=f"<< {shift}") ++ self.compare_with_numpy( ++ lambda x: x << shift, ++ lambda x: np.left_shift(x, shift), ++ input, ++ exact_dtype=exact_dtype, msg=f"<< {shift}" ++ ) ++ shift_right = input >> shift ++ self.assertEqual(shift_right, shift_right_expected, msg=f">> {shift}") ++ self.compare_with_numpy( ++ lambda x: x >> shift, ++ lambda x: np.right_shift(x, shift), ++ input, ++ exact_dtype=exact_dtype, msg=f">> {shift}" ++ ) ++ + @onlyNativeDeviceTypes + @dtypes( + *list( diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_fix-skip-decorators.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_fix-skip-decorators.patch new file mode 100644 index 00000000000..101849f4dbf --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_fix-skip-decorators.patch @@ -0,0 +1,122 @@ +The decorators are implemented to run when the function is called which is after +the test `setup` method spawned subprocesses which may use NCCL to sync failing when there are +not enough GPUs available. +So replace the custom code by calls to the `unittest` skip decorators. +See hhttps://github.com/pytorch/pytorch/pull/109491 + +Author: Alexander Grund (TU Dresden) + +diff --git a/torch/testing/_internal/common_distributed.py b/torch/testing/_internal/common_distributed.py +index 400aa80fdca..80a7375cfe1 100644 +--- a/torch/testing/_internal/common_distributed.py ++++ b/torch/testing/_internal/common_distributed.py +@@ -134,17 +134,7 @@ def skip_if_odd_worldsize(func): + + + def require_n_gpus_for_nccl_backend(n, backend): +- def decorator(func): +- @wraps(func) +- def wrapper(*args, **kwargs): +- if backend == "nccl" and torch.cuda.device_count() < n: +- sys.exit(TEST_SKIPS[f"multi-gpu-{n}"].exit_code) +- else: +- return func(*args, **kwargs) +- +- return wrapper +- +- return decorator ++ return skip_if_lt_x_gpu(n) if backend == "nccl" else unittest.skipIf(False, None) + + + def import_transformers_or_skip(): +@@ -167,32 +157,7 @@ def import_transformers_or_skip(): + + + def skip_if_lt_x_gpu(x): +- def decorator(func): +- @wraps(func) +- def wrapper(*args, **kwargs): +- if torch.cuda.is_available() and torch.cuda.device_count() >= x: +- return func(*args, **kwargs) +- sys.exit(TEST_SKIPS[f"multi-gpu-{x}"].exit_code) +- +- return wrapper +- +- return decorator +- +- +-# This decorator helps avoiding initializing cuda while testing other backends +-def nccl_skip_if_lt_x_gpu(backend, x): +- def decorator(func): +- @wraps(func) +- def wrapper(*args, **kwargs): +- if backend != "nccl": +- return func(*args, **kwargs) +- if torch.cuda.is_available() and torch.cuda.device_count() >= x: +- return func(*args, **kwargs) +- sys.exit(TEST_SKIPS[f"multi-gpu-{x}"].exit_code) +- +- return wrapper +- +- return decorator ++ return unittest.skipIf(torch.cuda.device_count() < x, TEST_SKIPS[f"multi-gpu-{x}"].message) + + + def verify_ddp_error_logged(model_DDP, err_substr): +diff --git a/torch/testing/_internal/distributed/distributed_test.py b/torch/testing/_internal/distributed/distributed_test.py +index eb5130f2963..25839618308 100644 +--- a/torch/testing/_internal/distributed/distributed_test.py ++++ b/torch/testing/_internal/distributed/distributed_test.py +@@ -56,7 +56,6 @@ from torch.testing._internal.common_distributed import ( + skip_if_small_worldsize, + skip_if_odd_worldsize, + skip_if_lt_x_gpu, +- nccl_skip_if_lt_x_gpu, + skip_if_no_gpu, + require_n_gpus_for_nccl_backend, + requires_nccl_version, +@@ -4960,7 +4959,7 @@ class DistributedTest: + BACKEND != "mpi" and BACKEND != "nccl" and BACKEND != "gloo", + "get_future is only supported on mpi, nccl and gloo", + ) +- @nccl_skip_if_lt_x_gpu(BACKEND, 2) ++ @require_n_gpus_for_nccl_backend(2, BACKEND) + def test_accumulate_gradients_no_sync(self): + """ + Runs _test_accumulate_gradients_no_sync using default inputs +@@ -4971,7 +4970,7 @@ class DistributedTest: + BACKEND != "mpi" and BACKEND != "nccl" and BACKEND != "gloo", + "get_future is only supported on mpi, nccl and gloo", + ) +- @nccl_skip_if_lt_x_gpu(BACKEND, 2) ++ @require_n_gpus_for_nccl_backend(2, BACKEND) + def test_accumulate_gradients_no_sync_grad_is_view(self): + """ + Runs _test_accumulate_gradients_no_sync using default inputs +@@ -4982,7 +4981,7 @@ class DistributedTest: + BACKEND != "mpi" and BACKEND != "nccl" and BACKEND != "gloo", + "get_future is only supported on mpi, nccl and gloo", + ) +- @nccl_skip_if_lt_x_gpu(BACKEND, 2) ++ @require_n_gpus_for_nccl_backend(2, BACKEND) + def test_accumulate_gradients_no_sync_allreduce_hook(self): + """ + Runs multiple iterations on _test_accumulate_gradients_no_sync +@@ -5010,7 +5009,7 @@ class DistributedTest: + BACKEND != "mpi" and BACKEND != "nccl" and BACKEND != "gloo", + "get_future is only supported on mpi, nccl and gloo", + ) +- @nccl_skip_if_lt_x_gpu(BACKEND, 2) ++ @require_n_gpus_for_nccl_backend(2, BACKEND) + def test_accumulate_gradients_no_sync_allreduce_with_then_hook(self): + """ + Runs multiple iterations on _test_accumulate_gradients_no_sync using allreduce +@@ -5044,7 +5043,7 @@ class DistributedTest: + BACKEND != "mpi" and BACKEND != "nccl" and BACKEND != "gloo", + "get_future is only supported on mpi, nccl and gloo", + ) +- @nccl_skip_if_lt_x_gpu(BACKEND, 2) ++ @require_n_gpus_for_nccl_backend(2, BACKEND) + def test_get_future(self): + def mult(fut): + return [t * 3 for t in fut.wait()] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_fix-test-ops-conf.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_fix-test-ops-conf.patch new file mode 100644 index 00000000000..6f3977c99a4 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_fix-test-ops-conf.patch @@ -0,0 +1,26 @@ +From 8581301957b0018a32433f85163535709bc9d332 Mon Sep 17 00:00:00 2001 +From: Masaki Kozuki +Date: Fri, 7 Oct 2022 21:25:07 -0700 +Subject: [PATCH] try using a different group name + +ref: +https://github.com/pytorch/pytorch/issues/85923#issuecomment-1272220271 + +Signed-off-by: Masaki Kozuki +--- + test/conftest.py | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/test/conftest.py b/test/conftest.py +index e5af19b760a..c9755322d16 100644 +--- a/test/conftest.py ++++ b/test/conftest.py +@@ -18,7 +18,7 @@ xml_key = StashKey["LogXMLReruns"]() + + + def pytest_addoption(parser: Parser) -> None: +- group = parser.getgroup("terminal reporting") ++ group = parser.getgroup("terminal reporting functorch") + group.addoption( + "--junit-xml-reruns", + action="store", diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_fix-test_memory_profiler.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_fix-test_memory_profiler.patch new file mode 100644 index 00000000000..b11903a6de3 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_fix-test_memory_profiler.patch @@ -0,0 +1,19 @@ +The test seems to be too sensitive and may fail due to a small temporary allocation. +Increase the filter size to make it pass. +See https://github.com/pytorch/pytorch/issues/109592 + +Author: Alexander Grund (TU Dresden) + +diff --git a/test/profiler/test_memory_profiler.py b/test/profiler/test_memory_profiler.py +index 70b21b6b610..176fe153638 100644 +--- a/test/profiler/test_memory_profiler.py ++++ b/test/profiler/test_memory_profiler.py +@@ -1480,7 +1480,7 @@ class TestMemoryProfilerE2E(TestCase): + + # We generally don't care about tiny allocations during memory + # profiling and they add a lot of noise to the unit test. +- if size >= 256 ++ if size >= 1024 + ] + + self.assertExpectedInline( diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_fix-torch.compile-on-ppc.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_fix-torch.compile-on-ppc.patch new file mode 100644 index 00000000000..0b064c8b4c7 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_fix-torch.compile-on-ppc.patch @@ -0,0 +1,39 @@ +commit 9942a14e96c539cb0195475d2cd660dcdc274123 +Author: Nisanth M P +Date: Fri Jul 14 04:09:14 2023 +0000 + + Fix torch.compile g++ flag error on ppc64le (#104956) + + g++ flag -march is not recognised on ppc64le. So adding a check for platform machine to be ppc64le and using -mcpu flag instead. Other architectures will still use -march flag + + This fixes the torch.compile feature failure on ppc64le + + Pull Request resolved: https://github.com/pytorch/pytorch/pull/104956 + Approved by: https://github.com/jgong5, https://github.com/jansel + +diff --git a/torch/_inductor/codecache.py b/torch/_inductor/codecache.py +--- a/torch/_inductor/codecache.py ++++ b/torch/_inductor/codecache.py +@@ -7,6 +7,7 @@ import json + import logging + import multiprocessing + import os ++import platform + import re + import shutil + import signal +@@ -378,7 +379,14 @@ def optimization_flags(): + # Also, `-march=native` is unrecognized option on M1 + base_flags += " -Xclang -fopenmp" + else: +- base_flags += " -march=native -fopenmp" ++ if platform.machine() == "ppc64le": ++ base_flags += " -mcpu=native" ++ else: ++ base_flags += " -march=native" ++ ++ # Internal cannot find libgomp.so ++ if not config.is_fbcode(): ++ base_flags += " -fopenmp" + return base_flags + diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_fix-ub-in-inductor-codegen.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_fix-ub-in-inductor-codegen.patch new file mode 100644 index 00000000000..5651f8fbbcf --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_fix-ub-in-inductor-codegen.patch @@ -0,0 +1,34 @@ +Casting negative floats to unsigned integers is undefined behavior so results vary between +different invocations and platforms. +This causes failures on e.g. PPC with test_comprehensive_byte in inductor/test_torchinductor_opinfo +See https://github.com/pytorch/pytorch/issues/110077 + +Fix by using `c10::convert` which handles that case. + +Author: Alexander Grund (TU Dresden) + +diff --git a/torch/_inductor/codegen/cpp.py b/torch/_inductor/codegen/cpp.py +index de6a32421c1..d16ae4cd91c 100644 +--- a/torch/_inductor/codegen/cpp.py ++++ b/torch/_inductor/codegen/cpp.py +@@ -577,7 +577,7 @@ class CppOverrides(OpOverrides): + @staticmethod + def to_dtype(x, dtype): + assert dtype in DTYPE_TO_CPP, f"{dtype} missing from {__name__}.DTYPE_TO_CPP" +- return f"static_cast<{DTYPE_TO_CPP[dtype]}>({x})" ++ return f"c10::convert<{DTYPE_TO_CPP[dtype]}>({x})" + + @staticmethod + def abs(x): +diff --git a/torch/_inductor/codegen/cpp_prefix.h b/torch/_inductor/codegen/cpp_prefix.h +index e0dba663144..9e17e481a89 100644 +--- a/torch/_inductor/codegen/cpp_prefix.h ++++ b/torch/_inductor/codegen/cpp_prefix.h +@@ -12,6 +12,7 @@ + #endif + #include + #include ++#include + + typedef at::Half half; + typedef at::BFloat16 bfloat16; diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_fix-vsx-loadu.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_fix-vsx-loadu.patch new file mode 100644 index 00000000000..5d8afb76fe5 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_fix-vsx-loadu.patch @@ -0,0 +1,31 @@ +Fix access to unitialized memory on PPC +See https://github.com/pytorch/pytorch/issues/32502 & https://github.com/pytorch/pytorch/pull/109487 + +Author: Alexander Grund (TU Dresden) + +diff --git a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_qint8_vsx.h b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_qint8_vsx.h +index 806f6731abb..648ed06afa6 100644 +--- a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_qint8_vsx.h ++++ b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_qint8_vsx.h +@@ -91,7 +91,7 @@ struct Vectorized { + vec_vsx_ld(offset0, reinterpret_cast(ptr)), + vec_vsx_ld(offset16, reinterpret_cast(ptr))}; + } +- __at_align__ value_type tmp_values[size()]; ++ __at_align__ value_type tmp_values[size()] = {}; + std::memcpy(tmp_values, ptr, std::min(count, size()) * sizeof(value_type)); + return {vec_vsx_ld(offset0, tmp_values), vec_vsx_ld(offset16, tmp_values)}; + } +diff --git a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_quint8_vsx.h b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_quint8_vsx.h +index 891c56b53ec..db3698804a7 100644 +--- a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_quint8_vsx.h ++++ b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_quint8_vsx.h +@@ -94,7 +94,7 @@ struct Vectorized { + vec_vsx_ld(offset0, reinterpret_cast(ptr)), + vec_vsx_ld(offset16, reinterpret_cast(ptr))}; + } +- __at_align__ value_type tmp_values[size()]; ++ __at_align__ value_type tmp_values[size()] = {}; + std::memcpy(tmp_values, ptr, std::min(count, size()) * sizeof(value_type)); + return {vec_vsx_ld(offset0, tmp_values), vec_vsx_ld(offset16, tmp_values)}; + } diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_no-cuda-stubs-rpath.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_no-cuda-stubs-rpath.patch new file mode 100644 index 00000000000..df699c5517e --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_no-cuda-stubs-rpath.patch @@ -0,0 +1,186 @@ +# PyTorch's CMAKE configuration by default sets RUNPATH on libraries if they link other libraries +# that are outside the build tree, which is done because of the CMAKE config on +# https://github.com/pytorch/pytorch/blob/v1.10.0/cmake/Dependencies.cmake#L10. +# This provides problems, since the cuda stubs library path then also gets added to the RUNPATH. +# As a result, at runtime, the stub version of things like libcuda.so.1 gets picked up, instead of the real drivers +# See https://github.com/easybuilders/easybuild-easyconfigs/issues/14359 +# This line https://github.com/pytorch/pytorch/blob/v1.10.0/cmake/Dependencies.cmake#L16 +# Makes sure that any path that is linked, is also added to the RUNPATH. +# This has been reported upstream in https://github.com/pytorch/pytorch/issues/35418 +# and a fix was attempted in https://github.com/pytorch/pytorch/pull/37737 but it was reverted +# +# This EasyBuild patch changes behavior for the libraries that were failing, i.e. the ones in this list: +# https://github.com/easybuilders/easybuild-easyconfigs/issues/14359#issuecomment-970479904 +# This is done by setting INSTALL_RPATH_USE_LINK_PATH to false, and instead, specifying the RPATH +# explicitely by defining INSTALL_RPATH, but only adding directories that do not match to the "stubs" regex +# +# Original patch: Caspar van Leeuwen +# Updated: Alexander Grund (TU Dresden) +# +# See https://github.com/pytorch/pytorch/pull/87593 + +diff --git a/caffe2/CMakeLists.txt b/caffe2/CMakeLists.txt +index 221e3f32b29..c3f24060f6a 100644 +--- a/caffe2/CMakeLists.txt ++++ b/caffe2/CMakeLists.txt +@@ -627,14 +627,13 @@ endif() + if(USE_CUDA) + list(APPEND Caffe2_GPU_CU_SRCS ${Caffe2_GPU_HIP_JIT_FUSERS_SRCS}) + add_library(caffe2_nvrtc SHARED ${ATen_NVRTC_STUB_SRCS}) ++ include(${Torch_SOURCE_DIR}/cmake/LinkCudaLibraries.cmake) ++ link_cuda_libraries(caffe2_nvrtc ${CUDA_NVRTC} ${CUDA_CUDA_LIB} ${CUDA_NVRTC_LIB}) + if(MSVC) + # Delay load nvcuda.dll so we can import torch compiled with cuda on a CPU-only machine +- set(DELAY_LOAD_FLAGS "-DELAYLOAD:nvcuda.dll;delayimp.lib") +- else() +- set(DELAY_LOAD_FLAGS "") ++ target_link_libraries(caffe2_nvrtc "-DELAYLOAD:nvcuda.dll;delayimp.lib") + endif() + +- target_link_libraries(caffe2_nvrtc ${CUDA_NVRTC} ${CUDA_CUDA_LIB} ${CUDA_NVRTC_LIB} ${DELAY_LOAD_FLAGS}) + target_include_directories(caffe2_nvrtc PRIVATE ${CUDA_INCLUDE_DIRS}) + install(TARGETS caffe2_nvrtc DESTINATION "${TORCH_INSTALL_LIB_DIR}") + if(USE_NCCL) +diff --git a/cmake/LinkCudaLibraries.cmake b/cmake/LinkCudaLibraries.cmake +new file mode 100644 +index 00000000000..005914ccc6f +--- /dev/null ++++ b/cmake/LinkCudaLibraries.cmake +@@ -0,0 +1,33 @@ ++# Link CUDA libraries to the given target, i.e.: `target_link_libraries(target )` ++# ++# Additionally makes sure CUDA stub libs don't end up being in RPath ++# ++# Example: link_cuda_libraries(mytarget PRIVATE ${CUDA_LIBRARIES}) ++function(link_cuda_libraries target) ++ set(libs ${ARGN}) ++ set(install_rpath "$ORIGIN") ++ set(filtered FALSE) ++ foreach(lib IN LISTS libs) ++ # CUDA stub libs are in form /prefix/lib/stubs/libcuda.so ++ # So extract the name of the parent folder, to check against "stubs" ++ # And the parent path which we need to add to the INSTALL_RPATH for non-stubs ++ get_filename_component(parent_path "${lib}" DIRECTORY) ++ get_filename_component(parent_name "${parent_path}" NAME) ++ if(parent_name STREQUAL "stubs") ++ message(STATUS "Filtering ${lib} from being set in ${target}'s RPATH, " ++ "because it appears to point to the CUDA stubs directory.") ++ set(filtered TRUE) ++ elseif(parent_path) ++ list(APPEND install_rpath ${parent_path}) ++ endif() ++ endforeach() ++ ++ # Regular link command ++ target_link_libraries(${target} ${libs}) ++ # Manually set INSTALL_RPATH when there were any stub libs ++ if(filtered) ++ list(REMOVE_DUPLICATES install_rpath) ++ set_target_properties(${target} PROPERTIES INSTALL_RPATH_USE_LINK_PATH FALSE) ++ set_target_properties(${target} PROPERTIES INSTALL_RPATH "${install_rpath}") ++ endif() ++endfunction() +diff --git a/test/cpp/api/CMakeLists.txt b/test/cpp/api/CMakeLists.txt +index 6b801a07318..6ac92870479 100644 +--- a/test/cpp/api/CMakeLists.txt ++++ b/test/cpp/api/CMakeLists.txt +@@ -54,7 +54,8 @@ if(NOT MSVC) + endif() + + if(USE_CUDA) +- target_link_libraries(test_api PRIVATE ++ include(${Torch_SOURCE_DIR}/cmake/LinkCudaLibraries.cmake) ++ link_cuda_libraries(test_api PRIVATE + ${CUDA_LIBRARIES} + ${CUDA_NVRTC_LIB} + ${CUDA_CUDA_LIB} +diff --git a/test/cpp/dist_autograd/CMakeLists.txt b/test/cpp/dist_autograd/CMakeLists.txt +index 9969c63e16d..356ba5be55c 100644 +--- a/test/cpp/dist_autograd/CMakeLists.txt ++++ b/test/cpp/dist_autograd/CMakeLists.txt +@@ -10,7 +10,8 @@ if(USE_DISTRIBUTED AND NOT WIN32) + target_link_libraries(test_dist_autograd PRIVATE torch gtest) + + if(USE_CUDA) +- target_link_libraries(test_dist_autograd PRIVATE ++ include(${Torch_SOURCE_DIR}/cmake/LinkCudaLibraries.cmake) ++ link_cuda_libraries(test_dist_autograd PRIVATE + ${CUDA_LIBRARIES} + ${CUDA_NVRTC_LIB} + ${CUDA_CUDA_LIB} +diff --git a/test/cpp/jit/CMakeLists.txt b/test/cpp/jit/CMakeLists.txt +index 2376f1bc43b..30fbb99fa6d 100644 +--- a/test/cpp/jit/CMakeLists.txt ++++ b/test/cpp/jit/CMakeLists.txt +@@ -139,7 +139,8 @@ if(LINUX) + endif() + + if(USE_CUDA) +- target_link_libraries(test_jit PRIVATE ++ include(${Torch_SOURCE_DIR}/cmake/LinkCudaLibraries.cmake) ++ link_cuda_libraries(test_jit PRIVATE + ${CUDA_LIBRARIES} + ${CUDA_NVRTC_LIB} + ${CUDA_CUDA_LIB} +diff --git a/test/cpp/rpc/CMakeLists.txt b/test/cpp/rpc/CMakeLists.txt +index 3997f8753e5..21fddbc645d 100644 +--- a/test/cpp/rpc/CMakeLists.txt ++++ b/test/cpp/rpc/CMakeLists.txt +@@ -33,7 +33,8 @@ target_include_directories( + target_link_libraries(test_cpp_rpc PRIVATE ${TORCH_RPC_TEST_DEPENDENCY_LIBS}) + + if(USE_CUDA) +- target_link_libraries(test_cpp_rpc PRIVATE ++ include(${Torch_SOURCE_DIR}/cmake/LinkCudaLibraries.cmake) ++ link_cuda_libraries(test_cpp_rpc PRIVATE + ${CUDA_LIBRARIES} + ${CUDA_NVRTC_LIB} + ${CUDA_CUDA_LIB} +diff --git a/test/cpp/tensorexpr/CMakeLists.txt b/test/cpp/tensorexpr/CMakeLists.txt +index 7dff70630d3..ecb83005492 100644 +--- a/test/cpp/tensorexpr/CMakeLists.txt ++++ b/test/cpp/tensorexpr/CMakeLists.txt +@@ -57,14 +57,15 @@ if(USE_PTHREADPOOL) + target_link_libraries(test_tensorexpr PRIVATE pthreadpool_interface) + endif() + if(USE_CUDA) +- target_link_libraries(test_tensorexpr PRIVATE ++ include(${Torch_SOURCE_DIR}/cmake/LinkCudaLibraries.cmake) ++ link_cuda_libraries(test_tensorexpr PRIVATE + ${CUDA_LIBRARIES} + ${CUDA_NVRTC_LIB} + ${CUDA_CUDA_LIB} + ${TORCH_CUDA_LIBRARIES}) + target_compile_definitions(test_tensorexpr PRIVATE USE_CUDA) + +- target_link_libraries(tutorial_tensorexpr PRIVATE ++ link_cuda_libraries(tutorial_tensorexpr PRIVATE + ${CUDA_LIBRARIES} + ${CUDA_NVRTC_LIB} + ${CUDA_CUDA_LIB} +diff --git a/test/test_torch.py b/test/test_torch.py +index c86535e22c0..6859311d806 100644 +--- a/test/test_torch.py ++++ b/test/test_torch.py +@@ -8833,6 +8833,21 @@ def add_neg_dim_tests(): + assert not hasattr(TestTorch, test_name), "Duplicated test name: " + test_name + setattr(TestTorch, test_name, make_neg_dim_test(name, tensor_arg, arg_constr, types, extra_dim)) + ++class TestRPATH(TestCase): ++ @unittest.skipIf(not sys.platform.startswith('linux'), "linux-only test") ++ def test_rpath(self): ++ """ ++ Make sure RPATH (or RUNPATH) in nvrtc does not contain a cuda stubs directory ++ issue gh-35418 ++ """ ++ libdir = os.path.join(os.path.dirname(torch._C.__file__), 'lib') ++ caffe2_nvrtc = os.path.join(libdir, 'libcaffe2_nvrtc.so') ++ if os.path.exists(caffe2_nvrtc): ++ output = subprocess.check_output(['objdump', '-x', caffe2_nvrtc]) ++ for line in output.split(b'\n'): ++ if b'RPATH' in line or b'RUNPATH' in line: ++ self.assertFalse(b'stubs' in line) ++ + # TODO: these empy classes are temporarily instantiated for XLA compatibility + # once XLA updates their test suite it should be removed + class TestViewOps(TestCase): diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_remove-test-requiring-online-access.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_remove-test-requiring-online-access.patch new file mode 100644 index 00000000000..4022d01c852 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_remove-test-requiring-online-access.patch @@ -0,0 +1,30 @@ +This downloads a Perl file from a Github repo which may fail in: + + File "test/test_cuda.py", line 4632, in test_memory_snapshot + torch.cuda.memory._save_segment_usage(f.name) + File "/torch/cuda/memory.py", line 610, in _save_segment_usage + f.write(_segments(snapshot)) + File "/torch/cuda/_memory_viz.py", line 60, in segments + return format_flamegraph(f.getvalue()) + File "/torch/cuda/_memory_viz.py", line 21, in format_flamegraph + urllib.request.urlretrieve( + +Author: Alexander Grund (TU Dresden) + +diff --git a/test/test_cuda.py b/test/test_cuda.py +index 7f2693b52c5..4bff69e5cad 100644 +--- a/test/test_cuda.py ++++ b/test/test_cuda.py +@@ -4993,12 +4993,6 @@ class TestCudaComm(TestCase): + found_it = True + self.assertTrue(found_it) + +- if not IS_WINDOWS: +- with tempfile.NamedTemporaryFile() as f: +- torch.cuda.memory._save_segment_usage(f.name) +- with open(f.name, 'r') as f2: +- self.assertTrue('test_cuda.py' in f2.read()) +- + del x + torch.cuda.empty_cache() + ss = torch.cuda.memory._snapshot() diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_skip-diff-test-on-ppc.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_skip-diff-test-on-ppc.patch new file mode 100644 index 00000000000..41d0da2eb03 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_skip-diff-test-on-ppc.patch @@ -0,0 +1,26 @@ +The workaround for over/underflow isn't implemented for PPC yet. +So skip the test. +See https://github.com/pytorch/pytorch/issues/109870 + +Author: Alexander Grund (TU Dresden) + +diff --git a/test/test_binary_ufuncs.py b/test/test_binary_ufuncs.py +index 57fc1b76f18..06c129e007a 100644 +--- a/test/test_binary_ufuncs.py ++++ b/test/test_binary_ufuncs.py +@@ -27,6 +27,7 @@ from torch.testing._internal.common_utils import ( + numpy_to_torch_dtype_dict, + TEST_SCIPY, + set_default_dtype, ++ IS_PPC, + ) + from torch.testing._internal.common_device_type import ( + expectedFailureMeta, +@@ -1091,6 +1092,7 @@ class TestBinaryUfuncs(TestCase): + ) + + @dtypes(*complex_types()) ++ @skipIf(IS_PPC, "Vectorized div fails on PPC: #109870") + def test_complex_div_underflow_overflow(self, device, dtype): + # test to make sure the complex division does not produce underflow or overflow + # in the intermediate of its calculations diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_skip-failing-gradtest.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_skip-failing-gradtest.patch new file mode 100644 index 00000000000..19d427b3049 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_skip-failing-gradtest.patch @@ -0,0 +1,16 @@ +test_fn_grad_linalg_det_singular_cpu_float64 fails not only on macos + +Author: Alexander Grund (TU Dresden) + +diff --git a/torch/testing/_internal/opinfo/definitions/linalg.py b/torch/testing/_internal/opinfo/definitions/linalg.py +index 616c8cf42f4..3a07d19df46 100644 +--- a/torch/testing/_internal/opinfo/definitions/linalg.py ++++ b/torch/testing/_internal/opinfo/definitions/linalg.py +@@ -1135,7 +1135,6 @@ op_db: List[OpInfo] = [ + "test_fn_grad", + device_type="cpu", + dtypes=(torch.float64,), +- active_if=IS_MACOS, + ), + DecorateInfo( + unittest.skip("Gradients are incorrect on macos"), diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_skip-test_shuffle_reproducibility.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_skip-test_shuffle_reproducibility.patch new file mode 100644 index 00000000000..f02e5d3ab0d --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_skip-test_shuffle_reproducibility.patch @@ -0,0 +1,20 @@ +The test fails on some systems with +> RuntimeError: Too many open files. Communication with the workers is no longer possible. +> Please increase the limit using `ulimit -n` in the shell or change the sharing strategy by calling `torch.multiprocessing.set_sharing_strategy('file_system')` at the beginning of your code + +So just skip it. + +Author: Alexander Grund (TU Dresden) + +diff --git a/test/test_dataloader.py b/test/test_dataloader.py +index 39d91876f0b..aff47063344 100644 +--- a/test/test_dataloader.py ++++ b/test/test_dataloader.py +@@ -1542,6 +1542,7 @@ except RuntimeError as e: + def test_shuffle_batch(self): + self._test_shuffle(self._get_data_loader(self.dataset, batch_size=2, shuffle=True)) + ++ @unittest.skip("May cause 'Too many open files' error due to potential `ulimit -n` restrictions") + def test_shuffle_reproducibility(self): + for fn in ( + lambda: DataLoader(self.dataset, shuffle=True, num_workers=0, generator=torch.Generator().manual_seed(42)), diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_skip-tests-skipped-in-subprocess.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_skip-tests-skipped-in-subprocess.patch new file mode 100644 index 00000000000..8e80dec749f --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_skip-tests-skipped-in-subprocess.patch @@ -0,0 +1,34 @@ +Use unittest.skip to skip tests skipped by subprocesses as otherwise skipped tests +marked as expectedFailure may succeed unexpectatly failing the testsuite. +E.g.: +> INFO:torch.testing._internal.common_distributed:Thread 0 skipping test > for following reason: PyTorch is built without MKL support +> INFO:torch.testing._internal.common_distributed:Thread 1 skipping test > for following reason: PyTorch is built without MKL support +> INFO:torch.testing._internal.common_distributed:Skipping > on sandcastle for the following reason: Test skipped at subprocess level, look at subprocess log for skip reason +> u +> ... +> FAILED (unexpected successes=1) + +Author: Alexander Grund (TU Dresden) + +diff --git a/torch/testing/_internal/common_distributed.py b/torch/testing/_internal/common_distributed.py +index 400aa80fdca..afea4a8f89f 100644 +--- a/torch/testing/_internal/common_distributed.py ++++ b/torch/testing/_internal/common_distributed.py +@@ -828,7 +828,7 @@ class MultiProcessTestCase(TestCase): + ) + for skip in TEST_SKIPS.values(): + if first_process.exitcode == skip.exit_code: +- if IS_SANDCASTLE: ++ if False: + # Don't use unittest.skip to skip the test on sandcastle + # since it creates tasks for skipped tests assuming there + # is some follow-up needed. Instead just "pass" the test +@@ -1123,7 +1123,7 @@ class MultiThreadedTestCase(TestCase): + if skip_code > 0: + for skip in TEST_SKIPS.values(): + if skip_code == skip.exit_code: +- if IS_SANDCASTLE: ++ if False: + # "pass" the test with an appropriate message. + logger.info( + f"Skipping {fn} on sandcastle for the following reason: {skip.message}" From c1c1ef069def6d08e76dfa426ba99be738905d59 Mon Sep 17 00:00:00 2001 From: Adam Huffman <12435+verdurin@users.noreply.github.com> Date: Tue, 24 Oct 2023 12:14:34 +0000 Subject: [PATCH 072/599] adding easyconfigs: Seurat-4.4.0-foss-2022b-R-4.2.2.eb --- .../Seurat/Seurat-4.4.0-foss-2022b-R-4.2.2.eb | 76 +++++++++++++++++++ 1 file changed, 76 insertions(+) create mode 100644 easybuild/easyconfigs/s/Seurat/Seurat-4.4.0-foss-2022b-R-4.2.2.eb diff --git a/easybuild/easyconfigs/s/Seurat/Seurat-4.4.0-foss-2022b-R-4.2.2.eb b/easybuild/easyconfigs/s/Seurat/Seurat-4.4.0-foss-2022b-R-4.2.2.eb new file mode 100644 index 00000000000..2b65e56b170 --- /dev/null +++ b/easybuild/easyconfigs/s/Seurat/Seurat-4.4.0-foss-2022b-R-4.2.2.eb @@ -0,0 +1,76 @@ +easyblock = 'Bundle' + +name = 'Seurat' +version = '4.4.0' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://satijalab.org/seurat' +description = "Seurat is an R package designed for QC, analysis, and exploration of single cell RNA-seq data." + +toolchain = {'name': 'foss', 'version': '2022b'} + +dependencies = [ + ('R', '4.2.2'), + ('R-bundle-Bioconductor', '3.16', versionsuffix), +] + +exts_defaultclass = 'RPackage' +exts_default_options = { + 'sources': ['%(name)s_%(version)s.tar.gz'], + '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 + ], +} + +exts_list = [ + ('Matrix', '1.6-1.1', { + 'checksums': ['331eb1f1fe9441d4224d8551072443596001b50e8c15618f59cb938b46ee8cc2'], + }), + ('sp', '1.5-1', { + 'checksums': ['69b9eab481d389bbb736d2adcf50c180aca248c3ffc4ebda8ffe2accc5f229df'], + }), + ('SeuratObject', '4.1.4', { + 'checksums': ['74e7649ad9795c962c0b12d039d7bf9b11a8a275a63c3a0fa1205b684e5310ef'], + }), + ('sctransform', '0.4.0', { + 'checksums': ['9aef10c196a9578e0d7a8e244c55cf28eb0685947d9df9e2d7790c2b99c6b4b3'], + }), + ('uwot', '0.1.14', { + 'checksums': ['8016e8192b7e72604ca71840cbe43fa1d2caed8a8ad7cbf20e85cd3b384a9fe0'], + }), + ('spatstat.utils', '3.0-1', { + 'checksums': ['cba1c7806564fd9145ca15edf77233d6ba5609f0989f7812221f5fc1ece0b91a'], + }), + ('spatstat.data', '3.0-0', { + 'checksums': ['cff9058a88489020a4a05b9576cd452f37fa9b42084873c474d06931f5187057'], + }), + ('spatstat.geom', '3.0-3', { + 'checksums': ['6e5b56c60e774a0cdcaa5a8ffde071225f233832446a341588bd8a7840913c84'], + }), + ('spatstat.random', '3.0-1', { + 'checksums': ['938c845c063b8781bf894c0a67537e7b2a7c425a4beba4a95ec9d2c37b43e5b6'], + }), + ('spatstat.sparse', '3.0-0', { + 'checksums': ['99be0a3c7592760fdf1668dc0811f75ed91c400390d1ecc3d5e643255f501ad2'], + }), + ('spatstat.explore', '3.0-5', { + 'checksums': ['9f438a12fac3f3e1d0bd550b1393c1e5732be694517b0878db09da557d6dc862'], + }), + ('scattermore', '1.2', { + 'checksums': ['5534a87b0bdd1375f0fbffc1a5c980ad64e33a108435a67469b8324b580602d1'], + }), + (name, version, { + 'checksums': ['0f17df9597642cfc1db4d8718f0b59ebab9fbed328b1f885f42ee85ea0dcb4dd'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +modextrapaths = {'R_LIBS_SITE': ''} + +moduleclass = 'bio' From 05c56f212f710533eb1b932d13666642cc93dde9 Mon Sep 17 00:00:00 2001 From: Orient Date: Tue, 24 Oct 2023 19:00:11 +0200 Subject: [PATCH 073/599] adding easyconfigs: gff3tool-2.1.0-foss-2022a.eb and patches: GFF3toolkit-2.1.0-remove_hardcode.patch --- .../GFF3toolkit-2.1.0-remove_hardcode.patch | 88 +++++++++++++++++++ .../g/gff3tool/gff3tool-2.1.0-foss-2022a.eb | 28 ++++++ 2 files changed, 116 insertions(+) create mode 100644 easybuild/easyconfigs/g/gff3tool/GFF3toolkit-2.1.0-remove_hardcode.patch create mode 100644 easybuild/easyconfigs/g/gff3tool/gff3tool-2.1.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/g/gff3tool/GFF3toolkit-2.1.0-remove_hardcode.patch b/easybuild/easyconfigs/g/gff3tool/GFF3toolkit-2.1.0-remove_hardcode.patch new file mode 100644 index 00000000000..99aa1e1e734 --- /dev/null +++ b/easybuild/easyconfigs/g/gff3tool/GFF3toolkit-2.1.0-remove_hardcode.patch @@ -0,0 +1,88 @@ +This patch removes the hardcoded part of the setup.py that downloads and installs BLAST+ +Author: Orient Kružík (INUITS) +diff -ruN gff3tool-2.1.0_orig/setup.py gff3tool-2.1.0/setup.py +--- gff3tool-2.1.0_orig/setup.py 2023-10-22 17:15:12.175583000 +0200 ++++ gff3tool-2.1.0/setup.py 2023-10-22 17:20:48.098956000 +0200 +@@ -6,69 +6,12 @@ + """ + # Always prefer setuptools over distutils + from setuptools import setup, find_packages +-from distutils.command.build import build + # To use a consistent encoding + from codecs import open +-from os import path, remove, mkdir +-import shutil +-import tarfile +-try: +- from urllib.request import urlretrieve +-except ImportError: +- from urllib import urlretrieve +- +-import platform +-import sys +-from wheel.bdist_wheel import bdist_wheel as _bdist_wheel +- ++from os import path + + here = path.abspath(path.dirname(__file__)) + +- +-class bdist_wheel(_bdist_wheel): +- def finalize_options(self): +- _bdist_wheel.finalize_options(self) +- # Mark us as not a pure python package +- self.root_is_pure = False +- +-class CustomBuildCommand(build): +- def run(self): +- platform_system = platform.system( +- ) # Linux: Linux; Mac:Darwin; Windows: Windows +- +- blast_path = path.join(here, 'gff3tool', 'lib', 'ncbi-blast+') +- blast_file = path.join(blast_path, 'blast.tgz') +- +- mkdir(blast_path) +- +- if platform_system == 'Linux': +- urlretrieve( +- 'https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.31/ncbi-blast-2.2.31+-x64-linux.tar.gz', +- blast_file) +- elif platform_system == 'Windows': +- urlretrieve( +- 'https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.31/ncbi-blast-2.2.31+-x64-win64.tar.gz', +- blast_file) +- elif platform_system == 'Darwin': +- urlretrieve( +- 'https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.31/ncbi-blast-2.2.31+-universal-macosx.tar.gz', +- blast_file) +- else: +- sys.error( +- 'GFF3 Toolkit currently only supports linux, windows, and MacOS' +- ) +- +- tar = tarfile.open(blast_file, 'r:gz') +- tar.extractall(blast_path) +- tar.close() +- +- extract_path = path.join(blast_path, 'ncbi-blast-2.2.31+') +- shutil.move(path.join(extract_path, 'bin'), blast_path) +- if path.exists(blast_file): +- remove(blast_file) +- if path.exists(extract_path): +- shutil.rmtree(extract_path) +- + # Get the long description from the README file + with open(path.join(here, 'README.md'), encoding='utf-8') as f: + long_description = f.read() +@@ -170,11 +113,6 @@ + # + packages=find_packages(exclude=['contrib', 'docs', 'tests']), # Required + +- cmdclass={ +- 'build': CustomBuildCommand, +- 'bdist_wheel': bdist_wheel +- }, +- + # This field lists other packages that your project depends on to run. + # Any package you put here will be installed by pip when your project is + # installed, so they must be valid existing projects. diff --git a/easybuild/easyconfigs/g/gff3tool/gff3tool-2.1.0-foss-2022a.eb b/easybuild/easyconfigs/g/gff3tool/gff3tool-2.1.0-foss-2022a.eb new file mode 100644 index 00000000000..ccc79b535ad --- /dev/null +++ b/easybuild/easyconfigs/g/gff3tool/gff3tool-2.1.0-foss-2022a.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'gff3tool' +version = '2.1.0' + +homepage = 'https://gff3toolkit.readthedocs.io' +description = 'Python programs for processing GFF3 files' + +toolchain = {'name': 'foss', 'version': '2022a'} + +sources = ['gff3tool-2.1.0.tar.gz'] +patches = ['GFF3toolkit-2.1.0-remove_hardcode.patch'] +checksums = [ + {'gff3tool-2.1.0.tar.gz': 'e842ef4afdb66926a2b63bf2619c7ef30bd9b76a5f1084a5c57bf8b39cc4f15d'}, + {'GFF3toolkit-2.1.0-remove_hardcode.patch': '03696635af25ab1e3d650b46c7aeaaaadb31e7eac766039c758150f3f3162cb7'}, +] + +local_blast_path = '%(installdir)s/lib/python%(pyshortver)s/site-packages/gff3tool/lib/ncbi-blast+' +preinstallopts = 'mkdir -p %s && ' % local_blast_path +preinstallopts += 'ln -s $EBROOTBLASTPLUS/bin %s && ' % local_blast_path + +dependencies = [ + ('Python', '3.10.4'), + ('BLAST+', '2.13.0'), +] + +use_pip = True +sanity_pip_check = True From 8366961f534d57a2ec2ccb8368c6cdedf0a3f8b0 Mon Sep 17 00:00:00 2001 From: Orient Date: Tue, 24 Oct 2023 21:01:25 +0200 Subject: [PATCH 074/599] Added moduleclass and set download_dep_fail --- easybuild/easyconfigs/g/gff3tool/gff3tool-2.1.0-foss-2022a.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/g/gff3tool/gff3tool-2.1.0-foss-2022a.eb b/easybuild/easyconfigs/g/gff3tool/gff3tool-2.1.0-foss-2022a.eb index ccc79b535ad..80f979fe27c 100644 --- a/easybuild/easyconfigs/g/gff3tool/gff3tool-2.1.0-foss-2022a.eb +++ b/easybuild/easyconfigs/g/gff3tool/gff3tool-2.1.0-foss-2022a.eb @@ -26,3 +26,6 @@ dependencies = [ use_pip = True sanity_pip_check = True +download_dep_fail = True + +moduleclass = "tools" From 4534cf815cd7de928b0e7ba8c3ce9ddb852e4788 Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Wed, 25 Oct 2023 14:26:01 +0000 Subject: [PATCH 075/599] adding easyconfigs: boto3-1.28.70-GCCcore-12.3.0.eb --- .../b/boto3/boto3-1.28.70-GCCcore-12.3.0.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/b/boto3/boto3-1.28.70-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/b/boto3/boto3-1.28.70-GCCcore-12.3.0.eb b/easybuild/easyconfigs/b/boto3/boto3-1.28.70-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..01896809767 --- /dev/null +++ b/easybuild/easyconfigs/b/boto3/boto3-1.28.70-GCCcore-12.3.0.eb @@ -0,0 +1,40 @@ +easyblock = 'PythonBundle' + +name = 'boto3' +version = '1.28.70' + +homepage = 'https://github.com/boto/boto3' +description = """Boto3 is the Amazon Web Services (AWS) Software Development Kit +(SDK) for Python, which allows Python developers to write software that makes +use of services like Amazon S3 and Amazon EC2.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), +] + +exts_list = [ + ('botocore', '1.31.70', { + 'checksums': ['5f49def4ec2e4216dd0195d23d9811027d02ee6c8a37b031e2b2fe38e8c77ddc'], + }), + ('jmespath', '1.0.1', { + 'checksums': ['90261b206d6defd58fdd5e85f478bf633a2901798906be2ad389150c5c60edbe'], + }), + ('s3transfer', '0.7.0', { + 'checksums': ['fd3889a66f5fe17299fe75b82eae6cf722554edca744ca5d5fe308b104883d2e'], + }), + (name, version, { + 'checksums': ['89002e1d8411c7c54110f9f8fc4a11d57d6d7977c0cb4ba064887ca5d4c788f7'], + }), +] + +use_pip = True +sanity_pip_check = True + +moduleclass = 'lib' From 89455ae5241460aafe8fe3abf676ea03de052aae Mon Sep 17 00:00:00 2001 From: WilleBell Date: Wed, 25 Oct 2023 16:36:49 +0200 Subject: [PATCH 076/599] use wrapt 1.15.0 as dep, remove binutils as builddep --- .../s/scikit-lego/scikit-lego-0.6.16-foss-2022a.eb | 8 +------- 1 file changed, 1 insertion(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/s/scikit-lego/scikit-lego-0.6.16-foss-2022a.eb b/easybuild/easyconfigs/s/scikit-lego/scikit-lego-0.6.16-foss-2022a.eb index b469cc61b1e..5ea30879467 100644 --- a/easybuild/easyconfigs/s/scikit-lego/scikit-lego-0.6.16-foss-2022a.eb +++ b/easybuild/easyconfigs/s/scikit-lego/scikit-lego-0.6.16-foss-2022a.eb @@ -14,16 +14,13 @@ toolchain = {'name': 'foss', 'version': '2022a'} github_account = 'koaning' -builddependencies = [ - ('binutils', '2.38'), -] - dependencies = [ ('Python', '3.10.4'), ('SciPy-bundle', '2022.05'), ('scikit-learn', '1.1.2'), ('matplotlib', '3.5.2'), ('umap-learn', '0.5.3'), + ('wrapt', '1.15.0'), ] use_pip = True @@ -38,9 +35,6 @@ exts_list = [ ('patsy', '0.5.3', { 'checksums': ['bdc18001875e319bc91c812c1eb6a10be4bb13cb81eb763f466179dca3b67277'], }), - ('wrapt', '1.14.1', { - 'checksums': ['380a85cf89e0e69b7cfbe2ea9f765f004ff419f34194018a6827ac0e3edfed4d'], - }), (name, version, { 'modulename': 'sklego', 'source_tmpl': 'v%(version)s.tar.gz', From 24c85cba46cb7a2c9b89511b3eb0ec11dc69804b Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 26 Oct 2023 11:13:52 +0200 Subject: [PATCH 077/599] Workaround test_torchinductor_opinfo failure --- .../p/PyTorch/PyTorch-2.0.1-foss-2022b.eb | 3 +++ ...success_in_test_torchinductor_opinfo.patch | 22 +++++++++++++++++++ 2 files changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_ignore_unexpected_success_in_test_torchinductor_opinfo.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1-foss-2022b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1-foss-2022b.eb index 59f471b813e..763167da5cc 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1-foss-2022b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1-foss-2022b.eb @@ -32,6 +32,7 @@ patches = [ 'PyTorch-2.0.1_fix-torch.compile-on-ppc.patch', 'PyTorch-2.0.1_fix-ub-in-inductor-codegen.patch', 'PyTorch-2.0.1_fix-vsx-loadu.patch', + 'PyTorch-2.0.1_ignore_unexpected_success_in_test_torchinductor_opinfo.patch', 'PyTorch-2.0.1_no-cuda-stubs-rpath.patch', 'PyTorch-2.0.1_remove-test-requiring-online-access.patch', 'PyTorch-2.0.1_skip-diff-test-on-ppc.patch', @@ -76,6 +77,8 @@ checksums = [ {'PyTorch-2.0.1_fix-ub-in-inductor-codegen.patch': '1b37194f55ae678f3657b8728dfb896c18ffe8babe90987ce468c4fa9274f357'}, {'PyTorch-2.0.1_fix-vsx-loadu.patch': 'a0ffa61da2d47c6acd09aaf6d4791e527d8919a6f4f1aa7ed38454cdcadb1f72'}, + {'PyTorch-2.0.1_ignore_unexpected_success_in_test_torchinductor_opinfo.patch': + '57e2985a5b7085c2786e4b0c4a5f0c81f6b2ae9d5804bbd552b06e8b1570f4c4'}, {'PyTorch-2.0.1_no-cuda-stubs-rpath.patch': '8902e58a762240f24cdbf0182e99ccdfc2a93492869352fcb4ca0ec7e407f83a'}, {'PyTorch-2.0.1_remove-test-requiring-online-access.patch': '721ab0d35ed0ff8a46cb84ced5a98c0fb8ce6143cf6cea80b1360d3d7f64f584'}, diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_ignore_unexpected_success_in_test_torchinductor_opinfo.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_ignore_unexpected_success_in_test_torchinductor_opinfo.patch new file mode 100644 index 00000000000..db8aa200deb --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_ignore_unexpected_success_in_test_torchinductor_opinfo.patch @@ -0,0 +1,22 @@ +Some tests may succeed although they are not expected to. E.g.: +> FAILED inductor/test_torchinductor_opinfo.py::TestInductorOpInfoCPU::test_comprehensive_index_add_cpu_float16 - RuntimeError: unexpected success index_add, torch.float16, cpu +> FAILED inductor/test_torchinductor_opinfo.py::TestInductorOpInfoCPU::test_comprehensive_scatter_add_cpu_float16 - RuntimeError: unexpected success scatter_add, torch.float16, cpu +> FAILED inductor/test_torchinductor_opinfo.py::TestInductorOpInfoCPU::test_comprehensive_scatter_reduce_sum_cpu_float16 - RuntimeError: unexpected success scatter_reduce.sum, torch.float16, cpu + +Disable that unexpected success check. + +Author: Alexander Grund (TU Dresden) + +diff --git a/test/inductor/test_torchinductor_opinfo.py b/test/inductor/test_torchinductor_opinfo.py +index d91a27684ba..1e6d247c8d4 100644 +--- a/test/inductor/test_torchinductor_opinfo.py ++++ b/test/inductor/test_torchinductor_opinfo.py +@@ -66,7 +66,7 @@ _ops = partial( + TestExpect = Enum("TestExpect", ("SUCCESS", "XFAILURE", "SKIP")) + + COLLECT_EXPECT = os.getenv("PYTORCH_COLLECT_EXPECT", "0") == "1" +-FAIL_ON_SUCCESS = os.getenv("PYTORCH_FAIL_ON_SUCCESS", "1") == "1" ++FAIL_ON_SUCCESS = False + ALL_SAMPLES = os.getenv("PYTORCH_ALL_SAMPLES", "0") == "1" + START = os.getenv("PYTORCH_TEST_RANGE_START", None) + END = os.getenv("PYTORCH_TEST_RANGE_END", None) From c110b159cbbe40bdf1a66c7f590c030c177e3350 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 26 Oct 2023 14:02:55 +0200 Subject: [PATCH 078/599] Add patch description --- easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1-foss-2022b.eb | 2 +- ...Torch-2.0.1_add-missing-vsx-vector-shift-functions.patch | 6 ++++++ 2 files changed, 7 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1-foss-2022b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1-foss-2022b.eb index 763167da5cc..6f869d07be5 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1-foss-2022b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1-foss-2022b.eb @@ -62,7 +62,7 @@ checksums = [ {'PyTorch-1.13.1_skip-tests-without-fbgemm.patch': '481e595f673baf8ae58b41697a6792b83048b0264aa79b422f48cd8c22948bb7'}, {'PyTorch-2.0.1_add-missing-vsx-vector-shift-functions.patch': - '245ee7f479f6f809b6ea52460113b2c49bbc2a550201f82bdfa0651c72b02ea8'}, + 'da44961d6c204403ba0c4b88cedccf06a7a3d24f29c4398545f96efae7a45c95'}, {'PyTorch-2.0.1_avoid-test_quantization-failures.patch': '02e3f47e4ed1d7d6077e26f1ae50073dc2b20426269930b505f4aefe5d2f33cd'}, {'PyTorch-2.0.1_disable-test-sharding.patch': 'a1ed7f21c9a269ea039a07a3d6574f885787b30ca5687143c96e096d31066cca'}, diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_add-missing-vsx-vector-shift-functions.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_add-missing-vsx-vector-shift-functions.patch index 57e334c908f..0f30c6b98c5 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_add-missing-vsx-vector-shift-functions.patch +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_add-missing-vsx-vector-shift-functions.patch @@ -1,3 +1,9 @@ +The `Vectorized` class template specializations for VSX are missing the +left and right shift operators. +Add a backported version of the fixed operators of https://github.com/pytorch/pytorch/pull/109886 + +Author: Alexander Grund (TU Dresden) + diff --git a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_int16_vsx.h b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_int16_vsx.h index 7c300c8087c..84c84286740 100644 --- a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_int16_vsx.h From ca39ec81d3b3ca010f134264065daa6e985b7451 Mon Sep 17 00:00:00 2001 From: xina Date: Thu, 26 Oct 2023 17:18:42 +0200 Subject: [PATCH 079/599] update fix patch and pythonpath --- .../w/waLBerla/waLBerla-6.1-foss-2021a.eb | 12 ++++++++---- .../waLBerla-6.1_fix_cmakelist_for_easybuild.patch | 12 ++++++++---- 2 files changed, 16 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb b/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb index e67edd92949..fe3ca95573a 100644 --- a/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb +++ b/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb @@ -17,10 +17,9 @@ patches = ['waLBerla-6.1_fix_cmakelist_for_easybuild.patch'] checksums = [ {'waLBerla-v6.1.tar.gz': 'f0acdd9ad6543bc9306c8aae953dd5065986271d4398916ae0469db8b21c007a'}, {'waLBerla-6.1_fix_cmakelist_for_easybuild.patch': - '13393d523d8f2e1856ae6acffc04bc74d35b5b6a7c800cfad75fb8e3678e4dad'}, + '4adbf15c336a47f7642524190d97d93a4baf8309de88f1f19278b5275377331d'}, ] - builddependencies = [('CMake', '3.20.1')] dependencies = [ @@ -35,10 +34,15 @@ configopts = "-DWALBERLA_BUILD_WITH_PYTHON=ON " configopts += "-DWALBERLA_BUILD_SHOWCASES=OFF " configopts += "-DWALBERLA_BUILD_DOC=OFF " configopts += "-DPython_ROOT_DIR=$EBROOTPYTHON " +configopts += "-DCMAKE_INSTALL_PREFIX=%(installdir)s " + +modextrapaths = {'PYTHONPATH': ['pythonmodule']} sanity_check_paths = { - 'files': ['walberla/waLBerlaDefinitions.h', 'walberla/pythonmodule/walberla_cpp.cpython-39-x86_64-linux-gnu.so'], - 'dirs': ['walberla/pythonmodule/'] + 'files': ['waLBerlaDefinitions.h', 'pythonmodule/walberla_cpp.cpython-39-x86_64-linux-gnu.so'], + 'dirs': ['pythonmodule'] } moduleclass = 'chem' + + diff --git a/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1_fix_cmakelist_for_easybuild.patch b/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1_fix_cmakelist_for_easybuild.patch index 62c8fad3044..7d796c2144c 100644 --- a/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1_fix_cmakelist_for_easybuild.patch +++ b/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1_fix_cmakelist_for_easybuild.patch @@ -1,12 +1,16 @@ diff -ruN walberla-v6.1.orig/CMakeLists.txt walberla-v6.1/CMakeLists.txt --- walberla-v6.1.orig/CMakeLists.txt 2023-10-17 13:06:02.619565000 +0200 -+++ walberla-v6.1/CMakeLists.txt 2023-10-18 14:47:35.047985995 +0200 -@@ -1314,7 +1314,7 @@ ++++ walberla-v6.1/CMakeLists.txt 2023-10-26 17:03:11.300212100 +0200 +@@ -1313,8 +1313,10 @@ + configure_file ( src/waLBerlaDefinitions.in.h src/waLBerlaDefinitions.h ) - install( FILES ${walberla_BINARY_DIR}/src/waLBerlaDefinitions.h DESTINATION walberla/ ) +-install( FILES ${walberla_BINARY_DIR}/src/waLBerlaDefinitions.h DESTINATION walberla/ ) - -+install( DIRECTORY ${walberla_BINARY_DIR}/apps/ DESTINATION walberla/ ) ++install( FILES ${walberla_BINARY_DIR}/src/waLBerlaDefinitions.h DESTINATION . ) ++install( DIRECTORY ${walberla_BINARY_DIR}/apps/pythonmodule/ DESTINATION . ) ++install( DIRECTORY ${walberla_BINARY_DIR}/apps/benchmarks/ DESTINATION . ) ++install( DIRECTORY ${walberla_BINARY_DIR}/apps/tutorials/ DESTINATION . ) # test if ( WALBERLA_BUILD_TESTS ) From 7f7c7c3bf3dd03b11b9b200c9cbca80a10f8386c Mon Sep 17 00:00:00 2001 From: Xin An <34663977+xinan1911@users.noreply.github.com> Date: Thu, 26 Oct 2023 19:22:16 +0200 Subject: [PATCH 080/599] Update waLBerla-6.1-foss-2021a.eb --- easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb b/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb index fe3ca95573a..c2e786ff87a 100644 --- a/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb +++ b/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb @@ -44,5 +44,3 @@ sanity_check_paths = { } moduleclass = 'chem' - - From ee7eaeb8df0c51d24897014365e680f1816934a8 Mon Sep 17 00:00:00 2001 From: Xin An <34663977+xinan1911@users.noreply.github.com> Date: Thu, 26 Oct 2023 19:26:00 +0200 Subject: [PATCH 081/599] Update waLBerla-6.1_fix_cmakelist_for_easybuild.patch --- .../waLBerla/waLBerla-6.1_fix_cmakelist_for_easybuild.patch | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1_fix_cmakelist_for_easybuild.patch b/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1_fix_cmakelist_for_easybuild.patch index 7d796c2144c..2397582632a 100644 --- a/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1_fix_cmakelist_for_easybuild.patch +++ b/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1_fix_cmakelist_for_easybuild.patch @@ -8,9 +8,9 @@ diff -ruN walberla-v6.1.orig/CMakeLists.txt walberla-v6.1/CMakeLists.txt -install( FILES ${walberla_BINARY_DIR}/src/waLBerlaDefinitions.h DESTINATION walberla/ ) - +install( FILES ${walberla_BINARY_DIR}/src/waLBerlaDefinitions.h DESTINATION . ) -+install( DIRECTORY ${walberla_BINARY_DIR}/apps/pythonmodule/ DESTINATION . ) -+install( DIRECTORY ${walberla_BINARY_DIR}/apps/benchmarks/ DESTINATION . ) -+install( DIRECTORY ${walberla_BINARY_DIR}/apps/tutorials/ DESTINATION . ) ++install( DIRECTORY ${walberla_BINARY_DIR}/apps/pythonmodule/ DESTINATION pythonmodule/ ) ++install( DIRECTORY ${walberla_BINARY_DIR}/apps/benchmarks/ DESTINATION benchmarks/ ) ++install( DIRECTORY ${walberla_BINARY_DIR}/apps/tutorials/ DESTINATION tutorials/ ) # test if ( WALBERLA_BUILD_TESTS ) From 9ad0ecc63dbf9e009b90a40c259096c0b430bad1 Mon Sep 17 00:00:00 2001 From: xina Date: Thu, 26 Oct 2023 19:36:28 +0200 Subject: [PATCH 082/599] fix install path --- easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb | 2 +- .../w/waLBerla/waLBerla-6.1_fix_cmakelist_for_easybuild.patch | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb b/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb index c2e786ff87a..5b98d3995e4 100644 --- a/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb +++ b/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb @@ -17,7 +17,7 @@ patches = ['waLBerla-6.1_fix_cmakelist_for_easybuild.patch'] checksums = [ {'waLBerla-v6.1.tar.gz': 'f0acdd9ad6543bc9306c8aae953dd5065986271d4398916ae0469db8b21c007a'}, {'waLBerla-6.1_fix_cmakelist_for_easybuild.patch': - '4adbf15c336a47f7642524190d97d93a4baf8309de88f1f19278b5275377331d'}, + '057066d07294e8f159c2545d2d5f9138d439dbb54bc70eb75eca1f82ae650c47'}, ] builddependencies = [('CMake', '3.20.1')] diff --git a/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1_fix_cmakelist_for_easybuild.patch b/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1_fix_cmakelist_for_easybuild.patch index 2397582632a..c5b275b6fe3 100644 --- a/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1_fix_cmakelist_for_easybuild.patch +++ b/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1_fix_cmakelist_for_easybuild.patch @@ -1,6 +1,6 @@ diff -ruN walberla-v6.1.orig/CMakeLists.txt walberla-v6.1/CMakeLists.txt --- walberla-v6.1.orig/CMakeLists.txt 2023-10-17 13:06:02.619565000 +0200 -+++ walberla-v6.1/CMakeLists.txt 2023-10-26 17:03:11.300212100 +0200 ++++ walberla-v6.1/CMakeLists.txt 2023-10-26 19:28:03.622447001 +0200 @@ -1313,8 +1313,10 @@ configure_file ( src/waLBerlaDefinitions.in.h src/waLBerlaDefinitions.h ) From 7e7c7d1d7f44d776152fc576dd5add72a67397af Mon Sep 17 00:00:00 2001 From: WilleBell Date: Fri, 27 Oct 2023 11:30:29 +0200 Subject: [PATCH 083/599] adding easyconfigs: PICRUSt2-2.5.2-foss-2022a.eb --- .../p/PICRUSt2/PICRUSt2-2.5.2-foss-2022a.eb | 49 +++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/p/PICRUSt2/PICRUSt2-2.5.2-foss-2022a.eb diff --git a/easybuild/easyconfigs/p/PICRUSt2/PICRUSt2-2.5.2-foss-2022a.eb b/easybuild/easyconfigs/p/PICRUSt2/PICRUSt2-2.5.2-foss-2022a.eb new file mode 100644 index 00000000000..9f766d3ffeb --- /dev/null +++ b/easybuild/easyconfigs/p/PICRUSt2/PICRUSt2-2.5.2-foss-2022a.eb @@ -0,0 +1,49 @@ +easyblock = 'PythonBundle' + +name = 'PICRUSt2' +version = '2.5.2' + +homepage = 'https://github.com/picrust/picrust2' +description = """PICRUSt2 (Phylogenetic Investigation of Communities by + Reconstruction of Unobserved States) is a software for predicting + functional abundances based only on marker gene sequences.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('h5py', '3.7.0'), + ('biom-format', '2.1.14'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('joblib', '1.3.1', { + 'checksums': ['1f937906df65329ba98013dc9692fe22a4c5e4a648112de500508b18a21b41e3'], + }), + (name, version, { + 'modulename': '%(namelower)s', + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/picrust/%(namelower)s/archive'], + 'checksums': ['a8c3832bf759233b52b41c56a0ffef72491e431fee347a7c05695596c76a1a4c'], + }), +] + +postinstallcmds = [ + "cp -a %(start_dir)s%(name)s/%(namelower)s-%(version)s/%(namelower)s/default_files" + " %(installdir)s/lib/python%(pyshortver)s/site-packages/%(namelower)s/" +] + +sanity_check_commands = [ + "python -c 'from picrust2.default import default_tables'" +] + +sanity_check_paths = { + 'files': ['bin/picrust2_pipeline.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/picrust2/default_files'], +} + +moduleclass = 'bio' From 91226f842b7b5d4325d507e882b5896442aea4b5 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Fri, 27 Oct 2023 14:07:30 +0200 Subject: [PATCH 084/599] Update checksum --- .../o/OpenImageIO/OpenImageIO-2.4.14.0-GCC-12.3.0.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenImageIO/OpenImageIO-2.4.14.0-GCC-12.3.0.eb b/easybuild/easyconfigs/o/OpenImageIO/OpenImageIO-2.4.14.0-GCC-12.3.0.eb index 3ca74380746..e0f24d0917d 100644 --- a/easybuild/easyconfigs/o/OpenImageIO/OpenImageIO-2.4.14.0-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/o/OpenImageIO/OpenImageIO-2.4.14.0-GCC-12.3.0.eb @@ -11,7 +11,10 @@ toolchain = {'name': 'GCC', 'version': '12.3.0'} source_urls = ['https://github.com/OpenImageIO/oiio/archive/refs/tags/'] sources = ['v%(version)s.tar.gz'] -checksums = ['92ad4b107394b273397baa1abe90207e1f8ef9fd52ffbfc23b46e3b0005d4439'] +checksums = [ + '92ad4b107394b273397baa1abe90207e1f8ef9fd52ffbfc23b46e3b0005d4439', + '40c2e6fe38f0460a92e3f9d24bf75bcc310c74585760a3b0ac1b1727582bb46c', +] builddependencies = [ ('CMake', '3.26.3'), From 1d4681d2b58f691d92e704af2e8c16b6428f7a55 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Fri, 27 Oct 2023 14:33:42 +0200 Subject: [PATCH 085/599] Fix checksum specification --- .../o/OpenImageIO/OpenImageIO-2.4.14.0-GCC-12.3.0.eb | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenImageIO/OpenImageIO-2.4.14.0-GCC-12.3.0.eb b/easybuild/easyconfigs/o/OpenImageIO/OpenImageIO-2.4.14.0-GCC-12.3.0.eb index e0f24d0917d..b0bc036fc2c 100644 --- a/easybuild/easyconfigs/o/OpenImageIO/OpenImageIO-2.4.14.0-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/o/OpenImageIO/OpenImageIO-2.4.14.0-GCC-12.3.0.eb @@ -11,10 +11,8 @@ toolchain = {'name': 'GCC', 'version': '12.3.0'} source_urls = ['https://github.com/OpenImageIO/oiio/archive/refs/tags/'] sources = ['v%(version)s.tar.gz'] -checksums = [ - '92ad4b107394b273397baa1abe90207e1f8ef9fd52ffbfc23b46e3b0005d4439', - '40c2e6fe38f0460a92e3f9d24bf75bcc310c74585760a3b0ac1b1727582bb46c', -] +checksums = [('92ad4b107394b273397baa1abe90207e1f8ef9fd52ffbfc23b46e3b0005d4439', + '40c2e6fe38f0460a92e3f9d24bf75bcc310c74585760a3b0ac1b1727582bb46c')] builddependencies = [ ('CMake', '3.26.3'), From f8832ffa7dd058d3561d1cb4a02ae97976efdf12 Mon Sep 17 00:00:00 2001 From: Orient Date: Fri, 27 Oct 2023 14:43:13 +0200 Subject: [PATCH 086/599] Made requested changes --- .../GFF3-toolkit-2.1.0-foss-2022a.eb} | 22 +++++++++++-------- .../GFF3-toolkit-2.1.0-remove-hardcode.patch} | 0 2 files changed, 13 insertions(+), 9 deletions(-) rename easybuild/easyconfigs/g/{gff3tool/gff3tool-2.1.0-foss-2022a.eb => GFF3-toolkit/GFF3-toolkit-2.1.0-foss-2022a.eb} (58%) rename easybuild/easyconfigs/g/{gff3tool/GFF3toolkit-2.1.0-remove_hardcode.patch => GFF3-toolkit/GFF3-toolkit-2.1.0-remove-hardcode.patch} (100%) diff --git a/easybuild/easyconfigs/g/gff3tool/gff3tool-2.1.0-foss-2022a.eb b/easybuild/easyconfigs/g/GFF3-toolkit/GFF3-toolkit-2.1.0-foss-2022a.eb similarity index 58% rename from easybuild/easyconfigs/g/gff3tool/gff3tool-2.1.0-foss-2022a.eb rename to easybuild/easyconfigs/g/GFF3-toolkit/GFF3-toolkit-2.1.0-foss-2022a.eb index 80f979fe27c..9db2550d17c 100644 --- a/easybuild/easyconfigs/g/gff3tool/gff3tool-2.1.0-foss-2022a.eb +++ b/easybuild/easyconfigs/g/GFF3-toolkit/GFF3-toolkit-2.1.0-foss-2022a.eb @@ -1,6 +1,6 @@ easyblock = 'PythonPackage' -name = 'gff3tool' +name = 'GFF3-toolkit' version = '2.1.0' homepage = 'https://gff3toolkit.readthedocs.io' @@ -8,24 +8,28 @@ description = 'Python programs for processing GFF3 files' toolchain = {'name': 'foss', 'version': '2022a'} -sources = ['gff3tool-2.1.0.tar.gz'] -patches = ['GFF3toolkit-2.1.0-remove_hardcode.patch'] +sources = ['gff3tool-%(version)s.tar.gz'] +source_urls = ['https://pypi.python.org/packages/source/g/gff3tool'] +patches = ['GFF3-toolkit-2.1.0-remove-hardcode.patch'] checksums = [ {'gff3tool-2.1.0.tar.gz': 'e842ef4afdb66926a2b63bf2619c7ef30bd9b76a5f1084a5c57bf8b39cc4f15d'}, - {'GFF3toolkit-2.1.0-remove_hardcode.patch': '03696635af25ab1e3d650b46c7aeaaaadb31e7eac766039c758150f3f3162cb7'}, + {'GFF3-toolkit-2.1.0-remove-hardcode.patch': '03696635af25ab1e3d650b46c7aeaaaadb31e7eac766039c758150f3f3162cb7'}, ] -local_blast_path = '%(installdir)s/lib/python%(pyshortver)s/site-packages/gff3tool/lib/ncbi-blast+' -preinstallopts = 'mkdir -p %s && ' % local_blast_path -preinstallopts += 'ln -s $EBROOTBLASTPLUS/bin %s && ' % local_blast_path - dependencies = [ ('Python', '3.10.4'), ('BLAST+', '2.13.0'), ] +#GFF3-toolkit has hardcoded path to BLAST+ libraries, so we have to add a symlink to the required path for this to work +local_blast_path = '%(installdir)s/lib/python%(pyshortver)s/site-packages/gff3tool/lib/ncbi-blast+' +preinstallopts = 'mkdir -p %s && ' % local_blast_path +preinstallopts += 'ln -s $EBROOTBLASTPLUS/bin %s && ' % local_blast_path + use_pip = True sanity_pip_check = True download_dep_fail = True -moduleclass = "tools" +options = {'modulename': 'gff3tool'} + +moduleclass = "bio" diff --git a/easybuild/easyconfigs/g/gff3tool/GFF3toolkit-2.1.0-remove_hardcode.patch b/easybuild/easyconfigs/g/GFF3-toolkit/GFF3-toolkit-2.1.0-remove-hardcode.patch similarity index 100% rename from easybuild/easyconfigs/g/gff3tool/GFF3toolkit-2.1.0-remove_hardcode.patch rename to easybuild/easyconfigs/g/GFF3-toolkit/GFF3-toolkit-2.1.0-remove-hardcode.patch From a3d99c8fcaf9ae146c583e4c572cf96d8830f351 Mon Sep 17 00:00:00 2001 From: Orient Date: Fri, 27 Oct 2023 14:52:59 +0200 Subject: [PATCH 087/599] adding easyconfigs: dynesty-2.1.3-foss-2023a.eb, typing-extensions-4.8.0-GCCcore-12.3.0.eb, pytest-7.4.2-GCCcore-12.3.0.eb, pytest-xdist-3.3.1-GCCcore-12.3.0.eb --- .../d/dynesty/dynesty-2.1.3-foss-2023a.eb | 41 ++++++++ .../pytest-xdist-3.3.1-GCCcore-12.3.0.eb | 61 ++++++++++++ .../p/pytest/pytest-7.4.2-GCCcore-12.3.0.eb | 96 +++++++++++++++++++ .../typing-extensions-4.8.0-GCCcore-12.3.0.eb | 22 +++++ 4 files changed, 220 insertions(+) create mode 100644 easybuild/easyconfigs/d/dynesty/dynesty-2.1.3-foss-2023a.eb create mode 100644 easybuild/easyconfigs/p/pytest-xdist/pytest-xdist-3.3.1-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/p/pytest/pytest-7.4.2-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/t/typing-extensions/typing-extensions-4.8.0-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/d/dynesty/dynesty-2.1.3-foss-2023a.eb b/easybuild/easyconfigs/d/dynesty/dynesty-2.1.3-foss-2023a.eb new file mode 100644 index 00000000000..d1a5101262a --- /dev/null +++ b/easybuild/easyconfigs/d/dynesty/dynesty-2.1.3-foss-2023a.eb @@ -0,0 +1,41 @@ +easyblock = 'PythonBundle' + +name = 'dynesty' +version = '2.1.3' + +homepage = 'https://dynesty.readthedocs.io/' +description = """dynesty is a Pure Python, MIT-licensed Dynamic Nested Sampling package +for estimating Bayesian posteriors and evidences.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('dill', '0.3.7'), + ('h5py', '3.9.0'), + ('tqdm', '4.66.1'), + ('pytest', '7.4.2'), + ('pytest-xdist', '3.3.1'), +] + +use_pip = True + +exts_list = [ + ('pytest-cov', '4.1.0', { + 'checksums': ['3904b13dfbfec47f003b8e77fd5b589cd11904a21ddf1ab38a64f204d6a10ef6'], + }), + ('coverage', '6.5.0', { + 'checksums': ['f642e90754ee3e06b0e7e51bce3379590e76b7f76b708e1a71ff043f87025c84'], + }), + ('coveralls', '3.3.1', { + 'checksums': ['b32a8bb5d2df585207c119d6c01567b81fba690c9c10a753bfe27a335bfc43ea'], + }), + (name, version, { + 'checksums': ['26b6c538ff59be4cfd27871b9b78e62c333052234f99c288e269ec022849a345'], + }), +] + +sanity_pip_check = True + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/pytest-xdist/pytest-xdist-3.3.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/pytest-xdist/pytest-xdist-3.3.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..47bba67554b --- /dev/null +++ b/easybuild/easyconfigs/p/pytest-xdist/pytest-xdist-3.3.1-GCCcore-12.3.0.eb @@ -0,0 +1,61 @@ +easyblock = 'PythonBundle' + +name = 'pytest-xdist' +version = '3.3.1' + +homepage = 'https://github.com/pytest-dev/pytest-xdist' +description = """xdist: pytest distributed testing plugin + +The pytest-xdist plugin extends pytest with some unique test execution modes: + + * test run parallelization: if you have multiple CPUs or hosts you + can use those for a combined test run. This allows to speed up + development or to use special resources of remote machines. + + * --looponfail: run your tests repeatedly in a subprocess. After + each run pytest waits until a file in your project changes and + then re-runs the previously failing tests. This is repeated + until all tests pass after which again a full run is + performed. + + * Multi-Platform coverage: you can specify different Python + interpreters or different platforms and run tests in parallel on + all of them. + +Before running tests remotely, pytest efficiently “rsyncs” your +program source code to the remote place. All test results are reported +back and displayed to your local terminal. You may specify different +Python versions and interpreters.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('Python', '3.11.3'), + ('pytest', '7.4.2'), + ('hatchling', '1.18.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('apipkg', '3.0.2', { + 'checksums': ['c7aa61a4f82697fdaa667e70af1505acf1f7428b1c27b891d204ba7a8a3c5e0d'], + }), + ('execnet', '2.0.2', { + 'checksums': ['cc59bc4423742fd71ad227122eb0dd44db51efb3dc4095b45ac9a08c770096af'], + }), + (name, version, { + 'modulename': 'xdist', + 'checksums': ['d5ee0520eb1b7bcca50a60a518ab7a7707992812c578198f8b44fdfac78e8c93'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' 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 new file mode 100644 index 00000000000..3d67f361036 --- /dev/null +++ b/easybuild/easyconfigs/p/pytest/pytest-7.4.2-GCCcore-12.3.0.eb @@ -0,0 +1,96 @@ +easyblock = 'PythonBundle' + +name = 'pytest' +version = '7.4.2' + +homepage = 'https://docs.pytest.org/en/latest/' +description = """The pytest framework makes it easy to write small, +readable tests, and can scale to support complex functional testing for +applications and libraries.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('typing-extensions', '4.8.0'), + ('hatchling', '1.18.0'), +] + +use_pip = True + +exts_default_options = {'source_urls': [PYPI_LOWER_SOURCE]} + +# Note! Some of the file system related tests may fail on shared file systems. +# Notably TestPOSIXLocalPath.test_copy_stat_file, TestPOSIXLocalPath.test_copy_stat_dir +# and test_source_mtime_long_long are known to fail on GPFS +# Build with buildpath and tmpdir set to a local file system to avoid this +# or use --ignore-test-failures +_skip_tests = [ + 'testing/io/test_terminalwriter.py', + 'testing/test_terminal.py', + 'testing/test_debugging.py', + 'testing/test_config.py', + 'testing/test_helpconfig.py', +] +_ignore_tests = ' --ignore='.join(_skip_tests) + +exts_list = [ + ('tomli', '2.0.1', { + 'checksums': ['de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f'], + }), + ('packaging', '23.2', { + 'checksums': ['048fb0e9405036518eaaf48a55953c750c11e1a1b68e0dd1a9d62ed0c092cfc5'], + }), + ('setuptools-scm', '8.0.4', { + 'checksums': ['b5f43ff6800669595193fd09891564ee9d1d7dcb196cab4b2506d53a2e1c95c7'], + }), + ('flit-core', '3.9.0', { + 'source_tmpl': 'flit_core-%(version)s.tar.gz', + 'checksums': ['72ad266176c4a3fcfab5f2930d76896059851240570ce9a98733b658cb786eba'], + }), + ('flit-scm', '1.7.0', { + 'source_tmpl': 'flit_scm-%(version)s.tar.gz', + 'checksums': ['961bd6fb24f31bba75333c234145fff88e6de0a90fc0f7e5e7c79deca69f6bb2'], + }), + ('exceptiongroup', '1.1.3', { + 'checksums': ['097acd85d473d75af5bb98e41b61ff7fe35efe6675e4f9370ec6ec5126d160e9'], + }), + ('attrs', '23.1.0', { + 'checksums': ['6279836d581513a26f1bf235f9acd333bc9115683f14f7e8fae46c98fc50e015'], + }), + ('sortedcontainers', '2.4.0', { + 'checksums': ['25caa5a06cc30b6b83d11423433f65d1f9d76c4c6a0c90e3379eaa43b9bfdb88'], + }), + ('hypothesis', '6.88.1', { + 'checksums': ['f4c2c004b9ec3e0e25332ad2cb6b91eba477a855557a7b5c6e79068809ff8b51'], + }), + ('elementpath', '4.1.5', { + 'checksums': ['c2d6dc524b29ef751ecfc416b0627668119d8812441c555d7471da41d4bacb8d'], + }), + ('xmlschema', '2.5.0', { + 'checksums': ['276a03e0fd3c94c148d528bff4d9482f9b99bf8c7b4056a2e8e703d28149d454'], + }), + ('iniconfig', '2.0.0', { + 'checksums': ['2d91e135bf72d31a410b17c16da610a82cb55f6b0477d1a902134b24a455b8b3'], + }), + ('pluggy', '1.3.0', { + 'checksums': ['cf61ae8f126ac6f7c451172cf30e3e43d3ca77615509771b3a984a0730651e12'], + }), + (name, version, { + 'checksums': ['a766259cfab564a2ad52cb1aae1b881a75c3eb7e34ca3779697c23ed47c47069'], + }), +] + +sanity_check_commands = [ + "python -c 'import pytest'", + 'cd %%(builddir)s/%%(name)s/%%(name)s-%%(version)s && %%(installdir)s/bin/pytest --ignore=%s testing' + % _ignore_tests, +] + +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/typing-extensions/typing-extensions-4.8.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/t/typing-extensions/typing-extensions-4.8.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..c1d6fc3757c --- /dev/null +++ b/easybuild/easyconfigs/t/typing-extensions/typing-extensions-4.8.0-GCCcore-12.3.0.eb @@ -0,0 +1,22 @@ +easyblock = 'PythonPackage' + +name = 'typing-extensions' +version = '4.8.0' + +homepage = 'https://github.com/python/typing/blob/master/typing_extensions/README.rst' +description = 'Typing Extensions - Backported and Experimental Type Hints for Python' + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +sources = ['typing_extensions-%(version)s.tar.gz'] +checksums = ['df8e4339e9cb77357558cbdbceca33c303714cf861d1eef15e1070055ae8b7ef'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [('Python', '3.11.3')] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'devel' From 097f893e476ef5071f59e7890a57a06365fc75bc Mon Sep 17 00:00:00 2001 From: Orient Date: Fri, 27 Oct 2023 21:06:02 +0200 Subject: [PATCH 088/599] Added a space to the beginning of a comment --- .../easyconfigs/g/GFF3-toolkit/GFF3-toolkit-2.1.0-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GFF3-toolkit/GFF3-toolkit-2.1.0-foss-2022a.eb b/easybuild/easyconfigs/g/GFF3-toolkit/GFF3-toolkit-2.1.0-foss-2022a.eb index 9db2550d17c..f1110ec02d4 100644 --- a/easybuild/easyconfigs/g/GFF3-toolkit/GFF3-toolkit-2.1.0-foss-2022a.eb +++ b/easybuild/easyconfigs/g/GFF3-toolkit/GFF3-toolkit-2.1.0-foss-2022a.eb @@ -21,7 +21,7 @@ dependencies = [ ('BLAST+', '2.13.0'), ] -#GFF3-toolkit has hardcoded path to BLAST+ libraries, so we have to add a symlink to the required path for this to work +# GFF3-toolkit has hardcoded path to BLAST+ libraries, so we have to add a symlink to the required path for this to work local_blast_path = '%(installdir)s/lib/python%(pyshortver)s/site-packages/gff3tool/lib/ncbi-blast+' preinstallopts = 'mkdir -p %s && ' % local_blast_path preinstallopts += 'ln -s $EBROOTBLASTPLUS/bin %s && ' % local_blast_path From a9dc9a6e0cdb411af843864fd664557ea12a7599 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sat, 28 Oct 2023 16:28:48 +0200 Subject: [PATCH 089/599] adding easyconfigs: virtualenv-20.24.6-GCCcore-13.2.0.eb, setuptools-rust-1.8.0-GCCcore-13.2.0.eb, scikit-build-0.17.6-GCCcore-13.2.0.eb, maturin-1.3.1-GCCcore-13.2.0.eb, poetry-1.6.1-GCCcore-13.2.0.eb, cryptography-41.0.5-GCCcore-13.2.0.eb, hatchling-1.18.0-GCCcore-13.2.0.eb --- .../cryptography-41.0.5-GCCcore-13.2.0.eb | 142 ++++ .../hatchling-1.18.0-GCCcore-13.2.0.eb | 65 ++ .../m/maturin/maturin-1.3.1-GCCcore-13.2.0.eb | 616 ++++++++++++++++++ .../p/poetry/poetry-1.6.1-GCCcore-13.2.0.eb | 162 +++++ .../scikit-build-0.17.6-GCCcore-13.2.0.eb | 37 ++ .../setuptools-rust-1.8.0-GCCcore-13.2.0.eb | 39 ++ .../virtualenv-20.24.6-GCCcore-13.2.0.eb | 47 ++ 7 files changed, 1108 insertions(+) create mode 100644 easybuild/easyconfigs/c/cryptography/cryptography-41.0.5-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/h/hatchling/hatchling-1.18.0-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/m/maturin/maturin-1.3.1-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/p/poetry/poetry-1.6.1-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/s/scikit-build/scikit-build-0.17.6-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/s/setuptools-rust/setuptools-rust-1.8.0-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/v/virtualenv/virtualenv-20.24.6-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/c/cryptography/cryptography-41.0.5-GCCcore-13.2.0.eb b/easybuild/easyconfigs/c/cryptography/cryptography-41.0.5-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..396020d6259 --- /dev/null +++ b/easybuild/easyconfigs/c/cryptography/cryptography-41.0.5-GCCcore-13.2.0.eb @@ -0,0 +1,142 @@ +easyblock = 'CargoPythonPackage' + +name = 'cryptography' +version = '41.0.5' + +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': '13.2.0'} +toolchainopts = {'pic': True} + +builddependencies = [ + ('binutils', '2.40'), + ('pkgconf', '2.0.3'), + ('Rust', '1.73.0'), # required for cryptography + ('hatchling', '1.18.0'), + ('setuptools-rust', '1.8.0'), +] + +dependencies = [ + ('Python', '3.11.5'), + ('cffi', '1.15.1'), +] + +crates = [ + ('Inflector', '0.11.4'), + ('aliasable', '0.1.3'), + ('asn1', '0.15.2'), + ('asn1_derive', '0.15.2'), + ('autocfg', '1.1.0'), + ('base64', '0.13.1'), + ('bitflags', '1.3.2'), + ('cc', '1.0.79'), + ('cfg-if', '1.0.0'), + ('foreign-types', '0.3.2'), + ('foreign-types-shared', '0.1.1'), + ('indoc', '1.0.9'), + ('libc', '0.2.144'), + ('lock_api', '0.4.9'), + ('memoffset', '0.8.0'), + ('once_cell', '1.17.2'), + ('openssl', '0.10.54'), + ('openssl-macros', '0.1.1'), + ('openssl-sys', '0.9.88'), + ('ouroboros', '0.15.6'), + ('ouroboros_macro', '0.15.6'), + ('parking_lot', '0.12.1'), + ('parking_lot_core', '0.9.7'), + ('pem', '1.1.1'), + ('pkg-config', '0.3.27'), + ('proc-macro-error', '1.0.4'), + ('proc-macro-error-attr', '1.0.4'), + ('proc-macro2', '1.0.64'), + ('pyo3', '0.18.3'), + ('pyo3-build-config', '0.18.3'), + ('pyo3-ffi', '0.18.3'), + ('pyo3-macros', '0.18.3'), + ('pyo3-macros-backend', '0.18.3'), + ('quote', '1.0.28'), + ('redox_syscall', '0.2.16'), + ('scopeguard', '1.1.0'), + ('smallvec', '1.10.0'), + ('syn', '1.0.109'), + ('syn', '2.0.18'), + ('target-lexicon', '0.12.7'), + ('unicode-ident', '1.0.9'), + ('unindent', '0.1.11'), + ('vcpkg', '0.2.15'), + ('version_check', '0.9.4'), + ('windows-sys', '0.45.0'), + ('windows-targets', '0.42.2'), + ('windows_aarch64_gnullvm', '0.42.2'), + ('windows_aarch64_msvc', '0.42.2'), + ('windows_i686_gnu', '0.42.2'), + ('windows_i686_msvc', '0.42.2'), + ('windows_x86_64_gnu', '0.42.2'), + ('windows_x86_64_gnullvm', '0.42.2'), + ('windows_x86_64_msvc', '0.42.2'), +] +sources = [SOURCE_TAR_GZ] +checksums = [ + {'cryptography-41.0.5.tar.gz': '392cb88b597247177172e02da6b7a63deeff1937fa6fec3bbf902ebd75d97ec7'}, + {'Inflector-0.11.4.tar.gz': 'fe438c63458706e03479442743baae6c88256498e6431708f6dfc520a26515d3'}, + {'aliasable-0.1.3.tar.gz': '250f629c0161ad8107cf89319e990051fae62832fd343083bea452d93e2205fd'}, + {'asn1-0.15.2.tar.gz': '28c19b9324de5b815b6487e0f8098312791b09de0dbf3d5c2db1fe2d95bab973'}, + {'asn1_derive-0.15.2.tar.gz': 'a045c3ccad89f244a86bd1e6cf1a7bf645296e7692698b056399b6efd4639407'}, + {'autocfg-1.1.0.tar.gz': 'd468802bab17cbc0cc575e9b053f41e72aa36bfa6b7f55e3529ffa43161b97fa'}, + {'base64-0.13.1.tar.gz': '9e1b586273c5702936fe7b7d6896644d8be71e6314cfe09d3167c95f712589e8'}, + {'bitflags-1.3.2.tar.gz': 'bef38d45163c2f1dde094a7dfd33ccf595c92905c8f8f4fdc18d06fb1037718a'}, + {'cc-1.0.79.tar.gz': '50d30906286121d95be3d479533b458f87493b30a4b5f79a607db8f5d11aa91f'}, + {'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'}, + {'indoc-1.0.9.tar.gz': 'bfa799dd5ed20a7e349f3b4639aa80d74549c81716d9ec4f994c9b5815598306'}, + {'libc-0.2.144.tar.gz': '2b00cc1c228a6782d0f076e7b232802e0c5689d41bb5df366f2a6b6621cfdfe1'}, + {'lock_api-0.4.9.tar.gz': '435011366fe56583b16cf956f9df0095b405b82d76425bc8981c0e22e60ec4df'}, + {'memoffset-0.8.0.tar.gz': 'd61c719bcfbcf5d62b3a09efa6088de8c54bc0bfcd3ea7ae39fcc186108b8de1'}, + {'once_cell-1.17.2.tar.gz': '9670a07f94779e00908f3e686eab508878ebb390ba6e604d3a284c00e8d0487b'}, + {'openssl-0.10.54.tar.gz': '69b3f656a17a6cbc115b5c7a40c616947d213ba182135b014d6051b73ab6f019'}, + {'openssl-macros-0.1.1.tar.gz': 'a948666b637a0f465e8564c73e89d4dde00d72d4d473cc972f390fc3dcee7d9c'}, + {'openssl-sys-0.9.88.tar.gz': 'c2ce0f250f34a308dcfdbb351f511359857d4ed2134ba715a4eadd46e1ffd617'}, + {'ouroboros-0.15.6.tar.gz': 'e1358bd1558bd2a083fed428ffeda486fbfb323e698cdda7794259d592ca72db'}, + {'ouroboros_macro-0.15.6.tar.gz': '5f7d21ccd03305a674437ee1248f3ab5d4b1db095cf1caf49f1713ddf61956b7'}, + {'parking_lot-0.12.1.tar.gz': '3742b2c103b9f06bc9fff0a37ff4912935851bee6d36f3c02bcc755bcfec228f'}, + {'parking_lot_core-0.9.7.tar.gz': '9069cbb9f99e3a5083476ccb29ceb1de18b9118cafa53e90c9551235de2b9521'}, + {'pem-1.1.1.tar.gz': 'a8835c273a76a90455d7344889b0964598e3316e2a79ede8e36f16bdcf2228b8'}, + {'pkg-config-0.3.27.tar.gz': '26072860ba924cbfa98ea39c8c19b4dd6a4a25423dbdf219c1eca91aa0cf6964'}, + {'proc-macro-error-1.0.4.tar.gz': 'da25490ff9892aab3fcf7c36f08cfb902dd3e71ca0f9f9517bea02a73a5ce38c'}, + {'proc-macro-error-attr-1.0.4.tar.gz': 'a1be40180e52ecc98ad80b184934baf3d0d29f979574e439af5a55274b35f869'}, + {'proc-macro2-1.0.64.tar.gz': '78803b62cbf1f46fde80d7c0e803111524b9877184cfe7c3033659490ac7a7da'}, + {'pyo3-0.18.3.tar.gz': 'e3b1ac5b3731ba34fdaa9785f8d74d17448cd18f30cf19e0c7e7b1fdb5272109'}, + {'pyo3-build-config-0.18.3.tar.gz': '9cb946f5ac61bb61a5014924910d936ebd2b23b705f7a4a3c40b05c720b079a3'}, + {'pyo3-ffi-0.18.3.tar.gz': 'fd4d7c5337821916ea2a1d21d1092e8443cf34879e53a0ac653fbb98f44ff65c'}, + {'pyo3-macros-0.18.3.tar.gz': 'a9d39c55dab3fc5a4b25bbd1ac10a2da452c4aca13bb450f22818a002e29648d'}, + {'pyo3-macros-backend-0.18.3.tar.gz': '97daff08a4c48320587b5224cc98d609e3c27b6d437315bd40b605c98eeb5918'}, + {'quote-1.0.28.tar.gz': '1b9ab9c7eadfd8df19006f1cf1a4aed13540ed5cbc047010ece5826e10825488'}, + {'redox_syscall-0.2.16.tar.gz': 'fb5a58c1855b4b6819d59012155603f0b22ad30cad752600aadfcb695265519a'}, + {'scopeguard-1.1.0.tar.gz': 'd29ab0c6d3fc0ee92fe66e2d99f700eab17a8d57d1c1d3b748380fb20baa78cd'}, + {'smallvec-1.10.0.tar.gz': 'a507befe795404456341dfab10cef66ead4c041f62b8b11bbb92bffe5d0953e0'}, + {'syn-1.0.109.tar.gz': '72b64191b275b66ffe2469e8af2c1cfe3bafa67b529ead792a6d0160888b4237'}, + {'syn-2.0.18.tar.gz': '32d41677bcbe24c20c52e7c70b0d8db04134c5d1066bf98662e2871ad200ea3e'}, + {'target-lexicon-0.12.7.tar.gz': 'fd1ba337640d60c3e96bc6f0638a939b9c9a7f2c316a1598c279828b3d1dc8c5'}, + {'unicode-ident-1.0.9.tar.gz': 'b15811caf2415fb889178633e7724bad2509101cde276048e013b9def5e51fa0'}, + {'unindent-0.1.11.tar.gz': 'e1766d682d402817b5ac4490b3c3002d91dfa0d22812f341609f97b08757359c'}, + {'vcpkg-0.2.15.tar.gz': 'accd4ea62f7bb7a82fe23066fb0957d48ef677f6eeb8215f372f52e48bb32426'}, + {'version_check-0.9.4.tar.gz': '49874b5167b65d7193b8aba1567f5c7d93d001cafc34600cee003eda787e483f'}, + {'windows-sys-0.45.0.tar.gz': '75283be5efb2831d37ea142365f009c02ec203cd29a3ebecbc093d52315b66d0'}, + {'windows-targets-0.42.2.tar.gz': '8e5180c00cd44c9b1c88adb3693291f1cd93605ded80c250a75d472756b4d071'}, + {'windows_aarch64_gnullvm-0.42.2.tar.gz': '597a5118570b68bc08d8d59125332c54f1ba9d9adeedeef5b99b02ba2b0698f8'}, + {'windows_aarch64_msvc-0.42.2.tar.gz': 'e08e8864a60f06ef0d0ff4ba04124db8b0fb3be5776a5cd47641e942e58c4d43'}, + {'windows_i686_gnu-0.42.2.tar.gz': 'c61d927d8da41da96a81f029489353e68739737d3beca43145c8afec9a31a84f'}, + {'windows_i686_msvc-0.42.2.tar.gz': '44d840b6ec649f480a41c8d80f9c65108b92d89345dd94027bfe06ac444d1060'}, + {'windows_x86_64_gnu-0.42.2.tar.gz': '8de912b8b8feb55c064867cf047dda097f92d51efad5b491dfb98f6bbb70cb36'}, + {'windows_x86_64_gnullvm-0.42.2.tar.gz': '26d41b46a36d453748aedef1486d5c7a85db22e56aff34643984ea85514e94a3'}, + {'windows_x86_64_msvc-0.42.2.tar.gz': '9aec5da331524158c6d1a4ac0ab1541149c0b9505fde06423b02f5ef0106b9f0'}, +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/hatchling/hatchling-1.18.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/h/hatchling/hatchling-1.18.0-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..765badccfff --- /dev/null +++ b/easybuild/easyconfigs/h/hatchling/hatchling-1.18.0-GCCcore-13.2.0.eb @@ -0,0 +1,65 @@ +easyblock = 'PythonBundle' + +name = 'hatchling' +version = '1.18.0' + +homepage = 'https://hatch.pypa.io' +description = """Extensible, standards compliant build backend used by Hatch, +a modern, extensible Python project manager.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('Python', '3.11.5'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('tomli', '2.0.1', { + 'checksums': ['de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f'], + }), + ('packaging', '23.2', { + 'checksums': ['048fb0e9405036518eaaf48a55953c750c11e1a1b68e0dd1a9d62ed0c092cfc5'], + }), + ('setuptools-scm', '8.0.4', { + 'checksums': ['b5f43ff6800669595193fd09891564ee9d1d7dcb196cab4b2506d53a2e1c95c7'], + }), + ('typing_extensions', '4.8.0', { + 'checksums': ['df8e4339e9cb77357558cbdbceca33c303714cf861d1eef15e1070055ae8b7ef'], + }), + ('pathspec', '0.11.2', { + 'checksums': ['e0d8d0ac2f12da61956eb2306b69f9469b42f4deb0f3cb6ed47b9cce9996ced3'], + }), + ('pluggy', '1.3.0', { + 'checksums': ['cf61ae8f126ac6f7c451172cf30e3e43d3ca77615509771b3a984a0730651e12'], + }), + ('editables', '0.5', { + 'checksums': ['309627d9b5c4adc0e668d8c6fa7bac1ba7c8c5d415c2d27f60f081f8e80d1de2'], + }), + ('trove_classifiers', '2023.10.18', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['20a3da8e3cb65587cc9f5d5b837bf74edeb480bba9bd8cd4f03ab056d6b06c4c'], + }), + (name, version, { + 'checksums': ['50e99c3110ce0afc3f7bdbadff1c71c17758e476731c27607940cfa6686489ca'], + }), + ('hatch_vcs', '0.3.0', { + 'checksums': ['cec5107cfce482c67f8bc96f18bbc320c9aa0d068180e14ad317bbee5a153fee'], + }), + ('hatch_fancy_pypi_readme', '23.1.0', { + 'checksums': ['b1df44063094af1e8248ceacd47a92c9cf313d6b9823bf66af8a927c3960287d'], + }), +] + +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-1.3.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/m/maturin/maturin-1.3.1-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..db1645e18a5 --- /dev/null +++ b/easybuild/easyconfigs/m/maturin/maturin-1.3.1-GCCcore-13.2.0.eb @@ -0,0 +1,616 @@ +easyblock = 'CargoPythonPackage' + +name = 'maturin' +version = '1.3.1' + +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': '13.2.0'} + +crates = [ + ('adler', '1.0.2'), + ('ahash', '0.7.6'), + ('aho-corasick', '0.7.20'), + ('anstream', '0.3.2'), + ('anstyle', '1.0.1'), + ('anstyle-parse', '0.2.1'), + ('anstyle-query', '1.0.0'), + ('anstyle-wincon', '1.0.2'), + ('anyhow', '1.0.75'), + ('autocfg', '1.1.0'), + ('base64', '0.13.1'), + ('base64', '0.21.2'), + ('bitflags', '1.3.2'), + ('block-buffer', '0.10.4'), + ('bstr', '1.6.0'), + ('bumpalo', '3.13.0'), + ('byteorder', '1.4.3'), + ('bytes', '1.4.0'), + ('bytesize', '1.2.0'), + ('bzip2', '0.4.4'), + ('bzip2-sys', '0.1.11+1.0.8'), + ('cab', '0.4.1'), + ('camino', '1.1.6'), + ('cargo-config2', '0.1.9'), + ('cargo-options', '0.6.0'), + ('cargo-platform', '0.1.3'), + ('cargo-xwin', '0.14.8'), + ('cargo-zigbuild', '0.17.3'), + ('cargo_metadata', '0.18.0'), + ('cbindgen', '0.25.0'), + ('cc', '1.0.82'), + ('cfb', '0.7.3'), + ('cfg-expr', '0.15.4'), + ('cfg-if', '1.0.0'), + ('charset', '0.1.3'), + ('chumsky', '0.9.2'), + ('clap', '4.1.14'), + ('clap_builder', '4.1.14'), + ('clap_complete', '4.2.3'), + ('clap_complete_command', '0.5.1'), + ('clap_complete_fig', '4.2.0'), + ('clap_complete_nushell', '0.1.11'), + ('clap_derive', '4.1.14'), + ('clap_lex', '0.4.1'), + ('cli-table', '0.4.7'), + ('colorchoice', '1.0.0'), + ('configparser', '3.0.2'), + ('console', '0.15.7'), + ('content_inspector', '0.2.4'), + ('core-foundation', '0.9.3'), + ('core-foundation-sys', '0.8.4'), + ('cpufeatures', '0.2.9'), + ('crc32fast', '1.3.2'), + ('crossbeam-channel', '0.5.8'), + ('crossbeam-deque', '0.8.3'), + ('crossbeam-epoch', '0.9.15'), + ('crossbeam-utils', '0.8.16'), + ('crypto-common', '0.1.6'), + ('data-encoding', '2.4.0'), + ('dialoguer', '0.10.4'), + ('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'), + ('either', '1.9.0'), + ('encode_unicode', '0.3.6'), + ('encoding_rs', '0.8.32'), + ('errno', '0.3.2'), + ('errno-dragonfly', '0.1.2'), + ('expect-test', '1.4.1'), + ('fastrand', '1.9.0'), + ('fat-macho', '0.4.7'), + ('filetime', '0.2.22'), + ('flate2', '1.0.27'), + ('fnv', '1.0.7'), + ('foreign-types', '0.3.2'), + ('foreign-types-shared', '0.1.1'), + ('form_urlencoded', '1.2.0'), + ('fs-err', '2.9.0'), + ('generic-array', '0.14.7'), + ('getrandom', '0.2.10'), + ('glob', '0.3.1'), + ('globset', '0.4.10'), + ('goblin', '0.7.1'), + ('hashbrown', '0.12.3'), + ('heck', '0.4.1'), + ('hermit-abi', '0.3.2'), + ('home', '0.5.5'), + ('humantime', '2.1.0'), + ('humantime-serde', '1.1.1'), + ('idna', '0.4.0'), + ('ignore', '0.4.20'), + ('indexmap', '1.9.3'), + ('indicatif', '0.17.6'), + ('indoc', '2.0.3'), + ('instant', '0.1.12'), + ('io-lifetimes', '1.0.11'), + ('is-terminal', '0.4.7'), + ('itertools', '0.11.0'), + ('itoa', '1.0.9'), + ('js-sys', '0.3.64'), + ('keyring', '2.0.5'), + ('lazy_static', '1.4.0'), + ('lddtree', '0.3.3'), + ('libc', '0.2.147'), + ('linux-keyutils', '0.2.3'), + ('linux-raw-sys', '0.3.8'), + ('lock_api', '0.4.10'), + ('log', '0.4.20'), + ('lzxd', '0.1.4'), + ('mailparse', '0.14.0'), + ('matchers', '0.1.0'), + ('memchr', '2.5.0'), + ('memoffset', '0.9.0'), + ('mime', '0.3.17'), + ('mime_guess', '2.0.4'), + ('minijinja', '1.0.8'), + ('minimal-lexical', '0.2.1'), + ('miniz_oxide', '0.7.1'), + ('msi', '0.6.0'), + ('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_cpus', '1.16.0'), + ('number_prefix', '0.4.0'), + ('once_cell', '1.18.0'), + ('openssl', '0.10.56'), + ('openssl-macros', '0.1.1'), + ('openssl-probe', '0.1.5'), + ('openssl-src', '111.27.0+1.1.1v'), + ('openssl-sys', '0.9.91'), + ('option-ext', '0.2.0'), + ('os_pipe', '1.1.4'), + ('overload', '0.1.1'), + ('parking_lot', '0.12.1'), + ('parking_lot_core', '0.9.8'), + ('paste', '1.0.14'), + ('path-slash', '0.2.1'), + ('pep440_rs', '0.3.6'), + ('pep508_rs', '0.2.1'), + ('percent-encoding', '2.3.0'), + ('pin-project-lite', '0.2.12'), + ('pkg-config', '0.3.27'), + ('plain', '0.2.3'), + ('platform-info', '2.0.2'), + ('portable-atomic', '1.4.2'), + ('ppv-lite86', '0.2.17'), + ('pretty_assertions', '1.4.0'), + ('proc-macro2', '1.0.66'), + ('psm', '0.1.21'), + ('pyproject-toml', '0.6.1'), + ('python-pkginfo', '0.6.0'), + ('quote', '1.0.33'), + ('quoted_printable', '0.4.8'), + ('rand', '0.8.5'), + ('rand_chacha', '0.3.1'), + ('rand_core', '0.6.4'), + ('rayon', '1.7.0'), + ('rayon-core', '1.11.0'), + ('redox_syscall', '0.2.16'), + ('redox_syscall', '0.3.5'), + ('redox_users', '0.4.3'), + ('regex', '1.7.3'), + ('regex-automata', '0.1.10'), + ('regex-syntax', '0.6.29'), + ('rfc2047-decoder', '0.2.2'), + ('ring', '0.16.20'), + ('rustc_version', '0.4.0'), + ('rustix', '0.37.25'), + ('rustls', '0.21.2'), + ('rustls-pemfile', '1.0.3'), + ('rustls-webpki', '0.100.2'), + ('rustversion', '1.0.14'), + ('ryu', '1.0.15'), + ('same-file', '1.0.6'), + ('schannel', '0.1.22'), + ('scopeguard', '1.2.0'), + ('scroll', '0.11.0'), + ('scroll_derive', '0.11.1'), + ('sct', '0.7.0'), + ('security-framework', '2.9.2'), + ('security-framework-sys', '2.9.1'), + ('semver', '1.0.18'), + ('serde', '1.0.183'), + ('serde_derive', '1.0.183'), + ('serde_json', '1.0.105'), + ('serde_spanned', '0.6.3'), + ('sha2', '0.10.7'), + ('sharded-slab', '0.1.4'), + ('shell-escape', '0.1.5'), + ('shell-words', '1.1.0'), + ('shlex', '1.1.0'), + ('similar', '2.2.1'), + ('smallvec', '1.11.0'), + ('smawk', '0.3.1'), + ('snapbox', '0.4.11'), + ('snapbox-macros', '0.3.4'), + ('socks', '0.3.4'), + ('spin', '0.5.2'), + ('stacker', '0.1.15'), + ('static_assertions', '1.1.0'), + ('strsim', '0.10.0'), + ('syn', '1.0.109'), + ('syn', '2.0.29'), + ('tar', '0.4.40'), + ('target-lexicon', '0.12.11'), + ('tempfile', '3.6.0'), + ('termcolor', '1.2.0'), + ('terminal_size', '0.2.6'), + ('textwrap', '0.16.0'), + ('thiserror', '1.0.47'), + ('thiserror-impl', '1.0.47'), + ('thread_local', '1.1.7'), + ('time', '0.3.20'), + ('time-core', '0.1.0'), + ('time-macros', '0.2.8'), + ('tinyvec', '1.6.0'), + ('tinyvec_macros', '0.1.1'), + ('toml', '0.5.11'), + ('toml', '0.7.4'), + ('toml_datetime', '0.6.2'), + ('toml_edit', '0.19.10'), + ('tracing', '0.1.37'), + ('tracing-attributes', '0.1.26'), + ('tracing-core', '0.1.31'), + ('tracing-log', '0.1.3'), + ('tracing-serde', '0.1.3'), + ('tracing-subscriber', '0.3.17'), + ('trycmd', '0.14.16'), + ('twox-hash', '1.6.3'), + ('typenum', '1.16.0'), + ('unicase', '2.6.0'), + ('unicode-bidi', '0.3.13'), + ('unicode-ident', '1.0.11'), + ('unicode-linebreak', '0.1.5'), + ('unicode-normalization', '0.1.22'), + ('unicode-width', '0.1.10'), + ('untrusted', '0.7.1'), + ('ureq', '2.7.1'), + ('url', '2.4.0'), + ('utf8parse', '0.2.1'), + ('uuid', '1.4.1'), + ('valuable', '0.1.0'), + ('vcpkg', '0.2.15'), + ('version_check', '0.9.4'), + ('versions', '5.0.1'), + ('wait-timeout', '0.2.0'), + ('walkdir', '2.3.3'), + ('wasi', '0.11.0+wasi-snapshot-preview1'), + ('wasm-bindgen', '0.2.87'), + ('wasm-bindgen-backend', '0.2.87'), + ('wasm-bindgen-macro', '0.2.87'), + ('wasm-bindgen-macro-support', '0.2.87'), + ('wasm-bindgen-shared', '0.2.87'), + ('web-sys', '0.3.64'), + ('webpki-roots', '0.23.1'), + ('which', '4.4.0'), + ('wild', '2.1.0'), + ('winapi', '0.3.9'), + ('winapi-i686-pc-windows-gnu', '0.4.0'), + ('winapi-util', '0.1.5'), + ('winapi-x86_64-pc-windows-gnu', '0.4.0'), + ('windows-sys', '0.45.0'), + ('windows-sys', '0.48.0'), + ('windows-targets', '0.42.2'), + ('windows-targets', '0.48.2'), + ('windows_aarch64_gnullvm', '0.42.2'), + ('windows_aarch64_gnullvm', '0.48.2'), + ('windows_aarch64_msvc', '0.42.2'), + ('windows_aarch64_msvc', '0.48.2'), + ('windows_i686_gnu', '0.42.2'), + ('windows_i686_gnu', '0.48.2'), + ('windows_i686_msvc', '0.42.2'), + ('windows_i686_msvc', '0.48.2'), + ('windows_x86_64_gnu', '0.42.2'), + ('windows_x86_64_gnu', '0.48.2'), + ('windows_x86_64_gnullvm', '0.42.2'), + ('windows_x86_64_gnullvm', '0.48.2'), + ('windows_x86_64_msvc', '0.42.2'), + ('windows_x86_64_msvc', '0.48.2'), + ('winnow', '0.4.7'), + ('xattr', '1.0.1'), + ('xwin', '0.3.1'), + ('yansi', '0.5.1'), + ('zeroize', '1.6.0'), + ('zip', '0.6.6'), +] +sources = [SOURCE_TAR_GZ] +checksums = [ + {'maturin-1.3.1.tar.gz': 'efa194e99ae5fff185263d8244acacb12ae256ea73aba62c9446f6075ffc7ac1'}, + {'adler-1.0.2.tar.gz': 'f26201604c87b1e01bd3d98f8d5d9a8fcbb815e8cedb41ffccbeb4bf593a35fe'}, + {'ahash-0.7.6.tar.gz': 'fcb51a0695d8f838b1ee009b3fbf66bda078cd64590202a864a8f3e8c4315c47'}, + {'aho-corasick-0.7.20.tar.gz': 'cc936419f96fa211c1b9166887b38e5e40b19958e5b895be7c1f93adec7071ac'}, + {'anstream-0.3.2.tar.gz': '0ca84f3628370c59db74ee214b3263d58f9aadd9b4fe7e711fd87dc452b7f163'}, + {'anstyle-1.0.1.tar.gz': '3a30da5c5f2d5e72842e00bcb57657162cdabef0931f40e2deb9b4140440cecd'}, + {'anstyle-parse-0.2.1.tar.gz': '938874ff5980b03a87c5524b3ae5b59cf99b1d6bc836848df7bc5ada9643c333'}, + {'anstyle-query-1.0.0.tar.gz': '5ca11d4be1bab0c8bc8734a9aa7bf4ee8316d462a08c6ac5052f888fef5b494b'}, + {'anstyle-wincon-1.0.2.tar.gz': 'c677ab05e09154296dd37acecd46420c17b9713e8366facafa8fc0885167cf4c'}, + {'anyhow-1.0.75.tar.gz': 'a4668cab20f66d8d020e1fbc0ebe47217433c1b6c8f2040faf858554e394ace6'}, + {'autocfg-1.1.0.tar.gz': 'd468802bab17cbc0cc575e9b053f41e72aa36bfa6b7f55e3529ffa43161b97fa'}, + {'base64-0.13.1.tar.gz': '9e1b586273c5702936fe7b7d6896644d8be71e6314cfe09d3167c95f712589e8'}, + {'base64-0.21.2.tar.gz': '604178f6c5c21f02dc555784810edfb88d34ac2c73b2eae109655649ee73ce3d'}, + {'bitflags-1.3.2.tar.gz': 'bef38d45163c2f1dde094a7dfd33ccf595c92905c8f8f4fdc18d06fb1037718a'}, + {'block-buffer-0.10.4.tar.gz': '3078c7629b62d3f0439517fa394996acacc5cbc91c5a20d8c658e77abd503a71'}, + {'bstr-1.6.0.tar.gz': '6798148dccfbff0fae41c7574d2fa8f1ef3492fba0face179de5d8d447d67b05'}, + {'bumpalo-3.13.0.tar.gz': 'a3e2c3daef883ecc1b5d58c15adae93470a91d425f3532ba1695849656af3fc1'}, + {'byteorder-1.4.3.tar.gz': '14c189c53d098945499cdfa7ecc63567cf3886b3332b312a5b4585d8d3a6a610'}, + {'bytes-1.4.0.tar.gz': '89b2fd2a0dcf38d7971e2194b6b6eebab45ae01067456a7fd93d5547a61b70be'}, + {'bytesize-1.2.0.tar.gz': '38fcc2979eff34a4b84e1cf9a1e3da42a7d44b3b690a40cdcb23e3d556cfb2e5'}, + {'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-config2-0.1.9.tar.gz': 'a393492158d1198da424057afeadc96af9330d76d12e56d131a7a5302524ac65'}, + {'cargo-options-0.6.0.tar.gz': '9b8e8daa6b2b84aa7cccd57317d9a9b36d969d75bb95923471f4eabbd36f2955'}, + {'cargo-platform-0.1.3.tar.gz': '2cfa25e60aea747ec7e1124f238816749faa93759c6ff5b31f1ccdda137f4479'}, + {'cargo-xwin-0.14.8.tar.gz': '11c08ee57b16103990269874220c0e8a4613b8096a314ce2f29ad1b54d4b6d02'}, + {'cargo-zigbuild-0.17.3.tar.gz': '2307bb523befb01f7e8cf299c2219439339316964c3a4e95e29bd1c7831fae89'}, + {'cargo_metadata-0.18.0.tar.gz': 'fb9ac64500cc83ce4b9f8dafa78186aa008c8dea77a09b94cd307fd0cd5022a8'}, + {'cbindgen-0.25.0.tar.gz': 'faeaa693e5a727975a79211b8f35c0cb09b031fdb6eaa4a788bc6713d01488ca'}, + {'cc-1.0.82.tar.gz': '305fe645edc1442a0fa8b6726ba61d422798d37a52e12eaecf4b022ebbb88f01'}, + {'cfb-0.7.3.tar.gz': 'd38f2da7a0a2c4ccf0065be06397cc26a81f4e528be095826eee9d4adbb8c60f'}, + {'cfg-expr-0.15.4.tar.gz': 'b40ccee03b5175c18cde8f37e7d2a33bcef6f8ec8f7cc0d81090d1bb380949c9'}, + {'cfg-if-1.0.0.tar.gz': 'baf1de4339761588bc0619e3cbc0120ee582ebb74b53b4efbf79117bd2da40fd'}, + {'charset-0.1.3.tar.gz': '18e9079d1a12a2cc2bffb5db039c43661836ead4082120d5844f02555aca2d46'}, + {'chumsky-0.9.2.tar.gz': '23170228b96236b5a7299057ac284a321457700bc8c41a4476052f0f4ba5349d'}, + {'clap-4.1.14.tar.gz': '906f7fe1da4185b7a282b2bc90172a496f9def1aca4545fe7526810741591e14'}, + {'clap_builder-4.1.14.tar.gz': '351f9ad9688141ed83dfd8f5fb998a06225ef444b48ff4dc43de6d409b7fd10b'}, + {'clap_complete-4.2.3.tar.gz': '1594fe2312ec4abf402076e407628f5c313e54c32ade058521df4ee34ecac8a8'}, + {'clap_complete_command-0.5.1.tar.gz': '183495371ea78d4c9ff638bfc6497d46fed2396e4f9c50aebc1278a4a9919a3d'}, + {'clap_complete_fig-4.2.0.tar.gz': 'f3af28956330989baa428ed4d3471b853715d445c62de21b67292e22cf8a41fa'}, + {'clap_complete_nushell-0.1.11.tar.gz': '5d02bc8b1a18ee47c4d2eec3fb5ac034dc68ebea6125b1509e9ccdffcddce66e'}, + {'clap_derive-4.1.14.tar.gz': '81d7dc0031c3a59a04fc2ba395c8e2dd463cba1859275f065d225f6122221b45'}, + {'clap_lex-0.4.1.tar.gz': '8a2dd5a6fe8c6e3502f568a6353e5273bbb15193ad9a89e457b9970798efbea1'}, + {'cli-table-0.4.7.tar.gz': 'adfbb116d9e2c4be7011360d0c0bee565712c11e969c9609b25b619366dc379d'}, + {'colorchoice-1.0.0.tar.gz': 'acbf1af155f9b9ef647e42cdc158db4b64a1b61f743629225fde6f3e0be2a7c7'}, + {'configparser-3.0.2.tar.gz': '5458d9d1a587efaf5091602c59d299696a3877a439c8f6d461a2d3cce11df87a'}, + {'console-0.15.7.tar.gz': 'c926e00cc70edefdc64d3a5ff31cc65bb97a3460097762bd23afb4d8145fccf8'}, + {'content_inspector-0.2.4.tar.gz': 'b7bda66e858c683005a53a9a60c69a4aca7eeaa45d124526e389f7aec8e62f38'}, + {'core-foundation-0.9.3.tar.gz': '194a7a9e6de53fa55116934067c844d9d749312f75c6f6d0980e8c252f8c2146'}, + {'core-foundation-sys-0.8.4.tar.gz': 'e496a50fda8aacccc86d7529e2c1e0892dbd0f898a6b5645b5561b89c3210efa'}, + {'cpufeatures-0.2.9.tar.gz': 'a17b76ff3a4162b0b27f354a0c87015ddad39d35f9c0c36607a3bdd175dde1f1'}, + {'crc32fast-1.3.2.tar.gz': 'b540bd8bc810d3885c6ea91e2018302f68baba2129ab3e88f32389ee9370880d'}, + {'crossbeam-channel-0.5.8.tar.gz': 'a33c2bf77f2df06183c3aa30d1e96c0695a313d4f9c453cc3762a6db39f99200'}, + {'crossbeam-deque-0.8.3.tar.gz': 'ce6fd6f855243022dcecf8702fef0c297d4338e226845fe067f6341ad9fa0cef'}, + {'crossbeam-epoch-0.9.15.tar.gz': 'ae211234986c545741a7dc064309f67ee1e5ad243d0e48335adc0484d960bcc7'}, + {'crossbeam-utils-0.8.16.tar.gz': '5a22b2d63d4d1dc0b7f1b6b2747dd0088008a9be28b6ddf0b1e7d335e3037294'}, + {'crypto-common-0.1.6.tar.gz': '1bfb12502f3fc46cca1bb51ac28df9d618d813cdc3d2f25b9fe775a34af26bb3'}, + {'data-encoding-2.4.0.tar.gz': 'c2e66c9d817f1720209181c316d28635c050fa304f9c79e47a520882661b7308'}, + {'dialoguer-0.10.4.tar.gz': '59c6f2989294b9a498d3ad5491a79c6deb604617378e1cdc4bfc1c1361fe2f87'}, + {'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'}, + {'either-1.9.0.tar.gz': 'a26ae43d7bcc3b814de94796a5e736d4029efb0ee900c12e2d54c993ad1a1e07'}, + {'encode_unicode-0.3.6.tar.gz': 'a357d28ed41a50f9c765dbfe56cbc04a64e53e5fc58ba79fbc34c10ef3df831f'}, + {'encoding_rs-0.8.32.tar.gz': '071a31f4ee85403370b58aca746f01041ede6f0da2730960ad001edc2b71b394'}, + {'errno-0.3.2.tar.gz': '6b30f669a7961ef1631673d2766cc92f52d64f7ef354d4fe0ddfd30ed52f0f4f'}, + {'errno-dragonfly-0.1.2.tar.gz': 'aa68f1b12764fab894d2755d2518754e71b4fd80ecfb822714a1206c2aab39bf'}, + {'expect-test-1.4.1.tar.gz': '30d9eafeadd538e68fb28016364c9732d78e420b9ff8853fa5e4058861e9f8d3'}, + {'fastrand-1.9.0.tar.gz': 'e51093e27b0797c359783294ca4f0a911c270184cb10f85783b118614a1501be'}, + {'fat-macho-0.4.7.tar.gz': '63fa117c7dcabeb8c83d5c229764cfa46518545d2dba5a9a08912014711f997b'}, + {'filetime-0.2.22.tar.gz': 'd4029edd3e734da6fe05b6cd7bd2960760a616bd2ddd0d59a0124746d6272af0'}, + {'flate2-1.0.27.tar.gz': 'c6c98ee8095e9d1dcbf2fcc6d95acccb90d1c81db1e44725c6a984b1dbdfb010'}, + {'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-1.2.0.tar.gz': 'a62bc1cf6f830c2ec14a513a9fb124d0a213a629668a4186f329db21fe045652'}, + {'fs-err-2.9.0.tar.gz': '0845fa252299212f0389d64ba26f34fa32cfe41588355f21ed507c59a0f64541'}, + {'generic-array-0.14.7.tar.gz': '85649ca51fd72272d7821adaf274ad91c288277713d9c18820d8499a7ff69e9a'}, + {'getrandom-0.2.10.tar.gz': 'be4136b2a15dd319360be1c07d9933517ccf0be8f16bf62a3bee4f0d618df427'}, + {'glob-0.3.1.tar.gz': 'd2fabcfbdc87f4758337ca535fb41a6d701b65693ce38287d856d1674551ec9b'}, + {'globset-0.4.10.tar.gz': '029d74589adefde59de1a0c4f4732695c32805624aec7b68d91503d4dba79afc'}, + {'goblin-0.7.1.tar.gz': 'f27c1b4369c2cd341b5de549380158b105a04c331be5db9110eef7b6d2742134'}, + {'hashbrown-0.12.3.tar.gz': '8a9ee70c43aaf417c914396645a0fa852624801b24ebb7ae78fe8272889ac888'}, + {'heck-0.4.1.tar.gz': '95505c38b4572b2d910cecb0281560f54b440a19336cbbcb27bf6ce6adc6f5a8'}, + {'hermit-abi-0.3.2.tar.gz': '443144c8cdadd93ebf52ddb4056d257f5b52c04d3c804e657d19eb73fc33668b'}, + {'home-0.5.5.tar.gz': '5444c27eef6923071f7ebcc33e3444508466a76f7a2b93da00ed6e19f30c1ddb'}, + {'humantime-2.1.0.tar.gz': '9a3a5bfb195931eeb336b2a7b4d761daec841b97f947d34394601737a7bba5e4'}, + {'humantime-serde-1.1.1.tar.gz': '57a3db5ea5923d99402c94e9feb261dc5ee9b4efa158b0315f788cf549cc200c'}, + {'idna-0.4.0.tar.gz': '7d20d6b07bfbc108882d88ed8e37d39636dcc260e15e30c45e6ba089610b917c'}, + {'ignore-0.4.20.tar.gz': 'dbe7873dab538a9a44ad79ede1faf5f30d49f9a5c883ddbab48bce81b64b7492'}, + {'indexmap-1.9.3.tar.gz': 'bd070e393353796e801d209ad339e89596eb4c8d430d18ede6a1cced8fafbd99'}, + {'indicatif-0.17.6.tar.gz': '0b297dc40733f23a0e52728a58fa9489a5b7638a324932de16b41adc3ef80730'}, + {'indoc-2.0.3.tar.gz': '2c785eefb63ebd0e33416dfcb8d6da0bf27ce752843a45632a67bf10d4d4b5c4'}, + {'instant-0.1.12.tar.gz': '7a5bbe824c507c5da5956355e86a746d82e0e1464f65d862cc5e71da70e94b2c'}, + {'io-lifetimes-1.0.11.tar.gz': 'eae7b9aee968036d54dce06cebaefd919e4472e753296daccd6d344e3e2df0c2'}, + {'is-terminal-0.4.7.tar.gz': 'adcf93614601c8129ddf72e2d5633df827ba6551541c6d8c59520a371475be1f'}, + {'itertools-0.11.0.tar.gz': 'b1c173a5686ce8bfa551b3563d0c2170bf24ca44da99c7ca4bfdab5418c3fe57'}, + {'itoa-1.0.9.tar.gz': 'af150ab688ff2122fcef229be89cb50dd66af9e01a4ff320cc137eecc9bacc38'}, + {'js-sys-0.3.64.tar.gz': 'c5f195fe497f702db0f318b07fdd68edb16955aed830df8363d837542f8f935a'}, + {'keyring-2.0.5.tar.gz': '9549a129bd08149e0a71b2d1ce2729780d47127991bfd0a78cc1df697ec72492'}, + {'lazy_static-1.4.0.tar.gz': 'e2abad23fbc42b3700f2f279844dc832adb2b2eb069b2df918f455c4e18cc646'}, + {'lddtree-0.3.3.tar.gz': '2f5bfec46830ad3a95199ae6804dfe9f51fdad43d7a95fbb6c185efa9824c295'}, + {'libc-0.2.147.tar.gz': 'b4668fb0ea861c1df094127ac5f1da3409a82116a4ba74fca2e58ef927159bb3'}, + {'linux-keyutils-0.2.3.tar.gz': '3f27bb67f6dd1d0bb5ab582868e4f65052e58da6401188a08f0da09cf512b84b'}, + {'linux-raw-sys-0.3.8.tar.gz': 'ef53942eb7bf7ff43a617b3e2c1c4a5ecf5944a7c1bc12d7ee39bbb15e5c1519'}, + {'lock_api-0.4.10.tar.gz': 'c1cc9717a20b1bb222f333e6a92fd32f7d8a18ddc5a3191a11af45dcbf4dcd16'}, + {'log-0.4.20.tar.gz': 'b5e6163cb8c49088c2c36f57875e58ccd8c87c7427f7fbd50ea6710b2f3f2e8f'}, + {'lzxd-0.1.4.tar.gz': '784462f20dddd9dfdb45de963fa4ad4a288cb10a7889ac5d2c34fb6481c6b213'}, + {'mailparse-0.14.0.tar.gz': '6b56570f5f8c0047260d1c8b5b331f62eb9c660b9dd4071a8c46f8c7d3f280aa'}, + {'matchers-0.1.0.tar.gz': '8263075bb86c5a1b1427b5ae862e8889656f126e9f77c484496e8b47cf5c5558'}, + {'memchr-2.5.0.tar.gz': '2dffe52ecf27772e601905b7522cb4ef790d2cc203488bbd0e2fe85fcb74566d'}, + {'memoffset-0.9.0.tar.gz': '5a634b1c61a95585bd15607c6ab0c4e5b226e695ff2800ba0cdccddf208c406c'}, + {'mime-0.3.17.tar.gz': '6877bb514081ee2a7ff5ef9de3281f14a4dd4bceac4c09388074a6b5df8a139a'}, + {'mime_guess-2.0.4.tar.gz': '4192263c238a5f0d0c6bfd21f336a313a4ce1c450542449ca191bb657b4642ef'}, + {'minijinja-1.0.8.tar.gz': '80084fa3099f58b7afab51e5f92e24c2c2c68dcad26e96ad104bd6011570461d'}, + {'minimal-lexical-0.2.1.tar.gz': '68354c5c6bd36d73ff3feceb05efa59b6acb7626617f4962be322a825e61f79a'}, + {'miniz_oxide-0.7.1.tar.gz': 'e7810e0be55b428ada41041c41f32c9f1a42817901b4ccf45fa3d4b6561e74c7'}, + {'msi-0.6.0.tar.gz': 'a7124fc3188eff23916d20d82bcbbb993914b22fba5603f9e7745e347a86cf67'}, + {'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_cpus-1.16.0.tar.gz': '4161fcb6d602d4d2081af7c3a45852d875a03dd337a6bfdd6e06407b61342a43'}, + {'number_prefix-0.4.0.tar.gz': '830b246a0e5f20af87141b25c173cd1b609bd7779a4617d6ec582abaf90870f3'}, + {'once_cell-1.18.0.tar.gz': 'dd8b5dd2ae5ed71462c540258bedcb51965123ad7e7ccf4b9a8cafaa4a63576d'}, + {'openssl-0.10.56.tar.gz': '729b745ad4a5575dd06a3e1af1414bd330ee561c01b3899eb584baeaa8def17e'}, + {'openssl-macros-0.1.1.tar.gz': 'a948666b637a0f465e8564c73e89d4dde00d72d4d473cc972f390fc3dcee7d9c'}, + {'openssl-probe-0.1.5.tar.gz': 'ff011a302c396a5197692431fc1948019154afc178baf7d8e37367442a4601cf'}, + {'openssl-src-111.27.0+1.1.1v.tar.gz': '06e8f197c82d7511c5b014030c9b1efeda40d7d5f99d23b4ceed3524a5e63f02'}, + {'openssl-sys-0.9.91.tar.gz': '866b5f16f90776b9bb8dc1e1802ac6f0513de3a7a7465867bfbc563dc737faac'}, + {'option-ext-0.2.0.tar.gz': '04744f49eae99ab78e0d5c0b603ab218f515ea8cfe5a456d7629ad883a3b6e7d'}, + {'os_pipe-1.1.4.tar.gz': '0ae859aa07428ca9a929b936690f8b12dc5f11dd8c6992a18ca93919f28bc177'}, + {'overload-0.1.1.tar.gz': 'b15813163c1d831bf4a13c3610c05c0d03b39feb07f7e09fa234dac9b15aaf39'}, + {'parking_lot-0.12.1.tar.gz': '3742b2c103b9f06bc9fff0a37ff4912935851bee6d36f3c02bcc755bcfec228f'}, + {'parking_lot_core-0.9.8.tar.gz': '93f00c865fe7cabf650081affecd3871070f26767e7b2070a3ffae14c654b447'}, + {'paste-1.0.14.tar.gz': 'de3145af08024dea9fa9914f381a17b8fc6034dfb00f3a84013f7ff43f29ed4c'}, + {'path-slash-0.2.1.tar.gz': '1e91099d4268b0e11973f036e885d652fb0b21fedcf69738c627f94db6a44f42'}, + {'pep440_rs-0.3.6.tar.gz': '3d6f6ead185985925c7e2b5ddb57ed5ef9d95835bf3994a5ce74403653898ab6'}, + {'pep508_rs-0.2.1.tar.gz': 'c0713d7bb861ca2b7d4c50a38e1f31a4b63a2e2df35ef1e5855cc29e108453e2'}, + {'percent-encoding-2.3.0.tar.gz': '9b2a4787296e9989611394c33f193f676704af1686e70b8f8033ab5ba9a35a94'}, + {'pin-project-lite-0.2.12.tar.gz': '12cc1b0bf1727a77a54b6654e7b5f1af8604923edc8b81885f8ec92f9e3f0a05'}, + {'pkg-config-0.3.27.tar.gz': '26072860ba924cbfa98ea39c8c19b4dd6a4a25423dbdf219c1eca91aa0cf6964'}, + {'plain-0.2.3.tar.gz': 'b4596b6d070b27117e987119b4dac604f3c58cfb0b191112e24771b2faeac1a6'}, + {'platform-info-2.0.2.tar.gz': 'd6259c4860e53bf665016f1b2f46a8859cadfa717581dc9d597ae4069de6300f'}, + {'portable-atomic-1.4.2.tar.gz': 'f32154ba0af3a075eefa1eda8bb414ee928f62303a54ea85b8d6638ff1a6ee9e'}, + {'ppv-lite86-0.2.17.tar.gz': '5b40af805b3121feab8a3c29f04d8ad262fa8e0561883e7653e024ae4479e6de'}, + {'pretty_assertions-1.4.0.tar.gz': 'af7cee1a6c8a5b9208b3cb1061f10c0cb689087b3d8ce85fb9d2dd7a29b6ba66'}, + {'proc-macro2-1.0.66.tar.gz': '18fb31db3f9bddb2ea821cde30a9f70117e3f119938b5ee630b7403aa6e2ead9'}, + {'psm-0.1.21.tar.gz': '5787f7cda34e3033a72192c018bc5883100330f362ef279a8cbccfce8bb4e874'}, + {'pyproject-toml-0.6.1.tar.gz': 'ee79feaa9d31e1c417e34219e610b67db4e786ce9b49d77dda549640abb9dc5f'}, + {'python-pkginfo-0.6.0.tar.gz': '037469c164f08c891bf6d69ca02f1d56210011451e229618669777df82124cfa'}, + {'quote-1.0.33.tar.gz': '5267fca4496028628a95160fc423a33e8b2e6af8a5302579e322e4b520293cae'}, + {'quoted_printable-0.4.8.tar.gz': '5a3866219251662ec3b26fc217e3e05bf9c4f84325234dfb96bf0bf840889e49'}, + {'rand-0.8.5.tar.gz': '34af8d1a0e25924bc5b7c43c079c942339d8f0a8b57c39049bef581b46327404'}, + {'rand_chacha-0.3.1.tar.gz': 'e6c10a63a0fa32252be49d21e7709d4d4baf8d231c2dbce1eaa8141b9b127d88'}, + {'rand_core-0.6.4.tar.gz': 'ec0be4795e2f6a28069bec0b5ff3e2ac9bafc99e6a9a7dc3547996c5c816922c'}, + {'rayon-1.7.0.tar.gz': '1d2df5196e37bcc87abebc0053e20787d73847bb33134a69841207dd0a47f03b'}, + {'rayon-core-1.11.0.tar.gz': '4b8f95bd6966f5c87776639160a66bd8ab9895d9d4ab01ddba9fc60661aebe8d'}, + {'redox_syscall-0.2.16.tar.gz': 'fb5a58c1855b4b6819d59012155603f0b22ad30cad752600aadfcb695265519a'}, + {'redox_syscall-0.3.5.tar.gz': '567664f262709473930a4bf9e51bf2ebf3348f2e748ccc50dea20646858f8f29'}, + {'redox_users-0.4.3.tar.gz': 'b033d837a7cf162d7993aded9304e30a83213c648b6e389db233191f891e5c2b'}, + {'regex-1.7.3.tar.gz': '8b1f693b24f6ac912f4893ef08244d70b6067480d2f1a46e950c9691e6749d1d'}, + {'regex-automata-0.1.10.tar.gz': '6c230d73fb8d8c1b9c0b3135c5142a8acee3a0558fb8db5cf1cb65f8d7862132'}, + {'regex-syntax-0.6.29.tar.gz': 'f162c6dd7b008981e4d40210aca20b4bd0f9b60ca9271061b07f78537722f2e1'}, + {'rfc2047-decoder-0.2.2.tar.gz': '61fc4b4e52897c3e30b12b7e9b04461215b647fbe66f6def60dd8edbce14ec2e'}, + {'ring-0.16.20.tar.gz': '3053cf52e236a3ed746dfc745aa9cacf1b791d846bdaf412f60a8d7d6e17c8fc'}, + {'rustc_version-0.4.0.tar.gz': 'bfa0f585226d2e68097d4f95d113b15b83a82e819ab25717ec0590d9584ef366'}, + {'rustix-0.37.25.tar.gz': 'd4eb579851244c2c03e7c24f501c3432bed80b8f720af1d6e5b0e0f01555a035'}, + {'rustls-0.21.2.tar.gz': 'e32ca28af694bc1bbf399c33a516dbdf1c90090b8ab23c2bc24f834aa2247f5f'}, + {'rustls-pemfile-1.0.3.tar.gz': '2d3987094b1d07b653b7dfdc3f70ce9a1da9c51ac18c1b06b662e4f9a0e9f4b2'}, + {'rustls-webpki-0.100.2.tar.gz': 'e98ff011474fa39949b7e5c0428f9b4937eda7da7848bbb947786b7be0b27dab'}, + {'rustversion-1.0.14.tar.gz': '7ffc183a10b4478d04cbbbfc96d0873219d962dd5accaff2ffbd4ceb7df837f4'}, + {'ryu-1.0.15.tar.gz': '1ad4cc8da4ef723ed60bced201181d83791ad433213d8c24efffda1eec85d741'}, + {'same-file-1.0.6.tar.gz': '93fc1dc3aaa9bfed95e02e6eadabb4baf7e3078b0bd1b4d7b6b0b68378900502'}, + {'schannel-0.1.22.tar.gz': '0c3733bf4cf7ea0880754e19cb5a462007c4a8c1914bff372ccc95b464f1df88'}, + {'scopeguard-1.2.0.tar.gz': '94143f37725109f92c262ed2cf5e59bce7498c01bcc1502d7b9afe439a4e9f49'}, + {'scroll-0.11.0.tar.gz': '04c565b551bafbef4157586fa379538366e4385d42082f255bfd96e4fe8519da'}, + {'scroll_derive-0.11.1.tar.gz': '1db149f81d46d2deba7cd3c50772474707729550221e69588478ebf9ada425ae'}, + {'sct-0.7.0.tar.gz': 'd53dcdb7c9f8158937a7981b48accfd39a43af418591a5d008c7b22b5e1b7ca4'}, + {'security-framework-2.9.2.tar.gz': '05b64fb303737d99b81884b2c63433e9ae28abebe5eb5045dcdd175dc2ecf4de'}, + {'security-framework-sys-2.9.1.tar.gz': 'e932934257d3b408ed8f30db49d85ea163bfe74961f017f405b025af298f0c7a'}, + {'semver-1.0.18.tar.gz': 'b0293b4b29daaf487284529cc2f5675b8e57c61f70167ba415a463651fd6a918'}, + {'serde-1.0.183.tar.gz': '32ac8da02677876d532745a130fc9d8e6edfa81a269b107c5b00829b91d8eb3c'}, + {'serde_derive-1.0.183.tar.gz': 'aafe972d60b0b9bee71a91b92fee2d4fb3c9d7e8f6b179aa99f27203d99a4816'}, + {'serde_json-1.0.105.tar.gz': '693151e1ac27563d6dbcec9dee9fbd5da8539b20fa14ad3752b2e6d363ace360'}, + {'serde_spanned-0.6.3.tar.gz': '96426c9936fd7a0124915f9185ea1d20aa9445cc9821142f0a73bc9207a2e186'}, + {'sha2-0.10.7.tar.gz': '479fb9d862239e610720565ca91403019f2f00410f1864c5aa7479b950a76ed8'}, + {'sharded-slab-0.1.4.tar.gz': '900fba806f70c630b0a382d0d825e17a0f19fcd059a2ade1ff237bcddf446b31'}, + {'shell-escape-0.1.5.tar.gz': '45bb67a18fa91266cc7807181f62f9178a6873bfad7dc788c42e6430db40184f'}, + {'shell-words-1.1.0.tar.gz': '24188a676b6ae68c3b2cb3a01be17fbf7240ce009799bb56d5b1409051e78fde'}, + {'shlex-1.1.0.tar.gz': '43b2853a4d09f215c24cc5489c992ce46052d359b5109343cbafbf26bc62f8a3'}, + {'similar-2.2.1.tar.gz': '420acb44afdae038210c99e69aae24109f32f15500aa708e81d46c9f29d55fcf'}, + {'smallvec-1.11.0.tar.gz': '62bb4feee49fdd9f707ef802e22365a35de4b7b299de4763d44bfea899442ff9'}, + {'smawk-0.3.1.tar.gz': 'f67ad224767faa3c7d8b6d91985b78e70a1324408abcb1cfcc2be4c06bc06043'}, + {'snapbox-0.4.11.tar.gz': 'f6bccd62078347f89a914e3004d94582e13824d4e3d8a816317862884c423835'}, + {'snapbox-macros-0.3.4.tar.gz': 'eaaf09df9f0eeae82be96290918520214530e738a7fe5a351b0f24cf77c0ca31'}, + {'socks-0.3.4.tar.gz': 'f0c3dbbd9ae980613c6dd8e28a9407b50509d3803b57624d5dfe8315218cd58b'}, + {'spin-0.5.2.tar.gz': '6e63cff320ae2c57904679ba7cb63280a3dc4613885beafb148ee7bf9aa9042d'}, + {'stacker-0.1.15.tar.gz': 'c886bd4480155fd3ef527d45e9ac8dd7118a898a46530b7b94c3e21866259fce'}, + {'static_assertions-1.1.0.tar.gz': 'a2eb9349b6444b326872e140eb1cf5e7c522154d69e7a0ffb0fb81c06b37543f'}, + {'strsim-0.10.0.tar.gz': '73473c0e59e6d5812c5dfe2a064a6444949f089e20eec9a2e5506596494e4623'}, + {'syn-1.0.109.tar.gz': '72b64191b275b66ffe2469e8af2c1cfe3bafa67b529ead792a6d0160888b4237'}, + {'syn-2.0.29.tar.gz': 'c324c494eba9d92503e6f1ef2e6df781e78f6a7705a0202d9801b198807d518a'}, + {'tar-0.4.40.tar.gz': 'b16afcea1f22891c49a00c751c7b63b2233284064f11a200fc624137c51e2ddb'}, + {'target-lexicon-0.12.11.tar.gz': '9d0e916b1148c8e263850e1ebcbd046f333e0683c724876bb0da63ea4373dc8a'}, + {'tempfile-3.6.0.tar.gz': '31c0432476357e58790aaa47a8efb0c5138f137343f3b5f23bd36a27e3b0a6d6'}, + {'termcolor-1.2.0.tar.gz': 'be55cf8942feac5c765c2c993422806843c9a9a45d4d5c407ad6dd2ea95eb9b6'}, + {'terminal_size-0.2.6.tar.gz': '8e6bf6f19e9f8ed8d4048dc22981458ebcf406d67e94cd422e5ecd73d63b3237'}, + {'textwrap-0.16.0.tar.gz': '222a222a5bfe1bba4a77b45ec488a741b3cb8872e5e499451fd7d0129c9c7c3d'}, + {'thiserror-1.0.47.tar.gz': '97a802ec30afc17eee47b2855fc72e0c4cd62be9b4efe6591edde0ec5bd68d8f'}, + {'thiserror-impl-1.0.47.tar.gz': '6bb623b56e39ab7dcd4b1b98bb6c8f8d907ed255b18de254088016b27a8ee19b'}, + {'thread_local-1.1.7.tar.gz': '3fdd6f064ccff2d6567adcb3873ca630700f00b5ad3f060c25b5dcfd9a4ce152'}, + {'time-0.3.20.tar.gz': 'cd0cbfecb4d19b5ea75bb31ad904eb5b9fa13f21079c3b92017ebdf4999a5890'}, + {'time-core-0.1.0.tar.gz': '2e153e1f1acaef8acc537e68b44906d2db6436e2b35ac2c6b42640fff91f00fd'}, + {'time-macros-0.2.8.tar.gz': 'fd80a657e71da814b8e5d60d3374fc6d35045062245d80224748ae522dd76f36'}, + {'tinyvec-1.6.0.tar.gz': '87cc5ceb3875bb20c2890005a4e226a4651264a5c75edb2421b52861a0a0cb50'}, + {'tinyvec_macros-0.1.1.tar.gz': '1f3ccbac311fea05f86f61904b462b55fb3df8837a366dfc601a0161d0532f20'}, + {'toml-0.5.11.tar.gz': 'f4f7f0dd8d50a853a531c426359045b1998f04219d88799810762cd4ad314234'}, + {'toml-0.7.4.tar.gz': 'd6135d499e69981f9ff0ef2167955a5333c35e36f6937d382974566b3d5b94ec'}, + {'toml_datetime-0.6.2.tar.gz': '5a76a9312f5ba4c2dec6b9161fdf25d87ad8a09256ccea5a556fef03c706a10f'}, + {'toml_edit-0.19.10.tar.gz': '2380d56e8670370eee6566b0bfd4265f65b3f432e8c6d85623f728d4fa31f739'}, + {'tracing-0.1.37.tar.gz': '8ce8c33a8d48bd45d624a6e523445fd21ec13d3653cd51f681abf67418f54eb8'}, + {'tracing-attributes-0.1.26.tar.gz': '5f4f31f56159e98206da9efd823404b79b6ef3143b4a7ab76e67b1751b25a4ab'}, + {'tracing-core-0.1.31.tar.gz': '0955b8137a1df6f1a2e9a37d8a6656291ff0297c1a97c24e0d8425fe2312f79a'}, + {'tracing-log-0.1.3.tar.gz': '78ddad33d2d10b1ed7eb9d1f518a5674713876e97e5bb9b7345a7984fbb4f922'}, + {'tracing-serde-0.1.3.tar.gz': 'bc6b213177105856957181934e4920de57730fc69bf42c37ee5bb664d406d9e1'}, + {'tracing-subscriber-0.3.17.tar.gz': '30a651bc37f915e81f087d86e62a18eec5f79550c7faff886f7090b4ea757c77'}, + {'trycmd-0.14.16.tar.gz': '2925e71868a12b173c1eb166018c2d2f9dfaedfcaec747bdb6ea2246785d258e'}, + {'twox-hash-1.6.3.tar.gz': '97fee6b57c6a41524a810daee9286c02d7752c4253064d0b05472833a438f675'}, + {'typenum-1.16.0.tar.gz': '497961ef93d974e23eb6f433eb5fe1b7930b659f06d12dec6fc44a8f554c0bba'}, + {'unicase-2.6.0.tar.gz': '50f37be617794602aabbeee0be4f259dc1778fabe05e2d67ee8f79326d5cb4f6'}, + {'unicode-bidi-0.3.13.tar.gz': '92888ba5573ff080736b3648696b70cafad7d250551175acbaa4e0385b3e1460'}, + {'unicode-ident-1.0.11.tar.gz': '301abaae475aa91687eb82514b328ab47a211a533026cb25fc3e519b86adfc3c'}, + {'unicode-linebreak-0.1.5.tar.gz': '3b09c83c3c29d37506a3e260c08c03743a6bb66a9cd432c6934ab501a190571f'}, + {'unicode-normalization-0.1.22.tar.gz': '5c5713f0fc4b5db668a2ac63cdb7bb4469d8c9fed047b1d0292cc7b0ce2ba921'}, + {'unicode-width-0.1.10.tar.gz': 'c0edd1e5b14653f783770bce4a4dabb4a5108a5370a5f5d8cfe8710c361f6c8b'}, + {'untrusted-0.7.1.tar.gz': 'a156c684c91ea7d62626509bce3cb4e1d9ed5c4d978f7b4352658f96a4c26b4a'}, + {'ureq-2.7.1.tar.gz': '0b11c96ac7ee530603dcdf68ed1557050f374ce55a5a07193ebf8cbc9f8927e9'}, + {'url-2.4.0.tar.gz': '50bff7831e19200a85b17131d085c25d7811bc4e186efdaf54bbd132994a88cb'}, + {'utf8parse-0.2.1.tar.gz': '711b9620af191e0cdc7468a8d14e709c3dcdb115b36f838e601583af800a370a'}, + {'uuid-1.4.1.tar.gz': '79daa5ed5740825c40b389c5e50312b9c86df53fccd33f281df655642b43869d'}, + {'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-2.3.3.tar.gz': '36df944cda56c7d8d8b7496af378e6b16de9284591917d307c9b4d313c44e698'}, + {'wasi-0.11.0+wasi-snapshot-preview1.tar.gz': '9c8d87e72b64a3b4db28d11ce29237c246188f4f51057d65a7eab63b7987e423'}, + {'wasm-bindgen-0.2.87.tar.gz': '7706a72ab36d8cb1f80ffbf0e071533974a60d0a308d01a5d0375bf60499a342'}, + {'wasm-bindgen-backend-0.2.87.tar.gz': '5ef2b6d3c510e9625e5fe6f509ab07d66a760f0885d858736483c32ed7809abd'}, + {'wasm-bindgen-macro-0.2.87.tar.gz': 'dee495e55982a3bd48105a7b947fd2a9b4a8ae3010041b9e0faab3f9cd028f1d'}, + {'wasm-bindgen-macro-support-0.2.87.tar.gz': '54681b18a46765f095758388f2d0cf16eb8d4169b639ab575a8f5693af210c7b'}, + {'wasm-bindgen-shared-0.2.87.tar.gz': 'ca6ad05a4870b2bf5fe995117d3728437bd27d7cd5f06f13c17443ef369775a1'}, + {'web-sys-0.3.64.tar.gz': '9b85cbef8c220a6abc02aefd892dfc0fc23afb1c6a426316ec33253a3877249b'}, + {'webpki-roots-0.23.1.tar.gz': 'b03058f88386e5ff5310d9111d53f48b17d732b401aeb83a8d5190f2ac459338'}, + {'which-4.4.0.tar.gz': '2441c784c52b289a054b7201fc93253e288f094e2f4be9058343127c4226a269'}, + {'wild-2.1.0.tar.gz': '05b116685a6be0c52f5a103334cbff26db643826c7b3735fc0a3ba9871310a74'}, + {'winapi-0.3.9.tar.gz': '5c839a674fcd7a98952e593242ea400abe93992746761e38641405d28b00f419'}, + {'winapi-i686-pc-windows-gnu-0.4.0.tar.gz': 'ac3b87c63620426dd9b991e5ce0329eff545bccbbb34f3be09ff6fb6ab51b7b6'}, + {'winapi-util-0.1.5.tar.gz': '70ec6ce85bb158151cae5e5c87f95a8e97d2c0c4b001223f33a334e3ce5de178'}, + {'winapi-x86_64-pc-windows-gnu-0.4.0.tar.gz': '712e227841d057c1ee1cd2fb22fa7e5a5461ae8e48fa2ca79ec42cfc1931183f'}, + {'windows-sys-0.45.0.tar.gz': '75283be5efb2831d37ea142365f009c02ec203cd29a3ebecbc093d52315b66d0'}, + {'windows-sys-0.48.0.tar.gz': '677d2418bec65e3338edb076e806bc1ec15693c5d0104683f2efe857f61056a9'}, + {'windows-targets-0.42.2.tar.gz': '8e5180c00cd44c9b1c88adb3693291f1cd93605ded80c250a75d472756b4d071'}, + {'windows-targets-0.48.2.tar.gz': 'd1eeca1c172a285ee6c2c84c341ccea837e7c01b12fbb2d0fe3c9e550ce49ec8'}, + {'windows_aarch64_gnullvm-0.42.2.tar.gz': '597a5118570b68bc08d8d59125332c54f1ba9d9adeedeef5b99b02ba2b0698f8'}, + {'windows_aarch64_gnullvm-0.48.2.tar.gz': 'b10d0c968ba7f6166195e13d593af609ec2e3d24f916f081690695cf5eaffb2f'}, + {'windows_aarch64_msvc-0.42.2.tar.gz': 'e08e8864a60f06ef0d0ff4ba04124db8b0fb3be5776a5cd47641e942e58c4d43'}, + {'windows_aarch64_msvc-0.48.2.tar.gz': '571d8d4e62f26d4932099a9efe89660e8bd5087775a2ab5cdd8b747b811f1058'}, + {'windows_i686_gnu-0.42.2.tar.gz': 'c61d927d8da41da96a81f029489353e68739737d3beca43145c8afec9a31a84f'}, + {'windows_i686_gnu-0.48.2.tar.gz': '2229ad223e178db5fbbc8bd8d3835e51e566b8474bfca58d2e6150c48bb723cd'}, + {'windows_i686_msvc-0.42.2.tar.gz': '44d840b6ec649f480a41c8d80f9c65108b92d89345dd94027bfe06ac444d1060'}, + {'windows_i686_msvc-0.48.2.tar.gz': '600956e2d840c194eedfc5d18f8242bc2e17c7775b6684488af3a9fff6fe3287'}, + {'windows_x86_64_gnu-0.42.2.tar.gz': '8de912b8b8feb55c064867cf047dda097f92d51efad5b491dfb98f6bbb70cb36'}, + {'windows_x86_64_gnu-0.48.2.tar.gz': 'ea99ff3f8b49fb7a8e0d305e5aec485bd068c2ba691b6e277d29eaeac945868a'}, + {'windows_x86_64_gnullvm-0.42.2.tar.gz': '26d41b46a36d453748aedef1486d5c7a85db22e56aff34643984ea85514e94a3'}, + {'windows_x86_64_gnullvm-0.48.2.tar.gz': '8f1a05a1ece9a7a0d5a7ccf30ba2c33e3a61a30e042ffd247567d1de1d94120d'}, + {'windows_x86_64_msvc-0.42.2.tar.gz': '9aec5da331524158c6d1a4ac0ab1541149c0b9505fde06423b02f5ef0106b9f0'}, + {'windows_x86_64_msvc-0.48.2.tar.gz': 'd419259aba16b663966e29e6d7c6ecfa0bb8425818bb96f6f1f3c3eb71a6e7b9'}, + {'winnow-0.4.7.tar.gz': 'ca0ace3845f0d96209f0375e6d367e3eb87eb65d27d445bdc9f1843a26f39448'}, + {'xattr-1.0.1.tar.gz': 'f4686009f71ff3e5c4dbcf1a282d0a44db3f021ba69350cd42086b3e5f1c6985'}, + {'xwin-0.3.1.tar.gz': '79db6a9fc6b665feccd1984e4e21ff588102652c317176fab0d6706b55d3e208'}, + {'yansi-0.5.1.tar.gz': '09041cd90cf85f7f8b2df60c646f853b7f535ce68f85244eb6731cf89fa498ec'}, + {'zeroize-1.6.0.tar.gz': '2a0956f1ba7c7909bfb66c2e9e4124ab6f6482560f6628b5aaeba39207c9aad9'}, + {'zip-0.6.6.tar.gz': '760394e246e4c28189f19d488c058bf16f564016aefac5d32bb1f3b51d5e9261'}, +] + +builddependencies = [ + ('binutils', '2.40'), + ('setuptools-rust', '1.8.0'), +] +dependencies = [ + ('Python', '3.11.5'), + ('Rust', '1.73.0'), +] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/poetry/poetry-1.6.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/poetry/poetry-1.6.1-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..62fcc19a0e4 --- /dev/null +++ b/easybuild/easyconfigs/p/poetry/poetry-1.6.1-GCCcore-13.2.0.eb @@ -0,0 +1,162 @@ +easyblock = 'PythonBundle' + +name = 'poetry' +version = '1.6.1' + +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': '13.2.0'} + +builddependencies = [ + ('binutils', '2.40'), + ('pkgconf', '2.0.3'), + ('scikit-build', '0.17.6'), +] + +dependencies = [ + ('Python', '3.11.5'), + ('hatchling', '1.18.0'), + ('cryptography', '41.0.5'), + ('virtualenv', '20.24.6'), +# ('maturin', '1.3.1'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('six', '1.16.0', { + 'checksums': ['1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926'], + }), + ('idna', '3.4', { + 'checksums': ['814f528e8dead7d329833b91c5faa87d60bf71824cd12a7530b5526063d02cb4'], + }), + ('certifi', '2023.7.22', { + 'checksums': ['539cc1d13202e33ca466e88b2807e29f4c13049d6d87031a3c110744495cb082'], + }), + ('urllib3', '2.0.7', { + 'checksums': ['c97dfde1f7bd43a71c8d2a58e369e9b2bf692d1334ea9f9cae55add7d0dd0f84'], + }), + ('charset-normalizer', '3.3.1', { + 'checksums': ['d9137a876020661972ca6eec0766d81aef8a5627df628b664b234b73396e727e'], + }), + ('dulwich', '0.21.6', { + 'checksums': ['30fbe87e8b51f3813c131e2841c86d007434d160bd16db586b40d47f31dd05b0'], + }), + ('crashtest', '0.4.1', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['8d23eac5fa660409f57472e3851dab7ac18aba459a8d19cbbba86d3d5aecd2a5'], + }), + ('zipp', '3.17.0', { + 'checksums': ['84e64a1c28cf7e91ed2078bb8cc8c259cb19b76942096c8d7b84947690cabaf0'], + }), + ('importlib_metadata', '6.8.0', { + 'checksums': ['dbace7892d8c0c4ac1ad096662232f831d4e64f4c4545bd53016a3e9d4654743'], + }), + ('jeepney', '0.8.0', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['c0a454ad016ca575060802ee4d590dd912e35c122fa04e70306de3d076cce755'], + }), + ('SecretStorage', '3.3.3', { + 'checksums': ['2403533ef369eca6d2ba81718576c5e0f564d5cca1b58f73a8b23e7d4eeebd77'], + }), + ('more-itertools', '10.1.0', { + 'checksums': ['626c369fa0eb37bac0291bce8259b332fd59ac792fa5497b59837309cd5b114a'], + }), + ('jaraco.classes', '3.3.0', { + 'checksums': ['c063dd08e89217cee02c8d5e5ec560f2c8ce6cdc2fcdc2e68f7b2e5547ed3621'], + }), + ('keyring', '24.2.0', { + 'modulename': False, + 'checksums': ['ca0746a19ec421219f4d713f848fa297a661a8a8c1504867e55bfb5e09091509'], + }), + ('pyproject_hooks', '1.0.0', { + 'checksums': ['f271b298b97f5955d53fb12b72c1fb1948c22c1a6b70b315c54cedaca0264ef5'], + }), + # poetry 1.6.1 has requirement build<0.11.0,>=0.10.0 + ('build', '0.10.0', { + 'checksums': ['d5b71264afdb5951d6704482aac78de887c80691c52b88a9ad195983ca2c9269'], + }), + ('installer', '0.7.0', { + 'checksums': ['a26d3e3116289bb08216e0d0f7d925fcef0b0194eedfa0c944bcaaa106c4b631'], + }), + ('webencodings', '0.5.1', { + 'checksums': ['b36a1c245f2d304965eb4e0a82848379241dc04b865afcc4aab16748587e1923'], + }), + ('html5lib', '1.1', { + 'checksums': ['b2e5b40261e20f354d198eae92afc10d750afb487ed5e50f9c4eaf07c184146f'], + }), + # poetry 1.5.1 has requirement rapidfuzz<3.0.0,>=2.2.0 + ('rapidfuzz', '2.15.2', { + 'checksums': ['bfc1d38a7adcbe8912f980a5f46f27a801dd8655582ff0d4a2c0431c02b7ce33'], + }), + ('cleo', '2.0.1', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['6eb133670a3ed1f3b052d53789017b6e50fca66d1287e6e6696285f4cb8ea448'], + }), + ('attrs', '23.1.0', { + 'modulename': 'attr', + 'checksums': ['6279836d581513a26f1bf235f9acd333bc9115683f14f7e8fae46c98fc50e015'], + }), + ('pyrsistent', '0.20.0', { + 'checksums': ['4c48f78f62ab596c679086084d0dd13254ae4f3d6c72a83ffdf5ebdef8f265a4'], + }), + ('requests-toolbelt', '1.0.0', { + 'checksums': ['7681a0a3d047012b5bdc0ee37d7f8f07ebe76ab08caeccfc3921ce23c88d5bc6'], + }), + ('pkginfo', '1.9.6', { + 'checksums': ['8fd5896e8718a4372f0ea9cc9d96f6417c9b986e23a4d116dda26b62cc29d046'], + }), + ('ptyprocess', '0.7.0', { + 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', + 'checksums': ['4b41f3967fce3af57cc7e94b888626c18bf37a083e3651ca8feeb66d492fef35'], + }), + ('pexpect', '4.8.0', { + 'checksums': ['fc65a43959d153d0114afe13997d439c22823a27cefceb5ff35c2178c6784c0c'], + }), + # poetry 1.6.1 has requirement jsonschema<4.18.0,>=4.10.0 + ('jsonschema', '4.17.3', { + 'checksums': ['0f864437ab8b6076ba6707453ef8f98a6a0d512a80e93f8abdb676f737ecb60d'], + }), + ('platformdirs', '3.11.0', { + 'checksums': ['cf8ee52a3afdb965072dcc652433e0c7e3e40cf5ea1477cd4b3b1d2eb75495b3'], + }), + ('shellingham', '1.5.4', { + 'checksums': ['8dbca0739d487e5bd35ab3ca4b36e11c4078f3a234bfce294b0a0291363404de'], + }), + ('tomlkit', '0.12.1', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['712cbd236609acc6a3e2e97253dfc52d4c2082982a88f61b640ecf0817eab899'], + }), + ('requests', '2.31.0', { + 'checksums': ['942c5a758f98d790eaed1a29cb6eefc7ffb0d1cf7af05c3d2791656dbd6ad1e1'], + }), + ('msgpack', '1.0.7', { + 'checksums': ['572efc93db7a4d27e404501975ca6d2d9775705c2d922390d878fcf768d92c87'], + }), + ('cachecontrol', '0.13.1', { + 'checksums': ['f012366b79d2243a6118309ce73151bf52a38d4a5dac8ea57f09bd29087e506b'], + }), + ('lockfile', '0.12.2', { + 'checksums': ['6aed02de03cba24efabcd600b30540140634fc06cfa603822d508d5361e9f799'], + }), + ('poetry_core', '1.7.0', { + 'modulename': 'poetry.core', + 'checksums': ['8f679b83bd9c820082637beca1204124d5d2a786e4818da47ec8acefd0353b74'], + }), + ('poetry_plugin_export', '1.5.0', { + 'checksums': ['ecc8738da0c81c3758e36b4e72e04ae59648a547492af2ffe6245af3594bb00f'], + }), + (name, version, { + 'checksums': ['0ab9b1a592731cc8b252b8d6aaeea19c72cc0a109d7468b829ad57e6c48039d2'], + }), +] + +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-13.2.0.eb b/easybuild/easyconfigs/s/scikit-build/scikit-build-0.17.6-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..d42d1fe3d0c --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-build/scikit-build-0.17.6-GCCcore-13.2.0.eb @@ -0,0 +1,37 @@ +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': '13.2.0'} + +builddependencies = [ + ('binutils', '2.40'), + ('hatchling', '1.18.0'), +] + +dependencies = [ + ('Python', '3.11.5'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('packaging', '23.1', { + 'checksums': ['a392980d2b6cffa644431898be54b0045151319d1e7ec34f0cfed48767dd334f'], + }), + ('distro', '1.8.0', { + 'checksums': ['02e111d1dc6a50abb8eed6bf31c3e48ed8b0830d1ea2a1b78c61765c2513fdd8'], + }), + ('scikit_build', version, { + 'modulename': 'skbuild', + 'checksums': ['b51a51a36b37c42650994b5047912f59b22e3210b23e321f287611f9ef6e5c9d'], + }), +] + +moduleclass = 'lib' 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 new file mode 100644 index 00000000000..669229c8f11 --- /dev/null +++ b/easybuild/easyconfigs/s/setuptools-rust/setuptools-rust-1.8.0-GCCcore-13.2.0.eb @@ -0,0 +1,39 @@ +easyblock = 'PythonBundle' + +name = 'setuptools-rust' +version = '1.8.0' + +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': '13.2.0'} +toolchainopts = {'pic': True} + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('Python', '3.11.5'), +] + +exts_default_options = { + 'download_dep_fail': True, + 'sanity_pip_check': True, + 'use_pip': True, +} + +exts_list = [ + ('typing_extensions', '4.8.0', { + 'checksums': ['df8e4339e9cb77357558cbdbceca33c303714cf861d1eef15e1070055ae8b7ef'], + }), + ('semantic_version', '2.10.0', { + 'checksums': ['bdabb6d336998cbb378d4b9db3a4b56a1e3235701dc05ea2690d9a997ed5041c'], + }), + (name, version, { + 'checksums': ['5e02b7a80058853bf64127314f6b97d0efed11e08b94c88ca639a20976f6adc4'], + }), +] + +moduleclass = 'tools' 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 new file mode 100644 index 00000000000..a0b9921fb5c --- /dev/null +++ b/easybuild/easyconfigs/v/virtualenv/virtualenv-20.24.6-GCCcore-13.2.0.eb @@ -0,0 +1,47 @@ +easyblock = 'PythonBundle' + +name = 'virtualenv' +version = '20.24.6' + +homepage = 'https://github.com/pypa/virtualenv' +description = "A tool for creating isolated virtual python environments." + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +builddependencies = [ + ('binutils', '2.40'), + ('hatchling', '1.18.0'), +] + +dependencies = [ + ('Python', '3.11.5'), +] + +exts_default_options = { + 'download_dep_fail': True, + 'sanity_pip_check': True, + 'use_pip': True, +} + +exts_list = [ + ('distlib', '0.3.7', { + 'checksums': ['9dafe54b34a028eafd95039d5e5d4851a13734540f1331060d31c9916e7147a8'], + }), + ('filelock', '3.13.0', { + 'checksums': ['63c6052c82a1a24c873a549fbd39a26982e8f35a3016da231ead11a5be9dad44'], + }), + ('platformdirs', '3.11.0', { + 'checksums': ['cf8ee52a3afdb965072dcc652433e0c7e3e40cf5ea1477cd4b3b1d2eb75495b3'], + }), + (name, version, { + 'checksums': ['02ece4f56fbf939dbbc33c0715159951d6bf14aaf5457b092e4548e1382455af'], + }), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], +} + +moduleclass = 'tools' From 1b01f9d525db83b13b6fbc20377c361aaa2eefd1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sat, 28 Oct 2023 17:59:26 +0200 Subject: [PATCH 090/599] Remove leftover comment --- easybuild/easyconfigs/p/poetry/poetry-1.6.1-GCCcore-13.2.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/p/poetry/poetry-1.6.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/poetry/poetry-1.6.1-GCCcore-13.2.0.eb index 62fcc19a0e4..b55799d2110 100644 --- a/easybuild/easyconfigs/p/poetry/poetry-1.6.1-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/p/poetry/poetry-1.6.1-GCCcore-13.2.0.eb @@ -20,7 +20,6 @@ dependencies = [ ('hatchling', '1.18.0'), ('cryptography', '41.0.5'), ('virtualenv', '20.24.6'), -# ('maturin', '1.3.1'), ] use_pip = True From 02dad8e402622df091cc2a13810c1c500d4cfe92 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 29 Oct 2023 14:28:25 +0100 Subject: [PATCH 091/599] add sanity check commands for recent GDB versions --- easybuild/easyconfigs/g/GDB/GDB-10.1-GCCcore-10.2.0.eb | 5 +++++ easybuild/easyconfigs/g/GDB/GDB-10.2-GCCcore-10.3.0.eb | 5 +++++ .../easyconfigs/g/GDB/GDB-10.2-GCCcore-9.3.0-Python-3.8.2.eb | 5 +++++ easybuild/easyconfigs/g/GDB/GDB-11.1-GCCcore-11.2.0.eb | 5 +++++ easybuild/easyconfigs/g/GDB/GDB-12.1-GCCcore-11.3.0.eb | 5 +++++ easybuild/easyconfigs/g/GDB/GDB-13.2-GCCcore-12.3.0.eb | 5 +++++ easybuild/easyconfigs/g/GDB/GDB-13.2-GCCcore-13.2.0.eb | 5 +++++ 7 files changed, 35 insertions(+) diff --git a/easybuild/easyconfigs/g/GDB/GDB-10.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/GDB/GDB-10.1-GCCcore-10.2.0.eb index ce542957783..0300093f744 100644 --- a/easybuild/easyconfigs/g/GDB/GDB-10.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/g/GDB/GDB-10.1-GCCcore-10.2.0.eb @@ -41,4 +41,9 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = [ + 'gdb --help', + 'gdbserver --help', +] + moduleclass = 'debugger' diff --git a/easybuild/easyconfigs/g/GDB/GDB-10.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/g/GDB/GDB-10.2-GCCcore-10.3.0.eb index a036bbe3b5d..887741cbd05 100644 --- a/easybuild/easyconfigs/g/GDB/GDB-10.2-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/g/GDB/GDB-10.2-GCCcore-10.3.0.eb @@ -41,4 +41,9 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = [ + 'gdb --help', + 'gdbserver --help', +] + moduleclass = 'debugger' diff --git a/easybuild/easyconfigs/g/GDB/GDB-10.2-GCCcore-9.3.0-Python-3.8.2.eb b/easybuild/easyconfigs/g/GDB/GDB-10.2-GCCcore-9.3.0-Python-3.8.2.eb index a232a09da3b..2ee9015802d 100644 --- a/easybuild/easyconfigs/g/GDB/GDB-10.2-GCCcore-9.3.0-Python-3.8.2.eb +++ b/easybuild/easyconfigs/g/GDB/GDB-10.2-GCCcore-9.3.0-Python-3.8.2.eb @@ -42,4 +42,9 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = [ + 'gdb --help', + 'gdbserver --help', +] + moduleclass = 'debugger' diff --git a/easybuild/easyconfigs/g/GDB/GDB-11.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/g/GDB/GDB-11.1-GCCcore-11.2.0.eb index fe451504a66..a456f0500a8 100644 --- a/easybuild/easyconfigs/g/GDB/GDB-11.1-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/g/GDB/GDB-11.1-GCCcore-11.2.0.eb @@ -41,4 +41,9 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = [ + 'gdb --help', + 'gdbserver --help', +] + moduleclass = 'debugger' diff --git a/easybuild/easyconfigs/g/GDB/GDB-12.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/GDB/GDB-12.1-GCCcore-11.3.0.eb index 0ff055c409e..3ade2afc70d 100644 --- a/easybuild/easyconfigs/g/GDB/GDB-12.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/g/GDB/GDB-12.1-GCCcore-11.3.0.eb @@ -41,4 +41,9 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = [ + 'gdb --help', + 'gdbserver --help', +] + moduleclass = 'debugger' diff --git a/easybuild/easyconfigs/g/GDB/GDB-13.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/GDB/GDB-13.2-GCCcore-12.3.0.eb index df3bd632ae8..431a3fa995e 100644 --- a/easybuild/easyconfigs/g/GDB/GDB-13.2-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/g/GDB/GDB-13.2-GCCcore-12.3.0.eb @@ -41,4 +41,9 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = [ + 'gdb --help', + 'gdbserver --help', +] + moduleclass = 'debugger' diff --git a/easybuild/easyconfigs/g/GDB/GDB-13.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/g/GDB/GDB-13.2-GCCcore-13.2.0.eb index 574aef91ec3..ac981628400 100644 --- a/easybuild/easyconfigs/g/GDB/GDB-13.2-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/g/GDB/GDB-13.2-GCCcore-13.2.0.eb @@ -41,4 +41,9 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = [ + 'gdb --help', + 'gdbserver --help', +] + moduleclass = 'debugger' From 7c83a553950c233943c7b0189762f8c05cfea852 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 29 Oct 2023 20:44:17 +0100 Subject: [PATCH 092/599] adding easyconfigs: EasyBuild-4.8.2.eb --- .../e/EasyBuild/EasyBuild-4.8.2.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.8.2.eb diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.8.2.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.8.2.eb new file mode 100644 index 00000000000..3ee367b47ec --- /dev/null +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.8.2.eb @@ -0,0 +1,44 @@ +easyblock = 'EB_EasyBuildMeta' + +name = 'EasyBuild' +version = '4.8.2' + +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/e5/40/17e4ddbe7aa160e67219a90c7c4f67baa4b0efc3a6c21ab0e2c858af8f4e/', + # easybuild-easyblocks + 'https://files.pythonhosted.org/packages/85/07/e59231a6f4a90f6bd7c24c9c3b923469024ab0072af95dac9409624796d1/', + # easybuild-easyconfigs + 'https://files.pythonhosted.org/packages/4b/1e/27f7d6785b35978ebb70a518bb1ea699ace8d05395c902a6d518de8590bb/', +] +sources = [ + 'easybuild-framework-%(version)s.tar.gz', + 'easybuild-easyblocks-%(version)s.tar.gz', + 'easybuild-easyconfigs-%(version)s.tar.gz', +] +checksums = [ + {'easybuild-framework-4.8.2.tar.gz': '87852289d099aed18e6778c556d8aed173ab1ff711c20e7d9ad32803336b3610'}, + {'easybuild-easyblocks-4.8.2.tar.gz': '796ba8268e2832c6cb78c681401ce401f4d3a6471e1407a3987e76e6f42b3fd7'}, + {'easybuild-easyconfigs-4.8.2.tar.gz': 'c191b09f68cc3a0be33d248edfb892a143424af119f6ae6fd076c7880343cd63'}, +] + +# 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 4310a29cc0e621470bea5a4169dd5c065b7f0405 Mon Sep 17 00:00:00 2001 From: Wendar Lin Date: Mon, 30 Oct 2023 09:37:16 +0800 Subject: [PATCH 093/599] the mdust --- .../m/mDust/mDust-20231029-GCC-10.3.0.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/m/mDust/mDust-20231029-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/m/mDust/mDust-20231029-GCC-10.3.0.eb b/easybuild/easyconfigs/m/mDust/mDust-20231029-GCC-10.3.0.eb new file mode 100644 index 00000000000..12a25eb3276 --- /dev/null +++ b/easybuild/easyconfigs/m/mDust/mDust-20231029-GCC-10.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'MakeCp' + +name = 'mDust' +version = '20231029' + +homepage = 'https://github.com/lh3/mdust' +description = "mdust from DFCI Gene Indices Software Tools (archived for a historical record only)" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +sources = [{ + 'filename': 'mdust.tar.gz', + 'git_config': { + 'url': 'https://github.com/lh3', + 'repo_name': 'mdust', + 'commit': '3e3fed8', + 'clone_into': 'mdustSrc', + }, +}] +# git clone, might have to adjust this checksum +checksums = ['6fe21806e6bcd3810babed8d83dfb9ff072fcb9d3a31cd43da9cb9670c0ec6f0'] + +configure_without_installdir = True + +files_to_copy = [] + +postinstallcmds = ['mkdir %(installdir)s/bin', + 'cp mdust %(installdir)s/bin'] + +sanity_check_paths = { + 'files': ['bin/mdust'], + 'dirs': [] +} + +sanity_check_commands = ["mdust < /dev/null"] + +moduleclass = 'bio' From d03ec7d4694b6422e113c1a8166113ed62b1da1a Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Mon, 30 Oct 2023 10:36:46 +0100 Subject: [PATCH 094/599] Only set flag --enable-asmjit when installing on x86_64 --- easybuild/easyconfigs/p/PLUMED/PLUMED-2.6.2-foss-2020b.eb | 3 ++- easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.0-foss-2020b.eb | 3 ++- easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.2-foss-2021a.eb | 3 ++- easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.3-foss-2021b.eb | 3 ++- easybuild/easyconfigs/p/PLUMED/PLUMED-2.8.0-foss-2021b.eb | 3 ++- easybuild/easyconfigs/p/PLUMED/PLUMED-2.8.1-foss-2022a.eb | 3 ++- easybuild/easyconfigs/p/PLUMED/PLUMED-2.9.0-foss-2022b.eb | 3 ++- 7 files changed, 14 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.6.2-foss-2020b.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.6.2-foss-2020b.eb index da1d6cc2774..dd7b7837215 100644 --- a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.6.2-foss-2020b.eb +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.6.2-foss-2020b.eb @@ -35,7 +35,8 @@ dependencies = [ preconfigopts = 'env FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' configopts = '--exec-prefix=%(installdir)s --enable-gsl --enable-modules=all --enable-python ' configopts += '--enable-boost_graph --enable-boost_serialization ' -configopts += '--enable-asmjit ' +if ARCH == 'x86_64': + configopts += '--enable-asmjit ' prebuildopts = 'source sourceme.sh && ' # make sure that ld.gold linker is used diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.0-foss-2020b.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.0-foss-2020b.eb index efbec7485f0..10d4af1198f 100644 --- a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.0-foss-2020b.eb +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.0-foss-2020b.eb @@ -33,7 +33,8 @@ dependencies = [ preconfigopts = 'env FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' configopts = '--exec-prefix=%(installdir)s --enable-gsl --enable-modules=all --enable-python ' configopts += '--enable-boost_graph --enable-boost_serialization ' -configopts += '--enable-asmjit ' +if ARCH == 'x86_64': + configopts += '--enable-asmjit ' prebuildopts = 'source sourceme.sh && ' # make sure that ld.gold linker is used diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.2-foss-2021a.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.2-foss-2021a.eb index 886f07ba021..e3a435b4dd6 100644 --- a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.2-foss-2021a.eb +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.2-foss-2021a.eb @@ -33,7 +33,8 @@ dependencies = [ preconfigopts = 'env FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' configopts = '--exec-prefix=%(installdir)s --enable-gsl --enable-modules=all --enable-python ' configopts += '--enable-boost_graph --enable-boost_serialization ' -configopts += '--enable-asmjit ' +if ARCH == 'x86_64': + configopts += '--enable-asmjit ' prebuildopts = 'source sourceme.sh && ' # make sure that ld.gold linker is used diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.3-foss-2021b.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.3-foss-2021b.eb index c7f467034e0..b28de440469 100644 --- a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.3-foss-2021b.eb +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.3-foss-2021b.eb @@ -33,7 +33,8 @@ dependencies = [ preconfigopts = 'env FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' configopts = '--exec-prefix=%(installdir)s --enable-gsl --enable-modules=all --enable-python ' configopts += '--enable-boost_graph --enable-boost_serialization ' -configopts += '--enable-asmjit ' +if ARCH == 'x86_64': + configopts += '--enable-asmjit ' prebuildopts = 'source sourceme.sh && ' # make sure that ld.gold linker is used diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.8.0-foss-2021b.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.8.0-foss-2021b.eb index 675fa899a60..8e04ba57a68 100644 --- a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.8.0-foss-2021b.eb +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.8.0-foss-2021b.eb @@ -33,7 +33,8 @@ dependencies = [ preconfigopts = 'env FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' configopts = '--exec-prefix=%(installdir)s --enable-gsl --enable-modules=all --enable-python ' configopts += '--enable-boost_graph --enable-boost_serialization ' -configopts += '--enable-asmjit ' +if ARCH == 'x86_64': + configopts += '--enable-asmjit ' prebuildopts = 'source sourceme.sh && ' # make sure that ld.gold linker is used diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.8.1-foss-2022a.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.8.1-foss-2022a.eb index 39272200991..67da6c4a802 100644 --- a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.8.1-foss-2022a.eb +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.8.1-foss-2022a.eb @@ -33,7 +33,8 @@ dependencies = [ preconfigopts = 'env FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' configopts = '--exec-prefix=%(installdir)s --enable-gsl --enable-modules=all --enable-python ' configopts += '--enable-boost_graph --enable-boost_serialization ' -configopts += '--enable-asmjit ' +if ARCH == 'x86_64': + configopts += '--enable-asmjit ' prebuildopts = 'source sourceme.sh && ' # make sure that ld.gold linker is used diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.9.0-foss-2022b.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.9.0-foss-2022b.eb index c0b69eef9b1..b959eaf678f 100644 --- a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.9.0-foss-2022b.eb +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.9.0-foss-2022b.eb @@ -33,7 +33,8 @@ dependencies = [ preconfigopts = 'env FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' configopts = '--exec-prefix=%(installdir)s --enable-gsl --enable-modules=all --enable-python ' configopts += '--enable-boost_graph --enable-boost_serialization ' -configopts += '--enable-asmjit ' +if ARCH == 'x86_64': + configopts += '--enable-asmjit ' prebuildopts = 'source sourceme.sh && ' # make sure that ld.gold linker is used From 410e26ab8a3421bf7f584a1723b5c63c4b207041 Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Mon, 30 Oct 2023 16:01:43 +0100 Subject: [PATCH 095/599] remove flag since it is auto-enabled since version 2.8 --- easybuild/easyconfigs/p/PLUMED/PLUMED-2.6.2-foss-2020b.eb | 1 + easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.0-foss-2020b.eb | 1 + easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.2-foss-2021a.eb | 1 + easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.3-foss-2021b.eb | 1 + easybuild/easyconfigs/p/PLUMED/PLUMED-2.8.0-foss-2021b.eb | 2 -- easybuild/easyconfigs/p/PLUMED/PLUMED-2.8.1-foss-2022a.eb | 2 -- easybuild/easyconfigs/p/PLUMED/PLUMED-2.9.0-foss-2022b.eb | 2 -- 7 files changed, 4 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.6.2-foss-2020b.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.6.2-foss-2020b.eb index dd7b7837215..73cd893be22 100644 --- a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.6.2-foss-2020b.eb +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.6.2-foss-2020b.eb @@ -36,6 +36,7 @@ preconfigopts = 'env FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' configopts = '--exec-prefix=%(installdir)s --enable-gsl --enable-modules=all --enable-python ' configopts += '--enable-boost_graph --enable-boost_serialization ' if ARCH == 'x86_64': + # the flag is not supported on aarch64 configopts += '--enable-asmjit ' prebuildopts = 'source sourceme.sh && ' diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.0-foss-2020b.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.0-foss-2020b.eb index 10d4af1198f..dc860859939 100644 --- a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.0-foss-2020b.eb +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.0-foss-2020b.eb @@ -34,6 +34,7 @@ preconfigopts = 'env FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' configopts = '--exec-prefix=%(installdir)s --enable-gsl --enable-modules=all --enable-python ' configopts += '--enable-boost_graph --enable-boost_serialization ' if ARCH == 'x86_64': + # the flag is not supported on aarch64 configopts += '--enable-asmjit ' prebuildopts = 'source sourceme.sh && ' diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.2-foss-2021a.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.2-foss-2021a.eb index e3a435b4dd6..3a0b31731ee 100644 --- a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.2-foss-2021a.eb +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.2-foss-2021a.eb @@ -34,6 +34,7 @@ preconfigopts = 'env FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' configopts = '--exec-prefix=%(installdir)s --enable-gsl --enable-modules=all --enable-python ' configopts += '--enable-boost_graph --enable-boost_serialization ' if ARCH == 'x86_64': + # the flag is not supported on aarch64 configopts += '--enable-asmjit ' prebuildopts = 'source sourceme.sh && ' diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.3-foss-2021b.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.3-foss-2021b.eb index b28de440469..c653aa77c5b 100644 --- a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.3-foss-2021b.eb +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.3-foss-2021b.eb @@ -34,6 +34,7 @@ preconfigopts = 'env FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' configopts = '--exec-prefix=%(installdir)s --enable-gsl --enable-modules=all --enable-python ' configopts += '--enable-boost_graph --enable-boost_serialization ' if ARCH == 'x86_64': + # the flag is not supported on aarch64 configopts += '--enable-asmjit ' prebuildopts = 'source sourceme.sh && ' diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.8.0-foss-2021b.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.8.0-foss-2021b.eb index 8e04ba57a68..8dcdc9293d7 100644 --- a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.8.0-foss-2021b.eb +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.8.0-foss-2021b.eb @@ -33,8 +33,6 @@ dependencies = [ preconfigopts = 'env FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' configopts = '--exec-prefix=%(installdir)s --enable-gsl --enable-modules=all --enable-python ' configopts += '--enable-boost_graph --enable-boost_serialization ' -if ARCH == 'x86_64': - configopts += '--enable-asmjit ' prebuildopts = 'source sourceme.sh && ' # make sure that ld.gold linker is used diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.8.1-foss-2022a.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.8.1-foss-2022a.eb index 67da6c4a802..846670014d4 100644 --- a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.8.1-foss-2022a.eb +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.8.1-foss-2022a.eb @@ -33,8 +33,6 @@ dependencies = [ preconfigopts = 'env FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' configopts = '--exec-prefix=%(installdir)s --enable-gsl --enable-modules=all --enable-python ' configopts += '--enable-boost_graph --enable-boost_serialization ' -if ARCH == 'x86_64': - configopts += '--enable-asmjit ' prebuildopts = 'source sourceme.sh && ' # make sure that ld.gold linker is used diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.9.0-foss-2022b.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.9.0-foss-2022b.eb index b959eaf678f..a2971db49f7 100644 --- a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.9.0-foss-2022b.eb +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.9.0-foss-2022b.eb @@ -33,8 +33,6 @@ dependencies = [ preconfigopts = 'env FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' configopts = '--exec-prefix=%(installdir)s --enable-gsl --enable-modules=all --enable-python ' configopts += '--enable-boost_graph --enable-boost_serialization ' -if ARCH == 'x86_64': - configopts += '--enable-asmjit ' prebuildopts = 'source sourceme.sh && ' # make sure that ld.gold linker is used From 7509385d663250aa7270ed21a7255f9d24ec2bc4 Mon Sep 17 00:00:00 2001 From: Xin An <34663977+xinan1911@users.noreply.github.com> Date: Mon, 30 Oct 2023 16:59:39 +0100 Subject: [PATCH 096/599] Add dependency SciPy-bundle numpy --- easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb b/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb index 5b98d3995e4..1a5e2a7b940 100644 --- a/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb +++ b/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb @@ -26,6 +26,7 @@ dependencies = [ ('pybind11', '2.6.2'), ('Python', '3.9.5'), ('Boost.MPI', '1.76.0'), + ('SciPy-bundle', '2021.05'), ] parallel = 1 From 2d394248ba1737b4927089d545ca597477aa42c4 Mon Sep 17 00:00:00 2001 From: fizwit Date: Mon, 30 Oct 2023 16:00:25 -0700 Subject: [PATCH 097/599] update Arriba-2.4.0 --- .../a/Arriba/Arriba-2.4.0-GCC-12.2.0.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/a/Arriba/Arriba-2.4.0-GCC-12.2.0.eb diff --git a/easybuild/easyconfigs/a/Arriba/Arriba-2.4.0-GCC-12.2.0.eb b/easybuild/easyconfigs/a/Arriba/Arriba-2.4.0-GCC-12.2.0.eb new file mode 100644 index 00000000000..446ed4277cf --- /dev/null +++ b/easybuild/easyconfigs/a/Arriba/Arriba-2.4.0-GCC-12.2.0.eb @@ -0,0 +1,48 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'MakeCp' + +name = 'Arriba' +version = '2.4.0' + +github_account = 'suhrig' +homepage = 'https://github.com/%(github_account)s/%(namelower)s' +description = """Arriba is a command-line tool for the detection of gene fusions from RNA-Seq data. + It was developed for the use in a clinical research setting. Therefore, short runtimes and high + sensitivity were important design criteria.""" + +toolchain = {'name': 'GCC', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/%(github_account)s/%(namelower)s/releases/download/v%(version)s'] +sources = ['%(namelower)s_v%(version)s.tar.gz'] +checksums = ['a5173f44195d7f864aab95972d0cc3da85671c4b7e602e5a4e1a4fc143810e4a'] + +dependencies = [ + ('bzip2', '1.0.8'), + ('HTSlib', '1.17'), + ('libdeflate', '1.15'), + ('STAR', '2.7.10b'), + ('zlib', '1.2.12'), + ('XZ', '5.2.7'), +] + +# make target with dynamically linked libraries is called bioconda, default is a statically linked binary +build_cmd_targets = 'bioconda' +# otherwise it fails to find sam.h +buildopts = 'CPATH=${EBROOTHTSLIB}/include/htslib:CPATH' + +postinstallcmds = ['mkdir %(installdir)s/database'] +files_to_copy = ['%(namelower)s', 'documentation', 'download_references.sh', 'draw_fusions.R', 'LICENSE', + 'README.md', 'run_%(namelower)s.sh'] + +modextrapaths = {'PATH': ''} + +sanity_check_paths = { + 'files': ['%(namelower)s'], + 'dirs': [] +} + +sanity_check_commands = [('%(namelower)s', '-h')] + +moduleclass = 'bio' From 9e6ab6895cdc92901d38e15aa118edaf14e0f361 Mon Sep 17 00:00:00 2001 From: Orient Date: Tue, 31 Oct 2023 00:16:56 +0100 Subject: [PATCH 098/599] Added requested changes --- .../d/dynesty/dynesty-2.1.3-foss-2023a.eb | 7 +++-- .../pytest-xdist-3.3.1-GCCcore-12.3.0.eb | 6 ++-- .../p/pytest/pytest-7.4.2-GCCcore-12.3.0.eb | 29 ++----------------- 3 files changed, 11 insertions(+), 31 deletions(-) diff --git a/easybuild/easyconfigs/d/dynesty/dynesty-2.1.3-foss-2023a.eb b/easybuild/easyconfigs/d/dynesty/dynesty-2.1.3-foss-2023a.eb index d1a5101262a..9835112f86e 100644 --- a/easybuild/easyconfigs/d/dynesty/dynesty-2.1.3-foss-2023a.eb +++ b/easybuild/easyconfigs/d/dynesty/dynesty-2.1.3-foss-2023a.eb @@ -9,14 +9,17 @@ for estimating Bayesian posteriors and evidences.""" toolchain = {'name': 'foss', 'version': '2023a'} +builddependencies = [ + ('pytest', '7.4.2'), + ('pytest-xdist', '3.3.1'), +] + dependencies = [ ('Python', '3.11.3'), ('SciPy-bundle', '2023.07'), ('dill', '0.3.7'), ('h5py', '3.9.0'), ('tqdm', '4.66.1'), - ('pytest', '7.4.2'), - ('pytest-xdist', '3.3.1'), ] use_pip = True diff --git a/easybuild/easyconfigs/p/pytest-xdist/pytest-xdist-3.3.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/pytest-xdist/pytest-xdist-3.3.1-GCCcore-12.3.0.eb index 47bba67554b..7330aa9e074 100644 --- a/easybuild/easyconfigs/p/pytest-xdist/pytest-xdist-3.3.1-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/pytest-xdist/pytest-xdist-3.3.1-GCCcore-12.3.0.eb @@ -29,12 +29,14 @@ Python versions and interpreters.""" toolchain = {'name': 'GCCcore', 'version': '12.3.0'} -builddependencies = [('binutils', '2.40')] +builddependencies = [ + ('binutils', '2.40'), + ('hatchling', '1.18.0'), +] dependencies = [ ('Python', '3.11.3'), ('pytest', '7.4.2'), - ('hatchling', '1.18.0'), ] use_pip = True 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 3d67f361036..9d0b6f0c25d 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 @@ -12,12 +12,12 @@ toolchain = {'name': 'GCCcore', 'version': '12.3.0'} builddependencies = [ ('binutils', '2.40'), + ('hatchling', '1.18.0'), ] dependencies = [ ('Python', '3.11.3'), - ('typing-extensions', '4.8.0'), - ('hatchling', '1.18.0'), + ('Python-bundle-PyPI', '2023.06'), ] use_pip = True @@ -39,12 +39,6 @@ _skip_tests = [ _ignore_tests = ' --ignore='.join(_skip_tests) exts_list = [ - ('tomli', '2.0.1', { - 'checksums': ['de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f'], - }), - ('packaging', '23.2', { - 'checksums': ['048fb0e9405036518eaaf48a55953c750c11e1a1b68e0dd1a9d62ed0c092cfc5'], - }), ('setuptools-scm', '8.0.4', { 'checksums': ['b5f43ff6800669595193fd09891564ee9d1d7dcb196cab4b2506d53a2e1c95c7'], }), @@ -52,19 +46,6 @@ exts_list = [ 'source_tmpl': 'flit_core-%(version)s.tar.gz', 'checksums': ['72ad266176c4a3fcfab5f2930d76896059851240570ce9a98733b658cb786eba'], }), - ('flit-scm', '1.7.0', { - 'source_tmpl': 'flit_scm-%(version)s.tar.gz', - 'checksums': ['961bd6fb24f31bba75333c234145fff88e6de0a90fc0f7e5e7c79deca69f6bb2'], - }), - ('exceptiongroup', '1.1.3', { - 'checksums': ['097acd85d473d75af5bb98e41b61ff7fe35efe6675e4f9370ec6ec5126d160e9'], - }), - ('attrs', '23.1.0', { - 'checksums': ['6279836d581513a26f1bf235f9acd333bc9115683f14f7e8fae46c98fc50e015'], - }), - ('sortedcontainers', '2.4.0', { - 'checksums': ['25caa5a06cc30b6b83d11423433f65d1f9d76c4c6a0c90e3379eaa43b9bfdb88'], - }), ('hypothesis', '6.88.1', { 'checksums': ['f4c2c004b9ec3e0e25332ad2cb6b91eba477a855557a7b5c6e79068809ff8b51'], }), @@ -74,12 +55,6 @@ exts_list = [ ('xmlschema', '2.5.0', { 'checksums': ['276a03e0fd3c94c148d528bff4d9482f9b99bf8c7b4056a2e8e703d28149d454'], }), - ('iniconfig', '2.0.0', { - 'checksums': ['2d91e135bf72d31a410b17c16da610a82cb55f6b0477d1a902134b24a455b8b3'], - }), - ('pluggy', '1.3.0', { - 'checksums': ['cf61ae8f126ac6f7c451172cf30e3e43d3ca77615509771b3a984a0730651e12'], - }), (name, version, { 'checksums': ['a766259cfab564a2ad52cb1aae1b881a75c3eb7e34ca3779697c23ed47c47069'], }), From e1ebcfef7ae9a933e21a12d2c7edec1d6ee27348 Mon Sep 17 00:00:00 2001 From: Orient Date: Tue, 31 Oct 2023 00:43:03 +0100 Subject: [PATCH 099/599] Removed trailing whitespace --- .../p/pytest-xdist/pytest-xdist-3.3.1-GCCcore-12.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/pytest-xdist/pytest-xdist-3.3.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/pytest-xdist/pytest-xdist-3.3.1-GCCcore-12.3.0.eb index 7330aa9e074..e9fc2a36b36 100644 --- a/easybuild/easyconfigs/p/pytest-xdist/pytest-xdist-3.3.1-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/pytest-xdist/pytest-xdist-3.3.1-GCCcore-12.3.0.eb @@ -31,7 +31,7 @@ toolchain = {'name': 'GCCcore', 'version': '12.3.0'} builddependencies = [ ('binutils', '2.40'), - ('hatchling', '1.18.0'), + ('hatchling', '1.18.0'), ] dependencies = [ From eb30ad9e8ed9f38887e53f62393a91482c2eba3a Mon Sep 17 00:00:00 2001 From: Sarah Walters Date: Tue, 31 Oct 2023 14:28:28 +1000 Subject: [PATCH 100/599] Add Miniconda3-23.9.0-0 --- .../m/Miniconda3/Miniconda3-23.9.0-0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/m/Miniconda3/Miniconda3-23.9.0-0.eb diff --git a/easybuild/easyconfigs/m/Miniconda3/Miniconda3-23.9.0-0.eb b/easybuild/easyconfigs/m/Miniconda3/Miniconda3-23.9.0-0.eb new file mode 100644 index 00000000000..890e89a8b08 --- /dev/null +++ b/easybuild/easyconfigs/m/Miniconda3/Miniconda3-23.9.0-0.eb @@ -0,0 +1,27 @@ +easyblock = 'EB_Anaconda' + +name = 'Miniconda3' +version = '23.9.0-0' + +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': + '43651393236cb8bb4219dcd429b3803a60f318e5507d8d84ca00dafa0c69f1bb', + '%(name)s-py311_%(version)s-Linux-ppc64le.sh': + '07b53e411c2e4423bd34c3526d6644b916c4b2143daa8fbcb36b8ead412239b9', + '%(name)s-py311_%(version)s-Linux-aarch64.sh': + '1242847b34b23353d429fcbcfb6586f0c373e63070ad7d6371c23ddbb577778a', + } +] + +moduleclass = 'lang' From 9bfd37f1ae4dc953b402e8bba7a9fe78ba5766e4 Mon Sep 17 00:00:00 2001 From: Sarah Walters Date: Tue, 31 Oct 2023 16:12:38 +1000 Subject: [PATCH 101/599] Correction to wrap lines From f9ee66654cca2089996cf184dbb5f90de7e121ef Mon Sep 17 00:00:00 2001 From: Tim Kok Date: Tue, 31 Oct 2023 11:31:27 +0100 Subject: [PATCH 102/599] Ensure right Python version is used in DP3, WSClean and dependencies --- .../easyconfigs/a/AOFlagger/AOFlagger-3.4.0-foss-2022a.eb | 3 +++ easybuild/easyconfigs/c/casacore/casacore-3.5.0-foss-2022a.eb | 4 +++- easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2022a.eb | 3 +++ .../easyconfigs/e/EveryBeam/EveryBeam-0.5.2-foss-2022a.eb | 3 +++ easybuild/easyconfigs/w/WSClean/WSClean-3.4-foss-2022a.eb | 3 +++ 5 files changed, 15 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/AOFlagger/AOFlagger-3.4.0-foss-2022a.eb b/easybuild/easyconfigs/a/AOFlagger/AOFlagger-3.4.0-foss-2022a.eb index eeb528a357b..fc5d1d7e3bd 100644 --- a/easybuild/easyconfigs/a/AOFlagger/AOFlagger-3.4.0-foss-2022a.eb +++ b/easybuild/easyconfigs/a/AOFlagger/AOFlagger-3.4.0-foss-2022a.eb @@ -32,6 +32,9 @@ dependencies = [ ('libxml2', '2.9.13'), ] +# make sure the right Python is used +configopts = '-DPython3_EXECUTABLE=$EBROOTPYTHON/bin/python ' + sanity_check_paths = { 'files': ['include/aoflagger.h', 'bin/aoflagger'], 'dirs': ['bin'], diff --git a/easybuild/easyconfigs/c/casacore/casacore-3.5.0-foss-2022a.eb b/easybuild/easyconfigs/c/casacore/casacore-3.5.0-foss-2022a.eb index 9c359a65e60..7209a109104 100644 --- a/easybuild/easyconfigs/c/casacore/casacore-3.5.0-foss-2022a.eb +++ b/easybuild/easyconfigs/c/casacore/casacore-3.5.0-foss-2022a.eb @@ -42,7 +42,9 @@ dependencies = [ ] configopts = '-DBUILD_PYTHON=NO -DBUILD_PYTHON3=YES -Wno-dev -DCXX11="ON" -DDATA_DIR=%(installdir)s/data ' -configopts += '-DUSE_OPENMP=ON -DUSE_HDF5=ON -DUSE_MPI=ON' +configopts += '-DUSE_OPENMP=ON -DUSE_HDF5=ON -DUSE_MPI=ON ' +# make sure the right Python is used +configopts += '-DPython3_EXECUTABLE=$EBROOTPYTHON/bin/python ' sanity_check_paths = { 'files': ['lib/libcasa_casa.%s' % SHLIB_EXT, 'lib/libcasa_mirlib.%s' % SHLIB_EXT, diff --git a/easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2022a.eb b/easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2022a.eb index 41dbbeb6af1..6ee878c3713 100644 --- a/easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2022a.eb +++ b/easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2022a.eb @@ -36,6 +36,9 @@ dependencies = [ ('AOFlagger', '3.4.0') ] +# make sure the right Python is used +configopts = '-DPython3_EXECUTABLE=$EBROOTPYTHON/bin/python ' + sanity_check_paths = { 'files': ['include/include/dp3/base/DP3.h', 'bin/DP3'], 'dirs': ['bin'], diff --git a/easybuild/easyconfigs/e/EveryBeam/EveryBeam-0.5.2-foss-2022a.eb b/easybuild/easyconfigs/e/EveryBeam/EveryBeam-0.5.2-foss-2022a.eb index 43f393b0dc7..48e5bd469f0 100644 --- a/easybuild/easyconfigs/e/EveryBeam/EveryBeam-0.5.2-foss-2022a.eb +++ b/easybuild/easyconfigs/e/EveryBeam/EveryBeam-0.5.2-foss-2022a.eb @@ -36,6 +36,9 @@ dependencies = [ ('libxml2', '2.9.13'), ] +# make sure the right Python is used +configopts = '-DPython3_EXECUTABLE=$EBROOTPYTHON/bin/python ' + sanity_check_paths = { 'files': ['include/EveryBeam/beamformer.h', 'lib/libeverybeam.so'], 'dirs': [], diff --git a/easybuild/easyconfigs/w/WSClean/WSClean-3.4-foss-2022a.eb b/easybuild/easyconfigs/w/WSClean/WSClean-3.4-foss-2022a.eb index de04e74ec1c..7822414a2b9 100644 --- a/easybuild/easyconfigs/w/WSClean/WSClean-3.4-foss-2022a.eb +++ b/easybuild/easyconfigs/w/WSClean/WSClean-3.4-foss-2022a.eb @@ -31,6 +31,9 @@ dependencies = [ ('Python', '3.10.4'), ] +# make sure the right Python is used +configopts = '-DPython3_EXECUTABLE=$EBROOTPYTHON/bin/python ' + sanity_check_paths = { 'files': ['include/wscleaninterface.h', 'bin/wsclean'], 'dirs': ['bin'], From c9c2627ae2f0fe4fcdc5181fe72cf69c3cd78904 Mon Sep 17 00:00:00 2001 From: "hung.tao" Date: Tue, 31 Oct 2023 14:00:13 +0100 Subject: [PATCH 103/599] adding easyconfigs: ctffind-4.1.14-foss-2022b.eb --- .../c/ctffind/ctffind-4.1.14-foss-2022b.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-foss-2022b.eb diff --git a/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-foss-2022b.eb b/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-foss-2022b.eb new file mode 100644 index 00000000000..ff2bc24f2a4 --- /dev/null +++ b/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-foss-2022b.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'ctffind' +version = '4.1.14' + +homepage = 'https://grigoriefflab.umassmed.edu/ctffind4' +description = """Program for finding CTFs of electron micrographs.""" + +toolchain = {'name': 'foss', 'version': '2022b'} +toolchainopts = {'openmp': True} + +source_urls = ['https://grigoriefflab.umassmed.edu/sites/default/files/'] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + '%(name)s-%(version)s_asm-fix.patch', + '%(name)s-%(version)s_void-functions.patch' +] +checksums = [ + 'db17b2ebeb3c3b2b3764e42b820cd50d19ccccf6956c64257bfe5d5ba6b40cb5', # ctffind-4.1.14.tar.gz + 'e6d468b3f1569e2d42e077573529dbc3035a03715c436d2349ccaaab63b64f28', # ctffind-4.1.14_asm-fix.patch + '0a578328062881d86b10585f1b0efa81b7a1826baf3e7bcc5c749bba73e96d10', # ctffind-4.1.14_void-functions.patch +] + +dependencies = [ + ('zlib', '1.2.12'), + ('libjpeg-turbo', '2.1.4'), + ('LibTIFF', '4.4.0'), + ('GSL', '2.7',), + ('wxWidgets', '3.2.2.1'), +] + +configopts = '--enable-openmp ' + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/ctffind'], + 'dirs': [], +} + +moduleclass = 'bio' From d7da9537361056ca65857887dd91ab6446c0875d Mon Sep 17 00:00:00 2001 From: Tim Kok Date: Tue, 31 Oct 2023 16:32:48 +0100 Subject: [PATCH 104/599] Improve comment by being more explicit --- .../easyconfigs/a/AOFlagger/AOFlagger-3.4.0-foss-2022a.eb | 4 +++- easybuild/easyconfigs/c/casacore/casacore-3.5.0-foss-2022a.eb | 4 +++- easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2022a.eb | 4 +++- .../easyconfigs/e/EveryBeam/EveryBeam-0.5.2-foss-2022a.eb | 4 +++- easybuild/easyconfigs/w/WSClean/WSClean-3.4-foss-2022a.eb | 4 +++- 5 files changed, 15 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/a/AOFlagger/AOFlagger-3.4.0-foss-2022a.eb b/easybuild/easyconfigs/a/AOFlagger/AOFlagger-3.4.0-foss-2022a.eb index fc5d1d7e3bd..ada37c804a9 100644 --- a/easybuild/easyconfigs/a/AOFlagger/AOFlagger-3.4.0-foss-2022a.eb +++ b/easybuild/easyconfigs/a/AOFlagger/AOFlagger-3.4.0-foss-2022a.eb @@ -32,7 +32,9 @@ dependencies = [ ('libxml2', '2.9.13'), ] -# make sure the right Python is used +# Without this, the wrong (system) python is picked up by cmake +# in cases where the system python is newer than the one used in these EasyConfigs +# See PR # 19119 configopts = '-DPython3_EXECUTABLE=$EBROOTPYTHON/bin/python ' sanity_check_paths = { diff --git a/easybuild/easyconfigs/c/casacore/casacore-3.5.0-foss-2022a.eb b/easybuild/easyconfigs/c/casacore/casacore-3.5.0-foss-2022a.eb index 7209a109104..d98f5af249e 100644 --- a/easybuild/easyconfigs/c/casacore/casacore-3.5.0-foss-2022a.eb +++ b/easybuild/easyconfigs/c/casacore/casacore-3.5.0-foss-2022a.eb @@ -43,7 +43,9 @@ dependencies = [ configopts = '-DBUILD_PYTHON=NO -DBUILD_PYTHON3=YES -Wno-dev -DCXX11="ON" -DDATA_DIR=%(installdir)s/data ' configopts += '-DUSE_OPENMP=ON -DUSE_HDF5=ON -DUSE_MPI=ON ' -# make sure the right Python is used +# Without this, the wrong (system) python is picked up by cmake +# in cases where the system python is newer than the one used in these EasyConfigs +# See PR # 19119 configopts += '-DPython3_EXECUTABLE=$EBROOTPYTHON/bin/python ' sanity_check_paths = { diff --git a/easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2022a.eb b/easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2022a.eb index 6ee878c3713..c18f4974acf 100644 --- a/easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2022a.eb +++ b/easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2022a.eb @@ -36,7 +36,9 @@ dependencies = [ ('AOFlagger', '3.4.0') ] -# make sure the right Python is used +# Without this, the wrong (system) python is picked up by cmake +# in cases where the system python is newer than the one used in these EasyConfigs +# See PR # 19119 configopts = '-DPython3_EXECUTABLE=$EBROOTPYTHON/bin/python ' sanity_check_paths = { diff --git a/easybuild/easyconfigs/e/EveryBeam/EveryBeam-0.5.2-foss-2022a.eb b/easybuild/easyconfigs/e/EveryBeam/EveryBeam-0.5.2-foss-2022a.eb index 48e5bd469f0..b61f0c86167 100644 --- a/easybuild/easyconfigs/e/EveryBeam/EveryBeam-0.5.2-foss-2022a.eb +++ b/easybuild/easyconfigs/e/EveryBeam/EveryBeam-0.5.2-foss-2022a.eb @@ -36,7 +36,9 @@ dependencies = [ ('libxml2', '2.9.13'), ] -# make sure the right Python is used +# Without this, the wrong (system) python is picked up by cmake +# in cases where the system python is newer than the one used in these EasyConfigs +# See PR # 19119 configopts = '-DPython3_EXECUTABLE=$EBROOTPYTHON/bin/python ' sanity_check_paths = { diff --git a/easybuild/easyconfigs/w/WSClean/WSClean-3.4-foss-2022a.eb b/easybuild/easyconfigs/w/WSClean/WSClean-3.4-foss-2022a.eb index 7822414a2b9..e3bdcb00894 100644 --- a/easybuild/easyconfigs/w/WSClean/WSClean-3.4-foss-2022a.eb +++ b/easybuild/easyconfigs/w/WSClean/WSClean-3.4-foss-2022a.eb @@ -31,7 +31,9 @@ dependencies = [ ('Python', '3.10.4'), ] -# make sure the right Python is used +# Without this, the wrong (system) python is picked up by cmake +# in cases where the system python is newer than the one used in these EasyConfigs +# See PR # 19119 configopts = '-DPython3_EXECUTABLE=$EBROOTPYTHON/bin/python ' sanity_check_paths = { From 158f1e6be41575a17af18bb0d32e932c47ca5517 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 1 Nov 2023 00:22:47 +0100 Subject: [PATCH 105/599] adding easyconfigs: LittleCMS-2.15-GCCcore-13.2.0.eb, libjxl-0.8.2-GCCcore-13.2.0.eb, gperftools-2.13-GCCcore-13.2.0.eb --- .../gperftools-2.13-GCCcore-13.2.0.eb | 38 ++++++++++++++ .../LittleCMS-2.15-GCCcore-13.2.0.eb | 26 ++++++++++ .../l/libjxl/libjxl-0.8.2-GCCcore-13.2.0.eb | 52 +++++++++++++++++++ 3 files changed, 116 insertions(+) create mode 100644 easybuild/easyconfigs/g/gperftools/gperftools-2.13-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.15-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/l/libjxl/libjxl-0.8.2-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/g/gperftools/gperftools-2.13-GCCcore-13.2.0.eb b/easybuild/easyconfigs/g/gperftools/gperftools-2.13-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..73a117d1b30 --- /dev/null +++ b/easybuild/easyconfigs/g/gperftools/gperftools-2.13-GCCcore-13.2.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'gperftools' +version = '2.13' + +homepage = 'https://github.com/gperftools/gperftools' +description = """ +gperftools is a collection of a high-performance multi-threaded malloc() +implementation, plus some pretty nifty performance analysis tools. +Includes TCMalloc, heap-checker, heap-profiler and cpu-profiler. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +github_account = 'gperftools' +source_urls = [GITHUB_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['fd43adbe0419cb0eaaa3e439845cc89fe7d42c22eff7fd2d6b7e87ae2acbce1d'] + +builddependencies = [ + ('Autotools', '20220317'), + ('binutils', '2.40'), +] + +dependencies = [ + ('libunwind', '1.6.2'), +] + +preconfigopts = "autoreconf -f -i && " +configopts = '--enable-libunwind' + +sanity_check_paths = { + 'files': ['bin/pprof', 'lib/libprofiler.a', 'lib/libprofiler.%s' % SHLIB_EXT, + 'lib/libtcmalloc.a', 'lib/libtcmalloc.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.15-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.15-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..31e22ec7db5 --- /dev/null +++ b/easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.15-GCCcore-13.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'LittleCMS' +version = '2.15' + +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': '13.2.0'} + +source_urls = ['https://sourceforge.net/projects/lcms/files/lcms/%s/' % '.'.join(version.split('.')[:2])] +sources = ['lcms2-%(version)s.tar.gz'] +checksums = ['b20cbcbd0f503433be2a4e81462106fa61050a35074dc24a4e356792d971ab39'] + +builddependencies = [('binutils', '2.40')] + +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/libjxl/libjxl-0.8.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/libjxl/libjxl-0.8.2-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..d5b0cc38223 --- /dev/null +++ b/easybuild/easyconfigs/l/libjxl/libjxl-0.8.2-GCCcore-13.2.0.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': 'GCCcore', 'version': '13.2.0'} + +github_account = 'libjxl' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['c70916fb3ed43784eb840f82f05d390053a558e2da106e40863919238fa7b420'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.27.6'), + ('googletest', '1.14.0'), + ('pkgconf', '2.0.3'), + ('Highway', '1.0.7'), # Highway only has a static library +] + +dependencies = [ + ('LittleCMS', '2.15'), + ('Brotli', '1.1.0'), + ('libjpeg-turbo', '3.0.1'), + ('libpng', '1.6.40'), + ('zlib', '1.2.13'), + ('giflib', '5.2.1'), + ('libwebp', '1.3.2'), + ('OpenEXR', '3.2.0'), + ('gperftools', '2.13'), +] + +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' From b11ffac9f4328404c64e9fdc446c41fe16885388 Mon Sep 17 00:00:00 2001 From: wdlingit <90846876+wdlingit@users.noreply.github.com> Date: Wed, 1 Nov 2023 17:49:10 +0800 Subject: [PATCH 106/599] Update and rename mDust-20231029-GCC-10.3.0.eb to mDust-20150102-GCC-10.3.0.eb modified as the suggested easyconfig practices --- ...-GCC-10.3.0.eb => mDust-20150102-GCC-10.3.0.eb} | 14 ++++---------- 1 file changed, 4 insertions(+), 10 deletions(-) rename easybuild/easyconfigs/m/mDust/{mDust-20231029-GCC-10.3.0.eb => mDust-20150102-GCC-10.3.0.eb} (65%) diff --git a/easybuild/easyconfigs/m/mDust/mDust-20231029-GCC-10.3.0.eb b/easybuild/easyconfigs/m/mDust/mDust-20150102-GCC-10.3.0.eb similarity index 65% rename from easybuild/easyconfigs/m/mDust/mDust-20231029-GCC-10.3.0.eb rename to easybuild/easyconfigs/m/mDust/mDust-20150102-GCC-10.3.0.eb index 12a25eb3276..81302e8e48d 100644 --- a/easybuild/easyconfigs/m/mDust/mDust-20231029-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/m/mDust/mDust-20150102-GCC-10.3.0.eb @@ -1,7 +1,7 @@ easyblock = 'MakeCp' -name = 'mDust' -version = '20231029' +name = 'mdust' +version = '20150102' homepage = 'https://github.com/lh3/mdust' description = "mdust from DFCI Gene Indices Software Tools (archived for a historical record only)" @@ -14,18 +14,12 @@ sources = [{ 'url': 'https://github.com/lh3', 'repo_name': 'mdust', 'commit': '3e3fed8', - 'clone_into': 'mdustSrc', }, }] # git clone, might have to adjust this checksum -checksums = ['6fe21806e6bcd3810babed8d83dfb9ff072fcb9d3a31cd43da9cb9670c0ec6f0'] +checksums = [None] -configure_without_installdir = True - -files_to_copy = [] - -postinstallcmds = ['mkdir %(installdir)s/bin', - 'cp mdust %(installdir)s/bin'] +files_to_copy = [(['mdust'], 'bin')] sanity_check_paths = { 'files': ['bin/mdust'], From 1422c1c7721889f5f67a6674fa047829898d7dbf Mon Sep 17 00:00:00 2001 From: wdlingit <90846876+wdlingit@users.noreply.github.com> Date: Wed, 1 Nov 2023 17:52:36 +0800 Subject: [PATCH 107/599] Rename mDust-20150102-GCC-10.3.0.eb to mdust-20150102-GCC-10.3.0.eb --- ...{mDust-20150102-GCC-10.3.0.eb => mdust-20150102-GCC-10.3.0.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/m/mDust/{mDust-20150102-GCC-10.3.0.eb => mdust-20150102-GCC-10.3.0.eb} (100%) diff --git a/easybuild/easyconfigs/m/mDust/mDust-20150102-GCC-10.3.0.eb b/easybuild/easyconfigs/m/mDust/mdust-20150102-GCC-10.3.0.eb similarity index 100% rename from easybuild/easyconfigs/m/mDust/mDust-20150102-GCC-10.3.0.eb rename to easybuild/easyconfigs/m/mDust/mdust-20150102-GCC-10.3.0.eb From d1477cfda67390a9d27e21ac2a8e652f8dfd684e Mon Sep 17 00:00:00 2001 From: Wendar Lin Date: Wed, 1 Nov 2023 18:06:40 +0800 Subject: [PATCH 108/599] rename the folder --- .../easyconfigs/m/{mDust => mdust}/mdust-20150102-GCC-10.3.0.eb | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/m/{mDust => mdust}/mdust-20150102-GCC-10.3.0.eb (100%) diff --git a/easybuild/easyconfigs/m/mDust/mdust-20150102-GCC-10.3.0.eb b/easybuild/easyconfigs/m/mdust/mdust-20150102-GCC-10.3.0.eb similarity index 100% rename from easybuild/easyconfigs/m/mDust/mdust-20150102-GCC-10.3.0.eb rename to easybuild/easyconfigs/m/mdust/mdust-20150102-GCC-10.3.0.eb From 0de1c03c962b3e02fc8e22f43da4772d88cfe833 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 1 Nov 2023 11:48:32 +0100 Subject: [PATCH 109/599] adding easyconfigs: DFT-D3-3.2.0-intel-compilers-2022.2.1.eb --- .../DFT-D3-3.2.0-intel-compilers-2022.2.1.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.2.0-intel-compilers-2022.2.1.eb diff --git a/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.2.0-intel-compilers-2022.2.1.eb b/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.2.0-intel-compilers-2022.2.1.eb new file mode 100644 index 00000000000..60c33ea0a87 --- /dev/null +++ b/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.2.0-intel-compilers-2022.2.1.eb @@ -0,0 +1,34 @@ +easyblock = 'MakeCp' + +name = 'DFT-D3' +version = '3.2.0' + +homepage = 'https://www.chemie.uni-bonn.de/grimme/de/software/dft-d3' +description = """DFT-D3 implements a dispersion correction for density functionals, Hartree-Fock and semi-empirical + quantum chemical methods.""" + +toolchain = {'name': 'intel-compilers', 'version': '2022.2.1'} + +source_urls = ['https://www.chemie.uni-bonn.de/grimme/de/software/dft-d3'] +# Note that the DFT-D3 tarball is named as "dftd3.tgz" with no version +# numbering. Also, the authors are prone (alas) to stealth upgrades, so that two +# tarballs with the same version number can have different checksums. For this +# reason, it is suggested to manually download and rename the tarball. The +# checksum may also need updating from time to time. +# Checksum last updated: 20 September 2018 +# Date tarball was reported to have been modified: 14 June 2016 +sources = [{'download_filename': 'dftd3.tgz', 'filename': SOURCELOWER_TGZ}] +checksums = ['d97cf9758f61aa81fd85425448fbf4a6e8ce07c12e9236739831a3af32880f59'] + +prebuildopts = "sed -i 's/OSTYPE=LINUXL/OSTYPE=LINUXI/' Makefile && " + +files_to_copy = [(['dftd3'], 'bin'), (['man.pdf'], 'doc')] + +sanity_check_paths = { + 'files': ['bin/dftd3'], + 'dirs': [], +} + +sanity_check_commands = ['dftd3'] + +moduleclass = 'chem' From f9bd47a6ed098072eb574a8edc0dbd1a711e46e4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Wed, 1 Nov 2023 13:58:50 +0100 Subject: [PATCH 110/599] remove comment --- easybuild/easyconfigs/m/mdust/mdust-20150102-GCC-10.3.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/m/mdust/mdust-20150102-GCC-10.3.0.eb b/easybuild/easyconfigs/m/mdust/mdust-20150102-GCC-10.3.0.eb index 81302e8e48d..5dea5b1bc57 100644 --- a/easybuild/easyconfigs/m/mdust/mdust-20150102-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/m/mdust/mdust-20150102-GCC-10.3.0.eb @@ -16,7 +16,6 @@ sources = [{ 'commit': '3e3fed8', }, }] -# git clone, might have to adjust this checksum checksums = [None] files_to_copy = [(['mdust'], 'bin')] From 2a73fc0874910a5ca25b1b8bb4cf8cc9bac36a4c Mon Sep 17 00:00:00 2001 From: Orient Date: Wed, 1 Nov 2023 16:03:22 +0100 Subject: [PATCH 111/599] adding easyconfigs: Oases-20180312-GCC-12.3.0.eb --- .../o/Oases/Oases-20180312-GCC-12.3.0.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/o/Oases/Oases-20180312-GCC-12.3.0.eb diff --git a/easybuild/easyconfigs/o/Oases/Oases-20180312-GCC-12.3.0.eb b/easybuild/easyconfigs/o/Oases/Oases-20180312-GCC-12.3.0.eb new file mode 100644 index 00000000000..357a853cb97 --- /dev/null +++ b/easybuild/easyconfigs/o/Oases/Oases-20180312-GCC-12.3.0.eb @@ -0,0 +1,39 @@ +easyblock = "MakeCp" + +name = 'Oases' +version = '20180312' +local_commit = '1b4c14c' + +homepage = 'http://www.ebi.ac.uk/~zerbino/oases/' +description = """Oases is a de novo transcriptome assembler designed to produce transcripts from + short read sequencing technologies, such as Illumina, SOLiD, or 454 in the absence of any genomic assembly.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +# This is taken from the Oases repo to avoid setting git_config in sources +velvet_commit = '9adf09f7ded7fedaf6b0e5e4edf9f46602e263d3' + +sources = [ + '%s.tar.gz' % local_commit, + '%s.tar.gz' % velvet_commit, +] + +source_urls = [ + 'https://github.com/dzerbino/%(namelower)s/archive/', + 'https://github.com/dzerbino/velvet/archive/', +] + +# listed make targets exclude 'doc' on purpose +buildopts = ['VELVET_DIR=../velvet-%s cleanobj velvet oases' % velvet_commit] +parallel = 1 + +files_to_copy = [(["oases"], 'bin'), "data", "scripts", "src", "doc", "LICENSE.txt", "README.md"] + +sanity_check_paths = { + 'files': ["bin/oases", "LICENSE.txt", "README.md"], + 'dirs': ["data", "scripts", "src", "doc"] +} + +sanity_check_commands = ['oases --version'] + +moduleclass = 'bio' From 39a5ec1d6e8e79f0758d23def1b9b89a90170f3b Mon Sep 17 00:00:00 2001 From: Orient Date: Wed, 1 Nov 2023 16:41:42 +0100 Subject: [PATCH 112/599] Renamed downloaded files + added checksums + added local_ to local vars --- .../o/Oases/Oases-20180312-GCC-12.3.0.eb | 17 ++++++++++------- 1 file changed, 10 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/o/Oases/Oases-20180312-GCC-12.3.0.eb b/easybuild/easyconfigs/o/Oases/Oases-20180312-GCC-12.3.0.eb index 357a853cb97..03ee0713e0f 100644 --- a/easybuild/easyconfigs/o/Oases/Oases-20180312-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/o/Oases/Oases-20180312-GCC-12.3.0.eb @@ -11,20 +11,23 @@ description = """Oases is a de novo transcriptome assembler designed to produce toolchain = {'name': 'GCC', 'version': '12.3.0'} # This is taken from the Oases repo to avoid setting git_config in sources -velvet_commit = '9adf09f7ded7fedaf6b0e5e4edf9f46602e263d3' - -sources = [ - '%s.tar.gz' % local_commit, - '%s.tar.gz' % velvet_commit, -] +local_velvet_commit = '9adf09f7ded7fedaf6b0e5e4edf9f46602e263d3' source_urls = [ 'https://github.com/dzerbino/%(namelower)s/archive/', 'https://github.com/dzerbino/velvet/archive/', ] +sources = [ + {'download_filename': '%s.tar.gz' % local_commit, 'filename': '%(namelower)s-%(version)s.tar.gz'}, + {'download_filename': '%s.tar.gz' % local_velvet_commit, 'filename': 'velvet-20140815.tar.gz'} +] +checksums = [ + {'oases-20180312.tar.gz': 'f526b84e9fa3e5f89b728f4a71b8bd23b336b8a6cd83a2d88414710592ec5e4e'}, + {'velvet-20140815.tar.gz': '8e952e3a4bf2ffae586a64e5e97029c9fdd53b5e1991106ef832d73e499b163b'}, +] # listed make targets exclude 'doc' on purpose -buildopts = ['VELVET_DIR=../velvet-%s cleanobj velvet oases' % velvet_commit] +buildopts = ['VELVET_DIR=../velvet-%s cleanobj velvet oases' % local_velvet_commit] parallel = 1 files_to_copy = [(["oases"], 'bin'), "data", "scripts", "src", "doc", "LICENSE.txt", "README.md"] From 75eb561c3c2803b925942b81f11e444628f79bcc Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 1 Nov 2023 17:02:29 +0100 Subject: [PATCH 113/599] Workaround GCC12 destructor bug --- .../p/PyTorch/PyTorch-2.0.1-foss-2022b.eb | 3 + ...round-gcc12-destructor-exception-bug.patch | 118 ++++++++++++++++++ 2 files changed, 121 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_workaround-gcc12-destructor-exception-bug.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1-foss-2022b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1-foss-2022b.eb index 6f869d07be5..318e4aacd4f 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1-foss-2022b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1-foss-2022b.eb @@ -39,6 +39,7 @@ patches = [ 'PyTorch-2.0.1_skip-failing-gradtest.patch', 'PyTorch-2.0.1_skip-test_shuffle_reproducibility.patch', 'PyTorch-2.0.1_skip-tests-skipped-in-subprocess.patch', + 'PyTorch-2.0.1_workaround-gcc12-destructor-exception-bug.patch', ] checksums = [ {'pytorch-v2.0.1.tar.gz': '9c564ca440265c69400ef5fdd48bf15e28af5aa4bed84c95efaad960a6699998'}, @@ -88,6 +89,8 @@ checksums = [ '7047862abc1abaff62954da59700f36d4f39fcf83167a638183b1b7f8fec78ae'}, {'PyTorch-2.0.1_skip-tests-skipped-in-subprocess.patch': '166c134573a95230e39b9ea09ece3ad8072f39d370c9a88fb2a1e24f6aaac2b5'}, + {'PyTorch-2.0.1_workaround-gcc12-destructor-exception-bug.patch': + '198f2244b7415958f96a2c248bab33491a95454091889824d98b0d4a55f114f3'}, ] osdependencies = [OS_PKG_IBVERBS_DEV] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_workaround-gcc12-destructor-exception-bug.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_workaround-gcc12-destructor-exception-bug.patch new file mode 100644 index 00000000000..cff643d4138 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_workaround-gcc12-destructor-exception-bug.patch @@ -0,0 +1,118 @@ +GCC 12 introduced a regression that may cause it to call the destructor twice on an object. +See https://gcc.gnu.org/bugzilla/show_bug.cgi?id=112301 +This is visible in e.g. `test_cpp_extensions_jit.py -k test_warning` +See also https://github.com/pytorch/pytorch/issues/112383 + +Workaround this by trying to avoid the throwing PyWarningHandler destructor. +Author: Alexander Grund (TU Dresden) + +diff --git a/torch/csrc/Exceptions.cpp b/torch/csrc/Exceptions.cpp +index 788f6782730..31d358528e3 100644 +--- a/torch/csrc/Exceptions.cpp ++++ b/torch/csrc/Exceptions.cpp +@@ -246,6 +246,10 @@ PyObject* map_warning_to_python_type(const c10::Warning& warning) { + /// NOLINTNEXTLINE(bugprone-exception-escape) + PyWarningHandler::~PyWarningHandler() noexcept(false) { + c10::WarningUtils::set_warning_handler(prev_handler_); ++ process_warnings(); ++} ++ ++void PyWarningHandler::process_warnings() { + auto& warning_buffer = internal_handler_.warning_buffer_; + + if (!warning_buffer.empty()) { +diff --git a/torch/csrc/Exceptions.h b/torch/csrc/Exceptions.h +index 7c448ddc67f..9779b21bcb7 100644 +--- a/torch/csrc/Exceptions.h ++++ b/torch/csrc/Exceptions.h +@@ -117,6 +117,13 @@ static inline void PyErr_SetString(PyObject* type, const std::string& message) { + retstmnt; \ + } + ++/** To be called inside a HANDLE_TH_ERRORS..END_HANDLE_TH_ERRORS_* block ++ * before returning a value / where no further warnings can occur. ++ * Avoids throwing an error in the destructor which triggers a bug in GCC 12+ ++ * See https://gcc.gnu.org/bugzilla/show_bug.cgi?id=112301 ++ */ ++#define FLUSH_TH_ERRORS __enforce_warning_buffer.process_warnings(); ++ + #define END_HANDLE_TH_ERRORS_PYBIND \ + } \ + catch (...) { \ +@@ -372,6 +379,9 @@ struct PyWarningHandler { + in_exception_ = true; + } + ++ // Trigger processing of warnings ++ TORCH_API void process_warnings(); ++ + private: + InternalHandler internal_handler_; + at::WarningHandler* prev_handler_; +@@ -379,26 +389,40 @@ struct PyWarningHandler { + }; + + namespace detail { ++ ++template ++struct conditional_gil_scoped_release: pybind11::gil_scoped_release{}; ++ ++template<> ++struct conditional_gil_scoped_release{ ++ conditional_gil_scoped_release() { ++ // suppress `unused variable` error messages at call sites ++ (void) (this != (this + 1)); ++ } ++}; ++ + template + using Arg = typename invoke_traits::template arg::type; + +-template ++template + auto wrap_pybind_function_impl_( + Func&& f, + std::index_sequence, +- bool release_gil) { ++ std::bool_constant) { + using result_type = typename invoke_traits::result_type; + namespace py = pybind11; + + // f=f is needed to handle function references on older compilers +- return [f = std::forward(f), +- release_gil](Arg... args) -> result_type { ++ return [f = std::forward(f)](Arg... args) -> result_type { + HANDLE_TH_ERRORS +- if (release_gil) { +- py::gil_scoped_release no_gil; +- return c10::guts::invoke(f, std::forward>(args)...); ++ conditional_gil_scoped_release no_gil; ++ if constexpr (std::is_void_v) { ++ c10::guts::invoke(f, std::forward>(args)...); ++ FLUSH_TH_ERRORS + } else { +- return c10::guts::invoke(f, std::forward>(args)...); ++ auto res = c10::guts::invoke(f, std::forward>(args)...); ++ FLUSH_TH_ERRORS ++ return res; + } + END_HANDLE_TH_ERRORS_PYBIND + }; +@@ -411,7 +435,7 @@ template + auto wrap_pybind_function(Func&& f) { + using traits = invoke_traits; + return torch::detail::wrap_pybind_function_impl_( +- std::forward(f), std::make_index_sequence{}, false); ++ std::forward(f), std::make_index_sequence{}, std::false_type{}); + } + + // Wrap a function with TH error, warning handling and releases the GIL. +@@ -420,7 +444,7 @@ template + auto wrap_pybind_function_no_gil(Func&& f) { + using traits = invoke_traits; + return torch::detail::wrap_pybind_function_impl_( +- std::forward(f), std::make_index_sequence{}, true); ++ std::forward(f), std::make_index_sequence{}, std::true_type{}); + } + + } // namespace torch From 0236dd2eaa3498a8990b29554deb1143ffd54a40 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 1 Nov 2023 17:56:38 +0100 Subject: [PATCH 114/599] Workaround potential crash in PyTorch 1.13.1 caused by GCC 12 compiler bug --- .../p/PyTorch/PyTorch-1.13.1-foss-2022b.eb | 3 + ...round-gcc12-destructor-exception-bug.patch | 68 +++++++++++++++++++ 2 files changed, 71 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_workaround-gcc12-destructor-exception-bug.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022b.eb index 896e238a874..132930e405c 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022b.eb @@ -42,6 +42,7 @@ patches = [ 'PyTorch-1.13.1_skip-failing-grad-test.patch', 'PyTorch-1.13.1_skip-failing-singular-grad-test.patch', 'PyTorch-1.13.1_skip-tests-without-fbgemm.patch', + 'PyTorch-1.13.1_workaround-gcc12-destructor-exception-bug.patch', ] checksums = [ {'pytorch-v1.13.1.tar.gz': 'dbc229ee9750b02b514937d017744443a269ea0241ed3f32b9af0703589d25d4'}, @@ -95,6 +96,8 @@ checksums = [ '72688a57b2bb617665ad1a1d5e362c5111ae912c10936bb38a089c0204729f48'}, {'PyTorch-1.13.1_skip-tests-without-fbgemm.patch': '481e595f673baf8ae58b41697a6792b83048b0264aa79b422f48cd8c22948bb7'}, + {'PyTorch-1.13.1_workaround-gcc12-destructor-exception-bug.patch': + '931142a3133ea8f6819123523b15cbc9dbdaf8c28e34396a09227f865e7c8829'}, ] osdependencies = [OS_PKG_IBVERBS_DEV] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_workaround-gcc12-destructor-exception-bug.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_workaround-gcc12-destructor-exception-bug.patch new file mode 100644 index 00000000000..0ebcb88930a --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_workaround-gcc12-destructor-exception-bug.patch @@ -0,0 +1,68 @@ +GCC 12 introduced a regression that may cause it to call the destructor twice on an object. +See https://gcc.gnu.org/bugzilla/show_bug.cgi?id=112301 +This is visible in e.g. `test_cpp_extensions_jit.py -k test_warning` +See also https://github.com/pytorch/pytorch/issues/112383 + +Workaround this by trying to avoid the throwing PyWarningHandler destructor. + +Author: Alexander Grund (TU Dresden) + +diff --git a/torch/csrc/Exceptions.cpp b/torch/csrc/Exceptions.cpp +index 5210d6f713d..3c91ed378e1 100644 +--- a/torch/csrc/Exceptions.cpp ++++ b/torch/csrc/Exceptions.cpp +@@ -226,6 +226,10 @@ PyWarningHandler::PyWarningHandler() noexcept(true) + /// NOLINTNEXTLINE(bugprone-exception-escape) + PyWarningHandler::~PyWarningHandler() noexcept(false) { + c10::Warning::set_warning_handler(prev_handler_); ++ process_warnings(); ++} ++ ++void PyWarningHandler::process_warnings() { + auto& warning_buffer = internal_handler_.warning_buffer_; + + if (warning_buffer.size() > 0) { +diff --git a/torch/csrc/Exceptions.h b/torch/csrc/Exceptions.h +index 89256c64bba..7e09d0ebc37 100644 +--- a/torch/csrc/Exceptions.h ++++ b/torch/csrc/Exceptions.h +@@ -110,6 +110,13 @@ static inline void PyErr_SetString(PyObject* type, const std::string& message) { + retstmnt; \ + } + ++/** To be called inside a HANDLE_TH_ERRORS..END_HANDLE_TH_ERRORS_* block ++ * before returning a value / where no further warnings can occur. ++ * Avoids throwing an error in the destructor which triggers a bug in GCC 12+ ++ * See https://gcc.gnu.org/bugzilla/show_bug.cgi?id=112301 ++ */ ++#define FLUSH_TH_ERRORS __enforce_warning_buffer.process_warnings(); ++ + #define END_HANDLE_TH_ERRORS_PYBIND \ + } \ + catch (...) { \ +@@ -381,6 +388,9 @@ struct PyWarningHandler { + in_exception_ = true; + } + ++ // Trigger processing of warnings ++ TORCH_API void process_warnings(); ++ + private: + InternalHandler internal_handler_; + at::WarningHandler* prev_handler_; +@@ -399,7 +409,14 @@ auto wrap_pybind_function_impl_(Func&& f, std::index_sequence) { + // f=f is needed to handle function references on older compilers + return [f = f](Arg... args) -> typename traits::result_type { + HANDLE_TH_ERRORS +- return f(std::forward>(args)...); ++ if constexpr (std::is_void_v) { ++ c10::guts::invoke(f, std::forward>(args)...); ++ FLUSH_TH_ERRORS ++ } else { ++ auto res = c10::guts::invoke(f, std::forward>(args)...); ++ FLUSH_TH_ERRORS ++ return res; ++ } + END_HANDLE_TH_ERRORS_PYBIND + }; + } From 44a85f20fdba3219490201815193a58cb13def61 Mon Sep 17 00:00:00 2001 From: Alexander Puck Neuwirth Date: Wed, 1 Nov 2023 20:10:48 +0100 Subject: [PATCH 115/599] adding easyconfigs: HepMC-2.06.11-gompi-2022a.eb --- .../h/HepMC/HepMC-2.06.11-gompi-2022a.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/h/HepMC/HepMC-2.06.11-gompi-2022a.eb diff --git a/easybuild/easyconfigs/h/HepMC/HepMC-2.06.11-gompi-2022a.eb b/easybuild/easyconfigs/h/HepMC/HepMC-2.06.11-gompi-2022a.eb new file mode 100644 index 00000000000..7d89e8ca6ac --- /dev/null +++ b/easybuild/easyconfigs/h/HepMC/HepMC-2.06.11-gompi-2022a.eb @@ -0,0 +1,30 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Alexander Puck Neuwirth + +easyblock = 'CMakeMake' + +name = 'HepMC' +version = '2.06.11' + +homepage = 'http://hepmc.web.cern.ch/hepmc/' +description = """HepMC is a standard for storing Monte Carlo event data.""" + +toolchain = {'name': 'gompi', 'version': '2022a'} + +source_urls = ['https://hepmc.web.cern.ch/hepmc/releases/'] +sources = ['hepmc%(version)s.tgz'] +checksums = ['86b66ea0278f803cde5774de8bd187dd42c870367f1cbf6cdaec8dc7cf6afc10'] + +builddependencies = [('CMake', '3.23.1')] + +dependencies = [ +] + +configopts = '-Dmomentum=GEV -Dlength=MM' + +sanity_check_paths = { + 'files': ["lib/libHepMC.so"], + 'dirs': ['include/HepMC'] +} + +moduleclass = 'phys' From 74c75fdd955d489366b47e62998c96da27c51d0a Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 2 Nov 2023 10:22:19 +0100 Subject: [PATCH 116/599] fix detection of newer Intel CPUs in OpenBLAS 0.3.20-0.3.23 --- .../o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb | 2 + .../o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb | 2 + .../OpenBLAS-0.3.20-NVHPC-22.7-CUDA-11.7.0.eb | 2 + .../OpenBLAS-0.3.20_fix-x86-cpuid.patch | 54 +++++++++++++++++++ .../o/OpenBLAS/OpenBLAS-0.3.21-GCC-12.2.0.eb | 2 + .../o/OpenBLAS/OpenBLAS-0.3.23-GCC-12.3.0.eb | 2 + 6 files changed, 64 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20_fix-x86-cpuid.patch diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb index ad53aa70e6b..03bd16ce48f 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb @@ -16,6 +16,7 @@ patches = [ ('large.tgz', '.'), ('timing.tgz', '.'), 'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch', + 'OpenBLAS-0.3.20_fix-x86-cpuid.patch', 'OpenBLAS-0.3.21_fix-order-vectorization.patch', 'OpenBLAS-0.3.21_disable-fma-in-cscal-zscal.patch', 'OpenBLAS-0.3.21_avoid-crash-in-zdot.patch', @@ -26,6 +27,7 @@ checksums = [ {'timing.tgz': '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af'}, {'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch': 'e6b326fb8c4a8a6fd07741d9983c37a72c55c9ff9a4f74a80e1352ce5f975971'}, + {'OpenBLAS-0.3.20_fix-x86-cpuid.patch': '57e8384404e136b9f0dafc26573adeb7dc69e60d84a7e189643b91d6299888fc'}, {'OpenBLAS-0.3.21_fix-order-vectorization.patch': '08af834e5d60441fd35c128758ed9c092ba6887c829e0471ecd489079539047d'}, {'OpenBLAS-0.3.21_disable-fma-in-cscal-zscal.patch': diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb index 1041b4ef6d3..5b104219e11 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb @@ -20,6 +20,7 @@ patches = [ 'OpenBLAS-0.3.21_disable-fma-in-cscal-zscal.patch', 'OpenBLAS-0.3.21_avoid-crash-in-zdot.patch', 'OpenBLAS-0.3.20_fix-cpuid-neoverse-v1-n2.patch', + 'OpenBLAS-0.3.20_fix-x86-cpuid.patch', ] checksums = [ {'v0.3.20.tar.gz': '8495c9affc536253648e942908e88e097f2ec7753ede55aca52e5dead3029e3c'}, @@ -34,6 +35,7 @@ checksums = [ {'OpenBLAS-0.3.21_avoid-crash-in-zdot.patch': '3dac2c1ec896df574f1b37cde81a16f24550b7f1eb81fbfacb0c4449b0dc7894'}, {'OpenBLAS-0.3.20_fix-cpuid-neoverse-v1-n2.patch': '1b495465f8dd1e151d74cf5aa4288120361d29164d6a377228a8d51c255b8a9e'}, + {'OpenBLAS-0.3.20_fix-x86-cpuid.patch': '57e8384404e136b9f0dafc26573adeb7dc69e60d84a7e189643b91d6299888fc'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-NVHPC-22.7-CUDA-11.7.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-NVHPC-22.7-CUDA-11.7.0.eb index 7b49821c348..cbf11c2a295 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-NVHPC-22.7-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-NVHPC-22.7-CUDA-11.7.0.eb @@ -16,6 +16,7 @@ patches = [ ('large.tgz', '.'), ('timing.tgz', '.'), 'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch', + 'OpenBLAS-0.3.20_fix-x86-cpuid.patch', 'OpenBLAS-0.3.21_fix-order-vectorization.patch', 'OpenBLAS-0.3.21_disable-fma-in-cscal-zscal.patch', 'OpenBLAS-0.3.21_avoid-crash-in-zdot.patch', @@ -26,6 +27,7 @@ checksums = [ {'timing.tgz': '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af'}, {'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch': 'e6b326fb8c4a8a6fd07741d9983c37a72c55c9ff9a4f74a80e1352ce5f975971'}, + {'OpenBLAS-0.3.20_fix-x86-cpuid.patch': '57e8384404e136b9f0dafc26573adeb7dc69e60d84a7e189643b91d6299888fc'}, {'OpenBLAS-0.3.21_fix-order-vectorization.patch': '08af834e5d60441fd35c128758ed9c092ba6887c829e0471ecd489079539047d'}, {'OpenBLAS-0.3.21_disable-fma-in-cscal-zscal.patch': diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20_fix-x86-cpuid.patch b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20_fix-x86-cpuid.patch new file mode 100644 index 00000000000..a26c184754c --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20_fix-x86-cpuid.patch @@ -0,0 +1,54 @@ +Fix C&P error causing misdetection of CPUs. +Allows auto-detection of Intel SapphireRapids +Backport from https://github.com/OpenMathLib/OpenBLAS/pull/4002 + +Author: Alexander Grund (TU Dresden) + +diff --git a/cpuid_x86.c b/cpuid_x86.c +index d7d85eb20..9a37aa3f1 100644 +--- a/cpuid_x86.c ++++ b/cpuid_x86.c +@@ -1900,7 +1900,8 @@ static char *corename[] = { + "ZEN", + "SKYLAKEX", + "DHYANA", +- "COOPERLAKE" ++ "COOPERLAKE", ++ "SAPPHIRERAPIDS", + }; + + static char *corename_lower[] = { +@@ -1934,7 +1935,8 @@ static char *corename_lower[] = { + "zen", + "skylakex", + "dhyana", +- "cooperlake" ++ "cooperlake", ++ "sapphirerapids", + }; + + +@@ -2240,16 +2242,18 @@ int get_coretype(void){ + return CORE_NEHALEM; + } + if (model == 15) { // Sapphire Rapids ++ if(support_amx_bf16()) ++ return CORE_SAPPHIRERAPIDS; + if(support_avx512_bf16()) +- return CPUTYPE_COOPERLAKE; ++ return CORE_COOPERLAKE; + if(support_avx512()) +- return CPUTYPE_SKYLAKEX; ++ return CORE_SKYLAKEX; + if(support_avx2()) +- return CPUTYPE_HASWELL; ++ return CORE_HASWELL; + if(support_avx()) +- return CPUTYPE_SANDYBRIDGE; ++ return CORE_SANDYBRIDGE; + else +- return CPUTYPE_NEHALEM; ++ return CORE_NEHALEM; + } + break; + diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21-GCC-12.2.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21-GCC-12.2.0.eb index 274aeeec351..66b40a6a8a1 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21-GCC-12.2.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21-GCC-12.2.0.eb @@ -16,6 +16,7 @@ patches = [ ('large.tgz', '.'), ('timing.tgz', '.'), 'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch', + 'OpenBLAS-0.3.20_fix-x86-cpuid.patch', 'OpenBLAS-0.3.21_fix-order-vectorization.patch', 'OpenBLAS-0.3.21-GCC-12.2.0_disable-fma-in-cscal-zscal.patch', 'OpenBLAS-0.3.21_avoid-crash-in-zdot.patch', @@ -26,6 +27,7 @@ checksums = [ {'timing.tgz': '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af'}, {'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch': 'e6b326fb8c4a8a6fd07741d9983c37a72c55c9ff9a4f74a80e1352ce5f975971'}, + {'OpenBLAS-0.3.20_fix-x86-cpuid.patch': '57e8384404e136b9f0dafc26573adeb7dc69e60d84a7e189643b91d6299888fc'}, {'OpenBLAS-0.3.21_fix-order-vectorization.patch': '08af834e5d60441fd35c128758ed9c092ba6887c829e0471ecd489079539047d'}, {'OpenBLAS-0.3.21-GCC-12.2.0_disable-fma-in-cscal-zscal.patch': diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.23-GCC-12.3.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.23-GCC-12.3.0.eb index abbc1f81fe9..8051da228f0 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.23-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.23-GCC-12.3.0.eb @@ -16,6 +16,7 @@ patches = [ ('large.tgz', '.'), ('timing.tgz', '.'), 'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch', + 'OpenBLAS-0.3.20_fix-x86-cpuid.patch', 'OpenBLAS-0.3.21_fix-order-vectorization.patch', 'OpenBLAS-0.3.23_fix-parallel-build.patch', 'OpenBLAS-0.3.23_fix-lapack-test.patch', @@ -28,6 +29,7 @@ checksums = [ {'timing.tgz': '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af'}, {'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch': 'e6b326fb8c4a8a6fd07741d9983c37a72c55c9ff9a4f74a80e1352ce5f975971'}, + {'OpenBLAS-0.3.20_fix-x86-cpuid.patch': '57e8384404e136b9f0dafc26573adeb7dc69e60d84a7e189643b91d6299888fc'}, {'OpenBLAS-0.3.21_fix-order-vectorization.patch': '08af834e5d60441fd35c128758ed9c092ba6887c829e0471ecd489079539047d'}, {'OpenBLAS-0.3.23_fix-parallel-build.patch': 'abe10ba3b0ca54772dbf235596e35325a5159018f6a60cfc88824c2c220d99d9'}, From 72995a2f9d4c86691d18e22b3bcd489482caf073 Mon Sep 17 00:00:00 2001 From: Xin An <34663977+xinan1911@users.noreply.github.com> Date: Thu, 2 Nov 2023 12:08:22 +0100 Subject: [PATCH 117/599] Add sanity check command --- easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb b/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb index 1a5e2a7b940..11881bde0f5 100644 --- a/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb +++ b/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb @@ -44,4 +44,6 @@ sanity_check_paths = { 'dirs': ['pythonmodule'] } +sanity_check_commands = [('python', "-c 'import waLBerla'")] + moduleclass = 'chem' From d45bf684e35a61ef001c0d2ddcacf9e77fbc05a6 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 2 Nov 2023 12:31:20 +0100 Subject: [PATCH 118/599] Fix missing type in patch --- .../p/PyTorch/PyTorch-1.13.1-foss-2022b.eb | 2 +- ..._workaround-gcc12-destructor-exception-bug.patch | 13 ++++++++++--- 2 files changed, 11 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022b.eb index 132930e405c..7d768022015 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022b.eb @@ -97,7 +97,7 @@ checksums = [ {'PyTorch-1.13.1_skip-tests-without-fbgemm.patch': '481e595f673baf8ae58b41697a6792b83048b0264aa79b422f48cd8c22948bb7'}, {'PyTorch-1.13.1_workaround-gcc12-destructor-exception-bug.patch': - '931142a3133ea8f6819123523b15cbc9dbdaf8c28e34396a09227f865e7c8829'}, + 'd46412fe917110c197e4e2c572fc577644bd6b117c99dc8c57fa96b69d5456dc'}, ] osdependencies = [OS_PKG_IBVERBS_DEV] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_workaround-gcc12-destructor-exception-bug.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_workaround-gcc12-destructor-exception-bug.patch index 0ebcb88930a..b1bd76bc125 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_workaround-gcc12-destructor-exception-bug.patch +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_workaround-gcc12-destructor-exception-bug.patch @@ -23,7 +23,7 @@ index 5210d6f713d..3c91ed378e1 100644 if (warning_buffer.size() > 0) { diff --git a/torch/csrc/Exceptions.h b/torch/csrc/Exceptions.h -index 89256c64bba..7e09d0ebc37 100644 +index 89256c64bba..8514d08c8d0 100644 --- a/torch/csrc/Exceptions.h +++ b/torch/csrc/Exceptions.h @@ -110,6 +110,13 @@ static inline void PyErr_SetString(PyObject* type, const std::string& message) { @@ -50,9 +50,16 @@ index 89256c64bba..7e09d0ebc37 100644 private: InternalHandler internal_handler_; at::WarningHandler* prev_handler_; -@@ -399,7 +409,14 @@ auto wrap_pybind_function_impl_(Func&& f, std::index_sequence) { +@@ -394,12 +404,20 @@ using Arg = typename function_traits::template arg::type; + template + auto wrap_pybind_function_impl_(Func&& f, std::index_sequence) { + using traits = function_traits; ++ using result_type = typename traits::result_type; + namespace py = pybind11; + // f=f is needed to handle function references on older compilers - return [f = f](Arg... args) -> typename traits::result_type { +- return [f = f](Arg... args) -> typename traits::result_type { ++ return [f = f](Arg... args) -> result_type { HANDLE_TH_ERRORS - return f(std::forward>(args)...); + if constexpr (std::is_void_v) { From 1fb8c91e1807080c57d00a28eb2e480e8024d373 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 2 Nov 2023 13:03:56 +0100 Subject: [PATCH 119/599] adding easyconfigs: Python-bundle-PyPI-2023.10-GCCcore-13.2.0.eb --- ...thon-bundle-PyPI-2023.10-GCCcore-13.2.0.eb | 480 ++++++++++++++++++ 1 file changed, 480 insertions(+) create mode 100644 easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2023.10-GCCcore-13.2.0.eb 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 new file mode 100644 index 00000000000..bfb44233a8f --- /dev/null +++ b/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2023.10-GCCcore-13.2.0.eb @@ -0,0 +1,480 @@ +easyblock = 'PythonBundle' + +name = 'Python-bundle-PyPI' +version = '2023.10' + +homepage = 'https://python.org/' +description = "Bundle of Python packages from PyPI" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +builddependencies = [ + ('binutils', '2.40'), + ('UnZip', '6.0'), + ('pkgconf', '2.0.3'), + ('git', '2.42.0'), # required for pbr + ('hatchling', '1.18.0'), + ('poetry', '1.6.1'), + ('scikit-build', '0.17.6'), + ('flit', '3.9.0'), +] + +dependencies = [ + ('Python', '3.11.5'), + ('cryptography', '41.0.5'), + ('virtualenv', '20.24.6'), +] + +exts_default_options = { + 'download_dep_fail': True, + 'sanity_pip_check': True, + 'use_pip': True, +} + +# order is important! +# package versions updated 2023-10-29 +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', '5.11.1', { + 'checksums': ['aefc51675b0b533d56bb5fd1c8c6c0522fe31896679882e1c4c63d5e4a0fccb3'], + }), + ('Cython', '3.0.4', { + 'checksums': ['2e379b491ee985d31e5faaf050f79f4a8f59f482835906efe4477b33b4fbe9ff'], + }), + ('six', '1.16.0', { + 'checksums': ['1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926'], + }), + ('toml', '0.10.2', { + 'checksums': ['b3bda1d108d5dd99f4a20d24d9c348e91c4db7ab1b749200bded2f839ccbe68f'], + }), + ('tomli', '2.0.1', { + 'checksums': ['de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f'], + }), + ('packaging', '23.2', { + 'checksums': ['048fb0e9405036518eaaf48a55953c750c11e1a1b68e0dd1a9d62ed0c092cfc5'], + }), + ('python-dateutil', '2.8.2', { + 'modulename': 'dateutil', + 'checksums': ['0123cacc1627ae19ddf3c27a5de5bd67ee4586fbdd6440d9748f8abb483d3e86'], + }), + ('decorator', '5.1.1', { + 'checksums': ['637996211036b6385ef91435e4fae22989472f9d571faba8927ba8253acbc330'], + }), + ('liac-arff', '2.5.0', { + 'modulename': 'arff', + 'checksums': ['3220d0af6487c5aa71b47579be7ad1d94f3849ff1e224af3bf05ad49a0b5c4da'], + }), + ('pycryptodome', '3.19.0', { + 'modulename': 'Crypto.PublicKey.RSA', + 'checksums': ['bc35d463222cdb4dbebd35e0784155c81e161b9284e567e7e933d722e533331e'], + }), + ('ecdsa', '0.18.0', { + 'checksums': ['190348041559e21b22a1d65cee485282ca11a6f81d503fddb84d5017e9ed1e49'], + }), + ('ipaddress', '1.0.23', { + 'checksums': ['b7f8e0369580bb4a24d5ba1d7cc29660a4a6987763faf1d8a8046830e020e7e2'], + }), + ('asn1crypto', '1.5.1', { + 'checksums': ['13ae38502be632115abf8a24cbe5f4da52e3b5231990aff31123c805306ccb9c'], + }), + ('idna', '3.4', { + 'checksums': ['814f528e8dead7d329833b91c5faa87d60bf71824cd12a7530b5526063d02cb4'], + }), + ('pycparser', '2.21', { + 'checksums': ['e644fdec12f7872f86c58ff790da456218b10f863970249516d60a5eaca77206'], + }), + ('cffi', '1.16.0', { + 'checksums': ['bcb3ef43e58665bbda2fb198698fcae6776483e0c4a631aa5647806c25e02cc0'], + }), + ('semantic_version', '2.10.0', { + 'checksums': ['bdabb6d336998cbb378d4b9db3a4b56a1e3235701dc05ea2690d9a997ed5041c'], + }), + ('typing_extensions', '4.8.0', { + 'checksums': ['df8e4339e9cb77357558cbdbceca33c303714cf861d1eef15e1070055ae8b7ef'], + }), + ('pyasn1', '0.5.0', { + 'checksums': ['97b7290ca68e62a832558ec3976f15cbf911bf5d7c7039d8b861c2a0ece69fde'], + }), + ('PyNaCl', '1.5.0', { + 'modulename': 'nacl', + 'checksums': ['8ac7448f09ab85811607bdd21ec2464495ac8b7c66d146bf545b0f08fb9220ba'], + }), + ('pyparsing', '3.1.1', { + 'checksums': ['ede28a1a32462f5a9705e07aea48001a08f7cf81a021585011deba701581a0db'], + }), + ('netifaces', '0.11.0', { + 'checksums': ['043a79146eb2907edf439899f262b3dfe41717d34124298ed281139a8b93ca32'], + }), + ('netaddr', '0.9.0', { + 'checksums': ['7b46fa9b1a2d71fd5de9e4a3784ef339700a53a08c8040f08baf5f1194da0128'], + }), + ('mock', '5.1.0', { + 'checksums': ['5e96aad5ccda4718e0a229ed94b2024df75cc2d55575ba5762d31f5767b8767d'], + }), + ('pytz', '2023.3.post1', { + 'checksums': ['7b4fddbeb94a1eba4b557da24f19fdf9db575192544270a9101d8509f9f43d7b'], + }), + ('bitarray', '2.8.2', { + 'checksums': ['f90b2f44b5b23364d5fbade2c34652e15b1fcfe813c46f828e008f68a709160f'], + }), + ('bitstring', '4.1.2', { + 'checksums': ['c22283d60fd3e1a8f386ccd4f1915d7fe13481d6349db39711421e24d4a9cccf'], + }), + ('appdirs', '1.4.4', { + 'checksums': ['7d5d0167b2b1ba821647616af46a749d1c653740dd0d2415100fe26e27afdf41'], + }), + ('distlib', '0.3.7', { + 'checksums': ['9dafe54b34a028eafd95039d5e5d4851a13734540f1331060d31c9916e7147a8'], + }), + ('zipp', '3.17.0', { + 'checksums': ['84e64a1c28cf7e91ed2078bb8cc8c259cb19b76942096c8d7b84947690cabaf0'], + }), + ('importlib_metadata', '6.8.0', { + 'checksums': ['dbace7892d8c0c4ac1ad096662232f831d4e64f4c4545bd53016a3e9d4654743'], + }), + ('backports.entry-points-selectable', '1.2.0', { + 'sources': ['backports.entry_points_selectable-%(version)s.tar.gz'], + 'checksums': ['4706f59179657ca7c1d325a543ee1370f8f46331f432bcac62fab242fdf0afa5'], + }), + ('pathspec', '0.11.2', { + 'checksums': ['e0d8d0ac2f12da61956eb2306b69f9469b42f4deb0f3cb6ed47b9cce9996ced3'], + }), + ('pluggy', '1.3.0', { + 'checksums': ['cf61ae8f126ac6f7c451172cf30e3e43d3ca77615509771b3a984a0730651e12'], + }), + ('editables', '0.5', { + 'checksums': ['309627d9b5c4adc0e668d8c6fa7bac1ba7c8c5d415c2d27f60f081f8e80d1de2'], + }), + ('filelock', '3.13.0', { + 'checksums': ['63c6052c82a1a24c873a549fbd39a26982e8f35a3016da231ead11a5be9dad44'], + }), + ('platformdirs', '3.11.0', { + 'checksums': ['cf8ee52a3afdb965072dcc652433e0c7e3e40cf5ea1477cd4b3b1d2eb75495b3'], + }), + ('scandir', '1.10.0', { + 'checksums': ['4d4631f6062e658e9007ab3149a9b914f3548cb38bfb021c64f39a025ce578ae'], + }), + ('pathlib2', '2.3.7.post1', { + 'checksums': ['9fe0edad898b83c0c3e199c842b27ed216645d2e177757b2dd67384d4113c641'], + }), + ('importlib_resources', '6.1.0', { + 'checksums': ['9d48dcccc213325e810fd723e7fbb45ccb39f6cf5c31f00cf2b965f5f10f3cb9'], + }), + ('docopt', '0.6.2', { + 'checksums': ['49b3a825280bd66b3aa83585ef59c4a8c82f2c8a522dbe754a8bc8d08c85c491'], + }), + ('joblib', '1.3.2', { + 'checksums': ['92f865e621e17784e7955080b6d042489e3b8e294949cc44c6eac304f59772b1'], + }), + ('chardet', '5.2.0', { + 'checksums': ['1b3b6ff479a8c414bc3fa2c0852995695c4a026dcd6d0633b2dd092ca39c1cf7'], + }), + ('certifi', '2023.7.22', { + 'checksums': ['539cc1d13202e33ca466e88b2807e29f4c13049d6d87031a3c110744495cb082'], + }), + ('urllib3', '2.0.7', { + 'checksums': ['c97dfde1f7bd43a71c8d2a58e369e9b2bf692d1334ea9f9cae55add7d0dd0f84'], + }), + ('charset-normalizer', '3.3.1', { + 'checksums': ['d9137a876020661972ca6eec0766d81aef8a5627df628b664b234b73396e727e'], + }), + ('requests', '2.31.0', { + 'checksums': ['942c5a758f98d790eaed1a29cb6eefc7ffb0d1cf7af05c3d2791656dbd6ad1e1'], + }), + ('xlrd', '2.0.1', { + 'checksums': ['f72f148f54442c6b056bf931dbc34f986fd0c3b0b6b5a58d013c9aef274d0c88'], + }), + ('py_expression_eval', '0.3.14', { + 'checksums': ['ea60f9404a18346d5a63854db21c50666dfb4274ae111000165b31c6f8ab93f1'], + }), + ('tabulate', '0.9.0', { + 'checksums': ['0095b12bf5966de529c0feb1fa08671671b3368eec77d7ef7ab114be2c068b3c'], + }), + ('ujson', '5.8.0', { + 'checksums': ['78e318def4ade898a461b3d92a79f9441e7e0e4d2ad5419abed4336d702c7425'], + }), + ('atomicwrites', '1.4.1', { + 'checksums': ['81b2c9071a49367a7f770170e5eec8cb66567cfbbc8c73d20ce5ca4a8d71cf11'], + }), + ('py', '1.11.0', { + 'checksums': ['51c75c4126074b472f746a24399ad32f6053d1b34b68d2fa41e558e6f4a98719'], + }), + ('more-itertools', '10.1.0', { + 'checksums': ['626c369fa0eb37bac0291bce8259b332fd59ac792fa5497b59837309cd5b114a'], + }), + ('attrs', '23.1.0', { + 'modulename': 'attr', + 'checksums': ['6279836d581513a26f1bf235f9acd333bc9115683f14f7e8fae46c98fc50e015'], + }), + ('backports.functools_lru_cache', '1.6.6', { + 'checksums': ['7b70e701ba4db58c0ed8671a9d3391b0abb9bd1bc24d4e90c3480f4baafcc2dc'], + }), + ('wcwidth', '0.2.8', { + 'checksums': ['8705c569999ffbb4f6a87c6d1b80f324bd6db952f5eb0b95bc07517f4c1813d4'], + }), + ('iniconfig', '2.0.0', { + 'checksums': ['2d91e135bf72d31a410b17c16da610a82cb55f6b0477d1a902134b24a455b8b3'], + }), + ('colorama', '0.4.6', { + 'checksums': ['08695f5cb7ed6e0531a20572697297273c47b8cae5a63ffc6d6ed5c201be6e44'], + }), + ('exceptiongroup', '1.1.3', { + 'checksums': ['097acd85d473d75af5bb98e41b61ff7fe35efe6675e4f9370ec6ec5126d160e9'], + }), + ('pytest', '7.4.3', { + 'checksums': ['d989d136982de4e3b29dabcc838ad581c64e8ed52c11fbe86ddebd9da0818cd5'], + }), + ('MarkupSafe', '2.1.3', { + 'checksums': ['af598ed32d6ae86f1b747b82783958b1a4ab8f617b06fe68795c7f026abbdcad'], + }), + ('Jinja2', '3.1.2', { + 'checksums': ['31351a702a408a9e7595a8fc6150fc3f43bb6bf7e319770cbc0db9df9437e852'], + }), + ('sphinxcontrib_serializinghtml', '1.1.9', { + 'modulename': 'sphinxcontrib.serializinghtml', + 'checksums': ['0c64ff898339e1fac29abd2bf5f11078f3ec413cfe9c046d3120d7ca65530b54'], + }), + ('sphinxcontrib_websupport', '1.2.6', { + 'modulename': 'sphinxcontrib.websupport', + 'checksums': ['d592be8e11261bbbc64668f258efc4fd42c93ab617411143b5245fe30c633d8c'], + }), + ('Pygments', '2.16.1', { + 'checksums': ['1daff0494820c69bc8941e407aa20f577374ee88364ee10a98fdbe0aece96e29'], + }), + ('imagesize', '1.4.1', { + 'checksums': ['69150444affb9cb0d5cc5a92b3676f0b2fb7cd9ae39e947a5e11a36b4497cd4a'], + }), + ('docutils', '0.20.1', { + 'checksums': ['f08a4e276c3a1583a86dce3e34aba3fe04d02bba2dd51ed16106244e8a923e3b'], + }), + ('snowballstemmer', '2.2.0', { + 'checksums': ['09b16deb8547d3412ad7b590689584cd0fe25ec8db3be37788be3810cbf19cb1'], + }), + ('alabaster', '0.7.13', { + 'checksums': ['a27a4a084d5e690e16e01e03ad2b2e552c61a65469419b907243193de1a84ae2'], + }), + ('sphinxcontrib_applehelp', '1.0.7', { + 'modulename': 'sphinxcontrib.applehelp', + 'checksums': ['39fdc8d762d33b01a7d8f026a3b7d71563ea3b72787d5f00ad8465bd9d6dfbfa'], + }), + ('sphinxcontrib_devhelp', '1.0.5', { + 'modulename': 'sphinxcontrib.devhelp', + 'checksums': ['63b41e0d38207ca40ebbeabcf4d8e51f76c03e78cd61abe118cf4435c73d4212'], + }), + ('sphinxcontrib_htmlhelp', '2.0.4', { + 'modulename': 'sphinxcontrib.htmlhelp', + 'checksums': ['6c26a118a05b76000738429b724a0568dbde5b72391a688577da08f11891092a'], + }), + ('sphinxcontrib-jsmath', '1.0.1', { + 'modulename': 'sphinxcontrib.jsmath', + 'checksums': ['a9925e4a4587247ed2191a22df5f6970656cb8ca2bd6284309578f2153e0c4b8'], + }), + ('sphinxcontrib_qthelp', '1.0.6', { + 'modulename': 'sphinxcontrib.qthelp', + 'checksums': ['62b9d1a186ab7f5ee3356d906f648cacb7a6bdb94d201ee7adf26db55092982d'], + }), + ('Babel', '2.13.1', { + 'checksums': ['33e0952d7dd6374af8dbf6768cc4ddf3ccfefc244f9986d4074704f2fbd18900'], + }), + ('sphinx', '7.2.6', { + 'checksums': ['9a5160e1ea90688d5963ba09a2dcd8bdd526620edbb65c328728f1b2228d5ab5'], + }), + ('sphinx-bootstrap-theme', '0.8.1', { + 'checksums': ['683e3b735448dadd0149f76edecf95ff4bd9157787e9e77e0d048ca6f1d680df'], + }), + ('click', '8.1.7', { + 'checksums': ['ca9853ad459e787e2192211578cc907e7594e294c7ccc834310722b41b9ca6de'], + }), + ('psutil', '5.9.6', { + 'checksums': ['e4b92ddcd7dd4cdd3f900180ea1e104932c7bce234fb88976e2a3b296441225a'], + }), + ('future', '0.18.3', { + 'checksums': ['34a17436ed1e96697a86f9de3d15a3b0be01d8bc8de9c1dffd59fb8234ed5307'], + }), + ('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', { + 'checksums': ['f463434305e0336248cac9c2dc8076b707d8a12d019dd349f5c1e382dd1ae1b9'], + }), + ('regex', '2023.10.3', { + 'checksums': ['3fef4f844d2290ee0ba57addcec17eec9e3df73f10a2748485dfd6a3a188cc0f'], + }), + ('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'], + }), + # clikit 0.6.2 has requirement crashtest<0.4.0,>=0.3.0 + # but poetry 1.5.1 has requirement crashtest>=0.4.1 + # and cleo 2.0.1 has requirement crashtest>=0.4.1 + # ('clikit', '0.6.2', { + # 'source_tmpl': SOURCE_WHL, + # 'checksums': ['71268e074e68082306e23d7369a7b99f824a0ef926e55ba2665e911f7208489e'], + # }), + ('jeepney', '0.8.0', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['c0a454ad016ca575060802ee4d590dd912e35c122fa04e70306de3d076cce755'], + }), + ('SecretStorage', '3.3.3', { + 'checksums': ['2403533ef369eca6d2ba81718576c5e0f564d5cca1b58f73a8b23e7d4eeebd77'], + }), + ('keyring', '24.2.0', { + 'modulename': False, + 'checksums': ['ca0746a19ec421219f4d713f848fa297a661a8a8c1504867e55bfb5e09091509'], + }), + ('jaraco.classes', '3.3.0', { + 'checksums': ['c063dd08e89217cee02c8d5e5ec560f2c8ce6cdc2fcdc2e68f7b2e5547ed3621'], + }), + ('keyrings.alt', '5.0.0', { + 'modulename': False, + 'checksums': ['9d446cb47bbcea90ffa2ecc3e8003acf41573fc201bf44b4bf13bd0e11484828'], + }), + ('tomlkit', '0.12.1', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['712cbd236609acc6a3e2e97253dfc52d4c2082982a88f61b640ecf0817eab899'], + }), + ('shellingham', '1.5.4', { + 'checksums': ['8dbca0739d487e5bd35ab3ca4b36e11c4078f3a234bfce294b0a0291363404de'], + }), + ('requests-toolbelt', '1.0.0', { + 'checksums': ['7681a0a3d047012b5bdc0ee37d7f8f07ebe76ab08caeccfc3921ce23c88d5bc6'], + }), + ('pyrsistent', '0.20.0', { + 'checksums': ['4c48f78f62ab596c679086084d0dd13254ae4f3d6c72a83ffdf5ebdef8f265a4'], + }), + ('pkginfo', '1.9.6', { + 'checksums': ['8fd5896e8718a4372f0ea9cc9d96f6417c9b986e23a4d116dda26b62cc29d046'], + }), + ('ptyprocess', '0.7.0', { + 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', + 'checksums': ['4b41f3967fce3af57cc7e94b888626c18bf37a083e3651ca8feeb66d492fef35'], + }), + ('pexpect', '4.8.0', { + 'checksums': ['fc65a43959d153d0114afe13997d439c22823a27cefceb5ff35c2178c6784c0c'], + }), + ('jsonschema', '4.17.3', { + 'checksums': ['0f864437ab8b6076ba6707453ef8f98a6a0d512a80e93f8abdb676f737ecb60d'], + }), + ('simplejson', '3.19.2', { + 'checksums': ['9eb442a2442ce417801c912df68e1f6ccfcd41577ae7274953ab3ad24ef7d82c'], + }), + ('webencodings', '0.5.1', { + 'checksums': ['b36a1c245f2d304965eb4e0a82848379241dc04b865afcc4aab16748587e1923'], + }), + ('html5lib', '1.1', { + 'checksums': ['b2e5b40261e20f354d198eae92afc10d750afb487ed5e50f9c4eaf07c184146f'], + }), + ('distro', '1.8.0', { + 'checksums': ['02e111d1dc6a50abb8eed6bf31c3e48ed8b0830d1ea2a1b78c61765c2513fdd8'], + }), + ('rapidfuzz', '2.15.2', { + 'checksums': ['bfc1d38a7adcbe8912f980a5f46f27a801dd8655582ff0d4a2c0431c02b7ce33'], + }), + ('cleo', '2.0.1', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['6eb133670a3ed1f3b052d53789017b6e50fca66d1287e6e6696285f4cb8ea448'], + }), + ('cachy', '0.3.0', { + 'checksums': ['186581f4ceb42a0bbe040c407da73c14092379b1e4c0e327fdb72ae4a9b269b1'], + }), + ('msgpack', '1.0.7', { + 'checksums': ['572efc93db7a4d27e404501975ca6d2d9775705c2d922390d878fcf768d92c87'], + }), + ('cachecontrol', '0.13.1', { + 'checksums': ['f012366b79d2243a6118309ce73151bf52a38d4a5dac8ea57f09bd29087e506b'], + }), + ('lockfile', '0.12.2', { + 'checksums': ['6aed02de03cba24efabcd600b30540140634fc06cfa603822d508d5361e9f799'], + }), + ('glob2', '0.7', { + 'checksums': ['85c3dbd07c8aa26d63d7aacee34fa86e9a91a3873bc30bf62ec46e531f92ab8c'], + }), + ('dulwich', '0.21.6', { + 'checksums': ['30fbe87e8b51f3813c131e2841c86d007434d160bd16db586b40d47f31dd05b0'], + }), + ('fsspec', '2023.10.0', { + 'checksums': ['330c66757591df346ad3091a53bd907e15348c2ba17d63fd54f5c39c4457d2a5'], + }), + ('threadpoolctl', '3.2.0', { + 'checksums': ['c96a0ba3bdddeaca37dc4cc7344aafad41cdb8c313f74fdfe387a867bba93355'], + }), + ('simplegeneric', '0.8.1', { + 'source_tmpl': 'simplegeneric-%(version)s.zip', + 'checksums': ['dc972e06094b9af5b855b3df4a646395e43d1c9d0d39ed345b7393560d0b9173'], + }), + ('pooch', '1.8.0', { + 'checksums': ['f59981fd5b9b5d032dcde8f4a11eaa492c2ac6343fae3596a2fdae35fc54b0a0'], + }), + ('doit', '0.36.0', { + 'checksums': ['71d07ccc9514cb22fe59d98999577665eaab57e16f644d04336ae0b4bae234bc'], + }), + ('cloudpickle', '3.0.0', { + 'checksums': ['996d9a482c6fb4f33c1a35335cf8afd065d2a56e973270364840712d9131a882'], + }), + ('pydevtool', '0.3.0', { + 'checksums': ['25e3ba4f3d33ccac33ee2b9775995848d49e9b318b7a146477fb5d52f786fc8a'], + }), + ('Pygments', '2.16.1', { + 'checksums': ['1daff0494820c69bc8941e407aa20f577374ee88364ee10a98fdbe0aece96e29'], + }), + ('mdurl', '0.1.2', { + 'checksums': ['bb413d29f5eea38f31dd4754dd7377d4465116fb207585f97bf925588687c1ba'], + }), + ('markdown-it-py', '3.0.0', { + 'modulename': 'markdown_it', + 'checksums': ['e3f60a94fa066dc52ec76661e37c851cb232d92f9886b15cb560aaada2df8feb'], + }), + ('rich', '13.6.0', { + 'checksums': ['5c14d22737e6d5084ef4771b62d5d4363165b403455a30a1c8ca39dc7b644bef'], + }), + ('rich-click', '1.7.0', { + 'checksums': ['ab34e5d9f7733c4e6072f4de79eb3b35ac9ae78e692ea8a543f3b2828b30fee4'], + }), + ('commonmark', '0.9.1', { + 'checksums': ['452f9dc859be7f06631ddcb328b6919c67984aca654e5fefb3914d54691aed60'], + }), + ('execnet', '2.0.2', { + 'checksums': ['cc59bc4423742fd71ad227122eb0dd44db51efb3dc4095b45ac9a08c770096af'], + }), + ('pytest-xdist', '3.3.1', { + 'modulename': 'xdist', + 'checksums': ['d5ee0520eb1b7bcca50a60a518ab7a7707992812c578198f8b44fdfac78e8c93'], + }), +] + +moduleclass = 'lang' From 39f1df415ce1511b83a41aef25ee87894dfdf36e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Thu, 2 Nov 2023 14:21:48 +0100 Subject: [PATCH 120/599] adding easyconfigs: FPM-1.15.1-GCCcore-12.2.0-Ruby-3.2.2.eb --- .../FPM-1.15.1-GCCcore-12.2.0-Ruby-3.2.2.eb | 71 +++++++++++++++++++ 1 file changed, 71 insertions(+) create mode 100644 easybuild/easyconfigs/f/FPM/FPM-1.15.1-GCCcore-12.2.0-Ruby-3.2.2.eb diff --git a/easybuild/easyconfigs/f/FPM/FPM-1.15.1-GCCcore-12.2.0-Ruby-3.2.2.eb b/easybuild/easyconfigs/f/FPM/FPM-1.15.1-GCCcore-12.2.0-Ruby-3.2.2.eb new file mode 100644 index 00000000000..833ef4f3068 --- /dev/null +++ b/easybuild/easyconfigs/f/FPM/FPM-1.15.1-GCCcore-12.2.0-Ruby-3.2.2.eb @@ -0,0 +1,71 @@ +easyblock = 'Bundle' + +name = 'FPM' +version = '1.15.1' + +local_rubyver = '3.2.2' +versionsuffix = '-Ruby-%s' % local_rubyver + +homepage = 'https://github.com/jordansissel/fpm' +description = """Effing package management! Build packages for multiple platforms (deb, rpm, etc) with great ease + and sanity.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +dependencies = [ + ('Ruby', local_rubyver), +] + +exts_default_options = { + 'source_urls': ['https://rubygems.org/downloads/'], + 'source_tmpl': '%(name)s-%(version)s.gem', +} + +exts_defaultclass = 'RubyGem' + +exts_list = [ + ('stud', '0.0.23', { + 'checksums': ['6ba26fa28fc50a8d59229b296a733b48d50f1473b1e3e7f5e339d5bbd829eb62'], + }), + ('dotenv', '2.8.1', { + 'checksums': ['c5944793349ae03c432e1780a2ca929d60b88c7d14d52d630db0508c3a8a17d8'], + }), + ('insist', '1.0.0', { + 'checksums': ['6f6759eee583dc4e00a6cc3f713cfa7c570572958ba1f5d65595046d795b832f'], + }), + ('mustache', '0.99.8', { + 'checksums': ['826a96db895819c13fffa4fa3c20b85e80b60aaec1f28f79e7db80092abdb0bc'], + }), + ('clamp', '1.0.1', { + 'checksums': ['5fa57e4337c30b384fc162a6391f477ce21e9b73ba2c16a18b3d99cb34a16649'], + }), + ('cabin', '0.9.0', { + 'checksums': ['91c5394289e993e7037a6c869e3f212f31a5984d2b1811ac934f591c87446b2c'], + }), + ('pleaserun', '0.0.32', { + 'checksums': ['4dd8db18b81b48e2a875ec0c7fff3869454d1f93a9f5e2e6c4eb88812870d3ab'], + }), + ('rexml', '3.2.6', { + 'checksums': ['e0669a2d4e9f109951cb1fde723d8acd285425d81594a2ea929304af50282816'], + }), + ('arr-pm', '0.0.12', { + 'checksums': ['fdff482f75239239201f4d667d93424412639aad0b3b0ad4d827e7c637e0ad39'], + }), + ('backports', '3.24.1', { + 'checksums': ['83a720ea9a3ee0cf5eab18b866e9282293ab4f54eb6430291b3c238481677fb8'], + }), + ('%(namelower)s', version, { + 'checksums': ['1ffbf342a89ca97fb5c02e66946c97e2bd5413810f7f440ddf32f00a16052dbf'], + }), +] + +sanity_check_paths = { + 'files': ['bin/fpm'], + 'dirs': ['gems/%(namelower)s-%(version)s'], +} + +sanity_check_commands = ["%(namelower)s --help"] + +modextrapaths = {'GEM_PATH': ['']} + +moduleclass = 'tools' From 703f2d8dfffc6df3a88a7f914a6ef4f5ad6475fc Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Thu, 2 Nov 2023 15:41:39 +0100 Subject: [PATCH 121/599] add missing build dependency --- .../easyconfigs/f/FPM/FPM-1.15.1-GCCcore-12.2.0-Ruby-3.2.2.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/f/FPM/FPM-1.15.1-GCCcore-12.2.0-Ruby-3.2.2.eb b/easybuild/easyconfigs/f/FPM/FPM-1.15.1-GCCcore-12.2.0-Ruby-3.2.2.eb index 833ef4f3068..2aa7b5d9ad2 100644 --- a/easybuild/easyconfigs/f/FPM/FPM-1.15.1-GCCcore-12.2.0-Ruby-3.2.2.eb +++ b/easybuild/easyconfigs/f/FPM/FPM-1.15.1-GCCcore-12.2.0-Ruby-3.2.2.eb @@ -12,6 +12,10 @@ description = """Effing package management! Build packages for multiple platform toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +builddependencies = [ + ('binutils', '2.39'), +] + dependencies = [ ('Ruby', local_rubyver), ] From 2ab7081deda77fa94305135410a7b2e9cae60113 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 2 Nov 2023 20:22:28 +0100 Subject: [PATCH 122/599] Add flit --- .../f/flit/flit-3.9.0-GCCcore-13.2.0.eb | 71 +++++++++++++++++++ 1 file changed, 71 insertions(+) create mode 100644 easybuild/easyconfigs/f/flit/flit-3.9.0-GCCcore-13.2.0.eb 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 new file mode 100644 index 00000000000..79b1a625e7e --- /dev/null +++ b/easybuild/easyconfigs/f/flit/flit-3.9.0-GCCcore-13.2.0.eb @@ -0,0 +1,71 @@ +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': '13.2.0'} +toolchainopts = {'pic': True} + +builddependencies = [ + ('binutils', '2.40'), + ('hatchling', '1.18.0'), +] + +dependencies = [ + ('Python', '3.11.5'), +] + +exts_default_options = { + 'download_dep_fail': True, + 'sanity_pip_check': True, + 'use_pip': True, +} + +exts_list = [ + ('idna', '3.4', { + 'checksums': ['814f528e8dead7d329833b91c5faa87d60bf71824cd12a7530b5526063d02cb4'], + }), + ('certifi', '2023.7.22', { + 'checksums': ['539cc1d13202e33ca466e88b2807e29f4c13049d6d87031a3c110744495cb082'], + }), + ('urllib3', '2.0.7', { + 'checksums': ['c97dfde1f7bd43a71c8d2a58e369e9b2bf692d1334ea9f9cae55add7d0dd0f84'], + }), + ('charset-normalizer', '3.3.1', { + 'checksums': ['d9137a876020661972ca6eec0766d81aef8a5627df628b664b234b73396e727e'], + }), + ('packaging', '23.2', { + 'checksums': ['048fb0e9405036518eaaf48a55953c750c11e1a1b68e0dd1a9d62ed0c092cfc5'], + }), + ('setuptools-scm', '8.0.4', { + 'checksums': ['b5f43ff6800669595193fd09891564ee9d1d7dcb196cab4b2506d53a2e1c95c7'], + }), + ('typing_extensions', '4.8.0', { + 'checksums': ['df8e4339e9cb77357558cbdbceca33c303714cf861d1eef15e1070055ae8b7ef'], + }), + ('flit_scm', '1.7.0', { + 'checksums': ['961bd6fb24f31bba75333c234145fff88e6de0a90fc0f7e5e7c79deca69f6bb2'], + }), + ('requests', '2.31.0', { + 'checksums': ['942c5a758f98d790eaed1a29cb6eefc7ffb0d1cf7af05c3d2791656dbd6ad1e1'], + }), + ('docutils', '0.20.1', { + 'checksums': ['f08a4e276c3a1583a86dce3e34aba3fe04d02bba2dd51ed16106244e8a923e3b'], + }), + ('tomli_w', '1.0.0', { + 'checksums': ['f463434305e0336248cac9c2dc8076b707d8a12d019dd349f5c1e382dd1ae1b9'], + }), + (name, version, { + 'checksums': ['d75edf5eb324da20d53570a6a6f87f51e606eee8384925cd66a90611140844c7'], + }), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], +} + +moduleclass = 'tools' From dfef4d879545817beee02c833eddfaa27d94d34e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Fri, 3 Nov 2023 10:18:57 +0100 Subject: [PATCH 123/599] remove version suffix --- ...e-12.2.0-Ruby-3.2.2.eb => FPM-1.15.1-GCCcore-12.2.0.eb} | 7 ++----- 1 file changed, 2 insertions(+), 5 deletions(-) rename easybuild/easyconfigs/f/FPM/{FPM-1.15.1-GCCcore-12.2.0-Ruby-3.2.2.eb => FPM-1.15.1-GCCcore-12.2.0.eb} (94%) diff --git a/easybuild/easyconfigs/f/FPM/FPM-1.15.1-GCCcore-12.2.0-Ruby-3.2.2.eb b/easybuild/easyconfigs/f/FPM/FPM-1.15.1-GCCcore-12.2.0.eb similarity index 94% rename from easybuild/easyconfigs/f/FPM/FPM-1.15.1-GCCcore-12.2.0-Ruby-3.2.2.eb rename to easybuild/easyconfigs/f/FPM/FPM-1.15.1-GCCcore-12.2.0.eb index 2aa7b5d9ad2..2ffd9eef466 100644 --- a/easybuild/easyconfigs/f/FPM/FPM-1.15.1-GCCcore-12.2.0-Ruby-3.2.2.eb +++ b/easybuild/easyconfigs/f/FPM/FPM-1.15.1-GCCcore-12.2.0.eb @@ -3,9 +3,6 @@ easyblock = 'Bundle' name = 'FPM' version = '1.15.1' -local_rubyver = '3.2.2' -versionsuffix = '-Ruby-%s' % local_rubyver - homepage = 'https://github.com/jordansissel/fpm' description = """Effing package management! Build packages for multiple platforms (deb, rpm, etc) with great ease and sanity.""" @@ -17,7 +14,7 @@ builddependencies = [ ] dependencies = [ - ('Ruby', local_rubyver), + ('Ruby', '3.2.2'), ] exts_default_options = { @@ -64,7 +61,7 @@ exts_list = [ ] sanity_check_paths = { - 'files': ['bin/fpm'], + 'files': ['bin/%(namelower)s'], 'dirs': ['gems/%(namelower)s-%(version)s'], } From ce57972218fe1cd6ea59a6d6d24b5de3ae48aa69 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 3 Nov 2023 10:19:24 +0100 Subject: [PATCH 124/599] Fix whl --- .../Python-bundle-PyPI-2023.10-GCCcore-13.2.0.eb | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) 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 bfb44233a8f..f1c29800a58 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 @@ -332,11 +332,11 @@ exts_list = [ 'checksums': ['9e77e941042ad3a4cc305dcdf2b2dec1aec2fbe3dd9015d2698ad02b173006d1'], }), ('pastel', '0.2.1', { - 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', + 'source_tmpl': SOURCE_WHL, 'checksums': ['4349225fcdf6c2bb34d483e523475de5bb04a5c10ef711263452cb37d7dd4364'], }), ('crashtest', '0.4.1', { - 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'source_tmpl': SOURCE_PY3_WHL, 'checksums': ['8d23eac5fa660409f57472e3851dab7ac18aba459a8d19cbbba86d3d5aecd2a5'], }), # clikit 0.6.2 has requirement crashtest<0.4.0,>=0.3.0 @@ -347,7 +347,7 @@ exts_list = [ # 'checksums': ['71268e074e68082306e23d7369a7b99f824a0ef926e55ba2665e911f7208489e'], # }), ('jeepney', '0.8.0', { - 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'source_tmpl': SOURCE_PY3_WHL, 'checksums': ['c0a454ad016ca575060802ee4d590dd912e35c122fa04e70306de3d076cce755'], }), ('SecretStorage', '3.3.3', { @@ -365,7 +365,7 @@ exts_list = [ 'checksums': ['9d446cb47bbcea90ffa2ecc3e8003acf41573fc201bf44b4bf13bd0e11484828'], }), ('tomlkit', '0.12.1', { - 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'source_tmpl': SOURCE_PY3_WHL, 'checksums': ['712cbd236609acc6a3e2e97253dfc52d4c2082982a88f61b640ecf0817eab899'], }), ('shellingham', '1.5.4', { @@ -381,7 +381,7 @@ exts_list = [ 'checksums': ['8fd5896e8718a4372f0ea9cc9d96f6417c9b986e23a4d116dda26b62cc29d046'], }), ('ptyprocess', '0.7.0', { - 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', + 'source_tmpl': SOURCE_WHL, 'checksums': ['4b41f3967fce3af57cc7e94b888626c18bf37a083e3651ca8feeb66d492fef35'], }), ('pexpect', '4.8.0', { @@ -406,7 +406,7 @@ exts_list = [ 'checksums': ['bfc1d38a7adcbe8912f980a5f46f27a801dd8655582ff0d4a2c0431c02b7ce33'], }), ('cleo', '2.0.1', { - 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'source_tmpl': SOURCE_PY3_WHL, 'checksums': ['6eb133670a3ed1f3b052d53789017b6e50fca66d1287e6e6696285f4cb8ea448'], }), ('cachy', '0.3.0', { From 33ceac484bd3991192468db0f0907f579dde5d1b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Fri, 3 Nov 2023 10:34:13 +0100 Subject: [PATCH 125/599] drop the empty list of dependencies --- easybuild/easyconfigs/h/HepMC/HepMC-2.06.11-gompi-2022a.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/h/HepMC/HepMC-2.06.11-gompi-2022a.eb b/easybuild/easyconfigs/h/HepMC/HepMC-2.06.11-gompi-2022a.eb index 7d89e8ca6ac..4a07aa2e8e5 100644 --- a/easybuild/easyconfigs/h/HepMC/HepMC-2.06.11-gompi-2022a.eb +++ b/easybuild/easyconfigs/h/HepMC/HepMC-2.06.11-gompi-2022a.eb @@ -17,9 +17,6 @@ checksums = ['86b66ea0278f803cde5774de8bd187dd42c870367f1cbf6cdaec8dc7cf6afc10'] builddependencies = [('CMake', '3.23.1')] -dependencies = [ -] - configopts = '-Dmomentum=GEV -Dlength=MM' sanity_check_paths = { From 7f036f9dbb53e27376cc61e84a99ba77486554a4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Fri, 3 Nov 2023 10:34:44 +0100 Subject: [PATCH 126/599] consistent use of quotes --- easybuild/easyconfigs/h/HepMC/HepMC-2.06.11-gompi-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/HepMC/HepMC-2.06.11-gompi-2022a.eb b/easybuild/easyconfigs/h/HepMC/HepMC-2.06.11-gompi-2022a.eb index 4a07aa2e8e5..ca033f0fd1c 100644 --- a/easybuild/easyconfigs/h/HepMC/HepMC-2.06.11-gompi-2022a.eb +++ b/easybuild/easyconfigs/h/HepMC/HepMC-2.06.11-gompi-2022a.eb @@ -20,7 +20,7 @@ builddependencies = [('CMake', '3.23.1')] configopts = '-Dmomentum=GEV -Dlength=MM' sanity_check_paths = { - 'files': ["lib/libHepMC.so"], + 'files': ['lib/libHepMC.so'], 'dirs': ['include/HepMC'] } From 01f54f62d2dab2197cd4d64e15ef9d8cbef4c4fd Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 3 Nov 2023 11:07:20 +0100 Subject: [PATCH 127/599] adding easyconfigs: CUDA-12.3.0.eb --- easybuild/easyconfigs/c/CUDA/CUDA-12.3.0.eb | 24 +++++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/c/CUDA/CUDA-12.3.0.eb diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-12.3.0.eb b/easybuild/easyconfigs/c/CUDA/CUDA-12.3.0.eb new file mode 100644 index 00000000000..6510fce6366 --- /dev/null +++ b/easybuild/easyconfigs/c/CUDA/CUDA-12.3.0.eb @@ -0,0 +1,24 @@ +name = 'CUDA' +version = '12.3.0' +local_nv_version = '545.23.06' + +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: + '7c13face3af64d6e1648d6e3101d31c8111e747143acb0077d973c1690820422', + 'cuda_%%(version)s_%s_linux_ppc64le.run' % local_nv_version: + 'de15c04380ec35b194c07503bf434837bac5b427cf77b19a63962b1653d195d5', + 'cuda_%%(version)s_%s_linux_sbsa.run' % local_nv_version: + '9a8fb8acf46b88faf0d711bda3149e1706efbbae02fcb40ab72addfd0e9ce5df' +}] + +moduleclass = 'system' From f8a760786377f99ffffa89b91669b795c4bd2f65 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 3 Nov 2023 13:38:12 +0100 Subject: [PATCH 128/599] adding easyconfigs: pixman-0.42.2-GCCcore-13.2.0.eb, GLib-2.78.1-GCCcore-13.2.0.eb, cairo-1.18.0-GCCcore-13.2.0.eb, GObject-Introspection-1.78.1-GCCcore-13.2.0.eb --- .../c/cairo/cairo-1.18.0-GCCcore-13.2.0.eb | 51 ++++++++++++++++++ .../g/GLib/GLib-2.78.1-GCCcore-13.2.0.eb | 53 +++++++++++++++++++ ...ect-Introspection-1.78.1-GCCcore-13.2.0.eb | 44 +++++++++++++++ .../p/pixman/pixman-0.42.2-GCCcore-13.2.0.eb | 28 ++++++++++ 4 files changed, 176 insertions(+) create mode 100644 easybuild/easyconfigs/c/cairo/cairo-1.18.0-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/g/GLib/GLib-2.78.1-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.78.1-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/p/pixman/pixman-0.42.2-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.18.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/c/cairo/cairo-1.18.0-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..e1033ed8ada --- /dev/null +++ b/easybuild/easyconfigs/c/cairo/cairo-1.18.0-GCCcore-13.2.0.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': '13.2.0'} + +source_urls = [ + 'https://cairographics.org/releases/', + 'https://cairographics.org/snapshots/' +] +sources = [SOURCE_TAR_XZ] +checksums = ['243a0736b978a33dee29f9cca7521733b78a65b5418206fef7bd1c3d4cf10b64'] + +builddependencies = [ + ('binutils', '2.40'), + ('pkgconf', '2.0.3'), + ('Ninja', '1.11.1'), + ('Meson', '1.2.3'), +] +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.2.13'), + ('libpng', '1.6.40'), + ('freetype', '2.13.2'), + ('pixman', '0.42.2'), + ('expat', '2.5.0'), + ('GLib', '2.78.1'), + ('X11', '20231019'), +] + +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/g/GLib/GLib-2.78.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/g/GLib/GLib-2.78.1-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..44fbd9759a5 --- /dev/null +++ b/easybuild/easyconfigs/g/GLib/GLib-2.78.1-GCCcore-13.2.0.eb @@ -0,0 +1,53 @@ +easyblock = 'MesonNinja' + +name = 'GLib' +version = '2.78.1' + +homepage = 'https://www.gtk.org/' +description = """GLib is one of the base libraries of the GTK+ project""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['915bc3d0f8507d650ead3832e2f8fb670fce59aac4d7754a7dab6f1e6fed78b2'] + +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', '3.11.5'), + ('Meson', '1.2.3'), + ('Ninja', '1.11.1'), + ('binutils', '2.40'), + ('pkgconf', '2.0.3'), +] + +dependencies = [ + ('libffi', '3.4.4'), + ('gettext', '0.22'), + ('libxml2', '2.11.5'), + ('PCRE2', '10.42'), + ('util-linux', '2.39'), +] + +# 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' diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.78.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.78.1-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..1a8a0f4320b --- /dev/null +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.78.1-GCCcore-13.2.0.eb @@ -0,0 +1,44 @@ +easyblock = 'MesonNinja' + +name = 'GObject-Introspection' +version = '1.78.1' + +homepage = 'https://gi.readthedocs.io/en/latest/' +description = """GObject introspection is a middleware layer between C libraries + (using GObject) and language bindings. The C library can be scanned at + compile time and generate a metadata file, in addition to the actual + native C library. Then at runtime, language bindings can read this + metadata and automatically provide bindings to call into the C library.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['bd7babd99af7258e76819e45ba4a6bc399608fe762d83fde3cac033c50841bb4'] + +builddependencies = [ + ('binutils', '2.40'), + ('pkgconf', '2.0.3'), + ('Meson', '1.2.3'), + ('Ninja', '1.11.1'), + ('flex', '2.6.4'), + ('Bison', '3.8.2'), + ('cairo', '1.18.0'), +] + +dependencies = [ + ('Python', '3.11.5'), + ('GLib', '2.78.1'), + ('libffi', '3.4.4'), + ('util-linux', '2.39'), +] + +preconfigopts = "env GI_SCANNER_DISABLE_CACHE=true " + +sanity_check_paths = { + 'files': ['bin/g-ir-%s' % x for x in ['annotation-tool', 'compiler', 'generate', 'scanner']] + + ['lib/libgirepository-1.0.' + SHLIB_EXT], + 'dirs': ['include', 'share'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/pixman/pixman-0.42.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/pixman/pixman-0.42.2-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..2d5befc2cf5 --- /dev/null +++ b/easybuild/easyconfigs/p/pixman/pixman-0.42.2-GCCcore-13.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'pixman' +version = '0.42.2' + +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': '13.2.0'} + +source_urls = ['https://cairographics.org/releases/'] +sources = [SOURCE_TAR_GZ] +checksums = ['ea1480efada2fd948bc75366f7c349e1c96d3297d09a3fe62626e38e234a625e'] + +builddependencies = [ + ('binutils', '2.40'), +] + +sanity_check_paths = { + 'files': ['lib/libpixman-1.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' From 5ea5c15f89deb42409baf09e42e642954d35f2ea Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 3 Nov 2023 14:02:20 +0100 Subject: [PATCH 129/599] Remove outdated configure option from FriBidi-1.0.12 --- .../easyconfigs/f/FriBidi/FriBidi-1.0.12-GCCcore-11.3.0.eb | 2 -- .../easyconfigs/f/FriBidi/FriBidi-1.0.12-GCCcore-12.2.0.eb | 2 -- .../easyconfigs/f/FriBidi/FriBidi-1.0.12-GCCcore-12.3.0.eb | 2 -- 3 files changed, 6 deletions(-) diff --git a/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.12-GCCcore-11.3.0.eb b/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.12-GCCcore-11.3.0.eb index 65c4eb01b1c..5bcf88c38fe 100644 --- a/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.12-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.12-GCCcore-11.3.0.eb @@ -21,8 +21,6 @@ builddependencies = [ ('pkgconf', '1.8.0'), ] -configopts = '--disable-docs' - sanity_check_paths = { 'files': ['bin/%(namelower)s', 'include/%(namelower)s/%(namelower)s.h', 'lib/lib%%(namelower)s.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.12-GCCcore-12.2.0.eb b/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.12-GCCcore-12.2.0.eb index 97c8eece78b..357b9f24de3 100644 --- a/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.12-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.12-GCCcore-12.2.0.eb @@ -21,8 +21,6 @@ builddependencies = [ ('pkgconf', '1.9.3'), ] -configopts = '--disable-docs' - sanity_check_paths = { 'files': ['bin/%(namelower)s', 'include/%(namelower)s/%(namelower)s.h', 'lib/lib%%(namelower)s.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.12-GCCcore-12.3.0.eb b/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.12-GCCcore-12.3.0.eb index df4dacf597f..4df1d5562a9 100644 --- a/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.12-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.12-GCCcore-12.3.0.eb @@ -21,8 +21,6 @@ builddependencies = [ ('Autotools', '20220317'), ] -configopts = '--disable-docs' - sanity_check_paths = { 'files': ['bin/%(namelower)s', 'include/%(namelower)s/%(namelower)s.h', 'lib/lib%%(namelower)s.%s' % SHLIB_EXT], From fb6632a91a6be556e646ee44bfb78af7275b3041 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 3 Nov 2023 14:04:39 +0100 Subject: [PATCH 130/599] Fix patch and C++ standard --- easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022b.eb | 4 +--- ...rch-1.13.1_workaround-gcc12-destructor-exception-bug.patch | 2 +- 2 files changed, 2 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022b.eb index 7d768022015..45ffe3f1e20 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022b.eb @@ -97,7 +97,7 @@ checksums = [ {'PyTorch-1.13.1_skip-tests-without-fbgemm.patch': '481e595f673baf8ae58b41697a6792b83048b0264aa79b422f48cd8c22948bb7'}, {'PyTorch-1.13.1_workaround-gcc12-destructor-exception-bug.patch': - 'd46412fe917110c197e4e2c572fc577644bd6b117c99dc8c57fa96b69d5456dc'}, + 'a09a2d7ebd428c65988729578bb3fa372565ba176ab9ed7abf11f6fcb15e903e'}, ] osdependencies = [OS_PKG_IBVERBS_DEV] @@ -126,8 +126,6 @@ dependencies = [ ('expecttest', '0.1.3'), ] -custom_opts = ['CMAKE_CXX_STANDARD=17'] - excluded_tests = { '': [ # This test seems to take too long on NVIDIA Ampere at least. diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_workaround-gcc12-destructor-exception-bug.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_workaround-gcc12-destructor-exception-bug.patch index b1bd76bc125..63c3ab6c425 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_workaround-gcc12-destructor-exception-bug.patch +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_workaround-gcc12-destructor-exception-bug.patch @@ -62,7 +62,7 @@ index 89256c64bba..8514d08c8d0 100644 + return [f = f](Arg... args) -> result_type { HANDLE_TH_ERRORS - return f(std::forward>(args)...); -+ if constexpr (std::is_void_v) { ++ if constexpr (std::is_void::value) { + c10::guts::invoke(f, std::forward>(args)...); + FLUSH_TH_ERRORS + } else { From 2f60f846be1b0bc0e308e47db12108b06756bb1f Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 3 Nov 2023 16:35:23 +0000 Subject: [PATCH 131/599] adding easyconfigs: Autoconf-archive-2023.02.20-GCCcore-11.3.0.eb --- ...oconf-archive-2023.02.20-GCCcore-11.3.0.eb | 53 +++++++++++++++++++ 1 file changed, 53 insertions(+) create mode 100644 easybuild/easyconfigs/a/Autoconf-archive/Autoconf-archive-2023.02.20-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/a/Autoconf-archive/Autoconf-archive-2023.02.20-GCCcore-11.3.0.eb b/easybuild/easyconfigs/a/Autoconf-archive/Autoconf-archive-2023.02.20-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..7b10ea408dd --- /dev/null +++ b/easybuild/easyconfigs/a/Autoconf-archive/Autoconf-archive-2023.02.20-GCCcore-11.3.0.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 +# 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': '11.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['71d4048479ae28f1f5794619c3d72df9c01df49b1c628ef85fde37596dc31a33'] + +builddependencies = [ + ('binutils', '2.38'), + ('Autotools', '20220317'), + ('makeinfo', '6.8'), +] + +preconfigopts = 'autoreconf -i -f &&' + +sanity_check_paths = { + 'files': [], + 'dirs': ['share/%s' % x for x in + ['aclocal', 'doc', 'info']], +} + +moduleclass = 'devel' From 4ce4e29f826448897ef7677ce234298f3e1e68e8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sat, 4 Nov 2023 00:08:15 +0100 Subject: [PATCH 132/599] adding easyconfigs: ICU-74.1-GCCcore-13.2.0.eb, nodejs-20.9.0-GCCcore-13.2.0.eb --- .../i/ICU/ICU-74.1-GCCcore-13.2.0.eb | 29 ++++++++++ .../n/nodejs/nodejs-20.9.0-GCCcore-13.2.0.eb | 54 +++++++++++++++++++ 2 files changed, 83 insertions(+) create mode 100644 easybuild/easyconfigs/i/ICU/ICU-74.1-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/n/nodejs/nodejs-20.9.0-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/i/ICU/ICU-74.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/i/ICU/ICU-74.1-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..db1bede945b --- /dev/null +++ b/easybuild/easyconfigs/i/ICU/ICU-74.1-GCCcore-13.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'ICU' +version = '74.1' + +homepage = 'https://icu.unicode.org' +description = """ICU is a mature, widely used set of C/C++ and Java libraries providing Unicode and Globalization + support for software applications.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/unicode-org/icu/releases/download/release-%(version_major)s-%(version_minor)s'] +sources = ['icu4c-%(version_major)s_%(version_minor)s-src.tgz'] +checksums = ['86ce8e60681972e60e4dcb2490c697463fcec60dd400a5f9bffba26d0b52b8d0'] + +builddependencies = [ + ('binutils', '2.40'), + ('Python', '3.11.5'), +] + +start_dir = 'source' + +sanity_check_paths = { + 'files': ['lib/libicu%s.%s' % (x, SHLIB_EXT) for x in ['data', 'i18n', 'io', 'test', 'tu', 'uc']], + 'dirs': ['bin', 'include/unicode', 'share/icu', 'share/man'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/nodejs/nodejs-20.9.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/n/nodejs/nodejs-20.9.0-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..24be2bb275b --- /dev/null +++ b/easybuild/easyconfigs/n/nodejs/nodejs-20.9.0-GCCcore-13.2.0.eb @@ -0,0 +1,54 @@ +easyblock = 'ConfigureMake' + +name = 'nodejs' +version = '20.9.0' # LTS on 2023-11-03 +local_libversion = '115' + +homepage = 'https://nodejs.org' +description = """Node.js is a platform built on Chrome's JavaScript runtime + for easily building fast, scalable network applications. Node.js uses an + event-driven, non-blocking I/O model that makes it lightweight and efficient, + perfect for data-intensive real-time applications that run across distributed devices.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://nodejs.org/dist/v%(version)s/'] +sources = ['node-v%(version)s.tar.gz'] +checksums = ['a7e6547a951406e4e546a74160ed27b26f9abd4baf7c44dd5a0fa992852d0cfa'] + +builddependencies = [ + ('binutils', '2.40'), + ('Python', '3.11.5'), + ('pkgconf', '2.0.3'), +] + +dependencies = [ + ('ICU', '74.1'), + ('OpenSSL', '1.1', '', SYSTEM), +] + +# Use ICU and OpenSSL from EasyBuild +local_common_configopts = "--with-intl=system-icu --shared-openssl " + +configopts = [ + local_common_configopts, # Static build + '--shared %s' % local_common_configopts, # Build libnode.so in a second run +] + +# Link libv8 libs to libnode +local_extra_sonames = ['libnode', 'libv8', 'libv8_libbase', 'libv8_libplatform'] +local_extra_libs = ['%s.%s' % (x, SHLIB_EXT) for x in local_extra_sonames] +local_libnode_real = "libnode.%s.%s" % (SHLIB_EXT, local_libversion) + +postinstallcmds = [ + "cd %%(installdir)s/lib && ln -s %s %s" % (local_libnode_real, x) for x in local_extra_libs +] + +sanity_check_paths = { + 'files': ['bin/node', 'bin/npm'] + ['lib/%s' % x for x in [local_libnode_real] + local_extra_libs], + 'dirs': ['lib/node_modules', 'include/node'] +} + +sanity_check_commands = ["node --help"] + +moduleclass = 'lang' From cd9666e43d7de50038b4e27d62326eabe99c8825 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sat, 4 Nov 2023 02:33:03 +0100 Subject: [PATCH 133/599] adding easyconfigs: FFmpeg-6.0-GCCcore-13.2.0.eb, LAME-3.100-GCCcore-13.2.0.eb, FriBidi-1.0.13-GCCcore-13.2.0.eb, SDL2-2.28.5-GCCcore-13.2.0.eb --- .../f/FFmpeg/FFmpeg-6.0-GCCcore-13.2.0.eb | 45 +++++++++++++++++++ .../FriBidi/FriBidi-1.0.13-GCCcore-13.2.0.eb | 32 +++++++++++++ .../l/LAME/LAME-3.100-GCCcore-13.2.0.eb | 36 +++++++++++++++ .../s/SDL2/SDL2-2.28.5-GCCcore-13.2.0.eb | 26 +++++++++++ 4 files changed, 139 insertions(+) create mode 100644 easybuild/easyconfigs/f/FFmpeg/FFmpeg-6.0-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.13-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/s/SDL2/SDL2-2.28.5-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-6.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-6.0-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..fab8972c089 --- /dev/null +++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-6.0-GCCcore-13.2.0.eb @@ -0,0 +1,45 @@ +easyblock = 'ConfigureMake' + +name = 'FFmpeg' +version = '6.0' + +homepage = 'https://www.ffmpeg.org/' +description = "A complete, cross-platform solution to record, convert and stream audio and video." + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://%(namelower)s.org/releases/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['47d062731c9f66a78380e35a19aac77cebceccd1c7cc309b9c82343ffc430c3d'] + +builddependencies = [ + ('binutils', '2.40'), + ('pkgconf', '2.0.3'), + ('ffnvcodec', '12.1.14.0', '', SYSTEM), # optional nvenc/dec support +] +dependencies = [ + ('NASM', '2.16.01'), + ('zlib', '1.2.13'), + ('bzip2', '1.0.8'), + ('x264', '20231019'), + ('LAME', '3.100'), + ('x265', '3.5'), + ('X11', '20231019'), + ('freetype', '2.13.2'), + ('fontconfig', '2.14.2'), + ('FriBidi', '1.0.13'), + ('SDL2', '2.28.5'), +] + +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' + +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-1.0.13-GCCcore-13.2.0.eb b/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.13-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..359c71849ca --- /dev/null +++ b/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.13-GCCcore-13.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'FriBidi' +version = '1.0.13' + +homepage = 'https://github.com/fribidi/fribidi' + +description = """ + The Free Implementation of the Unicode Bidirectional Algorithm. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://github.com/fribidi/fribidi/releases/download/v%(version)s'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['7fa16c80c81bd622f7b198d31356da139cc318a63fc7761217af4130903f54a2'] + +builddependencies = [ + ('binutils', '2.40'), + ('pkgconf', '2.0.3'), + ('Autotools', '20220317'), +] + +configopts = '--disable-docs' + +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/l/LAME/LAME-3.100-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..7b163dff699 --- /dev/null +++ b/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-13.2.0.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': '13.2.0'} + +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', '2.40'), + ('Autotools', '20220317'), +] + +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': [], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/SDL2/SDL2-2.28.5-GCCcore-13.2.0.eb b/easybuild/easyconfigs/s/SDL2/SDL2-2.28.5-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..5b5d1835fcb --- /dev/null +++ b/easybuild/easyconfigs/s/SDL2/SDL2-2.28.5-GCCcore-13.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'SDL2' +version = '2.28.5' + +homepage = 'https://www.libsdl.org/' +description = "SDL: Simple DirectMedia Layer, a cross-platform multimedia library" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://www.libsdl.org/release/'] +sources = [SOURCE_TAR_GZ] +checksums = ['332cb37d0be20cb9541739c61f79bae5a477427d79ae85e352089afdaf6666e4'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('X11', '20231019'), +] + +sanity_check_paths = { + 'files': ['bin/sdl2-config', 'lib/libSDL2.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' From a4293e61408598581d873a829c41f356a53547db Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sat, 4 Nov 2023 03:01:47 +0100 Subject: [PATCH 134/599] adding easyconfigs: re2c-3.1-GCCcore-13.2.0.eb, JasPer-4.0.0-GCCcore-13.2.0.eb, graphite2-1.3.14-GCCcore-13.2.0.eb, NSPR-4.35-GCCcore-13.2.0.eb, NSS-3.94-GCCcore-13.2.0.eb --- .../graphite2-1.3.14-GCCcore-13.2.0.eb | 27 ++++++++ .../j/JasPer/JasPer-4.0.0-GCCcore-13.2.0.eb | 36 +++++++++++ .../n/NSPR/NSPR-4.35-GCCcore-13.2.0.eb | 30 +++++++++ .../n/NSS/NSS-3.94-GCCcore-13.2.0.eb | 61 +++++++++++++++++++ .../r/re2c/re2c-3.1-GCCcore-13.2.0.eb | 32 ++++++++++ 5 files changed, 186 insertions(+) create mode 100644 easybuild/easyconfigs/g/graphite2/graphite2-1.3.14-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/j/JasPer/JasPer-4.0.0-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/n/NSPR/NSPR-4.35-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/n/NSS/NSS-3.94-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/r/re2c/re2c-3.1-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/g/graphite2/graphite2-1.3.14-GCCcore-13.2.0.eb b/easybuild/easyconfigs/g/graphite2/graphite2-1.3.14-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..f72fbb4cc7a --- /dev/null +++ b/easybuild/easyconfigs/g/graphite2/graphite2-1.3.14-GCCcore-13.2.0.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': '13.2.0'} + +source_urls = ['https://github.com/silnrsi/graphite/archive/'] +sources = ['%(version)s.zip'] +checksums = ['36e15981af3bf7a3ca3daf53295c8ffde04cf7d163e3474e4d0836e2728b4149'] + +builddependencies = [ + ('CMake', '3.27.6'), + ('binutils', '2.40'), +] + +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/j/JasPer/JasPer-4.0.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/j/JasPer/JasPer-4.0.0-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..ab5a601586c --- /dev/null +++ b/easybuild/easyconfigs/j/JasPer/JasPer-4.0.0-GCCcore-13.2.0.eb @@ -0,0 +1,36 @@ +easyblock = 'CMakeMake' + +name = 'JasPer' +version = '4.0.0' + +homepage = 'https://www.ece.uvic.ca/~frodo/jasper/' + +description = """ + The JasPer Project is an open-source initiative to provide a free + software-based reference implementation of the codec specified in + the JPEG-2000 Part-1 standard. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +github_account = 'jasper-software' +source_urls = [GITHUB_SOURCE] +sources = ['version-%(version)s.tar.gz'] +checksums = ['977c4c2e4210f4e37313cd2232d99e73d57ab561917b3c060bcdd5e83a0a13f1'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.27.6'), +] + +configopts = '-DJAS_ENABLE_DOC=OFF ' + +sanity_check_paths = { + 'files': ['bin/jasper', ('lib/libjasper.%s' % SHLIB_EXT, 'lib64/libjasper.%s' % SHLIB_EXT)], + 'dirs': ['include'], +} + +sanity_check_commands = ['jasper --version'] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/n/NSPR/NSPR-4.35-GCCcore-13.2.0.eb b/easybuild/easyconfigs/n/NSPR/NSPR-4.35-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..dd289fea3b1 --- /dev/null +++ b/easybuild/easyconfigs/n/NSPR/NSPR-4.35-GCCcore-13.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'NSPR' +version = '4.35' + +homepage = 'https://developer.mozilla.org/en-US/docs/Mozilla/Projects/NSPR' +description = """Netscape Portable Runtime (NSPR) provides a platform-neutral API for system level + and libc-like functions.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://ftp.mozilla.org/pub/nspr/releases/v%(version)s/src/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['7ea3297ea5969b5d25a5dd8d47f2443cda88e9ee746301f6e1e1426f8a6abc8f'] + +builddependencies = [('binutils', '2.40')] + +configopts = "--disable-debug --enable-optimize --enable-64bit" + +sanity_check_paths = { + 'files': ['bin/nspr-config', 'lib/libnspr%(version_major)s.a', 'lib/libnspr%%(version_major)s.%s' % SHLIB_EXT, + 'lib/libplc%(version_major)s.a', 'lib/libplc%%(version_major)s.%s' % SHLIB_EXT, + 'lib/libplds%(version_major)s.a', 'lib/libplds%%(version_major)s.%s' % SHLIB_EXT, + 'lib/pkgconfig/nspr.pc'], + 'dirs': ['include/nspr'], +} + +sanity_check_commands = ["nspr-config --version"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NSS/NSS-3.94-GCCcore-13.2.0.eb b/easybuild/easyconfigs/n/NSS/NSS-3.94-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..98dcf8eb5b5 --- /dev/null +++ b/easybuild/easyconfigs/n/NSS/NSS-3.94-GCCcore-13.2.0.eb @@ -0,0 +1,61 @@ +easyblock = 'MakeCp' + +name = 'NSS' +version = '3.94' + +homepage = 'https://developer.mozilla.org/en-US/docs/Mozilla/Projects/NSS' +description = """Network Security Services (NSS) is a set of libraries designed to support cross-platform development + of security-enabled client and server applications.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://ftp.mozilla.org/pub/security/nss/releases/NSS_%s_RTM/src/' % version.replace('.', '_')] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + 'NSS-3.39_pkgconfig.patch', + 'NSS-3.55_fix-ftbfs-glibc-invalid-oob-error.patch', +] +checksums = [ + {'nss-3.94.tar.gz': '463ae180ee9e5ee9e3ad4f629326657e236780cc865572a930a16520abad9dd8'}, + {'NSS-3.39_pkgconfig.patch': '5c4b55842e5afd1e8e67b90635f6474510b89242963c4ac2622d3e3da9062774'}, + {'NSS-3.55_fix-ftbfs-glibc-invalid-oob-error.patch': + '15768297c5dd6918132af281531afcfe3e358f45a00bc2655d20a6cbe4310a9b'}, +] + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('NSPR', '4.35'), + ('zlib', '1.2.13'), +] + +# building in parallel fails +parallel = 1 + +# disable use of -Werror to work around compilation errors with newer glibc versions, +# see also https://sourceware.org/bugzilla/show_bug.cgi?id=27476 +buildopts = "NSS_ENABLE_WERROR=0 " +# fix for not being able to find header files +buildopts += 'BUILD_OPT=1 USE_64=1 CPATH="$EBROOTNSPR/include/nspr:$CPATH" ' +# fix c standard causing missing functions +buildopts += 'OS_REL_CFLAGS="-D_XOPEN_SOURCE " && ' +# also install pkgconfig file (see patch) +buildopts += "cd config && make PREFIX=%(installdir)s BUILD_OPT=1 USE_64=1 && cd -" +# optional testsuite (takes a long time) +# buildopts += " && cd %(builddir)s/%(namelower)s-%(version)s/%(namelower)s/tests && BUILD_OPT=1 USE_64=1 ./all.sh " + +files_to_copy = ['../dist/Linux*.OBJ/*', (['../dist/public/*'], 'include')] + +sanity_check_paths = { + 'files': ['bin/nss-config', 'bin/multinit', 'lib/libnss.a'], + 'dirs': ['include/dbm', 'include/nss'], +} + +sanity_check_commands = [ + "multinit --help", + "nss-config --version", +] + +modextrapaths = {'CPATH': 'include/nss'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/r/re2c/re2c-3.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/r/re2c/re2c-3.1-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..4db6f2daf45 --- /dev/null +++ b/easybuild/easyconfigs/r/re2c/re2c-3.1-GCCcore-13.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 're2c' +version = '3.1' + +homepage = 'https://re2c.org' +description = """re2c is a free and open-source lexer generator for C and C++. Its main goal is generating +fast lexers: at least as fast as their reasonably optimized hand-coded counterparts. Instead of using +traditional table-driven approach, re2c encodes the generated finite state automata directly in the form +of conditional jumps and comparisons.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://github.com/skvadrik/re2c/releases/download/%(version)s'] +sources = ['%(name)s-%(version)s.tar.xz'] +checksums = ['0ac299ad359e3f512b06a99397d025cfff81d3be34464ded0656f8a96676c029'] + +builddependencies = [ + ('binutils', '2.40'), + ('Python', '3.11.5') +] + +configopts = "--disable-rust" + +sanity_check_paths = { + 'files': ['bin/re2c'], + 'dirs': [], +} + +sanity_check_commands = ["re2c --help"] + +moduleclass = 'tools' From bcbe5a69c70f4c3279fee3105ac168a537bebdc0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sat, 4 Nov 2023 12:18:40 +0100 Subject: [PATCH 135/599] Add ffnvcodec --- .../f/ffnvcodec/ffnvcodec-12.1.14.0.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/f/ffnvcodec/ffnvcodec-12.1.14.0.eb diff --git a/easybuild/easyconfigs/f/ffnvcodec/ffnvcodec-12.1.14.0.eb b/easybuild/easyconfigs/f/ffnvcodec/ffnvcodec-12.1.14.0.eb new file mode 100644 index 00000000000..ffab57a6520 --- /dev/null +++ b/easybuild/easyconfigs/f/ffnvcodec/ffnvcodec-12.1.14.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'ffnvcodec' +version = '12.1.14.0' + +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 = ['a7da1532e61dee98c2a917a7a3f9127b94a1d72d44aa1cce23e3d797b114d0c0'] + +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' From b52852afdfdc9152349b4ebb56ee3379202a2825 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sat, 4 Nov 2023 12:19:05 +0100 Subject: [PATCH 136/599] Drop fribidi configopts --- .../easyconfigs/f/FriBidi/FriBidi-1.0.13-GCCcore-13.2.0.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.13-GCCcore-13.2.0.eb b/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.13-GCCcore-13.2.0.eb index 359c71849ca..bd7cef70af5 100644 --- a/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.13-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.13-GCCcore-13.2.0.eb @@ -21,8 +21,6 @@ builddependencies = [ ('Autotools', '20220317'), ] -configopts = '--disable-docs' - sanity_check_paths = { 'files': ['bin/%(namelower)s', 'include/%(namelower)s/%(namelower)s.h', 'lib/lib%%(namelower)s.%s' % SHLIB_EXT], From 2674cd7d3183ef81b3e90aac28f6b10f4762a030 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Sat, 4 Nov 2023 11:27:46 +0000 Subject: [PATCH 137/599] No checksum for git download --- easybuild/easyconfigs/f/ffnvcodec/ffnvcodec-12.1.14.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/ffnvcodec/ffnvcodec-12.1.14.0.eb b/easybuild/easyconfigs/f/ffnvcodec/ffnvcodec-12.1.14.0.eb index ffab57a6520..cf37dfdf36b 100644 --- a/easybuild/easyconfigs/f/ffnvcodec/ffnvcodec-12.1.14.0.eb +++ b/easybuild/easyconfigs/f/ffnvcodec/ffnvcodec-12.1.14.0.eb @@ -18,7 +18,7 @@ sources = [{ }, 'filename': SOURCE_TAR_GZ, }] -checksums = ['a7da1532e61dee98c2a917a7a3f9127b94a1d72d44aa1cce23e3d797b114d0c0'] +checksums = [None] skipsteps = ['configure'] From 7cfd61b5632d16cf7c210d39243441be1db1127b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sat, 4 Nov 2023 14:00:54 +0100 Subject: [PATCH 138/599] adding easyconfigs: Wayland-1.22.0-GCCcore-13.2.0.eb, PyCairo-1.25.1-GCCcore-13.2.0.eb, ATK-2.38.0-GCCcore-13.2.0.eb, Gdk-Pixbuf-2.42.10-GCCcore-13.2.0.eb, at-spi2-core-2.50.0-GCCcore-13.2.0.eb, HarfBuzz-8.2.2-GCCcore-13.2.0.eb, PyGObject-3.46.0-GCCcore-13.2.0.eb, Graphene-1.10.8-GCCcore-13.2.0.eb, at-spi2-atk-2.38.0-GCCcore-13.2.0.eb, Pango-1.51.0-GCCcore-13.2.0.eb, elfutils-0.190-GCCcore-13.2.0.eb, libepoxy-1.5.10-GCCcore-13.2.0.eb --- .../a/ATK/ATK-2.38.0-GCCcore-13.2.0.eb | 39 ++++++++++++ .../at-spi2-atk-2.38.0-GCCcore-13.2.0.eb | 37 +++++++++++ .../at-spi2-core-2.50.0-GCCcore-13.2.0.eb | 40 ++++++++++++ .../elfutils/elfutils-0.190-GCCcore-13.2.0.eb | 41 ++++++++++++ .../Gdk-Pixbuf-2.42.10-GCCcore-13.2.0.eb | 46 ++++++++++++++ .../Graphene-1.10.8-GCCcore-13.2.0.eb | 32 ++++++++++ .../HarfBuzz/HarfBuzz-8.2.2-GCCcore-13.2.0.eb | 38 +++++++++++ .../libepoxy-1.5.10-GCCcore-13.2.0.eb | 37 +++++++++++ .../p/Pango/Pango-1.51.0-GCCcore-13.2.0.eb | 41 ++++++++++++ .../PyCairo/PyCairo-1.25.1-GCCcore-13.2.0.eb | 38 +++++++++++ .../PyGObject-3.46.0-GCCcore-13.2.0.eb | 38 +++++++++++ .../Wayland/Wayland-1.22.0-GCCcore-13.2.0.eb | 63 +++++++++++++++++++ 12 files changed, 490 insertions(+) create mode 100644 easybuild/easyconfigs/a/ATK/ATK-2.38.0-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/a/at-spi2-atk/at-spi2-atk-2.38.0-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.50.0-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/e/elfutils/elfutils-0.190-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.42.10-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/g/Graphene/Graphene-1.10.8-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-8.2.2-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.10-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/p/Pango/Pango-1.51.0-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/p/PyCairo/PyCairo-1.25.1-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/p/PyGObject/PyGObject-3.46.0-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/w/Wayland/Wayland-1.22.0-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/a/ATK/ATK-2.38.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/a/ATK/ATK-2.38.0-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..6093e7836d8 --- /dev/null +++ b/easybuild/easyconfigs/a/ATK/ATK-2.38.0-GCCcore-13.2.0.eb @@ -0,0 +1,39 @@ +easyblock = 'MesonNinja' + +name = 'ATK' +version = '2.38.0' + +homepage = 'https://developer.gnome.org/atk/' +description = """ + ATK provides the set of accessibility interfaces that are implemented by other + toolkits and applications. Using the ATK interfaces, accessibility tools have + full access to view and control running applications. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['ac4de2a4ef4bd5665052952fe169657e65e895c5057dffb3c2a810f6191a0c36'] + +builddependencies = [ + ('binutils', '2.40'), + ('Meson', '1.2.3'), + ('Ninja', '1.11.1'), + ('pkgconf', '2.0.3'), + ('GObject-Introspection', '1.78.1'), +] + +dependencies = [ + ('GLib', '2.78.1'), +] + +configopts = "--buildtype=release --default-library=both " +configopts += "-Dintrospection=true " + +sanity_check_paths = { + 'files': ['lib/libatk-1.0.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/a/at-spi2-atk/at-spi2-atk-2.38.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/a/at-spi2-atk/at-spi2-atk-2.38.0-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..4f2a709e36b --- /dev/null +++ b/easybuild/easyconfigs/a/at-spi2-atk/at-spi2-atk-2.38.0-GCCcore-13.2.0.eb @@ -0,0 +1,37 @@ +easyblock = 'MesonNinja' + +name = 'at-spi2-atk' +version = '2.38.0' + +homepage = 'https://wiki.gnome.org/Accessibility' +description = "AT-SPI 2 toolkit bridge" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['cfa008a5af822b36ae6287f18182c40c91dd699c55faa38605881ed175ca464f'] + +builddependencies = [ + ('binutils', '2.40'), + ('Meson', '1.2.3'), + ('Ninja', '1.11.1'), + ('pkgconf', '2.0.3'), +] + +dependencies = [ + ('GLib', '2.78.1'), + ('DBus', '1.15.8'), + ('at-spi2-core', '2.50.0'), + ('libxml2', '2.11.5'), + ('ATK', '2.38.0'), +] + +configopts = "--libdir lib " + +sanity_check_paths = { + 'files': ['lib/libatk-bridge-2.0.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.50.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.50.0-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..2a4ccd76bff --- /dev/null +++ b/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.50.0-GCCcore-13.2.0.eb @@ -0,0 +1,40 @@ +easyblock = 'MesonNinja' + +name = 'at-spi2-core' +version = '2.50.0' + +homepage = 'https://wiki.gnome.org/Accessibility' +description = """ + Assistive Technology Service Provider Interface. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['e9f5a8c8235c9dd963b2171de9120301129c677dde933955e1df618b949c4adc'] + +builddependencies = [ + ('binutils', '2.40'), + ('Meson', '1.2.3'), + ('Ninja', '1.11.1'), + ('GObject-Introspection', '1.78.1'), + ('gettext', '0.22'), + ('pkgconf', '2.0.3'), +] + +dependencies = [ + ('GLib', '2.78.1'), + ('DBus', '1.15.8'), + ('X11', '20231019'), +] + +# Hard disable Dbus broker detection and (potential) use of systemd +configopts = "--libdir lib -Duse_systemd=false -Ddefault_bus=dbus-daemon" + +sanity_check_paths = { + 'files': ['lib/libatspi.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/e/elfutils/elfutils-0.190-GCCcore-13.2.0.eb b/easybuild/easyconfigs/e/elfutils/elfutils-0.190-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..83b0be058ef --- /dev/null +++ b/easybuild/easyconfigs/e/elfutils/elfutils-0.190-GCCcore-13.2.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'elfutils' +version = '0.190' + +homepage = 'https://elfutils.org/' + +description = """ + The elfutils project provides libraries and tools for ELF files + and DWARF data. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://sourceware.org/elfutils/ftp/%(version)s/'] +sources = [SOURCE_TAR_BZ2] +checksums = ['39bd8f1a338e2b7cd4abc3ff11a0eddc6e690f69578a57478d8179b4148708c8'] + +builddependencies = [ + ('M4', '1.4.19'), + ('pkgconf', '2.0.3'), +] + +dependencies = [ + ('binutils', '2.40'), + ('bzip2', '1.0.8'), + ('libarchive', '3.7.2'), + ('XZ', '5.4.4'), + ('zstd', '1.5.5'), +] + +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/g/Gdk-Pixbuf/Gdk-Pixbuf-2.42.10-GCCcore-13.2.0.eb b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.42.10-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..a66201f8def --- /dev/null +++ b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.42.10-GCCcore-13.2.0.eb @@ -0,0 +1,46 @@ +easyblock = 'MesonNinja' + +name = 'Gdk-Pixbuf' +version = '2.42.10' + +homepage = 'https://docs.gtk.org/gdk-pixbuf/' +description = """ + The Gdk Pixbuf is a toolkit for image loading and pixel buffer manipulation. + It is used by GTK+ 2 and GTK+ 3 to load and manipulate images. In the past it + was distributed as part of GTK+ 2 but it was split off into a separate package + in preparation for the change to GTK+ 3. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['ee9b6c75d13ba096907a2e3c6b27b61bcd17f5c7ebeab5a5b439d2f2e39fe44b'] + +builddependencies = [ + ('binutils', '2.40'), + ('Meson', '1.2.3'), + ('Ninja', '1.11.1'), + ('pkgconf', '2.0.3'), + ('GObject-Introspection', '1.78.1'), +] + +dependencies = [ + ('GLib', '2.78.1'), + ('libjpeg-turbo', '3.0.1'), + ('libpng', '1.6.40'), + ('LibTIFF', '4.6.0'), + ('X11', '20231019'), +] + +configopts = "--buildtype=release --default-library=both " +configopts += "-Dgio_sniffing=false -Dintrospection=enabled -Dman=false" + +sanity_check_paths = { + 'files': ['lib/libgdk_pixbuf-%(version_major)s.0.a', 'lib/libgdk_pixbuf-%%(version_major)s.0.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include/gdk-pixbuf-%(version_major)s.0', 'lib/gdk-pixbuf-%(version_major)s.0', 'share'], +} + +sanity_check_commands = ["gdk-pixbuf-pixdata --help"] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/Graphene/Graphene-1.10.8-GCCcore-13.2.0.eb b/easybuild/easyconfigs/g/Graphene/Graphene-1.10.8-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..b8b16bdc898 --- /dev/null +++ b/easybuild/easyconfigs/g/Graphene/Graphene-1.10.8-GCCcore-13.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'MesonNinja' + +name = 'Graphene' +version = '1.10.8' + +homepage = 'https://ebassi.github.io/graphene/' +description = "Graphene is a thin layer of types for graphic libraries" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +github_account = 'ebassi' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['922dc109d2dc5dc56617a29bd716c79dd84db31721a8493a13a5f79109a4a4ed'] + +builddependencies = [ + ('Meson', '1.2.3'), + ('Ninja', '1.11.1'), + ('pkgconf', '2.0.3'), + ('GObject-Introspection', '1.78.1'), + ('binutils', '2.40'), +] +dependencies = [('GLib', '2.78.1')] + +configopts = "-Dgobject_types=true -Dintrospection=enabled" + +sanity_check_paths = { + 'files': ['lib/libgraphene-1.0.%s' % SHLIB_EXT, 'share/gir-1.0/Graphene-1.0.gir'], + 'dirs': ['include/graphene-1.0', 'lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-8.2.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-8.2.2-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..87c73c5219b --- /dev/null +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-8.2.2-GCCcore-13.2.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'HarfBuzz' +version = '8.2.2' + +homepage = 'https://www.freedesktop.org/wiki/Software/HarfBuzz' +description = """HarfBuzz is an OpenType text shaping engine.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +github_account = 'harfbuzz' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['77c8c903f4539b050a6d3a5be79705c7ccf7b1cb66d68152a651486e261edbd2'] + +builddependencies = [ + ('binutils', '2.40'), + ('GObject-Introspection', '1.78.1'), + ('pkgconf', '2.0.3'), + ('Autotools', '20220317'), +] + +dependencies = [ + ('GLib', '2.78.1'), + ('ICU', '74.1'), + ('cairo', '1.18.0'), + ('freetype', '2.13.2'), +] + +preconfigopts = "./autogen.sh && " +configopts = "--enable-introspection=yes --with-gobject=yes --enable-static --enable-shared --with-cairo " + +sanity_check_paths = { + 'files': ['lib/libharfbuzz.%s' % SHLIB_EXT, 'bin/hb-view'], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.10-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.10-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..a3a41bd2a7a --- /dev/null +++ b/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.10-GCCcore-13.2.0.eb @@ -0,0 +1,37 @@ +easyblock = 'MesonNinja' + +name = 'libepoxy' +version = '1.5.10' + +homepage = 'https://github.com/anholt/libepoxy' +description = "Epoxy is a library for handling OpenGL function pointer management for you" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +github_account = 'anholt' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['a7ced37f4102b745ac86d6a70a9da399cc139ff168ba6b8002b4d8d43c900c15'] + +builddependencies = [ + ('binutils', '2.40'), + ('Meson', '1.2.3'), + ('Ninja', '1.11.1'), + ('pkgconf', '2.0.3'), +] + +dependencies = [ + ('X11', '20231019'), + ('Mesa', '23.1.9'), +] + +configopts = '-Degl=yes --libdir %(installdir)s/lib ' + +sanity_check_paths = { + 'files': ['include/epoxy/%s.h' % x for x in ['common', 'egl_generated', 'egl', 'gl_generated', + 'gl', 'glx_generated', 'glx']] + + ['lib/libepoxy.%s' % SHLIB_EXT], + 'dirs': ['lib'] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.51.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/Pango/Pango-1.51.0-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..c1a1fd7284b --- /dev/null +++ b/easybuild/easyconfigs/p/Pango/Pango-1.51.0-GCCcore-13.2.0.eb @@ -0,0 +1,41 @@ +easyblock = 'MesonNinja' + +name = 'Pango' +version = '1.51.0' + +homepage = 'https://www.pango.org/' +description = """Pango is a library for laying out and rendering of text, with an emphasis on internationalization. +Pango can be used anywhere that text layout is needed, though most of the work on Pango so far has been done in the +context of the GTK+ widget toolkit. Pango forms the core of text and font handling for GTK+-2.x.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['1d67f205bfc318c27a29cfdfb6828568df566795df0cb51d2189cde7f2d581e8'] + +builddependencies = [ + ('binutils', '2.40'), + ('Meson', '1.2.3'), + ('Ninja', '1.11.1'), + ('GObject-Introspection', '1.78.1'), + ('pkgconf', '2.0.3'), +] + +dependencies = [ + ('X11', '20231019'), + ('GLib', '2.78.1'), + ('cairo', '1.18.0'), + ('HarfBuzz', '8.2.2'), + ('FriBidi', '1.0.13'), +] + +configopts = "--buildtype=release --default-library=both " + +sanity_check_paths = { + 'files': ['bin/pango-view', 'lib/libpango-1.0.%s' % SHLIB_EXT, 'lib/libpangocairo-1.0.%s' % SHLIB_EXT, + 'lib/libpangoft2-1.0.%s' % SHLIB_EXT, 'lib/libpangoxft-1.0.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/PyCairo/PyCairo-1.25.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/PyCairo/PyCairo-1.25.1-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..2f139f4093d --- /dev/null +++ b/easybuild/easyconfigs/p/PyCairo/PyCairo-1.25.1-GCCcore-13.2.0.eb @@ -0,0 +1,38 @@ +# Need to use Meson instead of the "pip" installation +# See: https://github.com/pygobject/pycairo/issues/312 +easyblock = 'MesonNinja' + +name = 'PyCairo' +version = '1.25.1' + +homepage = 'https://pycairo.readthedocs.io/' +description = """Python bindings for the cairo library""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://github.com/pygobject/%(namelower)s/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['fabe2a6ae082e7970084ce61b29087f2211f098a099b0d6de68caac4be1263fb'] + +builddependencies = [ + ('binutils', '2.40'), + ('pkgconf', '2.0.3'), + ('Meson', '1.2.3'), + ('Ninja', '1.11.1'), +] + +dependencies = [ + ('Python', '3.11.5'), + ('cairo', '1.18.0'), +] + +sanity_check_paths = { + 'files': ['%s/py3cairo.%s' % (p, e) for (p, e) in [('include/pycairo', 'h'), ('lib/pkgconfig', 'pc')]], + 'dirs': ['lib/python%(pyshortver)s/site-packages/cairo'], +} + +modextrapaths = { + 'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/PyGObject/PyGObject-3.46.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/PyGObject/PyGObject-3.46.0-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..a70381c6579 --- /dev/null +++ b/easybuild/easyconfigs/p/PyGObject/PyGObject-3.46.0-GCCcore-13.2.0.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonPackage' + +name = 'PyGObject' +version = '3.46.0' + +homepage = 'https://pygobject.readthedocs.io/' +description = """PyGObject is a Python package which provides bindings for GObject based +libraries such as GTK, GStreamer, WebKitGTK, GLib, GIO and many more.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['481437b05af0a66b7c366ea052710eb3aacbb979d22d30b797f7ec29347ab1e6'] + +builddependencies = [ + ('binutils', '2.40'), + ('pkgconf', '2.0.3'), +] + +dependencies = [ + ('Python', '3.11.5'), + ('GLib', '2.78.1'), + ('GObject-Introspection', '1.78.1'), + ('PyCairo', '1.25.1'), +] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +sanity_check_paths = { + 'files': ['include/pygobject-%(version_major)s.0/pygobject.h'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +options = {'modulename': 'gi'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/w/Wayland/Wayland-1.22.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/w/Wayland/Wayland-1.22.0-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..dac0641eed7 --- /dev/null +++ b/easybuild/easyconfigs/w/Wayland/Wayland-1.22.0-GCCcore-13.2.0.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 = '1.22.0' + +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': '13.2.0'} + +builddependencies = [ + ('CMake', '3.27.6'), + ('Meson', '1.2.3'), + ('Ninja', '1.11.1'), + ('pkgconf', '2.0.3'), + ('binutils', '2.40'), +] + +dependencies = [ + ('libffi', '3.4.4'), + ('expat', '2.5.0'), + ('libxml2', '2.11.5'), +] + +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': ['1540af1ea698a471c2d8e9d288332c7e0fd360c8f1d12936ebb7e7cbc2425842'], + 'sources': [SOURCE_TAR_XZ], + 'configopts': "-Ddocumentation=false", + }), + ('wayland-protocols', '1.32', { + 'source_urls': ['https://gitlab.freedesktop.org/wayland/%(namelower)s/-/releases/%(version)s/downloads'], + 'checksums': ['7459799d340c8296b695ef857c07ddef24c5a09b09ab6a74f7b92640d2b1ba11'], + '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 67a1a1381c9c2275bbf162fb7ec0383a7ddb88f7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sat, 4 Nov 2023 14:02:42 +0100 Subject: [PATCH 139/599] checksum --- .../easyconfigs/e/elfutils/elfutils-0.190-GCCcore-13.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/elfutils/elfutils-0.190-GCCcore-13.2.0.eb b/easybuild/easyconfigs/e/elfutils/elfutils-0.190-GCCcore-13.2.0.eb index 83b0be058ef..1e9d836097e 100644 --- a/easybuild/easyconfigs/e/elfutils/elfutils-0.190-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/e/elfutils/elfutils-0.190-GCCcore-13.2.0.eb @@ -14,7 +14,7 @@ toolchain = {'name': 'GCCcore', 'version': '13.2.0'} source_urls = ['https://sourceware.org/elfutils/ftp/%(version)s/'] sources = [SOURCE_TAR_BZ2] -checksums = ['39bd8f1a338e2b7cd4abc3ff11a0eddc6e690f69578a57478d8179b4148708c8'] +checksums = ['8e00a3a9b5f04bc1dc273ae86281d2d26ed412020b391ffcc23198f10231d692'] builddependencies = [ ('M4', '1.4.19'), From 1940044ba64011c3ae8dda5b11e70991015ddf63 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sat, 4 Nov 2023 14:37:28 +0100 Subject: [PATCH 140/599] checksum --- easybuild/easyconfigs/p/Pango/Pango-1.51.0-GCCcore-13.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.51.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/Pango/Pango-1.51.0-GCCcore-13.2.0.eb index c1a1fd7284b..9040f4ef2dc 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.51.0-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.51.0-GCCcore-13.2.0.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'GCCcore', 'version': '13.2.0'} source_urls = [FTPGNOME_SOURCE] sources = [SOURCELOWER_TAR_XZ] -checksums = ['1d67f205bfc318c27a29cfdfb6828568df566795df0cb51d2189cde7f2d581e8'] +checksums = ['74efc109ae6f903bbe6af77eaa2ac6094b8ee245a2e23f132a7a8f0862d1a9f5'] builddependencies = [ ('binutils', '2.40'), From 1e875905f4aa8da17301171e622e2a924514ae09 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sat, 4 Nov 2023 14:38:26 +0100 Subject: [PATCH 141/599] Add dbus --- .../d/DBus/DBus-1.15.8-GCCcore-13.2.0.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/d/DBus/DBus-1.15.8-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/d/DBus/DBus-1.15.8-GCCcore-13.2.0.eb b/easybuild/easyconfigs/d/DBus/DBus-1.15.8-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..ec0ca4a6233 --- /dev/null +++ b/easybuild/easyconfigs/d/DBus/DBus-1.15.8-GCCcore-13.2.0.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': '13.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://dbus.freedesktop.org/releases/dbus'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['84fc597e6ec82f05dc18a7d12c17046f95bad7be99fc03c15bc254c4701ed204'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.27.6'), + ('pkgconf', '2.0.3'), +] + +dependencies = [ + ('expat', '2.5.0'), +] + +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 a74f80811f6e5cc5c69dffb4976a52e80f03ffb7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sat, 4 Nov 2023 14:39:06 +0100 Subject: [PATCH 142/599] style --- .../g/Gdk-Pixbuf/Gdk-Pixbuf-2.42.10-GCCcore-13.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.42.10-GCCcore-13.2.0.eb b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.42.10-GCCcore-13.2.0.eb index a66201f8def..ac99b2584dd 100644 --- a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.42.10-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.42.10-GCCcore-13.2.0.eb @@ -1,7 +1,7 @@ easyblock = 'MesonNinja' name = 'Gdk-Pixbuf' -version = '2.42.10' +version = '2.42.10' homepage = 'https://docs.gtk.org/gdk-pixbuf/' description = """ From e412de696a67a3808a3dc6e7ccc1d5000c7bfe70 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sat, 4 Nov 2023 15:48:03 +0100 Subject: [PATCH 143/599] fix dbus --- easybuild/easyconfigs/d/DBus/DBus-1.15.8-GCCcore-13.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/DBus/DBus-1.15.8-GCCcore-13.2.0.eb b/easybuild/easyconfigs/d/DBus/DBus-1.15.8-GCCcore-13.2.0.eb index ec0ca4a6233..21251602a0c 100644 --- a/easybuild/easyconfigs/d/DBus/DBus-1.15.8-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/d/DBus/DBus-1.15.8-GCCcore-13.2.0.eb @@ -32,7 +32,7 @@ dependencies = [ configopts = '-DENABLE_SYSTEMD=OFF ' # disable documentation -configopts = '-DDBUS_ENABLE_XML_DOCS=OFF -DDBUS_ENABLE_QTHELP_DOCS=OFF -DDBUS_ENABLE_DOXYGEN_DOCS=OFF ' +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 From 26306ac4bd11d1794183e340fe0a4b3daf565d98 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Sat, 4 Nov 2023 17:33:16 +0100 Subject: [PATCH 144/599] add libiconv dependency to gettext --- easybuild/easyconfigs/g/gettext/gettext-0.22-GCCcore-13.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.22-GCCcore-13.2.0.eb b/easybuild/easyconfigs/g/gettext/gettext-0.22-GCCcore-13.2.0.eb index 2f4d3b3096a..3bf5207d463 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.22-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.22-GCCcore-13.2.0.eb @@ -19,6 +19,7 @@ builddependencies = [('binutils', '2.40')] dependencies = [ ('libxml2', '2.11.5'), ('ncurses', '6.4'), + ('libiconv', '1.17'), ] configopts = '--without-emacs --with-libxml2-prefix=$EBROOTLIBXML2' From c0f09497fad94b5c6f2f9a8341025e53c97c2b58 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Sat, 4 Nov 2023 18:51:45 +0000 Subject: [PATCH 145/599] update checksum Co-authored-by: SebastianAchilles --- .../easyconfigs/h/HarfBuzz/HarfBuzz-8.2.2-GCCcore-13.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-8.2.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-8.2.2-GCCcore-13.2.0.eb index 87c73c5219b..8521cf6e258 100644 --- a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-8.2.2-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-8.2.2-GCCcore-13.2.0.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'GCCcore', 'version': '13.2.0'} github_account = 'harfbuzz' source_urls = [GITHUB_SOURCE] sources = ['%(version)s.tar.gz'] -checksums = ['77c8c903f4539b050a6d3a5be79705c7ccf7b1cb66d68152a651486e261edbd2'] +checksums = ['0546aac7b2493b3681047914550860157f8799fc80bf5cb528927a9643d6ab3d'] builddependencies = [ ('binutils', '2.40'), From 1e2ba69709dcd11b51089032b845bd8dac844c14 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 4 Nov 2023 21:08:47 +0100 Subject: [PATCH 146/599] bump version to 4.9.0dev --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 1aaee4d4aab..6403cb7b383 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 = '4.8.2' +VERSION = '4.9.0.dev0' MAJ_VER = VERSION.split('.')[0] MAJMIN_VER = '.'.join(VERSION.split('.')[0:2]) From ad78d8f2eb2d3bbe6484b294dd45eba6ede438a6 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 6 Nov 2023 12:11:45 +0100 Subject: [PATCH 147/599] Add patch to fix duplicate definition --- .../p/PyTorch/PyTorch-1.13.1-foss-2022b.eb | 3 ++ ...duplicate-kDefaultTimeout-definition.patch | 31 +++++++++++++++++++ 2 files changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_fix-duplicate-kDefaultTimeout-definition.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022b.eb index 45ffe3f1e20..e567f93765a 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022b.eb @@ -25,6 +25,7 @@ patches = [ 'PyTorch-1.12.1_fix-vsx-vector-funcs.patch', 'PyTorch-1.12.1_skip-test_round_robin.patch', 'PyTorch-1.13.1_disable-test-sharding.patch', + 'PyTorch-1.13.1_fix-duplicate-kDefaultTimeout-definition.patch', 'PyTorch-1.13.1_fix-flaky-jit-test.patch', 'PyTorch-1.13.1_fix-fsdp-fp16-test.patch', 'PyTorch-1.13.1_fix-gcc-12-missing-includes.patch', @@ -68,6 +69,8 @@ checksums = [ {'PyTorch-1.12.1_fix-vsx-vector-funcs.patch': 'caccbf60f62eac313896c1eaec78b08f5d0fdfcb907079087490bb13d1561aa2'}, {'PyTorch-1.12.1_skip-test_round_robin.patch': '63d4849b78605aa088fdff695637d9473ea60dee603a3ff7f788690d70c55349'}, {'PyTorch-1.13.1_disable-test-sharding.patch': 'df2074adeba47998ce2993d99ca64eb6f1c79ab7057f553b436efdec264d3572'}, + {'PyTorch-1.13.1_fix-duplicate-kDefaultTimeout-definition.patch': + '882f8cfaf33490a4372928fb6673cbbfa40e5be1b64bf7e0cc2924d73cf872e8'}, {'PyTorch-1.13.1_fix-flaky-jit-test.patch': '71efdeb29b5e5b4982c9f5cb2182733654a34d52f85bb5487bc4d7d99b86101b'}, {'PyTorch-1.13.1_fix-fsdp-fp16-test.patch': '8ae68e60d6e1f92f50322b7f0381c7e65251fba32d7606e3a238a36a2f55b5cf'}, {'PyTorch-1.13.1_fix-gcc-12-missing-includes.patch': diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_fix-duplicate-kDefaultTimeout-definition.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_fix-duplicate-kDefaultTimeout-definition.patch new file mode 100644 index 00000000000..6e211b1f3a8 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_fix-duplicate-kDefaultTimeout-definition.patch @@ -0,0 +1,31 @@ +From 9a18968253e28ba8d8bdf646731087000c7876b7 Mon Sep 17 00:00:00 2001 +From: sclarkson +Date: Tue, 21 Mar 2023 21:44:49 +0000 +Subject: [PATCH] Fix kDefaultTimeout multiple definition build failure + (#97270) + +Make the namespace explicit to avoid the constexpr conflict on GCC 11. + +Fixes #90448 + +@ezyang + +Pull Request resolved: https://github.com/pytorch/pytorch/pull/97270 +Approved by: https://github.com/ezyang +--- + torch/csrc/distributed/c10d/ProcessGroupGloo.hpp | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/torch/csrc/distributed/c10d/ProcessGroupGloo.hpp b/torch/csrc/distributed/c10d/ProcessGroupGloo.hpp +index a64bc37c4de522..e4d2967c8604ea 100644 +--- a/torch/csrc/distributed/c10d/ProcessGroupGloo.hpp ++++ b/torch/csrc/distributed/c10d/ProcessGroupGloo.hpp +@@ -125,7 +125,7 @@ class TORCH_API ProcessGroupGloo : public Backend { + } + + void wait(const std::vector& keys) override { +- store_->wait(keys, Store::kDefaultTimeout); ++ store_->wait(keys, ::c10d::Store::kDefaultTimeout); + } + + void wait( From 7bb3337a47d2de958b9dc79608c534ebcc1c1345 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Mon, 6 Nov 2023 12:56:24 +0100 Subject: [PATCH 148/599] {cae}[system/system] STAR-CCM+ v18.06.006 w/ r8 (#19100) * adding easyconfigs: STAR-CCM+-18.06.006.eb, STAR-CCM+-18.06.006-r8.eb * Add user facing versions * Disable restrictive version check in modulerc --------- Co-authored-by: Ake Sandgren --- .../s/STAR-CCM+/STAR-CCM+-18.06.006-r8.eb | 15 +++++++++++++++ .../s/STAR-CCM+/STAR-CCM+-18.06.006.eb | 14 ++++++++++++++ .../s/STAR-CCM+/STAR-CCM+-2310-r8.eb | 18 ++++++++++++++++++ .../easyconfigs/s/STAR-CCM+/STAR-CCM+-2310.eb | 17 +++++++++++++++++ 4 files changed, 64 insertions(+) create mode 100644 easybuild/easyconfigs/s/STAR-CCM+/STAR-CCM+-18.06.006-r8.eb create mode 100644 easybuild/easyconfigs/s/STAR-CCM+/STAR-CCM+-18.06.006.eb create mode 100644 easybuild/easyconfigs/s/STAR-CCM+/STAR-CCM+-2310-r8.eb create mode 100644 easybuild/easyconfigs/s/STAR-CCM+/STAR-CCM+-2310.eb diff --git a/easybuild/easyconfigs/s/STAR-CCM+/STAR-CCM+-18.06.006-r8.eb b/easybuild/easyconfigs/s/STAR-CCM+/STAR-CCM+-18.06.006-r8.eb new file mode 100644 index 00000000000..49cda6093eb --- /dev/null +++ b/easybuild/easyconfigs/s/STAR-CCM+/STAR-CCM+-18.06.006-r8.eb @@ -0,0 +1,15 @@ +name = 'STAR-CCM+' +version = '18.06.006' +versionsuffix = '-r8' + +homepage = 'https://mdx.plm.automation.siemens.com/star-ccm-plus' +description = """STAR-CCM+ is a multiphysics computational fluid dynamics (CFD) software for the simulation of products +operating under real-world conditions.""" + +toolchain = SYSTEM + +download_instructions = 'Manually obtain tarball from Siemens' +sources = ['%%(name)s%%(version)s_01_linux-x86_64%s.tar.gz' % versionsuffix] +checksums = ['77a46b81e93d427a1c33b78fa9ae3fa0c1de4636c749e2f2692728b0f5bb1296'] + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/s/STAR-CCM+/STAR-CCM+-18.06.006.eb b/easybuild/easyconfigs/s/STAR-CCM+/STAR-CCM+-18.06.006.eb new file mode 100644 index 00000000000..7368da66b4e --- /dev/null +++ b/easybuild/easyconfigs/s/STAR-CCM+/STAR-CCM+-18.06.006.eb @@ -0,0 +1,14 @@ +name = 'STAR-CCM+' +version = '18.06.006' + +homepage = 'https://mdx.plm.automation.siemens.com/star-ccm-plus' +description = """STAR-CCM+ is a multiphysics computational fluid dynamics (CFD) software for the simulation of products +operating under real-world conditions.""" + +toolchain = SYSTEM + +download_instructions = 'Manually obtain tarball from Siemens' +sources = ['%(name)s%(version)s_01_linux-x86_64.tar.gz'] +checksums = ['476b75b859612cf816ba62ac36fdf98b47dd606114c612dea6869031582db4a5'] + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/s/STAR-CCM+/STAR-CCM+-2310-r8.eb b/easybuild/easyconfigs/s/STAR-CCM+/STAR-CCM+-2310-r8.eb new file mode 100644 index 00000000000..408462f98ca --- /dev/null +++ b/easybuild/easyconfigs/s/STAR-CCM+/STAR-CCM+-2310-r8.eb @@ -0,0 +1,18 @@ +easyblock = 'ModuleRC' + +name = 'STAR-CCM+' +version = '2310' +versionsuffix = '-r8' +local_version = '18.06.006' + +homepage = 'https://mdx.plm.automation.siemens.com/star-ccm-plus' +description = """STAR-CCM+ is a multiphysics computational fluid dynamics (CFD) software for the simulation of products +operating under real-world conditions.""" + +toolchain = SYSTEM + +dependencies = [('STAR-CCM+', local_version, versionsuffix)] + +check_version = False + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/s/STAR-CCM+/STAR-CCM+-2310.eb b/easybuild/easyconfigs/s/STAR-CCM+/STAR-CCM+-2310.eb new file mode 100644 index 00000000000..706662fbe6d --- /dev/null +++ b/easybuild/easyconfigs/s/STAR-CCM+/STAR-CCM+-2310.eb @@ -0,0 +1,17 @@ +easyblock = 'ModuleRC' + +name = 'STAR-CCM+' +version = '2310' +local_version = '18.06.006' + +homepage = 'https://mdx.plm.automation.siemens.com/star-ccm-plus' +description = """STAR-CCM+ is a multiphysics computational fluid dynamics (CFD) software for the simulation of products +operating under real-world conditions.""" + +toolchain = SYSTEM + +dependencies = [('STAR-CCM+', local_version)] + +check_version = False + +moduleclass = 'cae' From e8383fab0b548e25f784731deacbce0b638a9824 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Mon, 6 Nov 2023 12:56:54 +0100 Subject: [PATCH 149/599] adding easyconfigs: STAR-CCM+-2302.eb, STAR-CCM+-2302-r8.eb (#19158) --- .../s/STAR-CCM+/STAR-CCM+-2302-r8.eb | 18 ++++++++++++++++++ .../easyconfigs/s/STAR-CCM+/STAR-CCM+-2302.eb | 17 +++++++++++++++++ 2 files changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/s/STAR-CCM+/STAR-CCM+-2302-r8.eb create mode 100644 easybuild/easyconfigs/s/STAR-CCM+/STAR-CCM+-2302.eb diff --git a/easybuild/easyconfigs/s/STAR-CCM+/STAR-CCM+-2302-r8.eb b/easybuild/easyconfigs/s/STAR-CCM+/STAR-CCM+-2302-r8.eb new file mode 100644 index 00000000000..ad6e29a31b6 --- /dev/null +++ b/easybuild/easyconfigs/s/STAR-CCM+/STAR-CCM+-2302-r8.eb @@ -0,0 +1,18 @@ +easyblock = 'ModuleRC' + +name = 'STAR-CCM+' +version = '2302' +versionsuffix = '-r8' +local_version = '18.02.008' + +homepage = 'https://mdx.plm.automation.siemens.com/star-ccm-plus' +description = """STAR-CCM+ is a multiphysics computational fluid dynamics (CFD) software for the simulation of products +operating under real-world conditions.""" + +toolchain = SYSTEM + +dependencies = [('STAR-CCM+', local_version, versionsuffix)] + +check_version = False + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/s/STAR-CCM+/STAR-CCM+-2302.eb b/easybuild/easyconfigs/s/STAR-CCM+/STAR-CCM+-2302.eb new file mode 100644 index 00000000000..3f1ac40dc79 --- /dev/null +++ b/easybuild/easyconfigs/s/STAR-CCM+/STAR-CCM+-2302.eb @@ -0,0 +1,17 @@ +easyblock = 'ModuleRC' + +name = 'STAR-CCM+' +version = '2302' +local_version = '18.02.008' + +homepage = 'https://mdx.plm.automation.siemens.com/star-ccm-plus' +description = """STAR-CCM+ is a multiphysics computational fluid dynamics (CFD) software for the simulation of products +operating under real-world conditions.""" + +toolchain = SYSTEM + +dependencies = [('STAR-CCM+', local_version)] + +check_version = False + +moduleclass = 'cae' From 9b85f424474a4811c72448102c347c8f0253775f Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 6 Nov 2023 13:35:38 +0100 Subject: [PATCH 150/599] fix OpenBLAS on newer Intel CPUs --- .../o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb | 3 + .../o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb | 13 ++-- .../OpenBLAS-0.3.20-NVHPC-22.7-CUDA-11.7.0.eb | 3 + ...xASUM-microkernels-on-new-intel-cpus.patch | 65 +++++++++++++++++++ .../o/OpenBLAS/OpenBLAS-0.3.21-GCC-12.2.0.eb | 3 + .../o/OpenBLAS/OpenBLAS-0.3.23-GCC-12.3.0.eb | 3 + .../o/OpenBLAS/OpenBLAS-0.3.24-GCC-13.2.0.eb | 3 + 7 files changed, 88 insertions(+), 5 deletions(-) create mode 100644 easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20_use-xASUM-microkernels-on-new-intel-cpus.patch diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb index 03bd16ce48f..48991f92ef5 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb @@ -17,6 +17,7 @@ patches = [ ('timing.tgz', '.'), 'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch', 'OpenBLAS-0.3.20_fix-x86-cpuid.patch', + 'OpenBLAS-0.3.20_use-xASUM-microkernels-on-new-intel-cpus.patch', 'OpenBLAS-0.3.21_fix-order-vectorization.patch', 'OpenBLAS-0.3.21_disable-fma-in-cscal-zscal.patch', 'OpenBLAS-0.3.21_avoid-crash-in-zdot.patch', @@ -28,6 +29,8 @@ checksums = [ {'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch': 'e6b326fb8c4a8a6fd07741d9983c37a72c55c9ff9a4f74a80e1352ce5f975971'}, {'OpenBLAS-0.3.20_fix-x86-cpuid.patch': '57e8384404e136b9f0dafc26573adeb7dc69e60d84a7e189643b91d6299888fc'}, + {'OpenBLAS-0.3.20_use-xASUM-microkernels-on-new-intel-cpus.patch': + '1dbd0f9473963dbdd9131611b455d8a801f1e995eae82896186d3d3ffe6d5f03'}, {'OpenBLAS-0.3.21_fix-order-vectorization.patch': '08af834e5d60441fd35c128758ed9c092ba6887c829e0471ecd489079539047d'}, {'OpenBLAS-0.3.21_disable-fma-in-cscal-zscal.patch': diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb index 5b104219e11..96a3218f027 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb @@ -16,11 +16,12 @@ patches = [ ('large.tgz', '.'), ('timing.tgz', '.'), 'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch', + 'OpenBLAS-0.3.20_fix-cpuid-neoverse-v1-n2.patch', + 'OpenBLAS-0.3.20_fix-x86-cpuid.patch', + 'OpenBLAS-0.3.20_use-xASUM-microkernels-on-new-intel-cpus.patch', 'OpenBLAS-0.3.21_fix-order-vectorization.patch', 'OpenBLAS-0.3.21_disable-fma-in-cscal-zscal.patch', 'OpenBLAS-0.3.21_avoid-crash-in-zdot.patch', - 'OpenBLAS-0.3.20_fix-cpuid-neoverse-v1-n2.patch', - 'OpenBLAS-0.3.20_fix-x86-cpuid.patch', ] checksums = [ {'v0.3.20.tar.gz': '8495c9affc536253648e942908e88e097f2ec7753ede55aca52e5dead3029e3c'}, @@ -28,14 +29,16 @@ checksums = [ {'timing.tgz': '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af'}, {'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch': 'e6b326fb8c4a8a6fd07741d9983c37a72c55c9ff9a4f74a80e1352ce5f975971'}, + {'OpenBLAS-0.3.20_fix-cpuid-neoverse-v1-n2.patch': + '1b495465f8dd1e151d74cf5aa4288120361d29164d6a377228a8d51c255b8a9e'}, + {'OpenBLAS-0.3.20_fix-x86-cpuid.patch': '57e8384404e136b9f0dafc26573adeb7dc69e60d84a7e189643b91d6299888fc'}, + {'OpenBLAS-0.3.20_use-xASUM-microkernels-on-new-intel-cpus.patch': + '1dbd0f9473963dbdd9131611b455d8a801f1e995eae82896186d3d3ffe6d5f03'}, {'OpenBLAS-0.3.21_fix-order-vectorization.patch': '08af834e5d60441fd35c128758ed9c092ba6887c829e0471ecd489079539047d'}, {'OpenBLAS-0.3.21_disable-fma-in-cscal-zscal.patch': 'bd6836206a883208dc8bc997946f97e4c97d91d8e101fc54db414aaa56902fc3'}, {'OpenBLAS-0.3.21_avoid-crash-in-zdot.patch': '3dac2c1ec896df574f1b37cde81a16f24550b7f1eb81fbfacb0c4449b0dc7894'}, - {'OpenBLAS-0.3.20_fix-cpuid-neoverse-v1-n2.patch': - '1b495465f8dd1e151d74cf5aa4288120361d29164d6a377228a8d51c255b8a9e'}, - {'OpenBLAS-0.3.20_fix-x86-cpuid.patch': '57e8384404e136b9f0dafc26573adeb7dc69e60d84a7e189643b91d6299888fc'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-NVHPC-22.7-CUDA-11.7.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-NVHPC-22.7-CUDA-11.7.0.eb index cbf11c2a295..d7442a5c7d8 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-NVHPC-22.7-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-NVHPC-22.7-CUDA-11.7.0.eb @@ -17,6 +17,7 @@ patches = [ ('timing.tgz', '.'), 'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch', 'OpenBLAS-0.3.20_fix-x86-cpuid.patch', + 'OpenBLAS-0.3.20_use-xASUM-microkernels-on-new-intel-cpus.patch', 'OpenBLAS-0.3.21_fix-order-vectorization.patch', 'OpenBLAS-0.3.21_disable-fma-in-cscal-zscal.patch', 'OpenBLAS-0.3.21_avoid-crash-in-zdot.patch', @@ -28,6 +29,8 @@ checksums = [ {'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch': 'e6b326fb8c4a8a6fd07741d9983c37a72c55c9ff9a4f74a80e1352ce5f975971'}, {'OpenBLAS-0.3.20_fix-x86-cpuid.patch': '57e8384404e136b9f0dafc26573adeb7dc69e60d84a7e189643b91d6299888fc'}, + {'OpenBLAS-0.3.20_use-xASUM-microkernels-on-new-intel-cpus.patch': + '1dbd0f9473963dbdd9131611b455d8a801f1e995eae82896186d3d3ffe6d5f03'}, {'OpenBLAS-0.3.21_fix-order-vectorization.patch': '08af834e5d60441fd35c128758ed9c092ba6887c829e0471ecd489079539047d'}, {'OpenBLAS-0.3.21_disable-fma-in-cscal-zscal.patch': diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20_use-xASUM-microkernels-on-new-intel-cpus.patch b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20_use-xASUM-microkernels-on-new-intel-cpus.patch new file mode 100644 index 00000000000..a342b04b79f --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20_use-xASUM-microkernels-on-new-intel-cpus.patch @@ -0,0 +1,65 @@ +From 9019bc494514a74c2042152cdca0a36adea7b42f Mon Sep 17 00:00:00 2001 +From: Martin Kroeker +Date: Sat, 4 Nov 2023 22:10:06 +0100 +Subject: [PATCH] Use SkylakeX ?ASUM microkernel for Cooperlake/Sapphirerapids + as well + +--- + kernel/x86_64/casum.c | 2 +- + kernel/x86_64/dasum.c | 2 +- + kernel/x86_64/sasum.c | 2 +- + kernel/x86_64/zasum.c | 2 +- + 4 files changed, 4 insertions(+), 4 deletions(-) + +diff --git a/kernel/x86_64/casum.c b/kernel/x86_64/casum.c +index 60feec0ceb..e4d0543114 100644 +--- a/kernel/x86_64/casum.c ++++ b/kernel/x86_64/casum.c +@@ -4,7 +4,7 @@ + #define ABS_K(a) ((a) > 0 ? (a) : (-(a))) + #endif + +-#if defined(SKYLAKEX) ++#if defined(SKYLAKEX) || defined(COOPERLAKE) || defined(SAPPHIRERAPIDS) + #include "casum_microk_skylakex-2.c" + #endif + +diff --git a/kernel/x86_64/dasum.c b/kernel/x86_64/dasum.c +index a9c40f38f0..0147c6978a 100644 +--- a/kernel/x86_64/dasum.c ++++ b/kernel/x86_64/dasum.c +@@ -4,7 +4,7 @@ + #define ABS_K(a) ((a) > 0 ? (a) : (-(a))) + #endif + +-#if defined(SKYLAKEX) ++#if defined(SKYLAKEX) || defined(COOPERLAKE) || defined(SAPPHIRERAPIDS) + #include "dasum_microk_skylakex-2.c" + #elif defined(HASWELL) || defined(ZEN) + #include "dasum_microk_haswell-2.c" +diff --git a/kernel/x86_64/sasum.c b/kernel/x86_64/sasum.c +index 37a92468ff..3f22cb97a1 100644 +--- a/kernel/x86_64/sasum.c ++++ b/kernel/x86_64/sasum.c +@@ -9,7 +9,7 @@ + + #endif + +-#if defined(SKYLAKEX) ++#if defined(SKYLAKEX) || defined(COOPERLAKE) || defined(SAPPHIRERAPIDS) + #include "sasum_microk_skylakex-2.c" + #elif defined(HASWELL) || defined(ZEN) + #include "sasum_microk_haswell-2.c" +diff --git a/kernel/x86_64/zasum.c b/kernel/x86_64/zasum.c +index 80e95a2c89..3f17ab1cfa 100644 +--- a/kernel/x86_64/zasum.c ++++ b/kernel/x86_64/zasum.c +@@ -4,7 +4,7 @@ + #define ABS_K(a) ((a) > 0 ? (a) : (-(a))) + #endif + +-#if defined(SKYLAKEX) ++#if defined(SKYLAKEX) || defined(COOPERLAKE) || defined(SAPPHIRERAPIDS) + #include "zasum_microk_skylakex-2.c" + #endif + diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21-GCC-12.2.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21-GCC-12.2.0.eb index 66b40a6a8a1..7e7d8c4b75f 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21-GCC-12.2.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21-GCC-12.2.0.eb @@ -17,6 +17,7 @@ patches = [ ('timing.tgz', '.'), 'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch', 'OpenBLAS-0.3.20_fix-x86-cpuid.patch', + 'OpenBLAS-0.3.20_use-xASUM-microkernels-on-new-intel-cpus.patch', 'OpenBLAS-0.3.21_fix-order-vectorization.patch', 'OpenBLAS-0.3.21-GCC-12.2.0_disable-fma-in-cscal-zscal.patch', 'OpenBLAS-0.3.21_avoid-crash-in-zdot.patch', @@ -28,6 +29,8 @@ checksums = [ {'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch': 'e6b326fb8c4a8a6fd07741d9983c37a72c55c9ff9a4f74a80e1352ce5f975971'}, {'OpenBLAS-0.3.20_fix-x86-cpuid.patch': '57e8384404e136b9f0dafc26573adeb7dc69e60d84a7e189643b91d6299888fc'}, + {'OpenBLAS-0.3.20_use-xASUM-microkernels-on-new-intel-cpus.patch': + '1dbd0f9473963dbdd9131611b455d8a801f1e995eae82896186d3d3ffe6d5f03'}, {'OpenBLAS-0.3.21_fix-order-vectorization.patch': '08af834e5d60441fd35c128758ed9c092ba6887c829e0471ecd489079539047d'}, {'OpenBLAS-0.3.21-GCC-12.2.0_disable-fma-in-cscal-zscal.patch': diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.23-GCC-12.3.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.23-GCC-12.3.0.eb index 8051da228f0..490f623ac15 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.23-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.23-GCC-12.3.0.eb @@ -17,6 +17,7 @@ patches = [ ('timing.tgz', '.'), 'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch', 'OpenBLAS-0.3.20_fix-x86-cpuid.patch', + 'OpenBLAS-0.3.20_use-xASUM-microkernels-on-new-intel-cpus.patch', 'OpenBLAS-0.3.21_fix-order-vectorization.patch', 'OpenBLAS-0.3.23_fix-parallel-build.patch', 'OpenBLAS-0.3.23_fix-lapack-test.patch', @@ -30,6 +31,8 @@ checksums = [ {'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch': 'e6b326fb8c4a8a6fd07741d9983c37a72c55c9ff9a4f74a80e1352ce5f975971'}, {'OpenBLAS-0.3.20_fix-x86-cpuid.patch': '57e8384404e136b9f0dafc26573adeb7dc69e60d84a7e189643b91d6299888fc'}, + {'OpenBLAS-0.3.20_use-xASUM-microkernels-on-new-intel-cpus.patch': + '1dbd0f9473963dbdd9131611b455d8a801f1e995eae82896186d3d3ffe6d5f03'}, {'OpenBLAS-0.3.21_fix-order-vectorization.patch': '08af834e5d60441fd35c128758ed9c092ba6887c829e0471ecd489079539047d'}, {'OpenBLAS-0.3.23_fix-parallel-build.patch': 'abe10ba3b0ca54772dbf235596e35325a5159018f6a60cfc88824c2c220d99d9'}, 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 f3358f87771..eb7737a76aa 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 @@ -16,6 +16,7 @@ patches = [ ('large.tgz', '.'), ('timing.tgz', '.'), 'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch', + 'OpenBLAS-0.3.20_use-xASUM-microkernels-on-new-intel-cpus.patch', 'OpenBLAS-0.3.21_fix-order-vectorization.patch', 'OpenBLAS-0.3.23_fix-lapack-test.patch', 'OpenBLAS-0.3.23_disable-DDRGES3-LAPACK-test.patch', @@ -26,6 +27,8 @@ checksums = [ {'timing.tgz': '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af'}, {'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch': 'e6b326fb8c4a8a6fd07741d9983c37a72c55c9ff9a4f74a80e1352ce5f975971'}, + {'OpenBLAS-0.3.20_use-xASUM-microkernels-on-new-intel-cpus.patch': + '1dbd0f9473963dbdd9131611b455d8a801f1e995eae82896186d3d3ffe6d5f03'}, {'OpenBLAS-0.3.21_fix-order-vectorization.patch': '08af834e5d60441fd35c128758ed9c092ba6887c829e0471ecd489079539047d'}, {'OpenBLAS-0.3.23_fix-lapack-test.patch': 'f6b3d81061f136e34aaf5359bb80fb9d2bba28825cc1dd26179b8dd01a9a0054'}, From ec1476b059588160e7ac77456aefaf7e76018b31 Mon Sep 17 00:00:00 2001 From: appolloford Date: Mon, 6 Nov 2023 19:06:27 +0100 Subject: [PATCH 151/599] Add pkgconf build dependency --- .../easyconfigs/s/SuiteSparse/SuiteSparse-7.1.0-foss-2023a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-7.1.0-foss-2023a.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-7.1.0-foss-2023a.eb index 8eea586e45f..2a01bcd59bd 100644 --- a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-7.1.0-foss-2023a.eb +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-7.1.0-foss-2023a.eb @@ -13,6 +13,7 @@ checksums = ['4cd3d161f9aa4f98ec5fa725ee5dc27bca960a3714a707a7d12b3d0abb504679'] builddependencies = [ ('CMake', '3.26.3'), + ('pkgconf', '1.9.5'), # ('M4', '1.4.19'), ] From bfb5cb05121fd3c01fd975bebf6a1fd83688138a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Mon, 6 Nov 2023 19:18:16 +0100 Subject: [PATCH 152/599] adding easyconfigs: libxslt-1.1.38-GCCcore-13.2.0.eb, nettle-3.9.1-GCCcore-13.2.0.eb, Xvfb-21.1.9-GCCcore-13.2.0.eb, xproto-7.0.31-GCCcore-13.2.0.eb --- .../libxslt/libxslt-1.1.38-GCCcore-13.2.0.eb | 36 +++++ .../n/nettle/nettle-3.9.1-GCCcore-13.2.0.eb | 38 ++++++ .../x/Xvfb/Xvfb-21.1.9-GCCcore-13.2.0.eb | 126 ++++++++++++++++++ .../x/xproto/xproto-7.0.31-GCCcore-13.2.0.eb | 29 ++++ 4 files changed, 229 insertions(+) create mode 100644 easybuild/easyconfigs/l/libxslt/libxslt-1.1.38-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/n/nettle/nettle-3.9.1-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/x/Xvfb/Xvfb-21.1.9-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/x/xproto/xproto-7.0.31-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.38-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.38-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..7f763c378c9 --- /dev/null +++ b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.38-GCCcore-13.2.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'libxslt' +version = '1.1.38' + +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': '13.2.0'} + +source_urls = ['https://download.gnome.org/sources/libxslt/%(version_major_minor)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['1f32450425819a09acaff2ab7a5a7f8a2ec7956e505d7beeb45e843d0e1ecab1'] + +builddependencies = [ + ('binutils', '2.40'), + ('pkgconf', '2.0.3'), +] + +dependencies = [ + ('zlib', '1.2.13'), + ('libxml2', '2.11.5'), +] + +# 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' diff --git a/easybuild/easyconfigs/n/nettle/nettle-3.9.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/n/nettle/nettle-3.9.1-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..d29fc015efd --- /dev/null +++ b/easybuild/easyconfigs/n/nettle/nettle-3.9.1-GCCcore-13.2.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'nettle' +version = '3.9.1' + +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': '13.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['ccfeff981b0ca71bbd6fbcb054f407c60ffb644389a5be80d6716d5b550c6ce3'] + +builddependencies = [ + ('binutils', '2.40'), + ('Autotools', '20220317'), +] + +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/x/Xvfb/Xvfb-21.1.9-GCCcore-13.2.0.eb b/easybuild/easyconfigs/x/Xvfb/Xvfb-21.1.9-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..740256850ac --- /dev/null +++ b/easybuild/easyconfigs/x/Xvfb/Xvfb-21.1.9-GCCcore-13.2.0.eb @@ -0,0 +1,126 @@ +easyblock = 'Bundle' + +name = 'Xvfb' +version = '21.1.9' + +homepage = 'https://www.x.org/releases/X11R7.6/doc/man/man1/Xvfb.1.xhtml' +description = """Xvfb is an X server that can run on machines with no display hardware and no physical input devices. + It emulates a dumb framebuffer using virtual memory.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +builddependencies = [ + ('binutils', '2.40'), + ('pkgconf', '2.0.3'), + ('Python', '3.11.5'), + ('Meson', '1.2.3'), + ('Ninja', '1.11.1'), + ('libxslt', '1.1.38'), + ('gettext', '0.22'), + ('Bison', '3.8.2'), +] + +dependencies = [ + ('X11', '20231019'), + ('pixman', '0.42.2'), + ('libdrm', '2.4.117'), + ('Mesa', '23.1.9'), + ('nettle', '3.9.1'), + ('libunwind', '1.6.2'), + ('XZ', '5.4.4'), +] + +default_easyblock = 'ConfigureMake' + +local_xvfb_configopts = "--enable-xvfb --disable-xorg --disable-xnest --disable-xwin " +local_xvfb_configopts += "--disable-dri --disable-dri2 --disable-dri3 --disable-libunwind " +local_xvfb_configopts += "--with-fontrootdir=%(installdir)s/share/fonts/X11" + +# use 'make V=1' to see compiler commands +local_xvfb_buildopts = "V=1 " + +# use static libraries for nettle & libunwind, so avoid errors like "No rule to make target '-lnettle'" +local_xvfb_buildopts += 'SHA1_LIBS="$EBROOTNETTLE/lib*/libnettle.a" ' +local_xvfb_buildopts += 'LIBUNWIND_LIBS="$EBROOTLIBUNWIND/lib*/libunwind.a $EBROOTXZ/lib*/liblzma.a"' + +default_component_specs = { + 'sources': [SOURCE_TAR_GZ], + 'start_dir': '%(name)s-%(version)s', +} + +local_font_misc_preconfigopts = "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && " +local_font_misc_preconfigopts += "export PATH=%(installdir)s/bin:$PATH && " + +components = [ + ('mkfontscale', '1.2.2', { + 'source_urls': ['https://www.x.org/archive/individual/app/'], + 'checksums': ['4a5af55e670713024639a7f7d10826d905d86faf574cd77e0f5aef2d00e70168'], + }), + ('mkfontdir', '1.0.7', { + 'source_urls': ['https://www.x.org/archive/individual/app/'], + 'checksums': ['bccc5fb7af1b614eabe4a22766758c87bfc36d66191d08c19d2fa97674b7b5b7'], + }), + ('bdftopcf', '1.1', { + 'source_urls': ['https://www.x.org/archive/individual/app/'], + 'checksums': ['699d1a62012035b1461c7f8e3f05a51c8bd6f28f348983249fb89bbff7309b47'], + }), + ('font-util', '1.4.1', { + 'source_urls': ['https://www.x.org/archive/individual/font/'], + 'checksums': ['f029ae80cdd75d89bee7f7af61c21e07982adfb9f72344a158b99f91f77ef5ed'], + }), + ('font-misc-misc', '1.1.3', { + 'source_urls': ['https://www.x.org/archive/individual/font/'], + 'checksums': ['bece4a9482b3cb6f7fad2164fd3b394d22dfe1ad2f96f60030a703bcff30f5a5'], + 'preconfigopts': local_font_misc_preconfigopts, + }), + ('xkbcomp', '1.4.6', { + 'source_urls': ['https://www.x.org/archive/individual/app/'], + 'checksums': ['b216a2c8c0eab83f3dc4a3d5ee2bdf7827b30e49c8907035d0f222138eca0987'], + }), + ('xkeyboard-config', '2.40', { + 'easyblock': 'MesonNinja', + 'source_urls': ['https://www.x.org/archive/individual/data/xkeyboard-config/'], + 'sources': [SOURCE_TAR_XZ], + 'checksums': ['7a3dba1bec7dc7191432da021242d17c9cf6c89690e6c57b0de048ff8c9d2ae3'], + 'configopts': '-Dxorg-rules-symlinks=true', + }), + ('xauth', '1.1.2', { + 'source_urls': ['https://www.x.org/releases/individual/app/'], + 'checksums': ['84d27a1023d8da524c134f424b312e53cb96e08871f96868aa20316bfcbbc054'], + }), + ('libxcvt', '0.1.2', { + 'easyblock': 'MesonNinja', + 'source_urls': ['https://www.x.org/archive/individual/lib/'], + 'sources': [SOURCE_TAR_XZ], + 'checksums': ['0561690544796e25cfbd71806ba1b0d797ffe464e9796411123e79450f71db38'], + }), + (name, version, { + 'source_urls': ['https://www.x.org/releases/individual/xserver/'], + 'sources': ['xorg-server-%(version)s.tar.gz'], + 'patches': [('xvfb-run', '.')], + 'checksums': [ + '455ac22c411b3e74adb4d1b3fd48b9037b6b5ba9260247c59b669f67a08fd26e', # xorg-server-21.1.9.tar.gz + 'fd6d13182b77871d4f65fccdaebb8a72387a726426066d3f8e6aa26b010ea0e8', # xvfb-run + ], + 'start_dir': 'xorg-server-%(version)s', + 'configopts': local_xvfb_configopts, + 'buildopts': local_xvfb_buildopts, + 'installopts': local_xvfb_buildopts, + }), +] + +# enable exec permissions for xvfb-run after copying; +# need to also enable user write permissions on xvfb-run to ensure that copying with preserved permissions works +postinstallcmds = ["chmod u+w xvfb-run && cp -a xvfb-run %(installdir)s/bin/ && chmod a+x %(installdir)s/bin/xvfb-run"] + +sanity_check_paths = { + 'files': ['bin/Xvfb', 'bin/xvfb-run'], + 'dirs': ['lib/xorg', 'share/fonts/X11/misc', 'share/fonts/X11/util'], +} + +sanity_check_commands = [ + "xvfb-run --help", + "xvfb-run --error-file %(builddir)s/xvfb-run-test.err echo hello", +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.31-GCCcore-13.2.0.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.31-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..a1cf4fe28c7 --- /dev/null +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.31-GCCcore-13.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'xproto' +version = '7.0.31' + +homepage = 'https://www.freedesktop.org/wiki/Software/xlibs' +description = "X protocol and ancillary headers" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = [XORG_PROTO_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['6d755eaae27b45c5cc75529a12855fed5de5969b367ed05003944cf901ed43c7'] + +builddependencies = [ + ('binutils', '2.40'), + ('xorg-macros', '1.20.0'), +] + +sanity_check_paths = { + 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', 'Xatom.h', + 'XF86keysym.h', 'Xfuncs.h', 'Xmd.h', 'Xos.h', 'Xpoll.h', 'Xprotostr.h', + 'Xw32defs.h', 'Xwindows.h', 'DECkeysym.h', 'keysymdef.h', 'Sunkeysym.h', + 'Xarch.h', 'Xdefs.h', 'Xfuncproto.h', 'X.h', 'Xosdefs.h', 'Xos_r.h', + 'Xproto.h', 'Xthreads.h', 'XWDFile.h', 'Xwinsock.h']], + 'dirs': [] +} + +moduleclass = 'devel' From 4a0a28bd77202e7f39e788d8ccdd6a0fc9250077 Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Tue, 7 Nov 2023 11:45:54 +0100 Subject: [PATCH 153/599] update ScaFaCos for LAMMPS --- .../easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos.eb index e464d600e94..1abcc202d59 100644 --- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos.eb +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos.eb @@ -44,7 +44,7 @@ dependencies = [ ('kim-api', '2.3.0'), ('Eigen', '3.4.0'), ('PLUMED', '2.7.3'), - ('ScaFaCoS', '1.0.1'), + ('ScaFaCoS', '1.0.4'), ('SciPy-bundle', '2021.10'), # VTK package is auto-disabled if this dep is not available ('VTK', '9.1.0'), From eabda6df35d77295acb6eb1d99dd4c5df90969bd Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Tue, 7 Nov 2023 13:40:08 +0100 Subject: [PATCH 154/599] {bio}[foss/2022a] mrcfile v1.4.3 --- .../m/mrcfile/mrcfile-1.4.3-foss-2022a.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/m/mrcfile/mrcfile-1.4.3-foss-2022a.eb diff --git a/easybuild/easyconfigs/m/mrcfile/mrcfile-1.4.3-foss-2022a.eb b/easybuild/easyconfigs/m/mrcfile/mrcfile-1.4.3-foss-2022a.eb new file mode 100644 index 00000000000..dae89bc115f --- /dev/null +++ b/easybuild/easyconfigs/m/mrcfile/mrcfile-1.4.3-foss-2022a.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': 'foss', 'version': '2022a'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['43c358c59ff8f583fc4dc2079a0099028719109ebf92066e388772bab389c5f5'] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), +] + +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 b71452b2d3d4dcec49894da1b51564350af8b7bb Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann Date: Tue, 7 Nov 2023 13:55:14 +0000 Subject: [PATCH 155/599] remove Rust from builddeps --- .../easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb b/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb index 7e268e45acb..241eb2a55fd 100644 --- a/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb @@ -12,8 +12,7 @@ toolchain = {'name': 'GCCcore', 'version': '12.2.0'} toolchainopts = {'pic': True} builddependencies = [ - ('binutils', '2.39'), - ('Rust', '1.65.0'), + ('binutils', '2.39') ] dependencies = [ From 121dd592afa1f7fe9d65cf9a0052c00222172cb1 Mon Sep 17 00:00:00 2001 From: casparl Date: Tue, 7 Nov 2023 15:01:16 +0100 Subject: [PATCH 156/599] adding easyconfigs: Horovod-0.28.1-foss-2022a-PyTorch-1.12.0.eb --- ...orovod-0.28.1-foss-2022a-PyTorch-1.12.0.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/h/Horovod/Horovod-0.28.1-foss-2022a-PyTorch-1.12.0.eb diff --git a/easybuild/easyconfigs/h/Horovod/Horovod-0.28.1-foss-2022a-PyTorch-1.12.0.eb b/easybuild/easyconfigs/h/Horovod/Horovod-0.28.1-foss-2022a-PyTorch-1.12.0.eb new file mode 100644 index 00000000000..089c87eaf0a --- /dev/null +++ b/easybuild/easyconfigs/h/Horovod/Horovod-0.28.1-foss-2022a-PyTorch-1.12.0.eb @@ -0,0 +1,45 @@ +easyblock = 'PythonBundle' + +name = 'Horovod' +version = '0.28.1' +local_pt_version = '1.12.0' +versionsuffix = '-PyTorch-%s' % local_pt_version + +homepage = 'https://github.com/uber/horovod' +description = """Horovod is a distributed training framework for TensorFlow, PyTorch and MXnet. +This build only has PyTorch enabled.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +builddependencies = [ + ('CMake', '3.23.1'), +] +dependencies = [ + ('Python', '3.10.4'), + ('PyYAML', '6.0'), + ('PyTorch', local_pt_version), +] + +use_pip = True +sanity_pip_check = True + +preinstallopts = 'HOROVOD_WITH_MPI=1 ' +preinstallopts += 'HOROVOD_WITHOUT_TENSORFLOW=1 HOROVOD_WITH_PYTORCH=1 HOROVOD_WITHOUT_MXNET=1 ' + +exts_list = [ + ('cloudpickle', '2.2.1', { + 'checksums': ['d89684b8de9e34a2a43b3460fbca07d09d6e25ce858df4d5a44240403b6178f5'], + }), + ('horovod', version, { + 'checksums': ['92a43f5a94c43907a56805bad15f19700c62ffc83b7ca483f9e104e229f67ef0'], + }), +] + +sanity_check_paths = { + 'files': ['bin/horovodrun'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["horovodrun --help"] + +moduleclass = 'tools' From 358a027e5c3cdf151c1aa78627d3436380241128 Mon Sep 17 00:00:00 2001 From: appolloford Date: Tue, 7 Nov 2023 15:06:01 +0100 Subject: [PATCH 157/599] Remove unused dependencies --- .../easyconfigs/s/SuiteSparse/SuiteSparse-7.1.0-foss-2023a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-7.1.0-foss-2023a.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-7.1.0-foss-2023a.eb index 2a01bcd59bd..765f6e99944 100644 --- a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-7.1.0-foss-2023a.eb +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-7.1.0-foss-2023a.eb @@ -14,7 +14,6 @@ checksums = ['4cd3d161f9aa4f98ec5fa725ee5dc27bca960a3714a707a7d12b3d0abb504679'] builddependencies = [ ('CMake', '3.26.3'), ('pkgconf', '1.9.5'), - # ('M4', '1.4.19'), ] dependencies = [ From 94a39f8764b9a56fac571b5f54639cde5ed27be9 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Tue, 7 Nov 2023 17:04:54 +0100 Subject: [PATCH 158/599] update R to 4.3.2, add required dependencies and bump extensions --- .../l/libgit2/libgit2-1.7.0-GCCcore-12.3.0.eb | 34 --- ....1-gfbf-2023a.eb => R-4.3.2-gfbf-2023a.eb} | 195 +++++++++--------- 2 files changed, 98 insertions(+), 131 deletions(-) delete mode 100644 easybuild/easyconfigs/l/libgit2/libgit2-1.7.0-GCCcore-12.3.0.eb rename easybuild/easyconfigs/r/R/{R-4.3.1-gfbf-2023a.eb => R-4.3.2-gfbf-2023a.eb} (61%) diff --git a/easybuild/easyconfigs/l/libgit2/libgit2-1.7.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libgit2/libgit2-1.7.0-GCCcore-12.3.0.eb deleted file mode 100644 index df14e87ef74..00000000000 --- a/easybuild/easyconfigs/l/libgit2/libgit2-1.7.0-GCCcore-12.3.0.eb +++ /dev/null @@ -1,34 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'libgit2' -version = '1.7.0' - -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': '12.3.0'} - -github_account = 'libgit2' -source_urls = [GITHUB_SOURCE] -sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] -checksums = ['d9d0f84a86bf98b73e68997f5c1543cc5067d0ca9c7a5acaba3e8d117ecefef3'] - -builddependencies = [ - ('binutils', '2.40'), - ('CMake', '3.26.3'), - ('pkgconf', '1.9.5'), -] - -dependencies = [ - ('PCRE', '8.45'), - ('OpenSSL', '1.1', '', SYSTEM), -] - -sanity_check_paths = { - 'files': ['include/git2.h', 'lib64/libgit2.%s' % SHLIB_EXT, 'lib64/pkgconfig/libgit2.pc'], - 'dirs': [] -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/r/R/R-4.3.1-gfbf-2023a.eb b/easybuild/easyconfigs/r/R/R-4.3.2-gfbf-2023a.eb similarity index 61% rename from easybuild/easyconfigs/r/R/R-4.3.1-gfbf-2023a.eb rename to easybuild/easyconfigs/r/R/R-4.3.2-gfbf-2023a.eb index 24764c1cd82..ed664162bf5 100644 --- a/easybuild/easyconfigs/r/R/R-4.3.1-gfbf-2023a.eb +++ b/easybuild/easyconfigs/r/R/R-4.3.2-gfbf-2023a.eb @@ -1,5 +1,5 @@ name = 'R' -version = '4.3.1' +version = '4.3.2' homepage = 'https://www.r-project.org/' description = """R is a free software environment for statistical computing @@ -9,11 +9,10 @@ toolchain = {'name': 'gfbf', 'version': '2023a'} source_urls = ['https://cloud.r-project.org/src/base/R-%(version_major)s'] sources = [SOURCE_TAR_GZ] -checksums = ['8dd0bf24f1023c6f618c3b317383d291b4a494f40d73b983ac22ffea99e4ba99'] +checksums = ['b3f5760ac2eee8026a3f0eefcb25b47723d978038eee8e844762094c860c452a'] builddependencies = [ ('pkgconf', '1.9.5'), - #('Xvfb', '21.1.6'), ('Autotools', '20220317'), ] dependencies = [ @@ -32,13 +31,12 @@ dependencies = [ ('libjpeg-turbo', '2.1.5.1'), # for plottting in R ('LibTIFF', '4.5.0'), ('Java', '11', '', SYSTEM), - ('libgit2', '1.7.0'), + ('libgit2', '1.7.1'), ('OpenSSL', '1.1', '', SYSTEM), ('cURL', '8.0.1'), - #('Tk', '8.6.12'), # for tcltk - #('libxml2', '2.10.3'), # for XML - #('HarfBuzz', '5.3.1'), # for textshaping - #('FriBidi', '1.0.12'), # for textshaping + ('Tk', '8.6.13'), # for tcltk + ('HarfBuzz', '5.3.1'), # for textshaping + ('FriBidi', '1.0.12'), # for textshaping ] @@ -65,8 +63,11 @@ exts_default_options = { } # !! order of packages is important !! -# packages updated on 22nd June 2023 +# packages updated on 5th November 2023 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', @@ -81,11 +82,11 @@ exts_list = [ 'tcltk', 'tools', 'utils', - ('rlang', '1.1.1', { - 'checksums': ['5e5ec9a7796977216c39d94b1e342e08f0681746657067ba30de11b8fa8ada99'], + ('rlang', '1.1.2', { + 'checksums': ['2a0ee1dc6e5c59b283c32db5e74e869922a336197cb406fe92622b6ec66f8092'], }), - ('Rcpp', '1.0.10', { - 'checksums': ['1e65e24a9981251ab5fc4f9fd65fe4eab4ba0255be3400a8c5abe20b62b5d546'], + ('Rcpp', '1.0.11', { + 'checksums': ['df757c3068599c6c05367900bcad93547ba3422d59802dbaca20fd74d4d2fa5f'], }), ('R6', '2.5.1', { 'checksums': ['8d92bd29c2ed7bf15f2778618ffe4a95556193d21d8431a7f75e7e5fc102bf48'], @@ -96,11 +97,11 @@ exts_list = [ ('base64enc', '0.1-3', { 'checksums': ['6d856d8a364bcdc499a0bf38bfd283b7c743d08f0b288174fba7dbf0a04b688d'], }), - ('rprojroot', '2.0.3', { - 'checksums': ['50604247470e910cecfe9b76df754bf96a0d701f81b732f7aa9c90a20d30f897'], + ('rprojroot', '2.0.4', { + 'checksums': ['b5f463fb25a24dac7a4ca916be57dbe22b5262e1f41e53871ca83e57d4336e99'], }), - ('xfun', '0.39', { - 'checksums': ['d0ecaabb243dd3496da6029932fcdd4772914843de7ffd0b78a172efde1356c9'], + ('xfun', '0.41', { + 'checksums': ['2374c3b8f141f1e5ff01b291d8aa5c3dc807dd8e99ab4dc7a048c9534a7e3b02'], }), ('commonmark', '1.9.0', { 'checksums': ['6dd01a5a26c8d436486abf69c2f6ad0f8dd1c811f575c31983aeb4dbd376548f'], @@ -108,8 +109,8 @@ exts_list = [ ('highr', '0.10', { 'checksums': ['ec55bc1ff66390ed66806dc2a7b6c17dbfd089b3d73fe2e369017f8cb4bc347b'], }), - ('digest', '0.6.31', { - 'checksums': ['5a284f490eaca6750f695f00a584cfca3f180ca1046ac1107202141149d431b9'], + ('digest', '0.6.33', { + 'checksums': ['be702c886b1639be7eda4ea25a4261b30ce418c580f79bd78ec8d6cb4d327819'], }), ('desc', '1.4.2', { 'checksums': ['758acf14be478c09ba7e84ade3a7ce512becf35d44e5e6a997b932065f2a227c'], @@ -117,8 +118,8 @@ exts_list = [ ('ellipsis', '0.3.2', { 'checksums': ['a90266e5eb59c7f419774d5c6d6bd5e09701a26c9218c5933c9bce6765aa1558'], }), - ('prettyunits', '1.1.1', { - 'checksums': ['9a199aa80c6d5e50fa977bc724d6e39dae1fc597a96413053609156ee7fb75c5'], + ('prettyunits', '1.2.0', { + 'checksums': ['f059f27e2a5c82e351fe05b87ad712f7afc273c651450453f59d99af5deeacea'], }), ('crayon', '1.5.2', { 'checksums': ['70a9a505b5b3c0ee6682ad8b965e28b7e24d9f942160d0a2bad18eec22b45a7a'], @@ -129,56 +130,56 @@ exts_list = [ ('magrittr', '2.0.3', { 'checksums': ['a2bff83f792a1acb801bfe6330bb62724c74d5308832f2cb6a6178336ace55d2'], }), - ('evaluate', '0.21', { - 'checksums': ['3178c99cee8917d7d128806d064d4fecce7845ed07f42e759dcc0adda89c22b9'], + ('evaluate', '0.23', { + 'checksums': ['c9cf9c37502b8fbfa78e4eb96b8c3d1789060e49505c86c07cb7476da804a45c'], }), ('ps', '1.7.5', { 'checksums': ['1abc3ae3c55797b994973f7e43bf5c7bbb4da649a0dcfad36675e196dba4cb4e'], }), - ('processx', '3.8.1', { - 'checksums': ['e008472b81d4ca1a37a4ba7dd58e5e944f96ab2e44c8ccc8840d43e9fe99e93c'], + ('processx', '3.8.2', { + 'checksums': ['e91b87af5b23c14b71003ec880f749dca81fd74f0601ab59ea1847c7fe857ecd'], }), ('callr', '3.7.3', { 'checksums': ['567bfedf073a1d4c5785f0553341608a214938110567b9a6495ff20ebb2fd04e'], }), - ('pkgbuild', '1.4.1', { - 'checksums': ['cdb0ace14444f362be9725bd84e9752dab92f4771296504b63b9b8084f5e8a6b'], + ('pkgbuild', '1.4.2', { + 'checksums': ['2334a245d75420b2adf9f217a6bc4a5f7faaa4244a6aac2b774b26f199fc82c5'], }), - ('fs', '1.6.2', { - 'checksums': ['548b7c0ed5ab26dc4fbd88707ae12987bcaef834dbc6de4e17d453846dc436b2'], + ('fs', '1.6.3', { + 'checksums': ['fa82061e50d7a4d94b7e404f9f2b699e75ae8fbfb575fabdfc2c39f536c0f971'], }), - ('utf8', '1.2.3', { - 'checksums': ['c0a88686591f4ad43b52917d0964e9df4c62d8858fe25135a1bf357dfcbd6347'], + ('utf8', '1.2.4', { + 'checksums': ['418f824bbd9cd868d2d8a0d4345545c62151d321224cdffca8b1ffd98a167b7d'], }), - ('fansi', '1.0.4', { - 'checksums': ['3163214e6c40922bbb495229259ed8ce1bebd98b77098a6936d234e43da9c49f'], + ('fansi', '1.0.5', { + 'checksums': ['c616ce357fbfd43253c366da578549a38066459058c22fb99c82fc05992e23f6'], }), ('pkgconfig', '2.0.3', { 'checksums': ['330fef440ffeb842a7dcfffc8303743f1feae83e8d6131078b5a44ff11bc3850'], }), - ('withr', '2.5.0', { - 'checksums': ['37317b3ed790a08407072993a05ab255f6305f95a12a16e0e28aa6aa80fc8bc0'], + ('withr', '2.5.2', { + 'checksums': ['d5b6fa6d728fda5201310d6ad5921a43aae1c23029c25334bfc1e54cb13d4205'], }), ('glue', '1.6.2', { 'checksums': ['9da518f12be584c90e75fe8e07f711ee3f6fc0d03d817f72c25dc0f66499fdbf'], }), - ('rstudioapi', '0.14', { - 'checksums': ['469d0987b1ad728a96c363a422fba712a5cebc8b11a5f7e953b4a671044dafc4'], + ('rstudioapi', '0.15.0', { + 'checksums': ['935bc81dca37d3d6e77982bfe6e7fbd779e8606e5b7e00d0ba4c80fec0416ccf'], }), - ('pkgload', '1.3.2', { - 'checksums': ['35d19a032bfeeefcab92d76a768b4a420c2ede0920badaf48cca878592b46b2f'], + ('pkgload', '1.3.3', { + 'checksums': ['b0898122876479cc4a35cd566654b3a7b50f8ac105565dbf3f8b9d4283816959'], }), ('fastmap', '1.1.1', { 'checksums': ['3623809dd016ae8abd235200ba7834effc4b916915a059deb76044137c5c7173'], }), - ('htmltools', '0.5.5', { - 'checksums': ['c8b23fab855a89c6ed0f6d6c7cad0ff9c5ae329c0bdb479940443ee752f26659'], + ('htmltools', '0.5.7', { + 'checksums': ['ecb0d82619063f49e4d001c44fcc1b811a06928fd66c2bb8c86632798d98b386'], }), ('yaml', '2.3.7', { 'checksums': ['d20cb219e0f9c48aba02f132f81cfa9ecda5e22c925e36726840218ed56680ab'], }), - ('knitr', '1.43', { - 'checksums': ['3d29baea8c349aaa9310879ceb9a9d51bcaec39827ad46d422c3793c8a4ed53c'], + ('knitr', '1.45', { + 'checksums': ['ee2edea53bc53efa51d131ab5a0b0c829c0f950b79d3c6ee34705354bf7584fb'], }), ('mime', '0.12', { 'checksums': ['a9001051d6c1e556e881910b1816b42872a1ee41ab76d0040ce66a27135e3849'], @@ -189,14 +190,14 @@ exts_list = [ ('brio', '1.1.3', { 'checksums': ['eaa89041856189bee545bf1c42c7920a0bb0f1f70bb477487c467ee3e8fedcc6'], }), - ('jsonlite', '1.8.5', { - 'checksums': ['dc3cca4bdca1b6d6836c412760ea9656140683126c54cb89c3e42219dec4a3ad'], + ('jsonlite', '1.8.7', { + 'checksums': ['7d42b7784b72d728698ea02b97818df51e2015ffa39fec2eaa2400771b0f601c'], }), ('lifecycle', '1.0.3', { 'checksums': ['6459fdc3211585c0cdf120427579c12149b02161efe273a64b825c05e9aa69c2'], }), - ('vctrs', '0.6.3', { - 'checksums': ['93dc220dcde8b440586b2260460ef354e827a17dfec1ea6a9815585a10cfa5c2'], + ('vctrs', '0.6.4', { + 'checksums': ['8a80192356e724d21bd89a0ce3e5835856fd5bb1651e7fc205c6fee58fd001c8'], }), ('stringr', '1.5.0', { 'checksums': ['52b159d7700a139111b4caf939e7c9c6ab3e01185181400d70a74c552826633a'], @@ -213,29 +214,29 @@ exts_list = [ ('rematch2', '2.1.2', { 'checksums': ['fe9cbfe99dd7731a0a2a310900d999f80e7486775b67f3f8f388c30737faf7bb'], }), - ('waldo', '0.5.1', { - 'checksums': ['45bf076cff449e3c506c95857734bb73fdf30040333709b8845d09a12c6fdf46'], + ('waldo', '0.5.2', { + 'checksums': ['82cdae1ab2c5e7e5dbf5c6bdf832020b46e152732053fb45de7c9a81afdf2e05'], }), - ('testthat', '3.1.9', { - 'checksums': ['4da1f992549c9b8db211f205059ec4c5d91a45d5971d60ebae21058268448375'], + ('testthat', '3.2.0', { + 'checksums': ['5b0be53295fe509042e48711df091f7021e23512d1339a4f6f6d9f36d145650e'], }), - ('xml2', '1.3.4', { - 'checksums': ['340bb1a18e643a5008c0b4e92d71c3b0abacb44f1742e3a77d0cb33cb73b3030'], + ('xml2', '1.3.5', { + 'checksums': ['3d6a10a7ab76e0cc024b73d3fb8af65a662efe0e707681d9ffc2b3ff1f09e282'], }), - ('curl', '5.0.1', { - 'checksums': ['b7058f9cc7fa8f649505583584b61383fc08dccf746faa5381ba3d0b8bdf93a6'], + ('curl', '5.1.0', { + 'checksums': ['57218da84b85bd01ce7daa4bca3e271eda1bf688e0cdb211c397ccb272ecba97'], }), ('sys', '3.4.2', { 'checksums': ['b7bdce66f0fb681830ea6fb77b5a2c6babb43920abb1eddc733f95c0a63ce5b3'], }), - ('askpass', '1.1', { - 'checksums': ['db40827d1bdbb90c0aa2846a2961d3bf9d76ad1b392302f9dd84cc2fd18c001f'], + ('askpass', '1.2.0', { + 'checksums': ['b922369781934d0ffc8d0c0177e8ace56796c2e6a726f65e460c16f792592cef'], }), - ('openssl', '2.0.6', { - 'checksums': ['77f3032a16270f0d1734f269b8d348eedc75b277812854386091143082c1b3f3'], + ('openssl', '2.1.1', { + 'checksums': ['faa726f9af2a97d5fa1e1044f4a38ee2edd4c81f0beb5830f6a36ff249b64bdc'], }), - ('httr', '1.4.6', { - 'checksums': ['8d6d86cbef23738d2b4390490f7486d8cf7674f0a59c19f515f61cad35ec37b2'], + ('httr', '1.4.7', { + 'checksums': ['1555e6c2fb67bd38ff11b479f74aa287b2d93f4add487aec53b836ff07de3a3a'], }), ('jquerylib', '0.1.4', { 'checksums': ['f0bcc11dcde3a6ff180277e45c24642d3da3c8690900e38f44495efbc9064411'], @@ -243,11 +244,11 @@ exts_list = [ ('rappdirs', '0.3.3', { 'checksums': ['49959f65b45b0b189a2792d6c1339bef59674ecae92f8c2ed9f26ff9e488c184'], }), - ('sass', '0.4.6', { - 'checksums': ['2ee82ce709b7fdee78f7e2364d04f369f58fc2cda4bb5a235bd53c49d311c019'], + ('sass', '0.4.7', { + 'checksums': ['717a08b63615a4fd9e494f775c33f0f965db83677cf1cc37849afc3da1c5e9ee'], }), - ('purrr', '1.0.1', { - 'checksums': ['0a7911be3539355a4c40d136f2602befcaaad5a3f7222078500bfb969a6f2ba2'], + ('purrr', '1.0.2', { + 'checksums': ['2c1bc6bb88433dff0892b41136f2f5c23573b335ff35a4775c72aa57b48bbb63'], }), ('cachem', '1.0.8', { 'checksums': ['ea9ca919fe615dce8770758ecc2fc88ac99074f66ff1cde3a0b95d40007f45c2'], @@ -255,32 +256,32 @@ exts_list = [ ('memoise', '2.0.1', { 'checksums': ['f85034ee98c8ca07fb3cd826142c1cd1e1e5747075a94c75a45783bbc4fe2deb'], }), - ('bslib', '0.5.0', { - 'checksums': ['a2c6fbc62242806e10bb58c5d1ba04a6d3bf4e546bc53d7acf1b8eb1160bd115'], + ('bslib', '0.5.1', { + 'checksums': ['b175612322e3ba929cf67a9261dd253346a981ce15bbb63d4a6874f54d5ef00e'], }), - ('fontawesome', '0.5.0', { - 'checksums': ['4117b417a33e82d626881d7059eb54e7534cba202e75dae7e27021cb3796e90b'], + ('fontawesome', '0.5.2', { + 'checksums': ['da3de2a9717084d1400d48edd783f06c66b8c910ce9c8d753d1b7d99be1c5cc9'], }), - ('tinytex', '0.45', { - 'checksums': ['0c2fbbd09e80af80ca6b685bf0653f070da97b85413d39af966aba28f376e92c'], + ('tinytex', '0.48', { + 'checksums': ['1d0b989fa781a50a560b8d785f20c28bffc63b5b2e0fcd937c57fdd61d597695'], }), - ('rmarkdown', '2.22', { - 'checksums': ['c6635519503e0fcdd518696d3ac96d8d28d9d4ecd9db0532c53426002f6387b8'], + ('rmarkdown', '2.25', { + 'checksums': ['06e4662666fe018fbe3bef3531280a461c7bc24bb00f34b9d4c7b08d52210155'], }), - ('downlit', '0.4.2', { - 'checksums': ['33dff66909104d1a5ba8e57b1288986e82b61fd5e91dce0cd358d53724b37e3c'], + ('downlit', '0.4.3', { + 'checksums': ['6c0fbe98ece8a511973263f8e8a35574df0cfc45edea7452b53b8d326436b3bd'], }), - ('cpp11', '0.4.3', { - 'checksums': ['f1a60e4971a86dbbcf6a16bbd739b59bb66d9c45d93cfd8dedc2a87e302598f1'], + ('cpp11', '0.4.6', { + 'checksums': ['d1c56954671d3398078ad52aaa4efce0864e8166465c8c5e5e9a1e40599055b3'], }), - ('systemfonts', '1.0.4', { - 'checksums': ['ef766c75b942f147d382664a00d6a4930f1bfe0cce9d88943f571682a85a84c0'], + ('systemfonts', '1.0.5', { + 'checksums': ['840ffb1d8293739c79cbc868101d9f9a84f4a9de4c7b3625e30af2fb63e15823'], }), - ('textshaping', '0.3.6', { - 'checksums': ['80e2c087962f55ce2811fbc798b09f5638c06c6b28c10cd3cb3827005b902ada'], + ('textshaping', '0.3.7', { + 'checksums': ['fa924dbe1fb4138b80d6c26ee42f4203843f1d34f77e2a5e42514e6fcc97ec42'], }), - ('ragg', '1.2.5', { - 'checksums': ['936f4d75e0e01cdeefb9f57d121cdd7812d0de5a9e1a3a8315f92ce1c84da8f9'], + ('ragg', '1.2.6', { + 'checksums': ['1014dc493ab52e98e4114fbabfca753bebd4d64db7ef7946bd064fb404e0f7c7'], }), ('whisker', '0.4.1', { 'checksums': ['bf5151494508032f68ac41e211bda80da9087c65c7068ffdd12f16669bf1f2bc'], @@ -300,20 +301,20 @@ exts_list = [ ('later', '1.3.1', { 'checksums': ['23eed681f0b9eacebbc3c6a5ba14ee0b676a4bf6e69af194c5a36edfe11464ac'], }), - ('promises', '1.2.0.1', { - 'checksums': ['8d3a8217909e91f4c2a2eebba5ac8fc902a9ac1a9e9d8a30815c9dc0f162c4b7'], + ('promises', '1.2.1', { + 'checksums': ['3ce0a26df39ea27536877ec6db13083b2952108245024baa8b40ae856d2ce5be'], }), ('xtable', '1.8-4', { 'checksums': ['5abec0e8c27865ef0880f1d19c9f9ca7cc0fd24eadaa72bcd270c3fb4075fd1c'], }), - ('httpuv', '1.6.11', { - 'checksums': ['8ba79e0a8351274daf2dc566c71f88e891127cdedca62ad77a4b27a8103eeef5'], + ('httpuv', '1.6.12', { + 'checksums': ['b1d972b1c240702c38cb844a1040670d62876abf462256764b49c120a52f5e74'], }), ('sourcetools', '0.1.7-1', { 'checksums': ['96812bdb7a0dd99690d84e4b0a3def91389e4290f53f01919ef28a50554e31d1'], }), - ('shiny', '1.7.4', { - 'checksums': ['bbfcdd7375013b8f59248b3f3f4e752acd445feb25179f3f7f65cd69614da4b5'], + ('shiny', '1.7.5.1', { + 'checksums': ['2023d91cc8039580752f6ecc5010d4419b7d928724ce5b10b93a3b48e1e6fb46'], }), ('miniUI', '0.1.1.1', { 'checksums': ['452b41133289f630d8026507263744e385908ca025e9a7976925c1539816b0c0'], @@ -336,8 +337,8 @@ exts_list = [ ('rcmdcheck', '1.4.0', { 'checksums': ['bbd4ef7d514b8c2076196a7c4a6041d34623d55fbe73f2771758ce61fd32c9d0'], }), - ('remotes', '2.4.2', { - 'checksums': ['f2ef875f24a485bf4f55a8c830f87cdd5db868f9a8cdb624dc452d0bf66ba516'], + ('remotes', '2.4.2.1', { + 'checksums': ['7ba8ca9a652d60bcdea25dbd43bd1e055e97b031c05e0bc3fac43bf245c1209d'], }), ('clipr', '0.8.0', { 'checksums': ['32c2931992fbec9c31b71de3e27059f1cbb45b4b1f45fd42e0e8dbcec6de3be9'], @@ -354,17 +355,17 @@ exts_list = [ ('gh', '1.4.0', { 'checksums': ['68c69fcd18429b378e639a09652465a4e92b7b5b5704804d0c5b1ca2b9b58b71'], }), - ('credentials', '1.3.2', { - 'checksums': ['2ffa7c11bedbfa034adf553d0a2f2e4f6a496b858af753a09a89219cff9028b8'], + ('credentials', '2.0.1', { + 'checksums': ['2c7cfc45bd4afa9a2c2b85d43e907b212da3468781e1b617737bd095253c358b'], }), ('zip', '2.3.0', { 'checksums': ['33eba844922af9981732ee6ec1582d46cf04c562344f09a0f0f14a22c6f74543'], }), - ('gert', '1.9.2', { - 'checksums': ['42ca1b4bcafb1fdbbc7f54df0ee4476ecd19e9e7d563b53fe7064e0086ab665e'], + ('gert', '2.0.0', { + 'checksums': ['7c147c3740e7ece8764e6197f311d84e6191fddead1d96fbbfb29816ef5d6391'], }), - ('usethis', '2.2.0', { - 'checksums': ['2ccebe690aadebff96451cc9c226dc1a1e9ca5ac6ec83310e12a1312cb163b4f'], + ('usethis', '2.2.2', { + 'checksums': ['d9d8c1a789ae6fd0e717e174ac29da2e4a925df321e5cc0bfb3d65c87e4cbe46'], }), ('devtools', '2.4.5', { 'checksums': ['38160ebd839acdec7ebf0699a085b4ab1ebd5500d3c57a9fa7ae484f1909904b'], From 5fa0641a00b326468a1546d990a067f37797d8ba Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Tue, 7 Nov 2023 17:12:30 +0100 Subject: [PATCH 159/599] adding easyconfigs: R-bundle-CRAN-2023.11-foss-2023a.eb and patches: HWxtest-1.1.9_add-fcommon.patch, liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch --- .../HWxtest-1.1.9_add-fcommon.patch | 21 + .../R-bundle-CRAN-2023.11-foss-2023a.eb | 3399 +++++++++++++++++ ...dSVM-1.2.4-fix_ppc_and_aarch64_build.patch | 49 + 3 files changed, 3469 insertions(+) create mode 100644 easybuild/easyconfigs/r/R-bundle-CRAN/HWxtest-1.1.9_add-fcommon.patch create mode 100644 easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2023.11-foss-2023a.eb create mode 100644 easybuild/easyconfigs/r/R-bundle-CRAN/liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch diff --git a/easybuild/easyconfigs/r/R-bundle-CRAN/HWxtest-1.1.9_add-fcommon.patch b/easybuild/easyconfigs/r/R-bundle-CRAN/HWxtest-1.1.9_add-fcommon.patch new file mode 100644 index 00000000000..a4e41eea63e --- /dev/null +++ b/easybuild/easyconfigs/r/R-bundle-CRAN/HWxtest-1.1.9_add-fcommon.patch @@ -0,0 +1,21 @@ +fix "multiple definition" errors by adding -fcommon compiler options, +see https://www.gnu.org/software/gcc/gcc-10/porting_to.html + +author: Kenneth Hoste (HPC-UGent) + +diff -ruN HWxtest.orig/MD5 HWxtest/MD5 +--- HWxtest.orig/MD5 2020-11-08 21:15:03.612622261 +0100 ++++ HWxtest/MD5 2020-11-08 21:13:24.278691443 +0100 +@@ -40,6 +40,7 @@ + 4657a2011dc5363ed1cfd1d29a7040d5 *src/HWmtest.c + 08ec52ea231752fbb2bb11a529107806 *src/HWxcount.c + 23598383650c211dd18d54bded68b9bd *src/HWxtest.c ++8b6d9aec8b8cef60d1b245e0f290bfed *src/Makevars + 886a6d855fb0b59e565b919a1ff69eb0 *vignettes/HWxtest.Rmd + fcf857c5f98963f740c5c2f95e33ccc9 *vignettes/HWxtest.md + b93f768037a75ec9edd60ca89fd4c1db *vignettes/bibHW.txt +diff -ruN HWxtest.orig/src/Makevars HWxtest/src/Makevars +--- HWxtest.orig/src/Makevars 1970-01-01 01:00:00.000000000 +0100 ++++ HWxtest/src/Makevars 2020-11-08 21:15:51.340615023 +0100 +@@ -0,0 +1 @@ ++PKG_CFLAGS = -fcommon diff --git a/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2023.11-foss-2023a.eb b/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2023.11-foss-2023a.eb new file mode 100644 index 00000000000..8421d82323d --- /dev/null +++ b/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2023.11-foss-2023a.eb @@ -0,0 +1,3399 @@ +easyblock = 'Bundle' + +name = 'R-bundle-CRAN' +version = '2023.11' + +homepage = 'https://www.r-project.org/' +description = "Bundle of R packages from CRAN" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('pkgconf', '1.9.5'), + ('Xvfb', '21.1.8'), + ('Autotools', '20220317'), + ('CMake', '3.26.3'), +] + +dependencies = [ + ('R', '4.3.2'), + ('X11', '20230603'), + ('Mesa', '23.1.4'), + ('libGLU', '9.0.3'), + ('cairo', '1.17.8'), + ('libreadline', '8.2'), + ('ncurses', '6.4'), + ('bzip2', '1.0.8'), + ('XZ', '5.4.2'), + ('zlib', '1.2.13'), + ('SQLite', '3.42.0'), + ('PCRE2', '10.42'), + ('libpng', '1.6.39'), # for plotting in R + ('libjpeg-turbo', '2.1.5.1'), # for plottting in R + ('LibTIFF', '4.5.0'), + ('Java', '11', '', SYSTEM), + ('Tk', '8.6.13'), # for tcltk + ('cURL', '8.0.1'), # for RCurl + ('libxml2', '2.11.4'), # for XML + ('GMP', '6.2.1'), # for igraph + ('NLopt', '2.7.1'), # for nlopt + ('FFTW', '3.3.10'), # for fftw + ('libsndfile', '1.2.2'), # for seewave + ('ICU', '73.2'), # for rJava & gdsfmt + ('HDF5', '1.14.0'), # for hdf5r + ('UDUNITS', '2.2.28'), # for units + ('GSL', '2.7'), # for RcppGSL + ('ImageMagick', '7.1.1-15'), + ('GLPK', '5.0'), # for Rglpk + ('nodejs', '18.17.1'), # for V8 (required by rstan) + ('GDAL', '3.7.1'), # for sf + ('MPFR', '4.2.0'), # for Rmpfr + ('PostgreSQL', '16.0'), # for RPostgreSQL + ('libgit2', '1.7.1'), + ('OpenSSL', '1.1', '', SYSTEM), +] + +# 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" + +# specify that at least EasyBuild v3.5.0 is required, +# since we rely on the updated easyblock for R to configure correctly w.r.t. BLAS/LAPACK +easybuild_version = '3.5.0' + +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', +} + +# !! order of packages is important !! +# packages updated on 5th November 2023 +exts_list = [ + ('abind', '1.4-5', { + 'checksums': ['3a3ace5afbcb86e56889efcebf3bf5c3bb042a282ba7cc4412d450bb246a3f2c'], + }), + ('magic', '1.6-1', { + 'checksums': ['ca79ec7ae92b736cb128556c081abf547f49956c326e053a76579889cbcb7976'], + }), + ('RcppProgress', '0.4.2', { + 'checksums': ['b1624b21b7aeb1dafb30f092b2a4bef4c3504efd2d6b00b2cdf55dc9df194b48'], + }), + ('lpSolve', '5.6.19', { + 'checksums': ['49d5b49e64c6eba2bc4cea80eb615df21a2d0188b1bbffa05052dc978c94581b'], + }), + ('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', '4.0.9', { + 'checksums': ['722053271987a0c9673c3ff9e7968bbab47979d529a2fe6bb1a3179408ee3c4f'], + }), + ('bnlearn', '4.9', { + 'checksums': ['5159ab0e4b4785ce830726284bdd52d8e1e444a34109b657d022c07b14449227'], + }), + ('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', '3.9.4', { + 'checksums': ['59cf8b194fe98b1cc05dbb4d686810a1068f59d8b402b731548a898ece85f111'], + }), + ('gdata', '3.0.0', { + 'checksums': ['a456b9921765a705fe8e51780dfbbc6ca005abc948b2f80effeccd468601b17f'], + }), + ('GSA', '1.03.2', { + 'checksums': ['177d6059fc645d3d8883806d2dea1c5dfc68efdada9aadde8a96b6d57acf35b8'], + }), + ('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', '1.11', { + 'checksums': ['47fc61755a952ce9716c12de2daf7940fcf306747bd47ad31dd364bbccca5f14'], + }), + ('mlbench', '2.1-3.1', { + 'checksums': ['7afec6d58968ab526ea642e1df39bead2f479c14486b0a62032c999ba73d5cf0'], + }), + ('NLP', '0.2-1', { + 'checksums': ['05eaa453ad2757311c073fd30093c738b20a977c5089031eb454345a1d01f2b6'], + }), + ('mclust', '6.0.0', { + 'checksums': ['de7c306ecba1ef0f4e4a56c748ce08149417496b711beefb032d561a4c28122a'], + }), + ('RANN', '2.6.1', { + 'checksums': ['b299c3dfb7be17aa41e66eff5674fddd2992fb6dd3b10bc59ffbf0c401697182'], + }), + ('rmeta', '3.0', { + 'checksums': ['b9f9d405935cffcd7a5697ff13b033f9725de45f4dc7b059fd68a7536eb76b6e'], + }), + ('MASS', '7.3-60', { + 'checksums': ['b802410feab01464d112b27b3501176eb8e68511d4ba9d052ac4db1f2a72f0c2'], + }), + ('lattice', '0.22-5', { + 'checksums': ['ba1fbe5e18a133507dca9851b7f933002bdb6d1f3ea5f410a0a441103b6da5f1'], + }), + ('nlme', '3.1-163', { + 'checksums': ['7d46ff4c4fb7fda8df6129b28cd2aa7d32e814eac87dae8ea9fa7560593c128a'], + }), + ('segmented', '1.6-4', { + 'checksums': ['472c08ae3eb1c4e784aba45f3e745b0e946bef77c26fbb9f103fd35e1a349191'], + }), + ('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', '1.0-19', { + 'checksums': ['ba55bf193f1df9785a0e13b7ef727d5fd2415b318cd6a26b48a2db490c4dfe40'], + }), + ('timeDate', '4022.108', { + 'checksums': ['a5949b4fe2f6bdff751fc0793df8e3150cc25c078d48a28c066c10a6c4bfceef'], + }), + ('longmemo', '1.1-2', { + 'checksums': ['7964e982287427dd58f98e1144e468ae0cbd572d25a4bea6ca9ae9c7522f3207'], + }), + ('ADGofTest', '0.3', { + 'checksums': ['9cd9313954f6ecd82480d373f6c5371ca84ab33e3f5c39d972d35cfcf1096846'], + }), + ('pixmap', '0.4-12', { + 'checksums': ['893ba894d4348ba05e6edf9c1b4fd201191816b444a214f7a6b2c0a79b0a2aec'], + }), + ('sp', '2.1-1', { + 'checksums': ['2d34cde2a8d5c7876425f99d9d3b24ae192430d316bd2a397a62b52412b1405b'], + }), + ('hms', '1.1.3', { + 'checksums': ['e626f4c60af46efd53ea631b316a103e089470d8fd63c0e0c0efb99364990282'], + }), + ('progress', '1.2.2', { + 'checksums': ['b4a4d8ed55db99394b036a29a0fb20b5dd2a91c211a1d651c52a1023cc58ff35'], + }), + ('RcppArmadillo', '0.12.6.6.0', { + 'checksums': ['d35eb191c5a14e5a95498f43dff3984763ac3fecaf4016c12926f6031e753e9c'], + }), + ('ade4', '1.7-22', { + 'checksums': ['007df54e83a2a6cb8d6da8006f0aace011e7eaa7744dc5f8230ac2c002b393b4'], + }), + ('AlgDesign', '1.2.1', { + 'checksums': ['5989626c526bd7c3d9bdda326c962056879be03392065a0b7ddb9b8cf9309d05'], + }), + ('BH', '1.81.0-1', { + 'checksums': ['f51c8badd6f181e06353314e1d15a6ec1495cc498ee74b6fa4ea8aba6e97ff64'], + }), + ('Matrix', '1.6-1.1', { + 'checksums': ['331eb1f1fe9441d4224d8551072443596001b50e8c15618f59cb938b46ee8cc2'], + }), + ('Brobdingnag', '1.2-9', { + 'checksums': ['f9012d250bc2a0f47815d6a7c06df2d4ddf3d8bab2d3b75e8cdefd964d20e91e'], + }), + ('corpcor', '1.6.10', { + 'checksums': ['71a04c503c93ec95ddde09abe8c7ddeb36175b7da76365a14b27066383e10e09'], + }), + ('longitudinal', '1.1.13', { + 'checksums': ['57f04a0f387c1cc30d2feb945dc3ed35d2a304d94d21d3bc2cac8c92571fdc10'], + }), + ('backports', '1.4.1', { + 'checksums': ['845c3c59fbb05e5a892c4231b955a0afdd331d82b7cc815bcff0672023242474'], + }), + ('checkmate', '2.3.0', { + 'checksums': ['88721b851e489da0acf88a9d598c847eca22255d7afb86fcaa06f378768b81d4'], + }), + ('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', '3.4.1.1', { + 'checksums': ['d39d467537c336d20c4b501d36a421dd3e8309c9d1bdcf9b4a7abe994242851a'], + }), + ('nnls', '1.5', { + 'checksums': ['cd70feb286f86f6dead75da693a8f67c9bd3b91eb738e6e6ac659e3b8c7a3452'], + }), + ('sendmailR', '1.4-0', { + 'checksums': ['5b8b91fc13f6b07b9fc5a2cf7591cf760fad47c5ea17d87a2891898c506454ad'], + }), + ('dotCall64', '1.1-0', { + 'checksums': ['3484e32d5b2ff6e1b74963cc81e8dcb5c3dab0e1b1a5905898606cb6851370c5'], + }), + ('spam', '2.10-0', { + 'checksums': ['719c86a23801ecf051ffd8291912ee3567af4010e74af470fbf09e274728ac79'], + }), + ('subplex', '1.8', { + 'checksums': ['3bc31d8990380c9f790c9c7d84cb2e39f4945eff934eddfa1196d597465be5a5'], + }), + ('logspline', '2.1.21', { + 'checksums': ['8e3a3cf11f3261f010092aa657d938a69b604818afc123151c7d3e24e0980b77'], + }), + ('ncbit', '2013.03.29.1', { + 'checksums': ['847f570c035d849e775c1cb922d2775e6c535971eb4429cf62904319fd126504'], + }), + ('permute', '0.9-7', { + 'checksums': ['eff88ffb579aaeb994e9f8609b776b2d9d9d56bc2879ddf180e3a2ad19f48dc0'], + }), + ('plotrix', '3.8-3', { + 'checksums': ['b961d3b59ba0850e4c198b57fcceb1735c1c10d5ddcda0ecd6c2c731f114bc05'], + }), + ('randomForest', '4.7-1.1', { + 'checksums': ['f59ea87534480edbcd6baf53d7ec57e8c69f4532c2d2528eacfd48924efa2cd6'], + }), + ('scatterplot3d', '0.3-44', { + 'checksums': ['1c9c08348c3ed925f59df40cb73accc9e1a169ccfb1e8571f105f40fa98e6ec2'], + }), + ('SparseM', '1.81', { + 'checksums': ['bd838f381ace680fa38508ff70b3d83cb9ffa28ac1ab568509249bca53c34b33'], + }), + ('tripack', '1.3-9.1', { + 'checksums': ['7f82f8d63741c468767acc6fb35281bd9903f6c3c52e8fada60a6ae317511fbe'], + }), + ('irace', '3.5', { + 'checksums': ['d9928644a5a7e94838558d73afaaee8a914fd26fe68f691ad103331632060bf4'], + }), + ('rJava', '1.0-6', { + 'checksums': ['e290d0493317a5d6c452793e92baa914e37ef03faef19b2e436329b4ec8658c6'], + }), + ('RColorBrewer', '1.1-3', { + 'checksums': ['4f42f5423c45688b39f492c7892d93f37b4541831c8ffb140364d2bd89031ac0'], + }), + ('png', '0.1-8', { + 'checksums': ['5a36fabb6d62ba2533d3fc4cececd07891942cfb76fe689ec0d550d08762f61c'], + }), + ('jpeg', '0.1-10', { + 'checksums': ['c8d9f609c3088f91ec4853d6cc0e66511038a465811dea79ca6a0c09519178ca'], + }), + ('deldir', '1.0-9', { + 'checksums': ['127a24ec3aa7e41e441d5b2f5654f3b59fbe47bf61ba8038d81a6110c8670687'], + }), + ('RcppEigen', '0.3.3.9.4', { + 'checksums': ['41eabb8d034ffae0fcfcf23ca92b8f0fba5aec8f1ba108d922e19db7e10d5fb9'], + }), + ('interp', '1.1-4', { + 'checksums': ['4f7b5d388132a4d76e8635e2a7c4fa0d705df2b49e7d108faa16ce2236e34d06'], + }), + ('latticeExtra', '0.6-30', { + 'checksums': ['c550a76913624818482bf237d48883c58e368ba356ced8ed5e76146672279eed'], + }), + ('plyr', '1.8.9', { + 'checksums': ['15b5e7f711d53bf41b8687923983b8ef424563aa2f74c5195feb5b1df1aee103'], + }), + ('gtable', '0.3.4', { + 'checksums': ['7032039371a4ec1bde9d3e4b7dae450dcc9aab50bb0e6287ab26a1b0199c7977'], + }), + ('reshape2', '1.4.4', { + 'checksums': ['d88dcf9e2530fa9695fc57d0c78adfc5e361305fe8919fe09410b17da5ca12d8'], + }), + ('dichromat', '2.0-0.1', { + 'checksums': ['a10578e9ad8a581bd8fe0d8a8370051f3cdcf12c7d282f3af2a18dacda566081'], + }), + ('colorspace', '2.1-0', { + 'checksums': ['04078abb6b54119c90dc7085d62916bf292ccb163e213f9ea70567d1be82614c'], + }), + ('munsell', '0.5.0', { + 'checksums': ['d0f3a9fb30e2b5d411fa61db56d4be5733a2621c0edf017d090bdfa5e377e199'], + }), + ('labeling', '0.4.3', { + 'checksums': ['c62f4fc2cc74377d7055903c5f1913b7295f7587456fe468592738a483e264f2'], + }), + ('viridisLite', '0.4.2', { + 'checksums': ['893f111d31deccd2cc959bc9db7ba2ce9020a2dd1b9c1c009587e449c4cce1a1'], + }), + ('farver', '2.1.1', { + 'checksums': ['0dcfda6ca743f465372790bcff1bcbc6a7145fdac1c682b021f654e8c6c996ce'], + }), + ('scales', '1.2.1', { + 'checksums': ['59453e6dbdafee93dfb101e4d86048a62a12898134259d3ef02d65aeec57ed08'], + }), + ('zeallot', '0.1.0', { + 'checksums': ['439f1213c97c8ddef9a1e1499bdf81c2940859f78b76bc86ba476cebd88ba1e9'], + }), + ('assertthat', '0.2.1', { + 'checksums': ['85cf7fcc4753a8c86da9a6f454e46c2a58ffc70c4f47cac4d3e3bcefda2a9e9f'], + }), + ('lazyeval', '0.2.2', { + 'checksums': ['d6904112a21056222cfcd5eb8175a78aa063afe648a562d9c42c6b960a8820d4'], + }), + ('mgcv', '1.9-0', { + 'checksums': ['b2b10078c1f8b2ce3cadcca405496eedacc8d4632ee4357e17632cae1b043b70'], + }), + ('isoband', '0.2.7', { + 'checksums': ['7693223343b45b86de2b5b638ff148f0dafa6d7b1237e822c5272902f79cdf61'], + }), + ('ggplot2', '3.4.4', { + 'checksums': ['2d76ec065d3e604d019506f45b3b713ae20f38e47dbebfb5ba1648b47fe63e46'], + }), + ('pROC', '1.18.5', { + 'checksums': ['5593c841a6df5a2f2d209d0c14401971eb9427092ed9c3ac2059273807b42c89'], + }), + ('quadprog', '1.5-8', { + 'checksums': ['22128dd6b08d3516c44ff89276719ad4fe46b36b23fdd585274fa3a93e7a49cd'], + }), + ('BB', '2019.10-1', { + 'checksums': ['04d0b6ce6e5f070b109478a6005653dbe78613bb4e3ea4903203d851b5d3c94d'], + }), + ('data.table', '1.14.8', { + 'checksums': ['14b2ce5367df9c9bb58f373555066f5dcb629c156149b5565de36d69557139fd'], + }), + ('BBmisc', '1.13', { + 'checksums': ['1145dcf9fed15e7beeaa4a5c7075d8a8badd17c8246838cd63e40cd9551e4405'], + }), + ('fail', '1.3', { + 'checksums': ['ede8aa2a9f2371aff5874cd030ac625adb35c33954835b54ab4abf7aeb34d56d'], + }), + ('rlecuyer', '0.3-7', { + 'checksums': ['65ac447e809fa3f427fec58de7f615b5ccd6f1493fd03758fe7ceca5b911bf3c'], + }), + ('snow', '0.4-4', { + 'checksums': ['84587f46f222a96f3e2fde10ad6ec6ddbd878f4e917cd926d632f61a87db13c9'], + }), + ('tree', '1.0-43', { + 'checksums': ['9b0a996d013cce4f457abdbdc54bd2f8f4dbe4ef0b33e0a53925509c509d5287'], + }), + ('pls', '2.8-2', { + 'checksums': ['24424c3961cd52e6c72e3e46c4f2718da8b8b50ee2837110b8d508e8f721f2b8'], + }), + ('class', '7.3-22', { + 'checksums': ['b6994164e93843fcc7e08dfdc8c8b4af6a5a10ef7153d2e72a6855342508d15c'], + }), + ('proxy', '0.4-27', { + 'checksums': ['249991a4c4d70ad139e93f3a24e17f161ad1ec854951813ea192daf79478563f'], + }), + ('e1071', '1.7-13', { + 'checksums': ['da94e191af6e69aa0f9e3250d4b823674cc869339d914f761ebf2824177b6b2f'], + }), + ('nnet', '7.3-19', { + 'checksums': ['a9241f469270d3b03bbab7dc0d3c6a06a84010af16ba82fd3bd6660b35382ce7'], + }), + ('minqa', '1.2.6', { + 'checksums': ['51a7b8850e5f2fee79e8f460b9d9eca4221d9702087cca5fab5851ad3d594110'], + }), + ('MatrixModels', '0.5-2', { + 'checksums': ['1c06dbbc969eac965c75b0f4cf295d2895429917fa4ba727e5525fb1beabe32a'], + }), + ('matrixStats', '1.0.0', { + 'checksums': ['94876850e60ed16b50bf303cdfe4dd747ad2c28cae07bdc471a093eac23bad6f'], + }), + ('codetools', '0.2-19', { + 'checksums': ['c4b7e567c87f33dad85de92f79641e5e5b5deede6d19a9dfa47133d191782dab'], + }), + ('foreach', '1.5.2', { + 'checksums': ['56338d8753f9f68f262cf532fd8a6d0fe25a71a2ff0107f3ce378feb926bafe4'], + }), + ('ModelMetrics', '1.2.2.2', { + 'checksums': ['5e06f1926aebca5654e1329c66ef19b04058376b2277ebb16e3bf8c208d73457'], + }), + ('generics', '0.1.3', { + 'checksums': ['75046163bfa8b8a4f4214c1b689e796207f6447182f2e5062cf570302387d053'], + }), + ('tidyselect', '1.2.0', { + 'checksums': ['538d26b727e37d618e2efd3b00836048f103112a03e6994bf07a02392e269e3b'], + }), + ('dplyr', '1.1.3', { + 'checksums': ['6843a247db0fcbba6cbffc869efbdfb25247ee6cf2fbdc36fae7e36cccfe1742'], + }), + ('gower', '1.0.1', { + 'checksums': ['296a9d8e5efa8c3a8cc6b92cf38880915753afdef30281629af9dc8eae8315fc'], + }), + ('rpart', '4.1.21', { + 'checksums': ['e77c1c675b211705be18181913a97b67379ccae699c1406acf7814ad8a45622b'], + }), + ('survival', '3.5-7', { + 'checksums': ['d50e2dd32add39f0d148c17ec301eeff1ba9b74d9f9674324a9acd5ef234272e'], + }), + ('KernSmooth', '2.23-22', { + 'checksums': ['76e044904606cab79c9edf4eae3ad63ac9d91a2962b44e063075b4b40e8574e9'], + }), + ('globals', '0.16.2', { + 'checksums': ['682c26a95fa6c4e76a3a875be1a3192fc5b88e036c80dfa3b256add0336d770a'], + }), + ('listenv', '0.9.0', { + 'checksums': ['352841e04f0725d361b78cfdc75e00511f740d97237dd651ea86aa5484674887'], + }), + ('parallelly', '1.36.0', { + 'checksums': ['b9c0a29155944aae8fdb4cab00c521c7ed16af250450dd2a3dd69d5661427c88'], + }), + ('future', '1.33.0', { + 'checksums': ['4228eb9b35ce4b56bf4168977661fed4f83bb36131b2dc7120b2898d8747935b'], + }), + ('future.apply', '1.11.0', { + 'checksums': ['317b30ceb9b5b03eabaf367d52b8fbcbfeabce1da2ee1000ca1eec5adb4b01e8'], + }), + ('progressr', '0.14.0', { + 'checksums': ['9a2899f879a5577f043be99c18d52bfe4d655cc52a96cae834e8a301b36258af'], + }), + ('numDeriv', '2016.8-1.1', { + 'checksums': ['d8c4d19ff9aeb31b0c628bd4a16378e51c1c9a3813b525469a31fe89af00b345'], + }), + ('SQUAREM', '2021.1', { + 'checksums': ['66e5e18ca29903e4950750bbd810f0f9df85811ee4195ce0a86d939ba8183a58'], + }), + ('lava', '1.7.3', { + 'checksums': ['4e087df1350b05c3d0403597a1ad97f4b0e183047d5d8636a62143f26bd86a08'], + }), + ('shape', '1.4.6', { + 'checksums': ['b9103e5ed05c223c8147dbe3b87a0d73184697343634a353a2ae722f7ace0b7b'], + }), + ('diagram', '1.6.5', { + 'checksums': ['e9c03e7712e0282c5d9f2b760bafe2aac9e99a9723578d9e6369d60301f574e4'], + }), + ('prodlim', '2023.08.28', { + 'checksums': ['8002229f38bbe42e26b88ac542d9c028a9dbe8fd3b80af7552060bec3a555de8'], + }), + ('ipred', '0.9-14', { + 'checksums': ['81c83dc847d09c3db52ef15e36cd4dac38c50eead1008ddd458b9e89d7528f35'], + }), + ('timechange', '0.2.0', { + 'checksums': ['3d602008052123daef94a5c3f5154c5461b4ec0432ab70c37273d7ddd252f7f1'], + }), + ('lubridate', '1.9.3', { + 'checksums': ['2b6e1406d231b0a14d60b99cc406d159fea5465a5694725ad25343f12cf37fff'], + }), + ('tidyr', '1.3.0', { + 'checksums': ['8d532b9366fdd3ec9827b51830e559a49d073425007c766025f0e603964e0a9d'], + }), + ('hardhat', '1.3.0', { + 'checksums': ['fe9ff009e2ba6dd4d70cbb541430f88d85c0a28d6a1c2772e4910c79b81fe82e'], + }), + ('tzdb', '0.4.0', { + 'checksums': ['4253c66041bdddfd463c98183bf0052fbcacdb7c5cff9eadbb858b3dcf9d3a23'], + }), + ('clock', '0.7.0', { + 'checksums': ['54e57a3b3f8c308d67536e2a75d48f3493cf7fe821bfa4da9159b4fb2ceca874'], + }), + ('recipes', '1.0.8', { + 'checksums': ['d3d20824b36e1195ed072b632c3be89714c335f56c0a2e942386fdadcd78a00d'], + }), + ('caret', '6.0-94', { + 'checksums': ['2715e83ca260bb739cd926a55b0d2da1e3f6308b17b56862466e738d930d29a8'], + }), + ('conquer', '1.3.3', { + 'checksums': ['a2c6155ed74af0e2a279145843ec5229ae2f3707aa25169ae030c520aa97deba'], + }), + ('quantreg', '5.97', { + 'checksums': ['87e7de5776dee936ef0809dcc9ac2e0d51a7580368e6defa12ec21276a676da1'], + }), + ('robustbase', '0.99-0', { + 'checksums': ['437d422eec29c4345ea65efa6b2c7c21944059a79643d74f4187e06db6e35077'], + }), + ('zoo', '1.8-12', { + 'checksums': ['e6c3862668f9e3422bced3b6fba485c76a1e91b48f5d6153822d6a61863b2fb8'], + }), + ('lmtest', '0.9-40', { + 'checksums': ['64400d4d6cc635316531042971f1783539686e9015c76f5741c07304fa14d997'], + }), + ('vcd', '1.4-11', { + 'checksums': ['7a54e855689e1429d46e0d4d7a956f96b0ad2fd0c7084fa023902c55849e0932'], + }), + ('snowfall', '1.84-6.2', { + 'checksums': ['9b467ab2b992455c6e1aeabe375c5694761fa1cf8aaf4f003ca47102b656353b'], + }), + ('bindr', '0.1.1', { + 'checksums': ['7c785ca77ceb3ab9282148bcecf64d1857d35f5b800531d49483622fe67505d0'], + }), + ('plogr', '0.2.0', { + 'checksums': ['0e63ba2e1f624005fe25c67cdd403636a912e063d682eca07f2f1d65e9870d29'], + }), + ('bindrcpp', '0.2.2', { + 'checksums': ['48130709eba9d133679a0e959e49a7b14acbce4f47c1e15c4ab46bd9e48ae467'], + }), + ('tmvnsim', '1.0-2', { + 'checksums': ['97f63d0bab3b240cc7bdbe6e6e74e90ad25a4382a345ee51a26fe3959edeba0f'], + }), + ('mnormt', '2.1.1', { + 'checksums': ['95fca70378af0afd5a388982ba5528f5b27e02157eeb9940a0a9762d11511308'], + }), + ('foreign', '0.8-85', { + 'checksums': ['9079d20a1807122f3a6b5a72737d76eb4c011dd35d7099dfbf6171e84e52ecab'], + }), + ('psych', '2.3.9', { + 'checksums': ['04c2e81c161792aae9de458b15a373577569629c1b0a897e973bf4b3bd2019b1'], + }), + ('broom', '1.0.5', { + 'checksums': ['9d77ddee9ee32ffefdacddcb35adc0ac83035537c4e5ef5cfbd2f8bbd909d991'], + }), + ('nloptr', '2.0.3', { + 'checksums': ['7b26ac1246fd1bd890817b0c3a145456c11aec98458b8518de863650b99616d7'], + }), + ('boot', '1.3-28.1', { + 'checksums': ['d4cde76fcc8ccc7ffa329de69147b66a6a93a10188e89342fd18207b1d02ff53'], + }), + ('statmod', '1.5.0', { + 'checksums': ['d61c3ef9b09d55b42e038f8d767fa483ebbdec2a9c7172b1b0ccda0ae0016ec9'], + }), + ('lme4', '1.1-35.1', { + 'checksums': ['e4a411396f68bf93751dfd01c8cd431e2d4658340186c47d164ebb2b840afb5b'], + }), + ('ucminf', '1.2.0', { + 'checksums': ['5add8f84aeb0910a7ebf796c9514d4a3998606c3e45fe97e55d84f000a1d6df4'], + }), + ('ordinal', '2022.11-16', { + 'checksums': ['5488ad1dfa531a09d017d68d7393d376c8bc49cceeaa6a3e5f7d57b99168d493'], + }), + ('jomo', '2.7-6', { + 'checksums': ['3ffa2a5521d4969fe77b23cd3ab201afdf8db3f8f708b1276c33083c01d7e2da'], + }), + ('bit64', '4.0.5', { + 'checksums': ['25df6826ea5e93241c4874cad4fa8dadc87a40f4ff74c9107aa12a9e033e1578'], + }), + ('vroom', '1.6.4', { + 'checksums': ['8d46f96b2621409838a5d0bfa86a70146cc31f375bf3c8f66b64bbdcc62ae24d'], + }), + ('readr', '2.1.4', { + 'checksums': ['98144fa48c4fa61ef8c73ede8f87a2d2c5c44e9502b7875b266eb79984fbeb0d'], + }), + ('forcats', '1.0.0', { + 'checksums': ['c5bb157909d92e1e1a427c0dc5cb358ea00a43a14918a9088fa4f6630962254e'], + }), + ('haven', '2.5.3', { + 'checksums': ['9a5999afad09f0cf80515241b2ff19a0c480658c4bd3810638ad52762e04b7e3'], + }), + ('pan', '1.9', { + 'checksums': ['e37e184c3c1b7a34f54dd95335e6bc730fd5716d2d2dc20c24279401aa673c52'], + }), + ('mitml', '0.4-5', { + 'checksums': ['056aec823187cc3793640d8a5e74d74093bae74260a975ceb098a83a52e2eeeb'], + }), + ('glmnet', '4.1-8', { + 'checksums': ['1ddbe5ce07076d1bdf58b0202ebd0ceac8eeb4796c5175681adb9e58c30ddcfe'], + }), + ('mice', '3.16.0', { + 'checksums': ['29f0285185a540337e9dde2357690c82d174f115be701ee2f0a7083173a44040'], + }), + ('urca', '1.3-3', { + 'checksums': ['43baa8b6735f8325a69e6a43686f4fecd77a0eb7f60da25b4fc5c51b9271e9f1'], + }), + ('fracdiff', '1.5-2', { + 'checksums': ['ac5f881330287f5bc68b5cdce4fb74156a95356ffb875ee171538bc44200f437'], + }), + ('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', '1.2.0', { + 'checksums': ['4237baab35cd246a8a98fb9cf4ce53b6ddbc31d00742ded4edea0479613d1ea0'], + }), + ('plotly', '4.10.3', { + 'checksums': ['8b7a6c26443088c8aae4624e01cf726a91fee875c2e60b6c439375d1adaa5d8f'], + }), + ('mixtools', '2.0.0', { + 'checksums': ['854e7482230b9a5dde61bab191b78e06aa8f9b0cdfe3c03e046afa133b317e0d'], + }), + ('cluster', '2.1.4', { + 'checksums': ['c6f10ceca29a176ba833f24ebf71fd451629052c2338398ba286df5689d6f5b6'], + }), + ('gclus', '1.3.2', { + 'checksums': ['9cc61cdff206c11213e73afca3d570a7234250cf6044a9202c2589932278e0b3'], + }), + ('coda', '0.19-4', { + 'checksums': ['422d3cfd34797a3631e9c4812431940599c0ca4bb9937797bed07b7b1d6fe58f'], + }), + ('doMC', '1.3.8', { + 'checksums': ['b2186f851448251ae6af5d14b9e3e7f9221f90887e5f8de6a68c91caf16619a3'], + }), + ('DBI', '1.1.3', { + 'checksums': ['38bb33753da5bddb78893a5228a5d269dae3bf16f21dc5d9853ac9c24d31428d'], + }), + ('gam', '1.22-2', { + 'checksums': ['fe737f45229448b98b4fe2c0a3193d4cd2de43a1415f1fa25e4ec4c5a0ca02fa'], + }), + ('gamlss.data', '6.0-2', { + 'checksums': ['dbb3b6f855540928ccdbda497f8d552144895e34565799e8b595e704096db71e'], + }), + ('gamlss.dist', '6.1-1', { + 'checksums': ['d2db3a7658799c2ef212aa18cb75a3ecf4f73faf8c13dfdc3c14b21ae0129069'], + }), + ('gamlss', '5.4-20', { + 'checksums': ['a60c1e20e173f909a0df344016e64381e45a098b60f07f80fd2802bfba086873'], + }), + ('gamlss.tr', '5.1-7', { + 'checksums': ['8f9975bceaf8000b1d39317daf490e59c8385b5291326ed6a2630be11dae3137'], + }), + ('hwriter', '1.3.2.1', { + 'checksums': ['ed2fa254ab27cf65d397e181339976fc3261dfb4f6b600fea8c5689620dab6f3'], + }), + ('xts', '0.13.1', { + 'checksums': ['2c3907c6d0162e48d1898647105bbb32cfe0cb005788481a64ee675a941d825d'], + }), + ('TTR', '0.24.3', { + 'checksums': ['4d9aef32647664be5cf965b05f21ed62cde9425fa87c21530852e05ef7aaba87'], + }), + ('quantmod', '0.4.25', { + 'checksums': ['3f1896d45fbd4daea438fd2824bf4c91aba1a6729d93d20e6a0e60d2a0f95b32'], + }), + ('mvtnorm', '1.2-3', { + 'checksums': ['2adadc5df5e5303d51c9b0c1881930f51ff84bfb9b1a9754354e012f982bc6c7'], + }), + ('pcaPP', '2.0-3', { + 'checksums': ['1aac554f039753bf9d026090e47d66b82bf3f1f75479ed0adefa3f7bbb55d603'], + }), + ('pscl', '1.5.5.1', { + 'checksums': ['611367c3d34c78f2d4db79e630e38d7a5df8296bd7e72d258f6a115fbbe78d5b'], + }), + ('blob', '1.2.4', { + 'checksums': ['d08922ebc4147d930fe4762b1b289935217308c6d3fcaa5ae028ce3f5cf2728f'], + }), + ('RSQLite', '2.3.3', { + 'checksums': ['32b1d0ca464da2b61c1e7a11e979c35516a954ee94352285d9f451c630942c44'], + }), + ('BatchJobs', '1.9', { + 'checksums': ['5da9c381df461320ed4033523bad1ee97f88a4670d2714fec32be92964115c77'], + }), + ('sandwich', '3.0-2', { + 'checksums': ['6e30b6b554eb19430a60c45a8132fb7918ddb0013577bf6a62caeb163bdfe2b4'], + }), + ('sfsmisc', '1.1-16', { + 'checksums': ['511b4a661e3cfec540eb3d08f67b715f3cda398eb135a011b9be84305c11436c'], + }), + ('spatial', '7.3-17', { + 'checksums': ['f1003ed8cff2a47169a4787c8be46e8c2c501cc06c8b1e5f97bf62507e5f5dd7'], + }), + ('VGAM', '1.1-9', { + 'checksums': ['d4d411b020acaec32777c89e2b2265449e6855794442b2c4c51bcd9288b1afd0'], + }), + ('waveslim', '1.8.4', { + 'checksums': ['408eeea72a218ef3458f0934ff556733cacf1a63ddaa52491abcc1fce6ed2094'], + }), + ('profileModel', '0.6.1', { + 'checksums': ['91dc25e81f52506593f5c8d80a6131510b14525262f65b4ac10ae0cad0b2a506'], + }), + ('brglm', '0.7.2', { + 'checksums': ['56098d2ce238478e7a27cacc4cdec0bc65f287fe746b38fbb1edda20c1675023'], + }), + ('deSolve', '1.38', { + 'checksums': ['a0b4fe5c46ae560a3f36eb31e474b08ed85a928e86ae52dd59457409de188969'], + }), + ('tseriesChaos', '0.1-13.1', { + 'checksums': ['23cb5fea56409a305e02a523ff8b7642ec383942d415c9cffdc92208dacfd961'], + }), + ('tseries', '0.10-54', { + 'checksums': ['c3ca3263b58a22dd9f613b0be34a6f401caa9c88f0609c0b4e825f1efab4d028'], + }), + ('fastICA', '1.2-3', { + 'checksums': ['e9ef82644cb64bb49ae3b7b6e0885f4fb2dc08ae030f8c76fe8dd8507b658950'], + }), + ('R.methodsS3', '1.8.2', { + 'checksums': ['822d5e61dad4c91e8883be2b38d7b89f87492046d0fe345704eb5d2658927c2e'], + }), + ('R.oo', '1.25.0', { + 'checksums': ['b8b19061774918ee7d9d4330c16c0ea505f7cd02d01343df1e8b2e4fb847beef'], + }), + ('cgdsr', '1.3.0', { + 'checksums': ['4aa2a3564cee2449c3ff39ab2ad631deb165d4c78b8107e0ff77a9095340cc1f'], + }), + ('R.utils', '2.12.2', { + 'checksums': ['fe3cf1aa8641540634e96990294d0202d4d94ec79ce73aaf78e4eda30fcb8836'], + }), + ('R.matlab', '3.7.0', { + 'checksums': ['d713522268a1206555610938350137ea022e07e27fa9cdd73c02fae8d1a43dda'], + }), + ('gridExtra', '2.3', { + 'checksums': ['81b60ce6f237ec308555471ae0119158b115463df696d2eca9b177ded8988e3b'], + }), + ('gbm', '2.1.8.1', { + 'checksums': ['8d2456124552658ee9500707c4e9992cf42cb88705008c32ea258efb4f2be80b'], + }), + ('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', '0.6.4', { + 'checksums': ['0ba2a88bc38ff8be4d074ed2bc17fd9d746e96ed4dec03fa079d96a06541d6dc'], + }), + ('htmlTable', '2.4.2', { + 'checksums': ['6a83dd6172c13cad4a74f2660db94565814aaf8500237e2c418216be6db7360d'], + }), + ('Hmisc', '5.1-1', { + 'checksums': ['4971efa6d89d0002d688d160f9abca0185c5a9aa3ecc79f598a91a258db04a51'], + }), + ('fastcluster', '1.2.3', { + 'checksums': ['1f229129e1cddc78c7bb5ecc90c4d28ed810ee68cf210004c7cdfa12cfaf2a01'], + }), + ('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', '1.5.1', { + 'checksums': ['add90a1e77ad4a5d95641f0556553e3f1d1c4443cb2d5afb70171efd278ab14a'], + }), + ('GeneNet', '1.2.16', { + 'checksums': ['c1e98073ccdaa18f4952630bfe4fc0617106eeaf7ed94d347cb2773bd48333e4'], + }), + ('ape', '5.7-1', { + 'checksums': ['8b09c71218d8aa629e43bc807b433a4e30a61847d91b2810e31c366f0fe5057a'], + }), + ('RJSONIO', '1.3-1.8', { + 'checksums': ['f6f0576d3c7852b16295dfc897feebca064fe5dd29cdce7592f94c56823553f5'], + }), + ('caTools', '1.18.2', { + 'checksums': ['75d61115afec754b053ed1732cc034f2aeb27b13e6e1932aa0f26bf590cf0293'], + }), + ('gplots', '3.1.3', { + 'checksums': ['9f853b9e205264d087e61e8825f797ce36c9eb585b187dab794563613a526716'], + }), + ('ROCR', '1.0-11', { + 'checksums': ['57385a773220a3aaef5b221a68b2d9c2a94794d4f9e9fc3c1eb9521767debb2a'], + }), + ('rjson', '0.2.21', { + 'checksums': ['982b56d35ccc0c7db0b20c1d3eab5f5f47c620309646fdc278ff1cc3433ea2e2'], + }), + ('seqinr', '4.2-30', { + 'checksums': ['faf8fe533867eeef57fddfa6592e19d5984954d0670c6c7dbeab6411d55fee4b'], + }), + ('LearnBayes', '2.15.1', { + 'checksums': ['9b110858456523ca0b2a63f22013c4e1fbda6674b9d84dc1f4de8bffc5260532'], + }), + ('gmodels', '2.18.1.1', { + 'checksums': ['da7d48021b7cd2fd8a7cd8d0bb9658b12342a32698a13877b25ca94aa03f1e95'], + }), + ('expm', '0.999-7', { + 'checksums': ['28f249b914b8dd33eee16663fc793e57afd0e301e16067bf9f27fa8e591ba0f1'], + }), + ('terra', '1.7-55', { + 'checksums': ['7000bdfd8591be64921cf841ef29b2aad74661781865f29e1540e57a7d7231ec'], + }), + ('raster', '3.6-26', { + 'checksums': ['c65777225a46ada699e70098f54c60cf191d15e454fac9440aca439a4dbd5592'], + }), + ('spData', '2.3.0', { + 'checksums': ['4b2c1f597049f2c78a7e2b7538c067e2b57e2f12291d19210b1eef702664848b'], + }), + ('units', '0.8-4', { + 'checksums': ['499da1891e6167af42f501894444dcc9f5d8195017456bb6aca8aeec3515c7fc'], + }), + ('classInt', '0.4-10', { + 'checksums': ['c3561eafbc493ac02840191d4f1e4d2ef437ca8eb20f41fc5eca28f00ee42b8b'], + }), + ('vegan', '2.6-4', { + 'checksums': ['5d8ad4bebe79ae2bbd840a34100cf54c62f089c66ea484a542a201afcba21d06'], + }), + ('rncl', '0.8.7', { + 'checksums': ['1d876e4f5f2b8a24cc3ea1002c29eedbc0ca96011b0fa15b085e5b75cfc7993a'], + }), + ('XML', '3.99-0.15', { + 'checksums': ['98a14694670a8a1d9a03e184ec60203180fb8eca9fb3da086693b01ed7003b3e'], + }), + ('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', '1.4.0', { + 'checksums': ['8e50415e415702402473caf622d86b89ddc881f6e5d888079a4818a8807ac9a2'], + }), + ('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', '1.5.0', { + 'checksums': ['f8d0e6f04fb65f7ad9c1c068852a6a8b699ffe8d39edf1f3fa07d32d087e8ff0'], + }), + ('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', '1.1-1', { + 'checksums': ['1611240eb706e6f53400b25c9cf792ad90f151b72ed0918a1e756997f7abb716'], + }), + ('conditionz', '0.1.0', { + 'checksums': ['ccd81e4f2534d29cddf44cf697f76ff01417cbeb22001a93477edc61cdd35646'], + }), + ('taxize', '0.9.100', { + 'checksums': ['e2e578fc45eb5d1306332892c67535fa4bc32d63129532df2c6cde393993cd29'], + }), + ('RNeXML', '2.4.11', { + 'checksums': ['246913cbb0e816401bb8e37dda20646202547f5cc8379c9dadf832f61d6cfd46'], + }), + ('phylobase', '0.8.10', { + 'checksums': ['5a44380ff49bab333a56f6f96157324ade8afb4af0730e013194c4badb0bf94b'], + }), + ('magick', '2.8.1', { + 'checksums': ['d8fcd10e1817d42796102e85df05bb45fc8ced4c721b06fac37e61b6792b458e'], + }), + ('animation', '2.7', { + 'checksums': ['88418f1b04ec785963bad492f30eb48b05914e9e5d88c7eef705d949cbd7e469'], + }), + ('bigmemory.sri', '0.1.6', { + 'checksums': ['3bfa6ac966ce0ea93283f5856a853d0ee5ff85aedd7a7d1ca8a93d0aa642860c'], + }), + ('bigmemory', '4.6.1', { + 'checksums': ['b56e157c87ed6c4fc69d4cb9c697ae9a2001726e776e41aa7c48b35327b65141'], + }), + ('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'], + }), + ('phytools', '1.9-16', { + 'checksums': ['1b800b722a17679998efff40ab26adb127f61fcd57ea486ec1e129f34c79b29c'], + }), + ('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', '1.2.1', { + 'checksums': ['d12a3f35527f260f8d393ae842c7705df5656669a72907f78aa64a363c6dcb9b'], + }), + ('Rtsne', '0.16', { + 'checksums': ['52a05adc826c28212e97d11c54eba3fec45d14eb52039c0f47f62a8e338ffbd5'], + }), + ('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', '1.3-13', { + 'checksums': ['def05e7f0c59f1b1ecf0ab3929cff75ae8c2691aaf52292cad4371281b897e7b'], + }), + ('inum', '1.0-5', { + 'checksums': ['e696b7e0b31b3bbf405112e60691b6a72fedcaa02e08ee517c59f6bf9cd36bbd'], + }), + ('partykit', '1.2-20', { + 'checksums': ['63509aa3ed2d7417ad284c037cef66bc837fdb7a97967957e79b9fee8ed2e0da'], + }), + ('mboost', '2.9-8', { + 'checksums': ['d64c6bc630f9279ae5a672e86b296e947ab304df9e22a6af518a7d5a627fd1cb'], + }), + ('msm', '1.7', { + 'checksums': ['7f89f8e47966919e49ef8dfe1f9c82ac6553b2f404bb03840da5f42e73dd0db0'], + }), + ('nor1mix', '1.3-0', { + 'checksums': ['9ce4ee92f889a4a4041b5ea1ff09396780785a9f12ac46f40647f74a37e327a0'], + }), + ('np', '0.60-17', { + 'checksums': ['d97957cb234ec2e570fc2d02d305eadff3d71939484b3d1054ed8b67a3427f36'], + }), + ('polynom', '1.4-1', { + 'checksums': ['bc1edb7bb16c8b299103f80a52ab8c5fc200cd07a9056578c1f672e9f5019278'], + }), + ('polspline', '1.1.24', { + 'checksums': ['6641c3666727841d291e3bbeda548ca422e4f04e7ba92e806486ca741c3a5455'], + }), + ('rms', '6.7-1', { + 'checksums': ['1f836c12973b39c42230005767e94b075fb6767e6b8c9714476de9fe515a3da5'], + }), + ('RWekajars', '3.9.3-2', { + 'checksums': ['16e6b019aab1646f89c5203f0d6fc1cb800129e5169b15aaef30fd6236f5da1a'], + }), + ('RWeka', '0.4-46', { + 'checksums': ['660555781703c19b994c9dcfc9e7d8312c30b02539f38cd3948bfc33d9f94b67'], + }), + ('slam', '0.1-50', { + 'checksums': ['7899bf3266c204ecccefc1878f96940b117d4503af128f4fbc50fc409163f8bd'], + }), + ('tm', '0.7-11', { + 'checksums': ['9aab8b8493df4c62cff8adbba53be72295673ba8c546cdb129cdc52aabeae742'], + }), + ('leaps', '3.1', { + 'checksums': ['3d7c3a102ce68433ecf167ece96a7ebb4207729e4defd0ac8fc00e7003f5c3b6'], + }), + ('cNORM', '3.0.4', { + 'checksums': ['d766bfd86f8a871b972b9b9cd952fa2e5bb7c0fe6903b3f2c15eccf4612a17e2'], + }), + ('weights', '1.0.4', { + 'checksums': ['efbe65e8a9d05824a86095d45ed62ce24d82101d4ca3b94828d443e08e83ccba'], + }), + ('TraMineR', '2.2-8', { + 'checksums': ['052b905c067fb1fd71ed8a4f02ccf94579b344bc9e4d8153f5a7e4b520c2e762'], + }), + ('chemometrics', '1.4.4', { + 'checksums': ['fd0edb1ebe321ff7677d0a668d7dfc79a7cd55f408a53d1f13db4cf6347aa881'], + }), + ('FNN', '1.1.3.2', { + 'checksums': ['d701a13487979ebb07a071f4cc83fcf4daea5832d1f3923bce1e0d671dfe0e87'], + }), + ('miscTools', '0.6-28', { + 'checksums': ['bd4c2f2120948af538f9874df1ac745ff162817d0e53756f52f863eb4f593b21'], + }), + ('maxLik', '1.5-2', { + 'checksums': ['7cee05be0624b6a76911fa7b0d66f3e1b78460e0c55ed8bc904ce1e8af7bb15d'], + }), + ('gbRd', '0.4-11', { + 'checksums': ['0251f6dd6ca987a74acc4765838b858f1edb08b71dbad9e563669b58783ea91b'], + }), + ('rbibutils', '2.2.16', { + 'checksums': ['9c7c0fba47f63b1749005311c7174b40e72d95c863a67b736a84b8ff375a2aaf'], + }), + ('Rdpack', '2.5', { + 'checksums': ['4d4db2e1431feb9bd785eced8b44ca5af37b866992ec17dc28b605aee8e0c877'], + }), + ('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', '1.7.3', { + 'checksums': ['6287e1af051d4a65037900ce7b30bd962039450dd4eab63b6f2491eace6a07ed'], + }), + ('labelled', '2.12.0', { + 'checksums': ['fe043c2cd910e692c98bf7c79d20d0d8b9e27431eb26c266d863f1956b80d2b8'], + }), + ('R.cache', '0.16.0', { + 'checksums': ['7853409161571a790e0383f64f99e4eae43201a0ed7146d2baf157741a509291'], + }), + ('styler', '1.10.2', { + 'checksums': ['a6c055310f4be6f3c5d11314938cb592594a869bf9c9fa7fce588a53794f7b10'], + }), + ('questionr', '0.7.8', { + 'checksums': ['af72e59fe652c6063282a7e5b0f487993b9361cc9ed052a632d64a5a6db76ba9'], + }), + ('klaR', '1.7-2', { + 'checksums': ['8035c3edb8257973184ad5a2109fc7c77c32da913cb9dd0c2f1c373e6fccbd61'], + }), + ('neuRosim', '0.2-14', { + 'checksums': ['7fc264bb86f1edd7b39a2472330bbabb34eb6dfb722db016a6ee60444ebfafd9'], + }), + ('locfit', '1.5-9.8', { + 'checksums': ['0d0a9bfb32e50e8f8f97de771f91b17db1db7c5be35027f2d7840a7293e11de3'], + }), + ('GGally', '2.1.2', { + 'checksums': ['30352f36bf061bc98bdd5fa373ea0f23d007040bd908c7c018c8e627e0fb28e5'], + }), + ('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', '1.4.2', { + 'checksums': ['8f75633eb2b6349a07db347d5b6bf40781a8dab63b6cb858849a616e9b629027'], + }), + ('rio', '1.0.1', { + 'checksums': ['754c137c5588870f75665d0acc149f0ef28250edc057d5d4ac6fa25ba9547bee'], + }), + ('car', '3.1-2', { + 'checksums': ['89263491977ac8e9406b2f4b1638bf06c7ddd1b0e0e3ecda4be61420474674c8'], + }), + ('flashClust', '1.01-2', { + 'checksums': ['48a7849bb86530465ff3fbfac1c273f0df4b846e67d5eee87187d250c8bf9450'], + }), + ('ggrepel', '0.9.4', { + 'checksums': ['81abb47270593709587480ffbc88dce3d3f695bd6f1164729311b37c50d7cf3e'], + }), + ('DT', '0.30', { + 'checksums': ['2f1a53e32a9b493efc9041758810c6a744ebb17ad7a942b376389b7e95ff698e'], + }), + ('estimability', '1.4.1', { + 'checksums': ['c65aaf1e452f3947013d3ce05ae674d48492081f615a942592dc91db780f1124'], + }), + ('emmeans', '1.8.9', { + 'checksums': ['8a0cf0a1fd1d69fe7642644181b943bcf38db6cb1cbbb8b2282e7a1b11d2ffc6'], + }), + ('multcompView', '0.1-9', { + 'checksums': ['1f3993e9d51f3c7a711a881b6a20081a85ffab60c27828ceb3640a6b4c887397'], + }), + ('FactoMineR', '2.9', { + 'checksums': ['882698d399a641c80f63ffae69c334fc5306238fb8592e9b760e17d4621f5230'], + }), + ('flexclust', '1.4-1', { + 'checksums': ['d67977df059e622832358069509f8968d506074320a45d34bfd21c65f898538d'], + }), + ('flexmix', '2.3-19', { + 'checksums': ['adf5a40cbb6d45e3652c1666cb3ccdb9654e501fd685c091cad0686e62bc12e9'], + }), + ('prabclus', '2.3-3', { + 'checksums': ['005d000a9ac357e670de26e5b8fc4ddb1617351275fa43bf6d2e88b8774358c1'], + }), + ('diptest', '0.76-0', { + 'checksums': ['508a5ebb161519cd0fcd156dc047b51becb216d545d62c6522496463f94ec280'], + }), + ('trimcluster', '0.1-5', { + 'checksums': ['9239f20e4a06ac2fa89e5d5d89b23a45c8c534a7264d89bede8a35d43dda518b'], + }), + ('fpc', '2.2-10', { + 'checksums': ['99b4548f2eca1a092a31bc2fa4e4bd1d6b50fdfacf3218588c879ceec99147d2'], + }), + ('BiasedUrn', '2.0.11', { + 'checksums': ['6295f1a12cd9d425cc03ec05a993fba04f539007c1754f23d7043a585b9e7537'], + }), + ('TeachingDemos', '2.12', { + 'checksums': ['3e75405ce1affa406d6df85e06f96381412bc7a2810b25d8c81bfe64c4698644'], + }), + ('kohonen', '3.0.12', { + 'checksums': ['40944b916aa228d90862301beb9d93a521e6d98ba23c147d1bd9dded04ef0ca1'], + }), + ('base64', '2.0.1', { + 'checksums': ['4d22687c0195c2049e0af2c613b1ebcb908037010ad6e550bf47d69e842535f1'], + }), + ('doRNG', '1.8.6', { + 'checksums': ['5032ade083f1f9841ac2e8d4426faa07f189c25c0c338fa155c5dadbe5507de2'], + }), + ('nleqslv', '3.3.4', { + 'checksums': ['2783e7525bcd155dd8cedf5a41b7db65cd1fa0e095cd937371448316f3930fcf'], + }), + ('Deriv', '4.1.3', { + 'checksums': ['dbdbf5ed8babf706373ae33a937d013c46110a490aa821bcd158a70f761d0f8c'], + }), + ('RGCCA', '3.0.2', { + 'checksums': ['c965e9d106f0954ce940314e4d5d3f8f0f57b7fc5c5c8cbe913e43a9a3953f83'], + }), + ('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', '2.1-2', { + 'checksums': ['bd7fd9e35928d09d0e8fae9e4359a2b2bca6e6865b278436319e2f91db0e4b37'], + }), + ('forecast', '8.21.1', { + 'checksums': ['811eace27c7f6e99e1048b8f2522e67bb3620471c5431e0ef83c396612dc8127'], + }), + ('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', '3.0-4', { + 'checksums': ['5d418e39e0e20a14d44779fcde17caea9bf8075f1647baa59342e824b40f3cc4'], + }), + ('spatstat.data', '3.0-3', { + 'checksums': ['7642c0e41e905a287f9f319a4169d82bf41349cbc406e9c6d107a89f8d11ad3b'], + }), + ('spatstat.geom', '3.2-7', { + 'checksums': ['be9819b3abde9714629a06bc8d741c7a7f8352fb8f72d92b3156b48f422a688e'], + }), + ('spatstat.sparse', '3.0-3', { + 'checksums': ['6bbc4e42ae71eece63e8c3e390068a84eeeb6cd4f6bdb555d8815aa2ed988d69'], + }), + ('spatstat.random', '3.2-1', { + 'checksums': ['925421aeb7befa88a1f28d2bfa113630099b5edb75e04b04d3b0ed9bb1af31dc'], + }), + ('spatstat.core', '2.4-4', { + 'checksums': ['e38c39efe8b14d6e8fdbee8dd870b90c52f78ea571ab7988fd3685f48347d13b'], + }), + ('spatstat.explore', '3.2-5', { + 'checksums': ['4c0715a12af4f5691c493545ab7f6cad790e36a79f5354c0c57356c80fa27c14'], + }), + ('spatstat.model', '3.2-8', { + 'checksums': ['8d5c73abbd5e8fff4246d4ee3a5229cc1d774fb7fc4e69b26f08e720927703f4'], + }), + ('spatstat.linnet', '3.1-3', { + 'checksums': ['78649210eca810deae5bce0edbe85dd790cafe48f37318178d25a7cb58a172f9'], + }), + ('spatstat', '3.0-7', { + 'checksums': ['33779f4a4f881e98c4fa2f8faac8d3a8eb2d45149992cde77fb3a83a62b6cec0'], + }), + ('pracma', '2.4.2', { + 'checksums': ['1d50337fdfd9a8d704a64f01dae5d52b9a2bd6d872fdaa4a6685b8d3bde89c16'], + }), + ('RCurl', '1.98-1.13', { + 'checksums': ['05a52f6329b4ea91dc92ae23b2528b99d654532c8291712bd591521d6eacf306'], + }), + ('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', '2.0-28.1', { + 'checksums': ['752f11b99816f8d61c1ff411ea4d5bec5509f2a655d250e58baa48e8a0266ba6'], + }), + ('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', '1.3.13', { + 'checksums': ['e4a60a4e0950a3587db2a2d5958ab4fbe07b2548f7c3d4795912fe45c77a4eae'], + }), + ('RcppRoll', '0.3.0', { + 'checksums': ['cbff2096443a8a38a6f1dabf8c90b9e14a43d2196b412b5bfe5390393f743f6b'], + }), + ('rlist', '0.4.6.2', { + 'checksums': ['ebde658d897c8a27a90ebb892b9e2bad15e2ad75557a7352fb08cbb5604e0997'], + }), + ('ConsRank', '2.1.3', { + 'checksums': ['7ef9fd405d2f01a9b31fccbbfe0bdb1fd3dcbec6654f553db3ef3a21ffc92d6c'], + }), + ('adabag', '5.0', { + 'checksums': ['ec58756fda2e64753d21e28d9e27ed34f28020045b199a58dcea06a3e2c3d60e'], + }), + ('parallelMap', '1.5.1', { + 'checksums': ['c108a634a335ed47b0018f532a52b032487e239c5061f939ba32355dfefde7e1'], + }), + ('ParamHelpers', '1.14.1', { + 'checksums': ['0450ff8489b0d4d0842130f6a9713ede97da936d7909c43d43587bf2d5a01a21'], + }), + ('ggvis', '0.4.8', { + 'checksums': ['3d5480a0b97a57c26b595785f826b13d7695dab1f1dd8fcf5d7964fa8546a26a'], + }), + ('mlr', '2.19.1', { + 'checksums': ['9d52afd54d9d5746e798134d5675818cee65caa53d7eaf317d46ba88d5865202'], + }), + ('unbalanced', '2.0', { + 'checksums': ['9be32b1ce9d972f1abfff2fbe18f5bb5ba9c3f4fb1282063dc410b82ad4d1ea2'], + }), + ('RSNNS', '0.4-16', { + 'checksums': ['1a215fdb04a39e94eb3c21a9e66dff76f089d3310cb585cdfba5a66253a232d8'], + }), + ('abc.data', '1.0', { + 'checksums': ['b242f43c3d05de2e8962d25181c6b1bb6ca1852d4838868ae6241ca890b161af'], + }), + ('abc', '2.2.1', { + 'checksums': ['db52a397a204a0040ec1368ae217cf7b0d8e99e2567927dbe3ae89f93d1de598'], + }), + ('lhs', '1.1.6', { + 'checksums': ['e37fce44efe6a371677ba2f72f9e1e48270a0fdc60872d05def89270586cd23f'], + }), + ('tensorA', '0.36.2', { + 'checksums': ['8e8947566bd3b65a54de4269df1abaa3d49cf5bfd2a963c3274a524c8a819ca7'], + }), + ('EasyABC', '1.5.2', { + 'checksums': ['326c92e003866728729dc61473f168c3663106b1229e8513abd7ce520c18689c'], + }), + ('git2r', '0.32.0', { + 'checksums': ['1b5d254c0c684a56751d26d482823d0006964eb1f55c558f365d037f5e984671'], + }), + ('clisymbols', '1.2.0', { + 'checksums': ['0649f2ce39541820daee3ed408d765eddf83db5db639b493561f4e5fbf88efe0'], + }), + ('covr', '3.6.3', { + 'checksums': ['c0ce1846a4d12cd7d365ed1844c221cd8a40f50ea2c6d7d87f27c3e7deffa29e'], + }), + ('Rook', '1.2', { + 'checksums': ['c79ae4b5164daffd4e7cf74bd23c1b08a3948bf343dfe9570d57f39cbf8e5f62'], + }), + ('Cairo', '1.6-1', { + 'checksums': ['e64dcfc4d7081f909c947643ff08241e14a4e6e68bf9c8459c6d64ede0c23714'], + }), + ('RMTstat', '0.3.1', { + 'checksums': ['bb4827d76106f5377044cd2b230208881eb714cae65f512f4b95988d9b162ae4'], + }), + ('Lmoments', '1.3-1', { + 'checksums': ['7c9d489a08f93fa5877e2f233ab9732e0d1b2761596b3f6ac91f2295e41a865d'], + }), + ('distillery', '1.2-1', { + 'checksums': ['4b88f0b34e472b9134ad403fb32283424f1883a5943e52c55f1fe05995efb5fa'], + }), + ('extRemes', '2.1-3', { + 'checksums': ['e1ccf0dd542502eb9775682ff64ed358fce4aec271b98cd746e58fbfcf093c40'], + }), + ('tkrplot', '0.0-27', { + 'checksums': ['c99211919414400b0f579e1354407f2e154cfe85533d324bcf9c68172c2772a5'], + }), + ('misc3d', '0.9-1', { + 'checksums': ['a07bbb0de153e806cd79675ed478d2d9221cff825654f59a71a9cf61f4293d65'], + }), + ('multicool', '0.1-12', { + 'checksums': ['487d28d9c3c606be0cf56e2d8f8b0d79fb71949c68886ea9251fbb1c01664a36'], + }), + ('plot3D', '1.4', { + 'checksums': ['d04a45197646fb36bc38870c1c2351cb56b912bd772b1ebfa25eaeef35fda9c0'], + }), + ('plot3Drgl', '1.0.4', { + 'checksums': ['6d87a9a32aba3aa64f751268cabd14dbd3e0eca2bd5f0a4b11366cd1e2f51bdd'], + }), + ('OceanView', '1.0.6', { + 'checksums': ['2c5165975d6c49fdc83a892cb0406584928dd44000c9774fffc00fbd2fec86f3'], + }), + ('ks', '1.14.1', { + 'checksums': ['4543f53af412c368d7dedd1bf30c411290de3f37a5d5f77226112e8315dec76d'], + }), + ('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', '1.0.0', { + 'checksums': ['40674c90a5bd00f5185db9adbd221c6f1114043e69095249f5fa8b3044af3f5e'], + }), + ('influenceR', '0.1.5', { + 'checksums': ['8164e4820f769032fab97c9ca486d33e83309641fcc4875065d8f5a43b20f58c'], + }), + ('visNetwork', '2.1.2', { + 'checksums': ['47c99d42fc89e6ae929257b2648d998c5ffed60dff97ad7e47613f5a0c1ddc84'], + }), + ('downloader', '0.4', { + 'checksums': ['1890e75b028775154023f2135cafb3e3eed0fe908138ab4f7eff1fc1b47dafab'], + }), + ('DiagrammeR', '1.0.10', { + 'checksums': ['72f6a89708ae15277acbbab2dded5f461b6bdc9c5893112860fb34c8df3ff890'], + }), + ('randomForestSRC', '3.2.2', { + 'checksums': ['0b39ed80b5a86ab902e707b3910ca24051331003a26cfd6f81db52faf38157cb'], + }), + ('sm', '2.2-5.7.1', { + 'checksums': ['ea0cc32eb14f6c18beba0bede66ed37bc5341bd3f76c1a7ae56d7254693e1457'], + }), + ('pbivnorm', '0.6.0', { + 'checksums': ['07c37d507cb8f8d2d9ae51a9a6d44dfbebd8a53e93c242c4378eaddfb1cc5f16'], + }), + ('lavaan', '0.6-16', { + 'checksums': ['1def927393a2681b0a61f67b4d92ff05530bf75fab51e5c434140b32c7d70a94'], + }), + ('matrixcalc', '1.0-6', { + 'checksums': ['0bc7d2f11f62d8b1969474defe27c924a243ccba0c856d585f317f6caa07f326'], + }), + ('arm', '1.13-1', { + 'checksums': ['c02da290c1b9699b958431865fcedce94f00ccc80da5c0aa50ed1c3fb56de937'], + }), + ('mi', '1.1', { + 'checksums': ['4d7a9790dbdc675605d70755af9aa80c21a279be5a5d712b22d77465772cc785'], + }), + ('servr', '0.27', { + 'checksums': ['01c23c56bbe483486b9daac831953ce1d5d1814966b9044c03c69884065458c5'], + }), + ('rgexf', '0.16.2', { + 'checksums': ['6ee052b0de99d0c7492366b991d345a51b3d0cc890d10a68b8670e1bd4fc8201'], + }), + ('sem', '3.1-15', { + 'checksums': ['ad023b00e6e8eb20d107039caf1008c4b05104c7c69709e59c66fbddbf381316'], + }), + ('statnet.common', '4.9.0', { + 'checksums': ['a485dc6e363a993d87336fbd1027adb1cd7b9103447fd63904cae4dc3bfc2dd7'], + }), + ('network', '1.18.1', { + 'checksums': ['c80d70352967d8480cfa801f2a31bfe130e2ad4dbf2c07b0046e57f3013cd243'], + }), + ('rle', '0.9.2', { + 'checksums': ['803cbe310af6e882e27be61d37d660dbe5910ac1ee1eff61a480bcf724a04f69'], + }), + ('sna', '2.7-1', { + 'checksums': ['60daf217c15b6fa335804600dc1e6eb73594b6e794faa4f82a2275c4d8570ae3'], + }), + ('glasso', '1.11', { + 'checksums': ['4c37844b26f55985184a734e16b8fe880b192e3d2763614b0ab3f99b4530e30a'], + }), + ('huge', '1.3.5', { + 'checksums': ['9240866e2f773cd0ac8a02514871149d2babaa162a49e151eab9591ad42984ea'], + }), + ('d3Network', '0.5.2.1', { + 'checksums': ['5c798dc0c87c6d574abb7c1f1903346e6b0fec8adfd1df7aef5e4f9e7e3a09be'], + }), + ('BDgraph', '2.72', { + 'checksums': ['7cf9cc1bccf2a56b518c88030e00e88217f571afcb250aa95c3bd2771a8b83cd'], + }), + ('graphlayouts', '1.0.2', { + 'checksums': ['55c95490bc0625ea2fc187f58dc20ee4df325cc93b7987da5d0d5dc96692e0d5'], + }), + ('tweenr', '2.0.2', { + 'checksums': ['64bbfded418d4880e3636f434571c20303d2f66be6950d64583a864fbb661ff3'], + }), + ('ggforce', '0.4.1', { + 'checksums': ['b44219fb63c45fa003c64bca323452f16dcace635204bc0127d3244c0f451873'], + }), + ('tidygraph', '1.2.3', { + 'checksums': ['b09c06b12583ae57edd1ec01e61a0e1b7a4b82358361fb28a6046dbece475687'], + }), + ('ggraph', '2.1.0', { + 'checksums': ['686fdb22dc4f613273fb755ec42399a208b4d10348eecd1a217afd4612245c1f'], + }), + ('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', '1.3.9', { + 'checksums': ['a106fdf99a7070243c412f0117f0f4e3954b2bae81266fba272e9c85040dcde7'], + }), + ('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', '0.1-11', { + 'checksums': ['b8c3ea15114d972f8140541c7b01f5ce2e5322af1f63c1a083aaf766fd3eec75'], + }), + ('readbitmap', '0.1.5', { + 'checksums': ['737d7d585eb33de2c200da64d16781e3c9522400fe2af352e1460c6a402a0291'], + }), + ('imager', '0.45.2', { + 'checksums': ['49848bcb03dd3fc3605799893d39986b521921faaa5647815274eb204bb9bf56'], + }), + ('signal', '0.7-7', { + 'checksums': ['67a015c46d67de7548c3adb83a1b22524de75501a861d91668c3c2ea761a4e61'], + }), + ('tuneR', '1.4.5', { + 'checksums': ['f5d20d2dfa0e5ea08465d9fd57675ced3e20aa55b8904a32265766ca2ab252fb'], + }), + ('pastecs', '1.3.21', { + 'checksums': ['8c1ef2affe88627f0b23295aa5edb758b8fd6089ef09f60f37c46445128b8d7c'], + }), + ('audio', '0.1-11', { + 'checksums': ['1052f6335be4df4b2e145c077d82e781eaf6658f3ed4821033b07e57bb4ce17c'], + }), + ('fftw', '1.0-7', { + 'checksums': ['f69f63467b84e107f3e0b18d1f034a37140545e6f50e6be3b887df2b4eec3a1e'], + }), + ('seewave', '2.2.3', { + 'checksums': ['1f897af809e8e5f9d515d788f4b5ea14ba27b2b554a3ab8024d78f42ac46848d'], + }), + ('gsw', '1.1-1', { + 'checksums': ['d2a21dbcc3b285163d9cf1bc649a3de1bb1e713c64e4cb6cbc3e613c43f4dd82'], + }), + ('wk', '0.9.0', { + 'checksums': ['10fba9d5d24e9942c1b9cfdaf2a862d023f7d5a8d7c350f22483723d6e7bb9da'], + }), + ('s2', '1.1.4', { + 'checksums': ['be0b4925eaade52cf85b1cb6e851430bd4fe6ca30722dffcc3f9107e7a4e404c'], + }), + ('sf', '1.0-14', { + 'checksums': ['8b535648d537a1a95920c938e43692c1dfaac8d293ff3f506334001352c339f7'], + }), + ('oce', '1.8-1', { + 'checksums': ['22910a5a88b43ae60f12f3d4d4627777c54910c0fef71fa5c537e24af39fde67'], + }), + ('ineq', '0.2-13', { + 'checksums': ['e0876403f59a3dfc2ea7ffc0d965416e1ecfdecf154e5856e5f54800b3efda25'], + }), + ('soundecology', '1.3.3', { + 'checksums': ['276164d5eb92c78726c647be16232d2443acbf7061371ddde2672b4fdb7a069a'], + }), + ('memuse', '4.2-3', { + 'checksums': ['906fdff665e2aed0e98ee3181233a5c62bd521abfce6ab1cb215c71c95d12620'], + }), + ('pinfsc50', '1.2.0', { + 'checksums': ['ed1fe214b9261feef8abfbf724c2bd9070d68e99a6ea95208aff2c57bbef8794'], + }), + ('vcfR', '1.14.0', { + 'checksums': ['8576dbd2e5a707dabc20acbbea3fe18b6a783910e622423ac203609a386204cb'], + }), + ('glmmML', '1.1.5', { + 'checksums': ['17d13d90eaea3ba3477ac2453ea5ced8d2cc20b2d00d097003e4f3b2ad79dde9'], + }), + ('cowplot', '1.1.1', { + 'checksums': ['c7dce625b456dffc59ba100c816e16226048d12fdd29a7335dc1f6f6e12eed48'], + }), + ('tsne', '0.1-3.1', { + 'checksums': ['14abc65bc0a3f3ed63c04dda19620e483a21d1f5f33feb74aba9f3221434d888'], + }), + ('sn', '2.1.1', { + 'checksums': ['f9f6b56d91dc7cb18dc8308d0875b9648c90b268d1aaf8f4c5164ff016df22bd'], + }), + ('tclust', '1.5-4', { + 'checksums': ['2b55da5e351c5054c9627f57a43084518a138a1d8097e35a364db0eff63471a8'], + }), + ('ranger', '0.15.1', { + 'checksums': ['4d65d9ee7c5f2704a0e303a27222c02aa53e49f3c28dc0b4451371e37ada2b2e'], + }), + ('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', '0.5.2', { + 'checksums': ['22790f7157f23eb0b7b0b89e2ea53478fb3c0d15b5be8ad11525d3e6d5626cdc'], + }), + ('VIM', '6.2.2', { + 'checksums': ['afa7492c54508c46eff39ac66fa4b05627e0044253ebe4a61b2a78d459f715e4'], + }), + ('smoother', '1.1', { + 'checksums': ['91b55b82f805cfa1deedacc0a4e844a2132aa59df593f3b05676954cf70a195b'], + }), + ('dynamicTreeCut', '1.63-1', { + 'checksums': ['831307f64eddd68dcf01bbe2963be99e5cde65a636a13ce9de229777285e4db9'], + }), + ('beeswarm', '0.4.0', { + 'checksums': ['51f4339bf4080a2be84bb49a844c636625657fbed994abeaa42aead916c3d504'], + }), + ('vipor', '0.4.5', { + 'checksums': ['7d19251ac37639d6a0fed2d30f1af4e578785677df5e53dcdb2a22771a604f84'], + }), + ('ggbeeswarm', '0.7.2', { + 'checksums': ['fd7ca265bb892dde514d5f8d6a853fb8b32d7a673b05e9c8b50544a523299ce5'], + }), + ('shinydashboard', '0.7.2', { + 'checksums': ['a56ee48572649830cd8d82f1caa2099411461e19e19223cbad36a375299f3843'], + }), + ('rrcov', '1.7-4', { + 'checksums': ['6341eddc590fe11fb8545aa9084f5d99cd93415a599022ba63f1af890617754a'], + }), + ('WriteXLS', '6.4.0', { + 'checksums': ['644b90a82683c668b6e05bb4f940111a42cd634f63a5b559351e8cd4274a19b7'], + }), + ('bst', '0.3-24', { + 'checksums': ['64d96e13551d35ec32aabaa733bec86dbe8c9ca3f976a34ebbf1f49bb63e49f4'], + }), + ('pamr', '1.56.1', { + 'checksums': ['d0e527f2336ee4beee91eefb2a8f0dfa96413d9b5a5841d6fc7ff821e67c9779'], + }), + ('WeightSVM', '1.7-11', { + 'checksums': ['498f2d1d8329b7309b373c18afcdad8ed9d3d54169f310de3264a65364406e69'], + }), + ('mpath', '0.4-2.23', { + 'checksums': ['1608215dd7826dde0cb7c8890375568d286270024d52f01cb12c9402c817ed99'], + }), + ('timereg', '2.0.5', { + 'checksums': ['a0d1ddeaf6962c7f48e213430ec838cf8e880a6c41571e4c2e864d070f84f7ef'], + }), + ('peperr', '1.5', { + 'checksums': ['f7f9b3140bd8f0d00b7cacd55e9626e2333eb91ab0173e8f21237803045b8500'], + }), + ('heatmap3', '1.1.9', { + 'checksums': ['594c33947b2be2cc8a592075f41a0df2398c892add7d63a15c613a5eeb8fdb69'], + }), + ('GlobalOptions', '0.1.2', { + 'checksums': ['47890699668cfa9900a829c51f8a32e02a7a7764ad07cfac972aad66f839753e'], + }), + ('circlize', '0.4.15', { + 'checksums': ['d602d55313fe7c675109153d6ed3b99bdba5292e1deefed71d5a21e0db595cc7'], + }), + ('GetoptLong', '1.0.5', { + 'checksums': ['8c237986ed3dfb72d956ad865ef7768644eebf144675ad66140acfd1aca9d701'], + }), + ('dendextend', '1.17.1', { + 'checksums': ['87e96e119e7236b4f5df1c6f1b0d4d4e12aab606a2142e039f56d8ec71f9e521'], + }), + ('RInside', '0.2.18', { + 'checksums': ['805014f0f0a364633e0e3c59100665a089bc455dec80b24f04aaec96466cb736'], + }), + ('limSolve', '1.5.7', { + 'checksums': ['047766ff01171c67763f50103c4cfa97c37300e01dd84b0b2410e979e39c58f1'], + }), + ('dbplyr', '2.4.0', { + 'checksums': ['9154f35771fa818456c6c6ec566699f2e1e7569aaa48209de80b44274240f1e7'], + }), + ('modelr', '0.1.11', { + 'checksums': ['94ebd506e9ccf3bf25318be6a182f8f89c3669a77b41864a0b9dbcc1d4337bd3'], + }), + ('debugme', '1.1.0', { + 'checksums': ['4dae0e2450d6689a6eab560e36f8a7c63853abbab64994028220b8fd4b793ab1'], + }), + ('reprex', '2.0.2', { + 'checksums': ['a85b16e26112364a65c886efea050df08c17aadf1411fd14ec27d9ef13e87092'], + }), + ('selectr', '0.4-2', { + 'checksums': ['5588aed05f3f5ee63c0d29953ef53da5dac7afccfdd04b7b22ef24e1e3b0c127'], + }), + ('rvest', '1.0.3', { + 'checksums': ['a465ef7391afaa3c26eebe8c61db02314ac04c4d8de5aa53f090716763d21c1e'], + }), + ('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', '0.45.0', { + 'checksums': ['a58046d448b2fca15fb1bf5b5eec4da37b29175270c07e46d740066537435da4'], + }), + ('gdistance', '1.6.4', { + 'checksums': ['6af5fd3ea7e256f34d705d4817bb88056037ce1d68adfeb28d61c4a640d8992b'], + }), + ('vioplot', '0.4.0', { + 'checksums': ['5729b483e3a4f7c81d2cc22c8bc5211b64e289734e9da5b5696c4974067867b5'], + }), + ('emulator', '1.2-21', { + 'checksums': ['9b50b2c1e673dbc5e846a4fa72e8bd03434add9f659bde6d7b0c4f1bbd713346'], + }), + ('gmm', '1.8', { + 'checksums': ['7099fc5c6a9069924392995a726190e8d62f6e55375ef356084b0c73346d85d8'], + }), + ('tmvtnorm', '1.5', { + 'checksums': ['1c7a606bdce4319a6fdb4180fef499c293df3412d8583e296869521ece5460fe'], + }), + ('IDPmisc', '1.1.20', { + 'checksums': ['bcb9cd7b8097e5089d1936286ef310ac2030ea7791350df706382ba470afc67f'], + }), + ('gap.datasets', '0.0.6', { + 'checksums': ['1e14b06fac203016555ddca323225ccf18d784609dbf9bdfff423e6dccd297cb'], + }), + ('gap', '1.5-3', { + 'checksums': ['6e19f9d822460867fcb97fe917730ce0f87218893a6a7edae42caaa401b452ce'], + }), + ('qrnn', '2.1', { + 'checksums': ['4f597c9b1437388716db232bf4a33ad5afeca6aa261aaed6eb1cf6938fde8aa6'], + }), + ('TMB', '1.9.6', { + 'checksums': ['00da066f99fbd07910b17ff26207c73c26935a23d71cb5efabf10922755603ea'], + }), + ('glmmTMB', '1.1.8', { + 'checksums': ['4248f6c37a2f82543bc0160c71d6d409ff742a4b1b29b417a42f34460489bd14'], + }), + ('gmp', '0.7-2', { + 'checksums': ['7c9528b484197d13e69e91f8a1c9957729997b9e71e44ebebbf173a587042d8b'], + }), + ('ROI', '1.0-1', { + 'checksums': ['d4ff143304f1422ecc455eb1a00896530193c1a227ed7f3e9da2baa95d921616'], + }), + ('Rglpk', '0.6-5', { + 'checksums': ['aaeffc005a8febfe3422c8ae1347d5e17ea84320b959358670bb1083d6b57ca1'], + }), + ('ROI.plugin.glpk', '1.0-0', { + 'checksums': ['b361b0d4222d74b21432cdc6990762affecdbcec8fd6bbdb13b78b59cb04b444'], + }), + ('spaMM', '4.4.0', { + 'checksums': ['ff7299662dfa60b73f8792242a7480332468c9248f337b89c38dc95388762731'], + }), + ('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', '1.3.2', { + 'checksums': ['9b85be7b12b31ac076f2456853a5b18d8a79ce2b86d00055264529a0cd28515c'], + }), + ('cghFLasso', '0.2-1', { + 'checksums': ['6e697959b35a3ceb2baa1542ef81f0335006a5a9c937f0173c6483979cb4302c'], + }), + ('svd', '0.5.4.1', { + 'checksums': ['6b0e6f3dfda216882e7bddb2bddf206dbb081147b77c368476333a8f55d9962b'], + }), + ('Rssa', '1.0.5', { + 'checksums': ['475819636afb330a4467722b0a664fa54d6114d782b681f681ccb123f3be522d'], + }), + ('JBTools', '0.7.2.9', { + 'checksums': ['b33cfa17339df7113176ad1832cbb0533acf5d25c36b95e888f561d586c5d62f'], + }), + ('RUnit', '0.4.32', { + 'checksums': ['23a393059989000734898685d0d5509ece219879713eb09083f7707f167f81f1'], + }), + ('DistributionUtils', '0.6-1', { + 'checksums': ['31e79eaa8871b0b9fb8ac63a3fbd852f9ed3047bc584c233ac030b50e1b963d7'], + }), + ('gapfill', '0.9.6-1', { + 'checksums': ['22f04755873e34a9077bb1b1de8d16f5bc56cb8c395c4f797f9ad0b209b1b996'], + }), + ('gee', '4.13-25', { + 'checksums': ['e140881e2febe793a24086a2d179062b9995db901257d678f85d220441400e89'], + }), + ('Matching', '4.10-14', { + 'checksums': ['bfb4286a5da29dcfcc4ddee6299e2d91c0de177720b060b8946fd16f32f6a6b0'], + }), + ('chk', '0.9.1', { + 'checksums': ['f9b43dcf1002c6244dc87965f21dff6e65256eb634b826deb7b5cdfc26f505a7'], + }), + ('MatchIt', '4.5.5', { + 'checksums': ['ae39cafdd3a52487e3ebff1b49642f516cf64321fea90fa57ce3d545a259859e'], + }), + ('RItools', '0.3-3', { + 'checksums': ['2a08e2d2ea3abf5fad89c65fdba1d78dd5f4bd12f980436964fe535554d331d5'], + }), + ('mitools', '2.4', { + 'checksums': ['f204f3774e29d79810f579f128de892539518f2cbe6ed237e08c8e7283155d30'], + }), + ('survey', '4.2-1', { + 'checksums': ['cc3c61e132fb20bed98fa59a8254335a588780a5f4eeb51fab7489390aadf150'], + }), + ('rlemon', '0.2.1', { + 'checksums': ['4a18fa034f197c68daf48daf25c0e41f1b8acbe71d030c6bc1f55e3062a10375'], + }), + ('optmatch', '0.10.6', { + 'checksums': ['2b7661567fdfbdb39dae3779b4b7dea2b9eb759d3117311b3a7936b10cce1d35'], + }), + ('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', { + 'checksums': ['1d60ff13bb260630f797bde66a377a5d4cd65d78ae81a3936dc4374572ec786e'], + }), + ('distr', '2.9.2', { + 'checksums': ['b52a817ed66b75defb009e2f946472ab87f693f63c43638e86b5482cd39a2e30'], + }), + ('distrEx', '2.9.0', { + 'checksums': ['087d1847ad400141b5e0fd0858ef3e5c698b3018d7e2d33087be601a5740fb35'], + }), + ('minerva', '1.5.10', { + 'checksums': ['2f26353d8fcc989ac698c4e45bb683801b1a7bb60b14903d05a4d73c629c590f'], + }), + ('RcppTOML', '0.2.2', { + 'checksums': ['371391f9ca82221e76a424082ea9ebc5ea2c50f14e8408469b09d7dc3e6f63aa'], + }), + ('here', '1.0.1', { + 'checksums': ['08ed908033420d3d665c87248b3a14d1b6e2b37844bf736be620578c20ca346b'], + }), + ('reticulate', '1.34.0', { + 'checksums': ['8d0d8922cd811153836e95354357615968b005a4d0d4c5734441953c526e4206'], + }), + ('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', '0.5.4', { + 'checksums': ['2bf71c2034804cec637e6748dc51d8cadad01d3ea4d14ace754327f082e8d851'], + }), + ('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', '1.3.8', { + 'installopts': '--configure-args="--with-hdf5=$EBROOTHDF5/bin/h5pcc"', + 'preinstallopts': "unset LIBS && ", + 'checksums': ['b53281e2cf57447965849748e972de2f7fe8df0cee3538ef5813c33c7ed2302b'], + }), + ('DTRreg', '1.7', { + 'checksums': ['f0fad2244d960cec8fc33d9a1078df359ceb0aadff980ce6149aa9f01c62223b'], + }), + ('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', '2.0-6', { + 'checksums': ['45d374ebfdcc2c9f6cc738d196caf83a2297ed2aefe2cc99007fcbeb78a61c34'], + }), + ('clustree', '0.5.0', { + 'checksums': ['a87f65dc0489af77807ed27de67e905699f21f50bcfba6a84353b9a846a84ac1'], + }), + ('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', '5.5.2.0-17.10', { + 'checksums': ['4cb7ef25d32c1dace99455d5858bac0c57acca29e3a8e206b36e231e13da10b9'], + }), + ('ergm', '4.5.0', { + 'checksums': ['3372c7bd35b640518d65a62615cb7029652a65fe2851748847f1c16b657b6351'], + }), + ('networkLite', '1.0.5', { + 'checksums': ['aaab55d4f8f0b330fe7c1ecbab3c44746c52c2fda99c53c6b46042bb8775718b'], + }), + ('networkDynamic', '0.11.3', { + 'checksums': ['2c664fd0d85c0cdc099480d67a18e6afbb0cc1036963b6664a8a756874648e5b'], + }), + ('ergm.multi', '0.2.0', { + 'checksums': ['13e27ba59b087f09cfb3dc6fccaa360e4ae0159f13e7a20d2c3306b5fe74fb5a'], + }), + ('tergm', '4.2.0', { + 'checksums': ['dcf5a26cc2c4d165766706af08f8ea4f36e328158f5b682490c2a351f7fbda69'], + }), + ('ergm.count', '4.1.1', { + 'checksums': ['446893614ad8b41aa39c37c2bf45a167f575536bb6778b8ad1fbcddb7b934932'], + }), + ('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', '0.9-7', { + 'checksums': ['b7c4d3d5f9364c67a4a3cd49296a61c315ad9bd49324a22deccbacb314aa8260'], + }), + ('MCMCpack', '1.6-3', { + 'checksums': ['cb14ba20690b31fd813b05565484c866425f072a5ad99a5cbf1da63588958db3'], + }), + ('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', { + # Don't add optimization flags by liquidSVM which may not be known e.g. on PPC + 'patches': ['liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch'], + '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', '3.42.0.2', { + 'checksums': ['9aae531f4eb3ed90b5d3e31a9030ba0ca7c6bdc6e3c84aec2a5c4e3eb562929b'], + }), + ('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', '1.1.10.1', { + 'checksums': ['9093384941b5626aae2acf4835b591875193a6000d1f0b212abeaf682652949b'], + }), + ('parsedate', '1.3.1', { + 'checksums': ['1fc31ab9813b61680abf4f4c2705b8f484d56d1d3ef256df84b342b628b6d1b1'], + }), + ('circular', '0.5-0', { + 'checksums': ['4bf4da5de29e555d1a7ae7ea64f8a5dda037e5c423f1078944f0bbb6eb9a7b92'], + }), + ('cobs', '1.3-5', { + 'checksums': ['7fae7da8f940975d544120c836e2d3b874f9b0cbab9631851ce986709f51c611'], + }), + ('resample', '0.6', { + 'checksums': ['1b958009b18c92a47971847c782af76952ea4e85d5f1e3e1e70fa35c67b95265'], + }), + ('MIIVsem', '0.5.8', { + 'checksums': ['a908f51e1598290d25864c358d57201bd50c1c40775d4d0405cbc8077bee61e1'], + }), + ('medflex', '0.6-10', { + 'checksums': ['bd89a8fe939f3becd71a9dab30fe27fa43c96572d8309d2c1a70633117d4cb33'], + }), + ('Rserve', '1.8-11', { + 'checksums': ['9dfb1d68493f8cee5d2e12a1bfa604404834e11809f4c908d65b9100a9af1b85'], + }), + ('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', '2.0.0', { + 'checksums': ['8693cab745d426260227d522d9113078d720b1ac0eb0931a47fa8f74aab82fa7'], + }), + ('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', '1.3-6', { + 'checksums': ['f9c871d54378408902931792b3dbf8bda863d6aa67af6a0472a6ec1c420760bc'], + }), + ('fftwtools', '0.9-11', { + 'checksums': ['f1f0c9a9086c7b2f72c5fb0334717cc917213a004eaef8448eab4940c9852c7f'], + }), + ('imagerExtra', '1.3.2', { + 'checksums': ['0ebfa1eabb89459d774630ab73c7a97a93b9481ea5afc55482975475acebd5b8'], + }), + ('MALDIquant', '1.22.1', { + 'checksums': ['0a52a55dbe76a7e7ca50c5555fea4381eeda0c215c66e420d8dc9bfd2992411c'], + }), + ('threejs', '0.3.3', { + 'checksums': ['76c759c8b20fb34f4f7a01cbd1b961296e1f19f4df6dded69aae7f1bca80219c'], + }), + ('LaplacesDemon', '16.1.6', { + 'checksums': ['57b53882fd7a195b38bbdbbf0b17745405eb3159b1b42f7f11ce80c78ab94eb7'], + }), + ('rda', '1.2-1', { + 'checksums': ['37038a9131c9133519f5e64fa1a86dbe28b21f519cf6528503234648a139ae9a'], + }), + ('sampling', '2.10', { + 'checksums': ['fdec976ec0abfb5c690049d76f89ebcb8ab3650e2eb28a5b54c3984d17372775'], + }), + ('lda', '1.4.2', { + 'checksums': ['5606a1e1bc24706988853528023f7a004c725791ae1a7309f1aea2fc6681240f'], + }), + ('jiebaRD', '0.1', { + 'checksums': ['045ee670f5378fe325a45b40fd55136b355cbb225e088cb229f512c51abb4df1'], + }), + ('jiebaR', '0.11', { + 'checksums': ['adde8b0b21c01ec344735d49cd33929511086719c99f8e10dce4ca9479276623'], + }), + ('hdm', '0.3.1', { + 'checksums': ['ba087565e9e0a8ea30a6095919141895fd76b7f3c05a03e60e9e24e602732bce'], + }), + ('abe', '3.0.1', { + 'checksums': ['66d2e9ac78ba64b7d27b22b647fc00378ea832f868e51c18df50d6fffb8029b8'], + }), + ('SignifReg', '4.3', { + 'checksums': ['f755808fcb618582acb862729b20e267d9c2214f22e6e7a0c8d29073d8faa7b8'], + }), + ('bbmle', '1.0.25', { + 'checksums': ['86a8c69902fbf6caf337f9bc532afe89dc2a59dd24287a2423d781797010b255'], + }), + ('emdbook', '1.3.13', { + 'checksums': ['26044b7ea1b42304b4dfde48afa94dd487acf979da4db2bf670ba41222083c19'], + }), + ('SOAR', '0.99-11', { + 'checksums': ['d5a0fba3664087308ce5295a1d57d10bad149eb9771b4fe67478deae4b7f68d8'], + }), + ('rasterVis', '0.51.6', { + 'checksums': ['61bd0d19d045b50c6764f3a7c95ce1e734af9e5f964449825d002afe02109489'], + }), + ('tictoc', '1.2', { + 'checksums': ['f05ea4b4142a90b0dc5d10356be3748625ef86bbd0e4399c56455654165ff20c'], + }), + ('ISOcodes', '2022.09.29', { + 'checksums': ['4bae4fdf661a1c29694f9702240b84c933518ef70e66312cbaddaf35562d4fe5'], + }), + ('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', '0.2-14', { + 'checksums': ['acd40ff8ea973692bd9e9acf175afc5c74ccf54b93297a0a054c15caa44b5cc9'], + }), + ('tidytext', '0.4.1', { + 'checksums': ['526750a2cc8ac7b65be1093f4c9186aa27f0a22f00023a6d6b3b878e1310c815'], + }), + ('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', '1.0.3', { + 'checksums': ['38760abd8c8e8f69ad85ca7992803060acc44ce68358de1763bd2415fdf83c9f'], + }), + ('HiddenMarkov', '1.8-13', { + 'checksums': ['7186d23e561818f3e1f01376a4fb2af9ccee775ce5afc1e3175f3b07a81db515'], + }), + ('lmerTest', '3.1-3', { + 'checksums': ['35aa75e9f5f2871398ff56a482b013e6828135ef04916ced7d1d7e35257ea8fd'], + }), + ('loo', '2.6.0', { + 'checksums': ['66da60fdf53a62cbc93797fa696a4cc43bce77f1721dd4bc1a58d25b3f981210'], + }), + ('RcppParallel', '5.1.7', { + 'checksums': ['f9c30eb9ce1abffc590825d513d6d28dcbe970e36032dd7521febf04e905b29c'], + }), + ('StanHeaders', '2.26.28', { + 'checksums': ['938a8d96d3a64357b5fee73eea2923a2a2292a062ff516ea8c720756ec7e3de8'], + }), + ('V8', '4.4.0', { + 'installopts': '--configure-vars="INCLUDE_DIR=$CPATH LIB_DIR=$LIBRARY_PATH"', + 'preinstallopts': "export CPATH=$EBROOTNODEJS/include/node:$CPATH && ", + 'checksums': ['635bc20fb90206c357b0eba53d8af0789783241d300f0190fce9d6d0614c8f46'], + }), + ('QuickJSR', '1.0.7', { + 'checksums': ['3161c243fed64ea215084b44141bea9ee416fa1ef3910aeb78abe55f3d3e9893'], + }), + ('rstan', '2.32.3', { + 'checksums': ['a29d9e1abf6d7c7b5ce98e10e60f14f18bad076aff4c7affa4b6263945ba549d'], + }), + ('Rborist', '0.3-5', { + 'checksums': ['30cf41ae646e53ef5e4be0c924eca9c783ccec9e771aeba1429f801009be8abc'], + }), + ('VSURF', '1.2.0', { + 'checksums': ['c027b1e19762f1eaf4a559c2592f3530210fefd21ee3d7c787c73b776c683393'], + }), + ('mRMRe', '2.1.2.1', { + 'checksums': ['d53c392e82a437005b71d0e8b97350d0237608fffafe087700fe7f6770167fd9'], + }), + ('dHSIC', '2.1', { + 'checksums': ['94c86473790cf69f11c68ed8ba9d6ae98218c7c69b7a9a093f235d175cf83db0'], + }), + ('ggsci', '3.0.0', { + 'checksums': ['8901316516d78f82a2a8685d93ba479424bcfd8cb5e28a28adbd50e68964e129'], + }), + ('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', '1.0-33', { + 'checksums': ['58595262eb1bc9ffeeadca78664c418ea24b4e894744890c00252c5ebd02512c'], + }), + ('intrinsicDimension', '1.2.0', { + 'checksums': ['6cc9180a83aa0d123f1e420136bb959c0d5877867fa170b79536f5ee22106a32'], + }), + ('patchwork', '1.1.3', { + 'checksums': ['e976424f4bd88e075f2ca6836db2aa1eb5fa7ad6a20ad0a34a4d5047d59ad71e'], + }), + ('leiden', '0.4.3', { + 'checksums': ['6a464b4b860e621749b3b701bb7ceb07e23c1a36be241c3e13b18105eb980938'], + }), + ('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', '2.2.2', { + 'checksums': ['b62c9bf5e6ca35fb7a2e614a916815c04cbf6c6db3f89f99b4df76470a4a856d'], + }), + ('intergraph', '2.0-3', { + 'checksums': ['354640a8ac4a1186e6d229b6c25f0535be3e456c13b1e7224a1632d3a346a7e8'], + }), + ('ggnetwork', '0.5.12', { + 'checksums': ['74368662c1a225cdefc8addf606b398f14dafeff03faac56c15aa5e14819e9cd'], + }), + ('qqman', '0.1.9', { + 'checksums': ['3f6a931771d375174b78f220471ddd601def9b5c69631931b0992ebbc8c5bc13'], + }), + ('rstantools', '2.3.1.1', { + 'checksums': ['f260ee54c11461d0f80f447e6fa6909337ede09806cd48f4a89ae9d59804e22e'], + }), + ('distributional', '0.3.2', { + 'checksums': ['c883d633398233aee5a8ca6b587687f765bdfe0732a84e4961e7f71ac0d008f8'], + }), + ('posterior', '1.5.0', { + 'checksums': ['4a10307fcae321f2cd4ca7871504a0c6c9152b8473dc9a033721e8dcda18e2de'], + }), + ('bayesplot', '1.10.0', { + 'checksums': ['bb4cb92b1ae4cf8ae5f4b5cb092aba34af3d820d137e1f2265cca8f3e85113ff'], + }), + ('dygraphs', '1.1.1.6', { + 'checksums': ['c3d331f30012e721a048e04639f60ea738cd7e54e4f930ac9849b95f0f005208'], + }), + ('renv', '1.0.3', { + 'checksums': ['985a1432144a662d34af4b55a3e38c4fc030551ba077f68541af91a1a70f5eb4'], + }), + ('rsconnect', '1.1.1', { + 'checksums': ['77bce6f08ed376be1028b05db3526bb4587aa024d86b9117ab30af177c5608ed'], + }), + ('shinystan', '2.6.0', { + 'checksums': ['a084856a2d66d8744f2c72e3e19ca35e600a508ed7ef1f7ebed8c7fc0738d529'], + }), + ('optimx', '2023-10.21', { + 'checksums': ['0d732d5604c26af59cfb95b80ed4e226c9c10422e2d82a6cc06b92f9ba6a44b5'], + }), + ('gamm4', '0.2-6', { + 'checksums': ['57c5b66582b2adc32f6a3bb6a259f5b95198e283a96d966a6007e8e48b380c89'], + }), + ('memisc', '0.99.31.6', { + 'checksums': ['52336b4ffc6e60c3ed10ccc7417231582b0d2e4c5c3b2184396a7d3ca9c1d96e'], + }), + ('mclogit', '0.9.6', { + 'checksums': ['9adc5f6d8649960abe009c30d9b4c448ff7d174c455a594cbf104a33d5a36f69'], + }), + ('projpred', '2.7.0', { + 'checksums': ['b9e8336c1da7eea958e8aca8ecdb9e2aea1a3d9a3032bb288914db0fd69ecd37'], + }), + ('brms', '2.20.4', { + 'checksums': ['00a6f3ea690c4e6b3e645e0a366d8a93c9bd51151b9376d01011ab95e332072f'], + }), + ('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', '1.8.0', { + 'checksums': ['52a3eace87d73e3088d2eacc37c1840ca0436f6060498cc2520a2d9f9955dff3'], + }), + ('drugCombo', '1.2.1', { + 'checksums': ['9a605c655c159604033558d757711e6d83d33dfc286c1280f722d4cb7d130f80'], + }), + ('betareg', '3.1-4', { + 'checksums': ['5106986096a68b2b516215968158589b71969ce7912879253d6e930355a18101'], + }), + ('unmarked', '1.3.2', { + 'checksums': ['a1d21619c8627419e09646cc12e09457c0ea8989caf2e674d032e59b310cf883'], + }), + ('maxlike', '0.1-10', { + 'checksums': ['0c0af4c44140e6037b6b9700013fe2b87f750b4af41b7646b37e16bd7feb5133'], + }), + ('coxme', '2.2-18.1', { + 'checksums': ['aef691d74ee75095c43d7b6ab27e01641382cfb349a8eefad972c745ac0531f5'], + }), + ('AICcmodavg', '2.3-2', { + 'checksums': ['899e5edb0858c218184d01b7de32dee991090c6593ee60669767b96b7037f353'], + }), + ('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', '3.7.8', { + 'checksums': ['c0d3b84ce6fbbadf007c16ea93c3037faf451736d8ced5b0b9f529b53685b1a3'], + }), + ('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', '0.8.2', { + 'checksums': ['2de9a3ec33a213c7592b49cca1d510a25aef0625369376d9b1b4e5d0da519226'], + }), + ('ridigbio', '0.3.7', { + 'checksums': ['af2a90a8a90fbede4cf2178b758f00cc13066f4d0bd87dac8d156809050a6d59'], + }), + ('spocc', '1.2.2', { + 'checksums': ['af4b398dc02522629b9fee697ccf640b7654330419a8f94cb5d1c7d17c8784fc'], + }), + ('spThin', '0.2.0', { + 'checksums': ['2e997afb79a2a990eded34c71afaac83986669cfa9ac51b15ae3f2b558902048'], + }), + ('RPostgreSQL', '0.7-5', { + 'checksums': ['6b5401ee55bd948ae7bc84520d789ceb422533a7d5e5bd6e10e3b54447f29fa1'], + }), + ('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', '3.6.2', { + 'checksums': ['cde33a8ec558b12d8e11d7d0531e73f6678a25ee589b79897d2fc425a3fd353c'], + }), + ('earth', '5.3.2', { + 'checksums': ['c844d75edf9a2706a911bb05ed4287aad9acf6f3fed357e037763a300eac0bea'], + }), + ('mda', '0.5-4', { + 'checksums': ['f25f7f28807d0fa478b1b55eb9d026ebc30577d9d5ff288f9abfe1f3fdb8a759'], + }), + ('xgboost', '1.7.5.1', { + 'checksums': ['4ec0833f206f84e5983e9f373ea64903bec488f751fba6f75a6f4702b1c965bc'], + }), + ('biomod2', '4.2-4', { + 'checksums': ['c28163075df90a90fc1939e9ff24d40bace7de611ff7ddfe027e0ff980e7c64f'], + }), + ('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', '2.5-3', { + 'checksums': ['154ed68785de8c4a02db1916dfe50862cf544865901936e864207ada777e5108'], + }), + ('ruv', '0.9.7.1', { + 'checksums': ['a0c54e56ba3d8f6ae178ae4d0e417a79295abf5dcb68bbae26c4b874734d98d8'], + }), + ('mhsmm', '0.4.21', { + 'checksums': ['293544afb194934b1d58cf88c6f8c372f537745514b6e428cf83ae62e87d2bba'], + }), + ('dbarts', '0.9-23', { + 'checksums': ['e1ac65fd89c321895d4f0e77d9cd8dcda5f1103485008afd4e19e6c9137557a3'], + }), + ('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'], + }), + ('readODS', '2.1.0', { + 'checksums': ['3f3e557ac7cadeda4759c51f866ce9a942cb21a2b3dd24e55a082fc7d300d7fe'], + }), + ('nortest', '1.0-4', { + 'checksums': ['a3850a048181d5d059c1e74903437569873b430c915b709808237d71fee5209f'], + }), + ('EnvStats', '2.8.1', { + 'checksums': ['12952b9eaa64b7bdbaaa5c6b7acb3aa1028ddfa4e5de7ddfea54f900c452d6a6'], + }), + ('outliers', '0.15', { + 'checksums': ['cc31d7f2faefd2c3a27f8ce78c7e67d3b321dcd6690292fad2468125e5e635fb'], + }), + # elementR is too old and doesn't work anymore with other extensions, such as gdata and readODS + # ('elementR', '1.3.7', { + # 'checksums': ['4275f88f372a2efe96ccd0afc20f4f12be92f28c7db35c68b80bb0ffb2c2ab07'], + # }), + ('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 ", + # skip 'import' check with library(gWidgets2tcltk), since it also fails on headless systems... + 'modulename': False, + 'checksums': ['10399cc636eeeb5484c3379970c37c56df10d979bf866a35b66d0c75b7222c0a'], + }), + ('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', '0.99.50', { + 'checksums': ['1b9cf09de7c7625c30d2daca92b4f798476f10907d531267e773d379f6828eab'], + }), + ('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', '1.1.2', { + 'checksums': ['e9f6a4eab1be75fab63d9de5cc496b1812e2ec2d3e1d6a006ae6a9a6d2fd29ab'], + }), + ('RCAL', '2.0', { + 'checksums': ['10f5f938a8322d8737159e1e49ce9d12419a5130699b8a19c6ca53d6508da8cc'], + }), + ('stargazer', '5.2.3', { + 'checksums': ['208e9b48a11cf56ce142731c204f3d2bcb5b68719f84309a36362cd925414265'], + }), + ('sensemakr', '0.1.4', { + 'checksums': ['6a1354f05392fa9343b90f69a54022c995651fb3c3d05cb08fa088ef52258caf'], + }), + ('CompQuadForm', '1.4.3', { + 'checksums': ['042fc56c800dd8f5f47a017e2efa832caf74f0602824abf7099898d9708660c4'], + }), + ('nonnest2', '0.5-6', { + 'checksums': ['b59144f50fb264fd0d40ee770bf25047bf0f37fa154620d8fe0a91c0065061e8'], + }), + ('blavaan', '0.5-2', { + 'checksums': ['f3523ab082a0db524719c32ddc3397a7798ba146766356ac134c3973acc40758'], + }), + ('mathjaxr', '1.6-0', { + 'checksums': ['ecc47607111b788d84789459af7f4f9102719f98640b7a23bd5a4eb1a6d3c179'], + }), + ('metadat', '1.2-0', { + 'checksums': ['f0cce5e30c3d256eaf5a41e4f52ffc7108e195016a4b99409e0ab4c2ef58f5b8'], + }), + ('metafor', '4.4-0', { + 'checksums': ['62aca0c70b44205e885cf55f6cfb56c37efff74bdef79dbabd727d629d3087d4'], + }), + ('RNifti', '1.5.0', { + 'checksums': ['32e4dfd35643932e0f2021b22cfc26cedff51dff13b940d9a3abe6282bf5e905'], + }), + ('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'], + }), + ('DEoptim', '2.2-8', { + 'checksums': ['631eabdcf26ec25a759651f699db1971beca3ae193c7fbd1c63a78248fdbf54c'], + }), + ('optextras', '2019-12.4', { + 'checksums': ['59006383860826be502ea8757e39ed94338f04d246c4fc398a088e004d8b13eb'], + }), + ('setRNG', '2022.4-1', { + 'checksums': ['61c06e6bd6b43c295472c6990266fe87ca41e57db04d3460e756a35ef24e0824'], + }), + ('Rvmmin', '2018-4.17.1', { + 'checksums': ['55000ac4ff57d42f172c46c7d6b0a603da3b65866d6440d6b32bac4d2b81814e'], + }), + ('Rcgmin', '2022-4.30', { + 'checksums': ['2684b8e7fb970da2afbc00e482031cf4447416249d04c4c1740400ad112fb911'], + }), + ('optimr', '2019-12.16', { + 'checksums': ['73b1ed560ffd74599517e8baa4c5b293aa062e9c8d50219a3a24b63e72fa7c00'], + }), + ('DMCfun', '2.0.2', { + 'checksums': ['430cbc18f17db11a7941e6a8274a0eefbb8a6b0bdac8800970530d60d5881fde'], + }), + ('miceadds', '3.16-18', { + 'checksums': ['dbc56cd2b20aaaaa69ea28c15cfd61d48d072fe9c0dc8e392c81a569e280cf75'], + }), + ('visdat', '0.6.0', { + 'checksums': ['104acdbb9d41167b861ab24de0e1e1e14f61c1b476bac112fcbc6e47c157e598'], + }), + ('UpSetR', '1.4.0', { + 'checksums': ['351e5fee64204cf77fd378cf2a2c0456cc19d4d98a2fd5f3dac74b69a505f100'], + }), + ('norm', '1.0-11.1', { + 'checksums': ['c2ffe6c30fc203337bde49ef630a740141604d8e648c558e58c20116c47963bc'], + }), + ('naniar', '1.0.0', { + 'checksums': ['c2eda97de603e2daf4c1c5d12f9c9a65635910833a3c669e08e344e90d9394f4'], + }), + ('stringdist', '0.9.10', { + 'checksums': ['6fd42e0b7ff25843ca7f45acf9a183facfe14a6cde2dc7a97ef7126ab0f06ce8'], + }), + ('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', '0.33', { + 'checksums': ['3911bea32326bfc2e19d4f47d05e8ad7260da36fa2ae0bfde03540195081dbaa'], + }), + ('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', '0.2.9.4', { + 'checksums': ['7631cd29316a32050b9e72057754e053d7f9064a75900bb7e69b29ebca6c60b2'], + }), + ('DiceKriging', '1.6.0', { + 'checksums': ['ab5d1332809f2bb16d156ed234b102eb9fbd6de792e4291f9f6ea4652215cb49'], + }), + ('grf', '2.3.1', { + 'checksums': ['151878724a99d516fe3824299274f194e6c67c4bacc6f4cba9adfd64bc5b1c7c'], + }), + ('twang', '2.5', { + 'checksums': ['fc355527c57e4f6e0f60d26d7c690c4475fcd5fb165d125fea7cc6b9fafc4ce5'], + }), + ('neuralnet', '1.44.2', { + 'checksums': ['5f66cd255db633322c0bd158b9320cac5ceff2d56f93e4864a0540f936028826'], + }), + ('PCAmatchR', '0.3.3', { + 'checksums': ['5dc9d8bb4c0020b5e51a53a4fa71afa9adc6b907ea618b231f5cfc2877a49779'], + }), + ('origami', '1.0.7', { + 'checksums': ['b44034541ac358e0686682684c40e9a1de8d78c7913e56e4d3dbe41a2a55c62c'], + }), + ('hal9001', '0.4.3', { + 'checksums': ['f2489e7a0a16db6dc65da8ce13bfb7f0854e6f303c9ec05f6158d46c66b6588c'], + }), + ('cobalt', '4.5.1', { + 'checksums': ['799b68805033a92900c5a884862a315670b0379ed8fc8c3f3c20c61e402c27c0'], + }), + ('CBPS', '0.23', { + 'checksums': ['ed8fe09b642db459a516bdeb03a49e718a7d5ad915cbf82400029508efe9b32d'], + }), + ('SBdecomp', '1.2', { + 'checksums': ['0be4e1c9e8bed87fd1712e62346a97148a1a295ff56981e832921cc390006e5c'], + }), + ('naturalsort', '0.1.3', { + 'checksums': ['cd38a9c5f323f61459e6096cdbf4493851d40497baf671af4f8dfe9a7c00e857'], + }), + ('lwgeom', '0.2-13', { + 'checksums': ['f0822888c029af48bf0238e3d20d82d3c75018e7e63728765a6220a6a0151c67'], + }), + ('finalfit', '1.0.6', { + 'checksums': ['c12be933408b0a8ec4962ebe5e9b404ef99a0b1eafccf7f646627458f4af4b9a'], + }), + ('broom.helpers', '1.14.0', { + 'checksums': ['cdc12f35bfed5d3da55ac7c7e09974584c8e4cb7a2147429c53b7b1176c76a93'], + }), + ('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', '0.10.0', { + 'checksums': ['708a5f303ea131babd35e4ee5ce28dd30376001714eabcc967615f608fc76e3e'], + }), + ('gtsummary', '1.7.2', { + 'checksums': ['ddc225f1c3a629b47bce85b64229d2a99c46c7bf22b88a6bb6cc728e76d34b0a'], + }), + ('ncdf4', '1.21', { + 'checksums': ['2f5ae7def382c595c66b6ed0ea0529f8337108eb73de39939f9762f3fb21b30d'], + }), + ('geex', '1.1.1', { + 'checksums': ['a1aebb9f73ba8dfe26ee3dc7b0725ccb814b3db5358ba17e417bdfc7eb3e4143'], + }), + ('momentfit', '0.5', { + 'checksums': ['5f68e90545f123790d6ba149a21f07d1885361e4ca748cc93fb13bc443f7c720'], + }), + ('StatMatch', '1.4.1', { + 'checksums': ['0c5479c444cb831d21b6305fc4cdcdf2653723ff08a31427dc2b236ca4f25bc5'], + }), + ('stars', '0.6-4', { + 'checksums': ['424a4cfde4c3524f8bd44a1090c8d725662af8cc636f785d951d4aa45c130d57'], + }), + ('rapidjsonr', '1.2.0', { + 'checksums': ['62c94fcdcf5d0fbdfa2f6168affe526bf547c37c16d94e2e1b78d7bf608eed1f'], + }), + ('jsonify', '1.2.2', { + 'checksums': ['3745e962592f021a3deaed8b2f6b99c4f7181f28e095300a96d1c2b08af4af2f'], + }), + ('geometries', '0.2.3', { + 'checksums': ['642fd7b5b98be3197616b38c5eb7e59f93859ad327800ab8af65b8d5b18a9e77'], + }), + ('sfheaders', '0.4.3', { + 'checksums': ['a3a11b7297de2c85405fbdfcb6b47462cb053b727ef7a8d9ec9bd5977a8e4348'], + }), + ('geojsonsf', '2.0.3', { + 'checksums': ['275ca14672d982e6a95884515f49d8a0aad14f3be62ea01b675a91b0bffb46d1'], + }), + ('leaflet.providers', '2.0.0', { + 'checksums': ['c5ceeadc8088c9840a8249f0347501cdba0119be97219a01ea2050d1dd4a8666'], + }), + ('leaflet', '2.2.0', { + 'checksums': ['b801ef8d78c94a7337858499f0ed9e6088f08f40fa841603368dee0a17bd1f4c'], + }), + ('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', '2.0.3', { + 'checksums': ['fb8cea81b281bd40d8eccff777c998f7c5915d624623db4132044c9271c7c49b'], + }), + ('genoPlotR', '0.8.11', { + 'checksums': ['f127f7fe8b19c899ecfdf98bf69d2e18926afb593a72fc40097acca66d401607'], + }), + ('VineCopula', '2.5.0', { + 'checksums': ['51b99e6fe0a1f4c32c860fc24b0164f0ade5d81aee7235e0ef5b5256e2115b68'], + }), + ('Rmpfr', '0.9-3', { + 'checksums': ['828dbdc98e28a9f7beb0d9bec251a7387b54908753314d75c1400754560cf641'], + }), + ('scam', '1.2-14', { + 'checksums': ['cc5086aaab35d0e1969760af191ed7e76f97b65a26a9be623ac8cf0c45a93771'], + }), + ('copula', '1.1-2', { + 'checksums': ['88f9454d25e4dcdf53d8ca5156daf48e664769f5e13b1e835ed64f37251587d3'], + }), + ('evd', '2.3-6.1', { + 'checksums': ['662c592d3f5c5693dbf1c673d1137c4a60a347e330b71be1f3933f201d2c8971'], + }), + ('ismev', '1.42', { + 'checksums': ['0d57fbeca83bd478e84fcff795967d51d8448c629abe7adc6c4c18c7fb8bf1a5'], + }), + ('GJRM', '0.2-6.4', { + 'checksums': ['365a49ac4cc9dc6fb88953214b0e97b019cd1a1a8529c0ef640711c3bb8eec57'], + }), + ('penfa', '0.1.1', { + 'checksums': ['a22a8ac3d4a040c77e50ddc92328c1989eae536d79fe56013e9372ba27c114e5'], + }), + ('kde1d', '1.0.5', { + 'checksums': ['b5fab76a394a7819deee10afdff39ac64fccdb844735adfe51c92043016f2468'], + }), + ('RcppThread', '2.1.6', { + 'checksums': ['e9470c5e29e5e07ac5360d165ec96effad9115c03833b25c3acd8cd6809a27a5'], + }), + ('wdm', '0.2.4', { + 'checksums': ['e2d19c04ea2fb9394cc2b61899c7fd21ae7c6d5825bfdcb74822c7243cd335d3'], + }), + ('rvinecopulib', '0.6.3.1.1', { + 'checksums': ['df95d007552e7fa30aefad90a86acf5e14f6fe1e363ed4c71a74d501a08cbf32'], + }), + ('PearsonDS', '1.3.0', { + 'checksums': ['d37f1c38ca0ad457cff6c3e21d1b0c0d5e0d06832c5de3ee11d72b93803b57b5'], + }), + ('covsim', '1.0.0', { + 'checksums': ['3788e91ee7f7fd44b290feb22185637493e8301a64f9511ca80e1ed361c3f44f'], + }), + ('semTools', '0.5-6', { + 'checksums': ['f522ce3c02ac580ad49af7a7278141dae39fdfaeccc7d1379faf1266ce9fcaf2'], + }), + ('GPArotation', '2023.8-1', { + 'checksums': ['e445d479e477e2d42daac1d7f7db0daf6628aac6b3f8a2d51dbb95b4ad1ecfeb'], + }), + ('dcurver', '0.9.2', { + 'checksums': ['cc6c55090d3607910515981ea0c7221e40e7a29e0da0c5a5f42c3847012290ec'], + }), + ('mirt', '1.41', { + 'checksums': ['d01b2d2e8caf0f1569f1db9138839e698e17c46020dfaaab8a5496f649c6a863'], + }), + ('rpf', '1.0.14', { + 'checksums': ['e4bb090a810ec4e70a23547f95e1e07ce0229e38fbbbbe22abfad98e9b33f796'], + }), + ('OpenMx', '2.21.8', { + 'checksums': ['bfe13368360434ab5804496bb7f28053f75669b6b264e0e679261a3e705a74ef'], + }), + ('matlab', '1.0.4', { + 'checksums': ['1988a2220703444a575f2bad4eb090a0da71478599eb53081dd7237b7ec216ea'], + }), + ('FactorCopula', '0.9.3', { + 'checksums': ['df1675bb96431417cdbb9000ab80e15e12d82c8ed9809eeb3d7fe7b4855178d3'], + }), + ('rpact', '3.4.0', { + 'checksums': ['447e142f53437c070ad11b04a7d549207635114312147f358249be0d49b83674'], + }), + ('ldbounds', '2.0.1', { + 'checksums': ['1a23d56a619eff18eaf8a3538da8da47dfbeddddc8922047457de92e3e01aa1d'], + }), + ('catlearn', '1.0', { + 'checksums': ['c6ef66257b8a6968599876f53bd431b5d836f125b32cdb829b53fb972ffeffaf'], + }), + ('MetaUtility', '2.1.2', { + 'checksums': ['e38c21588c239aa8926e64d916aa0f3b04108c2992f0e801095e4c7920b9ad5d'], + }), + ('EValue', '4.1.3', { + 'checksums': ['52a8d4df8ddc80eddf7c2f6684ed6f0fd71f3bd1bfc096ed07cfe875a367e446'], + }), + ('dagitty', '0.3-1', { + 'checksums': ['7d44b5d259ec3fef776a7e3fcb21d1c379f930d6ae9ae5fbfff54494ad78e8a8'], + }), + ('ggdag', '0.2.10', { + 'checksums': ['66cdb226f63f44268fed0ef596d8849f8b70cd92cec20eb305db52a3bd1fc9ee'], + }), + ('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', '1.1.0', { + 'checksums': ['7bcdd5cb7e99e791e0aa11aa3e5316cbdb884270a3528f8a5fe5b8410169c167'], + }), + ('apcluster', '1.4.11', { + 'checksums': ['4497da8766802cb18a5729ddb629368a17a967436d696941deb4b21da73e3333'], + }), + ('DataCombine', '0.2.21', { + 'checksums': ['352b235612e2cf8234b3ab5f9aa6f7a394b006b98d24e315940ccc65c4218b47'], + }), + ('docstring', '1.0.0', { + 'checksums': ['14528bc85bbb299fb8fe1a7116034f8df49ae0c26fb299376185b5d56176e5a7'], + }), + ('gdalUtils', '2.0.3.2', { + 'checksums': ['4c6faabee2db8a87b7ea0f8e67e9fce3c5db7f4be353d7d86ea559507cbb2a4f'], + }), + ('openair', '2.18-0', { + 'checksums': ['e06febbe421a6493dff0a3c05b894bb1fffdfb1c4fed576288974f5dae597cc3'], + }), + ('pdp', '0.8.1', { + 'checksums': ['e23db66e5d575337d5c8fd664ccd0548cc85da2aca6613d90ce187be1dca376c'], + }), + ('date', '1.2-42', { + 'checksums': ['5a913f960a0071cf9db05df4de03055a21a1c243b3bdbf846375537a664bcb74'], + }), + ('cmprsk', '2.2-11', { + 'checksums': ['844027cb2c162cf7ef97034d01237ad7b81aa192fe302250d22d2c5528110e14'], + }), + ('mets', '1.3.2', { + 'checksums': ['1a8bd1678c92650c0637b69b807bfb43df4210806518d56c650967c72f3e21d8'], + }), + ('Publish', '2023.01.17', { + 'checksums': ['436cc2bf5cdca1b3fdf892c9d35227f01740f1a4b335ff7b42a37e12c0115953'], + }), + ('riskRegression', '2023.09.08', { + 'checksums': ['e4f08d4ebc19ce6ddb2c1cd9a52191d34f9b57da9498c52db416ef4216985f21'], + }), + ('pec', '2023.04.12', { + 'checksums': ['6552fe9843b0b59bfd97c0db70c1ac5b0291184b498a796803b9dca0dc70ef95'], + }), + ('pammtools', '0.5.92', { + 'checksums': ['ccf9d930521af76d441d82bf08b89e125f237f81df1f50a8152c13c9bf73e401'], + }), + ('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', '1.1.1', { + 'checksums': ['777f1b76b16837387b830e2b65304ede234b9299d17efd09c7fd403356122118'], + }), + ('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', '1.0.1', { + 'checksums': ['00310dd6bce81849e799326efdf49fdc89633d53411d2a89b01586180d5ed4f1'], + }), + ('LCFdata', '2.0', { + 'checksums': ['b58f4d93b9023dd1ba2db96a59ddfc058397085933d8de4cdb38ee064d5e7bf4'], + }), + ('LMERConvenienceFunctions', '3.0', { + 'checksums': ['eb430de9fbf836173f716960d60afc2de91de7f986471f406c3ca9027142e849'], + }), + ('HGNChelper', '0.8.1', { + 'checksums': ['aa3f0b3a8691ed93d63bec8f36d2954c6fcfd0b8b3efc705379248544c999363'], + }), + ('logger', '0.2.2', { + 'checksums': ['4f1be7d4381f2fc591f19fdbfb8f3cccbf26c9fdbae104612f6e6d5762a97e22'], + }), + ('parallelDist', '0.2.6', { + 'checksums': ['30c6b3b85cf78c04a7dcd17ea7ed64356971f6ce48d15794078a18c53b249e06'], + }), + ('roptim', '0.1.6', { + 'checksums': ['7ef0c2a2ddb3703efaabf337fa0026485875d5ffb35ba3ef5d60eb0c62c30686'], + }), + ('yulab.utils', '0.1.0', { + 'checksums': ['ef4fa9fc7e5fd458f84e0337cd08fd66961cb18be4508c59aa480d715e1fba10'], + }), + ('ggfun', '0.1.3', { + 'checksums': ['89232ea73b7bcf3262ce4f66c7f6d05b00c5c79927c9c16d3ba8f816332669ca'], + }), + ('gridGraphics', '0.5-1', { + 'checksums': ['29086e94e63891884c933b186b35511aac2a2f9c56967a72e4050e2980e7da8b'], + }), + ('ggplotify', '0.1.2', { + 'checksums': ['01bae5759e14e211bddb04413e094ba31399b513989894ea08602d202f990e87'], + }), + ('aplot', '0.2.2', { + 'checksums': ['c7f163fb0010e3a2d742f79d5a220cbfa5be2a40ae577ac56c422f2f59fe8b24'], + }), + ('tidytree', '0.4.5', { + 'checksums': ['d2708e5ff068102262eb3bc0577e34522263d70ed1e291ef196c931b51c89472'], + }), + ('ggvenn', '0.1.10', { + 'checksums': ['cde116f117266cca27d8cd20205512e602c23514db6d97caaa950b9b21fa873e'], + }), + ('scatterpie', '0.2.1', { + 'checksums': ['8b5ac54273f1d4a988e2ee8d3d8c863dc4e6307fe1bddd3019fc13bffd64d971'], + }), + ('shadowtext', '0.1.2', { + 'checksums': ['253c4e737dbb302aa0729e5074e84cbfde2a73bfd7a0fd2c74b557cb728bae7d'], + }), + ('random', '0.2.6', { + 'checksums': ['2b59f9bce0c3ebf8215ab42dffaf9a1c7eea7468964063215a8d422af953b069'], + }), + ('R2WinBUGS', '2.1-21', { + 'checksums': ['fa86cb5140f5dfce29f9517b94d6d08c316ddcffa4aa3085945b84d34910134d'], + }), + ('aricode', '1.0.3', { + 'checksums': ['10a739353feb4f552496d3a51d436088c92edbd241f80f7c33ee5f278de1d90a'], + }), + ('DepthProc', '2.1.5', { + 'checksums': ['e6b0afd54bb20e25a6bf5402c771848db20e9c844f0fc990ecc3d1078b9eee44'], + }), + ('dbscan', '1.1-11', { + 'checksums': ['f0498e67e612629340a2758fbe747c4d9d4ca648f002230a03499cb73735e62f'], + }), + ('ggh4x', '0.2.6', { + 'checksums': ['eb7929b4c3167dce644b13d655144b2893e320072e7a998f07c37c4f7d9b2b3b'], + }), + ('ComplexUpset', '1.3.3', { + 'checksums': ['5b2f99b4a38648641c7d31fc57f201a93e5bc1b85442a0b9726f72c166d964ea'], + }), + ('proxyC', '0.3.4', { + 'checksums': ['f39d1d3d34b4e26694e3916002ea370b2f4e745c0992e718bb024ed03a2b78ea'], + }), + ('changepoint', '2.2.4', { + 'checksums': ['ac636fde7610137385dde1e3d8a22a2ff856a8d5c917c7ad1a5cc49f98b8649b'], + }), + ('geeM', '0.10.1', { + 'checksums': ['fe76a32981b55835095041e777d1cf2e9ce43edb8d9488db56279f7cb6f43fe5'], + }), + ('ggstance', '0.3.6', { + 'checksums': ['cd9ad4fb83c583009ee45371c7d02d32b33d06238d3f0162b3ba9851e27a6372'], + }), + ('mosaicCore', '0.9.4.0', { + 'checksums': ['e25605d787d274eedd3de8584283c20204bcb7b94f4a409461304ce7cd867d6c'], + }), + ('ggformula', '0.10.4', { + 'checksums': ['b26d478e7e38bd9ec51777c14a7e0fef41e2c2742ca202532f0f44dc00d6a91d'], + }), + ('kinship2', '1.9.6', { + 'checksums': ['0150bd5974c2a19885f6ff2e99f3c1f6361054a0910dcfc9dd26a8e0cd73bbf6'], + }), + ('MESS', '0.5.12', { + 'checksums': ['41e07993e67a8aab52d9d4d07a06d654186ac8a8db9b740763ed5d481f01dcf7'], + }), + ('smoof', '1.6.0.3', { + 'checksums': ['af8664b152876c545f6545528de6e05a289d0714103fac7afc52960a9a855fb1'], + }), + ('mlrMBO', '1.1.5.1', { + 'checksums': ['0cf26e5e9b180d15b932541cf081a552703a60edf762aafca9933c24ea91dc99'], + }), + ('emoa', '0.5-0.2', { + 'checksums': ['d9e8bd286c4578be76a3dc7a1110bbb751eb8d0e451143273f0ced09878a243b'], + }), + ('webutils', '1.1', { + 'checksums': ['33e2b408d2b9ca12e158e0007d4a55a3ace6838341ad944344de2ceb806e4699'], + }), + ('swagger', '3.33.1', { + 'checksums': ['528369b04c6142112e05ee8b950ca1c01b3e390a4515eacb0fa17db98bafafd1'], + }), + ('varhandle', '2.0.6', { + 'checksums': ['4e7afd3ef77343c61508b0465b588751dc089c264faabf7bed60e9f4d9e1c577'], + }), + ('dlm', '1.1-6', { + 'checksums': ['89dd4130ea3a5213244c66b313fed0a74cdcc96d3e70285b14cf3fe5f354ae57'], + }), + ('PMA', '1.2-2', { + 'checksums': ['34f2a4236b5c9793cfea2c6367c61146687c277749dbbff0524425a8f335bdb9'], + }), + ('unikn', '0.9.0', { + 'checksums': ['5480f568bd182a96ac6b613347a659b3a506ff540713021692712f0b91c31c10'], + }), + ('ppcor', '1.1', { + 'checksums': ['6a78f0c4d9caa17ab0252c5d351c2371e4ffb9047ebd13964877018dd6142bf5'], + }), + ('berryFunctions', '1.22.0', { + 'checksums': ['8d8578d746e8e4f7a1deb0b1d49ff8603c5e51504d5fe549bcba54f20fe9d498'], + }), + ('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', '3.3.1', { + 'checksums': ['628542307d7ac45d4996fbc993a43ed5efcca73d97735ca74a10ccea401d4166'], + }), + ('ISOweek', '0.6-2', { + 'checksums': ['b58a37b61ee772ea2704d510e9fce69dea4dd641b45124d566242825df4530b8'], + }), + ('sentometrics', '1.0.0', { + 'checksums': ['b5c238bb72f36331cb1ed63b581a9a2a73cefc96f80bf770b0e064a89fe31b1b'], + }), + ('tau', '0.0-24', { + 'checksums': ['f08d9fc92ed11ec01f7da12ccf98862e36ef8bb69d5e42584a08b46cea6917e1'], + }), + ('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', '1.7-2', { + 'checksums': ['bde8008b5fc8f0023bdd84b3a14a7425aecf1edcdf79480dac861895de4a9a9b'], + }), + ('svglite', '2.1.2', { + 'checksums': ['c2c163e17de8174408062b969a1fc298aa1dba957dc0acc1c898384bb76c0030'], + }), + ('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', '1.2.0', { + 'checksums': ['e0c9b7060e0037f4213a5faad73f5910cf97bf93ecba93d35301cbc88cf45eed'], + }), + ('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', '0.6.3.2', { + 'checksums': ['18543b329a42be0f419dff4aa42f4401c2afb18f46276ce359853494dd803244'], + }), + ('CVXR', '1.0-11', { + 'checksums': ['e92a9638f35f4909e2a29c3b7106081e3dae7ff88b14bb6466b87fbdc80b972a'], + }), + ('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', '0.6.3', { + 'checksums': ['e51754029240d66fb1c8e6d524c63a275f6fafa19a22fef90d90c8ceb982777c'], + }), + ('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', '0.3.4', { + 'checksums': ['aad743033fba0b48aa05867df4bc9643802fa82542b559579105e8a0659aaa02'], + }), + ('flextable', '0.9.4', { + 'checksums': ['55ad11660325cf470cedf532df774f99748583eb53c0162e2dede8e1c3539ab6'], + }), + ('ridge', '3.3', { + 'checksums': ['5c2daecf6f97aa099ef5fa54f8448518c4f2ed6e44dd29fc60621a70721c60f5'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R-bundle-CRAN/liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch b/easybuild/easyconfigs/r/R-bundle-CRAN/liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch new file mode 100644 index 00000000000..56af45097b7 --- /dev/null +++ b/easybuild/easyconfigs/r/R-bundle-CRAN/liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch @@ -0,0 +1,49 @@ +The code requires C++11 but nvcc is not passed any flag for it, do that to avoid 'error: identifier "__ieee128" is undefined' on PPC +Use uppercase __PPC64__ to detect PPC 64bit (defined by GCC) +Use lowercase __aarch64__ to detect aarch64 (defined by GCC) +diff -aur liquidSVM-orig/MD5 liquidSVM/MD5 +--- liquidSVM-orig/MD5 2020-02-20 15:51:17.387058566 +0100 ++++ liquidSVM/MD5 2020-02-20 16:48:06.042078399 +0100 +@@ -66,7 +66,7 @@ + e0ea06f050a2ae8ed2f2e401d968f0ce *man/test.liquidSVM.Rd + 8874fc45419e3174bf06013d887f6582 *man/trainSVMs.Rd + 4cf2abf7c6d415a4a8cd7f5dee2df959 *man/write.liquidData.Rd +-854c1eecccd169acdb80b03ad6d768dc *src/Makevars.in ++8c4346267f7b7f649ff27fb5288d4e23 *src/Makevars.in + e6d47b428caa2cc55798b431cb5e504f *src/kernel_calculator.cpp + 13af8529f5c2bccd4ea03288e9adf908 *src/kernel_calculator.h + dc2c86cbe61e7b7c5dd433f9fa41fac6 *src/liquidSVM.cpp +@@ -155,7 +155,7 @@ + 8b39ec05680bf3416bc1de3ad92f043f *src/sources/shared/system_support/cuda_simple_vector_operations.h + 806ca83732bff4b1b89adfc3494e90da *src/sources/shared/system_support/full_64bit_support.h + dfb08cdb449d490d86dd33bee186aac5 *src/sources/shared/system_support/memory_allocation.cpp +-aec0000be577e69e88c040b641d6818a *src/sources/shared/system_support/memory_allocation.h ++f0231e65bd627116f1b5ebcc45ab1e66 *src/sources/shared/system_support/memory_allocation.h + 683d4ee517b1c760dc410c69c5508ce2 *src/sources/shared/system_support/memory_allocation.ins.cpp + cbd209324ad752e19be10d8975d65e2f *src/sources/shared/system_support/os_specifics.h + 54e8583d2e8e269ff2b6d7a79d57cbd5 *src/sources/shared/system_support/parallel_control.cpp +diff -aur liquidSVM-orig/src/Makevars.in liquidSVM/src/Makevars.in +--- liquidSVM-orig/src/Makevars.in 2020-02-20 15:51:17.377058962 +0100 ++++ liquidSVM/src/Makevars.in 2020-02-20 16:47:44.042949538 +0100 +@@ -39,7 +39,7 @@ + # The architecure flag can be set to higher values, if the hardware supports this. + # The value below should be safe for essentially all non stone-age systems. + +-NVCCFLAGS= -arch sm_30 -L$(CUDA_LIB_PATH) -DCOMPILE_WITH_CUDA__ -U__SSE2__ -U__AVX__ ++NVCCFLAGS= -arch sm_30 -L$(CUDA_LIB_PATH) -DCOMPILE_WITH_CUDA__ -U__SSE2__ -U__AVX__ -std=c++11 + + + #----------- CUDA related flags for GCC ---------------------------------------------------- +diff -aur liquidSVM-orig/src/sources/shared/system_support/memory_allocation.h liquidSVM/src/sources/shared/system_support/memory_allocation.h +--- liquidSVM-orig/src/sources/shared/system_support/memory_allocation.h 2020-02-20 15:51:17.377058962 +0100 ++++ liquidSVM/src/sources/shared/system_support/memory_allocation.h 2020-02-20 15:56:04.905673381 +0100 +@@ -42,7 +42,7 @@ + + // Check for GCC + #if __GNUC__ +- #if __x86_64__ || __ppc64__ ++ #if __x86_64__ || __ppc64__ || __PPC64__ || __aarch64__ + #define SYSTEM_WITH_64BIT + #else + #define SYSTEM_WITH_32BIT + From 00ab470fadad35a030b8af8193c60ddafc10a4b0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 7 Nov 2023 18:01:38 +0100 Subject: [PATCH 160/599] adding easyconfigs: Nextflow-23.10.0.eb --- .../n/Nextflow/Nextflow-23.10.0.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/n/Nextflow/Nextflow-23.10.0.eb diff --git a/easybuild/easyconfigs/n/Nextflow/Nextflow-23.10.0.eb b/easybuild/easyconfigs/n/Nextflow/Nextflow-23.10.0.eb new file mode 100644 index 00000000000..2c6f2b030c8 --- /dev/null +++ b/easybuild/easyconfigs/n/Nextflow/Nextflow-23.10.0.eb @@ -0,0 +1,35 @@ +easyblock = 'Binary' + +name = 'Nextflow' +version = '23.10.0' + +homepage = 'https://www.nextflow.io/' +description = """Nextflow is a reactive workflow framework and a programming DSL + that eases writing computational pipelines with complex data""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/nextflow-io/nextflow/releases/download/v%(version)s/'] +sources = ['nextflow-%(version)s-all'] +checksums = ['c69f6055c97741b828b6ee67de38125a42f1774f1621afd34c0eb72ffea171a6'] + +dependencies = [('Java', '11')] + +install_cmds = [ + "mkdir -p %(installdir)s/bin", + "cp %(builddir)s/nextflow-%(version)s-all %(installdir)s/bin", + "cd %(installdir)s/bin && ln -s nextflow-%(version)s-all nextflow", + "cd %(installdir)s/bin && chmod +x %(installdir)s/bin/nextflow-%(version)s-all", +] + +sanity_check_paths = { + 'files': ['bin/nextflow-%(version)s-all', 'bin/nextflow'], + 'dirs': [] +} + +sanity_check_commands = [ + "nextflow -v", + "nextflow help", +] + +moduleclass = 'tools' From 6bd356dde83f0a29da29dcb75079d7ef2a722095 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 7 Nov 2023 19:05:39 +0100 Subject: [PATCH 161/599] fix trivial code style issues in GFF3-toolkit easyconfig --- .../g/GFF3-toolkit/GFF3-toolkit-2.1.0-foss-2022a.eb | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/g/GFF3-toolkit/GFF3-toolkit-2.1.0-foss-2022a.eb b/easybuild/easyconfigs/g/GFF3-toolkit/GFF3-toolkit-2.1.0-foss-2022a.eb index f1110ec02d4..6698ca78b96 100644 --- a/easybuild/easyconfigs/g/GFF3-toolkit/GFF3-toolkit-2.1.0-foss-2022a.eb +++ b/easybuild/easyconfigs/g/GFF3-toolkit/GFF3-toolkit-2.1.0-foss-2022a.eb @@ -4,12 +4,12 @@ name = 'GFF3-toolkit' version = '2.1.0' homepage = 'https://gff3toolkit.readthedocs.io' -description = 'Python programs for processing GFF3 files' +description = "Python programs for processing GFF3 files" toolchain = {'name': 'foss', 'version': '2022a'} -sources = ['gff3tool-%(version)s.tar.gz'] source_urls = ['https://pypi.python.org/packages/source/g/gff3tool'] +sources = ['gff3tool-%(version)s.tar.gz'] patches = ['GFF3-toolkit-2.1.0-remove-hardcode.patch'] checksums = [ {'gff3tool-2.1.0.tar.gz': 'e842ef4afdb66926a2b63bf2619c7ef30bd9b76a5f1084a5c57bf8b39cc4f15d'}, @@ -23,8 +23,8 @@ dependencies = [ # GFF3-toolkit has hardcoded path to BLAST+ libraries, so we have to add a symlink to the required path for this to work local_blast_path = '%(installdir)s/lib/python%(pyshortver)s/site-packages/gff3tool/lib/ncbi-blast+' -preinstallopts = 'mkdir -p %s && ' % local_blast_path -preinstallopts += 'ln -s $EBROOTBLASTPLUS/bin %s && ' % local_blast_path +preinstallopts = "mkdir -p %s && " % local_blast_path +preinstallopts += "ln -s $EBROOTBLASTPLUS/bin %s && " % local_blast_path use_pip = True sanity_pip_check = True @@ -32,4 +32,4 @@ download_dep_fail = True options = {'modulename': 'gff3tool'} -moduleclass = "bio" +moduleclass = 'bio' From cb081c90f0e23375b41ba8d1ebfe78322f3161ed Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 7 Nov 2023 20:01:31 +0100 Subject: [PATCH 162/599] trivial style fixes for Oases easyconfig --- .../easyconfigs/o/Oases/Oases-20180312-GCC-12.3.0.eb | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/o/Oases/Oases-20180312-GCC-12.3.0.eb b/easybuild/easyconfigs/o/Oases/Oases-20180312-GCC-12.3.0.eb index 03ee0713e0f..ff28b8169fa 100644 --- a/easybuild/easyconfigs/o/Oases/Oases-20180312-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/o/Oases/Oases-20180312-GCC-12.3.0.eb @@ -1,4 +1,4 @@ -easyblock = "MakeCp" +easyblock = 'MakeCp' name = 'Oases' version = '20180312' @@ -27,16 +27,16 @@ checksums = [ ] # listed make targets exclude 'doc' on purpose -buildopts = ['VELVET_DIR=../velvet-%s cleanobj velvet oases' % local_velvet_commit] +buildopts = "VELVET_DIR=../velvet-%s cleanobj velvet oases" % local_velvet_commit parallel = 1 -files_to_copy = [(["oases"], 'bin'), "data", "scripts", "src", "doc", "LICENSE.txt", "README.md"] +files_to_copy = [(['oases'], 'bin'), 'data', 'scripts', 'src', 'doc', 'LICENSE.txt', 'README.md'] sanity_check_paths = { - 'files': ["bin/oases", "LICENSE.txt", "README.md"], - 'dirs': ["data", "scripts", "src", "doc"] + 'files': ['bin/oases', 'LICENSE.txt', 'README.md'], + 'dirs': ['data', 'scripts', 'src', 'doc'] } -sanity_check_commands = ['oases --version'] +sanity_check_commands = ["oases --version"] moduleclass = 'bio' From a96b92e6c481a73c5fe99a5b279f1170436f2ec4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 7 Nov 2023 20:02:24 +0100 Subject: [PATCH 163/599] remove easyconfig for typing-extensions 4.8.0 (since typing-extensions is already included with Python-bundle-PyPI) --- .../typing-extensions-4.8.0-GCCcore-12.3.0.eb | 22 ------------------- 1 file changed, 22 deletions(-) delete mode 100644 easybuild/easyconfigs/t/typing-extensions/typing-extensions-4.8.0-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/t/typing-extensions/typing-extensions-4.8.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/t/typing-extensions/typing-extensions-4.8.0-GCCcore-12.3.0.eb deleted file mode 100644 index c1d6fc3757c..00000000000 --- a/easybuild/easyconfigs/t/typing-extensions/typing-extensions-4.8.0-GCCcore-12.3.0.eb +++ /dev/null @@ -1,22 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'typing-extensions' -version = '4.8.0' - -homepage = 'https://github.com/python/typing/blob/master/typing_extensions/README.rst' -description = 'Typing Extensions - Backported and Experimental Type Hints for Python' - -toolchain = {'name': 'GCCcore', 'version': '12.3.0'} - -sources = ['typing_extensions-%(version)s.tar.gz'] -checksums = ['df8e4339e9cb77357558cbdbceca33c303714cf861d1eef15e1070055ae8b7ef'] - -builddependencies = [('binutils', '2.40')] - -dependencies = [('Python', '3.11.3')] - -use_pip = True -download_dep_fail = True -sanity_pip_check = True - -moduleclass = 'devel' From e5af9b028c27fb91b67a554b377984d579f39748 Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann <82444481+jkuhl-uni@users.noreply.github.com> Date: Tue, 7 Nov 2023 21:33:02 +0100 Subject: [PATCH 164/599] change patoolib to patool Co-authored-by: Sam Moors --- .../easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb b/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb index 241eb2a55fd..5af271bcfcd 100644 --- a/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb @@ -32,7 +32,7 @@ exts_list = [ ('fasteners', '0.18', { 'checksums': ['cb7c13ef91e0c7e4fe4af38ecaf6b904ec3f5ce0dda06d34924b6b74b869d953'], }), - ('patoolib', '1.12', { + ('patool', '1.12', { 'source_tmpl': 'patool-%(version)s.tar.gz', 'checksums': ['e3180cf8bfe13bedbcf6f5628452fca0c2c84a3b5ae8c2d3f55720ea04cb1097'], }), From 83d1a210fe7481832687b08a19de3014fa8cfe86 Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann Date: Tue, 7 Nov 2023 20:34:07 +0000 Subject: [PATCH 165/599] ... also use name fixture --- .../easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb b/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb index 5af271bcfcd..bf2d7474a2d 100644 --- a/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb @@ -33,7 +33,7 @@ exts_list = [ 'checksums': ['cb7c13ef91e0c7e4fe4af38ecaf6b904ec3f5ce0dda06d34924b6b74b869d953'], }), ('patool', '1.12', { - 'source_tmpl': 'patool-%(version)s.tar.gz', + 'source_tmpl': '%(name)s-%(version)s.tar.gz', 'checksums': ['e3180cf8bfe13bedbcf6f5628452fca0c2c84a3b5ae8c2d3f55720ea04cb1097'], }), ('annexremote', '1.6.0', { From e2f72ff32d3d208bb113dbe7873aa41d90e5f6b3 Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann Date: Tue, 7 Nov 2023 20:46:22 +0000 Subject: [PATCH 166/599] leave out souce templates alltogether --- .../easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb b/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb index bf2d7474a2d..3aad292130c 100644 --- a/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb @@ -33,7 +33,6 @@ exts_list = [ 'checksums': ['cb7c13ef91e0c7e4fe4af38ecaf6b904ec3f5ce0dda06d34924b6b74b869d953'], }), ('patool', '1.12', { - 'source_tmpl': '%(name)s-%(version)s.tar.gz', 'checksums': ['e3180cf8bfe13bedbcf6f5628452fca0c2c84a3b5ae8c2d3f55720ea04cb1097'], }), ('annexremote', '1.6.0', { @@ -45,8 +44,7 @@ exts_list = [ ('boto', '2.49.0', { 'checksums': ['ea0d3b40a2d852767be77ca343b58a9e3a4b00d9db440efb8da74b4e58025e5a'], }), - ('gitlab', '3.10.0', { - 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + ('python-gitlab', '3.10.0', { 'checksums': ['14930a16fdd7f36f67b9373e7d4d4720e8e374800028380289db3306e9f74614'], }), ('iso8601', '1.0.2', { From c6a2f3e4837cf4f31072aee266c2ba3244039e5c Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann Date: Tue, 7 Nov 2023 21:06:47 +0000 Subject: [PATCH 167/599] add module names for patool and python-gitlab --- .../easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb b/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb index 3aad292130c..c5bc906b649 100644 --- a/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb @@ -33,6 +33,7 @@ exts_list = [ 'checksums': ['cb7c13ef91e0c7e4fe4af38ecaf6b904ec3f5ce0dda06d34924b6b74b869d953'], }), ('patool', '1.12', { + 'modulename' : 'patoolib', 'checksums': ['e3180cf8bfe13bedbcf6f5628452fca0c2c84a3b5ae8c2d3f55720ea04cb1097'], }), ('annexremote', '1.6.0', { @@ -45,6 +46,7 @@ exts_list = [ 'checksums': ['ea0d3b40a2d852767be77ca343b58a9e3a4b00d9db440efb8da74b4e58025e5a'], }), ('python-gitlab', '3.10.0', { + 'modulename' : 'gitlab', 'checksums': ['14930a16fdd7f36f67b9373e7d4d4720e8e374800028380289db3306e9f74614'], }), ('iso8601', '1.0.2', { From f931f50e14f11b61c7240050f2b4c800f42b7ec0 Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann Date: Tue, 7 Nov 2023 21:22:53 +0000 Subject: [PATCH 168/599] lint --- .../easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb b/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb index c5bc906b649..8ec6b98f4fb 100644 --- a/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb @@ -33,7 +33,7 @@ exts_list = [ 'checksums': ['cb7c13ef91e0c7e4fe4af38ecaf6b904ec3f5ce0dda06d34924b6b74b869d953'], }), ('patool', '1.12', { - 'modulename' : 'patoolib', + 'modulename': 'patoolib', 'checksums': ['e3180cf8bfe13bedbcf6f5628452fca0c2c84a3b5ae8c2d3f55720ea04cb1097'], }), ('annexremote', '1.6.0', { @@ -46,7 +46,7 @@ exts_list = [ 'checksums': ['ea0d3b40a2d852767be77ca343b58a9e3a4b00d9db440efb8da74b4e58025e5a'], }), ('python-gitlab', '3.10.0', { - 'modulename' : 'gitlab', + 'modulename': 'gitlab', 'checksums': ['14930a16fdd7f36f67b9373e7d4d4720e8e374800028380289db3306e9f74614'], }), ('iso8601', '1.0.2', { From 9094e493a6c83a3e80effd4d3a408af78d79f175 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 8 Nov 2023 08:37:58 +0100 Subject: [PATCH 169/599] update OpenMx in R-bundle-CRAN 2023.11 --- .../r/R-bundle-CRAN/R-bundle-CRAN-2023.11-foss-2023a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2023.11-foss-2023a.eb b/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2023.11-foss-2023a.eb index 8421d82323d..786c88814f8 100644 --- a/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2023.11-foss-2023a.eb +++ b/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2023.11-foss-2023a.eb @@ -3023,8 +3023,8 @@ exts_list = [ ('rpf', '1.0.14', { 'checksums': ['e4bb090a810ec4e70a23547f95e1e07ce0229e38fbbbbe22abfad98e9b33f796'], }), - ('OpenMx', '2.21.8', { - 'checksums': ['bfe13368360434ab5804496bb7f28053f75669b6b264e0e679261a3e705a74ef'], + ('OpenMx', '2.21.10', { + 'checksums': ['d513227ca7a60faf1b16e9be64864401914482aac9a326676fe1d052632c94ce'], }), ('matlab', '1.0.4', { 'checksums': ['1988a2220703444a575f2bad4eb090a0da71478599eb53081dd7237b7ec216ea'], From 74599ba64d0253ab16b61d33b394354122da8600 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 8 Nov 2023 14:28:53 +0100 Subject: [PATCH 170/599] update R-bundle-CRAN 2023.11 --- .../R-bundle-CRAN-2023.11-foss-2023a.eb | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2023.11-foss-2023a.eb b/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2023.11-foss-2023a.eb index 786c88814f8..f87304d4c51 100644 --- a/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2023.11-foss-2023a.eb +++ b/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2023.11-foss-2023a.eb @@ -77,6 +77,12 @@ exts_default_options = { '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 5th November 2023 exts_list = [ @@ -3396,4 +3402,11 @@ exts_list = [ }), ] +modextrapaths = {'R_LIBS_SITE': ''} + +sanity_check_paths = { + 'files': [], + 'dirs': ['abind', 'base64', 'calibrate'], +} + moduleclass = 'lang' From ad5d94b6e5b6eb2388b866b642bbb0475f5ed2f5 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 8 Nov 2023 15:41:09 +0100 Subject: [PATCH 171/599] adding easyconfigs: PostgreSQL-16.0-GCCcore-12.3.0.eb --- .../PostgreSQL-16.0-GCCcore-12.3.0.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-16.0-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-16.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-16.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..978dbe9a5c0 --- /dev/null +++ b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-16.0-GCCcore-12.3.0.eb @@ -0,0 +1,43 @@ +easyblock = 'ConfigureMake' + +name = 'PostgreSQL' +version = '16.0' + +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': '12.3.0'} + +source_urls = ['http://ftp.postgresql.org/pub/source/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['58bd3a265a279a2754905ddf072a54d64d6236dcf786f20f92b5d30b916df516'] + +builddependencies = [ + ('binutils', '2.40'), + ('Bison', '3.8.2'), + ('flex', '2.6.4'), + ('Perl', '5.36.1'), + ('Python', '3.11.3'), +] + +dependencies = [ + ('libreadline', '8.2'), + ('zlib', '1.2.13'), + ('OpenSSL', '1.1', '', 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 5a136212b7ce6eac36183bac5ddcb3f62763d225 Mon Sep 17 00:00:00 2001 From: WilleBell Date: Wed, 8 Nov 2023 15:42:47 +0100 Subject: [PATCH 172/599] adding easyconfigs: castor-1.7.11-foss-2022a.eb --- .../c/castor/castor-1.7.11-foss-2022a.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/c/castor/castor-1.7.11-foss-2022a.eb diff --git a/easybuild/easyconfigs/c/castor/castor-1.7.11-foss-2022a.eb b/easybuild/easyconfigs/c/castor/castor-1.7.11-foss-2022a.eb new file mode 100644 index 00000000000..48f2a840462 --- /dev/null +++ b/easybuild/easyconfigs/c/castor/castor-1.7.11-foss-2022a.eb @@ -0,0 +1,37 @@ +easyblock = 'RPackage' + +name = 'castor' +version = '1.7.11' + +homepage = 'https://CRAN.R-project.org/package=castor' +description = """ +Efficient phylogenetic analyses on massive phylogenies comprising up to millions of tips. +Functions include pruning, rerooting, calculation of most-recent common ancestors, calculating +distances from the tree root and calculating pairwise distances. Calculation of phylogenetic +signal and mean trait depth (trait conservatism), ancestral state reconstruction and hidden +character prediction of discrete characters, simulating and fitting models of trait evolution, +fitting and simulating diversification models, dating trees, comparing trees, and +reading/writing trees in Newick format. +""" + + +toolchain = {'name': 'foss', 'version': '2022a'} + +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'] +checksums = ['c3fa63969ffbebc92878b857052110d3e22e9bbd06b28641604c32a5177fb2b3'] + +dependencies = [ + ('R', '4.2.1'), +] + +sanity_check_paths = { + 'files': ['%(name)s/R/%(name)s'], + 'dirs': [], +} + +moduleclass = 'bio' From 15558592d3045d0697c6279dd98431be42b4b3bd Mon Sep 17 00:00:00 2001 From: Chia-Jung Hsu Date: Wed, 8 Nov 2023 16:11:36 +0100 Subject: [PATCH 173/599] Support customizing cmake_options --- .../easyconfigs/s/SuiteSparse/SuiteSparse-7.1.0-foss-2023a.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-7.1.0-foss-2023a.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-7.1.0-foss-2023a.eb index 765f6e99944..359a382e7ff 100644 --- a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-7.1.0-foss-2023a.eb +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-7.1.0-foss-2023a.eb @@ -20,6 +20,7 @@ dependencies = [ ('MPFR', '4.2.0'), ] -prebuildopts = 'CMAKE_OPTIONS="-DCMAKE_INSTALL_PREFIX=%(installdir)s -DBLA_VENDOR=FlexiBLAS"' +# uncomment the next row if need customization +# cmake_options = '' moduleclass = 'numlib' From ca3323e972f2dec6f0b4e2c92129bb2fe63a1274 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 9 Nov 2023 10:51:49 +0100 Subject: [PATCH 174/599] fix regression in GCC 12+ on AVX512 systems --- .../easyconfigs/g/GCCcore/GCCcore-12.1.0.eb | 3 +++ .../easyconfigs/g/GCCcore/GCCcore-12.2.0.eb | 3 +++ ...re-12.2.0_fix-avx512-misoptimization.patch | 25 +++++++++++++++++++ .../easyconfigs/g/GCCcore/GCCcore-12.3.0.eb | 3 +++ .../easyconfigs/g/GCCcore/GCCcore-13.1.0.eb | 3 +++ .../easyconfigs/g/GCCcore/GCCcore-13.2.0.eb | 3 +++ 6 files changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/g/GCCcore/GCCcore-12.2.0_fix-avx512-misoptimization.patch diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-12.1.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-12.1.0.eb index 3482f6f3c16..4d35ae69304 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-12.1.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-12.1.0.eb @@ -35,6 +35,7 @@ patches = [ 'GCCcore-9.3.0_gmp-c99.patch', 'GCCcore-12.1.0_allow-pragma-wself-init.patch', 'GCCcore-12.1.0_fix-Wuninitialized-in-AVX-headers.patch', + 'GCCcore-12.2.0_fix-avx512-misoptimization.patch', 'GCCcore-12.2.0_fix-vectorizer.patch', ] checksums = [ @@ -51,6 +52,8 @@ checksums = [ '464f5faa9b23e805995d10dcdacca83df6321cac70826e9a3bc5bc9cd737f6a1'}, {'GCCcore-12.1.0_fix-Wuninitialized-in-AVX-headers.patch': '0ea675960795e238a43ae7d685a0082b21f0b63cf2fe499f6d55e89e0aaee392'}, + {'GCCcore-12.2.0_fix-avx512-misoptimization.patch': + 'bb3db707727b9975b0005346ef04230a96b3ad896f004a34262a82a244b5d436'}, {'GCCcore-12.2.0_fix-vectorizer.patch': '0b76fc379308fd189ee39c4a3a49facacf8ede08dbec4280f289341083f1632b'}, ] diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-12.2.0.eb index aa2a7e328a2..06a43b75d9c 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-12.2.0.eb @@ -35,6 +35,7 @@ patches = [ 'GCCcore-9.3.0_gmp-c99.patch', 'GCCcore-12.1.0_allow-pragma-wself-init.patch', 'GCCcore-12.1.0_fix-Wuninitialized-in-AVX-headers.patch', + 'GCCcore-12.2.0_fix-avx512-misoptimization.patch', 'GCCcore-12.2.0_fix-vectorizer.patch', 'GCCcore-12.2.0_improve-cuda-compatibility.patch', ] @@ -52,6 +53,8 @@ checksums = [ '464f5faa9b23e805995d10dcdacca83df6321cac70826e9a3bc5bc9cd737f6a1'}, {'GCCcore-12.1.0_fix-Wuninitialized-in-AVX-headers.patch': '0ea675960795e238a43ae7d685a0082b21f0b63cf2fe499f6d55e89e0aaee392'}, + {'GCCcore-12.2.0_fix-avx512-misoptimization.patch': + 'bb3db707727b9975b0005346ef04230a96b3ad896f004a34262a82a244b5d436'}, {'GCCcore-12.2.0_fix-vectorizer.patch': '0b76fc379308fd189ee39c4a3a49facacf8ede08dbec4280f289341083f1632b'}, {'GCCcore-12.2.0_improve-cuda-compatibility.patch': '91d00122554b56381592229398540e63baa26d03633292a7fdf338407a4a62d5'}, diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-12.2.0_fix-avx512-misoptimization.patch b/easybuild/easyconfigs/g/GCCcore/GCCcore-12.2.0_fix-avx512-misoptimization.patch new file mode 100644 index 00000000000..04f468739d8 --- /dev/null +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-12.2.0_fix-avx512-misoptimization.patch @@ -0,0 +1,25 @@ +Fix a typo causing inverted semantics when (even AVX2) code is compiled for AVX512 systems, e.g. via -march=native +See https://gcc.gnu.org/bugzilla/show_bug.cgi?id=112443 where the changeset is from. + +diff --git a/gcc/config/i386/sse.md b/gcc/config/i386/sse.md +index 2ce1aed4ad9..d7e058c2517 100644 +--- a/gcc/config/i386/sse.md ++++ b/gcc/config/i386/sse.md +@@ -16350,7 +16350,7 @@ + (match_dup 4))] + UNSPEC_BLENDV))] + { +- if (INTVAL (operands[5]) == 1) ++ if (INTVAL (operands[5]) == 5) + std::swap (operands[1], operands[2]); + operands[3] = gen_lowpart (mode, operands[3]); + }) +@@ -16380,7 +16380,7 @@ + (match_dup 4))] + UNSPEC_BLENDV))] + { +- if (INTVAL (operands[5]) == 1) ++ if (INTVAL (operands[5]) == 5) + std::swap (operands[1], operands[2]); + }) + diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-12.3.0.eb index c9fe0e62a87..eb7afd9a068 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-12.3.0.eb @@ -33,6 +33,7 @@ sources = [ patches = [ 'GCCcore-6.2.0-fix-find-isl.patch', 'GCCcore-9.3.0_gmp-c99.patch', + 'GCCcore-12.2.0_fix-avx512-misoptimization.patch', 'GCCcore-12.2.0_improve-cuda-compatibility.patch', ] checksums = [ @@ -45,6 +46,8 @@ checksums = [ {'nvptx-tools-20230122.tar.gz': 'af05fac26e9a83d337758a5495dc35f7a7bbfd90cd09f4a5d3242d059f235e08'}, {'GCCcore-6.2.0-fix-find-isl.patch': '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68'}, {'GCCcore-9.3.0_gmp-c99.patch': '0e135e1cc7cec701beea9d7d17a61bab34cfd496b4b555930016b98db99f922e'}, + {'GCCcore-12.2.0_fix-avx512-misoptimization.patch': + 'bb3db707727b9975b0005346ef04230a96b3ad896f004a34262a82a244b5d436'}, {'GCCcore-12.2.0_improve-cuda-compatibility.patch': '91d00122554b56381592229398540e63baa26d03633292a7fdf338407a4a62d5'}, ] diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-13.1.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-13.1.0.eb index 5805f7d8a96..005f4794d63 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-13.1.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-13.1.0.eb @@ -33,6 +33,7 @@ sources = [ patches = [ 'GCCcore-6.2.0-fix-find-isl.patch', 'GCCcore-9.3.0_gmp-c99.patch', + 'GCCcore-12.2.0_fix-avx512-misoptimization.patch', ] checksums = [ {'gcc-13.1.0.tar.gz': 'bacd4c614d8bd5983404585e53478d467a254249e0f1bb747c8bc6d787bd4fa2'}, @@ -44,6 +45,8 @@ checksums = [ {'nvptx-tools-20230122.tar.gz': 'af05fac26e9a83d337758a5495dc35f7a7bbfd90cd09f4a5d3242d059f235e08'}, {'GCCcore-6.2.0-fix-find-isl.patch': '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68'}, {'GCCcore-9.3.0_gmp-c99.patch': '0e135e1cc7cec701beea9d7d17a61bab34cfd496b4b555930016b98db99f922e'}, + {'GCCcore-12.2.0_fix-avx512-misoptimization.patch': + 'bb3db707727b9975b0005346ef04230a96b3ad896f004a34262a82a244b5d436'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-13.2.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-13.2.0.eb index c71dc05e7aa..3749681657f 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-13.2.0.eb @@ -33,6 +33,7 @@ sources = [ patches = [ 'GCCcore-6.2.0-fix-find-isl.patch', 'GCCcore-9.3.0_gmp-c99.patch', + 'GCCcore-12.2.0_fix-avx512-misoptimization.patch', ] checksums = [ {'gcc-13.2.0.tar.gz': '8cb4be3796651976f94b9356fa08d833524f62420d6292c5033a9a26af315078'}, @@ -44,6 +45,8 @@ checksums = [ {'nvptx-tools-20230725.tar.gz': '17ce1f2c64f09c6f1cb709e3af869bb90b0102c412f25da55f338e35bc74b2e2'}, {'GCCcore-6.2.0-fix-find-isl.patch': '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68'}, {'GCCcore-9.3.0_gmp-c99.patch': '0e135e1cc7cec701beea9d7d17a61bab34cfd496b4b555930016b98db99f922e'}, + {'GCCcore-12.2.0_fix-avx512-misoptimization.patch': + 'bb3db707727b9975b0005346ef04230a96b3ad896f004a34262a82a244b5d436'}, ] builddependencies = [ From 87d9d702eb8a7e100fc4864d2d884ae8e1368145 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 6 Nov 2023 17:16:06 +0100 Subject: [PATCH 175/599] Disable bogus warning --- .../p/PyTorch/PyTorch-2.0.1-foss-2022b.eb | 2 ++ .../PyTorch-2.0.1_disable-gcc12-warning.patch | 32 +++++++++++++++++++ 2 files changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_disable-gcc12-warning.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1-foss-2022b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1-foss-2022b.eb index 318e4aacd4f..27e6fe2c084 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1-foss-2022b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1-foss-2022b.eb @@ -23,6 +23,7 @@ patches = [ 'PyTorch-1.13.1_skip-tests-without-fbgemm.patch', 'PyTorch-2.0.1_add-missing-vsx-vector-shift-functions.patch', 'PyTorch-2.0.1_avoid-test_quantization-failures.patch', + 'PyTorch-2.0.1_disable-gcc12-warning.patch', 'PyTorch-2.0.1_disable-test-sharding.patch', 'PyTorch-2.0.1_fix-numpy-compat.patch', 'PyTorch-2.0.1_fix-shift-ops.patch', @@ -66,6 +67,7 @@ checksums = [ 'da44961d6c204403ba0c4b88cedccf06a7a3d24f29c4398545f96efae7a45c95'}, {'PyTorch-2.0.1_avoid-test_quantization-failures.patch': '02e3f47e4ed1d7d6077e26f1ae50073dc2b20426269930b505f4aefe5d2f33cd'}, + {'PyTorch-2.0.1_disable-gcc12-warning.patch': 'f558dfc8f7cdcdc74c4c58ef7e8fe6d67870aec6386ac0d923f1b745d108eec7'}, {'PyTorch-2.0.1_disable-test-sharding.patch': 'a1ed7f21c9a269ea039a07a3d6574f885787b30ca5687143c96e096d31066cca'}, {'PyTorch-2.0.1_fix-numpy-compat.patch': 'f3e5798193e0909a415d824f13772973200965db84476c1737824f2735f2db94'}, {'PyTorch-2.0.1_fix-shift-ops.patch': '5ee655d5dba56d801d5618543b6ca299fa874939a3471f7b5449bfcb7f3f18c7'}, diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_disable-gcc12-warning.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_disable-gcc12-warning.patch new file mode 100644 index 00000000000..e3091daf27a --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_disable-gcc12-warning.patch @@ -0,0 +1,32 @@ +GCC 12 has a false positive warning when compiled for some architectures, e.g. Intel Sapphire Rapids. +See https://gcc.gnu.org/bugzilla/show_bug.cgi?id=112370 + +Suppress this warning such that the build doesn't error. + +Author: Alexander Grund (TU Dresden) + +diff --git a/CMakeLists.txt b/CMakeLists.txt +index 471fc8a8d3d..5eb7b432630 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -557,6 +557,7 @@ string(APPEND CMAKE_CUDA_FLAGS " -Xfatbin -compress-all") + if(NOT MSVC) + string(APPEND CMAKE_CUDA_FLAGS_DEBUG " -g -lineinfo --source-in-ptx") + string(APPEND CMAKE_CUDA_FLAGS_RELWITHDEBINFO " -g -lineinfo --source-in-ptx") ++ append_cxx_flag_if_supported("-Wno-free-nonheap-object" CMAKE_CXX_FLAGS) + endif(NOT MSVC) + + # Set INTERN_BUILD_MOBILE for all mobile builds. Components that are not +diff --git a/cmake/public/utils.cmake b/cmake/public/utils.cmake +index 60cca5383dd..76c02d7479f 100644 +--- a/cmake/public/utils.cmake ++++ b/cmake/public/utils.cmake +@@ -548,6 +548,8 @@ function(torch_update_find_cuda_flags) + endif() + endfunction() + ++include(CheckCXXCompilerFlag) ++ + ############################################################################## + # CHeck if given flag is supported and append it to provided outputvar + # Also define HAS_UPPER_CASE_FLAG_NAME variable From 82f7472a97eeb9986d6273da52b8dfd9b21f4533 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Thu, 9 Nov 2023 13:33:10 +0100 Subject: [PATCH 176/599] adding easyconfigs: SUPPA-2.3-20231005-foss-2022b.eb --- .../s/SUPPA/SUPPA-2.3-20231005-foss-2022b.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/s/SUPPA/SUPPA-2.3-20231005-foss-2022b.eb diff --git a/easybuild/easyconfigs/s/SUPPA/SUPPA-2.3-20231005-foss-2022b.eb b/easybuild/easyconfigs/s/SUPPA/SUPPA-2.3-20231005-foss-2022b.eb new file mode 100644 index 00000000000..20cf5f81693 --- /dev/null +++ b/easybuild/easyconfigs/s/SUPPA/SUPPA-2.3-20231005-foss-2022b.eb @@ -0,0 +1,37 @@ +easyblock = 'Tarball' + +name = 'SUPPA' +version = '2.3-20231005' +local_commit = 'a5d5e89' + +homepage = 'https://github.com/comprna/SUPPA' +description = """Fast, accurate, and uncertainty-aware differential + splicing analysis across multiple conditions.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +github_account = 'comprna' +source_urls = [GITHUB_SOURCE] +sources = ['%s.tar.gz' % local_commit] +checksums = ['5e55911be2727c7abc7a4e3b6179f2f7cb0e3126bb443bce102fa7af97249e5d'] + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('statsmodels', '0.14.0'), + ('scikit-learn', '1.2.1'), +] + +modextrapaths = { + 'PATH': '', + 'PYTHONPATH': '', +} + +sanity_check_paths = { + 'files': ['suppa.py'], + 'dirs': [], +} + +sanity_check_commands = ['python suppa.py --help'] + +moduleclass = 'bio' From 2a7db4afd5649985dc6a39ab411bd79838c94c3d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Thu, 9 Nov 2023 13:59:11 +0100 Subject: [PATCH 177/599] add link to bin directory --- .../easyconfigs/s/SUPPA/SUPPA-2.3-20231005-foss-2022b.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SUPPA/SUPPA-2.3-20231005-foss-2022b.eb b/easybuild/easyconfigs/s/SUPPA/SUPPA-2.3-20231005-foss-2022b.eb index 20cf5f81693..f9a247220fd 100644 --- a/easybuild/easyconfigs/s/SUPPA/SUPPA-2.3-20231005-foss-2022b.eb +++ b/easybuild/easyconfigs/s/SUPPA/SUPPA-2.3-20231005-foss-2022b.eb @@ -22,6 +22,10 @@ dependencies = [ ('scikit-learn', '1.2.1'), ] +postinstallcmds = ['cd %(installdir)s && mkdir bin && ln -s suppa.py bin/suppa.py && chmod a+x suppa.py'] + +fix_python_shebang_for = ['suppa.py'] + modextrapaths = { 'PATH': '', 'PYTHONPATH': '', @@ -32,6 +36,6 @@ sanity_check_paths = { 'dirs': [], } -sanity_check_commands = ['python suppa.py --help'] +sanity_check_commands = ['suppa.py --help'] moduleclass = 'bio' From b0ecd1e94c618bf426decb8a109686ef427827a7 Mon Sep 17 00:00:00 2001 From: Viktor Rehnberg Date: Thu, 9 Nov 2023 16:03:38 +0100 Subject: [PATCH 178/599] adding easyconfigs: RFdiffusion-1.1.0-foss-2022a-CUDA-11.7.0.eb, e3nn-0.3.3-foss-2022a-CUDA-11.7.0.eb --- .../e3nn/e3nn-0.3.3-foss-2022a-CUDA-11.7.0.eb | 39 +++++++++++++ ...Fdiffusion-1.1.0-foss-2022a-CUDA-11.7.0.eb | 58 +++++++++++++++++++ 2 files changed, 97 insertions(+) create mode 100644 easybuild/easyconfigs/e/e3nn/e3nn-0.3.3-foss-2022a-CUDA-11.7.0.eb create mode 100644 easybuild/easyconfigs/r/RFdiffusion/RFdiffusion-1.1.0-foss-2022a-CUDA-11.7.0.eb diff --git a/easybuild/easyconfigs/e/e3nn/e3nn-0.3.3-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/e/e3nn/e3nn-0.3.3-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 00000000000..0dd9d35d940 --- /dev/null +++ b/easybuild/easyconfigs/e/e3nn/e3nn-0.3.3-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,39 @@ +easyblock = 'PythonBundle' + +name = 'e3nn' +version = '0.3.3' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://e3nn.org/' +description = """ +Euclidean neural networks (e3nn) is a python library based on pytorch to create equivariant +neural networks for the group O(3). +""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('PyTorch', '1.12.0', versionsuffix), + ('sympy', '1.10.1'), +] + +use_pip = True + +exts_list = [ + ('opt_einsum', '3.3.0', { + 'checksums': ['59f6475f77bbc37dcf7cd748519c0ec60722e91e63ca114e68821c0c54a46549'], + }), + ('opt_einsum_fx', '0.1.4', { + 'checksums': ['7eeb7f91ecb70be65e6179c106ea7f64fc1db6319e3d1289a4518b384f81e74f'], + }), + (name, version, { + 'checksums': ['532b34a5644153659253c59943fe4224cd9c3c46ce8a79f1dc7c00afccb44ecb'], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/RFdiffusion/RFdiffusion-1.1.0-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/r/RFdiffusion/RFdiffusion-1.1.0-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 00000000000..8ca5151696c --- /dev/null +++ b/easybuild/easyconfigs/r/RFdiffusion/RFdiffusion-1.1.0-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,58 @@ +easyblock = 'PythonBundle' + +name = 'RFdiffusion' +version = '1.1.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/RosettaCommons/RFdiffusion' +description = """ +RFdiffusion is an open source method for structure generation, with or without conditional information +(a motif, target etc). It can perform a whole range of protein design challenges as we have outlined +in the RFdiffusion paper. +""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('e3nn', '0.3.3', versionsuffix), + ('wandb', '0.13.4'), +] + +use_pip = True + +exts_list = [ + ('pynvml', '11.0.0', { + 'checksums': ['d5fc4a22d355b40c341d6ba0aa888a2d4d2253177d243900f8401b7e6cacb1bb'], + }), + ('dllogger', '1.0.0', { + 'source_urls': ['https://github.com/NVIDIA/dllogger/archive/refs/tags'], + 'sources': ['v%(version)s.zip'], + 'checksums': ['07d0cd9b9b56f454f0c186a0889137e9f94e1979fca3d35911967c874c93c191'], + }), + ('decorator', '5.1.1', { + 'checksums': ['637996211036b6385ef91435e4fae22989472f9d571faba8927ba8253acbc330'], + }), + ('se3-transformer', version, { + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/RosettaCommons/RFdiffusion/archive/refs/tags'], + 'start_dir': 'env/SE3Transformer', + 'checksums': ['57d82f0d43540c2912eda3f1d34ad90b13db14966ee069c427e217fe78f0297f'], + }), + (name, version, { + 'patches': ['%(name)s-%(version)s_fix-find-packages.patch'], + 'source_urls': ['https://github.com/RosettaCommons/RFdiffusion/archive/refs/tags'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': [ + {'v1.1.0.tar.gz': '57d82f0d43540c2912eda3f1d34ad90b13db14966ee069c427e217fe78f0297f'}, + {'RFdiffusion-1.1.0_fix-find-packages.patch': + 'e25da7f476acacb6af58bd84f40aca712538900b0b48532b22f9a133d6886da2'}, + ], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' From 9f188946ad29079e97215966e1d9814d10ba74d7 Mon Sep 17 00:00:00 2001 From: Viktor Rehnberg Date: Thu, 9 Nov 2023 16:59:26 +0100 Subject: [PATCH 179/599] Fix source being overwritten --- .../RFdiffusion-1.1.0-foss-2022a-CUDA-11.7.0.eb | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/r/RFdiffusion/RFdiffusion-1.1.0-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/r/RFdiffusion/RFdiffusion-1.1.0-foss-2022a-CUDA-11.7.0.eb index 8ca5151696c..9ebc11b3bd2 100644 --- a/easybuild/easyconfigs/r/RFdiffusion/RFdiffusion-1.1.0-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/r/RFdiffusion/RFdiffusion-1.1.0-foss-2022a-CUDA-11.7.0.eb @@ -43,10 +43,13 @@ exts_list = [ }), (name, version, { 'patches': ['%(name)s-%(version)s_fix-find-packages.patch'], - 'source_urls': ['https://github.com/RosettaCommons/RFdiffusion/archive/refs/tags'], - 'sources': ['v%(version)s.tar.gz'], + 'sources': { + 'filename': '%(name)s-%(version)s.tar.gz', + 'download_filename': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/RosettaCommons/RFdiffusion/archive/refs/tags'], + }, 'checksums': [ - {'v1.1.0.tar.gz': '57d82f0d43540c2912eda3f1d34ad90b13db14966ee069c427e217fe78f0297f'}, + {'RFdiffusion-1.1.0.tar.gz': '57d82f0d43540c2912eda3f1d34ad90b13db14966ee069c427e217fe78f0297f'}, {'RFdiffusion-1.1.0_fix-find-packages.patch': 'e25da7f476acacb6af58bd84f40aca712538900b0b48532b22f9a133d6886da2'}, ], From d26176e20afeadd1b30e7a6b53f4c7e0c8249bcb Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 10 Nov 2023 09:18:26 +0100 Subject: [PATCH 180/599] add pkgconf build dependency to libGLU --- .../easyconfigs/l/libGLU/libGLU-9.0.3-GCCcore-12.3.0.eb | 9 ++++++--- .../easyconfigs/l/libGLU/libGLU-9.0.3-GCCcore-13.2.0.eb | 9 ++++++--- 2 files changed, 12 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/l/libGLU/libGLU-9.0.3-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.3-GCCcore-12.3.0.eb index c636b6c6a9d..326dfd2626e 100644 --- a/easybuild/easyconfigs/l/libGLU/libGLU-9.0.3-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.3-GCCcore-12.3.0.eb @@ -13,9 +13,12 @@ source_urls = ['https://mesa.freedesktop.org/archive/glu/'] sources = ['glu-%(version)s.tar.xz'] checksums = ['bd43fe12f374b1192eb15fe20e45ff456b9bc26ab57f0eee919f96ca0f8a330f'] -builddependencies = [('binutils', '2.40'), - ('Ninja', '1.11.1'), - ('Meson', '1.1.1')] +builddependencies = [ + ('pkgconf', '1.9.5'), + ('binutils', '2.40'), + ('Ninja', '1.11.1'), + ('Meson', '1.1.1'), +] dependencies = [('Mesa', '23.1.4')] diff --git a/easybuild/easyconfigs/l/libGLU/libGLU-9.0.3-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.3-GCCcore-13.2.0.eb index 6de3d5baea2..b2c0581c7f6 100644 --- a/easybuild/easyconfigs/l/libGLU/libGLU-9.0.3-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.3-GCCcore-13.2.0.eb @@ -13,9 +13,12 @@ source_urls = ['https://mesa.freedesktop.org/archive/glu/'] sources = ['glu-%(version)s.tar.xz'] checksums = ['bd43fe12f374b1192eb15fe20e45ff456b9bc26ab57f0eee919f96ca0f8a330f'] -builddependencies = [('binutils', '2.40'), - ('Ninja', '1.11.1'), - ('Meson', '1.2.3')] +builddependencies = [ + ('pkgconf', '2.0.3'), + ('binutils', '2.40'), + ('Ninja', '1.11.1'), + ('Meson', '1.2.3'), +] dependencies = [('Mesa', '23.1.9')] From e6a32a5b9ae3358d8cd9aa2969261f8f8f91d5c5 Mon Sep 17 00:00:00 2001 From: Xin An <34663977+xinan1911@users.noreply.github.com> Date: Fri, 10 Nov 2023 11:39:08 +0100 Subject: [PATCH 181/599] Remove CMake installation path as easyblock takes care of it already --- easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb b/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb index 11881bde0f5..b033fcf10d9 100644 --- a/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb +++ b/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb @@ -35,7 +35,6 @@ configopts = "-DWALBERLA_BUILD_WITH_PYTHON=ON " configopts += "-DWALBERLA_BUILD_SHOWCASES=OFF " configopts += "-DWALBERLA_BUILD_DOC=OFF " configopts += "-DPython_ROOT_DIR=$EBROOTPYTHON " -configopts += "-DCMAKE_INSTALL_PREFIX=%(installdir)s " modextrapaths = {'PYTHONPATH': ['pythonmodule']} From 913276533aaaca0e45908829201b7601a4b56ecc Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Fri, 10 Nov 2023 14:45:22 +0100 Subject: [PATCH 182/599] updating ScaFaCoS is not enough to build LAMMPS on ARM --- .../l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos.eb | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos.eb index 1abcc202d59..ff105a29ce8 100644 --- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos.eb +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos.eb @@ -44,14 +44,17 @@ dependencies = [ ('kim-api', '2.3.0'), ('Eigen', '3.4.0'), ('PLUMED', '2.7.3'), - ('ScaFaCoS', '1.0.4'), ('SciPy-bundle', '2021.10'), # VTK package is auto-disabled if this dep is not available ('VTK', '9.1.0'), ] if ARCH == 'x86_64': - # TBB is an optional dependency when building on Intel arch - dependencies += [('tbb', '2020.3'), ] + # TBB and ScaFaCoSis an optional dependency when building on Intel arch + dependencies += [ + ('tbb', '2020.3'), + ('ScaFaCoS', '1.0.1'), + ] + # To use additional custom configuration options, use the 'configopts' easyconfig parameter # See docs and lammps easyblock for more information. From e84f046018fc118db2ec5e0dc100deb8cdee6534 Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Fri, 10 Nov 2023 15:39:22 +0100 Subject: [PATCH 183/599] Fix style errors --- .../easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos.eb index ff105a29ce8..e6f9a7d1940 100644 --- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos.eb +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos.eb @@ -52,9 +52,8 @@ if ARCH == 'x86_64': # TBB and ScaFaCoSis an optional dependency when building on Intel arch dependencies += [ ('tbb', '2020.3'), - ('ScaFaCoS', '1.0.1'), + ('ScaFaCoS', '1.0.1'), ] - # To use additional custom configuration options, use the 'configopts' easyconfig parameter # See docs and lammps easyblock for more information. From f89312a1dd5f8b831019fe544aa9ca691fcfefb7 Mon Sep 17 00:00:00 2001 From: Alan O'Cais Date: Fri, 10 Nov 2023 16:34:40 +0100 Subject: [PATCH 184/599] Sidestep some build issues with CUDA-Samples 12.1 --- .../CUDA-Samples-12.1-GCC-12.3.0-CUDA-12.1.1.eb | 13 ++++++++++++- 1 file changed, 12 insertions(+), 1 deletion(-) 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 438e0f44965..202d408d9dd 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 @@ -28,7 +28,9 @@ local_filters += "Samples/3_CUDA_Features/warpAggregatedAtomicsCG/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/4_CUDA_Libraries/freeImageInteropNPP/Makefile " +local_filters += "Samples/4_CUDA_Libraries/histEqualizationNPP/Makefile " +local_filters += "Samples/4_CUDA_Libraries/FilterBorderControlNPP/Makefile " local_filters += "Samples/5_Domain_Specific/simpleGL/Makefile " local_filters += "Samples/5_Domain_Specific/simpleVulkan/Makefile " local_filters += "Samples/5_Domain_Specific/simpleVulkanMMAP/Makefile " @@ -40,8 +42,17 @@ local_filters += "Samples/3_CUDA_Features/bf16TensorCoreGemm/Makefile " local_filters += "Samples/3_CUDA_Features/dmmaTensorCoreGemm/Makefile " local_filters += "Samples/3_CUDA_Features/globalToShmemAsyncCopy/Makefile " +# This give a link error under EESSI (ignoring for now) +local_filters += "Samples/4_CUDA_Libraries/simpleCUFFT_callback/Makefile " + +# Builds a shared lib that it sticks in `bin`! +local_filters += "Samples/2_Concepts_and_Techniques/cuHook/Makefile " + buildopts = "HOST_COMPILER=g++ FILTER_OUT='%s'" % local_filters +# Remove libraries in the bin dir after a successful 'make' +buildopts += " && rm bin/*/linux/release/lib*.so.*" + files_to_copy = [ (['bin/%s/linux/release/*' % ARCH], 'bin'), 'LICENSE', From e1db708cfb7aa0a14c6eba551b30d8f6a9f7daa5 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Fri, 10 Nov 2023 16:41:06 +0100 Subject: [PATCH 185/599] Update CUDA-Samples-12.1-GCC-12.3.0-CUDA-12.1.1.eb --- .../c/CUDA-Samples/CUDA-Samples-12.1-GCC-12.3.0-CUDA-12.1.1.eb | 1 + 1 file changed, 1 insertion(+) 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 202d408d9dd..c5c6afe7534 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 @@ -28,6 +28,7 @@ local_filters += "Samples/3_CUDA_Features/warpAggregatedAtomicsCG/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/4_CUDA_Libraries/freeImageInteropNPP/Makefile " local_filters += "Samples/4_CUDA_Libraries/histEqualizationNPP/Makefile " local_filters += "Samples/4_CUDA_Libraries/FilterBorderControlNPP/Makefile " From c3a677e18e113ce0e9e66ea30940f06d9f672057 Mon Sep 17 00:00:00 2001 From: sassy Date: Sat, 11 Nov 2023 00:37:48 +0000 Subject: [PATCH 186/599] adding easyconfigs: mctc-lib-0.3.1-GCCcore-12.2.0.eb, mctc-lib-0.3.1-intel-compilers-2022.2.1.eb --- .../mctc-lib/mctc-lib-0.3.1-GCCcore-12.2.0.eb | 42 +++++++++++++++++++ ...mctc-lib-0.3.1-intel-compilers-2022.2.1.eb | 42 +++++++++++++++++++ 2 files changed, 84 insertions(+) create mode 100644 easybuild/easyconfigs/m/mctc-lib/mctc-lib-0.3.1-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/m/mctc-lib/mctc-lib-0.3.1-intel-compilers-2022.2.1.eb diff --git a/easybuild/easyconfigs/m/mctc-lib/mctc-lib-0.3.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/m/mctc-lib/mctc-lib-0.3.1-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..9cb015c7bfa --- /dev/null +++ b/easybuild/easyconfigs/m/mctc-lib/mctc-lib-0.3.1-GCCcore-12.2.0.eb @@ -0,0 +1,42 @@ +easyblock = 'CMakeMake' + +name = 'mctc-lib' +version = '0.3.1' + +homepage = 'https://grimme-lab.github.io/mctc-lib' +description = """Common tool chain for working with molecular structure data in various +applications. This library provides a unified way to perform operations on +molecular structure data, like reading and writing to common geometry file +formats.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +github_account = 'grimme-lab' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['03dc8ccba37413da70e55a07cef8e8de53bce33f5bb52c1f8db5fec326abe083'] + +builddependencies = [ + ('binutils', '2.39'), + ('CMake', '3.24.3'), +] + +dependencies = [ + ('json-fortran', '8.3.0'), +] + +configopts = ['-DBUILD_SHARED_LIBS=ON', '-DBUILD_SHARED_LIBS=OFF'] + +sanity_check_paths = { + 'files': ['bin/mctc-convert', 'lib/libmctc-lib.%s' % SHLIB_EXT], + 'dirs': ['include/%(name)s', 'lib/cmake', 'lib/pkgconfig'], +} + +sanity_check_commands = ["mctc-convert --help"] + +# run suite of tests with ctest +test_cmd = 'ctest' +runtest = '' + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/m/mctc-lib/mctc-lib-0.3.1-intel-compilers-2022.2.1.eb b/easybuild/easyconfigs/m/mctc-lib/mctc-lib-0.3.1-intel-compilers-2022.2.1.eb new file mode 100644 index 00000000000..3f875046212 --- /dev/null +++ b/easybuild/easyconfigs/m/mctc-lib/mctc-lib-0.3.1-intel-compilers-2022.2.1.eb @@ -0,0 +1,42 @@ +easyblock = 'CMakeMake' + +name = 'mctc-lib' +version = '0.3.1' + +homepage = 'https://grimme-lab.github.io/mctc-lib' +description = """Common tool chain for working with molecular structure data in various +applications. This library provides a unified way to perform operations on +molecular structure data, like reading and writing to common geometry file +formats.""" + +toolchain = {'name': 'intel-compilers', 'version': '2022.2.1'} +toolchainopts = {'pic': True} + +github_account = 'grimme-lab' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['03dc8ccba37413da70e55a07cef8e8de53bce33f5bb52c1f8db5fec326abe083'] + +builddependencies = [ + ('binutils', '2.39'), + ('CMake', '3.24.3'), +] + +dependencies = [ + ('json-fortran', '8.3.0'), +] + +configopts = ['-DBUILD_SHARED_LIBS=ON', '-DBUILD_SHARED_LIBS=OFF'] + +sanity_check_paths = { + 'files': ['bin/mctc-convert', 'lib/libmctc-lib.%s' % SHLIB_EXT], + 'dirs': ['include/%(name)s', 'lib/cmake', 'lib/pkgconfig'], +} + +sanity_check_commands = ["mctc-convert --help"] + +# run suite of tests with ctest +test_cmd = 'ctest' +runtest = '' + +moduleclass = 'chem' From 39304f2d6e52b96566a00255d2ac51f163c13029 Mon Sep 17 00:00:00 2001 From: sassy Date: Sat, 11 Nov 2023 00:54:03 +0000 Subject: [PATCH 187/599] adding easyconfigs: json-fortran-8.3.0-GCCcore-12.2.0.eb --- .../json-fortran-8.3.0-GCCcore-12.2.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/j/json-fortran/json-fortran-8.3.0-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/j/json-fortran/json-fortran-8.3.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/j/json-fortran/json-fortran-8.3.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..e409adb3f77 --- /dev/null +++ b/easybuild/easyconfigs/j/json-fortran/json-fortran-8.3.0-GCCcore-12.2.0.eb @@ -0,0 +1,31 @@ +# J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'CMakeMake' + +name = 'json-fortran' +version = '8.3.0' + +homepage = 'https://github.com/jacobwilliams/json-fortran' +description = "JSON-Fortran: A Modern Fortran JSON API" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/jacobwilliams/json-fortran/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['5fe9ad709a726416cec986886503e0526419742e288c4e43f63c1c22026d1e8a'] + +builddependencies = [ + ('binutils', '2.39'), + ('CMake', '3.24.3'), +] + +configopts = '-DUSE_GNU_INSTALL_CONVENTION=TRUE' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libjsonfortran.a', 'lib/libjsonfortran.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'lib' From d39f2f5a10bf614521025dac296efc5c44fe668e Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Sat, 11 Nov 2023 14:58:28 +0800 Subject: [PATCH 188/599] adding easyconfigs: 4ti2-1.6.9-GCC-11.3.0.eb --- .../0/4ti2/4ti2-1.6.9-GCC-11.3.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/0/4ti2/4ti2-1.6.9-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/0/4ti2/4ti2-1.6.9-GCC-11.3.0.eb b/easybuild/easyconfigs/0/4ti2/4ti2-1.6.9-GCC-11.3.0.eb new file mode 100644 index 00000000000..1fd0b976427 --- /dev/null +++ b/easybuild/easyconfigs/0/4ti2/4ti2-1.6.9-GCC-11.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = '4ti2' +version = '1.6.9' + +homepage = 'https://4ti2.github.io/' +description = """A software package for algebraic, geometric and combinatorial problems on linear spaces""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +github_account = '4ti2' +source_urls = [GITHUB_SOURCE] +sources = ['Release_%s.tar.gz' % '_'.join(version.split('.'))] +checksums = ['7b1015718102d8cd4dc2de64f69094fdba0bc69a1878ada5960979b171ff89e4'] + +dependencies = [ + ('GMP', '6.2.1'), + ('GLPK', '5.0'), +] + +builddependencies = [('Autotools', '20220317')] + +preconfigopts = './autogen.sh && ' + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['4ti2gmp', '4ti2int32', '4ti2int64']], + 'dirs': ['include/4ti2', 'lib', 'share/4ti2'] +} + +moduleclass = 'math' From 9317fe94ea09b9b6c8c79071d054e33fd9063fc9 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Sat, 11 Nov 2023 15:16:57 +0800 Subject: [PATCH 189/599] adding easyconfigs: cddlib-0.94m-GCCcore-11.3.0.eb --- .../c/cddlib/cddlib-0.94m-GCCcore-11.3.0.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/c/cddlib/cddlib-0.94m-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/c/cddlib/cddlib-0.94m-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/cddlib/cddlib-0.94m-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..d5ef7861ad7 --- /dev/null +++ b/easybuild/easyconfigs/c/cddlib/cddlib-0.94m-GCCcore-11.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'cddlib' +version = '0.94m' + +homepage = 'https://github.com/cddlib/cddlib' +description = "An efficient implementation of the Double Description Method" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +github_account = 'cddlib' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['766d8ec2135989830748e5e2fe57f307ed0706431c135541c3c081cbec0bc34f'] + +builddependencies = [ + ('Autotools', '20220317'), + ('binutils', '2.38'), +] + +dependencies = [('GMP', '6.2.1')] + +preconfigopts = "autoreconf -f -i && " + +buildopts = "SUBDIRS='lib-src src'" # build sources but spare the documentation in latex +installopts = buildopts + +local_exes = ['adjacency', 'allfaces', 'cddexec', 'fourier', 'lcdd', 'projection', 'redcheck', 'scdd', 'testcdd1', + 'testcdd2', 'testlp1', 'testlp2', 'testlp3', 'testshoot'] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_exes] + ['bin/%s_gmp' % x for x in local_exes] + + ['lib/%s.%s' % (l, e) for l in ['libcdd', 'libcddgmp'] for e in ['a', SHLIB_EXT]] + + ['include/cddlib/%s.h' % h for h in ['cdd', 'cddmp', 'cddtypes', 'setoper', 'splitmix64']], + 'dirs': ['share/doc'] +} + +moduleclass = 'math' From e0bb3a39382a7477b9a2c20dabf18b3c29b732b3 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Sat, 11 Nov 2023 15:38:24 +0800 Subject: [PATCH 190/599] adding easyconfigs: CoCoALib-0.99818-GCC-11.3.0.eb --- .../c/CoCoALib/CoCoALib-0.99818-GCC-11.3.0.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/c/CoCoALib/CoCoALib-0.99818-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/c/CoCoALib/CoCoALib-0.99818-GCC-11.3.0.eb b/easybuild/easyconfigs/c/CoCoALib/CoCoALib-0.99818-GCC-11.3.0.eb new file mode 100644 index 00000000000..845ea2a2ccc --- /dev/null +++ b/easybuild/easyconfigs/c/CoCoALib/CoCoALib-0.99818-GCC-11.3.0.eb @@ -0,0 +1,42 @@ +easyblock = 'ConfigureMake' + +name = 'CoCoALib' +version = '0.99818' + +homepage = 'https://cocoa.dima.unige.it/cocoa/cocoalib/' +description = "CoCoALib is a free GPL3 C++ library for doing Computations in Commutative Algebra." + +toolchain = {'name': 'GCC', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://cocoa.dima.unige.it/cocoa/cocoalib/tgz'] +sources = [SOURCE_TGZ] +checksums = ['7c7d6bb0bc3004ea76caaeb5f8de10ed09c8052a9131fd98716c36c6fc96d1ea'] + +dependencies = [ + ('GMP', '6.2.1'), + ('cddlib', '0.94m'), # optional +] + +# libreadline only needed for CoCoA-5 +configopts = "--only-cocoalib --no-readline --threadsafe-hack " +# Use cddlib and GMP from EB +configopts += "--with-libcddgmp=${EBROOTCDDLIB}/lib/libcddgmp.a --with-libgmp=$EBROOTGMP/lib/libgmp.a " + +buildopts = 'CXX="$CXX" CXXFLAGS="$CXXFLAGS"' + +# Makefile is not smart enough to create missing directories +preinstallopts = "mkdir %(installdir)s/{include,lib} && " + +# Move doc and examples from include to share +postinstallcmds = [ + "mkdir %(installdir)s/share", + "mv %(installdir)s/include/CoCoA-%(version)s/{doc,examples} %(installdir)s/share/", +] + +sanity_check_paths = { + 'files': ['lib/libcocoa.a'], + 'dirs': ['include/CoCoA-%(version)s', 'share/doc', 'share/examples'] +} + +moduleclass = 'math' From c7d1e9e0deb3ea4f75098d5acea9f06ad6105621 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Sat, 11 Nov 2023 15:46:44 +0800 Subject: [PATCH 191/599] adding easyconfigs: Givaro-4.2.0-GCCcore-11.3.0.eb --- .../g/Givaro/Givaro-4.2.0-GCCcore-11.3.0.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/g/Givaro/Givaro-4.2.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/g/Givaro/Givaro-4.2.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/Givaro/Givaro-4.2.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..fc41e542efe --- /dev/null +++ b/easybuild/easyconfigs/g/Givaro/Givaro-4.2.0-GCCcore-11.3.0.eb @@ -0,0 +1,41 @@ +## +# This file is an EasyBuild recipe; see https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright (c) 2016 Riccardo Murri +# Authors:: Riccardo Murri +# License:: GPL +# +## + +easyblock = 'ConfigureMake' + +name = 'Givaro' +version = '4.2.0' + +homepage = 'https://github.com/linbox-team/givaro' +description = "C++ library for arithmetic and algebraic computations" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/linbox-team/givaro/archive'] +sources = ['v%(version)s.zip'] +checksums = ['bf51b47ac9a02be233fc39ac78d959d13630bcc78997007ffec410d940ed4c64'] + +builddependencies = [ + ('Autotools', '20220317'), + ('binutils', '2.38'), +] + +dependencies = [ + ('GMP', '6.2.1'), +] + +preconfigopts = "env NOCONFIGURE=1 ./autogen.sh && " +configopts = "--with-gmp=$EBROOTGMP --enable-inline" + +sanity_check_paths = { + 'files': ['bin/givaro-config', 'include/givaro-config.h'], + 'dirs': ['bin', 'include', 'lib'], +} + +moduleclass = 'math' From 99cc1d9d875428d78efbe15c43361581ba071088 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Sat, 11 Nov 2023 15:57:05 +0800 Subject: [PATCH 192/599] adding easyconfigs: lrslib-7.2-gompi-2022a.eb and patches: lrslib-7.2-use-EB-values.patch --- .../l/lrslib/lrslib-7.2-gompi-2022a.eb | 39 ++++ .../l/lrslib/lrslib-7.2-use-EB-values.patch | 183 ++++++++++++++++++ 2 files changed, 222 insertions(+) create mode 100644 easybuild/easyconfigs/l/lrslib/lrslib-7.2-gompi-2022a.eb create mode 100644 easybuild/easyconfigs/l/lrslib/lrslib-7.2-use-EB-values.patch diff --git a/easybuild/easyconfigs/l/lrslib/lrslib-7.2-gompi-2022a.eb b/easybuild/easyconfigs/l/lrslib/lrslib-7.2-gompi-2022a.eb new file mode 100644 index 00000000000..17ae62bb0c4 --- /dev/null +++ b/easybuild/easyconfigs/l/lrslib/lrslib-7.2-gompi-2022a.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'lrslib' +version = '7.2' + +homepage = 'http://cgm.cs.mcgill.ca/~avis/C/lrs.html' +description = """lrslib is a self-contained ANSI C implementation of the +reverse search algorithm for vertex enumeration/convex hull problems""" + +toolchain = {'name': 'gompi', 'version': '2022a'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = ['http://cgm.cs.mcgill.ca/~avis/C/lrslib/archive/'] +sources = ['lrslib-0%(version_major)s%(version_minor)s.tar.gz'] +patches = ['lrslib-%(version)s-use-EB-values.patch'] +checksums = [ + {'lrslib-072.tar.gz': 'fc48754a1ded1d8445d40ecfbe3546e4f27d53aaee95dc2c8c0c79fb9cd532f0'}, + {'lrslib-7.2-use-EB-values.patch': '16b0b4d987a751a45c7961bb7e0cb12aac50410a562dab3299335186456ab2ad'}, +] + +dependencies = [ + ('GMP', '6.2.1'), +] + +skipsteps = ['configure'] + +# Default built plus mplrs +buildopts = 'lrs lrsgmp mplrs CFLAGS="$CFLAGS"' + +installopts = 'prefix=%(installdir)s' + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['lrs', 'lrsnash']] + + ['include/lrslib/lrs%s.h' % h for h in ['driver', 'gmp', 'lib', 'long', 'mp', 'restart']] + + ['lib/liblrs.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/l/lrslib/lrslib-7.2-use-EB-values.patch b/easybuild/easyconfigs/l/lrslib/lrslib-7.2-use-EB-values.patch new file mode 100644 index 00000000000..c84ecf21b05 --- /dev/null +++ b/easybuild/easyconfigs/l/lrslib/lrslib-7.2-use-EB-values.patch @@ -0,0 +1,183 @@ +# Fix makefile to use EB environment +# Ward Poelmans, Alex Domingo (Vrije Universiteit Brussel) +# updated to version 7.2 by Miguel Dias Costa (National University of Singapore) +--- lrslib-072/makefile.orig 2023-11-06 13:50:57.098070000 +0800 ++++ lrslib-072/makefile 2023-11-06 13:58:17.056703000 +0800 +@@ -30,8 +30,8 @@ + #LIBDIR = /usr/lib + + #Kyoto machines usage +-INCLUDEDIR = /usr/local/include +-LIBDIR = /usr/local/lib ++#INCLUDEDIR = /usr/local/include ++#LIBDIR = /usr/local/lib + + CFLAGS ?= -O3 -Wall + #CFLAGS = -g -Wall +@@ -61,7 +61,7 @@ + MPLRSOBJ64=lrslong1-mplrs.o lrslib1-mplrs.o lrslibgmp-mplrs.o lrsgmp-mplrs.o lrsdriver-mplrs.o mplrs64.o + + lrs: ${LRSOBJ} +- $(CC) ${CFLAGS} -DMA ${BITS} -L${LIBDIR} -o lrs ${LRSOBJ} -lgmp ++ $(CC) ${CFLAGS} -DMA ${BITS} $(LDFLAGS) -o lrs ${LRSOBJ} -lgmp + $(CC) -O3 hvref.c -o hvref + ln -s -f lrs redund + +@@ -71,7 +71,7 @@ + ln -s -f lrs redund + + lrs64: ${LRSOBJ64} +- $(CC) ${CFLAGS} -DMA -L${LIBDIR} -o lrs ${LRSOBJ64} -lgmp ++ $(CC) ${CFLAGS} -DMA $(LDFLAGS) -o lrs ${LRSOBJ64} -lgmp + + lrs.o: lrs.c + $(CC) ${CFLAGS} -DMA ${BITS} -c -o lrs.o lrs.c +@@ -92,22 +92,22 @@ + $(CC) ${CFLAGS} -DMA -DSAFE ${BITS} -DLRSLONG -c -o lrslib2.o lrslib.c + + lrslibgmp.o: lrslib.c lrslib.h +- $(CC) ${CFLAGS} -DMA -DGMP -I${INCLUDEDIR} -c -o lrslibgmp.o lrslib.c ++ $(CC) ${CFLAGS} -DMA -DGMP $(CPPFLAGS) -c -o lrslibgmp.o lrslib.c + + lrslibmp.o: lrslib.c lrslib.h + $(CC) ${CFLAGS} -DMA -DMP -c -o lrslibmp.o lrslib.c + + lrsgmp.o: lrsgmp.c lrsgmp.h +- $(CC) ${CFLAGS} -DMA -DGMP -I${INCLUDEDIR} -c -o lrsgmp.o lrsgmp.c ++ $(CC) ${CFLAGS} -DMA -DGMP $(CPPFLAGS) -c -o lrsgmp.o lrsgmp.c + + lrsmp.o: lrsmp.c lrsmp.h + $(CC) ${CFLAGS} -DMA -DMP -c -o lrsmp.o lrsmp.c + + inedel: inedel.c lrsgmp.h lrsgmp.c +- $(CC) ${CFLAGS} -I${INCLUDEDIR} -L${LIBDIR} -DGMP -o inedel inedel.c lrsgmp.c -lgmp ++ $(CC) ${CFLAGS} $(CPPFLAGS) $(LDFLAGS) -DGMP -o inedel inedel.c lrsgmp.c -lgmp + + checkpred: checkpred.c lrsgmp.h lrsgmp.c +- $(CC) $(CFLAGS) -I${INCLUDEDIR} -L${LIBDIR} -DGMP -o checkpred checkpred.c lrsgmp.c -lgmp ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -DGMP -o checkpred checkpred.c lrsgmp.c -lgmp + + lrslong1-mplrs.o: lrslong.c lrslong.h + $(mpicxx) ${CFLAGS} -DTIMES -DSIGNALS -DMA -DSAFE -DLRSLONG -DPLRS -c -o lrslong1-mplrs.o lrslong.c +@@ -122,28 +122,28 @@ + $(mpicxx) ${CFLAGS} -DTIMES -DSIGNALS -DMA -DSAFE ${BITS} -DLRSLONG -DPLRS -c -o lrslib2-mplrs.o lrslib.c + + lrslibgmp-mplrs.o: lrslib.c lrslib.h +- $(mpicxx) ${CFLAGS} -DMA -DTIMES -DSIGNALS -DGMP -DPLRS -I${INCLUDEDIR} -c -o lrslibgmp-mplrs.o lrslib.c ++ $(mpicxx) ${CFLAGS} -DMA -DTIMES -DSIGNALS -DGMP -DPLRS $(CPPFLAGS) -c -o lrslibgmp-mplrs.o lrslib.c + + lrsgmp-mplrs.o: lrsgmp.c lrsgmp.h +- $(mpicxx) ${CFLAGS} -DMA -DTIMES -DSIGNALS -DGMP -DPLRS -I${INCLUDEDIR} -c -o lrsgmp-mplrs.o lrsgmp.c ++ $(mpicxx) ${CFLAGS} -DMA -DTIMES -DSIGNALS -DGMP -DPLRS $(CPPFLAGS) -c -o lrsgmp-mplrs.o lrsgmp.c + + lrsdriver-mplrs.o: lrsdriver.c lrsdriver.h lrslib.h + $(mpicxx) $(CFLAGS) -c -o lrsdriver-mplrs.o lrsdriver.c + + mplrs.o: mplrs.c mplrs.h lrslib.h lrsgmp.h +- $(mpicxx) ${CFLAGS} -I${INCLUDEDIR} -DMA -DPLRS -DTIMES ${BITS} -DSIGNALS -D_WITH_GETLINE -c -o mplrs.o mplrs.c ++ $(mpicxx) ${CFLAGS} $(CPPFLAGS) -DMA -DPLRS -DTIMES ${BITS} -DSIGNALS -D_WITH_GETLINE -c -o mplrs.o mplrs.c + + mplrs64.o: mplrs.c mplrs.h lrslib.h lrsgmp.h +- $(mpicxx) ${CFLAGS} -I${INCLUDEDIR} -DMA -DPLRS -DTIMES -DSIGNALS -D_WITH_GETLINE -c -o mplrs64.o mplrs.c ++ $(mpicxx) ${CFLAGS} $(CPPFLAGS) -DMA -DPLRS -DTIMES -DSIGNALS -D_WITH_GETLINE -c -o mplrs64.o mplrs.c + + mplrs: ${MPLRSOBJ} mplrsgmp +- $(mpicxx) ${CFLAGS} -DTIMES -DSIGNALS -D_WITH_GETLINE -DPLRS -DMA ${BITS} -L${LIBDIR} -o mplrs ${MPLRSOBJ} -lgmp ++ $(mpicxx) ${CFLAGS} -DTIMES -DSIGNALS -D_WITH_GETLINE -DPLRS -DMA ${BITS} $(LDFLAGS) -o mplrs ${MPLRSOBJ} -lgmp + + mplrs64: ${MPLRSOBJ64} mplrsgmp +- $(mpicxx) ${CFLAGS} -DTIMES -DSIGNALS -D_WITH_GETLINE -DPLRS -DMA -L${LIBDIR} -o mplrs ${MPLRSOBJ64} -lgmp ++ $(mpicxx) ${CFLAGS} -DTIMES -DSIGNALS -D_WITH_GETLINE -DPLRS -DMA $(LDFLAGS) -o mplrs ${MPLRSOBJ64} -lgmp + + mplrsgmp: mplrs.c mplrs.h lrslib.c lrslib.h lrsgmp.c lrsgmp.h lrsdriver.h lrsdriver.c +- $(mpicxx) ${CFLAGS} -DTIMES -DSIGNALS -D_WITH_GETLINE -DPLRS -DGMP -I${INCLUDEDIR} mplrs.c lrslib.c lrsgmp.c lrsdriver.c -L${LIBDIR} -o mplrsgmp -lgmp ++ $(mpicxx) ${CFLAGS} -DTIMES -DSIGNALS -D_WITH_GETLINE -DPLRS -DGMP $(CPPFLAGS) mplrs.c lrslib.c lrsgmp.c lrsdriver.c $(LDFLAGS) -o mplrsgmp -lgmp + + mplrs1: mplrs.c mplrs.h lrslib.c lrslib.h lrslong.c lrslong.h lrsdriver.h lrsdriver.c + $(mpicxx) ${CFLAGS} -DTIMES -DSIGNALS -D_WITH_GETLINE -DPLRS -DSAFE -DLRSLONG mplrs.c lrslib.c lrslong.c lrsdriver.c -o mplrs1 +@@ -157,17 +157,17 @@ + singlemplrs: mplrsgmp mplrs1 mplrs2 + + flint: lrs.c lrslib.c lrslib.h lrsgmp.c lrsgmp.h +- @test -d ${INCLUDEDIR}/flint || { echo ${INCLUDEDIR}/flint not found; exit 1; } +- $(CC) -O3 -DFLINT -I/usr/local/include/flint lrs.c lrslib.c lrsgmp.c lrsdriver.c -L/usr/local/lib -Wl,-rpath=/usr/local/lib -lflint -o lrsflint -lgmp +-# $(CC) -O3 -DFLINT -I${INCLUDEDIR} -I${INCLUDEDIR}/flint lrs.c lrsdriver.c lrslib.c lrsgmp.c -L${LIBDIR} -lflint -o lrsflint -lgmp ++# @test -d ${INCLUDEDIR}/flint || { echo ${INCLUDEDIR}/flint not found; exit 1; } ++ $(CC) -O3 -DFLINT lrs.c lrslib.c lrsgmp.c lrsdriver.c -Wl,-lflint -o lrsflint -lgmp ++# $(CC) -O3 -DFLINT $(CPPFLAGS) lrs.c lrsdriver.c lrslib.c lrsgmp.c $(LDFLAGS) -lflint -o lrsflint -lgmp + + mplrsflint: mplrs.c mplrs.h lrslib.c lrslib.h lrsgmp.c lrsgmp.h lrsdriver.c lrsdriver.h +- ${mpicxx} ${CFLAGS} -DTIMES -DSIGNALS -D_WITH_GETLINE -DFLINT -I${INCLUDEDIR}/flint -DPLRS -o mplrsflint mplrs.c lrsdriver.c lrslib.c lrsgmp.c -L${LIBDIR} -lflint -lgmp ++ ${mpicxx} ${CFLAGS} -DTIMES -DSIGNALS -D_WITH_GETLINE -DFLINT -DPLRS -o mplrsflint mplrs.c lrsdriver.c lrslib.c lrsgmp.c $(LDFLAGS) -lflint -lgmp + + #comment out lines with ${BITS} if __int128 not supported by your C compiler + + lrsgmp: lrs.c lrslib.c lrslib.h lrsgmp.c lrsgmp.h lrsdriver.h lrsdriver.c +- $(CC) ${CFLAGS} -DGMP -I${INCLUDEDIR} -o lrsgmp lrs.c lrslib.c lrsgmp.c lrsdriver.c -L${LIBDIR} -lgmp ++ $(CC) ${CFLAGS} -DGMP $(CPPFLAGS) -o lrsgmp lrs.c lrslib.c lrsgmp.c lrsdriver.c $(LDFLAGS) -lgmp + ln -s -f lrsgmp redundgmp + + single: lrs.c lrslong.c lrslong.h lrslib.c lrslib.h lrsgmp.c lrsgmp.h lrsdriver.h lrsdriver.c +@@ -188,23 +188,23 @@ + $(CC) -O3 -o 2nash 2nash.c + + demo: lpdemo1.c lrslib.c lrsdriver.c lrslib.h lrsgmp.c lrsgmp.h +- $(CC) -O3 -I${INCLUDEDIR} -L${LIBDIR} -o lpdemo1 lpdemo1.c lrslib.c lrsdriver.c lrsgmp.c -lgmp -DGMP +- $(CC) -O3 -I${INCLUDEDIR} -L${LIBDIR} -o lpdemo lpdemo.c lrslib.c lrsdriver.c lrsgmp.c -lgmp -DGMP +- $(CC) -O3 -I${INCLUDEDIR} -L${LIBDIR} -o lpdemo2 lpdemo2.c lrslib.c lrsdriver.c lrsgmp.c -lgmp -DGMP +- $(CC) -O3 -I${INCLUDEDIR} -L${LIBDIR} -o vedemo vedemo.c lrslib.c lrsdriver.c lrsgmp.c -lgmp -DGMP +- $(CC) -O3 -I${INCLUDEDIR} -L${LIBDIR} -o chdemo chdemo.c lrslib.c lrsdriver.c lrsgmp.c -lgmp -DGMP ++ $(CC) -O3 $(CPPFLAGS) $(LDFLAGS) -o lpdemo1 lpdemo1.c lrslib.c lrsdriver.c lrsgmp.c -lgmp -DGMP ++ $(CC) -O3 $(CPPFLAGS) $(LDFLAGS) -o lpdemo lpdemo.c lrslib.c lrsdriver.c lrsgmp.c -lgmp -DGMP ++ $(CC) -O3 $(CPPFLAGS) $(LDFLAGS) -o lpdemo2 lpdemo2.c lrslib.c lrsdriver.c lrsgmp.c -lgmp -DGMP ++ $(CC) -O3 $(CPPFLAGS) $(LDFLAGS) -o vedemo vedemo.c lrslib.c lrsdriver.c lrsgmp.c -lgmp -DGMP ++ $(CC) -O3 $(CPPFLAGS) $(LDFLAGS) -o chdemo chdemo.c lrslib.c lrsdriver.c lrsgmp.c -lgmp -DGMP + + lrsnash: lrsnash.c lrsnashlib.c lrslib.c lrsnashlib.h lrslib.h lrsgmp.c lrsgmp.h lrsdriver.h lrsdriver.c +- $(CC) -O3 -I${INCLUDEDIR} -L${LIBDIR} -o lrsnash lrsnash.c lrsnashlib.c lrslib.c lrsgmp.c lrsdriver.c -lgmp -DGMP ++ $(CC) -O3 $(CPPFLAGS) $(LDFLAGS) -o lrsnash lrsnash.c lrsnashlib.c lrslib.c lrsgmp.c lrsdriver.c -lgmp -DGMP + + alllrsnash: lrsnash.c nashdemo.c lrsnashlib.c lrslib.c lrsnashlib.h lrslib.h lrsgmp.c lrsgmp.h lrslong.h lrsdriver.h lrsdriver.c +- $(CC) -O3 -I${INCLUDEDIR} -L${LIBDIR} -o lrsnashgmp lrsnash.c lrsnashlib.c lrslib.c lrsgmp.c lrsdriver.c -lgmp -DGMP +- $(CC) -O3 -I${INCLUDEDIR} -L${LIBDIR} -o lrsnash1 lrsnash.c lrsnashlib.c lrslib.c lrslong.c lrsdriver.c -DLRSLONG -DSAFE +- $(CC) -O3 -I${INCLUDEDIR} -L${LIBDIR} -o lrsnash2 lrsnash.c lrsnashlib.c lrslib.c lrslong.c lrsdriver.c -DLRSLONG -DSAFE ${BITS} +- $(CC) -O3 -I${INCLUDEDIR} -L${LIBDIR} -o nashdemo nashdemo.c lrsnashlib.c lrslib.c lrsgmp.c lrsdriver.c -lgmp -DGMP ++ $(CC) -O3 $(CPPFLAGS) $(LDFLAGS) -o lrsnashgmp lrsnash.c lrsnashlib.c lrslib.c lrsgmp.c lrsdriver.c -lgmp -DGMP ++ $(CC) -O3 $(CPPFLAGS) $(LDFLAGS) -o lrsnash1 lrsnash.c lrsnashlib.c lrslib.c lrslong.c lrsdriver.c -DLRSLONG -DSAFE ++ $(CC) -O3 $(CPPFLAGS) $(LDFLAGS) -o lrsnash2 lrsnash.c lrsnashlib.c lrslib.c lrslong.c lrsdriver.c -DLRSLONG -DSAFE ${BITS} ++ $(CC) -O3 $(CPPFLAGS) $(LDFLAGS) -o nashdemo nashdemo.c lrsnashlib.c lrslib.c lrsgmp.c lrsdriver.c -lgmp -DGMP + $(CC) -O3 -DMP -o setupnash setupnash.c lrslib.c lrsdriver.c lrsmp.c + $(CC) -O3 -DMP -o setupnash2 setupnash2.c lrslib.c lrsdriver.c lrsmp.c +- $(CC) -O3 -I${INCLUDEDIR} -L${LIBDIR} -o 2nash 2nash.c ++ $(CC) -O3 $(CPPFLAGS) $(LDFLAGS) -o 2nash 2nash.c + cp lrsnashgmp lrsnash + + ###################################################################### +@@ -248,12 +248,12 @@ + + + lrsnash-shared: ${SHLINK} lrsnash.c +- $(CC) ${CFLAGS} -DGMP -DMA lrsnash.c lrsnashlib.c -I${INCLUDEDIR} -o $@ -L . -llrs -lgmp ++ $(CC) ${CFLAGS} -DGMP -DMA lrsnash.c lrsnashlib.c $(CPPFLAGS) -o $@ -L . -llrs -lgmp + + # driver object files + + lrs-shared.o: lrs.c +- $(CC) ${CFLAGS} -DMA ${BITS} -L${LIBDIR} -c -o $@ lrs.c ++ $(CC) ${CFLAGS} -DMA ${BITS} $(LDFLAGS) -c -o $@ lrs.c + + # build object files for the shared library + +@@ -270,10 +270,10 @@ + $(CC) ${CFLAGS} ${SHLIB_CFLAGS} -DMA -DSAFE ${BITS} -DLRSLONG -c -o $@ lrslong.c + + lrslibgmp-shr.o: lrslib.c lrslib.h +- $(CC) ${CFLAGS} ${SHLIB_CFLAGS} -DMA -DGMP -I${INCLUDEDIR} -c -o $@ lrslib.c ++ $(CC) ${CFLAGS} ${SHLIB_CFLAGS} -DMA -DGMP $(CPPFLAGS) -c -o $@ lrslib.c + + lrsgmp-shr.o: lrsgmp.c lrsgmp.h +- $(CC) ${CFLAGS} ${SHLIB_CFLAGS} -DMA -DGMP -I${INCLUDEDIR} -c -o $@ lrsgmp.c ++ $(CC) ${CFLAGS} ${SHLIB_CFLAGS} -DMA -DGMP $(CPPFLAGS) -c -o $@ lrsgmp.c + + lrslib2-shr.o: lrslib.c lrslib.h + $(CC) ${CFLAGS} ${SHLIB_CFLAGS} -DMA -DSAFE ${BITS} -DLRSLONG -c -o $@ lrslib.c From 78d60915b06ca579ce1243362b232e79a9d72bc0 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Sat, 11 Nov 2023 16:04:54 +0800 Subject: [PATCH 193/599] adding easyconfigs: nauty-2.8.6-GCC-11.3.0.eb --- .../n/nauty/nauty-2.8.6-GCC-11.3.0.eb | 51 +++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/n/nauty/nauty-2.8.6-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/n/nauty/nauty-2.8.6-GCC-11.3.0.eb b/easybuild/easyconfigs/n/nauty/nauty-2.8.6-GCC-11.3.0.eb new file mode 100644 index 00000000000..bc1a1036d2d --- /dev/null +++ b/easybuild/easyconfigs/n/nauty/nauty-2.8.6-GCC-11.3.0.eb @@ -0,0 +1,51 @@ +easyblock = 'MakeCp' + +name = 'nauty' +version = '2.8.6' + +homepage = 'https://pallini.di.uniroma1.it/' +description = """nauty and Traces are programs for computing automorphism groups of graphs and +digraphs. They can also produce a canonical label.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://pallini.di.uniroma1.it'] +sources = ['nauty%s.tar.gz' % version.replace('.', '_')] +checksums = ['f2ce98225ca8330f5bce35f7d707b629247e09dda15fc479dc00e726fee5e6fa'] + +local_executables = [ + 'addedgeg', 'amtog', 'assembleg', 'biplabg', 'catg', 'complg', 'converseg', 'copyg', 'countg', 'cubhamg', + 'deledgeg', 'delptg', 'directg', 'dreadnaut', 'dretodot', 'dretog', 'edgetransg', 'genbg', 'genbgL', 'geng', + 'gengL', 'genquarticg', 'genrang', 'genspecialg', 'gentourng', 'gentreeg', 'hamheuristic', 'labelg', 'linegraphg', + 'listg', 'multig', 'newedgeg', 'NRswitchg', 'pickg', 'planarg', 'ranlabg', 'shortg', 'showg', 'subdivideg', + 'twohamg', 'underlyingg', 'vcolg', 'watercluster2' +] +local_headers = [ + 'gtools.h', 'gutils.h', 'naugroup.h', 'naugstrings.h', 'naurng.h', 'nausparse.h', 'nautaux.h', 'nautinv.h', + 'naututil.h', 'nautycliquer.h', 'nauty.h', 'planarity.h', 'quarticirred28.h', 'schreier.h', 'traces.h' +] +local_libs = ['nauty%s.a' % l for l in ['', '1', 'L', 'L1', 'W', 'W1']] + +# Configure and enable thread-local variables +prebuildopts = "./configure --enable-tls && " + +runtest = "checks" + +files_to_copy = [ + (local_executables, "bin"), + (local_headers, "include/%(name)s"), + (local_libs, "lib"), +] + +# prepend "lib" to library files to standarize their name +postinstallcmds = ["cd %%(installdir)s/lib/ && mv %s lib%s" % (l, l) for l in local_libs] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_executables] + + ['include/%%(name)s/%s' % h for h in local_headers] + + ['lib/lib%s' % l for l in local_libs], + 'dirs': [''] +} + +moduleclass = 'math' From 2cb6228a4a6e09ea80d2df4ee0d7b305f4450a11 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Sat, 11 Nov 2023 16:10:36 +0800 Subject: [PATCH 194/599] adding easyconfigs: PARI-GP-2.15.4-GCCcore-11.3.0.eb --- .../PARI-GP/PARI-GP-2.15.4-GCCcore-11.3.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/p/PARI-GP/PARI-GP-2.15.4-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/p/PARI-GP/PARI-GP-2.15.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/PARI-GP/PARI-GP-2.15.4-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..eac0ec3c674 --- /dev/null +++ b/easybuild/easyconfigs/p/PARI-GP/PARI-GP-2.15.4-GCCcore-11.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'PARI-GP' +version = '2.15.4' + +homepage = 'http://pari.math.u-bordeaux.fr' +description = """PARI/GP is a widely used computer algebra system designed for fast computations in number theory + (factorizations, algebraic number theory, elliptic curves...), but also contains a large number of other useful + functions to compute with mathematical entities such as matrices, polynomials, power series, algebraic numbers etc., + and a lot of transcendental functions. PARI is also available as a C library to allow for faster computations. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['http://pari.math.u-bordeaux.fr/pub/pari/unix/'] +sources = ['pari-%(version)s.tar.gz'] +checksums = ['c3545bfee0c6dfb40b77fb4bbabaf999d82e60069b9f6d28bcb6cf004c8c5c0f'] + +builddependencies = [('binutils', '2.38')] + +dependencies = [ + ('libreadline', '8.1.2'), + ('ncurses', '6.3'), +] + +skipsteps = ['configure'] + +prebuildopts = './Configure --prefix=%(installdir)s &&' + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['gp', 'gp-2.15', 'gphelp', 'tex2mail']] + + ['include/pari/%s' % x for x in ['pari.h', 'genpari.h']], + 'dirs': ['bin', 'include'] +} + +moduleclass = 'math' From 682ecdfa8992df030f9e942db8bd3393ffbb1e46 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Sat, 11 Nov 2023 16:24:43 +0800 Subject: [PATCH 195/599] adding easyconfigs: Singular-4.3.2p10-gfbf-2022a.eb --- .../Singular/Singular-4.3.2p10-gfbf-2022a.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/s/Singular/Singular-4.3.2p10-gfbf-2022a.eb diff --git a/easybuild/easyconfigs/s/Singular/Singular-4.3.2p10-gfbf-2022a.eb b/easybuild/easyconfigs/s/Singular/Singular-4.3.2p10-gfbf-2022a.eb new file mode 100644 index 00000000000..97c0499a3ab --- /dev/null +++ b/easybuild/easyconfigs/s/Singular/Singular-4.3.2p10-gfbf-2022a.eb @@ -0,0 +1,45 @@ +easyblock = 'ConfigureMake' + +name = 'Singular' +version = '4.3.2p10' + +homepage = 'https://www.singular.uni-kl.de/' +description = """Singular is a computer algebra system for polynomial computations, +with special emphasis on commutative and non-commutative algebra, algebraic geometry, +and singularity theory.""" + +toolchain = {'name': 'gfbf', 'version': '2022a'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/Singular/Singular/archive/refs/tags/'] +sources = ['Release-%s.tar.gz' % version.replace('.', '-')] +checksums = ['692a09ef87be731f21b792721edd671ee98f1a4048539e628d92f123714279ab'] + +builddependencies = [ + ('Autotools', '20220317'), + ('Doxygen', '1.9.4'), + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('libreadline', '8.1.2'), + ('GMP', '6.2.1'), + ('MPFR', '4.1.0'), + ('FLINT', '2.9.0'), + ('NTL', '11.5.1'), + ('cddlib', '0.94m'), + ('4ti2', '1.6.9'), +] + +preconfigopts = "./autogen.sh && " +configopts = "--with-gmp=$EBROOTGMP --with-flint=$EBROOTFLINT --with-ntl=$EBROOTNTL" + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['ESingular', 'Singular', 'TSingular', 'libpolys-config', 'libsingular-config']] + + ['lib/lib%s.%s' % (l, e) for l in ['Singular', 'factory', 'omalloc', 'polys', 'singular_resources'] + for e in ['a', SHLIB_EXT]], + 'dirs': ['include/%s' % h for h in ['factory', 'omalloc', 'resources', 'singular']] + + ['libexec/singular', 'share'], +} + +moduleclass = 'math' From 27abd03b3258dd2e760dc3d71ebb10b4881b3c85 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Sat, 11 Nov 2023 16:28:33 +0800 Subject: [PATCH 196/599] switch to https --- .../easyconfigs/p/PARI-GP/PARI-GP-2.15.4-GCCcore-11.3.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PARI-GP/PARI-GP-2.15.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/PARI-GP/PARI-GP-2.15.4-GCCcore-11.3.0.eb index eac0ec3c674..4b8ff351b17 100644 --- a/easybuild/easyconfigs/p/PARI-GP/PARI-GP-2.15.4-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/PARI-GP/PARI-GP-2.15.4-GCCcore-11.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'PARI-GP' version = '2.15.4' -homepage = 'http://pari.math.u-bordeaux.fr' +homepage = 'https://pari.math.u-bordeaux.fr' description = """PARI/GP is a widely used computer algebra system designed for fast computations in number theory (factorizations, algebraic number theory, elliptic curves...), but also contains a large number of other useful functions to compute with mathematical entities such as matrices, polynomials, power series, algebraic numbers etc., @@ -12,7 +12,7 @@ description = """PARI/GP is a widely used computer algebra system designed for f toolchain = {'name': 'GCCcore', 'version': '11.3.0'} -source_urls = ['http://pari.math.u-bordeaux.fr/pub/pari/unix/'] +source_urls = ['https://pari.math.u-bordeaux.fr/pub/pari/unix/'] sources = ['pari-%(version)s.tar.gz'] checksums = ['c3545bfee0c6dfb40b77fb4bbabaf999d82e60069b9f6d28bcb6cf004c8c5c0f'] From 8d2129cae7cd7edee8bde9f01c486ba51ceffe4d Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Sat, 11 Nov 2023 16:37:49 +0800 Subject: [PATCH 197/599] adding easyconfigs: FFLAS-FFPACK-2.5.0-gfbf-2022a.eb --- .../FFLAS-FFPACK-2.5.0-gfbf-2022a.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/f/FFLAS-FFPACK/FFLAS-FFPACK-2.5.0-gfbf-2022a.eb diff --git a/easybuild/easyconfigs/f/FFLAS-FFPACK/FFLAS-FFPACK-2.5.0-gfbf-2022a.eb b/easybuild/easyconfigs/f/FFLAS-FFPACK/FFLAS-FFPACK-2.5.0-gfbf-2022a.eb new file mode 100644 index 00000000000..e162b0e9773 --- /dev/null +++ b/easybuild/easyconfigs/f/FFLAS-FFPACK/FFLAS-FFPACK-2.5.0-gfbf-2022a.eb @@ -0,0 +1,39 @@ +## +# This file is an EasyBuild recipe; see https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright (c) 2016 Riccardo Murri +# Authors:: Riccardo Murri +# License:: GPL +# +## + +easyblock = 'ConfigureMake' + +name = 'FFLAS-FFPACK' +version = '2.5.0' + +homepage = 'https://linbox-team.github.io/fflas-ffpack/' +description = "Finite Field Linear Algebra Subroutines / Package" + +toolchain = {'name': 'gfbf', 'version': '2022a'} + +source_urls = ['https://github.com/linbox-team/fflas-ffpack/releases/download/v%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['dafb4c0835824d28e4f823748579be6e4c8889c9570c6ce9cce1e186c3ebbb23'] + +dependencies = [ + ('GMP', '6.2.1'), + ('Givaro', '4.2.0'), +] + +configopts = '--with-blas-libs="$LIBBLAS_MT" --with-blas-cflags="-I$BLAS_INC_DIR" ' +configopts += '--with-gmp=$EBROOTGMP --with-givaro=$EBROOTGIVARO --enable-openmp' + +buildopts = " && make autotune " + +sanity_check_paths = { + 'files': ['bin/fflas-ffpack-config', 'include/fflas-ffpack/fflas-ffpack.h'], + 'dirs': ['bin', 'include', 'lib'], +} + +moduleclass = 'math' From 1c31a9d56d4187758295af7c8ec98dc627df6374 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Sat, 11 Nov 2023 16:53:35 +0800 Subject: [PATCH 198/599] adding easyconfigs: IML-1.0.5-gfbf-2022a.eb --- .../easyconfigs/i/IML/IML-1.0.5-gfbf-2022a.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/i/IML/IML-1.0.5-gfbf-2022a.eb diff --git a/easybuild/easyconfigs/i/IML/IML-1.0.5-gfbf-2022a.eb b/easybuild/easyconfigs/i/IML/IML-1.0.5-gfbf-2022a.eb new file mode 100644 index 00000000000..246ea7b40b6 --- /dev/null +++ b/easybuild/easyconfigs/i/IML/IML-1.0.5-gfbf-2022a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'IML' +version = '1.0.5' + +homepage = 'https://cs.uwaterloo.ca/~astorjoh/iml.html' +description = """IML is a free library of C source code which implements algorithms for computing + exact solutions to dense systems of linear equations over the integers.""" + +toolchain = {'name': 'gfbf', 'version': '2022a'} + +source_urls = ['http://www.cs.uwaterloo.ca/~astorjoh'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['1dad666850895a5709b00b97422e2273f293cfadea7697a9f90b90953e847c2a'] + +dependencies = [('GMP', '6.2.1')] + +configopts = '--with-cblas="$LIBBLAS" --with-gmp-include=$EBROOTGMP/include --with-gmp-lib=$EBROOTGMP/lib ' + +sanity_check_paths = { + 'files': ['include/iml.h', 'lib/libiml.a'], + 'dirs': ['share'], +} + +moduleclass = 'math' From 830478bc08f55d5d2993cf6e884dd9b4e71e6cd8 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Sat, 11 Nov 2023 17:02:09 +0800 Subject: [PATCH 199/599] adding easyconfigs: LinBox-1.7.0-gfbf-2022a.eb --- .../l/LinBox/LinBox-1.7.0-gfbf-2022a.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/l/LinBox/LinBox-1.7.0-gfbf-2022a.eb diff --git a/easybuild/easyconfigs/l/LinBox/LinBox-1.7.0-gfbf-2022a.eb b/easybuild/easyconfigs/l/LinBox/LinBox-1.7.0-gfbf-2022a.eb new file mode 100644 index 00000000000..0fecede9ee7 --- /dev/null +++ b/easybuild/easyconfigs/l/LinBox/LinBox-1.7.0-gfbf-2022a.eb @@ -0,0 +1,42 @@ +## +# This file is an EasyBuild recipe; see https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright (c) 2016 Riccardo Murri +# Authors:: Riccardo Murri +# License:: GPL +# +## + +easyblock = 'ConfigureMake' + +name = 'LinBox' +version = '1.7.0' + +homepage = 'https://linalg.org/' +description = "C++ library for exact, high-performance linear algebra" + +toolchain = {'name': 'gfbf', 'version': '2022a'} + +source_urls = ['https://github.com/linbox-team/linbox/releases/download/v%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['6d2159fd395be0298362dd37f6c696676237bc8e2757341fbc46520e3b466bcc'] + +dependencies = [ + ('FFLAS-FFPACK', '2.5.0'), + ('FLINT', '2.9.0'), + ('Givaro', '4.2.0'), + ('IML', '1.0.5'), + ('NTL', '11.5.1'), +] + +configopts = "--with-fflas-ffpack=$EBROOTFFLASMINFFPACK --with-flint=$EBROOTFLINT " +configopts += "--with-givaro=$EBROOTGIVARO --with-iml=$EBROOTIML --with-ntl=$EBROOTNTL " +configopts += "--enable-openmp --enable-shared " + +sanity_check_paths = { + 'files': ['bin/linbox-config', 'include/linbox/linbox-config.h'] + + ['lib/liblinbox.%s' % e for e in ['a', SHLIB_EXT]], + 'dirs': ['bin', 'include', 'lib'], +} + +moduleclass = 'math' From 0e037ac328a79d074824f256942f7d2aff779d04 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Sat, 11 Nov 2023 17:09:31 +0800 Subject: [PATCH 200/599] adding easyconfigs: ANTIC-0.2.5-gfbf-2022a.eb --- .../a/ANTIC/ANTIC-0.2.5-gfbf-2022a.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/a/ANTIC/ANTIC-0.2.5-gfbf-2022a.eb diff --git a/easybuild/easyconfigs/a/ANTIC/ANTIC-0.2.5-gfbf-2022a.eb b/easybuild/easyconfigs/a/ANTIC/ANTIC-0.2.5-gfbf-2022a.eb new file mode 100644 index 00000000000..8e320df93cd --- /dev/null +++ b/easybuild/easyconfigs/a/ANTIC/ANTIC-0.2.5-gfbf-2022a.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'ANTIC' +version = '0.2.5' + +homepage = 'https://github.com/flintlib/antic' +description = "Antic is an algebraic number theory library." + +toolchain = {'name': 'gfbf', 'version': '2022a'} +toolchainopts = {'pic': True} + +github_account = 'flintlib' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['7b236b6226d5730cf66d492f1562c34d4dcf1bdc8775fec2330f560332ab05c1'] + +dependencies = [('FLINT', '2.9.0')] + +configopts = "--with-gmp=$EBROOTGMP --with-mpfr=$EBROOTMPFR --with-flint=$EBROOTFLINT " + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libantic.%s' % e for e in ['a', SHLIB_EXT]] + + ['include/antic/%s.h' % h for h in ['nf', 'nf_elem', 'qfb']], + 'dirs': [], +} + +moduleclass = 'math' From 6e9196ab44d089a1a27c2c792c987bfda52cbfd6 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Sat, 11 Nov 2023 20:11:26 +0800 Subject: [PATCH 201/599] adding easyconfigs: cppyy-3.0.0-GCCcore-11.3.0.eb --- .../c/cppyy/cppyy-3.0.0-GCCcore-11.3.0.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/c/cppyy/cppyy-3.0.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/c/cppyy/cppyy-3.0.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/cppyy/cppyy-3.0.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..c9df1eeb8b8 --- /dev/null +++ b/easybuild/easyconfigs/c/cppyy/cppyy-3.0.0-GCCcore-11.3.0.eb @@ -0,0 +1,45 @@ +easyblock = 'PythonBundle' + +name = 'cppyy' +version = '3.0.0' + +homepage = "https://cppyy.readthedocs.io" +description = """cppyy is an automatic, run-time, Python-C++ bindings generator, + for calling C++ from Python and Python from C++.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.24.3'), +] + +dependencies = [ + ('Python', '3.10.4'), +] + +exts_list = [ + ('cppyy-cling', '6.28.0', { + 'modulename': False, + 'checksums': ['ae67fc338510d03b68dde08add5b519e2c6434d40fe07e23e7ebace3caa684e7'], + }), + ('cppyy-backend', '1.14.11', { + 'checksums': ['2d329adce65b421a4e8a1af36116fb1756571349dc6b22a9ac3dde54b2a30af1'], + }), + ('CPyCppyy', '1.12.13', { + 'modulename': False, + 'checksums': ['f8c8c05b1eb8f0ccaed07b5069efabecff791bbe5e1b5be86767d32974e833d4'], + }), + (name, version, { + 'checksums': ['9c7c1c113d771488cee0bf63f26d2bbf4f42de731eb63776e007cb0d9e23d3d8'], + }), + ('cppyythonizations', '1.2.2', { + 'source_tmpl': 'cppyythonizations-%(version)s-py3-none-any.whl', + 'checksums': ['fa7805cea410955583d0add18e6d5b2d17740310eed974fcc65271ee9ba6da20'], + }), +] + +use_pip = True +sanity_pip_check = True + +moduleclass = 'lang' From d215f41fa998a17292c0da32ff16e2d215ff331f Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Sat, 11 Nov 2023 20:16:07 +0800 Subject: [PATCH 202/599] adding easyconfigs: E-ANTIC-1.3.0-gfbf-2022a.eb --- .../e/E-ANTIC/E-ANTIC-1.3.0-gfbf-2022a.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/e/E-ANTIC/E-ANTIC-1.3.0-gfbf-2022a.eb diff --git a/easybuild/easyconfigs/e/E-ANTIC/E-ANTIC-1.3.0-gfbf-2022a.eb b/easybuild/easyconfigs/e/E-ANTIC/E-ANTIC-1.3.0-gfbf-2022a.eb new file mode 100644 index 00000000000..2d10a851d97 --- /dev/null +++ b/easybuild/easyconfigs/e/E-ANTIC/E-ANTIC-1.3.0-gfbf-2022a.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'E-ANTIC' +version = '1.3.0' + +homepage = 'https://github.com/flatsurf/e-antic' +description = """E-ANTIC is a C/C++ library to deal with real embedded number fields built on +top of ANTIC (https://github.com/wbhart/antic). Its aim is to have as fast as +possible exact arithmetic operations and comparisons.""" + +toolchain = {'name': 'gfbf', 'version': '2022a'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/flatsurf/e-antic/releases/download/%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['ae12cb87f09478f49c4acdf0f3ff888dc556267614c0a5a3bc8bfaa41b22deef'] + +dependencies = [ + ('ANTIC', '0.2.5'), + ('FLINT', '2.9.0'), + ('Arb', '2.23.0'), + ('Python', '3.10.4'), + ('cppyy', '3.0.0'), +] + +configopts = '--without-benchmark --without-byexample --without-pytest --without-doc' + +sanity_check_paths = { + 'files': ['lib/lib%s.%s' % (lib, ext) for lib in ['eantic', 'eanticxx'] for ext in ['a', SHLIB_EXT]] + + ['include/e-antic/%s.h' % h for h in ['e-antic', 'fmpq_poly_extra', 'renf', + 'renf_elem', 'renfxx']], + 'dirs': ['lib/python3.10/site-packages'], +} + +sanity_check_commands = ["python -c 'import pyeantic'"] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'math' From e641366e605dfd3395137dc6f38c8dfea6762754 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Sat, 11 Nov 2023 20:23:05 +0800 Subject: [PATCH 203/599] adding easyconfigs: Normaliz-3.10.1-gfbf-2022a.eb --- .../n/Normaliz/Normaliz-3.10.1-gfbf-2022a.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/n/Normaliz/Normaliz-3.10.1-gfbf-2022a.eb diff --git a/easybuild/easyconfigs/n/Normaliz/Normaliz-3.10.1-gfbf-2022a.eb b/easybuild/easyconfigs/n/Normaliz/Normaliz-3.10.1-gfbf-2022a.eb new file mode 100644 index 00000000000..d7f2cdf14cf --- /dev/null +++ b/easybuild/easyconfigs/n/Normaliz/Normaliz-3.10.1-gfbf-2022a.eb @@ -0,0 +1,46 @@ +easyblock = 'ConfigureMake' + +name = 'Normaliz' +version = '3.10.1' + +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': '2022a'} +toolchainopts = {'pic': True, 'openmp': True, 'cstd': 'c++11'} + +github_account = 'Normaliz' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['761b28884fa2af00498251803a3ce4e03fcb843b7471e77e4be9b9bcd3cd0a15'] + +builddependencies = [ + ('Autotools', '20220317'), +] + +dependencies = [ + ('Boost', '1.79.0'), + ('GMP', '6.2.1'), + ('CoCoALib', '0.99818'), + ('FLINT', '2.9.0'), + ('Arb', '2.23.0'), + ('E-ANTIC', '1.3.0'), + ('nauty', '2.8.6'), +] + +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'] +} + +moduleclass = 'math' From b020e8631c2c86cbd9eae6d1c7d78b33ca5f7ebc Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Sat, 11 Nov 2023 20:38:39 +0800 Subject: [PATCH 204/599] adding easyconfigs: gap-4.12.2-foss-2022a.eb --- .../g/gap/gap-4.12.2-foss-2022a.eb | 52 +++++++++++++++++++ 1 file changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/g/gap/gap-4.12.2-foss-2022a.eb diff --git a/easybuild/easyconfigs/g/gap/gap-4.12.2-foss-2022a.eb b/easybuild/easyconfigs/g/gap/gap-4.12.2-foss-2022a.eb new file mode 100644 index 00000000000..04d6ec24740 --- /dev/null +++ b/easybuild/easyconfigs/g/gap/gap-4.12.2-foss-2022a.eb @@ -0,0 +1,52 @@ +easyblock = 'ConfigureMake' + +name = 'gap' +version = '4.12.2' + +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': '2022a'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.gap-system.org/pub/gap/gap-%(version_major_minor)s/tar.gz/'] +sources = [SOURCE_TAR_GZ] +checksums = ['672308745eb78a222494ee8dd6786edd5bc331456fcc6456ac064bdb28d587a8'] + +unpack_options = '--strip-components=1' + +builddependencies = [ + ('Perl', '5.34.1'), # needed to install NormalizInterface +] + +dependencies = [ + ('GMP', '6.2.1'), + ('libreadline', '8.1.2'), + ('zlib', '1.2.12'), + ('4ti2', '1.6.9'), # needed by 4ti2Interface, HeLP + ('cddlib', '0.94m'), # needed by CddInterface + ('cURL', '7.83.0'), # needed by curlInterface + ('lrslib', '7.2'), # needed by HeLP + ('ncurses', '6.3'), # needed by Browse + ('Normaliz', '3.10.1'), # needed by NormalizInterface, HeLP + ('Singular', '4.3.2p10'), # needed by singular + ('ZeroMQ', '4.3.4'), # needed by ZeroMQInterface +] + +# 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' + +runtest = "testinstall" + +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'] +} + +moduleclass = 'math' From 38963ddbef4c11c9a0130af4e733d6ee2c4219c8 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Sat, 11 Nov 2023 20:55:59 +0800 Subject: [PATCH 205/599] adding easyconfigs: BRiAl-1.2.12-GCC-11.3.0.eb, m4ri-20200125-GCC-11.3.0.eb, m4rie-20200125-GCC-11.3.0.eb --- .../b/BRiAl/BRiAl-1.2.12-GCC-11.3.0.eb | 28 +++++++++++++++++++ .../m/m4ri/m4ri-20200125-GCC-11.3.0.eb | 25 +++++++++++++++++ .../m/m4rie/m4rie-20200125-GCC-11.3.0.eb | 27 ++++++++++++++++++ 3 files changed, 80 insertions(+) create mode 100644 easybuild/easyconfigs/b/BRiAl/BRiAl-1.2.12-GCC-11.3.0.eb create mode 100644 easybuild/easyconfigs/m/m4ri/m4ri-20200125-GCC-11.3.0.eb create mode 100644 easybuild/easyconfigs/m/m4rie/m4rie-20200125-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/b/BRiAl/BRiAl-1.2.12-GCC-11.3.0.eb b/easybuild/easyconfigs/b/BRiAl/BRiAl-1.2.12-GCC-11.3.0.eb new file mode 100644 index 00000000000..b4a8e727e88 --- /dev/null +++ b/easybuild/easyconfigs/b/BRiAl/BRiAl-1.2.12-GCC-11.3.0.eb @@ -0,0 +1,28 @@ +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': '11.3.0'} + +source_urls = ['https://github.com/BRiAl/BRiAl/releases/download/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['ca009e3722dd3f0a60d15501caed1413146c80abced57423e32ae0116f407494'] + +dependencies = [ + ('Boost', '1.79.0'), + ('CUDD', '3.0.0'), + ('Python', '3.10.4'), + ('m4ri', '20200125'), +] + +sanity_check_paths = { + 'files': ['include/polybori.h'] + + ['lib/libbrial.%s' % e for e in ['a', SHLIB_EXT]], + 'dirs': [], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/m4ri/m4ri-20200125-GCC-11.3.0.eb b/easybuild/easyconfigs/m/m4ri/m4ri-20200125-GCC-11.3.0.eb new file mode 100644 index 00000000000..25596bcadc4 --- /dev/null +++ b/easybuild/easyconfigs/m/m4ri/m4ri-20200125-GCC-11.3.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'm4ri' +version = '20200125' + +homepage = 'https://github.com/malb/m4ri' +description = "M4RI is a library for fast arithmetic with dense matrices over F2." + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://github.com/malb/m4ri/archive/refs/tags/'] +sources = ['release-%(version)s.tar.gz'] +checksums = ['7369adcecb72d4dacfb23fd437a6b59a956f76b26dee07f32558cb915a9d6e9d'] + +builddependencies = [('Autotools', '20220317')] + +preconfigopts = "autoreconf --install && " +configopts = "--enable-openmp " + +sanity_check_paths = { + 'files': ['include/m4ri/m4ri.h', 'lib/libm4ri.a', 'lib/libm4ri.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/m4rie/m4rie-20200125-GCC-11.3.0.eb b/easybuild/easyconfigs/m/m4rie/m4rie-20200125-GCC-11.3.0.eb new file mode 100644 index 00000000000..4fbe407e8aa --- /dev/null +++ b/easybuild/easyconfigs/m/m4rie/m4rie-20200125-GCC-11.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'm4rie' +version = '20200125' + +homepage = 'https://github.com/malb/m4rie' +description = "M4RIE is a library for fast arithmetic with dense matrices." + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://github.com/malb/m4rie/archive/refs/tags/'] +sources = ['release-%(version)s.tar.gz'] +checksums = ['bc5c515e6151203b7a483f6ca84a22ec8c0407ea3621d8e11de3c997b5009d69'] + +builddependencies = [('Autotools', '20220317')] + +dependencies = [('m4ri', version)] + +preconfigopts = "autoreconf --install && " +configopts = "--enable-openmp " + +sanity_check_paths = { + 'files': ['include/m4rie/m4rie.h'] + ['lib/libm4rie.%s' % e for e in ['a', SHLIB_EXT]], + 'dirs': [], +} + +moduleclass = 'math' From 4af9e24c1eb2e56e741c41edd2c90490c88aa039 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Sat, 11 Nov 2023 20:58:37 +0800 Subject: [PATCH 206/599] add CUDD easyconfig --- .../c/CUDD/CUDD-3.0.0-GCC-11.3.0.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/c/CUDD/CUDD-3.0.0-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/c/CUDD/CUDD-3.0.0-GCC-11.3.0.eb b/easybuild/easyconfigs/c/CUDD/CUDD-3.0.0-GCC-11.3.0.eb new file mode 100644 index 00000000000..c18f2d7cc9a --- /dev/null +++ b/easybuild/easyconfigs/c/CUDD/CUDD-3.0.0-GCC-11.3.0.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': '11.3.0'} + +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 814faca5b516f5d1a5d8110233d05dfe8d380204 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Sat, 11 Nov 2023 21:29:09 +0800 Subject: [PATCH 207/599] adding easyconfigs: eclib-20230424-GCC-11.3.0.eb --- .../e/eclib/eclib-20230424-GCC-11.3.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/e/eclib/eclib-20230424-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/e/eclib/eclib-20230424-GCC-11.3.0.eb b/easybuild/easyconfigs/e/eclib/eclib-20230424-GCC-11.3.0.eb new file mode 100644 index 00000000000..374895237c3 --- /dev/null +++ b/easybuild/easyconfigs/e/eclib/eclib-20230424-GCC-11.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'eclib' +version = '20230424' + +homepage = 'https://github.com/JohnCremona/eclib' +description = """The eclib package includes mwrank (for 2-descent on elliptic curves over Q) + and modular symbol code used to create the elliptic curve database.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://github.com/JohnCremona/eclib/releases/download/v%(version)s'] +sources = [SOURCE_TAR_BZ2] +checksums = ['1422decfcabebb0ad42f7f58c5aefe5bd8fa11757b45e31a186384fd037cd5c1'] + +builddependencies = [('Autotools', '20220317')] + +dependencies = [ + ('NTL', '11.5.1'), + ('PARI-GP', '2.15.4'), +] + +preconfigopts = "autoreconf --install && " + +configopts = "--with-ntl=$EBROOTNTL --with-pari=$EBROOTPARI" + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['ecnf', 'mwrank', 'pcurve', 'qexp']] + + ['include/eclib/%s.h' % h for h in ['curve', 'egr', 'vector']] + + ['lib/libec.%s' % e for e in ['a', SHLIB_EXT]], + 'dirs': ['share'], +} + +moduleclass = 'math' From 59e2856067df82c5c9171738eb5ae5b71d13e6ff Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Sat, 11 Nov 2023 21:56:29 +0800 Subject: [PATCH 208/599] adding easyconfigs: cliquer-1.21-GCCcore-11.3.0.eb --- .../c/cliquer/cliquer-1.21-GCCcore-11.3.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/c/cliquer/cliquer-1.21-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/c/cliquer/cliquer-1.21-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/cliquer/cliquer-1.21-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..c3c98e348d9 --- /dev/null +++ b/easybuild/easyconfigs/c/cliquer/cliquer-1.21-GCCcore-11.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'MakeCp' + +name = 'cliquer' +version = '1.21' + +homepage = 'https://users.aalto.fi/~pat/cliquer.html' +description = """Cliquer is a set of C routines for finding cliques in an arbitrary weighted graph. + It uses an exact branch-and-bound algorithm developed by Patric Ostergard. It is designed with + the aim of being efficient while still being flexible and easy to use.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['http://users.aalto.fi/~pat/cliquer/'] +sources = [SOURCE_TAR_GZ] +checksums = ['ff306d27eda82383c0257065e3ffab028415ac9af73bccfdd9c2405b797ed1f1'] + +builddependencies = [('binutils', '2.38')] + +local_headers = ['cliquer', 'set', 'graph', 'misc', 'reorder', 'cliquerconf'] + +files_to_copy = [ + (['cl'], 'bin'), + (['%s.h' % h for h in local_headers], 'include/cliquer'), +] + +sanity_check_paths = { + 'files': ['bin/cl'] + ['include/cliquer/%s.h' % h for h in local_headers], + 'dirs': [], +} + +moduleclass = 'math' From dd0b4c0890e3e5ab212f4978fddbd8b166c3832b Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Sat, 11 Nov 2023 22:07:14 +0800 Subject: [PATCH 209/599] adding easyconfigs: ECL-23.9.9-GCCcore-11.3.0.eb --- .../e/ECL/ECL-23.9.9-GCCcore-11.3.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/e/ECL/ECL-23.9.9-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/e/ECL/ECL-23.9.9-GCCcore-11.3.0.eb b/easybuild/easyconfigs/e/ECL/ECL-23.9.9-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..4a15b7330df --- /dev/null +++ b/easybuild/easyconfigs/e/ECL/ECL-23.9.9-GCCcore-11.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'ECL' +version = '23.9.9' + +homepage = 'https://ecl.common-lisp.dev/' +description = """ECL (Embeddable Common-Lisp) is an interpreter of the Common-Lisp language + as described in the X3J13 Ansi specification, featuring CLOS (Common-Lisp Object System), + conditions, loops, etc, plus a translator to C, which can produce standalone executables.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://common-lisp.net/project/ecl/static/files/release'] +sources = [SOURCELOWER_TGZ] +checksums = ['c51bdab4ca6c1173dd3fe9cfe9727bcefb97bb0a3d6434b627ca6bdaeb33f880'] + +builddependencies = [('binutils', '2.38')] + +dependencies = [ + ('GMP', '6.2.1'), +] + +configopts = "--enable-manual=no " + +sanity_check_paths = { + 'files': ['bin/ecl', 'bin/ecl-config', 'include/ecl/ecl.h', 'lib/libecl.%s' % SHLIB_EXT], + 'dirs': ['share'], +} + +moduleclass = 'lang' From 3180105d3738c6240900a1d5009eab5907b15d3d Mon Sep 17 00:00:00 2001 From: deniskristak Date: Sun, 12 Nov 2023 14:33:18 +0100 Subject: [PATCH 210/599] adding easyconfigs: tensorflow-probability-0.19.0-foss-2022a.eb, vaeda-0.0.30-foss-2022a.eb --- ...ensorflow-probability-0.19.0-foss-2022a.eb | 48 +++++++++++++++++++ .../v/vaeda/vaeda-0.0.30-foss-2022a.eb | 40 ++++++++++++++++ 2 files changed, 88 insertions(+) create mode 100644 easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.19.0-foss-2022a.eb create mode 100644 easybuild/easyconfigs/v/vaeda/vaeda-0.0.30-foss-2022a.eb diff --git a/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.19.0-foss-2022a.eb b/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.19.0-foss-2022a.eb new file mode 100644 index 00000000000..5f95682889d --- /dev/null +++ b/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.19.0-foss-2022a.eb @@ -0,0 +1,48 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Authors:: Dugan Witherick (University of Warwick) +# License:: MIT/GPL +# $Id$ +# +# Updated to 0.19.0 +# Author: J. Sassmannshausen (Imperial College London/UK) +## + +easyblock = 'PythonBundle' + +name = 'tensorflow-probability' +version = '0.19.0' + +homepage = 'https://www.tensorflow.org/probability' +description = """TensorFlow Probability (TFP) is a library for probabilistic reasoning and statistical analysis.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'usempi': True, 'pic': True} + +dependencies = [ + ('Python', '3.10.4'), + ('TensorFlow', '2.11.0'), + ('dm-tree', '0.1.8'), +] + +use_pip = True + +exts_list = [ + ('cloudpickle', '2.2.0', { + 'checksums': ['3f4219469c55453cfe4737e564b67c2a149109dabf7f242478948b895f61106f'], + }), + (name, version, { + 'installopts': '--install-option="--release"', + 'modulename': 'tensorflow_probability', + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/tensorflow/probability/archive/'], + 'checksums': ['b32d2ae211ec727df9791b501839619f5389134bd6d4fe951570f500b0e75f55'], + }), +] + +sanity_check_commands = ["python -c 'import tensorflow; import tensorflow_probability'"] + +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/v/vaeda/vaeda-0.0.30-foss-2022a.eb b/easybuild/easyconfigs/v/vaeda/vaeda-0.0.30-foss-2022a.eb new file mode 100644 index 00000000000..81be3ccd7c0 --- /dev/null +++ b/easybuild/easyconfigs/v/vaeda/vaeda-0.0.30-foss-2022a.eb @@ -0,0 +1,40 @@ +easyblock = 'PythonBundle' + +name = 'vaeda' +# recent vaeda version are also available via https://test.pypi.org/project/vaeda, +# but downloading from there doesn't seem like a good idea... +local_commit = '36cdc53' +version = '0.0.30' + +homepage = 'https://github.com/kostkalab/vaeda' +description = """vaeda (variaitonal auto-encoder (vae) for doublet annotation (da)) is a Python package for doublet +annotation in single cell RNA-sequencing.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('scikit-learn', '1.1.2'), + ('scanpy', '1.9.1'), + ('TensorFlow', '2.11.0'), + ('tensorflow-probability', '0.19.0'), +] + +use_pip = True + +exts_list = [ + ('kneed', '0.8.1', { + 'preinstallopts': "sed -i 's/install_requires = .*/install_requires = numpy;scipy/g' setup.cfg && ", + 'checksums': ['6addebca6a3742e51a173f4f40f789c704677c49bc0b02666e7d71152ca0e473'], + }), + (name, version, { + 'source_urls': ['https://github.com/kostkalab/vaeda/archive/'], + 'sources': [{'download_filename': '36cdc53.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['bef23d0496944a5b9c41645de0442db99ddb26e3fb69bda3437c00339832295e'], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' From 695ea0d4b7275bc130fa8dd0e6229a3ab01c76e5 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Sun, 12 Nov 2023 14:36:50 +0100 Subject: [PATCH 211/599] adding easyconfigs: scrublet-0.2.3-foss-2022a.eb --- .../s/scrublet/scrublet-0.2.3-foss-2022a.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/s/scrublet/scrublet-0.2.3-foss-2022a.eb diff --git a/easybuild/easyconfigs/s/scrublet/scrublet-0.2.3-foss-2022a.eb b/easybuild/easyconfigs/s/scrublet/scrublet-0.2.3-foss-2022a.eb new file mode 100644 index 00000000000..9e63514905b --- /dev/null +++ b/easybuild/easyconfigs/s/scrublet/scrublet-0.2.3-foss-2022a.eb @@ -0,0 +1,41 @@ +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': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('scikit-learn', '1.1.2'), + ('scikit-image', '0.19.3'), + ('matplotlib', '3.5.2'), + ('numba', '0.56.4'), + ('tqdm', '4.64.0'), +] + +use_pip = True + +exts_list = [ + ('annoy', '1.17.1', { + 'checksums': ['bf177dbeafb81f63b2ac1e1246b1f26a2acc82e73ba46638734d29d8258122da'], + }), + ('pynndescent', '0.5.7', { + 'checksums': ['ecb395255fa36a748b5870b4ba0300ea0f7da8b1964864b8edd62577a84dfd7d'], + }), + ('umap-learn', '0.5.3', { + 'modulename': 'umap', + 'checksums': ['dbd57cb181c2b66d238acb5635697526bf24c798082daed0cf9b87f6a3a6c0c7'], + }), + (name, version, { + 'checksums': ['2185f63070290267f82a36e5b4cae8c321f10415d2d0c9f7e5e97b1126bf653a'], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' From ecd73bd1d73a0071baf64d09977a34bf12b7fbfe Mon Sep 17 00:00:00 2001 From: deniskristak Date: Sun, 12 Nov 2023 14:41:16 +0100 Subject: [PATCH 212/599] adding easyconfigs: solo-1.3-foss-2022a.eb --- .../easyconfigs/s/solo/solo-1.3-foss-2022a.eb | 90 +++++++++++++++++++ 1 file changed, 90 insertions(+) create mode 100644 easybuild/easyconfigs/s/solo/solo-1.3-foss-2022a.eb diff --git a/easybuild/easyconfigs/s/solo/solo-1.3-foss-2022a.eb b/easybuild/easyconfigs/s/solo/solo-1.3-foss-2022a.eb new file mode 100644 index 00000000000..a9560982884 --- /dev/null +++ b/easybuild/easyconfigs/s/solo/solo-1.3-foss-2022a.eb @@ -0,0 +1,90 @@ +easyblock = 'PythonBundle' + +name = 'solo' +version = '1.3' + +homepage = 'https://github.com/calico/solo' +description = "Doublet detection via semi-supervised deep learning" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('IPython', '8.5.0'), + ('PyTorch', '1.12.0'), + ('tqdm', '4.64.0'), + ('Seaborn', '0.12.1'), + ('leidenalg', '0.9.1'), + ('scanpy', '1.9.1'), + ('openpyxl', '3.0.10'), + ('tensorboard', '2.10.0'), +] + +use_pip = True + +exts_list = [ + ('ConfigArgParse', '1.5.3', { + 'checksums': ['1b0b3cbf664ab59dada57123c81eff3d9737e0d11d8cf79e3d6eb10823f1739f'], + }), + ('docrep', '0.3.2', { + 'checksums': ['ed8a17e201abd829ef8da78a0b6f4d51fb99a4cbd0554adbed3309297f964314'], + }), + ('opt-einsum', '3.3.0', { + 'sources': ['opt_einsum-%(version)s.tar.gz'], + 'checksums': ['59f6475f77bbc37dcf7cd748519c0ec60722e91e63ca114e68821c0c54a46549'], + }), + ('pyro-api', '0.1.2', { + 'modulename': 'pyroapi', + 'checksums': ['a1b900d9580aa1c2fab3b123ab7ff33413744da7c5f440bd4aadc4d40d14d920'], + }), + ('pyro-ppl', '1.8.4', { + 'modulename': 'pyro', + 'checksums': ['766fad61e52df48885de96d41213da1f8e8c1b79ecf308ad53189fcd15c1cb41'], + }), + ('commonmark', '0.9.1', { + 'checksums': ['452f9dc859be7f06631ddcb328b6919c67984aca654e5fefb3914d54691aed60'], + }), + ('rich', '12.6.0', { + 'checksums': ['ba3a3775974105c221d31141f2c116f4fd65c5ceb0698657a11e9f295ec93fd0'], + }), + ('pyDeprecate', '0.3.2', { + 'modulename': 'deprecate', + 'checksums': ['d481116cc5d7f6c473e7c4be820efdd9b90a16b594b350276e9e66a6cb5bdd29'], + }), + ('torchmetrics', '0.7.3', { + 'checksums': ['875e744a6db63c88757260d63cb80919d0398734a7f456f8ea4181bb2db957d8'], + }), + ('PyYAML', '5.4.1', { + 'modulename': 'yaml', + 'checksums': ['607774cbba28732bfa802b54baa7484215f530991055bb562efbed5b2f20a45e'], + }), + ('pytorch-lightning', '1.3.8', { + 'preinstallopts': "sed -i 's/pyDeprecate==/pyDeprecate>=/g' requirements.txt && ", + 'checksums': ['60b0a3e464d394864dae4c8d251afa7aa453644a19bb7672f5ee400343cdf7b0'], + }), + ('scvi-tools', '0.14.6', { + 'modulename': 'scvi', + 'preinstallopts': "sed -i '/^setuptools/d' pyproject.toml && ", + 'checksums': ['f30a8a685624e49fa8a0d9b9d53152eb7b95e28b020ebd1c564387b2250bc38a'], + }), + ('solo-sc', version, { + 'modulename': 'solo', + 'preinstallopts': "sed -i 's/==/>=/g' requirements.txt && ", + 'checksums': ['e19e5697ad5e12b39dd2549682356171a438dfe70ec46277d4502bab047b624d'], + }), +] + +sanity_check_paths = { + 'files': ['bin/hashsolo', 'bin/solo'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "hashsolo --help", + "solo --help", +] + +sanity_pip_check = True + +moduleclass = 'bio' From 2dc76b4466155120b9ab09e1a7041d5122b20ee1 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Sun, 12 Nov 2023 17:13:24 +0100 Subject: [PATCH 213/599] adding easyconfigs: EUKulele-2.0.6-foss-2022a.eb --- .../e/EUKulele/EUKulele-2.0.6-foss-2022a.eb | 78 +++++++++++++++++++ 1 file changed, 78 insertions(+) create mode 100644 easybuild/easyconfigs/e/EUKulele/EUKulele-2.0.6-foss-2022a.eb diff --git a/easybuild/easyconfigs/e/EUKulele/EUKulele-2.0.6-foss-2022a.eb b/easybuild/easyconfigs/e/EUKulele/EUKulele-2.0.6-foss-2022a.eb new file mode 100644 index 00000000000..55e7e75e1b5 --- /dev/null +++ b/easybuild/easyconfigs/e/EUKulele/EUKulele-2.0.6-foss-2022a.eb @@ -0,0 +1,78 @@ +easyblock = 'PythonBundle' + +name = 'EUKulele' +version = '2.0.6' + +homepage = 'https://github.com/AlexanderLabWHOI/EUKulele' +description = "Formalizing environmental eukaryotic taxonomic assignment" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('Biopython', '1.79'), + ('SciPy-bundle', '2022.05'), + ('Seaborn', '0.12.1'), + ('PyYAML', '6.0'), + ('coverage', '7.2.7'), + ('matplotlib', '3.5.2'), + ('pytest-xdist', '2.5.0'), +] + +use_pip = True + +local_oset_sed = 'sed -i "s/collections import MutableSet/collections.abc import MutableSet/g" ./src/oset/pyoset.py ' +exts_list = [ + ('oset', '0.1.3', { + 'preinstallopts': 'sed -i "s/collections import MutableSet/collections.abc import MutableSet/g" ./src/oset/pyoset.py && ', + 'checksums': ['4c1fd7dec96eeff9d3260995a8e37f9f415d0bdb79975f57824e68716ac8f904'], + }), + ('dill', '0.3.6', { + 'checksums': ['e5db55f3687856d8fbdab002ed78544e1c4559a130302693d839dfe8f93f2373'], + }), + ('multiprocess', '0.70.14', { + 'checksums': ['3eddafc12f2260d27ae03fe6069b12570ab4764ab59a75e81624fac453fbf46a'], + }), + ('joblib', '1.3.1', { + 'checksums': ['1f937906df65329ba98013dc9692fe22a4c5e4a648112de500508b18a21b41e3'], + }), + ('python-coveralls', '2.9.3', { + 'modulename': 'coveralls', + 'checksums': ['bfaf7811e7dc5628e83b6b162962a4e2485dbff184b30e49f380374ed1bcee55'], + }), + ('pytest-cov', '4.1.0', { + 'checksums': ['3904b13dfbfec47f003b8e77fd5b589cd11904a21ddf1ab38a64f204d6a10ef6'], + }), + ('latexcodec', '2.0.1', { + 'checksums': ['2aa2551c373261cefe2ad3a8953a6d6533e68238d180eb4bb91d7964adb3fe9a'], + }), + ('pybtex', '0.24.0', { + 'checksums': ['818eae35b61733e5c007c3fcd2cfb75ed1bc8b4173c1f70b56cc4c0802d34755'], + }), + ('pybtex-docutils', '1.0.3', { + 'checksums': ['3a7ebdf92b593e00e8c1c538aa9a20bca5d92d84231124715acc964d51d93c6b'], + }), + ('sphinxcontrib-bibtex', '1.0.0', { + 'modulename': 'sphinxcontrib.bibtex', + 'checksums': ['629612b001f86784669d65e662377a482052decfd9a0a17c46860878eef7b9e0'], + }), + (name, version, { + 'modulename': 'EUKulele', + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/AlexanderLabWHOI/EUKulele/archive/'], + 'checksums': ['ab4efb692886f25c2b94e9405b98f3935d78b7c716b66b5f7d43f3bca02184b4'], + }), +] + +sanity_check_paths = { + 'files': ['bin/EUKulele', 'bin/create_protein_table.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "EUKulele --help" +] + +sanity_pip_check = True + +moduleclass = 'bio' From a8603e98abbc414f7e133210a4df64216cfed79e Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Sun, 12 Nov 2023 16:43:32 +0000 Subject: [PATCH 214/599] Update EUKulele-2.0.6-foss-2022a.eb --- easybuild/easyconfigs/e/EUKulele/EUKulele-2.0.6-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/EUKulele/EUKulele-2.0.6-foss-2022a.eb b/easybuild/easyconfigs/e/EUKulele/EUKulele-2.0.6-foss-2022a.eb index 55e7e75e1b5..ddaf11c8df9 100644 --- a/easybuild/easyconfigs/e/EUKulele/EUKulele-2.0.6-foss-2022a.eb +++ b/easybuild/easyconfigs/e/EUKulele/EUKulele-2.0.6-foss-2022a.eb @@ -24,7 +24,7 @@ use_pip = True local_oset_sed = 'sed -i "s/collections import MutableSet/collections.abc import MutableSet/g" ./src/oset/pyoset.py ' exts_list = [ ('oset', '0.1.3', { - 'preinstallopts': 'sed -i "s/collections import MutableSet/collections.abc import MutableSet/g" ./src/oset/pyoset.py && ', + 'preinstallopts': local_oset_sed + ' && ', 'checksums': ['4c1fd7dec96eeff9d3260995a8e37f9f415d0bdb79975f57824e68716ac8f904'], }), ('dill', '0.3.6', { From 7a2eb039d734e5e253577b7eed76b324872ca164 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 12 Nov 2023 21:08:46 +0100 Subject: [PATCH 215/599] add sanity check command for Givaro --- easybuild/easyconfigs/g/Givaro/Givaro-4.2.0-GCCcore-11.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/g/Givaro/Givaro-4.2.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/Givaro/Givaro-4.2.0-GCCcore-11.3.0.eb index fc41e542efe..ee09ead5dc2 100644 --- a/easybuild/easyconfigs/g/Givaro/Givaro-4.2.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/g/Givaro/Givaro-4.2.0-GCCcore-11.3.0.eb @@ -38,4 +38,6 @@ sanity_check_paths = { 'dirs': ['bin', 'include', 'lib'], } +sanity_check_commands = ["givaro-config --help"] + moduleclass = 'math' From a3c608a65c2ed6b927e549f29846e1b69305b007 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 12 Nov 2023 21:10:54 +0100 Subject: [PATCH 216/599] add sanity check command for lrslib --- easybuild/easyconfigs/l/lrslib/lrslib-7.2-gompi-2022a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/l/lrslib/lrslib-7.2-gompi-2022a.eb b/easybuild/easyconfigs/l/lrslib/lrslib-7.2-gompi-2022a.eb index 17ae62bb0c4..e9c03887918 100644 --- a/easybuild/easyconfigs/l/lrslib/lrslib-7.2-gompi-2022a.eb +++ b/easybuild/easyconfigs/l/lrslib/lrslib-7.2-gompi-2022a.eb @@ -36,4 +36,6 @@ sanity_check_paths = { 'dirs': [] } +sanity_check_commands = ["lrsnash --help 2>&1 | grep 'usage.*lrsnash'"] + moduleclass = 'math' From 321ccf2e1cf84bdf36ad75ea4e8ddd9028773f4a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 12 Nov 2023 21:31:25 +0100 Subject: [PATCH 217/599] add sanity check command for nauty --- easybuild/easyconfigs/n/nauty/nauty-2.8.6-GCC-11.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/n/nauty/nauty-2.8.6-GCC-11.3.0.eb b/easybuild/easyconfigs/n/nauty/nauty-2.8.6-GCC-11.3.0.eb index bc1a1036d2d..1fe2879b3c8 100644 --- a/easybuild/easyconfigs/n/nauty/nauty-2.8.6-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/n/nauty/nauty-2.8.6-GCC-11.3.0.eb @@ -48,4 +48,6 @@ sanity_check_paths = { 'dirs': [''] } +sanity_check_commands = ["dreadnaut --help"] + moduleclass = 'math' From cb355428d3db979d057ec1e1fc89fbb484da9a60 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 12 Nov 2023 21:33:19 +0100 Subject: [PATCH 218/599] add sanity check command for PARI-GP --- .../easyconfigs/p/PARI-GP/PARI-GP-2.15.4-GCCcore-11.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/p/PARI-GP/PARI-GP-2.15.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/PARI-GP/PARI-GP-2.15.4-GCCcore-11.3.0.eb index 4b8ff351b17..44c09806f4d 100644 --- a/easybuild/easyconfigs/p/PARI-GP/PARI-GP-2.15.4-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/PARI-GP/PARI-GP-2.15.4-GCCcore-11.3.0.eb @@ -33,4 +33,6 @@ sanity_check_paths = { 'dirs': ['bin', 'include'] } +sanity_check_commands = ["gp --help"] + moduleclass = 'math' From 695bd52189ca97274b9d71070b3bf8b42ce737a1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 12 Nov 2023 21:48:24 +0100 Subject: [PATCH 219/599] add sanity check command for FFLAS-FFPACK --- .../easyconfigs/f/FFLAS-FFPACK/FFLAS-FFPACK-2.5.0-gfbf-2022a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/f/FFLAS-FFPACK/FFLAS-FFPACK-2.5.0-gfbf-2022a.eb b/easybuild/easyconfigs/f/FFLAS-FFPACK/FFLAS-FFPACK-2.5.0-gfbf-2022a.eb index e162b0e9773..75c22cfa096 100644 --- a/easybuild/easyconfigs/f/FFLAS-FFPACK/FFLAS-FFPACK-2.5.0-gfbf-2022a.eb +++ b/easybuild/easyconfigs/f/FFLAS-FFPACK/FFLAS-FFPACK-2.5.0-gfbf-2022a.eb @@ -36,4 +36,6 @@ sanity_check_paths = { 'dirs': ['bin', 'include', 'lib'], } +sanity_check_commands = ["fflas-ffpack-config --help"] + moduleclass = 'math' From 4a9684381ba32fb142979a51a1817033aaead2ee Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Mon, 13 Nov 2023 07:57:14 +0800 Subject: [PATCH 220/599] add sanity check command for Singular --- .../easyconfigs/s/Singular/Singular-4.3.2p10-gfbf-2022a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/s/Singular/Singular-4.3.2p10-gfbf-2022a.eb b/easybuild/easyconfigs/s/Singular/Singular-4.3.2p10-gfbf-2022a.eb index 97c0499a3ab..9cbd46cd597 100644 --- a/easybuild/easyconfigs/s/Singular/Singular-4.3.2p10-gfbf-2022a.eb +++ b/easybuild/easyconfigs/s/Singular/Singular-4.3.2p10-gfbf-2022a.eb @@ -42,4 +42,6 @@ sanity_check_paths = { ['libexec/singular', 'share'], } +sanity_check_commands = ["Singular --help"] + moduleclass = 'math' From ad709ccf04f12fd9dbd282e582eb2401550a9733 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Mon, 13 Nov 2023 08:02:32 +0800 Subject: [PATCH 221/599] add sanity check command for LinBox --- easybuild/easyconfigs/l/LinBox/LinBox-1.7.0-gfbf-2022a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/l/LinBox/LinBox-1.7.0-gfbf-2022a.eb b/easybuild/easyconfigs/l/LinBox/LinBox-1.7.0-gfbf-2022a.eb index 0fecede9ee7..b8c32471efc 100644 --- a/easybuild/easyconfigs/l/LinBox/LinBox-1.7.0-gfbf-2022a.eb +++ b/easybuild/easyconfigs/l/LinBox/LinBox-1.7.0-gfbf-2022a.eb @@ -39,4 +39,6 @@ sanity_check_paths = { 'dirs': ['bin', 'include', 'lib'], } +sanity_check_commands = ["linbox-config --help"] + moduleclass = 'math' From 331e27bb1979d18b41d20691923b3cecb9c0f9fc Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Mon, 13 Nov 2023 08:09:03 +0800 Subject: [PATCH 222/599] add sanity check command for Normaliz --- easybuild/easyconfigs/n/Normaliz/Normaliz-3.10.1-gfbf-2022a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/n/Normaliz/Normaliz-3.10.1-gfbf-2022a.eb b/easybuild/easyconfigs/n/Normaliz/Normaliz-3.10.1-gfbf-2022a.eb index d7f2cdf14cf..97f691eb2d0 100644 --- a/easybuild/easyconfigs/n/Normaliz/Normaliz-3.10.1-gfbf-2022a.eb +++ b/easybuild/easyconfigs/n/Normaliz/Normaliz-3.10.1-gfbf-2022a.eb @@ -43,4 +43,6 @@ sanity_check_paths = { 'dirs': ['include/libnormaliz'] } +sanity_check_commands = ["normaliz --help"] + moduleclass = 'math' From 18b3ff79feb41251fac4c3871a10224ff23a6120 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Mon, 13 Nov 2023 08:10:15 +0800 Subject: [PATCH 223/599] add sanity check command for gap -x --- easybuild/easyconfigs/g/gap/gap-4.12.2-foss-2022a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/g/gap/gap-4.12.2-foss-2022a.eb b/easybuild/easyconfigs/g/gap/gap-4.12.2-foss-2022a.eb index 04d6ec24740..77a38aad37a 100644 --- a/easybuild/easyconfigs/g/gap/gap-4.12.2-foss-2022a.eb +++ b/easybuild/easyconfigs/g/gap/gap-4.12.2-foss-2022a.eb @@ -49,4 +49,6 @@ sanity_check_paths = { 'dirs': ['share/gap'] } +sanity_check_commands = ["gap --help"] + moduleclass = 'math' From c4ed8dc16c2ff63decc5e173c8021c88407a470e Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Mon, 13 Nov 2023 08:15:20 +0800 Subject: [PATCH 224/599] add sanity check command for eclib --- easybuild/easyconfigs/e/eclib/eclib-20230424-GCC-11.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/e/eclib/eclib-20230424-GCC-11.3.0.eb b/easybuild/easyconfigs/e/eclib/eclib-20230424-GCC-11.3.0.eb index 374895237c3..1c6d6c78a88 100644 --- a/easybuild/easyconfigs/e/eclib/eclib-20230424-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/e/eclib/eclib-20230424-GCC-11.3.0.eb @@ -31,4 +31,6 @@ sanity_check_paths = { 'dirs': ['share'], } +sanity_check_commands = ["mwrank -h"] + moduleclass = 'math' From cad123fe3674cbb8a7a14145a1c914c1acfe700b Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Mon, 13 Nov 2023 08:17:17 +0800 Subject: [PATCH 225/599] add sanity check command for cliquer --- easybuild/easyconfigs/c/cliquer/cliquer-1.21-GCCcore-11.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/c/cliquer/cliquer-1.21-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/cliquer/cliquer-1.21-GCCcore-11.3.0.eb index c3c98e348d9..8e68fac80d5 100644 --- a/easybuild/easyconfigs/c/cliquer/cliquer-1.21-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/c/cliquer/cliquer-1.21-GCCcore-11.3.0.eb @@ -28,4 +28,6 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = ["cl --help"] + moduleclass = 'math' From 3ad1af638e74e6669b5b836527237f5a0e172d16 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Mon, 13 Nov 2023 08:30:05 +0800 Subject: [PATCH 226/599] add sanity check command for ECL --- easybuild/easyconfigs/e/ECL/ECL-23.9.9-GCCcore-11.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/e/ECL/ECL-23.9.9-GCCcore-11.3.0.eb b/easybuild/easyconfigs/e/ECL/ECL-23.9.9-GCCcore-11.3.0.eb index 4a15b7330df..7785b55e3af 100644 --- a/easybuild/easyconfigs/e/ECL/ECL-23.9.9-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/e/ECL/ECL-23.9.9-GCCcore-11.3.0.eb @@ -27,4 +27,6 @@ sanity_check_paths = { 'dirs': ['share'], } +sanity_check_commands = ["ecl --help"] + moduleclass = 'lang' From 8392e0312d55bf38ec2bc7b95a2d1e8650c26921 Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 13 Nov 2023 12:45:47 +0000 Subject: [PATCH 227/599] adding easyconfigs: TOML-Fortran-0.4.1-GCC-12.2.0.eb, TOML-Fortran-0.4.1-intel-compilers-2022.2.1.eb --- .../TOML-Fortran-0.4.1-GCC-12.2.0.eb | 24 ++++++++++++++++++ ...-Fortran-0.4.1-intel-compilers-2022.2.1.eb | 25 +++++++++++++++++++ 2 files changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/t/TOML-Fortran/TOML-Fortran-0.4.1-GCC-12.2.0.eb create mode 100644 easybuild/easyconfigs/t/TOML-Fortran/TOML-Fortran-0.4.1-intel-compilers-2022.2.1.eb diff --git a/easybuild/easyconfigs/t/TOML-Fortran/TOML-Fortran-0.4.1-GCC-12.2.0.eb b/easybuild/easyconfigs/t/TOML-Fortran/TOML-Fortran-0.4.1-GCC-12.2.0.eb new file mode 100644 index 00000000000..e3b1d6f709e --- /dev/null +++ b/easybuild/easyconfigs/t/TOML-Fortran/TOML-Fortran-0.4.1-GCC-12.2.0.eb @@ -0,0 +1,24 @@ +easyblock = 'CMakeMake' + +name = 'TOML-Fortran' +version = '0.4.1' + +homepage = 'https://github.com/toml-f/toml-f' +description = 'TOML parser for Fortran projects' + +toolchain = {'name': 'GCC', 'version': '12.2.0'} + +source_urls = ['https://github.com/toml-f/toml-f/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['435f6c06dd7392ef282ed7567c9245ca64b8456d62cbf814ada9cbad60f21c00'] + +builddependencies = [ + ('CMake', '3.24.3'), +] + +sanity_check_paths = { + 'files': ['lib/libtoml-f.a'], + 'dirs': ['include/toml-f', 'lib/pkgconfig', 'share'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/t/TOML-Fortran/TOML-Fortran-0.4.1-intel-compilers-2022.2.1.eb b/easybuild/easyconfigs/t/TOML-Fortran/TOML-Fortran-0.4.1-intel-compilers-2022.2.1.eb new file mode 100644 index 00000000000..5acb344e912 --- /dev/null +++ b/easybuild/easyconfigs/t/TOML-Fortran/TOML-Fortran-0.4.1-intel-compilers-2022.2.1.eb @@ -0,0 +1,25 @@ +easyblock = 'CMakeMake' + +name = 'TOML-Fortran' +version = '0.4.1' + +homepage = 'https://github.com/toml-f/toml-f' +description = 'TOML parser for Fortran projects' + +toolchain = {'name': 'intel-compilers', 'version': '2022.2.1'} + +source_urls = ['https://github.com/toml-f/toml-f/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['435f6c06dd7392ef282ed7567c9245ca64b8456d62cbf814ada9cbad60f21c00'] + +builddependencies = [ + ('binutils', '2.39'), + ('CMake', '3.24.3'), +] + +sanity_check_paths = { + 'files': ['lib/libtoml-f.a'], + 'dirs': ['include/toml-f', 'lib/pkgconfig', 'share'], +} + +moduleclass = 'tools' From c826e71ff0bea11b23c3f4c399fbe7d4fbddd2a4 Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 13 Nov 2023 13:01:05 +0000 Subject: [PATCH 228/599] adding easyconfigs: multicharge-0.2.0-gfbf-2022b.eb, multicharge-0.2.0-iimkl-2022b.eb --- .../multicharge-0.2.0-gfbf-2022b.eb | 43 +++++++++++++++++++ .../multicharge-0.2.0-iimkl-2022b.eb | 43 +++++++++++++++++++ 2 files changed, 86 insertions(+) create mode 100644 easybuild/easyconfigs/m/multicharge/multicharge-0.2.0-gfbf-2022b.eb create mode 100644 easybuild/easyconfigs/m/multicharge/multicharge-0.2.0-iimkl-2022b.eb diff --git a/easybuild/easyconfigs/m/multicharge/multicharge-0.2.0-gfbf-2022b.eb b/easybuild/easyconfigs/m/multicharge/multicharge-0.2.0-gfbf-2022b.eb new file mode 100644 index 00000000000..ca33f9ac6d7 --- /dev/null +++ b/easybuild/easyconfigs/m/multicharge/multicharge-0.2.0-gfbf-2022b.eb @@ -0,0 +1,43 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'CMakeNinja' + +name = 'multicharge' +version = '0.2.0' + +homepage = 'https://github.com/grimme-lab/multicharge' +description = """Electronegativity equilibration model for atomic partial charges.""" + +toolchain = {'name': 'gfbf', 'version': '2022b'} + +github_account = 'grimme-lab' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['953e2ace2f4035b1fa8ecf680f90b5ce6ad5caae17c8d8ccbc2578b92b69d3e7'] + +builddependencies = [ + ('CMake', '3.24.3'), + ('Ninja', '1.11.1'), + ('binutils', '2.39'), +] + +dependencies = [ + ('mctc-lib', '0.3.1'), + ('mstore', '0.2.0'), +] + +# configopts = '-DBLAS_LIBRARIES="-lmkl_sequential -lmkl_intel_lp64 -lmkl_core" ' +# configopts += '-DLAPACK_LIBRARIES="-lmkl_sequential -lmkl_intel_lp64 -lmkl_core" ' + +sanity_check_paths = { + 'files': ['bin/multicharge', 'lib/libmulticharge.a'], + 'dirs': ['include/%(name)s', 'lib/cmake', 'lib/pkgconfig'], +} + +sanity_check_commands = ["multicharge --help"] + +# run suite of tests with ctest +test_cmd = 'ctest' +runtest = '' + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/m/multicharge/multicharge-0.2.0-iimkl-2022b.eb b/easybuild/easyconfigs/m/multicharge/multicharge-0.2.0-iimkl-2022b.eb new file mode 100644 index 00000000000..7988816274b --- /dev/null +++ b/easybuild/easyconfigs/m/multicharge/multicharge-0.2.0-iimkl-2022b.eb @@ -0,0 +1,43 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'CMakeNinja' + +name = 'multicharge' +version = '0.2.0' + +homepage = 'https://github.com/grimme-lab/multicharge' +description = """Electronegativity equilibration model for atomic partial charges.""" + +toolchain = {'name': 'iimkl', 'version': '2022b'} + +github_account = 'grimme-lab' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['953e2ace2f4035b1fa8ecf680f90b5ce6ad5caae17c8d8ccbc2578b92b69d3e7'] + +builddependencies = [ + ('CMake', '3.24.3'), + ('Ninja', '1.11.1'), + ('binutils', '2.39'), +] + +dependencies = [ + ('mctc-lib', '0.3.1'), + ('mstore', '0.2.0'), +] + +configopts = '-DBLAS_LIBRARIES="-lmkl_sequential -lmkl_intel_lp64 -lmkl_core" ' +configopts += '-DLAPACK_LIBRARIES="-lmkl_sequential -lmkl_intel_lp64 -lmkl_core" ' + +sanity_check_paths = { + 'files': ['bin/multicharge', 'lib/libmulticharge.a'], + 'dirs': ['include/%(name)s', 'lib/cmake', 'lib/pkgconfig'], +} + +sanity_check_commands = ["multicharge --help"] + +# run suite of tests with ctest +test_cmd = 'ctest' +runtest = '' + +moduleclass = 'chem' From 6c074533aae9122a0c2931f627ebf00cdd361d06 Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 13 Nov 2023 13:02:25 +0000 Subject: [PATCH 229/599] adding easyconfigs: mstore-0.2.0-intel-compilers-2022.2.1.eb, mstore-0.2.0-GCCcore-12.2.0.eb --- .../m/mstore/mstore-0.2.0-GCCcore-12.2.0.eb | 37 +++++++++++++++++++ .../mstore-0.2.0-intel-compilers-2022.2.1.eb | 37 +++++++++++++++++++ 2 files changed, 74 insertions(+) create mode 100644 easybuild/easyconfigs/m/mstore/mstore-0.2.0-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/m/mstore/mstore-0.2.0-intel-compilers-2022.2.1.eb diff --git a/easybuild/easyconfigs/m/mstore/mstore-0.2.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/m/mstore/mstore-0.2.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..9b307e46fbc --- /dev/null +++ b/easybuild/easyconfigs/m/mstore/mstore-0.2.0-GCCcore-12.2.0.eb @@ -0,0 +1,37 @@ +# J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'CMakeMake' + +name = 'mstore' +version = '0.2.0' + +homepage = 'https://github.com/grimme-lab/mstore' +description = """Molecular structure store for testing""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +github_account = 'grimme-lab' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['95edba88afbc8013f57f4c818a97c0500cc40b158bed11234c061b2b6d7e480d'] + +builddependencies = [ + ('binutils', '2.39'), + ('CMake', '3.24.3'), +] + +dependencies = [ + ('mctc-lib', '0.3.1'), +] + +configopts = '-DBUILD_SHARED_LIBS=ON' + +sanity_check_paths = { + 'files': ['bin/mstore-fortranize', 'bin/mstore-info', 'lib/libmstore.%s' % SHLIB_EXT], + 'dirs': ['include/%(name)s', 'lib/cmake', 'lib/pkgconfig'], +} + +sanity_check_commands = ["mstore-info --help"] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/m/mstore/mstore-0.2.0-intel-compilers-2022.2.1.eb b/easybuild/easyconfigs/m/mstore/mstore-0.2.0-intel-compilers-2022.2.1.eb new file mode 100644 index 00000000000..22c6dc7cd21 --- /dev/null +++ b/easybuild/easyconfigs/m/mstore/mstore-0.2.0-intel-compilers-2022.2.1.eb @@ -0,0 +1,37 @@ +# J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'CMakeMake' + +name = 'mstore' +version = '0.2.0' + +homepage = 'https://github.com/grimme-lab/mstore' +description = """Molecular structure store for testing""" + +toolchain = {'name': 'intel-compilers', 'version': '2022.2.1'} +toolchainopts = {'pic': True} + +github_account = 'grimme-lab' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['95edba88afbc8013f57f4c818a97c0500cc40b158bed11234c061b2b6d7e480d'] + +builddependencies = [ + ('binutils', '2.39'), + ('CMake', '3.24.3'), +] + +dependencies = [ + ('mctc-lib', '0.3.1'), +] + +configopts = '-DBUILD_SHARED_LIBS=ON' + +sanity_check_paths = { + 'files': ['bin/mstore-fortranize', 'bin/mstore-info', 'lib/libmstore.%s' % SHLIB_EXT], + 'dirs': ['include/%(name)s', 'lib/cmake', 'lib/pkgconfig'], +} + +sanity_check_commands = ["mstore-info --help"] + +moduleclass = 'chem' From 98af7b005894e16eb7200b289f1bb4e79306a573 Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 13 Nov 2023 13:04:36 +0000 Subject: [PATCH 230/599] adding easyconfigs: dftd4-3.4.0-iimkl-2022b.eb, dftd4-3.4.0-gfbf-2022b.eb --- .../d/dftd4/dftd4-3.4.0-gfbf-2022b.eb | 41 +++++++++++++++++ .../d/dftd4/dftd4-3.4.0-iimkl-2022b.eb | 44 +++++++++++++++++++ 2 files changed, 85 insertions(+) create mode 100644 easybuild/easyconfigs/d/dftd4/dftd4-3.4.0-gfbf-2022b.eb create mode 100644 easybuild/easyconfigs/d/dftd4/dftd4-3.4.0-iimkl-2022b.eb diff --git a/easybuild/easyconfigs/d/dftd4/dftd4-3.4.0-gfbf-2022b.eb b/easybuild/easyconfigs/d/dftd4/dftd4-3.4.0-gfbf-2022b.eb new file mode 100644 index 00000000000..0868fa75c7b --- /dev/null +++ b/easybuild/easyconfigs/d/dftd4/dftd4-3.4.0-gfbf-2022b.eb @@ -0,0 +1,41 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'CMakeNinja' + +name = 'dftd4' +version = '3.4.0' + +homepage = 'https://github.com/dftd4/dftd4' +description = """Generally Applicable Atomic-Charge Dependent London Dispersion Correction.""" + +toolchain = {'name': 'gfbf', 'version': '2022b'} + +github_account = 'dftd4' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['f3b0a16a952817ae48e819626e13676fba3b61c8beea47b0f8ada2fbb679fb7b'] + +builddependencies = [ + ('CMake', '3.24.3'), + ('Ninja', '1.11.1'), + ('binutils', '2.39'), +] + +dependencies = [ + ('mctc-lib', '0.3.1'), + ('mstore', '0.2.0'), + ('multicharge', '0.2.0'), +] +# +# run suite of tests with ctest +test_cmd = 'ctest --parallel 1' +runtest = '' + +sanity_check_paths = { + 'files': ['bin/dftd4', 'lib/libdftd4.a'], + 'dirs': ['include/%(name)s', 'lib/cmake', 'lib/pkgconfig'], +} + +sanity_check_commands = ["dftd4 --help"] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/d/dftd4/dftd4-3.4.0-iimkl-2022b.eb b/easybuild/easyconfigs/d/dftd4/dftd4-3.4.0-iimkl-2022b.eb new file mode 100644 index 00000000000..df1ee93ef68 --- /dev/null +++ b/easybuild/easyconfigs/d/dftd4/dftd4-3.4.0-iimkl-2022b.eb @@ -0,0 +1,44 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'CMakeNinja' + +name = 'dftd4' +version = '3.4.0' + +homepage = 'https://github.com/dftd4/dftd4' +description = """Generally Applicable Atomic-Charge Dependent London Dispersion Correction.""" + +toolchain = {'name': 'iimkl', 'version': '2022b'} + +github_account = 'dftd4' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['f3b0a16a952817ae48e819626e13676fba3b61c8beea47b0f8ada2fbb679fb7b'] + +builddependencies = [ + ('CMake', '3.24.3'), + ('Ninja', '1.11.1'), + ('binutils', '2.39'), +] + +dependencies = [ + ('mctc-lib', '0.3.1'), + ('mstore', '0.2.0'), + ('multicharge', '0.2.0'), +] + +configopts = '-DBLAS_LIBRARIES="-lmkl_sequential -lmkl_intel_lp64 -lmkl_core" ' +configopts += '-DLAPACK_LIBRARIES="-lmkl_sequential -lmkl_intel_lp64 -lmkl_core" ' + +# run suite of tests with ctest +test_cmd = 'ctest --parallel 2' +runtest = '' + +sanity_check_paths = { + 'files': ['bin/dftd4', 'lib/libdftd4.a'], + 'dirs': ['include/%(name)s', 'lib/cmake', 'lib/pkgconfig'], +} + +sanity_check_commands = ["dftd4 --help"] + +moduleclass = 'chem' From bf149f64a3924032551f61902f67adaa94a75d13 Mon Sep 17 00:00:00 2001 From: Alan O'Cais Date: Mon, 13 Nov 2023 14:38:59 +0100 Subject: [PATCH 231/599] Make Pillow easyconfigs aware of sysroot --- .../easyconfigs/p/Pillow/Pillow-10.0.0-GCCcore-12.3.0.eb | 7 +++++++ .../easyconfigs/p/Pillow/Pillow-6.0.0-GCCcore-8.2.0.eb | 7 +++++++ .../easyconfigs/p/Pillow/Pillow-6.2.1-GCCcore-8.3.0.eb | 7 +++++++ .../p/Pillow/Pillow-7.0.0-GCCcore-9.3.0-Python-3.8.2.eb | 7 +++++++ .../easyconfigs/p/Pillow/Pillow-8.0.1-GCCcore-10.2.0.eb | 7 +++++++ .../easyconfigs/p/Pillow/Pillow-8.2.0-GCCcore-10.3.0.eb | 7 +++++++ .../easyconfigs/p/Pillow/Pillow-8.3.1-GCCcore-11.2.0.eb | 7 +++++++ .../easyconfigs/p/Pillow/Pillow-8.3.2-GCCcore-11.2.0.eb | 7 +++++++ .../easyconfigs/p/Pillow/Pillow-9.1.0-GCCcore-10.3.0.eb | 7 +++++++ .../easyconfigs/p/Pillow/Pillow-9.1.1-GCCcore-11.2.0.eb | 7 +++++++ .../easyconfigs/p/Pillow/Pillow-9.1.1-GCCcore-11.3.0.eb | 7 +++++++ .../easyconfigs/p/Pillow/Pillow-9.2.0-GCCcore-10.2.0.eb | 7 +++++++ .../easyconfigs/p/Pillow/Pillow-9.4.0-GCCcore-12.2.0.eb | 7 +++++++ 13 files changed, 91 insertions(+) diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-10.0.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-10.0.0-GCCcore-12.3.0.eb index 21d8071c49b..db4238313ed 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-10.0.0-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-10.0.0-GCCcore-12.3.0.eb @@ -24,8 +24,15 @@ dependencies = [ ] download_dep_fail = True + +# If we have a sysroot, make sure it is picked up +# (should not affect non-sysroot as the template is empty in this scenario) +preinstallopts = "export CPATH=$CPATH:%(sysroot)s/usr/include && " +preinstallopts = "export LIBRARY_PATH=$LIBRARY_PATH:%(sysroot)s/usr/lib:%(sysroot)s/usr/lib64 && " + # avoid that hardcoded paths like /usr/include are used in build commands installopts = "--global-option=build_ext --global-option='--disable-platform-guessing' " + use_pip = True sanity_pip_check = True diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-6.0.0-GCCcore-8.2.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-6.0.0-GCCcore-8.2.0.eb index fa078fe683a..268240341d2 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-6.0.0-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-6.0.0-GCCcore-8.2.0.eb @@ -25,8 +25,15 @@ dependencies = [ ] download_dep_fail = True + +# If we have a sysroot, make sure it is picked up +# (should not affect non-sysroot as the template is empty in this scenario) +preinstallopts = "export CPATH=$CPATH:%(sysroot)s/usr/include && " +preinstallopts = "export LIBRARY_PATH=$LIBRARY_PATH:%(sysroot)s/usr/lib:%(sysroot)s/usr/lib64 && " + # avoid that hardcoded paths like /usr/include are used in build commands installopts = "--global-option=build_ext --global-option='--disable-platform-guessing' " + use_pip = True sanity_pip_check = True diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-6.2.1-GCCcore-8.3.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-6.2.1-GCCcore-8.3.0.eb index 5bd030dd974..a52368bb6ac 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-6.2.1-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-6.2.1-GCCcore-8.3.0.eb @@ -25,8 +25,15 @@ dependencies = [ ] download_dep_fail = True + +# If we have a sysroot, make sure it is picked up +# (should not affect non-sysroot as the template is empty in this scenario) +preinstallopts = "export CPATH=$CPATH:%(sysroot)s/usr/include && " +preinstallopts = "export LIBRARY_PATH=$LIBRARY_PATH:%(sysroot)s/usr/lib:%(sysroot)s/usr/lib64 && " + # avoid that hardcoded paths like /usr/include are used in build commands installopts = "--global-option=build_ext --global-option='--disable-platform-guessing' " + use_pip = True sanity_pip_check = True diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-7.0.0-GCCcore-9.3.0-Python-3.8.2.eb b/easybuild/easyconfigs/p/Pillow/Pillow-7.0.0-GCCcore-9.3.0-Python-3.8.2.eb index 0e9cf1b4445..dfcebb3a91d 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-7.0.0-GCCcore-9.3.0-Python-3.8.2.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-7.0.0-GCCcore-9.3.0-Python-3.8.2.eb @@ -29,8 +29,15 @@ dependencies = [ ] download_dep_fail = True + +# If we have a sysroot, make sure it is picked up +# (should not affect non-sysroot as the template is empty in this scenario) +preinstallopts = "export CPATH=$CPATH:%(sysroot)s/usr/include && " +preinstallopts = "export LIBRARY_PATH=$LIBRARY_PATH:%(sysroot)s/usr/lib:%(sysroot)s/usr/lib64 && " + # avoid that hardcoded paths like /usr/include are used in build commands installopts = "--global-option=build_ext --global-option='--disable-platform-guessing' " + use_pip = True sanity_pip_check = True diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-8.0.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-8.0.1-GCCcore-10.2.0.eb index 6c8f256ce9a..2195b83f130 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-8.0.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-8.0.1-GCCcore-10.2.0.eb @@ -28,8 +28,15 @@ dependencies = [ ] download_dep_fail = True + +# If we have a sysroot, make sure it is picked up +# (should not affect non-sysroot as the template is empty in this scenario) +preinstallopts = "export CPATH=$CPATH:%(sysroot)s/usr/include && " +preinstallopts = "export LIBRARY_PATH=$LIBRARY_PATH:%(sysroot)s/usr/lib:%(sysroot)s/usr/lib64 && " + # avoid that hardcoded paths like /usr/include are used in build commands installopts = "--global-option=build_ext --global-option='--disable-platform-guessing' " + use_pip = True sanity_pip_check = True diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-8.2.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-8.2.0-GCCcore-10.3.0.eb index 6274b50e9b0..87e923978b0 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-8.2.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-8.2.0-GCCcore-10.3.0.eb @@ -28,8 +28,15 @@ dependencies = [ ] download_dep_fail = True + +# If we have a sysroot, make sure it is picked up +# (should not affect non-sysroot as the template is empty in this scenario) +preinstallopts = "export CPATH=$CPATH:%(sysroot)s/usr/include && " +preinstallopts = "export LIBRARY_PATH=$LIBRARY_PATH:%(sysroot)s/usr/lib:%(sysroot)s/usr/lib64 && " + # avoid that hardcoded paths like /usr/include are used in build commands installopts = "--global-option=build_ext --global-option='--disable-platform-guessing' " + use_pip = True sanity_pip_check = True diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-8.3.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-8.3.1-GCCcore-11.2.0.eb index 4b4a35c2651..6ba7c115749 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-8.3.1-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-8.3.1-GCCcore-11.2.0.eb @@ -28,8 +28,15 @@ dependencies = [ ] download_dep_fail = True + +# If we have a sysroot, make sure it is picked up +# (should not affect non-sysroot as the template is empty in this scenario) +preinstallopts = "export CPATH=$CPATH:%(sysroot)s/usr/include && " +preinstallopts = "export LIBRARY_PATH=$LIBRARY_PATH:%(sysroot)s/usr/lib:%(sysroot)s/usr/lib64 && " + # avoid that hardcoded paths like /usr/include are used in build commands installopts = "--global-option=build_ext --global-option='--disable-platform-guessing' " + use_pip = True sanity_pip_check = True diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-8.3.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-8.3.2-GCCcore-11.2.0.eb index 098deac80fa..975b2bc89a8 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-8.3.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-8.3.2-GCCcore-11.2.0.eb @@ -24,8 +24,15 @@ dependencies = [ ] download_dep_fail = True + +# If we have a sysroot, make sure it is picked up +# (should not affect non-sysroot as the template is empty in this scenario) +preinstallopts = "export CPATH=$CPATH:%(sysroot)s/usr/include && " +preinstallopts = "export LIBRARY_PATH=$LIBRARY_PATH:%(sysroot)s/usr/lib:%(sysroot)s/usr/lib64 && " + # avoid that hardcoded paths like /usr/include are used in build commands installopts = "--global-option=build_ext --global-option='--disable-platform-guessing' " + use_pip = True sanity_pip_check = True diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-9.1.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-9.1.0-GCCcore-10.3.0.eb index caa9fcf574f..fcb88fb0431 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-9.1.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-9.1.0-GCCcore-10.3.0.eb @@ -24,8 +24,15 @@ dependencies = [ ] download_dep_fail = True + +# If we have a sysroot, make sure it is picked up +# (should not affect non-sysroot as the template is empty in this scenario) +preinstallopts = "export CPATH=$CPATH:%(sysroot)s/usr/include && " +preinstallopts = "export LIBRARY_PATH=$LIBRARY_PATH:%(sysroot)s/usr/lib:%(sysroot)s/usr/lib64 && " + # avoid that hardcoded paths like /usr/include are used in build commands installopts = "--global-option=build_ext --global-option='--disable-platform-guessing' " + use_pip = True sanity_pip_check = True diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-9.1.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-9.1.1-GCCcore-11.2.0.eb index 6516e4b933b..e2af6602733 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-9.1.1-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-9.1.1-GCCcore-11.2.0.eb @@ -24,8 +24,15 @@ dependencies = [ ] download_dep_fail = True + +# If we have a sysroot, make sure it is picked up +# (should not affect non-sysroot as the template is empty in this scenario) +preinstallopts = "export CPATH=$CPATH:%(sysroot)s/usr/include && " +preinstallopts = "export LIBRARY_PATH=$LIBRARY_PATH:%(sysroot)s/usr/lib:%(sysroot)s/usr/lib64 && " + # avoid that hardcoded paths like /usr/include are used in build commands installopts = "--global-option=build_ext --global-option='--disable-platform-guessing' " + use_pip = True sanity_pip_check = True diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-9.1.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-9.1.1-GCCcore-11.3.0.eb index 1105bf2154e..2e900babcb2 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-9.1.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-9.1.1-GCCcore-11.3.0.eb @@ -24,8 +24,15 @@ dependencies = [ ] download_dep_fail = True + +# If we have a sysroot, make sure it is picked up +# (should not affect non-sysroot as the template is empty in this scenario) +preinstallopts = "export CPATH=$CPATH:%(sysroot)s/usr/include && " +preinstallopts = "export LIBRARY_PATH=$LIBRARY_PATH:%(sysroot)s/usr/lib:%(sysroot)s/usr/lib64 && " + # avoid that hardcoded paths like /usr/include are used in build commands installopts = "--global-option=build_ext --global-option='--disable-platform-guessing' " + use_pip = True sanity_pip_check = True diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-9.2.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-9.2.0-GCCcore-10.2.0.eb index f925080a099..c304bb9fc68 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-9.2.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-9.2.0-GCCcore-10.2.0.eb @@ -26,8 +26,15 @@ dependencies = [ ] download_dep_fail = True + +# If we have a sysroot, make sure it is picked up +# (should not affect non-sysroot as the template is empty in this scenario) +preinstallopts = "export CPATH=$CPATH:%(sysroot)s/usr/include && " +preinstallopts = "export LIBRARY_PATH=$LIBRARY_PATH:%(sysroot)s/usr/lib:%(sysroot)s/usr/lib64 && " + # avoid that hardcoded paths like /usr/include are used in build commands installopts = "--global-option=build_ext --global-option='--disable-platform-guessing' " + use_pip = True sanity_pip_check = True diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-9.4.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-9.4.0-GCCcore-12.2.0.eb index cb1ef19b3f0..03cb9b29175 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-9.4.0-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-9.4.0-GCCcore-12.2.0.eb @@ -24,8 +24,15 @@ dependencies = [ ] download_dep_fail = True + +# If we have a sysroot, make sure it is picked up +# (should not affect non-sysroot as the template is empty in this scenario) +preinstallopts = "export CPATH=$CPATH:%(sysroot)s/usr/include && " +preinstallopts = "export LIBRARY_PATH=$LIBRARY_PATH:%(sysroot)s/usr/lib:%(sysroot)s/usr/lib64 && " + # avoid that hardcoded paths like /usr/include are used in build commands installopts = "--global-option=build_ext --global-option='--disable-platform-guessing' " + use_pip = True sanity_pip_check = True From 7b966e8c4db034e788dac93a483ede79df5442b4 Mon Sep 17 00:00:00 2001 From: Richard Top Date: Mon, 13 Nov 2023 13:39:07 +0000 Subject: [PATCH 232/599] adding easyconfigs: strace-6.6-GCCcore-12.2.0.eb --- .../s/strace/strace-6.6-GCCcore-12.2.0.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/s/strace/strace-6.6-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/s/strace/strace-6.6-GCCcore-12.2.0.eb b/easybuild/easyconfigs/s/strace/strace-6.6-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..a5f0699fc99 --- /dev/null +++ b/easybuild/easyconfigs/s/strace/strace-6.6-GCCcore-12.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'strace' +version = '6.6' + +homepage = 'https://strace.io/' +description = """ +strace is a diagnostic, debugging and instructional userspace utility for Linux. It is used to monitor and tamper with +interactions between processes and the Linux kernel, which include system calls, signal deliveries, and changes of +process state. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/strace/strace/releases/download/v%(version)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['421b4186c06b705163e64dc85f271ebdcf67660af8667283147d5e859fc8a96c'] + +builddependencies = [ + ('binutils', '2.40'), +] + +configopts = "--enable-mpers=check" + +sanity_check_paths = { + 'files': ['bin/strace-log-merge', 'bin/strace'], + 'dirs': ['share'] +} + +sanity_check_commands = ['strace --help'] + +moduleclass = 'system' From c0ad1ab06170b2261c75d94a29839c02a9e4408e Mon Sep 17 00:00:00 2001 From: Alan O'Cais Date: Mon, 13 Nov 2023 15:57:14 +0100 Subject: [PATCH 233/599] Fix typo --- easybuild/easyconfigs/p/Pillow/Pillow-10.0.0-GCCcore-12.3.0.eb | 2 +- easybuild/easyconfigs/p/Pillow/Pillow-6.0.0-GCCcore-8.2.0.eb | 2 +- easybuild/easyconfigs/p/Pillow/Pillow-6.2.1-GCCcore-8.3.0.eb | 2 +- .../p/Pillow/Pillow-7.0.0-GCCcore-9.3.0-Python-3.8.2.eb | 2 +- easybuild/easyconfigs/p/Pillow/Pillow-8.0.1-GCCcore-10.2.0.eb | 2 +- easybuild/easyconfigs/p/Pillow/Pillow-8.2.0-GCCcore-10.3.0.eb | 2 +- easybuild/easyconfigs/p/Pillow/Pillow-8.3.1-GCCcore-11.2.0.eb | 2 +- easybuild/easyconfigs/p/Pillow/Pillow-8.3.2-GCCcore-11.2.0.eb | 2 +- easybuild/easyconfigs/p/Pillow/Pillow-9.1.0-GCCcore-10.3.0.eb | 2 +- easybuild/easyconfigs/p/Pillow/Pillow-9.1.1-GCCcore-11.2.0.eb | 2 +- easybuild/easyconfigs/p/Pillow/Pillow-9.1.1-GCCcore-11.3.0.eb | 2 +- easybuild/easyconfigs/p/Pillow/Pillow-9.2.0-GCCcore-10.2.0.eb | 2 +- easybuild/easyconfigs/p/Pillow/Pillow-9.4.0-GCCcore-12.2.0.eb | 2 +- 13 files changed, 13 insertions(+), 13 deletions(-) diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-10.0.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-10.0.0-GCCcore-12.3.0.eb index db4238313ed..823fd234dfa 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-10.0.0-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-10.0.0-GCCcore-12.3.0.eb @@ -28,7 +28,7 @@ download_dep_fail = True # If we have a sysroot, make sure it is picked up # (should not affect non-sysroot as the template is empty in this scenario) preinstallopts = "export CPATH=$CPATH:%(sysroot)s/usr/include && " -preinstallopts = "export LIBRARY_PATH=$LIBRARY_PATH:%(sysroot)s/usr/lib:%(sysroot)s/usr/lib64 && " +preinstallopts += "export LIBRARY_PATH=$LIBRARY_PATH:%(sysroot)s/usr/lib:%(sysroot)s/usr/lib64 && " # avoid that hardcoded paths like /usr/include are used in build commands installopts = "--global-option=build_ext --global-option='--disable-platform-guessing' " diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-6.0.0-GCCcore-8.2.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-6.0.0-GCCcore-8.2.0.eb index 268240341d2..a8360e2bc0c 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-6.0.0-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-6.0.0-GCCcore-8.2.0.eb @@ -29,7 +29,7 @@ download_dep_fail = True # If we have a sysroot, make sure it is picked up # (should not affect non-sysroot as the template is empty in this scenario) preinstallopts = "export CPATH=$CPATH:%(sysroot)s/usr/include && " -preinstallopts = "export LIBRARY_PATH=$LIBRARY_PATH:%(sysroot)s/usr/lib:%(sysroot)s/usr/lib64 && " +preinstallopts += "export LIBRARY_PATH=$LIBRARY_PATH:%(sysroot)s/usr/lib:%(sysroot)s/usr/lib64 && " # avoid that hardcoded paths like /usr/include are used in build commands installopts = "--global-option=build_ext --global-option='--disable-platform-guessing' " diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-6.2.1-GCCcore-8.3.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-6.2.1-GCCcore-8.3.0.eb index a52368bb6ac..7624d218ee5 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-6.2.1-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-6.2.1-GCCcore-8.3.0.eb @@ -29,7 +29,7 @@ download_dep_fail = True # If we have a sysroot, make sure it is picked up # (should not affect non-sysroot as the template is empty in this scenario) preinstallopts = "export CPATH=$CPATH:%(sysroot)s/usr/include && " -preinstallopts = "export LIBRARY_PATH=$LIBRARY_PATH:%(sysroot)s/usr/lib:%(sysroot)s/usr/lib64 && " +preinstallopts += "export LIBRARY_PATH=$LIBRARY_PATH:%(sysroot)s/usr/lib:%(sysroot)s/usr/lib64 && " # avoid that hardcoded paths like /usr/include are used in build commands installopts = "--global-option=build_ext --global-option='--disable-platform-guessing' " diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-7.0.0-GCCcore-9.3.0-Python-3.8.2.eb b/easybuild/easyconfigs/p/Pillow/Pillow-7.0.0-GCCcore-9.3.0-Python-3.8.2.eb index dfcebb3a91d..8bb25ce9590 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-7.0.0-GCCcore-9.3.0-Python-3.8.2.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-7.0.0-GCCcore-9.3.0-Python-3.8.2.eb @@ -33,7 +33,7 @@ download_dep_fail = True # If we have a sysroot, make sure it is picked up # (should not affect non-sysroot as the template is empty in this scenario) preinstallopts = "export CPATH=$CPATH:%(sysroot)s/usr/include && " -preinstallopts = "export LIBRARY_PATH=$LIBRARY_PATH:%(sysroot)s/usr/lib:%(sysroot)s/usr/lib64 && " +preinstallopts += "export LIBRARY_PATH=$LIBRARY_PATH:%(sysroot)s/usr/lib:%(sysroot)s/usr/lib64 && " # avoid that hardcoded paths like /usr/include are used in build commands installopts = "--global-option=build_ext --global-option='--disable-platform-guessing' " diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-8.0.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-8.0.1-GCCcore-10.2.0.eb index 2195b83f130..34563e55acf 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-8.0.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-8.0.1-GCCcore-10.2.0.eb @@ -32,7 +32,7 @@ download_dep_fail = True # If we have a sysroot, make sure it is picked up # (should not affect non-sysroot as the template is empty in this scenario) preinstallopts = "export CPATH=$CPATH:%(sysroot)s/usr/include && " -preinstallopts = "export LIBRARY_PATH=$LIBRARY_PATH:%(sysroot)s/usr/lib:%(sysroot)s/usr/lib64 && " +preinstallopts += "export LIBRARY_PATH=$LIBRARY_PATH:%(sysroot)s/usr/lib:%(sysroot)s/usr/lib64 && " # avoid that hardcoded paths like /usr/include are used in build commands installopts = "--global-option=build_ext --global-option='--disable-platform-guessing' " diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-8.2.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-8.2.0-GCCcore-10.3.0.eb index 87e923978b0..66f47353838 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-8.2.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-8.2.0-GCCcore-10.3.0.eb @@ -32,7 +32,7 @@ download_dep_fail = True # If we have a sysroot, make sure it is picked up # (should not affect non-sysroot as the template is empty in this scenario) preinstallopts = "export CPATH=$CPATH:%(sysroot)s/usr/include && " -preinstallopts = "export LIBRARY_PATH=$LIBRARY_PATH:%(sysroot)s/usr/lib:%(sysroot)s/usr/lib64 && " +preinstallopts += "export LIBRARY_PATH=$LIBRARY_PATH:%(sysroot)s/usr/lib:%(sysroot)s/usr/lib64 && " # avoid that hardcoded paths like /usr/include are used in build commands installopts = "--global-option=build_ext --global-option='--disable-platform-guessing' " diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-8.3.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-8.3.1-GCCcore-11.2.0.eb index 6ba7c115749..8af0717a0b8 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-8.3.1-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-8.3.1-GCCcore-11.2.0.eb @@ -32,7 +32,7 @@ download_dep_fail = True # If we have a sysroot, make sure it is picked up # (should not affect non-sysroot as the template is empty in this scenario) preinstallopts = "export CPATH=$CPATH:%(sysroot)s/usr/include && " -preinstallopts = "export LIBRARY_PATH=$LIBRARY_PATH:%(sysroot)s/usr/lib:%(sysroot)s/usr/lib64 && " +preinstallopts += "export LIBRARY_PATH=$LIBRARY_PATH:%(sysroot)s/usr/lib:%(sysroot)s/usr/lib64 && " # avoid that hardcoded paths like /usr/include are used in build commands installopts = "--global-option=build_ext --global-option='--disable-platform-guessing' " diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-8.3.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-8.3.2-GCCcore-11.2.0.eb index 975b2bc89a8..f9a774e6a89 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-8.3.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-8.3.2-GCCcore-11.2.0.eb @@ -28,7 +28,7 @@ download_dep_fail = True # If we have a sysroot, make sure it is picked up # (should not affect non-sysroot as the template is empty in this scenario) preinstallopts = "export CPATH=$CPATH:%(sysroot)s/usr/include && " -preinstallopts = "export LIBRARY_PATH=$LIBRARY_PATH:%(sysroot)s/usr/lib:%(sysroot)s/usr/lib64 && " +preinstallopts += "export LIBRARY_PATH=$LIBRARY_PATH:%(sysroot)s/usr/lib:%(sysroot)s/usr/lib64 && " # avoid that hardcoded paths like /usr/include are used in build commands installopts = "--global-option=build_ext --global-option='--disable-platform-guessing' " diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-9.1.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-9.1.0-GCCcore-10.3.0.eb index fcb88fb0431..0805f5cb64c 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-9.1.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-9.1.0-GCCcore-10.3.0.eb @@ -28,7 +28,7 @@ download_dep_fail = True # If we have a sysroot, make sure it is picked up # (should not affect non-sysroot as the template is empty in this scenario) preinstallopts = "export CPATH=$CPATH:%(sysroot)s/usr/include && " -preinstallopts = "export LIBRARY_PATH=$LIBRARY_PATH:%(sysroot)s/usr/lib:%(sysroot)s/usr/lib64 && " +preinstallopts += "export LIBRARY_PATH=$LIBRARY_PATH:%(sysroot)s/usr/lib:%(sysroot)s/usr/lib64 && " # avoid that hardcoded paths like /usr/include are used in build commands installopts = "--global-option=build_ext --global-option='--disable-platform-guessing' " diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-9.1.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-9.1.1-GCCcore-11.2.0.eb index e2af6602733..79ced7c8c2a 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-9.1.1-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-9.1.1-GCCcore-11.2.0.eb @@ -28,7 +28,7 @@ download_dep_fail = True # If we have a sysroot, make sure it is picked up # (should not affect non-sysroot as the template is empty in this scenario) preinstallopts = "export CPATH=$CPATH:%(sysroot)s/usr/include && " -preinstallopts = "export LIBRARY_PATH=$LIBRARY_PATH:%(sysroot)s/usr/lib:%(sysroot)s/usr/lib64 && " +preinstallopts += "export LIBRARY_PATH=$LIBRARY_PATH:%(sysroot)s/usr/lib:%(sysroot)s/usr/lib64 && " # avoid that hardcoded paths like /usr/include are used in build commands installopts = "--global-option=build_ext --global-option='--disable-platform-guessing' " diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-9.1.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-9.1.1-GCCcore-11.3.0.eb index 2e900babcb2..6021839c820 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-9.1.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-9.1.1-GCCcore-11.3.0.eb @@ -28,7 +28,7 @@ download_dep_fail = True # If we have a sysroot, make sure it is picked up # (should not affect non-sysroot as the template is empty in this scenario) preinstallopts = "export CPATH=$CPATH:%(sysroot)s/usr/include && " -preinstallopts = "export LIBRARY_PATH=$LIBRARY_PATH:%(sysroot)s/usr/lib:%(sysroot)s/usr/lib64 && " +preinstallopts += "export LIBRARY_PATH=$LIBRARY_PATH:%(sysroot)s/usr/lib:%(sysroot)s/usr/lib64 && " # avoid that hardcoded paths like /usr/include are used in build commands installopts = "--global-option=build_ext --global-option='--disable-platform-guessing' " diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-9.2.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-9.2.0-GCCcore-10.2.0.eb index c304bb9fc68..bc254d1f99f 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-9.2.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-9.2.0-GCCcore-10.2.0.eb @@ -30,7 +30,7 @@ download_dep_fail = True # If we have a sysroot, make sure it is picked up # (should not affect non-sysroot as the template is empty in this scenario) preinstallopts = "export CPATH=$CPATH:%(sysroot)s/usr/include && " -preinstallopts = "export LIBRARY_PATH=$LIBRARY_PATH:%(sysroot)s/usr/lib:%(sysroot)s/usr/lib64 && " +preinstallopts += "export LIBRARY_PATH=$LIBRARY_PATH:%(sysroot)s/usr/lib:%(sysroot)s/usr/lib64 && " # avoid that hardcoded paths like /usr/include are used in build commands installopts = "--global-option=build_ext --global-option='--disable-platform-guessing' " diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-9.4.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-9.4.0-GCCcore-12.2.0.eb index 03cb9b29175..9c723fb6f2d 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-9.4.0-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-9.4.0-GCCcore-12.2.0.eb @@ -28,7 +28,7 @@ download_dep_fail = True # If we have a sysroot, make sure it is picked up # (should not affect non-sysroot as the template is empty in this scenario) preinstallopts = "export CPATH=$CPATH:%(sysroot)s/usr/include && " -preinstallopts = "export LIBRARY_PATH=$LIBRARY_PATH:%(sysroot)s/usr/lib:%(sysroot)s/usr/lib64 && " +preinstallopts += "export LIBRARY_PATH=$LIBRARY_PATH:%(sysroot)s/usr/lib:%(sysroot)s/usr/lib64 && " # avoid that hardcoded paths like /usr/include are used in build commands installopts = "--global-option=build_ext --global-option='--disable-platform-guessing' " From fc74053cb4ce12df82c7f492f948019a3a18ac34 Mon Sep 17 00:00:00 2001 From: TopRichard <121792457+TopRichard@users.noreply.github.com> Date: Mon, 13 Nov 2023 17:35:59 +0100 Subject: [PATCH 234/599] Update strace-6.6-GCCcore-12.2.0.eb --- easybuild/easyconfigs/s/strace/strace-6.6-GCCcore-12.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/strace/strace-6.6-GCCcore-12.2.0.eb b/easybuild/easyconfigs/s/strace/strace-6.6-GCCcore-12.2.0.eb index a5f0699fc99..d3187e80ef7 100644 --- a/easybuild/easyconfigs/s/strace/strace-6.6-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/s/strace/strace-6.6-GCCcore-12.2.0.eb @@ -17,7 +17,7 @@ sources = [SOURCE_TAR_XZ] checksums = ['421b4186c06b705163e64dc85f271ebdcf67660af8667283147d5e859fc8a96c'] builddependencies = [ - ('binutils', '2.40'), + ('binutils', '2.39'), ] configopts = "--enable-mpers=check" From b1210f45c18d7aecf9eddf778098dd33aaccdecc Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Mon, 13 Nov 2023 18:20:25 +0100 Subject: [PATCH 235/599] {bio}[foss/2022a] topaz-em w/ CUDA 11.7.0 w/ PyTorch 1.12.0 --- ...3-foss-2022a-CUDA-11.7.0-PyTorch-1.12.0.eb | 67 +++++++++++++++++++ ...az-em-0.2.5_install_relion3_wrappers.patch | 14 ++++ 2 files changed, 81 insertions(+) create mode 100644 easybuild/easyconfigs/t/topaz-em/topaz-em-0.2.5.2230923-foss-2022a-CUDA-11.7.0-PyTorch-1.12.0.eb create mode 100644 easybuild/easyconfigs/t/topaz-em/topaz-em-0.2.5_install_relion3_wrappers.patch diff --git a/easybuild/easyconfigs/t/topaz-em/topaz-em-0.2.5.2230923-foss-2022a-CUDA-11.7.0-PyTorch-1.12.0.eb b/easybuild/easyconfigs/t/topaz-em/topaz-em-0.2.5.2230923-foss-2022a-CUDA-11.7.0-PyTorch-1.12.0.eb new file mode 100644 index 00000000000..6a7315621a1 --- /dev/null +++ b/easybuild/easyconfigs/t/topaz-em/topaz-em-0.2.5.2230923-foss-2022a-CUDA-11.7.0-PyTorch-1.12.0.eb @@ -0,0 +1,67 @@ +# Thomas Hoffman, EMBL Heidelberg, structures-it@embl.de, 2023/1 +easyblock = 'PythonPackage' + +name = 'topaz-em' # named topaz-em instead of topaz to be consistent with pypi +_mainversion = '0.2.5' +_patchdate = '2230923' +_patchsha = 'dadfe725efa9181e55864054f492a41b4abe8c1c' +version = '%s.%s' % (_mainversion, _patchdate) +_cudasuffix = '-CUDA-%(cudaver)s' +_pytorch_ver = '1.12.0' +_pytorchsuffix = '-PyTorch-%s' % _pytorch_ver +versionsuffix = _cudasuffix + _pytorchsuffix +_mainversion = '0.2.5' +_patchdate = '2230923' +_patchsha = 'dadfe725efa9181e55864054f492a41b4abe8c1c' +version = '%s.%s' % (_mainversion, _patchdate) + +homepage = 'http://cb.csail.mit.edu/cb/topaz/' + +description = """Particle picking software for single particle cryo-electron microscopy using +convolutional neural networks and positive-unlabeled learning. Includes methods +for micrograph denoising.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +use_pip = True + +builddependencies = [ + ('pkg-config', '0.29.2'), +] +dependencies = [ + ('CUDA', '11.7.0', '', True), + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('PyTorch', _pytorch_ver, _cudasuffix), + ('scikit-learn', '1.1.2'), + ('torchvision', '0.13.1', _cudasuffix), +] + + +source_urls = [ + 'https://github.com/tbepler/topaz/archive', + 'https://github.com/tbepler/topaz/compare/' +] +sources = ['v%s.tar.gz' % _mainversion] +patches = [ + 'topaz-em-0.2.5_install_relion3_wrappers.patch', + 'v%s..%s.patch' % (_mainversion, _patchsha) +] +checksums = [ + {'v0.2.5.tar.gz': '33bba5fc071dcdf584cfc8c152ffe889a95b71ebad7ddefd15d3f81a96987417'}, + {'topaz-em-0.2.5_install_relion3_wrappers.patch': + '0fe23a0ecaf887aaa89641a7e7cf37fafd3134384b0a8f46acb4e17537d1a151'}, + {'v0.2.5..dadfe725efa9181e55864054f492a41b4abe8c1c.patch': + 'f0dc2f0613138cff856274e5367a767d97f46dd2b47ba2a932f8ca1d20b93de1'}, +] + +sanity_pip_check = True +options = {'modulename': 'topaz'} +_relion3_wrappers = ['denoise', 'pick', 'train', 'train_denoise'] +sanity_check_commands = ['run_topaz_%s.py --help' % x for x in _relion3_wrappers] + ['topaz --help'] +sanity_check_paths = { + 'files': ["bin/run_topaz_%s.py" % x for x in _relion3_wrappers], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/topaz-em/topaz-em-0.2.5_install_relion3_wrappers.patch b/easybuild/easyconfigs/t/topaz-em/topaz-em-0.2.5_install_relion3_wrappers.patch new file mode 100644 index 00000000000..533e6e11b93 --- /dev/null +++ b/easybuild/easyconfigs/t/topaz-em/topaz-em-0.2.5_install_relion3_wrappers.patch @@ -0,0 +1,14 @@ +# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2023/11 +# install relion3 wrappers into bin +diff -ru topaz-0.2.5/setup.py topaz-0.2.5_install_relion3_wrappers/setup.py +--- topaz-0.2.5/setup.py 2022-03-11 02:33:01.000000000 +0100 ++++ topaz-0.2.5_install_relion3_wrappers/setup.py 2023-11-13 17:46:28.306807471 +0100 +@@ -30,7 +30,7 @@ + #package_dir = {'': 'topaz'}, + entry_points = {'console_scripts': ['topaz = topaz.main:main']}, + include_package_data = True, +- ++ scripts=['relion_run_topaz/run_topaz_%s.py' % x for x in ['denoise','pick','train','train_denoise']], + install_requires=[ + 'torch>=1.0.0', + 'torchvision', From 3a75d06c8c6874dfb2e94f1c62a594760ab0981e Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Mon, 13 Nov 2023 18:29:04 +0100 Subject: [PATCH 236/599] fix typos and duplicates --- ...3-foss-2022a-CUDA-11.7.0-PyTorch-1.12.0.eb | 67 +++++++++++++++++++ 1 file changed, 67 insertions(+) create mode 100644 easybuild/easyconfigs/t/topaz-em/topaz-em-0.2.5.220923-foss-2022a-CUDA-11.7.0-PyTorch-1.12.0.eb diff --git a/easybuild/easyconfigs/t/topaz-em/topaz-em-0.2.5.220923-foss-2022a-CUDA-11.7.0-PyTorch-1.12.0.eb b/easybuild/easyconfigs/t/topaz-em/topaz-em-0.2.5.220923-foss-2022a-CUDA-11.7.0-PyTorch-1.12.0.eb new file mode 100644 index 00000000000..ff22ba3d5e6 --- /dev/null +++ b/easybuild/easyconfigs/t/topaz-em/topaz-em-0.2.5.220923-foss-2022a-CUDA-11.7.0-PyTorch-1.12.0.eb @@ -0,0 +1,67 @@ +# Thomas Hoffman, EMBL Heidelberg, structures-it@embl.de, 2023/11 +easyblock = 'PythonPackage' + +name = 'topaz-em' # named topaz-em instead of topaz to be consistent with pypi +_mainversion = '0.2.5' +_patchdate = '2230923' +_patchsha = 'dadfe725efa9181e55864054f492a41b4abe8c1c' +version = '%s.%s' % (_mainversion, _patchdate) +_cudasuffix = '-CUDA-%(cudaver)s' +_pytorch_ver = '1.12.0' +_pytorchsuffix = '-PyTorch-%s' % _pytorch_ver +versionsuffix = _cudasuffix + _pytorchsuffix +_mainversion = '0.2.5' +_patchdate = '220923' +_patchsha = 'dadfe725efa9181e55864054f492a41b4abe8c1c' +version = '%s.%s' % (_mainversion, _patchdate) + +homepage = 'http://cb.csail.mit.edu/cb/topaz/' + +description = """Particle picking software for single particle cryo-electron microscopy using +convolutional neural networks and positive-unlabeled learning. Includes methods +for micrograph denoising.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +use_pip = True + +builddependencies = [ + ('pkg-config', '0.29.2'), +] +dependencies = [ + ('CUDA', '11.7.0', '', True), + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('PyTorch', _pytorch_ver, _cudasuffix), + ('scikit-learn', '1.1.2'), + ('torchvision', '0.13.1', _cudasuffix), +] + + +source_urls = [ + 'https://github.com/tbepler/topaz/archive', + 'https://github.com/tbepler/topaz/compare/' +] +sources = ['v%s.tar.gz' % _mainversion] +patches = [ + 'topaz-em-0.2.5_install_relion3_wrappers.patch', + 'v%s..%s.patch' % (_mainversion, _patchsha) +] +checksums = [ + {'v0.2.5.tar.gz': '33bba5fc071dcdf584cfc8c152ffe889a95b71ebad7ddefd15d3f81a96987417'}, + {'topaz-em-0.2.5_install_relion3_wrappers.patch': + '0fe23a0ecaf887aaa89641a7e7cf37fafd3134384b0a8f46acb4e17537d1a151'}, + {'v0.2.5..dadfe725efa9181e55864054f492a41b4abe8c1c.patch': + 'f0dc2f0613138cff856274e5367a767d97f46dd2b47ba2a932f8ca1d20b93de1'}, +] + +sanity_pip_check = True +options = {'modulename': 'topaz'} +_relion3_wrappers = ['denoise', 'pick', 'train', 'train_denoise'] +sanity_check_commands = ['run_topaz_%s.py --help' % x for x in _relion3_wrappers] + ['topaz --help'] +sanity_check_paths = { + 'files': ["bin/run_topaz_%s.py" % x for x in _relion3_wrappers], + 'dirs': [], +} + +moduleclass = 'bio' From 190f7bccf4cb008e06b53ad8948639f5c4b585fd Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Mon, 13 Nov 2023 18:32:04 +0100 Subject: [PATCH 237/599] fix typos and duplicates --- ...6-foss-2022a-CUDA-11.7.0-PyTorch-1.12.0.eb | 63 +++++++++++++++++++ 1 file changed, 63 insertions(+) create mode 100644 easybuild/easyconfigs/t/topaz-em/topaz-em-0.2.5.230926-foss-2022a-CUDA-11.7.0-PyTorch-1.12.0.eb diff --git a/easybuild/easyconfigs/t/topaz-em/topaz-em-0.2.5.230926-foss-2022a-CUDA-11.7.0-PyTorch-1.12.0.eb b/easybuild/easyconfigs/t/topaz-em/topaz-em-0.2.5.230926-foss-2022a-CUDA-11.7.0-PyTorch-1.12.0.eb new file mode 100644 index 00000000000..2adbcba0f55 --- /dev/null +++ b/easybuild/easyconfigs/t/topaz-em/topaz-em-0.2.5.230926-foss-2022a-CUDA-11.7.0-PyTorch-1.12.0.eb @@ -0,0 +1,63 @@ +# Thomas Hoffman, EMBL Heidelberg, structures-it@embl.de, 2023/11 +easyblock = 'PythonPackage' + +name = 'topaz-em' # named topaz-em instead of topaz to be consistent with pypi +_mainversion = '0.2.5' +_patchdate = '230926' +_patchsha = 'dadfe725efa9181e55864054f492a41b4abe8c1c' +version = '%s.%s' % (_mainversion, _patchdate) +_cudasuffix = '-CUDA-%(cudaver)s' +_pytorch_ver = '1.12.0' +_pytorchsuffix = '-PyTorch-%s' % _pytorch_ver +versionsuffix = _cudasuffix + _pytorchsuffix + +homepage = 'http://cb.csail.mit.edu/cb/topaz/' + +description = """Particle picking software for single particle cryo-electron microscopy using +convolutional neural networks and positive-unlabeled learning. Includes methods +for micrograph denoising.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +use_pip = True + +builddependencies = [ + ('pkg-config', '0.29.2'), +] +dependencies = [ + ('CUDA', '11.7.0', '', True), + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('PyTorch', _pytorch_ver, _cudasuffix), + ('scikit-learn', '1.1.2'), + ('torchvision', '0.13.1', _cudasuffix), +] + + +source_urls = [ + 'https://github.com/tbepler/topaz/archive', + 'https://github.com/tbepler/topaz/compare/' +] +sources = ['v%s.tar.gz' % _mainversion] +patches = [ + 'topaz-em-0.2.5_install_relion3_wrappers.patch', + 'v%s..%s.patch' % (_mainversion, _patchsha) +] +checksums = [ + {'v0.2.5.tar.gz': '33bba5fc071dcdf584cfc8c152ffe889a95b71ebad7ddefd15d3f81a96987417'}, + {'topaz-em-0.2.5_install_relion3_wrappers.patch': + '0fe23a0ecaf887aaa89641a7e7cf37fafd3134384b0a8f46acb4e17537d1a151'}, + {'v0.2.5..dadfe725efa9181e55864054f492a41b4abe8c1c.patch': + 'f0dc2f0613138cff856274e5367a767d97f46dd2b47ba2a932f8ca1d20b93de1'}, +] + +sanity_pip_check = True +options = {'modulename': 'topaz'} +_relion3_wrappers = ['denoise', 'pick', 'train', 'train_denoise'] +sanity_check_commands = ['run_topaz_%s.py --help' % x for x in _relion3_wrappers] + ['topaz --help'] +sanity_check_paths = { + 'files': ["bin/run_topaz_%s.py" % x for x in _relion3_wrappers], + 'dirs': [], +} + +moduleclass = 'bio' From 41b7dd2f522a939a7a978aef9ab69725f6015ca4 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Mon, 13 Nov 2023 18:36:46 +0100 Subject: [PATCH 238/599] Delete easybuild/easyconfigs/t/topaz-em/topaz-em-0.2.5.220923-foss-2022a-CUDA-11.7.0-PyTorch-1.12.0.eb --- ...3-foss-2022a-CUDA-11.7.0-PyTorch-1.12.0.eb | 67 ------------------- 1 file changed, 67 deletions(-) delete mode 100644 easybuild/easyconfigs/t/topaz-em/topaz-em-0.2.5.220923-foss-2022a-CUDA-11.7.0-PyTorch-1.12.0.eb diff --git a/easybuild/easyconfigs/t/topaz-em/topaz-em-0.2.5.220923-foss-2022a-CUDA-11.7.0-PyTorch-1.12.0.eb b/easybuild/easyconfigs/t/topaz-em/topaz-em-0.2.5.220923-foss-2022a-CUDA-11.7.0-PyTorch-1.12.0.eb deleted file mode 100644 index ff22ba3d5e6..00000000000 --- a/easybuild/easyconfigs/t/topaz-em/topaz-em-0.2.5.220923-foss-2022a-CUDA-11.7.0-PyTorch-1.12.0.eb +++ /dev/null @@ -1,67 +0,0 @@ -# Thomas Hoffman, EMBL Heidelberg, structures-it@embl.de, 2023/11 -easyblock = 'PythonPackage' - -name = 'topaz-em' # named topaz-em instead of topaz to be consistent with pypi -_mainversion = '0.2.5' -_patchdate = '2230923' -_patchsha = 'dadfe725efa9181e55864054f492a41b4abe8c1c' -version = '%s.%s' % (_mainversion, _patchdate) -_cudasuffix = '-CUDA-%(cudaver)s' -_pytorch_ver = '1.12.0' -_pytorchsuffix = '-PyTorch-%s' % _pytorch_ver -versionsuffix = _cudasuffix + _pytorchsuffix -_mainversion = '0.2.5' -_patchdate = '220923' -_patchsha = 'dadfe725efa9181e55864054f492a41b4abe8c1c' -version = '%s.%s' % (_mainversion, _patchdate) - -homepage = 'http://cb.csail.mit.edu/cb/topaz/' - -description = """Particle picking software for single particle cryo-electron microscopy using -convolutional neural networks and positive-unlabeled learning. Includes methods -for micrograph denoising.""" - -toolchain = {'name': 'foss', 'version': '2022a'} - -use_pip = True - -builddependencies = [ - ('pkg-config', '0.29.2'), -] -dependencies = [ - ('CUDA', '11.7.0', '', True), - ('Python', '3.10.4'), - ('SciPy-bundle', '2022.05'), - ('PyTorch', _pytorch_ver, _cudasuffix), - ('scikit-learn', '1.1.2'), - ('torchvision', '0.13.1', _cudasuffix), -] - - -source_urls = [ - 'https://github.com/tbepler/topaz/archive', - 'https://github.com/tbepler/topaz/compare/' -] -sources = ['v%s.tar.gz' % _mainversion] -patches = [ - 'topaz-em-0.2.5_install_relion3_wrappers.patch', - 'v%s..%s.patch' % (_mainversion, _patchsha) -] -checksums = [ - {'v0.2.5.tar.gz': '33bba5fc071dcdf584cfc8c152ffe889a95b71ebad7ddefd15d3f81a96987417'}, - {'topaz-em-0.2.5_install_relion3_wrappers.patch': - '0fe23a0ecaf887aaa89641a7e7cf37fafd3134384b0a8f46acb4e17537d1a151'}, - {'v0.2.5..dadfe725efa9181e55864054f492a41b4abe8c1c.patch': - 'f0dc2f0613138cff856274e5367a767d97f46dd2b47ba2a932f8ca1d20b93de1'}, -] - -sanity_pip_check = True -options = {'modulename': 'topaz'} -_relion3_wrappers = ['denoise', 'pick', 'train', 'train_denoise'] -sanity_check_commands = ['run_topaz_%s.py --help' % x for x in _relion3_wrappers] + ['topaz --help'] -sanity_check_paths = { - 'files': ["bin/run_topaz_%s.py" % x for x in _relion3_wrappers], - 'dirs': [], -} - -moduleclass = 'bio' From 08a692a0c7a5b8da02e507b92e79d3b06310753b Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Mon, 13 Nov 2023 18:37:06 +0100 Subject: [PATCH 239/599] Delete easybuild/easyconfigs/t/topaz-em/topaz-em-0.2.5.2230923-foss-2022a-CUDA-11.7.0-PyTorch-1.12.0.eb --- ...3-foss-2022a-CUDA-11.7.0-PyTorch-1.12.0.eb | 67 ------------------- 1 file changed, 67 deletions(-) delete mode 100644 easybuild/easyconfigs/t/topaz-em/topaz-em-0.2.5.2230923-foss-2022a-CUDA-11.7.0-PyTorch-1.12.0.eb diff --git a/easybuild/easyconfigs/t/topaz-em/topaz-em-0.2.5.2230923-foss-2022a-CUDA-11.7.0-PyTorch-1.12.0.eb b/easybuild/easyconfigs/t/topaz-em/topaz-em-0.2.5.2230923-foss-2022a-CUDA-11.7.0-PyTorch-1.12.0.eb deleted file mode 100644 index 6a7315621a1..00000000000 --- a/easybuild/easyconfigs/t/topaz-em/topaz-em-0.2.5.2230923-foss-2022a-CUDA-11.7.0-PyTorch-1.12.0.eb +++ /dev/null @@ -1,67 +0,0 @@ -# Thomas Hoffman, EMBL Heidelberg, structures-it@embl.de, 2023/1 -easyblock = 'PythonPackage' - -name = 'topaz-em' # named topaz-em instead of topaz to be consistent with pypi -_mainversion = '0.2.5' -_patchdate = '2230923' -_patchsha = 'dadfe725efa9181e55864054f492a41b4abe8c1c' -version = '%s.%s' % (_mainversion, _patchdate) -_cudasuffix = '-CUDA-%(cudaver)s' -_pytorch_ver = '1.12.0' -_pytorchsuffix = '-PyTorch-%s' % _pytorch_ver -versionsuffix = _cudasuffix + _pytorchsuffix -_mainversion = '0.2.5' -_patchdate = '2230923' -_patchsha = 'dadfe725efa9181e55864054f492a41b4abe8c1c' -version = '%s.%s' % (_mainversion, _patchdate) - -homepage = 'http://cb.csail.mit.edu/cb/topaz/' - -description = """Particle picking software for single particle cryo-electron microscopy using -convolutional neural networks and positive-unlabeled learning. Includes methods -for micrograph denoising.""" - -toolchain = {'name': 'foss', 'version': '2022a'} - -use_pip = True - -builddependencies = [ - ('pkg-config', '0.29.2'), -] -dependencies = [ - ('CUDA', '11.7.0', '', True), - ('Python', '3.10.4'), - ('SciPy-bundle', '2022.05'), - ('PyTorch', _pytorch_ver, _cudasuffix), - ('scikit-learn', '1.1.2'), - ('torchvision', '0.13.1', _cudasuffix), -] - - -source_urls = [ - 'https://github.com/tbepler/topaz/archive', - 'https://github.com/tbepler/topaz/compare/' -] -sources = ['v%s.tar.gz' % _mainversion] -patches = [ - 'topaz-em-0.2.5_install_relion3_wrappers.patch', - 'v%s..%s.patch' % (_mainversion, _patchsha) -] -checksums = [ - {'v0.2.5.tar.gz': '33bba5fc071dcdf584cfc8c152ffe889a95b71ebad7ddefd15d3f81a96987417'}, - {'topaz-em-0.2.5_install_relion3_wrappers.patch': - '0fe23a0ecaf887aaa89641a7e7cf37fafd3134384b0a8f46acb4e17537d1a151'}, - {'v0.2.5..dadfe725efa9181e55864054f492a41b4abe8c1c.patch': - 'f0dc2f0613138cff856274e5367a767d97f46dd2b47ba2a932f8ca1d20b93de1'}, -] - -sanity_pip_check = True -options = {'modulename': 'topaz'} -_relion3_wrappers = ['denoise', 'pick', 'train', 'train_denoise'] -sanity_check_commands = ['run_topaz_%s.py --help' % x for x in _relion3_wrappers] + ['topaz --help'] -sanity_check_paths = { - 'files': ["bin/run_topaz_%s.py" % x for x in _relion3_wrappers], - 'dirs': [], -} - -moduleclass = 'bio' From e6ceb42223d550e574b994c72a7c7195a99160c3 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 13 Nov 2023 17:40:20 +0000 Subject: [PATCH 240/599] adding easyconfigs: GROMACS-2023.3-foss-2022a-CUDA-11.7.0.eb, GROMACS-2023.3-foss-2022a.eb --- .../GROMACS-2023.3-foss-2022a-CUDA-11.7.0.eb | 88 +++++++++++++++++++ .../g/GROMACS/GROMACS-2023.3-foss-2022a.eb | 86 ++++++++++++++++++ 2 files changed, 174 insertions(+) create mode 100755 easybuild/easyconfigs/g/GROMACS/GROMACS-2023.3-foss-2022a-CUDA-11.7.0.eb create mode 100755 easybuild/easyconfigs/g/GROMACS/GROMACS-2023.3-foss-2022a.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.3-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.3-foss-2022a-CUDA-11.7.0.eb new file mode 100755 index 00000000000..e2b86108e93 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.3-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,88 @@ +# 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 +# * Fotis Georgatos +# * George Tsouloupas +# * Kenneth Hoste +# * Adam Huffman +# * Ake Sandgren +# * J. Sassmannshausen +# * Dugan Witherick +# * Christoph Siegert +# License:: MIT/GPL + +name = 'GROMACS' +version = '2023.3' +versionsuffix = '-CUDA-%(cudaver)s' + +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 GPU enabled build, containing both MPI and threadMPI binaries. + +It also contains the gmxapi extension for the single precision MPI build. +""" + +toolchain = {'name': 'foss', 'version': '2022a'} +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', +] +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'}, +] + +builddependencies = [ + ('CMake', '3.24.3'), + ('scikit-build', '0.15.0'), +] + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('UCX-CUDA', '1.12.1', versionsuffix), + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('networkx', '2.8.4'), +] + +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' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.3-foss-2022a.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.3-foss-2022a.eb new file mode 100755 index 00000000000..9a72a3c43d4 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.3-foss-2022a.eb @@ -0,0 +1,86 @@ +# 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 +# * Fotis Georgatos +# * George Tsouloupas +# * Kenneth Hoste +# * Adam Huffman +# * Ake Sandgren +# * J. Sassmannshausen +# * Dugan Witherick +# * Christoph Siegert +# License:: MIT/GPL + +name = 'GROMACS' +version = '2023.3' + +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. +""" + +toolchain = {'name': 'foss', 'version': '2022a'} +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', +] +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'}, +] + +builddependencies = [ + ('CMake', '3.24.3'), + ('scikit-build', '0.15.0'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('networkx', '2.8.4'), +] + +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 1e7b15e6fb6579f1ffd512db412ab6c164923274 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 13 Nov 2023 19:06:56 +0000 Subject: [PATCH 241/599] no exe --- .../g/GROMACS/GROMACS-2023.3-foss-2022a-CUDA-11.7.0.eb | 0 easybuild/easyconfigs/g/GROMACS/GROMACS-2023.3-foss-2022a.eb | 0 2 files changed, 0 insertions(+), 0 deletions(-) mode change 100755 => 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-2023.3-foss-2022a-CUDA-11.7.0.eb mode change 100755 => 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-2023.3-foss-2022a.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.3-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.3-foss-2022a-CUDA-11.7.0.eb old mode 100755 new mode 100644 diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.3-foss-2022a.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.3-foss-2022a.eb old mode 100755 new mode 100644 From 7978703a427030c957bc12420be08e077caaa7d7 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Tue, 14 Nov 2023 09:39:51 +0100 Subject: [PATCH 242/599] fix typos and duplicates --- ...opaz-em-0.2.5.230926-foss-2022a-CUDA-11.7.0-PyTorch-1.12.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/t/topaz-em/topaz-em-0.2.5.230926-foss-2022a-CUDA-11.7.0-PyTorch-1.12.0.eb b/easybuild/easyconfigs/t/topaz-em/topaz-em-0.2.5.230926-foss-2022a-CUDA-11.7.0-PyTorch-1.12.0.eb index 2adbcba0f55..a83158b339f 100644 --- a/easybuild/easyconfigs/t/topaz-em/topaz-em-0.2.5.230926-foss-2022a-CUDA-11.7.0-PyTorch-1.12.0.eb +++ b/easybuild/easyconfigs/t/topaz-em/topaz-em-0.2.5.230926-foss-2022a-CUDA-11.7.0-PyTorch-1.12.0.eb @@ -51,6 +51,7 @@ checksums = [ 'f0dc2f0613138cff856274e5367a767d97f46dd2b47ba2a932f8ca1d20b93de1'}, ] +download_dep_fail = True sanity_pip_check = True options = {'modulename': 'topaz'} _relion3_wrappers = ['denoise', 'pick', 'train', 'train_denoise'] From 0ab5d9ec0f7fc608cf7e481cd0dcd6e7a9e0d335 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Tue, 14 Nov 2023 10:51:30 +0100 Subject: [PATCH 243/599] adding easyconfigs: NVHPC-23.7-CUDA-12.2.0.eb --- .../n/NVHPC/NVHPC-23.7-CUDA-12.2.0.eb | 66 +++++++++++++++++++ 1 file changed, 66 insertions(+) create mode 100644 easybuild/easyconfigs/n/NVHPC/NVHPC-23.7-CUDA-12.2.0.eb diff --git a/easybuild/easyconfigs/n/NVHPC/NVHPC-23.7-CUDA-12.2.0.eb b/easybuild/easyconfigs/n/NVHPC/NVHPC-23.7-CUDA-12.2.0.eb new file mode 100644 index 00000000000..46f5e66cea0 --- /dev/null +++ b/easybuild/easyconfigs/n/NVHPC/NVHPC-23.7-CUDA-12.2.0.eb @@ -0,0 +1,66 @@ +name = 'NVHPC' +version = '23.7' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://developer.nvidia.com/hpc-sdk/' +description = """C, C++ and Fortran compilers included with the NVIDIA HPC SDK (previously: PGI)""" + +toolchain = SYSTEM + +local_tarball_tmpl = 'nvhpc_2023_%%(version_major)s%%(version_minor)s_Linux_%s_cuda_multi.tar.gz' +# By downloading, you accept the HPC SDK Software License Agreement +# https://docs.nvidia.com/hpc-sdk/eula/index.html +# accept_eula = True +source_urls = ['https://developer.download.nvidia.com/hpc-sdk/%(version)s/'] +sources = [local_tarball_tmpl % '%(arch)s'] +checksums = ['fea91d95ff18bca1ce7afde50371caa02001ade8bed6ddfc5ff70862ccbebece'] + +local_gccver = '12.3.0' +dependencies = [ + ('GCCcore', local_gccver), + ('binutils', '2.40', '', ('GCCcore', local_gccver)), + # This is necessary to avoid cases where just libnuma.so.1 is present in the system and -lnuma fails + ('numactl', '2.0.16', '', ('GCCcore', local_gccver)), + ('CUDA', '12.2.0', '', SYSTEM), +] + +module_add_cuda = False + +# specify default CUDA version that should be used by NVHPC +# should match one of the CUDA versions that are included with this NVHPC version +# (see install_components/Linux_x86_64/$version/cuda/) where $version is the NVHPC version +# this version can be tweaked from the EasyBuild command line with +# --try-amend=default_cuda_version="11.0" (for example) +default_cuda_version = '%(cudaver)s' + +# NVHPC EasyBlock supports some features, which can be set via CLI or this easyconfig. +# The following list gives examples for the easyconfig +# +# NVHPC needs CUDA to work. Two options are available: 1) Use NVHPC-bundled CUDA, 2) use system CUDA +# 1) Bundled CUDA +# If no easybuild dependency to CUDA is present, the bundled CUDA is taken. A version needs to be specified with +# default_cuda_version = "11.0" +# in this easyconfig file; alternatively, it can be specified through the command line during installation with +# --try-amend=default_cuda_version="10.2" +# 2) CUDA provided via EasyBuild +# Use CUDA as a dependency, for example +# dependencies = [('CUDA', '11.5.0')] +# The parameter default_cuda_version still can be set as above. +# If not set, it will be deduced from the CUDA module (via $EBVERSIONCUDA) +# +# Define a NVHPC-default Compute Capability +# cuda_compute_capabilities = "8.0" +# Can also be specified on the EasyBuild command line via --cuda-compute-capabilities=8.0 +# Only single values supported, not lists of values! +# +# Options to add/remove things to/from environment module (defaults shown) +# module_byo_compilers = False # Remove compilers from PATH (Bring-your-own compilers) +# module_nvhpc_own_mpi = False # Add NVHPC's own pre-compiled OpenMPI +# module_add_math_libs = False # Add NVHPC's math libraries (which should be there from CUDA anyway) +# module_add_profilers = False # Add NVHPC's NVIDIA Profilers +# module_add_nccl = False # Add NVHPC's NCCL library +# module_add_nvshmem = False # Add NVHPC's NVSHMEM library +# module_add_cuda = False # Add NVHPC's bundled CUDA + +# this bundle serves as a compiler-only toolchain, so it should be marked as compiler (important for HMNS) +moduleclass = 'compiler' From 7dbdd505ff8ec6bd4ae78afae78ac416f3d053bd Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 14 Nov 2023 13:11:07 +0100 Subject: [PATCH 244/599] fix possible error/crash in NCCL on x86 due to cpuid --- .../NCCL-2.10.3-GCCcore-10.3.0-CUDA-11.3.1.eb | 6 ++- .../NCCL-2.10.3-GCCcore-11.2.0-CUDA-11.4.1.eb | 6 ++- .../NCCL-2.10.3-GCCcore-11.2.0-CUDA-11.5.2.eb | 6 ++- .../n/NCCL/NCCL-2.11.4-gcccuda-2019b.eb | 6 ++- ...NCCL-2.12.12-GCCcore-11.3.0-CUDA-11.7.0.eb | 6 ++- .../NCCL-2.16.2-GCCcore-12.2.0-CUDA-12.0.0.eb | 6 ++- .../n/NCCL/NCCL-2.16.2_fix-cpuid.patch | 43 +++++++++++++++++++ .../NCCL-2.18.3-GCCcore-12.3.0-CUDA-12.1.1.eb | 7 ++- .../NCCL-2.8.3-GCCcore-10.2.0-CUDA-11.1.1.eb | 10 +++-- .../NCCL-2.8.3-GCCcore-9.3.0-CUDA-11.0.2.eb | 10 +++-- 10 files changed, 92 insertions(+), 14 deletions(-) create mode 100644 easybuild/easyconfigs/n/NCCL/NCCL-2.16.2_fix-cpuid.patch diff --git a/easybuild/easyconfigs/n/NCCL/NCCL-2.10.3-GCCcore-10.3.0-CUDA-11.3.1.eb b/easybuild/easyconfigs/n/NCCL/NCCL-2.10.3-GCCcore-10.3.0-CUDA-11.3.1.eb index 16e18e8e36e..d4fb6614198 100644 --- a/easybuild/easyconfigs/n/NCCL/NCCL-2.10.3-GCCcore-10.3.0-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/n/NCCL/NCCL-2.10.3-GCCcore-10.3.0-CUDA-11.3.1.eb @@ -11,7 +11,11 @@ toolchain = {'name': 'GCCcore', 'version': '10.3.0'} github_account = 'NVIDIA' source_urls = [GITHUB_SOURCE] sources = ['v%(version)s-1.tar.gz'] -checksums = ['55de166eb7dcab9ecef2629cdb5fb0c5ebec4fae03589c469ebe5dcb5716b3c5'] +patches = ['NCCL-2.16.2_fix-cpuid.patch'] +checksums = [ + {'v2.10.3-1.tar.gz': '55de166eb7dcab9ecef2629cdb5fb0c5ebec4fae03589c469ebe5dcb5716b3c5'}, + {'NCCL-2.16.2_fix-cpuid.patch': '0459ecadcd32b2a7a000a2ce4f675afba908b2c0afabafde585330ff4f83e277'}, +] builddependencies = [('binutils', '2.36.1')] diff --git a/easybuild/easyconfigs/n/NCCL/NCCL-2.10.3-GCCcore-11.2.0-CUDA-11.4.1.eb b/easybuild/easyconfigs/n/NCCL/NCCL-2.10.3-GCCcore-11.2.0-CUDA-11.4.1.eb index 63927a18ac1..5dec7af894e 100644 --- a/easybuild/easyconfigs/n/NCCL/NCCL-2.10.3-GCCcore-11.2.0-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/n/NCCL/NCCL-2.10.3-GCCcore-11.2.0-CUDA-11.4.1.eb @@ -11,7 +11,11 @@ toolchain = {'name': 'GCCcore', 'version': '11.2.0'} github_account = 'NVIDIA' source_urls = [GITHUB_SOURCE] sources = ['v%(version)s-1.tar.gz'] -checksums = ['55de166eb7dcab9ecef2629cdb5fb0c5ebec4fae03589c469ebe5dcb5716b3c5'] +patches = ['NCCL-2.16.2_fix-cpuid.patch'] +checksums = [ + {'v2.10.3-1.tar.gz': '55de166eb7dcab9ecef2629cdb5fb0c5ebec4fae03589c469ebe5dcb5716b3c5'}, + {'NCCL-2.16.2_fix-cpuid.patch': '0459ecadcd32b2a7a000a2ce4f675afba908b2c0afabafde585330ff4f83e277'}, +] builddependencies = [('binutils', '2.37')] diff --git a/easybuild/easyconfigs/n/NCCL/NCCL-2.10.3-GCCcore-11.2.0-CUDA-11.5.2.eb b/easybuild/easyconfigs/n/NCCL/NCCL-2.10.3-GCCcore-11.2.0-CUDA-11.5.2.eb index e3a29b13334..da1b8400a0f 100644 --- a/easybuild/easyconfigs/n/NCCL/NCCL-2.10.3-GCCcore-11.2.0-CUDA-11.5.2.eb +++ b/easybuild/easyconfigs/n/NCCL/NCCL-2.10.3-GCCcore-11.2.0-CUDA-11.5.2.eb @@ -11,7 +11,11 @@ toolchain = {'name': 'GCCcore', 'version': '11.2.0'} github_account = 'NVIDIA' source_urls = [GITHUB_SOURCE] sources = ['v%(version)s-1.tar.gz'] -checksums = ['55de166eb7dcab9ecef2629cdb5fb0c5ebec4fae03589c469ebe5dcb5716b3c5'] +patches = ['NCCL-2.16.2_fix-cpuid.patch'] +checksums = [ + {'v2.10.3-1.tar.gz': '55de166eb7dcab9ecef2629cdb5fb0c5ebec4fae03589c469ebe5dcb5716b3c5'}, + {'NCCL-2.16.2_fix-cpuid.patch': '0459ecadcd32b2a7a000a2ce4f675afba908b2c0afabafde585330ff4f83e277'}, +] builddependencies = [('binutils', '2.37')] diff --git a/easybuild/easyconfigs/n/NCCL/NCCL-2.11.4-gcccuda-2019b.eb b/easybuild/easyconfigs/n/NCCL/NCCL-2.11.4-gcccuda-2019b.eb index a80da45c38a..407de136e21 100644 --- a/easybuild/easyconfigs/n/NCCL/NCCL-2.11.4-gcccuda-2019b.eb +++ b/easybuild/easyconfigs/n/NCCL/NCCL-2.11.4-gcccuda-2019b.eb @@ -10,6 +10,10 @@ toolchain = {'name': 'gcccuda', 'version': '2019b'} github_account = 'NVIDIA' source_urls = [GITHUB_SOURCE] sources = ['v%(version)s-1.tar.gz'] -checksums = ['db4e9a0277a64f9a31ea9b5eea22e63f10faaed36dded4587bbc8a0d8eceed10'] +patches = ['NCCL-2.16.2_fix-cpuid.patch'] +checksums = [ + {'v2.11.4-1.tar.gz': 'db4e9a0277a64f9a31ea9b5eea22e63f10faaed36dded4587bbc8a0d8eceed10'}, + {'NCCL-2.16.2_fix-cpuid.patch': '0459ecadcd32b2a7a000a2ce4f675afba908b2c0afabafde585330ff4f83e277'}, +] moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NCCL/NCCL-2.12.12-GCCcore-11.3.0-CUDA-11.7.0.eb b/easybuild/easyconfigs/n/NCCL/NCCL-2.12.12-GCCcore-11.3.0-CUDA-11.7.0.eb index 2282286a915..89fcfe9a013 100644 --- a/easybuild/easyconfigs/n/NCCL/NCCL-2.12.12-GCCcore-11.3.0-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/n/NCCL/NCCL-2.12.12-GCCcore-11.3.0-CUDA-11.7.0.eb @@ -11,7 +11,11 @@ toolchain = {'name': 'GCCcore', 'version': '11.3.0'} github_account = 'NVIDIA' source_urls = [GITHUB_SOURCE] sources = ['v%(version)s-1.tar.gz'] -checksums = ['49b4fbfeebf1f62f6ceb69e72504045d8d1b4e7609e3c2477906f3004c7e2d82'] +patches = ['NCCL-2.16.2_fix-cpuid.patch'] +checksums = [ + {'v2.12.12-1.tar.gz': '49b4fbfeebf1f62f6ceb69e72504045d8d1b4e7609e3c2477906f3004c7e2d82'}, + {'NCCL-2.16.2_fix-cpuid.patch': '0459ecadcd32b2a7a000a2ce4f675afba908b2c0afabafde585330ff4f83e277'}, +] builddependencies = [('binutils', '2.38')] diff --git a/easybuild/easyconfigs/n/NCCL/NCCL-2.16.2-GCCcore-12.2.0-CUDA-12.0.0.eb b/easybuild/easyconfigs/n/NCCL/NCCL-2.16.2-GCCcore-12.2.0-CUDA-12.0.0.eb index cd576dcb0e7..17636f6fb8b 100644 --- a/easybuild/easyconfigs/n/NCCL/NCCL-2.16.2-GCCcore-12.2.0-CUDA-12.0.0.eb +++ b/easybuild/easyconfigs/n/NCCL/NCCL-2.16.2-GCCcore-12.2.0-CUDA-12.0.0.eb @@ -11,7 +11,11 @@ toolchain = {'name': 'GCCcore', 'version': '12.2.0'} github_account = 'NVIDIA' source_urls = [GITHUB_SOURCE] sources = ['v%(version)s-1.tar.gz'] -checksums = ['7f7c738511a8876403fc574d13d48e7c250d934d755598d82e14bab12236fc64'] +patches = ['NCCL-2.16.2_fix-cpuid.patch'] +checksums = [ + {'v2.16.2-1.tar.gz': '7f7c738511a8876403fc574d13d48e7c250d934d755598d82e14bab12236fc64'}, + {'NCCL-2.16.2_fix-cpuid.patch': '0459ecadcd32b2a7a000a2ce4f675afba908b2c0afabafde585330ff4f83e277'}, +] builddependencies = [('binutils', '2.39')] diff --git a/easybuild/easyconfigs/n/NCCL/NCCL-2.16.2_fix-cpuid.patch b/easybuild/easyconfigs/n/NCCL/NCCL-2.16.2_fix-cpuid.patch new file mode 100644 index 00000000000..de293c36e76 --- /dev/null +++ b/easybuild/easyconfigs/n/NCCL/NCCL-2.16.2_fix-cpuid.patch @@ -0,0 +1,43 @@ +The 2nd CPUID asm code modifies registers used by other variables due to failure to list +EBX, ECX & EDX in the "clobbers" list. +This causes corruption leading to segfaults or wrong results depending on compiler optimization/register allocation. + +Fix by using the __cpuid GCC function. +See https://github.com/NVIDIA/nccl/pull/1070 + +Author: Alexander Grund (TU Dresden) + +diff --git a/src/graph/xml.cc b/src/graph/xml.cc +index 316d20f..d0d1272 100644 +--- a/src/graph/xml.cc ++++ b/src/graph/xml.cc +@@ -12,6 +12,9 @@ + #include "core.h" + #include "nvmlwrap.h" + #include "xml.h" ++#if defined(__x86_64__) ++#include ++#endif + + /*******************/ + /* XML File Parser */ +@@ -408,7 +411,8 @@ ncclResult_t ncclTopoGetXmlFromCpu(struct ncclXmlNode* cpuNode, struct ncclXml* + char vendor[12]; + } cpuid0; + +- asm volatile("cpuid" : "=b" (cpuid0.ebx), "=c" (cpuid0.ecx), "=d" (cpuid0.edx) : "a" (0) : "memory"); ++ unsigned unused; ++ __cpuid(0, unused, cpuid0.ebx, cpuid0.ecx, cpuid0.edx); + char vendor[13]; + strncpy(vendor, cpuid0.vendor, 12); + vendor[12] = '\0'; +@@ -430,7 +434,8 @@ ncclResult_t ncclTopoGetXmlFromCpu(struct ncclXmlNode* cpuNode, struct ncclXml* + }; + uint32_t val; + } cpuid1; +- asm volatile("cpuid" : "=a" (cpuid1.val) : "a" (1) : "memory"); ++ unsigned unused; ++ __cpuid(1, cpuid1.val, unused, unused, unused); + int familyId = cpuid1.familyId + (cpuid1.extFamilyId << 4); + int modelId = cpuid1.modelId + (cpuid1.extModelId << 4); + NCCLCHECK(xmlSetAttrInt(cpuNode, "familyid", familyId)); 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 d23741aa2c8..ade0f545d36 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 @@ -11,8 +11,11 @@ toolchain = {'name': 'GCCcore', 'version': '12.3.0'} github_account = 'NVIDIA' source_urls = [GITHUB_SOURCE] sources = ['v%(version)s-1.tar.gz'] -checksums = [('6477d83c9edbb34a0ebce6d751a1b32962bc6415d75d04972b676c6894ceaef9', - 'b4f5d7d9eea2c12e32e7a06fe138b2cfc75969c6d5c473aa6f819a792db2fc96')] +patches = ['NCCL-2.16.2_fix-cpuid.patch'] +checksums = [ + {'v2.18.3-1.tar.gz': '6477d83c9edbb34a0ebce6d751a1b32962bc6415d75d04972b676c6894ceaef9'}, + {'NCCL-2.16.2_fix-cpuid.patch': '0459ecadcd32b2a7a000a2ce4f675afba908b2c0afabafde585330ff4f83e277'}, +] builddependencies = [('binutils', '2.40')] diff --git a/easybuild/easyconfigs/n/NCCL/NCCL-2.8.3-GCCcore-10.2.0-CUDA-11.1.1.eb b/easybuild/easyconfigs/n/NCCL/NCCL-2.8.3-GCCcore-10.2.0-CUDA-11.1.1.eb index 81fa9b3dfaa..3c825519ba4 100644 --- a/easybuild/easyconfigs/n/NCCL/NCCL-2.8.3-GCCcore-10.2.0-CUDA-11.1.1.eb +++ b/easybuild/easyconfigs/n/NCCL/NCCL-2.8.3-GCCcore-10.2.0-CUDA-11.1.1.eb @@ -16,10 +16,14 @@ dependencies = [('CUDAcore', local_cuda_version, '', SYSTEM)] github_account = 'NVIDIA' source_urls = [GITHUB_SOURCE] sources = ['v%(version)s-1.tar.gz'] -patches = ['NCCL-2.8.3_fix-isend-irecv.patch'] +patches = [ + 'NCCL-2.8.3_fix-isend-irecv.patch', + 'NCCL-2.16.2_fix-cpuid.patch', +] checksums = [ - '3ae89ddb2956fff081e406a94ff54ae5e52359f5d645ce977c7eba09b3b782e6', # v2.8.3-1.tar.gz - '04d61ea9b9f0954bed05494017649a68950b6b5e5851d969244f9ab67d5ecc92', # NCCL-2.8.3_fix-isend-irecv.patch + {'v2.8.3-1.tar.gz': '3ae89ddb2956fff081e406a94ff54ae5e52359f5d645ce977c7eba09b3b782e6'}, + {'NCCL-2.8.3_fix-isend-irecv.patch': '04d61ea9b9f0954bed05494017649a68950b6b5e5851d969244f9ab67d5ecc92'}, + {'NCCL-2.16.2_fix-cpuid.patch': '0459ecadcd32b2a7a000a2ce4f675afba908b2c0afabafde585330ff4f83e277'}, ] moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NCCL/NCCL-2.8.3-GCCcore-9.3.0-CUDA-11.0.2.eb b/easybuild/easyconfigs/n/NCCL/NCCL-2.8.3-GCCcore-9.3.0-CUDA-11.0.2.eb index 140a12a4575..700f896be0e 100644 --- a/easybuild/easyconfigs/n/NCCL/NCCL-2.8.3-GCCcore-9.3.0-CUDA-11.0.2.eb +++ b/easybuild/easyconfigs/n/NCCL/NCCL-2.8.3-GCCcore-9.3.0-CUDA-11.0.2.eb @@ -16,10 +16,14 @@ dependencies = [('CUDAcore', local_cuda_version, '', SYSTEM)] github_account = 'NVIDIA' source_urls = [GITHUB_SOURCE] sources = ['v%(version)s-1.tar.gz'] -patches = ['NCCL-2.8.3_fix-isend-irecv.patch'] +patches = [ + 'NCCL-2.8.3_fix-isend-irecv.patch', + 'NCCL-2.16.2_fix-cpuid.patch', +] checksums = [ - '3ae89ddb2956fff081e406a94ff54ae5e52359f5d645ce977c7eba09b3b782e6', # v2.8.3-1.tar.gz - '04d61ea9b9f0954bed05494017649a68950b6b5e5851d969244f9ab67d5ecc92', # NCCL-2.8.3_fix-isend-irecv.patch + {'v2.8.3-1.tar.gz': '3ae89ddb2956fff081e406a94ff54ae5e52359f5d645ce977c7eba09b3b782e6'}, + {'NCCL-2.8.3_fix-isend-irecv.patch': '04d61ea9b9f0954bed05494017649a68950b6b5e5851d969244f9ab67d5ecc92'}, + {'NCCL-2.16.2_fix-cpuid.patch': '0459ecadcd32b2a7a000a2ce4f675afba908b2c0afabafde585330ff4f83e277'}, ] moduleclass = 'lib' From 79847f8e6764d4897df03dd6db5d53ffa7cadf7e Mon Sep 17 00:00:00 2001 From: Adam Huffman <12435+verdurin@users.noreply.github.com> Date: Tue, 14 Nov 2023 16:54:04 +0000 Subject: [PATCH 245/599] adding easyconfigs: Restrander-20230713-GCCcore-12.2.0.eb --- .../Restrander-20230713-GCCcore-12.2.0.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/r/Restrander/Restrander-20230713-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/r/Restrander/Restrander-20230713-GCCcore-12.2.0.eb b/easybuild/easyconfigs/r/Restrander/Restrander-20230713-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..2cedafa4643 --- /dev/null +++ b/easybuild/easyconfigs/r/Restrander/Restrander-20230713-GCCcore-12.2.0.eb @@ -0,0 +1,37 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'MakeCp' + +name = 'Restrander' +# No release or tag, so using the date of the last commit +version = '20230713' +github_account = 'mritchielab' +local_commit = '54a61fa' + +homepage = "https://github.com/mritchielab/restrander" +description = "A fast, accurate program for orienting and quality-checking cDNA sequencing reads." + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/%(github_account)s/%(name)s/archive/'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['8b23c9992f81896b54d73c05b447f9002fe9482d848de16e1622e09961196237'] + +builddependencies = [ + ('binutils', '2.39'), +] + +files_to_copy = [ + (["restrander"], "bin/"), + 'README.md', + 'config', + 'figures', + 'LICENSE', +] + +sanity_check_paths = { + 'files': ['bin/restrander', 'README.md'], + 'dirs': ['config', 'figures'], +} + +moduleclass = 'bio' From 5cc18b8d21cdd90e3dcab5c5c1958fcc07dcd3bd Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Wed, 15 Nov 2023 13:56:43 +0000 Subject: [PATCH 246/599] adding easyconfigs: STAR-2.7.11a-GCC-12.2.0.eb --- .../s/STAR/STAR-2.7.11a-GCC-12.2.0.eb | 51 +++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/s/STAR/STAR-2.7.11a-GCC-12.2.0.eb 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 new file mode 100644 index 00000000000..42f094bb67b --- /dev/null +++ b/easybuild/easyconfigs/s/STAR/STAR-2.7.11a-GCC-12.2.0.eb @@ -0,0 +1,51 @@ +# 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 = '2.7.11a' + +homepage = 'https://github.com/alexdobin/STAR' +description = "STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays." + +toolchain = {'name': 'GCC', 'version': '12.2.0'} +toolchainopts = {'openmp': True} + +github_account = 'alexdobin' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +patches = ['STAR-%(version)s_use-external-htslib.patch'] +checksums = [ + {'%(version)s.tar.gz': '542457b1a4fee73f27a581b1776e9f73ad2b4d7e790388b6dc71147bd039f99a'}, + {'STAR-%(version)s_use-external-htslib.patch': '2fdc3ed9372d983f77d861d6f16a60a553598358dce9ff8216f96eb20e63ce4e'}, +] + +dependencies = [ + ('HTSlib', '1.17'), + ('zlib', '1.2.12'), +] + +start_dir = 'source' + +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 a64b19e3202c9b4c8a3667e73269782cea696511 Mon Sep 17 00:00:00 2001 From: "A.H. Kole" Date: Wed, 15 Nov 2023 15:09:10 +0100 Subject: [PATCH 247/599] adding easyconfigs: libfdf-0.5.0-GCC-11.3.0.eb --- .../l/libfdf/libfdf-0.5.0-GCC-11.3.0.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/l/libfdf/libfdf-0.5.0-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/l/libfdf/libfdf-0.5.0-GCC-11.3.0.eb b/easybuild/easyconfigs/l/libfdf/libfdf-0.5.0-GCC-11.3.0.eb new file mode 100644 index 00000000000..245b4e41e57 --- /dev/null +++ b/easybuild/easyconfigs/l/libfdf/libfdf-0.5.0-GCC-11.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'CMakeMake' + +name = 'libfdf' +version = '0.5.0' + +homepage = 'https://gitlab.com/siesta-project/libraries/libfdf' +description = """LibFDF is the official implementation of the FDF specifications for use in client codes.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://gitlab.com/siesta-project/libraries/libfdf/-/archive/%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['a8ac07a0d27ec9a96ee0691221cee8a18b5c60aaa001fcdc6858a9bfa0782f5f'] + +builddependencies = [ + ('CMake', '3.23.1'), +] + +sanity_check_paths = { + 'files': ['lib/libfdf.a'], + 'dirs': ['include', 'lib/pkgconfig', 'lib/cmake/libfdf'], +} + +runtest = 'test' + +moduleclass = 'data' From 44a8fc58426c01e4bdfed5475e1d738fec8f8eb1 Mon Sep 17 00:00:00 2001 From: "A.H. Kole" Date: Wed, 15 Nov 2023 15:25:19 +0100 Subject: [PATCH 248/599] adding easyconfigs: flook-0.8.1-GCC-11.3.0.eb and patches: flook-0.8.1_flook.pc.in.patch --- .../f/flook/flook-0.8.1-GCC-11.3.0.eb | 33 +++++++++++++++++++ .../f/flook/flook-0.8.1_flook.pc.in.patch | 11 +++++++ 2 files changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/f/flook/flook-0.8.1-GCC-11.3.0.eb create mode 100644 easybuild/easyconfigs/f/flook/flook-0.8.1_flook.pc.in.patch diff --git a/easybuild/easyconfigs/f/flook/flook-0.8.1-GCC-11.3.0.eb b/easybuild/easyconfigs/f/flook/flook-0.8.1-GCC-11.3.0.eb new file mode 100644 index 00000000000..3c6df83f972 --- /dev/null +++ b/easybuild/easyconfigs/f/flook/flook-0.8.1-GCC-11.3.0.eb @@ -0,0 +1,33 @@ +name = 'flook' +version = '0.8.1' + +homepage = 'https://github.com/ElectronicStructureLibrary/flook' +description = """The fortran-Lua-hook library.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://github.com/ElectronicStructureLibrary/flook/archive/'] +sources = ['v%(version)s/flook-%(version)s.tar.gz'] +patches = [ + ('flook-%(version)s_setup.make', './setup.make'), + 'flook-%(version)s_flook.pc.in.patch', +] +checksums = [ + {'flook-0.8.1.tar.gz': 'beb15b8cb57b7a2facc7a5094326aaa877fda4fe35f8aabac023232c2e12d97e'}, + {'flook-0.8.1_setup.make': '6df3f53faa8a8fe61534ded997c5e748d0327c13b18972fbbf49eacbda30d6e0'}, + {'flook-0.8.1_flook.pc.in.patch': '1aa3635d83f0f9bad2ef2f9457183aefa94c8f07e66d3ef31e8897190752b42c'}, +] + +dependencies = [('Lua', '5.4.4')] + +parallel = 1 + +local_comp_flags = 'VENDOR="gnu" FFLAGS="$FFLAGS" CFLAGS="$CFLAGS"' +buildopts = 'liball %s' % local_comp_flags + +sanity_check_paths = { + 'files': ['include/flook.mod', 'lib/libflook.a', 'lib/libflookall.a'], + 'dirs': [], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/f/flook/flook-0.8.1_flook.pc.in.patch b/easybuild/easyconfigs/f/flook/flook-0.8.1_flook.pc.in.patch new file mode 100644 index 00000000000..86e8375df05 --- /dev/null +++ b/easybuild/easyconfigs/f/flook/flook-0.8.1_flook.pc.in.patch @@ -0,0 +1,11 @@ +diff --git a/flook.pc.in b/flook.pc.in +index 680b5e0..b46f8ad 100644 +--- a/flook.pc.in ++++ b/flook.pc.in +@@ -10,5 +10,5 @@ Version: @PROJECT_VERSION@ + URL: https://github.com/ElectronicStructureLibrary/flook + Cflags: -I${includedir} + Libs.private: -ldl +-Libs: -L${libdir} -lflookall ++Libs: -L${libdir} -lflookall -llua -ldl + From 6ebaa42549951a915b81733e89cfd20578117805 Mon Sep 17 00:00:00 2001 From: Sam Moors Date: Wed, 15 Nov 2023 15:37:39 +0100 Subject: [PATCH 249/599] remove empty lines --- easybuild/easyconfigs/c/castor/castor-1.7.11-foss-2022a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/c/castor/castor-1.7.11-foss-2022a.eb b/easybuild/easyconfigs/c/castor/castor-1.7.11-foss-2022a.eb index 48f2a840462..5095a3d9cb2 100644 --- a/easybuild/easyconfigs/c/castor/castor-1.7.11-foss-2022a.eb +++ b/easybuild/easyconfigs/c/castor/castor-1.7.11-foss-2022a.eb @@ -14,7 +14,6 @@ fitting and simulating diversification models, dating trees, comparing trees, an reading/writing trees in Newick format. """ - toolchain = {'name': 'foss', 'version': '2022a'} source_urls = [ From 18a25c8111b45828eb59e2b5fcefeb0101c47a06 Mon Sep 17 00:00:00 2001 From: "A.H. Kole" Date: Wed, 15 Nov 2023 16:04:10 +0100 Subject: [PATCH 250/599] Moved sanity check and buildopts to easyblock --- .../easyconfigs/f/flook/flook-0.8.1-GCC-11.3.0.eb | 10 ---------- 1 file changed, 10 deletions(-) diff --git a/easybuild/easyconfigs/f/flook/flook-0.8.1-GCC-11.3.0.eb b/easybuild/easyconfigs/f/flook/flook-0.8.1-GCC-11.3.0.eb index 3c6df83f972..aeab9ee569a 100644 --- a/easybuild/easyconfigs/f/flook/flook-0.8.1-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/f/flook/flook-0.8.1-GCC-11.3.0.eb @@ -20,14 +20,4 @@ checksums = [ dependencies = [('Lua', '5.4.4')] -parallel = 1 - -local_comp_flags = 'VENDOR="gnu" FFLAGS="$FFLAGS" CFLAGS="$CFLAGS"' -buildopts = 'liball %s' % local_comp_flags - -sanity_check_paths = { - 'files': ['include/flook.mod', 'lib/libflook.a', 'lib/libflookall.a'], - 'dirs': [], -} - moduleclass = 'data' From 3140cc08c6ae5a89aaf23764d16d2d2f257e770a Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Wed, 15 Nov 2023 17:02:58 +0100 Subject: [PATCH 251/599] rename; bugfix patch --- ...m-0.2.5.20230926-foss-2022a-CUDA-11.7.0.eb | 61 + ...e725efa9181e55864054f492a41b4abe8c1c.patch | 8128 +++++++++++++++++ 2 files changed, 8189 insertions(+) create mode 100644 easybuild/easyconfigs/t/topaz-em/topaz-em-0.2.5.20230926-foss-2022a-CUDA-11.7.0.eb create mode 100644 easybuild/easyconfigs/t/topaz-em/v0.2.5..dadfe725efa9181e55864054f492a41b4abe8c1c.patch diff --git a/easybuild/easyconfigs/t/topaz-em/topaz-em-0.2.5.20230926-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/t/topaz-em/topaz-em-0.2.5.20230926-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 00000000000..526b8270dda --- /dev/null +++ b/easybuild/easyconfigs/t/topaz-em/topaz-em-0.2.5.20230926-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,61 @@ +# Thomas Hoffman, EMBL Heidelberg, structures-it@embl.de, 2023/11 +easyblock = 'PythonPackage' + +name = 'topaz-em' # named topaz-em instead of topaz to be consistent with pypi +_mainversion = '0.2.5' +_patchdate = '20230926' +_patchsha = 'dadfe725efa9181e55864054f492a41b4abe8c1c' +version = '%s.%s' % (_mainversion, _patchdate) +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'http://cb.csail.mit.edu/cb/topaz/' + +description = """Particle picking software for single particle cryo-electron microscopy using +convolutional neural networks and positive-unlabeled learning. Includes methods +for micrograph denoising.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +use_pip = True + +builddependencies = [ + ('pkg-config', '0.29.2'), +] +dependencies = [ + ('CUDA', '11.7.0', '', True), + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('PyTorch', '1.12.0', versionsuffix), + ('scikit-learn', '1.1.2'), + ('torchvision', '0.13.1', versionsuffix), +] + + +source_urls = [ + 'https://github.com/tbepler/topaz/archive', + 'https://github.com/tbepler/topaz/compare/' +] +sources = ['v%s.tar.gz' % _mainversion] +patches = [ + 'topaz-em-0.2.5_install_relion3_wrappers.patch', + 'v%s..%s.patch' % (_mainversion, _patchsha) +] +checksums = [ + {'v0.2.5.tar.gz': '33bba5fc071dcdf584cfc8c152ffe889a95b71ebad7ddefd15d3f81a96987417'}, + {'topaz-em-0.2.5_install_relion3_wrappers.patch': + '0fe23a0ecaf887aaa89641a7e7cf37fafd3134384b0a8f46acb4e17537d1a151'}, + {'v0.2.5..dadfe725efa9181e55864054f492a41b4abe8c1c.patch': + 'f0dc2f0613138cff856274e5367a767d97f46dd2b47ba2a932f8ca1d20b93de1'}, +] + +download_dep_fail = True +sanity_pip_check = True +options = {'modulename': 'topaz'} +_relion3_wrappers = ['denoise', 'pick', 'train', 'train_denoise'] +sanity_check_commands = ['run_topaz_%s.py --help' % x for x in _relion3_wrappers] + ['topaz --help'] +sanity_check_paths = { + 'files': ["bin/run_topaz_%s.py" % x for x in _relion3_wrappers], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/topaz-em/v0.2.5..dadfe725efa9181e55864054f492a41b4abe8c1c.patch b/easybuild/easyconfigs/t/topaz-em/v0.2.5..dadfe725efa9181e55864054f492a41b4abe8c1c.patch new file mode 100644 index 00000000000..75d8b088944 --- /dev/null +++ b/easybuild/easyconfigs/t/topaz-em/v0.2.5..dadfe725efa9181e55864054f492a41b4abe8c1c.patch @@ -0,0 +1,8128 @@ +From 512ff354295d28c884ce0934f51705029bc78be9 Mon Sep 17 00:00:00 2001 +From: Darnell Granberry <40174000+DarnellGranberry@users.noreply.github.com> +Date: Fri, 11 Mar 2022 17:29:16 -0500 +Subject: [PATCH 01/28] BasicConv test file, sphinx quickstart + +--- + docs/Makefile | 20 ++++++++++++++ + docs/make.bat | 35 ++++++++++++++++++++++++ + docs/source/conf.py | 57 +++++++++++++++++++++++++++++++++++++++ + docs/source/index.md | 18 +++++++++++++ + test/models/test_basic.py | 35 ++++++++++++++++++++++++ + test/topaz/test_mrc.py | 21 +++++++++++++++ + 6 files changed, 186 insertions(+) + create mode 100644 docs/Makefile + create mode 100644 docs/make.bat + create mode 100644 docs/source/conf.py + create mode 100644 docs/source/index.md + +diff --git a/docs/Makefile b/docs/Makefile +new file mode 100644 +index 0000000..d0c3cbf +--- /dev/null ++++ b/docs/Makefile +@@ -0,0 +1,20 @@ ++# Minimal makefile for Sphinx documentation ++# ++ ++# You can set these variables from the command line, and also ++# from the environment for the first two. ++SPHINXOPTS ?= ++SPHINXBUILD ?= sphinx-build ++SOURCEDIR = source ++BUILDDIR = build ++ ++# Put it first so that "make" without argument is like "make help". ++help: ++ @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) ++ ++.PHONY: help Makefile ++ ++# Catch-all target: route all unknown targets to Sphinx using the new ++# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS). ++%: Makefile ++ @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) +diff --git a/docs/make.bat b/docs/make.bat +new file mode 100644 +index 0000000..061f32f +--- /dev/null ++++ b/docs/make.bat +@@ -0,0 +1,35 @@ ++@ECHO OFF ++ ++pushd %~dp0 ++ ++REM Command file for Sphinx documentation ++ ++if "%SPHINXBUILD%" == "" ( ++ set SPHINXBUILD=sphinx-build ++) ++set SOURCEDIR=source ++set BUILDDIR=build ++ ++if "%1" == "" goto help ++ ++%SPHINXBUILD% >NUL 2>NUL ++if errorlevel 9009 ( ++ echo. ++ echo.The 'sphinx-build' command was not found. Make sure you have Sphinx ++ echo.installed, then set the SPHINXBUILD environment variable to point ++ echo.to the full path of the 'sphinx-build' executable. Alternatively you ++ echo.may add the Sphinx directory to PATH. ++ echo. ++ echo.If you don't have Sphinx installed, grab it from ++ echo.https://www.sphinx-doc.org/ ++ exit /b 1 ++) ++ ++%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% ++goto end ++ ++:help ++%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% ++ ++:end ++popd +diff --git a/docs/source/conf.py b/docs/source/conf.py +new file mode 100644 +index 0000000..3651199 +--- /dev/null ++++ b/docs/source/conf.py +@@ -0,0 +1,57 @@ ++# Configuration file for the Sphinx documentation builder. ++# ++# This file only contains a selection of the most common options. For a full ++# list see the documentation: ++# https://www.sphinx-doc.org/en/master/usage/configuration.html ++ ++# -- Path setup -------------------------------------------------------------- ++ ++# If extensions (or modules to document with autodoc) are in another directory, ++# add these directories to sys.path here. If the directory is relative to the ++# documentation root, use os.path.abspath to make it absolute, like shown here. ++# ++# import os ++# import sys ++# sys.path.insert(0, os.path.abspath('.')) ++import sphinx_rtd_theme ++ ++ ++# -- Project information ----------------------------------------------------- ++ ++project = 'Topaz' ++copyright = '2022, Tristan Bepler, Alex Noble, Darnell Granberry' ++author = 'Tristan Bepler, Alex Noble, Darnell Granberry' ++ ++# The full version, including alpha/beta/rc tags ++release = '0.2.5' ++ ++ ++# -- General configuration --------------------------------------------------- ++ ++# Add any Sphinx extension module names here, as strings. They can be ++# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom ++# ones. ++extensions = [ ++ "myst_parser", ++] ++ ++# Add any paths that contain templates here, relative to this directory. ++templates_path = ['_templates'] ++ ++# List of patterns, relative to source directory, that match files and ++# directories to ignore when looking for source files. ++# This pattern also affects html_static_path and html_extra_path. ++exclude_patterns = [] ++ ++ ++# -- Options for HTML output ------------------------------------------------- ++ ++# The theme to use for HTML and HTML Help pages. See the documentation for ++# a list of builtin themes. ++# ++html_theme = 'sphinx_rtd_theme' ++ ++# Add any paths that contain custom static files (such as style sheets) here, ++# relative to this directory. They are copied after the builtin static files, ++# so a file named "default.css" will overwrite the builtin "default.css". ++html_static_path = ['_static'] +diff --git a/docs/source/index.md b/docs/source/index.md +new file mode 100644 +index 0000000..71ef567 +--- /dev/null ++++ b/docs/source/index.md +@@ -0,0 +1,18 @@ ++% Topaz documentation master file, created by ++% sphinx-quickstart on Fri Mar 11 15:57:59 2022. ++% You can adapt this file completely to your liking, but it should at least ++% contain the root `toctree` directive. ++ ++# Welcome to Topaz's documentation! ++ ++ ++```{include} ../../README.md ++:relative-images: ++``` ++ ++ ++ ++```{toctree} ++:caption: 'Contents:' ++:maxdepth: 2 ++``` +diff --git a/test/models/test_basic.py b/test/models/test_basic.py +index e69de29..bacc895 100644 +--- a/test/models/test_basic.py ++++ b/test/models/test_basic.py +@@ -0,0 +1,35 @@ ++from re import L ++import numpy as np ++from topaz.model.features.basic import BasicConv, Conv63, Conv127 ++ ++ ++class TestBasicConv(): ++ ++ def test_init(): ++ layers = [5] ++ units = [5] ++ model = BasicConv(layers, units) ++ ++ ++ def test_fill(): ++ pass ++ ++ ++ def test_unfill(): ++ pass ++ ++ ++ def test_forward(): ++ pass ++ ++ ++ ++class TestConv127(): ++ def test_conv127(): ++ pass ++ ++ ++ ++class TestConv63(): ++ def test_conv63(): ++ pass +\ No newline at end of file +diff --git a/test/topaz/test_mrc.py b/test/topaz/test_mrc.py +index e69de29..8aa55f5 100644 +--- a/test/topaz/test_mrc.py ++++ b/test/topaz/test_mrc.py +@@ -0,0 +1,21 @@ ++from topaz.mrc import get_mode, make_header, parse, write ++ ++ ++def test_parse(): ++ path = 'test/test_data/EMPIAR-10025/rawdata/micrographs/14sep05c_c_00003gr_00014sq_00004hl_00004es_c.mrc' ++ with open(path, 'rb') as f: ++ content = f.read() ++ image, header, extended_header = parse(content) ++ assert len(header) == 49 ++ ++ ++def test_get_mode(): ++ pass ++ ++ ++def test_make_header(): ++ pass ++ ++ ++def test_write(): ++ pass +\ No newline at end of file + +From 9e0f4d95a224903aba1465aee60e1aeb0746c6ef Mon Sep 17 00:00:00 2001 +From: Darnell Granberry <40174000+DarnellGranberry@users.noreply.github.com> +Date: Tue, 15 Mar 2022 20:52:50 -0400 +Subject: [PATCH 02/28] Created more doc pages for RTD + +--- + .readthedocs.yaml | 21 +++++ + docs/source/commands.md | 15 ++++ + docs/source/conf.py | 2 + + docs/source/cryosparc.md | 1 + + docs/source/description.md | 12 +++ + docs/source/index.md | 11 ++- + docs/source/installation.md | 172 ++++++++++++++++++++++++++++++++++++ + docs/source/models.md | 11 +++ + docs/source/relion.md | 1 + + docs/source/scripts.md | 1 + + docs/source/tutorial.md | 15 ++++ + topaz/model/classifier.py | 9 ++ + 12 files changed, 269 insertions(+), 2 deletions(-) + create mode 100644 .readthedocs.yaml + create mode 100644 docs/source/commands.md + create mode 100644 docs/source/cryosparc.md + create mode 100644 docs/source/description.md + create mode 100644 docs/source/installation.md + create mode 100644 docs/source/models.md + create mode 100644 docs/source/relion.md + create mode 100644 docs/source/scripts.md + create mode 100644 docs/source/tutorial.md + +diff --git a/.readthedocs.yaml b/.readthedocs.yaml +new file mode 100644 +index 0000000..b67d3bf +--- /dev/null ++++ b/.readthedocs.yaml +@@ -0,0 +1,21 @@ ++version: 2 ++ ++build: ++ os: "ubuntu-20.04" ++ tools: ++ python: "3.9" ++ ++sphinx: ++ configuration: docs/source/conf.py ++ ++python: ++ install: ++ - method: pip ++ path: . ++ extra_requirements: ++ - docs ++ - nbsphinx ++ - sphinx_rtd_theme ++ - sphinx-autobuild ++ - rst-to-myst ++ - myst-parser +\ No newline at end of file +diff --git a/docs/source/commands.md b/docs/source/commands.md +new file mode 100644 +index 0000000..44c4a21 +--- /dev/null ++++ b/docs/source/commands.md +@@ -0,0 +1,15 @@ ++# Topaz Commands ++ ++## downsample ++ ++## normalize ++ ++## preprocess ++ ++## train ++ ++## segment ++ ++## extract ++ ++## precision_recall_curve +diff --git a/docs/source/conf.py b/docs/source/conf.py +index 3651199..cac08bc 100644 +--- a/docs/source/conf.py ++++ b/docs/source/conf.py +@@ -33,6 +33,8 @@ + # ones. + extensions = [ + "myst_parser", ++ "nbsphinx", ++ "sphinx.ext.autodoc" + ] + + # Add any paths that contain templates here, relative to this directory. +diff --git a/docs/source/cryosparc.md b/docs/source/cryosparc.md +new file mode 100644 +index 0000000..789bd78 +--- /dev/null ++++ b/docs/source/cryosparc.md +@@ -0,0 +1 @@ ++## Use with CryoSPARC +\ No newline at end of file +diff --git a/docs/source/description.md b/docs/source/description.md +new file mode 100644 +index 0000000..dc12170 +--- /dev/null ++++ b/docs/source/description.md +@@ -0,0 +1,12 @@ ++# Topaz ++A pipeline for particle detection in cryo-electron microscopy images using convolutional neural networks trained from positive and unlabeled examples. Topaz also includes methods for micrograph and tomogram denoising using deep denoising models. ++ ++**Check out our [Discussion](https://github.com/tbepler/topaz/discussions) section for general help, suggestions, and tips on using Topaz.** ++ ++ +\ No newline at end of file +diff --git a/docs/source/index.md b/docs/source/index.md +index 71ef567..1ab1b7c 100644 +--- a/docs/source/index.md ++++ b/docs/source/index.md +@@ -6,8 +6,7 @@ + # Welcome to Topaz's documentation! + + +-```{include} ../../README.md +-:relative-images: ++```{include} ./description.md + ``` + + +@@ -15,4 +14,12 @@ + ```{toctree} + :caption: 'Contents:' + :maxdepth: 2 ++ ++installation ++tutorial ++commands ++relion ++cryosparc ++models ++scripts + ``` +diff --git a/docs/source/installation.md b/docs/source/installation.md +new file mode 100644 +index 0000000..fc4a774 +--- /dev/null ++++ b/docs/source/installation.md +@@ -0,0 +1,172 @@ ++# Installation ++ ++**
(Recommended) Click here to install *using Anaconda*

** ++ ++If you do not have the Anaconda python distribution, [please install it following the instructions on their website](https://www.anaconda.com/download). ++ ++We strongly recommend installing Topaz into a separate conda environment. To create a conda environment for Topaz: ++``` ++conda create -n topaz python=3.6 # or 2.7 if you prefer python 2 ++source activate topaz # this changes to the topaz conda environment, 'conda activate topaz' can be used with anaconda >= 4.4 if properly configured ++# source deactivate # returns to the base conda environment ++``` ++More information on conda environments can be found [here](https://conda.io/docs/user-guide/tasks/manage-environments.html). ++ ++## Install Topaz ++ ++To install the precompiled Topaz package and its dependencies, including pytorch: ++``` ++conda install topaz -c tbepler -c pytorch ++``` ++This installs pytorch from the official channel. To install pytorch for specific cuda versions, you will need to add the 'cudatoolkit=X.X' package. E.g. to install pytorch for CUDA 9.0: ++``` ++conda install cudatoolkit=9.0 -c pytorch ++``` ++or combined into a single command: ++``` ++conda install topaz cudatoolkit=9.0 -c tbepler -c pytorch ++``` ++See [here](https://pytorch.org/get-started/locally/) for additional pytorch installation instructions. ++ ++That's it! Topaz is now installed in your anaconda environment. ++ ++

++ ++**
Click here to install *using Pip*

** ++ ++We strongly recommend installing Topaz into a _virtual environment_. See [installation instructions](https://virtualenv.pypa.io/en/latest/installation/) and [user guide](https://virtualenv.pypa.io/en/latest/userguide/) for virtualenv. ++ ++### Install Topaz ++ ++To install Topaz for Python 3.X ++``` ++pip3 install topaz-em ++``` ++ ++for Python 2.7 ++``` ++pip install topaz-em ++``` ++See [here](https://pytorch.org/get-started/locally/) for additional pytorch installation instructions, including how to install pytorch for specific CUDA versions. ++ ++That's it! Topaz is now installed through pip. ++ ++

++ ++**
Click here to install *using Docker*

** ++ ++**

Do you have Docker installed? If not, *click here*

** ++ ++#### Linux/MacOS    *(command line)* ++ ++Download and install Docker 1.21 or greater for [Linux](https://docs.docker.com/engine/installation/) or [MacOS](https://store.docker.com/editions/community/docker-ce-desktop-mac). ++ ++> Consider using a Docker 'convenience script' to install (search on your OS's Docker installation webpage). ++ ++Launch docker according to your Docker engine's instructions, typically ``docker start``. ++ ++> **Note:** You must have sudo or root access to *install* Docker. If you do not wish to *run* Docker as sudo/root, you need to configure user groups as described here: https://docs.docker.com/install/linux/linux-postinstall/ ++ ++#### Windows    *(GUI & command line)* ++ ++Download and install [Docker Toolbox for Windows](https://docs.docker.com/toolbox/toolbox_install_windows/). ++ ++Launch Kitematic. ++ ++> If on first startup Kitematic displays a red error suggesting that you run using VirtualBox, do so. ++ ++> **Note:** [Docker Toolbox for MacOS](https://docs.docker.com/toolbox/toolbox_install_mac/) has not yet been tested. ++ ++ ++### What is Docker? ++ ++[This tutorial explains why Docker is useful.](https://www.youtube.com/watch?v=YFl2mCHdv24) ++ ++ ++ ++A Dockerfile is provided to build images with CUDA support. Build from the github repo: ++``` ++docker build -t topaz https://github.com/tbepler/topaz.git ++``` ++ ++or download the source code and build from the source directory ++``` ++git clone https://github.com/tbepler/topaz ++cd topaz ++docker build -t topaz . ++``` ++ ++

++ ++ ++**
Click here to install *using Singularity*

** ++ ++A prebuilt Singularity image for Topaz is available [here](https://singularity-hub.org/collections/2413) and can be installed with: ++``` ++singularity pull shub://nysbc/topaz ++``` ++ ++Then, you can run topaz from within the singularity image with (paths must be changed appropriately): ++``` ++singularity exec --nv -B /mounted_path:/mounted_path /path/to/singularity/container/topaz_latest.sif /usr/local/conda/bin/topaz ++``` ++ ++

++ ++ ++**
Click here to install *from source*

** ++ ++_Recommended: install Topaz into a virtual Python environment_ ++See https://conda.io/docs/user-guide/tasks/manage-environments.html or https://virtualenv.pypa.io/en/stable/ for setting one up. ++ ++#### Install the dependencies ++ ++Tested with python 3.6 and 2.7 ++ ++- pytorch (>= 1.0.0) ++- torchvision ++- pillow (>= 6.2.0) ++- numpy (>= 1.11) ++- pandas (>= 0.20.3) ++- scipy (>= 0.19.1) ++- scikit-learn (>= 0.19.0) ++ ++Easy installation of dependencies with conda ++``` ++conda install numpy pandas scikit-learn ++conda install -c pytorch pytorch torchvision ++``` ++For more info on installing pytorch for your CUDA version see https://pytorch.org/get-started/locally/ ++ ++#### Download the source code ++``` ++git clone https://github.com/tbepler/topaz ++``` ++ ++#### Install Topaz ++ ++Move to the source code directory ++``` ++cd topaz ++``` ++ ++By default, this will be the most recent version of the topaz source code. To install a specific older version, checkout that commit. For example, for v0.1.0 of Topaz: ++``` ++git checkout v0.1.0 ++``` ++Note that older Topaz versions may have different dependencies. Refer to the README for the specific Topaz version. ++ ++Install Topaz into your Python path including the topaz command line interface ++``` ++pip install . ++``` ++ ++To install for development use ++``` ++pip install -e . ++``` ++ ++

++

++ ++Topaz is also available through [SBGrid](https://sbgrid.org/software/titles/topaz). +\ No newline at end of file +diff --git a/docs/source/models.md b/docs/source/models.md +new file mode 100644 +index 0000000..574c6fb +--- /dev/null ++++ b/docs/source/models.md +@@ -0,0 +1,11 @@ ++# Models ++ ++```{eval-rst} ++.. autoclass:: topaz.model.classifier.LinearClassifier ++``` ++ ++## Features ++ ++```{eval-rst} ++.. autoclass:: topaz.model.features.basic.BasicConv ++``` +\ No newline at end of file +diff --git a/docs/source/relion.md b/docs/source/relion.md +new file mode 100644 +index 0000000..7c94e56 +--- /dev/null ++++ b/docs/source/relion.md +@@ -0,0 +1 @@ ++## Use with RELION +\ No newline at end of file +diff --git a/docs/source/scripts.md b/docs/source/scripts.md +new file mode 100644 +index 0000000..82916c1 +--- /dev/null ++++ b/docs/source/scripts.md +@@ -0,0 +1 @@ ++# Scripts +\ No newline at end of file +diff --git a/docs/source/tutorial.md b/docs/source/tutorial.md +new file mode 100644 +index 0000000..161a880 +--- /dev/null ++++ b/docs/source/tutorial.md +@@ -0,0 +1,15 @@ ++# Tutorial ++ +diff --git a/topaz/model/classifier.py b/topaz/model/classifier.py +index be1c3de..bb4710f 100644 +--- a/topaz/model/classifier.py ++++ b/topaz/model/classifier.py +@@ -6,6 +6,15 @@ + + class LinearClassifier(nn.Module): + def __init__(self, features): ++ ''' ++ A simple convolutional layer with no non-linear activation. ++ ++ Args: ++ features (:obj:): the sizes associated with the layer ++ ++ Attributes: ++ features (:obj:) ++ ''' + super(LinearClassifier, self).__init__() + self.features = features + self.classifier = nn.Conv2d(features.latent_dim, 1, 1) + +From e064f07d52ba152e79a664c16d64cbbbf46067e3 Mon Sep 17 00:00:00 2001 +From: Darnell Granberry <40174000+DarnellGranberry@users.noreply.github.com> +Date: Wed, 16 Mar 2022 10:49:08 -0400 +Subject: [PATCH 03/28] updated doc requirements for rtd + +--- + .readthedocs.yaml | 11 +++-------- + docs/requirements.txt | 15 +++++++++++++++ + 2 files changed, 18 insertions(+), 8 deletions(-) + create mode 100644 docs/requirements.txt + +diff --git a/.readthedocs.yaml b/.readthedocs.yaml +index b67d3bf..7468b70 100644 +--- a/.readthedocs.yaml ++++ b/.readthedocs.yaml +@@ -11,11 +11,6 @@ sphinx: + python: + install: + - method: pip +- path: . +- extra_requirements: +- - docs +- - nbsphinx +- - sphinx_rtd_theme +- - sphinx-autobuild +- - rst-to-myst +- - myst-parser +\ No newline at end of file ++ - requirements: docs/requirements.txt ++ - extra-requirements: ++ - doc +\ No newline at end of file +diff --git a/docs/requirements.txt b/docs/requirements.txt +new file mode 100644 +index 0000000..46d9223 +--- /dev/null ++++ b/docs/requirements.txt +@@ -0,0 +1,15 @@ ++# torch >= 1.0.0 ++# torchvision ++# numpy >= 1.11 ++# pandas ++# scikit-learn >= 0.19.0 ++# scipy >= 0.17.0 ++# pillow >= 6.2.0 ++# future ++ ++sphinx ++sphinx_rtd_theme ++sphinx-autobuild ++rst-to-myst ++myst-parser ++nbsphinx +\ No newline at end of file + +From d80d47b01d4e919d4e0be86e4790e65074158b18 Mon Sep 17 00:00:00 2001 +From: Darnell Granberry <40174000+DarnellGranberry@users.noreply.github.com> +Date: Wed, 16 Mar 2022 10:52:10 -0400 +Subject: [PATCH 04/28] Restored path in rtd.yaml + +--- + .readthedocs.yaml | 1 + + 1 file changed, 1 insertion(+) + +diff --git a/.readthedocs.yaml b/.readthedocs.yaml +index 7468b70..037a6c0 100644 +--- a/.readthedocs.yaml ++++ b/.readthedocs.yaml +@@ -11,6 +11,7 @@ sphinx: + python: + install: + - method: pip ++ - path: . + - requirements: docs/requirements.txt + - extra-requirements: + - doc +\ No newline at end of file + +From bba83e16c33c0614fa63a0f363677032f6086234 Mon Sep 17 00:00:00 2001 +From: Darnell Granberry <40174000+DarnellGranberry@users.noreply.github.com> +Date: Wed, 16 Mar 2022 14:14:58 -0400 +Subject: [PATCH 05/28] Corrected rtd yaml formatting + +--- + .readthedocs.yaml | 7 ++++--- + 1 file changed, 4 insertions(+), 3 deletions(-) + +diff --git a/.readthedocs.yaml b/.readthedocs.yaml +index 037a6c0..fc40b17 100644 +--- a/.readthedocs.yaml ++++ b/.readthedocs.yaml +@@ -11,7 +11,8 @@ sphinx: + python: + install: + - method: pip +- - path: . +- - requirements: docs/requirements.txt +- - extra-requirements: ++ path: . ++ requirements: docs/requirements.txt ++ requirements: requirements.txt ++ extra-requirements: + - doc +\ No newline at end of file + +From 1c5f11140f7f063a214e11e9787f779844423bd8 Mon Sep 17 00:00:00 2001 +From: Darnell Granberry <40174000+DarnellGranberry@users.noreply.github.com> +Date: Wed, 16 Mar 2022 14:36:29 -0400 +Subject: [PATCH 06/28] added docs requirements, edited rtd.yaml + +--- + .readthedocs.yaml | 5 +---- + docs/requirements.txt | 10 ++++------ + requirements.txt | 5 +++++ + 3 files changed, 10 insertions(+), 10 deletions(-) + +diff --git a/.readthedocs.yaml b/.readthedocs.yaml +index fc40b17..b9870ed 100644 +--- a/.readthedocs.yaml ++++ b/.readthedocs.yaml +@@ -12,7 +12,4 @@ python: + install: + - method: pip + path: . +- requirements: docs/requirements.txt +- requirements: requirements.txt +- extra-requirements: +- - doc +\ No newline at end of file ++ requirements: requirements.txt +\ No newline at end of file +diff --git a/docs/requirements.txt b/docs/requirements.txt +index 46d9223..e7f2aa5 100644 +--- a/docs/requirements.txt ++++ b/docs/requirements.txt +@@ -6,10 +6,8 @@ + # scipy >= 0.17.0 + # pillow >= 6.2.0 + # future +- +-sphinx ++sphinx==4.4.0 + sphinx_rtd_theme +-sphinx-autobuild +-rst-to-myst +-myst-parser +-nbsphinx +\ No newline at end of file ++rst-to-myst==0.3.2 ++myst-parser==0.17.0 ++nbsphinx==0.8.8 +\ No newline at end of file +diff --git a/requirements.txt b/requirements.txt +index 4e7245f..01c0804 100644 +--- a/requirements.txt ++++ b/requirements.txt +@@ -6,3 +6,8 @@ scikit-learn >= 0.19.0 + scipy >= 0.17.0 + pillow >= 6.2.0 + future ++sphinx==4.4.0 ++sphinx_rtd_theme ++rst-to-myst==0.3.2 ++myst-parser==0.17.0 ++nbsphinx==0.8.8 +\ No newline at end of file + +From ed7de9c2d2e89fc3a254b3c0882d6c2e2b981205 Mon Sep 17 00:00:00 2001 +From: Darnell Granberry <40174000+DarnellGranberry@users.noreply.github.com> +Date: Wed, 16 Mar 2022 14:46:51 -0400 +Subject: [PATCH 07/28] Reordered rtd.yaml args + +--- + .readthedocs.yaml | 4 +++- + 1 file changed, 3 insertions(+), 1 deletion(-) + +diff --git a/.readthedocs.yaml b/.readthedocs.yaml +index b9870ed..6722c59 100644 +--- a/.readthedocs.yaml ++++ b/.readthedocs.yaml +@@ -10,6 +10,8 @@ sphinx: + + python: + install: ++ - requirements: docs/requirements.txt + - method: pip + path: . +- requirements: requirements.txt +\ No newline at end of file ++ extra_requirements: ++ - docs +\ No newline at end of file + +From 683093572078eb20e9aebfa5daeb931ddb3c5bbc Mon Sep 17 00:00:00 2001 +From: Darnell Granberry <40174000+DarnellGranberry@users.noreply.github.com> +Date: Wed, 16 Mar 2022 14:50:07 -0400 +Subject: [PATCH 08/28] removed doc versions pkg version + +--- + docs/requirements.txt | 6 +++--- + 1 file changed, 3 insertions(+), 3 deletions(-) + +diff --git a/docs/requirements.txt b/docs/requirements.txt +index e7f2aa5..f12e5f7 100644 +--- a/docs/requirements.txt ++++ b/docs/requirements.txt +@@ -8,6 +8,6 @@ + # future + sphinx==4.4.0 + sphinx_rtd_theme +-rst-to-myst==0.3.2 +-myst-parser==0.17.0 +-nbsphinx==0.8.8 +\ No newline at end of file ++rst-to-myst ++myst-parser ++nbsphinx +\ No newline at end of file + +From c3415895c8515696be1a88c2bfde242c3c2999f7 Mon Sep 17 00:00:00 2001 +From: Darnell Granberry <40174000+DarnellGranberry@users.noreply.github.com> +Date: Wed, 16 Mar 2022 14:55:36 -0400 +Subject: [PATCH 09/28] Add docs status to readme + +--- + README.md | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/README.md b/README.md +index 5987691..f2b6433 100644 +--- a/README.md ++++ b/README.md +@@ -1,5 +1,5 @@ + [![Python package](https://github.com/tbepler/topaz/actions/workflows/ci.yml/badge.svg)](https://github.com/tbepler/topaz/actions/workflows/ci.yml) +- ++[![Documentation Status](https://readthedocs.org/projects/topaz-em/badge/?version=latest)](https://topaz-em.readthedocs.io/en/latest/?badge=latest) + + + # Topaz + +From 538286e7a4780d31f163e95011e89a68fc418b9f Mon Sep 17 00:00:00 2001 +From: Darnell Granberry <40174000+DarnellGranberry@users.noreply.github.com> +Date: Wed, 16 Mar 2022 15:00:17 -0400 +Subject: [PATCH 10/28] Added version and conda install badges + +--- + README.md | 2 ++ + 1 file changed, 2 insertions(+) + +diff --git a/README.md b/README.md +index f2b6433..f3832bd 100644 +--- a/README.md ++++ b/README.md +@@ -1,5 +1,7 @@ + [![Python package](https://github.com/tbepler/topaz/actions/workflows/ci.yml/badge.svg)](https://github.com/tbepler/topaz/actions/workflows/ci.yml) + [![Documentation Status](https://readthedocs.org/projects/topaz-em/badge/?version=latest)](https://topaz-em.readthedocs.io/en/latest/?badge=latest) ++[![Anaconda-Server Badge](https://anaconda.org/tbepler/topaz/badges/version.svg)](https://anaconda.org/tbepler/topaz) ++[![Anaconda-Server Badge](https://anaconda.org/tbepler/topaz/badges/installer/conda.svg)](https://conda.anaconda.org/tbepler) + + + # Topaz + +From 2c13c55fa3080741571b868f6275b1839456e45e Mon Sep 17 00:00:00 2001 +From: Darnell Granberry <40174000+DarnellGranberry@users.noreply.github.com> +Date: Wed, 16 Mar 2022 15:05:11 -0400 +Subject: [PATCH 11/28] removed duplicate docs requirements + +--- + requirements.txt | 7 +------ + 1 file changed, 1 insertion(+), 6 deletions(-) + +diff --git a/requirements.txt b/requirements.txt +index 01c0804..d83f97b 100644 +--- a/requirements.txt ++++ b/requirements.txt +@@ -5,9 +5,4 @@ pandas + scikit-learn >= 0.19.0 + scipy >= 0.17.0 + pillow >= 6.2.0 +-future +-sphinx==4.4.0 +-sphinx_rtd_theme +-rst-to-myst==0.3.2 +-myst-parser==0.17.0 +-nbsphinx==0.8.8 +\ No newline at end of file ++future +\ No newline at end of file + +From 06f301640ea566f9baae816edb0a908ffafca444 Mon Sep 17 00:00:00 2001 +From: Darnell Granberry <40174000+DarnellGranberry@users.noreply.github.com> +Date: Thu, 17 Mar 2022 17:50:20 -0400 +Subject: [PATCH 12/28] Created doc entries for most code except commands + +--- + docs/source/algorithms.md | 7 +++ + docs/source/conf.py | 4 +- + docs/source/denoising.md | 7 +++ + docs/source/index.md | 10 ++++- + docs/source/methods.md | 7 +++ + docs/source/metrics_stats.md | 14 ++++++ + docs/source/models.md | 52 +++++++++++++++++++++- + docs/source/transforms.md | 7 +++ + docs/source/utils.md | 81 +++++++++++++++++++++++++++++++++++ + topaz/_version.py | 2 +- + topaz/model/classifier.py | 12 +++++- + topaz/model/features/basic.py | 2 + + 12 files changed, 197 insertions(+), 8 deletions(-) + create mode 100644 docs/source/algorithms.md + create mode 100644 docs/source/denoising.md + create mode 100644 docs/source/methods.md + create mode 100644 docs/source/metrics_stats.md + create mode 100644 docs/source/transforms.md + create mode 100644 docs/source/utils.md + +diff --git a/docs/source/algorithms.md b/docs/source/algorithms.md +new file mode 100644 +index 0000000..0a617c9 +--- /dev/null ++++ b/docs/source/algorithms.md +@@ -0,0 +1,7 @@ ++# Algorithms ++ ++```{eval-rst} ++.. automodule:: topaz.algorithms ++ :members: ++ :undoc-members: ++``` +\ No newline at end of file +diff --git a/docs/source/conf.py b/docs/source/conf.py +index cac08bc..8a8b336 100644 +--- a/docs/source/conf.py ++++ b/docs/source/conf.py +@@ -34,7 +34,9 @@ + extensions = [ + "myst_parser", + "nbsphinx", +- "sphinx.ext.autodoc" ++ "sphinx.ext.autodoc", ++ "sphinx.ext.napoleon", ++ "sphinx.ext.autosectionlabel" + ] + + # Add any paths that contain templates here, relative to this directory. +diff --git a/docs/source/denoising.md b/docs/source/denoising.md +new file mode 100644 +index 0000000..036d4d5 +--- /dev/null ++++ b/docs/source/denoising.md +@@ -0,0 +1,7 @@ ++# Denoising ++ ++```{eval-rst} ++.. automodule:: topaz.denoise ++ :members: ++ :undoc-members: ++``` +\ No newline at end of file +diff --git a/docs/source/index.md b/docs/source/index.md +index 1ab1b7c..af67119 100644 +--- a/docs/source/index.md ++++ b/docs/source/index.md +@@ -18,8 +18,14 @@ + installation + tutorial + commands +-relion +-cryosparc ++algorithms ++denoising ++methods ++metrics_stats + models ++transforms ++utils + scripts ++relion ++cryosparc + ``` +diff --git a/docs/source/methods.md b/docs/source/methods.md +new file mode 100644 +index 0000000..aed5cfd +--- /dev/null ++++ b/docs/source/methods.md +@@ -0,0 +1,7 @@ ++# Methods ++ ++```{eval-rst} ++.. automodule:: topaz.methods ++ :members: ++ :undoc-members: ++``` +\ No newline at end of file +diff --git a/docs/source/metrics_stats.md b/docs/source/metrics_stats.md +new file mode 100644 +index 0000000..dcfe0c4 +--- /dev/null ++++ b/docs/source/metrics_stats.md +@@ -0,0 +1,14 @@ ++# Metrics and Statistics ++ ++```{eval-rst} ++.. automodule:: topaz.metrics ++ :members: ++ :undoc-members: ++``` ++ ++ ++```{eval-rst} ++.. automodule:: topaz.stats ++ :members: ++ :undoc-members: ++``` +\ No newline at end of file +diff --git a/docs/source/models.md b/docs/source/models.md +index 574c6fb..dbad6b1 100644 +--- a/docs/source/models.md ++++ b/docs/source/models.md +@@ -1,11 +1,59 @@ + # Models + ++## Feature Extractors ++ ++### Basic Conv Nets ++```{eval-rst} ++.. automodule:: topaz.model.features.basic ++ :members: ++ :undoc-members: ++``` ++ ++### DenseNets ++```{eval-rst} ++.. automodule:: topaz.model.features.densenet ++ :members: ++ :undoc-members: ++``` ++ ++### MSNets ++```{eval-rst} ++.. automodule:: topaz.model.features.msnet ++ :members: ++ :undoc-members: ++``` ++ ++### ResNets ++```{eval-rst} ++.. automodule:: topaz.model.features.resnet ++ :members: ++ :undoc-members: ++``` ++ ++## Linear Classifier + ```{eval-rst} + .. autoclass:: topaz.model.classifier.LinearClassifier ++ :members: ++ :undoc-members: + ``` + +-## Features ++## Model Factory ++```{eval-rst} ++.. automodule:: topaz.model.factory ++ :members: ++ :undoc-members: ++``` ++ ++## Model Generator ++```{eval-rst} ++.. automodule:: topaz.model.generative ++ :members: ++ :undoc-members: ++``` + ++## Model Utilities + ```{eval-rst} +-.. autoclass:: topaz.model.features.basic.BasicConv ++.. automodule:: topaz.model.utils ++ :members: ++ :undoc-members: + ``` +\ No newline at end of file +diff --git a/docs/source/transforms.md b/docs/source/transforms.md +new file mode 100644 +index 0000000..9bf1082 +--- /dev/null ++++ b/docs/source/transforms.md +@@ -0,0 +1,7 @@ ++# Transformations ++ ++```{eval-rst} ++.. automodule:: topaz.transform.scaled_gaussian_mixture ++ :members: ++ :undoc-members: ++``` +\ No newline at end of file +diff --git a/docs/source/utils.md b/docs/source/utils.md +new file mode 100644 +index 0000000..027f498 +--- /dev/null ++++ b/docs/source/utils.md +@@ -0,0 +1,81 @@ ++# Utilities ++ ++## Conversions ++```{eval-rst} ++.. automodule:: topaz.utils.conversions ++ :members: ++ :undoc-members: ++``` ++ ++## File Utilities ++```{eval-rst} ++.. automodule:: topaz.utils.conversions ++ :members: ++ :undoc-members: ++``` ++ ++ ++```{eval-rst} ++.. automodule:: topaz.mrc ++ :members: ++ :undoc-members: ++``` ++ ++ ++## Image Manipulations ++```{eval-rst} ++.. automodule:: topaz.utils.image ++ :members: ++ :undoc-members: ++``` ++ ++## Pick Masking ++```{eval-rst} ++.. automodule:: topaz.utils.picks ++ :members: ++ :undoc-members: ++``` ++ ++## Printing ++```{eval-rst} ++.. automodule:: topaz.utils.printing ++ :members: ++ :undoc-members: ++``` ++ ++## STAR File Manipulations ++```{eval-rst} ++.. automodule:: topaz.utils.star ++ :members: ++ :undoc-members: ++``` ++ ++## Data Utilities ++ ++### Coordinate Manipulations ++```{eval-rst} ++.. automodule:: topaz.utils.data.coordinates ++ :members: ++ :undoc-members: ++``` ++ ++### Image Loading ++```{eval-rst} ++.. automodule:: topaz.utils.data.loader ++ :members: ++ :undoc-members: ++``` ++ ++### Dataset Partitioning ++```{eval-rst} ++.. automodule:: topaz.utils.data.partition ++ :members: ++ :undoc-members: ++``` ++ ++### Dataset Sampling ++```{eval-rst} ++.. automodule:: topaz.utils.data.sampler ++ :members: ++ :undoc-members: ++``` +\ No newline at end of file +diff --git a/topaz/_version.py b/topaz/_version.py +index e723ff3..fe404ae 100644 +--- a/topaz/_version.py ++++ b/topaz/_version.py +@@ -1 +1 @@ +-__version__ = "0.2.5a" ++__version__ = "0.2.5" +diff --git a/topaz/model/classifier.py b/topaz/model/classifier.py +index bb4710f..d63d83c 100644 +--- a/topaz/model/classifier.py ++++ b/topaz/model/classifier.py +@@ -5,10 +5,10 @@ + import torch.nn.functional as F + + class LinearClassifier(nn.Module): ++ '''A simple convolutional layer without non-linear activation.''' ++ + def __init__(self, features): + ''' +- A simple convolutional layer with no non-linear activation. +- + Args: + features (:obj:): the sizes associated with the layer + +@@ -34,6 +34,14 @@ def unfill(self): + self.features.unfill() + + def forward(self, x): ++ '''Applies the classifier to an input. ++ ++ Args: ++ x (np.ndarray): the image from which features are extracted and classified ++ ++ Returns: ++ z (np.ndarray): output of the classifer ++ ''' + z = self.features(x) + y = self.classifier(z) + return y +diff --git a/topaz/model/features/basic.py b/topaz/model/features/basic.py +index 0ea1fe9..dff4e9f 100644 +--- a/topaz/model/features/basic.py ++++ b/topaz/model/features/basic.py +@@ -10,6 +10,8 @@ + from topaz.model.utils import insize_from_outsize + + class BasicConv(nn.Module): ++ '''A generic convolutional neural network scaffold.''' ++ + def __init__(self, layers, units, unit_scaling=1, dropout=0, bn=True + , pooling=None, activation=nn.PReLU): + super(BasicConv, self).__init__() + +From d2c9761c2fba8d996c1f117f3004eeaf5a2abad7 Mon Sep 17 00:00:00 2001 +From: Darnell Granberry <40174000+DarnellGranberry@users.noreply.github.com> +Date: Fri, 18 Mar 2022 15:44:56 -0400 +Subject: [PATCH 13/28] reorganized docs, began work on man pages + +--- + docs/requirements.txt | 3 +- + docs/source/commands.md | 20 ++- + docs/source/commands/convert.md | 1 + + docs/source/commands/denoise.md | 1 + + docs/source/commands/denoise3d.md | 1 + + docs/source/commands/downsample.md | 1 + + docs/source/commands/extract.md | 1 + + docs/source/commands/file_utilities.md | 11 ++ + docs/source/commands/gui.md | 1 + + docs/source/commands/image_processing.md | 12 ++ + docs/source/commands/normalize.md | 8 + + docs/source/commands/particle_picking.md | 11 ++ + docs/source/commands/particle_stack.md | 1 + + docs/source/commands/precision_recall.md | 1 + + docs/source/commands/preprocess.md | 1 + + docs/source/commands/segment.md | 1 + + docs/source/commands/split.md | 1 + + docs/source/commands/train.md | 1 + + docs/source/commands/train_test_split.md | 1 + + docs/source/conf.py | 3 +- + docs/source/index.md | 2 +- + docs/source/installation.md | 172 ++------------------- + docs/source/installation/conda_install.md | 32 ++++ + docs/source/installation/docker_install.md | 51 ++++++ + docs/source/installation/pip_install.md | 20 +++ + docs/source/installation/singularity.md | 11 ++ + docs/source/installation/source_install.md | 57 +++++++ + docs/source/tutorial.md | 5 +- + topaz/commands/normalize.py | 9 +- + 29 files changed, 264 insertions(+), 176 deletions(-) + create mode 100644 docs/source/commands/convert.md + create mode 100644 docs/source/commands/denoise.md + create mode 100644 docs/source/commands/denoise3d.md + create mode 100644 docs/source/commands/downsample.md + create mode 100644 docs/source/commands/extract.md + create mode 100644 docs/source/commands/file_utilities.md + create mode 100644 docs/source/commands/gui.md + create mode 100644 docs/source/commands/image_processing.md + create mode 100644 docs/source/commands/normalize.md + create mode 100644 docs/source/commands/particle_picking.md + create mode 100644 docs/source/commands/particle_stack.md + create mode 100644 docs/source/commands/precision_recall.md + create mode 100644 docs/source/commands/preprocess.md + create mode 100644 docs/source/commands/segment.md + create mode 100644 docs/source/commands/split.md + create mode 100644 docs/source/commands/train.md + create mode 100644 docs/source/commands/train_test_split.md + create mode 100644 docs/source/installation/conda_install.md + create mode 100644 docs/source/installation/docker_install.md + create mode 100644 docs/source/installation/pip_install.md + create mode 100644 docs/source/installation/singularity.md + create mode 100644 docs/source/installation/source_install.md + +diff --git a/docs/requirements.txt b/docs/requirements.txt +index f12e5f7..bd0b467 100644 +--- a/docs/requirements.txt ++++ b/docs/requirements.txt +@@ -10,4 +10,5 @@ sphinx==4.4.0 + sphinx_rtd_theme + rst-to-myst + myst-parser +-nbsphinx +\ No newline at end of file ++nbsphinx ++sphinx-argparse +\ No newline at end of file +diff --git a/docs/source/commands.md b/docs/source/commands.md +index 44c4a21..3c462c9 100644 +--- a/docs/source/commands.md ++++ b/docs/source/commands.md +@@ -1,15 +1,13 @@ +-# Topaz Commands ++# Topaz Commands (work in progress) + +-## downsample + +-## normalize ++```{toctree} ++:caption: 'Commands' ++:maxdepth: 2 + +-## preprocess ++commands/particle_picking ++commands/image_processing ++commands/file_utilities + +-## train +- +-## segment +- +-## extract +- +-## precision_recall_curve ++commands/gui ++``` +\ No newline at end of file +diff --git a/docs/source/commands/convert.md b/docs/source/commands/convert.md +new file mode 100644 +index 0000000..122f443 +--- /dev/null ++++ b/docs/source/commands/convert.md +@@ -0,0 +1 @@ ++# Convert +\ No newline at end of file +diff --git a/docs/source/commands/denoise.md b/docs/source/commands/denoise.md +new file mode 100644 +index 0000000..d995632 +--- /dev/null ++++ b/docs/source/commands/denoise.md +@@ -0,0 +1 @@ ++# Denoise +\ No newline at end of file +diff --git a/docs/source/commands/denoise3d.md b/docs/source/commands/denoise3d.md +new file mode 100644 +index 0000000..bf78fac +--- /dev/null ++++ b/docs/source/commands/denoise3d.md +@@ -0,0 +1 @@ ++# Denoise 3D +\ No newline at end of file +diff --git a/docs/source/commands/downsample.md b/docs/source/commands/downsample.md +new file mode 100644 +index 0000000..e0b15bf +--- /dev/null ++++ b/docs/source/commands/downsample.md +@@ -0,0 +1 @@ ++# Downsample +\ No newline at end of file +diff --git a/docs/source/commands/extract.md b/docs/source/commands/extract.md +new file mode 100644 +index 0000000..d0e6da9 +--- /dev/null ++++ b/docs/source/commands/extract.md +@@ -0,0 +1 @@ ++# Extract +\ No newline at end of file +diff --git a/docs/source/commands/file_utilities.md b/docs/source/commands/file_utilities.md +new file mode 100644 +index 0000000..b26444f +--- /dev/null ++++ b/docs/source/commands/file_utilities.md +@@ -0,0 +1,11 @@ ++# File Utilities ++ ++```{toctree} ++:caption: 'Commands' ++:maxdepth: 1 ++ ++convert ++split ++particle_stack ++train_test_split ++``` +\ No newline at end of file +diff --git a/docs/source/commands/gui.md b/docs/source/commands/gui.md +new file mode 100644 +index 0000000..93bd5f2 +--- /dev/null ++++ b/docs/source/commands/gui.md +@@ -0,0 +1 @@ ++# GUI +\ No newline at end of file +diff --git a/docs/source/commands/image_processing.md b/docs/source/commands/image_processing.md +new file mode 100644 +index 0000000..973048c +--- /dev/null ++++ b/docs/source/commands/image_processing.md +@@ -0,0 +1,12 @@ ++# Image Processing ++ ++```{toctree} ++:caption: 'Commands' ++:maxdepth: 1 ++ ++downsample ++normalize ++preprocess ++denoise ++denoise3d ++``` +\ No newline at end of file +diff --git a/docs/source/commands/normalize.md b/docs/source/commands/normalize.md +new file mode 100644 +index 0000000..ad442b2 +--- /dev/null ++++ b/docs/source/commands/normalize.md +@@ -0,0 +1,8 @@ ++# Normalize ++ ++```{eval-rst} ++.. argparse:: ++ :module: topaz.commands.normalize ++ :func: add_arguments ++ :prog: normalize ++``` +\ No newline at end of file +diff --git a/docs/source/commands/particle_picking.md b/docs/source/commands/particle_picking.md +new file mode 100644 +index 0000000..c32361a +--- /dev/null ++++ b/docs/source/commands/particle_picking.md +@@ -0,0 +1,11 @@ ++# Particle Picking ++ ++```{toctree} ++:caption: 'Commands' ++:maxdepth: 1 ++ ++train ++segment ++extract ++precision_recall ++``` +\ No newline at end of file +diff --git a/docs/source/commands/particle_stack.md b/docs/source/commands/particle_stack.md +new file mode 100644 +index 0000000..7bb5a5e +--- /dev/null ++++ b/docs/source/commands/particle_stack.md +@@ -0,0 +1 @@ ++# Particle Stack +\ No newline at end of file +diff --git a/docs/source/commands/precision_recall.md b/docs/source/commands/precision_recall.md +new file mode 100644 +index 0000000..dff8323 +--- /dev/null ++++ b/docs/source/commands/precision_recall.md +@@ -0,0 +1 @@ ++# Precision Recall Curve +\ No newline at end of file +diff --git a/docs/source/commands/preprocess.md b/docs/source/commands/preprocess.md +new file mode 100644 +index 0000000..8fd260d +--- /dev/null ++++ b/docs/source/commands/preprocess.md +@@ -0,0 +1 @@ ++# Preprocess +\ No newline at end of file +diff --git a/docs/source/commands/segment.md b/docs/source/commands/segment.md +new file mode 100644 +index 0000000..af21080 +--- /dev/null ++++ b/docs/source/commands/segment.md +@@ -0,0 +1 @@ ++# Segment +\ No newline at end of file +diff --git a/docs/source/commands/split.md b/docs/source/commands/split.md +new file mode 100644 +index 0000000..5e525aa +--- /dev/null ++++ b/docs/source/commands/split.md +@@ -0,0 +1 @@ ++# Split +\ No newline at end of file +diff --git a/docs/source/commands/train.md b/docs/source/commands/train.md +new file mode 100644 +index 0000000..44ac09a +--- /dev/null ++++ b/docs/source/commands/train.md +@@ -0,0 +1 @@ ++# Train +\ No newline at end of file +diff --git a/docs/source/commands/train_test_split.md b/docs/source/commands/train_test_split.md +new file mode 100644 +index 0000000..e28a8c8 +--- /dev/null ++++ b/docs/source/commands/train_test_split.md +@@ -0,0 +1 @@ ++# Train Test Split +\ No newline at end of file +diff --git a/docs/source/conf.py b/docs/source/conf.py +index 8a8b336..8f3a9d3 100644 +--- a/docs/source/conf.py ++++ b/docs/source/conf.py +@@ -36,7 +36,8 @@ + "nbsphinx", + "sphinx.ext.autodoc", + "sphinx.ext.napoleon", +- "sphinx.ext.autosectionlabel" ++ "sphinx.ext.autosectionlabel", ++ "sphinxarg.ext" + ] + + # Add any paths that contain templates here, relative to this directory. +diff --git a/docs/source/index.md b/docs/source/index.md +index af67119..13b414e 100644 +--- a/docs/source/index.md ++++ b/docs/source/index.md +@@ -13,7 +13,7 @@ + + ```{toctree} + :caption: 'Contents:' +-:maxdepth: 2 ++:maxdepth: 3 + + installation + tutorial +diff --git a/docs/source/installation.md b/docs/source/installation.md +index fc4a774..8eca25e 100644 +--- a/docs/source/installation.md ++++ b/docs/source/installation.md +@@ -1,172 +1,28 @@ + # Installation + +-**

(Recommended) Click here to install *using Anaconda*

** +- +-If you do not have the Anaconda python distribution, [please install it following the instructions on their website](https://www.anaconda.com/download). +- +-We strongly recommend installing Topaz into a separate conda environment. To create a conda environment for Topaz: +-``` +-conda create -n topaz python=3.6 # or 2.7 if you prefer python 2 +-source activate topaz # this changes to the topaz conda environment, 'conda activate topaz' can be used with anaconda >= 4.4 if properly configured +-# source deactivate # returns to the base conda environment +-``` +-More information on conda environments can be found [here](https://conda.io/docs/user-guide/tasks/manage-environments.html). +- +-## Install Topaz +- +-To install the precompiled Topaz package and its dependencies, including pytorch: +-``` +-conda install topaz -c tbepler -c pytorch +-``` +-This installs pytorch from the official channel. To install pytorch for specific cuda versions, you will need to add the 'cudatoolkit=X.X' package. E.g. to install pytorch for CUDA 9.0: +-``` +-conda install cudatoolkit=9.0 -c pytorch +-``` +-or combined into a single command: +-``` +-conda install topaz cudatoolkit=9.0 -c tbepler -c pytorch +-``` +-See [here](https://pytorch.org/get-started/locally/) for additional pytorch installation instructions. +- +-That's it! Topaz is now installed in your anaconda environment. +- +-

+- +-**
Click here to install *using Pip*

** +- +-We strongly recommend installing Topaz into a _virtual environment_. See [installation instructions](https://virtualenv.pypa.io/en/latest/installation/) and [user guide](https://virtualenv.pypa.io/en/latest/userguide/) for virtualenv. +- +-### Install Topaz +- +-To install Topaz for Python 3.X +-``` +-pip3 install topaz-em +-``` +- +-for Python 2.7 +-``` +-pip install topaz-em +-``` +-See [here](https://pytorch.org/get-started/locally/) for additional pytorch installation instructions, including how to install pytorch for specific CUDA versions. +- +-That's it! Topaz is now installed through pip. +- +-

+- +-**
Click here to install *using Docker*

** +- +-**

Do you have Docker installed? If not, *click here*

** +- +-#### Linux/MacOS    *(command line)* +- +-Download and install Docker 1.21 or greater for [Linux](https://docs.docker.com/engine/installation/) or [MacOS](https://store.docker.com/editions/community/docker-ce-desktop-mac). +- +-> Consider using a Docker 'convenience script' to install (search on your OS's Docker installation webpage). +- +-Launch docker according to your Docker engine's instructions, typically ``docker start``. +- +-> **Note:** You must have sudo or root access to *install* Docker. If you do not wish to *run* Docker as sudo/root, you need to configure user groups as described here: https://docs.docker.com/install/linux/linux-postinstall/ +- +-#### Windows    *(GUI & command line)* +- +-Download and install [Docker Toolbox for Windows](https://docs.docker.com/toolbox/toolbox_install_windows/). +- +-Launch Kitematic. +- +-> If on first startup Kitematic displays a red error suggesting that you run using VirtualBox, do so. +- +-> **Note:** [Docker Toolbox for MacOS](https://docs.docker.com/toolbox/toolbox_install_mac/) has not yet been tested. +- +- +-### What is Docker? +- +-[This tutorial explains why Docker is useful.](https://www.youtube.com/watch?v=YFl2mCHdv24) +- +- +- +-A Dockerfile is provided to build images with CUDA support. Build from the github repo: +-``` +-docker build -t topaz https://github.com/tbepler/topaz.git +-``` +- +-or download the source code and build from the source directory +-``` +-git clone https://github.com/tbepler/topaz +-cd topaz +-docker build -t topaz . +-``` +- +-

+- +- +-**
Click here to install *using Singularity*

** +- +-A prebuilt Singularity image for Topaz is available [here](https://singularity-hub.org/collections/2413) and can be installed with: +-``` +-singularity pull shub://nysbc/topaz +-``` +- +-Then, you can run topaz from within the singularity image with (paths must be changed appropriately): ++## Conda ++```{include} installation/conda_install.md + ``` +-singularity exec --nv -B /mounted_path:/mounted_path /path/to/singularity/container/topaz_latest.sif /usr/local/conda/bin/topaz +-``` +- +-

+- +- +-**
Click here to install *from source*

** +- +-_Recommended: install Topaz into a virtual Python environment_ +-See https://conda.io/docs/user-guide/tasks/manage-environments.html or https://virtualenv.pypa.io/en/stable/ for setting one up. +- +-#### Install the dependencies +- +-Tested with python 3.6 and 2.7 +- +-- pytorch (>= 1.0.0) +-- torchvision +-- pillow (>= 6.2.0) +-- numpy (>= 1.11) +-- pandas (>= 0.20.3) +-- scipy (>= 0.19.1) +-- scikit-learn (>= 0.19.0) +- +-Easy installation of dependencies with conda +-``` +-conda install numpy pandas scikit-learn +-conda install -c pytorch pytorch torchvision +-``` +-For more info on installing pytorch for your CUDA version see https://pytorch.org/get-started/locally/ +- +-#### Download the source code +-``` +-git clone https://github.com/tbepler/topaz +-``` +- +-#### Install Topaz ++

+ +-Move to the source code directory +-``` +-cd topaz ++## Pip ++```{include} installation/pip_install.md + ``` ++

+ +-By default, this will be the most recent version of the topaz source code. To install a specific older version, checkout that commit. For example, for v0.1.0 of Topaz: ++## Docker ++```{include} installation/docker_install.md + ``` +-git checkout v0.1.0 +-``` +-Note that older Topaz versions may have different dependencies. Refer to the README for the specific Topaz version. ++

+ +-Install Topaz into your Python path including the topaz command line interface +-``` +-pip install . ++## Singularity ++```{include} installation/singularity.md + ``` ++

+ +-To install for development use ++## From Source ++```{include} installation/source_install.md + ``` +-pip install -e . +-``` +- +-

+

+ + Topaz is also available through [SBGrid](https://sbgrid.org/software/titles/topaz). +\ No newline at end of file +diff --git a/docs/source/installation/conda_install.md b/docs/source/installation/conda_install.md +new file mode 100644 +index 0000000..06476c9 +--- /dev/null ++++ b/docs/source/installation/conda_install.md +@@ -0,0 +1,32 @@ ++**

(Recommended) Click here to install *using Anaconda*

** ++ ++If you do not have the Anaconda python distribution, [please install it following the instructions on their website](https://www.anaconda.com/download). ++ ++We strongly recommend installing Topaz into a separate conda environment. To create a conda environment for Topaz: ++``` ++conda create -n topaz python=3.6 # or 2.7 if you prefer python 2 ++source activate topaz # this changes to the topaz conda environment, 'conda activate topaz' can be used with anaconda >= 4.4 if properly configured ++# source deactivate # returns to the base conda environment ++``` ++More information on conda environments can be found [here](https://conda.io/docs/user-guide/tasks/manage-environments.html). ++ ++\ ++**Install Topaz** ++ ++To install the precompiled Topaz package and its dependencies, including pytorch: ++``` ++conda install topaz -c tbepler -c pytorch ++``` ++This installs pytorch from the official channel. To install pytorch for specific cuda versions, you will need to add the 'cudatoolkit=X.X' package. E.g. to install pytorch for CUDA 9.0: ++``` ++conda install cudatoolkit=9.0 -c pytorch ++``` ++or combined into a single command: ++``` ++conda install topaz cudatoolkit=9.0 -c tbepler -c pytorch ++``` ++See [here](https://pytorch.org/get-started/locally/) for additional pytorch installation instructions. ++ ++That's it! Topaz is now installed in your anaconda environment. ++ ++

+\ No newline at end of file +diff --git a/docs/source/installation/docker_install.md b/docs/source/installation/docker_install.md +new file mode 100644 +index 0000000..913ffd0 +--- /dev/null ++++ b/docs/source/installation/docker_install.md +@@ -0,0 +1,51 @@ ++**
Click here to install *using Docker*

** ++ ++**

What is Docker?

** ++ ++[This tutorial explains why Docker is useful.](https://www.youtube.com/watch?v=YFl2mCHdv24) ++

++ ++ ++**
Do you have Docker installed? If not, *click here*

** ++ ++**

Linux/MacOS    *(command line)*

** ++ ++

++Download and install Docker 1.21 or greater for [Linux](https://docs.docker.com/engine/installation/) or [MacOS](https://store.docker.com/editions/community/docker-ce-desktop-mac). ++ ++> Consider using a Docker 'convenience script' to install (search on your OS's Docker installation webpage). ++ ++Launch docker according to your Docker engine's instructions, typically ``docker start``. ++ ++> **Note:** You must have sudo or root access to *install* Docker. If you do not wish to *run* Docker as sudo/root, you need to configure user groups as described here: https://docs.docker.com/install/linux/linux-postinstall/ ++

++ ++ ++**
Windows    *(GUI & command line)*

** ++ ++

++Download and install [Docker Toolbox for Windows](https://docs.docker.com/toolbox/toolbox_install_windows/). ++ ++Launch Kitematic. ++ ++> If on first startup Kitematic displays a red error suggesting that you run using VirtualBox, do so. ++ ++> **Note:** [Docker Toolbox for MacOS](https://docs.docker.com/toolbox/toolbox_install_mac/) has not yet been tested. ++

++ ++

++

++ ++\ ++A Dockerfile is provided to build images with CUDA support. Build from the github repo: ++``` ++docker build -t topaz https://github.com/tbepler/topaz.git ++``` ++ ++or download the source code and build from the source directory ++``` ++git clone https://github.com/tbepler/topaz ++cd topaz ++docker build -t topaz . ++``` ++

+\ No newline at end of file +diff --git a/docs/source/installation/pip_install.md b/docs/source/installation/pip_install.md +new file mode 100644 +index 0000000..e65f64e +--- /dev/null ++++ b/docs/source/installation/pip_install.md +@@ -0,0 +1,20 @@ ++**
Click here to install *using Pip*

** ++ ++We strongly recommend installing Topaz into a _virtual environment_. See [installation instructions](https://virtualenv.pypa.io/en/latest/installation/) and [user guide](https://virtualenv.pypa.io/en/latest/userguide/) for virtualenv. ++ ++**Install Topaz** ++ ++To install Topaz for Python 3.X ++``` ++pip3 install topaz-em ++``` ++ ++for Python 2.7 ++``` ++pip install topaz-em ++``` ++See [here](https://pytorch.org/get-started/locally/) for additional pytorch installation instructions, including how to install pytorch for specific CUDA versions. ++ ++That's it! Topaz is now installed through pip. ++ ++

+\ No newline at end of file +diff --git a/docs/source/installation/singularity.md b/docs/source/installation/singularity.md +new file mode 100644 +index 0000000..401c819 +--- /dev/null ++++ b/docs/source/installation/singularity.md +@@ -0,0 +1,11 @@ ++**
Click here to install *using Singularity*

** ++A prebuilt Singularity image for Topaz is available [here](https://singularity-hub.org/collections/2413) and can be installed with: ++``` ++singularity pull shub://nysbc/topaz ++``` ++ ++Then, you can run topaz from within the singularity image with (paths must be changed appropriately): ++``` ++singularity exec --nv -B /mounted_path:/mounted_path /path/to/singularity/container/topaz_latest.sif /usr/local/conda/bin/topaz ++``` ++

+\ No newline at end of file +diff --git a/docs/source/installation/source_install.md b/docs/source/installation/source_install.md +new file mode 100644 +index 0000000..648dfc8 +--- /dev/null ++++ b/docs/source/installation/source_install.md +@@ -0,0 +1,57 @@ ++**
Click here to install *from source*

** ++ ++_Recommended: install Topaz into a virtual Python environment_ ++See https://conda.io/docs/user-guide/tasks/manage-environments.html or https://virtualenv.pypa.io/en/stable/ for setting one up. ++ ++\ ++**Install the dependencies** ++ ++Tested with python 3.6 and 2.7 ++ ++- pytorch (>= 1.0.0) ++- torchvision ++- pillow (>= 6.2.0) ++- numpy (>= 1.11) ++- pandas (>= 0.20.3) ++- scipy (>= 0.19.1) ++- scikit-learn (>= 0.19.0) ++ ++Easy installation of dependencies with conda ++``` ++conda install numpy pandas scikit-learn ++conda install -c pytorch pytorch torchvision ++``` ++For more info on installing pytorch for your CUDA version see https://pytorch.org/get-started/locally/ ++ ++\ ++**Download the source code** ++``` ++git clone https://github.com/tbepler/topaz ++``` ++ ++\ ++**Install Topaz** ++ ++Move to the source code directory ++``` ++cd topaz ++``` ++ ++By default, this will be the most recent version of the topaz source code. To install a specific older version, checkout that commit. For example, for v0.1.0 of Topaz: ++``` ++git checkout v0.1.0 ++``` ++Note that older Topaz versions may have different dependencies. Refer to the README for the specific Topaz version. ++ ++Install Topaz into your Python path including the topaz command line interface ++``` ++pip install . ++``` ++ ++To install for development use ++``` ++pip install -e . ++``` ++ ++

++

+\ No newline at end of file +diff --git a/docs/source/tutorial.md b/docs/source/tutorial.md +index 161a880..c2ebb97 100644 +--- a/docs/source/tutorial.md ++++ b/docs/source/tutorial.md +@@ -1,4 +1,7 @@ +-# Tutorial ++# Tutorials (coming soon) ++ ++Tutorial pages here are a work-in-progress. For the time being, please refer to the tutorial notebooks in topaz/tutorial. ++ + -\ No newline at end of file -diff --git a/docs/source/index.md b/docs/source/index.md -index 71ef567..1ab1b7c 100644 ---- a/docs/source/index.md -+++ b/docs/source/index.md -@@ -6,8 +6,7 @@ - # Welcome to Topaz's documentation! - - --```{include} ../../README.md --:relative-images: -+```{include} ./description.md - ``` - - -@@ -15,4 +14,12 @@ - ```{toctree} - :caption: 'Contents:' - :maxdepth: 2 -+ -+installation -+tutorial -+commands -+relion -+cryosparc -+models -+scripts - ``` -diff --git a/docs/source/installation.md b/docs/source/installation.md -new file mode 100644 -index 0000000..fc4a774 ---- /dev/null -+++ b/docs/source/installation.md -@@ -0,0 +1,172 @@ -+# Installation -+ -+**

(Recommended) Click here to install *using Anaconda*

** -+ -+If you do not have the Anaconda python distribution, [please install it following the instructions on their website](https://www.anaconda.com/download). -+ -+We strongly recommend installing Topaz into a separate conda environment. To create a conda environment for Topaz: -+``` -+conda create -n topaz python=3.6 # or 2.7 if you prefer python 2 -+source activate topaz # this changes to the topaz conda environment, 'conda activate topaz' can be used with anaconda >= 4.4 if properly configured -+# source deactivate # returns to the base conda environment -+``` -+More information on conda environments can be found [here](https://conda.io/docs/user-guide/tasks/manage-environments.html). -+ -+## Install Topaz -+ -+To install the precompiled Topaz package and its dependencies, including pytorch: -+``` -+conda install topaz -c tbepler -c pytorch -+``` -+This installs pytorch from the official channel. To install pytorch for specific cuda versions, you will need to add the 'cudatoolkit=X.X' package. E.g. to install pytorch for CUDA 9.0: -+``` -+conda install cudatoolkit=9.0 -c pytorch -+``` -+or combined into a single command: -+``` -+conda install topaz cudatoolkit=9.0 -c tbepler -c pytorch -+``` -+See [here](https://pytorch.org/get-started/locally/) for additional pytorch installation instructions. -+ -+That's it! Topaz is now installed in your anaconda environment. -+ -+

-+ -+**
Click here to install *using Pip*

** -+ -+We strongly recommend installing Topaz into a _virtual environment_. See [installation instructions](https://virtualenv.pypa.io/en/latest/installation/) and [user guide](https://virtualenv.pypa.io/en/latest/userguide/) for virtualenv. -+ -+### Install Topaz -+ -+To install Topaz for Python 3.X -+``` -+pip3 install topaz-em -+``` -+ -+for Python 2.7 -+``` -+pip install topaz-em -+``` -+See [here](https://pytorch.org/get-started/locally/) for additional pytorch installation instructions, including how to install pytorch for specific CUDA versions. -+ -+That's it! Topaz is now installed through pip. -+ -+

-+ -+**
Click here to install *using Docker*

** -+ -+**

Do you have Docker installed? If not, *click here*

** -+ -+#### Linux/MacOS    *(command line)* -+ -+Download and install Docker 1.21 or greater for [Linux](https://docs.docker.com/engine/installation/) or [MacOS](https://store.docker.com/editions/community/docker-ce-desktop-mac). -+ -+> Consider using a Docker 'convenience script' to install (search on your OS's Docker installation webpage). -+ -+Launch docker according to your Docker engine's instructions, typically ``docker start``. -+ -+> **Note:** You must have sudo or root access to *install* Docker. If you do not wish to *run* Docker as sudo/root, you need to configure user groups as described here: https://docs.docker.com/install/linux/linux-postinstall/ -+ -+#### Windows    *(GUI & command line)* -+ -+Download and install [Docker Toolbox for Windows](https://docs.docker.com/toolbox/toolbox_install_windows/). -+ -+Launch Kitematic. -+ -+> If on first startup Kitematic displays a red error suggesting that you run using VirtualBox, do so. -+ -+> **Note:** [Docker Toolbox for MacOS](https://docs.docker.com/toolbox/toolbox_install_mac/) has not yet been tested. -+ -+ -+### What is Docker? -+ -+[This tutorial explains why Docker is useful.](https://www.youtube.com/watch?v=YFl2mCHdv24) -+ -+ -+ -+A Dockerfile is provided to build images with CUDA support. Build from the github repo: -+``` -+docker build -t topaz https://github.com/tbepler/topaz.git -+``` -+ -+or download the source code and build from the source directory -+``` -+git clone https://github.com/tbepler/topaz -+cd topaz -+docker build -t topaz . -+``` -+ -+

-+ -+ -+**
Click here to install *using Singularity*

** -+ -+A prebuilt Singularity image for Topaz is available [here](https://singularity-hub.org/collections/2413) and can be installed with: -+``` -+singularity pull shub://nysbc/topaz -+``` -+ -+Then, you can run topaz from within the singularity image with (paths must be changed appropriately): -+``` -+singularity exec --nv -B /mounted_path:/mounted_path /path/to/singularity/container/topaz_latest.sif /usr/local/conda/bin/topaz -+``` -+ -+

-+ -+ -+**
Click here to install *from source*

** -+ -+_Recommended: install Topaz into a virtual Python environment_ -+See https://conda.io/docs/user-guide/tasks/manage-environments.html or https://virtualenv.pypa.io/en/stable/ for setting one up. -+ -+#### Install the dependencies -+ -+Tested with python 3.6 and 2.7 -+ -+- pytorch (>= 1.0.0) -+- torchvision -+- pillow (>= 6.2.0) -+- numpy (>= 1.11) -+- pandas (>= 0.20.3) -+- scipy (>= 0.19.1) -+- scikit-learn (>= 0.19.0) -+ -+Easy installation of dependencies with conda -+``` -+conda install numpy pandas scikit-learn -+conda install -c pytorch pytorch torchvision -+``` -+For more info on installing pytorch for your CUDA version see https://pytorch.org/get-started/locally/ -+ -+#### Download the source code -+``` -+git clone https://github.com/tbepler/topaz -+``` -+ -+#### Install Topaz -+ -+Move to the source code directory -+``` -+cd topaz -+``` -+ -+By default, this will be the most recent version of the topaz source code. To install a specific older version, checkout that commit. For example, for v0.1.0 of Topaz: -+``` -+git checkout v0.1.0 -+``` -+Note that older Topaz versions may have different dependencies. Refer to the README for the specific Topaz version. -+ -+Install Topaz into your Python path including the topaz command line interface -+``` -+pip install . -+``` -+ -+To install for development use -+``` -+pip install -e . -+``` -+ -+

-+

-+ -+Topaz is also available through [SBGrid](https://sbgrid.org/software/titles/topaz). -\ No newline at end of file -diff --git a/docs/source/models.md b/docs/source/models.md -new file mode 100644 -index 0000000..574c6fb ---- /dev/null -+++ b/docs/source/models.md -@@ -0,0 +1,11 @@ -+# Models -+ -+```{eval-rst} -+.. autoclass:: topaz.model.classifier.LinearClassifier -+``` -+ -+## Features -+ -+```{eval-rst} -+.. autoclass:: topaz.model.features.basic.BasicConv -+``` -\ No newline at end of file -diff --git a/docs/source/relion.md b/docs/source/relion.md -new file mode 100644 -index 0000000..7c94e56 ---- /dev/null -+++ b/docs/source/relion.md -@@ -0,0 +1 @@ -+## Use with RELION -\ No newline at end of file -diff --git a/docs/source/scripts.md b/docs/source/scripts.md -new file mode 100644 -index 0000000..82916c1 ---- /dev/null -+++ b/docs/source/scripts.md -@@ -0,0 +1 @@ -+# Scripts -\ No newline at end of file -diff --git a/docs/source/tutorial.md b/docs/source/tutorial.md -new file mode 100644 -index 0000000..161a880 ---- /dev/null -+++ b/docs/source/tutorial.md -@@ -0,0 +1,15 @@ -+# Tutorial -+ -diff --git a/topaz/model/classifier.py b/topaz/model/classifier.py -index be1c3de..bb4710f 100644 ---- a/topaz/model/classifier.py -+++ b/topaz/model/classifier.py -@@ -6,6 +6,15 @@ - - class LinearClassifier(nn.Module): - def __init__(self, features): -+ ''' -+ A simple convolutional layer with no non-linear activation. -+ -+ Args: -+ features (:obj:): the sizes associated with the layer -+ -+ Attributes: -+ features (:obj:) -+ ''' - super(LinearClassifier, self).__init__() - self.features = features - self.classifier = nn.Conv2d(features.latent_dim, 1, 1) - -From e064f07d52ba152e79a664c16d64cbbbf46067e3 Mon Sep 17 00:00:00 2001 -From: Darnell Granberry <40174000+DarnellGranberry@users.noreply.github.com> -Date: Wed, 16 Mar 2022 10:49:08 -0400 -Subject: [PATCH 03/28] updated doc requirements for rtd - ---- - .readthedocs.yaml | 11 +++-------- - docs/requirements.txt | 15 +++++++++++++++ - 2 files changed, 18 insertions(+), 8 deletions(-) - create mode 100644 docs/requirements.txt - -diff --git a/.readthedocs.yaml b/.readthedocs.yaml -index b67d3bf..7468b70 100644 ---- a/.readthedocs.yaml -+++ b/.readthedocs.yaml -@@ -11,11 +11,6 @@ sphinx: - python: - install: - - method: pip -- path: . -- extra_requirements: -- - docs -- - nbsphinx -- - sphinx_rtd_theme -- - sphinx-autobuild -- - rst-to-myst -- - myst-parser -\ No newline at end of file -+ - requirements: docs/requirements.txt -+ - extra-requirements: -+ - doc -\ No newline at end of file -diff --git a/docs/requirements.txt b/docs/requirements.txt -new file mode 100644 -index 0000000..46d9223 ---- /dev/null -+++ b/docs/requirements.txt -@@ -0,0 +1,15 @@ -+# torch >= 1.0.0 -+# torchvision -+# numpy >= 1.11 -+# pandas -+# scikit-learn >= 0.19.0 -+# scipy >= 0.17.0 -+# pillow >= 6.2.0 -+# future -+ -+sphinx -+sphinx_rtd_theme -+sphinx-autobuild -+rst-to-myst -+myst-parser -+nbsphinx -\ No newline at end of file - -From d80d47b01d4e919d4e0be86e4790e65074158b18 Mon Sep 17 00:00:00 2001 -From: Darnell Granberry <40174000+DarnellGranberry@users.noreply.github.com> -Date: Wed, 16 Mar 2022 10:52:10 -0400 -Subject: [PATCH 04/28] Restored path in rtd.yaml - ---- - .readthedocs.yaml | 1 + - 1 file changed, 1 insertion(+) - -diff --git a/.readthedocs.yaml b/.readthedocs.yaml -index 7468b70..037a6c0 100644 ---- a/.readthedocs.yaml -+++ b/.readthedocs.yaml -@@ -11,6 +11,7 @@ sphinx: - python: - install: - - method: pip -+ - path: . - - requirements: docs/requirements.txt - - extra-requirements: - - doc -\ No newline at end of file - -From bba83e16c33c0614fa63a0f363677032f6086234 Mon Sep 17 00:00:00 2001 -From: Darnell Granberry <40174000+DarnellGranberry@users.noreply.github.com> -Date: Wed, 16 Mar 2022 14:14:58 -0400 -Subject: [PATCH 05/28] Corrected rtd yaml formatting - ---- - .readthedocs.yaml | 7 ++++--- - 1 file changed, 4 insertions(+), 3 deletions(-) - -diff --git a/.readthedocs.yaml b/.readthedocs.yaml -index 037a6c0..fc40b17 100644 ---- a/.readthedocs.yaml -+++ b/.readthedocs.yaml -@@ -11,7 +11,8 @@ sphinx: - python: - install: - - method: pip -- - path: . -- - requirements: docs/requirements.txt -- - extra-requirements: -+ path: . -+ requirements: docs/requirements.txt -+ requirements: requirements.txt -+ extra-requirements: - - doc -\ No newline at end of file - -From 1c5f11140f7f063a214e11e9787f779844423bd8 Mon Sep 17 00:00:00 2001 -From: Darnell Granberry <40174000+DarnellGranberry@users.noreply.github.com> -Date: Wed, 16 Mar 2022 14:36:29 -0400 -Subject: [PATCH 06/28] added docs requirements, edited rtd.yaml - ---- - .readthedocs.yaml | 5 +---- - docs/requirements.txt | 10 ++++------ - requirements.txt | 5 +++++ - 3 files changed, 10 insertions(+), 10 deletions(-) - -diff --git a/.readthedocs.yaml b/.readthedocs.yaml -index fc40b17..b9870ed 100644 ---- a/.readthedocs.yaml -+++ b/.readthedocs.yaml -@@ -12,7 +12,4 @@ python: - install: - - method: pip - path: . -- requirements: docs/requirements.txt -- requirements: requirements.txt -- extra-requirements: -- - doc -\ No newline at end of file -+ requirements: requirements.txt -\ No newline at end of file -diff --git a/docs/requirements.txt b/docs/requirements.txt -index 46d9223..e7f2aa5 100644 ---- a/docs/requirements.txt -+++ b/docs/requirements.txt -@@ -6,10 +6,8 @@ - # scipy >= 0.17.0 - # pillow >= 6.2.0 - # future -- --sphinx -+sphinx==4.4.0 - sphinx_rtd_theme --sphinx-autobuild --rst-to-myst --myst-parser --nbsphinx -\ No newline at end of file -+rst-to-myst==0.3.2 -+myst-parser==0.17.0 -+nbsphinx==0.8.8 -\ No newline at end of file -diff --git a/requirements.txt b/requirements.txt -index 4e7245f..01c0804 100644 ---- a/requirements.txt -+++ b/requirements.txt -@@ -6,3 +6,8 @@ scikit-learn >= 0.19.0 - scipy >= 0.17.0 - pillow >= 6.2.0 - future -+sphinx==4.4.0 -+sphinx_rtd_theme -+rst-to-myst==0.3.2 -+myst-parser==0.17.0 -+nbsphinx==0.8.8 -\ No newline at end of file - -From ed7de9c2d2e89fc3a254b3c0882d6c2e2b981205 Mon Sep 17 00:00:00 2001 -From: Darnell Granberry <40174000+DarnellGranberry@users.noreply.github.com> -Date: Wed, 16 Mar 2022 14:46:51 -0400 -Subject: [PATCH 07/28] Reordered rtd.yaml args - ---- - .readthedocs.yaml | 4 +++- - 1 file changed, 3 insertions(+), 1 deletion(-) - -diff --git a/.readthedocs.yaml b/.readthedocs.yaml -index b9870ed..6722c59 100644 ---- a/.readthedocs.yaml -+++ b/.readthedocs.yaml -@@ -10,6 +10,8 @@ sphinx: - - python: - install: -+ - requirements: docs/requirements.txt - - method: pip - path: . -- requirements: requirements.txt -\ No newline at end of file -+ extra_requirements: -+ - docs -\ No newline at end of file - -From 683093572078eb20e9aebfa5daeb931ddb3c5bbc Mon Sep 17 00:00:00 2001 -From: Darnell Granberry <40174000+DarnellGranberry@users.noreply.github.com> -Date: Wed, 16 Mar 2022 14:50:07 -0400 -Subject: [PATCH 08/28] removed doc versions pkg version - ---- - docs/requirements.txt | 6 +++--- - 1 file changed, 3 insertions(+), 3 deletions(-) - -diff --git a/docs/requirements.txt b/docs/requirements.txt -index e7f2aa5..f12e5f7 100644 ---- a/docs/requirements.txt -+++ b/docs/requirements.txt -@@ -8,6 +8,6 @@ - # future - sphinx==4.4.0 - sphinx_rtd_theme --rst-to-myst==0.3.2 --myst-parser==0.17.0 --nbsphinx==0.8.8 -\ No newline at end of file -+rst-to-myst -+myst-parser -+nbsphinx -\ No newline at end of file - -From c3415895c8515696be1a88c2bfde242c3c2999f7 Mon Sep 17 00:00:00 2001 -From: Darnell Granberry <40174000+DarnellGranberry@users.noreply.github.com> -Date: Wed, 16 Mar 2022 14:55:36 -0400 -Subject: [PATCH 09/28] Add docs status to readme - ---- - README.md | 2 +- - 1 file changed, 1 insertion(+), 1 deletion(-) - -diff --git a/README.md b/README.md -index 5987691..f2b6433 100644 ---- a/README.md -+++ b/README.md -@@ -1,5 +1,5 @@ - [![Python package](https://github.com/tbepler/topaz/actions/workflows/ci.yml/badge.svg)](https://github.com/tbepler/topaz/actions/workflows/ci.yml) -- -+[![Documentation Status](https://readthedocs.org/projects/topaz-em/badge/?version=latest)](https://topaz-em.readthedocs.io/en/latest/?badge=latest) - - - # Topaz - -From 538286e7a4780d31f163e95011e89a68fc418b9f Mon Sep 17 00:00:00 2001 -From: Darnell Granberry <40174000+DarnellGranberry@users.noreply.github.com> -Date: Wed, 16 Mar 2022 15:00:17 -0400 -Subject: [PATCH 10/28] Added version and conda install badges - ---- - README.md | 2 ++ - 1 file changed, 2 insertions(+) - -diff --git a/README.md b/README.md -index f2b6433..f3832bd 100644 ---- a/README.md -+++ b/README.md -@@ -1,5 +1,7 @@ - [![Python package](https://github.com/tbepler/topaz/actions/workflows/ci.yml/badge.svg)](https://github.com/tbepler/topaz/actions/workflows/ci.yml) - [![Documentation Status](https://readthedocs.org/projects/topaz-em/badge/?version=latest)](https://topaz-em.readthedocs.io/en/latest/?badge=latest) -+[![Anaconda-Server Badge](https://anaconda.org/tbepler/topaz/badges/version.svg)](https://anaconda.org/tbepler/topaz) -+[![Anaconda-Server Badge](https://anaconda.org/tbepler/topaz/badges/installer/conda.svg)](https://conda.anaconda.org/tbepler) - - - # Topaz - -From 2c13c55fa3080741571b868f6275b1839456e45e Mon Sep 17 00:00:00 2001 -From: Darnell Granberry <40174000+DarnellGranberry@users.noreply.github.com> -Date: Wed, 16 Mar 2022 15:05:11 -0400 -Subject: [PATCH 11/28] removed duplicate docs requirements - ---- - requirements.txt | 7 +------ - 1 file changed, 1 insertion(+), 6 deletions(-) - -diff --git a/requirements.txt b/requirements.txt -index 01c0804..d83f97b 100644 ---- a/requirements.txt -+++ b/requirements.txt -@@ -5,9 +5,4 @@ pandas - scikit-learn >= 0.19.0 - scipy >= 0.17.0 - pillow >= 6.2.0 --future --sphinx==4.4.0 --sphinx_rtd_theme --rst-to-myst==0.3.2 --myst-parser==0.17.0 --nbsphinx==0.8.8 -\ No newline at end of file -+future -\ No newline at end of file - -From 06f301640ea566f9baae816edb0a908ffafca444 Mon Sep 17 00:00:00 2001 -From: Darnell Granberry <40174000+DarnellGranberry@users.noreply.github.com> -Date: Thu, 17 Mar 2022 17:50:20 -0400 -Subject: [PATCH 12/28] Created doc entries for most code except commands - ---- - docs/source/algorithms.md | 7 +++ - docs/source/conf.py | 4 +- - docs/source/denoising.md | 7 +++ - docs/source/index.md | 10 ++++- - docs/source/methods.md | 7 +++ - docs/source/metrics_stats.md | 14 ++++++ - docs/source/models.md | 52 +++++++++++++++++++++- - docs/source/transforms.md | 7 +++ - docs/source/utils.md | 81 +++++++++++++++++++++++++++++++++++ - topaz/_version.py | 2 +- - topaz/model/classifier.py | 12 +++++- - topaz/model/features/basic.py | 2 + - 12 files changed, 197 insertions(+), 8 deletions(-) - create mode 100644 docs/source/algorithms.md - create mode 100644 docs/source/denoising.md - create mode 100644 docs/source/methods.md - create mode 100644 docs/source/metrics_stats.md - create mode 100644 docs/source/transforms.md - create mode 100644 docs/source/utils.md - -diff --git a/docs/source/algorithms.md b/docs/source/algorithms.md -new file mode 100644 -index 0000000..0a617c9 ---- /dev/null -+++ b/docs/source/algorithms.md -@@ -0,0 +1,7 @@ -+# Algorithms -+ -+```{eval-rst} -+.. automodule:: topaz.algorithms -+ :members: -+ :undoc-members: -+``` -\ No newline at end of file -diff --git a/docs/source/conf.py b/docs/source/conf.py -index cac08bc..8a8b336 100644 ---- a/docs/source/conf.py -+++ b/docs/source/conf.py -@@ -34,7 +34,9 @@ - extensions = [ - "myst_parser", - "nbsphinx", -- "sphinx.ext.autodoc" -+ "sphinx.ext.autodoc", -+ "sphinx.ext.napoleon", -+ "sphinx.ext.autosectionlabel" - ] - - # Add any paths that contain templates here, relative to this directory. -diff --git a/docs/source/denoising.md b/docs/source/denoising.md -new file mode 100644 -index 0000000..036d4d5 ---- /dev/null -+++ b/docs/source/denoising.md -@@ -0,0 +1,7 @@ -+# Denoising -+ -+```{eval-rst} -+.. automodule:: topaz.denoise -+ :members: -+ :undoc-members: -+``` -\ No newline at end of file -diff --git a/docs/source/index.md b/docs/source/index.md -index 1ab1b7c..af67119 100644 ---- a/docs/source/index.md -+++ b/docs/source/index.md -@@ -18,8 +18,14 @@ - installation - tutorial - commands --relion --cryosparc -+algorithms -+denoising -+methods -+metrics_stats - models -+transforms -+utils - scripts -+relion -+cryosparc - ``` -diff --git a/docs/source/methods.md b/docs/source/methods.md -new file mode 100644 -index 0000000..aed5cfd ---- /dev/null -+++ b/docs/source/methods.md -@@ -0,0 +1,7 @@ -+# Methods -+ -+```{eval-rst} -+.. automodule:: topaz.methods -+ :members: -+ :undoc-members: -+``` -\ No newline at end of file -diff --git a/docs/source/metrics_stats.md b/docs/source/metrics_stats.md -new file mode 100644 -index 0000000..dcfe0c4 ---- /dev/null -+++ b/docs/source/metrics_stats.md -@@ -0,0 +1,14 @@ -+# Metrics and Statistics -+ -+```{eval-rst} -+.. automodule:: topaz.metrics -+ :members: -+ :undoc-members: -+``` -+ -+ -+```{eval-rst} -+.. automodule:: topaz.stats -+ :members: -+ :undoc-members: -+``` -\ No newline at end of file -diff --git a/docs/source/models.md b/docs/source/models.md -index 574c6fb..dbad6b1 100644 ---- a/docs/source/models.md -+++ b/docs/source/models.md -@@ -1,11 +1,59 @@ - # Models - -+## Feature Extractors -+ -+### Basic Conv Nets -+```{eval-rst} -+.. automodule:: topaz.model.features.basic -+ :members: -+ :undoc-members: -+``` -+ -+### DenseNets -+```{eval-rst} -+.. automodule:: topaz.model.features.densenet -+ :members: -+ :undoc-members: -+``` -+ -+### MSNets -+```{eval-rst} -+.. automodule:: topaz.model.features.msnet -+ :members: -+ :undoc-members: -+``` -+ -+### ResNets -+```{eval-rst} -+.. automodule:: topaz.model.features.resnet -+ :members: -+ :undoc-members: -+``` -+ -+## Linear Classifier - ```{eval-rst} - .. autoclass:: topaz.model.classifier.LinearClassifier -+ :members: -+ :undoc-members: - ``` - --## Features -+## Model Factory -+```{eval-rst} -+.. automodule:: topaz.model.factory -+ :members: -+ :undoc-members: -+``` -+ -+## Model Generator -+```{eval-rst} -+.. automodule:: topaz.model.generative -+ :members: -+ :undoc-members: -+``` - -+## Model Utilities - ```{eval-rst} --.. autoclass:: topaz.model.features.basic.BasicConv -+.. automodule:: topaz.model.utils -+ :members: -+ :undoc-members: - ``` -\ No newline at end of file -diff --git a/docs/source/transforms.md b/docs/source/transforms.md -new file mode 100644 -index 0000000..9bf1082 ---- /dev/null -+++ b/docs/source/transforms.md -@@ -0,0 +1,7 @@ -+# Transformations -+ -+```{eval-rst} -+.. automodule:: topaz.transform.scaled_gaussian_mixture -+ :members: -+ :undoc-members: -+``` -\ No newline at end of file -diff --git a/docs/source/utils.md b/docs/source/utils.md -new file mode 100644 -index 0000000..027f498 ---- /dev/null -+++ b/docs/source/utils.md -@@ -0,0 +1,81 @@ -+# Utilities -+ -+## Conversions -+```{eval-rst} -+.. automodule:: topaz.utils.conversions -+ :members: -+ :undoc-members: -+``` -+ -+## File Utilities -+```{eval-rst} -+.. automodule:: topaz.utils.conversions -+ :members: -+ :undoc-members: -+``` -+ -+ -+```{eval-rst} -+.. automodule:: topaz.mrc -+ :members: -+ :undoc-members: -+``` -+ -+ -+## Image Manipulations -+```{eval-rst} -+.. automodule:: topaz.utils.image -+ :members: -+ :undoc-members: -+``` -+ -+## Pick Masking -+```{eval-rst} -+.. automodule:: topaz.utils.picks -+ :members: -+ :undoc-members: -+``` -+ -+## Printing -+```{eval-rst} -+.. automodule:: topaz.utils.printing -+ :members: -+ :undoc-members: -+``` -+ -+## STAR File Manipulations -+```{eval-rst} -+.. automodule:: topaz.utils.star -+ :members: -+ :undoc-members: -+``` -+ -+## Data Utilities -+ -+### Coordinate Manipulations -+```{eval-rst} -+.. automodule:: topaz.utils.data.coordinates -+ :members: -+ :undoc-members: -+``` -+ -+### Image Loading -+```{eval-rst} -+.. automodule:: topaz.utils.data.loader -+ :members: -+ :undoc-members: -+``` -+ -+### Dataset Partitioning -+```{eval-rst} -+.. automodule:: topaz.utils.data.partition -+ :members: -+ :undoc-members: -+``` -+ -+### Dataset Sampling -+```{eval-rst} -+.. automodule:: topaz.utils.data.sampler -+ :members: -+ :undoc-members: -+``` -\ No newline at end of file -diff --git a/topaz/_version.py b/topaz/_version.py -index e723ff3..fe404ae 100644 ---- a/topaz/_version.py -+++ b/topaz/_version.py -@@ -1 +1 @@ --__version__ = "0.2.5a" -+__version__ = "0.2.5" -diff --git a/topaz/model/classifier.py b/topaz/model/classifier.py -index bb4710f..d63d83c 100644 ---- a/topaz/model/classifier.py -+++ b/topaz/model/classifier.py -@@ -5,10 +5,10 @@ - import torch.nn.functional as F - - class LinearClassifier(nn.Module): -+ '''A simple convolutional layer without non-linear activation.''' -+ - def __init__(self, features): - ''' -- A simple convolutional layer with no non-linear activation. -- - Args: - features (:obj:): the sizes associated with the layer - -@@ -34,6 +34,14 @@ def unfill(self): - self.features.unfill() - - def forward(self, x): -+ '''Applies the classifier to an input. -+ -+ Args: -+ x (np.ndarray): the image from which features are extracted and classified -+ -+ Returns: -+ z (np.ndarray): output of the classifer -+ ''' - z = self.features(x) - y = self.classifier(z) - return y -diff --git a/topaz/model/features/basic.py b/topaz/model/features/basic.py -index 0ea1fe9..dff4e9f 100644 ---- a/topaz/model/features/basic.py -+++ b/topaz/model/features/basic.py -@@ -10,6 +10,8 @@ - from topaz.model.utils import insize_from_outsize - - class BasicConv(nn.Module): -+ '''A generic convolutional neural network scaffold.''' -+ - def __init__(self, layers, units, unit_scaling=1, dropout=0, bn=True - , pooling=None, activation=nn.PReLU): - super(BasicConv, self).__init__() - -From d2c9761c2fba8d996c1f117f3004eeaf5a2abad7 Mon Sep 17 00:00:00 2001 -From: Darnell Granberry <40174000+DarnellGranberry@users.noreply.github.com> -Date: Fri, 18 Mar 2022 15:44:56 -0400 -Subject: [PATCH 13/28] reorganized docs, began work on man pages - ---- - docs/requirements.txt | 3 +- - docs/source/commands.md | 20 ++- - docs/source/commands/convert.md | 1 + - docs/source/commands/denoise.md | 1 + - docs/source/commands/denoise3d.md | 1 + - docs/source/commands/downsample.md | 1 + - docs/source/commands/extract.md | 1 + - docs/source/commands/file_utilities.md | 11 ++ - docs/source/commands/gui.md | 1 + - docs/source/commands/image_processing.md | 12 ++ - docs/source/commands/normalize.md | 8 + - docs/source/commands/particle_picking.md | 11 ++ - docs/source/commands/particle_stack.md | 1 + - docs/source/commands/precision_recall.md | 1 + - docs/source/commands/preprocess.md | 1 + - docs/source/commands/segment.md | 1 + - docs/source/commands/split.md | 1 + - docs/source/commands/train.md | 1 + - docs/source/commands/train_test_split.md | 1 + - docs/source/conf.py | 3 +- - docs/source/index.md | 2 +- - docs/source/installation.md | 172 ++------------------- - docs/source/installation/conda_install.md | 32 ++++ - docs/source/installation/docker_install.md | 51 ++++++ - docs/source/installation/pip_install.md | 20 +++ - docs/source/installation/singularity.md | 11 ++ - docs/source/installation/source_install.md | 57 +++++++ - docs/source/tutorial.md | 5 +- - topaz/commands/normalize.py | 9 +- - 29 files changed, 264 insertions(+), 176 deletions(-) - create mode 100644 docs/source/commands/convert.md - create mode 100644 docs/source/commands/denoise.md - create mode 100644 docs/source/commands/denoise3d.md - create mode 100644 docs/source/commands/downsample.md - create mode 100644 docs/source/commands/extract.md - create mode 100644 docs/source/commands/file_utilities.md - create mode 100644 docs/source/commands/gui.md - create mode 100644 docs/source/commands/image_processing.md - create mode 100644 docs/source/commands/normalize.md - create mode 100644 docs/source/commands/particle_picking.md - create mode 100644 docs/source/commands/particle_stack.md - create mode 100644 docs/source/commands/precision_recall.md - create mode 100644 docs/source/commands/preprocess.md - create mode 100644 docs/source/commands/segment.md - create mode 100644 docs/source/commands/split.md - create mode 100644 docs/source/commands/train.md - create mode 100644 docs/source/commands/train_test_split.md - create mode 100644 docs/source/installation/conda_install.md - create mode 100644 docs/source/installation/docker_install.md - create mode 100644 docs/source/installation/pip_install.md - create mode 100644 docs/source/installation/singularity.md - create mode 100644 docs/source/installation/source_install.md - -diff --git a/docs/requirements.txt b/docs/requirements.txt -index f12e5f7..bd0b467 100644 ---- a/docs/requirements.txt -+++ b/docs/requirements.txt -@@ -10,4 +10,5 @@ sphinx==4.4.0 - sphinx_rtd_theme - rst-to-myst - myst-parser --nbsphinx -\ No newline at end of file -+nbsphinx -+sphinx-argparse -\ No newline at end of file -diff --git a/docs/source/commands.md b/docs/source/commands.md -index 44c4a21..3c462c9 100644 ---- a/docs/source/commands.md -+++ b/docs/source/commands.md -@@ -1,15 +1,13 @@ --# Topaz Commands -+# Topaz Commands (work in progress) - --## downsample - --## normalize -+```{toctree} -+:caption: 'Commands' -+:maxdepth: 2 - --## preprocess -+commands/particle_picking -+commands/image_processing -+commands/file_utilities - --## train -- --## segment -- --## extract -- --## precision_recall_curve -+commands/gui -+``` -\ No newline at end of file -diff --git a/docs/source/commands/convert.md b/docs/source/commands/convert.md -new file mode 100644 -index 0000000..122f443 ---- /dev/null -+++ b/docs/source/commands/convert.md -@@ -0,0 +1 @@ -+# Convert -\ No newline at end of file -diff --git a/docs/source/commands/denoise.md b/docs/source/commands/denoise.md -new file mode 100644 -index 0000000..d995632 ---- /dev/null -+++ b/docs/source/commands/denoise.md -@@ -0,0 +1 @@ -+# Denoise -\ No newline at end of file -diff --git a/docs/source/commands/denoise3d.md b/docs/source/commands/denoise3d.md -new file mode 100644 -index 0000000..bf78fac ---- /dev/null -+++ b/docs/source/commands/denoise3d.md -@@ -0,0 +1 @@ -+# Denoise 3D -\ No newline at end of file -diff --git a/docs/source/commands/downsample.md b/docs/source/commands/downsample.md -new file mode 100644 -index 0000000..e0b15bf ---- /dev/null -+++ b/docs/source/commands/downsample.md -@@ -0,0 +1 @@ -+# Downsample -\ No newline at end of file -diff --git a/docs/source/commands/extract.md b/docs/source/commands/extract.md -new file mode 100644 -index 0000000..d0e6da9 ---- /dev/null -+++ b/docs/source/commands/extract.md -@@ -0,0 +1 @@ -+# Extract -\ No newline at end of file -diff --git a/docs/source/commands/file_utilities.md b/docs/source/commands/file_utilities.md -new file mode 100644 -index 0000000..b26444f ---- /dev/null -+++ b/docs/source/commands/file_utilities.md -@@ -0,0 +1,11 @@ -+# File Utilities -+ -+```{toctree} -+:caption: 'Commands' -+:maxdepth: 1 -+ -+convert -+split -+particle_stack -+train_test_split -+``` -\ No newline at end of file -diff --git a/docs/source/commands/gui.md b/docs/source/commands/gui.md -new file mode 100644 -index 0000000..93bd5f2 ---- /dev/null -+++ b/docs/source/commands/gui.md -@@ -0,0 +1 @@ -+# GUI -\ No newline at end of file -diff --git a/docs/source/commands/image_processing.md b/docs/source/commands/image_processing.md -new file mode 100644 -index 0000000..973048c ---- /dev/null -+++ b/docs/source/commands/image_processing.md -@@ -0,0 +1,12 @@ -+# Image Processing -+ -+```{toctree} -+:caption: 'Commands' -+:maxdepth: 1 -+ -+downsample -+normalize -+preprocess -+denoise -+denoise3d -+``` -\ No newline at end of file -diff --git a/docs/source/commands/normalize.md b/docs/source/commands/normalize.md -new file mode 100644 -index 0000000..ad442b2 ---- /dev/null -+++ b/docs/source/commands/normalize.md -@@ -0,0 +1,8 @@ -+# Normalize -+ -+```{eval-rst} -+.. argparse:: -+ :module: topaz.commands.normalize -+ :func: add_arguments -+ :prog: normalize -+``` -\ No newline at end of file -diff --git a/docs/source/commands/particle_picking.md b/docs/source/commands/particle_picking.md -new file mode 100644 -index 0000000..c32361a ---- /dev/null -+++ b/docs/source/commands/particle_picking.md -@@ -0,0 +1,11 @@ -+# Particle Picking -+ -+```{toctree} -+:caption: 'Commands' -+:maxdepth: 1 -+ -+train -+segment -+extract -+precision_recall -+``` -\ No newline at end of file -diff --git a/docs/source/commands/particle_stack.md b/docs/source/commands/particle_stack.md -new file mode 100644 -index 0000000..7bb5a5e ---- /dev/null -+++ b/docs/source/commands/particle_stack.md -@@ -0,0 +1 @@ -+# Particle Stack -\ No newline at end of file -diff --git a/docs/source/commands/precision_recall.md b/docs/source/commands/precision_recall.md -new file mode 100644 -index 0000000..dff8323 ---- /dev/null -+++ b/docs/source/commands/precision_recall.md -@@ -0,0 +1 @@ -+# Precision Recall Curve -\ No newline at end of file -diff --git a/docs/source/commands/preprocess.md b/docs/source/commands/preprocess.md -new file mode 100644 -index 0000000..8fd260d ---- /dev/null -+++ b/docs/source/commands/preprocess.md -@@ -0,0 +1 @@ -+# Preprocess -\ No newline at end of file -diff --git a/docs/source/commands/segment.md b/docs/source/commands/segment.md -new file mode 100644 -index 0000000..af21080 ---- /dev/null -+++ b/docs/source/commands/segment.md -@@ -0,0 +1 @@ -+# Segment -\ No newline at end of file -diff --git a/docs/source/commands/split.md b/docs/source/commands/split.md -new file mode 100644 -index 0000000..5e525aa ---- /dev/null -+++ b/docs/source/commands/split.md -@@ -0,0 +1 @@ -+# Split -\ No newline at end of file -diff --git a/docs/source/commands/train.md b/docs/source/commands/train.md -new file mode 100644 -index 0000000..44ac09a ---- /dev/null -+++ b/docs/source/commands/train.md -@@ -0,0 +1 @@ -+# Train -\ No newline at end of file -diff --git a/docs/source/commands/train_test_split.md b/docs/source/commands/train_test_split.md -new file mode 100644 -index 0000000..e28a8c8 ---- /dev/null -+++ b/docs/source/commands/train_test_split.md -@@ -0,0 +1 @@ -+# Train Test Split -\ No newline at end of file -diff --git a/docs/source/conf.py b/docs/source/conf.py -index 8a8b336..8f3a9d3 100644 ---- a/docs/source/conf.py -+++ b/docs/source/conf.py -@@ -36,7 +36,8 @@ - "nbsphinx", - "sphinx.ext.autodoc", - "sphinx.ext.napoleon", -- "sphinx.ext.autosectionlabel" -+ "sphinx.ext.autosectionlabel", -+ "sphinxarg.ext" - ] - - # Add any paths that contain templates here, relative to this directory. -diff --git a/docs/source/index.md b/docs/source/index.md -index af67119..13b414e 100644 ---- a/docs/source/index.md -+++ b/docs/source/index.md -@@ -13,7 +13,7 @@ - - ```{toctree} - :caption: 'Contents:' --:maxdepth: 2 -+:maxdepth: 3 - - installation - tutorial -diff --git a/docs/source/installation.md b/docs/source/installation.md -index fc4a774..8eca25e 100644 ---- a/docs/source/installation.md -+++ b/docs/source/installation.md -@@ -1,172 +1,28 @@ - # Installation - --**

(Recommended) Click here to install *using Anaconda*

** -- --If you do not have the Anaconda python distribution, [please install it following the instructions on their website](https://www.anaconda.com/download). -- --We strongly recommend installing Topaz into a separate conda environment. To create a conda environment for Topaz: --``` --conda create -n topaz python=3.6 # or 2.7 if you prefer python 2 --source activate topaz # this changes to the topaz conda environment, 'conda activate topaz' can be used with anaconda >= 4.4 if properly configured --# source deactivate # returns to the base conda environment --``` --More information on conda environments can be found [here](https://conda.io/docs/user-guide/tasks/manage-environments.html). -- --## Install Topaz -- --To install the precompiled Topaz package and its dependencies, including pytorch: --``` --conda install topaz -c tbepler -c pytorch --``` --This installs pytorch from the official channel. To install pytorch for specific cuda versions, you will need to add the 'cudatoolkit=X.X' package. E.g. to install pytorch for CUDA 9.0: --``` --conda install cudatoolkit=9.0 -c pytorch --``` --or combined into a single command: --``` --conda install topaz cudatoolkit=9.0 -c tbepler -c pytorch --``` --See [here](https://pytorch.org/get-started/locally/) for additional pytorch installation instructions. -- --That's it! Topaz is now installed in your anaconda environment. -- --

-- --**
Click here to install *using Pip*

** -- --We strongly recommend installing Topaz into a _virtual environment_. See [installation instructions](https://virtualenv.pypa.io/en/latest/installation/) and [user guide](https://virtualenv.pypa.io/en/latest/userguide/) for virtualenv. -- --### Install Topaz -- --To install Topaz for Python 3.X --``` --pip3 install topaz-em --``` -- --for Python 2.7 --``` --pip install topaz-em --``` --See [here](https://pytorch.org/get-started/locally/) for additional pytorch installation instructions, including how to install pytorch for specific CUDA versions. -- --That's it! Topaz is now installed through pip. -- --

-- --**
Click here to install *using Docker*

** -- --**

Do you have Docker installed? If not, *click here*

** -- --#### Linux/MacOS    *(command line)* -- --Download and install Docker 1.21 or greater for [Linux](https://docs.docker.com/engine/installation/) or [MacOS](https://store.docker.com/editions/community/docker-ce-desktop-mac). -- --> Consider using a Docker 'convenience script' to install (search on your OS's Docker installation webpage). -- --Launch docker according to your Docker engine's instructions, typically ``docker start``. -- --> **Note:** You must have sudo or root access to *install* Docker. If you do not wish to *run* Docker as sudo/root, you need to configure user groups as described here: https://docs.docker.com/install/linux/linux-postinstall/ -- --#### Windows    *(GUI & command line)* -- --Download and install [Docker Toolbox for Windows](https://docs.docker.com/toolbox/toolbox_install_windows/). -- --Launch Kitematic. -- --> If on first startup Kitematic displays a red error suggesting that you run using VirtualBox, do so. -- --> **Note:** [Docker Toolbox for MacOS](https://docs.docker.com/toolbox/toolbox_install_mac/) has not yet been tested. -- -- --### What is Docker? -- --[This tutorial explains why Docker is useful.](https://www.youtube.com/watch?v=YFl2mCHdv24) -- -- -- --A Dockerfile is provided to build images with CUDA support. Build from the github repo: --``` --docker build -t topaz https://github.com/tbepler/topaz.git --``` -- --or download the source code and build from the source directory --``` --git clone https://github.com/tbepler/topaz --cd topaz --docker build -t topaz . --``` -- --

-- -- --**
Click here to install *using Singularity*

** -- --A prebuilt Singularity image for Topaz is available [here](https://singularity-hub.org/collections/2413) and can be installed with: --``` --singularity pull shub://nysbc/topaz --``` -- --Then, you can run topaz from within the singularity image with (paths must be changed appropriately): -+## Conda -+```{include} installation/conda_install.md - ``` --singularity exec --nv -B /mounted_path:/mounted_path /path/to/singularity/container/topaz_latest.sif /usr/local/conda/bin/topaz --``` -- --

-- -- --**
Click here to install *from source*

** -- --_Recommended: install Topaz into a virtual Python environment_ --See https://conda.io/docs/user-guide/tasks/manage-environments.html or https://virtualenv.pypa.io/en/stable/ for setting one up. -- --#### Install the dependencies -- --Tested with python 3.6 and 2.7 -- --- pytorch (>= 1.0.0) --- torchvision --- pillow (>= 6.2.0) --- numpy (>= 1.11) --- pandas (>= 0.20.3) --- scipy (>= 0.19.1) --- scikit-learn (>= 0.19.0) -- --Easy installation of dependencies with conda --``` --conda install numpy pandas scikit-learn --conda install -c pytorch pytorch torchvision --``` --For more info on installing pytorch for your CUDA version see https://pytorch.org/get-started/locally/ -- --#### Download the source code --``` --git clone https://github.com/tbepler/topaz --``` -- --#### Install Topaz -+

- --Move to the source code directory --``` --cd topaz -+## Pip -+```{include} installation/pip_install.md - ``` -+

- --By default, this will be the most recent version of the topaz source code. To install a specific older version, checkout that commit. For example, for v0.1.0 of Topaz: -+## Docker -+```{include} installation/docker_install.md - ``` --git checkout v0.1.0 --``` --Note that older Topaz versions may have different dependencies. Refer to the README for the specific Topaz version. -+

- --Install Topaz into your Python path including the topaz command line interface --``` --pip install . -+## Singularity -+```{include} installation/singularity.md - ``` -+

- --To install for development use -+## From Source -+```{include} installation/source_install.md - ``` --pip install -e . --``` -- --

-

- - Topaz is also available through [SBGrid](https://sbgrid.org/software/titles/topaz). -\ No newline at end of file -diff --git a/docs/source/installation/conda_install.md b/docs/source/installation/conda_install.md -new file mode 100644 -index 0000000..06476c9 ---- /dev/null -+++ b/docs/source/installation/conda_install.md -@@ -0,0 +1,32 @@ -+**

(Recommended) Click here to install *using Anaconda*

** -+ -+If you do not have the Anaconda python distribution, [please install it following the instructions on their website](https://www.anaconda.com/download). -+ -+We strongly recommend installing Topaz into a separate conda environment. To create a conda environment for Topaz: -+``` -+conda create -n topaz python=3.6 # or 2.7 if you prefer python 2 -+source activate topaz # this changes to the topaz conda environment, 'conda activate topaz' can be used with anaconda >= 4.4 if properly configured -+# source deactivate # returns to the base conda environment -+``` -+More information on conda environments can be found [here](https://conda.io/docs/user-guide/tasks/manage-environments.html). -+ -+\ -+**Install Topaz** -+ -+To install the precompiled Topaz package and its dependencies, including pytorch: -+``` -+conda install topaz -c tbepler -c pytorch -+``` -+This installs pytorch from the official channel. To install pytorch for specific cuda versions, you will need to add the 'cudatoolkit=X.X' package. E.g. to install pytorch for CUDA 9.0: -+``` -+conda install cudatoolkit=9.0 -c pytorch -+``` -+or combined into a single command: -+``` -+conda install topaz cudatoolkit=9.0 -c tbepler -c pytorch -+``` -+See [here](https://pytorch.org/get-started/locally/) for additional pytorch installation instructions. -+ -+That's it! Topaz is now installed in your anaconda environment. -+ -+

-\ No newline at end of file -diff --git a/docs/source/installation/docker_install.md b/docs/source/installation/docker_install.md -new file mode 100644 -index 0000000..913ffd0 ---- /dev/null -+++ b/docs/source/installation/docker_install.md -@@ -0,0 +1,51 @@ -+**
Click here to install *using Docker*

** -+ -+**

What is Docker?

** -+ -+[This tutorial explains why Docker is useful.](https://www.youtube.com/watch?v=YFl2mCHdv24) -+

-+ -+ -+**
Do you have Docker installed? If not, *click here*

** -+ -+**

Linux/MacOS    *(command line)*

** -+ -+

-+Download and install Docker 1.21 or greater for [Linux](https://docs.docker.com/engine/installation/) or [MacOS](https://store.docker.com/editions/community/docker-ce-desktop-mac). -+ -+> Consider using a Docker 'convenience script' to install (search on your OS's Docker installation webpage). -+ -+Launch docker according to your Docker engine's instructions, typically ``docker start``. -+ -+> **Note:** You must have sudo or root access to *install* Docker. If you do not wish to *run* Docker as sudo/root, you need to configure user groups as described here: https://docs.docker.com/install/linux/linux-postinstall/ -+

-+ -+ -+**
Windows    *(GUI & command line)*

** -+ -+

-+Download and install [Docker Toolbox for Windows](https://docs.docker.com/toolbox/toolbox_install_windows/). -+ -+Launch Kitematic. -+ -+> If on first startup Kitematic displays a red error suggesting that you run using VirtualBox, do so. -+ -+> **Note:** [Docker Toolbox for MacOS](https://docs.docker.com/toolbox/toolbox_install_mac/) has not yet been tested. -+

-+ -+

-+

-+ -+\ -+A Dockerfile is provided to build images with CUDA support. Build from the github repo: -+``` -+docker build -t topaz https://github.com/tbepler/topaz.git -+``` -+ -+or download the source code and build from the source directory -+``` -+git clone https://github.com/tbepler/topaz -+cd topaz -+docker build -t topaz . -+``` -+

-\ No newline at end of file -diff --git a/docs/source/installation/pip_install.md b/docs/source/installation/pip_install.md -new file mode 100644 -index 0000000..e65f64e ---- /dev/null -+++ b/docs/source/installation/pip_install.md -@@ -0,0 +1,20 @@ -+**
Click here to install *using Pip*

** -+ -+We strongly recommend installing Topaz into a _virtual environment_. See [installation instructions](https://virtualenv.pypa.io/en/latest/installation/) and [user guide](https://virtualenv.pypa.io/en/latest/userguide/) for virtualenv. -+ -+**Install Topaz** -+ -+To install Topaz for Python 3.X -+``` -+pip3 install topaz-em -+``` -+ -+for Python 2.7 -+``` -+pip install topaz-em -+``` -+See [here](https://pytorch.org/get-started/locally/) for additional pytorch installation instructions, including how to install pytorch for specific CUDA versions. -+ -+That's it! Topaz is now installed through pip. -+ -+

-\ No newline at end of file -diff --git a/docs/source/installation/singularity.md b/docs/source/installation/singularity.md -new file mode 100644 -index 0000000..401c819 ---- /dev/null -+++ b/docs/source/installation/singularity.md -@@ -0,0 +1,11 @@ -+**
Click here to install *using Singularity*

** -+A prebuilt Singularity image for Topaz is available [here](https://singularity-hub.org/collections/2413) and can be installed with: -+``` -+singularity pull shub://nysbc/topaz -+``` -+ -+Then, you can run topaz from within the singularity image with (paths must be changed appropriately): -+``` -+singularity exec --nv -B /mounted_path:/mounted_path /path/to/singularity/container/topaz_latest.sif /usr/local/conda/bin/topaz -+``` -+

-\ No newline at end of file -diff --git a/docs/source/installation/source_install.md b/docs/source/installation/source_install.md -new file mode 100644 -index 0000000..648dfc8 ---- /dev/null -+++ b/docs/source/installation/source_install.md -@@ -0,0 +1,57 @@ -+**
Click here to install *from source*

** -+ -+_Recommended: install Topaz into a virtual Python environment_ -+See https://conda.io/docs/user-guide/tasks/manage-environments.html or https://virtualenv.pypa.io/en/stable/ for setting one up. -+ -+\ -+**Install the dependencies** -+ -+Tested with python 3.6 and 2.7 -+ -+- pytorch (>= 1.0.0) -+- torchvision -+- pillow (>= 6.2.0) -+- numpy (>= 1.11) -+- pandas (>= 0.20.3) -+- scipy (>= 0.19.1) -+- scikit-learn (>= 0.19.0) -+ -+Easy installation of dependencies with conda -+``` -+conda install numpy pandas scikit-learn -+conda install -c pytorch pytorch torchvision -+``` -+For more info on installing pytorch for your CUDA version see https://pytorch.org/get-started/locally/ -+ -+\ -+**Download the source code** -+``` -+git clone https://github.com/tbepler/topaz -+``` -+ -+\ -+**Install Topaz** -+ -+Move to the source code directory -+``` -+cd topaz -+``` -+ -+By default, this will be the most recent version of the topaz source code. To install a specific older version, checkout that commit. For example, for v0.1.0 of Topaz: -+``` -+git checkout v0.1.0 -+``` -+Note that older Topaz versions may have different dependencies. Refer to the README for the specific Topaz version. -+ -+Install Topaz into your Python path including the topaz command line interface -+``` -+pip install . -+``` -+ -+To install for development use -+``` -+pip install -e . -+``` -+ -+

-+

-\ No newline at end of file -diff --git a/docs/source/tutorial.md b/docs/source/tutorial.md -index 161a880..c2ebb97 100644 ---- a/docs/source/tutorial.md -+++ b/docs/source/tutorial.md -@@ -1,4 +1,7 @@ --# Tutorial -+# Tutorials (coming soon) -+ -+Tutorial pages here are a work-in-progress. For the time being, please refer to the tutorial notebooks in topaz/tutorial. -+ - +\ No newline at end of file +diff --git a/docs/source/index.md b/docs/source/index.md +index 71ef567..1ab1b7c 100644 +--- a/docs/source/index.md ++++ b/docs/source/index.md +@@ -6,8 +6,7 @@ + # Welcome to Topaz's documentation! + + +-```{include} ../../README.md +-:relative-images: ++```{include} ./description.md + ``` + + +@@ -15,4 +14,12 @@ + ```{toctree} + :caption: 'Contents:' + :maxdepth: 2 ++ ++installation ++tutorial ++commands ++relion ++cryosparc ++models ++scripts + ``` +diff --git a/docs/source/installation.md b/docs/source/installation.md +new file mode 100644 +index 0000000..fc4a774 +--- /dev/null ++++ b/docs/source/installation.md +@@ -0,0 +1,172 @@ ++# Installation ++ ++**

(Recommended) Click here to install *using Anaconda*

** ++ ++If you do not have the Anaconda python distribution, [please install it following the instructions on their website](https://www.anaconda.com/download). ++ ++We strongly recommend installing Topaz into a separate conda environment. To create a conda environment for Topaz: ++``` ++conda create -n topaz python=3.6 # or 2.7 if you prefer python 2 ++source activate topaz # this changes to the topaz conda environment, 'conda activate topaz' can be used with anaconda >= 4.4 if properly configured ++# source deactivate # returns to the base conda environment ++``` ++More information on conda environments can be found [here](https://conda.io/docs/user-guide/tasks/manage-environments.html). ++ ++## Install Topaz ++ ++To install the precompiled Topaz package and its dependencies, including pytorch: ++``` ++conda install topaz -c tbepler -c pytorch ++``` ++This installs pytorch from the official channel. To install pytorch for specific cuda versions, you will need to add the 'cudatoolkit=X.X' package. E.g. to install pytorch for CUDA 9.0: ++``` ++conda install cudatoolkit=9.0 -c pytorch ++``` ++or combined into a single command: ++``` ++conda install topaz cudatoolkit=9.0 -c tbepler -c pytorch ++``` ++See [here](https://pytorch.org/get-started/locally/) for additional pytorch installation instructions. ++ ++That's it! Topaz is now installed in your anaconda environment. ++ ++

++ ++**
Click here to install *using Pip*

** ++ ++We strongly recommend installing Topaz into a _virtual environment_. See [installation instructions](https://virtualenv.pypa.io/en/latest/installation/) and [user guide](https://virtualenv.pypa.io/en/latest/userguide/) for virtualenv. ++ ++### Install Topaz ++ ++To install Topaz for Python 3.X ++``` ++pip3 install topaz-em ++``` ++ ++for Python 2.7 ++``` ++pip install topaz-em ++``` ++See [here](https://pytorch.org/get-started/locally/) for additional pytorch installation instructions, including how to install pytorch for specific CUDA versions. ++ ++That's it! Topaz is now installed through pip. ++ ++

++ ++**
Click here to install *using Docker*

** ++ ++**

Do you have Docker installed? If not, *click here*

** ++ ++#### Linux/MacOS    *(command line)* ++ ++Download and install Docker 1.21 or greater for [Linux](https://docs.docker.com/engine/installation/) or [MacOS](https://store.docker.com/editions/community/docker-ce-desktop-mac). ++ ++> Consider using a Docker 'convenience script' to install (search on your OS's Docker installation webpage). ++ ++Launch docker according to your Docker engine's instructions, typically ``docker start``. ++ ++> **Note:** You must have sudo or root access to *install* Docker. If you do not wish to *run* Docker as sudo/root, you need to configure user groups as described here: https://docs.docker.com/install/linux/linux-postinstall/ ++ ++#### Windows    *(GUI & command line)* ++ ++Download and install [Docker Toolbox for Windows](https://docs.docker.com/toolbox/toolbox_install_windows/). ++ ++Launch Kitematic. ++ ++> If on first startup Kitematic displays a red error suggesting that you run using VirtualBox, do so. ++ ++> **Note:** [Docker Toolbox for MacOS](https://docs.docker.com/toolbox/toolbox_install_mac/) has not yet been tested. ++ ++ ++### What is Docker? ++ ++[This tutorial explains why Docker is useful.](https://www.youtube.com/watch?v=YFl2mCHdv24) ++ ++ ++ ++A Dockerfile is provided to build images with CUDA support. Build from the github repo: ++``` ++docker build -t topaz https://github.com/tbepler/topaz.git ++``` ++ ++or download the source code and build from the source directory ++``` ++git clone https://github.com/tbepler/topaz ++cd topaz ++docker build -t topaz . ++``` ++ ++

++ ++ ++**
Click here to install *using Singularity*

** ++ ++A prebuilt Singularity image for Topaz is available [here](https://singularity-hub.org/collections/2413) and can be installed with: ++``` ++singularity pull shub://nysbc/topaz ++``` ++ ++Then, you can run topaz from within the singularity image with (paths must be changed appropriately): ++``` ++singularity exec --nv -B /mounted_path:/mounted_path /path/to/singularity/container/topaz_latest.sif /usr/local/conda/bin/topaz ++``` ++ ++

++ ++ ++**
Click here to install *from source*

** ++ ++_Recommended: install Topaz into a virtual Python environment_ ++See https://conda.io/docs/user-guide/tasks/manage-environments.html or https://virtualenv.pypa.io/en/stable/ for setting one up. ++ ++#### Install the dependencies ++ ++Tested with python 3.6 and 2.7 ++ ++- pytorch (>= 1.0.0) ++- torchvision ++- pillow (>= 6.2.0) ++- numpy (>= 1.11) ++- pandas (>= 0.20.3) ++- scipy (>= 0.19.1) ++- scikit-learn (>= 0.19.0) ++ ++Easy installation of dependencies with conda ++``` ++conda install numpy pandas scikit-learn ++conda install -c pytorch pytorch torchvision ++``` ++For more info on installing pytorch for your CUDA version see https://pytorch.org/get-started/locally/ ++ ++#### Download the source code ++``` ++git clone https://github.com/tbepler/topaz ++``` ++ ++#### Install Topaz ++ ++Move to the source code directory ++``` ++cd topaz ++``` ++ ++By default, this will be the most recent version of the topaz source code. To install a specific older version, checkout that commit. For example, for v0.1.0 of Topaz: ++``` ++git checkout v0.1.0 ++``` ++Note that older Topaz versions may have different dependencies. Refer to the README for the specific Topaz version. ++ ++Install Topaz into your Python path including the topaz command line interface ++``` ++pip install . ++``` ++ ++To install for development use ++``` ++pip install -e . ++``` ++ ++

++

++ ++Topaz is also available through [SBGrid](https://sbgrid.org/software/titles/topaz). +\ No newline at end of file +diff --git a/docs/source/models.md b/docs/source/models.md +new file mode 100644 +index 0000000..574c6fb +--- /dev/null ++++ b/docs/source/models.md +@@ -0,0 +1,11 @@ ++# Models ++ ++```{eval-rst} ++.. autoclass:: topaz.model.classifier.LinearClassifier ++``` ++ ++## Features ++ ++```{eval-rst} ++.. autoclass:: topaz.model.features.basic.BasicConv ++``` +\ No newline at end of file +diff --git a/docs/source/relion.md b/docs/source/relion.md +new file mode 100644 +index 0000000..7c94e56 +--- /dev/null ++++ b/docs/source/relion.md +@@ -0,0 +1 @@ ++## Use with RELION +\ No newline at end of file +diff --git a/docs/source/scripts.md b/docs/source/scripts.md +new file mode 100644 +index 0000000..82916c1 +--- /dev/null ++++ b/docs/source/scripts.md +@@ -0,0 +1 @@ ++# Scripts +\ No newline at end of file +diff --git a/docs/source/tutorial.md b/docs/source/tutorial.md +new file mode 100644 +index 0000000..161a880 +--- /dev/null ++++ b/docs/source/tutorial.md +@@ -0,0 +1,15 @@ ++# Tutorial ++ +diff --git a/topaz/model/classifier.py b/topaz/model/classifier.py +index be1c3de..bb4710f 100644 +--- a/topaz/model/classifier.py ++++ b/topaz/model/classifier.py +@@ -6,6 +6,15 @@ + + class LinearClassifier(nn.Module): + def __init__(self, features): ++ ''' ++ A simple convolutional layer with no non-linear activation. ++ ++ Args: ++ features (:obj:): the sizes associated with the layer ++ ++ Attributes: ++ features (:obj:) ++ ''' + super(LinearClassifier, self).__init__() + self.features = features + self.classifier = nn.Conv2d(features.latent_dim, 1, 1) + +From e064f07d52ba152e79a664c16d64cbbbf46067e3 Mon Sep 17 00:00:00 2001 +From: Darnell Granberry <40174000+DarnellGranberry@users.noreply.github.com> +Date: Wed, 16 Mar 2022 10:49:08 -0400 +Subject: [PATCH 03/28] updated doc requirements for rtd + +--- + .readthedocs.yaml | 11 +++-------- + docs/requirements.txt | 15 +++++++++++++++ + 2 files changed, 18 insertions(+), 8 deletions(-) + create mode 100644 docs/requirements.txt + +diff --git a/.readthedocs.yaml b/.readthedocs.yaml +index b67d3bf..7468b70 100644 +--- a/.readthedocs.yaml ++++ b/.readthedocs.yaml +@@ -11,11 +11,6 @@ sphinx: + python: + install: + - method: pip +- path: . +- extra_requirements: +- - docs +- - nbsphinx +- - sphinx_rtd_theme +- - sphinx-autobuild +- - rst-to-myst +- - myst-parser +\ No newline at end of file ++ - requirements: docs/requirements.txt ++ - extra-requirements: ++ - doc +\ No newline at end of file +diff --git a/docs/requirements.txt b/docs/requirements.txt +new file mode 100644 +index 0000000..46d9223 +--- /dev/null ++++ b/docs/requirements.txt +@@ -0,0 +1,15 @@ ++# torch >= 1.0.0 ++# torchvision ++# numpy >= 1.11 ++# pandas ++# scikit-learn >= 0.19.0 ++# scipy >= 0.17.0 ++# pillow >= 6.2.0 ++# future ++ ++sphinx ++sphinx_rtd_theme ++sphinx-autobuild ++rst-to-myst ++myst-parser ++nbsphinx +\ No newline at end of file + +From d80d47b01d4e919d4e0be86e4790e65074158b18 Mon Sep 17 00:00:00 2001 +From: Darnell Granberry <40174000+DarnellGranberry@users.noreply.github.com> +Date: Wed, 16 Mar 2022 10:52:10 -0400 +Subject: [PATCH 04/28] Restored path in rtd.yaml + +--- + .readthedocs.yaml | 1 + + 1 file changed, 1 insertion(+) + +diff --git a/.readthedocs.yaml b/.readthedocs.yaml +index 7468b70..037a6c0 100644 +--- a/.readthedocs.yaml ++++ b/.readthedocs.yaml +@@ -11,6 +11,7 @@ sphinx: + python: + install: + - method: pip ++ - path: . + - requirements: docs/requirements.txt + - extra-requirements: + - doc +\ No newline at end of file + +From bba83e16c33c0614fa63a0f363677032f6086234 Mon Sep 17 00:00:00 2001 +From: Darnell Granberry <40174000+DarnellGranberry@users.noreply.github.com> +Date: Wed, 16 Mar 2022 14:14:58 -0400 +Subject: [PATCH 05/28] Corrected rtd yaml formatting + +--- + .readthedocs.yaml | 7 ++++--- + 1 file changed, 4 insertions(+), 3 deletions(-) + +diff --git a/.readthedocs.yaml b/.readthedocs.yaml +index 037a6c0..fc40b17 100644 +--- a/.readthedocs.yaml ++++ b/.readthedocs.yaml +@@ -11,7 +11,8 @@ sphinx: + python: + install: + - method: pip +- - path: . +- - requirements: docs/requirements.txt +- - extra-requirements: ++ path: . ++ requirements: docs/requirements.txt ++ requirements: requirements.txt ++ extra-requirements: + - doc +\ No newline at end of file + +From 1c5f11140f7f063a214e11e9787f779844423bd8 Mon Sep 17 00:00:00 2001 +From: Darnell Granberry <40174000+DarnellGranberry@users.noreply.github.com> +Date: Wed, 16 Mar 2022 14:36:29 -0400 +Subject: [PATCH 06/28] added docs requirements, edited rtd.yaml + +--- + .readthedocs.yaml | 5 +---- + docs/requirements.txt | 10 ++++------ + requirements.txt | 5 +++++ + 3 files changed, 10 insertions(+), 10 deletions(-) + +diff --git a/.readthedocs.yaml b/.readthedocs.yaml +index fc40b17..b9870ed 100644 +--- a/.readthedocs.yaml ++++ b/.readthedocs.yaml +@@ -12,7 +12,4 @@ python: + install: + - method: pip + path: . +- requirements: docs/requirements.txt +- requirements: requirements.txt +- extra-requirements: +- - doc +\ No newline at end of file ++ requirements: requirements.txt +\ No newline at end of file +diff --git a/docs/requirements.txt b/docs/requirements.txt +index 46d9223..e7f2aa5 100644 +--- a/docs/requirements.txt ++++ b/docs/requirements.txt +@@ -6,10 +6,8 @@ + # scipy >= 0.17.0 + # pillow >= 6.2.0 + # future +- +-sphinx ++sphinx==4.4.0 + sphinx_rtd_theme +-sphinx-autobuild +-rst-to-myst +-myst-parser +-nbsphinx +\ No newline at end of file ++rst-to-myst==0.3.2 ++myst-parser==0.17.0 ++nbsphinx==0.8.8 +\ No newline at end of file +diff --git a/requirements.txt b/requirements.txt +index 4e7245f..01c0804 100644 +--- a/requirements.txt ++++ b/requirements.txt +@@ -6,3 +6,8 @@ scikit-learn >= 0.19.0 + scipy >= 0.17.0 + pillow >= 6.2.0 + future ++sphinx==4.4.0 ++sphinx_rtd_theme ++rst-to-myst==0.3.2 ++myst-parser==0.17.0 ++nbsphinx==0.8.8 +\ No newline at end of file + +From ed7de9c2d2e89fc3a254b3c0882d6c2e2b981205 Mon Sep 17 00:00:00 2001 +From: Darnell Granberry <40174000+DarnellGranberry@users.noreply.github.com> +Date: Wed, 16 Mar 2022 14:46:51 -0400 +Subject: [PATCH 07/28] Reordered rtd.yaml args + +--- + .readthedocs.yaml | 4 +++- + 1 file changed, 3 insertions(+), 1 deletion(-) + +diff --git a/.readthedocs.yaml b/.readthedocs.yaml +index b9870ed..6722c59 100644 +--- a/.readthedocs.yaml ++++ b/.readthedocs.yaml +@@ -10,6 +10,8 @@ sphinx: + + python: + install: ++ - requirements: docs/requirements.txt + - method: pip + path: . +- requirements: requirements.txt +\ No newline at end of file ++ extra_requirements: ++ - docs +\ No newline at end of file + +From 683093572078eb20e9aebfa5daeb931ddb3c5bbc Mon Sep 17 00:00:00 2001 +From: Darnell Granberry <40174000+DarnellGranberry@users.noreply.github.com> +Date: Wed, 16 Mar 2022 14:50:07 -0400 +Subject: [PATCH 08/28] removed doc versions pkg version + +--- + docs/requirements.txt | 6 +++--- + 1 file changed, 3 insertions(+), 3 deletions(-) + +diff --git a/docs/requirements.txt b/docs/requirements.txt +index e7f2aa5..f12e5f7 100644 +--- a/docs/requirements.txt ++++ b/docs/requirements.txt +@@ -8,6 +8,6 @@ + # future + sphinx==4.4.0 + sphinx_rtd_theme +-rst-to-myst==0.3.2 +-myst-parser==0.17.0 +-nbsphinx==0.8.8 +\ No newline at end of file ++rst-to-myst ++myst-parser ++nbsphinx +\ No newline at end of file + +From c3415895c8515696be1a88c2bfde242c3c2999f7 Mon Sep 17 00:00:00 2001 +From: Darnell Granberry <40174000+DarnellGranberry@users.noreply.github.com> +Date: Wed, 16 Mar 2022 14:55:36 -0400 +Subject: [PATCH 09/28] Add docs status to readme + +--- + README.md | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/README.md b/README.md +index 5987691..f2b6433 100644 +--- a/README.md ++++ b/README.md +@@ -1,5 +1,5 @@ + [![Python package](https://github.com/tbepler/topaz/actions/workflows/ci.yml/badge.svg)](https://github.com/tbepler/topaz/actions/workflows/ci.yml) +- ++[![Documentation Status](https://readthedocs.org/projects/topaz-em/badge/?version=latest)](https://topaz-em.readthedocs.io/en/latest/?badge=latest) + + + # Topaz + +From 538286e7a4780d31f163e95011e89a68fc418b9f Mon Sep 17 00:00:00 2001 +From: Darnell Granberry <40174000+DarnellGranberry@users.noreply.github.com> +Date: Wed, 16 Mar 2022 15:00:17 -0400 +Subject: [PATCH 10/28] Added version and conda install badges + +--- + README.md | 2 ++ + 1 file changed, 2 insertions(+) + +diff --git a/README.md b/README.md +index f2b6433..f3832bd 100644 +--- a/README.md ++++ b/README.md +@@ -1,5 +1,7 @@ + [![Python package](https://github.com/tbepler/topaz/actions/workflows/ci.yml/badge.svg)](https://github.com/tbepler/topaz/actions/workflows/ci.yml) + [![Documentation Status](https://readthedocs.org/projects/topaz-em/badge/?version=latest)](https://topaz-em.readthedocs.io/en/latest/?badge=latest) ++[![Anaconda-Server Badge](https://anaconda.org/tbepler/topaz/badges/version.svg)](https://anaconda.org/tbepler/topaz) ++[![Anaconda-Server Badge](https://anaconda.org/tbepler/topaz/badges/installer/conda.svg)](https://conda.anaconda.org/tbepler) + + + # Topaz + +From 2c13c55fa3080741571b868f6275b1839456e45e Mon Sep 17 00:00:00 2001 +From: Darnell Granberry <40174000+DarnellGranberry@users.noreply.github.com> +Date: Wed, 16 Mar 2022 15:05:11 -0400 +Subject: [PATCH 11/28] removed duplicate docs requirements + +--- + requirements.txt | 7 +------ + 1 file changed, 1 insertion(+), 6 deletions(-) + +diff --git a/requirements.txt b/requirements.txt +index 01c0804..d83f97b 100644 +--- a/requirements.txt ++++ b/requirements.txt +@@ -5,9 +5,4 @@ pandas + scikit-learn >= 0.19.0 + scipy >= 0.17.0 + pillow >= 6.2.0 +-future +-sphinx==4.4.0 +-sphinx_rtd_theme +-rst-to-myst==0.3.2 +-myst-parser==0.17.0 +-nbsphinx==0.8.8 +\ No newline at end of file ++future +\ No newline at end of file + +From 06f301640ea566f9baae816edb0a908ffafca444 Mon Sep 17 00:00:00 2001 +From: Darnell Granberry <40174000+DarnellGranberry@users.noreply.github.com> +Date: Thu, 17 Mar 2022 17:50:20 -0400 +Subject: [PATCH 12/28] Created doc entries for most code except commands + +--- + docs/source/algorithms.md | 7 +++ + docs/source/conf.py | 4 +- + docs/source/denoising.md | 7 +++ + docs/source/index.md | 10 ++++- + docs/source/methods.md | 7 +++ + docs/source/metrics_stats.md | 14 ++++++ + docs/source/models.md | 52 +++++++++++++++++++++- + docs/source/transforms.md | 7 +++ + docs/source/utils.md | 81 +++++++++++++++++++++++++++++++++++ + topaz/_version.py | 2 +- + topaz/model/classifier.py | 12 +++++- + topaz/model/features/basic.py | 2 + + 12 files changed, 197 insertions(+), 8 deletions(-) + create mode 100644 docs/source/algorithms.md + create mode 100644 docs/source/denoising.md + create mode 100644 docs/source/methods.md + create mode 100644 docs/source/metrics_stats.md + create mode 100644 docs/source/transforms.md + create mode 100644 docs/source/utils.md + +diff --git a/docs/source/algorithms.md b/docs/source/algorithms.md +new file mode 100644 +index 0000000..0a617c9 +--- /dev/null ++++ b/docs/source/algorithms.md +@@ -0,0 +1,7 @@ ++# Algorithms ++ ++```{eval-rst} ++.. automodule:: topaz.algorithms ++ :members: ++ :undoc-members: ++``` +\ No newline at end of file +diff --git a/docs/source/conf.py b/docs/source/conf.py +index cac08bc..8a8b336 100644 +--- a/docs/source/conf.py ++++ b/docs/source/conf.py +@@ -34,7 +34,9 @@ + extensions = [ + "myst_parser", + "nbsphinx", +- "sphinx.ext.autodoc" ++ "sphinx.ext.autodoc", ++ "sphinx.ext.napoleon", ++ "sphinx.ext.autosectionlabel" + ] + + # Add any paths that contain templates here, relative to this directory. +diff --git a/docs/source/denoising.md b/docs/source/denoising.md +new file mode 100644 +index 0000000..036d4d5 +--- /dev/null ++++ b/docs/source/denoising.md +@@ -0,0 +1,7 @@ ++# Denoising ++ ++```{eval-rst} ++.. automodule:: topaz.denoise ++ :members: ++ :undoc-members: ++``` +\ No newline at end of file +diff --git a/docs/source/index.md b/docs/source/index.md +index 1ab1b7c..af67119 100644 +--- a/docs/source/index.md ++++ b/docs/source/index.md +@@ -18,8 +18,14 @@ + installation + tutorial + commands +-relion +-cryosparc ++algorithms ++denoising ++methods ++metrics_stats + models ++transforms ++utils + scripts ++relion ++cryosparc + ``` +diff --git a/docs/source/methods.md b/docs/source/methods.md +new file mode 100644 +index 0000000..aed5cfd +--- /dev/null ++++ b/docs/source/methods.md +@@ -0,0 +1,7 @@ ++# Methods ++ ++```{eval-rst} ++.. automodule:: topaz.methods ++ :members: ++ :undoc-members: ++``` +\ No newline at end of file +diff --git a/docs/source/metrics_stats.md b/docs/source/metrics_stats.md +new file mode 100644 +index 0000000..dcfe0c4 +--- /dev/null ++++ b/docs/source/metrics_stats.md +@@ -0,0 +1,14 @@ ++# Metrics and Statistics ++ ++```{eval-rst} ++.. automodule:: topaz.metrics ++ :members: ++ :undoc-members: ++``` ++ ++ ++```{eval-rst} ++.. automodule:: topaz.stats ++ :members: ++ :undoc-members: ++``` +\ No newline at end of file +diff --git a/docs/source/models.md b/docs/source/models.md +index 574c6fb..dbad6b1 100644 +--- a/docs/source/models.md ++++ b/docs/source/models.md +@@ -1,11 +1,59 @@ + # Models + ++## Feature Extractors ++ ++### Basic Conv Nets ++```{eval-rst} ++.. automodule:: topaz.model.features.basic ++ :members: ++ :undoc-members: ++``` ++ ++### DenseNets ++```{eval-rst} ++.. automodule:: topaz.model.features.densenet ++ :members: ++ :undoc-members: ++``` ++ ++### MSNets ++```{eval-rst} ++.. automodule:: topaz.model.features.msnet ++ :members: ++ :undoc-members: ++``` ++ ++### ResNets ++```{eval-rst} ++.. automodule:: topaz.model.features.resnet ++ :members: ++ :undoc-members: ++``` ++ ++## Linear Classifier + ```{eval-rst} + .. autoclass:: topaz.model.classifier.LinearClassifier ++ :members: ++ :undoc-members: + ``` + +-## Features ++## Model Factory ++```{eval-rst} ++.. automodule:: topaz.model.factory ++ :members: ++ :undoc-members: ++``` ++ ++## Model Generator ++```{eval-rst} ++.. automodule:: topaz.model.generative ++ :members: ++ :undoc-members: ++``` + ++## Model Utilities + ```{eval-rst} +-.. autoclass:: topaz.model.features.basic.BasicConv ++.. automodule:: topaz.model.utils ++ :members: ++ :undoc-members: + ``` +\ No newline at end of file +diff --git a/docs/source/transforms.md b/docs/source/transforms.md +new file mode 100644 +index 0000000..9bf1082 +--- /dev/null ++++ b/docs/source/transforms.md +@@ -0,0 +1,7 @@ ++# Transformations ++ ++```{eval-rst} ++.. automodule:: topaz.transform.scaled_gaussian_mixture ++ :members: ++ :undoc-members: ++``` +\ No newline at end of file +diff --git a/docs/source/utils.md b/docs/source/utils.md +new file mode 100644 +index 0000000..027f498 +--- /dev/null ++++ b/docs/source/utils.md +@@ -0,0 +1,81 @@ ++# Utilities ++ ++## Conversions ++```{eval-rst} ++.. automodule:: topaz.utils.conversions ++ :members: ++ :undoc-members: ++``` ++ ++## File Utilities ++```{eval-rst} ++.. automodule:: topaz.utils.conversions ++ :members: ++ :undoc-members: ++``` ++ ++ ++```{eval-rst} ++.. automodule:: topaz.mrc ++ :members: ++ :undoc-members: ++``` ++ ++ ++## Image Manipulations ++```{eval-rst} ++.. automodule:: topaz.utils.image ++ :members: ++ :undoc-members: ++``` ++ ++## Pick Masking ++```{eval-rst} ++.. automodule:: topaz.utils.picks ++ :members: ++ :undoc-members: ++``` ++ ++## Printing ++```{eval-rst} ++.. automodule:: topaz.utils.printing ++ :members: ++ :undoc-members: ++``` ++ ++## STAR File Manipulations ++```{eval-rst} ++.. automodule:: topaz.utils.star ++ :members: ++ :undoc-members: ++``` ++ ++## Data Utilities ++ ++### Coordinate Manipulations ++```{eval-rst} ++.. automodule:: topaz.utils.data.coordinates ++ :members: ++ :undoc-members: ++``` ++ ++### Image Loading ++```{eval-rst} ++.. automodule:: topaz.utils.data.loader ++ :members: ++ :undoc-members: ++``` ++ ++### Dataset Partitioning ++```{eval-rst} ++.. automodule:: topaz.utils.data.partition ++ :members: ++ :undoc-members: ++``` ++ ++### Dataset Sampling ++```{eval-rst} ++.. automodule:: topaz.utils.data.sampler ++ :members: ++ :undoc-members: ++``` +\ No newline at end of file +diff --git a/topaz/_version.py b/topaz/_version.py +index e723ff3..fe404ae 100644 +--- a/topaz/_version.py ++++ b/topaz/_version.py +@@ -1 +1 @@ +-__version__ = "0.2.5a" ++__version__ = "0.2.5" +diff --git a/topaz/model/classifier.py b/topaz/model/classifier.py +index bb4710f..d63d83c 100644 +--- a/topaz/model/classifier.py ++++ b/topaz/model/classifier.py +@@ -5,10 +5,10 @@ + import torch.nn.functional as F + + class LinearClassifier(nn.Module): ++ '''A simple convolutional layer without non-linear activation.''' ++ + def __init__(self, features): + ''' +- A simple convolutional layer with no non-linear activation. +- + Args: + features (:obj:): the sizes associated with the layer + +@@ -34,6 +34,14 @@ def unfill(self): + self.features.unfill() + + def forward(self, x): ++ '''Applies the classifier to an input. ++ ++ Args: ++ x (np.ndarray): the image from which features are extracted and classified ++ ++ Returns: ++ z (np.ndarray): output of the classifer ++ ''' + z = self.features(x) + y = self.classifier(z) + return y +diff --git a/topaz/model/features/basic.py b/topaz/model/features/basic.py +index 0ea1fe9..dff4e9f 100644 +--- a/topaz/model/features/basic.py ++++ b/topaz/model/features/basic.py +@@ -10,6 +10,8 @@ + from topaz.model.utils import insize_from_outsize + + class BasicConv(nn.Module): ++ '''A generic convolutional neural network scaffold.''' ++ + def __init__(self, layers, units, unit_scaling=1, dropout=0, bn=True + , pooling=None, activation=nn.PReLU): + super(BasicConv, self).__init__() + +From d2c9761c2fba8d996c1f117f3004eeaf5a2abad7 Mon Sep 17 00:00:00 2001 +From: Darnell Granberry <40174000+DarnellGranberry@users.noreply.github.com> +Date: Fri, 18 Mar 2022 15:44:56 -0400 +Subject: [PATCH 13/28] reorganized docs, began work on man pages + +--- + docs/requirements.txt | 3 +- + docs/source/commands.md | 20 ++- + docs/source/commands/convert.md | 1 + + docs/source/commands/denoise.md | 1 + + docs/source/commands/denoise3d.md | 1 + + docs/source/commands/downsample.md | 1 + + docs/source/commands/extract.md | 1 + + docs/source/commands/file_utilities.md | 11 ++ + docs/source/commands/gui.md | 1 + + docs/source/commands/image_processing.md | 12 ++ + docs/source/commands/normalize.md | 8 + + docs/source/commands/particle_picking.md | 11 ++ + docs/source/commands/particle_stack.md | 1 + + docs/source/commands/precision_recall.md | 1 + + docs/source/commands/preprocess.md | 1 + + docs/source/commands/segment.md | 1 + + docs/source/commands/split.md | 1 + + docs/source/commands/train.md | 1 + + docs/source/commands/train_test_split.md | 1 + + docs/source/conf.py | 3 +- + docs/source/index.md | 2 +- + docs/source/installation.md | 172 ++------------------- + docs/source/installation/conda_install.md | 32 ++++ + docs/source/installation/docker_install.md | 51 ++++++ + docs/source/installation/pip_install.md | 20 +++ + docs/source/installation/singularity.md | 11 ++ + docs/source/installation/source_install.md | 57 +++++++ + docs/source/tutorial.md | 5 +- + topaz/commands/normalize.py | 9 +- + 29 files changed, 264 insertions(+), 176 deletions(-) + create mode 100644 docs/source/commands/convert.md + create mode 100644 docs/source/commands/denoise.md + create mode 100644 docs/source/commands/denoise3d.md + create mode 100644 docs/source/commands/downsample.md + create mode 100644 docs/source/commands/extract.md + create mode 100644 docs/source/commands/file_utilities.md + create mode 100644 docs/source/commands/gui.md + create mode 100644 docs/source/commands/image_processing.md + create mode 100644 docs/source/commands/normalize.md + create mode 100644 docs/source/commands/particle_picking.md + create mode 100644 docs/source/commands/particle_stack.md + create mode 100644 docs/source/commands/precision_recall.md + create mode 100644 docs/source/commands/preprocess.md + create mode 100644 docs/source/commands/segment.md + create mode 100644 docs/source/commands/split.md + create mode 100644 docs/source/commands/train.md + create mode 100644 docs/source/commands/train_test_split.md + create mode 100644 docs/source/installation/conda_install.md + create mode 100644 docs/source/installation/docker_install.md + create mode 100644 docs/source/installation/pip_install.md + create mode 100644 docs/source/installation/singularity.md + create mode 100644 docs/source/installation/source_install.md + +diff --git a/docs/requirements.txt b/docs/requirements.txt +index f12e5f7..bd0b467 100644 +--- a/docs/requirements.txt ++++ b/docs/requirements.txt +@@ -10,4 +10,5 @@ sphinx==4.4.0 + sphinx_rtd_theme + rst-to-myst + myst-parser +-nbsphinx +\ No newline at end of file ++nbsphinx ++sphinx-argparse +\ No newline at end of file +diff --git a/docs/source/commands.md b/docs/source/commands.md +index 44c4a21..3c462c9 100644 +--- a/docs/source/commands.md ++++ b/docs/source/commands.md +@@ -1,15 +1,13 @@ +-# Topaz Commands ++# Topaz Commands (work in progress) + +-## downsample + +-## normalize ++```{toctree} ++:caption: 'Commands' ++:maxdepth: 2 + +-## preprocess ++commands/particle_picking ++commands/image_processing ++commands/file_utilities + +-## train +- +-## segment +- +-## extract +- +-## precision_recall_curve ++commands/gui ++``` +\ No newline at end of file +diff --git a/docs/source/commands/convert.md b/docs/source/commands/convert.md +new file mode 100644 +index 0000000..122f443 +--- /dev/null ++++ b/docs/source/commands/convert.md +@@ -0,0 +1 @@ ++# Convert +\ No newline at end of file +diff --git a/docs/source/commands/denoise.md b/docs/source/commands/denoise.md +new file mode 100644 +index 0000000..d995632 +--- /dev/null ++++ b/docs/source/commands/denoise.md +@@ -0,0 +1 @@ ++# Denoise +\ No newline at end of file +diff --git a/docs/source/commands/denoise3d.md b/docs/source/commands/denoise3d.md +new file mode 100644 +index 0000000..bf78fac +--- /dev/null ++++ b/docs/source/commands/denoise3d.md +@@ -0,0 +1 @@ ++# Denoise 3D +\ No newline at end of file +diff --git a/docs/source/commands/downsample.md b/docs/source/commands/downsample.md +new file mode 100644 +index 0000000..e0b15bf +--- /dev/null ++++ b/docs/source/commands/downsample.md +@@ -0,0 +1 @@ ++# Downsample +\ No newline at end of file +diff --git a/docs/source/commands/extract.md b/docs/source/commands/extract.md +new file mode 100644 +index 0000000..d0e6da9 +--- /dev/null ++++ b/docs/source/commands/extract.md +@@ -0,0 +1 @@ ++# Extract +\ No newline at end of file +diff --git a/docs/source/commands/file_utilities.md b/docs/source/commands/file_utilities.md +new file mode 100644 +index 0000000..b26444f +--- /dev/null ++++ b/docs/source/commands/file_utilities.md +@@ -0,0 +1,11 @@ ++# File Utilities ++ ++```{toctree} ++:caption: 'Commands' ++:maxdepth: 1 ++ ++convert ++split ++particle_stack ++train_test_split ++``` +\ No newline at end of file +diff --git a/docs/source/commands/gui.md b/docs/source/commands/gui.md +new file mode 100644 +index 0000000..93bd5f2 +--- /dev/null ++++ b/docs/source/commands/gui.md +@@ -0,0 +1 @@ ++# GUI +\ No newline at end of file +diff --git a/docs/source/commands/image_processing.md b/docs/source/commands/image_processing.md +new file mode 100644 +index 0000000..973048c +--- /dev/null ++++ b/docs/source/commands/image_processing.md +@@ -0,0 +1,12 @@ ++# Image Processing ++ ++```{toctree} ++:caption: 'Commands' ++:maxdepth: 1 ++ ++downsample ++normalize ++preprocess ++denoise ++denoise3d ++``` +\ No newline at end of file +diff --git a/docs/source/commands/normalize.md b/docs/source/commands/normalize.md +new file mode 100644 +index 0000000..ad442b2 +--- /dev/null ++++ b/docs/source/commands/normalize.md +@@ -0,0 +1,8 @@ ++# Normalize ++ ++```{eval-rst} ++.. argparse:: ++ :module: topaz.commands.normalize ++ :func: add_arguments ++ :prog: normalize ++``` +\ No newline at end of file +diff --git a/docs/source/commands/particle_picking.md b/docs/source/commands/particle_picking.md +new file mode 100644 +index 0000000..c32361a +--- /dev/null ++++ b/docs/source/commands/particle_picking.md +@@ -0,0 +1,11 @@ ++# Particle Picking ++ ++```{toctree} ++:caption: 'Commands' ++:maxdepth: 1 ++ ++train ++segment ++extract ++precision_recall ++``` +\ No newline at end of file +diff --git a/docs/source/commands/particle_stack.md b/docs/source/commands/particle_stack.md +new file mode 100644 +index 0000000..7bb5a5e +--- /dev/null ++++ b/docs/source/commands/particle_stack.md +@@ -0,0 +1 @@ ++# Particle Stack +\ No newline at end of file +diff --git a/docs/source/commands/precision_recall.md b/docs/source/commands/precision_recall.md +new file mode 100644 +index 0000000..dff8323 +--- /dev/null ++++ b/docs/source/commands/precision_recall.md +@@ -0,0 +1 @@ ++# Precision Recall Curve +\ No newline at end of file +diff --git a/docs/source/commands/preprocess.md b/docs/source/commands/preprocess.md +new file mode 100644 +index 0000000..8fd260d +--- /dev/null ++++ b/docs/source/commands/preprocess.md +@@ -0,0 +1 @@ ++# Preprocess +\ No newline at end of file +diff --git a/docs/source/commands/segment.md b/docs/source/commands/segment.md +new file mode 100644 +index 0000000..af21080 +--- /dev/null ++++ b/docs/source/commands/segment.md +@@ -0,0 +1 @@ ++# Segment +\ No newline at end of file +diff --git a/docs/source/commands/split.md b/docs/source/commands/split.md +new file mode 100644 +index 0000000..5e525aa +--- /dev/null ++++ b/docs/source/commands/split.md +@@ -0,0 +1 @@ ++# Split +\ No newline at end of file +diff --git a/docs/source/commands/train.md b/docs/source/commands/train.md +new file mode 100644 +index 0000000..44ac09a +--- /dev/null ++++ b/docs/source/commands/train.md +@@ -0,0 +1 @@ ++# Train +\ No newline at end of file +diff --git a/docs/source/commands/train_test_split.md b/docs/source/commands/train_test_split.md +new file mode 100644 +index 0000000..e28a8c8 +--- /dev/null ++++ b/docs/source/commands/train_test_split.md +@@ -0,0 +1 @@ ++# Train Test Split +\ No newline at end of file +diff --git a/docs/source/conf.py b/docs/source/conf.py +index 8a8b336..8f3a9d3 100644 +--- a/docs/source/conf.py ++++ b/docs/source/conf.py +@@ -36,7 +36,8 @@ + "nbsphinx", + "sphinx.ext.autodoc", + "sphinx.ext.napoleon", +- "sphinx.ext.autosectionlabel" ++ "sphinx.ext.autosectionlabel", ++ "sphinxarg.ext" + ] + + # Add any paths that contain templates here, relative to this directory. +diff --git a/docs/source/index.md b/docs/source/index.md +index af67119..13b414e 100644 +--- a/docs/source/index.md ++++ b/docs/source/index.md +@@ -13,7 +13,7 @@ + + ```{toctree} + :caption: 'Contents:' +-:maxdepth: 2 ++:maxdepth: 3 + + installation + tutorial +diff --git a/docs/source/installation.md b/docs/source/installation.md +index fc4a774..8eca25e 100644 +--- a/docs/source/installation.md ++++ b/docs/source/installation.md +@@ -1,172 +1,28 @@ + # Installation + +-**

(Recommended) Click here to install *using Anaconda*

** +- +-If you do not have the Anaconda python distribution, [please install it following the instructions on their website](https://www.anaconda.com/download). +- +-We strongly recommend installing Topaz into a separate conda environment. To create a conda environment for Topaz: +-``` +-conda create -n topaz python=3.6 # or 2.7 if you prefer python 2 +-source activate topaz # this changes to the topaz conda environment, 'conda activate topaz' can be used with anaconda >= 4.4 if properly configured +-# source deactivate # returns to the base conda environment +-``` +-More information on conda environments can be found [here](https://conda.io/docs/user-guide/tasks/manage-environments.html). +- +-## Install Topaz +- +-To install the precompiled Topaz package and its dependencies, including pytorch: +-``` +-conda install topaz -c tbepler -c pytorch +-``` +-This installs pytorch from the official channel. To install pytorch for specific cuda versions, you will need to add the 'cudatoolkit=X.X' package. E.g. to install pytorch for CUDA 9.0: +-``` +-conda install cudatoolkit=9.0 -c pytorch +-``` +-or combined into a single command: +-``` +-conda install topaz cudatoolkit=9.0 -c tbepler -c pytorch +-``` +-See [here](https://pytorch.org/get-started/locally/) for additional pytorch installation instructions. +- +-That's it! Topaz is now installed in your anaconda environment. +- +-

+- +-**
Click here to install *using Pip*

** +- +-We strongly recommend installing Topaz into a _virtual environment_. See [installation instructions](https://virtualenv.pypa.io/en/latest/installation/) and [user guide](https://virtualenv.pypa.io/en/latest/userguide/) for virtualenv. +- +-### Install Topaz +- +-To install Topaz for Python 3.X +-``` +-pip3 install topaz-em +-``` +- +-for Python 2.7 +-``` +-pip install topaz-em +-``` +-See [here](https://pytorch.org/get-started/locally/) for additional pytorch installation instructions, including how to install pytorch for specific CUDA versions. +- +-That's it! Topaz is now installed through pip. +- +-

+- +-**
Click here to install *using Docker*

** +- +-**

Do you have Docker installed? If not, *click here*

** +- +-#### Linux/MacOS    *(command line)* +- +-Download and install Docker 1.21 or greater for [Linux](https://docs.docker.com/engine/installation/) or [MacOS](https://store.docker.com/editions/community/docker-ce-desktop-mac). +- +-> Consider using a Docker 'convenience script' to install (search on your OS's Docker installation webpage). +- +-Launch docker according to your Docker engine's instructions, typically ``docker start``. +- +-> **Note:** You must have sudo or root access to *install* Docker. If you do not wish to *run* Docker as sudo/root, you need to configure user groups as described here: https://docs.docker.com/install/linux/linux-postinstall/ +- +-#### Windows    *(GUI & command line)* +- +-Download and install [Docker Toolbox for Windows](https://docs.docker.com/toolbox/toolbox_install_windows/). +- +-Launch Kitematic. +- +-> If on first startup Kitematic displays a red error suggesting that you run using VirtualBox, do so. +- +-> **Note:** [Docker Toolbox for MacOS](https://docs.docker.com/toolbox/toolbox_install_mac/) has not yet been tested. +- +- +-### What is Docker? +- +-[This tutorial explains why Docker is useful.](https://www.youtube.com/watch?v=YFl2mCHdv24) +- +- +- +-A Dockerfile is provided to build images with CUDA support. Build from the github repo: +-``` +-docker build -t topaz https://github.com/tbepler/topaz.git +-``` +- +-or download the source code and build from the source directory +-``` +-git clone https://github.com/tbepler/topaz +-cd topaz +-docker build -t topaz . +-``` +- +-

+- +- +-**
Click here to install *using Singularity*

** +- +-A prebuilt Singularity image for Topaz is available [here](https://singularity-hub.org/collections/2413) and can be installed with: +-``` +-singularity pull shub://nysbc/topaz +-``` +- +-Then, you can run topaz from within the singularity image with (paths must be changed appropriately): ++## Conda ++```{include} installation/conda_install.md + ``` +-singularity exec --nv -B /mounted_path:/mounted_path /path/to/singularity/container/topaz_latest.sif /usr/local/conda/bin/topaz +-``` +- +-

+- +- +-**
Click here to install *from source*

** +- +-_Recommended: install Topaz into a virtual Python environment_ +-See https://conda.io/docs/user-guide/tasks/manage-environments.html or https://virtualenv.pypa.io/en/stable/ for setting one up. +- +-#### Install the dependencies +- +-Tested with python 3.6 and 2.7 +- +-- pytorch (>= 1.0.0) +-- torchvision +-- pillow (>= 6.2.0) +-- numpy (>= 1.11) +-- pandas (>= 0.20.3) +-- scipy (>= 0.19.1) +-- scikit-learn (>= 0.19.0) +- +-Easy installation of dependencies with conda +-``` +-conda install numpy pandas scikit-learn +-conda install -c pytorch pytorch torchvision +-``` +-For more info on installing pytorch for your CUDA version see https://pytorch.org/get-started/locally/ +- +-#### Download the source code +-``` +-git clone https://github.com/tbepler/topaz +-``` +- +-#### Install Topaz ++

+ +-Move to the source code directory +-``` +-cd topaz ++## Pip ++```{include} installation/pip_install.md + ``` ++

+ +-By default, this will be the most recent version of the topaz source code. To install a specific older version, checkout that commit. For example, for v0.1.0 of Topaz: ++## Docker ++```{include} installation/docker_install.md + ``` +-git checkout v0.1.0 +-``` +-Note that older Topaz versions may have different dependencies. Refer to the README for the specific Topaz version. ++

+ +-Install Topaz into your Python path including the topaz command line interface +-``` +-pip install . ++## Singularity ++```{include} installation/singularity.md + ``` ++

+ +-To install for development use ++## From Source ++```{include} installation/source_install.md + ``` +-pip install -e . +-``` +- +-

+

+ + Topaz is also available through [SBGrid](https://sbgrid.org/software/titles/topaz). +\ No newline at end of file +diff --git a/docs/source/installation/conda_install.md b/docs/source/installation/conda_install.md +new file mode 100644 +index 0000000..06476c9 +--- /dev/null ++++ b/docs/source/installation/conda_install.md +@@ -0,0 +1,32 @@ ++**

(Recommended) Click here to install *using Anaconda*

** ++ ++If you do not have the Anaconda python distribution, [please install it following the instructions on their website](https://www.anaconda.com/download). ++ ++We strongly recommend installing Topaz into a separate conda environment. To create a conda environment for Topaz: ++``` ++conda create -n topaz python=3.6 # or 2.7 if you prefer python 2 ++source activate topaz # this changes to the topaz conda environment, 'conda activate topaz' can be used with anaconda >= 4.4 if properly configured ++# source deactivate # returns to the base conda environment ++``` ++More information on conda environments can be found [here](https://conda.io/docs/user-guide/tasks/manage-environments.html). ++ ++\ ++**Install Topaz** ++ ++To install the precompiled Topaz package and its dependencies, including pytorch: ++``` ++conda install topaz -c tbepler -c pytorch ++``` ++This installs pytorch from the official channel. To install pytorch for specific cuda versions, you will need to add the 'cudatoolkit=X.X' package. E.g. to install pytorch for CUDA 9.0: ++``` ++conda install cudatoolkit=9.0 -c pytorch ++``` ++or combined into a single command: ++``` ++conda install topaz cudatoolkit=9.0 -c tbepler -c pytorch ++``` ++See [here](https://pytorch.org/get-started/locally/) for additional pytorch installation instructions. ++ ++That's it! Topaz is now installed in your anaconda environment. ++ ++

+\ No newline at end of file +diff --git a/docs/source/installation/docker_install.md b/docs/source/installation/docker_install.md +new file mode 100644 +index 0000000..913ffd0 +--- /dev/null ++++ b/docs/source/installation/docker_install.md +@@ -0,0 +1,51 @@ ++**
Click here to install *using Docker*

** ++ ++**

What is Docker?

** ++ ++[This tutorial explains why Docker is useful.](https://www.youtube.com/watch?v=YFl2mCHdv24) ++

++ ++ ++**
Do you have Docker installed? If not, *click here*

** ++ ++**

Linux/MacOS    *(command line)*

** ++ ++

++Download and install Docker 1.21 or greater for [Linux](https://docs.docker.com/engine/installation/) or [MacOS](https://store.docker.com/editions/community/docker-ce-desktop-mac). ++ ++> Consider using a Docker 'convenience script' to install (search on your OS's Docker installation webpage). ++ ++Launch docker according to your Docker engine's instructions, typically ``docker start``. ++ ++> **Note:** You must have sudo or root access to *install* Docker. If you do not wish to *run* Docker as sudo/root, you need to configure user groups as described here: https://docs.docker.com/install/linux/linux-postinstall/ ++

++ ++ ++**
Windows    *(GUI & command line)*

** ++ ++

++Download and install [Docker Toolbox for Windows](https://docs.docker.com/toolbox/toolbox_install_windows/). ++ ++Launch Kitematic. ++ ++> If on first startup Kitematic displays a red error suggesting that you run using VirtualBox, do so. ++ ++> **Note:** [Docker Toolbox for MacOS](https://docs.docker.com/toolbox/toolbox_install_mac/) has not yet been tested. ++

++ ++

++

++ ++\ ++A Dockerfile is provided to build images with CUDA support. Build from the github repo: ++``` ++docker build -t topaz https://github.com/tbepler/topaz.git ++``` ++ ++or download the source code and build from the source directory ++``` ++git clone https://github.com/tbepler/topaz ++cd topaz ++docker build -t topaz . ++``` ++

+\ No newline at end of file +diff --git a/docs/source/installation/pip_install.md b/docs/source/installation/pip_install.md +new file mode 100644 +index 0000000..e65f64e +--- /dev/null ++++ b/docs/source/installation/pip_install.md +@@ -0,0 +1,20 @@ ++**
Click here to install *using Pip*

** ++ ++We strongly recommend installing Topaz into a _virtual environment_. See [installation instructions](https://virtualenv.pypa.io/en/latest/installation/) and [user guide](https://virtualenv.pypa.io/en/latest/userguide/) for virtualenv. ++ ++**Install Topaz** ++ ++To install Topaz for Python 3.X ++``` ++pip3 install topaz-em ++``` ++ ++for Python 2.7 ++``` ++pip install topaz-em ++``` ++See [here](https://pytorch.org/get-started/locally/) for additional pytorch installation instructions, including how to install pytorch for specific CUDA versions. ++ ++That's it! Topaz is now installed through pip. ++ ++

+\ No newline at end of file +diff --git a/docs/source/installation/singularity.md b/docs/source/installation/singularity.md +new file mode 100644 +index 0000000..401c819 +--- /dev/null ++++ b/docs/source/installation/singularity.md +@@ -0,0 +1,11 @@ ++**
Click here to install *using Singularity*

** ++A prebuilt Singularity image for Topaz is available [here](https://singularity-hub.org/collections/2413) and can be installed with: ++``` ++singularity pull shub://nysbc/topaz ++``` ++ ++Then, you can run topaz from within the singularity image with (paths must be changed appropriately): ++``` ++singularity exec --nv -B /mounted_path:/mounted_path /path/to/singularity/container/topaz_latest.sif /usr/local/conda/bin/topaz ++``` ++

+\ No newline at end of file +diff --git a/docs/source/installation/source_install.md b/docs/source/installation/source_install.md +new file mode 100644 +index 0000000..648dfc8 +--- /dev/null ++++ b/docs/source/installation/source_install.md +@@ -0,0 +1,57 @@ ++**
Click here to install *from source*

** ++ ++_Recommended: install Topaz into a virtual Python environment_ ++See https://conda.io/docs/user-guide/tasks/manage-environments.html or https://virtualenv.pypa.io/en/stable/ for setting one up. ++ ++\ ++**Install the dependencies** ++ ++Tested with python 3.6 and 2.7 ++ ++- pytorch (>= 1.0.0) ++- torchvision ++- pillow (>= 6.2.0) ++- numpy (>= 1.11) ++- pandas (>= 0.20.3) ++- scipy (>= 0.19.1) ++- scikit-learn (>= 0.19.0) ++ ++Easy installation of dependencies with conda ++``` ++conda install numpy pandas scikit-learn ++conda install -c pytorch pytorch torchvision ++``` ++For more info on installing pytorch for your CUDA version see https://pytorch.org/get-started/locally/ ++ ++\ ++**Download the source code** ++``` ++git clone https://github.com/tbepler/topaz ++``` ++ ++\ ++**Install Topaz** ++ ++Move to the source code directory ++``` ++cd topaz ++``` ++ ++By default, this will be the most recent version of the topaz source code. To install a specific older version, checkout that commit. For example, for v0.1.0 of Topaz: ++``` ++git checkout v0.1.0 ++``` ++Note that older Topaz versions may have different dependencies. Refer to the README for the specific Topaz version. ++ ++Install Topaz into your Python path including the topaz command line interface ++``` ++pip install . ++``` ++ ++To install for development use ++``` ++pip install -e . ++``` ++ ++

++

+\ No newline at end of file +diff --git a/docs/source/tutorial.md b/docs/source/tutorial.md +index 161a880..c2ebb97 100644 +--- a/docs/source/tutorial.md ++++ b/docs/source/tutorial.md +@@ -1,4 +1,7 @@ +-# Tutorial ++# Tutorials (coming soon) ++ ++Tutorial pages here are a work-in-progress. For the time being, please refer to the tutorial notebooks in topaz/tutorial. ++ + -\ No newline at end of file -diff --git a/docs/source/index.md b/docs/source/index.md -index 71ef567..1ab1b7c 100644 ---- a/docs/source/index.md -+++ b/docs/source/index.md -@@ -6,8 +6,7 @@ - # Welcome to Topaz's documentation! - - --```{include} ../../README.md --:relative-images: -+```{include} ./description.md - ``` - - -@@ -15,4 +14,12 @@ - ```{toctree} - :caption: 'Contents:' - :maxdepth: 2 -+ -+installation -+tutorial -+commands -+relion -+cryosparc -+models -+scripts - ``` -diff --git a/docs/source/installation.md b/docs/source/installation.md -new file mode 100644 -index 0000000..fc4a774 ---- /dev/null -+++ b/docs/source/installation.md -@@ -0,0 +1,172 @@ -+# Installation -+ -+**

(Recommended) Click here to install *using Anaconda*

** -+ -+If you do not have the Anaconda python distribution, [please install it following the instructions on their website](https://www.anaconda.com/download). -+ -+We strongly recommend installing Topaz into a separate conda environment. To create a conda environment for Topaz: -+``` -+conda create -n topaz python=3.6 # or 2.7 if you prefer python 2 -+source activate topaz # this changes to the topaz conda environment, 'conda activate topaz' can be used with anaconda >= 4.4 if properly configured -+# source deactivate # returns to the base conda environment -+``` -+More information on conda environments can be found [here](https://conda.io/docs/user-guide/tasks/manage-environments.html). -+ -+## Install Topaz -+ -+To install the precompiled Topaz package and its dependencies, including pytorch: -+``` -+conda install topaz -c tbepler -c pytorch -+``` -+This installs pytorch from the official channel. To install pytorch for specific cuda versions, you will need to add the 'cudatoolkit=X.X' package. E.g. to install pytorch for CUDA 9.0: -+``` -+conda install cudatoolkit=9.0 -c pytorch -+``` -+or combined into a single command: -+``` -+conda install topaz cudatoolkit=9.0 -c tbepler -c pytorch -+``` -+See [here](https://pytorch.org/get-started/locally/) for additional pytorch installation instructions. -+ -+That's it! Topaz is now installed in your anaconda environment. -+ -+

-+ -+**
Click here to install *using Pip*

** -+ -+We strongly recommend installing Topaz into a _virtual environment_. See [installation instructions](https://virtualenv.pypa.io/en/latest/installation/) and [user guide](https://virtualenv.pypa.io/en/latest/userguide/) for virtualenv. -+ -+### Install Topaz -+ -+To install Topaz for Python 3.X -+``` -+pip3 install topaz-em -+``` -+ -+for Python 2.7 -+``` -+pip install topaz-em -+``` -+See [here](https://pytorch.org/get-started/locally/) for additional pytorch installation instructions, including how to install pytorch for specific CUDA versions. -+ -+That's it! Topaz is now installed through pip. -+ -+

-+ -+**
Click here to install *using Docker*

** -+ -+**

Do you have Docker installed? If not, *click here*

** -+ -+#### Linux/MacOS    *(command line)* -+ -+Download and install Docker 1.21 or greater for [Linux](https://docs.docker.com/engine/installation/) or [MacOS](https://store.docker.com/editions/community/docker-ce-desktop-mac). -+ -+> Consider using a Docker 'convenience script' to install (search on your OS's Docker installation webpage). -+ -+Launch docker according to your Docker engine's instructions, typically ``docker start``. -+ -+> **Note:** You must have sudo or root access to *install* Docker. If you do not wish to *run* Docker as sudo/root, you need to configure user groups as described here: https://docs.docker.com/install/linux/linux-postinstall/ -+ -+#### Windows    *(GUI & command line)* -+ -+Download and install [Docker Toolbox for Windows](https://docs.docker.com/toolbox/toolbox_install_windows/). -+ -+Launch Kitematic. -+ -+> If on first startup Kitematic displays a red error suggesting that you run using VirtualBox, do so. -+ -+> **Note:** [Docker Toolbox for MacOS](https://docs.docker.com/toolbox/toolbox_install_mac/) has not yet been tested. -+ -+ -+### What is Docker? -+ -+[This tutorial explains why Docker is useful.](https://www.youtube.com/watch?v=YFl2mCHdv24) -+ -+ -+ -+A Dockerfile is provided to build images with CUDA support. Build from the github repo: -+``` -+docker build -t topaz https://github.com/tbepler/topaz.git -+``` -+ -+or download the source code and build from the source directory -+``` -+git clone https://github.com/tbepler/topaz -+cd topaz -+docker build -t topaz . -+``` -+ -+

-+ -+ -+**
Click here to install *using Singularity*

** -+ -+A prebuilt Singularity image for Topaz is available [here](https://singularity-hub.org/collections/2413) and can be installed with: -+``` -+singularity pull shub://nysbc/topaz -+``` -+ -+Then, you can run topaz from within the singularity image with (paths must be changed appropriately): -+``` -+singularity exec --nv -B /mounted_path:/mounted_path /path/to/singularity/container/topaz_latest.sif /usr/local/conda/bin/topaz -+``` -+ -+

-+ -+ -+**
Click here to install *from source*

** -+ -+_Recommended: install Topaz into a virtual Python environment_ -+See https://conda.io/docs/user-guide/tasks/manage-environments.html or https://virtualenv.pypa.io/en/stable/ for setting one up. -+ -+#### Install the dependencies -+ -+Tested with python 3.6 and 2.7 -+ -+- pytorch (>= 1.0.0) -+- torchvision -+- pillow (>= 6.2.0) -+- numpy (>= 1.11) -+- pandas (>= 0.20.3) -+- scipy (>= 0.19.1) -+- scikit-learn (>= 0.19.0) -+ -+Easy installation of dependencies with conda -+``` -+conda install numpy pandas scikit-learn -+conda install -c pytorch pytorch torchvision -+``` -+For more info on installing pytorch for your CUDA version see https://pytorch.org/get-started/locally/ -+ -+#### Download the source code -+``` -+git clone https://github.com/tbepler/topaz -+``` -+ -+#### Install Topaz -+ -+Move to the source code directory -+``` -+cd topaz -+``` -+ -+By default, this will be the most recent version of the topaz source code. To install a specific older version, checkout that commit. For example, for v0.1.0 of Topaz: -+``` -+git checkout v0.1.0 -+``` -+Note that older Topaz versions may have different dependencies. Refer to the README for the specific Topaz version. -+ -+Install Topaz into your Python path including the topaz command line interface -+``` -+pip install . -+``` -+ -+To install for development use -+``` -+pip install -e . -+``` -+ -+

-+

-+ -+Topaz is also available through [SBGrid](https://sbgrid.org/software/titles/topaz). -\ No newline at end of file -diff --git a/docs/source/models.md b/docs/source/models.md -new file mode 100644 -index 0000000..574c6fb ---- /dev/null -+++ b/docs/source/models.md -@@ -0,0 +1,11 @@ -+# Models -+ -+```{eval-rst} -+.. autoclass:: topaz.model.classifier.LinearClassifier -+``` -+ -+## Features -+ -+```{eval-rst} -+.. autoclass:: topaz.model.features.basic.BasicConv -+``` -\ No newline at end of file -diff --git a/docs/source/relion.md b/docs/source/relion.md -new file mode 100644 -index 0000000..7c94e56 ---- /dev/null -+++ b/docs/source/relion.md -@@ -0,0 +1 @@ -+## Use with RELION -\ No newline at end of file -diff --git a/docs/source/scripts.md b/docs/source/scripts.md -new file mode 100644 -index 0000000..82916c1 ---- /dev/null -+++ b/docs/source/scripts.md -@@ -0,0 +1 @@ -+# Scripts -\ No newline at end of file -diff --git a/docs/source/tutorial.md b/docs/source/tutorial.md -new file mode 100644 -index 0000000..161a880 ---- /dev/null -+++ b/docs/source/tutorial.md -@@ -0,0 +1,15 @@ -+# Tutorial -+ -diff --git a/topaz/model/classifier.py b/topaz/model/classifier.py -index be1c3de..bb4710f 100644 ---- a/topaz/model/classifier.py -+++ b/topaz/model/classifier.py -@@ -6,6 +6,15 @@ - - class LinearClassifier(nn.Module): - def __init__(self, features): -+ ''' -+ A simple convolutional layer with no non-linear activation. -+ -+ Args: -+ features (:obj:): the sizes associated with the layer -+ -+ Attributes: -+ features (:obj:) -+ ''' - super(LinearClassifier, self).__init__() - self.features = features - self.classifier = nn.Conv2d(features.latent_dim, 1, 1) - -From e064f07d52ba152e79a664c16d64cbbbf46067e3 Mon Sep 17 00:00:00 2001 -From: Darnell Granberry <40174000+DarnellGranberry@users.noreply.github.com> -Date: Wed, 16 Mar 2022 10:49:08 -0400 -Subject: [PATCH 03/28] updated doc requirements for rtd - ---- - .readthedocs.yaml | 11 +++-------- - docs/requirements.txt | 15 +++++++++++++++ - 2 files changed, 18 insertions(+), 8 deletions(-) - create mode 100644 docs/requirements.txt - -diff --git a/.readthedocs.yaml b/.readthedocs.yaml -index b67d3bf..7468b70 100644 ---- a/.readthedocs.yaml -+++ b/.readthedocs.yaml -@@ -11,11 +11,6 @@ sphinx: - python: - install: - - method: pip -- path: . -- extra_requirements: -- - docs -- - nbsphinx -- - sphinx_rtd_theme -- - sphinx-autobuild -- - rst-to-myst -- - myst-parser -\ No newline at end of file -+ - requirements: docs/requirements.txt -+ - extra-requirements: -+ - doc -\ No newline at end of file -diff --git a/docs/requirements.txt b/docs/requirements.txt -new file mode 100644 -index 0000000..46d9223 ---- /dev/null -+++ b/docs/requirements.txt -@@ -0,0 +1,15 @@ -+# torch >= 1.0.0 -+# torchvision -+# numpy >= 1.11 -+# pandas -+# scikit-learn >= 0.19.0 -+# scipy >= 0.17.0 -+# pillow >= 6.2.0 -+# future -+ -+sphinx -+sphinx_rtd_theme -+sphinx-autobuild -+rst-to-myst -+myst-parser -+nbsphinx -\ No newline at end of file - -From d80d47b01d4e919d4e0be86e4790e65074158b18 Mon Sep 17 00:00:00 2001 -From: Darnell Granberry <40174000+DarnellGranberry@users.noreply.github.com> -Date: Wed, 16 Mar 2022 10:52:10 -0400 -Subject: [PATCH 04/28] Restored path in rtd.yaml - ---- - .readthedocs.yaml | 1 + - 1 file changed, 1 insertion(+) - -diff --git a/.readthedocs.yaml b/.readthedocs.yaml -index 7468b70..037a6c0 100644 ---- a/.readthedocs.yaml -+++ b/.readthedocs.yaml -@@ -11,6 +11,7 @@ sphinx: - python: - install: - - method: pip -+ - path: . - - requirements: docs/requirements.txt - - extra-requirements: - - doc -\ No newline at end of file - -From bba83e16c33c0614fa63a0f363677032f6086234 Mon Sep 17 00:00:00 2001 -From: Darnell Granberry <40174000+DarnellGranberry@users.noreply.github.com> -Date: Wed, 16 Mar 2022 14:14:58 -0400 -Subject: [PATCH 05/28] Corrected rtd yaml formatting - ---- - .readthedocs.yaml | 7 ++++--- - 1 file changed, 4 insertions(+), 3 deletions(-) - -diff --git a/.readthedocs.yaml b/.readthedocs.yaml -index 037a6c0..fc40b17 100644 ---- a/.readthedocs.yaml -+++ b/.readthedocs.yaml -@@ -11,7 +11,8 @@ sphinx: - python: - install: - - method: pip -- - path: . -- - requirements: docs/requirements.txt -- - extra-requirements: -+ path: . -+ requirements: docs/requirements.txt -+ requirements: requirements.txt -+ extra-requirements: - - doc -\ No newline at end of file - -From 1c5f11140f7f063a214e11e9787f779844423bd8 Mon Sep 17 00:00:00 2001 -From: Darnell Granberry <40174000+DarnellGranberry@users.noreply.github.com> -Date: Wed, 16 Mar 2022 14:36:29 -0400 -Subject: [PATCH 06/28] added docs requirements, edited rtd.yaml - ---- - .readthedocs.yaml | 5 +---- - docs/requirements.txt | 10 ++++------ - requirements.txt | 5 +++++ - 3 files changed, 10 insertions(+), 10 deletions(-) - -diff --git a/.readthedocs.yaml b/.readthedocs.yaml -index fc40b17..b9870ed 100644 ---- a/.readthedocs.yaml -+++ b/.readthedocs.yaml -@@ -12,7 +12,4 @@ python: - install: - - method: pip - path: . -- requirements: docs/requirements.txt -- requirements: requirements.txt -- extra-requirements: -- - doc -\ No newline at end of file -+ requirements: requirements.txt -\ No newline at end of file -diff --git a/docs/requirements.txt b/docs/requirements.txt -index 46d9223..e7f2aa5 100644 ---- a/docs/requirements.txt -+++ b/docs/requirements.txt -@@ -6,10 +6,8 @@ - # scipy >= 0.17.0 - # pillow >= 6.2.0 - # future -- --sphinx -+sphinx==4.4.0 - sphinx_rtd_theme --sphinx-autobuild --rst-to-myst --myst-parser --nbsphinx -\ No newline at end of file -+rst-to-myst==0.3.2 -+myst-parser==0.17.0 -+nbsphinx==0.8.8 -\ No newline at end of file -diff --git a/requirements.txt b/requirements.txt -index 4e7245f..01c0804 100644 ---- a/requirements.txt -+++ b/requirements.txt -@@ -6,3 +6,8 @@ scikit-learn >= 0.19.0 - scipy >= 0.17.0 - pillow >= 6.2.0 - future -+sphinx==4.4.0 -+sphinx_rtd_theme -+rst-to-myst==0.3.2 -+myst-parser==0.17.0 -+nbsphinx==0.8.8 -\ No newline at end of file - -From ed7de9c2d2e89fc3a254b3c0882d6c2e2b981205 Mon Sep 17 00:00:00 2001 -From: Darnell Granberry <40174000+DarnellGranberry@users.noreply.github.com> -Date: Wed, 16 Mar 2022 14:46:51 -0400 -Subject: [PATCH 07/28] Reordered rtd.yaml args - ---- - .readthedocs.yaml | 4 +++- - 1 file changed, 3 insertions(+), 1 deletion(-) - -diff --git a/.readthedocs.yaml b/.readthedocs.yaml -index b9870ed..6722c59 100644 ---- a/.readthedocs.yaml -+++ b/.readthedocs.yaml -@@ -10,6 +10,8 @@ sphinx: - - python: - install: -+ - requirements: docs/requirements.txt - - method: pip - path: . -- requirements: requirements.txt -\ No newline at end of file -+ extra_requirements: -+ - docs -\ No newline at end of file - -From 683093572078eb20e9aebfa5daeb931ddb3c5bbc Mon Sep 17 00:00:00 2001 -From: Darnell Granberry <40174000+DarnellGranberry@users.noreply.github.com> -Date: Wed, 16 Mar 2022 14:50:07 -0400 -Subject: [PATCH 08/28] removed doc versions pkg version - ---- - docs/requirements.txt | 6 +++--- - 1 file changed, 3 insertions(+), 3 deletions(-) - -diff --git a/docs/requirements.txt b/docs/requirements.txt -index e7f2aa5..f12e5f7 100644 ---- a/docs/requirements.txt -+++ b/docs/requirements.txt -@@ -8,6 +8,6 @@ - # future - sphinx==4.4.0 - sphinx_rtd_theme --rst-to-myst==0.3.2 --myst-parser==0.17.0 --nbsphinx==0.8.8 -\ No newline at end of file -+rst-to-myst -+myst-parser -+nbsphinx -\ No newline at end of file - -From c3415895c8515696be1a88c2bfde242c3c2999f7 Mon Sep 17 00:00:00 2001 -From: Darnell Granberry <40174000+DarnellGranberry@users.noreply.github.com> -Date: Wed, 16 Mar 2022 14:55:36 -0400 -Subject: [PATCH 09/28] Add docs status to readme - ---- - README.md | 2 +- - 1 file changed, 1 insertion(+), 1 deletion(-) - -diff --git a/README.md b/README.md -index 5987691..f2b6433 100644 ---- a/README.md -+++ b/README.md -@@ -1,5 +1,5 @@ - [![Python package](https://github.com/tbepler/topaz/actions/workflows/ci.yml/badge.svg)](https://github.com/tbepler/topaz/actions/workflows/ci.yml) -- -+[![Documentation Status](https://readthedocs.org/projects/topaz-em/badge/?version=latest)](https://topaz-em.readthedocs.io/en/latest/?badge=latest) - - - # Topaz - -From 538286e7a4780d31f163e95011e89a68fc418b9f Mon Sep 17 00:00:00 2001 -From: Darnell Granberry <40174000+DarnellGranberry@users.noreply.github.com> -Date: Wed, 16 Mar 2022 15:00:17 -0400 -Subject: [PATCH 10/28] Added version and conda install badges - ---- - README.md | 2 ++ - 1 file changed, 2 insertions(+) - -diff --git a/README.md b/README.md -index f2b6433..f3832bd 100644 ---- a/README.md -+++ b/README.md -@@ -1,5 +1,7 @@ - [![Python package](https://github.com/tbepler/topaz/actions/workflows/ci.yml/badge.svg)](https://github.com/tbepler/topaz/actions/workflows/ci.yml) - [![Documentation Status](https://readthedocs.org/projects/topaz-em/badge/?version=latest)](https://topaz-em.readthedocs.io/en/latest/?badge=latest) -+[![Anaconda-Server Badge](https://anaconda.org/tbepler/topaz/badges/version.svg)](https://anaconda.org/tbepler/topaz) -+[![Anaconda-Server Badge](https://anaconda.org/tbepler/topaz/badges/installer/conda.svg)](https://conda.anaconda.org/tbepler) - - - # Topaz - -From 2c13c55fa3080741571b868f6275b1839456e45e Mon Sep 17 00:00:00 2001 -From: Darnell Granberry <40174000+DarnellGranberry@users.noreply.github.com> -Date: Wed, 16 Mar 2022 15:05:11 -0400 -Subject: [PATCH 11/28] removed duplicate docs requirements - ---- - requirements.txt | 7 +------ - 1 file changed, 1 insertion(+), 6 deletions(-) - -diff --git a/requirements.txt b/requirements.txt -index 01c0804..d83f97b 100644 ---- a/requirements.txt -+++ b/requirements.txt -@@ -5,9 +5,4 @@ pandas - scikit-learn >= 0.19.0 - scipy >= 0.17.0 - pillow >= 6.2.0 --future --sphinx==4.4.0 --sphinx_rtd_theme --rst-to-myst==0.3.2 --myst-parser==0.17.0 --nbsphinx==0.8.8 -\ No newline at end of file -+future -\ No newline at end of file - -From 06f301640ea566f9baae816edb0a908ffafca444 Mon Sep 17 00:00:00 2001 -From: Darnell Granberry <40174000+DarnellGranberry@users.noreply.github.com> -Date: Thu, 17 Mar 2022 17:50:20 -0400 -Subject: [PATCH 12/28] Created doc entries for most code except commands - ---- - docs/source/algorithms.md | 7 +++ - docs/source/conf.py | 4 +- - docs/source/denoising.md | 7 +++ - docs/source/index.md | 10 ++++- - docs/source/methods.md | 7 +++ - docs/source/metrics_stats.md | 14 ++++++ - docs/source/models.md | 52 +++++++++++++++++++++- - docs/source/transforms.md | 7 +++ - docs/source/utils.md | 81 +++++++++++++++++++++++++++++++++++ - topaz/_version.py | 2 +- - topaz/model/classifier.py | 12 +++++- - topaz/model/features/basic.py | 2 + - 12 files changed, 197 insertions(+), 8 deletions(-) - create mode 100644 docs/source/algorithms.md - create mode 100644 docs/source/denoising.md - create mode 100644 docs/source/methods.md - create mode 100644 docs/source/metrics_stats.md - create mode 100644 docs/source/transforms.md - create mode 100644 docs/source/utils.md - -diff --git a/docs/source/algorithms.md b/docs/source/algorithms.md -new file mode 100644 -index 0000000..0a617c9 ---- /dev/null -+++ b/docs/source/algorithms.md -@@ -0,0 +1,7 @@ -+# Algorithms -+ -+```{eval-rst} -+.. automodule:: topaz.algorithms -+ :members: -+ :undoc-members: -+``` -\ No newline at end of file -diff --git a/docs/source/conf.py b/docs/source/conf.py -index cac08bc..8a8b336 100644 ---- a/docs/source/conf.py -+++ b/docs/source/conf.py -@@ -34,7 +34,9 @@ - extensions = [ - "myst_parser", - "nbsphinx", -- "sphinx.ext.autodoc" -+ "sphinx.ext.autodoc", -+ "sphinx.ext.napoleon", -+ "sphinx.ext.autosectionlabel" - ] - - # Add any paths that contain templates here, relative to this directory. -diff --git a/docs/source/denoising.md b/docs/source/denoising.md -new file mode 100644 -index 0000000..036d4d5 ---- /dev/null -+++ b/docs/source/denoising.md -@@ -0,0 +1,7 @@ -+# Denoising -+ -+```{eval-rst} -+.. automodule:: topaz.denoise -+ :members: -+ :undoc-members: -+``` -\ No newline at end of file -diff --git a/docs/source/index.md b/docs/source/index.md -index 1ab1b7c..af67119 100644 ---- a/docs/source/index.md -+++ b/docs/source/index.md -@@ -18,8 +18,14 @@ - installation - tutorial - commands --relion --cryosparc -+algorithms -+denoising -+methods -+metrics_stats - models -+transforms -+utils - scripts -+relion -+cryosparc - ``` -diff --git a/docs/source/methods.md b/docs/source/methods.md -new file mode 100644 -index 0000000..aed5cfd ---- /dev/null -+++ b/docs/source/methods.md -@@ -0,0 +1,7 @@ -+# Methods -+ -+```{eval-rst} -+.. automodule:: topaz.methods -+ :members: -+ :undoc-members: -+``` -\ No newline at end of file -diff --git a/docs/source/metrics_stats.md b/docs/source/metrics_stats.md -new file mode 100644 -index 0000000..dcfe0c4 ---- /dev/null -+++ b/docs/source/metrics_stats.md -@@ -0,0 +1,14 @@ -+# Metrics and Statistics -+ -+```{eval-rst} -+.. automodule:: topaz.metrics -+ :members: -+ :undoc-members: -+``` -+ -+ -+```{eval-rst} -+.. automodule:: topaz.stats -+ :members: -+ :undoc-members: -+``` -\ No newline at end of file -diff --git a/docs/source/models.md b/docs/source/models.md -index 574c6fb..dbad6b1 100644 ---- a/docs/source/models.md -+++ b/docs/source/models.md -@@ -1,11 +1,59 @@ - # Models - -+## Feature Extractors -+ -+### Basic Conv Nets -+```{eval-rst} -+.. automodule:: topaz.model.features.basic -+ :members: -+ :undoc-members: -+``` -+ -+### DenseNets -+```{eval-rst} -+.. automodule:: topaz.model.features.densenet -+ :members: -+ :undoc-members: -+``` -+ -+### MSNets -+```{eval-rst} -+.. automodule:: topaz.model.features.msnet -+ :members: -+ :undoc-members: -+``` -+ -+### ResNets -+```{eval-rst} -+.. automodule:: topaz.model.features.resnet -+ :members: -+ :undoc-members: -+``` -+ -+## Linear Classifier - ```{eval-rst} - .. autoclass:: topaz.model.classifier.LinearClassifier -+ :members: -+ :undoc-members: - ``` - --## Features -+## Model Factory -+```{eval-rst} -+.. automodule:: topaz.model.factory -+ :members: -+ :undoc-members: -+``` -+ -+## Model Generator -+```{eval-rst} -+.. automodule:: topaz.model.generative -+ :members: -+ :undoc-members: -+``` - -+## Model Utilities - ```{eval-rst} --.. autoclass:: topaz.model.features.basic.BasicConv -+.. automodule:: topaz.model.utils -+ :members: -+ :undoc-members: - ``` -\ No newline at end of file -diff --git a/docs/source/transforms.md b/docs/source/transforms.md -new file mode 100644 -index 0000000..9bf1082 ---- /dev/null -+++ b/docs/source/transforms.md -@@ -0,0 +1,7 @@ -+# Transformations -+ -+```{eval-rst} -+.. automodule:: topaz.transform.scaled_gaussian_mixture -+ :members: -+ :undoc-members: -+``` -\ No newline at end of file -diff --git a/docs/source/utils.md b/docs/source/utils.md -new file mode 100644 -index 0000000..027f498 ---- /dev/null -+++ b/docs/source/utils.md -@@ -0,0 +1,81 @@ -+# Utilities -+ -+## Conversions -+```{eval-rst} -+.. automodule:: topaz.utils.conversions -+ :members: -+ :undoc-members: -+``` -+ -+## File Utilities -+```{eval-rst} -+.. automodule:: topaz.utils.conversions -+ :members: -+ :undoc-members: -+``` -+ -+ -+```{eval-rst} -+.. automodule:: topaz.mrc -+ :members: -+ :undoc-members: -+``` -+ -+ -+## Image Manipulations -+```{eval-rst} -+.. automodule:: topaz.utils.image -+ :members: -+ :undoc-members: -+``` -+ -+## Pick Masking -+```{eval-rst} -+.. automodule:: topaz.utils.picks -+ :members: -+ :undoc-members: -+``` -+ -+## Printing -+```{eval-rst} -+.. automodule:: topaz.utils.printing -+ :members: -+ :undoc-members: -+``` -+ -+## STAR File Manipulations -+```{eval-rst} -+.. automodule:: topaz.utils.star -+ :members: -+ :undoc-members: -+``` -+ -+## Data Utilities -+ -+### Coordinate Manipulations -+```{eval-rst} -+.. automodule:: topaz.utils.data.coordinates -+ :members: -+ :undoc-members: -+``` -+ -+### Image Loading -+```{eval-rst} -+.. automodule:: topaz.utils.data.loader -+ :members: -+ :undoc-members: -+``` -+ -+### Dataset Partitioning -+```{eval-rst} -+.. automodule:: topaz.utils.data.partition -+ :members: -+ :undoc-members: -+``` -+ -+### Dataset Sampling -+```{eval-rst} -+.. automodule:: topaz.utils.data.sampler -+ :members: -+ :undoc-members: -+``` -\ No newline at end of file -diff --git a/topaz/_version.py b/topaz/_version.py -index e723ff3..fe404ae 100644 ---- a/topaz/_version.py -+++ b/topaz/_version.py -@@ -1 +1 @@ --__version__ = "0.2.5a" -+__version__ = "0.2.5" -diff --git a/topaz/model/classifier.py b/topaz/model/classifier.py -index bb4710f..d63d83c 100644 ---- a/topaz/model/classifier.py -+++ b/topaz/model/classifier.py -@@ -5,10 +5,10 @@ - import torch.nn.functional as F - - class LinearClassifier(nn.Module): -+ '''A simple convolutional layer without non-linear activation.''' -+ - def __init__(self, features): - ''' -- A simple convolutional layer with no non-linear activation. -- - Args: - features (:obj:): the sizes associated with the layer - -@@ -34,6 +34,14 @@ def unfill(self): - self.features.unfill() - - def forward(self, x): -+ '''Applies the classifier to an input. -+ -+ Args: -+ x (np.ndarray): the image from which features are extracted and classified -+ -+ Returns: -+ z (np.ndarray): output of the classifer -+ ''' - z = self.features(x) - y = self.classifier(z) - return y -diff --git a/topaz/model/features/basic.py b/topaz/model/features/basic.py -index 0ea1fe9..dff4e9f 100644 ---- a/topaz/model/features/basic.py -+++ b/topaz/model/features/basic.py -@@ -10,6 +10,8 @@ - from topaz.model.utils import insize_from_outsize - - class BasicConv(nn.Module): -+ '''A generic convolutional neural network scaffold.''' -+ - def __init__(self, layers, units, unit_scaling=1, dropout=0, bn=True - , pooling=None, activation=nn.PReLU): - super(BasicConv, self).__init__() - -From d2c9761c2fba8d996c1f117f3004eeaf5a2abad7 Mon Sep 17 00:00:00 2001 -From: Darnell Granberry <40174000+DarnellGranberry@users.noreply.github.com> -Date: Fri, 18 Mar 2022 15:44:56 -0400 -Subject: [PATCH 13/28] reorganized docs, began work on man pages - ---- - docs/requirements.txt | 3 +- - docs/source/commands.md | 20 ++- - docs/source/commands/convert.md | 1 + - docs/source/commands/denoise.md | 1 + - docs/source/commands/denoise3d.md | 1 + - docs/source/commands/downsample.md | 1 + - docs/source/commands/extract.md | 1 + - docs/source/commands/file_utilities.md | 11 ++ - docs/source/commands/gui.md | 1 + - docs/source/commands/image_processing.md | 12 ++ - docs/source/commands/normalize.md | 8 + - docs/source/commands/particle_picking.md | 11 ++ - docs/source/commands/particle_stack.md | 1 + - docs/source/commands/precision_recall.md | 1 + - docs/source/commands/preprocess.md | 1 + - docs/source/commands/segment.md | 1 + - docs/source/commands/split.md | 1 + - docs/source/commands/train.md | 1 + - docs/source/commands/train_test_split.md | 1 + - docs/source/conf.py | 3 +- - docs/source/index.md | 2 +- - docs/source/installation.md | 172 ++------------------- - docs/source/installation/conda_install.md | 32 ++++ - docs/source/installation/docker_install.md | 51 ++++++ - docs/source/installation/pip_install.md | 20 +++ - docs/source/installation/singularity.md | 11 ++ - docs/source/installation/source_install.md | 57 +++++++ - docs/source/tutorial.md | 5 +- - topaz/commands/normalize.py | 9 +- - 29 files changed, 264 insertions(+), 176 deletions(-) - create mode 100644 docs/source/commands/convert.md - create mode 100644 docs/source/commands/denoise.md - create mode 100644 docs/source/commands/denoise3d.md - create mode 100644 docs/source/commands/downsample.md - create mode 100644 docs/source/commands/extract.md - create mode 100644 docs/source/commands/file_utilities.md - create mode 100644 docs/source/commands/gui.md - create mode 100644 docs/source/commands/image_processing.md - create mode 100644 docs/source/commands/normalize.md - create mode 100644 docs/source/commands/particle_picking.md - create mode 100644 docs/source/commands/particle_stack.md - create mode 100644 docs/source/commands/precision_recall.md - create mode 100644 docs/source/commands/preprocess.md - create mode 100644 docs/source/commands/segment.md - create mode 100644 docs/source/commands/split.md - create mode 100644 docs/source/commands/train.md - create mode 100644 docs/source/commands/train_test_split.md - create mode 100644 docs/source/installation/conda_install.md - create mode 100644 docs/source/installation/docker_install.md - create mode 100644 docs/source/installation/pip_install.md - create mode 100644 docs/source/installation/singularity.md - create mode 100644 docs/source/installation/source_install.md - -diff --git a/docs/requirements.txt b/docs/requirements.txt -index f12e5f7..bd0b467 100644 ---- a/docs/requirements.txt -+++ b/docs/requirements.txt -@@ -10,4 +10,5 @@ sphinx==4.4.0 - sphinx_rtd_theme - rst-to-myst - myst-parser --nbsphinx -\ No newline at end of file -+nbsphinx -+sphinx-argparse -\ No newline at end of file -diff --git a/docs/source/commands.md b/docs/source/commands.md -index 44c4a21..3c462c9 100644 ---- a/docs/source/commands.md -+++ b/docs/source/commands.md -@@ -1,15 +1,13 @@ --# Topaz Commands -+# Topaz Commands (work in progress) - --## downsample - --## normalize -+```{toctree} -+:caption: 'Commands' -+:maxdepth: 2 - --## preprocess -+commands/particle_picking -+commands/image_processing -+commands/file_utilities - --## train -- --## segment -- --## extract -- --## precision_recall_curve -+commands/gui -+``` -\ No newline at end of file -diff --git a/docs/source/commands/convert.md b/docs/source/commands/convert.md -new file mode 100644 -index 0000000..122f443 ---- /dev/null -+++ b/docs/source/commands/convert.md -@@ -0,0 +1 @@ -+# Convert -\ No newline at end of file -diff --git a/docs/source/commands/denoise.md b/docs/source/commands/denoise.md -new file mode 100644 -index 0000000..d995632 ---- /dev/null -+++ b/docs/source/commands/denoise.md -@@ -0,0 +1 @@ -+# Denoise -\ No newline at end of file -diff --git a/docs/source/commands/denoise3d.md b/docs/source/commands/denoise3d.md -new file mode 100644 -index 0000000..bf78fac ---- /dev/null -+++ b/docs/source/commands/denoise3d.md -@@ -0,0 +1 @@ -+# Denoise 3D -\ No newline at end of file -diff --git a/docs/source/commands/downsample.md b/docs/source/commands/downsample.md -new file mode 100644 -index 0000000..e0b15bf ---- /dev/null -+++ b/docs/source/commands/downsample.md -@@ -0,0 +1 @@ -+# Downsample -\ No newline at end of file -diff --git a/docs/source/commands/extract.md b/docs/source/commands/extract.md -new file mode 100644 -index 0000000..d0e6da9 ---- /dev/null -+++ b/docs/source/commands/extract.md -@@ -0,0 +1 @@ -+# Extract -\ No newline at end of file -diff --git a/docs/source/commands/file_utilities.md b/docs/source/commands/file_utilities.md -new file mode 100644 -index 0000000..b26444f ---- /dev/null -+++ b/docs/source/commands/file_utilities.md -@@ -0,0 +1,11 @@ -+# File Utilities -+ -+```{toctree} -+:caption: 'Commands' -+:maxdepth: 1 -+ -+convert -+split -+particle_stack -+train_test_split -+``` -\ No newline at end of file -diff --git a/docs/source/commands/gui.md b/docs/source/commands/gui.md -new file mode 100644 -index 0000000..93bd5f2 ---- /dev/null -+++ b/docs/source/commands/gui.md -@@ -0,0 +1 @@ -+# GUI -\ No newline at end of file -diff --git a/docs/source/commands/image_processing.md b/docs/source/commands/image_processing.md -new file mode 100644 -index 0000000..973048c ---- /dev/null -+++ b/docs/source/commands/image_processing.md -@@ -0,0 +1,12 @@ -+# Image Processing -+ -+```{toctree} -+:caption: 'Commands' -+:maxdepth: 1 -+ -+downsample -+normalize -+preprocess -+denoise -+denoise3d -+``` -\ No newline at end of file -diff --git a/docs/source/commands/normalize.md b/docs/source/commands/normalize.md -new file mode 100644 -index 0000000..ad442b2 ---- /dev/null -+++ b/docs/source/commands/normalize.md -@@ -0,0 +1,8 @@ -+# Normalize -+ -+```{eval-rst} -+.. argparse:: -+ :module: topaz.commands.normalize -+ :func: add_arguments -+ :prog: normalize -+``` -\ No newline at end of file -diff --git a/docs/source/commands/particle_picking.md b/docs/source/commands/particle_picking.md -new file mode 100644 -index 0000000..c32361a ---- /dev/null -+++ b/docs/source/commands/particle_picking.md -@@ -0,0 +1,11 @@ -+# Particle Picking -+ -+```{toctree} -+:caption: 'Commands' -+:maxdepth: 1 -+ -+train -+segment -+extract -+precision_recall -+``` -\ No newline at end of file -diff --git a/docs/source/commands/particle_stack.md b/docs/source/commands/particle_stack.md -new file mode 100644 -index 0000000..7bb5a5e ---- /dev/null -+++ b/docs/source/commands/particle_stack.md -@@ -0,0 +1 @@ -+# Particle Stack -\ No newline at end of file -diff --git a/docs/source/commands/precision_recall.md b/docs/source/commands/precision_recall.md -new file mode 100644 -index 0000000..dff8323 ---- /dev/null -+++ b/docs/source/commands/precision_recall.md -@@ -0,0 +1 @@ -+# Precision Recall Curve -\ No newline at end of file -diff --git a/docs/source/commands/preprocess.md b/docs/source/commands/preprocess.md -new file mode 100644 -index 0000000..8fd260d ---- /dev/null -+++ b/docs/source/commands/preprocess.md -@@ -0,0 +1 @@ -+# Preprocess -\ No newline at end of file -diff --git a/docs/source/commands/segment.md b/docs/source/commands/segment.md -new file mode 100644 -index 0000000..af21080 ---- /dev/null -+++ b/docs/source/commands/segment.md -@@ -0,0 +1 @@ -+# Segment -\ No newline at end of file -diff --git a/docs/source/commands/split.md b/docs/source/commands/split.md -new file mode 100644 -index 0000000..5e525aa ---- /dev/null -+++ b/docs/source/commands/split.md -@@ -0,0 +1 @@ -+# Split -\ No newline at end of file -diff --git a/docs/source/commands/train.md b/docs/source/commands/train.md -new file mode 100644 -index 0000000..44ac09a ---- /dev/null -+++ b/docs/source/commands/train.md -@@ -0,0 +1 @@ -+# Train -\ No newline at end of file -diff --git a/docs/source/commands/train_test_split.md b/docs/source/commands/train_test_split.md -new file mode 100644 -index 0000000..e28a8c8 ---- /dev/null -+++ b/docs/source/commands/train_test_split.md -@@ -0,0 +1 @@ -+# Train Test Split -\ No newline at end of file -diff --git a/docs/source/conf.py b/docs/source/conf.py -index 8a8b336..8f3a9d3 100644 ---- a/docs/source/conf.py -+++ b/docs/source/conf.py -@@ -36,7 +36,8 @@ - "nbsphinx", - "sphinx.ext.autodoc", - "sphinx.ext.napoleon", -- "sphinx.ext.autosectionlabel" -+ "sphinx.ext.autosectionlabel", -+ "sphinxarg.ext" - ] - - # Add any paths that contain templates here, relative to this directory. -diff --git a/docs/source/index.md b/docs/source/index.md -index af67119..13b414e 100644 ---- a/docs/source/index.md -+++ b/docs/source/index.md -@@ -13,7 +13,7 @@ - - ```{toctree} - :caption: 'Contents:' --:maxdepth: 2 -+:maxdepth: 3 - - installation - tutorial -diff --git a/docs/source/installation.md b/docs/source/installation.md -index fc4a774..8eca25e 100644 ---- a/docs/source/installation.md -+++ b/docs/source/installation.md -@@ -1,172 +1,28 @@ - # Installation - --**

(Recommended) Click here to install *using Anaconda*

** -- --If you do not have the Anaconda python distribution, [please install it following the instructions on their website](https://www.anaconda.com/download). -- --We strongly recommend installing Topaz into a separate conda environment. To create a conda environment for Topaz: --``` --conda create -n topaz python=3.6 # or 2.7 if you prefer python 2 --source activate topaz # this changes to the topaz conda environment, 'conda activate topaz' can be used with anaconda >= 4.4 if properly configured --# source deactivate # returns to the base conda environment --``` --More information on conda environments can be found [here](https://conda.io/docs/user-guide/tasks/manage-environments.html). -- --## Install Topaz -- --To install the precompiled Topaz package and its dependencies, including pytorch: --``` --conda install topaz -c tbepler -c pytorch --``` --This installs pytorch from the official channel. To install pytorch for specific cuda versions, you will need to add the 'cudatoolkit=X.X' package. E.g. to install pytorch for CUDA 9.0: --``` --conda install cudatoolkit=9.0 -c pytorch --``` --or combined into a single command: --``` --conda install topaz cudatoolkit=9.0 -c tbepler -c pytorch --``` --See [here](https://pytorch.org/get-started/locally/) for additional pytorch installation instructions. -- --That's it! Topaz is now installed in your anaconda environment. -- --

-- --**
Click here to install *using Pip*

** -- --We strongly recommend installing Topaz into a _virtual environment_. See [installation instructions](https://virtualenv.pypa.io/en/latest/installation/) and [user guide](https://virtualenv.pypa.io/en/latest/userguide/) for virtualenv. -- --### Install Topaz -- --To install Topaz for Python 3.X --``` --pip3 install topaz-em --``` -- --for Python 2.7 --``` --pip install topaz-em --``` --See [here](https://pytorch.org/get-started/locally/) for additional pytorch installation instructions, including how to install pytorch for specific CUDA versions. -- --That's it! Topaz is now installed through pip. -- --

-- --**
Click here to install *using Docker*

** -- --**

Do you have Docker installed? If not, *click here*

** -- --#### Linux/MacOS    *(command line)* -- --Download and install Docker 1.21 or greater for [Linux](https://docs.docker.com/engine/installation/) or [MacOS](https://store.docker.com/editions/community/docker-ce-desktop-mac). -- --> Consider using a Docker 'convenience script' to install (search on your OS's Docker installation webpage). -- --Launch docker according to your Docker engine's instructions, typically ``docker start``. -- --> **Note:** You must have sudo or root access to *install* Docker. If you do not wish to *run* Docker as sudo/root, you need to configure user groups as described here: https://docs.docker.com/install/linux/linux-postinstall/ -- --#### Windows    *(GUI & command line)* -- --Download and install [Docker Toolbox for Windows](https://docs.docker.com/toolbox/toolbox_install_windows/). -- --Launch Kitematic. -- --> If on first startup Kitematic displays a red error suggesting that you run using VirtualBox, do so. -- --> **Note:** [Docker Toolbox for MacOS](https://docs.docker.com/toolbox/toolbox_install_mac/) has not yet been tested. -- -- --### What is Docker? -- --[This tutorial explains why Docker is useful.](https://www.youtube.com/watch?v=YFl2mCHdv24) -- -- -- --A Dockerfile is provided to build images with CUDA support. Build from the github repo: --``` --docker build -t topaz https://github.com/tbepler/topaz.git --``` -- --or download the source code and build from the source directory --``` --git clone https://github.com/tbepler/topaz --cd topaz --docker build -t topaz . --``` -- --

-- -- --**
Click here to install *using Singularity*

** -- --A prebuilt Singularity image for Topaz is available [here](https://singularity-hub.org/collections/2413) and can be installed with: --``` --singularity pull shub://nysbc/topaz --``` -- --Then, you can run topaz from within the singularity image with (paths must be changed appropriately): -+## Conda -+```{include} installation/conda_install.md - ``` --singularity exec --nv -B /mounted_path:/mounted_path /path/to/singularity/container/topaz_latest.sif /usr/local/conda/bin/topaz --``` -- --

-- -- --**
Click here to install *from source*

** -- --_Recommended: install Topaz into a virtual Python environment_ --See https://conda.io/docs/user-guide/tasks/manage-environments.html or https://virtualenv.pypa.io/en/stable/ for setting one up. -- --#### Install the dependencies -- --Tested with python 3.6 and 2.7 -- --- pytorch (>= 1.0.0) --- torchvision --- pillow (>= 6.2.0) --- numpy (>= 1.11) --- pandas (>= 0.20.3) --- scipy (>= 0.19.1) --- scikit-learn (>= 0.19.0) -- --Easy installation of dependencies with conda --``` --conda install numpy pandas scikit-learn --conda install -c pytorch pytorch torchvision --``` --For more info on installing pytorch for your CUDA version see https://pytorch.org/get-started/locally/ -- --#### Download the source code --``` --git clone https://github.com/tbepler/topaz --``` -- --#### Install Topaz -+

- --Move to the source code directory --``` --cd topaz -+## Pip -+```{include} installation/pip_install.md - ``` -+

- --By default, this will be the most recent version of the topaz source code. To install a specific older version, checkout that commit. For example, for v0.1.0 of Topaz: -+## Docker -+```{include} installation/docker_install.md - ``` --git checkout v0.1.0 --``` --Note that older Topaz versions may have different dependencies. Refer to the README for the specific Topaz version. -+

- --Install Topaz into your Python path including the topaz command line interface --``` --pip install . -+## Singularity -+```{include} installation/singularity.md - ``` -+

- --To install for development use -+## From Source -+```{include} installation/source_install.md - ``` --pip install -e . --``` -- --

-

- - Topaz is also available through [SBGrid](https://sbgrid.org/software/titles/topaz). -\ No newline at end of file -diff --git a/docs/source/installation/conda_install.md b/docs/source/installation/conda_install.md -new file mode 100644 -index 0000000..06476c9 ---- /dev/null -+++ b/docs/source/installation/conda_install.md -@@ -0,0 +1,32 @@ -+**

(Recommended) Click here to install *using Anaconda*

** -+ -+If you do not have the Anaconda python distribution, [please install it following the instructions on their website](https://www.anaconda.com/download). -+ -+We strongly recommend installing Topaz into a separate conda environment. To create a conda environment for Topaz: -+``` -+conda create -n topaz python=3.6 # or 2.7 if you prefer python 2 -+source activate topaz # this changes to the topaz conda environment, 'conda activate topaz' can be used with anaconda >= 4.4 if properly configured -+# source deactivate # returns to the base conda environment -+``` -+More information on conda environments can be found [here](https://conda.io/docs/user-guide/tasks/manage-environments.html). -+ -+\ -+**Install Topaz** -+ -+To install the precompiled Topaz package and its dependencies, including pytorch: -+``` -+conda install topaz -c tbepler -c pytorch -+``` -+This installs pytorch from the official channel. To install pytorch for specific cuda versions, you will need to add the 'cudatoolkit=X.X' package. E.g. to install pytorch for CUDA 9.0: -+``` -+conda install cudatoolkit=9.0 -c pytorch -+``` -+or combined into a single command: -+``` -+conda install topaz cudatoolkit=9.0 -c tbepler -c pytorch -+``` -+See [here](https://pytorch.org/get-started/locally/) for additional pytorch installation instructions. -+ -+That's it! Topaz is now installed in your anaconda environment. -+ -+

-\ No newline at end of file -diff --git a/docs/source/installation/docker_install.md b/docs/source/installation/docker_install.md -new file mode 100644 -index 0000000..913ffd0 ---- /dev/null -+++ b/docs/source/installation/docker_install.md -@@ -0,0 +1,51 @@ -+**
Click here to install *using Docker*

** -+ -+**

What is Docker?

** -+ -+[This tutorial explains why Docker is useful.](https://www.youtube.com/watch?v=YFl2mCHdv24) -+

-+ -+ -+**
Do you have Docker installed? If not, *click here*

** -+ -+**

Linux/MacOS    *(command line)*

** -+ -+

-+Download and install Docker 1.21 or greater for [Linux](https://docs.docker.com/engine/installation/) or [MacOS](https://store.docker.com/editions/community/docker-ce-desktop-mac). -+ -+> Consider using a Docker 'convenience script' to install (search on your OS's Docker installation webpage). -+ -+Launch docker according to your Docker engine's instructions, typically ``docker start``. -+ -+> **Note:** You must have sudo or root access to *install* Docker. If you do not wish to *run* Docker as sudo/root, you need to configure user groups as described here: https://docs.docker.com/install/linux/linux-postinstall/ -+

-+ -+ -+**
Windows    *(GUI & command line)*

** -+ -+

-+Download and install [Docker Toolbox for Windows](https://docs.docker.com/toolbox/toolbox_install_windows/). -+ -+Launch Kitematic. -+ -+> If on first startup Kitematic displays a red error suggesting that you run using VirtualBox, do so. -+ -+> **Note:** [Docker Toolbox for MacOS](https://docs.docker.com/toolbox/toolbox_install_mac/) has not yet been tested. -+

-+ -+

-+

-+ -+\ -+A Dockerfile is provided to build images with CUDA support. Build from the github repo: -+``` -+docker build -t topaz https://github.com/tbepler/topaz.git -+``` -+ -+or download the source code and build from the source directory -+``` -+git clone https://github.com/tbepler/topaz -+cd topaz -+docker build -t topaz . -+``` -+

-\ No newline at end of file -diff --git a/docs/source/installation/pip_install.md b/docs/source/installation/pip_install.md -new file mode 100644 -index 0000000..e65f64e ---- /dev/null -+++ b/docs/source/installation/pip_install.md -@@ -0,0 +1,20 @@ -+**
Click here to install *using Pip*

** -+ -+We strongly recommend installing Topaz into a _virtual environment_. See [installation instructions](https://virtualenv.pypa.io/en/latest/installation/) and [user guide](https://virtualenv.pypa.io/en/latest/userguide/) for virtualenv. -+ -+**Install Topaz** -+ -+To install Topaz for Python 3.X -+``` -+pip3 install topaz-em -+``` -+ -+for Python 2.7 -+``` -+pip install topaz-em -+``` -+See [here](https://pytorch.org/get-started/locally/) for additional pytorch installation instructions, including how to install pytorch for specific CUDA versions. -+ -+That's it! Topaz is now installed through pip. -+ -+

-\ No newline at end of file -diff --git a/docs/source/installation/singularity.md b/docs/source/installation/singularity.md -new file mode 100644 -index 0000000..401c819 ---- /dev/null -+++ b/docs/source/installation/singularity.md -@@ -0,0 +1,11 @@ -+**
Click here to install *using Singularity*

** -+A prebuilt Singularity image for Topaz is available [here](https://singularity-hub.org/collections/2413) and can be installed with: -+``` -+singularity pull shub://nysbc/topaz -+``` -+ -+Then, you can run topaz from within the singularity image with (paths must be changed appropriately): -+``` -+singularity exec --nv -B /mounted_path:/mounted_path /path/to/singularity/container/topaz_latest.sif /usr/local/conda/bin/topaz -+``` -+

-\ No newline at end of file -diff --git a/docs/source/installation/source_install.md b/docs/source/installation/source_install.md -new file mode 100644 -index 0000000..648dfc8 ---- /dev/null -+++ b/docs/source/installation/source_install.md -@@ -0,0 +1,57 @@ -+**
Click here to install *from source*

** -+ -+_Recommended: install Topaz into a virtual Python environment_ -+See https://conda.io/docs/user-guide/tasks/manage-environments.html or https://virtualenv.pypa.io/en/stable/ for setting one up. -+ -+\ -+**Install the dependencies** -+ -+Tested with python 3.6 and 2.7 -+ -+- pytorch (>= 1.0.0) -+- torchvision -+- pillow (>= 6.2.0) -+- numpy (>= 1.11) -+- pandas (>= 0.20.3) -+- scipy (>= 0.19.1) -+- scikit-learn (>= 0.19.0) -+ -+Easy installation of dependencies with conda -+``` -+conda install numpy pandas scikit-learn -+conda install -c pytorch pytorch torchvision -+``` -+For more info on installing pytorch for your CUDA version see https://pytorch.org/get-started/locally/ -+ -+\ -+**Download the source code** -+``` -+git clone https://github.com/tbepler/topaz -+``` -+ -+\ -+**Install Topaz** -+ -+Move to the source code directory -+``` -+cd topaz -+``` -+ -+By default, this will be the most recent version of the topaz source code. To install a specific older version, checkout that commit. For example, for v0.1.0 of Topaz: -+``` -+git checkout v0.1.0 -+``` -+Note that older Topaz versions may have different dependencies. Refer to the README for the specific Topaz version. -+ -+Install Topaz into your Python path including the topaz command line interface -+``` -+pip install . -+``` -+ -+To install for development use -+``` -+pip install -e . -+``` -+ -+

-+

-\ No newline at end of file -diff --git a/docs/source/tutorial.md b/docs/source/tutorial.md -index 161a880..c2ebb97 100644 ---- a/docs/source/tutorial.md -+++ b/docs/source/tutorial.md -@@ -1,4 +1,7 @@ --# Tutorial -+# Tutorials (coming soon) -+ -+Tutorial pages here are a work-in-progress. For the time being, please refer to the tutorial notebooks in topaz/tutorial. -+ -