Skip to content

Commit

Permalink
Merge pull request #11261 from easybuilders/4.3.x
Browse files Browse the repository at this point in the history
release EasyBuild v4.3.0
  • Loading branch information
boegel authored Sep 13, 2020
2 parents c31bf3b + 4e67459 commit 43d13b7
Show file tree
Hide file tree
Showing 525 changed files with 17,024 additions and 1,355 deletions.
20 changes: 20 additions & 0 deletions .github/workflows/linting.yml
Original file line number Diff line number Diff line change
@@ -0,0 +1,20 @@
name: Static Analysis
on: [push, pull_request]
jobs:
python-linting:
runs-on: ubuntu-18.04
steps:
- uses: actions/checkout@v2

- name: set up Python
uses: actions/setup-python@v1
with:
python-version: 3.8

- name: install Python packages
run: |
pip install --upgrade pip
pip install --upgrade flake8
- name: Run flake8 to verify PEP8-compliance of Python code
run: flake8
2 changes: 0 additions & 2 deletions .pep8

This file was deleted.

69 changes: 0 additions & 69 deletions .travis.yml

This file was deleted.

14 changes: 2 additions & 12 deletions README.rst
Original file line number Diff line number Diff line change
@@ -1,3 +1,5 @@
.. image:: https://github.com/easybuilders/easybuild-easyconfigs/workflows/easyconfigs%20unit%20tests/badge.svg

.. image:: https://easybuilders.github.io/easybuild/images/easybuild_logo_small.png
:align: center

Expand Down Expand Up @@ -31,15 +33,3 @@ Related Python packages:
* a collection of easyblocks that implement support for building and installing (groups of) software packages
* GitHub repository: https://github.com/easybuilders/easybuild-easyblocks
* package on PyPi: https://pypi.python.org/pypi/easybuild-easyblocks

*Build status overview:*

* **master** branch:

.. image:: https://travis-ci.org/easybuilders/easybuild-easyconfigs.svg?branch=master
:target: https://travis-ci.org/easybuilders/easybuild-easyconfigs/branches

* **develop** branch:

.. image:: https://travis-ci.org/easybuilders/easybuild-easyconfigs.svg?branch=develop
:target: https://travis-ci.org/easybuilders/easybuild-easyconfigs/branches
101 changes: 100 additions & 1 deletion RELEASE_NOTES
Original file line number Diff line number Diff line change
Expand Up @@ -3,9 +3,108 @@ For more detailed information, please see the git log.

These release notes can also be consulted at http://easybuild.readthedocs.org/en/latest/Release_notes.html.

The latest version of easybuild-easyconfig provides 10,147 easyconfig files, for 2,013 different software packages,
The latest version of easybuild-easyconfig provides 10,384 easyconfig files, for 2,059 different software packages,
incl. 31 different (compiler) toolchains.

v4.3.0 (September 13th 2020)
----------------------------

feature release

- added easyconfigs for 2 new toolchains:
- gomkl/2020a and iomkl/2020a (#11036)
- added example easyconfig files for 49 new software packages:
- almosthere (#11152), arcasHLA (#10867), BioPP (#11113), Bracken (#10829), BUFRLIB (#11140), Calib (#11111),
CellRanger-ATAC (#11186), edlib (#10470, #11246), flatbuffers (#11109), gengetopt (#11117), graphite2 (#11168),
HeFFTe (#10990), hierfstat (#11249), immunedeconv (#11136), ioapi (#10959), itpp (#10958), LiBis (#11059),
libosmium (#11024), limix-bgen (#11152), minibar (#10470, #11246), misha (#11127), MOABS (#10747), moonjit (#11163),
NGLess (#11128), nsync (#11109), openCARP (#11117), OpenForceField (#11048), OpenMMTools (#11046), OpenMS (#10994),
PennCNV (#10986), plantcv (#10968), PlasmaPy (#10732), Portcullis (#11038), PycURL (#11169), PyGEOS (#11110),
pySCENIC (#11115), Reapr (#9296), RnBeads (#11142), sf (#11248), SLiM (#11172), stars (#11215, #11248), Sumo (#11071),
Telescope (#10943), tensorflow-probability (#10312), texlive (#11168), tidymodels (#11010), Trycycler (#11207),
umi4cPackage (#11127), variant_tools (#11169)
- added additional easyconfigs for various supported software packages, including:
- Bazel 3.4.1, Bonito 0.2.2, binutils 2.35, CP2K 7.1, Clang 10.0.1, ccache 3.7.11, ctffind 4.1.14, datamash 1.5,
ELPA 2020.05.001, Emacs 26.3, Flye 2.8.1, GCC(core) 10.2.0, googletest 1.10.0, HDF 4.2.15, Horovod 0.19.5,
imageio 2.9.0, JUBE 2.4.0, Julia 1.5.1, Kent_tools 401, Libint 2.6.0, libxsmm 1.16.1, MDSplus 7.96.8,
MDTraj 1.9.4, MariaDB 10.4.13, Meson 0.55.1, MotionCor2 1.3.2, NAMD 2.14, NCO 4.9.3, OpenFOAM 8, OpenMPI 4.0.5,
OptiX 6.5.0, Pandoc 2.10, Perl 5.32.0, PostgreSQL 12.4, PyCUDA 2019.1.2, PyFR 1.9.0, PyTorch 1.6.0,
PyZMQ 18.1.1, patchelf 0.12, pocl 1.5, pycocotools 2.0.1, pyproj 2.6.1.post1, QuantumESPRESSO 6.6,
RDKit 2020.03.3, rgdal 1.5, Salmon 1.3.0, Spark 3.0.0, scikit-image 0.17.1, scipy 1.4.1, snpEff 5.0,
sympy 1.6.2, TINKER 8.7.2, tqdm 4.47.0, Unicycler 0.4.8, VMD 1.9.4a43
- minor enhancements, including:
- also build Python libraries for ParaView 5.8.0 (#10927)
- add extensions to recent Bioconductor easyconfigs: FlowSorted.Blood.EPIC (#11021), DRIMSeq + stageR (#11053)
- add extensions to recent R easyconfigs: AICcmodavg + biomod2 (#11030), qqman (#11052), poLCA (#11081), coxed
(#11094), testit + data.tree (#11135), celestial + fasterize (#11206)
- add Config::Simple extension to Perl 5.30.x easyconfigs (#11051)
- update TensorFlow v2.1.0 (#11109) and v2.0.0 (#11233) easyconfigs to provide more dependencies via EasyBuild
- add CUDA compute capabilities to torchvision-0.5.0 (#11241)
- various bug fixes, including:
- patch to fix exporting images with PyQtGraph v0.10.0 (#10848)
- add missing Python dependency to PETSc 3.11.1 (#10907) and PETSc 3.12.x (#10908) easyconfigs
- use CMakeMake easyblock for installing magma to avoid C++11 related failures on POWER (#10929)
- fix source URL for Graphviz v2.40.1 (#10944)
- fix lapack.h for use with C++ in OpenBLAS 0.3.9 easyconfigs (#10960)
- add missing build dep on M4 for 2019b versions of netCDF-Fortran (#10972)
- update easyconfig for PyTorch 1.4 to use custom easyblock and run on POWER (#11000)
- create symlinks to incorrectly named directories in OpenBabel-3.1.1 so $BABEL_LIBDIR and $BABEL_DATADIR work properly (#11004)
- add missing Python build dep to recent ELPA easyconfigs (#11011)
- use is_generic_easyblock from filetools in easyconfigs test suite (#11020)
- fix sources in Portcullis v1.2.2 easyconfigs (#11038)
- add patch for FFTW 3.3.8 to avoid use of -no-gcc when building with Intel compilers, to fix installation on CentOS 8 (cfr. #10932) (#11050)
- add missing Python build dep for BEDTools 2.29.x (#11054)
- add missing SciPy-bundle and Kent_tools (for bedPartition command) dependencies to FLAIR (#11057)
- add patch to fix bug in LiBiS v20200428 easyconfig (#11059)
- use FFTW provided via EasyBuild for ScaFaCoS (#11060)
- fix undefined reference to 'qfloat16::mantissatable' in Qt5.14.1 (#11063)
- add alternative checksum for rstantools 2.0.0 extension (#11081)
- update checksums for R 3.6.0 packages and add patch for ppc (#11088)
- install scikit-learn 0.23.1 as a bundle and include required threadpoolctl extension (#11089)
- update pybind11 easyconfigs to use custom easyblock to install with pip (#11091)
- add recent six as extension to archspec installed on top of Python 3.7.4 (#11092)
- add missing Seaborn dependency to LiBis easyconfig (#11095)
- add missing dependencies for OpenPIV + switch to PythonBundle easyblock and include progressbar2 as extension (#11096)
- add missing argparse dep to TEtranscripts easyconfig (#11097)
- add missing pkg-config build dep in Octave 5.1.0 easyconfigs (#11100)
- don't statically link MUSCLE, to avoid requiring that glibc-static is installed in OS (#11102)
- add missing pkg-config build dependency in recent R-bundle-Bioconductor easyconfigs (#11104)
- add patch to h5py 2.8.0 (#11119) and 2.9.0 (#11118) easyconfigs to avoid MPI_Init on 'import h5py'
- add patch to support libbfd 2.34 API change in Score-P 6.0 (#11123)
- use pip to install protobuf-python in 2019b toolchain (requires re-downloading source tarball!) (#11143, #11260)
- add missing Keras-Applications extension to TensorFlow 2.2.0 easyconfigs with foss*/2019b toolchain (#11156)
- add missing pocl dependency in R 3.6.0 (#11157)
- update Meson build dep to 0.55.1 for GLib, X11, Mesa & co to fix aggressive RPATH stripping (#11178)
- disable generating of man pages in recent libdrm easyconfigs to avoid installation failure if docbook-xsl is not installed (#11182)
- add fontconfig and bzip2 as direct dependencies for Qt5 to fix installation with --rpath (#11183)
- fix failing 'make check' for MPFR 4.x (#11187) and GMP (#11188) when installing with 'eb --rpath'
- add pkg-config as a build dependency for libglvnd (#11189)
- add missing libiconv build dep in recent Doxygen easyconfigs (#11191, #11257)
- enhance Java/11 wrapper to also support for aarch64/Arm (#11192)
- add pkg-config as a build dependency to Ghostscript 9.52, needed on aarch64/arm (#11194)
- add patch for pycrypto extension in recent Python easyconfigs to remove hardcoded /usr/include which causes problems when 'eb --sysroot' is used (#11202)
- fix installation of R v3.6.3 and v4.0.0 with foss/2020a on Arm (aarch64) (#11213)
- update PyTorch 1.4 easyconfigs to use custom easyblock (and do less downloading during installations) (#11219)
- other changes:
- don't require custom sanity_check_paths for 'CUDA' bundle easyconfigs (#10936)
- move intervaltree and sortedcontainers to main Python easyconfigs (#10969, #10970)
- disable qtwayland in Qt5 v5.14.1 (#11107)
- remove mklml (small MKL) from PyTorch 1.3.1 and 1.4.0 easyconfigs (#11019)
- use pip to install h5py 2.10.0 (#11044)
- stop testing easyconfig PRs with Travis, only use GitHub Actions from now on (#11008, #11055)
- switch to Kent_tools built from source as dep for FusionCatcher (#11057)
- fall back to using PR target branch when determining "merge base" between PR branch & target branch fails in test suite (#11069)
- rename gtest to googletest (#11082)
- rename sdsl-lite to SDSL (to use one single name) (#11084)
- stop using 'remove_usr_bin'-patch in TensorFlow easyconfig, no longer required with updated TensorFlow easyblock (#11087)
- extend timeout for libxc-4.3.4 to avoid failing tests (#11126)
- move GitHub Actions status badge to top of README (#11138)
- fix code style issues in test (#11146)
- enable Flake8 on CI and fix issues (#11147)
- prefer gc GitHub site for source downloads (#11208)
- prefer https over ftp in source_urls of IgBLAST easyconfig (#11244)


v4.2.2 (July 8th 2020)
----------------------

Expand Down
35 changes: 35 additions & 0 deletions easybuild/easyconfigs/a/ACTC/ACTC-1.1-GCCcore-8.3.0.eb
Original file line number Diff line number Diff line change
@@ -0,0 +1,35 @@
easyblock = 'MakeCp'

name = 'ACTC'
version = '1.1'

homepage = 'https://sourceforge.net/projects/actc'
description = "ACTC converts independent triangles into triangle strips or fans."

toolchain = {'name': 'GCCcore', 'version': '8.3.0'}
toolchainopts = {'pic': True}

source_urls = [SOURCEFORGE_SOURCE]
sources = [SOURCELOWER_TAR_GZ]
checksums = ['3a1303291629b9de6008c3c9d7b020a4b854802408fb3f8222ec492808c8b44d']

builddependencies = [('binutils', '2.32')]

buildopts = 'CC="$CC" CFLAGS="$CFLAGS"'

files_to_copy = [
(['tcsample', 'tctest', 'tctest2'], 'bin'),
(['tc.h'], 'include/ac'),
(['libactc.a'], 'lib'),
'COPYRIGHT', 'manual.html', 'prims.gif', 'README',
]

sanity_check_paths = {
'files': ['bin/tctest', 'bin/tctest2', 'bin/tcsample', 'include/ac/tc.h', 'lib/libactc.a',
'COPYRIGHT', 'manual.html', 'prims.gif', 'README'],
'dirs': [],
}

modextrapaths = {'CPATH': 'include/ac'}

moduleclass = 'lib'
31 changes: 31 additions & 0 deletions easybuild/easyconfigs/a/ADOL-C/ADOL-C-2.7.2-gompi-2020a.eb
Original file line number Diff line number Diff line change
@@ -0,0 +1,31 @@
easyblock = 'ConfigureMake'

name = 'ADOL-C'
version = '2.7.2'

homepage = 'https://projects.coin-or.org/ADOL-C'

description = """The package ADOL-C (Automatic Differentiation by OverLoading in C++) facilitates
the evaluation of first and higher derivatives of vector functions that are defined
by computer programs written in C or C++. The resulting derivative evaluation
routines may be called from C/C++, Fortran, or any other language that can be linked
with C.
"""

toolchain = {'name': 'gompi', 'version': '2020a'}
toolchainopts = {'openmp': True, 'usempi': True, 'pic': True}

source_urls = ['https://github.com/coin-or/%(name)s/archive/releases']
sources = ['%(version)s.tar.gz']
checksums = ['701e0856baae91b98397960d5e0a87a549988de9d4002d0e9a56fa08f5455f6e']

builddependencies = [('Autotools', '20180311')]

preconfigopts = 'autoreconf -fi && '

sanity_check_paths = {
'files': ['lib64/libadolc.so'],
'dirs': ['include/adolc'],
}

moduleclass = 'system'
33 changes: 33 additions & 0 deletions easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-8.3.0-Java-11.eb
Original file line number Diff line number Diff line change
@@ -0,0 +1,33 @@
easyblock = 'ConfigureMake'

name = 'ANTLR'
version = '2.7.7'
versionsuffix = '-Java-%(javaver)s'

homepage = 'https://www.antlr2.org/'
description = """ANTLR, ANother Tool for Language Recognition, (formerly PCCTS)
is a language tool that provides a framework for constructing recognizers,
compilers, and translators from grammatical descriptions containing
Java, C#, C++, or Python actions."""

toolchain = {'name': 'GCCcore', 'version': '8.3.0'}

source_urls = ['https://www.antlr2.org/download/']
sources = [SOURCELOWER_TAR_GZ]
patches = ['%(name)s-%(version)s_includes.patch']
checksums = [
'853aeb021aef7586bda29e74a6b03006bcb565a755c86b66032d8ec31b67dbb9', # antlr-2.7.7.tar.gz
'd167d3248a03301bc93efcb37d5df959aae6794968e42231af0b0dd26d6a2e66', # ANTLR-2.7.7_includes.patch
]

builddependencies = [('binutils', '2.32')]
dependencies = [('Java', '11', '', True)]

configopts = '--disable-examples --disable-csharp --disable-python'

sanity_check_paths = {
'files': ['bin/antlr', 'bin/antlr-config'],
'dirs': ['include'],
}

moduleclass = 'tools'
Original file line number Diff line number Diff line change
@@ -0,0 +1,56 @@
easyblock = 'PythonBundle'

name = 'ASE'
version = '3.19.0'
versionsuffix = '-Python-%(pyver)s'

homepage = 'https://wiki.fysik.dtu.dk/ase'
description = """ASE is a python package providing an open source Atomic Simulation Environment
in the Python scripting language."""

toolchain = {'name': 'fosscuda', 'version': '2019b'}

dependencies = [
('Python', '3.7.4'),
('Tkinter', '%(pyver)s'),
('matplotlib', '3.1.1', '-Python-%(pyver)s'),
]

use_pip = True
sanity_pip_check = True

exts_default_options = {'source_urls': [PYPI_SOURCE]}

exts_list = [
('MarkupSafe', '1.1.1', {
'checksums': ['29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b'],
}),
('Jinja2', '2.10.3', {
'checksums': ['9fe95f19286cfefaa917656583d020be14e7859c6b0252588391e47db34527de'],
}),
('Werkzeug', '0.16.0', {
'checksums': ['7280924747b5733b246fe23972186c6b348f9ae29724135a6dfc1e53cea433e7'],
}),
('Click', '7.0', {
'checksums': ['5b94b49521f6456670fdb30cd82a4eca9412788a93fa6dd6df72c94d5a8ff2d7'],
}),
('itsdangerous', '1.1.0', {
'checksums': ['321b033d07f2a4136d3ec762eac9f16a10ccd60f53c0c91af90217ace7ba1f19'],
}),
('Flask', '1.1.1', {
'checksums': ['13f9f196f330c7c2c5d7a5cf91af894110ca0215ac051b5844701f2bfd934d52'],
}),
('ase', version, {
'checksums': ['a8378ab57e91cfe1ba09b3639d8409bb7fc1a40b59479c7822d206e673ad93f9'],
}),
]

sanity_check_paths = {
'files': ['bin/ase'],
'dirs': ['lib/python%(pyshortver)s/site-packages'],
}

# make sure Tkinter is available, otherwise 'ase gui' will not work
sanity_check_commands = ["python -c 'import tkinter' "]

moduleclass = 'chem'
2 changes: 1 addition & 1 deletion easybuild/easyconfigs/a/ATK/ATK-2.36.0-GCCcore-9.3.0.eb
Original file line number Diff line number Diff line change
Expand Up @@ -18,7 +18,7 @@ checksums = ['fb76247e369402be23f1f5c65d38a9639c1164d934e40f6a9cf3c9e96b652788']

builddependencies = [
('binutils', '2.34'),
('Meson', '0.53.2', '-Python-3.8.2'),
('Meson', '0.55.1', '-Python-3.8.2'),
('Ninja', '1.10.0'),
('pkg-config', '0.29.2'),
('GObject-Introspection', '1.64.0', '-Python-3.8.2'),
Expand Down
Loading

0 comments on commit 43d13b7

Please sign in to comment.