From 3a3be3ac7cef30ab20ec5866fc61dd6c24ec1848 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 29 Nov 2022 11:53:39 +0100 Subject: [PATCH 001/107] adding easyconfigs: NTPoly-2.7.1-foss-2022a.eb, ELSI-2.9.1-foss-2022a-PEXSI.eb, libmbd-0.12.6-foss-2022a.eb --- .../e/ELSI/ELSI-2.9.1-foss-2022a-PEXSI.eb | 45 ++++++++++++++ .../l/libmbd/libmbd-0.12.6-foss-2022a.eb | 59 +++++++++++++++++++ .../n/NTPoly/NTPoly-2.7.1-foss-2022a.eb | 28 +++++++++ 3 files changed, 132 insertions(+) create mode 100644 easybuild/easyconfigs/e/ELSI/ELSI-2.9.1-foss-2022a-PEXSI.eb create mode 100644 easybuild/easyconfigs/l/libmbd/libmbd-0.12.6-foss-2022a.eb create mode 100644 easybuild/easyconfigs/n/NTPoly/NTPoly-2.7.1-foss-2022a.eb diff --git a/easybuild/easyconfigs/e/ELSI/ELSI-2.9.1-foss-2022a-PEXSI.eb b/easybuild/easyconfigs/e/ELSI/ELSI-2.9.1-foss-2022a-PEXSI.eb new file mode 100644 index 00000000000..d5ef7e3da14 --- /dev/null +++ b/easybuild/easyconfigs/e/ELSI/ELSI-2.9.1-foss-2022a-PEXSI.eb @@ -0,0 +1,45 @@ +name = 'ELSI' +version = '2.9.1' +versionsuffix = '-PEXSI' + +homepage = 'https://wordpress.elsi-interchange.org/' +description = """ELSI provides and enhances scalable, open-source software library solutions for + electronic structure calculations in materials science, condensed matter physics, chemistry, and many other fields. + ELSI focuses on methods that solve or circumvent eigenvalue problems in electronic structure theory. + The ELSI infrastructure should also be useful for other challenging eigenvalue problems. +""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'usempi': True, 'pic': True, 'cstd': 'c++11', 'extra_fflags': '-fallow-argument-mismatch'} + +source_urls = ['https://wordpress.elsi-interchange.org/wp-content/uploads/2022/05'] +sources = ['elsi_interface-v%(version)s.tar.gz'] +patches = [ + 'pexsi-1.2.0-mpi30.patch', + 'ELSI-2.7.1_bison_3.7_compat.patch', +] +checksums = [ + {'elsi_interface-v2.9.1.tar.gz': 'ad3dc163159a79f7a83f360265f2446920c151ecce9c294136e630fe424f1d29'}, + {'pexsi-1.2.0-mpi30.patch': 'd5580de710cee652c27622f167a10933f792546481d9c08d62f452885cb63abb'}, + {'ELSI-2.7.1_bison_3.7_compat.patch': '986f95c2eb22c8a8bef13357a10242dcf0a0fac562c88bdc9bdf46cc6e7a1edb'}, +] + +builddependencies = [ + ('flex', '2.6.4'), + ('Bison', '3.8.2'), + ('CMake', '3.23.1'), +] + +dependencies = [ + ('ELPA', '2021.11.001'), + ('NTPoly', '2.7.1'), +] + +abs_path_compilers = True +build_internal_pexsi = True + +configopts = '-DENABLE_BSEPACK=ON ' + +runtest = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/l/libmbd/libmbd-0.12.6-foss-2022a.eb b/easybuild/easyconfigs/l/libmbd/libmbd-0.12.6-foss-2022a.eb new file mode 100644 index 00000000000..e0e689460f9 --- /dev/null +++ b/easybuild/easyconfigs/l/libmbd/libmbd-0.12.6-foss-2022a.eb @@ -0,0 +1,59 @@ +easyblock = 'CMakeMake' + +name = 'libmbd' +version = '0.12.6' + +homepage = 'https://libmbd.github.io/index.html' +description = """ +Libmbd implements the many-body dispersion (MBD) method in several programming languages and frameworks: + + - The Fortran implementation is the reference, most advanced implementation, with support for analytical + gradients and distributed parallelism, and additional functionality beyond the MBD method itself. + It provides a low-level and a high-level Fortran API, as well as a C API. Furthermore, Python bindings + to the C API are provided. + - The Python/Numpy implementation is intended for prototyping, and as a high-level language reference. + - The Python/Tensorflow implementation is an experiment that should enable rapid prototyping of machine + learning applications with MBD. + +The Python-based implementations as well as Python bindings to the Libmbd C API are accessible from the +Python package called Pymbd. +""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'usempi': True, 'pic': True} + +github_account = 'libmbd' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['9f8154b6b2f57e78a8e33d3b315a244185e8e5ecb03661a469808af7512e761e'] + +builddependencies = [ + ('CMake', '3.23.1'), + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('ELSI', '2.9.1', '-PEXSI'), +] + +# build scripts expect either a git repo or a defined version string in a file +_versiontag_file = '%(builddir)s/%(name)s-%(version)s/cmake/LibmbdVersionTag.cmake' +preconfigopts = "echo 'set(VERSION_TAG \"%%(version)s\")' > %s && " % _versiontag_file + +configopts = "-DENABLE_SCALAPACK_MPI=ON -DENABLE_ELSI=ON " +configopts += "-DMPIEXEC_MAX_NUMPROCS=1 " # number of procs in the tests + +# make sure that built libraries (libmbd.so) in build directory are picked when running tests +# this is required when RPATH linking is used +pretestopts = "export LD_LIBRARY_PATH=%(builddir)s/easybuild_obj:$LD_LIBRARY_PATH && " + +runtest = 'test' + +sanity_check_paths = { + 'files': ['lib/libmbd.%s' % SHLIB_EXT, 'include/mbd/mbd.h', 'include/mbd/mbd.mod'], + 'dirs': ['lib/cmake/mbd'], +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/n/NTPoly/NTPoly-2.7.1-foss-2022a.eb b/easybuild/easyconfigs/n/NTPoly/NTPoly-2.7.1-foss-2022a.eb new file mode 100644 index 00000000000..e6ef7ccfb3e --- /dev/null +++ b/easybuild/easyconfigs/n/NTPoly/NTPoly-2.7.1-foss-2022a.eb @@ -0,0 +1,28 @@ +easyblock = 'CMakeMake' + +name = 'NTPoly' +version = '2.7.1' + +homepage = 'https://github.com/william-dawson/NTPoly' +description = """is a massively parallel library for computing the functions of sparse, symmetric matrices based on +polynomial expansions. For sufficiently sparse matrices, most of the matrix functions +in NTPoly can be computed in linear time.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'openmp': False, 'usempi': True} + +source_urls = ['https://github.com/william-dawson/NTPoly/archive/ntpoly-v%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c15d9f51ac054b4ef0565ce5c4c8589c10bdbab4dc3442ebd109691e2bbfc7e2'] + +builddependencies = [('CMake', '3.23.1')] + +build_shared_libs = True + +sanity_check_paths = { + 'files': ['include/%s.mod' % x for x in ['datatypesmodule', 'densitymatrixsolversmodule']] + + ['lib64/libNTPoly.%s' % SHLIB_EXT, 'lib/libNTPoly.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'math' From b993aeed7c5023d8c65e082c778f0551268b0bd4 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 30 Apr 2024 19:59:21 +0200 Subject: [PATCH 002/107] adding easyconfigs: CAMPARI-4.0-foss-2023a.eb --- .../c/CAMPARI/CAMPARI-4.0-foss-2023a.eb | 54 +++++++++++++++++++ 1 file changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/c/CAMPARI/CAMPARI-4.0-foss-2023a.eb diff --git a/easybuild/easyconfigs/c/CAMPARI/CAMPARI-4.0-foss-2023a.eb b/easybuild/easyconfigs/c/CAMPARI/CAMPARI-4.0-foss-2023a.eb new file mode 100644 index 00000000000..af659719245 --- /dev/null +++ b/easybuild/easyconfigs/c/CAMPARI/CAMPARI-4.0-foss-2023a.eb @@ -0,0 +1,54 @@ +easyblock = 'ConfigureMake' + +name = 'CAMPARI' +version = '4.0' +_date = '12202020' + +homepage = 'http://campari.sourceforge.net/V4/index.html' +description = """ +CAMPARI is a joint package for performing and analyzing molecular simulations, in particular of systems of biological +relevance. It focuses on a wide availability of algorithms for (advanced) sampling and is capable of combining Monte +Carlo and molecular dynamics in seamless fashion.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['campari_v%s_%s.zip' % (version.split('.')[0], _date)] +checksums = ['bc627fb286b5461a5c68aa3e1a551ecd81016495163685800163c734f7c4f1bd'] + +builddependencies = [ + ('Autotools', '20220317'), +] + +dependencies = [ + ('netCDF-Fortran', '4.6.1'), + ('libtirpc', '1.3.3'), +] + +start_dir = 'source' + +# remove hardcoded paths in configure script +preconfigopts = 'sed -i "s|/usr/share|$EBROOTAUTOMAKE/share|" configure &&' +# ignore default compiler settings and use EB build environment +local_fcflags = '$FCFLAGS -fallow-argument-mismatch $CPPFLAGS' +configopts = '--enable-compiler=ignore --with-trailing-user-fcflags="%s" ' % local_fcflags +configopts += '--enable-mpi=auto ' +configopts += 'LIBS="$LIBS $LIBFFT $LIBBLAS -ltirpc"' + +buildopts = 'all' + +maxparallel = 10 + +postinstallcmds = ['cp -a %(builddir)s/campari/{data,doc,examples,params,tools,LICENSE} %(installdir)s/'] + +_binaries = ['campari', 'campari_mpi', 'campari_mpi_threads', 'campari_threads', 'camp_ncminer', 'camp_ncminer_threads'] +_libraries = ['lcampari.a', 'lcampari_mpi.a', 'lcampari_mpi_threads.a', 'lcampari_threads.a', 'libxdrf.a'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in _binaries] + ['lib/%s' % x for x in _libraries], + 'dirs': [], +} + +sanity_check_commands = ['campari -h | grep "USAGE: CAMPARI"'] + +moduleclass = 'bio' From 31925564e48688a549911a21b25134436081f865 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 30 Apr 2024 20:01:18 +0200 Subject: [PATCH 003/107] sync configopts in CAMPARI v4.0 on foss/2023a and intel/2023a --- easybuild/easyconfigs/c/CAMPARI/CAMPARI-4.0-intel-2023a.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/CAMPARI/CAMPARI-4.0-intel-2023a.eb b/easybuild/easyconfigs/c/CAMPARI/CAMPARI-4.0-intel-2023a.eb index 203b4e4cd9f..743bf47a462 100644 --- a/easybuild/easyconfigs/c/CAMPARI/CAMPARI-4.0-intel-2023a.eb +++ b/easybuild/easyconfigs/c/CAMPARI/CAMPARI-4.0-intel-2023a.eb @@ -30,9 +30,10 @@ start_dir = 'source' # remove hardcoded paths in configure script preconfigopts = 'sed -i "s|/usr/share|$EBROOTAUTOMAKE/share|" configure &&' # ignore default compiler settings and use EB build environment -configopts = '--enable-compiler=ignore --with-trailing-user-fcflags="$FCFLAGS" ' +local_fcflags = '$FCFLAGS -fallow-argument-mismatch $CPPFLAGS' +configopts = '--enable-compiler=ignore --with-trailing-user-fcflags="%s" ' % local_fcflags configopts += '--enable-mpi=auto ' -configopts += 'LIBS="$LIBS $LIBFFT -ltirpc"' +configopts += 'LIBS="$LIBS $LIBFFT $LIBBLAS -ltirpc"' buildopts = 'all' From dad682330109923e467e0d5ebb11f90e4f7ecd44 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 10 May 2024 13:29:03 +0200 Subject: [PATCH 004/107] adding easyconfigs: R-tesseract-5.2.1-foss-2023a.eb, tesseract-5.3.4-GCCcore-12.3.0.eb, Leptonica-1.84.1-GCCcore-12.3.0.eb --- .../Leptonica-1.84.1-GCCcore-12.3.0.eb | 32 +++++++++ .../R-tesseract-5.2.1-foss-2023a.eb | 51 ++++++++++++++ .../tesseract-5.3.4-GCCcore-12.3.0.eb | 66 +++++++++++++++++++ 3 files changed, 149 insertions(+) create mode 100644 easybuild/easyconfigs/l/Leptonica/Leptonica-1.84.1-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/r/R-tesseract/R-tesseract-5.2.1-foss-2023a.eb create mode 100644 easybuild/easyconfigs/t/tesseract/tesseract-5.3.4-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/l/Leptonica/Leptonica-1.84.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/Leptonica/Leptonica-1.84.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..ee92fb98c62 --- /dev/null +++ b/easybuild/easyconfigs/l/Leptonica/Leptonica-1.84.1-GCCcore-12.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'Leptonica' +version = '1.84.1' + +homepage = 'http://www.leptonica.org' +description = """Leptonica is a collection of pedagogically-oriented open source software + that is broadly useful for image processing and image analysis applications.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/DanBloomberg/leptonica/releases/download/%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['2b3e1254b1cca381e77c819b59ca99774ff43530209b9aeb511e1d46588a64f6'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('libpng', '1.6.39'), + ('LibTIFF', '4.5.0'), + ('libjpeg-turbo', '2.1.5.1'), + ('giflib', '5.2.1'), + ('libwebp', '1.3.1'), + ('zlib', '1.2.13'), +] + +sanity_check_paths = { + 'files': ['bin/convertformat'], + 'dirs': ['include/leptonica', 'lib/pkgconfig'] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/r/R-tesseract/R-tesseract-5.2.1-foss-2023a.eb b/easybuild/easyconfigs/r/R-tesseract/R-tesseract-5.2.1-foss-2023a.eb new file mode 100644 index 00000000000..4981b999b95 --- /dev/null +++ b/easybuild/easyconfigs/r/R-tesseract/R-tesseract-5.2.1-foss-2023a.eb @@ -0,0 +1,51 @@ +easyblock = 'Bundle' + +name = 'R-tesseract' +version = '5.2.1' + +homepage = 'https://cran.r-project.org/package=tesseract' +description = "The R extension for using tesseract" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [('pkgconf', '1.9.5')] + +dependencies = [ + ('R', '4.3.2'), + ('poppler', '23.09.0'), + ('tesseract', '5.3.4'), +] + +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', +} + +exts_list = [ + ('qpdf', '1.3.3', { + 'checksums': ['415610be6fa73f60a31872b81fea089288b07f9cb6d078088009207c5e60fe53'], + }), + ('pdftools', '3.4.0', { + 'checksums': ['0b9d7b2100a6d7959c56e144285b9638ca6ff4a7f484a31ff814a99d71482c64'], + }), + ('tesseract', version, { + 'preinstallopts': 'INCLUDE_DIR="$EBROOTTESSERACT/include/tesseract -I$EBROOTLEPTONICA/include/leptonica"' + ' LIB_DIR=$EBROOTTESSERACT/lib', + 'checksums': ['ffaba641c5d531a2b6d4ded3608a669206b1e0690cb5e013e3fc9db8aea117fe'], + }), +] + +sanity_check_paths = { + 'files': ['tesseract/libs/tesseract.%s' % SHLIB_EXT, 'tesseract/R/tesseract'], + 'dirs': ['qpdf', 'pdftools'], +} + +modextrapaths = {'R_LIBS_SITE': ''} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/t/tesseract/tesseract-5.3.4-GCCcore-12.3.0.eb b/easybuild/easyconfigs/t/tesseract/tesseract-5.3.4-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..94cf0915ff9 --- /dev/null +++ b/easybuild/easyconfigs/t/tesseract/tesseract-5.3.4-GCCcore-12.3.0.eb @@ -0,0 +1,66 @@ +easyblock = 'CMakeMake' + +name = 'tesseract' +version = '5.3.4' +_tessdata_ver = '4.1.0' + +homepage = 'https://github.com/tesseract-ocr/tesseract' +description = """Tesseract is an optical character recognition engine""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +github_account = 'tesseract-ocr' +source_urls = [GITHUB_SOURCE] +sources = [ + '%(version)s.tar.gz', + { + 'source_urls': ['https://github.com/tesseract-ocr/tessdata_best/archive/'], + 'download_filename': '%s.tar.gz' % _tessdata_ver, + 'filename': 'tessdata_best-%s.tar.gz' % _tessdata_ver, + }, +] +checksums = [ + {'5.3.4.tar.gz': '141afc12b34a14bb691a939b4b122db0d51bd38feda7f41696822bacea7710c7'}, + {'tessdata_best-4.1.0.tar.gz': 'bb05b738298ae73e7130e2913ed002b49d94cd1cea508e63be1928fe47770b32'}, +] + +builddependencies = [ + ('CMake', '3.26.3'), + ('binutils', '2.40'), + ('pkgconf', '1.9.5') +] + +dependencies = [ + ('zlib', '1.2.13'), + ('libpng', '1.6.39'), + ('libjpeg-turbo', '2.1.5.1'), + ('LibTIFF', '4.5.0'), + ('Leptonica', '1.84.1'), + ('libarchive', '3.6.2'), + ('ICU', '73.2'), + ('fontconfig', '2.14.2'), + ('GLib', '2.77.1'), + ('cairo', '1.17.8'), + ('Pango', '1.50.14'), +] + +configopts = ['-DBUILD_SHARED_LIBS=ON', '-DBUILD_SHARED_LIBS=OFF'] + +postinstallcmds = [ + 'rm %(builddir)s/tessdata_best-*/configs', + 'rm -rf %(builddir)s/tessdata_best-*/tessconfigs', + 'mv %(builddir)s/tessdata_best-*/* %(installdir)s/share/tessdata' +] + +modextrapaths = { + 'TESSDATA_PREFIX': 'share/tessdata', +} + +sanity_check_paths = { + 'files': ['bin/tesseract', 'lib/libtesseract.a', 'lib/libtesseract.%s' % SHLIB_EXT], + 'dirs': ['share/tessdata', 'include/tesseract'] +} + +sanity_check_commands = ['tesseract --version', 'tesseract --list-langs'] + +moduleclass = 'vis' From e2c3ef10c8193d142a647729c93858e5345ae576 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Wed, 15 May 2024 14:17:47 +0200 Subject: [PATCH 005/107] adding easyconfigs: sleuth-0.30.1-foss-2023a.eb --- .../s/sleuth/sleuth-0.30.1-foss-2023a.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/s/sleuth/sleuth-0.30.1-foss-2023a.eb diff --git a/easybuild/easyconfigs/s/sleuth/sleuth-0.30.1-foss-2023a.eb b/easybuild/easyconfigs/s/sleuth/sleuth-0.30.1-foss-2023a.eb new file mode 100644 index 00000000000..f03005cda38 --- /dev/null +++ b/easybuild/easyconfigs/s/sleuth/sleuth-0.30.1-foss-2023a.eb @@ -0,0 +1,25 @@ +easyblock = 'RPackage' + +name = 'sleuth' +version = '0.30.1' + +homepage = 'https://pachterlab.github.io/sleuth' +description = """Investigate RNA-Seq transcript abundance from kallisto and perform differential expression analysis.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/pachterlab/sleuth/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['4c8efca5d726471cb71187e8db07097a50f63aadf42f6fa25c59e7eed635f982'] + +dependencies = [ + ('R', '4.3.2'), + ('R-bundle-Bioconductor', '3.18', '-R-%(rver)s'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +moduleclass = 'bio' From a8646f52d10cf3ce89068b5545826c0c6c4cf988 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 27 May 2024 17:15:43 +0200 Subject: [PATCH 006/107] adding easyconfigs: Julia-1.10.3-linux-x86_64.eb, IJulia-1.24.2-Julia-1.10.3.eb --- .../i/IJulia/IJulia-1.24.2-Julia-1.10.3.eb | 84 +++++++++++++++++++ .../j/Julia/Julia-1.10.3-linux-x86_64.eb | 30 +++++++ 2 files changed, 114 insertions(+) create mode 100644 easybuild/easyconfigs/i/IJulia/IJulia-1.24.2-Julia-1.10.3.eb create mode 100644 easybuild/easyconfigs/j/Julia/Julia-1.10.3-linux-x86_64.eb diff --git a/easybuild/easyconfigs/i/IJulia/IJulia-1.24.2-Julia-1.10.3.eb b/easybuild/easyconfigs/i/IJulia/IJulia-1.24.2-Julia-1.10.3.eb new file mode 100644 index 00000000000..f2072785aa5 --- /dev/null +++ b/easybuild/easyconfigs/i/IJulia/IJulia-1.24.2-Julia-1.10.3.eb @@ -0,0 +1,84 @@ +easyblock = 'JuliaBundle' + +name = 'IJulia' +version = '1.24.2' +_julia_ver = '1.10.3' +versionsuffix = "-Julia-%s" % _julia_ver + +homepage = 'https://github.com/JuliaLang/IJulia.jl' +description = "Julia kernel for Jupyter" + +toolchain = SYSTEM + +dependencies = [ + ('Julia', _julia_ver, '-linux-%s' % ARCH, SYSTEM), +] + +exts_list = [ + ('Preferences', '1.4.3', { + 'source_urls': ['https://github.com/JuliaPackaging/Preferences.jl/archive/'], + 'checksums': ['02b995891818b91266f98bcb46eefc513dfb66b177b5a6a0d1cff97be3e4582d'], + }), + ('JLLWrappers', '1.5.0', { + 'source_urls': ['https://github.com/JuliaPackaging/JLLWrappers.jl/archive/'], + 'checksums': ['6e83b81afd0c57636e80bcf52ad51f6ba43d98643cac999727b958d9ab3d4a01'], + }), + ('SnoopPrecompile', '2.10.8', { + 'source_urls': ['https://github.com/timholy/SnoopCompile.jl/archive/'], + 'start_dir': '%(name)s', + 'checksums': ['9b3204ce72fa3d0f1a359428e9f2ae43db2ee91f7ba77407056aced39d74d9d6'], + }), + ('PrecompileTools', '1.2.1', { + 'source_urls': ['https://github.com/JuliaLang/PrecompileTools.jl/archive/'], + 'checksums': ['af58b384e08b488b2da5ad19e72817b8b0ddb026997f8cf85f2964cc2c26cd34'], + }), + ('Parsers', '2.8.1', { + 'source_urls': ['https://github.com/JuliaData/Parsers.jl/archive/'], + 'checksums': ['6ea035be48ef5daaecdff62ac8f29c6110aaf20f3349058a4f96e2503f55b693'], + }), + ('JSON', '0.21.4', { + 'source_urls': ['https://github.com/JuliaIO/JSON.jl/archive/'], + 'checksums': ['c6b620ad4150ec5a154367f50c9579af800e3a89a6d8f9cb5dd30215a5d3f552'], + }), + ('MbedTLS', '1.1.9', { + 'source_urls': ['https://github.com/JuliaLang/MbedTLS.jl/archive/'], + 'checksums': ['d421bb36f9eb7f8840bd7108c2c33a9a5532454ac9465861e2f7797f89c1f56b'], + }), + ('VersionParsing', '1.3.0', { + 'source_urls': ['https://github.com/JuliaInterop/VersionParsing.jl/archive/'], + 'checksums': ['f90fe419e1a40ef0eccfaaed1d1b7792d9115a059a82d0c23e3c04c944d0f8ca'], + }), + ('Conda', '1.10.0', { + 'source_urls': ['https://github.com/JuliaPy/Conda.jl/archive/'], + 'checksums': ['2007170cad58d6f27626500abd52bd782023b8ecb7a7d05a678d7aec3c0f9948'], + }), + ('SoftGlobalScope', '1.1.0', { + 'source_urls': ['https://github.com/stevengj/SoftGlobalScope.jl/archive/'], + 'checksums': ['8d4264386c859403938498cd9ddd5e94e10181deba4a3e71d391b16750e3848b'], + }), + ('libsodium_jll', '1.0.20+0', { + 'source_urls': ['https://github.com/JuliaBinaryWrappers/libsodium_jll.jl/archive/'], + 'sources': [{'filename': 'libsodium-v%(version)s.tar.gz'}], + 'checksums': ['f7c3a17acc3a478ec10a4a49a0dd04694140f4483644ec9db638706ea9844aba'], + }), + ('ZeroMQ_jll', '4.3.5+0', { + 'source_urls': ['https://github.com/JuliaBinaryWrappers/ZeroMQ_jll.jl/archive/'], + 'sources': [{'filename': 'ZeroMQ-v%(version)s.tar.gz'}], + 'checksums': ['29d1f35e48c1436743a6da28518cb7aeccb32af4b439c3976df1967c6a252e87'], + }), + ('ZMQ', '1.2.4', { + 'source_urls': ['https://github.com/JuliaInterop/ZMQ.jl/archive/'], + 'checksums': ['a15fe752d2b049ad7521d03909ae8ad6c28e4cf46fc823f666cbc1cc6f5795ba'], + }), + (name, version, { + 'preinstallopts': "mkdir -p %(installdir)s/jupyter && export JUPYTER_DATA_DIR=%(installdir)s/jupyter && ", + 'source_urls': ['https://github.com/JuliaLang/IJulia.jl/archive/'], + 'checksums': ['de215348c7c41e1ca15c0d21f5f9a78bedce77b02ef89d67f38702c4d57ee80d'], + }), +] + +modextrapaths = { + 'JUPYTER_PATH': 'jupyter', +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.10.3-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.10.3-linux-x86_64.eb new file mode 100644 index 00000000000..c93803c3f49 --- /dev/null +++ b/easybuild/easyconfigs/j/Julia/Julia-1.10.3-linux-x86_64.eb @@ -0,0 +1,30 @@ +easyblock = 'Tarball' + +name = 'Julia' +version = '1.10.3' +versionsuffix = '-linux-x86_64' + +homepage = 'https://julialang.org' +description = "Julia is a high-level, high-performance dynamic programming language for numerical computing" + +toolchain = SYSTEM + +source_urls = ['https://julialang-s3.julialang.org/bin/linux/x64/%(version_major_minor)s/'] +sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz'] +patches = [('julia.wrapper', 'bin/')] +checksums = [ + {'julia-1.10.3-linux-x86_64.tar.gz': '81b910c922fff0e27ae1f256f2cc803db81f3960215281eddd2d484721928c70'}, + {'julia.wrapper': 'a36a3e0cb98ab4d2b05e0ca8f0bf2724baafbd669a0db318a00e40737d2f02f9'}, +] + +# install wrapper with linking safeguards for Julia libraries +postinstallcmds = ["cd %(installdir)s/bin && mv julia julia.bin && mv julia.wrapper julia"] + +sanity_check_paths = { + 'files': ['bin/julia', 'bin/julia.bin', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT], + 'dirs': ['bin', 'etc', 'include', 'lib', 'lib/julia', 'share'] +} + +sanity_check_commands = ['julia --help'] + +moduleclass = 'lang' From 22620e9ada1f2624a8bcbe775d8040377ffd7704 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 3 Jul 2024 01:19:25 +0200 Subject: [PATCH 007/107] fix checksum of julia.wrapper in Julia-1.10.3-linux-x86_64.eb --- easybuild/easyconfigs/j/Julia/Julia-1.10.3-linux-x86_64.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.10.3-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.10.3-linux-x86_64.eb index c93803c3f49..599edfd33ea 100644 --- a/easybuild/easyconfigs/j/Julia/Julia-1.10.3-linux-x86_64.eb +++ b/easybuild/easyconfigs/j/Julia/Julia-1.10.3-linux-x86_64.eb @@ -14,7 +14,7 @@ sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz'] patches = [('julia.wrapper', 'bin/')] checksums = [ {'julia-1.10.3-linux-x86_64.tar.gz': '81b910c922fff0e27ae1f256f2cc803db81f3960215281eddd2d484721928c70'}, - {'julia.wrapper': 'a36a3e0cb98ab4d2b05e0ca8f0bf2724baafbd669a0db318a00e40737d2f02f9'}, + {'julia.wrapper': 'd10aeaff53cca9875f7b0ce9218eae3bd21870b654e26c4c52aa8bfcc9da702d'}, ] # install wrapper with linking safeguards for Julia libraries From 08fa65756d160d2b9b3bf0e5e0f0cb34aa40616e Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 15 Jul 2024 01:30:40 +0200 Subject: [PATCH 008/107] adding easyconfigs: GOMC-2.76-20230613-GCC-11.3.0-CUDA-11.7.0.eb --- ...MC-2.76-20230613-GCC-11.3.0-CUDA-11.7.0.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/g/GOMC/GOMC-2.76-20230613-GCC-11.3.0-CUDA-11.7.0.eb diff --git a/easybuild/easyconfigs/g/GOMC/GOMC-2.76-20230613-GCC-11.3.0-CUDA-11.7.0.eb b/easybuild/easyconfigs/g/GOMC/GOMC-2.76-20230613-GCC-11.3.0-CUDA-11.7.0.eb new file mode 100644 index 00000000000..4cd71cb5340 --- /dev/null +++ b/easybuild/easyconfigs/g/GOMC/GOMC-2.76-20230613-GCC-11.3.0-CUDA-11.7.0.eb @@ -0,0 +1,45 @@ +easyblock = 'CMakeMake' + +name = 'GOMC' +version = '2.76-20230613' +versionsuffix = '-CUDA-%(cudaver)s' +_commit = '9fc85fb' + +homepage = 'https://gomc-wsu.org/' +description = """GPU Optimized Monte Carlo (GOMC) is a parallel molecular +simulation code designed for high-performance simulation of large systems.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +sources = [ + { + 'source_urls': ['https://github.com/GOMC-WSU/GOMC/archive'], + 'download_filename': '%s.tar.gz' % _commit, + 'filename': SOURCE_TAR_GZ, + }, +] +checksums = ['14725836707e4525cc7daea219a6eb47a8aeb675d01ef6d16ad60a9986dd3c1e'] + +builddependencies = [ + ('CMake', '3.23.1'), +] +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('UCX-CUDA', '1.12.1', versionsuffix), +] + +# default CUDA compute capabilities to use (override via --cuda-compute-capabilities) +cuda_compute_capabilities = ['6.0', '7.0', '7.5', '8.0', '8.6'] +configopts = '-DCMAKE_CUDA_ARCHITECTURES="%(cuda_cc_cmake)s" ' + +preinstallopts = 'mkdir %(installdir)s/bin &&' +install_cmd = 'cp' +installopts = '%(builddir)s/easybuild_obj/%(name)s_{CPU,GPU}_* %(installdir)s/bin' + +_gomc_exe = ['GOMC_CPU_GCMC', 'GOMC_CPU_GEMC', 'GOMC_CPU_NPT', 'GOMC_CPU_NVT', 'GOMC_GPU_GCMC', 'GOMC_GPU_GEMC', 'GOMC_GPU_NPT', 'GOMC_GPU_NVT'] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in _gomc_exe], + 'dirs': [], +} + +moduleclass = 'chem' From 22a31b9b535b87a997d376c997f5d0de47022450 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 15 Jul 2024 11:15:56 +0200 Subject: [PATCH 009/107] fix too long line in GOMC-2.76-20230613-GCC-11.3.0-CUDA-11.7.0.eb --- .../g/GOMC/GOMC-2.76-20230613-GCC-11.3.0-CUDA-11.7.0.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GOMC/GOMC-2.76-20230613-GCC-11.3.0-CUDA-11.7.0.eb b/easybuild/easyconfigs/g/GOMC/GOMC-2.76-20230613-GCC-11.3.0-CUDA-11.7.0.eb index 4cd71cb5340..7b3db4cc18b 100644 --- a/easybuild/easyconfigs/g/GOMC/GOMC-2.76-20230613-GCC-11.3.0-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/g/GOMC/GOMC-2.76-20230613-GCC-11.3.0-CUDA-11.7.0.eb @@ -36,7 +36,9 @@ preinstallopts = 'mkdir %(installdir)s/bin &&' install_cmd = 'cp' installopts = '%(builddir)s/easybuild_obj/%(name)s_{CPU,GPU}_* %(installdir)s/bin' -_gomc_exe = ['GOMC_CPU_GCMC', 'GOMC_CPU_GEMC', 'GOMC_CPU_NPT', 'GOMC_CPU_NVT', 'GOMC_GPU_GCMC', 'GOMC_GPU_GEMC', 'GOMC_GPU_NPT', 'GOMC_GPU_NVT'] +_gomc_exe = ['GOMC_CPU_GCMC', 'GOMC_CPU_GEMC', 'GOMC_CPU_NPT', 'GOMC_CPU_NVT', 'GOMC_GPU_GCMC', + 'GOMC_GPU_GEMC', 'GOMC_GPU_NPT', 'GOMC_GPU_NVT'] + sanity_check_paths = { 'files': ['bin/%s' % x for x in _gomc_exe], 'dirs': [], From c62afab0f964a42584a3951f9a7f0a6b520f9608 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 20 Jul 2024 12:29:37 +0200 Subject: [PATCH 010/107] adding easyconfigs: Biotite-0.41.0-gfbf-2023a.eb, ESM3-3.0.0.post2-foss-2023a-CUDA-12.1.1.eb, ESM3-3.0.0.post2-foss-2023a.eb --- .../b/Biotite/Biotite-0.41.0-gfbf-2023a.eb | 32 ++++++++++++ ...ESM3-3.0.0.post2-foss-2023a-CUDA-12.1.1.eb | 49 +++++++++++++++++++ .../e/ESM3/ESM3-3.0.0.post2-foss-2023a.eb | 47 ++++++++++++++++++ 3 files changed, 128 insertions(+) create mode 100644 easybuild/easyconfigs/b/Biotite/Biotite-0.41.0-gfbf-2023a.eb create mode 100644 easybuild/easyconfigs/e/ESM3/ESM3-3.0.0.post2-foss-2023a-CUDA-12.1.1.eb create mode 100644 easybuild/easyconfigs/e/ESM3/ESM3-3.0.0.post2-foss-2023a.eb diff --git a/easybuild/easyconfigs/b/Biotite/Biotite-0.41.0-gfbf-2023a.eb b/easybuild/easyconfigs/b/Biotite/Biotite-0.41.0-gfbf-2023a.eb new file mode 100644 index 00000000000..8d4385e45f5 --- /dev/null +++ b/easybuild/easyconfigs/b/Biotite/Biotite-0.41.0-gfbf-2023a.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonBundle' + +name = 'Biotite' +version = '0.41.0' + +homepage = 'https://www.biotite-python.org/' +description = """Biotite is your Swiss army knife for bioinformatics. Whether you want to +identify homologous sequence regions in a protein family or you would like to +find disulfide bonds in a protein structure: Biotite has the right tool for +you. This package bundles popular tasks in computational molecular biology into +a uniform Python library.""" + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('networkx', '3.1'), +] + +use_pip = True + +exts_list = [ + ('biotite', version, { + 'checksums': ['a5fddb4d738291772735cf04dfa8b642e0bdd6b4c2c0c71e2db727c0a66bd106'], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/e/ESM3/ESM3-3.0.0.post2-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/e/ESM3/ESM3-3.0.0.post2-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..b316a1a4441 --- /dev/null +++ b/easybuild/easyconfigs/e/ESM3/ESM3-3.0.0.post2-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,49 @@ +easyblock = 'PythonBundle' + +name = 'ESM3' +version = '3.0.0.post2' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://www.evolutionaryscale.ai/' +description = """ESM3 is a frontier generative model for biology, able to jointly reason across +three fundamental biological properties of proteins: sequence, structure, and +function. These three data modalities are represented as tracks of discrete +tokens at the input and output of ESM3. You can present the model with a +combination of partial inputs across the tracks, and ESM3 will provide output +predictions for all the tracks. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('Python', '3.11.3'), + ('PyTorch-bundle', '2.1.2', versionsuffix), + ('Transformers', '4.39.3'), + ('Biopython', '1.83'), + ('Biotite', '0.41.0'), + ('Brotli-python', '1.0.9'), + ('einops', '0.7.0'), + ('IPython', '8.14.0'), + ('scikit-learn', '1.3.1'), +] + +use_pip = True + +exts_list = [ + ('msgpack-numpy', '0.4.8', { + 'checksums': ['c667d3180513422f9c7545be5eec5d296dcbb357e06f72ed39cc683797556e69'], + }), + ('cloudpathlib', '0.16.0', { + 'checksums': ['cdfcd35d46d529587d744154a0bdf962aca953b725c8784cd2ec478354ea63a3'], + }), + ('esm', version, { + 'source_urls': ['https://github.com/evolutionaryscale/esm/archive/'], + 'source_tmpl': 'v%(version)s.tar.gz', + 'checksums': ['6c6c803be285a7ba45f71c05bf9e09aeba463e0e8f359373ccd3073f7d589c06'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/e/ESM3/ESM3-3.0.0.post2-foss-2023a.eb b/easybuild/easyconfigs/e/ESM3/ESM3-3.0.0.post2-foss-2023a.eb new file mode 100644 index 00000000000..0470d9c4ec6 --- /dev/null +++ b/easybuild/easyconfigs/e/ESM3/ESM3-3.0.0.post2-foss-2023a.eb @@ -0,0 +1,47 @@ +easyblock = 'PythonBundle' + +name = 'ESM3' +version = '3.0.0.post2' + +homepage = 'https://www.evolutionaryscale.ai/' +description = """ESM3 is a frontier generative model for biology, able to jointly reason across +three fundamental biological properties of proteins: sequence, structure, and +function. These three data modalities are represented as tracks of discrete +tokens at the input and output of ESM3. You can present the model with a +combination of partial inputs across the tracks, and ESM3 will provide output +predictions for all the tracks. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('PyTorch-bundle', '2.1.2'), + ('Transformers', '4.39.3'), + ('Biopython', '1.83'), + ('Biotite', '0.41.0'), + ('Brotli-python', '1.0.9'), + ('einops', '0.7.0'), + ('IPython', '8.14.0'), + ('scikit-learn', '1.3.1'), +] + +use_pip = True + +exts_list = [ + ('msgpack-numpy', '0.4.8', { + 'checksums': ['c667d3180513422f9c7545be5eec5d296dcbb357e06f72ed39cc683797556e69'], + }), + ('cloudpathlib', '0.16.0', { + 'checksums': ['cdfcd35d46d529587d744154a0bdf962aca953b725c8784cd2ec478354ea63a3'], + }), + ('esm', version, { + 'source_urls': ['https://github.com/evolutionaryscale/esm/archive/'], + 'source_tmpl': 'v%(version)s.tar.gz', + 'checksums': ['6c6c803be285a7ba45f71c05bf9e09aeba463e0e8f359373ccd3073f7d589c06'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' From ce2dc5e7a30246e258f2cfd25df771353aea8a3c Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 24 Jul 2024 14:04:07 +0200 Subject: [PATCH 011/107] fix partial installation of ESM3 by swicthing to wheel sources --- .../ESM3/ESM3-3.0.0.post2-foss-2023a-CUDA-12.1.1.eb | 12 ++++++++---- .../e/ESM3/ESM3-3.0.0.post2-foss-2023a.eb | 12 ++++++++---- 2 files changed, 16 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/e/ESM3/ESM3-3.0.0.post2-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/e/ESM3/ESM3-3.0.0.post2-foss-2023a-CUDA-12.1.1.eb index b316a1a4441..1382c12efc6 100644 --- a/easybuild/easyconfigs/e/ESM3/ESM3-3.0.0.post2-foss-2023a-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/e/ESM3/ESM3-3.0.0.post2-foss-2023a-CUDA-12.1.1.eb @@ -38,12 +38,16 @@ exts_list = [ 'checksums': ['cdfcd35d46d529587d744154a0bdf962aca953b725c8784cd2ec478354ea63a3'], }), ('esm', version, { - 'source_urls': ['https://github.com/evolutionaryscale/esm/archive/'], - 'source_tmpl': 'v%(version)s.tar.gz', - 'checksums': ['6c6c803be285a7ba45f71c05bf9e09aeba463e0e8f359373ccd3073f7d589c06'], + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['5544b6974945d791205226408100429c2ea6e49b30265aea1d359caabe20bb14'], }), ] sanity_pip_check = True -moduleclass = 'lib' +sanity_check_commands = [ + "python -c 'import esm'", + "python -c 'from esm.models.esm3 import ESM3'", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/e/ESM3/ESM3-3.0.0.post2-foss-2023a.eb b/easybuild/easyconfigs/e/ESM3/ESM3-3.0.0.post2-foss-2023a.eb index 0470d9c4ec6..60125c1af46 100644 --- a/easybuild/easyconfigs/e/ESM3/ESM3-3.0.0.post2-foss-2023a.eb +++ b/easybuild/easyconfigs/e/ESM3/ESM3-3.0.0.post2-foss-2023a.eb @@ -36,12 +36,16 @@ exts_list = [ 'checksums': ['cdfcd35d46d529587d744154a0bdf962aca953b725c8784cd2ec478354ea63a3'], }), ('esm', version, { - 'source_urls': ['https://github.com/evolutionaryscale/esm/archive/'], - 'source_tmpl': 'v%(version)s.tar.gz', - 'checksums': ['6c6c803be285a7ba45f71c05bf9e09aeba463e0e8f359373ccd3073f7d589c06'], + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['5544b6974945d791205226408100429c2ea6e49b30265aea1d359caabe20bb14'], }), ] sanity_pip_check = True -moduleclass = 'lib' +sanity_check_commands = [ + "python -c 'import esm'", + "python -c 'from esm.models.esm3 import ESM3'", +] + +moduleclass = 'bio' From da7746aeed4c7841a988343ffee89e78c7e72f56 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 25 Jul 2024 16:50:23 +0200 Subject: [PATCH 012/107] enable support for Apache ORC to Arrow v14.0.1 and v16.1.0 --- easybuild/easyconfigs/a/Arrow/Arrow-14.0.1-gfbf-2023a.eb | 9 +++++---- easybuild/easyconfigs/a/Arrow/Arrow-16.1.0-gfbf-2023b.eb | 9 +++++---- 2 files changed, 10 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-14.0.1-gfbf-2023a.eb b/easybuild/easyconfigs/a/Arrow/Arrow-14.0.1-gfbf-2023a.eb index 85715fef495..0c588b9f16b 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-14.0.1-gfbf-2023a.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-14.0.1-gfbf-2023a.eb @@ -39,10 +39,10 @@ dependencies = [ start_dir = 'cpp' # see https://arrow.apache.org/docs/developers/python.html -configopts = "-DARROW_DATASET=on -DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_WITH_SNAPPY=ON " +configopts = "-DARROW_DATASET=on -DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_ORC=ON " configopts += "-DCMAKE_INSTALL_LIBDIR=lib -DPython3_ROOT_DIR=$EBROOTPYTHON " -configopts += "-DARROW_WITH_ZLIB=ON -DARROW_WITH_BZ2=ON -DARROW_WITH_ZSTD=ON -DARROW_WITH_LZ4=ON " -configopts += "-DZSTD_ROOT=$EBROOTZSTD " +configopts += "-DARROW_WITH_ZLIB=ON -DARROW_WITH_BZ2=ON -DARROW_WITH_LZ4=ON -DARROW_WITH_SNAPPY=ON " +configopts += "-DARROW_WITH_ZSTD=ON -DZSTD_ROOT=$EBROOTZSTD " # install Python bindings _pyarrow_preinstall_opts = "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && " @@ -52,7 +52,7 @@ _pyarrow_preinstall_opts += "export XDG_CACHE_HOME=$TMPDIR && " _pyarrow_preinstall_opts += "sed -i 's/numpy==[0-9.]*/numpy/g' pyproject.toml && " _pyarrow_preinstall_opts += "Python3_ROOT_DIR=$EBROOTPYTHON " _pyarrow_preinstall_opts += "PYARROW_CMAKE_OPTIONS='-DZSTD_LIB=$EBROOTZSTD/lib/libzstd.%s ' " % SHLIB_EXT -_pyarrow_preinstall_opts += "PYARROW_WITH_DATASET=1 PYARROW_WITH_PARQUET=1 " +_pyarrow_preinstall_opts += "PYARROW_WITH_DATASET=1 PYARROW_WITH_PARQUET=1 PYARROW_WITH_ORC=1 " exts_defaultclass = 'PythonPackage' exts_default_options = { @@ -81,6 +81,7 @@ sanity_check_commands = [ "python -c 'import pyarrow'", "python -c 'import pyarrow.dataset'", "python -c 'import pyarrow.parquet'", + "python -c 'import pyarrow.orc'", ] moduleclass = 'data' diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-16.1.0-gfbf-2023b.eb b/easybuild/easyconfigs/a/Arrow/Arrow-16.1.0-gfbf-2023b.eb index 87862215507..5219bd9c54f 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-16.1.0-gfbf-2023b.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-16.1.0-gfbf-2023b.eb @@ -39,10 +39,10 @@ dependencies = [ start_dir = 'cpp' # see https://arrow.apache.org/docs/developers/python.html -configopts = "-DARROW_DATASET=on -DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_WITH_SNAPPY=ON " +configopts = "-DARROW_DATASET=on -DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_ORC=ON " configopts += "-DCMAKE_INSTALL_LIBDIR=lib -DPython3_ROOT_DIR=$EBROOTPYTHON " -configopts += "-DARROW_WITH_ZLIB=ON -DARROW_WITH_BZ2=ON -DARROW_WITH_ZSTD=ON -DARROW_WITH_LZ4=ON " -configopts += "-DZSTD_ROOT=$EBROOTZSTD " +configopts += "-DARROW_WITH_ZLIB=ON -DARROW_WITH_BZ2=ON -DARROW_WITH_LZ4=ON -DARROW_WITH_SNAPPY=ON " +configopts += "-DARROW_WITH_ZSTD=ON -DZSTD_ROOT=$EBROOTZSTD " # install Python bindings _pyarrow_preinstall_opts = "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && " @@ -52,7 +52,7 @@ _pyarrow_preinstall_opts += "export XDG_CACHE_HOME=$TMPDIR && " _pyarrow_preinstall_opts += "sed -i 's/numpy==[0-9.]*/numpy/g' pyproject.toml && " _pyarrow_preinstall_opts += "Python3_ROOT_DIR=$EBROOTPYTHON " _pyarrow_preinstall_opts += "PYARROW_CMAKE_OPTIONS='-DZSTD_LIB=$EBROOTZSTD/lib/libzstd.%s ' " % SHLIB_EXT -_pyarrow_preinstall_opts += "PYARROW_WITH_DATASET=1 PYARROW_WITH_PARQUET=1 " +_pyarrow_preinstall_opts += "PYARROW_WITH_DATASET=1 PYARROW_WITH_PARQUET=1 PYARROW_WITH_ORC=1 " exts_defaultclass = 'PythonPackage' exts_default_options = { @@ -81,6 +81,7 @@ sanity_check_commands = [ "python -c 'import pyarrow'", "python -c 'import pyarrow.dataset'", "python -c 'import pyarrow.parquet'", + "python -c 'import pyarrow.orc'", ] moduleclass = 'data' From 324edb1a6927674324754a6fa4386ee51ae027e1 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 26 Jul 2024 19:15:29 +0200 Subject: [PATCH 013/107] adding easyconfigs: PCAngsd-1.2-gfbf-2023a.eb --- .../p/PCAngsd/PCAngsd-1.2-gfbf-2023a.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/p/PCAngsd/PCAngsd-1.2-gfbf-2023a.eb diff --git a/easybuild/easyconfigs/p/PCAngsd/PCAngsd-1.2-gfbf-2023a.eb b/easybuild/easyconfigs/p/PCAngsd/PCAngsd-1.2-gfbf-2023a.eb new file mode 100644 index 00000000000..d534bfa0f78 --- /dev/null +++ b/easybuild/easyconfigs/p/PCAngsd/PCAngsd-1.2-gfbf-2023a.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonBundle' + +name = 'PCAngsd' +version = '1.2' + +homepage = "https://www.popgen.dk/software/index.php/PCAngsd" +description = "Framework for analyzing low depth NGS data in heterogeneous populations using PCA." + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('Cython', '3.0.8'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'modulename': False, + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/Rosemeis/pcangsd/archive/refs/tags/'], + 'checksums': ['286f09851c37e380c9abf5859595e7cd0ad8cb49f1d48b1b0ae409aab0eae62e'], + }), +] + +sanity_check_commands = [ + 'pcangsd --help', +] + +moduleclass = 'bio' From 60ff433938da75ab1ce05b0c73bb6db9cdc59f87 Mon Sep 17 00:00:00 2001 From: WilleBell Date: Thu, 8 Aug 2024 10:04:11 +0200 Subject: [PATCH 014/107] adding easyconfigs: RHEIA-1.1.11-foss-2023a.eb --- .../r/RHEIA/RHEIA-1.1.11-foss-2023a.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/r/RHEIA/RHEIA-1.1.11-foss-2023a.eb diff --git a/easybuild/easyconfigs/r/RHEIA/RHEIA-1.1.11-foss-2023a.eb b/easybuild/easyconfigs/r/RHEIA/RHEIA-1.1.11-foss-2023a.eb new file mode 100644 index 00000000000..d218a83dc02 --- /dev/null +++ b/easybuild/easyconfigs/r/RHEIA/RHEIA-1.1.11-foss-2023a.eb @@ -0,0 +1,41 @@ +easyblock = 'PythonBundle' + +name = 'RHEIA' +version = '1.1.11' + +homepage = 'https://github.com/rheia-framework/RHEIA' +description = "Robust design optimization of renewable Hydrogen and dErIved energy cArrier systems" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), # deap, numpy, pandas, scipy + ('h5py', '3.9.0'), + ('matplotlib', '3.7.2'), +] + +use_pip = True + +exts_list = [ + ('pvlib', '0.11.0', { + 'checksums': ['88b31c44dc07f0435af1e2d5ddcac067e6ce15917251a9f270366f61e9bd015b'], + }), + ('pyDOE', '0.3.8', { + 'modulename': '%(name)s', + 'source_tmpl': '%(name)s-%(version)s.zip', + 'checksums': ['cbd6f14ae26d3c9f736013205f53ea1191add4567033c3ee77b7dd356566c4b6'], + }), + ('SobolSequence', '0.2.1', { + 'modulename': 'sobol', + 'checksums': ['b2b4b57451b8d2e79ddb07efa23bc471dfdd436ea357d6368666bdc364df3eb1'], + }), + ('rheia', version, { + 'sources': ['%(namelower)s-%(version)s.tar.gz'], + 'checksums': ['d6b1ea991f6338cca136b59e8e413bae2167c5ebd631163ec68fafe0040aa143'], + }), +] + +sanity_pip_check = True + +moduleclass = 'math' From 2335c2ed629398fe0772e1eb46f264c0ad7056e4 Mon Sep 17 00:00:00 2001 From: WilleBell Date: Fri, 16 Aug 2024 10:39:02 +0200 Subject: [PATCH 015/107] adding easyconfigs: gffread-0.12.7-GCCcore-12.3.0.eb --- .../gffread/gffread-0.12.7-GCCcore-12.3.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/g/gffread/gffread-0.12.7-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/g/gffread/gffread-0.12.7-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/gffread/gffread-0.12.7-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..eba4233b57f --- /dev/null +++ b/easybuild/easyconfigs/g/gffread/gffread-0.12.7-GCCcore-12.3.0.eb @@ -0,0 +1,34 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +easyblock = 'MakeCp' + +name = 'gffread' +version = '0.12.7' + +homepage = 'https://ccb.jhu.edu/software/stringtie/gff.shtml#gffread' +description = """GFF/GTF parsing utility providing format conversions, +region filtering, FASTA sequence extraction and more.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/gpertea/%(namelower)s/releases/download/v%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['bfde1c857495e578f5b3af3c007a9aa40593e69450eafcc6a42c3e8ef08ed1f5'] + +builddependencies = [('binutils', '2.40')] + +buildopts = " release" + +files_to_copy = [ + (['%(name)s'], 'bin'), + 'LICENSE', +] + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': [] +} + +sanity_check_commands = ['%(name)s'] + +moduleclass = 'bio' From 17de7b9d5a4eeb4c3d2631286857b774af338150 Mon Sep 17 00:00:00 2001 From: Louwrens van Dellen Date: Wed, 28 Aug 2024 18:31:28 +0200 Subject: [PATCH 016/107] add to gitignore: *.eb_bak_* *.out .venv/ Such paths should never be committed: - `.eb_bak` files are remnants after `eb --inject-checksums` - `.out` files are log remnants after `eb --job` - `.venv/` are probably created for ad-hoc testing --- .gitignore | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.gitignore b/.gitignore index c667a41e000..c2974194435 100644 --- a/.gitignore +++ b/.gitignore @@ -1,12 +1,15 @@ .pydevproject .project LICENSE_HEADER +*.eb.bak_* *.pyc *.pyo *.nja +*.out build/ dist/ *egg-info/ +.venv/ *.swp *.ropeproject/ eb-*.log From 11e6ad96ed4ecbd9e04c69cb1f8dd17de3c3f073 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 28 Aug 2024 19:01:23 +0200 Subject: [PATCH 017/107] adding easyconfigs: Single-cell-python-bundle-2024.02-foss-2023a-CUDA-12.1.1.eb --- .../CellRank-2.0.2-foss-2023a-CUDA-12.1.1.eb | 78 ++++++ .../Optax-0.2.2-foss-2023a-CUDA-12.1.1.eb | 43 +++ ...n-bundle-2024.02-foss-2023a-CUDA-12.1.1.eb | 247 ++++++++++++++++++ .../scArches-0.6.1-foss-2023a-CUDA-12.1.1.eb | 53 ++++ ...ib-metrics-0.5.1-foss-2023a-CUDA-12.1.1.eb | 55 ++++ ...scvi-tools-1.1.2-foss-2023a-CUDA-12.1.1.eb | 69 +++++ 6 files changed, 545 insertions(+) create mode 100644 easybuild/easyconfigs/c/CellRank/CellRank-2.0.2-foss-2023a-CUDA-12.1.1.eb create mode 100644 easybuild/easyconfigs/o/Optax/Optax-0.2.2-foss-2023a-CUDA-12.1.1.eb create mode 100644 easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a-CUDA-12.1.1.eb create mode 100644 easybuild/easyconfigs/s/scArches/scArches-0.6.1-foss-2023a-CUDA-12.1.1.eb create mode 100644 easybuild/easyconfigs/s/scib-metrics/scib-metrics-0.5.1-foss-2023a-CUDA-12.1.1.eb create mode 100644 easybuild/easyconfigs/s/scvi-tools/scvi-tools-1.1.2-foss-2023a-CUDA-12.1.1.eb diff --git a/easybuild/easyconfigs/c/CellRank/CellRank-2.0.2-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/c/CellRank/CellRank-2.0.2-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..3ec16f6ab04 --- /dev/null +++ b/easybuild/easyconfigs/c/CellRank/CellRank-2.0.2-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,78 @@ +easyblock = 'PythonBundle' + +name = 'CellRank' +version = '2.0.2' +versionsuffix = '-CUDA-12.1.1' + +homepage = 'https://cellrank.readthedocs.io/en/stable/' +description = """CellRank is a toolkit to uncover cellular dynamics based on + Markov state modeling of single-cell data. It contains two main modules: +kernels compute cell-cell transition probabilities and estimators generate +hypothesis based on these. """ + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [('poetry', '1.5.1')] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('anndata', '0.10.5.post1'), + ('matplotlib', '3.7.2'), + ('networkx', '3.1'), + ('numba', '0.58.1'), + ('scanpy', '1.9.8'), + ('scikit-learn', '1.3.1'), + ('scVelo', '0.3.1'), + ('Seaborn', '0.13.2'), + ('wrapt', '1.15.0'), + ('PyTorch', '2.1.2', versionsuffix), + ('wandb', '0.16.1'), + ('PyTorch-Lightning', '2.2.1', versionsuffix), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('loguru', '0.7.2', { + 'checksums': ['e671a53522515f34fd406340ee968cb9ecafbc4b36c679da03c18fd8d0bd51ac'], + }), + ('nam', '0.0.3', { + 'checksums': ['48400d12b5f29fdd1671aebdf78d7f41bcac4f5c8ab7ed48770ee0c4fbc0673b'], + }), + ('python-utils', '3.8.2', { + 'checksums': ['c5d161e4ca58ce3f8c540f035e018850b261a41e7cb98f6ccf8e1deb7174a1f1'], + }), + ('progressbar2', '4.4.1', { + 'modulename': 'progressbar', + 'checksums': ['97d323ba03ad3d017a4d047fd0b2d3e733c5a360c07f87d269f96641c3de729f'], + }), + ('dunamai', '1.19.2', { + 'checksums': ['3be4049890763e19b8df1d52960dbea60b3e263eb0c96144a677ae0633734d2e'], + }), + ('poetry_dynamic_versioning', '1.2.0', { + 'checksums': ['1a7bbdba2530499e73dfc6ac0af19de29020ab4aaa3e507573877114e6b71ed6'], + }), + ('pygpcca', '1.0.4', { + 'preinstallopts': "sed -i 's/jinja2==3.0.3/jinja2>=3.0.3/' requirements.txt && ", + 'checksums': ['5e3b49279abc62d25133811daeee050715f995ff02042c46e2a2034331d090d1'], + }), + ('pygam', '0.9.1', { + 'checksums': ['a321a017bf485ed93fc6233e02621f8e7eab3d4f8971371c9ae9e079c55be01d'], + }), + ('joblib', '1.3.2', { + 'checksums': ['92f865e621e17784e7955080b6d042489e3b8e294949cc44c6eac304f59772b1'], + }), + ('docrep', '0.3.2', { + 'checksums': ['ed8a17e201abd829ef8da78a0b6f4d51fb99a4cbd0554adbed3309297f964314'], + }), + (name, version, { + 'modulename': 'cellrank', + 'preinstallopts': "sed -i 's/matplotlib>=3.5.0,<3.7.2/matplotlib>=3.5.0/' pyproject.toml && ", + 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + 'checksums': ['47c1d2e953ac91f572937d816142b4ac5f0c876174c60f857562de76a9f8aa61'], + }), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/o/Optax/Optax-0.2.2-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/o/Optax/Optax-0.2.2-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..43b7ce4b7ef --- /dev/null +++ b/easybuild/easyconfigs/o/Optax/Optax-0.2.2-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,43 @@ +easyblock = 'PythonBundle' + +name = 'Optax' +version = '0.2.2' +versionsuffix = '-CUDA-12.1.1' + +homepage = 'https://github.com/deepmind/optax' +description = """Optax is a gradient processing and optimization library for JAX.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('jax', '0.4.25', versionsuffix), +] + +use_pip = True + +exts_list = [ + ('toolz', '0.12.1', { + 'checksums': ['ecca342664893f177a13dac0e6b41cbd8ac25a358e5f215316d43e2100224f4d'], + }), + ('flit_core', '3.9.0', { + 'checksums': ['72ad266176c4a3fcfab5f2930d76896059851240570ce9a98733b658cb786eba'], + }), + ('absl-py', '2.1.0', { + 'modulename': 'absl', + 'checksums': ['7820790efbb316739cde8b4e19357243fc3608a152024288513dd968d7d959ff'], + }), + ('chex', '0.1.86', { + 'checksums': ['e8b0f96330eba4144659e1617c0f7a57b161e8cbb021e55c6d5056c7378091d1'], + }), + ('optax', version, { + 'checksums': ['f09bf790ef4b09fb9c35f79a07594c6196a719919985f542dc84b0bf97812e0e'], + }), +] + +sanity_pip_check = True + +sanity_check_commands = ["python -c 'from optax import GradientTransformation'"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..22eca6d4ed4 --- /dev/null +++ b/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,247 @@ +easyblock = 'PythonBundle' + +name = 'Single-cell-python-bundle' +version = '2024.02' +versionsuffix = '-CUDA-12.1.1' + +homepage = (None) +description = """Bundle of tools for single-cell sequence analysis.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('poetry', '1.5.1'), + ('CMake', '3.26.3'), + ('hatchling', '1.18.0'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('matplotlib', '3.7.2'), + ('Seaborn', '0.13.2'), + ('PyTorch', '2.1.2', versionsuffix), + ('scanpy', '1.9.8'), + ('scib', '1.1.4'), + ('scVelo', '0.3.1'), + ('CellTypist', '1.6.2'), + ('epiScanpy', '0.4.0'), + ('scCODA', '0.1.9'), + ('infercnvpy', '0.4.3'), + ('pySCENIC', '0.12.1-20240311'), + ('CellRank', '2.0.2', versionsuffix), + ('Squidpy', '1.4.1'), + ('Cassiopeia', '2.0.0'), + ('scvi-tools', '1.1.2', versionsuffix), + ('scArches', '0.6.1', versionsuffix), + ('scib-metrics', '0.5.1', versionsuffix), + # deps of exts: + ('umap-learn', '0.5.5'), # bbknn + ('scikit-learn', '1.3.1'), # bbknn, sc_toolbox + ('PyYAML', '6.0'), # sc_toolbox + ('typing-extensions', '4.9.0'), # sc_toolbox + ('adjustText', '0.7.3'), # sc_toolbox + ('python-parasail', '1.3.4'), # scirpy + ('graph-tool', '2.59'), # schist + ('Pyomo', '6.7.3'), # pertpy + ('mpmath', '1.3.0'), # blitzgsea +] + +exts_list = [ + ('flit_core', '3.9.0', { + 'checksums': ['72ad266176c4a3fcfab5f2930d76896059851240570ce9a98733b658cb786eba'], + }), + ('annoy', '1.17.3', { + 'checksums': ['9cbfebefe0a5f843eba29c6be4c84d601f4f41ad4ded0486f1b88c3b07739c15'], + }), + ('pynndescent', '0.5.11', { + 'checksums': ['6f44ced9d5a9da2c87d9b2fff30bb5308540c0657605e4d5cde7ed3275bbad50'], + }), + ('bbknn', '1.6.0', { + 'checksums': ['1c01a9d6df2fc52a527de8a403617897a4b672724863299a7026f2132f1b041b'], + }), + ('tzlocal', '5.2', { + 'checksums': ['8d399205578f1a9342816409cc1e46a93ebd5755e39ea2d85334bea911bf0e6e'], + }), + ('anndata2ri', '1.3.1', { + 'checksums': ['0e3fa2f81789f682d19ef452fabdb401ec27899db9abe5a78e45e21dcc7caa42'], + }), + ('pypi-latest', '0.1.2', { + 'checksums': ['b195654567e6abaac6acfec37638d8e000838f419bc6b129962a896eedc4ed4e'], + }), + ('text-unidecode', '1.3', { + 'checksums': ['bad6603bb14d279193107714b288be206cac565dfa49aa5b105294dd5c4aab93'], + }), + ('python-slugify', '8.0.4', { + 'modulename': 'slugify', + 'checksums': ['59202371d1d05b54a9e7720c5e038f928f45daaffe41dd10822f3907b937c856'], + }), + ('prompt_toolkit', '3.0.36', { + 'checksums': ['3e163f254bef5a03b146397d7c1963bd3e2812f0964bb9a24e6ec761fd28db63'], + }), + ('binaryornot', '0.4.4', { + 'checksums': ['359501dfc9d40632edc9fac890e19542db1a287bbcfa58175b66658392018061'], + }), + ('types-python-dateutil', '2.9.0.20240316', { + 'modulename': False, + 'checksums': ['5d2f2e240b86905e40944dd787db6da9263f0deabef1076ddaed797351ec0202'], + }), + ('arrow', '1.3.0', { + 'checksums': ['d4540617648cb5f895730f1ad8c82a65f2dad0166f57b75f3ca54759c4d67a85'], + }), + ('cookiecutter', '2.6.0', { + 'checksums': ['db21f8169ea4f4fdc2408d48ca44859349de2647fbe494a9d6c3edfc0542c21c'], + }), + ('questionary', '2.0.1', { + 'checksums': ['bcce898bf3dbb446ff62830c86c5c6fb9a22a54146f0f5597d3da43b10d8fc8b'], + }), + ('rich', '13.7.1', { + 'checksums': ['9be308cb1fe2f1f57d67ce99e95af38a1e2bc71ad9813b0e247cf7ffbcc3a432'], + }), + ('sc_toolbox', '0.12.3', { + 'checksums': ['6ca22a364c269a095114e620eb3c6da8aac1950d8f43f58ceea08005a09cc2cb'], + }), + ('toolz', '0.12.1', { + 'checksums': ['ecca342664893f177a13dac0e6b41cbd8ac25a358e5f215316d43e2100224f4d'], + }), + ('altair', '5.2.0', { + 'checksums': ['2ad7f0c8010ebbc46319cc30febfb8e59ccf84969a201541c207bc3a4fa6cf81'], + }), + ('custom_inherit', '2.4.1', { + 'checksums': ['7052eb337bcce83551815264391cc4efc2bf70b295a3c52aba64f1ab57c3a8a2'], + }), + ('multipledispatch', '1.0.0', { + 'checksums': ['5c839915465c68206c3e9c473357908216c28383b425361e5d144594bf85a7e0'], + }), + ('pypng', '0.20220715.0', { + 'modulename': 'png', + 'checksums': ['739c433ba96f078315de54c0db975aee537cbc3e1d0ae4ed9aab0ca1e427e2c1'], + }), + ('reportlab', '4.1.0', { + 'checksums': ['3a99faf412691159c068b3ff01c15307ce2fd2cf6b860199434874e002040a84'], + }), + ('toyplot', '1.0.3', { + 'checksums': ['7b7b2bc5784fd75e5c695300bffc80d568c83bebef543bb54e6e6c2229912edd'], + }), + ('toytree', '2.0.5', { + 'checksums': ['7be04ca310067e0e9737449700d6ab1b68b4379b64e2d22f2f7697a70030ceb0'], + }), + ('tascCODA', '0.1.3', { + # strip out tensorflow-probability as required dependency, to ensure that 'pip check' passes + 'preinstallopts': "sed -i '/tensorflow-probability>=0.16/d' setup.py && ", + 'checksums': ['8c12ddccb72c41c96c6a5abceb52e7a76f439a9ab94fb092aa86ee3c1292383a'], + }), + ('harmonypy', '0.0.9', { + 'checksums': ['85bfdd4e6ec6e0fa8816a276639358d3598a40d60ba9f7a5d9dada8706be8c4d'], + }), + ('fbpca', '1.0', { + 'checksums': ['150677642479663f317fdbb5e06dab3f98721cf7031bb4a84113d7a631c472d1'], + }), + ('geosketch', '1.2', { + 'checksums': ['bbfe97366b91c5927b6076d5a6738d9cfbe094efb5ac1117aab7a30b6081cc4e'], + }), + ('python_circos', '0.3.0', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'modulename': 'pycircos', + 'checksums': ['410eaffc4eb2933cd688897356813da23310f5e2f14a8bceb003e9b96faa715b'], + }), + ('mizani', '0.9.3', { + 'checksums': ['fb61339e9e4711850e902ca286b1ae75255f483823d891aa0515b426d56c606d'], + }), + ('plotnine', '0.12.4', { + 'checksums': ['adc41a672503594445a8fa19872799253bd0784cdbd5a1cc16657a1dd20ba905'], + }), + ('ktplotspy', '0.2.3', { + 'checksums': ['9a1e3646217e6e99f59ab2258dfd76120cf1f50880c9cb2f9005de397c00f0a9'], + }), + ('cellphonedb', '5.0.0', { + 'checksums': ['1c96173d8527f1655216d265fc50a28ea3360d70486afa5050e3f5565fa3a8cd'], + }), + ('decoupler', '1.6.0', { + 'checksums': ['dde501f4d3e55a260f716e51b871bee403bc8aaa6b66799df0e42dee0787b98d'], + }), + ('mudata', '0.2.3', { + 'checksums': ['45288ac150bfc598d68acb7c2c1c43c38c5c39522107e04f7efbf3360c7f2035'], + }), + ('nodeenv', '1.9.0', { + 'checksums': ['07f144e90dae547bf0d4ee8da0ee42664a42a04e02ed68e06324348dafe4bdb1'], + }), + ('identify', '2.5.36', { + 'checksums': ['e5e00f54165f9047fbebeb4a560f9acfb8af4c88232be60a488e9b68d122745d'], + }), + ('cfgv', '3.4.0', { + 'checksums': ['e52591d4c5f5dead8e0f673fb16db7949d2cfb3f7da4582893288f0ded8fe560'], + }), + ('pre_commit', '3.7.1', { + 'checksums': ['8ca3ad567bc78a4972a3f1a477e94a79d4597e8140a6e0b651c5e33899c3654a'], + }), + ('muon', '0.1.6', { + 'checksums': ['762feeb6f52f865cf79d0d0332cc742fe91c1885f668ce15794b62b3952b02f9'], + }), + ('liana', '1.2.0', { + 'checksums': ['be899c69bfcbf3d0f8b61c04c35f225ac6b11fe1ea80e6ed4bdc0e6212cb2379'], + }), + ('squarify', '0.4.3', { + 'checksums': ['54091f6ad175f7f201f8934574e647ce1b50dedc478c5fd968688eb7d7469f95'], + }), + ('scikit_build_core', '0.9.3', { + 'checksums': ['341d113e473a5409dc62522e8b1b1b8b1647a0b95557ad15f6be2a36071fd390'], + }), + ('awkward-cpp', '33', { + 'checksums': ['550adebccd329d18d02e95226d0b89698188fd33e44f07450942c692881927d8'], + }), + ('awkward', '2.6.4', { + 'checksums': ['ee0cb27c64150f368749983dda499c108848c64dc830912480eb37b78c04300f'], + }), + ('yamlordereddictloader', '0.4.2', { + 'checksums': ['36af2f6210fcff5da4fc4c12e1d815f973dceb41044e795e1f06115d634bca13'], + }), + ('airr', '1.5.0', { + 'checksums': ['febc0a881bf46b1a9c29ac6a7089dd733ff9120d114585e75dede26403f68d42'], + }), + ('scirpy', '0.17.0', { + 'checksums': ['f61653a4f7387562ec89b00fbfd7cab762c0bf3320f21ccfc47df80a13cc5d41'], + }), + ('schist', '0.8.3', { + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/dawe/schist/archive/'], + 'checksums': ['9b98ec9d85554573288c24f18c4791ba7c4d315397cbc422ea25d4a7cdd42e6d'], + }), + ('typeguard', '2.13.3', { + 'checksums': ['00edaa8da3a133674796cf5ea87d9f4b4c367d77476e185e80251cc13dfbb8c4'], + }), + ('jaxtyping', '0.2.29', { + 'checksums': ['e1cd916ed0196e40402b0638449e7d051571562b2cd68d8b94961a383faeb409'], + }), + ('equinox', '0.11.4', { + 'checksums': ['0033d9731083f402a855b12a0777a80aa8507651f7aa86d9f0f9503bcddfd320'], + }), + ('lineax', '0.0.4', { + 'checksums': ['e68f1eba2f352122fdce9adc0556684f31eb8364b1a00acee484dd6e44a34e5e'], + }), + ('jaxopt', '0.8.3', { + 'checksums': ['4b06dfa6f915a4f3291699606245af6069371a48dc5c92d4c507840d62990646'], + }), + ('ott_jax', '0.4.6', { + 'modulename': 'ott', + 'checksums': ['bc91f8d512cdb344439f5584712d76cd0650b6716b6686d53b828cc67abdbcba'], + }), + ('sparsecca', '0.3.1', { + 'checksums': ['be1526baebac5ce6efbc7190fd62a1cec13288c493f5d427024f66ca6afaec13'], + }), + ('PubChemPy', '1.0.4', { + 'checksums': ['24e9dc2fc90ab153b2764bf805e510b1410700884faf0510a9e7cf0d61d8ed0e'], + }), + ('blitzgsea', '1.3.42', { + 'checksums': ['dcc997b5d29d190d8632474f3bb57b5ead7fb1370b478c7f824b42782325a1ca'], + }), + ('pertpy', '0.7.0', { + 'checksums': ['273723b5b70f3cb714bb36d3234462014b72e133111eeaf08aa47153c9df14aa'], + }), +] + +use_pip = True +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/scArches/scArches-0.6.1-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/s/scArches/scArches-0.6.1-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..cb33b614f6f --- /dev/null +++ b/easybuild/easyconfigs/s/scArches/scArches-0.6.1-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,53 @@ +easyblock = 'PythonBundle' + +name = 'scArches' +version = '0.6.1' +versionsuffix = '-CUDA-12.1.1' + +homepage = 'https://github.com/theislab/scarches' +description = """Single-cell architecture surgery (scArches) is a package for reference-based analysis of single-cell + data.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('Python-bundle-PyPI', '2023.06'), + ('matplotlib', '3.7.2'), + ('anndata', '0.10.5.post1'), + ('h5py', '3.9.0'), + ('leidenalg', '0.10.2'), + ('scanpy', '1.9.8'), + ('scikit-learn', '1.3.1'), + ('scvi-tools', '1.1.2', versionsuffix), + ('PyTorch', '2.1.2', versionsuffix), + ('tqdm', '4.66.1'), +] + +use_pip = True + +exts_list = [ + ('gdown', '5.1.0', { + 'checksums': ['550a72dc5ca2819fe4bcc15d80d05d7c98c0b90e57256254b77d0256b9df4683'], + }), + ('muon', '0.1.6', { + 'checksums': ['762feeb6f52f865cf79d0d0332cc742fe91c1885f668ce15794b62b3952b02f9'], + }), + ('newick', '1.9.0', { + 'checksums': ['9f81be96ec86aefca74d920fc0d6962d89a3156547003ca6915c2e6e31ad3ddf'], + }), + ('scHPL', '1.0.5', { + 'modulename': 'scHPL', + # unpin pandas and newick versions to be compatible with foss/2023a versions + 'preinstallopts': "sed -i 's/~=/>=/g' setup.py && sed -i 's/pandas>=1.1.2,<2/pandas/g' setup.py && ", + 'checksums': ['3eb62b2e65b1faba04b7bcb86f7bf6967a6301866a605551211b8f14fd27eced'], + }), + (name, version, { + 'checksums': ['187463c25781d5c5586c129ad137d96327a9f8604d530a696d5f568a9225d77c'], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/scib-metrics/scib-metrics-0.5.1-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/s/scib-metrics/scib-metrics-0.5.1-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..b021ceb3c20 --- /dev/null +++ b/easybuild/easyconfigs/s/scib-metrics/scib-metrics-0.5.1-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,55 @@ +easyblock = 'PythonBundle' + +name = 'scib-metrics' +version = '0.5.1' +versionsuffix = '-CUDA-12.1.1' + +homepage = 'https://scib-metrics.readthedocs.io' +description = "Accelerated and Python-only metrics for benchmarking single-cell integration outputs" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('hatchling', '1.18.0'), + ('poetry', '1.5.1'), +] +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('anndata', '0.10.5.post1'), + ('jax', '0.4.25', versionsuffix), + ('scikit-learn', '1.3.1'), + ('scanpy', '1.9.8'), + ('python-igraph', '0.11.4'), + ('matplotlib', '3.7.2'), + ('tqdm', '4.66.1'), + ('umap-learn', '0.5.5'), +] + +use_pip = True + +exts_list = [ + ('toolz', '0.12.1', { + 'checksums': ['ecca342664893f177a13dac0e6b41cbd8ac25a358e5f215316d43e2100224f4d'], + }), + ('plottable', '0.1.5', { + 'checksums': ['235d762a31c82129dc5bf74205c103a14b1e4393d0f921cc0231be5de884041d'], + }), + ('pynndescent', '0.5.11', { + 'checksums': ['6f44ced9d5a9da2c87d9b2fff30bb5308540c0657605e4d5cde7ed3275bbad50'], + }), + ('rich', '13.7.1', { + 'checksums': ['9be308cb1fe2f1f57d67ce99e95af38a1e2bc71ad9813b0e247cf7ffbcc3a432'], + }), + ('chex', '0.1.86', { + 'checksums': ['e8b0f96330eba4144659e1617c0f7a57b161e8cbb021e55c6d5056c7378091d1'], + }), + (name, version, { + 'sources': ['scib_metrics-%(version)s.tar.gz'], + 'checksums': ['74d10251acf1c11402b994faf063e55317881d7950fb78f6cef011d232a1e266'], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/scvi-tools/scvi-tools-1.1.2-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/s/scvi-tools/scvi-tools-1.1.2-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..7a284e4e0c0 --- /dev/null +++ b/easybuild/easyconfigs/s/scvi-tools/scvi-tools-1.1.2-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,69 @@ +easyblock = 'PythonBundle' + +name = 'scvi-tools' +version = '1.1.2' +versionsuffix = '-CUDA-12.1.1' + +homepage = 'https://github.com/scverse/scvi-tools' +description = """scvi-tools (single-cell variational inference tools) is a package for probabilistic modeling and +analysis of single-cell omics data, built on top of PyTorch and AnnData.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [('hatchling', '1.18.0')] +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('anndata', '0.10.5.post1'), + ('matplotlib', '3.7.2'), + ('scikit-learn', '1.3.1'), + ('tqdm', '4.66.1'), + ('jax', '0.4.25', versionsuffix), + ('h5py', '3.9.0'), + ('PyTorch-Lightning', '2.2.1', versionsuffix), + ('pyro-ppl', '1.9.0', versionsuffix), + ('ml-collections', '0.1.1'), + ('Optax', '0.2.2', versionsuffix), +] + +use_pip = True + +exts_list = [ + ('mudata', '0.2.3', { + 'checksums': ['45288ac150bfc598d68acb7c2c1c43c38c5c39522107e04f7efbf3360c7f2035'], + }), + ('multipledispatch', '1.0.0', { + 'checksums': ['5c839915465c68206c3e9c473357908216c28383b425361e5d144594bf85a7e0'], + }), + ('numpyro', '0.15.0', { + 'checksums': ['e16c9f47cc31e2aa259584a0b6c944312081d33ca92406022632ad584b0e600d'], + }), + ('nest_asyncio', '1.6.0', { + 'checksums': ['6f172d5449aca15afd6c646851f4e31e02c598d553a667e38cafa997cfec55fe'], + }), + ('orbax_checkpoint', '0.5.15', { + 'modulename': 'orbax.checkpoint', + 'checksums': ['15195e8d1b381b56f23a62a25599a3644f5d08655fa64f60bb1b938b8ffe7ef3'], + }), + ('tensorstore', '0.1.60', { + 'checksums': ['88da8f1978982101b8dbb144fd29ee362e4e8c97fc595c4992d555f80ce62a79'], + }), + ('flax', '0.8.4', { + 'checksums': ['968683f850198e1aa5eb2d9d1e20bead880ef7423c14f042db9d60848cb1c90b'], + }), + ('docrep', '0.3.2', { + 'checksums': ['ed8a17e201abd829ef8da78a0b6f4d51fb99a4cbd0554adbed3309297f964314'], + }), + ('lightning', '2.1.4', { + 'checksums': ['0e45098c700fa28c604a11ae233ce181b44aeffce2404debebc2616118431d9f'], + }), + (name, version, { + 'modulename': 'scvi', + 'sources': ['scvi_tools-%(version)s.tar.gz'], + 'checksums': ['104a11a30e8996f5ceaa907b8c81b48b1f4b380d492ef2dd9b9a5577ed81b0f9'], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' From fc75b68e28885d1c07d9c4fb273ca387c089f6a9 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 30 Aug 2024 16:47:05 +0200 Subject: [PATCH 018/107] remove exts_default_options from TensorFlow 2.3.1 This is a top-level parameter --- .../t/TensorFlow/TensorFlow-2.3.1-foss-2020a-Python-3.8.2.eb | 4 +--- .../TensorFlow-2.3.1-fosscuda-2020a-Python-3.8.2.eb | 4 +--- 2 files changed, 2 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.1-foss-2020a-Python-3.8.2.eb index 2cfb8444ca4..daa5022fb1f 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.1-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.1-foss-2020a-Python-3.8.2.eb @@ -40,9 +40,7 @@ dependencies = [ ('zlib', '1.2.11'), ] -exts_default_options = { - 'sanity_pip_check': True, -} +sanity_pip_check = True use_pip = True # Dependencies created and updated using findPythonDeps.sh: diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.1-fosscuda-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.1-fosscuda-2020a-Python-3.8.2.eb index 54fdbc44964..7a4a7766ca6 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.1-fosscuda-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.1-fosscuda-2020a-Python-3.8.2.eb @@ -42,9 +42,7 @@ dependencies = [ ('zlib', '1.2.11'), ] -exts_default_options = { - 'sanity_pip_check': True, -} +sanity_pip_check = True use_pip = True # Dependencies created and updated using findPythonDeps.sh: From d4ba4abf16cf85b53b488173fb8a3eec0aed68dd Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Tue, 3 Sep 2024 13:40:57 +0200 Subject: [PATCH 019/107] Add ReFrame 4.6.2 at system toolchain level --- .../easyconfigs/r/ReFrame/ReFrame-4.6.2.eb | 87 +++++++++++++++++++ 1 file changed, 87 insertions(+) create mode 100644 easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb new file mode 100644 index 00000000000..6a16ff28a3a --- /dev/null +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb @@ -0,0 +1,87 @@ +easyblock = 'PythonBundle' + +name = 'ReFrame' +version = '4.6.2' + +homepage = 'https://github.com/reframe-hpc/reframe' +description = '''ReFrame is a framework for writing regression tests for HPC systems.''' + +toolchain = SYSTEM + +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +# Required by lxml, which is installed by ReFrame's bootstrap installer +osdependencies = [ + ('libxml2'), + ('libxslt', 'libxslt1.1'), +] + +# Listed as python_requires in https://github.com/reframe-hpc/reframe/blob/v4.6.2/setup.cfg +req_py_majver = 3 +req_py_minver = 6 + +use_pip = True + +exts_list = [ + # stick to pip 21.3.1, which is compatible with Python 3.6 + # we still need pip outside of ReFrame's external dependencies, since the install cmd uses pip + ('pip', '21.3.1', { + 'use_pip': False, + 'checksums': ['fd11ba3d0fdb4c07fbc5ecbba0b1b719809420f25038f8ee3cd913d3faa3033a'], + }), + # Require new enough setuptools to install with e.g. pyproject.toml + # 59.6.0 is the latest compatible with Python 3.6 + ('setuptools', '59.6.0', { + 'use_pip': False, + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + 'checksums': ['22c7348c6d2976a52632c67f7ab0cdf40147db7789f9aed18734643fe9cf3373'], + }), + # stick to wheel 0.37.1, which is compatible with Python 3.6 + ('wheel', '0.37.1', { + 'source_tmpl': 'wheel-%(version)s-py2.py3-none-any.whl', + 'checksums': ['4bdcd7d840138086126cd09254dc6195fb4fc6f01c050a1d7236f2630db1d22a'], + }), + # ReFrame's bootstrap script is intended to run with zero dependencies. It downloads all python deps for ReFrame + # into a %(installdir)/external directory. ReFrame's main executable (reframe) adds this dir to python's sys.path + # so that ReFrame (and only ReFrame) will find & use all of these dependencies. + # In EasyBuild, we should adhere to this installation method because a) it is how ReFrame is meant to be used and + # b) it isolates all of ReFrame dependencies from any other python code you run. Thus, there is no chance that + # a test will pick up on any python deps from ReFrame itself. + # For this to work, we need to disable download_dep_fail and sanity_pip_check, as both are _expected_ to fail + # for this setup. + ('reframe', version, { + # Deps are downloaded to %(installdir)/external, which won't polute the PYTHONPATH, so is ok + 'download_dep_fail': False, + # ReFrame uses its custom sys.path to find necessary packages, they are not on PYTYHONPATH + # Thus, the regular pip sanity check is expected to fail, even if ReFrame would run just fine + 'sanity_pip_check': False, + # Set modulename to False, as to skip the sanity_check-step from extension.py (python -c "import reframe") + # This step would fail, since the regular python interpreter wouldn't find the additional packages in + # %(installdir)/external. That's fine, as ReFrame should never be imported directly, only through the + # reframe command. + 'modulename': False, + 'preinstallopts': "export PATH=%(installdir)s/bin:$PATH && " + "./bootstrap.sh +docs +pygelf && cp -r external %(installdir)s && ", + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/reframe-hpc/reframe/archive/'], + 'checksums': ['d3343815ee3d2c330b91a1cdb924ba184119ed7d9fc88a4a754b939a4259df82'], + }), +] + +postinstallcmds = [ + "cp -a tools examples %(installdir)s", + "mkdir -p %(installdir)s/share && cp -a share/completions %(installdir)s/share/completions", + r"sed -i 's@/\(python[0-9.]*\)$@/\1 -S@g' %(installdir)s/bin/reframe", +] + +sanity_check_paths = { + 'files': ['bin/reframe', + 'share/completions/reframe.bash', + 'share/completions/reframe.fish', + 'share/completions/reframe.tcsh'], + 'dirs': ['external', 'lib', 'tools', 'examples'] +} + +sanity_check_commands = ['reframe -V'] + +moduleclass = 'devel' From 893cf70a9964e48b934a7b19ada32563a0aeee80 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Tue, 3 Sep 2024 13:56:29 +0200 Subject: [PATCH 020/107] Make two EasyConfigs: one for Python 3.6, and one for Python 3.7 and above, including 3.12 --- .../r/ReFrame/ReFrame-4.6.2-Python-3.6.eb | 90 +++++++++++++++++++ .../easyconfigs/r/ReFrame/ReFrame-4.6.2.eb | 22 +++-- 2 files changed, 103 insertions(+), 9 deletions(-) create mode 100644 easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-Python-3.6.eb diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-Python-3.6.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-Python-3.6.eb new file mode 100644 index 00000000000..7b48610c6ee --- /dev/null +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-Python-3.6.eb @@ -0,0 +1,90 @@ +# This EasyConfig is made with older setuptools and wheel versions, so that it still works with Python-3.6.X +# For newer python versions, we suggest to use ReFrame-4.6.2.eb (without suffix) +easyblock = 'PythonBundle' + +name = 'ReFrame' +version = '4.6.2' +versionsuffix = '-Python-3.6' + +homepage = 'https://github.com/reframe-hpc/reframe' +description = '''ReFrame is a framework for writing regression tests for HPC systems.''' + +toolchain = SYSTEM + +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +# Required by lxml, which is installed by ReFrame's bootstrap installer +osdependencies = [ + ('libxml2'), + ('libxslt', 'libxslt1.1'), +] + +# Listed as python_requires in https://github.com/reframe-hpc/reframe/blob/v4.6.2/setup.cfg +req_py_majver = 3 +req_py_minver = 6 + +use_pip = True + +exts_list = [ + # stick to pip 21.3.1, which is compatible with Python 3.6 + # we still need pip outside of ReFrame's external dependencies, since the install cmd uses pip + ('pip', '21.3.1', { + 'use_pip': False, + 'checksums': ['fd11ba3d0fdb4c07fbc5ecbba0b1b719809420f25038f8ee3cd913d3faa3033a'], + }), + # Require new enough setuptools to install with e.g. pyproject.toml + # 59.6.0 is the latest compatible with Python 3.6 + ('setuptools', '59.6.0', { + 'use_pip': False, + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + 'checksums': ['22c7348c6d2976a52632c67f7ab0cdf40147db7789f9aed18734643fe9cf3373'], + }), + # stick to wheel 0.37.1, which is compatible with Python 3.6 + ('wheel', '0.37.1', { + 'source_tmpl': 'wheel-%(version)s-py2.py3-none-any.whl', + 'checksums': ['4bdcd7d840138086126cd09254dc6195fb4fc6f01c050a1d7236f2630db1d22a'], + }), + # ReFrame's bootstrap script is intended to run with zero dependencies. It downloads all python deps for ReFrame + # into a %(installdir)/external directory. ReFrame's main executable (reframe) adds this dir to python's sys.path + # so that ReFrame (and only ReFrame) will find & use all of these dependencies. + # In EasyBuild, we should adhere to this installation method because a) it is how ReFrame is meant to be used and + # b) it isolates all of ReFrame dependencies from any other python code you run. Thus, there is no chance that + # a test will pick up on any python deps from ReFrame itself. + # For this to work, we need to disable download_dep_fail and sanity_pip_check, as both are _expected_ to fail + # for this setup. + ('reframe', version, { + # Deps are downloaded to %(installdir)/external, which won't polute the PYTHONPATH, so is ok + 'download_dep_fail': False, + # ReFrame uses its custom sys.path to find necessary packages, they are not on PYTYHONPATH + # Thus, the regular pip sanity check is expected to fail, even if ReFrame would run just fine + 'sanity_pip_check': False, + # Set modulename to False, as to skip the sanity_check-step from extension.py (python -c "import reframe") + # This step would fail, since the regular python interpreter wouldn't find the additional packages in + # %(installdir)/external. That's fine, as ReFrame should never be imported directly, only through the + # reframe command. + 'modulename': False, + 'preinstallopts': "export PATH=%(installdir)s/bin:$PATH && " + "./bootstrap.sh +docs +pygelf && cp -r external %(installdir)s && ", + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/reframe-hpc/reframe/archive/'], + 'checksums': ['d3343815ee3d2c330b91a1cdb924ba184119ed7d9fc88a4a754b939a4259df82'], + }), +] + +postinstallcmds = [ + "cp -a tools examples %(installdir)s", + "mkdir -p %(installdir)s/share && cp -a share/completions %(installdir)s/share/completions", + r"sed -i 's@/\(python[0-9.]*\)$@/\1 -S@g' %(installdir)s/bin/reframe", +] + +sanity_check_paths = { + 'files': ['bin/reframe', + 'share/completions/reframe.bash', + 'share/completions/reframe.fish', + 'share/completions/reframe.tcsh'], + 'dirs': ['external', 'lib', 'tools', 'examples'] +} + +sanity_check_commands = ['reframe -V'] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb index 6a16ff28a3a..c6bbf9aa882 100644 --- a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb @@ -16,28 +16,32 @@ osdependencies = [ ('libxslt', 'libxslt1.1'), ] -# Listed as python_requires in https://github.com/reframe-hpc/reframe/blob/v4.6.2/setup.cfg +# We use pip, setuptools and wheel compatible with Python 3.7 and above +# Note that ReFrame itself is compatible also with Python 3.6 +# As listed in the python_requires in https://github.com/reframe-hpc/reframe/blob/v4.6.2/setup.cfg +# To use with Python 3.6, please install ReFrame-4.6.2-Python-3.6.eb instead req_py_majver = 3 -req_py_minver = 6 +req_py_minver = 7 use_pip = True exts_list = [ - # stick to pip 21.3.1, which is compatible with Python 3.6 + # stick to pip 24.0, which is compatible with Python 3.7 # we still need pip outside of ReFrame's external dependencies, since the install cmd uses pip - ('pip', '21.3.1', { + ('pip', '24.0', { 'use_pip': False, 'checksums': ['fd11ba3d0fdb4c07fbc5ecbba0b1b719809420f25038f8ee3cd913d3faa3033a'], }), - # Require new enough setuptools to install with e.g. pyproject.toml - # 59.6.0 is the latest compatible with Python 3.6 - ('setuptools', '59.6.0', { + # Require new enough setuptools to work with Python 3.12, which doesn't have pkgutil.ImpImporter anymore + # See https://github.com/pypa/setuptools/commit/6653e747c3815b140156249205397ef3719581ee + # 68.0.0 is the latest compatible with Python 3.7 + ('setuptools', '68.0.0', { 'use_pip': False, 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], 'checksums': ['22c7348c6d2976a52632c67f7ab0cdf40147db7789f9aed18734643fe9cf3373'], }), - # stick to wheel 0.37.1, which is compatible with Python 3.6 - ('wheel', '0.37.1', { + # stick to wheel 0.42.0, which is compatible with Python 3.7 + ('wheel', '0.42.0', { 'source_tmpl': 'wheel-%(version)s-py2.py3-none-any.whl', 'checksums': ['4bdcd7d840138086126cd09254dc6195fb4fc6f01c050a1d7236f2630db1d22a'], }), From 5ff26ab3323581ebd0afa4f8afd36504910216fe Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Tue, 3 Sep 2024 14:42:51 +0200 Subject: [PATCH 021/107] use correct checksum for pip 24.0 --- easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb index c6bbf9aa882..dcdff5b4b9a 100644 --- a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb @@ -30,7 +30,7 @@ exts_list = [ # we still need pip outside of ReFrame's external dependencies, since the install cmd uses pip ('pip', '24.0', { 'use_pip': False, - 'checksums': ['fd11ba3d0fdb4c07fbc5ecbba0b1b719809420f25038f8ee3cd913d3faa3033a'], + 'checksums': ['ea9bd1a847e8c5774a5777bb398c19e80bcd4e2aa16a4b301b718fe6f593aba2'], }), # Require new enough setuptools to work with Python 3.12, which doesn't have pkgutil.ImpImporter anymore # See https://github.com/pypa/setuptools/commit/6653e747c3815b140156249205397ef3719581ee From ed168ec0370d75319f0af68d41111258ef692ccf Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Tue, 3 Sep 2024 14:47:41 +0200 Subject: [PATCH 022/107] use correct checksum for setuptools 68.0.0 --- easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb index dcdff5b4b9a..7544d3640ba 100644 --- a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb @@ -38,7 +38,7 @@ exts_list = [ ('setuptools', '68.0.0', { 'use_pip': False, 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], - 'checksums': ['22c7348c6d2976a52632c67f7ab0cdf40147db7789f9aed18734643fe9cf3373'], + 'checksums': ['baf1fdb41c6da4cd2eae722e135500da913332ab3f2f5c7d33af9b492acb5235'], }), # stick to wheel 0.42.0, which is compatible with Python 3.7 ('wheel', '0.42.0', { From d7e047d98807d392ea488ba5f9efaa7df5563e15 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Tue, 3 Sep 2024 14:48:59 +0200 Subject: [PATCH 023/107] use correct filename for wheel 0.42.0 --- easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb index 7544d3640ba..1a2416ce023 100644 --- a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb @@ -42,7 +42,7 @@ exts_list = [ }), # stick to wheel 0.42.0, which is compatible with Python 3.7 ('wheel', '0.42.0', { - 'source_tmpl': 'wheel-%(version)s-py2.py3-none-any.whl', + 'source_tmpl': 'wheel-%(version)s-py3-none-any.whl', 'checksums': ['4bdcd7d840138086126cd09254dc6195fb4fc6f01c050a1d7236f2630db1d22a'], }), # ReFrame's bootstrap script is intended to run with zero dependencies. It downloads all python deps for ReFrame From 084b306b44df6970b01b301d60b01eeb70463806 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Tue, 3 Sep 2024 14:51:00 +0200 Subject: [PATCH 024/107] use correct checksum for wheel 0.42.0 --- easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb index 1a2416ce023..26e331c131e 100644 --- a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb @@ -43,7 +43,7 @@ exts_list = [ # stick to wheel 0.42.0, which is compatible with Python 3.7 ('wheel', '0.42.0', { 'source_tmpl': 'wheel-%(version)s-py3-none-any.whl', - 'checksums': ['4bdcd7d840138086126cd09254dc6195fb4fc6f01c050a1d7236f2630db1d22a'], + 'checksums': ['177f9c9b0d45c47873b619f5b650346d632cdc35fb5e4d25058e09c9e581433d'], }), # ReFrame's bootstrap script is intended to run with zero dependencies. It downloads all python deps for ReFrame # into a %(installdir)/external directory. ReFrame's main executable (reframe) adds this dir to python's sys.path From 94d34a5af7d222d00f783357a273964ad45c0709 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Wed, 4 Sep 2024 13:39:35 +0200 Subject: [PATCH 025/107] Use implementation from https://github.com/easybuilders/easybuild-easyblocks/pull/3431 to set a maximum version --- easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-Python-3.6.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-Python-3.6.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-Python-3.6.eb index 7b48610c6ee..4e58793cd0a 100644 --- a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-Python-3.6.eb +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-Python-3.6.eb @@ -23,6 +23,11 @@ osdependencies = [ req_py_majver = 3 req_py_minver = 6 +# The setuptools in this EasyConfig is the latest that works for Python 3.6, but is too old for Python 3.12 +# See https://github.com/easybuilders/easybuild-easyconfigs/pull/21269#discussion_r1741570244 +max_py_majver = 3 +max_py_minver = 11 + use_pip = True exts_list = [ From 4e6c8bcddc103717168884e896346b48454cad42 Mon Sep 17 00:00:00 2001 From: WilleBell Date: Wed, 4 Sep 2024 17:40:34 +0200 Subject: [PATCH 026/107] adding easyconfigs: Triton-2.1.0-foss-2023a-CUDA-12.1.1.eb, Clang-17.0.0_20230515-GCCcore-12.3.0-CUDA-12.1.1.eb and patches: Triton-2.1.0-disable_rocm_support.patch, Triton-2.1.0-use_eb_env_python_build.patch --- ...0.0_20230515-GCCcore-12.3.0-CUDA-12.1.1.eb | 61 ++++++++++++ .../Triton-2.1.0-disable_rocm_support.patch | 88 ++++++++++++++++++ .../Triton-2.1.0-foss-2023a-CUDA-12.1.1.eb | 56 +++++++++++ ...Triton-2.1.0-use_eb_env_python_build.patch | 93 +++++++++++++++++++ 4 files changed, 298 insertions(+) create mode 100644 easybuild/easyconfigs/c/Clang/Clang-17.0.0_20230515-GCCcore-12.3.0-CUDA-12.1.1.eb create mode 100644 easybuild/easyconfigs/t/Triton/Triton-2.1.0-disable_rocm_support.patch create mode 100644 easybuild/easyconfigs/t/Triton/Triton-2.1.0-foss-2023a-CUDA-12.1.1.eb create mode 100644 easybuild/easyconfigs/t/Triton/Triton-2.1.0-use_eb_env_python_build.patch diff --git a/easybuild/easyconfigs/c/Clang/Clang-17.0.0_20230515-GCCcore-12.3.0-CUDA-12.1.1.eb b/easybuild/easyconfigs/c/Clang/Clang-17.0.0_20230515-GCCcore-12.3.0-CUDA-12.1.1.eb new file mode 100644 index 00000000000..947a6afdad5 --- /dev/null +++ b/easybuild/easyconfigs/c/Clang/Clang-17.0.0_20230515-GCCcore-12.3.0-CUDA-12.1.1.eb @@ -0,0 +1,61 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2013-2015 Dmitri Gribenko, Ward Poelmans +# Authors:: Dmitri Gribenko +# Authors:: Ward Poelmans +# License:: GPLv2 or later, MIT, three-clause BSD. +# $Id$ +## + +name = 'Clang' +version = '17.0.0_20230515' +versionsuffix = '-CUDA-%(cudaver)s' +_commit = 'c5dede880d17' + +homepage = 'https://clang.llvm.org/' +description = """C, C++, Objective-C compiler, based on LLVM. Does not + include C++ standard library -- use libstdc++ from GCC.""" + +# Clang also depends on libstdc++ during runtime, but this dependency is +# already specified as the toolchain. +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +sources = [{ + 'source_urls': ["https://github.com/llvm/llvm-project/archive"], + 'download_filename': '%s.tar.gz' % _commit, + 'filename': 'llvm-project-%s.tar.gz' % version, +}] +checksums = ['6f371f9ac208b8e9dc57fc117b1a9c8565d7ea2bbb49a2768cb9c3c0fee0291d'] + +builddependencies = [ + ('CMake', '3.26.3'), + ('Perl', '5.36.1'), + # Including Python bindings would require this as a runtime dep + ('Python', '3.11.3'), +] +dependencies = [ + # since Clang is a compiler, binutils is a runtime dependency too + ('binutils', '2.40'), + ('hwloc', '2.9.1'), + ('libxml2', '2.11.4'), + ('ncurses', '6.4'), + ('GMP', '6.2.1'), + ('Z3', '4.12.2'), + ('CUDA', '12.1.1', '', SYSTEM), +] + +# enabling RTTI makes the flang compiler need to link to libc++ so instead of +# flang-new -flang-experimental-exec -fopenmp hello_openmp.f90 +# you would need +# flang-new -flang-experimental-exec -fopenmp hello_openmp.f90 -l c++ +enable_rtti = False + +assertions = True +python_bindings = False +skip_all_tests = True + +llvm_runtimes = ['libunwind', 'libcxx', 'libcxxabi'] +llvm_projects = ['polly', 'lld', 'lldb', 'clang-tools-extra', 'flang'] + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/t/Triton/Triton-2.1.0-disable_rocm_support.patch b/easybuild/easyconfigs/t/Triton/Triton-2.1.0-disable_rocm_support.patch new file mode 100644 index 00000000000..13d736b4bfc --- /dev/null +++ b/easybuild/easyconfigs/t/Triton/Triton-2.1.0-disable_rocm_support.patch @@ -0,0 +1,88 @@ +Disable experimental support for AMD GPUs +author: Alex Domingo (Vrije Universiteit Brussel) +author: Samuel Moors (Vrije Universiteit Brussel) +diff -ur triton-2.1.0.orig/CMakeLists.txt triton-2.1.0/CMakeLists.txt +--- triton-2.1.0.orig/CMakeLists.txt 2023-09-01 08:28:27.000000000 +0200 ++++ triton-2.1.0/CMakeLists.txt 2024-09-01 10:40:17.863374000 +0200 +@@ -70,7 +70,7 @@ + AMDGPUInfo AMDGPUcodegen + ) + else() +- find_package(LLVM 11 REQUIRED COMPONENTS "nvptx;amdgpu") ++ find_package(LLVM 11 REQUIRED COMPONENTS "nvptx") + endif() + + message(STATUS "Found LLVM ${LLVM_PACKAGE_VERSION}") +@@ -89,9 +89,7 @@ + LLVMNVPTXCodeGen + LLVMNVPTXDesc + LLVMNVPTXInfo +- LLVMAMDGPUDisassembler + LLVMMCDisassembler +- LLVMAMDGPUCodeGen + LLVMMIRParser + LLVMGlobalISel + LLVMSelectionDAG +@@ -116,10 +114,7 @@ + LLVMObject + LLVMTextAPI + LLVMBitReader +- LLVMAMDGPUAsmParser + LLVMMCParser +- LLVMAMDGPUDesc +- LLVMAMDGPUUtils + LLVMMC + LLVMDebugInfoCodeView + LLVMDebugInfoMSF +@@ -127,7 +122,6 @@ + LLVMRemarks + LLVMBitstreamReader + LLVMBinaryFormat +- LLVMAMDGPUInfo + LLVMSupport + LLVMDemangle + LLVMPasses +diff -ur triton-2.1.0.orig/lib/Target/HSACO/HSACOTranslation.cpp triton-2.1.0/lib/Target/HSACO/HSACOTranslation.cpp +--- triton-2.1.0.orig/lib/Target/HSACO/HSACOTranslation.cpp 2023-09-01 08:28:27.000000000 +0200 ++++ triton-2.1.0/lib/Target/HSACO/HSACOTranslation.cpp 2024-09-02 21:27:09.233712000 +0200 +@@ -37,13 +37,6 @@ + + namespace { + +-void init_llvm() { +- LLVMInitializeAMDGPUTarget(); +- LLVMInitializeAMDGPUTargetInfo(); +- LLVMInitializeAMDGPUTargetMC(); +- LLVMInitializeAMDGPUAsmParser(); +- LLVMInitializeAMDGPUAsmPrinter(); +-} + + std::unique_ptr + initialize_module(llvm::Module *module, const std::string &triple, +@@ -155,7 +148,6 @@ + llir_to_amdgcn_and_hsaco(llvm::Module *module, std::string gfx_arch, + std::string gfx_triple, std::string gfx_features) { + +- init_llvm(); + + // verify and store llvm + auto module_obj = llvm::CloneModule(*module); +diff -ur triton-2.1.0.orig/python/src/triton.cc triton-2.1.0/python/src/triton.cc +--- triton-2.1.0.orig/python/src/triton.cc 2023-09-01 08:28:27.000000000 +0200 ++++ triton-2.1.0/python/src/triton.cc 2024-09-01 10:41:29.146862440 +0200 +@@ -60,7 +60,6 @@ + enum backend_t { + HOST, + CUDA, +- ROCM, + }; + + void init_triton_runtime(py::module &&m) { +@@ -68,7 +67,6 @@ + py::enum_(m, "backend", py::module_local()) + .value("HOST", HOST) + .value("CUDA", CUDA) +- .value("ROCM", ROCM) + .export_values(); + } + diff --git a/easybuild/easyconfigs/t/Triton/Triton-2.1.0-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/t/Triton/Triton-2.1.0-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..a1cdbe87df3 --- /dev/null +++ b/easybuild/easyconfigs/t/Triton/Triton-2.1.0-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,56 @@ +easyblock = 'PythonPackage' + +name = 'Triton' +version = '2.1.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://triton-lang.org/' + +description = """Triton is a language and compiler for parallel programming. It aims to provide a +Python-based programming environment for productively writing custom DNN compute +kernels capable of running at maximal throughput on modern GPU hardware.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +github_account = 'openai' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = [ + '%(name)s-%(version)s-disable_rocm_support.patch', + '%(name)s-%(version)s-use_eb_env_python_build.patch', +] +checksums = [ + {'v2.1.0.tar.gz': '4338ca0e80a059aec2671f02bfc9320119b051f378449cf5f56a1273597a3d99'}, + {'Triton-2.1.0-disable_rocm_support.patch': 'e4d7c0947c3287b3f0871a004e8b483963f637c9fa3ef6212ac3a34660de2a7c'}, + {'Triton-2.1.0-use_eb_env_python_build.patch': 'd68bf766c699ad6a778d9449d3bccdadc2f20f1f86ba13e1359ad297b12fbf7c'}, +] + +builddependencies = [ + ('Clang', '17.0.0_20230515', versionsuffix), # this is the exact commit that would be downloaded by Triton + ('CMake', '3.26.3'), +] + +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('Python', '3.11.3'), + ('PyTorch', '2.1.2', versionsuffix), +] + +use_pip = True +download_dep_fail = True + +start_dir = 'python' + +preinstallopts = 'export LLVM_INCLUDE_DIRS=$EBROOTCLANG/include && ' +preinstallopts += 'export LLVM_LIBRARY_DIR=$EBROOTCLANG/lib && ' +preinstallopts += 'export LLVM_SYSPATH=$EBROOTCLANG && ' +preinstallopts += 'export TRITON_BUILD_WITH_CLANG_LLD=1 && ' + +# make pip print output of cmake +installopts = "-v " + +sanity_pip_check = True + +modluafooter = 'setenv("TRITON_PTXAS_PATH", pathJoin(os.getenv("CUDA_HOME"), "bin", "ptxas"))' + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/t/Triton/Triton-2.1.0-use_eb_env_python_build.patch b/easybuild/easyconfigs/t/Triton/Triton-2.1.0-use_eb_env_python_build.patch new file mode 100644 index 00000000000..650134e73be --- /dev/null +++ b/easybuild/easyconfigs/t/Triton/Triton-2.1.0-use_eb_env_python_build.patch @@ -0,0 +1,93 @@ +Fix Triton cmake build to use dependencies from EasyBuild +author: Alex Domingo (Vrije Universiteit Brussel) +author: Samuel Moors (Vrije Universiteit Brussel) +diff -ur triton-2.1.0.orig/lib/Target/LLVMIR/LLVMIRTranslation.cpp triton-2.1.0/lib/Target/LLVMIR/LLVMIRTranslation.cpp +--- triton-2.1.0.orig/lib/Target/LLVMIR/LLVMIRTranslation.cpp 2023-09-01 08:28:27.000000000 +0200 ++++ triton-2.1.0/lib/Target/LLVMIR/LLVMIRTranslation.cpp 2024-09-02 19:46:06.574421829 +0200 +@@ -35,6 +35,7 @@ + #endif + #include + #include ++#include // for getenv + + namespace fs = std::filesystem; + +@@ -177,6 +178,7 @@ + } + + if (!funcs.empty()) { ++ std::filesystem::path cuda_home = std::getenv("CUDA_HOME"); + static const std::string libdevice = "libdevice"; + // first search for environmental path + std::string env_path = ::triton::tools::getenv("TRITON_LIBDEVICE_PATH"); +@@ -189,8 +191,7 @@ + // `triton/third_party/cuda/lib/libdevice.10.bc` + static const auto this_library_path = getThisLibraryPath(); + static const auto runtime_path = +- this_library_path.parent_path().parent_path() / "third_party" / "cuda" / +- "lib" / "libdevice.10.bc"; ++ cuda_home / "nvvm" / "libdevice" / "libdevice.10.bc"; + if (fs::exists(runtime_path)) { + externLibs.try_emplace(libdevice, runtime_path.string()); + } else { +diff -ur triton-2.1.0.orig/python/setup.py triton-2.1.0/python/setup.py +--- triton-2.1.0.orig/python/setup.py 2023-09-01 08:28:27.000000000 +0200 ++++ triton-2.1.0/python/setup.py 2024-09-02 18:16:58.044760300 +0200 +@@ -202,13 +202,13 @@ + + def build_extension(self, ext): + lit_dir = shutil.which('lit') +- user_home = os.getenv("HOME") or os.getenv("USERPROFILE") or \ +- os.getenv("HOMEPATH") or None +- if not user_home: +- raise RuntimeError("Could not find user home directory") +- triton_cache_path = os.path.join(user_home, ".triton") ++ # user_home = os.getenv("HOME") or os.getenv("USERPROFILE") or \ ++ # os.getenv("HOMEPATH") or None ++ # if not user_home: ++ # raise RuntimeError("Could not find user home directory") ++ # triton_cache_path = os.path.join(user_home, ".triton") + # lit is used by the test suite +- thirdparty_cmake_args = get_thirdparty_packages(triton_cache_path) ++ # thirdparty_cmake_args = get_thirdparty_packages(triton_cache_path) + extdir = os.path.abspath(os.path.dirname(self.get_ext_fullpath(ext.path))) + # create build directories + if not os.path.exists(self.build_temp): +@@ -216,8 +216,9 @@ + # python directories + python_include_dir = sysconfig.get_path("platinclude") + cmake_args = [ ++ "-DCMAKE_VERBOSE_MAKEFILE:BOOL=ON", + "-DCMAKE_EXPORT_COMPILE_COMMANDS=ON", +- "-DLLVM_ENABLE_WERROR=ON", ++ # "-DLLVM_ENABLE_WERROR=ON", + "-DCMAKE_LIBRARY_OUTPUT_DIRECTORY=" + extdir, + "-DTRITON_BUILD_TUTORIALS=OFF", + "-DTRITON_BUILD_PYTHON_MODULE=ON", +@@ -227,7 +228,7 @@ + ] + if lit_dir is not None: + cmake_args.append("-DLLVM_EXTERNAL_LIT=" + lit_dir) +- cmake_args.extend(thirdparty_cmake_args) ++ # cmake_args.extend(thirdparty_cmake_args) + + # configuration + cfg = get_build_type() +@@ -245,7 +246,7 @@ + build_args += ["--", "/m"] + else: + cmake_args += ["-DCMAKE_BUILD_TYPE=" + cfg] +- max_jobs = os.getenv("MAX_JOBS", str(2 * os.cpu_count())) ++ max_jobs = os.getenv("MAX_JOBS", str(len(os.sched_getaffinity(0)))) + build_args += ['-j' + max_jobs] + + if check_env_flag("TRITON_BUILD_WITH_CLANG_LLD"): +@@ -262,7 +263,7 @@ + subprocess.check_call(["cmake", "--build", "."] + build_args, cwd=cmake_dir) + + +-download_and_copy_ptxas() ++# download_and_copy_ptxas() + + + setup( From b05d0afe9314f401f89ac9b3d2ebe4e76c79c41f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 4 Sep 2024 19:17:33 +0200 Subject: [PATCH 027/107] remove easyconfig for Optax using foss/2023a toolchain --- .../Optax-0.2.2-foss-2023a-CUDA-12.1.1.eb | 43 ------------------- 1 file changed, 43 deletions(-) delete mode 100644 easybuild/easyconfigs/o/Optax/Optax-0.2.2-foss-2023a-CUDA-12.1.1.eb diff --git a/easybuild/easyconfigs/o/Optax/Optax-0.2.2-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/o/Optax/Optax-0.2.2-foss-2023a-CUDA-12.1.1.eb deleted file mode 100644 index 43b7ce4b7ef..00000000000 --- a/easybuild/easyconfigs/o/Optax/Optax-0.2.2-foss-2023a-CUDA-12.1.1.eb +++ /dev/null @@ -1,43 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'Optax' -version = '0.2.2' -versionsuffix = '-CUDA-12.1.1' - -homepage = 'https://github.com/deepmind/optax' -description = """Optax is a gradient processing and optimization library for JAX.""" - -toolchain = {'name': 'foss', 'version': '2023a'} - -dependencies = [ - ('Python', '3.11.3'), - ('SciPy-bundle', '2023.07'), - ('jax', '0.4.25', versionsuffix), -] - -use_pip = True - -exts_list = [ - ('toolz', '0.12.1', { - 'checksums': ['ecca342664893f177a13dac0e6b41cbd8ac25a358e5f215316d43e2100224f4d'], - }), - ('flit_core', '3.9.0', { - 'checksums': ['72ad266176c4a3fcfab5f2930d76896059851240570ce9a98733b658cb786eba'], - }), - ('absl-py', '2.1.0', { - 'modulename': 'absl', - 'checksums': ['7820790efbb316739cde8b4e19357243fc3608a152024288513dd968d7d959ff'], - }), - ('chex', '0.1.86', { - 'checksums': ['e8b0f96330eba4144659e1617c0f7a57b161e8cbb021e55c6d5056c7378091d1'], - }), - ('optax', version, { - 'checksums': ['f09bf790ef4b09fb9c35f79a07594c6196a719919985f542dc84b0bf97812e0e'], - }), -] - -sanity_pip_check = True - -sanity_check_commands = ["python -c 'from optax import GradientTransformation'"] - -moduleclass = 'lib' From 42469bb2d883bec568b9e6966b404cd1cedce6a0 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Thu, 5 Sep 2024 14:07:40 +0200 Subject: [PATCH 028/107] adding easyconfigs: CLUMPP-1.1.2-Linux64.eb --- .../c/CLUMPP/CLUMPP-1.1.2-Linux64.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/c/CLUMPP/CLUMPP-1.1.2-Linux64.eb diff --git a/easybuild/easyconfigs/c/CLUMPP/CLUMPP-1.1.2-Linux64.eb b/easybuild/easyconfigs/c/CLUMPP/CLUMPP-1.1.2-Linux64.eb new file mode 100644 index 00000000000..fb71ad7ff19 --- /dev/null +++ b/easybuild/easyconfigs/c/CLUMPP/CLUMPP-1.1.2-Linux64.eb @@ -0,0 +1,32 @@ +easyblock = 'Tarball' + +name = 'CLUMPP' +version = '1.1.2' +versionsuffix = '-Linux64' + +homepage = 'https://rosenberglab.stanford.edu/clumpp.html' +description = """ +CLUMPP is a program that deals with label switching and multimodality problems +in population-genetic cluster analyses.""" + +toolchain = SYSTEM + +source_urls = ['https://rosenberglab.stanford.edu/software/'] +sources = ['%(name)s_Linux64.%(version)s.tar.gz'] +checksums = ['58cf3fe9e37f890621a76a244362256ffe4dde5e409346ae811d56af26cfe724'] + +postinstallcmds = [ + 'cd %(installdir)s && mkdir bin && mv CLUMPP bin/' +] + +sanity_check_paths = { + 'files': ['bin/CLUMPP'], + 'dirs': [], +} + +sanity_check_commands = [ + 'tmpdir=$(mktemp -d) && cp %(installdir)s/{paramfile,arabid.popfile,arabid.permutationfile} $tmpdir/ && ' + 'cd $tmpdir && CLUMPP', +] + +moduleclass = 'bio' From 9a50608a0d1f7478c2f001e11d38b30a71787509 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 6 Sep 2024 14:15:28 +0100 Subject: [PATCH 029/107] adding easyconfigs: rnamotif-20240904-GCCcore-12.3.0.eb --- .../rnamotif-20240904-GCCcore-12.3.0.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/r/rnamotif/rnamotif-20240904-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/r/rnamotif/rnamotif-20240904-GCCcore-12.3.0.eb b/easybuild/easyconfigs/r/rnamotif/rnamotif-20240904-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..bb1513a04b2 --- /dev/null +++ b/easybuild/easyconfigs/r/rnamotif/rnamotif-20240904-GCCcore-12.3.0.eb @@ -0,0 +1,42 @@ +# This easyconfig was created by the BEAR Software team at the University of Birmingham. +easyblock = 'MakeCp' + +name = 'rnamotif' +version = '20240904' +_commit = '697ee7fda4ff2f5181a33c0c3eac54d7b97409fa' + +homepage = "https://github.com/dacase/rnamotif" +description = """The rnamotif program searchs input sequences for portions that match a given descriptor or "motif". + Matching sequences can also be ranked by various scoring functions.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +github_account = 'dacase' +source_urls = [GITHUB_SOURCE] +sources = ['%s.tar.gz' % _commit] +checksums = ['e9432e128ce7f1bfcf4898a36d56435272ad9b4e2d37f1866a95aa159c81fdfe'] + +builddependencies = [ + ('binutils', '2.40'), + ('Bison', '3.8.2'), + ('flex', '2.6.4'), + +] + +prebuildopts = 'sed -i "s/CFLAGS= -O2 -Wall/CFLAGS=$CFLAGS/" config.h &&' +pretestopts = 'EFNDATA=%%(builddir)s/%%(name)s-%s/efndata' % _commit +runtest = 'test' + +files_to_copy = [ + (['src/rnamotif', 'src/rmprune', 'src/rmfmt', 'src/rm2ct'], 'bin'), + 'LICENSE', 'efndata', 'Ecoli.trna.example', +] + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': ['efndata'], +} + +modextravars = {'EFNDATA': 'efndata'} + +moduleclass = 'bio' From 736457464a1f3aaa307083a124d372ca02d195df Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 6 Sep 2024 16:01:52 +0200 Subject: [PATCH 030/107] unbundle tensorboard from TensorFlow v2.15.1 --- .../TensorFlow-2.15.1-foss-2023a.eb | 61 ------------------- 1 file changed, 61 deletions(-) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a.eb index 506cbafd52b..0f3a94f2cc4 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a.eb @@ -57,7 +57,6 @@ dependencies = [ # - portpicker for tests no longer needed (TF@e85860e838) # - opt_einsum now comes from ml_dtypes exts_list = [ - ('wrapt', '1.14.1', { 'checksums': ['380a85cf89e0e69b7cfbe2ea9f765f004ff419f34194018a6827ac0e3edfed4d'], }), @@ -68,48 +67,6 @@ exts_list = [ 'source_tmpl': 'tensorflow_estimator-%(version)s-py2.py3-none-any.whl', 'checksums': ['aedf21eec7fb2dc91150fc91a1ce12bc44dbb72278a08b58e79ff87c9e28f153'], }), - ('Werkzeug', '3.0.2', { - 'source_tmpl': SOURCELOWER_TAR_GZ, - 'checksums': ['e39b645a6ac92822588e7b39a692e7828724ceae0b0d702ef96701f90e70128d'], - }), - ('tensorboard-data-server', '0.7.2', { - 'source_tmpl': 'tensorboard_data_server-%(version)s-py3-none-any.whl', - 'checksums': ['7e0610d205889588983836ec05dc098e80f97b7e7bbff7e994ebb78f578d0ddb'], - }), - ('Markdown', '3.6', { - 'checksums': ['ed4f41f6daecbeeb96e576ce414c41d2d876daa9a16cb35fa8ed8c2ddfad0224'], - }), - ('oauthlib', '3.2.2', { - 'checksums': ['9859c40929662bec5d64f34d01c99e093149682a3f38915dc0655d5a633dd918'], - }), - ('requests-oauthlib', '2.0.0', { - 'checksums': ['b3dffaebd884d8cd778494369603a9e7b58d29111bf6b41bdc2dcd87203af4e9'], - }), - ('rsa', '4.9', { - 'checksums': ['e38464a49c6c85d7f1351b0126661487a7e0a14a50f1675ec50eb34d4f20ef21'], - }), - ('pyasn1-modules', '0.4.0', { - 'source_tmpl': 'pyasn1_modules-%(version)s.tar.gz', - 'checksums': ['831dbcea1b177b28c9baddf4c6d1013c24c3accd14a1873fffaa6a2e905f17b6'], - }), - ('cachetools', '5.3.3', { - 'checksums': ['ba29e2dfa0b8b556606f097407ed1aa62080ee108ab0dc5ec9d6a723a007d105'], - }), - ('google-auth', '2.29.0', { - 'modulename': 'google.auth', - 'checksums': ['672dff332d073227550ffc7457868ac4218d6c500b155fe6cc17d2b13602c360'], - }), - ('google-auth-oauthlib', '1.2.0', { - 'checksums': ['292d2d3783349f2b0734a0a0207b1e1e322ac193c2c09d8f7c613fb7cc501ea8'], - }), - ('absl-py', '2.1.0', { - 'modulename': 'absl', - 'checksums': ['7820790efbb316739cde8b4e19357243fc3608a152024288513dd968d7d959ff'], - }), - ('tensorboard', '2.15.2', { - 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', - 'checksums': ['a6f6443728064d962caea6d34653e220e34ef8df764cb06a8212c17e1a8f0622'], - }), ('keras', '2.15.0', { 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', 'checksums': ['2dcc6d2e30cf9c951064b63c1f4c404b966c59caf09e01f3549138ec8ee0dd1f'], @@ -128,15 +85,6 @@ exts_list = [ ('astor', '0.8.1', { 'checksums': ['6a6effda93f4e1ce9f618779b2dd1d9d84f1e32812c23a29b3fff6fd7f63fa5e'], }), - # Optional profile plugin + dependency - ('gviz-api', '1.10.0', { - 'source_tmpl': 'gviz_api-%(version)s.tar.gz', - 'checksums': ['846692dd8cc73224fc31b18e41589bd934e1cc05090c6576af4b4b26c2e71b90'], - }), - ('tensorboard-plugin-profile', '2.15.1', { - 'source_tmpl': 'tensorboard_plugin_profile-%(version)s.tar.gz', - 'checksums': ['84bb33e446eb4a9c0616f669fc6a42cdd40eadd9ae1d74bf756f4f0479993273'], - }), (name, version, { 'patches': [ 'TensorFlow-2.13.0_add-missing-system-protobuf-targets.patch', @@ -208,13 +156,4 @@ exts_list = [ }), ] -# Taken from tensorboard-2.15.1-gfbf-2023a.eb: -# Relax restriction on protobuf dependency as issue was fixed -# in https://github.com/protocolbuffers/upb/pull/1514 -# see also: https://github.com/easybuilders/easybuild-easyconfigs/pull/19671 -postinstallcmds = [ - 'sed -i "s/Requires-Dist: protobuf.*/Requires-Dist: protobuf >=3.19.6/g" ' + - '%(installdir)s/lib/python%(pyshortver)s/site-packages/tensorboard-2.15.2.dist-info/METADATA', -] - moduleclass = 'lib' From 099539e2dd5fa132b5c6c74d66ebd48a7ea0998c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 6 Sep 2024 17:00:53 +0200 Subject: [PATCH 031/107] adding easyconfigs: PLINK-1.90-beta-7.4-x86_64.eb --- .../p/PLINK/PLINK-1.90-beta-7.4-x86_64.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/p/PLINK/PLINK-1.90-beta-7.4-x86_64.eb diff --git a/easybuild/easyconfigs/p/PLINK/PLINK-1.90-beta-7.4-x86_64.eb b/easybuild/easyconfigs/p/PLINK/PLINK-1.90-beta-7.4-x86_64.eb new file mode 100644 index 00000000000..51357650dbb --- /dev/null +++ b/easybuild/easyconfigs/p/PLINK/PLINK-1.90-beta-7.4-x86_64.eb @@ -0,0 +1,22 @@ +easyblock = 'PackedBinary' + +name = 'PLINK' +version = '1.90-beta-7.4-x86_64' + +homepage = 'https://www.cog-genomics.org/plink/1.9/' +description = 'plink-1.9-x86_64: Whole-genome association analysis toolset' + +toolchain = SYSTEM + +source_urls = ['https://s3.amazonaws.com/plink1-assets/'] +sources = ['plink_linux_x86_64_20240818.zip'] +checksums = ['0ac294ffcd5d82f5b0d2d7f579ac85a87017f6fc46485b21793f5aff9c719e3d'] + +sanity_check_paths = { + 'files': ['plink', 'prettify', 'toy.map', 'toy.ped'], + 'dirs': [], +} + +sanity_check_commands = ["plink --help"] + +moduleclass = 'bio' From bf063e5a037c163d90834386f5c8b3b312fa3d5b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 6 Sep 2024 18:01:39 +0200 Subject: [PATCH 032/107] adding easyconfigs: SNAP-ESA-10.0.0-Java-11.eb --- .../s/SNAP-ESA/SNAP-ESA-10.0.0-Java-11.eb | 71 +++++++++++++++++++ 1 file changed, 71 insertions(+) create mode 100644 easybuild/easyconfigs/s/SNAP-ESA/SNAP-ESA-10.0.0-Java-11.eb diff --git a/easybuild/easyconfigs/s/SNAP-ESA/SNAP-ESA-10.0.0-Java-11.eb b/easybuild/easyconfigs/s/SNAP-ESA/SNAP-ESA-10.0.0-Java-11.eb new file mode 100644 index 00000000000..06a2de7582c --- /dev/null +++ b/easybuild/easyconfigs/s/SNAP-ESA/SNAP-ESA-10.0.0-Java-11.eb @@ -0,0 +1,71 @@ +easyblock = 'Binary' + +name = 'SNAP-ESA' +version = '10.0.0' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://step.esa.int/main/toolboxes/snap/' +description = """ +The Sentinel Application Platform (SNAP) is a common architecture for all +Sentinel Toolboxes being jointly developed by Brockmann Consult, SkyWatch and +C-S. +The SNAP architecture is ideal for Earth Observation processing and analysis +due to the following technological innovations: Extensibility, Portability, +Modular Rich Client Platform, Generic EO Data Abstraction, Tiled Memory +Management, and a Graph Processing Framework.""" + +toolchain = SYSTEM + +local_installer = 'esa-snap_all_linux-%(version)s.sh' +local_varfile = 'SNAP-ESA-8.0-response.varfile' + +source_urls = [ + 'https://download.esa.int/step/snap/%(version_major)s_%(version_minor)s/installers', + 'https://step.esa.int/downloads/%(version_major_minor)s/installers', +] +sources = [local_installer] +patches = [(local_varfile, '.')] +checksums = [ + {'esa-snap_all_linux-10.0.0.sh': 'c928fd886c983fa7c09c09a3c48593542e71b0636d493ae1401b4c964348698a'}, + {'SNAP-ESA-8.0-response.varfile': '5ea98e3376bb3df52b9c4c99ab4986015296b815021e16486b58e4aad58e21a4'}, +] + +# The installation is executed with the bundled JRE 1.8.0_242 (Zulu) +# At runtime we switch to an external JDK (SNAP developers recommend any OpenJDK distribution) +dependencies = [ + ('Java', '11'), +] + +install_cmd = "INSTALL4J_TEMP='%(builddir)s' " +install_cmd += "bash %s -dir '%%(installdir)s'" % local_installer +install_cmd += " -q -varfile '%s'" % local_varfile + +postinstallcmds = [ + # set paths + 'sed -i "s|jdkhome.*|jdkhome=$JAVA_HOME|" %(installdir)s/etc/snap.conf', + 'sed -i "s|#snap.home.*|snap.home=%(installdir)s|" %(installdir)s/etc/snap.properties', + # remove default maximum memory allocation pool + 'sed -i "s|-J-Xmx[0-9G]* ||" %(installdir)s/etc/snap.conf', + # disable update checks + "echo 'snap.versionCheck.interval=NEVER' >> %(installdir)s/etc/snap.properties", + "sed -i 's|dpiaware=false|& -J-Dplugin.manager.check.interval=NEVER|' %(installdir)s/etc/snap.conf", + # (optional) update all modules to latest version + # the update command is buggy and it hangs after doing the update, kill it whenever it prints "updates=0" + # see issue https://senbox.atlassian.net/browse/SNAP-927 + # ('LOG="$(mktemp -d)/snap-update.log"; mkfifo $LOG; trap "rm -f $LOG" EXIT;' + # 'SNAPCMD="%(installdir)s/bin/snap --nosplash --nogui --userdir "%(builddir)s/snap" --modules --update-all";' + # '$SNAPCMD 2>&1 > $LOG & SNAPPID=$!;' + # 'while read line; do echo "$line"; [ "$line" = "updates=0" ] && kill $SNAPPID; done < $LOG;'), +] + +sanity_check_paths = { + 'files': ['bin/snap', 'bin/gpt'], + 'dirs': ['rstb', 'smos', 'snap'], +} + +sanity_check_commands = [ + "snap --nosplash --nogui --modules --help | grep 'Additional module options'", + "gpt -h", +] + +moduleclass = 'geo' From d86580519347bfa7e87ffc36a5b0be4a212ad159 Mon Sep 17 00:00:00 2001 From: WilleBell Date: Mon, 9 Sep 2024 10:43:21 +0200 Subject: [PATCH 033/107] adding easyconfigs: xskillscore-0.0.26-foss-2023a.eb --- .../xskillscore-0.0.26-foss-2023a.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/x/xskillscore/xskillscore-0.0.26-foss-2023a.eb diff --git a/easybuild/easyconfigs/x/xskillscore/xskillscore-0.0.26-foss-2023a.eb b/easybuild/easyconfigs/x/xskillscore/xskillscore-0.0.26-foss-2023a.eb new file mode 100644 index 00000000000..c8454e53dbb --- /dev/null +++ b/easybuild/easyconfigs/x/xskillscore/xskillscore-0.0.26-foss-2023a.eb @@ -0,0 +1,37 @@ +easyblock = "PythonBundle" + +name = 'xskillscore' +version = '0.0.26' + +homepage = 'https://xskillscore.readthedocs.io' +description = """ +xskillscore is an open source project and Python package that provides verification metrics of +deterministic (and probabilistic from properscoring) forecasts with xarray. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('dask', '2023.9.2'), + ('SciPy-bundle', '2023.07'), + ('statsmodels', '0.14.1'), + ('xarray', '2023.9.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('properscoring', '0.1', { + 'checksums': ['b0cc4963cc218b728d6c5f77b3259c8f835ae00e32e82678cdf6936049b93961'], + }), + ('xhistogram', '0.3.2', { + 'checksums': ['56b0751e1469eaed81710f644c8ba5c574b51883baa2feee26a95f2f708f91a1'], + }), + (name, version, { + 'checksums': ['780a424c1ab3eedf526a45ba8e6cf6dca61b17339252115a4e25ea8c5833ada5'], + }), +] + +moduleclass = 'geo' From 524adde76ed4be7075e5b046b55ad1d9416c0e5e Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Mon, 9 Sep 2024 11:51:19 +0200 Subject: [PATCH 034/107] adding easyconfigs: MOKIT-1.2.6_20240830-gfbf-2023a.eb --- .../MOKIT/MOKIT-1.2.6_20240830-gfbf-2023a.eb | 64 +++++++++++++++++++ 1 file changed, 64 insertions(+) create mode 100644 easybuild/easyconfigs/m/MOKIT/MOKIT-1.2.6_20240830-gfbf-2023a.eb diff --git a/easybuild/easyconfigs/m/MOKIT/MOKIT-1.2.6_20240830-gfbf-2023a.eb b/easybuild/easyconfigs/m/MOKIT/MOKIT-1.2.6_20240830-gfbf-2023a.eb new file mode 100644 index 00000000000..ace55d37c66 --- /dev/null +++ b/easybuild/easyconfigs/m/MOKIT/MOKIT-1.2.6_20240830-gfbf-2023a.eb @@ -0,0 +1,64 @@ +easyblock = 'Bundle' + +name = 'MOKIT' +version = '1.2.6_20240830' +_commit = 'd66560a6a7926e5e21b45cbcc9213aaa26bd997d' + +homepage = 'https://github.com/1234zou/MOKIT' +description = """ +MOKIT offers various utilities and modules to transfer MOs among various quantum chemistry software packages.""" + +toolchain = {'name': 'gfbf', 'version': '2023a'} +toolchainopts = {'openmp': True} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), +] + +_makefile = 'Makefile.gnu_openblas_conda' +maxparallel = 1 + +default_component_specs = { + 'source_urls': ['https://github.com/1234zou/MOKIT/archive'], + 'checksums': ['b4e7224ac5b56e6d0116f7759a3017c57d527b1d35c32e3b2733904f7f7c4de5'], + 'sources': [{ + 'download_filename': '%s.tar.gz' % _commit, + 'filename': SOURCE_TAR_GZ, + }], +} + +components = [ + (name, version, { + 'easyblock': 'MakeCp', + 'start_dir': 'MOKIT-%s/src' % _commit, + 'prebuildopts': 'sed -i -e "s/^MKL_FLAGS.*/MKL_FLAGS = $LIBBLAS/" %s && ' % _makefile, + 'buildopts': 'all -f %s' % _makefile, + 'files_to_copy': ['../bin'], + }), + ('mokit', version, { + 'easyblock': 'PythonPackage', + 'start_dir': 'MOKIT-%s' % _commit, + 'use_pip': True, + 'download_dep_fail': True, + 'sanity_pip_check': True, + 'options': {'modulename': 'mokit'}, + }), +] + +modextrapaths = { + 'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages'] +} + +sanity_check_commands = [ + 'fch2inp | grep Example', + 'geom_opt | grep Example', + "python -c 'from mokit.lib.gaussian import load_mol_from_fch'", +] + +sanity_check_paths = { + 'files': ['bin/geom_opt', 'bin/fch2inp'], + 'dirs': ['lib/python3.11/site-packages/mokit'], +} + +moduleclass = 'chem' From a93463e20ada01bcba7667121989a2e0ff2220c4 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen Date: Mon, 9 Sep 2024 11:10:17 +0000 Subject: [PATCH 035/107] adding easyconfigs: rustworkx-0.12.1-foss-2023a.eb --- .../rustworkx/rustworkx-0.12.1-foss-2023a.eb | 170 ++++++++++++++++++ 1 file changed, 170 insertions(+) create mode 100644 easybuild/easyconfigs/r/rustworkx/rustworkx-0.12.1-foss-2023a.eb diff --git a/easybuild/easyconfigs/r/rustworkx/rustworkx-0.12.1-foss-2023a.eb b/easybuild/easyconfigs/r/rustworkx/rustworkx-0.12.1-foss-2023a.eb new file mode 100644 index 00000000000..2a86b64c9ae --- /dev/null +++ b/easybuild/easyconfigs/r/rustworkx/rustworkx-0.12.1-foss-2023a.eb @@ -0,0 +1,170 @@ +easyblock = "CargoPythonPackage" + +name = 'rustworkx' +version = '0.12.1' + +homepage = 'https://github.com/Qiskit/rustworkx' +description = """rustworkx (previously retworkx) is a general purpose graph library for Python written in Rust to take +advantage of the performance and safety that Rust provides. It is designed to provide a high performance general +purpose graph library for any Python application.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('Rust', '1.75.0'), + ('setuptools-rust', '1.6.0'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), +] + +crates = [ + ('ahash', '0.7.6'), + ('autocfg', '1.1.0'), + ('bitflags', '1.3.2'), + ('cfg-if', '1.0.0'), + ('crossbeam-channel', '0.5.4'), + ('crossbeam-deque', '0.8.1'), + ('crossbeam-epoch', '0.9.8'), + ('crossbeam-utils', '0.8.8'), + ('either', '1.6.1'), + ('fixedbitset', '0.4.2'), + ('getrandom', '0.2.6'), + ('hashbrown', '0.11.2'), + ('hermit-abi', '0.1.19'), + ('indexmap', '1.7.0'), + ('indoc', '1.0.6'), + ('instant', '0.1.12'), + ('itoa', '1.0.2'), + ('lazy_static', '1.4.0'), + ('libc', '0.2.126'), + ('lock_api', '0.4.7'), + ('matrixmultiply', '0.2.4'), + ('memchr', '2.5.0'), + ('memoffset', '0.6.5'), + ('ndarray', '0.13.1'), + ('num-bigint', '0.4.3'), + ('num-complex', '0.2.4'), + ('num-complex', '0.4.1'), + ('num-integer', '0.1.45'), + ('num-traits', '0.2.15'), + ('num_cpus', '1.13.1'), + ('numpy', '0.17.2'), + ('once_cell', '1.12.0'), + ('parking_lot', '0.11.2'), + ('parking_lot_core', '0.8.5'), + ('petgraph', '0.6.2'), + ('ppv-lite86', '0.2.16'), + ('priority-queue', '1.2.0'), + ('proc-macro2', '1.0.39'), + ('pyo3', '0.17.3'), + ('pyo3-build-config', '0.17.3'), + ('pyo3-ffi', '0.17.3'), + ('pyo3-macros', '0.17.3'), + ('pyo3-macros-backend', '0.17.3'), + ('quick-xml', '0.22.0'), + ('quote', '1.0.18'), + ('rand', '0.8.5'), + ('rand_chacha', '0.3.1'), + ('rand_core', '0.6.3'), + ('rand_pcg', '0.3.1'), + ('rawpointer', '0.2.1'), + ('rayon', '1.5.3'), + ('rayon-core', '1.9.3'), + ('redox_syscall', '0.2.13'), + ('ryu', '1.0.10'), + ('scopeguard', '1.1.0'), + ('serde', '1.0.145'), + ('serde_derive', '1.0.145'), + ('serde_json', '1.0.89'), + ('smallvec', '1.8.0'), + ('syn', '1.0.96'), + ('target-lexicon', '0.12.4'), + ('unicode-ident', '1.0.0'), + ('unindent', '0.1.9'), + ('version_check', '0.9.4'), + ('wasi', '0.10.2+wasi-snapshot-preview1'), + ('winapi', '0.3.9'), + ('winapi-i686-pc-windows-gnu', '0.4.0'), + ('winapi-x86_64-pc-windows-gnu', '0.4.0'), +] +sources = [SOURCELOWER_TAR_GZ] +checksums = [ + {'rustworkx-0.12.1.tar.gz': '13a19a2f64dff086b3bffffb294c4630100ecbc13634b4995d9d36a481ae130e'}, + {'ahash-0.7.6.tar.gz': 'fcb51a0695d8f838b1ee009b3fbf66bda078cd64590202a864a8f3e8c4315c47'}, + {'autocfg-1.1.0.tar.gz': 'd468802bab17cbc0cc575e9b053f41e72aa36bfa6b7f55e3529ffa43161b97fa'}, + {'bitflags-1.3.2.tar.gz': 'bef38d45163c2f1dde094a7dfd33ccf595c92905c8f8f4fdc18d06fb1037718a'}, + {'cfg-if-1.0.0.tar.gz': 'baf1de4339761588bc0619e3cbc0120ee582ebb74b53b4efbf79117bd2da40fd'}, + {'crossbeam-channel-0.5.4.tar.gz': '5aaa7bd5fb665c6864b5f963dd9097905c54125909c7aa94c9e18507cdbe6c53'}, + {'crossbeam-deque-0.8.1.tar.gz': '6455c0ca19f0d2fbf751b908d5c55c1f5cbc65e03c4225427254b46890bdde1e'}, + {'crossbeam-epoch-0.9.8.tar.gz': '1145cf131a2c6ba0615079ab6a638f7e1973ac9c2634fcbeaaad6114246efe8c'}, + {'crossbeam-utils-0.8.8.tar.gz': '0bf124c720b7686e3c2663cf54062ab0f68a88af2fb6a030e87e30bf721fcb38'}, + {'either-1.6.1.tar.gz': 'e78d4f1cc4ae33bbfc157ed5d5a5ef3bc29227303d595861deb238fcec4e9457'}, + {'fixedbitset-0.4.2.tar.gz': '0ce7134b9999ecaf8bcd65542e436736ef32ddca1b3e06094cb6ec5755203b80'}, + {'getrandom-0.2.6.tar.gz': '9be70c98951c83b8d2f8f60d7065fa6d5146873094452a1008da8c2f1e4205ad'}, + {'hashbrown-0.11.2.tar.gz': 'ab5ef0d4909ef3724cc8cce6ccc8572c5c817592e9285f5464f8e86f8bd3726e'}, + {'hermit-abi-0.1.19.tar.gz': '62b467343b94ba476dcb2500d242dadbb39557df889310ac77c5d99100aaac33'}, + {'indexmap-1.7.0.tar.gz': 'bc633605454125dec4b66843673f01c7df2b89479b32e0ed634e43a91cff62a5'}, + {'indoc-1.0.6.tar.gz': '05a0bd019339e5d968b37855180087b7b9d512c5046fbd244cf8c95687927d6e'}, + {'instant-0.1.12.tar.gz': '7a5bbe824c507c5da5956355e86a746d82e0e1464f65d862cc5e71da70e94b2c'}, + {'itoa-1.0.2.tar.gz': '112c678d4050afce233f4f2852bb2eb519230b3cf12f33585275537d7e41578d'}, + {'lazy_static-1.4.0.tar.gz': 'e2abad23fbc42b3700f2f279844dc832adb2b2eb069b2df918f455c4e18cc646'}, + {'libc-0.2.126.tar.gz': '349d5a591cd28b49e1d1037471617a32ddcda5731b99419008085f72d5a53836'}, + {'lock_api-0.4.7.tar.gz': '327fa5b6a6940e4699ec49a9beae1ea4845c6bab9314e4f84ac68742139d8c53'}, + {'matrixmultiply-0.2.4.tar.gz': '916806ba0031cd542105d916a97c8572e1fa6dd79c9c51e7eb43a09ec2dd84c1'}, + {'memchr-2.5.0.tar.gz': '2dffe52ecf27772e601905b7522cb4ef790d2cc203488bbd0e2fe85fcb74566d'}, + {'memoffset-0.6.5.tar.gz': '5aa361d4faea93603064a027415f07bd8e1d5c88c9fbf68bf56a285428fd79ce'}, + {'ndarray-0.13.1.tar.gz': 'ac06db03ec2f46ee0ecdca1a1c34a99c0d188a0d83439b84bf0cb4b386e4ab09'}, + {'num-bigint-0.4.3.tar.gz': 'f93ab6289c7b344a8a9f60f88d80aa20032336fe78da341afc91c8a2341fc75f'}, + {'num-complex-0.2.4.tar.gz': 'b6b19411a9719e753aff12e5187b74d60d3dc449ec3f4dc21e3989c3f554bc95'}, + {'num-complex-0.4.1.tar.gz': '97fbc387afefefd5e9e39493299f3069e14a140dd34dc19b4c1c1a8fddb6a790'}, + {'num-integer-0.1.45.tar.gz': '225d3389fb3509a24c93f5c29eb6bde2586b98d9f016636dff58d7c6f7569cd9'}, + {'num-traits-0.2.15.tar.gz': '578ede34cf02f8924ab9447f50c28075b4d3e5b269972345e7e0372b38c6cdcd'}, + {'num_cpus-1.13.1.tar.gz': '19e64526ebdee182341572e50e9ad03965aa510cd94427a4549448f285e957a1'}, + {'numpy-0.17.2.tar.gz': 'a462c1af5ba1fddec1488c4646993a23ae7931f9e170ccba23e9c7c834277797'}, + {'once_cell-1.12.0.tar.gz': '7709cef83f0c1f58f666e746a08b21e0085f7440fa6a29cc194d68aac97a4225'}, + {'parking_lot-0.11.2.tar.gz': '7d17b78036a60663b797adeaee46f5c9dfebb86948d1255007a1d6be0271ff99'}, + {'parking_lot_core-0.8.5.tar.gz': 'd76e8e1493bcac0d2766c42737f34458f1c8c50c0d23bcb24ea953affb273216'}, + {'petgraph-0.6.2.tar.gz': 'e6d5014253a1331579ce62aa67443b4a658c5e7dd03d4bc6d302b94474888143'}, + {'ppv-lite86-0.2.16.tar.gz': 'eb9f9e6e233e5c4a35559a617bf40a4ec447db2e84c20b55a6f83167b7e57872'}, + {'priority-queue-1.2.0.tar.gz': 'cf40e51ccefb72d42720609e1d3c518de8b5800d723a09358d4a6d6245e1f8ca'}, + {'proc-macro2-1.0.39.tar.gz': 'c54b25569025b7fc9651de43004ae593a75ad88543b17178aa5e1b9c4f15f56f'}, + {'pyo3-0.17.3.tar.gz': '268be0c73583c183f2b14052337465768c07726936a260f480f0857cb95ba543'}, + {'pyo3-build-config-0.17.3.tar.gz': '28fcd1e73f06ec85bf3280c48c67e731d8290ad3d730f8be9dc07946923005c8'}, + {'pyo3-ffi-0.17.3.tar.gz': '0f6cb136e222e49115b3c51c32792886defbfb0adead26a688142b346a0b9ffc'}, + {'pyo3-macros-0.17.3.tar.gz': '94144a1266e236b1c932682136dc35a9dee8d3589728f68130c7c3861ef96b28'}, + {'pyo3-macros-backend-0.17.3.tar.gz': 'c8df9be978a2d2f0cdebabb03206ed73b11314701a5bfe71b0d753b81997777f'}, + {'quick-xml-0.22.0.tar.gz': '8533f14c8382aaad0d592c812ac3b826162128b65662331e1127b45c3d18536b'}, + {'quote-1.0.18.tar.gz': 'a1feb54ed693b93a84e14094943b84b7c4eae204c512b7ccb95ab0c66d278ad1'}, + {'rand-0.8.5.tar.gz': '34af8d1a0e25924bc5b7c43c079c942339d8f0a8b57c39049bef581b46327404'}, + {'rand_chacha-0.3.1.tar.gz': 'e6c10a63a0fa32252be49d21e7709d4d4baf8d231c2dbce1eaa8141b9b127d88'}, + {'rand_core-0.6.3.tar.gz': 'd34f1408f55294453790c48b2f1ebbb1c5b4b7563eb1f418bcfcfdbb06ebb4e7'}, + {'rand_pcg-0.3.1.tar.gz': '59cad018caf63deb318e5a4586d99a24424a364f40f1e5778c29aca23f4fc73e'}, + {'rawpointer-0.2.1.tar.gz': '60a357793950651c4ed0f3f52338f53b2f809f32d83a07f72909fa13e4c6c1e3'}, + {'rayon-1.5.3.tar.gz': 'bd99e5772ead8baa5215278c9b15bf92087709e9c1b2d1f97cdb5a183c933a7d'}, + {'rayon-core-1.9.3.tar.gz': '258bcdb5ac6dad48491bb2992db6b7cf74878b0384908af124823d118c99683f'}, + {'redox_syscall-0.2.13.tar.gz': '62f25bc4c7e55e0b0b7a1d43fb893f4fa1361d0abe38b9ce4f323c2adfe6ef42'}, + {'ryu-1.0.10.tar.gz': 'f3f6f92acf49d1b98f7a81226834412ada05458b7364277387724a237f062695'}, + {'scopeguard-1.1.0.tar.gz': 'd29ab0c6d3fc0ee92fe66e2d99f700eab17a8d57d1c1d3b748380fb20baa78cd'}, + {'serde-1.0.145.tar.gz': '728eb6351430bccb993660dfffc5a72f91ccc1295abaa8ce19b27ebe4f75568b'}, + {'serde_derive-1.0.145.tar.gz': '81fa1584d3d1bcacd84c277a0dfe21f5b0f6accf4a23d04d4c6d61f1af522b4c'}, + {'serde_json-1.0.89.tar.gz': '020ff22c755c2ed3f8cf162dbb41a7268d934702f3ed3631656ea597e08fc3db'}, + {'smallvec-1.8.0.tar.gz': 'f2dd574626839106c320a323308629dcb1acfc96e32a8cba364ddc61ac23ee83'}, + {'syn-1.0.96.tar.gz': '0748dd251e24453cb8717f0354206b91557e4ec8703673a4b30208f2abaf1ebf'}, + {'target-lexicon-0.12.4.tar.gz': 'c02424087780c9b71cc96799eaeddff35af2bc513278cda5c99fc1f5d026d3c1'}, + {'unicode-ident-1.0.0.tar.gz': 'd22af068fba1eb5edcb4aea19d382b2a3deb4c8f9d475c589b6ada9e0fd493ee'}, + {'unindent-0.1.9.tar.gz': '52fee519a3e570f7df377a06a1a7775cdbfb7aa460be7e08de2b1f0e69973a44'}, + {'version_check-0.9.4.tar.gz': '49874b5167b65d7193b8aba1567f5c7d93d001cafc34600cee003eda787e483f'}, + {'wasi-0.10.2+wasi-snapshot-preview1.tar.gz': 'fd6fbd9a79829dd1ad0cc20627bf1ed606756a7f77edff7b66b7064f9cb327c6'}, + {'winapi-0.3.9.tar.gz': '5c839a674fcd7a98952e593242ea400abe93992746761e38641405d28b00f419'}, + {'winapi-i686-pc-windows-gnu-0.4.0.tar.gz': 'ac3b87c63620426dd9b991e5ce0329eff545bccbbb34f3be09ff6fb6ab51b7b6'}, + {'winapi-x86_64-pc-windows-gnu-0.4.0.tar.gz': '712e227841d057c1ee1cd2fb22fa7e5a5461ae8e48fa2ca79ec42cfc1931183f'}, +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'math' From 2aff166c8715067650ff83415a1ecc256c47e7fd Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 9 Sep 2024 13:20:19 +0200 Subject: [PATCH 036/107] replace grpio with tensorboard in TensorFlow v2.15.1 --- .../easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a.eb index 0f3a94f2cc4..ebca59072d6 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a.eb @@ -47,7 +47,7 @@ dependencies = [ ('libpng', '1.6.39'), ('snappy', '1.1.10'), ('zlib', '1.2.13'), - ('grpcio', '1.57.0'), + ('tensorboard', '2.15.1'), ] # Dependencies created and updated using findPythonDeps, see: From 0551a2fab2c7337ba8945e676dfc50de217fa3e1 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Mon, 9 Sep 2024 15:32:58 +0200 Subject: [PATCH 037/107] adding easyconfigs: PyBullet-3.2.6-gfbf-2023a.eb --- .../p/PyBullet/PyBullet-3.2.6-gfbf-2023a.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyBullet/PyBullet-3.2.6-gfbf-2023a.eb diff --git a/easybuild/easyconfigs/p/PyBullet/PyBullet-3.2.6-gfbf-2023a.eb b/easybuild/easyconfigs/p/PyBullet/PyBullet-3.2.6-gfbf-2023a.eb new file mode 100644 index 00000000000..71c469fc41f --- /dev/null +++ b/easybuild/easyconfigs/p/PyBullet/PyBullet-3.2.6-gfbf-2023a.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonBundle' + +name = 'PyBullet' +version = '3.2.6' + +homepage = 'https://github.com/bulletphysics/bullet3' +description = """Bullet Physics SDK: real-time collision detection and +multi-physics simulation for VR, games, visual effects, robotics, +machine learning etc.""" + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +exts_list = [ + ('pybullet', version, { + 'checksums': ['da27525433c88698dc9fd8bc20fa4ae4d07738b4656633659ebd82c2d2884e08'], + }), +] + +moduleclass = 'vis' From 8b1c946254c044cc07411fa3d446c73d8f6ab9af Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 9 Sep 2024 18:00:53 +0200 Subject: [PATCH 038/107] adding easyconfigs: LDC-1.39.0-GCCcore-13.2.0.eb --- .../l/LDC/LDC-1.39.0-GCCcore-13.2.0.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/l/LDC/LDC-1.39.0-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/l/LDC/LDC-1.39.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/LDC/LDC-1.39.0-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..f0d3a361152 --- /dev/null +++ b/easybuild/easyconfigs/l/LDC/LDC-1.39.0-GCCcore-13.2.0.eb @@ -0,0 +1,39 @@ +easyblock = 'CMakeNinja' + +name = 'LDC' +version = '1.39.0' + +homepage = 'https://wiki.dlang.org/LDC' +description = "The LLVM-based D Compiler" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://github.com/ldc-developers/ldc/releases/download/v%(version)s'] +sources = ['ldc-%(version)s-src.tar.gz'] +checksums = ['839bac36f6073318e36f0b163767e03bdbd3f57d99256b97494ac439b59a4562'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.27.6'), + ('Ninja', '1.11.1'), + # building LDC from source requires LDC + ('LDC', '1.24.0', '-%(arch)s', SYSTEM), +] + +dependencies = [ + ('LLVM', '16.0.6'), +] + +configopts = "-DLLVM_ROOT_DIR=$EBROOTLLVM" + +sanity_check_paths = { + 'files': ['bin/ldc2', 'bin/ldmd2'], + 'dirs': ['include/d', 'lib'], +} + +sanity_check_commands = [ + "ldc2 --help", + "ldmd2 --help", +] + +moduleclass = 'lang' From 23d696d4e92520cfecf6a94b636998444335d659 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 10 Sep 2024 11:01:50 +0200 Subject: [PATCH 039/107] PyBullet: drop download_dep_fail, default in PythonBundle easyblock --- easybuild/easyconfigs/p/PyBullet/PyBullet-3.2.6-gfbf-2023a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyBullet/PyBullet-3.2.6-gfbf-2023a.eb b/easybuild/easyconfigs/p/PyBullet/PyBullet-3.2.6-gfbf-2023a.eb index 71c469fc41f..47fce7ec459 100644 --- a/easybuild/easyconfigs/p/PyBullet/PyBullet-3.2.6-gfbf-2023a.eb +++ b/easybuild/easyconfigs/p/PyBullet/PyBullet-3.2.6-gfbf-2023a.eb @@ -16,7 +16,6 @@ dependencies = [ ] use_pip = True -download_dep_fail = True sanity_pip_check = True exts_list = [ From 9cc9c7028df5beaafc27830c4c8cb28150591b5a Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Tue, 10 Sep 2024 16:37:29 +0200 Subject: [PATCH 040/107] python no user site --- .../easyconfigs/m/MOKIT/MOKIT-1.2.6_20240830-gfbf-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MOKIT/MOKIT-1.2.6_20240830-gfbf-2023a.eb b/easybuild/easyconfigs/m/MOKIT/MOKIT-1.2.6_20240830-gfbf-2023a.eb index ace55d37c66..5b4aedbdadb 100644 --- a/easybuild/easyconfigs/m/MOKIT/MOKIT-1.2.6_20240830-gfbf-2023a.eb +++ b/easybuild/easyconfigs/m/MOKIT/MOKIT-1.2.6_20240830-gfbf-2023a.eb @@ -53,7 +53,7 @@ modextrapaths = { sanity_check_commands = [ 'fch2inp | grep Example', 'geom_opt | grep Example', - "python -c 'from mokit.lib.gaussian import load_mol_from_fch'", + "python -s -c 'from mokit.lib.gaussian import load_mol_from_fch'", ] sanity_check_paths = { From 954060586f3caba6ddd538afd17cf1f95337cec6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Wed, 11 Sep 2024 08:57:26 +0200 Subject: [PATCH 041/107] adding easyconfigs: NanoStat-1.6.0-foss-2023a.eb, nanoget-1.19.3-foss-2023a.eb, nanomath-1.4.0-foss-2023a.eb --- .../n/NanoStat/NanoStat-1.6.0-foss-2023a.eb | 32 ++++++++++++++++++ .../n/nanoget/nanoget-1.19.3-foss-2023a.eb | 30 +++++++++++++++++ .../n/nanomath/nanomath-1.4.0-foss-2023a.eb | 33 +++++++++++++++++++ 3 files changed, 95 insertions(+) create mode 100644 easybuild/easyconfigs/n/NanoStat/NanoStat-1.6.0-foss-2023a.eb create mode 100644 easybuild/easyconfigs/n/nanoget/nanoget-1.19.3-foss-2023a.eb create mode 100644 easybuild/easyconfigs/n/nanomath/nanomath-1.4.0-foss-2023a.eb diff --git a/easybuild/easyconfigs/n/NanoStat/NanoStat-1.6.0-foss-2023a.eb b/easybuild/easyconfigs/n/NanoStat/NanoStat-1.6.0-foss-2023a.eb new file mode 100644 index 00000000000..8f0fa5a053c --- /dev/null +++ b/easybuild/easyconfigs/n/NanoStat/NanoStat-1.6.0-foss-2023a.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'NanoStat' +version = '1.6.0' + +homepage = 'https://github.com/wdecoster/nanostat' +description = """Calculate various statistics from a long read sequencing dataset in fastq, + bam or albacore sequencing summary format.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['e45fa8d1ab49bdaed17596c26c0af148b44e4af46238391a8bb7a1b4cc940079'] + +dependencies = [ + ('Python', '3.11.3'), + ('nanoget', '1.19.3'), + ('nanomath', '1.4.0'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/NanoStat'], + 'dirs': [], +} + +sanity_check_commands = ["NanoStat --help"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/nanoget/nanoget-1.19.3-foss-2023a.eb b/easybuild/easyconfigs/n/nanoget/nanoget-1.19.3-foss-2023a.eb new file mode 100644 index 00000000000..2aeb2ceaf26 --- /dev/null +++ b/easybuild/easyconfigs/n/nanoget/nanoget-1.19.3-foss-2023a.eb @@ -0,0 +1,30 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 +# Update: Petr Král (INUITS) + +easyblock = 'PythonPackage' + +name = 'nanoget' +version = '1.19.3' + +homepage = 'https://github.com/wdecoster/nanoget' +description = "Functions to extract information from Oxford Nanopore sequencing data and alignments" + +toolchain = {'name': 'foss', 'version': '2023a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['da981810edb1cbe42cbbfbe5fcf753f29bf5555204cd51256b28a284a036a71b'] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('Biopython', '1.83'), + ('Pysam', '0.22.0'), + ('nanomath', '1.4.0'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/nanomath/nanomath-1.4.0-foss-2023a.eb b/easybuild/easyconfigs/n/nanomath/nanomath-1.4.0-foss-2023a.eb new file mode 100644 index 00000000000..2a2f56955cc --- /dev/null +++ b/easybuild/easyconfigs/n/nanomath/nanomath-1.4.0-foss-2023a.eb @@ -0,0 +1,33 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 +# Update: Petr Král (INUITS) + +easyblock = 'PythonBundle' + +name = 'nanomath' +version = '1.4.0' + +homepage = 'https://github.com/wdecoster/nanomath' +description = "A few simple math functions for other Oxford Nanopore processing scripts" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('Python-Deprecated', '1.1.0', { + 'modulename': 'deprecated', + 'checksums': ['a242b3c1721f97912330b12cd5529abfa5b3876084a6c60a2c683a87d4b0dd6f'], + }), + (name, version, { + 'checksums': ['ed7a38fbb156d9a68a95c2570fe3c2035321d0a3e234580496750afca4927ced'], + }), +] + +moduleclass = 'math' From 48ab4ab6abc8cbc49010f56444b2f1ebadea22a6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Wed, 11 Sep 2024 09:06:23 +0200 Subject: [PATCH 042/107] adding easyconfigs: NanoFilt-2.8.0-foss-2023a.eb --- .../n/NanoFilt/NanoFilt-2.8.0-foss-2023a.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/n/NanoFilt/NanoFilt-2.8.0-foss-2023a.eb diff --git a/easybuild/easyconfigs/n/NanoFilt/NanoFilt-2.8.0-foss-2023a.eb b/easybuild/easyconfigs/n/NanoFilt/NanoFilt-2.8.0-foss-2023a.eb new file mode 100644 index 00000000000..fed069c1e75 --- /dev/null +++ b/easybuild/easyconfigs/n/NanoFilt/NanoFilt-2.8.0-foss-2023a.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'NanoFilt' +version = '2.8.0' + +homepage = 'https://github.com/wdecoster/nanofilt' +description = """Filtering and trimming of long read sequencing data.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['47f4f4f8be834f011570a8d76d07cc12abe0686c8917607316a8ccfb3e20758c'] + +dependencies = [ + ('Python', '3.11.3'), + ('Biopython', '1.83'), +] + +download_dep_fail = True +use_pip = True + +sanity_check_commands = ["NanoFilt --help"] + +sanity_pip_check = True + +moduleclass = 'bio' From c1001dec254d845d3735a206895b23ed64643c40 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Wed, 11 Sep 2024 09:07:19 +0200 Subject: [PATCH 043/107] adding easyconfigs: NanoLyse-1.2.1-foss-2023a.eb --- .../n/NanoLyse/NanoLyse-1.2.1-foss-2023a.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/n/NanoLyse/NanoLyse-1.2.1-foss-2023a.eb diff --git a/easybuild/easyconfigs/n/NanoLyse/NanoLyse-1.2.1-foss-2023a.eb b/easybuild/easyconfigs/n/NanoLyse/NanoLyse-1.2.1-foss-2023a.eb new file mode 100644 index 00000000000..1b21ec42201 --- /dev/null +++ b/easybuild/easyconfigs/n/NanoLyse/NanoLyse-1.2.1-foss-2023a.eb @@ -0,0 +1,48 @@ +## +# This is a contribution from SIB Swiss Institute of Bioinformatics +# Homepage: https://www.sib.swiss/research-infrastructure/competence-centers/vital-it +# +# Authors:: Sebastien Moretti +# +# Update: Petr Král (INUITS) +## + +easyblock = 'PythonBundle' + +name = 'NanoLyse' +version = '1.2.1' + +homepage = 'https://github.com/wdecoster/nanolyse' +description = """Remove reads mapping to the lambda phage genome from a fastq file.""" +software_license = 'LicenseGPLv3' + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('Biopython', '1.83'), + ('minimap2', '2.26'), +] + +use_pip = True + +# Fetch the tar.gz, not the whl files! +exts_list = [ + ('mappy', '2.28', { + 'checksums': ['0ebf7a5d62bd668f5456028215e26176e180ca68161ac18d4f7b48045484cebb'], + }), + (name, version, { + 'checksums': ['933ee668da805fc9ec9fa86c9fca81a073438d45b5f64e23cf606c01e715b1d5'], + }), +] + +sanity_check_paths = { + 'files': ['bin/NanoLyse'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["NanoLyse --version"] + +sanity_pip_check = True + +moduleclass = 'bio' From f0f1e6b727136bd358d2fe0f17a940d777f67ba8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Wed, 11 Sep 2024 09:51:04 +0200 Subject: [PATCH 044/107] adding easyconfigs: nanoQC-0.9.4-foss-2023a.eb --- .../n/nanoQC/nanoQC-0.9.4-foss-2023a.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/n/nanoQC/nanoQC-0.9.4-foss-2023a.eb diff --git a/easybuild/easyconfigs/n/nanoQC/nanoQC-0.9.4-foss-2023a.eb b/easybuild/easyconfigs/n/nanoQC/nanoQC-0.9.4-foss-2023a.eb new file mode 100644 index 00000000000..d0efa23525d --- /dev/null +++ b/easybuild/easyconfigs/n/nanoQC/nanoQC-0.9.4-foss-2023a.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'nanoQC' +version = '0.9.4' + +homepage = 'https://github.com/wdecoster/nanoQC' +description = """Quality control tools for long read sequencing + data aiming to replicate some of the plots made by fastQC.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['05685656138cbaf099b18831d1ceeaca93faf3399881cc2efda44c04d3b316e3'] + +dependencies = [ + ('Python', '3.11.3'), + ('Biopython', '1.83'), + ('SciPy-bundle', '2023.07'), + ('bokeh', '3.2.2'), +] + +download_dep_fail = True +use_pip = True + +options = {'modulename': 'nanoQC'} + +sanity_check_commands = ["nanoQC --help"] + +sanity_pip_check = True + +moduleclass = 'tools' From afd298bbfc666f3a707991ca8d2d0b4aa6a536c7 Mon Sep 17 00:00:00 2001 From: ankekreuzer Date: Wed, 11 Sep 2024 12:33:34 +0200 Subject: [PATCH 045/107] Added ccache, PROJ, protobuf(-python), pytest-flakefinder, RDFlib, RapidJSON and Seaborn. --- .../c/ccache/ccache-4.10.2-GCCcore-13.3.0.eb | 49 +++++++++++++++++++ .../p/PROJ/PROJ-9.4.1-GCCcore-13.3.0.eb | 49 +++++++++++++++++++ .../protobuf-python-5.28.0-GCCcore-13.3.0.eb | 35 +++++++++++++ .../protobuf/protobuf-28.0-GCCcore-13.3.0.eb | 35 +++++++++++++ ...pytest-flakefinder-1.1.0-GCCcore-13.3.0.eb | 24 +++++++++ .../r/RDFlib/RDFlib-7.0.0-GCCcore-13.3.0.eb | 35 +++++++++++++ ...RapidJSON-1.1.0-20240815-GCCcore-13.3.0.eb | 31 ++++++++++++ .../s/Seaborn/Seaborn-0.13.2-gfbf-2024a.eb | 24 +++++++++ 8 files changed, 282 insertions(+) create mode 100644 easybuild/easyconfigs/c/ccache/ccache-4.10.2-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/p/PROJ/PROJ-9.4.1-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/p/protobuf-python/protobuf-python-5.28.0-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/p/protobuf/protobuf-28.0-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/p/pytest-flakefinder/pytest-flakefinder-1.1.0-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/r/RDFlib/RDFlib-7.0.0-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/r/RapidJSON/RapidJSON-1.1.0-20240815-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/s/Seaborn/Seaborn-0.13.2-gfbf-2024a.eb diff --git a/easybuild/easyconfigs/c/ccache/ccache-4.10.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/c/ccache/ccache-4.10.2-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..5a6b4ee2256 --- /dev/null +++ b/easybuild/easyconfigs/c/ccache/ccache-4.10.2-GCCcore-13.3.0.eb @@ -0,0 +1,49 @@ +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL + +easyblock = 'CMakeNinja' + +name = 'ccache' +version = '4.10.2' + +homepage = 'https://ccache.dev/' +description = """Ccache (or “ccache”) is a compiler cache. It speeds up recompilation by +caching previous compilations and detecting when the same compilation is being done again""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [GITHUB_RELEASE] +sources = [SOURCE_TAR_GZ] +checksums = ['108100960bb7e64573ea925af2ee7611701241abb36ce0aae3354528403a7d87'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), + ('Ninja', '1.12.1'), + ('zstd', '1.5.6'), + ('pkgconf', '2.2.0'), +] + +dependencies = [ + ('hiredis', '1.2.0'), +] + +# use BFD linker rather than default ld.gold (required on CentOS 8) +preconfigopts = 'LDFLAGS="-fuse-ld=bfd"' +configopts = ' '.join([ + '-DENABLE_DOCUMENTATION=OFF', + '-DENABLE_IPO=ON', + # Link most libraries statically + '-DSTATIC_LINK=ON', + # Disable downloading dependencies + '-DZSTD_FROM_INTERNET=OFF -DHIREDIS_FROM_INTERNET=OFF', +]) + +sanity_check_paths = { + 'files': ['bin/ccache'], + 'dirs': [] +} +sanity_check_commands = ['ccache --help'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/PROJ/PROJ-9.4.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/PROJ/PROJ-9.4.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..1307155f8f7 --- /dev/null +++ b/easybuild/easyconfigs/p/PROJ/PROJ-9.4.1-GCCcore-13.3.0.eb @@ -0,0 +1,49 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2014-2015 The Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# +## +easyblock = 'CMakeMake' + +name = 'PROJ' +version = '9.4.1' + +homepage = 'https://proj.org' +description = """Program proj is a standard Unix filter function which converts +geographic longitude and latitude coordinates into cartesian coordinates""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://download.osgeo.org/proj/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['ffe20170ee2b952207adf8a195e2141eab12cda181e49fdeb54425d98c7171d7'] + +builddependencies = [ + ('pkgconf', '2.2.0'), + ('binutils', '2.42'), + ('CMake', '3.29.3'), + ('googletest', '1.15.2'), +] + +dependencies = [ + ('SQLite', '3.45.3'), + ('LibTIFF', '4.6.0'), + ('cURL', '8.7.1'), + ('XZ', '5.4.5'), + ('nlohmann_json', '3.11.3'), +] + +# build twice, once for static, once for shared libraries +configopts = ['', '-DBUILD_SHARED_LIBS=OFF'] + +sanity_check_paths = { + 'files': ['bin/cct', 'bin/cs2cs', 'bin/geod', 'bin/gie', 'bin/proj', 'bin/projinfo', + 'lib/libproj.a', 'lib/libproj.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/protobuf-python/protobuf-python-5.28.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-5.28.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..ed4aac1448e --- /dev/null +++ b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-5.28.0-GCCcore-13.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonPackage' + +name = 'protobuf-python' +version = '5.28.0' + +homepage = 'https://github.com/google/protobuf/' +description = "Python Protocol Buffers runtime library." + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://pypi.python.org/packages/source/p/protobuf'] +sources = ['protobuf-%(version)s.tar.gz'] +checksums = ['dde74af0fa774fa98892209992295adbfb91da3fa98c8f67a88afe8f5a349add'] + +builddependencies = [('binutils', '2.42')] + +dependencies = [ + ('Python', '3.12.3'), + ('protobuf', version[2:]), # Major version is only used for the Python bindings +] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +options = {'modulename': 'google.protobuf'} + +# Make sure protobuf is installed as a regular folder or it will not be found if +# other google packages are installed in other site-packages folders +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/google/protobuf'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/protobuf/protobuf-28.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/protobuf/protobuf-28.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..b5f959fc06b --- /dev/null +++ b/easybuild/easyconfigs/p/protobuf/protobuf-28.0-GCCcore-13.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'CMakeMake' + +name = 'protobuf' +version = '28.0' + +homepage = 'https://github.com/protocolbuffers/protobuf' +description = """Protocol Buffers (a.k.a., protobuf) are Google's +language-neutral, platform-neutral, extensible mechanism for +serializing structured data.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +github_account = 'protocolbuffers' +source_urls = [GITHUB_RELEASE] +sources = [SOURCE_TAR_GZ] +checksums = ['13e7749c30bc24af6ee93e092422f9dc08491c7097efa69461f88eb5f61805ce'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), +] +dependencies = [ + ('Abseil', '20240722.0'), +] + +srcdir = '.' + +configopts = '-Dprotobuf_BUILD_TESTS=OFF -Dprotobuf_BUILD_SHARED_LIBS=ON -Dprotobuf_ABSL_PROVIDER="package" ' + +sanity_check_paths = { + 'files': ['bin/protoc', 'lib/libprotobuf.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/pytest-flakefinder/pytest-flakefinder-1.1.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/pytest-flakefinder/pytest-flakefinder-1.1.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..7a512df4e25 --- /dev/null +++ b/easybuild/easyconfigs/p/pytest-flakefinder/pytest-flakefinder-1.1.0-GCCcore-13.3.0.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'pytest-flakefinder' +version = '1.1.0' + +homepage = 'https://github.com/dropbox/pytest-flakefinder' +description = "Runs tests multiple times to expose flakiness." + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [('binutils', '2.42')] +dependencies = [ + ('Python', '3.12.3'), + ('Python-bundle-PyPI', '2024.06'), +] + +sources = [SOURCE_TAR_GZ] +checksums = ['e2412a1920bdb8e7908783b20b3d57e9dad590cc39a93e8596ffdd493b403e0e'] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/r/RDFlib/RDFlib-7.0.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/r/RDFlib/RDFlib-7.0.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..4be8dccf690 --- /dev/null +++ b/easybuild/easyconfigs/r/RDFlib/RDFlib-7.0.0-GCCcore-13.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonBundle' + +name = 'RDFlib' +version = '7.0.0' + +homepage = 'https://github.com/RDFLib/rdflib' +description = """RDFLib is a Python library for working with RDF, a simple yet powerful language + for representing information.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [ + ('binutils', '2.42'), + ('poetry', '1.8.3'), +] + +dependencies = [ + ('Python', '3.12.3'), + ('Python-bundle-PyPI', '2024.06'), +] + +use_pip = True + +exts_list = [ + ('isodate', '0.6.1', { + 'checksums': ['48c5881de7e8b0a0d648cb024c8062dc84e7b840ed81e864c7614fd3c127bde9'], + }), + ('rdflib', version, { + 'checksums': ['9995eb8569428059b8c1affd26b25eac510d64f5043d9ce8c84e0d0036e995ae'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/r/RapidJSON/RapidJSON-1.1.0-20240815-GCCcore-13.3.0.eb b/easybuild/easyconfigs/r/RapidJSON/RapidJSON-1.1.0-20240815-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..b296d76e7b7 --- /dev/null +++ b/easybuild/easyconfigs/r/RapidJSON/RapidJSON-1.1.0-20240815-GCCcore-13.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'CMakeMake' + +name = 'RapidJSON' +# no new release since Aug'16 so using latest commit; +# see also https://github.com/Tencent/rapidjson/issues/2202 +version = '1.1.0-20240815' +local_commit = '7c73dd7' + +homepage = 'https://rapidjson.org' +description = "A fast JSON parser/generator for C++ with both SAX/DOM style API" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/Tencent/%(namelower)s/archive/'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': 'v%(version)s.tar.gz'}] +checksums = ['91138ebc9c980e554e6bcf9d13537f9eebf42710e0b956fdca46181ad645f94d'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), +] + +# strip out hardcoded use of -march=native, EasyBuild should be in control of this +preconfigopts = "sed -i 's/-march=native//g' ../rapidjson-*/CMakeLists.txt && " + +sanity_check_paths = { + 'files': ['lib/pkgconfig/%(name)s.pc'], + 'dirs': ['include/%(namelower)s', 'lib/cmake', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/Seaborn/Seaborn-0.13.2-gfbf-2024a.eb b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.13.2-gfbf-2024a.eb new file mode 100644 index 00000000000..de14ff81ce9 --- /dev/null +++ b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.13.2-gfbf-2024a.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'Seaborn' +version = '0.13.2' + +homepage = 'https://seaborn.pydata.org/' +description = """ Seaborn is a Python visualization library based on matplotlib. + It provides a high-level interface for drawing attractive statistical graphics. """ + +toolchain = {'name': 'gfbf', 'version': '2024a'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['93e60a40988f4d65e9f4885df477e2fdaff6b73a9ded434c1ab356dd57eefff7'] + +dependencies = [ + ('Python', '3.12.3'), + ('matplotlib', '3.9.2'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'bio' From 6772363f449e4f05ac75e63b35c21bbc45a3b9b8 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 11 Sep 2024 15:36:16 +0200 Subject: [PATCH 046/107] unbundle tensorboard from TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb --- ...ensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb | 62 +------------------ 1 file changed, 1 insertion(+), 61 deletions(-) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb index 1d1c871f3d5..7b2f4888b23 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb @@ -51,7 +51,7 @@ dependencies = [ ('libpng', '1.6.39'), ('snappy', '1.1.10'), ('zlib', '1.2.13'), - ('grpcio', '1.57.0'), + ('tensorboard', '2.15.1'), ] # Dependencies created and updated using findPythonDeps, see: @@ -71,48 +71,6 @@ exts_list = [ 'source_tmpl': 'tensorflow_estimator-%(version)s-py2.py3-none-any.whl', 'checksums': ['aedf21eec7fb2dc91150fc91a1ce12bc44dbb72278a08b58e79ff87c9e28f153'], }), - ('Werkzeug', '3.0.2', { - 'source_tmpl': SOURCELOWER_TAR_GZ, - 'checksums': ['e39b645a6ac92822588e7b39a692e7828724ceae0b0d702ef96701f90e70128d'], - }), - ('tensorboard-data-server', '0.7.2', { - 'source_tmpl': 'tensorboard_data_server-%(version)s-py3-none-any.whl', - 'checksums': ['7e0610d205889588983836ec05dc098e80f97b7e7bbff7e994ebb78f578d0ddb'], - }), - ('Markdown', '3.6', { - 'checksums': ['ed4f41f6daecbeeb96e576ce414c41d2d876daa9a16cb35fa8ed8c2ddfad0224'], - }), - ('oauthlib', '3.2.2', { - 'checksums': ['9859c40929662bec5d64f34d01c99e093149682a3f38915dc0655d5a633dd918'], - }), - ('requests-oauthlib', '2.0.0', { - 'checksums': ['b3dffaebd884d8cd778494369603a9e7b58d29111bf6b41bdc2dcd87203af4e9'], - }), - ('rsa', '4.9', { - 'checksums': ['e38464a49c6c85d7f1351b0126661487a7e0a14a50f1675ec50eb34d4f20ef21'], - }), - ('pyasn1-modules', '0.4.0', { - 'source_tmpl': 'pyasn1_modules-%(version)s.tar.gz', - 'checksums': ['831dbcea1b177b28c9baddf4c6d1013c24c3accd14a1873fffaa6a2e905f17b6'], - }), - ('cachetools', '5.3.3', { - 'checksums': ['ba29e2dfa0b8b556606f097407ed1aa62080ee108ab0dc5ec9d6a723a007d105'], - }), - ('google-auth', '2.29.0', { - 'modulename': 'google.auth', - 'checksums': ['672dff332d073227550ffc7457868ac4218d6c500b155fe6cc17d2b13602c360'], - }), - ('google-auth-oauthlib', '1.2.0', { - 'checksums': ['292d2d3783349f2b0734a0a0207b1e1e322ac193c2c09d8f7c613fb7cc501ea8'], - }), - ('absl-py', '2.1.0', { - 'modulename': 'absl', - 'checksums': ['7820790efbb316739cde8b4e19357243fc3608a152024288513dd968d7d959ff'], - }), - ('tensorboard', '2.15.2', { - 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', - 'checksums': ['a6f6443728064d962caea6d34653e220e34ef8df764cb06a8212c17e1a8f0622'], - }), ('keras', '2.15.0', { 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', 'checksums': ['2dcc6d2e30cf9c951064b63c1f4c404b966c59caf09e01f3549138ec8ee0dd1f'], @@ -131,15 +89,6 @@ exts_list = [ ('astor', '0.8.1', { 'checksums': ['6a6effda93f4e1ce9f618779b2dd1d9d84f1e32812c23a29b3fff6fd7f63fa5e'], }), - # Optional profile plugin + dependency - ('gviz-api', '1.10.0', { - 'source_tmpl': 'gviz_api-%(version)s.tar.gz', - 'checksums': ['846692dd8cc73224fc31b18e41589bd934e1cc05090c6576af4b4b26c2e71b90'], - }), - ('tensorboard-plugin-profile', '2.15.1', { - 'source_tmpl': 'tensorboard_plugin_profile-%(version)s.tar.gz', - 'checksums': ['84bb33e446eb4a9c0616f669fc6a42cdd40eadd9ae1d74bf756f4f0479993273'], - }), (name, version, { 'patches': [ 'TensorFlow-2.1.0_fix-cuda-build.patch', @@ -226,13 +175,4 @@ exts_list = [ }), ] -# Taken from tensorboard-2.15.1-gfbf-2023a.eb: -# Relax restriction on protobuf dependency as issue was fixed -# in https://github.com/protocolbuffers/upb/pull/1514 -# see also: https://github.com/easybuilders/easybuild-easyconfigs/pull/19671 -postinstallcmds = [ - 'sed -i "s/Requires-Dist: protobuf.*/Requires-Dist: protobuf >=3.19.6/g" ' + - '%(installdir)s/lib/python%(pyshortver)s/site-packages/tensorboard-2.15.2.dist-info/METADATA', -] - moduleclass = 'lib' From 04ac5d75fe57aaaa19589ade51a2a34c1042c7a7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 11 Sep 2024 21:57:48 +0200 Subject: [PATCH 047/107] {phys}[GCC/12.3.0] GATE v9.4, CLHEP v2.4.7.1, Geant4 v11.2.2, Geant4-data v11.2 --- .../c/CLHEP/CLHEP-2.4.7.1-GCC-12.3.0.eb | 29 ++++++++++ .../easyconfigs/g/GATE/GATE-9.4-foss-2023a.eb | 29 ++++++++++ .../g/Geant4-data/Geant4-data-11.2.eb | 54 +++++++++++++++++++ .../g/Geant4/Geant4-11.2.2-GCC-12.3.0.eb | 48 +++++++++++++++++ 4 files changed, 160 insertions(+) create mode 100644 easybuild/easyconfigs/c/CLHEP/CLHEP-2.4.7.1-GCC-12.3.0.eb create mode 100644 easybuild/easyconfigs/g/GATE/GATE-9.4-foss-2023a.eb create mode 100644 easybuild/easyconfigs/g/Geant4-data/Geant4-data-11.2.eb create mode 100644 easybuild/easyconfigs/g/Geant4/Geant4-11.2.2-GCC-12.3.0.eb diff --git a/easybuild/easyconfigs/c/CLHEP/CLHEP-2.4.7.1-GCC-12.3.0.eb b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.4.7.1-GCC-12.3.0.eb new file mode 100644 index 00000000000..4bf02eab9a1 --- /dev/null +++ b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.4.7.1-GCC-12.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'CMakeMake' + +name = 'CLHEP' +version = '2.4.7.1' + +homepage = 'https://proj-clhep.web.cern.ch/proj-clhep/' +description = """The CLHEP project is intended to be a set of HEP-specific foundation and + utility classes such as random generators, physics vectors, geometry and linear algebra. + CLHEP is structured in a set of packages independent of any external package.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://proj-clhep.web.cern.ch/proj-clhep/dist1/'] +sources = [SOURCELOWER_TGZ] +checksums = ['1c8304a7772ac6b99195f1300378c6e3ddf4ad07c85d64a04505652abb8a55f9'] + +builddependencies = [ + ('CMake', '3.26.3'), +] + +sanity_check_paths = { + 'files': ['bin/clhep-config', 'lib/libCLHEP.a', 'lib/libCLHEP.%s' % SHLIB_EXT], + 'dirs': ['include/CLHEP'], +} + +sanity_check_commands = ["clhep-config --help"] + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/g/GATE/GATE-9.4-foss-2023a.eb b/easybuild/easyconfigs/g/GATE/GATE-9.4-foss-2023a.eb new file mode 100644 index 00000000000..6fd245d2079 --- /dev/null +++ b/easybuild/easyconfigs/g/GATE/GATE-9.4-foss-2023a.eb @@ -0,0 +1,29 @@ +name = 'GATE' +version = '9.4' + +homepage = 'http://www.opengatecollaboration.org/' +description = """GATE is an advanced opensource software developed by the international OpenGATE collaboration and + dedicated to the numerical simulations in medical imaging. It currently supports simulations of Emission Tomography + (Positron Emission Tomography - PET and Single Photon Emission Computed Tomography - SPECT), and Computed Tomography""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/OpenGATE/Gate/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['96c53f6ab1b25c0e540d8f9564bce0049371b378de80a7118a0ff8834c6c117c'] + +builddependencies = [ + ('CMake', '3.26.3'), +] +dependencies = [ + ('Geant4', '11.2.2'), + ('CLHEP', '2.4.7.1'), + ('ROOT', '6.30.06'), +] + +preinstallopts = "sed -i 's|/usr/local/bin|%(installdir)s/bin|g' Makefile &&" + +# enable extra capabilities (Davis requires Geant4 10.04 or newer) +configopts = "-DGATE_USE_OPTICAL=1 -DGATE_USE_DAVIS=1" + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/g/Geant4-data/Geant4-data-11.2.eb b/easybuild/easyconfigs/g/Geant4-data/Geant4-data-11.2.eb new file mode 100644 index 00000000000..a085843d7d2 --- /dev/null +++ b/easybuild/easyconfigs/g/Geant4-data/Geant4-data-11.2.eb @@ -0,0 +1,54 @@ +easyblock = 'Tarball' +name = 'Geant4-data' +version = '11.2' # version should somewhat match the Geant4 version it should be used in + +homepage = 'https://geant4.web.cern.ch/' +description = """Datasets for Geant4.""" + +toolchain = SYSTEM + +# Pick up the correct sets and versions from cmake/Modules/G4DatasetDefinitions.cmake +# in the Geant source, +# see also https://github.com/Geant4/geant4/blob/v11.2.2/cmake/Modules/G4DatasetDefinitions.cmake +local_datasets = [ + ('G4NDL', '4.7.1', 'G4NDL', 'G4NEUTRONHPDATA'), # NDL + ('G4EMLOW', '8.5', 'G4EMLOW', 'G4LEDATA'), # Low energy electromagnetics + ('PhotonEvaporation', '5.7', 'G4PhotonEvaporation', 'G4LEVELGAMMADATA'), # Photon evaporation + ('RadioactiveDecay', '5.6', 'G4RadioactiveDecay', 'G4RADIOACTIVEDATA'), # Radioisotopes + ('G4SAIDDATA', '2.0', 'G4SAIDDATA', 'G4SAIDXSDATA'), # SAID + ('G4PARTICLEXS', '4.0', 'G4PARTICLEXS', 'G4PARTICLEXSDATA'), # Particle XS - replaces Neutron XS + ('G4PII', '1.3', 'G4PII', 'G4PIIDATA'), # PII + ('RealSurface', '2.2', 'G4RealSurface', 'G4REALSURFACEDATA'), # Optical Surfaces + ('G4ABLA', '3.3', 'G4ABLA', 'G4ABLADATA'), # ABLA + ('G4INCL', '1.2', 'G4INCL', 'G4INCLDATA'), # INCL + ('G4ENSDFSTATE', '2.3', 'G4ENSDFSTATE', 'G4ENSDFSTATEDATA'), # ENSDFSTATE + ('G4TENDL', '1.4', 'G4TENDL', 'G4PARTICLEHPDATA'), # TENDL +] + +source_urls = ['https://cern.ch/geant4-data/datasets'] +sources = ['%s.%s.tar.gz' % (x[2], x[1]) for x in local_datasets] +checksums = [ + {'G4NDL.4.7.1.tar.gz': 'd3acae48622118d2579de24a54d533fb2416bf0da9dd288f1724df1485a46c7c'}, + {'G4EMLOW.8.5.tar.gz': '66baca49ac5d45e2ac10c125b4fb266225e511803e66981909ce9cd3e9bcef73'}, + {'G4PhotonEvaporation.5.7.tar.gz': '761e42e56ffdde3d9839f9f9d8102607c6b4c0329151ee518206f4ee9e77e7e5'}, + {'G4RadioactiveDecay.5.6.tar.gz': '3886077c9c8e5a98783e6718e1c32567899eeb2dbb33e402d4476bc2fe4f0df1'}, + {'G4SAIDDATA.2.0.tar.gz': '1d26a8e79baa71e44d5759b9f55a67e8b7ede31751316a9e9037d80090c72e91'}, + {'G4PARTICLEXS.4.0.tar.gz': '9381039703c3f2b0fd36ab4999362a2c8b4ff9080c322f90b4e319281133ca95'}, + {'G4PII.1.3.tar.gz': '6225ad902675f4381c98c6ba25fc5a06ce87549aa979634d3d03491d6616e926'}, + {'G4RealSurface.2.2.tar.gz': '9954dee0012f5331267f783690e912e72db5bf52ea9babecd12ea22282176820'}, + {'G4ABLA.3.3.tar.gz': '1e041b3252ee9cef886d624f753e693303aa32d7e5ef3bba87b34f36d92ea2b1'}, + {'G4INCL.1.2.tar.gz': 'f880b16073ee0a92d7494f3276a6d52d4de1d3677a0d4c7c58700396ed0e1a7e'}, + {'G4ENSDFSTATE.2.3.tar.gz': '9444c5e0820791abd3ccaace105b0e47790fadce286e11149834e79c4a8e9203'}, + {'G4TENDL.1.4.tar.gz': '4b7274020cc8b4ed569b892ef18c2e088edcdb6b66f39d25585ccee25d9721e0'}, +] + +start_dir = '..' + +modextrapaths = {x[3]: x[0] + x[1] for x in local_datasets} + +sanity_check_paths = { + 'files': [], + 'dirs': [x[0] + x[1] for x in local_datasets], +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/g/Geant4/Geant4-11.2.2-GCC-12.3.0.eb b/easybuild/easyconfigs/g/Geant4/Geant4-11.2.2-GCC-12.3.0.eb new file mode 100644 index 00000000000..d4cdf6c78cb --- /dev/null +++ b/easybuild/easyconfigs/g/Geant4/Geant4-11.2.2-GCC-12.3.0.eb @@ -0,0 +1,48 @@ +name = 'Geant4' +version = '11.2.2' + +homepage = 'https://geant4.web.cern.ch/' +description = """Geant4 is a toolkit for the simulation of the passage of particles through matter. + Its areas of application include high energy, nuclear and accelerator physics, + as well as studies in medical and space science.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +github_account = 'Geant4' +source_urls = [GITHUB_SOURCE] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCELOWER_TAR_GZ}] +patches = [ + 'Geant4-11.1.2_use_data_env_vars_from_Geant4-data_module.patch', +] +checksums = [ + {'geant4-11.2.2.tar.gz': '0b0cfce14e9143079c4440d27ee21f889c4c4172ac5ee7586746b940ffcf812a'}, + {'Geant4-11.1.2_use_data_env_vars_from_Geant4-data_module.patch': + '822265b7cbcaacdffd28b1094786a3c94122aff63338e514d5d3810cdf9218a6'}, +] + +builddependencies = [ + ('CMake', '3.26.3'), +] + +dependencies = [ + ('expat', '2.5.0'), + # recommended CLHEP version, see https://geant4.web.cern.ch/download/release-notes/notes-v11.1.0.html + ('CLHEP', '2.4.7.1'), + ('Xerces-C++', '3.2.4'), + ('Qt5', '5.15.10'), + ('Geant4-data', '11.2', '', SYSTEM), +] + +_copts = [ + "-DGEANT4_INSTALL_DATA=OFF", + "-DGEANT4_USE_SYSTEM_ZLIB=ON", + "-DGEANT4_USE_SYSTEM_EXPAT=ON", + "-DGEANT4_USE_SYSTEM_CLHEP=ON", + "-DGEANT4_USE_QT=ON", + "-DGEANT4_USE_GDML=ON", + "-DGEANT4_USE_OPENGL_X11=ON", + "-DGEANT4_USE_RAYTRACER_X11=ON", +] +configopts = ' '.join(_copts) + +moduleclass = 'phys' From c684b96d0e803f4f20f647152e64bfd380a63945 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 12 Sep 2024 12:45:48 +0200 Subject: [PATCH 048/107] adding easyconfigs: dub-1.38.1-GCCcore-13.2.0.eb --- .../d/dub/dub-1.38.1-GCCcore-13.2.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/d/dub/dub-1.38.1-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/d/dub/dub-1.38.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/d/dub/dub-1.38.1-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..cfd077260fb --- /dev/null +++ b/easybuild/easyconfigs/d/dub/dub-1.38.1-GCCcore-13.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'CmdCp' + +name = 'dub' +version = '1.38.1' + +homepage = 'https://github.com/dlang/dub' +description = "Package and build manager for D applications and libraries" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://github.com/dlang/dub/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['a7c9a2f819fdea7359f298cba76e81a24ca1536d756c3b4b98c2480463c37907'] + +builddependencies = [ + ('binutils', '2.40'), + ('LDC', '1.39.0'), +] + +cmds_map = [('.*', "ldmd2 -v -run build.d")] + +files_to_copy = [(['bin/dub'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/dub'], + 'dirs': [], +} + +sanity_check_commands = ["dub --help"] + +moduleclass = 'lang' From bd3714e0135d2196db6fb29d545d3618520a218f Mon Sep 17 00:00:00 2001 From: Paul Melis Date: Thu, 12 Sep 2024 15:32:24 +0200 Subject: [PATCH 049/107] Added libGLU-9.0.3-GCCcore-13.3.0.eb --- .../l/libGLU/libGLU-9.0.3-GCCcore-13.3.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/l/libGLU/libGLU-9.0.3-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/l/libGLU/libGLU-9.0.3-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.3-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..8a01a3ac439 --- /dev/null +++ b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.3-GCCcore-13.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'MesonNinja' + +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': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://mesa.freedesktop.org/archive/glu/'] +sources = ['glu-%(version)s.tar.xz'] +checksums = ['bd43fe12f374b1192eb15fe20e45ff456b9bc26ab57f0eee919f96ca0f8a330f'] + +builddependencies = [ + ('pkgconf', '2.2.0'), + ('binutils', '2.42'), + ('Ninja', '1.12.1'), + ('Meson', '1.4.0'), +] + +dependencies = [('Mesa', '24.1.3')] + +sanity_check_paths = { + 'files': ['lib/libGLU.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' From bfd5bf97147e7df26c34bbdf5edf8434d10c4ed2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Thu, 12 Sep 2024 16:07:42 +0200 Subject: [PATCH 050/107] adding easyconfigs: cramino-0.14.5-GCC-12.3.0.eb --- .../c/cramino/cramino-0.14.5-GCC-12.3.0.eb | 348 ++++++++++++++++++ 1 file changed, 348 insertions(+) create mode 100644 easybuild/easyconfigs/c/cramino/cramino-0.14.5-GCC-12.3.0.eb diff --git a/easybuild/easyconfigs/c/cramino/cramino-0.14.5-GCC-12.3.0.eb b/easybuild/easyconfigs/c/cramino/cramino-0.14.5-GCC-12.3.0.eb new file mode 100644 index 00000000000..2d7064097e7 --- /dev/null +++ b/easybuild/easyconfigs/c/cramino/cramino-0.14.5-GCC-12.3.0.eb @@ -0,0 +1,348 @@ +easyblock = 'Cargo' + +name = 'cramino' +version = '0.14.5' + +homepage = 'https://github.com/wdecoster/cramino' +description = """A tool for quick quality assessment of cram and bam files, intended for long read sequencing.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://github.com/wdecoster/cramino/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = [ + {'v0.14.5.tar.gz': 'd3b31ab76808ca76171e2539cfe30e66fe24cbd4af4ff9a941c282a0bc438032'}, + {'ahash-0.8.9.tar.gz': 'd713b3834d76b85304d4d525563c1276e2e30dc97cc67bfb4585a4a29fc2c89f'}, + {'aho-corasick-1.1.2.tar.gz': 'b2969dcb958b36655471fc61f7e416fa76033bdd4bfed0678d8fee1e2d07a1f0'}, + {'android-tzdata-0.1.1.tar.gz': 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('lexical-write-integer', '0.8.5'), + ('libc', '0.2.153'), + ('libm', '0.2.8'), + ('libz-sys', '1.1.15'), + ('linear-map', '1.2.0'), + ('log', '0.4.20'), + ('lzma-sys', '0.1.20'), + ('memchr', '2.7.1'), + ('newtype_derive', '0.1.6'), + ('num', '0.4.1'), + ('num-bigint', '0.4.4'), + ('num-complex', '0.4.5'), + ('num-integer', '0.1.46'), + ('num-iter', '0.1.44'), + ('num-rational', '0.4.1'), + ('num-traits', '0.2.18'), + ('once_cell', '1.19.0'), + ('openssl-src', '300.2.3+3.2.1'), + ('openssl-sys', '0.9.100'), + ('percent-encoding', '2.3.1'), + ('pkg-config', '0.3.30'), + ('proc-macro2', '1.0.78'), + ('quick-error', '1.2.3'), + ('quote', '1.0.35'), + ('rayon', '1.8.1'), + ('rayon-core', '1.12.1'), + ('regex', '1.10.3'), + ('regex-automata', '0.4.5'), + ('regex-syntax', '0.8.2'), + ('rust-htslib', '0.46.0'), + ('rustc_version', '0.1.7'), + ('rustc_version', '0.4.0'), + ('rustversion', '1.0.14'), + ('ryu', '1.0.17'), + ('semver', '0.1.20'), + ('semver', '1.0.22'), + ('serde', '1.0.197'), + ('serde_derive', '1.0.197'), + ('serde_json', '1.0.114'), + ('static_assertions', '1.1.0'), + ('strsim', '0.11.0'), + ('strum_macros', '0.25.3'), + ('syn', '1.0.109'), + ('syn', '2.0.50'), + ('thiserror', '1.0.57'), + ('thiserror-impl', '1.0.57'), + ('tiny-keccak', '2.0.2'), + ('tinyvec', '1.6.0'), + ('tinyvec_macros', '0.1.1'), + ('unicode-bidi', '0.3.15'), + ('unicode-ident', '1.0.12'), + ('unicode-normalization', '0.1.23'), + ('unzip-n', '0.1.2'), + ('url', '2.5.0'), + ('utf8parse', '0.2.1'), + ('vcpkg', '0.2.15'), + ('version_check', '0.9.4'), + ('wasi', '0.11.0+wasi-snapshot-preview1'), + ('wasm-bindgen', '0.2.91'), + ('wasm-bindgen-backend', '0.2.91'), + ('wasm-bindgen-macro', '0.2.91'), + ('wasm-bindgen-macro-support', '0.2.91'), + ('wasm-bindgen-shared', '0.2.91'), + ('windows-core', '0.52.0'), + ('windows-sys', '0.52.0'), + ('windows-targets', '0.52.0'), + ('windows_aarch64_gnullvm', '0.52.0'), + ('windows_aarch64_msvc', '0.52.0'), + ('windows_i686_gnu', '0.52.0'), + ('windows_i686_msvc', '0.52.0'), + ('windows_x86_64_gnu', '0.52.0'), + ('windows_x86_64_gnullvm', '0.52.0'), + ('windows_x86_64_msvc', '0.52.0'), + ('zerocopy', '0.7.32'), + ('zerocopy-derive', '0.7.32'), +] + +builddependencies = [ + ('Rust', '1.75.0'), + ('CMake', '3.26.3'), +] + +dependencies = [ + ('bzip2', '1.0.8'), +] + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': [], +} + +sanity_check_commands = ["%(name)s --help"] + +moduleclass = 'bio' From e88c4378baf599d49732fa5019f792bf7f8b5595 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 12 Sep 2024 16:48:24 +0200 Subject: [PATCH 051/107] adding easyconfigs: GObject-Introspection-1.80.1-GCCcore-13.3.0.eb and patches: GObject-Introspection-1.80.1_install-GLib-GIR-files.patch --- ...ect-Introspection-1.80.1-GCCcore-13.3.0.eb | 51 ++++++++++++++++++ ...ection-1.80.1_install-GLib-GIR-files.patch | 52 +++++++++++++++++++ 2 files changed, 103 insertions(+) create mode 100644 easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.80.1-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.80.1_install-GLib-GIR-files.patch diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.80.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.80.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..4f1620c0db9 --- /dev/null +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.80.1-GCCcore-13.3.0.eb @@ -0,0 +1,51 @@ +easyblock = 'MesonNinja' + +name = 'GObject-Introspection' +version = '1.80.1' + +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': '13.3.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +patches = ['GObject-Introspection-1.80.1_install-GLib-GIR-files.patch'] +checksums = [ + {'gobject-introspection-1.80.1.tar.xz': 'a1df7c424e15bda1ab639c00e9051b9adf5cea1a9e512f8a603b53cd199bc6d8'}, + {'GObject-Introspection-1.80.1_install-GLib-GIR-files.patch': + '2920b94cf33a41b424de2fb3a0f04b7a1076fd8f47417fa82cf4703ff1ba95fa'}, +] + +builddependencies = [ + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), + ('CMake', '3.29.3'), + ('Meson', '1.4.0'), + ('Ninja', '1.12.1'), + ('Python', '3.12.3'), + ('Bison', '3.8.2'), + ('cairo', '1.18.0'), + ('flex', '2.6.4'), +] + +dependencies = [ + ('GLib', '2.80.4'), + ('libffi', '3.4.5'), + ('util-linux', '2.40'), +] + +preconfigopts = "env GI_SCANNER_DISABLE_CACHE=true " +configopts = "-Dcairo=enabled" + +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/g/GObject-Introspection/GObject-Introspection-1.80.1_install-GLib-GIR-files.patch b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.80.1_install-GLib-GIR-files.patch new file mode 100644 index 00000000000..349eecf7c0b --- /dev/null +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.80.1_install-GLib-GIR-files.patch @@ -0,0 +1,52 @@ +This reverts a commit from upstream +> build: Do not install generated GLib GIR files +> +> GLib 2.79 ships its own introspection data. + +However GObject-Introspection requires (optionally) Cairo, which requires GLib +which requires GLib-Introspection for generating the introspection data. + +So there is a cyclib dependency, see https://gitlab.gnome.org/GNOME/gobject-introspection/-/issues/517 + +Author: Alexander Grund (TU Dresden) + +diff --git a/gir/meson.build b/gir/meson.build +index 3a016831..312aa886 100644 +--- a/gir/meson.build ++++ b/gir/meson.build +@@ -241,6 +241,8 @@ glib_gir = custom_target('gir-glib', + output: 'GLib-2.0.gir', + depends: [gir_giscanner_pymod, glib_gir_dep, gdump], + depend_files: gir_giscanner_built_files, ++ install: true, ++ install_dir: girdir, + env: g_ir_scanner_env, + command: glib_command + [ + '--cflags-begin'] + glib_includes + extra_giscanner_cflags + [ +@@ -308,6 +310,8 @@ gobject_gir = custom_target('gir-gobject', + output: 'GObject-2.0.gir', + depends: [glib_gir, gir_giscanner_pymod, gobject_gir_dep, gdump], + depend_files: gir_giscanner_built_files, ++ install: true, ++ install_dir: girdir, + env: g_ir_scanner_env, + command: gobject_command + [ + '--include-uninstalled=' + glib_gir.full_path(), +@@ -360,6 +364,8 @@ uninstalled_gir_files += custom_target('gir-gmodule', + output: 'GModule-2.0.gir', + depends: [glib_gir, gir_giscanner_pymod, gmodule_gir_dep, gdump], + depend_files: gir_giscanner_built_files, ++ install: true, ++ install_dir: girdir, + env: g_ir_scanner_env, + command: gmodule_command + [ + '--include-uninstalled=' + glib_gir.full_path(), +@@ -455,6 +461,8 @@ gio_gir = custom_target('gir-gio', + output: 'Gio-2.0.gir', + depends: [gobject_gir, gir_giscanner_pymod, gio_gir_dep, gdump], + depend_files: gir_giscanner_built_files, ++ install: true, ++ install_dir: girdir, + env: g_ir_scanner_env, + command: gio_command + [ + '--include-uninstalled=' + gobject_gir.full_path(), From 6a10ce129926783d3cae55eb68fe38da279ba451 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 12 Sep 2024 17:04:20 +0200 Subject: [PATCH 052/107] adding easyconfigs: Ghostscript-10.03.1-GCCcore-13.3.0.eb, HarfBuzz-9.0.0-GCCcore-13.3.0.eb, ImageMagick-7.1.1-38-GCCcore-13.3.0.eb, Pango-1.54.0-GCCcore-13.3.0.eb, JasPer-4.2.4-GCCcore-13.3.0.eb and patches: HarfBuzz-9.0.0_fix-subset-test.patch, ImageMagick-7.1.1-38_fix-linking.patch --- .../Ghostscript-10.03.1-GCCcore-13.3.0.eb | 58 +++++++++++++++++++ .../HarfBuzz/HarfBuzz-9.0.0-GCCcore-13.3.0.eb | 51 ++++++++++++++++ .../HarfBuzz-9.0.0_fix-subset-test.patch | 26 +++++++++ .../ImageMagick-7.1.1-38-GCCcore-13.3.0.eb | 50 ++++++++++++++++ .../ImageMagick-7.1.1-38_fix-linking.patch | 27 +++++++++ .../j/JasPer/JasPer-4.2.4-GCCcore-13.3.0.eb | 36 ++++++++++++ .../p/Pango/Pango-1.54.0-GCCcore-13.3.0.eb | 41 +++++++++++++ 7 files changed, 289 insertions(+) create mode 100644 easybuild/easyconfigs/g/Ghostscript/Ghostscript-10.03.1-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-9.0.0-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-9.0.0_fix-subset-test.patch create mode 100644 easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.1-38-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.1-38_fix-linking.patch create mode 100644 easybuild/easyconfigs/j/JasPer/JasPer-4.2.4-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/p/Pango/Pango-1.54.0-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-10.03.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-10.03.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..174aec3f515 --- /dev/null +++ b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-10.03.1-GCCcore-13.3.0.eb @@ -0,0 +1,58 @@ +easyblock = 'ConfigureMake' + +name = 'Ghostscript' +version = '10.03.1' + +homepage = 'https://ghostscript.com' +description = """Ghostscript is a versatile processor for PostScript data with the ability to render PostScript to + different targets. It used to be part of the cups printing stack, but is no longer used for that.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = [ + 'https://github.com/ArtifexSoftware/ghostpdl-downloads/releases/download/gs%s/' % version.replace('.', ''), +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['31cd01682ad23a801cc3bbc222a55f07c4ea3e068bdfb447792d54db21a2e8ad'] + +builddependencies = [ + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), +] + +dependencies = [ + ('zlib', '1.3.1'), + ('libpng', '1.6.43'), + ('freetype', '2.13.2'), + ('libjpeg-turbo', '3.0.1'), + ('expat', '2.6.2'), + ('GLib', '2.80.4'), + ('cairo', '1.18.0'), + ('LibTIFF', '4.6.0'), +] + +# Do not use local copies of zlib, jpeg, freetype, and png +preconfigopts = 'mv zlib zlib.no && mv jpeg jpeg.no && mv freetype freetype.no && ' +preconfigopts += 'mv libpng libpng.no && export LIBS="$LIBS -L$EBROOTZLIB/lib -lz" && ' +configopts = "--with-system-libtiff --enable-dynamic --disable-hidden-visibility" + +# also build and install shared libs +build_cmd_targets = ['', 'so'] +installopts = 'soinstall' + +postinstallcmds = [ + # install header files + "mkdir -p %(installdir)s/include/%(namelower)s", + "install -v -m644 base/*.h %(installdir)s/include/%(namelower)s", + "install -v -m644 psi/*.h %(installdir)s/include/%(namelower)s", +] + +sanity_check_paths = { + 'files': ['bin/gs', 'lib/libgs.%s' % SHLIB_EXT], + 'dirs': ['lib/%(namelower)s', 'include/%(namelower)s', 'share/man'], +} + +sanity_check_commands = ["gs --help"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-9.0.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-9.0.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..40540c3fcdc --- /dev/null +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-9.0.0-GCCcore-13.3.0.eb @@ -0,0 +1,51 @@ +easyblock = 'MesonNinja' + +name = 'HarfBuzz' +version = '9.0.0' + +homepage = 'https://www.freedesktop.org/wiki/Software/HarfBuzz' +description = """HarfBuzz is an OpenType text shaping engine.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +github_account = 'harfbuzz' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +patches = ['HarfBuzz-9.0.0_fix-subset-test.patch'] +checksums = [ + {'9.0.0.tar.gz': 'b7e481b109d19aefdba31e9f5888aa0cdfbe7608fed9a43494c060ce1f8a34d2'}, + {'HarfBuzz-9.0.0_fix-subset-test.patch': '1635505c27c312dca507863f2a865eb88d42e35ff4cc241cfa0e90c0ade8b790'}, +] + +builddependencies = [ + ('binutils', '2.42'), + ('GObject-Introspection', '1.80.1'), + ('pkgconf', '2.2.0'), + ('Ninja', '1.12.1'), + ('Meson', '1.4.0'), + ('fonttools', '4.53.1'), # For tests +] + +dependencies = [ + ('GLib', '2.80.4'), + ('ICU', '75.1'), + ('cairo', '1.18.0'), + ('freetype', '2.13.2'), +] + +configopts = '--default-library=both' # static and shared library +configopts += ' -Dgobject=enabled -Dintrospection=enabled' +configopts += ' -Dglib=enabled' +configopts += ' -Dicu=enabled' +configopts += ' -Dcairo=enabled' +configopts += ' -Dfreetype=enabled' + +runtest = 'meson' +testopts = 'test -C %(builddir)s/easybuild_obj -t 60' + +sanity_check_paths = { + 'files': ['lib/libharfbuzz.%s' % SHLIB_EXT, 'bin/hb-view'], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-9.0.0_fix-subset-test.patch b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-9.0.0_fix-subset-test.patch new file mode 100644 index 00000000000..25a2b619fc8 --- /dev/null +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-9.0.0_fix-subset-test.patch @@ -0,0 +1,26 @@ +The test "feature_variation_instance_collect_lookups" fails when run in environments +where the decimal separator is not a dot ("."). +Fix this by using the C locale. +See https://github.com/harfbuzz/harfbuzz/pull/4857 + +Author: Alexander Grund (TU Dresden) + +diff --git a/test/subset/run-tests.py b/test/subset/run-tests.py +index 9e09d95d1d9..c0c256d8974 100755 +--- a/test/subset/run-tests.py ++++ b/test/subset/run-tests.py +@@ -135,10 +135,13 @@ def check_ots (path): + + has_ots = has_ots() + ++env = os.environ.copy() ++env['LC_ALL'] = 'C' + process = subprocess.Popen ([hb_subset, '--batch'], + stdin=subprocess.PIPE, + stdout=subprocess.PIPE, +- stderr=sys.stdout) ++ stderr=sys.stdout, ++ env=env) + + fails = 0 + for path in args: diff --git a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.1-38-GCCcore-13.3.0.eb b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.1-38-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..776471b14b2 --- /dev/null +++ b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.1-38-GCCcore-13.3.0.eb @@ -0,0 +1,50 @@ +easyblock = 'ConfigureMake' + +name = 'ImageMagick' +version = '7.1.1-38' + +homepage = 'https://www.imagemagick.org/' +description = "ImageMagick is a software suite to create, edit, compose, or convert bitmap images" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/%(name)s/%(name)s/archive/'] +sources = ['%(version)s.tar.gz'] +patches = ['ImageMagick-7.1.1-38_fix-linking.patch'] +checksums = [ + {'7.1.1-38.tar.gz': '5e449530ccec8b85ae2bfd1ad773184fb7a4737d40fd9439db8a5d4beee4403e'}, + {'ImageMagick-7.1.1-38_fix-linking.patch': '0fbe8e3b6621e3e0d1efec59949fecb45924bc6e65851b9b6399bb3eff8d55d9'}, +] + +builddependencies = [ + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), +] +dependencies = [ + ('bzip2', '1.0.8'), + ('X11', '20240607'), + ('Ghostscript', '10.03.1'), + ('JasPer', '4.2.4'), + ('libjpeg-turbo', '3.0.1'), + ('LibTIFF', '4.6.0'), + ('LittleCMS', '2.16'), + ('Pango', '1.54.0'), + ('pixman', '0.43.4'), + ('FriBidi', '1.0.15'), +] + +preconfigopts = 'PKG_CONFIG=$EBROOTPKGCONF/bin/pkgconf' +configopts = "--with-gslib --with-x" + +sanity_check_paths = { + 'files': ['bin/magick'], + 'dirs': ['etc/%(name)s-%(version_major)s', 'include/%(name)s-%(version_major)s', 'lib', 'share'], +} + +sanity_check_commands = [ + 'magick --help', +] + +modextravars = {'MAGICK_HOME': '%(installdir)s'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.1-38_fix-linking.patch b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.1-38_fix-linking.patch new file mode 100644 index 00000000000..2c9d54a4ac0 --- /dev/null +++ b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.1-38_fix-linking.patch @@ -0,0 +1,27 @@ +The configure script sets this to a path inside the install location which is empty during build. +However this path(s) is/are used by the compiler/linker to find libraries. `pkg-config` used during configure assumes this is the same during build as on invocation of itself and omits any path already contained in the variable. + +This combination causes build failures due to dependent libraries not being found in the link step unless there happens to be some other way the paths get pulled in. E.g. if HarfBuzz is built using (the deprecated) configure&make it has `*.la` files which contain the required link flags. If HarfBuzz is built using the new Meson build system those files are no longer present and the linker paths will be missing. + +As there doesn't seem to be a specific reason for the variable to be set to an empty directory in the Makefile just remove it. + +See https://github.com/ImageMagick/ImageMagick/pull/7613 + +Author: Alexander Grund (TU Dresden) + +--- + Makefile.in | 1 - + 1 file changed, 1 deletion(-) + +diff --git a/Makefile.in b/Makefile.in +index 47b78566f0c..3a9761cfd5b 100644 +--- a/Makefile.in ++++ b/Makefile.in +@@ -3288,7 +3288,6 @@ LIBOBJS = @LIBOBJS@ + LIBOPENJP2_CFLAGS = @LIBOPENJP2_CFLAGS@ + LIBOPENJP2_LIBS = @LIBOPENJP2_LIBS@ + LIBRARY_EXTRA_CPPFLAGS = @LIBRARY_EXTRA_CPPFLAGS@ +-LIBRARY_PATH = @LIBRARY_PATH@ + LIBS = @LIBS@ + LIBSTDCLDFLAGS = @LIBSTDCLDFLAGS@ + LIBTOOL = @LIBTOOL@ diff --git a/easybuild/easyconfigs/j/JasPer/JasPer-4.2.4-GCCcore-13.3.0.eb b/easybuild/easyconfigs/j/JasPer/JasPer-4.2.4-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..14ce45ca6ad --- /dev/null +++ b/easybuild/easyconfigs/j/JasPer/JasPer-4.2.4-GCCcore-13.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'CMakeMake' + +name = 'JasPer' +version = '4.2.4' + +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': '13.3.0'} +toolchainopts = {'pic': True} + +github_account = 'jasper-software' +source_urls = [GITHUB_SOURCE] +sources = ['version-%(version)s.tar.gz'] +checksums = ['23a3d58cdeacf3abdf9fa1d81dcefee58da6ab330940790c0f27019703bfd2cd'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), +] + +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/p/Pango/Pango-1.54.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/Pango/Pango-1.54.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..cfbbc1eb16b --- /dev/null +++ b/easybuild/easyconfigs/p/Pango/Pango-1.54.0-GCCcore-13.3.0.eb @@ -0,0 +1,41 @@ +easyblock = 'MesonNinja' + +name = 'Pango' +version = '1.54.0' + +homepage = 'https://pango.gnome.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': '13.3.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['8a9eed75021ee734d7fc0fdf3a65c3bba51dfefe4ae51a9b414a60c70b2d1ed8'] + +builddependencies = [ + ('binutils', '2.42'), + ('Meson', '1.4.0'), + ('Ninja', '1.12.1'), + ('GObject-Introspection', '1.80.1'), + ('pkgconf', '2.2.0'), +] + +dependencies = [ + ('X11', '20240607'), + ('GLib', '2.80.4'), + ('cairo', '1.18.0'), + ('HarfBuzz', '9.0.0'), + ('FriBidi', '1.0.15'), +] + +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' From 7821c59138199c828095b6da83d37a6e41c57cc7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 12 Sep 2024 17:05:36 +0200 Subject: [PATCH 053/107] {bio}[foss/2023b] BiG-SCAPE v1.1.9, HMMER v3.4, FastTree v2.1.11 --- .../b/BiG-SCAPE/BiG-SCAPE-1.1.9-foss-2023b.eb | 66 ++++++++++++++++ .../FastTree-2.1.11-GCCcore-13.2.0.eb | 42 ++++++++++ .../h/HMMER/HMMER-3.4-gompi-2023b.eb | 78 +++++++++++++++++++ 3 files changed, 186 insertions(+) create mode 100644 easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.9-foss-2023b.eb create mode 100644 easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/h/HMMER/HMMER-3.4-gompi-2023b.eb diff --git a/easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.9-foss-2023b.eb b/easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.9-foss-2023b.eb new file mode 100644 index 00000000000..87ffb021f06 --- /dev/null +++ b/easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.9-foss-2023b.eb @@ -0,0 +1,66 @@ +easyblock = 'PythonPackage' + +name = 'BiG-SCAPE' +version = '1.1.9' + +homepage = 'https://bigscape-corason.secondarymetabolites.org/index.html' +description = """BiG-SCAPE and CORASON provide a set of tools to explore the diversity of biosynthetic gene clusters +(BGCs) across large numbers of genomes, by constructing BGC sequence similarity networks, grouping BGCs into gene +cluster families, and exploring gene cluster diversity linked to enzyme phylogenies.""" + +toolchain = {'name': 'foss', 'version': '2023b'} + +github_account = 'medema-group' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = [ + 'BiG-SCAPE-1.1.5_use_env_var_for_html.patch', + 'BiG-SCAPE-1.1.5_use_correct_name_for_FastTree.patch', +] +checksums = [ + {'v1.1.9.tar.gz': 'ef0ddb5b433e0b1467ae5f96037fd6d23ebcba6bc08201d1421eba35d072e534'}, + {'BiG-SCAPE-1.1.5_use_env_var_for_html.patch': '540be22396ab982c2aeaaed4ce5acdb8ccb8ce2b31d36bc69d37be7a29c7c42a'}, + {'BiG-SCAPE-1.1.5_use_correct_name_for_FastTree.patch': + 'e1572e4134c6163a3927ac32bd2a39b7f87cf01109f7913b3c55126e2381a771'}, +] + +dependencies = [ + ('Python', '3.11.5'), + ('SciPy-bundle', '2023.11'), + ('Biopython', '1.84'), + ('scikit-learn', '1.4.0'), + ('networkx', '3.2.1'), + ('HMMER', '3.4'), + ('FastTree', '2.1.11'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +options = {'modulename': 'bigscape'} + +sanity_check_paths = { + 'files': ['bin/bigscape'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + 'bigscape --help', +] + +modextravars = { + 'BIG_SCAPE_HTML_PATH': '%(installdir)s/lib/python%(pyshortver)s/site-packages/BiG-SCAPE', +} + +modloadmsg = "%(name)s needs processed Pfam database to work properly.\n" +modloadmsg += "For this, download the latest 'Pfam-A.hmm.gz' file from the Pfam website " +modloadmsg += "(http://ftp.ebi.ac.uk/pub/databases/Pfam/releases/), " +modloadmsg += "uncompress it and process it using the `hmmpress` command.\n" +modloadmsg += "For data files, like the domains_color_file.tsv and domain_includelist.txt, " +modloadmsg += "one can set the environment variable BIG_SCAPE_DATA_PATH, if that is not set " +modloadmsg += "it will use the directory where the bigscape command is started from.\n" +modloadmsg += "One can copy the domains_color_file.tsv from " +modloadmsg += "%(installdir)s/lib/python%(pyshortver)s/site-packages/BiG-SCAPE/domains_color_file.tsv\n" + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-13.2.0.eb b/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..b44229828a4 --- /dev/null +++ b/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-13.2.0.eb @@ -0,0 +1,42 @@ +# Updated from previous config +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'CmdCp' + +name = 'FastTree' +version = '2.1.11' + +homepage = 'http://www.microbesonline.org/fasttree/' +description = """FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide + or protein sequences. FastTree can handle alignments with up to a million of sequences in a reasonable amount of + time and memory. """ + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'openmp': True} + +# HTTPS cert error: +# hostname 'www.microbesonline.org' doesn't match either of 'genomics.lbl.gov', 'mojave.qb3.berkeley.edu', ... +source_urls = ['http://www.microbesonline.org/fasttree/'] +sources = [{'filename': '%(name)s-%(version)s.c', 'extract_cmd': 'cp %s FastTree.c'}] +checksums = ['9026ae550307374be92913d3098f8d44187d30bea07902b9dcbfb123eaa2050f'] + +builddependencies = [('binutils', '2.40')] + +cmds_map = [('%(name)s-%(version)s.c', '$CC -DOPENMP $CFLAGS $LIBS %%(source)s -o %(name)s')] + +files_to_copy = [(['FastTree'], 'bin')] + +# as FastTree is built with OpenMP, the correct binary is FastTreeMP +# the FastTree binary should normally be built without OpenMP, but let’s keep it as is for backward compatibility +# see http://www.microbesonline.org/fasttree/#OpenMP +postinstallcmds = ['cd %(installdir)s/bin && ln -s FastTree FastTreeMP'] + +sanity_check_paths = { + 'files': ['bin/FastTree'], + 'dirs': [], +} + +sanity_check_commands = ['FastTree 2>&1 | grep "FastTree Version %(version)s"'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/HMMER/HMMER-3.4-gompi-2023b.eb b/easybuild/easyconfigs/h/HMMER/HMMER-3.4-gompi-2023b.eb new file mode 100644 index 00000000000..bb76dc1e937 --- /dev/null +++ b/easybuild/easyconfigs/h/HMMER/HMMER-3.4-gompi-2023b.eb @@ -0,0 +1,78 @@ +## +# EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Nils Christian , +# Fotis Georgatos +# Updated by: Filip Kružík (INUITS) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a +# component of the policy: +# https://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = 'ConfigureMake' + +name = 'HMMER' +version = '3.4' + +homepage = 'http://hmmer.org/' +description = """HMMER is used for searching sequence databases for homologs + of protein sequences, and for making protein sequence alignments. It + implements methods using probabilistic models called profile hidden Markov + models (profile HMMs). Compared to BLAST, FASTA, and other sequence + alignment and database search tools based on older scoring methodology, + HMMER aims to be significantly more accurate and more able to detect remote + homologs because of the strength of its underlying mathematical models. In the + past, this strength came at significant computational expense, but in the new + HMMER3 project, HMMER is now essentially as fast as BLAST.""" + +toolchain = {'name': 'gompi', 'version': '2023b'} + +source_urls = [ + 'http://eddylab.org/software/hmmer/', + 'http://eddylab.org/software/hmmer%(version_major)s/%(version)s/', +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['ca70d94fd0cf271bd7063423aabb116d42de533117343a9b27a65c17ff06fbf3'] + +builddependencies = [ + ('Python', '3.11.5'), + ('Perl', '5.38.0'), +] + +# replace hardcoded /usr/bin/perl shebang lines with '/usr/bin/env perl' across all files +preconfigopts = "grep '/usr/bin/perl' . | cut -f1 -d: | xargs echo sed -i 's@/usr/bin/perl@/usr/bin/env perl@g' && " + +configopts = '--enable-mpi' + +buildopts = ' V=1 ' + +testopts = buildopts +runtest = 'check' + +installopts = ' && cd easel && make install' + +local_bin_files = ['alimask', 'esl-afetch', 'esl-alimanip', 'esl-alimap', 'esl-alimask', + 'esl-alimerge', 'esl-alipid', 'esl-alirev', 'esl-alistat', 'esl-compalign', + 'esl-compstruct', 'esl-construct', 'esl-histplot', 'esl-mask', 'esl-reformat', + 'esl-selectn', 'esl-seqrange', 'esl-seqstat', 'esl-sfetch', 'esl-shuffle', + 'esl-ssdraw', 'esl-translate', 'esl-weight', 'hmmalign', 'hmmbuild', + 'hmmconvert', 'hmmemit', 'hmmfetch', 'hmmlogo', 'hmmpgmd', 'hmmpress', + 'hmmscan', 'hmmsearch', 'hmmsim', 'hmmstat', 'jackhmmer', 'makehmmerdb', + 'nhmmer', 'nhmmscan', 'phmmer'] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in local_bin_files], + 'dirs': ['bin', 'share'], +} + +sanity_check_commands = [ + "esl-construct -h", + "hmmsearch -h", + "nhmmer -h", +] + +moduleclass = 'bio' From c6cc0232a089462e57b162169bb4e0b873c860cf Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Thu, 12 Sep 2024 17:39:38 +0200 Subject: [PATCH 054/107] add missing dependency --- easybuild/easyconfigs/c/cramino/cramino-0.14.5-GCC-12.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/c/cramino/cramino-0.14.5-GCC-12.3.0.eb b/easybuild/easyconfigs/c/cramino/cramino-0.14.5-GCC-12.3.0.eb index 2d7064097e7..7193a870648 100644 --- a/easybuild/easyconfigs/c/cramino/cramino-0.14.5-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/c/cramino/cramino-0.14.5-GCC-12.3.0.eb @@ -336,6 +336,7 @@ builddependencies = [ dependencies = [ ('bzip2', '1.0.8'), + ('OpenSSL', '1.1', '', SYSTEM), ] sanity_check_paths = { From 4ff7932b51a185f17e8686d6cd8e1f945c2c6ffe Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Thu, 12 Sep 2024 18:00:05 +0200 Subject: [PATCH 055/107] add missing dependencies --- easybuild/easyconfigs/c/cramino/cramino-0.14.5-GCC-12.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/c/cramino/cramino-0.14.5-GCC-12.3.0.eb b/easybuild/easyconfigs/c/cramino/cramino-0.14.5-GCC-12.3.0.eb index 7193a870648..49c61ff64fb 100644 --- a/easybuild/easyconfigs/c/cramino/cramino-0.14.5-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/c/cramino/cramino-0.14.5-GCC-12.3.0.eb @@ -337,6 +337,8 @@ builddependencies = [ dependencies = [ ('bzip2', '1.0.8'), ('OpenSSL', '1.1', '', SYSTEM), + ('Perl', '5.36.1'), + ('Perl-bundle-CPAN', '5.36.1'), ] sanity_check_paths = { From 545807433e6631ba3fe3c12c85867bdf064ee83c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Thu, 12 Sep 2024 18:41:12 +0200 Subject: [PATCH 056/107] change moduleclass --- easybuild/easyconfigs/n/nanoQC/nanoQC-0.9.4-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/nanoQC/nanoQC-0.9.4-foss-2023a.eb b/easybuild/easyconfigs/n/nanoQC/nanoQC-0.9.4-foss-2023a.eb index d0efa23525d..264a822a3ca 100644 --- a/easybuild/easyconfigs/n/nanoQC/nanoQC-0.9.4-foss-2023a.eb +++ b/easybuild/easyconfigs/n/nanoQC/nanoQC-0.9.4-foss-2023a.eb @@ -28,4 +28,4 @@ sanity_check_commands = ["nanoQC --help"] sanity_pip_check = True -moduleclass = 'tools' +moduleclass = 'bio' From 881e8f00be655c2ce5a1c8b169003e7861caa23f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Thu, 12 Sep 2024 18:57:45 +0200 Subject: [PATCH 057/107] adding easyconfigs: phasius-0.2.0-GCC-12.3.0.eb --- .../p/phasius/phasius-0.2.0-GCC-12.3.0.eb | 391 ++++++++++++++++++ 1 file changed, 391 insertions(+) create mode 100644 easybuild/easyconfigs/p/phasius/phasius-0.2.0-GCC-12.3.0.eb diff --git a/easybuild/easyconfigs/p/phasius/phasius-0.2.0-GCC-12.3.0.eb b/easybuild/easyconfigs/p/phasius/phasius-0.2.0-GCC-12.3.0.eb new file mode 100644 index 00000000000..0999294863b --- /dev/null +++ b/easybuild/easyconfigs/p/phasius/phasius-0.2.0-GCC-12.3.0.eb @@ -0,0 +1,391 @@ +easyblock = 'Cargo' + +name = 'phasius' +version = '0.2.0' + +homepage = 'https://github.com/wdecoster/phasius' +description = """A tool to visualize phase block structure from (many) BAM, + CRAM or VCF files together with BED annotation""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://github.com/wdecoster/phasius/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = [ + {'v0.2.0.tar.gz': 'a5b320303383b473661fccf7ec93f3b555b21d86d78d9cdaf5317cc9bcf3cb0e'}, + {'aho-corasick-1.1.3.tar.gz': '8e60d3430d3a69478ad0993f19238d2df97c507009a52b3c10addcd7f6bcb916'}, + {'android-tzdata-0.1.1.tar.gz': 'e999941b234f3131b00bc13c22d06e8c5ff726d1b6318ac7eb276997bbb4fef0'}, + {'android_system_properties-0.1.5.tar.gz': '819e7219dbd41043ac279b19830f2efc897156490d7fd6ea916720117ee66311'}, + {'anstream-0.6.15.tar.gz': '64e15c1ab1f89faffbf04a634d5e1962e9074f2741eef6d97f3c4e322426d526'}, + {'anstyle-1.0.8.tar.gz': '1bec1de6f59aedf83baf9ff929c98f2ad654b97c9510f4e70cf6f661d49fd5b1'}, + {'anstyle-parse-0.2.5.tar.gz': 'eb47de1e80c2b463c735db5b217a0ddc39d612e7ac9e2e96a5aed1f57616c1cb'}, + {'anstyle-query-1.1.1.tar.gz': '6d36fc52c7f6c869915e99412912f22093507da8d9e942ceaf66fe4b7c14422a'}, + {'anstyle-wincon-3.0.4.tar.gz': 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{'wasm-bindgen-macro-0.2.93.tar.gz': '585c4c91a46b072c92e908d99cb1dcdf95c5218eeb6f3bf1efa991ee7a68cccf'}, + {'wasm-bindgen-macro-support-0.2.93.tar.gz': 'afc340c74d9005395cf9dd098506f7f44e38f2b4a21c6aaacf9a105ea5e1e836'}, + {'wasm-bindgen-shared-0.2.93.tar.gz': 'c62a0a307cb4a311d3a07867860911ca130c3494e8c2719593806c08bc5d0484'}, + {'winapi-0.3.9.tar.gz': '5c839a674fcd7a98952e593242ea400abe93992746761e38641405d28b00f419'}, + {'winapi-i686-pc-windows-gnu-0.4.0.tar.gz': 'ac3b87c63620426dd9b991e5ce0329eff545bccbbb34f3be09ff6fb6ab51b7b6'}, + {'winapi-util-0.1.9.tar.gz': 'cf221c93e13a30d793f7645a0e7762c55d169dbb0a49671918a2319d289b10bb'}, + {'winapi-x86_64-pc-windows-gnu-0.4.0.tar.gz': '712e227841d057c1ee1cd2fb22fa7e5a5461ae8e48fa2ca79ec42cfc1931183f'}, + {'windows-core-0.52.0.tar.gz': '33ab640c8d7e35bf8ba19b884ba838ceb4fba93a4e8c65a9059d08afcfc683d9'}, + {'windows-sys-0.52.0.tar.gz': '282be5f36a8ce781fad8c8ae18fa3f9beff57ec1b52cb3de0789201425d9a33d'}, + {'windows-sys-0.59.0.tar.gz': '1e38bc4d79ed67fd075bcc251a1c39b32a1776bbe92e5bef1f0bf1f8c531853b'}, + {'windows-targets-0.52.6.tar.gz': '9b724f72796e036ab90c1021d4780d4d3d648aca59e491e6b98e725b84e99973'}, + {'windows_aarch64_gnullvm-0.52.6.tar.gz': '32a4622180e7a0ec044bb555404c800bc9fd9ec262ec147edd5989ccd0c02cd3'}, + {'windows_aarch64_msvc-0.52.6.tar.gz': '09ec2a7bb152e2252b53fa7803150007879548bc709c039df7627cabbd05d469'}, + {'windows_i686_gnu-0.52.6.tar.gz': '8e9b5ad5ab802e97eb8e295ac6720e509ee4c243f69d781394014ebfe8bbfa0b'}, + {'windows_i686_gnullvm-0.52.6.tar.gz': '0eee52d38c090b3caa76c563b86c3a4bd71ef1a819287c19d586d7334ae8ed66'}, + {'windows_i686_msvc-0.52.6.tar.gz': '240948bc05c5e7c6dabba28bf89d89ffce3e303022809e73deaefe4f6ec56c66'}, + {'windows_x86_64_gnu-0.52.6.tar.gz': '147a5c80aabfbf0c7d901cb5895d1de30ef2907eb21fbbab29ca94c5b08b1a78'}, + {'windows_x86_64_gnullvm-0.52.6.tar.gz': '24d5b23dc417412679681396f2b49f3de8c1473deb516bd34410872eff51ed0d'}, + {'windows_x86_64_msvc-0.52.6.tar.gz': '589f6da84c646204747d1270a2a5661ea66ed1cced2631d546fdfb155959f9ec'}, + {'zerocopy-0.7.35.tar.gz': '1b9b4fd18abc82b8136838da5d50bae7bdea537c574d8dc1a34ed098d6c166f0'}, + {'zerocopy-derive-0.7.35.tar.gz': 'fa4f8080344d4671fb4e831a13ad1e68092748387dfc4f55e356242fae12ce3e'}, +] + +crates = [ + ('aho-corasick', '1.1.3'), + ('android-tzdata', '0.1.1'), + ('android_system_properties', '0.1.5'), + ('anstream', '0.6.15'), + ('anstyle', '1.0.8'), + ('anstyle-parse', '0.2.5'), + ('anstyle-query', '1.1.1'), + ('anstyle-wincon', '3.0.4'), + ('askama', '0.12.1'), + ('askama_derive', '0.12.5'), + ('askama_escape', '0.10.3'), + ('askama_parser', '0.2.1'), + ('atty', '0.2.14'), + ('autocfg', '1.3.0'), + ('base64', '0.13.1'), + ('basic-toml', '0.1.9'), + ('bindgen', '0.69.4'), + ('bio-types', '1.0.4'), + ('bitflags', '1.3.2'), + ('bitflags', '2.6.0'), + ('bumpalo', '3.16.0'), + ('byteorder', '1.5.0'), + ('bzip2-sys', '0.1.11+1.0.8'), + ('cc', '1.1.15'), + ('cexpr', '0.6.0'), + ('cfg-if', '1.0.0'), + ('chrono', '0.4.38'), + ('clang-sys', '1.8.1'), + ('clap', '3.2.25'), + ('clap_derive', '3.2.25'), + ('clap_lex', '0.2.4'), + ('cmake', '0.1.51'), + ('colorchoice', '1.0.2'), + ('core-foundation-sys', '0.8.7'), + ('crossbeam-deque', '0.8.5'), + ('crossbeam-epoch', '0.9.18'), + ('crossbeam-utils', '0.8.20'), + ('ctor', '0.2.8'), + ('curl-sys', '0.4.74+curl-8.9.0'), + ('custom_derive', '0.1.7'), + ('darling', '0.20.10'), + ('darling_core', '0.20.10'), + ('darling_macro', '0.20.10'), + ('deranged', '0.3.11'), + ('derive-new', '0.5.9'), + ('derive-new', '0.6.0'), + ('dyn-clone', '1.0.17'), + ('either', '1.13.0'), + ('env_filter', '0.1.2'), + ('env_logger', '0.11.5'), + ('erased-serde', '0.4.5'), + ('fnv', '1.0.7'), + ('form_urlencoded', '1.2.1'), + ('fs-utils', '1.1.4'), + ('getrandom', '0.2.15'), + ('glob', '0.3.1'), + ('hashbrown', '0.12.3'), + ('heck', '0.4.1'), + ('heck', '0.5.0'), + ('hermit-abi', '0.1.19'), + ('hex', '0.4.3'), + ('hts-sys', '2.1.4'), + ('humansize', '2.1.3'), + ('humantime', '2.1.0'), + ('iana-time-zone', '0.1.60'), + ('iana-time-zone-haiku', '0.1.2'), + ('ident_case', '1.0.1'), + ('idna', '0.5.0'), + ('ieee754', '0.2.6'), + ('indexmap', '1.9.3'), + ('is_terminal_polyfill', '1.70.1'), + ('itertools', '0.12.1'), + ('itoa', '1.0.11'), + ('jobserver', '0.1.32'), + ('js-sys', '0.3.70'), + ('lazy_static', '1.5.0'), + ('lazycell', '1.3.0'), + ('libc', '0.2.158'), + ('libloading', '0.8.5'), + ('libm', '0.2.8'), + ('libz-sys', '1.1.20'), + ('linear-map', '1.2.0'), + ('log', '0.4.22'), + ('lzma-sys', '0.1.20'), + ('memchr', '2.7.4'), + ('mime', '0.3.17'), + ('mime_guess', '2.0.5'), + ('minimal-lexical', '0.2.1'), + ('newtype_derive', '0.1.6'), + ('nom', '7.1.3'), + ('num-conv', '0.1.0'), + ('num-traits', '0.2.19'), + ('once_cell', '1.19.0'), + ('openssl-src', '300.3.1+3.3.1'), + ('openssl-sys', '0.9.103'), + ('os_str_bytes', '6.6.1'), + ('percent-encoding', '2.3.1'), + ('pkg-config', '0.3.30'), + ('plotly', '0.9.0'), + ('plotly_derive', '0.9.0'), + ('powerfmt', '0.2.0'), + ('ppv-lite86', '0.2.20'), + ('proc-macro-error', '1.0.4'), + ('proc-macro-error-attr', '1.0.4'), + ('proc-macro2', '1.0.86'), + ('quick-error', '1.2.3'), + ('quote', '1.0.37'), + ('rand', '0.8.5'), + ('rand_chacha', '0.3.1'), + ('rand_core', '0.6.4'), + ('rayon', '1.10.0'), + ('rayon-core', '1.12.1'), + ('regex', '1.10.6'), + ('regex-automata', '0.4.7'), + ('regex-syntax', '0.8.4'), + ('rust-htslib', '0.47.0'), + ('rustc-hash', '1.1.0'), + ('rustc_version', '0.1.7'), + ('rustversion', '1.0.17'), + ('ryu', '1.0.18'), + ('semver', '0.1.20'), + ('serde', '1.0.209'), + ('serde_derive', '1.0.209'), + ('serde_json', '1.0.127'), + ('serde_repr', '0.1.19'), + ('serde_with', '2.3.3'), + ('serde_with_macros', '2.3.3'), + ('shlex', '1.3.0'), + ('strsim', '0.10.0'), + ('strsim', '0.11.1'), + ('strum_macros', '0.26.4'), + ('syn', '1.0.109'), + ('syn', '2.0.76'), + ('termcolor', '1.4.1'), + ('textwrap', '0.16.1'), + ('thiserror', '1.0.63'), + ('thiserror-impl', '1.0.63'), + ('time', '0.3.36'), + ('time-core', '0.1.2'), + ('time-macros', '0.2.18'), + ('tinyvec', '1.8.0'), + ('tinyvec_macros', '0.1.1'), + ('typeid', '1.0.2'), + ('unicase', '2.7.0'), + ('unicode-bidi', '0.3.15'), + ('unicode-ident', '1.0.12'), + ('unicode-normalization', '0.1.23'), + ('unzip-n', '0.1.2'), + ('url', '2.5.2'), + ('utf8parse', '0.2.2'), + ('vcpkg', '0.2.15'), + ('version_check', '0.9.5'), + ('wasi', '0.11.0+wasi-snapshot-preview1'), + ('wasm-bindgen', '0.2.93'), + ('wasm-bindgen-backend', '0.2.93'), + ('wasm-bindgen-macro', '0.2.93'), + ('wasm-bindgen-macro-support', '0.2.93'), + ('wasm-bindgen-shared', '0.2.93'), + ('winapi', '0.3.9'), + ('winapi-i686-pc-windows-gnu', '0.4.0'), + ('winapi-util', '0.1.9'), + ('winapi-x86_64-pc-windows-gnu', '0.4.0'), + ('windows-core', '0.52.0'), + ('windows-sys', '0.52.0'), + ('windows-sys', '0.59.0'), + ('windows-targets', '0.52.6'), + ('windows_aarch64_gnullvm', '0.52.6'), + ('windows_aarch64_msvc', '0.52.6'), + ('windows_i686_gnu', '0.52.6'), + ('windows_i686_gnullvm', '0.52.6'), + ('windows_i686_msvc', '0.52.6'), + ('windows_x86_64_gnu', '0.52.6'), + ('windows_x86_64_gnullvm', '0.52.6'), + ('windows_x86_64_msvc', '0.52.6'), + ('zerocopy', '0.7.35'), + ('zerocopy-derive', '0.7.35'), +] + +builddependencies = [ + ('Rust', '1.75.0'), + ('CMake', '3.26.3'), + ('Clang', '16.0.6'), +] + +dependencies = [ + ('bzip2', '1.0.8'), + ('OpenSSL', '1.1', '', SYSTEM), +] + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': [], +} + +sanity_check_commands = ["%(name)s --version"] + +moduleclass = 'bio' From 48b166808bf877e0e65463fb3b87e670d7a6245a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Thu, 12 Sep 2024 18:59:45 +0200 Subject: [PATCH 058/107] adding easyconfigs: NanoComp-1.24.0-foss-2023a.eb, plotly-orca-1.3.1-GCCcore-12.3.0.eb, joypy-0.2.6-foss-2023a.eb --- .../j/joypy/joypy-0.2.6-foss-2023a.eb | 28 +++++++++++++ .../n/NanoComp/NanoComp-1.24.0-foss-2023a.eb | 42 +++++++++++++++++++ .../plotly-orca-1.3.1-GCCcore-12.3.0.eb | 34 +++++++++++++++ 3 files changed, 104 insertions(+) create mode 100644 easybuild/easyconfigs/j/joypy/joypy-0.2.6-foss-2023a.eb create mode 100644 easybuild/easyconfigs/n/NanoComp/NanoComp-1.24.0-foss-2023a.eb create mode 100644 easybuild/easyconfigs/p/plotly-orca/plotly-orca-1.3.1-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/j/joypy/joypy-0.2.6-foss-2023a.eb b/easybuild/easyconfigs/j/joypy/joypy-0.2.6-foss-2023a.eb new file mode 100644 index 00000000000..db6e77ea520 --- /dev/null +++ b/easybuild/easyconfigs/j/joypy/joypy-0.2.6-foss-2023a.eb @@ -0,0 +1,28 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 +# Update: Petr Král (INUITS) + +easyblock = 'PythonPackage' + +name = 'joypy' +version = '0.2.6' + +homepage = 'https://github.com/sbebo/joypy' +description = "Joyplots in Python with matplotlib & pandas" + +toolchain = {'name': 'foss', 'version': '2023a'} + +sources = [SOURCE_WHL] +checksums = ['fffe882e8281e56e08b374a3148436cb448562ba39e4d566204c7e8ee2caddab'] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('matplotlib', '3.7.2'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/n/NanoComp/NanoComp-1.24.0-foss-2023a.eb b/easybuild/easyconfigs/n/NanoComp/NanoComp-1.24.0-foss-2023a.eb new file mode 100644 index 00000000000..94de23b83da --- /dev/null +++ b/easybuild/easyconfigs/n/NanoComp/NanoComp-1.24.0-foss-2023a.eb @@ -0,0 +1,42 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 +# Update: Petr Král (INUITS) + +easyblock = 'PythonPackage' + +name = 'NanoComp' +version = '1.24.0' + +homepage = 'https://github.com/wdecoster/NanoComp' +description = "Comparing runs of Oxford Nanopore sequencing data and alignments" + +toolchain = {'name': 'foss', 'version': '2023a'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['2ce02bb38c76137ee00ebcc68b6b2654a4a459993e901aebde436c4d54287b09'] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('Pysam', '0.22.0'), + ('nanomath', '1.4.0'), + ('nanoget', '1.19.3'), + ('NanoPlot', '1.43.0'), + ('plotly.py', '5.16.0'), + ('plotly-orca', '1.3.1'), + ('joypy', '0.2.6'), +] + +download_dep_fail = True +use_pip = True + +sanity_check_paths = { + 'files': ['bin/NanoComp'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["NanoComp --help"] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/plotly-orca/plotly-orca-1.3.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/plotly-orca/plotly-orca-1.3.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..fcf1a67d7ff --- /dev/null +++ b/easybuild/easyconfigs/p/plotly-orca/plotly-orca-1.3.1-GCCcore-12.3.0.eb @@ -0,0 +1,34 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 +# Update: Petr Král (INUITS) + +easyblock = 'Binary' + +name = 'plotly-orca' +version = '1.3.1' + +homepage = 'https://github.com/plotly/orca' +description = """Orca is an Electron app that generates images and reports of Plotly things like + plotly.js graphs, dash apps, dashboards from the command line.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/plotly/orca/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['25ebf207d75769c140dcea033a984e7a3a6d919bb8e110a14c890c8cf430f14d'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('nodejs', '18.17.1'), +] + +install_cmd = 'npm install --no-package-lock -g --prefix %(installdir)s electron@6.1.4 v%(version)s.tar.gz' + +sanity_check_paths = { + 'files': ['bin/orca'], + 'dirs': ['lib/node_modules/orca'], +} +sanity_check_commands = ['orca --help'] + +moduleclass = 'vis' From 7cfd8073e6cf8d104983f9fb6fbd291c50d45120 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Thu, 12 Sep 2024 19:01:10 +0200 Subject: [PATCH 059/107] adding easyconfigs: NanoPlot-1.43.0-foss-2023a.eb --- .../n/NanoPlot/NanoPlot-1.43.0-foss-2023a.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/n/NanoPlot/NanoPlot-1.43.0-foss-2023a.eb diff --git a/easybuild/easyconfigs/n/NanoPlot/NanoPlot-1.43.0-foss-2023a.eb b/easybuild/easyconfigs/n/NanoPlot/NanoPlot-1.43.0-foss-2023a.eb new file mode 100644 index 00000000000..4e547b9963b --- /dev/null +++ b/easybuild/easyconfigs/n/NanoPlot/NanoPlot-1.43.0-foss-2023a.eb @@ -0,0 +1,43 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 +# Update: Petr Král (INUITS) + +easyblock = 'PythonPackage' + +name = 'NanoPlot' +version = '1.43.0' + +homepage = 'https://github.com/wdecoster/NanoPlot' +description = "Plotting suite for long read sequencing data and alignments" + +toolchain = {'name': 'foss', 'version': '2023a'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['0f94096d689b552c32fd7246ad87cb6d5e5e2499dad5acc551091e0ff67f48df'] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('Biopython', '1.83'), + ('Pysam', '0.22.0'), + ('nanomath', '1.4.0'), + ('nanoget', '1.19.3'), + ('plotly.py', '5.16.0'), + ('statsmodels', '0.14.1'), + ('Arrow', '14.0.1'), # for pyarrow + ('Kaleido', '0.2.1'), +] + +download_dep_fail = True +use_pip = True + +sanity_check_paths = { + 'files': ['bin/NanoPlot'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["NanoPlot --help"] + +sanity_pip_check = True + +moduleclass = 'bio' From 8d427bbc6975332d95184a09ac6a6102f981b723 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Thu, 12 Sep 2024 19:23:26 +0200 Subject: [PATCH 060/107] add missing dependencies --- easybuild/easyconfigs/p/phasius/phasius-0.2.0-GCC-12.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/p/phasius/phasius-0.2.0-GCC-12.3.0.eb b/easybuild/easyconfigs/p/phasius/phasius-0.2.0-GCC-12.3.0.eb index 0999294863b..bc9d066a13d 100644 --- a/easybuild/easyconfigs/p/phasius/phasius-0.2.0-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/p/phasius/phasius-0.2.0-GCC-12.3.0.eb @@ -379,6 +379,8 @@ builddependencies = [ dependencies = [ ('bzip2', '1.0.8'), ('OpenSSL', '1.1', '', SYSTEM), + ('Perl', '5.36.1'), + ('Perl-bundle-CPAN', '5.36.1'), ] sanity_check_paths = { From 2006e7ae337c0feab2e81ef6d7231585842fdc94 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 13 Sep 2024 08:37:12 +0200 Subject: [PATCH 061/107] Fix test_easyconfig_locations when cache is present The test fails if the easyconfig cache file .eb-path-index is present. This is caused by checking all files instead of only easyconfigs. Fix that, directly ignore the TEMPLATE.eb and replace `assertTrue(False` --- test/easyconfigs/easyconfigs.py | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index dc24739ec01..a4684900718 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -1001,14 +1001,13 @@ def test_easyconfig_locations(self): # ignore git/svn dirs & archived easyconfigs if '/.git/' in dirpath or '/.svn/' in dirpath or '__archive__' in dirpath: continue - # check whether list of .eb files is non-empty - easyconfig_files = [fn for fn in filenames if fn.endswith('eb')] + # check whether list of .eb files is non-empty, only exception: TEMPLATE.eb + easyconfig_files = [fn for fn in filenames if fn.endswith('eb') and fn != 'TEMPLATE.eb'] if easyconfig_files: # check whether path matches required pattern if not easyconfig_dirs_regex.search(dirpath): - # only exception: TEMPLATE.eb - if not (dirpath.endswith('/easybuild/easyconfigs') and filenames == ['TEMPLATE.eb']): - self.assertTrue(False, "List of easyconfig files in %s is empty: %s" % (dirpath, filenames)) + if not dirpath.endswith('/easybuild/easyconfigs'): + self.fail("There should be no easyconfig files in %s, found %s" % (dirpath, easyconfig_files)) def test_easyconfig_name_clashes(self): """Make sure there is not a name clash when all names are lowercase""" @@ -1029,7 +1028,7 @@ def test_easyconfig_name_clashes(self): duplicates[name] = names[name] if duplicates: - self.assertTrue(False, "EasyConfigs with case-insensitive name clash: %s" % duplicates) + self.fail("EasyConfigs with case-insensitive name clash: %s" % duplicates) @skip_if_not_pr_to_non_main_branch() def test_pr_sha256_checksums(self): From f14cfd24a3040e012e3a95f1038f368a84ca5d78 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 13 Sep 2024 09:16:34 +0200 Subject: [PATCH 062/107] Fix typo in patch --- .../GObject-Introspection-1.80.1-GCCcore-13.3.0.eb | 2 +- .../GObject-Introspection-1.80.1_install-GLib-GIR-files.patch | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.80.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.80.1-GCCcore-13.3.0.eb index 4f1620c0db9..83ab6981ae3 100644 --- a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.80.1-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.80.1-GCCcore-13.3.0.eb @@ -18,7 +18,7 @@ patches = ['GObject-Introspection-1.80.1_install-GLib-GIR-files.patch'] checksums = [ {'gobject-introspection-1.80.1.tar.xz': 'a1df7c424e15bda1ab639c00e9051b9adf5cea1a9e512f8a603b53cd199bc6d8'}, {'GObject-Introspection-1.80.1_install-GLib-GIR-files.patch': - '2920b94cf33a41b424de2fb3a0f04b7a1076fd8f47417fa82cf4703ff1ba95fa'}, + 'c1909f1b7fd30784ae789ac0b5e45e0ca3dd2456890b864efa86a2f8c2e563aa'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.80.1_install-GLib-GIR-files.patch b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.80.1_install-GLib-GIR-files.patch index 349eecf7c0b..5c09ded1cb2 100644 --- a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.80.1_install-GLib-GIR-files.patch +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.80.1_install-GLib-GIR-files.patch @@ -6,7 +6,7 @@ This reverts a commit from upstream However GObject-Introspection requires (optionally) Cairo, which requires GLib which requires GLib-Introspection for generating the introspection data. -So there is a cyclib dependency, see https://gitlab.gnome.org/GNOME/gobject-introspection/-/issues/517 +So there is a cyclic dependency, see https://gitlab.gnome.org/GNOME/gobject-introspection/-/issues/517 Author: Alexander Grund (TU Dresden) From 0cc7bb5cf7ecabd958529b72572f2a82733c0a1d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 13 Sep 2024 11:22:38 +0200 Subject: [PATCH 063/107] adding easyconfigs: worker-1.6.13-iimpi-2023a.eb --- .../w/worker/worker-1.6.13-iimpi-2023a.eb | 49 +++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/w/worker/worker-1.6.13-iimpi-2023a.eb diff --git a/easybuild/easyconfigs/w/worker/worker-1.6.13-iimpi-2023a.eb b/easybuild/easyconfigs/w/worker/worker-1.6.13-iimpi-2023a.eb new file mode 100644 index 00000000000..f3b254591f5 --- /dev/null +++ b/easybuild/easyconfigs/w/worker/worker-1.6.13-iimpi-2023a.eb @@ -0,0 +1,49 @@ +easyblock = 'ConfigureMake' + +name = 'worker' +version = '1.6.13' + +homepage = 'https://github.com/gjbex/worker' +description = """The Worker framework has been developed to help deal with parameter exploration experiments + that would otherwise result in many jobs, forcing the user resort to scripting to retain her sanity; + see also https://vscentrum.be/neutral/documentation/cluster-doc/running-jobs/worker-framework.""" + +local_tcname = 'iimpi' +local_tcver = '2023a' +toolchain = {'name': local_tcname, 'version': local_tcver} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/gjbex/worker/archive/'] +sources = ['%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_fixintel.patch'] +checksums = [ + 'b42b8566d82048c706427913c8f7edcd9f5892d61f190ce1f49e428113b7e1bc', # 1.6.13.tar.gz + 'c28bbc837ec5d6fb3390df668b06e0b5169ca31dede907336a2b0637c4a81504', # worker-1.6.13_fixintel.patch +] + +dependencies = [ + ('Perl', '5.36.1'), + ('Perl-bundle-CPAN', '5.36.1'), +] + +# adjust worker configuration file +# note: tweak this to your local setup +postinstallcmds = [ + 'sed -i "s/ cores_per_node = .*/ cores_per_node = 16/g" %(installdir)s/conf/worker.conf', + 'sed -i "s@ qsub = .*@ qsub = `which qsub`@g" %(installdir)s/conf/worker.conf', + 'sed -i "s/ email = .*/ email = hpc-support@example.com/g" %(installdir)s/conf/worker.conf', + 'sed -i "s/ unload_modules = .*/ unload_modules = %s/g" %%(installdir)s/conf/worker.conf' % (local_tcname), + 'sed -i "s@ mpi_module = .*@ mpi_module = %s/%s@g" %%(installdir)s/conf/worker.conf' % (local_tcname, local_tcver), + 'sed -i "s@ module_path = .*@ module_path = %(installdir)s/../../../modules/all@g" %(installdir)s/conf/worker.conf', + "echo PERL=\\'`which perl`\\' > %(installdir)s/conf/worker_perl.sh", +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['wcat', 'wconvert', 'wload', 'worker', 'wreduce', 'wresume', 'wsub', + 'wsummarize']], + 'dirs': ['lib/perl', 'lib/tt'], +} + +sanity_check_commands = ["wsub -help"] + +moduleclass = 'tools' From 85e6c2bbc2fd515a1d4dab607b8d43d0a1ed668f Mon Sep 17 00:00:00 2001 From: Paul Melis Date: Fri, 13 Sep 2024 11:37:52 +0200 Subject: [PATCH 064/107] Added TurboVNC-3.1.2-GCCcore-13.3.0.eb, based on TurboVNC-3.0.1-GCCcore-11.3.0.eb. This one leaves out the patch, as the CMakeLists.txt being patched switched to using pkg-config --- .../TurboVNC/TurboVNC-3.1.2-GCCcore-13.3.0.eb | 63 +++++++++++++++++++ 1 file changed, 63 insertions(+) create mode 100644 easybuild/easyconfigs/t/TurboVNC/TurboVNC-3.1.2-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/t/TurboVNC/TurboVNC-3.1.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/t/TurboVNC/TurboVNC-3.1.2-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..5b532a99e9f --- /dev/null +++ b/easybuild/easyconfigs/t/TurboVNC/TurboVNC-3.1.2-GCCcore-13.3.0.eb @@ -0,0 +1,63 @@ +easyblock = 'CMakeMake' + +name = 'TurboVNC' +version = '3.1.2' + +homepage = 'https://www.turbovnc.org' +description = """TurboVNC is a derivative of VNC (Virtual Network Computing) that is tuned to provide + peak performance for 3D and video workloads.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/%(name)s/%(namelower)s/archive'] +sources = ['%(version)s.tar.gz'] + +checksums = [ + '98629cd2b676df5d30df51c69edd97cf99b395c3080cc55e2f997ac33a7d40de', # 3.0.1.tar.gz +] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), +] + +dependencies = [ + ('Java', '21.0.2', '', SYSTEM), + ('X11', '20240607'), + ('pixman', '0.43.4'), + ('libjpeg-turbo', '3.0.1'), + ('Mesa', '24.1.3'), + ('libGLU', '9.0.3'), + ('libglvnd', '1.7.0'), + ('OpenSSL', '3', '', SYSTEM), +] + +osdependencies = [('pam-devel', 'libpam0g-dev')] + +configopts = "-DTVNC_BUILDJAVA=0 -DTVNC_SYSTEMX11=1 " +configopts += "-DX11_X11_LIB=$EBROOTX11/lib/libX11.%s " % SHLIB_EXT +configopts += "-DX11_Xau_LIB=$EBROOTX11/lib/libXau.%s " % SHLIB_EXT +configopts += "-DX11_SM_LIB=$EBROOTX11/lib/libSM.%s " % SHLIB_EXT +configopts += "-DX11_ICE_LIB=$EBROOTX11/lib/libICE.%s " % SHLIB_EXT +configopts += "-DX11_Pixman_LIB=$EBROOTPIXMAN/lib/libpixman-1.%s.0 " % SHLIB_EXT +configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT +configopts += "-DOPENGL_egl_LIBRARY=$EBROOTLIBGLVND/lib/libEGL.%s " % SHLIB_EXT +configopts += "-DOPENGL_opengl_LIBRARY=$EBROOTLIBGLVND/lib/libOpenGL.%s " % SHLIB_EXT +configopts += "-DOPENGL_glx_LIBRARY=$EBROOTLIBGLVND/lib/libGLX.%s " % SHLIB_EXT + +# if installdir starts with /opt, i.e. /opt/xxx, CMake will set SYSCONFDIR to /etc/opt/xxx instead of /opt/xxx/etc +# https://cmake.org/cmake/help/latest/module/GNUInstallDirs.html +# the solution is to define CMAKE_INSTALL_SYSCONFDIR explicitly +configopts += "-DCMAKE_INSTALL_SYSCONFDIR=%(installdir)s/etc " + +# remove etc/turbovncserver-security.conf, to avoid errors like: +# (EE) Fatal server error: +# (EE) ERROR: .../TurboVNC/2.2.3-GCCcore-8.2.0/etc/turbovncserver-security.conf must be owned by you or by root +postinstallcmds = ['rm -rf %(installdir)s/etc/turbovncserver-security.conf'] + +sanity_check_paths = { + 'files': ['bin/vncserver', 'bin/vncpasswd', 'bin/Xvnc'], + 'dirs': [], +} + +moduleclass = 'vis' From a0e95b89941f4c1996e07702fed8690234056ab2 Mon Sep 17 00:00:00 2001 From: Paul Melis Date: Fri, 13 Sep 2024 13:19:36 +0200 Subject: [PATCH 065/107] Added VirtualGL-3.1.1-GCC-13.3.0.eb and its dep pocl-6.0-GCC-13.3.0.eb --- .../easyconfigs/p/pocl/pocl-6.0-GCC-13.3.0.eb | 48 +++++++++++++++++++ .../v/VirtualGL/VirtualGL-3.1.1-GCC-13.3.0.eb | 47 ++++++++++++++++++ 2 files changed, 95 insertions(+) create mode 100644 easybuild/easyconfigs/p/pocl/pocl-6.0-GCC-13.3.0.eb create mode 100644 easybuild/easyconfigs/v/VirtualGL/VirtualGL-3.1.1-GCC-13.3.0.eb diff --git a/easybuild/easyconfigs/p/pocl/pocl-6.0-GCC-13.3.0.eb b/easybuild/easyconfigs/p/pocl/pocl-6.0-GCC-13.3.0.eb new file mode 100644 index 00000000000..4a188f7473b --- /dev/null +++ b/easybuild/easyconfigs/p/pocl/pocl-6.0-GCC-13.3.0.eb @@ -0,0 +1,48 @@ +# https://github.com/pocl/pocl/issues/1219 +# "PoCL 3.1 supports LLVM only up to 15", so need 4.0 for working with Clang 16 +easyblock = 'CMakeNinja' + +name = 'pocl' +version = '6.0' + +homepage = 'http://portablecl.org' +description = """PoCL is a portable open source (MIT-licensed) implementation +of the OpenCL standard (1.2 with some 2.0 features supported).""" + +toolchain = {'name': 'GCC', 'version': '13.3.0'} + +source_urls = ['https://github.com/pocl/pocl/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = [] +checksums = [ + 'de9710223fc1855f833dbbf42ea2681e06aa8ec0464f0201104dc80a74dfd1f2', # v6.0.tar.gz +] + +builddependencies = [ + ('CMake', '3.29.3'), + ('Ninja', '1.12.1'), + ('pkgconf', '2.2.0'), +] + +dependencies = [ + ('Clang', '18.1.8'), + ('hwloc', '2.10.0'), + ('libtool', '2.4.7'), + ('libxml2', '2.12.7'), +] + +separate_build_dir = True + +# disable attempt to find an ICD loader, always build libOpenCL.so +configopts = "-DENABLE_ICD=0 -DINSTALL_OPENCL_HEADERS=1 " +# make sure we use the easybuild Clang +configopts += "-DWITH_LLVM_CONFIG=$EBROOTCLANG/bin/llvm-config -DSTATIC_LLVM=ON " +# avoid host CPU auto-detection (which may fail on recent CPUs) +configopts += "-DLLC_HOST_CPU=native " + +sanity_check_paths = { + 'files': ['bin/poclcc', 'lib64/libOpenCL.%s' % SHLIB_EXT], + 'dirs': ['include/CL', 'lib64/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/v/VirtualGL/VirtualGL-3.1.1-GCC-13.3.0.eb b/easybuild/easyconfigs/v/VirtualGL/VirtualGL-3.1.1-GCC-13.3.0.eb new file mode 100644 index 00000000000..72cd90736a4 --- /dev/null +++ b/easybuild/easyconfigs/v/VirtualGL/VirtualGL-3.1.1-GCC-13.3.0.eb @@ -0,0 +1,47 @@ +# Contribution from the Crick HPC team +# uploaded by J. Sassmannshausen +# updated by Valentin Plugaru 2019-09-26 +# updated by Paul Melis 2022-10-07, 2023-08-18 + +easyblock = 'CMakeMake' + +name = 'VirtualGL' +version = '3.1.1' + +homepage = 'https://virtualgl.org/' +description = """VirtualGL is an open source toolkit that gives any Linux or +Unix remote display software the ability to run OpenGL applications with full +hardware acceleration.""" + +toolchain = {'name': 'GCC', 'version': '13.3.0'} + +source_urls = ['https://github.com/VirtualGL/virtualgl/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['79c0d76993814d9ed9fdc29908de1cc6da08f41931bc8363084fdfae03f53ce8'] +patches = [] + +builddependencies = [ + ('CMake', '3.29.3'), + ('binutils', '2.42'), +] + +dependencies = [ + ('libjpeg-turbo', '3.0.1'), + ('Mesa', '24.1.3'), + ('libGLU', '9.0.3'), + ('pocl', '6.0'), + ('X11', '20240607'), +] + +local_binaries = [ + 'cpustat', 'glreadtest', 'glxinfo', 'glxspheres64', 'nettest', 'tcbench', + 'vglclient', 'vglconfig', 'vglconnect', 'vglgenkey', 'vgllogin', 'vglrun', + 'vglserver_config' +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_binaries], + 'dirs': ['lib64', 'share', 'include'], +} + +moduleclass = 'vis' From e898862e93d2b4414edee34dfa57bb64c4a580c1 Mon Sep 17 00:00:00 2001 From: ankekreuzer Date: Fri, 13 Sep 2024 13:35:49 +0200 Subject: [PATCH 066/107] Added ATK and Gdk-Pixbuf after the GObject-Introspection fix. --- .../a/ATK/ATK-2.38.0-GCCcore-13.3.0.eb | 39 ++++++++++++++++ .../Gdk-Pixbuf-2.42.11-GCCcore-13.3.0.eb | 46 +++++++++++++++++++ 2 files changed, 85 insertions(+) create mode 100644 easybuild/easyconfigs/a/ATK/ATK-2.38.0-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.42.11-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/a/ATK/ATK-2.38.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/a/ATK/ATK-2.38.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..506079ce98c --- /dev/null +++ b/easybuild/easyconfigs/a/ATK/ATK-2.38.0-GCCcore-13.3.0.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': '13.3.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['ac4de2a4ef4bd5665052952fe169657e65e895c5057dffb3c2a810f6191a0c36'] + +builddependencies = [ + ('binutils', '2.42'), + ('Meson', '1.4.0'), + ('Ninja', '1.12.1'), + ('pkgconf', '2.2.0'), + ('GObject-Introspection', '1.80.1'), +] + +dependencies = [ + ('GLib', '2.80.4'), +] + +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/g/Gdk-Pixbuf/Gdk-Pixbuf-2.42.11-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.42.11-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..2ac4237f4c0 --- /dev/null +++ b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.42.11-GCCcore-13.3.0.eb @@ -0,0 +1,46 @@ +easyblock = 'MesonNinja' + +name = 'Gdk-Pixbuf' +version = '2.42.11' + +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': '13.3.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['49dcb402388708647e8c321d56b6fb30f21e51e515d0c5a942268d23052a2f00'] + +builddependencies = [ + ('binutils', '2.42'), + ('Meson', '1.4.0'), + ('Ninja', '1.12.1'), + ('pkgconf', '2.2.0'), + ('GObject-Introspection', '1.80.1'), +] + +dependencies = [ + ('GLib', '2.80.4'), + ('libjpeg-turbo', '3.0.1'), + ('libpng', '1.6.43'), + ('LibTIFF', '4.6.0'), + ('X11', '20240607'), +] + +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' From ccd2d8d921cae09496001e344852e721f940ea3c Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Fri, 13 Sep 2024 15:14:24 +0000 Subject: [PATCH 067/107] adding easyconfigs: scikit-build-core-0.10.6-GCCcore-13.3.0.eb --- ...scikit-build-core-0.10.6-GCCcore-13.3.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/s/scikit-build-core/scikit-build-core-0.10.6-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/s/scikit-build-core/scikit-build-core-0.10.6-GCCcore-13.3.0.eb b/easybuild/easyconfigs/s/scikit-build-core/scikit-build-core-0.10.6-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..57e6f53d4c0 --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-build-core/scikit-build-core-0.10.6-GCCcore-13.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonBundle' + +name = 'scikit-build-core' +version = '0.10.6' + +homepage = 'https://scikit-build.readthedocs.io/en/latest/' +description = """Scikit-build-core is a complete ground-up rewrite of scikit-build on top of +modern packaging APIs. It provides a bridge between CMake and the Python build +system, allowing you to make Python modules with CMake.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [ + ('binutils', '2.42'), + ('hatchling', '1.24.2'), +] + +dependencies = [ + ('Python', '3.12.3'), + ('Python-bundle-PyPI', '2024.06'), + ('CMake', '3.29.3'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('scikit_build_core', version, { + 'checksums': ['5397db8f09ee050d145406c11deed06538bb0b261df95f8d2d6aaf8699f0126d'], + }), +] + +moduleclass = 'lib' From 9dfa69f4bead0ff5beedf9e3c545e19449667412 Mon Sep 17 00:00:00 2001 From: WilleBell Date: Fri, 13 Sep 2024 17:38:08 +0200 Subject: [PATCH 068/107] adding easyconfigs: DFTD4-3.7.0-foss-2023a.eb, mctc-lib-0.3.1-GCC-12.3.0.eb, json-fortran-9.0.2-GCC-12.3.0.eb, mstore-0.3.0-GCC-12.3.0.eb, TOML-Fortran-0.4.2-GCC-12.3.0.eb --- .../d/DFTD4/DFTD4-3.7.0-foss-2023a.eb | 49 +++++++++++++++++++ .../json-fortran-9.0.2-GCC-12.3.0.eb | 32 ++++++++++++ .../m/mctc-lib/mctc-lib-0.3.1-GCC-12.3.0.eb | 41 ++++++++++++++++ .../m/mstore/mstore-0.3.0-GCC-12.3.0.eb | 37 ++++++++++++++ .../TOML-Fortran-0.4.2-GCC-12.3.0.eb | 24 +++++++++ 5 files changed, 183 insertions(+) create mode 100644 easybuild/easyconfigs/d/DFTD4/DFTD4-3.7.0-foss-2023a.eb create mode 100644 easybuild/easyconfigs/j/json-fortran/json-fortran-9.0.2-GCC-12.3.0.eb create mode 100644 easybuild/easyconfigs/m/mctc-lib/mctc-lib-0.3.1-GCC-12.3.0.eb create mode 100644 easybuild/easyconfigs/m/mstore/mstore-0.3.0-GCC-12.3.0.eb create mode 100644 easybuild/easyconfigs/t/TOML-Fortran/TOML-Fortran-0.4.2-GCC-12.3.0.eb diff --git a/easybuild/easyconfigs/d/DFTD4/DFTD4-3.7.0-foss-2023a.eb b/easybuild/easyconfigs/d/DFTD4/DFTD4-3.7.0-foss-2023a.eb new file mode 100644 index 00000000000..36455d10ffe --- /dev/null +++ b/easybuild/easyconfigs/d/DFTD4/DFTD4-3.7.0-foss-2023a.eb @@ -0,0 +1,49 @@ +# A. Domingo (Vrije Universiteit Brussel) +# J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'CMakeNinja' + +name = 'DFTD4' +version = '3.7.0' + +homepage = 'https://dftd4.readthedocs.io' +description = """ +The dftd4 project provides an implementation of the generally applicable, charge dependent +London-dispersion correction, termed DFT-D4. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'usempi': False, 'openmp': True, 'pic': True} + +github_account = 'dftd4' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['f00b244759eff2c4f54b80a40673440ce951b6ddfa5eee1f46124297e056f69c'] + +builddependencies = [ + ('CMake', '3.26.3'), + ('Ninja', '1.11.1'), +] + +dependencies = [ + ('mctc-lib', '0.3.1'), # New EC + ('mstore', '0.3.0'), # New EC + ('TOML-Fortran', '0.4.2'), # New EC +] + +build_shared_libs = True + +configopts = '-DWITH_BLAS=1 -DWITH_OpenMP=1' + +# run suite of tests with ctest +test_cmd = 'ctest' +runtest = '' + +sanity_check_paths = { + 'files': ['bin/dftd4', 'lib/libdftd4.%s' % SHLIB_EXT, 'include/dftd4.h'], + 'dirs': ['include/dftd4', 'lib/cmake', 'lib/pkgconfig'], +} + +sanity_check_commands = ["dftd4 --help"] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/j/json-fortran/json-fortran-9.0.2-GCC-12.3.0.eb b/easybuild/easyconfigs/j/json-fortran/json-fortran-9.0.2-GCC-12.3.0.eb new file mode 100644 index 00000000000..03dceec3b87 --- /dev/null +++ b/easybuild/easyconfigs/j/json-fortran/json-fortran-9.0.2-GCC-12.3.0.eb @@ -0,0 +1,32 @@ +# J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'CMakeMake' + +name = 'json-fortran' +version = '9.0.2' + +homepage = 'https://github.com/jacobwilliams/json-fortran' +description = "JSON-Fortran: A Modern Fortran JSON API" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://github.com/jacobwilliams/json-fortran/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['a599a77e406e59cdb7672d780e69156b6ce57cb8ce515d21d1744c4065a85976'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), +] + +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' diff --git a/easybuild/easyconfigs/m/mctc-lib/mctc-lib-0.3.1-GCC-12.3.0.eb b/easybuild/easyconfigs/m/mctc-lib/mctc-lib-0.3.1-GCC-12.3.0.eb new file mode 100644 index 00000000000..64ab2ab3bb9 --- /dev/null +++ b/easybuild/easyconfigs/m/mctc-lib/mctc-lib-0.3.1-GCC-12.3.0.eb @@ -0,0 +1,41 @@ +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': 'GCC', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +github_account = 'grimme-lab' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['03dc8ccba37413da70e55a07cef8e8de53bce33f5bb52c1f8db5fec326abe083'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), +] + +dependencies = [ + ('json-fortran', '9.0.2'), # New EC +] + +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 +runtest = True + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/m/mstore/mstore-0.3.0-GCC-12.3.0.eb b/easybuild/easyconfigs/m/mstore/mstore-0.3.0-GCC-12.3.0.eb new file mode 100644 index 00000000000..a609b4e373b --- /dev/null +++ b/easybuild/easyconfigs/m/mstore/mstore-0.3.0-GCC-12.3.0.eb @@ -0,0 +1,37 @@ +# J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'CMakeMake' + +name = 'mstore' +version = '0.3.0' + +homepage = 'https://github.com/grimme-lab/mstore' +description = """Molecular structure store for testing""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +github_account = 'grimme-lab' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['56b3d778629eb74b8a515cd53c727d04609f858a07f8d3555fd5fd392a206dcc'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), +] + +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/t/TOML-Fortran/TOML-Fortran-0.4.2-GCC-12.3.0.eb b/easybuild/easyconfigs/t/TOML-Fortran/TOML-Fortran-0.4.2-GCC-12.3.0.eb new file mode 100644 index 00000000000..baa1d460ed6 --- /dev/null +++ b/easybuild/easyconfigs/t/TOML-Fortran/TOML-Fortran-0.4.2-GCC-12.3.0.eb @@ -0,0 +1,24 @@ +easyblock = 'CMakeMake' + +name = 'TOML-Fortran' +version = '0.4.2' + +homepage = 'https://github.com/toml-f/toml-f' +description = 'TOML parser for Fortran projects' + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://github.com/toml-f/toml-f/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['e66d0e355a8a2e65fd5fc7cd4f00078dfbdbf1b3cc47b60f028c19467df4c337'] + +builddependencies = [ + ('CMake', '3.26.3'), +] + +sanity_check_paths = { + 'files': ['lib/libtoml-f.a'], + 'dirs': ['include/toml-f', 'lib/pkgconfig', 'share'], +} + +moduleclass = 'tools' From 4275401631dfd515bbebd1605b430648d310e199 Mon Sep 17 00:00:00 2001 From: WilleBell Date: Fri, 13 Sep 2024 17:44:49 +0200 Subject: [PATCH 069/107] remove comments --- easybuild/easyconfigs/d/DFTD4/DFTD4-3.7.0-foss-2023a.eb | 6 +++--- .../easyconfigs/m/mctc-lib/mctc-lib-0.3.1-GCC-12.3.0.eb | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/d/DFTD4/DFTD4-3.7.0-foss-2023a.eb b/easybuild/easyconfigs/d/DFTD4/DFTD4-3.7.0-foss-2023a.eb index 36455d10ffe..12d97f5a8a4 100644 --- a/easybuild/easyconfigs/d/DFTD4/DFTD4-3.7.0-foss-2023a.eb +++ b/easybuild/easyconfigs/d/DFTD4/DFTD4-3.7.0-foss-2023a.eb @@ -26,9 +26,9 @@ builddependencies = [ ] dependencies = [ - ('mctc-lib', '0.3.1'), # New EC - ('mstore', '0.3.0'), # New EC - ('TOML-Fortran', '0.4.2'), # New EC + ('mctc-lib', '0.3.1'), + ('mstore', '0.3.0'), + ('TOML-Fortran', '0.4.2'), ] build_shared_libs = True diff --git a/easybuild/easyconfigs/m/mctc-lib/mctc-lib-0.3.1-GCC-12.3.0.eb b/easybuild/easyconfigs/m/mctc-lib/mctc-lib-0.3.1-GCC-12.3.0.eb index 64ab2ab3bb9..e8ec2b8435d 100644 --- a/easybuild/easyconfigs/m/mctc-lib/mctc-lib-0.3.1-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/m/mctc-lib/mctc-lib-0.3.1-GCC-12.3.0.eb @@ -23,7 +23,7 @@ builddependencies = [ ] dependencies = [ - ('json-fortran', '9.0.2'), # New EC + ('json-fortran', '9.0.2'), ] configopts = ['-DBUILD_SHARED_LIBS=ON', '-DBUILD_SHARED_LIBS=OFF'] From 166d673f9b3e612fe7c45c1e33a087721e1b4c76 Mon Sep 17 00:00:00 2001 From: WilleBell Date: Fri, 13 Sep 2024 17:53:54 +0200 Subject: [PATCH 070/107] adding easyconfigs: DFTB+-24.1-foss-2023a.eb, libmbd-0.12.6-foss-2023a.eb, ELSI-2.11.0-foss-2023a-PEXSI.eb, NTPoly-3.1.0-foss-2023a.eb and patches: ELSI-2.11.0_bison_3.8_compat.patch --- .../d/DFTB+/DFTB+-24.1-foss-2023a.eb | 93 +++++++++++++++++++ .../e/ELSI/ELSI-2.11.0-foss-2023a-PEXSI.eb | 43 +++++++++ .../e/ELSI/ELSI-2.11.0_bison_3.8_compat.patch | 14 +++ .../l/libmbd/libmbd-0.12.6-foss-2023a.eb | 59 ++++++++++++ .../n/NTPoly/NTPoly-3.1.0-foss-2023a.eb | 28 ++++++ 5 files changed, 237 insertions(+) create mode 100644 easybuild/easyconfigs/d/DFTB+/DFTB+-24.1-foss-2023a.eb create mode 100644 easybuild/easyconfigs/e/ELSI/ELSI-2.11.0-foss-2023a-PEXSI.eb create mode 100644 easybuild/easyconfigs/e/ELSI/ELSI-2.11.0_bison_3.8_compat.patch create mode 100644 easybuild/easyconfigs/l/libmbd/libmbd-0.12.6-foss-2023a.eb create mode 100644 easybuild/easyconfigs/n/NTPoly/NTPoly-3.1.0-foss-2023a.eb diff --git a/easybuild/easyconfigs/d/DFTB+/DFTB+-24.1-foss-2023a.eb b/easybuild/easyconfigs/d/DFTB+/DFTB+-24.1-foss-2023a.eb new file mode 100644 index 00000000000..c1e713bfa0d --- /dev/null +++ b/easybuild/easyconfigs/d/DFTB+/DFTB+-24.1-foss-2023a.eb @@ -0,0 +1,93 @@ +easyblock = 'CMakeMake' + +name = 'DFTB+' +version = '24.1' + +homepage = 'https://www.dftb-plus.info' +description = """DFTB+ is a fast and efficient versatile quantum mechanical simulation package. +It is based on the Density Functional Tight Binding (DFTB) method, containing +almost all of the useful extensions which have been developed for the DFTB +framework so far. Using DFTB+ you can carry out quantum mechanical simulations +like with ab-initio density functional theory based packages, but in an +approximate way gaining typically around two order of magnitude in speed.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'usempi': True, 'openmp': True, 'pic': True} + +_external_dir = '%%(builddir)s/dftbplus-%%(version)s/external/%s/origin/' +_external_extract = 'mkdir -p %s && tar -C %s' % (_external_dir, _external_dir) +_external_extract += ' --strip-components=1 -xzf %%s' + +source_urls = ['https://github.com/dftbplus/dftbplus/releases/download/%(version)s'] +sources = [ + 'dftbplus-%(version)s.tar.xz', + { + # Slater-Koster (slakos) data for testing + 'source_urls': ['https://github.com/dftbplus/testparams/archive'], + 'download_filename': 'fbe3d62127d86bd8e49ad25a1e5793e6a095e8e7.tar.gz', + 'filename': 'slakos-data-%(version)s.tar.gz', + 'extract_cmd': _external_extract % ('slakos', 'slakos'), + }, + { + # GBSA (gbsa) data for testing + 'source_urls': ['https://github.com/grimme-lab/gbsa-parameters/archive'], + 'download_filename': '6836c4d997e4135e418cfbe273c96b1a3adb13e2.tar.gz', + 'filename': 'gbsa-data-%(version)s.tar.gz', + 'extract_cmd': _external_extract % ('gbsa', 'gbsa'), + }, +] +checksums = [ + {'dftbplus-24.1.tar.xz': '3bc405d1ab834b6b145ca671fb44565ec50a6f576e9e18e7a1ae2c613a311321'}, + {'slakos-data-24.1.tar.gz': '78a0494c2ff9216d6a9199ba07d632b18b809e0198f43905c044b5748bde488d'}, + {'gbsa-data-24.1.tar.gz': 'd464f9f7b1883d1353b433d0c7eae2f5606af092d9b51d38e9ed15e072610a79'}, +] + +builddependencies = [ + ('CMake', '3.26.3'), + ('pkgconf', '1.9.5'), + ('git', '2.41.0', '-nodocs'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('DFTD4', '3.7.0'), + ('ELSI', '2.11.0', '-PEXSI'), + ('libmbd', '0.12.6'), +] + +# Prefer dependencies from EB than bundled sources +configopts = '-DHYBRID_CONFIG_METHODS="Find;Submodule;Fetch" ' +configopts += '-DWITH_MPI=1 -DWITH_OMP=1 -DWITH_SDFTD3=1 -DWITH_ELSI=1 -DWITH_MBD=1 -DWITH_UNIT_TESTS=1 ' +configopts += '-DBUILD_SHARED_LIBS=1 -DWITH_API=1 -DWITH_PYTHON=0 ' # Python bindings installed as extension +configopts += '-DSCALAPACK_LIBRARY="$LIBSCALAPACK" ' + +runtest = 'test' + +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'download_dep_fail': True, + 'use_pip': True, + 'runtest': False, +} +exts_list = [ + ('dptools', version, { + 'source_tmpl': 'dftbplus-%(version)s.tar.xz', + 'source_urls': ['https://github.com/dftbplus/dftbplus/releases/download/%(version)s'], + 'start_dir': 'tools/dptools', + 'checksums': ['3bc405d1ab834b6b145ca671fb44565ec50a6f576e9e18e7a1ae2c613a311321'], + }), +] + +sanity_check_paths = { + 'files': ['bin/' + x for x in ['dftb+', 'dp_bands', 'dp_dos', 'gen2cif', 'gen2xyz', 'makecube', + 'modes', 'repeatgen', 'straingen', 'waveplot', 'xyz2gen']] + + ['lib/libdftbplus.%s' % SHLIB_EXT, 'lib/libmpifx.%s' % SHLIB_EXT], + 'dirs': ['include/dftbplus', 'lib/cmake', 'lib/pkgconfig', 'lib/python%(pyshortver)s/site-packages'] +} + +sanity_check_commands = ["python -c 'import dptools'"] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/e/ELSI/ELSI-2.11.0-foss-2023a-PEXSI.eb b/easybuild/easyconfigs/e/ELSI/ELSI-2.11.0-foss-2023a-PEXSI.eb new file mode 100644 index 00000000000..1ac711b9cf5 --- /dev/null +++ b/easybuild/easyconfigs/e/ELSI/ELSI-2.11.0-foss-2023a-PEXSI.eb @@ -0,0 +1,43 @@ +name = 'ELSI' +version = '2.11.0' +versionsuffix = '-PEXSI' + +homepage = 'https://wordpress.elsi-interchange.org/' +description = """ELSI provides and enhances scalable, open-source software library solutions for + electronic structure calculations in materials science, condensed matter physics, chemistry, and many other fields. + ELSI focuses on methods that solve or circumvent eigenvalue problems in electronic structure theory. + The ELSI infrastructure should also be useful for other challenging eigenvalue problems. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'usempi': True, 'pic': True, 'cstd': 'c++11', 'extra_fflags': '-fallow-argument-mismatch'} + +source_urls = ['https://gitlab.com/elsi_project/elsi_interface/-/archive/v2.11.0/'] +sources = ['elsi_interface-v%(version)s.tar.gz'] +patches = [ + 'ELSI-2.11.0_bison_3.8_compat.patch', +] +checksums = [ + {'elsi_interface-v2.11.0.tar.gz': '2e6929827ed9c99a32381ed9da40482e862c28608d59d4f27db7dcbcaed1520d'}, + {'ELSI-2.11.0_bison_3.8_compat.patch': 'a1284f5c0f442129610aa0fb463cc2b54450e3511a2fd6c871fadc21a16e9504'}, +] + +builddependencies = [ + ('flex', '2.6.4'), + ('Bison', '3.8.2'), + ('CMake', '3.26.3'), +] + +dependencies = [ + ('ELPA', '2023.05.001'), + ('NTPoly', '3.1.0'), +] + +abs_path_compilers = True +build_internal_pexsi = True + +configopts = '-DENABLE_BSEPACK=ON ' + +runtest = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/e/ELSI/ELSI-2.11.0_bison_3.8_compat.patch b/easybuild/easyconfigs/e/ELSI/ELSI-2.11.0_bison_3.8_compat.patch new file mode 100644 index 00000000000..255ed4a5575 --- /dev/null +++ b/easybuild/easyconfigs/e/ELSI/ELSI-2.11.0_bison_3.8_compat.patch @@ -0,0 +1,14 @@ +Make it compatible with Bison 3.7 +Author: Åke Sandgren, 20211020 +Update: Cintia Willemyns (Vrije Universiteit Brussel) +--- elsi_interface-v2.11.0.orig/external/SCOTCH/CMakeLists.txt 2024-09-10 19:01:11.447551000 +0200 ++++ elsi_interface-v2.11.0/external/SCOTCH/CMakeLists.txt 2024-09-10 19:08:44.913993743 +0200 +@@ -56,7 +56,7 @@ + COMMAND mv ${PROJECT_BINARY_DIR}/generated/tmp2.c ${PROJECT_BINARY_DIR}/generated/parser_yy.c + # Versions of bison > 2.X insert a '#include tmp2.h' in tmp2.c. A simple 'mv' will not work. + # The file needs to remain in the directory with the old name. Hence the 'cp' +- COMMAND cp ${PROJECT_BINARY_DIR}/generated/tmp2.h ${PROJECT_BINARY_DIR}/generated/parser_ly.h ++ COMMAND ln -s ${PROJECT_BINARY_DIR}/generated/tmp2.h ${PROJECT_BINARY_DIR}/generated/parser_ly.h + COMMAND flex -Pscotchyy -o${PROJECT_BINARY_DIR}/generated/tmp1.c ${SCOTCH_DIR}/parser_ll.l + COMMAND mv ${PROJECT_BINARY_DIR}/generated/tmp1.c ${PROJECT_BINARY_DIR}/generated/parser_ll.c + DEPENDS ${SCOTCH_DIR}/parser_yy.y ${SCOTCH_DIR}/parser_ll.l ${SCOTCH_DIR}/parser_yy.h ${SCOTCH_DIR}/parser_ll.h diff --git a/easybuild/easyconfigs/l/libmbd/libmbd-0.12.6-foss-2023a.eb b/easybuild/easyconfigs/l/libmbd/libmbd-0.12.6-foss-2023a.eb new file mode 100644 index 00000000000..260ecb98ddb --- /dev/null +++ b/easybuild/easyconfigs/l/libmbd/libmbd-0.12.6-foss-2023a.eb @@ -0,0 +1,59 @@ +easyblock = 'CMakeMake' + +name = 'libmbd' +version = '0.12.6' + +homepage = 'https://libmbd.github.io/index.html' +description = """ +Libmbd implements the many-body dispersion (MBD) method in several programming languages and frameworks: + + - The Fortran implementation is the reference, most advanced implementation, with support for analytical + gradients and distributed parallelism, and additional functionality beyond the MBD method itself. + It provides a low-level and a high-level Fortran API, as well as a C API. Furthermore, Python bindings + to the C API are provided. + - The Python/Numpy implementation is intended for prototyping, and as a high-level language reference. + - The Python/Tensorflow implementation is an experiment that should enable rapid prototyping of machine + learning applications with MBD. + +The Python-based implementations as well as Python bindings to the Libmbd C API are accessible from the +Python package called Pymbd. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'usempi': True, 'pic': True} + +github_account = 'libmbd' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['9f8154b6b2f57e78a8e33d3b315a244185e8e5ecb03661a469808af7512e761e'] + +builddependencies = [ + ('CMake', '3.26.3'), + ('pkgconf', '1.9.5'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('ELSI', '2.11.0', '-PEXSI'), +] + +# build scripts expect either a git repo or a defined version string in a file +_versiontag_file = '%(builddir)s/%(name)s-%(version)s/cmake/LibmbdVersionTag.cmake' +preconfigopts = "echo 'set(VERSION_TAG \"%%(version)s\")' > %s && " % _versiontag_file + +configopts = "-DENABLE_SCALAPACK_MPI=ON -DENABLE_ELSI=ON " +configopts += "-DMPIEXEC_MAX_NUMPROCS=1 " # number of procs in the tests + +# make sure that built libraries (libmbd.so) in build directory are picked when running tests +# this is required when RPATH linking is used +pretestopts = "export LD_LIBRARY_PATH=%(builddir)s/easybuild_obj:$LD_LIBRARY_PATH && " + +runtest = 'test' + +sanity_check_paths = { + 'files': ['lib/libmbd.%s' % SHLIB_EXT, 'include/mbd/mbd.h', 'include/mbd/mbd.mod'], + 'dirs': ['lib/cmake/mbd'], +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/n/NTPoly/NTPoly-3.1.0-foss-2023a.eb b/easybuild/easyconfigs/n/NTPoly/NTPoly-3.1.0-foss-2023a.eb new file mode 100644 index 00000000000..8f7a531ce0e --- /dev/null +++ b/easybuild/easyconfigs/n/NTPoly/NTPoly-3.1.0-foss-2023a.eb @@ -0,0 +1,28 @@ +easyblock = 'CMakeMake' + +name = 'NTPoly' +version = '3.1.0' + +homepage = 'https://github.com/william-dawson/NTPoly' +description = """is a massively parallel library for computing the functions of sparse, symmetric matrices based on +polynomial expansions. For sufficiently sparse matrices, most of the matrix functions +in NTPoly can be computed in linear time.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'openmp': False, 'usempi': True} + +source_urls = ['https://github.com/william-dawson/NTPoly/archive/ntpoly-v%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['71cd6827f20c68e384555dbcfc85422d0690e21d21d7b5d4f7375544a2755271'] + +builddependencies = [('CMake', '3.26.3')] + +build_shared_libs = True + +sanity_check_paths = { + 'files': ['include/%s.mod' % x for x in ['datatypesmodule', 'densitymatrixsolversmodule']] + + ['lib64/libNTPoly.%s' % SHLIB_EXT, 'lib/libNTPoly.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'math' From a73038934f8f5076cc48f8d8e8070c3dd3c2203c Mon Sep 17 00:00:00 2001 From: WilleBell Date: Fri, 13 Sep 2024 18:51:41 +0200 Subject: [PATCH 071/107] fix dftd4 name, add multicharge and remove TOML-Fortran --- .../dftd4-3.7.0-foss-2023a.eb} | 5 ++- .../multicharge-0.3.0-gfbf-2023a.eb | 38 +++++++++++++++++++ .../TOML-Fortran-0.4.2-GCC-12.3.0.eb | 24 ------------ 3 files changed, 41 insertions(+), 26 deletions(-) rename easybuild/easyconfigs/d/{DFTD4/DFTD4-3.7.0-foss-2023a.eb => dftd4/dftd4-3.7.0-foss-2023a.eb} (92%) create mode 100644 easybuild/easyconfigs/m/multicharge/multicharge-0.3.0-gfbf-2023a.eb delete mode 100644 easybuild/easyconfigs/t/TOML-Fortran/TOML-Fortran-0.4.2-GCC-12.3.0.eb diff --git a/easybuild/easyconfigs/d/DFTD4/DFTD4-3.7.0-foss-2023a.eb b/easybuild/easyconfigs/d/dftd4/dftd4-3.7.0-foss-2023a.eb similarity index 92% rename from easybuild/easyconfigs/d/DFTD4/DFTD4-3.7.0-foss-2023a.eb rename to easybuild/easyconfigs/d/dftd4/dftd4-3.7.0-foss-2023a.eb index 12d97f5a8a4..912ed2baf4a 100644 --- a/easybuild/easyconfigs/d/DFTD4/DFTD4-3.7.0-foss-2023a.eb +++ b/easybuild/easyconfigs/d/dftd4/dftd4-3.7.0-foss-2023a.eb @@ -1,9 +1,10 @@ # A. Domingo (Vrije Universiteit Brussel) # J. Sassmannshausen (Imperial College London/UK) +# C. Willemyns (Vrije Universiteit Brussel) easyblock = 'CMakeNinja' -name = 'DFTD4' +name = 'dftd4' version = '3.7.0' homepage = 'https://dftd4.readthedocs.io' @@ -28,7 +29,7 @@ builddependencies = [ dependencies = [ ('mctc-lib', '0.3.1'), ('mstore', '0.3.0'), - ('TOML-Fortran', '0.4.2'), + ('multicharge', '0.3.0'), ] build_shared_libs = True diff --git a/easybuild/easyconfigs/m/multicharge/multicharge-0.3.0-gfbf-2023a.eb b/easybuild/easyconfigs/m/multicharge/multicharge-0.3.0-gfbf-2023a.eb new file mode 100644 index 00000000000..b6debf00815 --- /dev/null +++ b/easybuild/easyconfigs/m/multicharge/multicharge-0.3.0-gfbf-2023a.eb @@ -0,0 +1,38 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'CMakeNinja' + +name = 'multicharge' +version = '0.3.0' + +homepage = 'https://github.com/grimme-lab/multicharge' +description = """Electronegativity equilibration model for atomic partial charges.""" + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +github_account = 'grimme-lab' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] + +builddependencies = [ + ('CMake', '3.26.3'), + ('Ninja', '1.11.1'), + ('binutils', '2.40'), +] + +dependencies = [ + ('mctc-lib', '0.3.1'), + ('mstore', '0.3.0'), +] + +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 +runtest = True + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/t/TOML-Fortran/TOML-Fortran-0.4.2-GCC-12.3.0.eb b/easybuild/easyconfigs/t/TOML-Fortran/TOML-Fortran-0.4.2-GCC-12.3.0.eb deleted file mode 100644 index baa1d460ed6..00000000000 --- a/easybuild/easyconfigs/t/TOML-Fortran/TOML-Fortran-0.4.2-GCC-12.3.0.eb +++ /dev/null @@ -1,24 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'TOML-Fortran' -version = '0.4.2' - -homepage = 'https://github.com/toml-f/toml-f' -description = 'TOML parser for Fortran projects' - -toolchain = {'name': 'GCC', 'version': '12.3.0'} - -source_urls = ['https://github.com/toml-f/toml-f/archive/refs/tags/'] -sources = ['v%(version)s.tar.gz'] -checksums = ['e66d0e355a8a2e65fd5fc7cd4f00078dfbdbf1b3cc47b60f028c19467df4c337'] - -builddependencies = [ - ('CMake', '3.26.3'), -] - -sanity_check_paths = { - 'files': ['lib/libtoml-f.a'], - 'dirs': ['include/toml-f', 'lib/pkgconfig', 'share'], -} - -moduleclass = 'tools' From 95d84e1426f1a98bca00bb48160d2672e21ce7d9 Mon Sep 17 00:00:00 2001 From: WilleBell Date: Fri, 13 Sep 2024 18:59:48 +0200 Subject: [PATCH 072/107] fix dftd4 name --- easybuild/easyconfigs/d/DFTB+/DFTB+-24.1-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/DFTB+/DFTB+-24.1-foss-2023a.eb b/easybuild/easyconfigs/d/DFTB+/DFTB+-24.1-foss-2023a.eb index c1e713bfa0d..c862fcea552 100644 --- a/easybuild/easyconfigs/d/DFTB+/DFTB+-24.1-foss-2023a.eb +++ b/easybuild/easyconfigs/d/DFTB+/DFTB+-24.1-foss-2023a.eb @@ -51,7 +51,7 @@ builddependencies = [ dependencies = [ ('Python', '3.11.3'), ('SciPy-bundle', '2023.07'), - ('DFTD4', '3.7.0'), + ('dftd4', '3.7.0'), ('ELSI', '2.11.0', '-PEXSI'), ('libmbd', '0.12.6'), ] From 21fbc8d3017bbe7b268a51d60eda6f9720370fad Mon Sep 17 00:00:00 2001 From: Cintia Willemyns <115622907+WilleBell@users.noreply.github.com> Date: Fri, 13 Sep 2024 19:20:28 +0200 Subject: [PATCH 073/107] Add missing checksum to multicharge --- .../easyconfigs/m/multicharge/multicharge-0.3.0-gfbf-2023a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/m/multicharge/multicharge-0.3.0-gfbf-2023a.eb b/easybuild/easyconfigs/m/multicharge/multicharge-0.3.0-gfbf-2023a.eb index b6debf00815..b4ccfa2544f 100644 --- a/easybuild/easyconfigs/m/multicharge/multicharge-0.3.0-gfbf-2023a.eb +++ b/easybuild/easyconfigs/m/multicharge/multicharge-0.3.0-gfbf-2023a.eb @@ -13,6 +13,7 @@ toolchain = {'name': 'gfbf', 'version': '2023a'} github_account = 'grimme-lab' source_urls = [GITHUB_SOURCE] sources = ['v%(version)s.tar.gz'] +checksums = ['2fcc1f80871f404f005e9db458ffaec95bb28a19516a0245278cd3175b63a6b2'] builddependencies = [ ('CMake', '3.26.3'), From 84798df187db79668e55befb2b87cd1f9accb40e Mon Sep 17 00:00:00 2001 From: Sam Moors Date: Fri, 13 Sep 2024 22:09:15 +0200 Subject: [PATCH 074/107] add sanity_check_commands --- .../easyconfigs/r/rnamotif/rnamotif-20240904-GCCcore-12.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/r/rnamotif/rnamotif-20240904-GCCcore-12.3.0.eb b/easybuild/easyconfigs/r/rnamotif/rnamotif-20240904-GCCcore-12.3.0.eb index bb1513a04b2..742dabcaa85 100644 --- a/easybuild/easyconfigs/r/rnamotif/rnamotif-20240904-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/r/rnamotif/rnamotif-20240904-GCCcore-12.3.0.eb @@ -37,6 +37,8 @@ sanity_check_paths = { 'dirs': ['efndata'], } +sanity_check_commands = ['rnamotif -h 2>&1 | grep usage'] + modextravars = {'EFNDATA': 'efndata'} moduleclass = 'bio' From 82206bb1c68d8d9ccd551b36efb0a0cc2251147c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 14 Sep 2024 22:51:52 +0200 Subject: [PATCH 075/107] adding easyconfigs: EasyBuild-4.9.3.eb --- .../e/EasyBuild/EasyBuild-4.9.3.eb | 56 +++++++++++++++++++ 1 file changed, 56 insertions(+) create mode 100644 easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.9.3.eb diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.9.3.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.9.3.eb new file mode 100644 index 00000000000..4059b342213 --- /dev/null +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.9.3.eb @@ -0,0 +1,56 @@ +easyblock = 'EB_EasyBuildMeta' + +name = 'EasyBuild' +version = '4.9.3' + +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/10/a0/e5484d4078f7450042cd7b7a1af24fd3f8d0cb4818f4578e4c322ba488d8/', + # easybuild-easyblocks + 'https://files.pythonhosted.org/packages/ee/40/4f6412917f83429f9389b977903c8905f216cb211c8bf3111f28c3017677/', + # easybuild-easyconfigs + 'https://files.pythonhosted.org/packages/13/95/44d1e10ceaaf08219ef50d1d97d500ba3b6b34f2d76dd1ff64def71612dc/', +] +# note: subdirectory for each unpacked source tarball is renamed because custom easyblock in older EasyBuild version +# that is used for installing EasyBuild with EasyBuild expects subdirectories with '-' rather than '_'; +# see also https://github.com/easybuilders/easybuild-easyblocks/pull/3358 +sources = [ + { + 'filename': 'easybuild_framework-%(version)s.tar.gz', + 'extract_cmd': "tar xfvz %s && mv easybuild_framework-%(version)s easybuild-framework-%(version)s", + }, + { + 'filename': 'easybuild_easyblocks-%(version)s.tar.gz', + 'extract_cmd': "tar xfvz %s && mv easybuild_easyblocks-%(version)s easybuild-easyblocks-%(version)s", + }, + { + 'filename': 'easybuild_easyconfigs-%(version)s.tar.gz', + 'extract_cmd': "tar xfvz %s && mv easybuild_easyconfigs-%(version)s easybuild-easyconfigs-%(version)s", + }, +] +checksums = [ + {'easybuild_framework-4.9.3.tar.gz': '43bbcaa0a7b075eb6483054428ef4b1279a9fc850301171688f86899eaebfff8'}, + {'easybuild_easyblocks-4.9.3.tar.gz': '4f036be918f88fe2dadba87f15d696e9b4d3f8f06986c675b9fafc77b591649d'}, + {'easybuild_easyconfigs-4.9.3.tar.gz': 'f7f501c87cb16a8eb393f5e98cb3cd5f8e84314901e81ff50f8140681b415676'}, +] + +# 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 1f374568b1133e89a5faf07c872a531d5681ac46 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 14 Sep 2024 23:16:10 +0200 Subject: [PATCH 076/107] bump version to 4.9.4dev --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index ae4897821b1..47b7fc09bd1 100644 --- a/setup.py +++ b/setup.py @@ -44,7 +44,7 @@ # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like # UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0' # This causes problems further up the dependency chain... -VERSION = '4.9.3' +VERSION = '4.9.4.dev0' MAJ_VER = VERSION.split('.')[0] MAJMIN_VER = '.'.join(VERSION.split('.')[0:2]) From 04a1c44abd4ae39fe02e815110731f22aa055bdc Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Mon, 16 Sep 2024 10:25:51 +0200 Subject: [PATCH 077/107] adding easyconfigs: chopper-0.9.0-GCCcore-12.3.0.eb and patches: chopper-0.9.0_fix_incorrect_version.patch --- .../c/chopper/chopper-0.9.0-GCCcore-12.3.0.eb | 316 ++++++++++++++++++ .../chopper-0.9.0_fix_incorrect_version.patch | 28 ++ 2 files changed, 344 insertions(+) create mode 100644 easybuild/easyconfigs/c/chopper/chopper-0.9.0-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/c/chopper/chopper-0.9.0_fix_incorrect_version.patch diff --git a/easybuild/easyconfigs/c/chopper/chopper-0.9.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/c/chopper/chopper-0.9.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..df0b3abaa21 --- /dev/null +++ b/easybuild/easyconfigs/c/chopper/chopper-0.9.0-GCCcore-12.3.0.eb @@ -0,0 +1,316 @@ +easyblock = 'Cargo' + +name = 'chopper' +version = '0.9.0' + +homepage = 'https://github.com/wdecoster/chopper' +description = """Rust implementation of NanoFilt+NanoLyse, both +originally written in Python. This tool, intended for long read +sequencing such as PacBio or ONT, filters and trims a fastq file. +Filtering is done on average read quality and minimal or maximal read +length, and applying a headcrop (start of read) and tailcrop (end of +read) while printing the reads passing the filter.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +github_account = 'wdecoster' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = [ + 'chopper-0.9.0_fix_incorrect_version.patch', +] +checksums = [ + {'v0.9.0.tar.gz': 'ae5b6f8f5ffde45582998b63cb45b4221b25ee37a9fde7a256e653c7f3f12075'}, + {'adler-1.0.2.tar.gz': 'f26201604c87b1e01bd3d98f8d5d9a8fcbb815e8cedb41ffccbeb4bf593a35fe'}, + {'aho-corasick-1.1.3.tar.gz': '8e60d3430d3a69478ad0993f19238d2df97c507009a52b3c10addcd7f6bcb916'}, + {'anstream-0.6.13.tar.gz': 'd96bd03f33fe50a863e394ee9718a706f988b9079b20c3784fb726e7678b62fb'}, + {'anstyle-1.0.6.tar.gz': 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'bec47e5bfd1bff0eeaf6d8b485cc1074891a197ab4225d504cb7a1ab88b02bf0'}, + {'xz2-0.1.7.tar.gz': '388c44dc09d76f1536602ead6d325eb532f5c122f17782bd57fb47baeeb767e2'}, + {'chopper-0.9.0_fix_incorrect_version.patch': 'b3f3dfa620fbda6d00a73eafc8508a73ac4d96f6edfb0e804b3ff0bc149e37cd'}, +] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), + ('Rust', '1.75.0'), +] + +dependencies = [ + ('bzip2', '1.0.8'), + ('XZ', '5.4.2'), +] + +crates = [ + ('adler', '1.0.2'), + ('aho-corasick', '1.1.3'), + ('anstream', '0.6.13'), + ('anstyle', '1.0.6'), + ('anstyle-parse', '0.2.3'), + ('anstyle-query', '1.0.2'), + ('anstyle-wincon', '3.0.2'), + ('anyhow', '1.0.82'), + ('approx', '0.5.1'), + ('atty', '0.2.14'), + ('autocfg', '1.2.0'), + ('bio', '1.6.0'), + ('bio-types', '1.0.1'), + ('bit-set', '0.5.3'), + ('bit-vec', '0.6.3'), + ('buffer-redux', '1.0.1'), + ('bv', '0.11.1'), + ('bytecount', '0.6.8'), + ('bytemuck', '1.15.0'), + ('byteorder', '1.5.0'), + ('bzip2', '0.4.4'), + ('bzip2-sys', '0.1.11+1.0.8'), + ('cc', '1.0.94'), + ('cfg-if', '1.0.0'), + ('clap', '4.5.4'), + ('clap_builder', '4.5.2'), + ('clap_derive', '4.5.4'), + ('clap_lex', '0.7.0'), + ('cmake', '0.1.50'), + ('colorchoice', '1.0.0'), + ('crc32fast', '1.4.0'), + ('crossbeam-deque', '0.8.5'), + ('crossbeam-epoch', '0.9.18'), + ('crossbeam-utils', '0.8.19'), + ('csv', '1.3.0'), + ('csv-core', '0.1.11'), + ('custom_derive', '0.1.7'), + ('derive-new', '0.5.9'), + ('editdistancek', '1.0.2'), + ('either', '1.11.0'), + ('enum-map', '2.7.3'), + ('enum-map-derive', '0.17.0'), + ('equivalent', '1.0.1'), + ('feature-probe', '0.1.1'), + ('fixedbitset', '0.4.2'), + ('flate2', '1.0.28'), + ('fxhash', '0.2.1'), + ('getrandom', '0.2.14'), + ('hashbrown', '0.14.3'), + ('heck', '0.4.1'), + ('heck', '0.5.0'), + ('hermit-abi', '0.1.19'), + ('indexmap', '2.2.6'), + ('itertools', '0.11.0'), + ('itertools-num', '0.1.3'), + ('itoa', '1.0.11'), + ('lazy_static', '1.4.0'), + ('libc', '0.2.153'), + ('libm', '0.2.8'), + ('libz-ng-sys', '1.1.15'), + ('libz-sys', '1.1.16'), + ('lzma-sys', '0.1.20'), + ('matrixmultiply', '0.3.8'), + ('memchr', '2.7.2'), + ('minimap2', '0.1.17+minimap2.2.27'), + ('minimap2-sys', '0.1.18+minimap2.2.27'), + ('miniz_oxide', '0.7.2'), + ('multimap', '0.9.1'), + ('nalgebra', '0.29.0'), + ('nalgebra-macros', '0.1.0'), + ('ndarray', '0.15.6'), + ('needletail', '0.5.1'), + ('newtype_derive', '0.1.6'), + ('num-complex', '0.4.5'), + ('num-integer', '0.1.46'), + ('num-rational', '0.4.1'), + ('num-traits', '0.2.18'), + ('ordered-float', '3.9.2'), + ('paste', '1.0.14'), + ('petgraph', '0.6.4'), + ('pkg-config', '0.3.30'), + ('ppv-lite86', '0.2.17'), + ('proc-macro2', '1.0.81'), + ('quote', '1.0.36'), + ('rand', '0.8.5'), + ('rand_chacha', '0.3.1'), + ('rand_core', '0.6.4'), + ('rand_distr', '0.4.3'), + ('rawpointer', '0.2.1'), + ('rayon', '1.10.0'), + ('rayon-core', '1.12.1'), + ('regex', '1.10.4'), + ('regex-automata', '0.4.6'), + ('regex-syntax', '0.8.3'), + ('rustc_version', '0.1.7'), + ('rustversion', '1.0.15'), + ('ryu', '1.0.17'), + ('safe_arch', '0.7.1'), + ('semver', '0.1.20'), + ('serde', '1.0.198'), + ('serde_derive', '1.0.198'), + ('simba', '0.6.0'), + ('simdutf8', '0.1.4'), + ('statrs', '0.16.0'), + ('strsim', '0.11.1'), + ('strum', '0.25.0'), + ('strum_macros', '0.25.3'), + ('syn', '1.0.109'), + ('syn', '2.0.60'), + ('thiserror', '1.0.58'), + ('thiserror-impl', '1.0.58'), + ('triple_accel', '0.4.0'), + ('typenum', '1.17.0'), + ('unicode-ident', '1.0.12'), + ('utf8parse', '0.2.1'), + ('vcpkg', '0.2.15'), + ('vec_map', '0.8.2'), + ('wasi', '0.11.0+wasi-snapshot-preview1'), + ('wide', '0.7.16'), + ('winapi', '0.3.9'), + ('winapi-i686-pc-windows-gnu', '0.4.0'), + ('winapi-x86_64-pc-windows-gnu', '0.4.0'), + ('windows-sys', '0.52.0'), + ('windows-targets', '0.52.5'), + ('windows_aarch64_gnullvm', '0.52.5'), + ('windows_aarch64_msvc', '0.52.5'), + ('windows_i686_gnu', '0.52.5'), + ('windows_i686_gnullvm', '0.52.5'), + ('windows_i686_msvc', '0.52.5'), + ('windows_x86_64_gnu', '0.52.5'), + ('windows_x86_64_gnullvm', '0.52.5'), + ('windows_x86_64_msvc', '0.52.5'), + ('xz2', '0.1.7'), +] + +sanity_check_paths = { + 'files': ['bin/chopper'], + 'dirs': [], +} + +sanity_check_commands = [ + 'chopper --help', +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/chopper/chopper-0.9.0_fix_incorrect_version.patch b/easybuild/easyconfigs/c/chopper/chopper-0.9.0_fix_incorrect_version.patch new file mode 100644 index 00000000000..57c15b94db4 --- /dev/null +++ b/easybuild/easyconfigs/c/chopper/chopper-0.9.0_fix_incorrect_version.patch @@ -0,0 +1,28 @@ +Fix incorrect version number in the 0.9.0 tar file. + +Åke Sandgren, 2024-09-16 +diff --git a/Cargo.lock b/Cargo.lock +index 3e8f1fe..53fa5da 100644 +--- a/Cargo.lock ++++ b/Cargo.lock +@@ -236,7 +236,7 @@ checksum = "baf1de4339761588bc0619e3cbc0120ee582ebb74b53b4efbf79117bd2da40fd" + + [[package]] + name = "chopper" +-version = "0.8.0" ++version = "0.9.0" + dependencies = [ + "approx", + "atty", +diff --git a/Cargo.toml b/Cargo.toml +index f268dce..7f7277a 100644 +--- a/Cargo.toml ++++ b/Cargo.toml +@@ -1,6 +1,6 @@ + [package] + name = "chopper" +-version = "0.8.0" ++version = "0.9.0" + authors = ["wdecoster "] + edition = "2021" + From 905a8a835ebcb0221d30bcc16699e20cc8616ed1 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 16 Sep 2024 12:37:49 +0200 Subject: [PATCH 078/107] account for crates for easyconfigs using Cargo-based easyblock when determining checksums for patches --- test/easyconfigs/easyconfigs.py | 13 ++++++++----- 1 file changed, 8 insertions(+), 5 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index a4684900718..74f98af5cf8 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -1459,6 +1459,9 @@ def template_easyconfig_test(self, spec): ] failing_checks.extend("Old URL '%s' found" % old_url for old_url in old_urls if old_url in ec.rawtxt) + # Note the use of app.cfg which might contain sources populated by e.g. the Cargo easyblock + sources, patches, checksums = app.cfg['sources'], app.cfg['patches'], app.cfg['checksums'] + # make sure binutils is included as a (build) dep if toolchain is GCCcore if ec['toolchain']['name'] == 'GCCcore': # easyblocks without a build step @@ -1475,7 +1478,7 @@ def template_easyconfig_test(self, spec): requires_binutils &= bool(ec['name'] not in binutils_complete_dependencies) # if no sources/extensions/components are specified, it's just a bundle (nothing is being compiled) - requires_binutils &= bool(ec['sources'] or ec['exts_list'] or ec.get('components')) + requires_binutils &= bool(sources or ec['exts_list'] or ec.get('components')) if requires_binutils: # dependencies() returns both build and runtime dependencies @@ -1506,13 +1509,13 @@ def template_easyconfig_test(self, spec): if openssl_osdep: failing_checks.append("OpenSSL should not be listed as OS dependency") - src_cnt = len(ec['sources']) - patch_checksums = ec['checksums'][src_cnt:] + src_cnt = len(sources) + patch_checksums = checksums[src_cnt:] # make sure all patch files are available specdir = os.path.dirname(spec) basedir = os.path.dirname(os.path.dirname(specdir)) - for idx, patch in enumerate(ec['patches']): + for idx, patch in enumerate(patches): patch_dir = specdir if isinstance(patch, str): patch_name = patch @@ -1535,7 +1538,7 @@ def template_easyconfig_test(self, spec): # make sure 'source' step is not being skipped, # since that implies not verifying the checksum - if ec['checksums'] and ('source' in ec['skipsteps']): + if checksums and ('source' in ec['skipsteps']): failing_checks.append("'source' step should not be skipped, since that implies not verifying checksums") for ext in ec.get_ref('exts_list'): From 34ad2d1556fe85c86b3e957f04c77ca9b9787785 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Mon, 16 Sep 2024 16:10:58 +0200 Subject: [PATCH 079/107] adding easyconfigs: RepeatMasker-4.1.7-p1-foss-2023a.eb, RMBlast-2.14.1-gompi-2023a.eb, TRF-4.09.1-GCCcore-12.3.0.eb --- .../r/RMBlast/RMBlast-2.14.1-gompi-2023a.eb | 65 +++++++++++++++++++ .../RepeatMasker-4.1.7-p1-foss-2023a.eb | 57 ++++++++++++++++ .../t/TRF/TRF-4.09.1-GCCcore-12.3.0.eb | 30 +++++++++ 3 files changed, 152 insertions(+) create mode 100644 easybuild/easyconfigs/r/RMBlast/RMBlast-2.14.1-gompi-2023a.eb create mode 100644 easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.1.7-p1-foss-2023a.eb create mode 100644 easybuild/easyconfigs/t/TRF/TRF-4.09.1-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/r/RMBlast/RMBlast-2.14.1-gompi-2023a.eb b/easybuild/easyconfigs/r/RMBlast/RMBlast-2.14.1-gompi-2023a.eb new file mode 100644 index 00000000000..22e6ed85f93 --- /dev/null +++ b/easybuild/easyconfigs/r/RMBlast/RMBlast-2.14.1-gompi-2023a.eb @@ -0,0 +1,65 @@ +## +# EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos , Kenneth Hoste (UGent) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of +# the policy: https://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +# +# Update: Petr Král (INUITS) +## + +easyblock = 'ConfigureMake' + +name = 'RMBlast' +version = '2.14.1' + +homepage = 'https://www.repeatmasker.org/rmblast/' +description = """RMBlast is a RepeatMasker compatible version of the standard NCBI BLAST suite. The primary + difference between this distribution and the NCBI distribution is the addition of a new program 'rmblastn' + for use with RepeatMasker and RepeatModeler.""" + +toolchain = {'name': 'gompi', 'version': '2023a'} +toolchainopts = {'usempi': True} + +# RMBlast is distributed as a patch that applies on top of BLAST+ +source_urls = ['https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/%(version)s/'] +sources = ['ncbi-blast-%(version)s+-src.tar.gz'] +patches = [('https://www.repeatmasker.org/%(namelower)s/isb-%(version)s+-%(namelower)s.patch.gz', 2)] +checksums = [ + {'ncbi-blast-2.14.1+-src.tar.gz': '712c2dbdf0fb13cc1c2d4f4ef5dd1ce4b06c3b57e96dfea8f23e6e99f5b1650e'}, + {'isb-2.14.1+-rmblast.patch.gz': '9c8091eb2aec97ac83287859d2bfec83cb08c082d5a121cbefe3cc626f933763'}, +] + +dependencies = [ + ('zlib', '1.2.13'), + ('bzip2', '1.0.8'), + ('PCRE', '8.45'), + ('Boost.MPI', '1.82.0'), + ('GMP', '6.2.1'), + ('libpng', '1.6.39'), + ('libjpeg-turbo', '2.1.5.1'), + ('LMDB', '0.9.31'), +] + +# Disable auto-vectorization for the API on CPUs with AVX512 (Intel Skylake and onwards) +# Compilation fails on src/algo/blast/api/prelim_stage.cpp +local_apimake = 'src/algo/blast/api/Makefile.xblast.lib' +preconfigopts = "sed -i 's/FAST_CXXFLAGS)/FAST_CXXFLAGS) -fno-tree-vectorize/g' %s &&" % local_apimake + +configopts = "--with-64 --with-z=$EBROOTZLIB --with-bz2=$EBROOTBZIP2 " +configopts += "--with-pcre=$EBROOTPCRE --with-boost=$EBROOTBOOST " +configopts += "--with-gmp=$EBROOTGMP --with-png=$EBROOTLIBPNG " +configopts += "--with-jpeg=$EBROOTLIBJPEGMINTURBO --with-lmdb=$EBROOTLMDB" + +prebuildopts = "sed -i 's/LIBS =/LIBS = $(BLAST_THIRD_PARTY_LIBS)/' src/app/rmblastn/Makefile.rmblastn.app && " + +sanity_check_paths = { + 'files': ['bin/blastp', 'bin/blastn', 'bin/deltablast', 'bin/rmblastn'], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.1.7-p1-foss-2023a.eb b/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.1.7-p1-foss-2023a.eb new file mode 100644 index 00000000000..90b43c163a0 --- /dev/null +++ b/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.1.7-p1-foss-2023a.eb @@ -0,0 +1,57 @@ +easyblock = 'Tarball' + +name = 'RepeatMasker' +version = '4.1.7-p1' + +homepage = 'https://www.repeatmasker.org/' +description = """RepeatMasker is a program that screens DNA sequences for interspersed repeats + and low complexity DNA sequences.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://www.repeatmasker.org/%(name)s'] +sources = [ + SOURCE_TAR_GZ, + # optional but recommended: RepBase RepeatMasker Edition + # requires subscription and academic license, download from here: https://www.girinst.org/server/RepBase/index.php + # { + # 'filename': 'RepBaseRepeatMaskerEdition-20181026.tar.gz', + # 'extract_cmd': "tar -xzf %s -C %(builddir)s/%(name)s/Libraries --strip-components 1", + # }, +] +checksums = ['15222b39178f19c116282437190b64c5ba68f62b0f2044b3bbcbda5e02748993'] + +dependencies = [ + ('Python', '3.11.3'), + ('Perl', '5.36.1'), + ('TRF', '4.09.1'), + ('h5py', '3.9.0'), + # At least one search engine of: RMBlast, HMMER, ABBlast/WUBlast, Cross_Match + ('HMMER', '3.4'), + ('RMBlast', '2.14.1'), +] + +local_default_search_engine = 'RMBlast' + +local_config_command = 'cd %(installdir)s &&' +local_config_command += './configure -perlbin "$EBROOTPERL/bin/perl" -trf_prgm "$EBROOTTRF/bin/trf" ' +local_config_command += '-hmmer_dir "$EBROOTHMMER/bin" -rmblast_dir "$EBROOTRMBLAST/bin" ' +local_config_command += '-default_search_engine %s' % local_default_search_engine.lower() + +postinstallcmds = [local_config_command] + +fix_perl_shebang_for = ['RepeatMasker'] + +sanity_check_paths = { + 'files': ['RepeatMasker', 'RepeatMaskerConfig.pm'], + 'dirs': ['Libraries', 'util'], +} + +sanity_check_commands = ['RepeatMasker -help'] + +modextrapaths = { + 'PATH': '', + 'PERL5LIB': '', +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/TRF/TRF-4.09.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/t/TRF/TRF-4.09.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..cbf3e47917e --- /dev/null +++ b/easybuild/easyconfigs/t/TRF/TRF-4.09.1-GCCcore-12.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'TRF' +version = '4.09.1' + +homepage = 'https://tandem.bu.edu/trf/trf.html' +description = """Tandem Repeats Finder: a program to analyze DNA sequences.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +github_account = 'Benson-Genomics-Lab' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['516015b625473350c3d1c9b83cac86baea620c8418498ab64c0a67029c3fb28a'] + +builddependencies = [ + ('binutils', '2.40'), + ('Autotools', '20220317'), +] + +preconfigopts = "autoreconf -i -f && " + +sanity_check_paths = { + 'files': ['bin/trf'], + 'dirs': [], +} + +sanity_check_commands = ["trf -v"] + +moduleclass = 'bio' From f15cafbf3580cd077c444336882c65968a1770b8 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 16 Sep 2024 17:17:21 +0200 Subject: [PATCH 080/107] adding easyconfigs: pytest-workflow-2.1.0-GCCcore-13.3.0.eb, tqdm-4.66.5-GCCcore-13.3.0.eb, typing-extensions-4.11.0-GCCcore-13.3.0.eb --- .../pytest-workflow-2.1.0-GCCcore-13.3.0.eb | 34 +++++++++++++++++++ .../t/tqdm/tqdm-4.66.5-GCCcore-13.3.0.eb | 24 +++++++++++++ ...typing-extensions-4.11.0-GCCcore-13.3.0.eb | 21 ++++++++++++ 3 files changed, 79 insertions(+) create mode 100644 easybuild/easyconfigs/p/pytest-workflow/pytest-workflow-2.1.0-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/t/tqdm/tqdm-4.66.5-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/t/typing-extensions/typing-extensions-4.11.0-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/p/pytest-workflow/pytest-workflow-2.1.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/pytest-workflow/pytest-workflow-2.1.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..25aaab957da --- /dev/null +++ b/easybuild/easyconfigs/p/pytest-workflow/pytest-workflow-2.1.0-GCCcore-13.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonBundle' + +name = 'pytest-workflow' +version = '2.1.0' + +homepage = 'https://github.com/LUMC/pytest-workflow' +description = """Configure workflow/pipeline tests using yaml files. + +pytest-workflow is a workflow-system agnostic testing framework that aims to make pipeline/workflow testing easy by +using YAML files for the test configuration. +Whether you write your pipelines in WDL, snakemake, nextflow, bash or any other workflow framework, +pytest-workflow makes testing easy. +pytest-workflow is build on top of the pytest test framework.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [('binutils', '2.42')] +dependencies = [ + ('Python', '3.12.3'), + ('PyYAML', '6.0.2'), + ('python-isal', '1.7.0'), + ('zlib-ng', '2.2.1'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('zstandard', '0.23.0', {'checksums': ['b2d8c62d08e7255f68f7a740bae85b3c9b8e5466baa9cbf7f57f1cde0ac6bc09']}), + ('xopen', '2.0.2', {'checksums': ['f19d83de470f5a81725df0140180ec71d198311a1d7dad48f5467b4ad5df6154']}), + (name, version, {'checksums': ['dc86ad9a5f94482aec14926788f6b78b428be68ee0428cbca22f89b6326f8b7a']}), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/t/tqdm/tqdm-4.66.5-GCCcore-13.3.0.eb b/easybuild/easyconfigs/t/tqdm/tqdm-4.66.5-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..b9d92f49462 --- /dev/null +++ b/easybuild/easyconfigs/t/tqdm/tqdm-4.66.5-GCCcore-13.3.0.eb @@ -0,0 +1,24 @@ +# # +# Author: Robert Mijakovic +# # +easyblock = 'PythonPackage' + +name = 'tqdm' +version = '4.66.5' + +homepage = 'https://github.com/tqdm/tqdm' +description = "A fast, extensible progress bar for Python and CLI" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['e1020aef2e5096702d8a025ac7d16b1577279c9d63f8375b63083e9a5f0fcbad'] + +builddependencies = [('binutils', '2.42')] +dependencies = [('Python', '3.12.3')] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/typing-extensions/typing-extensions-4.11.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/t/typing-extensions/typing-extensions-4.11.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..552279e3ffe --- /dev/null +++ b/easybuild/easyconfigs/t/typing-extensions/typing-extensions-4.11.0-GCCcore-13.3.0.eb @@ -0,0 +1,21 @@ +easyblock = 'PythonPackage' + +name = 'typing-extensions' +version = '4.11.0' + +homepage = 'https://github.com/python/typing_extensions' +description = "Typing Extensions - Backported and Experimental Type Hints for Python" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +sources = ['typing_extensions-%(version)s.tar.gz'] +checksums = ['83f085bd5ca59c80295fc2a82ab5dac679cbe02b9f33f7d83af68e241bea51b0'] + +builddependencies = [('binutils', '2.42')] +dependencies = [('Python', '3.12.3')] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +moduleclass = 'devel' From e860d9244185ab88bcff035a5217f50afb0d1768 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 16 Sep 2024 17:18:47 +0200 Subject: [PATCH 081/107] adding easyconfigs: GitPython-3.1.43-GCCcore-13.3.0.eb, ISA-L-2.31.0-GCCcore-13.3.0.eb, Markdown-3.7-GCCcore-13.3.0.eb, prompt-toolkit-3.0.36-GCCcore-13.3.0.eb, python-isal-1.7.0-GCCcore-13.3.0.eb, versioningit-3.1.2-GCCcore-13.3.0.eb, zlib-ng-2.2.1-GCCcore-13.3.0.eb --- .../GitPython-3.1.43-GCCcore-13.3.0.eb | 33 ++++++++++++ .../i/ISA-L/ISA-L-2.31.0-GCCcore-13.3.0.eb | 45 +++++++++++++++++ .../m/Markdown/Markdown-3.7-GCCcore-13.3.0.eb | 24 +++++++++ .../prompt-toolkit-3.0.36-GCCcore-13.3.0.eb | 27 ++++++++++ .../python-isal-1.7.0-GCCcore-13.3.0.eb | 34 +++++++++++++ .../versioningit-3.1.2-GCCcore-13.3.0.eb | 27 ++++++++++ .../z/zlib-ng/zlib-ng-2.2.1-GCCcore-13.3.0.eb | 50 +++++++++++++++++++ 7 files changed, 240 insertions(+) create mode 100644 easybuild/easyconfigs/g/GitPython/GitPython-3.1.43-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/i/ISA-L/ISA-L-2.31.0-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/m/Markdown/Markdown-3.7-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-3.0.36-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/p/python-isal/python-isal-1.7.0-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/v/versioningit/versioningit-3.1.2-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.2.1-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/g/GitPython/GitPython-3.1.43-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/GitPython/GitPython-3.1.43-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..62484b4a3e8 --- /dev/null +++ b/easybuild/easyconfigs/g/GitPython/GitPython-3.1.43-GCCcore-13.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonBundle' + +name = 'GitPython' +version = '3.1.43' + +homepage = 'https://gitpython.readthedocs.org' +description = """ GitPython is a python library used to interact with Git repositories """ + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [('binutils', '2.42'),] +dependencies = [ + ('Python', '3.12.3'), + ('git', '2.45.1'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('smmap', '5.0.1', { + 'checksums': ['dceeb6c0028fdb6734471eb07c0cd2aae706ccaecab45965ee83f11c8d3b1f62'], + }), + ('gitdb', '4.0.11', { + 'checksums': ['bf5421126136d6d0af55bc1e7c1af1c397a34f5b7bd79e776cd3e89785c2b04b'], + }), + (name, version, { + 'modulename': 'git', + 'checksums': ['35f314a9f878467f5453cc1fee295c3e18e52f1b99f10f6cf5b1682e968a9e7c'], + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/i/ISA-L/ISA-L-2.31.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/i/ISA-L/ISA-L-2.31.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..1e79d2b10db --- /dev/null +++ b/easybuild/easyconfigs/i/ISA-L/ISA-L-2.31.0-GCCcore-13.3.0.eb @@ -0,0 +1,45 @@ +# Author: Jasper Grimm (UoY) + +easyblock = 'ConfigureMake' + +name = 'ISA-L' +version = '2.31.0' + +homepage = 'https://github.com/intel/isa-l' +description = "Intelligent Storage Acceleration Library" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +github_account = 'intel' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['e218b7b2e241cfb8e8b68f54a6e5eed80968cc387c4b1af03708b54e9fb236f1'] + +builddependencies = [ + ('Autotools', '20231222'), + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), +] +dependencies = [('NASM', '2.16.03')] + +preconfigopts = "autoreconf -i -f &&" + +runtest = 'check' + +local_bins = ['bin/igzip'] +local_includes = ['include/%(namelower)s.h'] +local_includes += ['include/isa-l/%s.h' % i for i in ['crc64', 'crc', 'erasure_code', 'gf_vect_mul', 'igzip_lib', + 'mem_routines', 'raid', 'test']] +local_libs = ['lib/libisal.%s' % k for k in ['a', 'la', SHLIB_EXT]] + +sanity_check_paths = { + 'files': local_bins + local_includes + local_libs, + 'dirs': ['bin', 'include', 'lib', 'share'], +} + +sanity_check_commands = [ + "igzip --help", + "igzip --version", +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/Markdown/Markdown-3.7-GCCcore-13.3.0.eb b/easybuild/easyconfigs/m/Markdown/Markdown-3.7-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..f5cc55d6ff3 --- /dev/null +++ b/easybuild/easyconfigs/m/Markdown/Markdown-3.7-GCCcore-13.3.0.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'Markdown' +version = '3.7' + +homepage = 'https://python-markdown.github.io/' +description = """This is a Python implementation of John Gruber's Markdown. +It is almost completely compliant with the reference implementation, though there are a few known issues. +Additional features are supported by the Available Extensions. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['2ae2471477cfd02dbbf038d5d9bc226d40def84b4fe2986e49b59b6b472bbed2'] + +builddependencies = [('binutils', '2.42'),] +dependencies = [('Python', '3.12.3'),] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-3.0.36-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-3.0.36-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..8cbde894708 --- /dev/null +++ b/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-3.0.36-GCCcore-13.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'prompt-toolkit' +version = '3.0.36' + +homepage = 'https://github.com/jonathanslenders/python-prompt-toolkit' +description = """prompt_toolkit is a Python library for building powerful interactive command lines and + terminal applications.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [('binutils', '2.42')] +dependencies = [ + ('Python', '3.12.3'), + ('Python-bundle-PyPI', '2024.06'), +] + +sources = ['prompt_toolkit-%(version)s-py3-none-any.whl'] +checksums = ['aa64ad242a462c5ff0363a7b9cfe696c20d55d9fc60c11fd8e632d064804d305'] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +options = {'modulename': 'prompt_toolkit'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/python-isal/python-isal-1.7.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/python-isal/python-isal-1.7.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..96885969511 --- /dev/null +++ b/easybuild/easyconfigs/p/python-isal/python-isal-1.7.0-GCCcore-13.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'python-isal' +version = '1.7.0' + +homepage = 'https://github.com/pycompression/python-isal' +description = """Faster zlib and gzip compatible compression and decompression + by providing python bindings for the isa-l library. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [ + ('binutils', '2.42'), + ('versioningit', '3.1.2'), +] +dependencies = [ + ('Python', '3.12.3'), + ('ISA-L', '2.31.0'), +] + +source_urls = [PYPI_SOURCE.replace('%(name)s', 'isal')] +sources = ['isal-%(version)s.tar.gz'] +checksums = ['9eb9457ed27fd0a8a7b403a5f4f9e6c8d1a44c2ca28ecd2f2bf3aed90b0a74bf'] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +preinstallopts = 'PYTHON_ISAL_LINK_DYNAMIC=true' + +options = {'modulename': 'isal'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/v/versioningit/versioningit-3.1.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/v/versioningit/versioningit-3.1.2-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..ab4e77dea46 --- /dev/null +++ b/easybuild/easyconfigs/v/versioningit/versioningit-3.1.2-GCCcore-13.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'versioningit' +version = '3.1.2' + +homepage = 'https://github.com/jwodder/versioningit' +description = """versioningit is yet another Python packaging plugin for automatically determining your +package’s version based on your version control repository’s tags. +Unlike others, it allows easy customization of the version format and even lets you easily override +the separate functions used for version extraction & calculation.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [ + ('binutils', '2.42'), + ('hatchling', '1.24.2'), +] +dependencies = [('Python', '3.12.3')] + +sources = [SOURCE_TAR_GZ] +checksums = ['4db83ed99f56b07d83940bee3445ca46ca120d13b6b304cdb5fb44e5aa4edec0'] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.2.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.2.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..266b927072a --- /dev/null +++ b/easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.2.1-GCCcore-13.3.0.eb @@ -0,0 +1,50 @@ +easyblock = 'PythonBundle' + +name = 'zlib-ng' +version = '2.2.1' + +homepage = 'https://github.com/zlib-ng/zlib-ng' +description = """zlib data compression library for the next generation systems""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [ + ('CMake', '3.29.3'), + ('binutils', '2.42'), + ('versioningit', '3.1.2'), +] + +dependencies = [ + ('Python', '3.12.3'), +] + +components = [ + (name, version, { + 'easyblock': 'CMakeMake', + 'source_urls': ['https://github.com/zlib-ng/zlib-ng/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], + 'checksums': ['ec6a76169d4214e2e8b737e0850ba4acb806c69eeace6240ed4481b9f5c57cdf'], + 'start_dir': '%(name)s-%(version)s', + 'configopts': '-DZLIB_ENABLE_TESTS=ON', + }), + +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, '0.5.0', { + 'source_tmpl': 'zlib_ng-%(version)s.tar.gz', + 'checksums': ['3322c4300253a054af3d3aafa2f3858dceee3a577810122ba55eff756bf35ef2'], + 'preinstallopts': 'PYTHON_ZLIB_NG_LINK_DYNAMIC=true', + 'modulename': 'zlib_ng', + }), +] + +sanity_check_paths = { + 'files': ['include/zconf-ng.h', 'include/zlib-ng.h', 'lib/libz-ng.a', 'lib/libz-ng.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'tools' From fa048953782740cea16a874946f5dc209644b2a7 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 16 Sep 2024 17:20:24 +0200 Subject: [PATCH 082/107] adding easyconfigs: giflib-5.2.2-GCCcore-13.3.0.eb, Pillow-10.4.0-GCCcore-13.3.0.eb --- .../g/giflib/giflib-5.2.2-GCCcore-13.3.0.eb | 31 +++++++++++++ .../p/Pillow/Pillow-10.4.0-GCCcore-13.3.0.eb | 43 +++++++++++++++++++ 2 files changed, 74 insertions(+) create mode 100644 easybuild/easyconfigs/g/giflib/giflib-5.2.2-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/p/Pillow/Pillow-10.4.0-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/g/giflib/giflib-5.2.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/giflib/giflib-5.2.2-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..d8db77830fe --- /dev/null +++ b/easybuild/easyconfigs/g/giflib/giflib-5.2.2-GCCcore-13.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'giflib' +version = '5.2.2' + +homepage = 'http://giflib.sourceforge.net/' +description = """giflib is a library for reading and writing gif images. +It is API and ABI compatible with libungif which was in wide use while +the LZW compression algorithm was patented.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['be7ffbd057cadebe2aa144542fd90c6838c6a083b5e8a9048b8ee3b66b29d5fb'] + +builddependencies = [ + ('binutils', '2.42'), + ('ImageMagick', '7.1.1-38'), +] + +skipsteps = ['configure'] + +installopts = 'PREFIX=%(installdir)s' + +sanity_check_paths = { + 'files': ['bin/giftool'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-10.4.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-10.4.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..34c086c859a --- /dev/null +++ b/easybuild/easyconfigs/p/Pillow/Pillow-10.4.0-GCCcore-13.3.0.eb @@ -0,0 +1,43 @@ +easyblock = 'PythonPackage' + +name = 'Pillow' +version = '10.4.0' + +homepage = 'https://pillow.readthedocs.org/' +description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. + PIL is the Python Imaging Library by Fredrik Lundh and Contributors.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['166c1cd4d24309b30d61f79f4a9114b7b2313d7450912277855ff5dfd7cd4a06'] + +builddependencies = [('binutils', '2.42')] +dependencies = [ + ('Python', '3.12.3'), + ('libjpeg-turbo', '3.0.1'), + ('libpng', '1.6.43'), + ('zlib', '1.3.1'), + ('LibTIFF', '4.6.0'), + ('freetype', '2.13.2'), + ('libwebp', '1.4.0'), + ('OpenJPEG', '2.5.2'), + ('LittleCMS', '2.16'), +] + +# patch setup.py to prefix hardcoded /usr/* and /lib paths with value of %(sysroot) template +# (which will be empty if EasyBuild is not configured to use an alternate sysroot); +# see also https://gitlab.com/eessi/support/-/issues/9 +preinstallopts = """sed -i 's@"/usr/@"%(sysroot)s/usr/@g' setup.py && """ +preinstallopts += """sed -i 's@"/lib@"%(sysroot)s/lib@g' setup.py && """ + +# avoid that hardcoded paths like /usr/include are used in build commands +installopts = "--global-option=build_ext --global-option='--disable-platform-guessing' " + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +options = {'modulename': 'PIL'} + +moduleclass = 'vis' From 6f238ee392ff66428d1a5e09dd2bad1874e3c553 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 17 Sep 2024 08:50:48 +0200 Subject: [PATCH 083/107] fix value for $BIG_SCAPE_HTML_PATH for BiG-SCAPE v1.1.9 --- .../easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.9-foss-2023b.eb | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.9-foss-2023b.eb b/easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.9-foss-2023b.eb index 87ffb021f06..59f7c1a7cd5 100644 --- a/easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.9-foss-2023b.eb +++ b/easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.9-foss-2023b.eb @@ -40,9 +40,11 @@ sanity_pip_check = True options = {'modulename': 'bigscape'} +local_lib_py_bigscape_path = 'lib/python%(pyshortver)s/site-packages/bigscape' + sanity_check_paths = { 'files': ['bin/bigscape'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], + 'dirs': [local_lib_py_bigscape_path], } sanity_check_commands = [ @@ -50,7 +52,7 @@ sanity_check_commands = [ ] modextravars = { - 'BIG_SCAPE_HTML_PATH': '%(installdir)s/lib/python%(pyshortver)s/site-packages/BiG-SCAPE', + 'BIG_SCAPE_HTML_PATH': '%(installdir)s/' + local_lib_py_bigscape_path, } modloadmsg = "%(name)s needs processed Pfam database to work properly.\n" From 09d918de048a1a7ff52ae99f68f744a598760899 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 17 Sep 2024 09:05:56 +0200 Subject: [PATCH 084/107] Fix style --- .../g/GitPython/GitPython-3.1.43-GCCcore-13.3.0.eb | 10 +++------- .../m/Markdown/Markdown-3.7-GCCcore-13.3.0.eb | 4 ++-- 2 files changed, 5 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/g/GitPython/GitPython-3.1.43-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/GitPython/GitPython-3.1.43-GCCcore-13.3.0.eb index 62484b4a3e8..e6ca0d7b0aa 100644 --- a/easybuild/easyconfigs/g/GitPython/GitPython-3.1.43-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/g/GitPython/GitPython-3.1.43-GCCcore-13.3.0.eb @@ -8,7 +8,7 @@ description = """ GitPython is a python library used to interact with Git reposi toolchain = {'name': 'GCCcore', 'version': '13.3.0'} -builddependencies = [('binutils', '2.42'),] +builddependencies = [('binutils', '2.42')] dependencies = [ ('Python', '3.12.3'), ('git', '2.45.1'), @@ -18,12 +18,8 @@ sanity_pip_check = True use_pip = True exts_list = [ - ('smmap', '5.0.1', { - 'checksums': ['dceeb6c0028fdb6734471eb07c0cd2aae706ccaecab45965ee83f11c8d3b1f62'], - }), - ('gitdb', '4.0.11', { - 'checksums': ['bf5421126136d6d0af55bc1e7c1af1c397a34f5b7bd79e776cd3e89785c2b04b'], - }), + ('smmap', '5.0.1', {'checksums': ['dceeb6c0028fdb6734471eb07c0cd2aae706ccaecab45965ee83f11c8d3b1f62']}), + ('gitdb', '4.0.11', {'checksums': ['bf5421126136d6d0af55bc1e7c1af1c397a34f5b7bd79e776cd3e89785c2b04b']}), (name, version, { 'modulename': 'git', 'checksums': ['35f314a9f878467f5453cc1fee295c3e18e52f1b99f10f6cf5b1682e968a9e7c'], diff --git a/easybuild/easyconfigs/m/Markdown/Markdown-3.7-GCCcore-13.3.0.eb b/easybuild/easyconfigs/m/Markdown/Markdown-3.7-GCCcore-13.3.0.eb index f5cc55d6ff3..04b5629d6bf 100644 --- a/easybuild/easyconfigs/m/Markdown/Markdown-3.7-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/m/Markdown/Markdown-3.7-GCCcore-13.3.0.eb @@ -14,8 +14,8 @@ toolchain = {'name': 'GCCcore', 'version': '13.3.0'} sources = [SOURCELOWER_TAR_GZ] checksums = ['2ae2471477cfd02dbbf038d5d9bc226d40def84b4fe2986e49b59b6b472bbed2'] -builddependencies = [('binutils', '2.42'),] -dependencies = [('Python', '3.12.3'),] +builddependencies = [('binutils', '2.42')] +dependencies = [('Python', '3.12.3')] download_dep_fail = True sanity_pip_check = True From 4f82480bbc82b2912a3befb929eb044719d0034e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 17 Sep 2024 09:29:54 +0200 Subject: [PATCH 085/107] remove whitespace from empty line in chopper easyconfig --- easybuild/easyconfigs/c/chopper/chopper-0.9.0-GCCcore-12.3.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/c/chopper/chopper-0.9.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/c/chopper/chopper-0.9.0-GCCcore-12.3.0.eb index df0b3abaa21..b1788fb34f9 100644 --- a/easybuild/easyconfigs/c/chopper/chopper-0.9.0-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/c/chopper/chopper-0.9.0-GCCcore-12.3.0.eb @@ -303,7 +303,6 @@ crates = [ ('windows_x86_64_msvc', '0.52.5'), ('xz2', '0.1.7'), ] - sanity_check_paths = { 'files': ['bin/chopper'], 'dirs': [], From 99107f64310990f97009e53f0119afd324212b9b Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 17 Sep 2024 10:03:19 +0200 Subject: [PATCH 086/107] avoid missing symbol in mclust extension of R-4.0.3-foss-2020b --- easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb index d8b9d1c97fe..9d09c819514 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb @@ -57,6 +57,10 @@ dependencies = [ osdependencies = [OS_PKG_OPENSSL_DEV] +# 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 From 1cfab50d0fa131df4d5108c42cce656c99a1ad78 Mon Sep 17 00:00:00 2001 From: WilleBell Date: Tue, 17 Sep 2024 17:14:30 +0200 Subject: [PATCH 087/107] Avoid test-suite fail for ELSI --- easybuild/easyconfigs/e/ELSI/ELSI-2.11.0-foss-2023a-PEXSI.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/e/ELSI/ELSI-2.11.0-foss-2023a-PEXSI.eb b/easybuild/easyconfigs/e/ELSI/ELSI-2.11.0-foss-2023a-PEXSI.eb index 1ac711b9cf5..a1be84f6de9 100644 --- a/easybuild/easyconfigs/e/ELSI/ELSI-2.11.0-foss-2023a-PEXSI.eb +++ b/easybuild/easyconfigs/e/ELSI/ELSI-2.11.0-foss-2023a-PEXSI.eb @@ -38,6 +38,10 @@ build_internal_pexsi = True configopts = '-DENABLE_BSEPACK=ON ' +# Tests use 4 MPI ranks, they require a minimum of 4 cores +# Map each MPI process to a single CPU core to avoid tests fails +pretestopts = "export OMPI_MCA_rmaps_base_mapping_policy=slot:PE=1 && " + runtest = True moduleclass = 'math' From 26b7160f205a46edf86305ed85423906ddb3e479 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 17 Sep 2024 16:41:06 +0100 Subject: [PATCH 088/107] adding easyconfigs: CREST-2.12-gfbf-2023b.eb and patches: CREST-2.12-longline.patch --- .../c/CREST/CREST-2.12-gfbf-2023b.eb | 44 +++++++++++++++++++ .../c/CREST/CREST-2.12-longline.patch | 16 +++++++ 2 files changed, 60 insertions(+) create mode 100644 easybuild/easyconfigs/c/CREST/CREST-2.12-gfbf-2023b.eb create mode 100644 easybuild/easyconfigs/c/CREST/CREST-2.12-longline.patch diff --git a/easybuild/easyconfigs/c/CREST/CREST-2.12-gfbf-2023b.eb b/easybuild/easyconfigs/c/CREST/CREST-2.12-gfbf-2023b.eb new file mode 100644 index 00000000000..87ae95876bf --- /dev/null +++ b/easybuild/easyconfigs/c/CREST/CREST-2.12-gfbf-2023b.eb @@ -0,0 +1,44 @@ +# Author: Jasper Grimm (UoY) +# Update to 2.12: +# Author: J. Sassmannshausen (Imperial College London) + +easyblock = 'CMakeMake' + +name = 'CREST' +version = '2.12' + +homepage = 'https://xtb-docs.readthedocs.io/en/latest/crest.html' +description = """CREST is an utility/driver program for the xtb program. Originally it was designed + as conformer sampling program, hence the abbreviation Conformer–Rotamer Ensemble Sampling Tool, + but now offers also some utility functions for calculations with the GFNn–xTB methods. Generally + the program functions as an IO based OMP scheduler (i.e., calculations are performed by the xtb + program) and tool for the creation and analysation of structure ensembles. +""" + +toolchain = {'name': 'gfbf', 'version': '2023b'} + +github_account = 'grimme-lab' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = ['CREST-2.12-longline.patch'] +checksums = [ + {'v2.12.tar.gz': '390f0ac0aedafbd6bb75974fcffefe7e0232ad6c4ea0ab4f1a77e656a3ce263d'}, + {'CREST-2.12-longline.patch': '596ca2bcce3bbdfe99a3849934f41b388fb763a4898240091593b9b6a454fea9'}, +] + +builddependencies = [('CMake', '3.27.6')] + +dependencies = [('xtb', '6.7.1')] # required to run the program + +# Simple test command just to check if the program is working: +test_cmd = 'export PATH=%(builddir)s/easybuild_obj:$PATH && ' +test_cmd += 'cd %(builddir)s/%(namelower)s-%(version)s/examples/expl-0/ && ./run.sh ' + +sanity_check_paths = { + 'files': ['bin/%s' % name.lower()], + 'dirs': [], +} + +sanity_check_commands = ["crest -h", "crest --cite"] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/c/CREST/CREST-2.12-longline.patch b/easybuild/easyconfigs/c/CREST/CREST-2.12-longline.patch new file mode 100644 index 00000000000..c3b84785f5f --- /dev/null +++ b/easybuild/easyconfigs/c/CREST/CREST-2.12-longline.patch @@ -0,0 +1,16 @@ +Dealing with a long line, which gfortran does not like +Author: J. Sassmannshausen (Imperial College London/UK) +diff --git a/crest-2.12.orig/src/qcg/solvtool.f90 b/crest-2.12/src/qcg/solvtool.f90 +index cec514c..f38b576 100644 +--- a/crest-2.12.orig/src/qcg/solvtool.f90 ++++ b/crest-2.12/src/qcg/solvtool.f90 +@@ -3158,7 +3158,8 @@ subroutine check_prog_path_iff(env) + str=trim(str) + open(unit=27, file=str, iostat=ios) + read(27,'(a)',iostat=ios) path +- if(ios .ne. 0) error stop 'No xtb-IFF found. This is currently required for QCG and available at https:/github.com/grimme-lab/xtbiff/releases/tag/v1.1' ++ if(ios .ne. 0) error stop 'No xtb-IFF found. This is currently required for QCG and available at & ++ https:/github.com/grimme-lab/xtbiff/releases/tag/v1.1' + + end subroutine check_prog_path_iff + From 27cbe9bf42c0bd0649750cd5df720c2fba796d8c Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 18 Sep 2024 12:38:01 +0200 Subject: [PATCH 089/107] fix build of librosa in somve environments --- easybuild/easyconfigs/l/librosa/librosa-0.10.1-foss-2023a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/l/librosa/librosa-0.10.1-foss-2023a.eb b/easybuild/easyconfigs/l/librosa/librosa-0.10.1-foss-2023a.eb index 444e2ba800d..c26fed6c2e3 100644 --- a/easybuild/easyconfigs/l/librosa/librosa-0.10.1-foss-2023a.eb +++ b/easybuild/easyconfigs/l/librosa/librosa-0.10.1-foss-2023a.eb @@ -27,7 +27,6 @@ use_pip = True exts_list = [ ('soxr', '0.3.7', { - 'preinstallopts': 'python -m build && ', 'checksums': ['436ddff00c6eb2c75b79c19cfdca7527b1e31b5fad738652f044045ba6258593'], }), ('audioread', '3.0.1', { From dfd515d50bb3c3e598035cccab7b4de55919d1fe Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 18 Sep 2024 12:56:22 +0200 Subject: [PATCH 090/107] Fix repeated sanity check runs in manta --- .../m/manta/manta-1.6.0-GCC-10.2.0-Python-2.7.18.eb | 4 +--- .../m/manta/manta-1.6.0-gompi-2019b-Python-2.7.16.eb | 2 +- .../m/manta/manta-1.6.0-gompi-2020a-Python-2.7.18.eb | 2 +- 3 files changed, 3 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/m/manta/manta-1.6.0-GCC-10.2.0-Python-2.7.18.eb b/easybuild/easyconfigs/m/manta/manta-1.6.0-GCC-10.2.0-Python-2.7.18.eb index 4587e8e91df..ff224b45ba2 100644 --- a/easybuild/easyconfigs/m/manta/manta-1.6.0-GCC-10.2.0-Python-2.7.18.eb +++ b/easybuild/easyconfigs/m/manta/manta-1.6.0-GCC-10.2.0-Python-2.7.18.eb @@ -62,9 +62,7 @@ sanity_check_paths = { 'dirs': ['libexec'], } -sanity_check_commands = [ - 'python %(installdir)s/bin/runMantaWorkflowDemo.py' -] +sanity_check_commands = ['cd "$(mktemp -d)" && runMantaWorkflowDemo.py'] modextrapaths = { 'PATH': 'libexec', diff --git a/easybuild/easyconfigs/m/manta/manta-1.6.0-gompi-2019b-Python-2.7.16.eb b/easybuild/easyconfigs/m/manta/manta-1.6.0-gompi-2019b-Python-2.7.16.eb index 8e5943d0213..2d6c80a9b71 100644 --- a/easybuild/easyconfigs/m/manta/manta-1.6.0-gompi-2019b-Python-2.7.16.eb +++ b/easybuild/easyconfigs/m/manta/manta-1.6.0-gompi-2019b-Python-2.7.16.eb @@ -41,7 +41,7 @@ sanity_check_paths = { 'dirs': ['lib/python', 'share'], } -sanity_check_commands = ['runMantaWorkflowDemo.py'] +sanity_check_commands = ['cd "$(mktemp -d)" && runMantaWorkflowDemo.py'] modextrapaths = { 'PATH': 'libexec', diff --git a/easybuild/easyconfigs/m/manta/manta-1.6.0-gompi-2020a-Python-2.7.18.eb b/easybuild/easyconfigs/m/manta/manta-1.6.0-gompi-2020a-Python-2.7.18.eb index 0b2b3af8477..7633e9131e0 100644 --- a/easybuild/easyconfigs/m/manta/manta-1.6.0-gompi-2020a-Python-2.7.18.eb +++ b/easybuild/easyconfigs/m/manta/manta-1.6.0-gompi-2020a-Python-2.7.18.eb @@ -41,7 +41,7 @@ sanity_check_paths = { 'dirs': ['lib/python', 'share'], } -sanity_check_commands = ['runMantaWorkflowDemo.py'] +sanity_check_commands = ['cd "$(mktemp -d)" && runMantaWorkflowDemo.py'] modextrapaths = { 'PATH': 'libexec', From a025c619b617c24a2be3a86dcad69d1bb25b477d Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann Date: Wed, 18 Sep 2024 13:32:29 +0000 Subject: [PATCH 091/107] use eb-built libnsl for git-annex --- .../git-annex-10.20230802-GCCcore-12.2.0.eb | 1 + .../git-annex-10.20230802-GCCcore-12.3.0.eb | 1 + .../git-annex-10.20240731-GCCcore-13.3.0.eb | 1 + .../l/libnsl/libnsl-2.0.1-GCCcore-13.3.0.eb | 33 +++++++++++++++++++ .../libtirpc/libtirpc-1.3.5-GCCcore-13.3.0.eb | 28 ++++++++++++++++ 5 files changed, 64 insertions(+) create mode 100644 easybuild/easyconfigs/l/libnsl/libnsl-2.0.1-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/l/libtirpc/libtirpc-1.3.5-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.2.0.eb index 2e2696826f6..58d3de407c2 100644 --- a/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.2.0.eb @@ -16,6 +16,7 @@ dependencies = [ ('GHC', '9.2.2', '-x86_64', SYSTEM), ('Stack', '2.11.1', '-x86_64', SYSTEM), ('git', '2.38.1', '-nodocs'), + ('libnsl', '2.0.0'), ] sources = [{ diff --git a/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.3.0.eb index 6b6af7f9eba..0e7cce68755 100644 --- a/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.3.0.eb @@ -18,6 +18,7 @@ dependencies = [ ('GHC', '9.4.6', '-x86_64', SYSTEM), ('Stack', '2.13.1', '-x86_64', SYSTEM), ('git', '2.41.0', '-nodocs'), + ('libnsl', '2.0.1' ), ] sources = [{ diff --git a/easybuild/easyconfigs/g/git-annex/git-annex-10.20240731-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/git-annex/git-annex-10.20240731-GCCcore-13.3.0.eb index 89c70af2f45..8b981e6ea6c 100644 --- a/easybuild/easyconfigs/g/git-annex/git-annex-10.20240731-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/g/git-annex/git-annex-10.20240731-GCCcore-13.3.0.eb @@ -18,6 +18,7 @@ dependencies = [ ('GHC', '9.10.1', '-x86_64', SYSTEM), ('Stack', '3.1.1', '-x86_64', SYSTEM), ('git', '2.45.1'), + ('libnsl', '2.0.1'), ] sources = [{ diff --git a/easybuild/easyconfigs/l/libnsl/libnsl-2.0.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libnsl/libnsl-2.0.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..ee8ad125324 --- /dev/null +++ b/easybuild/easyconfigs/l/libnsl/libnsl-2.0.1-GCCcore-13.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libnsl' +version = '2.0.1' + +homepage = 'https://github.com/thkukuk/libnsl' +description = """The libnsl package contains the public client interface for NIS(YP).""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/thkukuk/%(name)s/releases/download/v%(version)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['5c9e470b232a7acd3433491ac5221b4832f0c71318618dc6aa04dd05ffcd8fd9'] + +builddependencies = [ + ('binutils', '2.42'), +] + +dependencies = [ + ('libtirpc', '1.3.3'), +] + +# Provide a symlink for libnsl.so.1, which used to be part of glibc. +# This new version of libnsl should be backwards compatible. +postinstallcmds = ['ln -s libnsl.so %(installdir)s/lib/libnsl.so.1'] + +sanity_check_paths = { + 'files': ['include/rpcsvc/yp.h', 'lib/libnsl.a', + 'lib/libnsl.%s' % SHLIB_EXT, 'lib/libnsl.%s.1' % SHLIB_EXT], + 'dirs': ['include'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libtirpc/libtirpc-1.3.5-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libtirpc/libtirpc-1.3.5-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..30a34609ef9 --- /dev/null +++ b/easybuild/easyconfigs/l/libtirpc/libtirpc-1.3.5-GCCcore-13.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'libtirpc' +version = '1.3.5' + +homepage = 'https://sourceforge.net/projects/libtirpc/' +description = "Libtirpc is a port of Suns Transport-Independent RPC library to Linux." + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_BZ2] +checksums = ['1e0b0c7231c5fa122e06c0609a76723664d068b0dba3b8219b63e6340b347860'] + +configopts = '--enable-static --enable-shared --disable-gssapi' + +builddependencies = [ + ('binutils', '2.42') +] + +sanity_check_paths = { + 'files': ['lib/libtirpc.%s' % (x,) for x in ['a', SHLIB_EXT]], + 'dirs': ['include/tirpc', 'lib'], +} + +modextrapaths = {'CPATH': 'include/tirpc'} + +moduleclass = 'lib' From 199e765b7a77699c90c8069fd967bc0c92df0277 Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann Date: Wed, 18 Sep 2024 13:36:54 +0000 Subject: [PATCH 092/107] correct libtirpc version --- easybuild/easyconfigs/l/libnsl/libnsl-2.0.1-GCCcore-13.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libnsl/libnsl-2.0.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libnsl/libnsl-2.0.1-GCCcore-13.3.0.eb index ee8ad125324..818f1687a15 100644 --- a/easybuild/easyconfigs/l/libnsl/libnsl-2.0.1-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/l/libnsl/libnsl-2.0.1-GCCcore-13.3.0.eb @@ -17,7 +17,7 @@ builddependencies = [ ] dependencies = [ - ('libtirpc', '1.3.3'), + ('libtirpc', '1.3.5'), ] # Provide a symlink for libnsl.so.1, which used to be part of glibc. From b8489cccbd65868ee040eebcf6ab58848d0bf12f Mon Sep 17 00:00:00 2001 From: WilleBell Date: Wed, 18 Sep 2024 16:37:52 +0200 Subject: [PATCH 093/107] adding easyconfigs: CREST-3.0.2-foss-2023a.eb --- .../c/CREST/CREST-3.0.2-foss-2023a.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/c/CREST/CREST-3.0.2-foss-2023a.eb diff --git a/easybuild/easyconfigs/c/CREST/CREST-3.0.2-foss-2023a.eb b/easybuild/easyconfigs/c/CREST/CREST-3.0.2-foss-2023a.eb new file mode 100644 index 00000000000..5490dcf0578 --- /dev/null +++ b/easybuild/easyconfigs/c/CREST/CREST-3.0.2-foss-2023a.eb @@ -0,0 +1,47 @@ +easyblock = 'CMakeMake' + +name = 'CREST' +version = '3.0.2' + +homepage = 'https://xtb-docs.readthedocs.io/en/latest/crest.html' +description = """CREST is an utility/driver program for the xtb program. Originally it was designed + as conformer sampling program, hence the abbreviation Conformer–Rotamer Ensemble Sampling Tool, + but now offers also some utility functions for calculations with the GFNn–xTB methods. Generally + the program functions as an IO based OMP scheduler (i.e., calculations are performed by the xtb + program) and tool for the creation and analysation of structure ensembles. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'opt': True} + +sources = [{ + 'filename': SOURCE_TAR_GZ, + 'git_config': { + 'url': 'https://github.com/crest-lab', + 'repo_name': 'crest', + 'tag': 'v%s' % version, + 'recursive': True, + }, +}] +checksums = ['010637e0c47a9cb89d8507e5f5ed9e4494f333fe21cd0fd3cbaa983d566eeccc'] + +builddependencies = [('CMake', '3.26.3')] + +dependencies = [ + ('dftd4', '3.7.0'), + ('mctc-lib', '0.3.1'), + ('mstore', '0.3.0'), + ('multicharge', '0.3.0'), + ('xtb', '6.6.1'), +] + +runtest = "test" + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [], +} + +sanity_check_commands = ["crest -h", "crest --cite"] + +moduleclass = 'chem' From 7272e21b6dae3abd9680d8f77f0567ccc4708e35 Mon Sep 17 00:00:00 2001 From: Cintia Willemyns <115622907+WilleBell@users.noreply.github.com> Date: Wed, 18 Sep 2024 16:50:40 +0200 Subject: [PATCH 094/107] remove checksum --- easybuild/easyconfigs/c/CREST/CREST-3.0.2-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CREST/CREST-3.0.2-foss-2023a.eb b/easybuild/easyconfigs/c/CREST/CREST-3.0.2-foss-2023a.eb index 5490dcf0578..38fc051e0fb 100644 --- a/easybuild/easyconfigs/c/CREST/CREST-3.0.2-foss-2023a.eb +++ b/easybuild/easyconfigs/c/CREST/CREST-3.0.2-foss-2023a.eb @@ -23,7 +23,7 @@ sources = [{ 'recursive': True, }, }] -checksums = ['010637e0c47a9cb89d8507e5f5ed9e4494f333fe21cd0fd3cbaa983d566eeccc'] +checksums = [None] builddependencies = [('CMake', '3.26.3')] From 729d84cee11662133e6fb8d6c1aaa4c26a889b96 Mon Sep 17 00:00:00 2001 From: WilleBell Date: Wed, 18 Sep 2024 17:38:46 +0200 Subject: [PATCH 095/107] Fix name of CREST to indicate it is a pre-release --- ...240319-gfbf-2023a.eb => CREST-3.0pre-20240319-gfbf-2023a.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/c/CREST/{CREST-20240319-gfbf-2023a.eb => CREST-3.0pre-20240319-gfbf-2023a.eb} (98%) diff --git a/easybuild/easyconfigs/c/CREST/CREST-20240319-gfbf-2023a.eb b/easybuild/easyconfigs/c/CREST/CREST-3.0pre-20240319-gfbf-2023a.eb similarity index 98% rename from easybuild/easyconfigs/c/CREST/CREST-20240319-gfbf-2023a.eb rename to easybuild/easyconfigs/c/CREST/CREST-3.0pre-20240319-gfbf-2023a.eb index 7649571fc62..4247fa23773 100644 --- a/easybuild/easyconfigs/c/CREST/CREST-20240319-gfbf-2023a.eb +++ b/easybuild/easyconfigs/c/CREST/CREST-3.0pre-20240319-gfbf-2023a.eb @@ -5,7 +5,7 @@ easyblock = 'CMakeMake' name = 'CREST' -version = '20240319' +version = '3.0pre-20240319' _commit = '2719412edf8bb606cebdd4cd6bbb4cdbd249e1e5' homepage = 'https://xtb-docs.readthedocs.io/en/latest/crest.html' From 4a91a8842b05c7a0f154f33547d61065f1f5c863 Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann Date: Thu, 19 Sep 2024 07:01:27 +0000 Subject: [PATCH 096/107] correct checksum --- .../easyconfigs/l/libtirpc/libtirpc-1.3.5-GCCcore-13.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libtirpc/libtirpc-1.3.5-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libtirpc/libtirpc-1.3.5-GCCcore-13.3.0.eb index 30a34609ef9..a9fc2a5d749 100644 --- a/easybuild/easyconfigs/l/libtirpc/libtirpc-1.3.5-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/l/libtirpc/libtirpc-1.3.5-GCCcore-13.3.0.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'GCCcore', 'version': '13.3.0'} source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCE_TAR_BZ2] -checksums = ['1e0b0c7231c5fa122e06c0609a76723664d068b0dba3b8219b63e6340b347860'] +checksums = ['9b31370e5a38d3391bf37edfa22498e28fe2142467ae6be7a17c9068ec0bf12f'] configopts = '--enable-static --enable-shared --disable-gssapi' From 9c622192222fbe0e615d09c54a1daf24e263b058 Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann Date: Thu, 19 Sep 2024 08:54:09 +0000 Subject: [PATCH 097/107] lint --- .../g/git-annex/git-annex-10.20230802-GCCcore-12.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.3.0.eb index 0e7cce68755..5b362fb5873 100644 --- a/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.3.0.eb @@ -18,7 +18,7 @@ dependencies = [ ('GHC', '9.4.6', '-x86_64', SYSTEM), ('Stack', '2.13.1', '-x86_64', SYSTEM), ('git', '2.41.0', '-nodocs'), - ('libnsl', '2.0.1' ), + ('libnsl', '2.0.1'), ] sources = [{ From 07f3b358137c09fd8a7b37bfc05181b4f7cee086 Mon Sep 17 00:00:00 2001 From: maximm Date: Thu, 19 Sep 2024 12:30:50 +0200 Subject: [PATCH 098/107] adding easyconfigs: MPICH-4.2.2-GCC-13.3.0.eb --- .../m/MPICH/MPICH-4.2.2-GCC-13.3.0.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/m/MPICH/MPICH-4.2.2-GCC-13.3.0.eb diff --git a/easybuild/easyconfigs/m/MPICH/MPICH-4.2.2-GCC-13.3.0.eb b/easybuild/easyconfigs/m/MPICH/MPICH-4.2.2-GCC-13.3.0.eb new file mode 100644 index 00000000000..629c5f4dcbc --- /dev/null +++ b/easybuild/easyconfigs/m/MPICH/MPICH-4.2.2-GCC-13.3.0.eb @@ -0,0 +1,21 @@ +name = 'MPICH' +version = '4.2.2' + +homepage = 'https://www.mpich.org/' +description = """MPICH is a high-performance and widely portable implementation +of the Message Passing Interface (MPI) standard (MPI-1, MPI-2 and MPI-3).""" + +toolchain = {'name': 'GCC', 'version': '13.3.0'} + +source_urls = ['https://www.%(namelower)s.org/static/downloads/%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['883f5bb3aeabf627cb8492ca02a03b191d09836bbe0f599d8508351179781d41'] + +dependencies = [ + ('UCX', '1.16.0'), +] + +configopts = 'FFLAGS="-w -fallow-argument-mismatch -O2" --with-devices=ch4:ucx --with-ucx=$EBROOTUCX' + + +moduleclass = 'mpi' From be3e4102b2f512a31e2b98add3d59bb1101492ed Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Thu, 19 Sep 2024 14:03:00 +0200 Subject: [PATCH 099/107] adding easyconfigs: decona-1.4-20240731-foss-2023a.eb, qcat-1.1.0-foss-2023a.eb --- .../decona/decona-1.4-20240731-foss-2023a.eb | 41 +++++++++++++++++++ .../q/qcat/qcat-1.1.0-foss-2023a.eb | 35 ++++++++++++++++ 2 files changed, 76 insertions(+) create mode 100644 easybuild/easyconfigs/d/decona/decona-1.4-20240731-foss-2023a.eb create mode 100644 easybuild/easyconfigs/q/qcat/qcat-1.1.0-foss-2023a.eb diff --git a/easybuild/easyconfigs/d/decona/decona-1.4-20240731-foss-2023a.eb b/easybuild/easyconfigs/d/decona/decona-1.4-20240731-foss-2023a.eb new file mode 100644 index 00000000000..3e1eb388a12 --- /dev/null +++ b/easybuild/easyconfigs/d/decona/decona-1.4-20240731-foss-2023a.eb @@ -0,0 +1,41 @@ +easyblock = 'Tarball' + +name = 'decona' +version = '1.4-20240731' +local_commit = 'f7488ad' + +homepage = 'https://github.com/Saskia-Oosterbroek/decona' +description = "fastq to polished sequenses: pipeline suitable for mixed samples and long (Nanopore) reads" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/Saskia-Oosterbroek/decona/archive'] +sources = ['%s.tar.gz' % local_commit] +checksums = ['7504160481ccdd3410fc79348c01a9a3bf0795ad73679cc305e1dcdf3e395962'] + +dependencies = [ + ('Python', '3.11.3'), + ('NanoFilt', '2.8.0'), + ('qcat', '1.1.0'), + ('CD-HIT', '4.8.1'), + ('minimap2', '2.26'), + ('Racon', '1.5.0'), + ('medaka', '1.11.3'), + ('BLAST+', '2.14.1'), +] + +fix_python_shebang_for = ['decona'] + +modextrapaths = { + 'PATH': '', + 'PYTHONPATH': '', +} + +sanity_check_paths = { + 'files': ['decona'], + 'dirs': [], +} + +sanity_check_commands = ["decona -v | grep 'This is Decona %s'" % version.split('-')[0]] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/q/qcat/qcat-1.1.0-foss-2023a.eb b/easybuild/easyconfigs/q/qcat/qcat-1.1.0-foss-2023a.eb new file mode 100644 index 00000000000..0c20434dec2 --- /dev/null +++ b/easybuild/easyconfigs/q/qcat/qcat-1.1.0-foss-2023a.eb @@ -0,0 +1,35 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 +# Update: Petr Král (INUITS) +easyblock = 'PythonPackage' + +name = 'qcat' +version = '1.1.0' + +homepage = 'https://github.com/nanoporetech/qcat' +description = "qcat is a Python command-line tool for demultiplexing Oxford Nanopore reads from FASTQ files" + +toolchain = {'name': 'foss', 'version': '2023a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['56f225321a48eef43e2b83a33cbbb47bf1b1edcd569f3db4d088a1bc0199e20a'] + +dependencies = [ + ('Python', '3.11.3'), + ('Biopython', '1.83'), + ('python-parasail', '1.3.4'), + ('PyYAML', '6.0'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/qcat'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["qcat --help"] + +moduleclass = 'bio' From c371929a82a584ba60fa72fe29be88bd9a52c935 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Thu, 19 Sep 2024 16:22:19 +0200 Subject: [PATCH 100/107] adding easyconfigs: awscli-2.17.54-GCCcore-13.2.0.eb --- .../a/awscli/awscli-2.17.54-GCCcore-13.2.0.eb | 73 +++++++++++++++++++ 1 file changed, 73 insertions(+) create mode 100644 easybuild/easyconfigs/a/awscli/awscli-2.17.54-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/a/awscli/awscli-2.17.54-GCCcore-13.2.0.eb b/easybuild/easyconfigs/a/awscli/awscli-2.17.54-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..9b70b1a9008 --- /dev/null +++ b/easybuild/easyconfigs/a/awscli/awscli-2.17.54-GCCcore-13.2.0.eb @@ -0,0 +1,73 @@ +easyblock = 'PythonBundle' + +name = 'awscli' +version = '2.17.54' + +homepage = 'https://pypi.python.org/pypi/awscli' +description = 'Universal Command Line Environment for AWS' + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.27.6'), # required for awscrt +] + +dependencies = [ + ('Python', '3.11.5'), + ('PyYAML', '6.0.1'), + ('ruamel.yaml', '0.18.6'), +] + +use_pip = True + +exts_list = [ + ('jmespath', '1.0.1', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['02e2e4cc71b5bcab88332eebf907519190dd9e6e82107fa7f83b1003a6252980'], + }), + ('botocore', '1.35.22', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['d9bc656e7dde0b3e3f3080fc54bacff6a97fd7806b98acbcc21c7f9d4d0102b9'], + }), + ('s3transfer', '0.10.2', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['eca1c20de70a39daee580aef4986996620f365c4e0fda6a86100231d62f1bf69'], + }), + ('prompt_toolkit', '3.0.47', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['0d7bfa67001d5e39d02c224b663abc33687405033a8c422d0d675a5a13361d10'], + }), + ('distro', '1.9.0', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['7bffd925d65168f85027d8da9af6bddab658135b840670a223589bc0c8ef02b2'], + }), + ('awscrt', '0.21.5', { + 'preinstallopts': "export AWS_CRT_BUILD_USE_SYSTEM_LIBCRYPTO=1 && ", + 'checksums': ['7ec2a67af30fbf386494df00bbdf996f7024000df6b01ab160014afef2b91005'], + }), + # older version of `urllib3` to avoid `ImportError: cannot import name 'DEFAULT_CIPHERS' from 'urllib3.util.ssl_'` + # see https://github.com/aws/aws-cli/issues/7905#issuecomment-1559817550 + ('urllib3', '1.26.20', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['0ed14ccfbf1c30a9072c7ca157e4319b70d65f623e91e7b32fadb2853431016e'], + }), + (name, version, { + # version requirements are too strict + 'preinstallopts': """sed -i 's/>[^"]*//g' pyproject.toml && """, + 'source_tmpl': '%(version)s.tar.gz', + 'source_urls': ['https://github.com/aws/aws-cli/archive/'], + 'checksums': ['c0a37eeb52b7df336e117667b67a275929701e9f6dad0ddb7de59a6f834e5b48'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/aws'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +sanity_check_commands = ["aws help"] + +moduleclass = 'tools' From 100bc746fac841c86af68e76ba344f2ad04d5a9a Mon Sep 17 00:00:00 2001 From: Sam Moors Date: Thu, 19 Sep 2024 19:28:29 +0200 Subject: [PATCH 101/107] don't use name template in url --- easybuild/easyconfigs/m/MPICH/MPICH-4.2.2-GCC-13.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MPICH/MPICH-4.2.2-GCC-13.3.0.eb b/easybuild/easyconfigs/m/MPICH/MPICH-4.2.2-GCC-13.3.0.eb index 629c5f4dcbc..2b2b2185ecc 100644 --- a/easybuild/easyconfigs/m/MPICH/MPICH-4.2.2-GCC-13.3.0.eb +++ b/easybuild/easyconfigs/m/MPICH/MPICH-4.2.2-GCC-13.3.0.eb @@ -7,7 +7,7 @@ of the Message Passing Interface (MPI) standard (MPI-1, MPI-2 and MPI-3).""" toolchain = {'name': 'GCC', 'version': '13.3.0'} -source_urls = ['https://www.%(namelower)s.org/static/downloads/%(version)s'] +source_urls = ['https://www.mpich.org/static/downloads/%(version)s'] sources = [SOURCELOWER_TAR_GZ] checksums = ['883f5bb3aeabf627cb8492ca02a03b191d09836bbe0f599d8508351179781d41'] From af0c51f8e3b48ddfbb073442c1d06317e3fcaf07 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Thu, 19 Sep 2024 21:06:09 +0200 Subject: [PATCH 102/107] avoid writing to ~/.stack file for git-annex --- .../g/git-annex/git-annex-10.20230802-GCCcore-12.2.0.eb | 2 +- .../g/git-annex/git-annex-10.20230802-GCCcore-12.3.0.eb | 2 +- .../g/git-annex/git-annex-10.20240731-GCCcore-13.3.0.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.2.0.eb index 2e2696826f6..efe47052c14 100644 --- a/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.2.0.eb @@ -29,7 +29,7 @@ sources = [{ checksums = [None] -prebuildopts = "stack setup && stack build && " +prebuildopts = "export STACK_ROOT=$(mktemp -d) && stack setup && stack build && " buildopts = "install-bins BUILDER=stack PREFIX=%(builddir)s" files_to_copy = [ diff --git a/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.3.0.eb index 6b6af7f9eba..9761a2d03a6 100644 --- a/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.3.0.eb @@ -31,7 +31,7 @@ sources = [{ checksums = [None] -prebuildopts = "stack setup && stack build && " +prebuildopts = "export STACK_ROOT=$(mktemp -d) && stack setup && stack build && " buildopts = "install-bins BUILDER=stack PREFIX=%(builddir)s" files_to_copy = [ diff --git a/easybuild/easyconfigs/g/git-annex/git-annex-10.20240731-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/git-annex/git-annex-10.20240731-GCCcore-13.3.0.eb index 89c70af2f45..b04d3b5f5bb 100644 --- a/easybuild/easyconfigs/g/git-annex/git-annex-10.20240731-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/g/git-annex/git-annex-10.20240731-GCCcore-13.3.0.eb @@ -31,7 +31,7 @@ sources = [{ checksums = [None] -prebuildopts = "stack setup && stack build && " +prebuildopts = "export STACK_ROOT=$(mktemp -d) && stack setup && stack build && " buildopts = "install-bins BUILDER=stack PREFIX=%(builddir)s" files_to_copy = [ From 985ed3c6e5fda49a1197530c0859a295ad4d86e4 Mon Sep 17 00:00:00 2001 From: Sam Moors Date: Fri, 20 Sep 2024 15:11:44 +0200 Subject: [PATCH 103/107] add sanity_check_commands --- .../g/GOMC/GOMC-2.76-20230613-GCC-11.3.0-CUDA-11.7.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/g/GOMC/GOMC-2.76-20230613-GCC-11.3.0-CUDA-11.7.0.eb b/easybuild/easyconfigs/g/GOMC/GOMC-2.76-20230613-GCC-11.3.0-CUDA-11.7.0.eb index 7b3db4cc18b..fbe1458a01a 100644 --- a/easybuild/easyconfigs/g/GOMC/GOMC-2.76-20230613-GCC-11.3.0-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/g/GOMC/GOMC-2.76-20230613-GCC-11.3.0-CUDA-11.7.0.eb @@ -44,4 +44,6 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = ['%s | grep "Info: GOMC"' % x for x in _gomc_exe] + moduleclass = 'chem' From bde569eaea07f752c0adb28bae0a4cdce71b8ed4 Mon Sep 17 00:00:00 2001 From: Sam Moors Date: Fri, 20 Sep 2024 15:27:11 +0200 Subject: [PATCH 104/107] minor change Co-authored-by: Alex Domingo --- easybuild/easyconfigs/c/CLUMPP/CLUMPP-1.1.2-Linux64.eb | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/CLUMPP/CLUMPP-1.1.2-Linux64.eb b/easybuild/easyconfigs/c/CLUMPP/CLUMPP-1.1.2-Linux64.eb index fb71ad7ff19..3b42e01a2be 100644 --- a/easybuild/easyconfigs/c/CLUMPP/CLUMPP-1.1.2-Linux64.eb +++ b/easybuild/easyconfigs/c/CLUMPP/CLUMPP-1.1.2-Linux64.eb @@ -24,9 +24,15 @@ sanity_check_paths = { 'dirs': [], } +_clumpp_test_cmd = [ + "tmpdir=$(mktemp -d)", + "cp %(installdir)s/{paramfile,arabid.popfile,arabid.permutationfile} $tmpdir", + "cd $tmpdir", + "CLUMPP", +] + sanity_check_commands = [ - 'tmpdir=$(mktemp -d) && cp %(installdir)s/{paramfile,arabid.popfile,arabid.permutationfile} $tmpdir/ && ' - 'cd $tmpdir && CLUMPP', + " && ".join(_clumpp_test_cmd), ] moduleclass = 'bio' From 364089ed5444765ecfdf949083dcc931673affd9 Mon Sep 17 00:00:00 2001 From: WilleBell Date: Fri, 20 Sep 2024 15:42:57 +0200 Subject: [PATCH 105/107] Remove broken easyconfig for pre-release --- .../CREST/CREST-3.0pre-20240319-gfbf-2023a.eb | 44 ------------------- 1 file changed, 44 deletions(-) delete mode 100644 easybuild/easyconfigs/c/CREST/CREST-3.0pre-20240319-gfbf-2023a.eb diff --git a/easybuild/easyconfigs/c/CREST/CREST-3.0pre-20240319-gfbf-2023a.eb b/easybuild/easyconfigs/c/CREST/CREST-3.0pre-20240319-gfbf-2023a.eb deleted file mode 100644 index 4247fa23773..00000000000 --- a/easybuild/easyconfigs/c/CREST/CREST-3.0pre-20240319-gfbf-2023a.eb +++ /dev/null @@ -1,44 +0,0 @@ -# Author: Jasper Grimm (UoY) -# Update to 2.12: -# Author: J. Sassmannshausen (Imperial College London) - -easyblock = 'CMakeMake' - -name = 'CREST' -version = '3.0pre-20240319' -_commit = '2719412edf8bb606cebdd4cd6bbb4cdbd249e1e5' - -homepage = 'https://xtb-docs.readthedocs.io/en/latest/crest.html' -description = """CREST is an utility/driver program for the xtb program. Originally it was designed - as conformer sampling program, hence the abbreviation Conformer–Rotamer Ensemble Sampling Tool, - but now offers also some utility functions for calculations with the GFNn–xTB methods. Generally - the program functions as an IO based OMP scheduler (i.e., calculations are performed by the xtb - program) and tool for the creation and analysation of structure ensembles. -""" - -toolchain = {'name': 'gfbf', 'version': '2023a'} -toolchainopts = {'opt': True, 'optarch': True, 'extra_fflags': '-ffree-line-length-none'} - -separate_build_dir = False - -github_account = 'grimme-lab' -source_urls = [GITHUB_LOWER_SOURCE] -sources = [{'download_filename': '%s.tar.gz' % _commit, 'filename': SOURCE_TAR_GZ}] -checksums = ['770b7ca72bc47bc4e1ffd8ca56566df7b03f4d3b702b04ec6b83bad9a125884d'] - -builddependencies = [('CMake', '3.26.3')] - -dependencies = [('xtb', '6.6.1')] # required to run the program - -# Simple test command just to check if the program is working: -test_cmd = 'export PATH=%%(builddir)s/%%(namelower)s-%s:$PATH && ' % _commit -test_cmd += 'cd %%(builddir)s/%%(namelower)s-%s/examples/expl-0/ && ./run.sh ' % _commit - -sanity_check_paths = { - 'files': ['bin/%s' % name.lower()], - 'dirs': [], -} - -sanity_check_commands = ["crest -h", "crest --cite"] - -moduleclass = 'chem' From fa7e7e41a87024ac86c073405793108e3a6ca4b4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 22 Sep 2024 10:02:33 +0200 Subject: [PATCH 106/107] prepare release notes for EasyBuild v4.9.4 + bump version to 4.9.4 --- RELEASE_NOTES | 33 +++++++++++++++++++++++++++++++++ setup.py | 2 +- 2 files changed, 34 insertions(+), 1 deletion(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index 590c5db69f2..9d2bef5bef9 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -7,6 +7,39 @@ The latest version of easybuild-easyconfig provides 20,561 easyconfig files, for incl. 41 different (compiler) toolchains. +v4.9.4 (22 september 2024) +-------------------------- + +update/bugfix release + +- added example easyconfig files for XXX new software packages: + - Biotite (#21026), chopper (#21418), CLUMPP (#21329), cramino (#21382), dub (#21378), ESM3 (#21026), GOMC (#21008), + MOKIT (#21352), nanoQC (#21371), phasius (#21389), PyBullet (#21356), rnamotif (#21336), versioningit (#21424), + xskillscore (#21351) +- added additional easyconfigs for various supported software packages, including: + - awscli 2.17.54, BiG-SCAPE-1.1.9, ccache 4.10.2, CLHEP 2.4.7.1, CREST 3.0.2, decona 1.4-2024073, dftd4 3.7.0, + GATE 9.4, Gdk-Pixbuf 2.42.11, Geant4 11.2.2, Geant4-data 11.2, Ghostscript 10.03.1, GitPython 3.1.43, + GObject-Introspection 1.80.1, HarfBuzz 9.0.0, ImageMagick 7.1.1-38, JasPer 4.2.4, joypy 0.2.6, Julia 1.10.4, + LDC 1.39.0, Leptonica 1.84.1, Markdown 3.7, MPICH 4.2.2, NanoComp 1.24.0, nanoget 1.19.3, nanomath 1.4.0, + NanoPlot 1.43.0, Pango 1.54.0, PCAngsd 1.2, Pillow 10.4.0, python-isal 1.7.0, pocl 6.0, PROJ 9.4.1, protobuf 28.0, + protobuf-python 5.28.0, R-tesseract 5.2.1, RepeatMasker 4.1.7-p1, RHEIA 1.1.11, RMBlast 2.14.1, + scikit-build-core 0.10.6, sleuth 0.30.1, SNAP-ESA 10.0.0, tesseract 5.3.4, Triton 2.1.0, TurboVNC 3.1.2, + VirtualGL 3.1.1, zlib-ng 2.2.1 +- minor enhancements, including: + - enable support for Apache ORC to Arrow v14.0.1 and v16.1.0 (#21056) + - use proper dependency for tensorboard in easyconfigs for TensorFlow v2.15.1 (#21337) +- various bug fixes, including: + - account for crates for easyconfigs using Cargo-based easyblock when determining checksums for patches in easyconfigs test suite (#21419) + - avoid missing symbol in mclust extension of R-4.0.3 w/ foss/2020b (#21429) + - fix build of librosa 0.10.1 in some environments by removing "python -m build" for soxr extension (#21434) + - fix repeated sanity check runs in manta easyconfigs (#21435) + - fix test_easyconfig_locations when easyconfigs index is present (#21394) + - use proper dependency for libnsl in git-annex (#21441) + - avoid writing into ~/.stack directory during build for git-annex (#21452) +- other changes: + - remove exts_default_options from TensorFlow 2.3.1 (#21290) + + v4.9.3 (14 September 2024) -------------------------- diff --git a/setup.py b/setup.py index 47b7fc09bd1..a2774a7bbe2 100644 --- a/setup.py +++ b/setup.py @@ -44,7 +44,7 @@ # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like # UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0' # This causes problems further up the dependency chain... -VERSION = '4.9.4.dev0' +VERSION = '4.9.4' MAJ_VER = VERSION.split('.')[0] MAJMIN_VER = '.'.join(VERSION.split('.')[0:2]) From 6d1f4b973a5c2ef81be505bfd3cdcaee5dec5809 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 22 Sep 2024 15:02:27 +0200 Subject: [PATCH 107/107] fix counts in release notes for EasyBuild v4.9.4 --- RELEASE_NOTES | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index 9d2bef5bef9..457e390f6b9 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -3,7 +3,7 @@ For more detailed information, please see the git log. These release notes can also be consulted at https://docs.easybuild.io/en/latest/Release_notes.html. -The latest version of easybuild-easyconfig provides 20,561 easyconfig files, for 3,656 different software packages, +The latest version of easybuild-easyconfig provides 20,670 easyconfig files, for 3,670 different software packages, incl. 41 different (compiler) toolchains. @@ -12,7 +12,7 @@ v4.9.4 (22 september 2024) update/bugfix release -- added example easyconfig files for XXX new software packages: +- added example easyconfig files for 14 new software packages: - Biotite (#21026), chopper (#21418), CLUMPP (#21329), cramino (#21382), dub (#21378), ESM3 (#21026), GOMC (#21008), MOKIT (#21352), nanoQC (#21371), phasius (#21389), PyBullet (#21356), rnamotif (#21336), versioningit (#21424), xskillscore (#21351)