Merge remote-tracking branch 'origin/develop' into new_pr_python-casa…

…core-foss-2023b

easybuild/easyconfigs/a/AMICA/AMICA-2024.1.19-intel-2023a.eb

@@ -0,0 +1,30 @@
+easyblock = 'CmdCp'
+
+name = 'AMICA'
+version = '2024.1.19'
+local_commit = 'e0db55f07c8c410641cd5b0df5498a5a53129ce6'
+
+homepage = 'https://github.com/sccn/amica'
+description = """Code for AMICA: Adaptive Mixture ICA with shared components"""
+
+toolchain = {'name': 'intel', 'version': '2023a'}
+toolchainopts = {'openmp': True}
+
+source_urls = ['https://github.com/sccn/amica/archive/']
+sources = [{'download_filename': '%s.zip' % local_commit, 'filename': '%(name)s-%(version)s.zip'}]
+checksums = ['d856ef1bf4bd09b2aacf5da6832b9af5d7fb70976786f43585c72acd1a52443b']
+
+# original command: 
+# $ mpif90 -static-intel -fpp -O3 -march=core-avx2 -heap-arrays -qopenmp -mkl -DMKL -o amica17 funmod2.f90 amica17.f90
+cmds_map = [('.*', "$MPIF90 $F90FLAGS -static-intel -fpp  -heap-arrays -mkl -DMKL -o amica17 funmod2.f90 amica17.f90")]
+
+test_cmd = "./amica17 ./amicadefs.param"
+
+files_to_copy = [(['amica17', 'amicadefs.param'], 'bin')]
+
+sanity_check_paths = {
+    'files': ["bin/amica17", "bin/amicadefs.param"],
+    'dirs': [],
+}
+
+moduleclass = 'math'

easybuild/easyconfigs/a/AMOS/AMOS-3.1.0-foss-2023a.eb

@@ -0,0 +1,44 @@
+##
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+#
+# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA
+# Authors::   Cedric Laczny <[email protected]>, Fotis Georgatos <[email protected]>
+# License::   MIT/GPL
+# $Id$
+#
+# This work implements a part of the HPCBIOS project and is a component of the policy:
+# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html
+##
+
+easyblock = 'ConfigureMake'
+
+name = 'AMOS'
+version = '3.1.0'
+
+homepage = 'http://amos.sourceforge.net'
+description = """The AMOS consortium is committed to the development of open-source whole genome assembly software"""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+toolchainopts = {'pic': True, 'cstd': 'c++98'}
+
+source_urls = [SOURCEFORGE_SOURCE]
+sources = [SOURCELOWER_TAR_GZ]
+patches = ['AMOS-%(version)s_GCC-4.7.patch']
+checksums = [
+    '2d9f50e39186ad3dde3d3b28cc265e8d632430657f40fc3978ce34ab1b3db43b',  # amos-3.1.0.tar.gz
+    '8633ff196568e208cc12932f25f46fa35f7e9a9e80e0bbf4288ae070dd7b8844',  # AMOS-3.1.0_GCC-4.7.patch
+]
+
+dependencies = [
+    ('expat', '2.5.0'),
+    ('MUMmer', '4.0.0rc1'),
+]
+
+sanity_check_paths = {
+    'files': ['bin/AMOScmp', 'bin/AMOScmp-shortReads', 'bin/AMOScmp-shortReads-alignmentTrimmed'],
+    'dirs': []
+}
+
+parallel = 1  # make crashes otherwise
+
+moduleclass = 'bio'

easybuild/easyconfigs/a/ASAP3/ASAP3-3.13.3-foss-2023a.eb

@@ -0,0 +1,36 @@
+easyblock = "PythonPackage"
+
+name = 'ASAP3'
+version = '3.13.3'
+
+homepage = 'https://wiki.fysik.dtu.dk/asap/'
+description = """ASAP is a calculator for doing large-scale classical molecular
+dynamics within the Campos Atomic Simulation Environment (ASE)."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+toolchainopts = {'pic': True, 'usempi': True, 'openmp': False}
+
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['78aa4c9ee11315b6e7f8cd9b1fda6ab9a240cc4f4ff418972ea079612e26d369']
+
+builddependencies = [
+    ('pkgconf', '1.9.5'),
+]
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('ASE', '3.22.1'),
+    ('kim-api', '2.3.0'),
+]
+
+use_pip = True
+download_dep_fail = True
+sanity_pip_check = True
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s']
+}
+
+moduleclass = 'phys'

easybuild/easyconfigs/a/ASAP3/ASAP3-3.13.3-intel-2023a.eb

@@ -0,0 +1,42 @@
+easyblock = "PythonPackage"
+
+name = 'ASAP3'
+version = '3.13.3'
+
+homepage = 'https://wiki.fysik.dtu.dk/asap/'
+description = """ASAP is a calculator for doing large-scale classical molecular
+dynamics within the Campos Atomic Simulation Environment (ASE)."""
+
+toolchain = {'name': 'intel', 'version': '2023a'}
+toolchainopts = {
+    'pic': True,
+    'usempi': True,
+    'openmp': False,
+    'extra_cflags': '-fp-speculation=fast -fp-model fast'
+}
+
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['78aa4c9ee11315b6e7f8cd9b1fda6ab9a240cc4f4ff418972ea079612e26d369']
+
+builddependencies = [
+    ('pkgconf', '1.9.5'),
+]
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('ASE', '3.22.1'),
+    ('kim-api', '2.3.0'),
+]
+
+installopts = '--verbose'
+use_pip = True
+download_dep_fail = True
+sanity_pip_check = True
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s']
+}
+
+moduleclass = 'phys'

easybuild/easyconfigs/a/ArchR/ArchR-1.0.2-foss-2023a-R-4.3.2.eb

@@ -0,0 +1,27 @@
+easyblock = 'RPackage'
+
+name = 'ArchR'
+version = '1.0.2'
+versionsuffix = '-R-%(rver)s'
+
+homepage = 'https://www.archrproject.com'
+description = "ArchR is a full-featured R package for processing and analyzing single-cell ATAC-seq data."
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+source_urls = ['https://github.com/GreenleafLab/ArchR/archive/refs/tags/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['afe4d82975e9d75018e9ec9fda3d116f34f99ad1d45990cbc5a2be7dea8df352']
+
+dependencies = [
+    ('R', '4.3.2'),
+    ('R-bundle-Bioconductor', '3.18', versionsuffix),
+    ('presto', '1.0.0-20230501', versionsuffix),
+]
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['%(name)s'],
+}
+
+moduleclass = 'bio'

easybuild/easyconfigs/a/Arrow/Arrow-14.0.1-gfbf-2023a.eb

@@ -44,18 +44,30 @@ 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 "
 
-# also install Python bindings
-local_install_pyarrow_cmds = "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && "
-local_install_pyarrow_cmds += "export Arrow_DIR=%(installdir)s && export ArrowDataset_DIR=%(installdir)s && "
-local_install_pyarrow_cmds += "export ArrowAcero_DIR=%(installdir)s && export Parquet_DIR=%(installdir)s && "
-local_install_pyarrow_cmds += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && "
-local_install_pyarrow_cmds += "cd %(builddir)s/*arrow-%(version)s/python && export XDG_CACHE_HOME=$TMPDIR && "
-local_install_pyarrow_cmds += "sed -i 's/numpy==[0-9.]*/numpy/g' pyproject.toml && "
-local_install_pyarrow_cmds += "Python3_ROOT_DIR=$EBROOTPYTHON "
-local_install_pyarrow_cmds += "PYARROW_CMAKE_OPTIONS='-DZSTD_LIB=$EBROOTZSTD/lib/libzstd.%s ' " % SHLIB_EXT
-local_install_pyarrow_cmds += "PYARROW_WITH_DATASET=1 PYARROW_WITH_PARQUET=1 "
-local_install_pyarrow_cmds += "python -m pip install --prefix %(installdir)s --no-build-isolation ."
-postinstallcmds = [local_install_pyarrow_cmds]
+# install Python bindings
+_pyarrow_preinstall_opts = "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && "
+_pyarrow_preinstall_opts += "export Arrow_DIR=%(installdir)s && export ArrowDataset_DIR=%(installdir)s && "
+_pyarrow_preinstall_opts += "export ArrowAcero_DIR=%(installdir)s && export Parquet_DIR=%(installdir)s && "
+_pyarrow_preinstall_opts += "export XDG_CACHE_HOME=$TMPDIR && "
+_pyarrow_preinstall_opts += "sed -i 's/numpy==[0-9.]*/numpy/g' pyproject.toml && "
+_pyarrow_preinstall_opts += "Python3_ROOT_DIR=$EBROOTPYTHON "
+_pyarrow_preinstall_opts += "PYARROW_CMAKE_OPTIONS='-DZSTD_LIB=$EBROOTZSTD/lib/libzstd.%s ' " % SHLIB_EXT
+_pyarrow_preinstall_opts += "PYARROW_WITH_DATASET=1 PYARROW_WITH_PARQUET=1 "
+
+exts_defaultclass = 'PythonPackage'
+exts_default_options = {
+    'download_dep_fail': True,
+    'use_pip': True,
+    'sanity_pip_check': True,
+}
+exts_list = [
+    ('pyarrow', version, {
+        'sources': ['apache-arrow-%(version)s.tar.gz'],
+        'checksums': ['5c70eafb1011f9d124bafb328afe54f62cc5b9280b7080e1e3d668f78c0e407e'],
+        'start_dir': '%(builddir)s/apache-arrow-%(version)s/python',
+        'preinstallopts': _pyarrow_preinstall_opts,
+    }),
+]
 
 modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'}
 

easybuild/easyconfigs/a/anndata/anndata-0.10.5.post1-foss-2023a.eb

@@ -0,0 +1,44 @@
+easyblock = 'PythonBundle'
+
+name = 'anndata'
+version = '0.10.5.post1'
+
+homepage = 'https://github.com/scverse/anndata'
+description = """anndata is a Python package for handling annotated data matrices in memory and on disk,
+ positioned between pandas and xarray"""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('h5py', '3.9.0'),
+    ('hatchling', '1.18.0'),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    ('packaging', '23.2', {
+        'checksums': ['048fb0e9405036518eaaf48a55953c750c11e1a1b68e0dd1a9d62ed0c092cfc5'],
+    }),
+    ('array_api_compat', '1.4.1', {
+        'checksums': ['053103b7c0ba73626bff7380abf27a29dc80de144394137bc7455b7eba23d8c0'],
+    }),
+    ('natsort', '8.4.0', {
+        'checksums': ['45312c4a0e5507593da193dedd04abb1469253b601ecaf63445ad80f0a1ea581'],
+    }),
+    (name, version, {
+        'checksums': ['9a17c6eda9fc40759b3f5f81742f5d18c1a0a1acdf02f13e1646700ec082c155'],
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['bin/natsort'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = ["natsort --help"]
+
+moduleclass = 'bio'

easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.9.0-foss-2023b.eb

@@ -1,6 +1,5 @@
-# #
 # Author:    Robert Mijakovic <[email protected]>
-# #
+
 easyblock = 'ConfigureMake'
 
 name = 'arpack-ng'

easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.9.1-foss-2023b.eb

@@ -0,0 +1,32 @@
+easyblock = 'ConfigureMake'
+
+name = 'arpack-ng'
+version = '3.9.1'
+
+homepage = 'https://github.com/opencollab/arpack-ng'
+description = """ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems."""
+
+toolchain = {'name': 'foss', 'version': '2023b'}
+toolchainopts = {'pic': True, 'usempi': True}
+
+github_account = 'opencollab'
+source_urls = [GITHUB_SOURCE]
+sources = ['%(version)s.tar.gz']
+checksums = ['f6641deb07fa69165b7815de9008af3ea47eb39b2bb97521fbf74c97aba6e844']
+
+builddependencies = [
+    ('Autotools', '20220317'),
+    ('pkgconf', '2.0.3'),
+    ('Eigen', '3.4.0')
+]
+
+preconfigopts = "sh bootstrap && "
+configopts = '--enable-mpi --with-pic --with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK"'
+
+sanity_check_paths = {
+    'files': ['lib64/libarpack.la', 'lib64/libarpack.%s' % SHLIB_EXT,
+              'lib64/libparpack.la', 'lib64/libparpack.%s' % SHLIB_EXT],
+    'dirs': [],
+}
+
+moduleclass = 'numlib'

easybuild/easyconfigs/b/BWA/BWA-0.7.17-20220923-GCCcore-12.3.0.eb

@@ -0,0 +1,50 @@
+##
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+#
+# Copyright:: Copyright 2012-2014 Cyprus Institute / CaSToRC, Uni.Lu/LCSB, NTUA
+# Authors::   George Tsouloupas <[email protected]>, Fotis Georgatos <[email protected]>
+# License::   MIT/GPL
+# $Id$
+#
+# This work implements a part of the HPCBIOS project and is a component of the policy:
+# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html
+#
+# Version >= 0.7.15
+# Author: Adam Huffman
+# The Francis Crick Institute
+#
+# Note that upstream development is mainly at: https://github.com/lh3/bwa
+##
+
+name = 'BWA'
+local_commit = '139f68f'
+version = '0.7.17-20220923'
+
+homepage = 'http://bio-bwa.sourceforge.net/'
+description = """
+ Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively
+ short nucleotide sequences against a long reference sequence such as the human
+ genome.
+"""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://github.com/lh3/bwa/archive']
+sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}]
+checksums = ['be460d6e13ddf34896aafae00bad71e05a0b9f7e23490eeeca8ad257065f5e60']
+
+builddependencies = [('binutils', '2.40')]
+
+dependencies = [
+    ('Perl', '5.36.1'),
+    ('zlib', '1.2.13'),
+]
+
+# Allow use of x86 intrinsics on PPC
+prebuildopts = 'export CFLAGS="$CFLAGS -fcommon -DNO_WARN_X86_INTRINSICS" && '
+prebuildopts += "sed -i 's|^CC=|#CC=|g' Makefile && "
+prebuildopts += "sed -i 's|^CFLAGS=|#CFLAGS=|g' Makefile && "
+prebuildopts += "sed -i 's|^LIBS=|LIBS= $(LDFLAGS) |g' Makefile && "
+
+moduleclass = 'bio'

easybuild/easyconfigs/b/Boost.MPI/Boost.MPI-1.79.0-gompi-2022b.eb

@@ -0,0 +1,29 @@
+easyblock = 'EB_Boost'
+
+name = 'Boost.MPI'
+version = '1.79.0'
+
+homepage = 'https://www.boost.org/'
+description = """Boost provides free peer-reviewed portable C++ source libraries."""
+
+toolchain = {'name': 'gompi', 'version': '2022b'}
+toolchainopts = {'pic': True, 'usempi': True}
+
+source_urls = ['https://boostorg.jfrog.io/artifactory/main/release/%(version)s/source/']
+sources = ['boost_%s.tar.gz' % '_'.join(version.split('.'))]
+checksums = ['273f1be93238a068aba4f9735a4a2b003019af067b9c183ed227780b8f36062c']
+
+dependencies = [
+    ('bzip2', '1.0.8'),
+    ('zlib', '1.2.12'),
+    ('XZ', '5.2.7'),
+    ('zstd', '1.5.2'),
+    ('ICU', '72.1'),
+]
+
+configopts = '--without-libraries=python'
+
+boost_mpi = True
+tagged_layout = True
+
+moduleclass = 'devel'