Merge branch 'develop' into 20240122145841_new_pr_tensorboard2151

easybuild/easyconfigs/a/ASE/ASE-3.22.1-iimkl-2023a.eb

@@ -0,0 +1,64 @@
+easyblock = 'PythonBundle'
+
+name = 'ASE'
+version = '3.22.1'
+
+homepage = 'https://wiki.fysik.dtu.dk/ase'
+description = """ASE is a python package providing an open source Atomic Simulation Environment
+ in the Python scripting language.
+
+From version 3.20.1 we also include the ase-ext package, it contains optional reimplementations
+in C of functions in ASE.  ASE uses it automatically when installed."""
+
+toolchain = {'name': 'iimkl', 'version': '2023a'}
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('Python-bundle-PyPI', '2023.06'),
+    ('SciPy-bundle', '2023.07'),
+    ('Flask', '2.3.3'),
+    ('matplotlib', '3.7.2'),
+    ('Tkinter', '%(pyver)s'),     # Needed by GUI of ASE
+    ('spglib-python', '2.1.0'),  # optional
+]
+
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    ('pytest-mock', '3.11.1', {
+        'checksums': ['7f6b125602ac6d743e523ae0bfa71e1a697a2f5534064528c6ff84c2f7c2fc7f'],
+    }),
+    ('ase', version, {
+        'patches': [
+            'ASE-3.22.1-Compatibility-with-pytest-from-Python-3-10.patch',
+            'ASE-3.22.1-Compatibility-with-pytest-part-2.patch',
+            'ASE-3.22.1-Compatibility-with-Scipy-2022-05.patch',
+            'ASE-3.22.1-Compatibility-with-Flask-2-2-2.patch',
+        ],
+        'checksums': [
+            {'ase-3.22.1.tar.gz': '004df6b0ea04b1114c790fadfe45d4125eb0e53125c66a93425af853d82ab432'},
+            {'ASE-3.22.1-Compatibility-with-pytest-from-Python-3-10.patch':
+             '8184765ecc9e14081b183fee5c4470da716d77caa67c25164018ac1fdd225eac'},
+            {'ASE-3.22.1-Compatibility-with-pytest-part-2.patch':
+             '3a3473912f5f96ffc625119d87227781ba4ea581de15d4af6a58ba960cdf4601'},
+            {'ASE-3.22.1-Compatibility-with-Scipy-2022-05.patch':
+             'c1cb07160b063d432f098efd40dd4b3c9f015b7966572c838a908613a482e0c8'},
+            {'ASE-3.22.1-Compatibility-with-Flask-2-2-2.patch':
+             '2a05f98291dc970cb759904988783d1ecc3512ba6a0da852af1d3205667b398d'},
+        ],
+    }),
+    ('ase-ext', '20.9.0', {
+        'checksums': ['a348b0e42cf9fdd11f04b3df002b0bf150002c8df2698ff08d3c8fc7a1223aed'],
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['bin/ase'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+# make sure Tkinter is available, otherwise 'ase gui' will not work
+sanity_check_commands = ["python -c 'import tkinter' "]
+
+moduleclass = 'chem'

easybuild/easyconfigs/a/atools/atools-1.5.1-GCCcore-12.3.0.eb

@@ -0,0 +1,36 @@
+easyblock = 'ConfigureMake'
+
+name = 'atools'
+version = '1.5.1'
+
+homepage = 'https://github.com/gjbex/atools'
+description = """Tools to make using job arrays a lot more convenient."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+source_urls = ['https://github.com/gjbex/atools/archive']
+sources = [SOURCE_TAR_GZ]
+checksums = ['540714c39aa83dd5f1a7367d76f8d6f491336fa5fc00077591a22151ef5d31f4']
+
+builddependencies = [('binutils', '2.40')]
+
+dependencies = [('Python', '3.11.3')]
+
+# to enable SLURM integration (site-specific) (options are torque, moab, sge, slurm)
+configopts = '--with-batchsystem=slurm'
+
+sanity_check_paths = {
+    'files': ['bin/%s' % x for x in ['acreate', 'aenv', 'aload', 'alog', 'arange', 'areduce']],
+    'dirs': ['lib/vsc/atools']
+}
+
+sanity_check_commands = [
+    'acreate -h',
+    'aenv -h',
+    'aload -h',
+    'alog -h',
+    'arange -h',
+    'areduce -h',
+]
+
+moduleclass = 'tools'

easybuild/easyconfigs/b/Blosc/Blosc-1.21.5-GCCcore-12.3.0.eb

@@ -0,0 +1,28 @@
+easyblock = 'CMakeMake'
+
+name = 'Blosc'
+version = '1.21.5'
+
+homepage = 'https://www.blosc.org/'
+
+description = "Blosc, an extremely fast, multi-threaded, meta-compressor library"
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://github.com/Blosc/c-blosc/archive/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['32e61961bbf81ffea6ff30e9d70fca36c86178afd3e3cfa13376adec8c687509']
+
+builddependencies = [
+    ('binutils', '2.40'),
+    ('CMake', '3.26.3'),
+]
+
+sanity_check_paths = {
+    'files': ['include/blosc-export.h', 'include/blosc.h', 'lib/libblosc.a',
+              'lib/libblosc.%s' % SHLIB_EXT],
+    'dirs': [],
+}
+
+moduleclass = 'lib'

easybuild/easyconfigs/b/Blosc2/Blosc2-2.8.0-GCCcore-12.3.0.eb

@@ -0,0 +1,31 @@
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+# Author: Denis Kristak
+# Update: Thomas Hoffmann (EMBL)
+easyblock = 'CMakeMake'
+
+name = 'Blosc2'
+version = '2.8.0'
+
+homepage = 'https://www.blosc.org/'
+
+description = "Blosc, an extremely fast, multi-threaded, meta-compressor library"
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://github.com/Blosc/c-blosc2/archive/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['be608cdf68deb02e0d3ee62e183942a0fe5d5d3185375b9b6566e2ae35a9bdbd']
+
+builddependencies = [
+    ('binutils', '2.40'),
+    ('CMake', '3.26.3'),
+]
+
+sanity_check_paths = {
+    'files': ['include/blosc2/blosc2-export.h', 'include/blosc2.h', 'lib/libblosc2.a',
+              'lib/libblosc2.%s' % SHLIB_EXT],
+    'dirs': [],
+}
+
+moduleclass = 'lib'

easybuild/easyconfigs/b/bx-python/bx-python-0.10.0-foss-2023a.eb

@@ -0,0 +1,34 @@
+easyblock = 'PythonBundle'
+
+name = 'bx-python'
+version = '0.10.0'
+
+homepage = 'https://github.com/bxlab/bx-python'
+description = """The bx-python project is a Python library and associated set of scripts to allow for rapid
+ implementation of genome scale analyses."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('LZO', '2.10'),
+    ('SciPy-bundle', '2023.07'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('python-lzo', '1.15', {
+        'modulename': 'lzo',
+        'preinstallopts': "export PREFIX=$EBROOTLZO && ",
+        'checksums': ['a57aaa00c5c3a0515dd9f7426ba2cf601767dc19dc023d8b99d4a13b0a327b49'],
+    }),
+    (name, version, {
+        'modulename': 'bx',
+        'checksums': ['bfe9541d7b18a98e907b085e31f58d3989fbca4dc667c4ae48c33b753e0e2da8'],
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'bio'

easybuild/easyconfigs/c/CDO/CDO-2.0.5-gompi-2021b.eb

@@ -42,6 +42,9 @@ configopts += "--with-curl=$EBROOTCURL --with-eccodes=$EBROOTECCODES --with-fftw
 configopts += "--with-netcdf=$EBROOTNETCDF --with-proj=$EBROOTPROJ --with-szlib=$EBROOTSZIP "
 configopts += "--with-udunits2=$EBROOTUDUNITS --with-util-linux-uuid=$EBROOTUTILMINLINUX "
 
+# Make sure that right Fortran compiler is used, also on non-x86_64 architectures
+configopts += 'CPPFLAGS="$CPPFLAGS -DgFortran" '
+
 sanity_check_paths = {
     'files': ['bin/cdo', 'lib/libcdi.a', 'lib/libcdi.%s' % SHLIB_EXT],
     'dirs': ['include'],

easybuild/easyconfigs/c/CDO/CDO-2.0.6-gompi-2022a.eb

@@ -43,6 +43,9 @@ configopts += "--with-curl=$EBROOTCURL --with-eccodes=$EBROOTECCODES --with-fftw
 configopts += "--with-netcdf=$EBROOTNETCDF --with-proj=$EBROOTPROJ --with-szlib=$EBROOTSZIP "
 configopts += "--with-udunits2=$EBROOTUDUNITS --with-util-linux-uuid=$EBROOTUTILMINLINUX "
 
+# Make sure that right Fortran compiler is used, also on non-x86_64 architectures
+configopts += 'CPPFLAGS="$CPPFLAGS -DgFortran" '
+
 sanity_check_paths = {
     'files': ['bin/cdo', 'lib/libcdi.a', 'lib/libcdi.%s' % SHLIB_EXT],
     'dirs': ['include'],

easybuild/easyconfigs/c/CDO/CDO-2.1.1-gompi-2021a.eb

@@ -43,6 +43,9 @@ configopts += "--with-curl=$EBROOTCURL --with-eccodes=$EBROOTECCODES --with-fftw
 configopts += "--with-netcdf=$EBROOTNETCDF --with-proj=$EBROOTPROJ --with-szlib=$EBROOTSZIP "
 configopts += "--with-udunits2=$EBROOTUDUNITS --with-util-linux-uuid=$EBROOTUTILMINLINUX "
 
+# Make sure that right Fortran compiler is used, also on non-x86_64 architectures
+configopts += 'CPPFLAGS="$CPPFLAGS -DgFortran" '
+
 sanity_check_paths = {
     'files': ['bin/cdo', 'lib/libcdi.a', 'lib/libcdi.%s' % SHLIB_EXT],
     'dirs': ['include'],

easybuild/easyconfigs/c/CDO/CDO-2.2.2-gompi-2023a.eb

@@ -43,6 +43,9 @@ configopts += "--with-curl=$EBROOTCURL --with-eccodes=$EBROOTECCODES --with-fftw
 configopts += "--with-netcdf=$EBROOTNETCDF --with-proj=$EBROOTPROJ --with-szlib=$EBROOTSZIP "
 configopts += "--with-udunits2=$EBROOTUDUNITS --with-util-linux-uuid=$EBROOTUTILMINLINUX "
 
+# Make sure that right Fortran compiler is used, also on non-x86_64 architectures
+configopts += 'CPPFLAGS="$CPPFLAGS -DgFortran" '
+
 sanity_check_paths = {
     'files': ['bin/cdo', 'lib/libcdi.a', 'lib/libcdi.%s' % SHLIB_EXT],
     'dirs': ['include'],

easybuild/easyconfigs/c/CPPE/CPPE-0.3.1-GCC-12.2.0.eb

@@ -0,0 +1,47 @@
+easyblock = 'CMakeMake'
+
+name = 'CPPE'
+version = '0.3.1'
+
+homepage = 'https://github.com/maxscheurer/cppe'
+description = """CPPE is an open-source, light-weight C++ and Python library for Polarizable
+Embedding (PE)1,2 calculations. It provides an easy-to-use API to implement PE
+for ground-state self-consistent field (SCF) calculations and post-SCF methods.
+A convenient Python interface is also available."""
+
+toolchain = {'name': 'GCC', 'version': '12.2.0'}
+
+github_account = 'maxscheurer'
+source_urls = [GITHUB_LOWER_SOURCE]
+sources = ['v%(version)s.tar.gz']
+checksums = ['38d4230ba3ace78936049c23ad4b1fe9e704fd250ec57cc9733cb3904b62cf7c']
+
+builddependencies = [
+    ('CMake', '3.24.3'),
+    ('pybind11', '2.10.3'),
+]
+
+dependencies = [
+    ('Python', '3.10.8'),
+]
+
+exts_defaultclass = 'PythonPackage'
+exts_default_options = {
+    'download_dep_fail': True,
+    'use_pip': True,
+}
+exts_list = [
+    ('cppe', version, {
+        'source_urls': [PYPI_SOURCE],
+        'checksums': ['b0aef578d6919f8c103d4d4a9fcd3db481bd73c59c157985f52bf62477425d6c'],
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['lib/libcppe.%s' % SHLIB_EXT],
+    'dirs': ['include/cppe', 'lib/python%(pyshortver)s/site-packages', 'share/cmake'],
+}
+
+modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'}
+
+moduleclass = 'chem'

easybuild/easyconfigs/c/CalculiX-CrunchiX/CalculiX-CrunchiX-2.20-foss-2023a.eb

@@ -0,0 +1,50 @@
+# Author: Jasper Grimm (UoY)
+easyblock = 'MakeCp'
+
+name = 'CalculiX-CrunchiX'
+version = '2.20'
+
+homepage = 'http://www.calculix.de'
+description = 'A Free Software Three-Dimensional Structural Finite Element Program'
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+source_urls = ['http://www.dhondt.de']
+sources = ['ccx_%(version)s.src.tar.bz2']
+patches = ['CalculiX-CrunchiX-2.20_improve-makefile.patch']
+checksums = [
+    {'ccx_2.20.src.tar.bz2': '63bf6ea09e7edcae93e0145b1bb0579ea7ae82e046f6075a27c8145b72761bcf'},
+    {'CalculiX-CrunchiX-2.20_improve-makefile.patch':
+     'ada15598029d231f804f61d959ce91e2bb3a58749fe5955398f42fbe87dc970c'},
+]
+
+builddependencies = [
+    ('Perl', '5.36.1'),
+]
+
+dependencies = [
+    ('arpack-ng', '3.9.0'),
+    ('SPOOLES', '2.2'),
+]
+
+start_dir = 'CalculiX/ccx_%(version)s/src'
+
+prebuildopts = 'CFLAGS="$CFLAGS $CPPFLAGS" FFLAGS="$FFLAGS -fallow-argument-mismatch"'
+buildopts = 'SPOOLES_INC_DIR="$EBROOTSPOOLES/include/spooles"'
+
+files_to_copy = [(['ccx_%(version)s'], 'bin')]
+
+postinstallcmds = ['cd %(installdir)s/bin && ln -sf ccx_%(version)s ccx']
+
+sanity_check_paths = {
+    'files': ['bin/ccx'],
+    'dirs': [],
+}
+
+sanity_check_commands = [
+    # ccx {,-v} exit with code 201
+    "ccx | grep 'Usage: CalculiX.exe -i jobname'",
+    "ccx -v | grep 'Version %(version)s'",
+]
+
+moduleclass = 'math'

easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.8.12-foss-2022b.eb

@@ -0,0 +1,30 @@
+easyblock = 'CMakeMake'
+
+name = 'CheMPS2'
+version = '1.8.12'
+
+homepage = 'https://github.com/SebWouters/CheMPS2'
+description = """CheMPS2 is a scientific library which contains a spin-adapted implementation of the
+density matrix renormalization group (DMRG) for ab initio quantum chemistry."""
+
+toolchain = {'name': 'foss', 'version': '2022b'}
+
+source_urls = ['https://github.com/SebWouters/CheMPS2/archive/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['eef1b92d74ac07fde58c043f64e8cac02b5400c209c44dcbb51641f86e0c7c83']
+
+builddependencies = [('CMake', '3.24.3')]
+
+dependencies = [
+    ('HDF5', '1.14.0')
+]
+
+pretestopts = 'export OMP_NUM_THREADS=1 && '
+runtest = 'test'
+
+sanity_check_paths = {
+    'files': ['bin/chemps2', 'lib64/libchemps2.%s' % SHLIB_EXT, 'lib64/libchemps2.a'],
+    'dirs': ['include/chemps2']
+}
+
+moduleclass = 'chem'

easybuild/easyconfigs/c/CmdStanR/CmdStanR-0.7.1-foss-2023a-R-4.3.2.eb

@@ -0,0 +1,28 @@
+easyblock = 'RPackage'
+
+name = 'CmdStanR'
+version = '0.7.1'
+versionsuffix = '-R-%(rver)s'
+
+homepage = 'https://mc-stan.org/cmdstanr'
+description = "CmdStanR is a lightweight interface to Stan for R users"
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+source_urls = ['https://github.com/stan-dev/cmdstanr/archive/refs/tags/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['62e552c641c4faaf64edaf0951a8c39dde8758193154bb79c6b7df114bce233c']
+
+dependencies = [
+    ('R', '4.3.2'),
+    ('R-bundle-CRAN', '2023.12'),
+]
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['%(namelower)s'],
+}
+
+options = {'modulename': '%(namelower)s'}
+
+moduleclass = 'bio'