Merge branch 'develop' of https://github.com/easybuilders/easybuild-e…

…asyconfigs into 20221013153130_new_pr_motif238

.github/workflows/unit_tests.yml

@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-20.04
     strategy:
       matrix:
-        python: [3.6]
+        python: [3.6, '3.11']
         modules_tool: [Lmod-7.8.22, Lmod-8.6.8]
         module_syntax: [Lua, Tcl]
         # exclude some configurations: only test Tcl module syntax with Lmod 8.x and Python 3.6
@@ -147,10 +147,6 @@ jobs:
           eb --search '^foss-2019b.eb' | tee eb_search_foss.out
           grep '/foss-2019b.eb$' eb_search_foss.out
 
-          # make sure CVS easyconfigs are included in installation (cfr. issue #10325)
-          echo "Searching for CVS easyconfigs..."
-          eb --search '^CVS-' | grep '/CVS-'
-
           # try installing M4 with system toolchain (requires ConfigureMake easyblock + easyconfig)
           # use /tmp/sources because that has cached downloads (see cache step above)
           eb --prefix /tmp/$USER/$GITHUB_SHA --sourcepath /tmp/sources M4-1.4.18.eb
@@ -159,7 +155,7 @@ jobs:
     runs-on: ubuntu-20.04
     strategy:
       matrix:
-        python: [3.6]
+        python: [3.6, '3.11']
     steps:
     - uses: actions/checkout@v2
 
@@ -184,12 +180,3 @@ jobs:
           else
             echo "No .git folders found in source tarball: OK"
           fi
-
-          # CVS easyconfigs must be included in source tarball,
-          # see https://github.com/easybuilders/easybuild-easyconfigs/issues/10325
-          cvs_easyconfigs=$(find . -name 'CVS-*.eb')
-          if [ -z "$cvs_easyconfigs" ]; then
-            echo "CVS easyconfigs not found" && false
-          else
-            echo "Found CVS easyconfigs: $cvs_easyconfigs"
-          fi

.gitignore

@@ -11,3 +11,4 @@ dist/
 *.ropeproject/
 eb-*.log
 /MANIFEST
+/easybuild/easyconfigs/.eb-path-index

easybuild/easyconfigs/0/4ti2/4ti2-1.6.9-GCC-11.3.0.eb

@@ -0,0 +1,30 @@
+easyblock = 'ConfigureMake'
+
+name = '4ti2'
+version = '1.6.9'
+
+homepage = 'https://4ti2.github.io/'
+description = """A software package for algebraic, geometric and combinatorial problems on linear spaces"""
+
+toolchain = {'name': 'GCC', 'version': '11.3.0'}
+
+github_account = '4ti2'
+source_urls = [GITHUB_SOURCE]
+sources = ['Release_%s.tar.gz' % '_'.join(version.split('.'))]
+checksums = ['7b1015718102d8cd4dc2de64f69094fdba0bc69a1878ada5960979b171ff89e4']
+
+dependencies = [
+    ('GMP', '6.2.1'),
+    ('GLPK', '5.0'),
+]
+
+builddependencies = [('Autotools', '20220317')]
+
+preconfigopts = './autogen.sh && '
+
+sanity_check_paths = {
+    'files': ['bin/%s' % x for x in ['4ti2gmp', '4ti2int32', '4ti2int64']],
+    'dirs': ['include/4ti2', 'lib', 'share/4ti2']
+}
+
+moduleclass = 'math'

easybuild/easyconfigs/TEMPLATE.eb

@@ -24,7 +24,7 @@ dependencies = []
 # The sanity test MUST be tuned before going production and submitting your contribution to upstream git repositories
 sanity_check_paths = {
     'files': [],
-    'dirs': ["."]
+    'dirs': [],
 }
 
 # You SHOULD change the following line; Kindly consult other easyconfigs for possible options

easybuild/easyconfigs/a/ABINIT/ABINIT-9.10.3-intel-2022a.eb

@@ -0,0 +1,68 @@
+easyblock = 'ConfigureMake'
+
+name = 'ABINIT'
+version = '9.10.3'
+
+homepage = 'https://www.abinit.org/'
+description = """
+ABINIT is a package whose main program allows one to find the total energy, charge density and electronic structure of
+systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using
+pseudopotentials and a planewave or wavelet basis.
+"""
+
+toolchain = {'name': 'intel', 'version': '2022a'}
+toolchainopts = {'usempi': True, 'openmp': True, 'pic': True}
+
+source_urls = ['https://www.abinit.org/sites/default/files/packages/']
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['3f2a9aebbf1fee9855a09dd687f88d2317b8b8e04f97b2628ab96fb898dce49b']
+
+builddependencies = [
+    ('Python', '3.10.4'),
+]
+dependencies = [
+    ('libxc', '5.2.3'),
+    ('netCDF', '4.9.0'),
+    ('netCDF-Fortran', '4.6.0'),
+    ('HDF5', '1.12.2'),
+    ('Wannier90', '3.1.0'),
+]
+
+# Ensure MPI with intel wrappers.
+configopts = '--with-mpi="yes" '
+configopts += ' FC="mpiifort" CC="mpiicc" CXX="mpiicpc" '
+
+# Enable OpenMP
+configopts += '--enable-openmp="yes" '
+
+# BLAS/Lapack from MKL
+configopts += '--with-linalg-flavor=mkl '
+
+# FFTW from MKL
+configopts += '--with-fft-flavor=dfti '
+
+# libxc support
+configopts += '--with-libxc=${EBROOTLIBXC} '
+
+# hdf5/netcdf4 support
+configopts += '--with-netcdf="${EBROOTNETCDF}" '
+configopts += '--with-netcdf-fortran="${EBROOTNETCDFMINFORTRAN}" '
+configopts += '--with-hdf5="${EBROOTHDF5}" '
+
+# Wannier90
+configopts += '--with-wannier90="${EBROOTWANNIER90}" '
+preconfigopts = 'export WANNIER90_LIBS="-L$EBROOTWANNIER90/lib -lwannier" && '
+
+# Enable double precision for GW calculations
+configopts += '--enable-gw-dpc '
+
+# 'make check' is just executing some basic unit tests.
+# Also running 'make tests_v1' to have some basic validation
+runtest = "check && make test_v1"
+
+sanity_check_paths = {
+    'files': ['bin/%s' % x for x in ['abinit', 'aim', 'cut3d', 'conducti', 'mrgddb', 'mrgscr', 'optic']],
+    'dirs': ['lib/pkgconfig'],
+}
+
+moduleclass = 'chem'

easybuild/easyconfigs/a/AICSImageIO/AICSImageIO-4.14.0-foss-2022a.eb

@@ -0,0 +1,64 @@
+easyblock = 'PythonBundle'
+
+name = 'AICSImageIO'
+version = '4.14.0'
+
+homepage = 'https://github.com/AllenCellModeling/aicsimageio'
+description = """Image Reading, Metadata Conversion, and Image Writing for Microscopy Images in Pure Python"""
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('dask', '2022.10.0'),
+    ('imagecodecs', '2022.9.26'),
+    ('lxml', '4.9.1'),
+    ('SciPy-bundle', '2022.05'),
+    ('PyYAML', '6.0'),
+    ('wrapt', '1.15.0'),
+    ('xarray', '2022.6.0'),
+    ('zarr', '2.13.3'),
+    ('aiohttp', '3.8.3'),
+    ('scikit-image', '0.19.3'),
+    ('pydantic', '1.10.4'),
+]
+
+sanity_pip_check = True
+use_pip = True
+
+exts_list = [
+    ('pydantic_compat', '0.1.2', {
+        'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl',
+        'checksums': ['37a4df48565a35aedc947f0fde5edbdff270a30836d995923287292bb59d5677'],
+    }),
+    ('xsdata', '23.8', {
+        'checksums': ['55f03d4c88236f047266affe550ba0dd19476adfce6a01f3e0aefac7c8078e56'],
+    }),
+    ('ome_types', '0.4.3', {
+        'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl',
+        'checksums': ['3d97ce595d0f2f9c37dce3dd359fb30c7dbcad8c8c806604c40f18f99be8c1b2'],
+    }),
+    # Overwrites installed version because aicsimageio 4.14.0 has requirement fsspec<2023.9.0,>=2022.8.0
+    ('fsspec', '2023.6.0', {
+        'checksums': ['d0b2f935446169753e7a5c5c55681c54ea91996cc67be93c39a154fb3a2742af'],
+    }),
+    ('ome-zarr', '0.8.3', {
+        'checksums': ['e98762e6a3cc82e8f6ef50c938e23fc579498d94d1991f3476ccf9726209997b'],
+    }),
+    ('resource_backed_dask_array', '0.1.0', {
+        'checksums': ['8fabcccf5c7e29059b5badd6786dd7675a258a203c58babf10077d9c90ada54f'],
+    }),
+    ('elementpath', '4.1.5', {
+        'checksums': ['c2d6dc524b29ef751ecfc416b0627668119d8812441c555d7471da41d4bacb8d'],
+    }),
+    ('xmlschema', '2.5.0', {
+        'checksums': ['276a03e0fd3c94c148d528bff4d9482f9b99bf8c7b4056a2e8e703d28149d454'],
+    }),
+    ('%(namelower)s', version, {
+        'checksums': ['0f6684587b1d833ce5b10f3e81314e2a89269cd94bd09747fcd6460f3119855c'],
+    }),
+]
+
+sanity_check_commands = ["python -c 'from aicsimageio.writers import OmeTiffWriter'"]
+
+moduleclass = 'lib'

easybuild/easyconfigs/a/ALAMODE/ALAMODE-1.4.2-foss-2022b.eb

@@ -0,0 +1,57 @@
+# with thanks to ComputeCanada for the initial easyconfig for 1.0.2-iomkl-2017.5.211.eb
+# updated for 1.4.2 by BEAR Software team at University of Birmingham
+easyblock = "CMakeMakeCp"
+
+name = 'ALAMODE'
+version = '1.4.2'
+
+homepage = 'http://alamode.readthedocs.io/en/latest/index.html'
+description = """ALAMODE is an open source software designed for analyzing lattice anharmonicity
+ and lattice thermal conductivity of solids. By using an external DFT package such as VASP and
+ Quantum ESPRESSO, you can extract harmonic and anharmonic force constants straightforwardly with ALAMODE.
+ Using the calculated anharmonic force constants, you can also estimate lattice thermal conductivity,
+ phonon linewidth, and other anharmonic phonon properties from first principles.
+"""
+
+toolchain = {'name': 'foss', 'version': '2022b'}
+toolchainopts = {'usempi': True, 'pic': True}
+
+source_urls = ['https://github.com/ttadano/alamode/archive/']
+sources = ['v.%(version)s.tar.gz']
+checksums = ['18fb80a183c2a9b68488aeeccd6efa95e8c21d4cb21b08319a557389d55c067a']
+
+builddependencies = [
+    ('binutils', '2.39'),
+    ('CMake', '3.24.3'),
+]
+
+dependencies = [
+    ('Boost', '1.81.0'),
+    ('Eigen', '3.4.0'),
+    ('spglib', '2.0.2'),
+    ('FFTW', '3.3.10'),
+    ('HDF5', '1.14.0'),
+    ('Python', '3.10.8'),
+]
+
+configopts = ' '.join([
+    "-DWITH_HDF5_SUPPORT=yes",
+    "-DUSE_MKL_FFT=no",
+    "-DSPGLIB_ROOT=$EBROOTSPGLIB"
+])
+
+local_binary_files = [
+    "alm/alm", "anphon/anphon", "tools/analyze_phonons", "tools/dfc2", "tools/fc_virtual",
+    "tools/parse_fcsxml", "tools/qe2alm", "tools/analyze_phonons.py", "tools/displace.py", "tools/extract.py",
+    "tools/GenDisplacement.py", "tools/makedisp_qe.py", "tools/plotband.py", "tools/plotdos.py",
+    "tools/scph_to_qefc.py",
+]
+
+files_to_copy = [([x for x in local_binary_files], 'bin'), 'docs', 'example']
+
+sanity_check_paths = {
+    'files': ['bin/alm'],
+    'dirs': ["docs", "example"]
+}
+
+moduleclass = 'chem'

easybuild/easyconfigs/a/ALL/ALL-0.9.2-foss-2022b.eb

@@ -0,0 +1,41 @@
+easyblock = 'CMakeMake'
+
+name = 'ALL'
+version = '0.9.2'
+
+homepage = 'https://gitlab.jsc.fz-juelich.de/SLMS/loadbalancing'
+description = """A Load Balancing Library (ALL) aims to provide an easy way to include dynamic
+domain-based load balancing into particle based simulation codes. The library
+is developed in the Simulation Laboratory Molecular Systems of the Jülich
+Supercomputing Centre at Forschungszentrum Jülich."""
+
+toolchain = {'name': 'foss', 'version': '2022b'}
+toolchainopts = {'usempi': True}
+
+source_urls = ["https://gitlab.jsc.fz-juelich.de/SLMS/loadbalancing/-/archive/v%(version)s/"]
+sources = ['loadbalancing-v%(version)s.tar.gz']
+checksums = ['2b4ef52c604c3c0c467712d0912a33c82177610b67edc14df1e034779c6ddb71']
+
+builddependencies = [
+    ('CMake', '3.24.3'),
+    ('Boost', '1.81.0'),  # only needed for tests
+]
+
+dependencies = [
+    ('VTK', '9.2.6'),
+]
+
+configopts = '-DCM_ALL_FORTRAN=ON -DCM_ALL_USE_F08=ON -DCM_ALL_VORONOI=ON -DCM_ALL_VTK_OUTPUT=ON '
+configopts += '-DCM_ALL_TESTS=ON -DCM_ALL_AUTO_DOC=OFF -DVTK_DIR=$EBROOTVTK '
+
+runtest = 'test'
+
+sanity_check_paths = {
+    'files': [
+        'include/ALL.hpp', 'include/ALL_Voronoi.hpp', 'lib/all_module.mod',
+        'lib/libALL.a', 'lib/libALL_fortran.a'
+    ],
+    'dirs': ['lib/cmake'],
+}
+
+moduleclass = 'lib'