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

…asyconfigs into 20230318125117_new_pr_OpenMPI500rc10

.github/workflows/linting.yml

@@ -28,4 +28,4 @@ jobs:
       run: flake8
 
     - name: Run flake8 to verify PEP8-compliance of Easyconfigs
-      run: flake8 --select W605  --filename '*.eb'
+      run: flake8 --select F,W605  --filename '*.eb'

.github/workflows/unit_tests.yml

@@ -13,10 +13,10 @@ jobs:
     runs-on: ubuntu-20.04
     strategy:
       matrix:
-        python: [2.7, 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 2.7 & 3.6
+        # exclude some configurations: only test Tcl module syntax with Lmod 8.x and Python 3.6
         exclude:
           - modules_tool: Lmod-7.8.22
             module_syntax: Tcl
@@ -34,7 +34,7 @@ jobs:
         key: eb-sourcepath
 
     - name: set up Python
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: ${{matrix.python}}
         architecture: x64
@@ -147,10 +147,6 @@ jobs:
           eb --search '^foss-2019b.eb' | tee eb_search_foss.out
           grep '/foss-2019b.eb$' 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
@@ -159,12 +155,12 @@ jobs:
     runs-on: ubuntu-20.04
     strategy:
       matrix:
-        python: [2.7, 3.6, 3.7]
+        python: [3.6, '3.11']
     steps:
     - uses: actions/checkout@v2
 
     - name: set up Python
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v4
       with:
         python-version: ${{matrix.python}}
 
@@ -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/0/3d-dna/3d-dna-180922-GCCcore-8.2.0-Python-2.7.15.eb

@@ -0,0 +1,35 @@
+easyblock = 'Tarball'
+
+name = '3d-dna'
+version = '180922'
+versionsuffix = '-Python-%(pyver)s'
+local_githash = '529ccf46599825b3047e58a69091d599e9858a19'
+
+homepage = 'https://github.com/theaidenlab/3d-dna'
+description = """3D de novo assembly (3D DNA) pipeline"""
+
+toolchain = {'name': 'GCCcore', 'version': '8.2.0'}
+
+source_urls = ['https://github.com/theaidenlab/%(name)s/archive']
+sources = [{'download_filename': '%s.zip' % local_githash, 'filename': SOURCE_ZIP}]
+checksums = ['348c3e019ea29e47382eb2d85228a56bc11b316c130afabae016ad8e7d7640ca']
+
+dependencies = [
+    ('Python', '2.7.15'),
+    ('LASTZ', '1.02.00'),
+    ('Java', '1.8', '', SYSTEM),
+    ('parallel', '20190622'),
+]
+
+postinstallcmds = ['chmod 755 %(installdir)s/*.sh']
+
+sanity_check_paths = {
+    'files': ['run-asm-pipeline.sh', 'run-asm-pipeline-post-review.sh'],
+    'dirs': [],
+}
+
+sanity_check_commands = ["run-asm-pipeline.sh --help"]
+
+modextrapaths = {'PATH': ''}
+
+moduleclass = 'bio'

easybuild/easyconfigs/0/4ti2/4ti2-1.6.10-GCC-13.2.0.eb

@@ -0,0 +1,30 @@
+easyblock = 'ConfigureMake'
+
+name = '4ti2'
+version = '1.6.10'
+
+homepage = 'https://4ti2.github.io/'
+description = """A software package for algebraic, geometric and combinatorial problems on linear spaces"""
+
+toolchain = {'name': 'GCC', 'version': '13.2.0'}
+
+github_account = '4ti2'
+source_urls = [GITHUB_SOURCE]
+sources = ['Release_%s.tar.gz' % '_'.join(version.split('.'))]
+checksums = ['2f1bce3203da65b651d68cbd0ace0f89a16d1f436cf5f24e22bc15ec22df936a']
+
+dependencies = [
+    ('GMP', '6.3.0'),
+    ('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']
+}
+
+moduleclass = 'math'

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/__archive__/f/f90nml/f90nml-1.4.4-GCCcore-10.2.0.eb

@@ -0,0 +1,27 @@
+easyblock = 'PythonPackage'
+
+name = 'f90nml'
+version = '1.4.4'
+
+homepage = 'https://github.com/marshallward/f90nml'
+description = """A Python module and command line tool for parsing
+    Fortran namelist files"""
+
+toolchain = {'name': 'GCCcore', 'version': '10.2.0'}
+
+sources = [SOURCE_TAR_GZ]
+checksums = ['65e8e135779895245238cbf6be5b1b80d6c2b8c9350c9cdce6183a31bdfd7622']
+
+builddependencies = [
+    ('binutils', '2.35'),
+]
+dependencies = [
+    ('Python', '3.8.6'),
+    ('PyYAML', '5.3.1')
+]
+
+use_pip = True
+download_dep_fail = True
+sanity_pip_check = True
+
+moduleclass = 'tools'

easybuild/easyconfigs/__archive__/l/libunwind/libunwind-1.1-foss-2015a.eb

@@ -15,7 +15,7 @@ toolchain = {'version': '2015a', 'name': 'foss'}
 sources = [SOURCE_TAR_GZ]
 source_urls = [GNU_SAVANNAH_SOURCE]
 
-checksums = ['fb4ea2f6fbbe45bf032cd36e586883ce']
+checksums = ['9dfe0fcae2a866de9d3942c66995e4b460230446887dbdab302d41a8aee8d09a']
 
 dependencies = [
     ('XZ', '5.2.2'),

easybuild/easyconfigs/__archive__/l/libunwind/libunwind-1.1-goolf-1.4.10.eb

@@ -15,7 +15,7 @@ toolchain = {'version': '1.4.10', 'name': 'goolf'}
 sources = [SOURCE_TAR_GZ]
 source_urls = [GNU_SAVANNAH_SOURCE]
 
-checksums = ['fb4ea2f6fbbe45bf032cd36e586883ce']
+checksums = ['9dfe0fcae2a866de9d3942c66995e4b460230446887dbdab302d41a8aee8d09a']
 
 dependencies = [
     ('XZ', '5.2.2'),
@@ -24,7 +24,6 @@ dependencies = [
 preconfigopts = 'export LIBS="$LIBS -llzma" && '
 
 sanity_check_paths = {
-    'files': ["include/libunwind.h", "lib/libunwind.%s" % SHLIB_EXT],
     'files': ['include/libunwind.h', ('lib/libunwind.%s' % SHLIB_EXT, 'lib64/libunwind.%s' % SHLIB_EXT)],
     'dirs': []
 }

easybuild/easyconfigs/__archive__/l/libunwind/libunwind-1.1-ictce-5.3.0.eb

@@ -15,7 +15,7 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'}
 sources = [SOURCE_TAR_GZ]
 source_urls = [GNU_SAVANNAH_SOURCE]
 
-checksums = ['fb4ea2f6fbbe45bf032cd36e586883ce']
+checksums = ['9dfe0fcae2a866de9d3942c66995e4b460230446887dbdab302d41a8aee8d09a']
 
 dependencies = [
     ('XZ', '5.2.2'),
@@ -24,7 +24,6 @@ dependencies = [
 preconfigopts = 'export LIBS="$LIBS -llzma" && '
 
 sanity_check_paths = {
-    'files': ["include/libunwind.h", "lib/libunwind.%s" % SHLIB_EXT],
     'files': ['include/libunwind.h', ('lib/libunwind.%s' % SHLIB_EXT, 'lib64/libunwind.%s' % SHLIB_EXT)],
     'dirs': []
 }

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/ABINIT/ABINIT-9.2.1-foss-2019b.eb

@@ -0,0 +1,59 @@
+#
+easyblock = 'ConfigureMake'
+
+name = 'ABINIT'
+version = '9.2.1'
+
+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': 'foss', 'version': '2019b'}
+toolchainopts = {'usempi': True, 'pic': True}
+
+source_urls = ['https://www.abinit.org/sites/default/files/packages/']
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['4aa2deaeec385ff1624669a59768e1a6655f6367f8f109e69944244e000142a0']
+
+builddependencies = [
+    ('Python', '3.7.4'),
+]
+dependencies = [
+    ('libxc', '4.3.4'),
+    ('netCDF', '4.7.1'),
+    ('netCDF-Fortran', '4.5.2'),
+    ('HDF5', '1.10.5'),
+]
+
+# Ensure MPI.
+configopts = '--with-mpi="yes" --enable-openmp="no" '
+
+# BLAS/Lapack
+configopts += '--with-linalg-flavor="openblas"  LINALG_LIBS="-L${EBROOTOPENBLAS}/lib -lopenblas" '
+
+# FFTW3 support
+configopts += '--with-fft-flavor=fftw3 FFTW3_LIBS="-L${EBROOTFFTW} -lfftw3f -lfftw3" '
+
+# libxc support
+configopts += '--with-libxc=${EBROOTLIBXC} '
+
+# hdf5/netcdf4 support
+configopts += '--with-netcdf="${EBROOTNETCDF}" '
+configopts += '--with-netcdf-fortran="${EBROOTNETCDFMINFORTRAN}" '
+configopts += '--with-hdf5="${EBROOTHDF5}" '
+
+# make sure --free-line-length-none is added to FCFLAGS
+configopts += 'FCFLAGS="${FCFLAGS} --free-line-length-none" '
+
+# `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'