Merge branch 'develop' into tests_python311

.github/workflows/unit_tests.yml

@@ -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
@@ -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/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/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'

easybuild/easyconfigs/a/ABINIT/ABINIT-9.2.1-intel-2019b.eb

@@ -0,0 +1,57 @@
+#
+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': 'intel', '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 with intel wrappers.
+configopts = '--with-mpi="yes" --enable-openmp="no" '
+configopts += ' FC="mpiifort" CC="mpiicc" CXX="mpiicpc" '
+
+# 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}" '
+
+# `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/AGAT/AGAT-1.1.0-GCC-12.2.0.eb

@@ -0,0 +1,69 @@
+# easybuild easyconfig
+#
+# John Dey <[email protected]> Fred Hutchinson Cancer Center
+# Thomas Eylenbosch - Gluo NV
+#
+easyblock = 'Bundle'
+
+name = 'AGAT'
+version = '1.1.0'
+
+homepage = 'https://agat.readthedocs.io/en/latest/'
+description = """AGAT: Another GTF/GFF Analysis Toolkit. Suite of tools to handle gene annotations
+ in any GTF/GFF format."""
+
+toolchain = {'name': 'GCC', 'version': '12.2.0'}
+
+builddependencies = [('binutils', '2.39')]
+
+dependencies = [
+    ('Perl', '5.36.0'),
+    ('BioPerl', '1.7.8'),
+]
+
+exts_defaultclass = 'PerlModule'
+exts_filter = ("perl -e 'require %(ext_name)s'", '')
+
+exts_list = [
+    ('Set::Object', '1.42', {
+        'source_tmpl': 'Set-Object-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/R/RU/RURBAN'],
+        'checksums': ['d18c5a8a233eabbd0206cf3da5b00fcdd7b37febf12a93dcc3d1c026e6fdec45'],
+    }),
+    ('File::Share', '0.27', {
+        'source_tmpl': 'File-Share-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/I/IN/INGY'],
+        'checksums': ['d6e8f4b55ebd38e0bb45e44392e3fa27dc1fde16abc5d1ff53e157e19a5755be'],
+    }),
+    ('Sort::Naturally', '1.03', {
+        'source_tmpl': 'Sort-Naturally-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'],
+        'checksums': ['eaab1c5c87575a7826089304ab1f8ffa7f18e6cd8b3937623e998e865ec1e746'],
+    }),
+    ('Class::MethodMaker', '2.24', {
+        'source_tmpl': 'Class-MethodMaker-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/S/SC/SCHWIGON/class-methodmaker'],
+        'checksums': ['5eef58ccb27ebd01bcde5b14bcc553b5347a0699e5c3e921c7780c3526890328'],
+    }),
+    ('Term::ProgressBar', '2.23', {
+        'source_tmpl': 'Term-ProgressBar-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MANWAR'],
+        'checksums': ['defc03fb9f4ac1c9df1359d312bff3c0865ddefbf3aba64cd42a69a86215d49d'],
+    }),
+    (name, version, {
+        'modulename': 'AGAT::Utilities',
+        'source_urls': ['https://github.com/NBISweden/AGAT/archive/refs/tags'],
+        'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}],
+        'checksums': ['38e3df0d0a3817a38e8d824e9d865926c7da6eccc83d583f890faf72e62d7002'],
+    }),
+]
+
+modextrapaths = {'PERL5LIB': 'lib/perl5/site_perl/%(perlver)s/'}
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['bin', 'lib/perl5/site_perl/%(perlver)s/%(name)s'],
+}
+
+sanity_check_commands = ['agat_convert_bed2gff.pl --help']
+moduleclass = 'bio'