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

…asyconfigs into 20221004152047_new_pr_StringTie221

.github/workflows/linting.yml

@@ -1,5 +1,13 @@
 name: Static Analysis
 on: [push, pull_request]
+
+permissions:
+  contents: read # to fetch code (actions/checkout)
+
+concurrency:
+  group: ${{format('{0}:{1}:{2}', github.repository, github.ref, github.workflow)}}
+  cancel-in-progress: true
+
 jobs:
   python-linting:
     runs-on: ubuntu-20.04
@@ -18,3 +26,6 @@ jobs:
 
     - name: Run flake8 to verify PEP8-compliance of Python code
       run: flake8
+
+    - name: Run flake8 to verify PEP8-compliance of Easyconfigs
+      run: flake8 --select W605  --filename '*.eb'

.github/workflows/unit_tests.yml

@@ -1,14 +1,22 @@
 name: easyconfigs unit tests
 on: [push, pull_request]
+
+permissions:
+  contents: read # to fetch code (actions/checkout)
+
+concurrency:
+  group: ${{format('{0}:{1}:{2}', github.repository, github.ref, github.workflow)}}
+  cancel-in-progress: true
+
 jobs:
   test-suite:
     runs-on: ubuntu-20.04
     strategy:
       matrix:
-        python: [2.7, 3.6]
+        python: [3.6]
         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
@@ -26,7 +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
@@ -151,12 +159,12 @@ jobs:
     runs-on: ubuntu-20.04
     strategy:
       matrix:
-        python: [2.7, 3.6, 3.7]
+        python: [3.6]
     steps:
     - uses: actions/checkout@v2
 
     - name: set up Python
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v4
       with:
         python-version: ${{matrix.python}}
 

.gitignore

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

README.rst

@@ -1,9 +1,10 @@
-.. image:: https://github.com/easybuilders/easybuild-easyconfigs/workflows/easyconfigs%20unit%20tests/badge.svg
-
-.. image:: https://easybuilders.github.io/easybuild/images/easybuild_logo_small.png
+.. image:: https://github.com/easybuilders/easybuild/raw/develop/logo/png/easybuild_logo_2022_horizontal_dark_bg_transparent.png
    :align: center
+   :height: 400px
+
+.. image:: https://github.com/easybuilders/easybuild-easyconfigs/workflows/easyconfigs%20unit%20tests/badge.svg
 
-`EasyBuild <https://easybuilders.github.io/easybuild>`_ is a software build
+`EasyBuild <https://easybuild.io>`_ is a software build
 and installation framework that allows you to manage (scientific) software
 on High Performance Computing (HPC) systems in an efficient way.
 
@@ -13,7 +14,7 @@ Easyconfig files are used to specify which software to build, which
 version of the software (and its dependencies), which build parameters
 to use (e.g., which compiler toolchain to use), etc.
 
-The EasyBuild documentation is available at http://easybuild.readthedocs.org/.
+The EasyBuild documentation is available at http://docs.easybuild.io/.
 
 The easybuild-easyconfigs package is hosted on GitHub, along
 with an issue tracker for bug reports and feature requests, see

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/__archive__/a/AFNI/AFNI-20150717-intel-2015a.eb

@@ -43,13 +43,13 @@ skipsteps = ['configure', 'install']
 
 prebuildopts = "cp Makefile.linux_openmp_64 Makefile && "
 buildopts = 'totality LGIFTI="$EBROOTEXPAT/lib/libexpat.a" LDPYTHON="-lpython%s" ' % majpyver
-buildopts += 'CC="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" '
-buildopts += 'CCVOL="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" '
-buildopts += 'CCFAST="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" '
-buildopts += 'CCOLD="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" '
-buildopts += 'CCMIN="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" '
-buildopts += 'CCSVD="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" '
-buildopts += 'LD="${CC} \$(CPROF)" LZLIB="${EBROOTZLIB}/lib/libz.a" XLIBS="-lXm -lXt" '
+buildopts += r'CC="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" '
+buildopts += r'CCVOL="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" '
+buildopts += r'CCFAST="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" '
+buildopts += r'CCOLD="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" '
+buildopts += r'CCMIN="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" '
+buildopts += r'CCSVD="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" '
+buildopts += r'LD="${CC} \$(CPROF)" LZLIB="${EBROOTZLIB}/lib/libz.a" XLIBS="-lXm -lXt" '
 buildopts += 'IFLAGS="-I. -I$EBROOTPYTHON/include/python%s ' % majpyver
 buildopts += '-I$EBROOTGLIB/lib/glib-2.0/include -I$EBROOTGLIB/include/glib-2.0"'
 buildopts += ' INSTALLDIR=%(installdir)s'

easybuild/easyconfigs/__archive__/c/CGAL/CGAL-4.7-intel-2015b-Python-2.7.10.eb

@@ -25,7 +25,7 @@ dependencies = [
     ('libGLU', '9.0.0'),
 ]
 
-configopts = "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include "
+configopts = r"-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include "
 configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.so -DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.so "
 
 builddependencies = [

easybuild/easyconfigs/__archive__/c/CGAL/CGAL-4.7-intel-2015b-Python-2.7.11.eb

@@ -25,7 +25,7 @@ dependencies = [
     ('libGLU', '9.0.0', '-Mesa-%s' % mesaver),
 ]
 
-configopts = "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include "
+configopts = r"-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include "
 configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT
 configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT
 

easybuild/easyconfigs/__archive__/c/CGAL/CGAL-4.8.1-foss-2015a-GLib-2.48.2-Python-2.7.11.eb

@@ -26,7 +26,7 @@ dependencies = [
 ]
 
 configopts = "-DCMAKE_VERBOSE_MAKEFILE=ON "
-configopts += "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include "
+configopts += r"-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include "
 configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT
 configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT
 

easybuild/easyconfigs/__archive__/c/ChIP-Seq/ChIP-Seq-1.5-1-goolf-1.4.10.eb

@@ -44,7 +44,7 @@ modextrapaths = {
 }
 
 # fix shebang line in all provided perl scripts in tools folder
-postinstallcmds = ["sed -i -e 's|/usr/bin/perl|/usr/bin/env\ perl|' %(installdir)s/tools/*.pl",
-                   "sed -i -e 's|/usr/local/bin/perl|/usr/bin/env\ perl|' %(installdir)s/tools/*.pl"]
+postinstallcmds = ["sed -i -e 's|/usr/bin/perl|/usr/bin/env perl|' %(installdir)s/tools/*.pl",
+                   "sed -i -e 's|/usr/local/bin/perl|/usr/bin/env perl|' %(installdir)s/tools/*.pl"]
 
 moduleclass = 'bio'

easybuild/easyconfigs/__archive__/c/ChIP-Seq/ChIP-Seq-1.5-1-goolf-1.7.20.eb

@@ -44,7 +44,7 @@ modextrapaths = {
 }
 
 # fix shebang line in all provided perl scripts in tools folder
-postinstallcmds = ["sed -i -e 's|/usr/bin/perl|/usr/bin/env\ perl|' %(installdir)s/tools/*.pl",
-                   "sed -i -e 's|/usr/local/bin/perl|/usr/bin/env\ perl|' %(installdir)s/tools/*.pl"]
+postinstallcmds = [r"sed -i -e 's|/usr/bin/perl|/usr/bin/env\ perl|' %(installdir)s/tools/*.pl",
+                   r"sed -i -e 's|/usr/local/bin/perl|/usr/bin/env\ perl|' %(installdir)s/tools/*.pl"]
 
 moduleclass = 'bio'

easybuild/easyconfigs/__archive__/p/PRINSEQ/PRINSEQ-0.20.4-foss-2015b-Perl-5.20.3.eb

@@ -106,7 +106,7 @@ modextrapaths = {
 }
 
 postinstallcmds = [
-    "sed -i -e 's|/usr/bin/perl|/usr/bin/env\ perl|' %(installdir)s/*.pl",  # fix shebang line
+    r"sed -i -e 's|/usr/bin/perl|/usr/bin/env\ perl|' %(installdir)s/*.pl",  # fix shebang line
     "chmod +x %(installdir)s/*.pl"  # add execution permission
 ]
 

easybuild/easyconfigs/__archive__/p/PRINSEQ/PRINSEQ-0.20.4-goolf-1.4.10-Perl-5.16.3.eb

@@ -104,7 +104,7 @@ modextrapaths = {
 }
 
 postinstallcmds = [
-    "sed -i -e 's|/usr/bin/perl|/usr/bin/env\ perl|' %(installdir)s/*.pl",  # fix shebang line
+    r"sed -i -e 's|/usr/bin/perl|/usr/bin/env\ perl|' %(installdir)s/*.pl",  # fix shebang line
     "chmod +x %(installdir)s/*.pl"  # add execution permission
 ]
 

easybuild/easyconfigs/a/ABAQUS/ABAQUS-2022-hotfix-2214.eb

@@ -34,6 +34,4 @@ checksums = [
     '88b5c0b182e2dc3e09c14f89be338993cf7edcfeb2f388f405022c63f5512029',
 ]
 
-dependencies = [('Java', '11')]
-
 moduleclass = 'cae'

easybuild/easyconfigs/a/ABAQUS/ABAQUS-2022-hotfix-2223.eb

@@ -0,0 +1,34 @@
+name = 'ABAQUS'
+version = '2022'
+local_hotfix = '2223'
+versionsuffix = '-hotfix-%s' % local_hotfix
+
+homepage = 'https://www.simulia.com/products/abaqus_fea.html'
+description = """Finite Element Analysis software for modeling, visualization and best-in-class implicit and explicit
+ dynamics FEA."""
+
+toolchain = SYSTEM
+
+sources = [
+    '%(version)s.AM_SIM_Abaqus_Extend.AllOS.1-5.tar',
+    '%(version)s.AM_SIM_Abaqus_Extend.AllOS.2-5.tar',
+    '%(version)s.AM_SIM_Abaqus_Extend.AllOS.3-5.tar',
+    '%(version)s.AM_SIM_Abaqus_Extend.AllOS.4-5.tar',
+    '%(version)s.AM_SIM_Abaqus_Extend.AllOS.5-5.tar',
+    # hotfixes
+    '%%(version)s.FP.CFA.%s.Part_SIMULIA_EstPrd.Linux64.tar' % local_hotfix,
+    '%%(version)s.FP.CFA.%s.Part_SIMULIA_FlexNet.Linux64.tar' % local_hotfix,
+]
+checksums = [
+    '9025c9bc2d0345c13d96e88c1c422b1979a14bf7ba281bd32dfe093c1446945d',  # 2022.AM_SIM_Abaqus_Extend.AllOS.1-5.tar
+    '14c23b3fdfddb723d84a02eb27edc25162e1d27e8fdce053193f72d28ff0a12c',  # 2022.AM_SIM_Abaqus_Extend.AllOS.2-5.tar
+    '561d54d688ea2f2dcf329701e20502642aecf5526eb56db3a586cbcadfbf20fb',  # 2022.AM_SIM_Abaqus_Extend.AllOS.3-5.tar
+    'c085066ae2df68c9c61ea345808042ddb205c642d649f1ec3b7db4aaffb3d544',  # 2022.AM_SIM_Abaqus_Extend.AllOS.4-5.tar
+    'bfbc2c1a402881308f68f054e1e376fe153053b4287018ddbc80e76710f6969f',  # 2022.AM_SIM_Abaqus_Extend.AllOS.5-5.tar
+    # 2022.FP.CFA.2223.Part_SIMULIA_EstPrd.Linux64.tar
+    'bb05b07072ded86944eb44908875e6813c6ea18b2e6ab4dc7f8ef1ef368851e2',
+    # 2022.FP.CFA.2223.Part_SIMULIA_FlexNet.Linux64.tar
+    '32895726d409af8f7055b0f2bad53d10e7c32e36712e3eda8ff860f02622ee6f',
+]
+
+moduleclass = 'cae'

easybuild/easyconfigs/a/ABAQUS/ABAQUS-2022.eb

@@ -22,6 +22,4 @@ checksums = [
     'bfbc2c1a402881308f68f054e1e376fe153053b4287018ddbc80e76710f6969f',  # 2022.AM_SIM_Abaqus_Extend.AllOS.5-5.tar
 ]
 
-dependencies = [('Java', '11')]
-
 moduleclass = 'cae'

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'