Merge pull request #20294 from easybuilders/4.9.x

release EasyBuild v4.9.1

.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'

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/ABySS/ABySS-2.3.7-foss-2023a.eb

@@ -0,0 +1,34 @@
+easyblock = 'ConfigureMake'
+
+name = 'ABySS'
+version = '2.3.7'
+
+homepage = 'https://www.bcgsc.ca/platform/bioinfo/software/abyss'
+description = """Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler"""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+toolchainopts = {'usempi': True, 'cstd': 'c++17'}
+
+source_urls = ['http://github.com/bcgsc/abyss/releases/download/%(version)s/']
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['ba37780e79ec3aa359b6003e383caef13479a87f4d0022af01b86398f9ffca1f']
+
+dependencies = [
+    ('Autoconf', '2.71'),
+    ('Automake', '1.16.5'),
+    ('Boost', '1.82.0'),
+    ('sparsehash', '2.0.4'),
+    ('btllib', '1.7.0'),
+]
+
+preconfigopts = "./autogen.sh && "
+configopts = 'CXXFLAGS="$CXXFLAGS -Wno-error"'
+
+sanity_check_paths = {
+    'files': ["bin/ABYSS", "bin/ABYSS-P"],
+    'dirs': []
+}
+
+sanity_check_commands = ['ABYSS --help']
+
+moduleclass = 'bio'

easybuild/easyconfigs/a/AMICA/AMICA-2024.1.19-intel-2023a.eb

@@ -0,0 +1,30 @@
+easyblock = 'CmdCp'
+
+name = 'AMICA'
+version = '2024.1.19'
+local_commit = 'e0db55f07c8c410641cd5b0df5498a5a53129ce6'
+
+homepage = 'https://github.com/sccn/amica'
+description = """Code for AMICA: Adaptive Mixture ICA with shared components"""
+
+toolchain = {'name': 'intel', 'version': '2023a'}
+toolchainopts = {'openmp': True}
+
+source_urls = ['https://github.com/sccn/amica/archive/']
+sources = [{'download_filename': '%s.zip' % local_commit, 'filename': '%(name)s-%(version)s.zip'}]
+checksums = ['d856ef1bf4bd09b2aacf5da6832b9af5d7fb70976786f43585c72acd1a52443b']
+
+# original command: 
+# $ mpif90 -static-intel -fpp -O3 -march=core-avx2 -heap-arrays -qopenmp -mkl -DMKL -o amica17 funmod2.f90 amica17.f90
+cmds_map = [('.*', "$MPIF90 $F90FLAGS -static-intel -fpp  -heap-arrays -mkl -DMKL -o amica17 funmod2.f90 amica17.f90")]
+
+test_cmd = "./amica17 ./amicadefs.param"
+
+files_to_copy = [(['amica17', 'amicadefs.param'], 'bin')]
+
+sanity_check_paths = {
+    'files': ["bin/amica17", "bin/amicadefs.param"],
+    'dirs': [],
+}
+
+moduleclass = 'math'

easybuild/easyconfigs/a/AMOS/AMOS-3.1.0-foss-2023a.eb

@@ -0,0 +1,52 @@
+##
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+#
+# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA
+# Authors::   Cedric Laczny <cedric.laczny@uni.lu>, Fotis Georgatos <fotis@cern.ch>
+# License::   MIT/GPL
+# $Id$
+#
+# This work implements a part of the HPCBIOS project and is a component of the policy:
+# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html
+##
+
+easyblock = 'ConfigureMake'
+
+name = 'AMOS'
+version = '3.1.0'
+
+homepage = 'http://amos.sourceforge.net'
+description = """The AMOS consortium is committed to the development of open-source whole genome assembly software"""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+toolchainopts = {'pic': True, 'cstd': 'c++98'}
+
+source_urls = [SOURCEFORGE_SOURCE]
+sources = [SOURCELOWER_TAR_GZ]
+patches = [
+    'AMOS-%(version)s_GCC-4.7.patch',
+    'AMOS-3.1.0_fix_deprecated_maxmatch-flag.patch',
+    'AMOS-3.1.0_link_correctly_to_DELTAFILER_SHOWCOORDS.patch',
+]
+checksums = [
+    {'amos-3.1.0.tar.gz': '2d9f50e39186ad3dde3d3b28cc265e8d632430657f40fc3978ce34ab1b3db43b'},
+    {'AMOS-3.1.0_GCC-4.7.patch': '8633ff196568e208cc12932f25f46fa35f7e9a9e80e0bbf4288ae070dd7b8844'},
+    {'AMOS-3.1.0_fix_deprecated_maxmatch-flag.patch':
+     '80379cee8e8c8228590af89d37ea3fdb734c7e0ebe5bb357eaf2af71d1399fc6'},
+    {'AMOS-3.1.0_link_correctly_to_DELTAFILER_SHOWCOORDS.patch':
+     'e291d87b8cd27752474ee0e1f3acb44f9657cac50d5d6dcceca0efc6436f1fe1'},
+]
+
+dependencies = [
+    ('expat', '2.5.0'),
+    ('MUMmer', '4.0.0rc1'),
+]
+
+sanity_check_paths = {
+    'files': ['bin/AMOScmp', 'bin/AMOScmp-shortReads', 'bin/AMOScmp-shortReads-alignmentTrimmed'],
+    'dirs': []
+}
+
+parallel = 1  # make crashes otherwise
+
+moduleclass = 'bio'

easybuild/easyconfigs/a/AMOS/AMOS-3.1.0_fix_deprecated_maxmatch-flag.patch

@@ -0,0 +1,14 @@
+Replace deprecate NUCMER flag -maxmatch with --maxmatch (from MUMmer 4.0.0rc)
+see https://github.com/sanger-pathogens/circlator/issues/121 and https://github.com/mummer4/mummer/issues/49
+diff -ru amos-3.1.0.orig/src/Pipeline/minimus2.acf amos-3.1.0/src/Pipeline/minimus2.acf
+--- amos-3.1.0.orig/src/Pipeline/minimus2.acf	2011-07-25 01:27:26.000000000 +0200
++++ amos-3.1.0/src/Pipeline/minimus2.acf	2024-03-13 17:03:35.981707768 +0100
+@@ -54,7 +54,7 @@
+ 13: $(BINDIR)/dumpreads $(BANK) -m $(REFCOUNT) > $(QRYSEQ)
+
+ ## Getting overlaps 
+-20: $(NUCMER) -maxmatch -c $(OVERLAP) $(REFSEQ) $(QRYSEQ) -p $(PREFIX)
++20: $(NUCMER) --maxmatch -c $(OVERLAP) $(REFSEQ) $(QRYSEQ) -p $(PREFIX)
+ 21: $(SHOWCOORDS) -H -c -l -o -r -I $(MINID) $(ALIGN) | $(BINDIR)/nucmerAnnotate | egrep 'BEGIN|END|CONTAIN|IDENTITY' > $(COORDS) 
+ 22: $(BINDIR)/nucmer2ovl -ignore $(MAXTRIM) -tab $(COORDS) | $(BINDIR)/sort2 > $(OVLTAB)
+

easybuild/easyconfigs/a/AMOS/AMOS-3.1.0_link_correctly_to_DELTAFILER_SHOWCOORDS.patch

@@ -0,0 +1,15 @@
+minimus2 needs delta-filter and show-coords but these were not set correctly like NUCMER
+author: Lara Peeters (HPC-UGent)
+diff -ru amos-3.1.0.orig/src/Pipeline/Makefile.in amos-3.1.0/src/Pipeline/Makefile.in
+--- amos-3.1.0.orig/src/Pipeline/Makefile.in	2011-08-05 05:08:07.000000000 +0200
++++ amos-3.1.0/src/Pipeline/Makefile.in	2024-03-14 12:31:16.218067000 +0100
+@@ -477,7 +477,8 @@
+                 echo '#!$(bindir)/runAmos -C' > "$(DESTDIR)$(bindir)/$$b"; \
+                 sed -e 's|^BINDIR[ 	]*=.*$$|BINDIR=$(bindir)|' \
+                     -e 's|^NUCMER[ 	]*=.*$$|NUCMER=$(NUCMER)|' \
+-                    -e 's|^DELTAFILTER[        ]*=.*$$|DELTAFILTER=$(DELTAFILTER)|' \
++                    -e 's|^DELTAFILTER[ 	]*=.*$$|DELTAFILTER=$(DELTAFILTER)|' \
++                    -e 's|^SHOWCOORDS[ 	]*=.*$$|SHOWCOORDS=$(SHOWCOORDS)|' \
+                     "$(DESTDIR)$(bindir)/$$f" >> "$(DESTDIR)$(bindir)/$$b" \
+                 || exit 1; \
+                 ;; \

easybuild/easyconfigs/a/AMS/AMS-2023.104-iimpi-2022b-intelmpi.eb

@@ -0,0 +1,47 @@
+easyblock = 'Tarball'
+
+name = 'AMS'
+version = '2023.104'
+versionsuffix = '-intelmpi'
+
+homepage = 'https://www.scm.com/amsterdam-modeling-suite/'
+description = """
+The Amsterdam Modeling Suite (AMS) provides a comprehensive set of modules for
+computational chemistry and materials science, from quantum mechanics to fluid
+thermodynamics.
+"""
+
+toolchain = {'name': 'iimpi', 'version': '2022b'}
+
+sources = ['ams%(version)s.pc64_linux.intelmpi.bin.tgz']
+checksums = ['c977014f14291f7f210be7e48bc28f71ab0a076a5af257e92f2c873f54d208af']
+
+dependencies = [('libGLU', '9.0.2')]
+
+keepsymlinks = True
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['atomicdata', 'bin', 'examples'],
+}
+
+# check if license file is installed
+# sanity_check_commands = ['dirac check']
+
+modextrapaths = {
+    'AMSHOME': '',
+    'AMSBIN': 'bin',
+    'AMSRESOURCES': 'atomicdata',
+}
+
+modextravars = {
+    # use Intel MPI from EasyBuild
+    'SCM_USE_LOCAL_IMPI': '1',
+}
+
+modloadmsg = """These environment variables need to be defined before using AMS:
+  * $SCMLICENSE: path to AMS license file
+  * $SCM_TMPDIR: path to user scratch directory
+"""
+
+moduleclass = 'chem'

easybuild/easyconfigs/a/AOFlagger/AOFlagger-3.4.0-foss-2023b.eb

@@ -0,0 +1,46 @@
+easyblock = 'CMakeMake'
+
+name = 'AOFlagger'
+version = '3.4.0'
+
+homepage = 'https://aoflagger.readthedocs.io/'
+description = """The AOFlagger is a tool that can find and remove radio-frequency interference (RFI)
+in radio astronomical observations. It can make use of Lua scripts to make flagging strategies flexible,
+and the tools are applicable to a wide set of telescopes."""
+
+toolchain = {'name': 'foss', 'version': '2023b'}
+
+sources = [
+    {
+        'source_urls': [
+            'https://gitlab.com/aroffringa/%(namelower)s/-/package_files/96704214/'
+        ],
+        'filename': '%(namelower)s-v%(version)s.tar.bz2',
+        'download_filename': 'download'
+    },
+]
+checksums = ['9560b7381b68f37d842599f222a8aa2a5d3d3d501d1277471e1a0ba3d7b2aeba']
+
+builddependencies = [
+    ('CMake', '3.27.6'),
+]
+dependencies = [
+    ('casacore', '3.5.0'),
+    ('Boost', '1.83.0'),
+    ('CFITSIO', '4.3.1'),
+    ('GSL', '2.7'),
+    ('HDF5', '1.14.3'),
+    ('Python', '3.11.5'),
+    ('Lua', '5.4.6'),
+    ('libpng', '1.6.40'),
+    ('libxml2', '2.11.5'),
+]
+
+sanity_check_paths = {
+    'files': ['include/%(namelower)s.h', 'bin/%(namelower)s'],
+    'dirs': ['bin'],
+}
+
+sanity_check_commands = [('%(namelower)s', '-v')]
+
+moduleclass = 'lib'

easybuild/easyconfigs/a/ASAP3/ASAP3-3.13.3-foss-2023a.eb

@@ -0,0 +1,36 @@
+easyblock = "PythonPackage"
+
+name = 'ASAP3'
+version = '3.13.3'
+
+homepage = 'https://wiki.fysik.dtu.dk/asap/'
+description = """ASAP is a calculator for doing large-scale classical molecular
+dynamics within the Campos Atomic Simulation Environment (ASE)."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+toolchainopts = {'pic': True, 'usempi': True, 'openmp': False}
+
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['78aa4c9ee11315b6e7f8cd9b1fda6ab9a240cc4f4ff418972ea079612e26d369']
+
+builddependencies = [
+    ('pkgconf', '1.9.5'),
+]
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('ASE', '3.22.1'),
+    ('kim-api', '2.3.0'),
+]
+
+use_pip = True
+download_dep_fail = True
+sanity_pip_check = True
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s']
+}
+
+moduleclass = 'phys'