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

…asyconfigs into 20240118182910_new_pr_maturin140

easybuild/easyconfigs/a/alsa-lib/alsa-lib-1.2.4-GCCcore-9.3.0.eb

@@ -9,7 +9,7 @@ description = """The Advanced Linux Sound Architecture (ALSA) provides audio and
 
 toolchain = {'name': 'GCCcore', 'version': '9.3.0'}
 
-source_urls = ['ftp://ftp.alsa-project.org/pub/lib/']
+source_urls = ['https://www.alsa-project.org/files/pub/lib/']
 sources = [SOURCE_TAR_BZ2]
 checksums = ['f7554be1a56cdff468b58fc1c29b95b64864c590038dd309c7a978c7116908f7']
 

easybuild/easyconfigs/a/alsa-lib/alsa-lib-1.2.8-GCCcore-10.2.0.eb

@@ -9,7 +9,7 @@ description = """The Advanced Linux Sound Architecture (ALSA) provides audio and
 
 toolchain = {'name': 'GCCcore', 'version': '10.2.0'}
 
-source_urls = ['ftp://ftp.alsa-project.org/pub/lib/']
+source_urls = ['https://www.alsa-project.org/files/pub/lib/']
 sources = [SOURCE_TAR_BZ2]
 checksums = ['1ab01b74e33425ca99c2e36c0844fd6888273193bd898240fe8f93accbcbf347']
 

easybuild/easyconfigs/a/alsa-lib/alsa-lib-1.2.8-GCCcore-11.2.0.eb

@@ -9,7 +9,7 @@ description = """The Advanced Linux Sound Architecture (ALSA) provides audio and
 
 toolchain = {'name': 'GCCcore', 'version': '11.2.0'}
 
-source_urls = ['ftp://ftp.alsa-project.org/pub/lib/']
+source_urls = ['https://www.alsa-project.org/files/pub/lib/']
 sources = [SOURCE_TAR_BZ2]
 checksums = ['1ab01b74e33425ca99c2e36c0844fd6888273193bd898240fe8f93accbcbf347']
 

easybuild/easyconfigs/a/alsa-lib/alsa-lib-1.2.8-GCCcore-11.3.0.eb

@@ -9,7 +9,7 @@ description = """The Advanced Linux Sound Architecture (ALSA) provides audio and
 
 toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
 
-source_urls = ['ftp://ftp.alsa-project.org/pub/lib/']
+source_urls = ['https://www.alsa-project.org/files/pub/lib/']
 sources = [SOURCE_TAR_BZ2]
 checksums = ['1ab01b74e33425ca99c2e36c0844fd6888273193bd898240fe8f93accbcbf347']
 

easybuild/easyconfigs/v/VSCode-cli/VSCode-cli-1.85.1-x64.eb → easybuild/easyconfigs/c/code-cli/code-cli-1.85.1-x64.eb

@@ -1,6 +1,6 @@
 easyblock = 'Tarball'
 
-name = 'VSCode-cli'
+name = 'code-cli'
 version = '1.85.1'
 versionsuffix = '-x64'
 

easybuild/easyconfigs/f/fastjet-contrib/fastjet-contrib-1.053-gompi-2023a.eb

@@ -0,0 +1,32 @@
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+# Author: Alexander Puck Neuwirth <[email protected]>
+
+easyblock = 'ConfigureMake'
+
+name = 'fastjet-contrib'
+version = '1.053'
+
+homepage = 'https://fastjet.hepforge.org/contrib/'
+description = """3rd party extensions of FastJet"""
+
+toolchain = {'name': 'gompi', 'version': '2023a'}
+
+toolchainopts = {'optarch': True, 'pic': True}
+
+source_urls = ['https://fastjet.hepforge.org/contrib/downloads/']
+sources = ['fjcontrib-' + version + '.tar.gz']
+checksums = ['b12a248e0b143934c99e3b7c8dd83265122f6c6c09533c2a03df44f5eff1e6fa']
+
+dependencies = [
+    ('fastjet', '3.4.2')
+]
+
+build_cmd_targets = ['', 'fragile-shared']
+install_cmd = "make install && make fragile-shared-install"
+
+sanity_check_paths = {
+    'files': ['lib/libfastjetcontribfragile.%s' % SHLIB_EXT],
+    'dirs': ['include/fastjet/contrib']
+}
+
+moduleclass = 'phys'

easybuild/easyconfigs/f/fastjet/fastjet-3.4.2-gompi-2023a.eb

@@ -0,0 +1,43 @@
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+# Author: Alexander Puck Neuwirth <[email protected]>
+
+easyblock = 'ConfigureMake'
+
+name = 'fastjet'
+version = '3.4.2'
+
+homepage = 'https://fastjet.fr/'
+description = """A software package for jet finding in pp and e+e- collisions"""
+
+toolchain = {'name': 'gompi', 'version': '2023a'}
+toolchainopts = {'optarch': True, 'pic': True}
+
+source_urls = ['https://fastjet.fr/repo/']
+sources = [SOURCELOWER_TAR_GZ]
+patches = ['fastjet-3.4.0_excludeSISCone.patch']
+checksums = [
+    {'fastjet-3.4.2.tar.gz': 'b3d33155b55ce43f420cd6d99b525acf7bdc2593a7bb7ea898a9ddb3d8ca38e3'},
+    {'fastjet-3.4.0_excludeSISCone.patch': '698902b4c4d54873d640239461cccc036234986ae8d6a33ceb649462ade971d3'},
+]
+
+builddependencies = [
+    ('Autotools', '20220317'),
+]
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('siscone', '3.0.6'),
+    ('CGAL', '5.6'),
+]
+configopts = '--enable-cgal-header-only --enable-pyext --enable-allplugins --enable-allcxxplugins '
+configopts += "--enable-shared"
+
+sanity_check_paths = {
+    'files': ['lib/libfastjet.%s' % SHLIB_EXT, 'bin/fastjet-config'],
+    'dirs': ['include/fastjet'],
+}
+sanity_check_commands = ["python -c 'import fastjet'"]
+
+modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'}
+
+moduleclass = 'phys'

easybuild/easyconfigs/g/GSL/GSL-2.7-GCC-13.2.0.eb

@@ -0,0 +1,25 @@
+easyblock = 'ConfigureMake'
+
+name = 'GSL'
+version = '2.7'
+
+homepage = 'https://www.gnu.org/software/gsl/'
+description = """The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers.
+ The library provides a wide range of mathematical routines such as random number generators, special functions
+ and least-squares fitting."""
+
+toolchain = {'name': 'GCC', 'version': '13.2.0'}
+toolchainopts = {'unroll': True, 'pic': True}
+
+source_urls = [GNU_SOURCE]
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['efbbf3785da0e53038be7907500628b466152dbc3c173a87de1b5eba2e23602b']
+
+sanity_check_paths = {
+    'files': ['bin/%s' % x for x in ['gsl-config', 'gsl-histogram', 'gsl-randist']] +
+             ['include/gsl/gsl_types.h'] +
+             ['lib/lib%s.%s' % (x, SHLIB_EXT) for x in ['gsl', 'gslcblas']],
+    'dirs': [],
+}
+
+moduleclass = 'numlib'

easybuild/easyconfigs/g/GUIDANCE/GUIDANCE-2.02-GCC-12.3.0.eb

@@ -0,0 +1,40 @@
+easyblock = 'MakeCp'
+
+name = 'GUIDANCE'
+version = '2.02'
+
+homepage = 'https://taux.evolseq.net/guidance/'
+description = """
+GUIDANCE is a software package for aligning biological sequences (DNA or
+amino acids) using either MAFFT, PRANK, or CLUSTALW, and calculating
+confidence scores for each column, sequence and residue in the alignment."""
+
+toolchain = {'name': 'GCC', 'version': '12.3.0'}
+
+source_urls = ['https://taux.evolseq.net/guidance/static/download/']
+sources = ['%(namelower)s.v%(version)s.tar.gz']
+checksums = ['825e105dde526759fb5bda1cd539b24db0b90b8b586f26b1df74d9c5abaa7844']
+
+dependencies = [
+    ('Perl', '5.36.1'),
+    ('BioPerl', '1.7.8'),
+    ('Ruby', '3.3.0'),
+    ('MAFFT', '7.520', '-with-extensions'),
+    ('PRANK', '170427'),
+    ('ClustalW2', '2.1'),
+    ('MUSCLE', '5.1.0'),
+    ('PAGAN2', '1.53_20230824', '-linux64', SYSTEM),
+]
+
+_bins = ['isEqualTree', 'msa_set_score', 'removeTaxa', 'semphy']
+
+files_to_copy = [(['programs/%s/%s' % (x, x) for x in _bins], 'bin'), 'www']
+
+sanity_check_paths = {
+    'files': ['bin/%s' % x for x in _bins],
+    'dirs': [],
+}
+
+sanity_check_commands = ['msa_set_score -h', 'semphy -h']
+
+moduleclass = 'bio'

easybuild/easyconfigs/h/HepMC3/HepMC3-3.2.6-GCC-12.3.0.eb

@@ -0,0 +1,36 @@
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+# Author: Alexander Puck Neuwirth <[email protected]>
+
+easyblock = 'CMakeMake'
+
+name = 'HepMC3'
+version = '3.2.6'
+
+homepage = 'http://hepmc.web.cern.ch/hepmc/'
+description = """HepMC is a standard for storing Monte Carlo event data."""
+
+toolchain = {'name': 'GCC', 'version': '12.3.0'}
+
+source_urls = ['https://hepmc.web.cern.ch/hepmc/releases/']
+sources = [SOURCE_TAR_GZ]
+checksums = ['248f3b5b36dd773844cbe73d51f60891458334b986b259754c59dbf4bbf1d525']
+
+builddependencies = [('CMake', '3.26.3')]
+
+dependencies = [
+    ('Python', '3.11.3')
+]
+
+configopts = '-DHEPMC3_ENABLE_ROOTIO=OFF -Dmomentum=GEV -Dlength=MM '
+configopts += '-DHEPMC3_ENABLE_PYTHON=ON '
+configopts += '-DHEPMC3_Python_SITEARCH311=%(installdir)s/lib/python%(pyshortver)s/site-packages'
+
+modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'}
+
+sanity_check_paths = {
+    'files': ['lib/libHepMC3.%s' % SHLIB_EXT],
+    'dirs': ['include/HepMC3']
+}
+sanity_check_commands = ["python -c 'import pyHepMC3'"]
+
+moduleclass = 'phys'

easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-2.1.0-foss-2022a-PyTorch-1.12.0.eb

@@ -0,0 +1,59 @@
+easyblock = 'PythonBundle'
+
+name = 'PyTorch-Geometric'
+version = '2.1.0'
+local_pytorchver = '1.12.0'
+versionsuffix = '-PyTorch-%s' % local_pytorchver
+
+homepage = 'https://github.com/rusty1s/pytorch_geometric'
+description = "PyTorch Geometric (PyG) is a geometric deep learning extension library for PyTorch."
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('PyTorch', local_pytorchver),
+    ('scikit-learn', '1.1.2'),
+    ('scikit-image', '0.19.3'),
+    ('numba', '0.56.4'),
+    ('h5py', '3.7.0'),
+    ('tqdm', '4.64.0'),
+    ('RDFlib', '6.2.0'),
+    ('ASE', '3.22.1'),
+    ('YACS', '0.1.8'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('googledrivedownloader', '0.4', {
+        'modulename': 'google_drive_downloader',
+        'checksums': ['4b34c1337b2ff3bf2bd7581818efbdcaea7d50ffd484ccf80809688f5ca0e204'],
+    }),
+    ('plyfile', '0.7.4', {
+        'checksums': ['9e9a18d22a3158fcd74df38761d43a7facc6df75126f2ab9f4e9a5d4d2188652'],
+    }),
+    ('torch_scatter', version, {
+        'checksums': ['3a7124c2a033552febbdc72407f7d4d8cb6dce465720e84ab831512e81c1d208'],
+    }),
+    ('torch_sparse', '0.6.15', {
+        'checksums': ['3a741ae8a7cc19247a44de549fa4d593c4257b5f741e1eb5110b712a14209dd9'],
+    }),
+    ('torch_cluster', '1.6.0', {
+        'checksums': ['249c1bd8c33a887b22bf569a59d0868545804032123594dd8c76ba1885859c39'],
+    }),
+    ('torch_spline_conv', '1.2.1', {
+        'checksums': ['364f658e0ecb4c5263a728c2961553e022fc44c11a633d5a1bf986cf169ab438'],
+    }),
+    ('python-louvain', '0.16', {
+        'modulename': 'community.community_louvain',
+        'checksums': ['b7ba2df5002fd28d3ee789a49532baad11fe648e4f2117cf0798e7520a1da56b'],
+    }),
+    ('torch_geometric', version, {
+        'checksums': ['72653deca925885e4d613eb5c72268bb9710325d9c717516922499fbe1197079'],
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'lib'

easybuild/easyconfigs/r/Rivet/Rivet-3.1.9-gompi-2023a-HepMC3-3.2.6.eb

@@ -0,0 +1,52 @@
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+# Author: Alexander Puck Neuwirth <[email protected]>
+
+easyblock = 'ConfigureMake'
+
+name = 'Rivet'
+version = '3.1.9'
+local_hepmc = "HepMC3"
+local_hepmcver = "3.2.6"
+versionsuffix = '-%s-%s' % (local_hepmc, local_hepmcver)
+
+homepage = 'https://gitlab.com/hepcedar/rivet'
+description = """
+Rivet toolkit (Robust Independent Validation of Experiment and Theory)
+
+To use your own analysis you must append the path to `RIVET_ANALYSIS_PATH`.
+"""
+
+toolchain = {'name': 'gompi', 'version': '2023a'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://www.hepforge.org/archive/rivet/']
+sources = [SOURCE_TAR_GZ]
+checksums = ['ddf0f13f722d0b4fc61969f3db06416b6b68f721dba36ca5d2a85c2759bf9fd7']
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('YODA', '1.9.9'),
+    ('fastjet', '3.4.2'),
+    ('fastjet-contrib', '1.053'),
+    ('HepMC3', '3.2.6'),
+    ('GSL', '2.7'),
+]
+
+configopts = "--with-yoda=$EBROOTYODA --with-fastjet=$EBROOTFASTJET --with-hepmc3=$EBROOTHEPMC3"
+
+sanity_check_paths = {
+    'files': ['bin/rivet-config', 'lib/libRivet.%s' % SHLIB_EXT],
+    'dirs': ['share/Rivet', 'lib/Rivet']
+}
+sanity_check_commands = ["python -c 'import rivet'"]
+
+modloadmsg = """
+To use your own analysis you must append the path to `RIVET_ANALYSIS_PATH`.
+You might want to load `texlive` or `matplotlib` if you want to create plots.
+"""
+modextrapaths = {
+    'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages',
+    # 'RIVET_ANALYSIS_PATH': '/path/to/share/Rivet/',  # please adapt for system-wided shared non-default analysis
+}
+
+moduleclass = 'phys'

easybuild/easyconfigs/r/Rust/Rust-1.75.0-GCCcore-12.3.0.eb

@@ -0,0 +1,31 @@
+name = 'Rust'
+version = '1.75.0'
+
+homepage = 'https://www.rust-lang.org'
+description = """Rust is a systems programming language that runs blazingly fast, prevents segfaults,
+ and guarantees thread safety."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+source_urls = ['https://static.rust-lang.org/dist/']
+sources = ['rustc-%(version)s-src.tar.gz']
+patches = ['Rust-1.70_sysroot-fix-interpreter.patch']
+checksums = [
+    {'rustc-1.75.0-src.tar.gz': '5b739f45bc9d341e2d1c570d65d2375591e22c2d23ef5b8a37711a0386abc088'},
+    {'Rust-1.70_sysroot-fix-interpreter.patch': '220129db55e022a98d25028da5dcc9f26b252dd995c3ac92f6312dbb1e362cb1'},
+]
+
+builddependencies = [
+    ('binutils', '2.40'),
+    ('CMake', '3.26.3'),
+    ('Python', '3.11.3'),
+    ('Ninja', '1.11.1'),
+    ('pkgconf', '1.9.5'),
+    ('patchelf', '0.18.0'),  # only required when RPATH linking is enabled
+]
+
+dependencies = [
+    ('OpenSSL', '1.1', '', SYSTEM),
+]
+
+moduleclass = 'lang'

easybuild/easyconfigs/s/siscone/siscone-3.0.6-GCCcore-12.3.0.eb

@@ -0,0 +1,27 @@
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+# Author: Alexander Puck Neuwirth <[email protected]>
+
+easyblock = 'ConfigureMake'
+
+name = 'siscone'
+version = '3.0.6'
+
+homepage = 'https://siscone.hepforge.org/'
+description = """Hadron Seedless Infrared-Safe Cone jet algorithm"""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+source_urls = ['https://siscone.hepforge.org/downloads/']
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['f9f19e87433305d073e5715a175d8ef0a56101f97203e5bd36a09b3eeb5cb04a']
+
+builddependencies = [
+    ('binutils', '2.40'),
+]
+
+sanity_check_paths = {
+    'files': ["lib/libsiscone.so"],
+    'dirs': ["include/siscone"],
+}
+
+moduleclass = 'phys'