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

…asyconfigs into 20230903170925_new_pr_OpenMPI415

easybuild/easyconfigs/a/Autoconf/Autoconf-2.71-GCCcore-13.2.0.eb

@@ -0,0 +1,48 @@
+easyblock = 'ConfigureMake'
+
+name = 'Autoconf'
+version = '2.71'
+
+homepage = 'https://www.gnu.org/software/autoconf/'
+
+description = """
+ Autoconf is an extensible package of M4 macros that produce shell scripts
+ to automatically configure software source code packages. These scripts can
+ adapt the packages to many kinds of UNIX-like systems without manual user
+ intervention. Autoconf creates a configuration script for a package from a
+ template file that lists the operating system features that the package can
+ use, in the form of M4 macro calls.
+"""
+
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
+
+source_urls = [GNU_SOURCE]
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['431075ad0bf529ef13cb41e9042c542381103e80015686222b8a9d4abef42a1c']
+
+builddependencies = [
+    ('binutils', '2.40'),
+]
+
+dependencies = [
+    ('M4', '1.4.19'),
+    # non-standard Perl modules are required,
+    # see https://github.com/easybuilders/easybuild-easyconfigs/issues/1822
+    ('Perl', '5.38.0'),
+]
+
+preconfigopts = "export PERL='/usr/bin/env perl' && "
+
+sanity_check_paths = {
+    'files': ["bin/%s" % x
+              for x in ["autoconf", "autoheader", "autom4te", "autoreconf",
+                        "autoscan", "autoupdate", "ifnames"]],
+    'dirs': [],
+}
+
+sanity_check_commands = [
+    "autoconf --help",
+    "autom4te --help",
+]
+
+moduleclass = 'devel'

easybuild/easyconfigs/a/Automake/Automake-1.16.5-GCCcore-13.2.0.eb

@@ -0,0 +1,39 @@
+easyblock = 'ConfigureMake'
+
+name = 'Automake'
+version = '1.16.5'
+
+homepage = 'https://www.gnu.org/software/automake/automake.html'
+
+description = "Automake: GNU Standards-compliant Makefile generator"
+
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
+
+source_urls = [GNU_SOURCE]
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['07bd24ad08a64bc17250ce09ec56e921d6343903943e99ccf63bbf0705e34605']
+
+builddependencies = [
+    ('binutils', '2.40'),
+]
+
+dependencies = [
+    ('Autoconf', '2.71'),
+    # non-standard Perl modules are required,
+    # see https://github.com/easybuilders/easybuild-easyconfigs/issues/1822
+    ('Perl', '5.38.0'),
+]
+
+preconfigopts = "export PERL='/usr/bin/env perl' && "
+
+sanity_check_paths = {
+    'files': ['bin/aclocal', 'bin/automake'],
+    'dirs': []
+}
+
+sanity_check_commands = [
+    "aclocal --help",
+    "automake --help",
+]
+
+moduleclass = 'devel'

easybuild/easyconfigs/a/Autotools/Autotools-20220317-GCCcore-13.2.0.eb

@@ -0,0 +1,24 @@
+easyblock = 'Bundle'
+
+name = 'Autotools'
+version = '20220317'  # date of the most recent change
+
+homepage = 'https://autotools.io'
+
+description = """
+ This bundle collect the standard GNU build tools: Autoconf, Automake
+ and libtool
+"""
+
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
+
+dependencies = [
+    ('Autoconf', '2.71'),    # 20210128
+    ('Automake', '1.16.5'),  # 20211003
+    ('libtool', '2.4.7'),    # 20220317
+]
+
+# Pure bundle -- no need to specify 'binutils' used when building GCCcore
+# toolchain as build dependency
+
+moduleclass = 'devel'

easybuild/easyconfigs/b/Biopython/Biopython-1.76-foss-2021b-Python-2.7.18.eb

@@ -0,0 +1,43 @@
+easyblock = 'PythonPackage'
+
+name = 'Biopython'
+version = '1.76'
+versionsuffix = '-Python-%(pyver)s'
+
+homepage = 'https://www.biopython.org'
+description = """Biopython is a set of freely available tools for biological
+ computation written in Python by an international team of developers. It is
+ a distributed collaborative effort to develop Python libraries and
+ applications which address the needs of current and future work in
+ bioinformatics. """
+
+toolchain = {'name': 'foss', 'version': '2021b'}
+
+source_urls = ['https://biopython.org/DIST']
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['3873cb98dad5e28d5e3f2215a012565345a398d3d2c4eebf7cd701757b828c72']
+
+dependencies = [
+    ('Python', '2.7.18'),
+    ('SciPy-bundle', '2021.10', versionsuffix),
+]
+
+download_dep_fail = True
+use_pip = True
+sanity_pip_check = True
+
+# Run only tests that don't require internet connection
+runtest = 'python setup.py test --offline'
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['lib/python%(pyshortver)s/site-packages/Bio',
+             'lib/python%(pyshortver)s/site-packages/BioSQL']
+}
+
+# extra check to ensure numpy dependency is available
+sanity_check_commands = ["python -c 'import Bio.MarkovModel'"]
+
+options = {'modulename': 'Bio'}
+
+moduleclass = 'bio'

easybuild/easyconfigs/c/CUDA/CUDA-12.2.2.eb

@@ -0,0 +1,24 @@
+name = 'CUDA'
+version = '12.2.2'
+local_nv_version = '535.104.05'
+
+homepage = 'https://developer.nvidia.com/cuda-toolkit'
+description = """CUDA (formerly Compute Unified Device Architecture) is a parallel
+ computing platform and programming model created by NVIDIA and implemented by the
+ graphics processing units (GPUs) that they produce. CUDA gives developers access
+ to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs."""
+
+toolchain = SYSTEM
+
+source_urls = ['https://developer.download.nvidia.com/compute/cuda/%(version)s/local_installers/']
+sources = ['cuda_%%(version)s_%s_linux%%(cudaarch)s.run' % local_nv_version]
+checksums = [{
+    'cuda_%%(version)s_%s_linux.run' % local_nv_version:
+        '2b39aae3e7618d9f59a3c8fa1f1bc61f29c0b0e0df75fb05076badb352952ef2',
+    'cuda_%%(version)s_%s_linux_ppc64le.run' % local_nv_version:
+        '18848278e7f2bd4b4481f5665633d7e3d46e9a562d175d5ff278218188b01342',
+    'cuda_%%(version)s_%s_linux_sbsa.run' % local_nv_version:
+        '4113a15e6b27a02638c72edeb5f89de4c9ea312febba12fc4cefff2edc882268'
+}]
+
+moduleclass = 'system'

easybuild/easyconfigs/c/CatBoost/CatBoost-1.2-gfbf-2023a.eb

@@ -0,0 +1,41 @@
+easyblock = 'PythonBundle'
+
+name = 'CatBoost'
+version = '1.2'
+
+homepage = 'https://catboost.ai'
+description = """CatBoost is a high-performance open source library for gradient boosting on decision trees"""
+
+toolchain = {'name': 'gfbf', 'version': '2023a'}
+
+builddependencies = [
+    ('CMake', '3.26.3'),
+    ('conan', '1.60.2'),
+]
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('Clang', '16.0.6'),
+    ('SciPy-bundle', '2023.07'),
+    ('matplotlib', '3.7.2'),
+    ('plotly.py', '5.16.0'),
+    ('graphviz-python', '0.20.1'),
+    ('Ninja', '1.11.1'),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    (name, version, {
+        'patches': ['%(name)s-%(version)s_disable-widget.patch'],
+        'source_urls': ['https://pypi.python.org/packages/source/c/catboost'],
+        'sources': ['catboost-%(version)s.tar.gz'],
+        'checksums': [
+            {'catboost-1.2.tar.gz': '39e53403727ecfbb48156773ef3006b4e71cc35ab49cc9a0cf044b474c34be0c'},
+            {'CatBoost-1.2_disable-widget.patch': '468be5b5e9eaf655d407a342b786bb419d4ceaeb9df5c753c256a8bd6d69f9df'},
+        ],
+    }),
+]
+
+moduleclass = 'ai'

easybuild/easyconfigs/c/CatBoost/CatBoost-1.2_disable-widget.patch

@@ -0,0 +1,14 @@
+Disabling optional widget, as it requires `yarn`
+Author: Denis Kristak (Inuits)
+diff -ruN catboost-1.2_pypi_orig/setup.py catboost-1.2_pypi/setup.py
+--- catboost-1.2_pypi_orig/setup.py	2023-08-08 13:41:49.501481901 +0200
++++ catboost-1.2_pypi/setup.py	2023-08-08 13:43:39.744105439 +0200
+@@ -245,7 +245,7 @@
+
+     @staticmethod
+     def initialize_options(command):
+-        command.no_widget = False
++        command.no_widget = True
+         command.prebuilt_widget = False
+
+     @staticmethod

easybuild/easyconfigs/c/ccache/ccache-4.8.3.eb

@@ -0,0 +1,54 @@
+# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA
+# Authors::   Fotis Georgatos <fotis@cern.ch>
+# License::   MIT/GPL
+
+easyblock = 'CMakeNinja'
+
+name = 'ccache'
+version = '4.8.3'
+
+homepage = 'https://ccache.dev/'
+description = """Ccache (or “ccache”) is a compiler cache. It speeds up recompilation by
+caching previous compilations and detecting when the same compilation is being done again"""
+
+toolchain = SYSTEM
+
+source_urls = ['https://github.com/ccache/ccache/releases/download/v%(version)s/']
+sources = [SOURCE_TAR_GZ]
+checksums = ['d59dd569ad2bbc826c0bc335c8ebd73e78ed0f2f40ba6b30069347e63585d9ef']
+
+osdependencies = [('glibc-static', 'libc6-dev')]
+
+local_gccver = '12.3.0'
+builddependencies = [
+    ('GCC', local_gccver),
+    ('CMake', '3.26.3', '', ('GCCcore', local_gccver)),
+    ('Ninja', '1.11.1', '', ('GCCcore', local_gccver)),
+    ('hiredis', '1.2.0', '', ('GCCcore', local_gccver)),
+    ('zstd', '1.5.5', '', ('GCCcore', local_gccver)),
+]
+
+# use BFD linker rather than default ld.gold (required on CentOS 8)
+preconfigopts = 'LDFLAGS="-fuse-ld=bfd"'
+configopts = ' '.join([
+    '-DENABLE_DOCUMENTATION=OFF',
+    '-DENABLE_IPO=ON',
+    # Link dependencies and binary statically
+    '-DCMAKE_EXE_LINKER_FLAGS="-static"',
+    '-DZSTD_LIBRARY="$EBROOTZSTD/lib/libzstd.a"',
+    '-DHIREDIS_LIBRARY="$EBROOTHIREDIS/lib/libhiredis.a"',
+    # Disable downloading dependencies
+    '-DZSTD_FROM_INTERNET=OFF -DHIREDIS_FROM_INTERNET=OFF',
+])
+
+sanity_check_paths = {
+    'files': ['bin/ccache'],
+    'dirs': []
+}
+sanity_check_commands = [
+    'ccache --help',
+    # Ensure that the binary does not depend on any shared library
+    'LC_ALL=C ldd $(which ccache) | grep -q "not a dynamic executable"',
+]
+
+moduleclass = 'tools'

easybuild/easyconfigs/c/conan/conan-1.60.2-GCCcore-12.3.0.eb

@@ -0,0 +1,64 @@
+easyblock = 'PythonBundle'
+
+name = 'conan'
+version = '1.60.2'  # have to stick to an older version because catboost is not compatible with newer one
+
+homepage = 'https://conan.io'
+description = "Decentralized, open-source (MIT), C/C++ package manager."
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+builddependencies = [
+    ('binutils', '2.40'),
+]
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('PyYAML', '6.0'),
+    ('tqdm', '4.66.1'),
+    ('Python-bundle-PyPI', '2023.06'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('bottle', '0.12.25', {
+        'checksums': ['e1a9c94970ae6d710b3fb4526294dfeb86f2cb4a81eff3a4b98dc40fb0e5e021'],
+    }),
+    ('distro', '1.8.0', {
+        'checksums': ['02e111d1dc6a50abb8eed6bf31c3e48ed8b0830d1ea2a1b78c61765c2513fdd8'],
+    }),
+    ('fasteners', '0.18', {
+        'checksums': ['cb7c13ef91e0c7e4fe4af38ecaf6b904ec3f5ce0dda06d34924b6b74b869d953'],
+    }),
+    ('node-semver', '0.6.1', {
+        'modulename': 'semver',
+        'checksums': ['4016f7c1071b0493f18db69ea02d3763e98a633606d7c7beca811e53b5ac66b7'],
+    }),
+    ('patch-ng', '1.17.4', {
+        'checksums': ['627abc5bd723c8b481e96849b9734b10065426224d4d22cd44137004ac0d4ace'],
+    }),
+    ('pluginbase', '1.0.1', {
+        'checksums': ['ff6c33a98fce232e9c73841d787a643de574937069f0d18147028d70d7dee287'],
+    }),
+    ('PyJWT', '2.8.0', {
+        'modulename': 'jwt',
+        'checksums': ['57e28d156e3d5c10088e0c68abb90bfac3df82b40a71bd0daa20c65ccd5c23de'],
+    }),
+    (name, version, {
+        'source_tmpl': '%(version)s.tar.gz',
+        'source_urls': ['https://github.com/conan-io/conan/archive/'],
+        'checksums': ['63dc6e92fc7f1d77fe08488bd78cd8a20fdddf454e55e1244107d1aec974377c'],
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['bin/conan'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = ["conan --help"]
+
+sanity_pip_check = True
+
+moduleclass = 'devel'