adding easyconfigs: MUSCLE3-0.7.1-gfbf-2023b.eb, ruamel.yaml-0.18.5-G…

…CCcore-13.2.0.eb, msgpack-c-6.0.0-GCC-13.2.0.eb and patches: muscle3-0.7.1_fix_setup.patch, ymmsl-0.13.0_fix_setup.patch, yatiml-0.10.0_fix_setup.patch

easybuild/easyconfigs/m/MUSCLE3/MUSCLE3-0.7.1-gfbf-2023b.eb

@@ -0,0 +1,115 @@
+easyblock = 'ConfigureMakePythonPackage'
+
+name = 'MUSCLE3'
+version = '0.7.1'
+
+homepage = 'https://muscle3.readthedocs.io/en/latest/index.html'
+
+description = """MUSCLE3 allows connecting multiple simulation models
+ together into a multiscale simulation. Simulation models can be as
+ simple as a single Python file, or as complex as a combination of
+ multiple separate simulation codes written in C++ or Fortran, and
+ running on an HPC machine."""
+
+toolchain = {'name': 'gfbf', 'version': '2023b'}
+
+source_urls = ['https://github.com/multiscale/%(namelower)s/archive/refs/tags/']
+sources = ['%(version)s.tar.gz']
+checksums = ['b3023387c21af4d924b5cd240bdba376804ae166eb2c4b812e5222b4e0d3c8e0']
+
+builddependencies = [
+    ('googletest', '1.14.0'),
+]
+
+dependencies = [
+    ('msgpack-c', '6.0.0'),
+    ('zlib', '1.2.13'),
+    ('Python', '3.11.5'),
+    ('SciPy-bundle', '2023.11'),
+    ('QCG-PilotJob', '0.13.1'),
+    ('ruamel.yaml', '0.18.5'),
+    ('matplotlib', '3.8.2'),
+]
+
+skipsteps = ['configure']
+
+prebuildopts = 'msgpack_ROOT=$EBROOTMSGPACKMINC '
+preinstallopts = 'PREFIX=%(installdir)s '
+testopts = 'googletest_ROOT=$EBROOTGOOGLETEST'
+
+exts_defaultclass = 'PythonPackage'
+
+exts_default_options = {
+    'source_urls': [PYPI_SOURCE],
+    'use_pip': True,
+    'download_dep_fail': True,
+    'sanity_pip_check': True,
+}
+
+exts_list = [
+    ('typing_extensions', '4.9.0', {
+        'checksums': ['23478f88c37f27d76ac8aee6c905017a143b0b1b886c3c9f66bc2fd94f9f5783'],
+    }),
+    ('msgpack', '1.0.7', {
+        'checksums': ['572efc93db7a4d27e404501975ca6d2d9775705c2d922390d878fcf768d92c87'],
+    }),
+    ('click', '8.1.7', {
+        'checksums': ['ca9853ad459e787e2192211578cc907e7594e294c7ccc834310722b41b9ca6de'],
+    }),
+    ('yatiml', '0.10.0', {
+        'patches': ['yatiml-0.10.0_fix_setup.patch'],
+        'checksums': [
+            {'yatiml-0.10.0.tar.gz': '4d23bfd7bbf45ae603c08fcb70d0c86404934a0cef24fb77b532705ff195fc92'},
+            {'yatiml-0.10.0_fix_setup.patch': '7b88cc59bc45254d28c9d59110caaf3954e3e479def5d6dc987f63fdedccb849'},
+        ],
+    }),
+    ('ymmsl', '0.13.0', {
+        'patches': ['ymmsl-0.13.0_fix_setup.patch'],
+        'checksums': [
+            {'ymmsl-0.13.0.tar.gz': '861c8b728d2808b8e8eb31592af42c5c4317b441fbd83d050ccf91fa24a9212e'},
+            {'ymmsl-0.13.0_fix_setup.patch': 'b8574b51c8b252817604b136acd84109c08900f9f563d2a742b525da980841ca'},
+        ],
+    }),
+    ('netifaces', '0.11.0', {
+        'checksums': ['043a79146eb2907edf439899f262b3dfe41717d34124298ed281139a8b93ca32'],
+    }),
+    ('muscle3', version, {
+        'patches': ['muscle3-0.7.1_fix_setup.patch'],
+        'source_tmpl': '%(version)s.tar.gz',
+        'source_urls': ['https://github.com/multiscale/muscle3/archive/refs/tags/'],
+        'checksums': [
+            {'0.7.1.tar.gz': 'b3023387c21af4d924b5cd240bdba376804ae166eb2c4b812e5222b4e0d3c8e0'},
+            {'muscle3-0.7.1_fix_setup.patch': '5c36a507b9fe8dc762dc5054000be10a05be3d277aed4036be378b728676dda5'},
+        ],
+    }),
+]
+
+modextrapaths = {
+    'MUSCLE3_HOME': '',
+}
+
+sanity_check_paths = {
+    'files': ['include/libmuscle.f90',
+              'include/libmuscle.mod',
+              'include/libmuscle/libmuscle.hpp',
+              'include/ymmsl/ymmsl.hpp',
+              'lib/libmuscle.a',
+              'lib/libmuscle.%s' % SHLIB_EXT,
+              'lib/libmuscle_fortran.a',
+              'lib/libmuscle_fortran.%s' % SHLIB_EXT,
+              'lib/libymmsl.a',
+              'lib/libymmsl.%s' % SHLIB_EXT,
+              'lib/libymmsl_fortran.a',
+              'lib/libymmsl_fortran.%s' % SHLIB_EXT,
+              'lib/pkgconfig/libmuscle.pc',
+              'lib/pkgconfig/libmuscle_fortran.pc',
+              'lib/pkgconfig/ymmsl.pc',
+              'lib/pkgconfig/ymmsl_fortran.pc'],
+    'dirs':  ['bin',
+              'include/libmuscle/mcp',
+              'include/ymmsl',
+              'lib/pkgconfig',
+              'lib64']
+}
+
+moduleclass = 'tools'

easybuild/easyconfigs/m/MUSCLE3/muscle3-0.7.1_fix_setup.patch

@@ -0,0 +1,12 @@
+diff -Nru muscle3-0.7.1-orig/setup.py muscle3-0.7.1/setup.py
+--- muscle3-0.7.1-orig/setup.py	2023-10-01 18:50:49.000000000 +0200
++++ muscle3-0.7.1/setup.py	2024-01-11 11:22:30.494825000 +0100
+@@ -57,7 +57,7 @@
+         'msgpack>=1,<2',
+         'netifaces==0.11.0',
+         "numpy<1.22; python_version=='3.7'",
+-        "numpy>=1.22,<=1.25; python_version>='3.8'",
++        "numpy>=1.22; python_version>='3.8'",
+         'qcg-pilotjob==0.13.1',
+         'typing_extensions>=4.4.0,<5',
+         'ymmsl>=0.13.0,<0.14'          # Also in CI, update there as well

easybuild/easyconfigs/m/MUSCLE3/yatiml-0.10.0_fix_setup.patch

@@ -0,0 +1,12 @@
+diff -Nru yatiml-0.10.0-orig/setup.py yatiml-0.10.0/setup.py
+--- yatiml-0.10.0-orig/setup.py	2022-12-19 15:16:27.000000000 +0100
++++ yatiml-0.10.0/setup.py	2024-01-11 11:21:08.019950000 +0100
+@@ -33,7 +33,7 @@
+         'Programming Language :: Python :: 3.11'
+     ],
+     install_requires=[
+-        'ruamel.yaml>=0.15.71,<=0.17.21,!=0.17.5',
++        'ruamel.yaml',
+         'typing_extensions'
+     ]
+ )

easybuild/easyconfigs/m/MUSCLE3/ymmsl-0.13.0_fix_setup.patch

@@ -0,0 +1,12 @@
+diff -Nru ymmsl-0.13.0-orig/setup.py ymmsl-0.13.0/setup.py
+--- ymmsl-0.13.0-orig/setup.py	2023-01-17 22:00:21.000000000 +0100
++++ ymmsl-0.13.0/setup.py	2024-01-11 11:32:59.149099000 +0100
+@@ -37,7 +37,7 @@
+     python_requires='>=3.7, <4',
+     test_suite='tests',
+     install_requires=[
+-        'ruamel.yaml<=0.17.21,!=0.17.5',
++        'ruamel.yaml',
+         'yatiml>=0.10.0,<0.11.0'
+     ],
+ )

easybuild/easyconfigs/m/msgpack-c/msgpack-c-6.0.0-GCC-13.2.0.eb

@@ -0,0 +1,37 @@
+# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2021/04
+easyblock = 'CMakeMake'
+
+name = 'msgpack-c'
+version = '6.0.0'
+
+homepage = 'http://msgpack.org/'
+description = """MessagePack is an efficient binary serialization format, which lets you exchange
+data among multiple languages like JSON, except that it's faster and smaller.   
+Small integers are encoded into a single byte while typical short strings       
+require only one extra byte in addition to the strings themselves."""
+
+toolchain = {'name': 'GCC', 'version': '13.2.0'}
+
+source_urls = ['https://github.com/msgpack/msgpack-c/releases/download/c-%(version)s']
+sources = ['msgpack-c-%(version)s.tar.gz']
+checksums = ['3654f5e2c652dc52e0a993e270bb57d5702b262703f03771c152bba51602aeba']
+
+builddependencies = [
+    ('CMake', '3.27.6'),
+    ('binutils', '2.40'),
+    ('googletest', '1.14.0'),
+]
+
+dependencies = [
+    ('Boost', '1.83.0'),
+]
+
+sanity_check_paths = {
+    'files': [
+        ['lib/libmsgpack-c.%s' % x for x in ['a', '%s' % SHLIB_EXT]],
+        ['include/msgpack.%s' % x for x in ['h']]
+    ],
+    'dirs': ['lib/pkgconfig', 'include/msgpack'],
+}
+
+moduleclass = 'lib'

easybuild/easyconfigs/r/ruamel.yaml/ruamel.yaml-0.18.5-GCCcore-13.2.0.eb

@@ -0,0 +1,71 @@
+easyblock = 'PythonBundle'
+
+name = 'ruamel.yaml'
+version = '0.18.5'
+
+homepage = 'https://sourceforge.net/projects/ruamel-yaml'
+description = "ruamel.yaml is a YAML 1.2 loader/dumper package for Python."
+
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
+
+builddependencies = [
+    ('binutils', '2.40'),
+]
+
+dependencies = [
+    ('Python', '3.11.5'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('ruamel.yaml.clib', '0.2.8', {
+        'modulename': False,
+        'checksums': ['beb2e0404003de9a4cab9753a8805a8fe9320ee6673136ed7f04255fe60bb512'],
+    }),
+    (name, version, {
+        'checksums': ['61917e3a35a569c1133a8f772e1226961bf5a1198bea7e23f06a0841dea1ab0e'],
+    }),
+    ('six', '1.16.0', {
+        'checksums': ['1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926'],
+    }),
+    ('configobj', '5.0.8', {
+        'checksums': ['6f704434a07dc4f4dc7c9a745172c1cad449feb548febd9f7fe362629c627a97'],
+    }),
+    ('lz4', '4.3.3', {
+        'patches': ['lz4-4.3.3_fix_setup.patch'],
+        'checksums': [
+            {'lz4-4.3.3.tar.gz': '01fe674ef2889dbb9899d8a67361e0c4a2c833af5aeb37dd505727cf5d2a131e'},
+            {'lz4-4.3.3_fix_setup.patch': '6dd189426fd8bee330642c3dd75b8fe0322235c4d66073e12a08f75a5ee6c13a'},
+        ],
+    }),
+    ('ruamel.yaml.base', '0.3.2', {
+        'checksums': ['88b6edc8ace60c12d98f05fda22e5d9d69ba9a4b531cf54783142151145b0372'],
+    }),
+    ('python-dateutil', '2.8.2', {
+        'modulename': 'dateutil',
+        'patches': ['python-dateutil-2.8.2_fix_setup.patch'],
+        'checksums': [
+            {'python-dateutil-2.8.2.tar.gz': '0123cacc1627ae19ddf3c27a5de5bd67ee4586fbdd6440d9748f8abb483d3e86'},
+            {'python-dateutil-2.8.2_fix_setup.patch':
+             '085d4287ab8484031503b63fdf302c26fb3f00668ceef3b0e9a5a13c0f2f2129'},
+        ],
+    }),
+    ('ruamel.yaml.convert', '0.3.2', {
+        'checksums': ['065ed9492a3189291d5bc0256709afc0231b52e4a01376fc91cf1757560ac9c4'],
+    }),
+    ('ruamel.yaml.cmd', '0.6.5', {
+        'checksums': ['49af59514cb87d7637d1186e31c9345c9947120a9ce49cf6975435aa7abd5aa8'],
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['bin/yaml'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = ["yaml --help"]
+
+sanity_pip_check = True
+
+moduleclass = 'lang'