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branfosj merged 3 commits into from
Feb 4, 2026
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build(MacSyFinder): ✅ 2.1.6 #774

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10702f4
build(MacSyFinder): :white_check_mark: 2.1.6
Jan 29, 2026
04ad8db
test(MacSyFinder): unittests
Jan 29, 2026
7924df6
style(MacSyFinder): :pencil2: trailing whitespaces
Jan 29, 2026
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75 changes: 75 additions & 0 deletions easyconfigs/m/MacSyFinder/MacSyFinder-2.1.6-foss-2024a.eb
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# This easyconfig was created by the BEAR Software team at the University of Birmingham.
easyblock = 'PythonBundle'

name = 'MacSyFinder'
version = '2.1.6'

homepage = "https://github.com/gem-pasteur/macsyfinder"
description = """MacSyFinder - Detection of macromolecular systems in protein datasets
using systems modelling and similarity search"""
citing = """MacSyFinder v2: Néron, Bertrand; Denise, Rémi; Coluzzi, Charles;
Touchon, Marie; Rocha, Eduardo P.C.; Abby, Sophie S. MacSyFinder v2:
Improved modelling and search engine to identify molecular systems in genomes.
Peer Community Journal, Volume 3 (2023), article no. e28.
doi : 10.24072/pcjournal.250. https://peercommunityjournal.org/articles/10.24072/pcjournal.250/"""

toolchain = {'name': 'foss', 'version': '2024a'}

dependencies = [
('Python', '3.12.3'),
('HMMER', '3.4'),
('GitPython', '3.1.43'), # for macsylib[model]
('lxml', '5.3.0'), # for macsylyb[model]
('networkx', '3.4.2'),
('PyYAML', '6.0.2'),
('SciPy-bundle', '2024.05'),
('flit', '3.9.0'),

]

exts_list = [
('colorlog', '6.9.0', {
'checksums': ['bfba54a1b93b94f54e1f4fe48395725a3d92fd2a4af702f6bd70946bdc0c6ac2'],
}),
('macsylib', '1.0.4', {
'patches': ['%(name)s-%(version)s_licence.patch'],
'use_pip_extras': 'model',
'testinstall': True,
# 'runtest': '%(python)s -m unittest discover -vv', # fails to resolve in _pre_sanity_check_hook
'runtest': 'python -m unittest discover -vv',
'checksums': [
{'macsylib-1.0.4.tar.gz': '084cf0ff7c89642d925bd1457f6ed32089d0be50b8ad726c5d75026efa438abb'},
{'macsylib-1.0.4_licence.patch': 'e6b67d40815b3910f5f6d72499f4d1cea96f113c580e061325cba70bb2555d45'},
],
}),
('macsyfinder', version, {
'patches': ['%(name)s-%(version)s_licence.patch'],
'use_pip_extras': 'model',
'testinstall': True,
# 'runtest': '%(python)s -m unittest discover -vv', # fails to resolve template python_cmd
'runtest': 'python -m unittest discover -vv',
'checksums': [
{'macsyfinder-2.1.6.tar.gz': 'd05f5eb46b03c62e2183111225aa869a97ca1e4353c07fe342ac28be22cd523e'},
{'macsyfinder-2.1.6_licence.patch': 'f67604332e40c30287dbd58fa2aad0c77fd169e4e861cb18f56adf9548657a9b'},
],
}),
]

sanity_check_paths = {
'files': [
'bin/macsyconfig',
'bin/macsydata',
'bin/macsyfinder',
'bin/macsyprofile',
'bin/msf_config',
'bin/msf_data',
'bin/msf_merge',
'bin/msf_profile',
'bin/msf_split',
'bin/msl_data',
],
'dirs': ['bin', 'lib/python%(pyshortver)s/site-packages/']
}


moduleclass = 'bio'
14 changes: 14 additions & 0 deletions easyconfigs/m/MacSyFinder/macsyfinder-2.1.6_licence.patch
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diff --git a/pyproject.toml b/pyproject.toml
index 324447b6..91387a75 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -15,8 +15,7 @@ maintainers = [
description = 'MacSyFinder: Detection of macromolecular systems in protein datasets using systems modelling and similarity search'
keywords = ['science', 'research', 'bioinformatic', 'microbiology', 'genomic', 'prokaryote', 'functional gene annotation']
readme = "README.md"
-license = "GPL-3.0-or-later"
-license-files = ["COPYING"]
+license = {file = 'COPYING'}

classifiers = [
"Programming Language :: Python :: 3",
14 changes: 14 additions & 0 deletions easyconfigs/m/MacSyFinder/macsylib-1.0.4_licence.patch
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diff --git a/pyproject.toml b/pyproject.toml
index a60ff60..15d9a5b 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -15,8 +15,7 @@ maintainers = [
description = 'MacSyLib: Python library that help to detect of macromolecular, systems genetic pathways… in prokaryotes protein datasets using systems modelling and similarity search.'
keywords = ['science', 'research', 'bioinformatic', 'microbiology', 'genomic', 'prokaryote', 'functional gene annotation']
readme = "README.md"
-license = 'GPL-3.0-or-later'
-license-files = ["COPYING"]
+license = {file = "COPYING"}

classifiers = [
"Programming Language :: Python :: 3",