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[BUGFIX:GROMACS] Build with gmxapi distributed with the GROMACS source code #25188

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[BUGFIX:GROMACS] Build with gmxapi distributed with the GROMACS source code #25188

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37f8ec1
[BUGFIX:GROMACS] Build with `gmxapi` distributed with the GROMACS sou…
gkaf89 Jan 29, 2026
ea1e4b2
Fix style errors
gkaf89 Jan 30, 2026
cb44479
Remove configuration script patch as it is no longer used
gkaf89 Feb 18, 2026
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15 changes: 15 additions & 0 deletions easybuild/easyconfigs/g/GROMACS/GROMACS-2024.1-fix-gmxapi-version.patch
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Original file line number Diff line number Diff line change
@@ -0,0 +1,15 @@
Version information is located in file: /python_packaging/gmxapi/src/gmxapi/version.py

This patch overrides the outdated data in the TOML file.
diff -ruN gromacs-v2024.1.orig/python_packaging/gmxapi/pyproject.toml gromacs-v2024.1/python_packaging/gmxapi/pyproject.toml
--- gromacs-v2024.1.orig/python_packaging/gmxapi/pyproject.toml 2024-02-28 14:31:24.000000000 +0100
+++ gromacs-v2024.1/python_packaging/gmxapi/pyproject.toml 2026-01-29 17:05:01.426362279 +0100
@@ -4,7 +4,7 @@

[project]
name = "gmxapi"
-version = "0.4.1"
+version = "0.5.0a1"
description = "gmxapi Python interface for GROMACS."
readme = "README.rst"
license = { text = "GNU LESSER GENERAL PUBLIC LICENSE" }
15 changes: 9 additions & 6 deletions easybuild/easyconfigs/g/GROMACS/GROMACS-2024.1-foss-2023b.eb
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Original file line number Diff line number Diff line change
Expand Up @@ -71,17 +71,20 @@ dependencies = [

exts_defaultclass = 'PythonPackage'

exts_default_options = {
'source_urls': [PYPI_SOURCE],
}
_gmxapi_source_version = version

exts_list = [
('gmxapi', '0.5.0', {
('gmxapi', '0.5.0a1', {
'patches': ['GROMACS-2024.1-fix-gmxapi-version.patch'],
'preinstallopts': 'export CMAKE_ARGS="-Dgmxapi_ROOT=%(installdir)s ' +
'-C %(installdir)s/share/cmake/gromacs_mpi/gromacs-hints_mpi.cmake" && ',
'source_tmpl': 'gromacs-2024.1.tar.gz',
'source_tmpl': 'gromacs-%s.tar.gz' % _gmxapi_source_version,
'start_dir': 'python_packaging/gmxapi',
'checksums': ['937d8f12a36fffbf2af7add71adbb5aa5c5537892d46c9a76afbecab1aa0aac7'],
'checksums': [
{'gromacs-2024.1.tar.gz': '937d8f12a36fffbf2af7add71adbb5aa5c5537892d46c9a76afbecab1aa0aac7'},
{'GROMACS-2024.1-fix-gmxapi-version.patch':
'df30b21352a26d8e01d693e2822db0ea45015c23f900a6ceb68522d44e6e790c'},
],
}),
]

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15 changes: 10 additions & 5 deletions easybuild/easyconfigs/g/GROMACS/GROMACS-2024.3-foss-2023b-PLUMED-2.9.2.eb
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Original file line number Diff line number Diff line change
Expand Up @@ -73,15 +73,20 @@ ignore_plumed_version_check = True

exts_defaultclass = 'PythonPackage'

exts_default_options = {
'source_urls': [PYPI_SOURCE],
}
_gmxapi_source_version = version

exts_list = [
('gmxapi', '0.4.2', {
('gmxapi', '0.5.0a1', {
'patches': ['GROMACS-2024.1-fix-gmxapi-version.patch'],
'preinstallopts': 'export CMAKE_ARGS="-Dgmxapi_ROOT=%(installdir)s ' +
'-C %(installdir)s/share/cmake/gromacs_mpi/gromacs-hints_mpi.cmake" && ',
'checksums': ['c746c6498c73a75913d7fcb01c13cc001d4bcb82999e9bf91d63578565ed1a1f'],
'source_tmpl': 'gromacs-%s.tar.gz' % _gmxapi_source_version,
'start_dir': 'python_packaging/gmxapi',
'checksums': [
{'gromacs-2024.3.tar.gz': 'bbda056ee59390be7d58d84c13a9ec0d4e3635617adf2eb747034922cba1f029'},
{'GROMACS-2024.1-fix-gmxapi-version.patch':
'df30b21352a26d8e01d693e2822db0ea45015c23f900a6ceb68522d44e6e790c'},
],
}),
]

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16 changes: 10 additions & 6 deletions easybuild/easyconfigs/g/GROMACS/GROMACS-2024.3-foss-2023b.eb
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Original file line number Diff line number Diff line change
Expand Up @@ -65,16 +65,20 @@ dependencies = [

exts_defaultclass = 'PythonPackage'

exts_default_options = {
'source_urls': [PYPI_SOURCE],
}
_gmxapi_source_version = version

exts_list = [
('gmxapi', '0.4.2', {
('gmxapi', '0.5.0a1', {
'patches': ['GROMACS-2024.1-fix-gmxapi-version.patch'],
'preinstallopts': 'export CMAKE_ARGS="-Dgmxapi_ROOT=%(installdir)s ' +
'-C %(installdir)s/share/cmake/gromacs_mpi/gromacs-hints_mpi.cmake" && ',
'checksums': ['c746c6498c73a75913d7fcb01c13cc001d4bcb82999e9bf91d63578565ed1a1f'],
'source_tmpl': 'gromacs-%s.tar.gz' % _gmxapi_source_version,
'start_dir': 'python_packaging/gmxapi',
'checksums': [
{'gromacs-2024.3.tar.gz': 'bbda056ee59390be7d58d84c13a9ec0d4e3635617adf2eb747034922cba1f029'},
{'GROMACS-2024.1-fix-gmxapi-version.patch':
'df30b21352a26d8e01d693e2822db0ea45015c23f900a6ceb68522d44e6e790c'},
],
}),
]

moduleclass = 'bio'
15 changes: 10 additions & 5 deletions easybuild/easyconfigs/g/GROMACS/GROMACS-2024.4-foss-2023b-CUDA-12.4.0-PLUMED-2.9.2.eb
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Original file line number Diff line number Diff line change
Expand Up @@ -78,15 +78,20 @@ ignore_plumed_version_check = True

exts_defaultclass = 'PythonPackage'

exts_default_options = {
'source_urls': [PYPI_SOURCE],
}
_gmxapi_source_version = version

exts_list = [
('gmxapi', '0.4.2', {
('gmxapi', '0.5.0a1', {
'patches': ['GROMACS-2024.1-fix-gmxapi-version.patch'],
'preinstallopts': 'export CMAKE_ARGS="-Dgmxapi_ROOT=%(installdir)s ' +
'-C %(installdir)s/share/cmake/gromacs_mpi/gromacs-hints_mpi.cmake" && ',
'checksums': ['c746c6498c73a75913d7fcb01c13cc001d4bcb82999e9bf91d63578565ed1a1f'],
'source_tmpl': 'gromacs-%s.tar.gz' % _gmxapi_source_version,
'start_dir': 'python_packaging/gmxapi',
'checksums': [
{'gromacs-2024.4.tar.gz': 'ac618ece2e58afa86b536c5a2c4fcb937f0760318f12d18f10346b6bdebd86a8'},
{'GROMACS-2024.1-fix-gmxapi-version.patch':
'df30b21352a26d8e01d693e2822db0ea45015c23f900a6ceb68522d44e6e790c'},
],
}),
]

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15 changes: 10 additions & 5 deletions easybuild/easyconfigs/g/GROMACS/GROMACS-2024.4-foss-2023b-CUDA-12.4.0.eb
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Original file line number Diff line number Diff line change
Expand Up @@ -71,15 +71,20 @@ configopts = "-DGMX_TEST_TIMEOUT_FACTOR=3"

exts_defaultclass = 'PythonPackage'

exts_default_options = {
'source_urls': [PYPI_SOURCE],
}
_gmxapi_source_version = version

exts_list = [
('gmxapi', '0.4.2', {
('gmxapi', '0.5.0a1', {
'patches': ['GROMACS-2024.1-fix-gmxapi-version.patch'],
'preinstallopts': 'export CMAKE_ARGS="-Dgmxapi_ROOT=%(installdir)s ' +
'-C %(installdir)s/share/cmake/gromacs_mpi/gromacs-hints_mpi.cmake" && ',
'checksums': ['c746c6498c73a75913d7fcb01c13cc001d4bcb82999e9bf91d63578565ed1a1f'],
'source_tmpl': 'gromacs-%s.tar.gz' % _gmxapi_source_version,
'start_dir': 'python_packaging/gmxapi',
'checksums': [
{'gromacs-2024.4.tar.gz': 'ac618ece2e58afa86b536c5a2c4fcb937f0760318f12d18f10346b6bdebd86a8'},
{'GROMACS-2024.1-fix-gmxapi-version.patch':
'df30b21352a26d8e01d693e2822db0ea45015c23f900a6ceb68522d44e6e790c'},
],
}),
]

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15 changes: 10 additions & 5 deletions easybuild/easyconfigs/g/GROMACS/GROMACS-2024.4-foss-2023b-PLUMED-2.9.2.eb
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Original file line number Diff line number Diff line change
Expand Up @@ -77,15 +77,20 @@ configopts = "-DGMX_TEST_TIMEOUT_FACTOR=3"

exts_defaultclass = 'PythonPackage'

exts_default_options = {
'source_urls': [PYPI_SOURCE],
}
_gmxapi_source_version = version

exts_list = [
('gmxapi', '0.4.2', {
('gmxapi', '0.5.0a1', {
'patches': ['GROMACS-2024.1-fix-gmxapi-version.patch'],
'preinstallopts': 'export CMAKE_ARGS="-Dgmxapi_ROOT=%(installdir)s ' +
'-C %(installdir)s/share/cmake/gromacs_mpi/gromacs-hints_mpi.cmake" && ',
'checksums': ['c746c6498c73a75913d7fcb01c13cc001d4bcb82999e9bf91d63578565ed1a1f'],
'source_tmpl': 'gromacs-%s.tar.gz' % _gmxapi_source_version,
'start_dir': 'python_packaging/gmxapi',
'checksums': [
{'gromacs-2024.4.tar.gz': 'ac618ece2e58afa86b536c5a2c4fcb937f0760318f12d18f10346b6bdebd86a8'},
{'GROMACS-2024.1-fix-gmxapi-version.patch':
'df30b21352a26d8e01d693e2822db0ea45015c23f900a6ceb68522d44e6e790c'},
],
}),
]

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15 changes: 10 additions & 5 deletions easybuild/easyconfigs/g/GROMACS/GROMACS-2024.4-foss-2023b.eb
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Original file line number Diff line number Diff line change
Expand Up @@ -69,15 +69,20 @@ configopts = "-DGMX_TEST_TIMEOUT_FACTOR=3"

exts_defaultclass = 'PythonPackage'

exts_default_options = {
'source_urls': [PYPI_SOURCE],
}
_gmxapi_source_version = version

exts_list = [
('gmxapi', '0.4.2', {
('gmxapi', '0.5.0a1', {
'patches': ['GROMACS-2024.1-fix-gmxapi-version.patch'],
'preinstallopts': 'export CMAKE_ARGS="-Dgmxapi_ROOT=%(installdir)s ' +
'-C %(installdir)s/share/cmake/gromacs_mpi/gromacs-hints_mpi.cmake" && ',
'checksums': ['c746c6498c73a75913d7fcb01c13cc001d4bcb82999e9bf91d63578565ed1a1f'],
'source_tmpl': 'gromacs-%s.tar.gz' % _gmxapi_source_version,
'start_dir': 'python_packaging/gmxapi',
'checksums': [
{'gromacs-2024.4.tar.gz': 'ac618ece2e58afa86b536c5a2c4fcb937f0760318f12d18f10346b6bdebd86a8'},
{'GROMACS-2024.1-fix-gmxapi-version.patch':
'df30b21352a26d8e01d693e2822db0ea45015c23f900a6ceb68522d44e6e790c'},
],
}),
]

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16 changes: 8 additions & 8 deletions easybuild/easyconfigs/g/GROMACS/GROMACS-2025.2-foss-2025a.eb
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Original file line number Diff line number Diff line change
Expand Up @@ -70,19 +70,19 @@ configopts = "-DGMX_TEST_TIMEOUT_FACTOR=3"

exts_defaultclass = 'PythonPackage'

exts_default_options = {
'source_urls': [PYPI_SOURCE],
}
_gmxapi_source_version = version

exts_list = [
('gmxapi', '0.4.2', {
'patches': ['GROMACS-2025.2_gmxapi-remove-builddependencies.patch'],
('gmxapi', '0.5.0a1', {
'patches': ['GROMACS-2024.1-fix-gmxapi-version.patch'],
'preinstallopts': 'export CMAKE_ARGS="-Dgmxapi_ROOT=%(installdir)s ' +
'-C %(installdir)s/share/cmake/gromacs_mpi/gromacs-hints_mpi.cmake" && ',
'source_tmpl': 'gromacs-%s.tar.gz' % _gmxapi_source_version,
'start_dir': 'python_packaging/gmxapi',
'checksums': [
{'gmxapi-0.4.2.tar.gz': 'c746c6498c73a75913d7fcb01c13cc001d4bcb82999e9bf91d63578565ed1a1f'},
{'GROMACS-2025.2_gmxapi-remove-builddependencies.patch':
'd35eedea75167a88cd1c74df4c201b666ec9f8aef00f0fc6136380e36eb1e0e5'},
{'gromacs-2025.2.tar.gz': '0df09f9d45a99ef00e66b9baa9493a27e906813763a3b6c7672217c66b43ea11'},
{'GROMACS-2024.1-fix-gmxapi-version.patch':
'df30b21352a26d8e01d693e2822db0ea45015c23f900a6ceb68522d44e6e790c'},
],
}),
]
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16 changes: 8 additions & 8 deletions easybuild/easyconfigs/g/GROMACS/GROMACS-2025.2-foss-2025b.eb
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Original file line number Diff line number Diff line change
Expand Up @@ -70,19 +70,19 @@ configopts = "-DGMX_TEST_TIMEOUT_FACTOR=3"

exts_defaultclass = 'PythonPackage'

exts_default_options = {
'source_urls': [PYPI_SOURCE],
}
_gmxapi_source_version = version

exts_list = [
('gmxapi', '0.4.2', {
'patches': ['GROMACS-2025.2_gmxapi-remove-builddependencies.patch'],
('gmxapi', '0.5.0a1', {
'patches': ['GROMACS-2024.1-fix-gmxapi-version.patch'],
'preinstallopts': 'export CMAKE_ARGS="-Dgmxapi_ROOT=%(installdir)s ' +
'-C %(installdir)s/share/cmake/gromacs_mpi/gromacs-hints_mpi.cmake" && ',
'source_tmpl': 'gromacs-%s.tar.gz' % _gmxapi_source_version,
'start_dir': 'python_packaging/gmxapi',
'checksums': [
{'gmxapi-0.4.2.tar.gz': 'c746c6498c73a75913d7fcb01c13cc001d4bcb82999e9bf91d63578565ed1a1f'},
{'GROMACS-2025.2_gmxapi-remove-builddependencies.patch':
'd35eedea75167a88cd1c74df4c201b666ec9f8aef00f0fc6136380e36eb1e0e5'},
{'gromacs-2025.2.tar.gz': '0df09f9d45a99ef00e66b9baa9493a27e906813763a3b6c7672217c66b43ea11'},
{'GROMACS-2024.1-fix-gmxapi-version.patch':
'df30b21352a26d8e01d693e2822db0ea45015c23f900a6ceb68522d44e6e790c'},
],
}),
]
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16 changes: 8 additions & 8 deletions easybuild/easyconfigs/g/GROMACS/GROMACS-2025.2-lfoss-2025b.eb
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Original file line number Diff line number Diff line change
Expand Up @@ -70,19 +70,19 @@ configopts = "-DGMX_TEST_TIMEOUT_FACTOR=3"

exts_defaultclass = 'PythonPackage'

exts_default_options = {
'source_urls': [PYPI_SOURCE],
}
_gmxapi_source_version = version

exts_list = [
('gmxapi', '0.4.2', {
'patches': ['GROMACS-2025.2_gmxapi-remove-builddependencies.patch'],
('gmxapi', '0.5.0a1', {
'patches': ['GROMACS-2024.1-fix-gmxapi-version.patch'],
'preinstallopts': 'export CMAKE_ARGS="-Dgmxapi_ROOT=%(installdir)s ' +
'-C %(installdir)s/share/cmake/gromacs_mpi/gromacs-hints_mpi.cmake" && ',
'source_tmpl': 'gromacs-%s.tar.gz' % _gmxapi_source_version,
'start_dir': 'python_packaging/gmxapi',
'checksums': [
{'gmxapi-0.4.2.tar.gz': 'c746c6498c73a75913d7fcb01c13cc001d4bcb82999e9bf91d63578565ed1a1f'},
{'GROMACS-2025.2_gmxapi-remove-builddependencies.patch':
'd35eedea75167a88cd1c74df4c201b666ec9f8aef00f0fc6136380e36eb1e0e5'},
{'gromacs-2025.2.tar.gz': '0df09f9d45a99ef00e66b9baa9493a27e906813763a3b6c7672217c66b43ea11'},
{'GROMACS-2024.1-fix-gmxapi-version.patch':
'df30b21352a26d8e01d693e2822db0ea45015c23f900a6ceb68522d44e6e790c'},
],
}),
]
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16 changes: 8 additions & 8 deletions easybuild/easyconfigs/g/GROMACS/GROMACS-2025.2-lmpflf-2025b.eb
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Original file line number Diff line number Diff line change
Expand Up @@ -73,19 +73,19 @@ configopts = "-DGMX_TEST_TIMEOUT_FACTOR=3"

exts_defaultclass = 'PythonPackage'

exts_default_options = {
'source_urls': [PYPI_SOURCE],
}
_gmxapi_source_version = version

exts_list = [
('gmxapi', '0.4.2', {
'patches': ['GROMACS-2025.2_gmxapi-remove-builddependencies.patch'],
('gmxapi', '0.5.0a1', {
'patches': ['GROMACS-2024.1-fix-gmxapi-version.patch'],
'preinstallopts': 'export CMAKE_ARGS="-Dgmxapi_ROOT=%(installdir)s ' +
'-C %(installdir)s/share/cmake/gromacs_mpi/gromacs-hints_mpi.cmake" && ',
'source_tmpl': 'gromacs-%s.tar.gz' % _gmxapi_source_version,
'start_dir': 'python_packaging/gmxapi',
'checksums': [
{'gmxapi-0.4.2.tar.gz': 'c746c6498c73a75913d7fcb01c13cc001d4bcb82999e9bf91d63578565ed1a1f'},
{'GROMACS-2025.2_gmxapi-remove-builddependencies.patch':
'd35eedea75167a88cd1c74df4c201b666ec9f8aef00f0fc6136380e36eb1e0e5'},
{'gromacs-2025.2.tar.gz': '0df09f9d45a99ef00e66b9baa9493a27e906813763a3b6c7672217c66b43ea11'},
{'GROMACS-2024.1-fix-gmxapi-version.patch':
'df30b21352a26d8e01d693e2822db0ea45015c23f900a6ceb68522d44e6e790c'},
],
}),
]
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17 changes: 0 additions & 17 deletions easybuild/easyconfigs/g/GROMACS/GROMACS-2025.2_gmxapi-remove-builddependencies.patch
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This file was deleted.

16 changes: 8 additions & 8 deletions easybuild/easyconfigs/g/GROMACS/GROMACS-2025.3-foss-2025b.eb
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Original file line number Diff line number Diff line change
Expand Up @@ -71,19 +71,19 @@ configopts = "-DGMX_TEST_TIMEOUT_FACTOR=3"

exts_defaultclass = 'PythonPackage'

exts_default_options = {
'source_urls': [PYPI_SOURCE],
}
_gmxapi_source_version = version

exts_list = [
('gmxapi', '0.4.2', {
'patches': ['GROMACS-2025.2_gmxapi-remove-builddependencies.patch'],
('gmxapi', '0.5.0a1', {
'patches': ['GROMACS-2024.1-fix-gmxapi-version.patch'],
'preinstallopts': 'export CMAKE_ARGS="-Dgmxapi_ROOT=%(installdir)s ' +
'-C %(installdir)s/share/cmake/gromacs_mpi/gromacs-hints_mpi.cmake" && ',
'source_tmpl': 'gromacs-%s.tar.gz' % _gmxapi_source_version,
'start_dir': 'python_packaging/gmxapi',
'checksums': [
{'gmxapi-0.4.2.tar.gz': 'c746c6498c73a75913d7fcb01c13cc001d4bcb82999e9bf91d63578565ed1a1f'},
{'GROMACS-2025.2_gmxapi-remove-builddependencies.patch':
'd35eedea75167a88cd1c74df4c201b666ec9f8aef00f0fc6136380e36eb1e0e5'},
{'gromacs-2025.3.tar.gz': '8bdfca0268f3f10a7ca3c06e59b62f73ea02420c67211c0ff3912f32d7833c65'},
{'GROMACS-2024.1-fix-gmxapi-version.patch':
'df30b21352a26d8e01d693e2822db0ea45015c23f900a6ceb68522d44e6e790c'},
],
}),
]
Expand Down