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Merge pull request #309076 from natsukium/mdtraj/fix

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python312Packages.mdtraj: fix runtime error and support python3.12
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OTABI Tomoya 2024-05-12 10:04:30 +09:00 committed by GitHub
commit 5cdadbba38
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1 changed files with 28 additions and 2 deletions
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30
pkgs/development/python-modules/mdtraj/default.nix
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@ -11,6 +11,7 @@
, wheel
, astunparse
, numpy
, packaging
, pyparsing
, scipy
, gsd
@ -39,9 +40,31 @@ buildPythonPackage rec {
url = "https://github.com/mdtraj/mdtraj/commit/81209d00817ab07cfc4668bf5ec88088d16904c0.patch";
hash = "sha256-ttNmij7csxF0Z5wPPwhGumRX055W2IgFjRAe6nI6GNY=";
})
# remove pkg_resources usage
# https://github.com/mdtraj/mdtraj/pull/1837
(fetchpatch {
name = "fix-runtime-error.patch";
url = "https://github.com/mdtraj/mdtraj/commit/02d44d4db7039fceb199c85b4f993244804f470d.patch";
hash = "sha256-nhbi3iOrDSM87DyIp1KVt383Vvb6aYOgkjuYzviqiq8=";
})
# remove distutils usage
# https://github.com/mdtraj/mdtraj/pull/1834
(fetchpatch {
name = "python312-compatibility.patch";
url = "https://github.com/mdtraj/mdtraj/commit/95d79747deef42c976ca362a57806b61933409f3.patch";
hash = "sha256-Cq7/d745q6ZgAyWGM4ULnSsWezsbnu1CjSz5eqYSb+g=";
})
# disable intrinsics when SIMD is not available
# TODO: enable SIMD with python3.12
# https://github.com/mdtraj/mdtraj/pull/1884
(fetchpatch {
name = "fix-intrinsics-flag.patch";
url = "https://github.com/mdtraj/mdtraj/commit/d6041c645d51898e2a09030633210213eec7d4c5.patch";
hash = "sha256-kcnlHMoA/exJzV8iQltH+LWXrvSk7gsUV+yWK6xn0jg=";
})
];
nativeBuildInputs = [
build-system = [
cython_0
oldest-supported-numpy
setuptools
@ -54,9 +77,10 @@ buildPythonPackage rec {
llvmPackages.openmp
];
propagatedBuildInputs = [
dependencies = [
astunparse
numpy
packaging
pyparsing
scipy
];
@ -87,7 +111,9 @@ buildPythonPackage rec {
"test_read_atomindices_2"
# flaky test
"test_compare_rdf_t_master"
"test_distances_t"
"test_precentered_2"
];
pythonImportsCheck = [ "mdtraj" ];