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{
lib,
stdenv,
buildPythonPackage,
fetchFromGitHub,
fetchpatch,
llvmPackages,
zlib,
cython_0,
oldest-supported-numpy,
setuptools,
wheel,
astunparse,
numpy,
packaging,
pyparsing,
scipy,
gsd,
networkx,
pandas,
pytest-xdist,
pytestCheckHook,
tables,
}:
buildPythonPackage rec {
pname = "mdtraj";
version = "1.9.9";
pyproject = true;
src = fetchFromGitHub {
owner = "mdtraj";
repo = "mdtraj";
rev = "refs/tags/${version}";
hash = "sha256-2Jg6DyVJlRBLD/6hMtcsrAdxKF5RkpUuhAQm/lqVGeE=";
};
patches = [
(fetchpatch {
name = "gsd_3-compatibility.patch";
url = "https://github.com/mdtraj/mdtraj/commit/81209d00817ab07cfc4668bf5ec88088d16904c0.patch";
hash = "sha256-ttNmij7csxF0Z5wPPwhGumRX055W2IgFjRAe6nI6GNY=";
})
# remove pkg_resources usage
# https://github.com/mdtraj/mdtraj/pull/1837
(fetchpatch {
name = "fix-runtime-error.patch";
url = "https://github.com/mdtraj/mdtraj/commit/02d44d4db7039fceb199c85b4f993244804f470d.patch";
hash = "sha256-nhbi3iOrDSM87DyIp1KVt383Vvb6aYOgkjuYzviqiq8=";
})
# remove distutils usage
# https://github.com/mdtraj/mdtraj/pull/1834
(fetchpatch {
name = "python312-compatibility.patch";
url = "https://github.com/mdtraj/mdtraj/commit/95d79747deef42c976ca362a57806b61933409f3.patch";
hash = "sha256-Cq7/d745q6ZgAyWGM4ULnSsWezsbnu1CjSz5eqYSb+g=";
})
# disable intrinsics when SIMD is not available
# TODO: enable SIMD with python3.12
# https://github.com/mdtraj/mdtraj/pull/1884
(fetchpatch {
name = "fix-intrinsics-flag.patch";
url = "https://github.com/mdtraj/mdtraj/commit/d6041c645d51898e2a09030633210213eec7d4c5.patch";
hash = "sha256-kcnlHMoA/exJzV8iQltH+LWXrvSk7gsUV+yWK6xn0jg=";
})
];
build-system = [
cython_0
oldest-supported-numpy
setuptools
wheel
];
buildInputs = [ zlib ] ++ lib.optionals stdenv.cc.isClang [ llvmPackages.openmp ];
dependencies = [
astunparse
numpy
packaging
pyparsing
scipy
];
env.NIX_CFLAGS_COMPILE = lib.optionalString stdenv.cc.isClang "-Wno-incompatible-function-pointer-types";
nativeCheckInputs = [
gsd
networkx
pandas
pytest-xdist
pytestCheckHook
tables
];
preCheck = ''
cd tests
export PATH=$out/bin:$PATH
'';
disabledTests = [
# require network access
"test_pdb_from_url"
"test_1vii_url_and_gz"
# fail due to data race
"test_read_atomindices_1"
"test_read_atomindices_2"
# flaky test
"test_compare_rdf_t_master"
"test_distances_t"
"test_precentered_2"
];
pythonImportsCheck = [ "mdtraj" ];
meta = with lib; {
description = "Open library for the analysis of molecular dynamics trajectories";
homepage = "https://github.com/mdtraj/mdtraj";
changelog = "https://github.com/mdtraj/mdtraj/releases/tag/${src.rev}";
license = licenses.lgpl21Plus;
maintainers = with maintainers; [ natsukium ];
};
}
|
