Merge pull request #309076 from natsukium/mdtraj/fix (5cdadbba) · Commits · nix / nixpkgs

pkgs/development/python-modules/mdtraj/default.nix

+28 −2

Original line number	Diff line number	Diff line
		@@ -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" ];