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