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{ lib
, stdenv
, buildPythonPackage
, fetchFromGitHub
, fetchpatch
, llvmPackages
, zlib
, cython_0
, oldest-supported-numpy
, setuptools
, wheel
, astunparse
, numpy
, 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/${version}";
hash = "sha256-2Jg6DyVJlRBLD/6hMtcsrAdxKF5RkpUuhAQm/lqVGeE=";
};
patches = [
(fetchpatch {
name = "gsd_3-compatibility.patch";
url = "https://github.com/mdtraj/mdtraj/commit/81209d00817ab07cfc4668bf5ec88088d16904c0.patch";
hash = "sha256-ttNmij7csxF0Z5wPPwhGumRX055W2IgFjRAe6nI6GNY=";
})
];
nativeBuildInputs = [
cython_0
oldest-supported-numpy
setuptools
wheel
];
buildInputs = [
zlib
] ++ lib.optionals stdenv.cc.isClang [
llvmPackages.openmp
];
propagatedBuildInputs = [
astunparse
numpy
pyparsing
scipy
];
env.NIX_CFLAGS_COMPILE = lib.optionalString stdenv.cc.isClang "-Wno-incompatible-function-pointer-types";
nativeCheckInputs = [
gsd
networkx
pandas
pytest-xdist
pytestCheckHook
tables
];
preCheck = ''
cd tests
export PATH=$out/bin:$PATH
'';
disabledTests = [
# require network access
"test_pdb_from_url"
"test_1vii_url_and_gz"
# fail due to data race
"test_read_atomindices_1"
"test_read_atomindices_2"
# flaky test
"test_distances_t"
];
pythonImportsCheck = [ "mdtraj" ];
meta = with lib; {
description = "An open library for the analysis of molecular dynamics trajectories";
homepage = "https://github.com/mdtraj/mdtraj";
changelog = "https://github.com/mdtraj/mdtraj/releases/tag/${src.rev}";
license = licenses.lgpl21Plus;
maintainers = with maintainers; [ natsukium ];
};
}
|