102 lines
1.9 KiB
Nix
102 lines
1.9 KiB
Nix
{ 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 ];
|
|
};
|
|
}
|