1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
|
{
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,
pythonAtLeast,
}:
buildPythonPackage rec {
pname = "mdtraj";
version = "1.10.0";
pyproject = true;
src = fetchFromGitHub {
owner = "mdtraj";
repo = "mdtraj";
rev = "refs/tags/${version}";
hash = "sha256-hNv/humEZOX4W7cOlJSAodk9pIi18//YJNSWNiEFiVg=";
};
patches = [
# disable intrinsics when SIMD is not available
# TODO: enable SIMD with python3.12
# https://github.com/mdtraj/mdtraj/pull/1884
(fetchpatch {
name = "fix-intrinsics-flag.patch";
url = "https://github.com/mdtraj/mdtraj/commit/d6041c645d51898e2a09030633210213eec7d4c5.patch";
hash = "sha256-kcnlHMoA/exJzV8iQltH+LWXrvSk7gsUV+yWK6xn0jg=";
})
];
build-system = [
cython_0
oldest-supported-numpy
setuptools
wheel
];
buildInputs = [ zlib ] ++ lib.optionals stdenv.cc.isClang [ llvmPackages.openmp ];
dependencies = [
astunparse
numpy
packaging
pyparsing
scipy
];
env.NIX_CFLAGS_COMPILE = lib.optionalString stdenv.cc.isClang "-Wno-incompatible-function-pointer-types";
nativeCheckInputs = [
gsd
networkx
pandas
pytest-xdist
pytestCheckHook
tables
];
preCheck = ''
cd tests
export PATH=$out/bin:$PATH
'';
disabledTests = [
# require network access
"test_pdb_from_url"
"test_1vii_url_and_gz"
# fail due to data race
"test_read_atomindices_1"
"test_read_atomindices_2"
# flaky test
"test_compare_rdf_t_master"
"test_distances_t"
"test_precentered_2"
];
# these files import distutils
# remove once https://github.com/mdtraj/mdtraj/pull/1916 is merged
disabledTestPaths = lib.optionals (pythonAtLeast "3.12") [
"test_mol2.py"
"test_netcdf.py"
];
pythonImportsCheck = [ "mdtraj" ];
meta = with lib; {
description = "Open library for the analysis of molecular dynamics trajectories";
homepage = "https://github.com/mdtraj/mdtraj";
changelog = "https://github.com/mdtraj/mdtraj/releases/tag/${lib.removePrefix "refs/tags/" src.rev}";
license = licenses.lgpl21Plus;
maintainers = with maintainers; [ natsukium ];
};
}
|
