pyrox.dev
1{ lib
2, buildPythonPackage
3, fetchPypi
4, fetchpatch
5, oldest-supported-numpy
6, setuptools-scm
7, wheel
8, pythonOlder
9, gsl
10, numpy
11, newick
12, tskit
13, demes
14, pytestCheckHook
15, pytest-xdist
16, scipy
17}:
18
19buildPythonPackage rec {
20 pname = "msprime";
21 version = "1.2.0";
22 format = "pyproject";
23 disabled = pythonOlder "3.8";
24
25 src = fetchPypi {
26 inherit pname version;
27 hash = "sha256-YAJa2f0w2CenKubnYLbP8HodDhabLB2hAkyw/CPkp6o=";
28 };
29
30 patches = [
31 # upstream patch fixes 2 failing unittests. remove on update
32 (fetchpatch {
33 name = "python311.patch";
34 url = "https://github.com/tskit-dev/msprime/commit/639125ec942cb898cf4a80638f229e11ce393fbc.patch";
35 hash = "sha256-peli4tdu8Bv21xIa5H8SRdfjQnTMO72IPFqybmSBSO8=";
36 includes = [ "tests/test_ancestry.py" ];
37 })
38 ];
39
40 nativeBuildInputs = [
41 gsl
42 oldest-supported-numpy
43 setuptools-scm
44 wheel
45 ];
46
47 buildInputs = [
48 gsl
49 ];
50
51 propagatedBuildInputs = [
52 numpy
53 newick
54 tskit
55 demes
56 ];
57
58 nativeCheckInputs = [
59 pytestCheckHook
60 pytest-xdist
61 scipy
62 ];
63 disabledTests = [
64 "tests/test_ancestry.py::TestSimulator::test_debug_logging"
65 "tests/test_ancestry.py::TestSimulator::test_debug_logging_dtw"
66 ];
67 disabledTestPaths = [
68 "tests/test_demography.py"
69 "tests/test_algorithms.py"
70 "tests/test_provenance.py"
71 "tests/test_dict_encoding.py"
72 ];
73
74 # `python -m pytest` puts $PWD in sys.path, which causes the extension
75 # modules imported as `msprime._msprime` to be unavailable, failing the
76 # tests. This deletes the `msprime` folder such that only what's installed in
77 # $out is used for the imports. See also discussion at:
78 # https://github.com/NixOS/nixpkgs/issues/255262
79 preCheck = ''
80 rm -r msprime
81 '';
82 pythonImportsCheck = [
83 "msprime"
84 ];
85
86 meta = with lib; {
87 description = "Simulate genealogical trees and genomic sequence data using population genetic models";
88 homepage = "https://github.com/tskit-dev/msprime";
89 license = licenses.gpl3Plus;
90 maintainers = with maintainers; [ alxsimon ];
91 };
92}