pkgs/development/python-modules/msprime/default.nix

   1 {
   2   lib,
   3   buildPythonPackage,
   4   demes,
   5   fetchPypi,
   6   gsl,
   7   newick,
   8   numpy,
   9   oldest-supported-numpy,
  10   pytest-xdist,
  11   pytestCheckHook,
  12   pythonOlder,
  13   scipy,
  14   setuptools-scm,
  15   tskit,
  16   wheel,
  17 }:
  18
  19 buildPythonPackage rec {
  20   pname = "msprime";
  21   version = "1.3.3";
  22   pyproject = true;
  23
  24   disabled = pythonOlder "3.8";
  25
  26   src = fetchPypi {
  27     inherit pname version;
  28     hash = "sha256-2K55gHYWf2Mrj9fszVCJ+qqEyQNMppQi+IZCX5SlsBs=";
  29   };
  30
  31   postPatch = ''
  32     # build-time constriant, used to ensure forward and backward compat
  33     substituteInPlace pyproject.toml \
  34       --replace-fail "numpy>=2" "numpy"
  35   '';
  36
  37   nativeBuildInputs = [
  38     gsl
  39     oldest-supported-numpy
  40     setuptools-scm
  41     wheel
  42   ];
  43
  44   buildInputs = [ gsl ];
  45
  46   propagatedBuildInputs = [
  47     numpy
  48     newick
  49     tskit
  50     demes
  51   ];
  52
  53   nativeCheckInputs = [
  54     pytestCheckHook
  55     pytest-xdist
  56     scipy
  57   ];
  58
  59   disabledTests = [
  60     "tests/test_ancestry.py::TestSimulator::test_debug_logging"
  61     "tests/test_ancestry.py::TestSimulator::test_debug_logging_dtw"
  62   ];
  63
  64   disabledTestPaths = [
  65     "tests/test_demography.py"
  66     "tests/test_algorithms.py"
  67     "tests/test_provenance.py"
  68     "tests/test_dict_encoding.py"
  69   ];
  70
  71   # `python -m pytest` puts $PWD in sys.path, which causes the extension
  72   # modules imported as `msprime._msprime` to be unavailable, failing the
  73   # tests. This deletes the `msprime` folder such that only what's installed in
  74   # $out is used for the imports. See also discussion at:
  75   # https://github.com/NixOS/nixpkgs/issues/255262
  76   preCheck = ''
  77     rm -r msprime
  78   '';
  79   pythonImportsCheck = [ "msprime" ];
  80
  81   meta = with lib; {
  82     description = "Simulate genealogical trees and genomic sequence data using population genetic models";
  83     homepage = "https://github.com/tskit-dev/msprime";
  84     changelog = "https://github.com/tskit-dev/msprime/blob/${version}/CHANGELOG.md";
  85     license = licenses.gpl3Plus;
  86     maintainers = with maintainers; [ alxsimon ];
  87   };
  88 }