1 files changed, 85 insertions, 0 deletions
diff --git a/nixpkgs/pkgs/development/python-modules/msprime/default.nix b/nixpkgs/pkgs/development/python-modules/msprime/default.nix
new file mode 100644
index 000000000000..c09b3b8d7609
--- /dev/null
+++ b/nixpkgs/pkgs/development/python-modules/msprime/default.nix
@@ -0,0 +1,85 @@
+{ lib
+, buildPythonPackage
+, demes
+, fetchPypi
+, gsl
+, newick
+, numpy
+, oldest-supported-numpy
+, pytest-xdist
+, pytestCheckHook
+, pythonOlder
+, scipy
+, setuptools-scm
+, tskit
+, wheel
+}:
+
+buildPythonPackage rec {
+  pname = "msprime";
+  version = "1.3.1";
+  pyproject = true;
+
+  disabled = pythonOlder "3.8";
+
+  src = fetchPypi {
+    inherit pname version;
+    hash = "sha256-s/Ys1RatLkPIQS6h8kKsrRvJOTkc/pyqGWJYdOLjSDU=";
+  };
+
+  nativeBuildInputs = [
+    gsl
+    oldest-supported-numpy
+    setuptools-scm
+    wheel
+  ];
+
+  buildInputs = [
+    gsl
+  ];
+
+  propagatedBuildInputs = [
+    numpy
+    newick
+    tskit
+    demes
+  ];
+
+  nativeCheckInputs = [
+    pytestCheckHook
+    pytest-xdist
+    scipy
+  ];
+
+  disabledTests = [
+    "tests/test_ancestry.py::TestSimulator::test_debug_logging"
+    "tests/test_ancestry.py::TestSimulator::test_debug_logging_dtw"
+  ];
+
+  disabledTestPaths = [
+    "tests/test_demography.py"
+    "tests/test_algorithms.py"
+    "tests/test_provenance.py"
+    "tests/test_dict_encoding.py"
+  ];
+
+  # `python -m pytest` puts $PWD in sys.path, which causes the extension
+  # modules imported as `msprime._msprime` to be unavailable, failing the
+  # tests. This deletes the `msprime` folder such that only what's installed in
+  # $out is used for the imports. See also discussion at:
+  # https://github.com/NixOS/nixpkgs/issues/255262
+  preCheck = ''
+    rm -r msprime
+  '';
+  pythonImportsCheck = [
+    "msprime"
+  ];
+
+  meta = with lib; {
+    description = "Simulate genealogical trees and genomic sequence data using population genetic models";
+    homepage = "https://github.com/tskit-dev/msprime";
+    changelog = "https://github.com/tskit-dev/msprime/blob/${version}/CHANGELOG.md";
+    license = licenses.gpl3Plus;
+    maintainers = with maintainers; [ alxsimon ];
+  };
+}