python310Packages.msprime: init at version 1.2.0

Co-authored-by: OTABI Tomoya <tomoya.otabi@gmail.com>

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

@@ -0,0 +1,81 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+, setuptools-scm
+, pythonOlder
+, gsl
+, numpy
+, newick
+, tskit
+, demes
+, pytest
+, pytest-xdist
+, scipy
+}:
+
+buildPythonPackage rec {
+  pname = "msprime";
+  version = "1.2.0";
+  format = "pyproject";
+  disabled = pythonOlder "3.8";
+
+  src = fetchPypi {
+    inherit pname version;
+    hash = "sha256-YAJa2f0w2CenKubnYLbP8HodDhabLB2hAkyw/CPkp6o=";
+  };
+
+  nativeBuildInputs = [
+    setuptools-scm
+    gsl
+  ];
+
+  buildInputs = [
+    gsl
+  ];
+
+  propagatedBuildInputs = [
+    numpy
+    newick
+    tskit
+    demes
+  ];
+
+  nativeCheckInputs = [
+    pytest
+    pytest-xdist
+    scipy
+  ];
+
+  checkPhase = ''
+    runHook preCheck
+
+    # avoid adding the current directory to sys.path
+    # https://docs.pytest.org/en/7.1.x/explanation/pythonpath.html#invoking-pytest-versus-python-m-pytest
+    # need pythonPackages.stdpopsim
+    # need pythonPackages.bintrees
+    # need pythonPachages.python_jsonschema_objects
+    # ModuleNotFoundError: No module named 'lwt_interface.dict_encoding_testlib'
+    # fails for python311
+    # fails for python311
+    pytest -v --import-mode append \
+      --ignore=tests/test_demography.py \
+      --ignore=tests/test_algorithms.py \
+      --ignore=tests/test_provenance.py \
+      --ignore=tests/test_dict_encoding.py \
+      --deselect=tests/test_ancestry.py::TestSimulator::test_debug_logging \
+      --deselect=tests/test_ancestry.py::TestSimulator::test_debug_logging_dtwf
+
+    runHook postCheck
+  '';
+
+  pythonImportsCheck = [
+    "msprime"
+  ];
+
+  meta = with lib; {
+    description = "Simulate genealogical trees and genomic sequence data using population genetic models";
+    homepage = "https://github.com/tskit-dev/msprime";
+    license = licenses.gpl3Plus;
+    maintainers = with maintainers; [ alxsimon ];
+  };
+}

pkgs/top-level/python-packages.nix

@@ -6526,6 +6526,8 @@ self: super: with self; {
 
   msoffcrypto-tool = callPackage ../development/python-modules/msoffcrypto-tool { };
 
+  msprime = callPackage ../development/python-modules/msprime { };
+
   mss = callPackage ../development/python-modules/mss { };
 
   msrestazure = callPackage ../development/python-modules/msrestazure { };