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{
lib,
buildPythonPackage,
demes,
fetchPypi,
gsl,
newick,
numpy,
oldest-supported-numpy,
pytest-xdist,
pytestCheckHook,
scipy,
setuptools-scm,
tskit,
wheel,
}:
buildPythonPackage rec {
pname = "msprime";
version = "1.3.4";
pyproject = true;
src = fetchPypi {
inherit pname version;
hash = "sha256-0PlEo3pREx34zZZ5fyR5gXPEC6L/XAlFgdHKVvxRFzA=";
};
postPatch = ''
# build-time constriant, used to ensure forward and backward compat
substituteInPlace pyproject.toml \
--replace-fail "numpy>=2" "numpy"
'';
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
# $out is used for the imports. See also discussion at:
# https://github.com/NixOS/nixpkgs/issues/255262
preCheck = ''
rm -r msprime
'';
pythonImportsCheck = [ "msprime" ];
meta = {
description = "Simulate genealogical trees and genomic sequence data using population genetic models";
homepage = "https://github.com/tskit-dev/msprime";
changelog = "https://github.com/tskit-dev/msprime/blob/${version}/CHANGELOG.md";
license = lib.licenses.gpl3Plus;
maintainers = [ ];
};
}
|
