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{ lib
, buildPythonPackage
, fetchPypi
, oldest-supported-numpy
, setuptools-scm
, wheel
, 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 = [
gsl
oldest-supported-numpy
setuptools-scm
wheel
];
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 ];
};
}
|
