mirror of
https://github.com/NixOS/nixpkgs.git
synced 2026-06-13 16:53:53 +00:00
86 lines
1.9 KiB
Nix
86 lines
1.9 KiB
Nix
{
|
|
lib,
|
|
buildPythonPackage,
|
|
demes,
|
|
fetchPypi,
|
|
gsl,
|
|
newick,
|
|
numpy,
|
|
oldest-supported-numpy,
|
|
pytest-xdist,
|
|
pytestCheckHook,
|
|
scipy,
|
|
setuptools-scm,
|
|
tskit,
|
|
wheel,
|
|
}:
|
|
|
|
buildPythonPackage rec {
|
|
pname = "msprime";
|
|
version = "1.4.2";
|
|
pyproject = true;
|
|
|
|
src = fetchPypi {
|
|
inherit pname version;
|
|
hash = "sha256-hpGz7fdPl5ZBFieXDmps0Q7Fhcmr9K3ULZPimzhl/SI=";
|
|
};
|
|
|
|
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 = [ ];
|
|
};
|
|
}
|