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