942d0482e3
Instead of manually specifying the disabled tests and test paths in `checkPhase`, use the pytestCheckHook for that, and avoid the issue described at https://github.com/NixOS/nixpkgs/issues/255262 by removing the source directory.
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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, oldest-supported-numpy
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, setuptools-scm
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, wheel
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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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, pytestCheckHook
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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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gsl
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oldest-supported-numpy
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setuptools-scm
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wheel
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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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pytestCheckHook
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pytest-xdist
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scipy
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];
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disabledTests = [
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"tests/test_ancestry.py::TestSimulator::test_debug_logging"
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"tests/test_ancestry.py::TestSimulator::test_debug_logging_dtw"
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];
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disabledTestPaths = [
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"tests/test_demography.py"
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"tests/test_algorithms.py"
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"tests/test_provenance.py"
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"tests/test_dict_encoding.py"
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];
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# `python -m pytest` puts $PWD in sys.path, which causes the extension
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# modules imported as `msprime._msprime` to be unavailable, failing the
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# tests. This deletes the `msprime` folder such that only what's installed in
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# $out is used for the imports. See also discussion at:
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# https://github.com/NixOS/nixpkgs/issues/255262
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preCheck = ''
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rm -r msprime
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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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