tjh.dev
nixpkgs mirror (for testing)
github.com/NixOS/nixpkgs
nix
python3.pkgs.msprime: use pytestCheckHook
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.
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+19
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pkgs/development/python-modules/msprime/default.nix
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pkgs/development/python-modules/msprime/default.nix
···
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, newick
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, tskit
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, demes
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-
, pytest
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, pytestCheckHook
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, pytest-xdist
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, scipy
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}:
···
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];
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nativeCheckInputs = [
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-
pytest
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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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checkPhase = ''
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runHook preCheck
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-
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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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-
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runHook postCheck
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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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-
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pythonImportsCheck = [
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"msprime"
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];