Ihar Hrachyshka
567e8dfd8e
This commit was created by a combination of scripts and tools: - an ast-grep script to prefix things in meta with `lib.`, - a modified nixf-diagnose / nixf combination to remove unused `with lib;`, and - regular nixfmt. Co-authored-by: Wolfgang Walther <walther@technowledgy.de>
89 lines
1.9 KiB
Nix
89 lines
1.9 KiB
Nix
{
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lib,
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buildPythonPackage,
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demes,
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fetchPypi,
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gsl,
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newick,
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numpy,
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oldest-supported-numpy,
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pytest-xdist,
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pytestCheckHook,
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pythonOlder,
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scipy,
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setuptools-scm,
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tskit,
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wheel,
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}:
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buildPythonPackage rec {
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pname = "msprime";
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version = "1.3.4";
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pyproject = true;
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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 = "sha256-0PlEo3pREx34zZZ5fyR5gXPEC6L/XAlFgdHKVvxRFzA=";
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};
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postPatch = ''
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# build-time constriant, used to ensure forward and backward compat
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substituteInPlace pyproject.toml \
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--replace-fail "numpy>=2" "numpy"
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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 = [ gsl ];
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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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# $out is used for the imports. See also discussion at:
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# https://github.com/NixOS/nixpkgs/issues/255262
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preCheck = ''
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rm -r msprime
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'';
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pythonImportsCheck = [ "msprime" ];
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meta = {
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description = "Simulate genealogical trees and genomic sequence data using population genetic models";
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homepage = "https://github.com/tskit-dev/msprime";
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changelog = "https://github.com/tskit-dev/msprime/blob/${version}/CHANGELOG.md";
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license = lib.licenses.gpl3Plus;
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maintainers = [ ];
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};
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}
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