Gaetan Lepage
76 lines
1.5 KiB
Nix
76 lines
1.5 KiB
Nix
{
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lib,
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buildPythonPackage,
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fetchFromGitHub,
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# build-system
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cython,
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numpy,
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setuptools,
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# dependencies
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click,
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h5py,
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pandas,
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scipy,
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# tests
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pytestCheckHook,
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}:
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buildPythonPackage (finalAttrs: {
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pname = "biom-format";
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version = "2.1.17";
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pyproject = true;
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src = fetchFromGitHub {
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owner = "biocore";
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repo = "biom-format";
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tag = finalAttrs.version;
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hash = "sha256-FjIC21LoqltixBstbbANByjTNxVm/3YCxdWaD9KbOQ0=";
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};
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# https://numpy.org/doc/stable//release/2.4.0-notes.html#removed-numpy-in1d
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postPatch = ''
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substituteInPlace biom/table.py \
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--replace-fail "np.in1d" "np.isin"
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'';
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build-system = [
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cython
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numpy
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setuptools
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];
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dependencies = [
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click
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h5py
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numpy
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pandas
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scipy
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];
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# make pytest resolve the package from $out
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# some tests don't work if we change the level of directory nesting
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preCheck = ''
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mkdir biom_tests
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mv biom/tests biom_tests/tests
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rm -r biom
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'';
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nativeCheckInputs = [ pytestCheckHook ];
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enabledTestPaths = [ "biom_tests/tests" ];
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pythonImportsCheck = [ "biom" ];
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meta = {
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description = "Biological Observation Matrix (BIOM) format";
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homepage = "http://biom-format.org/";
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downloadPage = "https://github.com/biocore/biom-format";
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changelog = "https://github.com/biocore/biom-format/blob/${finalAttrs.src.tag}/ChangeLog.md";
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license = lib.licenses.bsd3;
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maintainers = with lib.maintainers; [ tomasajt ];
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};
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})
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