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12345678910111213141516171819202122232425262728293031323334353637383940414243444546474849505152535455565758596061626364656667686970717273747576{ lib, buildPythonPackage, fetchFromGitHub,
# build-system cython, numpy, setuptools,
# dependencies click, h5py, pandas, scipy,
# tests pytestCheckHook,}:
buildPythonPackage (finalAttrs: { pname = "biom-format"; version = "2.1.17"; pyproject = true;
src = fetchFromGitHub { owner = "biocore"; repo = "biom-format"; tag = finalAttrs.version; hash = "sha256-FjIC21LoqltixBstbbANByjTNxVm/3YCxdWaD9KbOQ0="; };
# https://numpy.org/doc/stable//release/2.4.0-notes.html#removed-numpy-in1d postPatch = '' substituteInPlace biom/table.py \ --replace-fail "np.in1d" "np.isin" '';
build-system = [ cython numpy setuptools ];
dependencies = [ click h5py numpy pandas scipy ];
# make pytest resolve the package from $out # some tests don't work if we change the level of directory nesting preCheck = '' mkdir biom_tests mv biom/tests biom_tests/tests rm -r biom '';
nativeCheckInputs = [ pytestCheckHook ];
enabledTestPaths = [ "biom_tests/tests" ];
pythonImportsCheck = [ "biom" ];
meta = { description = "Biological Observation Matrix (BIOM) format"; homepage = "http://biom-format.org/"; downloadPage = "https://github.com/biocore/biom-format"; changelog = "https://github.com/biocore/biom-format/blob/${finalAttrs.src.tag}/ChangeLog.md"; license = lib.licenses.bsd3; maintainers = with lib.maintainers; [ tomasajt ]; };})