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{
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 ];
};
})
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