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{
lib,
buildPythonPackage,
fetchFromGitHub,
fetchpatch,
setuptools,
cython,
click,
numpy,
scipy,
pandas,
h5py,
pytestCheckHook,
}:
buildPythonPackage rec {
pname = "biom-format";
version = "2.1.15";
pyproject = true;
src = fetchFromGitHub {
owner = "biocore";
repo = "biom-format";
rev = "refs/tags/${version}";
hash = "sha256-WRBc+C/UWme7wYogy4gH4KTIdIqU3KmBm2jWzGNxGQg=";
};
patches = [
# fixes a test, can be removed in next version after 2.1.15
(fetchpatch {
name = "fix-dataframe-comparison.patch";
url = "https://github.com/biocore/biom-format/commit/5d1c921ca2cde5d7332508503ce990a7209d1fdc.patch";
hash = "sha256-nyHi469ivjJSQ01yIk/6ZMXFdoo9wVuazJHnFdy2nBg=";
})
];
build-system = [
setuptools
cython
numpy
];
dependencies = [
click
numpy
scipy
pandas
h5py
];
# 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 ];
pytestFlagsArray = [ "biom_tests/tests" ];
pythonImportsCheck = [ "biom" ];
meta = {
homepage = "http://biom-format.org/";
description = "Biological Observation Matrix (BIOM) format";
license = lib.licenses.bsd3;
maintainers = with lib.maintainers; [ tomasajt ];
};
}
|
