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{
lib,
fetchFromGitHub,
buildPythonPackage,
numpy,
pyparsing,
cython,
zlib,
python-lzo,
pytestCheckHook,
setuptools,
oldest-supported-numpy,
}:
buildPythonPackage rec {
pname = "bx-python";
version = "0.14.0";
pyproject = true;
src = fetchFromGitHub {
owner = "bxlab";
repo = "bx-python";
tag = "v${version}";
hash = "sha256-WZjCPggAlC+L/SagC4TXJXNrFG85BmjO7FaV2GxrYYA=";
};
postPatch = ''
# pytest-cython, which provides this option, isn't packaged
substituteInPlace pytest.ini \
--replace-fail "--doctest-cython" ""
'';
build-system = [
setuptools
cython
oldest-supported-numpy
];
buildInputs = [ zlib ];
dependencies = [
numpy
pyparsing
];
nativeCheckInputs = [
python-lzo
pytestCheckHook
];
# https://github.com/bxlab/bx-python/issues/101
doCheck = false;
postInstall = ''
cp -r scripts/* $out/bin
# This is a small hack; the test suite uses the scripts which need to
# be patched. Linking the patched scripts in $out back to the
# working directory allows the tests to run
rm -rf scripts
ln -s $out/bin scripts
'';
meta = {
description = "Tools for manipulating biological data, particularly multiple sequence alignments";
homepage = "https://github.com/bxlab/bx-python";
changelog = "https://github.com/bxlab/bx-python/releases/tag/${src.tag}";
license = lib.licenses.mit;
maintainers = with lib.maintainers; [ jbedo ];
platforms = [ "x86_64-linux" ];
};
}
|
