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# Copyright 1999-2026 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=8
PYTHON_COMPAT=( python3_{12..13} )
DISTUTILS_USE_PEP517=setuptools
PYPI_NO_NORMALIZE=1
inherit distutils-r1
DESCRIPTION="A python library to analyze and manipulate molecular dynamics trajectories"
HOMEPAGE="https://www.mdanalysis.org"
SRC_URI="https://github.com/${PN}/${PN}/archive/refs/tags/package-${PV}.tar.gz -> ${P}.gh.tar.gz"
S="${WORKDIR}/mdanalysis-package-${PV}/package"
LICENSE="GPL-2"
SLOT="0"
KEYWORDS="~amd64"
# TODO: fix this
# ImportError: MDAnalysis not installed properly. This can happen if your C extensions have not been built.
RESTRICT="test"
RDEPEND="
>=dev-python/numpy-1.16.0[${PYTHON_USEDEP}]
>=dev-python/scipy-1.0.0[${PYTHON_USEDEP}]
>=sci-biology/biopython-1.71[${PYTHON_USEDEP}]
>=dev-python/networkx-1.0[${PYTHON_USEDEP}]
>=dev-python/griddataformats-0.4.0[${PYTHON_USEDEP}]
>=dev-python/joblib-0.12[${PYTHON_USEDEP}]
>=dev-python/matplotlib-1.5.1[${PYTHON_USEDEP}]
>=dev-python/mmtf-python-1.0.0[${PYTHON_USEDEP}]
>=dev-python/tqdm-4.43.0[${PYTHON_USEDEP}]
>=dev-python/gsd-1.9.3[${PYTHON_USEDEP}]
dev-python/threadpoolctl[${PYTHON_USEDEP}]
"
BDEPEND="${RDEPEND}"
distutils_enable_tests pytest
src_prepare() {
# fix deprecated NPY API
sed \
-e "s:NPY_IN_ARRAY:NPY_ARRAY_IN_ARRAY:g" \
-e "s:NPY_ALIGNED:NPY_ARRAY_ALIGNED:g" \
-e "s:NPY_ENSURECOPY:NPY_ARRAY_ENSURECOPY:g" \
-i MDAnalysis/lib/src/transformations/transformations.c || die
distutils-r1_src_prepare
}
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