From d0dc560983dfef94fd73bdba1d6822304f5bec49 Mon Sep 17 00:00:00 2001 From: Pacho Ramos Date: Thu, 2 Jul 2026 12:09:27 +0200 Subject: [PATCH] sci-chemistry/MDAnalysis: add 2.10.0 Closes: https://bugs.gentoo.org/974083 Closes: https://bugs.gentoo.org/970033 Signed-off-by: Pacho Ramos --- .../MDAnalysis/MDAnalysis-2.10.0.ebuild | 56 +++++++++++++++++++ sci-chemistry/MDAnalysis/Manifest | 1 + 2 files changed, 57 insertions(+) create mode 100644 sci-chemistry/MDAnalysis/MDAnalysis-2.10.0.ebuild diff --git a/sci-chemistry/MDAnalysis/MDAnalysis-2.10.0.ebuild b/sci-chemistry/MDAnalysis/MDAnalysis-2.10.0.ebuild new file mode 100644 index 0000000000000..1451c3c0ad03e --- /dev/null +++ b/sci-chemistry/MDAnalysis/MDAnalysis-2.10.0.ebuild @@ -0,0 +1,56 @@ +# Copyright 1999-2026 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{12..14} ) + +DISTUTILS_USE_PEP517=setuptools +DISTUTILS_EXT=1 +PYPI_NO_NORMALIZE=1 + +inherit distutils-r1 + +DESCRIPTION="A python library to analyze and manipulate molecular dynamics trajectories" +HOMEPAGE="https://www.mdanalysis.org https://github.com/MDAnalysis/mdanalysis" +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="${RDEPEND} + dev-python/cython[${PYTHON_USEDEP}] +" + +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 +} diff --git a/sci-chemistry/MDAnalysis/Manifest b/sci-chemistry/MDAnalysis/Manifest index a3cbff31c9f34..7a7b7c6717542 100644 --- a/sci-chemistry/MDAnalysis/Manifest +++ b/sci-chemistry/MDAnalysis/Manifest @@ -1 +1,2 @@ +DIST MDAnalysis-2.10.0.gh.tar.gz 63494206 BLAKE2B 03fd8726bd5ef487bcf8475ada6a06d624a8da918a258aa8468469ea4de6e7ec3315e6cd7430a7beedd289a34640ebc4ba929ca86b83e95ee882a919dfd6a2a8 SHA512 b0fdbb4f75418be1b05a042b1be06320a0702c3dc7e50d3c161f1ade5f885e9548ec40c296b4bd65435e6552219142304dbe7db4c6af432feb2d2657f0071aa9 DIST MDAnalysis-2.9.0.gh.tar.gz 62932576 BLAKE2B 785c1919c383d646222943375e5ce7fa886c32d3db51ce3973da516cf629ce6081f2d16fe548cd32aaf9e5435374532266046fd54e8ad63870e7e3e17ef18c27 SHA512 fa13da003ede823a4a9ffb6e396f80a8b7e5a858431e9c0a78ded734d9872fa4f7ebf28e5e1a0bb45add5a2a9c05206be571371607879df0d5ff0eda750d1885