sci-chemistry/MDAnalysis: add 2.10.0

Closes: https://bugs.gentoo.org/974083
Closes: https://bugs.gentoo.org/970033
Signed-off-by: Pacho Ramos <pacho@gentoo.org>

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
+}

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