commit: 10caada046daf3195d2df0285b6dbad230a18e3e Author: Nicolas PARLANT <nicolas.parlant <AT> parhuet <DOT> fr> AuthorDate: Fri Feb 13 09:20:17 2026 +0000 Commit: Sam James <sam <AT> gentoo <DOT> org> CommitDate: Sat Feb 14 05:17:17 2026 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=10caada0
sci-libs/avogadrolibs: add 1.103.0 jkqtplotter is now optional, restore genXrd for amd64 Signed-off-by: Nicolas PARLANT <nicolas.parlant <AT> parhuet.fr> Part-of: https://codeberg.org/gentoo/gentoo/pulls/48 Signed-off-by: Sam James <sam <AT> gentoo.org> sci-libs/avogadrolibs/Manifest | 6 + sci-libs/avogadrolibs/avogadrolibs-1.103.0.ebuild | 215 ++++++++++++++++++++++ sci-libs/avogadrolibs/metadata.xml | 1 + 3 files changed, 222 insertions(+) diff --git a/sci-libs/avogadrolibs/Manifest b/sci-libs/avogadrolibs/Manifest index 2a53139e3177..4736d34f4098 100644 --- a/sci-libs/avogadrolibs/Manifest +++ b/sci-libs/avogadrolibs/Manifest @@ -2,12 +2,18 @@ DIST avogadrolibs-1.101.0-data.tar.gz 18043657 BLAKE2B 469d1b675c1ca39577f50db33 DIST avogadrolibs-1.101.0.tar.gz 4714237 BLAKE2B fddb27e8d59f4bd8664c35f1a29c769487ea5d8a75671a6720aadf926e8f8d9c439dd3d68b3aefc8e57df8451d872238fca116b2a33a30ddaa7921f797e9e8ad SHA512 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9b9fe03631822bb7df19259acaebc5fdb8e7050e646bd08bfbb48e1335c73dda14e1386a82e85f379df8c8498d9e77ef75bad97e809df954d3b3b45135929523 DIST avogadrolibs-molecules-1.102.1.tar.gz 9979117 BLAKE2B 73acd92d9eaddddfeff5cba83611039b502f712025bf6ee80f22ade18415ff77ec826b07f0f8b1c11129ae76b1e257ff44afff64597b963c29673b6962c426ea SHA512 839321afc1c1267dd74a8cace70f3ef7126e83ab4f9668cf4fe4eeb05049152c86a8878efb16c8a788cc06c5341ca5ae6a32cc5d6cee6938f5bdb797ca43bbeb +DIST avogadrolibs-molecules-1.103.0.tar.gz 9978990 BLAKE2B 151cf8fde97fa1a88d21a373351aa5825e4b1b7043fb74b713cda5610e8af0d9266cd4c9f1a778bf43e323cfaa7dbc4731ac34e3d0fb2182610529a823d1220b SHA512 d3ebcc4f5da4e5f92e6e36e2ccfdce74a8f109408e2ff604dc31179db949fafce572d41e3e12545482429b2e75d77771a46aaf33f80675faf47a5acc88fec047 diff --git a/sci-libs/avogadrolibs/avogadrolibs-1.103.0.ebuild b/sci-libs/avogadrolibs/avogadrolibs-1.103.0.ebuild new file mode 100644 index 000000000000..2014484abb2c --- /dev/null +++ b/sci-libs/avogadrolibs/avogadrolibs-1.103.0.ebuild @@ -0,0 +1,215 @@ +# Copyright 1999-2026 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{11..14} ) +inherit cmake dot-a python-single-r1 + +MY_PV_GENXRD=1.1 +MY_PV_AVOGEN=${PV} +MY_PV_CRYSTALS=${PV} +MY_PV_FRAGMENTS=${PV} +MY_PV_MOLECULES=${PV} + +DESCRIPTION="Advanced molecule editor and visualizer 2 - libraries" +HOMEPAGE="https://two.avogadro.cc/ https://www.openchemistry.org/"; +SRC_URI=" + https://github.com/OpenChemistry/${PN}/archive/${PV}.tar.gz + -> ${P}.tar.gz + qt6? ( + https://github.com/OpenChemistry/avogenerators/archive/refs/tags/${MY_PV_AVOGEN}.tar.gz + -> ${PN}-avogenerators-${MY_PV_AVOGEN}.tar.gz + https://github.com/OpenChemistry/crystals/archive/refs/tags/${MY_PV_CRYSTALS}.tar.gz + -> ${PN}-crystals-${MY_PV_CRYSTALS}.tar.gz + https://github.com/OpenChemistry/fragments/archive/refs/tags/${MY_PV_FRAGMENTS}.tar.gz + -> ${PN}-fragments-${MY_PV_FRAGMENTS}.tar.gz + https://github.com/OpenChemistry/molecules/archive/refs/tags/${MY_PV_MOLECULES}.tar.gz + -> ${PN}-molecules-${MY_PV_MOLECULES}.tar.gz + ) + jkqtplotter? ( + amd64? ( https://github.com/psavery/genXrdPattern/releases/download/${MY_PV_GENXRD}-linux/linux64-genXrdPattern + -> ${PN}-linux64-genXrdPattern-${MY_PV_GENXRD} ) + ) + test? ( https://github.com/OpenChemistry/avogadrodata/archive/refs/tags/${PV}.tar.gz + -> ${P}-data.tar.gz ) +" + +LICENSE="BSD GPL-2+" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="archive doc hdf5 jkqtplotter python qt6 spglib static-libs test" +RESTRICT="!test? ( test )" +REQUIRED_USE=" + jkqtplotter? ( qt6 ) + python? ( ${PYTHON_REQUIRED_USE} ) + test? ( qt6 ) +" + +# TODO: Not yet packaged: +# sci-libs/libmsym (https://github.com/mcodev31/libmsym) +RDEPEND=" + dev-cpp/nlohmann_json + dev-libs/pugixml + hdf5? ( sci-libs/hdf5:= ) + python? ( + ${PYTHON_DEPS} + $(python_gen_cond_dep 'dev-python/pybind11[${PYTHON_USEDEP}]') + ) + qt6? ( + dev-qt/qtbase:6[concurrent,gui,network,opengl,widgets] + dev-qt/qtsvg:6 + media-libs/glew:0= + >=sci-chemistry/openbabel-3.1.1_p20241221:=[json] + virtual/opengl + archive? ( app-arch/libarchive:= ) + jkqtplotter? ( sci-libs/jkqtplotter:= ) + ) + spglib? ( >=sci-libs/spglib-2.6.0:= ) +" +DEPEND=" + ${RDEPEND} + dev-cpp/eigen:3 +" +BDEPEND=" + doc? ( app-text/doxygen ) + test? ( dev-cpp/gtest ) +" + +PATCHES=( + "${FILESDIR}/"${PN}-1.91.0_pre20180406-bundled-genxrdpattern.patch +) + +# Static binary (requires ObjCryst++ to build otherwise) +QA_FLAGS_IGNORED="usr/bin/genXrdPattern" + +pkg_setup() { + use python && python-single-r1_pkg_setup +} + +src_unpack() { + default + + rm -rf thirdparty/{nlohmann,pugixml} || die + + if use jkqtplotter && use amd64; then + cp "${DISTDIR}"/${PN}-linux64-genXrdPattern-${MY_PV_GENXRD} "${WORKDIR}/genXrdPattern" || die + fi + + if use qt6; then + # hardcoded assumptions in + # avogadro/qtplugins/insertfragment/CMakeLists.txt + mv crystals-${MY_PV_CRYSTALS} crystals || die + mv molecules-${MY_PV_MOLECULES} molecules || die + # avogadro/qtplugins/quantuminput/CMakeLists.txt + mv avogenerators-${MY_PV_AVOGEN} avogenerators || die + # avogadro/qtplugins/templatetool/CMakeLists.txt + mv fragments-${MY_PV_FRAGMENTS} fragments || die + fi + + if use test; then + mv avogadrodata-${PV} avogadrodata || die + fi +} + +src_prepare() { + # fix default value for BABEL_LIBDIR + sed -i -e "s:/../lib/openbabel:/../$(get_libdir)/openbabel:g" \ + avogadro/qtplugins/forcefield/obenergy.cpp \ + avogadro/qtplugins/forcefield/obmmenergy.cpp \ + avogadro/qtplugins/openbabel/obprocess.cpp || die + + # avoid cmake_min warning w/ this unused file + rm thirdparty/tinycolormap/CMakeLists.txt || die + + if use doc; then + doxygen -u docs/doxyfile.in 2>/dev/null || die + fi + + # restore user-LDFLAGS + if use python; then + sed -e 's:CMAKE_MODULE_LINKER_FLAGS "":CMAKE_MODULE_LINKER_FLAGS "'"${LDFLAGS}"'":' \ + -i "${S}"/python/CMakeLists.txt || die + fi + + cmake_src_prepare +} + +src_configure() { + local mycmakeargs=( + -DCMAKE_SKIP_RPATH=ON + -DUSE_EXTERNAL_NLOHMANN=ON + -DUSE_EXTERNAL_PUGIXML=ON + -DUSE_LIBARCHIVE=$(usex archive $(usex qt6)) + -DBUILD_DOCUMENTATION=$(usex doc) + -DUSE_HDF5=$(usex hdf5) + # https://github.com/OpenChemistry/avogadrolibs/issues/2200 + -DUSE_MMTF=OFF + -DUSE_OPENGL=$(usex qt6) + -DUSE_PLOTTER=$(usex jkqtplotter) + -DUSE_PYTHON=$(usex python) + -DUSE_QT=$(usex qt6) + -DUSE_SPGLIB=$(usex spglib) + -DENABLE_TESTING=$(usex test) + # disabled libraries + -DUSE_LIBMSYM=OFF + ) + + if use jkqtplotter && use amd64; then + mycmakeargs+=( + -DBUNDLED_GENXRDPATTERN="${WORKDIR}/genXrdPattern" + -DUSE_SYSTEM_GENXRDPATTERN=OFF + ) + fi + + if use qt6; then + mycmakeargs+=( + -DBUILD_GPL_PLUGINS=ON + -DBUILD_STATIC_PLUGINS=$(usex static-libs) + -DQT_VERSION=6 + ) + # use python's abilities to define the interpreter path for qtplugins, + # it can also be set with: + # - AVO_PYTHON_INTERPRETER (absolute path) + # - extensions settings + # otherwise default is python + use python && mycmakeargs+=( -DPython3_EXECUTABLE="${PYTHON}" ) + + # even w/o static-libs due to libgwavi.a, required for avogadro2 + lto-guarantee-fat + fi + + cmake_src_configure +} + +src_compile() { + cmake_src_compile + + use doc && cmake_build documentation +} + +src_test() { + local -x LD_LIBRARY_PATH="${BUILD_DIR}/lib" + cmake_src_test +} + +src_install() { + if use doc; then + local DOCS+=( "${BUILD_DIR}"/docs/xml ) + local HTML_DOCS=( "${BUILD_DIR}"/docs/html/. ) + docompress -x /usr/share/doc/${PF}/xml + fi + + cmake_src_install + + if use python; then + python_fix_shebang "${ED}" + python_optimize "${ED}" + fi + + # always strip due to libgwavi.a + use qt6 && strip-lto-bytecode "${ED}" + + # remove CONTRIBUTING, LICENSE and duplicate README + rm -r "${ED}/usr/share/doc/${PF}/avogadrolibs" || die +} diff --git a/sci-libs/avogadrolibs/metadata.xml b/sci-libs/avogadrolibs/metadata.xml index f06ec6e3cfc5..74296c075dd7 100644 --- a/sci-libs/avogadrolibs/metadata.xml +++ b/sci-libs/avogadrolibs/metadata.xml @@ -7,6 +7,7 @@ </maintainer> <use> <flag name="archive">Enable archive support using <pkg>app-arch/libarchive</pkg></flag> + <flag name="jkqtplotter">Enable charts and spectra using <pkg>sci-libs/jkqtplotter</pkg></flag> <flag name="spglib">Find and set the Hall number for a crystal using <pkg>sci-libs/spglib</pkg></flag> <flag name="vtk">Enable <pkg>sci-libs/vtk</pkg> support</flag> </use>
