commit: 8b295bba664c496c6e923c02313b3808300cd75a Author: Nicolas PARLANT <nicolas.parlant <AT> parhuet <DOT> fr> AuthorDate: Tue Mar 11 14:28:07 2025 +0000 Commit: Sam James <sam <AT> gentoo <DOT> org> CommitDate: Mon Mar 24 09:30:11 2025 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=8b295bba
sci-libs/avogadrolibs: add 1.100.0, qt6 update HOMEPAGE switch to qt6 iuse : add spglib (Hall number for a crystal using sci-libs/spglib) fetch avogadrodata for more tests deps : rm molequeue, abandoned and without Qt6 support, client-only bundled rm linguist-tools, no longer required (qm) add dev-cpp/nlohmann_json (since 1.98) add dev-libs/pugixml (since 1.98) add sci-chemistry/openbabel[json] (qtplugins) add dev-libs/mmtf-cpp (mmtf useflag) build opt : rm USE_PROTOCALL (dropped since 1.98.0) rm BUILD_STATIC_PLUGINS, on by default rm OpenGL_GL_PREFERENCE=GLVND, value by default add USE_SYSTEM_GENXRDPATTERN=OFF to use workaround w/ DownloadGenXrdPattern patches : cmake detection for openbabel conditionnal test: Spacegroup (spglib) Closes: https://bugs.gentoo.org/926352 Signed-off-by: Nicolas PARLANT <nicolas.parlant <AT> parhuet.fr> Signed-off-by: Sam James <sam <AT> gentoo.org> sci-libs/avogadrolibs/Manifest | 7 + sci-libs/avogadrolibs/avogadrolibs-1.100.0.ebuild | 174 +++++++++++++++++++++ .../files/avogadrolibs-1.100-fix-openbabel3.patch | 13 ++ .../files/avogadrolibs-1.100-tests.patch | 21 +++ sci-libs/avogadrolibs/metadata.xml | 2 + 5 files changed, 217 insertions(+) diff --git a/sci-libs/avogadrolibs/Manifest b/sci-libs/avogadrolibs/Manifest index af9a44e3a35f..c615c4afbd3c 100644 --- a/sci-libs/avogadrolibs/Manifest +++ b/sci-libs/avogadrolibs/Manifest @@ -1,4 +1,11 @@ +DIST avogadrolibs-1.100.0-data.tar.gz 17378761 BLAKE2B 6900869f5056b02648a95bcacb98f35689f6b90f57f920c2678a0b8f7c043d4adc37b5c83de671ba7554b040a898bcaaa6cb36f29df84ce5221ee9f706ee93ff SHA512 71616ab1c197919fe1337654e698c0a52d86266bf64ca9453b89913c957b473c74e58a8a9483682dbaba56d296a2f56154bd94e5fdf9e4795b7457371215b0c3 +DIST avogadrolibs-1.100.0.tar.gz 4979722 BLAKE2B 1a47d9636ff5c978e2fbe84f782b8bd9b24fd23b44de93bd2b9f7790d3e077a92e2ac62a3823466ffd0e8ec664514d18c47ef5d0ff874d83b4c7571e046960d2 SHA512 8f0e9a6659a3190b12667da948468b83952e5017929ab802e4153682ed8b1a8ac97e874c20773c45e6e5c67fb3d2fd0ae55e99e49a8d03305b5a66e87ccbd2fd DIST avogadrolibs-1.97.0.tar.gz 11456702 BLAKE2B 2f9229a0525dc151ef636c4c101ea21d3713efb033f6a007c43689bfd078b07081d695bb3ec32715c3ccf9d67e7bb85a617a08eeb0e6fc8c80e479a3cb3f1553 SHA512 a0ad3ba294db5f0fff35087ff0f616fdcaefc7b4abfa470c9fd26326ad14f73e3584c18a7111b671998d8a23a50091307520f01f79295fc7ea52ae2d78716c7e +DIST avogadrolibs-avogenerators-1.98.0.tar.gz 15676 BLAKE2B 647050636cd93e2055dacbd5c8c1c7b98b1c61ac891b836ec990d75be80ff62c452f54d7225550b9fd5e4126c1b9cf3d806121d759aabca571bfff5e6bc69028 SHA512 87f42a538af6418ce33813b8e263ca349dca455142f476413b93ba9b0c5762b7e66f8fc1cd2535a5e284b6df3e7acc226fd7c223d1d20318fca9fa69536c6f4e DIST avogadrolibs-crystals-1.0.1.tar.gz 151829 BLAKE2B 0a1353392a4c087977452f50ffb7db0b2976a2993651b6f7e0df7a9ce6fa8f7960223cac2916dd9f667d37518b85606d73d05e86f7489193a6a609700fc60223 SHA512 c5d6500d8472807b8d2e62888e4a09279c6aeafec81bc4981edaa74e36724b1e7f0381250c79ad297f9f0331bcb5cd8a45fce3f13ad65b9870e901a6424c0650 +DIST avogadrolibs-crystals-1.98.0.tar.gz 55935019 BLAKE2B 1750369af8a259bdccb3b0babf4e46ecc7f780f12ff8d00fcc230c7d3689bdc690bd9856ece49afca1b0f4b717360462577e618a54351c80c983a1d90de58065 SHA512 3ed07b598841c8dbc1536bd8f2a992abe73e1dc13bb9c14a4db0b60be7ba085c834d982ceb22ade3a5f0f4d05a7681567bd0c926995e78ebb9d56e2923bd4706 +DIST avogadrolibs-fragments-1.99.0.tar.gz 2553232 BLAKE2B 3d2b25bbf73e0c239634726005fb737a88199882059a8f0f57638749e06593d6156df382957126d8bc010ab75b1de872de64e559d56921a51d442d915c9cd389 SHA512 fa1341a482f184960a0167c601e3bd8faac2f4e312c7a603146c63ad563cb3b943e37c0d3fe785eb134c0bf4dd3dda6e21b8276e760237f5b6b2e883af5a268a +DIST avogadrolibs-linux64-genXrdPattern-1.1 14315976 BLAKE2B bed67aa2bb015843c20af8b89e1276a3e509cbebb32b36bb4002cb8fcfa557acfeefff37ccae2b7d67ca80e09f654c924c6d6227d1d0e1fcfa43438aef81de08 SHA512 e98395e1dd831779af7a613e9c6460a4f048e0a7973d6156e8ebd0bebe2d32b4c19df9875e91185b73ddc6f0d3637d35e955b3bd393c0893986555763b61492a DIST avogadrolibs-molecules-1.0.0.tar.gz 206924 BLAKE2B 70eea3d5eb440ab2c7f29c56111f2b8cf780cc84983aa145bc4f2fe144c981978218333ba3c33cf1f620dd3180cca706dfa4e94ffaee6167f89bd3e372172218 SHA512 06891ea7ad3e65c5b0c0ad73ea01916478fcd13fd9ff0d6905d28159678a50371ba9fa2c1f68ef32604dee0c2165de29bd5d50ffbc345bfe752ef0bcb13126f2 +DIST avogadrolibs-molecules-1.98.0.tar.gz 9953630 BLAKE2B eabc9604a68efb5db912c45ec19b731e51d5405e50dad597289f07ce1faeca9c2c296b9005ecfe21c2695ca9d536d79ec42e7e58aa6fb67f753187abc6f96649 SHA512 297bf73b290c099267ff011c68f40c636094a9ca632be7bc6d71db99d55eb16bfa9b1eee7504ada8a15534690aa80840e7d731880346fcd8b68e08b00b1e2bf6 DIST linux64-genXrdPattern-avogadrolibs-1.97.0 7480152 BLAKE2B dca8285c41aadfaa20c72f337e0f02db8ee07ce30c11ae84bf3aa7bd0b2220273d33f484d63f761d41a8946c6a0b77a0fb27906c480bcae01ae49b1531ae5cbb SHA512 538bde12e1e52600a21640d5907f43fcc853c6f3c111880f39eb238093e3d1358ccdfa1f45e944ec8b8e5ee3c2dff269cefe5334db5d73300e6ca327c95520b8 diff --git a/sci-libs/avogadrolibs/avogadrolibs-1.100.0.ebuild b/sci-libs/avogadrolibs/avogadrolibs-1.100.0.ebuild new file mode 100644 index 000000000000..19472b5c3b31 --- /dev/null +++ b/sci-libs/avogadrolibs/avogadrolibs-1.100.0.ebuild @@ -0,0 +1,174 @@ +# Copyright 1999-2025 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit cmake + +MY_PV_AVOGEN=1.98.0 +MY_PV_CRYSTALS=1.98.0 +MY_PV_FRAGMENTS=1.99.0 +MY_PV_GENXRD=1.1 +MY_PV_MOLECULES=1.98.0 + +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 + ) + test? ( https://github.com/OpenChemistry/avogadrodata/archive/refs/tags/${PV}.tar.gz + -> ${P}-data.tar.gz ) + vtk? ( https://github.com/psavery/genXrdPattern/releases/download/${MY_PV_GENXRD}-linux/linux64-genXrdPattern + -> ${PN}-linux64-genXrdPattern-${MY_PV_GENXRD} ) +" + +LICENSE="BSD GPL-2+" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="archive doc hdf5 mmtf qt6 spglib test vtk" +RESTRICT="!test? ( test )" +REQUIRED_USE=" + test? ( qt6 ) + vtk? ( 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:= ) + qt6? ( + >=sci-chemistry/openbabel-3.1.1_p20241221:=[json] + dev-qt/qtbase:6[concurrent,gui,network,opengl,widgets] + dev-qt/qtsvg:6 + media-libs/glew:0= + virtual/opengl + archive? ( app-arch/libarchive:= ) + ) + spglib? ( >=sci-libs/spglib-2.6.0:= ) + vtk? ( sci-libs/vtk:=[qt6,views] ) +" +DEPEND="${RDEPEND} + dev-cpp/eigen:3 + mmtf? ( dev-libs/mmtf-cpp ) +" +BDEPEND=" + doc? ( app-text/doxygen ) + test? ( dev-cpp/gtest ) +" + +PATCHES=( + "${FILESDIR}/"${PN}-1.91.0_pre20180406-bundled-genxrdpattern.patch + "${FILESDIR}/"${PN}-1.100-tests.patch + # https://github.com/OpenChemistry/avogadrolibs/issues/1633 + "${FILESDIR}/"${PN}-1.100-fix-openbabel3.patch +) + +# Static binary (requires ObjCryst++ to build otherwise) +QA_FLAGS_IGNORED="usr/bin/genXrdPattern" + +src_unpack() { + default + + rm -rf thirdparty/{nlohmann,pugixml} || die + + if use vtk; then + cp "${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} avogadrogenerators || 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:/../$(get_libdir)/openbabel:g" \ + avogadro/qtplugins/forcefield/obenergy.cpp \ + avogadro/qtplugins/forcefield/obmmenergy.cpp \ + avogadro/qtplugins/openbabel/obprocess.cpp || die + + if use doc; then + doxygen -u docs/doxyfile.in 2>/dev/null || die + fi + + cmake_src_prepare +} + +src_configure() { + local mycmakeargs=( + -DCMAKE_SKIP_RPATH=ON + -DUSE_EXTERNAL_NLOHMANN=ON + -DUSE_EXTERNAL_PUGIXML=ON + -DUSE_LIBARCHIVE=$(usex archive $(usex qt6)) + -DBUILD_DOCUMENTATION=$(usex doc) + -DUSE_HDF5=$(usex hdf5) + -DUSE_MMTF=$(usex mmtf) + -DUSE_OPENGL=$(usex qt6) + -DUSE_QT=$(usex qt6) + -DUSE_SPGLIB=$(usex spglib) + -DENABLE_TESTING=$(usex test) + -DUSE_VTK=$(usex vtk) + # disabled libraries + -DUSE_PYTHON=OFF + -DUSE_LIBMSYM=OFF + ) + + use qt6 && mycmakeargs+=( + -DBUILD_GPL_PLUGINS=ON + -DQT_VERSION=6 + ) + + use vtk && mycmakeargs+=( + -DBUNDLED_GENXRDPATTERN="${WORKDIR}/genXrdPattern" + -DUSE_SYSTEM_GENXRDPATTERN=OFF + ) + + 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 + + # remove CONTRIBUTING, LICENSE and duplicate README + rm -r "${ED}/usr/share/doc/${PF}/avogadrolibs" || die +} diff --git a/sci-libs/avogadrolibs/files/avogadrolibs-1.100-fix-openbabel3.patch b/sci-libs/avogadrolibs/files/avogadrolibs-1.100-fix-openbabel3.patch new file mode 100644 index 000000000000..6395dc83359b --- /dev/null +++ b/sci-libs/avogadrolibs/files/avogadrolibs-1.100-fix-openbabel3.patch @@ -0,0 +1,13 @@ +FindOpenBabel3.cmake is not fully functional +(confusion between OpenBabel3_INCLUDE_DIR / OPENBABEL3_INCLUDE_DIR) +The easiest way is to amend here. +--- a/cmake/FindOpenBabel3.cmake ++++ b/cmake/FindOpenBabel3.cmake +@@ -26,6 +26,6 @@ + set_target_properties(OpenBabel3 PROPERTIES + IMPORTED_LOCATION "${OpenBabel3_LIBRARY}" + IMPORTED_IMPLIB "${OpenBabel3_LIBRARY}" +- INTERFACE_INCLUDE_DIRECTORIES "${OpenBabel3_INCLUDE_DIR}") ++ INTERFACE_INCLUDE_DIRECTORIES "${OpenBabel3_INCLUDE_DIR}/openbabel3") + endif() + endif() diff --git a/sci-libs/avogadrolibs/files/avogadrolibs-1.100-tests.patch b/sci-libs/avogadrolibs/files/avogadrolibs-1.100-tests.patch new file mode 100644 index 000000000000..6c9cc4faf99d --- /dev/null +++ b/sci-libs/avogadrolibs/files/avogadrolibs-1.100-tests.patch @@ -0,0 +1,21 @@ +Spacegroup test requires spglib feature, see tests/core/spacegrouptest.cpp:17 +--- a/tests/core/CMakeLists.txt ++++ b/tests/core/CMakeLists.txt +@@ -16,13 +16,16 @@ + Mutex + NeighborPerceiver + RingPerceiver +- Spacegroup + Utilities + UnitCell + Variant + VariantMap + ) + ++if(USE_SPGLIB) ++ list(APPEND tests Spacegroup) ++endif() ++ + # Build up the source file names. + set(testSrcs "") + foreach(TestName ${tests}) diff --git a/sci-libs/avogadrolibs/metadata.xml b/sci-libs/avogadrolibs/metadata.xml index 672fc1a05040..ff776fffbddf 100644 --- a/sci-libs/avogadrolibs/metadata.xml +++ b/sci-libs/avogadrolibs/metadata.xml @@ -7,6 +7,8 @@ </maintainer> <use> <flag name="archive">Enable archive support using <pkg>app-arch/libarchive</pkg></flag> + <flag name="mmtf">Enable support of MMTF format using <pkg>dev-libs/mmtf-cpp</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> <upstream>
