commit: 52b295d43de6f90960c0c9319fd19d37751b8e96 Author: Nicolas PARLANT <nicolas.parlant <AT> parhuet <DOT> fr> AuthorDate: Mon Oct 27 14:21:08 2025 +0000 Commit: Sam James <sam <AT> gentoo <DOT> org> CommitDate: Tue Nov 4 11:16:04 2025 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=52b295d4
sci-libs/avogadrolibs, sci-chemistry/avogadro2: remove old Signed-off-by: Nicolas PARLANT <nicolas.parlant <AT> parhuet.fr> Part-of: https://github.com/gentoo/gentoo/pull/44352 Closes: https://github.com/gentoo/gentoo/pull/44352 Signed-off-by: Sam James <sam <AT> gentoo.org> sci-chemistry/avogadro2/Manifest | 2 - .../avogadro2/avogadro2-1.100.0-r1.ebuild | 81 --------- sci-libs/avogadrolibs/Manifest | 6 - .../avogadrolibs/avogadrolibs-1.100.0-r1.ebuild | 194 --------------------- .../files/avogadrolibs-1.100-cmake4.patch | 38 ---- .../files/avogadrolibs-1.100-fix-openbabel3.patch | 13 -- .../files/avogadrolibs-1.100-fix_odr.patch | 98 ----------- .../files/avogadrolibs-1.100-tests.patch | 21 --- sci-libs/avogadrolibs/metadata.xml | 1 - 9 files changed, 454 deletions(-) diff --git a/sci-chemistry/avogadro2/Manifest b/sci-chemistry/avogadro2/Manifest index 0701163d70e5..d4f8c94a612f 100644 --- a/sci-chemistry/avogadro2/Manifest +++ b/sci-chemistry/avogadro2/Manifest @@ -1,5 +1,3 @@ -DIST avogadro2-1.100.0-i18n.tar.gz 1225588 BLAKE2B a548952828764c3bbb2b487ecdfa649dd290473e3b241fcdb85c0fcf21e2b163e47e2007de2eb62845c2cfc368a2d8a115698c8988113d802504895a3ea5419d SHA512 261a1c3c165529731107346eca1b423fad6e64e790bf694dde64245e640cb3164735535574efac895d17f2b3ff1e236eb64535bf29de7d55ad4f008854e45164 -DIST avogadro2-1.100.0.tar.gz 3079141 BLAKE2B f9ddd73b9c85099db8594300976fcb64d9b74ac8349a611c536efacaf57aa7f10b7f5b2325b6a9cc8f64354768bbb4af9bc280784a9042c9226af68d06e519c7 SHA512 689999bad26d575c879bf3e64a32afb3a2b95ece26b7338b417a4f8a552ef97908c75cf4aa09880b657b74255ead18e9025b0faf46dfb6e3329e00647ce12c48 DIST avogadro2-1.101.0-i18n.tar.gz 1403440 BLAKE2B 595e76179350a3aebf9fe66df97dcc73d037b96c5dbf860e995cc5c3a8098a4a2f1d447398108584c22234cccc2cc1b7425361b5ba30b86d7d4143f1d5975868 SHA512 4cdecdb75bd5f1a1adbcdc56652489d87fd7c118bbf69305bf2b8d46a11a85f8ff45dffdbb4bf533531419902edc48dfb040e7b3a235e3ef0521302eda5180ec DIST avogadro2-1.101.0.tar.gz 3474642 BLAKE2B 6c973855c9440ef9b5d52f9d95ad597821704057850e7403a7824d2e053404dcb35889d63bdbf717206a75485e4994025401230662f05b2215c13ae83540424f SHA512 1d3b096f9d89f0bac3e4e9ee1095eb030409595c3eb2890785fd1f0991a9cf4eee30ba02ff2babf33d1f05a40aeb6fb18bad36845942e1c9201de6c3b49884fa DIST avogadro2-1.102.1-i18n.tar.gz 1450971 BLAKE2B 187cd08f1ae674776bb9d72ef70a107e10e94cdd75d546864c4dc9812825c2b8090333b19ecea8dd97f9207283dc6a724e1cbe3155549f5b8be4407a7291900f SHA512 e425ac58cffea2798425dacd9418349242e82b4dee4ab74289483bbd408a1aa374a36e1a05f743522bace48700145ba4cfdb693d8e4b2d743f79ecbafb00aafe diff --git a/sci-chemistry/avogadro2/avogadro2-1.100.0-r1.ebuild b/sci-chemistry/avogadro2/avogadro2-1.100.0-r1.ebuild deleted file mode 100644 index ce8df32481bb..000000000000 --- a/sci-chemistry/avogadro2/avogadro2-1.100.0-r1.ebuild +++ /dev/null @@ -1,81 +0,0 @@ -# Copyright 1999-2025 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -MY_PN=avogadroapp -inherit cmake xdg - -DESCRIPTION="Advanced molecule editor and visualizer 2" -HOMEPAGE="https://www.openchemistry.org/ https://two.avogadro.cc/"; -SRC_URI=" - https://github.com/OpenChemistry/${MY_PN}/archive/${PV}.tar.gz -> ${P}.tar.gz - https://github.com/OpenChemistry/avogadro-i18n/archive/${PV}.tar.gz -> ${P}-i18n.tar.gz -" -S="${WORKDIR}/${MY_PN}-${PV}" - -LICENSE="BSD GPL-2+" -SLOT="0" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="doc vtk" - -RDEPEND=" - dev-qt/qtbase:6[concurrent,gui,network,opengl,ssl,widgets] - >=sci-libs/avogadrolibs-${PV}[qt6,vtk?] - vtk? ( sci-libs/vtk:= ) -" -DEPEND="${RDEPEND} - dev-cpp/eigen:3 - vtk? ( dev-libs/pegtl ) -" -BDEPEND="doc? ( app-text/doxygen )" - -src_unpack() { - default - mv "${WORKDIR}"/avogadro-i18n-${PV} "${WORKDIR}"/avogadro-i18n || die -} - -src_prepare() { - if use doc; then - doxygen -u docs/doxyfile.in 2>/dev/null || die - fi - - cmake_src_prepare -} - -src_configure() { - local mycmakeargs=( - -DCMAKE_SKIP_RPATH=ON - -DBUILD_DOCUMENTATION=$(usex doc) - # rpc/molequeue is abandoned - # see https://github.com/OpenChemistry/avogadroapp/issues/561 - -DAvogadro_ENABLE_RPC=OFF - # test requires qttesting/paraview - -DENABLE_TESTING=OFF - -DQT_VERSION=6 - -DUSE_VTK=$(usex vtk) - ) - - # Need this to prevent overwriting the documentation OUTDIR - use doc && mycmakeargs+=( - -DChemData_SOURCE_DIR="${S}" - -DChemData_BINARY_DIR="${BUILD_DIR}" - ) - - cmake_src_configure -} - -src_compile() { - cmake_src_compile - - use doc && cmake_build documentation -} - -src_install() { - use doc && local HTML_DOCS=( "${BUILD_DIR}"/docs/html/. ) - - cmake_src_install - - # remove CONTRIBUTING, LICENSE and duplicate README - rm -r "${ED}"/usr/share/doc/${PF}/avogadro2 || die -} diff --git a/sci-libs/avogadrolibs/Manifest b/sci-libs/avogadrolibs/Manifest index 57b0a68d1537..2a53139e3177 100644 --- a/sci-libs/avogadrolibs/Manifest +++ b/sci-libs/avogadrolibs/Manifest @@ -1,19 +1,13 @@ -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-1.101.0-data.tar.gz 18043657 BLAKE2B 469d1b675c1ca39577f50db33f5641c940b077166a15fcd34c7f70c428c1b6585ab12099f24406501c8a1d312a36e7fdd6dcc663eadbfe1659b20d2ba6e3aba4 SHA512 9930a4925abcdfd28756f614ebe4e3f00d72933d9452e2041c3991a5a0b9d240261e49de9c6a814e17cc1aa6ceac1cd3bee89cffda86c0dd84a7fb8751e70340 DIST avogadrolibs-1.101.0.tar.gz 4714237 BLAKE2B fddb27e8d59f4bd8664c35f1a29c769487ea5d8a75671a6720aadf926e8f8d9c439dd3d68b3aefc8e57df8451d872238fca116b2a33a30ddaa7921f797e9e8ad SHA512 a084736345f781eb2a770333440594f0fddda73a520f436a570648766a5c6f5a9c59fcd7671ba3c700129b6bf110c81a677a6461dbf10cb4f2816ba4c013d250 DIST avogadrolibs-1.102.1-data.tar.gz 23208807 BLAKE2B 1fd5428e1952de9fc4950c920858f9cc0070678aede4e6e7d0cfd10b60c26f00cd9fd32def178d6bb6b1895f29ccbac21358503b9b7ebf4fd45ca62fc40f9f2c SHA512 06024993b0cb652c5cc59c16d4ebbe44feb7b76f083f64863da13142f96c01e579b0445452164ef75830fde28e21c76a46da8361111d757f694a9f7e517359c9 DIST avogadrolibs-1.102.1.tar.gz 4802785 BLAKE2B 8e6f0ec091469886ba0b1c6b86cfc5f08502f865216e47284584dcc265b019f780c15941a207a489f4d65d9ebc5da30b09c512f9942bf40b81774320650529d7 SHA512 34706a1bcf9e483c305193ba45fb9463df9bf2087a3075a889b50aacabfaf6feecf10747e7074e4639b630616d707401e797ad8e8a4a313e2a9547bd21c2ee5e DIST avogadrolibs-avogenerators-1.101.0.tar.gz 16185 BLAKE2B 4d562133d5ff7e4a10192712a7623002a72c7633d82fc2c87a8803afc27dca8ac36da06d8b1e384053bc74d14effb89557a0f5333552f480a383979b9667bd72 SHA512 2a2b5686c1494b66e82a02a38c07971e38a10403b87c7e3107de6d196ba9a43440602b6df04ff6dc2bfb5d1e872eb5dd394a00c6c56ccb22323bc9b82b6e6667 DIST avogadrolibs-avogenerators-1.102.1.tar.gz 15131 BLAKE2B 2bcc92e377f2501b16639c8ea86e8f6fe578660577274be3d1ff37de75fe7f24f09bc98b62fc88eb9bf6ae27fe8bbb7f8f86ab234fbccbdcecd8e8c3302981c0 SHA512 f46cfc201d10bb11a871bab5f901cdbeb34446fead5f82653a39b2d11095e663fae6ddcd2d43624fdfc787347785fbd0e8418cee64fa718cce8d8dee0e1ae462 -DIST avogadrolibs-avogenerators-1.98.0.tar.gz 15676 BLAKE2B 647050636cd93e2055dacbd5c8c1c7b98b1c61ac891b836ec990d75be80ff62c452f54d7225550b9fd5e4126c1b9cf3d806121d759aabca571bfff5e6bc69028 SHA512 87f42a538af6418ce33813b8e263ca349dca455142f476413b93ba9b0c5762b7e66f8fc1cd2535a5e284b6df3e7acc226fd7c223d1d20318fca9fa69536c6f4e DIST avogadrolibs-crystals-1.101.0.tar.gz 21674415 BLAKE2B 57b0693d86bec0e7f429d336822c0e2d84b0f911e572b0e8628b15e811fe82e1d578b850ea1a9ed6986a4ca671f83029b37d5da7573aea5c4ce5feb0b8cf74ab SHA512 327fbfa1d3239f62d585fafee25f8236929b0fac439c1232b2fb1cd08722de97937b50978ac7144ef1755a37e09eea79ac26ab7e0a8576e2fbdb6095c0030375 DIST avogadrolibs-crystals-1.102.1.tar.gz 21674416 BLAKE2B f70386438ab6214f2b123debd549a14caf5d475bd000a7e909a5cacb9664c43686b2e6e8a559effbb0916c6bb8383831eefe2cf07cf26efb80f3a03afde2baed SHA512 73efa4ddf870f7dd7762c83176bf562f5d592722e4d333ea3669f2e7c434372f58b65b516b8d16392f4d54e08bc671a9acc7281a1b95ce35d313aff2e1f66574 -DIST avogadrolibs-crystals-1.98.0.tar.gz 55935019 BLAKE2B 1750369af8a259bdccb3b0babf4e46ecc7f780f12ff8d00fcc230c7d3689bdc690bd9856ece49afca1b0f4b717360462577e618a54351c80c983a1d90de58065 SHA512 3ed07b598841c8dbc1536bd8f2a992abe73e1dc13bb9c14a4db0b60be7ba085c834d982ceb22ade3a5f0f4d05a7681567bd0c926995e78ebb9d56e2923bd4706 DIST avogadrolibs-fragments-1.101.0.tar.gz 1616263 BLAKE2B 8d68917fb5bd99933c39384f87c2d07ab815347e76668b25a344e69797bed1184688cd5f7c09d4293b10fcfc2e835642df4c726380973bfac6c29f57c2dab5ff SHA512 d76e75910c806a6bc9bc1149ee31cc64e4c23ee464cd3fd2c46377d4d233ac2fd231db238c50f40628252ca5ccc9167c264d09ed2d1d7ff5c1064b50b19a138b DIST avogadrolibs-fragments-1.102.1.tar.gz 1616241 BLAKE2B 1ce20f4c7e299b75970c012e009e71c98a8c324753d09c8755ce403f26047f299e04a81de398f63957279a9ca88a880fb630a671e15676ce62b58168d81feda9 SHA512 81fd3c0e330538a4d6e7e293cb75391abababcd0b9829ffe652d271331242822e1cde47398ba491838a0c50934f38c1eb0904cb4ddf49dd9c65a5d1bf1f0620d -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-1.101.0.tar.gz 9979718 BLAKE2B ed026b16e3e3fc9d330e96afb915442113ac7cb3b620f4c5ca5b1330a4ced1ad3430e960f683b8d9ae71332e383f0a22077aa0bae8aeca0a101361a18ffa6e30 SHA512 9b9fe03631822bb7df19259acaebc5fdb8e7050e646bd08bfbb48e1335c73dda14e1386a82e85f379df8c8498d9e77ef75bad97e809df954d3b3b45135929523 DIST avogadrolibs-molecules-1.102.1.tar.gz 9979117 BLAKE2B 73acd92d9eaddddfeff5cba83611039b502f712025bf6ee80f22ade18415ff77ec826b07f0f8b1c11129ae76b1e257ff44afff64597b963c29673b6962c426ea SHA512 839321afc1c1267dd74a8cace70f3ef7126e83ab4f9668cf4fe4eeb05049152c86a8878efb16c8a788cc06c5341ca5ae6a32cc5d6cee6938f5bdb797ca43bbeb -DIST avogadrolibs-molecules-1.98.0.tar.gz 9953630 BLAKE2B eabc9604a68efb5db912c45ec19b731e51d5405e50dad597289f07ce1faeca9c2c296b9005ecfe21c2695ca9d536d79ec42e7e58aa6fb67f753187abc6f96649 SHA512 297bf73b290c099267ff011c68f40c636094a9ca632be7bc6d71db99d55eb16bfa9b1eee7504ada8a15534690aa80840e7d731880346fcd8b68e08b00b1e2bf6 diff --git a/sci-libs/avogadrolibs/avogadrolibs-1.100.0-r1.ebuild b/sci-libs/avogadrolibs/avogadrolibs-1.100.0-r1.ebuild deleted file mode 100644 index d6004b49916c..000000000000 --- a/sci-libs/avogadrolibs/avogadrolibs-1.100.0-r1.ebuild +++ /dev/null @@ -1,194 +0,0 @@ -# Copyright 1999-2025 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -inherit cmake dot-a flag-o-matic - -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 static-libs 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="${RDEPEND} - dev-cpp/eigen:3 - mmtf? ( dev-libs/mmtf-cpp ) - vtk? ( dev-libs/pegtl ) -" -BDEPEND=" - doc? ( app-text/doxygen ) - test? ( dev-cpp/gtest ) -" - -PATCHES=( - "${FILESDIR}/"${PN}-1.91.0_pre20180406-bundled-genxrdpattern.patch - "${FILESDIR}/"${PN}-1.100-tests.patch - # https://github.com/OpenChemistry/avogadrolibs/issues/1633 - "${FILESDIR}/"${PN}-1.100-fix-openbabel3.patch - # fix lto - ODR violations (except with vtk) - "${FILESDIR}/"${PN}-1.100-fix_odr.patch - # bump cmake_min. From upstream, to be removed with next version - "${FILESDIR}/"${PN}-1.100-cmake4.patch -) - -# Static binary (requires ObjCryst++ to build otherwise) -QA_FLAGS_IGNORED="usr/bin/genXrdPattern" - -src_unpack() { - default - - rm -rf thirdparty/{nlohmann,pugixml} || die - - if use vtk; then - cp "${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=$(usex vtk) - # disabled libraries - -DUSE_PYTHON=OFF - -DUSE_LIBMSYM=OFF - ) - - if use qt6; then - mycmakeargs+=( - -DBUILD_GPL_PLUGINS=ON - -DBUILD_STATIC_PLUGINS=$(usex static-libs) - -DQT_VERSION=6 - ) - - # even w/o static-libs due to libgwavi.a, required for avogadro2 - lto-guarantee-fat - fi - - if use vtk; then - mycmakeargs+=( - -DBUNDLED_GENXRDPATTERN="${WORKDIR}/genXrdPattern" - -DUSE_SYSTEM_GENXRDPATTERN=OFF - ) - - # -Werror=odr -Werror=lto-type-mismatch - # https://github.com/OpenChemistry/avogadrolibs/issues/2060 - filter-lto - fi - - cmake_src_configure -} - -src_compile() { - cmake_src_compile - - use doc && cmake_build documentation -} - -src_test() { - local -x LD_LIBRARY_PATH="${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/${PF}/xml - fi - - cmake_src_install - - # always strip due to libgwavi.a - use qt6 && strip-lto-bytecode "${ED}" - - # remove CONTRIBUTING, LICENSE and duplicate README - rm -r "${ED}/usr/share/doc/${PF}/avogadrolibs" || die -} diff --git a/sci-libs/avogadrolibs/files/avogadrolibs-1.100-cmake4.patch b/sci-libs/avogadrolibs/files/avogadrolibs-1.100-cmake4.patch deleted file mode 100644 index 07595281b5b6..000000000000 --- a/sci-libs/avogadrolibs/files/avogadrolibs-1.100-cmake4.patch +++ /dev/null @@ -1,38 +0,0 @@ -PR merged -https://github.com/OpenChemistry/avogadrolibs/pull/2022.patch -From 7edee1178f5cd95c3b81964ce39d529b413dbe22 Mon Sep 17 00:00:00 2001 -From: Eisuke Kawashima <[email protected]> -Date: Thu, 5 Jun 2025 09:58:13 +0900 -Subject: [PATCH] build: bump cmake_minimum_required - -CMake 4 drops support of 3.4 or earlier - -note: FindPython is introduced in 3.12 -https://cmake.org/cmake/help/v3.12/release/3.12.html#modules - -Signed-off-by: Eisuke Kawashima <[email protected]> ---- - python/CMakeLists.txt | 2 +- - thirdparty/tinycolormap/CMakeLists.txt | 2 +- - 2 files changed, 2 insertions(+), 2 deletions(-) - -diff --git a/python/CMakeLists.txt b/python/CMakeLists.txt -index 2cb3d0e17b..ab6b073746 100644 ---- a/python/CMakeLists.txt -+++ b/python/CMakeLists.txt -@@ -1,4 +1,4 @@ --cmake_minimum_required(VERSION 3.3 FATAL_ERROR) -+cmake_minimum_required(VERSION 3.12 FATAL_ERROR) - - if (NOT TARGET Avogadro::Core) - find_package(AvogadroLibs REQUIRED) -diff --git a/thirdparty/tinycolormap/CMakeLists.txt b/thirdparty/tinycolormap/CMakeLists.txt -index ee88bf4878..d4c9096175 100644 ---- a/thirdparty/tinycolormap/CMakeLists.txt -+++ b/thirdparty/tinycolormap/CMakeLists.txt -@@ -1,4 +1,4 @@ --cmake_minimum_required(VERSION 3.1) -+cmake_minimum_required(VERSION 3.5) - - project(tinycolormap CXX) - set(CMAKE_CXX_STANDARD 11) diff --git a/sci-libs/avogadrolibs/files/avogadrolibs-1.100-fix-openbabel3.patch b/sci-libs/avogadrolibs/files/avogadrolibs-1.100-fix-openbabel3.patch deleted file mode 100644 index 6395dc83359b..000000000000 --- a/sci-libs/avogadrolibs/files/avogadrolibs-1.100-fix-openbabel3.patch +++ /dev/null @@ -1,13 +0,0 @@ -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-fix_odr.patch b/sci-libs/avogadrolibs/files/avogadrolibs-1.100-fix_odr.patch deleted file mode 100644 index 307466464b1e..000000000000 --- a/sci-libs/avogadrolibs/files/avogadrolibs-1.100-fix_odr.patch +++ /dev/null @@ -1,98 +0,0 @@ -https://github.com/OpenChemistry/avogadrolibs/pull/2059.patch -From ef234b94bcff5e4416e7ae0546c3e8977d3ad3a2 Mon Sep 17 00:00:00 2001 -From: Nicolas PARLANT <[email protected]> -Date: Tue, 24 Jun 2025 02:23:13 +0200 -Subject: [PATCH] Fix ODR violations, move enums into class scope -MIME-Version: 1.0 -Content-Type: text/plain; charset=UTF-8 -Content-Transfer-Encoding: 8bit - -avogadrolibs-1.100.0/avogadro/qtplugins/cp2kinput/cp2kinputdialog.cpp:61:6: -error: type ‘Avogadro::QtPlugins::BasisOption’ violates the C++ One Definition Rule [-Werror=odr] - 61 | enum BasisOption - | ^ -avogadrolibs-1.100.0/work/avogadrolibs-1.100.0/avogadro/qtplugins/cp2kinput/cp2kinputdialog.cpp:40:6: -error: type ‘Avogadro::QtPlugins::CalculateOption’ violates the C++ One Definition Rule [-Werror=odr] - 40 | enum CalculateOption - | ^ - -Signed-off-by: Nicolas PARLANT <[email protected]> ---- - .../qtplugins/cp2kinput/cp2kinputdialog.cpp | 21 ------------------- - .../qtplugins/cp2kinput/cp2kinputdialog.h | 21 +++++++++++++++++++ - 2 files changed, 21 insertions(+), 21 deletions(-) - -diff --git a/avogadro/qtplugins/cp2kinput/cp2kinputdialog.cpp b/avogadro/qtplugins/cp2kinput/cp2kinputdialog.cpp -index 5eec8b6d..97f583a3 100644 ---- a/avogadro/qtplugins/cp2kinput/cp2kinputdialog.cpp -+++ b/avogadro/qtplugins/cp2kinput/cp2kinputdialog.cpp -@@ -37,16 +37,6 @@ using Avogadro::MoleQueue::JobObject; - - namespace Avogadro::QtPlugins { - --enum CalculateOption --{ -- CalculateEnergy = 0, -- CalculateEnergyAndForces, -- CalculateMolecularDynamics, -- CalculateGeometryOptimization, -- -- CalculateCount --}; -- - enum FunctionalOption - { - FunctionalBLYP = 0, -@@ -58,17 +48,6 @@ enum FunctionalOption - FunctionalCount - }; - --enum BasisOption --{ -- BasisSZVGTH = 0, -- BasisDZVGTH, -- BasisDZVPGTH, -- BasisTZVPGTH, -- BasisTZV2PGTH, -- -- BasisCount --}; -- - enum MethodOption - { - DFT = 0, -diff --git a/avogadro/qtplugins/cp2kinput/cp2kinputdialog.h b/avogadro/qtplugins/cp2kinput/cp2kinputdialog.h -index dc24594f..52be8dcd 100644 ---- a/avogadro/qtplugins/cp2kinput/cp2kinputdialog.h -+++ b/avogadro/qtplugins/cp2kinput/cp2kinputdialog.h -@@ -31,6 +31,27 @@ class Cp2kInputDialog : public QDialog - { - Q_OBJECT - -+ enum CalculateOption -+ { -+ CalculateEnergy = 0, -+ CalculateEnergyAndForces, -+ CalculateMolecularDynamics, -+ CalculateGeometryOptimization, -+ -+ CalculateCount -+ }; -+ -+ enum BasisOption -+ { -+ BasisSZVGTH = 0, -+ BasisDZVGTH, -+ BasisDZVPGTH, -+ BasisTZVPGTH, -+ BasisTZV2PGTH, -+ -+ BasisCount -+ }; -+ - public: - explicit Cp2kInputDialog(QWidget* parent_ = nullptr, - Qt::WindowFlags f = Qt::WindowFlags()); --- -2.49.0 - diff --git a/sci-libs/avogadrolibs/files/avogadrolibs-1.100-tests.patch b/sci-libs/avogadrolibs/files/avogadrolibs-1.100-tests.patch deleted file mode 100644 index 6c9cc4faf99d..000000000000 --- a/sci-libs/avogadrolibs/files/avogadrolibs-1.100-tests.patch +++ /dev/null @@ -1,21 +0,0 @@ -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 ff776fffbddf..f06ec6e3cfc5 100644 --- a/sci-libs/avogadrolibs/metadata.xml +++ b/sci-libs/avogadrolibs/metadata.xml @@ -7,7 +7,6 @@ </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>
