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-rw-r--r--sci-libs/Manifest.gzbin40366 -> 40366 bytes
-rw-r--r--sci-libs/avogadrolibs/Manifest18
-rw-r--r--sci-libs/avogadrolibs/avogadrolibs-1.100.0.ebuild174
-rw-r--r--sci-libs/avogadrolibs/avogadrolibs-1.97.0.ebuild93
-rw-r--r--sci-libs/avogadrolibs/files/avogadrolibs-1.100-fix-openbabel3.patch13
-rw-r--r--sci-libs/avogadrolibs/files/avogadrolibs-1.100-tests.patch21
-rw-r--r--sci-libs/avogadrolibs/files/avogadrolibs-1.95.1-tests.patch13
-rw-r--r--sci-libs/avogadrolibs/metadata.xml2
-rw-r--r--sci-libs/spglib/Manifest6
-rw-r--r--sci-libs/spglib/files/spglib-2.6.0-dist_sources.patch48
-rw-r--r--sci-libs/spglib/files/spglib-2.6.0-pyproject.patch29
-rw-r--r--sci-libs/spglib/metadata.xml4
-rw-r--r--sci-libs/spglib/spglib-2.6.0.ebuild100
13 files changed, 407 insertions, 114 deletions
diff --git a/sci-libs/Manifest.gz b/sci-libs/Manifest.gz
index 21c21b98f516..137d31086cfe 100644
--- a/sci-libs/Manifest.gz
+++ b/sci-libs/Manifest.gz
Binary files differ
diff --git a/sci-libs/avogadrolibs/Manifest b/sci-libs/avogadrolibs/Manifest
index 2cae521a3bb6..63474ec0e77d 100644
--- a/sci-libs/avogadrolibs/Manifest
+++ b/sci-libs/avogadrolibs/Manifest
@@ -1,8 +1,12 @@
+AUX avogadrolibs-1.100-fix-openbabel3.patch 539 BLAKE2B 8981fea4b94a604fada965523a8ceb0272530b5155ebcded0c30c2c055ddd3d20d431a688fb22a9e018e9479aa482c068a24a51861a98097601368fc2e6abc0b SHA512 b73225b3ab20e798940d0be4dcbed3b09722dca1dcf75272b411b721d6ed80cd8f2dcdcfc9443bda7f8f702cad823c4c7541940a5b6289a4da3f9e18078a1fd1
+AUX avogadrolibs-1.100-tests.patch 421 BLAKE2B e573ae107eae855b5ae0d03f2acc1cec989ecaefc8d183f9060d93d2eff3e5152b234e43070ff96e598269dbe1e56454780871df7ba7e488cb37935ded9e68c6 SHA512 063260ddad3164e02c5ba16ac54780d7ec80f4e60f0e346fc334b2a5add84ffdd89a629946ab72854f81b4aa662de53a69a18bf49ddea9f48f02aa9e435aa309
AUX avogadrolibs-1.91.0_pre20180406-bundled-genxrdpattern.patch 1644 BLAKE2B 3b25bc2648b323b803b5d0b6e10be2689ef9e4c988d0c55abe172bf4312da8f5f9b527262a2f8e48d0b2391b01a03a976bc36cc22c467ac9a44fb85cc43c7a6d SHA512 515c7029e6f99c5e88a37f43387e656b2873b99e14e8d8e9b1b20bf82604f70be8f669d8b97383e80969b0f80d43439647fdfd17566bbf6fbd32cb75ce2fb4e3
-AUX avogadrolibs-1.95.1-tests.patch 263 BLAKE2B 463e2fb995354253e25cd2a0ee53603faefbf5ed5ca92c74154694df02ab488ffae155f08b3d1019e5713cb6c4e6fa340ead9fb93bd2ea91d79af0b646d86bb7 SHA512 00facd6927fe84ca65971a723531df6653ea9379fdaaae17401645508fb6ccce2f4b5efc5e53c6d2851611ffcc2ce382840da4a82366b26d1c7f368dceeb549b
-DIST avogadrolibs-1.97.0.tar.gz 11456702 BLAKE2B 2f9229a0525dc151ef636c4c101ea21d3713efb033f6a007c43689bfd078b07081d695bb3ec32715c3ccf9d67e7bb85a617a08eeb0e6fc8c80e479a3cb3f1553 SHA512 a0ad3ba294db5f0fff35087ff0f616fdcaefc7b4abfa470c9fd26326ad14f73e3584c18a7111b671998d8a23a50091307520f01f79295fc7ea52ae2d78716c7e
-DIST avogadrolibs-crystals-1.0.1.tar.gz 151829 BLAKE2B 0a1353392a4c087977452f50ffb7db0b2976a2993651b6f7e0df7a9ce6fa8f7960223cac2916dd9f667d37518b85606d73d05e86f7489193a6a609700fc60223 SHA512 c5d6500d8472807b8d2e62888e4a09279c6aeafec81bc4981edaa74e36724b1e7f0381250c79ad297f9f0331bcb5cd8a45fce3f13ad65b9870e901a6424c0650
-DIST avogadrolibs-molecules-1.0.0.tar.gz 206924 BLAKE2B 70eea3d5eb440ab2c7f29c56111f2b8cf780cc84983aa145bc4f2fe144c981978218333ba3c33cf1f620dd3180cca706dfa4e94ffaee6167f89bd3e372172218 SHA512 06891ea7ad3e65c5b0c0ad73ea01916478fcd13fd9ff0d6905d28159678a50371ba9fa2c1f68ef32604dee0c2165de29bd5d50ffbc345bfe752ef0bcb13126f2
-DIST linux64-genXrdPattern-avogadrolibs-1.97.0 7480152 BLAKE2B dca8285c41aadfaa20c72f337e0f02db8ee07ce30c11ae84bf3aa7bd0b2220273d33f484d63f761d41a8946c6a0b77a0fb27906c480bcae01ae49b1531ae5cbb SHA512 538bde12e1e52600a21640d5907f43fcc853c6f3c111880f39eb238093e3d1358ccdfa1f45e944ec8b8e5ee3c2dff269cefe5334db5d73300e6ca327c95520b8
-EBUILD avogadrolibs-1.97.0.ebuild 2483 BLAKE2B 34a3d859318c57095af34849ff412a2f1e4b0783ea198decbae5904c6b33efc84a1de442f84038d2b02de128898c3be035c43ee354aadd914a247f21e393d6ca SHA512 ece7e8d0758de73ac9a753e5223c10ae92faef26a544ee329035af0fcb16072ba97cb1f56285f86b0071800fbb0b3a8fe7bd82991772d8237e59b374bdbe409d
-MISC metadata.xml 580 BLAKE2B 6947845054474e20335743a41d96511981b4eb0bf9ae1c4ab23cb20fc2ead0dff6055c406ae96604312fe348d636f4b9557e98b051ddcf33ba13e9d68df01045 SHA512 81e34367a52b6d1ce417ce086d11e72e071ca7193862bfac1b6c7e4160716e50aaf40a157f3e05dfd0a18a00388fe39a254332c548e101c478d93aa8b38b8e4c
+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-avogenerators-1.98.0.tar.gz 15676 BLAKE2B 647050636cd93e2055dacbd5c8c1c7b98b1c61ac891b836ec990d75be80ff62c452f54d7225550b9fd5e4126c1b9cf3d806121d759aabca571bfff5e6bc69028 SHA512 87f42a538af6418ce33813b8e263ca349dca455142f476413b93ba9b0c5762b7e66f8fc1cd2535a5e284b6df3e7acc226fd7c223d1d20318fca9fa69536c6f4e
+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-1.98.0.tar.gz 9953630 BLAKE2B eabc9604a68efb5db912c45ec19b731e51d5405e50dad597289f07ce1faeca9c2c296b9005ecfe21c2695ca9d536d79ec42e7e58aa6fb67f753187abc6f96649 SHA512 297bf73b290c099267ff011c68f40c636094a9ca632be7bc6d71db99d55eb16bfa9b1eee7504ada8a15534690aa80840e7d731880346fcd8b68e08b00b1e2bf6
+EBUILD avogadrolibs-1.100.0.ebuild 4565 BLAKE2B c35545571b19c80bcd766a6a9468b68f89360ec9e40c269e572a235f4958df7f57f46f5e3ac7e7a3df5c15143a5b524a9cb6de1c55dbc95900707eaae865b917 SHA512 ef4512b589b8599db1bafa6a3e4d0c7b102e754e906bf4b9b2e7a553ab99cbc719806f61664b147818aae24d83756961bd3729d3509c0f3eea3fb64f1d17c107
+MISC metadata.xml 777 BLAKE2B 01bb2f067dcc73acae3437c4caa4c768d88eec9f6606083c4ad94c67fc7c437498b20e8435d626ffe003b40e9323e157309687120ebb49c4ea7c32974d4d1951 SHA512 f895440aa9299130bb1f7cd4fba9147a9c5dd514aa05fff049a081dadc6ae17e247111a3184be86765ffd45ac97a787c27bec35b9537843647bf9a6b10c93022
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/avogadrolibs-1.97.0.ebuild b/sci-libs/avogadrolibs/avogadrolibs-1.97.0.ebuild
deleted file mode 100644
index 6d9cb22617aa..000000000000
--- a/sci-libs/avogadrolibs/avogadrolibs-1.97.0.ebuild
+++ /dev/null
@@ -1,93 +0,0 @@
-# Copyright 1999-2024 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit cmake
-
-DESCRIPTION="Advanced molecule editor and visualizer 2 - libraries"
-HOMEPAGE="https://www.openchemistry.org/ https://github.com/OpenChemistry/avogadrolibs"
-SRC_URI="
- https://github.com/OpenChemistry/${PN}/archive/${PV}.tar.gz -> ${P}.tar.gz
- https://github.com/OpenChemistry/molecules/archive/refs/tags/1.0.0.tar.gz -> ${PN}-molecules-1.0.0.tar.gz
- https://github.com/OpenChemistry/crystals/archive/refs/tags/1.0.1.tar.gz -> ${PN}-crystals-1.0.1.tar.gz
- vtk? ( https://github.com/psavery/genXrdPattern/releases/download/1.0-static/linux64-genXrdPattern -> linux64-genXrdPattern-${P} )"
-
-LICENSE="BSD GPL-2+"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="archive doc hdf5 qt5 test vtk"
-RESTRICT="!test? ( test )"
-REQUIRED_USE="vtk? ( qt5 )"
-
-# TODO: Not yet packaged:
-# sci-libs/libmsym (https://github.com/mcodev31/libmsym)
-RDEPEND="
- >=sci-chemistry/molequeue-0.7
- archive? ( app-arch/libarchive:= )
- hdf5? ( sci-libs/hdf5:= )
- qt5? (
- dev-qt/qtconcurrent:5
- dev-qt/qtcore:5
- dev-qt/qtgui:5
- dev-qt/qtnetwork:5
- dev-qt/qtsvg:5
- dev-qt/qtwidgets:5
- media-libs/glew:0=
- virtual/opengl
- )
- vtk? ( sci-libs/vtk[qt5,views] )"
-DEPEND="${RDEPEND}
- dev-cpp/eigen:3
- test? ( dev-cpp/gtest )"
-BDEPEND="
- doc? ( app-text/doxygen[dot] )
- qt5? ( dev-qt/linguist-tools:5 )"
-
-PATCHES=(
- "${FILESDIR}/"${PN}-1.91.0_pre20180406-bundled-genxrdpattern.patch
- "${FILESDIR}/"${PN}-1.95.1-tests.patch
-)
-
-src_unpack() {
- default
-
- if use vtk; then
- cp "${DISTDIR}"/linux64-genXrdPattern-${P} "${WORKDIR}/genXrdPattern" || die
- fi
-
- # hardcoded assumptions in
- # avogadro/qtplugins/insertfragment/CMakeLists.txt
- mv crystals-1.0.1 crystals || die
- mv molecules-1.0.0 molecules || die
-}
-
-src_configure() {
- local mycmakeargs=(
- -DUSE_LIBARCHIVE=$(usex archive)
- -DBUILD_DOCUMENTATION=$(usex doc)
- -DUSE_HDF5=$(usex hdf5)
- -DENABLE_TRANSLATIONS=$(usex qt5)
- -DUSE_OPENGL=$(usex qt5)
- -DUSE_QT=$(usex qt5)
- -DENABLE_TESTING=$(usex test)
- -DUSE_VTK=$(usex vtk)
- # disabled libraries
- -DUSE_PYTHON=OFF
- -DUSE_PROTOCALL=OFF
- -DUSE_MMTF=OFF
- -DUSE_LIBMSYM=OFF
- # find_package(Spglib) completely broken
- -DUSE_SPGLIB=OFF
- )
- use qt5 && mycmakeargs+=(
- -DBUILD_GPL_PLUGINS=ON
- -DBUILD_STATIC_PLUGINS=ON
- -DOpenGL_GL_PREFERENCE=GLVND
- )
- use vtk && mycmakeargs+=(
- -DBUNDLED_GENXRDPATTERN="${WORKDIR}/genXrdPattern"
- )
-
- cmake_src_configure
-}
diff --git a/sci-libs/avogadrolibs/files/avogadrolibs-1.100-fix-openbabel3.patch b/sci-libs/avogadrolibs/files/avogadrolibs-1.100-fix-openbabel3.patch
new file mode 100644
index 000000000000..6395dc83359b
--- /dev/null
+++ b/sci-libs/avogadrolibs/files/avogadrolibs-1.100-fix-openbabel3.patch
@@ -0,0 +1,13 @@
+FindOpenBabel3.cmake is not fully functional
+(confusion between OpenBabel3_INCLUDE_DIR / OPENBABEL3_INCLUDE_DIR)
+The easiest way is to amend here.
+--- a/cmake/FindOpenBabel3.cmake
++++ b/cmake/FindOpenBabel3.cmake
+@@ -26,6 +26,6 @@
+ set_target_properties(OpenBabel3 PROPERTIES
+ IMPORTED_LOCATION "${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/files/avogadrolibs-1.95.1-tests.patch b/sci-libs/avogadrolibs/files/avogadrolibs-1.95.1-tests.patch
deleted file mode 100644
index 5feea804632e..000000000000
--- a/sci-libs/avogadrolibs/files/avogadrolibs-1.95.1-tests.patch
+++ /dev/null
@@ -1,13 +0,0 @@
-exclude test that unconditionally requires sci-libs/spglib
-* https://bugs.gentoo.org/765811
-
---- a/tests/core/CMakeLists.txt
-+++ b/tests/core/CMakeLists.txt
-@@ -15,7 +15,6 @@
- Molecule
- Mutex
- RingPerceiver
-- Spacegroup
- Utilities
- UnitCell
- Variant
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>
diff --git a/sci-libs/spglib/Manifest b/sci-libs/spglib/Manifest
index 70966755d741..3b228714cd5b 100644
--- a/sci-libs/spglib/Manifest
+++ b/sci-libs/spglib/Manifest
@@ -1,3 +1,7 @@
+AUX spglib-2.6.0-dist_sources.patch 1811 BLAKE2B 7396c62994256c1bcfb888934342a2efc3b3c5badc82ef5ea33af4d9fc6d2ed1f375dbdb72f6c13de4a6e32620b5804e0dd22174c5808506411e32f407aa3cb1 SHA512 2db3fe2119b6bb7e46c55b28e6a687e8a8dd25be01339489f09709c486bc73bbc7033970541bdc2e4a7de31a2323e9dfa4ee41ab658108843a81b00310a96d65
+AUX spglib-2.6.0-pyproject.patch 832 BLAKE2B 2a6112705e38eff263f453b022e2c4a763178982debf26f2567d31bb216105907772acd5bf135f6a4b6220a8b9447c2e6282029b5e87841aa735cdfc54e4d81a SHA512 b524b467c568546769b5cd953bc9574e4b99ffe51582f1c8f0599a556e7be1ef30d5eb34c5a88b7614e932a136e3d05d48797d7e238d6b23a8712914250d4231
DIST spglib-1.14.1.tar.gz 1994323 BLAKE2B 69c16d4b1b7f23b652247df01f88d88917083bf4394e4a5e2e6636b49950ae3e06e395d117ba92ed4fc7c4295f61bab53cda25c2b7b3b7073bc888719ac2dee1 SHA512 77f65af957b1cc956bbd7ab555b5d62297b13228187c54cc4f6e48efba84b0fd60e57f79a4cf22a160a550ca0a19c5d71de0219fccd0b370d2ce413d41a5cfb0
+DIST spglib-2.6.0.tar.gz 2438640 BLAKE2B 99befe83edf51fbffdb815315e89e5bc9a882298e08ca79631ce2fbb17d302be529b6f4f326d60ee07bef330b8f217aa0111acaa1ec8f0562f2fb12be498db24 SHA512 a70a318dcfb0cfffca1d68605ec3afea6c5ff18ada6a4a1c0ea1c09f23ab8585d093aaf322939bc83cff28e8bb3b1b42ec65edce9208e4f69288504326e4cf2f
EBUILD spglib-1.14.1.ebuild 592 BLAKE2B 16533821ff23f6a96435da7a3bc6a55aa52392aa660f153859da34913b013f1675d52e37cd2a5407e8c74c1ab4791329d374aecd585639a06b4ad7d0cba32e2e SHA512 5e72af6ad26709197d41f6ddfd9f9b552169b8d6858f8930277250c34d2ff161c184b9a3611069dff91bcc4e3557fbfa88f12a6acb9003350d4044065fd73608
-MISC metadata.xml 266 BLAKE2B a03b1fcf7148cf43fb829f619c218219bcd4e66c45d12f563113401e3ae0b06cb0df9a8c0af01ea97e21453638d627d420e7df5b9b0d330ef1752253faa8aa32 SHA512 1dc293fa0d0296eba18ac2cbcd57f47ffc6cc822bf0d76e1cc86cb046700201f703d705375b5555b88cbe8780ef3750be05b8f9f8de092693e6d165c1734e049
+EBUILD spglib-2.6.0.ebuild 2236 BLAKE2B d6a12daaabb1e8d95ab146e97ed09bf508db8b3cb94e30459747d65e5a1434ae76c35da173454a6e7d104b6b9320001bfe1ac39ce5e66dc186521e4b9b2ca6ac SHA512 66e9a8da287cf4c1895b3cbebdef6cf07bafcc10415fed796e234fc7559156e690f56d7ef35b102e506726ed5f7413e4937b0a6cdda9d891b631efa05836aa79
+MISC metadata.xml 410 BLAKE2B edc506e79948baa46687eb8c08a3cb17e3e1a22f5041460d7510607f9676232818ef5f4fb97fce154ddb8a43e86b55153af5267b78e5df49985ad2f217f3350f SHA512 7a9fbf1be6be2c8dd7e2606da9f74d395b64748672fd505d3ebcada5230a0166b72c042335435fe6aeff6979deb130c3c9e2d793655c801b27bc6cf386586eda
diff --git a/sci-libs/spglib/files/spglib-2.6.0-dist_sources.patch b/sci-libs/spglib/files/spglib-2.6.0-dist_sources.patch
new file mode 100644
index 000000000000..4b628ba2fae7
--- /dev/null
+++ b/sci-libs/spglib/files/spglib-2.6.0-dist_sources.patch
@@ -0,0 +1,48 @@
+Always use sources instead of a hypothetical installed package.
+diff '--color=auto' -uNr a/fortran/CMakeLists.txt b/fortran/CMakeLists.txt
+--- a/fortran/CMakeLists.txt 2025-03-12 19:45:47.109635926 -0000
++++ b/fortran/CMakeLists.txt 2025-03-12 19:46:51.964594152 -0000
+@@ -77,11 +77,8 @@
+
+ # Get Spglib if it's run as stand-alone project
+ if (NOT TARGET Spglib::symspg)
+- find_package(Spglib CONFIG)
+- if (NOT Spglib_FOUND)
+ message(STATUS "Using bundled spglib sources")
+ add_subdirectory(${PROJECT_SOURCE_DIR}/.. _deps/spglib-build)
+- endif ()
+ endif ()
+
+ #[=============================================================================[
+diff '--color=auto' -uNr a/python/CMakeLists.txt b/python/CMakeLists.txt
+--- a/python/CMakeLists.txt 2025-03-12 19:45:47.113635861 -0000
++++ b/python/CMakeLists.txt 2025-03-12 19:47:13.720244693 -0000
+@@ -47,11 +47,8 @@
+
+ # Get Spglib if it's run as stand-alone project
+ if (NOT TARGET Spglib::symspg)
+- find_package(Spglib CONFIG)
+- if (NOT Spglib_FOUND)
+ message(STATUS "Using bundled spglib sources")
+ add_subdirectory(${PROJECT_SOURCE_DIR}/.. _deps/spglib-build)
+- endif ()
+ endif ()
+
+ #[=============================================================================[
+diff '--color=auto' -uNr a/test/CMakeLists.txt b/test/CMakeLists.txt
+--- a/test/CMakeLists.txt 2025-03-12 19:45:47.113635861 -0000
++++ b/test/CMakeLists.txt 2025-03-12 19:47:43.499766319 -0000
+@@ -75,13 +75,11 @@
+
+ # Get Spglib if it's run as stand-alone project
+ if (NOT TARGET Spglib::symspg)
+- set(spglib_find_package_args)
+ if (SPGLIB_WITH_Fortran)
+ list(APPEND
+ COMPONENTS Fortran
+ )
+ endif ()
+- find_package(Spglib REQUIRED CONFIG ${spglib_find_package_args})
+ endif ()
+
+ set(BUILD_GMOCK OFF)
diff --git a/sci-libs/spglib/files/spglib-2.6.0-pyproject.patch b/sci-libs/spglib/files/spglib-2.6.0-pyproject.patch
new file mode 100644
index 000000000000..523d55c3baa5
--- /dev/null
+++ b/sci-libs/spglib/files/spglib-2.6.0-pyproject.patch
@@ -0,0 +1,29 @@
+Invalid type for license
+Prevent variables relevant only for a standalone python-pkg
+--- a/pyproject.toml
++++ b/pyproject.toml
+@@ -8,7 +8,6 @@
+ name = "spglib"
+ requires-python = ">=3.9"
+ description = "This is the spglib module."
+-license = "BSD-3-Clause"
+ license-files = ["COPYING"]
+ readme = "python/README.rst"
+ dynamic = ["version"]
+@@ -89,16 +88,6 @@
+ metadata.version.provider = "scikit_build_core.metadata.setuptools_scm"
+ sdist.include = ["python/spglib/_version.py"]
+
+-[tool.scikit-build.cmake.define]
+-SPGLIB_WITH_Python = "ON"
+-SPGLIB_WITH_TESTS = "OFF"
+-SPGLIB_USE_OMP = "OFF"
+-
+-[[tool.scikit-build.overrides]]
+-if.env.CIBUILDWHEEL = true
+-# Make sure cibuildwheel builds with a bundled spglib
+-cmake.define.CMAKE_DISABLE_FIND_PACKAGE_Spglib = "ON"
+-
+ [tool.setuptools_scm]
+ write_to = "python/spglib/_version.py"
+
diff --git a/sci-libs/spglib/metadata.xml b/sci-libs/spglib/metadata.xml
index d4ff1000a775..9363fa8ccdbe 100644
--- a/sci-libs/spglib/metadata.xml
+++ b/sci-libs/spglib/metadata.xml
@@ -5,4 +5,8 @@
<email>sci-chemistry@gentoo.org</email>
<name>Gentoo Chemistry Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">atztogo/spglib</remote-id><!-- old -->
+ <remote-id type="github">spglib/spglib</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-libs/spglib/spglib-2.6.0.ebuild b/sci-libs/spglib/spglib-2.6.0.ebuild
new file mode 100644
index 000000000000..41e008c55e7d
--- /dev/null
+++ b/sci-libs/spglib/spglib-2.6.0.ebuild
@@ -0,0 +1,100 @@
+# Copyright 1999-2025 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_EXT=1
+DISTUTILS_OPTIONAL=1
+DISTUTILS_SINGLE_IMPL=1
+DISTUTILS_USE_PEP517=scikit-build-core
+PYTHON_COMPAT=( python3_{10..13} )
+FORTRAN_NEEDED=fortran
+inherit cmake distutils-r1 fortran-2 toolchain-funcs
+
+DESCRIPTION="Spglib is a C library for finding and handling crystal symmetries"
+HOMEPAGE="https://github.com/spglib/spglib/"
+SRC_URI="https://github.com/spglib/spglib/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="BSD"
+SLOT="0/2"
+KEYWORDS="~amd64 ~x86"
+IUSE="fortran openmp python test"
+REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )"
+RESTRICT="!test? ( test )"
+
+RDEPEND="
+ python? (
+ ${PYTHON_DEPS}
+ $(python_gen_cond_dep '
+ dev-python/numpy[${PYTHON_USEDEP}]
+ dev-python/ruamel-yaml[${PYTHON_USEDEP}]
+ ')
+ $(python_gen_cond_dep '
+ dev-python/typing-extensions[${PYTHON_USEDEP}]
+ ' 3.10 3.11 3.12)
+ )
+"
+DEPEND="${RDEPEND}"
+BDEPEND="
+ python? (
+ ${DISTUTILS_DEPS}
+ ${PYTHON_DEPS}
+ test? ( $(python_gen_cond_dep 'dev-python/pyyaml[${PYTHON_USEDEP}]') )
+ )
+ test? ( dev-cpp/gtest )
+"
+
+PATCHES=(
+ "${FILESDIR}"/${PN}-2.6.0-pyproject.patch
+ "${FILESDIR}"/${PN}-2.6.0-dist_sources.patch
+)
+
+distutils_enable_tests pytest
+
+pkg_pretend() {
+ [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
+}
+
+pkg_setup() {
+ [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
+ use fortran && fortran-2_pkg_setup
+ use python && python-single-r1_pkg_setup
+}
+
+src_prepare() {
+ cmake_src_prepare
+ use python && distutils-r1_src_prepare
+}
+
+src_configure() {
+ local mycmakeargs=(
+ -DCMAKE_SKIP_RPATH=ON
+ -DSPGLIB_SHARED_LIBS=ON
+ -DSPGLIB_USE_OMP="$(usex openmp)"
+ -DSPGLIB_WITH_Fortran="$(usex fortran)"
+ -DSPGLIB_WITH_Python="$(usex python)"
+ -DSPGLIB_WITH_TESTS="$(usex test)"
+ )
+ cmake_src_configure
+}
+
+src_compile() {
+ cmake_src_compile
+ use python && distutils-r1_src_compile
+}
+
+src_test() {
+ local -x LD_LIBRARY_PATH="${BUILD_DIR}"
+ cmake_src_test
+ use python && distutils-r1_src_test
+}
+
+src_install() {
+ cmake_src_install
+ if use python; then
+ distutils-r1_src_install
+
+ # remove duplicate headers/lib
+ rm -r "${ED}"/$(python_get_sitedir)/spglib/{$(get_libdir),include} || die
+ fi
+}
generated by cgit v1.2.3 (git 2.25.1) at 2025-04-15 11:39:09 +0000