gentoo resync : 20.03.2022

4 files changed, 53 insertions, 51 deletions

diff --git a/sci-libs/avogadrolibs/Manifest b/sci-libs/avogadrolibs/Manifest
index 313c0ef35af1..9465dd7ee146 100644
--- a/sci-libs/avogadrolibs/Manifest
+++ b/sci-libs/avogadrolibs/Manifest
@@ -1,6 +1,8 @@
 AUX avogadrolibs-1.91.0_pre20180406-bundled-genxrdpattern.patch 1644 BLAKE2B 3b25bc2648b323b803b5d0b6e10be2689ef9e4c988d0c55abe172bf4312da8f5f9b527262a2f8e48d0b2391b01a03a976bc36cc22c467ac9a44fb85cc43c7a6d SHA512 515c7029e6f99c5e88a37f43387e656b2873b99e14e8d8e9b1b20bf82604f70be8f669d8b97383e80969b0f80d43439647fdfd17566bbf6fbd32cb75ce2fb4e3
-AUX avogadrolibs-1.93.0-fix_AvogadroLibsConfig.patch 695 BLAKE2B 40feb1bfe132fe5ddbef435b4d611a55650c0348c943f0796a87fc0761c99c4aebcbc54fb4d29e545c66384ad7352067f3ff5549e9e26bdd2cfe602974f56425 SHA512 7e5198bb3b6c7e83372bd6b54d3f50347ff8519fd24adcb0c59fdc50593be1c08cc2b1d7d12dc530de10c80bfaacad17679a6b1b90ded82947fe94d6dfa51f56
-DIST avogadrolibs-1.93.0.tar.gz 2735862 BLAKE2B b5d696f23aeeab27358ee390a30b2cf146e7119185a0d2e8d71b34d2744e534cd8b50b36d12928b5aa723118db470272b6428514593d64770d172c4bde730cf6 SHA512 1af220e5614cbd96656679c2879cb7f7c46acd135b4e6f2e5f8d0ba98601ce004e78f019a0a71c643f005451309bd194eb73eb9f66707685e5855b47e95f7eae
-DIST linux64-genXrdPattern-avogadrolibs-1.93.0 7480152 BLAKE2B dca8285c41aadfaa20c72f337e0f02db8ee07ce30c11ae84bf3aa7bd0b2220273d33f484d63f761d41a8946c6a0b77a0fb27906c480bcae01ae49b1531ae5cbb SHA512 538bde12e1e52600a21640d5907f43fcc853c6f3c111880f39eb238093e3d1358ccdfa1f45e944ec8b8e5ee3c2dff269cefe5334db5d73300e6ca327c95520b8
-EBUILD avogadrolibs-1.93.0.ebuild 2647 BLAKE2B df0837f311d0acca43d12920c6d9e34df7e225a59f9ed959ac92c70764a483174693529ea49644fa3355ff30f816b7225dd406a780cb7fef22436e6333e3b1fd SHA512 93453289e331bfd812b3a199df45657ee4815ae137c09a0eece04790bc53b2aafbb39af43b9982ac385dd4833f154925c4146c5dcb29c10d3bba5360235748a6
+AUX avogadrolibs-1.95.1-tests.patch 263 BLAKE2B 463e2fb995354253e25cd2a0ee53603faefbf5ed5ca92c74154694df02ab488ffae155f08b3d1019e5713cb6c4e6fa340ead9fb93bd2ea91d79af0b646d86bb7 SHA512 00facd6927fe84ca65971a723531df6653ea9379fdaaae17401645508fb6ccce2f4b5efc5e53c6d2851611ffcc2ce382840da4a82366b26d1c7f368dceeb549b
+DIST avogadrolibs-1.95.1.tar.gz 11015910 BLAKE2B 27cb43a22e489c0279e1ed912b1e81f3c850983f367ffb89bef3a63d11204cbf761f2bce6501988ed5ef9b21b44cc5194dad4367da3ae6af65efd0cec5e7d711 SHA512 b4734c732b1686eba74055c4834fef2f9fb66d4a67cd1199c84e81965c3f6e783911e7c7c8d09386c4ff9f1322bab91fe490d3606784ae49acf5531a65a58beb
+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-1.95.1 7480152 BLAKE2B dca8285c41aadfaa20c72f337e0f02db8ee07ce30c11ae84bf3aa7bd0b2220273d33f484d63f761d41a8946c6a0b77a0fb27906c480bcae01ae49b1531ae5cbb SHA512 538bde12e1e52600a21640d5907f43fcc853c6f3c111880f39eb238093e3d1358ccdfa1f45e944ec8b8e5ee3c2dff269cefe5334db5d73300e6ca327c95520b8
+EBUILD avogadrolibs-1.95.1.ebuild 2477 BLAKE2B d8902fdb0f40ebe7a1c0bacb2a6c7d7c7ee2fe4cfbebd5a679a5b08cbdb4637896186f2331607f6f37c0a852365f572cc5f8216a2892382978aff17b9a451d36 SHA512 3174b74c5f2abbbaa63532fd29ab827ba0bd3c5788a5ca8074395f789c348afc10d71c8f9d220043a4ab1b09dd0e55bd2a591da32528d68b0c2241422c3c6b7a
 MISC metadata.xml 580 BLAKE2B 6947845054474e20335743a41d96511981b4eb0bf9ae1c4ab23cb20fc2ead0dff6055c406ae96604312fe348d636f4b9557e98b051ddcf33ba13e9d68df01045 SHA512 81e34367a52b6d1ce417ce086d11e72e071ca7193862bfac1b6c7e4160716e50aaf40a157f3e05dfd0a18a00388fe39a254332c548e101c478d93aa8b38b8e4c
diff --git a/sci-libs/avogadrolibs/avogadrolibs-1.93.0.ebuild b/sci-libs/avogadrolibs/avogadrolibs-1.95.1.ebuild
index 4db9d9a0c2b9..2a3a1c7cdb9b 100644
--- a/sci-libs/avogadrolibs/avogadrolibs-1.93.0.ebuild
+++ b/sci-libs/avogadrolibs/avogadrolibs-1.95.1.ebuild
@@ -1,95 +1,93 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=7
-inherit cmake-utils flag-o-matic
+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 -> ${P}.tar.gz
-	vtk? ( https://github.com/psavery/genXrdPattern/releases/download/1.0-static/linux64-genXrdPattern -> linux64-genXrdPattern-${P} )
-"
+	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} )"
 
-SLOT="0"
 LICENSE="BSD GPL-2+"
+SLOT="0"
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-
-# static-plugins needs to be enabled until upstream fixes
-# https://github.com/OpenChemistry/avogadrolibs/issues/436
-#IUSE="archive doc hdf5 qt5 static-plugins test vtk"
 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)
-# sci-libs/spglib (https://atztogo.github.io/spglib/)
 RDEPEND="
-	dev-libs/jsoncpp:=
 	>=sci-chemistry/molequeue-0.7
-	sci-libs/spglib
-	archive? ( app-arch/libarchive )
+	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] )
-"
+	vtk? ( sci-libs/vtk[qt5,views] )"
 DEPEND="${RDEPEND}
 	dev-cpp/eigen:3
-	qt5? ( dev-qt/linguist-tools:5 )
 	test? ( dev-cpp/gtest )"
+BDEPEND="
+	doc? ( app-doc/doxygen )
+	qt5? ( dev-qt/linguist-tools:5 )"
 
 PATCHES=(
-	# https://github.com/OpenChemistry/avogadrolibs/issues/449
-	"${FILESDIR}"/${PN}-1.93.0-fix_AvogadroLibsConfig.patch
 	"${FILESDIR}/"${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() {
-	# Seems to be what upstream are using too. Apply the old hdf5lib workaround.
-	# https://github.com/OpenChemistry/avogadrolibs/commit/32e3dd8ce9f48f74e3960dc9afcc614496d87c7f
-	# bug #810505
-	append-cppflags -DH5_USE_110_API
-
-	# -DBUILD_STATIC_PLUGINS=$(usex static-plugins)
 	local mycmakeargs=(
-		-DCMAKE_INSTALL_DOCDIR="${EPREFIX}/usr/share/doc/${PF}"
-		-DUSE_PROTOCALL=OFF
-		-DBUILD_GPL_PLUGINS=ON
-		-DUSE_MOLEQUEUE=ON
-		-DUSE_MMTF=OFF
-		-DUSE_LIBMSYM=OFF
-		-DUSE_SPGLIB=OFF
-		-DUSE_PYTHON=OFF
 		-DUSE_LIBARCHIVE=$(usex archive)
 		-DBUILD_DOCUMENTATION=$(usex doc)
 		-DUSE_HDF5=$(usex hdf5)
 		-DENABLE_TRANSLATIONS=$(usex qt5)
 		-DUSE_OPENGL=$(usex qt5)
 		-DUSE_QT=$(usex qt5)
-		-DBUILD_STATIC_PLUGINS=ON
 		-DENABLE_TESTING=$(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-utils_src_configure
+	cmake_src_configure
 }
diff --git a/sci-libs/avogadrolibs/files/avogadrolibs-1.93.0-fix_AvogadroLibsConfig.patch b/sci-libs/avogadrolibs/files/avogadrolibs-1.93.0-fix_AvogadroLibsConfig.patch
deleted file mode 100644
index 5eb316af9414..000000000000
--- a/sci-libs/avogadrolibs/files/avogadrolibs-1.93.0-fix_AvogadroLibsConfig.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- a/cmake/AvogadroLibsConfig.cmake.orig.in	2016-12-01 22:17:48.000000000 +0100
-+++ b/cmake/AvogadroLibsConfig.cmake.in	2017-03-11 20:39:36.462581381 +0100
-@@ -10,7 +10,7 @@
- 
- set(AvogadroLibs_INSTALL_PREFIX  "@CMAKE_INSTALL_PREFIX@")
- set(AvogadroLibs_INCLUDE_DIRS    "${AvogadroLibs_INSTALL_PREFIX}/@INSTALL_INCLUDE_DIR@")
--set(AvogadroLibs_LIBRARY_DIR     "${AvogadroLibs_INSTALL_PREFIX}/@INSTALL_LIBRARY_DIR@@LIB_SUFFIX@")
-+set(AvogadroLibs_LIBRARY_DIR     "${AvogadroLibs_INSTALL_PREFIX}/@INSTALL_LIBRARY_DIR@")
- set(AvogadroLibs_RUNTIME_DIR     "${AvogadroLibs_INSTALL_PREFIX}/@INSTALL_RUNTIME_DIR@")
- set(AvogadroLibs_CMAKE_DIR       "${AvogadroLibs_LIBRARY_DIR}/cmake/avogadrolibs")
- 
diff --git a/sci-libs/avogadrolibs/files/avogadrolibs-1.95.1-tests.patch b/sci-libs/avogadrolibs/files/avogadrolibs-1.95.1-tests.patch
new file mode 100644
index 000000000000..5feea804632e
--- /dev/null
+++ b/sci-libs/avogadrolibs/files/avogadrolibs-1.95.1-tests.patch
@@ -0,0 +1,13 @@
+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