gentoo auto-resync : 07:09:2022 - 16:36:21

5 files changed, 181 insertions, 2 deletions

diff --git a/sci-libs/Manifest.gz b/sci-libs/Manifest.gz
index b7c13033bf0a..b595b8f085b3 100644
--- a/sci-libs/Manifest.gz
+++ b/sci-libs/Manifest.gz
diff --git a/sci-libs/avogadrolibs/Manifest b/sci-libs/avogadrolibs/Manifest
index 9465dd7ee146..a8d1fdfea022 100644
--- a/sci-libs/avogadrolibs/Manifest
+++ b/sci-libs/avogadrolibs/Manifest
@@ -1,8 +1,12 @@
 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
+AUX avogadrolibs-1.95.1-usability_backport.patch 3189 BLAKE2B 7668450eaa3daab4474cf87ad0ce97aa1c98f7fbfc13586ae94b84653387d30ff2aaa34ae9cc7a359b1723c4ea92b1620fece5266da0a1ca0bcbd16e50a33a6d SHA512 a8143e940008981f62bd128bc1b2ebcba012c46fcdac4a2e9b1e08537b9c51ce4e21d7423dfd9380c4cc822d0cb8dbc87231142f5d85fac5b472b0d60368ab9b
 DIST avogadrolibs-1.95.1.tar.gz 11015910 BLAKE2B 27cb43a22e489c0279e1ed912b1e81f3c850983f367ffb89bef3a63d11204cbf761f2bce6501988ed5ef9b21b44cc5194dad4367da3ae6af65efd0cec5e7d711 SHA512 b4734c732b1686eba74055c4834fef2f9fb66d4a67cd1199c84e81965c3f6e783911e7c7c8d09386c4ff9f1322bab91fe490d3606784ae49acf5531a65a58beb
+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-1.95.1 7480152 BLAKE2B dca8285c41aadfaa20c72f337e0f02db8ee07ce30c11ae84bf3aa7bd0b2220273d33f484d63f761d41a8946c6a0b77a0fb27906c480bcae01ae49b1531ae5cbb SHA512 538bde12e1e52600a21640d5907f43fcc853c6f3c111880f39eb238093e3d1358ccdfa1f45e944ec8b8e5ee3c2dff269cefe5334db5d73300e6ca327c95520b8
-EBUILD avogadrolibs-1.95.1.ebuild 2477 BLAKE2B d8902fdb0f40ebe7a1c0bacb2a6c7d7c7ee2fe4cfbebd5a679a5b08cbdb4637896186f2331607f6f37c0a852365f572cc5f8216a2892382978aff17b9a451d36 SHA512 3174b74c5f2abbbaa63532fd29ab827ba0bd3c5788a5ca8074395f789c348afc10d71c8f9d220043a4ab1b09dd0e55bd2a591da32528d68b0c2241422c3c6b7a
+DIST linux64-genXrdPattern-avogadrolibs-1.97.0 7480152 BLAKE2B dca8285c41aadfaa20c72f337e0f02db8ee07ce30c11ae84bf3aa7bd0b2220273d33f484d63f761d41a8946c6a0b77a0fb27906c480bcae01ae49b1531ae5cbb SHA512 538bde12e1e52600a21640d5907f43fcc853c6f3c111880f39eb238093e3d1358ccdfa1f45e944ec8b8e5ee3c2dff269cefe5334db5d73300e6ca327c95520b8
+EBUILD avogadrolibs-1.95.1-r1.ebuild 2530 BLAKE2B 525cadfd80efa1556865bc702008a00a9109260f20f91d916202a88c46f7e195b1e160fa811d46e3f108d401a8ef07f46288058c1c09416580910dc0068fc2b1 SHA512 cdf479756217c1da11a60158c195d0a847e87a3d6b212bfb78269b34700afedea6bd5988f25f9c9241032effac25fdeeb13960e18f96161e0abd0d4a28562239
+EBUILD avogadrolibs-1.97.0.ebuild 2482 BLAKE2B 4dab120d4fce755a8bbcd7e6ebc558a9f0c2c16246a2c1da71803c883a20f67865178a95784c059d3578b167b34b0d2da52c4b0da9107a4dbc7891eefd6b08fa SHA512 0b7358854b317124577b5751d14a8f5d8a11df9fc47ca06717cd8c8ed28184460bd016fb6dc93da8e3453c4ccd50fcb767cc6784ca483a5bc9c153f7ad8fc2ec
 MISC metadata.xml 580 BLAKE2B 6947845054474e20335743a41d96511981b4eb0bf9ae1c4ab23cb20fc2ead0dff6055c406ae96604312fe348d636f4b9557e98b051ddcf33ba13e9d68df01045 SHA512 81e34367a52b6d1ce417ce086d11e72e071ca7193862bfac1b6c7e4160716e50aaf40a157f3e05dfd0a18a00388fe39a254332c548e101c478d93aa8b38b8e4c
diff --git a/sci-libs/avogadrolibs/avogadrolibs-1.95.1-r1.ebuild b/sci-libs/avogadrolibs/avogadrolibs-1.95.1-r1.ebuild
new file mode 100644
index 000000000000..ea0659f222d9
--- /dev/null
+++ b/sci-libs/avogadrolibs/avogadrolibs-1.95.1-r1.ebuild
@@ -0,0 +1,94 @@
+# Copyright 1999-2022 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="${RDEPEND}
+	dev-cpp/eigen:3
+	test? ( dev-cpp/gtest )"
+BDEPEND="
+	doc? ( app-doc/doxygen )
+	qt5? ( dev-qt/linguist-tools:5 )"
+
+PATCHES=(
+	"${FILESDIR}/"${PN}-1.91.0_pre20180406-bundled-genxrdpattern.patch
+	"${FILESDIR}/"${PN}-1.95.1-tests.patch
+	"${FILESDIR}/"${PN}-1.95.1-usability_backport.patch
+)
+
+src_unpack() {
+	default
+
+	if use vtk; then
+		cp "${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="${WORKDIR}/genXrdPattern"
+	)
+
+	cmake_src_configure
+}
diff --git a/sci-libs/avogadrolibs/avogadrolibs-1.95.1.ebuild b/sci-libs/avogadrolibs/avogadrolibs-1.97.0.ebuild
index 2a3a1c7cdb9b..e702d214d629 100644
--- a/sci-libs/avogadrolibs/avogadrolibs-1.95.1.ebuild
+++ b/sci-libs/avogadrolibs/avogadrolibs-1.97.0.ebuild
@@ -41,7 +41,7 @@ DEPEND="${RDEPEND}
 	dev-cpp/eigen:3
 	test? ( dev-cpp/gtest )"
 BDEPEND="
-	doc? ( app-doc/doxygen )
+	doc? ( app-doc/doxygen[dot] )
 	qt5? ( dev-qt/linguist-tools:5 )"
 
 PATCHES=(
diff --git a/sci-libs/avogadrolibs/files/avogadrolibs-1.95.1-usability_backport.patch b/sci-libs/avogadrolibs/files/avogadrolibs-1.95.1-usability_backport.patch
new file mode 100644
index 000000000000..07a32023600e
--- /dev/null
+++ b/sci-libs/avogadrolibs/files/avogadrolibs-1.95.1-usability_backport.patch
@@ -0,0 +1,81 @@
+From 56c67fff7dd7ec84b2f2b5c2e5beaec13981e408 Mon Sep 17 00:00:00 2001
+From: Aritz Erkiaga <aerkiaga3@gmail.com>
+Date: Sat, 3 Sep 2022 16:54:55 +0200
+Subject: [PATCH 1/3] Fix erratic editing behavior
+
+Signed-off-by: Aritz Erkiaga <aerkiaga3@gmail.com>
+---
+ avogadro/qtgui/rwmolecule_undo.h | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/avogadro/qtgui/rwmolecule_undo.h b/avogadro/qtgui/rwmolecule_undo.h
+index de5bdd33..20768066 100644
+--- a/avogadro/qtgui/rwmolecule_undo.h
++++ b/avogadro/qtgui/rwmolecule_undo.h
+@@ -89,7 +89,7 @@ public:
+   {
+     assert(m_molecule.atomCount() == m_atomId);
+     if (m_usingPositions)
+-      m_molecule.addAtom(m_atomicNumber, Vector3::Zero(), m_atomId);
++      m_molecule.addAtom(m_atomicNumber, Vector3::Zero(), m_atomUid);
+     else
+       m_molecule.addAtom(m_atomicNumber, m_atomUid);
+     m_molecule.layer().addAtom(m_layer, m_atomId);
+-- 
+2.34.1
+
+
+From 5159ea1a9629ad82130670767cc25c5065f9627c Mon Sep 17 00:00:00 2001
+From: Aritz Erkiaga <aerkiaga3@gmail.com>
+Date: Sat, 3 Sep 2022 16:55:26 +0200
+Subject: [PATCH 2/3] Fix Manipulator Tool not working at all
+
+Signed-off-by: Aritz Erkiaga <aerkiaga3@gmail.com>
+---
+ avogadro/qtplugins/manipulator/manipulator.cpp | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/avogadro/qtplugins/manipulator/manipulator.cpp b/avogadro/qtplugins/manipulator/manipulator.cpp
+index 19dc51ac..29559dd0 100644
+--- a/avogadro/qtplugins/manipulator/manipulator.cpp
++++ b/avogadro/qtplugins/manipulator/manipulator.cpp
+@@ -129,7 +129,7 @@ QUndoCommand* Manipulator::mouseMoveEvent(QMouseEvent* e)
+   Vector2f windowPos(e->localPos().x(), e->localPos().y());
+ 
+   if (mol->isSelectionEmpty() && m_object.type == Rendering::AtomType &&
+-      m_object.molecule == mol) {
++      m_object.molecule == &m_molecule->molecule()) {
+     // translate single atom position
+     RWAtom atom = m_molecule->atom(m_object.index);
+     Vector3f oldPos(atom.position3d().cast<float>());
+-- 
+2.34.1
+
+
+From f38bfbc88f0722a66ab298ff26073874b5f73634 Mon Sep 17 00:00:00 2001
+From: Aritz Erkiaga <aerkiaga3@gmail.com>
+Date: Sat, 3 Sep 2022 16:55:59 +0200
+Subject: [PATCH 3/3] Fix Bond Centric Tool not working at all
+
+Signed-off-by: Aritz Erkiaga <aerkiaga3@gmail.com>
+---
+ avogadro/qtplugins/bondcentrictool/bondcentrictool.cpp | 3 +--
+ 1 file changed, 1 insertion(+), 2 deletions(-)
+
+diff --git a/avogadro/qtplugins/bondcentrictool/bondcentrictool.cpp b/avogadro/qtplugins/bondcentrictool/bondcentrictool.cpp
+index 79112899..3a853057 100644
+--- a/avogadro/qtplugins/bondcentrictool/bondcentrictool.cpp
++++ b/avogadro/qtplugins/bondcentrictool/bondcentrictool.cpp
+@@ -342,8 +342,7 @@ QUndoCommand* BondCentricTool::mousePressEvent(QMouseEvent* e)
+   Rendering::Identifier ident = m_renderer->hit(e->pos().x(), e->pos().y());
+ 
+   // If no hits, return. Also ensure that the hit molecule is the one we expect.
+-  const Core::Molecule* mol = &m_molecule->molecule();
+-  if (!ident.isValid() || ident.molecule != mol)
++  if (!ident.isValid() || ident.molecule != &m_molecule->molecule())
+     return nullptr;
+ 
+   // If the hit is a left click on a bond, make it the selected bond and map
+-- 
+2.34.1
+