sci-visualization/paraview: version bump to 5.6.1

 - Version bump to 5.6.1
 - OpenMP 4.0 compatibility
 - Fix various dependencies

Closes: https://bugs.gentoo.org/661860
Closes: https://bugs.gentoo.org/686362
Closes: https://bugs.gentoo.org/686990
Closes: https://bugs.gentoo.org/687534
Closes: https://bugs.gentoo.org/687790
Package-Manager: Portage-2.3.67, Repoman-2.3.16
Signed-off-by: Matthias Maier <tamiko@gentoo.org>

3 files changed, 345 insertions, 0 deletions

diff --git a/sci-visualization/paraview/Manifest b/sci-visualization/paraview/Manifest
index 9b7d008bf85e..396d42620be1 100644
--- a/sci-visualization/paraview/Manifest
+++ b/sci-visualization/paraview/Manifest
@@ -1,2 +1,3 @@
 DIST ParaView-v5.5.2.tar.gz 51418473 BLAKE2B 3300ccbd3fdb522889e9689bd3ad3b37602168658332438d1403f0fcd235722b1751e5acdf01536e4398d759ad26abc4d87f98902f09f64e067a1025e4dcd7a3 SHA512 3150d01cdeaf04aba449b7ffdc22d425d4bace8f17923b56aaf9393695e61fc96406ca49a9ca33ff57f1a2b94a3111b080d4fce5763cce5d082cfbc5c68ea94a
 DIST ParaView-v5.6.0.tar.gz 54085457 BLAKE2B a99a320f87af19ad4d39336e148f4ab1989225111299341ff3ebb095c652f1392362e42ce90dab8fe7390c44f9200637e76c1076e07d61c7e6cd4aad93df3a83 SHA512 4d7c1b9f5781411cdd290a0ef105221deca1af28bb29b8e6e6c077f3377b110e7c86637c11514559d2d826d36f189d5b5c1caa9e5f9c53820cf35c3ade1ae1f6
+DIST ParaView-v5.6.1.tar.xz 38756076 BLAKE2B 65515a61493e5b9518c42b8b255c59086629bc863de9bfd5651b06ea96dce108ce93f559192d76411bfacaa93660add8ee181e68c46e36ba26b65d32dc141534 SHA512 33ca0b29d4dae8f2ecdad3148c30b5cecb4dc64a4fc898206f5f855cacbc18e554c86d6e259b39fb2f56d190cf76cdefe103009b233ce04ad2573caa34b9ca45
diff --git a/sci-visualization/paraview/files/paraview-5.6.1-fix_openmp_4.0.patch b/sci-visualization/paraview/files/paraview-5.6.1-fix_openmp_4.0.patch
new file mode 100644
index 000000000000..515624150315
--- /dev/null
+++ b/sci-visualization/paraview/files/paraview-5.6.1-fix_openmp_4.0.patch
@@ -0,0 +1,32 @@
+diff -urNd ParaView-v5.6.0/VTK/ThirdParty/vtkm/vtk-m/vtkm/cont/openmp/internal/FunctorsOpenMP.h ParaView-v5.6.0-openmp/VTK/ThirdParty/vtkm/vtk-m/vtkm/cont/openmp/internal/FunctorsOpenMP.h
+--- ParaView-v5.6.0/VTK/ThirdParty/vtkm/vtk-m/vtkm/cont/openmp/internal/FunctorsOpenMP.h	2018-11-07 05:05:18.000000000 +1000
++++ ParaView-v5.6.0-openmp/VTK/ThirdParty/vtkm/vtk-m/vtkm/cont/openmp/internal/FunctorsOpenMP.h	2019-06-28 14:04:02.292922908 +1000
+@@ -290,7 +290,7 @@
+     std::unique_ptr<ReturnType[]> threadData;
+ 
+     VTKM_OPENMP_DIRECTIVE(parallel default(none) firstprivate(f)
+-                            shared(data, doParallel, numThreads, threadData))
++                            shared(data, doParallel, numThreads, threadData, numVals))
+     {
+ 
+       int tid = omp_get_thread_num();
+@@ -422,7 +422,7 @@
+   vtkm::Id outIdx = 0;
+ 
+   VTKM_OPENMP_DIRECTIVE(parallel default(none) firstprivate(keysIn, valuesIn, keysOut, valuesOut, f)
+-                          shared(outIdx))
++                          shared(outIdx, numValues))
+   {
+     int tid = omp_get_thread_num();
+     int numThreads = omp_get_num_threads();
+diff -urNd ParaView-v5.6.0/VTK/ThirdParty/vtkm/vtk-m/vtkm/cont/openmp/internal/ParallelSortOpenMP.h ParaView-v5.6.0-openmp/VTK/ThirdParty/vtkm/vtk-m/vtkm/cont/openmp/internal/ParallelSortOpenMP.h
+--- ParaView-v5.6.0/VTK/ThirdParty/vtkm/vtk-m/vtkm/cont/openmp/internal/ParallelSortOpenMP.h	2018-11-07 05:05:18.000000000 +1000
++++ ParaView-v5.6.0-openmp/VTK/ThirdParty/vtkm/vtk-m/vtkm/cont/openmp/internal/ParallelSortOpenMP.h	2019-06-28 13:54:33.132064191 +1000
+@@ -133,6 +133,7 @@
+       VTKM_OPENMP_DIRECTIVE(parallel for
+                             default(none)
+                             firstprivate(valuesInPortal, indexPortal, valuesOutPortal)
++                            shared(size)
+                             schedule(static))
+       for (vtkm::Id i = 0; i < size; ++i)
+       {
diff --git a/sci-visualization/paraview/paraview-5.6.1.ebuild b/sci-visualization/paraview/paraview-5.6.1.ebuild
new file mode 100644
index 000000000000..a1cc1d76516b
--- /dev/null
+++ b/sci-visualization/paraview/paraview-5.6.1.ebuild
@@ -0,0 +1,312 @@
+# Copyright 1999-2019 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+PYTHON_COMPAT=( python{2_7,3_5,3_6} )
+inherit cmake-utils desktop gnome2-utils python-single-r1 toolchain-funcs
+
+MAIN_PV=$(ver_cut 0-1)
+MAJOR_PV=$(ver_cut 1-2)
+MY_P="ParaView-v${PV}"
+
+DESCRIPTION="Powerful scientific data visualization application"
+HOMEPAGE="https://www.paraview.org"
+SRC_URI="https://www.paraview.org/files/v${MAJOR_PV}/${MY_P}.tar.xz"
+
+LICENSE="paraview GPL-2"
+KEYWORDS="~amd64 ~x86"
+SLOT="0"
+IUSE="boost cg coprocessing development doc examples ffmpeg mpi mysql nvcontrol openmp offscreen plugins python +qt5 sqlite tcl test tk"
+
+RESTRICT="mirror test"
+
+# "vtksqlite, needed by vtkIOSQL" and "vtkIOSQL, needed by vtkIOMySQL"
+REQUIRED_USE="python? ( mpi ${PYTHON_REQUIRED_USE} )
+	mysql? ( sqlite )
+	?? ( offscreen qt5 )"
+
+RDEPEND="
+	app-arch/lz4
+	dev-libs/expat
+	dev-libs/jsoncpp
+	dev-libs/libxml2:2
+	dev-libs/protobuf:=
+	dev-libs/pugixml
+	media-libs/freetype
+	media-libs/glew:0
+	media-libs/libpng:0
+	media-libs/libtheora
+	media-libs/tiff:0=
+	sci-libs/cgnslib
+	sci-libs/hdf5:=[mpi=]
+	>=sci-libs/netcdf-4.2[hdf5]
+	>=sci-libs/netcdf-cxx-4.2:3
+	sys-libs/zlib
+	virtual/glu
+	virtual/jpeg:0
+	x11-libs/libX11
+	x11-libs/libXext
+	x11-libs/libXmu
+	x11-libs/libXt
+	coprocessing? (
+		plugins? (
+			dev-python/PyQt5
+			dev-qt/qtgui:5[-gles2]
+		)
+	)
+	ffmpeg? ( virtual/ffmpeg )
+	mpi? ( virtual/mpi[cxx,romio] )
+	mysql? ( dev-db/mysql-connector-c )
+	offscreen? ( >=media-libs/mesa-18.3.6[osmesa] )
+	!offscreen? ( virtual/opengl )
+	python? (
+		${PYTHON_DEPS}
+		dev-python/constantly[${PYTHON_USEDEP}]
+		dev-python/incremental[${PYTHON_USEDEP}]
+		dev-python/matplotlib[${PYTHON_USEDEP}]
+		dev-python/numpy[${PYTHON_USEDEP}]
+		dev-python/pygments[${PYTHON_USEDEP}]
+		dev-python/sip[${PYTHON_USEDEP}]
+		dev-python/six[${PYTHON_USEDEP}]
+		|| ( dev-python/twisted[${PYTHON_USEDEP}]
+			dev-python/twisted-core[${PYTHON_USEDEP}]
+		)
+		dev-python/zope-interface[${PYTHON_USEDEP}]
+		mpi? ( dev-python/mpi4py )
+		qt5? ( dev-python/PyQt5[opengl,webkit,${PYTHON_USEDEP}] )
+	)
+	qt5? (
+		dev-qt/designer:5
+		dev-qt/qtgui:5[-gles2]
+		dev-qt/qthelp:5
+		dev-qt/qtopengl:5[-gles2]
+		dev-qt/qtsql:5
+		dev-qt/qttest:5
+		dev-qt/qtwebkit:5
+		dev-qt/qtx11extras:5
+	)
+	sqlite? ( dev-db/sqlite:3 )
+	tcl? ( dev-lang/tcl:0= )
+	tk? ( dev-lang/tk:0= )"
+DEPEND="${RDEPEND}
+	${PYTHON_DEPS}
+	boost? ( dev-libs/boost[mpi?,${PYTHON_USEDEP}] )
+	doc? ( app-doc/doxygen )"
+
+S="${WORKDIR}/${MY_P}"
+
+PATCHES=(
+	"${FILESDIR}"/${PN}-4.0.1-xdmf-cstring.patch
+	"${FILESDIR}"/${PN}-5.3.0-fix_buildsystem.patch
+	"${FILESDIR}"/${PN}-5.5.0-allow_custom_build_type.patch
+	"${FILESDIR}"/${PN}-5.6.1-fix_openmp_4.0.patch
+)
+
+CMAKE_MAKEFILE_GENERATOR="emake" #579474
+
+pkg_setup() {
+	[[ ${MERGE_TYPE} != "binary" ]] && use openmp && tc-check-openmp
+	python-single-r1_pkg_setup
+	PVLIBDIR=$(get_libdir)/${PN}-${MAJOR_PV}
+}
+
+src_prepare() {
+
+	# Bug #661812
+	mkdir -p Plugins/StreamLinesRepresentation/doc || die
+
+	cmake-utils_src_prepare
+
+	# lib64 fixes
+	sed -i \
+		-e "s:/lib/python:/$(get_libdir)/python:g" \
+		VTK/ThirdParty/xdmf3/vtkxdmf3/CMakeLists.txt || die
+	sed -i \
+		-e "s:lib/paraview-:$(get_libdir)/paraview-:g" \
+		ParaViewCore/ServerManager/SMApplication/vtkInitializationHelper.cxx || die
+}
+
+src_configure() {
+	if use qt5; then
+		export QT_SELECT=qt5
+	fi
+
+	local mycmakeargs=(
+		-DCMAKE_INSTALL_LIBDIR="${PVLIBDIR}"
+		-DCMAKE_INSTALL_PREFIX="${EPREFIX}"/usr
+		-DEXPAT_INCLUDE_DIR="${EPREFIX}"/usr/include
+		-DEXPAT_LIBRARY="${EPREFIX}"/usr/$(get_libdir)/libexpat.so
+		-DBUILD_SHARED_LIBS=ON
+		-DCMAKE_VERBOSE_MAKEFILE=ON
+
+		-DVTK_Group_StandAlone=ON
+		-DVTK_DEFAULT_RENDER_WINDOW_OFFSCREEN=TRUE
+
+		-DVTK_USE_OGGTHEORA_ENCODER=TRUE
+		-DVTK_USE_SYSTEM_CGNS=ON
+		-DVTK_USE_SYSTEM_PUGIXML=ON
+		-DVTK_USE_SYSTEM_EXPAT=ON
+		-DVTK_USE_SYSTEM_FREETYPE=ON
+		-DVTK_USE_SYSTEM_GL2PS=OFF # doesn't compile, requires modified sources
+		-DVTK_USE_SYSTEM_GLEW=ON
+		-DVTK_USE_SYSTEM_HDF5=ON
+		-DVTK_USE_SYSTEM_JPEG=ON
+		-DVTK_USE_SYSTEM_JSONCPP=ON
+		-DVTK_USE_SYSTEM_LIBXML2=ON
+		-DVTK_USE_SYSTEM_LZ4=ON
+		-DVTK_USE_SYSTEM_NETCDF=ON
+		-DVTK_USE_SYSTEM_PNG=ON
+		-DVTK_USE_SYSTEM_PROTOBUF=ON
+		-DVTK_USE_SYSTEM_TIFF=ON
+		-DVTK_USE_SYSTEM_XDMF2=OFF # does not compile with sci-libs/xdmf2-1.0_p141226
+		-DVTK_USE_SYSTEM_ZLIB=ON
+
+		# boost
+		-DModule_vtkInfovisBoost="$(usex boost)"
+
+		# coprocessing
+		-DPARAVIEW_ENABLE_CATALYST="$(usex coprocessing)"
+
+		# doc
+		-DBUILD_DOCUMENTATION="$(usex doc)"
+
+		# examples
+		-DBUILD_EXAMPLES="$(usex examples)"
+
+		# ffmpeg
+		-DPARAVIEW_ENABLE_FFMPEG="$(usex ffmpeg)"
+		-DVTK_USE_FFMPEG_ENCODER="$(usex ffmpeg)"
+		-DModule_vtkIOFFMPEG="$(usex ffmpeg)"
+
+		# mpi
+		-DPARAVIEW_USE_ICE_T="$(usex mpi)"
+		-DPARAVIEW_USE_MPI_SSEND="$(usex mpi)"
+		-DPARAVIEW_USE_MPI="$(usex mpi)"
+		-DVTK_Group_MPI="$(usex mpi)"
+		-DVTK_XDMF_USE_MPI="$(usex mpi)"
+		-DXDMF_BUILD_MPI="$(usex mpi)"
+
+		# mysql
+		-DModule_vtkIOMySQL="$(usex mysql)"
+
+		# offscreen
+		-DVTK_USE_X=$(usex !offscreen)
+		-DVTK_OPENGL_HAS_OSMESA=$(usex offscreen)
+		-DVTK_OPENGL_HAS_OSMESA=$(usex offscreen)
+
+		# plugins
+		-DPARAVIEW_BUILD_PLUGIN_AdiosReader="$(usex plugins)"
+		-DPARAVIEW_BUILD_PLUGIN_AnalyzeNIfTIIO="$(usex plugins)"
+		-DPARAVIEW_BUILD_PLUGIN_ArrowGlyph="$(usex plugins)"
+		-DPARAVIEW_BUILD_PLUGIN_EyeDomeLighting="$(usex plugins)"
+		-DPARAVIEW_BUILD_PLUGIN_GMVReader="$(usex plugins)"
+		-DPARAVIEW_BUILD_PLUGIN_Moments="$(usex plugins)"
+		-DPARAVIEW_BUILD_PLUGIN_NonOrthogonalSource="$(usex plugins)"
+		-DPARAVIEW_BUILD_PLUGIN_PacMan="$(usex plugins)"
+		-DPARAVIEW_BUILD_PLUGIN_SierraPlotTools="$(usex plugins)"
+		-DPARAVIEW_BUILD_PLUGIN_SLACTools="$(usex plugins)"
+		-DPARAVIEW_BUILD_PLUGIN_StreamingParticles="$(usex plugins)"
+		-DPARAVIEW_BUILD_PLUGIN_SurfaceLIC="$(usex plugins)"
+		# these are always needed for plugins
+		-DModule_vtkFiltersFlowPaths="$(usex plugins)"
+		-DModule_vtkPVServerManagerApplication="$(usex plugins)"
+		# force this module due to incorrect build system deps wrt bug 460528
+		-DModule_vtkUtilitiesProcessXML=ON
+
+		# python
+		-DModule_pqPython="$(usex python)"
+		-DModule_vtkmpi4py="$(usex python)"
+		-DModule_vtkPython="$(usex python)"
+		-DModule_vtkWrappingPythonCore="$(usex python)"
+		-DPARAVIEW_ENABLE_PYTHON="$(usex python)"
+		-DXDMF_WRAP_PYTHON="$(usex python)"
+
+		# qt5
+		-DPARAVIEW_INSTALL_DEVELOPMENT_FILES="$(usex development)"
+		-DModule_vtkGUISupportQtSQL="$(usex qt5)"
+		-DModule_vtkRenderingQt="$(usex qt5)"
+		-DModule_vtkViewsQt="$(usex qt5)"
+		-DPARAVIEW_BUILD_QT_GUI="$(usex qt5)"
+		-DVTK_Group_ParaViewQt="$(usex qt5)"
+		-DVTK_Group_Qt="$(usex qt5)"
+		-DModule_pqPython="$(usex qt5 "$(usex python)" "off")"
+		$(usex qt5 "-DPARAVIEW_QT_VERSION=5" "")
+		-DVTK_USE_NVCONTROL="$(usex nvcontrol)"
+
+		# sqlite
+		-DModule_vtksqlite="$(usex sqlite)"
+
+		# tcl
+		-DModule_vtkTclTk="$(usex tcl)"
+
+		# test
+		-DBUILD_TESTING="$(usex test)"
+
+		# tk
+		-DVTK_Group_Tk="$(usex tk)"
+		-DVTK_USE_TK="$(usex tk)"
+		-DModule_vtkRenderingTk="$(usex tk)"
+	)
+
+	if use openmp; then
+		mycmakeargs+=( -DVTK_SMP_IMPLEMENTATION_TYPE=OpenMP )
+	fi
+
+	if use python; then
+		mycmakeargs+=(
+			-DVTK_USE_SYSTEM_TWISTED=ON
+			-DVTK_USE_SYSTEM_AUTOBAHN=ON
+			-DVTK_USE_SYSTEM_ZOPE=ON
+		)
+	fi
+
+	if use qt5; then
+		mycmakeargs+=(
+			-DVTK_USE_QVTK=ON
+			-DOPENGL_gl_LIBRARY="${EPREFIX}"/usr/$(get_libdir)/libGL.so
+			-DOPENGL_glu_LIBRARY="${EPREFIX}"/usr/$(get_libdir)/libGLU.so
+			-DVTK_QT_VERSION=5
+			-DQT_MOC_EXECUTABLE="$(qt5_get_bindir)/moc"
+			-DQT_UIC_EXECUTABLE="$(qt5_get_bindir)/uic"
+			-DQT_QMAKE_EXECUTABLE="$(qt5_get_bindir)/qmake"
+			-DVTK_Group_Qt:BOOL=ON
+		)
+	fi
+
+	cmake-utils_src_configure
+}
+
+src_install() {
+	cmake-utils_src_install
+
+		# remove wrapper binaries and put the actual executable in place
+		for i in {paraview-config,pvserver,pvdataserver,pvrenderserver,pvbatch,pvpython,paraview}; do
+			if [ -f "${ED}"/usr/lib/"$i" ]; then
+				mv "${ED}"/usr/lib/"$i" "${ED}"/usr/bin/"$i" || die
+			fi
+		done
+
+		# install libraries into correct directory respecting get_libdir:
+		mv "${ED}"/usr/lib "${ED}"/usr/lib_tmp || die
+		mkdir -p "${ED}"/usr/"${PVLIBDIR}" || die
+		mv "${ED}"/usr/lib_tmp/* "${ED}"/usr/"${PVLIBDIR}" || die
+		rmdir "${ED}"/usr/lib_tmp || die
+
+		# set up the environment
+		echo "LDPATH=${EPREFIX}/usr/${PVLIBDIR}" > "${T}"/40${PN} || die
+		doenvd "${T}"/40${PN}
+
+		newicon "${S}"/Applications/ParaView/pvIcon-32x32.png paraview.png
+		make_desktop_entry paraview "Paraview" paraview
+
+		use python && python_optimize "${D}"/usr/$(get_libdir)/${PN}-${MAJOR_PV}
+	}
+
+	pkg_postinst() {
+		gnome2_icon_cache_update
+	}
+
+	pkg_postrm() {
+		gnome2_icon_cache_update
+	}