sci-libs/vtk: improve all-modules USE flag

- add missing flags to REQUIRED_USE
- add new mysql USE flag - needed by all-modules, adds new dependency on
	dev-db/mysql-connector-c. Dev-db/mariadb-connector-c isn't supported
	by this version. Fix an issue with using of deprecated my_bool when
	using mysql-connector-c.
- remove xdmf2 USE flag, block sci-libs/xdmf2 with all-modules:
	sci-libs/xdmf2 doesn't ship any cmake configuration files, which leads
	to configuration errors when trying to build against external xdmf2
- block sci-libs/xdmf2: when built against internal xdmf2, there are header
	file collisions with the header files installed by sci-libs/xdmf2
- add dependency on sci-libs/kissfft, bug #754684) and drop bundled
- fix an issue with xdmf3 library being installed in both library locations,
	lib and lib64
- fix QA issues with RPATH
- byte compile python files
- disable searching for zfp (no package in tree)
- addresses some QA issues with defined but unused cmake variables: fixing all
	of them would need a thorough testing of each single USE flag and checking
	where these belong to, in this over-complex build system (bug #660582)

Closes: https://bugs.gentoo.org/793839
Closes: https://bugs.gentoo.org/754684
Closes: https://bugs.gentoo.org/646846
Bug: https://bugs.gentoo.org/660582
Package-Manager: Portage-3.0.19, Repoman-3.0.3
Signed-off-by: Bernd Waibel <waebbl-gentoo@posteo.net>
Signed-off-by: Sam James <sam@gentoo.org>

2 files changed, 439 insertions, 0 deletions

diff --git a/sci-libs/vtk/files/vtk-8.2.0-0001-fix-library-installation-dir-for-xdmf3.patch b/sci-libs/vtk/files/vtk-8.2.0-0001-fix-library-installation-dir-for-xdmf3.patch
new file mode 100644
index 000000000000..d03cab326f4f
--- /dev/null
+++ b/sci-libs/vtk/files/vtk-8.2.0-0001-fix-library-installation-dir-for-xdmf3.patch
@@ -0,0 +1,57 @@
+From 3aad9ec6004b7e3a82817f2f1e2840fc5f07c050 Mon Sep 17 00:00:00 2001
+From: Bernd Waibel <waebbl-gentoo@posteo.net>
+Date: Thu, 3 Jun 2021 13:13:38 +0200
+Subject: [PATCH] fix library installation dir for xdmf3
+
+Signed-off-by: Bernd Waibel <waebbl-gentoo@posteo.net>
+---
+ ThirdParty/xdmf3/vtkxdmf3/core/CMakeLists.txt | 14 +++++++-------
+ 1 file changed, 7 insertions(+), 7 deletions(-)
+
+diff --git a/ThirdParty/xdmf3/vtkxdmf3/core/CMakeLists.txt b/ThirdParty/xdmf3/vtkxdmf3/core/CMakeLists.txt
+index 86d688f8..7d009dfe 100644
+--- a/ThirdParty/xdmf3/vtkxdmf3/core/CMakeLists.txt
++++ b/ThirdParty/xdmf3/vtkxdmf3/core/CMakeLists.txt
+@@ -269,10 +269,10 @@ endif()
+ 
+ if(UNIX)
+     if (BUILD_SHARED_LIBS)
+-      set(XDMFCORE_LIBRARY ${CMAKE_INSTALL_PREFIX}/lib/libXdmfCore.so
++      set(XDMFCORE_LIBRARY ${CMAKE_INSTALL_PREFIX}/lib${LIB_SUFFIX}/libXdmfCore.so
+           PARENT_SCOPE)
+     else()
+-      set(XDMFCORE_LIBRARY ${CMAKE_INSTALL_PREFIX}/lib/libXdmfCore.a
++      set(XDMFCORE_LIBRARY ${CMAKE_INSTALL_PREFIX}/lib${LIB_SUFFIX}/libXdmfCore.a
+           PARENT_SCOPE)
+     endif()
+ endif()
+@@ -297,13 +297,13 @@ if (NOT XDMF_INSTALL_NO_DEVELOPMENT)
+ endif()
+ install(TARGETS XdmfCore
+   RUNTIME DESTINATION bin
+-  LIBRARY DESTINATION lib
+-  ARCHIVE DESTINATION lib)
++  LIBRARY DESTINATION lib${LIB_SUFFIX}
++  ARCHIVE DESTINATION lib${LIB_SUFFIX})
+ if (XDMF_STATIC_AND_SHARED AND BUILD_SHARED_LIBS)
+   install(TARGETS XdmfCore_Static
+     RUNTIME DESTINATION bin
+-    LIBRARY DESTINATION lib
+-    ARCHIVE DESTINATION lib)
++    LIBRARY DESTINATION lib${LIB_SUFFIX}
++    ARCHIVE DESTINATION lib${LIB_SUFFIX})
+ endif ()
+ 
+ if (Boost_FOUND)
+@@ -329,7 +329,7 @@ set(XdmfCore_INCLUDE_DIRS
+   CACHE INTERNAL "")
+ 
+ set(XDMF_INCLUDE_DIRS ${CMAKE_INSTALL_PREFIX}/include PARENT_SCOPE)
+-set(XDMF_LIBRARIES ${XDMF_LIBRARIES} ${CMAKE_INSTALL_PREFIX}/lib)
++set(XDMF_LIBRARIES ${XDMF_LIBRARIES} ${CMAKE_INSTALL_PREFIX}/lib${LIB_SUFFIX})
+ set(XDMF_DIR ${CMAKE_INSTALL_PREFIX} PARENT_SCOPE)
+ set(XDMF_BINARIES ${XDMF_BINARIES} ${CMAKE_INSTALL_PREFIX}/bin)
+ 
+-- 
+2.31.1
+
diff --git a/sci-libs/vtk/vtk-8.2.0-r2.ebuild b/sci-libs/vtk/vtk-8.2.0-r2.ebuild
new file mode 100644
index 000000000000..4335d1c44a2f
--- /dev/null
+++ b/sci-libs/vtk/vtk-8.2.0-r2.ebuild
@@ -0,0 +1,382 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+PYTHON_COMPAT=( python3_{7,8,9} )
+WEBAPP_OPTIONAL=yes
+WEBAPP_MANUAL_SLOT=yes
+
+# Short package version
+SPV="$(ver_cut 1-2)"
+inherit flag-o-matic java-pkg-opt-2 python-single-r1 qmake-utils toolchain-funcs cmake virtualx webapp
+
+DESCRIPTION="The Visualization Toolkit"
+HOMEPAGE="https://www.vtk.org/"
+SRC_URI="
+	https://www.vtk.org/files/release/${SPV}/VTK-${PV}.tar.gz
+	doc? ( https://www.vtk.org/files/release/${SPV}/vtkDocHtml-${PV}.tar.gz )
+	examples? (
+		https://www.vtk.org/files/release/${SPV}/VTKData-${PV}.tar.gz
+		https://www.vtk.org/files/release/${SPV}/VTKLargeData-${PV}.tar.gz
+	)"
+
+LICENSE="BSD LGPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~arm ~arm64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="all-modules aqua boost doc examples ffmpeg gdal imaging java json mpi
+	mysql odbc offscreen postgres python qt5 R rendering tbb tcl theora tk
+	video_cards_nvidia views web +X"
+
+REQUIRED_USE="
+	all-modules? ( boost ffmpeg gdal mpi mysql odbc postgres python qt5 )
+	java? ( qt5 )
+	python? ( ${PYTHON_REQUIRED_USE} )
+	tcl? ( rendering )
+	examples? ( python )
+	tk? ( tcl )
+	web? ( python )
+	^^ ( X aqua offscreen )"
+
+RDEPEND="
+	app-arch/lz4
+	dev-cpp/eigen
+	dev-db/sqlite
+	dev-libs/double-conversion:0=
+	dev-libs/expat
+	dev-libs/jsoncpp:=
+	dev-libs/libxml2:2
+	>=dev-libs/pugixml-1.11
+	>=media-libs/freetype-2.5.4
+	media-libs/glew:0=
+	>=media-libs/libharu-2.3.0-r2
+	media-libs/libpng:0=
+	media-libs/libtheora
+	media-libs/mesa
+	media-libs/tiff:0
+	sci-libs/exodusii
+	sci-libs/hdf5:=
+	sci-libs/netcdf:0=
+	sci-libs/netcdf-cxx:3
+	sys-libs/zlib
+	virtual/jpeg:0
+	virtual/opengl
+	x11-libs/libX11
+	x11-libs/libXmu
+	x11-libs/libXt
+	all-modules? (
+		!sci-libs/xdmf2
+		<dev-libs/pegtl-3
+		sci-libs/kissfft
+	)
+	boost? ( dev-libs/boost:=[mpi?] )
+	examples? (
+		dev-qt/qtcore:5
+		dev-qt/qtgui:5
+	)
+	ffmpeg? ( media-video/ffmpeg )
+	gdal? ( sci-libs/gdal )
+	java? ( >=virtual/jdk-1.8:* )
+	mpi? (
+		virtual/mpi[cxx,romio]
+		$(python_gen_cond_dep '
+			python? ( dev-python/mpi4py[${PYTHON_MULTI_USEDEP}] )
+		')
+	)
+	mysql? ( dev-db/mysql-connector-c )
+	odbc? ( dev-db/unixODBC )
+	offscreen? ( media-libs/mesa[osmesa] )
+	postgres? ( dev-db/postgresql:= )
+	python? (
+		${PYTHON_DEPS}
+		$(python_gen_cond_dep '
+			dev-python/sip[${PYTHON_MULTI_USEDEP}]
+		')
+	)
+	qt5? (
+		dev-qt/designer:5
+		dev-qt/qtcore:5
+		dev-qt/qtgui:5
+		dev-qt/qtopengl:5
+		dev-qt/qtsql:5
+		dev-qt/qtx11extras:5
+		$(python_gen_cond_dep '
+			python? ( dev-python/PyQt5[${PYTHON_MULTI_USEDEP}] )
+		')
+	)
+	R? ( dev-lang/R )
+	tbb? ( dev-cpp/tbb )
+	tcl? ( dev-lang/tcl:0= )
+	tk? ( dev-lang/tk:0= )
+	video_cards_nvidia? ( x11-drivers/nvidia-drivers[tools,static-libs] )
+	web? (
+		${WEBAPP_DEPEND}
+		$(python_gen_cond_dep '
+			dev-python/autobahn[${PYTHON_MULTI_USEDEP}]
+			dev-python/constantly[${PYTHON_MULTI_USEDEP}]
+			dev-python/hyperlink[${PYTHON_MULTI_USEDEP}]
+			dev-python/incremental[${PYTHON_MULTI_USEDEP}]
+			dev-python/six[${PYTHON_MULTI_USEDEP}]
+			dev-python/twisted[${PYTHON_MULTI_USEDEP}]
+			dev-python/txaio[${PYTHON_MULTI_USEDEP}]
+			dev-python/zope-interface[${PYTHON_MULTI_USEDEP}]
+		')
+	)
+"
+DEPEND="${RDEPEND}"
+BDEPEND="
+	doc? ( app-doc/doxygen )
+	mpi? ( app-admin/chrpath )
+"
+
+S="${WORKDIR}"/VTK-${PV}
+
+PATCHES=(
+	"${FILESDIR}"/${PN}-8.1.0-openmpi-4-compatibility.patch
+	"${FILESDIR}"/${P}-qt-5.15.patch # bug 726960
+	"${FILESDIR}"/${P}-gcc-10.patch # bug 723374
+	"${FILESDIR}"/${P}-fno-common.patch # bug 721048
+	"${FILESDIR}"/${P}-py38.patch
+	"${FILESDIR}"/${P}-freetype-2.10.3-provide-FT_CALLBACK_DEF.patch # bug #751088
+	"${FILESDIR}"/${P}-pugixml.patch
+	"${FILESDIR}"/${P}-0001-fix-library-installation-dir-for-xdmf3.patch
+)
+
+RESTRICT="test"
+
+pkg_setup() {
+	use java && java-pkg-opt-2_pkg_setup
+	use python && python-single-r1_pkg_setup
+	use web && webapp_pkg_setup
+}
+
+src_prepare() {
+	cmake_src_prepare
+
+	local x
+	# missing: VPIC freerange libproj4 mrmpi sqlite utf8 verdict xmdf2 xmdf3 zfp
+	for x in expat freetype hdf5 jpeg jsoncpp kissfft libharu libxml2 lz4 netcdf pugixml png tiff zlib; do
+		ebegin "Dropping bundled ${x}"
+		rm -r ThirdParty/${x}/vtk${x} || die
+		eend $?
+	done
+
+	sed -i -e '/add_subdirectory(vtkpugixml)/d' ThirdParty/pugixml/CMakeLists.txt || die
+	sed -i -e '/vtk_target_export(vtkpugixml)/d' ThirdParty/pugixml/CMakeLists.txt || die
+
+	# my_bool is no longer used in MySQL and MariaDB isn't supported in vtk-8
+	sed -e 's/my_bool/bool/' -i IO/MySQL/vtkMySQL{Database,Query}.cxx || die
+
+	if use doc; then
+		einfo "Removing .md5 files from documents."
+		rm -f "${WORKDIR}"/html/*.md5 || die "Failed to remove superfluous hashes"
+		sed -e "s|\${VTK_BINARY_DIR}/Utilities/Doxygen/doc|${WORKDIR}|" \
+			-i Utilities/Doxygen/CMakeLists.txt || die
+	fi
+}
+
+src_configure() {
+	# general configuration
+	local mycmakeargs=(
+		-Wno-dev
+		-DVTK_DIR="${S}"
+		-DVTK_INSTALL_LIBRARY_DIR=$(get_libdir)
+		-DVTK_INSTALL_PACKAGE_DIR="$(get_libdir)/cmake/${PN}-${SPV}"
+		-DVTK_INSTALL_DOC_DIR="${EPREFIX}/usr/share/doc/${PF}"
+		-DVTK_DATA_ROOT="${EPREFIX}/usr/share/${PN}/data"
+		-DVTK_CUSTOM_LIBRARY_SUFFIX=""
+		-DBUILD_SHARED_LIBS=ON
+		-DVTK_USE_SYSTEM_AUTOBAHN=ON
+		-DVTK_USE_SYSTEM_EXPAT=ON
+		-DVTK_USE_SYSTEM_FREETYPE=ON
+		-DVTK_USE_SYSTEM_FreeType=ON
+		# Use bundled gl2ps (bundled version is a patched version of 1.3.9. Post 1.3.9 versions should be compatible)
+		-DVTK_USE_SYSTEM_GL2PS=OFF
+		-DVTK_USE_SYSTEM_HDF5=ON
+		-DVTK_USE_SYSTEM_JPEG=ON
+		-DVTK_USE_SYSTEM_LIBPROJ=OFF
+		-DVTK_USE_SYSTEM_LIBXML2=ON
+		-DVTK_USE_SYSTEM_LibXml2=ON
+		-DVTK_USE_SYSTEM_NETCDF=ON
+		-DVTK_USE_SYSTEM_OGGTHEORA=ON
+		-DVTK_USE_SYSTEM_PUGIXML=ON
+		-DVTK_USE_SYSTEM_PNG=ON
+		-DVTK_USE_SYSTEM_TIFF=ON
+		-DVTK_USE_SYSTEM_TWISTED=ON
+		-DVTK_USE_SYSTEM_XDMF2=OFF
+		-DVTK_USE_SYSTEM_XDMF3=OFF
+		-DVTK_USE_SYSTEM_ZLIB=ON
+		-DVTK_USE_SYSTEM_ZOPE=ON
+		-DVTK_USE_SYSTEM_LIBRARIES=ON
+		# Use bundled diy2 (no gentoo package / upstream does not provide a Finddiy2.cmake or diy2Config.cmake / diy2-config.cmake)
+		-DVTK_USE_SYSTEM_DIY2=OFF
+		-DVTK_USE_GL2PS=ON
+		-DVTK_USE_LARGE_DATA=ON
+		-DVTK_USE_PARALLEL=ON
+		-DVTK_EXTRA_COMPILER_WARNINGS=ON
+		-DVTK_Group_StandAlone=ON
+		-DBUILD_DOCUMENTATION=$(usex doc)
+		-DBUILD_EXAMPLES=$(usex examples)
+		-DBUILD_VTK_BUILD_ALL_MODULES_FOR_TESTS=off
+		-DVTK_BUILD_ALL_MODULES=$(usex all-modules)
+		-DUSE_DOCUMENTATION_HTML_HELP=$(usex doc)
+		-DVTK_Group_Imaging=$(usex imaging)
+		-DVTK_Group_MPI=$(usex mpi)
+		-DVTK_Group_Rendering=$(usex rendering)
+		-DVTK_Group_Tk=$(usex tk)
+		-DVTK_Group_Views=$(usex views)
+		-DVTK_Group_Web=$(usex web)
+		-DVTK_SMP_IMPLEMENTATION_TYPE="$(usex tbb TBB Sequential)"
+		-DVTK_WWW_DIR="${EPREFIX}/${MY_HTDOCSDIR}"
+		-DVTK_WRAP_JAVA=$(usex java)
+		-DVTK_WRAP_PYTHON=$(usex python)
+		-DVTK_WRAP_PYTHON_SIP=$(usex python)
+		-DVTK_WRAP_TCL=$(usex tcl)
+		-DVTK_USE_BOOST=$(usex boost)
+		-DUSE_VTK_USE_BOOST=$(usex boost)
+		-DModule_vtkInfovisBoost=$(usex boost)
+		-DModule_vtkInfovisBoostGraphAlgorithms=$(usex boost)
+		-DVTK_USE_ODBC=$(usex odbc)
+		-DModule_vtkIOODBC=$(usex odbc)
+		-DVTK_USE_OFFSCREEN=$(usex offscreen)
+		-DVTK_OPENGL_HAS_OSMESA=$(usex offscreen)
+		-DVTK_USE_OGGTHEORA_ENCODER=$(usex theora)
+		-DVTK_USE_NVCONTROL=$(usex video_cards_nvidia)
+		-DModule_vtkFiltersStatisticsGnuR=$(usex R)
+		-DVTK_USE_X=$(usex X)
+	# IO
+		-DVTK_USE_FFMPEG_ENCODER=$(usex ffmpeg)
+		-DModule_vtkIOGDAL=$(usex gdal)
+		-DModule_vtkIOGeoJSON=$(usex json)
+		-DModule_vtkIOXdmf2=$(usex all-modules)
+		-DBUILD_TESTING=$(usex examples)
+	# Apple stuff, does it really work?
+		-DVTK_USE_COCOA=$(usex aqua)
+	)
+
+	if use all-modules; then
+		mycmakeargs+=(
+			-DVTK_MODULE_USE_EXTERNAL_VTK_pegtl=ON
+			# we don't have a package for zfp yet
+			-DVTK_USE_SYSTEM_ZFP=OFF
+		)
+	fi
+
+	if use java; then
+		local javacargs=$(java-pkg_javac-args)
+		mycmakeargs+=( -DJAVAC_OPTIONS=${javacargs// /;} )
+	fi
+
+	if use mpi; then
+		mycmakeargs+=( -DVTK_USE_SYSTEM_MPI4PY=ON )
+	fi
+
+	if use python; then
+		mycmakeargs+=(
+			-DVTK_INSTALL_PYTHON_MODULES_DIR="$(python_get_sitedir)"
+			-DPYTHON_INCLUDE_DIR="$(python_get_includedir)"
+			-DPYTHON_LIBRARY="$(python_get_library_path)"
+			-DSIP_PYQT_DIR="${EPREFIX}/usr/share/sip"
+			-DSIP_INCLUDE_DIR="$(python_get_includedir)"
+			-DVTK_PYTHON_INCLUDE_DIR="$(python_get_includedir)"
+			-DVTK_PYTHON_LIBRARY="$(python_get_library_path)"
+#			-DVTK_PYTHON_SETUP_ARGS:STRING="--prefix=${EPREFIX} --root=${D}"
+			-DVTK_USE_SYSTEM_SIX=ON
+		)
+	fi
+
+	if use qt5; then
+		mycmakeargs+=(
+			-DVTK_USE_QVTK=ON
+			-DVTK_USE_QVTK_OPENGL=ON
+			-DVTK_USE_QVTK_QTOPENGL=ON
+			-DQT_WRAP_CPP=ON
+			-DQT_WRAP_UI=ON
+			-DVTK_INSTALL_QT_DIR="$(basename $(qt5_get_libdir))/qt5/plugins/designer"
+			-DDESIRED_QT_VERSION=5
+			-DVTK_QT_VERSION=5
+			-DQT_MOC_EXECUTABLE="$(qt5_get_bindir)/moc"
+			-DQT_UIC_EXECUTABLE="$(qt5_get_bindir)/uic"
+			-DQT_INCLUDE_DIR="${EPREFIX}/usr/include/qt5"
+			-DQT_QMAKE_EXECUTABLE="$(qt5_get_bindir)/qmake"
+			-DVTK_Group_Qt:BOOL=ON
+			-DCMAKE_DISABLE_FIND_PACKAGE_Qt5WebKitWidgets=ON
+		)
+	fi
+
+	if use R; then
+		mycmakeargs+=(
+			-DR_LIBRARY_BLAS=/usr/$(get_libdir)/R/lib/libR.so
+			-DR_LIBRARY_LAPACK=/usr/$(get_libdir)/R/lib/libR.so
+		)
+	fi
+
+	append-cppflags -D__STDC_CONSTANT_MACROS -D_UNICODE
+
+	use java && export JAVA_HOME="${EPREFIX}/etc/java-config-2/current-system-vm"
+
+	if use mpi; then
+		export CC=mpicc
+		export CXX=mpicxx
+		export FC=mpif90
+		export F90=mpif90
+		export F77=mpif77
+	fi
+
+	cmake_src_configure
+}
+
+src_install() {
+	use web && webapp_src_preinst
+
+	cmake_src_install
+
+	use java && java-pkg_regjar "${ED}"/usr/$(get_libdir)/${PN}.jar
+
+	# Stop web page images from being compressed
+	use doc && docompress -x /usr/share/doc/${PF}/doxygen
+
+	if use tcl; then
+		# install Tcl docs
+		docinto vtk_tcl
+		docinto .
+	fi
+
+	# install examples
+	if use examples; then
+		einfo "Installing examples"
+		mv -v {E,e}xamples || die
+		dodoc -r examples
+		docompress -x /usr/share/doc/${PF}/examples
+	fi
+
+	# with MPI, rpaths are not deleted properly
+	if use mpi; then
+		chrpath -d "${ED}"/usr/$(get_libdir)/*.so.* || die
+		if use python; then
+			chrpath -d "${ED}"/$(python_get_sitedir)/vtkmodules/*.so || die
+			chrpath -d "${ED}"/usr/bin/{,p}vtkpython || die
+		fi
+	fi
+
+	use python && python_optimize
+
+	# environment
+	cat >> "${T}"/40${PN} <<- EOF || die
+		VTK_DATA_ROOT=${EPREFIX}/usr/share/${PN}/data
+		VTK_DIR=${EPREFIX}/usr/$(get_libdir)/${PN}-${SPV}
+		VTKHOME=${EPREFIX}/usr
+		EOF
+	doenvd "${T}"/40${PN}
+
+	use web && webapp_src_install
+}
+
+# webapp.eclass exports these but we want it optional #534036
+pkg_postinst() {
+	use web && webapp_pkg_postinst
+}
+
+pkg_prerm() {
+	use web && webapp_pkg_prerm
+}