[gentoo-commits] proj/sci:master commit in: sci-libs/itk/, sci-libs/itk/files/

["Horea Christian" <horea.christ@gmail.com>]

commit:     445eb95b61c9b12481b24f962123d0f13e940ab6
Author:     Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Mon Sep  9 08:25:49 2019 +0000
Commit:     Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Mon Sep  9 08:25:49 2019 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=445eb95b

sci-libs/itk: version bump to 5.0.1

And removed deprecated versions on account of gccxml removal

Package-Manager: Portage-2.3.72, Repoman-2.3.17
Signed-off-by: Horea Christian <chr <AT> chymera.eu>

 sci-libs/itk/files/ITKModuleRemote.patch           |  45 ++++++
 sci-libs/itk/files/tests.patch                     |  41 ++++++
 sci-libs/itk/itk-4.12.0.ebuild                     | 136 ------------------
 sci-libs/itk/itk-4.4.2-r1.ebuild                   | 135 ------------------
 sci-libs/itk/itk-4.4.2.ebuild                      | 115 ---------------
 sci-libs/itk/itk-4.5.1.ebuild                      | 155 ---------------------
 .../itk/{itk-5.0_rc1.ebuild => itk-5.0.1.ebuild}   |  50 +++++--
 sci-libs/itk/metadata.xml                          |   1 -
 8 files changed, 124 insertions(+), 554 deletions(-)

diff --git a/sci-libs/itk/files/ITKModuleRemote.patch b/sci-libs/itk/files/ITKModuleRemote.patch
new file mode 100644
index 000000000..eb130159a
--- /dev/null
+++ b/sci-libs/itk/files/ITKModuleRemote.patch
@@ -0,0 +1,45 @@
+Disable automatic git clone attempt for modules:
+https://github.com/InsightSoftwareConsortium/ITK/issues/1157
+
+--- a/CMake/ITKModuleRemote.cmake	2019-08-13 18:10:33.385472767 +0200
++++ b/CMake/ITKModuleRemote.cmake	2019-08-13 18:12:04.020198966 +0200
+@@ -165,39 +165,4 @@
+     set(Module_${_name} ON CACHE FORCE "${_description}")
+   endif()
+ 
+-  if(Module_${_name})
+-    itk_download_attempt_check(Module_${_name})
+-    include(CMakeParseArguments)
+-    cmake_parse_arguments(_fetch_options "" "GIT_REPOSITORY;GIT_TAG" "" ${ARGN})
+-    find_package(Git)
+-    if(NOT GIT_EXECUTABLE)
+-      message(FATAL_ERROR "error: could not find git for clone of ${_name}")
+-    endif()
+-    execute_process(
+-      COMMAND "${GIT_EXECUTABLE}" --version
+-      OUTPUT_VARIABLE ov
+-      OUTPUT_STRIP_TRAILING_WHITESPACE
+-      )
+-    string(REGEX REPLACE "^git version (.+)$" "\\1" _version "${ov}")
+-    if("${_version}" VERSION_LESS 1.6.6)
+-      message(FATAL_ERROR "Git version 1.6.6 or later is required.")
+-    endif()
+-
+-    set(REMOTE_GIT_TAG "${_fetch_options_GIT_TAG}")
+-
+-    if( DEFINED REMOTE_GIT_TAG_${_name} AND NOT "${REMOTE_GIT_TAG_${_name}}" STREQUAL "${_fetch_options_GIT_TAG}")
+-      set(REMOTE_GIT_TAG "${REMOTE_GIT_TAG_${_name}}")
+-      message(STATUS "NOTE: Using override 'REMOTE_GIT_TAG_${_name}=${REMOTE_GIT_TAG}'\n"
+-                     "      instead of value 'GIT_TAG=${_fetch_options_GIT_TAG}'\n"
+-                     "      specified in file ${ITK_SOURCE_DIR}/Modules/Remote/${_name}.remote.cmake'")
+-    endif()
+-    set(REMOTE_GIT_TAG_${_name} "${REMOTE_GIT_TAG}" CACHE STRING "Override default GIT_TAG value for remote module ${_name}")
+-    mark_as_advanced(REMOTE_GIT_TAG_${_name})
+-
+-    _fetch_with_git("${GIT_EXECUTABLE}"
+-      "${_fetch_options_GIT_REPOSITORY}"
+-      "${REMOTE_GIT_TAG}"
+-      "${ITK_SOURCE_DIR}/Modules/Remote/${_name}"
+-      )
+-  endif()
+ endfunction()

diff --git a/sci-libs/itk/files/tests.patch b/sci-libs/itk/files/tests.patch
new file mode 100644
index 000000000..c24714e4d
--- /dev/null
+++ b/sci-libs/itk/files/tests.patch
@@ -0,0 +1,41 @@
+Known to fail by upstream:
+https://github.com/InsightSoftwareConsortium/ITK/issues/1212#issuecomment-527998115
+
+--- a/Modules/Bridge/VtkGlue/test/CMakeLists.txt	2019-09-09 00:45:14.736032139 +0200
++++ b/Modules/Bridge/VtkGlue/test/CMakeLists.txt	2019-09-09 00:49:42.183935497 +0200
+@@ -7,8 +7,6 @@
+ if(NOT VTK_RENDERING_BACKEND STREQUAL "None")
+   list(APPEND ITKVtkGlueTests
+     itkVtkMedianFilterTest.cxx
+-    itkVtkConnectedComponentImageFilterTest.cxx
+-    QuickViewTest.cxx
+     # ### runViewImage ###
+     # No test generated. Use it for view images (2D or 3D) with:
+     # ITKVtkGlueTestDriver runViewImage image_file
+@@ -40,26 +38,3 @@
+   NAME itkVTKImageToImageFilterTest
+   COMMAND ITKVtkGlueTestDriver
+     itkVTKImageToImageFilterTest)
+-
+-if(NOT VTK_RENDERING_BACKEND STREQUAL "None")
+-  itk_add_test(
+-    NAME itkVtkMedianImageFilterTest
+-    COMMAND ITKVtkGlueTestDriver
+-      itkVtkMedianFilterTest DATA{${ITK_DATA_ROOT}/Input/cthead1.png} 2)
+-  set_property(TEST itkVtkMedianImageFilterTest APPEND PROPERTY LABELS REQUIRES_DISPLAY)
+-
+-  itk_add_test(
+-    NAME QuickViewTest
+-    COMMAND ITKVtkGlueTestDriver
+-             --compare DATA{Baseline/QuickViewTest.png,:}
+-                       ${ITK_TEST_OUTPUT_DIR}/QuickViewTest0.png
+-             --compareNumberOfPixelsTolerance 1500
+-      QuickViewTest DATA{${ITK_DATA_ROOT}/Input/peppers.png} ${ITK_TEST_OUTPUT_DIR})
+-  set_property(TEST QuickViewTest APPEND PROPERTY LABELS REQUIRES_DISPLAY)
+-
+-  itk_add_test(
+-    NAME itkVtkConnectedComponentImageFilterTest
+-    COMMAND ITKVtkGlueTestDriver
+-      itkVtkConnectedComponentImageFilterTest DATA{${ITK_DATA_ROOT}/Input/cthead1.png})
+-  set_property(TEST itkVtkConnectedComponentImageFilterTest APPEND PROPERTY LABELS REQUIRES_DISPLAY)
+-endif()

diff --git a/sci-libs/itk/itk-4.12.0.ebuild b/sci-libs/itk/itk-4.12.0.ebuild
deleted file mode 100644
index a9633748b..000000000
--- a/sci-libs/itk/itk-4.12.0.ebuild
+++ /dev/null
@@ -1,136 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit eutils toolchain-funcs cmake-utils python-single-r1
-
-MYPN=InsightToolkit
-MYP=${MYPN}-${PV}
-DOC_PV=4.5.0
-
-DESCRIPTION="NLM Insight Segmentation and Registration Toolkit"
-HOMEPAGE="http://www.itk.org"
-SRC_URI="mirror://sourceforge/${PN}/${MYP}.tar.xz
-	doc? ( mirror://sourceforge/${PN}/Doxygen${MYPN}-${DOC_PV}.tar.gz )"
-RESTRICT="primaryuri"
-
-LICENSE="Apache-2.0"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="debug doc examples +fftw itkv3compat python review cpu_flags_x86_sse2 test vtkglue"
-
-RDEPEND="
-	dev-libs/double-conversion:0=
-	media-libs/libpng:0=
-	media-libs/tiff:0=
-	sci-libs/dcmtk:0=
-	sci-libs/hdf5:0=[cxx]
-	sys-libs/zlib:0=
-	virtual/jpeg:0=
-	fftw? ( sci-libs/fftw:3.0= )
-	vtkglue? ( sci-libs/vtk:0=[python?] )
-"
-DEPEND="${RDEPEND}
-	python? (
-		${PYTHON_DEPS}
-		>=dev-lang/swig-2.0:0
-		>=dev-cpp/gccxml-0.9.0_pre20120309
-	)
-	doc? ( app-doc/doxygen )
-"
-
-REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )"
-
-S="${WORKDIR}/${MYP}"
-
-PATCHES=(
-	"${FILESDIR}/nrrdio-linking.patch"
-)
-
-get_memory() {
-	free --giga | grep Mem | cut -d ' ' -f 15 || die 'unable to get memory size'
-}
-
-src_configure() {
-	sed -i \
-		-e '/find_package/d' \
-		Modules/ThirdParty/DoubleConversion/CMakeLists.txt || die
-
-	local mycmakeargs=(
-		-DBUILD_SHARED_LIBS=ON
-		-DITK_USE_SYSTEM_DCMTK=ON
-		-DITK_USE_SYSTEM_DOUBLECONVERSION=ON
-		-DITK_USE_SYSTEM_HDF5=ON
-		-DITK_USE_SYSTEM_JPEG=ON
-		-DITK_USE_SYSTEM_PNG=ON
-		-DITK_USE_SYSTEM_SWIG=ON
-		-DITK_USE_SYSTEM_TIFF=ON
-		-DITK_USE_SYSTEM_ZLIB=ON
-		-DITK_BUILD_DEFAULT_MODULES=ON
-		-DITK_COMPUTER_MEMORY_SIZE="$(get_memory)"
-		-DITK_WRAP_JAVA=OFF
-		-DITK_WRAP_TCL=OFF
-		-DBUILD_TESTING=$(usex test)
-		-DBUILD_EXAMPLES=$(usex examples)
-		-DITK_USE_REVIEW=$(usex review)
-		-DITKV3_COMPATIBILITY=$(usex itkv3compat)
-		-DVNL_CONFIG_ENABLE_SSE2=$(usex cpu_flags_x86_sse2)
-	)
-	if use fftw; then
-		mycmakeargs+=(
-			-DUSE_FFTWD=ON
-			-DUSE_FFTWF=ON
-			-DUSE_SYSTEM_FFTW=ON
-			-DITK_USE_SYSTEM_FFTW=ON
-			-DITK_WRAPPING=ON
-			-DITK_WRAP_double=ON
-			-DITK_WRAP_vector_double=ON
-			-DITK_WRAP_covariant_vector_double=ON
-			-DITK_WRAP_complex_double=ON
-		)
-	fi
-	if use vtkglue; then
-		mycmakeargs+=(
-			-DModule_ITKVtkGlue=ON
-		)
-	fi
-	mycmakeargs+=(
-		-DITK_WRAP_PYTHON=$(usex python ON OFF)
-	)
-
-	cmake-utils_src_configure
-}
-
-src_install() {
-	cmake-utils_src_install
-
-	if use examples; then
-		insinto /usr/share/doc/${PF}/examples
-		docompress -x /usr/share/doc/${PF}/examples
-		doins -r "${S}"/Examples/*
-	fi
-
-	echo "ITK_DATA_ROOT=${EROOT%/}/usr/share/${PN}/data" > ${T}/40${PN}
-	local ldpath="${EROOT%/}/usr/$(get_libdir)/InsightToolkit"
-	if use python; then
-		echo "PYTHONPATH=${EROOT%/}/usr/$(get_libdir)/InsightToolkit/WrapITK/Python" >> "${T}"/40${PN}
-		ldpath="${ldpath}:${EROOT%/}/usr/$(get_libdir)/InsightToolkit/WrapITK/lib"
-	fi
-	echo "LDPATH=${ldpath}" >> "${T}"/40${PN}
-	doenvd "${T}"/40${PN}
-
-	if use doc; then
-		insinto /usr/share/doc/${PF}/api-docs
-		cd "${WORKDIR}"/html
-		rm  *.md5 || die "Failed to remove superfluous hashes"
-		einfo "Installing API docs. This may take some time."
-		insinto /usr/share/doc/${PF}/api-docs
-		doins -r *
-	fi
-
-	mv "${D}/usr/lib" "${D}/usr/$(get_libdir)" || \
-		die 'unable to fix libdir'
-}

diff --git a/sci-libs/itk/itk-4.4.2-r1.ebuild b/sci-libs/itk/itk-4.4.2-r1.ebuild
deleted file mode 100644
index 93a03a5f8..000000000
--- a/sci-libs/itk/itk-4.4.2-r1.ebuild
+++ /dev/null
@@ -1,135 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit eutils toolchain-funcs cmake-utils python-single-r1
-
-MYPN=InsightToolkit
-MYP=${MYPN}-${PV}
-
-DESCRIPTION="NLM Insight Segmentation and Registration Toolkit"
-HOMEPAGE="http://www.itk.org"
-SRC_URI="
-	mirror://sourceforge/${PN}/${MYP}.tar.gz
-	doc? ( mirror://sourceforge/${PN}/Doxygen${MYPN}-4.4.0.tar.gz )"
-RESTRICT="primaryuri"
-
-LICENSE="Apache-2.0"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="debug doc examples fftw itkv3compat python review cpu_flags_x86_sse2 test vtkglue"
-
-RDEPEND="
-	sci-libs/hdf5[cxx]
-	virtual/jpeg:0=
-	media-libs/libpng:0=
-	media-libs/tiff:0=
-	sys-libs/zlib
-	fftw? ( sci-libs/fftw:3.0 )
-	vtkglue? ( sci-libs/vtk )
-"
-DEPEND="${RDEPEND}
-	python? (
-		${PYTHON_DEPS}
-		>=dev-lang/swig-2.0:0
-		>=dev-cpp/gccxml-0.9.0_pre20120309
-	)
-	doc? ( app-doc/doxygen )
-"
-
-S="${WORKDIR}/${MYP}"
-
-pkg_pretend() {
-	if [[ -z ${ITK_COMPUTER_MEMORY_SIZE} ]]; then
-		elog "To tune ITK to make the best use ouf working memory you can set"
-		elog "    ITK_COMPUTER_MEMORY_SIZE=XX"
-		elog "in make.conf, default is 1 (unit is GB)"
-	fi
-	if use python && [[ -z ${ITK_WRAP_DIMS} ]]; then
-		elog "For Python language bindings, you can define the dimensions"
-		elog "you want to create bindings for by setting"
-		elog "    ITK_WRAP_DIMS=X;Y;Z..."
-		elog "in make.conf, default is 2;3 for 2D and 3D data"
-	fi
-}
-
-src_configure() {
-	local mycmakeargs=(
-		-DWRAP_ITK_JAVA=OFF
-		-DWRAP_ITK_TCL=OFF
-		-DITK_USE_SYSTEM_HDF5=ON
-		-DITK_USE_SYSTEM_JPEG=ON
-		-DITK_USE_SYSTEM_PNG=ON
-		-DITK_USE_SYSTEM_TIFF=ON
-		-DITK_USE_SYSTEM_ZLIB=ON
-		-DITK_USE_SYSTEM_GCCXML=ON
-		-DITK_USE_SYSTEM_SWIG=ON
-		-DITK_BUILD_ALL_MODULES=ON
-		-DBUILD_SHARED_LIBS=ON
-		-DBUILD_EXAMPLES=OFF
-		-DITK_COMPUTER_MEMORY_SIZE="${ITK_COMPUTER_MEMORY_SIZE:-1}"
-		$(cmake-utils_use_build test TESTING)
-		$(cmake-utils_use review ITK_USE_REVIEW)
-		$(cmake-utils_use itkv3compat ITKV3_COMPATIBILITY)
-		$(cmake-utils_use cpu_flags_x86_sse2 VNL_CONFIG_ENABLE_SSE2)
-	)
-	if use fftw; then
-		mycmakeargs+=(
-			-DUSE_FFTWD=ON
-			-DUSE_FFTWF=ON
-			-DUSE_SYSTEM_FFTW=ON
-			-DITK_WRAP_double=ON
-			-DITK_WRAP_vector_double=ON
-			-DITK_WRAP_covariant_vector_double=ON
-			-DITK_WRAP_complex_double=ON
-		)
-	fi
-	if use vtkglue; then
-		mycmakeargs+=(
-			-DModule_ITKVtkGlue=ON
-		)
-	fi
-	if use python; then
-		mycmakeargs+=(
-			-DITK_WRAP_PYTHON=ON
-			-DITK_WRAP_DIMS="${ITK_WRAP_DIMS:-2;3}"
-		)
-	else
-		mycmakeargs+=(
-			-DITK_WRAP_PYTHON=OFF
-		)
-	fi
-	cmake-utils_src_configure
-}
-
-src_install() {
-	cmake-utils_src_install
-
-	if use examples; then
-		insinto /usr/share/doc/${PF}/examples
-		docompress -x /usr/share/doc/${PF}/examples
-		doins -r "${S}"/Examples/*
-	fi
-
-	echo "ITK_DATA_ROOT=${EROOT}/usr/share/${PN}/data" > ${T}/40${PN}
-	local ldpath="${EROOT}/usr/$(get_libdir)/InsightToolkit"
-	if use python; then
-		echo "PYTHONPATH=${EROOT}/usr/$(get_libdir)/InsightToolkit/WrapITK/Python" >> ${T}/40${PN}
-		ldpath="${ldpath}:${EROOT}/usr/$(get_libdir)/InsightToolkit/WrapITK/lib"
-	fi
-	echo "LDPATH=${ldpath}" >> ${T}/40${PN}
-
-	if use doc; then
-		insinto "/usr/share/doc/${PF}/api-docs"
-		cd "${WORKDIR}"/html
-		rm -f *.md5 || die "Failed to remove superfluous hashes"
-		einfo "Installing API docs. This may take some time."
-		insinto "/usr/share/doc/${PF}/api-docs"
-		doins -r ./*
-	fi
-
-	doenvd "${T}"/40${PN}
-}

diff --git a/sci-libs/itk/itk-4.4.2.ebuild b/sci-libs/itk/itk-4.4.2.ebuild
deleted file mode 100644
index 2d3b9f961..000000000
--- a/sci-libs/itk/itk-4.4.2.ebuild
+++ /dev/null
@@ -1,115 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit eutils toolchain-funcs cmake-utils python-single-r1
-
-MYP=InsightToolkit-${PV}
-
-DESCRIPTION="NLM Insight Segmentation and Registration Toolkit"
-HOMEPAGE="http://www.itk.org"
-SRC_URI="mirror://sourceforge/${PN}/${MYP}.tar.gz"
-
-LICENSE="Apache-2.0"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="debug examples fftw itkv3compat python review cpu_flags_x86_sse2 test"
-
-RDEPEND="
-	sci-libs/hdf5[cxx]
-	virtual/jpeg:0=
-	media-libs/libpng:0=
-	media-libs/tiff:0=
-	sys-libs/zlib
-	fftw? ( sci-libs/fftw:3.0 )
-"
-DEPEND="${RDEPEND}
-	python? (
-		${PYTHON_DEPS}
-		>=dev-lang/swig-2.0:0
-		>=dev-cpp/gccxml-0.9.0_pre20120309
-	)
-"
-
-S="${WORKDIR}/${MYP}"
-
-pkg_pretend() {
-	if [[ -z ${ITK_COMPUTER_MEMORY_SIZE} ]]; then
-		elog "To tune ITK to make the best use ouf working memory you can set"
-		elog "    ITK_COMPUTER_MEMORY_SIZE=XX"
-		elog "in make.conf, default is 1 (unit is GB)"
-	fi
-	if use python && [[ -z ${ITK_WRAP_DIMS} ]]; then
-		elog "For Python language bindings, you can define the dimensions"
-		elog "you want to create bindings for by setting"
-		elog "    ITK_WRAP_DIMS=X;Y;Z..."
-		elog "in make.conf, default is 2;3 for 2D and 3D data"
-	fi
-}
-
-src_configure() {
-	local mycmakeargs=(
-		-DWRAP_ITK_JAVA=OFF
-		-DWRAP_ITK_TCL=OFF
-		-DITK_USE_SYSTEM_HDF5=ON
-		-DITK_USE_SYSTEM_JPEG=ON
-		-DITK_USE_SYSTEM_PNG=ON
-		-DITK_USE_SYSTEM_TIFF=ON
-		-DITK_USE_SYSTEM_ZLIB=ON
-		-DITK_USE_SYSTEM_GCCXML=ON
-		-DITK_USE_SYSTEM_SWIG=ON
-		-DITK_BUILD_ALL_MODULES=ON
-		-DBUILD_SHARED_LIBS=ON
-		-DBUILD_EXAMPLES=OFF
-		-DITK_COMPUTER_MEMORY_SIZE="${ITK_COMPUTER_MEMORY_SIZE:-1}"
-		$(cmake-utils_use_build test TESTING)
-		$(cmake-utils_use review ITK_USE_REVIEW)
-		$(cmake-utils_use itkv3compat ITKV3_COMPATIBILITY)
-		$(cmake-utils_use cpu_flags_x86_sse2 VNL_CONFIG_ENABLE_SSE2)
-	)
-	if use fftw; then
-		mycmakeargs+=(
-			-DUSE_FFTWD=ON
-			-DUSE_FFTWF=ON
-			-DUSE_SYSTEM_FFTW=ON
-			-DITK_WRAP_double=ON
-			-DITK_WRAP_vector_double=ON
-			-DITK_WRAP_covariant_vector_double=ON
-			-DITK_WRAP_complex_double=ON
-		)
-	fi
-	if use python; then
-		mycmakeargs+=(
-			-DITK_WRAP_PYTHON=ON
-			-DITK_WRAP_DIMS="${ITK_WRAP_DIMS:-2;3}"
-		)
-	else
-		mycmakeargs+=(
-			-DITK_WRAP_PYTHON=OFF
-		)
-	fi
-	cmake-utils_src_configure
-}
-
-src_install() {
-	cmake-utils_src_install
-
-	if use examples; then
-		insinto /usr/share/doc/${PF}/examples
-		docompress -x /usr/share/doc/${PF}/examples
-		doins -r "${S}"/Examples/*
-	fi
-
-	echo "ITK_DATA_ROOT=${EROOT}/usr/share/${PN}/data" > ${T}/40${PN}
-	local ldpath="${EROOT}/usr/$(get_libdir)/InsightToolkit"
-	if use python; then
-		echo "PYTHONPATH=${EROOT}/usr/$(get_libdir)/InsightToolkit/WrapITK/Python" >> ${T}/40${PN}
-		ldpath="${ldpath}:${EROOT}/usr/$(get_libdir)/InsightToolkit/WrapITK/lib"
-	fi
-	echo "LDPATH=${ldpath}" >> ${T}/40${PN}
-
-	doenvd "${T}"/40${PN}
-}

diff --git a/sci-libs/itk/itk-4.5.1.ebuild b/sci-libs/itk/itk-4.5.1.ebuild
deleted file mode 100644
index 199c03659..000000000
--- a/sci-libs/itk/itk-4.5.1.ebuild
+++ /dev/null
@@ -1,155 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit eutils toolchain-funcs cmake-utils python-single-r1
-
-MYPN=InsightToolkit
-MYP=${MYPN}-${PV}
-DOC_PV=4.5.0
-
-DESCRIPTION="NLM Insight Segmentation and Registration Toolkit"
-HOMEPAGE="http://www.itk.org"
-SRC_URI="mirror://sourceforge/${PN}/${MYP}.tar.xz
-	doc? ( mirror://sourceforge/${PN}/Doxygen${MYPN}-${DOC_PV}.tar.gz )"
-RESTRICT="primaryuri"
-
-LICENSE="Apache-2.0"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="debug doc examples fftw itkv3compat python review cpu_flags_x86_sse2 test vtkglue"
-
-RDEPEND="
-	dev-libs/double-conversion:0=
-	media-libs/libpng:0=
-	media-libs/tiff:0=
-	sci-libs/dcmtk:0=
-	sci-libs/hdf5:0=[cxx]
-	sys-libs/zlib:0=
-	virtual/jpeg:0=
-	fftw? ( sci-libs/fftw:3.0= )
-	vtkglue? ( sci-libs/vtk:0=[python?] )
-"
-DEPEND="${RDEPEND}
-	python? (
-		${PYTHON_DEPS}
-		>=dev-lang/swig-2.0:0
-		>=dev-cpp/gccxml-0.9.0_pre20120309
-	)
-	doc? ( app-doc/doxygen )
-"
-
-REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )"
-
-S="${WORKDIR}/${MYP}"
-
-PATCHES=(
-	"${FILESDIR}"/0001-BUG-Wrap-TransformFileReader-TransformFileWriter.patch
-	"${FILESDIR}"/0002-COMP-Fixed-itkQuasiNewtonOptimizerv4-wrapping-warnin.patch
-	"${FILESDIR}"/0003-COMP-Fixed-itkGradientDescentOptimizerv4-wrapping-wa.patch
-	"${FILESDIR}"/0004-COMP-Warp-OptimizerParameterScalesEstimatorTemplate.patch
-	"${FILESDIR}"/0005-make-gdcm-helper-library-static.patch
-	"${FILESDIR}"/nrrdio-linking.patch
-)
-
-pkg_pretend() {
-	if [[ -z ${ITK_COMPUTER_MEMORY_SIZE} ]]; then
-		elog "To tune ITK to make the best use of working memory you can set"
-		elog "    ITK_COMPUTER_MEMORY_SIZE=XX"
-		elog "in make.conf, default is 1 (unit is GB)"
-	fi
-	if use python && [[ -z ${ITK_WRAP_DIMS} ]]; then
-		elog "For Python language bindings, you can define the dimensions"
-		elog "you want to create bindings for by setting"
-		elog "    ITK_WRAP_DIMS=X;Y;Z..."
-		elog "in make.conf, default is 2;3 for 2D and 3D data"
-	fi
-}
-
-src_configure() {
-	sed -i \
-		-e '/find_package/d' \
-		Modules/ThirdParty/DoubleConversion/CMakeLists.txt || die
-
-	local mycmakeargs=(
-		-DBUILD_SHARED_LIBS=ON
-		-DITK_USE_SYSTEM_DCMTK=ON
-		-DITK_USE_SYSTEM_DOUBLECONVERSION=ON
-		-DITK_USE_SYSTEM_GCCXML=ON
-		-DITK_USE_SYSTEM_HDF5=ON
-		-DITK_USE_SYSTEM_JPEG=ON
-		-DITK_USE_SYSTEM_PNG=ON
-		-DITK_USE_SYSTEM_SWIG=ON
-		-DITK_USE_SYSTEM_TIFF=ON
-		-DITK_USE_SYSTEM_ZLIB=ON
-		-DITK_BUILD_DEFAULT_MODULES=ON
-		-DITK_COMPUTER_MEMORY_SIZE="${ITK_COMPUTER_MEMORY_SIZE:-1}"
-		-DWRAP_ITK_JAVA=OFF
-		-DWRAP_ITK_TCL=OFF
-		-Ddouble-conversion_INCLUDE_DIRS="${EPREFIX}/usr/include/double-conversion"
-		-Ddouble-conversion_LIBRARIES="-ldouble-conversion"
-		$(cmake-utils_use_build test TESTING)
-		$(cmake-utils_use_build examples EXAMPLES)
-		$(cmake-utils_use review ITK_USE_REVIEW)
-		$(cmake-utils_use itkv3compat ITKV3_COMPATIBILITY)
-		$(cmake-utils_use cpu_flags_x86_sse2 VNL_CONFIG_ENABLE_SSE2)
-	)
-	if use fftw; then
-		mycmakeargs+=(
-			-DUSE_FFTWD=ON
-			-DUSE_FFTWF=ON
-			-DUSE_SYSTEM_FFTW=ON
-			-DITK_WRAP_double=ON
-			-DITK_WRAP_vector_double=ON
-			-DITK_WRAP_covariant_vector_double=ON
-			-DITK_WRAP_complex_double=ON
-		)
-	fi
-	if use vtkglue; then
-		mycmakeargs+=(
-			-DModule_ITKVtkGlue=ON
-		)
-	fi
-	if use python; then
-		mycmakeargs+=(
-			-DITK_WRAP_PYTHON=ON
-			-DITK_WRAP_DIMS="${ITK_WRAP_DIMS:-2;3}"
-		)
-	else
-		mycmakeargs+=(
-			-DITK_WRAP_PYTHON=OFF
-		)
-	fi
-	cmake-utils_src_configure
-}
-
-src_install() {
-	cmake-utils_src_install
-
-	if use examples; then
-		insinto /usr/share/doc/${PF}/examples
-		docompress -x /usr/share/doc/${PF}/examples
-		doins -r "${S}"/Examples/*
-	fi
-
-	echo "ITK_DATA_ROOT=${EROOT%/}/usr/share/${PN}/data" > ${T}/40${PN}
-	local ldpath="${EROOT%/}/usr/$(get_libdir)/InsightToolkit"
-	if use python; then
-		echo "PYTHONPATH=${EROOT%/}/usr/$(get_libdir)/InsightToolkit/WrapITK/Python" >> "${T}"/40${PN}
-		ldpath="${ldpath}:${EROOT%/}/usr/$(get_libdir)/InsightToolkit/WrapITK/lib"
-	fi
-	echo "LDPATH=${ldpath}" >> "${T}"/40${PN}
-	doenvd "${T}"/40${PN}
-
-	if use doc; then
-		insinto /usr/share/doc/${PF}/api-docs
-		cd "${WORKDIR}"/html
-		rm  *.md5 || die "Failed to remove superfluous hashes"
-		einfo "Installing API docs. This may take some time."
-		insinto /usr/share/doc/${PF}/api-docs
-		doins -r *
-	fi
-}

diff --git a/sci-libs/itk/itk-5.0_rc1.ebuild b/sci-libs/itk/itk-5.0.1.ebuild
similarity index 69%
rename from sci-libs/itk/itk-5.0_rc1.ebuild
rename to sci-libs/itk/itk-5.0.1.ebuild
index f6433e551..e1ec7166a 100644
--- a/sci-libs/itk/itk-5.0_rc1.ebuild
+++ b/sci-libs/itk/itk-5.0.1.ebuild
@@ -1,19 +1,26 @@
 # Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
 PYTHON_COMPAT=( python2_7 python3_{5,6,7} )
 
-inherit eutils toolchain-funcs cmake-utils python-single-r1
+inherit toolchain-funcs cmake-utils python-single-r1
 
-MY_PV="5.0rc01"
+MY_PN="InsightToolkit"
+MY_P="${MY_PN}-${PV}"
+GLI_HASH="187ab99b7d42718c99e5017f0acd3900d7469bd1"
+GLI_TEST_HASH="57b5d5de8d777f10f269445a"
 
 DESCRIPTION="NLM Insight Segmentation and Registration Toolkit"
 HOMEPAGE="http://www.itk.org"
 SRC_URI="
-	https://github.com/InsightSoftwareConsortium/ITK/archive/v${MY_PV}.tar.gz
-	test? ( https://github.com/InsightSoftwareConsortium/ITK/releases/download/v5.0rc01/InsightData-${MY_PV}.tar.gz )
+	https://github.com/InsightSoftwareConsortium/ITK/releases/download/v${PV}/${MY_P}.tar.gz
+	https://github.com/InsightSoftwareConsortium/ITKGenericLabelInterpolator/archive/${GLI_HASH}.zip -> ITKGenericLabelInterpolator-${PV}.zip
+	test? (
+		https://data.kitware.com/api/v1/folder/${GLI_TEST_HASH}/download -> ITKGenericLabelInterpolator_test-${PV}.zip
+		https://github.com/InsightSoftwareConsortium/ITK/releases/download/v${PV}/InsightData-${PV}.tar.gz
+		)
 	"
 RESTRICT="primaryuri"
 
@@ -21,6 +28,9 @@ LICENSE="Apache-2.0"
 SLOT="0"
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
 IUSE="debug doc examples fftw python review test vtkglue"
+# python will not work, this is a know issue upstream:
+# https://github.com/InsightSoftwareConsortium/ITK/issues/1229
+# https://github.com/InsightSoftwareConsortium/ITKGenericLabelInterpolator/issues/10
 
 RDEPEND="
 	dev-libs/double-conversion:0=
@@ -32,20 +42,25 @@ RDEPEND="
 	sys-libs/zlib:0=
 	virtual/jpeg:0=
 	fftw? ( sci-libs/fftw:3.0= )
-	vtkglue? ( sci-libs/vtk:0=[python?] )
+	vtkglue? ( sci-libs/vtk:0=[rendering,python?] )
 "
 DEPEND="${RDEPEND}
+	sys-apps/coreutils
 	python? (
-		${PYTHON_DEPS}
 		>=dev-lang/swig-2.0:0
-		>=dev-cpp/gccxml-0.9.0_pre20120309
+		dev-cpp/castxml
 	)
 	doc? ( app-doc/doxygen )
 "
 
 REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )"
 
-S="${WORKDIR}/ITK-${MY_PV}"
+S="${WORKDIR}/${MY_P}"
+
+PATCHES=(
+	"${FILESDIR}"/ITKModuleRemote.patch
+	"${FILESDIR}"/tests.patch
+)
 
 pkg_pretend() {
 	if [[ -z ${ITK_COMPUTER_MEMORY_SIZE} ]]; then
@@ -64,14 +79,23 @@ pkg_pretend() {
 src_prepare() {
 	sed -i -e "s/find_package(OpenJPEG 2.0.0/find_package(OpenJPEG/g"\
 		Modules/ThirdParty/GDCM/src/gdcm/CMakeLists.txt
-	default
+	ln -sr ../ITKGenericLabelInterpolator-* Modules/Remote/ITKGenericLabelInterpolator || die
+	if use test; then
+		for filename in ../GenericLabelInterpolator/test/*/*mha; do
+			MD5=$(md5sum $filename) || die
+			MD5=${MD5%  *} || die
+			cp "$filename" ".ExternalData/MD5/${MD5}" || die
+		done
+	fi
+	cmake-utils_src_prepare
 }
 
 src_configure() {
 	local mycmakeargs=(
 		-DBUILD_SHARED_LIBS=ON
-		-DITK_USE_SYSTEM_DCMTK=ON
 		-DGDCM_USE_SYSTEM_OPENJPEG=ON
+		-DITK_FORBID_DOWNLOADS:BOOL=OFF
+		-DITK_USE_SYSTEM_DCMTK=ON
 		-DITK_USE_SYSTEM_DOUBLECONVERSION=ON
 		-DITK_USE_SYSTEM_CASTXML=ON
 		-DITK_USE_SYSTEM_HDF5=ON
@@ -86,7 +110,9 @@ src_configure() {
 		-DWRAP_ITK_JAVA=OFF
 		-DWRAP_ITK_TCL=OFF
 		-Ddouble-conversion_INCLUDE_DIRS="${EPREFIX}/usr/include/double-conversion"
-		-DExternalData_OBJECT_STORES="${WORKDIR}/InsightToolkit-${MY_PV}/.ExternalData"
+		-DExternalData_OBJECT_STORES="${WORKDIR}/InsightToolkit-${PV}/.ExternalData"
+		-DModule_GenericLabelInterpolator:BOOL=ON
+		-DModule_ITKReview:BOOL=ON
 		-DBUILD_TESTING="$(usex test ON OFF)"
 		-DBUILD_EXAMPLES="$(usex examples ON OFF)"
 		-DITK_USE_REVIEW="$(usex review ON OFF)"

diff --git a/sci-libs/itk/metadata.xml b/sci-libs/itk/metadata.xml
index 8485fb7e1..7c4535324 100644
--- a/sci-libs/itk/metadata.xml
+++ b/sci-libs/itk/metadata.xml
@@ -14,7 +14,6 @@ that provides developers with an extensive suite of tools for image
 analysis.
 </longdescription>
 	<use>
-		<flag name="itkv3compat">Enable compatibility with ITK version 3</flag>
 		<flag name="review">Enable compilation of methods under review</flag>
 		<flag name="vtkglue">PLEASE FIX MY DESCRIPTION</flag>
 	</use>