sci-libs/itk: version bump 5.1.0 ahead of Gentoo Science

Package-Manager: Portage-3.0.0, Repoman-2.3.23
Signed-off-by: Horea Christian <chr@chymera.eu>

sci-libs/itk/ChangeLog

@@ -0,0 +1,5 @@
+*itk-5.1.0 (04 Aug 2020)
+
+  04 Aug 2020;  <chymera@gentoo.org> +files/itk-5.1.0-downloads.patch,
+  +files/tests.patch, +itk-5.1.0.ebuild, +metadata.xml:
+  sci-libs/itk: version bump 5.1.0 ahead of Gentoo Science

sci-libs/itk/Manifest

@@ -0,0 +1,3 @@
+DIST ITKGenericLabelInterpolator-5.1.0.zip 161970 SHA256 8c6cda6d4d8bac95347576b35355cc7a0fe127396b2c96fb8688b413045ff704 SHA512 26304168d2dc6f825ba085912c50a179e101da281b3d646109250c5ac9d12f2ad2216f967a81fb12d54ebd55ff7b17a355658282d7c65efb16dafb311fb3fc2c WHIRLPOOL d183ea141b212fa2247f595155836710cee5c05049caa0c67326a9ebb9eaf16f192464580ac616ab5970242704a797afb5fda9ecd79a19f3e41b2556c42bdd8d
+DIST InsightData-5.1.0.tar.gz 292322103 SHA256 777f587c587b47d76157a0ee87a5942b944742f334b801abe0e6dc1ad1d8424f SHA512 458c2959ba5e0745eee23e16ff7178230a7bae94d7dff065b3b38136e238becff96554693e3b2149d2307949c23a6c695c92676f8d44e6f7305dbb8bed48c9fa WHIRLPOOL d5785f862c627cabc97c469ac9fb84d1493e1827fd993c68ed5019e7062adc7fe68efe6ab2471c7c6b2a9d542cbfdb1a00c6633fa7be498cbc9e09fa12d3710a
+DIST InsightToolkit-5.1.0.tar.gz 20694338 SHA256 121020a1611508cec8123eb5226215598cec07be627d843a2e6b6da891e61d13 SHA512 413b6ef549b59d8f507038130446ccb704794c6d0980d8ab631d1b1051cb91f399e77c26b69fab6a1e9b9bb4cc233d49996c3ee735cd4de065993d4379b4ed4c WHIRLPOOL bbe7368cc46dc1a0869d8ab47218d0777e689be17114048653a537fbe792dfc0eb0e687b06fa894218cc35ef95143df75a46c17ffd6b072233e9f72a3c811825

sci-libs/itk/files/itk-5.1.0-downloads.patch

@@ -0,0 +1,20 @@
+--- a/CMake/ITKDownloadSetup.cmake	2020-07-30 19:03:10.330325423 -0400
++++ b/CMake/ITKDownloadSetup.cmake	2020-07-30 19:03:10.330325423 -0400
+@@ -11,7 +11,7 @@
+
+ macro(itk_download_attempt_check _name)
+   if(ITK_FORBID_DOWNLOADS)
+-    message(SEND_ERROR "Attempted to download ${_name} when ITK_FORBID_DOWNLOADS is ON")
++    message("Warning: Attempted to download ${_name} when ITK_FORBID_DOWNLOADS is ON")
+   endif()
+ endmacro()
+
+--- a/Modules/Remote/GenericLabelInterpolator.remote.cmake	2020-04-25 14:30:53.000000000 -0400
++++ b/Modules/Remote/GenericLabelInterpolator.remote.cmake	2020-04-25 14:30:53.000000000 -0400
+@@ -44,6 +44,4 @@
+ itk_fetch_module(GenericLabelInterpolator
+   "A generic interpolator for multi-label images."
+   MODULE_COMPLIANCE_LEVEL 2
+-  GIT_REPOSITORY ${git_protocol}://github.com/InsightSoftwareConsortium/ITKGenericLabelInterpolator.git
+-  GIT_TAG b95fe46c7f4fe8002af67c67e6fe4e1f087bf6b7
+   )

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()

sci-libs/itk/itk-5.1.0.ebuild

@@ -0,0 +1,177 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+PYTHON_COMPAT=( python2_7 python3_{5,6,7} )
+
+inherit toolchain-funcs cmake python-single-r1
+
+MY_PN="InsightToolkit"
+MY_P="${MY_PN}-${PV}"
+GLI_HASH="a02cbeaf28cb3d28ac66b9ac651073530eb6ab78"
+GLI_TEST_HASH="57b5d5de8d777f10f269445a"
+
+DESCRIPTION="NLM Insight Segmentation and Registration Toolkit"
+HOMEPAGE="http://www.itk.org"
+SRC_URI="
+	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://github.com/InsightSoftwareConsortium/ITK/releases/download/v${PV}/InsightData-${PV}.tar.gz
+		)
+	"
+#https://github.com/InsightSoftwareConsortium/ITKGenericLabelInterpolator/archive/${GLI_HASH}.zip -> ITKGenericLabelInterpolator-${PV}.zip
+#https://data.kitware.com/api/v1/folder/${GLI_TEST_HASH}/download -> ITKGenericLabelInterpolator_test-${PV}.zip
+RESTRICT="primaryuri"
+
+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=
+	media-libs/openjpeg:2
+	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=[rendering,python?] )
+"
+DEPEND="${RDEPEND}
+	sys-apps/coreutils
+	python? (
+		>=dev-lang/swig-2.0:0
+		dev-cpp/castxml
+	)
+	doc? ( app-doc/doxygen )
+"
+
+REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )"
+
+S="${WORKDIR}/${MY_P}"
+
+PATCHES=(
+	"${FILESDIR}"/tests.patch
+	"${FILESDIR}"/${P}-downloads.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 ${ITK_WRAP_DIMS} ]]; then
+		elog "For Python language bindings, you can define the dimensions"
+		elog "you want to create bindings for by setting"
+		elog "    ITK_WRAP_DIMS=X;Y;Z..."
+		elog "in make.conf, default is 2;3 for 2D and 3D data"
+	fi
+}
+
+src_prepare() {
+	sed -i -e "s/find_package(OpenJPEG 2.0.0/find_package(OpenJPEG/g"\
+		Modules/ThirdParty/GDCM/src/gdcm/CMakeLists.txt
+	ln -sr ../ITKGenericLabelInterpolator-* Modules/External/ITKGenericLabelInterpolator || die
+	#if use test; then
+	#	for filename in ../GenericLabelInterpolator/test/*/*mha; do
+	#		MD5=$(md5sum $filename) || die
+	#		MD5=${MD5%  *} || die
+	#		cp "$filename" ".ExternalData/MD5/${MD5}" || die
+	#	done
+	#fi
+	cmake_src_prepare
+}
+
+src_configure() {
+	local mycmakeargs=(
+		-DBUILD_EXAMPLES="$(usex examples ON OFF)"
+		-DBUILD_SHARED_LIBS=ON
+		-DBUILD_TESTING="$(usex test ON OFF)"
+		-Ddouble-conversion_INCLUDE_DIRS="${EPREFIX}/usr/include/double-conversion"
+		-DExternalData_OBJECT_STORES="${WORKDIR}/InsightToolkit-${PV}/.ExternalData"
+		-DGDCM_USE_SYSTEM_OPENJPEG=ON
+		-DITK_FORBID_DOWNLOADS:BOOL=ON
+		-DITK_INSTALL_LIBRARY_DIR=$(get_libdir)
+		-DITK_USE_REVIEW="$(usex review ON OFF)"
+		-DITK_USE_SYSTEM_DCMTK=ON
+		-DITK_USE_SYSTEM_DOUBLECONVERSION=ON
+		-DITK_USE_SYSTEM_CASTXML=ON
+		-DITK_USE_SYSTEM_HDF5=ON
+		-DITK_USE_SYSTEM_JPEG=ON
+		-DITK_USE_SYSTEM_PNG=ON
+		-DITK_USE_SYSTEM_SWIG=ON
+		-DITK_USE_SYSTEM_TIFF=ON
+		-DITK_USE_SYSTEM_ZLIB=ON
+		-DITK_USE_KWSTYLE=OFF
+		-DITK_BUILD_DEFAULT_MODULES=ON
+		-DITK_COMPUTER_MEMORY_SIZE="${ITK_COMPUTER_MEMORY_SIZE:-1}"
+		-DModule_GenericLabelInterpolator:BOOL=ON
+		-DModule_ITKReview:BOOL=ON
+		-DWRAP_ITK_JAVA=OFF
+		-DWRAP_ITK_TCL=OFF
+	)
+	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="${ITK_WRAP_DIMS:-2;3}"
+		)
+	else
+		mycmakeargs+=(
+			-DITK_WRAP_PYTHON=OFF
+		)
+	fi
+	cmake_src_configure
+}
+
+src_install() {
+	cmake_src_install
+
+	if use examples; then
+		insinto /usr/share/doc/${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
+}

sci-libs/itk/metadata.xml

@@ -0,0 +1,23 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>maintainer-wanted@gentoo.org</email>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci-biology@gentoo.org</email>
+		<name>Gentoo Biology Project</name>
+	</maintainer>
+	<longdescription lang="en">
+Insight Segmentation and Registration Toolkit (ITK) is a library
+that provides developers with an extensive suite of tools for image
+analysis.
+</longdescription>
+	<use>
+		<flag name="review">Enable compilation of methods under review</flag>
+		<flag name="vtkglue">PLEASE FIX MY DESCRIPTION</flag>
+	</use>
+	<upstream>
+		<remote-id type="sourceforge">itk</remote-id>
+	</upstream>
+</pkgmetadata>