sci-libs/itk: bump to 5.0.1

Package-Manager: Portage-2.3.72, Repoman-2.3.17 Signed-off-by: Horea Christian <chr@chymera.eu>
2019-09-09 06:49:59 +02:00 · 2019-09-09 06:49:59 +02:00 · 91b6270255
parent efa17741b3
commit 91b6270255
7 changed files with 149 additions and 28 deletions
--- a/sci-libs/itk/ChangeLog
+++ b/sci-libs/itk/ChangeLog
@ -1,3 +1,10 @@
+*itk-5.0.1 (09 Sep 2019)
+
+  09 Sep 2019;  <chymera@gentoo.org> +files/ITKModuleRemote.patch,
+  +files/tests.patch, +itk-5.0.1.ebuild, -itk-4.13.2.ebuild, itk-5.0.0.ebuild,
+  metadata.xml:
+  sci-libs/itk: bump to 5.0.1
+
 *itk-5.0_rc1 (18 May 2019)

  18 May 2019;  <chymera@gentoo.org>
--- a/sci-libs/itk/Manifest
+++ b/sci-libs/itk/Manifest
@ -1,5 +1,8 @@
+DIST ITKGenericLabelInterpolator-5.0.1.zip 157566 SHA256 18a0f078bcfeee15b4d4c6e61fe67188746f15e7d765d029f537c9c1ad8615d0 SHA512 0783ec5b336bba6f89a1e8ecf92bb9a488f331b839c4ccf6ca11e40e530e4a46232d257a8814b14238695275b48ff57d63600c103c49e9b7895c385f756c533c WHIRLPOOL 5fc5e862d3f0a677945e13fcc2213e76a0a028092464d92866c36cb53501a79c5f680d55df7912962a6b8f7b834d2f930ece744e6ad6bd8c35f94ca19ab59f76
+DIST ITKGenericLabelInterpolator_test-5.0.1.zip 430662 SHA256 1fc57394b08c8cb72d145d8779c73f17095a5c32cb7ca6d60c0b3da7307a68cf SHA512 18e2fb9b2ee210250937b4c7d6dd0e5482c1d251413c50df9f3f212261b6f47d8cd120cbb923dc279f1113a86826e629df03c887e0cd41589cfe85c07cbb17a9 WHIRLPOOL 063157fb2c73c22a19894ebc3008647921a7f2c3a521dcf598c7a02a2d99a3aabbeee2c487f30af762892abc631bb89c0a89486b66009089e7ebe4e7fc55ae38
 DIST InsightData-5.0.0.tar.gz 290800449 SHA256 8c29831687ee8bd75292edf1d78c7df889b099a33480f0acc504d1fea4ed010f SHA512 0a2b55971ca04040cd7b9732a66100a848437a36768902bb81a20103232fb25dc4766177a2dba1537e1888b56a7dd1dd5ec93f30273993b826453fe8c36adf14 WHIRLPOOL 6b46ed472fe152159a74443d8616d556613edb62021b2d6123f8c5fa47eb13671940c328c2856f506a31713670bae0672a790ebbcab9740cd2b3fbae03de2cb7
+DIST InsightData-5.0.1.tar.gz 290801718 SHA256 5fc343de9ae8e5fd14ac743a8321f5fb699928c08bf8f426aab7835a92fc805e SHA512 eb766c115049949937d6527937f1f49ef84304a71dc4924581a53173f45c4e5a0c5a0e180550e75ecd840314609580b9d1fe9b2358c5a87c82a2c6aff8e9f50e WHIRLPOOL e123f5e69f4253daa1db2c2f9535cfa00a666a95b80606974b65c5d1f485a6db5656f6db0e9489cd80e550fb3d9c8e10acda7e2d2045497218619bf394a758e9
 DIST InsightData-5.0rc01.tar.gz 290621965 SHA256 c4b6172809fd86ee623311001bdf7b79e801bddb9bbb8cb7123b2e5cc04f5c4f SHA512 0be5568b75017a4c4cbfc4a4e7b0339537cd2dc23d5d5637a95002e040b96f923851bc354f3a1447d3802444a951b62d2ef66ad2a0db0961bf2bd9f47399fd9a WHIRLPOOL 35668bb25fc4fd6db3b63683cb26d62f46467f3304998ec3ddcd93cd55c9532f9701feda6f9e9e14c9d3a695434ce8c3e68ba916b1e26e3bb53df2f8aae7836b
 DIST InsightToolkit-5.0.0.tar.gz 20617888 SHA256 6ef73c8972e775632e4022a3a3158eacd039f095bb660d235b0affb9a9282b38 SHA512 7cbff9e555fe0f351cb83828ef7c1a5fbd698290d53faa438b76192685ca188f7f65a506c31e7d0d637409ea19d56467b6a1177b93b9093055104f2ec031ecd8 WHIRLPOOL a5f97080f0deed2f81e2c0d3bcfc05b9b1351a444eb31072e088ce6001e8ad9573d8d9eb6cc17df874e6e08162099161188aa125559f6bbd4e26ac6c64ef9ed8
-DIST itk-4.13.2.tar.gz 19343413 SHA256 313422d9fedd94851133aad26a65ad9541b9c40099d22b5629d010603ad17f7c SHA512 86641537f804cc2d1ddf935a36e260033a53242e8286da43fd493e48cd2530e5562440a3ce2c61f491c12461b0f5e4fb855bb22a2611417ec8faaa54b97aea96 WHIRLPOOL 0198735615c296a72bd4b1016c90f15e80d7fc724af6ff1c7415512d820cf4ebd19183b514f9607b8907de57159a03c1b23b29eaf5b00bd487f8b4fe2a29940c
+DIST InsightToolkit-5.0.1.tar.gz 20627889 SHA256 613b125cbf58481e8d1e36bdeacf7e21aba4b129b4e524b112f70c4d4e6d15a6 SHA512 f36613ff72c513ded3d32504f71308a94fe75555cf9fd22b77485d1375601f6e1f1539cc5ac82a9e1e229bcf514a88ccb55122a7dfc74a6ae1b6604aa70bd814 WHIRLPOOL 8d3f1b426c894c3ecc63981d60a763d92450b08cb00fb82e5f1afc7d034dd784580e2271ca8dba358e49af14f69a1ac52bf1321c8bcc327d1409002edfafd66a
 DIST v5.0rc01.tar.gz 20944543 SHA256 fa6cd61bc39ccdc53808b9b0df5dd95d63a3c08be130e63ab0f4b77ca9594e46 SHA512 30e327708c7717bb2131911c86802c4104730d146b4263c68ae89384d3f01a6675b3abf5962af14cc7f40984cb1e8eedd911fe0f084a8deb4c79b4239b309728 WHIRLPOOL 6447eccbb17573233f750e3462dadd4c44c177613ca88520787579cc6e10ac523488e44dbf0f3e690a0cc009443b5adccdf62b588bdf6180dbda4a98b7d03cef
--- a/sci-libs/itk/files/ITKModuleRemote.patch
+++ 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/${_name}"
+-      )
+-  endif()
+ endfunction()
--- a/sci-libs/itk/files/tests.patch
+++ b/sci-libs/itk/files/tests.patch
@ -0,0 +1,41 @@
+Known to fail by upstream:
+https://github.com/InsightSoftwareConsortium/ITK/issues/1212#issuecomment-527998115
+
+--- a/Modules/Bridge/VtkGlue/test/CMakeLists.txt	2019-09-09 00:45:14.736032139 +0200
+++ b/Modules/Bridge/VtkGlue/test/CMakeLists.txt	2019-09-09 00:49:42.183935497 +0200
+@@ -7,8 +7,6 @@
+ if(NOT VTK_RENDERING_BACKEND STREQUAL "None")
+   list(APPEND ITKVtkGlueTests
+     itkVtkMedianFilterTest.cxx
+-    itkVtkConnectedComponentImageFilterTest.cxx
+-    QuickViewTest.cxx
+     # ### runViewImage ###
+     # No test generated. Use it for view images (2D or 3D) with:
+     # ITKVtkGlueTestDriver runViewImage image_file
+@@ -40,26 +38,3 @@
+   NAME itkVTKImageToImageFilterTest
+   COMMAND ITKVtkGlueTestDriver
+     itkVTKImageToImageFilterTest)
+-
+-if(NOT VTK_RENDERING_BACKEND STREQUAL "None")
+-  itk_add_test(
+-    NAME itkVtkMedianImageFilterTest
+-    COMMAND ITKVtkGlueTestDriver
+-      itkVtkMedianFilterTest DATA{${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()
--- a/sci-libs/itk/itk-5.0.0.ebuild
+++ b/sci-libs/itk/itk-5.0.0.ebuild
@ -86,7 +86,7 @@ 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-${PV}/.ExternalData"
 		-DBUILD_TESTING="$(usex test ON OFF)"
 		-DBUILD_EXAMPLES="$(usex examples ON OFF)"
 		-DITK_USE_REVIEW="$(usex review ON OFF)"
--- a/sci-libs/itk/itk-4.13.2.ebuild
+++ b/sci-libs/itk/itk-4.13.2.ebuild
@ -1,28 +1,40 @@
-# Copyright 1999-2019 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2

-EAPI=5
+EAPI=7

-PYTHON_COMPAT=( python2_7 )
+PYTHON_COMPAT=( python2_7 python3_{5,6,7} )

 inherit eutils toolchain-funcs cmake-utils python-single-r1

-MY_HASH="3ee6f1e5c9a18235ca9ab88f7bba6056c09db56d"
+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/dzenanz/ITK/archive/${MY_HASH}.tar.gz -> ${P}.tar.gz
+	https://github.com/InsightSoftwareConsortium/ITK/releases/download/v${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-${PV}.tar.gz
+		)
 	"
-	#https://github.com/InsightSoftwareConsortium/ITK/archive/v${PV}.tar.gz -> ${P}.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"
+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=
@ -30,24 +42,24 @@ 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="${WORKDIR}/${MYP}"
-S="${WORKDIR}/ITK-${MY_HASH}"
+S="${WORKDIR}/${MY_P}"

 PATCHES=(
-	"${FILESDIR}"/nrrdio-linking.patch
+	"${FILESDIR}"/ITKModuleRemote.patch
+	"${FILESDIR}"/tests.patch
 )

 pkg_pretend() {
@ -64,34 +76,48 @@ pkg_pretend() {
 	fi
 }

-src_configure() {
-	#sed -i \
-	#	-e 's/find_package(double-conversion REQUIRED)/find_package(double-conversion CONFIG REQUIRED)/g' \
-	#	Modules/ThirdParty/DoubleConversion/CMakeLists.txt || die
+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
+}

+src_configure() {
 	local mycmakeargs=(
 		-DBUILD_SHARED_LIBS=ON
+		-DGDCM_USE_SYSTEM_OPENJPEG=ON
+		-DITK_FORBID_DOWNLOADS:BOOL=OFF
 		-DITK_USE_SYSTEM_DCMTK=ON
 		-DITK_USE_SYSTEM_DOUBLECONVERSION=ON
-		-DITK_USE_SYSTEM_GCCXML=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}"
 		-DWRAP_ITK_JAVA=OFF
 		-DWRAP_ITK_TCL=OFF
-		$(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)
-		$(cmake-utils_use cpu_flags_x86_sse2 VNL_CONFIG_ENABLE_SSE2)
+		-Ddouble-conversion_INCLUDE_DIRS="${EPREFIX}/usr/include/double-conversion"
+		-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="$(usex review ON OFF)"
+		-DITK_INSTALL_LIBRARY_DIR=$(get_libdir)
 	)
-		#-Ddouble-conversion_INCLUDE_DIRS="${EPREFIX}/usr/include/double-conversion"
-		#-Ddouble-conversion_LIBRARIES="-ldouble-conversion"
 	if use fftw; then
 		mycmakeargs+=(
 			-DUSE_FFTWD=ON
--- 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>