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>
