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>
This commit is contained in:
Horea Christian
parent
23f513cd9b
commit
4124c531d9
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*itk-5.1.0 (04 Aug 2020)
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04 Aug 2020; <chymera@gentoo.org> +files/itk-5.1.0-downloads.patch,
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+files/tests.patch, +itk-5.1.0.ebuild, +metadata.xml:
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sci-libs/itk: version bump 5.1.0 ahead of Gentoo Science
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DIST ITKGenericLabelInterpolator-5.1.0.zip 161970 SHA256 8c6cda6d4d8bac95347576b35355cc7a0fe127396b2c96fb8688b413045ff704 SHA512 26304168d2dc6f825ba085912c50a179e101da281b3d646109250c5ac9d12f2ad2216f967a81fb12d54ebd55ff7b17a355658282d7c65efb16dafb311fb3fc2c WHIRLPOOL d183ea141b212fa2247f595155836710cee5c05049caa0c67326a9ebb9eaf16f192464580ac616ab5970242704a797afb5fda9ecd79a19f3e41b2556c42bdd8d
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DIST InsightData-5.1.0.tar.gz 292322103 SHA256 777f587c587b47d76157a0ee87a5942b944742f334b801abe0e6dc1ad1d8424f SHA512 458c2959ba5e0745eee23e16ff7178230a7bae94d7dff065b3b38136e238becff96554693e3b2149d2307949c23a6c695c92676f8d44e6f7305dbb8bed48c9fa WHIRLPOOL d5785f862c627cabc97c469ac9fb84d1493e1827fd993c68ed5019e7062adc7fe68efe6ab2471c7c6b2a9d542cbfdb1a00c6633fa7be498cbc9e09fa12d3710a
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DIST InsightToolkit-5.1.0.tar.gz 20694338 SHA256 121020a1611508cec8123eb5226215598cec07be627d843a2e6b6da891e61d13 SHA512 413b6ef549b59d8f507038130446ccb704794c6d0980d8ab631d1b1051cb91f399e77c26b69fab6a1e9b9bb4cc233d49996c3ee735cd4de065993d4379b4ed4c WHIRLPOOL bbe7368cc46dc1a0869d8ab47218d0777e689be17114048653a537fbe792dfc0eb0e687b06fa894218cc35ef95143df75a46c17ffd6b072233e9f72a3c811825
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--- a/CMake/ITKDownloadSetup.cmake 2020-07-30 19:03:10.330325423 -0400
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+++ b/CMake/ITKDownloadSetup.cmake 2020-07-30 19:03:10.330325423 -0400
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@@ -11,7 +11,7 @@
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macro(itk_download_attempt_check _name)
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if(ITK_FORBID_DOWNLOADS)
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- message(SEND_ERROR "Attempted to download ${_name} when ITK_FORBID_DOWNLOADS is ON")
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+ message("Warning: Attempted to download ${_name} when ITK_FORBID_DOWNLOADS is ON")
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endif()
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endmacro()
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--- a/Modules/Remote/GenericLabelInterpolator.remote.cmake 2020-04-25 14:30:53.000000000 -0400
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+++ b/Modules/Remote/GenericLabelInterpolator.remote.cmake 2020-04-25 14:30:53.000000000 -0400
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@@ -44,6 +44,4 @@
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itk_fetch_module(GenericLabelInterpolator
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"A generic interpolator for multi-label images."
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MODULE_COMPLIANCE_LEVEL 2
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- GIT_REPOSITORY ${git_protocol}://github.com/InsightSoftwareConsortium/ITKGenericLabelInterpolator.git
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- GIT_TAG b95fe46c7f4fe8002af67c67e6fe4e1f087bf6b7
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)
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Known to fail by upstream:
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https://github.com/InsightSoftwareConsortium/ITK/issues/1212#issuecomment-527998115
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--- a/Modules/Bridge/VtkGlue/test/CMakeLists.txt 2019-09-09 00:45:14.736032139 +0200
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+++ b/Modules/Bridge/VtkGlue/test/CMakeLists.txt 2019-09-09 00:49:42.183935497 +0200
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@@ -7,8 +7,6 @@
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if(NOT VTK_RENDERING_BACKEND STREQUAL "None")
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list(APPEND ITKVtkGlueTests
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itkVtkMedianFilterTest.cxx
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- itkVtkConnectedComponentImageFilterTest.cxx
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- QuickViewTest.cxx
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# ### runViewImage ###
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# No test generated. Use it for view images (2D or 3D) with:
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# ITKVtkGlueTestDriver runViewImage image_file
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@@ -40,26 +38,3 @@
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NAME itkVTKImageToImageFilterTest
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COMMAND ITKVtkGlueTestDriver
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itkVTKImageToImageFilterTest)
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-
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-if(NOT VTK_RENDERING_BACKEND STREQUAL "None")
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- itk_add_test(
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- NAME itkVtkMedianImageFilterTest
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- COMMAND ITKVtkGlueTestDriver
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- itkVtkMedianFilterTest DATA{${ITK_DATA_ROOT}/Input/cthead1.png} 2)
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- set_property(TEST itkVtkMedianImageFilterTest APPEND PROPERTY LABELS REQUIRES_DISPLAY)
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-
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- itk_add_test(
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- NAME QuickViewTest
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- COMMAND ITKVtkGlueTestDriver
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- --compare DATA{Baseline/QuickViewTest.png,:}
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- ${ITK_TEST_OUTPUT_DIR}/QuickViewTest0.png
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- --compareNumberOfPixelsTolerance 1500
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- QuickViewTest DATA{${ITK_DATA_ROOT}/Input/peppers.png} ${ITK_TEST_OUTPUT_DIR})
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- set_property(TEST QuickViewTest APPEND PROPERTY LABELS REQUIRES_DISPLAY)
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-
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- itk_add_test(
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- NAME itkVtkConnectedComponentImageFilterTest
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- COMMAND ITKVtkGlueTestDriver
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- itkVtkConnectedComponentImageFilterTest DATA{${ITK_DATA_ROOT}/Input/cthead1.png})
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- set_property(TEST itkVtkConnectedComponentImageFilterTest APPEND PROPERTY LABELS REQUIRES_DISPLAY)
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-endif()
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# Copyright 1999-2020 Gentoo Authors
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# Distributed under the terms of the GNU General Public License v2
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EAPI=7
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PYTHON_COMPAT=( python2_7 python3_{5,6,7} )
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inherit toolchain-funcs cmake python-single-r1
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MY_PN="InsightToolkit"
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MY_P="${MY_PN}-${PV}"
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GLI_HASH="a02cbeaf28cb3d28ac66b9ac651073530eb6ab78"
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GLI_TEST_HASH="57b5d5de8d777f10f269445a"
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DESCRIPTION="NLM Insight Segmentation and Registration Toolkit"
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HOMEPAGE="http://www.itk.org"
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SRC_URI="
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https://github.com/InsightSoftwareConsortium/ITK/releases/download/v${PV}/${MY_P}.tar.gz
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https://github.com/InsightSoftwareConsortium/ITKGenericLabelInterpolator/archive/${GLI_HASH}.zip -> ITKGenericLabelInterpolator-${PV}.zip
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test? (
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https://github.com/InsightSoftwareConsortium/ITK/releases/download/v${PV}/InsightData-${PV}.tar.gz
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)
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"
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#https://github.com/InsightSoftwareConsortium/ITKGenericLabelInterpolator/archive/${GLI_HASH}.zip -> ITKGenericLabelInterpolator-${PV}.zip
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#https://data.kitware.com/api/v1/folder/${GLI_TEST_HASH}/download -> ITKGenericLabelInterpolator_test-${PV}.zip
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RESTRICT="primaryuri"
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LICENSE="Apache-2.0"
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SLOT="0"
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KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
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IUSE="debug doc examples fftw python review test vtkglue"
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# python will not work, this is a know issue upstream:
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# https://github.com/InsightSoftwareConsortium/ITK/issues/1229
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# https://github.com/InsightSoftwareConsortium/ITKGenericLabelInterpolator/issues/10
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RDEPEND="
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dev-libs/double-conversion:0=
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media-libs/openjpeg:2
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media-libs/libpng:0=
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media-libs/tiff:0=
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sci-libs/dcmtk:0=
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sci-libs/hdf5:0=[cxx]
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sys-libs/zlib:0=
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virtual/jpeg:0=
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fftw? ( sci-libs/fftw:3.0= )
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vtkglue? ( sci-libs/vtk:0=[rendering,python?] )
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"
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DEPEND="${RDEPEND}
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sys-apps/coreutils
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python? (
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>=dev-lang/swig-2.0:0
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dev-cpp/castxml
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)
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doc? ( app-doc/doxygen )
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"
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REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )"
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S="${WORKDIR}/${MY_P}"
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PATCHES=(
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"${FILESDIR}"/tests.patch
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"${FILESDIR}"/${P}-downloads.patch
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)
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pkg_pretend() {
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if [[ -z ${ITK_COMPUTER_MEMORY_SIZE} ]]; then
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elog "To tune ITK to make the best use of working memory you can set"
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elog " ITK_COMPUTER_MEMORY_SIZE=XX"
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elog "in make.conf, default is 1 (unit is GB)"
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fi
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if use python && [[ -z ${ITK_WRAP_DIMS} ]]; then
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elog "For Python language bindings, you can define the dimensions"
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elog "you want to create bindings for by setting"
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elog " ITK_WRAP_DIMS=X;Y;Z..."
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elog "in make.conf, default is 2;3 for 2D and 3D data"
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fi
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}
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src_prepare() {
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sed -i -e "s/find_package(OpenJPEG 2.0.0/find_package(OpenJPEG/g"\
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Modules/ThirdParty/GDCM/src/gdcm/CMakeLists.txt
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ln -sr ../ITKGenericLabelInterpolator-* Modules/External/ITKGenericLabelInterpolator || die
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#if use test; then
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# for filename in ../GenericLabelInterpolator/test/*/*mha; do
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# MD5=$(md5sum $filename) || die
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# MD5=${MD5% *} || die
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# cp "$filename" ".ExternalData/MD5/${MD5}" || die
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# done
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#fi
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cmake_src_prepare
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}
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src_configure() {
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local mycmakeargs=(
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-DBUILD_EXAMPLES="$(usex examples ON OFF)"
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-DBUILD_SHARED_LIBS=ON
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-DBUILD_TESTING="$(usex test ON OFF)"
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-Ddouble-conversion_INCLUDE_DIRS="${EPREFIX}/usr/include/double-conversion"
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-DExternalData_OBJECT_STORES="${WORKDIR}/InsightToolkit-${PV}/.ExternalData"
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-DGDCM_USE_SYSTEM_OPENJPEG=ON
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-DITK_FORBID_DOWNLOADS:BOOL=ON
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-DITK_INSTALL_LIBRARY_DIR=$(get_libdir)
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-DITK_USE_REVIEW="$(usex review ON OFF)"
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-DITK_USE_SYSTEM_DCMTK=ON
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-DITK_USE_SYSTEM_DOUBLECONVERSION=ON
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-DITK_USE_SYSTEM_CASTXML=ON
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-DITK_USE_SYSTEM_HDF5=ON
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-DITK_USE_SYSTEM_JPEG=ON
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-DITK_USE_SYSTEM_PNG=ON
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-DITK_USE_SYSTEM_SWIG=ON
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-DITK_USE_SYSTEM_TIFF=ON
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-DITK_USE_SYSTEM_ZLIB=ON
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-DITK_USE_KWSTYLE=OFF
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-DITK_BUILD_DEFAULT_MODULES=ON
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-DITK_COMPUTER_MEMORY_SIZE="${ITK_COMPUTER_MEMORY_SIZE:-1}"
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-DModule_GenericLabelInterpolator:BOOL=ON
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-DModule_ITKReview:BOOL=ON
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-DWRAP_ITK_JAVA=OFF
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-DWRAP_ITK_TCL=OFF
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)
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if use fftw; then
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mycmakeargs+=(
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-DUSE_FFTWD=ON
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-DUSE_FFTWF=ON
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-DUSE_SYSTEM_FFTW=ON
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-DITK_WRAP_double=ON
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-DITK_WRAP_vector_double=ON
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-DITK_WRAP_covariant_vector_double=ON
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-DITK_WRAP_complex_double=ON
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)
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fi
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if use vtkglue; then
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mycmakeargs+=(
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-DModule_ITKVtkGlue=ON
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)
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fi
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if use python; then
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mycmakeargs+=(
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-DITK_WRAP_PYTHON=ON
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-DITK_WRAP_DIMS="${ITK_WRAP_DIMS:-2;3}"
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)
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else
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mycmakeargs+=(
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-DITK_WRAP_PYTHON=OFF
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)
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fi
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cmake_src_configure
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}
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src_install() {
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cmake_src_install
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if use examples; then
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insinto /usr/share/doc/${PF}/examples
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docompress -x /usr/share/doc/${PF}/examples
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doins -r "${S}"/Examples/*
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fi
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echo "ITK_DATA_ROOT=${EROOT%/}/usr/share/${PN}/data" > ${T}/40${PN}
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local ldpath="${EROOT%/}/usr/$(get_libdir)/InsightToolkit"
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if use python; then
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echo "PYTHONPATH=${EROOT%/}/usr/$(get_libdir)/InsightToolkit/WrapITK/Python" >> "${T}"/40${PN}
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ldpath="${ldpath}:${EROOT%/}/usr/$(get_libdir)/InsightToolkit/WrapITK/lib"
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fi
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echo "LDPATH=${ldpath}" >> "${T}"/40${PN}
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doenvd "${T}"/40${PN}
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if use doc; then
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insinto /usr/share/doc/${PF}/api-docs
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cd "${WORKDIR}"/html
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rm *.md5 || die "Failed to remove superfluous hashes"
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einfo "Installing API docs. This may take some time."
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insinto /usr/share/doc/${PF}/api-docs
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doins -r *
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fi
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}
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@ -0,0 +1,23 @@
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<?xml version="1.0" encoding="UTF-8"?>
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<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
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<pkgmetadata>
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<maintainer type="project">
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<email>maintainer-wanted@gentoo.org</email>
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</maintainer>
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<maintainer type="project">
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<email>sci-biology@gentoo.org</email>
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<name>Gentoo Biology Project</name>
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</maintainer>
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<longdescription lang="en">
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Insight Segmentation and Registration Toolkit (ITK) is a library
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that provides developers with an extensive suite of tools for image
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analysis.
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</longdescription>
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<use>
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<flag name="review">Enable compilation of methods under review</flag>
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<flag name="vtkglue">PLEASE FIX MY DESCRIPTION</flag>
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</use>
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<upstream>
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<remote-id type="sourceforge">itk</remote-id>
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</upstream>
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</pkgmetadata>
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