diff --git a/sci-libs/itk/ChangeLog b/sci-libs/itk/ChangeLog new file mode 100644 index 0000000..9aadba5 --- /dev/null +++ b/sci-libs/itk/ChangeLog @@ -0,0 +1,5 @@ +*itk-5.1.0 (04 Aug 2020) + + 04 Aug 2020; +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 diff --git a/sci-libs/itk/Manifest b/sci-libs/itk/Manifest new file mode 100644 index 0000000..30580bd --- /dev/null +++ b/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 diff --git a/sci-libs/itk/files/itk-5.1.0-downloads.patch b/sci-libs/itk/files/itk-5.1.0-downloads.patch new file mode 100644 index 0000000..c4eb04e --- /dev/null +++ b/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 ${git_protocol}://github.com/InsightSoftwareConsortium/ITKGenericLabelInterpolator.git +- GIT_TAG b95fe46c7f4fe8002af67c67e6fe4e1f087bf6b7 + ) diff --git a/sci-libs/itk/files/tests.patch b/sci-libs/itk/files/tests.patch new file mode 100644 index 0000000..c24714e --- /dev/null +++ b/sci-libs/itk/files/tests.patch @@ -0,0 +1,41 @@ +Known to fail by upstream: +https://github.com/InsightSoftwareConsortium/ITK/issues/1212#issuecomment-527998115 + +--- a/Modules/Bridge/VtkGlue/test/CMakeLists.txt 2019-09-09 00:45:14.736032139 +0200 ++++ b/Modules/Bridge/VtkGlue/test/CMakeLists.txt 2019-09-09 00:49:42.183935497 +0200 +@@ -7,8 +7,6 @@ + if(NOT VTK_RENDERING_BACKEND STREQUAL "None") + list(APPEND ITKVtkGlueTests + itkVtkMedianFilterTest.cxx +- itkVtkConnectedComponentImageFilterTest.cxx +- QuickViewTest.cxx + # ### runViewImage ### + # No test generated. Use it for view images (2D or 3D) with: + # ITKVtkGlueTestDriver runViewImage image_file +@@ -40,26 +38,3 @@ + NAME itkVTKImageToImageFilterTest + COMMAND ITKVtkGlueTestDriver + itkVTKImageToImageFilterTest) +- +-if(NOT VTK_RENDERING_BACKEND STREQUAL "None") +- itk_add_test( +- NAME itkVtkMedianImageFilterTest +- COMMAND ITKVtkGlueTestDriver +- itkVtkMedianFilterTest DATA{${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-5.1.0.ebuild b/sci-libs/itk/itk-5.1.0.ebuild new file mode 100644 index 0000000..e91046b --- /dev/null +++ b/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 +} diff --git a/sci-libs/itk/metadata.xml b/sci-libs/itk/metadata.xml new file mode 100644 index 0000000..7c45353 --- /dev/null +++ b/sci-libs/itk/metadata.xml @@ -0,0 +1,23 @@ + + + + + maintainer-wanted@gentoo.org + + + sci-biology@gentoo.org + Gentoo Biology Project + + +Insight Segmentation and Registration Toolkit (ITK) is a library +that provides developers with an extensive suite of tools for image +analysis. + + + Enable compilation of methods under review + PLEASE FIX MY DESCRIPTION + + + itk + +