From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from lists.gentoo.org (pigeon.gentoo.org [208.92.234.80]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by finch.gentoo.org (Postfix) with ESMTPS id E8A76138334 for ; Mon, 9 Sep 2019 08:26:10 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 215BEE09C6; Mon, 9 Sep 2019 08:26:10 +0000 (UTC) Received: from smtp.gentoo.org (smtp.gentoo.org [140.211.166.183]) (using TLSv1.2 with cipher ECDHE-RSA-AES128-GCM-SHA256 (128/128 bits)) (No client certificate requested) by pigeon.gentoo.org (Postfix) with ESMTPS id EBAE3E09C6 for ; Mon, 9 Sep 2019 08:26:09 +0000 (UTC) Received: from oystercatcher.gentoo.org (unknown [IPv6:2a01:4f8:202:4333:225:90ff:fed9:fc84]) (using TLSv1.2 with cipher ECDHE-RSA-AES128-GCM-SHA256 (128/128 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id B411F34AED5 for ; Mon, 9 Sep 2019 08:26:08 +0000 (UTC) Received: from localhost.localdomain (localhost [IPv6:::1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id 6808A780 for ; Mon, 9 Sep 2019 08:26:07 +0000 (UTC) From: "Horea Christian" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Horea Christian" Message-ID: <1568017549.445eb95b61c9b12481b24f962123d0f13e940ab6.chymera@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: sci-libs/itk/, sci-libs/itk/files/ X-VCS-Repository: proj/sci X-VCS-Files: sci-libs/itk/files/ITKModuleRemote.patch sci-libs/itk/files/tests.patch sci-libs/itk/itk-4.12.0.ebuild sci-libs/itk/itk-4.4.2-r1.ebuild sci-libs/itk/itk-4.4.2.ebuild sci-libs/itk/itk-4.5.1.ebuild sci-libs/itk/itk-5.0.1.ebuild sci-libs/itk/itk-5.0_rc1.ebuild sci-libs/itk/metadata.xml X-VCS-Directories: sci-libs/itk/ sci-libs/itk/files/ X-VCS-Committer: chymera X-VCS-Committer-Name: Horea Christian X-VCS-Revision: 445eb95b61c9b12481b24f962123d0f13e940ab6 X-VCS-Branch: master Date: Mon, 9 Sep 2019 08:26:07 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org X-Auto-Response-Suppress: DR, RN, NRN, OOF, AutoReply X-Archives-Salt: 845a7abf-8891-449c-bc85-9d6614e801fd X-Archives-Hash: 7914af0bc1a616c31dfa90be6666a172 commit: 445eb95b61c9b12481b24f962123d0f13e940ab6 Author: Horea Christian chymera eu> AuthorDate: Mon Sep 9 08:25:49 2019 +0000 Commit: Horea Christian gmail 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 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. - Enable compatibility with ITK version 3 Enable compilation of methods under review PLEASE FIX MY DESCRIPTION