From 0e89672299b6e896fb56810cf5e8a249aba6fc23 Mon Sep 17 00:00:00 2001 From: Horea Christian Date: Fri, 25 Sep 2020 03:51:52 -0400 Subject: [PATCH] sci-libs/itk: Pushed to Gentoo Science https://gitweb.gentoo.org/proj/sci.git/commit/?id=7112647657d76049ee42f5e2c86c05c2c1330760 --- sci-libs/itk/ChangeLog | 14 -- sci-libs/itk/Manifest | 6 - sci-libs/itk/files/itk-5.1.0-downloads.patch | 20 -- sci-libs/itk/files/tests.patch | 41 ---- sci-libs/itk/itk-5.1.0.ebuild | 196 ------------------- sci-libs/itk/metadata.xml | 23 --- 6 files changed, 300 deletions(-) delete mode 100644 sci-libs/itk/ChangeLog delete mode 100644 sci-libs/itk/Manifest delete mode 100644 sci-libs/itk/files/itk-5.1.0-downloads.patch delete mode 100644 sci-libs/itk/files/tests.patch delete mode 100644 sci-libs/itk/itk-5.1.0.ebuild delete mode 100644 sci-libs/itk/metadata.xml diff --git a/sci-libs/itk/ChangeLog b/sci-libs/itk/ChangeLog deleted file mode 100644 index 12b5b1b..0000000 --- a/sci-libs/itk/ChangeLog +++ /dev/null @@ -1,14 +0,0 @@ - 21 Sep 2020; itk-5.1.0.ebuild: - sci-libs/itk: requiring jpeg support from media-libs/tiff - - 19 Sep 2020; itk-5.1.0.ebuild: - sci-libs/itk: fetching test files - - 08 Aug 2020; files/itk-5.1.0-downloads.patch: - sci-libs/itk: better syntax for warning - -*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 deleted file mode 100644 index a7614d8..0000000 --- a/sci-libs/itk/Manifest +++ /dev/null @@ -1,6 +0,0 @@ -DIST 0eb202e23ae81be123b1b26cf31a9ba743824700.tar.gz 2409232372 SHA256 bac8365cb56a6c5f68e565445e00012f31453b06e8f7879bc7c3238796a67948 SHA512 8b451608cb3f75d3ba6a78fd23e79495948c2792a98d831e0f0c93745595df84d3c2a8d76389976f67ac7e7e1f5a44a18d201e51d2ee659cdb708ae28536df8f WHIRLPOOL 4c9f65bb51a0714a24db6c1e739fff32b454e0289135cd190146df0fd6dece736ff348d9aeae388dff8ce9ccc9010c979f1a6051065f92bbb0bc98c8628aab4e -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 -DIST a5e11ea71164ff78c65fcf259db01ea5db981a9d868e60045ff2bffca92984df1174bf984a1076e450f0d5d69b4f0191ed1a61465c220e2c91a893b5df150c0a 214819 SHA256 6b62bd25168bebf9a3bc14403952c2bf326f787a055a757bced6d2d76b459706 SHA512 a5e11ea71164ff78c65fcf259db01ea5db981a9d868e60045ff2bffca92984df1174bf984a1076e450f0d5d69b4f0191ed1a61465c220e2c91a893b5df150c0a WHIRLPOOL 0e97d37fff5e205d5784be8f44209f22218c31723a6461eed6dd2497cc6345c98cf41e20a9c650b8c990735ef45e533cc979d0054a37a201191cab8bdaabcb05 -DIST bcdbb347f3704262d1f00be7179d6a0a6e68aed56c0653e8072ee5a94985c713bd229c935b1226a658af84fb7f1fffc2458c98364fc35303a2303b12f9f7ce2f 215417 SHA256 aa1e713ed84c9a45337df1e2754c6f5a073e1b74ee33b38d59d3f8e449928378 SHA512 bcdbb347f3704262d1f00be7179d6a0a6e68aed56c0653e8072ee5a94985c713bd229c935b1226a658af84fb7f1fffc2458c98364fc35303a2303b12f9f7ce2f WHIRLPOOL 6ec2cf4178fa52242fb323100e0ec69046bf6bc304cf4b6f8899ccfc8267b790a4133565e7677a73ce7dc1852cdeee7e0b42f7e99c20ec1615bd9089b2613582 diff --git a/sci-libs/itk/files/itk-5.1.0-downloads.patch b/sci-libs/itk/files/itk-5.1.0-downloads.patch deleted file mode 100644 index 34fdb76..0000000 --- a/sci-libs/itk/files/itk-5.1.0-downloads.patch +++ /dev/null @@ -1,20 +0,0 @@ ---- 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 ${git_protocol}://github.com/InsightSoftwareConsortium/ITKGenericLabelInterpolator.git -- GIT_TAG b95fe46c7f4fe8002af67c67e6fe4e1f087bf6b7 - ) diff --git a/sci-libs/itk/files/tests.patch b/sci-libs/itk/files/tests.patch deleted file mode 100644 index c24714e..0000000 --- a/sci-libs/itk/files/tests.patch +++ /dev/null @@ -1,41 +0,0 @@ -Known to fail by upstream: -https://github.com/InsightSoftwareConsortium/ITK/issues/1212#issuecomment-527998115 - ---- a/Modules/Bridge/VtkGlue/test/CMakeLists.txt 2019-09-09 00:45:14.736032139 +0200 -+++ b/Modules/Bridge/VtkGlue/test/CMakeLists.txt 2019-09-09 00:49:42.183935497 +0200 -@@ -7,8 +7,6 @@ - if(NOT VTK_RENDERING_BACKEND STREQUAL "None") - list(APPEND ITKVtkGlueTests - itkVtkMedianFilterTest.cxx -- itkVtkConnectedComponentImageFilterTest.cxx -- QuickViewTest.cxx - # ### runViewImage ### - # No test generated. Use it for view images (2D or 3D) with: - # ITKVtkGlueTestDriver runViewImage image_file -@@ -40,26 +38,3 @@ - NAME itkVTKImageToImageFilterTest - COMMAND ITKVtkGlueTestDriver - itkVTKImageToImageFilterTest) -- --if(NOT VTK_RENDERING_BACKEND STREQUAL "None") -- itk_add_test( -- NAME itkVtkMedianImageFilterTest -- COMMAND ITKVtkGlueTestDriver -- itkVtkMedianFilterTest DATA{${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 deleted file mode 100644 index f129bab..0000000 --- a/sci-libs/itk/itk-5.1.0.ebuild +++ /dev/null @@ -1,196 +0,0 @@ -# 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" -TEST_HASH="0eb202e23ae81be123b1b26cf31a9ba743824700" -#declare -a GIT_TEST_HASHES=( -# "a5e11ea71164ff78c65fcf259db01ea5db981a9d868e60045ff2bffca92984df1174bf984a1076e450f0d5d69b4f0191ed1a61465c220e2c91a893b5df150c0a" -# "bcdbb347f3704262d1f00be7179d6a0a6e68aed56c0653e8072ee5a94985c713bd229c935b1226a658af84fb7f1fffc2458c98364fc35303a2303b12f9f7ce2f" -#) -GLI_TEST_HASH1="a5e11ea71164ff78c65fcf259db01ea5db981a9d868e60045ff2bffca92984df1174bf984a1076e450f0d5d69b4f0191ed1a61465c220e2c91a893b5df150c0a" -GLI_TEST_HASH2="bcdbb347f3704262d1f00be7179d6a0a6e68aed56c0653e8072ee5a94985c713bd229c935b1226a658af84fb7f1fffc2458c98364fc35303a2303b12f9f7ce2f" - -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/ITKTestingData/archive/${TEST_HASH}.tar.gz - https://data.kitware.com/api/v1/file/hashsum/sha512/${GLI_TEST_HASH1}/download -> ${GLI_TEST_HASH1} - https://data.kitware.com/api/v1/file/hashsum/sha512/${GLI_TEST_HASH2}/download -> ${GLI_TEST_HASH2} - ) - " -#https://github.com/InsightSoftwareConsortium/ITKGenericLabelInterpolator/archive/${GLI_HASH}.zip -> ITKGenericLabelInterpolator-${PV}.zip -#https://data.kitware.com/api/v1/folder/${GLI_TEST_HASH}/download -> ITKGenericLabelInterpolator_test-${PV}.zip -RESTRICT="primaryuri" - -LICENSE="Apache-2.0" -SLOT="0" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="debug doc examples fftw python review test vtkglue" -# python will not work, this is a know issue upstream: -# https://github.com/InsightSoftwareConsortium/ITK/issues/1229 -# https://github.com/InsightSoftwareConsortium/ITKGenericLabelInterpolator/issues/10 - -RDEPEND=" - dev-libs/double-conversion:0= - media-libs/openjpeg:2 - media-libs/libpng:0= - media-libs/tiff:0=[jpeg] - sci-libs/dcmtk:0= - sci-libs/hdf5:0=[cxx] - sys-libs/zlib:0= - virtual/jpeg:0= - fftw? ( sci-libs/fftw:3.0= ) - vtkglue? ( sci-libs/vtk:0=[rendering,python?] ) -" -DEPEND="${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 - #pwd - #echo ${S} - #echo ${WORKDIR} - #die - cmake_src_prepare - if use test; then - cp -rf "../ITKTestingData-${TEST_HASH}/"* ".ExternalData/" || die - mv "../ITKTestingData-${TEST_HASH}" "${BUILD_DIR}/.ExternalData" || die - cp "${DISTDIR}/${GLI_TEST_HASH1}" ".ExternalData/SHA512/" || die - cp "${DISTDIR}/${GLI_TEST_HASH1}" "${BUILD_DIR}/.ExternalData/SHA512/" || die - cp "${DISTDIR}/${GLI_TEST_HASH2}" ".ExternalData/SHA512/" || die - cp "${DISTDIR}/${GLI_TEST_HASH2}" "${BUILD_DIR}/.ExternalData/SHA512/" || die - fi - #pwd - #echo ${S} - #echo ${WORKDIR} - #echo ${BUILD_DIR} - #die -} - -src_configure() { - local mycmakeargs=( - -DBUILD_EXAMPLES="$(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 deleted file mode 100644 index 7c45353..0000000 --- a/sci-libs/itk/metadata.xml +++ /dev/null @@ -1,23 +0,0 @@ - - - - - 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 - -