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 DD43F138359 for ; Fri, 25 Sep 2020 07:33:34 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id EA3B7E0830; Fri, 25 Sep 2020 07:33:33 +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 BC1B8E0830 for ; Fri, 25 Sep 2020 07:33:33 +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 D5C2D33BDE6 for ; Fri, 25 Sep 2020 07:33:31 +0000 (UTC) Received: from localhost.localdomain (localhost [IPv6:::1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id 5385E373 for ; Fri, 25 Sep 2020 07:33:30 +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: <1601019200.7112647657d76049ee42f5e2c86c05c2c1330760.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/itk-5.1.0-downloads.patch sci-libs/itk/itk-5.1.0.ebuild X-VCS-Directories: sci-libs/itk/ sci-libs/itk/files/ X-VCS-Committer: chymera X-VCS-Committer-Name: Horea Christian X-VCS-Revision: 7112647657d76049ee42f5e2c86c05c2c1330760 X-VCS-Branch: master Date: Fri, 25 Sep 2020 07:33:30 +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: bdbaeb0e-660e-4557-8029-a36588fdd0ea X-Archives-Hash: 696271801ac9d5a2d7e4320406e2c691 commit: 7112647657d76049ee42f5e2c86c05c2c1330760 Author: Horea Christian chymera eu> AuthorDate: Fri Sep 25 07:33:20 2020 +0000 Commit: Horea Christian gmail com> CommitDate: Fri Sep 25 07:33:20 2020 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=71126476 sci-libs/itk: version bump 5.1.0 Package-Manager: Portage-3.0.8, Repoman-3.0.1 Signed-off-by: Horea Christian chymera.eu> sci-libs/itk/files/itk-5.1.0-downloads.patch | 20 +++ sci-libs/itk/itk-5.1.0.ebuild | 188 +++++++++++++++++++++++++++ 2 files changed, 208 insertions(+) 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 000000000..34fdb76d1 --- /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 ${git_protocol}://github.com/InsightSoftwareConsortium/ITKGenericLabelInterpolator.git +- GIT_TAG b95fe46c7f4fe8002af67c67e6fe4e1f087bf6b7 + ) diff --git a/sci-libs/itk/itk-5.1.0.ebuild b/sci-libs/itk/itk-5.1.0.ebuild new file mode 100644 index 000000000..64fd555cb --- /dev/null +++ b/sci-libs/itk/itk-5.1.0.ebuild @@ -0,0 +1,188 @@ +# Copyright 1999-2020 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 + +PYTHON_COMPAT=( python2_7 python3_{5,6,7} ) + +inherit toolchain-funcs cmake python-single-r1 + +MY_PN="InsightToolkit" +MY_P="${MY_PN}-${PV}" +GLI_HASH="a02cbeaf28cb3d28ac66b9ac651073530eb6ab78" +TEST_HASH="0eb202e23ae81be123b1b26cf31a9ba743824700" +declare -a GLI_TEST_HASHES=( + "a5e11ea71164ff78c65fcf259db01ea5db981a9d868e60045ff2bffca92984df1174bf984a1076e450f0d5d69b4f0191ed1a61465c220e2c91a893b5df150c0a" + "bcdbb347f3704262d1f00be7179d6a0a6e68aed56c0653e8072ee5a94985c713bd229c935b1226a658af84fb7f1fffc2458c98364fc35303a2303b12f9f7ce2f" +) + +GLI_TEST_SRC="" +for i in "${GLI_TEST_HASHES[@]}"; do + GLI_TEST_SRC+="https://data.kitware.com/api/v1/file/hashsum/sha512/${i} -> ${i} " +done + +DESCRIPTION="NLM Insight Segmentation and Registration Toolkit" +HOMEPAGE="http://www.itk.org" +SRC_URI=" + https://github.com/InsightSoftwareConsortium/ITK/releases/download/v${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 + ${GLI_TEST_SRC} + ) + " +RESTRICT="primaryuri" + +LICENSE="Apache-2.0" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="debug doc examples fftw python review test vtkglue" +# python will not work, this is a know issue upstream: +# https://github.com/InsightSoftwareConsortium/ITK/issues/2005 +# https://github.com/InsightSoftwareConsortium/ITK/issues/1229 +# https://github.com/InsightSoftwareConsortium/ITKGenericLabelInterpolator/issues/10 + +RDEPEND=" + dev-libs/double-conversion:0= + media-libs/openjpeg:2 + media-libs/libpng:0= + media-libs/tiff:0=[jpeg] + sci-libs/dcmtk:0= + sci-libs/hdf5:0=[cxx] + sys-libs/zlib:0= + virtual/jpeg:0= + fftw? ( sci-libs/fftw:3.0= ) + vtkglue? ( sci-libs/vtk:0=[rendering,python?] ) +" +DEPEND="${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 ${ITK_WRAP_DIMS} ]]; then + elog "For Python language bindings, you can define the dimensions" + elog "you want to create bindings for by setting" + elog " ITK_WRAP_DIMS=X;Y;Z..." + elog "in make.conf, default is 2;3 for 2D and 3D data" + fi +} + +src_prepare() { + sed -i -e "s/find_package(OpenJPEG 2.0.0/find_package(OpenJPEG/g"\ + Modules/ThirdParty/GDCM/src/gdcm/CMakeLists.txt + ln -sr ../ITKGenericLabelInterpolator-* Modules/External/ITKGenericLabelInterpolator || die + cmake_src_prepare + if use test; then + cp -rf "../ITKTestingData-${TEST_HASH}/"* ".ExternalData/" || die + mv "../ITKTestingData-${TEST_HASH}" "${BUILD_DIR}/.ExternalData" || die + for i in "${GLI_TEST_HASHES[@]}"; do + cp "${DISTDIR}/${i}" ".ExternalData/SHA512/" || die + cp "${DISTDIR}/${i}" "${BUILD_DIR}/.ExternalData/SHA512/" || die + done + fi +} + +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 +}