[gentoo-commits] proj/sci:master commit in: sci-libs/itk/, sci-libs/itk/files/

["Horea Christian" <horea.christ@gmail.com>]

commit:     7112647657d76049ee42f5e2c86c05c2c1330760
Author:     Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Fri Sep 25 07:33:20 2020 +0000
Commit:     Horea Christian <horea.christ <AT> gmail <DOT> 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 <chr <AT> 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
+}