[gentoo-commits] proj/sci:master commit in: sci-biology/fsl/

["Andrew Ammerlaan" <andrewammerlaan@gentoo.org>]

commit:     9a7852ed945ad222d4969f29460c12a230ec8c1e
Author:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Sat Jan 15 15:59:34 2022 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Sat Jan 15 15:59:34 2022 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=9a7852ed

sci-biology/fsl: drop old

Closes: https://github.com/gentoo/sci/issues/974
Package-Manager: Portage-3.0.30, Repoman-3.0.3
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>

 sci-biology/fsl/fsl-6.0.2-r1.ebuild | 203 ------------------------------------
 sci-biology/fsl/fsl-6.0.2.ebuild    | 167 -----------------------------
 2 files changed, 370 deletions(-)

diff --git a/sci-biology/fsl/fsl-6.0.2-r1.ebuild b/sci-biology/fsl/fsl-6.0.2-r1.ebuild
deleted file mode 100644
index e9918bbeb..000000000
--- a/sci-biology/fsl/fsl-6.0.2-r1.ebuild
+++ /dev/null
@@ -1,203 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit cuda toolchain-funcs prefix
-
-DESCRIPTION="Analysis of functional, structural, and diffusion MRI brain imaging data"
-HOMEPAGE="https://www.fmrib.ox.ac.uk/fsl"
-SRC_URI="https://fsl.fmrib.ox.ac.uk/fsldownloads/${P}-sources.tar.gz -> ${P}.tar.gz"
-
-LICENSE="FSL BSD-2 newmat"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE="cuda"
-
-DEPEND="
-	dev-libs/boost
-	<dev-python/fslpy-3
-	media-gfx/graphviz
-	media-libs/gd
-	media-libs/glu
-	media-libs/libpng:0=
-	sci-libs/ciftilib
-	sci-libs/nlopt
-	sys-libs/zlib
-	dev-lang/tcl:0=
-	dev-lang/tk:0=
-	>=virtual/lapack-3.8
-	>=virtual/blas-3.8
-
-	cuda? (
-		|| (
-			( =dev-util/nvidia-cuda-toolkit-10* =sys-devel/gcc-8*:* )
-			( =dev-util/nvidia-cuda-toolkit-11* =sys-devel/gcc-9*:* )
-		   )
-	)
-	"
-RDEPEND="${DEPEND}"
-
-S=${WORKDIR}/${PN}
-UPSTREAM_FSLDIR="/usr/share/fsl"
-
-PATCHES=(
-	"${FILESDIR}/${PN}"-6.0.2-gcc10_include.patch
-	"${FILESDIR}/${PN}"-6.0.2-setup.patch
-	"${FILESDIR}/${PN}"-6.0.2-template.patch
-	"${FILESDIR}/${PN}"-6.0.2-no_xmlpp.patch
-	"${FILESDIR}/${PN}"-5.0.11-niftiio_var_fix.patch
-	"${FILESDIR}/${PN}"-5.0.11-ifstream_use.patch
-	"${FILESDIR}/${PN}"-5.0.11-fslsurface_parallel_make.patch
-	"${FILESDIR}/${PN}"-6.0.2-qstring_compat.patch
-	"${FILESDIR}/${PN}"-5.0.9-headers.patch
-	"${FILESDIR}/${PN}"-6.0.2-fsldir_redux-p1.patch
-	"${FILESDIR}/${PN}"-6.0.2-fsldir_redux-p2.patch
-)
-
-src_prepare() {
-	default
-
-	sed -i \
-		-e "s:@@GENTOO_RANLIB@@:$(tc-getRANLIB):" \
-		-e "s:@@GENTOO_CC@@:$(tc-getCC):" \
-		-e "s:@@GENTOO_CXX@@:$(tc-getCXX):" \
-		config/buildSettings.mk || die
-
-	eprefixify $(grep -rl GENTOO_PORTAGE_EPREFIX src/*) \
-		etc/js/label-div.html
-
-	# Disable mist-clean the hard way for now.
-	rm -rf src/mist-clean
-
-	makefilelist=$(find src/ -name Makefile)
-
-	sed -i \
-		-e "s:-I\${INC_BOOST}::" \
-		-e "s:-I\${INC_ZLIB}::" \
-		-e "s:-I\${INC_GD}::" \
-		-e "s:-I\${INC_PNG}::" \
-		-e "s:-L\${LIB_GD}::" \
-		-e "s:-L\${LIB_PNG}::" \
-		-e "s:-L\${LIB_ZLIB}::" \
-		${makefilelist} || die
-
-	sed -e "s:\${FSLDIR}/bin/::g" \
-		-e "s:\$FSLDIR/bin/::g" \
-		-i $(grep -rl "\${FSLDIR}/bin" src/*) \
-		-i $(grep -rl "\$FSLDIR/bin" src/*) \
-		$(grep -rl "\${FSLDIR}/bin" etc/matlab/*)\
-		$(grep -rl "\$FSLDIR/bin" etc/matlab/*) || die
-
-	sed -e "s:\$FSLDIR/data:${EPREFIX}/usr/share/fsl/data:g" \
-		-e "s:\${FSLDIR}/data:${EPREFIX}/usr/share/fsl/data:g" \
-		-i $(grep -rl "\$FSLDIR/data" src/*) \
-		$(grep -rl "\${FSLDIR}/data" src/*) || die
-
-	sed -e "s:\$FSLDIR/doc:${EPREFIX}/usr/share/fsl/doc:g" \
-		-e "s:\${FSLDIR}/doc:${EPREFIX}/usr/share/fsl/doc:g" \
-		-i $(grep -rl "\$FSLDIR/doc" src/*) \
-		$(grep -rl "\${FSLDIR}/doc" src/*) || die
-
-	sed -e "s:/usr/share/fsl/doc:${EPREFIX}/usr/share/fsl/doc:g" \
-		-i $(grep -rl "/usr/share/fsl/doc" src/*) || die
-
-	sed -e "s:\$FSLDIR/etc:${EPREFIX}/etc:g" \
-		-e "s:\${FSLDIR}/etc:${EPREFIX}/etc:g" \
-		-i $(grep -rlI "\$FSLDIR/etc" *) \
-		-i $(grep -rlI "\${FSLDIR}/etc" *) || die
-
-	# Use generic blas/lapack rather than openblas
-	sed -e "s:-lopenblas:-llapack -lblas:g" \
-		-i $(grep -rlI lopenblas *) || die
-
-	# script wanting to have access to flsversion at buildtime
-	sed -e "s:/etc/fslversion:${S}/etc/fslversion:g" \
-		-i ${makefilelist} || die
-
-	if use cuda; then
-		einfo
-
-		gcc_ver=`gcc-fullversion`
-		einfo "GCC version: ${gcc_ver}"
-
-		cuda_gcc=`cuda_gccdir`
-		cuda_NVCC_flags=`cuda_gccdir -f`
-		einfo "CUDA GCC path: ${cuda_gcc}"
-		einfo "  ${cuda_NVCC_flags}"
-
-		CUDA_INSTALLATION="/opt/cuda"
-		CUDAVER=`cuda_toolkit_version`
-
-		eapply "${FILESDIR}/${PN}-6.0.2-eddy_cuda.patch"
-		eapply "${FILESDIR}/${PN}-6.0.2-cuda_buildsettings.patch"
-
-		sed -i \
-			-e "s:@@GENTOO_NVCC_FLAGS@@:${cuda_NVCC_flags}:" \
-			src/eddy/Makefile || die
-
-		cuda_sanitize
-	fi
-}
-
-src_compile() {
-	export FSLDIR=${WORKDIR}/${PN}
-	export FSLCONDIR=${WORKDIR}/${PN}/config
-	export FSLMACHTYPE=generic
-
-	export USERLDFLAGS="${LDFLAGS}"
-	export USERCFLAGS="${CFLAGS}"
-	export USERCXXFLAGS="${CXXFLAGS}"
-
-	export CIFTICFLAGS="$($(tc-getPKG_CONFIG) --cflags CiftiLib)"
-	export CIFTILIBS="$($(tc-getPKG_CONFIG) --libs-only-l CiftiLib)"
-
-	if use cuda; then
-		einfo "CUDA_INSTALLATION: ${CUDA_INSTALLATION}"
-		einfo "CUDAVER: ${CUDAVER}"
-	fi
-
-	./build || die
-}
-
-src_install() {
-	sed -i "s:\${FSLDIR}/tcl:/usr/libexec/fsl:g" \
-		$(grep -lI "\${FSLDIR}/tcl" bin/*) \
-		$(grep -l "\${FSLDIR}/tcl"  tcl/*) || die
-	sed -i "s:\$FSLDIR/tcl:/usr/libexec/fsl:g" \
-		$(grep -l "\$FSLDIR/tcl" tcl/*) || die
-
-	dobin bin/*
-
-	insinto /usr/share/${PN}
-	doins -r data
-	dodoc -r doc/. refdoc
-
-	insinto /usr/libexec/fsl
-	doins -r tcl/*
-
-	insinto /etc/fslconf
-	doins etc/fslconf/fsl.sh
-
-	insinto /etc
-	doins etc/fslversion
-	doins -r etc/default_flobs.flobs etc/flirtsch etc/js etc/luts
-
-	#the following is needed for FSL and depending programs to be able
-	#to find its files, since FSL uses an uncommon installation path:
-	#https://github.com/gentoo-science/sci/pull/612#r60289295
-	dosym ../../../etc ${UPSTREAM_FSLDIR}/etc
-	dosym ../doc/${PF} ${UPSTREAM_FSLDIR}/doc
-	dosym ../../bin ${UPSTREAM_FSLDIR}/bin
-
-	doenvd "$(prefixify_ro "${FILESDIR}"/99fsl)"
-	mv "${ED}"/usr/bin/{,fsl_}cluster || die
-}
-
-pkg_postinst() {
-	echo
-	einfo "Please run the following commands if you"
-	einfo "intend to use fsl from an existing shell:"
-	einfo "env-update && source /etc/profile"
-	echo
-}

diff --git a/sci-biology/fsl/fsl-6.0.2.ebuild b/sci-biology/fsl/fsl-6.0.2.ebuild
deleted file mode 100644
index f7b0e9b73..000000000
--- a/sci-biology/fsl/fsl-6.0.2.ebuild
+++ /dev/null
@@ -1,167 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit toolchain-funcs prefix
-
-DESCRIPTION="Analysis of functional, structural, and diffusion MRI brain imaging data"
-HOMEPAGE="https://www.fmrib.ox.ac.uk/fsl"
-SRC_URI="https://fsl.fmrib.ox.ac.uk/fsldownloads/${P}-sources.tar.gz -> ${P}.tar.gz"
-
-LICENSE="FSL BSD-2 newmat"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-DEPEND="
-	dev-libs/boost
-	<dev-python/fslpy-3
-	media-gfx/graphviz
-	media-libs/gd
-	media-libs/glu
-	media-libs/libpng:0=
-	sci-libs/ciftilib
-	sci-libs/nlopt
-	sys-libs/zlib
-	dev-lang/tcl:0=
-	dev-lang/tk:0=
-	>=virtual/lapack-3.8
-	>=virtual/blas-3.8
-	"
-RDEPEND="${DEPEND}"
-
-S=${WORKDIR}/${PN}
-UPSTREAM_FSLDIR="/usr/share/fsl"
-
-PATCHES=(
-	"${FILESDIR}/${PN}"-6.0.2-gcc10_include.patch
-	"${FILESDIR}/${PN}"-6.0.2-setup.patch
-	"${FILESDIR}/${PN}"-6.0.2-template.patch
-	"${FILESDIR}/${PN}"-6.0.2-no_xmlpp.patch
-	"${FILESDIR}/${PN}"-5.0.11-niftiio_var_fix.patch
-	"${FILESDIR}/${PN}"-5.0.11-ifstream_use.patch
-	"${FILESDIR}/${PN}"-5.0.11-fslsurface_parallel_make.patch
-	"${FILESDIR}/${PN}"-6.0.2-qstring_compat.patch
-	"${FILESDIR}/${PN}"-5.0.9-headers.patch
-	"${FILESDIR}/${PN}"-6.0.2-fsldir_redux-p1.patch
-	"${FILESDIR}/${PN}"-6.0.2-fsldir_redux-p2.patch
-)
-
-src_prepare(){
-	default
-
-	sed -i \
-		-e "s:@@GENTOO_RANLIB@@:$(tc-getRANLIB):" \
-		-e "s:@@GENTOO_CC@@:$(tc-getCC):" \
-		-e "s:@@GENTOO_CXX@@:$(tc-getCXX):" \
-		config/buildSettings.mk || die
-
-	eprefixify $(grep -rl GENTOO_PORTAGE_EPREFIX src/*) \
-		etc/js/label-div.html
-
-	# Disable mist-clean the hard way for now.
-	rm -rf src/mist-clean
-
-	makefilelist=$(find src/ -name Makefile)
-
-	sed -i \
-		-e "s:-I\${INC_BOOST}::" \
-		-e "s:-I\${INC_ZLIB}::" \
-		-e "s:-I\${INC_GD}::" \
-		-e "s:-I\${INC_PNG}::" \
-		-e "s:-L\${LIB_GD}::" \
-		-e "s:-L\${LIB_PNG}::" \
-		-e "s:-L\${LIB_ZLIB}::" \
-		${makefilelist} || die
-
-	sed -e "s:\${FSLDIR}/bin/::g" \
-		-e "s:\$FSLDIR/bin/::g" \
-		-i $(grep -rl "\${FSLDIR}/bin" src/*) \
-		-i $(grep -rl "\$FSLDIR/bin" src/*) \
-		$(grep -rl "\${FSLDIR}/bin" etc/matlab/*)\
-		$(grep -rl "\$FSLDIR/bin" etc/matlab/*) || die
-
-	sed -e "s:\$FSLDIR/data:${EPREFIX}/usr/share/fsl/data:g" \
-		-e "s:\${FSLDIR}/data:${EPREFIX}/usr/share/fsl/data:g" \
-		-i $(grep -rl "\$FSLDIR/data" src/*) \
-		$(grep -rl "\${FSLDIR}/data" src/*) || die
-
-	sed -e "s:\$FSLDIR/doc:${EPREFIX}/usr/share/fsl/doc:g" \
-		-e "s:\${FSLDIR}/doc:${EPREFIX}/usr/share/fsl/doc:g" \
-		-i $(grep -rl "\$FSLDIR/doc" src/*) \
-		$(grep -rl "\${FSLDIR}/doc" src/*) || die
-
-	sed -e "s:/usr/share/fsl/doc:${EPREFIX}/usr/share/fsl/doc:g" \
-		-i $(grep -rl "/usr/share/fsl/doc" src/*) || die
-
-	sed -e "s:\$FSLDIR/etc:${EPREFIX}/etc:g" \
-		-e "s:\${FSLDIR}/etc:${EPREFIX}/etc:g" \
-		-i $(grep -rlI "\$FSLDIR/etc" *) \
-		-i $(grep -rlI "\${FSLDIR}/etc" *) || die
-
-	# Use generic blas/lapack rather than openblas
-	sed -e "s:-lopenblas:-llapack -lblas:g" \
-		-i $(grep -rlI lopenblas *) || die
-
-	# script wanting to have access to flsversion at buildtime
-	sed -e "s:/etc/fslversion:${S}/etc/fslversion:g" \
-		-i ${makefilelist} || die
-}
-
-src_compile() {
-	export FSLDIR=${WORKDIR}/${PN}
-	export FSLCONDIR=${WORKDIR}/${PN}/config
-	export FSLMACHTYPE=generic
-
-	export USERLDFLAGS="${LDFLAGS}"
-	export USERCFLAGS="${CFLAGS}"
-	export USERCXXFLAGS="${CXXFLAGS}"
-
-	export CIFTICFLAGS="$($(tc-getPKG_CONFIG) --cflags CiftiLib)"
-	export CIFTILIBS="$($(tc-getPKG_CONFIG) --libs-only-l CiftiLib)"
-
-	./build || die
-}
-
-src_install() {
-	sed -i "s:\${FSLDIR}/tcl:/usr/libexec/fsl:g" \
-		$(grep -lI "\${FSLDIR}/tcl" bin/*) \
-		$(grep -l "\${FSLDIR}/tcl"  tcl/*) || die
-	sed -i "s:\$FSLDIR/tcl:/usr/libexec/fsl:g" \
-		$(grep -l "\$FSLDIR/tcl" tcl/*) || die
-
-	dobin bin/*
-
-	insinto /usr/share/${PN}
-	doins -r data
-	dodoc -r doc/. refdoc
-
-	insinto /usr/libexec/fsl
-	doins -r tcl/*
-
-	insinto /etc/fslconf
-	doins etc/fslconf/fsl.sh
-
-	insinto /etc
-	doins etc/fslversion
-	doins -r etc/default_flobs.flobs etc/flirtsch etc/js etc/luts
-
-	#the following is needed for FSL and depending programs to be able
-	#to find its files, since FSL uses an uncommon installation path:
-	#https://github.com/gentoo-science/sci/pull/612#r60289295
-	dosym ../../../etc ${UPSTREAM_FSLDIR}/etc
-	dosym ../doc/${PF} ${UPSTREAM_FSLDIR}/doc
-	dosym ../../bin ${UPSTREAM_FSLDIR}/bin
-
-	doenvd "$(prefixify_ro "${FILESDIR}"/99fsl)"
-	mv "${ED}"/usr/bin/{,fsl_}cluster || die
-}
-
-pkg_postinst() {
-	echo
-	einfo "Please run the following commands if you"
-	einfo "intend to use fsl from an existing shell:"
-	einfo "env-update && source /etc/profile"
-	echo
-}