* [gentoo-commits] proj/sci:master commit in: sci-biology/afni/, sci-biology/afni/files/
@ 2022-04-01 9:06 Andrew Ammerlaan
0 siblings, 0 replies; 3+ messages in thread
From: Andrew Ammerlaan @ 2022-04-01 9:06 UTC (permalink / raw
To: gentoo-commits
commit: 34f54dc027e97c6df729cede84253f6555e6c45e
Author: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Fri Apr 1 09:05:26 2022 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Fri Apr 1 09:05:38 2022 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=34f54dc0
sci-biology/afni: add 22.0.21, drop 22.0.03
Restore patch dropping py2.7 dep
TODO: make build system respect *FLAGS
TODO: Switch to cmake? This is non-trivial because the
cmake build system wants to fetch deps from the internet
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>
.../afni/{afni-22.0.03.ebuild => afni-22.0.21.ebuild} | 19 +++++++++++++------
sci-biology/afni/files/afni-22.0.21-python.patch | 13 +++++++++++++
2 files changed, 26 insertions(+), 6 deletions(-)
diff --git a/sci-biology/afni/afni-22.0.03.ebuild b/sci-biology/afni/afni-22.0.21.ebuild
similarity index 91%
rename from sci-biology/afni/afni-22.0.03.ebuild
rename to sci-biology/afni/afni-22.0.21.ebuild
index 9e831b018..5a015dafc 100644
--- a/sci-biology/afni/afni-22.0.03.ebuild
+++ b/sci-biology/afni/afni-22.0.21.ebuild
@@ -8,14 +8,16 @@ inherit toolchain-funcs
DESCRIPTION="An open-source environment for processing and displaying functional MRI data"
HOMEPAGE="http://afni.nimh.nih.gov/"
SRC_URI="https://github.com/afni/afni/archive/AFNI_${PV}.tar.gz -> ${P}.tar.gz"
+S="${WORKDIR}/${PN}-AFNI_${PV}/src"
LICENSE="GPL-3+"
SLOT="0"
-# fully broken due to upstream cmake migration
-KEYWORDS=""
-IUSE=""
+KEYWORDS="~amd64"
-RDEPEND="dev-libs/expat
+RDEPEND="
+ dev-libs/libf2c
+ dev-libs/expat
+ media-libs/freeglut
media-libs/glu
media-libs/netpbm
media-libs/qhull
@@ -31,9 +33,14 @@ RDEPEND="dev-libs/expat
"
DEPEND="${RDEPEND}
- app-shells/tcsh"
+ app-shells/tcsh
+"
+
+PATCHES=(
+ # Drop python2.7 dependency
+ "${FILESDIR}/${P}-python.patch"
+)
-S="${WORKDIR}/${PN}-AFNI_${PV}/src"
BUILD="linux_fedora_19_64"
BIN_CONFLICTS=(qdelaunay whirlgif djpeg cjpeg qhull rbox count)
diff --git a/sci-biology/afni/files/afni-22.0.21-python.patch b/sci-biology/afni/files/afni-22.0.21-python.patch
new file mode 100644
index 000000000..f31cc051b
--- /dev/null
+++ b/sci-biology/afni/files/afni-22.0.21-python.patch
@@ -0,0 +1,13 @@
+diff --git a/other_builds/Makefile.linux_fedora_19_64 b/other_builds/Makefile.linux_fedora_19_64
+index ebaa9d5..1471081 100644
+--- a/other_builds/Makefile.linux_fedora_19_64
++++ b/other_builds/Makefile.linux_fedora_19_64
+@@ -11,8 +11,6 @@ LGIFTI = -lexpat
+
+ # ------------------------------
+ # python from C
+-IPYTHON = -DSELENIUM_READY -I/usr/include/python2.7
+-LDPYTHON = -lpython2.7
+
+ # ----------------------------------------------------------------------
+ # X configuration
^ permalink raw reply related [flat|nested] 3+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/afni/, sci-biology/afni/files/
@ 2024-02-28 23:30 Horea Christian
0 siblings, 0 replies; 3+ messages in thread
From: Horea Christian @ 2024-02-28 23:30 UTC (permalink / raw
To: gentoo-commits
commit: fa3769352840642eb37e6125ee2fa69fef802cd4
Author: Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Wed Feb 28 23:30:07 2024 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Wed Feb 28 23:30:07 2024 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=fa376935
sci-biology/afni: drop 20.1.16, 20.3.03, 22.0.21
Signed-off-by: Horea Christian <chr <AT> chymera.eu>
sci-biology/afni/afni-20.1.16.ebuild | 73 -----------------------
sci-biology/afni/afni-20.3.03.ebuild | 73 -----------------------
sci-biology/afni/afni-22.0.21.ebuild | 75 ------------------------
sci-biology/afni/files/afni-20.1.16-python.patch | 11 ----
4 files changed, 232 deletions(-)
diff --git a/sci-biology/afni/afni-20.1.16.ebuild b/sci-biology/afni/afni-20.1.16.ebuild
deleted file mode 100644
index e3e16f834..000000000
--- a/sci-biology/afni/afni-20.1.16.ebuild
+++ /dev/null
@@ -1,73 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit toolchain-funcs
-
-DESCRIPTION="An open-source environment for processing and displaying functional MRI data"
-HOMEPAGE="http://afni.nimh.nih.gov/"
-SRC_URI="https://github.com/afni/afni/archive/AFNI_${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="GPL-3+"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND="dev-libs/expat
- media-libs/glu
- media-libs/netpbm
- media-libs/qhull
- media-video/mpeg-tools
- sci-libs/gsl
- sys-devel/llvm:*
- media-libs/libjpeg-turbo:0
- x11-libs/libGLw
- x11-libs/libXft
- x11-libs/libXi
- x11-libs/libXpm
- x11-libs/motif[-static-libs]"
-
-# x11-libs/motif[static-libs] breaks the build.
-# See upstream discussion
-# http://afni.nimh.nih.gov/afni/community/board/read.php?1,85348,85348#msg-85348
-
-DEPEND="${RDEPEND}
- app-shells/tcsh"
-
-S="${WORKDIR}/${PN}-AFNI_${PV}/src"
-BUILD="linux_fedora_19_64"
-BIN_CONFLICTS=(qdelaunay whirlgif djpeg cjpeg qhull rbox count mpeg_encode)
-
-src_prepare() {
- eapply "${FILESDIR}/${P}-python.patch" || die
- find -type f -exec sed -i -e "s/-lXp //g" {} +
- cp other_builds/Makefile.${BUILD} Makefile || die "Could not copy Makefile"
- # Unbundle imcat
- sed -e "s/ imcat / /g" \
- -i Makefile.INCLUDE || die "Could not edit includes files."
- sed -e "s~CC = /usr/bin/gcc -O2 -m64~CC = $(tc-getCC) \$(CFLAGS)~" \
- -e "s~CCMIN = /usr/bin/gcc -m64~CCMIN = $(tc-getCC) \$(CFLAGS)~" \
- -e "s~LD = /usr/bin/gcc~LD = $(tc-getCC)~" \
- -e "s~AR = /usr/bin/ar~AR = $(tc-getAR)~" \
- -e "s~RANLIB = /usr/bin/ranlib~RANLIB = $(tc-getRANLIB)~" \
- -i Makefile || die "Could not edit Makefile"
- # they provide somewhat problematic makefiles :(
- sed -e "s~ifeq ($(CC),gcc)~ifeq (1,1)~"\
- -i SUMA/SUMA_Makefile || die "Could not edit SUMA/SUMA_Makefile"
- # upstream checks if $CC is EXACTLY gcc, else sets variables for Mac
- find "${S}" -iname "*Makefile*" | xargs sed -e "s~/usr/~${EPREFIX}/usr/~g;" -i
- default
-}
-
-src_compile() {
- emake -j1 all plugins suma_exec
-}
-
-src_install() {
- emake INSTALLDIR="${ED}/usr/bin" -j1 install install_plugins
- emake INSTALLDIR="${ED}/usr/$(get_libdir)" install_lib
- for CONFLICT in ${BIN_CONFLICTS[@]}; do
- rm "${ED}/usr/bin/${CONFLICT}"
- done
-}
diff --git a/sci-biology/afni/afni-20.3.03.ebuild b/sci-biology/afni/afni-20.3.03.ebuild
deleted file mode 100644
index 1d9043ebb..000000000
--- a/sci-biology/afni/afni-20.3.03.ebuild
+++ /dev/null
@@ -1,73 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit toolchain-funcs
-
-DESCRIPTION="An open-source environment for processing and displaying functional MRI data"
-HOMEPAGE="http://afni.nimh.nih.gov/"
-SRC_URI="https://github.com/afni/afni/archive/AFNI_${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="GPL-3+"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND="dev-libs/expat
- media-libs/glu
- media-libs/netpbm
- media-libs/qhull
- media-video/mpeg-tools
- sci-libs/gsl
- sys-devel/llvm:*
- media-libs/libjpeg-turbo:0
- x11-libs/libGLw
- x11-libs/libXft
- x11-libs/libXi
- x11-libs/libXpm
- x11-libs/motif[-static-libs]"
-
-# x11-libs/motif[static-libs] breaks the build.
-# See upstream discussion
-# http://afni.nimh.nih.gov/afni/community/board/read.php?1,85348,85348#msg-85348
-
-DEPEND="${RDEPEND}
- app-shells/tcsh"
-
-S="${WORKDIR}/${PN}-AFNI_${PV}/src"
-BUILD="linux_fedora_19_64"
-BIN_CONFLICTS=(qdelaunay whirlgif djpeg cjpeg qhull rbox count mpeg_encode)
-
-src_prepare() {
- eapply "${FILESDIR}/${PN}-20.1.16-python.patch" || die
- find -type f -exec sed -i -e "s/-lXp //g" {} +
- cp other_builds/Makefile.${BUILD} Makefile || die "Could not copy Makefile"
- # Unbundle imcat
- sed -e "s/ imcat / /g" \
- -i Makefile.INCLUDE || die "Could not edit includes files."
- sed -e "s~CC = /usr/bin/gcc -O2 -m64~CC = $(tc-getCC) \$(CFLAGS)~" \
- -e "s~CCMIN = /usr/bin/gcc -m64~CCMIN = $(tc-getCC) \$(CFLAGS)~" \
- -e "s~LD = /usr/bin/gcc~LD = $(tc-getCC)~" \
- -e "s~AR = /usr/bin/ar~AR = $(tc-getAR)~" \
- -e "s~RANLIB = /usr/bin/ranlib~RANLIB = $(tc-getRANLIB)~" \
- -i Makefile || die "Could not edit Makefile"
- # they provide somewhat problematic makefiles :(
- sed -e "s~ifeq ($(CC),gcc)~ifeq (1,1)~"\
- -i SUMA/SUMA_Makefile || die "Could not edit SUMA/SUMA_Makefile"
- # upstream checks if $CC is EXACTLY gcc, else sets variables for Mac
- find "${S}" -iname "*Makefile*" | xargs sed -e "s~/usr/~${EPREFIX}/usr/~g;" -i
- default
-}
-
-src_compile() {
- emake -j1 all plugins suma_exec
-}
-
-src_install() {
- emake INSTALLDIR="${ED}/usr/bin" -j1 install install_plugins
- emake INSTALLDIR="${ED}/usr/$(get_libdir)" install_lib
- for CONFLICT in ${BIN_CONFLICTS[@]}; do
- rm "${ED}/usr/bin/${CONFLICT}"
- done
-}
diff --git a/sci-biology/afni/afni-22.0.21.ebuild b/sci-biology/afni/afni-22.0.21.ebuild
deleted file mode 100644
index 149deede8..000000000
--- a/sci-biology/afni/afni-22.0.21.ebuild
+++ /dev/null
@@ -1,75 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit toolchain-funcs
-
-DESCRIPTION="An open-source environment for processing and displaying functional MRI data"
-HOMEPAGE="http://afni.nimh.nih.gov/"
-SRC_URI="https://github.com/afni/afni/archive/AFNI_${PV}.tar.gz -> ${P}.tar.gz"
-S="${WORKDIR}/${PN}-AFNI_${PV}/src"
-
-LICENSE="GPL-3+"
-SLOT="0"
-# SUMA error: https://ppb.chymera.eu/4223de.log
-KEYWORDS=""
-
-RDEPEND="
- dev-libs/libf2c
- dev-libs/expat
- media-libs/freeglut
- media-libs/glu
- media-libs/netpbm
- media-libs/qhull
- media-video/mpeg-tools
- sci-libs/gsl
- sys-devel/llvm:*
- media-libs/libjpeg-turbo:0
- x11-libs/libGLw
- x11-libs/libXft
- x11-libs/libXi
- x11-libs/libXpm
- x11-libs/motif
-"
-
-DEPEND="${RDEPEND}
- app-shells/tcsh
-"
-
-BUILD="linux_fedora_19_64"
-BIN_CONFLICTS=(qdelaunay whirlgif djpeg cjpeg qhull rbox count)
-
-src_prepare() {
- # more easily applied here than via PATCHES at phase end.
- eapply "${FILESDIR}/${PN}-20.1.16-python.patch" || die
- find -type f -exec sed -i -e "s/-lXp //g" {} + || die
- cp other_builds/Makefile.${BUILD} Makefile || die "Could not copy Makefile"
- # Unbundle imcat
- sed -e "s/ imcat / /g" \
- -i Makefile.INCLUDE || die "Could not edit includes files."
- sed -e "s~CC = /usr/bin/gcc -O2 -m64~CC = $(tc-getCC) \$(CFLAGS)~" \
- -e "s~CCMIN = /usr/bin/gcc -m64~CCMIN = $(tc-getCC) \$(CFLAGS)~" \
- -e "s~LD = /usr/bin/gcc~LD = $(tc-getCC)~" \
- -e "s~AR = /usr/bin/ar~AR = $(tc-getAR)~" \
- -e "s~RANLIB = /usr/bin/ranlib~RANLIB = $(tc-getRANLIB)~" \
- -i Makefile || die "Could not edit Makefile"
- # they provide somewhat problematic makefiles :(
- sed -e "s~ifeq (\$(CC),gcc)~ifeq (1,1)~"\
- -i SUMA/SUMA_Makefile || die "Could not edit SUMA/SUMA_Makefile"
- # upstream checks if $CC is EXACTLY gcc, else sets variables for Mac
- find "${S}" -iname "*Makefile*" | xargs sed -e "s~/usr/~${EPREFIX}/usr/~g;" -i || die
- default
-}
-
-src_compile() {
- emake -j1 all plugins suma_exec
-}
-
-src_install() {
- emake INSTALLDIR="${ED}/usr/bin" install install_plugins
- emake INSTALLDIR="${ED}/usr/$(get_libdir)" install_lib
- for CONFLICT in ${BIN_CONFLICTS[@]}; do
- rm "${ED}/usr/bin/${CONFLICT}" || die
- done
-}
diff --git a/sci-biology/afni/files/afni-20.1.16-python.patch b/sci-biology/afni/files/afni-20.1.16-python.patch
deleted file mode 100644
index 8c3e859f5..000000000
--- a/sci-biology/afni/files/afni-20.1.16-python.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- a/other_builds/Makefile.linux_fedora_19_64 2020-10-09 07:07:58.348874414 -0400
-+++ b/other_builds/Makefile.linux_fedora_19_64 2020-10-10 01:15:22.337755934 -0400
-@@ -11,8 +11,6 @@
-
- # ------------------------------
- # python from C
--IPYTHON = -DSELENIUM_READY -I/usr/include/python2.7
--LDPYTHON = -lpython2.7
-
- # ----------------------------------------------------------------------
- # X configuration
^ permalink raw reply related [flat|nested] 3+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/afni/, sci-biology/afni/files/
@ 2024-02-28 23:30 Horea Christian
0 siblings, 0 replies; 3+ messages in thread
From: Horea Christian @ 2024-02-28 23:30 UTC (permalink / raw
To: gentoo-commits
commit: 19c71d97b19391b8797187494008509914db24ed
Author: Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Wed Feb 28 22:43:04 2024 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Wed Feb 28 22:43:04 2024 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=19c71d97
sci-biology/afni: add 24.0.04, 24.0.08
Signed-off-by: Horea Christian <chr <AT> chymera.eu>
sci-biology/afni/afni-24.0.04.ebuild | 111 ++++++++++++++++++++
sci-biology/afni/afni-24.0.08.ebuild | 115 +++++++++++++++++++++
sci-biology/afni/files/afni-24.0.04-whirlgif.patch | 39 +++++++
sci-biology/afni/metadata.xml | 3 +
4 files changed, 268 insertions(+)
diff --git a/sci-biology/afni/afni-24.0.04.ebuild b/sci-biology/afni/afni-24.0.04.ebuild
new file mode 100644
index 000000000..c00ef846f
--- /dev/null
+++ b/sci-biology/afni/afni-24.0.04.ebuild
@@ -0,0 +1,111 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..12} )
+
+DISTUTILS_USE_PEP517=setuptools
+inherit cmake distutils-r1 toolchain-funcs
+
+GTS_HASH="962155a01f5a1b87bd64e3e3d880b4dbc2347ac7"
+NIFTI_HASH="da476fd27f46098f37f5c9c4c1baee01e559572c"
+GIFTI_HASH="d3e873d8539d9b469daf7db04093da1d7e73d4f7"
+
+DESCRIPTION="Advanced Normalitazion Tools for neuroimaging"
+HOMEPAGE="http://stnava.github.io/ANTs/"
+SRC_URI="
+ https://github.com/afni/afni/archive/refs/tags/AFNI_${PV}.tar.gz -> ${P}.gh.tar.gz
+ https://github.com/NIFTI-Imaging/nifti_clib/archive/${NIFTI_HASH}.tar.gz -> nifti-${NIFTI_HASH}.tar.gz
+ https://github.com/NIFTI-Imaging/gifti_clib/archive/${GIFTI_HASH}.tar.gz -> gifti-${GIFTI_HASH}.tar.gz
+ "
+
+SLOT="0"
+LICENSE="GPL-3+"
+KEYWORDS="~amd64 ~x86"
+IUSE="test whirlgif"
+RESTRICT="!test? ( test )"
+
+RDEPEND="
+ dev-libs/glib:2
+ dev-libs/libf2c
+ dev-libs/expat
+ dev-build/ninja
+ media-libs/freeglut
+ media-libs/glu
+ media-libs/netpbm
+ media-libs/qhull
+ media-video/mpeg-tools
+ sci-libs/gsl
+ sci-libs/gts
+ sys-devel/llvm:*
+ sys-libs/libomp
+ dev-libs/libpthread-stubs
+ virtual/jpeg-compat:62
+ x11-libs/libGLw
+ x11-libs/libXft
+ x11-libs/libXi
+ x11-libs/libXmu
+ x11-libs/libXpm
+ x11-libs/libXt
+ x11-libs/motif[-static-libs]
+ "
+DEPEND="
+ ${RDEPEND}
+ app-shells/tcsh
+ "
+
+S="${WORKDIR}/afni-AFNI_${PV}"
+
+src_prepare() {
+ tar xf "${DISTDIR}/nifti-${NIFTI_HASH}.tar.gz" || die
+ tar xf "${DISTDIR}/gifti-${GIFTI_HASH}.tar.gz" || die
+ cmake_src_prepare
+ default
+ }
+
+src_configure() {
+ if use !whirlgif; then
+ eapply "${FILESDIR}/${P}-whirlgif.patch"
+ fi
+ export CFLAGS="-pthread ${CFLAGS}"
+ export GIT_REPO_VERSION=3.0.1.1
+ local mycmakeargs=(
+ -DLIBDIR=/usr/$(get_libdir)
+ -DNIFTI_INSTALL_LIBRARY_DIR=/usr/$(get_libdir)
+ -DGIFTI_INSTALL_LIBRARY_DIR=/usr/$(get_libdir)
+ -DGIFTI_INSTALL_LIB_DIR=/usr/$(get_libdir)
+ -DAFNI_INSTALL_LIBRARY_DIR=/usr/$(get_libdir)
+ -DCMAKE_INSTALL_LIBDIR=/usr/$(get_libdir)
+ -DCOMP_COREBINARIES=ON
+ -DUSE_SYSTEM_NIFTI=OFF
+ -DUSE_SYSTEM_GIFTI=OFF
+ -DUSE_SYSTEM_XMHTML=OFF
+ -DUSE_SYSTEM_GTS=ON
+ -DFETCHCONTENT_SOURCE_DIR_NIFTI_CLIB="${WORKDIR}/nifti_clib-${NIFTI_HASH}"
+ -DFETCHCONTENT_SOURCE_DIR_GIFTI_CLIB="${WORKDIR}/gifti_clib-${GIFTI_HASH}"
+ -DCOMP_GUI=ON
+ -DCOMP_PLUGINS=ON
+ -DUSE_OMP=ON
+ -DCOMP_PYTHON=OFF
+ -DUSE_SYSTEM_F2C=ON
+ )
+ tc-export CC
+ cmake_src_configure
+}
+
+src_compile() {
+ cmake_src_compile
+ pushd src/python_scripts
+ distutils-r1_src_compile
+ popd
+}
+
+src_install() {
+ cmake_src_install
+ pushd src/python_scripts
+ distutils-r1_src_install
+ popd
+ cd "${D}"
+ rm usr/bin/mpeg_encode
+}
diff --git a/sci-biology/afni/afni-24.0.08.ebuild b/sci-biology/afni/afni-24.0.08.ebuild
new file mode 100644
index 000000000..75ff5b6b6
--- /dev/null
+++ b/sci-biology/afni/afni-24.0.08.ebuild
@@ -0,0 +1,115 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..12} )
+
+DISTUTILS_USE_PEP517=setuptools
+inherit cmake distutils-r1 toolchain-funcs
+
+GTS_HASH="962155a01f5a1b87bd64e3e3d880b4dbc2347ac7"
+NIFTI_HASH="da476fd27f46098f37f5c9c4c1baee01e559572c"
+GIFTI_HASH="d3e873d8539d9b469daf7db04093da1d7e73d4f7"
+
+DESCRIPTION="Advanced Normalitazion Tools for neuroimaging"
+HOMEPAGE="http://stnava.github.io/ANTs/"
+SRC_URI="
+ https://github.com/afni/afni/archive/refs/tags/AFNI_${PV}.tar.gz -> ${P}.gh.tar.gz
+ https://github.com/NIFTI-Imaging/nifti_clib/archive/${NIFTI_HASH}.tar.gz -> nifti-${NIFTI_HASH}.tar.gz
+ https://github.com/NIFTI-Imaging/gifti_clib/archive/${GIFTI_HASH}.tar.gz -> gifti-${GIFTI_HASH}.tar.gz
+ "
+
+SLOT="0"
+LICENSE="GPL-3+"
+KEYWORDS="~amd64 ~x86"
+IUSE="test whirlgif"
+RESTRICT="!test? ( test )"
+
+RDEPEND="
+ dev-libs/glib:2
+ dev-libs/libf2c
+ dev-libs/expat
+ dev-build/ninja
+ media-libs/freeglut
+ media-libs/glu
+ media-libs/netpbm
+ media-libs/qhull
+ media-video/mpeg-tools
+ sci-libs/gsl
+ sci-libs/gts
+ sys-devel/llvm:*
+ sys-libs/libomp
+ dev-libs/libpthread-stubs
+ virtual/jpeg-compat:62
+ x11-libs/libGLw
+ x11-libs/libXft
+ x11-libs/libXi
+ x11-libs/libXmu
+ x11-libs/libXpm
+ x11-libs/libXt
+ x11-libs/motif[-static-libs]
+ "
+DEPEND="
+ ${RDEPEND}
+ app-shells/tcsh
+ "
+# Prospectively:
+#Update jpeg-compat to virtual/jpeg:0
+# look for xmhtlm
+
+S="${WORKDIR}/afni-AFNI_${PV}"
+
+ #tar xf "${DISTDIR}/${GTS_HASH}.tar.gz" || die
+src_prepare() {
+ tar xf "${DISTDIR}/nifti-${NIFTI_HASH}.tar.gz" || die
+ tar xf "${DISTDIR}/gifti-${GIFTI_HASH}.tar.gz" || die
+ cmake_src_prepare
+ default
+ }
+
+src_configure() {
+ if use !whirlgif; then
+ eapply "${FILESDIR}/${PN}-24.0.04-whirlgif.patch"
+ fi
+ export CFLAGS="-pthread ${CFLAGS}"
+ export GIT_REPO_VERSION=3.0.1.1
+ local mycmakeargs=(
+ -DLIBDIR=/usr/$(get_libdir)
+ -DNIFTI_INSTALL_LIBRARY_DIR=/usr/$(get_libdir)
+ -DGIFTI_INSTALL_LIBRARY_DIR=/usr/$(get_libdir)
+ -DGIFTI_INSTALL_LIB_DIR=/usr/$(get_libdir)
+ -DAFNI_INSTALL_LIBRARY_DIR=/usr/$(get_libdir)
+ -DCMAKE_INSTALL_LIBDIR=/usr/$(get_libdir)
+ -DCOMP_COREBINARIES=ON
+ -DUSE_SYSTEM_NIFTI=OFF
+ -DUSE_SYSTEM_GIFTI=OFF
+ -DUSE_SYSTEM_XMHTML=OFF
+ -DUSE_SYSTEM_GTS=ON
+ -DFETCHCONTENT_SOURCE_DIR_NIFTI_CLIB="${WORKDIR}/nifti_clib-${NIFTI_HASH}"
+ -DFETCHCONTENT_SOURCE_DIR_GIFTI_CLIB="${WORKDIR}/gifti_clib-${GIFTI_HASH}"
+ -DCOMP_GUI=ON
+ -DCOMP_PLUGINS=ON
+ -DUSE_OMP=ON
+ -DCOMP_PYTHON=OFF
+ -DUSE_SYSTEM_F2C=ON
+ )
+ tc-export CC
+ cmake_src_configure
+}
+
+src_compile() {
+ cmake_src_compile
+ pushd src/python_scripts
+ distutils-r1_src_compile
+ popd
+}
+
+src_install() {
+ cmake_src_install
+ pushd src/python_scripts
+ distutils-r1_src_install
+ popd
+ cd "${D}"
+ rm usr/bin/mpeg_encode
+}
diff --git a/sci-biology/afni/files/afni-24.0.04-whirlgif.patch b/sci-biology/afni/files/afni-24.0.04-whirlgif.patch
new file mode 100644
index 000000000..a357799e6
--- /dev/null
+++ b/sci-biology/afni/files/afni-24.0.04-whirlgif.patch
@@ -0,0 +1,39 @@
+diff --git a/packaging/installation_components.txt b/packaging/installation_components.txt
+index 127193338..ba8825a7b 100644
+--- a/packaging/installation_components.txt
++++ b/packaging/installation_components.txt
+@@ -347,7 +347,6 @@ uniq_images, corebinaries
+ unu, corebinaries
+ waver, corebinaries
+ whereami, corebinaries
+-whirlgif, corebinaries
+ 3dMax, tcsh
+ 3dPAR2AFNI.pl, tcsh
+ @1dDiffMag, tcsh
+diff --git a/src/CMakeLists_binaries.txt b/src/CMakeLists_binaries.txt
+index d53368390..8c8e9e1fb 100644
+--- a/src/CMakeLists_binaries.txt
++++ b/src/CMakeLists_binaries.txt
+@@ -209,7 +209,6 @@ foreach(
+ uniq_images
+ unu
+ whereami
+- whirlgif
+ )
+
+ add_afni_executable(${target} ${target}.c)
+diff --git a/src/Makefile.INCLUDE b/src/Makefile.INCLUDE
+index f44103def..7ac08a87d 100644
+--- a/src/Makefile.INCLUDE
++++ b/src/Makefile.INCLUDE
+@@ -3495,11 +3495,6 @@ help_format:help_format.o
+ ibinom:ibinom.o
+ $(CC) -o ibinom ibinom.o $(LFLAGS) $(LLIBS)
+
+-## GIF animation
+-
+-whirlgif:whirlgif.h whirlgif.c
+- $(CC) -o whirlgif whirlgif.c $(INFLAGS) $(LFLAGS) $(LLIBS)
+-
+ extor.o:extor.c
+ $(CCFAST) -c extor.c $(INFLAGS)
diff --git a/sci-biology/afni/metadata.xml b/sci-biology/afni/metadata.xml
index cbb8a4299..39ec69d08 100644
--- a/sci-biology/afni/metadata.xml
+++ b/sci-biology/afni/metadata.xml
@@ -13,6 +13,9 @@
Analysis of Functional NeuroImages (AFNI) is an open-source environment for processing and displaying
functional MRI data—a technique for mapping human brain activity.
</longdescription>
+ <use>
+ <flag name="whirlgif">Build optional whirlgif binary</flag>
+ </use>
<upstream>
<remote-id type="github">afni/afni</remote-id>
</upstream>
^ permalink raw reply related [flat|nested] 3+ messages in thread
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2022-04-01 9:06 [gentoo-commits] proj/sci:master commit in: sci-biology/afni/, sci-biology/afni/files/ Andrew Ammerlaan
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2024-02-28 23:30 Horea Christian
2024-02-28 23:30 Horea Christian
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