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

2024-05-29 Thread Horea Christian 
commit: 6d9b772f10ed51682604e5c1cb6f9c278a5c6c72
Author: Horea Christian  chymera  eu>
AuthorDate: Wed May 29 08:31:29 2024 +
Commit: Horea Christian  gmail  com>
CommitDate: Wed May 29 08:31:29 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=6d9b772f

sci-biology/afni: correct version annotation

Signed-off-by: Horea Christian  chymera.eu>

 sci-biology/afni/afni-24.0.08-r3.ebuild | 125 
 1 file changed, 125 insertions(+)

diff --git a/sci-biology/afni/afni-24.0.08-r3.ebuild 
b/sci-biology/afni/afni-24.0.08-r3.ebuild
new file mode 100644
index 0..12d6c8f87
--- /dev/null
+++ b/sci-biology/afni/afni-24.0.08-r3.ebuild
@@ -0,0 +1,125 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..13} )
+
+DISTUTILS_USE_PEP517=setuptools
+inherit cmake distutils-r1 toolchain-funcs
+
+GTS_HASH="962155a01f5a1b87bd64e3e3d880b4dbc2347ac7"
+NIFTI_HASH="da476fd27f46098f37f5c9c4c1baee01e559572c"
+GIFTI_HASH="d3e873d8539d9b469daf7db04093da1d7e73d4f7"
+
+DESCRIPTION="Analysis of Functional Neuroimages by NIMH"
+HOMEPAGE="https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/;
+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-${GIFTI_HASH}.tar.gz
+   "
+
+S="${WORKDIR}/afni-AFNI_${PV}"
+
+LICENSE="GPL-3+"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="test whirlgif"
+RESTRICT="!test? ( test )"
+
+RDEPEND="
+   dev-build/ninja
+   dev-libs/expat
+   dev-libs/glib:2
+   dev-libs/libf2c
+   media-libs/freeglut
+   media-libs/glu
+   media-libs/netpbm
+   media-libs/qhull
+   media-video/mpeg-tools
+   sci-biology/afni-datasets
+   sci-libs/gsl
+   sci-libs/gts
+   sys-devel/llvm:*
+   sys-libs/libomp
+   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="
+   ${RDEPEND}
+   app-shells/tcsh
+   "
+# Prospectively:
+#Update jpeg-compat to virtual/jpeg:0
+# look for xmhtlm
+
+   #tar xf "${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
+   # Fix AFNI version, no better way seemed to work
+   sed -i -e "s/GIT_REPO_VERSION \"99\.99\.99\"/GIT_REPO_VERSION ${PV}/g" 
cmake/get_git_repo_version.cmake
+   export CFLAGS="-pthread ${CFLAGS}"
+   local mycmakeargs=(
+   -DLIBDIR=/usr/$(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
+   doenvd "${FILESDIR}/97afni"
+}
+
+pkg_postinst() {
+   echo
+   einfo "Please run the following commands if you"
+   einfo "intend to use afni binaries from an existing shell:"
+   einfo "source /etc/profile"
+   echo
+}

[gentoo-commits] proj/sci:master commit in: sci-biology/afni/files/, sci-biology/afni/

2024-05-28 Thread Horea Christian 
commit: 0075b0aa4f9993e0bc54e9d627329332555d16e0
Author: Horea Christian  chymera  eu>
AuthorDate: Tue May 28 17:10:35 2024 +
Commit: Horea Christian  gmail  com>
CommitDate: Tue May 28 17:10:35 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=0075b0aa

sci-biology/afni: env variable for AFNI data

Signed-off-by: Horea Christian  chymera.eu>

 sci-biology/afni/afni-24.0.08-r2.ebuild | 124 
 sci-biology/afni/files/97afni   |   1 +
 2 files changed, 125 insertions(+)

diff --git a/sci-biology/afni/afni-24.0.08-r2.ebuild 
b/sci-biology/afni/afni-24.0.08-r2.ebuild
new file mode 100644
index 0..270100c0b
--- /dev/null
+++ b/sci-biology/afni/afni-24.0.08-r2.ebuild
@@ -0,0 +1,124 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..13} )
+
+DISTUTILS_USE_PEP517=setuptools
+inherit cmake distutils-r1 toolchain-funcs
+
+GTS_HASH="962155a01f5a1b87bd64e3e3d880b4dbc2347ac7"
+NIFTI_HASH="da476fd27f46098f37f5c9c4c1baee01e559572c"
+GIFTI_HASH="d3e873d8539d9b469daf7db04093da1d7e73d4f7"
+
+DESCRIPTION="Analysis of Functional Neuroimages by NIMH"
+HOMEPAGE="https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/;
+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-${GIFTI_HASH}.tar.gz
+   "
+
+S="${WORKDIR}/afni-AFNI_${PV}"
+
+LICENSE="GPL-3+"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="test whirlgif"
+RESTRICT="!test? ( test )"
+
+RDEPEND="
+   dev-build/ninja
+   dev-libs/expat
+   dev-libs/glib:2
+   dev-libs/libf2c
+   media-libs/freeglut
+   media-libs/glu
+   media-libs/netpbm
+   media-libs/qhull
+   media-video/mpeg-tools
+   sci-biology/afni-datasets
+   sci-libs/gsl
+   sci-libs/gts
+   sys-devel/llvm:*
+   sys-libs/libomp
+   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="
+   ${RDEPEND}
+   app-shells/tcsh
+   "
+# Prospectively:
+#Update jpeg-compat to virtual/jpeg:0
+# look for xmhtlm
+
+   #tar xf "${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
+   doenvd "${FILESDIR}/97afni"
+}
+
+pkg_postinst() {
+   echo
+   einfo "Please run the following commands if you"
+   einfo "intend to use afni binaries from an existing shell:"
+   einfo "source /etc/profile"
+   echo
+}

diff --git a/sci-biology/afni/files/97afni b/sci-biology/afni/files/97afni
new file mode 100644
index 0..dbf463f47
--- /dev/null
+++ b/sci-biology/afni/files/97afni
@@ -0,0 +1 @@
+export AFNI_ATLAS_PATH=/usr/share/afni-datasets

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

2024-05-28 Thread Horea Christian 
commit: f3153dcbca91b2c127a05f04a8eec9db28ef7024
Author: Horea Christian  chymera  eu>
AuthorDate: Tue May 28 16:13:32 2024 +
Commit: Horea Christian  gmail  com>
CommitDate: Tue May 28 16:13:32 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=f3153dcb

sci-biology/afni-datasets: new package, add 20240503

Signed-off-by: Horea Christian  chymera.eu>

 .../afni-datasets/afni-datasets-20240503.ebuild  | 20 
 sci-biology/afni-datasets/metadata.xml   | 12 
 2 files changed, 32 insertions(+)

diff --git a/sci-biology/afni-datasets/afni-datasets-20240503.ebuild 
b/sci-biology/afni-datasets/afni-datasets-20240503.ebuild
new file mode 100644
index 0..4d554a633
--- /dev/null
+++ b/sci-biology/afni-datasets/afni-datasets-20240503.ebuild
@@ -0,0 +1,20 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+MY_P="afni_atlases_dist_2024_0503"
+
+DESCRIPTION="Datasets for using and testing sci-biology/afni"
+HOMEPAGE="https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/;
+SRC_URI="https://afni.nimh.nih.gov/pub/dist/atlases/${MY_P}.tgz -> ${P}.tar.gz"
+
+S="${WORKDIR}/${MY_P}"
+LICENSE="GPL-3+"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+src_install() {
+   insinto /usr/share/${PN}
+   doins -r *
+}

diff --git a/sci-biology/afni-datasets/metadata.xml 
b/sci-biology/afni-datasets/metadata.xml
new file mode 100644
index 0..cb6710311
--- /dev/null
+++ b/sci-biology/afni-datasets/metadata.xml
@@ -0,0 +1,12 @@
+
+http://www.gentoo.org/dtd/metadata.dtd;>
+
+   
+   gen...@chymera.eu
+   Horea Christian
+   
+   
+   s...@gentoo.org
+   Gentoo Science Project
+   
+

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

2024-05-24 Thread Horea Christian 
commit: b5ce4a1154c05787fe20c3074b2bc91f5146bacf
Author: Horea Christian  chymera  eu>
AuthorDate: Fri May 24 13:49:20 2024 +
Commit: Horea Christian  gmail  com>
CommitDate: Fri May 24 13:49:20 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=b5ce4a11

sci-biology/afni: update DESCRIPTION, HOMEPAGE

Signed-off-by: Horea Christian  chymera.eu>

 sci-biology/afni/afni-24.0.04-r1.ebuild | 12 ++--
 sci-biology/afni/afni-24.0.08-r1.ebuild | 12 ++--
 2 files changed, 12 insertions(+), 12 deletions(-)

diff --git a/sci-biology/afni/afni-24.0.04-r1.ebuild 
b/sci-biology/afni/afni-24.0.04-r1.ebuild
index 557fbd579..c5adfb6d8 100644
--- a/sci-biology/afni/afni-24.0.04-r1.ebuild
+++ b/sci-biology/afni/afni-24.0.04-r1.ebuild
@@ -3,7 +3,7 @@
 
 EAPI=8
 
-PYTHON_COMPAT=( python3_{10..12} )
+PYTHON_COMPAT=( python3_{10..13} )
 
 DISTUTILS_USE_PEP517=setuptools
 inherit cmake distutils-r1 toolchain-funcs
@@ -12,16 +12,18 @@ GTS_HASH="962155a01f5a1b87bd64e3e3d880b4dbc2347ac7"
 NIFTI_HASH="da476fd27f46098f37f5c9c4c1baee01e559572c"
 GIFTI_HASH="d3e873d8539d9b469daf7db04093da1d7e73d4f7"
 
-DESCRIPTION="Advanced Normalitazion Tools for neuroimaging"
-HOMEPAGE="http://stnava.github.io/ANTs/;
+DESCRIPTION="Analysis of Functional Neuroimages by NIMH"
+HOMEPAGE="https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/;
 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"
+S="${WORKDIR}/afni-AFNI_${PV}"
+
 LICENSE="GPL-3+"
+SLOT="0"
 KEYWORDS="~amd64 ~x86"
 IUSE="test whirlgif"
 RESTRICT="!test? ( test )"
@@ -54,8 +56,6 @@ DEPEND="
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

diff --git a/sci-biology/afni/afni-24.0.08-r1.ebuild 
b/sci-biology/afni/afni-24.0.08-r1.ebuild
index 20293877f..21ecf81a1 100644
--- a/sci-biology/afni/afni-24.0.08-r1.ebuild
+++ b/sci-biology/afni/afni-24.0.08-r1.ebuild
@@ -3,7 +3,7 @@
 
 EAPI=8
 
-PYTHON_COMPAT=( python3_{10..12} )
+PYTHON_COMPAT=( python3_{10..13} )
 
 DISTUTILS_USE_PEP517=setuptools
 inherit cmake distutils-r1 toolchain-funcs
@@ -12,16 +12,18 @@ GTS_HASH="962155a01f5a1b87bd64e3e3d880b4dbc2347ac7"
 NIFTI_HASH="da476fd27f46098f37f5c9c4c1baee01e559572c"
 GIFTI_HASH="d3e873d8539d9b469daf7db04093da1d7e73d4f7"
 
-DESCRIPTION="Advanced Normalitazion Tools for neuroimaging"
-HOMEPAGE="http://stnava.github.io/ANTs/;
+DESCRIPTION="Analysis of Functional Neuroimages by NIMH"
+HOMEPAGE="https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/;
 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"
+S="${WORKDIR}/afni-AFNI_${PV}"
+
 LICENSE="GPL-3+"
+SLOT="0"
 KEYWORDS="~amd64 ~x86"
 IUSE="test whirlgif"
 RESTRICT="!test? ( test )"
@@ -57,8 +59,6 @@ DEPEND="
 #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

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

2024-03-22 Thread Horea Christian 
commit: bf635e42b9e981623432224920b21940f4feda56
Author: Horea Christian  chymera  eu>
AuthorDate: Fri Mar 22 21:18:40 2024 +
Commit: Horea Christian  gmail  com>
CommitDate: Fri Mar 22 21:18:40 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=bf635e42

sci-biology/afni: removed deprecated deps

Signed-off-by: Horea Christian  chymera.eu>

 sci-biology/afni/{afni-24.0.04.ebuild => afni-24.0.04-r1.ebuild} | 1 -
 sci-biology/afni/{afni-24.0.08.ebuild => afni-24.0.08-r1.ebuild} | 1 -
 2 files changed, 2 deletions(-)

diff --git a/sci-biology/afni/afni-24.0.04.ebuild 
b/sci-biology/afni/afni-24.0.04-r1.ebuild
similarity index 98%
rename from sci-biology/afni/afni-24.0.04.ebuild
rename to sci-biology/afni/afni-24.0.04-r1.ebuild
index c00ef846f..557fbd579 100644
--- a/sci-biology/afni/afni-24.0.04.ebuild
+++ b/sci-biology/afni/afni-24.0.04-r1.ebuild
@@ -40,7 +40,6 @@ RDEPEND="
sci-libs/gts
sys-devel/llvm:*
sys-libs/libomp
-   dev-libs/libpthread-stubs
virtual/jpeg-compat:62
x11-libs/libGLw
x11-libs/libXft

diff --git a/sci-biology/afni/afni-24.0.08.ebuild 
b/sci-biology/afni/afni-24.0.08-r1.ebuild
similarity index 99%
rename from sci-biology/afni/afni-24.0.08.ebuild
rename to sci-biology/afni/afni-24.0.08-r1.ebuild
index 75ff5b6b6..20293877f 100644
--- a/sci-biology/afni/afni-24.0.08.ebuild
+++ b/sci-biology/afni/afni-24.0.08-r1.ebuild
@@ -40,7 +40,6 @@ RDEPEND="
sci-libs/gts
sys-devel/llvm:*
sys-libs/libomp
-   dev-libs/libpthread-stubs
virtual/jpeg-compat:62
x11-libs/libGLw
x11-libs/libXft

[gentoo-commits] proj/sci:master commit in: sci-biology/afni/, sci-biology/afni/files/

2024-02-28 Thread Horea Christian 
commit: fa3769352840642eb37e6125ee2fa69fef802cd4
Author: Horea Christian  chymera  eu>
AuthorDate: Wed Feb 28 23:30:07 2024 +
Commit: Horea Christian  gmail  com>
CommitDate: Wed Feb 28 23:30:07 2024 +
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  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..0
--- 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..0
--- 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
-

[gentoo-commits] proj/sci:master commit in: sci-biology/afni/, sci-biology/afni/files/

2024-02-28 Thread Horea Christian 
commit: 19c71d97b19391b8797187494008509914db24ed
Author: Horea Christian  chymera  eu>
AuthorDate: Wed Feb 28 22:43:04 2024 +
Commit: Horea Christian  gmail  com>
CommitDate: Wed Feb 28 22:43:04 2024 +
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  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 0..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 0..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="
+

[gentoo-commits] proj/sci:master commit in: sci-biology/afni/files/, sci-biology/afni/

2022-04-03 Thread Horea Christian 
commit: 48589a716ae0690d1f7968fa42eb3c8686cef7a8
Author: Horea Christian  chymera  eu>
AuthorDate: Sun Apr  3 08:13:53 2022 +
Commit: Horea Christian  gmail  com>
CommitDate: Sun Apr  3 08:13:53 2022 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=48589a71

sci-biology/afni: version patches are identical

Package-Manager: Portage-3.0.30, Repoman-3.0.3
Signed-off-by: Horea Christian  chymera.eu>

 sci-biology/afni/afni-20.3.03.ebuild |  2 +-
 sci-biology/afni/afni-22.0.21.ebuild |  2 +-
 sci-biology/afni/files/afni-20.3.03-python.patch | 11 ---
 sci-biology/afni/files/afni-22.0.21-python.patch | 13 -
 4 files changed, 2 insertions(+), 26 deletions(-)

diff --git a/sci-biology/afni/afni-20.3.03.ebuild 
b/sci-biology/afni/afni-20.3.03.ebuild
index a95a34cfb..1cc1a3246 100644
--- a/sci-biology/afni/afni-20.3.03.ebuild
+++ b/sci-biology/afni/afni-20.3.03.ebuild
@@ -40,7 +40,7 @@ BUILD="linux_fedora_19_64"
 BIN_CONFLICTS=(qdelaunay whirlgif djpeg cjpeg qhull rbox count mpeg_encode)
 
 src_prepare() {
-   eapply "${FILESDIR}/${P}-python.patch" || die
+   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

diff --git a/sci-biology/afni/afni-22.0.21.ebuild 
b/sci-biology/afni/afni-22.0.21.ebuild
index 6694c9525..6d791e6e1 100644
--- a/sci-biology/afni/afni-22.0.21.ebuild
+++ b/sci-biology/afni/afni-22.0.21.ebuild
@@ -42,7 +42,7 @@ BIN_CONFLICTS=(qdelaunay whirlgif djpeg cjpeg qhull rbox 
count)
 
 src_prepare() {
# more easily applied here than via PATCHES at phase end.
-   eapply "${FILESDIR}/${P}-python.patch" || die
+   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

diff --git a/sci-biology/afni/files/afni-20.3.03-python.patch 
b/sci-biology/afni/files/afni-20.3.03-python.patch
deleted file mode 100644
index 8c3e859f5..0
--- a/sci-biology/afni/files/afni-20.3.03-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

diff --git a/sci-biology/afni/files/afni-22.0.21-python.patch 
b/sci-biology/afni/files/afni-22.0.21-python.patch
deleted file mode 100644
index f31cc051b..0
--- a/sci-biology/afni/files/afni-22.0.21-python.patch
+++ /dev/null
@@ -1,13 +0,0 @@
-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

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

2022-04-03 Thread Horea Christian 
commit: 65c6f547d13f0bf646544e6aef04a70e0d8976c3
Author: Horea Christian  chymera  eu>
AuthorDate: Sun Apr  3 08:11:12 2022 +
Commit: Horea Christian  gmail  com>
CommitDate: Sun Apr  3 08:11:12 2022 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=65c6f547

sci-biology/afni: corrected patch application

ebuild still fails, though, log included in comment and reposited here:
https://ppb.chymera.eu/4223de.log

Package-Manager: Portage-3.0.30, Repoman-3.0.3
Signed-off-by: Horea Christian  chymera.eu>

 sci-biology/afni/afni-22.0.21.ebuild | 10 +++---
 1 file changed, 3 insertions(+), 7 deletions(-)

diff --git a/sci-biology/afni/afni-22.0.21.ebuild 
b/sci-biology/afni/afni-22.0.21.ebuild
index d8ad693bf..6694c9525 100644
--- a/sci-biology/afni/afni-22.0.21.ebuild
+++ b/sci-biology/afni/afni-22.0.21.ebuild
@@ -12,8 +12,7 @@ S="${WORKDIR}/${PN}-AFNI_${PV}/src"
 
 LICENSE="GPL-3+"
 SLOT="0"
-# Depends on some python version withoug pulling it in
-# `thd_selenium.c:18:10: fatal error: Python.h: No such file or directory`
+# SUMA error: https://ppb.chymera.eu/4223de.log
 KEYWORDS=""
 
 RDEPEND="
@@ -38,15 +37,12 @@ DEPEND="${RDEPEND}
app-shells/tcsh
 "
 
-PATCHES=(
-   # Drop python2.7 dependency
-   "${FILESDIR}/${P}-python.patch"
-)
-
 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 "${FILESDIR}/${P}-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

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

2022-04-01 Thread Horea Christian 
commit: e076bdf17bc9d27acebb0294bc5fab198ffd91f5
Author: Horea Christian  chymera  eu>
AuthorDate: Fri Apr  1 15:41:23 2022 +
Commit: Horea Christian  gmail  com>
CommitDate: Fri Apr  1 15:41:23 2022 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=e076bdf1

sci-biology/afni: bump ebuild still fails

Package-Manager: Portage-3.0.30, Repoman-3.0.3
Signed-off-by: Horea Christian  chymera.eu>

 sci-biology/afni/afni-22.0.21.ebuild | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/sci-biology/afni/afni-22.0.21.ebuild 
b/sci-biology/afni/afni-22.0.21.ebuild
index 5a015dafc..d8ad693bf 100644
--- a/sci-biology/afni/afni-22.0.21.ebuild
+++ b/sci-biology/afni/afni-22.0.21.ebuild
@@ -12,7 +12,9 @@ S="${WORKDIR}/${PN}-AFNI_${PV}/src"
 
 LICENSE="GPL-3+"
 SLOT="0"
-KEYWORDS="~amd64"
+# Depends on some python version withoug pulling it in
+# `thd_selenium.c:18:10: fatal error: Python.h: No such file or directory`
+KEYWORDS=""
 
 RDEPEND="
dev-libs/libf2c

[gentoo-commits] proj/sci:master commit in: sci-biology/afni/, sci-biology/afni/files/

2022-04-01 Thread Andrew Ammerlaan 
commit: 34f54dc027e97c6df729cede84253f6555e6c45e
Author: Andrew Ammerlaan  gentoo  org>
AuthorDate: Fri Apr  1 09:05:26 2022 +
Commit: Andrew Ammerlaan  gentoo  org>
CommitDate: Fri Apr  1 09:05:38 2022 +
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  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 0..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

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

2022-04-01 Thread Horea Christian 
commit: e3ed6312407f673e0d8d544fd54d625b6492a27a
Author: Horea Christian  chymera  eu>
AuthorDate: Fri Apr  1 08:22:33 2022 +
Commit: Horea Christian  gmail  com>
CommitDate: Fri Apr  1 08:22:33 2022 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=e3ed6312

sci-biology/afni: cleaned up whitespace and unneeded code

Package-Manager: Portage-3.0.30, Repoman-3.0.3
Signed-off-by: Horea Christian  chymera.eu>

 sci-biology/afni/afni-20.1.16.ebuild | 8 
 sci-biology/afni/afni-20.3.03.ebuild | 6 +-
 2 files changed, 5 insertions(+), 9 deletions(-)

diff --git a/sci-biology/afni/afni-20.1.16.ebuild 
b/sci-biology/afni/afni-20.1.16.ebuild
index 98fdb2397..a95a34cfb 100644
--- a/sci-biology/afni/afni-20.1.16.ebuild
+++ b/sci-biology/afni/afni-20.1.16.ebuild
@@ -46,17 +46,17 @@ src_prepare() {
# 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)~" 
\
+   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~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/~${EROOT}/usr/~g;" -i
+   find "${S}" -iname "*Makefile*" | xargs sed -e 
"s~/usr/~${EPREFIX}/usr/~g;" -i
default
 }
 

diff --git a/sci-biology/afni/afni-20.3.03.ebuild 
b/sci-biology/afni/afni-20.3.03.ebuild
index fab7446bf..a95a34cfb 100644
--- a/sci-biology/afni/afni-20.3.03.ebuild
+++ b/sci-biology/afni/afni-20.3.03.ebuild
@@ -39,10 +39,6 @@ S="${WORKDIR}/${PN}-AFNI_${PV}/src"
 BUILD="linux_fedora_19_64"
 BIN_CONFLICTS=(qdelaunay whirlgif djpeg cjpeg qhull rbox count mpeg_encode)
 
-#PATCHES=(
-#   "${FILESDIR}/${P}-python.patch"
-#)
-
 src_prepare() {
eapply "${FILESDIR}/${P}-python.patch" || die
find -type f -exec sed -i -e "s/-lXp //g" {} +
@@ -60,7 +56,7 @@ src_prepare() {
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/~${EROOT}/usr/~g;" -i
+   find "${S}" -iname "*Makefile*" | xargs sed -e 
"s~/usr/~${EPREFIX}/usr/~g;" -i
default
 }

[gentoo-commits] proj/sci:master commit in: sci-biology/afni/files/, sci-biology/afni/

2022-04-01 Thread Horea Christian 
commit: da45c12e15c1bfde33d4c8e0919eccec25b426b8
Author: Horea Christian  chymera  eu>
AuthorDate: Fri Apr  1 07:48:43 2022 +
Commit: Horea Christian  gmail  com>
CommitDate: Fri Apr  1 07:48:43 2022 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=da45c12e

sci-biology/afni: reinstated working versions

Package-Manager: Portage-3.0.30, Repoman-3.0.3
Signed-off-by: Horea Christian  chymera.eu>

 .../{afni-22.0.03.ebuild => afni-20.1.16.ebuild}   | 26 +++
 .../{afni-22.0.03.ebuild => afni-20.3.03.ebuild}   | 30 ++
 sci-biology/afni/afni-22.0.03.ebuild   |  3 ++-
 sci-biology/afni/files/afni-20.1.16-python.patch   | 11 
 sci-biology/afni/files/afni-20.3.03-python.patch   | 11 
 5 files changed, 58 insertions(+), 23 deletions(-)

diff --git a/sci-biology/afni/afni-22.0.03.ebuild 
b/sci-biology/afni/afni-20.1.16.ebuild
similarity index 66%
copy from sci-biology/afni/afni-22.0.03.ebuild
copy to sci-biology/afni/afni-20.1.16.ebuild
index 920bf7189..98fdb2397 100644
--- a/sci-biology/afni/afni-22.0.03.ebuild
+++ b/sci-biology/afni/afni-20.1.16.ebuild
@@ -26,33 +26,37 @@ RDEPEND="dev-libs/expat
x11-libs/libXft
x11-libs/libXi
x11-libs/libXpm
-   x11-libs/motif
-"
+   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)
+BIN_CONFLICTS=(qdelaunay whirlgif djpeg cjpeg qhull rbox count mpeg_encode)
 
 src_prepare() {
-   find -type f -exec sed -i -e "s/-lXp //g" {} + || die
+   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)~" \
+   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~LD = /usr/bin/gcc~LD   = $(tc-getCC)~" \
+   -e "s~AR = /usr/bin/ar~AR   = $(tc-getAR)~" \
-e "s~RANLIB = /usr/bin/ranlib~RANLIB = $(tc-getRANLIB)~" \
-i Makefile || die "Could not edit Makefile"
# they provide somewhat problematic makefiles :(
-   sed -e "s~ifeq (\$(CC),gcc)~ifeq (1,1)~"\
+   sed -e "s~ifeq ($(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/~${EPREFIX}/usr/~g;" -i || die
+   find "${S}" -iname "*Makefile*" | xargs sed -e 
"s~/usr/~${EROOT}/usr/~g;" -i
default
 }
 
@@ -61,9 +65,9 @@ src_compile() {
 }
 
 src_install() {
-   emake INSTALLDIR="${ED}/usr/bin" install install_plugins
+   emake INSTALLDIR="${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/${CONFLICT}" || die
+   rm "${ED}/usr/bin/${CONFLICT}"
done
 }

diff --git a/sci-biology/afni/afni-22.0.03.ebuild 
b/sci-biology/afni/afni-20.3.03.ebuild
similarity index 65%
copy from sci-biology/afni/afni-22.0.03.ebuild
copy to sci-biology/afni/afni-20.3.03.ebuild
index 920bf7189..fab7446bf 100644
--- a/sci-biology/afni/afni-22.0.03.ebuild
+++ b/sci-biology/afni/afni-20.3.03.ebuild
@@ -26,33 +26,41 @@ RDEPEND="dev-libs/expat
x11-libs/libXft
x11-libs/libXi
x11-libs/libXpm
-   x11-libs/motif
-"
+   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_${PV}/src"
 BUILD="linux_fedora_19_64"
-BIN_CONFLICTS=(qdelaunay whirlgif djpeg cjpeg qhull rbox count)
+BIN_CONFLICTS=(qdelaunay whirlgif djpeg cjpeg qhull rbox count mpeg_encode)
+
+#PATCHES=(
+#   "${FILESDIR}/${P}-python.patch"
+#)
 
 src_prepare() {
-   find -type f -exec sed -i -e "s/-lXp //g" {} + || die
+   eapply "${FILESDIR}/${P}-python.patch" || die
+   find -type f -exec sed -i -e "s/-lXp //g" {} +
cp other_builds/Makefile.${BUILD}

[gentoo-commits] proj/sci:master commit in: sci-biology/afni/files/, sci-biology/afni/

2022-01-25 Thread Andrew Ammerlaan 
commit: 7c2d62f11603cc64279a72f03d2b7b18d61b9de0
Author: Andrew Ammerlaan  gentoo  org>
AuthorDate: Tue Jan 25 15:34:00 2022 +
Commit: Andrew Ammerlaan  gentoo  org>
CommitDate: Tue Jan 25 15:34:00 2022 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=7c2d62f1

sci-biology/afni: bump to version 22.0.03

Package-Manager: Portage-3.0.30, Repoman-3.0.3
Signed-off-by: Andrew Ammerlaan  gentoo.org>

 sci-biology/afni/afni-19.3.12.ebuild   | 72 
 sci-biology/afni/afni-20.3.03.ebuild   | 77 --
 .../{afni-20.1.16.ebuild => afni-22.0.03.ebuild}   | 24 +++
 sci-biology/afni/afni-.ebuild  | 70 
 sci-biology/afni/files/afni-20.1.16-python.patch   | 11 
 sci-biology/afni/files/afni-20.3.03-python.patch   | 11 
 6 files changed, 10 insertions(+), 255 deletions(-)

diff --git a/sci-biology/afni/afni-19.3.12.ebuild 
b/sci-biology/afni/afni-19.3.12.ebuild
deleted file mode 100644
index db19930fd..0
--- a/sci-biology/afni/afni-19.3.12.ebuild
+++ /dev/null
@@ -1,72 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-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 -> ${P}.tar.gz"
-
-LICENSE="GPL-3+"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND="dev-libs/expat
-   media-libs/glu
-   media-libs/netpbm
-   media-libs/qhull
-   media-video/mpeg-tools
-   sci-libs/gsl
-   sys-devel/llvm:*
-   virtual/jpeg:0
-   x11-libs/libGLw
-   x11-libs/libXft
-   x11-libs/libXi
-   x11-libs/libXpm
-   x11-libs/motif[-static-libs]"
-
-# x11-libs/motif[static-libs] breaks the build.
-# See upstream discussion
-# 
http://afni.nimh.nih.gov/afni/community/board/read.php?1,85348,85348#msg-85348
-
-DEPEND="${RDEPEND}
-   app-shells/tcsh"
-
-S="${WORKDIR}/${PN}-AFNI_${PV}/src"
-BUILD="linux_fedora_19_64"
-BIN_CONFLICTS=(qdelaunay whirlgif djpeg cjpeg qhull rbox count mpeg_encode)
-
-src_prepare() {
-   find -type f -exec sed -i -e "s/-lXp //g" {} +
-   cp other_builds/Makefile.${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/~${EROOT}/usr/~g;" -i
-   eapply_user
-}
-
-src_compile() {
-   emake -j1 all plugins suma_exec
-}
-
-src_install() {
-   emake INSTALLDIR="${ED}/usr/bin" -j1 install install_plugins
-   emake INSTALLDIR="${ED}/usr/$(get_libdir)" -j1 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 3185a297a..0
--- a/sci-biology/afni/afni-20.3.03.ebuild
+++ /dev/null
@@ -1,77 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-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 -> ${P}.tar.gz"
-
-LICENSE="GPL-3+"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND="dev-libs/expat
-   media-libs/glu
-   media-libs/netpbm
-   media-libs/qhull
-   media-video/mpeg-tools
-   sci-libs/gsl
-   sys-devel/llvm:*
-   virtual/jpeg:0
-   x11-libs/libGLw
-   x11-libs/libXft
-   x11-libs/libXi
-   x11-libs/libXpm
-   x11-libs/motif[-static-libs]"
-
-# x11-libs/motif[static-libs] breaks the build.
-# See upstream discussion
-# 
http://afni.nimh.nih.gov/afni/community/board/read.php?1,85348,85348#msg-85348
-
-DEPEND="${RDEPEND}
-   app-shells/tcsh"
-
-S="${WORKDIR}/${PN}-AFNI_${PV}/src"
-BUILD="linux_fedora_19_64"
-BIN_CONFLICTS=(qdelaunay whirlgif djpeg cjpeg qhull rbox

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

2021-01-31 Thread Horea Christian 
commit: dad08138c6043026d67cf7e54b610a084a9e6780
Author: Horea Christian  chymera  eu>
AuthorDate: Mon Feb  1 03:52:44 2021 +
Commit: Horea Christian  gmail  com>
CommitDate: Mon Feb  1 03:52:44 2021 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=dad08138

sci-biology/afni: added missing patch file

Package-Manager: Portage-3.0.13, Repoman-3.0.2
Signed-off-by: Horea Christian  chymera.eu>

 sci-biology/afni/files/afni-20.3.03-python.patch | 11 +++
 1 file changed, 11 insertions(+)

diff --git a/sci-biology/afni/files/afni-20.3.03-python.patch 
b/sci-biology/afni/files/afni-20.3.03-python.patch
new file mode 100644
index 0..24ed98405
--- /dev/null
+++ b/sci-biology/afni/files/afni-20.3.03-python.patch
@@ -0,0 +1,11 @@
+--- 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

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

2021-01-02 Thread Horea Christian 
commit: 5c191a775d0dedfe49d26f2bc38342791f8750b7
Author: Horea Christian  chymera  eu>
AuthorDate: Sun Jan  3 03:46:05 2021 +
Commit: Horea Christian  gmail  com>
CommitDate: Sun Jan  3 03:46:05 2021 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=5c191a77

sci-biology/afni: version bump 20.3.03

Package-Manager: Portage-3.0.12, Repoman-3.0.2
Signed-off-by: Horea Christian  chymera.eu>

 sci-biology/afni/afni-20.3.03.ebuild | 77 
 1 file changed, 77 insertions(+)

diff --git a/sci-biology/afni/afni-20.3.03.ebuild 
b/sci-biology/afni/afni-20.3.03.ebuild
new file mode 100644
index 0..ed100cb3c
--- /dev/null
+++ b/sci-biology/afni/afni-20.3.03.ebuild
@@ -0,0 +1,77 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit eutils multilib pax-utils 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 -> ${P}.tar.gz"
+
+LICENSE="GPL-3+"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+RDEPEND="dev-libs/expat
+   media-libs/glu
+   media-libs/netpbm
+   media-libs/qhull
+   media-video/mpeg-tools
+   sci-libs/gsl
+   sys-devel/llvm:*
+   virtual/jpeg:0
+   x11-libs/libGLw
+   x11-libs/libXft
+   x11-libs/libXi
+   x11-libs/libXpm
+   x11-libs/motif[-static-libs]"
+
+# x11-libs/motif[static-libs] breaks the build.
+# See upstream discussion
+# 
http://afni.nimh.nih.gov/afni/community/board/read.php?1,85348,85348#msg-85348
+
+DEPEND="${RDEPEND}
+   app-shells/tcsh"
+
+S="${WORKDIR}/${PN}-AFNI_${PV}/src"
+BUILD="linux_fedora_19_64"
+BIN_CONFLICTS=(qdelaunay whirlgif djpeg cjpeg qhull rbox count mpeg_encode)
+
+#PATCHES=(
+#  "${FILESDIR}/${P}-python.patch"
+#)
+
+src_prepare() {
+   eapply "${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/~${EROOT}/usr/~g;" -i
+   default
+}
+
+src_compile() {
+   emake -j1 all plugins suma_exec
+}
+
+src_install() {
+   emake INSTALLDIR="${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
+}

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

2021-01-02 Thread Horea Christian 
commit: f225be3cfea18d5fedcc3c7f77f402effa123dea
Author: Horea Christian  chymera  eu>
AuthorDate: Sun Jan  3 03:44:38 2021 +
Commit: Horea Christian  gmail  com>
CommitDate: Sun Jan  3 03:44:38 2021 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=f225be3c

sci-biology/afni: applying patch at start of prepare phase

Package-Manager: Portage-3.0.12, Repoman-3.0.2
Signed-off-by: Horea Christian  chymera.eu>

 sci-biology/afni/afni-20.1.16.ebuild | 7 ++-
 1 file changed, 2 insertions(+), 5 deletions(-)

diff --git a/sci-biology/afni/afni-20.1.16.ebuild 
b/sci-biology/afni/afni-20.1.16.ebuild
index 09e2b7def..da68d2d6d 100644
--- a/sci-biology/afni/afni-20.1.16.ebuild
+++ b/sci-biology/afni/afni-20.1.16.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=7
@@ -39,11 +39,8 @@ S="${WORKDIR}/${PN}-AFNI_${PV}/src"
 BUILD="linux_fedora_19_64"
 BIN_CONFLICTS=(qdelaunay whirlgif djpeg cjpeg qhull rbox count mpeg_encode)
 
-PATCHES=(
-   "${FILESDIR}/${P}-python.patch"
-)
-
 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

[gentoo-commits] proj/sci:master commit in: sci-biology/afni/files/, sci-biology/afni/

2020-10-23 Thread Horea Christian 
commit: 83fd8b496d322f3f6130ff251f0567486f35a14a
Author: Horea Christian  chymera  eu>
AuthorDate: Sat Oct 24 04:31:12 2020 +
Commit: Horea Christian  gmail  com>
CommitDate: Sat Oct 24 04:31:12 2020 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=83fd8b49

sci-biology/afni: fixed build issues for systems missing python 2.7

Package-Manager: Portage-3.0.8, Repoman-3.0.2
Signed-off-by: Horea Christian  chymera.eu>

 sci-biology/afni/afni-20.1.16.ebuild |  6 +-
 sci-biology/afni/files/afni-20.1.16-python.patch | 11 +++
 2 files changed, 16 insertions(+), 1 deletion(-)

diff --git a/sci-biology/afni/afni-20.1.16.ebuild 
b/sci-biology/afni/afni-20.1.16.ebuild
index 4953408d6..09e2b7def 100644
--- a/sci-biology/afni/afni-20.1.16.ebuild
+++ b/sci-biology/afni/afni-20.1.16.ebuild
@@ -39,6 +39,10 @@ S="${WORKDIR}/${PN}-AFNI_${PV}/src"
 BUILD="linux_fedora_19_64"
 BIN_CONFLICTS=(qdelaunay whirlgif djpeg cjpeg qhull rbox count mpeg_encode)
 
+PATCHES=(
+   "${FILESDIR}/${P}-python.patch"
+)
+
 src_prepare() {
find -type f -exec sed -i -e "s/-lXp //g" {} +
cp other_builds/Makefile.${BUILD} Makefile || die "Could not copy 
Makefile"
@@ -56,7 +60,7 @@ src_prepare() {
-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/~${EROOT}/usr/~g;" -i
-   eapply_user
+   default
 }
 
 src_compile() {

diff --git a/sci-biology/afni/files/afni-20.1.16-python.patch 
b/sci-biology/afni/files/afni-20.1.16-python.patch
new file mode 100644
index 0..24ed98405
--- /dev/null
+++ b/sci-biology/afni/files/afni-20.1.16-python.patch
@@ -0,0 +1,11 @@
+--- 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

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

2020-06-19 Thread Horea Christian 
commit: 644434c14f22d95edcf230733955076ecab0cf31
Author: Horea Christian  chymera  eu>
AuthorDate: Fri Jun 19 16:01:29 2020 +
Commit: Horea Christian  gmail  com>
CommitDate: Fri Jun 19 16:01:29 2020 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=644434c1

sci-biology/afni: version bump 20.1.16

Package-Manager: Portage-2.3.101, Repoman-2.3.22
Signed-off-by: Horea Christian  chymera.eu>

 sci-biology/afni/afni-20.1.16.ebuild | 72 
 1 file changed, 72 insertions(+)

diff --git a/sci-biology/afni/afni-20.1.16.ebuild 
b/sci-biology/afni/afni-20.1.16.ebuild
new file mode 100644
index 0..4953408d6
--- /dev/null
+++ b/sci-biology/afni/afni-20.1.16.ebuild
@@ -0,0 +1,72 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit eutils multilib pax-utils 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 -> ${P}.tar.gz"
+
+LICENSE="GPL-3+"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+RDEPEND="dev-libs/expat
+   media-libs/glu
+   media-libs/netpbm
+   media-libs/qhull
+   media-video/mpeg-tools
+   sci-libs/gsl
+   sys-devel/llvm:*
+   virtual/jpeg:0
+   x11-libs/libGLw
+   x11-libs/libXft
+   x11-libs/libXi
+   x11-libs/libXpm
+   x11-libs/motif[-static-libs]"
+
+# x11-libs/motif[static-libs] breaks the build.
+# See upstream discussion
+# 
http://afni.nimh.nih.gov/afni/community/board/read.php?1,85348,85348#msg-85348
+
+DEPEND="${RDEPEND}
+   app-shells/tcsh"
+
+S="${WORKDIR}/${PN}-AFNI_${PV}/src"
+BUILD="linux_fedora_19_64"
+BIN_CONFLICTS=(qdelaunay whirlgif djpeg cjpeg qhull rbox count mpeg_encode)
+
+src_prepare() {
+   find -type f -exec sed -i -e "s/-lXp //g" {} +
+   cp other_builds/Makefile.${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/~${EROOT}/usr/~g;" -i
+   eapply_user
+}
+
+src_compile() {
+   emake -j1 all plugins suma_exec
+}
+
+src_install() {
+   emake INSTALLDIR="${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
+}

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

2020-01-16 Thread Horea Christian 
commit: ab307a97b24eb48f5e7c7e7570a0486d0748
Author: Horea Christian  chymera  eu>
AuthorDate: Thu Jan 16 18:27:52 2020 +
Commit: Horea Christian  gmail  com>
CommitDate: Thu Jan 16 18:27:52 2020 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=ab307a97

sci-biology/afni: deprecated old hard-masked versions

Package-Manager: Portage-2.3.84, Repoman-2.3.20
Signed-off-by: Horea Christian  chymera.eu>

 sci-biology/afni/afni-18.1.04.ebuild | 69 
 sci-biology/afni/afni-19.0.21.ebuild | 69 
 2 files changed, 138 deletions(-)

diff --git a/sci-biology/afni/afni-18.1.04.ebuild 
b/sci-biology/afni/afni-18.1.04.ebuild
deleted file mode 100644
index c3f1be074..0
--- a/sci-biology/afni/afni-18.1.04.ebuild
+++ /dev/null
@@ -1,69 +0,0 @@
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit eutils multilib pax-utils 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 -> ${P}.tar.gz"
-
-LICENSE="GPL-3+"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND="dev-libs/expat
-   media-libs/glu
-   media-libs/netpbm
-   media-libs/qhull
-   media-video/mpeg-tools
-   sci-libs/gsl
-   sys-devel/llvm:*
-   virtual/jpeg:0
-   x11-libs/libGLw
-   x11-libs/libXft
-   x11-libs/libXi
-   x11-libs/libXpm
-   x11-libs/motif[-static-libs]"
-
-# x11-libs/motif[static-libs] breaks the build.
-# See upstream discussion
-# 
http://afni.nimh.nih.gov/afni/community/board/read.php?1,85348,85348#msg-85348
-
-DEPEND="${RDEPEND}
-   app-shells/tcsh"
-
-S="${WORKDIR}/${PN}-AFNI_${PV}/src"
-BUILD="linux_fedora_19_64"
-BIN_CONFLICTS=(qdelaunay whirlgif djpeg cjpeg qhull rbox count mpeg_encode)
-
-src_prepare() {
-   find -type f -exec sed -i -e "s/-lXp //g" {} +
-   cp other_builds/Makefile.${BUILD} Makefile || die "Could not copy 
Makefile"
-   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/~${EROOT}/usr/~g;" -i
-   eapply_user
-}
-
-src_compile() {
-   emake -j1 all plugins suma_exec
-}
-
-src_install() {
-   emake INSTALLDIR="${ED}/usr/bin" -j1 install install_plugins
-   emake INSTALLDIR="${ED}/usr/$(get_libdir)" -j1 install_lib
-   for CONFLICT in ${BIN_CONFLICTS[@]}; do
-   rm "${ED}/usr/bin/${CONFLICT}"
-   done
-}

diff --git a/sci-biology/afni/afni-19.0.21.ebuild 
b/sci-biology/afni/afni-19.0.21.ebuild
deleted file mode 100644
index c3f1be074..0
--- a/sci-biology/afni/afni-19.0.21.ebuild
+++ /dev/null
@@ -1,69 +0,0 @@
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit eutils multilib pax-utils 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 -> ${P}.tar.gz"
-
-LICENSE="GPL-3+"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND="dev-libs/expat
-   media-libs/glu
-   media-libs/netpbm
-   media-libs/qhull
-   media-video/mpeg-tools
-   sci-libs/gsl
-   sys-devel/llvm:*
-   virtual/jpeg:0
-   x11-libs/libGLw
-   x11-libs/libXft
-   x11-libs/libXi
-   x11-libs/libXpm
-   x11-libs/motif[-static-libs]"
-
-# x11-libs/motif[static-libs] breaks the build.
-# See upstream discussion
-# 
http://afni.nimh.nih.gov/afni/community/board/read.php?1,85348,85348#msg-85348
-
-DEPEND="${RDEPEND}
-   app-shells/tcsh"
-
-S="${WORKDIR}/${PN}-AFNI_${PV}/src"
-BUILD="linux_fedora_19_64"
-BIN_CONFLICTS=(qdelaunay whirlgif djpeg cjpeg qhull rbox count mpeg_encode)
-
-src_prepare() {
-   find -type f -exec sed -i -e "s/-lXp //g" {} +
-   cp other_builds/Makefile.${BUILD} Makefile || die "Could not copy 
Makefile"
-   sed -e "s~CC = /usr/bin/gcc -O2 -m64~CC = $(tc-getCC) 
\$(CFLAGS)~" \
-   -e "s~CCMIN  = /usr/bin/gcc -m64~CCMIN  = $(tc-getCC) 
\$(CFLAGS)~" \
-

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

2019-11-25 Thread Horea Christian 
commit: b3db3a9c0d4b6e6a7c24003a12eef93e4a79c73d
Author: Horea Christian  chymera  eu>
AuthorDate: Mon Nov 25 18:30:38 2019 +
Commit: Horea Christian  gmail  com>
CommitDate: Mon Nov 25 18:30:38 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=b3db3a9c

sci-biology/afni: version bump 19.3.12 (non-masked version)

Package-Manager: Portage-2.3.79, Repoman-2.3.18
Signed-off-by: Horea Christian  chymera.eu>

 sci-biology/afni/afni-19.3.12.ebuild | 72 
 1 file changed, 72 insertions(+)

diff --git a/sci-biology/afni/afni-19.3.12.ebuild 
b/sci-biology/afni/afni-19.3.12.ebuild
new file mode 100644
index 0..c60a87138
--- /dev/null
+++ b/sci-biology/afni/afni-19.3.12.ebuild
@@ -0,0 +1,72 @@
+# Copyright 1999-2019 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit eutils multilib pax-utils 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 -> ${P}.tar.gz"
+
+LICENSE="GPL-3+"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+RDEPEND="dev-libs/expat
+   media-libs/glu
+   media-libs/netpbm
+   media-libs/qhull
+   media-video/mpeg-tools
+   sci-libs/gsl
+   sys-devel/llvm:*
+   virtual/jpeg:0
+   x11-libs/libGLw
+   x11-libs/libXft
+   x11-libs/libXi
+   x11-libs/libXpm
+   x11-libs/motif[-static-libs]"
+
+# x11-libs/motif[static-libs] breaks the build.
+# See upstream discussion
+# 
http://afni.nimh.nih.gov/afni/community/board/read.php?1,85348,85348#msg-85348
+
+DEPEND="${RDEPEND}
+   app-shells/tcsh"
+
+S="${WORKDIR}/${PN}-AFNI_${PV}/src"
+BUILD="linux_fedora_19_64"
+BIN_CONFLICTS=(qdelaunay whirlgif djpeg cjpeg qhull rbox count mpeg_encode)
+
+src_prepare() {
+   find -type f -exec sed -i -e "s/-lXp //g" {} +
+   cp other_builds/Makefile.${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/~${EROOT}/usr/~g;" -i
+   eapply_user
+}
+
+src_compile() {
+   emake -j1 all plugins suma_exec
+}
+
+src_install() {
+   emake INSTALLDIR="${ED}/usr/bin" -j1 install install_plugins
+   emake INSTALLDIR="${ED}/usr/$(get_libdir)" -j1 install_lib
+   for CONFLICT in ${BIN_CONFLICTS[@]}; do
+   rm "${ED}/usr/bin/${CONFLICT}"
+   done
+}

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

2019-04-25 Thread Horea Christian 
commit: d4ca0e569b7e7f01c39bd08adb2b8c42efa96be0
Author: Horea Christian  chymera  eu>
AuthorDate: Thu Apr 25 08:48:41 2019 +
Commit: Horea Christian  gmail  com>
CommitDate: Thu Apr 25 08:50:33 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=d4ca0e56

sci-biology/afni: dependency update

Package-Manager: Portage-2.3.63, Repoman-2.3.12
Signed-off-by: Horea Christian  chymera.eu>

 sci-biology/afni/afni-18.1.04.ebuild | 3 ++-
 sci-biology/afni/afni-19.0.21.ebuild | 1 +
 sci-biology/afni/afni-.ebuild| 3 ++-
 3 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/sci-biology/afni/afni-18.1.04.ebuild 
b/sci-biology/afni/afni-18.1.04.ebuild
index ba1a0bcd9..c3f1be074 100644
--- a/sci-biology/afni/afni-18.1.04.ebuild
+++ b/sci-biology/afni/afni-18.1.04.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=7
@@ -15,6 +15,7 @@ KEYWORDS="~amd64 ~x86"
 IUSE=""
 
 RDEPEND="dev-libs/expat
+   media-libs/glu
media-libs/netpbm
media-libs/qhull
media-video/mpeg-tools

diff --git a/sci-biology/afni/afni-19.0.21.ebuild 
b/sci-biology/afni/afni-19.0.21.ebuild
index 104015772..c3f1be074 100644
--- a/sci-biology/afni/afni-19.0.21.ebuild
+++ b/sci-biology/afni/afni-19.0.21.ebuild
@@ -15,6 +15,7 @@ KEYWORDS="~amd64 ~x86"
 IUSE=""
 
 RDEPEND="dev-libs/expat
+   media-libs/glu
media-libs/netpbm
media-libs/qhull
media-video/mpeg-tools

diff --git a/sci-biology/afni/afni-.ebuild 
b/sci-biology/afni/afni-.ebuild
index e73bef8cc..e30be5542 100644
--- a/sci-biology/afni/afni-.ebuild
+++ b/sci-biology/afni/afni-.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=7
@@ -16,6 +16,7 @@ KEYWORDS=""
 IUSE=""
 
 RDEPEND="dev-libs/expat
+   media-libs/glu
media-libs/netpbm
media-libs/qhull
media-video/mpeg-tools

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

2018-06-25 Thread Horea Christian 
commit: 8536fe8cb8687e2b585d3f805affbf17971b9653
Author: Horea Christian  yandex  com>
AuthorDate: Tue Jun 26 01:16:34 2018 +
Commit: Horea Christian  gmail  com>
CommitDate: Tue Jun 26 01:16:34 2018 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=8536fe8c

sci-biology/afni: Added unstable x86 keyword

Package-Manager: Portage-2.3.40, Repoman-2.3.9

 sci-biology/afni/afni-18.1.04.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-biology/afni/afni-18.1.04.ebuild 
b/sci-biology/afni/afni-18.1.04.ebuild
index 3a646ffb7..ba1a0bcd9 100644
--- a/sci-biology/afni/afni-18.1.04.ebuild
+++ b/sci-biology/afni/afni-18.1.04.ebuild
@@ -11,7 +11,7 @@ 
SRC_URI="https://github.com/afni/afni/archive/AFNI_${PV}.tar.gz -> ${P}.tar.gz"
 
 LICENSE="GPL-3+"
 SLOT="0"
-KEYWORDS="~amd64"
+KEYWORDS="~amd64 ~x86"
 IUSE=""
 
 RDEPEND="dev-libs/expat