diff options
Diffstat (limited to 'sci-biology/afni')
-rw-r--r-- | sci-biology/afni/Manifest | 9 | ||||
-rw-r--r-- | sci-biology/afni/afni-20.1.16.ebuild | 73 | ||||
-rw-r--r-- | sci-biology/afni/afni-20.3.03.ebuild | 73 | ||||
-rw-r--r-- | sci-biology/afni/afni-22.0.21.ebuild | 75 | ||||
-rw-r--r-- | sci-biology/afni/afni-24.0.08-r3.ebuild | 125 | ||||
-rw-r--r-- | sci-biology/afni/afni-24.1.15.ebuild | 125 | ||||
-rw-r--r-- | sci-biology/afni/afni-24.1.16.ebuild | 127 | ||||
-rw-r--r-- | sci-biology/afni/files/97afni | 1 | ||||
-rw-r--r-- | sci-biology/afni/files/afni-20.1.16-python.patch | 11 | ||||
-rw-r--r-- | sci-biology/afni/files/afni-24.0.04-whirlgif.patch | 39 | ||||
-rw-r--r-- | sci-biology/afni/files/afni-24.1.16-niftiio.patch | 27 | ||||
-rw-r--r-- | sci-biology/afni/metadata.xml | 3 |
12 files changed, 453 insertions, 235 deletions
diff --git a/sci-biology/afni/Manifest b/sci-biology/afni/Manifest index e8caa43d1..cc0d96468 100644 --- a/sci-biology/afni/Manifest +++ b/sci-biology/afni/Manifest @@ -1,3 +1,6 @@ -DIST afni-20.1.16.tar.gz 43355499 BLAKE2B ad7750e64dd9f4c2ca7e5c67bd99faeb8595a41d8a16192e77202f3d307e912083affc11dcbb5da3530079b9e3cf3c2b6b470050f57d5d7af2bb35cc2322772f SHA512 e6fdb8baea6165865bae5bb186375bd65e862564c48470523a8fe026a12f00715fd21bd852bd77c4077ea444a97642c4c3d2ca8060640ba5ddd57bd7883901a6 -DIST afni-20.3.03.tar.gz 43263734 BLAKE2B 7fdaf3de874edff9b32950a2724ba8b4cbcdda538b09effb12658a042326d5c8badf48f1a4dfb4555eb069347099cf3cdb08c4fe1a12999e6eca3ca6f8dca639 SHA512 3c5007f59d6c46093d38f9419c72aa36fb5701314690811f757d9568561b386cf3cd602ddf910ae08fd071ea7ae1e51f5762081217f7a29b23e32f1490f5db65 -DIST afni-22.0.21.tar.gz 43934548 BLAKE2B 3efd5b7fcbbb7b98000e8de51c363ec936a691fcbd505871ff406824ba6ecd5fef358102f6dd2e4d0991b0a40589db6416c1ef14966138c5c36499d7efa3b089 SHA512 1c741e36227075bd8b4f9983510eef95528084cbc4971f9d6d028726ffc2bb211da7a74df98991538d8f6caed041633fdceb0c4366e04d6594faa0160a0e6d2b +DIST afni-24.0.08.gh.tar.gz 52917832 BLAKE2B 4cf61f3474c2c69d8373fbf9413c2236fbda77408535b142e6860effbf49ebcc6007ef9fb18943c07299b4815be6692477cc79423d7ac5a09bfe3d125565058c SHA512 90a9c8a48e1084dcc19d90e62b313057f0e71e87740f6ac63a305d19a4ded8ee01722b55546d2aaa2d4dfbfd0a206d4a9d25969592646c101cabe4743b8962c6 +DIST afni-24.1.15.gh.tar.gz 53136605 BLAKE2B aab19b572b3d3f32e4d91414c127a8ef5cfd5cef04cb55836060298340c3d0e6cf0ec2f5f324590ce432e920842358007858a278198b37b47e6eeb8f318855b3 SHA512 ca8e3d26a32feea0118e4219c5915f8541bf5194f0db8e4b51637fb79a08c15d1772bc75499b71a47af5cac831bbd484efb3fce848d499f51ef002f9f52a6e10 +DIST afni-24.1.16.gh.tar.gz 53139168 BLAKE2B dff31b9b6e89cd2c62e2ab8cb1b7d1ed28e7bc3bbeb586ae7218ccc276237b0632d06c65928469560684871b8fd25dc382e5bdffcc4c5181c5b9855565398df8 SHA512 c507bc8d3bbad8b61daef3321e48bd88c2f020c940c61a7c3ff4dafe1d2823dad5c87b96080716ab6c59d5312b7fa33c8289426f3fcc4938d3ef049df54134b3 +DIST gifti-d3e873d8539d9b469daf7db04093da1d7e73d4f7.tar.gz 107745 BLAKE2B b8162fe08446d5c934762e8dce051e93c8c90fd574dca55757988ccc45be20bfdd07b7a401ef6c536afbe097e6bc05fd3b7f09c4404af4fad4e21fbada7109de SHA512 c458074c6976245cffc48c1e1e57811ec3c0cc5959345bdbc8d674eed6c8a8f93e9f9762bf3acce7142e004dc37930d14bed8cfb97c5b7e92b3f39598da924e2 +DIST nifti-da476fd27f46098f37f5c9c4c1baee01e559572c.tar.gz 451578 BLAKE2B 6bb92ae3ab48dba435b067f7ec0b6d417658ee1a46efe05070bf18fd6d46b8339eaffd09c2fea4971d2685f211496a700b36c255ffb164994636e535b64fe4f5 SHA512 df92345ed580e8bf0579f2ea3ed55a4c4c678a0fe3bfad1e62379e5bf16961272bb2d3e7fda89b96b503cda51c1bf2fb8eb74adba6aad9c73b6830d7d884d1f5 +DIST nifti-f24bec503f1a5d501c0413c1bb8aa3d6e04aebda.tar.gz 451555 BLAKE2B d83e8e265d996bb041fa7c712e4f67f6ab3c4e7e7b9713f5d5a0e045b11c2c5c34a193a0d6f69594d37ff1ac09bb295f9be6b04a7a29711cfad8d27167c15058 SHA512 8a4707edfd11112bdb0c359223bb39c6e1d9281234759ebf65bffe34b52a0530053b2e9368c36a77b788194113db5ac66ddf44204036983fffda3d81699e1d5b 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/${CONFLICT}" || die - done -} diff --git a/sci-biology/afni/afni-24.0.08-r3.ebuild b/sci-biology/afni/afni-24.0.08-r3.ebuild new file mode 100644 index 000000000..12d6c8f87 --- /dev/null +++ b/sci-biology/afni/afni-24.0.08-r3.ebuild @@ -0,0 +1,125 @@ +# Copyright 1999-2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..13} ) + +DISTUTILS_USE_PEP517=setuptools +inherit cmake distutils-r1 toolchain-funcs + +GTS_HASH="962155a01f5a1b87bd64e3e3d880b4dbc2347ac7" +NIFTI_HASH="da476fd27f46098f37f5c9c4c1baee01e559572c" +GIFTI_HASH="d3e873d8539d9b469daf7db04093da1d7e73d4f7" + +DESCRIPTION="Analysis of Functional Neuroimages by NIMH" +HOMEPAGE="https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/" +SRC_URI=" + https://github.com/afni/afni/archive/refs/tags/AFNI_${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 "${FILESDIR}/97afni" +} + +pkg_postinst() { + echo + einfo "Please run the following commands if you" + einfo "intend to use afni binaries from an existing shell:" + einfo "source /etc/profile" + echo +} diff --git a/sci-biology/afni/afni-24.1.15.ebuild b/sci-biology/afni/afni-24.1.15.ebuild new file mode 100644 index 000000000..12d6c8f87 --- /dev/null +++ b/sci-biology/afni/afni-24.1.15.ebuild @@ -0,0 +1,125 @@ +# Copyright 1999-2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..13} ) + +DISTUTILS_USE_PEP517=setuptools +inherit cmake distutils-r1 toolchain-funcs + +GTS_HASH="962155a01f5a1b87bd64e3e3d880b4dbc2347ac7" +NIFTI_HASH="da476fd27f46098f37f5c9c4c1baee01e559572c" +GIFTI_HASH="d3e873d8539d9b469daf7db04093da1d7e73d4f7" + +DESCRIPTION="Analysis of Functional Neuroimages by NIMH" +HOMEPAGE="https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/" +SRC_URI=" + https://github.com/afni/afni/archive/refs/tags/AFNI_${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 "${FILESDIR}/97afni" +} + +pkg_postinst() { + echo + einfo "Please run the following commands if you" + einfo "intend to use afni binaries from an existing shell:" + einfo "source /etc/profile" + echo +} diff --git a/sci-biology/afni/afni-24.1.16.ebuild b/sci-biology/afni/afni-24.1.16.ebuild new file mode 100644 index 000000000..0759d30a0 --- /dev/null +++ b/sci-biology/afni/afni-24.1.16.ebuild @@ -0,0 +1,127 @@ +# Copyright 1999-2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..13} ) + +DISTUTILS_USE_PEP517=setuptools +inherit cmake distutils-r1 toolchain-funcs + +GTS_HASH="962155a01f5a1b87bd64e3e3d880b4dbc2347ac7" +NIFTI_HASH="f24bec503f1a5d501c0413c1bb8aa3d6e04aebda" +GIFTI_HASH="d3e873d8539d9b469daf7db04093da1d7e73d4f7" + +DESCRIPTION="Analysis of Functional Neuroimages by NIMH" +HOMEPAGE="https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/" +SRC_URI=" + https://github.com/afni/afni/archive/refs/tags/AFNI_${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=" + ${RDEPEND} + app-shells/tcsh + " +# Prospectively: +#Update jpeg-compat to virtual/jpeg:0 +# look for xmhtlm + +PATCHES=("${FILESDIR}/afni-24.1.16-niftiio.patch") + + #tar xf "${DISTDIR}/${GTS_HASH}.tar.gz" || die +src_prepare() { + # We need a name without the hash to reference in patches + mv "${WORKDIR}/nifti_clib-${NIFTI_HASH}" "${WORKDIR}/afni-AFNI_24.1.16/nifti_clib_from_github" + mv "${WORKDIR}/gifti_clib-${GIFTI_HASH}" "${WORKDIR}/afni-AFNI_24.1.16/gifti_clib_from_github" + cmake_src_prepare +} + +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}/afni-AFNI_24.1.16/nifti_clib_from_github" + -DFETCHCONTENT_SOURCE_DIR_GIFTI_CLIB="${WORKDIR}/afni-AFNI_24.1.16/gifti_clib_from_github" + -DCOMP_GUI=ON + -DCOMP_PLUGINS=ON + -DUSE_OMP=ON + -DCOMP_PYTHON=OFF + -DUSE_SYSTEM_F2C=ON + ) + tc-export CC + cmake_src_configure +} + +src_compile() { + cmake_src_compile + pushd src/python_scripts + distutils-r1_src_compile + popd +} + +src_install() { + cmake_src_install + pushd src/python_scripts + distutils-r1_src_install + popd + cd "${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 000000000..dbf463f47 --- /dev/null +++ b/sci-biology/afni/files/97afni @@ -0,0 +1 @@ +export AFNI_ATLAS_PATH=/usr/share/afni-datasets 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 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 $(INFLAGS) diff --git a/sci-biology/afni/files/afni-24.1.16-niftiio.patch b/sci-biology/afni/files/afni-24.1.16-niftiio.patch new file mode 100644 index 000000000..a4eb35435 --- /dev/null +++ b/sci-biology/afni/files/afni-24.1.16-niftiio.patch @@ -0,0 +1,27 @@ +From 05dbcd2659fa6177b221a2686300036e4ae435d6 Mon Sep 17 00:00:00 2001 +From: Yaroslav Halchenko <debian@onerussian.com> +Date: Mon, 3 Jun 2024 19:28:21 -0400 +Subject: [PATCH] Announce niftiio as PRIVATE for linking to prevent + propagating linking against it + +I am just a messanger from the cmake-wise @leej3 at +https://github.com/afni/afni/issues/639#issuecomment-2145703256 + +Supposedly closes #639 +--- + src/nifti/nifticdf/CMakeLists.txt | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/src/nifti/nifticdf/CMakeLists.txt b/src/nifti/nifticdf/CMakeLists.txt +index 473be7e3be..01b18a14d8 100644 +--- a/nifti_clib_from_github/nifticdf/CMakeLists.txt ++++ b/nifti_clib_from_github/nifticdf/CMakeLists.txt +@@ -8,7 +8,7 @@ set_target_properties( + "${CMAKE_CURRENT_LIST_DIR}/nifticdf.h" + ) + target_compile_options(${NIFTI_CDFLIB_NAME} PRIVATE "-D__COMPILE_UNUSED_FUNCTIONS__") +-target_link_libraries(${NIFTI_CDFLIB_NAME} PUBLIC ${NIFTI_PACKAGE_PREFIX}niftiio) ++target_link_libraries(${NIFTI_CDFLIB_NAME} PRIVATE ${NIFTI_PACKAGE_PREFIX}niftiio) + get_lib_version_vars("nifticdf_version.h" NIFTICDF_VERSION NIFTICDF_MAJOR_VERSION) + if(BUILD_SHARED_LIBS) + set_target_properties(${NIFTI_CDFLIB_NAME} 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> |