sci-biology/afni: add 24.1.15, 24.1.16

Signed-off-by: Horea Christian <chr@chymera.eu>

4 files changed, 282 insertions, 0 deletions

diff --git a/sci-biology/afni/Manifest b/sci-biology/afni/Manifest
index ef61a42fb..cc0d96468 100644
--- a/sci-biology/afni/Manifest
+++ b/sci-biology/afni/Manifest
@@ -1,3 +1,6 @@
 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-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 "${FILESDIR}/97afni"
+}
+
+pkg_postinst() {
+	echo
+	einfo "Please run the following commands if you"
+	einfo "intend to use afni binaries from an existing shell:"
+	einfo "source /etc/profile"
+	echo
+}
diff --git a/sci-biology/afni/files/afni-24.1.16-niftiio.patch b/sci-biology/afni/files/afni-24.1.16-niftiio.patch
new file mode 100644
index 000000000..a4eb35435
--- /dev/null
+++ b/sci-biology/afni/files/afni-24.1.16-niftiio.patch
@@ -0,0 +1,27 @@
+From 05dbcd2659fa6177b221a2686300036e4ae435d6 Mon Sep 17 00:00:00 2001
+From: Yaroslav Halchenko <debian@onerussian.com>
+Date: Mon, 3 Jun 2024 19:28:21 -0400
+Subject: [PATCH] Announce niftiio as PRIVATE for linking to prevent
+ propagating linking against it
+
+I am just a messanger from the cmake-wise @leej3 at
+https://github.com/afni/afni/issues/639#issuecomment-2145703256
+
+Supposedly closes #639
+---
+ src/nifti/nifticdf/CMakeLists.txt | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/src/nifti/nifticdf/CMakeLists.txt b/src/nifti/nifticdf/CMakeLists.txt
+index 473be7e3be..01b18a14d8 100644
+--- a/nifti_clib_from_github/nifticdf/CMakeLists.txt
++++ b/nifti_clib_from_github/nifticdf/CMakeLists.txt
+@@ -8,7 +8,7 @@ set_target_properties(
+     "${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}