[gentoo-commits] proj/sci:master commit in: sci-chemistry/relion/

[Alexey Shvetsov]

commit:     c2861a35cb4f890544347dc141403e8dc32c8ff5
Author:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
AuthorDate: Wed Feb  1 12:03:34 2023 +0000
Commit:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
CommitDate: Wed Feb  1 12:03:34 2023 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=c2861a35

sci-chemistry/relion: Update relion ebuilds

Signed-off-by: Alexey Shvetsov <alexxy <AT> gentoo.org>

 sci-chemistry/relion/metadata.xml        |  1 +
 sci-chemistry/relion/relion-4.0.0.ebuild | 30 +++++++++++++-
 sci-chemistry/relion/relion-9999.ebuild  | 69 ++++++++++++++++++++++++++++++++
 3 files changed, 98 insertions(+), 2 deletions(-)

diff --git a/sci-chemistry/relion/metadata.xml b/sci-chemistry/relion/metadata.xml
index 33e6e7e5d..101a056b9 100644
--- a/sci-chemistry/relion/metadata.xml
+++ b/sci-chemistry/relion/metadata.xml
@@ -11,6 +11,7 @@
 	</maintainer>
 	<use>
 		<flag name="gui">Enable relion gui</flag>
+		<flag name="cuda">Enable CUDA support</flag>
 	</use>
 	<upstream>
 		<remote-id type="github">3dem/relion</remote-id>

diff --git a/sci-chemistry/relion/relion-4.0.0.ebuild b/sci-chemistry/relion/relion-4.0.0.ebuild
index a40375f64..c6d7d90db 100644
--- a/sci-chemistry/relion/relion-4.0.0.ebuild
+++ b/sci-chemistry/relion/relion-4.0.0.ebuild
@@ -7,11 +7,22 @@ inherit cmake
 
 DESCRIPTION="Image-processing software for cryo-electron microscopy"
 HOMEPAGE="https://www3.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page"
-SRC_URI="https://github.com/3dem/relion/archive/${PV}.tar.gz -> ${P}.tar.gz"
+
+if [[ ${PV} = *9999* ]]; then
+	EGIT_REPO_URI="https://github.com/3dem/relion.git"
+	[[ ${PV} = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="ver${PV:0:4}"
+	inherit git-r3
+	SRC_URI="ftp://ftp.mrc-lmb.cam.ac.uk/pub/dari/class_ranker_0.1.3_torch_1.0.1.pt.tar.gz"
+else
+	SRC_URI="
+	https://github.com/3dem/relion/archive/${PV}.tar.gz -> ${P}.tar.gz
+	ftp://ftp.mrc-lmb.cam.ac.uk/pub/dari/class_ranker_0.1.3_torch_1.0.1.pt.tar.gz
+	"
+	KEYWORDS="~amd64"
+fi
 
 LICENSE="GPL-2"
 SLOT="0"
-KEYWORDS="~amd64"
 IUSE="+gui cuda"
 
 DEPEND="
@@ -30,6 +41,21 @@ BDEPEND="${DEPEND}"
 
 PATCHES=( "${FILESDIR}/${PN}-4.0.0-build.patch" )
 
+src_unpack() {
+	git-r3_src_unpack
+	default
+}
+
+src_prepare() {
+	cmake_src_prepare
+	mkdir -p "${S}/external/torch_models/"
+	cp "${DISTDIR}/class_ranker_0.1.3_torch_1.0.1.pt.tar.gz" "${S}/external/torch_models/"
+	mkdir -p "${S}/external/torch_models/class_ranker/"
+	cp "${WORKDIR}/class_ranker_0.1.3_torch_1.0.1.pt" "${S}/external/torch_models/class_ranker/"
+	sed -e "s:{CMAKE_INSTALL_PREFIX}/lib:{CMAKE_INSTALL_PREFIX}/$(get_libdir):g" -i CMakeLists.txt || die
+	sed -e "s:LIBRARY DESTINATION lib:LIBRARY DESTINATION $(get_libdir):g" -i src/apps/CMakeLists.txt || die
+}
+
 src_configure() {
 	CMAKE_BUILD_TYPE=Release
 	mycmakeargs=(

diff --git a/sci-chemistry/relion/relion-9999.ebuild b/sci-chemistry/relion/relion-9999.ebuild
new file mode 100644
index 000000000..12e09d2fe
--- /dev/null
+++ b/sci-chemistry/relion/relion-9999.ebuild
@@ -0,0 +1,69 @@
+# Copyright 2019-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit cmake
+
+DESCRIPTION="Image-processing software for cryo-electron microscopy"
+HOMEPAGE="https://www3.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page"
+
+if [[ ${PV} = *9999* ]]; then
+	EGIT_REPO_URI="https://github.com/3dem/relion.git"
+	[[ ${PV} = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="ver${PV:0:4}"
+	inherit git-r3
+	SRC_URI="ftp://ftp.mrc-lmb.cam.ac.uk/pub/dari/class_ranker_0.1.3_torch_1.0.1.pt.tar.gz"
+else
+	SRC_URI="
+	https://github.com/3dem/relion/archive/${PV}.tar.gz -> ${P}.tar.gz
+	ftp://ftp.mrc-lmb.cam.ac.uk/pub/dari/class_ranker_0.1.3_torch_1.0.1.pt.tar.gz
+	"
+	KEYWORDS="~amd64"
+fi
+
+LICENSE="GPL-2"
+SLOT="0"
+IUSE="+gui cuda"
+
+DEPEND="
+	gui? ( x11-libs/fltk )
+	cuda? ( dev-util/nvidia-cuda-toolkit )
+	dev-cpp/tbb
+	sci-libs/fftw:3.0
+	media-libs/tiff
+	virtual/mpi
+"
+RDEPEND="
+	${DEPEND}
+	sci-chemistry/ctffind
+"
+BDEPEND="${DEPEND}"
+
+src_unpack() {
+	git-r3_src_unpack
+	default
+}
+
+src_prepare() {
+	cmake_src_prepare
+	mkdir -p "${S}/external/torch_models/"
+	cp "${DISTDIR}/class_ranker_0.1.3_torch_1.0.1.pt.tar.gz" "${S}/external/torch_models/"
+	mkdir -p "${S}/external/torch_models/class_ranker/"
+	cp "${WORKDIR}/class_ranker_0.1.3_torch_1.0.1.pt" "${S}/external/torch_models/class_ranker/"
+	sed -e "s:{CMAKE_INSTALL_PREFIX}/lib:{CMAKE_INSTALL_PREFIX}/$(get_libdir):g" -i CMakeLists.txt || die
+	sed -e "s:LIBRARY DESTINATION lib:LIBRARY DESTINATION $(get_libdir):g" -i src/apps/CMakeLists.txt || die
+}
+
+src_configure() {
+	CMAKE_BUILD_TYPE=Release
+	mycmakeargs=(
+		-DBUILD_SHARED_LIBS=ON
+		-DALTCPU=$(usex !cuda)
+		-DFORCE_OWN_FFTW=OFF
+		-DFORCE_OWN_FLTK=OFF
+		-DFORCE_OWN_TBB=OFF
+		-DCUDA=$(usex cuda)
+		-DGUI=$(usex gui)
+	)
+	cmake_src_configure
+}