[med-svn] [Git][med-team/relion][debian/2.1-1] 2 commits: Add d/dir from 1.4+dfsg-4 version
Roland Fehrenbacher
gitlab at salsa.debian.org
Thu Oct 1 12:28:18 BST 2020
Roland Fehrenbacher pushed to tag debian/2.1-1 at Debian Med / relion
Commits:
e43b0f49 by Roland Fehrenbacher at 2019-02-04T16:26:28+00:00
Add d/dir from 1.4+dfsg-4 version
- - - - -
330a59cd by Roland Fehrenbacher at 2019-02-07T11:38:45+01:00
d/dir changes for new 2.1
- - - - -
24 changed files:
- + debian/README.source
- + debian/changelog
- + debian/compat
- + debian/control
- + debian/copyright
- + debian/gbp.conf
- + debian/relion-cuda.docs
- + debian/relion-cuda.install
- + debian/relion-cuda.lintian-overrides
- + debian/relion-cuda.triggers
- + debian/relion-gui-cuda.install
- + debian/relion-gui-cuda.lintian-overrides
- + debian/relion-gui-cuda.triggers
- + debian/relion-gui.install
- + debian/relion-gui.lintian-overrides
- + debian/relion-gui.triggers
- + debian/relion.docs
- + debian/relion.install
- + debian/relion.lintian-overrides
- + debian/relion.triggers
- + debian/rules
- + debian/source/format
- + debian/upstream/metadata
- + debian/watch
Changes:
=====================================
debian/README.source
=====================================
@@ -0,0 +1,52 @@
+This package is maintained from the upstream git repository located at
+https://github.com/3dem/relion.git
+using Dep14 (http://dep.debian.net/deps/dep14/) layout/workflow.
+
+New versions should usually be built from the debian/master branch.
+There is a d/gbp.conf, so building with 'gbp buildpackage' is supported.
+The upstream branch is master (there are old upstream branches called upstream
+and upstream-branch that were used for intermediate package versions but are now
+obsolete).
+
+Patches are managed within the patch-queue/debian/master branch (if there are
+any). This branch should always be based on the (upstream) master branch. The
+contents of the d/patches directory is then auto-generated using:
+$ gbp pq export
+
+To clone this repo use:
+$ gbp clone --pristine-tar git at salsa.debian.org:med-team/relion.git
+
+To build the package after cloning:
+$ gbp buildpackage
+
+To be able to receive new upstream releases/commits, after cloning, you need to
+add the upstream repo address as a 'git remote' as follows:
+$ git remote add upstream https://github.com/3dem/relion.git
+Then you can pull upstream changes as follows:
+$ git branch master
+$ git pull upstream
+
+Handling new upstream releases (e.g. for new release 2.1):
+- Set an upstream tag 'alias' (original upstream tag would be 2.1):
+ $ git tag upstream/2.1 2.1
+- Rebase patch-queue branch (if it exists and contains needed patches)
+ $ git checkout patch-queue/debian/master
+ $ git rebase -i upstream/2.1
+ Review patches, possibly fix conflicts, when done:
+ $ gbp pq export
+ This puts you into the debian/master branch automatically. Review the changes
+ and commit.
+- Merge new upstream release to the debian/master branch:
+ $ git checkout debian/master (probably you're already there)
+ $ git merge upstream/2.1
+- Adjust debian files for new release ...
+- Set debian release tag when done (assuming debian version 2.1-1)
+ $ git tag debian/2.1-1
+- Build new package including new pristine-tar generation:
+ $ gbp buildpackage --git-pristine-tar --git-pristine-tar-commit \
+ --git-compression=xz
+- When all is fine, push the new version
+ $ git push --all
+ $ git push --tags
+
+ -- Roland Fehrenbacher <rfehren at debian.org>, Thu, 07 Feb 2019 10:36:56 +0000
=====================================
debian/changelog
=====================================
@@ -0,0 +1,94 @@
+relion (2.1-1) unstable; urgency=medium
+
+ * New upstream version 2.1
+ * Rename available binary packages, since MPI support is now default.
+ The MPI enabled binaries carry a suffix _mpi, serial versions are still
+ available.
+ * Dropped librelion* packages. Shared libraries are not meant to be used
+ outside of the package and are now part of the relion* packages.
+ * Add versions with CUDA/GPU support (these are in the Debian contrib
+ archive area). They are named relion-cuda and relion-gui-cuda.
+ * Moved to dep14 layout to work directly with the upstream git repo (see
+ README.source in the source archive).
+
+ -- Roland Fehrenbacher <rfehren at debian.org> Mon, 04 Feb 2019 17:58:47 +0000
+
+relion (1.4+dfsg-4) unstable; urgency=medium
+
+ * Team upload.
+ * Add watch file (and delete README.source that explains why there is no
+ watch file)
+ * New upstream version
+ * debhelper 11
+ * Point Vcs fields to salsa.debian.org
+ * Standards-Version: 4.1.4
+ * Restrict architectures to amd64 and i386
+ Closes: #897239
+
+ -- Andreas Tille <tille at debian.org> Thu, 14 Jun 2018 14:10:42 +0200
+
+relion (1.4+dfsg-3) unstable; urgency=medium
+
+ * Team upload
+ * d/control: Enable all archs, Closes: #873865
+ * d/control: Update standards to 4.1.1 (no changes)
+
+ -- Gert Wollny <gewo at debian.org> Thu, 07 Dec 2017 10:27:59 +0100
+
+relion (1.4+dfsg-2) unstable; urgency=medium
+
+ [ Gert Wollny ]
+ * Team upload.
+ * d/p/0005: Correct compilation with gcc-6, Closes: #811641
+ * d/p/0006: Correctly copy only 4 byte, corresponding to the
+ target array size
+ * d/control: Update standards version to 3.9.8
+
+ [ Andreas Tille ]
+ * hardening=+bindnow
+
+ -- Gert Wollny <gw.fossdev at gmail.com> Wed, 29 Jun 2016 13:32:34 +0000
+
+relion (1.4+dfsg-1) unstable; urgency=medium
+
+ [ Roland Fehrenbacher ]
+ * New upstream version 1.4
+ * Bug fix: "file conflicts between librelion{+mpi}{+gui}-1.3-1{v5}
+ packages", thanks to Ralf Treinen (Closes: #797825).
+
+ [ Andreas Tille ]
+ * Enable building architecture independant files separately
+ Closes: #806103
+
+ -- Roland Fehrenbacher <rf at q-leap.de> Tue, 08 Dec 2015 19:04:50 +0100
+
+relion (1.3+dfsg-3) unstable; urgency=medium
+
+ [ Andreas Tille ]
+ * Rename library packages for g++5 ABI transition.
+ (Thanks for the patch to Iain Lane <iain at orangesquash.org.uk>)
+ Closes: #791267
+
+ [ Roland Fehrenbacher ]
+ * Fix permissions of d/lib*.install files (needed for dh-exec)
+
+ -- Roland Fehrenbacher <rf at q-leap.de> Mon, 24 Aug 2015 16:08:36 +0000
+
+relion (1.3+dfsg-2) unstable; urgency=medium
+
+ * Drop build-dep on openmpi-gcc
+ Closes: #766821
+
+ -- Andreas Tille <tille at debian.org> Sun, 26 Oct 2014 07:40:11 +0100
+
+relion (1.3+dfsg-1) unstable; urgency=low
+
+ * Initial upload (Closes: #766324)
+
+ -- Roland Fehrenbacher <rf at q-leap.de> Thu, 23 Oct 2014 11:52:48 +0000
+
+relion (0.0) stable; urgency=low
+
+ * New repository
+
+ -- Roland Fehrenbacher <rf at q-leap.de> Tue, 29 Jul 2014 14:11:18 +0200
=====================================
debian/compat
=====================================
@@ -0,0 +1 @@
+11
=====================================
debian/control
=====================================
@@ -0,0 +1,118 @@
+Source: relion
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Roland Fehrenbacher <rfehren at debian.org>,
+ Andreas Tille <tille at debian.org>,
+Section: science
+Priority: optional
+Build-Depends: cmake,
+ debhelper (>= 11),
+ dh-exec,
+ libfftw3-dev,
+ libfltk1.3-dev,
+ libopenmpi-dev,
+ nvidia-cuda-toolkit,
+Standards-Version: 4.3.0
+Vcs-Browser: https://salsa.debian.org/med-team/relion
+Vcs-Git: https://salsa.debian.org/med-team/relion.git
+Homepage: https://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page
+
+Package: relion
+Architecture: amd64 i386
+Depends: openmpi-gcc | openmpi-bin,
+ ${misc:Depends},
+ ${shlibs:Depends},
+Breaks: relion-bin,
+ relion-bin+gui,
+ relion-bin+mpi,
+ relion-bin+mpi+gui,
+Replaces: relion-bin,
+ relion-bin+gui,
+ relion-bin+mpi,
+ relion-bin+mpi+gui,
+Conflicts: relion-cuda,
+Description: toolkit for 3D reconstructions in cryo-electron microscopy
+ RELION (for REgularised LIkelihood OptimisatioN) is a stand-alone
+ computer program for Maximum A Posteriori refinement of (multiple) 3D
+ reconstructions or 2D class averages in cryo-electron microscopy.
+ .
+ RELION provides a GUI, several command-line tools in parallel (MPI) and serial
+ versions, optionally with CUDA/GPU support.
+ .
+ relion provides the serial and parallel (MPI) command-line tools without
+ CUDA/GPU support.
+
+Package: relion-gui
+Architecture: amd64 i386
+Depends: openmpi-gcc | openmpi-bin,
+ relion,
+ ${misc:Depends},
+ ${shlibs:Depends},
+Breaks: relion-bin,
+ relion-bin+gui,
+ relion-bin+mpi,
+ relion-bin+mpi+gui,
+Replaces: relion-bin,
+ relion-bin+gui,
+ relion-bin+mpi,
+ relion-bin+mpi+gui,
+Conflicts: relion-cuda-gui,
+Description: parallel toolkit for 3D reconstructions in cryo-electron microscopy
+ RELION (for REgularised LIkelihood OptimisatioN) is a stand-alone
+ computer program for Maximum A Posteriori refinement of (multiple) 3D
+ reconstructions or 2D class averages in cryo-electron microscopy.
+ .
+ RELION provides a GUI, several command-line tools in parallel (MPI) and serial
+ versions, optionally with CUDA/GPU support.
+ .
+ relion-gui provides the graphical user interface without CUDA/GPU support.
+
+Package: relion-cuda
+Section: contrib/science
+Architecture: amd64 i386
+Depends: openmpi-gcc | openmpi-bin,
+ ${misc:Depends},
+ ${shlibs:Depends},
+Breaks: relion-bin,
+ relion-bin+gui,
+ relion-bin+mpi,
+ relion-bin+mpi+gui,
+Replaces: relion-bin,
+ relion-bin+gui,
+ relion-bin+mpi,
+ relion-bin+mpi+gui,
+Conflicts: relion,
+Description: parallel toolkit for 3D reconstructions in cryo-electron microscopy
+ RELION (for REgularised LIkelihood OptimisatioN) is a stand-alone
+ computer program for Maximum A Posteriori refinement of (multiple) 3D
+ reconstructions or 2D class averages in cryo-electron microscopy.
+ .
+ RELION provides a GUI, several command-line tools in parallel (MPI) and serial
+ versions, optionally with CUDA/GPU support.
+ .
+ relion-cuda provides the serial and parallel (MPI) command-line tools with
+ CUDA/GPU support.
+
+Package: relion-gui-cuda
+Architecture: amd64 i386
+Depends: openmpi-gcc | openmpi-bin,
+ relion-cuda,
+ ${misc:Depends},
+ ${shlibs:Depends},
+Breaks: relion-bin,
+ relion-bin+gui,
+ relion-bin+mpi,
+ relion-bin+mpi+gui,
+Replaces: relion-bin,
+ relion-bin+gui,
+ relion-bin+mpi,
+ relion-bin+mpi+gui,
+Conflicts: relion-gui,
+Description: parallel toolkit for 3D reconstructions in cryo-electron microscopy
+ RELION (for REgularised LIkelihood OptimisatioN) is a stand-alone
+ computer program for Maximum A Posteriori refinement of (multiple) 3D
+ reconstructions or 2D class averages in cryo-electron microscopy.
+ .
+ RELION provides a GUI, several command-line tools in parallel (MPI) and serial
+ versions, optionally with CUDA/GPU support.
+ .
+ relion-gui-cuda provides the graphical user interface with CUDA/GPU support.
=====================================
debian/copyright
=====================================
@@ -0,0 +1,45 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: relion
+Upstream-Contact: scheres at mrc-lmb.cam.ac.uk
+Source: http://www2.mrc-lmb.cam.ac.uk/groups/scheres/download_relion.html
+Files-Excluded: external
+
+Files: *
+Copyright: 2014, Sjors Scheres at the MRC Laboratory of Molecular Biology
+License: GPL-2+
+
+Files: debian/*
+Copyright: 2014-2018, Q-Leap Networks GmbH <info at q-leap.de>
+License: GPL-2+
+
+Files: src/CPlot2D.cpp
+ src/CPlot2D.h
+Copyright: 2014, AMZs.
+License: GPL-2+
+
+Files: src/Healpix_2.15a/*
+Copyright: 2002-2007, Max-Planck-Society
+License: GPL-2+
+
+Files: src/Healpix_2.15a/NOTES
+ src/Healpix_2.15a/lsconstants.h
+Copyright: 2014, Sjors Scheres at the MRC Laboratory of Molecular Biology
+License: GPL-2+
+
+License: GPL-2+
+ This program is free software: you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation, either version 2 of the License, or
+ (at your option) any later version.
+ .
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+ .
+ On Debian systems, the full text of the GNU General Public
+ License version 2 can be found in the file
+ `/usr/share/common-licenses/GPL-2'.
=====================================
debian/gbp.conf
=====================================
@@ -0,0 +1,5 @@
+[DEFAULT]
+upstream-branch = master
+debian-branch = debian/master
+ignore-branch = False
+pristine-tar = True
=====================================
debian/relion-cuda.docs
=====================================
@@ -0,0 +1,2 @@
+AUTHORS
+README.md
=====================================
debian/relion-cuda.install
=====================================
@@ -0,0 +1,3 @@
+#! /usr/bin/dh-exec
+cuda/usr/bin/* usr/bin/
+cuda/usr/lib/*.so usr/lib/${DEB_HOST_MULTIARCH}/
=====================================
debian/relion-cuda.lintian-overrides
=====================================
@@ -0,0 +1,3 @@
+relion-cuda: binary-without-manpage
+relion-cuda: package-name-doesnt-match-sonames
+relion-cuda: shlib-without-versioned-soname
=====================================
debian/relion-cuda.triggers
=====================================
@@ -0,0 +1 @@
+activate-noawait ldconfig
=====================================
debian/relion-gui-cuda.install
=====================================
@@ -0,0 +1,3 @@
+#! /usr/bin/dh-exec
+cuda-gui/usr/bin/* usr/bin/
+cuda-gui/usr/lib/*.so usr/lib/${DEB_HOST_MULTIARCH}/
=====================================
debian/relion-gui-cuda.lintian-overrides
=====================================
@@ -0,0 +1,3 @@
+relion-gui-cuda: binary-without-manpage
+relion-gui-cuda: package-name-doesnt-match-sonames
+relion-gui-cuda: shlib-without-versioned-soname
=====================================
debian/relion-gui-cuda.triggers
=====================================
@@ -0,0 +1 @@
+activate-noawait ldconfig
=====================================
debian/relion-gui.install
=====================================
@@ -0,0 +1,3 @@
+#! /usr/bin/dh-exec
+no-cuda-gui/usr/bin/* usr/bin/
+no-cuda-gui/usr/lib/*.so usr/lib/${DEB_HOST_MULTIARCH}/
=====================================
debian/relion-gui.lintian-overrides
=====================================
@@ -0,0 +1,3 @@
+relion-gui: binary-without-manpage
+relion-gui: package-name-doesnt-match-sonames
+relion-gui: shlib-without-versioned-soname
=====================================
debian/relion-gui.triggers
=====================================
@@ -0,0 +1 @@
+activate-noawait ldconfig
=====================================
debian/relion.docs
=====================================
@@ -0,0 +1,2 @@
+AUTHORS
+README.md
=====================================
debian/relion.install
=====================================
@@ -0,0 +1,3 @@
+#! /usr/bin/dh-exec
+no-cuda/usr/bin/* usr/bin/
+no-cuda/usr/lib/*.so usr/lib/${DEB_HOST_MULTIARCH}/
=====================================
debian/relion.lintian-overrides
=====================================
@@ -0,0 +1,3 @@
+relion: binary-without-manpage
+relion: package-name-doesnt-match-sonames
+relion: shlib-without-versioned-soname
=====================================
debian/relion.triggers
=====================================
@@ -0,0 +1 @@
+activate-noawait ldconfig
=====================================
debian/rules
=====================================
@@ -0,0 +1,84 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+export DEB_BUILD_MAINT_OPTIONS = hardening=+bindnow
+
+DEBVENDOR := $(shell dpkg-vendor --query Vendor)
+
+ifeq ($(DEBVENDOR), Qlustar)
+ # Qlustar specific stuff
+ include /usr/share/ql-deb-utils/Makefile
+ MPICXX := mpicxx.openmpi-gcc
+else
+ NUMJOBS := $(patsubst parallel=%,%,$(filter parallel=%,$(DEB_BUILD_OPTIONS)))
+ MAKE_-J := $(addprefix -j, $(NUMJOBS))
+ MPICXX := mpicxx.openmpi
+endif
+
+# include defs of all DEB_HOST_*/DEB_BUILD_* vars
+include /usr/share/dpkg/architecture.mk
+
+CONFIGURE_COMMON := CC=gcc-7 CXX=g++-7 cmake -DCMAKE_INSTALL_PREFIX=/usr \
+ -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON "-GUnix Makefiles" \
+ -DCMAKE_VERBOSE_MAKEFILE=ON \
+ -DCMAKE_SKIP_RPATH=TRUE \
+ -DDoublePrec_GPU=ON
+
+%:
+ dh $@
+
+override_dh_auto_configure:
+
+override_dh_auto_build:
+ for build_type in no-cuda cuda; do \
+ mkdir $(CURDIR)/build-$$build_type; done
+ # We need to build 2 different versions for the 2 different types of
+ # binary packages. The CUDA version will go to contrib
+ # First no CUDA (for relion, relion-gui) ...
+ cd $(CURDIR)/build-no-cuda; \
+ $(CONFIGURE_COMMON) -DGUI=ON -DCUDA=OFF $(CURDIR); \
+ make $(MAKE_-J); DESTDIR=$(CURDIR)/debian/tmp/no-cuda make install
+ mkdir -p $(CURDIR)/debian/tmp/no-cuda-gui/usr/bin \
+ $(CURDIR)/debian/tmp/no-cuda-gui/usr/lib
+ rm $(CURDIR)/debian/tmp/no-cuda/usr/bin/*.csh # Useless ...
+ for prog in relion relion_display relion_maingui relion_manualpick \
+ relion_pipeliner; do \
+ mv $(CURDIR)/debian/tmp/no-cuda/usr/bin/$$prog \
+ $(CURDIR)/debian/tmp/no-cuda-gui/usr/bin; done
+ mv $(CURDIR)/debian/tmp/no-cuda/usr/lib/librelion_gui_lib.so \
+ $(CURDIR)/debian/tmp/no-cuda-gui/usr/lib
+ # ... then add CUDA support (for relion-cuda, relion-gui-cuda) ...
+ cd $(CURDIR)/build-cuda; \
+ $(CONFIGURE_COMMON) -DGUI=ON -DCUDA=ON $(CURDIR); \
+ make $(MAKE_-J); DESTDIR=$(CURDIR)/debian/tmp/cuda make install
+ mkdir -p $(CURDIR)/debian/tmp/cuda-gui/usr/bin \
+ $(CURDIR)/debian/tmp/cuda-gui/usr/lib
+ rm $(CURDIR)/debian/tmp/cuda/usr/bin/*.csh # Useless ...
+ for prog in relion relion_display relion_maingui relion_manualpick \
+ relion_pipeliner; do \
+ mv $(CURDIR)/debian/tmp/cuda/usr/bin/$$prog \
+ $(CURDIR)/debian/tmp/cuda-gui/usr/bin; done
+ mv $(CURDIR)/debian/tmp/cuda/usr/lib/librelion_gui_lib.so \
+ $(CURDIR)/debian/tmp/cuda-gui/usr/lib
+
+override_dh_prep:
+ # We don't want debian/tmp to be removed again ...
+ dh_prep -X debian/tmp
+
+override_dh_auto_install:
+
+override_dh_install-arch:
+ dh_install -a
+
+override_dh_clean:
+ dh_clean
+ -rm -rf build*
+
+describe-current-version:
+ git describe --tags upstream | sed 's,^release-,,;s,-,+,;s,-,~,;'
+
+get-orig-source:
+ uscan --download-current-version --force-download --rename --repack-compression xz
=====================================
debian/source/format
=====================================
@@ -0,0 +1 @@
+3.0 (quilt)
=====================================
debian/upstream/metadata
=====================================
@@ -0,0 +1,20 @@
+Reference:
+ Author: Sjors H. W. Scheres
+ Title: >
+ RELION: implementation of a Bayesian approach to
+ cryo-EM structure determination
+ Journal: J Struct Biol.
+ Year: 2012
+ Year: 180
+ Number: 3
+ Pages: 519-30
+ DOI: 10.1016/j.jsb.2012.09.006
+ PMID: 23000701
+ URL: http://www.sciencedirect.com/science/article/pii/S1047847712002481
+Registry:
+ - Name: OMICtools
+ Entry: OMICS_15597
+ - Name: bio.tools
+ Entry: NA
+ - Name: SciCrunch
+ Entry: NA
=====================================
debian/watch
=====================================
@@ -0,0 +1,3 @@
+version=4
+
+https://github.com/3dem/relion/releases .*/archive/(\d[\d.]+)@ARCHIVE_EXT@
View it on GitLab: https://salsa.debian.org/med-team/relion/-/compare/47819caf95c06f466b3e7d35573fef3070e2f540...330a59cd79a45d2d51e2707221f88b84a2d4503b
--
View it on GitLab: https://salsa.debian.org/med-team/relion/-/compare/47819caf95c06f466b3e7d35573fef3070e2f540...330a59cd79a45d2d51e2707221f88b84a2d4503b
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