[med-svn] [Git][med-team/relion][debian/master] Separate non-cuda/cuda packages
Roland Fehrenbacher
gitlab at salsa.debian.org
Thu Oct 1 12:25:22 BST 2020
Roland Fehrenbacher pushed to branch debian/master at Debian Med / relion
Commits:
ccd7eec7 by Roland Fehrenbacher at 2020-10-01T11:21:07+02:00
Separate non-cuda/cuda packages
cuda packages will now be built from the branch debian-contrib/master
- - - - -
13 changed files:
- debian/README.source
- debian/changelog
- debian/control
- − 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.install
- debian/rules
Changes:
=====================================
debian/README.source
=====================================
@@ -3,7 +3,8 @@ 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.
+Note that a cuda enabled version can be built from the debian-contrib/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).
@@ -26,22 +27,22 @@ 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
+Handling new upstream releases (e.g. for new release 3.1.0):
+- Set an upstream tag 'alias' (original upstream tag would be 3.1.0):
+ $ git tag upstream/3.1.0 3.1.0
- Rebase patch-queue branch (if it exists and contains needed patches)
$ git checkout patch-queue/debian/master
- $ git rebase -i upstream/2.1
+ $ git rebase -i upstream/3.1.0
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
+ $ git merge upstream/3.1.0
- Adjust debian files for new release ...
-- Set debian release tag when done (assuming debian version 2.1-1)
- $ git tag debian/2.1-1
+- Set debian release tag when done (assuming debian version 3.1.0-1)
+ $ git tag debian/3.1.0-1
- Build new package including new pristine-tar generation:
$ gbp buildpackage --git-pristine-tar --git-pristine-tar-commit \
--git-compression=xz
@@ -49,4 +50,5 @@ Handling new upstream releases (e.g. for new release 2.1):
$ git push --all
$ git push --tags
- -- Roland Fehrenbacher <rfehren at debian.org>, Thu, 07 Feb 2019 10:36:56 +0000
+ -- Roland Fehrenbacher <rfehren at debian.org> Thu, 01 Oct 2020 10:37:37 +0200
+
=====================================
debian/changelog
=====================================
@@ -1,24 +1,17 @@
-relion (3.1.0-2) unstable; urgency=medium
+relion (3.1.0-3) unstable; urgency=medium
* New upstream version 3.1.0
* Update to Standards-Version: 4.5.0
-
- -- Roland Fehrenbacher <rfehren at debian.org> Tue, 29 Sep 2020 19:01:31 +0000
-
-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.
+ * Dropped librelion* packages. No shared libraries are created by relion
+ anymore.
* Moved to dep14 layout to work directly with the upstream git repo (see
README.source in the source archive).
+ * Added a simple autopkgtest
- -- Roland Fehrenbacher <rfehren at debian.org> Mon, 04 Feb 2019 17:58:47 +0000
+ -- Roland Fehrenbacher <rfehren at debian.org> Thu, 01 Oct 2020 10:37:37 +0200
relion (1.4+dfsg-4) unstable; urgency=medium
=====================================
debian/control
=====================================
@@ -10,7 +10,6 @@ Build-Depends: cmake,
libfltk1.3-dev,
libopenmpi-dev,
libtiff-dev,
- nvidia-cuda-toolkit,
Standards-Version: 4.5.0
Vcs-Browser: https://salsa.debian.org/med-team/relion
Vcs-Git: https://salsa.debian.org/med-team/relion.git
@@ -65,54 +64,3 @@ Description: parallel toolkit for 3D reconstructions in cryo-electron microscopy
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/relion-cuda.docs deleted
=====================================
@@ -1,2 +0,0 @@
-AUTHORS
-README.md
=====================================
debian/relion-cuda.install deleted
=====================================
@@ -1,2 +0,0 @@
-cuda/usr/bin/* usr/bin/
-
=====================================
debian/relion-cuda.lintian-overrides deleted
=====================================
@@ -1 +0,0 @@
-relion-cuda: binary-without-manpage
=====================================
debian/relion-cuda.triggers deleted
=====================================
@@ -1 +0,0 @@
-activate-noawait ldconfig
=====================================
debian/relion-gui-cuda.install deleted
=====================================
@@ -1 +0,0 @@
-cuda-gui/usr/bin/* usr/bin/
=====================================
debian/relion-gui-cuda.lintian-overrides deleted
=====================================
@@ -1 +0,0 @@
-relion-gui-cuda: binary-without-manpage
=====================================
debian/relion-gui-cuda.triggers deleted
=====================================
@@ -1 +0,0 @@
-activate-noawait ldconfig
=====================================
debian/relion-gui.install
=====================================
@@ -1,2 +1,2 @@
-no-cuda-gui/usr/bin/* usr/bin/
+gui/usr/bin/* usr/bin/
=====================================
debian/relion.install
=====================================
@@ -1 +1 @@
-no-cuda/usr/bin/* usr/bin/
+cli/usr/bin/* usr/bin/
=====================================
debian/rules
=====================================
@@ -32,31 +32,15 @@ CONFIGURE_COMMON := cmake -DCMAKE_INSTALL_PREFIX=/usr \
override_dh_auto_configure:
override_dh_auto_build:
- for build_type in no-cuda cuda; do \
- mkdir $(CURDIR)/build-$$build_type; done
- # We need to build 2 different versions for the 2 different types of
- # binary packages. The CUDA version will go to contrib
- # First no CUDA (for relion, relion-gui) ...
- cd $(CURDIR)/build-no-cuda; \
- CC=gcc-10 CXX=g++-10 $(CONFIGURE_COMMON) -DGUI=ON -DCUDA=OFF $(CURDIR);\
- make $(MAKE_-J); DESTDIR=$(CURDIR)/debian/tmp/no-cuda make install
- mkdir -p $(CURDIR)/debian/tmp/no-cuda-gui/usr/bin
- rm $(CURDIR)/debian/tmp/no-cuda/usr/bin/*.csh # Useless ...
+ mkdir $(CURDIR)/build
+ cd $(CURDIR)/build; \
+ CC=gcc CXX=g++ $(CONFIGURE_COMMON) -DGUI=ON -DCUDA=OFF $(CURDIR);\
+ make $(MAKE_-J); DESTDIR=$(CURDIR)/debian/tmp/cli make install
+ mkdir -p $(CURDIR)/debian/tmp/gui/usr/bin
+ rm $(CURDIR)/debian/tmp/cli/usr/bin/*.csh # Useless ...
for prog in relion relion_display relion_maingui relion_manualpick; do \
- mv $(CURDIR)/debian/tmp/no-cuda/usr/bin/$$prog \
- $(CURDIR)/debian/tmp/no-cuda-gui/usr/bin; done
- # ... then add CUDA support (for relion-cuda, relion-gui-cuda) ...
- # We have to use gcc 8 here, since some parts of CUDA don't work with
- # later versions.
- cd $(CURDIR)/build-cuda; \
- CC=gcc-8 CXX=g++-8 $(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; do \
- mv $(CURDIR)/debian/tmp/cuda/usr/bin/$$prog \
- $(CURDIR)/debian/tmp/cuda-gui/usr/bin; done
+ mv $(CURDIR)/debian/tmp/cli/usr/bin/$$prog \
+ $(CURDIR)/debian/tmp/gui/usr/bin; done
override_dh_prep:
# We don't want debian/tmp to be removed again ...
@@ -69,7 +53,7 @@ override_dh_install-arch:
override_dh_clean:
dh_clean
- -rm -rf build*
+ -rm -rf build
get-orig-source:
uscan --download-current-version --force-download --rename
View it on GitLab: https://salsa.debian.org/med-team/relion/-/commit/ccd7eec747542e5a7e8e3744655dad38e53fd56e
--
View it on GitLab: https://salsa.debian.org/med-team/relion/-/commit/ccd7eec747542e5a7e8e3744655dad38e53fd56e
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