[med-svn] [qiime] branch master created (now 4be3af6)
Andreas Tille
tille at debian.org
Fri Nov 17 09:08:25 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch master
in repository qiime.
at 4be3af6 Moved packaging from SVN to Git
This branch includes the following new commits:
new c9b8c83 Rudimentary packaging attempt
new 2afbc08 Fixed watch, added README.source.
new e4d4dda Cleanups.
new 5f1a758 Update of debian policy
new 9be7c97 Correcting for group management.
new e9918a1 Series of changes to qiime that apparently were forgotten to commit.
new b8ce524 Uploaded 1.2.1 to experimental ... volunteers for improvements welcome.
new e17f1fc Fixed python 2.6 incompatibility
new 523b2e2 Qiime is a work in progress. This package will build, but it won't work right now. Also, there are mentions of Bio-Linux packages which I had to put in to get it working properly for my Bio-Linux testers. Hopefully these will be cleaned out long before Qiime becomes a candidate for Debian.
new 52f1071 Pushing a few more changes for the day. Awaiting feedback from Bio-Linux testers. Still a work in progress.
new 752d642 * Dropped cdbs in favour of dh * Debhelper 8 (compat+control) * Use debian/{install,dirs) to enable better readable debian/rules * debian/rules: - override_dh_compress - override_dh_installchangelogs Hope this simplifies maintaining the debian/rules file
new fe16ad3 Uploaded all those nice improvements to Qiime by Tim and Andreas.
new b99f09a New upstream version - we need to clarify changes about all->any / inclusion of Denoiser
new 12efff3 Some updates parallel to the ubuntu branch.
new 3665cfa Qiime is a beast. Errors are not found easily. If at all. Whatever we do, we need to make sure that we do it coherently across all our installations. With Tim doing all the verification on Lucid, and without such Debian should not ship anything, we should adopt his exact packaging also for Debian.
new 7b6e8ac Move from contrib to main; hopefully better up to date and better understandable README.Debian
new 95dfdef New binary package qiime-denoiser which makes sure that the large amount of payload does not need to be arch any; There is another way to go: strip out qiime-tutorial as arch all.
new c279c71 Fix Vcs fields
new 08407a1 DM-Upload-Allowed: yes
new 7fe4572 Several changes merging BioLinux (lucid) branch with current Debian packaging; not finished yet
new b0b4540 Take over changes in scripts from BioLinux branch
new 4b0dfcd Fix installed files
new 7008cd4 Drop qiime-denoiser extra packaging but rather move documentation to qiime-doc package; TODO: doc-base + manpages
new 74f5977 Created qiime-doc package, incl. doc-base; upstream-metadata.yaml with citation information
new 33f6bcd allow overriding python2 by environemnt which helps backporters like Tim for BioLinux; uploaded to unstable
new d28c0be Create packaging dir for cd-hit (and commit uncommited change of qiime/README.source)
new 65cc3da Renamed debian/upstream-metadata.yaml to debian/upstream.
new 17a79ae debian/upstream: Moved DOI and PMID to the Reference namespace.
new 58a0618 Somehow the original text of the previous released package was lost - restoring
new db1e651 Documented rename of debian/upstream; New standards-version
new d1ff5e4 Try to fix FTBFS issue using a patch provided by Tim Booth but problem is not fully solved
new 949c17c Replace old fix_system_exit.patch by ghc_7.4.2_compatibility.patch provided by Joachim Breitner which finally solves the build problem
new dc01b92 Upload to unstable
new aac5d9e Missed to update debian/copyright in latest upload -> now DEP5
new 89b0280 New upstream version
new 290cd5a Upload new version to unstable
new 445c0d6 Add address where patch was forwarded to
new 085a88c Install the needed Python files which were just lacking from the binary deb
new 4a0f0ce Upload to unstable
new 3980d2a * debian/upstream: - more complete authors information in BibTeX conform format - Moved DOI+PMID to References
new e4bc0f5 New upstream version + strip binary JAR from source tarball
new f2142aa Adapted patches to new upstream version; link king.jar
new 2ca326f Upload to unstable with debhelper 9; however, Makefile might need some work to enable hardening (or lintian is simply wrong)
new 7affa44 Depends python >= 2.7; Recommends: python-biom-format; use xz compression for next source version
new 3810d70 xz compression; upload zu unstable
new 7765619 Remove one unneeded patch and cleanup cleanup
new 4ed1fbf See changelog Still need to test this properly Older packages had the various data files in place but they seem to have vanished in the later version so I added them back
new f9d5661 Some minor fixes, mainly due to my repackaging of rdp-classifier.
new 81d4e8d Add Files-Excluded to document what was removed from original source
new 45d45f9 Added some patches to address QIIME bugs. The patches are tested but not pretty, especially the make_qiime_accept_new_rdp_classifier patch which is a hatchet job.
new 40aa442 Move to be uploaded Debian changelog entry on top
new 0b1c6b5 Usual changes to debian/control
new 50d1192 FIx Build-Depends and upload to unstable
new 09c096d Use xz compression for binary packages
new 3b181ae SVN is giving me stupid errors again. Trying to delete and re-add stuff until it stops bitching at me.
new 0ed699e still trying to get SVN to play ball
new 3a03e21 I can't get SVN to accept my commits :-(
new 21da16c Trying to get changelog straight
new 6245e60 Various changes for QIIME 1.7 in Bio-Linux, which should also be ready for Debian.
new f2d2b81 I guess this dir is simply some remaining in SVN - otherwise I see no need for *.bak dirs when using version control
new 6ed5f8e Upload to debian (and totally forgot to mention the addition of a get-orig-source target in debian/rules)
new 9064816 Suggests: torque-client
new 80f8eff FIx watch file to detect new version
new be0c2d4 cme fix dpkg-control
new b0c9cfb rdp-classifier can only be suggested since it is not in Debian and currently it seems that it can only go into non-free
new a3e3c94 Canonical Vcs URLs
new 5aa27e2 Adapted patches to new upstream version
new 8afc357 Remove Google Addsense from user documentation to save user privacy
new 7e283ed Upload to unstable
new 0ec5767 Fix links to new biom_format
new 198733a New dependency: python-qcli
new f273682 Try to get rid of calls to uclust in test cases which is not distributable in Debian and since we can not run the tests (there are more tests to exclude but for the moment I'll drop the strategy here.
new a0a61de Clean up after testing
new ee372bf Recommends: python-mpi4py since this is used in some tests
new 902409a Upload to unstable
new a53eb1f It is possible to replace king by invue http://sourceforge.net/apps/mediawiki/invue/ but this needs to be packaged first. The advantage would be that this way we could easily deal with #731190 and other side effects of the fact that king is using deprecated libjogl-java
new de66245 Move debian/upstream to debian/upstream/metadata
new 311cb2b QIIME 1.8.0 as put onto Bio-Linux
new 811bd7d cme fix dpkg-control (remove useless Pre-Depends)
new 1d2f695 DEP5 syntax
new 28b727c Fixed watch file
new b8050d7 Normalise patches, DEP3
new 6b95bc5 Prevent download when building
new bb31ace Make sure dependencies are installable on Debian systems
new f1de198 Remove hack to link to biom-format tools
new a7324e9 Fix copyright
new e28fe7e Added conflict with newer rdp-classifier. I know it makes no sense to conflict with a package that doesn't yet exist in Debian but I'm developing for Bio-Linux here! QIIME 1.9 will be out very soon and then all the loose ends will be tied up! Hold off any updates until then.
new e43f0bd Adapt watch and get-orig-source target to new uscan
new 3da2a3a New upstream version
new c8b3bbf Commit all changes done by BioLinux in one rush
new 892d433 Also commit BioLinux Changelog
new a918fe5 cme fix dpkg-control
new 4673b47 Add TODO item python-burrito
new 712b47c Remove denoiser from d/control since there is no such package any more
new 84f97ae This completes the sync between Bio-Linux and Debian.
new 42c7b8f This now builds and passes all my tests on Ubuntu LTS.
new 958e349 DEP5 fixes, Add lintian override for false positive about JS without source
new 7b41ba6 Enable building arch independent packages separately, upload to unstable
new 1c65857 Fix target distribution
new 80770fa Introduced EDAM annotation.
new d9472a8 Minimizing EDAM annotation for QIIME - just a bit, to be more consistent also with what we did for Mothur.
new 6843e60 Cherry-pick Ubuntu build fix by adding python-biom-format build-dependency
new a222905 Added references to registries.
new 8bd922c New upstream version 1.9.1+dfsg
new 039d950 Updated version 1.9.1+dfsg from 'upstream/1.9.1+dfsg'
new 4be3af6 Moved packaging from SVN to Git
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