transrate Debian packaging

[mr-c]

Oh my, 16 dependencies! Alas the biggest delay will be waiting for leaf packages to be accepted so those packages that depend on them can be sent in.

Dependencies that need packaging (default) or updates (as marked):

[ ] transrate
 + [x] transrate-tools
 + [x] salmon
 |  + [x] libcereal-dev
 |  + [x] libgff-dev
 |  + [x] libspdlog-dev
 |  + [x] libjellyfish-2.0-dev (update)
 |  + [x] libbwa-dev (update)
 + [x] snap-aligner
 + [x] ruby-crb-blast
 |  + [x] ruby-threach
 |  + [x] ruby-fixwhich
 |  |  + [x] ruby-pathname2
 |  |  |  + [x] ruby-facade
 + [x] ruby-fix-trinity-output
 + [x] ruby-yell
 + [x] ruby-colorize (update from 0.7.3 to 0.7.7)

• [x] Get membership to Debian Ruby team (my application has been submitted) https://wiki.debian.org/Teams/Ruby/Packaging#Joining_the_pkg-ruby-extras_team

http://anonscm.debian.org/cgit/debian-med/cereal.git https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=800335 https://ftp-master.debian.org/new/cereal_1.1.2-1.html http://tracker.debian.org/pkg/libcereal

• [x] libcereal-dev: needs Intent To Package (ITP) bug filed
• [x] libcereal-dev: fix debian/copyright
• [x] libcereal-dev: drop extra license files from usr/include/cereal/external/
• [x] libcereal-dev: sponsored upload
• [x] libcereal-dev: acceptance!

http://anonscm.debian.org/cgit/debian-med/libgff.git https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=800336 https://ftp-master.debian.org/new/libgff_1.0-1.html https://packages.qa.debian.org/libg/libgff.html

• [x] libgff-dev: ITP bug filed
• [x] libgff-dev: needs description
• [x] libgff-dev: needs watch file
• [x] libgff-dev: sponsored upload
• [x] libgff-dev: acceptance!

http://anonscm.debian.org/cgit/debian-med/spdlog.git https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=800337 https://ftp-master.debian.org/new/spdlog_1.4-1.html https://tracker.debian.org/pkg/spdlog

• [x] libspdlog: ITP bug
• [x] libspdlog: better description
• [x] libspdlog: sponsored upload
• [x] libspdlog: acceptance!

http://anonscm.debian.org/cgit/debian-med/jellyfish.git

• [x] libjellyfish-2.0-dev: sponsored upload
• [x] libjellyfish-2.0-dev: acceptance!

http://anonscm.debian.org/cgit/debian-med/bwa.git https://ftp-master.debian.org/new/bwa_0.7.12-5.html

• [x] libbwa-dev: sponsored upload
• [x] libbwa-dev: acceptance!

http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=800339 http://anonscm.debian.org/cgit/debian-med/salmon.git https://ftp-master.debian.org/new/salmon_0.4.2+ds1-1.html https://tracker.debian.org/pkg/salmon

• [x] salmon: ITP bug
• [x] salmon: manpage
• [x] salmon: track down missing source issue re: doc/build/html/_static/jquery.js & underscore.js
• [x] salmon: tweak build to link dynamically to libraries.
• [x] salmon: sponsored upload
• [x] salmon: acceptance!

http://anonscm.debian.org/cgit/debian-med/snap-aligner.git http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=800340 https://tracker.debian.org/pkg/snap-aligner

• [x] snap-aligner: ITP bug
• [x] snap-aligner: man page for snap-aligner
• [x] snap-aligner: man page for SNAPCommand
• [x] snap-aligner: upstream paper metadata
• [x] snap-aligner: sponsored upload
• [x] snap-aligner: acceptance!

http://anonscm.debian.org/cgit/debian-med/transrate-tools.git https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=800412 https://ftp-master.debian.org/new/transrate-tools_1.0.0-1.html https://tracker.debian.org/pkg/transrate-tools

• [x] transrate-tools: ITP bug
• [x] transrate-tools: patch descriptions
• [x] transrate-tools: copyright
• [x] transrate-tools: manpage
• [x] transrate-tools: sponsored upload
• [x] transrate-tools: acceptance!

Ruby packages: https://wiki.debian.org/Teams/Ruby/Packaging

https://anonscm.debian.org/cgit/pkg-ruby-extras/transrate.git https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=800733

• [x] transrate: ITP bug
• [x] transrate: gem2deb -p transrate & create repo
• [x] transrate: add patch to remove use of ruby-bindeps
• [x] transrate: fix tests
• [ ] transrate: fix excessive linking to libgmp.so, libidl.so, libcrypt.so, libpthread.so, libm.so
• [x] transrate: manpage for transrate
• [ ] transrate: sponsored upload
• [ ] transrate: acceptance!

https://anonscm.debian.org/cgit/pkg-ruby-extras/ruby-fix-trinity-output.git https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=800489 https://tracker.debian.org/pkg/ruby-fix-trinity-output

• [x] ruby-fix-trinity-output: ITP bug
• [x] ruby-fix-trinity-output: gem2deb & create repo
• [x] ruby-fix-trinity-output: fix tests
• [x] ruby-fix-trinity-output: man page for fix-trinity-output
• [x] ruby-fix-trinity-output: sponsored upload
• [x] ruby-fix-trinity-output: acceptance!

https://anonscm.debian.org/cgit/pkg-ruby-extras/ruby-yell.git http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=800494 http://tracker.debian.org/pkg/ruby-yell

• [x] ruby-yell: ITP bug
• [x] ruby-yell: gem2deb & create repo
• [x] ruby-yell: add ruby-rr, ruby-timecop to build dep dependencies list
• [x] ruby-yell: fix tests
• [x] ruby-yell: sponsored upload
• [x] ruby-yell: acceptance!

https://anonscm.debian.org/cgit/pkg-ruby-extras/ruby-threach.git https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=800734 https://ftp-master.debian.org/new/ruby-threach_0.2.0-1.html https://tracker.debian.org/pkg/ruby-threach

• [x] ruby-threach: ITP bug
• [x] ruby-threach: gem2deb & create repo
• [x] ruby-threach: fix tests
• [x] ruby-threach: sponsored upload
• [x] ruby-threach: acceptance!

https://anonscm.debian.org/cgit/pkg-ruby-extras/ruby-crb-blast.git https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=800737 https://ftp-master.debian.org/new/ruby-crb-blast_0.6.4-1.html https://tracker.debian.org/pkg/ruby-crb-blast

• [x] ruby-crb-blast: ITP bug
• [x] ruby-crb-blast: gem2deb & create repo
• [x] ruby-crb-blast: remove builddep on ruby-bindeps
• [x] ruby-crb-blast: man page for crb-blast
• [x] ruby-crb-blast: fix tests
• [x] ruby-crb-blast: sponsored upload
• [x] ruby-crb-blast: acceptance!

https://anonscm.debian.org/cgit/pkg-ruby-extras/ruby-pathname2.git https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=800740 https://ftp-master.debian.org/new/ruby-pathname2_1.7.4-1.html http://tracker.debian.org/pkg/ruby-pathname2

• [x] ruby-pathname2: ITP bug
• [x] ruby-pathname2: gem2deb & create repo
• [x] ruby-pathname2: sponsored upload
• [x] ruby-pathname2: acceptance!

https://anonscm.debian.org/cgit/pkg-ruby-extras/ruby-fixwhich.git http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=800742 https://tracker.debian.org/pkg/ruby-fixwhich

• [x] ruby-fixwhich: ITP bug
• [x] ruby-fixwhich: gem2deb & create repo
• [x] ruby-fixwhich: sponsored upload
• [x] ruby-fixwhich: acceptance!

https://anonscm.debian.org/cgit/pkg-ruby-extras/ruby-facade.git https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=800488 https://ftp-master.debian.org/new/ruby-facade_1.0.7-1.html

• [x] ruby-facade: ITP bug
• [x] ruby-facade: gem2deb & create repo
• [x] ruby-facade: sponsored upload
• [x] ruby-facade: acceptance!

https://tracker.debian.org/news/718538

• [x] ruby-colorize: update to 0.7.7
• [x] ruby-colorize: sponsored upload & acceptance

[mr-c]

This will be a five-phase submission:

1) transrate-tools, snap-aligner, ruby-fix-trinity-output, ruby-yell, libcereal-dev, libgff-dev, libspdlog-dev, libjellyfish-2.0-dev, libbwa-dev (update), ruby-facade, ruby-colorize (update from 0.7.3 to 0.7.7), ruby-threach 2) salmon, ruby-pathname2 3) ruby-fixwhich 4) ruby-crb-blast 5) transrate itself

[blahah]

@mr-c this is heroic! And very much appreciated. What can we do to support it?

[mr-c]

@Blahah Thanks :-) The licenses need clarifying, see https://github.com/Blahah/transrate/issues/159.

In general it seems that the Ruby community is a fan of the MIT license and not putting this in each file nor having a copyright line. Alas this is rather confusing as multiple versions exist, all with the same name. When documenting the license for Debian I can use the short name 'expat' if it exactly matches that variant; otherwise it creates a delay.

Ideally the program licensecheck (from the devscripts package) would give me the correct information when scanning source trees.

(sid)255 mcrusoe@localhost:~/debian/transrate-tools$ licensecheck `git ls-files`
src/bam-read.cpp: *No copyright* UNKNOWN
src/bam-read.h: *No copyright* UNKNOWN
src/pileup.cpp: *No copyright* UNKNOWN
src/pileup.h: *No copyright* UNKNOWN
src/segmenter.cpp: *No copyright* UNKNOWN
src/segmenter.h: *No copyright* UNKNOWN

[blahah]

Can I deal with that by just putting a LICENSE file in the repo (see https://github.com/Blahah/transrate-tools/commit/215f661ac19fe847da62f49f56e6b3599aa81b72)?

[mr-c]

For transrate-tools & #159 yes, that is required; thanks!

A copyright line in each file would be nice too.

[blahah]

You're right, I never put the license in every file because I find it aesthetically unpleasant - a distraction from the pure utility of the code. But now that you mention it, I see why it would be useful!

Is there some convention for stating the license/copyright as simply as possible?

[mr-c]

:-)

I know of no convention, alas. Some licenses give specific guidance on how to use them in a source file; many do not.

For the MIT family of licenses it appears that the best bet is to include the entire license in the header as it is unversioned and so short. See: https://anonscm.debian.org/cgit/collab-maint/devscripts.git/tree/scripts/licensecheck.pl#n593

(DIB lab had the same issue with the BSD license; I ended up adding the full text of the license to every file during a copyright/license audit brought about because seqan didn't declare all of its constituent copyrights and licenses)

[blahah]

Putting the whole MIT license in seems horrible. Would a two-liner like this suffice?

# Copyright Richard Smith-Unna and Chris Boursnell 2015. This file is MIT licensed.
# Full license at: https://github.com/Blahah/transrate/blob/master/LICENSE

[blahah]

Because honestly I'd rather just waive all rights in a short one-liner than have a big header in every file! I would feel sick every time I saw it!

[mr-c]

:-)

This variation allows both the copyright and license to be detected:

mcrusoe@localhost:~$ cat test.py
#!/usr/bin/env python
# Copyright 2015 Richard Smith-Unna and Chris Boursnell.
# This file is MIT licensed.
# Full license at: http://opensource.org/licenses/mit-license.php

import this
mcrusoe@localhost:~$ licensecheck --copyright test.py 
test.py: MIT/X11 (BSD like)
  [Copyright: 2015 Richard Smith-Unna and Chris Boursnell]

[blahah]

OK, deal ;).

[mr-c]

@Blahah https://wiki.debian.org/Teams/Ruby/RubyExtras/UpstreamDevelopers :-)

[mr-c]

Transrate-tools has been accepted into Debian! https://tracker.debian.org/pkg/transrate-tools

[mr-c]

snap-aligner has been accepted: https://tracker.debian.org/pkg/snap-aligner

I've received a series of apologies from a debian-ruby team member apologizing for the delays in reviewing my ruby packages.

[mr-c]

I'm preparing the salmon package (0.4.1) and I see that version 0.6 is out. @Blahah, when do you expect transrate to be updated to handle the format changes?

[blahah]

@mr-c we'll push a small patch soon addressing reviewer's comments, after which the next release will support the latest salmon. I guess late feb.

Thanks for all your hard work on this :)