transrate Debian packaging #160

mr-c · 2015-09-20T03:18:31Z

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)

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

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

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

libspdlog: ITP bug
libspdlog: better description
libspdlog: sponsored upload
libspdlog: acceptance!

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

libjellyfish-2.0-dev: sponsored upload
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~~

libbwa-dev: sponsored upload
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

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

snap-aligner: ITP bug
snap-aligner: man page for snap-aligner
snap-aligner: man page for SNAPCommand
snap-aligner: upstream paper metadata
snap-aligner: sponsored upload
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

transrate-tools: ITP bug
transrate-tools: patch descriptions
transrate-tools: copyright
transrate-tools: manpage
transrate-tools: sponsored upload
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

transrate: ITP bug
transrate: gem2deb -p transrate & create repo
transrate: add patch to remove use of ruby-bindeps
transrate: fix tests
transrate: fix excessive linking to libgmp.so, libidl.so, libcrypt.so, libpthread.so, libm.so
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

ruby-fix-trinity-output: ITP bug
ruby-fix-trinity-output: gem2deb & create repo
ruby-fix-trinity-output: fix tests
ruby-fix-trinity-output: man page for fix-trinity-output
ruby-fix-trinity-output: sponsored upload
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

ruby-yell: ITP bug
ruby-yell: gem2deb & create repo
ruby-yell: add ruby-rr, ruby-timecop to build dep dependencies list
ruby-yell: fix tests
ruby-yell: sponsored upload
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

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

ruby-crb-blast: ITP bug
ruby-crb-blast: gem2deb & create repo
ruby-crb-blast: remove builddep on ruby-bindeps
ruby-crb-blast: man page for crb-blast
ruby-crb-blast: fix tests
ruby-crb-blast: sponsored upload
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

ruby-pathname2: ITP bug
ruby-pathname2: gem2deb & create repo
ruby-pathname2: sponsored upload
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

ruby-fixwhich: ITP bug
ruby-fixwhich: gem2deb & create repo
ruby-fixwhich: sponsored upload
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

ruby-facade: ITP bug
ruby-facade: gem2deb & create repo
ruby-facade: sponsored upload
ruby-facade: acceptance!

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

ruby-colorize: update to 0.7.7
ruby-colorize: sponsored upload & acceptance

The text was updated successfully, but these errors were encountered:

mr-c · 2015-09-20T04:11:46Z

This will be a five-phase submission:

~~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~~
~~salmon~~, ~~ruby-pathname2~~
~~ruby-fixwhich~~
~~ruby-crb-blast~~
transrate itself

blahah · 2015-09-20T13:28:51Z

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

mr-c · 2015-09-27T20:52:10Z

@blahah Thanks :-) The licenses need clarifying, see #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 · 2015-09-27T21:52:01Z

Can I deal with that by just putting a LICENSE file in the repo (see blahah/transrate-tools@215f661)?

mr-c · 2015-09-27T21:55:37Z

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

A copyright line in each file would be nice too.

blahah · 2015-09-27T21:58:05Z

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 · 2015-09-27T22:17:24Z

:-)

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 · 2015-09-28T17:37:23Z

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 · 2015-09-28T17:39:00Z

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 · 2015-09-28T18:29:18Z

:-)

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 · 2015-09-28T21:40:14Z

OK, deal ;).

mr-c · 2015-09-30T04:45:00Z

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

mr-c · 2015-10-01T20:13:38Z

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

mr-c · 2016-01-22T11:55:51Z

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 · 2016-01-30T08:00:40Z

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 · 2016-01-30T09:10:26Z

@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 :)

mr-c mentioned this issue Oct 1, 2015

upgrade CMakeLists.txt to use external copies of dependencies & no downloading COMBINE-lab/salmon#19

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7 tasks

blahah added enhancement devops labels Feb 19, 2016

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transrate Debian packaging #160

transrate Debian packaging #160

mr-c commented Sep 20, 2015

mr-c commented Sep 20, 2015

blahah commented Sep 20, 2015

mr-c commented Sep 27, 2015

blahah commented Sep 27, 2015

mr-c commented Sep 27, 2015

blahah commented Sep 27, 2015

mr-c commented Sep 27, 2015

blahah commented Sep 28, 2015

blahah commented Sep 28, 2015

mr-c commented Sep 28, 2015

blahah commented Sep 28, 2015

mr-c commented Sep 30, 2015

mr-c commented Oct 1, 2015

mr-c commented Jan 22, 2016

mr-c commented Jan 30, 2016

blahah commented Jan 30, 2016

transrate Debian packaging #160

transrate Debian packaging #160

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mr-c commented Sep 20, 2015

mr-c commented Sep 20, 2015

blahah commented Sep 20, 2015

mr-c commented Sep 27, 2015

blahah commented Sep 27, 2015

mr-c commented Sep 27, 2015

blahah commented Sep 27, 2015

mr-c commented Sep 27, 2015

blahah commented Sep 28, 2015

blahah commented Sep 28, 2015

mr-c commented Sep 28, 2015

blahah commented Sep 28, 2015

mr-c commented Sep 30, 2015

mr-c commented Oct 1, 2015

mr-c commented Jan 22, 2016

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blahah commented Jan 30, 2016