[Debian-med-packaging] Packaging CSB Toolbox

Mon Oct 29 09:46:48 UTC 2012

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Hello Tomas!

In a somewhat mixed up order:

 * I can not decide for you if you should use your regular machine for packaging work (when you have 'unstable' on it). It can be unsafe, of
course, installing new packages for testing. You have to decide if you take the risk. A chroot probably would not be a bad idea. It also depends
of how much you trust the upstream.

 * For ideas for convincing people about freeing up software: perhaps fellow Team Members can point you (us) to some page with good arguments -
I am sure it exists. This also should be linked/included in the UpstreamAuthorsContacting page, I think. [1]

 * Packaging the CSB Toolbox - python framework for building applications in the domain of structural bioinformatics - seems like a good idea to
me. Some of the dependencies seem to be listed here already [2]. This is Python software, so at one point we should involve the Python Modules
Team as well [4]. Jakub Wilk of that team has been especially helpful.

   1: Pick up at [3]: file the WNPP-ITP bug. Then, once you are member of the Debian Med Team, create the repository directory (svn preferably,
with mergeWithUpstream=1) on Alioth. Have a look at the librcsb-core-wrapper, you may want to use this package as an example [5,6]. This also is
a Python module, which is a wrapper for a C++ library. I think you could start by adapting this to the CSB Toolbox. Use debhelper (dh) as your
packaging aid. I have tried CDBS as well, and chose dh in the end.

   2: Once you have debian/{changelog,compat,control,copyright,rules,source/format(=3.0 (quilt)),watch}, you can use:
      .
      $ uscan --verbose --force-download --destdir ../tarballs/
      .
      to get the upstream, and get started with building. I recommend you use these config files:

~/.quiltrc:
QUILT_PATCH_OPTS="--reject-format=unified"
QUILT_DIFF_ARGS="-p ab --no-timestamps --no-index --color=always"
QUILT_REFRESH_ARGS="-p ab --no-timestamps --no-index"

~/.lintianrc:
color=always
display-experimental=yes
display-info=yes
pedantic=yes
show-overrides=yes

~/.svn-buildpackage.conf:
svn-lintian

~/.dput.cf: (for later, when you are a DM)
[DEFAULT]
run_lintian		= 1

~/.bashrc:
export DEBEMAIL="Your GPG Signing Identity <with at your.email>"

   3: When you use svn-buildpackage to work on your package, your build is kept in ../build-area/{package}/ compared to your trunk directory
with 'debian' in it. Have an alias like "svn-b='svn-buildpackage --svn-reuse'", and use this to build a package you plan to work on, as this
will keep the build directory. Once this command exits (with failure, likely, at first), do:

$ cd ../build-area/{package}/
$ rm -rf debian (make sure you are in the right dir in build-area)
$ ln -s ../../trunk/debian

      The purpose of this is to link the debian directory of the volatile build-area to the 'debian' in trunk, that is versioned. You now can
test your build in the build dir after patching with debuild -b. You can not do a source build because of the symlink (so use that -b), but that
usually is not a problem. Are you familiar with quilt(1)? Learn about it, and keep your patches small, addressing only one issue at a time.

Let me know if/when you need more help. By the way: what is your GPG key? Make sure it is generated with 4096 bits!

Andreas Tille (in cc) regularly organizes the 'Mentoring of the Month' [7], where he teaches newcomers the details of packaging. I think it
would be great if you became his student with this package. @Andreas: what say you?

Best regards,

Laszlo

[1] http://wiki.debian.org/DebianScience/UpstreamAuthorsContactingQA
[2] http://pypi.python.org/pypi/csb/1.0.0
[3] http://debian-med.alioth.debian.org/docs/policy.html#packaging
[4] http://wiki.debian.org/Teams/PythonModulesTeam
[5] svn+ssh://tdido-guest@svn.debian.org/svn/debian-med/trunk/packages/rcsb-core-wrapper
[6] http://svn.debian.org/wsvn/debian-med/trunk/packages/rcsb-core-wrapper/
[7] http://wiki.debian.org/DebianMed/MoM

On 27/10/12 12:57, Tomás Di Domenico wrote:
> Greets, Laszlo!
> 
> Well, I'm having a bit of trouble trying to convince people at the lab
> to free some packages.
> 
> There's a new structural bioinformatics toolbox, that I've been using,
> however, that ocurred to me could be a good addition to Debian. I've
> been using it for a while and I think it's very good. The developers are
> quite responsive checking bugs I filled and helping out, and they've
> agreed to support my effor to package the library into Debian.
> 
> The address is https://csb.codeplex.com/. Would you let me know what you
> think?
> 
> Also, I've just requested membership to the Debian Med team, and am busy
> reading all the package maintaining docs I can find. I do think I'll be
> needing your help though, as it seems like quite a big universe of new
> things.
> 
> About the unstable distro, that's what I run as my main OS. Would that
> suffice, or would it still be better to have an isolated installation?
> 
> Thanks!
> 
> On 10/10/12 15:41, Laszlo Kajan wrote:
>> Hello Tomas!
>>
>> Ok, so the next step for you is to join the Debian Med Team. That will be good when you start working on something. Until then, you could read
>> this document [1]. It will give you a good foundation for the packaging work.
>>
>> [1] http://debian-med.alioth.debian.org/docs/policy.html
>>
>> Also, since Debian packages should be prepared on an 'unstable' installation, you could establish this somewhere: either in a chroot, or in a
>> virtual machine, or in user-mode linux, or on a real machine. If you want, I can help you with either of these. I recommend the virtual machine
>> with kvm.
>>
>> Write to me again when you want to start a new package - and don't delay that, because such work /begins/ with putting a special bug into
>> Debian. So we can do that as soon as you have the name and a description for your package.
>>
>> Best regards,
>>
>> Laszlo
>>
>> On 10/10/12 15:35, Tomás Di Domenico wrote:
>>> Greets, Laszlo! Hopefully the subject gets through your filters ;)
>>>
>>> I'm Tomás, the argentinean working in Padova who was asking you
>>> questions about Debian on the Oktoberfest table.
>>>
>>> Anyway, I just wanted to drop a line so we stay in touch. Next week,
>>> when my boss is back from his trip, I'll start advocating for freeing
>>> some of the methods. Hopefully I'll convince him and I can start
>>> thinking about including them in Debian.
>>>
>>> As you instructed me, I've created an account in alioth: "tdido-guest".
>>> I suppose there's not much to do until I have something to contribute
>>> though.
>>>
>>> In any case, I'll contact you again soon.
>>>
>>> Cheers!
>>>
>>
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