Re: Fwd: Re: Bug#763275: ITP: opencfu -- A C++ program to count cell colonies (CFUs) on agar plates by processing digital pictures

[Andreas Tille <tille@debian.org>]

Hi Quentin,

thanks for your ITP which is in fact interesting for Debian Med.  I hope
Steffen warned you that I do only open discussion and feel private mails
as a waste of resources for other team members - in this case they would
miss your interesting ITP.  So I'll answer on our public mailing list
and I hope you don't mind to much of the violating of netiquette - I
have not seen any private content and ITPs are public anyway.

On Sun, Sep 28, 2014 at 09:36:01PM +0100, Quentin Geissmann wrote:
> Dear Andreas,
> 
> Steffen advised me to contact you in order to get some help with
> debian packaging of opencfu (http://opencfu.sourceforge.net/).
> I am at the point where I have a makefile that automatically
> generates a debian package, which I then succeed to install, but I
> am not quite sure about what to do next…

I'd recommend joining the Debian Med team and read our team policy[1]
which gives some useful hints also to packaging documentation.  As
Steffen also mentioned you could join "Mentoring of the Month"[2] where
I'm teaching newcomers how to properly package bio-medical software
for Debian.
 
> A reproducible example can be done by cloning
> https://github.com/qgeissmann/OpenCFU/tree/devel.
> 
> Then, by installing dependencies with |# apt-get install
> build-essential automake autoconf libopencv-dev libgtkmm-2.4-dev|.
> 
> And running |autoreconf -i && ./configure && make && make deb|
> The last make recipe creates a temporary dir with the package files.
> The original debian packaging files are in
> |packagingScripts/debian|.

I had a look into this.  This is not really how packaging works even if
it results in probably usable (but not distributable) Debian packages.
Not distributable is specifically for a zero-byte debian/copyright file
but there are more issues.

Usually you start with a source tarball (see the packaging guide we have
linked from Debian Med policy[1]).  The canonical way to create a Debian
package is to download the tarball, add a debian/ dir and then you build
the package.  The `autoreconf -i && ./configure && make` steps are done
at package build time (usually triggere by dh) and not before.
 
> My understanding is that I am almost there, but I don’t really know
> 1) if my package is correct 2) what to do next.

I tend to disagree that you are almost there but I'm very optimistic
that we will be able to bring you there. :-)  I'd recommend to register
on alioth.debian.org to get commit permission to the Debian Med
repository where the packaging code is maintained.  Usually it is not a
good idea to keep the packaging code in the same archive as the source
(the reasons were frequently discussed - feel free to ask if you want me
to be more verbose about this.)

> ps. Do not hesitate to send pull requests directly if you feel like
> modifying the package

I would insist in maintaining the packaging code at git.debian.org to
enable all members of Debian Med team to work on the packaging.

> pps. I can also upload whatever file you would like, if it is simpler

As far as I can see you have set a release tag[3] which is good.  You
need to write a proper debian/watch file to fetch the resulting tarball
and detect new versions.  This should be pretty simple if you are using
the package_template (see policy[1]).
 
> ———— Forwarded Message ————
> 
> Hi Quentin, I am too swamped with too many things to be of direct
> help, I am afraid. Andreas Tille kindly initiated his “Mentoring of
> the Month” project for Debian Med
> https://wiki.debian.org/DebianMed/MoM and I just suggest you contact
> Andreas tille@debian.org <http://mailto:tille@debian.org>

I wished Steffen would have used mailto:debian-med@lists.debian.org
instead of my e-mail address.  Hi should know that I prefer open
discussion ... :-)

> The package is a published scientific software
> (http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0054072).

You can specify this in a debian/upstream/metadata file (see also
package_template).

Your software is actually really interesting for Debian Med and I admit
I'm keen to include it.  But for a real release we can not diverge from
the formalisms of Debian Policy in general and I also would like to be
strict in using the well established workflow in the Debian Med team.

Kind regards

         Andreas.

[1] http://debian-med.alioth.debian.org/docs/policy.html ​
[2] https://wiki.debian.org/DebianMed/MoM
[3] https://github.com/qgeissmann/OpenCFU/releases

-- 
http://fam-tille.de