[PLUG] FOSS med software (Fwd: Bits from Debian Med team)

Coincidentally this came across the Debian developer announce list last night...

---------- Forwarded message ----------
From: Andreas Tille <andreas@an3as.eu>
Date: Fri, Nov 14, 2014 at 1:57 AM
Subject: Bits from Debian Med team
To: debian-devel-announce@lists.debian.org
Cc: Debian Med Project List <debian-med@lists.debian.org>

Hi,

Jessie is frozen now and so we want to make you aware of some interesting
things in Debian Med

1. New set of metapackages
2. Some support for Hospital Information Systems
3. Packages moved from non-free to main
4. Autopkgtest in Debian Med packages
5. General quality assurance
6. Publication with Debian Med involvement
7. Updated team metrics
8. Blends installable via d-i?
9. Debian Med Bug Squashing Advent Calendar 2014

1. New set of metapackages
==========================

The version number of debian-med metapackages was bumped to 1.99 as a
signal that we plan to release version 2.0 with Jessie. As usual the
metapackages will be recreated shortly before the final release to
include potential changes in the package pool. Feel free to install the
metapackages med-* with the package installer of your choice.

As always you can have a look at the packages in our focus by visiting
our tasks pages[1a]. Please note that there may be new packages that
aren’t ready for release and that won’t be installed by using the
current metapackages. This is because we don’t stop packaging software
when the current testing is in freeze.

[1a] http://blends.debian.org/med/tasks

2. Some support for Hospital Information Systems
================================================

This release contains, for the first time some support for Hospital
Information Systems (HIS) with the dependency fis-gtm of the med-his
metapackage. This was made possible due to the work of Luis Ibanez (at
kitware at the time when working on the packaging) and Amul Shah
(fisglobal). Thanks to a fruitful cooperation between upstream FIS and
Debian the build system of fis-gtm was adapted to enable an easier
packaging.

The availability of fis-gtm will simplify running Vista-foia[2a] on
Debian systems and we are finally working on packaging Vista as well
to make Debian fit for running inside hospitals.

There was some interesting work done by Emilien Klein who was working
hard to get GNUHealth[2b] packaged. Emilien has given a detailed
explanation on the Debian Med mailing list[2c] giving reasons why he
removed the existing packages from the Debian package pool again. While
this is a shame for GNUHealth users there might be an opportunity to
revive this effort if there was better coordination between upstream and
Tryton (which is the framework GNUHealth is based upon). In any case
the packaging code in SVN[2d] as a useful resource to base private
packages on. Feel free to contact us via the Debian Med mailing list if
you consider creating GNUHealth Debian packages.

[2a] http://www.osehra.org/
[2b] http://health.gnu.org/
[2c] https://lists.debian.org/debian-med/2014/09/msg00103.html
[2d] http://svn.debian.org/wsvn/debian-med/trunk/packages/gnuhealth/trunk/

3. Packages moved from non-free to main
=======================================

The Debian Med team worked hard to finally enable DFSG free licenses for
PHYLIP[3a] and other package based on this tool. PHYLIP is well known
in bioinformatics and actually one of the first packages in this field
inside Debian (oldest changelog entry 28 Aug 1998). Since then it was
considered non-free because its use was restricted to scientific /
non-commercial use and also has the condition that you need to pay a
fee to the University of Washington if you intend to use it
commercially.

Since Debian Med was started we were in continuous discussion with the
author Joe Felsenstein. We even started an online petition[3b] to show
how large the interest in a DFSG free PHYLIP might be. As a side note:
This petition was *not* presented to the authors since they happily
decided to move to a free license because of previous discussion and
since they realised that the money they "gained" over they years was
minimal. The petition is mentioned here to demonstrate that it is
possible to gather support to see positive changes implemented that
benefit all users and that this approach can be used for similar cases.

So finally PHYLIP was released in September under a BSD-2-clause license
and in turn SeaView[3c] (a similarly famous program and also long term
non-free citizen) depending on PHYLIP code was freed as well. There are
several other tools like python-biopython and python-cogent which are
calling PHYLIP if it exists. So not only is PHYLIP freed we can now
stop removing those parts of the test suites of these other tools that
are using PHYLIP.

Thanks to all who participated in freeing PHYLIP specifically its author
Joe Felsenstein.

[3a] http://evolution.genetics.washington.edu/phylip.html
[3b] https://wiki.debian.org/DebianMed/Meeting/Southport2012/ePetition_Phylip
[3c] http://doua.prabi.fr/software/seaview

4. Autopkgtest in Debian Med packages
=====================================

We tried hard to add autopkgtests to all packages where some upstream
test suite exists and we also tried to create some tests on our own.
Since we consider testing of scientific software a very important
feature this work was highly focused on for the Jessie release. When
doing so we were able to drastically enhance the reliability of packages
and found new formerly hidden dependency relations. Perhaps the hardest
work was to run the full test suite of python-biopython[4a] which also
has uncovered some hidden bugs in the upstream code on architectures
that are not so frequently used in the field of bioinformatics. This
was made possible by the very good support of upstream who were very
helpful in solving the issues we reported.

However, we are not at 100% coverage of autopkgtest and we will keep on
working on our packages in the next release cycle for Jessie+1.

[4a] http://biopython.org

5. General quality assurance
============================

A general inspection of all Debian Med packages was done to check all
packages which were uploaded before the Wheezy release and never touched
since then. Those packages where checked for changed upstream locations
which might have been hidden from uscan and in some cases new upstream
releases were spotted by doing this investigation. Other old packages
were re-uploaded conforming to current policy and packaging tools also
polishing lintian issues.

6. Publication with Debian Med involvement
==========================================

The Debian Med team is involved in a paper which is in BioMed
Central[5a] (in press). The title will be "Community-driven development
for computational biology at Sprints, Hackathons and Codefests"

[6a] http://www.biomedcentral.com/

7. Updated team metrics
=======================

The team metrics graphs on the Debian Med Blend entry page[7a] were
updated. At the bottom you will find a 3D Bar chart of dependencies of
selected metapackages over different versions. It shows our continuous
work in several fields. Thanks to all Debian Med team members for their
rigorous work on our common goal to make Debian the best operating
system for medicine and biology.

Please note that VCS stat calculation is currently broken and does not
reflect the latest commits this year.

[7a] http://blends.debian.org/med/

8. Blends installable via d-i?
==============================

In bug #758116 it is requested to list all Blends and thus also Debian
Med in the initial tasksel selection. This would solve a long term open
issue which was addessed more than eleven years ago (in #186085) in a
more general and better way. This would add a frequently requested
feature by our users who always wonder how to install Debian Med.

While there is no final decision on bug #758116 and we are quite late
with the request to get this implemented in Jessie feel free to
contribute ideas so that this selection of Blends can be done in the
best possible manner.

9. Debian Med Bug Squashing Advent Calendar 2014
================================================

The Debian Med team will again do the Bug Squashing Advent Calendar.
Feel free to join us in our bug squashing effort where we *close*
bugs while other people are *opening* doors. :-)

[9a] http://debian-med.alteholz.de/advent/

Thanks for your interest and kind regards

Andreas.