Thursday, 13 November 2014

Bits from Debian Med team (by Andreas Tille)

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. 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.

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 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 packaged. Emilien has given a detailed explanation on the Debian Med mailing list 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 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.

Packages moved from non-free to main

The Debian Med team worked hard to finally enable DFSG free licenses for PHYLIP 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 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 only 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 (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.

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 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.

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.

Publication with Debian Med involvement

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

Updated team metrics

The team metrics graphs on the Debian Med Blend entry page 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.

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.

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. :-)

1 comment:

  1. I do believe all of the ideas you've offered to your post. They are very convincing and will definitely work. Nonetheless, the posts are too short for newbies. May you please lengthen them a little from next time? Thank you for the post.

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