[med-svn] r18479 - trunk/community/bits

Thu Nov 13 14:25:50 UTC 2014

Author: tille
Date: 2014-11-13 14:25:48 +0000 (Thu, 13 Nov 2014)
New Revision: 18479

Added:
   trunk/community/bits/2014-11.bits.html
Modified:
   trunk/community/bits/2014-11.bits
Log:
Prepare HTML version of bits for publishing in Blog.  If you want to add/fix something please do not hesitate since i'll publish tomorrow


Modified: trunk/community/bits/2014-11.bits
===================================================================

--- trunk/community/bits/2014-11.bits	2014-11-12 13:48:06 UTC (rev 18478)
+++ trunk/community/bits/2014-11.bits	2014-11-13 14:25:48 UTC (rev 18479)
@@ -53,7 +53,7 @@
 shame for GNUHealth users there might be chances to revive this effort
 if there would be some better coordination between upstream and Tryton
 (which is the framework GNUHealth is based upon).  In any case you can
-consider the packaging code in SVN as a useful resource to base your
+consider the packaging code in SVN[2d] as a useful resource to base your
 private packages on.  Feel free to contact us via the Debian Med mailing
 list in case you consider creating GNUHealth Debian packages.
 

Added: trunk/community/bits/2014-11.bits.html
===================================================================
--- trunk/community/bits/2014-11.bits.html	                        (rev 0)
+++ trunk/community/bits/2014-11.bits.html	2014-11-13 14:25:48 UTC (rev 18479)
@@ -0,0 +1,158 @@
+<h2>New set of metapackages</h2>
+<p>
+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 short before the final release to reflect
+potential changes in the package pool.  Feel free to install the
+metapackages med-* with the package installer of your choice.
+</p><p>
+As always you can have a look at the packages in our focus by visiting
+our <a href="http://blends.debian.org/med/tasks">tasks pages</a>.
+Please note that there might be some new packages residing only in
+unstable which are not installed by using the current metapackages
+since we will not stop packaging software only because the current
+testing is in freeze.
+</p>
+
+<h2>Some support for Hospital Information Systems</h2>
+<p>
+This release contains 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
+this time at kitware) and Amul Shah (fisglobal).  Thanks to a fruitful
+cooperation between upstream FIS and Debian the build system of fis-gtm
+was adapted to enable a more easy packaging.
+</p><p>
+The availability of fis-gtm will simplify
+running <a href="http://www.osehra.org/">Vista-foia</a> on Debian
+systems and we finally are working on packaging Vista as well to make
+Debian fit for running inside hospitals.
+</p><p>
+There was some interesting work done by Emilien Klein who was working
+pretty hard to get <a href="http://health.gnu.org/">GNUHealth</a>
+packaged.  Emilien has given a detailed explanation on the
+<a href="https://lists.debian.org/debian-med/2014/09/msg00103.html">Debian
+Med mailing list</a> why he removed the existing packages from the
+Debian package pool again.  While this is a shame for GNUHealth users
+there might be chances to revive this effort if there would be some
+better coordination between upstream and Tryton (which is the
+framework GNUHealth is based upon).  In any case you can consider the
+<a href="http://svn.debian.org/wsvn/debian-med/trunk/packages/gnuhealth/trunk/">packaging
+code in SVN</a> as a useful resource to base your private packages on.
+Feel free to contact us via the Debian Med mailing list in case you
+consider creating GNUHealth Debian packages.
+</p>
+
+<h2>Packages moved from non-free to main</h2>
+<p>
+The Debian Med team worked hard to finally enable DFSG free licenses for
+<a href="http://evolution.genetics.washington.edu/phylip.html">PHYLIP</a>
+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
+some fee to the University of Washington if you intend to use it in a
+commercial setup.
+</p><p>
+Since Debian Med was started we were in continuous discussion with the
+author Joe Felsenstein.  We even started
+an <a href="https://wiki.debian.org/DebianMed/Meeting/Southport2012/ePetition_Phylip">online
+petition</a> 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 a few dollars.  The petition is just
+mentioned for the purpose that readers of these bits get some idea
+what you can do in similar cases to show what a large team behind a
+certain topic can approach.
+</p><p>
+So finally PHYLIP was released in September under a BSD-2-clause
+license and in
+turn <a href="http://doua.prabi.fr/software/seaview">SeaView</a> (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.  We can now stop removing those parts of the test suites
+of these tools that are using PHYLIP which is for the profit of those
+indirect PHYLIP usage.
+</p><p>
+Thanks to all who participated in freeing PHYLIP specifically its author
+Joe Felsenstein.
+</p>
+
+<h2>Autopkgtest in Debian Med packages</h2>
+<p>
+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 in focus 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 <a href="http://biopython.org">python-biopython</a> 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 to solve the issues we reported.
+</p><p>
+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.
+</p>
+
+<h2>General quality assurance</h2>
+<p>
+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 current policy and packaging tools also
+polishing lintian issues.
+</p>
+
+<h2>Publication with Debian Med involvement</h2>
+<p>
+The Debian Med team is involved in a paper which is in press of
+<a href="http://www.biomedcentral.com/">BioMed Central</a>.  The title
+will be "Community-driven development for computational biology at
+Sprints, Hackathons and Codefests"
+</p>
+
+<h2>Updated team metrics</h2>
+<p>
+The team metrics graphs on
+the <a href="http://blends.debian.org/med/">Debian Med Blend entry
+page</a> were updated.  At the bottom you find a 3D Bar chart of
+dependencies of selected metapackages over different versions in time.
+It shows or continuous work in several fields.  Thanks to all Debian
+Med team members for their sedulous work on or common goal to make
+Debian the best operating system for medicine and biology.
+</p><p>
+Please note that VCS stat calculation is currently broken and do not
+really reflect the latest commits this year.
+</p>
+
+<h2>Blends installable via d-i?</h2>
+<p>
+In bug <a href="http://bugs.debian.org/758116">#758116</a> 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 <a href="http://bugs.debian.org/186085">#186085</a>) 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.
+</p><p>
+While there is no final decision drawn about bug #758116 and we are
+quite late with the request to get this implemented in Jessie feel free
+to contribute ideas this selection of Blends can be done in the best
+possible manner.
+</p>
+
+<h2>Debian Med Bug Squashing Advent Calendar 2014</h2>
+<p>
+The Debian Med team will again do
+the <a href="http://debian-med.alteholz.de/advent/">Bug Squashing
+Advent Calendar</a>.  Feel free to join us in our bug squashing effort
+where we *close* bugs while other people are *opening* doors. :-)
+</p>


