When Building python-biopython as much tests as possible should be run
to confirm the integrity of the build result.  There are three types of
tests that can not be run:

  1. which need online access since the build should work in an
     offline chroot
  2. tests needing a ready setup database server (MySQL and PostgreSQL)
  3. non-free tools
  4. tools that are not packaged for Debian yet
  5. packages only available on some architectures are only tested there
  6. packages failing tests for some other reasons (phyml)

The according tests are moved away from the test directory in the
debian/rules file.  Please look there if you want to know what tests
are affected.

Since the Build of the package is done in a chroot and in this chroot
the setup of the database servers is not done it is not possible to run
the database connection tests (item 2.)  This affects the tests:

  BioSQL_MySQLdb  for MySQL connections
  BioSQL_psycopg2 for PostgreSQL connections

The non-free tools (item 3.) which are packaged are:

  paml            for test_PAML_tools.py
  embassy-phylip  for test_EmbossPhylipNew.py

you might like to install these manually if you are interested in these
tests.

The tools which are not packaged yet (item 4.) are:

  MSAProbs:  http://msaprobs.sourceforge.net/

  naccess:   http://www.e-lucid.com/i/software/bioinformatics/naccess.html
             It says: A non-commercial use only licence for academic
             researchers is available from the following website:
               http://www.bioinf.manchester.ac.uk/naccess/
             but the later site seems to have no content

  Dfdist:    http://tomato.biol.trinity.edu/programs/index.php/DFDIST

  fdist2:    It will be described at
               https://courses.washington.edu/popgen/Software.htm
             as "relatively old but still widely used program based on
             Beaumont & Nichols 1996. Uses simuations to derive confidence
             limits around mean FSTs - outliers from these limits may be
             under selection.
             The linked page is not available.

  GenePop:   http://genepop.curtin.edu.au/
             Download at http://kimura.univ-montp2.fr/~rousset/Genepop.htm
             Recently updated CeCILL Licence

  SIMCOAL2:  http://cmpg.unibe.ch/software/simcoal2/

  XXmotif:   http://xxmotif.genzentrum.lmu.de/index.php?id=about
             http://xxmotif.genzentrum.lmu.de/index.php?id=download

  fastsimcoal: Non-free, see
             https://lists.debian.org/debian-med/2014/09/msg00016.html
             But it does not need to be explicitly excluded since the
             test suite itself checks the existence

 -- Andreas Tille <tille@debian.org>  Tue, 04 Mar 2014 11:16:02 +0100
