[med-svn] r16439 - trunk/packages/python-biopython/trunk/debian

[Andreas Tille]

Author: tille
Date: 2014-03-12 21:41:39 +0000 (Wed, 12 Mar 2014)
New Revision: 16439

Modified:
   trunk/packages/python-biopython/trunk/debian/README.source
   trunk/packages/python-biopython/trunk/debian/rules
Log:
Better documentation of the excluded database tests


Modified: trunk/packages/python-biopython/trunk/debian/README.source
===================================================================
--- trunk/packages/python-biopython/trunk/debian/README.source	2014-03-12 21:33:53 UTC (rev 16438)
+++ trunk/packages/python-biopython/trunk/debian/README.source	2014-03-12 21:41:39 UTC (rev 16439)
@@ -4,28 +4,32 @@
 
   1. which need online access since the build should work in an
      offline chroot
-  2. non-free tools
-  3. tools that are not packaged for Debian yet
+  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
 
 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:
 
-The non-free tools (item 2.) which are packaged are:
+  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.
 
-Other packages that are excluded:
+The tools which are not packaged yet (item 4.) are:
 
-  bwa:       The package is limited to amd64 only.
-
-The tools which are not packaged yet (item 3.) are:
-
   MSAProbs:  http://msaprobs.sourceforge.net/
 
   naccess:   http://www.e-lucid.com/i/software/bioinformatics/naccess.html
@@ -54,6 +58,14 @@
              http://xxmotif.genzentrum.lmu.de/index.php?id=download
 
 
+Finally there is a package only available on amd64 architectures:
+
+  bwa:       The package is limited to amd64 only.
+
+So the Build-Depends from bwa is only on these architectures and the
+test is consequently only run there.
+
+
 The test test_Phylo_CDAO for Python3 also needs python3-rdflib, but this is
 currently only avialable in experimental, so this will be ignored for the
 moment.

Modified: trunk/packages/python-biopython/trunk/debian/rules
===================================================================
--- trunk/packages/python-biopython/trunk/debian/rules	2014-03-12 21:33:53 UTC (rev 16438)
+++ trunk/packages/python-biopython/trunk/debian/rules	2014-03-12 21:41:39 UTC (rev 16439)
@@ -24,7 +24,7 @@
 
 override_dh_auto_test:
 	# 1. avoid some tests which need online access
-	# 2. avoid tests needing a ready setup database server (MySQL and PostgreSQL
+	# 2. avoid tests needing a ready setup database server (MySQL and PostgreSQL)
 	# 3. avoid PAML_tools and EmbossPhylipNew since paml resp. embassy-phylip are non-free
 	# 4. avoid testing tools that are not packaged for Debian yet
 	# 5. avoid amd64 only tools on other architectures