[med-svn] r16389 - trunk/packages/python-biopython/trunk/debian

[Andreas Tille]

Author: tille
Date: 2014-03-05 09:24:34 +0000 (Wed, 05 Mar 2014)
New Revision: 16389

Modified:
   trunk/packages/python-biopython/trunk/debian/README.source
   trunk/packages/python-biopython/trunk/debian/control
   trunk/packages/python-biopython/trunk/debian/rules
Log:
Enhanced testing and documentation of the testing in README.source


Modified: trunk/packages/python-biopython/trunk/debian/README.source
===================================================================
--- trunk/packages/python-biopython/trunk/debian/README.source	2014-03-04 21:15:55 UTC (rev 16388)
+++ trunk/packages/python-biopython/trunk/debian/README.source	2014-03-05 09:24:34 UTC (rev 16389)
@@ -1,4 +1,44 @@
-01-enable-mmCIF.patch:
- Enable building mmCIF support
+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:
 
- -- Philipp Benner <philipp at debian.org>, Wed, 30 Sep 2009 11:50:43 +0000
+  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
+
+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.
+
+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
+             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
+
+
+ -- Andreas Tille <tille at debian.org>  Tue, 04 Mar 2014 11:16:02 +0100

Modified: trunk/packages/python-biopython/trunk/debian/control
===================================================================
--- trunk/packages/python-biopython/trunk/debian/control	2014-03-04 21:15:55 UTC (rev 16388)
+++ trunk/packages/python-biopython/trunk/debian/control	2014-03-05 09:24:34 UTC (rev 16389)
@@ -15,9 +15,22 @@
                python3-reportlab,
                python3-numpy,
                bwa,
+               clustalo,
+               clustalw,
+               dialign,
+               dssp,
+               emboss,
+               fasttree,
+               mafft,
                muscle,
                ncbi-blast+,
+               phyml,
+               prank,
+               probcons,
                python-mysqldb,
+               python-matplotlib,
+               python3-matplotlib,
+               python-rdflib,
                python-psycopg2,
                python3-psycopg2,
                t-coffee,

Modified: trunk/packages/python-biopython/trunk/debian/rules
===================================================================
--- trunk/packages/python-biopython/trunk/debian/rules	2014-03-04 21:15:55 UTC (rev 16388)
+++ trunk/packages/python-biopython/trunk/debian/rules	2014-03-05 09:24:34 UTC (rev 16389)
@@ -16,9 +16,17 @@
 	dh_numpy3 -ppython3-biopython
 
 override_dh_auto_test:
-	# avoid some tests which need online access
+	# 1. avoid some tests which need online access
+	# 2. avoid PAML_tools since paml is non-free
+	# 3. avoid testing tools that are not packaged for Debian yet
+        # While 2. and 3. do not create errors there is no point in bloating
+	# the build log and this kind of documentation makes things more transparent
 	mkdir -p Tests_avoid
-	for avoid in Entrez_online HotRand NCBI_qblast SCOP_online SeqIO_online TogoWS; do \
+	for avoid in \
+			Entrez_online HotRand NCBI_qblast SCOP_online SeqIO_online TogoWS \
+			PAML_tools \
+			MSAProbs_tool NACCESS_tool PopGen_DFDist PopGen_FDist PopGen_GenePop PopGen_GenePop_EasyController PopGen_SimCoal XXmotif_tool \
+		    ; do \
 	    mv Tests/test_$${avoid}.py Tests_avoid ; \
 	done
 	dh_auto_test -- --test --system=custom --test-args='env PYTHONPATH={build_dir} {interpreter} setup.py test'