[med-svn] r16773 - in trunk/packages/python-biopython/trunk/debian: . tests

[Andreas Tille]

Author: tille
Date: 2014-04-24 14:08:10 +0000 (Thu, 24 Apr 2014)
New Revision: 16773

Added:
   trunk/packages/python-biopython/trunk/debian/python-biopython-doc.lintian-overrides
Modified:
   trunk/packages/python-biopython/trunk/debian/python-biopython-doc.docs
   trunk/packages/python-biopython/trunk/debian/rules
   trunk/packages/python-biopython/trunk/debian/tests/run-unit-test
Log:
More enhancements of testing


Modified: trunk/packages/python-biopython/trunk/debian/python-biopython-doc.docs
===================================================================
--- trunk/packages/python-biopython/trunk/debian/python-biopython-doc.docs	2014-04-24 13:44:55 UTC (rev 16772)
+++ trunk/packages/python-biopython/trunk/debian/python-biopython-doc.docs	2014-04-24 14:08:10 UTC (rev 16773)
@@ -1,4 +1,3 @@
 Doc/
-debian/tmp_tests/*
 debian/README.test
 debian/tests/run-unit-test

Added: trunk/packages/python-biopython/trunk/debian/python-biopython-doc.lintian-overrides
===================================================================
--- trunk/packages/python-biopython/trunk/debian/python-biopython-doc.lintian-overrides	                        (rev 0)
+++ trunk/packages/python-biopython/trunk/debian/python-biopython-doc.lintian-overrides	2014-04-24 14:08:10 UTC (rev 16773)
@@ -0,0 +1,4 @@
+# We really need this zero byte file for running the test suite
+# and there was actually done some means to keep it since
+# dh_installdocs ignores the file
+python-biopython-doc: zero-byte-file-in-doc-directory usr/share/doc/python-biopython-doc/Tests/Blast/tab_2226_tblastn_002.txt

Modified: trunk/packages/python-biopython/trunk/debian/rules
===================================================================
--- trunk/packages/python-biopython/trunk/debian/rules	2014-04-24 13:44:55 UTC (rev 16772)
+++ trunk/packages/python-biopython/trunk/debian/rules	2014-04-24 14:08:10 UTC (rev 16773)
@@ -27,6 +27,7 @@
 	# 2. avoid PAML_tools and EmbossPhylipNew since paml resp. embassy-phylip are non-free
 	# 3. avoid testing tools that are not packaged for Debian yet
 	# 4. avoid amd64 only tools on other architectures
+        # 5. avoid tests with data base connections if no server is running while we are doing the build
         # 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
@@ -35,6 +36,7 @@
 			PAML_tools EmbossPhylipNew \
 			MSAProbs_tool NACCESS_tool PopGen_DFDist PopGen_FDist PopGen_GenePop PopGen_GenePop_EasyController PopGen_SimCoal XXmotif_tool \
 			$(EXCLUDEBWA) \
+                        BioSQL_MySQLdb BioSQL_psycopg2 \
 		    ; do \
 	    mv Tests/test_$${avoid}.py Tests_avoid ; \
 	done
@@ -57,6 +59,8 @@
 	dh_installdocs
 	find debian -name __pycache__ -type d | xargs rm -rf
 	find debian -name example.fastq.gz
+	# dh_installdocs seems to refuse copying zero length files (for instance Tests/Blast/tab_2226_tblastn_002.txt) but these are needed for the tests as well
+	cp -a debian/tmp_tests/* $(CURDIR)/debian/python-biopython-doc/usr/share/doc/python-biopython-doc/
 
 override_dh_auto_clean:
 	dh_auto_clean

Modified: trunk/packages/python-biopython/trunk/debian/tests/run-unit-test
===================================================================
--- trunk/packages/python-biopython/trunk/debian/tests/run-unit-test	2014-04-24 13:44:55 UTC (rev 16772)
+++ trunk/packages/python-biopython/trunk/debian/tests/run-unit-test	2014-04-24 14:08:10 UTC (rev 16773)
@@ -7,7 +7,7 @@
 cp -a /usr/share/doc/python-biopython-doc/Tests $ADTTMP
 mkdir -p Doc
 cp -a /usr/share/doc/python-biopython-doc/Doc/Tutorial.tex* Doc
-gunzip -r */*.gz Tests/*/*.gz
+find . -name "*.gz" -exec gunzip \{\} \;
 cd Tests
 
 # bwa is only available on amd64