[med-svn] r16455 - in trunk/packages/python-biopython/trunk/debian: . tests

[Andreas Tille]

Author: tille
Date: 2014-03-17 13:41:01 +0000 (Mon, 17 Mar 2014)
New Revision: 16455

Modified:
   trunk/packages/python-biopython/trunk/debian/control
   trunk/packages/python-biopython/trunk/debian/rules
   trunk/packages/python-biopython/trunk/debian/tests/control
Log:
Please leave the possibility to test the package at build time ... at least as long as the issue discussed on Debian Python list is open.  BTW, the test control file becomes *way* more simple if we leave it this way and as I wrote on the mainling list both tests make perfectly sense.


Modified: trunk/packages/python-biopython/trunk/debian/control
===================================================================
--- trunk/packages/python-biopython/trunk/debian/control	2014-03-17 12:46:57 UTC (rev 16454)
+++ trunk/packages/python-biopython/trunk/debian/control	2014-03-17 13:41:01 UTC (rev 16455)
@@ -11,7 +11,37 @@
                python3-all-dev,
 	       python-numpy,
 	       python3-numpy,
-               flex
+               flex,
+               python-reportlab,
+               python3-reportlab,
+               bwa [any-amd64],
+               clustalo,
+               clustalw,
+               dialign,
+               dssp,
+               emboss,
+               fasttree,
+               mafft,
+               muscle,
+               ncbi-blast+,
+               phyml,
+               prank,
+               probcons,
+               python-mysqldb,
+               python-matplotlib,
+               python3-matplotlib,
+               python-numpy,
+               python3-numpy,
+               python-pil,
+               python3-pil,
+               python-rdflib,
+               python-renderpm,
+               python3-renderpm,
+               python-psycopg2,
+               python3-psycopg2,
+               raxml,
+               t-coffee,
+               wise
 Standards-Version: 3.9.5
 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/python-biopython/trunk/
 Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/python-biopython/trunk/

Modified: trunk/packages/python-biopython/trunk/debian/rules
===================================================================
--- trunk/packages/python-biopython/trunk/debian/rules	2014-03-17 12:46:57 UTC (rev 16454)
+++ trunk/packages/python-biopython/trunk/debian/rules	2014-03-17 13:41:01 UTC (rev 16455)
@@ -7,6 +7,13 @@
 #export PYBUILD_DESTDIR_python2=debian/python-biopython/
 #export PYBUILD_DESTDIR_python3=debian/python3-biopython/
 
+BUILDARCH := $(shell dpkg-architecture -qDEB_BUILD_ARCH)
+ifeq ($(BUILDARCH),amd64)
+    EXCLUDEBWA=
+else
+    EXCLUDEBWA=BWA_tool
+endif
+
 %:
 	dh $@ --with python2,python3 --buildsystem=pybuild
 
@@ -16,7 +23,36 @@
 	dh_numpy3 -ppython3-biopython
 
 override_dh_auto_test:
+	# 1. avoid some tests which need online access
+	# 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
+        # 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 \
+			PAML_tools EmbossPhylipNew \
+			MSAProbs_tool NACCESS_tool PopGen_DFDist PopGen_FDist PopGen_GenePop PopGen_GenePop_EasyController PopGen_SimCoal XXmotif_tool \
+			$(EXCLUDEBWA) \
+		    ; do \
+	    mv Tests/test_$${avoid}.py Tests_avoid ; \
+	done
+	# in the Debian package dialign it is not needed to set DIALIGN2_DIR but the test is verifying this dir 
+	# to run the EMBOSS test test_Emboss also requires to have the environment variable EMBOSS_ROOT set
+	#  dh_auto_test -- --test --system=custom --test-args='env DIALIGN2_DIR=/usr/share/dialign EMBOSS_ROOT=/usr/lib/emboss PYTHONPATH={build_dir} {interpreter} setup.py test'
+	#  (the line above prefers package's root directory over sys.path; according to Piotr Ożarowski this can be prevented by:
+	dh_auto_test -- --test --system=custom --test-args='cd {build_dir}; env DIALIGN2_DIR=/usr/share/dialign EMBOSS_ROOT=/usr/lib/emboss {interpreter} ../setup.py test'
+	mv Tests_avoid/* Tests
+	rmdir Tests_avoid
 
 override_dh_installdocs:
 	dh_installdocs
 	find debian -name __pycache__ -type d | xargs rm -rf
+
+override_dh_auto_clean:
+	dh_auto_clean
+	if [ -d Tests_avoid ] ; then \
+	    mv Tests_avoid/* Tests ; \
+	    rmdir Tests_avoid ; \
+	fi

Modified: trunk/packages/python-biopython/trunk/debian/tests/control
===================================================================
--- trunk/packages/python-biopython/trunk/debian/tests/control	2014-03-17 12:46:57 UTC (rev 16454)
+++ trunk/packages/python-biopython/trunk/debian/tests/control	2014-03-17 13:41:01 UTC (rev 16455)
@@ -1,36 +1,2 @@
 Tests: upstream
-Depends: python-all-dev,
-	 python3-all-dev,
-	 flex,
-         python-reportlab,
-         python-numpy,
-         python3-reportlab,
-         python3-numpy,
-         bwa [any-amd64],
-         clustalo,
-         clustalw,
-         dialign,
-         dssp,
-         emboss,
-         fasttree,
-         mafft,
-         muscle,
-         ncbi-blast+,
-         phyml,
-         prank,
-         probcons,
-         python-mysqldb,
-         python-matplotlib,
-         python3-matplotlib,
-         python-numpy,
-         python3-numpy,
-         python-pil,
-         python3-pil,
-         python-rdflib,
-         python-renderpm,
-         python3-renderpm,
-         python-psycopg2,
-         python3-psycopg2,
-         raxml,
-         t-coffee,
-         wise
+Depends: @builddeps@