debian/changelog

 pbgenomicconsensus (2.3.2-2) UNRELEASED; urgency=medium
 
+  [ Afif Elghraoui ]
+  * Remove myself from Uploaders
+
+  [ Andreas Tille ]
+  * Add myself to Uploaders
   * python-pbgenomicconsensus Depends: python-pbconsensuscore
   * Test Depends: poa
   * Ignore some warnings which are breaking test results, remove
     tests that are based on non-existing input data
+  * Move exclusion of tests to upstream Makefile via patch rather than
+    in d/rules.  This is needed to run autopkgtest successfully
     Closes: #925909
 
- -- Andreas Tille <tille@debian.org>  Thu, 28 Mar 2019 13:40:21 +0100
+ -- Andreas Tille <tille@debian.org>  Thu, 28 Mar 2019 17:14:15 +0100
 
 pbgenomicconsensus (2.3.2-1) unstable; urgency=medium
 

debian/control

 Source: pbgenomicconsensus
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+Uploaders: Andreas Tille <tille@debian.org>
 Section: science
 Priority: optional
 Build-Depends: debhelper (>= 12~),

debian/patches/ignore_test_requiring_pbtestdata.patch

@@ -9,12 +9,13 @@ Last-Update: Thu, 28 Mar 2019 13:40:21 +0100
  
  unit-tests:
  	# Unit tests
-+	mkdir -p tmp_test_ignore
-+	# This test requires https://github.com/PacificBiosciences/PacBioTestData which is not packaged
-+	mv tests/unit/test_tool_contract.py tmp_test_ignore
- 	py.test --junit-xml=nosetests.xml tests/unit
-+	mv tmp_test_ignore/* tests/unit
-+	rmdir tmp_test_ignore
+-	py.test --junit-xml=nosetests.xml tests/unit
++	# ignore tests requiring https://github.com/PacificBiosciences/PacBioTestData which is not packaged
++	TMPDIR=$$(mktemp -d /tmp/test_ignore_XXXXXX) ; \
++	mv tests/unit/test_tool_contract.py $${TMPDIR} ; \
++	py.test --junit-xml=nosetests.xml tests/unit ; \
++	mv $${TMPDIR}/* tests/unit ; \
++	rmdir $${TMPDIR}
  
  # Note: We need at least cram/0.7 for '--xunit-file'
  # Note: The cram tests often need h5py.

debian/patches/ignore_test_using_local_data.patch

@@ -5,20 +5,24 @@ Last-Update: Thu, 28 Mar 2019 13:40:21 +0100
 
 --- a/Makefile
 +++ b/Makefile
-@@ -21,7 +21,15 @@ unit-tests:
+@@ -20,8 +20,18 @@ unit-tests:
+ 
  basic-tests:
  	# End-to-end tests
- 	# One of these now needs mummer and exonerate.
+-	# One of these now needs mummer and exonerate.
 -	PATH=`pwd`:$(PATH) cram --verbose --xunit-file=gc-cram.xml `ls tests/cram/*.t | grep -v -e arrow -e bad_input`
-+	mkdir -p tmp_test_ignore
-+	# this test requires an input file on a local mount of upstream
-+	mv tests/cram/alignment_summary.t tmp_test_ignore
-+	mv tests/cram/quiver-tinyLambda-coverage-islands.t tmp_test_ignore
-+	# this test contains a wrong syntax in calling poa - no idea how to fix this thus ignoring the test
-+	mv tests/cram/poa-all4mer.t tmp_test_ignore
-+	PATH=`pwd`:$(PATH) cram --verbose --xunit-file=gc-cram.xml `ls tests/cram/*.t | grep -v -e arrow -e bad_input` || \
-+	mv tmp_test_ignore/* tests/cram/
-+	rmdir tmp_test_ignore
++	# some tests require a input files on a local mount of upstream
++	# The test poa-all4mer.t contains a wrong syntax in calling poa - no idea how to fix this thus ignoring the test
++	TMPDIR=$$(mktemp -d /tmp/test_ignore_XXXXXX) ; \
++	for nt in $$(grep -Rl /mnt/secondary/Share/Quiver/ tests/*) ; do \
++	    mkdir -p $${TMPDIR}/$$(dirname $${nt}) ; \
++	    mv $${nt} $${TMPDIR}/$$(dirname $${nt}) ; \
++	done ; \
++	mkdir -p $${TMPDIR}/tests/cram ; \
++	mv tests/cram/poa-all4mer.t $${TMPDIR}/tests/cram ; \
++	PATH=`pwd`:$(PATH) cram --verbose --xunit-file=gc-cram.xml `ls tests/cram/*.t | grep -v -e arrow -e bad_input` ; \
++	cp -a -v $${TMPDIR}/tests/* tests ; \
++	rm -r $${TMPDIR}
  
  extra-tests:
  	# Tests that need to be run by Jenkins but are slowing

debian/rules

@@ -24,20 +24,8 @@ variantCaller.1.md \
 override_dh_auto_test:
 ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
 	chmod +x bin/gffToBed
-	mv tests/unit/test_tool_contract.py .	# move test requiring pbtestdata out of the way
-	# move tests accessing developers local data out of the way
-	mkdir no_tests
-	for nt in `grep -Rl /mnt/secondary/Share/Quiver/ tests/*` ; do \
-	    mkdir -p no_`dirname $${nt}` ; \
-	    mv $${nt} no_`dirname $${nt}` ; \
-	done
 	unset GZIP ; \
-	PYTHONPATH=$(CURDIR) PATH=$(CURDIR)/bin:$$PATH $(MAKE) tests
-	for nt in `find no_tests -name "*.t"` ; do \
-	    mv $${nt} `dirname $${nt} | sed 's/^no_//'` ; \
-	done
-	rm -rf no_tests
-	mv test_tool_contract.py tests/unit	# restore test data
+	PYTHONPATH=$(CURDIR) PATH=$(CURDIR)/bin:$$PATH $(MAKE) -j1 tests
 	chmod -x bin/gffToBed
 endif