debian/changelog

+pbgenomicconsensus (2.3.2-3) unstable; urgency=medium
+
+  * Really fix autopkgtest
+
+ -- Andreas Tille <tille@debian.org>  Tue, 02 Apr 2019 21:29:59 +0200
+
 pbgenomicconsensus (2.3.2-2) unstable; urgency=medium
 
   [ Afif Elghraoui ]

debian/patches/ignore_test_requiring_pbtestdata.patch

@@ -5,15 +5,17 @@ Last-Update: Thu, 28 Mar 2019 13:40:21 +0100
 
 --- a/Makefile
 +++ b/Makefile
-@@ -8,7 +8,12 @@ tests: unit-tests basic-tests
+@@ -8,7 +8,14 @@ tests: unit-tests basic-tests
  
  unit-tests:
  	# Unit tests
 -	py.test --junit-xml=nosetests.xml tests/unit
 +	# ignore tests requiring https://github.com/PacificBiosciences/PacBioTestData which is not packaged
++	set -e ; \
 +	TMPDIR=$$(mktemp -d /tmp/test_ignore_XXXXXX) ; \
 +	mv tests/unit/test_tool_contract.py $${TMPDIR} ; \
 +	py.test --junit-xml=nosetests.xml tests/unit ; \
++	rm -rf tests/unit/__pycache__ ; \
 +	mv $${TMPDIR}/* tests/unit ; \
 +	rmdir $${TMPDIR}
  

debian/patches/ignore_test_using_local_data.patch

@@ -5,7 +5,7 @@ Last-Update: Thu, 28 Mar 2019 13:40:21 +0100
 
 --- a/Makefile
 +++ b/Makefile
-@@ -20,8 +20,18 @@ unit-tests:
+@@ -22,8 +22,19 @@ unit-tests:
  
  basic-tests:
  	# End-to-end tests
@@ -13,6 +13,7 @@ Last-Update: Thu, 28 Mar 2019 13:40:21 +0100
 -	PATH=`pwd`:$(PATH) cram --verbose --xunit-file=gc-cram.xml `ls tests/cram/*.t | grep -v -e arrow -e bad_input`
 +	# 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
++	set -e ; \
 +	TMPDIR=$$(mktemp -d /tmp/test_ignore_XXXXXX) ; \
 +	for nt in $$(grep -Rl /mnt/secondary/Share/Quiver/ tests/*) ; do \
 +	    mkdir -p $${TMPDIR}/$$(dirname $${nt}) ; \

debian/tests/control

 Test-Command:
-	make unit-tests || true # due to warnings caused by python-pbcore some non-zero value is returned despite all tests are passing - thus adding '|| true'
+	cp -r Makefile tests $AUTOPKGTEST_TMP
+	&& cd $AUTOPKGTEST_TMP
+	&& make tests
 Depends:
 	@,
 	python-nose,
 	python-cram,
 	make,
-	poa
+	poa,
 Restrictions: allow-stderr
 
 Test-Command:
-	make basic-tests
-Depends:
-	@,
-	python-nose,
-	python-cram,
-	make,
-	poa
-Restrictions: allow-stderr
-
-Test-Command:
-	make extra-tests
+	cp -r Makefile tests $AUTOPKGTEST_TMP
+	&& cd $AUTOPKGTEST_TMP
+	&& make extra-tests
 Depends:
 	@,
 	python-cram,