[med-svn] [Git][med-team/pbgenomicconsensus][master] 6 commits: Mark autopkgtest that is forced to succeed "superficial"

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / pbgenomicconsensus


Commits:
b52deeaf by Andreas Tille at 2019-04-02T18:11:16Z
Mark autopkgtest that is forced to succeed "superficial"

- - - - -
5ed0a59d by Andreas Tille at 2019-04-02T18:32:08Z
Make test more sensible

- - - - -
60725a61 by Andreas Tille at 2019-04-02T19:20:59Z
Restore old autopkgtest file

- - - - -
23150713 by Andreas Tille at 2019-04-02T19:23:36Z
Document what really was done

- - - - -
ee6d69fe by Andreas Tille at 2019-04-02T19:25:08Z
No debugging noise

- - - - -
304e988e by Andreas Tille at 2019-04-02T19:33:06Z
Upload to unstable

- - - - -


4 changed files:

- debian/changelog
- debian/patches/ignore_test_requiring_pbtestdata.patch
- debian/patches/ignore_test_using_local_data.patch
- debian/tests/control


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,9 @@
+pbgenomicconsensus (2.3.2-3) unstable; urgency=medium
+
+  * Really fix autopkgtest
+
+ -- Andreas Tille <tille at 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
=====================================
@@ -1,25 +1,19 @@
 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,



View it on GitLab: https://salsa.debian.org/med-team/pbgenomicconsensus/compare/b10335c1c862e91e440b83b5941e2416386a28cd...304e988ecae787fc26b97888f681a276ec9922d0

-- 
View it on GitLab: https://salsa.debian.org/med-team/pbgenomicconsensus/compare/b10335c1c862e91e440b83b5941e2416386a28cd...304e988ecae787fc26b97888f681a276ec9922d0
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