[med-svn] [Git][med-team/kineticstools][master] 3 commits: Make sure cram3 is used in tests

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / kineticstools


Commits:
05e0e396 by Andreas Tille at 2020-04-21T11:05:50+02:00
Make sure cram3 is used in tests

- - - - -
4acd59e6 by Andreas Tille at 2020-04-21T11:11:37+02:00
replace further python calls by pathon3 - just to be sure

- - - - -
c0d17084 by Andreas Tille at 2020-04-21T11:26:47+02:00
Upload to unstable

- - - - -


2 changed files:

- debian/changelog
- debian/patches/tests2to3.patch


Changes:

=====================================
debian/changelog
=====================================
@@ -1,7 +1,6 @@
-kineticstools (0.6.1+git20200325.3558942-1) UNRELEASED; urgency=medium
+kineticstools (0.6.1+git20200325.3558942-1) unstable; urgency=medium
 
   [ Steffen Moeller ]
-  * Team upload.
   * New upstream version
   * d/control
     - Standards-Version: 4.5.0 (routine-update)
@@ -41,7 +40,7 @@ kineticstools (0.6.1+git20200325.3558942-1) UNRELEASED; urgency=medium
   * Reported alignment issue in the manual.rst to upstream:
     https://github.com/PacificBiosciences/kineticsTools/pull/74
 
- -- Steffen Moeller <moeller at debian.org>  Sun, 19 Apr 2020 13:03:11 +0200
+ -- Andreas Tille <tille at debian.org>  Tue, 21 Apr 2020 11:12:01 +0200
 
 kineticstools (0.6.1+git20180425.27a1878-2) unstable; urgency=medium
 


=====================================
debian/patches/tests2to3.patch
=====================================
@@ -2,10 +2,8 @@ Author: Steffen Moeller
 Last-Update: 2020-03-26 04:21:08 +0100
 Description: Use Python3 in test
 
-Index: kineticstools/test/test_gather_bigwig.py
-===================================================================
---- kineticstools.orig/test/test_gather_bigwig.py
-+++ kineticstools/test/test_gather_bigwig.py
+--- a/test/test_gather_bigwig.py
++++ b/test/test_gather_bigwig.py
 @@ -72,7 +72,7 @@ class TestGatherBigwig:
      def test_gather_bigwig_cli(self):
          tmp_dir = tempfile.mkdtemp()
@@ -15,3 +13,49 @@ Index: kineticstools/test/test_gather_bigwig.py
                  ofn] + self._data_files
          log.info("Output will be in %s", tmp_dir)
          with open(op.join(tmp_dir, "stdout"), "w") as stdout:
+--- a/Makefile
++++ b/Makefile
+@@ -6,17 +6,17 @@ utest:
+ all: build install
+ 
+ build:
+-	python setup.py build --executable="/usr/bin/env python"
++	python3 setup.py build --executable="/usr/bin/env python"
+ 
+ bdist:
+-	python setup.py build --executable="/usr/bin/env python"
+-	python setup.py bdist --formats=egg
++	python3 setup.py build --executable="/usr/bin/env python"
++	python3 setup.py bdist --formats=egg
+ 
+ install:
+-	python setup.py install
++	python3 setup.py install
+ 
+ develop:
+-	python setup.py develop
++	python3 setup.py develop
+ 
+ clean:
+ 	rm -rf build/;\
+@@ -29,17 +29,17 @@ check: tests
+ tests: cram-tests py-tests extra-tests
+ 
+ cram-tests:
+-	cram --verbose --xunit-file=cramtests.xml `ls test/cram/*.t | grep -v detection_bam`
++	cram3 --verbose --xunit-file=cramtests.xml `ls test/cram/*.t | grep -v detection_bam`
+ 
+ long-tests:
+-	cram test/cram/long_running/*.t
++	cram3 test/cram/long_running/*.t
+ 
+ py-tests:
+ 	# pytest --cov=kineticsTools  # does not quite work since we run in test/ dir.
+ 	cd test/; pytest -s -v -p no:warnings -n auto --dist=loadscope --durations=20 --junitxml=../nosetests.xml --cov-report=xml:../coverage.xml test_*.py
+ 
+ extra-tests:
+-	#cram --verbose --xunit-file=cramtests-extra.xml test/cram/extra/*.t
++	#cram3 --verbose --xunit-file=cramtests-extra.xml test/cram/extra/*.t
+ 	# TODO: Fix chemistry and re-enable this test.
+ 
+ pylint:



View it on GitLab: https://salsa.debian.org/med-team/kineticstools/-/compare/3206ba0549a1da7c0296fad46761cfaa88173fbb...c0d1708469f90f945f1932dd15215f5768fb7503

-- 
View it on GitLab: https://salsa.debian.org/med-team/kineticstools/-/compare/3206ba0549a1da7c0296fad46761cfaa88173fbb...c0d1708469f90f945f1932dd15215f5768fb7503
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