[med-svn] [Git][med-team/toil][master] Autopkgtests: skip collection of s3 tests

[Michael R. Crusoe (@crusoe)]

Michael R. Crusoe pushed to branch master at Debian Med / toil


Commits:
93ad57da by Michael R. Crusoe at 2021-10-03T13:35:50+02:00
Autopkgtests: skip collection of s3 tests

- - - - -


4 changed files:

- debian/changelog
- + debian/patches/cwl_test_path
- debian/patches/series
- debian/tests/run-unit-tests


Changes:

=====================================
debian/changelog
=====================================
@@ -1,8 +1,9 @@
-toil (5.5.0-3) UNRELEASED; urgency=medium
+toil (5.5.0-3) unstable; urgency=medium
 
   * toil binary package depedency on recent cwltool as well.
+  * Autopkgtests: skip collection of s3 tests
 
- -- Michael R. Crusoe <crusoe at debian.org>  Fri, 01 Oct 2021 00:18:15 +0200
+ -- Michael R. Crusoe <crusoe at debian.org>  Sun, 03 Oct 2021 13:20:18 +0200
 
 toil (5.5.0-2) unstable; urgency=medium
 


=====================================
debian/patches/cwl_test_path
=====================================
@@ -0,0 +1,14 @@
+From: Michael R. Crusoe <crusoe at debian.org>
+Subject: CWL: safer test path generation for post-install testing
+Forwarded: https://github.com/DataBiosphere/toil/pull/3818
+--- toil.orig/src/toil/test/cwl/cwlTest.py
++++ toil/src/toil/test/cwl/cwlTest.py
+@@ -632,7 +632,7 @@
+         option_1 = '--strict-memory-limit'
+         option_2 = '--force-docker-pull'
+         option_3 = '--clean=always'
+-        cwl = os.path.join(self._projectRootPath(), 'src/toil/test/cwl/echo_string.cwl')
++        cwl = os.path.join(os.path.dirname(__file__), 'echo_string.cwl')
+         cmd = [toil, jobstore, option_1, option_2, option_3, cwl]
+         log.debug(f'Now running: {" ".join(cmd)}')
+         p = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE)


=====================================
debian/patches/series
=====================================
@@ -1,3 +1,4 @@
+cwl_test_path
 spelling
 setting_version.patch
 no_galaxy_lib


=====================================
debian/tests/run-unit-tests
=====================================
@@ -10,4 +10,4 @@ export LC_ALL=C.UTF-8
 # 
 # cd "${AUTOPKGTEST_TMP}"
 
-TMP=AUTOPKGTEST_TMP TOIL_TEST_QUICK=True TOIL_SKIP_DOCKER=True python3 -m pytest -vv -W ignore -k "not test_bioconda and not AWSJobStoreTest and not awsjobstoretest and not testCwlexample and not CWLv10Test and not CWLv11Test and not CWLv12Test" --ignore-glob '*cwlTest*' --pyargs toil.test
+TMP=AUTOPKGTEST_TMP TOIL_TEST_QUICK=True TOIL_SKIP_DOCKER=True python3 -m pytest -vv -rs -W ignore -k "not (test_bioconda or AWSJobStoreTest or awsjobstoretest or testCwlexample or CWLv10Test or CWLv11Test or CWLv12Test or AWSAutoscaleTest or AWSStaticAutoscaleTest or AWSManagedAutoscaleTest or AWSAutoscaleTestMultipleNodeTypes or AWSRestartTest or PreemptableDeficitCompensationTest)" --ignore-glob '*cwlTest*' --ignore /usr/lib/python3/dist-packages/toil/test/lib/aws/test_s3.py --pyargs toil.test



View it on GitLab: https://salsa.debian.org/med-team/toil/-/commit/93ad57da4d43522ac726aae93ae3322523caa29f

-- 
View it on GitLab: https://salsa.debian.org/med-team/toil/-/commit/93ad57da4d43522ac726aae93ae3322523caa29f
You're receiving this email because of your account on salsa.debian.org.


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20211003/5556da2a/attachment-0001.htm>