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 <[email protected]> Fri, 01 Oct 2021 00:18:15 +0200 + -- Michael R. Crusoe <[email protected]> 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 <[email protected]> +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.
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