Santiago Vila pushed to branch master at Debian Med / toil
Commits: e27aeca6 by Santiago Vila at 2026-04-29T16:05:00+02:00 Conditionally skip tests requiring more CPUs than available. Closes: #1108056. - - - - - ed292b60 by Santiago Vila at 2026-04-29T16:10:00+02:00 Upload for unstable as 9.3.0-3 - - - - - 3 changed files: - debian/changelog - + debian/patches/conditionally-skip-tests.patch - debian/patches/series Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,11 @@ +toil (9.3.0-3) unstable; urgency=medium + + * Team upload. + * Conditionally skip tests requiring more CPUs than available. + Closes: #1108056. + + -- Santiago Vila <[email protected]> Wed, 29 Apr 2026 16:10:00 +0200 + toil (9.3.0-2) unstable; urgency=medium * Resume autopkgtests on i386. ===================================== debian/patches/conditionally-skip-tests.patch ===================================== @@ -0,0 +1,68 @@ +From: Santiago Vila <[email protected]> +Subject: Conditionally skip tests requiring more CPUs than available +Bug-Debian: https://bugs.debian.org/1108056 +Forwarded: https://github.com/DataBiosphere/toil/issues/5482 + +--- a/src/toil/test/src/jobServiceTest.py ++++ b/src/toil/test/src/jobServiceTest.py +@@ -116,6 +116,10 @@ + # Check we get expected output + assert outFile.read_text() == "woot1 woot2 woot3" + ++ @pytest.mark.skipif( ++ SingleMachineBatchSystem.numCores < 4, ++ reason="Need at least four cores to run this test", ++ ) + def testServiceWithCheckpoints(self, tmp_path: Path) -> None: + """ + Tests the creation of a Job.Service with random failures of the worker, making the root job use checkpointing to +--- a/src/toil/test/batchSystems/batchSystemTest.py ++++ b/src/toil/test/batchSystems/batchSystemTest.py +@@ -530,6 +530,10 @@ + _, maxValue = getCounters(counterPath) + assert maxValue == (self.cpuCount // coresPerJob) + ++ @pytest.mark.skipif( ++ SingleMachineBatchSystem.numCores < 2, ++ reason="Need at least two cores to run this test", ++ ) + def test_omp_threads(self, tmp_path: Path) -> None: + """ + Test if the OMP_NUM_THREADS env var is set correctly based on jobs.cores. +--- a/src/toil/test/docs/scriptsTest.py ++++ b/src/toil/test/docs/scriptsTest.py +@@ -69,6 +69,10 @@ + n = re.search(pattern, outerr) + self.assertNotEqual(n, None, f"Pattern:\n{expectedPattern}\nOutput:\n{outerr}") + ++ @pytest.mark.skipif( ++ os.cpu_count() < 2, ++ reason="Need at least two cores to run this test", ++ ) + def testStats(self): + # This script asks for 4 cores but we might need to run the tests in only 3. + self.checkExitCode("tutorial_stats.py", ["--scale=0.5"]) +--- a/src/toil/test/src/promisedRequirementTest.py ++++ b/src/toil/test/src/promisedRequirementTest.py +@@ -121,6 +121,10 @@ + assert (minValue, maxValue) == (0, 0) + return counterPath + ++ @pytest.mark.skipif( ++ os.cpu_count() < 2, ++ reason="Need at least two cores to run this test", ++ ) + def testPromisesWithJobStoreFileObjects( + self, tmp_path: Path, caching: bool = True + ) -> None: +@@ -145,6 +149,10 @@ + + Job.Runner.startToil(F1, self.getOptions(tmp_path, caching=caching)) + ++ @pytest.mark.skipif( ++ os.cpu_count() < 2, ++ reason="Need at least two cores to run this test", ++ ) + def testPromisesWithNonCachingFileStore(self, tmp_path: Path) -> None: + self.testPromisesWithJobStoreFileObjects(tmp_path, caching=False) + ===================================== debian/patches/series ===================================== @@ -8,3 +8,4 @@ atomic_copy_as_alternative.patch soften-cwltool-dep.patch accept_debian_packaged_docker_version.patch allow_newer_requests +conditionally-skip-tests.patch View it on GitLab: https://salsa.debian.org/med-team/toil/-/compare/0c125b8cc35bcde02c47e6f242b3a4491b3e52a6...ed292b606b88f26be27550ff122696ad73a410a7 -- View it on GitLab: https://salsa.debian.org/med-team/toil/-/compare/0c125b8cc35bcde02c47e6f242b3a4491b3e52a6...ed292b606b88f26be27550ff122696ad73a410a7 You're receiving this email because of your account on salsa.debian.org. Manage all notifications: https://salsa.debian.org/-/profile/notifications | Help: https://salsa.debian.org/help
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