[med-svn] [Git][med-team/toil][master] 2 commits: Conditionally skip tests requiring more CPUs than available. Closes: #1108056.

[Santiago Vila (@sanvila)]

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 <sanvila at debian.org>  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 <sanvila at debian.org>
+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
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