[Debian-med-packaging] Bug#1135228: trixie-pu: package toil/8.0.0-5+deb13u1

[Santiago Vila]

Package: release.debian.org
Severity: normal
Tags: trixie
X-Debbugs-Cc: toil at packages.debian.org, sanvila at debian.org
Control: affects -1 + src:toil
User: release.debian.org at packages.debian.org
Usertags: pu

[ Reason ]
Fix FTBFS Bug #1108056. Some tests fail on single-CPU systems.

[ Impact ]
Anybody trying to build the package on a single-CPU system will unexpectedly
find that the package does not build.

[ Tests ]
I've checked that the package builds ok again on the systems where it used to fail.

[ Risks ]
Very low. No real code changes. Only some tests are disabled, and only
when it's detected that they would fail.

[ Checklist ]
   [X] *all* changes are documented in the d/changelog
   [X] I reviewed all changes and I approve them
   [X] attach debdiff against the package in (old)stable
   [X] the issue is verified as fixed in unstable

[ Changes ]
See changelog.

[ Other info ]
I've already uploaded the package.
-------------- next part --------------
diff -Nru toil-8.0.0/debian/changelog toil-8.0.0/debian/changelog
--- toil-8.0.0/debian/changelog	2025-04-09 13:42:27.000000000 +0200
+++ toil-8.0.0/debian/changelog	2026-04-29 20:30:00.000000000 +0200
@@ -1,3 +1,11 @@
+toil (8.0.0-5+deb13u1) trixie; urgency=medium
+
+  * Team upload.
+  * Conditionally skip tests requiring more CPUs than available.
+    Closes: #1108056.
+
+ -- Santiago Vila <sanvila at debian.org>  Wed, 29 Apr 2026 20:30:00 +0200
+
 toil (8.0.0-5) unstable; urgency=medium
 
   * d/rules: skip flaky testServices. Closes: #1101085
diff -Nru toil-8.0.0/debian/patches/conditionally-skip-tests.patch toil-8.0.0/debian/patches/conditionally-skip-tests.patch
--- toil-8.0.0/debian/patches/conditionally-skip-tests.patch	1970-01-01 01:00:00.000000000 +0100
+++ toil-8.0.0/debian/patches/conditionally-skip-tests.patch	2026-04-29 18:14:00.000000000 +0200
@@ -0,0 +1,73 @@
+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/batchSystems/batchSystemTest.py
++++ b/src/toil/test/batchSystems/batchSystemTest.py
+@@ -24,6 +24,8 @@
+ from fractions import Fraction
+ from unittest import skipIf
+ 
++import pytest
++
+ from toil.batchSystems.abstractBatchSystem import (
+     AbstractBatchSystem,
+     BatchSystemSupport,
+@@ -505,6 +507,10 @@
+                 _, maxValue = getCounters(counterPath)
+                 self.assertEqual(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):
+             """
+             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
+@@ -68,6 +68,10 @@
+         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
+@@ -16,6 +16,8 @@
+ import os
+ import time
+ 
++import pytest
++
+ import toil.test.batchSystems.batchSystemTest as batchSystemTest
+ from toil.batchSystems.mesos.test import MesosTestSupport
+ from toil.job import Job, PromisedRequirement
+@@ -127,6 +129,10 @@
+             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, caching=True):
+             """
+             Check whether FileID objects are being pickled properly when used as return
+@@ -153,6 +159,10 @@
+                 F1, self.getOptions(self._createTempDir("testFiles"), caching=caching)
+             )
+ 
++        @pytest.mark.skipif(
++            os.cpu_count() < 2,
++            reason="Need at least two cores to run this test",
++        )
+         def testPromisesWithNonCachingFileStore(self):
+             self.testPromisesWithJobStoreFileObjects(caching=False)
+ 
diff -Nru toil-8.0.0/debian/patches/series toil-8.0.0/debian/patches/series
--- toil-8.0.0/debian/patches/series	2025-03-17 19:11:04.000000000 +0100
+++ toil-8.0.0/debian/patches/series	2026-04-29 18:00:00.000000000 +0200
@@ -11,3 +11,4 @@
 accept_debian_packaged_docker_version.patch
 allow_newer_requests
 soften-psutil
+conditionally-skip-tests.patch