Bug#1058586: bullseye-pu: package python-cogent/2020.12.21a+dfsg-4+deb11u1
Package: release.debian.org
Severity: normal
Tags: bullseye
User: release.debian.org@packages.debian.org
Usertags: pu
X-Debbugs-Cc: python-cogent@packages.debian.org, sanvila@debian.org
Control: affects -1 + src:python-cogent
[ Reason ]
This upload fixes Bug #1030885: FTBFS on single-CPU systems.
[ Impact ]
Anybody trying to build the package using a single-CPU system
will see that the build will fail unexpectedly.
[ Tests ]
I've checked that the fixed package builds again on single-CPU
systems and also that it still builds ok on multi-core systems.
[ Risks ]
Low risk. No real code changes. The only change is that
some tests are skipped when we know 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 ]
Skip parallel tests when the build machine has only one CPU.
[ Other info ]
The package is already uploaded.
diff -Nru python-cogent-2020.12.21a+dfsg/debian/changelog python-cogent-2020.12.21a+dfsg/debian/changelog
--- python-cogent-2020.12.21a+dfsg/debian/changelog 2021-02-09 14:42:13.000000000 +0100
+++ python-cogent-2020.12.21a+dfsg/debian/changelog 2023-12-13 12:30:00.000000000 +0100
@@ -1,3 +1,10 @@
+python-cogent (2020.12.21a+dfsg-4+deb11u1) bullseye; urgency=medium
+
+ * Team upload.
+ * Skip parallel tests on single-CPU systems. Closes: #1030885.
+
+ -- Santiago Vila <sanvila@debian.org> Wed, 13 Dec 2023 12:30:00 +0100
+
python-cogent (2020.12.21a+dfsg-4) unstable; urgency=high
* Team upload.
diff -Nru python-cogent-2020.12.21a+dfsg/debian/patches/series python-cogent-2020.12.21a+dfsg/debian/patches/series
--- python-cogent-2020.12.21a+dfsg/debian/patches/series 2021-02-07 17:23:21.000000000 +0100
+++ python-cogent-2020.12.21a+dfsg/debian/patches/series 2023-12-13 12:30:00.000000000 +0100
@@ -1,3 +1,4 @@
sphinx.patch
fix_interpreter.patch
py39_union_dict
+skip-parallel-tests-on-single-cpu-systems.patch
diff -Nru python-cogent-2020.12.21a+dfsg/debian/patches/skip-parallel-tests-on-single-cpu-systems.patch python-cogent-2020.12.21a+dfsg/debian/patches/skip-parallel-tests-on-single-cpu-systems.patch
--- python-cogent-2020.12.21a+dfsg/debian/patches/skip-parallel-tests-on-single-cpu-systems.patch 1970-01-01 01:00:00.000000000 +0100
+++ python-cogent-2020.12.21a+dfsg/debian/patches/skip-parallel-tests-on-single-cpu-systems.patch 2023-12-13 12:30:00.000000000 +0100
@@ -0,0 +1,73 @@
+Author: Santiago Vila <sanvila@debian.org>
+Last-Update: 2023-12-13
+Bug-Debian: https://bugs.debian.org/1030885
+Description: Skip parallel tests on single-cpu systems
+
+--- a/tests/test_app/test_evo.py
++++ b/tests/test_app/test_evo.py
+@@ -1,5 +1,7 @@
++import multiprocessing
++
+ from os.path import dirname, join
+-from unittest import TestCase, main
++from unittest import TestCase, main, skipIf
+ from unittest.mock import MagicMock
+
+ from numpy.testing import assert_allclose, assert_raises
+@@ -670,6 +672,7 @@
+ got = deserialise_object(json)
+ self.assertIsInstance(got, evo_app.bootstrap_result)
+
++ @skipIf(multiprocessing.cpu_count() == 1, "Does not work on single-cpu systems")
+ def test_bstrap_parallel(self):
+ """exercising bootstrap with parallel"""
+ aln = load_aligned_seqs(join(data_dir, "brca1.fasta"), moltype="dna")
+--- a/tests/test_app/test_io.py
++++ b/tests/test_app/test_io.py
+@@ -3,10 +3,11 @@
+ import pathlib
+ import shutil
+ import zipfile
++import multiprocessing
+
+ from os.path import basename, join
+ from tempfile import TemporaryDirectory
+-from unittest import TestCase, main
++from unittest import TestCase, main, skipIf
+ from unittest.mock import Mock, patch
+
+ import numpy
+@@ -532,6 +533,7 @@
+ w = io_app.write_db(outdir, create=True, if_exists="skip")
+ w.data_store.close()
+
++ @skipIf(multiprocessing.cpu_count() == 1, "Does not work on single-cpu systems")
+ def test_write_db_parallel(self):
+ """writing with overwrite in parallel should reset db"""
+ dstore = io_app.get_data_store(self.basedir, suffix="fasta")
+--- a/tests/test_util/test_parallel.py
++++ b/tests/test_util/test_parallel.py
+@@ -35,6 +35,7 @@
+
+
+ class ParallelTests(TestCase):
++ @skipIf(multiprocessing.cpu_count() == 1, "Does not work on single-cpu systems")
+ def test_create_processes(self):
+ """Procressor pool should create multiple distingue processes"""
+ max_worker_count = multiprocessing.cpu_count() - 1
+@@ -45,6 +46,7 @@
+ self.assertEqual(sorted(list(result_values)), index)
+ self.assertEqual(len(set(result_processes)), max_worker_count)
+
++ @skipIf(multiprocessing.cpu_count() == 1, "Does not work on single-cpu systems")
+ def test_random_seeding(self):
+ """Random seed should be set every function call"""
+ # On Windows process ids are not guaranteed to be sequential(1,2,3,4...)
+@@ -56,6 +58,7 @@
+ self.assertEqual(result1[0], result2[0])
+ self.assertNotEqual(result1, result2)
+
++ @skipIf(multiprocessing.cpu_count() == 1, "Does not work on single-cpu systems")
+ @skipIf(sys.version_info[1] < 7, "method exclusive to Python 3.7 and above")
+ def test_is_master_process(self):
+ """
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