Santiago Vila pushed to branch master at Debian Med / python-cogent
Commits: 8da22a9e by Santiago Vila at 2024-07-05T18:48:15+02:00 Update skip-parallel-tests-on-single-cpu-systems.patch to skip "test_write_db_parallel" again. Closes: #1030885. - - - - - 61224724 by Santiago Vila at 2024-07-05T18:49:27+02:00 Upload to unstable as 2024.5.7a1+dfsg-3 - - - - - 2 changed files: - debian/changelog - debian/patches/skip-parallel-tests-on-single-cpu-systems.patch Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,11 @@ +python-cogent (2024.5.7a1+dfsg-3) unstable; urgency=medium + + * Team upload. + * Update skip-parallel-tests-on-single-cpu-systems.patch + to skip "test_write_db_parallel" again. Closes: #1030885. + + -- Santiago Vila <[email protected]> Fri, 05 Jul 2024 18:45:00 +0200 + python-cogent (2024.5.7a1+dfsg-2) unstable; urgency=medium * Fix binary-any build ===================================== debian/patches/skip-parallel-tests-on-single-cpu-systems.patch ===================================== @@ -1,11 +1,55 @@ Author: Santiago Vila <[email protected]> -Last-Update: 2023-10-28 +Last-Update: 2024-07-05 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 +@@ -2,10 +2,11 @@ + + from os.path import dirname, join + from tempfile import TemporaryDirectory +-from unittest import TestCase ++from unittest import TestCase, skipIf + from unittest.mock import MagicMock + + import pytest ++import multiprocessing + + from numpy.testing import assert_allclose, assert_raises + +@@ -846,6 +847,7 @@ + _ = io.load_db() + evo_app.bootstrap(hyp, num_reps=2) + writer + + ++@skipIf(multiprocessing.cpu_count() == 1, "Does not work on single-cpu systems") + def test_bstrap_parallel(): + """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 +@@ -9,8 +9,10 @@ + + import numpy + import pytest ++import multiprocessing + + from numpy.testing import assert_allclose ++from unittest import skipIf + + from cogent3 import DNA, get_app, open_data_store + from cogent3.app import io as io_app +@@ -481,6 +483,7 @@ + assert isinstance(writer.data_store.summary_not_completed, Table) + + ++@skipIf(multiprocessing.cpu_count() == 1, "Does not work on single-cpu systems") + def test_write_db_parallel(tmp_dir, fasta_dir): + """writing with overwrite in parallel should reset db""" + dstore = open_data_store(fasta_dir, suffix="fasta") --- a/tests/test_util/test_parallel.py +++ b/tests/test_util/test_parallel.py -@@ -25,6 +25,7 @@ def check_is_master_process(n): +@@ -25,6 +25,7 @@ class ParallelTests(TestCase): @@ -13,7 +57,7 @@ Description: Skip parallel tests on single-cpu systems def test_create_processes(self): """Procressor pool should create multiple distingue processes""" max_worker_count = multiprocessing.cpu_count() - 1 -@@ -35,6 +36,7 @@ class ParallelTests(TestCase): +@@ -35,6 +36,7 @@ self.assertEqual(sorted(list(result_values)), index) self.assertEqual(len(set(result_processes)), max_worker_count) @@ -21,7 +65,7 @@ Description: Skip parallel tests 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...) -@@ -46,6 +48,7 @@ class ParallelTests(TestCase): +@@ -46,6 +48,7 @@ self.assertEqual(result1[0], result2[0]) self.assertNotEqual(result1, result2) @@ -29,26 +73,3 @@ Description: Skip parallel tests on single-cpu systems @skipIf(sys.version_info[1] < 7, "method exclusive to Python 3.7 and above") def test_is_master_process(self): """ ---- a/tests/test_app/test_evo.py -+++ b/tests/test_app/test_evo.py -@@ -2,10 +2,11 @@ import pathlib - - from os.path import dirname, join - from tempfile import TemporaryDirectory --from unittest import TestCase -+from unittest import TestCase, skipIf - from unittest.mock import MagicMock - - import pytest -+import multiprocessing - - from numpy.testing import assert_allclose, assert_raises - -@@ -846,6 +847,7 @@ class TestBootstrap(TestCase): - _ = io.load_db() + evo_app.bootstrap(hyp, num_reps=2) + writer - - -+@skipIf(multiprocessing.cpu_count() == 1, "Does not work on single-cpu systems") - def test_bstrap_parallel(): - """exercising bootstrap with parallel""" - aln = load_aligned_seqs(join(data_dir, "brca1.fasta"), moltype="dna") View it on GitLab: https://salsa.debian.org/med-team/python-cogent/-/compare/ec8bb7568e78a1daddc6fa2d8c0ace459fc2b598...61224724024ca36fd08a506a49bea294ed7ea126 -- This project does not include diff previews in email notifications. View it on GitLab: https://salsa.debian.org/med-team/python-cogent/-/compare/ec8bb7568e78a1daddc6fa2d8c0ace459fc2b598...61224724024ca36fd08a506a49bea294ed7ea126 You're receiving this email because of your account on salsa.debian.org.
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