Bug#1054286: bookworm-pu: package python-cogent/2023.2.12a1+dfsg-2+deb12u1
Sorry, forgot the debdiff. Here it is.
Thanks.
diff -Nru python-cogent-2023.2.12a1+dfsg/debian/changelog python-cogent-2023.2.12a1+dfsg/debian/changelog
--- python-cogent-2023.2.12a1+dfsg/debian/changelog 2023-02-24 14:18:01.000000000 +0100
+++ python-cogent-2023.2.12a1+dfsg/debian/changelog 2023-10-20 19:04:00.000000000 +0200
@@ -1,3 +1,11 @@
+python-cogent (2023.2.12a1+dfsg-2+deb12u1) bookworm; urgency=medium
+
+ * Team upload.
+ * Update fix-build-on-single-cpu-systems.patch to skip
+ "test_write_db_parallel" again. Closes: #1030885.
+
+ -- Santiago Vila <sanvila@debian.org> Fri, 20 Oct 2023 19:04:00 +0200
+
python-cogent (2023.2.12a1+dfsg-2) unstable; urgency=medium
* Restrict to 64 bit architectures
diff -Nru python-cogent-2023.2.12a1+dfsg/debian/patches/fix-build-on-single-cpu-systems.patch python-cogent-2023.2.12a1+dfsg/debian/patches/fix-build-on-single-cpu-systems.patch
--- python-cogent-2023.2.12a1+dfsg/debian/patches/fix-build-on-single-cpu-systems.patch 2023-02-24 14:18:01.000000000 +0100
+++ python-cogent-2023.2.12a1+dfsg/debian/patches/fix-build-on-single-cpu-systems.patch 2023-10-20 19:03:12.000000000 +0200
@@ -1,11 +1,11 @@
-Author:: Santiago Vila <sanvila@debian.org>
-Last-Upate: Wed, 8 Feb 2023 19:40:13 +0100
+Author: Santiago Vila <sanvila@debian.org>
+Last-Update: 2023-10-20
Bug-Debian: https://bugs.debian.org/1030885
Description: Skip tests that are failing on single-cpu systems
--- a/tests/test_app/test_evo.py
+++ b/tests/test_app/test_evo.py
-@@ -2,7 +2,7 @@ import pathlib
+@@ -2,7 +2,7 @@
from os.path import dirname, join
from tempfile import TemporaryDirectory
@@ -14,7 +14,7 @@
from unittest.mock import MagicMock
from numpy.testing import assert_allclose, assert_raises
-@@ -854,6 +854,7 @@ class TestBootstrap(TestCase):
+@@ -854,6 +854,7 @@
# correct message being relayed
self.assertTrue("ValueError: '-' at" in result.message)
@@ -24,7 +24,7 @@
aln = load_aligned_seqs(join(data_dir, "brca1.fasta"), moltype="dna")
--- a/tests/test_util/test_parallel.py
+++ b/tests/test_util/test_parallel.py
-@@ -2,7 +2,7 @@ import multiprocessing
+@@ -2,7 +2,7 @@
import sys
import time
@@ -33,7 +33,7 @@
import numpy
-@@ -35,6 +35,7 @@ def check_is_master_process(n):
+@@ -35,6 +35,7 @@
class ParallelTests(TestCase):
@@ -41,7 +41,7 @@
def test_create_processes(self):
"""Procressor pool should create multiple distingue processes"""
max_worker_count = multiprocessing.cpu_count() - 1
-@@ -45,6 +46,7 @@ class ParallelTests(TestCase):
+@@ -45,6 +46,7 @@
self.assertEqual(sorted(list(result_values)), index)
self.assertEqual(len(set(result_processes)), max_worker_count)
@@ -49,7 +49,7 @@
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 @@ class ParallelTests(TestCase):
+@@ -56,6 +58,7 @@
self.assertEqual(result1[0], result2[0])
self.assertNotEqual(result1, result2)
@@ -57,3 +57,21 @@
@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_io_new.py
++++ b/tests/test_app/test_io_new.py
+@@ -6,6 +6,7 @@
+ import pickle
+
+ from pathlib import Path
++from unittest import skip
+
+ import numpy
+ import pytest
+@@ -479,6 +480,7 @@
+ assert isinstance(writer.data_store.summary_not_completed, Table)
+
+
++@skip("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")
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