[med-svn] [Git][med-team/python-cogent][master] 2 commits: Update fix-build-on-single-cpu-systems.patch to skip "test_write_db_parallel"...

[Santiago Vila (@sanvila)]

Santiago Vila pushed to branch master at Debian Med / python-cogent


Commits:
8b7e34e0 by Santiago Vila at 2023-10-20T14:07:42+02:00
Update fix-build-on-single-cpu-systems.patch to skip "test_write_db_parallel" again. Closes: #1030885

- - - - -
7d6026b3 by Santiago Vila at 2023-10-20T14:07:49+02:00
Upload to unstable as 2023.2.12a1+dfsg-3

- - - - -


2 changed files:

- debian/changelog
- debian/patches/fix-build-on-single-cpu-systems.patch


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+python-cogent (2023.2.12a1+dfsg-3) unstable; urgency=medium
+
+  * Team upload.
+  * Update fix-build-on-single-cpu-systems.patch to skip
+    "test_write_db_parallel" again. Closes: #1030885.
+
+ -- Santiago Vila <sanvila at debian.org>  Fri, 20 Oct 2023 14:02:00 +0200
+
 python-cogent (2023.2.12a1+dfsg-2) unstable; urgency=medium
 
   * Restrict to 64 bit architectures


=====================================
debian/patches/fix-build-on-single-cpu-systems.patch
=====================================
@@ -1,11 +1,11 @@
-Author:: Santiago Vila <sanvila at debian.org>
-Last-Upate: Wed, 8 Feb 2023 19:40:13 +0100
+Author: Santiago Vila <sanvila at 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 @@ Description: Skip tests that are failing on single-cpu systems
  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 @@ Description: Skip tests that are failing on single-cpu systems
          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 @@ Description: Skip tests that are failing on single-cpu systems
  
  import numpy
  
-@@ -35,6 +35,7 @@ def check_is_master_process(n):
+@@ -35,6 +35,7 @@
  
  
  class ParallelTests(TestCase):
@@ -41,7 +41,7 @@ Description: Skip tests that are failing 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 @@ 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 @@ Description: Skip tests that are failing 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 @@ class ParallelTests(TestCase):
+@@ -56,6 +58,7 @@
          self.assertEqual(result1[0], result2[0])
          self.assertNotEqual(result1, result2)
  
@@ -57,3 +57,21 @@ Description: Skip tests that are failing 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_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)
+ 
+ 
++ at 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")



View it on GitLab: https://salsa.debian.org/med-team/python-cogent/-/compare/acbe2de871ad3e7cd596854e2031fcfd7d0dab82...7d6026b3efad0afea2117bb8a12e367103ca1141

-- 
View it on GitLab: https://salsa.debian.org/med-team/python-cogent/-/compare/acbe2de871ad3e7cd596854e2031fcfd7d0dab82...7d6026b3efad0afea2117bb8a12e367103ca1141
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