[med-svn] [Git][med-team/python-cogent][master] 3 commits: Finally the new version builds and is closing bug #1030884
Andreas Tille (@tille)
gitlab at salsa.debian.org
Thu Feb 9 14:36:48 GMT 2023
Andreas Tille pushed to branch master at Debian Med / python-cogent
Commits:
20205714 by Andreas Tille at 2023-02-09T15:19:07+01:00
Finally the new version builds and is closing bug #1030884
- - - - -
d7f67a0f by Andreas Tille at 2023-02-09T15:24:14+01:00
Skip tests that are failing on single-cpu systems
- - - - -
35cf15b0 by Andreas Tille at 2023-02-09T15:31:45+01:00
Upload to unstable
- - - - -
5 changed files:
- debian/changelog
- + debian/patches/fix-build-on-single-cpu-systems.patch
- debian/patches/remove-jupyter-sphinx.patch
- debian/patches/series
- debian/patches/sphinx.patch
Changes:
=====================================
debian/changelog
=====================================
@@ -1,13 +1,18 @@
-python-cogent (2022.10.31a1+dfsg-1) UNRELEASED; urgency=medium
+python-cogent (2022.10.31a1+dfsg-1) unstable; urgency=medium
[ Andreas Tille ]
* New upstream version
+ Closes: #1030884
* Build-Depends: python3-typing-extensions
[ Étienne Mollier ]
* d/{control,rules}: migrate from flit to generic pyproject.
- -- Étienne Mollier <emollier at debian.org> Sat, 03 Dec 2022 12:28:36 +0100
+ [ Santiago Vila ]
+ * Skip tests that are failing on single-cpu systems
+ Closes: 1030885
+
+ -- Andreas Tille <tille at debian.org> Thu, 09 Feb 2023 15:24:31 +0100
python-cogent (2022.8.24a1+dfsg-1) unstable; urgency=medium
=====================================
debian/patches/fix-build-on-single-cpu-systems.patch
=====================================
@@ -0,0 +1,77 @@
+Author:: Santiago Vila <sanvila at debian.org>
+Last-Upate: Wed, 8 Feb 2023 19:40:13 +0100
+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
+@@ -1,6 +1,6 @@
+ from os.path import dirname, join
+ from tempfile import TemporaryDirectory
+-from unittest import TestCase, main
++from unittest import TestCase, main, skip
+ from unittest.mock import MagicMock
+
+ from numpy.testing import assert_allclose, assert_raises
+@@ -847,6 +847,7 @@ class TestBootstrap(TestCase):
+ # correct message being relayed
+ self.assertTrue("ValueError: '-' at" in result.message)
+
++ @skip("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
+@@ -6,7 +6,7 @@ import zipfile
+
+ from os.path import join
+ from tempfile import TemporaryDirectory
+-from unittest import TestCase, main
++from unittest import TestCase, main, skip
+
+ import numpy
+
+@@ -505,6 +505,7 @@ class TestIo(TestCase):
+ w = io_app.write_db(outdir, create=True, if_exists="skip")
+ w.data_store.close()
+
++ @skip("Does not work on single-cpu systems")
+ def test_write_db_parallel(self):
+ """writing with overwrite in parallel should reset db"""
+ with TemporaryDirectory(dir=".") as dirname:
+--- a/tests/test_util/test_parallel.py
++++ b/tests/test_util/test_parallel.py
+@@ -2,7 +2,7 @@ import multiprocessing
+ import sys
+ import time
+
+-from unittest import TestCase, main, skipIf
++from unittest import TestCase, main, skipIf, skip
+
+ import numpy
+
+@@ -35,6 +35,7 @@ def check_is_master_process(n):
+
+
+ class ParallelTests(TestCase):
++ @skip("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 @@ class ParallelTests(TestCase):
+ self.assertEqual(sorted(list(result_values)), index)
+ self.assertEqual(len(set(result_processes)), max_worker_count)
+
++ @skip("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 @@ class ParallelTests(TestCase):
+ self.assertEqual(result1[0], result2[0])
+ self.assertNotEqual(result1, result2)
+
++ @skip("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):
+ """
=====================================
debian/patches/remove-jupyter-sphinx.patch
=====================================
@@ -4,7 +4,7 @@ Forwarded: not-needed
Last-Update: 2022-02-20
--- a/pyproject.toml
+++ b/pyproject.toml
-@@ -52,7 +52,6 @@ doc = ["click",
+@@ -57,7 +57,6 @@ doc = ["click",
"ipykernel",
"ipython",
"ipywidgets",
@@ -12,7 +12,7 @@ Last-Update: 2022-02-20
"jupyter_client",
"jupyterlab",
"jupytext",
-@@ -80,7 +79,6 @@ dev = ["black",
+@@ -86,7 +85,6 @@ dev = ["black",
"ipython",
"ipywidgets",
"isort",
=====================================
debian/patches/series
=====================================
@@ -2,3 +2,4 @@ sphinx.patch
fix_interpreter.patch
remove-jupyter-sphinx.patch
ignore_tests_accessing_network.patch
+fix-build-on-single-cpu-systems.patch
=====================================
debian/patches/sphinx.patch
=====================================
@@ -5,7 +5,7 @@ Forwarded: not-needed
--- a/doc/conf.py
+++ b/doc/conf.py
-@@ -30,17 +30,18 @@ add_module_names = False # don't includ
+@@ -31,17 +31,18 @@ add_module_names = False # don't includ
numpydoc_class_members_toctree = False
extensions = [
View it on GitLab: https://salsa.debian.org/med-team/python-cogent/-/compare/b696d81ce4d0c45ab1a1010b08af00e4418068e5...35cf15b03479924e031c8db03d6a5a54a08f03ce
--
View it on GitLab: https://salsa.debian.org/med-team/python-cogent/-/compare/b696d81ce4d0c45ab1a1010b08af00e4418068e5...35cf15b03479924e031c8db03d6a5a54a08f03ce
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