[med-svn] [Git][med-team/python-skbio][master] Cherry-picked patch from upstream to fix test that failed under Python 3.13.
Michael R. Crusoe (@crusoe)
gitlab at salsa.debian.org
Mon Nov 18 10:11:09 GMT 2024
Michael R. Crusoe pushed to branch master at Debian Med / python-skbio
Commits:
1cdaed1e by Michael R. Crusoe at 2024-11-18T09:59:20+00:00
Cherry-picked patch from upstream to fix test that failed under Python 3.13.
Closes: #1087690
- - - - -
3 changed files:
- debian/changelog
- + debian/patches/45127698e270024bacb670cdd0bd2e4850104b6f.patch
- debian/patches/series
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+python-skbio (0.6.2-4) UNRELEASED; urgency=medium
+
+ * Team upload.
+ * Cherry-picked patch from upstream to fix test that failed under Python
+ 3.13. Closes: #1087690
+
+ -- Michael R. Crusoe <crusoe at debian.org> Mon, 18 Nov 2024 09:55:29 +0000
+
python-skbio (0.6.2-3) unstable; urgency=medium
* Team upload.
=====================================
debian/patches/45127698e270024bacb670cdd0bd2e4850104b6f.patch
=====================================
@@ -0,0 +1,90 @@
+From 45127698e270024bacb670cdd0bd2e4850104b6f Mon Sep 17 00:00:00 2001
+From: Matt Aton <matthewaton2 at gmail.com>
+Date: Wed, 6 Nov 2024 17:31:40 -0700
+Subject: [PATCH] Python 3.13 Support (#2146)
+
+* Rewrite tests and add Python 3.13 to CI workflow
+
+* Update CHANGELOG
+
+* Make doctest for permdisp pass on different platforms
+---
+ .github/workflows/ci.yml | 4 +--
+ .github/workflows/release.yml | 2 +-
+ .github/workflows/website.yml | 2 +-
+ CHANGELOG.md | 1 +
+ setup.py | 1 +
+ skbio/stats/distance/_permdisp.py | 4 +--
+ skbio/util/tests/test_misc.py | 43 ++++++++++++++++++-------------
+ 7 files changed, 33 insertions(+), 24 deletions(-)
+
+
+--- a/setup.py
++++ b/setup.py
+@@ -129,6 +129,7 @@
+ Programming Language :: Python :: 3.10
+ Programming Language :: Python :: 3.11
+ Programming Language :: Python :: 3.12
++ Programming Language :: Python :: 3.13
+ Operating System :: Unix
+ Operating System :: POSIX
+ Operating System :: MacOS :: MacOS X
+--- a/skbio/util/tests/test_misc.py
++++ b/skbio/util/tests/test_misc.py
+@@ -8,6 +8,7 @@
+
+ import io
+ import unittest
++import re
+
+ import numpy as np
+
+@@ -103,24 +104,30 @@
+ self.registry.interpolate(SomethingToInterpolate, "interpolate_me")
+ subclass_registry.interpolate(Subclass, "interpolate_me")
+
+- self.assertEqual(SomethingToInterpolate.interpolate_me.__doc__,
+- "First line\n\n Some description of th"
+- "ings, also this:\n\n\t'a'\n\t x\n\t'b'\n\t y\n\t'c"
+- "'\n\t z\n\n Other things are happeni"
+- "ng now.\n ")
+- self.assertEqual(SomethingToInterpolate.dont_interpolate_me.__doc__,
+- "First line\n\n Some description of th"
+- "ings, also this:\n\n Other things are"
+- " happening now.\n ")
+- self.assertEqual(Subclass.interpolate_me.__doc__,
+- "First line\n\n Some description of th"
+- "ings, also this:\n\n\t'a'\n\t x\n\t'b'\n\t y\n\t'c"
+- "'\n\t z\n\t'o'\n\t p\n\n Other thin"
+- "gs are happening now.\n ")
+- self.assertEqual(Subclass.dont_interpolate_me.__doc__,
+- "First line\n\n Some description of th"
+- "ings, also this:\n\n Other things are"
+- " happening now.\n ")
++ # Python 3.13+ removes leading whitespaces from a docstring, therefore it is
++ # necessary to make this edit.
++ def _strip_spaces(s):
++ return re.sub(r'^\s+', '', s, flags=re.MULTILINE)
++
++ obs = _strip_spaces(SomethingToInterpolate.interpolate_me.__doc__)
++ exp = ("First line\nSome description of things, also this:\n'a'\nx"
++ "\n'b'\ny\n'c'\nz\nOther things are happening now.\n")
++ self.assertEqual(obs, exp)
++
++ obs = _strip_spaces(SomethingToInterpolate.dont_interpolate_me.__doc__)
++ exp = ("First line\nSome description of things, also this:\nOther things "
++ "are happening now.\n")
++ self.assertEqual(obs, exp)
++
++ obs = _strip_spaces(Subclass.interpolate_me.__doc__)
++ exp = ("First line\nSome description of things, also this:\n'a'\nx\n'b'\ny\n"
++ "'c'\nz\n'o'\np\nOther things are happening now.\n")
++ self.assertEqual(obs, exp)
++
++ obs = _strip_spaces(Subclass.dont_interpolate_me.__doc__)
++ exp = ("First line\nSome description of things, also this:\nOther things "
++ "are happening now.\n")
++ self.assertEqual(obs, exp)
+
+
+ class ResolveKeyTests(unittest.TestCase):
=====================================
debian/patches/series
=====================================
@@ -5,3 +5,4 @@ no_privacy_breach_logo.patch
local_inventory
docs-no-version-switch
0007-Fix-cython-segmentation-error-2090.patch
+45127698e270024bacb670cdd0bd2e4850104b6f.patch
View it on GitLab: https://salsa.debian.org/med-team/python-skbio/-/commit/1cdaed1edf1d4ec5c9086ca666e064821a13bf6f
--
View it on GitLab: https://salsa.debian.org/med-team/python-skbio/-/commit/1cdaed1edf1d4ec5c9086ca666e064821a13bf6f
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