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 <[email protected]> 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 <[email protected]> +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 You're receiving this email because of your account on salsa.debian.org.
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