[med-svn] [Git][med-team/python-skbio][master] 3 commits: Take over changes from NMU

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Med / python-skbio


Commits:
a5b59c09 by Andreas Tille at 2023-12-10T11:16:28+01:00
Take over changes from NMU

- - - - -
6e807695 by Andreas Tille at 2023-12-10T11:25:30+01:00
Fix patch

- - - - -
a5265a38 by Andreas Tille at 2023-12-10T11:35:43+01:00
Upload to unstable

- - - - -


5 changed files:

- debian/changelog
- debian/control
- debian/patches/local_inventory
- + debian/patches/python3.12-xfail-tests.patch
- debian/patches/series


Changes:

=====================================
debian/changelog
=====================================
@@ -1,11 +1,19 @@
-python-skbio (0.5.9-1) UNRELEASED; urgency=medium
+python-skbio (0.5.9-1) unstable; urgency=medium
 
   * New upstream version
   * Build-Depends: s/dh-python/dh-sequence-python3/ (routine-update)
   * Remove patch numpy-1.24_32bit.patch that is missing from debian/patches/series.
   * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository, Repository-Browse.
 
- -- Andreas Tille <tille at debian.org>  Sat, 09 Dec 2023 10:31:25 +0100
+ -- Andreas Tille <tille at debian.org>  Sun, 10 Dec 2023 11:16:54 +0100
+
+python-skbio (0.5.8-4.1) unstable; urgency=medium
+
+  * Non-maintainer upload
+  * Xfail tests known to fail with Python 3.12, see #1056047
+  * Build with cython3-legacy for now (Closes: #1056873)
+
+ -- Graham Inggs <ginggs at debian.org>  Sun, 10 Dec 2023 07:58:34 +0000
 
 python-skbio (0.5.8-4) unstable; urgency=medium
 


=====================================
debian/control
=====================================
@@ -5,7 +5,7 @@ Uploaders: Andreas Tille <tille at debian.org>,
 Section: python
 Priority: optional
 Build-Depends: debhelper-compat (= 13),
-               cython3,
+               cython3-legacy,
                dh-sequence-python3,
                python3-all-dev,
                python3-setuptools,


=====================================
debian/patches/local_inventory
=====================================
@@ -8,7 +8,7 @@ Forwarded: not-needed
  # -----------------------------------------------------------------------------
  intersphinx_mapping = {
 -        'Python': ('http://docs.python.org/dev', None),
-+        'Python': ('http://docs.python.org/dev', '/usr/share/doc/python{}.{}/html/objects.inv'.format(*sys.version_info[:2]),
++        'Python': ('http://docs.python.org/dev', '/usr/share/doc/python{}.{}/html/objects.inv'.format(*sys.version_info[:2])),
          'NumPy': ('http://docs.scipy.org/doc/numpy', None),
 -        'SciPy': ('http://docs.scipy.org/doc/scipy/reference', None),
 +        'SciPy': ('http://docs.scipy.org/doc/scipy/reference', '/usr/share/doc/python-scipy-doc/html/objects.inv'),


=====================================
debian/patches/python3.12-xfail-tests.patch
=====================================
@@ -0,0 +1,48 @@
+Description: xfail tests known to fail with Python 3.12
+Bug: https://github.com/scikit-bio/scikit-bio/issues/1897
+Bug-Debian: https://bugs.debian.org/1056047
+Author: Graham Inggs <ginggs at debian.org>
+Last-Update: 2023-11-20
+
+--- a/skbio/io/tests/test_util.py
++++ b/skbio/io/tests/test_util.py
+@@ -11,6 +11,7 @@
+ import shutil
+ import io
+ import os.path
++import pytest
+ 
+ try:
+     import httpretty
+@@ -336,6 +337,7 @@
+         self.assertEqual(self.get_contents(self.binary_file),
+                          self.binary_contents)
+ 
++    @pytest.mark.xfail
+     def test_open_gzip(self):
+         self.check_open_state_contents(self.gzip_file, self.text_contents,
+                                        False, compression='gzip')
+@@ -357,6 +359,7 @@
+         self.assertEqual(self.get_contents(self.big5_file),
+                          self.encoded_contents)
+ 
++    @pytest.mark.xfail
+     def test_open_gzip_encoding(self):
+         self.check_open_state_contents(self.gzip_encoded_file,
+                                        self.decoded_contents, False,
+@@ -486,6 +489,7 @@
+     def get_contents(self, file):
+         return file.getvalue()
+ 
++    @pytest.mark.xfail
+     def test_open_gzip(self):
+         self.check_open_state_contents(self.gzip_file, self.text_contents,
+                                        False, compression='gzip')
+@@ -493,6 +497,7 @@
+         self.compare_gzip_file_contents(self.get_contents(self.gzip_file),
+                                         self.gzip_contents)
+ 
++    @pytest.mark.xfail
+     def test_open_gzip_encoding(self):
+         self.check_open_state_contents(self.gzip_encoded_file,
+                                        self.decoded_contents, False,


=====================================
debian/patches/series
=====================================
@@ -6,3 +6,4 @@ local_inventory
 #older-scipy.patch
 modify-test.patch
 numpy-1.24.patch
+python3.12-xfail-tests.patch



View it on GitLab: https://salsa.debian.org/med-team/python-skbio/-/compare/e0d98b5376728c4f57b1aca5747192b4f9a01a1f...a5265a38e22b3686ca1411291ef07e3f584cce7e

-- 
View it on GitLab: https://salsa.debian.org/med-team/python-skbio/-/compare/e0d98b5376728c4f57b1aca5747192b4f9a01a1f...a5265a38e22b3686ca1411291ef07e3f584cce7e
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