[med-svn] [Git][med-team/python-skbio][master] 3 commits: Explicitly specify mode="rb" in GzipCompressor.get_reader Closes: #1146889

[Andreas Tille (@tille)]

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


Commits:
5bbbb38c by Andreas Tille at 2026-09-09T13:49:58+02:00
Explicitly specify mode="rb" in GzipCompressor.get_reader Closes: #1146889

- - - - -
58f1d8b7 by Andreas Tille at 2026-09-09T13:52:54+02:00
Simplify d/salsa-ci.yml

- - - - -
784ecb03 by Andreas Tille at 2026-09-09T14:02:48+02:00
Upload to unstable

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4 changed files:

- debian/changelog
- + debian/patches/fix-gzip-reader-mode.patch
- debian/patches/series
- debian/salsa-ci.yml


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,14 @@
+python-skbio (0.7.3-2) unstable; urgency=medium
+
+  [ Maximiliano Curia ]
+  * Explicitly specify mode="rb" in GzipCompressor.get_reader
+    Closes: #1146889
+
+  [ Andreas Tille ]
+  * Simplify d/salsa-ci.yml
+
+ -- Andreas Tille <tille at debian.org>  Wed, 09 Sep 2026 13:52:58 +0200
+
 python-skbio (0.7.3-1) unstable; urgency=medium
 
   [ Karsten Schöke ]


=====================================
debian/patches/fix-gzip-reader-mode.patch
=====================================
@@ -0,0 +1,18 @@
+Author: Maximiliano Curia <maxy at debian.org>
+Last-Update: 2026-09-06
+Description: Explicitly specify mode="rb" in GzipCompressor.get_reader
+ GzipFile without explicit mode defaults to fileobj.mode (e.g. 'w+b' for
+ temporary files), causing it to open for writing instead of reading.
+Bug-Debian: https://bugs.debian.org/1146889
+
+--- a/skbio/io/_iosources.py
++++ b/skbio/io/_iosources.py
+@@ -215,7 +215,7 @@ class GzipCompressor(Compressor):
+         return self.file.peek(2)[:2] == b"\x1f\x8b"
+ 
+     def get_reader(self):
+-        return gzip.GzipFile(fileobj=self.file)
++        return gzip.GzipFile(fileobj=self.file, mode="rb")
+ 
+     def get_writer(self):
+         return gzip.GzipFile(


=====================================
debian/patches/series
=====================================
@@ -3,3 +3,4 @@ Fix-missing-variable-declarations-in-Cython-code.patch
 remove-google-analytics_id.patch
 set-expliziet-mathjax_path.patch
 Use-setuptools-package-discovery-for-all-scikit-bio-modul.patch
+fix-gzip-reader-mode.patch


=====================================
debian/salsa-ci.yml
=====================================
@@ -1,9 +1,6 @@
-# https://salsa.debian.org/salsa-ci-team/pipeline#advanced-use
-
 ---
 include:
-  - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml
-  - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml
+  - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/recipes/debian.yml
 
 variables:
   # Build against scipy 1.10 in experimental



View it on GitLab: https://salsa.debian.org/med-team/python-skbio/-/compare/f0417d31dca95090b3437cab2693bed6f9702cf4...784ecb03b47c3d59ba6f16f8a5c454a7e89d8323

-- 
View it on GitLab: https://salsa.debian.org/med-team/python-skbio/-/compare/f0417d31dca95090b3437cab2693bed6f9702cf4...784ecb03b47c3d59ba6f16f8a5c454a7e89d8323
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