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 - - - - - 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 <[email protected]> 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 <[email protected]> +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 You're receiving this email because of your account on salsa.debian.org. Manage all notifications: https://salsa.debian.org/-/profile/notifications | Help: https://salsa.debian.org/help
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