Your message dated Mon, 10 Aug 2026 07:33:41 +0000
with message-id <[email protected]>
and subject line Subject: Fixed in 2.1.17-4
has caused the Debian Bug report #1120294,
regarding python3-biom-format: possibly vendors old numpydoc with SyntaxWarning
to be marked as done.
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--
1120294: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1120294
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: python3-biom-format
Version: 2.1.17-1
Severity: normal
Hi,
I got some SyntaxWarning when installing python3-biom-format.
These files looks like vendored copies of numpydoc.
At worst the filenames down /usr/lib/python3/dist-packages/doc/sphinxext/ could
clash
and makes this not installable with the real numpydoc.
Please se if these files could be de-vendored.
Greetings
Alexandre
https://github.com/biocore/biom-format/blob/master/doc/sphinxext/numpydoc/numpydoc/docscrape.py
Paramétrage de python3-biom-format (2.1.17-1) ...
/usr/lib/python3/dist-packages/doc/sphinxext/numpydoc/numpydoc/docscrape.py:274:
SyntaxWarning: invalid escape sequence '\w'
if re.compile('^([\w., ]+=)?\s*[\w\.]+\(.*\)$').match(summary_str):
/usr/lib/python3/dist-packages/doc/sphinxext/numpydoc/numpydoc/docscrape.py:316:
SyntaxWarning: invalid escape sequence '\*'
return [self['Signature'].replace('*','\*')] + ['']
/usr/lib/python3/dist-packages/doc/sphinxext/numpydoc/numpydoc/docscrape.py:438:
SyntaxWarning: invalid escape sequence '\*'
argspec = argspec.replace('*','\*')
/usr/lib/python3/dist-packages/doc/sphinxext/numpydoc/numpydoc/docscrape.py:456:
SyntaxWarning: invalid escape sequence '\*'
signature = self['Signature'].replace('*', '\*')
/usr/lib/python3/dist-packages/doc/sphinxext/numpydoc/numpydoc/docscrape.py:274:
SyntaxWarning: "\w" is an invalid escape sequence. Such sequences will not
work in the future. Did you mean "\\w"? A raw string is also an option.
if re.compile('^([\w., ]+=)?\s*[\w\.]+\(.*\)$').match(summary_str):
/usr/lib/python3/dist-packages/doc/sphinxext/numpydoc/numpydoc/docscrape.py:316:
SyntaxWarning: "\*" is an invalid escape sequence. Such sequences will not
work in the future. Did you mean "\\*"? A raw string is also an option.
return [self['Signature'].replace('*','\*')] + ['']
/usr/lib/python3/dist-packages/doc/sphinxext/numpydoc/numpydoc/docscrape.py:438:
SyntaxWarning: "\*" is an invalid escape sequence. Such sequences will not
work in the future. Did you mean "\\*"? A raw string is also an option.
argspec = argspec.replace('*','\*')
/usr/lib/python3/dist-packages/doc/sphinxext/numpydoc/numpydoc/docscrape.py:456:
SyntaxWarning: "\*" is an invalid escape sequence. Such sequences will not
work in the future. Did you mean "\\*"? A raw string is also an option.
signature = self['Signature'].replace('*', '\*')
-- System Information:
Debian Release: forky/sid
APT prefers testing
APT policy: (501, 'testing'), (450, 'unstable'), (400, 'experimental')
Architecture: amd64 (x86_64)
Foreign Architectures: i386
Kernel: Linux 6.16.12+deb14+1-amd64 (SMP w/4 CPU threads; PREEMPT)
Locale: LANG=fr_BE.UTF-8, LC_CTYPE=fr_BE.UTF-8 (charmap=UTF-8),
LANGUAGE=fr_BE:fr
Shell: /bin/sh linked to /usr/bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled
Versions of packages python3-biom-format depends on:
ii libc6 2.41-12
ii python3 3.13.7-2
ii python3-click 8.2.0+0.really.8.1.8-1
ii python3-h5py 3.15.1-3
ii python3-numpy [python3-numpy2-abi0] 1:2.3.4+ds-3
ii python3-pandas 2.3.3+dfsg-2
ii python3-scipy 1.15.3-1.1
python3-biom-format recommends no packages.
Versions of packages python3-biom-format suggests:
pn python-biom-format-doc <none>
-- no debconf information
--- End Message ---
--- Begin Message ---
The bug has been fixed in version 2.1.17-4, which has already been uploaded.
--- End Message ---
