#1120294 python3-biom-format: possibly vendors old numpydoc with SyntaxWarning

Package:
python3-biom-format
Source:
python3-biom-format
Description:
Biological Observation Matrix (BIOM) format (Python 3)
Submitter:
Alexandre Detiste
Date:
2026-08-10 07:35:02 UTC
Severity:
normal
#1120294#5
Date:
2025-11-07 06:41:59 UTC
From:
To:
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('*', '\*')

#1120294#10
Date:
2026-08-10 07:33:41 UTC
From:
To:
 The bug has been fixed in version 2.1.17-4, which has already been uploaded.