[Debian-med-packaging] Bug#1120294: python3-biom-format: possibly vendors old numpydoc with SyntaxWarning

[Alexandre Detiste]

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