[Debian-med-packaging] Bug#1085900: python-csb: Python SyntaxWarning

[Graham Inggs]

Source: python-csb
Version: 1.2.5+dfsg-10
User: debian-python at lists.debian.org
Usertags: syntaxwarning

Hi Maintainer

The SyntaxWarning below were emitted when this package was tested with
pipuarts[1].

Regards
Graham


[1] https://piuparts.debian.org/sid/source/p/python-csb.html


  Setting up python3-csb (1.2.5+dfsg-10) ...
  /usr/lib/python3/dist-packages/csb/bio/io/hhpred.py:210:
SyntaxWarning: invalid escape sequence '\d'
    m = re.search('(\d+)\D+(\d+)', line).groups()
  /usr/lib/python3/dist-packages/csb/bio/io/hhpred.py:260:
SyntaxWarning: invalid escape sequence '\s'
    seq = re.sub('\s+', '', ''.join(lines[1:]))
  /usr/lib/python3/dist-packages/csb/bio/io/hhpred.py:307:
SyntaxWarning: invalid escape sequence '\-'
    pattern = re.compile('^[A-Z\-]\s[0-9]+\s+')
  /usr/lib/python3/dist-packages/csb/bio/io/procheck.py:31:
SyntaxWarning: invalid escape sequence '\s'
    input_file_name = re.compile('>>>-----.*?\n.*?\n\s*\|\s*(\S+)\s+')
  /usr/lib/python3/dist-packages/csb/bio/io/procheck.py:32:
SyntaxWarning: invalid escape sequence '\d'
    residues = re.compile('(\d+)\s*residues\s\|')
  /usr/lib/python3/dist-packages/csb/bio/io/procheck.py:33:
SyntaxWarning: invalid escape sequence '\s'
    ramachandran_plot = re.compile('Ramachandran\splot:\s*(\d+\.\d+)' +
  /usr/lib/python3/dist-packages/csb/bio/io/procheck.py:34:
SyntaxWarning: invalid escape sequence '\s'
    '%\s*core\s*(\d+\.\d+)%\s*allow\s*(\d+\.\d+)' +
  /usr/lib/python3/dist-packages/csb/bio/io/procheck.py:35:
SyntaxWarning: invalid escape sequence '\s'
    '%\s*gener\s*(\d+\.\d+)%\s*disall')
  /usr/lib/python3/dist-packages/csb/bio/io/procheck.py:36:
SyntaxWarning: invalid escape sequence '\s'
    labelled_all = re.compile('Ramachandrans:\s*(\d+)\s*.*?out\sof\s*(\d+)')
  /usr/lib/python3/dist-packages/csb/bio/io/procheck.py:37:
SyntaxWarning: invalid escape sequence '\s'
    labelled_chi = re.compile('Chi1-chi2\splots:\s*(\d+)\s*.*?out\sof\s*(\d+)')
  /usr/lib/python3/dist-packages/csb/bio/io/procheck.py:38:
SyntaxWarning: invalid escape sequence '\s'
    bad_contacts = re.compile('Bad\scontacts:\s*(\d+)')
  /usr/lib/python3/dist-packages/csb/bio/io/procheck.py:39:
SyntaxWarning: invalid escape sequence '\s'
    g_factors = re.compile('G-factors\s*Dihedrals:\s*([0-9-+.]+)' +
  /usr/lib/python3/dist-packages/csb/bio/io/procheck.py:40:
SyntaxWarning: invalid escape sequence '\s'
    '\s*Covalent:\s*([0-9-+.]+)\s*Overall:\s*([0-9-+.]+)')
  /usr/lib/python3/dist-packages/csb/bio/io/whatif.py:32:
SyntaxWarning: invalid escape sequence '\s'
    re_ramachandran = re.compile('Ramachandran\s*Z-score\s*:\s*([0-9.Ee-]+)')
  /usr/lib/python3/dist-packages/csb/bio/io/whatif.py:33:
SyntaxWarning: invalid escape sequence '\s'
    re_1st = re.compile('1st\s*generation\s*packing\s*quality\s*:\s*([0-9.Ee-]+)')
  /usr/lib/python3/dist-packages/csb/bio/io/whatif.py:34:
SyntaxWarning: invalid escape sequence '\s'
    re_2nd = re.compile('2nd\s*generation\s*packing\s*quality\s*:\s*([0-9.Ee-]+)')
  /usr/lib/python3/dist-packages/csb/bio/io/whatif.py:35:
SyntaxWarning: invalid escape sequence '\s'
    re_backbone =
re.compile('Backbone\s*conformation\s*Z-score\s*:\s*([0-9.Ee-]+)')
  /usr/lib/python3/dist-packages/csb/bio/io/whatif.py:36:
SyntaxWarning: invalid escape sequence '\S'
    re_rotamer =
re.compile('chi-1\S*chi-2\s*rotamer\s*normality\s*:\s*([0-9.Ee-]+)')
  /usr/lib/python3/dist-packages/csb/bio/io/wwpdb.py:1222:
SyntaxWarning: invalid escape sequence '\d'
    res = re.search("(\d+(?:\.\d+)?)\s+ANGSTROM", line)
  /usr/lib/python3/dist-packages/csb/bio/sequence/__init__.py:566:
SyntaxWarning: invalid escape sequence '\w'
    self._residues += re.sub('([^\w\-\.])+', '', string)
  /usr/lib/python3/dist-packages/csb/bio/structure/__init__.py:2129:
SyntaxWarning: invalid escape sequence '\s'
    string = ''.join(re.split('\s+', string))
  /usr/lib/python3/dist-packages/csb/bio/structure/__init__.py:2131:
SyntaxWarning: invalid escape sequence '\s'
    conf_string = ''.join(re.split('\s+', conf_string))
  /usr/lib/python3/dist-packages/csb/statistics/__init__.py:341:
SyntaxWarning: invalid escape sequence '\s'
    """
  /usr/lib/python3/dist-packages/csb/test/cases/io/__init__.py:482:
SyntaxWarning: invalid escape sequence '\w'
    "([0-9a-zA-Z]([-.\w]*[0-9a-zA-Z])"]