[Debian-med-packaging] Bug#1085745: obitools: Python SyntaxWarning

[Graham Inggs]

Source: obitools
Version: 1.2.13+dfsg-9
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/o/obitools.html


  Setting up obitools (1.2.13+dfsg-9+b1) ...
  /usr/lib/python3/dist-packages/obitools/align/ssearch.py:9:
SyntaxWarning: invalid escape sequence '\d'
    _matchLQuery = re.compile("^Query:.+\n.+?(\d+)(?= nt\n)", re.MULTILINE)
  /usr/lib/python3/dist-packages/obitools/alignment/ace.py:11:
SyntaxWarning: invalid escape sequence '\S'
    _contigIterator.addParseAction('AF', '\nAF +(\S+) +([UC]) +(-?[0-9]+)')
  /usr/lib/python3/dist-packages/obitools/alignment/ace.py:12:
SyntaxWarning: invalid escape sequence '\S'
    _contigIterator.addParseAction('RD', '\nRD +(\S+) +([0-9]+)
+([0-9]+) +([0-9]+) *\n([A-Za-z\n*]+?)\n\n')
  /usr/lib/python3/dist-packages/obitools/alignment/ace.py:14:
SyntaxWarning: invalid escape sequence '\S'
    _contigIterator.addParseAction('CO',  '^CO (\S+)')
  /usr/lib/python3/dist-packages/obitools/fnaqual/__init__.py:2:
SyntaxWarning: invalid escape sequence '\s'
    fnaTag=' %s *= *([^\s]+)'
  /usr/lib/python3/dist-packages/obitools/location/__init__.py:479:
SyntaxWarning: invalid escape sequence '\.'
    __simplelocparser =
re.compile('(?P<before><?)(?P<from>[0-9]+)(\.\.(?P<after>>?)(?P<to>[0-9]+))?')
  /usr/lib/python3/dist-packages/obitools/location/__init__.py:523:
SyntaxWarning: invalid escape sequence '\.'
    _matchExternalRef = re.compile('[A-Za-z0-9_|]+(\.[0-9]+)?(?=:)')
  /usr/lib/python3/dist-packages/obitools/location/feature.py:67:
SyntaxWarning: invalid escape sequence '\S'
    _ftmatcher = re.compile('(?<=^ {5})\S+')
  /usr/lib/python3/dist-packages/obitools/location/feature.py:69:
SyntaxWarning: invalid escape sequence '\s'
    _cleanloc  = re.compile('[\s\n]+')
  /usr/lib/python3/dist-packages/obitools/obo/parser.py:54:
SyntaxWarning: invalid escape sequence '\ '
    _match_brace = re.compile('(?<=\ {)[^\]]*(\}) *( !|$)')
  /usr/lib/python3/dist-packages/obitools/obo/parser.py:102:
SyntaxWarning: invalid escape sequence '\['
    _match_bracket = re.compile('\[[^\]]*\]')
  /usr/lib/python3/dist-packages/obitools/obo/parser.py:230:
SyntaxWarning: invalid escape sequence '\['
    _match_scope = re.compile('(?<="")[^\[]*(?=\[|$)')
  /usr/lib/python3/dist-packages/obitools/obo/parser.py:520:
SyntaxWarning: invalid escape sequence '\['
    _match_stanza_name = re.compile('(?<=^\[)[^\]]*(?=\])')
  /usr/lib/python3/dist-packages/obitools/phylogeny/newick.py:25:
SyntaxWarning: invalid escape sequence '\s'
    _nodeParser=re.compile('\s*(?P<subnodes>\(.*\))?(?P<name>[^ :]+)?
*(?P<bootstrap>[0-9.]+)?(:(?P<distance>-?[0-9.]+))?')
  /usr/lib/python3/dist-packages/obitools/phylogeny/newick.py:47:
SyntaxWarning: invalid escape sequence '\s'
    _cleanTreeData=re.compile('\s+')
  /usr/lib/python3/dist-packages/obitools/phylogeny/newick.py:73:
SyntaxWarning: invalid escape sequence '\['
    _treecomment=re.compile('\[.*\]')
  /usr/lib/python3/dist-packages/obitools/table/csv.py:25:
SyntaxWarning: invalid escape sequence '\s'
    valueMatcher=re.compile('\s*((")(([^"]|"")*)"|([^%s]*?))\s*(%s|$)'
% (sep,sep))
  /usr/lib/python3/dist-packages/obitools/tagmatcher/parser.py:11:
SyntaxWarning: invalid escape sequence '\('
    _loMatcher     = re.compile('(?<=LO   ) *([ACGTRYMKWSBDHVN]+) +([^
]+) +([^ ]+) +\(([0-9]+)\)')
  /usr/lib/python3/dist-packages/obitools/tree/newick.py:25:
SyntaxWarning: invalid escape sequence '\s'
    _nodeParser=re.compile('\s*(?P<subnodes>\(.*\))?(?P<name>[^ :]+)?
*(?P<bootstrap>[0-9.]+)?(:(?P<distance>-?[0-9.]+))?')
  /usr/lib/python3/dist-packages/obitools/tree/newick.py:47:
SyntaxWarning: invalid escape sequence '\s'
    _cleanTreeData=re.compile('\s+')
  /usr/lib/python3/dist-packages/obitools/tree/newick.py:67:
SyntaxWarning: invalid escape sequence '\['
    _treecomment=re.compile('\[.*\]')
  /usr/lib/python3/dist-packages/obitools/utils/__init__.py:192:
SyntaxWarning: invalid escape sequence '\w'
    extraformat='([a-zA-Z]\w*) *= *([^;]+);'):