Your message dated Mon, 9 Dec 2024 20:26:06 +0100
with message-id <[email protected]>
and subject line Simply closing bug Python SyntaxWarning since not present in
current upstream version any more
has caused the Debian Bug report #1085745,
regarding obitools: Python SyntaxWarning
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
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--
1085745: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1085745
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: obitools
Version: 1.2.13+dfsg-9
User: [email protected]
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*) *= *([^;]+);'):
--- End Message ---
--- Begin Message ---
Simply closing bug Python SyntaxWarning since not present in current upstream
version any more.
--- End Message ---
