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Linting fix for W605 #888

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Merged
mvdbeek merged 2 commits into from
Nov 8, 2018
Merged

Linting fix for W605 #888

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5d59002
use strin gliteral prefix for regex
martenson Nov 7, 2018
30292a4
prefix the rest of the regexes
martenson Nov 7, 2018
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2 changes: 1 addition & 1 deletion planemo/bioconda_scripts/bioconductor_skeleton.py
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Original file line number Diff line number Diff line change
Expand Up @@ -120,7 +120,7 @@ def bioaRchive_url(self):
@property
def bioconductor_tarball_url(self):
"""Return the url to the tarball from the bioconductor site."""
r = re.compile('{0}.*\.tar.gz'.format(self.package))
r = re.compile(r'{0}.*\.tar.gz'.format(self.package))

def f(href):
return href and r.search(href)
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2 changes: 1 addition & 1 deletion planemo/galaxy/run.py
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Expand Up @@ -19,7 +19,7 @@
'if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then $create_virtualenv; fi',
)
PRINT_VENV_COMMAND = shell_join(
'echo "Set \$GALAXY_VIRTUAL_ENV to $GALAXY_VIRTUAL_ENV"',
r'echo "Set \$GALAXY_VIRTUAL_ENV to $GALAXY_VIRTUAL_ENV"',
('if [ -e "$GALAXY_VIRTUAL_ENV" ]; ',
'then echo "Virtual environment directory exists."; ',
'else echo "Virtual environment directory does not exist."; fi'),
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2 changes: 1 addition & 1 deletion planemo/rscript_parse.py
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Expand Up @@ -62,7 +62,7 @@ def __init__(self, script):
def _prune_library(self, line):
"""Prune line to get the names in library."""
import re
split_words = re.compile('\w+').findall(line)
split_words = re.compile(r'\w+').findall(line)
lib = [w for w in split_words if w != "library"]
return lib[0]

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4 changes: 2 additions & 2 deletions planemo/shed/__init__.py
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Expand Up @@ -95,8 +95,8 @@
REPO_TYPE_SUITE = "repository_suite_definition"

# TODO: sync this with tool shed impl someday
VALID_REPOSITORYNAME_RE = re.compile("^[a-z0-9\_]+$")
VALID_PUBLICNAME_RE = re.compile("^[a-z0-9\-]+$")
VALID_REPOSITORYNAME_RE = re.compile(r"^[a-z0-9\_]+$")
VALID_PUBLICNAME_RE = re.compile(r"^[a-z0-9\-]+$")

# Generate with python scripts/categories.py
CURRENT_CATEGORIES = [
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4 changes: 2 additions & 2 deletions planemo/tool_builder.py
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Expand Up @@ -836,9 +836,9 @@ def __str__(self):


def param_type(value):
if re.match("^\d+$", value):
if re.match(r"^\d+$", value):
return "int"
elif re.match("^\d+?\.\d+?$", value):
elif re.match(r"^\d+?\.\d+?$", value):
return "float"
else:
return "string"
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6 changes: 3 additions & 3 deletions planemo/training/tutorial.py
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Expand Up @@ -258,7 +258,7 @@ def init_from_existing_tutorial(self, tuto_name):
# get the metadata information of the tutorial (from the top of the tutorial.md)
with open(self.tuto_fp, "r") as tuto_f:
tuto_content = tuto_f.read()
regex = '^---\n(?P<metadata>[\s\S]*)\n---(?P<body>[\s\S]*)'
regex = r'^---\n(?P<metadata>[\s\S]*)\n---(?P<body>[\s\S]*)'
tuto_split_regex = re.search(regex, tuto_content)
if not tuto_split_regex:
raise Exception("No metadata found at the top of the tutorial")
Expand Down Expand Up @@ -507,9 +507,9 @@ def get_wf_inputs(step_inp):
inputs = {}
for inp_n, inp in step_inp.items():
if '|' in inp_n:
repeat_regex = '(?P<prefix>[^\|]*)_(?P<nb>\d+)\|(?P<suffix>.+).+'
repeat_regex = r'(?P<prefix>[^\|]*)_(?P<nb>\d+)\|(?P<suffix>.+).+'
repeat_search = re.search(repeat_regex, inp_n)
hier_regex = '(?P<prefix>[^\|]*)\|(?P<suffix>.+)'
hier_regex = r'(?P<prefix>[^\|]*)\|(?P<suffix>.+)'
hier_regex = re.search(hier_regex, inp_n)
if repeat_search and repeat_search.start(0) <= hier_regex.start(0):
inputs.setdefault(repeat_search.group('prefix'), {})
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