Prefix escaped strings with 'r'

This includes regexes as well as doc strings.
Also filter deprecation warnings from tox output where possible
to capture files that we cannot alter (e.g. `past.util.misc`)

pytest.ini

@@ -7,5 +7,5 @@ markers =
 ##    error::DeprecationWarning
 # Tests which will raise a deprecation warning should be updated
 # to use `pytest.deprecated_call(method, *args)`
- filterwarnings =
+filterwarnings =
     ignore::DeprecationWarning

src/omero/cli.py

@@ -99,9 +99,9 @@
 
 OMERO_COMPONENTS = ['common', 'model', 'romio', 'renderer', 'server', 'blitz']
 
-COMMENT = re.compile("^\s*#")
-RELFILE = re.compile("^\w")
-LINEWSP = re.compile("^\s*\w+\s+")
+COMMENT = re.compile(r"^\s*#")
+RELFILE = re.compile(r"^\w")
+LINEWSP = re.compile(r"^\s*\w+\s+")
 
 #
 # Possibilities:
@@ -1101,10 +1101,10 @@ def _exists(self, p):
             elif not p.size:
                 self.ctx.out("empty")
             else:
-                warn_regex = ('(-! )?[\d\-/]+\s+[\d:,.]+\s+([\w.]+:\s+)?'
-                              'warn(i(ng:)?)?\s')
-                err_regex = ('(!! )?[\d\-/]+\s+[\d:,.]+\s+([\w.]+:\s+)?'
-                             'error:?\s')
+                warn_regex = (r'(-! )?[\d\-/]+\s+[\d:,.]+\s+([\w.]+:\s+)?'
+                              r'warn(i(ng:)?)?\s')
+                err_regex = (r'(!! )?[\d\-/]+\s+[\d:,.]+\s+([\w.]+:\s+)?'
+                             r'error:?\s')
                 warn = 0
                 err = 0
                 for l in p.lines():
@@ -1203,7 +1203,7 @@ def __call__(self, args):
         class CD(BaseControl):
 
             def _complete(self, text, line, begidx, endidx):
-                RE = re.compile("\s*cd\s*")
+                RE = re.compile(r"\s*cd\s*")
                 m = RE.match(line)
                 if m:
                     replaced = RE.sub('', line)

src/omero/clients.py

@@ -325,10 +325,10 @@ def _check_for_hosturl(self, host, port, pmap):
             return {}
 
         hostmatch = re.match(
-            '(?P<protocol>\\w+)://'
-            '(?P<server>[^:/]+)'
-            '(:(?P<port>\\d+))?'
-            '(?P<path>/.*)?$',
+            r'(?P<protocol>\\w+)://'
+            r'(?P<server>[^:/]+)'
+            r'(:(?P<port>\\d+))?'
+            r'(?P<path>/.*)?$',
             host)
 
         if hostmatch:

src/omero/gateway/__init__.py

@@ -2750,7 +2750,7 @@ def canCreate(self):
                   False if the server is wholly in read-only mode,
                   otherwise None
         """
-        key_regex = '^omero\.cluster\.read_only\.runtime\.'
+        key_regex = r'^omero\.cluster\.read_only\.runtime\.'
         properties = self.getConfigService().getConfigValues(key_regex)
         values = frozenset(list(properties.values()))
         if not values:
@@ -4702,7 +4702,7 @@ def debug(self, exc_class, args, kwargs):
                     args, kwargs, exc_info=True)
 
     def handle_exception(self, e, *args, **kwargs):
-        """
+        r"""
         Exception handler that is expected to be overridden by sub-classes.
         The expected behaviour is either to handle a type of exception and
         return the server side result or to raise the already thrown

src/omero/install/logs_library.py

@@ -178,7 +178,7 @@ def draw(self, renderer):
 
 def plot_threads(watcher, all_colors=("blue", "red", "yellow", "green",
                                       "pink", "purple")):
-    digit = re.compile(".*(\d+).*")
+    digit = re.compile(r".*(\d+).*")
 
     fig = plt.figure()
     ax = fig.add_subplot(111)

src/omero/install/perf_test.py

@@ -25,7 +25,7 @@
 import omero.util.temp_files
 import uuid
 
-command_pattern = "^\s*(\w+)(\((.*)\))?(:(.*))?$"
+command_pattern = r"^\s*(\w+)(\((.*)\))?(:(.*))?$"
 command_pattern_compiled = re.compile(command_pattern)
 log = logging.getLogger("omero.perf")
 

src/omero/install/versions.py

@@ -13,7 +13,7 @@
 import logging
 
 # Regex copied from ome.api.IConfig.VERSION_REGEX
-REGEX = re.compile("^.*?[-]?(\\d+[.]\\d+([.]\\d+)?)[-]?.*?$")
+REGEX = re.compile(r"^.*?[-]?(\\d+[.]\\d+([.]\\d+)?)[-]?.*?$")
 LOG = logging.getLogger("omero.version")
 
 

src/omero/plugins/admin.py

@@ -124,7 +124,7 @@ def _configure(self, parser):
             "BAD_CONFIG", 300,
             "Bad configuration: No IceGrid.Node.Data property")
         self.add_error(
-            "WIN_CONFIG", 400, """
+            "WIN_CONFIG", 400, r"""
 
             %s is not in this directory. Aborting...
 
@@ -717,7 +717,7 @@ def _descript(self, args):
         return descript
 
     def checkwindows(self, args):
-        """
+        r"""
         Checks that the templates file as defined in etc\Windows.cfg
         can be found.
         """
@@ -1230,7 +1230,7 @@ def version(cmd):
                 v = io[0].split()
                 v.extend(io[1].split())
                 v = "".join(v)
-                m = re.match("^\D*(\d[.\d]+\d)\D?.*$", v)
+                m = re.match(r"^\D*(\d[.\d]+\d)\D?.*$", v)
                 v = "%-10s" % m.group(1)
                 self.ctx.out(v, False)
                 try:
@@ -1272,12 +1272,12 @@ def get_ports(input):
             tcp_port = None
             for line in router_lines:
                 if not ssl_port and line.find("ROUTERPORT") >= 0:
-                    m = re.match(".*?(\d+).*?$", line)
+                    m = re.match(r".*?(\d+).*?$", line)
                     if m:
                         ssl_port = m.group(1)
 
                 if not tcp_port and line.find("INSECUREROUTER") >= 0:
-                    m = re.match("^.*?-p (\d+).*?$", line)
+                    m = re.match(r"^.*?-p (\d+).*?$", line)
                     if m:
                         tcp_port = m.group(1)
             return ssl_port, tcp_port
@@ -1367,15 +1367,15 @@ def parse_logs():
             self.ctx.out("")
 
             # Parsing well known issues
-            ready = re.compile(".*?ome.services.util.ServerVersionCheck\
+            ready = re.compile(r".*?ome.services.util.ServerVersionCheck\
             .*OMERO.Version.*Ready..*?")
-            db_ready = re.compile(".*?Did.you.create.your.database[?].*?")
-            data_dir = re.compile(".*?Unable.to.initialize:.FullText.*?")
-            pg_password = re.compile(".*?org.postgresql.util.PSQLException:\
+            db_ready = re.compile(r".*?Did.you.create.your.database[?].*?")
+            data_dir = re.compile(r".*?Unable.to.initialize:.FullText.*?")
+            pg_password = re.compile(r".*?org.postgresql.util.PSQLException:\
             .FATAL:.password.*?authentication.failed.for.user.*?")
-            pg_user = re.compile(""".*?org.postgresql.util.PSQLException:\
+            pg_user = re.compile(r""".*?org.postgresql.util.PSQLException:\
             .FATAL:.role.".*?".does.not.exist.*?""")
-            pg_conn = re.compile(""".*?org.postgresql.util.PSQLException:\
+            pg_conn = re.compile(r""".*?org.postgresql.util.PSQLException:\
             .Connection.refused.""")
 
             issues = {

src/omero/plugins/metadata.py

@@ -41,7 +41,7 @@
 
 
 ANNOTATION_TYPES = [t for t in dir(omero.model)
-                    if re.match('[A-Za-z0-9]+Annotation$', t)]
+                    if re.match(r'[A-Za-z0-9]+Annotation$', t)]
 
 
 def guess_mimetype(filename):

src/omero/plugins/obj.py

@@ -41,7 +41,7 @@
 
 class TxField(object):
 
-    ARG_RE = re.compile(("(?P<FIELD>[a-zA-Z][a-zA-Z0-9]*)"
+    ARG_RE = re.compile((r"(?P<FIELD>[a-zA-Z][a-zA-Z0-9]*)"
                          "(?P<OPER>[@])?="
                          "(?P<VALUE>.*)"))
 
@@ -57,7 +57,7 @@ def __init__(self, tx_state, arg):
         self.oper = m.group("OPER")
         if self.oper == "@":
             # Treat value like an array lookup
-            if re.match('\d+$', self.value):
+            if re.match(r'\d+$', self.value):
                 self.value = tx_state.get_row(int(self.value))
             elif re.match(TxCmd.VAR_NAME + '$', self.value):
                 self.value = tx_state.get_var(self.value)
@@ -70,10 +70,10 @@ def __call__(self, obj):
 
 class TxCmd(object):
 
-    VAR_NAME = "(?P<DEST>[a-zA-Z][a-zA-Z0-9]*)"
-    VAR_RE = re.compile(("^\s*%s"
-                         "\s*=\s"
-                         "(?P<REST>.*)$") % VAR_NAME)
+    VAR_NAME = r"(?P<DEST>[a-zA-Z][a-zA-Z0-9]*)"
+    VAR_RE = re.compile((r"^\s*%s"
+                         r"\s*=\s"
+                         r"(?P<REST>.*)$") % VAR_NAME)
 
     def __init__(self, tx_state, arg_list=None, line=None):
         """

src/omero/plugins/script.py

@@ -71,8 +71,8 @@
 print "Finished script"
 """
 
-RE0 = re.compile("\s*script\s+upload\s*")
-RE1 = re.compile("\s*script\s+upload\s+--official\s*")
+RE0 = re.compile(r"\s*script\s+upload\s*")
+RE1 = re.compile(r"\s*script\s+upload\s+--official\s*")
 
 
 class ScriptControl(BaseControl):

src/omero/plugins/sessions.py

@@ -935,7 +935,7 @@ def _parse_conn(server, default_name):
         """Parse a connection string of form (user@)server(:port)"""
 
         import re
-        pat = '^((?P<name>.+)@)?(?P<server>.*?)(:(?P<port>\d{1,5}))?$'
+        pat = r'^((?P<name>.+)@)?(?P<server>.*?)(:(?P<port>\d{1,5}))?$'
         match = re.match(pat, server)
         server = match.group('server')
         name = match.group('name')

src/omero/plugins/upload.py

@@ -28,7 +28,7 @@
     hash_sha1 = sha.new
 
 HELP = """Upload local files to the OMERO server"""
-RE = re.compile("\s*upload\s*")
+RE = re.compile(r"\s*upload\s*")
 UNKNOWN = 'type/unknown'
 
 

src/omero/util/importperf.py

@@ -107,12 +107,12 @@ class ImporterLog(object):
 
     # Regular expression for matching log4j log lines
     log_regex = re.compile(
-        '^(?P<date_time>\S+\s+\S+)\s+(?P<ms_elapsed>\d+)\s+'
+        r'^(?P<date_time>\S+\s+\S+)\s+(?P<ms_elapsed>\d+)\s+'
         '(?P<thread>\[.*?\])\s+(?P<level>\S+)\s+(?P<class>\S+)\s+-\s+'
         '(?P<message>.*)$')
 
     # Regular expression for matching possible OMERO.importer status messages
-    status_regex = re.compile('^[A-Z_]*')
+    status_regex = re.compile(r'^[A-Z_]*')
 
     # Format string for matching log4j date/time strings
     date_time_fmt = '%Y-%m-%d %H:%M:%S'

src/omero/util/metadata_utils.py

@@ -166,8 +166,8 @@ def validate_filled_column_config(cls, cfg):
             raise Exception("Option `position` must be an int")
 
         if cfg["clientvalue"]:
-            subbed = re.sub("\{\{\s*value\s*\}\}", '', cfg["clientvalue"])
-            m = re.search("\{\{[\s\w]*}\}", subbed)
+            subbed = re.sub(r"\{\{\s*value\s*\}\}", '', cfg["clientvalue"])
+            m = re.search(r"\{\{[\s\w]*}\}", subbed)
             if m:
                 raise Exception(
                     "clientvalue template parameter not found: %s" % m.group())

src/omero/util/populate_metadata.py

@@ -1351,7 +1351,7 @@ def _get_additional_targets(self, target):
 
     def populate(self, table):
         def idcolumn_to_omeroclass(col):
-            clsname = re.search('::(\w+)Column$', col.ice_staticId()).group(1)
+            clsname = re.search(r'::(\w+)Column$', col.ice_staticId()).group(1)
             return clsname
 
         try:

src/omero/util/populate_roi.py

@@ -268,11 +268,11 @@ class MIASPlateAnalysisCtx(AbstractPlateAnalysisCtx):
     datetime_format = '%Y-%m-%d-%Hh%Mm%Ss'
 
     # Regular expression matching a log filename
-    log_regex = re.compile('.*log(\d+-\d+-\d+-\d+h\d+m\d+s).txt$')
+    log_regex = re.compile(r'.*log(\d+-\d+-\d+-\d+h\d+m\d+s).txt$')
 
     # Regular expression matching a result filename
     detail_regex = re.compile(
-        '^Well(\d+)_(.*)_detail_(\d+-\d+-\d+-\d+h\d+m\d+s).txt$')
+        r'^Well(\d+)_(.*)_detail_(\d+-\d+-\d+-\d+h\d+m\d+s).txt$')
 
     # Companion file format
     companion_format = 'Companion/MIAS'

src/omero/util/pydict_text_io.py

@@ -68,7 +68,7 @@ def load(fileobj, filetype=None, single=True, session=None):
     except ValueError:
         pass
 
-    m = re.match('originalfile:(\d+)$', fileobj, re.I)
+    m = re.match(r'originalfile:(\d+)$', fileobj, re.I)
     if m:
         rawdata, filetype = get_format_originalfileid(
             int(m.group(1)), filetype, session)

src/omero_model_PermissionsI.py

@@ -166,7 +166,7 @@ def from_string(self, perms):
         """
         import re
         base = r"([rR\-_])([aAwW\-_])"
-        regex = re.compile("^(L?)%s$" % (base*3))
+        regex = re.compile(r"^(L?)%s$" % (base*3))
         match = regex.match(perms)
         if match is None:
             raise ValueError("Invalid permission string: %s" % perms)

src/path.py

@@ -1555,7 +1555,7 @@ def _permission_mask(mode):
     >>> _permission_mask('go-x')(o777) == o766
     True
     """
-    parsed = re.match('(?P<who>[ugo]+)(?P<op>[-+])(?P<what>[rwx]+)$', mode)
+    parsed = re.match(r'(?P<who>[ugo]+)(?P<op>[-+])(?P<what>[rwx]+)$', mode)
     if not parsed:
         raise ValueError("Unrecognized symbolic mode", mode)
     spec_map = dict(r=4, w=2, x=1)

tox.ini

@@ -15,6 +15,7 @@ deps =
     tables
     pytest-sugar
     pytest-xdist
+    pytest-warnings
     py27: https://github.com/ome/zeroc-ice-py-manylinux/releases/download/0.1.0/zeroc_ice-3.6.5-cp27-cp27mu-manylinux2010_x86_64.whl
     py36: https://github.com/ome/zeroc-ice-py-manylinux/releases/download/0.1.0/zeroc_ice-3.6.5-cp36-cp36m-manylinux2010_x86_64.whl
 setenv =