pep8 and flake

Author: cjayb

stormdb/access.py

@@ -106,8 +106,8 @@ def _get_login_code(self):
         try:
             with open(os.path.expanduser(self._stormdblogin), 'r') as fid:
                 if self._verbose:
-                    print('Reading login credentials from ' +
-                          self._stormdblogin)
+                    print('Reading login credentials from {:s}'.format(
+                        self._stormdblogin))
                 self._login_code = fid.readline()
         except IOError:
             print('Login credentials not found, please enter them here')
@@ -193,7 +193,7 @@ def _send_request(self, url, verbose=None):
 
         try:
             req = requests.get(full_url)
-        except:
+        except ConnectionError:
             print('hyades00 is not responding, it may be down.')
             print('Contact a system administrator for confirmation.')
             raise
@@ -240,12 +240,12 @@ def get_subjects(self,
             raise ValueError(
                 'You can only specify a modality OR a series, not both.')
         type_err = '{} must be a string, not {}.'
-        if (has_modality is not None
-                and not isinstance(has_modality, string_types)):
+        if (has_modality is not None and not
+                isinstance(has_modality, string_types)):
             raise ValueError(
                 type_err.format('has_modality', type(has_modality)))
-        if (has_series is not None
-                and not isinstance(has_series, string_types)):
+        if (has_series is not None and not
+                isinstance(has_series, string_types)):
             raise ValueError(type_err.format('has_series', type(has_series)))
 
         # using 'subjecs' here would return only numeric ID, not code
@@ -278,8 +278,8 @@ def get_subjects(self,
             subj_list = [
                 ser['subjectcode'] for ser in all_series
                 if ser['subjectcode'] not in used and (
-                    used.append(ser['subjectcode']) or True)
-                and ser['subjectcode'] in subj_list
+                    used.append(ser['subjectcode']) or True) and (
+                        ser['subjectcode'] in subj_list)
             ]
             # The following also works, but is slower?
             # pop_inds = []
@@ -297,8 +297,8 @@ def get_subjects(self,
             subj_list = [
                 ser['subjectcode'] for ser in all_series
                 if ser['subjectcode'] not in used and (
-                    used.append(ser['subjectcode']) or True)
-                and ser['subjectcode'] in subj_list
+                    used.append(ser['subjectcode']) or True) and (
+                        ser['subjectcode'] in subj_list)
             ]
 
         return (subj_list)
@@ -618,7 +618,7 @@ def filter_series(self,
                     format(study_metas['name'],
                            study_metas['comparison'],
                            study_metas['value'])
-            except:
+            except KeyError:
                 print('Problem with study_metas:')
                 print(study_metas)
                 raise
@@ -653,7 +653,7 @@ def filter_series(self,
                     key_val_pair[1].sort(key=lambda x: os.path.splitext(x)[0])
 
                 elif 'path' in key_val_pair[0]:
-                    m = re.search('\d{3}\.(.+?)/files', key_val_pair[1])
+                    m = re.search(r'\d{3}\.(.+?)/files', key_val_pair[1])
                     info.append(['seriename', m.group(1)])
                 info.append(key_val_pair)
             info_dict = {key: value for (key, value) in info}
@@ -664,8 +664,8 @@ def filter_series(self,
                 study_date_range = [study_date_range, study_date_range]
             info_dict_list = [
                 s for s in info_dict_list
-                if s['study'][:8] >= study_date_range[0]
-                and s['study'][:8] <= study_date_range[1]
+                if s['study'][:8] >= study_date_range[0] and (
+                    s['study'][:8] <= study_date_range[1])
             ]
         return (info_dict_list)
 

stormdb/cluster.py

@@ -103,19 +103,19 @@ def get_memlimit_per_process(self, queue):
         if queue not in self.queues:
             raise ValueError('Unknown queue: {:s}'.format(queue))
 
-        lim = self._query('qconf -sq ' + queue +
-                          '| grep h_vmem | awk {\'print $2\'}')[0]
+        lim = self._query('qconf -sq ' + queue + (
+            '| grep h_vmem | awk {\'print $2\'}'))[0]
 
-        _, lim_int, lim_units = re.split('(\d+)', lim)
+        _, lim_int, lim_units = re.split(r'(\d+)', lim)
         assert isinstance(int(lim_int), int)
         assert isinstance(lim_units, string_types)
 
         return (lim)
 
     def _check_parallel_env(self, queue, pe_name):
         """Check that a PE is in the pe_list for a given queue"""
-        pes = self._query('qconf -sq ' + queue +
-                          '| grep pe_list')[0]  # just one line
+        pes = self._query('qconf -sq ' + queue + (
+                          '| grep pe_list'))[0]  # just one line
         pe_list = pes.split()[1:]
         if pe_name not in pe_list:
             raise ValueError('Queue \'{0}\' does not support the \'{1}\' '
@@ -238,14 +238,14 @@ def __init__(self,
                     'Maximum number of parallel threads is one (1) when total '
                     'memory consumption is specified.')
             # XXX would be nice with some sanity checking here...
-            _, totmem, totmem_unit = re.split('(\d+)', self.total_memory)
-            _, memlim, memlim_unit = re.split('(\d+)', h_vmem)
+            _, totmem, totmem_unit = re.split(r'(\d+)', self.total_memory)
+            _, memlim, memlim_unit = re.split(r'(\d+)', h_vmem)
 
             if totmem_unit != memlim_unit:
                 units = dict(k=1e3, m=1e6, g=1e9, t=1e12)
                 try:
                     ratio = units[totmem_unit.lower()] /\
-                                units[memlim_unit.lower()]
+                        units[memlim_unit.lower()]
                 except KeyError:
                     raise ValueError('Something is wrong with the memory units'
                                      ', likely {:s}'.format(self.total_memory))
@@ -310,9 +310,9 @@ def _initialise_cmd(self, value):
     def _create_qsub_script(self, job_name, cwd_flag, opt_threaded_flag,
                             opt_h_vmem_flag, log_name_prefix):
         """All variables should be defined"""
-        if (self.cmd is None or self.queue is None or job_name is None
-                or cwd_flag is None or opt_threaded_flag is None
-                or opt_h_vmem_flag is None):
+        if (self.cmd is None or self.queue is None or job_name is None or
+            cwd_flag is None or opt_threaded_flag is None or
+                opt_h_vmem_flag is None):
             raise ValueError('This should not happen, please report an Issue!')
 
         self._qsub_script =\
@@ -367,7 +367,7 @@ def submit(self, fake=False, sh_file='~/submit_job.sh'):
         else:
             # py2-3 safety
             output = output.decode('ascii', 'ignore').rstrip()
-            m = re.search('(\d+)', output)
+            m = re.search(r'(\d+)', output)
             self._jobid = m.group(1)
             if self._cleanup_qsub_job:
                 self._delete_qsub_job()
@@ -387,8 +387,8 @@ def _check_status(self):
                                      ' | awk \'{print $5, $8}\'')[0]  # ONLY
 
         if len(output) == 0:
-            if (self._submitted and not self._running and not self._completed
-                    and not self._waiting):
+            if (self._submitted and not self._running and not
+                    self._completed and not self._waiting):
                 self._status_msg = ('Submission failed, see log for'
                                     ' output errors!')
             elif self._submitted and not self._completed:
@@ -485,8 +485,8 @@ def verbose(self, value):
     def kill(self, jobid=None):
         """Kill (delete) all the jobs in the batch."""
         for job in self._joblist:
-            if (jobid is None
-                    or (jobid is not None and int(job._jobid) == int(jobid))):
+            if (jobid is None or (
+                    jobid is not None and int(job._jobid) == int(jobid))):
                 job.kill()
 
     def build_cmd(self):