Refactored docstrings to obey to PEP. Patch for pharmbio#56

Author: Luca Venturini

sciluigi/audit.py

@@ -1,6 +1,6 @@
-'''
+"""
 This module contains functionality for the audit-trail logging functionality
-'''
+"""
 
 import logging
 import luigi
@@ -15,20 +15,22 @@
 
 # ==============================================================================
 
+
 class AuditTrailHelpers(object):
-    '''
+    """
     Mixin for luigi.Task:s, with functionality for writing audit logs of running tasks
-    '''
+    """
     def add_auditinfo(self, infotype, infoval):
-        '''
+        """
         Alias to _add_auditinfo(), that can be overridden.
-        '''
+        """
         return self._add_auditinfo(self.instance_name, infotype, infoval)
 
+
     def _add_auditinfo(self, instance_name, infotype, infoval):
-        '''
+        """
         Save audit information in a designated file, specific for this task.
-        '''
+        """
         dirpath = self.workflow_task.get_auditdirpath()
         if not os.path.isdir(dirpath):
             time.sleep(random.random())
@@ -42,32 +44,35 @@ def _add_auditinfo(self, instance_name, infotype, infoval):
         with open(auditfile, 'a') as afile:
             afile.write('%s: %s\n' % (infotype, infoval))
 
+
     def get_instance_name(self):
-        '''
+        """
         Return the luigi instance_name
-        '''
+        """
         instance_name = None
         if self.instance_name is not None:
             instance_name = self.instance_name
         else:
             instance_name = self.task_id
         return instance_name
 
+
     @luigi.Task.event_handler(luigi.Event.START)
     def save_start_time(self):
-        '''
+        """
         Log start of execution of task.
-        '''
+        """
         if hasattr(self, 'workflow_task') and self.workflow_task is not None:
             msg = 'Task {task} started'.format(
                 task=self.get_instance_name())
             log.info(msg)
 
+
     @luigi.Task.event_handler(luigi.Event.PROCESSING_TIME)
     def save_end_time(self, task_exectime_sec):
-        '''
+        """
         Log end of execution of task, with execution time.
-        '''
+        """
         if hasattr(self, 'workflow_task') and self.workflow_task is not None:
             msg = 'Task {task} finished after {proctime:.3f}s'.format(
                 task=self.get_instance_name(),

sciluigi/dependencies.py

@@ -1,7 +1,7 @@
-'''
+"""
 This module contains functionality for dependency resolution for constructing
 the dependency graph of workflows.
-'''
+"""
 
 import luigi
 from luigi.contrib.postgres import PostgresTarget
@@ -10,11 +10,12 @@
 
 # ==============================================================================
 
+
 class TargetInfo(object):
-    '''
+    """
     Class to be used for sending specification of which target, from which
     task, to use, when stitching workflow tasks' outputs and inputs together.
-    '''
+    """
     task = None
     path = None
     target = None
@@ -25,21 +26,24 @@ def __init__(self, task, path, format=None, is_tmp=False):
         self.target = luigi.LocalTarget(path, format, is_tmp)
 
     def open(self, *args, **kwargs):
-        '''
+        """
         Forward open method, from luigi's target class
-        '''
+        """
         return self.target.open(*args, **kwargs)
 
 # ==============================================================================
 
+
 class S3TargetInfo(TargetInfo):
+
     def __init__(self, task, path, format=None, client=None):
         self.task = task
         self.path = path
         self.target = S3Target(path, format=format, client=client)
 
 # ==============================================================================
 
+
 class PostgresTargetInfo(TargetInfo):
     def __init__(self, task, host, database, user, password, update_id, table=None, port=None):
         self.task = task
@@ -54,28 +58,30 @@ def __init__(self, task, host, database, user, password, update_id, table=None,
 
 # ==============================================================================
 
+
 class DependencyHelpers(object):
-    '''
+
+    """
     Mixin implementing methods for supporting dynamic, and target-based
     workflow definition, as opposed to the task-based one in vanilla luigi.
-    '''
+    """
 
     # --------------------------------------------------------
     # Handle inputs
     # --------------------------------------------------------
 
     def requires(self):
-        '''
+        """
         Implement luigi API method by returning upstream tasks
-        '''
+        """
         return self._upstream_tasks()
 
     def _upstream_tasks(self):
-        '''
+        """
         Extract upstream tasks from the TargetInfo objects
         or functions returning those (or lists of both the earlier)
         for use in luigi's requires() method.
-        '''
+        """
         upstream_tasks = []
         for attrname, attrval in iteritems(self.__dict__):
             if 'in_' == attrname[0:3]:
@@ -84,11 +90,11 @@ def _upstream_tasks(self):
         return upstream_tasks
 
     def _parse_inputitem(self, val, tasks):
-        '''
+        """
         Recursively loop through lists of TargetInfos, or
         callables returning TargetInfos, or lists of ...
         (repeat recursively) ... and return all tasks.
-        '''
+        """
         if callable(val):
             val = val()
         if isinstance(val, TargetInfo):
@@ -108,17 +114,17 @@ def _parse_inputitem(self, val, tasks):
     # --------------------------------------------------------
 
     def output(self):
-        '''
+        """
         Implement luigi API method
-        '''
+        """
         return self._output_targets()
 
     def _output_targets(self):
-        '''
+        """
         Extract output targets from the TargetInfo objects
         or functions returning those (or lists of both the earlier)
         for use in luigi's output() method.
-        '''
+        """
         output_targets = []
         for attrname in dir(self):
             attrval = getattr(self, attrname)
@@ -128,11 +134,11 @@ def _output_targets(self):
         return output_targets
 
     def _parse_outputitem(self, val, targets):
-        '''
+        """
         Recursively loop through lists of TargetInfos, or
         callables returning TargetInfos, or lists of ...
         (repeat recursively) ... and return all targets.
-        '''
+        """
         if callable(val):
             val = val()
         if isinstance(val, TargetInfo):

sciluigi/interface.py

@@ -1,6 +1,6 @@
-'''
+"""
 This module contains mappings of methods that are part of the sciluigi API
-'''
+"""
 
 import luigi
 import logging
@@ -11,10 +11,11 @@
 LOGFMT_SCILUIGI = '%(asctime)s %(levelname)8s SCILUIGI %(message)s'
 DATEFMT = '%Y-%m-%d %H:%M:%S'
 
+
 def setup_logging():
-    '''
+    """
     Set up SciLuigi specific logging
-    '''
+    """
     sciluigi.util.ensuredir('log')
     log_path = 'log/sciluigi_run_%s_detailed.log' % sciluigi.util.timepath()
 
@@ -49,16 +50,19 @@ def setup_logging():
     sciluigi_logger.addHandler(sciluigi_file_handler)
     sciluigi_logger.setLevel(logging.DEBUG)
 
+
 setup_logging()
 
+
 def run(*args, **kwargs):
-    '''
+    """
     Forwarding luigi's run method
-    '''
+    """
     luigi.run(*args, **kwargs)
 
+
 def run_local(*args, **kwargs):
-    '''
+    """
     Forwarding luigi's run method, with local scheduler
-    '''
+    """
     run(local_scheduler=True, *args, **kwargs)

sciluigi/parameter.py

@@ -1,12 +1,13 @@
-'''
+"""
 This module contains a sciluigi subclass of luigi's Parameter, where
 custom functionality might be added in the future.
-'''
+"""
 
 import luigi
 
+
 class Parameter(luigi.Parameter):
-    '''
+    """
     Subclass of luigi's Parameter, where custom functionality might be added in the future.
-    '''
+    """
     pass