Class Hierarchy

• src.pyflow.Bunch: generic struct with named argument constructor
• src.pyflow.GlobalConstants
• src.pyflow.GlobalSync: Control total memory usage in non-local run modes by limiting the number of simultaneous subprocess calls
• src.pyflow.LogGlobals
• src.pyflow.LogState: A simple logging enum
• object: The most base type
  • exceptions.BaseException: Common base class for all exceptions
    • exceptions.Exception: Common base class for all non-exit exceptions.
      • src.pyflow.DataDirException
      • src.pyflow.WorkflowRunner._AbortWorkflowException
  • src.pyflow.CmdPayload
  • src.pyflow.Command: Commands can be presented as strings or argument lists (or none)
  • src.pyflowConfig.DefaultSiteConfig: Default configuration settings are designed to work with as many sites as technically feasible
    • src.pyflowConfig.hvmemSGEConfig: This config assumes 'h_vmem' is defined on the SGE instance
  • src.pyflow.DotConfig: A static container of configuration data for dot graph output
  • src.pyflow.ExpWaiter: Convenience object to setup exponentially increasing wait/polling times
  • src.pyflow.ModeInfo: Stores default values associated with each runmode: local,sge,...
  • src.pyflow.RetryParam: parameters pertaining to task retry behavior
  • src.pyflow.RunMode
  • src.pyflow.RunningTaskStatus: simple object allowing remote task threads to communicate their status back to the TaskManager
  • src.pyflowTaskWrapper.SimpleFifo: Store up to last N objects, not thread safe.
  • src.pyflow.StrFileObject: fakes a filehandle for library functions which write to a stream, and captures output in a string
  • src.pyflowTaskWrapper.StringBling
  • src.pyflow.TaskDAG: Holds all tasks and their dependencies.
  • src.pyflow.TaskNode: Represents an individual task in the task graph
  • src.pyflow.TaskNodeConstants
  • src.pyflow.WorkflowPayload
  • src.pyflow.WorkflowRunner: This object is designed to be inherited by a class in client code.
  • src.pyflow.WorkflowRunnerThreadSharedData: All data used by the WorkflowRunner which will be constant over the lifetime of a TaskManager instance.
  • threading._Verbose
    • threading.Thread: A class that represents a thread of control.
      • src.pyflow.QCaller: Calls to both qsub and qstat go through this run() method so that we can time them out:
      • src.pyflow.StoppableThread: Thread class with a stop() method.
        • src.pyflow.BaseTaskRunner: Each individual command-task or sub workflow task is run on its own thread using a class inherited from BaseTaskRunner
          • src.pyflow.CommandTaskRunner: Parent to local and SGE TaskRunner specializations for command tasks
            • src.pyflow.LocalTaskRunner
            • src.pyflow.SGETaskRunner
          • src.pyflow.WorkflowTaskRunner: Manages a sub-workflow task
        • src.pyflow.TaskFileWriter: This class runs on a separate thread and is responsible for updating the state and info task files
        • src.pyflow.TaskManager: This class runs on a separate thread from workflowRunner, launching jobs based on the current state of the TaskDAG