woom.workflow.Workflow

class woom.workflow.Workflow(cfgfile, taskmanager)

__init__(cfgfile, taskmanager)

Initialize a workflow

Parameters:

• cfgfile (str or configobj.ConfigObj) – Path to workflow configuration file or configuration object

• taskmanager (TaskManager) – Task manager instance

Attributes

config	Workflow ConfigObj configuration instance
context	Context to be used for rendering
cycles	List of Cycle
host	Current Host instance
jobmanager	Current job manager instance
members	List of Member
nmembers	Number of ensemble members
output_directories
paths	dict of standard paths that must be prepended
submission_dirs	Generator of submission directories computed from the task tree
task_tree	Current TaskTree
taskmanager	Current TaskManager instance
workflow_dir	Where we are running the workflow

Methods

clean([submission_dirs, log_files, ...])	Remove working files and directories
clean_task(task_name[, cycle, member])	Remove job specific files for this task
fill_templates()	Fill template file of a task in a context
get_app_path([sep])	Typically app/conf/exp or ''
get_artifacts([task_name, cycle, member])	Get artifacts as a pandas.DataFrame
get_context([task_name, cycle, member, ...])	Get an instance of woom.context.Context task rendering
get_cycle(cycle)	Get a valid Cycle instance from a token string
get_member(member)	Get a valid Member instance from its :attr:`~woom.iters.Member.label ` string .
get_run_dirs()	Get the run directories as pandas.DataFrame
get_status([running, colorize])	Get the workflow task status as a pandas.DataFrame
get_submission_dirs()	Get the submission directories as pandas.DataFrame
get_task(task_name)	Shortcut to self.taskmanager.get_task(task_name)
get_task_artifact_paths(artifact_name, task_name)	Get the paths of an artifact of a given task across cycles and members
get_task_artifacts(task_name[, cycle, ...])	Get the paths of all artifacts of a given task across cycles and members
get_task_cycle(task_name, cycle)	Like get_cycle() but check that it is compatible with a given task
get_task_items(getter, task_name[, cycle, ...])	Loop on cycles and members to retreive task items
get_task_member(task_name, member)	Like get_member() but check that it is compatible with a given task
get_task_members(task_name)	Get the list of members if applicable or None
get_task_path(task_name[, cycle, member, sep])	Concatenate the app_path, the cycle and, task_name and the member label
get_task_run_dir(task_name[, cycle, member, ...])	Get where the command lines are executed in the script
get_task_status(task_name[, cycle, member])	Get the job status of a task
get_task_submission_dir(task_name[, cycle, ...])	Where the batch script is created and submitted
is_task_blocking(task_name)	Is this task blocking?
is_task_skipped(task_name)	Is this task skipped?
kill([jobid, task_name, cycle, member])	Kill all running jobs specific to this workflow
run([dry, force, skip])	Run the workflow by submiting all tasks
set_context([task_name, cycle, member, ...])	Get and set the context used for rendering
show_artifacts([tablefmt])	Show the status of all the tasks of the wokflow
show_overview()	Display an overview of the workflow, like its task tree and cycles
show_run_dirs([tablefmt])	Show the run directory of all the tasks of the wokflow
show_status([running, tablefmt, colorize])	Show the status of all the tasks of the wokflow
show_submission_dirs([tablefmt])	Show the submission directory of all the tasks of the wokflow
submit_sentinel()	Submit a sentinel job that regularly checks the status of all task jobs
submit_task([depend, blocking])	Submit a task
submit_task_fake([depend, blocking])	Don't submit a task, just display it
terminate_blocking_jobs()	Terminate blocking jobs
to_json_entry()