schrodinger.tasks.cmdline module

schrodinger.tasks.cmdline.start_task(task)

Wrapper around task.start that runs preprocessing, handles any pre- processing errors or warnings, starts the task, and prints a message if the task fails during start.

schrodinger.tasks.cmdline.run_task_from_cmdline(TaskClass, args=None)

Given a TaskClass, create a task and pass it arguments from the command- line. Arguments take the form of -foo.bar.x VALUE', where `foo is a subparam on the input of the task, bar is a subparam on the foo, and x is a subparam on bar. Any omitted arguments will take the default value as specified by their corresponding params.

Parameters

args (list[str]) – A list of strings describing the arguments to the task. If None, the args will be parsed from the command-line.

Returns

The finished task.

Return type

TaskClass

schrodinger.tasks.cmdline.build_task_from_args(TaskClass, args)

schrodinger.tasks.cmdline.run_jobtask_from_cmdline(JobTaskClass, args=None)

schrodinger.tasks.cmdline.build_jobtask_from_args(JobTaskClass, args=None)

schrodinger.tasks.cmdline.write_output(task)

Write out each task output subparam of an allowed type to its own file.

Parameters

task (tasks.AbstractTask) – A task instance with output to be written.

schrodinger.tasks.cmdline.preprocessing_callback(result)

schrodinger.tasks.cmdline.make_get_job_spec_from_args(TaskClass)

Create a get_job_spec_from_args based on the specified task class. Example usage:

get_job_spec_from_args = cmdline.make_get_job_spec_from_args(CounterComboJobTask)

Note: task.job_config will not be populated to match the cmdline job flags

Parameters

TaskClass – the ComboJobTask class to run under jobcontrol

Returns

a get_job_spec_from_args function

schrodinger.tasks.cmdline.make_main(task_source: Union[type, Dict[str, type]], auto_write_output: bool = False) → Callable

Create a main function for running any combo task directly from the command line in-process (no job control). Example usage:

main = cmdline.make_main(CounterComboJobTask)

if __name__ == '__main__':
    main()

Alternatively, a dictionary of subparser names to task classes can be supplied, giving users the option to pick between different tasks to run:

task_dict = {
    'scaffold-search': ScaffoldSearchTask,
    'grafting': GraftingTask,
}
main = cmdline.make_main(task_dict)

if __name__ == '__main__':
    main()

Note

A subparser is automatically created for each task in the dictionary. They are named using the keys of the dictionary.

Parameters

• task_source – the source of combo task class(es) to use. Can be either a single combo task class or a dictionary mapping subparser names to task classes.

• auto_write_output – Whether to automatically write the task output to files if possible. Turn off output writing if the task already writes output to files in the backend.

Returns

a main function