pydra.engine.helpers module

Administrative support for the engine framework.

class pydra.engine.helpers.PydraFileLock(lockfile)

Bases: object

Wrapper for filelock’s SoftFileLock that makes it work with asyncio.

pydra.engine.helpers.allowed_values_validator(_, attribute, value): checking if the values is in allowed_values

pydra.engine.helpers.argstr_formatting(argstr, inputs, value_updates=None): formatting argstr that have form {field_name}, using values from inputs and updating with value_update if provided

pydra.engine.helpers.copyfile_workflow(wf_path: PathLike, result): if file in the wf results, the file will be copied to the workflow directory

pydra.engine.helpers.create_checksum(name, inputs)

Generate a checksum name for a given combination of task name and inputs.

Parameters:

name (str) – Task name.
inputs (str) – String of inputs.

pydra.engine.helpers.ensure_list(obj, tuple2list=False)

Return a list whatever the input object is.

Examples

>>> ensure_list(list("abc"))
['a', 'b', 'c']
>>> ensure_list("abc")
['abc']
>>> ensure_list(tuple("abc"))
[('a', 'b', 'c')]
>>> ensure_list(tuple("abc"), tuple2list=True)
['a', 'b', 'c']
>>> ensure_list(None)
[]
>>> ensure_list(5.0)
[5.0]

pydra.engine.helpers.execute(cmd, strip=False)

Run the event loop with coroutine.

Uses read_and_display_async() unless a loop is already running, in which case read_and_display() is used.

Parameters:

cmd (list or tuple) – The command line to be executed.
strip (bool) – TODO

pydra.engine.helpers.from_list_if_single(obj): Converts a list to a single item if it is of length == 1

pydra.engine.helpers.gather_runtime_info(fname)

Extract runtime information from a file.

Parameters:: fname (os.pathlike) – The file containing runtime information
Returns:: runtime – A runtime object containing the collected information.
Return type:: Runtime

pydra.engine.helpers.get_available_cpus()

Return the number of CPUs available to the current process or, if that is not available, the total number of CPUs on the system.

Returns:: n_proc – The number of available CPUs.
Return type:: int

pydra.engine.helpers.get_open_loop()

Get current event loop.

If the loop is closed, a new loop is created and set as the current event loop.

Returns:: loop – The current event loop
Return type:: asyncio.EventLoop

pydra.engine.helpers.load_and_run(task_pkl, ind=None, rerun=False, submitter=None, plugin=None, **kwargs): loading a task from a pickle file, settings proper input and running the task

async pydra.engine.helpers.load_and_run_async(task_pkl, ind=None, submitter=None, rerun=False, **kwargs): loading a task from a pickle file, settings proper input and running the workflow

pydra.engine.helpers.load_result(checksum, cache_locations)

Restore a result from the cache.

Parameters:

checksum (str) – Unique identifier of the task to be loaded.
cache_locations (list of os.pathlike) – List of cache directories, in order of priority, where the checksum will be looked for.

pydra.engine.helpers.load_task(task_pkl, ind=None): loading a task from a pickle file, settings proper input for the specific ind

pydra.engine.helpers.make_klass(spec)

Create a data class given a spec.

Parameters:: spec – TODO

pydra.engine.helpers.output_from_inputfields(output_spec, input_spec)

Collect values from output from input fields. If names_only is False, the output_spec is updated, if names_only is True only the names are returned

Parameters:

output_spec – TODO
input_spec – TODO

pydra.engine.helpers.parse_copyfile(fld: Attribute, default_collation=CopyCollation.any): Gets the copy mode from the ‘copyfile’ value from a field attribute

pydra.engine.helpers.position_sort(args)

Sort objects by position, following Python indexing conventions.

Ordering is positive positions, lowest to highest, followed by unspecified positions (None) and negative positions, lowest to highest.

>>> position_sort([(None, "d"), (-3, "e"), (2, "b"), (-2, "f"), (5, "c"), (1, "a")])
['a', 'b', 'c', 'd', 'e', 'f']

Parameters:: args (list of (int/None, object) tuples)
Return type:: list of objects

pydra.engine.helpers.print_help(obj): Visit a task object and print its input/output interface.

pydra.engine.helpers.read_and_display(*cmd, strip=False, hide_display=False): Capture a process’ standard output.

async pydra.engine.helpers.read_and_display_async(*cmd, hide_display=False, strip=False)

Capture standard input and output of a process, displaying them as they arrive.

Works line-by-line.

async pydra.engine.helpers.read_stream_and_display(stream, display): Read from stream line by line until EOF, display, and capture the lines.

See also

This discussion on StackOverflow.

pydra.engine.helpers.record_error(error_path, error): Write an error file.

pydra.engine.helpers.save(task_path: Path, result=None, task=None, name_prefix=None)

Save a TaskBase object and/or results.

Parameters:

task_path (Path) – Write directory
result (Result) – Result to pickle and write
task (TaskBase) – Task to pickle and write