skbio.workflow.Workflow

class skbio.workflow.Workflow(state, short_circuit=True, debug=False, options=None, **kwargs)[source]

Arbitrary workflow support structure

Methods that are considered to be directly part of the workflow must be decorated with method. The workflow methods offer a mechanism to logically group functionality together, and are free to make subsequent calls to other methods.

All methods of a subclass of Workflow (those with and without the method decoration) can take advantage of the requires decorator to specify any option or state requirements for the decorated function.

Parameters
  • state (object) – State can be anything or nothing. This is dependent on the workflow as in some cases, it is useful to preallocate state while in other workflows state may be ignored.

  • short_circuit (bool) – if True, enables ignoring function methods when a given item has failed

  • debug (bool) – Enable debug mode

  • options (dict) – runtime options, {‘option’:values}, that the requires decorator can interrogate.

  • kwargs (dict) – Additional arguments will be added as member variables to self. This is handy if additional contextual information is needed by a workflow method (e.g., a lookup table).

Built-ins

__call__(iter_[, success_callback, ...])

Operate on all the data

__eq__(value, /)

Return self==value.

__ge__(value, /)

Return self>=value.

__gt__(value, /)

Return self>value.

__hash__()

Return hash(self).

__init_subclass__

This method is called when a class is subclassed.

__le__(value, /)

Return self<=value.

__lt__(value, /)

Return self<value.

__ne__(value, /)

Return self!=value.

__str__()

Return str(self).

Methods

initialize_state(item)

Initialize state