pipen-annotate

pipen-annotate

Use docstring to annotate pipen processes

Installation

pip install -U pipen-annotate

Usage

from pprint import pprint
from pipen import Proc
from pipen_annotate import annotate


class Process(Proc):
    """Short description

    Long description

    Input:
        infile: An input file
        invar: An input variable

    Output:
        outfile: The output file

    Envs:
        ncores (type=int): Number of cores
    """
    input = "infile:file, invar"
    output = "outfile:file:output.txt"
    args = {'ncores': 1}

annotated = annotate(Process)
# returns:
{'Envs': {'ncores': {'attrs': {'type': 'int'},
                     'help': 'Number of cores',
                     'name': 'ncores',
                     'terms': {}}},
 'Input': {'infile': {'attrs': {'action': 'extend',
                                'itype': 'file',
                                'nargs': '+'},
                      'help': 'An input file',
                      'name': 'infile',
                      'terms': {}},
           'invar': {'attrs': {'action': 'extend',
                               'itype': 'var',
                               'nargs': '+'},
                     'help': 'An input variable',
                     'name': 'invar',
                     'terms': {}}},
 'Output': {'outfile': {'attrs': {'default': 'output.txt', 'otype': 'file'},
                        'help': 'The output file',
                        'name': 'outfile',
                        'terms': {}}},
 'Summary': {'long': 'Long description', 'short': 'Short description'}}