pipen-args

Command line argument parser for pipen

Usage

from pipen import Proc, Pipen


class Process(Proc):
    """My process

    Input:
        a: Input data
    """
    input = 'a'
    input_data = range(10)
    script = 'echo {{in.a}}'

Pipen().set_start(Process).run()

$ python example.py --help
Usage: test.py [-h | -h+] [options]

Undescribed process.
Use `@configfile` to load default values for the options.

Pipeline Options:
  --name NAME           The name for the pipeline, will affect the default workdir and
                        outdir. [default: pipen-0]
  --profile PROFILE     The default profile from the configuration to run the pipeline.
                        This profile will be used unless a profile is specified in the
                        process or in the .run method of pipen. You can check the
                        available profiles by running `pipen profile`
  --outdir OUTDIR       The output directory of the pipeline [default: ./<name>-output]
  --forks FORKS         How many jobs to run simultaneously by the scheduler
  --scheduler SCHEDULER
                        The scheduler to run the jobs

Namespace <in>:
  --in.a A [A ...]      Input data

Optional Arguments:
  -h, --help, -h+, --help+
                        show help message (with + to show more options) and exit

See more examples in tests/pipelines/ folder.

Plugin options

• args_hide: (process level) Hide the arguments in the help message. Default: False
• args_group: (pipeline level) The group name for the arguments. Default: pipeline options
• args_flatten: (pipeline level) Flatten the arguments in the help message when there is only one process in the pipeline. Default: auto (flatten if single process, otherwise not)

Metadata for Proc envs items

The metadata in the docstring of env items determines how the arguments are defined.

class Process(Proc):
    """My process

    # other docstring sections

    Envs:
        a (<metadata>): ...
    """

The metadata could be key-value pairs separated by ;. The separator : or = is used to separate the key and value. The value is optional. If the value is not specified, it will be set to True. The keys are valid arguments of argx.ArgumentParser.add_argument, except that hidden will be interpreted as show=False in argx.ArgumentParser.add_argument. If the value of choices is not specified, the subkeys of the env item will be used as the choices.