Command line argument parser for pipen
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 exitSee more examples in tests/pipelines/ folder.
-
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)
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.
