Command-line argument parser for pipen.
Project description
pipen-args
Command line argument parser for pipen
Usage
from pipen import Proc, Pipen
# Note that unlike other plugins, you need to import install
# to activate the plugin
from pipen_args import install # noqa: F401
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>_results]
--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.
Metadata for env 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.
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