# pipen-args
Command line argument parser for [pipen][1]
## Usage
```python
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()
```
```shell
$ 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.
```python
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.
[1]: https://github.com/pwwang/pipen
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"description": "# pipen-args\n\nCommand line argument parser for [pipen][1]\n\n## Usage\n\n```python\nfrom pipen import Proc, Pipen\n\n\nclass Process(Proc):\n \"\"\"My process\n\n Input:\n a: Input data\n \"\"\"\n input = 'a'\n input_data = range(10)\n script = 'echo {{in.a}}'\n\nPipen().set_start(Process).run()\n```\n\n```shell\n$ python example.py --help\nUsage: test.py [-h | -h+] [options]\n\nUndescribed process.\nUse `@configfile` to load default values for the options.\n\nPipeline Options:\n --name NAME The name for the pipeline, will affect the default workdir and\n outdir. [default: pipen-0]\n --profile PROFILE The default profile from the configuration to run the pipeline.\n This profile will be used unless a profile is specified in the\n process or in the .run method of pipen. You can check the\n available profiles by running `pipen profile`\n --outdir OUTDIR The output directory of the pipeline [default: ./<name>-output]\n --forks FORKS How many jobs to run simultaneously by the scheduler\n --scheduler SCHEDULER\n The scheduler to run the jobs\n\nNamespace <in>:\n --in.a A [A ...] Input data\n\nOptional Arguments:\n -h, --help, -h+, --help+\n show help message (with + to show more options) and exit\n```\n\nSee more examples in `tests/pipelines/` folder.\n\n## Plugin options\n\n- `args_hide`: (process level) Hide the arguments in the help message. Default: `False`\n- `args_group`: (pipeline level) The group name for the arguments. Default: `pipeline options`\n- `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)\n\n\n## Metadata for Proc envs items\n\nThe metadata in the docstring of env items determines how the arguments are defined.\n\n```python\nclass Process(Proc):\n \"\"\"My process\n\n # other docstring sections\n\n Envs:\n a (<metadata>): ...\n \"\"\"\n```\n\nThe metadata could be key-value pairs separated by `;`. The separator `:` or `=` is used to\nseparate the key and value. The value is optional. If the value is not specified, it\nwill 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.\n\n[1]: https://github.com/pwwang/pipen\n",
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