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Scientific Compute Container Spec Parser

Project Description

About

KLIKO is a specification, validator and parser for the KLIKO Scientific Compute Container specification. It enables a developer of scientific software to structure the input, output and parameters of a dockerized compute task. KLIKO is written in Python.

Installation

You can install Kliko inside a docker container or just on your system:

$ python setup.py install

or from pypi:

$ pip install kliko

Usage

from a Python script inside a container:

from kliko.validate import validate
parameters = validate()

or to check if a kliko file has a valid syntax:

$ kliko-validate /kliko.yml

or try to run the docker image from the examples folder directly:

$ kliko-run kliko/minimal --help

    usage: kliko-run [-h] [--target_folder TARGET_FOLDER] --choice {second,first}
                     --char CHAR [--float FLOAT] --file FILE --int INT
                     image_name

    positional arguments:
      image_name

    optional arguments:
      -h, --help            show this help message and exit
      --target_folder TARGET_FOLDER
      --choice {second,first}
                            choice field (default: second)
      --char CHAR           char field, maximum of 10 chars (default: empty)
      --float FLOAT         float field (default: 0.0)
      --file FILE           file field, this file will be put in /input in case of
                            split io, /work in case of join io
      --int INT             int field

Documentation

The documentation can be found on http://kliko.readthedocs.org

Example

There are examples of a kliko and parameters file in the examples folder.

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