Metadata-Version: 2.1
Name: data-pipeline-api
Version: 0.7.5
Summary: Python api to interact with the Fair Data Pipeline
Home-page: https://www.fairdatapipeline.org/
License: GNU General Public License v3.0
Keywords: FAIR Data Pipeline,FAIR,Data Management,Provenance
Author: Ryan J Field
Author-email: ryan.field@glasgow.ac.uk
Requires-Python: >=3.7.1,<3.11
Classifier: License :: Other/Proprietary License
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Requires-Dist: PyYAML (>=6.0,<7.0)
Requires-Dist: h5py (>=3.6.0,<4.0.0)
Requires-Dist: matplotlib (>=3.5.1,<4.0.0)
Requires-Dist: requests (>=2.27.1,<3.0.0)
Requires-Dist: scipy (>=1.7.3,<2.0.0)
Project-URL: Issue Tracker, https://github.com/FAIRDataPipeline/pyDataPipeline/issues
Project-URL: Repository, https://github.com/FAIRDataPipeline/pyDataPipeline
Description-Content-Type: text/markdown

# pyDataPipeline

[![pyDataPipeline](https://github.com/FAIRDataPipeline/pyDataPipeline/actions/workflows/pyDataPipeline.yaml/badge.svg?branch=dev)](https://github.com/FAIRDataPipeline/pyDataPipeline/actions/workflows/pyDataPipeline.yaml)
[![codecov](https://codecov.io/gh/FAIRDataPipeline/pyDataPipeline/branch/dev/graph/badge.svg?token=Eax5AmrDxx)](https://codecov.io/gh/FAIRDataPipeline/pyDataPipeline)
[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5562602.svg)](https://doi.org/10.5281/zenodo.5562602)
[![CII Best Practices](https://bestpractices.coreinfrastructure.org/projects/5461/badge)](https://bestpractices.coreinfrastructure.org/projects/5461)

Welcome to pyDataPipeline a Python api to interact with the Fair Data Pipeline.

Full documention of the pyDataPipeline is avaialable at [https://www.fairdatapipeline.org/pyDataPipeline/](https://www.fairdatapipeline.org/pyDataPipeline/)

## Installation
pyDataPipeline can be installed from PyPi:
```
pip3 install data-pipeline-api
```

Or from the Repository:
```
git clone https://github.com/FAIRDataPipeline/pythonFDP.git

git checkout dev

pip3 install -e .
```
**NB. PyDataPipeline requires Python3.**

## Example submission_script

Assume FDP_CONFIG_DIR, storage_locations and objects have been set by CLI tool

```
import os
import fairdatapipeline as pipeline

token = os.environ.get('FDP_LOCAL_TOKEN')
config_path = os.environ.get('FDP_CONFIG_DIR') + '/config.yaml'
script_path = os.environ.get('FDP_CONFIG_DIR') + '/script.sh'

handle = pipeline.initialise(token, config_path, script_path)

pipeline.finalise(token, handle)

```

## SEIRS Model Example

The SEIRS Model Example is available at: [https://www.fairdatapipeline.org/pyDataPipeline/examples/SEIRS.html](https://www.fairdatapipeline.org/pyDataPipeline/examples/SEIRS.html)

