phydra 0.0.2

A library of marine ecosystem models using the XSO frammework (xarray-simlab-ode)

phydra

A library of plankton community models utilizing the XSO frammework (Xarray-simlab-ODE).

Disclaimer: The library and framework are in the early stages of development. Feedback, testing, and contributions are very welcome.

What is phydra?

Phydra is a Python package that provides a library of modular plankton community models built using the XSO framework. XSO provides a streamlined, interactive and reproducible workflow for building and running models. The model input and output data is an Xarray-Dataset directly compatible with a wealth of tools of the Python scientific ecosystem.

Usage

See the included notebooks for an interactive presentation of the usage of the Phydra library.

Package structure

The plankton community models included in the Phydra package are available to the user at multiple hierarchical levels: as a library of pre-built XSO model components, as pre-assembled model objects, and as exemplary model simulations in interactive Jupyter notebooks. These levels are described below.

• Components: The first version of the library will contain all components used to create the three model applications presented in the notebooks.

• Model objects: The first release of Phydra contains the model objects defined in the three model applications presented in section UseCases. The model objects can be imported from the library and can be readily setup, modified, and run by a user.

• Example notebooks: Model objects only define the collection of components. To run a model, the input parameters still need to be defined and supplied at runtime. The Phydra library comes with three fully documented model applications that are presented in interactive Jupyter notebooks. These notebooks show all steps from creating the model setup object to analyzing model output and provide a template for further exploration and experimentation with the provided plankton community models.

Motivation

The open-source and extensible nature of Phydra and XSO enables users to customize and develop processes that accurately describe a particular ecosystem. In a collaborative effort to promote efficient, transparent, and reproducible marine ecosystem modeling, Phydra encourages users to contribute their own components and models to the core library. The Phydra library could potentially offer a comprehensive, well-documented, and peer-reviewed codebase for the scientific exploration of marine ecosystem models.

Installation

$ pip install phydra

Contributing

Interested in contributing? Check out the contributing guidelines. Please note that this project is released with a Code of Conduct. By contributing to this project, you agree to abide by its terms.

License

phydra was created by Benjamin Post. It is licensed under the terms of the BSD 3-Clause license.

Credits

phydra was created with cookiecutter and the py-pkgs-cookiecutter template.