/ocean-bgc-cookbook

This Project Pythia Cookbook covers working with various sources of ocean biogeochemistry data, including Community Earth System Model (CESM) output and observational data.

Primary LanguageJupyter NotebookApache License 2.0Apache-2.0

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Ocean Biogeochemistry Cookbook

nightly-build Binder DOI

This Project Pythia Cookbook covers working with various sources of ocean biogeochemistry data, including Community Earth System Model (CESM) output and observational data.

Motivation

(Add a few sentences stating why this cookbook will be useful. What skills will you, "the chef", gain once you have reached the end of the cookbook?)

Authors

Lev Romashkov, Kristen Krumhardt

Contributors

Structure

Intro

(Add content for this section, e.g., "The foundational content includes ... ")

Nutrients

(Add content for this section, e.g., "Example workflows include ... ")

Plankton

(Add content for this section, e.g., "Example workflows include ... ")

Running the Notebooks

You can either run the notebook using Binder or on your local machine.

Running on Binder

The simplest way to interact with a Jupyter Notebook is through Binder, which enables the execution of a Jupyter Book in the cloud. The details of how this works are not important for now. All you need to know is how to launch a Pythia Cookbooks chapter via Binder. Simply navigate your mouse to the top right corner of the book chapter you are viewing and click on the rocket ship icon, (see figure below), and be sure to select “launch Binder”. After a moment you should be presented with a notebook that you can interact with. I.e. you’ll be able to execute and even change the example programs. You’ll see that the code cells have no output at first, until you execute them by pressing {kbd}Shift+{kbd}Enter. Complete details on how to interact with a live Jupyter notebook are described in Getting Started with Jupyter.

Running on Your Own Machine

If you are interested in running this material locally on your computer, you will need to follow this workflow:

  1. Clone the https://github.com/ProjectPythia/ocean-bgc-cookbook repository:

     git clone https://github.com/ProjectPythia/cookbook-example.git
  2. Move into the ocean-bgc-cookbook directory

    cd ocean-bgc-cookbook
  3. Create and activate your conda environment from the environment.yml file

    conda env create -f environment.yml
    conda activate ocean-bgc-cookbook-dev
  4. Move into the notebooks directory and start up Jupyterlab

    cd notebooks/
    jupyter lab