ILCI-NotebookTemplates

Overview

In this repository we expect to host a collection on Jupyter Notebook templates suitable for data access and analysis of breeding data.

The goal is to use these templates with the BrAPI helper JupyterLab extension, however these templates will be usable as standalone notebooks in cookie cutter fashion.

The repository is experimental; expect things to break.

Templates

Templates are located in the src/templates/ directory. For each template write to a text file a brief one liner (just a few words) that describes what the template does, name this file with the following pattern template_name.info. For example, to describe what template_rtassel_demo.ipynb does we would create template_rtassel_demo.info with these contents in a single line:

Process data from BrAPI sources with rTASSEL

The metadata contained in the info files is used by create_catalog.py to generate a catalog of all the templates in src/templates/ in JSON format. The contents of catalog.json are very similar to this:

{
    "data": [
        {
            "name": "some_template.ipynb",
            "description": "brief description"
        },
        {
            "name": "template_rtassel_demo.ipynb",
            "description": "Process data from BrAPI sources with rTASSEL"
        },
        {
            "name": "sommer_evals.ipynb",
            "description": "mixed model analysis with Sommer"
        }
    ]
}

BrAPI Helper

To install the experimental BrAPI Helper extension open the command line and run:

/opt/shared/test_dir/brapi_helper_installer.run

This extension is only available for a subset of users for testing.

Using templates (not implemented yet!!)

The BrAPI extension reads templates from the $HOME/templates directory (not implemented yet). If you wish to use the templates from this repo with the extension directly you, could create a symlink to the this repo's contents. For instance, let's assume you clone this repo from your $HOME directory, this will create $HOME/ILCI-NotebookTemplates

ln -s $HOME/ILCI-NotebookTemplates/src/templates $HOME

Notes

We would also like to look at how templates are used and managed by the jupytemplate and the jupyterlab_templates extensions.