Contributing to the Project

Documentation

The documentation is created using sphinx and read-the-docs, which uses the reStructuredText format to create documents. To add documentation, go to the docs folder, where you will find a list of .rst files, the home page is written in index.rst, and links to the other subpages which are in the other .rst files.

These documents can be opened in any text editor of your choice, to learn more about how to write in reStructuredText, you can read:

• https://www.sphinx-doc.org/en/master/usage/restructuredtext/basics.html

• https://sublime-and-sphinx-guide.readthedocs.io/en/latest/index.html

A brief guide to building the documentation website on your computer before pushing changes to github:

• (Optional by recommended) Set up a virtual python environment (eg. using anaconda)

• Install the required python packages: change your directory to pip install MEA-NAP/docs/requirements.txt

• To build the website fromthe .rst files, change your directory to MEA-NAP/docs, then do make html

• If there are no error messages, the website is built, you can open docs/_build/html/index.html, which should open a website on your default internet browser, and navigate as normal. Note, this does not mean you have updated the online documentation, to do that, you need to push the changes of your rst files to github.

Code

To contribute code to the project, create a new branch of the analysis pipeline from the github site, make your changes, and create a pull request.

Suggestions / Troubleshooting

For general code suggestions, such as adding new features, or troubleshooting, open up a new issue in the issues page of the github site. You can see an example issue here.