Dockstore Documentation

Dockstore is using Read the Docs for documentation! Please take a look at our style guide to learn about our approach to documentation.

Below are some tips for setting up the documentation locally and updating the code.

Setting up locally

Install pip dependencies (Requires Python 3.9+) pip install -r requirements.txt

Go to the docs directory cd docs

Generate the HTML to generate HTML pages in a new folder called _build make html

Check for broken links make linkcheck

Open the _build/html/index.html in your browser!

OICR affilates can view additional developer docs here: https://wiki.oicr.on.ca/display/DOC/Read+The+Docs

Writing/Maintaining docs

Most of our docs are written in RST. A handful are written are in markdown. Both the RST and markdown documents will be rendered as HTML using the Python-based documentation manager Sphinx.

Most of our docs can be maintained by modifying individual RST and MD files directly. There are a few exceptions:

• When creating a new page, it must exist on the table of contents (toctree) which forms the sidebar on the left — in most cases this requires adding a new entry to index.rst
• dictionary.rst is generated from entries in docs/_attic/glossary_entries.py by docs/_attic/glossary_generator.py in order to easily handle the complexities of large RST documents — dictionary.rst is regenerated upon every make command (changes will not appear in git unless docs/_attic/glossary_entries.py is modified), but this regeneration can also be called explictly with make glossary
• Certain doi.org links, plus any images that link to internal documents, must have those links added to linkcheck_ignore in conf.py