Docs

This folder hosts our tutorial documents used for our readthedocs page as well as functions to create our docs dynamically.

Our readthedocs page is here.

Software Dependencies

Pandoc must be installed to use our PandocConverter class.

You can install it using the pypandoc package as well.

pip install pypandoc

# expects an installed pypandoc: pip install pypandoc
from pypandoc.pandoc_download import download_pandoc
# see the documentation how to customize the installation path
# but be aware that you then need to include it in the `PATH`
download_pandoc()

How-To: Create Our Docs

1. Run createdocs.py using python createdocs.py to regenerate docs.
2. Edit docs for specific add ins. For example, for main documentation in subfolders such as orthologs, reference the documentation files of submodules using submodule <submodulereadme.rst>__
3. Test the docs by running make html in the source folder.
4. Commit the changes and push to the branch.

Creating the modules directory for apidocs

Perform the below command in the root directory of this package. First, remove all of the existing files.

rm -rf Docs/docs/source/modules/*.rst

sphinx-apidoc OrthoEvol/ -o Docs/docs/source/modules