Source repository for the Sphinx documentation of the bigbio/quantms Nextflow pipeline.

Docs Creation

The documentation is built by ReadTheDocs. You can see previews of your changes for a PR-specific build on ReadTheDocs project builds, and under the Actions tab of this PR.

Local Build

In order to build the docs, you need to

1. Install sphinx and additional support packages
2. Build the package reference files
3. Run sphinx to create a local html version

Install the docs dependencies of the package (as specified in requirements.txt):

# in main folder
pip install -r requirements.txt

Run the following command inside the docs folder to build the HTML:

# build page in docs folder
python setup_docs.py # downloads files from bigbio/quantms/docs folder, 
                     # called in conf.py if built on Read The Docs.
sphinx-build -n -W --keep-going -b html ./ ./_build/