docs/README.md

Useful Tips on How to Build the Documentation

Steps

1. Install sphinx and sphinx_rtd_theme:

   pip install sphinx sphinx_rtd_theme
   

2. Create a docs directory in the root of the project:

    mkdir docs
   

3. Create the documentation structure:

   cd docs
   sphinx-quickstart
   

   • Answer the questions as follows:
     • Separate source and build directories (y/n) [n]: n
     • Project name: PROTAC-Degradation-Predictor
     • Author name(s): Your Name
     • Project version: v1.0.1

4. Edit the conf.py file:
   • Add the following lines:

     import os
     import sys
     sys.path.insert(0, os.path.abspath('..'))
     

   • Add the following line to the extensions list:

     'sphinx.ext.autodoc',
     

   • Check the current conf.py file in this repository for more details.
5. Create modules rst files: sphinx-apidoc -o docs/source/ ./protac_degradation_predictor
6. To include modules in the documentation, in index.rst, add the following line: source/modules
7. Setup the gh-pages branch:

   git checkout --orphan gh-pages
   git reset --hard
   git commit --allow-empty -m "Init"
   git push origin gh-pages
   git checkout main
   

8. Generate the specific workflow Action file:
   • See file .github/workflows/gh-pages.yml in this repository.
9. The start page is in the file index.rst.

Miscellaneous

• Useful guide
• Automatically create modules rst files: sphinx-apidoc -o source/ ../protac_degradation_predictor
  • Then, in index.rst, add the following line: source/modules
• Build the documentation: make clean ; make html