README.md

Funannotate2 Documentation

This directory contains the documentation for Funannotate2.

Building the Documentation

To build the documentation, you need to have Sphinx installed:

pip install sphinx sphinx_rtd_theme

Then, you can build the documentation:

cd docs
make html

The built documentation will be in the _build/html directory.

Documentation Structure

• index.rst: Main index file
• installation.rst: Installation instructions
• usage.rst: Usage guide
• modules.rst: Module reference
• API.rst: API reference
• tutorial.rst: Tutorial
• faq.rst: Frequently asked questions
• changelog.rst: Changelog
• API/: Directory containing API documentation for each module
  • clean.rst: Documentation for the clean module
  • predict.rst: Documentation for the predict module
  • annotate.rst: Documentation for the annotate module
  • compare.rst: Documentation for the compare module
  • search.rst: Documentation for the search module
  • utilities.rst: Documentation for the utilities module
  • log.rst: Documentation for the log module