Create Documentation Script (create_documentation.sh)

Overview

The create_documentation.sh script automates the process of generating local documentation for the bionemo.moco project and ensures its accuracy by performing a post-generation cleanup. This process enhances discoverability and maintainability of the project's codebase including local changes.

Usage

./create_documentation.sh

Step-by-Step Process Explained

1. Generating Documentation with pydoc-markdown

• Command: pydoc-markdown -I src/bionemo --render-toc > documentation.md
• Description: This step leverages pydoc-markdown to parse the src/bionemo directory, generating Markdown documentation. The --render-toc flag includes a Table of Contents for easier navigation. The output is redirected to a file named documentation.md.

2. Cleaning and Refining Documentation

• Command: python scripts/clean_documentation.py
• Description: Following the initial documentation generation, this Python script (clean_documentation.py) is executed to:
  • Remove redundant or unnecessary sections.
  • Ensure proper linkage within the documentation (e.g., fixing internal references).
  • Optionally, format code blocks and tables for better readability.

Output

• Location: The refined documentation will be available in the project's root directory as documentation.md.
• Content: A comprehensive, readable, and accurately linked documentation for bionemo.moco, covering modules, classes, functions, and variables documented within the src/bionemo directory.