quartodoc integration

docs/api/README.md

@@ -0,0 +1,59 @@
+# Axolotl API Documentation with quartodoc
+
+This directory contains the API documentation for Axolotl, automatically generated using quartodoc.
+
+## Setup
+
+1. Make sure quartodoc is installed:
+   ```
+   pip install quartodoc
+   ```
+
+2. Install Quarto (required to render the documentation):
+   ```
+   # Download and install the latest Quarto release
+   # Visit https://quarto.org/docs/get-started/ for installation instructions
+   ```
+
+## Generating Documentation
+
+Run the documentation generation script:
+```
+python scripts/generate_docs.py
+```
+
+This will:
+- Read the configuration from `_quarto.yml`
+- Extract documentation from the Python source code
+- Generate Quarto markdown files (.qmd) in the `docs/api` directory
+
+## Preview the Documentation
+
+After generating the documentation, preview it with:
+```
+quarto preview
+```
+
+## Building the Site
+
+Build the complete site with:
+```
+quarto render
+```
+
+This will create a `_site` directory with the static HTML site.
+
+## Configuration
+
+The documentation generation is configured in two places:
+
+1. `_quarto.yml` - Contains the `quartodoc` section that defines which modules to document
+2. The API section in the Quarto website sidebar configuration (also in `_quarto.yml`)
+
+## Customization
+
+To customize the documentation, you can:
+
+1. Add more modules to document in the `quartodoc` section of `_quarto.yml`
+2. Create template files in the `quartodoc_templates` directory
+3. Adjust the layout in the Quarto configuration