Updating documentation

The R2DT documentation is generated using Sphinx and MyST. The docs are deployed automatically to Read the Docs.

To generate documentation locally:

Start local server and watch for changes:
```
just docs
```
Open http://0.0.0.0:8000 in your browser to view the docs.

Note

An alternative port can be specified using the port variable: just port=3000 docs

Regenerating doc images

The viral genome diagrams in docs/images/ are generated from example inputs in examples/viral/ and examples/hcv-alignment.stk. To regenerate all of them:

just docs-images

This runs viral-annotate, stitch, and stockholm inside Docker against the checked-in example FASTA and Stockholm files, then copies the resulting SVGs into docs/images/. Run this after any algorithm change that affects diagram output, and commit the updated images alongside the code change.

Tip

Use just docs-images some-tag to regenerate against a specific Docker image tag.

Verifying documentation

To check that all hyperlinks are live:

just check-links