2025-sourmash-databases-doc-template

This repo uses Jinja2 templating to automatically produce Markdown files describing the available sourmash databases. It also produces automated scripts that check that the relevant files are available for download.

Basic instructions

Run make. Then look at outputs/md to see output markdown.

Previewing formatting with mkdocs

Run mkdocs serve to see the generated files.

Updating the database list in the sourmash docs

Copy all the files in outputs/md/ into the sourmash repo under doc/databases-md/.

Adding databases

Edit scripts/databases.py to add databases.

You'll also need to:

• add the new db to 'collections' list at top of scripts/make-md.py.
• update mkdocs.yml if you want to preview the new db;
• update doc/databases.md in sourmash to include a direct link to the generated file.

Validating database links

Run outputs/scripts/check-urls.py to check that all the database and taxonomy URLs are valid.

Notes on database naming conventions:

• all NCBI databases will be date-stamped
• all GTDB databases will be version-stamped