Configuration

Biofilter resolves settings from:

  1. command-line options (highest priority)

  2. environment variables (DATABASE_URL or BIOFILTER_DB_URI)

  3. .biofilter.toml

  4. internal defaults

Common Commands

Show resolved config:

biofilter config show

Get one value:

biofilter config get database.db_uri

Set one value:

biofilter config set database.db_uri "sqlite:///biofilter_dev.db"

Initialize template:

biofilter config init --path .

Typical Keys

  • database.db_uri

  • etl.data_root

Tips

  • Prefer --db-uri in CI or one-off commands.

  • Prefer DATABASE_URL in containers and orchestrators.

  • Prefer .biofilter.toml for local development defaults.