Offline mode

load_expanded_taxa helps you work without a network connection. It downloads a prebuilt SQLite dump of the expanded_taxa table (or converts a TSV file) and caches it locally.

from pathlib import Path
from typus.services.sqlite_loader import load_expanded_taxa

load_expanded_taxa(Path("expanded_taxa.sqlite"))

CLI

typus-load-sqlite --sqlite expanded_taxa.sqlite  # creates recommended indexes

Pass --replace to overwrite, --tsv my.tsv to use a local dump. Downloads are stored in ~/.cache/typus unless $TYPUS_CACHE_DIR is set. Override the source URL with --url or $TYPUS_EXPANDED_TAXA_URL.

Indexes: By default the loader creates expression indexes to accelerate case-insensitive name search and rank filters, and runs ANALYZE. To opt out, pass --no-with-indexes or set create_indexes=False in the programmatic API (expect slower queries).

Sample LCA dataset & tests

The test-suite uses a tiny dataset defined in tests/sample_tsv/expanded_taxa_sample.tsv. Build the corresponding expanded_taxa_sample.sqlite with:

python scripts/gen_fixture_sqlite.py

The resulting file stays well under 100 KB so CI can fetch it quickly.