polli-typus 0.3.0

Taxonomic types, projections and async taxonomy services for Polli-Labs.

Typus

Shared taxonomy & geo‑temporal types for the Polli‑Labs ecological stack

Typus centralises every domain object that the rest of our platform — linnaeus, pollinalysis-server, dashboards … — needs: taxon records, clades, hierarchical classification results, projection helpers and async database services. Anything that speaks taxonomy imports Typus and stays DRY.

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Features

• Wide ancestry view – expanded_taxa ORM exposes each rank (L10 → L70) on a single row for constant‑time lineage queries.
• Async services – PostgresTaxonomyService (ltree) & SQLiteTaxonomyService (fixture) share one interface.
• Pydantic v2 models – Taxon, Clade, HierarchicalClassificationResult, all JSON‑Schema‑exportable.
• Projection utils – lat/lon ↔ unit‑sphere, cyclical‑time features, multi‑scale elevation sinusoids.
• Optional drivers only when you need them – install polli-typus[postgres] or [sqlite]; core install stays lightweight.
• Offline SQLite loader – typus-load-sqlite CLI builds and caches the offline dataset

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Requirements

• Python ≥ 3.10

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Installation

Core (no DB drivers)

uv pip install polli-typus        # import typus

With Postgres backend

uv pip install "polli-typus[postgres]"    # adds asyncpg

With SQLite only (CI, offline, sandboxes)

uv pip install "polli-typus[sqlite]"

Development / tests / lint

uv pip install -e ".[dev,sqlite]"   # pytest, pytest-asyncio, ruff, pre-commit, aiosqlite …

Install with plain pip:

pip install -e ".[dev,sqlite]"

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Quick start

from typus import PostgresTaxonomyService, RankLevel, latlon_to_unit_sphere

svc = PostgresTaxonomyService("postgresql+asyncpg://user:pw@host/db")
bee = await svc.get_taxon(630955)           # Anthophila
print(bee.scientific_name, bee.rank_level)  # Anthophila RankLevel.L32

print(latlon_to_unit_sphere(31.5, -110.4))  # → x, y, z on S²

Offline mode (SQLite fixture)

from pathlib import Path
from typus.services import SQLiteTaxonomyService, load_expanded_taxa

db = Path("expanded_taxa.sqlite")
load_expanded_taxa(db)  # downloads if missing
svc = SQLiteTaxonomyService(db)

typus-load-sqlite --sqlite expanded_taxa.sqlite

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Developer guide

• Lint & tests (one‑liner)

  ruff check . && ruff format . && pytest -q
  

• Format whole repo

  ruff format .
  

• JSON Schemas – python -m typus.export_schemas → typus/schemas/

• SQLite fixture – python scripts/gen_fixture_sqlite.py

• Pre‑commit hooks – pre-commit install

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Publishing (maintainers)

See build/typus_publish.md for tag → TestPyPI → PyPI workflow.

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License

MIT © 2025 Polli Labs