bijux-pollenomics

bijux-pollenomics is the canonical runtime for the Pollenomics evidence and publication system. It keeps pollen, environmental archaeology, boundaries, lake registries, human ancient DNA, and curated animal ancient DNA in distinct evidence roles while collecting, reviewing, ranking, and publishing governed products.

The runtime applies contracts; it is not a bundled evidence database. Source captures, curated records, review decisions, and report products are supplied through explicit filesystem roots and retain versions independent of the package version.

Install

python3.11 -m pip install bijux-pollenomics
bijux-pollenomics --version
bijux-pollenomics product-scope --json

Python 3.11 or newer is required. Inspection commands work without repository data. Collection, review, and publication commands require explicit governed roots; their defaults are relative to the current working directory.

Distribution Boundary

The repository checkout is the reference environment when runtime, governed evidence, and checked-in products must be inspected together. A wheel version identifies behavior; a data revision identifies evidence state; a product manifest identifies publication membership.

Choose The Runtime Context Deliberately

These contexts can run identical Python code while answering different questions. An installed-wheel result cannot identify which repository evidence revision was intended. A checkout does not make every tracked product rebuildable when its lifecycle matrix declares missing preparation stages. A candidate proves only the state it contains until its identities and semantic diff are accepted into a governed root.

Choose An Operation

Begin with the read-only contract. A writer is appropriate only when its input identity, output roots, replacement behavior, and post-write review are known.

Runtime Architecture

flowchart LR
    Command["command and explicit roots"] --> Collect["source collection"]
    Collect --> Normalize["family-aware normalization"]
    Normalize --> Evidence["owned evidence objects and relations"]
    Evidence --> Review["claim-specific review"]
    Review --> Gate{"publication contract"}
    Gate -->|admit or qualify| Product["manifested product"]
    Gate -->|exclude or refuse| Negative["gap, caveat, or refusal"]

Command Surface

bijux-pollenomics --help
bijux-pollenomics source-support --json
bijux-pollenomics adna-species-review --species ovis_aries --json
bijux-pollenomics collect-data --help
bijux-pollenomics publish-reports --help

Collection and publication are state-changing operations. Pass source, data, context, AADR, and output roots explicitly in automation so a valid command cannot silently address the wrong filesystem state.

Python Surface

The supported public namespace is bijux_pollenomics:

from bijux_pollenomics import (
    build_product_scope,
    collect_data,
    generate_published_reports,
)

Use the top-level API where possible. Import implementation modules only when the integration deliberately owns that narrower contract. Public API schemas are frozen under apis/bijux-pollenomics/v1/ in the repository.

Evidence guarantees

The runtime guarantees contract behavior, not universal evidence quality:

• captured source identity remains distinct from repository interpretation;
• normalization does not imply scientific or publication fitness;
• review may qualify or refuse unsupported precision and comparison;
• publication membership is explicit in a versioned manifest;
• product descendants cannot strengthen their governing evidence;
• missing lifecycle stages remain missing rather than being inferred from a final export; and
• evidence, decision, and product identifiers remain independently auditable.

A reusable handoff records the package version, explicit roots, source or data revision, governed object IDs, decision IDs, product manifest and members, and focused verification. A dataframe, GeoJSON file, or rendered map without that packet is a transport form, not a complete evidence product.

Canonical And Short Names

bijux-pollenomics and bijux_pollenomics are the canonical distribution, command, and import identities. The pollenomics distribution forwards a short command and import prefix to this runtime. It does not define independent schemas, scientific behavior, or evidence state.

Read Next

• Product handbook
• Runtime architecture
• CLI and Python interfaces
• Evidence database
• Runtime package boundaries