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Public Interfaces

This section describes the runtime contracts that readers are expected to use directly.

It has to show more than a list of commands. The runtime exposes several different entry surfaces because different readers need different depths of control and different artifact guarantees.

Interface Families

  • CLI commands for end-to-end workflows and reviewer-facing files
  • workflow Python surfaces under bijux_phylogenetics.api
  • native Python contracts for runtime objects and inference results
  • benchmark and evidence-adjacent runtime contracts
  • emitted artifact and report families

What Each Interface Unlocks

Interface family Best for What the reader gets back
CLI governed command execution files, reports, manifests, and reproducible output directories
Workflow Python notebooks and pipelines typed workflow results with stable writers
Native Python lower-level scientific control direct owned contracts for trees, likelihood, inference, and analysis
Artifact surfaces review and downstream inspection explicit schemas, output families, and consumption rules

Interface Selection Heuristic

If you need Start here Why
one governed workflow or report CLI easiest path to durable artifacts
notebook or pipeline composition workflow Python typed results and stable writers
lower-level runtime control native Python direct access to owned contracts
trust or schema review artifact pages explicit output families and boundaries 
flowchart LR
    A[Need an interface] --> B[CLI]
    A --> C[Workflow Python]
    A --> D[Native Python]
    A --> E[Artifact surfaces]
    B --> F[Files and reports]
    C --> G[Typed workflow results]
    D --> H[Lower-level owned contracts]
    E --> I[Schema and output review]

Why This Section Matters

The package looks smaller than it is when all interfaces are described as if they were one generic API. They are not:

  • the CLI is optimized for governed runs and durable outputs
  • the workflow API is optimized for typed orchestration in Python
  • the native runtime surface is optimized for readers who need owned lower-level scientific contracts
  • the artifact pages are optimized for downstream consumers and reviewers

Start Here

  • If you need help choosing an entry point, use the surface selection guide.
  • If you already know the entry point, continue to the matching reference page below.

Section Map

The surface selection guide and artifact consumption guide are the two fastest ways to orient a new reader before they drop into the larger CLI and Python reference pages.