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ABIO infra

Infrastructure: entity base classes, serialization, data management, and configuration.

Entities

Core data classes and identity patterns that all biology objects inherit from. - Entity - Base class every biology object carries, with the tree and its dat anchor. - ABIO IO - Entity I/O: prefix bindings, formatting, parsing, persistence.

The Expr Class and Interpreter pages that stood here were retired 2026-10-07 (T068): both described an M1 design in which expression trees were evaluated by an Interpreter object with a do-manager and a lua: escape hatch. The language that shipped is alienbio.expr — forms (Name / Call / Quoted / Include / PyRef), an environment and evaluate(form, env), with three spellings — and it is documented as built in ABIO Expr Spec and ABIO Expr Python API.

Data Management

  • ABIO Data - Organization of the data/ folder and intent-based categories.
  • ABIO DAT - the dvc-dat 3.0 surface the package actually uses (Dat as a duck-typed anchor, MockDat everywhere synthetic).
  • the M1 Bio facade (deleted in M47.7) - Higher-level fetch/store/run for biology objects.
  • ABIO Expr Spec — the Expr language by example: the three spellings, the head catalog, the special forms.
  • ABIO Expr Python API - @biotype for hydration, @scoring/@action/@measurement/@rate for functions.

Installed Packages

  • pydantic - Data validation and settings management.
  • numpy - Numerical arrays for concentration vectors, rate calculations.
  • matplotlib - Plotting concentration curves, debugging visualizations.
  • pyyaml - YAML serialization for entities.
  • pytest - Unit and integration testing.
  • hypothesis - Property-based testing.
  • ruff - Fast linting and formatting.
  • pyright - Static type checking.

Configuration

System configuration and settings management.

(Protocols to be added)

Testing

  • Testing - Testing paradigm for Python and Rust code.