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 protocol for all biology objects. - Expr - Functional expression trees for computations and rate equations. - Interpreter - Evaluates Expr trees, handles language dispatch and template expansion. - IO - Entity I/O: prefix bindings, formatting, parsing, persistence.

Data Management¶

ABIO Data - Organization of the data/ folder and intent-based categories.
ABIO DAT - dvc_dat integration, name resolution, and _spec_.yaml format.
Bio - Higher-level fetch/store/run for biology objects.
Spec Language Reference — YAML syntax extensions (!ev, !_, !ref, !include, typed keys).
Decorators - @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.
pyo3 - Rust-Python bindings for high-performance simulator.
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.