Default axis inheritance for states

[jc-macdonald]

Summary

States should inherit all declared axes by default, with bracket syntax only needed for asymmetric (per-state) overrides.

Problem

Currently every state gets an empty axis set unless explicitly listed in state_axes. This means a model with 3 axes and 5 states requires a state_axes block mapping every state to every axis, even when they all share the same structure. The talk and proposed spec syntax show bare state: [S, E, I, R] with the expectation that all states expand over all declared axes automatically.

Proposed Behavior

1. Default: All states inherit all declared axes (full Cartesian product).
2. Override via bracket syntax: S[age] means S only carries the age axis. I[age,strain] means I carries both. A bare S means "inherit all axes."
3. Explicit state_axes: Still supported as an alternative to bracket syntax for backward compatibility.
4. Interaction with constraints (Add axis masking to avoid empty compartments #31/Constraint filtering for state, alias, and transition expansion #37): Default inheritance + constraints gives the same effect as asymmetric membership but with less boilerplate.

Proposed Syntax

spec:
  axes:
    - {name: age, type: continuous, coords: [0, 5, 18, 50, 65, 100]}
    - {name: vax, coords: [unvaccinated, 1dose, waned]}
  # All states get both axes by default:
  state: [S, E, I, R]

  # Or override per-state:
  state: [S[age,vax], E[age,vax], I[age,vax,strain], R[age]]

Scope

• When no state_axes block and no bracket syntax: every state inherits all axes
• Parse bracket syntax in state list entries to extract per-state axis overrides
• Validate bracket axis references against declared axes
• Preserve backward compatibility with explicit state_axes block
• Update tests and documentation

Related

• Shown in InsightNet talk slides 3, 4, 5 as assumed behavior
• Constraint filtering for state, alias, and transition expansion #37 — constraint filtering (alternative to asymmetric membership)
• Model specification guide: defining compartmental systems #45 — model specification guide (must document this feature)
• Add coord_shift transition type for axis-coordinate transitions #47 — coord_shift (relies on states carrying the shifted axis)