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Package Design

PlantBiophysics owns scientific model kernels. PlantSimEngine owns scenario assembly, dependency compilation, scheduling, object selection, environments, and output retention.

Each model declares:

  • a process identity;
  • inputs_ and outputs_;
  • optional meteorology inputs;
  • optional model-author dependency defaults through dep;
  • one-timestep equations through run!.

The same kernel can therefore run on one leaf or on millions of leaves without knowing its plant, species, timestep, or coupling context.

Variable Ownership

Keep each value in the contract that owns its lifecycle:

  • inputs_ declares object state read through status, including values bound from another application;
  • environment_inputs_ declares forcing read directly through environment;
  • model fields hold fixed parameters, while the constants argument holds shared physical constants;
  • dep declares hard calls that a model invokes itself;
  • distributed outputs remain outputs of their producer application and are connected with ModelSpec(...; inputs=...) or outputs_to=.... They do not become meteorological inputs merely because they vary over time.

The values in environment_inputs_ are schema representatives, not fallback forcing. PlantSimEngine validates their names against the bound environment before numerical execution. For example, Beer declares Ri_PAR_f, while Monteith declares the meteorological fields used by its energy-balance loop.

Soft Value Dependencies

When one application produces a variable consumed by another application on the same object, PlantSimEngine infers the value binding when it is unique. Cross-object values are declared explicitly with ModelSpec(...; inputs=...).

Manual Calls

Some PlantBiophysics models control an iterative call stack:

  • Monteith calls a photosynthesis model while solving leaf temperature;
  • Fvcb, FvcbIter, and ConstantAGs call stomatal conductance.

These are Call(...) defaults returned by dep(model). PlantSimEngine compiles them to concrete call targets. The parent model decides when to call them and when an accepted result should be published.

State And Generic Values

Runtime variables live in Status. Same-rate coupling uses shared references where possible, and multi-object inputs use reference vectors. PlantBiophysics does not require Float64; units, dual numbers, and uncertainty wrappers can flow through models when their operations are defined.

Scenario Assembly

leaf_scene(models...; status, environment, timestep, type_promotion, status_transform) is the convenience API for one leaf. It delegates to PlantSimEngine's concise CompositeModel constructor after preparing PlantBiophysics model defaults. Larger simulations use PlantSimEngine directly:

ModelSpec(model; name=:application, on=Many(scale=:Leaf), every=Dates.Hour(1))

Plant architecture and scene composition remain outside PlantBiophysics.