Example models missing parameter values/distributions, rate laws, observables, and state initial values

[SamWitty]

A fully specified AMR should contain all of the following components:

• Parameter values/distributions
• Rate laws expressions
• Observables (Optional)
• State Initial values

Currently, none of the examples in this repository contain all 4 of these components. The following list summarizes my current accounting of which models contain which components. Completion of this issue will involve updating each example accordingly.

Parameter values/distributions

• [ ] petrinet/flux_typed
• [ ] petrinet/flux_typed_aug
• [ ] petrinet/ont_pop_vax
• [x] petrinet/sir
• [x] petrinet/sir_flux_span
• [x] petrinet/sir_typed
• [x] petrinet/sir_typed_aug
• [x] regnet/lotka_volterra
• [x] regnet/syntax_edge_cases
• [x] stockflow/sir

Rate Law expressions

• [ ] petrinet/flux_typed
• [ ] petrinet/flux_typed_aug
• [ ] petrinet/ont_pop_vax
• [x] petrinet/sir
• [x] petrinet/sir_flux_span
• [x] petrinet/sir_typed
• [x] petrinet/sir_typed_aug
• [ ] regnet/lotka_volterra
• [ ] regnet/syntax_edge_cases
• [x] stockflow/sir

Observables

• [ ] petrinet/flux_typed
• [ ] petrinet/flux_typed_aug
• [ ] petrinet/ont_pop_vax
• [x] petrinet/sir
• [ ] petrinet/sir_flux_span
• [ ] petrinet/sir_typed
• [ ] petrinet/sir_typed_aug
• [ ] regnet/lotka_volterra
• [ ] regnet/syntax_edge_cases
• [ ] stockflow/sir

State initial values

• [ ] petrinet/flux_typed
• [ ] petrinet/flux_typed_aug
• [ ] petrinet/ont_pop_vax
• [x] petrinet/sir
• [x] petrinet/sir_flux_span
• [x] petrinet/sir_typed
• [x] petrinet/sir_typed_aug
• [x] regnet/lotka_volterra
• [x] regnet/syntax_edge_cases
• [x] stockflow/sir

[JosephCottam]

Model-checker (draft) now available in https://github.com/ciemss/Model-Representations/tree/jc-model-checks

Tries to compute the checkmarks @SamWitty listed above. Run as python validation/model_inventory.py petrinet/examples/*.json.

@SamWitty -- Does this checking make sense? Right now it looks at both pdeandodeinsemantics`, but I don't know if that is the right thing (I only have a few examples to go off of).

@djinnome -- The check_schema function validation/model_inventory.py is what I plan to use as the filter for my model-loading function.

[SamWitty]

@JosephCottam, sorry I missed this message. I never received an email notification for some reason, which usually happens ...

These checks looks great. Could you make a PR to this repo? I'd recommend assigning @bgyori as a reviewer.