jpfairbanks/SemanticModels.jl: Release v0.3.0

Release v0.3.0

Release v0.3.0 is a major enhancement to the new model augmentation tools introduced the the last release. This includes a more robust design, easier model implementation, and more built in features to augment and compose models.

• New submodules
  • ModelTools
    • SemanticModels.ModelTools.CategoryTheory the main module that contains the category theory based building blocks for model augmentation
      • SemanticModels.ModelTools.CategoryTheory.AbstractMorph abstract type for representing morphisms
      • SemanticModels.ModelTools.CategoryTheory.FinSetMorph morphism in the category of finite sets
      • SemanticModels.ModelTools.CategoryTheory.GraphMorph morphism in the category of graphs
      • SemanticModels.ModelTools.CategoryTheory.⊔ get the union of two categorically defined models or morphisms
      • SemanticModels.ModelTools.CategoryTheory.Decorated a type representing a decoration applied to the objects of a morphism
      • SemanticModels.ModelTools.CategoryTheory.AbstractSpan an abstract type for representing spans
      • SemanticModels.ModelTools.CategoryTheory.Span general span of two morphisms
      • SemanticModels.ModelTools.CategoryTheory.AbstractCospan an abstract type for representing cospans
      • SemanticModels.ModelTools.CategoryTheory.Cospan general cospan of two morphisms
      • SemanticModels.ModelTools.CategoryTheory.pushout solve the pushout defined by a span
    • SemanticModels.ModelTools.PetriModels Extends ModelTools and the new CategoryTheory API to support models defined in Petri.jl
    • SemanticModels.ModelTools.OpenModels module for defining an open model where there are defined inputs and outputs, domain and codomain
    • SemanticModels.ModelTools.OpenPetris module for implementing the open petri model, and converting a PetriModel to an OpenPetri
      • SemanticModels.ModelTools.OpenPetris.otimes combine two open petri models in parallel
      • SemanticModels.ModelTools.OpenPetris.compose combine two open petri models in series
• New examples
  • decorations/graphs.jl example of using the new Category Theory based Morphism API to combine graphs and Petri models
  • petri/malaria.ipynb example of utilizing the new OpenModel API to combine a Lotka Volterra model and an Epidemiology model to simulate Malaria spreading between a population
  • petri/rewrite_demo.jl example of using rewrite rules to augment a Petri model
  • petri/rewrite.jl more detailed example of using rewrite rules to augment a Petri model and then solving the new models using both agent based models and differential equations
  • petri/wiring_petri.jl example of creating a model using wiring diagrams, converting that to a Petri model, and solving
• New docs pages
  • Removed Dubstep
  • Updates to ModelTools
  • Updates to Theory
  • Replaced Flu Model walkthrough with Malaria example