Refactor Julia interop to use elaborated model/diagram

packages/algjulia-interop/Project.toml

@@ -18,15 +18,14 @@ IJulia = "7073ff75-c697-5162-941a-fcdaad2a7d2a"
 JSON3 = "0f8b85d8-7281-11e9-16c2-39a750bddbf1"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 MLStyle = "d8e11817-5142-5d16-987a-aa16d5891078"
+OrderedCollections = "bac558e1-5e72-5ebc-8fee-abe8a469f55d"
 OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
+PackageCompiler = "9b87118b-4619-50d2-8e1e-99f35a4d4d9d"
 Preferences = "21216c6a-2e73-6563-6e65-726566657250"
 REPL = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb"
 Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
 StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
 
-[weakdeps]
-PackageCompiler = "9b87118b-4619-50d2-8e1e-99f35a4d4d9d"
-
 [extensions]
 SysImageExt = "PackageCompiler"
 
@@ -44,6 +43,7 @@ IJulia = "1.26.0"
 JSON3 = "1"
 LinearAlgebra = "1"
 MLStyle = "0.4"
+OrderedCollections = "1.8.1"
 OrdinaryDiffEq = "6.101.0"
 PackageCompiler = "2.2.1"
 Preferences = "1.5.0"

packages/algjulia-interop/docs/literate/json.jl

@@ -0,0 +1,5 @@
+using CatColabInterop
+
+using JSON3
+
+json = JSON3.read(read("test/test_jsons/_payload.json"))

packages/algjulia-interop/src/CatColabInterop.jl

@@ -1,86 +1,33 @@
 module CatColabInterop
 
+import Base: run
+using JSON3
 using MLStyle
 using Reexport
 
 # this code tracks integrations and allows for basic theory/model-building code to dispatch from it.
 # the intent is that this is an interface for AlgebraicJulia code to interoperate with CatColab 
 abstract type AlgebraicJuliaIntegration end 
 
-# cells in the JSON are tagged. these are just objects for dispatching `to_model`
-@data ModelElementTag begin
-    ObTag()
-    HomTag()
-end
-export ObTag, HomTag
-
-#=
-@active patterns are MLStyle-implementations of F# active patterns that forces us to work in the Maybe/Option pattern. 
-Practically, yet while a matter of opinion, they make @match statements cleaner; a statement amounts to a helpful pattern
-name and the variables we intend to capture.
-=# 
-@active IsObject(x) begin; x[:content][:tag] == "object" ? Some(x[:content]) : nothing end
-@active IsMorphism(x) begin; x[:content][:tag] == "morphism" ? Some(x[:content]) : nothing end
-export IsObject, IsMorphism
-
-# Obs, Homs
-@data ModelElementValue begin
-    ObValue()
-    HomValue(dom,cod)
-end
-export ObValue, HomValue
-
-""" 
-Struct capturing the name of the object and its relevant information. 
-ModelElementValue may be objects or homs, each of which has different data. 
-"""
-struct ModelElement
-    name::Union{Symbol, Nothing}
-    val::Union{<:ModelElementValue, Nothing}
-    function ModelElement(;name::Symbol=nothing,val::Any=nothing)
-        new(name, val)
-    end
-end
-export ModelElement
-
-Base.nameof(t::ModelElement) = t.name
-
-""" Struct wrapping a dictionary """
-struct Model{T<:AlgebraicJuliaIntegration}
-    data::Dict{String, ModelElement}
-end
-export Model
-
-function Model(::T) where T<:AlgebraicJuliaIntegration
-    Model{T}(Dict{String, ModelElement}())
-end
-
-Base.values(model::Model) = values(model.data)
-
-""" 
-Functions to build a dictionary associating ids in the theory to elements in the model
-"""
-function to_model end
-export to_model
-
-
-# TODO supposes bijection between theories, models, diagrams, etc.
-abstract type AbstractDiagram{T<:AlgebraicJuliaIntegration} end
-
-abstract type AbstractAnalysis{T<:AlgebraicJuliaIntegration} end
+#= These files are responsible for parsing the model and diagram in the CCL payload =#
+include("qualified_name.jl")
+include("model.jl")
+include("diagram.jl")
+include("payload.jl") # payload and analysis are here
 
 struct ImplError <: Exception
     name::String
 end
 export ImplError
-
 Base.showerror(io::IO, e::ImplError) = print(io, "$(e.name) not implemented")
 
-include("result.jl")
-include("kernel_management.jl")
-include("kernel_support.jl")
+# Kernel utilities
+include("kernel/KernelUtility.jl")
+
+#= The Decapodes service contains an analysis =#
 include("decapodes-service/DecapodesService.jl")
 
+@reexport using .KernelUtility
 @reexport using .DecapodesService
 
 end

packages/algjulia-interop/src/decapodes-service/DecapodesService.jl

@@ -1,5 +1,7 @@
 module DecapodesService
 
+import Base: run
+
 # algebraicjulia dependencies
 using ACSets
 using DiagrammaticEquations
@@ -17,26 +19,37 @@ using Distributions # for initial conditions
 # meshing
 using CoordRefSystems
 using GeometryBasics: Point2, Point3
-Point3D = Point3{Float64};
+Point3D = Point3{Float64}
 
 # simulation
 using OrdinaryDiffEq
 
 using ..CatColabInterop
 using ..CatColabInterop: AlgebraicJuliaIntegration, AbstractDiagram, AbstractAnalysis
-import ..CatColabInterop: Model, to_model
+import ..CatColabInterop: Model, ObGenerator, MorGenerator, DiagramObGenerator, DiagramMorGenerator
 
 # necessary to export
-export infer_types!, evalsim, default_dec_generate, default_dec_matrix_generate,
-    DiagonalHodge, ComponentArray
+export infer_types!, evalsim, default_dec_generate, default_dec_matrix_generate, DiagonalHodge, ComponentArray
 
 struct ThDecapode <: AlgebraicJuliaIntegration end
 export ThDecapode
 
-# funcitons for geometry and initial conditions
+# functions for geometry and initial conditions
 include("geometry.jl")
-include("model.jl") ## model-building
-include("diagram.jl") ## diagram-building
-include("analysis/Analysis.jl")
+
+# responsible for constructing a valid model 
+include("model.jl")
+
+# helper functions for Navier-Stokes
+include("ns_helper.jl")
+
+# constructing initial conditions
+include("initial_conditions.jl")
+
+# parses a payload to a valid analysis 
+include("parse.jl")
+
+# executes the analysis 
+include("execute.jl")
 
 end