Merge branch 'main' into jpf/formulas-examples

.github/workflows/TagBot.yml

@@ -27,4 +27,4 @@ jobs:
     steps:
       - uses: JuliaRegistries/TagBot@v1
         with:
-          token: ${{ secrets.RELEASE_TOKEN }}
+          token: ${{ secrets.SERVICE_TOKEN }}

Project.toml

@@ -2,25 +2,25 @@ name = "SyntacticModels"
 uuid = "22bb929c-8bcf-4852-b455-eb3e1675e09c"
 license = "MIT"
 authors = ["James Fairbanks <[email protected]>"]
-version = "0.1.0"
+version = "0.2.0"
 
 [deps]
 ACSets = "227ef7b5-1206-438b-ac65-934d6da304b8"
 Catlab = "134e5e36-593f-5add-ad60-77f754baafbe"
-Decapodes = "679ab3ea-c928-4fe6-8d59-fd451142d391"
+DiagrammaticEquations = "6f00c28b-6bed-4403-80fa-30e0dc12f317"
 JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
 JSON3 = "0f8b85d8-7281-11e9-16c2-39a750bddbf1"
 MLStyle = "d8e11817-5142-5d16-987a-aa16d5891078"
 Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
 StructTypes = "856f2bd8-1eba-4b0a-8007-ebc267875bd4"
 
 [compat]
-Reexport = "1"
-Catlab = "0.15"
-JSON = "0.21"
 ACSets = "0.2"
-Decapodes = "0.4"
-StructTypes = "1"
+Catlab = "0.16"
+DiagrammaticEquations = "0.1.1"
+JSON = "0.21"
 JSON3 = "1"
 MLStyle = "0.4"
-julia = "1.9"
+Reexport = "1"
+StructTypes = "1"
+julia = "1.10"

README.md

@@ -2,11 +2,11 @@
 
 [![Stable Documentation](https://img.shields.io/badge/docs-stable-blue.svg)](https://AlgebraicJulia.github.io/SyntacticModels.jl/stable)
 [![Development Documentation](https://img.shields.io/badge/docs-dev-blue.svg)](https://AlgebraicJulia.github.io/SyntacticModels.jl/dev)
-[![Code Coverage](https://codecov.io/gh/AlgebraicJulia/SyntacticModels.jl/branch/main/graph/badge.svg)](https://codecov.io/gh/AlgebraicJulia/SyntacticModelse.jl)
+[![Code Coverage](https://codecov.io/gh/AlgebraicJulia/SyntacticModels.jl/branch/main/graph/badge.svg)](https://codecov.io/gh/AlgebraicJulia/SyntacticModels.jl)
 [![CI/CD](https://github.com/AlgebraicJulia/SyntacticModels.jl/actions/workflows/julia_ci.yml/badge.svg)](https://github.com/AlgebraicJulia/SyntacticModels.jl/actions/workflows/julia_ci.yml)
 
 A package for building languages for model representations.
 
 ## 🛠️ Usage
 
-See the literate code examples in the [documentation](https://AlgebraicJulia.github.io/SyntacticModels.jl/dev).
+See the literate code examples in the [documentation](https://AlgebraicJulia.github.io/SyntacticModels.jl/dev).

docs/Project.toml

@@ -1,7 +1,7 @@
 [deps]
 ACSets = "227ef7b5-1206-438b-ac65-934d6da304b8"
 Catlab = "134e5e36-593f-5add-ad60-77f754baafbe"
-Decapodes = "679ab3ea-c928-4fe6-8d59-fd451142d391"
+DiagrammaticEquations = "6f00c28b-6bed-4403-80fa-30e0dc12f317"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 JSON3 = "0f8b85d8-7281-11e9-16c2-39a750bddbf1"
 Literate = "98b081ad-f1c9-55d3-8b20-4c87d4299306"

docs/literate/composite_models_examples.jl

@@ -14,6 +14,7 @@ import SyntacticModels.ASKEMDecapodes.Decapodes as Decapodes
 using Catlab
 using Catlab.RelationalPrograms
 using Catlab.WiringDiagrams
+using DiagrammaticEquations
 using Test
 using JSON3
 
@@ -58,7 +59,7 @@ h = AMR.Header("harmonic_oscillator",
 
 # The easiest way to write down a DecaExpr is in our DSL and calling the parser.
 # This formula is $$∂ₜ(∂ₜ(x)) = -kx$$.
-dexpr = Decapodes.parse_decapode(quote
+dexpr = DiagrammaticEquations.parse_decapode(quote
   X::Form0{Point}
   V::Form0{Point}
 
@@ -81,7 +82,7 @@ d2 = ASKEMDecaExpr(
    "modelreps.io/SummationDecapode",
    "Velocity makes it get hot, but you dissipate heat away from Q₀",
    "SummationDecapode", "v1.0"),
-    Decapodes.parse_decapode(quote
+    DiagrammaticEquations.parse_decapode(quote
       V::Form0{Point}
       Q::Form0{Point}
       κ::Constant{Point}
@@ -134,7 +135,7 @@ uwdʰ = UWDExpr([v, Q], [Statement(:drag, [v, Q₊]), Statement(:cooling, [Q₋,
 #
 drag = ASKEMDecaExpr(
   AMR.Header("DragHeat", "modelreps.io/SummationDecapode", "velocity makes it get hot", "SummationDecapode", "v1.0"),
-  Decapodes.parse_decapode(quote
+  DiagrammaticEquations.parse_decapode(quote
     V::Form0{Point}
     Q₊::Form0{Point}
     κ::Constant{Point}
@@ -148,7 +149,7 @@ drag = ASKEMDecaExpr(
 
 cooling = ASKEMDecaExpr(
   AMR.Header("NetwonCooling", "modelreps.io/SummationDecapode", "heat dissipates to the enviornment", "SummationDecapode", "v1.0"),
-  Decapodes.parse_decapode(quote
+  DiagrammaticEquations.parse_decapode(quote
     Q₋::Form0{Point}
     Q₀::Parameter{Point}
     Q::Form0{Point}
@@ -162,7 +163,7 @@ cooling = ASKEMDecaExpr(
 
 superposition = ASKEMDecaExpr(
   AMR.Header("LinearSuperpositon", "modelreps.io/SummationDecapode", "variables be addin", "SummationDecapode", "v1.0"),
-  Decapodes.parse_decapode(quote
+  DiagrammaticEquations.parse_decapode(quote
     X::Form0{Point}
     Y::Form0{Point}
     T::Form0{Point}

docs/literate/decapodes_examples.jl

@@ -15,7 +15,7 @@ using JSON3
 using Catlab
 using ACSets
 using ACSets.JSONACSets
-using Decapodes
+using DiagrammaticEquations
 using Test
 
 # Build the header object describing the model.
@@ -29,7 +29,7 @@ h = AMR.Header("harmonic_oscillator",
 # The easiest way to write down a DecaExpr is in our DSL and calling the parser.
 # This example is $$x'' = -kx$$. We have manual transformed this into first order ODE
 # by introducing a velocity variable for $$x'$$.
-dexpr = Decapodes.parse_decapode(quote
+dexpr = DiagrammaticEquations.parse_decapode(quote
   X::Form0{Point}
   V::Form0{Point}
 
@@ -46,7 +46,7 @@ mexpr = ASKEMDecaExpr(h, dexpr)
 # Convert a the DecaExpr to a SummationDecapode which is the
 # combinatorial representation. The converter lives in Decapodes/src/language.jl.
 
-d = Decapodes.SummationDecapode(mexpr.model)
+d = DiagrammaticEquations.SummationDecapode(mexpr.model)
 
 # To visualize the Decapode as a compute graph, you can use Graphviz
 

src/SyntacticModelsBase.jl

@@ -1,6 +1,7 @@
 module SyntacticModelsBase
 
 using StructTypes
+using DiagrammaticEquations
 using JSON3
 import Base: Dict
 
@@ -23,6 +24,7 @@ _dict(x::Symbol) = x
 _dict(x::String) = x
 _dict(x::Number) = x
 _dict(x::AbstractVector) = map(_dict, x)
+_dict(x::DiagrammaticEquations.decapodes.Judgement) = x
 
 """    _dict(x::T) where T <: AbstractTerm
 
@@ -60,4 +62,4 @@ StructTypes.StructType(::Type{AbstractTerm}) = StructTypes.AbstractType()
 This is how you tell StructTypes where to look for the name of a type when reading the type back in from JSON.
 """
 StructTypes.subtypekey(::Type{AbstractTerm}) = :_type
-end
+end

src/amr.jl

@@ -4,13 +4,15 @@ export Math, MathML, ExpressionFormula, Unit, Distribution, Observable, Expressi
  Rate, Initial, Parameter, Time,
  StandardUniform, Uniform, StandardNormal, Normal, PointMass,
  Semantic, Header, ODERecord, ODEList, Typing, ASKEModel,
- distro_string, amr_to_string
+ distro_string, amr_to_string,
+ Annotation, Note, Name, Description, Grounding, Units
 
 using Reexport
 @reexport using MLStyle
 @reexport using ACSets
 using ACSets.ADTs
 using ACSets.ACSetInterface
+using StructTypes
 
 using ..SyntacticModelsBase
 
@@ -64,6 +66,24 @@ end
   # Stratification
 end
 
+@data Note <: AbstractTerm begin
+  Name(str::String)
+  Description(str::String)
+  Grounding(ontology::String, identifier::String)
+  Units(expression::String)
+end
+
+StructTypes.StructType(::Type{Note}) = StructTypes.AbstractType()
+StructTypes.subtypekey(::Type{Note}) = :_type
+StructTypes.subtypes(::Type{Note}) =
+  (Name=Name,Description=Description,Grounding=Grounding,Units=Units,)
+
+@as_record struct Annotation{E,T} <: AbstractTerm
+  entity::E
+  type::T
+  note::Note
+end
+
 @as_record struct Header <: AbstractTerm
   name::String
   schema::String
@@ -92,6 +112,19 @@ function distro_expr(d::Distribution)
   return Base.Meta.parse(distro_string(d))
 end
 
+function note_string(n::Note)
+  @match n begin
+    Name(n)           => "Name($n)"
+    Description(d)    => "Description($d)"
+    Grounding(ont, ident) => "Grounding($ont,$ident)"
+    Units(e)          => "Units($e)"
+  end
+end
+
+function note_expr(n::Note)
+  return Base.Meta.parse(note_string(n))
+end
+
 padlines(ss::Vector, n) = map(ss) do s
   " "^n * s
 end
@@ -119,6 +152,7 @@ function amr_to_string(amr)
       xs::Vector                       => map(!, xs)
       Typing(system, map)              => "Typing = begin\n$(padlines(!system, 2))\nTypeMap = [\n$(padlines(!map, 2))]\nend"
       ASKEModel(h, m, s)               => "$(!h)\n$(!m)\n\n$(!s)"
+      Annotation(e,t,n)                => "Annotation = $(String(e)),$(String(t)): $(note_string(n))"
     end
   end
 end
@@ -155,6 +189,7 @@ function amr_to_expr(amr)
       xs::Vector                       => begin ys = map(!, xs); block(ys) end
       Typing(system, map)              => :(Typing = $(!system); TypeMap = $(block(map)))
       ASKEModel(h, m, s)               => :($(!h);$(!m);$(!s))
+      Annotation(e,t,n)                => "Annotation = $(String(e)),$(String(t)): $(note_expr(n))"
     end
   end
 end
@@ -225,6 +260,17 @@ end
 
 load(::Type{Distribution}, ::Nothing) = PointMass(missing)
 
+function load(::Type{Note}, d::AbstractDict)
+  @match d begin
+    Dict("type"=>"Name", "parameters"=>p) => Name(p["str"])
+    Dict("type"=>"Description", "parameters"=>p) => Description(p["str"])
+    Dict("type"=>"Grounding", "parameters"=>p) => Grounding(p["ontology"], p["identifier"])
+    Dict("type"=>"Units", "parameters"=>p) => Units(p["expression"])
+  end
+end
+function load(::Type{Annotation}, d::AbstractDict)
+  Annotation(d["entity"], d["type"], load(Note,d["note"]))
+end
 
 function load(::Type{Parameter}, d::AbstractDict)
   u = load(Unit, d)
@@ -332,7 +378,6 @@ function load(d::Type{Distribution}, ex::Expr)
   end
 end
 
-
 function load(::Type{Parameter}, ex::Expr)
   name, desc, ex = docval(ex)
   id, u, val, dist = @matchast ex quote

src/composite_models.jl

@@ -4,7 +4,7 @@ export CompositeModelExpr, OpenModel, OpenDecapode, CompositeModel, interface, o
 
 using MLStyle
 using Catlab
-using Decapodes
+using DiagrammaticEquations
 using StructTypes
 
 using ..SyntacticModelsBase
@@ -83,4 +83,4 @@ function OpenDecapode(m::CompositeModel)
   OpenDecapode(ASKEMDecapode(m.header,apex(composite)), feet)
 end
 
-end
+end

src/decapodes.jl

@@ -6,12 +6,13 @@ using ..SyntacticModelsBase
 using ..AMR
 
 using StructTypes
-using Decapodes
+using DiagrammaticEquations
+using DiagrammaticEquations.Deca
 using MLStyle
 
 @data ASKEMDeca <: AbstractTerm begin
-  ASKEMDecaExpr(header::AMR.Header, model::Decapodes.DecaExpr)
-  ASKEMDecapode(header::AMR.Header, model::Decapodes.SummationDecapode)
+  ASKEMDecaExpr(header::AMR.Header, model::DiagrammaticEquations.DecaExpr, annotations::Vector{AMR.Annotation{Symbol,Symbol}})
+  ASKEMDecapode(header::AMR.Header, model::DiagrammaticEquations.SummationDecapode, annotations::Vector{AMR.Annotation{Symbol,Symbol}})
 end
 
 @doc """    ASKEMDeca
@@ -25,37 +26,37 @@ ASKEMDeca
 Stores the syntactic expression of a Decapode Expression with the
 model metadata for ASKEM AMR conformance.
 """
-ASKEMDecaExpr
+ASKEMDecaExpr(header::AMR.Header, model::DiagrammaticEquations.DecaExpr) = ASKEMDecaExpr(header,model,Vector{AMR.Annotation{Symbol,Symbol}}())
 
 @doc """    ASKEMDecapode
 
 Stores the combinatorial representation of a Decapode with the
 model metadata for ASKEM AMR conformance.
 """
-ASKEMDecapode
+ASKEMDecapode(header::AMR.Header, model::DiagrammaticEquations.SummationDecapode) = ASKEMDecapode(header,model,Vector{AMR.Annotation{Symbol,Symbol}}())
 
 StructTypes.StructType(::Type{ASKEMDeca}) = StructTypes.AbstractType()
 StructTypes.subtypekey(::Type{ASKEMDeca}) = :_type
 StructTypes.subtypes(::Type{ASKEMDeca}) = (ASKEMDecaExpr=ASKEMDecaExpr, ASKEMDecapode=ASKEMDecapode)
 
-SyntacticModelsBase._dict(x::T) where {T<:Union{Decapodes.DecaExpr, Decapodes.Equation, Decapodes.Term}} = begin
+SyntacticModelsBase._dict(x::T) where {T<:Union{DiagrammaticEquations.DecaExpr, DiagrammaticEquations.Equation, DiagrammaticEquations.Term}} = begin
   Dict(:_type => typename_last(T), [k=>_dict(getfield(x, k)) for k in fieldnames(T)]...)
 end
 
-StructTypes.StructType(::Type{Decapodes.Equation}) = StructTypes.AbstractType()
-StructTypes.subtypekey(::Type{Decapodes.Equation}) = :_type
-StructTypes.subtypes(::Type{Decapodes.Equation}) = (Eq=Eq,)
-
-StructTypes.StructType(::Type{Decapodes.Term}) = StructTypes.AbstractType()
-StructTypes.subtypekey(::Type{Decapodes.Term}) = :_type
-StructTypes.subtypes(::Type{Decapodes.Term}) = (Var=Decapodes.Var,
-  Lit=Decapodes.Lit,
-  Judgement=Decapodes.Judgement,
-  AppCirc1=Decapodes.AppCirc1,
-  App1=Decapodes.App1,
-  App2=Decapodes.App2,
-  Plus=Decapodes.Plus,
-  Mult=Decapodes.Mult,
-  Tan=Decapodes.Tan)
-
-end
+StructTypes.StructType(::Type{DiagrammaticEquations.Equation}) = StructTypes.AbstractType()
+StructTypes.subtypekey(::Type{DiagrammaticEquations.Equation}) = :_type
+StructTypes.subtypes(::Type{DiagrammaticEquations.Equation}) = (Eq=Eq,)
+
+StructTypes.StructType(::Type{DiagrammaticEquations.Term}) = StructTypes.AbstractType()
+StructTypes.subtypekey(::Type{DiagrammaticEquations.Term}) = :_type
+StructTypes.subtypes(::Type{DiagrammaticEquations.Term}) = (Var=DiagrammaticEquations.Var,
+  Lit=DiagrammaticEquations.Lit,
+  Judgement=DiagrammaticEquations.Judgement,
+  AppCirc1=DiagrammaticEquations.AppCirc1,
+  App1=DiagrammaticEquations.App1,
+  App2=DiagrammaticEquations.App2,
+  Plus=DiagrammaticEquations.Plus,
+  Mult=DiagrammaticEquations.Mult,
+  Tan=DiagrammaticEquations.Tan)
+
+end

test/Project.toml

@@ -1,11 +1,14 @@
 [deps]
-SyntacticModels = "22bb929c-8bcf-4852-b455-eb3e1675e09c"
-Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+ACSets = "227ef7b5-1206-438b-ac65-934d6da304b8"
+Catlab = "134e5e36-593f-5add-ad60-77f754baafbe"
+DiagrammaticEquations = "6f00c28b-6bed-4403-80fa-30e0dc12f317"
 JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
 JSON3 = "0f8b85d8-7281-11e9-16c2-39a750bddbf1"
 MLStyle = "d8e11817-5142-5d16-987a-aa16d5891078"
+Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
 StructTypes = "856f2bd8-1eba-4b0a-8007-ebc267875bd4"
-ACSets = "227ef7b5-1206-438b-ac65-934d6da304b8"
-Catlab = "134e5e36-593f-5add-ad60-77f754baafbe"
-Decapodes = "679ab3ea-c928-4fe6-8d59-fd451142d391"
-Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
+SyntacticModels = "22bb929c-8bcf-4852-b455-eb3e1675e09c"
+Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+
+[compat]
+Catlab = "0.16"