first pass at decapodes dependencing on DEq

Project.toml

@@ -1,12 +1,6 @@
 name = "Decapodes"
 uuid = "679ab3ea-c928-4fe6-8d59-fd451142d391"
-authors = [
-  "James Fairbanks",
-  "Andrew Baas",
-  "Evan Patterson",
-  "Luke Morris",
-  "George Rauta",
-]
+authors = ["James Fairbanks", "Andrew Baas", "Evan Patterson", "Luke Morris", "George Rauta"]
 version = "0.4.0"
 
 [deps]
@@ -15,6 +9,7 @@ Artifacts = "56f22d72-fd6d-98f1-02f0-08ddc0907c33"
 Catlab = "134e5e36-593f-5add-ad60-77f754baafbe"
 CombinatorialSpaces = "b1c52339-7909-45ad-8b6a-6e388f7c67f2"
 DataStructures = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"
+DiagrammaticEquations = "b66562e1-fa90-4e8b-9505-c909188fab76"
 Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
 FileIO = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549"
 GLMakie = "e9467ef8-e4e7-5192-8a1a-b1aee30e663a"

src/Decapodes.jl

@@ -8,38 +8,40 @@ using Catlab.CategoricalAlgebra
 using Catlab.WiringDiagrams
 using Catlab.WiringDiagrams.DirectedWiringDiagrams
 using Catlab.ACSetInterface
-using LinearAlgebra
 using MLStyle
 using Base.Iterators
 
+# TODO: Matt - Delete
 import Unicode
 
-export normalize_unicode, DerivOp, append_dot, unicode!, vec_to_dec!,
-  SchDecapode, SchNamedDecapode, AbstractDecapode, AbstractNamedDecapode, Decapode, NamedDecapode, SummationDecapode, fill_names!, dot_rename!, expand_operators, add_constant!, add_parameter, infer_types!, resolve_overloads!, op1_inf_rules_1D, op2_inf_rules_1D, op1_inf_rules_2D, op2_inf_rules_2D, op1_res_rules_1D, op2_res_rules_1D, op1_res_rules_2D, op2_res_rules_2D,
-  Term, Var, Judgement, Eq, AppCirc1, AppCirc2, App1, App2, Plus, Tan, term, parse_decapode,
-  VectorForm, PhysicsState, findname, findnode,
-  compile, compile_env, gensim, evalsim, closest_point, flat_op,
-  AbstractMeshKey, loadmesh, Icosphere, Rectangle_30x10, Torus_30x10, Point_Map,
-  Open, OpenSummationDecapodeOb, OpenSummationDecapode, unique_by, unique_by!, oapply,
-  CartesianPoint, SpherePoint, r, theta, phi, TangentBasis, θhat, ϕhat,
-  average_rewrite, recursive_delete_parents, contract_operators,
-  default_dec_matrix_generate, default_dec_generate, 
-  Collage,
-  @decapode
+using DiagrammaticEquations
 
-normalize_unicode(s::String) = Unicode.normalize(s, compose=true, stable=true, chartransform=Unicode.julia_chartransform)
-normalize_unicode(s::Symbol)  = Symbol(normalize_unicode(String(s)))
-DerivOp = Symbol("∂ₜ")
+export
+# DerivOp,
+# append_dot,
+# normalize_unicode, 
+findname, flat_op,
+gensim, evalsim, closest_point, findnode, compile, compile_env,  PhysicsState,  default_dec_matrix_generate, default_dec_generate, default_dec_generate, VectorForm,
+## meshes
+AbstractMeshKey, loadmesh, Icosphere, Rectangle_30x10, Torus_30x10, Point_Map,
+## coordinates 
+CartesianPoint, SpherePoint, r, theta, phi, TangentBasis, θhat, ϕhat  
+
+# TODO - Matt: Delete
+# normalize_unicode(s::String) = Unicode.normalize(s, compose=true, stable=true, chartransform=Unicode.julia_chartransform)
+# normalize_unicode(s::Symbol)  = Symbol(normalize_unicode(String(s)))
+# DerivOp = Symbol("∂ₜ")
+# TODO - Matt: this stays, but DE still has it
 append_dot(s::Symbol) = Symbol(string(s)*'\U0307')
 
-include("decapodeacset.jl")
-include("language.jl")
-include("composition.jl")
-include("collages.jl")
+# include("migrate/decapodeacset.jl")
+# include("migrate/language.jl")
+# include("migrate/composition.jl")
+# include("migrate/collages.jl")
 include("coordinates.jl")
-include("visualization.jl")
+# include("migrate/visualization.jl")
 include("simulation.jl")
 include("meshes.jl")
-include("rewrite.jl")
+# include("migrate/rewrite.jl")
 
 end

src/coordinates.jl

@@ -1,5 +1,5 @@
 using GeometryBasics
-using LinearAlgebra
+# using LinearAlgebra
 
 """    CartesianPoint{T}(p)