From e4af515eb0aaac9797174d8e92d55ead1dcf5019 Mon Sep 17 00:00:00 2001
From: Matt <cuffaro.matt@gmail.com>
Date: Thu, 5 Dec 2024 23:14:03 -0500
Subject: [PATCH] BUG: fixing indexing error in state_at_time + removing some
 comments

---
 .../src/decapodes-service/DecapodesService.jl                | 5 ++---
 packages/algjulia-service/src/decapodes-service/geometry.jl  | 1 -
 .../src/decapodes-service/initial_conditions.jl              | 3 +--
 packages/algjulia-service/test/runtests.jl                   | 5 -----
 4 files changed, 3 insertions(+), 11 deletions(-)

diff --git a/packages/algjulia-service/src/decapodes-service/DecapodesService.jl b/packages/algjulia-service/src/decapodes-service/DecapodesService.jl
index 311785f6..5e9712b8 100644
--- a/packages/algjulia-service/src/decapodes-service/DecapodesService.jl
+++ b/packages/algjulia-service/src/decapodes-service/DecapodesService.jl
@@ -56,8 +56,7 @@ end
 Construct a `PodeSystem` object from a JSON string.
 """
 function PodeSystem(json_object::AbstractDict, hodge=GeometricHodge())
-    # converts the JSON of (the fragment of) the theory
-    # into theory of the DEC, valued in Julia
+    # make a theory of the DEC, valued in Julia
     theory = Theory(json_object[:model])
 
     # this is a diagram in the model of the DEC. it wants to be a decapode!
@@ -160,7 +159,7 @@ end
 
 function state_at_time(soln::ODESolution, domain::Rectangle, var::Symbol, t::Int) # last two args can be one Point2
     (x, y) = indexing_bounds(domain)
-    [SVector(i, j, getproperty(soln.u[t], var)[x*(i-1) + j]) for i in 1:x+1, j in 1:y+1]
+    [SVector(i, j, getproperty(soln.u[t], var)[(x+1)*(i-1) + j]) for i in 1:x+1, j in 1:y+1]
 end
 
 # TODO just separated this from the SimResult function and added type parameters, but need to generalize
diff --git a/packages/algjulia-service/src/decapodes-service/geometry.jl b/packages/algjulia-service/src/decapodes-service/geometry.jl
index 0fef00b8..329abdec 100644
--- a/packages/algjulia-service/src/decapodes-service/geometry.jl
+++ b/packages/algjulia-service/src/decapodes-service/geometry.jl
@@ -79,7 +79,6 @@ function Geometry(json_object::AbstractDict)
     domain = PREDEFINED_MESHES[mesh_name]
     Geometry(domain)
 end
-# TODO PREDEFINED_MESHES is a dictionary of default methods
 
 # function Geometry(d::Domain, args...)
 #     throw(ImplError("The mesh ($(d)) is"))
diff --git a/packages/algjulia-service/src/decapodes-service/initial_conditions.jl b/packages/algjulia-service/src/decapodes-service/initial_conditions.jl
index dcd3251e..40e8ee7a 100644
--- a/packages/algjulia-service/src/decapodes-service/initial_conditions.jl
+++ b/packages/algjulia-service/src/decapodes-service/initial_conditions.jl
@@ -14,7 +14,7 @@ function GaussianData(μ::Vector{Float64}, Σ::Vector{Float64})
     GaussianData(μ, LinearAlgebra.Diagonal(abs.(Σ)))
 end
 
-# DEFAULT METHOD. A Moshi-like Default impl. would be nice!
+# default method
 function GaussianData(r::Rectangle)
     μ = middle(r)
     GaussianData(μ, μ/10)
@@ -42,7 +42,6 @@ end
 GaussianIC(r::Rectangle) = GaussianIC(r, GaussianData(r))
 TaylorVortexIC(d::Sphere) = TaylorVortexIC(d, TaylorVortexData())
 
-
 function initial_conditions(json_object::AbstractDict, geometry::Geometry, uuid2symb::Dict{String, Symbol})
     ic_specs = json_object[:initialConditions] # this is "C" 
     dict = Dict([uuid2symb[string(uuid)] => ic_specs[string(uuid)] for uuid ∈ keys(ic_specs)]...)
diff --git a/packages/algjulia-service/test/runtests.jl b/packages/algjulia-service/test/runtests.jl
index c50bf13c..76f00592 100644
--- a/packages/algjulia-service/test/runtests.jl
+++ b/packages/algjulia-service/test/runtests.jl
@@ -93,11 +93,6 @@ end
     f = simulator(system.geometry.dualmesh, default_dec_generate, DiagonalHodge())
 
     soln = run_sim(f, system.init, 50.0, ComponentArray(k=0.5,));
-    # returns ::ODESolution
-    #     - retcode
-    #     - interpolation
-    #     - t
-    #     - u::Vector{ComponentVector}
 
     @test soln.retcode == ReturnCode.Success