temp commit

Author: AayushSabharwal

src/systems/codegen.jl

@@ -125,7 +125,7 @@ function calculate_jacobian(sys::System;
         sparse = false, simplify = false, dvs = unknowns(sys))
     obs = Dict(eq.lhs => eq.rhs for eq in observed(sys))
     rhs = map(eq -> fixpoint_sub(eq.rhs - eq.lhs, obs), equations(sys))
-
+    @show rhs
     if sparse
         jac = sparsejacobian(rhs, dvs; simplify)
         if get_iv(sys) !== nothing

src/systems/nonlinear/homotopy_continuation.jl

@@ -394,7 +394,6 @@ function transform_system(sys::System, transformation::PolynomialTransformation;
     @set! sys2.unknowns = new_dvs
     # remove observed equations to avoid adding them in codegen
     @set! sys2.observed = Equation[]
-    @set! sys2.substitutions = nothing
     return PolynomialTransformationResult(sys2, denoms)
 end
 

src/systems/system.jl

@@ -107,7 +107,9 @@ struct System <: AbstractSystem
 end
 
 function default_consolidate(costs, subcosts)
-    return sum(costs; init = 0.0) + sum(subcosts; init = 0.0)
+    # `reduce` instead of `sum` because the rrule for `sum` doesn't
+    # handle the `init` kwarg.
+    return reduce(+, costs; init = 0.0) + reduce(+, subcosts; init = 0.0)
 end
 
 function System(eqs::Vector{Equation}, iv, dvs, ps, brownians = [];

test/labelledarrays.jl

@@ -13,8 +13,8 @@ eqs = [D(x) ~ σ * (y - x),
     D(z) ~ x * y - β * z]
 
 @named de = System(eqs, t)
-de = complete(de)
-ff = ODEFunction(de, [x, y, z], [σ, ρ, β], jac = true)
+de2 = complete(de)
+ff = ODEFunction(de; jac = true)
 
 a = @SVector [1.0, 2.0, 3.0]
 b = SLVector(x = 1.0, y = 2.0, z = 3.0)

test/runtests.jl

@@ -136,9 +136,9 @@ end
 
     if GROUP == "All" || GROUP == "Extensions"
         activate_extensions_env()
-        @safetestset "Dynamic Optimization Collocation Solvers" include("extensions/dynamic_optimization.jl")
-        @safetestset "HomotopyContinuation Extension Test" include("extensions/homotopy_continuation.jl")
-        @safetestset "Auto Differentiation Test" include("extensions/ad.jl")
+        # @safetestset "Dynamic Optimization Collocation Solvers" include("extensions/dynamic_optimization.jl")
+        # @safetestset "HomotopyContinuation Extension Test" include("extensions/homotopy_continuation.jl")
+        # @safetestset "Auto Differentiation Test" include("extensions/ad.jl")
         @safetestset "LabelledArrays Test" include("labelledarrays.jl")
         @safetestset "BifurcationKit Extension Test" include("extensions/bifurcationkit.jl")
         @safetestset "InfiniteOpt Extension Test" include("extensions/test_infiniteopt.jl")