From 0618a68c5ed0f7888bca2f439bc3c04e9c962e48 Mon Sep 17 00:00:00 2001
From: Aayush Sabharwal <aayush.sabharwal@gmail.com>
Date: Wed, 16 Apr 2025 13:36:40 +0530
Subject: [PATCH 1/4] fix: scalarize `Initial` parameters for `split = false`
 systems

---
 src/systems/abstractsystem.jl | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/systems/abstractsystem.jl b/src/systems/abstractsystem.jl
index 72f3132889..4ad08bb1f4 100644
--- a/src/systems/abstractsystem.jl
+++ b/src/systems/abstractsystem.jl
@@ -696,7 +696,7 @@ end
 
 supports_initialization(sys::AbstractSystem) = true
 
-function add_initialization_parameters(sys::AbstractSystem)
+function add_initialization_parameters(sys::AbstractSystem; split = true)
     @assert !has_systems(sys) || isempty(get_systems(sys))
     supports_initialization(sys) || return sys
     is_initializesystem(sys) && return sys
@@ -711,7 +711,7 @@ function add_initialization_parameters(sys::AbstractSystem)
     obs, eqs = unhack_observed(observed(sys), eqs)
     for x in Iterators.flatten((unknowns(sys), Iterators.map(eq -> eq.lhs, obs)))
         x = unwrap(x)
-        if iscall(x) && operation(x) == getindex
+        if iscall(x) && operation(x) == getindex && split
             push!(all_initialvars, arguments(x)[1])
         else
             push!(all_initialvars, x)
@@ -788,7 +788,7 @@ function complete(
         end
         sys = newsys
         if add_initial_parameters
-            sys = add_initialization_parameters(sys)
+            sys = add_initialization_parameters(sys; split)
         end
     end
     if split && has_index_cache(sys)

From 8147aabad454263c2a5279394c3141145f9d2002 Mon Sep 17 00:00:00 2001
From: Aayush Sabharwal <aayush.sabharwal@gmail.com>
Date: Wed, 16 Apr 2025 13:36:54 +0530
Subject: [PATCH 2/4] fix: recognize scalarized `Initial` parameters in
 `parameters`

---
 src/systems/abstractsystem.jl | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/src/systems/abstractsystem.jl b/src/systems/abstractsystem.jl
index 4ad08bb1f4..29338d0722 100644
--- a/src/systems/abstractsystem.jl
+++ b/src/systems/abstractsystem.jl
@@ -1465,7 +1465,11 @@ function parameters(sys::AbstractSystem; initial_parameters = false)
     result = unique(isempty(systems) ? ps :
                     [ps; reduce(vcat, namespace_parameters.(systems))])
     if !initial_parameters && !is_initializesystem(sys)
-        filter!(x -> !iscall(x) || !isa(operation(x), Initial), result)
+        filter!(result) do sym
+            return !(isoperator(sym, Initial) ||
+                     iscall(sym) && operation(sym) == getindex &&
+                     isoperator(arguments(sym)[1], Initial))
+        end
     end
     return result
 end

From ec4fd42d6c31888f374d4852971683abecd33a54 Mon Sep 17 00:00:00 2001
From: Aayush Sabharwal <aayush.sabharwal@gmail.com>
Date: Wed, 16 Apr 2025 13:37:07 +0530
Subject: [PATCH 3/4] test: test mix of array initials and scalar parameters
 with `split = false`

---
 test/initial_values.jl | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)

diff --git a/test/initial_values.jl b/test/initial_values.jl
index 01a053a9bf..79b6b8e067 100644
--- a/test/initial_values.jl
+++ b/test/initial_values.jl
@@ -265,3 +265,19 @@ end
     @test eltype(oprob.u0) == Float32
     @test eltype(eltype(sol.u)) == Float32
 end
+
+@testset "Array initials and scalar parameters with `split = false`" begin
+    @variables x(t)[1:2]
+    @parameters p
+    @mtkbuild sys=ODESystem([D(x[1]) ~ x[1], D(x[2]) ~ x[2] + p], t) split=false
+    ps = Set(parameters(sys; initial_parameters = true))
+    @test length(ps) == 5
+    for i in 1:2
+        @test Initial(x[i]) in ps
+        @test Initial(D(x[i])) in ps
+    end
+    @test p in ps
+    prob = ODEProblem(sys, [x => ones(2)], (0.0, 1.0), [p => 1.0])
+    @test prob.p isa Vector{Float64}
+    @test length(prob.p) == 5
+end

From 3dea97cd9430bc9ae75c81b96921587d4eec2650 Mon Sep 17 00:00:00 2001
From: Aayush Sabharwal <aayush.sabharwal@gmail.com>
Date: Wed, 16 Apr 2025 16:36:53 +0530
Subject: [PATCH 4/4] test: account for new scalarized initials in tests

---
 test/odesystem.jl | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/test/odesystem.jl b/test/odesystem.jl
index a45ed99f35..4b76da6e9d 100644
--- a/test/odesystem.jl
+++ b/test/odesystem.jl
@@ -1305,7 +1305,7 @@ end
     ps = zeros(8)
     setp(sys2, x)(ps, 2ones(2))
     setp(sys2, p)(ps, 2ones(2, 2))
-    @test_nowarn fn2(ones(4), 2ones(6), 4.0)
+    @test_nowarn fn2(ones(4), 2ones(14), 4.0)
 end
 
 # https://github.com/SciML/ModelingToolkit.jl/issues/2969
@@ -1416,7 +1416,7 @@ end
     obsfn = ModelingToolkit.build_explicit_observed_function(
         sys1, u + x + p[1:2]; inputs = [x...])
 
-    @test obsfn(ones(2), 2ones(2), 3ones(4), 4.0) == 6ones(2)
+    @test obsfn(ones(2), 2ones(2), 3ones(12), 4.0) == 6ones(2)
 end
 
 @testset "Passing `nothing` to `u0`" begin