From b049203069c4b8835268fd68cea327184f957250 Mon Sep 17 00:00:00 2001
From: jClugstor <jadonclugston@gmail.com>
Date: Tue, 30 Jul 2024 15:16:37 -0400
Subject: [PATCH 1/5] use full_equations so ovservables work

---
 ext/MTKBifurcationKitExt.jl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/ext/MTKBifurcationKitExt.jl b/ext/MTKBifurcationKitExt.jl
index b709b2eec0..ca161d8c04 100644
--- a/ext/MTKBifurcationKitExt.jl
+++ b/ext/MTKBifurcationKitExt.jl
@@ -144,7 +144,7 @@ function BifurcationKit.BifurcationProblem(osys::ODESystem, args...; kwargs...)
     if !ModelingToolkit.iscomplete(osys)
         error("A completed `ODESystem` is required. Call `complete` or `structural_simplify` on the system before creating a `BifurcationProblem`")
     end
-    nsys = NonlinearSystem([0 ~ eq.rhs for eq in equations(osys)],
+    nsys = NonlinearSystem([0 ~ eq.rhs for eq in full_equations(osys)],
         unknowns(osys),
         parameters(osys);
         name = nameof(osys))

From 06de5949c7eec64524e4cd1558de83389d6202fe Mon Sep 17 00:00:00 2001
From: jClugstor <jadonclugston@gmail.com>
Date: Thu, 1 Aug 2024 13:15:48 -0400
Subject: [PATCH 2/5] add observed to NonlinearSystem

---
 ext/MTKBifurcationKitExt.jl | 1 +
 1 file changed, 1 insertion(+)

diff --git a/ext/MTKBifurcationKitExt.jl b/ext/MTKBifurcationKitExt.jl
index ca161d8c04..6bc536958f 100644
--- a/ext/MTKBifurcationKitExt.jl
+++ b/ext/MTKBifurcationKitExt.jl
@@ -147,6 +147,7 @@ function BifurcationKit.BifurcationProblem(osys::ODESystem, args...; kwargs...)
     nsys = NonlinearSystem([0 ~ eq.rhs for eq in full_equations(osys)],
         unknowns(osys),
         parameters(osys);
+        observed = observed(osys),
         name = nameof(osys))
     return BifurcationKit.BifurcationProblem(complete(nsys), args...; kwargs...)
 end

From 85618710133284bd5205d47bf8420881e33b5d45 Mon Sep 17 00:00:00 2001
From: jClugstor <jadonclugston@gmail.com>
Date: Tue, 6 Aug 2024 16:21:06 -0400
Subject: [PATCH 3/5] add test

---
 test/extensions/bifurcationkit.jl | 32 +++++++++++++++++++++++++++++++
 1 file changed, 32 insertions(+)

diff --git a/test/extensions/bifurcationkit.jl b/test/extensions/bifurcationkit.jl
index 861d8f45f9..9581a9b17e 100644
--- a/test/extensions/bifurcationkit.jl
+++ b/test/extensions/bifurcationkit.jl
@@ -133,3 +133,35 @@ let
     @test length(fold_points) == 2
     @test fold_points ≈ [-1.1851851706940317, -5.6734983580551894e-6] # test that they occur at the correct parameter values).
 end
+
+let 
+
+    @mtkmodel FOL begin
+        @parameters begin
+            τ # parameters
+        end
+        @variables begin
+            x(t) # dependent variables
+            RHS(t)
+        end
+        @equations begin
+            RHS ~ τ + x^2 - 0.1
+            D(x) ~ RHS
+        end
+    end
+
+    @mtkbuild fol = FOL()
+
+    par = [fol.τ => 0.0]
+    u0 = [fol.x => -1.0]
+    #prob = ODEProblem(fol, u0, (0.0, 1.), par)
+
+    bif_par = fol.τ
+    bp = BifurcationProblem(fol, u0, par, bif_par)
+    opts_br = ContinuationPar(p_min = -1.0,
+        p_max = 1.0)
+    bf = bifurcationdiagram(bp, PALC(), 2, opts_br).γ.specialpoint[1] ≈ 0.1
+
+    @test bf.γ.specialpoint[1].param≈0.1 atol=1e-4 rtol=1e-4
+
+end
\ No newline at end of file

From 088185eac22ded899360f5f0b0c73517d792c10d Mon Sep 17 00:00:00 2001
From: jClugstor <jadonclugston@gmail.com>
Date: Tue, 13 Aug 2024 12:02:00 -0400
Subject: [PATCH 4/5] fix test

---
 test/extensions/bifurcationkit.jl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/extensions/bifurcationkit.jl b/test/extensions/bifurcationkit.jl
index 9581a9b17e..efba8e68fc 100644
--- a/test/extensions/bifurcationkit.jl
+++ b/test/extensions/bifurcationkit.jl
@@ -160,7 +160,7 @@ let
     bp = BifurcationProblem(fol, u0, par, bif_par)
     opts_br = ContinuationPar(p_min = -1.0,
         p_max = 1.0)
-    bf = bifurcationdiagram(bp, PALC(), 2, opts_br).γ.specialpoint[1] ≈ 0.1
+    bf = bifurcationdiagram(bp, PALC(), 2, opts_br)
 
     @test bf.γ.specialpoint[1].param≈0.1 atol=1e-4 rtol=1e-4
 

From d4899bc206bdd1544c567d259215e1c278afba12 Mon Sep 17 00:00:00 2001
From: jClugstor <jadonclugston@gmail.com>
Date: Tue, 13 Aug 2024 12:06:23 -0400
Subject: [PATCH 5/5] format

---
 test/extensions/bifurcationkit.jl | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/test/extensions/bifurcationkit.jl b/test/extensions/bifurcationkit.jl
index efba8e68fc..698dd085c8 100644
--- a/test/extensions/bifurcationkit.jl
+++ b/test/extensions/bifurcationkit.jl
@@ -134,8 +134,7 @@ let
     @test fold_points ≈ [-1.1851851706940317, -5.6734983580551894e-6] # test that they occur at the correct parameter values).
 end
 
-let 
-
+let
     @mtkmodel FOL begin
         @parameters begin
             τ # parameters
@@ -163,5 +162,4 @@ let
     bf = bifurcationdiagram(bp, PALC(), 2, opts_br)
 
     @test bf.γ.specialpoint[1].param≈0.1 atol=1e-4 rtol=1e-4
-
-end
\ No newline at end of file
+end