From ea6a4917ec0dc2dfd282be44a8d9705e189c438b Mon Sep 17 00:00:00 2001
From: "Edward A. Lee" <eal@berkeley.edu>
Date: Sat, 27 Apr 2024 08:40:08 -0700
Subject: [PATCH 1/4] Added tests for instance-in-mode bug

---
 test/C/src/ImportInstanceInMode.lf |  9 +++++++++
 test/C/src/lib/InstanceInMode.lf   | 11 +++++++++++
 2 files changed, 20 insertions(+)
 create mode 100644 test/C/src/ImportInstanceInMode.lf
 create mode 100644 test/C/src/lib/InstanceInMode.lf

diff --git a/test/C/src/ImportInstanceInMode.lf b/test/C/src/ImportInstanceInMode.lf
new file mode 100644
index 0000000000..5e91370bef
--- /dev/null
+++ b/test/C/src/ImportInstanceInMode.lf
@@ -0,0 +1,9 @@
+// Test that importing from a file with a reactor that is only instantiated in
+// a mode does not trigger a NPE.
+target C {
+  timeout: 0s
+}
+import B from "lib/InstanceInMode.lf"
+main reactor {
+  b = new B()
+}
\ No newline at end of file
diff --git a/test/C/src/lib/InstanceInMode.lf b/test/C/src/lib/InstanceInMode.lf
new file mode 100644
index 0000000000..c8c7dd2379
--- /dev/null
+++ b/test/C/src/lib/InstanceInMode.lf
@@ -0,0 +1,11 @@
+// Define a reactor that is only instantiated inside a mode.
+target C
+reactor U {
+  reaction(startup) {==}
+}
+reactor B {
+  reaction(startup) {==}
+  initial mode A {
+    u = new U()   
+  }
+}

From 6d057c7ccb4831b168f8442f88b5ef6c9135f3bc Mon Sep 17 00:00:00 2001
From: "Edward A. Lee" <eal@berkeley.edu>
Date: Sat, 27 Apr 2024 08:40:28 -0700
Subject: [PATCH 2/4] Include instantiations in modes

---
 .../java/org/lflang/graph/InstantiationGraph.java     | 11 +++++++----
 1 file changed, 7 insertions(+), 4 deletions(-)

diff --git a/core/src/main/java/org/lflang/graph/InstantiationGraph.java b/core/src/main/java/org/lflang/graph/InstantiationGraph.java
index dca5492fd0..04d52d826d 100644
--- a/core/src/main/java/org/lflang/graph/InstantiationGraph.java
+++ b/core/src/main/java/org/lflang/graph/InstantiationGraph.java
@@ -31,10 +31,7 @@
 import java.util.Set;
 import org.eclipse.emf.ecore.resource.Resource;
 import org.lflang.ast.ASTUtils;
-import org.lflang.lf.Instantiation;
-import org.lflang.lf.Model;
-import org.lflang.lf.Reactor;
-import org.lflang.lf.ReactorDecl;
+import org.lflang.lf.*;
 import org.lflang.util.IteratorUtil;
 
 /**
@@ -154,6 +151,12 @@ private void buildGraph(final Instantiation instantiation, final Set<Instantiati
         for (final Instantiation inst : reactor.getInstantiations()) {
           this.buildGraph(inst, visited);
         }
+        // Also have to look for instantiations inside modes.
+        for (final Mode mode : reactor.getModes()) {
+          for (final Instantiation inst : mode.getInstantiations()) {
+            this.buildGraph(inst, visited);
+          }
+        }
       }
     }
   }

From c234ef7aa5275f18a0496a5276acb21a1a039531 Mon Sep 17 00:00:00 2001
From: "Edward A. Lee" <eal@berkeley.edu>
Date: Sat, 27 Apr 2024 09:39:26 -0700
Subject: [PATCH 3/4] Spotless

---
 test/C/src/ImportInstanceInMode.lf | 6 ++++--
 test/C/src/lib/InstanceInMode.lf   | 9 ++++++---
 2 files changed, 10 insertions(+), 5 deletions(-)

diff --git a/test/C/src/ImportInstanceInMode.lf b/test/C/src/ImportInstanceInMode.lf
index 5e91370bef..59355841a4 100644
--- a/test/C/src/ImportInstanceInMode.lf
+++ b/test/C/src/ImportInstanceInMode.lf
@@ -1,9 +1,11 @@
 // Test that importing from a file with a reactor that is only instantiated in
 // a mode does not trigger a NPE.
 target C {
-  timeout: 0s
+  timeout: 0 s
 }
+
 import B from "lib/InstanceInMode.lf"
+
 main reactor {
   b = new B()
-}
\ No newline at end of file
+}
diff --git a/test/C/src/lib/InstanceInMode.lf b/test/C/src/lib/InstanceInMode.lf
index c8c7dd2379..531bcaee86 100644
--- a/test/C/src/lib/InstanceInMode.lf
+++ b/test/C/src/lib/InstanceInMode.lf
@@ -1,11 +1,14 @@
 // Define a reactor that is only instantiated inside a mode.
 target C
+
 reactor U {
-  reaction(startup) {==}
+  reaction(startup) {=  =}
 }
+
 reactor B {
-  reaction(startup) {==}
+  reaction(startup) {=  =}
+
   initial mode A {
-    u = new U()   
+    u = new U()
   }
 }

From 04917acddc92ee56f7b8b99d0c352b5061b051c5 Mon Sep 17 00:00:00 2001
From: Marten Lohstroh <marten@berkeley.edu>
Date: Sat, 27 Apr 2024 22:25:52 -0700
Subject: [PATCH 4/4] Update
 core/src/main/java/org/lflang/graph/InstantiationGraph.java

---
 core/src/main/java/org/lflang/graph/InstantiationGraph.java | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/core/src/main/java/org/lflang/graph/InstantiationGraph.java b/core/src/main/java/org/lflang/graph/InstantiationGraph.java
index 04d52d826d..8966bf10ee 100644
--- a/core/src/main/java/org/lflang/graph/InstantiationGraph.java
+++ b/core/src/main/java/org/lflang/graph/InstantiationGraph.java
@@ -31,7 +31,11 @@
 import java.util.Set;
 import org.eclipse.emf.ecore.resource.Resource;
 import org.lflang.ast.ASTUtils;
-import org.lflang.lf.*;
+import org.lflang.lf.Instantiation;
+import org.lflang.lf.Mode;
+import org.lflang.lf.Model;
+import org.lflang.lf.Reactor;
+import org.lflang.lf.ReactorDecl;
 import org.lflang.util.IteratorUtil;
 
 /**