From 4f8b93243879d4f05185be759f57ec0fcee94e07 Mon Sep 17 00:00:00 2001
From: eal <eal@eecs.berkeley.edu>
Date: Tue, 8 Mar 2022 10:48:33 -0800
Subject: [PATCH 01/36] First step at supporting modal models in Python

---
 org.lflang/src/lib/c/reactor-c                |   2 +-
 org.lflang/src/lib/py/reactor-c-py            |   2 +-
 .../org/lflang/generator/GeneratorBase.java   |  47 ++++--
 .../org/lflang/generator/c/CGenerator.xtend   |  91 +++++------
 .../generator/c/CReactionGenerator.java       |   6 +-
 .../generator/python/PythonGenerator.java     |  36 ++---
 .../python/PythonReactionGenerator.java       |  39 ++---
 .../src/modal_models/ConvertCaseTest.lf       | 144 ++++++++++++++++++
 test/Python/src/modal_models/Count3Modes.lf   |  61 ++++++++
 .../src/modal_models/util/TraceTesting.lf     |  83 ++++++++++
 10 files changed, 403 insertions(+), 108 deletions(-)
 create mode 100644 test/Python/src/modal_models/ConvertCaseTest.lf
 create mode 100644 test/Python/src/modal_models/Count3Modes.lf
 create mode 100644 test/Python/src/modal_models/util/TraceTesting.lf

diff --git a/org.lflang/src/lib/c/reactor-c b/org.lflang/src/lib/c/reactor-c
index 3d7c4f10f4..c649f166b5 160000
--- a/org.lflang/src/lib/c/reactor-c
+++ b/org.lflang/src/lib/c/reactor-c
@@ -1 +1 @@
-Subproject commit 3d7c4f10f4a93379b5a550639ab3ea836a38835f
+Subproject commit c649f166b52ecc325d7915f2456f4bde77084cc2
diff --git a/org.lflang/src/lib/py/reactor-c-py b/org.lflang/src/lib/py/reactor-c-py
index 9e78ad3596..58558873f5 160000
--- a/org.lflang/src/lib/py/reactor-c-py
+++ b/org.lflang/src/lib/py/reactor-c-py
@@ -1 +1 @@
-Subproject commit 9e78ad35961e559d88abfaf950f76a5f2d4323e7
+Subproject commit 58558873f592216b9904bdca03c4a977b0340ed1
diff --git a/org.lflang/src/org/lflang/generator/GeneratorBase.java b/org.lflang/src/org/lflang/generator/GeneratorBase.java
index 8f82df6746..5261445251 100644
--- a/org.lflang/src/org/lflang/generator/GeneratorBase.java
+++ b/org.lflang/src/org/lflang/generator/GeneratorBase.java
@@ -29,7 +29,6 @@
 import java.nio.file.Path;
 import java.nio.file.Paths;
 import java.util.ArrayList;
-import java.util.Collection;
 import java.util.HashSet;
 import java.util.LinkedHashMap;
 import java.util.LinkedHashSet;
@@ -40,12 +39,10 @@
 import java.util.regex.Pattern;
 import java.util.stream.Collectors;
 
-import com.google.common.base.Objects;
-import com.google.common.collect.Iterables;
-
 import org.eclipse.core.resources.IMarker;
 import org.eclipse.emf.ecore.EObject;
 import org.eclipse.emf.ecore.resource.Resource;
+import org.eclipse.emf.ecore.util.EcoreUtil;
 import org.eclipse.xtext.util.CancelIndicator;
 import org.eclipse.xtext.xbase.lib.CollectionLiterals;
 import org.eclipse.xtext.xbase.lib.IterableExtensions;
@@ -70,6 +67,7 @@
 import org.lflang.lf.Delay;
 import org.lflang.lf.Instantiation;
 import org.lflang.lf.LfFactory;
+import org.lflang.lf.Mode;
 import org.lflang.lf.Model;
 import org.lflang.lf.Parameter;
 import org.lflang.lf.Reaction;
@@ -79,6 +77,9 @@
 import org.lflang.lf.VarRef;
 import org.lflang.validation.AbstractLFValidator;
 
+import com.google.common.base.Objects;
+import com.google.common.collect.Iterables;
+
 /**
  * Generator base class for specifying core functionality
  * that all code generators should have.
@@ -594,20 +595,48 @@ private void transformConflictingConnectionsInModalReactors() {
         for (LFResource r : resources) {
             var transform = ASTUtils.findConflictingConnectionsInModalReactors(r.eResource);
             if (!transform.isEmpty()) {
-                transformConflictingConnectionsInModalReactors(transform);
+                var factory = LfFactory.eINSTANCE;
+                for (Connection connection : transform) {
+                    // Currently only simple transformations are supported
+                    if (connection.isPhysical() || connection.getDelay() != null || connection.isIterated() || 
+                        connection.getLeftPorts().size() > 1 || connection.getRightPorts().size() > 1
+                    ) {
+                        errorReporter.reportError(connection, "Cannot transform connection in modal reactor. Connection uses currently not supported features.");
+                    } else {
+                        var reaction = factory.createReaction();
+                        ((Mode)connection.eContainer()).getReactions().add(reaction);
+                        
+                        var sourceRef = connection.getLeftPorts().get(0);
+                        var destRef = connection.getRightPorts().get(0);
+                        reaction.getTriggers().add(sourceRef);
+                        reaction.getEffects().add(destRef);
+                        
+                        var code = factory.createCode();
+                        var source = (sourceRef.getContainer() != null ?
+                                sourceRef.getContainer().getName() + "." : "") + sourceRef.getVariable().getName();
+                        var dest = (destRef.getContainer() != null ? 
+                                destRef.getContainer().getName() + "." : "") + destRef.getVariable().getName();
+                        code.setBody(getConflictingConnectionsInModalReactorsBody(source, dest));
+                        reaction.setCode(code);
+                        
+                        EcoreUtil.remove(connection);
+                    }
+                }
             }
         }
     }
     /**
-     * Transforms connections into forwarding reactions iff the connections have the same destination as other
-     * connections or reaction in mutually exclusive modes.
+     * Return target code for forwarding reactions iff the connections have the
+     * same destination as other connections or reaction in mutually exclusive modes.
      * 
-     * This methods needs to be overridden in target specific code generators that support modal reactors.
+     * This methods needs to be overridden in target specific code generators that
+     * support modal reactors.
      */
-    protected void transformConflictingConnectionsInModalReactors(Collection<Connection> transform) {
+    protected String getConflictingConnectionsInModalReactorsBody(String source, String dest) {
         errorReporter.reportError("The currently selected code generation " +
                                   "is missing an implementation for conflicting " +
                                   "transforming connections in modal reactors.");
+        return "MODAL MODELS NOT SUPPORTED";
     }
 
     /**
diff --git a/org.lflang/src/org/lflang/generator/c/CGenerator.xtend b/org.lflang/src/org/lflang/generator/c/CGenerator.xtend
index 56c7ba5fc2..f0b5f115ed 100644
--- a/org.lflang/src/org/lflang/generator/c/CGenerator.xtend
+++ b/org.lflang/src/org/lflang/generator/c/CGenerator.xtend
@@ -29,7 +29,6 @@ package org.lflang.generator.c
 import java.io.File
 import java.nio.file.Files
 import java.util.ArrayList
-import java.util.Collection
 import java.util.HashSet
 import java.util.LinkedHashMap
 import java.util.LinkedHashSet
@@ -39,12 +38,11 @@ import java.util.concurrent.Executors
 import java.util.concurrent.TimeUnit
 import java.util.regex.Pattern
 import org.eclipse.emf.ecore.resource.Resource
-import org.eclipse.emf.ecore.util.EcoreUtil
 import org.eclipse.xtext.util.CancelIndicator
+import org.lflang.ASTUtils
 import org.lflang.ErrorReporter
 import org.lflang.FileConfig
 import org.lflang.InferredType
-import org.lflang.ASTUtils
 import org.lflang.Target
 import org.lflang.TargetConfig
 import org.lflang.TargetProperty
@@ -61,8 +59,8 @@ import org.lflang.federated.serialization.SupportedSerializers
 import org.lflang.generator.CodeBuilder
 import org.lflang.generator.GeneratorBase
 import org.lflang.generator.GeneratorResult
-import org.lflang.generator.IntegratedBuilder
 import org.lflang.generator.GeneratorUtils
+import org.lflang.generator.IntegratedBuilder
 import org.lflang.generator.LFGeneratorContext
 import org.lflang.generator.ModeInstance
 import org.lflang.generator.PortInstance
@@ -74,11 +72,9 @@ import org.lflang.generator.SubContext
 import org.lflang.generator.TriggerInstance
 import org.lflang.lf.Action
 import org.lflang.lf.ActionOrigin
-import org.lflang.lf.Connection
 import org.lflang.lf.Delay
 import org.lflang.lf.Input
 import org.lflang.lf.Instantiation
-import org.lflang.lf.LfFactory
 import org.lflang.lf.Mode
 import org.lflang.lf.Model
 import org.lflang.lf.Output
@@ -93,7 +89,6 @@ import org.lflang.lf.Variable
 import org.lflang.util.FileUtil
 import org.lflang.util.XtendUtil
 
-import static extension org.lflang.ASTUtils.*
 import static extension org.lflang.ASTUtils.*
 
 /** 
@@ -949,35 +944,12 @@ class CGenerator extends GeneratorBase {
         super.checkModalReactorSupport(!isFederated);
     }
     
-    override transformConflictingConnectionsInModalReactors(Collection<Connection> transform) {
-        val factory = LfFactory.eINSTANCE
-        for (connection : transform) {
-            // Currently only simple transformations are supported
-            if (connection.physical || connection.delay !== null || connection.iterated || 
-                connection.leftPorts.size > 1 || connection.rightPorts.size > 1
-            ) {
-                errorReporter.reportError(connection, "Cannot transform connection in modal reactor. Connection uses currently not supported features.");
-            } else {
-                var reaction = factory.createReaction();
-                (connection.eContainer() as Mode).getReactions().add(reaction);
-                
-                var sourceRef = connection.getLeftPorts().head
-                var destRef = connection.getRightPorts().head
-                reaction.getTriggers().add(sourceRef);
-                reaction.getEffects().add(destRef);
-                
-                var code = factory.createCode();
-                var source = (sourceRef.container !== null ? sourceRef.container.name + "." : "") + sourceRef.variable.name
-                var dest = (destRef.container !== null ? destRef.container.name + "." : "") + destRef.variable.name
-                code.setBody('''
-                    // Generated forwarding reaction for connections with the same destination but located in mutually exclusive modes.
-                    SET(«dest», «source»->value);
-                ''');
-                reaction.setCode(code);
-                
-                EcoreUtil.remove(connection);
-            }
-        }
+    override protected String getConflictingConnectionsInModalReactorsBody(String source, String dest) {
+        return String.join("\n",
+            "// Generated forwarding reaction for connections with the same destination",
+            "// but located in mutually exclusive modes.",
+            "SET("+dest+", "+source+"->value);"
+        );
     }
     
     /**
@@ -2098,17 +2070,17 @@ class CGenerator extends GeneratorBase {
             // Reactor's mode instances and its state.
             body.pr('''
                 reactor_mode_t _lf__modes[«reactor.modes.size»];
-                reactor_mode_state_t _lf__mode_state;
             ''')
             
             // Initialize the mode instances
             constructorCode.pr('''
                 // Initialize modes
+                self_base_t* _lf_self_base = (self_base_t*)self;
             ''')
             for (modeAndIdx : reactor.allModes.indexed) {
                 val mode = modeAndIdx.value
                 constructorCode.pr(mode, '''
-                    self->_lf__modes[«modeAndIdx.key»].state = &self->_lf__mode_state;
+                    self->_lf__modes[«modeAndIdx.key»].state = &_lf_self_base->_lf__mode_state;
                     self->_lf__modes[«modeAndIdx.key»].name = "«mode.name»";
                     self->_lf__modes[«modeAndIdx.key»].deactivation_time = 0;
                 ''')
@@ -2117,11 +2089,11 @@ class CGenerator extends GeneratorBase {
             // Initialize mode state with initial mode active upon start
             constructorCode.pr('''
                 // Initialize mode state
-                self->_lf__mode_state.parent_mode = NULL;
-                self->_lf__mode_state.initial_mode = &self->_lf__modes[«reactor.modes.indexed.findFirst[it.value.initial].key»];
-                self->_lf__mode_state.active_mode = self->_lf__mode_state.initial_mode;
-                self->_lf__mode_state.next_mode = NULL;
-                self->_lf__mode_state.mode_change = 0;
+                _lf_self_base->_lf__mode_state.parent_mode = NULL;
+                _lf_self_base->_lf__mode_state.initial_mode = &self->_lf__modes[«reactor.modes.indexed.findFirst[it.value.initial].key»];
+                _lf_self_base->_lf__mode_state.active_mode = _lf_self_base->_lf__mode_state.initial_mode;
+                _lf_self_base->_lf__mode_state.next_mode = NULL;
+                _lf_self_base->_lf__mode_state.mode_change = no_transition;
             ''')
         }
 
@@ -3443,7 +3415,7 @@ class CGenerator extends GeneratorBase {
                 }
             } else { // Otherwise, only reactions outside modes must be linked and the mode state itself gets a parent relation
                 initializeTriggerObjects.pr('''
-                    «nameOfSelfStruct»->_lf__mode_state.parent_mode = «parentModeRef»;
+                    ((self_base_t*)«nameOfSelfStruct»)->_lf__mode_state.parent_mode = «parentModeRef»;
                 ''')
                 for (reaction : instance.reactions.filter[it.getMode(true) === null]) {
                     initializeTriggerObjects.pr('''
@@ -3456,7 +3428,7 @@ class CGenerator extends GeneratorBase {
         if (!instance.modes.empty) {
             initializeTriggerObjects.pr('''
                 // Register for transition handling
-                _lf_modal_reactor_states[«modalReactorCount++»] = &«nameOfSelfStruct»->_lf__mode_state;
+                _lf_modal_reactor_states[«modalReactorCount++»] = &((self_base_t*)«nameOfSelfStruct»)->_lf__mode_state;
             ''')
         }
     }
@@ -4144,7 +4116,10 @@ class CGenerator extends GeneratorBase {
      * Generate code that needs to appear at the top of the generated
      * C file, such as #define and #include statements.
      */
-    def generatePreamble() {
+    def void generatePreamble() {
+        code.prComment("Code generated by the Lingua Franca compiler from:")
+        code.prComment("file:/" + FileUtil.toUnixString(fileConfig.srcFile))
+
         code.pr(this.defineLogLevel)
                 
         if (isFederated) {
@@ -4155,6 +4130,9 @@ class CGenerator extends GeneratorBase {
         }
         
         if (hasModalReactors) {
+            // So that each separate compile knows about modal reactors, do this:
+            targetConfig.compileDefinitions.put("MODAL_REACTORS", "");
+            // For readability, put this in the generated code.
             code.pr('''
                 #define MODAL_REACTORS
             ''')
@@ -4174,14 +4152,7 @@ class CGenerator extends GeneratorBase {
         
         // Do this after the above includes so that the preamble can
         // call built-in functions.
-        code.prComment("Code generated by the Lingua Franca compiler from:")
-        code.prComment("file:/" + FileUtil.toUnixString(fileConfig.srcFile))
-        if (this.mainDef !== null) {
-            val mainModel = this.mainDef.reactorClass.toDefinition.eContainer as Model
-            for (p : mainModel.preambles) {
-                code.pr(p.code.toText)
-            }
-        }
+        generateTopLevelPreambles();
 
         parseTargetParameters()
         
@@ -4189,6 +4160,18 @@ class CGenerator extends GeneratorBase {
         fileConfig.getSrcGenPath.toFile.mkdirs
     }
 
+    /**
+     * Generate top-level preamble code.
+     */
+    protected def void generateTopLevelPreambles() {
+        if (this.mainDef !== null) {
+            val mainModel = this.mainDef.reactorClass.toDefinition.eContainer as Model
+            for (p : mainModel.preambles) {
+                code.pr(p.code.toText)
+            }
+        }
+    }
+     
     /**
      * Print the main function.
      */
diff --git a/org.lflang/src/org/lflang/generator/c/CReactionGenerator.java b/org.lflang/src/org/lflang/generator/c/CReactionGenerator.java
index 135a855c37..de263bb097 100644
--- a/org.lflang/src/org/lflang/generator/c/CReactionGenerator.java
+++ b/org.lflang/src/org/lflang/generator/c/CReactionGenerator.java
@@ -11,7 +11,6 @@
 import org.lflang.ASTUtils;
 import org.lflang.ErrorReporter;
 import org.lflang.InferredType;
-import org.lflang.ASTUtils;
 import org.lflang.generator.CodeBuilder;
 import org.lflang.generator.ModeInstance.ModeTransitionType;
 import org.lflang.lf.Action;
@@ -162,8 +161,9 @@ public static String generateInitializationForReaction(String body,
                     if (idx >= 0) {
                         reactionInitialization.pr(
                             "reactor_mode_t* " + name + " = &self->_lf__modes[" + idx + "];\n"
-                            + "char _lf_" + name + "_change_type = "
-                            + (ModeTransitionType.getModeTransitionType(effect) == ModeTransitionType.HISTORY ? 2 : 1) 
+                            + "lf_mode_change_type_t _lf_" + name + "_change_type = "
+                            + (ModeTransitionType.getModeTransitionType(effect) == ModeTransitionType.HISTORY ?
+                                    "history_transition" : "reset_transition") 
                             + ";"
                         );
                     } else {
diff --git a/org.lflang/src/org/lflang/generator/python/PythonGenerator.java b/org.lflang/src/org/lflang/generator/python/PythonGenerator.java
index 58c4443d96..a1ac4daaff 100644
--- a/org.lflang/src/org/lflang/generator/python/PythonGenerator.java
+++ b/org.lflang/src/org/lflang/generator/python/PythonGenerator.java
@@ -48,7 +48,6 @@
 import org.lflang.ErrorReporter;
 import org.lflang.FileConfig;
 import org.lflang.InferredType;
-import org.lflang.ASTUtils;
 import org.lflang.Target;
 import org.lflang.federated.FedFileConfig;
 import org.lflang.federated.FederateInstance;
@@ -65,7 +64,6 @@
 import org.lflang.generator.SubContext;
 import org.lflang.generator.TargetTypes;
 import org.lflang.generator.c.CGenerator;
-import org.lflang.generator.c.CPreambleGenerator;
 import org.lflang.generator.c.CUtil;
 import org.lflang.lf.Action;
 import org.lflang.lf.Delay;
@@ -342,15 +340,11 @@ public void pythonCompileCode(LFGeneratorContext context) {
     }
 
     /** 
-     * Generate top-level preambles and #include of pqueue.c and either reactor.c or reactor_threaded.c
-     *  depending on whether threads are specified in target directive.
-     *  As a side effect, this populates the runCommand and compileCommand
-     *  private variables if such commands are specified in the target directive.
-     * 
-     * TODO: This function returns a boolean because xtend-generated parent function in CGenerator returns boolean
+     * Override generate top-level preambles, but put the preambles in the
+     * .py file rather than the C file.
      */
     @Override
-    public boolean generatePreamble() {
+    protected void generateTopLevelPreambles() {
         Set<Model> models = new LinkedHashSet<>();
         for (Reactor r : ASTUtils.convertToEmptyListIfNull(reactors)) {
             // The following assumes all reactors have a container.
@@ -365,19 +359,6 @@ public boolean generatePreamble() {
         for (Model m : models) {
             pythonPreamble.pr(PythonPreambleGenerator.generatePythonPreambles(m.getPreambles()));
         }
-        code.pr(CGenerator.defineLogLevel(this));
-        if (isFederated) {
-            code.pr(CPreambleGenerator.generateFederatedDirective(targetConfig.coordination));
-            // Handle target parameters.
-            // First, if there are federates, then ensure that threading is enabled.
-            targetConfig.threads = CUtil.minThreadsToHandleInputPorts(federates);
-        }
-        includeTargetLanguageHeaders();
-        code.pr(CPreambleGenerator.generateNumFederatesDirective(federates.size()));
-        code.pr(CPreambleGenerator.generateMixedRadixIncludeHeader());
-        super.includeTargetLanguageSourceFiles();
-        super.parseTargetParameters();
-        return false; // placeholder return value. See comment above
     }
 
     /**
@@ -919,6 +900,17 @@ public void writeDockerFile(File dockerComposeDir, String dockerFileName, String
         }
         System.out.println(getDockerBuildCommand(dockerFile, dockerComposeDir, federateName));
     }
+    
+    @Override
+    protected String getConflictingConnectionsInModalReactorsBody(String source, String dest) {
+        // NOTE: Strangely, a newline is needed at the beginning or indentation
+        // gets swallowed.
+        return String.join("\n",
+            "\n# Generated forwarding reaction for connections with the same destination",
+            "# but located in mutually exclusive modes.",
+            dest+".set("+source+".value)\n"
+        );
+    }
 
     private static String addDoubleQuotes(String str) {
         return "\""+str+"\"";
diff --git a/org.lflang/src/org/lflang/generator/python/PythonReactionGenerator.java b/org.lflang/src/org/lflang/generator/python/PythonReactionGenerator.java
index 8aa4494a29..11b6066848 100644
--- a/org.lflang/src/org/lflang/generator/python/PythonReactionGenerator.java
+++ b/org.lflang/src/org/lflang/generator/python/PythonReactionGenerator.java
@@ -1,31 +1,31 @@
 package org.lflang.generator.python;
 
-import java.util.Set;
 import java.util.ArrayList;
 import java.util.LinkedHashSet;
 import java.util.List;
+import java.util.Set;
 
-import org.lflang.lf.ReactorDecl;
-import org.lflang.lf.Reaction;
-import org.lflang.lf.Reactor;
-import org.lflang.lf.Action;
-import org.lflang.lf.TriggerRef;
-import org.lflang.lf.VarRef;
-import org.lflang.lf.Instantiation;
-import org.lflang.lf.Port;
-import org.lflang.lf.Input;
-import org.lflang.lf.Output;
-import org.lflang.generator.c.CReactionGenerator;
-import org.lflang.generator.c.CTypes;
-import org.lflang.generator.c.CUtil;
+import org.lflang.ASTUtils;
+import org.lflang.ErrorReporter;
+import org.lflang.Target;
 import org.lflang.generator.CodeBuilder;
 import org.lflang.generator.GeneratorBase;
 import org.lflang.generator.ReactionInstance;
 import org.lflang.generator.ReactorInstance;
-import org.lflang.ErrorReporter;
-import org.lflang.ASTUtils;
-import org.lflang.Target;
-import org.lflang.ASTUtils;
+import org.lflang.generator.c.CReactionGenerator;
+import org.lflang.generator.c.CTypes;
+import org.lflang.generator.c.CUtil;
+import org.lflang.lf.Action;
+import org.lflang.lf.Input;
+import org.lflang.lf.Instantiation;
+import org.lflang.lf.Mode;
+import org.lflang.lf.Output;
+import org.lflang.lf.Port;
+import org.lflang.lf.Reaction;
+import org.lflang.lf.Reactor;
+import org.lflang.lf.ReactorDecl;
+import org.lflang.lf.TriggerRef;
+import org.lflang.lf.VarRef;
 
 public class PythonReactionGenerator {
     /**
@@ -198,6 +198,9 @@ private static String generateCPythonInitializers(Reaction reaction,
                         PythonPortGenerator.generateActionVariableToSendToPythonReaction(pyObjects,
                             (Action) effect.getVariable(), decl);
                     }
+                } else if (effect.getVariable() instanceof Mode) {
+                    String name = effect.getVariable().getName();
+                    pyObjects.add("convert_C_mode_to_py("+name+",(self_base_t*)self, _lf_"+name+"_change_type)");
                 } else {
                     if (effect.getVariable() instanceof Output) {
                         PythonPortGenerator.generateOutputVariablesToSendToPythonReaction(pyObjects, (Output) effect.getVariable());
diff --git a/test/Python/src/modal_models/ConvertCaseTest.lf b/test/Python/src/modal_models/ConvertCaseTest.lf
new file mode 100644
index 0000000000..6855e3797d
--- /dev/null
+++ b/test/Python/src/modal_models/ConvertCaseTest.lf
@@ -0,0 +1,144 @@
+/*
+ * Modal Reactor Test.
+ * Tests nested reactors with modes.
+ */
+target Python {
+    fast: false,
+    timeout: 4 sec,
+//    logging: debug
+}
+
+// import TraceTesting from "util/TraceTesting.lf"
+
+reactor ResetProcessor {
+    input discard
+    input character
+    output converted
+    
+    initial mode Converting {
+        converter = new Converter()
+        character -> converter.raw
+        converter.converted -> converted
+        
+        reaction(discard) -> Discarding {=
+            Discarding.set()
+        =}
+    }
+    
+    mode Discarding {
+        reaction(character) -> converted {=
+            converted.set('_')
+        =}
+
+        reaction(character) -> Converting {=
+            Converting.set()
+        =}
+    }
+}
+
+reactor HistoryProcessor {
+    input discard
+    input character
+    output converted
+    
+    initial mode Converting {
+        converter = new Converter()
+        character -> converter.raw
+        converter.converted -> converted
+        
+        reaction(discard) -> Discarding {=
+            Discarding.set()
+        =}
+    }
+    
+    mode Discarding {
+        reaction(character) -> converted {=
+            converted.set('_')
+        =}
+
+        reaction(character) -> continue(Converting) {=
+            Converting.set()
+        =}
+    }
+}
+
+reactor Converter {
+    input raw
+    output converted
+
+    initial mode Upper {
+        reaction(raw) -> converted, Lower {=
+            character = raw.value.upper()
+            converted.set(character)
+            if character == ' ':
+                Lower.set()
+        =}
+    }
+    mode Lower {
+        reaction(raw) -> converted, Upper {=
+            character = raw.value.lower()
+            converted.set(character)
+            if character == ' ':
+                Upper.set()
+        =}
+    }
+}
+
+reactor InputFeeder(message("")) {
+    output character
+    state idx(0)
+    
+    timer t(0, 250 msec)
+    
+    reaction(t) -> character {=
+        if self.idx < len(self.message):
+            character.set(self.message[self.idx])
+            self.idx += 1
+    =}
+}
+
+main reactor {
+    timer stepper(500msec, 1sec)
+    
+    feeder = new InputFeeder(message="Hello World!")
+    reset_processor = new ResetProcessor()
+    history_processor = new HistoryProcessor()
+    
+    feeder.character -> reset_processor.character
+    feeder.character -> history_processor.character
+    
+    /*
+    test = new TraceTesting(
+        events_size = 2,
+        trace_size = 60, 
+        trace = (
+            0,1,72,1,72,
+            250000000,1,69,1,69,
+            250000000,1,76,1,76,
+            250000000,1,95,1,95,
+            250000000,1,79,1,79,
+            250000000,1,32,1,32,
+            250000000,1,119,1,119,
+            250000000,1,95,1,95,
+            250000000,1,82,1,114,
+            250000000,1,76,1,108,
+            250000000,1,68,1,100,
+            250000000,1,95,1,95
+        ), training = false)
+    */
+    // Trigger mode change
+    reaction(stepper) -> reset_processor.discard, history_processor.discard {=
+        reset_processor.discard.set(True)
+        history_processor.discard.set(True)
+    =}
+    
+    reaction(reset_processor.converted) {=
+        print(f"Reset: {reset_processor.converted.value}")
+    =}
+    
+    reaction(history_processor.converted) {=
+        print(f"History: {history_processor.converted.value}")
+    =}
+    
+    // reset_processor.converted, history_processor.converted -> test.events
+}
\ No newline at end of file
diff --git a/test/Python/src/modal_models/Count3Modes.lf b/test/Python/src/modal_models/Count3Modes.lf
new file mode 100644
index 0000000000..ac3661505e
--- /dev/null
+++ b/test/Python/src/modal_models/Count3Modes.lf
@@ -0,0 +1,61 @@
+/*
+ * Modal Reactor Test.
+ * Tests cycling through modes.
+ */
+target Python {
+    fast: false,
+    timeout: 2 sec
+};
+
+reactor CounterCycle {
+    input next;
+    output count;
+    
+    initial mode One {
+        reaction(next) -> count, Two {=
+            count.set(1)
+            Two.set()
+        =}
+    }
+    mode Two {
+        reaction(next) -> count, Three {=
+            count.set(2)
+            Three.set()
+        =}
+    }
+    mode Three {
+        reaction(next) -> count, One {=
+            count.set(3)
+            One.set()
+        =}
+    }
+}
+
+main reactor {
+    timer stepper(0, 250msec);
+    counter = new CounterCycle();
+    
+    state expected_value(1);
+    
+    // Trigger
+    reaction(stepper) -> counter.next {=
+        counter.next.set(True)
+    =}
+
+    // Check
+    reaction(stepper) counter.count {=
+        print(f"{counter.count.value}")
+        
+        if counter.count.is_present is not True:
+            sys.stderr.write("ERROR: Missing mode change.\n")
+            exit(1)
+        elif counter.count.value != self.expected_value:
+            sys.stderr.write("ERROR: Wrong mode.\n")
+            exit(2)
+        
+        if self.expected_value == 3:
+            self.expected_value = 1
+        else:
+            self.expected_value += 1
+    =}
+}
\ No newline at end of file
diff --git a/test/Python/src/modal_models/util/TraceTesting.lf b/test/Python/src/modal_models/util/TraceTesting.lf
new file mode 100644
index 0000000000..db0359c04c
--- /dev/null
+++ b/test/Python/src/modal_models/util/TraceTesting.lf
@@ -0,0 +1,83 @@
+/*
+ * Utility reactor to record and test execution traces.
+ */
+target C;
+
+preamble {=
+    #include <stdio.h>
+=}
+    
+reactor TraceTesting(events_size:int(0), trace_size:int(0), trace:int[](0), training:bool(false)) {
+    input [events_size]events:int
+    
+    state last_reaction_time:int(0)
+    state trace_idx:int(0)
+    state recorded_events:int*(0)
+    state recorded_events_next:int(0)
+    
+    reaction(startup) {=
+        self->last_reaction_time = get_logical_time();
+    =}
+    
+    reaction(events) {=
+        // Time passed since last reaction
+        int curr_reaction_delay = get_logical_time() - self->last_reaction_time;
+        
+        if (self->training) {
+            // Save time
+            self->recorded_events = (int*) realloc(self->recorded_events, sizeof(int) * (self->recorded_events_next + 1 + 2 * self->events_size));
+            self->recorded_events[self->recorded_events_next++] = curr_reaction_delay; 
+        } else {
+            if (self->trace_idx >= self->trace_size) {
+                printf("ERROR: Trace Error: Current execution exceeds given trace.\n");
+                exit(1);
+            }
+            
+            int trace_reaction_delay = self->trace[self->trace_idx++];
+            
+            if (curr_reaction_delay != trace_reaction_delay) {
+                printf("ERROR: Trace Mismatch: Unexpected reaction timing. (delay: %d, expected: %d)\n", curr_reaction_delay, trace_reaction_delay);
+                exit(2);
+            }
+        }
+        
+        for (int i = 0; i < self->events_size; i++) {
+            int curr_present = events[i]->is_present;
+            int curr_value = events[i]->value;
+            
+            if (self->training) {
+                // Save event
+                self->recorded_events[self->recorded_events_next++] = curr_present;
+                self->recorded_events[self->recorded_events_next++] = curr_value;
+            } else {
+                int trace_present = self->trace[self->trace_idx++];
+                int trace_value = self->trace[self->trace_idx++];
+                
+                if (trace_present != curr_present) {
+                    printf("ERROR: Trace Mismatch: Unexpected event presence. (event: %d, presence: %d, expected: %d)\n", i, curr_present, trace_present);
+                    exit(3);
+                } else if (curr_present && trace_value != curr_value) {
+                    printf("ERROR: Trace Mismatch: Unexpected event value. (event: %d, presence: %d, expected: %d)\n", i, curr_value, trace_value);
+                    exit(4);
+                }
+            }
+        }
+        
+        self->last_reaction_time = get_logical_time();
+    =}
+    
+    reaction(shutdown) {=
+        if (self->training) {
+            printf("Recorded event trace (%d): (", self->recorded_events_next);
+            for (int i = 0; i < self->recorded_events_next; i++) {
+                printf("%d", self->recorded_events[i]);
+                if (i < self->recorded_events_next - 1) {
+                    printf(",");
+                }
+            }
+            printf(")\n");
+            
+            free(self->recorded_events);
+        }
+    =}
+}
\ No newline at end of file

From e3f84ef77db0b1b7bfd82f2c7345886c05b55fb4 Mon Sep 17 00:00:00 2001
From: eal <eal@eecs.berkeley.edu>
Date: Tue, 8 Mar 2022 13:24:40 -0800
Subject: [PATCH 02/36] Updated reactor-c

---
 org.lflang/src/lib/c/reactor-c | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/org.lflang/src/lib/c/reactor-c b/org.lflang/src/lib/c/reactor-c
index c649f166b5..3c96abe46f 160000
--- a/org.lflang/src/lib/c/reactor-c
+++ b/org.lflang/src/lib/c/reactor-c
@@ -1 +1 @@
-Subproject commit c649f166b52ecc325d7915f2456f4bde77084cc2
+Subproject commit 3c96abe46fdb8b0dd8468e195499ff90741e787c

From 093450cf3942775b2873afb849ddfd5c7e10823e Mon Sep 17 00:00:00 2001
From: eal <eal@eecs.berkeley.edu>
Date: Tue, 8 Mar 2022 15:30:06 -0800
Subject: [PATCH 03/36] Updated comments

---
 .../org/lflang/generator/python/PythonReactionGenerator.java | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/org.lflang/src/org/lflang/generator/python/PythonReactionGenerator.java b/org.lflang/src/org/lflang/generator/python/PythonReactionGenerator.java
index 11b6066848..2409843eca 100644
--- a/org.lflang/src/org/lflang/generator/python/PythonReactionGenerator.java
+++ b/org.lflang/src/org/lflang/generator/python/PythonReactionGenerator.java
@@ -154,10 +154,9 @@ public static String generateCReaction(Reaction reaction,
      * 
      * @param reaction The reaction to generate Python-specific initialization for.
      * @param decl The reactor to which <code>reaction<code> belongs to.
-     * @param pyObjectDescriptor For each port object created, a Python-specific descriptor will be added to this that
-     *  then can be used as an argument to <code>Py_BuildValue<code> 
+     * @param pyObjects A list of expressions that can be used as additional arguments to <code>Py_BuildValue<code>
      *  (@see <a href="https://docs.python.org/3/c-api/arg.html#c.Py_BuildValue">docs.python.org/3/c-api</a>).
-     * @param pyObjects A "," delimited list of expressions that would be (or result in a creation of) a PyObject.
+     *  We will use as a format string, "(O...O)" where the number of O's is equal to the length of the list.
      */
     private static String generateCPythonInitializers(Reaction reaction,
                                                       ReactorDecl decl,

From e5720f71bed01276e4ea865acdeac73cc0d8440b Mon Sep 17 00:00:00 2001
From: Soroush Bateni <soroosh129@gmail.com>
Date: Tue, 8 Mar 2022 17:40:41 -0600
Subject: [PATCH 04/36] Moved code related to modal models into separate files

---
 org.lflang/src/lib/py/reactor-c-py             |  2 +-
 .../org/lflang/generator/python/PyUtil.java    | 18 ++++++++----------
 .../generator/python/PythonGenerator.java      |  5 +++++
 3 files changed, 14 insertions(+), 11 deletions(-)

diff --git a/org.lflang/src/lib/py/reactor-c-py b/org.lflang/src/lib/py/reactor-c-py
index 58558873f5..6aaf075ce8 160000
--- a/org.lflang/src/lib/py/reactor-c-py
+++ b/org.lflang/src/lib/py/reactor-c-py
@@ -1 +1 @@
-Subproject commit 58558873f592216b9904bdca03c4a977b0340ed1
+Subproject commit 6aaf075ce82f4104875f0aa809a1300445442720
diff --git a/org.lflang/src/org/lflang/generator/python/PyUtil.java b/org.lflang/src/org/lflang/generator/python/PyUtil.java
index b75cabf960..58b5996421 100644
--- a/org.lflang/src/org/lflang/generator/python/PyUtil.java
+++ b/org.lflang/src/org/lflang/generator/python/PyUtil.java
@@ -178,17 +178,15 @@ public static void copyTargetFiles(FileConfig fileConfig) throws IOException {
         // Copy the required target language files into the target file system.
         // This will also overwrite previous versions.
         final Path srcGen = fileConfig.getSrcGenPath();
-        FileUtil.copyFileFromClassPath(
-            "/lib/py/reactor-c-py/include/pythontarget.h",
-             srcGen.resolve("pythontarget.h")
+        FileUtil.copyDirectoryFromClassPath(
+            "/lib/py/reactor-c-py/include",
+             srcGen,
+             true
         );
-        FileUtil.copyFileFromClassPath(
-            "/lib/py/reactor-c-py/lib/pythontarget.c",
-            srcGen.resolve("pythontarget.c")
-        );
-        FileUtil.copyFileFromClassPath(
-            "/lib/c/reactor-c/include/ctarget.h",
-            srcGen.resolve("ctarget.h")
+        FileUtil.copyDirectoryFromClassPath(
+            "/lib/py/reactor-c-py/lib",
+             srcGen,
+             true
         );
     }
 }
\ No newline at end of file
diff --git a/org.lflang/src/org/lflang/generator/python/PythonGenerator.java b/org.lflang/src/org/lflang/generator/python/PythonGenerator.java
index a1ac4daaff..82a910710f 100644
--- a/org.lflang/src/org/lflang/generator/python/PythonGenerator.java
+++ b/org.lflang/src/org/lflang/generator/python/PythonGenerator.java
@@ -606,6 +606,11 @@ public void includeTargetLanguageHeaders() {
         if (targetConfig.tracing != null) {
             code.pr("#include \"core/trace.c\"");
         }
+        
+        if (hasModalReactors) {
+            code.pr("#include \"modal_models/definitions.h\"");
+            targetConfig.compileAdditionalSources.add("modal_models/impl.c");
+        }
     }
 
     /**

From 1f5d82dd2f4a0c77ac3b707b3eb142be8ed8308c Mon Sep 17 00:00:00 2001
From: Soroush Bateni <soroosh129@gmail.com>
Date: Tue, 8 Mar 2022 17:51:07 -0600
Subject: [PATCH 05/36] Updated pointer to reactor-c-py

---
 org.lflang/src/lib/py/reactor-c-py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/org.lflang/src/lib/py/reactor-c-py b/org.lflang/src/lib/py/reactor-c-py
index 6aaf075ce8..0dfd9dc2fe 160000
--- a/org.lflang/src/lib/py/reactor-c-py
+++ b/org.lflang/src/lib/py/reactor-c-py
@@ -1 +1 @@
-Subproject commit 6aaf075ce82f4104875f0aa809a1300445442720
+Subproject commit 0dfd9dc2feae0303bd987f4bad7eaf8d42a246f1

From 0d7a758fdef843274e3d9c7e9ca21fa7c3182a44 Mon Sep 17 00:00:00 2001
From: Soroush Bateni <soroosh129@gmail.com>
Date: Tue, 8 Mar 2022 17:57:51 -0600
Subject: [PATCH 06/36] Updated pointer to reactor-c-py

---
 org.lflang/src/lib/py/reactor-c-py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/org.lflang/src/lib/py/reactor-c-py b/org.lflang/src/lib/py/reactor-c-py
index 0dfd9dc2fe..c4e40d11be 160000
--- a/org.lflang/src/lib/py/reactor-c-py
+++ b/org.lflang/src/lib/py/reactor-c-py
@@ -1 +1 @@
-Subproject commit 0dfd9dc2feae0303bd987f4bad7eaf8d42a246f1
+Subproject commit c4e40d11be543705917305b3069d713f0351c107

From efc38f8c267fbbd71b33073e46bcd8bef58c2089 Mon Sep 17 00:00:00 2001
From: eal <eal@eecs.berkeley.edu>
Date: Tue, 8 Mar 2022 16:54:12 -0800
Subject: [PATCH 07/36] Updated reactor-c

---
 org.lflang/src/lib/c/reactor-c | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/org.lflang/src/lib/c/reactor-c b/org.lflang/src/lib/c/reactor-c
index 3c96abe46f..bd27e76c12 160000
--- a/org.lflang/src/lib/c/reactor-c
+++ b/org.lflang/src/lib/c/reactor-c
@@ -1 +1 @@
-Subproject commit 3c96abe46fdb8b0dd8468e195499ff90741e787c
+Subproject commit bd27e76c12d5f9cb8b3eab1f9e6aec52b790358c

From 89aa41fa4235c485d56307075e9e070b1c386516 Mon Sep 17 00:00:00 2001
From: Soroush Bateni <soroosh129@gmail.com>
Date: Tue, 8 Mar 2022 19:01:34 -0600
Subject: [PATCH 08/36] Bug fix

---
 .../src/org/lflang/generator/python/PythonPortGenerator.java   | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/org.lflang/src/org/lflang/generator/python/PythonPortGenerator.java b/org.lflang/src/org/lflang/generator/python/PythonPortGenerator.java
index efbb111e1d..5b5c2b122a 100644
--- a/org.lflang/src/org/lflang/generator/python/PythonPortGenerator.java
+++ b/org.lflang/src/org/lflang/generator/python/PythonPortGenerator.java
@@ -248,7 +248,8 @@ public static String generatePythonPortVariableInReaction(VarRef port) {
             );
         } else {
             return String.join("\n",
-                containerName+" = Make",
+                "try: "+containerName+"",
+                "except NameError: "+containerName+" = Make()",
                 containerName+"."+variableName+" = "+containerName+"_"+variableName
             );
         }

From 9e9bcba525a79e05b582eb89b4e295ae6b4155de Mon Sep 17 00:00:00 2001
From: Soroush Bateni <soroosh129@gmail.com>
Date: Tue, 8 Mar 2022 19:13:31 -0600
Subject: [PATCH 09/36] More bug fixes

---
 org.lflang/src/lib/c/reactor-c                           | 2 +-
 org.lflang/src/org/lflang/generator/python/PyUtil.java   | 4 ++--
 .../org/lflang/generator/python/PythonPortGenerator.java | 9 +++++----
 3 files changed, 8 insertions(+), 7 deletions(-)

diff --git a/org.lflang/src/lib/c/reactor-c b/org.lflang/src/lib/c/reactor-c
index bd27e76c12..3c96abe46f 160000
--- a/org.lflang/src/lib/c/reactor-c
+++ b/org.lflang/src/lib/c/reactor-c
@@ -1 +1 @@
-Subproject commit bd27e76c12d5f9cb8b3eab1f9e6aec52b790358c
+Subproject commit 3c96abe46fdb8b0dd8468e195499ff90741e787c
diff --git a/org.lflang/src/org/lflang/generator/python/PyUtil.java b/org.lflang/src/org/lflang/generator/python/PyUtil.java
index 58b5996421..8623a9bedb 100644
--- a/org.lflang/src/org/lflang/generator/python/PyUtil.java
+++ b/org.lflang/src/org/lflang/generator/python/PyUtil.java
@@ -181,12 +181,12 @@ public static void copyTargetFiles(FileConfig fileConfig) throws IOException {
         FileUtil.copyDirectoryFromClassPath(
             "/lib/py/reactor-c-py/include",
              srcGen,
-             true
+             false
         );
         FileUtil.copyDirectoryFromClassPath(
             "/lib/py/reactor-c-py/lib",
              srcGen,
-             true
+             false
         );
     }
 }
\ No newline at end of file
diff --git a/org.lflang/src/org/lflang/generator/python/PythonPortGenerator.java b/org.lflang/src/org/lflang/generator/python/PythonPortGenerator.java
index 5b5c2b122a..9c0f1a0e89 100644
--- a/org.lflang/src/org/lflang/generator/python/PythonPortGenerator.java
+++ b/org.lflang/src/org/lflang/generator/python/PythonPortGenerator.java
@@ -240,15 +240,16 @@ public static String generatePythonPortVariableInReaction(VarRef port) {
         String variableName = port.getVariable().getName();
         if (port.getContainer().getWidthSpec() != null) {
             // It's a bank
-            return String.join("\n", 
-                containerName+" = [None] * len("+containerName+"_"+variableName+")",
+            return String.join("\n",
+                "try: "+containerName,
+                "except NameError: "+containerName+" = [None] * len("+containerName+"_"+variableName+")",
                 "for i in range(len("+containerName+"_"+variableName+")):",
-                "    "+containerName+"[i] = Make()",
+                "    if "+containerName+"[i] is None: "+containerName+"[i] = Make()",
                 "    "+containerName+"[i]."+variableName+" = "+containerName+"_"+variableName+"[i]"
             );
         } else {
             return String.join("\n",
-                "try: "+containerName+"",
+                "try: "+containerName,
                 "except NameError: "+containerName+" = Make()",
                 containerName+"."+variableName+" = "+containerName+"_"+variableName
             );

From b7d2d2b3c278c199c1ef8a1a3c3a0e7b50937b45 Mon Sep 17 00:00:00 2001
From: Soroush Bateni <soroosh129@gmail.com>
Date: Tue, 8 Mar 2022 19:14:15 -0600
Subject: [PATCH 10/36] Updated pointer to reactor-c

---
 org.lflang/src/lib/c/reactor-c | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/org.lflang/src/lib/c/reactor-c b/org.lflang/src/lib/c/reactor-c
index 3c96abe46f..bd27e76c12 160000
--- a/org.lflang/src/lib/c/reactor-c
+++ b/org.lflang/src/lib/c/reactor-c
@@ -1 +1 @@
-Subproject commit 3c96abe46fdb8b0dd8468e195499ff90741e787c
+Subproject commit bd27e76c12d5f9cb8b3eab1f9e6aec52b790358c

From d2e75061044096de54df447873eec7e17c6f1602 Mon Sep 17 00:00:00 2001
From: Soroush Bateni <soroosh129@gmail.com>
Date: Tue, 8 Mar 2022 19:28:40 -0600
Subject: [PATCH 11/36] Updated pointer to reactor-c-py

---
 org.lflang/src/lib/py/reactor-c-py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/org.lflang/src/lib/py/reactor-c-py b/org.lflang/src/lib/py/reactor-c-py
index c4e40d11be..78dc0b241d 160000
--- a/org.lflang/src/lib/py/reactor-c-py
+++ b/org.lflang/src/lib/py/reactor-c-py
@@ -1 +1 @@
-Subproject commit c4e40d11be543705917305b3069d713f0351c107
+Subproject commit 78dc0b241d2797423d824080df7e7f685fd45b30

From a294ab48d8d086406ce52f5b7da86068c3d638e9 Mon Sep 17 00:00:00 2001
From: eal <eal@eecs.berkeley.edu>
Date: Tue, 8 Mar 2022 17:43:34 -0800
Subject: [PATCH 12/36] Moved MultipleContained test to the right directory
 matching the C tests.

---
 test/Python/src/{multiport => }/MultipleContained.lf | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename test/Python/src/{multiport => }/MultipleContained.lf (100%)

diff --git a/test/Python/src/multiport/MultipleContained.lf b/test/Python/src/MultipleContained.lf
similarity index 100%
rename from test/Python/src/multiport/MultipleContained.lf
rename to test/Python/src/MultipleContained.lf

From 13b748a95567f3a2f771b6cce105c494be97b318 Mon Sep 17 00:00:00 2001
From: eal <eal@eecs.berkeley.edu>
Date: Tue, 8 Mar 2022 17:49:02 -0800
Subject: [PATCH 13/36] Updated tests to verify that both inputs arrive

---
 test/C/src/MultipleContained.lf      | 8 ++++++++
 test/Python/src/MultipleContained.lf | 8 ++++++++
 2 files changed, 16 insertions(+)

diff --git a/test/C/src/MultipleContained.lf b/test/C/src/MultipleContained.lf
index 6d09798527..7c05f1fbe2 100644
--- a/test/C/src/MultipleContained.lf
+++ b/test/C/src/MultipleContained.lf
@@ -5,6 +5,7 @@ reactor Contained {
     output trigger:int;
     input in1:int;
     input in2:int;
+    state count:int(0);
     reaction(startup) -> trigger {=
         SET(trigger, 42);
     =}
@@ -14,6 +15,7 @@ reactor Contained {
             fprintf(stderr, "FAILED: Expected 42.\n");
             exit(1);
         }
+        self->count++;
     =}
     reaction(in2) {=
         printf("in2 received %d.\n", in2->value);
@@ -21,6 +23,12 @@ reactor Contained {
             fprintf(stderr, "FAILED: Expected 42.\n");
             exit(1);
         }
+        self->count++;
+    =}
+    reaction(shutdown) {=
+        if (self->count != 2) {
+            error_print_and_exit("FAILED: Expected two inputs!");
+        }
     =}
 }
 main reactor MultipleContained {
diff --git a/test/Python/src/MultipleContained.lf b/test/Python/src/MultipleContained.lf
index 3c9c29ddbd..cc549b5be2 100644
--- a/test/Python/src/MultipleContained.lf
+++ b/test/Python/src/MultipleContained.lf
@@ -3,6 +3,7 @@
 target Python;
 reactor Contained {
     output trigger;
+    state count(0);
     input in1;
     input in2;
     reaction(startup) -> trigger {=
@@ -13,12 +14,19 @@ reactor Contained {
         if in1.value != 42:
             sys.stderr.write("FAILED: Expected 42.\n")
             exit(1)
+        self.count += 1
     =}
     reaction(in2) {=
         print("in2 received ", in2.value)
         if in2.value != 42:
             sys.stderr.write("FAILED: Expected 42.\n")
             exit(1)
+        self.count += 1
+    =}
+    reaction(shutdown) {=
+        if self.count != 2:
+            sys.stderr.write("FAILED: Should have received two inputs.\n")
+            exit(1)
     =}
 }
 main reactor MultipleContained {

From e7741d3c1b8adb11ba20967fc56677c47995d0c1 Mon Sep 17 00:00:00 2001
From: eal <eal@eecs.berkeley.edu>
Date: Tue, 8 Mar 2022 18:33:29 -0800
Subject: [PATCH 14/36] Converted ConvertCaseTest to Python.

---
 .../src/modal_models/ConvertCaseTest.lf       |  13 +--
 .../src/modal_models/util/TraceTesting.lf     | 105 ++++++++----------
 2 files changed, 49 insertions(+), 69 deletions(-)

diff --git a/test/Python/src/modal_models/ConvertCaseTest.lf b/test/Python/src/modal_models/ConvertCaseTest.lf
index 6855e3797d..e80fd5429b 100644
--- a/test/Python/src/modal_models/ConvertCaseTest.lf
+++ b/test/Python/src/modal_models/ConvertCaseTest.lf
@@ -5,10 +5,9 @@
 target Python {
     fast: false,
     timeout: 4 sec,
-//    logging: debug
 }
 
-// import TraceTesting from "util/TraceTesting.lf"
+import TraceTesting from "util/TraceTesting.lf"
 
 reactor ResetProcessor {
     input discard
@@ -107,10 +106,8 @@ main reactor {
     feeder.character -> reset_processor.character
     feeder.character -> history_processor.character
     
-    /*
     test = new TraceTesting(
         events_size = 2,
-        trace_size = 60, 
         trace = (
             0,1,72,1,72,
             250000000,1,69,1,69,
@@ -124,9 +121,9 @@ main reactor {
             250000000,1,76,1,108,
             250000000,1,68,1,100,
             250000000,1,95,1,95
-        ), training = false)
-    */
-    // Trigger mode change
+        ), training = False)
+
+    # Trigger mode change
     reaction(stepper) -> reset_processor.discard, history_processor.discard {=
         reset_processor.discard.set(True)
         history_processor.discard.set(True)
@@ -140,5 +137,5 @@ main reactor {
         print(f"History: {history_processor.converted.value}")
     =}
     
-    // reset_processor.converted, history_processor.converted -> test.events
+    reset_processor.converted, history_processor.converted -> test.events
 }
\ No newline at end of file
diff --git a/test/Python/src/modal_models/util/TraceTesting.lf b/test/Python/src/modal_models/util/TraceTesting.lf
index db0359c04c..82b2f6a4b1 100644
--- a/test/Python/src/modal_models/util/TraceTesting.lf
+++ b/test/Python/src/modal_models/util/TraceTesting.lf
@@ -1,83 +1,66 @@
 /*
  * Utility reactor to record and test execution traces.
  */
-target C;
+target Python
 
-preamble {=
-    #include <stdio.h>
-=}
+reactor TraceTesting(events_size(0), trace({=[]=}), training(False)) {
+    input [events_size]events
     
-reactor TraceTesting(events_size:int(0), trace_size:int(0), trace:int[](0), training:bool(false)) {
-    input [events_size]events:int
-    
-    state last_reaction_time:int(0)
-    state trace_idx:int(0)
-    state recorded_events:int*(0)
-    state recorded_events_next:int(0)
+    state last_reaction_time(0)
+    state trace_idx(0)
+    state recorded_events({=[]=})
+    state recorded_events_next(0)
     
     reaction(startup) {=
-        self->last_reaction_time = get_logical_time();
+        self.last_reaction_time = get_logical_time()
     =}
     
     reaction(events) {=
-        // Time passed since last reaction
-        int curr_reaction_delay = get_logical_time() - self->last_reaction_time;
+        # Time passed since last reaction
+        curr_reaction_delay = get_logical_time() - self.last_reaction_time
         
-        if (self->training) {
-            // Save time
-            self->recorded_events = (int*) realloc(self->recorded_events, sizeof(int) * (self->recorded_events_next + 1 + 2 * self->events_size));
-            self->recorded_events[self->recorded_events_next++] = curr_reaction_delay; 
-        } else {
-            if (self->trace_idx >= self->trace_size) {
-                printf("ERROR: Trace Error: Current execution exceeds given trace.\n");
-                exit(1);
-            }
+        if self.training:
+            # Save the time
+            self.recorded_events.append(curr_reaction_delay)
+        else:
+            if self.trace_idx >= len(self.trace):
+                sys.stderr.write("ERROR: Trace Error: Current execution exceeds given trace.\n")
+                exit(1)
             
-            int trace_reaction_delay = self->trace[self->trace_idx++];
+            trace_reaction_delay = self.trace[self.trace_idx]
+            self.trace_idx += 1
             
-            if (curr_reaction_delay != trace_reaction_delay) {
-                printf("ERROR: Trace Mismatch: Unexpected reaction timing. (delay: %d, expected: %d)\n", curr_reaction_delay, trace_reaction_delay);
-                exit(2);
-            }
-        }
+            if curr_reaction_delay != trace_reaction_delay:
+                sys.stderr.write(f"ERROR: Trace Mismatch: Unexpected reaction timing. (delay: {curr_reaction_delay}, expected: {trace_reaction_delay})\n")
+                exit(2)
         
-        for (int i = 0; i < self->events_size; i++) {
-            int curr_present = events[i]->is_present;
-            int curr_value = events[i]->value;
+        for i in range(self.events_size):
+            curr_present = events[i].is_present
+            curr_value = events[i].value
             
-            if (self->training) {
-                // Save event
-                self->recorded_events[self->recorded_events_next++] = curr_present;
-                self->recorded_events[self->recorded_events_next++] = curr_value;
-            } else {
-                int trace_present = self->trace[self->trace_idx++];
-                int trace_value = self->trace[self->trace_idx++];
+            if self.training:
+                # Save the event
+                self.recorded_events.append(curr_present)
+                self.recorded_events.append(curr_value)
+            else:
+                trace_present = self.trace[self.trace_idx]
+                self.trace_idx += 1
+                trace_value = self.trace[self.trace_idx]
+                self.trace_idx += 1
                 
-                if (trace_present != curr_present) {
-                    printf("ERROR: Trace Mismatch: Unexpected event presence. (event: %d, presence: %d, expected: %d)\n", i, curr_present, trace_present);
-                    exit(3);
-                } else if (curr_present && trace_value != curr_value) {
-                    printf("ERROR: Trace Mismatch: Unexpected event value. (event: %d, presence: %d, expected: %d)\n", i, curr_value, trace_value);
-                    exit(4);
-                }
-            }
-        }
+                if trace_present != curr_present:
+                    sys.stderr.write(f"ERROR: Trace Mismatch: Unexpected event presence. (event: {i}, presence: {curr_present}, expected: {trace_present})\n")
+                    exit(3)
+                elif curr_present and trace_value != curr_value:
+                    sys.stderr.write(f"ERROR: Trace Mismatch: Unexpected event presence. (event: {i}, value: {curr_value}, expected: {trace_value})\n")
+                    exit(4)
         
-        self->last_reaction_time = get_logical_time();
+        self.last_reaction_time = get_logical_time()
     =}
     
     reaction(shutdown) {=
-        if (self->training) {
-            printf("Recorded event trace (%d): (", self->recorded_events_next);
-            for (int i = 0; i < self->recorded_events_next; i++) {
-                printf("%d", self->recorded_events[i]);
-                if (i < self->recorded_events_next - 1) {
-                    printf(",");
-                }
-            }
-            printf(")\n");
-            
-            free(self->recorded_events);
-        }
+        if self.training:
+            print(f"Recorded event trace ({self.recorded_events_next}):")
+            print(self.recorded_events)
     =}
 }
\ No newline at end of file

From d40d42835dcaa6a99863ac623d2245391a750e6a Mon Sep 17 00:00:00 2001
From: eal <eal@eecs.berkeley.edu>
Date: Thu, 10 Mar 2022 09:55:46 -0800
Subject: [PATCH 15/36] Fixed test to remove reaction self-loop cycle that was
 masked.

---
 .../generator/ReactionInstanceGraph.java       | 18 ++++++++----------
 test/C/src/modal_models/ModalCycleBreaker.lf   |  4 ++--
 2 files changed, 10 insertions(+), 12 deletions(-)

diff --git a/org.lflang/src/org/lflang/generator/ReactionInstanceGraph.java b/org.lflang/src/org/lflang/generator/ReactionInstanceGraph.java
index ccd5090a3e..5f99791a04 100644
--- a/org.lflang/src/org/lflang/generator/ReactionInstanceGraph.java
+++ b/org.lflang/src/org/lflang/generator/ReactionInstanceGraph.java
@@ -135,15 +135,13 @@ protected void addDownstreamReactions(PortInstance port, ReactionInstance reacti
                         List<Runtime> dstRuntimes = dstReaction.getRuntimeInstances();
                         Runtime srcRuntime = srcRuntimes.get(srcIndex);
                         Runtime dstRuntime = dstRuntimes.get(dstIndex);
-                        if (dstRuntime != srcRuntime) {
-                            // Only add this dependency if the reactions are not in modes at all or in the same mode or in modes of separate reactors
-                            // This allows modes to break cycles since modes are always mutually exclusive.
-                            if (srcRuntime.getReaction().getMode(true) == null ||
-                                    dstRuntime.getReaction().getMode(true) == null ||
-                                    srcRuntime.getReaction().getMode(true) == dstRuntime.getReaction().getMode(true) ||
-                                    srcRuntime.getReaction().getParent() != dstRuntime.getReaction().getParent()) {
-                                addEdge(dstRuntime, srcRuntime);
-                            }
+                        // Only add this dependency if the reactions are not in modes at all or in the same mode or in modes of separate reactors
+                        // This allows modes to break cycles since modes are always mutually exclusive.
+                        if (srcRuntime.getReaction().getMode(true) == null ||
+                                dstRuntime.getReaction().getMode(true) == null ||
+                                srcRuntime.getReaction().getMode(true) == dstRuntime.getReaction().getMode(true) ||
+                                srcRuntime.getReaction().getParent() != dstRuntime.getReaction().getParent()) {
+                            addEdge(dstRuntime, srcRuntime);
                         }
 
                         // Propagate the deadlines, if any.
@@ -263,7 +261,7 @@ private void assignLevels() {
             Set<Runtime> toRemove = new LinkedHashSet<Runtime>();
             Set<Runtime> downstreamAdjacentNodes = getDownstreamAdjacentNodes(origin);
             // All downstream adjacent nodes start with a level 0. Adjust the
-            // <code>maxNumOfReactionPerLevel<code> field accordingly (to be
+            // <code>numReactionsPerLevel<code> field accordingly (to be
             // updated in the for loop below).
             adjustNumReactionsPerLevel(0, downstreamAdjacentNodes.size());
             // Visit effect nodes.
diff --git a/test/C/src/modal_models/ModalCycleBreaker.lf b/test/C/src/modal_models/ModalCycleBreaker.lf
index b4e1b8af8f..ce8298fd03 100644
--- a/test/C/src/modal_models/ModalCycleBreaker.lf
+++ b/test/C/src/modal_models/ModalCycleBreaker.lf
@@ -18,8 +18,8 @@ reactor Modal {
     mode Two { // Defining reaction to in2 before in1 would cause cycle if no mode were present
         timer wait(150msec, 1sec)
               
-        reaction(in2) -> out {=
-            SET(out, in2->value);
+        reaction(in2) {=
+            // SET(out, in2->value);
         =}
         
         reaction(wait) -> One {=

From f1ea738304c90089f46078b9df6ee98132f24b0a Mon Sep 17 00:00:00 2001
From: eal <eal@eecs.berkeley.edu>
Date: Thu, 10 Mar 2022 11:51:17 -0800
Subject: [PATCH 16/36] Update reactor-c to point to branch

---
 org.lflang/src/lib/c/reactor-c | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/org.lflang/src/lib/c/reactor-c b/org.lflang/src/lib/c/reactor-c
index ff11e7bfde..01b0defbf9 160000
--- a/org.lflang/src/lib/c/reactor-c
+++ b/org.lflang/src/lib/c/reactor-c
@@ -1 +1 @@
-Subproject commit ff11e7bfdeb5aeac962ee18ac7a031b5b9f3b864
+Subproject commit 01b0defbf91c8938cc742e75a02d9d8fb88b86db

From e64abe240c621b93e80425db3beead96ba37c6a2 Mon Sep 17 00:00:00 2001
From: eal <eal@eecs.berkeley.edu>
Date: Thu, 10 Mar 2022 11:52:49 -0800
Subject: [PATCH 17/36] Added another modal model test to Python

---
 .../src/modal_models/ModalCycleBreaker.lf     | 81 +++++++++++++++++++
 1 file changed, 81 insertions(+)
 create mode 100644 test/Python/src/modal_models/ModalCycleBreaker.lf

diff --git a/test/Python/src/modal_models/ModalCycleBreaker.lf b/test/Python/src/modal_models/ModalCycleBreaker.lf
new file mode 100644
index 0000000000..30a373618e
--- /dev/null
+++ b/test/Python/src/modal_models/ModalCycleBreaker.lf
@@ -0,0 +1,81 @@
+/*
+ * Modal Reactor Test.
+ * 
+ * Tests if connections in the same reactor that have the same destination work if they are located in separate modes.
+ */
+target Python {
+    fast: false,
+    timeout: 1 sec
+}
+
+import TraceTesting from "util/TraceTesting.lf"
+
+reactor Modal {
+    input in1
+    input in2
+    output out
+    
+    mode Two { # Defining reaction to in2 before in1 would cause cycle if no mode were present
+        timer wait(150msec, 1sec)
+              
+        reaction(in2) {=
+        =}
+        
+        reaction(wait) -> One {=
+            One.set()
+            print("Switching to mode One")
+        =}
+    }
+    initial mode One {
+        reaction(in1) -> out {=
+            out.set(in1.value)
+        =}
+
+        reaction(in1) -> Two {=
+            if in1.value % 5 == 4:
+                Two.set()
+                print("Switching to mode Two")
+        =}
+    }
+}
+
+reactor Counter(period(1 sec)) {
+    output value
+    
+    timer t(0, period)
+    state curval(0)
+    
+    reaction(t) -> value {=
+        value.set(self.curval)
+        self.curval += 1
+    =}
+}
+
+main reactor {
+    counter = new Counter(period=100msec)    
+    modal = new Modal()
+    test = new TraceTesting(
+        events_size = 1,
+        trace = (
+            0,1,0,
+            100000000,1,1,
+            100000000,1,2,
+            100000000,1,3,
+            100000000,1,4,
+            200000000,1,6,
+            100000000,1,7,
+            100000000,1,8,
+            100000000,1,9
+        ), training = False)
+    
+    counter.value -> modal.in1
+    modal.out -> modal.in2
+    
+    modal.out
+    -> test.events
+
+    // Print
+    reaction(modal.out) {=
+        print(modal.out.value)
+    =}
+}
\ No newline at end of file

From 5aa8ac60cc822e93d8ff00b5b923b86d2792fe54 Mon Sep 17 00:00:00 2001
From: eal <eal@eecs.berkeley.edu>
Date: Thu, 10 Mar 2022 12:06:38 -0800
Subject: [PATCH 18/36] Added one more passing test and several unported tests
 that will fail

---
 test/Python/src/modal_models/ModalActions.lf  |  98 ++++++++++++++++
 test/Python/src/modal_models/ModalAfter.lf    | 106 ++++++++++++++++++
 .../src/modal_models/ModalNestedReactions.lf  |  78 +++++++++++++
 .../src/modal_models/ModalStateReset.lf       |  98 ++++++++++++++++
 test/Python/src/modal_models/ModalTimers.lf   |  79 +++++++++++++
 .../MultipleOutputFeeder_2Connections.lf      |  85 ++++++++++++++
 ...ultipleOutputFeeder_ReactionConnections.lf |  88 +++++++++++++++
 7 files changed, 632 insertions(+)
 create mode 100644 test/Python/src/modal_models/ModalActions.lf
 create mode 100644 test/Python/src/modal_models/ModalAfter.lf
 create mode 100644 test/Python/src/modal_models/ModalNestedReactions.lf
 create mode 100644 test/Python/src/modal_models/ModalStateReset.lf
 create mode 100644 test/Python/src/modal_models/ModalTimers.lf
 create mode 100644 test/Python/src/modal_models/MultipleOutputFeeder_2Connections.lf
 create mode 100644 test/Python/src/modal_models/MultipleOutputFeeder_ReactionConnections.lf

diff --git a/test/Python/src/modal_models/ModalActions.lf b/test/Python/src/modal_models/ModalActions.lf
new file mode 100644
index 0000000000..da16feea30
--- /dev/null
+++ b/test/Python/src/modal_models/ModalActions.lf
@@ -0,0 +1,98 @@
+/*
+ * Modal Reactor Test.
+ * Tests actions, their suspension during mode inactivity and continuation of delays with history transitions.
+ */
+target Python {
+    fast: false,
+    timeout: 4 sec
+}
+
+import TraceTesting from "util/TraceTesting.lf"
+
+reactor Modal {
+    input next
+    
+    output mode_switch
+    output action1_sched
+    output action1_exec
+    output action2_sched
+    output action2_exec
+    
+    initial mode One {
+        timer T1(0, 750msec)
+        logical action delay1(500msec)
+        
+        reaction(T1) -> delay1, action1_sched {=
+            print("Scheduled Action")
+            delay1.schedule(0)
+            action1_sched.set(1)
+        =}
+        reaction(delay1) -> action1_exec {=
+            print("Executed Action")
+            action1_exec.set(1)
+        =}
+        
+        reaction(next) -> reset(Two), mode_switch {=
+            print("Transitioning to mode Two (reset)")
+            mode_switch.set(1)
+            Two.set()
+        =}
+    }
+    mode Two {
+        timer T2(0, 750 msec)
+        logical action delay2(500 msec)
+        
+        reaction(T2) -> delay2, action2_sched {=
+            print("Scheduled Action2")
+            delay2.schedule(0)
+            action2_sched.set(1)
+        =}
+        reaction(delay2) -> action2_exec {=
+            print("Executed Action2")
+            action2_exec.set(1)
+        =}
+        
+        reaction(next) -> continue(One), mode_switch {=
+            print("Transitioning to mode One (continue)")
+            mode_switch.set(1)
+            One.set()
+        =}
+    }
+}
+
+main reactor {
+    timer stepper(1sec, 1sec)
+    
+    modal = new Modal()
+    test = new TraceTesting(
+        events_size = 5,
+        trace = (
+            0,0,0,1,1,0,0,0,0,0,0,
+            500000000,0,0,0,1,1,1,0,0,0,0,
+            250000000,0,0,1,1,0,1,0,0,0,0,
+            250000000,1,1,0,1,0,1,0,0,0,0,
+            0,0,1,0,1,0,1,1,1,0,0,
+            500000000,0,1,0,1,0,1,0,1,1,1,
+            250000000,0,1,0,1,0,1,1,1,0,1,
+            250000000,1,1,0,1,0,1,0,1,0,1,
+            250000000,0,1,0,1,1,1,0,1,0,1,
+            250000000,0,1,1,1,0,1,0,1,0,1,
+            500000000,1,1,0,1,1,1,0,1,0,1,
+            0,0,1,0,1,0,1,1,1,0,1,
+            500000000,0,1,0,1,0,1,0,1,1,1,
+            250000000,0,1,0,1,0,1,1,1,0,1,
+            250000000,1,1,0,1,0,1,0,1,0,1
+        ), training = False)
+
+    // Trigger mode change
+    reaction(stepper) -> modal.next {=
+        modal.next.set(True)
+    =}
+    
+    modal.mode_switch,
+    modal.action1_sched,
+    modal.action1_exec,
+    modal.action2_sched,
+    modal.action2_exec
+    -> test.events
+}
\ No newline at end of file
diff --git a/test/Python/src/modal_models/ModalAfter.lf b/test/Python/src/modal_models/ModalAfter.lf
new file mode 100644
index 0000000000..c162d347c9
--- /dev/null
+++ b/test/Python/src/modal_models/ModalAfter.lf
@@ -0,0 +1,106 @@
+/*
+ * Modal Reactor Test.
+ * Tests after delays, its suspension during mode inactivity and continuation with history transitions.
+ */
+target Python {
+    fast: false,
+    timeout: 4 sec
+};
+
+import TraceTesting from "util/TraceTesting.lf"
+
+reactor Modal {
+    input next:bool
+    
+    output mode_switch:int
+    output produced1:int
+    output consumed1:int
+    output produced2:int
+    output consumed2:int
+    
+    initial mode One {
+        producer1 = new Producer(mode_id=1)
+        consumer1 = new Consumer(mode_id=1)
+        producer1.product -> produced1
+        producer1.product -> consumer1.product after 500msec;
+        consumer1.report -> consumed1;
+        
+        reaction(next) -> reset(Two), mode_switch {=
+            printf("Transitioning to mode Two (reset)\n");
+            SET(mode_switch, 1);
+            SET_MODE(Two);
+        =}
+    }
+    mode Two {
+        producer2 = new Producer(mode_id=2)
+        consumer2 = new Consumer(mode_id=2)
+        producer2.product -> produced2
+        producer2.product -> consumer2.product after 500msec;
+        consumer2.report -> consumed2;
+        
+        reaction(next) -> continue(One), mode_switch {=
+            printf("Transitioning to mode One (continue)\n");
+            SET(mode_switch, 1);
+            SET_MODE(One);
+        =}
+    }
+}
+
+reactor Producer(mode_id:int(0)) {
+    output product:int
+    
+    timer t(0, 750msec)
+    
+    reaction(t) -> product {=
+        printf("Produced in %d\n", self->mode_id);
+        SET(product, 1);
+    =}
+}
+
+reactor Consumer(mode_id:int(0)) {
+    input product:int
+    output report:int
+    
+    reaction(product) -> report {=
+        printf("Consumed in %d\n", self->mode_id);
+        SET(report, 1);
+    =}
+}
+
+main reactor {
+    timer stepper(1sec, 1sec)
+    
+    modal = new Modal()
+    test = new TraceTesting(
+        events_size = 5,
+        trace_size = 165, 
+        trace = (
+            0,0,0,1,1,0,0,0,0,0,0,
+            500000000,0,0,0,1,1,1,0,0,0,0,
+            250000000,0,0,1,1,0,1,0,0,0,0,
+            250000000,1,1,0,1,0,1,0,0,0,0,
+            0,0,1,0,1,0,1,1,1,0,0,
+            500000000,0,1,0,1,0,1,0,1,1,1,
+            250000000,0,1,0,1,0,1,1,1,0,1,
+            250000000,1,1,0,1,0,1,0,1,0,1,
+            250000000,0,1,0,1,1,1,0,1,0,1,
+            250000000,0,1,1,1,0,1,0,1,0,1,
+            500000000,1,1,0,1,1,1,0,1,0,1,
+            0,0,1,0,1,0,1,1,1,0,1,
+            500000000,0,1,0,1,0,1,0,1,1,1,
+            250000000,0,1,0,1,0,1,1,1,0,1,
+            250000000,1,1,0,1,0,1,0,1,0,1
+        ), training = false)
+
+    // Trigger mode change
+    reaction(stepper) -> modal.next {=
+        SET(modal.next, true);
+    =}
+    
+    modal.mode_switch,
+    modal.produced1,
+    modal.consumed1,
+    modal.produced2,
+    modal.consumed2
+    -> test.events
+}
\ No newline at end of file
diff --git a/test/Python/src/modal_models/ModalNestedReactions.lf b/test/Python/src/modal_models/ModalNestedReactions.lf
new file mode 100644
index 0000000000..cbb5db417f
--- /dev/null
+++ b/test/Python/src/modal_models/ModalNestedReactions.lf
@@ -0,0 +1,78 @@
+/**
+ * Modal Reactor Test.
+ * Checks disabling of reactions indirectly nested in an inactive mode
+ */
+target Python {
+    fast: false,
+    timeout: 2 sec
+};
+
+reactor CounterCycle {
+	input next:bool;
+	
+    output count:int;
+    output only_in_two:bool;
+	output never:int;
+    
+    initial mode One {
+		reaction(next) -> count, Two {=
+            SET(count, 1);
+            SET_MODE(Two);
+		=}
+    }
+    mode Two {
+		fwd = new Forward()
+		next -> fwd.in
+		fwd.out -> only_in_two
+		
+		reaction(next) -> count, One {=
+            SET(count, 2);
+            SET_MODE(One);
+		=}
+    }
+    mode Three {
+		reaction(next) -> never {=
+            SET(never, true);
+		=}
+    }
+}
+
+reactor Forward {
+    input in:bool;
+    output out:bool;
+    
+    reaction(in) -> out {=
+        SET(out, in->value);
+    =}
+}
+
+main reactor {
+    timer stepper(0, 250msec)
+    counter = new CounterCycle()
+    
+    // Trigger
+    reaction(stepper) -> counter.next {=
+        SET(counter.next, true);
+    =}
+
+    // Check
+    reaction(stepper) counter.count, counter.only_in_two {=
+        printf("%d\n", counter.count->value);
+        
+        if (!counter.count->is_present) {
+            printf("ERROR: Missing mode change.\n");
+            exit(1);
+        } else if (counter.only_in_two->is_present && counter.count->value != 2) {
+            printf("ERROR: Indirectly nested reaction was not properly deactivated.\n");
+            exit(2);
+        } else if (!counter.only_in_two->is_present && counter.count->value == 2) {
+            printf("ERROR: Missing output from indirectly nested reaction.\n");
+            exit(3);
+        }
+    =}
+    
+    reaction(counter.never) {=
+        printf("ERROR: Detected output from unreachable mode.\n");
+        exit(4);
+    =}
+}
diff --git a/test/Python/src/modal_models/ModalStateReset.lf b/test/Python/src/modal_models/ModalStateReset.lf
new file mode 100644
index 0000000000..2239a7fa80
--- /dev/null
+++ b/test/Python/src/modal_models/ModalStateReset.lf
@@ -0,0 +1,98 @@
+/*
+ * Modal Reactor Test.
+ * Tests reset of state variables in modes.
+ */
+target Python {
+    fast: false,
+    timeout: 4 sec
+};
+
+import TraceTesting from "util/TraceTesting.lf"
+
+reactor Modal {
+    input next:bool;
+    
+    output mode_switch:int
+    output count0:int;
+    output count1:int;
+    output count2:int;
+    
+    state counter0:int(0);
+    
+    reaction(next) -> count0 {=
+        printf("Counter0: %d\n", self->counter0);
+        SET(count0, self->counter0++);
+    =}
+    
+    initial mode One {
+        state counter1:int(0);
+        timer T1(0msec, 250msec);
+        
+        reaction(T1) -> count1 {=
+            printf("Counter1: %d\n", self->counter1);
+            SET(count1, self->counter1++);
+        =}
+        
+        reaction(next) -> reset(Two), mode_switch {=
+            printf("Transitioning to mode Two (reset)\n");
+            SET(mode_switch, 1);
+            SET_MODE(Two);
+        =}
+    }
+    mode Two {
+        state counter2:int(-2);
+        timer T2(0msec, 250msec);
+        
+        reaction(T2) -> count2 {=
+            printf("Counter2: %d\n", self->counter2);
+            SET(count2, self->counter2++);
+        =}
+        
+        reaction(next) -> continue(One), mode_switch {=
+            printf("Transitioning to mode One (continue)\n");
+            SET(mode_switch, 1);
+            SET_MODE(One);
+        =}
+    }
+}
+
+main reactor {
+    timer stepper(1sec, 1sec)
+    
+    modal = new Modal()
+    test = new TraceTesting(
+        events_size = 4,
+        trace_size = 171, 
+        trace = (
+            0,0,0,0,0,1,0,0,0,
+            250000000,0,0,0,0,1,1,0,0,
+            250000000,0,0,0,0,1,2,0,0,
+            250000000,0,0,0,0,1,3,0,0,
+            250000000,1,1,1,0,1,4,0,0,
+            0,0,1,0,0,0,4,1,-2,
+            250000000,0,1,0,0,0,4,1,-1,
+            250000000,0,1,0,0,0,4,1,0,
+            250000000,0,1,0,0,0,4,1,1,
+            250000000,1,1,1,1,0,4,1,2,
+            250000000,0,1,0,1,1,5,0,2,
+            250000000,0,1,0,1,1,6,0,2,
+            250000000,0,1,0,1,1,7,0,2,
+            250000000,1,1,1,2,1,8,0,2,
+            0,0,1,0,2,0,8,1,-2,
+            250000000,0,1,0,2,0,8,1,-1,
+            250000000,0,1,0,2,0,8,1,0,
+            250000000,0,1,0,2,0,8,1,1,
+            250000000,1,1,1,3,0,8,1,2
+        ), training = false)
+
+    // Trigger mode change
+    reaction(stepper) -> modal.next {=
+        SET(modal.next, true);
+    =}
+    
+    modal.mode_switch,
+    modal.count0,
+    modal.count1,
+    modal.count2
+    -> test.events
+}
\ No newline at end of file
diff --git a/test/Python/src/modal_models/ModalTimers.lf b/test/Python/src/modal_models/ModalTimers.lf
new file mode 100644
index 0000000000..02ce11ab3b
--- /dev/null
+++ b/test/Python/src/modal_models/ModalTimers.lf
@@ -0,0 +1,79 @@
+/*
+ * Modal Reactor Test.
+ * Tests timers, their deactivation and reset in modes.
+ */
+target Python {
+    fast: false,
+    timeout: 4 sec
+};
+
+import TraceTesting from "util/TraceTesting.lf"
+
+reactor Modal {
+    input next:bool
+    
+    output mode_switch:int
+    output timer1:int
+    output timer2:int
+    
+    initial mode One {
+        timer T1(0, 750msec)
+        
+        reaction(T1) -> timer1 {=
+            printf("T1\n");
+            SET(timer1, 1);
+        =}
+        
+        reaction(next) -> reset(Two), mode_switch {=
+            printf("Transitioning to mode Two (reset)\n");
+            SET(mode_switch, 1);
+            SET_MODE(Two);
+        =}
+    }
+    mode Two {
+        timer T2(0, 750msec)
+        
+        reaction(T2) -> timer2 {=
+            printf("T2\n");
+            SET(timer2, 1);
+        =}
+        
+        reaction(next) -> continue(One), mode_switch {=
+            printf("Transitioning to mode One (continue)\n");
+            SET(mode_switch, 1);
+            SET_MODE(One);
+        =}
+    }
+}
+
+main reactor {
+    timer stepper(1sec, 1sec)
+    
+    modal = new Modal()
+    test = new TraceTesting(
+        events_size = 3,
+        trace_size = 77, 
+        trace = (
+            0,0,0,1,1,0,0,
+            750000000,0,0,1,1,0,0,
+            250000000,1,1,0,1,0,0,
+            0,0,1,0,1,1,1,
+            750000000,0,1,0,1,1,1,
+            250000000,1,1,0,1,0,1,
+            500000000,0,1,1,1,0,1,
+            500000000,1,1,0,1,0,1,
+            0,0,1,0,1,1,1,
+            750000000,0,1,0,1,1,1,
+            250000000,1,1,0,1,0,1
+        ), training = false)
+
+    // Trigger mode change
+    reaction(stepper) -> modal.next {=
+        SET(modal.next, true);
+    =}
+    
+    modal.mode_switch,
+    modal.timer1,
+    modal.timer2
+    -> test.events
+}
\ No newline at end of file
diff --git a/test/Python/src/modal_models/MultipleOutputFeeder_2Connections.lf b/test/Python/src/modal_models/MultipleOutputFeeder_2Connections.lf
new file mode 100644
index 0000000000..36e399ceb1
--- /dev/null
+++ b/test/Python/src/modal_models/MultipleOutputFeeder_2Connections.lf
@@ -0,0 +1,85 @@
+/*
+ * Modal Reactor Test.
+ * 
+ * Tests if connections in the same reactor that have the same destination work if they are located in separate modes.
+ */
+target Python {
+    fast: false,
+    timeout: 2 sec
+};
+
+import TraceTesting from "util/TraceTesting.lf"
+
+reactor Modal {
+	input next:bool;
+	output count:int;
+	
+    initial mode One {
+		counter1 = new Counter(period=250msec);
+		counter1.value -> count;
+		
+		reaction(next) -> Two {=
+            SET_MODE(Two);
+		=}
+    }
+    mode Two {
+		counter2 = new Counter(period=100msec);
+		counter2.value -> count;
+        
+		reaction(next) -> continue(One) {=
+            SET_MODE(One);
+		=}
+    }
+}
+
+reactor Counter(period:time(1sec)) {
+    output value:int
+    
+    timer t(0, period)
+    state curval:int(0)
+    
+    reaction(t) -> value {=
+        SET(value, self->curval++);
+    =}
+}
+
+main reactor {
+    timer stepper(500msec, 500msec)
+    
+    modal = new Modal()
+    test = new TraceTesting(
+        events_size = 1,
+        trace_size = 51, 
+        trace = (
+            0,1,0,
+            250000000,1,1,
+            250000000,1,2,
+            0,1,0,
+            100000000,1,1,
+            100000000,1,2,
+            100000000,1,3,
+            100000000,1,4,
+            100000000,1,5,
+            250000000,1,3,
+            250000000,1,4,
+            0,1,0,
+            100000000,1,1,
+            100000000,1,2,
+            100000000,1,3,
+            100000000,1,4,
+            100000000,1,5
+        ), training = false)
+
+    // Trigger mode change
+    reaction(stepper) -> modal.next {=
+        SET(modal.next, true);
+    =}
+    
+    // Print
+    reaction(modal.count) {=
+        printf("%d\n", modal.count->value);
+    =}
+    
+    modal.count
+    -> test.events
+}
\ No newline at end of file
diff --git a/test/Python/src/modal_models/MultipleOutputFeeder_ReactionConnections.lf b/test/Python/src/modal_models/MultipleOutputFeeder_ReactionConnections.lf
new file mode 100644
index 0000000000..52b9e834c6
--- /dev/null
+++ b/test/Python/src/modal_models/MultipleOutputFeeder_ReactionConnections.lf
@@ -0,0 +1,88 @@
+/*
+ * Modal Reactor Test.
+ * 
+ * Tests if a connection and a reaction in the same reactor can have the same destination if they are located in separate modes.
+ */
+target Python {
+    fast: false,
+    timeout: 2 sec
+};
+
+import TraceTesting from "util/TraceTesting.lf"
+
+reactor Modal {
+    input next:bool;
+    output count:int;
+    
+    initial mode One {
+        counter1 = new Counter(period=250msec);
+        counter1.value -> count;
+        
+        reaction(next) -> Two {=
+            SET_MODE(Two);
+        =}
+    }
+    mode Two {
+        counter2 = new Counter(period=100msec);
+        
+        reaction(counter2.value) -> count {=
+            SET(count, counter2.value->value * 10);
+        =}
+        
+        reaction(next) -> continue(One) {=
+            SET_MODE(One);
+        =}
+    }
+}
+
+reactor Counter(period:time(1sec)) {
+    output value:int
+    
+    timer t(0, period)
+    state curval:int(0)
+    
+    reaction(t) -> value {=
+        SET(value, self->curval++);
+    =}
+}
+
+main reactor {
+    timer stepper(500msec, 500msec)
+    
+    modal = new Modal()
+    test = new TraceTesting(
+        events_size = 1,
+        trace_size = 51, 
+        trace = (
+            0,1,0,
+            250000000,1,1,
+            250000000,1,2,
+            0,1,0,
+            100000000,1,10,
+            100000000,1,20,
+            100000000,1,30,
+            100000000,1,40,
+            100000000,1,50,
+            250000000,1,3,
+            250000000,1,4,
+            0,1,0,
+            100000000,1,10,
+            100000000,1,20,
+            100000000,1,30,
+            100000000,1,40,
+            100000000,1,50
+        ), training = false)
+
+    // Trigger mode change
+    reaction(stepper) -> modal.next {=
+        SET(modal.next, true);
+    =}
+    
+    // Print
+    reaction(modal.count) {=
+        printf("%d\n", modal.count->value);
+    =}
+    
+    modal.count
+    -> test.events
+}
\ No newline at end of file

From 6978981afadc903c2aafabf0745d1a180423a046 Mon Sep 17 00:00:00 2001
From: Soroush Bateni <soroosh129@gmail.com>
Date: Thu, 10 Mar 2022 15:17:12 -0600
Subject: [PATCH 19/36] Finished porting tests. Three tests fail because of
 missing features

---
 test/Python/src/modal_models/ModalAfter.lf    | 57 +++++++++----------
 .../src/modal_models/ModalNestedReactions.lf  | 57 +++++++++----------
 .../src/modal_models/ModalStateReset.lf       | 54 +++++++++---------
 test/Python/src/modal_models/ModalTimers.lf   | 35 ++++++------
 .../MultipleOutputFeeder_2Connections.lf      | 34 +++++------
 ...ultipleOutputFeeder_ReactionConnections.lf | 34 +++++------
 6 files changed, 135 insertions(+), 136 deletions(-)

diff --git a/test/Python/src/modal_models/ModalAfter.lf b/test/Python/src/modal_models/ModalAfter.lf
index c162d347c9..4202311b4f 100644
--- a/test/Python/src/modal_models/ModalAfter.lf
+++ b/test/Python/src/modal_models/ModalAfter.lf
@@ -5,65 +5,65 @@
 target Python {
     fast: false,
     timeout: 4 sec
-};
+}
 
 import TraceTesting from "util/TraceTesting.lf"
 
 reactor Modal {
-    input next:bool
+    input next
     
-    output mode_switch:int
-    output produced1:int
-    output consumed1:int
-    output produced2:int
-    output consumed2:int
+    output mode_switch
+    output produced1
+    output consumed1
+    output produced2
+    output consumed2
     
     initial mode One {
         producer1 = new Producer(mode_id=1)
         consumer1 = new Consumer(mode_id=1)
         producer1.product -> produced1
-        producer1.product -> consumer1.product after 500msec;
-        consumer1.report -> consumed1;
+        producer1.product -> consumer1.product after 500msec
+        consumer1.report -> consumed1
         
         reaction(next) -> reset(Two), mode_switch {=
-            printf("Transitioning to mode Two (reset)\n");
-            SET(mode_switch, 1);
-            SET_MODE(Two);
+            print("Transitioning to mode Two (reset)")
+            mode_switch.set(1)
+            Two.set()
         =}
     }
     mode Two {
         producer2 = new Producer(mode_id=2)
         consumer2 = new Consumer(mode_id=2)
         producer2.product -> produced2
-        producer2.product -> consumer2.product after 500msec;
-        consumer2.report -> consumed2;
+        producer2.product -> consumer2.product after 500msec
+        consumer2.report -> consumed2
         
         reaction(next) -> continue(One), mode_switch {=
-            printf("Transitioning to mode One (continue)\n");
-            SET(mode_switch, 1);
-            SET_MODE(One);
+            print("Transitioning to mode One (continue)")
+            mode_switch.set(1)
+            One.set()
         =}
     }
 }
 
-reactor Producer(mode_id:int(0)) {
-    output product:int
+reactor Producer(mode_id(0)) {
+    output product
     
     timer t(0, 750msec)
     
     reaction(t) -> product {=
-        printf("Produced in %d\n", self->mode_id);
-        SET(product, 1);
+        print(f"Produced in {self.mode_id}")
+        product.set(1)
     =}
 }
 
-reactor Consumer(mode_id:int(0)) {
-    input product:int
-    output report:int
+reactor Consumer(mode_id(0)) {
+    input product
+    output report
     
     reaction(product) -> report {=
-        printf("Consumed in %d\n", self->mode_id);
-        SET(report, 1);
+        print("Consumed in {self.mode_id}")
+        report.set(1)
     =}
 }
 
@@ -73,7 +73,6 @@ main reactor {
     modal = new Modal()
     test = new TraceTesting(
         events_size = 5,
-        trace_size = 165, 
         trace = (
             0,0,0,1,1,0,0,0,0,0,0,
             500000000,0,0,0,1,1,1,0,0,0,0,
@@ -90,11 +89,11 @@ main reactor {
             500000000,0,1,0,1,0,1,0,1,1,1,
             250000000,0,1,0,1,0,1,1,1,0,1,
             250000000,1,1,0,1,0,1,0,1,0,1
-        ), training = false)
+        ), training = False)
 
     // Trigger mode change
     reaction(stepper) -> modal.next {=
-        SET(modal.next, true);
+        modal.next.set(True)
     =}
     
     modal.mode_switch,
diff --git a/test/Python/src/modal_models/ModalNestedReactions.lf b/test/Python/src/modal_models/ModalNestedReactions.lf
index cbb5db417f..5f134ea33f 100644
--- a/test/Python/src/modal_models/ModalNestedReactions.lf
+++ b/test/Python/src/modal_models/ModalNestedReactions.lf
@@ -5,44 +5,44 @@
 target Python {
     fast: false,
     timeout: 2 sec
-};
+}
 
 reactor CounterCycle {
-	input next:bool;
+	input next
 	
-    output count:int;
-    output only_in_two:bool;
-	output never:int;
+    output count
+    output only_in_two
+	output never
     
     initial mode One {
 		reaction(next) -> count, Two {=
-            SET(count, 1);
-            SET_MODE(Two);
+            count.set(1)
+            Two.set()
 		=}
     }
     mode Two {
 		fwd = new Forward()
-		next -> fwd.in
+		next -> fwd.inp
 		fwd.out -> only_in_two
 		
 		reaction(next) -> count, One {=
-            SET(count, 2);
-            SET_MODE(One);
+            count.set(2)
+            One.set()
 		=}
     }
     mode Three {
 		reaction(next) -> never {=
-            SET(never, true);
+            never.set(True)
 		=}
     }
 }
 
 reactor Forward {
-    input in:bool;
-    output out:bool;
+    input inp
+    output out
     
-    reaction(in) -> out {=
-        SET(out, in->value);
+    reaction(inp) -> out {=
+        out.set(inp.value)
     =}
 }
 
@@ -52,27 +52,26 @@ main reactor {
     
     // Trigger
     reaction(stepper) -> counter.next {=
-        SET(counter.next, true);
+        counter.next.set(True)
     =}
 
     // Check
     reaction(stepper) counter.count, counter.only_in_two {=
-        printf("%d\n", counter.count->value);
+        print(counter.count.value)
         
-        if (!counter.count->is_present) {
-            printf("ERROR: Missing mode change.\n");
-            exit(1);
-        } else if (counter.only_in_two->is_present && counter.count->value != 2) {
-            printf("ERROR: Indirectly nested reaction was not properly deactivated.\n");
-            exit(2);
-        } else if (!counter.only_in_two->is_present && counter.count->value == 2) {
-            printf("ERROR: Missing output from indirectly nested reaction.\n");
-            exit(3);
-        }
+        if counter.count.is_present is not True:
+            sys.stderr.write("ERROR: Missing mode change.\n")
+            exit(1)
+        elif counter.only_in_two.is_present and (counter.count.value != 2):
+            sys.stderr.write("ERROR: Indirectly nested reaction was not properly deactivated.\n")
+            exit(2)
+        elif counter.only_in_two.is_present is not True and (counter.count.value == 2):
+            sys.stderr.write("ERROR: Missing output from indirectly nested reaction.\n")
+            exit(3)
     =}
     
     reaction(counter.never) {=
-        printf("ERROR: Detected output from unreachable mode.\n");
-        exit(4);
+        sys.stderr.write("ERROR: Detected output from unreachable mode.\n")
+        exit(4)
     =}
 }
diff --git a/test/Python/src/modal_models/ModalStateReset.lf b/test/Python/src/modal_models/ModalStateReset.lf
index 2239a7fa80..3ee796508e 100644
--- a/test/Python/src/modal_models/ModalStateReset.lf
+++ b/test/Python/src/modal_models/ModalStateReset.lf
@@ -5,53 +5,56 @@
 target Python {
     fast: false,
     timeout: 4 sec
-};
+}
 
 import TraceTesting from "util/TraceTesting.lf"
 
 reactor Modal {
-    input next:bool;
+    input next
     
-    output mode_switch:int
-    output count0:int;
-    output count1:int;
-    output count2:int;
+    output mode_switch
+    output count0
+    output count1
+    output count2
     
-    state counter0:int(0);
+    state counter0(0)
     
     reaction(next) -> count0 {=
-        printf("Counter0: %d\n", self->counter0);
-        SET(count0, self->counter0++);
+        print(f"Counter0: {self.counter0}")
+        count0.set(self.counter0)
+        self.counter0 += 1
     =}
     
     initial mode One {
-        state counter1:int(0);
-        timer T1(0msec, 250msec);
+        state counter1(0)
+        timer T1(0msec, 250msec)
         
         reaction(T1) -> count1 {=
-            printf("Counter1: %d\n", self->counter1);
-            SET(count1, self->counter1++);
+            print(f"Counter1: {self.counter1}")
+            count1.set(self.counter1)
+            self.counter1 += 1
         =}
         
         reaction(next) -> reset(Two), mode_switch {=
-            printf("Transitioning to mode Two (reset)\n");
-            SET(mode_switch, 1);
-            SET_MODE(Two);
+            print("Transitioning to mode Two (reset)")
+            mode_switch.set(1)
+            Two.set()
         =}
     }
     mode Two {
-        state counter2:int(-2);
-        timer T2(0msec, 250msec);
+        state counter2(-2)
+        timer T2(0msec, 250msec)
         
         reaction(T2) -> count2 {=
-            printf("Counter2: %d\n", self->counter2);
-            SET(count2, self->counter2++);
+            print(f"Counter2: {self.counter2}")
+            count2.set(self.counter2)
+            self.counter2 += 1
         =}
         
         reaction(next) -> continue(One), mode_switch {=
-            printf("Transitioning to mode One (continue)\n");
-            SET(mode_switch, 1);
-            SET_MODE(One);
+            print("Transitioning to mode One (continue)")
+            mode_switch.set(1)
+            One.set()
         =}
     }
 }
@@ -62,7 +65,6 @@ main reactor {
     modal = new Modal()
     test = new TraceTesting(
         events_size = 4,
-        trace_size = 171, 
         trace = (
             0,0,0,0,0,1,0,0,0,
             250000000,0,0,0,0,1,1,0,0,
@@ -83,11 +85,11 @@ main reactor {
             250000000,0,1,0,2,0,8,1,0,
             250000000,0,1,0,2,0,8,1,1,
             250000000,1,1,1,3,0,8,1,2
-        ), training = false)
+        ), training = False)
 
     // Trigger mode change
     reaction(stepper) -> modal.next {=
-        SET(modal.next, true);
+        modal.next.set(True)
     =}
     
     modal.mode_switch,
diff --git a/test/Python/src/modal_models/ModalTimers.lf b/test/Python/src/modal_models/ModalTimers.lf
index 02ce11ab3b..8883a4819d 100644
--- a/test/Python/src/modal_models/ModalTimers.lf
+++ b/test/Python/src/modal_models/ModalTimers.lf
@@ -5,43 +5,43 @@
 target Python {
     fast: false,
     timeout: 4 sec
-};
+}
 
 import TraceTesting from "util/TraceTesting.lf"
 
 reactor Modal {
-    input next:bool
+    input next
     
-    output mode_switch:int
-    output timer1:int
-    output timer2:int
+    output mode_switch
+    output timer1
+    output timer2
     
     initial mode One {
         timer T1(0, 750msec)
         
         reaction(T1) -> timer1 {=
-            printf("T1\n");
-            SET(timer1, 1);
+            print("T1")
+            timer1.set(1)
         =}
         
         reaction(next) -> reset(Two), mode_switch {=
-            printf("Transitioning to mode Two (reset)\n");
-            SET(mode_switch, 1);
-            SET_MODE(Two);
+            print("Transitioning to mode Two (reset)")
+            mode_switch.set(1)
+            Two.set()
         =}
     }
     mode Two {
         timer T2(0, 750msec)
         
         reaction(T2) -> timer2 {=
-            printf("T2\n");
-            SET(timer2, 1);
+            print("T2")
+            timer2.set(1)
         =}
         
         reaction(next) -> continue(One), mode_switch {=
-            printf("Transitioning to mode One (continue)\n");
-            SET(mode_switch, 1);
-            SET_MODE(One);
+            print("Transitioning to mode One (continue)")
+            mode_switch.set(1)
+            One.set()
         =}
     }
 }
@@ -52,7 +52,6 @@ main reactor {
     modal = new Modal()
     test = new TraceTesting(
         events_size = 3,
-        trace_size = 77, 
         trace = (
             0,0,0,1,1,0,0,
             750000000,0,0,1,1,0,0,
@@ -65,11 +64,11 @@ main reactor {
             0,0,1,0,1,1,1,
             750000000,0,1,0,1,1,1,
             250000000,1,1,0,1,0,1
-        ), training = false)
+        ), training = False)
 
     // Trigger mode change
     reaction(stepper) -> modal.next {=
-        SET(modal.next, true);
+        modal.next.set(True)
     =}
     
     modal.mode_switch,
diff --git a/test/Python/src/modal_models/MultipleOutputFeeder_2Connections.lf b/test/Python/src/modal_models/MultipleOutputFeeder_2Connections.lf
index 36e399ceb1..6a6ef990d4 100644
--- a/test/Python/src/modal_models/MultipleOutputFeeder_2Connections.lf
+++ b/test/Python/src/modal_models/MultipleOutputFeeder_2Connections.lf
@@ -6,40 +6,41 @@
 target Python {
     fast: false,
     timeout: 2 sec
-};
+}
 
 import TraceTesting from "util/TraceTesting.lf"
 
 reactor Modal {
-	input next:bool;
-	output count:int;
+	input next
+	output count
 	
     initial mode One {
-		counter1 = new Counter(period=250msec);
-		counter1.value -> count;
+		counter1 = new Counter(period=250msec)
+		counter1.value -> count
 		
 		reaction(next) -> Two {=
-            SET_MODE(Two);
+            Two.set()
 		=}
     }
     mode Two {
-		counter2 = new Counter(period=100msec);
-		counter2.value -> count;
+		counter2 = new Counter(period=100msec)
+		counter2.value -> count
         
 		reaction(next) -> continue(One) {=
-            SET_MODE(One);
+            One.set()
 		=}
     }
 }
 
-reactor Counter(period:time(1sec)) {
-    output value:int
+reactor Counter(period(1sec)) {
+    output value
     
     timer t(0, period)
-    state curval:int(0)
+    state curval(0)
     
     reaction(t) -> value {=
-        SET(value, self->curval++);
+        value.set(self.curval)
+        self.curval += 1
     =}
 }
 
@@ -49,7 +50,6 @@ main reactor {
     modal = new Modal()
     test = new TraceTesting(
         events_size = 1,
-        trace_size = 51, 
         trace = (
             0,1,0,
             250000000,1,1,
@@ -68,16 +68,16 @@ main reactor {
             100000000,1,3,
             100000000,1,4,
             100000000,1,5
-        ), training = false)
+        ), training = False)
 
     // Trigger mode change
     reaction(stepper) -> modal.next {=
-        SET(modal.next, true);
+        modal.next.set(True)
     =}
     
     // Print
     reaction(modal.count) {=
-        printf("%d\n", modal.count->value);
+        print(modal.count.value)
     =}
     
     modal.count
diff --git a/test/Python/src/modal_models/MultipleOutputFeeder_ReactionConnections.lf b/test/Python/src/modal_models/MultipleOutputFeeder_ReactionConnections.lf
index 52b9e834c6..5bb5d18fdc 100644
--- a/test/Python/src/modal_models/MultipleOutputFeeder_ReactionConnections.lf
+++ b/test/Python/src/modal_models/MultipleOutputFeeder_ReactionConnections.lf
@@ -6,43 +6,44 @@
 target Python {
     fast: false,
     timeout: 2 sec
-};
+}
 
 import TraceTesting from "util/TraceTesting.lf"
 
 reactor Modal {
-    input next:bool;
-    output count:int;
+    input next
+    output count
     
     initial mode One {
-        counter1 = new Counter(period=250msec);
-        counter1.value -> count;
+        counter1 = new Counter(period=250msec)
+        counter1.value -> count
         
         reaction(next) -> Two {=
-            SET_MODE(Two);
+            Two.set()
         =}
     }
     mode Two {
-        counter2 = new Counter(period=100msec);
+        counter2 = new Counter(period=100msec)
         
         reaction(counter2.value) -> count {=
-            SET(count, counter2.value->value * 10);
+            count.set(counter2.value.value * 10)
         =}
         
         reaction(next) -> continue(One) {=
-            SET_MODE(One);
+            One.set()
         =}
     }
 }
 
-reactor Counter(period:time(1sec)) {
-    output value:int
+reactor Counter(period(1sec)) {
+    output value
     
     timer t(0, period)
-    state curval:int(0)
+    state curval(0)
     
     reaction(t) -> value {=
-        SET(value, self->curval++);
+        value.set(self.curval)
+        self.curval += 1
     =}
 }
 
@@ -52,7 +53,6 @@ main reactor {
     modal = new Modal()
     test = new TraceTesting(
         events_size = 1,
-        trace_size = 51, 
         trace = (
             0,1,0,
             250000000,1,1,
@@ -71,16 +71,16 @@ main reactor {
             100000000,1,30,
             100000000,1,40,
             100000000,1,50
-        ), training = false)
+        ), training = False)
 
     // Trigger mode change
     reaction(stepper) -> modal.next {=
-        SET(modal.next, true);
+        modal.next.set(True)
     =}
     
     // Print
     reaction(modal.count) {=
-        printf("%d\n", modal.count->value);
+        print(modal.count.value)
     =}
     
     modal.count

From e68a4c78fe40b3b5044e0914f2d06ff42b20850e Mon Sep 17 00:00:00 2001
From: Steven <stevenhouseng@gmail.com>
Date: Fri, 11 Mar 2022 11:36:46 -0800
Subject: [PATCH 20/36] bug fix

---
 org.lflang/src/org/lflang/generator/c/CModesGenerator.java | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/org.lflang/src/org/lflang/generator/c/CModesGenerator.java b/org.lflang/src/org/lflang/generator/c/CModesGenerator.java
index 198a7a3fc2..bbb3c7a8ab 100644
--- a/org.lflang/src/org/lflang/generator/c/CModesGenerator.java
+++ b/org.lflang/src/org/lflang/generator/c/CModesGenerator.java
@@ -58,7 +58,7 @@ public static void generateDeclarations(
                 "// Initialize mode state",
                 "_lf_self_base->_lf__mode_state.parent_mode = NULL;",
                 "_lf_self_base->_lf__mode_state.initial_mode = &self->_lf__modes["+initialMode+"];",
-                "_lf_self_base->_lf__mode_state.active_mode = self->_lf__mode_state.initial_mode;",
+                "_lf_self_base->_lf__mode_state.active_mode = _lf_self_base->_lf__mode_state.initial_mode;",
                 "_lf_self_base->_lf__mode_state.next_mode = NULL;",
                 "_lf_self_base->_lf__mode_state.mode_change = 0;"
             ));

From 08486bef5bdf159d704139c22ab65b924504befc Mon Sep 17 00:00:00 2001
From: Steven <stevenhouseng@gmail.com>
Date: Fri, 11 Mar 2022 13:31:42 -0800
Subject: [PATCH 21/36] bug fix

---
 org.lflang/src/org/lflang/generator/c/CModesGenerator.java | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/org.lflang/src/org/lflang/generator/c/CModesGenerator.java b/org.lflang/src/org/lflang/generator/c/CModesGenerator.java
index bbb3c7a8ab..c887198d4f 100644
--- a/org.lflang/src/org/lflang/generator/c/CModesGenerator.java
+++ b/org.lflang/src/org/lflang/generator/c/CModesGenerator.java
@@ -60,7 +60,7 @@ public static void generateDeclarations(
                 "_lf_self_base->_lf__mode_state.initial_mode = &self->_lf__modes["+initialMode+"];",
                 "_lf_self_base->_lf__mode_state.active_mode = _lf_self_base->_lf__mode_state.initial_mode;",
                 "_lf_self_base->_lf__mode_state.next_mode = NULL;",
-                "_lf_self_base->_lf__mode_state.mode_change = 0;"
+                "_lf_self_base->_lf__mode_state.mode_change = no_transition;"
             ));
         }
     }

From 7639be74c36d60a00a7bc2f43e8189cbd7ecda17 Mon Sep 17 00:00:00 2001
From: eal <eal@eecs.berkeley.edu>
Date: Fri, 11 Mar 2022 11:50:33 -0800
Subject: [PATCH 22/36] Align reactor-c

---
 org.lflang/src/lib/c/reactor-c | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/org.lflang/src/lib/c/reactor-c b/org.lflang/src/lib/c/reactor-c
index 01b0defbf9..8d0972f7a4 160000
--- a/org.lflang/src/lib/c/reactor-c
+++ b/org.lflang/src/lib/c/reactor-c
@@ -1 +1 @@
-Subproject commit 01b0defbf91c8938cc742e75a02d9d8fb88b86db
+Subproject commit 8d0972f7a44cee8efc7448e140e834f97f2fad73

From 5728000ba0440660a5fcd75ccb347792c1f69de0 Mon Sep 17 00:00:00 2001
From: eal <eal@eecs.berkeley.edu>
Date: Fri, 11 Mar 2022 18:41:48 -0800
Subject: [PATCH 23/36] Retrained test to get the right data types for training
 data

---
 .../src/modal_models/ConvertCaseTest.lf       | 24 +++++++++----------
 1 file changed, 12 insertions(+), 12 deletions(-)

diff --git a/test/Python/src/modal_models/ConvertCaseTest.lf b/test/Python/src/modal_models/ConvertCaseTest.lf
index e80fd5429b..2c5150da21 100644
--- a/test/Python/src/modal_models/ConvertCaseTest.lf
+++ b/test/Python/src/modal_models/ConvertCaseTest.lf
@@ -109,18 +109,18 @@ main reactor {
     test = new TraceTesting(
         events_size = 2,
         trace = (
-            0,1,72,1,72,
-            250000000,1,69,1,69,
-            250000000,1,76,1,76,
-            250000000,1,95,1,95,
-            250000000,1,79,1,79,
-            250000000,1,32,1,32,
-            250000000,1,119,1,119,
-            250000000,1,95,1,95,
-            250000000,1,82,1,114,
-            250000000,1,76,1,108,
-            250000000,1,68,1,100,
-            250000000,1,95,1,95
+            0, True, 'H', True, 'H',
+            250000000, True, 'E', True, 'E',
+            250000000, True, 'L', True, 'L',
+            250000000, True, '_', True, '_',
+            250000000, True, 'O', True, 'O',
+            250000000, True, ' ', True, ' ',
+            250000000, True, 'w', True, 'w',
+            250000000, True, '_', True, '_',
+            250000000, True, 'R', True, 'r',
+            250000000, True, 'L', True, 'l',
+            250000000, True, 'D', True, 'd',
+            250000000, True, '_', True, '_'
         ), training = False)
 
     # Trigger mode change

From a02a4325ffcf54bf90c69c917838c4f836611452 Mon Sep 17 00:00:00 2001
From: eal <eal@eecs.berkeley.edu>
Date: Fri, 11 Mar 2022 18:44:30 -0800
Subject: [PATCH 24/36] Print tags

---
 test/Python/src/modal_models/ModalTimers.lf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/test/Python/src/modal_models/ModalTimers.lf b/test/Python/src/modal_models/ModalTimers.lf
index 8883a4819d..cddd17aa6a 100644
--- a/test/Python/src/modal_models/ModalTimers.lf
+++ b/test/Python/src/modal_models/ModalTimers.lf
@@ -20,7 +20,7 @@ reactor Modal {
         timer T1(0, 750msec)
         
         reaction(T1) -> timer1 {=
-            print("T1")
+            print(f"T1: at tag ({get_elapsed_logical_time()}, {get_microstep()})")
             timer1.set(1)
         =}
         
@@ -34,7 +34,7 @@ reactor Modal {
         timer T2(0, 750msec)
         
         reaction(T2) -> timer2 {=
-            print("T2")
+            print(f"T2: at tag ({get_elapsed_logical_time()}, {get_microstep()})")
             timer2.set(1)
         =}
         

From 2d278c40b23cf17817a5cef6a8df5d0f40ae059f Mon Sep 17 00:00:00 2001
From: Soroush Bateni <soroosh129@gmail.com>
Date: Sat, 12 Mar 2022 09:34:00 -0600
Subject: [PATCH 25/36] Added AST transformation for startup triggers in modes
 (not behaving as expected)

---
 .../org/lflang/generator/GeneratorBase.java   | 46 ++++++++++++
 test/C/src/modal_models/ModalStartup.lf       | 75 +++++++++++++++++++
 2 files changed, 121 insertions(+)
 create mode 100644 test/C/src/modal_models/ModalStartup.lf

diff --git a/org.lflang/src/org/lflang/generator/GeneratorBase.java b/org.lflang/src/org/lflang/generator/GeneratorBase.java
index f5a7895e1c..227df44e7e 100644
--- a/org.lflang/src/org/lflang/generator/GeneratorBase.java
+++ b/org.lflang/src/org/lflang/generator/GeneratorBase.java
@@ -381,6 +381,7 @@ public void doGenerate(Resource resource, LFGeneratorContext context) {
         // Check for existence and support of modes
         hasModalReactors = IterableExtensions.exists(reactors, it -> !it.getModes().isEmpty());
         checkModalReactorSupport(false);
+        transformStartupTriggersInModalReactors();
         
         enableSupportForSerializationIfApplicable(context.getCancelIndicator());
     }
@@ -643,6 +644,51 @@ protected String getConflictingConnectionsInModalReactorsBody(String source, Str
                                   "transforming connections in modal reactors.");
         return "MODAL MODELS NOT SUPPORTED";
     }
+    
+    /**
+     * Transform the startup trigger in modes to a timer with an offset and a period of zero.
+     * 
+     * This allows reactions in modes with startup in their trigger to be triggered when the mode
+     * is entered for the first time or via a reset transition.
+     */
+    protected void transformStartupTriggersInModalReactors() {
+        for (Reactor reactor : reactors) {
+            var reactorModes = reactor.getModes();
+            if (!reactorModes.isEmpty()) {
+                for (Mode mode : reactorModes) {
+                    // Create the timer with an offset and period of zero
+                    var zeroTime = LfFactory.eINSTANCE.createTime();
+                    zeroTime.setInterval(0);
+                    zeroTime.setUnit("msec");
+                    var zeroValue = LfFactory.eINSTANCE.createValue();
+                    zeroValue.setTime(zeroTime);
+                    var timer = LfFactory.eINSTANCE.createTimer();
+                    timer.setOffset(zeroValue);
+                    timer.setPeriod(zeroValue);
+                    timer.setName("_lf_startup_timer_for_mode_"+mode.getName());
+
+                    // Replace startup triggers
+                    boolean foundAtLeastOneStartupTriggerInMode = false;
+                    for (Reaction reaction : mode.getReactions()) {
+                        var hadStartupTrigger = reaction.getTriggers()
+                                .removeIf(trigger -> trigger.isStartup());
+                        if (hadStartupTrigger) {
+                            var timerRef = LfFactory.eINSTANCE.createVarRef();
+                            timerRef.setVariable(timer);
+                            reaction.getTriggers().add(timerRef);
+
+                            foundAtLeastOneStartupTriggerInMode = true;
+                        }
+                    }
+
+                    if (foundAtLeastOneStartupTriggerInMode) {
+                        // Add the timer to the mode
+                        mode.getTimers().add(timer);
+                    }
+                }
+            }
+        }
+    }
 
     /**
      * Generate code for the body of a reaction that handles the
diff --git a/test/C/src/modal_models/ModalStartup.lf b/test/C/src/modal_models/ModalStartup.lf
new file mode 100644
index 0000000000..5d772edb5b
--- /dev/null
+++ b/test/C/src/modal_models/ModalStartup.lf
@@ -0,0 +1,75 @@
+/*
+ * Modal Reactor Test.
+ * Test startup reactions in modes.
+ */
+target C {
+    fast: false,
+    timeout: 4 sec
+};
+
+import TraceTesting from "util/TraceTesting.lf"
+
+reactor Modal {
+    input next:bool
+    
+    output mode_switch:int
+    output timer1:int
+    output timer2:int
+    
+    initial mode One {
+        reaction(startup) -> timer1 {=
+            printf("T1\n");
+            SET(timer1, 1);
+        =}
+        
+        reaction(next) -> reset(Two), mode_switch {=
+            printf("Transitioning to mode Two (reset)\n");
+            SET(mode_switch, 1);
+            SET_MODE(Two);
+        =}
+    }
+    mode Two {        
+        reaction(startup) -> timer2 {=
+            printf("T2\n");
+            SET(timer2, 1);
+        =}
+        
+        reaction(next) -> continue(One), mode_switch {=
+            printf("Transitioning to mode One (continue)\n");
+            SET(mode_switch, 1);
+            SET_MODE(One);
+        =}
+    }
+}
+
+main reactor {
+    timer stepper(1sec, 1sec)
+    
+    modal = new Modal()
+    test = new TraceTesting(
+        events_size = 3,
+        trace_size = 77, 
+        trace = (
+            0,0,0,1,1,0,0,
+            750000000,0,0,1,1,0,0,
+            250000000,1,1,0,1,0,0,
+            0,0,1,0,1,1,1,
+            750000000,0,1,0,1,1,1,
+            250000000,1,1,0,1,0,1,
+            500000000,0,1,1,1,0,1,
+            500000000,1,1,0,1,0,1,
+            0,0,1,0,1,1,1,
+            750000000,0,1,0,1,1,1,
+            250000000,1,1,0,1,0,1
+        ), training = true)
+
+    // Trigger mode change
+    reaction(stepper) -> modal.next {=
+        SET(modal.next, true);
+    =}
+    
+    modal.mode_switch,
+    modal.timer1,
+    modal.timer2
+    -> test.events
+}

From a0fac1889e96cc526bc9819f634132a1ef155581 Mon Sep 17 00:00:00 2001
From: Soroush Bateni <soroosh129@gmail.com>
Date: Sat, 12 Mar 2022 09:56:39 -0600
Subject: [PATCH 26/36] Cleaned up the code a bit

---
 .../org/lflang/generator/GeneratorBase.java   | 20 +++++++++++--------
 1 file changed, 12 insertions(+), 8 deletions(-)

diff --git a/org.lflang/src/org/lflang/generator/GeneratorBase.java b/org.lflang/src/org/lflang/generator/GeneratorBase.java
index 227df44e7e..0aa3d3b98d 100644
--- a/org.lflang/src/org/lflang/generator/GeneratorBase.java
+++ b/org.lflang/src/org/lflang/generator/GeneratorBase.java
@@ -652,19 +652,23 @@ protected String getConflictingConnectionsInModalReactorsBody(String source, Str
      * is entered for the first time or via a reset transition.
      */
     protected void transformStartupTriggersInModalReactors() {
+        // Construct a timer with an offset and a period of zero
+        var zeroTime = LfFactory.eINSTANCE.createTime();
+        zeroTime.setInterval(0);
+        zeroTime.setUnit("msec");
+        var zeroValue = LfFactory.eINSTANCE.createValue();
+        zeroValue.setTime(zeroTime);
+        var baseTimer = LfFactory.eINSTANCE.createTimer();
+        baseTimer.setOffset(zeroValue);
+        baseTimer.setPeriod(zeroValue);
+        
+        // Look for reactors with modes
         for (Reactor reactor : reactors) {
             var reactorModes = reactor.getModes();
             if (!reactorModes.isEmpty()) {
                 for (Mode mode : reactorModes) {
                     // Create the timer with an offset and period of zero
-                    var zeroTime = LfFactory.eINSTANCE.createTime();
-                    zeroTime.setInterval(0);
-                    zeroTime.setUnit("msec");
-                    var zeroValue = LfFactory.eINSTANCE.createValue();
-                    zeroValue.setTime(zeroTime);
-                    var timer = LfFactory.eINSTANCE.createTimer();
-                    timer.setOffset(zeroValue);
-                    timer.setPeriod(zeroValue);
+                    var timer = EcoreUtil.copy(baseTimer);
                     timer.setName("_lf_startup_timer_for_mode_"+mode.getName());
 
                     // Replace startup triggers

From 924e9e86cd09c56c36867894edccdb50684f8894 Mon Sep 17 00:00:00 2001
From: Soroush Bateni <soroosh129@gmail.com>
Date: Sat, 12 Mar 2022 16:50:20 -0600
Subject: [PATCH 27/36] Pass the appropriate arguments to
 _lf_handle_mode_changes. Cleaned up the imports.

---
 .../org/lflang/generator/c/CGenerator.xtend   | 146 +++++++++---------
 1 file changed, 69 insertions(+), 77 deletions(-)

diff --git a/org.lflang/src/org/lflang/generator/c/CGenerator.xtend b/org.lflang/src/org/lflang/generator/c/CGenerator.xtend
index 22c4f04f9d..032829c753 100644
--- a/org.lflang/src/org/lflang/generator/c/CGenerator.xtend
+++ b/org.lflang/src/org/lflang/generator/c/CGenerator.xtend
@@ -26,82 +26,67 @@ THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
 package org.lflang.generator.c;
 
-import java.io.File;
-import java.nio.file.Files;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.HashSet;
-import java.util.LinkedHashMap;
-import java.util.LinkedHashSet;
-import java.util.LinkedList;
-import java.util.concurrent.Executors;
-import java.util.concurrent.TimeUnit;
-import java.util.regex.Pattern;
-import org.eclipse.emf.ecore.resource.Resource;
-import org.eclipse.emf.ecore.util.EcoreUtil;
-import org.eclipse.xtext.util.CancelIndicator;
-import org.lflang.ErrorReporter;
-import org.lflang.FileConfig;
-import org.lflang.InferredType;
-import org.lflang.ASTUtils;
-import org.lflang.Target;
-import org.lflang.TargetConfig;
-import org.lflang.TargetProperty;
-import org.lflang.TargetProperty.ClockSyncMode;
-import org.lflang.TargetProperty.CoordinationType;
-import org.lflang.TargetProperty.LogLevel;
-import org.lflang.TimeValue;
-import org.lflang.federated.CGeneratorExtension;
-import org.lflang.federated.FedFileConfig;
-import org.lflang.federated.FederateInstance;
-import org.lflang.federated.launcher.FedCLauncher;
-import org.lflang.federated.serialization.FedROS2CPPSerialization;
-import org.lflang.federated.serialization.SupportedSerializers;
-import org.lflang.generator.CodeBuilder;
-import org.lflang.generator.GeneratorBase;
-import org.lflang.generator.DockerComposeGenerator;
-import org.lflang.generator.GeneratorResult;
-import org.lflang.generator.IntegratedBuilder;
-import org.lflang.generator.GeneratorUtils;
-import org.lflang.generator.LFGeneratorContext;
-import org.lflang.generator.PortInstance;
-import org.lflang.generator.ReactionInstance;
-import org.lflang.generator.ReactorInstance;
-import org.lflang.generator.RuntimeRange;
-import org.lflang.generator.SendRange;
-import org.lflang.generator.SubContext;
-import org.lflang.generator.TriggerInstance;
-import org.lflang.generator.c.CActionGenerator;
-import org.lflang.generator.c.CTimerGenerator;
-import org.lflang.generator.c.CStateGenerator;
-import org.lflang.generator.c.CTracingGenerator;
-import org.lflang.generator.c.CPortGenerator;
-import org.lflang.generator.c.CModesGenerator;
-import org.lflang.generator.c.CMainGenerator;
-import org.lflang.generator.c.CFederateGenerator;
-import org.lflang.generator.c.CNetworkGenerator;
-import org.lflang.generator.c.InteractingContainedReactors;
-import org.lflang.lf.Action;
-import org.lflang.lf.ActionOrigin;
-import org.lflang.lf.Connection;
-import org.lflang.lf.Delay;
-import org.lflang.lf.Input;
-import org.lflang.lf.Instantiation;
-import org.lflang.lf.LfFactory;
-import org.lflang.lf.Mode;
-import org.lflang.lf.Model;
-import org.lflang.lf.Output;
-import org.lflang.lf.Port;
-import org.lflang.lf.Reaction;
-import org.lflang.lf.Reactor;
-import org.lflang.lf.ReactorDecl;
-import org.lflang.lf.VarRef;
-import org.lflang.lf.Variable;
-import org.lflang.util.FileUtil;
-import org.lflang.util.XtendUtil;
-
-import static extension org.lflang.ASTUtils.*;
-import static extension org.lflang.ASTUtils.*;
+import java.io.File
+import java.nio.file.Files
+import java.util.ArrayList
+import java.util.HashSet
+import java.util.LinkedHashMap
+import java.util.LinkedHashSet
+import java.util.LinkedList
+import java.util.concurrent.Executors
+import java.util.concurrent.TimeUnit
+import java.util.regex.Pattern
+import org.eclipse.emf.ecore.resource.Resource
+import org.eclipse.xtext.util.CancelIndicator
+import org.lflang.ASTUtils
+import org.lflang.ErrorReporter
+import org.lflang.FileConfig
+import org.lflang.InferredType
+import org.lflang.Target
+import org.lflang.TargetConfig
+import org.lflang.TargetProperty
+import org.lflang.TargetProperty.ClockSyncMode
+import org.lflang.TargetProperty.CoordinationType
+import org.lflang.TargetProperty.LogLevel
+import org.lflang.TimeValue
+import org.lflang.federated.CGeneratorExtension
+import org.lflang.federated.FedFileConfig
+import org.lflang.federated.FederateInstance
+import org.lflang.federated.launcher.FedCLauncher
+import org.lflang.federated.serialization.FedROS2CPPSerialization
+import org.lflang.federated.serialization.SupportedSerializers
+import org.lflang.generator.CodeBuilder
+import org.lflang.generator.DockerComposeGenerator
+import org.lflang.generator.GeneratorBase
+import org.lflang.generator.GeneratorResult
+import org.lflang.generator.GeneratorUtils
+import org.lflang.generator.IntegratedBuilder
+import org.lflang.generator.LFGeneratorContext
+import org.lflang.generator.PortInstance
+import org.lflang.generator.ReactionInstance
+import org.lflang.generator.ReactorInstance
+import org.lflang.generator.RuntimeRange
+import org.lflang.generator.SendRange
+import org.lflang.generator.SubContext
+import org.lflang.generator.TriggerInstance
+import org.lflang.lf.Action
+import org.lflang.lf.ActionOrigin
+import org.lflang.lf.Delay
+import org.lflang.lf.Input
+import org.lflang.lf.Instantiation
+import org.lflang.lf.Mode
+import org.lflang.lf.Model
+import org.lflang.lf.Output
+import org.lflang.lf.Port
+import org.lflang.lf.Reaction
+import org.lflang.lf.Reactor
+import org.lflang.lf.ReactorDecl
+import org.lflang.lf.VarRef
+import org.lflang.lf.Variable
+import org.lflang.util.FileUtil
+import org.lflang.util.XtendUtil
+
+import static extension org.lflang.ASTUtils.*
 
 /** 
  * Generator for C target. This class generates C code defining each reactor
@@ -763,7 +748,14 @@ class CGenerator extends GeneratorBase {
                     // Generate mode change detection
                     code.pr('''
                         void _lf_handle_mode_changes() {
-                            _lf_process_mode_changes(_lf_modal_reactor_states, _lf_modal_reactor_states_size, «modalStateResetCount > 0 ? "_lf_modal_state_reset" : "NULL"», «modalStateResetCount > 0 ? "_lf_modal_state_reset_size" : 0»);
+                            _lf_process_mode_changes(
+                                _lf_modal_reactor_states, 
+                                _lf_modal_reactor_states_size, 
+                                «modalStateResetCount > 0 ? "_lf_modal_state_reset" : "NULL"», 
+                                «modalStateResetCount > 0 ? "_lf_modal_state_reset_size" : 0»,
+                                _lf_timer_triggers,
+                                _lf_timer_triggers_size
+                            );
                         }
                     ''')
                 }

From a38bab602a83472d2e5ab85284dbb95427e037ff Mon Sep 17 00:00:00 2001
From: Soroush Bateni <soroosh129@gmail.com>
Date: Sat, 12 Mar 2022 16:52:25 -0600
Subject: [PATCH 28/36] Updated test to test startup triggers

---
 org.lflang/src/lib/c/reactor-c                |  2 +-
 .../org/lflang/generator/GeneratorBase.java   |  2 +-
 test/C/src/modal_models/ModalStartup.lf       | 65 ++++++++++++-------
 3 files changed, 43 insertions(+), 26 deletions(-)

diff --git a/org.lflang/src/lib/c/reactor-c b/org.lflang/src/lib/c/reactor-c
index 8d0972f7a4..e0e3451f50 160000
--- a/org.lflang/src/lib/c/reactor-c
+++ b/org.lflang/src/lib/c/reactor-c
@@ -1 +1 @@
-Subproject commit 8d0972f7a44cee8efc7448e140e834f97f2fad73
+Subproject commit e0e3451f5068cabce0cd185e44ea65fdbed05c8e
diff --git a/org.lflang/src/org/lflang/generator/GeneratorBase.java b/org.lflang/src/org/lflang/generator/GeneratorBase.java
index 0aa3d3b98d..562b0aa308 100644
--- a/org.lflang/src/org/lflang/generator/GeneratorBase.java
+++ b/org.lflang/src/org/lflang/generator/GeneratorBase.java
@@ -671,7 +671,7 @@ protected void transformStartupTriggersInModalReactors() {
                     var timer = EcoreUtil.copy(baseTimer);
                     timer.setName("_lf_startup_timer_for_mode_"+mode.getName());
 
-                    // Replace startup triggers
+                    // Replace startup triggers with the timer
                     boolean foundAtLeastOneStartupTriggerInMode = false;
                     for (Reaction reaction : mode.getReactions()) {
                         var hadStartupTrigger = reaction.getTriggers()
diff --git a/test/C/src/modal_models/ModalStartup.lf b/test/C/src/modal_models/ModalStartup.lf
index 5d772edb5b..b4324a47cd 100644
--- a/test/C/src/modal_models/ModalStartup.lf
+++ b/test/C/src/modal_models/ModalStartup.lf
@@ -4,7 +4,7 @@
  */
 target C {
     fast: false,
-    timeout: 4 sec
+    timeout: 4100 msec
 };
 
 import TraceTesting from "util/TraceTesting.lf"
@@ -13,13 +13,14 @@ reactor Modal {
     input next:bool
     
     output mode_switch:int
-    output timer1:int
-    output timer2:int
+    output startup1:int
+    output startup2:int
+    output startup3:int
     
     initial mode One {
-        reaction(startup) -> timer1 {=
-            printf("T1\n");
-            SET(timer1, 1);
+        reaction(startup) -> startup1 {=
+            printf("Startup 1 at (%ld, %u).\n", get_elapsed_logical_time(), get_microstep());
+            SET(startup1, 1);
         =}
         
         reaction(next) -> reset(Two), mode_switch {=
@@ -29,9 +30,22 @@ reactor Modal {
         =}
     }
     mode Two {        
-        reaction(startup) -> timer2 {=
-            printf("T2\n");
-            SET(timer2, 1);
+        reaction(startup) -> startup2 {=
+            printf("Startup 2 at (%ld, %u).\n", get_elapsed_logical_time(), get_microstep());
+            SET(startup2, 1);
+        =}
+        
+        reaction(next) -> continue(Three), mode_switch {=
+            printf("Transitioning to mode Three (continue)\n");
+            SET(mode_switch, 1);
+            SET_MODE(Three);
+        =}
+    }
+
+    mode Three {        
+        reaction(startup) -> startup3 {=
+            printf("Startup 3 at (%ld, %u).\n", get_elapsed_logical_time(), get_microstep());
+            SET(startup3, 1);
         =}
         
         reaction(next) -> continue(One), mode_switch {=
@@ -47,21 +61,23 @@ main reactor {
     
     modal = new Modal()
     test = new TraceTesting(
-        events_size = 3,
-        trace_size = 77, 
+        events_size = 4,
+        trace_size = 72, 
         trace = (
             0,0,0,1,1,0,0,
-            750000000,0,0,1,1,0,0,
-            250000000,1,1,0,1,0,0,
-            0,0,1,0,1,1,1,
-            750000000,0,1,0,1,1,1,
-            250000000,1,1,0,1,0,1,
-            500000000,0,1,1,1,0,1,
-            500000000,1,1,0,1,0,1,
-            0,0,1,0,1,1,1,
-            750000000,0,1,0,1,1,1,
-            250000000,1,1,0,1,0,1
-        ), training = true)
+            0,0,1000000000,
+            1,1,0,1,0,0,0,
+            0,0,0,1,0,1,1,
+            1,0,0,1000000000,
+            1,1,0,1,0,1,0,0,
+            0,0,1,0,1,0,1,1,1,
+            1000000000,1,1,0,
+            1,0,1,0,1,
+            1000000000,1,1,0,1,
+            0,1,0,1,0,0,1,0,1,
+            1,1,0,1), 
+        training = false
+    )
 
     // Trigger mode change
     reaction(stepper) -> modal.next {=
@@ -69,7 +85,8 @@ main reactor {
     =}
     
     modal.mode_switch,
-    modal.timer1,
-    modal.timer2
+    modal.startup1,
+    modal.startup2,
+    modal.startup3
     -> test.events
 }

From 3bf7a1d1a2526b48a0e2bc9008458ff0dcc6685e Mon Sep 17 00:00:00 2001
From: Soroush Bateni <soroosh129@gmail.com>
Date: Sat, 12 Mar 2022 17:04:58 -0600
Subject: [PATCH 29/36] Ported the startup test to Python

---
 test/Python/src/modal_models/ModalStartup.lf | 91 ++++++++++++++++++++
 1 file changed, 91 insertions(+)
 create mode 100644 test/Python/src/modal_models/ModalStartup.lf

diff --git a/test/Python/src/modal_models/ModalStartup.lf b/test/Python/src/modal_models/ModalStartup.lf
new file mode 100644
index 0000000000..ff33f9fbcb
--- /dev/null
+++ b/test/Python/src/modal_models/ModalStartup.lf
@@ -0,0 +1,91 @@
+/*
+ * Modal Reactor Test.
+ * Test startup reactions in modes.
+ */
+target Python {
+    fast: false,
+    timeout: 4100 msec
+};
+
+import TraceTesting from "util/TraceTesting.lf"
+
+reactor Modal {
+    input next
+    
+    output mode_switch
+    output startup1
+    output startup2
+    output startup3
+    
+    initial mode One {
+        reaction(startup) -> startup1 {=
+            print(f"Startup 1 at ({get_elapsed_logical_time()}, {get_microstep()}).")
+            startup1.set(1)
+        =}
+        
+        reaction(next) -> reset(Two), mode_switch {=
+            print("Transitioning to mode Two (reset)")
+            mode_switch.set(1)
+            Two.set()
+        =}
+    }
+    mode Two {        
+        reaction(startup) -> startup2 {=
+            print(f"Startup 2 at at ({get_elapsed_logical_time()}, {get_microstep()}).")
+            startup2.set(1)
+        =}
+        
+        reaction(next) -> continue(Three), mode_switch {=
+            print("Transitioning to mode Three (continue)")
+            mode_switch.set(1)
+            Three.set()
+        =}
+    }
+
+    mode Three {        
+        reaction(startup) -> startup3 {=
+            print(f"Startup 3 at at ({get_elapsed_logical_time()}, {get_microstep()}).")
+            startup3.set(1)
+        =}
+        
+        reaction(next) -> continue(One), mode_switch {=
+            print("Transitioning to mode One (continue)")
+            mode_switch.set(1)
+            One.set()
+        =}
+    }
+}
+
+main reactor {
+    timer stepper(1sec, 1sec)
+    
+    modal = new Modal()
+    test = new TraceTesting(
+        events_size = 4,
+        trace = (
+            0,0,0,1,1,0,0,
+            0,0,1000000000,
+            1,1,0,1,0,0,0,
+            0,0,0,1,0,1,1,
+            1,0,0,1000000000,
+            1,1,0,1,0,1,0,0,
+            0,0,1,0,1,0,1,1,1,
+            1000000000,1,1,0,
+            1,0,1,0,1,
+            1000000000,1,1,0,1,
+            0,1,0,1,0,0,1,0,1,
+            1,1,0,1), 
+        training = False
+    )
+
+    // Trigger mode change
+    reaction(stepper) -> modal.next {=
+        modal.next.set(True)
+    =}
+    
+    modal.mode_switch,
+    modal.startup1,
+    modal.startup2,
+    modal.startup3
+    -> test.events
+}

From 7a890b0742f3482aaa344e95bf6952f0cb329693 Mon Sep 17 00:00:00 2001
From: Soroush Bateni <soroosh129@gmail.com>
Date: Sat, 12 Mar 2022 19:54:04 -0600
Subject: [PATCH 30/36] Revert seemingly faulty strategy of replacing startup
 triggers with timers

---
 .../org/lflang/generator/GeneratorBase.java   | 55 +++----------------
 1 file changed, 9 insertions(+), 46 deletions(-)

diff --git a/org.lflang/src/org/lflang/generator/GeneratorBase.java b/org.lflang/src/org/lflang/generator/GeneratorBase.java
index 562b0aa308..64538cd901 100644
--- a/org.lflang/src/org/lflang/generator/GeneratorBase.java
+++ b/org.lflang/src/org/lflang/generator/GeneratorBase.java
@@ -381,7 +381,7 @@ public void doGenerate(Resource resource, LFGeneratorContext context) {
         // Check for existence and support of modes
         hasModalReactors = IterableExtensions.exists(reactors, it -> !it.getModes().isEmpty());
         checkModalReactorSupport(false);
-        transformStartupTriggersInModalReactors();
+        generateStartupReactionsInModesIfNeeded();
         
         enableSupportForSerializationIfApplicable(context.getCancelIndicator());
     }
@@ -646,52 +646,15 @@ protected String getConflictingConnectionsInModalReactorsBody(String source, Str
     }
     
     /**
-     * Transform the startup trigger in modes to a timer with an offset and a period of zero.
+     * Generate startup reactions in modes.
      * 
-     * This allows reactions in modes with startup in their trigger to be triggered when the mode
-     * is entered for the first time or via a reset transition.
-     */
-    protected void transformStartupTriggersInModalReactors() {
-        // Construct a timer with an offset and a period of zero
-        var zeroTime = LfFactory.eINSTANCE.createTime();
-        zeroTime.setInterval(0);
-        zeroTime.setUnit("msec");
-        var zeroValue = LfFactory.eINSTANCE.createValue();
-        zeroValue.setTime(zeroTime);
-        var baseTimer = LfFactory.eINSTANCE.createTimer();
-        baseTimer.setOffset(zeroValue);
-        baseTimer.setPeriod(zeroValue);
-        
-        // Look for reactors with modes
-        for (Reactor reactor : reactors) {
-            var reactorModes = reactor.getModes();
-            if (!reactorModes.isEmpty()) {
-                for (Mode mode : reactorModes) {
-                    // Create the timer with an offset and period of zero
-                    var timer = EcoreUtil.copy(baseTimer);
-                    timer.setName("_lf_startup_timer_for_mode_"+mode.getName());
-
-                    // Replace startup triggers with the timer
-                    boolean foundAtLeastOneStartupTriggerInMode = false;
-                    for (Reaction reaction : mode.getReactions()) {
-                        var hadStartupTrigger = reaction.getTriggers()
-                                .removeIf(trigger -> trigger.isStartup());
-                        if (hadStartupTrigger) {
-                            var timerRef = LfFactory.eINSTANCE.createVarRef();
-                            timerRef.setVariable(timer);
-                            reaction.getTriggers().add(timerRef);
-
-                            foundAtLeastOneStartupTriggerInMode = true;
-                        }
-                    }
-
-                    if (foundAtLeastOneStartupTriggerInMode) {
-                        // Add the timer to the mode
-                        mode.getTimers().add(timer);
-                    }
-                }
-            }
-        }
+     * Startup reactions (reactions that have startup in their list of triggers)
+     * will be triggered when the mode is entered for the first time and on each subsequent
+     * reset transition to that mode. These reactions could be useful for targets
+     * to perform cleanups, for example, to reset state variables.
+     */
+    protected void generateStartupReactionsInModesIfNeeded() {
+        // Do nothing
     }
 
     /**

From b2fc05c88584153c1008cab16cba979622dfba82 Mon Sep 17 00:00:00 2001
From: Soroush Bateni <soroosh129@gmail.com>
Date: Sat, 12 Mar 2022 19:55:24 -0600
Subject: [PATCH 31/36] Added AST transformation for Python that adds startup
 reactions to all reactors and their modes to reset state variables

---
 org.lflang/src/lib/c/reactor-c                |  2 +-
 .../generator/python/PythonGenerator.java     |  8 ++
 .../generator/python/PythonModeGenerator.java | 93 +++++++++++++++++++
 .../python/PythonStateGenerator.java          |  2 +-
 4 files changed, 103 insertions(+), 2 deletions(-)
 create mode 100644 org.lflang/src/org/lflang/generator/python/PythonModeGenerator.java

diff --git a/org.lflang/src/lib/c/reactor-c b/org.lflang/src/lib/c/reactor-c
index e0e3451f50..522854333e 160000
--- a/org.lflang/src/lib/c/reactor-c
+++ b/org.lflang/src/lib/c/reactor-c
@@ -1 +1 @@
-Subproject commit e0e3451f5068cabce0cd185e44ea65fdbed05c8e
+Subproject commit 522854333e6461aeaa8322149730760e553a0381
diff --git a/org.lflang/src/org/lflang/generator/python/PythonGenerator.java b/org.lflang/src/org/lflang/generator/python/PythonGenerator.java
index 64b89741a2..4777069c7d 100644
--- a/org.lflang/src/org/lflang/generator/python/PythonGenerator.java
+++ b/org.lflang/src/org/lflang/generator/python/PythonGenerator.java
@@ -887,6 +887,14 @@ protected void setUpParameters(LFGeneratorContext context) {
             targetConfig.compileAdditionalSources.add("modal_models/impl.c");
         }
     }
+    
+    @Override
+    protected void generateStartupReactionsInModesIfNeeded() {
+        if (!hasModalReactors) {
+            return;
+        }
+        PythonModeGenerator.generateStartupReactionsInModesIfNeeded(reactors);
+    }
 
     private static String generateMacroEntry(String key, String val) {
         return "(" + StringUtil.addDoubleQuotes(key) + ", " + StringUtil.addDoubleQuotes(val) + ")";
diff --git a/org.lflang/src/org/lflang/generator/python/PythonModeGenerator.java b/org.lflang/src/org/lflang/generator/python/PythonModeGenerator.java
new file mode 100644
index 0000000000..35491de90b
--- /dev/null
+++ b/org.lflang/src/org/lflang/generator/python/PythonModeGenerator.java
@@ -0,0 +1,93 @@
+package org.lflang.generator.python;
+
+import java.util.List;
+
+import org.eclipse.emf.ecore.util.EcoreUtil;
+import org.lflang.generator.CodeBuilder;
+import org.lflang.lf.LfFactory;
+import org.lflang.lf.Mode;
+import org.lflang.lf.Reaction;
+import org.lflang.lf.Reactor;
+import org.lflang.lf.TriggerRef;
+
+/**
+ * Helper class to handle modes in Python programs.
+ * 
+ * @author{Soroush Bateni <soroush@utdallas.edu>}
+ *
+ */
+public class PythonModeGenerator {
+    /**
+     * Generate startup reactions in modes.
+     * 
+     * Startup reactions (reactions that have startup in their list of triggers)
+     * will be triggered when the mode is entered for the first time and on each subsequent
+     * reset transition to that mode. These reactions could be useful for targets
+     * to perform cleanups, for example, to reset state variables.
+     * 
+     * @param reactors A list of reactors in the program, some of which could contain modes.
+     */
+    public static void generateStartupReactionsInModesIfNeeded(List<Reactor> reactors) {
+        for (Reactor reactor : reactors) {
+            generateStartupReactionsInReactor(reactor);
+        }
+    }
+    
+    /**
+     * Generate startup reactions that reset state variables in 
+     * - the reactor, and,
+     * - the modes within the reactor.
+     * 
+     * @param reactor The reactor.
+     */
+    private static void generateStartupReactionsInReactor(Reactor reactor) {
+        
+        // Create a reaction with a startup trigger
+        TriggerRef startupTrigger = LfFactory.eINSTANCE.createTriggerRef();
+        startupTrigger.setStartup(true);
+        Reaction baseReaction = LfFactory.eINSTANCE.createReaction();
+        baseReaction.getTriggers().add(startupTrigger);
+        
+        // Create a reaction body that resets all state variables to their initial value.
+        var reactionBody = LfFactory.eINSTANCE.createCode();
+        CodeBuilder code = new CodeBuilder();
+        for (var state: reactor.getStateVars()) {
+            code.pr("self."+state.getName()+" = "+PythonStateGenerator.generatePythonInitializer(state));
+        }
+        reactionBody.setBody(code.toString());
+        baseReaction.setCode(reactionBody);
+        
+        reactor.getReactions().add(0, baseReaction);
+            
+        
+        var reactorModes = reactor.getModes();
+        if (!reactorModes.isEmpty()) {
+            for (Mode mode : reactorModes) {
+                if (mode.getStateVars().isEmpty()) {
+                    continue;
+                }
+                Reaction reaction = EcoreUtil.copy(baseReaction);
+                
+                // Create a reaction body that resets all state variables to their initial value.
+                reactionBody = LfFactory.eINSTANCE.createCode();
+                code = new CodeBuilder();
+                for (var state: mode.getStateVars()) {
+                    code.pr("self."+state.getName()+" = "+PythonStateGenerator.generatePythonInitializer(state));
+                }
+                reactionBody.setBody(code.toString());
+                reaction.setCode(reactionBody);
+                
+                try {
+                    mode.getReactions().add(0, reaction);
+                } catch (IndexOutOfBoundsException e) {
+                    // There are no scoping for state variables.
+                    // We add this reaction for now so that it
+                    // still resets state variables even if there
+                    // are no reactions in this mode.
+                    mode.getReactions().add(reaction);
+                }
+                
+            }
+        }
+    }
+}
diff --git a/org.lflang/src/org/lflang/generator/python/PythonStateGenerator.java b/org.lflang/src/org/lflang/generator/python/PythonStateGenerator.java
index 7441f53225..78745d24d5 100644
--- a/org.lflang/src/org/lflang/generator/python/PythonStateGenerator.java
+++ b/org.lflang/src/org/lflang/generator/python/PythonStateGenerator.java
@@ -31,7 +31,7 @@ public static String generatePythonInstantiations(ReactorDecl decl) {
      * Handle initialization for state variable
      * @param state a state variable
      */
-    private static String generatePythonInitializer(StateVar state) {
+    public static String generatePythonInitializer(StateVar state) {
         if (!ASTUtils.isInitialized(state)) {
             return "None";
         }

From 76db8db5f367261131cacc7d2506e996665ec9d3 Mon Sep 17 00:00:00 2001
From: Soroush Bateni <soroosh129@gmail.com>
Date: Sat, 12 Mar 2022 20:01:00 -0600
Subject: [PATCH 32/36] Only generate startup reactions if there are state vars

---
 .../generator/python/PythonModeGenerator.java | 26 +++++++++++--------
 1 file changed, 15 insertions(+), 11 deletions(-)

diff --git a/org.lflang/src/org/lflang/generator/python/PythonModeGenerator.java b/org.lflang/src/org/lflang/generator/python/PythonModeGenerator.java
index 35491de90b..eeca3d59c5 100644
--- a/org.lflang/src/org/lflang/generator/python/PythonModeGenerator.java
+++ b/org.lflang/src/org/lflang/generator/python/PythonModeGenerator.java
@@ -48,16 +48,19 @@ private static void generateStartupReactionsInReactor(Reactor reactor) {
         Reaction baseReaction = LfFactory.eINSTANCE.createReaction();
         baseReaction.getTriggers().add(startupTrigger);
         
-        // Create a reaction body that resets all state variables to their initial value.
-        var reactionBody = LfFactory.eINSTANCE.createCode();
-        CodeBuilder code = new CodeBuilder();
-        for (var state: reactor.getStateVars()) {
-            code.pr("self."+state.getName()+" = "+PythonStateGenerator.generatePythonInitializer(state));
+        if (!reactor.getStateVars().isEmpty()) {
+            // Create a reaction body that resets all state variables to their initial value.
+            var reactionBody = LfFactory.eINSTANCE.createCode();
+            CodeBuilder code = new CodeBuilder();
+            code.pr("# Reset the following state variables to their initial value.");
+            for (var state: reactor.getStateVars()) {
+                code.pr("self."+state.getName()+" = "+PythonStateGenerator.generatePythonInitializer(state));
+            }
+            reactionBody.setBody(code.toString());
+            baseReaction.setCode(reactionBody);
+            
+            reactor.getReactions().add(0, baseReaction);
         }
-        reactionBody.setBody(code.toString());
-        baseReaction.setCode(reactionBody);
-        
-        reactor.getReactions().add(0, baseReaction);
             
         
         var reactorModes = reactor.getModes();
@@ -69,8 +72,9 @@ private static void generateStartupReactionsInReactor(Reactor reactor) {
                 Reaction reaction = EcoreUtil.copy(baseReaction);
                 
                 // Create a reaction body that resets all state variables to their initial value.
-                reactionBody = LfFactory.eINSTANCE.createCode();
-                code = new CodeBuilder();
+                var reactionBody = LfFactory.eINSTANCE.createCode();
+                CodeBuilder code = new CodeBuilder();
+                code.pr("# Reset the following state variables to their initial value.");
                 for (var state: mode.getStateVars()) {
                     code.pr("self."+state.getName()+" = "+PythonStateGenerator.generatePythonInitializer(state));
                 }

From aad8f5fd7e6ab06af892347c131edfb525c64513 Mon Sep 17 00:00:00 2001
From: Soroush Bateni <soroosh129@gmail.com>
Date: Mon, 14 Mar 2022 02:07:42 -0500
Subject: [PATCH 33/36] First working prototype for startup reactions (only for
 reset transitions)

---
 org.lflang/src/lib/c/reactor-c                |  2 +-
 .../org/lflang/generator/c/CGenerator.xtend   | 22 +++++--------------
 .../generator/python/PythonModeGenerator.java |  3 ++-
 test/C/src/modal_models/ModalStartup.lf       | 20 ++++++++---------
 4 files changed, 18 insertions(+), 29 deletions(-)

diff --git a/org.lflang/src/lib/c/reactor-c b/org.lflang/src/lib/c/reactor-c
index 522854333e..9ea25d0d90 160000
--- a/org.lflang/src/lib/c/reactor-c
+++ b/org.lflang/src/lib/c/reactor-c
@@ -1 +1 @@
-Subproject commit 522854333e6461aeaa8322149730760e553a0381
+Subproject commit 9ea25d0d909251ebe3200b2cfd346a4ec13a2381
diff --git a/org.lflang/src/org/lflang/generator/c/CGenerator.xtend b/org.lflang/src/org/lflang/generator/c/CGenerator.xtend
index 032829c753..5aa71440c0 100644
--- a/org.lflang/src/org/lflang/generator/c/CGenerator.xtend
+++ b/org.lflang/src/org/lflang/generator/c/CGenerator.xtend
@@ -596,22 +596,7 @@ class CGenerator extends GeneratorBase {
                         int _lf_timer_triggers_size = 0;
                     ''')
                 }
-                
-                // If there are startup reactions, store them in an array.
-                if (startupReactionCount > 0) {
-                    code.pr('''
-                        // Array of pointers to reactions to be scheduled in _lf_trigger_startup_reactions().
-                        reaction_t* _lf_startup_reactions[«startupReactionCount»];
-                        int _lf_startup_reactions_size = «startupReactionCount»;
-                    ''')
-                } else {
-                    code.pr('''
-                        // Array of pointers to reactions to be scheduled in _lf_trigger_startup_reactions().
-                        reaction_t** _lf_startup_reactions = NULL;
-                        int _lf_startup_reactions_size = 0;
-                    ''')
-                }
-                
+                                
                 // If there are shutdown reactions, create a table of triggers.
                 if (shutdownReactionCount > 0) {
                     code.pr('''
@@ -1010,6 +995,11 @@ class CGenerator extends GeneratorBase {
                 _lf_is_present_fields_abbreviated_size = 0;
             ''')
         }
+        
+        code.pr('''
+             _lf_startup_reactions = (reaction_t**)calloc(«startupReactionCount», sizeof(reaction_t*));
+             _lf_startup_reactions_size = «startupReactionCount»;
+        ''')
 
         // Allocate the memory for triggers used in federated execution
         code.pr(CGeneratorExtension.allocateTriggersForFederate(federate, this, startTimeStepIsPresentCount));
diff --git a/org.lflang/src/org/lflang/generator/python/PythonModeGenerator.java b/org.lflang/src/org/lflang/generator/python/PythonModeGenerator.java
index eeca3d59c5..dc465c357b 100644
--- a/org.lflang/src/org/lflang/generator/python/PythonModeGenerator.java
+++ b/org.lflang/src/org/lflang/generator/python/PythonModeGenerator.java
@@ -49,7 +49,8 @@ private static void generateStartupReactionsInReactor(Reactor reactor) {
         baseReaction.getTriggers().add(startupTrigger);
         
         if (!reactor.getStateVars().isEmpty()) {
-            // Create a reaction body that resets all state variables to their initial value.
+            // Create a reaction body that resets all state variables (that are not in a mode)
+            // to their initial value.
             var reactionBody = LfFactory.eINSTANCE.createCode();
             CodeBuilder code = new CodeBuilder();
             code.pr("# Reset the following state variables to their initial value.");
diff --git a/test/C/src/modal_models/ModalStartup.lf b/test/C/src/modal_models/ModalStartup.lf
index b4324a47cd..5244f16b01 100644
--- a/test/C/src/modal_models/ModalStartup.lf
+++ b/test/C/src/modal_models/ModalStartup.lf
@@ -64,18 +64,16 @@ main reactor {
         events_size = 4,
         trace_size = 72, 
         trace = (
-            0,0,0,1,1,0,0,
-            0,0,1000000000,
-            1,1,0,1,0,0,0,
-            0,0,0,1,0,1,1,
-            1,0,0,1000000000,
-            1,1,0,1,0,1,0,0,
-            0,0,1,0,1,0,1,1,1,
-            1000000000,1,1,0,
-            1,0,1,0,1,
+            0,0,0,1,1,0,0,0,0,
             1000000000,1,1,0,1,
-            0,1,0,1,0,0,1,0,1,
-            1,1,0,1), 
+            0,0,0,0,0,0,1,0,1,1,
+            1,0,0,1000000000,1,
+            1,0,1,0,1,0,0,
+            1000000000,1,1,0,1,0,
+            1,0,0,1000000000,1,1,
+            0,1,0,1,0,0,0,0,1,0,
+            1,1,1,0,0
+        ), 
         training = false
     )
 

From 348692fe05ef1abf612b61b99862ac29dde7257d Mon Sep 17 00:00:00 2001
From: Soroush Bateni <soroosh129@gmail.com>
Date: Mon, 14 Mar 2022 02:21:15 -0500
Subject: [PATCH 34/36] Updated test and reactor-c

---
 org.lflang/src/lib/c/reactor-c                |  2 +-
 test/Python/src/modal_models/ModalStartup.lf  | 21 ++++++++-----------
 .../MultipleOutputFeeder_2Connections.lf      |  2 +-
 3 files changed, 11 insertions(+), 14 deletions(-)

diff --git a/org.lflang/src/lib/c/reactor-c b/org.lflang/src/lib/c/reactor-c
index 9ea25d0d90..9445252028 160000
--- a/org.lflang/src/lib/c/reactor-c
+++ b/org.lflang/src/lib/c/reactor-c
@@ -1 +1 @@
-Subproject commit 9ea25d0d909251ebe3200b2cfd346a4ec13a2381
+Subproject commit 9445252028c51dd774d7075195d00766f90436b9
diff --git a/test/Python/src/modal_models/ModalStartup.lf b/test/Python/src/modal_models/ModalStartup.lf
index ff33f9fbcb..ef8e929131 100644
--- a/test/Python/src/modal_models/ModalStartup.lf
+++ b/test/Python/src/modal_models/ModalStartup.lf
@@ -63,19 +63,16 @@ main reactor {
     test = new TraceTesting(
         events_size = 4,
         trace = (
-            0,0,0,1,1,0,0,
-            0,0,1000000000,
-            1,1,0,1,0,0,0,
-            0,0,0,1,0,1,1,
-            1,0,0,1000000000,
-            1,1,0,1,0,1,0,0,
-            0,0,1,0,1,0,1,1,1,
-            1000000000,1,1,0,
-            1,0,1,0,1,
+            0,0,0,1,1,0,0,0,0,
             1000000000,1,1,0,1,
-            0,1,0,1,0,0,1,0,1,
-            1,1,0,1), 
-        training = False
+            0,0,0,0,0,0,1,0,1,1,
+            1,0,0,1000000000,1,
+            1,0,1,0,1,0,0,
+            1000000000,1,1,0,1,0,
+            1,0,0,1000000000,1,1,
+            0,1,0,1,0,0,0,0,1,0,
+            1,1,1,0,0
+        ), training = False
     )
 
     // Trigger mode change
diff --git a/test/Python/src/modal_models/MultipleOutputFeeder_2Connections.lf b/test/Python/src/modal_models/MultipleOutputFeeder_2Connections.lf
index 6a6ef990d4..ab4d032b91 100644
--- a/test/Python/src/modal_models/MultipleOutputFeeder_2Connections.lf
+++ b/test/Python/src/modal_models/MultipleOutputFeeder_2Connections.lf
@@ -82,4 +82,4 @@ main reactor {
     
     modal.count
     -> test.events
-}
\ No newline at end of file
+}

From 2e46b407feb5579553179db517d36dc6c05c1282 Mon Sep 17 00:00:00 2001
From: Soroush Bateni <soroosh129@gmail.com>
Date: Mon, 14 Mar 2022 02:21:52 -0500
Subject: [PATCH 35/36] Updated test and reactor-c

---
 org.lflang/src/lib/c/reactor-c | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/org.lflang/src/lib/c/reactor-c b/org.lflang/src/lib/c/reactor-c
index 9445252028..e61d28d7d6 160000
--- a/org.lflang/src/lib/c/reactor-c
+++ b/org.lflang/src/lib/c/reactor-c
@@ -1 +1 @@
-Subproject commit 9445252028c51dd774d7075195d00766f90436b9
+Subproject commit e61d28d7d68c682cefc740f012db8aaeb17e2914

From db6bb6760752f637e3840409b5756b353513e2bb Mon Sep 17 00:00:00 2001
From: Soroush Bateni <soroosh129@gmail.com>
Date: Mon, 14 Mar 2022 02:49:17 -0500
Subject: [PATCH 36/36] Also handle startup reactions for history transitions

---
 org.lflang/src/lib/c/reactor-c                         | 2 +-
 org.lflang/src/org/lflang/generator/c/CGenerator.xtend | 8 ++++++++
 test/C/src/modal_models/ModalStartup.lf                | 8 ++++----
 test/Python/src/modal_models/ModalStartup.lf           | 8 ++++----
 4 files changed, 17 insertions(+), 9 deletions(-)

diff --git a/org.lflang/src/lib/c/reactor-c b/org.lflang/src/lib/c/reactor-c
index e61d28d7d6..b20c870cb1 160000
--- a/org.lflang/src/lib/c/reactor-c
+++ b/org.lflang/src/lib/c/reactor-c
@@ -1 +1 @@
-Subproject commit e61d28d7d68c682cefc740f012db8aaeb17e2914
+Subproject commit b20c870cb1f0f11a918348162dc884fbd01b56d9
diff --git a/org.lflang/src/org/lflang/generator/c/CGenerator.xtend b/org.lflang/src/org/lflang/generator/c/CGenerator.xtend
index 5aa71440c0..c377e0b882 100644
--- a/org.lflang/src/org/lflang/generator/c/CGenerator.xtend
+++ b/org.lflang/src/org/lflang/generator/c/CGenerator.xtend
@@ -934,6 +934,14 @@ class CGenerator extends GeneratorBase {
                 «IF startupReactionCount > 0»
                 for (int i = 0; i < _lf_startup_reactions_size; i++) {
                     if (_lf_startup_reactions[i] != NULL) {
+                        #ifdef MODAL_REACTORS
+                        if (!_lf_mode_is_active(_lf_startup_reactions[i]->mode)) {
+                            // Mode is not active. Remember to trigger startup when the mode
+                            // becomes active.
+                            _lf_startup_reactions[i]->mode->should_trigger_startup = true;
+                            continue;
+                        }
+                        #endif
                         _lf_trigger_reaction(_lf_startup_reactions[i], -1);
                     }
                 }
diff --git a/test/C/src/modal_models/ModalStartup.lf b/test/C/src/modal_models/ModalStartup.lf
index 5244f16b01..4ff25a2ab8 100644
--- a/test/C/src/modal_models/ModalStartup.lf
+++ b/test/C/src/modal_models/ModalStartup.lf
@@ -68,11 +68,11 @@ main reactor {
             1000000000,1,1,0,1,
             0,0,0,0,0,0,1,0,1,1,
             1,0,0,1000000000,1,
-            1,0,1,0,1,0,0,
+            1,0,1,0,1,0,0,0,0,1,
+            0,1,0,1,1,1,1000000000,
+            1,1,0,1,0,1,0,1,
             1000000000,1,1,0,1,0,
-            1,0,0,1000000000,1,1,
-            0,1,0,1,0,0,0,0,1,0,
-            1,1,1,0,0
+            1,0,1,0,0,1,0,1,1,1,0,1
         ), 
         training = false
     )
diff --git a/test/Python/src/modal_models/ModalStartup.lf b/test/Python/src/modal_models/ModalStartup.lf
index ef8e929131..a5a42240b6 100644
--- a/test/Python/src/modal_models/ModalStartup.lf
+++ b/test/Python/src/modal_models/ModalStartup.lf
@@ -67,11 +67,11 @@ main reactor {
             1000000000,1,1,0,1,
             0,0,0,0,0,0,1,0,1,1,
             1,0,0,1000000000,1,
-            1,0,1,0,1,0,0,
+            1,0,1,0,1,0,0,0,0,1,
+            0,1,0,1,1,1,1000000000,
+            1,1,0,1,0,1,0,1,
             1000000000,1,1,0,1,0,
-            1,0,0,1000000000,1,1,
-            0,1,0,1,0,0,0,0,1,0,
-            1,1,1,0,0
+            1,0,1,0,0,1,0,1,1,1,0,1
         ), training = False
     )