Add javadocs and remove unused imports

contrib/src/main/java/gov/nasa/jpl/aerie/contrib/streamline/core/CellRefV2.java

@@ -1,7 +1,6 @@
 package gov.nasa.jpl.aerie.contrib.streamline.core;
 
 import gov.nasa.jpl.aerie.contrib.streamline.core.monads.ErrorCatchingMonad;
-import gov.nasa.jpl.aerie.contrib.streamline.debugging.Naming;
 import gov.nasa.jpl.aerie.merlin.framework.CellRef;
 import gov.nasa.jpl.aerie.merlin.protocol.model.CellType;
 import gov.nasa.jpl.aerie.merlin.protocol.model.EffectTrait;
@@ -15,6 +14,9 @@
 import static gov.nasa.jpl.aerie.contrib.streamline.debugging.Naming.*;
 import static gov.nasa.jpl.aerie.merlin.protocol.types.Duration.ZERO;
 
+/**
+ * Utility class for a simplified allocate method.
+ */
 public final class CellRefV2 {
   private CellRefV2() {}
 
@@ -89,6 +91,9 @@ public static <D extends Dynamics<?, D>> EffectTrait<DynamicsEffect<D>> autoEffe
    * correctly comparing expiry and error information in the process.
    */
   public static <D> Predicate<CommutativityTestInput<ErrorCatching<Expiring<D>>>> testing(Predicate<CommutativityTestInput<D>> test) {
+    // If both expiring, compare expiry and data
+    // If both error, compare error contents
+    // If one is expiring and the other is error, return false
     return input -> input.leftResult.match(
         leftExpiring -> input.rightResult.match(
             rightExpiring -> leftExpiring.expiry().equals(rightExpiring.expiry()) && test.test(new CommutativityTestInput<>(

contrib/src/main/java/gov/nasa/jpl/aerie/contrib/streamline/core/Dynamics.java

@@ -14,6 +14,8 @@ public interface Dynamics<V, D extends Dynamics<V, D>> {
 
     /**
      * Evolve for the given time.
+     *
+     * @apiNote This method should always return the same value when called on the same object with the same duration
      */
     D step(Duration t);
 }

contrib/src/main/java/gov/nasa/jpl/aerie/contrib/streamline/core/Reactions.java

@@ -3,7 +3,6 @@
 import gov.nasa.jpl.aerie.contrib.streamline.modeling.discrete.Discrete;
 import gov.nasa.jpl.aerie.merlin.framework.Condition;
 import gov.nasa.jpl.aerie.merlin.protocol.types.Duration;
-import org.apache.commons.lang3.mutable.MutableObject;
 
 import java.util.function.Consumer;
 import java.util.function.Supplier;

contrib/src/main/java/gov/nasa/jpl/aerie/contrib/streamline/modeling/Registrar.java

@@ -70,6 +70,9 @@ public Registrar(final gov.nasa.jpl.aerie.merlin.framework.Registrar baseRegistr
     this.errorBehavior = errorBehavior;
     errors = resource(Discrete.discrete(Map.of()));
     var errorString = map(errors, errors$ -> errors$.entrySet().stream().map(entry -> formatError(entry.getKey(), entry.getValue())).collect(joining("\n\n")));
+
+    // Register the errors and number of errors resources for output
+    // TODO consider using serializable events, rather than resources, to log errors
     discrete("errors", errorString, new StringValueMapper());
     discrete("numberOfErrors", map(errors, Map::size), new IntegerValueMapper());
   }
@@ -99,7 +102,7 @@ public void setProfile() {
   }
 
   public void clearProfile() {
-    profile = true;
+    profile = false;
   }
 
   public <Value> void discrete(final String name, final Resource<Discrete<Value>> resource, final ValueMapper<Value> mapper) {
@@ -145,7 +148,7 @@ private <D extends Dynamics<?, D>> void logErrors(String name, Resource<D> resou
     });
   }
 
-  // TODO: Consider pulling in a Guava MultiMap instead of doing this by hand below
+  // TODO: Consider using a MultiMap instead of doing this by hand below
   private Unit logError(String resourceName, Throwable e) {
     errors.emit(effect(s -> {
       var s$ = new HashMap<>(s);
@@ -163,6 +166,9 @@ private Unit logError(String resourceName, Throwable e) {
     return Unit.UNIT;
   }
 
+  /**
+   * Include the resource name in the error to give context
+   */
   private static <D> gov.nasa.jpl.aerie.merlin.framework.Resource<D> wrapErrors(String resourceName, gov.nasa.jpl.aerie.merlin.framework.Resource<D> resource) {
     return () -> {
       try {

contrib/src/main/java/gov/nasa/jpl/aerie/contrib/streamline/modeling/black_box/UnstructuredResources.java

@@ -1,7 +1,6 @@
 package gov.nasa.jpl.aerie.contrib.streamline.modeling.black_box;
 
 import gov.nasa.jpl.aerie.contrib.streamline.core.Dynamics;
-import gov.nasa.jpl.aerie.contrib.streamline.core.MutableResource;
 import gov.nasa.jpl.aerie.contrib.streamline.core.Resource;
 import gov.nasa.jpl.aerie.contrib.streamline.modeling.black_box.SecantApproximation.ErrorEstimates;
 import gov.nasa.jpl.aerie.contrib.streamline.modeling.black_box.monads.UnstructuredResourceApplicative;
@@ -32,7 +31,7 @@ public static <A> Resource<Unstructured<A>> timeBased(Function<Duration, A> f) {
     // Put this in a cell so it'll be stepped up appropriately
     return resource(Unstructured.timeBased(f));
   }
-  
+
   public static <A, D extends Dynamics<A, D>> Resource<Unstructured<A>> asUnstructured(Resource<D> resource) {
     return map(resource, Unstructured::unstructured);
   }

contrib/src/main/java/gov/nasa/jpl/aerie/contrib/streamline/modeling/polynomial/Polynomial.java

@@ -25,9 +25,20 @@
 import static gov.nasa.jpl.aerie.merlin.protocol.types.Duration.ZERO;
 import static org.apache.commons.math3.analysis.polynomials.PolynomialsUtils.shift;
 
+/**
+ * An implementation of Polynomial Dynamics
+ * @param coefficients an array of polynomial coefficients, where an entry's index in the array corresponds to the degree of that coefficient
+ *
+ * @apiNote The units of `t` are seconds
+ */
 public record Polynomial(double[] coefficients) implements Dynamics<Double, Polynomial> {
 
   // TODO: Add Duration parameter for unit of formal parameter?
+  /**
+   *
+   * @param coefficients the polynomial coefficients, from least to most significant
+   * @return a Polynomial with the given coefficients
+   */
   public static Polynomial polynomial(double... coefficients) {
     int n = coefficients.length;
     if (n == 0) {

examples/streamline-demo/src/main/java/gov/nasa/jpl/aerie/streamline_demo/ErrorTestingModel.java

@@ -10,7 +10,7 @@
 import gov.nasa.jpl.aerie.contrib.streamline.modeling.polynomial.Polynomial;
 import gov.nasa.jpl.aerie.contrib.streamline.modeling.polynomial.PolynomialResources;
 
-import static gov.nasa.jpl.aerie.contrib.streamline.modeling.discrete.DiscreteResources.discreteResource;
+import static gov.nasa.jpl.aerie.contrib.streamline.debugging.Naming.name;
 import static gov.nasa.jpl.aerie.contrib.streamline.modeling.discrete.monads.DiscreteResourceMonad.map;
 import static gov.nasa.jpl.aerie.contrib.streamline.modeling.polynomial.PolynomialResources.*;
 
@@ -23,7 +23,7 @@ public class ErrorTestingModel {
       asPolynomial(map(counter, c -> (double) c)),
       asPolynomial(map(bool, $ -> $ ? 1.0 : -1.0)));
 
-  public MutableResource<Polynomial> upperBound = PolynomialResources.polynomialResource(5);
+  public MutableResource<Polynomial> upperBound = name(PolynomialResources.polynomialResource(5), "upperBound");
   public MutableResource<Polynomial> lowerBound = PolynomialResources.polynomialResource(-5);
   public Resource<Polynomial> clamped = clamp(constant(10), lowerBound, upperBound);