Rename comp/lat/loc packages in core

.github/config/checks.xml

@@ -93,7 +93,7 @@
 
         <!-- Checks for imports -->
         <module name="AvoidStarImport">
-            <property name="excludes" value="arcade.core.agent.cell, arcade.core.agent.module, arcade.core.agent.helper, arcade.core.env.loc, arcade.core.env.grid, arcade.core.env.grid, arcade.core.env.lat, arcade.core.sim, arcade.core.sim.input, arcade.core.sim.output, arcade.core.vis"/>
+            <property name="excludes" value="arcade.core.agent.cell, arcade.core.agent.module, arcade.core.agent.helper, arcade.core.env.location, arcade.core.env.grid, arcade.core.env.grid, arcade.core.env.lattice, arcade.core.sim, arcade.core.sim.input, arcade.core.sim.output, arcade.core.vis"/>
             <property name="allowStaticMemberImports" value="true" />
         </module>
         <module name="IllegalImport" />

src/arcade/core/agent/action/Action.java

@@ -19,7 +19,7 @@
  * {@code Action} objects can affect {@link arcade.core.agent.cell.Cell}
  * populations or cell {@link arcade.core.agent.module.Module} or
  * {@link arcade.core.agent.process.Process} instances.
- * {@code Action} objects are analogs to {@link arcade.core.env.comp.Component}
+ * {@code Action} objects are analogs to {@link arcade.core.env.component.Component}
  * for steppables that affect agents.
  */
 

src/arcade/core/agent/cell/Cell.java

@@ -5,7 +5,7 @@
 import ec.util.MersenneTwisterFast;
 import arcade.core.agent.module.Module;
 import arcade.core.agent.process.Process;
-import arcade.core.env.loc.Location;
+import arcade.core.env.location.Location;
 import arcade.core.util.MiniBox;
 import static arcade.core.util.Enums.Domain;
 import static arcade.core.util.Enums.Region;

src/arcade/core/agent/cell/CellContainer.java

@@ -1,6 +1,6 @@
 package arcade.core.agent.cell;
 
-import arcade.core.env.loc.Location;
+import arcade.core.env.location.Location;
 
 /**
  * Container class for {@link Cell} objects.

src/arcade/core/env/comp/Component.java → src/arcade/core/env/component/Component.java

@@ -1,4 +1,4 @@
-package arcade.core.env.comp;
+package arcade.core.env.component;
 
 import sim.engine.Schedule;
 import sim.engine.Steppable;
@@ -17,7 +17,7 @@
  *     capillary beds or matrix scaffolding</li>
  * </ul>
  * <p>
- * {@code Component} objects can affect {@link arcade.core.env.lat.Lattice}
+ * {@code Component} objects can affect {@link arcade.core.env.lattice.Lattice}
  * layers or layer {@link arcade.core.env.operation.Operation} instances.
  * {@code Component} objects are analogs to
  * {@link arcade.core.agent.action.Action} for steppables that affect the

src/arcade/core/env/grid/Grid.java

@@ -1,14 +1,14 @@
 package arcade.core.env.grid;
 
 import sim.util.Bag;
-import arcade.core.env.loc.Location;
+import arcade.core.env.location.Location;
 
 /**
  * A {@code Grid} represents the environment for agents.
  * <p>
  * Calculations for geometry, bounds, size, etc. can be handled either by the
- * {@link arcade.core.env.loc.Location} object that is passed in with the agent
- * (using the {@code Grid} as a container class) or vice versa.
+ * {@link Location} object that is passed in with the agent (using the
+ * {@code Grid} as a container class) or vice versa.
  */
 
 public interface Grid {

src/arcade/core/env/lat/Lattice.java → src/arcade/core/env/lattice/Lattice.java

@@ -1,8 +1,8 @@
-package arcade.core.env.lat;
+package arcade.core.env.lattice;
 
 import sim.engine.Schedule;
 import sim.engine.Steppable;
-import arcade.core.env.loc.Location;
+import arcade.core.env.location.Location;
 import arcade.core.env.operation.Operation;
 import arcade.core.util.MiniBox;
 import static arcade.core.util.Enums.Category;

src/arcade/core/env/lat/LatticeFactory.java → src/arcade/core/env/lattice/LatticeFactory.java

@@ -1,4 +1,4 @@
-package arcade.core.env.lat;
+package arcade.core.env.lattice;
 
 import ec.util.MersenneTwisterFast;
 import arcade.core.sim.Series;

src/arcade/core/env/loc/Location.java → src/arcade/core/env/location/Location.java

@@ -1,4 +1,4 @@
-package arcade.core.env.loc;
+package arcade.core.env.location;
 
 import java.util.EnumSet;
 import static arcade.core.util.Enums.Region;
@@ -8,7 +8,7 @@
  * <p>
  * Each agent has a {@code Location} that identifies where they are within the
  * {@link arcade.core.env.grid.Grid} (relative to other agents) and the
- * {@link arcade.core.env.lat.Lattice} (local molecule concentrations).
+ * {@link arcade.core.env.lattice.Lattice} (local molecule concentrations).
  */
 
 public interface Location {

src/arcade/core/env/loc/LocationContainer.java → src/arcade/core/env/location/LocationContainer.java

@@ -1,4 +1,4 @@
-package arcade.core.env.loc;
+package arcade.core.env.location;
 
 import arcade.core.agent.cell.CellContainer;
 

src/arcade/core/env/loc/LocationFactory.java → src/arcade/core/env/location/LocationFactory.java

@@ -1,4 +1,4 @@
-package arcade.core.env.loc;
+package arcade.core.env.location;
 
 import ec.util.MersenneTwisterFast;
 import arcade.core.sim.Series;

src/arcade/core/env/operation/Operation.java

@@ -7,15 +7,15 @@
  * An {@code Operation} object is a non-exclusive environmental layer steppable.
  * <p>
  * {@code Operation} objects represent environmental behaviors or mechanisms
- * within a {@link arcade.core.env.lat.Lattice} object, such as diffusion.
+ * within a {@link arcade.core.env.lattice.Lattice} object, such as diffusion.
  * The {@code Operation} should be called during the step method of the
- * corresponding {@link arcade.core.env.lat.Lattice} object.
+ * corresponding {@link arcade.core.env.lattice.Lattice} object.
  * An {@code Operation} can be implemented with different versions; the specific
  * class can be selected when instantiating the
- * {@link arcade.core.env.lat.Lattice} object.
+ * {@link arcade.core.env.lattice.Lattice} object.
  * <p>
  * More than one {@code Operation} can be active for a given
- * {@link arcade.core.env.lat.Lattice} object.
+ * {@link arcade.core.env.lattice.Lattice} object.
  * <p>
  * {@code Operation} objects are analogs to
  * {@link arcade.core.agent.process.Process} for steppables that affect the
@@ -25,7 +25,7 @@
 public interface Operation {
     /**
      * Performs the actions of the process during the
-     * {@link arcade.core.env.lat.Lattice} step.
+     * {@link arcade.core.env.lattice.Lattice} step.
      *
      * @param random  the random number generator
      * @param sim  the simulation instance

src/arcade/core/sim/Simulation.java

@@ -6,10 +6,10 @@
 import sim.engine.Schedule;
 import arcade.core.agent.action.Action;
 import arcade.core.agent.cell.CellContainer;
-import arcade.core.env.comp.Component;
+import arcade.core.env.component.Component;
 import arcade.core.env.grid.Grid;
-import arcade.core.env.lat.Lattice;
-import arcade.core.env.loc.LocationContainer;
+import arcade.core.env.lattice.Lattice;
+import arcade.core.env.location.LocationContainer;
 
 /**
  * A {@code Simulation} sets up agents and environments for a simulation.
@@ -128,7 +128,7 @@ public interface Simulation {
     void setupEnvironment();
 
     /**
-     * Schedules any {@link arcade.core.agent.action.Action} instances.
+     * Schedules any {@link Action} instances.
      * <p>
      * The concrete implementing class calls this and other schedule methods
      * from the MASON library {@code start()} method, which is called before the
@@ -137,7 +137,7 @@ public interface Simulation {
     void scheduleActions();
 
     /**
-     * Schedules any {@link arcade.core.env.comp.Component} instances.
+     * Schedules any {@link Component} instances.
      * <p>
      * The concrete implementing class calls this and other schedule methods
      * from the MASON library {@code start()} method, which is called before the

src/arcade/core/sim/output/OutputDeserializer.java

@@ -10,7 +10,7 @@
 import com.google.gson.JsonObject;
 import com.google.gson.JsonParseException;
 import arcade.core.agent.cell.CellContainer;
-import arcade.core.env.loc.LocationContainer;
+import arcade.core.env.location.LocationContainer;
 import static arcade.core.sim.Simulation.DEFAULT_CELL_TYPE;
 import static arcade.core.sim.Simulation.DEFAULT_LOCATION_TYPE;
 

src/arcade/core/sim/output/OutputLoader.java

@@ -9,7 +9,7 @@
 import java.util.logging.Logger;
 import com.google.gson.Gson;
 import arcade.core.agent.cell.CellContainer;
-import arcade.core.env.loc.LocationContainer;
+import arcade.core.env.location.LocationContainer;
 import arcade.core.sim.Series;
 import arcade.core.sim.Simulation;
 import static arcade.core.sim.Simulation.DEFAULT_CELL_TYPE;

src/arcade/core/sim/output/OutputSaver.java

@@ -94,7 +94,7 @@ public void saveCells(int tick) {
     }
 
     /**
-     * Save a list of {@link arcade.core.env.loc.LocationContainer} to a JSON.
+     * Save a list of {@link arcade.core.env.location.LocationContainer} to a JSON.
      *
      * @param tick  the simulation tick
      */

src/arcade/core/sim/output/OutputSerializer.java

@@ -11,7 +11,7 @@
 import com.google.gson.JsonSerializationContext;
 import com.google.gson.JsonSerializer;
 import arcade.core.agent.cell.CellContainer;
-import arcade.core.env.loc.LocationContainer;
+import arcade.core.env.location.LocationContainer;
 import arcade.core.sim.Series;
 import arcade.core.util.MiniBox;
 import static arcade.core.sim.Simulation.DEFAULT_CELL_TYPE;

test/arcade/core/sim/SeriesTest.java

@@ -11,10 +11,10 @@
 import sim.engine.Steppable;
 import arcade.core.agent.action.Action;
 import arcade.core.agent.cell.CellContainer;
-import arcade.core.env.comp.Component;
+import arcade.core.env.component.Component;
 import arcade.core.env.grid.Grid;
-import arcade.core.env.lat.Lattice;
-import arcade.core.env.loc.LocationContainer;
+import arcade.core.env.lattice.Lattice;
+import arcade.core.env.location.LocationContainer;
 import arcade.core.util.Box;
 import arcade.core.util.MiniBox;
 import arcade.core.vis.*;

test/arcade/core/sim/output/OutputDeserializerTest.java

@@ -14,7 +14,7 @@
 import com.google.gson.internal.bind.TreeTypeAdapter;
 import com.google.gson.reflect.TypeToken;
 import arcade.core.agent.cell.CellContainer;
-import arcade.core.env.loc.LocationContainer;
+import arcade.core.env.location.LocationContainer;
 import static org.junit.Assert.*;
 import static org.mockito.Mockito.*;
 import static arcade.core.ARCADETestUtilities.*;

test/arcade/core/sim/output/OutputLoaderTest.java

@@ -10,7 +10,7 @@
 import org.junit.rules.TemporaryFolder;
 import com.google.gson.Gson;
 import arcade.core.agent.cell.CellContainer;
-import arcade.core.env.loc.LocationContainer;
+import arcade.core.env.location.LocationContainer;
 import arcade.core.sim.*;
 import static org.junit.Assert.*;
 import static org.mockito.Mockito.*;

test/arcade/core/sim/output/OutputSaverTest.java

@@ -12,7 +12,7 @@
 import sim.engine.Schedule;
 import sim.engine.SimState;
 import arcade.core.agent.cell.CellContainer;
-import arcade.core.env.loc.LocationContainer;
+import arcade.core.env.location.LocationContainer;
 import arcade.core.sim.*;
 import static org.junit.Assert.*;
 import static org.mockito.Mockito.*;

test/arcade/core/sim/output/OutputSerializerTest.java

@@ -13,7 +13,7 @@
 import com.google.gson.internal.bind.TreeTypeAdapter;
 import com.google.gson.reflect.TypeToken;
 import arcade.core.agent.cell.CellContainer;
-import arcade.core.env.loc.LocationContainer;
+import arcade.core.env.location.LocationContainer;
 import arcade.core.sim.Series;
 import arcade.core.util.MiniBox;
 import static org.junit.Assert.*;