handle SpotBugs warnings

agents/src/main/java/uk/ac/ox/poseidon/agents/behaviours/Action.java

@@ -19,6 +19,7 @@
 
 package uk.ac.ox.poseidon.agents.behaviours;
 
+import edu.umd.cs.findbugs.annotations.SuppressFBWarnings;
 import lombok.Data;
 import sim.engine.SimState;
 import sim.engine.Steppable;
@@ -37,6 +38,7 @@ public abstract class Action implements Steppable {
     private final Duration duration;
     private final Vessel vessel;
 
+    @SuppressFBWarnings("EI_EXPOSE_REP2")
     public Action(
         final LocalDateTime start,
         final Duration duration,

agents/src/main/java/uk/ac/ox/poseidon/agents/behaviours/destination/ChooseRandomDestinationBehaviour.java

@@ -19,6 +19,7 @@
 
 package uk.ac.ox.poseidon.agents.behaviours.destination;
 
+import com.google.common.collect.ImmutableList;
 import ec.util.MersenneTwisterFast;
 import sim.util.Int2D;
 import uk.ac.ox.poseidon.agents.behaviours.travel.TravelBehaviour;
@@ -30,7 +31,7 @@
 
 public class ChooseRandomDestinationBehaviour extends DestinationBehaviour {
 
-    private final List<Int2D> possibleDestinations;
+    private final ImmutableList<Int2D> possibleDestinations;
     private final MersenneTwisterFast rng;
 
     public ChooseRandomDestinationBehaviour(
@@ -39,7 +40,7 @@ public ChooseRandomDestinationBehaviour(
         final MersenneTwisterFast rng
     ) {
         super(travelBehaviour);
-        this.possibleDestinations = possibleDestinations;
+        this.possibleDestinations = ImmutableList.copyOf(possibleDestinations);
         this.rng = rng;
     }
 

agents/src/main/java/uk/ac/ox/poseidon/agents/vessels/Vessel.java

@@ -19,6 +19,7 @@
 
 package uk.ac.ox.poseidon.agents.vessels;
 
+import edu.umd.cs.findbugs.annotations.SuppressFBWarnings;
 import lombok.Getter;
 import lombok.NonNull;
 import lombok.Setter;
@@ -40,9 +41,10 @@ public class Vessel implements Oriented2D {
     private double cruisingSpeed;
     private double heading;
 
+    @SuppressFBWarnings("EI_EXPOSE_REP2")
     public Vessel(
         final String id,
-        @NonNull final Port homePort,
+        final Port homePort,
         final double cruisingSpeed,
         final VesselField vesselField
     ) {

biology/src/main/java/uk/ac/ox/poseidon/biology/biomass/BiomassDiffuser.java

@@ -20,6 +20,7 @@
 package uk.ac.ox.poseidon.biology.biomass;
 
 import ec.util.MersenneTwisterFast;
+import edu.umd.cs.findbugs.annotations.SuppressFBWarnings;
 import sim.engine.SimState;
 import sim.engine.Steppable;
 import sim.util.Double2D;
@@ -49,6 +50,7 @@ public class BiomassDiffuser implements Steppable {
 
     private final Map<Int2D, List<Int2D>> habitableNeighbours;
 
+    @SuppressFBWarnings("EI_EXPOSE_REP2")
     public BiomassDiffuser(
         final BiomassGrid biomassGrid,
         final CarryingCapacityGrid carryingCapacityGrid,

core/src/main/java/uk/ac/ox/poseidon/core/PathFactory.java

@@ -19,6 +19,7 @@
 
 package uk.ac.ox.poseidon.core;
 
+import com.google.common.collect.ImmutableList;
 import com.google.common.collect.Streams;
 import lombok.*;
 
@@ -27,14 +28,36 @@
 import java.util.List;
 import java.util.Optional;
 
+import static com.google.common.base.Preconditions.checkState;
+import static com.google.common.collect.ImmutableList.toImmutableList;
+
 @Getter
 @Setter
 @NoArgsConstructor
 @AllArgsConstructor
 public class PathFactory extends GlobalScopeFactory<Path> {
 
     private Factory<? extends Path> parent;
-    @NonNull private List<String> pathElements;
+    @NonNull private ImmutableList<String> pathElements;
+
+    public static PathFactory from(
+        final String path
+    ) {
+        return from(null, Path.of(path));
+    }
+
+    public static PathFactory from(
+        final Path path
+    ) {
+        return from(null, path);
+    }
+
+    public static PathFactory from(
+        final PathFactory parent,
+        final String path
+    ) {
+        return from(parent, Path.of(path));
+    }
 
     public static PathFactory from(
         final PathFactory parent,
@@ -48,13 +71,17 @@ public static PathFactory from(
                     Streams.stream(path)
                 )
                 .map(Path::toString)
-                .toList()
+                .collect(toImmutableList())
         );
     }
 
     @Override
     protected Path newInstance(final Simulation simulation) {
-        final Path path = Paths.get(pathElements.getFirst(), pathElements.removeFirst());
+        checkState(!pathElements.isEmpty());
+        final Path path = Path.of(
+            pathElements.getFirst(),
+            pathElements.subList(1, pathElements.size()).toArray(String[]::new)
+        );
         return parent == null ? path : parent.get(null).resolve(path);
     }
 }

core/src/main/java/uk/ac/ox/poseidon/core/Simulation.java

@@ -22,6 +22,7 @@
  */
 package uk.ac.ox.poseidon.core;
 
+import edu.umd.cs.findbugs.annotations.SuppressFBWarnings;
 import lombok.Getter;
 import sim.engine.SimState;
 import uk.ac.ox.poseidon.core.schedule.TemporalSchedule;
@@ -64,6 +65,7 @@ public Simulation(
         );
     }
 
+    @SuppressFBWarnings("EI_EXPOSE_REP2")
     public Simulation(
         final long seed,
         final TemporalSchedule schedule,

core/src/test/java/uk/ac/ox/poseidon/core/PathFactoryTest.java

@@ -0,0 +1,58 @@
+/*
+ * POSEIDON: an agent-based model of fisheries
+ * Copyright (c) 2024 CoHESyS Lab [email protected]
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
+package uk.ac.ox.poseidon.core;
+
+import com.google.common.collect.ImmutableList;
+import org.junit.jupiter.api.Test;
+
+import java.nio.file.Path;
+
+import static org.junit.jupiter.api.Assertions.*;
+
+class PathFactoryTest {
+
+    private static final String FOLDERS = "/a/b/c/";
+    private static final String FILENAME = "file.txt";
+
+    @Test
+    void newInstanceSimpleFile() {
+        final PathFactory pathFactory = PathFactory.from(FILENAME);
+        assertNull(pathFactory.getParent());
+        assertEquals(ImmutableList.of(FILENAME), pathFactory.getPathElements());
+        assertEquals(Path.of(FILENAME), pathFactory.newInstance(null));
+    }
+
+    @Test
+    void newInstanceFileInFolder() {
+        final PathFactory pathFactory = PathFactory.from(FOLDERS + FILENAME);
+        assertNull(pathFactory.getParent());
+        assertEquals(ImmutableList.of("/", "a", "b", "c", FILENAME), pathFactory.getPathElements());
+        assertEquals(Path.of(FOLDERS + FILENAME), pathFactory.newInstance(null));
+    }
+
+    @Test
+    void newInstanceWithParent() {
+        final PathFactory pathFactory = PathFactory.from(PathFactory.from(FOLDERS), FILENAME);
+        assertEquals(Path.of(FOLDERS), pathFactory.getParent().get(null));
+        assertEquals(ImmutableList.of(FILENAME), pathFactory.getPathElements());
+        assertEquals(Path.of(FOLDERS + FILENAME), pathFactory.newInstance(null));
+    }
+
+}

examples/src/test/java/uk/ac/ox/poseidon/gui/palettes/PaletteColorMapTest.java

@@ -29,20 +29,20 @@
 
 class PaletteColorMapTest {
 
-    private final double max = 5;
-    private final double min = -max;
-    private final PaletteColorMap colorMap = new PaletteColorMap(OLERON, min, max);
+    private static final double MAX = 5;
+    private static final double MIN = -MAX;
+    private final PaletteColorMap colorMap = new PaletteColorMap(OLERON, MIN, MAX);
 
     @Test
     void getColor() {
         final Color[] palette = colorMap.getColors();
         Map.of(
-            min - 1, 0,
-            min, 0,
+            MIN - 1, 0,
+            MIN, 0,
             -1E-10, 127,
             0.0, 128,
-            max, palette.length - 1,
-            max + 1, palette.length - 1
+            MAX, palette.length - 1,
+            MAX + 1, palette.length - 1
         ).forEach((value, index) -> {
             final Color expected = palette[index];
             final Color actual = colorMap.getColor(value);

geography/src/main/java/uk/ac/ox/poseidon/geography/bathymetry/BathymetricGrid.java

@@ -25,14 +25,24 @@
 
 import java.util.List;
 
+import static com.google.common.collect.ImmutableList.toImmutableList;
+
 public interface BathymetricGrid extends NumberGrid<Double, DoubleGrid2D> {
 
     default List<Int2D> getWaterCells() {
-        return getGridExtent().getAllCells().stream().filter(this::isWater).toList();
+        return getGridExtent()
+            .getAllCells()
+            .stream()
+            .filter(this::isWater)
+            .collect(toImmutableList());
     }
 
     default List<Int2D> getLandCells() {
-        return getGridExtent().getAllCells().stream().filter(this::isLand).toList();
+        return getGridExtent()
+            .getAllCells()
+            .stream()
+            .filter(this::isLand)
+            .collect(toImmutableList());
     }
 
     default List<Int2D> getAllCells() {

geography/src/main/java/uk/ac/ox/poseidon/geography/paths/CachingPathFinder.java

@@ -20,13 +20,15 @@
 package uk.ac.ox.poseidon.geography.paths;
 
 import com.google.common.collect.ImmutableList;
+import edu.umd.cs.findbugs.annotations.SuppressFBWarnings;
 
 import java.util.Optional;
 
 public class CachingPathFinder<P> implements PathFinder<P> {
     private final PathFinder<P> pathFinder;
     private final PathCache<P> cache;
 
+    @SuppressFBWarnings("EI_EXPOSE_REP2")
     public CachingPathFinder(
         final PathFinder<P> pathFinder,
         final PathCache<P> cache