add "external biomass grid process" using gRPC and tables using TableSaw

A bit of a sloppy commit since I tackled those two things in parallel.
They could have been better separated...

agents/build.gradle.kts

@@ -24,4 +24,5 @@ plugins {
 dependencies {
     api(project(":biology"))
     api(project(":geography"))
+    api(project(":io"))
 }

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

@@ -49,7 +49,8 @@ private Evaluation(final Vessel vessel) {
                 vessel.getEventManager(),
                 FishingAction.class,
                 0.0,
-                (caughtSoFar, fishingAction) -> caughtSoFar + fishingAction.getTotalBiomassCaught(),
+                (caughtSoFar, fishingAction) -> caughtSoFar +
+                    fishingAction.getFishCaught().getTotalBiomass().getValue(),
                 Action.class,
                 0.0,
                 (hoursSoFar, action) ->

agents/src/main/java/uk/ac/ox/poseidon/agents/behaviours/fishing/DefaultFishingBehaviour.java

@@ -65,11 +65,6 @@ private Fishing(
             super(start, duration, vessel, vessel.getCurrentCell());
         }
 
-        @Override
-        public double getTotalBiomassCaught() {
-            return fishCaught.getTotalBiomass().getValue();
-        }
-
         @Override
         protected Action complete(
             final LocalDateTime dateTime

agents/src/main/java/uk/ac/ox/poseidon/agents/behaviours/fishing/FishingAction.java

@@ -22,6 +22,7 @@
 import sim.util.Int2D;
 import uk.ac.ox.poseidon.agents.behaviours.GridAction;
 import uk.ac.ox.poseidon.agents.vessels.Vessel;
+import uk.ac.ox.poseidon.biology.Bucket;
 
 import java.time.Duration;
 import java.time.LocalDateTime;
@@ -37,5 +38,6 @@ public FishingAction(
         super(start, duration, vessel, cell);
     }
 
-    public abstract double getTotalBiomassCaught();
+    public abstract Bucket<?> getFishCaught();
+
 }

agents/src/main/java/uk/ac/ox/poseidon/agents/tables/ActionListenerTable.java

@@ -0,0 +1,51 @@
+/*
+ * 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.agents.tables;
+
+import tech.tablesaw.api.DateTimeColumn;
+import tech.tablesaw.api.StringColumn;
+import tech.tablesaw.api.Table;
+import uk.ac.ox.poseidon.agents.behaviours.Action;
+import uk.ac.ox.poseidon.io.tables.ListenerTable;
+
+public abstract class ActionListenerTable<A extends Action> implements ListenerTable<A> {
+    private final StringColumn vesselId = StringColumn.create("vessel_id");
+    private final DateTimeColumn actionStart = DateTimeColumn.create("action_start");
+    private final DateTimeColumn actionEnd = DateTimeColumn.create("action_end");
+
+    private final Table table =
+        Table.create(
+            vesselId,
+            actionStart,
+            actionEnd
+        );
+
+    @Override
+    public void receive(final A action) {
+        actionStart.append(action.getStart());
+        actionEnd.append(action.getEnd());
+        vesselId.append(action.getVessel().getId());
+    }
+
+    @Override
+    public Table get() {
+        return table;
+    }
+}

agents/src/main/java/uk/ac/ox/poseidon/agents/tables/FishingActionListenerTable.java

@@ -0,0 +1,50 @@
+/*
+ * 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.agents.tables;
+
+import tech.tablesaw.api.DoubleColumn;
+import tech.tablesaw.api.StringColumn;
+import uk.ac.ox.poseidon.agents.behaviours.fishing.FishingAction;
+import uk.ac.ox.poseidon.geography.grids.GridExtent;
+
+public class FishingActionListenerTable extends GridActionListenerTable<FishingAction> {
+
+    private final StringColumn speciesCode = StringColumn.create("species_code");
+    private final DoubleColumn biomassCaught = DoubleColumn.create("biomass_caught");
+
+    public FishingActionListenerTable(final GridExtent gridExtent) {
+        super(gridExtent);
+        get().addColumns(speciesCode, biomassCaught);
+    }
+
+    @Override
+    public void receive(final FishingAction fishingAction) {
+        super.receive(fishingAction);
+        fishingAction.getFishCaught().getMap().forEach((species, content) -> {
+            speciesCode.append(species.getCode());
+            biomassCaught.append(content.asBiomass().getValue());
+        });
+    }
+
+    @Override
+    public Class<FishingAction> getEventClass() {
+        return FishingAction.class;
+    }
+}

agents/src/main/java/uk/ac/ox/poseidon/agents/tables/FishingActionListenerTableFactory.java

@@ -0,0 +1,46 @@
+/*
+ * 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.agents.tables;
+
+import lombok.AllArgsConstructor;
+import lombok.Getter;
+import lombok.NoArgsConstructor;
+import lombok.Setter;
+import uk.ac.ox.poseidon.agents.behaviours.fishing.FishingAction;
+import uk.ac.ox.poseidon.core.Factory;
+import uk.ac.ox.poseidon.core.Simulation;
+import uk.ac.ox.poseidon.geography.grids.GridExtent;
+import uk.ac.ox.poseidon.io.tables.ListenerTableFactory;
+
+@Getter
+@Setter
+@NoArgsConstructor
+@AllArgsConstructor
+public class FishingActionListenerTableFactory
+    extends ListenerTableFactory<FishingAction, FishingActionListenerTable> {
+
+    private Factory<? extends GridExtent> gridExtent;
+
+    @Override
+    protected FishingActionListenerTable newTable(final Simulation simulation) {
+        return new FishingActionListenerTable(gridExtent.get(simulation));
+    }
+
+}

agents/src/main/java/uk/ac/ox/poseidon/agents/tables/GridActionListenerTable.java

@@ -0,0 +1,45 @@
+/*
+ * 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.agents.tables;
+
+import com.vividsolutions.jts.geom.Coordinate;
+import tech.tablesaw.api.DoubleColumn;
+import uk.ac.ox.poseidon.agents.behaviours.GridAction;
+import uk.ac.ox.poseidon.geography.grids.GridExtent;
+
+public abstract class GridActionListenerTable<A extends GridAction> extends ActionListenerTable<A> {
+    private final GridExtent gridExtent;
+    private final DoubleColumn lon = DoubleColumn.create("lon");
+    private final DoubleColumn lat = DoubleColumn.create("lat");
+
+    public GridActionListenerTable(final GridExtent gridExtent) {
+        super();
+        get().addColumns(lon, lat);
+        this.gridExtent = gridExtent;
+    }
+
+    @Override
+    public void receive(final A action) {
+        super.receive(action);
+        final Coordinate coordinate = gridExtent.toCoordinate(action.getCell());
+        lon.append(coordinate.x);
+        lat.append(coordinate.y);
+    }
+}

core/src/main/java/uk/ac/ox/poseidon/core/time/DistributedDurationSupplier.java → core/src/main/java/uk/ac/ox/poseidon/core/time/DurationSupplier.java

@@ -20,19 +20,18 @@
 package uk.ac.ox.poseidon.core.time;
 
 import lombok.RequiredArgsConstructor;
-import sim.util.distribution.AbstractDistribution;
 
 import java.time.Duration;
 import java.util.function.Supplier;
 
 @RequiredArgsConstructor
-public class DistributedDurationSupplier implements Supplier<Duration> {
+public class DurationSupplier implements Supplier<Duration> {
 
-    private final AbstractDistribution distribution;
+    private final Supplier<Long> secondsSupplier;
 
     @Override
     public Duration get() {
-        return Duration.ofSeconds(distribution.nextInt());
+        return Duration.ofSeconds(secondsSupplier.get());
     }
 
 }

core/src/main/java/uk/ac/ox/poseidon/core/time/ExponentiallyDistributedDurationSupplierFactory.java

@@ -42,11 +42,13 @@ public class ExponentiallyDistributedDurationSupplierFactory
 
     @Override
     protected Supplier<Duration> newInstance(final Simulation simulation) {
-        return new DistributedDurationSupplier(
+        final Exponential exponential =
             new Exponential(
                 1.0 / meanDuration.get(simulation).getSeconds(),
                 simulation.random
-            )
+            );
+        return new DurationSupplier(
+            () -> (long) (1 + exponential.nextInt())
         );
     }
 }

examples/src/main/java/uk/ac/ox/poseidon/examples/BasicScenario.java

@@ -23,6 +23,7 @@
 import lombok.Setter;
 import sim.engine.Steppable;
 import sim.util.Int2D;
+import tech.tablesaw.api.Table;
 import uk.ac.ox.poseidon.agents.behaviours.BackToInitialBehaviourFactory;
 import uk.ac.ox.poseidon.agents.behaviours.WaitBehaviourFactory;
 import uk.ac.ox.poseidon.agents.behaviours.choices.BestOptionsFromFriendsSupplierFactory;
@@ -39,6 +40,7 @@
 import uk.ac.ox.poseidon.agents.registers.Register;
 import uk.ac.ox.poseidon.agents.registers.RegisterFactory;
 import uk.ac.ox.poseidon.agents.registers.RegisteringFactory;
+import uk.ac.ox.poseidon.agents.tables.FishingActionListenerTableFactory;
 import uk.ac.ox.poseidon.agents.vessels.RandomHomePortFactory;
 import uk.ac.ox.poseidon.agents.vessels.VesselFactory;
 import uk.ac.ox.poseidon.agents.vessels.VesselScopeFactory;
@@ -50,7 +52,6 @@
 import uk.ac.ox.poseidon.core.Factory;
 import uk.ac.ox.poseidon.core.GlobalScopeFactory;
 import uk.ac.ox.poseidon.core.Scenario;
-import uk.ac.ox.poseidon.core.Simulation;
 import uk.ac.ox.poseidon.core.schedule.ScheduledRepeatingFactory;
 import uk.ac.ox.poseidon.core.schedule.SteppableSequenceFactory;
 import uk.ac.ox.poseidon.core.suppliers.PoissonIntSupplierFactory;
@@ -72,7 +73,9 @@
 
 import java.nio.file.Path;
 import java.time.LocalDate;
+import java.time.Period;
 import java.util.List;
+import java.util.function.Supplier;
 
 @SuppressWarnings("MagicNumber")
 @Getter
@@ -84,9 +87,9 @@ public class BasicScenario extends Scenario {
     private Factory<? extends Species> speciesA = new SpeciesFactory("A");
     private Factory<? extends Species> speciesB = new SpeciesFactory("B");
     private Factory<? extends BiomassDiffusionRule> biomassDiffusionRule =
-        new SmoothBiomassDiffusionRuleFactory(0.001, 0.01);
+        new SmoothBiomassDiffusionRuleFactory(0.01, 0.01);
     private Factory<? extends BiomassGrowthRule> biomassGrowthRule =
-        new LogisticGrowthRuleFactory(0.7);
+        new LogisticGrowthRuleFactory(0.1);
 
     private GlobalScopeFactory<? extends GridExtent> gridExtent =
         new GridExtentFactory(
@@ -97,6 +100,8 @@ public class BasicScenario extends Scenario {
             -5,
             5
         );
+    private Factory<? extends Supplier<Table>> catchTable =
+        new FishingActionListenerTableFactory(gridExtent);
     private Factory<? extends VesselField> vesselField = new VesselFieldFactory(gridExtent);
     private Factory<? extends Distance> distance = new EquirectangularDistanceFactory(gridExtent);
     private Factory<? extends BathymetricGrid> bathymetricGrid =
@@ -117,7 +122,6 @@ public class BasicScenario extends Scenario {
             3,
             2
         );
-
     private Factory<? extends GridPathFinder> pathFinder =
         new DefaultPathFinderFactory(
             bathymetricGrid,
@@ -200,20 +204,20 @@ public class BasicScenario extends Scenario {
                     ),
                     new ChooseDestinationBehaviourFactory(
                         new EpsilonGreedyDestinationSupplierFactory(
-                            0.2,
+                            0.25,
                             optionValues,
                             new NeighbourhoodGridExplorerFactory(
                                 optionValues,
                                 pathFinder,
                                 new ShiftedIntSupplierFactory(
-                                    new PoissonIntSupplierFactory(5),
+                                    new PoissonIntSupplierFactory(1),
                                     1
                                 )
                             ),
                             new ImitatingPickerFactory<>(
                                 optionValues,
                                 new BestOptionsFromFriendsSupplierFactory<>(
-                                    2,
+                                    5,
                                     optionValuesRegister
                                 )
                             ),
@@ -222,7 +226,7 @@ public class BasicScenario extends Scenario {
                         new TravelAlongPathBehaviourFactory(
                             new DefaultFishingBehaviourFactory<>(
                                 new FixedBiomassProportionGearFactory(
-                                    0.05,
+                                    0.1,
                                     new DurationFactory(0, 1, 0, 0)
                                 ),
                                 new VoidHoldFactory<>(),
@@ -263,16 +267,7 @@ public static void main(final String[] args) {
             scenario,
             Path.of("/home/nicolas/Desktop/scenario.yaml")
         );
-        final Simulation simulation = scenario.newSimulation();
-        simulation.start();
-        while (
-            simulation
-                .getTemporalSchedule()
-                .getDateTime()
-                .isBefore(LocalDate.of(LocalDate.now().getYear() + 10, 1, 1).atStartOfDay())
-        ) {
-            simulation.schedule.step(simulation);
-        }
-        simulation.finish();
+        new QuickRunner(scenario).runFor(Period.ofYears(1));
+
     }
 }