Fix bugs in genome and codecs + implement mutation manager

src/main/java/forestry/api/genetics/ClimateHelper.java

@@ -6,39 +6,15 @@
 package forestry.api.genetics;
 
 import java.util.Locale;
-import java.util.Set;
 
 import net.minecraft.network.chat.Component;
 import net.minecraft.network.chat.MutableComponent;
 
-import forestry.api.core.ForestryError;
 import forestry.api.core.HumidityType;
-import forestry.api.core.IError;
 import forestry.api.core.TemperatureType;
 import forestry.api.core.ToleranceType;
 
 public class ClimateHelper {
-	public static void addClimateErrorStates(TemperatureType temperature, HumidityType humidity,
-			TemperatureType baseTemp, ToleranceType tolTemp,
-			HumidityType baseHumid, ToleranceType tolHumid, Set<IError> errorStates) {
-
-		if (!isWithinLimits(temperature, baseTemp, tolTemp)) {
-			if (baseTemp.ordinal() > temperature.ordinal()) {
-				errorStates.add(ForestryError.TOO_COLD);
-			} else {
-				errorStates.add(ForestryError.TOO_HOT);
-			}
-		}
-
-		if (!isWithinLimits(humidity, baseHumid, tolHumid)) {
-			if (baseHumid.ordinal() > humidity.ordinal()) {
-				errorStates.add(ForestryError.TOO_ARID);
-			} else {
-				errorStates.add(ForestryError.TOO_HUMID);
-			}
-		}
-	}
-
 	public static int getColor(TemperatureType temperature) {
 		return switch (temperature) {
 			case ICY -> 0xe6e6fa;

src/main/java/forestry/api/genetics/IIndividual.java

@@ -1,6 +1,7 @@
 package forestry.api.genetics;
 
 import javax.annotation.Nullable;
+import java.util.Optional;
 
 import net.minecraft.resources.ResourceLocation;
 import net.minecraft.world.item.ItemStack;
@@ -44,9 +45,18 @@ public int hashCode() {
 
 	void setMate(@Nullable IGenome mate);
 
+	/**
+	 * @return The genome of this individual's mate, or {@code null} if this individual has no mate.
+	 */
 	@Nullable
 	IGenome getMate();
 
+	/**
+	 * An optional getter for {@link #getMate}. Used only for Codec purposes, prefer {@link #getMate} when possible.
+	 * @return An optional containing this individual's mate genome, or empty if this individual has no mate.
+	 */
+	Optional<IGenome> getMateOptional();
+
 	/**
 	 * @return {@code true} if this individual has been analyzed and a summary of its genome should be displayed in its tooltip.
 	 */
@@ -76,7 +86,7 @@ default boolean isSecret() {
 	 * Copies this individual and all of its properties EXCEPT FOR ITS MATE.
 	 * Override this method in subclasses to make sure all information is copied.
 	 *
-	 * @return An exact copy of this individual.
+	 * @return An exact copy of this individual WITHOUT A MATE.
 	 */
 	IIndividual copy();
 

src/main/java/forestry/api/genetics/IMutation.java

@@ -58,9 +58,9 @@ public interface IMutation<S extends ISpecies<?>> {
 	List<IMutationCondition> getConditions();
 
 	/**
-	 * @return {@code true} if the passed allele is one of the alleles participating in this mutation.
+	 * @return {@code true} if the passed species is one of the alleles participating in this mutation.
 	 */
-	boolean isPartner(ISpecies<?> allele);
+	boolean isPartner(ISpecies<?> species);
 
 	/**
 	 * @return The other parent in this mutation besides the given species.

src/main/java/forestry/api/genetics/IMutationManager.java

@@ -2,11 +2,8 @@
 
 import java.util.List;
 
-import net.minecraft.Util;
 import net.minecraft.util.RandomSource;
 
-import it.unimi.dsi.fastutil.objects.ObjectArrayList;
-
 /**
  * Keeps track of mutations involving members of a certain species type.
  *
@@ -29,16 +26,12 @@ public interface IMutationManager<S extends ISpecies<?>> {
 	List<IMutation<S>> getCombinations(S firstParent, S secondParent);
 
 	/**
-	 * @return All mutations within the species type of this mutation manager.
+	 * @return A shuffled list of all mutations within the species type of this mutation manager.
 	 */
-	List<IMutation<S>> getAllMutations();
+	List<? extends IMutation<S>> getCombinationsShuffled(S firstParent, S secondParent, RandomSource rand);
 
 	/**
-	 * @return A shuffled list of all mutations within the species type of this mutation manager.
+	 * @return All mutations within the species type of this mutation manager.
 	 */
-	default ObjectArrayList<? extends IMutation<S>> getAllMutations(RandomSource rand) {
-		ObjectArrayList<? extends IMutation<S>> mutations = new ObjectArrayList<>(getAllMutations());
-		Util.shuffle(mutations, rand);
-		return mutations;
-	}
+	List<IMutation<S>> getAllMutations();
 }

src/main/java/forestry/api/genetics/ISpeciesType.java

@@ -15,6 +15,7 @@
 import net.minecraft.world.level.LevelAccessor;
 
 import com.mojang.authlib.GameProfile;
+import com.mojang.datafixers.util.Pair;
 import com.mojang.serialization.Codec;
 
 import forestry.api.ForestryCapabilities;
@@ -43,6 +44,7 @@ public interface ISpeciesType<S extends ISpecies<I>, I extends IIndividual> exte
 
 	/**
 	 * @return The mutation manager for this species type.
+	 * @throws IllegalStateException If not all mutations have been registered.
 	 */
 	IMutationManager<S> getMutations();
 
@@ -208,17 +210,19 @@ default boolean isMember(ItemStack stack) {
 	 * checking if the plugin implements that interface.
 	 *
 	 * @param plugins The list of plugins responsible for registering species and data.
-	 * @return The map of every species registered to this species type, which later gets passed to {@link #onSpeciesRegistered}.
+	 * @return The map of every species registered to this species type, which later gets passed
+	 * to {@link #onSpeciesRegistered}, and the completed mutations manager for this species type.
 	 * @see IForestryPlugin#registerApiculture(IApicultureRegistration) for an example of what data is registered.
 	 */
-	ImmutableMap<ResourceLocation, S> handleSpeciesRegistration(List<IForestryPlugin> plugins);
+	Pair<ImmutableMap<ResourceLocation, S>, IMutationManager<S>> handleSpeciesRegistration(List<IForestryPlugin> plugins);
 
 	/**
 	 * Called when all species of this type have been registered and modified.
 	 *
 	 * @param allSpecies The map of every species ID to its species.
+	 * @param mutations  The mutations for this species type.
 	 */
-	void onSpeciesRegistered(ImmutableMap<ResourceLocation, S> allSpecies);
+	void onSpeciesRegistered(ImmutableMap<ResourceLocation, S> allSpecies, IMutationManager<S> mutations);
 
 	/**
 	 * @return This species type casted to a subclass of ISpeciesType.

src/main/java/forestry/api/lepidopterology/genetics/IButterfly.java

@@ -7,14 +7,12 @@
 
 import javax.annotation.Nullable;
 import java.util.List;
-import java.util.Set;
 
 import net.minecraft.core.BlockPos;
 import net.minecraft.network.chat.Component;
 import net.minecraft.world.item.ItemStack;
 import net.minecraft.world.level.Level;
 
-import forestry.api.core.IError;
 import forestry.api.genetics.IIndividualLiving;
 import forestry.api.lepidopterology.IButterflyCocoon;
 import forestry.api.lepidopterology.IButterflyNursery;
@@ -43,26 +41,6 @@ default boolean isAcceptedEnvironment(Level level, double x, double y, double z)
 	@Nullable
 	IButterfly spawnCaterpillar(IButterflyNursery nursery);
 
-	/**
-	 * Determines whether the caterpillar can grow.
-	 *
-	 * @param cocoon  the {@link IButterflyCocoon} the caterpillar resides in.
-	 * @param nursery the {@link IButterflyNursery} of the caterpillar.
-	 * @return an empty set if the caterpillar can grow, a set of error states if the caterpillar can not grow
-	 * @since 5.3.3
-	 */
-	Set<IError> getCanGrow(IButterflyNursery nursery, @Nullable IButterflyCocoon cocoon);
-
-	/**
-	 * Determines whether the caterpillar can spawn. (Used to auto-spawn butterflies out of a cocoon.)
-	 *
-	 * @param cocoon  the {@link IButterflyCocoon} the caterpillar resides in.
-	 * @param nursery the {@link IButterflyNursery} of the caterpillar.
-	 * @return an empty set if the caterpillar can spawn, a set of error states if the caterpillar can not spawn
-	 * @since 5.3.3
-	 */
-	Set<IError> getCanSpawn(IButterflyNursery nursery, @Nullable IButterflyCocoon cocoon);
-
 	/**
 	 * @param playerKill Whether or not the butterfly was killed by a player.
 	 * @param lootLevel  Loot level according to the weapon used to kill the butterfly.

src/main/java/forestry/api/plugin/IMutationBuilder.java

@@ -5,20 +5,23 @@
  ******************************************************************************/
 package forestry.api.plugin;
 
+import com.google.common.collect.ImmutableMap;
+
 import java.time.Month;
 
+import net.minecraft.resources.ResourceLocation;
 import net.minecraft.tags.TagKey;
 import net.minecraft.world.level.biome.Biome;
 import net.minecraft.world.level.block.state.BlockState;
 
 import forestry.api.core.HumidityType;
 import forestry.api.core.TemperatureType;
+import forestry.api.genetics.IMutation;
 import forestry.api.genetics.IMutationCondition;
 import forestry.api.genetics.ISpecies;
 import forestry.api.genetics.ISpeciesType;
 import forestry.api.genetics.alleles.IAllele;
 import forestry.api.genetics.alleles.IChromosome;
-import forestry.core.genetics.mutations.Mutation;
 
 /**
  * Set custom mutation requirements
@@ -85,5 +88,12 @@ default IMutationBuilder restrictDateRange(Month startMonth, int startDay, Month
 	 */
 	IMutationBuilder setChance(int chance);
 
-	<S extends ISpecies<?>> Mutation<S> build(ISpeciesType<S, ?> speciesType);
+	/**
+	 * Builds the mutation. Used internally.
+	 *
+	 * @param speciesType   Species type of the mutation. Do not call {@link ISpeciesType#getSpecies}.
+	 * @param speciesLookup The species by ID lookup, since species type might not have the registry yet.
+	 * @return The completed Mutation object with immutable data.
+	 */
+	<S extends ISpecies<?>> IMutation<S> build(ISpeciesType<S, ?> speciesType, ImmutableMap<ResourceLocation, S> speciesLookup);
 }

src/main/java/forestry/api/plugin/ISpeciesBuilder.java

@@ -1,12 +1,16 @@
 package forestry.api.plugin;
 
+import com.google.common.collect.ImmutableMap;
+
+import java.util.List;
 import java.util.function.Consumer;
 
 import net.minecraft.resources.ResourceLocation;
 
 import forestry.api.core.HumidityType;
 import forestry.api.core.TemperatureType;
 import forestry.api.genetics.IGenome;
+import forestry.api.genetics.IMutation;
 import forestry.api.genetics.ISpecies;
 import forestry.api.genetics.ISpeciesType;
 
@@ -103,6 +107,8 @@ public interface ISpeciesBuilder<T extends ISpeciesType<S, ?>, S extends ISpecie
 
 	ISpeciesFactory<T, S, B> createSpeciesFactory();
 
+	List<IMutation<S>> buildMutations(ISpeciesType<S, ?> speciesType, ImmutableMap<ResourceLocation, S> speciesLookup);
+
 	@FunctionalInterface
 	interface ISpeciesFactory<T extends ISpeciesType<S, ?>, S extends ISpecies<?>, B extends ISpeciesBuilder<T, S, B>> {
 		S create(ResourceLocation id, T speciesType, IGenome defaultGenome, B builder);

src/main/java/forestry/apiculture/genetics/Bee.java

@@ -18,6 +18,7 @@
 import java.util.HashSet;
 import java.util.Iterator;
 import java.util.List;
+import java.util.Optional;
 import java.util.Set;
 
 import net.minecraft.core.BlockPos;
@@ -72,26 +73,23 @@ public class Bee extends IndividualLiving<IBeeSpecies, IBee, IBeeSpeciesType> im
 	public static final Codec<Bee> CODEC = RecordCodecBuilder.create(instance -> {
 		Codec<IGenome> genomeCodec = SpeciesUtil.BEE_TYPE.get().getKaryotype().getGenomeCodec();
 
-		return instance.group(
-				genomeCodec.fieldOf("genome").forGetter(IIndividual::getGenome),
-				genomeCodec.optionalFieldOf("mate", null).forGetter(IIndividual::getMate),
+		return IndividualLiving.livingFields(instance, genomeCodec).and(instance.group(
 				Codec.BOOL.fieldOf("pristine").forGetter(IBee::isPristine),
 				Codec.INT.optionalFieldOf("generation", 0).forGetter(IBee::getGeneration)
-		).apply(instance, Bee::new);
+		)).apply(instance, Bee::new);
 	});
 
-	private int generation;
 	private boolean pristine = true;
+	private int generation;
 
 	public Bee(IGenome genome) {
 		super(genome);
 	}
 
-	// for codec. other places should use setters
-	private Bee(IGenome genome, @Nullable IGenome mate, boolean pristine, int generation) {
-		super(genome);
+	// For codec
+	private Bee(IGenome genome, Optional<IGenome> mate, boolean analyzed, int health, int maxHealth, boolean pristine, int generation) {
+		super(genome, mate, analyzed, health, maxHealth);
 
-		this.mate = mate;
 		this.pristine = pristine;
 		this.generation = generation;
 	}
@@ -168,15 +166,6 @@ private IEffectData doFX(IBeeEffect effect, IEffectData storedData, IBeeHousing
 		return effect.doFX(genome, storedData, housing);
 	}
 
-	// / INFORMATION
-
-	/*@Override
-	public IBee copy() {
-		CompoundTag compound = new CompoundTag();
-		this.write(compound);
-		return new Bee(compound);
-	}*/
-
 	@Override
 	public boolean canSpawn() {
 		return mate != null;
@@ -216,43 +205,41 @@ public Set<IError> getCanWork(IBeeHousing housing) {
 			}
 		}
 
-		// / Check for the sky, except if in hell
-		if (!world.dimensionType().hasCeiling()) {//TODO: We used 'isNether' earlier not sure if 'hasCeiling' is the right replacment method
+		// Check for the sky, except if in hell
+		if (!world.dimensionType().hasCeiling()) {
 			if (!housing.canBlockSeeTheSky() && !canWorkUnderground(beeModifier)) {
 				errorStates.add(ForestryError.NO_SKY);
 			}
 		}
 
-		// / And finally climate check
-		IBeeSpecies species = genome.getActiveValue(BeeChromosomes.SPECIES);
-		{
-			TemperatureType actualTemperature = housing.temperature();
-			TemperatureType beeBaseTemperature = species.getTemperature();
-			ToleranceType beeToleranceTemperature = genome.getActiveValue(BeeChromosomes.TEMPERATURE_TOLERANCE);
-
-			if (!ClimateHelper.isWithinLimits(actualTemperature, beeBaseTemperature, beeToleranceTemperature)) {
-				if (beeBaseTemperature.ordinal() > actualTemperature.ordinal()) {
-					errorStates.add(ForestryError.TOO_COLD);
-				} else {
-					errorStates.add(ForestryError.TOO_HOT);
-				}
+		// And finally climate check
+		IBeeSpecies species = this.species;
+
+		TemperatureType actualTemperature = housing.temperature();
+		TemperatureType beeBaseTemperature = species.getTemperature();
+		ToleranceType beeToleranceTemperature = genome.getActiveValue(BeeChromosomes.TEMPERATURE_TOLERANCE);
+
+		if (!ClimateHelper.isWithinLimits(actualTemperature, beeBaseTemperature, beeToleranceTemperature)) {
+			if (beeBaseTemperature.ordinal() > actualTemperature.ordinal()) {
+				errorStates.add(ForestryError.TOO_COLD);
+			} else {
+				errorStates.add(ForestryError.TOO_HOT);
 			}
 		}
 
-		{
-			HumidityType actualHumidity = housing.humidity();
-			HumidityType beeBaseHumidity = species.getHumidity();
-			ToleranceType beeToleranceHumidity = genome.getActiveValue(BeeChromosomes.HUMIDITY_TOLERANCE);
+		HumidityType actualHumidity = housing.humidity();
+		HumidityType beeBaseHumidity = species.getHumidity();
+		ToleranceType beeToleranceHumidity = genome.getActiveValue(BeeChromosomes.HUMIDITY_TOLERANCE);
 
-			if (!ClimateHelper.isWithinLimits(actualHumidity, beeBaseHumidity, beeToleranceHumidity)) {
-				if (beeBaseHumidity.ordinal() > actualHumidity.ordinal()) {
-					errorStates.add(ForestryError.TOO_ARID);
-				} else {
-					errorStates.add(ForestryError.TOO_HUMID);
-				}
+		if (!ClimateHelper.isWithinLimits(actualHumidity, beeBaseHumidity, beeToleranceHumidity)) {
+			if (beeBaseHumidity.ordinal() > actualHumidity.ordinal()) {
+				errorStates.add(ForestryError.TOO_ARID);
+			} else {
+				errorStates.add(ForestryError.TOO_HUMID);
 			}
 		}
 
+
 		return errorStates;
 	}
 
@@ -444,7 +431,7 @@ private IBee createOffspring(IBeeHousing housing, IGenome mate, int generation)
 
 		return SpeciesUtil.createOffspring(housing.getWorldObj().random, this.genome, mate, mutator, genome -> {
 			//IBeekeepingMode mode = BeeManager.beeRoot.getBeekeepingMode(level);
-			return new Bee(genome, null, this.pristine, generation); /*mode.isOffspringPristine(this)*/
+			return new Bee(genome, null, false, this.health, this.maxHealth, this.pristine, generation); /*mode.isOffspringPristine(this)*/
 		});
 	}