Food chain related miche data saving and loading (#5554)

* Made saving/loading miche trees work

* Made food chain show initially after load

src/auto-evo/Miche.cs

@@ -3,6 +3,7 @@
 using System;
 using System.Collections.Generic;
 using System.Linq;
+using Newtonsoft.Json;
 
 /// <summary>
 ///   A node for the Miche Tree
@@ -15,10 +16,24 @@
 ///     For a fuller explanation see docs/auto_evo.md
 ///   </para>
 /// </remarks>
+/// <remarks>
+///   <para>
+///     This is partially saved to be able to display info about the auto-evo run in the editor after loading a save.
+///     This has to be a reference to work with the parent miche reference. This uses Thrive serializer as the fields
+///     can already refer back to this object.
+///   </para>
+/// </remarks>
+[JsonObject(IsReference = true)]
+[UseThriveSerializer]
 public class Miche
 {
+    [JsonProperty]
     public readonly SelectionPressure Pressure;
+
+    [JsonProperty]
     public readonly List<Miche> Children = new();
+
+    [JsonProperty]
     public Miche? Parent;
 
     /// <summary>
@@ -29,6 +44,7 @@ public class Miche
     ///     Occupant should always be null if this Miche is not a leaf node (children is not empty).
     ///   </para>
     /// </remarks>
+    [JsonProperty]
     public Species? Occupant;
 
     public Miche(SelectionPressure pressure)

src/auto-evo/RunResults.cs

@@ -35,6 +35,12 @@ public class RunResults
     // afterwards when loading from a save
     private readonly List<PossibleSpecies> modifiedSpecies = new();
 
+    /// <summary>
+    ///   Miche tree generated for this auto-evo run. This is partially saved (some subobjects are excluded) so that
+    ///   food chain tab information can be displayed after loading a save.
+    /// </summary>
+    [JsonProperty]
+    [JsonConverter(typeof(DictionaryWithJSONKeysConverter<Patch, Miche>))]
     private readonly Dictionary<Patch, Miche> micheByPatch = new();
 
     public enum NewSpeciesType

src/auto-evo/mutation_strategy/IMutationStrategy.cs

@@ -2,10 +2,12 @@
 
 using System;
 using System.Collections.Generic;
+using Newtonsoft.Json;
 
 public interface IMutationStrategy<T>
     where T : Species
 {
+    [JsonIgnore]
     public bool Repeatable { get; }
 
     /// <summary>

src/auto-evo/selection_pressure/AvoidPredationSelectionPressure.cs

@@ -1,7 +1,11 @@
 namespace AutoEvo;
 
+using Newtonsoft.Json;
+
+[JSONDynamicTypeAllowed]
 public class AvoidPredationSelectionPressure : SelectionPressure
 {
+    [JsonProperty]
     public readonly Species Predator;
 
     // Needed for translation extraction
@@ -29,6 +33,7 @@ public AvoidPredationSelectionPressure(Species predator, float weight) : base(we
         Predator = predator;
     }
 
+    [JsonIgnore]
     public override LocalizedString Name => NameString;
 
     public override float Score(Species species, Patch patch, SimulationCache cache)

src/auto-evo/selection_pressure/ChunkCompoundPressure.cs

@@ -1,7 +1,9 @@
 namespace AutoEvo;
 
 using System;
+using Newtonsoft.Json;
 
+[JSONDynamicTypeAllowed]
 public class ChunkCompoundPressure : SelectionPressure
 {
     // Needed for translation extraction
@@ -12,18 +14,28 @@ public class ChunkCompoundPressure : SelectionPressure
 
     private readonly CompoundDefinition atp = SimulationParameters.GetCompound(Compound.ATP);
 
+    [JsonProperty]
     private readonly string chunkType;
+
+    [JsonProperty]
     private readonly LocalizedString readableName;
+
     private readonly CompoundDefinition compound;
 
+    // Needed for saving to work
+    [JsonProperty(nameof(compound))]
+    private readonly Compound compoundRaw;
+
     public ChunkCompoundPressure(string chunkType, LocalizedString readableName, Compound compound, float weight) :
         base(weight, [])
     {
+        compoundRaw = compound;
         this.compound = SimulationParameters.GetCompound(compound);
         this.chunkType = chunkType;
         this.readableName = readableName;
     }
 
+    [JsonIgnore]
     public override LocalizedString Name => NameString;
 
     public override float Score(Species species, Patch patch, SimulationCache cache)

src/auto-evo/selection_pressure/CompoundCloudPressure.cs

@@ -1,7 +1,9 @@
 namespace AutoEvo;
 
 using System;
+using Newtonsoft.Json;
 
+[JSONDynamicTypeAllowed]
 public class CompoundCloudPressure : SelectionPressure
 {
     // Needed for translation extraction
@@ -10,8 +12,12 @@ public class CompoundCloudPressure : SelectionPressure
 
     // ReSharper restore ArrangeObjectCreationWhenTypeEvident
 
+    [JsonProperty]
     private readonly Compound compound;
+
     private readonly CompoundDefinition compoundDefinition;
+
+    [JsonProperty]
     private readonly bool isDayNightCycleEnabled;
 
     public CompoundCloudPressure(Compound compound, bool isDayNightCycleEnabled, float weight) :
@@ -29,6 +35,7 @@ public CompoundCloudPressure(Compound compound, bool isDayNightCycleEnabled, flo
         this.isDayNightCycleEnabled = isDayNightCycleEnabled;
     }
 
+    [JsonIgnore]
     public override LocalizedString Name => NameString;
 
     public override float Score(Species species, Patch patch, SimulationCache cache)

src/auto-evo/selection_pressure/CompoundConversionEfficiencyPressure.cs

@@ -1,8 +1,14 @@
 namespace AutoEvo;
 
+using Newtonsoft.Json;
+
+[JSONDynamicTypeAllowed]
 public class CompoundConversionEfficiencyPressure : SelectionPressure
 {
+    [JsonIgnore]
     public readonly CompoundDefinition FromCompound;
+
+    [JsonIgnore]
     public readonly CompoundDefinition ToCompound;
 
     // Needed for translation extraction
@@ -11,16 +17,27 @@ public class CompoundConversionEfficiencyPressure : SelectionPressure
 
     // ReSharper restore ArrangeObjectCreationWhenTypeEvident
 
+    // These two are needed purely for saving to work
+    [JsonProperty]
+    private readonly Compound compound;
+
+    [JsonProperty]
+    private readonly Compound outCompound;
+
     public CompoundConversionEfficiencyPressure(Compound compound, Compound outCompound, float weight) :
         base(weight, [
             AddOrganelleAnywhere.ThatConvertBetweenCompounds(compound, outCompound),
             RemoveOrganelle.ThatCreateCompound(outCompound),
         ])
     {
+        this.compound = compound;
+        this.outCompound = outCompound;
+
         FromCompound = SimulationParameters.GetCompound(compound);
         ToCompound = SimulationParameters.GetCompound(outCompound);
     }
 
+    [JsonIgnore]
     public override LocalizedString Name => NameString;
 
     public override float Score(Species species, Patch patch, SimulationCache cache)

src/auto-evo/selection_pressure/EnvironmentalCompoundPressure.cs

@@ -1,7 +1,9 @@
 namespace AutoEvo;
 
 using System;
+using Newtonsoft.Json;
 
+[JSONDynamicTypeAllowed]
 public class EnvironmentalCompoundPressure : SelectionPressure
 {
     // Needed for translation extraction
@@ -14,14 +16,26 @@ public class EnvironmentalCompoundPressure : SelectionPressure
 
     private readonly CompoundDefinition createdCompound;
     private readonly CompoundDefinition compound;
+
+    [JsonProperty]
     private readonly float energyMultiplier;
 
+    // These two are needed purely for saving to work
+    [JsonProperty(nameof(compound))]
+    private readonly Compound compoundRaw;
+
+    [JsonProperty(nameof(createdCompound))]
+    private readonly Compound createdCompoundRaw;
+
     public EnvironmentalCompoundPressure(Compound compound, Compound createdCompound, float energyMultiplier,
         float weight) :
         base(weight, [
             AddOrganelleAnywhere.ThatUseCompound(compound),
         ])
     {
+        compoundRaw = compound;
+        createdCompoundRaw = createdCompound;
+
         this.compound = SimulationParameters.GetCompound(compound);
 
         if (this.compound.IsCloud)
@@ -36,6 +50,7 @@ public EnvironmentalCompoundPressure(Compound compound, Compound createdCompound
         this.energyMultiplier = energyMultiplier;
     }
 
+    [JsonIgnore]
     public override LocalizedString Name => NameString;
 
     public override float Score(Species species, Patch patch, SimulationCache cache)

src/auto-evo/selection_pressure/MaintainCompoundPressure.cs

@@ -1,7 +1,9 @@
 namespace AutoEvo;
 
 using System;
+using Newtonsoft.Json;
 
+[JSONDynamicTypeAllowed]
 public class MaintainCompoundPressure : SelectionPressure
 {
     // Needed for translation extraction
@@ -12,14 +14,20 @@ public class MaintainCompoundPressure : SelectionPressure
 
     private readonly CompoundDefinition compound;
 
+    // Needed for saving to work
+    [JsonProperty(nameof(compound))]
+    private readonly Compound compoundRaw;
+
     public MaintainCompoundPressure(Compound compound, float weight) : base(weight, [
         AddOrganelleAnywhere.ThatCreateCompound(compound),
         RemoveOrganelle.ThatUseCompound(compound),
     ])
     {
+        compoundRaw = compound;
         this.compound = SimulationParameters.GetCompound(compound);
     }
 
+    [JsonIgnore]
     public override LocalizedString Name => NameString;
 
     public override float Score(Species species, Patch patch, SimulationCache cache)

src/auto-evo/selection_pressure/MetabolicStabilityPressure.cs

@@ -1,5 +1,8 @@
 namespace AutoEvo;
 
+using Newtonsoft.Json;
+
+[JSONDynamicTypeAllowed]
 public class MetabolicStabilityPressure : SelectionPressure
 {
     // Needed for translation extraction
@@ -15,6 +18,7 @@ public MetabolicStabilityPressure(float weight) : base(weight, [
     {
     }
 
+    [JsonIgnore]
     public override LocalizedString Name => NameString;
 
     public override float Score(Species species, Patch patch, SimulationCache cache)

src/auto-evo/selection_pressure/NoOpPressure.cs

@@ -1,8 +1,11 @@
 namespace AutoEvo;
 
+using Newtonsoft.Json;
+
 /// <summary>
 ///   This pressure does nothing, but is used as a placeholder node in the Miche Tree
 /// </summary>
+[JSONDynamicTypeAllowed]
 public class NoOpPressure : SelectionPressure
 {
     // Needed for translation extraction
@@ -15,6 +18,7 @@ public NoOpPressure() : base(1, [])
     {
     }
 
+    [JsonIgnore]
     public override LocalizedString Name => NameString;
 
     public override float Score(Species species, Patch patch, SimulationCache cache)

src/auto-evo/selection_pressure/PredationEffectivenessPressure.cs

@@ -1,7 +1,11 @@
 namespace AutoEvo;
 
+using Newtonsoft.Json;
+
+[JSONDynamicTypeAllowed]
 public class PredationEffectivenessPressure : SelectionPressure
 {
+    [JsonProperty]
     public readonly Species Prey;
 
     // Needed for translation extraction
@@ -28,6 +32,7 @@ public PredationEffectivenessPressure(Species prey, float weight) :
         Prey = prey;
     }
 
+    [JsonIgnore]
     public override LocalizedString Name => NameString;
 
     public override float Score(Species species, Patch patch, SimulationCache cache)

src/auto-evo/selection_pressure/PredatorRoot.cs

@@ -1,5 +1,8 @@
 namespace AutoEvo;
 
+using Newtonsoft.Json;
+
+[JSONDynamicTypeAllowed]
 public class PredatorRoot : SelectionPressure
 {
     // Needed for translation extraction
@@ -17,6 +20,7 @@ public PredatorRoot(float weight) : base(weight, [
     {
     }
 
+    [JsonIgnore]
     public override LocalizedString Name => NameString;
 
     public override float Score(Species species, Patch patch, SimulationCache cache)

src/auto-evo/selection_pressure/RootPressure.cs

@@ -1,5 +1,8 @@
 namespace AutoEvo;
 
+using Newtonsoft.Json;
+
+[JSONDynamicTypeAllowed]
 public class RootPressure : SelectionPressure
 {
     // Needed for translation extraction
@@ -16,6 +19,7 @@ public RootPressure() : base(1, [
     {
     }
 
+    [JsonIgnore]
     public override LocalizedString Name => NameString;
 
     public override float Score(Species species, Patch patch, SimulationCache cache)