Fix processes' toggle buttons not matching their actual state

src/general/world_effects/PhotosynthesisProductionEffect.cs

@@ -50,6 +50,8 @@ private void ApplyCompoundsAddition()
             float oxygenBalance = 0;
             float co2Balance = 0;
 
+            Dictionary<BioProcess, float> tempStorage = new();
+
             foreach (var species in patch.SpeciesInPatch)
             {
                 // Only microbial photosynthesis and respiration are taken into account
@@ -67,7 +69,7 @@ private void ApplyCompoundsAddition()
                 if (balance.TotalConsumption < balance.TotalProduction)
                     balanceModifier = balance.TotalConsumption / balance.TotalProduction;
 
-                ProcessSystem.ComputeActiveProcessList(microbeSpecies.Organelles, ref microbeProcesses);
+                ProcessSystem.ComputeActiveProcessList(microbeSpecies.Organelles, ref microbeProcesses, tempStorage);
 
                 foreach (var process in microbeProcesses)
                 {

src/gui_common/ChemicalEquation.cs

@@ -59,8 +59,6 @@ public partial class ChemicalEquation : VBoxContainer
     /// </summary>
     private bool hasNoInputs;
 
-    private bool lastToggle = true;
-
     [Signal]
     public delegate void ToggleProcessPressedEventHandler(ChemicalEquation thisEquation);
 
@@ -102,14 +100,22 @@ public bool ShowToggle
 
     public bool ProcessEnabled
     {
-        get => lastToggle;
+        get
+        {
+            if (EquationFromProcess == null)
+                return true;
+
+            return EquationFromProcess.Enabled;
+        }
         set
         {
-            if (value == lastToggle)
+            if (EquationFromProcess == null)
+            {
+                GD.PrintErr("Display info isn't assigned to a ChemicalEquation, can't toggle process");
                 return;
+            }
 
-            lastToggle = value;
-            ApplyProcessToggleValue();
+            EmitSignal(SignalName.ToggleProcessPressed, this, value);
         }
     }
 
@@ -149,7 +155,6 @@ public bool ShowFullSecondText
     public override void _Ready()
     {
         UpdateEquation();
-        ApplyProcessToggleValue();
     }
 
     public override void _EnterTree()
@@ -245,6 +250,8 @@ private void UpdateEquation()
 
         // Environment conditions
         UpdateEnvironmentPart(environmentalInputs);
+
+        ApplyProcessToggleValue();
     }
 
     private void UpdateHeader()
@@ -376,8 +383,6 @@ private string GetEnvironmentLabelText()
     private void ToggleButtonPressed(bool toggled)
     {
         ProcessEnabled = toggled;
-
-        EmitSignal(SignalName.ToggleProcessPressed, this);
     }
 
     private void ApplyProcessToggleValue()

src/microbe_stage/IProcessDisplayInfo.cs

@@ -43,6 +43,8 @@ public interface IProcessDisplayInfo : IEquatable<IProcessDisplayInfo>
     /// </summary>
     public float CurrentSpeed { get; }
 
+    public bool Enabled { get; }
+
     /// <summary>
     ///   The limiting compounds in speed. Or null if not set
     /// </summary>

src/microbe_stage/MicrobeHUD.cs

@@ -841,7 +841,7 @@ private void OnTranslationsChanged()
         UpdateColonySizeForMacroscopic();
     }
 
-    private void ToggleProcessPressed(ChemicalEquation equation)
+    private void ToggleProcessPressed(ChemicalEquation equation, bool enabled)
     {
         if (!stage!.HasAlivePlayer || !stage.Player.Has<BioProcesses>())
             return;
@@ -852,9 +852,26 @@ private void ToggleProcessPressed(ChemicalEquation equation)
             return;
         }
 
-        ref var processes = ref stage.Player.Get<BioProcesses>();
+        if (stage.Player.Has<MicrobeColony>())
+        {
+            ref var colony = ref stage.Player.Get<MicrobeColony>();
+
+            foreach (var colonyMember in colony.ColonyMembers)
+            {
+                ref var bioProcesses = ref colonyMember.Get<BioProcesses>();
+                ToggleProcessOnEntity(equation, enabled, ref bioProcesses);
+            }
+        }
+        else
+        {
+            ref var bioProcesses = ref stage.Player.Get<BioProcesses>();
+            ToggleProcessOnEntity(equation, enabled, ref bioProcesses);
+        }
+    }
 
-        var activeProcesses = processes.ActiveProcesses;
+    private void ToggleProcessOnEntity(ChemicalEquation equation, bool enabled, ref BioProcesses bioProcesses)
+    {
+        var activeProcesses = bioProcesses.ActiveProcesses;
 
         if (activeProcesses == null)
             return;
@@ -864,10 +881,10 @@ private void ToggleProcessPressed(ChemicalEquation equation)
         for (int i = 0; i < processesCount; ++i)
         {
             // Update speed of the process controlled by the GUI control that signaled this change
-            if (equation.EquationFromProcess.MatchesUnderlyingProcess(activeProcesses[i].Process))
+            if (equation.EquationFromProcess!.MatchesUnderlyingProcess(activeProcesses[i].Process))
             {
                 var process = activeProcesses[i];
-                process.SpeedMultiplier = equation.ProcessEnabled ? 1 : 0;
+                process.SpeedMultiplier = enabled ? 1 : 0;
                 activeProcesses[i] = process;
             }
         }

src/microbe_stage/MicrobeStage.cs

@@ -634,6 +634,7 @@ public override void OnReturnFromEditor()
 
         var workData1 = new List<Hex>();
         var workData2 = new List<Hex>();
+        var tempMemory = new Dictionary<BioProcess, float>();
 
         var playerSpecies = Player.Get<SpeciesMember>().Species;
 
@@ -650,13 +651,13 @@ public override void OnReturnFromEditor()
             earlySpeciesType.MulticellularCellType = earlySpeciesType.Species.Cells[0].CellType;
 
             cellProperties.ReApplyCellTypeProperties(Player, earlySpeciesType.MulticellularCellType,
-                earlySpeciesType.Species, WorldSimulation, workData1, workData2);
+                earlySpeciesType.Species, WorldSimulation, workData1, workData2, tempMemory);
         }
         else
         {
             ref var species = ref Player.Get<MicrobeSpeciesMember>();
             cellProperties.ReApplyCellTypeProperties(Player, species.Species, species.Species, WorldSimulation,
-                workData1, workData2);
+                workData1, workData2, tempMemory);
         }
 
         var playerPosition = Player.Get<WorldPosition>().Position;

src/microbe_stage/MicrobeVisualOnlySimulation.cs

@@ -15,6 +15,7 @@ public sealed class MicrobeVisualOnlySimulation : WorldSimulation
 
     private readonly List<Hex> hexWorkData1 = new();
     private readonly List<Hex> hexWorkData2 = new();
+    private readonly Dictionary<BioProcess, float> tempProcessListMemory = new();
 
     // Base systems
     private AnimationControlSystem animationControlSystem = null!;
@@ -143,7 +144,8 @@ public void ApplyNewVisualisationMicrobeSpecies(Entity microbe, MicrobeSpecies s
 
         // Do a full update apply with the general code method
         ref var cellProperties = ref microbe.Get<CellProperties>();
-        cellProperties.ReApplyCellTypeProperties(microbe, species, species, this, hexWorkData1, hexWorkData2);
+        cellProperties.ReApplyCellTypeProperties(microbe, species, species, this, hexWorkData1, hexWorkData2,
+            tempProcessListMemory);
 
         // TODO: update species member component if species changed?
     }

src/microbe_stage/ProcessList.cs

@@ -88,8 +88,6 @@ private ChemicalEquation CreateEquation(StrictProcessDisplayInfoEquality process
 
         equation.Connect(SignalName.ToggleProcessPressed, new Callable(this, nameof(HandleToggleProcess)));
 
-        equation.ProcessEnabled = process.DisplayInfo.CurrentSpeed > 0;
-
         if (ProcessesTitleColour != null)
             equation.DefaultTitleFont = ProcessesTitleColour;
 
@@ -99,8 +97,8 @@ private ChemicalEquation CreateEquation(StrictProcessDisplayInfoEquality process
         return equation;
     }
 
-    private void HandleToggleProcess(ChemicalEquation equation)
+    private void HandleToggleProcess(ChemicalEquation equation, bool enabled)
     {
-        EmitSignal(SignalName.ToggleProcessPressed, equation);
+        EmitSignal(SignalName.ToggleProcessPressed, equation, enabled);
     }
 }

src/microbe_stage/ProcessPanel.cs

@@ -64,8 +64,8 @@ protected override void Dispose(bool disposing)
         base.Dispose(disposing);
     }
 
-    private void ToggleProcessToggled(ChemicalEquation equation)
+    private void ToggleProcessToggled(ChemicalEquation equation, bool enabled)
     {
-        EmitSignal(SignalName.ToggleProcessPressed, equation);
+        EmitSignal(SignalName.ToggleProcessPressed, equation, enabled);
     }
 }

src/microbe_stage/ProcessSpeedInformation.cs

@@ -39,6 +39,8 @@ public ProcessSpeedInformation(BioProcess process)
 
     public float CurrentSpeed { get; set; }
 
+    public bool Enabled => true;
+
     /// <summary>
     ///   Efficiency is a measure of how well the environment is favorable to the process.
     /// </summary>

src/microbe_stage/ProcessStatistics.cs

@@ -15,24 +15,19 @@ public class ProcessStatistics
     ///   a ThreadLocal in <see cref="Systems.ProcessSystem"/> as that was causing the game process to lock up in
     ///   Godot 4 (for unknown reasons). See: https://github.com/Revolutionary-Games/Thrive/issues/4989 for context.
     /// </summary>
-    private List<BioProcess>? temporaryRemovedItems;
+    private List<TweakedProcess>? temporaryRemovedItems;
 
     /// <summary>
     ///   The processes and their associated speed statistics
     /// </summary>
     /// <remarks>
     ///   <para>
-    ///     This uses <see cref="BioProcess"/> rather than <see cref="TweakedProcess"/> as the key so that equality
-    ///     comparison matches based on the process type not the process type and speed. All processables should
-    ///     combine their processes to run correctly with speed tracking.
-    ///   </para>
-    ///   <para>
     ///     This is JSON ignore to ensure that this object can exist in saves, but won't store non-savable information
     ///     like the process statistics object. That's the situation now but maybe some other design would be better...
     ///   </para>
     /// </remarks>
     [JsonIgnore]
-    public Dictionary<BioProcess, SingleProcessStatistics> Processes { get; } = new();
+    public Dictionary<TweakedProcess, SingleProcessStatistics> Processes { get; } = new();
 
     public void MarkAllUnused()
     {
@@ -49,7 +44,7 @@ public void RemoveUnused()
     {
         lock (Processes)
         {
-            temporaryRemovedItems ??= new List<BioProcess>();
+            temporaryRemovedItems ??= new List<TweakedProcess>();
 
             foreach (var entry in Processes)
             {
@@ -71,13 +66,12 @@ public void RemoveUnused()
         }
     }
 
-    public SingleProcessStatistics GetAndMarkUsed(BioProcess forProcess)
+    public SingleProcessStatistics GetAndMarkUsed(TweakedProcess forProcess)
     {
 #if DEBUG
-        if (forProcess == null!)
+        if (forProcess.Process == null!)
             throw new ArgumentException("Invalid process marked used");
 #endif
-
         lock (Processes)
         {
             if (Processes.TryGetValue(forProcess, out var entry))
@@ -109,7 +103,7 @@ public class SingleProcessStatistics : IProcessDisplayInfo
 
     private Dictionary<Compound, float>? precomputedEnvironmentInputs;
 
-    public SingleProcessStatistics(BioProcess process,
+    public SingleProcessStatistics(TweakedProcess process,
         float keepSnapshotTime = Constants.DEFAULT_PROCESS_STATISTICS_AVERAGE_INTERVAL)
     {
         this.keepSnapshotTime = keepSnapshotTime;
@@ -120,11 +114,11 @@ public SingleProcessStatistics(BioProcess process,
     /// <summary>
     ///   The process these statistics are for
     /// </summary>
-    public BioProcess Process { get; }
+    public TweakedProcess Process { get; }
 
     public bool Used { get; internal set; }
 
-    public string Name => Process.Name;
+    public string Name => Process.Process.Name;
 
     public IEnumerable<KeyValuePair<Compound, float>> Inputs =>
         LatestSnapshot?.Inputs.Where(p => !IProcessDisplayInfo.IsEnvironmental(p.Key)) ??
@@ -135,7 +129,7 @@ public SingleProcessStatistics(BioProcess process,
         throw new InvalidOperationException("No snapshot set");
 
     public IReadOnlyDictionary<Compound, float> FullSpeedRequiredEnvironmentalInputs =>
-        precomputedEnvironmentInputs ??= Process.Inputs
+        precomputedEnvironmentInputs ??= Process.Process.Inputs
             .Where(p => IProcessDisplayInfo.IsEnvironmental(p.Key.ID))
             .ToDictionary(p => p.Key.ID, p => p.Value);
 
@@ -154,6 +148,8 @@ public float CurrentSpeed
         }
     }
 
+    public bool Enabled => Process.SpeedMultiplier > 0.5f;
+
     public IReadOnlyList<Compound>? LimitingCompounds => LatestSnapshot?.LimitingCompounds;
 
     private SingleProcessStatisticsSnapshot? LatestSnapshot =>
@@ -296,7 +292,7 @@ public void Clear()
 
     public bool MatchesUnderlyingProcess(BioProcess process)
     {
-        return Process == process;
+        return Process.Process == process;
     }
 
     public bool Equals(IProcessDisplayInfo? other)
@@ -394,9 +390,13 @@ public AverageProcessStatistics(SingleProcessStatistics owner)
     public float CurrentSpeed { get; set; }
     public IReadOnlyList<Compound> LimitingCompounds => WritableLimitingCompounds;
 
+    public TweakedProcess Process => owner.Process;
+
+    public bool Enabled => owner.Process.SpeedMultiplier > 0.5f;
+
     public bool MatchesUnderlyingProcess(BioProcess process)
     {
-        return owner.Process == process;
+        return owner.Process.Process == process;
     }
 
     public bool Equals(IProcessDisplayInfo? other)

src/microbe_stage/Spawners.cs

@@ -571,9 +571,10 @@ public static float SpawnMicrobeWithoutFinalizing(IWorldSimulation worldSimulati
             // just need to accept that spawning a microbe allocates a bit of temporary unnecessary memory
             var workData1 = new List<Hex>();
             var workData2 = new List<Hex>();
+            var tempMemory = new Dictionary<BioProcess, float>();
 
             container.CreateOrganelleLayout(usedCellDefinition, workData1, workData2);
-            container.RecalculateOrganelleBioProcesses(ref bioProcesses);
+            container.RecalculateOrganelleBioProcesses(ref bioProcesses, tempMemory);
 
             organelleCount = container.Organelles!.Count;
 

src/microbe_stage/TweakedProcess.cs

@@ -50,7 +50,8 @@ public bool Equals(TweakedProcess other)
             return false;
 
         // ReSharper disable once CompareOfFloatsByEqualityOperator
-        return Rate == other.Rate && ReferenceEquals(Process, other.Process);
+        return Rate == other.Rate && SpeedMultiplier == other.SpeedMultiplier
+            && ReferenceEquals(Process, other.Process);
     }
 
     public TweakedProcess Clone()

src/microbe_stage/components/CellProperties.cs

@@ -521,9 +521,10 @@ public static Vector3 CalculateExternalOrganellePosition(this ref CellProperties
     /// </param>
     /// <param name="workMemory1">Temporary memory used for organelle copying</param>
     /// <param name="workMemory2">More temporary memory</param>
+    /// <param name="tempStorage">Even more temporary memory</param>
     public static void ReApplyCellTypeProperties(this ref CellProperties cellProperties, in Entity entity,
         ICellDefinition newDefinition, Species baseReproductionCostFrom, IWorldSimulation worldSimulation,
-        List<Hex> workMemory1, List<Hex> workMemory2)
+        List<Hex> workMemory1, List<Hex> workMemory2, Dictionary<BioProcess, float> tempStorage)
     {
         // Copy new cell type properties
         cellProperties.MembraneType = newDefinition.MembraneType;
@@ -550,7 +551,7 @@ public static void ReApplyCellTypeProperties(this ref CellProperties cellPropert
         // Reset all the duplicates organelles / reproduction progress of the entity
         // This also resets multicellular creature's reproduction progress
         organelleContainer.ResetOrganelleLayout(ref entity.Get<CompoundStorage>(), ref entity.Get<BioProcesses>(),
-            entity, newDefinition, baseReproductionCostFrom, worldSimulation, workMemory1, workMemory2);
+            entity, newDefinition, baseReproductionCostFrom, worldSimulation, workMemory1, workMemory2, tempStorage);
 
         // Reset runtime colour
         if (entity.Has<ColourAnimation>())