Renamed main MicrobeSpecies organelles to ModifiableOrganelles

Thrive.csproj

@@ -103,8 +103,7 @@
   <ItemGroup>
     <ProjectReference Include="RevolutionaryGamesCommon\LauncherThriveShared\LauncherThriveShared.csproj" />
     <ProjectReference Include="RevolutionaryGamesCommon\SharedBase\SharedBase.csproj" />
-    <ProjectReference Include="third_party\Arch.Extended\Arch.System.SourceGenerator\Arch.System.SourceGenerator.csproj" 
-                      OutputItemType="Analyzer" ReferenceOutputAssembly="false" />
+    <ProjectReference Include="third_party\Arch.Extended\Arch.System.SourceGenerator\Arch.System.SourceGenerator.csproj" OutputItemType="Analyzer" ReferenceOutputAssembly="false" />
     <ProjectReference Include="third_party\Arch.Extended\Arch.System\Arch.System.csproj" />
     <ProjectReference Include="third_party\Arch\src\Arch\Arch.csproj" />
     <ProjectReference Include="third_party\ThirdParty.csproj" />

Thrive.csproj.old.1

@@ -0,0 +1,119 @@
+<?xml version="1.0" encoding="utf-8"?>
+<Project Sdk="Godot.NET.Sdk/4.5.1">
+  <PropertyGroup>
+    <TreatWarningsAsErrors>false</TreatWarningsAsErrors>
+    <TargetFramework>net10.0</TargetFramework>
+    <TargetFramework Condition=" '$(GodotTargetPlatform)' == 'android' ">net9.0</TargetFramework>
+    <TargetFramework Condition=" '$(GodotTargetPlatform)' == 'ios' ">net8.0</TargetFramework>
+    <EnableDynamicLoading>true</EnableDynamicLoading>
+    <LangVersion>14</LangVersion>
+    <Nullable>enable</Nullable>
+    <Company>Revolutionary Games Studio</Company>
+    <Version>1.0.0.0</Version>
+    <!--<InformationalVersion>-beta</InformationalVersion>-->
+    <CopyLocalLockFileAssemblies>true</CopyLocalLockFileAssemblies>
+  </PropertyGroup>
+  <!-- Ignore the subproject source files -->
+  <PropertyGroup>
+    <DefaultItemExcludes>
+      $(DefaultItemExcludes);Scripts\**\*;ThriveScriptsShared\**\*;test\code_tests\**\*;test\code_benchmarks\**\*;RevolutionaryGamesCommon\**\*;third_party\**\*
+    </DefaultItemExcludes>
+  </PropertyGroup>
+  <!-- Ignore exporting tests when making release build of Thrive -->
+  <PropertyGroup>
+    <DefaultItemExcludes Condition="'$(Configuration)' == 'ExportRelease'">
+      $(DefaultItemExcludes);test/**/*;addons\gdUnit4\**\*
+    </DefaultItemExcludes>
+  </PropertyGroup>
+  <!-- Non-Steam build needs to skip this file -->
+  <ItemGroup>
+    <Compile Remove="src\steam\SteamClient.cs" />
+  </ItemGroup>
+  <!-- In case the hot reload in Godot editor would fail with the system JSON referenced, this single file is picked out -->
+  <ItemGroup>
+    <Compile Include="RevolutionaryGamesCommon\DevCenterCommunication\Models\Enums\PrecompiledTag.cs" />
+  </ItemGroup>
+  <ItemGroup>
+    <Folder Include="shaders\" />
+    <Folder Include="src\auto-evo\steps\" />
+    <Folder Include="src\auto-evo\simulation\" />
+  </ItemGroup>
+  <!-- Test resources -->
+  <ItemGroup Condition="'$(Configuration)' != 'ExportRelease'">
+    <PackageReference Include="gdUnit4.api" Version="5.1.0-rc3" />
+    <PackageReference Include="gdUnit4.test.adapter" Version="3.0.0" />
+    <!-- Re-enable this this once newer compiler versions are deployed everywhere
+    <PackageReference Include="gdUnit4.analyzers" Version="1.0.0">
+      <PrivateAssets>none</PrivateAssets>
+      <IncludeAssets>runtime; build; native; contentfiles; analyzers; buildtransitive</IncludeAssets>
+    </PackageReference> -->
+    <PackageReference Include="Microsoft.NET.Test.Sdk" Version="18.0.1" />
+  </ItemGroup>
+  <ItemGroup>
+    <PackageReference Include="AngleSharp" Version="1.4.0" />
+    <PackageReference Include="GraphShape" Version="1.2.1" />
+    <PackageReference Include="JetBrains.Annotations" Version="2025.2.4" />
+    <PackageReference Include="Newtonsoft.Json" Version="13.0.4" />
+    <PackageReference Include="System.IO.Hashing" Version="10.0.1" />
+    <PackageReference Include="Nito.Collections.Deque" Version="1.2.1" />
+    <PackageReference Include="XoshiroPRNG.Net" Version="1.6.0" />
+    <PackageReference Include="YamlDotNet" Version="16.3.0" />
+    <PackageReference Include="StyleCop.Analyzers" Version="1.2.0-beta.556" PrivateAssets="all" />
+    <PackageReference Include="Microsoft.CodeAnalysis.NetAnalyzers" Version="10.0.101" PrivateAssets="all" />
+  </ItemGroup>
+  <ItemGroup>
+    <Content Include=".config\dotnet-tools.json" />
+    <Content Include="export_presets.cfg" />
+    <Content Include="global.json" />
+    <Content Include="README.md" />
+    <Content Include="RevolutionaryGamesCommon\stylecop.json" />
+    <Content Include="RevolutionaryGamesCommon\StyleCop.ruleset" />
+    <Content Include="simulation_parameters\awakening_stage\crafting_recipes.json" />
+    <Content Include="simulation_parameters\awakening_stage\equipment.json" />
+    <Content Include="simulation_parameters\awakening_stage\structures.json" />
+    <Content Include="simulation_parameters\awakening_stage\technologies.json" />
+    <Content Include="simulation_parameters\awakening_stage\world_resources.json" />
+    <Content Include="simulation_parameters\common\achievements.json" />
+    <Content Include="simulation_parameters\common\auto-evo_parameters.json" />
+    <Content Include="simulation_parameters\common\credits.json" />
+    <Content Include="simulation_parameters\common\difficulty_presets.json" />
+    <Content Include="simulation_parameters\common\gallery.json" />
+    <Content Include="simulation_parameters\common\help_texts.json" />
+    <Content Include="simulation_parameters\common\input_options.json" />
+    <Content Include="simulation_parameters\common\music_tracks.json" />
+    <Content Include="simulation_parameters\common\patch_notes.yml" />
+    <Content Include="simulation_parameters\common\screen_effects.json" />
+    <Content Include="simulation_parameters\common\stage_resources.json" />
+    <Content Include="simulation_parameters\common\translations_info.json" />
+    <Content Include="simulation_parameters\common\visual_resources.json" />
+    <Content Include="simulation_parameters\common\wiki.json" />
+    <Content Include="simulation_parameters\industrial_stage\units.json" />
+    <Content Include="simulation_parameters\microbe_stage\backgrounds.json" />
+    <Content Include="simulation_parameters\microbe_stage\biomes.json" />
+    <Content Include="simulation_parameters\microbe_stage\bio_processes.json" />
+    <Content Include="simulation_parameters\microbe_stage\compounds.json" />
+    <Content Include="simulation_parameters\microbe_stage\enzymes.json" />
+    <Content Include="simulation_parameters\microbe_stage\membranes.json" />
+    <Content Include="simulation_parameters\microbe_stage\meteors.json" />
+    <Content Include="simulation_parameters\microbe_stage\organelles.json" />
+    <Content Include="simulation_parameters\microbe_stage\patch_syllables.json" />
+    <Content Include="simulation_parameters\microbe_stage\species_names.json" />
+    <Content Include="simulation_parameters\space_stage\space_structures.json" />
+  </ItemGroup>
+  <ItemGroup>
+    <ProjectReference Include="RevolutionaryGamesCommon\LauncherThriveShared\LauncherThriveShared.csproj" />
+    <ProjectReference Include="RevolutionaryGamesCommon\SharedBase\SharedBase.csproj" />
+    <ProjectReference Include="third_party\Arch.Extended\Arch.System.SourceGenerator\Arch.System.SourceGenerator.csproj" OutputItemType="Analyzer" ReferenceOutputAssembly="false" />
+    <ProjectReference Include="third_party\Arch.Extended\Arch.System\Arch.System.csproj" />
+    <ProjectReference Include="third_party\Arch\src\Arch\Arch.csproj" />
+    <ProjectReference Include="third_party\ThirdParty.csproj" />
+    <ProjectReference Include="ThriveScriptsShared\ThriveScriptsShared.csproj" />
+  </ItemGroup>
+  <!-- StyleCop Analyzers configuration -->
+  <PropertyGroup>
+    <CodeAnalysisRuleSet>$(MSBuildThisFileDirectory)RevolutionaryGamesCommon/StyleCop.ruleset</CodeAnalysisRuleSet>
+  </PropertyGroup>
+  <ItemGroup>
+    <AdditionalFiles Include="$(MSBuildThisFileDirectory)RevolutionaryGamesCommon/stylecop.json" Link="stylecop.json" />
+  </ItemGroup>
+</Project>

src/auto-evo/AutoEvoExploringTool.Export.cs

@@ -100,11 +100,11 @@ private void ExportCurrentWorldSpeciesHistory(string basePath)
                         microbeSpecies.BaseRotationSpeed.ToString(CultureInfo.InvariantCulture),
                         microbeSpecies.StorageCapacities.Nominal.ToString(CultureInfo.InvariantCulture),
                         microbeSpecies.IsBacteria.ToString(),
-                        microbeSpecies.Organelles.Count.ToString(),
+                        microbeSpecies.ReadonlyOrganelles.Count.ToString(),
                     });
 
                     data.AddRange(allOrganelles
-                        .Select(d => microbeSpecies.Organelles.Count(t => t.Definition == d).ToString()));
+                        .Select(d => microbeSpecies.ReadonlyOrganelles.Count(t => t.Definition == d).ToString()));
                 }
                 else
                 {

src/auto-evo/AutoEvoExploringTool.cs

@@ -1169,18 +1169,20 @@ public void UpdateWorldStatistics()
             foreach (var organelle in SimulationParameters.Instance.GetAllOrganelles())
             {
                 MicrobeSpeciesOrganelleStatistics[organelle] = (
-                    microbeSpecies.Average(s => s.Organelles.Any(o => o.Definition == organelle) ? 1 : 0),
-                    microbeSpecies.Average(s => s.Organelles.Count(o => o.Definition == organelle)));
+                    microbeSpecies.Average(s => s.ReadonlyOrganelles.Any(o => o.Definition == organelle) ? 1 : 0),
+                    microbeSpecies.Average(s => s.ReadonlyOrganelles.Count(o => o.Definition == organelle)));
             }
 
             foreach (var upgradeName in MicrobeSpeciesUpgradesStatistics.Keys)
             {
                 MicrobeSpeciesUpgradesStatistics[upgradeName] = (
                     MicrobeSpeciesUpgradesStatistics[upgradeName].Name,
                     microbeSpecies.Average(s =>
-                        s.Organelles.Any(o => o.Upgrades?.UnlockedFeatures.Contains(upgradeName) ?? false) ? 1 : 0),
+                        s.ReadonlyOrganelles.Any(o => o.Upgrades?.UnlockedFeatures.Contains(upgradeName) ?? false) ?
+                            1 :
+                            0),
                     microbeSpecies.Average(s =>
-                        s.Organelles.Count(o => o.Upgrades?.UnlockedFeatures.Contains(upgradeName) ?? false)));
+                        s.ReadonlyOrganelles.Count(o => o.Upgrades?.UnlockedFeatures.Contains(upgradeName) ?? false)));
             }
 
             foreach (var membrane in SimulationParameters.Instance.GetAllMembranes())
@@ -1192,11 +1194,11 @@ public void UpdateWorldStatistics()
             foreach (var enzyme in MicrobeSpeciesEnzymesStatistics.Keys)
             {
                 MicrobeSpeciesEnzymesStatistics[enzyme] = (
-                    microbeSpecies.Average(s => s.Organelles.Any(o =>
+                    microbeSpecies.Average(s => s.ReadonlyOrganelles.Any(o =>
                         o.Definition.Enzymes.TryGetValue(enzyme, out var value) && value > 0) ?
                         1 :
                         0),
-                    microbeSpecies.Average(s => s.Organelles.Count(o =>
+                    microbeSpecies.Average(s => s.ReadonlyOrganelles.Count(o =>
                         o.Definition.Enzymes.TryGetValue(enzyme, out var value) && value > 0)));
             }
         }

src/auto-evo/mutation_strategy/AddOrganelleAnywhere.cs

@@ -113,7 +113,7 @@ public static AddOrganelleAnywhere ThatConvertBetweenCompounds(Compound fromComp
                 continue;
 
             // Don't add duplicate unique organelles
-            if (organelle.Unique && baseSpecies.Organelles.Select(x => x.Definition).Contains(organelle))
+            if (organelle.Unique && baseSpecies.ModifiableOrganelles.Select(x => x.Definition).Contains(organelle))
                 continue;
 
             var newSpecies = (MicrobeSpecies)baseSpecies.Clone();

src/auto-evo/mutation_strategy/ModifyOrganelleBase.cs

@@ -42,7 +42,7 @@ public ModifyOrganelleBase(Func<OrganelleDefinition, bool> criteria, bool should
         List<int>? organelleIndexesToMutate = null;
 
         // Manual looping to avoid one enumerator allocation per call
-        var organelleList = baseSpecies.Organelles.Organelles;
+        var organelleList = baseSpecies.ModifiableOrganelles.Organelles;
         var organelleCount = organelleList.Count;
         for (var i = 0; i < organelleCount; ++i)
         {
@@ -98,14 +98,14 @@ public ModifyOrganelleBase(Func<OrganelleDefinition, bool> criteria, bool should
 
                     // We did not change the position at all, so we can safely put down the organelle as upgrades
                     // cannot affect the shape
-                    newSpecies.Organelles.AddAutoEvoAttemptOrganelle(upgradedOrganelle);
+                    newSpecies.ModifiableOrganelles.AddAutoEvoAttemptOrganelle(upgradedOrganelle);
                     mutatedOrganelle = true;
                 }
                 else
                 {
                     // TODO: switch away from cloning again once ensured that auto-evo does not modify original
                     // organelles
-                    newSpecies.Organelles.AddAutoEvoAttemptOrganelle(organelleList[j].Clone());
+                    newSpecies.ModifiableOrganelles.AddAutoEvoAttemptOrganelle(organelleList[j].Clone());
 
                     // newSpecies.Organelles.AddAutoEvoAttemptOrganelle(organelleList[j]);
                 }

src/auto-evo/mutation_strategy/MoveOrganelleBack.cs

@@ -28,11 +28,12 @@ public MoveOrganelleBack(Func<OrganelleDefinition, bool> criteria)
         var workMemory2 = new List<Hex>();
         var workMemory3 = new HashSet<Hex>();
 
-        foreach (OrganelleTemplate organelle in baseSpecies.Organelles.Where(x => allOrganelles.Contains(x.Definition)))
+        foreach (OrganelleTemplate organelle in baseSpecies.ModifiableOrganelles.Where(x =>
+                     allOrganelles.Contains(x.Definition)))
         {
             MicrobeSpecies newSpecies = (MicrobeSpecies)baseSpecies.Clone();
 
-            newSpecies.Organelles.Remove(organelle);
+            newSpecies.ModifiableOrganelles.Remove(organelle);
 
             if (CommonMutationFunctions.AddOrganelle(organelle.Definition, CommonMutationFunctions.Direction.Rear,
                     newSpecies, workMemory1, workMemory2, workMemory3, random))

src/auto-evo/mutation_strategy/RemoveOrganelle.cs

@@ -52,7 +52,7 @@ public static RemoveOrganelle ThatCreateCompound(Compound compound)
         if (mp < Constants.ORGANELLE_REMOVE_COST)
             return null;
 
-        var organelles = baseSpecies.Organelles.Where(x => Criteria(x.Definition))
+        var organelles = baseSpecies.ModifiableOrganelles.Where(x => Criteria(x.Definition))
             .OrderBy(_ => random.Next()).Take(Constants.AUTO_EVO_ORGANELLE_REMOVE_ATTEMPTS);
 
         List<Tuple<MicrobeSpecies, double>>? mutated = null;
@@ -73,8 +73,8 @@ public static RemoveOrganelle ThatCreateCompound(Compound compound)
             // Is this the best way to do this? Probably not, but this is how mutations.cs does is
             // and the other way outright did not work
             // This is now slightly improved - hhyyrylainen
-            var baseOrganelles = baseSpecies.Organelles.Organelles;
-            var count = baseSpecies.Organelles.Count;
+            var baseOrganelles = baseSpecies.ReadonlyOrganelles.Organelles;
+            var count = baseSpecies.ReadonlyOrganelles.Count;
 
             for (var i = 0; i < count; ++i)
             {
@@ -85,10 +85,11 @@ public static RemoveOrganelle ThatCreateCompound(Compound compound)
 
                 // Copy the organelle
                 var newOrganelle = parentOrganelle.Clone();
-                newSpecies.Organelles.AddIfPossible(newOrganelle, workMemory.WorkingMemory1, workMemory.WorkingMemory2);
+                newSpecies.ModifiableOrganelles.AddIfPossible(newOrganelle, workMemory.WorkingMemory1,
+                    workMemory.WorkingMemory2);
             }
 
-            CommonMutationFunctions.AttachIslandHexes(newSpecies.Organelles, workMemory);
+            CommonMutationFunctions.AttachIslandHexes(newSpecies.ModifiableOrganelles, workMemory);
 
             mutated ??= new List<Tuple<MicrobeSpecies, double>>();
             mutated.Add(Tuple.Create(newSpecies, mp - Constants.ORGANELLE_REMOVE_COST));

src/auto-evo/mutations/CommonMutationFunctions.cs

@@ -90,7 +90,7 @@ public static MicrobeSpecies GenerateRandomSpecies(MicrobeSpecies mutated, Patch
             MutationLogicFunctions.ColourNewMicrobeSpecies(random, mutated);
         }
 
-        mutated.ModifiableTolerances.CopyFrom(forPatch.GenerateTolerancesForMicrobe(mutated.Organelles));
+        mutated.ModifiableTolerances.CopyFrom(forPatch.GenerateTolerancesForMicrobe(mutated.ReadonlyOrganelles));
 
         // Override the default species starting name to have more variability in the names
         var nameGenerator = SimulationParameters.Instance.NameGenerator;
@@ -119,17 +119,18 @@ public static bool AddOrganelleWithStrategy(OrganelleAddStrategy strategy, Organ
         switch (strategy)
         {
             case OrganelleAddStrategy.Realistic:
-                position = GetRealisticPosition(organelle, newSpecies.Organelles, direction, workMemory1, workMemory3,
+                position = GetRealisticPosition(organelle, newSpecies.ModifiableOrganelles, direction, workMemory1,
+                    workMemory3,
                     random);
                 break;
             case OrganelleAddStrategy.Spiral:
-                position = GetSpiralPosition(organelle, newSpecies.Organelles, workMemory1, workMemory3);
+                position = GetSpiralPosition(organelle, newSpecies.ModifiableOrganelles, workMemory1, workMemory3);
                 break;
             case OrganelleAddStrategy.Front:
-                position = GetFrontPosition(organelle, newSpecies.Organelles, workMemory1, workMemory3);
+                position = GetFrontPosition(organelle, newSpecies.ModifiableOrganelles, workMemory1, workMemory3);
                 break;
             case OrganelleAddStrategy.Back:
-                position = GetBackPosition(organelle, newSpecies.Organelles, workMemory1, workMemory3);
+                position = GetBackPosition(organelle, newSpecies.ModifiableOrganelles, workMemory1, workMemory3);
                 break;
             default:
                 throw new ArgumentOutOfRangeException(nameof(strategy), strategy, null);
@@ -139,7 +140,7 @@ public static bool AddOrganelleWithStrategy(OrganelleAddStrategy strategy, Organ
         if (position == null)
             return false;
 
-        newSpecies.Organelles.AddFast(position, workMemory1, workMemory2);
+        newSpecies.ModifiableOrganelles.AddFast(position, workMemory1, workMemory2);
 
         // If the new species is eukaryotic, mark this as such.
         if (organelle == Nucleus)

src/auto-evo/mutations/MutationLogicFunctions.cs

@@ -68,8 +68,8 @@ public static void ColourNewMicrobeSpecies(Random random, MicrobeSpecies newSpec
 
     private static bool MicrobeSpeciesIsNewGenus(MicrobeSpecies species1, MicrobeSpecies species2)
     {
-        var species1UniqueOrganelles = species1.Organelles.Select(o => o.Definition).ToHashSet();
-        var species2UniqueOrganelles = species2.Organelles.Select(o => o.Definition).ToHashSet();
+        var species1UniqueOrganelles = species1.ReadonlyOrganelles.Select(o => o.Definition).ToHashSet();
+        var species2UniqueOrganelles = species2.ReadonlyOrganelles.Select(o => o.Definition).ToHashSet();
 
         return species1UniqueOrganelles.Union(species2UniqueOrganelles).Count()
             - species1UniqueOrganelles.Intersect(species2UniqueOrganelles).Count()

src/auto-evo/selection_pressure/CompoundConversionEfficiencyPressure.cs

@@ -71,7 +71,7 @@ public override float Score(Species species, Patch patch, SimulationCache cache)
         // being in a colony no longer reduces osmoregulation cost.
         var bindingModifier = 1.0f;
 
-        MicrobeInternalCalculations.GetBindingAndSignalling(microbeSpecies.Organelles.Organelles,
+        MicrobeInternalCalculations.GetBindingAndSignalling(microbeSpecies.ReadonlyOrganelles.Organelles,
             out var hasBindingAgent, out var hasSignallingAgent);
 
         if (hasBindingAgent)