Genetics: GenomeTemplate (per-organism gene allotment) + breed override

Adds the species/organism layer on top of the gene foundation.
GenomeTemplate carries which GeneDefs an individual has plus the
per-organism base value and spread its alleles are drawn around (and an
optional discrete-variant override), so the same shared GeneDef expresses
different centres for different species — Generate() draws an individual,
Registry() feeds breeding and trait computation.

Genome.Breed gains an optional mutationChance that overrides every gene's
fixed MutationChance, so a caller can drive mutation from an evolvable
trait. Allele sampling (numeric spread+clamp, weighted discrete pick) is
factored into a shared GeneSampling used by both Generate paths.

Covered by GenomeTemplateTests (per-species centres, registry-driven
breeding, mutation override on/off).

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

src/MrGameEng.Content/Genetics/GeneSampling.cs

@@ -0,0 +1,56 @@
+namespace MrGameEng.Genetics;
+
+/// <summary>
+/// Shared, deterministic allele sampling used by both <see cref="Genome.Generate"/> (gene defaults)
+/// and <see cref="GenomeTemplate"/> (per-individual base overrides). Centralizes the numeric
+/// spread+clamp and the weighted discrete pick so the two paths stay consistent.
+/// </summary>
+internal static class GeneSampling
+{
+    /// <summary>A numeric allele drawn as <c>baseValue ± spread·|baseValue|</c>, clamped to the gene's range.</summary>
+    public static float Numeric(GeneDef gene, float baseValue, float spread, Random random)
+    {
+        var value = baseValue + (random.NextSingle() * 2f - 1f) * spread * MathF.Abs(baseValue);
+        return Math.Clamp(value, gene.Min, gene.Max);
+    }
+
+    /// <summary>
+    /// A discrete variant index in <c>[0, Variants)</c>, picked from <paramref name="weights"/> when
+    /// they match the variant count, otherwise the gene's own weights, otherwise uniformly.
+    /// </summary>
+    public static float Variant(GeneDef gene, float[]? weights, Random random)
+    {
+        var variants = Math.Max(1, gene.Variants);
+        var w =
+            weights is { Length: > 0 } && weights.Length == variants
+                ? weights
+                : gene.VariantWeights;
+        if (w.Length != variants)
+        {
+            return random.Next(variants);
+        }
+
+        var total = 0f;
+        foreach (var value in w)
+        {
+            total += MathF.Max(0f, value);
+        }
+
+        if (total <= 0f)
+        {
+            return random.Next(variants);
+        }
+
+        var roll = random.NextSingle() * total;
+        for (var i = 0; i < variants; i++)
+        {
+            roll -= MathF.Max(0f, w[i]);
+            if (roll < 0f)
+            {
+                return i;
+            }
+        }
+
+        return variants - 1;
+    }
+}

src/MrGameEng.Content/Genetics/Genome.cs

@@ -77,12 +77,16 @@ public sealed class Genome
     /// carries, it is inherited (from that parent, on both sides) with 50% probability. Every
     /// inherited allele may then mutate per its <see cref="GeneDef"/>. <paramref name="registry"/>
     /// supplies the def for each gene id; genes absent from it are skipped.
+    /// <paramref name="mutationChance"/>, when given, overrides every gene's
+    /// <see cref="GeneDef.MutationChance"/> — letting the caller drive mutation from an evolvable
+    /// trait rather than a fixed per-gene constant.
     /// </summary>
     public static Genome Breed(
         Genome a,
         Genome b,
         IReadOnlyDictionary<string, GeneDef> registry,
-        Random random
+        Random random,
+        float? mutationChance = null
     )
     {
         var child = new Genome();
@@ -93,21 +97,22 @@ public sealed class Genome
                 continue;
             }
 
+            var chance = mutationChance ?? gene.MutationChance;
             var inA = a.Has(geneId);
             var inB = b.Has(geneId);
             if (inA && inB)
             {
                 child._alleles[geneId] = new Allele(
-                    Meiosis(gene, a[geneId], random),
-                    Meiosis(gene, b[geneId], random)
+                    Meiosis(gene, a[geneId], chance, random),
+                    Meiosis(gene, b[geneId], chance, random)
                 );
             }
             else if (random.NextSingle() < 0.5f)
             {
                 var parent = inA ? a : b;
                 child._alleles[geneId] = new Allele(
-                    Meiosis(gene, parent[geneId], random),
-                    Meiosis(gene, parent[geneId], random)
+                    Meiosis(gene, parent[geneId], chance, random),
+                    Meiosis(gene, parent[geneId], chance, random)
                 );
             }
         }
@@ -116,17 +121,17 @@ public sealed class Genome
     }
 
     // One inherited allele: pick one of the parent slot's two alleles, then maybe mutate it.
-    private static float Meiosis(GeneDef gene, Allele parent, Random random)
+    private static float Meiosis(GeneDef gene, Allele parent, float mutationChance, Random random)
     {
         var inherited = random.NextSingle() < 0.5f ? parent.A : parent.B;
-        if (random.NextSingle() >= gene.MutationChance)
+        if (random.NextSingle() >= mutationChance)
         {
             return inherited;
         }
 
         if (gene.Kind == GeneKind.Discrete)
         {
-            return PickVariant(gene, random);
+            return GeneSampling.Variant(gene, null, random);
         }
 
         var shifted =
@@ -135,49 +140,10 @@ public sealed class Genome
         return Math.Clamp(shifted, gene.Min, gene.Max);
     }
 
-    private static float GenerateAllele(GeneDef gene, Random random)
-    {
-        if (gene.Kind == GeneKind.Discrete)
-        {
-            return PickVariant(gene, random);
-        }
-
-        var value =
-            gene.Default + (random.NextSingle() * 2f - 1f) * gene.Spread * MathF.Abs(gene.Default);
-        return Math.Clamp(value, gene.Min, gene.Max);
-    }
-
-    private static float PickVariant(GeneDef gene, Random random)
-    {
-        var variants = Math.Max(1, gene.Variants);
-        if (gene.VariantWeights.Length != variants)
-        {
-            return random.Next(variants);
-        }
-
-        var total = 0f;
-        foreach (var w in gene.VariantWeights)
-        {
-            total += MathF.Max(0f, w);
-        }
-
-        if (total <= 0f)
-        {
-            return random.Next(variants);
-        }
-
-        var roll = random.NextSingle() * total;
-        for (var i = 0; i < variants; i++)
-        {
-            roll -= MathF.Max(0f, gene.VariantWeights[i]);
-            if (roll < 0f)
-            {
-                return i;
-            }
-        }
-
-        return variants - 1;
-    }
+    private static float GenerateAllele(GeneDef gene, Random random) =>
+        gene.Kind == GeneKind.Discrete
+            ? GeneSampling.Variant(gene, null, random)
+            : GeneSampling.Numeric(gene, gene.Default, gene.Spread, random);
 
     // Deterministic union of both parents' gene ids (ordered) so breeding is reproducible.
     private static IEnumerable<string> UnionKeys(Genome a, Genome b)

src/MrGameEng.Content/Genetics/GenomeTemplate.cs

@@ -0,0 +1,61 @@
+namespace MrGameEng.Genetics;
+
+/// <summary>
+/// A species' (or any organism kind's) gene allotment: which <see cref="GeneDef"/>s an individual
+/// carries and the per-organism base values its alleles are generated around. The same
+/// <see cref="GeneDef"/> (e.g. "optimal light") is shared by every species, while the template
+/// supplies the species-specific centre and spread — so an oak and grass differ in values, not in
+/// machinery. <see cref="Generate"/> draws a fresh individual; <see cref="Registry"/> feeds breeding
+/// and trait computation.
+/// </summary>
+public sealed class GenomeTemplate
+{
+    /// <summary>
+    /// One gene in the allotment. <paramref name="Base"/>/<paramref name="Spread"/> centre a numeric
+    /// gene's alleles; <paramref name="VariantWeights"/> (optional) override a discrete gene's
+    /// variant distribution for this organism.
+    /// </summary>
+    public readonly record struct Entry(
+        GeneDef Gene,
+        float Base,
+        float Spread,
+        float[]? VariantWeights = null
+    );
+
+    private readonly List<Entry> _entries;
+    private readonly Dictionary<string, GeneDef> _registry;
+
+    /// <summary>Builds a template from its gene entries.</summary>
+    public GenomeTemplate(IEnumerable<Entry> entries)
+    {
+        _entries = entries.ToList();
+        _registry = new Dictionary<string, GeneDef>(StringComparer.Ordinal);
+        foreach (var entry in _entries)
+        {
+            _registry[entry.Gene.DefName] = entry.Gene;
+        }
+    }
+
+    /// <summary>The gene entries that make up the allotment.</summary>
+    public IReadOnlyList<Entry> Entries => _entries;
+
+    /// <summary>Gene id → def for every carried gene; pass to <see cref="Genome.Breed"/> and <see cref="Phenotype.Compute"/>.</summary>
+    public IReadOnlyDictionary<string, GeneDef> Registry => _registry;
+
+    /// <summary>Generates a fresh individual: two alleles per gene drawn around each entry's base/variant.</summary>
+    public Genome Generate(Random random)
+    {
+        var genome = new Genome();
+        foreach (var entry in _entries)
+        {
+            genome[entry.Gene.DefName] = new Allele(Draw(entry, random), Draw(entry, random));
+        }
+
+        return genome;
+    }
+
+    private static float Draw(Entry entry, Random random) =>
+        entry.Gene.Kind == GeneKind.Discrete
+            ? GeneSampling.Variant(entry.Gene, entry.VariantWeights, random)
+            : GeneSampling.Numeric(entry.Gene, entry.Base, entry.Spread, random);
+}