2 Commits

Include renames

Author	SHA1	Message	Date
Leonid PershinandClaude Opus 4.8	ead22517ee	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>	2026-06-12 23:51:02 +03:00
Leonid PershinandClaude Opus 4.8	bc18db5df6	Add gene foundation: GeneDef, Genome, trait phenotype (Content) ... The organism-agnostic core of the gene system, built on the formula engine. GeneDef is a def describing a gene's kind (numeric/discrete), allele generation range/spread, mutation, variant distribution and its effects on named traits as formulas. Genome is a managed, variable- composition map (geneId -> Allele pair): generated from a gene set, bred meiotically with per-gene mutation, expressed to a phenotype (numeric mean / discrete lower-allele dominance); open composition allows hybrids. Phenotype.Compute aggregates each gene's effect formulas into a trait map (variable `value` = the gene's expressed phenotype, other gene ids and an environment context resolve too), so systems read traits, never genes. Nothing here is species-specific. Def JSON now supports string-named enums (JsonStringEnumConverter) so a gene's kind reads as "Discrete". Covered by GeneticsTests (generation/expression/breeding/traits) and GeneDefLoadTests (GeneDef through the real DefDatabase). Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-12 23:43:01 +03:00