GEN-1: add vitest suite (worked example, SpSp renorm, wildcards) + erasable-enum fix

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

gerbil-manager-web/src/genetics/__tests__/genetics.test.ts

@@ -0,0 +1,210 @@
+import { describe, expect, it } from 'vitest'
+import {
+  add,
+  divide,
+  frac,
+  multiply,
+  toNumber,
+  toString,
+  equals,
+} from '../fraction'
+import {
+  fromDisplayString,
+  makeGenotype,
+  toDisplayString,
+  toJSON,
+  fromJSON,
+  wildType,
+} from '../genotype'
+import { combineLocus } from '../punnett'
+import { farbschlagFor, CATALOG_SIZE } from '../catalog'
+import { breed } from '../breed'
+import { GeneticsWarningCode } from '../warnings'
+
+describe('Fraction', () => {
+  it('reduces and does exact arithmetic', () => {
+    expect(toString(frac(2, 4))).toBe('1/2')
+    expect(toString(add(frac(1, 4), frac(1, 4)))).toBe('1/2')
+    expect(toString(multiply(frac(1, 2), frac(1, 2)))).toBe('1/4')
+    expect(toString(divide(frac(1, 4), frac(3, 4)))).toBe('1/3')
+    expect(equals(frac(3, 6), frac(1, 2))).toBe(true)
+  })
+})
+
+describe('Genotype serialization', () => {
+  it('round-trips display string <-> structured form', () => {
+    const g = fromDisplayString('Aa CC Dd EE GG Pp Spsp rere')
+    expect(toDisplayString(g)).toBe('Aa CC Dd EE GG Pp Spsp rere')
+    expect(toDisplayString(fromJSON(toJSON(g)))).toBe('Aa CC Dd EE GG Pp Spsp rere')
+  })
+
+  it('parses multi-char C-series alleles via maximal munch', () => {
+    const g = fromDisplayString('aa cchmch DD EE GG PP spsp rere')
+    expect(g.C).toEqual(['cchm', 'ch'])
+  })
+
+  it('orders allele pairs most-dominant-first', () => {
+    const g = makeGenotype({
+      A: ['a', 'A'],
+      C: ['ch', 'C'],
+      D: ['D', 'D'],
+      E: ['E', 'E'],
+      G: ['G', 'G'],
+      P: ['p', 'P'],
+      Sp: ['sp', 'sp'],
+      Re: ['re', 're'],
+    })
+    expect(g.A).toEqual(['A', 'a'])
+    expect(g.C).toEqual(['C', 'ch'])
+    expect(g.P).toEqual(['P', 'p'])
+  })
+
+  it('wild type is AA CC DD EE GG PP spsp rere', () => {
+    expect(toDisplayString(wildType())).toBe('AA CC DD EE GG PP spsp rere')
+  })
+})
+
+describe('Punnett single locus', () => {
+  it('Aa x Aa -> 1/4 AA, 1/2 Aa, 1/4 aa', () => {
+    const dist = combineLocus('A', ['A', 'a'], ['A', 'a'])
+    expect(toString(dist.get('AA')!.probability)).toBe('1/4')
+    expect(toString(dist.get('Aa')!.probability)).toBe('1/2')
+    expect(toString(dist.get('aa')!.probability)).toBe('1/4')
+  })
+
+  it('AA x aa -> all Aa', () => {
+    const dist = combineLocus('A', ['A', 'A'], ['a', 'a'])
+    expect(dist.size).toBe(1)
+    expect(toString(dist.get('Aa')!.probability)).toBe('1')
+  })
+})
+
+describe('Worked example from research report', () => {
+  // Agouti AA CC DD EE GG PP  x  Platin aa CC DD EE GG pp  ->  all Aa Cc Dd Ee Gg Pp
+  // (every locus where parents differ becomes heterozygous with prob 1)
+  it('Agouti x Platin yields a single uniform heterozygous genotype', () => {
+    const father = fromDisplayString('AA CC DD EE GG PP spsp rere')
+    const mother = fromDisplayString('aa CC DD EE GG pp spsp rere')
+    const result = breed(father, mother)
+
+    expect(result.offspring).toHaveLength(1)
+    const only = result.offspring[0]
+    expect(only.genotype).toBe('Aa CC DD EE GG Pp spsp rere')
+    expect(only.probability.text).toBe('1')
+    expect(result.warnings).toHaveLength(0)
+  })
+})
+
+describe('Schecke × Schecke lethality (SpSp)', () => {
+  it('removes SpSp, renormalises, and warns ~25% fewer young', () => {
+    // Spsp x Spsp at the Sp locus -> 1/4 SpSp (lethal), 1/2 Spsp, 1/4 spsp.
+    // After removing SpSp the survivors renormalise to 2/3 Spsp : 1/3 spsp.
+    const father = fromDisplayString('AA CC DD EE GG PP Spsp rere')
+    const mother = fromDisplayString('AA CC DD EE GG PP Spsp rere')
+    const result = breed(father, mother)
+
+    // No surviving genotype is SpSp.
+    expect(result.offspring.every((o) => !o.genotype.includes('SpSp'))).toBe(true)
+
+    // Probabilities renormalise to sum to exactly 1.
+    const sum = result.offspring.reduce((acc, o) => acc + o.probability.value, 0)
+    expect(sum).toBeCloseTo(1, 10)
+
+    // Survivors: 2/3 checkered (Spsp), 1/3 non-checkered (spsp).
+    const spsp = result.offspring.find((o) => o.genotype.includes('Spsp'))!
+    const homRec = result.offspring.find((o) => o.genotype.includes('spsp'))!
+    expect(spsp.probability.text).toBe('2/3')
+    expect(homRec.probability.text).toBe('1/3')
+
+    // Warning emitted, carrying the 1/4 young-lost stat.
+    const warn = result.warnings.find((w) => w.code === GeneticsWarningCode.ScheckeLethal)
+    expect(warn).toBeDefined()
+    expect(warn!.detail?.youngLostFraction).toBe('1/4')
+  })
+})
+
+describe('Rex × Rex semi-lethality (ReRe)', () => {
+  it('keeps ReRe but emits a semi-lethal warning', () => {
+    const father = fromDisplayString('AA CC DD EE GG PP spsp Rere')
+    const mother = fromDisplayString('AA CC DD EE GG PP spsp Rere')
+    const result = breed(father, mother)
+
+    // ReRe survives (semi-lethal, not removed).
+    expect(result.offspring.some((o) => o.genotype.includes('ReRe'))).toBe(true)
+    const sum = result.offspring.reduce((acc, o) => acc + o.probability.value, 0)
+    expect(sum).toBeCloseTo(1, 10)
+
+    const warn = result.warnings.find((w) => w.code === GeneticsWarningCode.RexSemiLethal)
+    expect(warn).toBeDefined()
+  })
+})
+
+describe('Farbschlag catalog', () => {
+  it('names the wild type Agouti', () => {
+    expect(farbschlagFor(wildType()).name).toBe('Agouti')
+  })
+
+  it('names Platin (aa CC DD EE GG pp)', () => {
+    expect(farbschlagFor(fromDisplayString('aa CC DD EE GG pp spsp rere')).name).toBe('Platin')
+  })
+
+  it('names Schwarz (aa CC DD EE GG PP)', () => {
+    expect(farbschlagFor(fromDisplayString('aa CC DD EE GG PP spsp rere')).name).toBe('Schwarz')
+  })
+
+  it('appends Schecke and Rex modifiers', () => {
+    expect(farbschlagFor(fromDisplayString('AA CC DD EE GG PP Spsp rere')).name).toBe('Agouti Schecke')
+    expect(farbschlagFor(fromDisplayString('AA CC DD EE GG PP Spsp Rere')).name).toBe(
+      'Agouti Schecke Rex',
+    )
+  })
+
+  it('falls back to Unbekannter Farbschlag for uncatalogued genotypes', () => {
+    // Colourpoint marked + dilute + grey combo not in the catalog.
+    const match = farbschlagFor(fromDisplayString('aa cchmcchm dd ee gg PP spsp rere'))
+    expect(match.unknown).toBe(true)
+    expect(match.name).toBe('Unbekannter Farbschlag')
+  })
+
+  it('has the expected catalogue coverage', () => {
+    expect(CATALOG_SIZE).toBe(18)
+  })
+})
+
+describe('Partially-unknown parents (wildcards)', () => {
+  it('handles an A? parent (phenotype agouti, genotype unknown)', () => {
+    // A? x aa at the A locus -> father gamete: 1/2 A, 1/4 (each of A,a) from "?"
+    //   = effectively 3/4 A, 1/4 a ; mother always a.
+    // Offspring: 3/4 Aa, 1/4 aa.
+    const father = makeGenotype({
+      A: ['A', '?'],
+      C: ['C', 'C'],
+      D: ['D', 'D'],
+      E: ['E', 'E'],
+      G: ['G', 'G'],
+      P: ['P', 'P'],
+      Sp: ['sp', 'sp'],
+      Re: ['re', 're'],
+    })
+    const mother = fromDisplayString('aa CC DD EE GG PP spsp rere')
+    const result = breed(father, mother)
+
+    const agouti = result.byFarbschlag.find((f) => f.farbschlag === 'Agouti')!
+    const schwarz = result.byFarbschlag.find((f) => f.farbschlag === 'Schwarz')!
+    expect(agouti.probability.text).toBe('3/4')
+    expect(schwarz.probability.text).toBe('1/4')
+  })
+})
+
+describe('Probabilities are exact fractions summing to 1', () => {
+  it('Aa Cc x Aa Cc -> 9 genotypes summing to 1', () => {
+    const father = fromDisplayString('Aa Cch DD EE GG PP spsp rere')
+    const mother = fromDisplayString('Aa Cch DD EE GG PP spsp rere')
+    const result = breed(father, mother)
+    const sum = result.offspring.reduce(
+      (acc, o) => add(acc, o.probability.fraction),
+      frac(0, 1),
+    )
+    expect(toNumber(sum)).toBeCloseTo(1, 10)
+  })
+})

gerbil-manager-web/src/genetics/warnings.ts

@@ -1,13 +1,19 @@
 /**
  * Warning codes emitted by the genetics engine. The engine is language-neutral:
  * it emits CODES only. German texts are mapped in de.ts (UI layer).
+ *
+ * Modelled as a const object (not a TS `enum`) because the project's tsconfig
+ * enables `erasableSyntaxOnly`.
  */
-export enum GeneticsWarningCode {
+export const GeneticsWarningCode = {
   /** Schecke × Schecke: SpSp embryos die in utero; ~25% fewer live young. */
-  ScheckeLethal = 'SCHECKE_LETHAL',
+  ScheckeLethal: 'SCHECKE_LETHAL',
   /** Rex × Rex: ReRe is semi-lethal; reduced viability of homozygous young. */
-  RexSemiLethal = 'REX_SEMI_LETHAL',
+  RexSemiLethal: 'REX_SEMI_LETHAL',
-}
+} as const
+
+export type GeneticsWarningCode =
+  (typeof GeneticsWarningCode)[keyof typeof GeneticsWarningCode]
 
 export interface GeneticsWarning {
   readonly code: GeneticsWarningCode