From 2b9a0cd64880e63f64b621d425906092792d0798 Mon Sep 17 00:00:00 2001 From: Gulum Date: Fri, 5 Jun 2026 23:37:53 +0200 Subject: [PATCH] GEN-1: add vitest + exact Fraction utility Co-Authored-By: Claude Opus 4.8 (1M context) --- gerbil-manager-web/package-lock.json | 374 +++++++++++++++++++- gerbil-manager-web/package.json | 7 +- gerbil-manager-web/src/genetics/fraction.ts | 70 ++++ 3 files changed, 448 insertions(+), 3 deletions(-) create mode 100644 gerbil-manager-web/src/genetics/fraction.ts diff --git a/gerbil-manager-web/package-lock.json b/gerbil-manager-web/package-lock.json index d1288e7..f118bda 100644 --- a/gerbil-manager-web/package-lock.json +++ b/gerbil-manager-web/package-lock.json @@ -24,7 +24,8 @@ "globals": "^17.6.0", "typescript": "~6.0.2", "typescript-eslint": "^8.59.2", - "vite": "^8.0.12" + "vite": "^8.0.12", + "vitest": "^4.1.8" } }, "node_modules/@babel/code-frame": { @@ -838,6 +839,13 @@ "dev": true, "license": "MIT" }, + "node_modules/@standard-schema/spec": { + "version": "1.1.0", + "resolved": "https://registry.npmjs.org/@standard-schema/spec/-/spec-1.1.0.tgz", + "integrity": "sha512-l2aFy5jALhniG5HgqrD6jXLi/rUWrKvqN/qJx6yoJsgKhblVd+iqqU4RCXavm/jPityDo5TCvKMnpjKnOriy0w==", + "dev": true, + "license": "MIT" + }, "node_modules/@tybys/wasm-util": { "version": "0.10.2", "resolved": "https://registry.npmjs.org/@tybys/wasm-util/-/wasm-util-0.10.2.tgz", @@ -849,6 +857,24 @@ "tslib": "^2.4.0" } }, + "node_modules/@types/chai": { + "version": "5.2.3", + "resolved": "https://registry.npmjs.org/@types/chai/-/chai-5.2.3.tgz", + "integrity": "sha512-Mw558oeA9fFbv65/y4mHtXDs9bPnFMZAL/jxdPFUpOHHIXX91mcgEHbS5Lahr+pwZFR8A7GQleRWeI6cGFC2UA==", + "dev": true, + "license": "MIT", + "dependencies": { + "@types/deep-eql": "*", + "assertion-error": "^2.0.1" + } + }, + "node_modules/@types/deep-eql": { + "version": "4.0.2", + "resolved": "https://registry.npmjs.org/@types/deep-eql/-/deep-eql-4.0.2.tgz", + "integrity": "sha512-c9h9dVVMigMPc4bwTvC5dxqtqJZwQPePsWjPlpSOnojbor6pGqdk541lfA7AqFQr5pB1BRdq0juY9db81BwyFw==", + "dev": true, + "license": "MIT" + }, "node_modules/@types/esrecurse": { "version": "4.3.1", "resolved": "https://registry.npmjs.org/@types/esrecurse/-/esrecurse-4.3.1.tgz", @@ -1169,6 +1195,119 @@ } } }, + "node_modules/@vitest/expect": { + "version": "4.1.8", + "resolved": "https://registry.npmjs.org/@vitest/expect/-/expect-4.1.8.tgz", + "integrity": "sha512-h3nDO677RDLEGlBxyQ5CW8RlMThSKSRLUePLOx09gNIWRL40edgA1GCZSZgf1W55MFAG6/Sw14KeaAnqv0NKdQ==", + "dev": true, + "license": "MIT", + "dependencies": { + "@standard-schema/spec": "^1.1.0", + "@types/chai": "^5.2.2", + "@vitest/spy": "4.1.8", + "@vitest/utils": "4.1.8", + "chai": "^6.2.2", + "tinyrainbow": "^3.1.0" + }, + "funding": { + "url": "https://opencollective.com/vitest" + } + }, + "node_modules/@vitest/mocker": { + "version": "4.1.8", + "resolved": "https://registry.npmjs.org/@vitest/mocker/-/mocker-4.1.8.tgz", + "integrity": "sha512-LEiN/xe4OSIbKe9HQIp5OC24agGD9J5CnmMgsLohVVoOPWL9a2sBoR6VBx43jQZb7Kr1l4RCuyCJzcAa0+dojw==", + "dev": true, + "license": "MIT", + "dependencies": { + "@vitest/spy": "4.1.8", + "estree-walker": "^3.0.3", + "magic-string": "^0.30.21" + }, + "funding": { + "url": "https://opencollective.com/vitest" + }, + "peerDependencies": { + "msw": "^2.4.9", + "vite": "^6.0.0 || ^7.0.0 || ^8.0.0" + }, + "peerDependenciesMeta": { + "msw": { + "optional": true + }, + "vite": { + "optional": true + } + } + }, + "node_modules/@vitest/pretty-format": { + "version": "4.1.8", + "resolved": "https://registry.npmjs.org/@vitest/pretty-format/-/pretty-format-4.1.8.tgz", + "integrity": "sha512-9GasEBxpZ1VYIpqHf/0+YGg121uSNwCKOJqIrTwWP/TB7DmFCiaBpNl3aPZzoLWfWkuqhbH8vJIVobZkvdo2cA==", + "dev": true, + "license": "MIT", + "dependencies": { + "tinyrainbow": "^3.1.0" + }, + "funding": { + "url": "https://opencollective.com/vitest" + } + }, + "node_modules/@vitest/runner": { + "version": "4.1.8", + "resolved": "https://registry.npmjs.org/@vitest/runner/-/runner-4.1.8.tgz", + "integrity": "sha512-EmVxeBAfMJvycdjd6Hm+RbFBbA9fKvo0Kx37hNpBYoYeavH3RNsBXWDooR1mgD52dCrxIIuP7UotpfiwOikvcg==", + "dev": true, + "license": "MIT", + "dependencies": { + "@vitest/utils": "4.1.8", + "pathe": "^2.0.3" + }, + "funding": { + "url": "https://opencollective.com/vitest" + } + }, + "node_modules/@vitest/snapshot": { + "version": "4.1.8", + "resolved": "https://registry.npmjs.org/@vitest/snapshot/-/snapshot-4.1.8.tgz", + "integrity": "sha512-acfZboRmAIf05DEKcBQy33VXojFJjtUdLyo7oOmV9kebb2xdU01UknNiPuPZoJZQyO7DF0gZdTGTpeAzET9QPQ==", + "dev": true, + "license": "MIT", + "dependencies": { + "@vitest/pretty-format": "4.1.8", + "@vitest/utils": "4.1.8", + "magic-string": "^0.30.21", + "pathe": "^2.0.3" + }, + "funding": { + "url": "https://opencollective.com/vitest" + } + }, + "node_modules/@vitest/spy": { + "version": "4.1.8", + "resolved": "https://registry.npmjs.org/@vitest/spy/-/spy-4.1.8.tgz", + "integrity": 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"https://registry.npmjs.org/assertion-error/-/assertion-error-2.0.1.tgz", + "integrity": "sha512-Izi8RQcffqCeNVgFigKli1ssklIbpHnCYc6AknXGYoB6grJqyeby7jv12JUQgmTAnIDnbck1uxksT4dzN3PWBA==", + "dev": true, + "license": "MIT", + "engines": { + "node": ">=12" + } + }, "node_modules/balanced-match": { "version": "4.0.4", "resolved": "https://registry.npmjs.org/balanced-match/-/balanced-match-4.0.4.tgz", @@ -1300,6 +1449,16 @@ ], "license": "CC-BY-4.0" }, + "node_modules/chai": { + "version": "6.2.2", + "resolved": "https://registry.npmjs.org/chai/-/chai-6.2.2.tgz", + "integrity": "sha512-NUPRluOfOiTKBKvWPtSD4PhFvWCqOi0BGStNWs57X9js7XGTprSmFoz5F0tWhR4WPjNeR9jXqdC7/UpSJTnlRg==", + "dev": true, + "license": "MIT", + "engines": { + "node": ">=18" + } + }, "node_modules/convert-source-map": { "version": "2.0.0", "resolved": "https://registry.npmjs.org/convert-source-map/-/convert-source-map-2.0.0.tgz", @@ -1384,6 +1543,13 @@ "dev": true, "license": "ISC" }, + "node_modules/es-module-lexer": { + "version": "2.1.0", + "resolved": "https://registry.npmjs.org/es-module-lexer/-/es-module-lexer-2.1.0.tgz", + "integrity": "sha512-n27zTYMjYu1aj4MjCWzSP7G9r75utsaoc8m61weK+W8JMBGGQybd43GstCXZ3WNmSFtGT9wi59qQTW6mhTR5LQ==", + "dev": true, + "license": "MIT" + }, "node_modules/escalade": { "version": "3.2.0", "resolved": "https://registry.npmjs.org/escalade/-/escalade-3.2.0.tgz", @@ -1579,6 +1745,16 @@ "node": ">=4.0" } }, + "node_modules/estree-walker": { + "version": "3.0.3", + "resolved": "https://registry.npmjs.org/estree-walker/-/estree-walker-3.0.3.tgz", + "integrity": "sha512-7RUKfXgSMMkzt6ZuXmqapOurLGPPfgj6l9uRZ7lRGolvk0y2yocc35LdcxKC5PQZdn2DMqioAQ2NoWcrTKmm6g==", + "dev": true, + "license": "MIT", + "dependencies": { + "@types/estree": "^1.0.0" + } + }, "node_modules/esutils": { "version": "2.0.3", "resolved": "https://registry.npmjs.org/esutils/-/esutils-2.0.3.tgz", @@ -1589,6 +1765,16 @@ "node": ">=0.10.0" } }, + "node_modules/expect-type": { + "version": "1.3.0", + "resolved": "https://registry.npmjs.org/expect-type/-/expect-type-1.3.0.tgz", + "integrity": "sha512-knvyeauYhqjOYvQ66MznSMs83wmHrCycNEN6Ao+2AeYEfxUIkuiVxdEa1qlGEPK+We3n0THiDciYSsCcgW/DoA==", + "dev": true, + "license": "Apache-2.0", + "engines": { + "node": ">=12.0.0" + } + }, "node_modules/fast-deep-equal": { "version": "3.1.3", "resolved": "https://registry.npmjs.org/fast-deep-equal/-/fast-deep-equal-3.1.3.tgz", @@ -2162,6 +2348,16 @@ "yallist": "^3.0.2" } }, + "node_modules/magic-string": { + "version": "0.30.21", + "resolved": "https://registry.npmjs.org/magic-string/-/magic-string-0.30.21.tgz", + "integrity": "sha512-vd2F4YUyEXKGcLHoq+TEyCjxueSeHnFxyyjNp80yg0XV4vUhnDer/lvvlqM/arB5bXQN5K2/3oinyCRyx8T2CQ==", + "dev": true, + "license": "MIT", + "dependencies": { + "@jridgewell/sourcemap-codec": "^1.5.5" + } + }, "node_modules/minimatch": { "version": "10.2.5", "resolved": "https://registry.npmjs.org/minimatch/-/minimatch-10.2.5.tgz", @@ -2221,6 +2417,20 @@ "node": ">=18" } }, + "node_modules/obug": { + "version": "2.1.2", + "resolved": "https://registry.npmjs.org/obug/-/obug-2.1.2.tgz", + "integrity": "sha512-AWGB9WFcRXOQs48Z/udjI5ZcZMHXwX8XPByNpOydgcGsDLIzjGizhoMWJyKAWze7AVW/2W1i+/gPX4YtKe5cyg==", + "dev": true, + "funding": [ + "https://github.com/sponsors/sxzz", + "https://opencollective.com/debug" + ], + "license": "MIT", + "engines": { + "node": ">=12.20.0" + } + }, "node_modules/optionator": { "version": "0.9.4", "resolved": "https://registry.npmjs.org/optionator/-/optionator-0.9.4.tgz", @@ -2291,6 +2501,13 @@ "node": ">=8" } }, + "node_modules/pathe": { + "version": "2.0.3", + "resolved": "https://registry.npmjs.org/pathe/-/pathe-2.0.3.tgz", + "integrity": "sha512-WUjGcAqP1gQacoQe+OBJsFA7Ld4DyXuUIjZ5cc75cLHvJ7dtNsTugphxIADwspS+AraAUePCKrSVtPLFj/F88w==", + "dev": true, + "license": "MIT" + }, "node_modules/picocolors": { "version": "1.1.1", "resolved": "https://registry.npmjs.org/picocolors/-/picocolors-1.1.1.tgz", @@ -2498,6 +2715,13 @@ "node": ">=8" } }, + "node_modules/siginfo": { + "version": "2.0.0", + "resolved": "https://registry.npmjs.org/siginfo/-/siginfo-2.0.0.tgz", + "integrity": "sha512-ybx0WO1/8bSBLEWXZvEd7gMW3Sn3JFlW3TvX1nREbDLRNQNaeNN8WK0meBwPdAaOI7TtRRRJn/Es1zhrrCHu7g==", + "dev": true, + "license": "ISC" + }, "node_modules/source-map-js": { "version": "1.2.1", "resolved": "https://registry.npmjs.org/source-map-js/-/source-map-js-1.2.1.tgz", @@ -2508,6 +2732,37 @@ "node": ">=0.10.0" } }, + "node_modules/stackback": { + "version": "0.0.2", + "resolved": "https://registry.npmjs.org/stackback/-/stackback-0.0.2.tgz", + "integrity": "sha512-1XMJE5fQo1jGH6Y/7ebnwPOBEkIEnT4QF32d5R1+VXdXveM0IBMJt8zfaxX1P3QhVwrYe+576+jkANtSS2mBbw==", + "dev": true, + "license": "MIT" + }, + "node_modules/std-env": { + "version": "4.1.0", + "resolved": "https://registry.npmjs.org/std-env/-/std-env-4.1.0.tgz", + "integrity": "sha512-Rq7ybcX2RuC55r9oaPVEW7/xu3tj8u4GeBYHBWCychFtzMIr86A7e3PPEBPT37sHStKX3+TiX/Fr/ACmJLVlLQ==", + "dev": true, + "license": "MIT" + }, + "node_modules/tinybench": { + "version": "2.9.0", + "resolved": "https://registry.npmjs.org/tinybench/-/tinybench-2.9.0.tgz", + "integrity": "sha512-0+DUvqWMValLmha6lr4kD8iAMK1HzV0/aKnCtWb9v9641TnP/MFb7Pc2bxoxQjTXAErryXVgUOfv2YqNllqGeg==", + "dev": true, + "license": "MIT" + }, + "node_modules/tinyexec": { + "version": "1.2.4", + "resolved": "https://registry.npmjs.org/tinyexec/-/tinyexec-1.2.4.tgz", + "integrity": "sha512-SHf/r48b7vOrjve9PxJo3MN5v5yuyjHvdUcrQffT3WXMUfnGmHDVbC4k3sHJaJTgZCwpUplIaAo5ANtMyp3YHg==", + "dev": true, + "license": "MIT", + "engines": { + "node": ">=18" + } + }, "node_modules/tinyglobby": { "version": "0.2.17", "resolved": "https://registry.npmjs.org/tinyglobby/-/tinyglobby-0.2.17.tgz", @@ -2525,6 +2780,16 @@ "url": "https://github.com/sponsors/SuperchupuDev" } }, + "node_modules/tinyrainbow": { + "version": "3.1.0", + "resolved": "https://registry.npmjs.org/tinyrainbow/-/tinyrainbow-3.1.0.tgz", + "integrity": "sha512-Bf+ILmBgretUrdJxzXM0SgXLZ3XfiaUuOj/IKQHuTXip+05Xn+uyEYdVg0kYDipTBcLrCVyUzAPz7QmArb0mmw==", + "dev": true, + "license": "MIT", + "engines": { + "node": ">=14.0.0" + } + }, "node_modules/ts-api-utils": { "version": "2.5.0", "resolved": "https://registry.npmjs.org/ts-api-utils/-/ts-api-utils-2.5.0.tgz", @@ -2723,6 +2988,96 @@ } } }, + "node_modules/vitest": { + "version": "4.1.8", + "resolved": "https://registry.npmjs.org/vitest/-/vitest-4.1.8.tgz", + "integrity": "sha512-flY6ScbCIt9HThs+C5HS7jvGOB560DJtk/Z15IQROTA6zEy49Nh8T/dofWTQL+n3vswqn87sbJNiuqw1SDp5Ig==", + "dev": true, + "license": "MIT", + "dependencies": { + "@vitest/expect": "4.1.8", + "@vitest/mocker": "4.1.8", + "@vitest/pretty-format": "4.1.8", + "@vitest/runner": "4.1.8", + "@vitest/snapshot": "4.1.8", + "@vitest/spy": "4.1.8", + "@vitest/utils": "4.1.8", + "es-module-lexer": "^2.0.0", + "expect-type": "^1.3.0", + "magic-string": "^0.30.21", + "obug": "^2.1.1", + "pathe": "^2.0.3", + "picomatch": "^4.0.3", + "std-env": "^4.0.0-rc.1", + "tinybench": "^2.9.0", + "tinyexec": "^1.0.2", + "tinyglobby": "^0.2.15", + "tinyrainbow": "^3.1.0", + "vite": "^6.0.0 || ^7.0.0 || ^8.0.0", + "why-is-node-running": "^2.3.0" + }, + "bin": { + "vitest": "vitest.mjs" + }, + "engines": { + "node": "^20.0.0 || ^22.0.0 || >=24.0.0" + }, + "funding": { + "url": "https://opencollective.com/vitest" + }, + "peerDependencies": { + "@edge-runtime/vm": "*", + "@opentelemetry/api": "^1.9.0", + "@types/node": "^20.0.0 || ^22.0.0 || >=24.0.0", + "@vitest/browser-playwright": "4.1.8", + "@vitest/browser-preview": "4.1.8", + "@vitest/browser-webdriverio": "4.1.8", + "@vitest/coverage-istanbul": "4.1.8", + "@vitest/coverage-v8": "4.1.8", + "@vitest/ui": "4.1.8", + "happy-dom": "*", + "jsdom": "*", + "vite": "^6.0.0 || ^7.0.0 || ^8.0.0" + }, + "peerDependenciesMeta": { + "@edge-runtime/vm": { + "optional": true + }, + "@opentelemetry/api": { + "optional": true + }, + "@types/node": { + "optional": true + }, + "@vitest/browser-playwright": { + "optional": true + }, + "@vitest/browser-preview": { + "optional": true + }, + "@vitest/browser-webdriverio": { + "optional": true + }, + "@vitest/coverage-istanbul": { + "optional": true + }, + "@vitest/coverage-v8": { + "optional": true + }, + "@vitest/ui": { + "optional": true + }, + "happy-dom": { + "optional": true + }, + "jsdom": { + "optional": true + }, + "vite": { + "optional": false + } + } + }, "node_modules/which": { "version": "2.0.2", "resolved": "https://registry.npmjs.org/which/-/which-2.0.2.tgz", @@ -2739,6 +3094,23 @@ "node": ">= 8" } }, + "node_modules/why-is-node-running": { + "version": "2.3.0", + "resolved": "https://registry.npmjs.org/why-is-node-running/-/why-is-node-running-2.3.0.tgz", + "integrity": "sha512-hUrmaWBdVDcxvYqnyh09zunKzROWjbZTiNy8dBEjkS7ehEDQibXJ7XvlmtbwuTclUiIyN+CyXQD4Vmko8fNm8w==", + "dev": true, + "license": "MIT", + "dependencies": { + "siginfo": "^2.0.0", + "stackback": "0.0.2" + }, + "bin": { + "why-is-node-running": "cli.js" + }, + "engines": { + "node": ">=8" + } + }, "node_modules/word-wrap": { "version": "1.2.5", "resolved": "https://registry.npmjs.org/word-wrap/-/word-wrap-1.2.5.tgz", diff --git a/gerbil-manager-web/package.json b/gerbil-manager-web/package.json index cb1b0c5..d8e784f 100644 --- a/gerbil-manager-web/package.json +++ b/gerbil-manager-web/package.json @@ -7,7 +7,9 @@ "dev": "vite", "build": "tsc -b && vite build", "lint": "eslint .", - "preview": "vite preview" + "preview": "vite preview", + "test": "vitest run", + "test:watch": "vitest" }, "dependencies": { "react": "^19.2.6", @@ -26,6 +28,7 @@ "globals": "^17.6.0", "typescript": "~6.0.2", "typescript-eslint": "^8.59.2", - "vite": "^8.0.12" + "vite": "^8.0.12", + "vitest": "^4.1.8" } } diff --git a/gerbil-manager-web/src/genetics/fraction.ts b/gerbil-manager-web/src/genetics/fraction.ts new file mode 100644 index 0000000..3b80919 --- /dev/null +++ b/gerbil-manager-web/src/genetics/fraction.ts @@ -0,0 +1,70 @@ +/** + * Exact rational arithmetic for genetics probabilities. + * + * Punnett distributions are unions of dyadic/rational fractions (1/4, 3/16, …). + * Using exact fractions instead of floats keeps probabilities precise and lets + * us assert e.g. "exactly 1/4 of young are lost" after renormalisation. + */ +export interface Fraction { + readonly num: number + readonly den: number +} + +function gcd(a: number, b: number): number { + a = Math.abs(a) + b = Math.abs(b) + while (b !== 0) { + ;[a, b] = [b, a % b] + } + return a +} + +/** Create a normalised (reduced, positive-denominator) fraction. */ +export function frac(num: number, den: number): Fraction { + if (den === 0) throw new Error('Fraction denominator must not be zero') + if (den < 0) { + num = -num + den = -den + } + if (num === 0) return { num: 0, den: 1 } + const g = gcd(num, den) + return { num: num / g, den: den / g } +} + +export const ZERO: Fraction = { num: 0, den: 1 } +export const ONE: Fraction = { num: 1, den: 1 } + +export function add(a: Fraction, b: Fraction): Fraction { + return frac(a.num * b.den + b.num * a.den, a.den * b.den) +} + +export function multiply(a: Fraction, b: Fraction): Fraction { + return frac(a.num * b.num, a.den * b.den) +} + +export function divide(a: Fraction, b: Fraction): Fraction { + if (b.num === 0) throw new Error('Cannot divide by zero fraction') + return frac(a.num * b.den, a.den * b.num) +} + +export function equals(a: Fraction, b: Fraction): boolean { + return a.num * b.den === b.num * a.den +} + +export function toNumber(f: Fraction): number { + return f.num / f.den +} + +/** Human-readable "3/16" (or "0" / "1"). */ +export function toString(f: Fraction): string { + if (f.num === 0) return '0' + if (f.den === 1) return String(f.num) + return `${f.num}/${f.den}` +} + +/** "18.75 %" style label for display (rounded to `digits` decimals). */ +export function toPercentString(f: Fraction, digits = 2): string { + const pct = (f.num / f.den) * 100 + const rounded = Number(pct.toFixed(digits)) + return `${rounded} %` +}