@yalehwang/archguard 0.1.31 → 0.1.33

package/dist/analysis/jl/history-writer.js

@@ -0,0 +1,74 @@
+import path from 'path';
+import crypto from 'crypto';
+import fs from 'fs-extra';
+import { HISTORY_SCHEMA_VERSION, MAX_SNAPSHOTS } from './types.js';
+export const HISTORY_FILENAME = 'arch-health-history.json';
+export function historyFilePath(archDir) {
+    return path.join(archDir, HISTORY_FILENAME);
+}
+async function readRawHistory(archDir) {
+    const filePath = historyFilePath(archDir);
+    if (!(await fs.pathExists(filePath)))
+        return null;
+    let raw;
+    try {
+        raw = await fs.readJson(filePath);
+    }
+    catch {
+        return null;
+    }
+    if (typeof raw !== 'object' || raw === null)
+        return null;
+    return raw;
+}
+export async function readHistoryFile(archDir) {
+    const raw = await readRawHistory(archDir);
+    if (raw === null)
+        return null;
+    if (typeof raw.schemaVersion !== 'number')
+        return null;
+    if (raw.schemaVersion !== HISTORY_SCHEMA_VERSION)
+        return null;
+    if (!Array.isArray(raw.snapshots))
+        return null;
+    return {
+        schemaVersion: HISTORY_SCHEMA_VERSION,
+        language: typeof raw.language === 'string' ? raw.language : 'unknown',
+        snapshots: raw.snapshots,
+    };
+}
+export async function writeHistoryFile(archDir, history) {
+    const filePath = historyFilePath(archDir);
+    await fs.ensureDir(archDir);
+    const suffix = crypto.randomUUID().slice(0, 8);
+    const tmpPath = `${filePath}.tmp.${suffix}`;
+    await fs.writeJson(tmpPath, history, { spaces: 2 });
+    await fs.rename(tmpPath, filePath);
+}
+export async function appendSnapshot(archDir, language, snapshot) {
+    const raw = await readRawHistory(archDir);
+    if (raw !== null && raw.schemaVersion !== HISTORY_SCHEMA_VERSION) {
+        return {
+            ok: false,
+            reason: `history schemaVersion ${String(raw.schemaVersion)} is not compatible with ${HISTORY_SCHEMA_VERSION}`,
+            previous: null,
+        };
+    }
+    const existingSnapshots = raw !== null && Array.isArray(raw.snapshots)
+        ? raw.snapshots
+        : [];
+    const previous = existingSnapshots.length > 0 ? existingSnapshots[existingSnapshots.length - 1] : null;
+    const snapshots = [...existingSnapshots, snapshot];
+    snapshots.sort((a, b) => a.timestamp.localeCompare(b.timestamp));
+    if (snapshots.length > MAX_SNAPSHOTS) {
+        snapshots.splice(0, snapshots.length - MAX_SNAPSHOTS);
+    }
+    const history = {
+        schemaVersion: HISTORY_SCHEMA_VERSION,
+        language,
+        snapshots,
+    };
+    await writeHistoryFile(archDir, history);
+    return { ok: true, previous };
+}
+//# sourceMappingURL=history-writer.js.map

package/dist/analysis/jl/history-writer.js.map

@@ -0,0 +1 @@
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package/dist/analysis/jl/intrinsic-dimension.d.ts

@@ -0,0 +1,14 @@
+import type { IntrinsicDimensionResult, ProjectionMode } from './types.js';
+export interface ComputeIntrinsicDimensionInput {
+    matrix: number[][];
+    entityCount: number;
+    mode: ProjectionMode;
+    k: number | null;
+    epsilon: number | null;
+    featureVersion?: string;
+    timestamp?: string;
+    commitSha?: string;
+    varianceThreshold?: number;
+}
+export declare function computeIntrinsicDimension(input: ComputeIntrinsicDimensionInput): IntrinsicDimensionResult;
+//# sourceMappingURL=intrinsic-dimension.d.ts.map

package/dist/analysis/jl/intrinsic-dimension.d.ts.map

@@ -0,0 +1 @@
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package/dist/analysis/jl/intrinsic-dimension.js

@@ -0,0 +1,80 @@
+import { SVD } from 'ml-matrix';
+import { FEATURE_VERSION, VARIANCE_THRESHOLD } from './types.js';
+function round4(value) {
+    return Math.round(value * 10000) / 10000;
+}
+function centerColumns(matrix) {
+    const rows = matrix.length;
+    const cols = rows > 0 ? matrix[0].length : 0;
+    if (rows === 0 || cols === 0)
+        return [];
+    const means = new Array(cols).fill(0);
+    for (let j = 0; j < cols; j++) {
+        let sum = 0;
+        for (let i = 0; i < rows; i++)
+            sum += matrix[i][j];
+        means[j] = sum / rows;
+    }
+    return matrix.map((row) => row.map((value, j) => value - means[j]));
+}
+export function computeIntrinsicDimension(input) {
+    const { matrix, entityCount, mode, k, epsilon, featureVersion = FEATURE_VERSION, timestamp = new Date().toISOString(), commitSha, varianceThreshold = VARIANCE_THRESHOLD, } = input;
+    if (entityCount < 3) {
+        console.warn(`[jl] low entity count (${entityCount} < 3): d_int is not meaningful`);
+    }
+    const rows = matrix.length;
+    const cols = rows > 0 ? matrix[0].length : 0;
+    const isZeroMatrix = rows === 0 || cols === 0;
+    let singularValues = [];
+    if (!isZeroMatrix) {
+        const centered = centerColumns(matrix);
+        const svd = new SVD(centered);
+        singularValues = Array.from(svd.diagonal);
+    }
+    const totalEnergy = singularValues.reduce((sum, s) => sum + s * s, 0);
+    const noDependencies = isZeroMatrix || totalEnergy < 1e-12;
+    let dInt;
+    let varianceExplained;
+    if (noDependencies) {
+        console.warn('[jl] no dependencies detected (zero adjacency matrix): d_int = 0, varianceExplained = []');
+        dInt = 0;
+        varianceExplained = [];
+    }
+    else {
+        let cumulative = 0;
+        dInt = 0;
+        for (let i = 0; i < singularValues.length; i++) {
+            cumulative += singularValues[i] * singularValues[i];
+            if (cumulative / totalEnergy >= varianceThreshold) {
+                dInt = i + 1;
+                break;
+            }
+        }
+        if (dInt === 0)
+            dInt = singularValues.length;
+        const length = Math.min(dInt + 10, singularValues.length);
+        varianceExplained = new Array(length);
+        cumulative = 0;
+        for (let i = 0; i < length; i++) {
+            cumulative += singularValues[i] * singularValues[i];
+            varianceExplained[i] = cumulative / totalEnergy;
+        }
+        if (varianceExplained.length > 0) {
+            varianceExplained[varianceExplained.length - 1] = 1.0;
+        }
+    }
+    const dIntNormalized = entityCount > 0 ? round4(dInt / entityCount) : 0;
+    return {
+        timestamp,
+        commitSha,
+        entityCount,
+        mode,
+        featureVersion,
+        k,
+        dInt,
+        dIntNormalized,
+        varianceExplained,
+        epsilon,
+    };
+}
+//# sourceMappingURL=intrinsic-dimension.js.map

package/dist/analysis/jl/intrinsic-dimension.js.map

@@ -0,0 +1 @@
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package/dist/analysis/jl/jl-projector.d.ts

@@ -0,0 +1,7 @@
+import type { JLConfig, ProjectionMode } from './types.js';
+export declare function computeMode(entityCount: number, config: JLConfig): ProjectionMode;
+export declare function computeK(entityCount: number, epsilon: number): number;
+export declare function mulberry32(seed: number): () => number;
+export declare function buildAchlioptas(k: number, n: number, seed: number): number[][];
+export declare function project(matrix: number[][], achlioptas: number[][], k: number): number[][];
+//# sourceMappingURL=jl-projector.d.ts.map

package/dist/analysis/jl/jl-projector.d.ts.map

@@ -0,0 +1 @@
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package/dist/analysis/jl/jl-projector.js

@@ -0,0 +1,52 @@
+export function computeMode(entityCount, config) {
+    return entityCount < config.directModeThreshold ? 'direct' : 'jl';
+}
+export function computeK(entityCount, epsilon) {
+    return Math.ceil((4 * Math.log(entityCount)) / (epsilon * epsilon));
+}
+export function mulberry32(seed) {
+    let a = seed >>> 0;
+    return function next() {
+        a |= 0;
+        a = (a + 0x6d2b79f5) | 0;
+        let t = Math.imul(a ^ (a >>> 15), 1 | a);
+        t = (t + Math.imul(t ^ (t >>> 7), 61 | t)) ^ t;
+        return ((t ^ (t >>> 14)) >>> 0) / 4294967296;
+    };
+}
+export function buildAchlioptas(k, n, seed) {
+    const rand = mulberry32(seed);
+    const matrix = new Array(k);
+    for (let i = 0; i < k; i++) {
+        const row = new Array(n);
+        for (let j = 0; j < n; j++) {
+            const r = rand();
+            if (r < 1 / 6)
+                row[j] = 1;
+            else if (r < 2 / 6)
+                row[j] = -1;
+            else
+                row[j] = 0;
+        }
+        matrix[i] = row;
+    }
+    return matrix;
+}
+export function project(matrix, achlioptas, k) {
+    const rows = matrix.length;
+    const result = new Array(rows);
+    const invSqrtK = 1 / Math.sqrt(k);
+    for (let i = 0; i < rows; i++) {
+        const outRow = new Array(k);
+        for (let col = 0; col < k; col++) {
+            let sum = 0;
+            for (let j = 0; j < matrix[i].length; j++) {
+                sum += matrix[i][j] * achlioptas[col][j];
+            }
+            outRow[col] = sum * invSqrtK;
+        }
+        result[i] = outRow;
+    }
+    return result;
+}
+//# sourceMappingURL=jl-projector.js.map

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package/dist/analysis/jl/kmeans.d.ts

@@ -0,0 +1,11 @@
+import type { KMeansOptions, KMeansResult } from './types.js';
+export declare function detectOrphans(matrix: number[][]): number[];
+export declare class KMeansClusterer {
+    static cluster(matrix: number[][], options?: KMeansOptions): KMeansResult;
+    private static selectK;
+    private static runKMeans;
+    private static kmeanspp;
+    private static lloydIterate;
+    private static silhouette;
+}
+//# sourceMappingURL=kmeans.d.ts.map

package/dist/analysis/jl/kmeans.d.ts.map

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package/dist/analysis/jl/kmeans.js

@@ -0,0 +1,273 @@
+import { mulberry32 } from './jl-projector.js';
+const DEFAULT_MAX_ITERATIONS = 100;
+const DEFAULT_CONVERGENCE_THRESHOLD = 0.001;
+const DEFAULT_SEED = 42;
+const DEFAULT_SAMPLE_SIZE = 500;
+const DEFAULT_SAMPLE_THRESHOLD = 2000;
+export function detectOrphans(matrix) {
+    const orphans = [];
+    for (let i = 0; i < matrix.length; i++) {
+        const row = matrix[i];
+        let zero = true;
+        for (let j = 0; j < row.length; j++) {
+            if (row[j] !== 0) {
+                zero = false;
+                break;
+            }
+        }
+        if (zero)
+            orphans.push(i);
+    }
+    return orphans;
+}
+function euclidean(a, b) {
+    const len = Math.min(a.length, b.length);
+    let sum = 0;
+    for (let i = 0; i < len; i++) {
+        const d = (a[i] ?? 0) - (b[i] ?? 0);
+        sum += d * d;
+    }
+    return Math.sqrt(sum);
+}
+function nearestCentroid(point, centroids) {
+    let bestIndex = 0;
+    let bestDistance = Infinity;
+    for (let c = 0; c < centroids.length; c++) {
+        const d = euclidean(point, centroids[c]);
+        if (d < bestDistance) {
+            bestDistance = d;
+            bestIndex = c;
+        }
+    }
+    return bestIndex;
+}
+export class KMeansClusterer {
+    static cluster(matrix, options = {}) {
+        const seed = options.seed ?? DEFAULT_SEED;
+        const maxIterations = options.maxIterations ?? DEFAULT_MAX_ITERATIONS;
+        const convergenceThreshold = options.convergenceThreshold ?? DEFAULT_CONVERGENCE_THRESHOLD;
+        const sampleSize = options.sampleSize ?? DEFAULT_SAMPLE_SIZE;
+        const sampleThreshold = options.sampleThreshold ?? DEFAULT_SAMPLE_THRESHOLD;
+        const orphanSet = new Set(detectOrphans(matrix));
+        const entityIndices = [];
+        const clean = [];
+        for (let i = 0; i < matrix.length; i++) {
+            if (!orphanSet.has(i)) {
+                entityIndices.push(i);
+                clean.push(matrix[i]);
+            }
+        }
+        const orphanIndices = Array.from(orphanSet).sort((a, b) => a - b);
+        const n = clean.length;
+        if (n === 0) {
+            return {
+                k: 0,
+                assignments: [],
+                centroids: [],
+                silhouetteScore: 0,
+                converged: true,
+                iterations: 0,
+                orphanIndices,
+                entityIndices,
+            };
+        }
+        if (n === 1) {
+            return {
+                k: 1,
+                assignments: [0],
+                centroids: [clean[0]],
+                silhouetteScore: 0,
+                converged: true,
+                iterations: 1,
+                orphanIndices,
+                entityIndices,
+            };
+        }
+        const kInit = Math.max(2, options.kInit ?? 2);
+        const minK = Math.min(Math.max(2, kInit - 2), n);
+        const maxK = Math.min(kInit + 3, n);
+        const kRange = [];
+        for (let k = minK; k <= maxK; k++)
+            kRange.push(k);
+        const selected = this.selectK(clean, kRange, {
+            maxIterations,
+            convergenceThreshold,
+            seed,
+            sampleSize,
+            sampleThreshold,
+        });
+        const base = {
+            k: selected.k,
+            assignments: selected.assignments,
+            centroids: selected.centroids,
+            silhouetteScore: selected.silhouetteScore,
+            converged: selected.converged,
+            iterations: selected.iterations,
+            orphanIndices,
+            entityIndices,
+        };
+        if (selected.silhouetteScore < 0.2) {
+            return { ...base, warning: 'no clear cluster structure detected' };
+        }
+        return base;
+    }
+    static selectK(matrix, kRange, options) {
+        let best = null;
+        for (const k of kRange) {
+            const run = this.runKMeans(matrix, k, options);
+            const sil = this.silhouette(matrix, run.assignments, options);
+            if (best === null || sil > best.silhouetteScore) {
+                best = {
+                    k,
+                    assignments: run.assignments,
+                    centroids: run.centroids,
+                    silhouetteScore: sil,
+                    converged: run.converged,
+                    iterations: run.iterations,
+                };
+            }
+        }
+        return best;
+    }
+    static runKMeans(matrix, k, options) {
+        const rng = mulberry32(options.seed);
+        const initial = this.kmeanspp(matrix, k, rng);
+        return this.lloydIterate(matrix, initial, options.maxIterations, options.convergenceThreshold);
+    }
+    static kmeanspp(matrix, k, rng) {
+        const n = matrix.length;
+        const centroids = [];
+        const first = Math.floor(rng() * n);
+        centroids.push([...matrix[first]]);
+        const d2 = new Array(n).fill(0);
+        for (let c = 1; c < k; c++) {
+            let total = 0;
+            for (let i = 0; i < n; i++) {
+                const nearest = nearestCentroid(matrix[i], centroids);
+                d2[i] = euclidean(matrix[i], centroids[nearest]) ** 2;
+                total += d2[i];
+            }
+            if (total === 0) {
+                centroids.push([...matrix[Math.floor(rng() * n)]]);
+            }
+            else {
+                let r = rng() * total;
+                let idx = n - 1;
+                for (let i = 0; i < n; i++) {
+                    r -= d2[i];
+                    if (r <= 0) {
+                        idx = i;
+                        break;
+                    }
+                }
+                centroids.push([...matrix[idx]]);
+            }
+        }
+        return centroids;
+    }
+    static lloydIterate(matrix, initialCentroids, maxIterations, convergenceThreshold) {
+        const n = matrix.length;
+        const k = initialCentroids.length;
+        const dim = matrix[0].length;
+        let centroids = initialCentroids.map((c) => [...c]);
+        const assignments = new Array(n).fill(0);
+        let converged = false;
+        let iterations = 0;
+        for (let iter = 1; iter <= maxIterations; iter++) {
+            iterations = iter;
+            for (let i = 0; i < n; i++)
+                assignments[i] = nearestCentroid(matrix[i], centroids);
+            const counts = new Array(k).fill(0);
+            const sums = Array.from({ length: k }, () => new Array(dim).fill(0));
+            for (let i = 0; i < n; i++) {
+                const c = assignments[i];
+                counts[c]++;
+                const row = matrix[i];
+                for (let d = 0; d < dim; d++)
+                    sums[c][d] += row[d];
+            }
+            const newCentroids = new Array(k);
+            for (let c = 0; c < k; c++) {
+                if (counts[c] === 0) {
+                    let farIndex = 0;
+                    let farDist = -1;
+                    for (let i = 0; i < n; i++) {
+                        const d = euclidean(matrix[i], centroids[assignments[i]]);
+                        if (d > farDist) {
+                            farDist = d;
+                            farIndex = i;
+                        }
+                    }
+                    newCentroids[c] = [...matrix[farIndex]];
+                }
+                else {
+                    newCentroids[c] = sums[c].map((s) => s / counts[c]);
+                }
+            }
+            let maxShift = 0;
+            for (let c = 0; c < k; c++) {
+                const shift = euclidean(centroids[c], newCentroids[c]);
+                if (shift > maxShift)
+                    maxShift = shift;
+            }
+            centroids = newCentroids;
+            if (maxShift < convergenceThreshold) {
+                converged = true;
+                break;
+            }
+        }
+        return { assignments, centroids, converged, iterations };
+    }
+    static silhouette(matrix, assignments, options) {
+        const n = matrix.length;
+        const k = assignments.length > 0 ? Math.max(...assignments) + 1 : 0;
+        const members = Array.from({ length: k }, () => []);
+        for (let i = 0; i < n; i++)
+            members[assignments[i]].push(i);
+        let sample;
+        if (n > options.sampleThreshold) {
+            const rng = mulberry32(options.seed);
+            const size = Math.min(options.sampleSize, n);
+            sample = new Array(size);
+            for (let s = 0; s < size; s++)
+                sample[s] = Math.floor(rng() * n);
+        }
+        else {
+            sample = Array.from({ length: n }, (_, i) => i);
+        }
+        let sum = 0;
+        let count = 0;
+        for (const i of sample) {
+            const ci = assignments[i];
+            const same = members[ci];
+            let aSum = 0;
+            let aCount = 0;
+            for (const j of same) {
+                if (j === i)
+                    continue;
+                aSum += euclidean(matrix[i], matrix[j]);
+                aCount++;
+            }
+            const a = aCount > 0 ? aSum / aCount : 0;
+            let b = Infinity;
+            for (let c = 0; c < k; c++) {
+                if (c === ci)
+                    continue;
+                const other = members[c];
+                if (other.length === 0)
+                    continue;
+                let bSum = 0;
+                for (const j of other)
+                    bSum += euclidean(matrix[i], matrix[j]);
+                const bMean = bSum / other.length;
+                if (bMean < b)
+                    b = bMean;
+            }
+            const s = aCount === 0 || b === Infinity ? 0 : (b - a) / Math.max(a, b);
+            sum += s;
+            count++;
+        }
+        return count > 0 ? sum / count : 0;
+    }
+}
+//# sourceMappingURL=kmeans.js.map

package/dist/analysis/jl/kmeans.js.map

@@ -0,0 +1 @@
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