@monoes/monograph 1.5.6 → 1.5.7

package/src/__tests__/analysis/dependency-health.test.ts

@@ -1,105 +0,0 @@
-import { describe, it, expect } from 'vitest';
-import {
-  dependencyHealth,
-  type DependencyHealthInput,
-} from '../../analysis/dependency-health.js';
-
-describe('dependencyHealth', () => {
-  it('returns score 1 for a perfectly healthy small graph', () => {
-    const input: DependencyHealthInput = {
-      nodes: ['a', 'b', 'c'],
-      edges: [
-        { sourceId: 'a', targetId: 'b' },
-        { sourceId: 'b', targetId: 'c' },
-      ],
-      cycleCount: 0,
-      deadNodeCount: 0,
-    };
-    const result = dependencyHealth(input);
-    expect(result.score).toBeGreaterThan(0.8);
-  });
-
-  it('penalizes cycles', () => {
-    const baseline: DependencyHealthInput = {
-      nodes: ['a', 'b', 'c'],
-      edges: [
-        { sourceId: 'a', targetId: 'b' },
-        { sourceId: 'b', targetId: 'c' },
-      ],
-      cycleCount: 0,
-      deadNodeCount: 0,
-    };
-    const withCycle: DependencyHealthInput = {
-      ...baseline,
-      edges: [
-        ...baseline.edges,
-        { sourceId: 'c', targetId: 'a' },
-      ],
-      cycleCount: 1,
-    };
-    expect(dependencyHealth(withCycle).score).toBeLessThan(dependencyHealth(baseline).score);
-  });
-
-  it('penalizes dead code', () => {
-    const baseline: DependencyHealthInput = {
-      nodes: ['a', 'b', 'c'],
-      edges: [{ sourceId: 'a', targetId: 'b' }],
-      cycleCount: 0,
-      deadNodeCount: 0,
-    };
-    const withDead: DependencyHealthInput = { ...baseline, deadNodeCount: 2 };
-    expect(dependencyHealth(withDead).score).toBeLessThan(dependencyHealth(baseline).score);
-  });
-
-  it('penalizes high fan-in concentration (god nodes)', () => {
-    // One node targeted by all others → god node
-    const nodes = ['a', 'b', 'c', 'd', 'e', 'hub'];
-    const edges = nodes.slice(0, 5).map(n => ({ sourceId: n, targetId: 'hub' }));
-    const input: DependencyHealthInput = {
-      nodes,
-      edges,
-      cycleCount: 0,
-      deadNodeCount: 0,
-    };
-    const result = dependencyHealth(input);
-    expect(result.score).toBeLessThan(1);
-    expect(result.details.godNodeConcentration).toBeGreaterThan(0);
-  });
-
-  it('returns score in [0, 1] range', () => {
-    const input: DependencyHealthInput = {
-      nodes: ['a', 'b'],
-      edges: [{ sourceId: 'a', targetId: 'b' }, { sourceId: 'b', targetId: 'a' }],
-      cycleCount: 1,
-      deadNodeCount: 1,
-    };
-    const result = dependencyHealth(input);
-    expect(result.score).toBeGreaterThanOrEqual(0);
-    expect(result.score).toBeLessThanOrEqual(1);
-  });
-
-  it('exposes details breakdown', () => {
-    const input: DependencyHealthInput = {
-      nodes: ['a', 'b', 'c'],
-      edges: [{ sourceId: 'a', targetId: 'b' }],
-      cycleCount: 0,
-      deadNodeCount: 1,
-    };
-    const { details } = dependencyHealth(input);
-    expect(typeof details.cyclePenalty).toBe('number');
-    expect(typeof details.deadCodeRatio).toBe('number');
-    expect(typeof details.fanSkew).toBe('number');
-    expect(typeof details.godNodeConcentration).toBe('number');
-  });
-
-  it('handles empty graph without throwing', () => {
-    const input: DependencyHealthInput = {
-      nodes: [],
-      edges: [],
-      cycleCount: 0,
-      deadNodeCount: 0,
-    };
-    expect(() => dependencyHealth(input)).not.toThrow();
-    expect(dependencyHealth(input).score).toBe(1);
-  });
-});

package/src/__tests__/analysis/file-classifier.test.ts

@@ -1,50 +0,0 @@
-import { describe, it, expect } from 'vitest';
-import { classifyFile, classifyContent } from '../../analysis/file-classifier.js';
-
-describe('classifyFile', () => {
-  it('classifies TypeScript as CODE', () => {
-    expect(classifyFile('src/app.ts')).toBe('CODE');
-  });
-  it('classifies Python as CODE', () => {
-    expect(classifyFile('main.py')).toBe('CODE');
-  });
-  it('classifies markdown as DOCUMENT', () => {
-    expect(classifyFile('README.md')).toBe('DOCUMENT');
-  });
-  it('classifies PDF as DOCUMENT', () => {
-    expect(classifyFile('report.pdf')).toBe('DOCUMENT');
-  });
-  it('classifies PNG as IMAGE', () => {
-    expect(classifyFile('logo.png')).toBe('IMAGE');
-  });
-  it('classifies mp4 as VIDEO', () => {
-    expect(classifyFile('demo.mp4')).toBe('VIDEO');
-  });
-  it('classifies arxiv URL as PAPER', () => {
-    expect(classifyFile('https://arxiv.org/abs/2401.00001')).toBe('PAPER');
-  });
-  it('returns UNKNOWN for unrecognized extension', () => {
-    expect(classifyFile('Makefile')).toBe('UNKNOWN');
-  });
-  it('detects paper signals in filename', () => {
-    expect(classifyFile('attention_is_all_you_need.pdf')).toBe('PAPER');
-  });
-});
-
-describe('paper detection signals', () => {
-  it('detects LaTeX cite command', () => {
-    expect(classifyContent('We show \\cite{smith2020} that...')).toBe('PAPER');
-  });
-  it('detects numbered citations', () => {
-    expect(classifyContent('The results [1][2][3] confirm...')).toBe('PAPER');
-  });
-  it('detects DOI pattern', () => {
-    expect(classifyContent('doi:10.1145/3491102.3501993')).toBe('PAPER');
-  });
-  it('detects abstract keyword', () => {
-    expect(classifyContent('Abstract\nIn this paper we propose...')).toBe('PAPER');
-  });
-  it('does not classify random text as PAPER', () => {
-    expect(classifyContent('Hello world this is a readme.')).not.toBe('PAPER');
-  });
-});

package/src/__tests__/analysis/node-similarity.test.ts

@@ -1,81 +0,0 @@
-import { describe, it, expect } from 'vitest';
-import {
-  jaccardSimilarity,
-  findSimilarNodes,
-  buildNeighborMap,
-} from '../../analysis/node-similarity.js';
-
-describe('jaccardSimilarity', () => {
-  it('returns 1 for identical sets', () => {
-    expect(jaccardSimilarity(new Set(['a', 'b', 'c']), new Set(['a', 'b', 'c']))).toBeCloseTo(1);
-  });
-
-  it('returns 0 for disjoint sets', () => {
-    expect(jaccardSimilarity(new Set(['a', 'b']), new Set(['c', 'd']))).toBeCloseTo(0);
-  });
-
-  it('returns 1/3 for sets with one shared and two unique elements', () => {
-    // intersection={b}, union={a,b,c} => 1/3
-    expect(jaccardSimilarity(new Set(['a', 'b']), new Set(['b', 'c']))).toBeCloseTo(1 / 3);
-  });
-
-  it('returns 0 for two empty sets', () => {
-    expect(jaccardSimilarity(new Set(), new Set())).toBeCloseTo(0);
-  });
-
-  it('returns 0 when one set is empty and other is not', () => {
-    expect(jaccardSimilarity(new Set(['a']), new Set())).toBeCloseTo(0);
-  });
-});
-
-describe('buildNeighborMap', () => {
-  it('builds an undirected adjacency map', () => {
-    const edges = [
-      { sourceId: 'a', targetId: 'b' },
-      { sourceId: 'b', targetId: 'c' },
-    ];
-    const map = buildNeighborMap(edges);
-    expect(map.get('a')).toEqual(new Set(['b']));
-    expect(map.get('b')).toEqual(new Set(['a', 'c']));
-    expect(map.get('c')).toEqual(new Set(['b']));
-  });
-});
-
-describe('findSimilarNodes', () => {
-  const edges = [
-    { sourceId: 'a', targetId: 'b' },
-    { sourceId: 'a', targetId: 'c' },
-    { sourceId: 'a', targetId: 'd' },
-    { sourceId: 'x', targetId: 'b' },
-    { sourceId: 'x', targetId: 'c' },
-    { sourceId: 'x', targetId: 'd' },
-    { sourceId: 'y', targetId: 'e' },
-  ];
-
-  it('returns nodes sorted by jaccard similarity descending', () => {
-    const results = findSimilarNodes('a', edges, 5);
-    // 'x' shares all 3 neighbors (b,c,d) — should be top result
-    expect(results[0]?.nodeId).toBe('x');
-    expect(results[0]?.score).toBeGreaterThan(0.5);
-  });
-
-  it('respects the k limit', () => {
-    const results = findSimilarNodes('a', edges, 1);
-    expect(results.length).toBe(1);
-  });
-
-  it('excludes the query node itself', () => {
-    const results = findSimilarNodes('a', edges, 10);
-    expect(results.every(r => r.nodeId !== 'a')).toBe(true);
-  });
-
-  it('returns empty array for unknown node', () => {
-    const results = findSimilarNodes('unknown', edges, 5);
-    expect(results).toHaveLength(0);
-  });
-
-  it('returns only nodes with score > 0', () => {
-    const results = findSimilarNodes('a', edges, 10);
-    expect(results.every(r => r.score > 0)).toBe(true);
-  });
-});

package/src/__tests__/cache/augment-cache.test.ts

@@ -1,55 +0,0 @@
-import { describe, it, expect, beforeEach } from 'vitest';
-import { createAugmentCache, type AugmentCache } from '../../cache/augment-cache.js';
-
-describe('AugmentCache', () => {
-  let cache: AugmentCache;
-
-  beforeEach(() => {
-    cache = createAugmentCache({ maxSize: 3, ttlMs: 60_000 });
-  });
-
-  it('stores and retrieves a value by key', () => {
-    cache.set('k1', 'result1');
-    expect(cache.get('k1')).toBe('result1');
-  });
-
-  it('returns undefined for a missing key', () => {
-    expect(cache.get('missing')).toBeUndefined();
-  });
-
-  it('evicts the oldest entry when maxSize is exceeded', () => {
-    cache.set('k1', 'v1');
-    cache.set('k2', 'v2');
-    cache.set('k3', 'v3');
-    cache.set('k4', 'v4');
-    expect(cache.get('k1')).toBeUndefined();
-    expect(cache.get('k4')).toBe('v4');
-  });
-
-  it('expires entries after TTL', async () => {
-    const shortCache = createAugmentCache({ maxSize: 10, ttlMs: 10 });
-    shortCache.set('k1', 'v1');
-    await new Promise(r => setTimeout(r, 20));
-    expect(shortCache.get('k1')).toBeUndefined();
-  });
-
-  it('reports size correctly', () => {
-    cache.set('k1', 'v1');
-    cache.set('k2', 'v2');
-    expect(cache.size()).toBe(2);
-  });
-
-  it('clears all entries', () => {
-    cache.set('k1', 'v1');
-    cache.set('k2', 'v2');
-    cache.clear();
-    expect(cache.size()).toBe(0);
-  });
-
-  it('provides a makeKey helper that encodes all relevant params', () => {
-    const { makeKey } = cache;
-    const k = makeKey('query', '/repo', 10, 'markdown');
-    expect(k).toContain('query');
-    expect(k).toContain('/repo');
-  });
-});

package/src/__tests__/cli/check-update.test.ts

@@ -1,42 +0,0 @@
-import { describe, it, expect } from 'vitest';
-import Database from 'better-sqlite3';
-import { checkUpdate } from '../../cli/check-update.js';
-
-function makeDb(indexedAt: string | null = null): Database.Database {
-  const db = new Database(':memory:');
-  db.exec(`
-    CREATE TABLE index_meta (key TEXT PRIMARY KEY, value TEXT);
-  `);
-  if (indexedAt) {
-    db.prepare("INSERT INTO index_meta VALUES ('indexed_at', ?)").run(indexedAt);
-  }
-  return db;
-}
-
-describe('checkUpdate', () => {
-  it('returns needsUpdate=true when index is very old', () => {
-    const db = makeDb('2020-01-01T00:00:00.000Z');
-    const result = checkUpdate(db, { maxAgeMs: 1000 });
-    expect(result.needsUpdate).toBe(true);
-  });
-
-  it('returns needsUpdate=false when index is fresh', () => {
-    const db = makeDb(new Date().toISOString());
-    const result = checkUpdate(db, { maxAgeMs: 60_000 });
-    expect(result.needsUpdate).toBe(false);
-  });
-
-  it('returns needsUpdate=true when index_meta has no indexed_at', () => {
-    const db = makeDb(null);
-    const result = checkUpdate(db, {});
-    expect(result.needsUpdate).toBe(true);
-  });
-
-  it('returns indexedAt and ageMs in result', () => {
-    const now = new Date().toISOString();
-    const db = makeDb(now);
-    const result = checkUpdate(db, { maxAgeMs: 60_000 });
-    expect(result.indexedAt).toBe(now);
-    expect(typeof result.ageMs).toBe('number');
-  });
-});

package/src/__tests__/cli/hooks-install.test.ts

@@ -1,56 +0,0 @@
-import { describe, it, expect, beforeEach, afterEach } from 'vitest';
-import { mkdtempSync, rmSync, mkdirSync, readFileSync, existsSync } from 'fs';
-import { join } from 'path';
-import { tmpdir } from 'os';
-import { installGitHooks, uninstallGitHooks, listInstalledHooks } from '../../cli/hooks-install.js';
-
-describe('installGitHooks', () => {
-  let tmpDir: string;
-  let hooksDir: string;
-
-  beforeEach(() => {
-    tmpDir = mkdtempSync(join(tmpdir(), 'hooks-test-'));
-    hooksDir = join(tmpDir, '.git', 'hooks');
-    mkdirSync(hooksDir, { recursive: true });
-  });
-
-  afterEach(() => {
-    rmSync(tmpDir, { recursive: true, force: true });
-  });
-
-  it('creates pre-commit hook with monograph build command', () => {
-    installGitHooks(tmpDir, ['pre-commit']);
-    const hookPath = join(hooksDir, 'pre-commit');
-    expect(existsSync(hookPath)).toBe(true);
-    const content = readFileSync(hookPath, 'utf8');
-    expect(content).toContain('monograph');
-    expect(content).toContain('#!/');
-  });
-
-  it('creates post-merge hook', () => {
-    installGitHooks(tmpDir, ['post-merge']);
-    expect(existsSync(join(hooksDir, 'post-merge'))).toBe(true);
-  });
-
-  it('creates both hooks when both specified', () => {
-    installGitHooks(tmpDir, ['pre-commit', 'post-merge']);
-    expect(existsSync(join(hooksDir, 'pre-commit'))).toBe(true);
-    expect(existsSync(join(hooksDir, 'post-merge'))).toBe(true);
-  });
-
-  it('throws when .git directory does not exist', () => {
-    expect(() => installGitHooks('/nonexistent/repo', ['pre-commit'])).toThrow();
-  });
-
-  it('lists installed hooks', () => {
-    installGitHooks(tmpDir, ['pre-commit']);
-    const installed = listInstalledHooks(tmpDir);
-    expect(installed).toContain('pre-commit');
-  });
-
-  it('uninstalls a hook', () => {
-    installGitHooks(tmpDir, ['pre-commit']);
-    uninstallGitHooks(tmpDir, ['pre-commit']);
-    expect(existsSync(join(hooksDir, 'pre-commit'))).toBe(false);
-  });
-});

package/src/__tests__/cli/hooks-marker.test.ts

@@ -1,138 +0,0 @@
-/**
- * Tests for marker-based hook management enhancements.
- * Covers: append-not-overwrite, uninstall-only-marker-block, post-checkout,
- * Husky detection, rebase guards, and per-hook status details.
- */
-import { describe, it, expect, beforeEach, afterEach } from 'vitest';
-import { mkdtempSync, rmSync, mkdirSync, writeFileSync, readFileSync } from 'fs';
-import { join } from 'path';
-import { tmpdir } from 'os';
-import {
-  installGitHooks,
-  uninstallGitHooks,
-  getHookStatus,
-  HOOK_MARKER_START,
-  HOOK_MARKER_END,
-  type PerHookStatus,
-} from '../../cli/hooks-install.js';
-
-function makeRepo(): string {
-  const dir = mkdtempSync(join(tmpdir(), 'mhook-'));
-  mkdirSync(join(dir, '.git', 'hooks'), { recursive: true });
-  return dir;
-}
-
-describe('marker-based append (not overwrite)', () => {
-  let tmpDir: string;
-  afterEach(() => rmSync(tmpDir, { recursive: true, force: true }));
-
-  it('appends monograph block to existing hook content', () => {
-    tmpDir = makeRepo();
-    const hookPath = join(tmpDir, '.git', 'hooks', 'pre-commit');
-    const existing = '#!/bin/sh\necho "my custom hook"\n';
-    writeFileSync(hookPath, existing, 'utf8');
-
-    installGitHooks(tmpDir, ['pre-commit']);
-    const content = readFileSync(hookPath, 'utf8');
-    expect(content).toContain('my custom hook'); // existing preserved
-    expect(content).toContain(HOOK_MARKER_START);
-    expect(content).toContain('monograph');
-  });
-
-  it('does not duplicate the block on repeated installs', () => {
-    tmpDir = makeRepo();
-    installGitHooks(tmpDir, ['pre-commit']);
-    installGitHooks(tmpDir, ['pre-commit']);
-    const content = readFileSync(join(tmpDir, '.git', 'hooks', 'pre-commit'), 'utf8');
-    const count = (content.match(new RegExp(HOOK_MARKER_START, 'g')) ?? []).length;
-    expect(count).toBe(1);
-  });
-});
-
-describe('marker-based uninstall (only removes block)', () => {
-  let tmpDir: string;
-  afterEach(() => rmSync(tmpDir, { recursive: true, force: true }));
-
-  it('removes only the monograph block, leaves rest of hook intact', () => {
-    tmpDir = makeRepo();
-    const hookPath = join(tmpDir, '.git', 'hooks', 'pre-commit');
-    writeFileSync(hookPath, '#!/bin/sh\necho "keep this"\n', 'utf8');
-
-    installGitHooks(tmpDir, ['pre-commit']);
-    uninstallGitHooks(tmpDir, ['pre-commit']);
-
-    const content = readFileSync(hookPath, 'utf8');
-    expect(content).toContain('keep this');
-    expect(content).not.toContain(HOOK_MARKER_START);
-    expect(content).not.toContain('monograph build');
-  });
-
-  it('deletes the file if it was created entirely by monograph (no prior content)', () => {
-    tmpDir = makeRepo();
-    installGitHooks(tmpDir, ['pre-commit']);
-    uninstallGitHooks(tmpDir, ['pre-commit']);
-    // file should no longer contain the marker block
-    const hookPath = join(tmpDir, '.git', 'hooks', 'pre-commit');
-    try {
-      const content = readFileSync(hookPath, 'utf8');
-      expect(content).not.toContain(HOOK_MARKER_START);
-    } catch {
-      // file deleted entirely is also acceptable
-    }
-  });
-});
-
-describe('post-checkout hook support', () => {
-  let tmpDir: string;
-  afterEach(() => rmSync(tmpDir, { recursive: true, force: true }));
-
-  it('installs post-checkout hook', () => {
-    tmpDir = makeRepo();
-    installGitHooks(tmpDir, ['post-checkout']);
-    const content = readFileSync(join(tmpDir, '.git', 'hooks', 'post-checkout'), 'utf8');
-    expect(content).toContain('monograph');
-  });
-
-  it('post-checkout hook includes rebase/merge skip guard', () => {
-    tmpDir = makeRepo();
-    installGitHooks(tmpDir, ['post-checkout']);
-    const content = readFileSync(join(tmpDir, '.git', 'hooks', 'post-checkout'), 'utf8');
-    // Should skip during rebase or merge operations
-    expect(content).toMatch(/rebase|MERGE|cherry-pick/i);
-  });
-});
-
-describe('rebase guard in hook scripts', () => {
-  let tmpDir: string;
-  afterEach(() => rmSync(tmpDir, { recursive: true, force: true }));
-
-  it('pre-commit hook includes rebase skip guard', () => {
-    tmpDir = makeRepo();
-    installGitHooks(tmpDir, ['pre-commit']);
-    const content = readFileSync(join(tmpDir, '.git', 'hooks', 'pre-commit'), 'utf8');
-    expect(content).toMatch(/rebase|MERGE|cherry-pick/i);
-  });
-});
-
-describe('per-hook status (getHookStatus with details)', () => {
-  let tmpDir: string;
-  afterEach(() => rmSync(tmpDir, { recursive: true, force: true }));
-
-  it('returns per-hook detail objects', () => {
-    tmpDir = makeRepo();
-    installGitHooks(tmpDir, ['pre-commit', 'post-checkout']);
-    const status = getHookStatus(tmpDir);
-    expect(status.perHook).toBeDefined();
-    const preCommit = status.perHook!['pre-commit'];
-    expect(preCommit).toBeDefined();
-    expect((preCommit as PerHookStatus).installed).toBe(true);
-  });
-
-  it('perHook shows not-installed for hooks that were not set up', () => {
-    tmpDir = makeRepo();
-    installGitHooks(tmpDir, ['pre-commit']);
-    const status = getHookStatus(tmpDir);
-    const postMerge = status.perHook?.['post-merge'];
-    expect(postMerge?.installed ?? false).toBe(false);
-  });
-});

package/src/__tests__/cli/hooks-status.test.ts

@@ -1,42 +0,0 @@
-import { describe, it, expect, beforeEach, afterEach } from 'vitest';
-import { mkdtempSync, rmSync, mkdirSync } from 'fs';
-import { join } from 'path';
-import { tmpdir } from 'os';
-import { installGitHooks, getHookStatus, type HookStatus } from '../../cli/hooks-install.js';
-
-describe('getHookStatus', () => {
-  let tmpDir: string;
-
-  beforeEach(() => {
-    tmpDir = mkdtempSync(join(tmpdir(), 'hook-status-'));
-    mkdirSync(join(tmpDir, '.git', 'hooks'), { recursive: true });
-  });
-
-  afterEach(() => { rmSync(tmpDir, { recursive: true, force: true }); });
-
-  it('returns installed=false when no hooks present', () => {
-    const status = getHookStatus(tmpDir);
-    expect(status.installed).toBe(false);
-    expect(status.hooks).toEqual([]);
-  });
-
-  it('returns installed=true when hooks are present', () => {
-    installGitHooks(tmpDir, ['pre-commit', 'post-merge']);
-    const status = getHookStatus(tmpDir);
-    expect(status.installed).toBe(true);
-    expect(status.hooks).toContain('pre-commit');
-    expect(status.hooks).toContain('post-merge');
-  });
-
-  it('returns hooksDir path', () => {
-    const status = getHookStatus(tmpDir);
-    expect(status.hooksDir).toContain('.git/hooks');
-  });
-
-  it('returns installed=false when .git dir missing', () => {
-    const noGitDir = mkdtempSync(join(tmpdir(), 'no-git-'));
-    const status = getHookStatus(noGitDir);
-    expect(status.installed).toBe(false);
-    rmSync(noGitDir, { recursive: true, force: true });
-  });
-});