monomind 1.10.0 → 1.10.2

package/packages/@monomind/cli/bundled-graph/dist/src/pipeline.js

@@ -0,0 +1,269 @@
+import { join } from 'path';
+import { existsSync, mkdirSync, readFileSync, writeFileSync } from 'fs';
+import { collectFiles, corpusHealth } from './detect.js';
+import { FileCache } from './cache.js';
+import { buildGraph as buildGraphologyGraph } from './build.js';
+import { detectCommunities, cohesionScore } from './cluster.js';
+import { buildAnalysis, suggestQuestions } from './analyze.js';
+import { saveGraph } from './export.js';
+import { exportHTML } from './visualize.js';
+import { generateReport } from './report.js';
+import { typescriptExtractor } from './extract/languages/typescript.js';
+import { parseFile } from './extract/tree-sitter-runner.js';
+const DEFAULT_OUTPUT_SUBDIR = '.monomind/graph';
+// ---------------------------------------------------------------------------
+// Experiment loop — adapted from autoresearch's program.md protocol
+//
+// Every buildGraph call appends one row to results.tsv with a quality scalar,
+// then decides BASELINE / KEEP / DISCARD by comparing against the best known
+// result.  The quality metric mirrors autoresearch's val_bpb (a single number
+// to optimise), but for graph structure rather than language model perplexity.
+// ---------------------------------------------------------------------------
+const RESULTS_TSV_HEADER = 'timestamp\tnodes\tedges\tcommunities\tavg_cohesion\tavg_degree\tgraph_quality\tfiles_processed\tstatus\tdescription\n';
+/**
+ * Graph quality scalar.
+ *
+ * avgCohesion × ln(1 + avgDegree)
+ *
+ * Rewards both tight community structure (cohesion) and overall connectivity
+ * (avgDegree).  Higher is better — directly comparable across builds, like
+ * autoresearch's vocab-size-independent bits-per-byte metric.
+ */
+function computeGraphQuality(avgCohesion, nodes, edges) {
+    const avgDegree = nodes > 0 ? (2 * edges) / nodes : 0;
+    return avgCohesion * Math.log(1 + avgDegree);
+}
+/** Read results.tsv and return the best graph_quality seen so far (BASELINE or KEEP rows). */
+function readBestQuality(tsvPath) {
+    if (!existsSync(tsvPath))
+        return -Infinity;
+    try {
+        const lines = readFileSync(tsvPath, 'utf-8').split('\n').filter(Boolean);
+        let best = -Infinity;
+        for (const line of lines.slice(1)) { // skip header
+            const cols = line.split('\t');
+            const status = cols[8]; // status column
+            const quality = parseFloat(cols[6] ?? '0'); // graph_quality column
+            if ((status === 'BASELINE' || status === 'KEEP') && !isNaN(quality)) {
+                if (quality > best)
+                    best = quality;
+            }
+        }
+        return best;
+    }
+    catch {
+        return -Infinity;
+    }
+}
+/** Append one experiment row to results.tsv. Creates file + header if needed. */
+function appendResultsTsv(tsvPath, metrics) {
+    const avgDegree = metrics.nodes > 0 ? (2 * metrics.edges) / metrics.nodes : 0;
+    const description = `${metrics.nodes}n/${metrics.edges}e coh=${metrics.avgCohesion.toFixed(3)} deg=${avgDegree.toFixed(1)}`;
+    const row = [
+        new Date().toISOString(),
+        metrics.nodes,
+        metrics.edges,
+        metrics.communities,
+        metrics.avgCohesion.toFixed(4),
+        avgDegree.toFixed(2),
+        metrics.graphQuality.toFixed(6),
+        metrics.filesProcessed,
+        metrics.status,
+        description,
+    ].join('\t') + '\n';
+    try {
+        if (!existsSync(tsvPath)) {
+            writeFileSync(tsvPath, RESULTS_TSV_HEADER + row, 'utf-8');
+        }
+        else {
+            const existing = readFileSync(tsvPath, 'utf-8');
+            writeFileSync(tsvPath, existing + row, 'utf-8');
+        }
+    }
+    catch { /* TSV tracking is non-fatal */ }
+}
+// Map language identifiers to the extractors we have available.
+// python and go extractors are loaded lazily when their modules exist.
+const EXTRACTOR_MAP = {
+    typescript: typescriptExtractor,
+    javascript: typescriptExtractor, // TS extractor handles JS via regex + tree-sitter-javascript
+};
+/** Attempt to load python/go extractors that may be present in the extract/languages dir. */
+async function tryLoadExtractor(language) {
+    if (EXTRACTOR_MAP[language])
+        return EXTRACTOR_MAP[language];
+    try {
+        const mod = await import(`./extract/languages/${language}.js`);
+        const extractor = (mod[`${language}Extractor`] ?? mod['default']);
+        if (extractor)
+            EXTRACTOR_MAP[language] = extractor;
+        return extractor;
+    }
+    catch {
+        return undefined;
+    }
+}
+export async function buildGraph(projectPath, options = {}) {
+    // Resolve output directory
+    const outputDir = options.outputDir ?? join(projectPath, DEFAULT_OUTPUT_SUBDIR);
+    mkdirSync(outputDir, { recursive: true });
+    const cache = new FileCache(outputDir);
+    // 1. Collect files + corpus health check
+    const files = collectFiles(projectPath, options);
+    const corpusWarnings = corpusHealth(files);
+    // 2. Extract nodes/edges from each file (cache-aware)
+    const merged = {
+        nodes: [],
+        edges: [],
+        hyperedges: [],
+        filesProcessed: 0,
+        fromCache: 0,
+        errors: [],
+    };
+    for (const file of files) {
+        let content;
+        try {
+            content = readFileSync(file.path, 'utf-8');
+        }
+        catch (err) {
+            merged.errors.push(`Cannot read ${file.path}: ${String(err)}`);
+            continue;
+        }
+        const cacheKey = cache.key(file.path, content);
+        let result = cache.get(cacheKey);
+        if (result) {
+            merged.fromCache += 1;
+        }
+        else {
+            const extractor = file.language
+                ? await tryLoadExtractor(file.language)
+                : undefined;
+            if (extractor) {
+                result = parseFile(file.path, content, extractor);
+            }
+            else {
+                result = extractGeneric(file.path, content);
+            }
+            cache.set(cacheKey, result);
+        }
+        merged.nodes.push(...result.nodes);
+        merged.edges.push(...result.edges);
+        if (result.hyperedges)
+            merged.hyperedges.push(...result.hyperedges);
+        merged.filesProcessed += 1;
+        merged.errors.push(...result.errors);
+    }
+    // 3. Build graphology graph (dedup + stub endpoints)
+    const graph = buildGraphologyGraph(merged);
+    // 4. Community detection (Louvain with directory-based fallback)
+    await detectCommunities(graph);
+    // 5. Degree annotation
+    graph.forEachNode((id) => {
+        graph.setNodeAttribute(id, 'degree', graph.degree(id));
+    });
+    // 6. Build analysis (god nodes, surprise edges, communities, stats)
+    const analysis = buildAnalysis(graph, outputDir);
+    // 6b. Suggest questions the graph can answer
+    const questions = suggestQuestions(graph, analysis.communities);
+    // 6c. Compute cohesion scores per community
+    const cohesionScores = {};
+    for (const [cidStr, memberIds] of Object.entries(analysis.communities)) {
+        cohesionScores[Number(cidStr)] = cohesionScore(graph, memberIds);
+    }
+    // 6d. Graph quality metric + experiment loop (autoresearch protocol)
+    const cohesionValues = Object.values(cohesionScores);
+    const avgCohesion = cohesionValues.length > 0
+        ? cohesionValues.reduce((a, b) => a + b, 0) / cohesionValues.length
+        : 0;
+    const graphQuality = computeGraphQuality(avgCohesion, graph.order, graph.size);
+    const tsvPath = join(outputDir, 'results.tsv');
+    const prevBest = readBestQuality(tsvPath);
+    const experimentStatus = prevBest === -Infinity
+        ? 'BASELINE'
+        : graphQuality > prevBest * 1.001 // 0.1% improvement threshold
+            ? 'KEEP'
+            : 'DISCARD';
+    appendResultsTsv(tsvPath, {
+        nodes: graph.order,
+        edges: graph.size,
+        communities: analysis.stats.communities,
+        avgCohesion,
+        graphQuality,
+        filesProcessed: merged.filesProcessed,
+        status: experimentStatus,
+    });
+    // 7. Persist to disk
+    saveGraph(graph, outputDir, projectPath);
+    const graphPath = join(outputDir, 'graph.json');
+    // 7b. Generate and save markdown report (non-fatal)
+    const reportPath = join(outputDir, 'GRAPH_REPORT.md');
+    try {
+        const totalWords = merged.nodes.reduce((sum, n) => sum + (n.linesOfCode ?? 0) * 10, 0);
+        const reportMd = generateReport(graph, analysis, cohesionScores, {
+            projectPath,
+            questions,
+            corpusStats: corpusWarnings.length > 0
+                ? { totalFiles: files.length, totalWords, warning: corpusWarnings[0] }
+                : { totalFiles: files.length, totalWords },
+        });
+        writeFileSync(reportPath, reportMd, 'utf-8');
+    }
+    catch { /* report generation is non-fatal */ }
+    // 8. Serialize to the public return type
+    const serialized = {
+        version: '1.0.0',
+        builtAt: new Date().toISOString(),
+        projectPath,
+        directed: true,
+        multigraph: false,
+        nodes: graph.nodes().map((id) => ({
+            id,
+            ...graph.getNodeAttributes(id),
+        })),
+        links: graph.edges().map((edgeId) => ({
+            source: graph.source(edgeId),
+            target: graph.target(edgeId),
+            ...graph.getEdgeAttributes(edgeId),
+        })),
+    };
+    // 9. Generate interactive HTML visualization (non-fatal)
+    try {
+        exportHTML(serialized, outputDir);
+    }
+    catch {
+        // Visualization is best-effort; never block the build
+    }
+    return {
+        graph: serialized,
+        analysis,
+        questions,
+        corpusWarnings,
+        filesProcessed: merged.filesProcessed,
+        fromCache: merged.fromCache,
+        graphPath,
+        reportPath,
+        graphQuality,
+        experimentStatus,
+    };
+}
+// ---------------------------------------------------------------------------
+// Internal: minimal fallback for languages without a dedicated extractor
+// ---------------------------------------------------------------------------
+function extractGeneric(filePath, content) {
+    return {
+        nodes: [
+            {
+                id: filePath,
+                label: filePath.split('/').pop() ?? filePath,
+                fileType: 'code',
+                sourceFile: filePath,
+                linesOfCode: content.split('\n').length,
+            },
+        ],
+        edges: [],
+        filesProcessed: 1,
+        fromCache: 0,
+        errors: [],
+    };
+}
+//# sourceMappingURL=pipeline.js.map

package/packages/@monomind/cli/bundled-graph/dist/src/pipeline.js.map

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package/packages/@monomind/cli/bundled-graph/dist/src/report.d.ts

@@ -0,0 +1,26 @@
+import type Graph from 'graphology';
+import type { GraphAnalysis, GraphQuestion } from './types.js';
+export interface CorpusStats {
+    totalFiles: number;
+    totalWords: number;
+    warning?: string;
+}
+export interface ReportOptions {
+    projectPath?: string;
+    tokenCost?: {
+        input: number;
+        output: number;
+    };
+    corpusStats?: CorpusStats;
+    questions?: GraphQuestion[];
+}
+/**
+ * Generate the full markdown report string.
+ *
+ * @param graph     - The annotated Graphology graph (with `community` attributes set)
+ * @param analysis  - Result of buildAnalysis()
+ * @param cohesionScores - Map of communityId → cohesion score (0–1)
+ * @param options   - Optional metadata (projectPath, tokenCost, corpusStats, questions)
+ */
+export declare function generateReport(graph: Graph, analysis: GraphAnalysis, cohesionScores?: Record<number, number>, options?: ReportOptions): string;
+//# sourceMappingURL=report.d.ts.map

package/packages/@monomind/cli/bundled-graph/dist/src/report.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"report.d.ts","sourceRoot":"","sources":["../../src/report.ts"],"names":[],"mappings":"AAKA,OAAO,KAAK,KAAK,MAAM,YAAY,CAAC;AACpC,OAAO,KAAK,EAAE,aAAa,EAAE,aAAa,EAAE,MAAM,YAAY,CAAC;AAG/D,MAAM,WAAW,WAAW;IAC1B,UAAU,EAAE,MAAM,CAAC;IACnB,UAAU,EAAE,MAAM,CAAC;IACnB,OAAO,CAAC,EAAE,MAAM,CAAC;CAClB;AAED,MAAM,WAAW,aAAa;IAC5B,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,SAAS,CAAC,EAAE;QAAE,KAAK,EAAE,MAAM,CAAC;QAAC,MAAM,EAAE,MAAM,CAAA;KAAE,CAAC;IAC9C,WAAW,CAAC,EAAE,WAAW,CAAC;IAC1B,SAAS,CAAC,EAAE,aAAa,EAAE,CAAC;CAC7B;AAkCD;;;;;;;GAOG;AACH,wBAAgB,cAAc,CAC5B,KAAK,EAAE,KAAK,EACZ,QAAQ,EAAE,aAAa,EACvB,cAAc,CAAC,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,EACvC,OAAO,GAAE,aAAkB,GAC1B,MAAM,CAkMR"}

package/packages/@monomind/cli/bundled-graph/dist/src/report.js

@@ -0,0 +1,214 @@
+/**
+ * Generate GRAPH_REPORT.md — the human-readable audit trail.
+ * Mirrors the output format of Python graphify's report.py.
+ */
+import { basename } from 'path';
+import { cohesionScore } from './cluster.js';
+// ---------------------------------------------------------------------------
+// Helpers
+// ---------------------------------------------------------------------------
+/** True if the node label matches its own filename — AST file-hub node. */
+function isFileNode(graph, nodeId) {
+    const label = graph.getNodeAttribute(nodeId, 'label') || '';
+    const sourceFile = graph.getNodeAttribute(nodeId, 'sourceFile') || '';
+    if (!label || !sourceFile)
+        return false;
+    if (label === basename(sourceFile))
+        return true;
+    if (label.startsWith('.') && label.endsWith('()'))
+        return true;
+    return false;
+}
+/** Auto-derive a community label from its member nodes' source directories. */
+function communityLabel(graph, memberIds) {
+    const dirCounts = {};
+    for (const id of memberIds) {
+        const src = graph.getNodeAttribute(id, 'sourceFile') || '';
+        if (!src)
+            continue;
+        const parts = src.split('/');
+        const dir = parts.length > 1 ? parts[parts.length - 2] : parts[0];
+        dirCounts[dir] = (dirCounts[dir] ?? 0) + 1;
+    }
+    const sorted = Object.entries(dirCounts).sort(([, a], [, b]) => b - a);
+    return sorted.length > 0 ? sorted[0][0] : 'misc';
+}
+// ---------------------------------------------------------------------------
+// Main generator
+// ---------------------------------------------------------------------------
+/**
+ * Generate the full markdown report string.
+ *
+ * @param graph     - The annotated Graphology graph (with `community` attributes set)
+ * @param analysis  - Result of buildAnalysis()
+ * @param cohesionScores - Map of communityId → cohesion score (0–1)
+ * @param options   - Optional metadata (projectPath, tokenCost, corpusStats, questions)
+ */
+export function generateReport(graph, analysis, cohesionScores, options = {}) {
+    const today = new Date().toISOString().split('T')[0];
+    const root = options.projectPath ?? '.';
+    const scores = cohesionScores ?? {};
+    // Confidence breakdown
+    const totalEdges = graph.size || 1;
+    const confCounts = {};
+    const infScores = [];
+    graph.forEachEdge((_, attrs) => {
+        const c = attrs.confidence || 'EXTRACTED';
+        confCounts[c] = (confCounts[c] ?? 0) + 1;
+        if (c === 'INFERRED') {
+            const cs = attrs.confidenceScore;
+            if (cs !== undefined)
+                infScores.push(cs);
+        }
+    });
+    const extPct = Math.round((confCounts['EXTRACTED'] ?? 0) / totalEdges * 100);
+    const infPct = Math.round((confCounts['INFERRED'] ?? 0) / totalEdges * 100);
+    const ambPct = Math.round((confCounts['AMBIGUOUS'] ?? 0) / totalEdges * 100);
+    const infAvg = infScores.length > 0
+        ? (infScores.reduce((a, b) => a + b, 0) / infScores.length).toFixed(2)
+        : null;
+    const lines = [
+        `# Graph Report - ${root}  (${today})`,
+        '',
+        '## Corpus Check',
+    ];
+    // Corpus check
+    const cs = options.corpusStats;
+    if (cs?.warning) {
+        lines.push(`- ${cs.warning}`);
+    }
+    else if (cs) {
+        lines.push(`- ${cs.totalFiles} files · ~${cs.totalWords.toLocaleString()} words`);
+        lines.push('- Verdict: corpus is large enough that graph structure adds value.');
+    }
+    // Summary
+    const infEdgeCount = confCounts['INFERRED'] ?? 0;
+    const infTag = infAvg !== null
+        ? ` · INFERRED: ${infEdgeCount} edges (avg confidence: ${infAvg})`
+        : '';
+    const tokenCost = options.tokenCost;
+    lines.push('', '## Summary');
+    lines.push(`- ${graph.order} nodes · ${graph.size} edges · ${analysis.stats.communities} communities detected`);
+    lines.push(`- Extraction: ${extPct}% EXTRACTED · ${infPct}% INFERRED · ${ambPct}% AMBIGUOUS${infTag}`);
+    if (tokenCost) {
+        lines.push(`- Token cost: ${tokenCost.input.toLocaleString()} input · ${tokenCost.output.toLocaleString()} output`);
+    }
+    // God nodes
+    lines.push('', '## God Nodes (most connected - your core abstractions)');
+    analysis.godNodes.forEach((node, i) => {
+        lines.push(`${i + 1}. \`${node.label}\` - ${node.degree} edges`);
+    });
+    // Surprising connections
+    lines.push('', '## Surprising Connections (you probably didn\'t know these)');
+    if (analysis.surprises.length > 0) {
+        for (const s of analysis.surprises) {
+            const conf = s.confidence;
+            const confTag = conf === 'INFERRED'
+                ? `INFERRED ${s.confidenceScore?.toFixed(2) ?? ''}`
+                : conf;
+            const semTag = s.relation === 'semantically_similar_to' ? ' [semantically similar]' : '';
+            lines.push(`- \`${s.from}\` --${s.relation}--> \`${s.to}\`  [${confTag}]${semTag}`);
+            lines.push(`  ${s.fromFile} → ${s.toFile}`);
+        }
+    }
+    else {
+        lines.push('- None detected - all connections are within the same source files.');
+    }
+    // Hyperedges (stored in graph metadata)
+    const hyperedges = graph.getAttribute('hyperedges') ?? [];
+    if (hyperedges.length > 0) {
+        lines.push('', '## Hyperedges (group relationships)');
+        for (const h of hyperedges) {
+            const he = h;
+            const nodeLabels = (he.nodes ?? []).join(', ');
+            const conf = he.confidence ?? 'INFERRED';
+            const cs2 = he.confidenceScore;
+            const confTag = cs2 !== undefined ? `${conf} ${cs2.toFixed(2)}` : conf;
+            lines.push(`- **${he.label ?? ''}** — ${nodeLabels} [${confTag}]`);
+        }
+    }
+    // Communities
+    lines.push('', '## Communities');
+    for (const [cidStr, memberIds] of Object.entries(analysis.communities)) {
+        const cid = Number(cidStr);
+        const label = communityLabel(graph, memberIds);
+        const score = scores[cid] !== undefined ? scores[cid] : cohesionScore(graph, memberIds);
+        const realNodes = memberIds.filter((id) => graph.hasNode(id) && !isFileNode(graph, id));
+        const display = realNodes
+            .slice(0, 8)
+            .map((id) => graph.getNodeAttribute(id, 'label') || id);
+        const suffix = realNodes.length > 8 ? ` (+${realNodes.length - 8} more)` : '';
+        lines.push('');
+        lines.push(`### Community ${cid} - "${label}"`);
+        lines.push(`Cohesion: ${score.toFixed(2)}`);
+        lines.push(`Nodes (${realNodes.length}): ${display.join(', ')}${suffix}`);
+    }
+    // Ambiguous edges
+    const ambiguous = [];
+    graph.forEachEdge((_, attrs, source, target) => {
+        if (attrs.confidence === 'AMBIGUOUS') {
+            ambiguous.push({ u: source, v: target, attrs: attrs });
+        }
+    });
+    if (ambiguous.length > 0) {
+        lines.push('', '## Ambiguous Edges - Review These');
+        for (const { u, v, attrs } of ambiguous) {
+            const ul = graph.getNodeAttribute(u, 'label') || u;
+            const vl = graph.getNodeAttribute(v, 'label') || v;
+            lines.push(`- \`${ul}\` → \`${vl}\`  [AMBIGUOUS]`);
+            lines.push(`  ${attrs.sourceFile || ''} · relation: ${attrs.relation || 'unknown'}`);
+        }
+    }
+    // Knowledge gaps
+    const isolated = [];
+    graph.forEachNode((id) => {
+        if (graph.degree(id) <= 1 && !isFileNode(graph, id)) {
+            isolated.push(id);
+        }
+    });
+    const thinCommunities = Object.entries(analysis.communities).filter(([, nodes]) => nodes.length < 3);
+    const gapCount = isolated.length + thinCommunities.length;
+    if (gapCount > 0 || ambPct > 20) {
+        lines.push('', '## Knowledge Gaps');
+        if (isolated.length > 0) {
+            const labels = isolated
+                .slice(0, 5)
+                .map((id) => graph.getNodeAttribute(id, 'label') || id);
+            const suffix = isolated.length > 5 ? ` (+${isolated.length - 5} more)` : '';
+            lines.push(`- **${isolated.length} isolated node(s):** ${labels.map((l) => `\`${l}\``).join(', ')}${suffix}`);
+            lines.push('  These have ≤1 connection - possible missing edges or undocumented components.');
+        }
+        for (const [cidStr, nodes] of thinCommunities) {
+            const cid = Number(cidStr);
+            const label = communityLabel(graph, nodes);
+            const nodeLabels = nodes
+                .map((id) => graph.getNodeAttribute(id, 'label') || id);
+            lines.push(`- **Thin community \`${label}\`** (${nodes.length} nodes): ${nodeLabels.map((l) => `\`${l}\``).join(', ')}`);
+            lines.push('  Too small to be a meaningful cluster - may be noise or needs more connections extracted.');
+        }
+        if (ambPct > 20) {
+            lines.push(`- **High ambiguity: ${ambPct}% of edges are AMBIGUOUS.** Review the Ambiguous Edges section above.`);
+        }
+    }
+    // Suggested questions
+    const questions = options.questions ?? [];
+    if (questions.length > 0) {
+        lines.push('', '## Suggested Questions');
+        const noSignal = questions.length === 1 && questions[0].type === 'ISOLATED_NODE' && questions[0].nodes.length === 0;
+        if (noSignal) {
+            lines.push(`_${questions[0].question}_`);
+        }
+        else {
+            lines.push('_Questions this graph is uniquely positioned to answer:_');
+            lines.push('');
+            for (const q of questions) {
+                if (q.question) {
+                    lines.push(`- **${q.question}**`);
+                    lines.push(`  _Priority: ${q.priority}. Nodes: ${q.nodes.slice(0, 3).map((n) => `\`${n}\``).join(', ')}_`);
+                }
+            }
+        }
+    }
+    return lines.join('\n');
+}
+//# sourceMappingURL=report.js.map

package/packages/@monomind/cli/bundled-graph/dist/src/report.js.map

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