symbiote-cli 0.1.0

package/dist/src/commands/install.js

@@ -0,0 +1,67 @@
+import fs from 'node:fs';
+import path from 'node:path';
+import { fileURLToPath } from 'node:url';
+import * as p from '@clack/prompts';
+import pc from 'picocolors';
+import { ensureSymbioteHome } from '#utils/config.js';
+const __dirname = path.dirname(fileURLToPath(import.meta.url));
+const CLAUDE_SKILLS_DIR = path.join(process.env.HOME ?? process.env.USERPROFILE ?? '', '.claude', 'skills');
+function getSkillSourceDir() {
+    return path.resolve(__dirname, '../../../skills/symbiote-init');
+}
+function installSkill() {
+    try {
+        const skillSource = path.join(getSkillSourceDir(), 'SKILL.md');
+        if (!fs.existsSync(skillSource)) {
+            return { success: false, message: 'Skill source not found' };
+        }
+        const destDir = path.join(CLAUDE_SKILLS_DIR, 'symbiote-init');
+        fs.mkdirSync(destDir, { recursive: true });
+        fs.copyFileSync(skillSource, path.join(destDir, 'SKILL.md'));
+        return { success: true, message: 'Skill installed' };
+    }
+    catch (err) {
+        return {
+            success: false,
+            message: err instanceof Error ? err.message : 'Skill install failed',
+        };
+    }
+}
+export async function cmdInstall() {
+    const { ensureClaudeHooks, detectInstalledAgents, connectAgent } = await import('#init/agent-connector.js');
+    p.intro(pc.bold('Symbiote') + pc.dim(' — Installing globally'));
+    ensureSymbioteHome();
+    const agents = detectInstalledAgents();
+    const installed = agents.filter((a) => a.installed);
+    for (const agent of installed) {
+        const result = connectAgent(agent);
+        if (result.success) {
+            p.log.success(`${agent.name}: MCP registered`);
+        }
+        else {
+            p.log.error(`${agent.name}: ${result.message}`);
+        }
+    }
+    const hasClaude = installed.some((a) => a.id === 'claude-code');
+    if (hasClaude) {
+        const hooksResult = ensureClaudeHooks();
+        if (hooksResult.success) {
+            p.log.success('Claude Code: hooks registered');
+        }
+        else {
+            p.log.error(`Claude Code hooks failed: ${hooksResult.message}`);
+        }
+        const skillResult = installSkill();
+        if (skillResult.success) {
+            p.log.success('Claude Code: skill /symbiote-init installed');
+        }
+        else {
+            p.log.error(`Skill failed: ${skillResult.message}`);
+        }
+    }
+    if (installed.length === 0) {
+        p.log.warn('No supported AI editors detected');
+    }
+    p.outro(`Run ${pc.cyan('/symbiote-init')} in Claude Code to set up your project.`);
+}
+//# sourceMappingURL=install.js.map

package/dist/src/commands/install.js.map

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package/dist/src/commands/mcp.d.ts

@@ -0,0 +1,2 @@
+export declare function cmdMcp(): Promise<void>;
+//# sourceMappingURL=mcp.d.ts.map

package/dist/src/commands/mcp.d.ts.map

@@ -0,0 +1 @@
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package/dist/src/commands/mcp.js

@@ -0,0 +1,51 @@
+import path from 'node:path';
+import { fileURLToPath } from 'node:url';
+import { createDatabase } from '#storage/db.js';
+import { ensureBrainDir, ensureSymbioteHome, getBrainDbPath, getProjectPort, writePortFile, clearPortFile, } from '#utils/config.js';
+import { createMcpServer } from '#mcp/server.js';
+import { createServerContext } from '#mcp/context.js';
+import { handleHttpRequest } from './shared.js';
+const __dirname = path.dirname(fileURLToPath(import.meta.url));
+export async function cmdMcp() {
+    const { StdioServerTransport } = await import('@modelcontextprotocol/sdk/server/stdio.js');
+    const http = await import('node:http');
+    const projectRoot = process.cwd();
+    const brainDir = ensureBrainDir(projectRoot);
+    const symbioteHome = ensureSymbioteHome();
+    const dbPath = getBrainDbPath(projectRoot);
+    const db = await createDatabase(dbPath);
+    const ctx = await createServerContext({
+        db,
+        brainDir,
+        symbioteHome,
+        rootDir: projectRoot,
+    });
+    const { server } = createMcpServer(ctx);
+    const transport = new StdioServerTransport();
+    await server.connect(transport);
+    const port = getProjectPort(projectRoot);
+    const webDistDir = path.resolve(__dirname, '../../../../web/dist');
+    const httpServer = http.createServer((req, res) => {
+        const url = new URL(req.url ?? '/', `http://localhost:${port}`);
+        handleHttpRequest(ctx, webDistDir, port, url, req, res).catch((err) => {
+            if (!res.headersSent) {
+                res.writeHead(500, { 'Content-Type': 'application/json' });
+                res.end(JSON.stringify({ error: String(err) }));
+            }
+        });
+    });
+    httpServer.listen(port, () => {
+        writePortFile(projectRoot, port);
+        process.stderr.write(`[symbiote] Web UI available at http://localhost:${port}\n`);
+    });
+    httpServer.on('error', () => {
+        // Port already in use — skip HTTP server silently
+    });
+    process.on('SIGINT', () => {
+        clearPortFile(projectRoot);
+        httpServer.close();
+        db.close();
+        process.exit(0);
+    });
+}
+//# sourceMappingURL=mcp.js.map

package/dist/src/commands/mcp.js.map

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package/dist/src/commands/scan.d.ts

@@ -0,0 +1,2 @@
+export declare function cmdScan(flags: Record<string, string | boolean>): Promise<void>;
+//# sourceMappingURL=scan.d.ts.map

package/dist/src/commands/scan.d.ts.map

@@ -0,0 +1 @@
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package/dist/src/commands/scan.js

@@ -0,0 +1,46 @@
+import * as p from '@clack/prompts';
+import pc from 'picocolors';
+import { ensureBrainDir, getBrainDbPath } from '#utils/config.js';
+import { createDatabaseWithRetry } from './shared.js';
+import { CortexRepository } from '#cortex/repository.js';
+import { CortexEngine } from '#cortex/engine.js';
+import { createCortexSchema, refreshSymbolsTable } from '#cortex/schema.js';
+export async function cmdScan(flags) {
+    const projectRoot = process.cwd();
+    ensureBrainDir(projectRoot);
+    const dbPath = getBrainDbPath(projectRoot);
+    const db = await createDatabaseWithRetry(dbPath);
+    await createCortexSchema(db);
+    const cortexRepo = new CortexRepository(db);
+    const engine = new CortexEngine(cortexRepo);
+    const s = p.spinner();
+    s.start('Scanning codebase (cortex pipeline)...');
+    const result = await engine.run({
+        rootDir: projectRoot,
+        force: flags.force === true,
+    });
+    await refreshSymbolsTable(db);
+    await db.close();
+    const stageNames = [
+        'Structure',
+        'Symbols',
+        'Resolution',
+        'Call Graph',
+        'Type Inference',
+        'Flow Analysis',
+        'Topology',
+        'Intelligence',
+    ];
+    const completedStages = result.stages
+        .map((st, i) => st.filesProcessed > 0 || st.nodesCreated > 0 || st.edgesCreated > 0
+        ? stageNames[i]
+        : null)
+        .filter(Boolean);
+    s.stop(`Depth ${result.maxDepth + 1}/8` +
+        pc.dim(` · ${result.totalFiles} files · ${result.totalNodes} nodes · ${result.totalEdges} edges` +
+            ` · ${Math.round(result.totalDurationMs / 1000)}s`));
+    if (completedStages.length > 0) {
+        p.log.info(pc.dim(`Stages: ${completedStages.join(' → ')}`));
+    }
+}
+//# sourceMappingURL=scan.js.map

package/dist/src/commands/scan.js.map

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package/dist/src/commands/serve.d.ts

@@ -0,0 +1,2 @@
+export declare function cmdServe(flags: Record<string, string | boolean>): Promise<void>;
+//# sourceMappingURL=serve.d.ts.map

package/dist/src/commands/serve.d.ts.map

@@ -0,0 +1 @@
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package/dist/src/commands/serve.js

@@ -0,0 +1,93 @@
+import path from 'node:path';
+import { fileURLToPath } from 'node:url';
+import * as p from '@clack/prompts';
+import pc from 'picocolors';
+import { ensureBrainDir, ensureSymbioteHome, getBrainDbPath, getProjectPort, writePortFile, clearPortFile, } from '#utils/config.js';
+import { createMcpServer } from '#mcp/server.js';
+import { createServerContext } from '#mcp/context.js';
+import { createDatabaseWithRetry, isPortServing, openBrowser, handleHttpRequest, } from './shared.js';
+const __dirname = path.dirname(fileURLToPath(import.meta.url));
+export async function cmdServe(flags) {
+    const http = await import('node:http');
+    const projectRoot = process.cwd();
+    const port = typeof flags.port === 'string' ? parseInt(flags.port, 10) : getProjectPort(projectRoot);
+    const noOpen = !!flags['no-open'];
+    const alreadyRunning = await isPortServing(port);
+    if (alreadyRunning) {
+        const url = `http://localhost:${port}`;
+        p.intro(pc.bold('Symbiote') + pc.dim(' — Brain is alive'));
+        p.log.info(`${pc.dim('Web UI:')}  ${url}`);
+        if (!noOpen) {
+            p.outro(pc.dim('Opening browser...'));
+            openBrowser(url);
+        }
+        else {
+            p.outro(pc.dim('Already running.'));
+        }
+        return;
+    }
+    const brainDir = ensureBrainDir(projectRoot);
+    const symbioteHome = ensureSymbioteHome();
+    const dbPath = getBrainDbPath(projectRoot);
+    const db = await createDatabaseWithRetry(dbPath);
+    const ctx = await createServerContext({
+        db,
+        brainDir,
+        symbioteHome,
+        rootDir: projectRoot,
+    });
+    const { SSEServerTransport } = await import('@modelcontextprotocol/sdk/server/sse.js');
+    const sessions = new Map();
+    const webDistDir = path.resolve(__dirname, '../../../../web/dist');
+    const httpServer = http.createServer((req, res) => {
+        const url = new URL(req.url ?? '/', `http://localhost:${port}`);
+        if (url.pathname === '/sse' && req.method === 'GET') {
+            const transport = new SSEServerTransport('/messages', res);
+            const { server } = createMcpServer(ctx);
+            sessions.set(transport.sessionId, { transport, server });
+            server.connect(transport).catch((err) => {
+                sessions.delete(transport.sessionId);
+                if (!res.headersSent) {
+                    res.writeHead(500);
+                    res.end(String(err));
+                }
+            });
+            return;
+        }
+        if (url.pathname === '/messages' && req.method === 'POST') {
+            const sessionId = url.searchParams.get('sessionId');
+            const session = sessionId ? sessions.get(sessionId) : undefined;
+            if (!session) {
+                res.writeHead(404);
+                res.end('Session not found');
+                return;
+            }
+            session.transport.handlePostMessage(req, res);
+            return;
+        }
+        handleHttpRequest(ctx, webDistDir, port, url, req, res).catch((err) => {
+            if (!res.headersSent) {
+                res.writeHead(500, { 'Content-Type': 'application/json' });
+                res.end(JSON.stringify({ error: String(err) }));
+            }
+        });
+    });
+    httpServer.listen(port, () => {
+        writePortFile(projectRoot, port);
+        const url = `http://localhost:${port}`;
+        p.intro(pc.bold('Symbiote') + pc.dim(' — Brain is alive'));
+        p.log.info(`${pc.dim('Web UI:')}       ${url}\n` +
+            `${pc.dim('MCP SSE:')}      http://localhost:${port}/sse\n` +
+            `${pc.dim('Health:')}       http://localhost:${port}/internal/health`);
+        p.outro(pc.dim('Press Ctrl+C to stop.'));
+        if (!noOpen)
+            openBrowser(url);
+    });
+    process.on('SIGINT', () => {
+        clearPortFile(projectRoot);
+        httpServer.close();
+        db.close();
+        process.exit(0);
+    });
+}
+//# sourceMappingURL=serve.js.map

package/dist/src/commands/serve.js.map

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package/dist/src/commands/shared.d.ts

@@ -0,0 +1,11 @@
+import type { IncomingMessage, ServerResponse } from 'node:http';
+import { createDatabase } from '#storage/db.js';
+import type { createServerContext } from '#mcp/context.js';
+export type SymbioteDB = Awaited<ReturnType<typeof createDatabase>>;
+export declare function serveStatic(webDistDir: string, pathname: string, res: ServerResponse): boolean;
+export declare function openBrowser(url: string): void;
+export declare function killSymbioteProcesses(): Promise<boolean>;
+export declare function createDatabaseWithRetry(dbPath: string): Promise<SymbioteDB>;
+export declare function isPortServing(port: number): Promise<boolean>;
+export declare function handleHttpRequest(ctx: Awaited<ReturnType<typeof createServerContext>>, webDistDir: string, _port: number, url: URL, req: IncomingMessage, res: ServerResponse): Promise<void>;
+//# sourceMappingURL=shared.d.ts.map

package/dist/src/commands/shared.d.ts.map

@@ -0,0 +1 @@
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package/dist/src/commands/shared.js

@@ -0,0 +1,137 @@
+import fs from 'node:fs';
+import path from 'node:path';
+import { createDatabase } from '#storage/db.js';
+import { handleApiRequest, handleInternalEvent, handleSseConnection, handleHookContext, handleHookRequest, handleSessionStartRequest, } from '#mcp/http-api.js';
+const MIME_TYPES = {
+    '.html': 'text/html',
+    '.js': 'application/javascript',
+    '.css': 'text/css',
+    '.json': 'application/json',
+    '.png': 'image/png',
+    '.svg': 'image/svg+xml',
+    '.ico': 'image/x-icon',
+    '.woff2': 'font/woff2',
+    '.woff': 'font/woff',
+    '.map': 'application/json',
+};
+export function serveStatic(webDistDir, pathname, res) {
+    const safePath = path.normalize(pathname).replace(/^(\.\.[/\\])+/, '');
+    let filePath = path.join(webDistDir, safePath);
+    if (!filePath.startsWith(webDistDir))
+        return false;
+    if (!fs.existsSync(filePath) || fs.statSync(filePath).isDirectory()) {
+        filePath = path.join(webDistDir, 'index.html');
+    }
+    if (!fs.existsSync(filePath))
+        return false;
+    const ext = path.extname(filePath);
+    const contentType = MIME_TYPES[ext] ?? 'application/octet-stream';
+    res.writeHead(200, { 'Content-Type': contentType });
+    fs.createReadStream(filePath).pipe(res);
+    return true;
+}
+export function openBrowser(url) {
+    const cmd = process.platform === 'darwin'
+        ? 'open'
+        : process.platform === 'win32'
+            ? 'start'
+            : 'xdg-open';
+    import('node:child_process').then(({ execFile }) => execFile(cmd, [url]));
+}
+export async function killSymbioteProcesses() {
+    const { execSync: exec } = await import('node:child_process');
+    try {
+        const output = exec('pgrep -f "symbiote-cli mcp|symbiote mcp"', {
+            encoding: 'utf-8',
+        }).trim();
+        if (!output)
+            return false;
+        const pids = output
+            .split('\n')
+            .map((p) => parseInt(p, 10))
+            .filter((pid) => pid && pid !== process.pid);
+        if (pids.length === 0)
+            return false;
+        for (const pid of pids) {
+            try {
+                process.kill(pid, 'SIGTERM');
+            }
+            catch {
+                // already dead
+            }
+        }
+        await new Promise((r) => setTimeout(r, 1000));
+        return true;
+    }
+    catch {
+        return false;
+    }
+}
+export async function createDatabaseWithRetry(dbPath) {
+    try {
+        return await createDatabase(dbPath);
+    }
+    catch (err) {
+        const msg = err instanceof Error ? err.message : String(err);
+        if (!msg.includes('lock'))
+            throw err;
+        const killed = await killSymbioteProcesses();
+        if (!killed)
+            throw err;
+        await new Promise((r) => setTimeout(r, 500));
+        return await createDatabase(dbPath);
+    }
+}
+export async function isPortServing(port) {
+    const http = await import('node:http');
+    return new Promise((resolve) => {
+        const req = http.request({ hostname: '127.0.0.1', port, path: '/internal/health', timeout: 1000 }, (res) => {
+            res.resume();
+            resolve(res.statusCode === 200);
+        });
+        req.on('error', () => resolve(false));
+        req.on('timeout', () => {
+            req.destroy();
+            resolve(false);
+        });
+        req.end();
+    });
+}
+export async function handleHttpRequest(ctx, webDistDir, _port, url, req, res) {
+    if (url.pathname === '/internal/health') {
+        res.writeHead(200, { 'Content-Type': 'application/json' });
+        res.end(JSON.stringify({ status: 'ok' }));
+        return;
+    }
+    if (url.pathname === '/internal/events' && req.method === 'POST') {
+        await handleInternalEvent(ctx.eventBus, req, res);
+        return;
+    }
+    if (url.pathname === '/internal/hook-context' && req.method === 'GET') {
+        await handleHookContext(ctx, req, res);
+        return;
+    }
+    if (url.pathname.startsWith('/internal/hooks/') && req.method === 'POST') {
+        await handleHookRequest(ctx, url.pathname, req, res);
+        return;
+    }
+    if (url.pathname === '/internal/hooks/session-start' && req.method === 'GET') {
+        await handleSessionStartRequest(ctx, url.searchParams, res);
+        return;
+    }
+    if (url.pathname === '/events' && req.method === 'GET') {
+        handleSseConnection(ctx.eventBus, req, res);
+        return;
+    }
+    if (url.pathname.startsWith('/api/')) {
+        if (await handleApiRequest(ctx, url.pathname, req, res))
+            return;
+    }
+    if (fs.existsSync(webDistDir)) {
+        if (serveStatic(webDistDir, url.pathname, res))
+            return;
+    }
+    res.writeHead(404);
+    res.end('Not found');
+}
+//# sourceMappingURL=shared.js.map

package/dist/src/commands/shared.js.map

@@ -0,0 +1 @@
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package/dist/src/commands/unbond.d.ts

@@ -0,0 +1,2 @@
+export declare function cmdUnbond(targetId?: string): Promise<void>;
+//# sourceMappingURL=unbond.d.ts.map

package/dist/src/commands/unbond.d.ts.map

@@ -0,0 +1 @@
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package/dist/src/commands/unbond.js

@@ -0,0 +1,29 @@
+import * as p from '@clack/prompts';
+import pc from 'picocolors';
+export async function cmdUnbond(targetId) {
+    const { detectInstalledAgents, isBonded, disconnectWithHooks } = await import('#init/agent-connector.js');
+    p.intro(pc.bold('Symbiote') + pc.dim(' — Detaching'));
+    const agents = detectInstalledAgents();
+    const bonded = agents.filter((a) => a.installed && isBonded(a));
+    if (bonded.length === 0) {
+        p.outro('No bonded hosts found.');
+        return;
+    }
+    const toUnbond = targetId ? bonded.filter((a) => a.id === targetId) : bonded;
+    if (targetId && toUnbond.length === 0) {
+        p.log.error(`Host not found or not bonded: ${targetId}`);
+        p.outro('');
+        return;
+    }
+    for (const agent of toUnbond) {
+        const result = disconnectWithHooks(agent);
+        if (result.mcp.success) {
+            p.log.success(`Detached from ${agent.name}`);
+        }
+        else {
+            p.log.error(`Failed to detach from ${agent.name}: ${result.mcp.message}`);
+        }
+    }
+    p.outro('Symbiote detached.');
+}
+//# sourceMappingURL=unbond.js.map

package/dist/src/commands/unbond.js.map

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package/dist/src/core/algorithms.d.ts

@@ -0,0 +1,19 @@
+import type { Repository } from '#storage/repository.js';
+import type { GraphInstance } from './types.js';
+export interface AlgorithmResults {
+    communities: Record<string, number>;
+    pageRank: Record<string, number>;
+    betweenness: Record<string, number>;
+}
+/** @deprecated Use Stage6Topology from cortex/stage-6-topology.ts instead. */
+export declare class GraphAlgorithms {
+    private repo;
+    constructor(repo: Repository);
+    loadGraph(): Promise<GraphInstance>;
+    runLouvain(preloaded?: GraphInstance): Promise<Record<string, number>>;
+    runPageRank(preloaded?: GraphInstance): Promise<Record<string, number>>;
+    runBetweennessCentrality(preloaded?: GraphInstance): Promise<Record<string, number>>;
+    runAll(): Promise<AlgorithmResults>;
+    private computeLouvain;
+}
+//# sourceMappingURL=algorithms.d.ts.map

package/dist/src/core/algorithms.d.ts.map

@@ -0,0 +1 @@
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package/dist/src/core/algorithms.js

@@ -0,0 +1,98 @@
+import { createRequire } from 'node:module';
+import { Graph } from './types.js';
+/**
+ * @deprecated Use packages/cli/src/cortex/stage-6-topology.ts instead.
+ * This module uses the legacy Repository. Will be removed in next major version.
+ */
+const req = createRequire(import.meta.url);
+const louvain = req('graphology-communities-louvain');
+const centrality = req('graphology-metrics/centrality');
+/** @deprecated Use Stage6Topology from cortex/stage-6-topology.ts instead. */
+export class GraphAlgorithms {
+    repo;
+    constructor(repo) {
+        this.repo = repo;
+    }
+    async loadGraph() {
+        const nodes = await this.repo.getAllNodes();
+        const edges = await this.repo.getAllEdges();
+        const graph = new Graph({ multi: true, type: 'directed' });
+        for (const node of nodes) {
+            graph.addNode(node.id, {
+                type: node.type,
+                name: node.name,
+                filePath: node.filePath,
+                lineStart: node.lineStart,
+                lineEnd: node.lineEnd,
+                metadata: node.metadata,
+            });
+        }
+        for (const edge of edges) {
+            if (graph.hasNode(edge.sourceId) && graph.hasNode(edge.targetId)) {
+                graph.addEdge(edge.sourceId, edge.targetId, {
+                    type: edge.type,
+                });
+            }
+        }
+        return graph;
+    }
+    async runLouvain(preloaded) {
+        const graph = preloaded ?? (await this.loadGraph());
+        if (graph.order === 0)
+            return {};
+        return this.computeLouvain(graph);
+    }
+    async runPageRank(preloaded) {
+        const graph = preloaded ?? (await this.loadGraph());
+        if (graph.order === 0)
+            return {};
+        return centrality.pagerank(graph);
+    }
+    async runBetweennessCentrality(preloaded) {
+        const graph = preloaded ?? (await this.loadGraph());
+        if (graph.order === 0)
+            return {};
+        return centrality.betweenness(graph);
+    }
+    async runAll() {
+        const graph = await this.loadGraph();
+        if (graph.order === 0) {
+            return { communities: {}, pageRank: {}, betweenness: {} };
+        }
+        const communities = this.computeLouvain(graph);
+        const ranks = centrality.pagerank(graph);
+        const betweenness = centrality.betweenness(graph);
+        const updatedNodes = [];
+        graph.forEachNode((nodeId, attrs) => {
+            updatedNodes.push({
+                id: nodeId,
+                type: attrs.type,
+                name: attrs.name,
+                filePath: attrs.filePath,
+                lineStart: attrs.lineStart,
+                lineEnd: attrs.lineEnd,
+                metadata: {
+                    ...(attrs.metadata ?? {}),
+                    community: communities[nodeId] ?? -1,
+                    pageRank: ranks[nodeId] ?? 0,
+                    betweenness: betweenness[nodeId] ?? 0,
+                },
+            });
+        });
+        await this.repo.insertNodes(updatedNodes);
+        return { communities, pageRank: ranks, betweenness };
+    }
+    computeLouvain(graph) {
+        const undirected = new Graph({ multi: false, type: 'undirected' });
+        graph.forEachNode((node, attrs) => {
+            undirected.addNode(node, attrs);
+        });
+        graph.forEachEdge((_edge, _attrs, source, target) => {
+            if (source !== target && !undirected.hasEdge(source, target)) {
+                undirected.addEdge(source, target);
+            }
+        });
+        return louvain(undirected);
+    }
+}
+//# sourceMappingURL=algorithms.js.map