Helix Context

Genome-based context compression for local LLMs, with a machine-tagged know/miss agent contract.

Coordinate-index engine for LLM agents. Helix retrieves, weighs, and compresses your codebase into a context window — without a single LLM call on the retrieval path.

At a glance

• Compression: collapses ~9k tokens of raw working set into a ~600 effective-token assembled context (28.7× headline on production workloads, 5.4× median across 15 query shapes).
• Agent contract: every /context response carries a top-level know{} (grounded, you may answer) or miss{} (do_not_answer_from_genome:true, plus escalate_to tools or refresh_targets paths). Stale know blocks downgrade to miss(reason="stale"|"cold"|"superseded") via the Stage 7 freshness gate.
• LLM-free retrieval: /context runs spaCy NER, SQLite FTS5 BM25, BGE-M3 dense recall, RRF fusion, Howard-2005 TCM, and Hebbian co-activation — zero ribosome calls. The only LLM call is downstream at /v1/chat/completions.
• Three install paths: compact tray flow (start-helix-tray.bat) for the daily driver, proxy-only for OPENAI_BASE_URL redirection, agent-SDK fragment for frontier-model integration.

Quick navigation

• Setup guide — extras matrix, OS-specific install paths, calibration runbook
• Troubleshooting — common errors and recovery
• /context API reference — request/response schema, render branches, field-by-field
• Operator runbooks — backfill, calibrate, consolidate, vacuum
• Config reference — every key in helix.toml
• Agent SDK integration — frontier prompt fragment + compliance eval
• Environment variables — runtime overrides

Quick Start

# 1. Install
pip install -e ".[all,launcher,otel]"
python -m spacy download en_core_web_sm

# 2. Pull a small model for the ribosome (optional — disabled by default)
ollama pull gemma3:e4b

# 3. Start the proxy
python -m uvicorn helix_context._asgi:app --host 127.0.0.1 --port 11437

# 4. Or, daily-driver tray (Windows):
start-helix-tray.bat

# 5. Seed your genome (one-time)
python examples/seed_genome.py path/to/your/docs/

# 6. Post-merge: backfill 1024-dim BGE-M3 vectors for Stage 2 dense recall
python scripts/backfill_bgem3_v2.py genomes/main/genome.db

For full options including the extras matrix, see docs/SETUP.md.

Pipeline

A transparent OpenAI-compatible proxy that intercepts LLM requests and injects compressed context from a persistent SQLite genome. Six stages per turn, all LLM-free except step 4 splice (optional ribosome) and the downstream completion call:

• 0a. Classify — rule-based query classifier picks decoder mode + assembly cap (no model call).
• 1. Extract — heuristic keyword extraction from query (no model call).
• 2. Express — SQLite promoter-tag lookup + BGE-M3 dense recall + synonym expansion + co-activation. Ranks candidates via Reciprocal Rank Fusion over {dense, FTS5, promoter, harmonic, SR} when [retrieval] fusion_mode = "rrf" (default "additive", see Gotchas).
• 3. Re-rank — small CPU model scores candidates for relevance.
• 4. Splice — small CPU model trims introns, keeps exons (batched single call; optional).
• 5. Assemble — join spliced parts, enforce token budget, wrap in tags. The Stage 7 health pass downgrades to MissBlock(reason="stale") when the top-1 source mtime exceeds last_verified_at.
• 6. Replicate — pack query + response into the genome (background).

→ Swim-lane reference: docs/architecture/PIPELINE_LANES.md → Retrieval dimensions: docs/architecture/DIMENSIONS.md

Agent integration

Every /context response carries one of two top-level blocks:

• know { found, confidence, gene_id_match, ... } — retrieval succeeded; the expressed_context bytes are grounded. The agent may answer from them.
• miss { reason, escalate_to | refresh_targets, do_not_answer_from_genome:true } — retrieval did NOT find it (or found it but it is stale, cold, or superseded). The agent should NOT answer from the genome; it should call an escalation tool from escalate_to (grep | rag | web | ask_human) or refetch from refresh_targets.

To make a frontier model honor the contract, prepend the helix-context prompt fragment to your system prompt:

from helix_context.agent_prompt import full_fragment

system_prompt = full_fragment() + "\n\n" + your_existing_system_prompt

Without the fragment, frontier models will paper over do_not_answer_from_genome and confabulate. See docs/agent-sdk-fragment.md for the full template, the <helix:no_match/> token semantics, and the compliance eval recipe.

Caller model class

/context accepts an optional caller_model_class: "generic" | "small_moe" | "frontier" field that selects the render branch:

• frontier (Claude Opus, GPT-5, Gemini 3 Pro): forward rank-1-first ordering, larger assembly cap, full decoder mode.
• small_moe (qwen3:4b, gemma3:e4b): foveated reverse-rank order, JSON-shaped char-bounded answer slate, condensed decoder.
• generic (default): regression-locked byte-identical to pre-Stage-5 behavior.

See docs/api/context-endpoint.md §7 for the full behavior matrix.

Surfaces and endpoints

Endpoint	Purpose
POST /context	know/miss + expressed_context (primary integration).
POST /context/packet	Agent-safe bundle: verified / stale_risk / refresh_targets.
POST /context/refresh-plan	refresh_targets only — reread plan, no evidence items.
POST /fingerprint	Navigation-first payload (scores + metadata, no body).
POST /consolidate	Rewrite stale gene bodies from their source fingerprints (Stage 7 counterpart to refresh_targets).
POST /sessions/register	Register an agent participant (taude / laude / …) for attribution.
POST /admin/refresh	Force a retrieval-layer refresh (admin only).
POST /admin/vacuum	Reclaim SQLite pages after compaction (admin only).
POST /ingest	Add a document or exchange to the genome.
GET /stats	Genome metrics + compression ratio.
GET /health	Ribosome model, gene count, upstream URL, calibration provenance (Stage 4).
POST /v1/chat/completions	OpenAI-compatible proxy with automatic context injection.

→ Full endpoint reference: docs/api/endpoints.md and docs/api/context-endpoint.md → MCP tool schemas: docs/api/mcp-tools.md

Two surfaces, two caller types:

	/context	/context/packet
Returns	Assembled compressed window	Pointer + verdict + refresh plan
LLM reads?	Directly	No — agent fetches if needed
Verdict emitted?	Top-level know / miss	First-class: verified / stale_risk / needs_refresh
Best for	Chat clients, Continue	MCP agents, programmatic use

Continue IDE Integration

Add to ~/.continue/config.yaml:

models:
  - name: Helix (Local)
    provider: openai
    model: gemma3:e4b           # or whatever is loaded in Ollama
    apiBase: http://127.0.0.1:11437/v1
    apiKey: EMPTY
    roles: [chat]
    defaultCompletionOptions:
      contextLength: 128000     # Helix handles compression downstream
      maxTokens: 4096

MCP setup (Claude Code / Cursor / Claude Desktop)

Add to ~/.claude/settings.json:

{
  "mcpServers": {
    "helix-context": {
      "command": "python",
      "args": ["-m", "helix_context.mcp_server"],
      "cwd": "/absolute/path/to/your/project",
      "env": {
        "HELIX_MCP_URL": "http://127.0.0.1:11437"
      }
    }
  }
}

OpenAI-compatible proxy (zero code changes)

ANTHROPIC_BASE_URL=http://localhost:11437 claude
OPENAI_BASE_URL=http://localhost:11437/v1 your-app

Genome management

Genome path

Set path in [genome] to a file or directory:

[genome]
path = "genomes/main/genome.db"   # relative to helix run directory
# Put this on your fastest NVMe for best ingest throughput.
# Example: path = "D:/helix/genome.db"

One helix instance per genome — each reads its own helix.toml. Use the helix_context.hgt Python API to share genes across instances (Horizontal Gene Transfer).

Backup

SQLite WAL mode makes it safe to copy the .db file while helix is running:

# cron / Linux
cp genomes/main/genome.db backups/genome-$(date +%Y%m%d).db

# PowerShell / Windows
Copy-Item genomes\main\genome.db backups\genome-$(Get-Date -Format yyyyMMdd).db

DAL — source-content fetching

/context/packet returns source_id pointers. Callers resolve them to bytes via the DAL:

from helix_context.adapters.dal import DAL

dal = DAL()                          # file + HTTP built-in
dal.register("s3", my_s3_fetcher)    # register additional schemes
text, meta = dal.fetch("s3://bucket/schema.json")

Native observability (default)

The tray (start-helix-tray.bat) manages the native OpenTelemetry binaries in tools/native-otel/ automatically. A balloon notification confirms the sidecar is running. To opt out: HELIX_OBSERVABILITY=0 start-helix-tray.bat.

Advanced — Docker stack: if you prefer a full Docker-compose observability stack (Prometheus, Tempo, Loki, Grafana), see deploy/otel/README.md.

Architecture

Doc	Topic
PIPELINE_LANES.md	Swim-lane reference: ingest, context, packet, fingerprint flows
DIMENSIONS.md	The 9 retrieval dimensions — schema, data, bench status
LAUNCHER.md	Supervisor, tray, observability stack lifecycle
SESSION_REGISTRY.md	Multi-agent session + party isolation
OBSERVABILITY.md	Prometheus metrics, Grafana dashboards, alert rules
KNOWLEDGE_GRAPH.md	Entity graph, harmonic links, co-activation

Gotchas

• Model swap latency: the ribosome (small model) and the generation model share Ollama. Use keep_alive = "30m" in helix.toml to pin the ribosome in memory.
• Synonym map is critical: if queries return "no relevant context", check that query keywords map to the promoter tags the ribosome assigned. Add synonyms in [synonyms] of helix.toml.
• Short content may fail ingestion: the ribosome struggles with very short inputs (<200 chars). Pad with context or combine small files before ingesting.
• genome.db persists: delete it to start fresh. It auto-creates on first use.
• Continue Agent mode: use Chat mode, not Agent mode. The proxy does not handle tool routing.
• know/miss block requires the agent prompt fragment to be honored — without it, frontier models confabulate. Import helix_context.agent_prompt.full_fragment() and prepend it to your system prompt.
• Stage 2 backfill is a one-time post-merge action — embedding_dense_v2 IS NULL until you run scripts/backfill_bgem3_v2.py. Symptom: /context retrieval rate plateaus low; check coverage via sqlite3 genome.db "SELECT COUNT(*) FROM genes WHERE embedding_dense_v2 IS NOT NULL".
• Default [retrieval] fusion_mode = "additive" is back-compat; flip to "rrf" after running scripts/calibrate_thresholds.py so the absolute-floor gates do not strand every query in BROAD.
• Default [abstain].mode = "global" is back-compat; flip to "per_classifier" after calibration to use the bench-derived floors.

Testing

# All mock tests (no Ollama needed, ~6s)
python -m pytest tests/ -m "not live" -v

# Live tests (requires Ollama running)
python -m pytest tests/ -m live -v -s

# Full suite
python -m pytest tests/ -v

The 7-stage retrieval-fix added Stage-by-Stage contract tests: tests/test_dense_recall.py (Stage 2), tests/test_fusion_rrf.py (Stage 3), tests/test_calibration.py (Stage 4), tests/test_caller_model_class.py (Stage 5), tests/test_know_miss_block.py (Stage 6), tests/test_freshness_gate.py (Stage 7).

Acknowledgments

Built on: spaCy NER · Howard 2005 TCM · Stachenfeld 2017 SR · SQLite FTS5 BM25 · Kompress · Headroom

Licensed under Apache-2.0. See NOTICE for third-party attributions.

Further reading

• Setup guide
• Troubleshooting
• /context API reference
• Operator runbooks
• Config reference
• Agent SDK integration
• Environment variables
• Agentome paper