Cymatix Context

Cymatix Context

[](https://opensource.org/licenses/Apache-2.0) [](https://pypi.org/project/helix-context/) [](https://www.python.org/downloads/) [](tests/) [](docs/architecture/PIPELINE_LANES.md) [](https://mbachaud.substack.com/p/agentome)

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

---

Proof (30 seconds)

WIP benchmark numbers — compressor disabled (default LLM-free config), N=15 query shapes, May 2026:

| metric | tokens | vs standard RAG (top-5 @ 1500) | |--------|--------|-------------------------------| | median | 2,757 | 2.9× fewer tokens | | best (focused query) | 1,410 | 5.7× | | worst (broad 12-doc) | 3,755 | 2.1× |

With the optional compressor enabled (Claude Haiku splice), median improves to ~5×. In multi-turn sessions, the session delivery register elides already-seen documents — observed 37× reduction on repeated retrievals within a conversation.

Reproducer: python benchmarks/bench_rag_vs_sike_tokens.py against your own genome.

Agent contract: every /context response carries know { found, confidence } (grounded — you may answer) or miss { reason, escalate_to } (not found — don't answer from genome). Stale results downgrade to miss(reason="stale"|"cold"|"superseded") via the freshness gate.

Get started (60 seconds)

# 1. Install
pip install helix-context
python -m spacy download en_core_web_sm

# 2. Ingest your codebase
helix ingest path/to/your/project/ --recursive

# 3. Query it
helix query "how does the splice step work?"

# 4. Or start the proxy for IDE integration
helix-server   # binds to 127.0.0.1:11437

For extras matrix, BGE-M3 backfill, and tray setup: [docs/SETUP.md](docs/SETUP.md).

Agent surfaces

Three ways to drive Helix — same retrieval primitives, same JSON shapes:

| Surface | Best for | Example | |---------|----------|---------| | CLI | Scripts, CI, cold-start agents | helix query "..." --json | | MCP | Claude Code, Cursor, Claude Desktop | Add to settings.json | | HTTP proxy | Continue IDE, OPENAI_BASE_URL redirect | POST /context |

# CLI — no server, no daemon, subprocess-drivable
helix query    "what does the splice step do?" --json
helix packet   "edit the splice step" --task-type edit --json
helix gene get abc123 --json
helix neighbors "splice step" --k 10 --json
helix refresh-targets "edit the splice step" --json
helix status
helix diag corpus

Full CLI reference: [docs/clients/cli.md](docs/clients/cli.md). MCP tool schemas: [docs/api/mcp-tools.md](docs/api/mcp-tools.md).

Pipeline (2 minutes)

Seven stages per turn, all LLM-free except optional splice:

  query
    │
    ▼
┌──────────────┐
│ 0. Classify  │  rule-based: decoder mode + assembly cap
└──────┬───────┘
       ▼
┌──────────────┐
│ 1. Extract   │  heuristic keyword + entity extraction
└──────┬───────┘
       ▼
┌──────────────┐  FTS5 BM25 + BGE-M3 dense (1024-dim) + tags
│ 2. Retrieve  │  + synonym expansion + co-activation + SR
│              │  ranked via RRF or additive fusion
└──────┬───────┘
       ▼
┌──────────────┐
│ 3. Re-rank   │  CPU classifier scores (optional)
└──────┬───────┘
       ▼
┌──────────────┐
│ 4. Splice    │  Headroom Kompress (CPU) or LLM compressor
└──────┬───────┘
       ▼
┌──────────────┐  token budget + legibility headers (fired tiers,
│ 5. Assemble  │  confidence ◆/◇/⬦, compression ratio) +
│   + Stage 7  │  freshness gate (stale/cold/superseded → miss)
└──────┬───────┘  + session delivery (elide already-seen docs)
       ▼
┌──────────────┐
│ 6. Persist   │  query+response → knowledge store (background)
└──────┘───────┘
       ▼
   know { } or miss { }

• know/miss contract: know means the context is grounded, agent may answer. miss means don't answer from genome — escalate via escalate_to tools or refetch from refresh_targets.
• Caller model class: /context accepts caller_model_class: "generic" | "small_moe" | "frontier" to select render branch (ordering, assembly cap, decoder mode). See [docs/api/context-endpoint.md §7](docs/api/context-endpoint.md).

Configuration (17 sections in helix.toml)

| Section | Key settings | |---------|-------------| | [ribosome] | enabled, backend ("none" / "litellm" / "claude" / "deberta"), queryexpansion | | [hardware] | Device auto-detection (CUDA → ROCm → MPS → CPU) | | [budget] | expression_tokens (7k default), max_genes_per_turn, spliceaggressiveness, legibility_enabled, session_delivery_enabled | | [session] | Synthetic session windows, default partyid | | [genome] | path (genomes/main/genome.db), compactinterval, replicas | | [server] | host, port, upstream | | [headroom] | Optional Headroom proxy lifecycle | | [ingestion] | backend ("cpu" / "ollama"), spladeenabled, entitygraph | | [context] | Cold-tier retrieval: enabled, k, mincosine | | [cymatics] | Frequency-domain scoring, harmoniclinks, distancemetric | | [classifier] | Rule-based query classification thresholds | | [retrieval] | fusion_mode ("rrf" default / "additive" legacy), SR, raytracetheta, seedededges | | [plr] | Piecewise linear reranker model | | [know] | Know/miss calibration: emitfloor, betas, sref, gref, staleafterdays | | [mem_sync] | Auto-memory → helix sync: watchdirs, interval | | [synonyms] | Query expansion map (e.g., "cache" → ["redis", "ttl"]) | | [abstain] | Low-confidence abstention thresholds |

Full reference: [docs/config-reference.md](docs/config-reference.md).

Full endpoint reference

Core retrieval: | Endpoint | Purpose | |----------|---------| | POST /context | know/miss + expressedcontext (primary) | | POST /context/packet | Agent-safe bundle: verified / stalerisk / refreshtargets | | POST /context/refresh-plan | Refresh targets only (reread plan) | | POST /fingerprint | Navigation-first payload (scores, no body) | | GET /context/expand | 1-hop neighborhood from a geneid | | POST /v1/chat/completions | OpenAI-compatible proxy |

Ingestion + maintenance: | Endpoint | Purpose | |----------|---------| | POST /ingest | Add content to the knowledge store | | POST /consolidate | Rewrite stale docs from source fingerprints | | POST /admin/refresh | Force retrieval-layer refresh | | POST /admin/vacuum | Reclaim SQLite pages | | POST /admin/swap-db | Hot-swap the .db file without restart |

Identity + sessions: | Endpoint | Purpose | |----------|---------| | POST /sessions/register | Register agent participant | | GET /sessions | List registered participants | | GET /session/{id}/manifest | Session delivery log | | POST /hitl/emit | Record HITL pause event |

Diagnostics: | Endpoint | Purpose | |----------|---------| | GET /stats | Corpus metrics + compression ratio | | GET /health | Model, doc count, calibration provenance | | GET /genes/{gene_id} | Single document detail | | GET /debug/resonance | Tier activation profile | | GET /metrics/tokens | Token usage counters |

Full schema: [docs/api/endpoints.md](docs/api/endpoints.md).

Package structure (15 packages, post-PR #90)

| Package | Purpose | |---------|---------| | adapters/ | Cache, DAL, external retriever protocol | | backends/ | Compressor, BGE-M3 codec, DeBERTa, NLI, SEMA, SPLADE | | cli/ | helix CLI: query, packet, gene, neighbors, ingest, diag, config, status | | encoding/ | Chunking, fragments, legibility headers, Headroom bridge | | identity/ | CWoLa logger, session delivery, registry, provenance, claims | | pipeline/ | Tier logic, stage helpers | | retrieval/ | Expand, freshness, RRF/additive fusion, PLR, intent router, SR, seeded edges, query classifier | | scoring/ | Cymatics, know-calibration, know-decision, ray-trace, TCM | | server/ | FastAPI app factory + route modules (context, ingest, registry, admin) | | storage/ | DDL, indexes, co-activation graph | | telemetry/ | OTel metrics, histogram instrumentation | | vault/ | Obsidian vault export (diagnostic traces) | | launcher/ | System-tray supervisor | | mcp/ | MCP tool surface for Claude Code / Desktop | | integrations/ | ScoreRift bridge |

Back-compat shims: genome.py, ribosome.py, server.py, replication.py, hgt.py re-export from new locations. Lexicon: [docs/ROSETTA.md](docs/ROSETTA.md).

IDE + MCP integration

MCP setup (Claude Code / Cursor / Claude Desktop)

{
  "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" }
    }
  }
}

Continue IDE

models:
  - name: Helix (Local)
    provider: openai
    model: gemma3:e4b
    apiBase: http://127.0.0.1:11437/v1
    apiKey: EMPTY
    roles: [chat]
    defaultCompletionOptions:
      contextLength: 128000
      maxTokens: 4096

OpenAI-compatible proxy (zero code changes)

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

Knowledge store management

[genome]
path = "genomes/main/genome.db"   # relative to helix run directory

Backup (safe while running — WAL mode):

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

BGE-M3 backfill (one-time, after install):

python scripts/backfill_bgem3_v2.py genomes/main/genome.db

Observability

scripts\setup-grafana-telem.ps1     # Windows
scripts/setup-grafana-telem.sh      # Linux / macOS

Dashboard: . Full surface: [docs/architecture/OBSERVABILITY.md](docs/architecture/OBSERVABILITY.md).

Gotchas

• Knowledge store path is genomes/main/genome.db (not project root). Delete to start fresh.
• BGE-M3 backfill is one-time post-install — embedding_dense_v2 IS NULL until you run scripts/backfill_bgem3_v2.py. Low retrieval rate without it.
• Fusion mode defaults to "additive" (back-compat). Flip to "rrf" in [retrieval] after running scripts/calibrate_thresholds.py.
• Session delivery (session_delivery_enabled = true) tracks delivered docs per session, elides repeats. ~40% token savings on multi-turn. Pass ignore_delivered: true in /context body for benchmarks.
• know/miss contract requires the agent prompt fragment to be honored — without it, frontier models confabulate. Import helix_context.agent_prompt.full_fragment().
• Naming lexicon: biology terms (gene, genome, ribosome) have canonical software equivalents (document, knowledge store, compressor). Both work in code; new code uses software terms. See [docs/ROSETTA.md](docs/ROSETTA.md).

Testing

python -m pytest tests/ -m "not live" -v   # ~2,750 tests, no external services

Documentation

| Start here | Go deeper | |-----------|-----------| | [Setup guide](docs/SETUP.md) | [Pipeline lanes](docs/architecture/PIPELINELANES.md) | | [Troubleshooting](docs/TROUBLESHOOTING.md) | [Retrieval dimensions](docs/architecture/DIMENSIONS.md) | | [/context API](docs/api/context-endpoint.md) | [Knowledge graph](docs/architecture/KNOWLEDGEGRAPH.md) | | [Config reference](docs/config-reference.md) | [Session registry](docs/architecture/SESSIONREGISTRY.md) | | [Agent SDK fragment](docs/agent-sdk-fragment.md) | [Observability](docs/architecture/OBSERVABILITY.md) | | [Operator runbooks](docs/operator-runbooks.md) | [Launcher architecture](docs/architecture/LAUNCHER.md) | | [Dense ingest on ≤12 GB VRAM](docs/operations/DENSEVRAM.md) | |

Acknowledgments

Built on: spaCy NER · Howard 2005 TCM · Stachenfeld 2017 SR · SQLite FTS5 BM25 · BGE-M3 · Kompress · Headroom

License

[Apache-2.0](LICENSE). See [NOTICE](NOTICE) for third-party attributions.

Source & license

This open-source MCP server is cataloged on AgentStack and links to its original source — we do not rehost the code.

• Author: mbachaud
• Source: mbachaud/Cymatix-Context
• License: Apache-2.0

Install and usage instructions live in the source repository linked above.