genefoundry-router: Instructions file for Codex

AGENTS.md

genefoundry-router AGENTS.md is an instructions file for Codex, OpenCode from berntpopp/genefoundry-router. It costs 1,509 tokens per session, scanned A, original, MIT.

Repository instructions for GeneFoundry Router, a gateway that connects one coding tool interface to 21 biomedical data servers. It groups their tools behind one endpoint and keeps their names distinct.

In plain words
What is it for?
They guide work on biomedical tool routing, configuration, authentication, search, tests and deployment.
Why use it?
They explain the project structure, coding rules and required checks, helping agents avoid incorrect changes in a fast-moving codebase.

Instructions file for CodexOpenCode

Written for Codex and OpenCode: the file is AGENTS.md. Also seen: mentions AGENTS.md.

This is berntpopp/genefoundry-router's own configuration. It tells Codex and OpenCode how to work on genefoundry-router itself, so it is not a mod to install elsewhere. Copy it as a starting point and replace the rules that are about this project. Everything genefoundry-router configures →

Reuse

Borrowing it

Nothing to install: this file belongs to berntpopp/genefoundry-router. Take a copy, put it at the same path in your own repository, and replace the rules that are about this project with yours.

Copy the file
curl -O https://raw.githubusercontent.com/berntpopp/genefoundry-router/main/AGENTS.md
Clone the repo
git clone --depth 1 https://github.com/berntpopp/genefoundry-router

Made for: Codex, OpenCode.

Wrote this? Show the measurements

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README.md
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Per session 1,509 This file is loaded in full into every session.
When invoked 1,509 The same file — it is already loaded in full.
Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe.
Origin original No closer match found in the catalogue.
Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

ModelPer sessionOnce invoked
Fable 5.1 $0.01509 $0.01509
Opus 5 $0.00754 $0.00754
Sonnet 5 $0.00302 $0.00302
Haiku 4.5 $0.00151 $0.00151

Measured 3d ago against content hash 7eb6947583c7, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-07, from the pricing page.

Security

Grade A, and why

genefoundry-router AGENTS.md scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 3d ago.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Nothing flagged

None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.

AGENTS.md · 96 lines

How it starts

The opening of the file, as written. The whole thing — 96 lines — stays where its author put it; the contents beside it link to each section on GitHub.

AGENTS.md

Shared instructions for AI coding agents working in this repository.

What this project is

genefoundry-router is a thin FastMCP 3.x aggregator (a router/gateway), NOT a data server. It federates the GeneFoundry *-link MCP fleet behind one Streamable-HTTP endpoint (genefoundry) with collision-free namespacing, BM25 tool-search, pluggable auth, and a config-driven registry. It is a client to each backend and a server to hosts.

  • Primary code area: genefoundry_router/
  • Source of truth for backends: servers.yaml (structure) + .env (URLs/secrets) + uv.lock
  • Design spec: docs/specs/2026-06-13-genefoundry-router-design.md
  • Implementation plan: docs/plans/2026-06-13-genefoundry-router-implementation.md

Required check before handoff

make ci-local      # format-check, lint, lint-loc (600-LOC budget), mypy, unit + integration tests

Other useful targets: make test, make test-integration, make test-cov (coverage ≥70), make lint, make typecheck, make run, make validate, make doctor, make list-tools, make docker-build, make docker-prod-config, make docker-npm-config.

Coding standards

  • Python 3.12+; dependency + venv management via uv (uv sync --group dev, uv run).
  • Modern typing (X | None, builtin generics); ruff (lint + format) and mypy must pass.
  • 600-LOC per module budget, enforced by scripts/check_file_size.py (make lint-loc).
  • TDD: write a failing test, see it fail, implement minimally, see it pass; one atomic commit per change.
  • FastMCP 3.x symbols are post-training-cutoff and fast-moving — verify imports against the installed package before relying on them (see the import smoke in the implementation plan, Task 2). Adapt to the installed API; the integration test is the contract.

Project-specific guidance

  • Namespacing is the gateway's job. Keep per-backend transform blocks minimal and delete them from servers.yaml as source repos adopt Tool-Naming Standard v1.
  • No token passthrough: never forward the caller's Authorization header to backends.
  • Streamable HTTP only (transport="http"); SSE is not offered.
  • Container & deployment hardening is a fleet standard. The router and every -link server follow docs/CONTAINER-HARDENING-STANDARD-v1.md (non-root, read-only rootfs, cap_drop: ALL, no-new-privileges, resource limits, expose-only behind the proxy, digest-pinned base, CI image scan + SBOM). The router's docker/ is the reference implementation; copy it, don't reinvent.
  • Backends are unauthenticated by design (the router owns edge auth at the trust boundary) — they MUST be reachable only through the router/reverse proxy, never published directly.

Read the full file on GitHub · 96 lines

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

  1. 3d ago Changed · +26 lines · +471 tokens per session 7eb6947583c7
  2. 7d ago First seen · 70 lines · 1,038 tokens per session scan A f385a1042d8f

Subscribe to this mod's changes

genefoundry-router AGENTS.md is an instructions file published in the GitHub repository berntpopp/genefoundry-router (4 stars, last pushed yesterday), licensed MIT. It adds 1,509 tokens to every session, about $0.0075 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-31.

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