noctua-mcp: Instructions file for Codex

AGENTS.md

noctua-mcp AGENTS.md is an instructions file for Codex, OpenCode from geneontology/noctua-mcp. It costs 429 tokens per session, scanned A, original, BSD-3-Clause.

A set of project instructions for geneontology/noctua-mcp, a Python server that lets Barista control Noctua editing. It documents the repository layout, dependency management, documentation, testing, and coding practices.

In plain words
What is it for?
Use it when working on the noctua-mcp repository, especially when changing source code, documentation, dependencies, doctests, or pytest tests.
Why use it?
It gives an agent the project-specific rules needed to manage dependencies, choose the right commands, and keep tests and documentation consistent.

Instructions file for CodexOpenCode

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

This is geneontology/noctua-mcp's own configuration. It tells Codex and OpenCode how to work on noctua-mcp 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 noctua-mcp configures →

Reuse

Borrowing it

Nothing to install: this file belongs to geneontology/noctua-mcp. 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/geneontology/noctua-mcp/main/AGENTS.md
Clone the repo
git clone --depth 1 https://github.com/geneontology/noctua-mcp

Made for: Codex, OpenCode.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

agentmods badge for noctua-mcp AGENTS.md

README.md
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Your own site
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Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.

agentmods 80×15 button for noctua-mcp AGENTS.md

Your own site · 80×15
<a href="https://agentmods.dev/instructions/geneontology/noctua-mcp/agents-md"><img src="https://agentmods.dev/badge/instructions/geneontology/noctua-mcp/agents-md.svg" alt="Reviewed on agentmods" width="80" height="20"></a>
Per session 429 This file is loaded in full into every session.
When invoked 429 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 $0.00429 $0.00429
Opus 5 $0.00215 $0.00215
Sonnet 5 $0.00086 $0.00086
Haiku 4.5 $0.00043 $0.00043

Measured 9d ago against content hash 731fe1871e2f, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-10, from the pricing page.

Security

Grade A, and why

noctua-mcp 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 9d 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.

Origin

Copies of this mod

1 near-identical copy found in the catalogue:

AGENTS.md · 45 lines

What it actually says

AGENTS.md for noctua-mcp

MCP server for Barista to control Noctua editing

TODO: fill in extra description here

Repo management

This repo uses uv for managing dependencies. Never use commands like pip to add or manage dependencies. uv run is the best way to run things, unless you are using justfile or makefile target

mkdocs is used for documentation.## This is a Python repository

Layout:

  • src/noctua_mcp/ - Code goes here
  • docs - mkdocs docs
  • mkdocs.yml - index of docs
  • tests/input - example files

Building and testing:

  • just --list to see all commands
  • just test performs unit tests, doctests, ruff/liniting
  • just test-full as above plus integration tests

You can run the underlying commands (with uv run ...) but in general justfile targets should be favored.

Best practice:

  • Use doctests liberally - these serve as both explanatory examples for humans and as unit tests
  • For longer examples, write pytest tests
  • always write pytest functional style rather than unittest OO style
  • use modern pytest idioms, including @pytest.mark.parametrize to test for combinations of inputs
  • NEVER write mock tests unless requested. I need to rely on tests to know if something breaks
  • For tests that have external dependencies, you can do @pytest.mark.integration
  • Do not "fix" issues by changing or weakening test conditions. Try harder, or ask questions if a test fails.
  • Avoid try/except blocks, these can mask bugs
  • Fail fast is a good principle
  • Follow the DRY principle
  • Avoid repeating chunks of code, but also avoid premature over-abstraction
  • Pydantic or LinkML is favored for data objects
  • For state in engine-style OO classes, dataclasses is favored
  • Declarative principles are favored
  • Always use type hints, always document methods and classes
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. 9d ago First seen · 45 lines · 429 tokens per session scan A 731fe1871e2f

Subscribe to this mod's changes

noctua-mcp AGENTS.md is an instructions file published in the GitHub repository geneontology/noctua-mcp (0 stars, last pushed 10mo ago), licensed BSD-3-Clause. It adds 429 tokens to every session, about $0.0021 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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