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Noctua MCP Server

Official
by geneontology
CLAUDE.md1.82 kB
# 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

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