Cline rules

1---
2paths:
3  - "src/**/*.py"
4  - "tests/**/*.py"
5  - "scripts/**/*.py"
6  - "pyproject.toml"
7  - "uv.lock"
8---
9 
10# PubMed Python Rules
11 
12## Environment
13 
14- Use `uv` for all Python commands.
15- Prefer `uv run ...` so checks execute in the right environment.
16- Do not introduce raw package-manager calls in docs, CI, or code paths.
17 
18## Architecture Guardrails
19 
20- Keep `domain/` free of I/O, environment reads, and framework imports.
21- Keep external API calls in `infrastructure/`.
22- Put orchestration in `application/`.
23- Keep MCP presentation code as thin wrappers around services.
24- Read configuration through shared settings, not scattered `os.environ` reads.
25 
26## Validation Gates
27 
28- Lint: `uv run ruff check .`
29- Format: `uv run ruff format --check .`
30- Types: `uv run mypy src/ tests/`
31- Tests: `uv run pytest`
32 
33## Test Rules
34 
35- Use async tests and `AsyncMock` for async methods.
36- Preserve xdist-friendly tests; avoid singleton state leaks.
37- Mock external APIs unless a test is explicitly marked integration.
38- Add regression tests for parsing, query expansion, ranking, source counts, and MCP tool contracts.
39