.cursorrules

# Cursor Rules for BioNeMo Framework

## Pre-commit and Linting

1. **Always run pre-commit hooks after making changes:**
   - After editing any file, run `pre-commit run --all-files` or `pre-commit run` to check modified files
   - If pre-commit hooks fail, fix the issues before considering the task complete
   - Pre-commit hooks include:
     - Ruff linting and formatting (with auto-fix)
     - Markdown formatting
     - License header checks
     - Trailing whitespace and end-of-file fixes
     - YAML validation
     - Secret detection

2. **Fix linter errors immediately:**
   - When making code changes, check for linter errors using `read_lints` tool
   - Fix all linter errors before completing the task
   - The project uses:
     - Ruff for Python linting and formatting (configured in pyproject.toml)
     - Pyright for type checking (configured in pyproject.toml)
   - Ruff will auto-fix many issues, but you should verify all fixes are appropriate

3. **Code quality standards:**
   - Follow the project's ruff configuration (line-length: 119, specific ignores)
   - Ensure all Python files follow Google-style docstrings (pydocstyle convention)
   - Import sorting follows isort configuration (2 lines after imports)
   - Test files and `__init__.py` files have relaxed linting rules as configured

4. **Workflow:**
   - Make code changes
   - Check for linter errors with `read_lints`
   - Fix any linter errors
   - Run pre-commit: `pre-commit run --all-files` or `pre-commit run` for changed files
   - If pre-commit fails, fix the issues and re-run until all checks pass
   - Only mark a task as complete when all linter errors are resolved and pre-commit passes

5. **Exceptions:**
   - If a linting rule genuinely conflicts with the required change or is a false positive, document why in comments
   - Some files may have per-file ignores configured in pyproject.toml - respect those configurations