Fix code quality: resolve all ruff and mypy errors

[Copilot]

Addressed all code quality issues across the codebase by fixing linting errors and type checking violations.

Changes

Formatting and Linting

• Auto-fixed 125 ruff errors (unused imports, line length, security issues)
• Replaced subprocess.run() with shell=True to use list arguments
• Added per-file ignores for legitimate subprocess and temp directory usage in build/service files

Type Checking

TypedDict syntax errors: Fixed invalid subscript syntax used for type hints

# Before
def _get_model_root(engine_id: str, model_id: ModelMetadata["id"]) -> Path | None:

# After  
def _get_model_root(engine_id: str, model_id: str) -> Path | None:

Literal types for discriminated unions:

# Before
def create_model(...) -> Tuple[True, ModelMetadata] | Tuple[False, str]:

# After
def create_model(...) -> tuple[Literal[True], ModelMetadata] | tuple[Literal[False], str]:

Path vs str mismatches: Changed TypedDict fields expecting Path objects to receive Path instead of str(path)

Missing type annotations: Added explicit type hints for class attributes and variables where mypy couldn't infer them

Function signature mismatches: Aligned overridden method signatures with base class definitions

Verification

• ✅ ruff format --check (73 files)
• ✅ ruff check (0 errors)
• ✅ mypy (73 source files, 0 errors)

Warning

Firewall rules blocked me from connecting to one or more addresses (expand for details)

I tried to connect to the following addresses, but was blocked by firewall rules:

• https://api.github.com/repos/BrainBehaviorAnalyticsLab/PyPLLRComputer/commits/HEAD
  • Triggering command: /home/REDACTED/.local/bin/uv uv sync (http block)

If you need me to access, download, or install something from one of these locations, you can either:

• Configure Actions setup steps to set up my environment, which run before the firewall is enabled
• Add the appropriate URLs or hosts to the custom allowlist in this repository's Copilot coding agent settings (admins only)

Original prompt

Do what you do, be minimally invasive.

Custom agent used: code-quality-agent
Fixes linting, formatting, and type checking issues by running make commands until all checks pass

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