Fix critical import errors and add missing test coverage for security features

[Copilot]

Addressed unresolved PR review feedback from #24, prioritizing issues blocking runtime execution and test validation.

Critical runtime fixes:

• Added missing Union type import in agent_skills.py - function signature at L158 used Union[Tuple[int], Tuple[int, int]] without import, causing NameError
• Fixed function name mismatch in test suite - 9 call sites referenced fibonacciCoherenceBoost when actual export is applyFibonacciWeightedBoost

Test coverage for security features:

• 11 tests for qubit range validation (MAX_QUBIT_INDEX enforcement)
  • Boundary conditions (0, 100), invalid ranges (negative, >100)
  • Error message specificity for single-qubit vs two-qubit gates
• 10 tests for ATOM provenance tracking
  • Decision persistence to .atom-trail/decisions/*.json
  • Tag format validation (ATOM-TYPE-YYYYMMDD-NNN-slug)
  • Keyword detection and cascade integration

Code hygiene:

• Removed unused sanitizeInput function from workflow (34 lines of dead code)
• Removed unused imports: os (agent_skills.py), json (test_agent_skills.py)
• Fixed README.md list indentation to match document style
• Added explanatory comment to empty except clause per linter feedback
• Removed unused pytest markers from config

# Before: runtime error
def _extract_qubit_indices(gate_str: str) -> Optional[Union[Tuple[int], Tuple[int, int]]]:
    # NameError: name 'Union' is not defined

# After: correct import
from typing import Optional, Tuple, Union

Validation:

• 71 tests passing (21 new)
• CodeQL scan clean
• Code review approved

---

💡 You can make Copilot smarter by setting up custom instructions, customizing its development environment and configuring Model Context Protocol (MCP) servers. Learn more Copilot coding agent tips in the docs.

[github-actions]

🌀 Agent Review: Coherence >60%. Ethical quantum sims validated. Ready for merge.

[Copilot]

Pull request overview

This pull request addresses technical debt and adds comprehensive test coverage for quantum coding agent features. It resolves critical import issues, function naming mismatches, removes dead code, and adds 21 new tests for qubit validation and ATOM decision tracking.

Changes:

• Fixed critical import and function naming issues in both Python and TypeScript code
• Removed unused code (imports, functions, pytest markers) improving code cleanliness
• Added 21 new tests covering qubit range validation and ATOM decision functionality
• Improved documentation with better comments and consistent formatting

Reviewed changes

Copilot reviewed 4 out of 5 changed files in this pull request and generated no comments.

Show a summary per file

File	Description
tests/test_agent_skills.py	Removed unused json import, added 11 tests for qubit range validation and 10 tests for ATOM decision functionality
pytest.ini	Removed unused slow and integration test markers
packages/quantum-ethics/src/tests/vortex-wavespec.test.ts	Updated function name from fibonacciCoherenceBoost to applyFibonacciWeightedBoost throughout tests, removed unnecessary function existence check
agent_skills.py	Added Union to typing imports (required for type hints), removed unused os import, added explanatory comment to empty except clause
README.md	Fixed indentation inconsistency in contributing section to use proper markdown list formatting
.github/workflows/coding-agent.yml	Removed unused sanitizeInput function, added security reminder comment for future reference

Comments suppressed due to low confidence (1)

tests/test_agent_skills.py:727

• The new ATOM decision tests create file system side effects (directories and JSON files in .atom-trail/) without cleanup. This can cause test pollution where tests may pass or fail depending on execution order or previous test runs. Consider adding setup/teardown methods or pytest fixtures to ensure clean test isolation. For example, you could add a fixture that creates a temporary directory for the ATOM trail and cleans it up after each test.

        assert result['status'] == 'error'
        assert 'error' in result
        assert 'out of range' in result['error'].lower()
    
    def test_error_message_format_single_qubit(self):
        """Test error message format for single-qubit gate"""
        result = agent_skills.simulate_circuit("h(150)")
        assert result['status'] == 'error'
        expected_msg = "Qubit index 150 out of range. Must be between 0 and 100."
        assert result['error'] == expected_msg
    
    def test_error_message_format_cx_control(self):
        """Test error message format for CX gate with invalid control"""
        result = agent_skills.simulate_circuit("cx(150,0)")
        assert result['status'] == 'error'
        expected_msg = "Control qubit index 150 out of range. Must be between 0 and 100."
        assert result['error'] == expected_msg
    
    def test_error_message_format_cx_target(self):
        """Test error message format for CX gate with invalid target"""
        result = agent_skills.simulate_circuit("cx(0,150)")
        assert result['status'] == 'error'
        expected_msg = "Target qubit index 150 out of range. Must be between 0 and 100."
        assert result['error'] == expected_msg


class TestErrorHandling:
    """Test error handling in various scenarios"""
    
    def test_invalid_circuit_returns_error(self):
        """Test invalid circuit syntax returns error"""
        result = agent_skills.simulate_circuit("bad_gate()")

---

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.