empathy-framework 5.2.1__py3-none-any.whl → 5.4.0__py3-none-any.whl

empathy_llm_toolkit/code_health.py

@@ -1,1313 +0,0 @@
-"""Code Health Assistant Module
-
-A comprehensive system for running health checks, tracking trends,
-and auto-fixing common issues in codebases.
-
-Copyright 2025 Smart AI Memory, LLC
-Licensed under Fair Source 0.9
-"""
-
-import asyncio
-import json
-import logging
-import shutil
-import subprocess
-from dataclasses import dataclass, field
-from datetime import datetime, timedelta
-from enum import Enum
-from pathlib import Path
-from typing import Any
-
-logger = logging.getLogger(__name__)
-
-
-class HealthStatus(Enum):
-    """Health check result status."""
-
-    PASS = "pass"
-    WARN = "warn"
-    FAIL = "fail"
-    SKIP = "skip"
-    ERROR = "error"
-
-
-class CheckCategory(Enum):
-    """Categories of health checks."""
-
-    LINT = "lint"
-    FORMAT = "format"
-    TYPES = "types"
-    TESTS = "tests"
-    COVERAGE = "coverage"
-    SECURITY = "security"
-    DEPS = "deps"
-
-
-# Priority weights for health check categories
-CHECK_WEIGHTS = {
-    CheckCategory.SECURITY: 100,
-    CheckCategory.TYPES: 90,
-    CheckCategory.TESTS: 85,
-    CheckCategory.LINT: 70,
-    CheckCategory.FORMAT: 50,
-    CheckCategory.COVERAGE: 40,
-    CheckCategory.DEPS: 30,
-}
-
-# Default thresholds
-DEFAULT_THRESHOLDS = {
-    "good": 85,
-    "warning": 70,
-    "critical": 50,
-}
-
-# Default configuration
-DEFAULT_CONFIG = {
-    "checks": {
-        "lint": {"enabled": True, "tool": "ruff", "weight": 70},
-        "format": {"enabled": True, "tool": "black", "weight": 50},
-        "types": {"enabled": True, "tool": "pyright", "weight": 90},
-        "tests": {"enabled": True, "tool": "pytest", "weight": 85, "coverage_target": 80},
-        "security": {"enabled": True, "tool": "bandit", "weight": 100},
-        "deps": {"enabled": True, "tool": "pip-audit", "weight": 30},
-    },
-    "thresholds": DEFAULT_THRESHOLDS,
-    "auto_fix": {
-        "safe_fixes": True,
-        "prompt_fixes": True,
-        "categories": ["lint", "format"],
-    },
-}
-
-
-@dataclass
-class HealthIssue:
-    """A single health check issue."""
-
-    category: CheckCategory
-    file_path: str
-    line: int | None
-    code: str
-    message: str
-    severity: str = "warning"  # warning, error
-    fixable: bool = False
-    fix_command: str | None = None
-
-    def to_dict(self) -> dict:
-        """Convert to dictionary."""
-        return {
-            "category": self.category.value,
-            "file_path": self.file_path,
-            "line": self.line,
-            "code": self.code,
-            "message": self.message,
-            "severity": self.severity,
-            "fixable": self.fixable,
-            "fix_command": self.fix_command,
-        }
-
-
-@dataclass
-class CheckResult:
-    """Result of a single health check."""
-
-    category: CheckCategory
-    status: HealthStatus
-    score: int  # 0-100
-    issues: list[HealthIssue] = field(default_factory=list)
-    details: dict[str, Any] = field(default_factory=dict)
-    duration_ms: int = 0
-    tool_used: str = ""
-
-    @property
-    def issue_count(self) -> int:
-        """Return total issue count."""
-        return len(self.issues)
-
-    @property
-    def fixable_count(self) -> int:
-        """Return fixable issue count."""
-        return sum(1 for i in self.issues if i.fixable)
-
-    def to_dict(self) -> dict:
-        """Convert to dictionary."""
-        return {
-            "category": self.category.value,
-            "status": self.status.value,
-            "score": self.score,
-            "issue_count": self.issue_count,
-            "fixable_count": self.fixable_count,
-            "issues": [i.to_dict() for i in self.issues],
-            "details": self.details,
-            "duration_ms": self.duration_ms,
-            "tool_used": self.tool_used,
-        }
-
-
-@dataclass
-class HealthReport:
-    """Complete health report from all checks."""
-
-    results: list[CheckResult] = field(default_factory=list)
-    overall_score: int = 100
-    status: HealthStatus = HealthStatus.PASS
-    generated_at: str = field(default_factory=lambda: datetime.now().isoformat())
-    project_root: str = "."
-
-    def add_result(self, result: CheckResult) -> None:
-        """Add a check result to the report."""
-        self.results.append(result)
-        self._recalculate_score()
-
-    def _recalculate_score(self) -> None:
-        """Recalculate overall score based on weighted results."""
-        if not self.results:
-            self.overall_score = 100
-            self.status = HealthStatus.PASS
-            return
-
-        total_weight = 0
-        weighted_score = 0
-
-        for result in self.results:
-            if result.status != HealthStatus.SKIP:
-                weight = CHECK_WEIGHTS.get(result.category, 50)
-                weighted_score += result.score * weight
-                total_weight += weight
-
-        if total_weight > 0:
-            self.overall_score = int(weighted_score / total_weight)
-        else:
-            self.overall_score = 100
-
-        # Determine overall status
-        if self.overall_score >= DEFAULT_THRESHOLDS["good"]:
-            self.status = HealthStatus.PASS
-        elif self.overall_score >= DEFAULT_THRESHOLDS["warning"]:
-            self.status = HealthStatus.WARN
-        else:
-            self.status = HealthStatus.FAIL
-
-    @property
-    def total_issues(self) -> int:
-        """Return total issues across all checks."""
-        return sum(r.issue_count for r in self.results)
-
-    @property
-    def total_fixable(self) -> int:
-        """Return total fixable issues."""
-        return sum(r.fixable_count for r in self.results)
-
-    def get_result(self, category: CheckCategory) -> CheckResult | None:
-        """Get result for a specific category."""
-        for result in self.results:
-            if result.category == category:
-                return result
-        return None
-
-    def to_dict(self) -> dict:
-        """Convert to dictionary."""
-        return {
-            "overall_score": self.overall_score,
-            "status": self.status.value,
-            "total_issues": self.total_issues,
-            "total_fixable": self.total_fixable,
-            "generated_at": self.generated_at,
-            "project_root": self.project_root,
-            "results": [r.to_dict() for r in self.results],
-        }
-
-
-class HealthCheckRunner:
-    """Run configurable health checks and aggregate results."""
-
-    def __init__(
-        self,
-        project_root: str = ".",
-        config: dict | None = None,
-    ):
-        """Initialize the health check runner.
-
-        Args:
-            project_root: Root directory of the project
-            config: Configuration dictionary (uses defaults if not provided)
-
-        """
-        self.project_root = Path(project_root).resolve()
-        self.config = {**DEFAULT_CONFIG, **(config or {})}
-        self._check_handlers = {
-            CheckCategory.LINT: self._run_lint_check,
-            CheckCategory.FORMAT: self._run_format_check,
-            CheckCategory.TYPES: self._run_type_check,
-            CheckCategory.TESTS: self._run_test_check,
-            CheckCategory.SECURITY: self._run_security_check,
-            CheckCategory.DEPS: self._run_deps_check,
-        }
-
-    def _is_tool_available(self, tool: str) -> bool:
-        """Check if a tool is available on the system."""
-        return shutil.which(tool) is not None
-
-    async def run_all(self) -> HealthReport:
-        """Run all enabled health checks."""
-        report = HealthReport(project_root=str(self.project_root))
-
-        tasks = []
-        for category in CheckCategory:
-            check_config = self.config["checks"].get(category.value, {})
-            if check_config.get("enabled", False):
-                handler = self._check_handlers.get(category)
-                if handler:
-                    tasks.append(self._run_check_async(category, handler, check_config))
-
-        results = await asyncio.gather(*tasks, return_exceptions=True)
-
-        for result in results:
-            if isinstance(result, CheckResult):
-                report.add_result(result)
-            elif isinstance(result, Exception):
-                # Log error but continue with other checks
-                pass
-
-        return report
-
-    async def run_quick(self) -> HealthReport:
-        """Run fast checks only (lint, format, types)."""
-        report = HealthReport(project_root=str(self.project_root))
-
-        quick_checks = [CheckCategory.LINT, CheckCategory.FORMAT, CheckCategory.TYPES]
-        tasks = []
-
-        for category in quick_checks:
-            check_config = self.config["checks"].get(category.value, {})
-            if check_config.get("enabled", False):
-                handler = self._check_handlers.get(category)
-                if handler:
-                    tasks.append(self._run_check_async(category, handler, check_config))
-
-        results = await asyncio.gather(*tasks, return_exceptions=True)
-
-        for result in results:
-            if isinstance(result, CheckResult):
-                report.add_result(result)
-
-        return report
-
-    async def run_check(self, category: CheckCategory) -> CheckResult:
-        """Run a specific health check."""
-        check_config = self.config["checks"].get(category.value, {})
-        handler = self._check_handlers.get(category)
-
-        if not handler:
-            return CheckResult(
-                category=category,
-                status=HealthStatus.ERROR,
-                score=0,
-                details={"error": f"No handler for {category.value}"},
-            )
-
-        return await self._run_check_async(category, handler, check_config)
-
-    async def _run_check_async(
-        self,
-        category: CheckCategory,
-        handler,
-        config: dict,
-    ) -> CheckResult:
-        """Run a check handler asynchronously.
-
-        This uses broad exception handling intentionally for graceful degradation.
-        Health checks are optional features - the system should continue even if some checks fail.
-
-        Note:
-            Full exception context is preserved via logger.exception() for debugging.
-        """
-        start_time = datetime.now()
-        try:
-            result: CheckResult = await asyncio.to_thread(handler, config)
-            result.duration_ms = int((datetime.now() - start_time).total_seconds() * 1000)
-            return result
-        except Exception as e:
-            # INTENTIONAL: Broad exception handler for graceful degradation of optional checks
-            # Full traceback preserved for debugging
-            logger.exception(f"Health check failed for {category.value}: {e}")
-            return CheckResult(
-                category=category,
-                status=HealthStatus.ERROR,
-                score=0,
-                details={"error": str(e)},
-                duration_ms=int((datetime.now() - start_time).total_seconds() * 1000),
-            )
-
-    def _run_lint_check(self, config: dict) -> CheckResult:
-        """Run linting check using ruff or flake8."""
-        tool = config.get("tool", "ruff")
-        issues = []
-
-        if not self._is_tool_available(tool):
-            return CheckResult(
-                category=CheckCategory.LINT,
-                status=HealthStatus.SKIP,
-                score=100,
-                tool_used=tool,
-                details={"skip_reason": f"{tool} not available"},
-            )
-
-        try:
-            if tool == "ruff":
-                result = subprocess.run(
-                    ["ruff", "check", "--output-format=json", str(self.project_root)],
-                    check=False,
-                    capture_output=True,
-                    text=True,
-                    cwd=str(self.project_root),
-                )
-                if result.stdout:
-                    ruff_issues = json.loads(result.stdout)
-                    for item in ruff_issues:
-                        issues.append(
-                            HealthIssue(
-                                category=CheckCategory.LINT,
-                                file_path=item.get("filename", ""),
-                                line=item.get("location", {}).get("row"),
-                                code=item.get("code", ""),
-                                message=item.get("message", ""),
-                                severity=(
-                                    "warning" if item.get("code", "").startswith("W") else "error"
-                                ),
-                                fixable=item.get("fix") is not None,
-                                fix_command="ruff check --fix" if item.get("fix") else None,
-                            ),
-                        )
-            else:
-                # Fallback to flake8
-                result = subprocess.run(
-                    ["flake8", "--format=json", str(self.project_root)],
-                    check=False,
-                    capture_output=True,
-                    text=True,
-                    cwd=str(self.project_root),
-                )
-                # Parse flake8 output...
-
-            # Calculate score based on issues
-            score = max(0, 100 - len(issues) * 5)  # -5 per issue
-            status = HealthStatus.PASS if not issues else HealthStatus.WARN
-
-            return CheckResult(
-                category=CheckCategory.LINT,
-                status=status,
-                score=score,
-                issues=issues,
-                tool_used=tool,
-                details={"total_files_checked": len({i.file_path for i in issues}) or "all"},
-            )
-
-        except json.JSONDecodeError as e:
-            # Tool output not in expected JSON format
-            logger.warning(f"Lint check JSON parse error ({tool}): {e}")
-            return CheckResult(
-                category=CheckCategory.LINT,
-                status=HealthStatus.ERROR,
-                score=0,
-                tool_used=tool,
-                details={"error": f"Failed to parse {tool} output: {e}"},
-            )
-        except subprocess.SubprocessError as e:
-            # Tool execution failed
-            logger.error(f"Lint check subprocess error ({tool}): {e}")
-            return CheckResult(
-                category=CheckCategory.LINT,
-                status=HealthStatus.ERROR,
-                score=0,
-                tool_used=tool,
-                details={"error": f"Failed to run {tool}: {e}"},
-            )
-        except Exception as e:
-            # Unexpected errors - preserve full context for debugging
-            # INTENTIONAL: Broad handler for graceful degradation of optional check
-            logger.exception(f"Unexpected error in lint check ({tool}): {e}")
-            return CheckResult(
-                category=CheckCategory.LINT,
-                status=HealthStatus.ERROR,
-                score=0,
-                tool_used=tool,
-                details={"error": str(e)},
-            )
-
-    def _run_format_check(self, config: dict) -> CheckResult:
-        """Run formatting check using black or prettier."""
-        tool = config.get("tool", "black")
-        issues = []
-
-        if not self._is_tool_available(tool):
-            return CheckResult(
-                category=CheckCategory.FORMAT,
-                status=HealthStatus.SKIP,
-                score=100,
-                tool_used=tool,
-                details={"skip_reason": f"{tool} not available"},
-            )
-
-        try:
-            if tool == "black":
-                result = subprocess.run(
-                    ["black", "--check", "--diff", str(self.project_root)],
-                    check=False,
-                    capture_output=True,
-                    text=True,
-                    cwd=str(self.project_root),
-                )
-
-                if result.returncode != 0:
-                    # Parse diff output to find files needing formatting
-                    lines = result.stdout.split("\n") if result.stdout else []
-                    current_file = None
-                    for line in lines:
-                        if line.startswith("--- "):
-                            current_file = line[4:].split("\t")[0]
-                        elif current_file and line.startswith("would reformat"):
-                            issues.append(
-                                HealthIssue(
-                                    category=CheckCategory.FORMAT,
-                                    file_path=current_file,
-                                    line=None,
-                                    code="FORMAT",
-                                    message="File needs reformatting",
-                                    severity="warning",
-                                    fixable=True,
-                                    fix_command=f"black {current_file}",
-                                ),
-                            )
-
-                    # Also check stderr for files that would be reformatted
-                    if result.stderr:
-                        for line in result.stderr.split("\n"):
-                            if "would reformat" in line:
-                                file_path = line.replace("would reformat ", "").strip()
-                                if file_path and not any(i.file_path == file_path for i in issues):
-                                    issues.append(
-                                        HealthIssue(
-                                            category=CheckCategory.FORMAT,
-                                            file_path=file_path,
-                                            line=None,
-                                            code="FORMAT",
-                                            message="File needs reformatting",
-                                            severity="warning",
-                                            fixable=True,
-                                            fix_command=f"black {file_path}",
-                                        ),
-                                    )
-
-            score = max(0, 100 - len(issues) * 10)  # -10 per file
-            status = HealthStatus.PASS if not issues else HealthStatus.WARN
-
-            return CheckResult(
-                category=CheckCategory.FORMAT,
-                status=status,
-                score=score,
-                issues=issues,
-                tool_used=tool,
-                details={"files_need_formatting": len(issues)},
-            )
-
-        except subprocess.SubprocessError as e:
-            # Tool execution failed
-            logger.error(f"Format check subprocess error ({tool}): {e}")
-            return CheckResult(
-                category=CheckCategory.FORMAT,
-                status=HealthStatus.ERROR,
-                score=0,
-                tool_used=tool,
-                details={"error": f"Failed to run {tool}: {e}"},
-            )
-        except Exception as e:
-            # Unexpected errors - preserve full context for debugging
-            # INTENTIONAL: Broad handler for graceful degradation of optional check
-            logger.exception(f"Unexpected error in format check ({tool}): {e}")
-            return CheckResult(
-                category=CheckCategory.FORMAT,
-                status=HealthStatus.ERROR,
-                score=0,
-                tool_used=tool,
-                details={"error": str(e)},
-            )
-
-    def _run_type_check(self, config: dict) -> CheckResult:
-        """Run type checking using pyright or mypy."""
-        tool = config.get("tool", "pyright")
-        issues = []
-
-        if not self._is_tool_available(tool):
-            return CheckResult(
-                category=CheckCategory.TYPES,
-                status=HealthStatus.SKIP,
-                score=100,
-                tool_used=tool,
-                details={"skip_reason": f"{tool} not available"},
-            )
-
-        try:
-            if tool == "pyright":
-                result = subprocess.run(
-                    ["pyright", "--outputjson"],
-                    check=False,
-                    capture_output=True,
-                    text=True,
-                    cwd=str(self.project_root),
-                )
-
-                if result.stdout:
-                    try:
-                        data = json.loads(result.stdout)
-                        diagnostics = data.get("generalDiagnostics", [])
-                        for diag in diagnostics:
-                            issues.append(
-                                HealthIssue(
-                                    category=CheckCategory.TYPES,
-                                    file_path=diag.get("file", ""),
-                                    line=diag.get("range", {}).get("start", {}).get("line"),
-                                    code=diag.get("rule", "TYPE"),
-                                    message=diag.get("message", ""),
-                                    severity="error" if diag.get("severity") == 1 else "warning",
-                                    fixable=False,
-                                ),
-                            )
-                    except json.JSONDecodeError:
-                        pass
-
-            elif tool == "mypy":
-                result = subprocess.run(
-                    ["mypy", "--show-error-codes", "--no-error-summary", str(self.project_root)],
-                    check=False,
-                    capture_output=True,
-                    text=True,
-                    cwd=str(self.project_root),
-                )
-
-                if result.stdout:
-                    for line in result.stdout.split("\n"):
-                        if ": error:" in line or ": note:" in line:
-                            parts = line.split(":", 3)
-                            if len(parts) >= 4:
-                                issues.append(
-                                    HealthIssue(
-                                        category=CheckCategory.TYPES,
-                                        file_path=parts[0],
-                                        line=int(parts[1]) if parts[1].isdigit() else None,
-                                        code="TYPE",
-                                        message=parts[3].strip() if len(parts) > 3 else "",
-                                        severity="error",
-                                        fixable=False,
-                                    ),
-                                )
-
-            score = max(0, 100 - len(issues) * 10)  # -10 per type error
-            status = (
-                HealthStatus.PASS
-                if not issues
-                else (HealthStatus.FAIL if len(issues) > 5 else HealthStatus.WARN)
-            )
-
-            return CheckResult(
-                category=CheckCategory.TYPES,
-                status=status,
-                score=score,
-                issues=issues,
-                tool_used=tool,
-                details={"type_errors": len(issues)},
-            )
-
-        except json.JSONDecodeError as e:
-            # Tool output not in expected JSON format (pyright specific)
-            logger.warning(f"Type check JSON parse error ({tool}): {e}")
-            return CheckResult(
-                category=CheckCategory.TYPES,
-                status=HealthStatus.ERROR,
-                score=0,
-                tool_used=tool,
-                details={"error": f"Failed to parse {tool} output: {e}"},
-            )
-        except subprocess.SubprocessError as e:
-            # Tool execution failed
-            logger.error(f"Type check subprocess error ({tool}): {e}")
-            return CheckResult(
-                category=CheckCategory.TYPES,
-                status=HealthStatus.ERROR,
-                score=0,
-                tool_used=tool,
-                details={"error": f"Failed to run {tool}: {e}"},
-            )
-        except Exception as e:
-            # Unexpected errors - preserve full context for debugging
-            # INTENTIONAL: Broad handler for graceful degradation of optional check
-            logger.exception(f"Unexpected error in type check ({tool}): {e}")
-            return CheckResult(
-                category=CheckCategory.TYPES,
-                status=HealthStatus.ERROR,
-                score=0,
-                tool_used=tool,
-                details={"error": str(e)},
-            )
-
-    def _run_test_check(self, config: dict) -> CheckResult:
-        """Run test suite using pytest."""
-        tool = config.get("tool", "pytest")
-
-        if not self._is_tool_available(tool):
-            return CheckResult(
-                category=CheckCategory.TESTS,
-                status=HealthStatus.SKIP,
-                score=100,
-                tool_used=tool,
-                details={"skip_reason": f"{tool} not available"},
-            )
-
-        try:
-            result = subprocess.run(
-                ["pytest", "--tb=no", "-q", "--co", "-q"],  # Collect only, quiet
-                check=False,
-                capture_output=True,
-                text=True,
-                cwd=str(self.project_root),
-            )
-
-            # Count collected tests
-            test_count = 0
-            for line in result.stdout.split("\n"):
-                if "test" in line.lower() and "::" in line:
-                    test_count += 1
-
-            # Run actual tests
-            result = subprocess.run(
-                ["pytest", "--tb=short", "-q"],
-                check=False,
-                capture_output=True,
-                text=True,
-                cwd=str(self.project_root),
-                timeout=300,  # 5 minute timeout
-            )
-
-            passed = 0
-            failed = 0
-            issues = []
-
-            # Parse pytest output
-            for line in result.stdout.split("\n"):
-                if " passed" in line:
-                    parts = line.split()
-                    for i, part in enumerate(parts):
-                        if part == "passed" and i > 0:
-                            try:
-                                passed = int(parts[i - 1])
-                            except ValueError:
-                                pass
-                if " failed" in line:
-                    parts = line.split()
-                    for i, part in enumerate(parts):
-                        if part == "failed" and i > 0:
-                            try:
-                                failed = int(parts[i - 1])
-                            except ValueError:
-                                pass
-
-            # Create issues for failed tests
-            if result.returncode != 0 and result.stdout:
-                lines = result.stdout.split("\n")
-                for line in lines:
-                    if "FAILED" in line:
-                        # Extract test name and file
-                        if "::" in line:
-                            test_path = (
-                                line.split("FAILED")[1].strip() if "FAILED" in line else line
-                            )
-                            test_path = test_path.split(" -")[0].strip()
-                            file_part = test_path.split("::")[0] if "::" in test_path else test_path
-                            issues.append(
-                                HealthIssue(
-                                    category=CheckCategory.TESTS,
-                                    file_path=file_part,
-                                    line=None,
-                                    code="TEST_FAIL",
-                                    message=f"Test failed: {test_path}",
-                                    severity="error",
-                                    fixable=False,
-                                ),
-                            )
-
-            total = passed + failed
-            score = int((passed / total) * 100) if total > 0 else 100
-            status = HealthStatus.PASS if failed == 0 else HealthStatus.FAIL
-
-            return CheckResult(
-                category=CheckCategory.TESTS,
-                status=status,
-                score=score,
-                issues=issues,
-                tool_used=tool,
-                details={
-                    "passed": passed,
-                    "failed": failed,
-                    "total": total,
-                },
-            )
-
-        except subprocess.TimeoutExpired:
-            # Tests took too long - specific timeout error
-            logger.error(f"Test check timeout ({tool}): Tests took longer than 5 minutes")
-            return CheckResult(
-                category=CheckCategory.TESTS,
-                status=HealthStatus.ERROR,
-                score=0,
-                tool_used=tool,
-                details={"error": "Test suite timed out after 5 minutes"},
-            )
-        except subprocess.SubprocessError as e:
-            # Tool execution failed
-            logger.error(f"Test check subprocess error ({tool}): {e}")
-            return CheckResult(
-                category=CheckCategory.TESTS,
-                status=HealthStatus.ERROR,
-                score=0,
-                tool_used=tool,
-                details={"error": f"Failed to run {tool}: {e}"},
-            )
-        except Exception as e:
-            # Unexpected errors - preserve full context for debugging
-            # INTENTIONAL: Broad handler for graceful degradation of optional check
-            logger.exception(f"Unexpected error in test check ({tool}): {e}")
-            return CheckResult(
-                category=CheckCategory.TESTS,
-                status=HealthStatus.ERROR,
-                score=0,
-                tool_used=tool,
-                details={"error": str(e)},
-            )
-
-    def _run_security_check(self, config: dict) -> CheckResult:
-        """Run security check using bandit."""
-        tool = config.get("tool", "bandit")
-        issues = []
-
-        if not self._is_tool_available(tool):
-            return CheckResult(
-                category=CheckCategory.SECURITY,
-                status=HealthStatus.SKIP,
-                score=100,
-                tool_used=tool,
-                details={"skip_reason": f"{tool} not available"},
-            )
-
-        try:
-            result = subprocess.run(
-                ["bandit", "-r", "-f", "json", str(self.project_root)],
-                check=False,
-                capture_output=True,
-                text=True,
-                cwd=str(self.project_root),
-            )
-
-            if result.stdout:
-                try:
-                    data = json.loads(result.stdout)
-                    for item in data.get("results", []):
-                        severity = item.get("issue_severity", "LOW")
-                        issues.append(
-                            HealthIssue(
-                                category=CheckCategory.SECURITY,
-                                file_path=item.get("filename", ""),
-                                line=item.get("line_number"),
-                                code=item.get("test_id", ""),
-                                message=item.get("issue_text", ""),
-                                severity="error" if severity in ["HIGH", "MEDIUM"] else "warning",
-                                fixable=False,
-                            ),
-                        )
-                except json.JSONDecodeError:
-                    pass
-
-            # Weight by severity
-            high_count = sum(1 for i in issues if i.severity == "error")
-            low_count = len(issues) - high_count
-            score = max(0, 100 - high_count * 20 - low_count * 5)
-            status = (
-                HealthStatus.PASS
-                if not issues
-                else (HealthStatus.FAIL if high_count > 0 else HealthStatus.WARN)
-            )
-
-            return CheckResult(
-                category=CheckCategory.SECURITY,
-                status=status,
-                score=score,
-                issues=issues,
-                tool_used=tool,
-                details={
-                    "high_severity": high_count,
-                    "low_severity": low_count,
-                },
-            )
-
-        except json.JSONDecodeError as e:
-            # Tool output not in expected JSON format
-            logger.warning(f"Security check JSON parse error ({tool}): {e}")
-            return CheckResult(
-                category=CheckCategory.SECURITY,
-                status=HealthStatus.ERROR,
-                score=0,
-                tool_used=tool,
-                details={"error": f"Failed to parse {tool} output: {e}"},
-            )
-        except subprocess.SubprocessError as e:
-            # Tool execution failed
-            logger.error(f"Security check subprocess error ({tool}): {e}")
-            return CheckResult(
-                category=CheckCategory.SECURITY,
-                status=HealthStatus.ERROR,
-                score=0,
-                tool_used=tool,
-                details={"error": f"Failed to run {tool}: {e}"},
-            )
-        except Exception as e:
-            # Unexpected errors - preserve full context for debugging
-            # INTENTIONAL: Broad handler for graceful degradation of optional check
-            logger.exception(f"Unexpected error in security check ({tool}): {e}")
-            return CheckResult(
-                category=CheckCategory.SECURITY,
-                status=HealthStatus.ERROR,
-                score=0,
-                tool_used=tool,
-                details={"error": str(e)},
-            )
-
-    def _run_deps_check(self, config: dict) -> CheckResult:
-        """Run dependency check using pip-audit."""
-        tool = config.get("tool", "pip-audit")
-        issues = []
-
-        if not self._is_tool_available(tool):
-            return CheckResult(
-                category=CheckCategory.DEPS,
-                status=HealthStatus.SKIP,
-                score=100,
-                tool_used=tool,
-                details={"skip_reason": f"{tool} not available"},
-            )
-
-        try:
-            result = subprocess.run(
-                ["pip-audit", "--format=json"],
-                check=False,
-                capture_output=True,
-                text=True,
-                cwd=str(self.project_root),
-            )
-
-            if result.stdout:
-                try:
-                    data = json.loads(result.stdout)
-                    for item in data:
-                        issues.append(
-                            HealthIssue(
-                                category=CheckCategory.DEPS,
-                                file_path="requirements.txt",
-                                line=None,
-                                code=item.get("id", "VULN"),
-                                message=f"{item.get('name')}: {item.get('description', 'Vuln')}",
-                                severity="error" if item.get("fix_versions") else "warning",
-                                fixable=bool(item.get("fix_versions")),
-                                fix_command=self._get_fix_cmd(item),
-                            ),
-                        )
-                except json.JSONDecodeError:
-                    pass
-
-            score = max(0, 100 - len(issues) * 15)
-            status = HealthStatus.PASS if not issues else HealthStatus.WARN
-
-            return CheckResult(
-                category=CheckCategory.DEPS,
-                status=status,
-                score=score,
-                issues=issues,
-                tool_used=tool,
-                details={"vulnerable_packages": len(issues)},
-            )
-
-        except json.JSONDecodeError as e:
-            # Tool output not in expected JSON format
-            logger.warning(f"Dependency check JSON parse error ({tool}): {e}")
-            return CheckResult(
-                category=CheckCategory.DEPS,
-                status=HealthStatus.ERROR,
-                score=0,
-                tool_used=tool,
-                details={"error": f"Failed to parse {tool} output: {e}"},
-            )
-        except subprocess.SubprocessError as e:
-            # Tool execution failed
-            logger.error(f"Dependency check subprocess error ({tool}): {e}")
-            return CheckResult(
-                category=CheckCategory.DEPS,
-                status=HealthStatus.ERROR,
-                score=0,
-                tool_used=tool,
-                details={"error": f"Failed to run {tool}: {e}"},
-            )
-        except Exception as e:
-            # Unexpected errors - preserve full context for debugging
-            # INTENTIONAL: Broad handler for graceful degradation of optional check
-            logger.exception(f"Unexpected error in dependency check ({tool}): {e}")
-            return CheckResult(
-                category=CheckCategory.DEPS,
-                status=HealthStatus.ERROR,
-                score=0,
-                tool_used=tool,
-                details={"error": str(e)},
-            )
-
-    def _get_fix_cmd(self, item: dict) -> str | None:
-        """Get pip install command to fix a vulnerable package."""
-        fix_versions = item.get("fix_versions")
-        if fix_versions:
-            return f"pip install {item.get('name')}=={fix_versions[0]}"
-        return None
-
-
-class AutoFixer:
-    """Apply automatic fixes to code health issues."""
-
-    def __init__(self, config: dict[str, Any] | None = None):
-        """Initialize the auto-fixer."""
-        self.config: dict[str, Any] = config or DEFAULT_CONFIG.get("auto_fix", {})  # type: ignore[assignment]
-        self.safe_fixes = self.config.get("safe_fixes", True)
-        self.prompt_fixes = self.config.get("prompt_fixes", True)
-
-    def preview_fixes(self, report: HealthReport) -> list[dict]:
-        """Show what would be fixed without applying."""
-        fixes = []
-        for result in report.results:
-            for issue in result.issues:
-                if issue.fixable and issue.fix_command:
-                    fixes.append(
-                        {
-                            "category": issue.category.value,
-                            "file": issue.file_path,
-                            "issue": issue.message,
-                            "fix_command": issue.fix_command,
-                            "safe": self._is_safe_fix(issue),
-                        },
-                    )
-        return fixes
-
-    def _is_safe_fix(self, issue: HealthIssue) -> bool:
-        """Determine if a fix is safe to apply automatically."""
-        safe_codes = ["FORMAT", "W291", "W292", "W293", "I001"]  # Whitespace, imports
-        return issue.code in safe_codes or issue.category == CheckCategory.FORMAT
-
-    async def fix_all(self, report: HealthReport, interactive: bool = False) -> dict[str, Any]:
-        """Apply all safe fixes, optionally prompt for others."""
-        results: dict[str, Any] = {
-            "fixed": [],
-            "skipped": [],
-            "failed": [],
-        }
-
-        for result in report.results:
-            for issue in result.issues:
-                if issue.fixable and issue.fix_command:
-                    if self._is_safe_fix(issue):
-                        success = await self._apply_fix(issue)
-                        if success:
-                            results["fixed"].append(issue.to_dict())
-                        else:
-                            results["failed"].append(issue.to_dict())
-                    elif interactive and self.prompt_fixes:
-                        # In interactive mode, we'd prompt here
-                        results["skipped"].append(issue.to_dict())
-                    else:
-                        results["skipped"].append(issue.to_dict())
-
-        return results
-
-    async def fix_category(self, report: HealthReport, category: CheckCategory) -> dict[str, Any]:
-        """Fix issues in a specific category."""
-        results: dict[str, Any] = {
-            "fixed": [],
-            "skipped": [],
-            "failed": [],
-        }
-
-        result = report.get_result(category)
-        if not result:
-            return results
-
-        for issue in result.issues:
-            if issue.fixable and issue.fix_command:
-                success = await self._apply_fix(issue)
-                if success:
-                    results["fixed"].append(issue.to_dict())
-                else:
-                    results["failed"].append(issue.to_dict())
-
-        return results
-
-    async def _apply_fix(self, issue: HealthIssue) -> bool:
-        """Apply a single fix.
-
-        This uses broad exception handling intentionally for graceful degradation.
-        Auto-fixes are optional - the system should continue even if some fixes fail.
-
-        Note:
-            Full exception context is preserved via logger.exception() for debugging.
-        """
-        if not issue.fix_command:
-            return False
-
-        try:
-            result = await asyncio.to_thread(
-                subprocess.run,
-                issue.fix_command.split(),
-                capture_output=True,
-                text=True,
-            )
-            return result.returncode == 0
-        except subprocess.SubprocessError as e:
-            # Fix command execution failed
-            logger.error(f"Auto-fix subprocess error for {issue.file_path}: {e}")
-            return False
-        except Exception as e:
-            # Unexpected errors - preserve full context for debugging
-            # INTENTIONAL: Broad handler for graceful degradation of optional auto-fix
-            logger.exception(f"Unexpected error applying fix to {issue.file_path}: {e}")
-            return False
-
-
-class HealthTrendTracker:
-    """Track code health trends and identify patterns."""
-
-    def __init__(self, project_root: str = "."):
-        """Initialize the trend tracker."""
-        self.project_root = Path(project_root)
-        self.history_dir = self.project_root / ".empathy" / "health_history"
-        self.history_dir.mkdir(parents=True, exist_ok=True)
-
-    def record_check(self, report: HealthReport) -> None:
-        """Save health check to history."""
-        today = datetime.now().strftime("%Y-%m-%d")
-        filepath = self.history_dir / f"{today}.json"
-
-        # Load existing or create new
-        history = []
-        if filepath.exists():
-            try:
-                history = json.loads(filepath.read_text())
-            except json.JSONDecodeError:
-                history = []
-
-        # Add new entry
-        history.append(
-            {
-                "timestamp": datetime.now().isoformat(),
-                "overall_score": report.overall_score,
-                "status": report.status.value,
-                "total_issues": report.total_issues,
-                "results": {r.category.value: r.score for r in report.results},
-            },
-        )
-
-        filepath.write_text(json.dumps(history, indent=2))
-
-    def get_trends(self, days: int = 30) -> dict[str, Any]:
-        """Analyze health trends over time."""
-        trends: dict[str, Any] = {
-            "period_days": days,
-            "data_points": [],
-            "average_score": 0,
-            "trend_direction": "stable",
-            "score_change": 0,
-        }
-
-        scores = []
-        for i in range(days):
-            date = (datetime.now() - timedelta(days=i)).strftime("%Y-%m-%d")
-            filepath = self.history_dir / f"{date}.json"
-
-            if filepath.exists():
-                try:
-                    data = json.loads(filepath.read_text())
-                    if data:
-                        # Get last entry of the day
-                        entry = data[-1]
-                        scores.append(entry.get("overall_score", 0))
-                        trends["data_points"].append(
-                            {
-                                "date": date,
-                                "score": entry.get("overall_score", 0),
-                            },
-                        )
-                except json.JSONDecodeError:
-                    pass
-
-        if scores:
-            trends["average_score"] = int(sum(scores) / len(scores))
-
-            if len(scores) >= 2:
-                recent = scores[:7] if len(scores) >= 7 else scores[: len(scores) // 2]
-                older = scores[7:] if len(scores) >= 7 else scores[len(scores) // 2 :]
-
-                recent_avg = sum(recent) / len(recent) if recent else 0
-                older_avg = sum(older) / len(older) if older else 0
-
-                trends["score_change"] = int(recent_avg - older_avg)
-
-                if trends["score_change"] > 5:
-                    trends["trend_direction"] = "improving"
-                elif trends["score_change"] < -5:
-                    trends["trend_direction"] = "declining"
-                else:
-                    trends["trend_direction"] = "stable"
-
-        return trends
-
-    def identify_hotspots(self) -> list[dict]:
-        """Find files that consistently have issues."""
-        file_issues: dict[str, int] = {}
-
-        for filepath in self.history_dir.glob("*.json"):
-            try:
-                data = json.loads(filepath.read_text())
-                for entry in data:
-                    for result in entry.get("results", {}).values():
-                        if isinstance(result, dict):
-                            for issue in result.get("issues", []):
-                                file_path = issue.get("file_path", "")
-                                if file_path:
-                                    file_issues[file_path] = file_issues.get(file_path, 0) + 1
-            except (json.JSONDecodeError, KeyError):
-                pass
-
-        # Sort by issue count
-        sorted_files = sorted(file_issues.items(), key=lambda x: x[1], reverse=True)
-
-        return [{"file": f, "issue_count": c} for f, c in sorted_files[:10]]
-
-
-def format_health_output(
-    report: HealthReport,
-    level: int = 1,
-    thresholds: dict | None = None,
-) -> str:
-    """Format health report for display.
-
-    Args:
-        report: The health report to format
-        level: Detail level (1=summary, 2=details, 3=full)
-        thresholds: Score thresholds for status icons
-
-    """
-    thresholds = thresholds or DEFAULT_THRESHOLDS
-    lines = []
-
-    # Overall score
-    score = report.overall_score
-    if score >= thresholds["good"]:
-        status_word = "Good"
-        status_icon = "🟢"
-    elif score >= thresholds["warning"]:
-        status_word = "Warning"
-        status_icon = "🟡"
-    else:
-        status_word = "Critical"
-        status_icon = "🔴"
-
-    lines.append(f"{status_icon} Code Health: {status_word} ({score}/100)")
-    lines.append("")
-
-    # Level 1: Summary
-    for result in report.results:
-        if result.status == HealthStatus.SKIP:
-            continue
-
-        if result.score >= thresholds["good"]:
-            icon = "🟢"
-        elif result.score >= thresholds["warning"]:
-            icon = "🟡"
-        else:
-            icon = "🔴"
-
-        category_name = result.category.value.capitalize()
-
-        if result.category == CheckCategory.TESTS:
-            details = result.details
-            lines.append(
-                f"{icon} {category_name}: {details.get('passed', 0)}P/{details.get('failed', 0)}F",
-            )
-        elif result.category == CheckCategory.LINT:
-            lines.append(f"{icon} {category_name}: {result.issue_count} warnings")
-        elif result.category == CheckCategory.TYPES:
-            lines.append(f"{icon} {category_name}: {result.issue_count} errors")
-        elif result.category == CheckCategory.SECURITY:
-            details = result.details
-            high = details.get("high_severity", 0)
-            low = details.get("low_severity", 0)
-            if high or low:
-                lines.append(f"{icon} {category_name}: {high} high, {low} low severity")
-            else:
-                lines.append(f"{icon} {category_name}: No vulnerabilities")
-        elif result.category == CheckCategory.FORMAT:
-            if result.issue_count:
-                lines.append(f"{icon} {category_name}: {result.issue_count} files need formatting")
-            else:
-                lines.append(f"{icon} {category_name}: All files formatted")
-        elif result.category == CheckCategory.DEPS:
-            if result.issue_count:
-                lines.append(f"{icon} {category_name}: {result.issue_count} vulnerable packages")
-            else:
-                lines.append(f"{icon} {category_name}: All dependencies secure")
-
-    # Level 2: Details
-    if level >= 2:
-        lines.append("")
-        lines.append("━" * 40)
-        lines.append("Details:")
-        lines.append("")
-
-        for result in report.results:
-            if result.issues:
-                lines.append(f"  {result.category.value.upper()} ({len(result.issues)} issues)")
-                for issue in result.issues[:5]:  # Show first 5
-                    loc = f":{issue.line}" if issue.line else ""
-                    lines.append(f"    {issue.file_path}{loc}")
-                    lines.append(f"      {issue.code}: {issue.message}")
-                if len(result.issues) > 5:
-                    lines.append(f"    ... and {len(result.issues) - 5} more")
-                lines.append("")
-
-    # Level 3: Full report
-    if level >= 3:
-        lines.append("")
-        lines.append("━" * 40)
-        lines.append("Full Report")
-        lines.append(f"Generated: {report.generated_at}")
-        lines.append(f"Project: {report.project_root}")
-        lines.append("")
-
-        for result in report.results:
-            lines.append(f"## {result.category.value.capitalize()} (Score: {result.score}/100)")
-            lines.append(f"   Tool: {result.tool_used}")
-            lines.append(f"   Duration: {result.duration_ms}ms")
-            if result.details:
-                for key, value in result.details.items():
-                    lines.append(f"   {key}: {value}")
-            lines.append("")
-
-    # Action prompt
-    if report.total_fixable > 0:
-        lines.append("")
-        lines.append("━" * 40)
-        lines.append(
-            f"[1] Fix {report.total_fixable} auto-fixable issues  [2] See details  [3] Full report",
-        )
-
-    return "\n".join(lines)