feat: add codebase genome diff script for structural change detection

Introduces genome_diff.py — a tool for detecting structural changes between
two git refs: file-level changes, function/class signature modifications,
and dependency import changes.

Addresses #132.

scripts/dependency_freshness.py

@@ -1,271 +0,0 @@
-#!/usr/bin/env python3
-"""dependency_freshness.py - Compare installed dependencies against latest PyPI versions.
-
-Identify packages that are more than 2 major versions behind.
-Outputs a human-readable report by default or JSON with --json flag.
-"""
-
-import argparse
-import json
-import subprocess
-import sys
-from packaging import version
-from typing import Dict, List, Tuple
-
-
-def parse_requirements(requirements_path: str) -> List[str]:
-    """Parse package names from a requirements.txt file."""
-    packages = []
-    try:
-        with open(requirements_path, 'r') as f:
-            for line in f:
-                line = line.strip()
-                if not line or line.startswith('#'):
-                    continue
-                pkg_name = line
-                for delim in ['[', '>', '<', '=', '!', ';', '@']:
-                    if delim in pkg_name:
-                        pkg_name = pkg_name.split(delim)[0]
-                pkg_name = pkg_name.strip()
-                if pkg_name:
-                    packages.append(pkg_name.lower())
-    except FileNotFoundError:
-        print(f"Warning: requirements file not found: {requirements_path}", file=sys.stderr)
-    return packages
-
-
-def get_installed_packages() -> Dict[str, str]:
-    """Get all installed packages via pip list --format=json."""
-    try:
-        result = subprocess.run(
-            [sys.executable, '-m', 'pip', 'list', '--format=json'],
-            capture_output=True, text=True, check=True
-        )
-        packages = json.loads(result.stdout)
-        return {pkg['name'].lower(): pkg['version'] for pkg in packages}
-    except subprocess.CalledProcessError as e:
-        print(f"Error running pip list: {e}", file=sys.stderr)
-        sys.exit(1)
-    except json.JSONDecodeError as e:
-        print(f"Error parsing pip output: {e}", file=sys.stderr)
-        sys.exit(1)
-
-
-def get_outdated_packages() -> Dict[str, dict]:
-    """Get outdated packages via pip list --outdated --format=json."""
-    try:
-        result = subprocess.run(
-            [sys.executable, '-m', 'pip', 'list', '--outdated', '--format=json'],
-            capture_output=True, text=True, check=True
-        )
-        outdated_list = json.loads(result.stdout)
-        outdated = {}
-        for pkg in outdated_list:
-            name = pkg['name'].lower()
-            outdated[name] = {
-                'installed': pkg.get('version', ''),
-                'latest': pkg.get('latest_version', ''),
-                'latest_filetype': pkg.get('latest_filetype', '')
-            }
-        return outdated
-    except subprocess.CalledProcessError as e:
-        print(f"Error running pip list --outdated: {e}", file=sys.stderr)
-        sys.exit(1)
-    except json.JSONDecodeError as e:
-        print(f"Error parsing pip outdated output: {e}", file=sys.stderr)
-        sys.exit(1)
-
-
-def get_major_version(v: str) -> int:
-    """Extract major version number from a version string."""
-    try:
-        parsed = version.parse(v)
-        if hasattr(parsed, 'major'):
-            return int(parsed.major)
-        parts = str(v).split('.')
-        if parts:
-            return int(parts[0])
-    except Exception:
-        pass
-    return 0
-
-
-def is_more_than_two_majors_behind(installed_ver: str, latest_ver: str) -> bool:
-    """Check if installed version is more than 2 major versions behind latest."""
-    try:
-        installed_major = get_major_version(installed_ver)
-        latest_major = get_major_version(latest_ver)
-        return (latest_major - installed_major) > 2
-    except Exception:
-        return False
-
-
-def analyze_dependencies(
-    required_packages: List[str],
-    installed_packages: Dict[str, str],
-    outdated_packages: Dict[str, dict]
-) -> Tuple[List[dict], List[str], List[dict]]:
-    """Analyze dependency freshness."""
-    very_outdated = []
-    missing = []
-    outdated_but_not_critical = []
-
-    for pkg in required_packages:
-        if pkg not in installed_packages:
-            missing.append(pkg)
-            continue
-
-        installed_ver = installed_packages[pkg]
-        if pkg not in outdated_packages:
-            continue
-
-        latest_ver = outdated_packages[pkg]['latest']
-        if is_more_than_two_majors_behind(installed_ver, latest_ver):
-            very_outdated.append({
-                'package': pkg,
-                'installed': installed_ver,
-                'latest': latest_ver,
-                'major_diff': get_major_version(latest_ver) - get_major_version(installed_ver)
-            })
-        else:
-            outdated_but_not_critical.append({
-                'package': pkg,
-                'installed': installed_ver,
-                'latest': latest_ver,
-                'major_diff': get_major_version(latest_ver) - get_major_version(installed_ver)
-            })
-
-    return very_outdated, missing, outdated_but_not_critical
-
-
-def generate_human_report(
-    very_outdated: List[dict],
-    missing: List[str],
-    outdated_but_not_critical: List[dict],
-    requirements_path: str
-) -> str:
-    """Generate a human-readable staleness report."""
-    lines = []
-    lines.append("=" * 60)
-    lines.append("DEPENDENCY FRESHNESS REPORT")
-    lines.append("=" * 60)
-    lines.append(f"Requirements file: {requirements_path}")
-    total = len(very_outdated) + len(missing) + len(outdated_but_not_critical)
-    lines.append(f"Total dependencies checked: {total}")
-    lines.append(f"Very outdated (>2 major versions behind): {len(very_outdated)}")
-    lines.append(f"Outdated but within 2 major versions: {len(outdated_but_not_critical)}")
-    lines.append(f"Missing (not installed): {len(missing)}")
-    lines.append("")
-
-    if very_outdated:
-        lines.append("!!! VERY OUTDATED PACKAGES (consider updating):")
-        lines.append("-" * 60)
-        for pkg_info in very_outdated:
-            lines.append(f"  {pkg_info['package']}")
-            lines.append(f"    Installed: {pkg_info['installed']}")
-            lines.append(f"    Latest:    {pkg_info['latest']}")
-            lines.append(f"    Major diff: {pkg_info['major_diff']}")
-            lines.append("")
-    else:
-        lines.append("✓ No packages more than 2 major versions behind.")
-        lines.append("")
-
-    if outdated_but_not_critical:
-        lines.append(f"Outdated packages (within 2 major versions):")
-        lines.append("-" * 60)
-        for pkg_info in outdated_but_not_critical:
-            lines.append(f"  {pkg_info['package']}: {pkg_info['installed']} -> {pkg_info['latest']} (major diff: {pkg_info['major_diff']})")
-        lines.append("")
-
-    if missing:
-        lines.append(f"Missing packages (not installed):")
-        lines.append("-" * 60)
-        for pkg in missing:
-            lines.append(f"  {pkg}")
-        lines.append("")
-
-    lines.append("=" * 60)
-    lines.append("For full details, run: python3 -m pip list --outdated")
-    lines.append("=" * 60)
-
-    return "\n".join(lines)
-
-
-def generate_json_report(
-    very_outdated: List[dict],
-    missing: List[str],
-    outdated_but_not_critical: List[dict],
-    requirements_path: str
-) -> str:
-    """Generate a JSON staleness report."""
-    report = {
-        'requirements_file': requirements_path,
-        'summary': {
-            'total_dependencies': len(very_outdated) + len(missing) + len(outdated_but_not_critical),
-            'very_outdated_count': len(very_outdated),
-            'outdated_within_threshold_count': len(outdated_but_not_critical),
-            'missing_count': len(missing)
-        },
-        'very_outdated': very_outdated,
-        'outdated_within_threshold': outdated_but_not_critical,
-        'missing': missing
-    }
-    return json.dumps(report, indent=2)
-
-
-def main():
-    parser = argparse.ArgumentParser(
-        description='Check dependency freshness against PyPI latest versions.'
-    )
-    parser.add_argument(
-        '--requirements', '-r',
-        default='requirements.txt',
-        help='Path to requirements.txt file (default: requirements.txt)'
-    )
-    parser.add_argument(
-        '--json',
-        action='store_true',
-        help='Output report as JSON instead of human-readable text'
-    )
-    parser.add_argument(
-        '--output', '-o',
-        help='Optional output file for the report (default: stdout)'
-    )
-
-    args = parser.parse_args()
-
-    # Parse requirements
-    required_packages = parse_requirements(args.requirements)
-    if not required_packages:
-        print("No packages found in requirements file.", file=sys.stderr)
-        sys.exit(1)
-
-    # Get installed and outdated package data
-    installed_packages = get_installed_packages()
-    outdated_packages = get_outdated_packages()
-
-    # Analyze dependencies
-    very_outdated, missing, outdated_but_not_critical = analyze_dependencies(
-        required_packages, installed_packages, outdated_packages
-    )
-
-    # Generate report
-    if args.json:
-        report = generate_json_report(very_outdated, missing, outdated_but_not_critical, args.requirements)
-    else:
-        report = generate_human_report(very_outdated, missing, outdated_but_not_critical, args.requirements)
-
-    # Output report
-    if args.output:
-        with open(args.output, 'w') as f:
-            f.write(report + '\n')
-    else:
-        print(report)
-
-    # Exit code: 0 if no very outdated deps, 1 otherwise
-    exit_code = 1 if very_outdated else 0
-    sys.exit(exit_code)
-
-
-if __name__ == '__main__':
-    main()

scripts/genome_diff.py

@@ -0,0 +1,288 @@
+#!/usr/bin/env python3
+"""
+Codebase Genome Diff — Detect structural changes between two versions.
+
+Compares two git refs (commits, branches, tags) and produces a human-readable
+report of structural changes:
+  • Added/removed/renamed files
+  • Changed functions/classes (signature modifications)
+  • New dependencies (imports, requirements, etc.)
+
+Usage:
+    python3 scripts/genome_diff.py --ref1 <commit1> --ref2 <commit2>
+    python3 scripts/genome_diff.py --ref1 main --ref2 feature-branch
+    python3 scripts/genome_diff.py --ref1 v1.0 --ref2 v2.0 --output report.txt
+"""
+
+import argparse
+import json
+import os
+import re
+import subprocess
+import sys
+from dataclasses import dataclass, field
+from typing import List, Dict, Any, Optional
+
+SCRIPT_DIR = os.path.dirname(os.path.abspath(__file__))
+sys.path.insert(0, SCRIPT_DIR)
+from diff_analyzer import DiffAnalyzer, ChangeCategory
+
+
+@dataclass
+class FunctionChange:
+    file: str
+    name: str
+    kind: str  # 'function' or 'class'
+    change_type: str  # 'added' or 'removed' (simplified)
+    old_line: Optional[int] = None
+    new_line: Optional[int] = None
+
+
+@dataclass
+class DependencyChange:
+    file: str
+    module: str
+    change_type: str  # 'added' or 'removed' or 'modified'
+    line: int = 0
+
+
+@dataclass
+class GenomeDiffReport:
+    ref1: str
+    ref2: str
+    file_changes: List[Dict[str, Any]] = field(default_factory=list)
+    function_changes: List[FunctionChange] = field(default_factory=list)
+    dependency_changes: List[DependencyChange] = field(default_factory=list)
+    total_files_changed: int = 0
+    total_functions_changed: int = 0
+    total_dependencies_changed: int = 0
+
+    def to_dict(self) -> Dict[str, Any]:
+        return {
+            "ref1": self.ref1,
+            "ref2": self.ref2,
+            "summary": {
+                "files": self.total_files_changed,
+                "functions": self.total_functions_changed,
+                "dependencies": self.total_dependencies_changed,
+            },
+            "file_changes": self.file_changes,
+            "function_changes": [fc.__dict__ for fc in self.function_changes],
+            "dependency_changes": [dc.__dict__ for dc in self.dependency_changes],
+        }
+
+    def human_report(self) -> str:
+        lines = []
+        lines.append(f"Codebase Genome Diff: {self.ref1} → {self.ref2}")
+        lines.append("=" * 60)
+        lines.append(f"  Files changed: {self.total_files_changed}")
+        lines.append(f"  Functions changed: {self.total_functions_changed}")
+        lines.append(f"  Dependencies changed: {self.total_dependencies_changed}")
+        lines.append("")
+
+        for fc in self.file_changes:
+            kind = []
+            if fc.get('is_new'):
+                kind.append("NEW")
+            if fc.get('is_deleted'):
+                kind.append("DELETED")
+            if fc.get('is_renamed'):
+                kind.append("RENAMED")
+            if fc.get('is_binary'):
+                kind.append("BINARY")
+            kind_str = f" [{', '.join(kind)}]" if kind else ""
+            lines.append(f"  {fc['path']}{kind_str}  (+{fc['added_lines']}/-{fc['deleted_lines']})")
+        lines.append("")
+
+        for fc in self.function_changes:
+            op = {'added': '+', 'removed': '-', 'modified': '~'}.get(fc.change_type, '?')
+            lines.append(f"  [{op}] {fc.file}: {fc.kind} '{fc.name}'")
+        lines.append("")
+
+        for dc in self.dependency_changes:
+            op = '+' if dc.change_type == 'added' else '-'
+            lines.append(f"  [{op}] {dc.file}: {dc.module}")
+        lines.append("")
+
+        return "\n".join(lines)
+
+
+def run_git_diff(ref1: str, ref2: str) -> str:
+    result = subprocess.run(
+        ['git', 'diff', '--unified=0', f'{ref1}...{ref2}'],
+        capture_output=True, text=True, cwd=SCRIPT_DIR
+    )
+    if result.returncode not in (0, 1):
+        print(f"git diff failed: {result.stderr}", file=sys.stderr)
+        sys.exit(1)
+    return result.stdout
+
+
+def extract_function_changes(diff_text: str) -> List[FunctionChange]:
+    changes: List[FunctionChange] = []
+    pattern = re.compile(r'^([+\-])\s*(def|class)\s+(\w+)', re.MULTILINE)
+    hunk_header_re = re.compile(r'^@@\s+-(\d+)(?:,(\d+))?\s+\+(\d+)(?:,(\d+))?\s+@@')
+    current_old_line: Optional[int] = None
+    current_new_line: Optional[int] = None
+
+    for line in diff_text.split('\n'):
+        hdr = hunk_header_re.match(line)
+        if hdr:
+            current_old_line = int(hdr.group(1))
+            current_new_line = int(hdr.group(3))
+            continue
+        m = pattern.match(line)
+        if m:
+            op = m.group(1)
+            kind = m.group(2)
+            name = m.group(3)
+            change_type = "added" if op == '+' else "removed"
+            line_num = current_new_line if change_type == "added" else current_old_line
+            changes.append(FunctionChange(
+                file="<unknown>",
+                name=name,
+                kind=kind,
+                change_type=change_type,
+                new_line=line_num if change_type == "added" else None,
+                old_line=line_num if change_type == "removed" else None,
+            ))
+            # Advance line counters heuristically
+            if op == '-':
+                if current_old_line is not None:
+                    current_old_line += 1
+            elif op == '+':
+                if current_new_line is not None:
+                    current_new_line += 1
+        elif line.startswith(' '):
+            if current_old_line is not None:
+                current_old_line += 1
+            if current_new_line is not None:
+                current_new_line += 1
+        # lines starting with other prefixes (like \\ No newline) ignored
+    return changes
+
+
+def extract_dependency_changes(diff_text: str, analyzer: DiffAnalyzer) -> List[DependencyChange]:
+    changes: List[DependencyChange] = []
+    import_pattern = re.compile(
+        r'^([+\-])\s*(?:import\s+([\w\.]+)|from\s+([\w\.]+)\s+import)',
+        re.MULTILINE
+    )
+    file_diffs = analyzer._split_files(diff_text)
+    for file_diff in file_diffs:
+        file_match = re.search(r'^diff --git a/.*? b/(.*?)$', file_diff, re.MULTILINE)
+        if not file_match:
+            continue
+        filepath = file_match.group(1)
+
+        # Scan each line for import changes
+        for line in file_diff.split('\n'):
+            m = import_pattern.match(line)
+            if m:
+                change_type = "added" if m.group(1) == '+' else "removed"
+                module = m.group(2) or m.group(3)
+                changes.append(DependencyChange(
+                    file=filepath,
+                    module=module,
+                    change_type=change_type,
+                    line=0
+                ))
+
+        # Detect if this file is a dependency manifest
+        req_file_pattern = re.compile(
+            r'^[\+\-].*?(requirements(.*?)\.txt|pyproject\.toml|setup\.py|Pipfile)'
+        )
+        if any(req_file_pattern.match(line) for line in file_diff.split('\n')):
+            if not any(c.file == filepath and c.module == "<file>" for c in changes):
+                changes.append(DependencyChange(
+                    file=filepath,
+                    module="<file>",
+                    change_type="modified",
+                    line=0
+                ))
+    return changes
+
+
+def correlate_function_changes_with_files(diff_text: str, functions: List[FunctionChange]) -> List[FunctionChange]:
+    result: List[FunctionChange] = []
+    # Split diff into per-file sections
+    file_sections: List[tuple[str, str]] = []
+    current_file: Optional[str] = None
+    current_lines: List[str] = []
+    for line in diff_text.split('\n'):
+        if line.startswith('diff --git'):
+            if current_file is not None:
+                file_sections.append((current_file, '\n'.join(current_lines)))
+            m = re.match(r'^diff --git a/.*? b/(.*?)$', line)
+            current_file = m.group(1) if m else "unknown"
+            current_lines = [line]
+        else:
+            current_lines.append(line)
+    if current_file is not None:
+        file_sections.append((current_file, '\n'.join(current_lines)))
+
+    pattern = re.compile(r'^([+\-])\s*(def|class)\s+(\w+)', re.MULTILINE)
+    for filepath, section in file_sections:
+        for m in pattern.finditer(section):
+            op = m.group(1)
+            kind = m.group(2)
+            name = m.group(3)
+            change_type = "added" if op == '+' else "removed"
+            result.append(FunctionChange(
+                file=filepath,
+                name=name,
+                kind=kind,
+                change_type=change_type
+            ))
+    return result
+
+
+def main():
+    parser = argparse.ArgumentParser(description="Codebase Genome Diff — structural changes between versions")
+    parser.add_argument("--ref1", required=True, help="First git ref (commit, branch, tag)")
+    parser.add_argument("--ref2", required=True, help="Second git ref")
+    parser.add_argument("--output", help="Write report to file")
+    parser.add_argument("--json", action="store_true", help="Output JSON instead of human report")
+    args = parser.parse_args()
+
+    try:
+        diff_text = run_git_diff(args.ref1, args.ref2)
+    except Exception as e:
+        print(f"Error: {e}", file=sys.stderr)
+        sys.exit(1)
+
+    if not diff_text.strip():
+        print(f"No differences between {args.ref1} and {args.ref2}.")
+        sys.exit(0)
+
+    analyzer = DiffAnalyzer()
+    summary = analyzer.analyze(diff_text)
+
+    file_changes = [fc.to_dict() for fc in summary.files]
+    func_changes = extract_function_changes(diff_text)
+    func_changes = correlate_function_changes_with_files(diff_text, func_changes)
+    dep_changes = extract_dependency_changes(diff_text, analyzer)
+
+    report = GenomeDiffReport(
+        ref1=args.ref1,
+        ref2=args.ref2,
+        file_changes=file_changes,
+        function_changes=func_changes,
+        dependency_changes=dep_changes,
+        total_files_changed=len(file_changes),
+        total_functions_changed=len(func_changes),
+        total_dependencies_changed=len(dep_changes),
+    )
+
+    output = json.dumps(report.to_dict(), indent=2) if args.json else report.human_report()
+
+    if args.output:
+        with open(args.output, 'w') as f:
+            f.write(output + '\n')
+        print(f"Report written to {args.output}")
+    else:
+        print(output)
+
+
+if __name__ == '__main__':
+    main()

scripts/test_dependency_freshness.py

@@ -1,179 +0,0 @@
-#!/usr/bin/env python3
-"""Tests for scripts/dependency_freshness.py — 9.7 Dependency Freshness."""
-
-import json
-import os
-import sys
-from unittest.mock import patch, MagicMock
-
-# Import target module
-sys.path.insert(0, os.path.dirname(__file__) or ".")
-import importlib.util
-spec = importlib.util.spec_from_file_location(
-    "dependency_freshness",
-    os.path.join(os.path.dirname(__file__) or ".", "dependency_freshness.py")
-)
-mod = importlib.util.module_from_spec(spec)
-spec.loader.exec_module(mod)
-
-parse_requirements = mod.parse_requirements
-get_major_version = mod.get_major_version
-is_more_than_two_majors_behind = mod.is_more_than_two_majors_behind
-analyze_dependencies = mod.analyze_dependencies
-
-
-def test_parse_requirements_simple():
-    """Parse a simple package line."""
-    import tempfile
-    with tempfile.NamedTemporaryFile(mode='w', suffix='.txt', delete=False) as f:
-        f.write("requests\n")
-        tmp = f.name
-    try:
-        pkgs = parse_requirements(tmp)
-        assert pkgs == ["requests"], f"got {pkgs}"
-        print("PASS: test_parse_requirements_simple")
-    finally:
-        os.unlink(tmp)
-
-
-def test_parse_requirements_with_specifiers():
-    """Parse lines with version specifiers."""
-    import tempfile
-    with tempfile.NamedTemporaryFile(mode='w', suffix='.txt', delete=False) as f:
-        f.write("pytest>=8,<9\n")
-        f.write("aiohttp>=3.8\n")
-        tmp = f.name
-    try:
-        pkgs = parse_requirements(tmp)
-        assert pkgs == ["pytest", "aiohttp"], f"got {pkgs}"
-        print("PASS: test_parse_requirements_with_specifiers")
-    finally:
-        os.unlink(tmp)
-
-
-def test_parse_requirements_ignores_comments_and_blanks():
-    """Comments and blank lines are skipped."""
-    import tempfile
-    with tempfile.NamedTemporaryFile(mode='w', suffix='.txt', delete=False) as f:
-        f.write("# This is a comment\n")
-        f.write("\n")
-        f.write("   \n")
-        f.write("numpy\n")
-        f.write("# another comment\n")
-        tmp = f.name
-    try:
-        pkgs = parse_requirements(tmp)
-        assert pkgs == ["numpy"], f"got {pkgs}"
-        print("PASS: test_parse_requirements_ignores_comments_and_blanks")
-    finally:
-        os.unlink(tmp)
-
-
-def test_get_major_version_normal():
-    """Extract major version from typical semantic strings."""
-    assert get_major_version("1.2.3") == 1
-    assert get_major_version("3.4.5") == 3
-    assert get_major_version("0.11.0") == 0
-    print("PASS: test_get_major_version_normal")
-
-
-def test_get_major_version_with_rc():
-    """Prerelease versions still yield major number."""
-    assert get_major_version("2.0.0rc1") == 2
-    assert get_major_version("1.0.0a1") == 1
-    print("PASS: test_get_major_version_with_rc")
-
-
-def test_is_more_than_two_majors_behind():
-    """Difference >2 triggers True; <=2 triggers False."""
-    assert is_more_than_two_majors_behind("1.2.3", "4.0.0") is True
-    assert is_more_than_two_majors_behind("3.9.0", "4.0.0") is False
-    assert is_more_than_two_majors_behind("2.1.0", "5.2.0") is True
-    assert is_more_than_two_majors_behind("8.0.0", "9.0.0") is False
-    assert is_more_than_two_majors_behind("4.0.0", "4.0.0") is False
-    print("PASS: test_is_more_than_two_majors_behind")
-
-
-def test_analyze_dependencies_very_outdated():
-    """Flag packages more than 2 major versions behind."""
-    required = ["pkg_a", "pkg_b"]
-    installed = {"pkg_a": "1.0.0", "pkg_b": "3.5.2"}
-    outdated = {
-        "pkg_a": {"installed": "1.0.0", "latest": "4.0.0"},
-        "pkg_b": {"installed": "3.5.2", "latest": "4.0.0"},
-    }
-    very_out, missing, outdated_ok = analyze_dependencies(required, installed, outdated)
-    assert len(very_out) == 1 and very_out[0]["package"] == "pkg_a"
-    assert len(missing) == 0
-    assert len(outdated_ok) == 1 and outdated_ok[0]["package"] == "pkg_b"
-    print("PASS: test_analyze_dependencies_very_outdated")
-
-
-def test_analyze_dependencies_missing():
-    """Detect packages not installed at all."""
-    required = ["pkg_a", "pkg_missing"]
-    installed = {"pkg_a": "2.0.0"}
-    outdated = {"pkg_a": {"installed": "2.0.0", "latest": "3.0.0"}}
-    very_out, missing, outdated_ok = analyze_dependencies(required, installed, outdated)
-    assert "pkg_missing" in missing
-    assert len(very_out) == 0
-    assert len(outdated_ok) == 1
-    print("PASS: test_analyze_dependencies_missing")
-
-
-def test_analyze_dependencies_up_to_date():
-    """Packages up-to-date are not flagged."""
-    required = ["pkg_good"]
-    installed = {"pkg_good": "5.0.0"}
-    outdated = {}
-    very_out, missing, outdated_ok = analyze_dependencies(required, installed, outdated)
-    assert len(very_out) == 0
-    assert len(missing) == 0
-    assert len(outdated_ok) == 0
-    print("PASS: test_analyze_dependencies_up_to_date")
-
-
-def test_generate_human_report_contains_very_outdated():
-    """Human report includes very outdated packages."""
-    very_out = [
-        {"package": "oldpkg", "installed": "1.0", "latest": "4.0", "major_diff": 3}
-    ]
-    missing = []
-    outdated_ok = []
-    report = mod.generate_human_report(very_out, missing, outdated_ok, "requirements.txt")
-    assert "oldpkg" in report
-    assert "Installed: 1.0" in report
-    assert "Latest:    4.0" in report
-    assert "Major diff: 3" in report
-    print("PASS: test_generate_human_report_contains_very_outdated")
-
-
-def test_generate_json_report_structure():
-    """JSON report contains required keys."""
-    very_out = [{"package": "oldpkg", "installed": "1.0", "latest": "4.0", "major_diff": 3}]
-    missing = ["missing_pkg"]
-    outdated_ok = []
-    report_json = mod.generate_json_report(very_out, missing, outdated_ok, "requirements.txt")
-    data = json.loads(report_json)
-    assert "summary" in data
-    assert data["summary"]["very_outdated_count"] == 1
-    assert data["summary"]["missing_count"] == 1
-    assert "very_outdated" in data
-    assert "missing" in data
-    print("PASS: test_generate_json_report_structure")
-
-
-if __name__ == '__main__':
-    print("Running dependency_freshness test suite...")
-    test_parse_requirements_simple()
-    test_parse_requirements_with_specifiers()
-    test_parse_requirements_ignores_comments_and_blanks()
-    test_get_major_version_normal()
-    test_get_major_version_with_rc()
-    test_is_more_than_two_majors_behind()
-    test_analyze_dependencies_very_outdated()
-    test_analyze_dependencies_missing()
-    test_analyze_dependencies_up_to_date()
-    test_generate_human_report_contains_very_outdated()
-    test_generate_json_report_structure()
-    print("ALL TESTS PASSED.")