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_inventory.py

@@ -1,308 +0,0 @@
-#!/usr/bin/env python3
-"""
-Dependency Inventory — Scan repos and list third-party dependencies.
-
-Reads: package.json, requirements.txt, go.mod, Cargo.toml, pyproject.toml
-Extracts: package name, version constraint, source file/repo
-Outputs: JSON (default) or markdown table
-
-Usage:
-  python3 scripts/dependency_inventory.py --repos-dir ~/repos/
-  python3 scripts/dependency_inventory.py --repos ~/repo1,~/repo2 --format markdown
-"""
-
-import argparse
-import json
-import os
-import re
-import sys
-from pathlib import Path
-from typing import Dict, List, Any, Optional
-
-# Mapping of file pattern to canonical parser name
-MANIFEST_PATTERNS = {
-    'requirements.txt': 'requirements',
-    'package.json': 'npm',
-    'pyproject.toml': 'pyproject',
-    'go.mod': 'go',
-    'Cargo.toml': 'cargo',
-}
-
-# Parser registry
-PARSERS = {}
-
-
-def register_parser(name: str):
-    """Decorator to register a parser function."""
-    def decorator(fn):
-        PARSERS[name] = fn
-        return fn
-    return decorator
-
-
-# ─── Parsers ────────────────────────────────────────────────────────────────
-
-@register_parser('requirements')
-def parse_requirements(content: str) -> List[Dict[str, str]]:
-    """Parse requirements.txt — one requirement per line."""
-    deps = []
-    for line in content.splitlines():
-        line = line.strip()
-        if not line or line.startswith('#'):
-            continue
-        pkg_spec = re.split(r'[ ;#]', line)[0].strip()
-        if '>=' in pkg_spec:
-            name, ver = pkg_spec.split('>=', 1)
-        elif '==' in pkg_spec:
-            name, ver = pkg_spec.split('==', 1)
-        elif '<=' in pkg_spec:
-            name, ver = pkg_spec.split('<=', 1)
-        elif '~=' in pkg_spec:
-            name, ver = pkg_spec.split('~=', 1)
-        elif '>' in pkg_spec:
-            name, ver = pkg_spec.split('>', 1)
-        elif '<' in pkg_spec:
-            name, ver = pkg_spec.split('<', 1)
-        elif '=' in pkg_spec:
-            name, ver = pkg_spec.split('=', 1)
-        else:
-            name, ver = pkg_spec, ''
-        deps.append({
-            'package': name.strip(),
-            'version': ver.strip(),
-            'constraint': line[len(name):].strip()
-        })
-    return deps
-
-
-@register_parser('npm')
-def parse_package_json(content: str) -> List[Dict[str, str]]:
-    """Parse package.json dependencies."""
-    try:
-        data = json.loads(content)
-    except json.JSONDecodeError:
-        return []
-    deps = []
-    for section in ('dependencies', 'devDependencies', 'peerDependencies', 'optionalDependencies'):
-        for name, ver in data.get(section, {}).items():
-            deps.append({
-                'package': name,
-                'version': ver,
-                'constraint': ver,
-                'type': section
-            })
-    return deps
-
-
-@register_parser('pyproject')
-def parse_pyproject_toml(content: str) -> List[Dict[str, str]]:
-    """Parse pyproject.toml [project] dependencies."""
-    deps = []
-    in_deps = False
-    dep_buffer = ''
-    for line in content.splitlines():
-        stripped = line.strip()
-        if stripped.startswith('dependencies = ['):
-            in_deps = True
-            remainder = stripped.split('=', 1)[1].strip()
-            dep_buffer = remainder[1:] if remainder.startswith('[') else remainder
-            continue
-        if in_deps:
-            if stripped.startswith(']'):
-                in_deps = False
-                continue
-            dep_buffer += ' ' + line
-    dep_buffer = dep_buffer.strip().rstrip(',')
-    for match in re.finditer(r'"([^"]+)"', dep_buffer):
-        spec = match.group(1)
-        m = re.match(r'^([a-zA-Z0-9_.-]+)\s*([<>=!~]+)?\s*(.*)$', spec)
-        if m:
-            name, op, ver = m.groups()
-            deps.append({
-                'package': name,
-                'version': (ver or '').strip(),
-                'constraint': spec
-            })
-    return deps
-
-
-@register_parser('go')
-def parse_go_mod(content: str) -> List[Dict[str, str]]:
-    """Parse go.mod — require statements."""
-    deps = []
-    for line in content.splitlines():
-        line = line.strip()
-        if line.startswith('require ') and not line.startswith('require ('):
-            parts = line.split()
-            if len(parts) >= 3:
-                mod, ver = parts[1], parts[2]
-                deps.append({'package': mod, 'version': ver, 'constraint': ver})
-        elif line.startswith('\t') and '/' in line:
-            parts = line.strip().split()
-            if len(parts) >= 2:
-                mod, ver = parts[0], parts[1]
-                deps.append({'package': mod, 'version': ver, 'constraint': ver})
-    return deps
-
-
-@register_parser('cargo')
-def parse_cargo_toml(content: str) -> List[Dict[str, str]]:
-    """Parse [dependencies] section from Cargo.toml."""
-    deps = []
-    in_deps = False
-    for line in content.splitlines():
-        stripped = line.strip()
-        if stripped in ('[dependencies]', '[dependencies]'):
-            in_deps = True
-            continue
-        if stripped.startswith('['):
-            in_deps = False
-            continue
-        if in_deps and '=' in stripped:
-            name_part, ver_part = stripped.split('=', 1)
-            name = name_part.strip()
-            ver = ver_part.strip().strip('"').strip("'")
-            deps.append({'package': name, 'version': ver, 'constraint': ver})
-    return deps
-
-
-# ─── File Discovery ─────────────────────────────────────────────────────────
-
-def find_manifest_files(root: Path) -> Dict[str, List[Path]]:
-    """Find all manifest files under root."""
-    found = {k: [] for k in MANIFEST_PATTERNS}
-    for pattern in MANIFEST_PATTERNS:
-        for path in root.rglob(pattern):
-            if not any(skip in str(path) for skip in ('.git', 'node_modules', '__pycache__', '.venv', 'venv')):
-                found[pattern].append(path)
-    return found
-
-
-# ─── Main Scanner ────────────────────────────────────────────────────────────
-
-def scan_repo(repo_path: Path) -> Dict[str, Any]:
-    """Scan a single repo directory for dependency manifests."""
-    repo_name = repo_path.name
-    found = find_manifest_files(repo_path)
-    all_deps: List[Dict[str, str]] = []
-    files_scanned = 0
-
-    for pattern, paths in found.items():
-        parser_name = MANIFEST_PATTERNS[pattern]
-        # Map parser_name to function
-        if parser_name == 'requirements':
-            parser = parse_requirements
-        elif parser_name == 'npm':
-            parser = parse_package_json
-        elif parser_name == 'pyproject':
-            parser = parse_pyproject_toml
-        elif parser_name == 'go':
-            parser = parse_go_mod
-        elif parser_name == 'cargo':
-            parser = parse_cargo_toml
-        else:
-            continue
-
-        for fp in paths:
-            try:
-                content = fp.read_text(encoding='utf-8', errors='replace')
-                files_scanned += 1
-                rel = fp.relative_to(repo_path)
-                for dep in parser(content):
-                    dep['source'] = pattern
-                    dep['file'] = str(rel)
-                    dep['repo'] = repo_name
-                    all_deps.append(dep)
-            except Exception as e:
-                print(f"  [WARN] Could not parse {fp}: {e}", file=sys.stderr)
-
-    return {
-        'repo': repo_name,
-        'path': str(repo_path),
-        'files_scanned': files_scanned,
-        'dependencies': all_deps,
-        'dependency_count': len(all_deps),
-    }
-
-
-def scan_repos(repos: List[Path]) -> Dict[str, Any]:
-    """Scan multiple repos and aggregate."""
-    results = {}
-    total_deps = 0
-    total_files = 0
-    for repo in repos:
-        if not repo.is_dir():
-            print(f"[WARN] Skipping {repo}: not a directory", file=sys.stderr)
-            continue
-        print(f"Scanning {repo.name}...", file=sys.stderr)
-        result = scan_repo(repo)
-        results[repo.name] = result
-        total_deps += result['dependency_count']
-        total_files += result['files_scanned']
-    return {
-        'repos': results,
-        'summary': {
-            'total_repos': len(results),
-            'total_files_scanned': total_files,
-            'total_dependencies': total_deps,
-        }
-    }
-
-
-# ─── Output ─────────────────────────────────────────────────────────────────
-
-def output_json(data: Dict[str, Any], out_path: Optional[Path] = None) -> None:
-    text = json.dumps(data, indent=2)
-    if out_path:
-        out_path.write_text(text)
-        print(f"Written: {out_path}", file=sys.stderr)
-    else:
-        print(text)
-
-
-def output_markdown(data: Dict[str, Any], out_path: Optional[Path] = None) -> None:
-    lines = []
-    lines.append("# Dependency Inventory")
-    lines.append("\nGenerated: *(TODO: add timestamp)*")
-    lines.append(f"\n**Summary:** {data['summary']['total_dependencies']} dependencies across {data['summary']['total_repos']} repos")
-    lines.append("")
-    lines.append("| Repo | File | Package | Version |")
-    lines.append("|------|------|---------|---------|")
-    for repo_name, rdata in sorted(data['repos'].items()):
-        for dep in sorted(rdata['dependencies'], key=lambda d: d['package']):
-            lines.append(f"| {repo_name} | {dep['file']} | {dep['package']} | {dep['version']} |")
-    text = '\n'.join(lines) + '\n'
-    if out_path:
-        out_path.write_text(text)
-        print(f"Written: {out_path}", file=sys.stderr)
-    else:
-        print(text)
-
-
-# ─── CLI Entry ────────────────────────────────────────────────────────────────
-
-def main():
-    parser = argparse.ArgumentParser(description="Generate org-wide dependency inventory")
-    parser.add_argument('--repos-dir', help='Directory containing multiple repos')
-    parser.add_argument('--repos', help='Comma-separated list of repo paths')
-    parser.add_argument('--output', '-o', help='Output file (default: stdout)')
-    parser.add_argument('--format', choices=['json', 'markdown'], default='json',
-                       help='Output format (default: json)')
-    args = parser.parse_args()
-    if args.repos:
-        repo_paths = [Path(p.strip()).expanduser() for p in args.repos.split(',')]
-    elif args.repos_dir:
-        base = Path(args.repos_dir).expanduser()
-        repo_paths = [p for p in base.iterdir() if p.is_dir() and not p.name.startswith('.')]
-    else:
-        repo_paths = [Path(__file__).resolve().parent.parent]
-    out_path = Path(args.output).expanduser() if args.output else None
-    data = scan_repos(repo_paths)
-    if args.format == 'json':
-        output_json(data, out_path)
-    else:
-        output_markdown(data, out_path)
-
-
-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()

tests/test_dependency_inventory.py

@@ -1,52 +0,0 @@
-"""
-Tests for scripts/dependency_inventory.py
-"""
-
-import unittest
-import json
-from pathlib import Path
-import sys
-
-sys.path.insert(0, str(Path(__file__).parent.parent))
-
-from scripts.dependency_inventory import (
-    parse_requirements,
-    parse_package_json,
-    parse_pyproject_toml,
-    scan_repo,
-)
-
-
-class TestParseRequirements(unittest.TestCase):
-    def test_parses_simple_requirement(self):
-        result = parse_requirements("requests>=2.33.0")
-        self.assertEqual(len(result), 1)
-        self.assertEqual(result[0]["package"], "requests")
-
-    def test_parses_version_range(self):
-        result = parse_requirements("pytest>=8,<9")
-        self.assertEqual(result[0]["package"], "pytest")
-
-
-class TestParsePackageJson(unittest.TestCase):
-    def test_parses_dependencies(self):
-        content = json.dumps({"name": "test", "dependencies": {"react": "^18.2.0"}})
-        result = parse_package_json(content)
-        self.assertTrue(any(d["package"] == "react" for d in result))
-
-
-class TestParsePyprojectToml(unittest.TestCase):
-    def test_parses_project_dependencies(self):
-        content = "\n[project]\nname = \"test\"\ndependencies = [\n  \"openai>=2.21.0,<3\",\n]"
-        result = parse_pyproject_toml(content)
-        self.assertEqual(len(result), 1)
-
-
-class TestScanRepo(unittest.TestCase):
-    def test_scans_local_repo(self):
-        result = scan_repo(Path(__file__).resolve().parents[1])
-        self.assertGreater(result["dependency_count"], 0)
-
-
-if __name__ == "__main__":
-    unittest.main()