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/docstring_generator.py

@@ -1,203 +0,0 @@
-#!/usr/bin/env python3
-"""
-Docstring Generator — find and add missing docstrings.
-
-Scans Python files for functions/async functions lacking docstrings.
-Generates Google-style docstrings from function signature and body.
-Inserts them in place.
-
-Usage:
-    python3 docstring_generator.py scripts/            # Fix in place
-    python3 docstring_generator.py --dry-run scripts/  # Preview changes
-    python3 docstring_generator.py --json scripts/     # Machine-readable output
-    python3 docstring_generator.py path/to/file.py
-"""
-
-import argparse
-import ast
-import json
-import os
-import sys
-from pathlib import Path
-from typing import Optional, Tuple, List
-
-
-# --- Helper: turn snake_case into Title Case phrase ---
-def name_to_title(name: str) -> str:
-    """Convert snake_case function name to a Title Case description."""
-    words = name.replace('_', ' ').split()
-    if not words:
-        return ''
-    titled = []
-    for w in words:
-        if len(w) <= 2:
-            titled.append(w.upper())
-        else:
-            titled.append(w[0].upper() + w[1:])
-    return ' '.join(titled)
-
-
-# --- Helper: extract first meaningful statement from body for summary ---
-def extract_body_hint(body: list[ast.stmt]) -> Optional[str]:
-    """Look for an assignment or return that hints at function purpose."""
-    for stmt in body:
-        if isinstance(stmt, ast.Expr) and isinstance(stmt.value, ast.Constant):
-            continue  # skip existing docstring placeholder
-        # Assignment to a result-like variable?
-        if isinstance(stmt, ast.Assign):
-            for target in stmt.targets:
-                if isinstance(target, ast.Name):
-                    var_name = target.id
-                    if var_name in ('result', 'msg', 'output', 'retval', 'value', 'response', 'data'):
-                        val = ast.unparse(stmt.value).strip()
-                        if val:
-                            return f"Compute or return {val}"
-        # Return statement
-        if isinstance(stmt, ast.Return) and stmt.value:
-            ret = ast.unparse(stmt.value).strip()
-            if ret:
-                return f"Return {ret}"
-        break
-    return None
-
-
-# --- Generate a docstring string for a function ---
-def generate_docstring(func_node: ast.FunctionDef | ast.AsyncFunctionDef) -> str:
-    """Build a Google-style docstring for the given function node."""
-    parts: list[str] = []
-
-    # Summary line
-    summary = name_to_title(func_node.name)
-    body_hint = extract_body_hint(func_node.body)
-    if body_hint:
-        summary = f"{summary}. {body_hint}"
-    parts.append(summary)
-
-    # Args section if there are parameters (excluding self/cls)
-    args = func_node.args.args
-    if args:
-        arg_lines = []
-        for arg in args:
-            if arg.arg in ('self', 'cls'):
-                continue
-            type_ann = ast.unparse(arg.annotation) if arg.annotation else 'Any'
-            arg_lines.append(f"{arg.arg} ({type_ann}): Parameter {arg.arg}")
-        if arg_lines:
-            parts.append("\nArgs:\n    " + "\n    ".join(arg_lines))
-
-    # Returns section
-    if func_node.returns:
-        ret_type = ast.unparse(func_node.returns)
-        parts.append(f"\nReturns:\n    {ret_type}: Return value")
-    elif any(isinstance(s, ast.Return) and s.value is not None for s in ast.walk(func_node)):
-        parts.append("\nReturns:\n    Return value")
-
-    return '"""' + '\n'.join(parts) + '\n"""'
-
-
-# --- Transform source AST ---
-def process_source(source: str, filename: str) -> Tuple[str, List[str]]:
-    """Add docstrings to all undocumented functions. Returns (new_source, [func_names])."""
-    try:
-        tree = ast.parse(source)
-    except SyntaxError as e:
-        print(f"  WARNING: Could not parse {filename}: {e}", file=sys.stderr)
-        return source, []
-
-    class DocstringInserter(ast.NodeTransformer):
-        def __init__(self):
-            self.modified_funcs: list[str] = []
-
-        def visit_FunctionDef(self, node: ast.FunctionDef) -> ast.FunctionDef:
-            return self._process(node)
-
-        def visit_AsyncFunctionDef(self, node: ast.AsyncFunctionDef) -> ast.AsyncFunctionDef:
-            return self._process(node)
-
-        def _process(self, node):
-            existing_doc = ast.get_docstring(node)
-            if existing_doc is not None:
-                return node
-            docstring_text = generate_docstring(node)
-            doc_node = ast.Expr(value=ast.Constant(value=docstring_text))
-            node.body.insert(0, doc_node)
-            ast.fix_missing_locations(node)
-            self.modified_funcs.append(node.name)
-            return node
-
-    inserter = DocstringInserter()
-    new_tree = inserter.visit(tree)
-    if inserter.modified_funcs:
-        return ast.unparse(new_tree), inserter.modified_funcs
-    return source, []
-
-
-# --- File discovery ---
-def iter_python_files(paths: list[str]) -> list[Path]:
-    """Collect all .py files from provided paths."""
-    files: set[Path] = set()
-    for p in paths:
-        path = Path(p)
-        if not path.exists():
-            print(f"WARNING: Path not found: {p}", file=sys.stderr)
-            continue
-        if path.is_file() and path.suffix == '.py':
-            files.add(path.resolve())
-        elif path.is_dir():
-            for child in path.rglob('*.py'):
-                if '.git' in child.parts or '__pycache__' in child.parts:
-                    continue
-                files.add(child.resolve())
-    return sorted(files)
-
-
-def main():
-    parser = argparse.ArgumentParser(description="Generate docstrings for functions missing them")
-    parser.add_argument('paths', nargs='+', help='Python files or directories to process')
-    parser.add_argument('--dry-run', action='store_true', help='Show what would change without writing')
-    parser.add_argument('--json', action='store_true', help='Output machine-readable JSON summary')
-    parser.add_argument('-v', '--verbose', action='store_true', help='Print each file processed')
-
-    args = parser.parse_args()
-
-    files = iter_python_files(args.paths)
-    if not files:
-        print("No Python files found to process", file=sys.stderr)
-        sys.exit(1)
-
-    results = []
-    total_funcs = 0
-
-    for pyfile in files:
-        try:
-            original = pyfile.read_text(encoding='utf-8')
-        except Exception as e:
-            print(f"  ERROR reading {pyfile}: {e}", file=sys.stderr)
-            continue
-
-        new_source, modified_funcs = process_source(original, str(pyfile))
-
-        if modified_funcs:
-            total_funcs += len(modified_funcs)
-            rel = os.path.relpath(pyfile)
-            if args.verbose:
-                print(f"  {rel}: +{len(modified_funcs)} docstrings")
-            results.append({'file': str(pyfile), 'functions': modified_funcs})
-            if not args.dry_run:
-                pyfile.write_text(new_source, encoding='utf-8')
-        elif args.verbose:
-            print(f"  {rel}: no changes")
-
-    if args.json:
-        summary = {'total_files_modified': len(results), 'total_functions': total_funcs, 'files': results}
-        print(json.dumps(summary, indent=2))
-    else:
-        print(f"Generated docstrings for {total_funcs} functions across {len(results)} files")
-        if args.dry_run:
-            print("  (dry run — no files written)")
-
-    return 0
-
-
-if __name__ == '__main__':
-    sys.exit(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_docstring_generator.py

@@ -1,128 +0,0 @@
-"""Tests for docstring_generator module (Issue #96)."""
-
-import ast
-import sys
-import tempfile
-from pathlib import Path
-
-import pytest
-
-sys.path.insert(0, str(Path(__file__).parent.parent / "scripts"))
-
-from docstring_generator import (
-    name_to_title,
-    extract_body_hint,
-    generate_docstring,
-    process_source,
-    iter_python_files,
-)
-
-
-class TestNameToTitle:
-    def test_snake_to_title(self):
-        assert name_to_title("validate_fact") == "Validate Fact"
-        assert name_to_title("docstring_generator") == "Docstring Generator"
-        assert name_to_title("main") == "Main"
-        assert name_to_title("__init__") == "Init"
-
-
-class TestExtractBodyHint:
-    def test_assignment_hint(self):
-        body = [ast.parse("result = compute()").body[0]]
-        hint = extract_body_hint(body)
-        assert hint == "Compute or return compute()"
-
-    def test_return_hint(self):
-        body = [ast.parse("return data").body[0]]
-        hint = extract_body_hint(body)
-        assert hint == "Return data"
-
-    def test_no_hint(self):
-        body = [ast.parse("pass").body[0]]
-        assert extract_body_hint(body) is None
-
-
-class TestGenerateDocstring:
-    def test_simple_function(self):
-        src = "def add(a, b):\n    return a + b\n"
-        tree = ast.parse(src)
-        func = tree.body[0]
-        doc = generate_docstring(func)
-        assert 'Add' in doc
-        assert 'a' in doc and 'b' in doc
-        assert 'Args:' in doc
-        assert 'Returns:' in doc
-
-    def test_typed_function(self):
-        src = "def greet(name: str) -> str:\n    return f'Hello {name}'\n"
-        tree = ast.parse(src)
-        func = tree.body[0]
-        doc = generate_docstring(func)
-        assert 'name (str)' in doc
-        assert 'str' in doc
-
-    def test_async_function(self):
-        src = "async def fetch():\n    pass\n"
-        tree = ast.parse(src)
-        func = tree.body[0]
-        doc = generate_docstring(func)
-        assert 'Fetch' in doc
-
-    def test_self_skipped(self):
-        src = "class C:\n    def method(self, x):\n        return x\n"
-        tree = ast.parse(src)
-        cls = tree.body[0]
-        method = cls.body[0]
-        doc = generate_docstring(method)
-        # 'self' should not appear in Args section
-        args_start = doc.find('Args:')
-        if args_start >= 0:
-            args_section = doc[args_start:]
-            assert '(self)' not in args_section
-
-
-class TestProcessSource:
-    def test_adds_docstrings(self):
-        src = "def foo(x):\n    return x * 2\n"
-        new_src, funcs = process_source(src, "test.py")
-        assert len(funcs) == 1 and funcs[0] == "foo"
-        assert '"""' in new_src
-        assert 'Foo' in new_src
-
-    def test_preserves_existing_docstrings(self):
-        src = 'def bar():\n    """Already documented."""\n    return 1\n'
-        new_src, funcs = process_source(src, "test.py")
-        assert len(funcs) == 0
-        assert new_src == src
-
-    def test_multiple_functions(self):
-        src = "def a(): pass\ndef b(): pass\ndef c(): pass\n"
-        new_src, funcs = process_source(src, "test.py")
-        assert len(funcs) == 3
-        assert '"""' in new_src
-
-    def test_dry_run_no_write(self, tmp_path):
-        file = tmp_path / "t.py"
-        file.write_text("def f(): pass\n")
-        original_mtime = file.stat().st_mtime
-        new_src, funcs = process_source(file.read_text(), str(file))
-        assert funcs  # detected
-        # When caller handles write, dry-run leaves file unchanged
-        current_mtime = file.stat().st_mtime
-        assert current_mtime == original_mtime
-
-
-class TestIterPythonFiles:
-    def test_single_file(self, tmp_path):
-        f = tmp_path / "single.py"
-        f.write_text("x = 1")
-        files = iter_python_files([str(f)])
-        assert len(files) == 1
-        assert files[0].name == "single.py"
-
-    def test_directory_recursion(self, tmp_path):
-        (tmp_path / "sub").mkdir()
-        (tmp_path / "sub" / "a.py").write_text("a=1")
-        (tmp_path / "b.py").write_text("b=2")
-        files = iter_python_files([str(tmp_path)])
-        assert len(files) == 2