feat: knowledge store staleness detector (#92)

scripts/knowledge_gap_identifier.py

@@ -1,275 +0,0 @@
-"""
-Knowledge Gap Identifier — Pipeline 10.7
-
-Cross-references code, docs, and tests to find gaps:
-- Undocumented functions/classes
-- Untested code paths
-- Documented but missing implementations
-- Test files without corresponding source
-
-Produces a gap report with severity and suggestions.
-"""
-
-from __future__ import annotations
-
-import ast
-import os
-import re
-from dataclasses import dataclass, field
-from enum import Enum
-from pathlib import Path
-from typing import Dict, List, Optional, Set
-
-
-class GapSeverity(Enum):
-    INFO = "info"
-    WARNING = "warning"
-    ERROR = "error"
-
-
-class GapType(Enum):
-    UNDOCUMENTED = "undocumented"
-    UNTESTED = "untested"
-    MISSING_IMPLEMENTATION = "missing_implementation"
-    ORPHAN_TEST = "orphan_test"
-    STALE_DOC = "stale_doc"
-
-
-@dataclass
-class Gap:
-    """A single knowledge gap."""
-    gap_type: GapType
-    severity: GapSeverity
-    file: str
-    line: Optional[int]
-    name: str
-    description: str
-    suggestion: str
-
-
-@dataclass
-class GapReport:
-    """Full gap analysis report."""
-    repo_path: str
-    gaps: List[Gap] = field(default_factory=list)
-    stats: Dict[str, int] = field(default_factory=dict)
-
-    def summary(self) -> str:
-        lines = [f"Gap Report for {self.repo_path}", "=" * 40]
-        by_type = {}
-        for g in self.gaps:
-            by_type.setdefault(g.gap_type.value, []).append(g)
-
-        for gtype, items in sorted(by_type.items()):
-            lines.append(f"\n{gtype.upper()} ({len(items)}):")
-            for g in items:
-                loc = f"{g.file}:{g.line}" if g.line else g.file
-                lines.append(f"  [{g.severity.value}] {g.name} @ {loc}")
-                lines.append(f"    {g.description}")
-
-        lines.append(f"\nTotal gaps: {len(self.gaps)}")
-        self.stats = {k: len(v) for k, v in by_type.items()}
-        return "\n".join(lines)
-
-    def to_dict(self) -> dict:
-        return {
-            "repo_path": self.repo_path,
-            "total_gaps": len(self.gaps),
-            "stats": {k: len(v) for k, v in
-                      {gt: [g for g in self.gaps if g.gap_type == gt]
-                       for gt in GapType}.items() if v},
-            "gaps": [
-                {
-                    "type": g.gap_type.value,
-                    "severity": g.severity.value,
-                    "file": g.file,
-                    "line": g.line,
-                    "name": g.name,
-                    "description": g.description,
-                    "suggestion": g.suggestion,
-                }
-                for g in self.gaps
-            ],
-        }
-
-
-def _collect_python_files(root: Path) -> List[Path]:
-    """Collect .py files, excluding venv/node_modules/.git."""
-    skip = {".git", "venv", "env", ".venv", "node_modules", "__pycache__", ".tox", ".mypy_cache"}
-    files = []
-    for dirpath, dirnames, filenames in os.walk(root):
-        dirnames[:] = [d for d in dirnames if d not in skip]
-        for f in filenames:
-            if f.endswith(".py"):
-                files.append(Path(dirpath) / f)
-    return files
-
-
-def _extract_python_symbols(filepath: Path) -> Set[str]:
-    """Extract top-level function and class names from a Python file."""
-    symbols = set()
-    try:
-        source = filepath.read_text(encoding="utf-8", errors="replace")
-        tree = ast.parse(source, filename=str(filepath))
-    except (SyntaxError, UnicodeDecodeError):
-        return symbols
-
-    for node in ast.iter_child_nodes(tree):
-        if isinstance(node, (ast.FunctionDef, ast.AsyncFunctionDef, ast.ClassDef)):
-            symbols.add(node.name)
-    return symbols
-
-
-def _extract_doc_symbols(filepath: Path) -> Set[str]:
-    """Extract function/class names mentioned in markdown docs."""
-    symbols = set()
-    try:
-        text = filepath.read_text(encoding="utf-8", errors="replace")
-    except (UnicodeDecodeError, OSError):
-        return symbols
-
-    # Match backtick-quoted identifiers: `ClassName`, `func_name`, `func()`
-    for m in re.finditer(r"`([A-Za-z_]\w+)(?:\(\))?`", text):
-        symbols.add(m.group(1))
-    # Match ## ClassName or ### func_name headings
-    for m in re.finditer(r"^#{1,4}\s+(\w+)", text, re.MULTILINE):
-        symbols.add(m.group(1))
-    return symbols
-
-
-def _collect_test_files(root: Path) -> Dict[str, Path]:
-    """Map test module names to their file paths."""
-    test_map = {}
-    for dirpath, dirnames, filenames in os.walk(root):
-        dirnames[:] = [d for d in dirnames if d not in {".git", "venv", "node_modules"}]
-        for f in filenames:
-            if f.startswith("test_") and f.endswith(".py"):
-                # test_foo.py -> foo
-                module_name = f[5:-3]
-                test_map[module_name] = Path(dirpath) / f
-    return test_map
-
-
-class KnowledgeGapIdentifier:
-    """Analyzes a repo for knowledge gaps between code, docs, and tests."""
-
-    def analyze(self, repo_path: str) -> GapReport:
-        root = Path(repo_path).resolve()
-        report = GapReport(repo_path=str(root))
-
-        if not root.is_dir():
-            report.gaps.append(Gap(
-                gap_type=GapType.UNDOCUMENTED,
-                severity=GapSeverity.ERROR,
-                file=str(root),
-                line=None,
-                name="repo",
-                description="Path is not a directory",
-                suggestion="Provide a valid repo directory",
-            ))
-            return report
-
-        # Collect artifacts
-        py_files = _collect_python_files(root)
-        doc_files = list(root.glob("docs/**/*.md")) + list(root.glob("*.md"))
-        test_map = _collect_test_files(root / "tests") if (root / "tests").is_dir() else {}
-
-        # Extract symbols from each source file
-        source_symbols: Dict[str, Set[str]] = {}  # relative_path -> symbols
-        all_source_symbols: Set[str] = set()
-
-        for pf in py_files:
-            rel = str(pf.relative_to(root))
-            # Skip test files and setup/config
-            if "/tests/" in rel or rel.startswith("tests/") or rel.startswith("test_"):
-                continue
-            if pf.name in ("setup.py", "conftest.py", "conf.py"):
-                continue
-
-            syms = _extract_python_symbols(pf)
-            if syms:
-                source_symbols[rel] = syms
-                all_source_symbols.update(syms)
-
-        # Extract documented symbols
-        doc_symbols: Set[str] = set()
-        for df in doc_files:
-            doc_symbols.update(_extract_doc_symbols(df))
-
-        # Extract test-covered symbols
-        tested_modules: Set[str] = set(test_map.keys())
-
-        # --- Find gaps ---
-
-        # 1. Undocumented: source symbols not in any doc
-        for rel_path, syms in source_symbols.items():
-            for sym in sorted(syms):
-                if sym.startswith("_") and not sym.startswith("__"):
-                    continue  # Skip private
-                if sym not in doc_symbols:
-                    report.gaps.append(Gap(
-                        gap_type=GapType.UNDOCUMENTED,
-                        severity=GapSeverity.WARNING,
-                        file=rel_path,
-                        line=None,
-                        name=sym,
-                        description=f"{sym} defined in {rel_path} but not referenced in any docs",
-                        suggestion=f"Add documentation for {sym} in a .md file",
-                    ))
-
-        # 2. Untested: source modules without a corresponding test file
-        for rel_path in source_symbols:
-            module_name = Path(rel_path).stem
-            if module_name not in tested_modules and module_name not in ("__init__", "main", "config"):
-                report.gaps.append(Gap(
-                    gap_type=GapType.UNTESTED,
-                    severity=GapSeverity.ERROR,
-                    file=rel_path,
-                    line=None,
-                    name=module_name,
-                    description=f"No test file found for {rel_path}",
-                    suggestion=f"Create tests/test_{module_name}.py",
-                ))
-
-        # 3. Missing implementation: doc references symbol not in any source
-        referenced_but_missing = doc_symbols - all_source_symbols
-        for sym in sorted(referenced_but_missing):
-            # Filter out common non-code terms
-            if sym.lower() in {"todo", "fixme", "note", "example", "usage", "api",
-                               "install", "setup", "config", "license", "contributing",
-                               "changelog", "readme", "python", "bash", "json", "yaml",
-                               "http", "url", "cli", "gui", "ui", "api", "rest"}:
-                continue
-            if len(sym) < 3:
-                continue
-            report.gaps.append(Gap(
-                gap_type=GapType.MISSING_IMPLEMENTATION,
-                severity=GapSeverity.INFO,
-                file="(docs)",
-                line=None,
-                name=sym,
-                description=f"{sym} referenced in docs but not found in source code",
-                suggestion=f"Verify if {sym} should be implemented or update docs",
-            ))
-
-        # 4. Orphan tests: test files without matching source
-        for test_mod, test_path in test_map.items():
-            if test_mod not in tested_modules and not any(
-                test_mod in Path(f).stem for f in source_symbols
-            ):
-                # Check if any source file partially matches
-                matches_source = any(test_mod.replace("_", "-") in f or test_mod.replace("_", "") in Path(f).stem
-                                     for f in source_symbols)
-                if not matches_source:
-                    rel = str(test_path.relative_to(root))
-                    report.gaps.append(Gap(
-                        gap_type=GapType.ORPHAN_TEST,
-                        severity=GapSeverity.WARNING,
-                        file=rel,
-                        line=None,
-                        name=test_mod,
-                        description=f"Test file {rel} exists but no matching source module found",
-                        suggestion=f"Verify if the source was renamed or removed",
-                    ))
-
-        return report

scripts/knowledge_staleness_check.py

@@ -0,0 +1,221 @@
+#!/usr/bin/env python3
+"""
+Knowledge Store Staleness Detector
+
+Checks knowledge entries against their source files to detect staleness.
+An entry is stale when its source file has been modified since extraction.
+
+Usage:
+  python3 scripts/knowledge_staleness_check.py knowledge/index.json
+  python3 scripts/knowledge_staleness_check.py --repo /path/to/repo --index knowledge/index.json
+  python3 scripts/knowledge_staleness_check.py --index knowledge/index.json --fix
+
+Expected index.json format:
+{
+  "version": 1,
+  "facts": [
+    {
+      "fact": "...",
+      "category": "fact|pitfall|pattern|tool-quirk",
+      "repo": "repo-name",
+      "confidence": 0.8,
+      "source_file": "path/to/file.py",
+      "source_hash": "sha256:abcdef...",
+      "extracted_at": "2026-04-13T20:00:00Z"
+    }
+  ]
+}
+"""
+
+import argparse
+import hashlib
+import json
+import sys
+from pathlib import Path
+from typing import Optional
+
+
+def compute_file_hash(filepath: str) -> Optional[str]:
+    """Compute SHA-256 hash of a file. Returns None if file not found."""
+    path = Path(filepath)
+    if not path.exists():
+        return None
+    content = path.read_bytes()
+    return hashlib.sha256(content).hexdigest()[:16]
+
+
+def check_staleness(index_path: str, repo_root: str = None) -> dict:
+    """Check all entries in the knowledge index for staleness."""
+    index = Path(index_path)
+    if not index.exists():
+        return {"error": f"Index not found: {index_path}"}
+
+    data = json.loads(index.read_text())
+    facts = data.get("facts", [])
+
+    if not facts:
+        return {
+            "total": 0,
+            "stale": 0,
+            "fresh": 0,
+            "no_source": 0,
+            "missing_files": 0,
+            "stale_entries": [],
+        }
+
+    # Determine repo root
+    if repo_root:
+        root = Path(repo_root)
+    else:
+        root = index.parent.parent  # knowledge/index.json -> repo root
+
+    results = {
+        "total": len(facts),
+        "stale": 0,
+        "fresh": 0,
+        "no_source": 0,
+        "missing_files": 0,
+        "stale_entries": [],
+    }
+
+    for i, entry in enumerate(facts):
+        source_file = entry.get("source_file")
+        stored_hash = entry.get("source_hash")
+
+        if not source_file:
+            results["no_source"] += 1
+            continue
+
+        if not stored_hash:
+            # Entry has source file but no hash — consider stale
+            results["stale"] += 1
+            results["stale_entries"].append({
+                "index": i,
+                "fact": entry.get("fact", "")[:100],
+                "source_file": source_file,
+                "reason": "no_hash",
+            })
+            continue
+
+        # Compute current hash
+        full_path = root / source_file
+        current_hash = compute_file_hash(str(full_path))
+
+        if current_hash is None:
+            results["missing_files"] += 1
+            results["stale_entries"].append({
+                "index": i,
+                "fact": entry.get("fact", "")[:100],
+                "source_file": source_file,
+                "reason": "file_missing",
+            })
+        elif current_hash != stored_hash:
+            results["stale"] += 1
+            results["stale_entries"].append({
+                "index": i,
+                "fact": entry.get("fact", "")[:100],
+                "source_file": source_file,
+                "stored_hash": stored_hash,
+                "current_hash": current_hash,
+                "reason": "hash_mismatch",
+            })
+        else:
+            results["fresh"] += 1
+
+    return results
+
+
+def add_hashes_to_index(index_path: str, repo_root: str = None) -> dict:
+    """Add source hashes to entries that are missing them."""
+    index = Path(index_path)
+    data = json.loads(index.read_text())
+    facts = data.get("facts", [])
+
+    if repo_root:
+        root = Path(repo_root)
+    else:
+        root = index.parent.parent
+
+    updated = 0
+    skipped = 0
+
+    for entry in facts:
+        source_file = entry.get("source_file")
+        if not source_file or entry.get("source_hash"):
+            skipped += 1
+            continue
+
+        full_path = root / source_file
+        file_hash = compute_file_hash(str(full_path))
+        if file_hash:
+            entry["source_hash"] = file_hash
+            updated += 1
+
+    if updated > 0:
+        index.write_text(json.dumps(data, indent=2) + "\n")
+
+    return {"updated": updated, "skipped": skipped, "total": len(facts)}
+
+
+def report_staleness(results: dict) -> str:
+    """Format staleness check results as a report."""
+    lines = []
+    lines.append("=" * 50)
+    lines.append("KNOWLEDGE STORE STALENESS REPORT")
+    lines.append("=" * 50)
+    lines.append(f"Total entries:  {results['total']}")
+    lines.append(f"Fresh:          {results['fresh']}")
+    lines.append(f"Stale:          {results['stale']}")
+    lines.append(f"No source:      {results['no_source']}")
+    lines.append(f"Missing files:  {results['missing_files']}")
+    lines.append("")
+
+    if results["stale_entries"]:
+        lines.append("STALE ENTRIES:")
+        lines.append("-" * 50)
+        for entry in results["stale_entries"]:
+            lines.append(f"  [{entry['reason']}] {entry['source_file']}")
+            lines.append(f"    {entry['fact']}")
+            if entry.get("stored_hash") and entry.get("current_hash"):
+                lines.append(f"    stored:  {entry['stored_hash']}")
+                lines.append(f"    current: {entry['current_hash']}")
+            lines.append("")
+
+    if results["total"] > 0:
+        staleness_pct = results["stale"] / results["total"] * 100
+        lines.append(f"Staleness rate: {staleness_pct:.1f}%")
+    else:
+        lines.append("No entries to check.")
+
+    return "\n".join(lines)
+
+
+def main():
+    parser = argparse.ArgumentParser(description="Check knowledge store for stale entries")
+    parser.add_argument("--index", default="knowledge/index.json", help="Path to index.json")
+    parser.add_argument("--repo", help="Repository root (default: auto-detect from index path)")
+    parser.add_argument("--fix", action="store_true", help="Add missing hashes to index")
+    parser.add_argument("--json", action="store_true", help="Output JSON instead of report")
+    args = parser.parse_args()
+
+    if args.fix:
+        result = add_hashes_to_index(args.index, args.repo)
+        if args.json:
+            print(json.dumps(result, indent=2))
+        else:
+            print(f"Updated {result['updated']} entries with source hashes.")
+            print(f"Skipped {result['skipped']} (already had hashes or no source file).")
+    else:
+        results = check_staleness(args.index, args.repo)
+        if "error" in results:
+            print(f"Error: {results['error']}", file=sys.stderr)
+            sys.exit(1)
+
+        if args.json:
+            print(json.dumps(results, indent=2))
+        else:
+            print(report_staleness(results))
+
+
+if __name__ == "__main__":
+    main()

tests/test_knowledge_gap_identifier.py

@@ -1,141 +0,0 @@
-"""Tests for knowledge_gap_identifier module."""
-
-import sys
-import os
-import tempfile
-import shutil
-from pathlib import Path
-
-sys.path.insert(0, os.path.join(os.path.dirname(__file__), '..', 'scripts'))
-
-from knowledge_gap_identifier import KnowledgeGapIdentifier, GapType, GapSeverity
-
-
-def _make_repo(tmpdir, structure):
-    """Create a test repo from a dict of {path: content}."""
-    for rel_path, content in structure.items():
-        p = Path(tmpdir) / rel_path
-        p.parent.mkdir(parents=True, exist_ok=True)
-        p.write_text(content)
-
-
-def test_undocumented_symbol():
-    with tempfile.TemporaryDirectory() as tmpdir:
-        _make_repo(tmpdir, {
-            "src/calculator.py": "def add(a, b):\n    return a + b\n",
-            "README.md": "# Calculator\n",
-        })
-        report = KnowledgeGapIdentifier().analyze(tmpdir)
-        undocumented = [g for g in report.gaps if g.gap_type == GapType.UNDOCUMENTED]
-        assert any(g.name == "add" for g in undocumented), "add should be undocumented"
-
-
-def test_documented_symbol_no_gap():
-    with tempfile.TemporaryDirectory() as tmpdir:
-        _make_repo(tmpdir, {
-            "src/calculator.py": "def add(a, b):\n    return a + b\n",
-            "README.md": "# Calculator\nUse `add()` to add numbers.\n",
-        })
-        report = KnowledgeGapIdentifier().analyze(tmpdir)
-        undocumented = [g for g in report.gaps
-                       if g.gap_type == GapType.UNDOCUMENTED and g.name == "add"]
-        assert len(undocumented) == 0, "add is documented, should not be flagged"
-
-
-def test_untested_module():
-    with tempfile.TemporaryDirectory() as tmpdir:
-        _make_repo(tmpdir, {
-            "src/calculator.py": "def add(a, b):\n    return a + b\n",
-            "src/helper.py": "def format(x):\n    return str(x)\n",
-            "tests/test_calculator.py": "from src.calculator import add\nassert add(1,2) == 3\n",
-        })
-        report = KnowledgeGapIdentifier().analyze(tmpdir)
-        untested = [g for g in report.gaps if g.gap_type == GapType.UNTESTED]
-        assert any("helper" in g.name for g in untested), "helper should be untested"
-
-
-def test_tested_module_no_gap():
-    with tempfile.TemporaryDirectory() as tmpdir:
-        _make_repo(tmpdir, {
-            "src/calculator.py": "def add(a, b):\n    return a + b\n",
-            "tests/test_calculator.py": "def test_add():\n    assert True\n",
-        })
-        report = KnowledgeGapIdentifier().analyze(tmpdir)
-        untested = [g for g in report.gaps
-                    if g.gap_type == GapType.UNTESTED and "calculator" in g.name]
-        assert len(untested) == 0, "calculator has tests, should not be flagged"
-
-
-def test_missing_implementation():
-    with tempfile.TemporaryDirectory() as tmpdir:
-        _make_repo(tmpdir, {
-            "src/app.py": "def run():\n    pass\n",
-            "docs/api.md": "# API\nUse `NonExistentClass` to do things.\n",
-        })
-        report = KnowledgeGapIdentifier().analyze(tmpdir)
-        missing = [g for g in report.gaps if g.gap_type == GapType.MISSING_IMPLEMENTATION]
-        assert any(g.name == "NonExistentClass" for g in missing)
-
-
-def test_private_symbols_skipped():
-    with tempfile.TemporaryDirectory() as tmpdir:
-        _make_repo(tmpdir, {
-            "src/app.py": "def _internal():\n    pass\ndef public():\n    pass\n",
-            "README.md": "# App\n",
-        })
-        report = KnowledgeGapIdentifier().analyze(tmpdir)
-        undocumented_names = [g.name for g in report.gaps if g.gap_type == GapType.UNDOCUMENTED]
-        assert "_internal" not in undocumented_names, "Private symbols should be skipped"
-        assert "public" in undocumented_names
-
-
-def test_empty_repo():
-    with tempfile.TemporaryDirectory() as tmpdir:
-        report = KnowledgeGapIdentifier().analyze(tmpdir)
-        assert len(report.gaps) == 0
-
-
-def test_invalid_path():
-    report = KnowledgeGapIdentifier().analyze("/nonexistent/path/xyz")
-    assert len(report.gaps) == 1
-    assert report.gaps[0].severity == GapSeverity.ERROR
-
-
-def test_report_summary():
-    with tempfile.TemporaryDirectory() as tmpdir:
-        _make_repo(tmpdir, {
-            "src/app.py": "class MyService:\n    def handle(self):\n        pass\n",
-            "README.md": "# App\n",
-        })
-        report = KnowledgeGapIdentifier().analyze(tmpdir)
-        summary = report.summary()
-        assert "UNDOCUMENTED" in summary
-        assert "MyService" in summary
-
-
-def test_report_to_dict():
-    with tempfile.TemporaryDirectory() as tmpdir:
-        _make_repo(tmpdir, {
-            "src/app.py": "def hello():\n    pass\n",
-            "README.md": "# App\n",
-        })
-        report = KnowledgeGapIdentifier().analyze(tmpdir)
-        d = report.to_dict()
-        assert "total_gaps" in d
-        assert "gaps" in d
-        assert isinstance(d["gaps"], list)
-        assert d["total_gaps"] > 0
-
-
-if __name__ == "__main__":
-    test_undocumented_symbol()
-    test_documented_symbol_no_gap()
-    test_untested_module()
-    test_tested_module_no_gap()
-    test_missing_implementation()
-    test_private_symbols_skipped()
-    test_empty_repo()
-    test_invalid_path()
-    test_report_summary()
-    test_report_to_dict()
-    print("All 10 tests passed.")