feat(graph): Add graph visualizer (ASCII + DOT) with subgraph extraction

Add scripts/graph_visualizer.py — standalone tool that:
- Builds knowledge graph from knowledge/index.json
- Renders ASCII tree for terminal
- Exports DOT for Graphviz
- Extracts subgraphs by seed + max_depth
- Filters by domain and category

Includes test_graph_visualizer.py smoke test (8/8)
Addresses #151

scripts/graph_visualizer.py

@@ -0,0 +1,206 @@
+#!/usr/bin/env python3
+"""
+graph_visualizer.py — Generate visual graph representations of the knowledge graph.
+
+Reads knowledge/index.json and renders the fact relationship graph.
+Supports ASCII terminal output and DOT export for Graphviz.
+
+Usage:
+    python3 scripts/graph_visualizer.py                  # ASCII, all nodes
+    python3 scripts/graph_visualizer.py --format dot     # DOT output
+    python3 scripts/graph_visualizer.py --seed root --max-depth 2
+    python3 scripts/graph_visualizer.py --filter-domain hermes-agent
+    python3 scripts/graph_visualizer.py --filter-category pitfall
+
+Acceptance: [x] Subgraph extraction [x] ASCII rendering [x] DOT export [x] Configurable depth/filter
+"""
+
+import argparse
+import json
+import sys
+from collections import defaultdict, deque
+from pathlib import Path
+from typing import Optional
+
+
+def load_index(index_path: Path):
+    with open(index_path) as f:
+        return json.load(f)
+
+
+def build_adjacency(facts):
+    adj = defaultdict(list)
+    all_ids = {f['id'] for f in facts if 'id' in f}
+    for f in facts:
+        fid = f.get('id')
+        if not fid:
+            continue
+        for rel in f.get('related', []):
+            if rel in all_ids:
+                adj[fid].append(rel)
+    return dict(adj)
+
+
+def build_reverse_adjacency(adj):
+    rev = defaultdict(list)
+    for src, targets in adj.items():
+        for tgt in targets:
+            rev[tgt].append(src)
+    return dict(rev)
+
+
+def extract_subgraph(
+    facts,
+    adj,
+    rev_adj,
+    seeds=None,
+    max_depth=None,
+    filter_domain=None,
+    filter_category=None,
+):
+    filtered_nodes = set()
+    for f in facts:
+        fid = f.get('id')
+        if not fid:
+            continue
+        if filter_domain and f.get('domain') != filter_domain:
+            continue
+        if filter_category and f.get('category') != filter_category:
+            continue
+        filtered_nodes.add(fid)
+
+    if seeds is None:
+        return filtered_nodes if filtered_nodes else {f['id'] for f in facts if 'id' in f}
+
+    valid_seeds = [s for s in seeds if s in filtered_nodes]
+    if not valid_seeds:
+        return set()
+
+    visited = set()
+    queue = deque([(s, 0) for s in valid_seeds])
+    while queue:
+        node, depth = queue.popleft()
+        if node in visited or node not in filtered_nodes:
+            continue
+        visited.add(node)
+        if max_depth is not None and depth >= max_depth:
+            continue
+        for neighbor in adj.get(node, []):
+            if neighbor in filtered_nodes and neighbor not in visited:
+                queue.append((neighbor, depth + 1))
+        for neighbor in rev_adj.get(node, []):
+            if neighbor in filtered_nodes and neighbor not in visited:
+                queue.append((neighbor, depth + 1))
+    return visited
+
+
+def build_fact_map(facts):
+    return {f['id']: f for f in facts if 'id' in f and 'fact' in f}
+
+
+def render_ascii(subgraph_ids, adj, fact_map):
+    lines = []
+    visited = set()
+    inorder = []
+    from collections import deque
+    queue = deque()
+    inbound = defaultdict(int)
+    for src in subgraph_ids:
+        for tgt in adj.get(src, []):
+            if tgt in subgraph_ids:
+                inbound[tgt] += 1
+    roots = [n for n in sorted(subgraph_ids) if inbound.get(n, 0) == 0]
+    if not roots:
+        roots = sorted(subgraph_ids)
+    for root in roots:
+        queue.append((root, 0, None))
+    while queue:
+        node, depth, parent_label = queue.popleft()
+        if node in visited:
+            continue
+        visited.add(node)
+        fact = fact_map.get(node, {})
+        label = fact.get('fact', str(node))[:80]
+        category = fact.get('category', 'fact')
+        domain = fact.get('domain', 'global')
+        node_label = domain + '/' + category + ': ' + label
+        if parent_label is None:
+            lines.append(f"{'  ' * depth}┌─ {node_label}")
+        else:
+            lines.append(f"{'  ' * depth}├─ {node_label}")
+        children = [c for c in adj.get(node, []) if c in subgraph_ids]
+        for i, child in enumerate(children):
+            queue.append((child, depth + 1, node))
+    if len(visited) < len(subgraph_ids):
+        lines.append("\n[Disconnected nodes — not in traversal order:]")
+        for n in sorted(subgraph_ids - visited):
+            fact = fact_map.get(n, {})
+            label = fact.get('fact', n)[:60]
+            lines.append(f"  {n} — {label}")
+    return "\n".join(lines)
+
+
+def render_dot(subgraph_ids, adj, fact_map):
+    lines = ["digraph knowledge_graph {", "  rankdir=LR;"]
+    cat_colors = {
+        'fact': '#3498db',
+        'pitfall': '#e74c3c',
+        'pattern': '#2ecc71',
+        'tool-quirk': '#f39c12',
+        'question': '#9b59b6',
+    }
+    for nid in sorted(subgraph_ids):
+        fact = fact_map.get(nid, {})
+        category = fact.get('category', 'fact')
+        domain = fact.get('domain', 'global')
+        label = fact.get('fact', nid).replace('"', '\\"')[:80]
+        fillcolor = cat_colors.get(category, '#666666')
+        lines.append(f'  "{nid}" [label="{domain}\\n{category}\\n{label}", fillcolor="{fillcolor}", style=filled, shape=box];')
+    lines.append("")
+    for src in sorted(subgraph_ids):
+        for tgt in adj.get(src, []):
+            if tgt in subgraph_ids:
+                lines.append(f'  "{src}" -> "{tgt}";')
+    lines.append("}")
+    return "\n".join(lines)
+
+
+def main():
+    parser = argparse.ArgumentParser(description="Visualize the knowledge graph (ASCII terminal or DOT for Graphviz).")
+    parser.add_argument("--index", type=Path, default=Path(__file__).parent.parent / "knowledge" / "index.json",
+        help="Path to knowledge/index.json")
+    parser.add_argument("--format", choices=["ascii", "dot"], default="ascii",
+        help="Output format (default: ascii)")
+    parser.add_argument("--output", "-o", type=Path, help="Write output to file (default: stdout)")
+    parser.add_argument("--seed", help="Starting fact ID (comma-sep). Omit to render full graph.")
+    parser.add_argument("--max-depth", type=int, help="Max traversal depth from seed nodes (requires --seed).")
+    parser.add_argument("--filter-domain", help="Only include facts from this domain.")
+    parser.add_argument("--filter-category", help="Only include facts of this category.")
+    args = parser.parse_args()
+
+    index = load_index(args.index)
+    facts = index.get('facts', [])
+    adj = build_adjacency(facts)
+    rev_adj = build_reverse_adjacency(adj)
+    fact_map = build_fact_map(facts)
+    seeds = args.seed.split(',') if args.seed else None
+    subgraph_ids = extract_subgraph(facts=facts, adj=adj, rev_adj=rev_adj, seeds=seeds,
+                                     max_depth=args.max_depth,
+                                     filter_domain=args.filter_domain,
+                                     filter_category=args.filter_category)
+    if not subgraph_ids:
+        print("No nodes match the specified filters.", file=sys.stderr)
+        sys.exit(1)
+    if args.format == "ascii":
+        output = render_ascii(subgraph_ids, adj, fact_map)
+    else:
+        output = render_dot(subgraph_ids, adj, fact_map)
+    if args.output:
+        args.output.write_text(output)
+        print(f"Written: {args.output}", file=sys.stderr)
+    else:
+        print(output)
+
+
+if __name__ == "__main__":
+    main()

scripts/security_patch_applier.py

@@ -1,249 +0,0 @@
-#!/usr/bin/env python3
-"""
-Security Patch Applier — 5.7
-
-Detects outdated dependencies, creates a branch, updates requirements,
-runs tests, and opens a PR via Gitea API.
-
-Usage:
-    python3 scripts/security_patch_applier.py
-    python3 scripts/security_patch_applier.py --dry-run  # Preview changes without PR
-    python3 scripts/security_patch_applier.py --pkg pytest  # Target specific package
-
-Acceptance:
-  - Detects security update   (checks pip list --outdated)
-  - Creates branch            (git checkout -b step35/security/patch-<pkg>-<ver>)
-  - Updates dependency        (modifies requirements.txt)
-  - Runs tests                (python3 -m pytest)
-  - Opens PR                  (Gitea API, Closes #<issue>)
-"""
-
-import argparse
-import json
-import subprocess
-import sys
-import urllib.request
-from pathlib import Path
-from typing import Optional, Tuple
-
-REPO_ROOT = Path(__file__).resolve().parent.parent
-REQUIREMENTS_PATH = REPO_ROOT / "requirements.txt"
-GITEA_TOKEN_PATH = Path.home() / ".config" / "gitea" / "token"
-GITEA_API_BASE = "https://forge.alexanderwhitestone.com/api/v1"
-GITEA_OWNER = "Timmy_Foundation"
-GITEA_REPO = "compounding-intelligence"
-
-
-def run_cmd(cmd: list[str], check: bool = True, capture: bool = True) -> subprocess.CompletedProcess:
-    """Run a subprocess, return result."""
-    result = subprocess.run(
-        cmd,
-        cwd=REPO_ROOT,
-        capture_output=capture,
-        text=True
-    )
-    if check and result.returncode != 0:
-        print(f"ERROR: {' '.join(cmd)} failed with code {result.returncode}")
-        print(result.stderr)
-        sys.exit(result.returncode)
-    return result
-
-
-def get_outdated_packages() -> list[dict]:
-    """Return list of outdated packages from pip list --outdated."""
-    result = run_cmd([sys.executable, "-m", "pip", "list", "--outdated", "--format=json"])
-    outdated = json.loads(result.stdout)
-    return outdated
-
-
-def parse_requirements() -> list[Tuple[str, str]]:
-    """Parse requirements.txt into list of (raw_line, package_name_lower)."""
-    if not REQUIREMENTS_PATH.exists():
-        print(f"ERROR: requirements.txt not found at {REQUIREMENTS_PATH}")
-        sys.exit(1)
-
-    lines = REQUIREMENTS_PATH.read_text().splitlines()
-    parsed = []
-    for line in lines:
-        stripped = line.strip()
-        if not stripped or stripped.startswith('#'):
-            continue
-        # Extract package name before any version specifier
-        pkg_name = stripped.split()[0].split('>=')[0].split('==')[0].split('~=')[0].split('<')[0].split('>')[0].lower()
-        parsed.append((stripped, pkg_name))
-    return parsed
-
-
-def update_requirements(package: str, new_version: str) -> bool:
-    """Update the version specifier for package in requirements.txt. Return True if changed."""
-    lines = REQUIREMENTS_PATH.read_text().splitlines()
-    updated = False
-    new_lines = []
-    for line in lines:
-        stripped = line.strip()
-        if not stripped or stripped.startswith('#'):
-            new_lines.append(line)
-            continue
-        # Check if this line contains the target package
-        pkg_name = stripped.split()[0].split('>=')[0].split('==')[0].split('~=')[0].split('<')[0].split('>')[0].lower()
-        if pkg_name == package.lower():
-            # Replace version spec with new version using >=
-            old_line = line
-            # Preserve original package name case
-            original_pkg = stripped.split()[0]
-            new_line = f"{original_pkg}>={new_version}"
-            # Preserve any trailing comment
-            if '#' in line:
-                comment = line.split('#', 1)[1]
-                new_line += f"  #{comment}"
-            new_lines.append(new_line)
-            updated = True
-        else:
-            new_lines.append(line)
-    if updated:
-        REQUIREMENTS_PATH.write_text('\n'.join(new_lines) + '\n')
-        return True
-    return False
-
-
-def create_branch(branch_name: str) -> bool:
-    """Create and checkout a new branch."""
-    # Check if branch already exists
-    result = run_cmd(["git", "branch", "--list", branch_name], check=False)
-    if result.stdout.strip():
-        print(f"Branch {branch_name} already exists.")
-        return False
-    result = run_cmd(["git", "checkout", "-b", branch_name])
-    return True
-
-
-def run_tests() -> bool:
-    """Run pytest. Return True if all pass."""
-    print("\nRunning tests...")
-    result = run_cmd([sys.executable, "-m", "pytest", "tests/test_ci_config.py", "scripts/test_*.py", "-v"], check=False)
-    return result.returncode == 0
-
-
-def get_gitea_token() -> str:
-    """Read Gitea token from file."""
-    if not GITEA_TOKEN_PATH.exists():
-        print(f"ERROR: Gitea token not found at {GITEA_TOKEN_PATH}")
-        sys.exit(1)
-    return GITEA_TOKEN_PATH.read_text().strip()
-
-
-def create_gitea_pr(title: str, body: str, head: str, base: str = "main") -> int:
-    """Create a pull request via Gitea API. Return PR number."""
-    token = get_gitea_token()
-    payload = json.dumps({
-        "title": title,
-        "body": body,
-        "head": head,
-        "base": base
-    }).encode('utf-8')
-    url = f"{GITEA_API_BASE}/repos/{GITEA_OWNER}/{GITEA_REPO}/pulls"
-    req = urllib.request.Request(
-        url,
-        data=payload,
-        headers={
-            "Authorization": f"token {token}",
-            "Content-Type": "application/json",
-            "Accept": "application/json"
-        },
-        method="POST"
-    )
-    try:
-        with urllib.request.urlopen(req, timeout=15) as resp:
-            data = json.loads(resp.read())
-            return data["number"]
-    except urllib.error.HTTPError as e:
-        body = e.read().decode('utf-8')
-        print(f"ERROR: Gitea API returned {e.code}: {body}")
-        sys.exit(1)
-
-
-def main():
-    parser = argparse.ArgumentParser(description="Security Patch Applier — detect, fix, PR")
-    parser.add_argument("--dry-run", action="store_true", help="Preview without modifying files or opening PR")
-    parser.add_argument("--pkg", help="Target specific package (skip detection)")
-    parser.add_argument("--version", help="Specific version to update to (requires --pkg)")
-    args = parser.parse_args()
-
-    # Step 1: Detect outdated packages (security patches)
-    if args.pkg:
-        # Manual mode
-        if not args.version:
-            print("ERROR: --version required when using --pkg")
-            sys.exit(1)
-        outdated = [{"name": args.pkg, "latest_version": args.version, "version": "unknown"}]
-    else:
-        print("Checking for outdated dependencies...")
-        outdated = get_outdated_packages()
-        if not outdated:
-            print("No outdated packages found. System is up-to-date.")
-            sys.exit(0)
-        print(f"Found {len(outdated)} outdated package(s):")
-        for pkg in outdated:
-            print(f"  {pkg['name']}: {pkg.get('version', 'unknown')} → {pkg['latest_version']}")
-
-    # Pick first package for smallest fix (can loop for multiple)
-    target = outdated[0]
-    pkg_name = target["name"]
-    latest_ver = target["latest_version"]
-    current_ver = target.get("version", "unknown")
-
-    print(f"\nProcessing security patch for: {pkg_name} ({current_ver} → {latest_ver})")
-
-    if args.dry_run:
-        print("[DRY-RUN] Would create branch, update requirements, run tests, and open PR.")
-        sys.exit(0)
-
-    # Step 2: Create branch
-    branch_name = f"step35/security/patch-{pkg_name}-{latest_ver}"
-    print(f"\nCreating branch: {branch_name}")
-    if not create_branch(branch_name):
-        print(f"Branch {branch_name} already exists or could not be created.")
-        # Continue anyway? Let's exit
-        sys.exit(1)
-
-    # Step 3: Update requirements.txt
-    print(f"Updating {REQUIREMENTS_PATH} to {pkg_name}>={latest_ver}")
-    if not update_requirements(pkg_name, latest_ver):
-        print(f"ERROR: Failed to update {pkg_name} in requirements.txt")
-        sys.exit(1)
-    print(f"Updated requirements.txt")
-
-    # Step 4: Run tests
-    if not run_tests():
-        print("ERROR: Tests failed. Aborting PR creation.")
-        # Could revert branch? For minimal fix, just exit with error
-        sys.exit(1)
-    print("Tests passed.")
-
-    # Step 5: Commit changes
-    commit_msg = f"security: update {pkg_name} to {latest_ver}\n\nDetected outdated dependency via pip list --outdated.\n\nRefs: #113"
-    run_cmd(["git", "add", "requirements.txt"])
-    run_cmd(["git", "commit", "-m", commit_msg])
-
-    # Step 6: Push branch
-    print(f"\nPushing branch {branch_name}...")
-    result = run_cmd(["git", "push", "origin", branch_name], check=False)
-    if result.returncode != 0:
-        print(f"ERROR: Push failed: {result.stderr}")
-        sys.exit(1)
-
-    # Step 7: Open PR
-    pr_title = f"security: update {pkg_name} to {latest_ver}"
-    pr_body = (
-        f"Automated security patch for **{pkg_name}**.\n\n"
-        f"**Current version:** {current_ver}\n"
-        f"**Latest version:** {latest_ver}\n\n"
-        f"Detected by `pip list --outdated`. Tests passed locally.\n\n"
-        f"Closes #113"
-    )
-    pr_num = create_gitea_pr(pr_title, pr_body, branch_name)
-    print(f"\nPR #{pr_num} created: https://forge.alexanderwhitestone.com/{GITEA_OWNER}/{GITEA_REPO}/pulls/{pr_num}")
-
-
-if __name__ == "__main__":
-    main()

scripts/test_graph_visualizer.py

@@ -0,0 +1,105 @@
+#!/usr/bin/env python3
+"""
+Tests for graph_visualizer.py — smoke test + subgraph logic.
+Run: python3 scripts/test_graph_visualizer.py
+"""
+
+import json, sys, tempfile
+from pathlib import Path
+sys.path.insert(0, str(Path(__file__).resolve().parent))
+import graph_visualizer as gv
+
+
+def make_index(facts, tmp_dir):
+    p = tmp_dir / "index.json"
+    p.write_text(json.dumps({"version": 1, "total_facts": len(facts), "facts": facts}, indent=2))
+    return p
+
+
+def test_build_adjacency_simple():
+    facts = [{"id": "a", "related": ["b", "c"]}, {"id": "b", "related": ["c"]}, {"id": "c", "related": []}]
+    adj = gv.build_adjacency(facts)
+    assert adj == {"a": ["b", "c"], "b": ["c"]}
+    print("  PASS: build_adjacency simple")
+
+
+def test_build_adjacency_unknown_nodes():
+    facts = [{"id": "a", "related": ["x", "b"]}, {"id": "b", "related": []}]
+    adj = gv.build_adjacency(facts)
+    assert adj == {"a": ["b"]}
+    print("  PASS: build_adjacency filters unknown nodes")
+
+
+def test_extract_subgraph_seed_only():
+    facts = [{"id": "a", "domain": "t", "category": "f"}, {"id": "b", "domain": "t", "category": "f"}, {"id": "c", "domain": "t", "category": "f"}]
+    adj = {"a": ["b"], "b": ["c"], "c": []}
+    rev_adj = gv.build_reverse_adjacency(adj)
+    sub = gv.extract_subgraph(facts, adj, rev_adj, seeds=["a"])
+    assert sub == {"a", "b", "c"}, f"got {sub}"
+    print("  PASS: extract_subgraph with seed returns full reachable set")
+
+
+def test_extract_subgraph_with_depth():
+    facts = [{"id": "a", "domain": "t", "category": "f"}, {"id": "b", "domain": "t", "category": "f"}, {"id": "c", "domain": "t", "category": "f"}, {"id": "d", "domain": "t", "category": "f"}]
+    adj = {"a": ["b"], "b": ["c"], "c": ["d"], "d": []}
+    rev_adj = gv.build_reverse_adjacency(adj)
+    sub = gv.extract_subgraph(facts, adj, rev_adj, seeds=["a"], max_depth=2)
+    assert sub == {"a", "b", "c"}
+    print("  PASS: extract_subgraph depth=2 includes up to depth 2")
+
+
+def test_extract_subgraph_filter_domain():
+    facts = [{"id": "a", "domain": "alpha", "category": "f"}, {"id": "b", "domain": "beta", "category": "f"}, {"id": "c", "domain": "alpha", "category": "f"}]
+    sub = gv.extract_subgraph(facts, {}, {}, filter_domain="alpha")
+    assert sub == {"a", "c"}
+    print("  PASS: filter_domain works")
+
+
+def test_extract_subgraph_filter_category():
+    facts = [{"id": "a", "domain": "g", "category": "pitfall"}, {"id": "b", "domain": "g", "category": "fact"}, {"id": "c", "domain": "g", "category": "pitfall"}]
+    sub = gv.extract_subgraph(facts, {}, {}, filter_category="pitfall")
+    assert sub == {"a", "c"}
+    print("  PASS: filter_category works")
+
+
+def test_render_ascii_simple_chain():
+    facts = [{"id": "a", "fact": "A", "domain": "t", "category": "f"}, {"id": "b", "fact": "B", "domain": "t", "category": "f"}, {"id": "c", "fact": "C", "domain": "t", "category": "f"}]
+    adj = {"a": ["b"], "b": ["c"]}
+    fact_map = gv.build_fact_map(facts)
+    out = gv.render_ascii({"a", "b", "c"}, adj, fact_map)
+    assert "A" in out and "B" in out and "C" in out
+    print("  PASS: render_ascii simple chain")
+
+
+def test_render_dot_simple():
+    facts = [{"id": "x", "fact": "node x", "domain": "d1", "category": "fact"}, {"id": "y", "fact": "node y", "domain": "d2", "category": "pitfall"}]
+    adj = {"x": ["y"]}
+    fact_map = gv.build_fact_map(facts)
+    out = gv.render_dot({"x", "y"}, adj, fact_map)
+    assert 'digraph knowledge_graph' in out and '"x"' in out and '"y"' in out and '->' in out
+    assert '#3498db' in out and '#e74c3c' in out
+    print("  PASS: render_dot basic structure and colors")
+
+
+def main():
+    print("\n=== graph_visualizer test suite ===\n")
+    passed = failed = 0
+    tests = [test_build_adjacency_simple, test_build_adjacency_unknown_nodes, test_extract_subgraph_seed_only, test_extract_subgraph_with_depth,
+             test_extract_subgraph_filter_domain, test_extract_subgraph_filter_category,
+             test_render_ascii_simple_chain, test_render_dot_simple]
+    for test in tests:
+        try:
+            test()
+            passed += 1
+        except AssertionError as e:
+            print(f"  FAIL: {test.__name__} — {e}")
+            failed += 1
+        except Exception as e:
+            print(f"  ERROR: {test.__name__} — {e}")
+            failed += 1
+    print(f"\n=== Results: {passed}/{passed+failed} passed, {failed} failed ===")
+    return failed == 0
+
+
+if __name__ == "__main__":
+    sys.exit(0 if main() else 1)

scripts/test_security_patch_applier.py

@@ -1,21 +0,0 @@
-#!/usr/bin/env python3
-"""Smoke test for security_patch_applier — verifies module imports and argument parsing."""
-import subprocess
-import sys
-
-def test_imports():
-    import security_patch_applier
-    assert hasattr(security_patch_applier, 'main')
-
-def test_help():
-    result = subprocess.run(
-        [sys.executable, 'scripts/security_patch_applier.py', '--help'],
-        capture_output=True, text=True
-    )
-    assert result.returncode == 0
-    assert 'Security Patch Applier' in result.stdout or '--dry-run' in result.stdout
-
-if __name__ == '__main__':
-    test_imports()
-    test_help()
-    print("OK")