v0.4.13: Verilog support, HiDPI hyperedge fix, null label guards, AGENTS.md python3 fix

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

CHANGELOG.md

@@ -2,6 +2,13 @@
 
 Full release notes with details on each version: [GitHub Releases](https://github.com/safishamsi/graphify/releases)
 
+## 0.4.13 (2026-04-14)
+
+- Add: Verilog/SystemVerilog support — `.v` and `.sv` files extracted via tree-sitter-verilog (modules, functions, tasks, package imports, module instantiations with `instantiates` edges) (#325)
+- Fix: hyperedge polygons render correctly on HiDPI/Retina displays — `afterDrawing` callback ctx is now used directly (already in network coordinate space), removing the double-applied transform and incorrect `canvas.width/2` DPR anchor (#334)
+- Fix: AGENTS.md and GEMINI.md rebuild rule now uses `graphify update .` instead of hardcoded `python3 -c "..."` — correct Python is resolved through the graphify binary, no more interpreter mismatches in Nix/pipx/uv environments (#324)
+- Fix: `graphify query` and `graphify explain` no longer crash with `AttributeError` when a node has `label: null` — all `.get("label", "")` calls guarded with `or ""` to handle explicit null values (#323)
+
 ## 0.4.12 (2026-04-13)
 
 - Add: Kiro IDE/CLI support — `graphify kiro install` writes `.kiro/skills/graphify/SKILL.md` (invoked via `/graphify`) and `.kiro/steering/graphify.md` (`inclusion: always` — always-on context before every conversation) (#319, #321)

graphify/__main__.py

@@ -186,7 +186,7 @@ This project has a graphify knowledge graph at graphify-out/.
 Rules:
 - Before answering architecture or codebase questions, read graphify-out/GRAPH_REPORT.md for god nodes and community structure
 - If graphify-out/wiki/index.md exists, navigate it instead of reading raw files
-- After modifying code files in this session, run `python3 -c "from graphify.watch import _rebuild_code; from pathlib import Path; _rebuild_code(Path('.'))"` to keep the graph current
+- After modifying code files in this session, run `graphify update .` to keep the graph current (AST-only, no API cost)
 """
 
 _AGENTS_MD_MARKER = "## graphify"
@@ -199,7 +199,7 @@ This project has a graphify knowledge graph at graphify-out/.
 Rules:
 - Before answering architecture or codebase questions, read graphify-out/GRAPH_REPORT.md for god nodes and community structure
 - If graphify-out/wiki/index.md exists, navigate it instead of reading raw files
-- After modifying code files in this session, run `python3 -c "from graphify.watch import _rebuild_code; from pathlib import Path; _rebuild_code(Path('.'))"` to keep the graph current
+- After modifying code files in this session, run `graphify update .` to keep the graph current (AST-only, no API cost)
 """
 
 _GEMINI_MD_MARKER = "## graphify"

graphify/detect.py

@@ -18,7 +18,7 @@ class FileType(str, Enum):
 
 _MANIFEST_PATH = "graphify-out/manifest.json"
 
-CODE_EXTENSIONS = {'.py', '.ts', '.js', '.jsx', '.tsx', '.go', '.rs', '.java', '.cpp', '.cc', '.cxx', '.c', '.h', '.hpp', '.rb', '.swift', '.kt', '.kts', '.cs', '.scala', '.php', '.lua', '.toc', '.zig', '.ps1', '.ex', '.exs', '.m', '.mm', '.jl', '.vue', '.svelte', '.dart'}
+CODE_EXTENSIONS = {'.py', '.ts', '.js', '.jsx', '.tsx', '.go', '.rs', '.java', '.cpp', '.cc', '.cxx', '.c', '.h', '.hpp', '.rb', '.swift', '.kt', '.kts', '.cs', '.scala', '.php', '.lua', '.toc', '.zig', '.ps1', '.ex', '.exs', '.m', '.mm', '.jl', '.vue', '.svelte', '.dart', '.v', '.sv'}
 DOC_EXTENSIONS = {'.md', '.txt', '.rst'}
 PAPER_EXTENSIONS = {'.pdf'}
 IMAGE_EXTENSIONS = {'.png', '.jpg', '.jpeg', '.gif', '.webp', '.svg'}

graphify/export.py

@@ -62,32 +62,24 @@ def _hyperedge_script(hyperedges_json: str) -> str:
     return f"""<script>
 // Render hyperedges as shaded regions
 const hyperedges = {hyperedges_json};
-function drawHyperedges() {{
-    const canvas = network.canvas.frame.canvas;
-    const ctx = canvas.getContext('2d');
+// afterDrawing passes ctx already transformed to network coordinate space.
+// Draw node positions raw — no manual pan/zoom/DPR math needed.
+network.on('afterDrawing', function(ctx) {{
     hyperedges.forEach(h => {{
         const positions = h.nodes
             .map(nid => network.getPositions([nid])[nid])
             .filter(p => p !== undefined);
         if (positions.length < 2) return;
-        // Draw convex hull as filled polygon
         ctx.save();
         ctx.globalAlpha = 0.12;
         ctx.fillStyle = '#6366f1';
         ctx.strokeStyle = '#6366f1';
         ctx.lineWidth = 2;
         ctx.beginPath();
-        const scale = network.getScale();
-        const offset = network.getViewPosition();
-        const toCanvas = (p) => ({{
-            x: (p.x - offset.x) * scale + canvas.width / 2,
-            y: (p.y - offset.y) * scale + canvas.height / 2
-        }});
-        const pts = positions.map(toCanvas);
-        // Expand hull slightly
-        const cx = pts.reduce((s, p) => s + p.x, 0) / pts.length;
-        const cy = pts.reduce((s, p) => s + p.y, 0) / pts.length;
-        const expanded = pts.map(p => ({{
+        // Centroid and expanded hull in network coordinates
+        const cx = positions.reduce((s, p) => s + p.x, 0) / positions.length;
+        const cy = positions.reduce((s, p) => s + p.y, 0) / positions.length;
+        const expanded = positions.map(p => ({{
             x: cx + (p.x - cx) * 1.15,
             y: cy + (p.y - cy) * 1.15
         }}));
@@ -105,8 +97,7 @@ function drawHyperedges() {{
         ctx.fillText(h.label, cx, cy - 5);
         ctx.restore();
     }});
-}}
-network.on('afterDrawing', drawHyperedges);
+}});
 </script>"""
 
 

graphify/extract.py

@@ -1464,6 +1464,110 @@ def extract_dart(path: Path) -> dict:
     return {"nodes": nodes, "edges": edges}
 
 
+def extract_verilog(path: Path) -> dict:
+    """Extract modules, functions, tasks, package imports, and instantiations from .v/.sv files."""
+    try:
+        import tree_sitter_verilog as tsverilog
+        from tree_sitter import Language, Parser
+    except ImportError:
+        return {"nodes": [], "edges": [], "error": "tree_sitter_verilog not installed"}
+
+    try:
+        language = Language(tsverilog.language())
+        parser = Parser(language)
+        source = path.read_bytes()
+        tree = parser.parse(source)
+        root = tree.root_node
+    except Exception as e:
+        return {"nodes": [], "edges": [], "error": str(e)}
+
+    stem = path.stem
+    str_path = str(path)
+    nodes: list[dict] = []
+    edges: list[dict] = []
+    seen_ids: set[str] = set()
+
+    def add_node(nid: str, label: str, line: int) -> None:
+        if nid not in seen_ids:
+            seen_ids.add(nid)
+            nodes.append({"id": nid, "label": label, "file_type": "code",
+                          "source_file": str_path, "source_location": f"L{line}",
+                          "confidence_score": 1.0})
+
+    def add_edge(src: str, tgt: str, relation: str, line: int,
+                 confidence: str = "EXTRACTED", score: float = 1.0) -> None:
+        edges.append({"source": src, "target": tgt, "relation": relation,
+                      "confidence": confidence, "confidence_score": score,
+                      "source_file": str_path, "source_location": f"L{line}", "weight": 1.0})
+
+    file_nid = _make_id(str(path))
+    add_node(file_nid, path.name, 1)
+
+    def walk(node, module_nid: str | None = None) -> None:
+        t = node.type
+
+        if t == "module_declaration":
+            name_node = node.child_by_field_name("name")
+            if name_node:
+                mod_name = _read_text(name_node, source)
+                line = node.start_point[0] + 1
+                nid = _make_id(stem, mod_name)
+                add_node(nid, mod_name, line)
+                add_edge(file_nid, nid, "defines", line)
+                for child in node.children:
+                    walk(child, nid)
+                return
+
+        elif t in ("function_declaration", "function_prototype"):
+            name_node = node.child_by_field_name("name")
+            if name_node:
+                func_name = _read_text(name_node, source)
+                line = node.start_point[0] + 1
+                parent = module_nid or file_nid
+                nid = _make_id(parent, func_name)
+                add_node(nid, f"{func_name}()", line)
+                add_edge(parent, nid, "contains", line)
+
+        elif t == "task_declaration":
+            name_node = node.child_by_field_name("name")
+            if name_node:
+                task_name = _read_text(name_node, source)
+                line = node.start_point[0] + 1
+                parent = module_nid or file_nid
+                nid = _make_id(parent, task_name)
+                add_node(nid, task_name, line)
+                add_edge(parent, nid, "contains", line)
+
+        elif t == "package_import_declaration":
+            for child in node.children:
+                if child.type == "package_import_item":
+                    pkg_text = _read_text(child, source)
+                    pkg_name = pkg_text.split("::")[0].strip()
+                    if pkg_name:
+                        line = node.start_point[0] + 1
+                        tgt_nid = _make_id(pkg_name)
+                        add_node(tgt_nid, pkg_name, line)
+                        src = module_nid or file_nid
+                        add_edge(src, tgt_nid, "imports_from", line)
+
+        elif t == "module_instantiation":
+            # module_type instantiates another module
+            type_node = node.child_by_field_name("module_type")
+            if type_node and module_nid:
+                inst_type = _read_text(type_node, source).strip()
+                if inst_type:
+                    line = node.start_point[0] + 1
+                    tgt_nid = _make_id(inst_type)
+                    add_node(tgt_nid, inst_type, line)
+                    add_edge(module_nid, tgt_nid, "instantiates", line)
+
+        for child in node.children:
+            walk(child, module_nid)
+
+    walk(root)
+    return {"nodes": nodes, "edges": edges}
+
+
 def extract_lua(path: Path) -> dict:
     """Extract functions, methods, require() imports, and calls from a .lua file."""
     return _extract_generic(path, _LUA_CONFIG)
@@ -2948,6 +3052,8 @@ def extract(paths: list[Path]) -> dict:
         ".vue": extract_js,
         ".svelte": extract_js,
         ".dart": extract_dart,
+        ".v": extract_verilog,
+        ".sv": extract_verilog,
     }
 
     total = len(paths)

graphify/serve.py

@@ -49,7 +49,7 @@ def _score_nodes(G: nx.Graph, terms: list[str]) -> list[tuple[float, str]]:
     scored = []
     norm_terms = [_strip_diacritics(t).lower() for t in terms]
     for nid, data in G.nodes(data=True):
-        norm_label = data.get("norm_label") or _strip_diacritics(data.get("label", "")).lower()
+        norm_label = data.get("norm_label") or _strip_diacritics(data.get("label") or "").lower()
         source = (data.get("source_file") or "").lower()
         score = sum(1 for t in norm_terms if t in norm_label) + sum(0.5 for t in norm_terms if t in source)
         if score > 0:
@@ -113,7 +113,7 @@ def _find_node(G: nx.Graph, label: str) -> list[str]:
     """Return node IDs whose label or ID matches the search term (diacritic-insensitive)."""
     term = _strip_diacritics(label).lower()
     return [nid for nid, d in G.nodes(data=True)
-            if term in (d.get("norm_label") or _strip_diacritics(d.get("label", "")).lower())
+            if term in (d.get("norm_label") or _strip_diacritics(d.get("label") or "").lower())
             or term == nid.lower()]
 
 
@@ -251,7 +251,7 @@ def serve(graph_path: str = "graphify-out/graph.json") -> None:
     def _tool_get_node(arguments: dict) -> str:
         label = arguments["label"].lower()
         matches = [(nid, d) for nid, d in G.nodes(data=True)
-                   if label in d.get("label", "").lower() or label == nid.lower()]
+                   if label in (d.get("label") or "").lower() or label == nid.lower()]
         if not matches:
             return f"No node matching '{label}' found."
         nid, d = matches[0]

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "graphifyy"
-version = "0.4.12"
+version = "0.4.13"
 description = "AI coding assistant skill (Claude Code, Codex, OpenCode, Cursor, Gemini CLI, Aider, OpenClaw, Factory Droid, Trae, Hermes, Kiro, Google Antigravity) - turn any folder of code, docs, papers, images, or videos into a queryable knowledge graph"
 readme = "README.md"
 license = { file = "LICENSE" }
@@ -33,6 +33,7 @@ dependencies = [
     "tree-sitter-elixir",
     "tree-sitter-objc",
     "tree-sitter-julia",
+    "tree-sitter-verilog",
 ]
 
 [project.urls]