v0.3.16: NetworkX <3.4 compat, .jsx support, pipx follow-up fix

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

CHANGELOG.md

@@ -2,6 +2,12 @@
 
 Full release notes with details on each version: [GitHub Releases](https://github.com/safishamsi/graphify/releases)
 
+## 0.3.16 (2026-04-08)
+
+- Fix: `graphify query`, `serve`, and `benchmark` now work on NetworkX < 3.4 — version-safe shim for `node_link_graph()` at all call sites (#95)
+- Fix: `.jsx` files now detected and extracted via the JS extractor — added to `CODE_EXTENSIONS` and `_DISPATCH` (#94)
+- Fix: `.graphify_python` no longer deleted in Step 9 cleanup across all 6 skill files — pipx users no longer hit `ModuleNotFoundError` on follow-up commands (#92)
+
 ## 0.3.15 (2026-04-08)
 
 - Feat: Trae and Trae CN platform support (`graphify install --platform trae` / `trae-cn`)

graphify/__main__.py

@@ -502,7 +502,11 @@ def main() -> None:
         try:
             import json as _json
             import networkx as _nx
-            G = json_graph.node_link_graph(_json.loads(gp.read_text(encoding="utf-8")), edges="links")
+            _raw = _json.loads(gp.read_text(encoding="utf-8"))
+            try:
+                G = json_graph.node_link_graph(_raw, edges="links")
+            except TypeError:
+                G = json_graph.node_link_graph(_raw)
         except Exception as exc:
             print(f"error: could not load graph: {exc}", file=sys.stderr)
             sys.exit(1)

graphify/benchmark.py

@@ -76,7 +76,10 @@ def run_benchmark(
     Returns dict with: corpus_tokens, avg_query_tokens, reduction_ratio, per_question
     """
     data = json.loads(Path(graph_path).read_text())
-    G = json_graph.node_link_graph(data, edges="links")
+    try:
+        G = json_graph.node_link_graph(data, edges="links")
+    except TypeError:
+        G = json_graph.node_link_graph(data)
 
     if corpus_words is None:
         # Rough estimate: each node label is ~3 words, plus source context

graphify/detect.py

@@ -17,7 +17,7 @@ class FileType(str, Enum):
 
 _MANIFEST_PATH = "graphify-out/manifest.json"
 
-CODE_EXTENSIONS = {'.py', '.ts', '.js', '.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'}
+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'}
 DOC_EXTENSIONS = {'.md', '.txt', '.rst'}
 PAPER_EXTENSIONS = {'.pdf'}
 IMAGE_EXTENSIONS = {'.png', '.jpg', '.jpeg', '.gif', '.webp', '.svg'}

graphify/extract.py

@@ -2362,6 +2362,7 @@ def extract(paths: list[Path]) -> dict:
     _DISPATCH: dict[str, Any] = {
         ".py": extract_python,
         ".js": extract_js,
+        ".jsx": extract_js,
         ".ts": extract_js,
         ".tsx": extract_js,
         ".go": extract_go,

graphify/serve.py

@@ -12,7 +12,10 @@ def _load_graph(graph_path: str) -> nx.Graph:
     try:
         safe = validate_graph_path(graph_path)
         data = json.loads(safe.read_text())
-        return json_graph.node_link_graph(data, edges="links")
+        try:
+            return json_graph.node_link_graph(data, edges="links")
+        except TypeError:
+            return json_graph.node_link_graph(data)
     except (ValueError, FileNotFoundError) as exc:
         print(f"error: {exc}", file=sys.stderr)
         sys.exit(1)

graphify/skill-claw.md

@@ -594,7 +594,7 @@ cost_path.write_text(json.dumps(cost, indent=2))
 print(f'This run: {input_tok:,} input tokens, {output_tok:,} output tokens')
 print(f'All time: {cost[\"total_input_tokens\"]:,} input, {cost[\"total_output_tokens\"]:,} output ({len(cost[\"runs\"])} runs)')
 "
-rm -f .graphify_detect.json .graphify_extract.json .graphify_ast.json .graphify_semantic.json .graphify_analysis.json .graphify_labels.json .graphify_python
+rm -f .graphify_detect.json .graphify_extract.json .graphify_ast.json .graphify_semantic.json .graphify_analysis.json .graphify_labels.json
 rm -f graphify-out/.needs_update 2>/dev/null || true
 ```
 

graphify/skill-codex.md

@@ -650,7 +650,7 @@ cost_path.write_text(json.dumps(cost, indent=2))
 print(f'This run: {input_tok:,} input tokens, {output_tok:,} output tokens')
 print(f'All time: {cost[\"total_input_tokens\"]:,} input, {cost[\"total_output_tokens\"]:,} output ({len(cost[\"runs\"])} runs)')
 "
-rm -f .graphify_detect.json .graphify_extract.json .graphify_ast.json .graphify_semantic.json .graphify_analysis.json .graphify_labels.json .graphify_python
+rm -f .graphify_detect.json .graphify_extract.json .graphify_ast.json .graphify_semantic.json .graphify_analysis.json .graphify_labels.json
 rm -f graphify-out/.needs_update 2>/dev/null || true
 ```
 

graphify/skill-droid.md

@@ -647,7 +647,7 @@ cost_path.write_text(json.dumps(cost, indent=2))
 print(f'This run: {input_tok:,} input tokens, {output_tok:,} output tokens')
 print(f'All time: {cost[\"total_input_tokens\"]:,} input, {cost[\"total_output_tokens\"]:,} output ({len(cost[\"runs\"])} runs)')
 "
-rm -f .graphify_detect.json .graphify_extract.json .graphify_ast.json .graphify_semantic.json .graphify_analysis.json .graphify_labels.json .graphify_python
+rm -f .graphify_detect.json .graphify_extract.json .graphify_ast.json .graphify_semantic.json .graphify_analysis.json .graphify_labels.json
 rm -f graphify-out/.needs_update 2>/dev/null || true
 ```
 

graphify/skill-opencode.md

@@ -646,7 +646,7 @@ cost_path.write_text(json.dumps(cost, indent=2))
 print(f'This run: {input_tok:,} input tokens, {output_tok:,} output tokens')
 print(f'All time: {cost[\"total_input_tokens\"]:,} input, {cost[\"total_output_tokens\"]:,} output ({len(cost[\"runs\"])} runs)')
 "
-rm -f .graphify_detect.json .graphify_extract.json .graphify_ast.json .graphify_semantic.json .graphify_analysis.json .graphify_labels.json .graphify_python
+rm -f .graphify_detect.json .graphify_extract.json .graphify_ast.json .graphify_semantic.json .graphify_analysis.json .graphify_labels.json
 rm -f graphify-out/.needs_update 2>/dev/null || true
 ```
 

graphify/skill-trae.md

@@ -625,7 +625,7 @@ cost_path.write_text(json.dumps(cost, indent=2))
 print(f'This run: {input_tok:,} input tokens, {output_tok:,} output tokens')
 print(f'All time: {cost[\"total_input_tokens\"]:,} input, {cost[\"total_output_tokens\"]:,} output ({len(cost[\"runs\"])} runs)')
 "
-rm -f .graphify_detect.json .graphify_extract.json .graphify_ast.json .graphify_semantic.json .graphify_analysis.json .graphify_labels.json .graphify_python
+rm -f .graphify_detect.json .graphify_extract.json .graphify_ast.json .graphify_semantic.json .graphify_analysis.json .graphify_labels.json
 rm -f graphify-out/.needs_update 2>/dev/null || true
 ```
 

graphify/skill.md

@@ -650,7 +650,7 @@ cost_path.write_text(json.dumps(cost, indent=2))
 print(f'This run: {input_tok:,} input tokens, {output_tok:,} output tokens')
 print(f'All time: {cost[\"total_input_tokens\"]:,} input, {cost[\"total_output_tokens\"]:,} output ({len(cost[\"runs\"])} runs)')
 "
-rm -f graphify-out/.graphify_detect.json graphify-out/.graphify_extract.json graphify-out/.graphify_ast.json graphify-out/.graphify_semantic.json graphify-out/.graphify_analysis.json graphify-out/.graphify_labels.json graphify-out/.graphify_python
+rm -f graphify-out/.graphify_detect.json graphify-out/.graphify_extract.json graphify-out/.graphify_ast.json graphify-out/.graphify_semantic.json graphify-out/.graphify_analysis.json graphify-out/.graphify_labels.json
 rm -f graphify-out/.needs_update 2>/dev/null || true
 ```
 

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "graphifyy"
-version = "0.3.15"
+version = "0.3.16"
 description = "AI coding assistant skill (Claude Code, Codex, OpenCode, OpenClaw) - turn any folder of code, docs, papers, or images into a queryable knowledge graph"
 readme = "README.md"
 license = { file = "LICENSE" }