chore: reduce release tooling dependencies

.agents/requirements-graphify.in

@@ -1 +1 @@
-graphifyy==0.9.96
+graphifyy==0.4.23

.agents/requirements-graphify.txt

@@ -1,20 +1,13 @@
-graphifyy==0.9.96
+graphifyy==0.4.23
 networkx==3.6.1
-numpy==2.4.6
-pyyaml==6.0.3
-rapidfuzz==3.14.6
 tree-sitter==0.25.2
-tree-sitter-bash==0.25.1
 tree-sitter-c==0.24.2
 tree-sitter-c-sharp==0.23.5
 tree-sitter-cpp==0.23.4
 tree-sitter-elixir==0.3.5
-tree-sitter-fortran==0.6.0
 tree-sitter-go==0.25.0
-tree-sitter-groovy==0.1.2
 tree-sitter-java==0.23.5
 tree-sitter-javascript==0.25.0
-tree-sitter-json==0.24.8
 tree-sitter-julia==0.23.1
 tree-sitter-kotlin==1.1.0
 tree-sitter-lua==0.5.0

.agents/skills/datadesigner-docs/SKILL.md

@@ -356,7 +356,7 @@ Notebook tutorials are JS-driven via `<NotebookViewer>` rendering converted `.ip
 
 ```
 docs/notebook_source/*.py            (jupytext format — canonical source, edit here)
-        │ make convert-execute-notebooks      # jupytext --execute (needs NVIDIA_API_KEY)
+        │ make convert-execute-notebooks      # jupytext → jupyter-execute (needs NVIDIA_API_KEY)
         ▼
 docs/notebooks/*.ipynb               (executed; outputs captured)
         │

.agents/tests/test_structural_impact.py

@@ -19,10 +19,15 @@
 EXPORT_FAILURE = """
 import runpy
 import sys
+from pathlib import Path
 from unittest.mock import patch
 
+def fail_export(graph, communities, output_path):
+    Path(output_path).write_text('{')
+    raise OSError("graph export failed")
+
 sys.argv = sys.argv[1:]
-with patch("graphify.export.to_json", return_value=False):
+with patch("graphify.export.to_json", side_effect=fail_export):
     runpy.run_path(sys.argv[0], run_name="__main__")
 """
 
@@ -99,7 +104,7 @@ def test_full_graph_round_trip(repo_root: Path, run_tool: Callable[..., subproce
     assert "**no changes**" in run_tool("--full", "--previous-graph", str(graph_path)).stdout
 
 
-@pytest.mark.parametrize("metadata", [{}, {"graphify_version": "0.4.23"}, {"schema_version": -1}])
+@pytest.mark.parametrize("metadata", [{}, {"graphify_version": "0.9.96"}, {"schema_version": -1}])
 def test_incompatible_baseline_is_reset(
     repo_root: Path, run_tool: Callable[..., subprocess.CompletedProcess[str]], metadata: dict[str, object]
 ) -> None:
@@ -139,13 +144,16 @@ def test_rejected_export_preserves_baselines(
     run_tool("--full")
     baselines = repo_root / "graphify-out/baselines.json"
     previous = baselines.read_bytes()
+    graph_path = baselines.with_name("graph.json")
+    previous_graph = graph_path.read_bytes()
     (repo_root / INTERFACE).unlink()
 
     result = run_tool("--full", reject_export=True, check=False)
 
     assert result.returncode != 0
-    assert "baselines were not updated" in result.stderr
+    assert "graph export failed" in result.stderr
     assert baselines.read_bytes() == previous
+    assert graph_path.read_bytes() == previous_graph
 
 
 def test_empty_scan_preserves_baselines(

.agents/tools/structural_impact.py

@@ -22,13 +22,15 @@
 from graphify.analyze import god_nodes, graph_diff
 from graphify.build import build_from_json
 from graphify.cluster import cluster, score_all
-from graphify.export import GRAPH_SCHEMA_VERSION, to_json
+from graphify.export import to_json
 from graphify.extract import extract
 from networkx.readwrite import json_graph
 
 _REPO_ROOT_DEFAULT = Path(__file__).resolve().parent.parent.parent
 _REPO_ROOT = _REPO_ROOT_DEFAULT
 _GRAPHIFY_VERSION = version("graphifyy")
+# Graphify 0.4.x does not stamp its exports, so version our saved report format.
+GRAPH_SCHEMA_VERSION = 1
 
 # DD layering: interface -> engine -> config (left depends on right).
 _LEGAL_DIRECTIONS = {("interface", "engine"), ("interface", "config"), ("engine", "config")}
@@ -111,8 +113,12 @@ def _build_graph(files: list[Path]) -> _Analysis:
     """Extract, build directed graph, cluster, and find god nodes."""
     if not files:
         raise ValueError(f"No Python source files found under {_REPO_ROOT}")
-    ext = extract(files, root=_REPO_ROOT, cache_root=_REPO_ROOT)
+    ext = extract(files, cache_root=_REPO_ROOT)
     G = build_from_json(ext, directed=True)
+    G.graph.update(graphify_version=_GRAPHIFY_VERSION, schema_version=GRAPH_SCHEMA_VERSION)
+    for _, node in G.nodes(data=True):
+        if node.get("source_file"):
+            node["source_file"] = _rel(node["source_file"])
     comms = cluster(G)
     return _Analysis(graph=G, communities=comms, cohesion=score_all(G, comms), god_nodes=god_nodes(G, top_n=15))
 
@@ -370,8 +376,13 @@ def _full_mode(previous_graph_path: str | None = None) -> str:
     out_dir = _REPO_ROOT / "graphify-out"
     out_dir.mkdir(exist_ok=True)
     # This is a complete source snapshot, so deletions must replace the old graph.
-    if not to_json(G, communities, str(out_dir / "graph.json"), force=True):
-        raise RuntimeError("Could not save the structural graph; baselines were not updated")
+    graph_path = out_dir / "graph.json"
+    export_path = graph_path.with_suffix(".tmp")
+    try:
+        to_json(G, communities, str(export_path))
+        export_path.replace(graph_path)
+    finally:
+        export_path.unlink(missing_ok=True)
     (out_dir / "baselines.json").write_text(
         json.dumps(
             {

.github/dependabot.yml

@@ -14,6 +14,13 @@ updates:
     directory: /.agents
     schedule:
       interval: weekly
+    # Hold routine upgrades for the 0.4 adapter; keep security updates enabled.
+    ignore:
+      - dependency-name: graphifyy
+        update-types:
+          - version-update:semver-major
+          - version-update:semver-minor
+          - version-update:semver-patch
     groups:
       graphify:
         patterns:

DEVELOPMENT.md

@@ -25,13 +25,12 @@ cd DataDesigner
 # Install with dev dependencies
 make install-dev
 
-# Or, if you use Jupyter / IPython for development
+# Or, to execute the tutorial and documentation notebooks
 make install-dev-notebooks
 ```
 
-Notebook setup uses the patched nbconvert PyPI release, including its HTML stylesheets.
-The `install-notebook-css` target reuses existing stylesheets and can restore missing assets from a
-checksum-pinned wheel. Use `NOTEBOOK_CSS=0` to skip that restoration check in execution-only environments.
+Notebook setup installs the kernel and execution tools used by Jupytext and the Fern notebook pipeline.
+Install a Jupyter frontend separately if you want to edit notebooks in its browser interface.
 
 ### Verify Your Setup
 

Makefile

@@ -87,7 +87,6 @@ help:
 	@echo "  generate-fern-notebooks   - Convert docs/notebook_source/*.py → fern/components/notebooks/{json,ts}"
 	@echo "  generate-fern-notebooks-with-outputs - Full pipeline: execute notebooks (needs API key), colabify, convert to Fern"
 	@echo "  install-docs-deps        - Install docs and notebook dependencies"
-	@echo "  install-notebook-css     - Restore nbconvert HTML export stylesheets"
 	@echo "  prepare-fern-release VERSION=X.Y.Z - Add or refresh Fern version files for release preview"
 	@echo "  check-fern-release-version VERSION=X.Y.Z - Verify Fern has a version entry for release publishing"
 	@echo "  prepare-fern-docs         - Generate local Fern artifacts"
@@ -179,9 +178,8 @@ test-graphify: install-graphify
 install-dev-notebooks:
 	@echo "📦 Installing DataDesigner workspace with notebook dependencies..."
 	@echo "   Packages: data-designer-config → data-designer-engine → data-designer"
-	@echo "   Groups: dev + docs + notebooks (Jupyter, jupytext, etc.)"
+	@echo "   Groups: dev + docs + notebooks (Jupytext, kernel, execution tools)"
 	uv sync --all-packages --group dev --group docs --group notebooks
-	@$(MAKE) install-notebook-css
 	$(call install-pre-commit-hooks)
 	@echo "✅ Dev + docs + notebooks installation complete!"
 	@echo ""
@@ -511,7 +509,7 @@ update-license-headers:
 DOCS_PYTHON_VERSION ?= 3.13
 DOCS_PYTHON ?= .venv/bin/python
 DOCS_JUPYTEXT ?= .venv/bin/jupytext
-NOTEBOOK_CSS ?= 1
+DOCS_NBCLIENT ?= $(if $(findstring /,$(DOCS_JUPYTEXT)),$(dir $(DOCS_JUPYTEXT)),)jupyter-execute
 FERN_VERSION ?= $(shell jq -r .version fern/fern.config.json)
 FERN ?= npx -y fern-api@$(FERN_VERSION)
 FERN_ORG ?= $(shell jq -r .organization fern/fern.config.json)
@@ -526,16 +524,6 @@ DOCS_CERTS = SSL_CERT_FILE=$$($(DOCS_PYTHON) -c "import certifi; print(certifi.w
 install-docs-deps:
 	@echo "📦 Installing docs dependencies (Python $(DOCS_PYTHON_VERSION))..."
 	uv sync --python $(DOCS_PYTHON_VERSION) --all-packages --group docs --group notebooks
-	@$(MAKE) install-notebook-css
-
-install-notebook-css:
-ifeq ($(NOTEBOOK_CSS),1)
-	$(DOCS_CERTS) $(DOCS_PYTHON) docs/scripts/prepare_nbconvert_css.py
-else ifeq ($(NOTEBOOK_CSS),0)
-	@echo "Skipping nbconvert CSS (notebook execution only)."
-else
-	$(error NOTEBOOK_CSS must be 0 or 1)
-endif
 
 prepare-fern-release:
 ifndef VERSION
@@ -599,7 +587,7 @@ serve-fern-docs-local-theme:
 convert-execute-notebooks:
 ifeq ($(USE_CACHE),1)
 	@echo "📓 Converting Python tutorials to notebooks (with caching)..."
-	@$(DOCS_CERTS) DOCS_JUPYTEXT=$(DOCS_JUPYTEXT) bash docs/scripts/build_notebooks_cached.sh
+	@$(DOCS_CERTS) DOCS_JUPYTEXT=$(DOCS_JUPYTEXT) DOCS_NBCLIENT=$(DOCS_NBCLIENT) bash docs/scripts/build_notebooks_cached.sh
 else
 	@echo "📓 Converting Python tutorials to notebooks and executing ($(DOCS_PYTHON))..."
 	@rm -rf docs/notebooks
@@ -611,7 +599,10 @@ else
 		for f in docs/notebook_source/*.py; do \
 			[ -f "$$f" ] || continue; \
 			echo "▶ executing $$f"; \
-			$(DOCS_JUPYTEXT) --to ipynb --execute "$$f" || failed="$$failed\n   • $$f"; \
+			if ! { $(DOCS_JUPYTEXT) --to ipynb "$$f" && $(DOCS_NBCLIENT) --inplace "$${f%.py}.ipynb"; }; then \
+				rm -f "$${f%.py}.ipynb"; \
+				failed="$$failed\n   • $$f"; \
+			fi; \
 		done; \
 		for f in docs/notebook_source/*.ipynb; do [ -f "$$f" ] && mv "$$f" docs/notebooks/; done; \
 		rm -rf docs/notebook_source/artifacts; \
@@ -818,7 +809,7 @@ clean-test-coverage:
         format format-check format-check-config format-check-engine format-check-interface \
         format-config format-engine format-interface \
         generate-colab-notebooks generate-fern-notebooks generate-fern-notebooks-with-outputs help \
-        install install-dev install-dev-notebooks install-dev-recipes install-docs-deps install-graphify install-notebook-css \
+        install install-dev install-dev-notebooks install-dev-recipes install-docs-deps install-graphify \
         lint lint-config lint-engine lint-fix lint-fix-config lint-fix-engine lint-fix-interface lint-interface lock-graphify \
         perf-import perf-import-runtime prepare-fern-docs prepare-fern-release publish serve-fern-docs-dev serve-fern-docs-local-theme serve-fern-docs-locally show-versions \
         health-checks \

constraints.txt

@@ -4,7 +4,6 @@
 #           uv pip install data-designer -c constraints.txt
 #           uv add data-designer -c constraints.txt
 anyio>=4.14.2
-bleach>=6.4.0
 cryptography>=50.0.0
 filelock>=4.2.1
 idna>=3.15

docs/scripts/build_notebooks_cached.sh

@@ -25,6 +25,7 @@ SOURCE_DIR="$REPO_ROOT/docs/notebook_source"
 OUTPUT_DIR="$REPO_ROOT/docs/notebooks"
 CACHE_DIR="${1:-$REPO_ROOT/.notebook-cache}"
 DOCS_JUPYTEXT="${DOCS_JUPYTEXT:-$REPO_ROOT/.venv/bin/jupytext}"
+DOCS_NBCLIENT="${DOCS_NBCLIENT:-$(dirname "$DOCS_JUPYTEXT")/jupyter-execute}"
 NOTEBOOK_EXECUTION_ATTEMPTS="${NOTEBOOK_EXECUTION_ATTEMPTS:-1}"
 NOTEBOOK_RETRY_DELAY_SECONDS="${NOTEBOOK_RETRY_DELAY_SECONDS:-15}"
 
@@ -37,11 +38,13 @@ if [[ ! "$NOTEBOOK_RETRY_DELAY_SECONDS" =~ ^[0-9]+$ ]]; then
     exit 1
 fi
 
-if [ ! -x "$DOCS_JUPYTEXT" ]; then
-    echo "❌ Missing jupytext executable: $DOCS_JUPYTEXT"
-    echo "Run 'make install-dev-notebooks' first."
-    exit 1
-fi
+for notebook_tool in "$DOCS_JUPYTEXT" "$DOCS_NBCLIENT"; do
+    if [ ! -x "$notebook_tool" ]; then
+        echo "❌ Missing notebook executable: $notebook_tool"
+        echo "Run 'make install-dev-notebooks' first."
+        exit 1
+    fi
+done
 
 execute_notebook() {
     local src="$1"
@@ -51,7 +54,7 @@ execute_notebook() {
 
     for ((attempt = 1; attempt <= NOTEBOOK_EXECUTION_ATTEMPTS; attempt++)); do
         rm -f "$output"
-        if "$DOCS_JUPYTEXT" --to ipynb --execute "$src"; then
+        if "$DOCS_JUPYTEXT" --to ipynb "$src" && "$DOCS_NBCLIENT" --inplace "$output"; then
             return 0
         fi
         rm -f "$output"

fern/components/NotebookViewer.tsx

@@ -26,7 +26,7 @@ import type { ReactNode } from "react";
  * The trust boundary is the converter pipeline:
  *
  *   docs/notebook_source/*.py  (jupytext source — code-reviewed at PR time)
- *     └─> jupytext --execute    (runs in CI/maintainer shell with NVIDIA_API_KEY)
+ *     └─> jupytext + jupyter-execute (runs in CI/maintainer shell with NVIDIA_API_KEY)
  *           └─> *.ipynb         (real outputs captured)
  *                 └─> fern/scripts/ipynb-to-fern-json.py
  *                       └─> fern/components/notebooks/*.{json,ts}  (committed)