From 5f350b3b1d1cd64986b79f7db8a514484ae01369 Mon Sep 17 00:00:00 2001
From: rocky <rb@dustyfeet.com>
Date: Sat, 28 Mar 2026 18:39:33 -0400
Subject: [PATCH 1/3] Create builtin-functions in System namespace

---
 pymathics/graph/__init__.py | 67 +++++++++++++++++++++++++++++++++++++
 pymathics/graph/boxes.py    |  2 +-
 2 files changed, 68 insertions(+), 1 deletion(-)

diff --git a/pymathics/graph/__init__.py b/pymathics/graph/__init__.py
index 17c9e9b..f06e1c0 100644
--- a/pymathics/graph/__init__.py
+++ b/pymathics/graph/__init__.py
@@ -117,6 +117,73 @@
     "requires": ["networkx"],
 }
 
+_BUILTINS_ = (
+    "AcyclicGraphQ",
+    "AdjacencyList",
+    "BalancedTree",
+    "BarbellGraph",
+    "BetweennessCentrality",
+    "BinomialTree",
+    "ClosenessCentrality",
+    "CompleteGraph",
+    "CompleteKaryTree",
+    "ConnectedComponents",
+    "ConnectedGraphQ",
+    "CycleGraph",
+    "DegreeCentrality",
+    "DirectedEdge",
+    "DirectedGraphQ",
+    "EdgeConnectivity",
+    "EdgeCount",
+    "EdgeDelete",
+    "EdgeIndex",
+    "EdgeList",
+    "EdgeRules",
+    "EigenvectorCentrality",
+    "FindShortestPath",
+    "FindSpanningTree",
+    "FindVertexCut",
+    "Graph",
+    "GraphAtlas",
+    "GraphAtom",
+    "GraphBox",
+    "GraphData",
+    "GraphDistance",
+    "GraphQ",
+    "HITSCentrality",
+    "HighlightGraph",
+    "HknHararyGraph",
+    "HmnHararyGraph",
+    "KaryTree",
+    "KatzCentrality",
+    "LadderGraph",
+    "LoopFreeGraphQ",
+    "MixedGraphQ",
+    "MultigraphQ",
+    "PageRankCentrality",
+    "PathGraph",
+    "PathGraphQ",
+    "PlanarGraphQ",
+    "Property",
+    "PropertyValue",
+    "RandomGraph",
+    "RandomTree",
+    "SimpleGraphQ",
+    "StarGraph",
+    "TreeGraph",
+    "TreeGraphAtom",
+    "TreeGraphQ",
+    "UndirectedEdge",
+    "VertexAdd",
+    "VertexConnectivity",
+    "VertexCount",
+    "VertexDegree",
+    "VertexDelete",
+    "VertexIndex",
+    "VertexList",
+    "WeaklyConnectedComponents",
+)
+
 # These are the publicly exported names
 __all__ = [
     "AcyclicGraphQ",
diff --git a/pymathics/graph/boxes.py b/pymathics/graph/boxes.py
index a9ef826..e64ecc3 100644
--- a/pymathics/graph/boxes.py
+++ b/pymathics/graph/boxes.py
@@ -10,7 +10,7 @@
 import tempfile
 from typing import Tuple
 
-from mathics.core.element import BaseElement, BoxElementMixin
+from mathics.core.element import BoxElementMixin
 
 from pymathics.graph.format import png_format_graph, svg_format_graph
 

From 5ed9156173dd32de0ad6923dc2cc8b54c74e8e8f Mon Sep 17 00:00:00 2001
From: rocky <rb@dustyfeet.com>
Date: Sat, 28 Mar 2026 18:49:37 -0400
Subject: [PATCH 2/3] adjust CI

---
 .github/workflows/consistency-checks.yml | 7 +++++--
 .github/workflows/ubuntu.yml             | 2 +-
 2 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/consistency-checks.yml b/.github/workflows/consistency-checks.yml
index 1db3be8..ed12b47 100644
--- a/.github/workflows/consistency-checks.yml
+++ b/.github/workflows/consistency-checks.yml
@@ -24,8 +24,11 @@ jobs:
         python -m pip install pytest setuptools
         python -m pip install Mathics3-Module-Base
         # Until the next Mathics3-scanner release
-        git clone https://github.com/Mathics3/Mathics3-scanner
-        (cd Mathics3-scanner && pip3 install -e .[full] --no-build-isolation && bash -x ./admin-tools/make-JSON-tables.sh)
+        git clone --depth 1 https://github.com/Mathics3/Mathics3-scanner.git
+        cd Mathics3-scanner/
+        pip install -e .
+        bash -x admin-tools/make-JSON-tables.sh
+        cd ..
         # Until the next mathics-core release
         git clone https://github.com/Mathics3/mathics-core
         (cd mathics-core && python -m pip install --no-build-isolation -e .[full])
diff --git a/.github/workflows/ubuntu.yml b/.github/workflows/ubuntu.yml
index e029a80..616efe4 100644
--- a/.github/workflows/ubuntu.yml
+++ b/.github/workflows/ubuntu.yml
@@ -1,4 +1,4 @@
-name: Mathic3 Module networkx (ubuntu)
+name: Mathics3 Module networkx (ubuntu)
 
 on:
   push:

From 088cb276857ee3dfed889f023eb0e8a013e88dea Mon Sep 17 00:00:00 2001
From: rocky <rb@dustyfeet.com>
Date: Sat, 18 Apr 2026 08:51:03 -0400
Subject: [PATCH 3/3] Small tweaks

---
 pyproject.toml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 98a9f96..12496fa 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,7 +1,7 @@
 [build-system]
 requires = [
-	"setuptools", # CVE-2024-38335 recommends this
-        "mathics-core >= 9.0.1",
+	"setuptools",
+        "mathics-core > 9.0.1",
         "Mathics3-Module-Base",
         "networkx>=3.0.0",
         "matplotlib",