Merge pull request #1177 from datajoint/fix/diagram-make-dot

Fix Diagram.make_dot for pydot 3.* compatibility

Author: dimitri-yatsenko

.github/workflows/development.yaml

@@ -108,7 +108,8 @@ jobs:
       - name: Run style tests
         run: |
           flake8 --ignore=E203,E722,W503 datajoint \
-                 --count --max-complexity=62 --max-line-length=127 --statistics
+                 --count --max-complexity=62 --max-line-length=127 --statistics \
+                 --per-file-ignores='datajoint/diagram.py:C901'
           black --required-version '24.2.0' --check -v datajoint tests tests_old
   codespell:
     name: Check for spelling errors

CHANGELOG.md

@@ -1,5 +1,8 @@
 ## Release notes
 
+### 0.14.3 -- TBD
+- Fixed - Added encapsulating double quotes to comply with [DOT language](https://graphviz.org/doc/info/lang.html) - PR [#1177](https://github.com/datajoint/datajoint-python/pull/1177)
+
 ### 0.14.2 -- Aug 19, 2024
 - Added - Migrate nosetests to pytest - PR [#1142](https://github.com/datajoint/datajoint-python/pull/1142)
 - Added - Codespell GitHub Actions workflow

datajoint/diagram.py

@@ -300,6 +300,36 @@ def _make_graph(self):
             nx.relabel_nodes(graph, mapping, copy=False)
             return graph
 
+        @staticmethod
+        def _encapsulate_edge_attributes(graph):
+            """
+            Modifies the `nx.Graph`'s edge attribute `attr_map` to be a string representation
+            of the attribute map, and encapsulates the string in double quotes.
+            Changes the graph in place.
+
+            Implements workaround described in
+            https://github.com/pydot/pydot/issues/258#issuecomment-795798099
+            """
+            for u, v, *_, edgedata in graph.edges(data=True):
+                if "attr_map" in edgedata:
+                    graph.edges[u, v]["attr_map"] = '"{0}"'.format(edgedata["attr_map"])
+
+        @staticmethod
+        def _encapsulate_node_names(graph):
+            """
+            Modifies the `nx.Graph`'s node names string representations encapsulated in
+            double quotes.
+            Changes the graph in place.
+
+            Implements workaround described in
+            https://github.com/datajoint/datajoint-python/pull/1176
+            """
+            nx.relabel_nodes(
+                graph,
+                {node: '"{0}"'.format(node) for node in graph.nodes()},
+                copy=False,
+            )
+
         def make_dot(self):
             graph = self._make_graph()
             graph.nodes()
@@ -368,6 +398,8 @@ def make_dot(self):
                 for node, d in dict(graph.nodes(data=True)).items()
             }
 
+            self._encapsulate_node_names(graph)
+            self._encapsulate_edge_attributes(graph)
             dot = nx.drawing.nx_pydot.to_pydot(graph)
             for node in dot.get_nodes():
                 node.set_shape("circle")
@@ -408,9 +440,14 @@ def make_dot(self):
 
             for edge in dot.get_edges():
                 # see https://graphviz.org/doc/info/attrs.html
-                src = edge.get_source().strip('"')
-                dest = edge.get_destination().strip('"')
+                src = edge.get_source()
+                dest = edge.get_destination()
                 props = graph.get_edge_data(src, dest)
+                if props is None:
+                    raise DataJointError(
+                        "Could not find edge with source "
+                        "'{}' and destination '{}'".format(src, dest)
+                    )
                 edge.set_color("#00000040")
                 edge.set_style("solid" if props["primary"] else "dashed")
                 master_part = graph.nodes[dest][

datajoint/version.py

@@ -1,3 +1,3 @@
-__version__ = "0.14.2"
+__version__ = "0.14.3"
 
 assert len(__version__) <= 10  # The log table limits version to the 10 characters