DataJoint Diagram does not work with the latest version of pydot/networkx across Python 3.10-3.12; encapsulating double quotes needed

[tabedzki]

Bug Report

Description

DataJoint's Diagram feature does not work properly with recent versions of pydot and networkx packages because node_ids containing . are not encapsulated in double quotes " an required by DOT language specification for graphviz. This is seen when examining the dot string representation generated by networkx.drawing.nx_pydot.to_pydot

# Generate the diagram
diagram = dj.Diagram(ephys_element)
pydot_graph = diagram.make_dot()
dot_str = pydot_graph.to_string()
print(dot_str)

Trunctaed dot_str below. This fails when run through dot -Tsvg but passes if wrapped in ".

strict digraph  {
ephys_element.AcquisitionSoftware;
}

Testing of networkx

Here is a working example using networkx directly:

import networkx as nx
from networkx.drawing.nx_pydot import to_pydot

# Create a new graph
G = nx.DiGraph()

# Add two nodes
node_1 = '"a.a"'
G.add_node(node_1)
# Convert the graph to a pydot object
pydot_graph = to_pydot(G)

and excluding the double quotes results in the same error as calling Diagram()

import networkx as nx
from networkx.drawing.nx_pydot import to_pydot

# Create a new graph
G = nx.DiGraph()

# Add two nodes
node_1 = 'a.a'
G.add_node(node_1)
# Convert the graph to a pydot object
pydot_graph = to_pydot(G)

"dot" with args ['-Tsvg', '/var/folders/98/ncnp2y1n00qc_4y4ndc9mw240000gp/T/tmpj1xh62up'] returned code: 1

stdout, stderr:
 b''
b"Error: [/var/folders/98/ncnp2y1n00qc_4y4ndc9mw240000gp/T/tmpj1xh62up](https://file+.vscode-resource.vscode-cdn.net/var/folders/98/ncnp2y1n00qc_4y4ndc9mw240000gp/T/tmpj1xh62up): syntax error in line 2 near '.'\n"

Reproducibility

Include:

• OS ( MACOS)
• Python Version: 3.10-3.12
• MySQL Version: N/A
• MySQL Deployment Strategy (local-native | local-docker | remote): N/A
• DataJoint Version: 0.14.2
• Minimum number of steps to reliably reproduce the issue: 1
• Complete error stack as a result of evaluating the above steps

[ethho]

Duplicates #1169