Networkx 2.x

[clbarnes]

Old networkx is making some dependencies clash

[clbarnes]

At time of writing, the only place networkx is used is in the export application, to run node_link_graph on JSON data pulled from CATMAID.

In this format, there is an array of nodes, and edges are defined by their source and target nodes.

In networkx 1.x, these nodes are addressed by their index in the nodes array.

In networkx 2.x, these nodes are addressed by their ID.

Whether or not catpy changes, at this point in time, CATMAID currently uses networkx 1.x and so that is the format which will be returned. Obviously the networkx maintainers didn't think to include a schema version in the JSON.

I want networkx 2 so I'll write a converter; catpy will work with either networkx1 or 2 in this instance (more complex graph-manipulating stuff will probably break nx1 compatibility). CATMAID will continue to emit nx1-format JSON, and will break catpy if that changes.

This issue should be left open for informational purposes.