JGraphT

[pnrobinson]

phenol is at version 1.2.0. There are API changes for version 1.5.0 (the current one). Investigate how to update.

[julesjacobsen]

Migrate to Guava? I think it has a nicer API to JGraphT, but that might no longer be the case with 1.5.0. Sorry, that wasn't helpful!

[pnrobinson]

Didn't know that guava has a graph library. If so we could switch to save a dependency
We do not do anything really sophisticated with graphs, and it might be simpler just to implement this ourselves.
We need to do traversals mainly.

[julesjacobsen]

https://github.com/google/guava/wiki/GraphsExplained

[julesjacobsen]

It has a ValueGraph implementation

MutableValueGraph<Integer, Double> weightedGraph = ValueGraphBuilder.directed().build();
weightedGraph.addNode(1);
weightedGraph.putEdgeValue(2, 3, 1.5);  // also adds nodes 2 and 3 if not already present
weightedGraph.putEdgeValue(3, 5, 1.5);  // edge values (like Map values) need not be unique
...
weightedGraph.putEdgeValue(2, 3, 2.0);  // updates the value for (2,3) to 2.0

and I think Phenol has its own traversal code, right?

[julesjacobsen]

However JGraphT has sparse representations for immutable graphs, (https://github.com/jgrapht/jgrapht/tree/master/jgrapht-opt/src/main/java/org/jgrapht/opt/graph/sparse) so it might be worth looking into this although these don't appear to support generic value graphs. I had a go at creating a CSR graph based on the Guava API some time back but never quite got it finished :( I could try and dig-up the code if you like.

[pnrobinson]

CSR would be great!
I implemented one in Python that worked.
We could probably do this in pure Java, to reduce dependencies; We should check where and how TGraph is being used in phenol and figure out how much work this would be and whether we need a library.

[ielis]

Thanks to the recent development, we have a pure Java CSR graph implementation and unless we have really good reasons, I will remove JGraphT without replacement in v3.0.0.

[ielis]

#450

[pnrobinson]

@ielis I think we can probably go ahead and just remove the old APIs, let's simplify things and move towards a first documented release next year! Are we ready to remove the jgraphT import?

[ielis]

There is one site left in Phenol which uses the JGraphT graph: the ShortestPathTable.

Otherwise, getGraph() is not used anywhere else, hence ready to be removed. The removal will be part of the next major release - v3.