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cytoscape / cytoscape-automation

Collection of scripts that include programmatic io and control of Cytoscape
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Replacement for using py2cytoscape.data? #56

Closed JamesPino closed 4 years ago

JamesPino commented 4 years ago

I see a deprecation warning for using any of the entries to py2cytoscape.data. Are there any examples of doing the same type of function calls without it? I have started to use the cyclient api directly, but there are some things that don't seem to translate. For example, passing a networkX DiGraph to create a network or lack of batch updates for setting properties to nodes (seems to do them individually now which takes a long time for 10k nodes). I like the cyrest api a lot more, I just can't seem to find examples for the same type of modules that I am building so have to create them manually.

AlexanderPico commented 4 years ago

As far as I'm aware, py2cytoscape is no longer supported. Current development is focused on py4cytoscape (https://github.com/bdemchak/py4cytoscape). We are in the middle of updating documentation, tutorials, links, etc, as the package is finalized.

JamesPino commented 4 years ago

Thanks! Any estimate for when py4cytoscape will be finalized?

AlexanderPico commented 4 years ago

It's ready to go today. There is just always more to do... :)

AlexanderPico commented 4 years ago

It's more mature and robust than the current py2cytoscape, for example.

bdemchak commented 4 years ago

Hi, James –

I’m Barry Demchak, main author (for now) of py4cytoscape.

The first goal of py4cytoscape is to reach feature parity with RCy3, which includes matching function signatures and functionality. They’re almost there (mostly) and will evolve in lock step over time. The reasons are pretty simple and obvious: sharing good ideas, easing cross-language workflow porting, easing instruction, and easing documentation.

A py4cytoscape bonus: it’s likely that workflows in remote Jupyter Notebooks running py4cytoscape will be able to control Cytoscape on a desktop. This will make sharing workflows much more feasible than now, and will enable a number of other nice scenarios. I don’t know whether there’s a plan for this for RCy3, but it seems to me that it could be possible.

Once parity is reached, we’ll be in a position to incorporate new features, including those found only in py2cytoscape. We hope to do this, but would make concrete plans only after py4cytoscape rolls out.

I would be very pleased to include your voice in our plans, and for you to give us feedback on py4cytoscape (as it is now), too. Users with real needs are gold!

Are you interested? And how could you see yourself working with us?