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LoLab-MSM / pysb

Python framework for Systems Biology modeling [Lopez Lab Mods]
BSD 2-Clause "Simplified" License
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Visualization cytoscape #37

Closed ortega2247 closed 7 years ago

ortega2247 commented 8 years ago

this is the visualization class of PySB models. To run the models it is necessary to have cytoscape open

JamesPino commented 8 years ago

There are some files that depend on earm being installed. Maybe you can use the earm from examples?

Also there is a place where you set parameters from your local directory path. Will default parameters work?

It looks like you also need to add helper_functions to path.

ortega2247 commented 8 years ago

@JamesPino Thanks for the comments. I changed the code to use earm1.0 and the default parameters. What do you mean that i need to helper_functions to path?

JamesPino commented 8 years ago

I thought the previous travis test showed that it failed because there wasn't a module 'helper_functions'. You might have already changed it to pysb.tools.helper_functions. I can't seem to find the error in the output anymore.

I do see that it failed with no module PIL. File "/home/travis/build/LoLab-VU/pysb/build/lib/pysb/tools/model_visualization.py", line 15, in <module> from PIL import ImageFont ImportError: No module named PIL

I'll keep looking. Maybe that was something else

ortega2247 commented 8 years ago

You were right. I already fixed the PIL ImportErro, the error that throws now is related to cytoscape, as it needs to be open to run the code. I think @alubbock said that it is not possible to get rid of that error because there is no a headles cytoscape. However, i found this version: https://github.com/cytoscape/cytoscape-headless-distribution should i try to use it?

JamesPino commented 8 years ago

It looks like it isn't being developed any more. I wonder if turning of tests for that in Travis is the short term solution? Since it is specific for a tool.