Transition away from graphviz

[kirichoi]

Few functions in Tellurium (namely draw()) utilizes graphviz which is an external application to Python. It would be nice to transition into something purely Python as graphviz support in Windows is not ideal. Something like networkx or plotly might do it.

[hsauro]

Talk to Matthias about this.

Herbert

On Mon, Apr 10, 2017 at 4:14 PM, Kiri Choi notifications@github.com wrote:

Few functions in Tellurium (namely draw()) utilizes graphviz which is an external application to Python. It would be nice to transition into something purely Python as graphviz support in Windows is not ideal. Something like networkx or plotly might do it.

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[kirichoi]

I am thinking of keeping graphviz functionality but add a Python-based graphing tool and set that as the default. Using graphviz as backend can be done through something like:

rr.draw(backend='graphviz')

@matthiaskoenig: how does that sound?

[matthiaskoenig]

Sounds good to me.

On Apr 13, 2017 2:23 AM, "Kiri Choi" notifications@github.com wrote:

I am thinking of keeping graphviz functionality but add a Python-based graphing tool and set that as the default. Using graphviz as backend can be done through something like:

rr.draw(backend='graphviz')

@matthiaskoenig https://github.com/matthiaskoenig: how does that sound?

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[kirichoi]

Did some preliminary work on this and realized that networkx using matplotlib backend is functional but very limited and ugly. It might be even better to focus on figuring out good way to distribute graphviz. Another solution might be utilizing our network viewer.

[kirichoi]

NetworkX now supports directed graph. I have a simple package I built that takes antimony strings and plots out network diagrams and it looks okay.

[hsauro]

Can you post an image.

H

On Mon, Oct 15, 2018 at 1:53 PM Kiri Choi notifications@github.com wrote:

NetworkX now supports directed graph. I have a simple package I built that takes antimony strings and plots out network diagrams and it looks okay.

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[kirichoi]

Looks something like this:

Still needs a lot of polishing, but seems functional and the fact that it does not require any external binaries is a huge plus.

[hsauro]

Looks ok. What does it do for bimolecualar reactions?

H

On Mon, Oct 15, 2018 at 2:57 PM Kiri Choi notifications@github.com wrote:

Looks something like this:

[image: image] https://user-images.githubusercontent.com/7672320/46980693-32bb4c80-d08a-11e8-97db-28c23d9b17cd.png

Still needs a lot of polishing, but seems functional and the fact that it does not require any external binaries is a huge plus.

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-- Herbert Sauro, Associate Professor University of Washington, Bioengineering 206-685-2119, www.sys-bio.org hsauro@uw.edu Books: http://books.analogmachine.org/

[kirichoi]

I am working on those right now. I should be able to implement activation and inhibition in next few days. Also working on curved arrows.