Graph representation of biological model #131
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…aph.py. Minor changes to exec_model.py to make create_graph callable on model object.
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This pull request introduces 1 alert when merging 92640c6 into f7d3484 - view on LGTM.com new alerts:
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for more information, see https://pre-commit.ci
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This pull request introduces 1 alert when merging cda1212 into f7d3484 - view on LGTM.com new alerts:
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This pull request introduces 1 alert when merging bce630c into f7d3484 - view on LGTM.com new alerts:
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Hi @formersbach, Thanks a million for implementing a graph visualization method!
Overall, this update is amazing. The code needs minor update before merging into master.
biomass/graph.py
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| import os | ||
| import re | ||
| import warnings | ||
| from ast import Is |
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@formersbach from ast import Is Can you please remove this unused import?
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Weirdly this import was not added by me (at least not intentionally). I'll remove it, but do you have any idea where it might've come from?
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I guess it is from VScode auto-import when you type "Is". I sometimes face the same problem.
biomass/graph.py
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| def to_graph( | ||
| self, | ||
| save_path: str, | ||
| gviz_prog: str = "dot", | ||
| ): | ||
| """ | ||
| Constructs and draws a directed graph of the model using ode.py/reaction_network.py as text files. | ||
| """ |
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@formersbach It would be better to add Parameters and Examples section to docstring. I would like you to follow numpydoc style.
…o pass graphviz arguments
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Thanks @formersbach! I have updated docs and will soon merge your work into master. |
Will add support for graphic representation of biological model.
Requires graphviz program and pygraphviz package.
Minor changes to exec_model.py to make create_graph callable on model object.