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Showing progress during flux variability analysis. #1279

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achillesrasquinha opened this issue Sep 19, 2022 · 3 comments · May be fixed by #1283
Open
1 task

Showing progress during flux variability analysis. #1279

achillesrasquinha opened this issue Sep 19, 2022 · 3 comments · May be fixed by #1283

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@achillesrasquinha
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achillesrasquinha commented Sep 19, 2022

Checklist

Is your feature related to a problem? Please describe it.

Describe the solution you would like.

The currently implementation of FVA within cobrapy is generally slow (definitely improved using the processes flag. Would be nice to see the current progress since the program sometimes seems stalled for large networks. What say? I was planning on using tqdm within variability.py at line 247.

e.g.

Screen Shot 2022-09-19 at 2 57 36 PM

Describe alternatives you considered

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@cdiener
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cdiener commented Sep 19, 2022

Good idea. We already have rich as a dependency, so would be better to use rich.progress.track for that. There should also be a toggle to turn that on and off, since some workloads may run an FVA for thousands of models and may not want a progress bar for each iteration. Or one could couple it to the logging level and only show it on INFO...

@achillesrasquinha
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I'll do that accordingly.

@achillesrasquinha achillesrasquinha linked a pull request Sep 20, 2022 that will close this issue
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@achillesrasquinha
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@cdiener Done. PF Pull Request.

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