cobrapy icon indicating copy to clipboard operation
cobrapy copied to clipboard

Showing progress during flux variability analysis.

Open achillesrasquinha opened this issue 2 years ago • 3 comments

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

Additional context

achillesrasquinha avatar Sep 19 '22 19:09 achillesrasquinha

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...

cdiener avatar Sep 19 '22 23:09 cdiener

I'll do that accordingly.

achillesrasquinha avatar Sep 20 '22 14:09 achillesrasquinha

@cdiener Done. PF Pull Request.

achillesrasquinha avatar Sep 21 '22 01:09 achillesrasquinha