opencobra / cobrapy

COBRApy is a package for constraint-based modeling of metabolic networks.
http://opencobra.github.io/cobrapy/
GNU General Public License v2.0
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gapfilling.ipynb bug fix #1331

Closed pablodig closed 1 year ago

pablodig commented 1 year ago

Hi, I noticed that the gapfilling.ipynb notebook in the documentation has an error in the second cell: First the reaction is not called correctly. I changed add_reaction() for add_reactions() which the correct way of calling it. Second, the argument in the add_reactions() function needs to be an iterable so I enclosed the reaction.copy() in []. Third, the cell needs to import cobra to work.

Finally, some of the output that I got in the following cells differ a little bit from what you have in the original notebook.

I hope you find these changes useful.

codecov-commenter commented 1 year ago

Codecov Report

Patch and project coverage have no change.

Comparison is base (c99fb7e) 83.80% compared to head (9a96a7a) 83.80%.

:exclamation: Current head 9a96a7a differs from pull request most recent head 9978b82. Consider uploading reports for the commit 9978b82 to get more accurate results

Additional details and impacted files ```diff @@ Coverage Diff @@ ## devel #1331 +/- ## ======================================= Coverage 83.80% 83.80% ======================================= Files 66 66 Lines 5495 5495 Branches 1256 1256 ======================================= Hits 4605 4605 Misses 573 573 Partials 317 317 ```

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cdiener commented 1 year ago

Perfect, thanks!

pablodig commented 1 year ago

Sure. Im happy to help. Great package by the way.