Issue updating COBRA Toolbox from within MATLAB

[Bhushan Dhamale]

After initializing COBRA Toolbox using initCobraToolbox, I did updateCobraToolbox() and got the following output:
 > Checking for available updates ...
 > There are 60 new commit(s) on <master> and 0 new commit(s) on <develop> [70b700 @ master]
 > The COBRA Toolbox cannot be updated as you have unstaged files. Commits should only be made in your local and cloned fork.

Please suggest me a fix to this.

[Thomas Pfau]

Hello Bhushan,

This happens, if you modify files in your local cobra toolbox. Since we do not want people loosing modifications, the update function stops if it notices changed files in the cobra folder.

Now, there are a few options:

1. delete your current version and reinstall the toolbox as described in the documentation.

2. go to a command line (cmd on windows, any shell on unix/mac
navigate to the folder where your cobra toolbox is located.
type:
git diff

This will show you all files in your toolbox which were modified locally. If there is nothing you want to keep, type:

git stash

This will remove all modification you have made.

If there are modifications you want to keep, I strongly suggest to use the COBRA toolbox devtools (https://github.com/opencobra/MATLAB.devTools) and either commit the changes to the toolbox or create a local branch with these changes.

Best

Thomas

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[Bhushan Dhamale]

That fixed it. Thank you Thomas.