Cleanup of JSBML's history completed

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Andreas Dräger

Sep 17, 2018, 9:28:59 AM9/17/18
Dear all,

As announced last week, the git history of the JSBML repository has been thoroughly cleaned up. In this process, more than 500 duplicate commits were merged and 5 contributors could be linked to their commits.

To minimize the necessity of future cleanup operations, we like to ask all those of you who contribute to JSBML or want to contribute in the future, so please make sure that your name and e-mail address are correctly configured in git. There are two ways of achieving that:

1) You can define your account just for use in JSBML with this command:

git commit --amend --author="John M. Doe <>"

where “John M. Doe” is your full name and the given e-mail address is the one that you used to register in GitHub. Please make sure to execute the command above using the identical name and e-mail address as it appears in the list you obtain when executing

git log | grep Author: | sort | uniq

2) You can also use the 'git config' command to set the value properly for all repositories you contribute to:

git config --global ""
git config --global "John M. Doe"

The '--global' option can be removed if you have different GitHub usernames.

Now, in case that you have already cloned JSBML and want to continue working with the latest version from GitHub, you need to execute

git pull --rebase

If you have local changes or uncommitted modification, you need to use 'git stash' before and after as I indicated earlier in this discussion.

You have to rebase to avoid problems and don't push anything if you are not sure. There should be nothing to push after executing rebase.

If you have any further questions, don't hesitate to ask.

With best regards

Dr. Andreas Draeger
Assistant Professor
University of Tübingen
Center for Bioinformatics Tübingen (ZBIT)
Computational Systems Biology of Infection and Antimicrobial-Resistant Pathogens
Sand 14 · Office #C320 · 72076 Tübingen · Germany
Phone: +49-7071-29-70459 · Fax: +49-7071-29-5152
Web: · Twitter: @dr_drae

Michael Hucka

Sep 30, 2018, 10:49:22 PM9/30/18
Thank you for doing this great cleanup effort!

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