Re: [AMBER-Developers] updating Amber.lyx

From: B. Lachele Foley <>
Date: Tue, 18 Mar 2014 20:57:40 +0000

I think you can edit elsewhere if you do this. If this is wrong, I need to know, so please say. :-)

1. Make a branch for your changes. Don't pull from main into that branch until you are finished with the changes. The latter is important.

2. When done, be sure you have the branch checked out and copy your file over to it. Commit the file(s). (use "git status" first to be sure all changes committed are expected.)

3. Switch back to the master branch and pull the updates from the main AMBER repo into master.

4. Merge your changes from the branch into master.

This way, git knows that the work in the branch is from an older common ancestor, and it will do a more intelligent merge -- or ask you to deal with conflicts.

:-) Lachele

Dr. B. Lachele Foley
Complex Carbohydrate Research Center
The University of Georgia
Athens, GA USA

From: David A Case <>
Sent: Tuesday, March 18, 2014 4:44 PM
To: homeyer
Subject: Re: [AMBER-Developers] updating Amber.lyx

On Tue, Mar 18, 2014, Nadine Homeyer wrote:

> As I edited Amber.lyx under windows I had to copy it back to Linux. Does
> copying files into git from another location generally overwrite the
> changes others did in these files?

Yes, exactly. Git, or any other revision control program, has no way of
knowing whether you *intended* to reverse the changes that were made during
the time you were editing things in Windows, or whether this was an
inadvertent change.

It is the copying of files from Windows (or any other place outside of the
repository) into the git repository that does the damage. You really have to
either set up git on Windows (not hard at all), or do your editing on the
Linux machine. Then, if someone else updates the file while you are editing
it, git will recognize that and give an error message.

I'm cc-ing this to the Amber developers' list, so others won't make a similar
error. And, perhaps others on the list can give a clearer explanation of the
problem, or knows a pointer to a web site that goes over this issue. It's
actually a very common mistake, so don't feel bad. No real harm was done.


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Received on Tue Mar 18 2014 - 14:00:03 PDT
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