Track Upstream Mothur Branch and Update Our Master Branch from That

[azmfaridee]

Our code-base has been forked from mothur code-base. Since then there has been numerous commits in the upstream but we have not been able to follow that up. This is because we are not tracking the upstream branch in our code-base.

Follow the tutorial at http://help.github.com/fork-a-repo/ and add upstream branch so that we can track newest changes made by the core developers and and update our code from that.

[azmfaridee]

Here are some of the things that we need to do to track the upstream code:

$ git remote add upstream https://github.com/mothur/mothur.git
$ git fetch upstream
$ git merge upstream/master

I'm getting some conflict right now. Here are the details of the conflict.

Abu-Zahers-MacBook:mothur abuzaher$ git merge upstream/master
Auto-merging uchime_src/usort.cpp
Auto-merging uchime_src/uchime_main.cpp
Auto-merging uchime_src/uc.h
Auto-merging uchime_src/myutils.cpp
CONFLICT (content): Merge conflict in uchime_src/myutils.cpp
Auto-merging uchime_src/globalalign2.cpp
Auto-merging uchime_src/addtargets2.cpp
Removing phylodiversity.h
Removing phylodiversity.cpp
Auto-merging makefile
Auto-merging consensus.h
Auto-merging consensus.cpp
Removing bootstrapsharedcommand.h
Removing bootstrapsharedcommand.cpp
Auto-merging Mothur.xcodeproj/project.pbxproj
CONFLICT (content): Merge conflict in Mothur.xcodeproj/project.pbxproj
Automatic merge failed; fix conflicts and then commit the result.

I'm trying to fix it right now.

[mothur-westcott]

If you are going to do any development with Xcode 4, it has a really nice gui interface for merging and resolving conflicts with git repositories.

[azmfaridee]

@mothur-westcott Thanks for the tip, I'd be using Xcode 4.3 in Lion, so that would definitely help a lot.

I managed to fix the conflict and merge the upstream changes in this commit.