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A selection of commands

Check git commit status

git status

See all the commits

git log

Which files are tracked

git ls-files

Remove files from repo

git rm file.txt

git commit -m "remove file.txt"

Move files within or from repo

git mv file.txt ~

git commit -m "file.txt moved to home-dir"

Stash and drop changes when conflict between versions

git stash save --keep-index

A general workflow

  1. Fork a repository (e.g. music.features from the gallantlab organization into fatmai/music.features)

  2. Create a new branch for each logically connected work unit you will change

    git checkout -b <branch-name>

  3. Do whatever changes you want to make in this branch. Make several commits.

  4. Push all the changes to your github repository e.g. fatmai

    git push fatmai <branch-name>

  5. Make a pull request on github

CAUTION

Everything that can go wrong should come here.

Examine a pull request without merging it

  1. Remote add the repository if not yet done.

    git remote add fatmai  https://github.com/fatmai/music.features.git

  2. Fetch all data (don't merge!)

    git fetch fatmai

  3. Check if fetch worked

    git branch -v -a

  4. Checkout the remote repositories branch

    git checkout fatmai/branchname

Sync a fork with the upstream

  1. Fetch the branches and their commits from the upstream.

    git fetch upstream

  2. Checkout your fork's local master branch

    git checkout master

  3. Bring your fork's master branch into sync with the upstream repository. Merge changes from upstream/master into your local master branch.

    git merge upstream/master

DEALING WITH Changing the Repositories owner

Scenario:

I changed the github repository "music.features" under the user fatmai to be under the organisation gallantlab. Subsequently on github, I forked the gallantlab/music.features repository to fatmai/music.features. These changes now need to be made effective in the local machines that already had a clone from the fatmai/music.features repository.

  • First check what remote repositories you have access to

     $ git remote -v
 
 origin	https://github.com/fatmai/music.features.git (fetch)
 origin	https://github.com/fatmai/music.features.git (push)

  • Remove this local repository that is pointing to nirvana

     $ git remote rm origin

  • Add the new repository under gallantlab organization as the origin remote repository

     $ git remote add origin https://github.com/gallantlab/music.features.git

  • Add the new repository under fatmai organization as the fatmai remote repository

     $ git remote add fatmai https://github.com/fatmai/music.features.git

  • Check the remote repositories again

     $ git remote -v

 fatmai	https://github.com/fatmai/music.features.git (fetch)
 fatmai	https://github.com/fatmai/music.features.git (push)
 origin	https://github.com/gallantlab/music.features.git (fetch)
 origin	https://github.com/gallantlab/music.features.git (push)

  • One last complain: Pull request from the master branch will result in the following

     $ git pull
 
 From https://github.com/gallantlab/music.features
 * [new branch]      master     -> origin/master
 * [new branch]      test_fixes -> origin/test_fixes
 There is no tracking information for the current branch.
 Please specify which branch you want to merge with.
 See git-pull(1) for details

 git pull <remote> <branch>

 If you wish to set tracking information for this branch you can do so with:

 git branch --set-upstream master <remote>/<branch>

  • Tell your local git which repositories the branches belong to

     $ git branch --set-upstream master origin/master

  • this should work now:

     $ git pull

A solution to "Your branch is X commits ahead"

Scenario: You made changes in your local master copy but did not push them. (You can compare the git logs between your local and remote branch to see what has not been commited.) There are different solutions:

  • If you want to keep these commits, you can push your local changes to the remote repository:

     $ git push origin assuming origin is your remote

  • If you don't want to keep these changes then remove them or reset your local master to the state on remote by doing:

     $ git reset --hard origin/master

How to avoid this message in the future:

  • In general your remote master repository should be the clean repository and the local master repository a copy of the remote one.

DEALING WITH Reference has invalid format 'refs/heads/master'

Schenario: This is usually caused when you are using a cloud service (e.g. dropbox) to store your data.

The solution is from this stackoverflow link

  • Go to your repo

     $ cd my_repo

  • Search for the conflicted files and delete them

     $ find . -type f -name "* conflicted copy*" -exec rm -f {} \;

  • Remove all "conflicted" references from git's packed-refs file

     $ awk '!/conflicted/' .git/packed-refs > temp && mv temp .git/packed-refs

DEALING WITH SWC Pull requests

  • Create your own change-whatever branch

     git checkot -b change-whatever

  • Check what remote branches you have access

     git remote -v

  • Add remote upstream swcarpentery/shell-novice branch

     git remote add upstream https://github.com/swcarpentry/shell-novice.git

  • Now you should be able to see https://github.com/swcarpentry/shell-novice.git as upstream when you do

     git remote -v

  • Pull changes from swcarpentery/shell-novice, which is your upstream. You want to be up-to-date before moving forward.

     git pull upstream gh-pages

  • Make your changes *

     vi 06-find.md

  • Commit your changes. Commit them line by line and push after each commit.

     git commit -am "Comment from @r-gaia-cs. Adds backticks to line 116"

  • Push to origin branch gh-pages

  •  git push origin gh-pages

    ==> Now when you go on github the open issue will be gone. So if there are many comments to one issue, first clean everything. make commits to each separately and then when you have finalized push it to the origin branch.

Creating/adding a new SWC lesson for a workshop

  • Fork the SWC workshop github page (e.g. the workshop 2015-08-16-ucdavis-wise) in your github

  • Clone your forked version of the SWC workshop github page (e.g. the workshop 2015-08-16-ucdavis-wise)

     git clone https://github.com/fatmai/2015-08-16-ucdavis-wise

  • Create your own change-whatever branch

     git checkot -b change-whatever

  • Check what remote branches you have access

     git remote -v

  • Add remote upstream workshop repository

     git remote add upstream https://github.com/camillescott/2015-08-16-ucdavis-wise.git

  • Now you should be able to see the workshop repository as upstream when you do

     git remote -v

  • Pull changes from the workshop repository, which is your upstream. You want to be up-to-date before moving forward.

     git pull upstream gh-pages

  • Make your changes *

     vi 06-find.md

  • Commit your changes. Commit them line by line and push after each commit.

     git commit -am "New excercise added."

  • Push to origin branch gh-pages

     git push origin gh-pages

    ==> Now when you go on your own github you will have an option to create a Pull request against the workshop repository. Push that button to create a Pull request and wait for the lead instructor to merge it.