Reproducible Research Course by Eric C. Anderson for (NOAA/SWFSC)

Conflicts, stashing, remotes

  • Goals for this lecture
    1. Help everyone get there core editor configured for git
    2. Have everyone create some merge conflicts and resolve them, finding that they really aren’t a big deal.
    3. Discuss git’s rules to avoid clobbering uncommitted work by checking out new branches and let everyone play around with stashing, git’s convenient way to store uncommitted work.
    4. Remote brances: learn how git interacts with remote repositories via remote branches. Let everyone set up their very own, distinct repository on GitHub.

Configuring your text editor

Git needs messages from you

  • When you make commits, git wants you to comment on them
  • If you don’t write a commit message, the commit gets aborted
  • Writing comit comments in RStudio is easy: there is a “commit message” box
  • When you are merging branches on the command line, git tries to load up a text editor.
    • Note that a text editor is any program used to edit text files. Microsoft Word is not a text editor…
  • On Mac: Popular Unix terminal text editors include emacs and vi or vim
    • These can seem mysterious to the unitiated.
  • On PC: did any people on PC’s have an awkward time writing or saving their commit messages?

What editor does git use?

  • You can configure it:
    • On my system, I can look at the git configurations in effect like this (in the shell)

      git config --list
      # which tells me this: C. Anderson
      difftool.twdiff.cmd=/usr/bin/twdiff --wait --resume $LOCAL $REMOTE
      mergetool.twdiff.cmd=/usr/bin/twdiff --wait --resume $LOCAL $REMOTE
  • There actually isn’t a core.editor in there, because git uses my Unix system definition:

    env | grep EDITOR
    # which gives:

What should you use?

  • In my opinion, the most hassle free terminal editor for newcomers is nano which should already be intsalled on OS X.
  • If you want a reasonable editor for git, on Mac, do this:

    git config --global core.editor nano
  • Then, when you find git asking you to edit a commit message, you get an editor that has hints about what to do.
    • Three steps to saving your commit message after editing it:
      1. ^X = control-x (to exit file)
      2. Y to save “Yes, save that thing”
      3. RETURN to choose the default name for the file. (Don’t change the name)
    • Note that your commit message can’t be empty (or git will abort the commit).

Don’t be afraid of merge conflicts

Conflicts happen

  • Git will report a merge conflict when merging two commits in which the same part of the same file has been modified.
  • What is meant by the same part of the same file
    • Same line? Same word? Same “paragraph”?, etc.

Class activity to explore conflicts

Here is what I did

  1. Create new RStudio project with a git repository and call it explore_conflict
  2. Create a new R file called three_lines.R and fill it with this:

    # Line 1
    # Line 2
    # Line 3
  3. commit that file. After committing you have a master branch.
  4. Immediately make some new branches:

    git branch a1
    git branch a3
    git branch a13
    git branch b2
  5. Then checkout each of those branches in turn and modify the file three-lines.R in them according to their names (add an a at the end of line 1 in a1, add an a at the end of lines 1 and 3 in a13, etc.), i.e. in a13 the file will look like:

    # Line 1 a
    # Line 2  
    # Line 3 a
    • After this it is easy to view all those branches in RStudio’s git History viewer.
  6. Now, we don’t want to modify these, but we want to see what we can merge with what else. So, checkout new branches like this:
    1. Can we merge b2 into a13 without a conflict?

      git checkout a13
      git checkout -b a13-and-b2
      git merge b2  # Lo and behold we get a conflict even though there no changes on the same lines
      • But, conflicts aren’t necessarily scary. Here is the run down.
        1. You get a message that looks like

          Auto-merging three_lines.R
          CONFLICT (content): Merge conflict in three_lines.R
          Automatic merge failed; fix conflicts and then commit the result.
        2. In RStudio’s git panel the files with conflicts appear orange, and the file has this in it:

          <<<<<<< HEAD
          # Line 1 a
          # Line 2
          # Line 3 a
          # Line 1
          # Line 2 b
          # Line 3
          >>>>>>> b2
          which shows you that year HEAD branch a13-and-b2 in this case, has the part above the ====== and the b2 has the part below the ======.
        3. To successfully merge these branches, all you need to do is modfify the file to your liking, stage it and commit it. Maybe it should look like:

          # Line 1 a
          # Line 2 b
          # Line 3 a
          Edit it to look like that and commit it.
        4. What if you get cold feet? At any point in the process before you actually commit the merge, if you do

          git merge --abort
          git will return your working directory the way it was before you tried doing the merge.
    2. How about a3 into a1?

      git checkout a1
      git checkout -b a1-with-a3
      git merge a3  # No conflicts!
    3. How about a3 into a2? (Conflict!) So, it appears that if you make a change on an adjacent line it gives you a conflict.
    4. How about if the same change is made in each file? Like a13 onto a1? Success!!
    5. How about we make a new branch off master called wrap-it and then add stuff to the top and the bottom of the file, but we don’t touch the three lines at all. Will we be able to merge it with b2 without conflicts?
      • Yes! Git is smart enough to recognize the three lines even though they are no longer the only three lines in the file!

When git doesn’t let me switch branches (or merge)

Git will typically not lot you clobber your working area

  • If your working directory is clean, you can switch branches or merge without git shrieking at you.
  • If you working directory is dirty, you might see this:

    2014-10-30 13:29 /explore_conflict/--% (wrap-it-and-b2) git checkout master
    error: Your local changes to the following files would be overwritten by checkout:
    Please, commit your changes or stash them before you can switch branches.
    2014-10-30 14:10 /explore_conflict/--% (wrap-it-and-b2) git merge a2
    error: Your local changes to the following files would be overwritten by merge:
    Please, commit your changes or stash them before you can merge.
  • Remember, a dirty state in your working directory means that there are changes to some files that have not been committed.
  • For a detailed discussion of when git will and won’t let you switch branches check out this link
  • Big Note: If uncommitted changes wouldn’t be clobbered by switching to a new branch, then that dirty state gets carried over to the branch you are switching to.

What can be done when you can’t switch branches

  • First, try to understand just which files will get clobbered.
  • Then you have the choice of:
    1. Discarding your changes (easiest to do in the RStudio Diff window)
    2. Committing your changes
    3. Stashing your changes.
  • Number 1 is fine if you are sure you want to toss your changes.
  • Number 2 is good if you really want to commit that work
  • If neither #1 or #2 are good for you, then #3 is a good choice.

What does stashing do?

  • Stashing saves the changes that have been made to the current branch (and the state of the index) AND then wipes them away to return your branch to a clean state.
  • Then you can switch branches, work on something else, and when you come back to the original branch you stashed on, you can bring those changes back up.
  • You can also learn other things about your stashes:

    git stash list
    git stash show
    git stash show -v
    git stash show stash@{1}  # to see stashes other than the most recent
    # and finally, if you want to bring your stashed work back to life you can do:
    git stash apply 
    # The above restores the last stash you made
    # This can restore earlier stashes
    git stash apply stash@{i}  # where i is 0, 1, 2, ... depending on which stash you want.

Applying stashes up on branches they weren’t stashed off of

  • This gets complicated. Not recommended for now.
  • If you have moved way on from where you stashed, you can do:

    git stash new-branch-name
    # OR
    git stash new-branch-name stash@{i}
    which will give you a whole new branch off of the branch you stashed off of, and all the changes on top.
    • Note: it also drops your stash from the list of stashes!

Remote branches

  • We will leave a full discussion of these points:
    • Fetch, Merge, Pull, Push.
    • Tracking branches until later.
  • Until then, let’s have everyone create their own repository on GitHub if there is time.
  1. Make a repository to put on GitHub (just make a new RStudio project with git version control)
  2. Make a commit on it.
  3. Go to the GitHub website and click the “+” button…and follow the instructions from there.
  4. Don’t let them add a README or LICENSE file.

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