git-ing the course materials

We are maintaining course material using the version control software git, and distributing it through github. We’re doing this for our own sake (git makes our lives much easier!) but this also makes it easy for you to get the course material (and our updates), and to keep them updated. You can download files individuals from github’s web interface. But we don’t suggest that! “Gitting” them all together will give you a little bit of practice using git; if you don’t already, we encourage you to get to know it well.

Here is the basic procedure for obtaining the course material and keeping it updated. After you have git installed, in a console…

1. Go to the directory you want to put this course’s directory in, and run

    git clone https://github.com/UO-Biostats/UO_ABS
   

2. That should have created a new directory, called UO_ABS/ with everything in it. Check, by pointing your web browser to the subdirectory UO_ABS/CLASS_MATERIALS/Lectures and opening Week_01_Lecture.slides.html.

3. When we update the material, you can update your local copy by running

    git fetch
    git merge origin/master
   

It’s that easy!

But what if I want to take notes on the slides?

Well, there’s one more thing. If you change the files then the next time you try to get our updates, git will complain that your changes conflict with ours. So, we recommend that if you want to edit one of the files we have, to first make a copy of it, and edit the copy. For instance, you could copy Week_01_Lecture.Rmd to Week_01_Lecture_NOTES.Rmd, and then edit the NOTES version. git will ignore your new file, unless you ask it not to.

But what if I already did edit some of the files?

If you do modify some of the files, when you try to merge you could get an error like this:

error: Your local changes to the following files would be overwritten by checkout:
    (names of some files you changed)
Please commit your changes or stash them before you switch branches.
Aborting

To deal with this, you should (1) get rid of your local changes, and then (2) merge away. First, you should probably do

    git status

to see what’s changed. The message this prints out even gives you a nice reminder of how to remove any local changes: say you edited Week_01_Lecture.Rmd but didn’t mean to. You could make those changes go away by doing

    git checkout -- Week_01_Lecture.Rmd

This makes the changes go away permanently, so make sure if you actually wanted to keep them, that you first copy the file elsewhere. Another way to make all your changes go away at once is to do

    git stash

This is reversible - doing git stash pop will bring them back… if nothing else changes in the meantime.

After you make the local changes dissappear, doing git status should tell you

nothing added to commit but untracked files present (use "git add" to track)

(Maybe there’s some “untracked files”; those are OK.) after which you can finally

    git merge origin/master