This video shows a basic workflow using branches.
In the lecture, I cautioned against using branches when you are beginning with Git. Even through I work on many Git repositories and develop public R packages, it is rare that I need to use branches. Normal scientific workflow does not involve branches and IMO most scientists won’t gain much by adding that to their workflow. The GitHub features I talked about so far are things that are already part of our workflow (taking notes on what we are doing, saving copies along the way, reviewing work with collaborators, sharing our work) but Git/GitHub allows us to do it more efficiently, better and faster.
I do use branches regularly with certain R package projects and when I use them, it is in very specific ways
gh-pages
branch to serve that up.But usually other features of GitHub are sufficient and more appropriate.
That said, they are definitely helpful in certain situations. Before you start working with branches make sure think through some of the aspects of how they affect your file system and how that will affect your current workflow and the workflow of any users of your repository.
Switching branches changes your file system state. A branch is
not a separate ‘space’. When you switch branches, you tell Git to change
your files to reflect the branch state. Do you have any code that
‘sources’ the folder/repository with branches? For example, do you have
any code in other folders with lines like
source("Documents/myrepowithbranches/plot.R"). Do you do
things like that in practice? That kind of workflow will cause problems
because they will reference the branch state when you switch branches.
Your file system state will remain in the branch state until you switch
back to the main branch.
File time stamps. Video Because switching branches on your computer causes Git to change your file system to that branch state, the file time stamps of any files that differ between branches will update to the time that you switched branches. It is possible to make Git change the file time stamps back to the last modification time. This video shows how.
Are you working in a team with users who are not Git-saavy but will need to access branches? If you only have them access branches on GitHub, then it is probably fine but if you will have them switches branches using RStudio or GitHub Desktop on their computer then they are likely to get confused when they accidentally leave their file system in a branch state.
Pulling and Pushing work a bit differently when you have branches. When you do a pull from GitHub, you will get the changes across all branches, but when you push, the push is branch specific. So if you have changes on the main branch and another branch, you need to push from main then switch to the other branch(es) and push from them too. Video
Are you using a cloud backup system that syncs across devices/computers? Dropbox and iCloud are examples. Syncing repositories outside of Git (so not using the push/pull system) can definitely cause problems especially if you are using branches. If your backup system is linear, one computer being backed up, with no syncing across devices, and you are not working off-line then you are probably ok.
How to I clone just one branch? For this you will use Git from
the command line. Open a terminal window, change to the directory where
you keep repositories (e.g. cd Documents/GitHub). Then
issue the command
git clone -b <branchname> --single-branch <remote-repo-url>
You can add the name of the folder optionally at the end. So the command I issued in the video was
git clone -b test --single-branch https://github.com/eeholmes/Week2 Week2-testHere’s a screen recording of this Video.
Here is the post-checkout code used in this video to show you how to fix time stamps when you switch branches.
#!/bin/sh -e
OS=${OS:-`uname`}
if [ "$OS" = 'Darwin' ]; then
get_touch_time() {
date -r ${unixtime} '+%Y%m%d%H%M.%S'
}
else
get_touch_time() {
date -d @${unixtime} '+%Y%m%d%H%M.%S'
}
fi
# all git files
git ls-tree -r --name-only HEAD > .git_ls-tree_r_name-only_HEAD
# modified git files
git diff --name-only > .git_diff_name-only
# only restore files not modified
comm -2 -3 .git_ls-tree_r_name-only_HEAD .git_diff_name-only | while read filename; do
unixtime=$(git log -1 --format="%at" -- "${filename}")
touchtime=$(get_touch_time)
echo ${touchtime} "${filename}"
touch -t ${touchtime} "${filename}"
done
rm .git_ls-tree_r_name-only_HEAD .git_diff_name-onlyI want to link RStudio to Git, but I am getting an error that RStudio cannot find Git
Open RStudio. Go to Tools > Global Options… > Git/SVN . The paste in the location of the git.exe file.
On a Mac? location is usr/bin/git
Finding that location if you are on a PC can be onerous. First make
sure you can see hidden folders. In a finder window, you click View and
make sure the hidden files checkbox is checked. Then here are some ideas
of where to find git.exe. Note you might not see
.exe . You might only see git. It depends if
you have show file endings selected in preferences.
If you only installed GitHub Desktop, look here
C:\Users\UserName\AppData\Local\GitHubDesktop\app-2.8.3\resources\app\git\cmd\git.exeYou have to change app-x.x.x to whatever version you have.
If you installed Git for Windows, look in these places.
C:/Program Files/Git/bin/git.exeIf you installed Git for Windows locally, look here
C:\Users\UserName\AppData\Local\Programs\Git\bin\git.exe