Introductory course on git and GitHub by Chris Grandin and Andrew Edwards.
This course motivated parts of the stand-alone e-book Building Skills in Quantitative Biology. The book is written to be worked through alone, whereas these materials are for a taught workshop.
Departure Bay Room A/B, Vancouver Island Conference Centre.
Tuesday November 27, 2018.
Basically, git works on your computer and saves all versions of documents as you continually work on them ('version control'). GitHub is a copy of everything on a website that allows users to share code with each other.
See the git-course-setup.pdf file that we email to you.
You will then have all the files from this git-course repository on your computer.
From the GitHub glossary: "A repository is the most basic element of GitHub. They're easiest to imagine as a project's folder. A repository contains all of the project files (including documentation), and stores each file's revision history. Repositories can have multiple collaborators and can be either public or private."
beamer/ - our slides for the course, created using beamer (which is an alternative to Powerpoint). To build the slides (with Latex installed) click on the .bat file in each subdirectory.
beamer/git-course.sty is the common style file that is used for each set of slides.
In the order to be presented, the subdirectories are:
beamer/git-setup/ - instructions for setting up prior to course (filenames ending in -17 are those from our two-day course in 2017).
beamer/git-outline/ - outline of course
beamer/git-motivation/ - motivation for using Git
beamer/git-intro/ - introduction including some exercises (day 1)
beamer/git-advanced/ - more advanced understanding (day 2)
beamer/hake-example/ - simple example of using knitr
beamer/git-forRworkshop/ - stealing slides from other presentations to give a background talk for PBS R workshop on 28th June 2017.
exercise-files/ - contains files needed for exercises
content/ - contains .gitconfig needed for setup
.gitignore - files to be ignored by Git
On the repository's GitHub page, click 'Fork'. This puts a copy of the repository under your username on GitHub.
Navigate to your GitHub version of the repo.
To clone it onto your local machine, open your git shell, check you are in C:/github or wherever you are putting your GitHub work (remember no spaces in folder names), and type :
git clone https://github.com/YOUR-GITHUB-USER-NAME/REPO-NAME
(just copy and paste the http:// address from your web browser).
To start your own repository just click New Repository on your GitHub home page, and do the above git clone command.
The git clone command creates a new folder that is automatically given the name of the repository.
Once you have got going with a repository, all you really need are:
git s <View status of the repository>
git add FILENAME <One-time command to add FILENAME (including path) to the
list of files being tracked by git>
git com "MESSAGE" <Commit changes with descriptive MESSAGE>
git push <Push your changes to GitHub>
For collaborating you need:
git remote add NAME URL <One-time command to enable fetching and merging from
NAME'S GitHub repo at URL, e.g:>
git remote add pbs-assess https://github.com/pbs-assess/git-course
<The first pbs-assess is an alias - could be anything>
git r <Look at all remote data sources (URLs)>
git fetch pbs-assess <Fetch changes that pbs-assess has made>
git diff ..origin/master <Compare your local repo with the fetched version
(useful before merging; difftool also works)>
git merge pbs-assess/master <Merge the fetched changes with your local repository>
git merge p<TAB> <This will auto-complete the above command (if unique)>
git push <Remember to push after doing a merge, then check Network Graph>
Other useful commands are:
git help <command> <Open a help page in your browser for the command>
git s -sb <View status of the repository in very concise form>
git s -u <Show all untracked files, not just directories>
git rm --cached FILENAME <Remove FILENAME from the git repo, but not from local directory>
git rm FILENAME <Remove FILENAME from the git repo AND from local directory>
git difftool <options> <Compare changes using difftool; options can be branches,
other repos you have fetched but not merged, or leave blank
to compare to latest commit>
git log <View commit log>
git help <List git commands>
git cb BRANCH-NAME <Create and switch to branch BRANCH-NAME>
git co BRANCH-NAME <Checkout (switch to) branch BRANCH-NAME>
git branch <List all branches>
git branch -d NAME <Safely delete the branch called NAME>
git branch -D NAME <Forcibly delete the branch called NAME>
git push origin --delete NAME <Delete the branch NAME from the remote>
git reset --merge ORIG_HEAD <Undo a merge
(or maybe any commit?) that you haven't pushed*>
*See here for more details on git reset - the above command was one of the listed answers (and I think works for other commits).
git s git status
git com "MESSAGE" git commit -a -m "MESSAGE"
git r git remote -v
git cb BRANCH-NAME git checkout -b BRANCH-NAME
git co BRANCH-NAME git checkout BRANCH-NAME
When there is a conflict you will get a message. Then open the relevant file in a text editor, and you will see
<<<<<<< HEAD
Line(s) of text/code which are currently in your file.
=======
Line(s) of text/code which are trying to merge in, but conflict.
>>>>>>> BRANCH-NAME
where BRANCH-NAME is the name of the branch (or remote) you are trying to merge in from the previously-issued command:
git merge BRANCH-NAME
Choose one of the line(s) of text/code to keep, or edit the line(s) to be something else entirely.
Then remove the bracketing and separation lines
<<<...
>>>...
=======
Once you are done fixing each conflicted file, you need to
git add FILENAME
to confirm that's the one you want (that step is not completely obvious), then commit and push.
See https://help.github.com/articles/resolving-a-merge-conflict-from-the-command-line/ for an example.
Generally we try and work on different files so that there are no conflicts when we merge.
For example, we migrated this repo from cgrandin/git-course to pbs-assess/git-course. Then (if you already have the repo on our computer, but fetched from our forked version), you have to:
git remote rm origin
git remote add origin https://github.com/pbs-assess/git-course
Then the first time you pull:
git pull origin master
and the first time you push (to origin, if you are a member of pbs-assess):
git push --set-upstream origin master
A readable introduction to the general ideas of 'version control' is the manuscript Good Enough Practices in Scientific Computing.
We (Chris and Andy) are willing to put another course if someone can do the logistics. Basically:
- Vancouver Island Conference Centre (VCC), Departure Bay Rooms A and B for two days (we need to be on a wireless network);
- Set up in a U-shape configuration with space for about 25 people, and about 20 attended which worked well;
- We brought two projectors (ARRAD one and the one from Gloria's office, check the connections as one needs an HDMI cable and one has no HDMI connection);
- We brought a box of power bars from Groundfish (Malcolm's office) for everyone to plug into, plus a box of about six extension cords - there are plugs in the floors of the rooms, but I think we used some of the power bars and cords;
- We had VICC set up two projector screens ("Client's Own LCD Projector Package", includes audio visual cart and long VGA cable to the tables);
- Total bill from VICC was $856.80;
- We send out the git-course-setup.pdf file a couple of weeks beforehand - almost everyone had everything working fine so we could get going fairly quickly.