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https://github.com/pbs-assess/git-course
A repository for teaching the fundamentals of GIT
https://github.com/pbs-assess/git-course
Last synced: 18 days ago
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A repository for teaching the fundamentals of GIT
- Host: GitHub
- URL: https://github.com/pbs-assess/git-course
- Owner: pbs-assess
- Created: 2017-05-03T19:14:23.000Z (over 7 years ago)
- Default Branch: master
- Last Pushed: 2024-09-04T18:08:39.000Z (5 months ago)
- Last Synced: 2024-11-10T13:28:07.748Z (3 months ago)
- Language: TeX
- Homepage:
- Size: 1.97 MB
- Stars: 5
- Watchers: 4
- Forks: 80
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
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README
# git-course
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](http://quantitative-biology.ca). 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.
## Setting up
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](https://help.github.com/articles/github-glossary/#repository): "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."
## Contents of repository
**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
## Summary of most common commands
### To use someone else's repository or to create your own
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.
### The basic commands we use
[//]: # (https://mislav.net/2010/07/git-tips/)
Once you have got going with a repository, all you really need are:
git s
git add FILENAME
git com "MESSAGE"
git push
For collaborating you need:
git remote add NAME URL
git remote add pbs-assess https://github.com/pbs-assess/git-course
git r
git fetch pbs-assess
git diff ..origin/master
git merge pbs-assess/master
git merge p
git push
Other useful commands are:
git help
git s -sb
git s -u
git rm --cached FILENAME
git rm FILENAME
git difftool
git log
git help
git cb BRANCH-NAME
git co BRANCH-NAME
git branch
git branch -d NAME
git branch -D NAME
git push origin --delete NAME
git reset --merge ORIG_HEAD
*See [here](https://stackoverflow.com/questions/2389361/undo-a-git-merge-that-hasnt-been-pushed-yet) for more details on **git reset** - the above command was one of the listed answers (and I think works for other commits).
### Some of those are aliases (from your .gitconfig file):
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
### Fixing a conflict
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 for an example.
Generally we try and work on different files so that there are no conflicts when we merge.
### If the GitHub repository changes user
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
```
## General introduction
A readable introduction to the general ideas of 'version control' is the manuscript Good Enough Practices in Scientific Computing.
## Putting on a course
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.