Tutorial modeled on this Plos tutorial
Ensure that you have a valid account and that you know your username and the name that you have associated with the account.
Once you have done that please add your github username to this google sheet so that I can add you to our collaborative repository for step 6.
1. Log in to google cloud console
In the upper right corner there is a small box with ">_" click on that and activate the cloud shell.
On the google cloud console command line, run the following commands. For the first part of this tutorial we are going to pretend that we are creating a repository for storing notes in a markdown file. This is a really great way of keeping a lab notebook that ensures everything is dated, and that it is stored remotely so if something happens to your laptop you don't lose your notes.
Now make a directory and a notes file.
mkdir notes
cd notes/
nano Labnotebook.md
Copy the text below into Labnotebook.md. We are using a markup language called Markdown for this purpose. This is the language we use to create those neatly formatted README pages you may have seen on github (and this tutorial). For more info on markdown here is an intro you can look at later for formatting your own markdown files.
## 9/18/23
BME Bootcamp git tutorial
git config --global user.name "Firstname Lastname"
git config --global user.email "user@domain"
git init
You should see the following message
Initialized empty Git repository in /home/hailloucks/notes/.git/
Then run
git add Labnotebook.md
git commit -m "first commit"
git branch -M main
Now go back to github on your web browser and click the green "New" button to create a new repository.
Set the repository name to be the same as the name of the directory you executed git init in, which should be notes
I also recomend setting this to private as you likely want your research notes to not be published publically.
Click "Create Repository"
Now copy the HTTPS link for the repo you've just created and sub it in for the URL in the command below
git remote add origin https://github.com/username/notes.git
For the next step you will need to be logged in to your github account. You can do this by running
gh auth login
And select GitHub.com, HTTPS, Yes, and whatever method you would like to login with. Login with the web browser might be easier, and then follow the instructions.
This will save your login information so that you don't have to provide your credentials every time you push to a repo. If you don't want to save your credentials you can also create a personal access token which you provide every time you log in more information here
Now we are finally ready to push our file to our new repo!
git push -u origin main
Now refresh your github repo in the browser, you should be able to see your file in the browser and look at it.
Alright now lets make some changes to our existing lab notebook and add a new file to our repository. Back on the google command line open up your Lab notebook with nano and add some notes.
Let's also create a new file for noting useful bash commands we might want to reference in the future. Let's create a file called Bashtricks.md and add some of our bash commands to it to reference later.
nano Bashtricks.md
Here are a few commands I've found useful you can copy in to the file - you can add your own as you work
### view total disk space used by directories in current directory
du -sh ./*
### To time a script
`time Script.sh`
## Create a Screen with name
screen -S [name]
## reconect to a screen
screen -r [name]
## git basics
git add filename
git commit -m "Message about commit"
git push
Now that we have created a new file we can do the same process of adding, committing, and pushing it. You can check that state of your working directory with git status, which will show that your local repo is 1 commit ahead of your github repo.
git add Bashtricks.md
git commit -m "Adding bash tricks file"
git status
git push
Once again if you check the web interface you should see the updated repository with your new file. The process will be the same whether you've created a new file or just want to commit some changes
So far you've created and made changes in your own personal repository. This is great to be familiar with for keeping your own files in order, but is not the only use for version control. One of the most powerful use cases for git is when you have many people working on a project who all are contributing to a code base. This is where things can get tricky, as you want to be able to make changes without messing up code that someone else is working on. Here is more information on creating a remote branch.
We are going to be working on this repository https://github.com/shanksc/BootcampGitTutorial where we will clone the repo, create a new branch, then push our changes on the new branch.
Before you can push to this repo you will need to accept my invitation to join the repo. Check your notifications on github and accept the invitation to edit the BootcampGitTutorial repo.
cd
gh repo clone shanksc/BootcampGitTutorial
cd BootcampGitTutorial
# create a new branch with your name
git checkout -b Namebranch
# now you create a file with your name and add some text in the file
nano myname.txt
git add myname.txt
git commit -m "My Name"
# now push to the branch that you created
git push -u origin Namebranch
Now if you look back at github in your browser you should be able to find your branch. In the web interface click on your branch and then "New pull request" to create a pull request. Add some notes about the time and context, then. When you are working collaboratively and are ready to merge your code in to the main code base this is how you can start that process. Now the owner of the repo can review and merge your code if there are no issues. The pull request is also an opportunity for collaborators to view your code, so they will likely provide feedback on the readability and style of your changes.