Content from Automated Version Control


Last updated on 2025-05-22 | Edit this page

Estimated time: 5 minutes

Overview

Questions

  • What is version control and why should I use it?

Objectives

  • Understand the benefits of an automated version control system.
  • Understand the basics of how automated version control systems work.

We’ll start by exploring how version control can be used to keep track of what one person did and when. Even if you aren’t collaborating with other people, automated version control is much better than this situation:

Comic: a PhD student sends "FINAL.doc" to their supervisor, but after several increasingly intense and frustrating rounds of comments and revisions they end up with a file named "FINAL_rev.22.comments49.corrections.10.#@$%WHYDIDCOMETOGRADSCHOOL????.doc"
“notFinal.doc” by Jorge Cham, https://www.phdcomics.com

We’ve all been in this situation before: it seems unnecessary to have multiple nearly-identical versions of the same document. Some word processors let us deal with this a little better, such as Microsoft Word’s Track Changes, Google Docs’ version history, or LibreOffice’s Recording and Displaying Changes.

Version control systems start with a base version of the document and then record changes you make each step of the way. You can think of it as a recording of your progress: you can rewind to start at the base document and play back each change you made, eventually arriving at your more recent version.

Changes Are Saved Sequentially

Once you think of changes as separate from the document itself, you can then think about “playing back” different sets of changes on the base document, ultimately resulting in different versions of that document. For example, two users can make independent sets of changes on the same document.

Different Versions Can be Saved

Unless multiple users make changes to the same section of the document - a conflict - you can incorporate two sets of changes into the same base document.

Multiple Versions Can be Merged

A version control system is a tool that keeps track of these changes for us, effectively creating different versions of our files. It allows us to decide which changes will be made to the next version (each record of these changes is called a commit), and keeps useful metadata about them. The complete history of commits for a particular project and their metadata make up a repository. Repositories can be kept in sync across different computers, facilitating collaboration among different people.

Automated version control systems are nothing new. Tools like RCS, CVS, or Subversion have been around since the early 1980s and are used by many large companies. However, many of these are now considered legacy systems (i.e., outdated) due to various limitations in their capabilities. More modern systems, such as Git and Mercurial, are distributed, meaning that they do not need a centralized server to host the repository. These modern systems also include powerful merging tools that make it possible for multiple authors to work on the same files concurrently.

Paper Writing

  • Imagine you drafted an excellent paragraph for a paper you are writing, but later ruin it. How would you retrieve the excellent version of your conclusion? Is it even possible?

  • Imagine you have 5 co-authors. How would you manage the changes and comments they make to your paper? If you use LibreOffice Writer or Microsoft Word, what happens if you accept changes made using the Track Changes option? Do you have a history of those changes?

  • Recovering the excellent version is only possible if you created a copy of the old version of the paper. The danger of losing good versions often leads to the problematic workflow illustrated in the PhD Comics cartoon at the top of this page.

  • Collaborative writing with traditional word processors is cumbersome. Either every collaborator has to work on a document sequentially (slowing down the process of writing), or you have to send out a version to all collaborators and manually merge their comments into your document. The ‘track changes’ or ‘record changes’ option can highlight changes for you and simplifies merging, but as soon as you accept changes you will lose their history. You will then no longer know who suggested that change, why it was suggested, or when it was merged into the rest of the document. Even online word processors like Google Docs or Microsoft Office Online do not fully resolve these problems.

Key Points

  • Version control is like an unlimited ‘undo’.
  • Version control also allows many people to work in parallel.

Content from Setting Up Git


Last updated on 2025-05-22 | Edit this page

Estimated time: 10 minutes

Overview

Questions

  • How do I get set up to use Git?

Objectives

  • Configure git the first time it is used on a computer.
  • Understand the meaning of the --global configuration flag.

There are no slides for this episode. Explain what a command line is, why it is useful, and why we use it in this workshop. Participants are often new to the command line and don’t get why we not use a git gui. Only focus on the bare essentials for setting up git. We shall use nano editor so that everyone is on the same page.

When we use Git on a new computer for the first time, we need to configure a few things. Below are a few examples of configurations we will set as we get started with Git:

  • our name and email address,
  • what our preferred text editor is,
  • and that we want to use these settings globally (i.e. for every project).

On a command line, Git commands are written as git verb options, where verb is what we actually want to do and options is additional optional information which may be needed for the verb. So here is how Dracula sets up his new laptop:

BASH

$ git config --global user.name "Vlad Dracula"
$ git config --global user.email "vlad@tran.sylvan.ia"

Please use your own name and email address instead of Dracula’s. This user name and email will be associated with your subsequent Git activity, which means that any changes pushed to GitHub, BitBucket, GitLab or another Git host server after this lesson will include this information.

For this lesson, we will be interacting with GitHub and so the email address used should be the same as the one used when setting up your GitHub account. If you are concerned about privacy, please review GitHub’s instructions for keeping your email address private.

If you elect to use a private email address with GitHub, then use GitHub’s no-reply email address for the user.email value. It looks like ID+username@users.noreply.github.com. You can look up your own address in your GitHub email settings.

When working with git bash, you may run into a warning on line endings:

As with other keys, when you hit Enter or or on Macs, Return on your keyboard, your computer encodes this input as a character. Different operating systems use different character(s) to represent the end of a line. (You may also hear these referred to as newlines or line breaks.) Because Git uses these characters to compare files, it may cause unexpected issues when editing a file on different machines. Though it is beyond the scope of this lesson, you can read more about this issue in the Pro Git book.

You can change the way Git recognizes and encodes line endings using the core.autocrlf command to git config. The following settings are recommended:

On macOS and Linux:

BASH

$ git config --global core.autocrlf input

And on Windows:

BASH

$ git config --global core.autocrlf true

Set your text editor to nano. nano is a simple to use command-line editor, and we recommend to use it during this lesson.

Execute the following command:

BASH

$ git config --global core.editor "nano"

You can configure a different editor than nano if you wish. Here are a few examples:

Editor Configuration command
Atom $ git config --global core.editor "atom --wait"
BBEdit (Mac, with command line tools) $ git config --global core.editor "bbedit -w"
Sublime Text (Mac) $ git config --global core.editor "/Applications/Sublime\ Text.app/Contents/SharedSupport/bin/subl -n -w"
Sublime Text (Win, 32-bit install) $ git config --global core.editor "'c:/program files (x86)/sublime text 3/sublime_text.exe' -w"
Sublime Text (Win, 64-bit install) $ git config --global core.editor "'c:/program files/sublime text 3/sublime_text.exe' -w"
Notepad (Win) $ git config --global core.editor "c:/Windows/System32/notepad.exe"
Notepad++ (Win, 32-bit install) $ git config --global core.editor "'c:/program files (x86)/Notepad++/notepad++.exe' -multiInst -notabbar -nosession -noPlugin"
Notepad++ (Win, 64-bit install) $ git config --global core.editor "'c:/program files/Notepad++/notepad++.exe' -multiInst -notabbar -nosession -noPlugin"
Kate (Linux) $ git config --global core.editor "kate"
Gedit (Linux) $ git config --global core.editor "gedit --wait --new-window"
Scratch (Linux) $ git config --global core.editor "scratch-text-editor"
Emacs $ git config --global core.editor "emacs"
Vim $ git config --global core.editor "vim"
VS Code $ git config --global core.editor "code --wait"

It is possible to reconfigure the text editor for Git whenever you want to change it.

Default Git branch naming

Source file changes are associated with a “branch.” For new learners in this lesson, it’s enough to know that branches exist, and this lesson uses one branch.
Previously, by default, Git would create a branch called master instead of main, when you create a new repository with git init (as explained in the next Episode). This term evokes the racist practice of human slavery and the software development community has moved to adopt more inclusive language.

In 2020, most Git code hosting services transitioned to using main as the default branch.

The five commands we just ran above only need to be run once: the flag --global tells Git to use the settings for every project, in your user account, on this computer.

Let’s review those settings and test our core.editor right away:

BASH

$ git config --global --edit

Let’s close the file without making any additional changes. Remember, since typos in the config file will cause issues, it’s safer to view the configuration with:

BASH

$ git config --list

And if necessary, change your configuration using the same commands to choose another editor or update your email address. This can be done as many times as you want.

Git Help and Manual

Always remember that if you forget the subcommands or options of a git command, you can access the relevant list of options typing git <command> -h or access the corresponding Git manual by typing git <command> --help, e.g.:

BASH

$ git config -h
$ git config --help

While viewing the manual, remember the : is a prompt waiting for commands and you can press Q to exit the manual.

More generally, you can get the list of available git commands and further resources of the Git manual typing:

BASH

$ git help

Key Points

  • Use git config with the --global option to configure a user name, email address, editor, and other preferences once per machine.

Content from Creating a Repository


Last updated on 2025-05-15 | Edit this page

Estimated time: 15 minutes

Overview

Questions

  • Where does Git store information?

Objectives

  • Create a local Git repository.
  • Describe the purpose of the .git directory.

Introduce here the story of Wolfman and Dracula. The examples make more sense if you introduce the story. Here we suggest referring to ‘The Holy Realms of Git’ slide: https://esciencecenter-digital-skills.github.io/digital-skills-slides/modules/git-lesson/git-slides#/5 to introduce the idea of repository and .git.

Once Git is configured, we can start using it.

We will continue with the story of Wolfman and Dracula who are investigating if it is possible to send a planetary lander to Mars.

motivatingexampleWerewolf vs dracula by b-maze / Deviant Art. Mars by European Space Agency / CC-BY-SA 3.0 IGO. Pluto / Courtesy NASA/JPL-Caltech. Mummy © Gilad Fried / The Noun Project / CC BY 3.0. Moon © Luc Viatour / https://lucnix.be / CC BY-SA 3.0.

First, let’s create a new directory in the Desktop folder for our work and then change the current working directory to the newly created one:

BASH

$ cd ~/Desktop
$ mkdir planets
$ cd planets

Then we tell Git to make planets a repository -- a place where Git can store versions of our files:

BASH

$ git init

It is important to note that git init will create a repository that can include subdirectories and their files—there is no need to create separate repositories nested within the planets repository, whether subdirectories are present from the beginning or added later. Also, note that the creation of the planets directory and its initialization as a repository are completely separate processes.

If we use ls to show the directory’s contents, it appears that nothing has changed:

BASH

$ ls

But if we add the -a flag to show everything, we can see that Git has created a hidden directory within planets called .git:

BASH

$ ls -a

OUTPUT

.	..	.git

Git uses this special subdirectory to store all the information about the project, including the tracked files and sub-directories located within the project’s directory. If we ever delete the .git subdirectory, we will lose the project’s history.

Next, we will change the default branch to be called main. This might be the default branch depending on your settings and version of git. See the setup episode for more information on this change.

BASH

$ git switch -c main

OUTPUT

Switched to a new branch 'main'

We can check that everything is set up correctly by asking Git to tell us the status of our project:

BASH

$ git status

OUTPUT

On branch main

No commits yet

nothing to commit (create/copy files and use "git add" to track)

If you are using a different version of git, the exact wording of the output might be slightly different.

Places to Create Git Repositories

Along with tracking information about planets (the project we have already created), Dracula would also like to track information about moons. Despite Wolfman’s concerns, Dracula creates a moons project inside his planets project with the following sequence of commands:

BASH

$ cd ~/Desktop   # return to Desktop directory
$ cd planets     # go into planets directory, which is already a Git repository
$ ls -a          # ensure the .git subdirectory is still present in the planets directory
$ mkdir moons    # make a subdirectory planets/moons
$ cd moons       # go into moons subdirectory
$ git init       # make the moons subdirectory a Git repository
$ ls -a          # ensure the .git subdirectory is present indicating we have created a new Git repository

Is the git init command, run inside the moons subdirectory, required for tracking files stored in the moons subdirectory?

No. Dracula does not need to make the moons subdirectory a Git repository because the planets repository can track any files, sub-directories, and subdirectory files under the planets directory. Thus, in order to track all information about moons, Dracula only needed to add the moons subdirectory to the planets directory.

Additionally, Git repositories can interfere with each other if they are “nested”: the outer repository will try to version-control the inner repository. Therefore, it’s best to create each new Git repository in a separate directory. To be sure that there is no conflicting repository in the directory, check the output of git status. If it looks like the following, you are good to go to create a new repository as shown above:

BASH

$ git status

OUTPUT

fatal: Not a git repository (or any of the parent directories): .git

Key Points

  • git init initializes a repository.
  • Git stores all of its repository data in the .git directory.

Content from Tracking Changes


Last updated on 2025-05-22 | Edit this page

Estimated time: 25 minutes

Overview

Questions

  • How do I record changes in Git?
  • How do I check the status of my version control repository?
  • How do I record notes about what changes I made and why?

Objectives

  • Go through the modify-add-commit cycle for one or more files.
  • Explain where information is stored at each stage of that cycle.
  • Distinguish between descriptive and non-descriptive commit messages.

We suggest to use slides. From slide 5 onwards: https://esciencecenter-digital-skills.github.io/digital-skills-slides/modules/git-lesson/git-slides#/5 Please switch back and forth between command line and slides when necessary.

First let’s make sure we’re still in the right directory. You should be in the planets directory.

BASH

$ cd ~/Desktop/planets

Let’s create a file called mars.txt that contains some notes about the Red Planet’s suitability as a base. We’ll use nano to edit the file; you can use whatever editor you like. In particular, this does not have to be the core.editor you set globally earlier. But remember, the bash command to create or edit a new file will depend on the editor you choose (it might not be nano). For a refresher on text editors, check out “Which Editor?” in The Unix Shell lesson.

BASH

$ nano mars.txt

Type the text below into the mars.txt file:

OUTPUT

Cold and dry, but everything is my favorite color

Let’s first verify that the file was properly created by running the list command (ls):

BASH

$ ls

OUTPUT

mars.txt

mars.txt contains a single line, which we can see by running:

BASH

$ cat mars.txt

OUTPUT

Cold and dry, but everything is my favorite color

If we check the status of our project again, Git tells us that it’s noticed the new file:

BASH

$ git status

OUTPUT

On branch main

No commits yet

Untracked files:
   (use "git add <file>..." to include in what will be committed)

	mars.txt

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

The “untracked files” message means that there’s a file in the directory that Git isn’t keeping track of. We can tell Git to track a file using git add:

BASH

$ git add mars.txt

and then check that the right thing happened:

BASH

$ git status

OUTPUT

On branch main

No commits yet

Changes to be committed:
  (use "git rm --cached <file>..." to unstage)

	new file:   mars.txt

Git now knows that it’s supposed to keep track of mars.txt, but it hasn’t recorded these changes as a commit yet. To get it to do that, we need to run one more command:

BASH

$ git commit -m "Start notes on Mars as a base"

OUTPUT

[main (root-commit) f22b25e] Start notes on Mars as a base
 1 file changed, 1 insertion(+)
 create mode 100644 mars.txt

When we run git commit, Git takes everything we have told it to save by using git add and stores a copy permanently inside the special .git directory. This permanent copy is called a commit (or revision) and its short identifier is f22b25e. Your commit may have another identifier.

We use the -m flag (for “message”) to record a short, descriptive, and specific comment that will help us remember later on what we did and why. If we just run git commit without the -m option, Git will launch nano (or whatever other editor we configured as core.editor) so that we can write a longer message.

Good commit messages start with a brief (<50 characters) statement about the changes made in the commit. Generally, the message should complete the sentence “If applied, this commit will” . If you want to go into more detail, add a blank line between the summary line and your additional notes. Use this additional space to explain why you made changes and/or what their impact will be.

Choosing a Commit Message

You are making changes to your code, where you added a new function to calculate the mean. During this you also realise that you made a typo in the use guide.

Which of the following commit messages would be most appropriate?

  1. “Changes”
  2. “Added calc_mean to stats.py and fixed typos”
  3. “Add a function to calculate the mean” “Fix typos in introduction of the user guide”

Answer 1 is not descriptive enough, and the purpose of the commit is unclear; and answer 2 is redundant to using “git diff” to see what changed in this commit and the commit is combining different changes; but answer 3 is good: short, descriptive, and imperative. It also separates the changes into 2 commits

If we run git status now:

BASH

$ git status

OUTPUT

On branch main
nothing to commit, working tree clean

it tells us everything is up to date. If we want to know what we’ve done recently, we can ask Git to show us the project’s history using git log:

BASH

$ git log

OUTPUT

commit f22b25e3233b4645dabd0d81e651fe074bd8e73b
Author: Vlad Dracula <vlad@tran.sylvan.ia>
Date:   Thu Aug 22 09:51:46 2013 -0400

    Start notes on Mars as a base

git log lists all commits made to a repository in reverse chronological order. The listing for each commit includes the commit’s full identifier (which starts with the same characters as the short identifier printed by the git commit command earlier), the commit’s author, when it was created, and the log message Git was given when the commit was created.

Where Are My Changes?

If we run ls at this point, we will still see just one file called mars.txt. That’s because Git saves information about files’ history in the special .git directory mentioned earlier so that our filesystem doesn’t become cluttered (and so that we can’t accidentally edit or delete an old version).

Now suppose Dracula adds more information to the file. (Again, we’ll edit with nano and then cat the file to show its contents; you may use a different editor, and don’t need to cat.)

BASH

$ nano mars.txt
$ cat mars.txt

OUTPUT

Cold and dry, but everything is my favorite color
The two moons may be a problem for Wolfman

When we run git status now, it tells us that a file it already knows about has been modified:

BASH

$ git status

OUTPUT

On branch main
Changes not staged for commit:
  (use "git add <file>..." to update what will be committed)
  (use "git restore <file>..." to discard changes in working directory)

	modified:   mars.txt

no changes added to commit (use "git add" and/or "git commit -a")

The last line is the key phrase: “no changes added to commit”. We have changed this file, but we haven’t told Git we will want to save those changes (which we do with git add) nor have we saved them (which we do with git commit). So let’s do that now. It is good practice to always review our changes before saving them. We do this using git diff. This shows us the differences between the current state of the file and the most recently saved version:

BASH

$ git diff

OUTPUT

diff --git a/mars.txt b/mars.txt
index df0654a..315bf3a 100644
--- a/mars.txt
+++ b/mars.txt
@@ -1 +1,2 @@
 Cold and dry, but everything is my favorite color
+The two moons may be a problem for Wolfman

The output is cryptic because it is actually a series of commands for tools like editors and patch telling them how to reconstruct one file given the other. If we break it down into pieces:

  1. The first line tells us that Git is producing output similar to the Unix diff command comparing the old and new versions of the file.
  2. The second line tells exactly which versions of the file Git is comparing; df0654a and 315bf3a are unique computer-generated labels for those versions.
  3. The third and fourth lines once again show the name of the file being changed.
  4. The remaining lines are the most interesting, they show us the actual differences and the lines on which they occur. In particular, the + marker in the first column shows where we added a line.

After reviewing our change, it’s time to commit it:

BASH

$ git commit -m "Add concerns about effects of Mars' moons on Wolfman"

OUTPUT

On branch main
Changes not staged for commit:
  (use "git add <file>..." to update what will be committed)
  (use "git restore <file>..." to discard changes in working directory)

	modified:   mars.txt

no changes added to commit (use "git add" and/or "git commit -a")

Whoops: Git won’t commit because we didn’t use git add first. Let’s fix that:

BASH

$ git add mars.txt
$ git commit -m "Add concerns about effects of Mars' moons on Wolfman"

OUTPUT

[main 34961b1] Add concerns about effects of Mars' moons on Wolfman
 1 file changed, 1 insertion(+)

Git insists that we add files to the set we want to commit before actually committing anything. This allows us to commit our changes in stages and capture changes in logical portions rather than only large batches. For example, suppose we’re adding a few citations to relevant research to our thesis. We might want to commit those additions, and the corresponding bibliography entries, but not commit some of our work drafting the conclusion (which we haven’t finished yet).

To allow for this, Git has a special staging area where it keeps track of things that have been added to the current changeset but not yet committed.

If you think of Git as taking snapshots of changes over the life of a project, git add specifies what will go in a snapshot (putting things in the staging area), and git commit then actually takes the snapshot, and makes a permanent record of it (as a commit). If you don’t have anything staged when you type git commit, Git will prompt you to use git commit -a or git commit --all, which is kind of like gathering everyone to take a group photo! However, it’s almost always better to explicitly add things to the staging area, because you might commit changes you forgot you made. (Going back to the group photo simile, you might get an extra with incomplete makeup walking on the stage for the picture because you used -a!)

If you do accidentally add a file and you want to undo it, you can use: git restore <filename> or git revert <filename> to do this. However, these functionalities of git are beyond the scope of this course.

Try to stage things manually, or you might find yourself searching for “git undo commit” more than you would like!

The Git Staging Area

Let’s watch as our changes to a file move from our editor to the staging area and into long-term storage. First, we’ll add another line to the file:

BASH

$ nano mars.txt
$ cat mars.txt

OUTPUT

Cold and dry, but everything is my favorite color
The two moons may be a problem for Wolfman
But the Mummy will appreciate the lack of humidity

BASH

$ git diff

OUTPUT

diff --git a/mars.txt b/mars.txt
index 315bf3a..b36abfd 100644
--- a/mars.txt
+++ b/mars.txt
@@ -1,2 +1,3 @@
 Cold and dry, but everything is my favorite color
 The two moons may be a problem for Wolfman
+But the Mummy will appreciate the lack of humidity

So far, so good: we’ve added one line to the end of the file (shown with a + in the first column). Now let’s put that change in the staging area and see what git diff reports:

BASH

$ git add mars.txt
$ git diff

There is no output: as far as Git can tell, there’s no difference between what it’s been asked to save permanently and what’s currently in the directory. However, if we do this:

BASH

$ git diff --staged

OUTPUT

diff --git a/mars.txt b/mars.txt
index 315bf3a..b36abfd 100644
--- a/mars.txt
+++ b/mars.txt
@@ -1,2 +1,3 @@
 Cold and dry, but everything is my favorite color
 The two moons may be a problem for Wolfman
+But the Mummy will appreciate the lack of humidity

it shows us the difference between the last committed change and what’s in the staging area. Let’s save our changes:

BASH

$ git commit -m "Discuss concerns about Mars' climate for Mummy"

OUTPUT

[main 005937f] Discuss concerns about Mars' climate for Mummy
 1 file changed, 1 insertion(+)

check our status:

BASH

$ git status

OUTPUT

On branch main
nothing to commit, working tree clean

and look at the history of what we’ve done so far:

BASH

$ git log

OUTPUT

commit 005937fbe2a98fb83f0ade869025dc2636b4dad5 (HEAD -> main)
Author: Vlad Dracula <vlad@tran.sylvan.ia>
Date:   Thu Aug 22 10:14:07 2013 -0400

    Discuss concerns about Mars' climate for Mummy

commit 34961b159c27df3b475cfe4415d94a6d1fcd064d
Author: Vlad Dracula <vlad@tran.sylvan.ia>
Date:   Thu Aug 22 10:07:21 2013 -0400

    Add concerns about effects of Mars' moons on Wolfman

commit f22b25e3233b4645dabd0d81e651fe074bd8e73b
Author: Vlad Dracula <vlad@tran.sylvan.ia>
Date:   Thu Aug 22 09:51:46 2013 -0400

    Start notes on Mars as a base

Sometimes, e.g. in the case of the text documents a line-wise diff is too coarse. That is where the --color-words option of git diff comes in very useful as it highlights the changed words using colors.

When the output of git log is too long to fit in your screen, git uses a program to split it into pages of the size of your screen. When this “pager” is called, you will notice that the last line in your screen is a :, instead of your usual prompt.

  • To get out of the pager, press Q.
  • To move to the next page, press Spacebar.
  • To search for some_word in all pages, press / and type some_word. Navigate through matches pressing N.

To avoid having git log cover your entire terminal screen, you can limit the number of commits that Git lists by using -N, where N is the number of commits that you want to view. For example, if you only want information from the last commit you can use:

BASH

$ git log -1

OUTPUT

commit 005937fbe2a98fb83f0ade869025dc2636b4dad5 (HEAD -> main)
Author: Vlad Dracula <vlad@tran.sylvan.ia>
Date:   Thu Aug 22 10:14:07 2013 -0400

   Discuss concerns about Mars' climate for Mummy

You can also reduce the quantity of information using the --oneline option:

BASH

$ git log --oneline

OUTPUT

005937f (HEAD -> main) Discuss concerns about Mars' climate for Mummy
34961b1 Add concerns about effects of Mars' moons on Wolfman
f22b25e Start notes on Mars as a base

You can also combine the --oneline option with others. One useful combination adds --graph to display the commit history as a text-based graph and to indicate which commits are associated with the current HEAD, the current branch main, or other Git references:

BASH

$ git log --oneline --graph

OUTPUT

* 005937f (HEAD -> main) Discuss concerns about Mars' climate for Mummy
* 34961b1 Add concerns about effects of Mars' moons on Wolfman
* f22b25e Start notes on Mars as a base

Directories

Two important facts you should know about directories in Git.

  1. Git does not track directories on their own, only files within them. Try it for yourself:

BASH

$ mkdir spaceships
$ git status
$ git add spaceships
$ git status

Note, our newly created empty directory spaceships does not appear in the list of untracked files even if we explicitly add it (via git add) to our repository. This is the reason why you will sometimes see .gitkeep files in otherwise empty directories. Unlike .gitignore, these files are not special and their sole purpose is to populate a directory so that Git adds it to the repository. In fact, you can name such files anything you like.

  1. If you create a directory in your Git repository and populate it with files, you can add all files in the directory at once by:

BASH

git add <directory-with-files>

Try it for yourself:

BASH

$ touch spaceships/apollo-11 spaceships/sputnik-1
$ git status
$ git add spaceships
$ git status

Before moving on, we will commit these changes.

BASH

$ git commit -m "Add some initial thoughts on spaceships"

To recap, when we want to add changes to our repository, we first need to add the changed files to the staging area (git add) and then commit the staged changes to the repository (git commit):

The Git Commit Workflow

Committing Changes to Git

Which command(s) below would save the changes of myfile.txt to my local Git repository?

  1. BASH

       $ git commit -m "my recent changes"
  2. BASH

       $ git init myfile.txt
       $ git commit -m "my recent changes"
  3. BASH

       $ git add myfile.txt
       $ git commit -m "my recent changes"
  4. BASH

       $ git commit -m myfile.txt "my recent changes"
  1. Would only create a commit if files have already been staged.
  2. Would try to create a new repository.
  3. Is correct: first add the file to the staging area, then commit.
  4. Would try to commit a file “my recent changes” with the message myfile.txt.

Committing Multiple Files

The staging area can hold changes from any number of files that you want to commit as a single snapshot.

  1. Add some text to mars.txt noting your decision to consider Venus as a base
  2. Create a new file venus.txt with your initial thoughts about Venus as a base for you and your friends
  3. Add changes from both files to the staging area, and commit those changes.

The output below from cat mars.txt reflects only content added during this exercise. Your output may vary.

First we make our changes to the mars.txt and venus.txt files:

BASH

$ nano mars.txt
$ cat mars.txt

OUTPUT

Maybe I should start with a base on Venus.

BASH

$ nano venus.txt
$ cat venus.txt

OUTPUT

Venus is a nice planet and I definitely should consider it as a base.

Now you can add both files to the staging area. We can do that in one line:

BASH

$ git add mars.txt venus.txt

Or with multiple commands:

BASH

$ git add mars.txt
$ git add venus.txt

Now the files are ready to commit. You can check that using git status. If you are ready to commit use:

BASH

$ git commit -m "Write plans to start a base on Venus"

OUTPUT

[main cc127c2]
 Write plans to start a base on Venus
 2 files changed, 2 insertions(+)
 create mode 100644 venus.txt

This is an optional aside if it comes up or if there is enough time to address it.

Briefly mention the concept of ignoring files with a .gitignore file and direct learners to additional resources.

Along the lines of “What if we have files that we do not want Git to track for us, like backup files created by our editor or intermediate files created during data analysis? Putting these files under version control would be a waste of disk space. What’s worse, having them all listed could distract us from changes that actually matter, so we can tell Git to ignore them. We can do this by creating a file in the root directory of our project called .gitignore. As a bonus, using .gitignore helps us avoid accidentally adding files to the repository that we don’t want to track.”

Key Points

  • git status shows the status of a repository.
  • Files can be stored in a project’s working directory (which users see), the staging area (where the next commit is being built up) and the local repository (where commits are permanently recorded).
  • git add puts files in the staging area.
  • git commit saves the staged content as a new commit in the local repository.
  • git log shows the commit history & git diff the difference between 2 commits.
  • Write a commit message that accurately describes your changes.

Content from Remotes in GitHub


Last updated on 2025-05-22 | Edit this page

Estimated time: 45 minutes

Overview

Questions

  • How do I share my changes with others on the web?

Objectives

  • Explain what remote repositories are and why they are useful.
  • Push to or pull from a remote repository.

There are no slides associated with this episode. Take a dedicated moment right before this episode to check succesful completion of particpants’ SSH setup and help out people who did not succeed yet. You will need 15-30 minutes for this, so prepare an optional exercise for people that are correctly setup.

Version control really comes into its own when we begin to collaborate with other people. We already have most of the machinery we need to do this; the only thing missing is to copy changes from one repository to another.

Systems like Git allow us to move work between any two repositories. In practice, though, it’s easiest to use one copy as a central hub, and to keep it on the web rather than on someone’s laptop. Most programmers use hosting services like GitHub, Bitbucket or GitLab to hold those main copies.

Let’s start by sharing the changes we’ve made to our current project with the world. To this end we are going to create a remote repository that will be linked to our local repository.

1. Create a remote repository


Log in to GitHub, then click on the icon in the top right corner to create a new repository called planets:

Creating a Repository on GitHub (Step 1)

Name your repository “planets” and then click “Create Repository”.

Note: Since this repository will be connected to a local repository, it needs to be empty. Leave “Initialize this repository with a README” unchecked, and keep “None” as options for both “Add .gitignore” and “Add a license.” See the “GitHub License and README files” exercise below for a full explanation of why the repository needs to be empty.

Creating a Repository on GitHub (Step 2)

As soon as the repository is created, GitHub displays a page with a URL and some information on how to configure your local repository:

Creating a Repository on GitHub (Step 3)

This effectively does the following on GitHub’s servers:

BASH

$ mkdir planets
$ cd planets
$ git init

If you remember back to the earlier episode where we added and committed our earlier work on mars.txt, we had a diagram of the local repository which looked like this:

The Local Repository with Git Staging Area

Now that we have two repositories, we need a diagram like this:

Freshly-Made GitHub Repository

Note that our local repository still contains our earlier work on mars.txt, but the remote repository on GitHub appears empty as it doesn’t contain any files yet.

2. Connect local to remote repository


Now we connect the two repositories. We do this by making the GitHub repository a remote for the local repository. The home page of the repository on GitHub includes the URL string we need to identify it:

Where to Find Repository URL on GitHub

Click on the ‘SSH’ link to change the protocol from HTTPS to SSH.

HTTPS vs. SSH

We use SSH here because, while it requires some additional configuration, it is a security protocol widely used by many applications. The steps below describe SSH at a minimum level for GitHub.

Changing the Repository URL on GitHub

Copy that URL from the browser, go into the local planets repository, and run this command:

BASH

$ git remote add origin git@github.com:vlad/planets.git

Make sure to use the URL for your repository rather than Vlad’s: the only difference should be your username instead of vlad.

origin is a local name used to refer to the remote repository. It could be called anything, but origin is a convention that is often used by default in git and GitHub, so it’s helpful to stick with this unless there’s a reason not to.

We can check that the command has worked by running git remote -v:

BASH

$ git remote -v

OUTPUT

origin   git@github.com:vlad/planets.git (fetch)
origin   git@github.com:vlad/planets.git (push)

We’ll discuss remotes in more detail in the next episode, while talking about how they might be used for collaboration.

3. Push local changes to a remote


Now that authentication is setup, we can return to the remote. This command will push the changes from our local repository to the repository on GitHub:

BASH

$ git push origin main

Since Dracula set up a passphrase, it will prompt him for it. If you completed advanced settings for your authentication, it will not prompt for a passphrase.

OUTPUT

Enumerating objects: 16, done.
Counting objects: 100% (16/16), done.
Delta compression using up to 8 threads.
Compressing objects: 100% (11/11), done.
Writing objects: 100% (16/16), 1.45 KiB | 372.00 KiB/s, done.
Total 16 (delta 2), reused 0 (delta 0)
remote: Resolving deltas: 100% (2/2), done.
To https://github.com/vlad/planets.git
 * [new branch]      main -> main

If the network you are connected to uses a proxy, there is a chance that your last command failed with “Could not resolve hostname” as the error message. To solve this issue, you need to tell Git about the proxy:

BASH

$ git config --global http.proxy http://user:password@proxy.url
$ git config --global https.proxy https://user:password@proxy.url

When you connect to another network that doesn’t use a proxy, you will need to tell Git to disable the proxy using:

BASH

$ git config --global --unset http.proxy
$ git config --global --unset https.proxy

If your operating system has a password manager configured, git push will try to use it when it needs your username and password. For example, this is the default behavior for Git Bash on Windows. If you want to type your username and password at the terminal instead of using a password manager, type:

BASH

$ unset SSH_ASKPASS

in the terminal, before you run git push. Despite the name, Git uses SSH_ASKPASS for all credential entry, so you may want to unset SSH_ASKPASS whether you are using Git via SSH or https.

You may also want to add unset SSH_ASKPASS at the end of your ~/.bashrc to make Git default to using the terminal for usernames and passwords.

Our local and remote repositories are now in this state:

GitHub Repository After First Push

The ‘-u’ Flag

You may see a -u option used with git push in some documentation. This option is synonymous with the --set-upstream-to option for the git branch command, and is used to associate the current branch with a remote branch so that the git pull command can be used without any arguments. To do this, simply use git push -u origin main once the remote has been set up.

We can pull changes from the remote repository to the local one as well:

BASH

$ git pull origin main

OUTPUT

From https://github.com/vlad/planets
 * branch            main     -> FETCH_HEAD
Already up-to-date.

Pulling has no effect in this case because the two repositories are already synchronized. If someone else had pushed some changes to the repository on GitHub, though, this command would download them to our local repository.

Spend some time showing student around the repository and where to find history on commits etc.

Github also allows you to skip the command line and upload files directly to your repository without having to leave the browser. There are two options. First you can click the “Upload files” button in the toolbar at the top of the file tree. Or, you can drag and drop files from your desktop onto the file tree. You can read more about this on this GitHub page.

Push vs. Commit

In this episode, we introduced the “git push” command. How is “git push” different from “git commit”?

When we push changes, we’re interacting with a remote repository to update it with the changes we’ve made locally (often this corresponds to sharing the changes we’ve made with others). Commit only updates your local repository.

In this episode we learned about creating a remote repository on GitHub, but when you initialized your GitHub repo, you didn’t add a README.md or a license file. If we had, we’d see a merge conflict due to unrelated histories. When GitHub creates a README.md file, it performs a commit in the remote repository. When you try to pull the remote repository to your local repository, Git detects that they have histories that do not share a common origin and refuses to merge.

You can force git to merge the two repositories with the option --allow-unrelated-histories. Be careful when you use this option and carefully examine the contents of local and remote repositories before merging.

BASH

$ git pull --allow-unrelated-histories origin main

Another option would be to first create the repository on GitHub before writing any code and pull the repository locally with:

BASH

git clone git@github.com:[link-to-repo]

Take students through the workflow of creating and cloning a repo from GitHub or cloning an existing repository that you want to work with.

Key Points

  • A local Git repository can be connected to one or more remote repositories.
  • Use the SSH protocol to connect to remote repositories.
  • git push copies changes from a local repository to a remote repository.
  • git pull copies changes from a remote repository to a local repository.

Content from Branches


Last updated on 2025-04-28 | Edit this page

Estimated time: 5 minutes

Overview

Questions

  • Understand what branches are and when to use them

Objectives

  • What are branches?

Using the slides, explain what branches are and when to use them. You can choose to introduce the commands here, but we will practice with the git commands in the next episode as well.

What are branches and when to use them?


Have a look at these slides introducing branches.


Here are some commands related to branches that you often use in practice.

Create a new branch and switch onto it:

git switch -c new-branch-name

OUTPUT

Switched to a new branch 'new-branch-name'

Switch to an existing branch, for example back to main:

git switch main

OUTPUT

Switched to branch 'main'

Often while working on a branch, the main branch has changes that you want to apply to the branch you are working on. You can do this by pulling changes from the main branch into the branch that you are working on:

git switch branch-name # Make sure you are on the branch into which you want to pull changes from main
git pull origin main

Key Points

  • A branch represents an independent line of development.
  • Subsequent changes are considered to belong to that branch.

Content from Collaborative Version Control - Centralized


Last updated on 2025-05-22 | Edit this page

Estimated time: 120 minutes

Overview

Questions

  • How can I use version control to collaborate with internal collaborators?

Objectives

  • Understand the basics of collaborative version control with git and Github
  • Understand the centralized workflow

Teaching is done as a pair of instructors. Instructor A acts as the owner of the repository, instructor B as a collaborator (internal or external).

First we show the centralized workflow all in the browser using Github:

  • instructor A creates an issue (for example create ‘sum’ function)
  • instructor B picks up the issue
  • Instructor B clones the repository
  • Instructor B creates a new branch, using git switch -c new_feature
  • Instructor B does some reviewable changes (a simple ‘sum’ function)
  • Instructor B pushes the changes to the remote repository on GitHub using git push origin new_feature
  • Instructor B opens a new pull request.
  • Instructor A reviews and approves the PR.
  • Instructor B merges the pull request.
  • Use Github repo’s insights -> network to visualize what just happened

Exercise: Working as a project collaborator (in pairs):

  • PERSON A: Create an issue in the repository
  • PERSON B: Clone this repository to your system
  • PERSON B: Create a new branch, using git switch -c new_feature
  • PERSON B: Make the changes requested in the issue
  • PERSON B: Push the changes to the remote repository on GitHub using git push origin new_feature
  • PERSON B: Submit a Pull Request, refer to the issue (e.g. “Closes #1”)
  • PERSON A: Review the Pull Request
  • PERSON B: Address the comments
  • PERSON A: Approve the Pull Request
  • PERSON B: Merge the Pull Request

Key Points

  • Git and Github are superpowerful, not just for version control, but as tools for collaborative development
  • Do code reviews and be constructive in them!
  • Use centralized flow for internal collaborations