Content from Automated Version Control
Last updated on 2024-09-23 | 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.
Original lesson material: https://swcarpentry.github.io/git-novice/ Slides: https://esciencecenter-digital-skills.github.io/digital-skills-slides/modules/git-lesson/git-slides, until https://esciencecenter-digital-skills.github.io/digital-skills-slides/modules/git-lesson/git-slides#/4. Please note that slides will be deployed in the ‘right place’ in due time. Right now nobody knows where that is.
The slides provide visual context to the concepts that are used in the live coding. It would be best to have both the live coding screen and the slides screen side by side. As this is in general not possible, it is best to switch back and forth between command line and slides when necessary (you can use the images in the teaching material as indication when to switch to the slides).
Teach what you think is most useful. See how far you get, usually we get to episode 7 (Remotes in GitHub) in one morning. Ignore the temptation to answer advanced questions. (You can of course do this individually during exercises).
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:
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.
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.
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.
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.
The Long History of Version Control Systems
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 Changesoption? 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 2024-06-26 | Edit this page
Estimated time: 10 minutes
Overview
Questions
- How do I get set up to use Git?
Objectives
- Configure
gitthe first time it is used on a computer. - Understand the meaning of the
--globalconfiguration 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.
Keeping your email 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.
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:
And on Windows:
Dracula also has to set his favorite text editor, following this table:
| Editor | Configuration command |
|---|---|
| Atom | $ git config --global core.editor "atom --wait" |
| nano | $ git config --global core.editor "nano -w" |
| 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.
Exiting Vim
Note that Vim is the default editor for many programs. If you haven’t
used Vim before and wish to exit a session without saving your changes,
press Esc then type :q! and hit Enter
or ↵ or on Macs, Return. If you want to save your
changes and quit, press Esc then type :wq and
hit Enter or ↵ or on Macs, Return.
Git (2.28+) allows configuration of the name of the branch created
when you initialize any new repository. Dracula decides to use that
feature to set it to main so it matches the cloud service
he will eventually use.
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.
By default, Git will create a branch called master 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. As an example, any new
repository that is opened in GitHub and GitLab default to
main. However, Git has not yet made the same change. As a
result, local repositories must be manually configured have the same
main branch name as most cloud services.
For versions of Git prior to 2.28, the change can be made on an
individual repository level. The command for this is in the next
episode. Note that if this value is unset in your local Git
configuration, the init.defaultBranch value defaults to
master.
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:
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:
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.
Proxy
In some networks you need to use a proxy. If this is the case, you may also need to tell Git about the proxy:
To disable the proxy, use
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.:
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:
Key Points
- Use
git configwith the--globaloption to configure a user name, email address, editor, and other preferences once per machine.
Content from Creating a Repository
Last updated on 2024-09-23 | 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
.gitdirectory.
Introduce here the story of Wolfman and Dracula. we all feel it is a bit silly example, but it suits the purpose. 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.
Werewolf
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:
Then we tell Git to make planets a repository -- a place where Git can
store versions of our files:
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:
But if we add the -a flag to show everything, we can see
that Git has created a hidden directory within planets
called .git:
OUTPUT
. .. .gitGit 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.
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:
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 repositoryIs 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:
OUTPUT
fatal: Not a git repository (or any of the parent directories): .gitCorrecting git init Mistakes
Wolfman explains to Dracula how a nested repository is redundant and
may cause confusion down the road. Dracula would like to remove the
nested repository. How can Dracula undo his last git init
in the moons subdirectory?
Background
Removing files from a Git repository needs to be done with caution. But we have not learned yet how to tell Git to track a particular file; we will learn this in the next episode. Files that are not tracked by Git can easily be removed like any other “ordinary” files with
Similarly a directory can be removed using rm -r dirname
or rm -rf dirname. If the files or folder being removed in
this fashion are tracked by Git, then their removal becomes another
change that we will need to track, as we will see in the next
episode.
Solution
Git keeps all of its files in the .git directory. To
recover from this little mistake, Dracula can just remove the
.git folder in the moons subdirectory by running the
following command from inside the planets directory:
But be careful! Running this command in the wrong directory will
remove the entire Git history of a project you might want to keep.
Therefore, always check your current directory using the command
pwd.
Key Points
-
git initinitializes a repository. - Git stores all of its repository data in the
.gitdirectory.
Content from Tracking Changes
Last updated on 2024-09-23 | 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.
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.
Type the text below into the mars.txt file:
OUTPUT
Cold and dry, but everything is my favorite colorLet’s first verify that the file was properly created by running the
list command (ls):
OUTPUT
mars.txtmars.txt contains a single line, which we can see by
running:
OUTPUT
Cold and dry, but everything is my favorite colorIf we check the status of our project again, Git tells us that it’s noticed the new file:
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:
and then check that the right thing happened:
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:
OUTPUT
[main (root-commit) f22b25e] Start notes on Mars as a base
1 file changed, 1 insertion(+)
create mode 100644 mars.txtWhen 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 we run git status now:
OUTPUT
On branch main
nothing to commit, working tree cleanit 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:
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 basegit 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.)
OUTPUT
Cold and dry, but everything is my favorite color
The two moons may be a problem for WolfmanWhen we run git status now, it tells us that a file it
already knows about has been modified:
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:
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 WolfmanThe 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:
- The first line tells us that Git is producing output similar to the
Unix
diffcommand comparing the old and new versions of the file. - The second line tells exactly which versions of the file Git is
comparing;
df0654aand315bf3aare unique computer-generated labels for those versions. - The third and fourth lines once again show the name of the file being changed.
- 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:
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:
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.
Staging Area
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!)
Try to stage things manually, or you might find yourself searching for
“git undo commit” more than you would like!
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:
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 humidityOUTPUT
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 humiditySo 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:
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:
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 humidityit shows us the difference between the last committed change and what’s in the staging area. Let’s save our changes:
OUTPUT
[main 005937f] Discuss concerns about Mars' climate for Mummy
1 file changed, 1 insertion(+)check our status:
OUTPUT
On branch main
nothing to commit, working tree cleanand look at the history of what we’ve done so far:
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 baseWord-based diffing
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.
Paging the Log
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_wordin all pages, press / and typesome_word. Navigate through matches pressing N.
Limit Log Size
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:
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 MummyYou can also reduce the quantity of information using the
--oneline option:
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 baseYou 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:
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 baseDirectories
Two important facts you should know about directories in Git.
- Git does not track directories on their own, only files within them. Try it for yourself:
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.
- 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:
Try it for yourself:
BASH
$ touch spaceships/apollo-11 spaceships/sputnik-1
$ git status
$ git add spaceships
$ git statusBefore moving on, we will commit these changes.
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):
Choosing a Commit Message
Which of the following commit messages would be most appropriate for
the last commit made to mars.txt?
- “Changes”
- “Added line ‘But the Mummy will appreciate the lack of humidity’ to mars.txt”
- “Discuss effects of Mars’ climate on the Mummy”
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; but answer 3 is good: short, descriptive, and imperative.
Committing Changes to Git
Which command(s) below would save the changes of
myfile.txt to my local Git repository?
- Would only create a commit if files have already been staged.
- Would try to create a new repository.
- Is correct: first add the file to the staging area, then commit.
- 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.
- Add some text to
mars.txtnoting your decision to consider Venus as a base - Create a new file
venus.txtwith your initial thoughts about Venus as a base for you and your friends - 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:
OUTPUT
Maybe I should start with a base on Venus.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:
Or with multiple commands:
Now the files are ready to commit. You can check that using
git status. If you are ready to commit use:
OUTPUT
[main cc127c2]
Write plans to start a base on Venus
2 files changed, 2 insertions(+)
create mode 100644 venus.txt
bio Repository
- Create a new Git repository on your computer called
bio. - Write a three-line biography for yourself in a file called
me.txt, commit your changes - Modify one line, add a fourth line
- Display the differences between its updated state and its original state.
If needed, move out of the planets folder:
Create a new folder called bio and ‘move’ into it:
Initialise git:
Create your biography file me.txt using
nano or another text editor. Once in place, add and commit
it to the repository:
Modify the file as described (modify one line, add a fourth line). To
display the differences between its updated state and its original
state, use git diff:
Key Points
-
git statusshows 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 addputs files in the staging area. -
git commitsaves the staged content as a new commit in the local repository. - Write a commit message that accurately describes your changes.
Content from Exploring History
Last updated on 2024-08-05 | Edit this page
Estimated time: 25 minutes
Overview
Questions
- How can I identify old versions of files?
- How do I review my changes?
- How can I recover old versions of files?
Objectives
- Explain what the HEAD of a repository is and how to use it.
- Identify and use Git commit numbers.
- Compare various versions of tracked files.
- Restore old versions of files.
There are no specific slides for this episode. You could consider keeping the slides open to the episode on the basics of Git, to show the visual representation of the changes in the repository.
Consider doing this episode as a demo and not going into the details. The aim is to demonstrate to participants the possiblity to go back and forth through the git log, which is enough for an introduction to git. In practice you only use this occasionally.
Make use of git switch and git restore instead of the confusing git checkout. This is probably much clearer for participants. We haven’t tried this yet and it is not in the training material, so you have to do some pioneering.
As we saw in the previous episode, we can refer to commits by their
identifiers. You can refer to the most recent commit of the
working directory by using the identifier HEAD.
We’ve been adding one line at a time to mars.txt, so
it’s easy to track our progress by looking, so let’s do that using our
HEADs. Before we start, let’s make a change to
mars.txt, adding yet another line.
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
An ill-considered changeNow, let’s see what we get.
OUTPUT
diff --git a/mars.txt b/mars.txt
index b36abfd..0848c8d 100644
--- a/mars.txt
+++ b/mars.txt
@@ -1,3 +1,4 @@
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
+An ill-considered change.which is the same as what you would get if you leave out
HEAD (try it). The real goodness in all this is when you
can refer to previous commits. We do that by adding ~1
(where “~” is “tilde”, pronounced [til-duh])
to refer to the commit one before HEAD.
If we want to see the differences between older commits we can use
git diff again, but with the notation HEAD~1,
HEAD~2, and so on, to refer to them:
OUTPUT
diff --git a/mars.txt b/mars.txt
index df0654a..b36abfd 100644
--- a/mars.txt
+++ b/mars.txt
@@ -1 +1,4 @@
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
+An ill-considered changeWe could also use git show which shows us what changes
we made at an older commit as well as the commit message, rather than
the differences between a commit and our working directory that
we see by using git diff.
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
diff --git a/mars.txt b/mars.txt
new file mode 100644
index 0000000..df0654a
--- /dev/null
+++ b/mars.txt
@@ -0,0 +1 @@
+Cold and dry, but everything is my favorite colorIn this way, we can build up a chain of commits. The most recent end
of the chain is referred to as HEAD; we can refer to
previous commits using the ~ notation, so
HEAD~1 means “the previous commit”, while
HEAD~123 goes back 123 commits from where we are now.
We can also refer to commits using those long strings of digits and
letters that git log displays. These are unique IDs for the
changes, and “unique” really does mean unique: every change to any set
of files on any computer has a unique 40-character identifier. Our first
commit was given the ID
f22b25e3233b4645dabd0d81e651fe074bd8e73b, so let’s try
this:
OUTPUT
diff --git a/mars.txt b/mars.txt
index df0654a..93a3e13 100644
--- a/mars.txt
+++ b/mars.txt
@@ -1 +1,4 @@
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
+An ill-considered changeThat’s the right answer, but typing out random 40-character strings is annoying, so Git lets us use just the first few characters (typically seven for normal size projects):
OUTPUT
diff --git a/mars.txt b/mars.txt
index df0654a..93a3e13 100644
--- a/mars.txt
+++ b/mars.txt
@@ -1 +1,4 @@
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
+An ill-considered changeAll right! So we can save changes to files and see what we’ve
changed. Now, how can we restore older versions of things? Let’s suppose
we change our mind about the last update to mars.txt (the
“ill-considered change”).
git status now tells us that the file has been changed,
but those changes haven’t been staged:
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")We can put things back the way they were by using
git restore:
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 humidityAs you might guess from its name, git restore restores
an old version of a file. In this case, we’re telling Git that we want
to recover the version of the file recorded in HEAD, which
is the last saved commit. If we want to go back even further, we can use
the ‘source’ flag -s to specify a commit identifier
instead:
OUTPUT
Cold and dry, but everything is my favorite colorOUTPUT
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
Again, we can put things back the way they were by using
git restore:
It’s important to remember that we must use the commit number that
identifies the state of the repository before the change we’re
trying to undo. A common mistake is to use the number of the commit in
which we made the change we’re trying to discard. In the example below,
we want to retrieve the state from before the most recent commit
(HEAD~1), which is commit f22b25e:
So, to put it all together, here’s how Git works in cartoon form:
Simplifying the Common Case
If you read the output of git status carefully, you’ll
see that it includes this hint:
OUTPUT
(use "git restore <file>..." to discard changes in working directory)As it says, git restore without a version identifier
restores files to the state saved in HEAD.
The fact that files can be reverted one by one tends to change the way people organize their work. If everything is in one large document, it’s hard (but not impossible) to undo changes to the introduction without also undoing changes made later to the conclusion. If the introduction and conclusion are stored in separate files, on the other hand, moving backward and forward in time becomes much easier.
Recovering Older Versions of a File
Jennifer has made changes to the Python script that she has been working on for weeks, and the modifications she made this morning “broke” the script and it no longer runs. She has spent ~ 1hr trying to fix it, with no luck…
Luckily, she has been keeping track of her project’s versions using
Git! Which commands below will let her recover the last committed
version of her Python script called data_cruncher.py?
$ git restore$ git restore data_cruncher.py$ git restore -s HEAD~1 data_cruncher.py$ git restore -s <unique ID of last commit> data_cruncher.pyBoth 2 and 4
The answer is (5)-Both 2 and 4.
The restore command restores files from the repository,
overwriting the files in your working directory. Answers 2 and 4 both
restore the latest version in the repository of the
file data_cruncher.py. Answer 2 doesn’t specify a commit,
which means it automatically refers to the latest, whereas
answer 4 uses the unique ID of the last commit, which would be the same
as using HEAD instead.
Answer 3 gets the version of data_cruncher.py from the
commit before HEAD, which is NOT what we
wanted.
Answer 1 reports an error
fatal: you must specify path(s) to restore: you haven’t
specified which file(s) to restore. It’s a good idea to be specific
about which files you mean,so you don’t accidentally restore more files
than you need. If you do want to restore all previously committed files
in your repository, you can use . to specify the current
folder (and all subfolders), i.e., git restore ..
Reverting a Commit
Jennifer is collaborating with colleagues on her Python script. She
realizes her last commit to the project’s repository contained an error,
and wants to undo it. Jennifer wants to undo correctly so everyone in
the project’s repository gets the correct change. The command
git revert [erroneous commit ID] will create a new commit
that reverses the erroneous commit.
The command git revert is different from
git restore -s [commit ID] because git restore
returns the files not yet committed within the local repository to a
previous state, whereas git revert reverses changes
committed to the local and project repositories.
Below are the right steps and explanations for Jennifer to use
git revert, what is the missing command?
________ # Look at the git history of the project to find the commit IDCopy the ID (the first few characters of the ID, e.g. 0b1d055).
git revert [commit ID]Type in the new commit message.
Save and close
The command git log lists project history with commit
IDs.
The command git show HEAD shows changes made at the
latest commit, and lists the commit ID; however, Jennifer should
double-check it is the correct commit, and no one else has committed
changes to the repository.
Understanding Workflow and History
What is the output of the last command in
BASH
$ cd planets
$ echo "Venus is beautiful and full of love" > venus.txt
$ git add venus.txt
$ echo "Venus is too hot to be suitable as a base" >> venus.txt
$ git commit -m "Comment on Venus as an unsuitable base"
$ git restore venus.txt
$ cat venus.txt #this will print the contents of venus.txt to the screenOUTPUT
Venus is too hot to be suitable as a baseOUTPUT
Venus is beautiful and full of loveOUTPUT
Venus is beautiful and full of love Venus is too hot to be suitable as a baseOUTPUT
Error because you have changed venus.txt without committing the changes
The answer is 2.
The command git add venus.txt places the current version
of venus.txt into the staging area. The changes to the file
from the second echo command are only applied to the
working copy, not the version in the staging area.
So, when
git commit -m "Comment on Venus as an unsuitable base" is
executed, the version of venus.txt committed to the
repository is the one from the staging area and has only one line.
At this time, the working copy still has the second line (and
git status will show that the file is modified). However,
git restore venus.txt replaces the working copy with the
most recently committed version of venus.txt.
So, cat venus.txt will output
OUTPUT
Venus is beautiful and full of love.Checking Understanding of
git diff
Consider this command: git diff HEAD~9 mars.txt. What do
you predict this command will do if you execute it? What happens when
you do execute it? Why?
Try another command, git diff [ID] mars.txt, where [ID]
is replaced with the unique identifier for your most recent commit. What
do you think will happen, and what does happen?
Getting Rid of Staged Changes
git restore can be used to restore a previous commit
when unstaged changes have been made, but will it also work for changes
that have been staged but not committed? Make a change to
mars.txt, add that change using git add, then
use git restore to see if you can remove your change.
After adding a change, git restore can not be used
directly. Let’s look at the output of git status:
OUTPUT
On branch main
Changes to be committed:
(use "git restore --staged <file>..." to unstage)
modified: mars.txt
Note that if you don’t have the same output you may either have forgotten to change the file, or you have added it and committed it.
Using the command git restore mars.txt now does not give
an error, but it does not restore the file either. Git helpfully tells
us that we need to use git restore --staged instead to
unstage the file:
Now, git status gives us:
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")This means we can now use git restore to restore the
file to the previous commit:
OUTPUT
On branch main
nothing to commit, working tree cleanExplore and Summarize Histories
Exploring history is an important part of Git, and often it is a challenge to find the right commit ID, especially if the commit is from several months ago.
Imagine the planets project has more than 50 files. You
would like to find a commit that modifies some specific text in
mars.txt. When you type git log, a very long
list appeared. How can you narrow down the search?
Recall that the git diff command allows us to explore
one specific file, e.g., git diff mars.txt. We can apply a
similar idea here.
Unfortunately some of these commit messages are very ambiguous, e.g.,
update files. How can you search through these files?
Both git diff and git log are very useful
and they summarize a different part of the history for you. Is it
possible to combine both? Let’s try the following:
You should get a long list of output, and you should be able to see both commit messages and the difference between each commit.
Question: What does the following command do?
Key Points
-
git diffdisplays differences between commits. -
git restorerecovers old versions of files.
Content from Ignoring Things
Last updated on 2024-06-26 | Edit this page
Estimated time: 10 minutes
Overview
Questions
- How can I tell Git to ignore files I don’t want to track?
Objectives
- Configure Git to ignore specific files.
- Explain why ignoring files can be useful.
There are no slides associated with this episode. Focus on the main concept of ignoring files with a .gitignore file, instead of fully learning the syntax.
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? Let’s create a few dummy files:
and see what Git says:
OUTPUT
On branch main
Untracked files:
(use "git add <file>..." to include in what will be committed)
a.csv
b.csv
c.csv
results/
nothing added to commit but untracked files present (use "git add" to track)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 let’s tell Git to ignore them.
We do this by creating a file in the root directory of our project
called .gitignore:
OUTPUT
*.csv
results/These patterns tell Git to ignore any file whose name ends in
.csv and everything in the results directory.
(If any of these files were already being tracked, Git would continue to
track them.)
Once we have created this file, the output of git status
is much cleaner:
OUTPUT
On branch main
Untracked files:
(use "git add <file>..." to include in what will be committed)
.gitignore
nothing added to commit but untracked files present (use "git add" to track)The only thing Git notices now is the newly-created
.gitignore file. You might think we wouldn’t want to track
it, but everyone we’re sharing our repository with will probably want to
ignore the same things that we’re ignoring. Let’s add and commit
.gitignore:
OUTPUT
On branch main
nothing to commit, working tree cleanAs a bonus, using .gitignore helps us avoid accidentally
adding files to the repository that we don’t want to track:
OUTPUT
The following paths are ignored by one of your .gitignore files:
a.csv
Use -f if you really want to add them.If we really want to override our ignore settings, we can use
git add -f to force Git to add something. For example,
git add -f a.csv. We can also always see the status of
ignored files if we want:
OUTPUT
On branch main
Ignored files:
(use "git add -f <file>..." to include in what will be committed)
a.csv
b.csv
c.csv
results/
nothing to commit, working tree cleanIf you only want to ignore the contents of
results/plots, you can change your .gitignore
to ignore only the /plots/ subfolder by adding the
following line to your .gitignore:
OUTPUT
results/plots/This line will ensure only the contents of results/plots
is ignored, and not the contents of results/data.
As with most programming issues, there are a few alternative ways that one may ensure this ignore rule is followed. The “Ignoring Nested Files: Variation” exercise has a slightly different directory structure that presents an alternative solution. Further, the discussion page has more detail on ignore rules.
Including Specific Files
How would you ignore all .csv files in your root
directory except for final.csv? Hint: Find out what
! (the exclamation point operator) does
You would add the following two lines to your .gitignore:
OUTPUT
*.csv # ignore all data files
!final.csv # except final.csvThe exclamation point operator will include a previously excluded entry.
Note also that because you’ve previously committed .csv
files in this lesson they will not be ignored with this new rule. Only
future additions of .csv files added to the root directory
will be ignored.
Ignoring Nested Files: Variation
Given a directory structure that looks similar to the earlier Nested Files exercise, but with a slightly different directory structure:
How would you ignore all of the contents in the results folder, but
not results/data?
Hint: think a bit about how you created an exception with the
! operator before.
If you want to ignore the contents of results/ but not
those of results/data/, you can change your
.gitignore to ignore the contents of results folder, but
create an exception for the contents of the results/data
subfolder. Your .gitignore would look like this:
OUTPUT
results/* # ignore everything in results folder
!results/data/ # do not ignore results/data/ contentsIgnoring all data Files in a Directory
Assuming you have an empty .gitignore file, and given a directory structure that looks like:
BASH
results/data/position/gps/a.csv
results/data/position/gps/b.csv
results/data/position/gps/c.csv
results/data/position/gps/info.txt
results/plotsWhat’s the shortest .gitignore rule you could write to
ignore all .csv files in
result/data/position/gps? Do not ignore the
info.txt.
Appending results/data/position/gps/*.csv will match
every file in results/data/position/gps that ends with
.csv. The file
results/data/position/gps/info.txt will not be ignored.
Ignoring all data Files in the repository
Let us assume you have many .csv files in different
subdirectories of your repository. For example, you might have:
BASH
results/a.csv
data/experiment_1/b.csv
data/experiment_2/c.csv
data/experiment_2/variation_1/d.csvHow do you ignore all the .csv files, without explicitly
listing the names of the corresponding folders?
In the .gitignore file, write:
OUTPUT
**/*.csvThis will ignore all the .csv files, regardless of their
position in the directory tree. You can still include some specific
exception with the exclamation point operator.
The ! modifier will negate an entry from a previously
defined ignore pattern. Because the !*.csv entry negates
all of the previous .csv files in the
.gitignore, none of them will be ignored, and all
.csv files will be tracked.
Log Files
You wrote a script that creates many intermediate log-files of the
form log_01, log_02, log_03, etc.
You want to keep them but you do not want to track them through
git.
Write one
.gitignoreentry that excludes files of the formlog_01,log_02, etc.Test your “ignore pattern” by creating some dummy files of the form
log_01, etc.You find that the file
log_01is very important after all, add it to the tracked files without changing the.gitignoreagain.Discuss with your neighbor what other types of files could reside in your directory that you do not want to track and thus would exclude via
.gitignore.
- append either
log_*orlog*as a new entry in your .gitignore - track
log_01usinggit add -f log_01
Key Points
- The
.gitignorefile tells Git what files to ignore.
Content from Remotes in GitHub
Last updated on 2024-08-05 | 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.
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:
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.
As soon as the repository is created, GitHub displays a page with a URL and some information on how to configure your local repository:
This effectively does the following on GitHub’s servers:
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:
Now that we have two repositories, we need a diagram like this:
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:
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.
Copy that URL from the browser, go into the local
planets repository, and run this command:
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:
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. SSH Background and Setup
Before Dracula can connect to a remote repository, he needs to set up a way for his computer to authenticate with GitHub so it knows it’s him trying to connect to his remote repository.
We are going to set up the method that is commonly used by many different services to authenticate access on the command line. This method is called Secure Shell Protocol (SSH). SSH is a cryptographic network protocol that allows secure communication between computers using an otherwise insecure network.
SSH uses what is called a key pair. This is two keys that work together to validate access. One key is publicly known and called the public key, and the other key called the private key is kept private. Very descriptive names.
You can think of the public key as a padlock, and only you have the key (the private key) to open it. You use the public key where you want a secure method of communication, such as your GitHub account. You give this padlock, or public key, to GitHub and say “lock the communications to my account with this so that only computers that have my private key can unlock communications and send git commands as my GitHub account.”
What we will do now is the minimum required to set up the SSH keys and add the public key to a GitHub account.
Advanced SSH
A supplemental episode in this lesson discusses SSH and key pairs in more depth and detail.
The first thing we are going to do is check if this has already been done on the computer you’re on. Because generally speaking, this setup only needs to happen once and then you can forget about it.
Keeping your keys secure
You shouldn’t really forget about your SSH keys, since they keep your account secure. It’s good practice to audit your secure shell keys every so often. Especially if you are using multiple computers to access your account.
We will run the list command to check what key pairs already exist on your computer.
Your output is going to look a little different depending on whether or not SSH has ever been set up on the computer you are using.
Dracula has not set up SSH on his computer, so his output is
OUTPUT
ls: cannot access '/c/Users/Vlad Dracula/.ssh': No such file or directoryIf SSH has been set up on the computer you’re using, the public and
private key pairs will be listed. The file names are either
id_ed25519/id_ed25519.pub or
id_rsa/id_rsa.pub depending on how the key
pairs were set up.
Since they don’t exist on Dracula’s computer, he uses this command to
create them.
3.1 Create an SSH key pair
To create an SSH key pair Vlad uses this command, where the
-t option specifies which type of algorithm to use and
-C attaches a comment to the key (here, Vlad’s email):
If you are using a legacy system that doesn’t support the Ed25519
algorithm, use:
$ ssh-keygen -t rsa -b 4096 -C "your_email@example.com"
OUTPUT
Generating public/private ed25519 key pair.
Enter file in which to save the key (/c/Users/Vlad Dracula/.ssh/id_ed25519):We want to use the default file, so just press Enter.
OUTPUT
Created directory '/c/Users/Vlad Dracula/.ssh'.
Enter passphrase (empty for no passphrase):Now, it is prompting Dracula for a passphrase. Since he is using his lab’s laptop that other people sometimes have access to, he wants to create a passphrase. Be sure to use something memorable or save your passphrase somewhere, as there is no “reset my password” option.
OUTPUT
Enter same passphrase again:After entering the same passphrase a second time, we receive the confirmation
OUTPUT
Your identification has been saved in /c/Users/Vlad Dracula/.ssh/id_ed25519
Your public key has been saved in /c/Users/Vlad Dracula/.ssh/id_ed25519.pub
The key fingerprint is:
SHA256:SMSPIStNyA00KPxuYu94KpZgRAYjgt9g4BA4kFy3g1o vlad@tran.sylvan.ia
The key's randomart image is:
+--[ED25519 256]--+
|^B== o. |
|%*=.*.+ |
|+=.E =.+ |
| .=.+.o.. |
|.... . S |
|.+ o |
|+ = |
|.o.o |
|oo+. |
+----[SHA256]-----+The “identification” is actually the private key. You should never share it. The public key is appropriately named. The “key fingerprint” is a shorter version of a public key.
Now that we have generated the SSH keys, we will find the SSH files when we check.
OUTPUT
drwxr-xr-x 1 Vlad Dracula 197121 0 Jul 16 14:48 ./
drwxr-xr-x 1 Vlad Dracula 197121 0 Jul 16 14:48 ../
-rw-r--r-- 1 Vlad Dracula 197121 419 Jul 16 14:48 id_ed25519
-rw-r--r-- 1 Vlad Dracula 197121 106 Jul 16 14:48 id_ed25519.pub3.2 Copy the public key to GitHub
Now we have a SSH key pair and we can run this command to check if GitHub can read our authentication.
OUTPUT
The authenticity of host 'github.com (192.30.255.112)' can't be established.
RSA key fingerprint is SHA256:nThbg6kXUpJWGl7E1IGOCspRomTxdCARLviKw6E5SY8.
This key is not known by any other names
Are you sure you want to continue connecting (yes/no/[fingerprint])? y
Please type 'yes', 'no' or the fingerprint: yes
Warning: Permanently added 'github.com' (RSA) to the list of known hosts.
git@github.com: Permission denied (publickey).Right, we forgot that we need to give GitHub our public key!
First, we need to copy the public key. Be sure to include the
.pub at the end, otherwise you’re looking at the private
key.
OUTPUT
ssh-ed25519 AAAAC3NzaC1lZDI1NTE5AAAAIDmRA3d51X0uu9wXek559gfn6UFNF69yZjChyBIU2qKI vlad@tran.sylvan.iaNow, going to GitHub.com, click on your profile icon in the top right corner to get the drop-down menu. Click “Settings,” then on the settings page, click “SSH and GPG keys,” on the left side “Account settings” menu. Click the “New SSH key” button on the right side. Now, you can add the title (Dracula uses the title “Vlad’s Lab Laptop” so he can remember where the original key pair files are located), paste your SSH key into the field, and click the “Add SSH key” to complete the setup.
Now that we’ve set that up, let’s check our authentication again from the command line.
OUTPUT
Hi Vlad! You've successfully authenticated, but GitHub does not provide shell access.Good! This output confirms that the SSH key works as intended. We are now ready to push our work to the remote repository.
4. 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:
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 -> mainProxy
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.urlWhen you connect to another network that doesn’t use a proxy, you will need to tell Git to disable the proxy using:
Password Managers
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:
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:
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:
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.
GitHub GUI
Browse to your planets repository on GitHub. Underneath
the Code button, find and click on the text that says “XX commits”
(where “XX” is some number). Hover over, and click on, the three buttons
to the right of each commit. What information can you gather/explore
from these buttons? How would you get that same information in the
shell?
The left-most button (with the picture of a clipboard) copies the
full identifier of the commit to the clipboard. In the shell,
git log will show you the full commit identifier for each
commit.
When you click on the middle button, you’ll see all of the changes
that were made in that particular commit. Green shaded lines indicate
additions and red ones removals. In the shell we can do the same thing
with git diff. In particular,
git diff ID1..ID2 where ID1 and ID2 are commit identifiers
(e.g. git diff a3bf1e5..041e637) will show the differences
between those two commits.
The right-most button lets you view all of the files in the
repository at the time of that commit. To do this in the shell, we’d
need to restore the files in the repository to that particular time. We
can do this with git restore -s ID <files> where ID
is the identifier of the commit we want to look at, and
<files> is the list of files we want to view. To view
all files at at the time of that commit, you can use
git restore -s ID .. If we do this, we need to remember to
put the repository back to the right state afterwards!
Uploading files directly in GitHub browser
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.
GitHub Timestamp
Create a remote repository on GitHub. Push the contents of your local repository to the remote. Make changes to your local repository and push these changes. Go to the repo you just created on GitHub and check the timestamps of the files. How does GitHub record times, and why?
GitHub displays timestamps in a human readable relative format (i.e. “22 hours ago” or “three weeks ago”). However, if you hover over the timestamp, you can see the exact time at which the last change to the file occurred.
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.
GitHub License and README files
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 you had, what do you think would have happened when you tried to link your local and remote repositories?
In this case, 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.
OUTPUT
warning: no common commits
remote: Enumerating objects: 3, done.
remote: Counting objects: 100% (3/3), done.
remote: Total 3 (delta 0), reused 0 (delta 0), pack-reused 0
Unpacking objects: 100% (3/3), done.
From https://github.com/vlad/planets
* branch main -> FETCH_HEAD
* [new branch] main -> origin/main
fatal: refusing to merge unrelated historiesYou 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.
OUTPUT
From https://github.com/vlad/planets
* branch main -> FETCH_HEAD
Merge made by the 'recursive' strategy.
README.md | 1 +
1 file changed, 1 insertion(+)
create mode 100644 README.mdKey Points
- A local Git repository can be connected to one or more remote repositories.
- Use the SSH protocol to connect to remote repositories.
-
git pushcopies changes from a local repository to a remote repository. -
git pullcopies changes from a remote repository to a local repository.
Content from Collaborative Version Control - Centralized
Last updated on 2024-06-26 | 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 creates a new branch (good to do this explicitly)
- Instructor B does some reviewable changes (a simple ‘sum’ function)
- 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
- PERSON B: Make the changes requested in the issue
- PERSON B: Push the changes to the remote repository on GitHub
- 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
Content from Collaborative Version Control - Distributed
Last updated on 2024-06-26 | Edit this page
Estimated time: 70 minutes
Overview
Questions
- How can I use version control to collaborate with external collaborators?
Objectives
- Understand distributed workflow and when to use it
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).
Now we show distributed workflow. All in the browser using Github:
- Instructor A removes instructor B
- Instructor B now submits an issue
- Instructor A responds to issue asking instructor B to pick it up
- Instructor B forks repo, does some changes, and submits PR
- Instructor A reviews the changes
- Instructor B implements the changes
- Instructor A merges the pull request
- Use Github repo’s insights -> network to visualize what just happened
Exercise: Working as an external contributor (in pairs)
- PERSON A: Create an issue in Person B’s repository
- PERSON A: Fork the repository to their own (= Person A’s) account
- PERSON A: Clone the repository, make changes, push them back to the fork
- PERSON A: Submit a Pull Request from the fork to the original repository
- PERSON B: Make a change in the original repository in the same place as person A’s proposed changes
- PERSON A: Solve the merge conflict in the Pull Request
- PERSON B: Review/Approve the Pull Request
- PERSON B: merge the Pull Request
Key Points
- Use distributed flow for external collaborations