• 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?

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:

$ 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?

Which of the following commit messages would be most appropriate for the last commit made to mars.txt?

1. “Changes”
2. “Added line ‘But the Mummy will appreciate the lack of humidity’ to mars.txt”
3. “Discuss effects of Mars’ climate on the Mummy”

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"

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.

• 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.

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?

1. $ git checkout HEAD

2. $ git checkout HEAD data_cruncher.py

3. $ git checkout HEAD~1 data_cruncher.py

4. $ git checkout <unique ID of last commit> data_cruncher.py

5. Both 2 and 4

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 checkout [commit ID] because git checkout 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?

1. ________ # Look at the git history of the project to find the commit ID

2. Copy the ID (the first few characters of the ID, e.g. 0b1d055).

3. git revert [commit ID]

4. Type in the new commit message.

5. Save and close

What is the output of the last command in

$ 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 checkout HEAD venus.txt
$ cat venus.txt #this will print the contents of venus.txt to the screen

1. output Venus is too hot to be suitable as a base

2. output Venus is beautiful and full of love

3. output Venus is beautiful and full of love Venus is too hot to be suitable as a base

4. output Error because you have changed venus.txt without committing the changes

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?

git checkout 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 checkout to see if you can remove your change.

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.

$ git log mars.txt

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:

$ git log --patch mars.txt

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?

$ git log --patch HEAD~9 *.txt

Given a directory structure that looks like:

results/data
results/plots

How would you ignore only results/plots and not results/data?

How would you ignore all .csv files in your root directory except for final.csv? Hint: Find out what ! (the exclamation point operator) does

Given a directory structure that looks similar to the earlier Nested Files exercise, but with a slightly different directory structure:

results/data
results/images
results/plots
results/analysis

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.

Assuming you have an empty .gitignore file, and given a directory structure that looks like:

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/plots

What’s the shortest .gitignore rule you could write to ignore all .csv files in result/data/position/gps? Do not ignore the info.txt.

Let us assume you have many .csv files in different subdirectories of your repository. For example, you might have:

results/a.csv
data/experiment_1/b.csv
data/experiment_2/c.csv
data/experiment_2/variation_1/d.csv

How do you ignore all the .csv files, without explicitly listing the names of the corresponding folders?

Given a .gitignore file with the following contents:

*.csv
!*.csv

What will be the result?

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.

1. Write one .gitignore entry that excludes files of the form log_01, log_02, etc.

2. Test your “ignore pattern” by creating some dummy files of the form log_01, etc.

3. You find that the file log_01 is very important after all, add it to the tracked files without changing the .gitignore again.

4. 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.

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?

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?

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

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?

Switch roles and repeat the whole process.

The Owner pushed commits to the repository without giving any information to the Collaborator. How can the Collaborator find out what has changed with command line? And on GitHub?

The Collaborator has some questions about one line change made by the Owner and has some suggestions to propose.

With GitHub, it is possible to comment on the diff of a commit. Over the line of code to comment, a blue comment icon appears to open a comment window.

The Collaborator posts her comments and suggestions using the GitHub interface.

Some backup software can keep a history of the versions of your files. They also allows you to recover specific versions. How is this functionality different from version control? What are some of the benefits of using version control, Git and GitHub?

Clone the repository created by your instructor. Add a new file to it, and modify an existing file (your instructor will tell you which one). When asked by your instructor, pull her changes from the repository to create a conflict, then resolve it.

What does Git do when there is a conflict in an image or some other non-textual file that is stored in version control?

You sit down at your computer to work on a shared project that is tracked in a remote Git repository. During your work session, you take the following actions, but not in this order:

• Make changes by appending the number 100 to a text file numbers.txt
• Update remote repository to match the local repository
• Celebrate your success with some fancy beverage(s)
• Update local repository to match the remote repository
• Stage changes to be committed
• Commit changes to the local repository

In what order should you perform these actions to minimize the chances of conflicts? Put the commands above in order in the action column of the table below. When you have the order right, see if you can write the corresponding commands in the command column. A few steps are populated to get you started.

Ask one of your labmates to reproduce a result you recently obtained using only what they can find in your papers or on the web. Try to do the same for one of their results, then try to do it for a result from a lab you work with.

Surf the internet for a couple of minutes and check out the data repositories mentioned above: Figshare, Zenodo, Dryad. Depending on your field of research, you might find community-recognized repositories that are well-known in your field. You might also find useful these data repositories recommended by Nature. Discuss with your neighbor which data repository you might want to approach for your current project and explain why.

Large data or image files such as .md5 or .psd file types can be tracked within a github repository using the Git Large File Storage open source extension tool. This tool automatically uploads large file contents to a remote server and replaces the file with a text pointer within the github repository.

Try downloading and installing the Git Large File Storage extension tool, then add tracking of a large file to your github repository. Ask a colleague to clone your repository and describe what they see when they access that large file.

Find out whether you are allowed to apply an open license to your software. Can you do this unilaterally, or do you need permission from someone in your institution? If so, who?

Many of the software tools we use on a daily basis (including in this workshop) are released as open-source software. Pick a project on GitHub from the list below, or one of your own choosing. Find its license (usually in a file called LICENSE or COPYING) and talk about how it restricts your use of the software. Is it one of the licenses discussed in this session? How is it different?

• Git, the source-code management tool
• CPython, the standard implementation of the Python language
• Jupyter, the project behind the web-based Python notebooks we’ll be using
• EtherPad, a real-time collaborative editor

Find out whether you are allowed to host your work openly in a public repository. Can you do this unilaterally, or do you need permission from someone in your institution? If so, who?

Does your institution have a repository or repositories that you can use to share your papers, data and software? How do institutional repositories differ from services like arXiV, figshare, GitHub or GitLab?

1. Create a new directory within your project called graphs.
2. Modify the .gitignore so that the graphs directory is not version controlled.