Preparation

Please make sure that you do not clone repositories inside an already tracked folder:

$ git status

If you are inside an existing Git repository, step out of it. You need to find a different location since we will clone a new repository.

If you see this message, this is good in this case:

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

Our toolbox for history inspection

First the instructor demonstrates few commands on a real life example repository https://github.com/networkx/networkx (mentioned in the amazing site The Programming Historian). Later we will practice these in groups in an archaeology exercise (below).

1. git grep to search through the repository

With git grep you can find all lines in a repository which contain some string or regular expression. This is useful to find out where in the code some variable is used or some error message printed:

$ git grep sometext

In the networkx repository you can try:

$ git clone https://github.com/networkx/networkx
$ cd networkx
$ git grep -i fixme

2. git log -S to search through the history of changes

While git grep searches the current state of the repository, it is possible to search also through all changes for “sometext”:

$ git log -S sometext

In the networkx repository you can try:

$ git log -S test_weakly_connected_component

3. git show to inspect commits

We have seen this one before already. Using git show we can inspect an individual commit if we know its hash:

$ git show somehash

For instance:

$ git show 759d589bdfa61aff99e0535938f14f67b01c83f7

4. git annotate to annotate code with commit metadata

Try it out on a file - with git annotate you can see line by line who and when the line was modified last. It also prints the precise hash of the last change which modified each line. Incredibly useful for reproducibility.

$ git annotate somefile

Example:

$ git annotate networkx/convert_matrix.py

If you annotate in a terminal and the file is longer than the screen, Git by default uses the program less to scroll the output. Use /sometext <ENTER> to find “sometext” and you can cycle through the results with n (next) and N (last). You can also use page up/down to scroll. You can quit with q.

Discussion

Discuss how these two affect the annotation:

• wrapping long lines of text/code into shorter lines
• autoformatting tools such as black

5. git checkout -b to inspect code in the past

We can create branches pointing to a commit in the past. This is the recommended mechanism to inspect old code:

$ git checkout -b branchname somehash

Example:

  # create branch called "older-code" from hash 347e6292419b
$ git checkout -b older-code 347e6292419bd0e4bff077fe971f983932d7a0e9

  # now you can navigate and inspect the code as it was back then
  # ...

  # after we are done we can switch back to "master"
$ git checkout master

  # if we like we can delete the "older-code" branch
$ git branch -d older-code

On newer Git versions this is the preferred command:

$ git switch --create branchname somehash

6. git bisect to locate the commit that changed a behavior

We have a separate section about this command below.

Archaeology exercise

Let us explore the value of these commands in an exercise.

In-person workshops: We recommend that you do this exercise in groups of two and discuss with your neighbors.

Video workshops: We will group you in breakout rooms of ~4 persons where you can work and discuss together. A helper or instructor will pop in to help out. In the group one participant can share their screen and others in the group help out, discuss, and try to follow along. Please write down questions in the collaborative notes. After 15 minutes we will bring you back into the main room and discuss.

Exercise steps:

1. Clone this repository: https://github.com/tidyverse/rvest. Then step into the new directory:

   $ git clone --branch v0.3.5 https://github.com/tidyverse/rvest.git
   $ cd rvest
   

2. Find the code line which contains 'No links matched that expression'
3. Find out when this line was last modified. Find the actual commit which modified that line.
4. Inspect that commit with git show.
5. Create a branch pointing to the past when that commit was created to be able to browse and use the code as it was back then.
6. How would can you bring the code to the commit precisely before that line was last modified?

Finding out when something broke with git bisect

But I am sure it used to work! Strange.

• Sometimes you realize that something broke.
• You know that it used to work.
• You do not know when it broke.

How would you solve this?

Before we go on first discuss how you would solve this problem: You know that it worked 500 commits ago but it does not work now.

• How would you find the commit which changed it?
• Why could it be useful to know the commit that changed it?

Video workshops: Write down ideas on how you would solve it in the collaborative note and we will discuss various approaches.

We will probably arrive at a solution which is similar to git bisect:

• First find out a commit in past when it worked.
• Then bisect your way until you find the commit that broke it.

$ git bisect start
$ git bisect good f0ea950  # this is a commit that worked
$ git bisect bad master    # last commit is broken
  # now compile and/or run
  # after that decide whether
$ git bisect good
  # or
$ git bisect bad
  # now compile and/or run
  # after that decide whether
$ git bisect good
  # or
$ git bisect bad
  # iterate until commit is found

• This can even be automatized with git bisect run <script>.
• For this you write a script that returns zero/non-zero (success/failure).

Git bisect exercise

Clone https://gitext.gfz-potsdam.de/swc-bb/swc-lessons/2020-11-05-potsdam-berlin/git-bisect-exercise.

Motivation

The motivation for this exercise is to be able to do archaeology with Git on a source code where the bug is difficult to see visually. Finding the offending commit is often more than half the debugging.

Background

The script get_pi.py approximates pi using terms of the Nilakantha series. It should produce 3.14 but it does not. The script broke at some point and produces 3.57 using the last commit:

$ python get_pi.py

3.57

At some point within the 500 first commits, an error was introduced. The only thing we know is that the first commit worked correctly.

Your task

• Clone this repository and use git bisect to find the commit which broke the computation (solution - spoiler alert!).
• Once you have found the offending commit, also practice navigating to the last good commit.
• Bonus exercise: Write a script that checks for a correct result and use git bisect run to find the offending commit automatically (solution - spoiler alert!).

Video workshops: We will group you in breakout rooms of ~4 persons where you can work and discuss together. A helper or instructor will pop in to help out. Please write down questions in the collaborative notes. After 15-20 minutes we will bring you back into the main room and discuss.

Hints

Finding the first commit:

$ git log --oneline | tail -n 1

How to navigate to the parent of a commit with hash somehash:

  # create branch pointing to the parent of somehash
$ git checkout -b branchname somehash~1

  # instead of a tilde you can also use this
$ git checkout -b branchname somehash^