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COMP0233: Research Software Engineering With Python

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Debugging With Git Bisect

NOTE: using bash/git commands is not fully supported on jupyterlite yet (due to single thread/process restriction), and the cells below might error out on the browser (jupyterlite) version of this notebook

You can use

git bisect

to find out which commit caused a bug.

An example repository

In a nice open source example, I found an arbitrary exemplar on github

In [1]:
import os
top_dir = os.getcwd()
git_dir = os.path.join(top_dir, 'learning_git')
os.chdir(git_dir)
In [2]:
%%bash
rm -rf bisectdemo
git clone https://github.com/UCL-ARC-RSEing-with-Python/bisectdemo.git
Cloning into 'bisectdemo'...
In [3]:
bisect_dir=os.path.join(git_dir,'bisectdemo')
os.chdir(bisect_dir)
In [4]:
%%bash
python squares.py 2 # 4
4

This has been set up to break itself at a random commit, and leave you to use bisect to work out where it has broken:

In [5]:
%%bash
./breakme.sh > break_output
Switched to a new branch 'buggy'

Which will make a bunch of commits, of which one is broken, and leave you in the broken final state

In [6]:
%%bash
python squares.py 2 # Error message
Traceback (most recent call last):
  File "/home/runner/work/rsd-engineeringcourse/rsd-engineeringcourse/ch00git/learning_git/bisectdemo/squares.py", line 9, in <module>
    print(integer**2)
          ~~~~~~~^^~
TypeError: unsupported operand type(s) for ** or pow(): 'str' and 'int'
---------------------------------------------------------------------------
CalledProcessError                        Traceback (most recent call last)
Cell In[6], line 1
----> 1 get_ipython().run_cell_magic('bash', '', 'python squares.py 2 #\xa0Error message\n')

File /opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/IPython/core/interactiveshell.py:2541, in InteractiveShell.run_cell_magic(self, magic_name, line, cell)
   2539 with self.builtin_trap:
   2540     args = (magic_arg_s, cell)
-> 2541     result = fn(*args, **kwargs)
   2543 # The code below prevents the output from being displayed
   2544 # when using magics with decorator @output_can_be_silenced
   2545 # when the last Python token in the expression is a ';'.
   2546 if getattr(fn, magic.MAGIC_OUTPUT_CAN_BE_SILENCED, False):

File /opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/IPython/core/magics/script.py:155, in ScriptMagics._make_script_magic.<locals>.named_script_magic(line, cell)
    153 else:
    154     line = script
--> 155 return self.shebang(line, cell)

File /opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/IPython/core/magics/script.py:315, in ScriptMagics.shebang(self, line, cell)
    310 if args.raise_error and p.returncode != 0:
    311     # If we get here and p.returncode is still None, we must have
    312     # killed it but not yet seen its return code. We don't wait for it,
    313     # in case it's stuck in uninterruptible sleep. -9 = SIGKILL
    314     rc = p.returncode or -9
--> 315     raise CalledProcessError(rc, cell)

CalledProcessError: Command 'b'python squares.py 2 #\xc2\xa0Error message\n'' returned non-zero exit status 1.

Bisecting manually

In [7]:
%%bash
git bisect start
git bisect bad # We know the current state is broken
git switch main
git bisect good # We know the main branch state is OK
status: waiting for both good and bad commits
status: waiting for good commit(s), bad commit known
warning: you are switching branch while bisecting
Switched to branch 'main'
Your branch is up to date with 'origin/main'.
Bisecting: 500 revisions left to test after this (roughly 9 steps)
[e3daf46d9f18cf08753996ecd60a113da5062a23] Comment 499

Bisect needs one known good and one known bad commit to get started

Solving Manually

python squares.py 2 # 4
git bisect good
python squares.py 2 # 4
git bisect good
python squares.py 2 # 4
git bisect good
python squares.py 2 # Crash
git bisect bad
python squares.py 2 # Crash
git bisect bad
python squares.py 2 # Crash
git bisect bad
python squares.py 2 #Crash
git bisect bad
python squares.py 2 # 4
git bisect good
python squares.py 2 # 4
git bisect good
python squares.py 2 # 4
git bisect good

And eventually:

git bisect good
    Bisecting: 0 revisions left to test after this (roughly 0 steps)

python squares.py 2
    4

git bisect good
2777975a2334c2396ccb9faf98ab149824ec465b is the first bad commit
commit 2777975a2334c2396ccb9faf98ab149824ec465b
Author: Shawn Siefkas <shawn.siefkas@meredith.com>
Date:   Thu Nov 14 09:23:55 2013 -0600

    Breaking argument type

Stop the bisect process with:

git bisect reset

Solving automatically

If we have an appropriate unit test, we can do all this automatically:

(NOTE: You don't need to redirect the stderr and stdout (with &>) of git bisect run to a file when running these commands outside a jupyter notebook (i.e., on a shell). This is done here so the errors appears with the right commits)

In [8]:
%%bash
git bisect start
git bisect bad HEAD # We know the current state is broken
git bisect good main # We know main is good
git bisect run python squares.py 2 &> gitbisect.out
cat gitbisect.out
Previous HEAD position was e3daf46 Comment 499
Switched to branch 'buggy'
status: waiting for both good and bad commits
status: waiting for good commit(s), bad commit known
Bisecting: 500 revisions left to test after this (roughly 9 steps)
[e3daf46d9f18cf08753996ecd60a113da5062a23] Comment 499
running 'python' 'squares.py' '2'
Traceback (most recent call last):
  File "/home/runner/work/rsd-engineeringcourse/rsd-engineeringcourse/ch00git/learning_git/bisectdemo/squares.py", line 9, in <module>
    print(integer**2)
          ~~~~~~~^^~
TypeError: unsupported operand type(s) for ** or pow(): 'str' and 'int'
Bisecting: 249 revisions left to test after this (roughly 8 steps)
[b558992d23f58e3ec728d551150d0e81bc9b8996] Comment 249
running 'python' 'squares.py' '2'
Traceback (most recent call last):
  File "/home/runner/work/rsd-engineeringcourse/rsd-engineeringcourse/ch00git/learning_git/bisectdemo/squares.py", line 9, in <module>
    print(integer**2)
          ~~~~~~~^^~
TypeError: unsupported operand type(s) for ** or pow(): 'str' and 'int'
Bisecting: 124 revisions left to test after this (roughly 7 steps)
[54a83f8d7955381203b099de090e39bb728cc49f] Comment 125
running 'python' 'squares.py' '2'
4
Bisecting: 62 revisions left to test after this (roughly 6 steps)
[cbce9fa1e98f55302c8412a8d07f77a69ec4176c] Comment 186
running 'python' 'squares.py' '2'
Traceback (most recent call last):
  File "/home/runner/work/rsd-engineeringcourse/rsd-engineeringcourse/ch00git/learning_git/bisectdemo/squares.py", line 9, in <module>
    print(integer**2)
          ~~~~~~~^^~
TypeError: unsupported operand type(s) for ** or pow(): 'str' and 'int'
Bisecting: 30 revisions left to test after this (roughly 5 steps)
[f485a8363df4903df40df583fece6b59ce8494fb] Comment 155
running 'python' 'squares.py' '2'
Traceback (most recent call last):
  File "/home/runner/work/rsd-engineeringcourse/rsd-engineeringcourse/ch00git/learning_git/bisectdemo/squares.py", line 9, in <module>
    print(integer**2)
          ~~~~~~~^^~
TypeError: unsupported operand type(s) for ** or pow(): 'str' and 'int'
Bisecting: 15 revisions left to test after this (roughly 4 steps)
[b3963378c4d1faabc4351a8ad64cf9a9467c1aec] Comment 140
running 'python' 'squares.py' '2'
4
Bisecting: 7 revisions left to test after this (roughly 3 steps)
[b9becf6f2d242e78f44f9b48a6ef73e081ff0d8e] Comment 147
running 'python' 'squares.py' '2'
Traceback (most recent call last):
  File "/home/runner/work/rsd-engineeringcourse/rsd-engineeringcourse/ch00git/learning_git/bisectdemo/squares.py", line 9, in <module>
    print(integer**2)
          ~~~~~~~^^~
TypeError: unsupported operand type(s) for ** or pow(): 'str' and 'int'
Bisecting: 3 revisions left to test after this (roughly 2 steps)
[0a53337e13c06d9125657eb41c6511a38be2a7bb] Comment 144
running 'python' 'squares.py' '2'
4
Bisecting: 1 revision left to test after this (roughly 1 step)
[8d9ba0df080793decd832b7984f095863b624b70] Comment 145
running 'python' 'squares.py' '2'
Traceback (most recent call last):
  File "/home/runner/work/rsd-engineeringcourse/rsd-engineeringcourse/ch00git/learning_git/bisectdemo/squares.py", line 9, in <module>
    print(integer**2)
          ~~~~~~~^^~
TypeError: unsupported operand type(s) for ** or pow(): 'str' and 'int'
Bisecting: 0 revisions left to test after this (roughly 0 steps)
[609601015a73fc9c2da563f60480f290df484774] Breaking argument type
running 'python' 'squares.py' '2'
Traceback (most recent call last):
  File "/home/runner/work/rsd-engineeringcourse/rsd-engineeringcourse/ch00git/learning_git/bisectdemo/squares.py", line 9, in <module>
    print(integer**2)
          ~~~~~~~^^~
TypeError: unsupported operand type(s) for ** or pow(): 'str' and 'int'
609601015a73fc9c2da563f60480f290df484774 is the first bad commit
commit 609601015a73fc9c2da563f60480f290df484774
Author: Shawn Siefkas <shawn.siefkas@meredith.com>
Date:   Thu Nov 14 09:23:55 2013 -0600

    Breaking argument type

 squares.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)
bisect found first bad commit

Boom!