Using a debugger

Stepping through the code

Debuggers are programs that can be used to test other programs. They allow programmers to suspend execution of the target program and inspect variables at that point.

NB. If you are using the Windows command prompt, you will have to replace all %%bash directives in this notebook with %%cmd

Using the python debugger

Unfortunately this doesn’t work nicely in the notebook. But from the command line, you can run a python program with:

python -m pdb

Basic navigation:

Basic command to navigate the code and the python debugger:

  • help: prints the help

  • help n: prints help about command n

  • n(ext): executes one line of code. Executes and steps over functions.

  • s(tep): step into current function in line of code

  • l(ist): list program around current position

  • w(where): prints current stack (where we are in code)

  • [enter]: repeats last command

  • anypythonvariable: print the value of that variable

The python debugger is a python shell: it can print and compute values, and even change the values of the variables at that point in the program.


Break points tell debugger where and when to stop We say

  • b somefunctionname

from diffusion.model import energy

print(energy([5, 6, 7, 8, 0, 1]))

The debugger is, of course, most used interactively, but here I’m showing a prewritten debugger script:

%%writefile commands
restart        # restart session
b energy       # program will stop when entering energy
c              # continue program until break point is reached
print(density) # We are now "inside" the energy function and can print any variable.
Overwriting commands
python -m pdb < commands
> /home/runner/work/rse-course/rse-course/module05_testing_your_code/<module>()
-> from diffusion.model import energy
(Pdb) Restarting /home/runner/work/rse-course/rse-course/module05_testing_your_code/ with arguments:
	# restart session
> /home/runner/work/rse-course/rse-course/module05_testing_your_code/<module>()
-> from diffusion.model import energy
(Pdb) > /home/runner/work/rse-course/rse-course/module05_testing_your_code/<module>()
-> print(energy([5, 6, 7, 8, 0, 1]))
(Pdb) Breakpoint 1 at /home/runner/work/rse-course/rse-course/module05_testing_your_code/diffusion/
(Pdb) > /home/runner/work/rse-course/rse-course/module05_testing_your_code/diffusion/
-> density = array(density)
(Pdb) [5, 6, 7, 8, 0, 1]

Alternatively, break-points can be set on files: b will stop on line 20 of


Debugging when something goes wrong:

  1. Have a crash somewhere in the code

  2. run python -m pdb or run the cell with %pdb on

The program should stop where the exception was raised

  1. use w and l for position in code and in call stack

  2. use up and down to navigate up and down the call stack

  3. inspect variables along the way to understand failure

Note Running interactively like in the following example does work in the notebook. Try it out!

%pdb on
from diffusion.model import energy
partial_derivative(energy, [5, 6, 7, 8, 0, 1], 5)