Estimated time for this notebook: 10 minutes
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
Unfortunately this doesn't work nicely in the notebook. But from the command line, you can run a python program with:
python -m pdb my_program.py
Basic command to navigate the code and the python debugger:
help
: prints the helphelp 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 codel
(ist): list program around current positionw
(where): prints current stack (where we are in code)[enter]
: repeats last commandanypythonvariable
: print the value of that variableThe 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
%%writefile energy_example.py
from diffusion.model import energy
print(energy([5, 6, 7, 8, 0, 1]))
Overwriting energy_example.py
The debugger is, of course, most used interactively, but here I'm showing a prewritten debugger script:
%%writefile commands
restart # restart session
n
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
%%bash
python -m pdb energy_example.py < commands
>/home/turingdev/projects/research-software/rse-course/ch03tests/energy_example.py(1)<module>() -> from diffusion.model import energy (Pdb) Restarting energy_example.py with arguments: energy_example.py >/home/turingdev/projects/research-software/rse-course/ch03tests/energy_example.py(1)<module>() -> from diffusion.model import energy (Pdb) >/home/turingdev/projects/research-software/rse-course/ch03tests/energy_example.py(3)<module>() -> print(energy([5, 6, 7, 8, 0, 1])) (Pdb) Breakpoint 1 at/home/turingdev/projects/research-software/rse-course/ch03tests/diffusion/model.py:5 (Pdb) >/home/turingdev/projects/research-software/rse-course/ch03tests/diffusion/model.py(13)energy() -> density = array(density) (Pdb) [5, 6, 7, 8, 0, 1] (Pdb)
Alternatively, break-points can be set on files: b file.py:20
will stop on line 20 of file.py
.
Debugging when something goes wrong:
python -m pdb file.py
or run the cell with %pdb on
The program should stop where the exception was raised
w
and l
for position in code and in call stackup
and down
to navigate up and down the call stackNote 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)