Debugging in Python (using PyCharm) – Part 1

This blog post is the first of a multi-part series (here are the second and third debugging blog posts) intended to provide discussion of some basic debugging tools that I have found to be helpful in developing a pure Python simulation model using a Python Integrated Development Environment (IDE) called PyCharm. (Some of this discussion surely applies to other languages and development environments as well. I just want folks to know that I’ve prepared this post with Python/PyCharm in mind).  The post was updated with some additional tips from Joe Kasprzyk, on 10/15/2015.

If you didn’t catch my previous post, I strongly recommend PyCharm as a Python IDE, and have described in that post how to get access to PyCharm. PyCharm can be a bit heavy just for scientific computing, but in developing a large, object-oriented simulation model, I have found PyCharm’s code completion and debugging features to be a major asset for coding quickly and efficiently.

When I am debugging a program, there are often two fundamental issues at hand. The first is to make sure the program runs without any syntax errors (or any other errors generated while interpreting your code). The second is to be confident that your code is doing what you think it is. That is, even if it runs, there may be problems within the implementation of the routines you have coded. Python’s highly intelligent code editor is very helpful for solving the former problem before you even run your program: it will highlight errors on the fly, help you complete code to avoid variable misspellings, etc. However, to handle the latter issue, you may want to glimpse into the code’s functioning (e.g., variable values) as the program executes. I will now describe some of PyCharm’s debugging features that I have found to be very helpful in this regard.

I prepared the instructions and figures that appear below with the Professional version of PyCharm (JetBrains PyCharm 4.5.2), and I’m using it in Windows 7.

I am going to show examples of how to use the Pycharm’s debug features on a very simple Python script, which appears below. However, clearly you can follow these same steps for your own files. This script should work, so it shouldn’t need to be debugged, but I’ll show how I would use debugging tools to check the script anyway.

# My program file
import matplotlib.pyplot as plt
import numpy as np

# Initialize empty arrays
array_len = 10000  # Desired length of arrays
var1 = np.zeros(array_len)
var2 = np.zeros(array_len)
var3 = np.zeros(array_len)
var4 = np.zeros(array_len)

# Define two functions:

def function_1(input):
    # Function 1
    for i in range(array_len):
        var1[i] = 2 + i*input
        var2[i] = 2*var1[i]
    return var1, var2

def function_2(input):
    # Function 2
    for j in range(array_len):
        var3[j] = 3 + j*input
        var4[j] = 2*var3[j]
    return var3, var4

# Add var1 and var3, and plot result:
Output = function_1(1)[0] + function_2(2)[0]

Step 1. Open your files.

In PyCharm, open a file (or files) that you have coded, or are in the process of coding, and want to debug. For example, a screenshot of my open file appears below.

Fig 1

Step 2. Turn on the debugger.

There are numerous ways to do this. I prefer to open up a Python console to work from, and turn it on from there (as is shown in the screenshot below). To do this, click on the “Python console” button at the bottom of the screen, then click on the green bug icon on the console menu on the left to turn on the debugger. Note that you can actually have open multiple consoles (by clicking the “plus” icon on the console menu), and you can have debugging turned on in whichever consoles you prefer.

If you can’t figure out how to open up a Python console, you can also just click on the green bug icon in the menu at the top of the screen next to the play button, while your script is open. This may actually run the debugger as well, which is a step that comes later on in my post.

Fig 2

Step 3. Create breakpoints.

Breakpoints are spots in your code where you want to temporarily interrupt execution so you can glimpse into the program’s operation (e.g., view values of variables as the program runs). If you left click in the area just to the left of where the code editor stops, a closed red circle will appear, denoting a breakpoint.

In my example, I will set breakpoints on the lines where variables var2 and var4 are defined. (Note that I like to have line numbers turned on, particularly when debugging. You can access this features in PyCharm’s settings menu).

Breakpoints are only used when running the program in debug mode. That is, when you turn debugging off (e.g., by clicking once again on the bug icon in the console menu), the program will execute without stopping on breakpoints. Also, note that breakpoints are useful not only for viewing the program’s variable values and so forth, but also to see if the program is entering particular sections of code. If the program doesn’t stop on a breakpoint you’ve set, then the program is not entering the section of code where that breakpoint is located, which can be very valuable information.

Fig 3

Step 4. Create a run configuration and run the debugger.

There are several ways to do this as well. You can simply click on the green bug icon at the top of the screen again to run the debugger. Or, highlight your code, right click, and select the option to “Debug” your file.

Joe adds: If you want to do a quick debug of an uncomplicated script, the above will work well.  However sometimes you may want to debug a Python file that has command line arguments, such as  In order to create a configuration, right click on the configuration pull down menu in the upper right hand corner of the program, and click Edit Configurations…  Then you can add the command line arguments by typing them into the “Script parameters” box in that dialog window.  Then, you can continue debugging as usual.  Back to your regularly scheduled programming…

I have noticed that my programs execute significantly more slowly in debug mode, so you may experience the same. A debugger pane should appear as below.

Fig 4

Step 5. Set “Watches”.

Note the program execution has been interrupted on the “var1” line. Suppose we want to know the value of this local variable in its current loop. In the debugger pane, go to the “Watches” window, click the “plus” symbol, and enter “var1”. Repeat this process for the rest of the variables.

Fig 5

The debugger still shows no value for var1. This is because when the Pycharm debugger stops on a breakpoint, it interrupts execution before the breakpoint line is run, rather than after.

If you click on the “play” icon to resume execution in the debugger, you will see values appear in your “Watches” pane. (If you hold your cursor over the different icons in the debugging pane, an icon description at the bottom of the window appears, so you can figure out which buttons I’m referring to this way).

PyCharm will also display values of watch variables (as well as the counter i) in the actual code editor as well (note the new text in gray in the figure below). Watches are helpful for more complex programs than this one, where you could have hundreds or thousands of variables, attributes, objects, etc., and want to track the values only of specific ones, so you can check them as you debug.

Fig 6

Joe adds:

Step 6. Add some exception handling to find information about an error.

Sometimes it is unclear why it is that you’re getting a particular error, such as “list index out of range.”  The Python run may give you information about what line number caused the problem, but that may not be enough.  Exception handling provides a way to create a ‘soft landing’ when the program runs into a problem.  Check out the Python documentation of this here.

For example, I had a problem with the function ‘withobjectives’ within  It was telling me list index out of range.  This seemed strange to me, and setting a breakpoint would be a lot of work because I didn’t know when the actual error was happening.  But exception handling saves the day.  Here’s the original offending line:

for oo in oindices:

I add ‘try’ and ‘except’ statements around the offending line:

for oo in oindices:
        print "You messed up. Here is row:"
        print "%s" % row

Now, there will be a line printed to the console that shows you the variable that caused the problem. In this case, there was an error in the text file, and I can go and use a find command in a text editor to realize that there was an extra column somewhere in the file that should not have been there.

We return to the original post:

I have described just a few basic features. Other neat ones include:

  • If you want to temporarily turn off all breakpoints during the debug run, use “mute breakpoints”.
  • If you want the breakpoints only to turn on when particular conditions are satisfied, click on the “view breakpoints” icon. In the image below I am setting a rule that means the breakpoint will only interrupt execution when the counter (i) is >= 9998.

Fig 7

  • If you’ve been scrolling around in a big file and can’t find where the breakpoint is, click on the “Show Execution Point” icon.
  • You can change your code as you are debugging without any problem. So, if you discover and fix an error, you don’t have to stop the debugger and start over again. (In many cases, though, it obviously might be a good idea to just start again, in which case you can click on the “Stop” and/or “Rerun” icons).
  • In addition to watches, and values displayed by PyCharm in the editor, you can see the values of a variable (or attribute, etc.) by holding your mouse over that variable.
  • If you want to see plots of variables as you are debugging, you can import matplotlib and insert code in your script to generate a plot of those variables. PyCharm will print such figures during the debug. More details on matplotlib integration with the PyCharm debugger can be found here.

In a future post I will demonstrate PyCharm’s Coverage and Profile features, which are very useful for debugging by allowing you to see what parts of your program (e.g., modules) are/are not being accessed, how frequently, and how much time is being spent in them.


4 thoughts on “Debugging in Python (using PyCharm) – Part 1

  1. Pingback: PyCharm as a Python IDE for Generating UML Diagrams | Water Programming: A Collaborative Research Blog

  2. Pingback: Debugging in Python (using PyCharm) – Part 2 | Water Programming: A Collaborative Research Blog

  3. Pingback: Debugging in Python (using PyCharm) – Part 3 – Water Programming: A Collaborative Research Blog

  4. Pingback: Water Programming Blog Guide (Part I) – Water Programming: A Collaborative Research Blog

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