Debugging C extensions#

pandas uses Cython and C/C++ extension modules to optimize performance. Unfortunately, the standard Python debugger does not allow you to step into these extensions. Cython extensions can be debugged with the Cython debugger and C/C++ extensions can be debugged using the tools shipped with your platform’s compiler.

For Python developers with limited or no C/C++ experience this can seem a daunting task. Core developer Will Ayd has written a 3 part blog series to help guide you from the standard Python debugger into these other tools:

Debugging locally#

By default building pandas from source will generate a release build. To generate a development build you can type:

pip install -ve . --no-build-isolation --config-settings=builddir="debug" --config-settings=setup-args="-Dbuildtype=debug"


conda environments update CFLAGS/CPPFLAGS with flags that are geared towards generating releases. If using conda, you may need to set CFLAGS="$CFLAGS -O0" and CPPFLAGS="$CPPFLAGS -O0" to ensure optimizations are turned off for debugging

By specifying builddir="debug" all of the targets will be built and placed in the debug directory relative to the project root. This helps to keep your debug and release artifacts separate; you are of course able to choose a different directory name or omit altogether if you do not care to separate build types.

Using Docker#

To simplify the debugging process, pandas has created a Docker image with a debug build of Python and the gdb/Cython debuggers pre-installed. You may either docker pull pandas/pandas-debug to get access to this image or build it from the tooling/debug folder locallly.

You can then mount your pandas repository into this image via:

docker run --rm -it -w /data -v ${PWD}:/data pandas/pandas-debug

Inside the image, you can use meson to build/install pandas and place the build artifacts into a debug folder using a command as follows:

python -m pip install -ve . --no-build-isolation --config-settings=builddir="debug" --config-settings=setup-args="-Dbuildtype=debug"

If planning to use cygdb, the files required by that application are placed within the build folder. So you have to first cd to the build folder, then start that application.

cd debug

Within the debugger you can use cygdb commands to navigate cython extensions.

Editor support#

The meson build system generates a compilation database automatically and places it in the build directory. Many language servers and IDEs can use this information to provide code-completion, go-to-definition and error checking support as you type.

How each language server / IDE chooses to look for the compilation database may vary. When in doubt you may want to create a symlink at the root of the project that points to the compilation database in your build directory. Assuming you used debug as your directory name, you can run:

ln -s debug/compile_commands.json .