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C Extension

This repository interfaces with clustering.c via nanobind to efficiently generate C extensions.

Building

Build inplace with:

pip install nanobind scikit-build-core
pip install -e . --no-build-isolation

Run tests with

pip install pytest
pytest -x

Before committing and pushing code, ensure you've run pre-commit. Install and run with:

pip install pre-commit
pre-commit install

Then commit. pre-commit will run automatically`.

Emacs configuration

If using emacs and helm, generate the project configuration files using -DCMAKE_EXPORT_COMPILE_COMMANDS=ON. Here's a sample configuration for C++11 on Linux:

pip install nanobind
export NANOBIND_INCLUDE=$(python -c "import nanobind, os; print(os.path.join(os.path.dirname(nanobind.__file__), 'cmake'))")
cmake -Dnanobind_DIR=$NANOBIND_INCLUDE -DCMAKE_EXPORT_COMPILE_COMMANDS=ON -DCMAKE_CXX_STANDARD_INCLUDE_DIRECTORIES="/usr/include/c++/11;/usr/include/x86_64-linux-gnu/c++/11/;/usr/lib/gcc/x86_64-linux-gnu/11/include/"

These will be necessary for helm and treesit to determine the locations of the header files.

Debug Build

This can be helpful when debugging segfaults since this extension often uses raw pointers.

Set the cmake build type to debug in `pyproject.toml``

[tool.scikit-build]
cmake.build-type = "Debug"

Set the target compile options to build debug symbols with -g and -O0 in CMakeLists.txt:

target_compile_options(_utilities PRIVATE -g -O0)
target_compile_options(pfh PRIVATE -g -O0)

Finally, run using gdb. For example:

$ gdb --args python test_ext.py
(gdb) b qual.cpp:4872
Make breakpoint pending on future shared library load? (y or [n]) y
Breakpoint 1 (qual.cpp:4872) pending.
(gdb) run
Thread 1 "python" hit Breakpoint 1, ComputeWeights<float> (offset=0x1fe5830, neigh=0x20432e0,
indices=0x1bb8ec0, points=0x1d6a7a0, n_neigh=108, n_points=27, fac=-0.75, num_threads=4) at /home/user/library-path/src/qual.cpp:4872
4872      T *weights = new T[n_neigh];
(gdb)

Debugging memory leaks

These can be challenging to find. Use valgrind with the following to identify memory leaks. Be sure to download valgrind-python.supp.

 valgrind --leak-check=full --log-file=val.txt --suppressions=valgrind-python.supp pytest -k clus && grep 'new\[\]' val.txt