Migrate from pybind11 to nanobind

[msimberg]

This is still work in progress, but functional, at least according to GHEX tests.

This was heavily assisted by LLMs (various models). All bugs are mine.

[Copilot]

Pull request overview

Migrates the project’s Python bindings from pybind11 to nanobind, updating the C++ binding layer, CMake integration, and CI/test setup accordingly.

Changes:

• Switch Python binding implementation from pybind11 APIs/macros to nanobind equivalents across structured/unstructured bindings.
• Update build configuration to locate and build against nanobind (CMake + pyproject build requirements).
• Adjust test/CI workflows and packaging metadata to reflect the new binding backend.

Reviewed changes

Copilot reviewed 27 out of 27 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
test/bindings/python/CMakeLists.txt	Uses Python_EXECUTABLE and refactors test target dependencies.
pyproject.toml	Replaces pybind11 build requirement with nanobind.
include/ghex/structured/regular/halo_generator.hpp	Adds missing <vector> include.
cmake/ghex_python.cmake	Switches to FindPython + nanobind discovery via python module + CMake config.
bindings/python/src/ghex/pyghex/init.py	Updates documentation comment to nanobind.
bindings/python/src/ghex/CMakeLists.txt	Adds pyghex_files target to refresh Python files for tests.
bindings/python/src/_pyghex/unstructured/pattern.cpp	Ports bindings from pybind11 to nanobind.
bindings/python/src/_pyghex/unstructured/halo_generator.cpp	Ports bindings from pybind11 to nanobind; adjusts constructors.
bindings/python/src/_pyghex/unstructured/field_descriptor.cpp	Reworks buffer/ndarray handling using nanobind::ndarray.
bindings/python/src/_pyghex/unstructured/domain_descriptor.cpp	Ports bindings and adds NB v1/v2 constructor handling.
bindings/python/src/_pyghex/unstructured/communication_object.cpp	Ports bindings + CUDA stream extraction to nanobind.
bindings/python/src/_pyghex/structured/regular/pattern.cpp	Ports bindings from pybind11 to nanobind.
bindings/python/src/_pyghex/structured/regular/halo_generator.cpp	Ports bindings; adjusts __call__ return handling for nanobind.
bindings/python/src/_pyghex/structured/regular/field_descriptor.cpp	Reworks buffer/ndarray handling using nanobind::ndarray.
bindings/python/src/_pyghex/structured/regular/domain_descriptor.cpp	Ports bindings from pybind11 to nanobind.
bindings/python/src/_pyghex/structured/regular/communication_object.cpp	Ports bindings from pybind11 to nanobind.
bindings/python/src/_pyghex/register_class.hpp	Updates helper to return nanobind::class_ and properties.
bindings/python/src/_pyghex/py_dtype_to_cpp_name.cpp	Reimplements dtype mapping using nanobind + NumPy dtype canonicalization.
bindings/python/src/_pyghex/mpi_comm_shim.hpp	Switches shim API from pybind11 to nanobind.
bindings/python/src/_pyghex/mpi_comm_shim.cpp	Ports MPI shim registration and conversion logic to nanobind.
bindings/python/src/_pyghex/module.cpp	Replaces PYBIND11_MODULE with NB_MODULE and updates registrations.
bindings/python/src/_pyghex/context_shim.cpp	Ports context bindings to nanobind.
bindings/python/src/_pyghex/config.cpp	Ports config bindings to nanobind and updates version reporting.
bindings/python/src/_pyghex/CMakeLists.txt	Builds Python extension via nanobind_add_module.
README.md	Updates dependency list to Nanobind.
.github/workflows/test_pip.yml	Removes pybind11 system package install in pip workflow.
.github/workflows/CI.yml	Replaces python3-pybind11 with nanobind-dev in CI apt dependencies.

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[Copilot]

convert_to_mpi_comm does not actually call py2f(). o.attr("py2f") returns the bound method object, so casting it to MPI_Fint will fail at runtime. Call the method and cast its result (i.e., invoke py2f before converting to MPI_Comm).

Suggested change

	return MPI_Comm_f2c(nanobind::cast<MPI_Fint>(o.attr("py2f")()));
	auto py2f_method = o.attr("py2f");
	auto f_comm_obj = py2f_method();
	MPI_Fint f_comm = nanobind::cast<MPI_Fint>(f_comm_obj);
	return MPI_Comm_f2c(f_comm);

[Copilot]

The __cuda_stream__ protocol version check is inverted: version 0 is the expected value per the CUDA stream protocol, but the code throws when protocol_version == 0. This will reject valid stream objects. Flip the condition so that only non-zero protocol versions raise an error.

[msimberg]

@philip-paul-mueller this note looks very legit. Can you comment if it's right to complain or if the error message itself is wrong?

[msimberg]

Fixed by @philip-paul-mueller in #202. I'll apply the change here as well.