ci(deps): update c++ dependencies (main)

[renovate]

This PR contains the following updates:

Package	Update	Change
doctest	patch	v2.5.1 → v2.5.2
pybind11	patch	v3.0.1 → v3.0.4

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Release Notes

doctest/doctest (doctest)

v2.5.2

Compare Source

What's Changed

• build(cmake): Use single-source doctest.cpp for doctest_with_main target by @​mitchgrout in #​1106
• chore(release): v2.5.2 by @​mitchgrout in #​1107

Full Changelog: doctest/doctest@v2.5.1...v2.5.2

pybind/pybind11 (pybind11)

v3.0.4: Version 3.0.4

Compare Source

Bug fixes:

• Fixed test builds with installed Eigen 5 by improving Eigen3 CMake package detection.
  #​6036

• Fixed move semantics of scoped_ostream_redirect to preserve buffered output and avoid crashes when moved redirects restore stream buffers.
  #​6033

• Fixed py::dynamic_attr() traversal on Python 3.13+ to correctly propagate PyObject_VisitManagedDict() results.
  #​6032

• Fixed std::shared_ptr<T> fallback casting to avoid unnecessary copy-constructor instantiation in reference_internal paths.
  #​6028

CI:

• Updated setup-uv to the maintained GitHub Action tag scheme.
  #​6035

• Updated pre-commit hooks.
  #​6029

• Updated GitHub Actions dependencies, including actions-setup-cmake and cibuildwheel.
  #​6027

v3.0.3: Version 3.0.3

Compare Source

Bug fixes:

• Fixed TSS key exhaustion in implicitly_convertible() when many implicit conversions are registered across large module sets.
  #​6020

• Fixed heap-buffer-overflow in pythonbuf with undersized buffers by enforcing a minimum buffer size.
  #​6019

• Fixed virtual-inheritance pointer offset crashes when dispatching inherited methods through virtual bases.
  #​6017

• Fixed free(): invalid pointer crashes during interpreter shutdown with py::enum_<> by duplicating late-added def_property_static argument strings.
  #​6015

• Fixed function_record heap-type deallocation to call PyObject_Free() and decref the type.
  #​6010

• Hardened PYBIND11_MODULE_PYINIT and get_internals() against module-initialization crashes.
  #​6018

• Fixed static_pointer_cast build failure with virtual inheritance in holder_caster_foreign_helpers.h.
  #​6014

• Fixed ambiguous factory template specialization that caused compilation failures with nvcc + GCC 14.
  #​6011

• Fixed crash in def_readwrite for non-smart-holder properties of smart-holder classes.
  #​6008

• Fixed memory leak for py::dynamic_attr() objects on Python 3.13+ by clearing managed __dict__ contents during deallocation.
  #​5999

• Fixed binding of noexcept and ref-qualified (&, &&) methods inherited from unregistered base classes.
  #​5992

Internal:

• Moved tomlkit dependency to the dev dependency group.
  #​5990

• Switched to newer public CPython APIs (PyType_GetFlags and public vectorcall APIs where available).
  #​6005

Tests:

• Made an async callback test deterministic by replacing fixed sleep with bounded waiting.
  #​5986

CI:

• Re-enabled Android tests in the cibuildwheel workflow.
  #​6001

v3.0.2: Version 3.0.2

Compare Source

New Features:

• Added helper functions to py::array that return shape and strides as std::span when available.
  #​5974

Bug fixes:

• Added fallback locking for Python 3.13t where PyCriticalSection_BeginMutex is unavailable.
  #​5981

• Fixed race condition in py::make_key_iterator with free-threaded Python.
  #​5971

• MSVC 19.16 and earlier were blocked from using std::launder due to internal compiler errors.
  #​5968

• Internals destructors were updated to check the owning interpreter before clearing Python objects.
  #​5965

• Internals shutdown handling was refined in two iterations before release: an initial finalization-time cleanup was followed by a safety adjustment to avoid late-shutdown py::cast segfaults.
  #​5958
  #​5972

• Fixed ambiguous str(handle) construction for object-derived types like kwargs or dict by templatizing the constructor with SFINAE.
  #​5949

• Fixed concurrency consistency for internals_pp_manager under multiple-interpreters.
  #​5947

• Fixed MSVC LNK2001 in C++20 builds when /GL (whole program optimization) is enabled.
  #​5939

• Added per-interpreter storage for gil_safe_call_once_and_store to make it safe under multi-interpreters.
  #​5933

• A workaround for a GCC -Warray-bounds false positive in argument_vector was added.
  #​5908

• Corrected a mistake where support for __index__ was added, but the type hints did not reflect acceptance of SupportsIndex objects. Also fixed a long-standing bug: the complex-caster did not accept __index__ in convert mode.
  #​5891

• Fixed *args/**kwargs return types. Added type hinting to py::make_tuple.
  #​5881

• Fixed compiler error in type_caster_generic when casting a T implicitly convertible from T*.
  #​5873

• Updated py::native_enum bindings to unregister enum types on destruction, preventing a use-after-free when returning a destroyed enum instance.
  #​5871

• Fixed undefined behavior that occurred when importing pybind11 modules from non-main threads created by C API modules or embedded python interpreters.
  #​5870

• Fixed dangling pointer in internals::registered_types_cpp_fast.
  #​5867

• Added support for std::shared_ptr<T> when loading module-local or conduit types from other modules.
  #​5862

• Fixed thread-safety issues if types were concurrently registered while get_local_type_info() was called in free threaded Python.
  #​5856

• Fixed py::float_ casting and py::int_ and py::float_ type hints.
  #​5839

• Fixed two smart_holder bugs in shared_ptr and unique_ptr adoption with multiple/virtual inheritance:

  • shared_ptr to-Python caster was updated to register the correct subobject pointer (fixes #​5786).
  • unique_ptr adoption was updated to own the proper object start while aliasing subobject pointers for registration, which fixed MSVC crashes during destruction.
    #​5836

• Constrained accessor::operator= templates to avoid obscuring special members.
  #​5832

• Fixed crash that can occur when finalizers acquire and release the GIL.
  #​5828

• Fixed compiler detection in pybind11/detail/pybind11_namespace_macros.h for clang-cl on Windows, to address warning suppression macros.
  #​5816

• Fixed compatibility with CMake policy CMP0190 by not always requiring a Python interpreter when cross-compiling.
  #​5829

• Added a static assertion to disallow keep_alive and call_guard on properties.
  #​5533

Internal:

• CMake policy limit was set to 4.1.
  #​5944

• Improved performance of function calls between Python and C++ by switching to the "vectorcall" calling protocol.
  #​5948

• Many C-style casts were replaced with C++-style casts.
  #​5930

• Added cast_sources abstraction to type_caster_generic.
  #​5866

• Improved the performance of from-Python conversions of legacy pybind11 enum objects bound by py::enum_.
  #​5860

• Reduced size overhead by deduplicating functions' readable signatures and type information.
  #​5857

• Used new Python 3.14 C APIs when available.
  #​5854

• Improved performance of function dispatch and type casting by porting two-level type info lookup strategy from nanobind.
  #​5842

• Updated .gitignore to exclude __pycache__/ directories.
  #​5838

• Changed internals to use thread_local instead of thread_specific_storage for increased performance.
  #​5834

• Reduced function call overhead by using thread_local for loader_life_support when possible.
  #​5830

• Removed heap allocation for the C++ argument array when dispatching functions with 6 or fewer arguments.
  #​5824

Documentation:

• Fixed docstring for long double complex types to use numpy.clongdouble instead of the deprecated numpy.longcomplex (removed in NumPy 2.0).
  #​5952

• The "Supported compilers" and "Supported platforms" sections in the main README.rst were replaced with a new "Supported platforms & compilers" section that points to the CI test matrix as the living source of truth.
  #​5910

• Fixed documentation formatting.
  #​5903

• Updated upgrade notes for py::native_enum.
  #​5885

• Clarified in the docs to what extent bindings are global.
  #​5859

Tests:

• Fixed deadlock in a free-threading test by releasing the GIL while waiting on synchronization.
  #​5973

• Calls to env.deprecated_call() were replaced with direct calls to pytest.deprecated_call().
  #​5893

• Updated pytest configuration to use log_level instead of log_cli_level.
  #​5890

CI:

• Added CI tests for windows-11-arm with clang/MSVC (currently python 3.13), windows-11-arm with clang/mingw (currently python 3.12).
  #​5932

• These clang-tidy rules were added: readability-redundant-casting, readability-redundant-inline-specifier, readability-redundant-member-init
  #​5924

• Replaced deprecated macos-13 runners with macos-15-intel in CI.
  #​5916

• Restored runs-on: windows-latest in CI.
  #​5835

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[overlap-benchmarks]

C++ benchmark results

Benchmark	Reference (797c5e8)	Current (d4bca65)
construction[hex]	888 ns	885 ns: 1.00x faster
construction[tet]	304 ns	294 ns: 1.03x faster
construction[wedge]	597 ns	605 ns: 1.01x slower
hex_overlap_volume[sphere-in-hex]	564 ns	558 ns: 1.01x faster
normal_newell	50.5 ns	50.9 ns: 1.01x slower
tet_overlap_volume[sphere-in-hex]	1.22 us	1.21 us: 1.01x faster
Geometric mean	(ref)	1.00x faster

Benchmark hidden because not significant (6): hex_overlap_volume[AABB], hex_overlap_volume[hex-in-sphere], hex_overlap_volume[random], regularized_wedge, tet_overlap_volume[AABB], tet_overlap_volume[hex-in-sphere]

Python benchmark results

Benchmark	Reference	Current
hex_overlap_volume[sphere-in-hex]	2.45 us	2.19 us: 1.12x faster
hex_overlap_volume[hex-in-sphere]	1.70 us	1.52 us: 1.11x faster
hex_overlap_volume[AABB]	1.68 us	1.51 us: 1.11x faster
tet_overlap_volume[sphere-in-tet]	1.29 us	1.06 us: 1.21x faster
tet_overlap_volume[tet-in-sphere]	300 ns	196 ns: 1.53x faster
tet_overlap_volume[AABB]	288 ns	184 ns: 1.57x faster
construction[tet]	3.23 us	2.97 us: 1.09x faster
construction[wedge]	4.34 us	4.05 us: 1.07x faster
construction[hex]	5.73 us	5.32 us: 1.08x faster
hex_overlap_volume[random]	10.2 us	9.45 us: 1.07x faster
Geometric mean	(ref)	1.18x faster