pybind11: v2.10.1+

.github/workflows/macos.yml

@@ -25,6 +25,7 @@ jobs:
         brew install adios2 || true
         brew install hdf5-mpi || true
         brew install python || true
+        python3 -m pip install -U mpi4py numpy pandas
         set -e
     - name: Build
       env: {CXXFLAGS: -Werror -DTOML11_DISABLE_STD_FILESYSTEM, MACOSX_DEPLOYMENT_TARGET: 10.13}
@@ -41,7 +42,7 @@ jobs:
           -DopenPMD_USE_ADIOS2=ON \
           -DopenPMD_USE_INVASIVE_TESTS=ON
         cmake --build build --parallel 2
-        ctest --test-dir build --output-on-failure
+        ctest --test-dir build --verbose
 
 # TODO: apple_conda_ompi_all (similar to conda_ompi_all on Linux)
 #   both OpenMPI and MPICH cause startup (MPI_Init) issues on GitHub Actions

CHANGELOG.rst

@@ -18,7 +18,7 @@ Features
 """"""""
 
 - include internally shipped toml11 v3.7.1 #1148 #1227
-- pybind11: require version 2.9.1+ #1220
+- pybind11: require version 2.10.1+ #1220 #1322
 
 Bug Fixes
 """""""""

CMakeLists.txt

@@ -401,9 +401,9 @@ if(openPMD_USE_PYTHON STREQUAL AUTO)
         if(openPMD_USE_INTERNAL_PYBIND11)
             add_subdirectory("${openPMD_SOURCE_DIR}/share/openPMD/thirdParty/pybind11")
             set(openPMD_HAVE_PYTHON TRUE)
-            message(STATUS "pybind11: Using INTERNAL version 2.9.1")
+            message(STATUS "pybind11: Using INTERNAL version 2.10.1")
         else()
-            find_package(pybind11 2.9.1 CONFIG)
+            find_package(pybind11 2.10.1 CONFIG)
             if(pybind11_FOUND)
                 set(openPMD_HAVE_PYTHON TRUE)
                 message(STATUS "pybind11: Found version '${pybind11_VERSION}'")
@@ -419,9 +419,9 @@ elseif(openPMD_USE_PYTHON)
     if(openPMD_USE_INTERNAL_PYBIND11)
         add_subdirectory("${openPMD_SOURCE_DIR}/share/openPMD/thirdParty/pybind11")
         set(openPMD_HAVE_PYTHON TRUE)
-        message(STATUS "pybind11: Using INTERNAL version 2.9.1")
+        message(STATUS "pybind11: Using INTERNAL version 2.10.1")
     else()
-        find_package(pybind11 2.9.1 REQUIRED CONFIG)
+        find_package(pybind11 2.10.1 REQUIRED CONFIG)
         set(openPMD_HAVE_PYTHON TRUE)
         message(STATUS "pybind11: Found version '${pybind11_VERSION}'")
     endif()

NEWS.rst

@@ -11,7 +11,7 @@ Building openPMD-api now requires a compiler that supports C++17 or newer.
 
 Python 3.10 is now supported.
 openPMD-api now depends on `toml11 <https://github.com/ToruNiina/toml11>`__ 3.7.1+.
-pybind11 2.9.1 is now the minimally supported version for Python support.
+pybind11 2.10.1 is now the minimally supported version for Python support.
 Catch2 2.13.9 is now the minimally supported version for tests.
 
 The following backend-specific members of the ``Dataset`` class have been removed: ``Dataset::setChunkSize()``, ``Dataset::setCompression()``, ``Dataset::setCustomTransform()``, ``Dataset::chunkSize``, ``Dataset::compression``, ``Dataset::transform``.

README.md

@@ -104,7 +104,7 @@ Required:
 
 Shipped internally in `share/openPMD/thirdParty/`:
 * [Catch2](https://github.com/catchorg/Catch2) 2.13.9+ ([BSL-1.0](https://github.com/catchorg/Catch2/blob/master/LICENSE.txt))
-* [pybind11](https://github.com/pybind/pybind11) 2.9.1+ ([new BSD](https://github.com/pybind/pybind11/blob/master/LICENSE))
+* [pybind11](https://github.com/pybind/pybind11) 2.10.1+ ([new BSD](https://github.com/pybind/pybind11/blob/master/LICENSE))
 * [NLohmann-JSON](https://github.com/nlohmann/json) 3.9.1+ ([MIT](https://github.com/nlohmann/json/blob/develop/LICENSE.MIT))
 * [toml11](https://github.com/ToruNiina/toml11) 3.7.1+ ([MIT](https://github.com/ToruNiina/toml11/blob/master/LICENSE))
 
@@ -120,7 +120,7 @@ while those can be built either with or without:
 Optional language bindings:
 * Python:
   * Python 3.6 - 3.10
-  * pybind11 2.9.1+
+  * pybind11 2.10.1+
   * numpy 1.15+
   * mpi4py 2.1+ (optional, for MPI)
   * pandas 1.0+ (optional, for dataframes)
@@ -272,7 +272,7 @@ The following options allow to switch to external installs:
 | CMake Option                    | Values     | Library       | Version |
 |---------------------------------|------------|---------------|---------|
 | `openPMD_USE_INTERNAL_CATCH`    | **ON**/OFF | Catch2        | 2.13.9+ |
-| `openPMD_USE_INTERNAL_PYBIND11` | **ON**/OFF | pybind11      |  2.9.1+ |
+| `openPMD_USE_INTERNAL_PYBIND11` | **ON**/OFF | pybind11      | 2.10.1+ |
 | `openPMD_USE_INTERNAL_JSON`     | **ON**/OFF | NLohmann-JSON |  3.9.1+ |
 | `openPMD_USE_INTERNAL_TOML11`   | **ON**/OFF | toml11        |  3.7.1+ |
 

docs/source/dev/buildoptions.rst

@@ -69,7 +69,7 @@ The following options allow to switch to external installs of dependencies:
 CMake Option                      Values      Installs Library       Version
 ================================= =========== ======== ============= ========
 ``openPMD_USE_INTERNAL_CATCH``    **ON**/OFF  No       Catch2         2.13.9+
-``openPMD_USE_INTERNAL_PYBIND11`` **ON**/OFF  No       pybind11        2.9.1+
+``openPMD_USE_INTERNAL_PYBIND11`` **ON**/OFF  No       pybind11       2.10.1+
 ``openPMD_USE_INTERNAL_JSON``     **ON**/OFF  No       NLohmann-JSON   3.9.1+
 ``openPMD_USE_INTERNAL_TOML11``   **ON**/OFF  No       toml11          3.7.1+
 ================================= =========== ======== ============= ========

docs/source/dev/dependencies.rst

@@ -18,7 +18,7 @@ Shipped internally
 The following libraries are shipped internally in ``share/openPMD/thirdParty/`` for convenience:
 
 * `Catch2 <https://github.com/catchorg/Catch2>`_ 2.13.9+ (`BSL-1.0 <https://github.com/catchorg/Catch2/blob/master/LICENSE.txt>`__)
-* `pybind11 <https://github.com/pybind/pybind11>`_ 2.9.1+ (`new BSD <https://github.com/pybind/pybind11/blob/master/LICENSE>`_)
+* `pybind11 <https://github.com/pybind/pybind11>`_ 2.10.1+ (`new BSD <https://github.com/pybind/pybind11/blob/master/LICENSE>`_)
 * `NLohmann-JSON <https://github.com/nlohmann/json>`_ 3.9.1+ (`MIT <https://github.com/nlohmann/json/blob/develop/LICENSE.MIT>`_)
 * `toml11 <https://github.com/ToruNiina/toml11>`_ 3.7.1+ (`MIT <https://github.com/ToruNiina/toml11/blob/master/LICENSE>`__)
 
@@ -40,7 +40,7 @@ Optional: language bindings
 * Python:
 
   * Python 3.6 - 3.10
-  * pybind11 2.9.1+
+  * pybind11 2.10.1+
   * numpy 1.15+
   * mpi4py 2.1+ (optional, for MPI)
   * pandas 1.0+ (optional, for dataframes)

pyproject.toml

@@ -3,6 +3,6 @@ requires = [
     "setuptools>=42",
     "wheel",
     "cmake>=3.15.0,<4.0.0",
-    "pybind11>=2.9.1,<3.0.0"
+    "pybind11>=2.10.1,<3.0.0"
 ]
 build-backend = "setuptools.build_meta"

share/openPMD/thirdParty/pybind11/CMakeLists.txt

@@ -91,10 +91,16 @@ endif()
 option(PYBIND11_INSTALL "Install pybind11 header files?" ${PYBIND11_MASTER_PROJECT})
 option(PYBIND11_TEST "Build pybind11 test suite?" ${PYBIND11_MASTER_PROJECT})
 option(PYBIND11_NOPYTHON "Disable search for Python" OFF)
+option(PYBIND11_SIMPLE_GIL_MANAGEMENT
+       "Use simpler GIL management logic that does not support disassociation" OFF)
 set(PYBIND11_INTERNALS_VERSION
     ""
     CACHE STRING "Override the ABI version, may be used to enable the unstable ABI.")
 
+if(PYBIND11_SIMPLE_GIL_MANAGEMENT)
+  add_compile_definitions(PYBIND11_SIMPLE_GIL_MANAGEMENT)
+endif()
+
 cmake_dependent_option(
   USE_PYTHON_INCLUDE_DIR
   "Install pybind11 headers in Python include directory instead of default installation prefix"
@@ -198,6 +204,9 @@ else()
 endif()
 
 include("${CMAKE_CURRENT_SOURCE_DIR}/tools/pybind11Common.cmake")
+# https://github.com/jtojnar/cmake-snips/#concatenating-paths-when-building-pkg-config-files
+# TODO: cmake 3.20 adds the cmake_path() function, which obsoletes this snippet
+include("${CMAKE_CURRENT_SOURCE_DIR}/tools/JoinPaths.cmake")
 
 # Relative directory setting
 if(USE_PYTHON_INCLUDE_DIR AND DEFINED Python_INCLUDE_DIRS)
@@ -262,6 +271,16 @@ if(PYBIND11_INSTALL)
     NAMESPACE "pybind11::"
     DESTINATION ${PYBIND11_CMAKECONFIG_INSTALL_DIR})
 
+  # pkg-config support
+  if(NOT prefix_for_pc_file)
+    set(prefix_for_pc_file "${CMAKE_INSTALL_PREFIX}")
+  endif()
+  join_paths(includedir_for_pc_file "\${prefix}" "${CMAKE_INSTALL_INCLUDEDIR}")
+  configure_file("${CMAKE_CURRENT_SOURCE_DIR}/tools/pybind11.pc.in"
+                 "${CMAKE_CURRENT_BINARY_DIR}/pybind11.pc" @ONLY)
+  install(FILES "${CMAKE_CURRENT_BINARY_DIR}/pybind11.pc"
+          DESTINATION "${CMAKE_INSTALL_DATAROOTDIR}/pkgconfig/")
+
   # Uninstall target
   if(PYBIND11_MASTER_PROJECT)
     configure_file("${CMAKE_CURRENT_SOURCE_DIR}/tools/cmake_uninstall.cmake.in"

share/openPMD/thirdParty/pybind11/MANIFEST.in

@@ -1,6 +1,5 @@
 recursive-include pybind11/include/pybind11 *.h
 recursive-include pybind11 *.py
 recursive-include pybind11 py.typed
-recursive-include pybind11 *.pyi
 include pybind11/share/cmake/pybind11/*.cmake
 include LICENSE README.rst pyproject.toml setup.py setup.cfg

share/openPMD/thirdParty/pybind11/README.rst

@@ -32,9 +32,9 @@ this heavy machinery has become an excessively large and unnecessary
 dependency.
 
 Think of this library as a tiny self-contained version of Boost.Python
-with everything stripped away that isn’t relevant for binding
+with everything stripped away that isn't relevant for binding
 generation. Without comments, the core header files only require ~4K
-lines of code and depend on Python (2.7 or 3.5+, or PyPy) and the C++
+lines of code and depend on Python (3.6+, or PyPy) and the C++
 standard library. This compact implementation was possible thanks to
 some of the new C++11 language features (specifically: tuples, lambda
 functions and variadic templates). Since its creation, this library has
@@ -78,8 +78,8 @@ Goodies
 In addition to the core functionality, pybind11 provides some extra
 goodies:
 
-- Python 2.7, 3.5+, and PyPy/PyPy3 7.3 are supported with an
-  implementation-agnostic interface.
+- Python 3.6+, and PyPy3 7.3 are supported with an implementation-agnostic
+  interface (pybind11 2.9 was the last version to support Python 2 and 3.5).
 
 - It is possible to bind C++11 lambda functions with captured
   variables. The lambda capture data is stored inside the resulting
@@ -88,8 +88,8 @@ goodies:
 - pybind11 uses C++11 move constructors and move assignment operators
   whenever possible to efficiently transfer custom data types.
 
-- It’s easy to expose the internal storage of custom data types through
-  Pythons’ buffer protocols. This is handy e.g. for fast conversion
+- It's easy to expose the internal storage of custom data types through
+  Pythons' buffer protocols. This is handy e.g. for fast conversion
   between C++ matrix classes like Eigen and NumPy without expensive
   copy operations.
 
@@ -119,10 +119,10 @@ goodies:
 Supported compilers
 -------------------
 
-1. Clang/LLVM 3.3 or newer (for Apple Xcode’s clang, this is 5.0.0 or
+1. Clang/LLVM 3.3 or newer (for Apple Xcode's clang, this is 5.0.0 or
    newer)
 2. GCC 4.8 or newer
-3. Microsoft Visual Studio 2015 Update 3 or newer
+3. Microsoft Visual Studio 2017 or newer
 4. Intel classic C++ compiler 18 or newer (ICC 20.2 tested in CI)
 5. Cygwin/GCC (previously tested on 2.5.1)
 6. NVCC (CUDA 11.0 tested in CI)