Update Pybind to 2.11.1 (#1489)

* Update Pybind to 2.11.1 * Document version change --------- Co-authored-by: Ralf W. Grosse-Kunstleve <[email protected]>
openPMD · Aug 8, 2023 · 1df8049 · 1df8049
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diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -17,6 +17,8 @@ Changes to "0.15.0"
 Features
 """"""""
 
+- pybind11: require version 2.11.1+ #1220 #1322
+
 Bug Fixes
 """""""""
 

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -402,9 +402,9 @@ if(openPMD_USE_PYTHON STREQUAL AUTO)
         if(openPMD_USE_INTERNAL_PYBIND11)
             add_subdirectory("${openPMD_SOURCE_DIR}/share/openPMD/thirdParty/pybind11")
             set(openPMD_HAVE_PYTHON TRUE)
-            message(STATUS "pybind11: Using INTERNAL version 2.10.1")
+            message(STATUS "pybind11: Using INTERNAL version 2.11.1")
         else()
-            find_package(pybind11 2.10.1 CONFIG)
+            find_package(pybind11 2.11.1 CONFIG)
             if(pybind11_FOUND)
                 set(openPMD_HAVE_PYTHON TRUE)
                 message(STATUS "pybind11: Found version '${pybind11_VERSION}'")
@@ -420,9 +420,9 @@ elseif(openPMD_USE_PYTHON)
     if(openPMD_USE_INTERNAL_PYBIND11)
         add_subdirectory("${openPMD_SOURCE_DIR}/share/openPMD/thirdParty/pybind11")
         set(openPMD_HAVE_PYTHON TRUE)
-        message(STATUS "pybind11: Using INTERNAL version 2.10.1")
+        message(STATUS "pybind11: Using INTERNAL version 2.11.1")
     else()
-        find_package(pybind11 2.10.1 REQUIRED CONFIG)
+        find_package(pybind11 2.11.1 REQUIRED CONFIG)
         set(openPMD_HAVE_PYTHON TRUE)
         message(STATUS "pybind11: Found version '${pybind11_VERSION}'")
     endif()

diff --git a/NEWS.rst b/NEWS.rst
@@ -13,6 +13,8 @@ Please transition to ADIOS2.
 For reading legacy ADIOS1 BP3 files, either use an older version of openPMD-api or the BP3 backend in ADIOS2.
 Note that ADIOS2 does not support compression in BP3 files.
 
+pybind11 2.11.1 is now the minimally supported version for Python support.
+
 
 0.15.0
 ------

diff --git a/README.md b/README.md
@@ -7,9 +7,9 @@ C++ & Python API for Scientific I/O with openPMD
 [![Gitter chat](https://img.shields.io/gitter/room/openPMD/API)](https://gitter.im/openPMD/API)
 ![Supported Platforms][api-platforms]
 [![License](https://img.shields.io/badge/license-LGPLv3-blue)](https://www.gnu.org/licenses/lgpl-3.0.html)
-[![DOI](https://rodare.hzdr.de/badge/DOI/10.14278/rodare.27.svg)](https://doi.org/10.14278/rodare.27)  
+[![DOI](https://rodare.hzdr.de/badge/DOI/10.14278/rodare.27.svg)](https://doi.org/10.14278/rodare.27)
 [![CodeFactor](https://www.codefactor.io/repository/github/openpmd/openpmd-api/badge)](https://www.codefactor.io/repository/github/openpmd/openpmd-api)
-[![Coverage Status](https://coveralls.io/repos/github/openPMD/openPMD-api/badge)](https://coveralls.io/github/openPMD/openPMD-api)  
+[![Coverage Status](https://coveralls.io/repos/github/openPMD/openPMD-api/badge)](https://coveralls.io/github/openPMD/openPMD-api)
 [![Documentation Status](https://readthedocs.org/projects/openpmd-api/badge/?version=latest)](https://openpmd-api.readthedocs.io/en/latest/?badge=latest)
 [![Linux/OSX Build Status dev](https://travis-ci.com/openPMD/openPMD-api.svg?branch=dev)](https://travis-ci.com/openPMD/openPMD-api)
 [![Windows Build Status dev](https://ci.appveyor.com/api/projects/status/x95q4n620pqk0e0t/branch/dev?svg=true)](https://ci.appveyor.com/project/ax3l/openpmd-api/branch/dev)
@@ -101,7 +101,7 @@ Required:
 
 Shipped internally in `share/openPMD/thirdParty/`:
 * [Catch2](https://github.com/catchorg/Catch2) 2.13.10+ ([BSL-1.0](https://github.com/catchorg/Catch2/blob/master/LICENSE.txt))
-* [pybind11](https://github.com/pybind/pybind11) 2.10.1+ ([new BSD](https://github.com/pybind/pybind11/blob/master/LICENSE))
+* [pybind11](https://github.com/pybind/pybind11) 2.11.1+ ([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))
 
@@ -116,7 +116,7 @@ while those can be built either with or without:
 Optional language bindings:
 * Python:
   * Python 3.7 - 3.11
-  * pybind11 2.10.1+
+  * pybind11 2.11.1+
   * numpy 1.15+
   * mpi4py 2.1+ (optional, for MPI)
   * pandas 1.0+ (optional, for dataframes)
@@ -267,7 +267,7 @@ The following options allow to switch to external installs:
 | CMake Option                    | Values     | Library       | Version  |
 |---------------------------------|------------|---------------|----------|
 | `openPMD_USE_INTERNAL_CATCH`    | **ON**/OFF | Catch2        | 2.13.10+ |
-| `openPMD_USE_INTERNAL_PYBIND11` | **ON**/OFF | pybind11      |  2.10.1+ |
+| `openPMD_USE_INTERNAL_PYBIND11` | **ON**/OFF | pybind11      |  2.11.1+ |
 | `openPMD_USE_INTERNAL_JSON`     | **ON**/OFF | NLohmann-JSON |   3.9.1+ |
 | `openPMD_USE_INTERNAL_TOML11`   | **ON**/OFF | toml11        |   3.7.1+ |
 

diff --git a/docs/source/dev/buildoptions.rst b/docs/source/dev/buildoptions.rst
@@ -67,7 +67,7 @@ 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        2.13.10+
-``openPMD_USE_INTERNAL_PYBIND11`` **ON**/OFF  No       pybind11       2.10.1+
+``openPMD_USE_INTERNAL_PYBIND11`` **ON**/OFF  No       pybind11       2.11.1+
 ``openPMD_USE_INTERNAL_JSON``     **ON**/OFF  No       NLohmann-JSON   3.9.1+
 ``openPMD_USE_INTERNAL_TOML11``   **ON**/OFF  No       toml11          3.7.1+
 ================================= =========== ======== ============= ========

diff --git a/docs/source/dev/dependencies.rst b/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>`_ 2.13.10+ (`BSL-1.0 <https://github.com/catchorg/Catch2/blob/master/LICENSE.txt>`__)
-* `pybind11 <https://github.com/pybind/pybind11>`_ 2.10.1+ (`new BSD <https://github.com/pybind/pybind11/blob/master/LICENSE>`_)
+* `pybind11 <https://github.com/pybind/pybind11>`_ 2.11.1+ (`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 3.7 - 3.11
-  * pybind11 2.10.1+
+  * pybind11 2.11.1+
   * numpy 1.15+
   * mpi4py 2.1+ (optional, for MPI)
   * pandas 1.0+ (optional, for dataframes)

diff --git a/pyproject.toml b/pyproject.toml
@@ -3,6 +3,6 @@ requires = [
     "setuptools>=42",
     "wheel",
     "cmake>=3.15.0,<4.0.0",
-    "pybind11>=2.10.1,<3.0.0"
+    "pybind11>=2.11.1,<3.0.0"
 ]
 build-backend = "setuptools.build_meta"
diff --git a/share/openPMD/thirdParty/pybind11/CMakeLists.txt b/share/openPMD/thirdParty/pybind11/CMakeLists.txt
@@ -5,15 +5,15 @@
 # All rights reserved. Use of this source code is governed by a
 # BSD-style license that can be found in the LICENSE file.
 
-cmake_minimum_required(VERSION 3.4)
+cmake_minimum_required(VERSION 3.5)
 
-# The `cmake_minimum_required(VERSION 3.4...3.22)` syntax does not work with
+# The `cmake_minimum_required(VERSION 3.5...3.26)` syntax does not work with
 # some versions of VS that have a patched CMake 3.11. This forces us to emulate
 # the behavior using the following workaround:
-if(${CMAKE_VERSION} VERSION_LESS 3.22)
+if(${CMAKE_VERSION} VERSION_LESS 3.26)
   cmake_policy(VERSION ${CMAKE_MAJOR_VERSION}.${CMAKE_MINOR_VERSION})
 else()
-  cmake_policy(VERSION 3.22)
+  cmake_policy(VERSION 3.26)
 endif()
 
 # Avoid infinite recursion if tests include this as a subdirectory
@@ -126,6 +126,9 @@ set(PYBIND11_HEADERS
     include/pybind11/complex.h
     include/pybind11/options.h
     include/pybind11/eigen.h
+    include/pybind11/eigen/common.h
+    include/pybind11/eigen/matrix.h
+    include/pybind11/eigen/tensor.h
     include/pybind11/embed.h
     include/pybind11/eval.h
     include/pybind11/gil.h
@@ -137,7 +140,8 @@ set(PYBIND11_HEADERS
     include/pybind11/pytypes.h
     include/pybind11/stl.h
     include/pybind11/stl_bind.h
-    include/pybind11/stl/filesystem.h)
+    include/pybind11/stl/filesystem.h
+    include/pybind11/type_caster_pyobject_ptr.h)
 
 # Compare with grep and warn if mismatched
 if(PYBIND11_MASTER_PROJECT AND NOT CMAKE_VERSION VERSION_LESS 3.12)

diff --git a/share/openPMD/thirdParty/pybind11/MANIFEST.in b/share/openPMD/thirdParty/pybind11/MANIFEST.in
@@ -1,5 +1,6 @@
+prune tests
 recursive-include pybind11/include/pybind11 *.h
 recursive-include pybind11 *.py
 recursive-include pybind11 py.typed
 include pybind11/share/cmake/pybind11/*.cmake
-include LICENSE README.rst pyproject.toml setup.py setup.cfg
+include LICENSE README.rst SECURITY.md pyproject.toml setup.py setup.cfg
diff --git a/share/openPMD/thirdParty/pybind11/README.rst b/share/openPMD/thirdParty/pybind11/README.rst
@@ -135,7 +135,7 @@ This project was created by `Wenzel
 Jakob <http://rgl.epfl.ch/people/wjakob>`_. Significant features and/or
 improvements to the code were contributed by Jonas Adler, Lori A. Burns,
 Sylvain Corlay, Eric Cousineau, Aaron Gokaslan, Ralf Grosse-Kunstleve, Trent Houliston, Axel
-Huebl, @hulucc, Yannick Jadoul, Sergey Lyskov Johan Mabille, Tomasz Miąsko,
+Huebl, @hulucc, Yannick Jadoul, Sergey Lyskov, Johan Mabille, Tomasz Miąsko,
 Dean Moldovan, Ben Pritchard, Jason Rhinelander, Boris Schäling, Pim
 Schellart, Henry Schreiner, Ivan Smirnov, Boris Staletic, and Patrick Stewart.
 

diff --git a/share/openPMD/thirdParty/pybind11/include/pybind11/attr.h b/share/openPMD/thirdParty/pybind11/include/pybind11/attr.h
@@ -26,6 +26,9 @@ struct is_method {
     explicit is_method(const handle &c) : class_(c) {}
 };
 
+/// Annotation for setters
+struct is_setter {};
+
 /// Annotation for operators
 struct is_operator {};
 
@@ -188,8 +191,8 @@ struct argument_record {
 struct function_record {
     function_record()
         : is_constructor(false), is_new_style_constructor(false), is_stateless(false),
-          is_operator(false), is_method(false), has_args(false), has_kwargs(false),
-          prepend(false) {}
+          is_operator(false), is_method(false), is_setter(false), has_args(false),
+          has_kwargs(false), prepend(false) {}
 
     /// Function name
     char *name = nullptr; /* why no C++ strings? They generate heavier code.. */
@@ -230,6 +233,9 @@ struct function_record {
     /// True if this is a method
     bool is_method : 1;
 
+    /// True if this is a setter
+    bool is_setter : 1;
+
     /// True if the function has a '*args' argument
     bool has_args : 1;
 
@@ -399,7 +405,7 @@ struct process_attribute<doc> : process_attribute_default<doc> {
 template <>
 struct process_attribute<const char *> : process_attribute_default<const char *> {
     static void init(const char *d, function_record *r) { r->doc = const_cast<char *>(d); }
-    static void init(const char *d, type_record *r) { r->doc = const_cast<char *>(d); }
+    static void init(const char *d, type_record *r) { r->doc = d; }
 };
 template <>
 struct process_attribute<char *> : process_attribute<const char *> {};
@@ -426,6 +432,12 @@ struct process_attribute<is_method> : process_attribute_default<is_method> {
     }
 };
 
+/// Process an attribute which indicates that this function is a setter
+template <>
+struct process_attribute<is_setter> : process_attribute_default<is_setter> {
+    static void init(const is_setter &, function_record *r) { r->is_setter = true; }
+};
+
 /// Process an attribute which indicates the parent scope of a method
 template <>
 struct process_attribute<scope> : process_attribute_default<scope> {

diff --git a/share/openPMD/thirdParty/pybind11/include/pybind11/buffer_info.h b/share/openPMD/thirdParty/pybind11/include/pybind11/buffer_info.h
@@ -37,6 +37,9 @@ inline std::vector<ssize_t> f_strides(const std::vector<ssize_t> &shape, ssize_t
     return strides;
 }
 
+template <typename T, typename SFINAE = void>
+struct compare_buffer_info;
+
 PYBIND11_NAMESPACE_END(detail)
 
 /// Information record describing a Python buffer object
@@ -150,6 +153,17 @@ struct buffer_info {
     Py_buffer *view() const { return m_view; }
     Py_buffer *&view() { return m_view; }
 
+    /* True if the buffer item type is equivalent to `T`. */
+    // To define "equivalent" by example:
+    // `buffer_info::item_type_is_equivalent_to<int>(b)` and
+    // `buffer_info::item_type_is_equivalent_to<long>(b)` may both be true
+    // on some platforms, but `int` and `unsigned` will never be equivalent.
+    // For the ground truth, please inspect `detail::compare_buffer_info<>`.
+    template <typename T>
+    bool item_type_is_equivalent_to() const {
+        return detail::compare_buffer_info<T>::compare(*this);
+    }
+
 private:
     struct private_ctr_tag {};
 
@@ -170,9 +184,10 @@ struct buffer_info {
 
 PYBIND11_NAMESPACE_BEGIN(detail)
 
-template <typename T, typename SFINAE = void>
+template <typename T, typename SFINAE>
 struct compare_buffer_info {
     static bool compare(const buffer_info &b) {
+        // NOLINTNEXTLINE(bugprone-sizeof-expression) Needed for `PyObject *`
         return b.format == format_descriptor<T>::format() && b.itemsize == (ssize_t) sizeof(T);
     }
 };