pybind11: v2.4.3+ (#821)

* Doc: pybind11 2.4.3+

* Internal: pybind11 2.4.3

Update the internal version of pybind11, version 2.4.3.

This release includes several fixes, such as
  - add fix pybind/pybind11#1851

  https://github.com/pybind/pybind11/blob/v2.4.3/docs/changelog.rst

Modifications from the releases:
  - remove test dirs
  - remove wheel packaging (setup.py/cfg)
  - remove github templates

Co-authored-by: Wenzel Jakob <[email protected]>

Author: ax3l

CMakeLists.txt

@@ -252,9 +252,9 @@ if(openPMD_USE_PYTHON STREQUAL AUTO)
     if(openPMD_USE_INTERNAL_PYBIND11)
         add_subdirectory("${openPMD_SOURCE_DIR}/share/openPMD/thirdParty/pybind11")
         set(openPMD_HAVE_PYTHON TRUE)
-        message(STATUS "pybind11: Using INTERNAL version 2.3.0")
+        message(STATUS "pybind11: Using INTERNAL version 2.4.3")
     else()
-        find_package(pybind11 2.3.0 CONFIG)
+        find_package(pybind11 2.4.3 CONFIG)
         if(pybind11_FOUND)
             set(openPMD_HAVE_PYTHON TRUE)
             message(STATUS "pybind11: Found version '${pybind11_VERSION}'")
@@ -275,9 +275,9 @@ elseif(openPMD_USE_PYTHON)
     if(openPMD_USE_INTERNAL_PYBIND11)
         add_subdirectory("${openPMD_SOURCE_DIR}/share/openPMD/thirdParty/pybind11")
         set(openPMD_HAVE_PYTHON TRUE)
-        message(STATUS "pybind11: Using INTERNAL version 2.3.0")
+        message(STATUS "pybind11: Using INTERNAL version 2.4.3")
     else()
-        find_package(pybind11 2.3.0 REQUIRED CONFIG)
+        find_package(pybind11 2.4.3 REQUIRED CONFIG)
         set(openPMD_HAVE_PYTHON TRUE)
         message(STATUS "pybind11: Found version '${pybind11_VERSION}'")
     endif()

README.md

@@ -105,7 +105,7 @@ Required:
 Shipped internally in `share/openPMD/thirdParty/`:
 * [MPark.Variant](https://github.com/mpark/variant) 1.4.0+ ([BSL-1.0](https://github.com/mpark/variant/blob/master/LICENSE.md))
 * [Catch2](https://github.com/catchorg/Catch2) 2.6.1+ ([BSL-1.0](https://github.com/catchorg/Catch2/blob/master/LICENSE.txt))
-* [pybind11](https://github.com/pybind/pybind11) 2.3.0+ ([new BSD](https://github.com/pybind/pybind11/blob/master/LICENSE))
+* [pybind11](https://github.com/pybind/pybind11) 2.4.3+ ([new BSD](https://github.com/pybind/pybind11/blob/master/LICENSE))
 * [NLohmann-JSON](https://github.com/nlohmann/json) 3.7.0+ ([MIT](https://github.com/nlohmann/json/blob/develop/LICENSE.MIT))
 
 I/O backends:
@@ -120,7 +120,7 @@ while those can be built either with or without:
 Optional language bindings:
 * Python:
   * Python 3.5 - 3.8
-  * pybind 2.3.0+
+  * pybind 2.4.3+
   * numpy 1.15+
   * mpi4py 2.1+
 
@@ -260,7 +260,7 @@ The following options allow to switch to external installs:
 |---------------------------------|------------|---------------|---------|
 | `openPMD_USE_INTERNAL_VARIANT`  | **ON**/OFF | MPark.Variant |  1.4.0+ |
 | `openPMD_USE_INTERNAL_CATCH`    | **ON**/OFF | Catch2        |  2.6.1+ |
-| `openPMD_USE_INTERNAL_PYBIND11` | **ON**/OFF | pybind11      |  2.3.0+ |
+| `openPMD_USE_INTERNAL_PYBIND11` | **ON**/OFF | pybind11      |  2.4.3+ |
 | `openPMD_USE_INTERNAL_JSON`     | **ON**/OFF | NLohmann-JSON |  3.7.0+ |
 
 By default, this will build as a shared library (`libopenPMD.[so|dylib|dll]`) and installs also its headers.

docs/source/dev/buildoptions.rst

@@ -69,7 +69,7 @@ CMake Option                      Values      Installs Library       Version
 ================================= =========== ======== ============= ========
 ``openPMD_USE_INTERNAL_VARIANT``  **ON**/OFF  Yes      MPark.Variant   1.4.0+
 ``openPMD_USE_INTERNAL_CATCH``    **ON**/OFF  No       Catch2          2.6.1+
-``openPMD_USE_INTERNAL_PYBIND11`` **ON**/OFF  No       pybind11        2.3.0+
+``openPMD_USE_INTERNAL_PYBIND11`` **ON**/OFF  No       pybind11        2.4.3+
 ``openPMD_USE_INTERNAL_JSON``     **ON**/OFF  No       NLohmann-JSON   3.7.0+
 ================================= =========== ======== ============= ========
 

docs/source/dev/dependencies.rst

@@ -19,7 +19,7 @@ The following libraries are shipped internally in ``share/openPMD/thirdParty/``
 
 * `MPark.Variant <https://github.com/mpark/variant>`_ 1.4.0+ (`BSL-1.0 <https://github.com/mpark/variant/blob/master/LICENSE.md>`_)
 * `Catch2 <https://github.com/catchorg/Catch2>`_ 2.6.1+ (`BSL-1.0 <https://github.com/catchorg/Catch2/blob/master/LICENSE.txt>`__)
-* `pybind11 <https://github.com/pybind/pybind11>`_ 2.3.0+ (`new BSD <https://github.com/pybind/pybind11/blob/master/LICENSE>`_)
+* `pybind11 <https://github.com/pybind/pybind11>`_ 2.4.3+ (`new BSD <https://github.com/pybind/pybind11/blob/master/LICENSE>`_)
 * `NLohmann-JSON <https://github.com/nlohmann/json>`_ 3.7.0+ (`MIT <https://github.com/nlohmann/json/blob/develop/LICENSE.MIT>`_)
 
 Optional: I/O backends
@@ -40,7 +40,7 @@ Optional: language bindings
 * Python:
 
   * Python 3.5 - 3.8
-  * pybind11 2.3.0+
+  * pybind11 2.4.3+
   * numpy 1.15+
   * mpi4py 2.1+
 

pyproject.toml

@@ -1,2 +1,2 @@
 [build-system]
-requires = ["setuptools>38.6", "wheel", "cmake>=3.12.0,<4.0.0", "pybind11>=2.3.0,<3.0.0"]
+requires = ["setuptools>38.6", "wheel", "cmake>=3.12.0,<4.0.0", "pybind11>=2.4.3,<3.0.0"]

share/openPMD/thirdParty/pybind11/README.md

@@ -105,6 +105,7 @@ In addition to the core functionality, pybind11 provides some extra goodies:
 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,
 Trent Houliston,
 Axel Huebl,
@@ -117,6 +118,7 @@ Ben Pritchard,
 Jason Rhinelander,
 Boris Schäling,
 Pim Schellart,
+Henry Schreiner,
 Ivan Smirnov, and
 Patrick Stewart.
 

share/openPMD/thirdParty/pybind11/include/pybind11/cast.h

@@ -775,7 +775,9 @@ template <typename T, typename SFINAE = void> struct is_copy_constructible : std
 // so, copy constructability depends on whether the value_type is copy constructible.
 template <typename Container> struct is_copy_constructible<Container, enable_if_t<all_of<
         std::is_copy_constructible<Container>,
-        std::is_same<typename Container::value_type &, typename Container::reference>
+        std::is_same<typename Container::value_type &, typename Container::reference>,
+        // Avoid infinite recursion
+        negation<std::is_same<Container, typename Container::value_type>>
     >::value>> : is_copy_constructible<typename Container::value_type> {};
 
 #if !defined(PYBIND11_CPP17)
@@ -995,9 +997,11 @@ struct type_caster<T, enable_if_t<std::is_arithmetic<T>::value && !is_std_char_t
         }
 
         bool py_err = py_value == (py_type) -1 && PyErr_Occurred();
+
+        // Protect std::numeric_limits::min/max with parentheses
         if (py_err || (std::is_integral<T>::value && sizeof(py_type) != sizeof(T) &&
-                       (py_value < (py_type) std::numeric_limits<T>::min() ||
-                        py_value > (py_type) std::numeric_limits<T>::max()))) {
+                       (py_value < (py_type) (std::numeric_limits<T>::min)() ||
+                        py_value > (py_type) (std::numeric_limits<T>::max)()))) {
             bool type_error = py_err && PyErr_ExceptionMatches(
 #if PY_VERSION_HEX < 0x03000000 && !defined(PYPY_VERSION)
                 PyExc_SystemError

share/openPMD/thirdParty/pybind11/include/pybind11/chrono.h

@@ -106,20 +106,42 @@ template <typename Duration> class type_caster<std::chrono::time_point<std::chro
         if (!PyDateTimeAPI) { PyDateTime_IMPORT; }
 
         if (!src) return false;
+
+        std::tm cal;
+        microseconds msecs;
+
         if (PyDateTime_Check(src.ptr())) {
-            std::tm cal;
             cal.tm_sec   = PyDateTime_DATE_GET_SECOND(src.ptr());
             cal.tm_min   = PyDateTime_DATE_GET_MINUTE(src.ptr());
             cal.tm_hour  = PyDateTime_DATE_GET_HOUR(src.ptr());
             cal.tm_mday  = PyDateTime_GET_DAY(src.ptr());
             cal.tm_mon   = PyDateTime_GET_MONTH(src.ptr()) - 1;
             cal.tm_year  = PyDateTime_GET_YEAR(src.ptr()) - 1900;
             cal.tm_isdst = -1;
-
-            value = system_clock::from_time_t(std::mktime(&cal)) + microseconds(PyDateTime_DATE_GET_MICROSECOND(src.ptr()));
-            return true;
+            msecs        = microseconds(PyDateTime_DATE_GET_MICROSECOND(src.ptr()));
+        } else if (PyDate_Check(src.ptr())) {
+            cal.tm_sec   = 0;
+            cal.tm_min   = 0;
+            cal.tm_hour  = 0;
+            cal.tm_mday  = PyDateTime_GET_DAY(src.ptr());
+            cal.tm_mon   = PyDateTime_GET_MONTH(src.ptr()) - 1;
+            cal.tm_year  = PyDateTime_GET_YEAR(src.ptr()) - 1900;
+            cal.tm_isdst = -1;
+            msecs        = microseconds(0);
+        } else if (PyTime_Check(src.ptr())) {
+            cal.tm_sec   = PyDateTime_TIME_GET_SECOND(src.ptr());
+            cal.tm_min   = PyDateTime_TIME_GET_MINUTE(src.ptr());
+            cal.tm_hour  = PyDateTime_TIME_GET_HOUR(src.ptr());
+            cal.tm_mday  = 1;   // This date (day, month, year) = (1, 0, 70)
+            cal.tm_mon   = 0;   // represents 1-Jan-1970, which is the first
+            cal.tm_year  = 70;  // earliest available date for Python's datetime
+            cal.tm_isdst = -1;
+            msecs        = microseconds(PyDateTime_TIME_GET_MICROSECOND(src.ptr()));
         }
         else return false;
+
+        value = system_clock::from_time_t(std::mktime(&cal)) + msecs;
+        return true;
     }
 
     static handle cast(const std::chrono::time_point<std::chrono::system_clock, Duration> &src, return_value_policy /* policy */, handle /* parent */) {
@@ -128,7 +150,7 @@ template <typename Duration> class type_caster<std::chrono::time_point<std::chro
         // Lazy initialise the PyDateTime import
         if (!PyDateTimeAPI) { PyDateTime_IMPORT; }
 
-        std::time_t tt = system_clock::to_time_t(src);
+        std::time_t tt = system_clock::to_time_t(time_point_cast<system_clock::duration>(src));
         // this function uses static memory so it's best to copy it out asap just in case
         // otherwise other code that is using localtime may break this (not just python code)
         std::tm localtime = *std::localtime(&tt);

share/openPMD/thirdParty/pybind11/include/pybind11/detail/class.h

@@ -350,13 +350,19 @@ extern "C" inline void pybind11_object_dealloc(PyObject *self) {
     auto type = Py_TYPE(self);
     type->tp_free(self);
 
+#if PY_VERSION_HEX < 0x03080000
     // `type->tp_dealloc != pybind11_object_dealloc` means that we're being called
     // as part of a derived type's dealloc, in which case we're not allowed to decref
     // the type here. For cross-module compatibility, we shouldn't compare directly
     // with `pybind11_object_dealloc`, but with the common one stashed in internals.
     auto pybind11_object_type = (PyTypeObject *) get_internals().instance_base;
     if (type->tp_dealloc == pybind11_object_type->tp_dealloc)
         Py_DECREF(type);
+#else
+    // This was not needed before Python 3.8 (Python issue 35810)
+    // https://github.com/pybind/pybind11/issues/1946
+    Py_DECREF(type);
+#endif
 }
 
 /** Create the type which can be used as a common base for all classes.  This is
@@ -586,6 +592,9 @@ inline PyObject* make_new_python_type(const type_record &rec) {
     type->tp_as_number = &heap_type->as_number;
     type->tp_as_sequence = &heap_type->as_sequence;
     type->tp_as_mapping = &heap_type->as_mapping;
+#if PY_VERSION_HEX >= 0x03050000
+    type->tp_as_async = &heap_type->as_async;
+#endif
 
     /* Flags */
     type->tp_flags |= Py_TPFLAGS_DEFAULT | Py_TPFLAGS_BASETYPE | Py_TPFLAGS_HEAPTYPE;

share/openPMD/thirdParty/pybind11/include/pybind11/detail/common.h

@@ -93,8 +93,8 @@
 #endif
 
 #define PYBIND11_VERSION_MAJOR 2
-#define PYBIND11_VERSION_MINOR 3
-#define PYBIND11_VERSION_PATCH 0
+#define PYBIND11_VERSION_MINOR 4
+#define PYBIND11_VERSION_PATCH 3
 
 /// Include Python header, disable linking to pythonX_d.lib on Windows in debug mode
 #if defined(_MSC_VER)
@@ -113,10 +113,6 @@
 #include <frameobject.h>
 #include <pythread.h>
 
-#if defined(_WIN32) && (defined(min) || defined(max))
-#  error Macro clash with min and max -- define NOMINMAX when compiling your program on Windows
-#endif
-
 #if defined(isalnum)
 #  undef isalnum
 #  undef isalpha
@@ -168,7 +164,9 @@
 #define PYBIND11_STR_TYPE ::pybind11::str
 #define PYBIND11_BOOL_ATTR "__bool__"
 #define PYBIND11_NB_BOOL(ptr) ((ptr)->nb_bool)
+// Providing a separate declaration to make Clang's -Wmissing-prototypes happy
 #define PYBIND11_PLUGIN_IMPL(name) \
+    extern "C" PYBIND11_EXPORT PyObject *PyInit_##name();   \
     extern "C" PYBIND11_EXPORT PyObject *PyInit_##name()
 
 #else
@@ -192,8 +190,10 @@
 #define PYBIND11_STR_TYPE ::pybind11::bytes
 #define PYBIND11_BOOL_ATTR "__nonzero__"
 #define PYBIND11_NB_BOOL(ptr) ((ptr)->nb_nonzero)
+// Providing a separate PyInit decl to make Clang's -Wmissing-prototypes happy
 #define PYBIND11_PLUGIN_IMPL(name) \
     static PyObject *pybind11_init_wrapper();               \
+    extern "C" PYBIND11_EXPORT void init##name();           \
     extern "C" PYBIND11_EXPORT void init##name() {          \
         (void)pybind11_init_wrapper();                      \
     }                                                       \
@@ -673,6 +673,7 @@ PYBIND11_RUNTIME_EXCEPTION(index_error, PyExc_IndexError)
 PYBIND11_RUNTIME_EXCEPTION(key_error, PyExc_KeyError)
 PYBIND11_RUNTIME_EXCEPTION(value_error, PyExc_ValueError)
 PYBIND11_RUNTIME_EXCEPTION(type_error, PyExc_TypeError)
+PYBIND11_RUNTIME_EXCEPTION(buffer_error, PyExc_BufferError)
 PYBIND11_RUNTIME_EXCEPTION(cast_error, PyExc_RuntimeError) /// Thrown when pybind11::cast or handle::call fail due to a type casting error
 PYBIND11_RUNTIME_EXCEPTION(reference_cast_error, PyExc_RuntimeError) /// Used internally
 
@@ -719,10 +720,6 @@ struct error_scope {
 /// Dummy destructor wrapper that can be used to expose classes with a private destructor
 struct nodelete { template <typename T> void operator()(T*) { } };
 
-// overload_cast requires variable templates: C++14
-#if defined(PYBIND11_CPP14)
-#define PYBIND11_OVERLOAD_CAST 1
-
 NAMESPACE_BEGIN(detail)
 template <typename... Args>
 struct overload_cast_impl {
@@ -742,19 +739,23 @@ struct overload_cast_impl {
 };
 NAMESPACE_END(detail)
 
+// overload_cast requires variable templates: C++14
+#if defined(PYBIND11_CPP14)
+#define PYBIND11_OVERLOAD_CAST 1
 /// Syntax sugar for resolving overloaded function pointers:
 ///  - regular: static_cast<Return (Class::*)(Arg0, Arg1, Arg2)>(&Class::func)
 ///  - sweet:   overload_cast<Arg0, Arg1, Arg2>(&Class::func)
 template <typename... Args>
 static constexpr detail::overload_cast_impl<Args...> overload_cast = {};
 // MSVC 2015 only accepts this particular initialization syntax for this variable template.
+#endif
 
 /// Const member function selector for overload_cast
 ///  - regular: static_cast<Return (Class::*)(Arg) const>(&Class::func)
 ///  - sweet:   overload_cast<Arg>(&Class::func, const_)
 static constexpr auto const_ = std::true_type{};
 
-#else // no overload_cast: providing something that static_assert-fails:
+#if !defined(PYBIND11_CPP14) // no overload_cast: providing something that static_assert-fails:
 template <typename... Args> struct overload_cast {
     static_assert(detail::deferred_t<std::false_type, Args...>::value,
                   "pybind11::overload_cast<...> requires compiling in C++14 mode");