Merge branch 'master' into sh_merge_master_after_clang-format_etc

First pass manually resolving the many merge conflicts.
This commit is contained in:
Ralf W. Grosse-Kunstleve
2022-02-14 14:31:13 -08:00
175 changed files with 9294 additions and 7536 deletions

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@@ -18,5 +18,4 @@ ALIASES += "endrst=\endverbatim"
QUIET = YES
WARNINGS = YES
WARN_IF_UNDOCUMENTED = NO
PREDEFINED = PY_MAJOR_VERSION=3 \
PYBIND11_NOINLINE
PREDEFINED = PYBIND11_NOINLINE

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@@ -167,5 +167,4 @@ as arguments and return values, refer to the section on binding :ref:`classes`.
+------------------------------------+---------------------------+-----------------------------------+
.. [#] ``std::filesystem::path`` is converted to ``pathlib.Path`` and
``os.PathLike`` is converted to ``std::filesystem::path``, but this requires
Python 3.6 (for ``__fspath__`` support).
``os.PathLike`` is converted to ``std::filesystem::path``.

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@@ -87,8 +87,6 @@ included to tell pybind11 how to visit the variant.
pybind11 only supports the modern implementation of ``boost::variant``
which makes use of variadic templates. This requires Boost 1.56 or newer.
Additionally, on Windows, MSVC 2017 is required because ``boost::variant``
falls back to the old non-variadic implementation on MSVC 2015.
.. _opaque:

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@@ -1,14 +1,6 @@
Strings, bytes and Unicode conversions
######################################
.. note::
This section discusses string handling in terms of Python 3 strings. For
Python 2.7, replace all occurrences of ``str`` with ``unicode`` and
``bytes`` with ``str``. Python 2.7 users may find it best to use ``from
__future__ import unicode_literals`` to avoid unintentionally using ``str``
instead of ``unicode``.
Passing Python strings to C++
=============================
@@ -58,9 +50,9 @@ Passing bytes to C++
--------------------
A Python ``bytes`` object will be passed to C++ functions that accept
``std::string`` or ``char*`` *without* conversion. On Python 3, in order to
make a function *only* accept ``bytes`` (and not ``str``), declare it as taking
a ``py::bytes`` argument.
``std::string`` or ``char*`` *without* conversion. In order to make a function
*only* accept ``bytes`` (and not ``str``), declare it as taking a ``py::bytes``
argument.
Returning C++ strings to Python
@@ -204,11 +196,6 @@ decoded to Python ``str``.
}
);
.. warning::
Wide character strings may not work as described on Python 2.7 or Python
3.3 compiled with ``--enable-unicode=ucs2``.
Strings in multibyte encodings such as Shift-JIS must transcoded to a
UTF-8/16/32 before being returned to Python.

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@@ -133,14 +133,14 @@ a virtual method call.
>>> from example import *
>>> d = Dog()
>>> call_go(d)
u'woof! woof! woof! '
'woof! woof! woof! '
>>> class Cat(Animal):
... def go(self, n_times):
... return "meow! " * n_times
...
>>> c = Cat()
>>> call_go(c)
u'meow! meow! meow! '
'meow! meow! meow! '
If you are defining a custom constructor in a derived Python class, you *must*
ensure that you explicitly call the bound C++ constructor using ``__init__``,
@@ -813,26 +813,21 @@ An instance can now be pickled as follows:
.. code-block:: python
try:
import cPickle as pickle # Use cPickle on Python 2.7
except ImportError:
import pickle
import pickle
p = Pickleable("test_value")
p.setExtra(15)
data = pickle.dumps(p, 2)
data = pickle.dumps(p)
.. note::
Note that only the cPickle module is supported on Python 2.7.
The second argument to ``dumps`` is also crucial: it selects the pickle
protocol version 2, since the older version 1 is not supported. Newer
versions are also fine—for instance, specify ``-1`` to always use the
latest available version. Beware: failure to follow these instructions
will cause important pybind11 memory allocation routines to be skipped
during unpickling, which will likely lead to memory corruption and/or
segmentation faults.
If given, the second argument to ``dumps`` must be 2 or larger - 0 and 1 are
not supported. Newer versions are also fine; for instance, specify ``-1`` to
always use the latest available version. Beware: failure to follow these
instructions will cause important pybind11 memory allocation routines to be
skipped during unpickling, which will likely lead to memory corruption
and/or segmentation faults. Python defaults to version 3 (Python 3-3.7) and
version 4 for Python 3.8+.
.. seealso::
@@ -849,11 +844,9 @@ Python normally uses references in assignments. Sometimes a real copy is needed
to prevent changing all copies. The ``copy`` module [#f5]_ provides these
capabilities.
On Python 3, a class with pickle support is automatically also (deep)copy
A class with pickle support is automatically also (deep)copy
compatible. However, performance can be improved by adding custom
``__copy__`` and ``__deepcopy__`` methods. With Python 2.7, these custom methods
are mandatory for (deep)copy compatibility, because pybind11 only supports
cPickle.
``__copy__`` and ``__deepcopy__`` methods.
For simple classes (deep)copy can be enabled by using the copy constructor,
which should look as follows:
@@ -1125,13 +1118,6 @@ described trampoline:
py::class_<A, Trampoline>(m, "A") // <-- `Trampoline` here
.def("foo", &Publicist::foo); // <-- `Publicist` here, not `Trampoline`!
.. note::
MSVC 2015 has a compiler bug (fixed in version 2017) which
requires a more explicit function binding in the form of
``.def("foo", static_cast<int (A::*)() const>(&Publicist::foo));``
where ``int (A::*)() const`` is the type of ``A::foo``.
Binding final classes
=====================

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@@ -328,8 +328,8 @@ an invalid state.
Chaining exceptions ('raise from')
==================================
In Python 3.3 a mechanism for indicating that exceptions were caused by other
exceptions was introduced:
Python has a mechanism for indicating that exceptions were caused by other
exceptions:
.. code-block:: py
@@ -340,7 +340,7 @@ exceptions was introduced:
To do a similar thing in pybind11, you can use the ``py::raise_from`` function. It
sets the current python error indicator, so to continue propagating the exception
you should ``throw py::error_already_set()`` (Python 3 only).
you should ``throw py::error_already_set()``.
.. code-block:: cpp

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@@ -372,7 +372,7 @@ like so:
Keyword-only arguments
======================
Python 3 introduced keyword-only arguments by specifying an unnamed ``*``
Python implements keyword-only arguments by specifying an unnamed ``*``
argument in a function definition:
.. code-block:: python
@@ -395,19 +395,18 @@ argument annotations when registering the function:
m.def("f", [](int a, int b) { /* ... */ },
py::arg("a"), py::kw_only(), py::arg("b"));
Note that you currently cannot combine this with a ``py::args`` argument. This
feature does *not* require Python 3 to work.
.. versionadded:: 2.6
As of pybind11 2.9, a ``py::args`` argument implies that any following arguments
are keyword-only, as if ``py::kw_only()`` had been specified in the same
relative location of the argument list as the ``py::args`` argument. The
``py::kw_only()`` may be included to be explicit about this, but is not
required. (Prior to 2.9 ``py::args`` may only occur at the end of the argument
list, or immediately before a ``py::kwargs`` argument at the end).
A ``py::args`` argument implies that any following arguments are keyword-only,
as if ``py::kw_only()`` had been specified in the same relative location of the
argument list as the ``py::args`` argument. The ``py::kw_only()`` may be
included to be explicit about this, but is not required.
.. versionchanged:: 2.9
This can now be combined with ``py::args``. Before, ``py::args`` could only
occur at the end of the argument list, or immediately before a ``py::kwargs``
argument at the end.
.. versionadded:: 2.9
Positional-only arguments
=========================

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@@ -395,11 +395,9 @@ uses of ``py::array``:
Ellipsis
========
Python 3 provides a convenient ``...`` ellipsis notation that is often used to
Python provides a convenient ``...`` ellipsis notation that is often used to
slice multidimensional arrays. For instance, the following snippet extracts the
middle dimensions of a tensor with the first and last index set to zero.
In Python 2, the syntactic sugar ``...`` is not available, but the singleton
``Ellipsis`` (of type ``ellipsis``) can still be used directly.
.. code-block:: python
@@ -414,8 +412,6 @@ operation on the C++ side:
py::array a = /* A NumPy array */;
py::array b = a[py::make_tuple(0, py::ellipsis(), 0)];
.. versionchanged:: 2.6
``py::ellipsis()`` is now also available in Python 2.
Memory view
===========
@@ -455,9 +451,5 @@ We can also use ``memoryview::from_memory`` for a simple 1D contiguous buffer:
);
})
.. note::
``memoryview::from_memory`` is not available in Python 2.
.. versionchanged:: 2.6
``memoryview::from_memory`` added.

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@@ -32,8 +32,7 @@ The last line will both compile and run the tests.
Windows
-------
On Windows, only **Visual Studio 2015** and newer are supported since pybind11 relies
on various C++11 language features that break older versions of Visual Studio.
On Windows, only **Visual Studio 2017** and newer are supported.
.. Note::
@@ -166,12 +165,12 @@ load and execute the example:
.. code-block:: pycon
$ python
Python 2.7.10 (default, Aug 22 2015, 20:33:39)
[GCC 4.2.1 Compatible Apple LLVM 7.0.0 (clang-700.0.59.1)] on darwin
Python 3.9.10 (main, Jan 15 2022, 11:48:04)
[Clang 13.0.0 (clang-1300.0.29.3)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import example
>>> example.add(1, 2)
3L
3
>>>
.. _keyword_args:

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@@ -1,4 +1,3 @@
# -*- coding: utf-8 -*-
import datetime as dt
import os
import random
@@ -12,20 +11,20 @@ def generate_dummy_code_pybind11(nclasses=10):
bindings = ""
for cl in range(nclasses):
decl += "class cl%03i;\n" % cl
decl += f"class cl{cl:03};\n"
decl += "\n"
for cl in range(nclasses):
decl += "class cl%03i {\n" % cl
decl += f"class {cl:03} {{\n"
decl += "public:\n"
bindings += ' py::class_<cl%03i>(m, "cl%03i")\n' % (cl, cl)
bindings += f' py::class_<cl{cl:03}>(m, "cl{cl:03}")\n'
for fn in range(nfns):
ret = random.randint(0, nclasses - 1)
params = [random.randint(0, nclasses - 1) for i in range(nargs)]
decl += " cl%03i *fn_%03i(" % (ret, fn)
decl += ", ".join("cl%03i *" % p for p in params)
decl += f" cl{ret:03} *fn_{fn:03}("
decl += ", ".join(f"cl{p:03} *" for p in params)
decl += ");\n"
bindings += ' .def("fn_%03i", &cl%03i::fn_%03i)\n' % (fn, cl, fn)
bindings += f' .def("fn_{fn:03}", &cl{cl:03}::fn_{fn:03})\n'
decl += "};\n\n"
bindings += " ;\n"
@@ -43,23 +42,20 @@ def generate_dummy_code_boost(nclasses=10):
bindings = ""
for cl in range(nclasses):
decl += "class cl%03i;\n" % cl
decl += f"class cl{cl:03};\n"
decl += "\n"
for cl in range(nclasses):
decl += "class cl%03i {\n" % cl
decl += "public:\n"
bindings += ' py::class_<cl%03i>("cl%03i")\n' % (cl, cl)
bindings += f' py::class_<cl{cl:03}>("cl{cl:03}")\n'
for fn in range(nfns):
ret = random.randint(0, nclasses - 1)
params = [random.randint(0, nclasses - 1) for i in range(nargs)]
decl += " cl%03i *fn_%03i(" % (ret, fn)
decl += ", ".join("cl%03i *" % p for p in params)
decl += f" cl{ret:03} *fn_{fn:03}("
decl += ", ".join(f"cl{p:03} *" for p in params)
decl += ");\n"
bindings += (
' .def("fn_%03i", &cl%03i::fn_%03i, py::return_value_policy<py::manage_new_object>())\n'
% (fn, cl, fn)
)
bindings += f' .def("fn_{fn:03}", &cl{cl:03}::fn_{fn:03}, py::return_value_policy<py::manage_new_object>())\n'
decl += "};\n\n"
bindings += " ;\n"
@@ -75,7 +71,7 @@ def generate_dummy_code_boost(nclasses=10):
for codegen in [generate_dummy_code_pybind11, generate_dummy_code_boost]:
print("{")
for i in range(0, 10):
nclasses = 2 ** i
nclasses = 2**i
with open("test.cpp", "w") as f:
f.write(codegen(nclasses))
n1 = dt.datetime.now()

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@@ -800,7 +800,7 @@ Packaging / building improvements:
`#2338 <https://github.com/pybind/pybind11/pull/2338>`_ and
`#2370 <https://github.com/pybind/pybind11/pull/2370>`_
* Full integration with CMakes C++ standard system and compile features
* Full integration with CMake's C++ standard system and compile features
replaces ``PYBIND11_CPP_STANDARD``.
* Generated config file is now portable to different Python/compiler/CMake

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@@ -48,10 +48,10 @@ interactive Python session demonstrating this example is shown below:
>>> print(p)
<example.Pet object at 0x10cd98060>
>>> p.getName()
u'Molly'
'Molly'
>>> p.setName("Charly")
>>> p.getName()
u'Charly'
'Charly'
.. seealso::
@@ -124,10 +124,10 @@ This makes it possible to write
>>> p = example.Pet("Molly")
>>> p.name
u'Molly'
'Molly'
>>> p.name = "Charly"
>>> p.name
u'Charly'
'Charly'
Now suppose that ``Pet::name`` was a private internal variable
that can only be accessed via setters and getters.
@@ -282,9 +282,9 @@ expose fields and methods of both types:
>>> p = example.Dog("Molly")
>>> p.name
u'Molly'
'Molly'
>>> p.bark()
u'woof!'
'woof!'
The C++ classes defined above are regular non-polymorphic types with an
inheritance relationship. This is reflected in Python:
@@ -332,7 +332,7 @@ will automatically recognize this:
>>> type(p)
PolymorphicDog # automatically downcast
>>> p.bark()
u'woof!'
'woof!'
Given a pointer to a polymorphic base, pybind11 performs automatic downcasting
to the actual derived type. Note that this goes beyond the usual situation in
@@ -434,8 +434,7 @@ you can use ``py::detail::overload_cast_impl`` with an additional set of parenth
.def("set", overload_cast_<int>()(&Pet::set), "Set the pet's age")
.def("set", overload_cast_<const std::string &>()(&Pet::set), "Set the pet's name");
.. [#cpp14] A compiler which supports the ``-std=c++14`` flag
or Visual Studio 2015 Update 2 and newer.
.. [#cpp14] A compiler which supports the ``-std=c++14`` flag.
.. note::

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@@ -417,10 +417,10 @@ existing targets instead:
.. code-block:: cmake
cmake_minimum_required(VERSION 3.15...3.19)
cmake_minimum_required(VERSION 3.15...3.22)
project(example LANGUAGES CXX)
find_package(Python COMPONENTS Interpreter Development REQUIRED)
find_package(Python 3.6 COMPONENTS Interpreter Development REQUIRED)
find_package(pybind11 CONFIG REQUIRED)
# or add_subdirectory(pybind11)
@@ -433,9 +433,8 @@ algorithms from the CMake invocation, with ``-DPYBIND11_FINDPYTHON=ON``.
.. warning::
If you use FindPython2 and FindPython3 to dual-target Python, use the
individual targets listed below, and avoid targets that directly include
Python parts.
If you use FindPython to multi-target Python versions, use the individual
targets listed below, and avoid targets that directly include Python parts.
There are `many ways to hint or force a discovery of a specific Python
installation <https://cmake.org/cmake/help/latest/module/FindPython.html>`_),
@@ -462,11 +461,8 @@ available in all modes. The targets provided are:
``pybind11::headers``
Just the pybind11 headers and minimum compile requirements
``pybind11::python2_no_register``
Quiets the warning/error when mixing C++14 or higher and Python 2
``pybind11::pybind11``
Python headers + ``pybind11::headers`` + ``pybind11::python2_no_register`` (Python 2 only)
Python headers + ``pybind11::headers``
``pybind11::python_link_helper``
Just the "linking" part of pybind11:module
@@ -475,7 +471,7 @@ available in all modes. The targets provided are:
Everything for extension modules - ``pybind11::pybind11`` + ``Python::Module`` (FindPython CMake 3.15+) or ``pybind11::python_link_helper``
``pybind11::embed``
Everything for embedding the Python interpreter - ``pybind11::pybind11`` + ``Python::Embed`` (FindPython) or Python libs
Everything for embedding the Python interpreter - ``pybind11::pybind11`` + ``Python::Python`` (FindPython) or Python libs
``pybind11::lto`` / ``pybind11::thin_lto``
An alternative to `INTERPROCEDURAL_OPTIMIZATION` for adding link-time optimization.
@@ -577,21 +573,12 @@ On Linux, you can compile an example such as the one given in
$ c++ -O3 -Wall -shared -std=c++11 -fPIC $(python3 -m pybind11 --includes) example.cpp -o example$(python3-config --extension-suffix)
The flags given here assume that you're using Python 3. For Python 2, just
change the executable appropriately (to ``python`` or ``python2``).
The ``python3 -m pybind11 --includes`` command fetches the include paths for
both pybind11 and Python headers. This assumes that pybind11 has been installed
using ``pip`` or ``conda``. If it hasn't, you can also manually specify
``-I <path-to-pybind11>/include`` together with the Python includes path
``python3-config --includes``.
Note that Python 2.7 modules don't use a special suffix, so you should simply
use ``example.so`` instead of ``example$(python3-config --extension-suffix)``.
Besides, the ``--extension-suffix`` option may or may not be available, depending
on the distribution; in the latter case, the module extension can be manually
set to ``.so``.
On macOS: the build command is almost the same but it also requires passing
the ``-undefined dynamic_lookup`` flag so as to ignore missing symbols when
building the module:

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@@ -1,5 +1,4 @@
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
#
# pybind11 documentation build configuration file, created by
# sphinx-quickstart on Sun Oct 11 19:23:48 2015.
@@ -345,9 +344,9 @@ def generate_doxygen_xml(app):
subprocess.call(["doxygen", "--version"])
retcode = subprocess.call(["doxygen"], cwd=app.confdir)
if retcode < 0:
sys.stderr.write("doxygen error code: {}\n".format(-retcode))
sys.stderr.write(f"doxygen error code: {-retcode}\n")
except OSError as e:
sys.stderr.write("doxygen execution failed: {}\n".format(e))
sys.stderr.write(f"doxygen execution failed: {e}\n")
def prepare(app):

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@@ -8,9 +8,7 @@ Frequently asked questions
filename of the extension library (without suffixes such as ``.so``).
2. If the above did not fix the issue, you are likely using an incompatible
version of Python (for instance, the extension library was compiled against
Python 2, while the interpreter is running on top of some version of Python
3, or vice versa).
version of Python that does not match what you compiled with.
"Symbol not found: ``__Py_ZeroStruct`` / ``_PyInstanceMethod_Type``"
========================================================================
@@ -147,7 +145,7 @@ using C++14 template metaprogramming.
.. _`faq:hidden_visibility`:
"SomeClass declared with greater visibility than the type of its field SomeClass::member [-Wattributes]"
"'SomeClass' declared with greater visibility than the type of its field 'SomeClass::member' [-Wattributes]"
============================================================================================================
This error typically indicates that you are compiling without the required
@@ -222,20 +220,6 @@ In addition to decreasing binary size, ``-fvisibility=hidden`` also avoids
potential serious issues when loading multiple modules and is required for
proper pybind operation. See the previous FAQ entry for more details.
Working with ancient Visual Studio 2008 builds on Windows
=========================================================
The official Windows distributions of Python are compiled using truly
ancient versions of Visual Studio that lack good C++11 support. Some users
implicitly assume that it would be impossible to load a plugin built with
Visual Studio 2015 into a Python distribution that was compiled using Visual
Studio 2008. However, no such issue exists: it's perfectly legitimate to
interface DLLs that are built with different compilers and/or C libraries.
Common gotchas to watch out for involve not ``free()``-ing memory region
that that were ``malloc()``-ed in another shared library, using data
structures with incompatible ABIs, and so on. pybind11 is very careful not
to make these types of mistakes.
How can I properly handle Ctrl-C in long-running functions?
===========================================================
@@ -289,27 +273,7 @@ Conflicts can arise, however, when using pybind11 in a project that *also* uses
the CMake Python detection in a system with several Python versions installed.
This difference may cause inconsistencies and errors if *both* mechanisms are
used in the same project. Consider the following CMake code executed in a
system with Python 2.7 and 3.x installed:
.. code-block:: cmake
find_package(PythonInterp)
find_package(PythonLibs)
find_package(pybind11)
It will detect Python 2.7 and pybind11 will pick it as well.
In contrast this code:
.. code-block:: cmake
find_package(pybind11)
find_package(PythonInterp)
find_package(PythonLibs)
will detect Python 3.x for pybind11 and may crash on
``find_package(PythonLibs)`` afterwards.
used in the same project.
There are three possible solutions:

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@@ -1,5 +1,5 @@
breathe==4.31.0
sphinx==3.5.4
breathe==4.32.0
sphinx==4.4.0
sphinx_rtd_theme==1.0.0
sphinxcontrib-moderncmakedomain==3.19
sphinxcontrib-svg2pdfconverter==1.1.1
sphinxcontrib-moderncmakedomain==3.21.4
sphinxcontrib-svg2pdfconverter==1.2.0

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@@ -524,7 +524,7 @@ include a declaration of the form:
PYBIND11_DECLARE_HOLDER_TYPE(T, std::shared_ptr<T>)
Continuing to do so wont cause an error or even a deprecation warning,
Continuing to do so won't cause an error or even a deprecation warning,
but it's completely redundant.