Hardcopy of pybind11 instead of using git submodules (#552)

* removed pybind as submodule
* added hardcopy of pybind11 2.10.0
* rename pybind11 folder to avoid conflicts when changing branch

Co-authored-by: Dhanya Thattil <dhanya.thattil@psi.ch>

libs/pybind/pybind11/__init__.py

@@ -0,0 +1,16 @@
+import sys
+
+if sys.version_info < (3, 6):
+    msg = "pybind11 does not support Python < 3.6. 2.9 was the last release supporting Python 2.7 and 3.5."
+    raise ImportError(msg)
+
+
+from ._version import __version__, version_info
+from .commands import get_cmake_dir, get_include
+
+__all__ = (
+    "version_info",
+    "__version__",
+    "get_include",
+    "get_cmake_dir",
+)

libs/pybind/pybind11/__main__.py

@@ -0,0 +1,49 @@
+# pylint: disable=missing-function-docstring
+
+import argparse
+import sys
+import sysconfig
+
+from .commands import get_cmake_dir, get_include
+
+
+def print_includes() -> None:
+    dirs = [
+        sysconfig.get_path("include"),
+        sysconfig.get_path("platinclude"),
+        get_include(),
+    ]
+
+    # Make unique but preserve order
+    unique_dirs = []
+    for d in dirs:
+        if d and d not in unique_dirs:
+            unique_dirs.append(d)
+
+    print(" ".join("-I" + d for d in unique_dirs))
+
+
+def main() -> None:
+
+    parser = argparse.ArgumentParser()
+    parser.add_argument(
+        "--includes",
+        action="store_true",
+        help="Include flags for both pybind11 and Python headers.",
+    )
+    parser.add_argument(
+        "--cmakedir",
+        action="store_true",
+        help="Print the CMake module directory, ideal for setting -Dpybind11_ROOT in CMake.",
+    )
+    args = parser.parse_args()
+    if not sys.argv[1:]:
+        parser.print_help()
+    if args.includes:
+        print_includes()
+    if args.cmakedir:
+        print(get_cmake_dir())
+
+
+if __name__ == "__main__":
+    main()

libs/pybind/pybind11/_version.py

@@ -0,0 +1,12 @@
+from typing import Union
+
+
+def _to_int(s: str) -> Union[int, str]:
+    try:
+        return int(s)
+    except ValueError:
+        return s
+
+
+__version__ = "2.10.0"
+version_info = tuple(_to_int(s) for s in __version__.split("."))

libs/pybind/pybind11/commands.py

@@ -0,0 +1,25 @@
+import os
+
+DIR = os.path.abspath(os.path.dirname(__file__))
+
+
+def get_include(user: bool = False) -> str:  # pylint: disable=unused-argument
+    """
+    Return the path to the pybind11 include directory. The historical "user"
+    argument is unused, and may be removed.
+    """
+    installed_path = os.path.join(DIR, "include")
+    source_path = os.path.join(os.path.dirname(DIR), "include")
+    return installed_path if os.path.exists(installed_path) else source_path
+
+
+def get_cmake_dir() -> str:
+    """
+    Return the path to the pybind11 CMake module directory.
+    """
+    cmake_installed_path = os.path.join(DIR, "share", "cmake", "pybind11")
+    if os.path.exists(cmake_installed_path):
+        return cmake_installed_path
+
+    msg = "pybind11 not installed, installation required to access the CMake files"
+    raise ImportError(msg)

libs/pybind/pybind11/setup_helpers.py

@@ -0,0 +1,504 @@
+"""
+This module provides helpers for C++11+ projects using pybind11.
+
+LICENSE:
+
+Copyright (c) 2016 Wenzel Jakob <wenzel.jakob@epfl.ch>, All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its contributors
+   may be used to endorse or promote products derived from this software
+   without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+"""
+
+# IMPORTANT: If you change this file in the pybind11 repo, also review
+# setup_helpers.pyi for matching changes.
+#
+# If you copy this file in, you don't
+# need the .pyi file; it's just an interface file for static type checkers.
+
+import contextlib
+import os
+import platform
+import shlex
+import shutil
+import sys
+import sysconfig
+import tempfile
+import threading
+import warnings
+from functools import lru_cache
+from pathlib import Path
+from typing import (
+    Any,
+    Callable,
+    Dict,
+    Iterable,
+    Iterator,
+    List,
+    Optional,
+    Tuple,
+    TypeVar,
+    Union,
+)
+
+try:
+    from setuptools import Extension as _Extension
+    from setuptools.command.build_ext import build_ext as _build_ext
+except ImportError:
+    from distutils.command.build_ext import build_ext as _build_ext
+    from distutils.extension import Extension as _Extension
+
+import distutils.ccompiler
+import distutils.errors
+
+WIN = sys.platform.startswith("win32") and "mingw" not in sysconfig.get_platform()
+MACOS = sys.platform.startswith("darwin")
+STD_TMPL = "/std:c++{}" if WIN else "-std=c++{}"
+
+
+# It is recommended to use PEP 518 builds if using this module. However, this
+# file explicitly supports being copied into a user's project directory
+# standalone, and pulling pybind11 with the deprecated setup_requires feature.
+# If you copy the file, remember to add it to your MANIFEST.in, and add the current
+# directory into your path if it sits beside your setup.py.
+
+
+class Pybind11Extension(_Extension):  # type: ignore[misc]
+    """
+    Build a C++11+ Extension module with pybind11. This automatically adds the
+    recommended flags when you init the extension and assumes C++ sources - you
+    can further modify the options yourself.
+
+    The customizations are:
+
+    * ``/EHsc`` and ``/bigobj`` on Windows
+    * ``stdlib=libc++`` on macOS
+    * ``visibility=hidden`` and ``-g0`` on Unix
+
+    Finally, you can set ``cxx_std`` via constructor or afterwards to enable
+    flags for C++ std, and a few extra helper flags related to the C++ standard
+    level. It is _highly_ recommended you either set this, or use the provided
+    ``build_ext``, which will search for the highest supported extension for
+    you if the ``cxx_std`` property is not set. Do not set the ``cxx_std``
+    property more than once, as flags are added when you set it. Set the
+    property to None to disable the addition of C++ standard flags.
+
+    If you want to add pybind11 headers manually, for example for an exact
+    git checkout, then set ``include_pybind11=False``.
+    """
+
+    # flags are prepended, so that they can be further overridden, e.g. by
+    # ``extra_compile_args=["-g"]``.
+
+    def _add_cflags(self, flags: List[str]) -> None:
+        self.extra_compile_args[:0] = flags
+
+    def _add_ldflags(self, flags: List[str]) -> None:
+        self.extra_link_args[:0] = flags
+
+    def __init__(self, *args: Any, **kwargs: Any) -> None:
+
+        self._cxx_level = 0
+        cxx_std = kwargs.pop("cxx_std", 0)
+
+        if "language" not in kwargs:
+            kwargs["language"] = "c++"
+
+        include_pybind11 = kwargs.pop("include_pybind11", True)
+
+        super().__init__(*args, **kwargs)
+
+        # Include the installed package pybind11 headers
+        if include_pybind11:
+            # If using setup_requires, this fails the first time - that's okay
+            try:
+                import pybind11
+
+                pyinc = pybind11.get_include()
+
+                if pyinc not in self.include_dirs:
+                    self.include_dirs.append(pyinc)
+            except ModuleNotFoundError:
+                pass
+
+        self.cxx_std = cxx_std
+
+        cflags = []
+        ldflags = []
+        if WIN:
+            cflags += ["/EHsc", "/bigobj"]
+        else:
+            cflags += ["-fvisibility=hidden"]
+            env_cflags = os.environ.get("CFLAGS", "")
+            env_cppflags = os.environ.get("CPPFLAGS", "")
+            c_cpp_flags = shlex.split(env_cflags) + shlex.split(env_cppflags)
+            if not any(opt.startswith("-g") for opt in c_cpp_flags):
+                cflags += ["-g0"]
+            if MACOS:
+                cflags += ["-stdlib=libc++"]
+                ldflags += ["-stdlib=libc++"]
+        self._add_cflags(cflags)
+        self._add_ldflags(ldflags)
+
+    @property
+    def cxx_std(self) -> int:
+        """
+        The CXX standard level. If set, will add the required flags. If left at
+        0, it will trigger an automatic search when pybind11's build_ext is
+        used. If None, will have no effect.  Besides just the flags, this may
+        add a macos-min 10.9 or 10.14 flag if MACOSX_DEPLOYMENT_TARGET is
+        unset.
+        """
+        return self._cxx_level
+
+    @cxx_std.setter
+    def cxx_std(self, level: int) -> None:
+
+        if self._cxx_level:
+            warnings.warn("You cannot safely change the cxx_level after setting it!")
+
+        # MSVC 2015 Update 3 and later only have 14 (and later 17) modes, so
+        # force a valid flag here.
+        if WIN and level == 11:
+            level = 14
+
+        self._cxx_level = level
+
+        if not level:
+            return
+
+        cflags = [STD_TMPL.format(level)]
+        ldflags = []
+
+        if MACOS and "MACOSX_DEPLOYMENT_TARGET" not in os.environ:
+            # C++17 requires a higher min version of macOS. An earlier version
+            # (10.12 or 10.13) can be set manually via environment variable if
+            # you are careful in your feature usage, but 10.14 is the safest
+            # setting for general use. However, never set higher than the
+            # current macOS version!
+            current_macos = tuple(int(x) for x in platform.mac_ver()[0].split(".")[:2])
+            desired_macos = (10, 9) if level < 17 else (10, 14)
+            macos_string = ".".join(str(x) for x in min(current_macos, desired_macos))
+            macosx_min = f"-mmacosx-version-min={macos_string}"
+            cflags += [macosx_min]
+            ldflags += [macosx_min]
+
+        self._add_cflags(cflags)
+        self._add_ldflags(ldflags)
+
+
+# Just in case someone clever tries to multithread
+tmp_chdir_lock = threading.Lock()
+
+
+@contextlib.contextmanager
+def tmp_chdir() -> Iterator[str]:
+    "Prepare and enter a temporary directory, cleanup when done"
+
+    # Threadsafe
+    with tmp_chdir_lock:
+        olddir = os.getcwd()
+        try:
+            tmpdir = tempfile.mkdtemp()
+            os.chdir(tmpdir)
+            yield tmpdir
+        finally:
+            os.chdir(olddir)
+            shutil.rmtree(tmpdir)
+
+
+# cf http://bugs.python.org/issue26689
+def has_flag(compiler: Any, flag: str) -> bool:
+    """
+    Return the flag if a flag name is supported on the
+    specified compiler, otherwise None (can be used as a boolean).
+    If multiple flags are passed, return the first that matches.
+    """
+
+    with tmp_chdir():
+        fname = Path("flagcheck.cpp")
+        # Don't trigger -Wunused-parameter.
+        fname.write_text("int main (int, char **) { return 0; }", encoding="utf-8")
+
+        try:
+            compiler.compile([str(fname)], extra_postargs=[flag])
+        except distutils.errors.CompileError:
+            return False
+        return True
+
+
+# Every call will cache the result
+cpp_flag_cache = None
+
+
+@lru_cache()
+def auto_cpp_level(compiler: Any) -> Union[str, int]:
+    """
+    Return the max supported C++ std level (17, 14, or 11). Returns latest on Windows.
+    """
+
+    if WIN:
+        return "latest"
+
+    levels = [17, 14, 11]
+
+    for level in levels:
+        if has_flag(compiler, STD_TMPL.format(level)):
+            return level
+
+    msg = "Unsupported compiler -- at least C++11 support is needed!"
+    raise RuntimeError(msg)
+
+
+class build_ext(_build_ext):  # type: ignore[misc] # noqa: N801
+    """
+    Customized build_ext that allows an auto-search for the highest supported
+    C++ level for Pybind11Extension. This is only needed for the auto-search
+    for now, and is completely optional otherwise.
+    """
+
+    def build_extensions(self) -> None:
+        """
+        Build extensions, injecting C++ std for Pybind11Extension if needed.
+        """
+
+        for ext in self.extensions:
+            if hasattr(ext, "_cxx_level") and ext._cxx_level == 0:
+                ext.cxx_std = auto_cpp_level(self.compiler)
+
+        super().build_extensions()
+
+
+def intree_extensions(
+    paths: Iterable[str], package_dir: Optional[Dict[str, str]] = None
+) -> List[Pybind11Extension]:
+    """
+    Generate Pybind11Extensions from source files directly located in a Python
+    source tree.
+
+    ``package_dir`` behaves as in ``setuptools.setup``.  If unset, the Python
+    package root parent is determined as the first parent directory that does
+    not contain an ``__init__.py`` file.
+    """
+    exts = []
+
+    if package_dir is None:
+        for path in paths:
+            parent, _ = os.path.split(path)
+            while os.path.exists(os.path.join(parent, "__init__.py")):
+                parent, _ = os.path.split(parent)
+            relname, _ = os.path.splitext(os.path.relpath(path, parent))
+            qualified_name = relname.replace(os.path.sep, ".")
+            exts.append(Pybind11Extension(qualified_name, [path]))
+        return exts
+
+    for path in paths:
+        for prefix, parent in package_dir.items():
+            if path.startswith(parent):
+                relname, _ = os.path.splitext(os.path.relpath(path, parent))
+                qualified_name = relname.replace(os.path.sep, ".")
+                if prefix:
+                    qualified_name = prefix + "." + qualified_name
+                exts.append(Pybind11Extension(qualified_name, [path]))
+                break
+        else:
+            msg = (
+                f"path {path} is not a child of any of the directories listed "
+                f"in 'package_dir' ({package_dir})"
+            )
+            raise ValueError(msg)
+
+    return exts
+
+
+def naive_recompile(obj: str, src: str) -> bool:
+    """
+    This will recompile only if the source file changes. It does not check
+    header files, so a more advanced function or Ccache is better if you have
+    editable header files in your package.
+    """
+    return os.stat(obj).st_mtime < os.stat(src).st_mtime
+
+
+def no_recompile(obg: str, src: str) -> bool:  # pylint: disable=unused-argument
+    """
+    This is the safest but slowest choice (and is the default) - will always
+    recompile sources.
+    """
+    return True
+
+
+S = TypeVar("S", bound="ParallelCompile")
+
+CCompilerMethod = Callable[
+    [
+        distutils.ccompiler.CCompiler,
+        List[str],
+        Optional[str],
+        Optional[Union[Tuple[str], Tuple[str, Optional[str]]]],
+        Optional[List[str]],
+        bool,
+        Optional[List[str]],
+        Optional[List[str]],
+        Optional[List[str]],
+    ],
+    List[str],
+]
+
+
+# Optional parallel compile utility
+# inspired by: http://stackoverflow.com/questions/11013851/speeding-up-build-process-with-distutils
+# and: https://github.com/tbenthompson/cppimport/blob/stable/cppimport/build_module.py
+# and NumPy's parallel distutils module:
+#              https://github.com/numpy/numpy/blob/master/numpy/distutils/ccompiler.py
+class ParallelCompile:
+    """
+    Make a parallel compile function. Inspired by
+    numpy.distutils.ccompiler.CCompiler.compile and cppimport.
+
+    This takes several arguments that allow you to customize the compile
+    function created:
+
+    envvar:
+        Set an environment variable to control the compilation threads, like
+        NPY_NUM_BUILD_JOBS
+    default:
+        0 will automatically multithread, or 1 will only multithread if the
+        envvar is set.
+    max:
+        The limit for automatic multithreading if non-zero
+    needs_recompile:
+        A function of (obj, src) that returns True when recompile is needed.  No
+        effect in isolated mode; use ccache instead, see
+        https://github.com/matplotlib/matplotlib/issues/1507/
+
+    To use::
+
+        ParallelCompile("NPY_NUM_BUILD_JOBS").install()
+
+    or::
+
+        with ParallelCompile("NPY_NUM_BUILD_JOBS"):
+            setup(...)
+
+    By default, this assumes all files need to be recompiled. A smarter
+    function can be provided via needs_recompile.  If the output has not yet
+    been generated, the compile will always run, and this function is not
+    called.
+    """
+
+    __slots__ = ("envvar", "default", "max", "_old", "needs_recompile")
+
+    def __init__(
+        self,
+        envvar: Optional[str] = None,
+        default: int = 0,
+        max: int = 0,  # pylint: disable=redefined-builtin
+        needs_recompile: Callable[[str, str], bool] = no_recompile,
+    ) -> None:
+        self.envvar = envvar
+        self.default = default
+        self.max = max
+        self.needs_recompile = needs_recompile
+        self._old: List[CCompilerMethod] = []
+
+    def function(self) -> CCompilerMethod:
+        """
+        Builds a function object usable as distutils.ccompiler.CCompiler.compile.
+        """
+
+        def compile_function(
+            compiler: distutils.ccompiler.CCompiler,
+            sources: List[str],
+            output_dir: Optional[str] = None,
+            macros: Optional[Union[Tuple[str], Tuple[str, Optional[str]]]] = None,
+            include_dirs: Optional[List[str]] = None,
+            debug: bool = False,
+            extra_preargs: Optional[List[str]] = None,
+            extra_postargs: Optional[List[str]] = None,
+            depends: Optional[List[str]] = None,
+        ) -> Any:
+
+            # These lines are directly from distutils.ccompiler.CCompiler
+            macros, objects, extra_postargs, pp_opts, build = compiler._setup_compile(  # type: ignore[attr-defined]
+                output_dir, macros, include_dirs, sources, depends, extra_postargs
+            )
+            cc_args = compiler._get_cc_args(pp_opts, debug, extra_preargs)  # type: ignore[attr-defined]
+
+            # The number of threads; start with default.
+            threads = self.default
+
+            # Determine the number of compilation threads, unless set by an environment variable.
+            if self.envvar is not None:
+                threads = int(os.environ.get(self.envvar, self.default))
+
+            def _single_compile(obj: Any) -> None:
+                try:
+                    src, ext = build[obj]
+                except KeyError:
+                    return
+
+                if not os.path.exists(obj) or self.needs_recompile(obj, src):
+                    compiler._compile(obj, src, ext, cc_args, extra_postargs, pp_opts)  # type: ignore[attr-defined]
+
+            try:
+                # Importing .synchronize checks for platforms that have some multiprocessing
+                # capabilities but lack semaphores, such as AWS Lambda and Android Termux.
+                import multiprocessing.synchronize
+                from multiprocessing.pool import ThreadPool
+            except ImportError:
+                threads = 1
+
+            if threads == 0:
+                try:
+                    threads = multiprocessing.cpu_count()
+                    threads = self.max if self.max and self.max < threads else threads
+                except NotImplementedError:
+                    threads = 1
+
+            if threads > 1:
+                with ThreadPool(threads) as pool:
+                    for _ in pool.imap_unordered(_single_compile, objects):
+                        pass
+            else:
+                for ob in objects:
+                    _single_compile(ob)
+
+            return objects
+
+        return compile_function
+
+    def install(self: S) -> S:
+        """
+        Installs the compile function into distutils.ccompiler.CCompiler.compile.
+        """
+        distutils.ccompiler.CCompiler.compile = self.function()  # type: ignore[assignment]
+        return self
+
+    def __enter__(self: S) -> S:
+        self._old.append(distutils.ccompiler.CCompiler.compile)
+        return self.install()
+
+    def __exit__(self, *args: Any) -> None:
+        distutils.ccompiler.CCompiler.compile = self._old.pop()  # type: ignore[assignment]