pybind11: v2.6.1+ (openPMD#857)

* Internal: pybind11 2.6.1 Update the internal version of pybind11, version 2.6.1. Modifications from the releases: - remove test & doc dirs - remove wheel packaging (setup.py/cfg, pyproject.toml) - remove github templates & CI * Doc: pybind11 2.6.1+ * CMake: 3.15.0+ For new FindPython support (unifying FindPythonLibs and FindPythonInterp). * CMake: Adopt to FindPython.cmake * pybind11: replace non-ascii * Changelog: PR number * CI: Update Python Hints (none needed) Co-authored-by: Wenzel Jakob <wenzel.jakob@epfl.ch>
franzpoeschel · Dec 23, 2020 · 5889e06 · 5889e06
1 parent a90e494
commit 5889e06
Show file tree

Hide file tree

Showing 63 changed files with 3,832 additions and 1,836 deletions.
diff --git a/.github/workflows/unix.yml b/.github/workflows/unix.yml
@@ -98,7 +98,7 @@ jobs:
       run: |
         mkdir build && cd build
         ../share/openPMD/download_samples.sh && chmod u-w samples/git-sample/*.h5
-        cmake -S .. -B . -DopenPMD_USE_PYTHON=ON -DPYTHON_EXECUTABLE=$(which python3) -DopenPMD_USE_MPI=OFF -DopenPMD_USE_HDF5=ON -DopenPMD_USE_INVASIVE_TESTS=ON -DCMAKE_VERBOSE_MAKEFILE=ON
+        cmake -S .. -B . -DopenPMD_USE_PYTHON=ON -DopenPMD_USE_MPI=OFF -DopenPMD_USE_HDF5=ON -DopenPMD_USE_INVASIVE_TESTS=ON -DCMAKE_VERBOSE_MAKEFILE=ON
         cmake --build . --parallel 2
         ctest --output-on-failure
 
@@ -130,7 +130,7 @@ jobs:
       run: |
         mkdir build && cd build
         ../share/openPMD/download_samples.sh && chmod u-w samples/git-sample/*.h5
-        cmake -S .. -B . -DopenPMD_USE_PYTHON=ON -DPYTHON_EXECUTABLE=$(which python3) -DopenPMD_USE_MPI=ON -DopenPMD_USE_HDF5=ON -DopenPMD_USE_ADIOS2=ON -DopenPMD_USE_INVASIVE_TESTS=ON
+        cmake -S .. -B . -DopenPMD_USE_PYTHON=ON -DopenPMD_USE_MPI=ON -DopenPMD_USE_HDF5=ON -DopenPMD_USE_ADIOS2=ON -DopenPMD_USE_INVASIVE_TESTS=ON
         cmake --build . --parallel 2
         ctest --output-on-failure
 
@@ -167,7 +167,7 @@ jobs:
 
         mkdir build && cd build
         ../share/openPMD/download_samples.sh && chmod u-w samples/git-sample/*.h5
-        cmake -S .. -B . -DopenPMD_USE_PYTHON=ON -DPYTHON_EXECUTABLE=$(which python3) -DopenPMD_USE_MPI=ON -DopenPMD_USE_HDF5=ON -DopenPMD_USE_ADIOS1=ON -DopenPMD_USE_ADIOS2=ON -DopenPMD_USE_INVASIVE_TESTS=ON
+        cmake -S .. -B . -DopenPMD_USE_PYTHON=ON -DopenPMD_USE_MPI=ON -DopenPMD_USE_HDF5=ON -DopenPMD_USE_ADIOS1=ON -DopenPMD_USE_ADIOS2=ON -DopenPMD_USE_INVASIVE_TESTS=ON
         cmake --build . --parallel 2
         ctest --output-on-failure
 
@@ -185,6 +185,6 @@ jobs:
         mkdir build && cd build
         ../share/openPMD/download_samples.sh && chmod u-w samples/git-sample/*.h5
         find /usr -name adios.pc
-        cmake -S .. -B . -DopenPMD_USE_PYTHON=ON -DPYTHON_EXECUTABLE=$(which python3) -DopenPMD_USE_MPI=ON -DopenPMD_USE_HDF5=ON -DopenPMD_USE_INVASIVE_TESTS=ON
+        cmake -S .. -B . -DopenPMD_USE_PYTHON=ON -DopenPMD_USE_MPI=ON -DopenPMD_USE_HDF5=ON -DopenPMD_USE_INVASIVE_TESTS=ON
         cmake --build . --parallel 2
         ctest --output-on-failure
diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -24,8 +24,10 @@ Other
 """""
 
 - switch to C++14 #825
+- CMake: require version 3.15.0+ #857
 - Python: support 3.6 - 3.9 #828
 - NLohmann-JSON dependency updated to 3.9.1+ #839
+- pybind11 dependency updated 2.6.1+ #857
 - Docs:
 
   - Release cibuildwheel example #775

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -1,6 +1,6 @@
 # Preamble ####################################################################
 #
-cmake_minimum_required(VERSION 3.12.0)
+cmake_minimum_required(VERSION 3.15.0)
 
 project(openPMD VERSION 0.12.1) # LANGUAGES CXX
 
@@ -249,53 +249,38 @@ endif()
 
 # external library: pybind11 (optional)
 if(openPMD_USE_PYTHON STREQUAL AUTO)
-    if(openPMD_USE_INTERNAL_PYBIND11)
-        add_subdirectory("${openPMD_SOURCE_DIR}/share/openPMD/thirdParty/pybind11")
-        set(openPMD_HAVE_PYTHON TRUE)
-        message(STATUS "pybind11: Using INTERNAL version 2.4.3")
-    else()
-        find_package(pybind11 2.4.3 CONFIG)
-        if(pybind11_FOUND)
+    find_package(Python 3.6.0 COMPONENTS Interpreter Development)
+    if(Python_FOUND)
+        if(openPMD_USE_INTERNAL_PYBIND11)
+            add_subdirectory("${openPMD_SOURCE_DIR}/share/openPMD/thirdParty/pybind11")
             set(openPMD_HAVE_PYTHON TRUE)
-            message(STATUS "pybind11: Found version '${pybind11_VERSION}'")
+            message(STATUS "pybind11: Using INTERNAL version 2.6.1")
         else()
-            set(openPMD_HAVE_PYTHON FALSE)
+            find_package(pybind11 2.6.1 CONFIG)
+            if(pybind11_FOUND)
+                set(openPMD_HAVE_PYTHON TRUE)
+                message(STATUS "pybind11: Found version '${pybind11_VERSION}'")
+            else()
+                set(openPMD_HAVE_PYTHON FALSE)
+            endif()
         endif()
-    endif()
-    if(openPMD_HAVE_PYTHON AND
-       PYTHON_VERSION_MAJOR LESS 3)
+    else()
         set(openPMD_HAVE_PYTHON FALSE)
-        message(STATUS "python: Found version '"
-                       "${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR}' "
-                       "is NOT supported. Set for example "
-                       "-DPYTHON_EXECUTABLE=$(which python3) "
-                       "to use 3.6+.")
     endif()
 elseif(openPMD_USE_PYTHON)
+    find_package(Python COMPONENTS Interpreter Development REQUIRED)
     if(openPMD_USE_INTERNAL_PYBIND11)
         add_subdirectory("${openPMD_SOURCE_DIR}/share/openPMD/thirdParty/pybind11")
         set(openPMD_HAVE_PYTHON TRUE)
-        message(STATUS "pybind11: Using INTERNAL version 2.4.3")
+        message(STATUS "pybind11: Using INTERNAL version 2.6.1")
     else()
-        find_package(pybind11 2.4.3 REQUIRED CONFIG)
+        find_package(pybind11 2.6.1 REQUIRED CONFIG)
         set(openPMD_HAVE_PYTHON TRUE)
         message(STATUS "pybind11: Found version '${pybind11_VERSION}'")
     endif()
-    if(PYTHON_VERSION_MAJOR LESS 3)
-        message(FATAL_ERROR "python: Found version '"
-                            "${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR}' "
-                            "is NOT supported. Set for example "
-                            "-DPYTHON_EXECUTABLE=$(which python3) "
-                            "to use 3.6+.")
-    endif()
 else()
     set(openPMD_HAVE_PYTHON FALSE)
 endif()
-if(openPMD_HAVE_PYTHON)
-    add_library(openPMD::thirdparty::pybind11 INTERFACE IMPORTED)
-    target_link_libraries(openPMD::thirdparty::pybind11
-        INTERFACE pybind11::pybind11)
-endif()
 
 
 # Targets #####################################################################
@@ -535,7 +520,7 @@ endif()
 
 # python bindings
 if(openPMD_HAVE_PYTHON)
-    pybind11_add_module(openPMD.py MODULE SYSTEM
+    add_library(openPMD.py MODULE
         src/binding/python/openPMD.cpp
         src/binding/python/Access.cpp
         src/binding/python/Attributable.cpp
@@ -560,6 +545,13 @@ if(openPMD_HAVE_PYTHON)
         src/binding/python/UnitDimension.cpp
     )
     target_link_libraries(openPMD.py PRIVATE openPMD)
+    target_link_libraries(openPMD.py PRIVATE pybind11::module pybind11::lto pybind11::windows_extras)
+
+    pybind11_extension(openPMD.py)
+    pybind11_strip(openPMD.py)
+
+    set_target_properties(openPMD.py PROPERTIES CXX_VISIBILITY_PRESET "hidden"
+                                                CUDA_VISIBILITY_PRESET "hidden")
 
     # ancient Clang releases
     #   https://github.com/openPMD/openPMD-api/issues/542
@@ -581,7 +573,7 @@ if(openPMD_HAVE_PYTHON)
         )
     else()
         set(CMAKE_INSTALL_PYTHONDIR_DEFAULT
-            "${CMAKE_INSTALL_LIBDIR}/python${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR}/site-packages"
+            "${CMAKE_INSTALL_LIBDIR}/python${Python_VERSION_MAJOR}.${Python_VERSION_MINOR}/site-packages"
         )
     endif()
     set(CMAKE_INSTALL_PYTHONDIR "${CMAKE_INSTALL_PYTHONDIR_DEFAULT}"
@@ -926,7 +918,7 @@ if(BUILD_TESTING)
     if(openPMD_HAVE_PYTHON)
         # do we have mpi4py for MPI-parallel Python tests?
         if(openPMD_HAVE_MPI)
-            execute_process(COMMAND ${PYTHON_EXECUTABLE}
+            execute_process(COMMAND ${Python_EXECUTABLE}
                 -m mpi4py
                 -c "import mpi4py.MPI"
                 RESULT_VARIABLE MPI4PY_RETURN
@@ -962,7 +954,7 @@ if(BUILD_TESTING)
         if(openPMD_HAVE_HDF5)
             if(EXAMPLE_DATA_FOUND)
                 add_test(NAME Unittest.py
-                    COMMAND ${PYTHON_EXECUTABLE}
+                    COMMAND ${Python_EXECUTABLE}
                         ${openPMD_SOURCE_DIR}/test/python/unittest/Test.py -v
                     WORKING_DIRECTORY
                         ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}
@@ -1035,7 +1027,7 @@ if(BUILD_TESTING)
         #  console scripts and replace the all-binary CLI tools.)
         foreach(pymodulename ${openPMD_PYTHON_CLI_MODULE_NAMES})
              add_test(NAME CLI.py.help.${pymodulename}
-                 COMMAND ${PYTHON_EXECUTABLE} -m openpmd_api.${pymodulename} --help
+                 COMMAND ${Python_EXECUTABLE} -m openpmd_api.${pymodulename} --help
                  WORKING_DIRECTORY ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}
             )
             if(WIN32)
@@ -1068,7 +1060,7 @@ if(BUILD_TESTING)
                         if(openPMD_HAVE_MPI AND MPI4PY_RETURN EQUAL 0)
                             # see https://mpi4py.readthedocs.io/en/stable/mpi4py.run.html
                             add_test(NAME Example.py.${examplename}
-                                COMMAND ${MPI_TEST_EXE} ${PYTHON_EXECUTABLE} -m mpi4py
+                                COMMAND ${MPI_TEST_EXE} ${Python_EXECUTABLE} -m mpi4py
                                     ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/${examplename}.py
                                 WORKING_DIRECTORY ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}
                             )
@@ -1077,7 +1069,7 @@ if(BUILD_TESTING)
                         endif()
                     else()
                         add_test(NAME Example.py.${examplename}
-                            COMMAND ${PYTHON_EXECUTABLE}
+                            COMMAND ${Python_EXECUTABLE}
                                 ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/${examplename}.py
                             WORKING_DIRECTORY
                                 ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}

diff --git a/Dockerfile b/Dockerfile
@@ -101,7 +101,7 @@ RUN        cd /opt/src; \
 #RUN        mkdir build \
 #           && cd build \
 #           && /opt/cmake/bin/cmake \
-#               -DPYTHON_EXECUTABLE=$(which /opt/python/cp${PY_TARGET}-cp${PY_TARGET}m/bin/python) \
+#               -DPython_ROOT_DIR=$(which /opt/python/cp${PY_TARGET}-cp${PY_TARGET}m) \
 #               -DHDF5_USE_STATIC_LIBRARIES=ON \
 #               -DBUILD_SHARED_LIBS=OFF \
 #               -DBUILD_TESTING=OFF \

diff --git a/NEWS.rst b/NEWS.rst
@@ -8,6 +8,7 @@ Upgrade Guide
 
 Building openPMD-api now requires a compiler that supports C++14 or newer.
 Supported Python version are now 3.6 to 3.9.
+CMake 3.15.0 is now the minimally supported version for CMake.
 
 Python
 ^^^^^^

diff --git a/README.md b/README.md
@@ -99,13 +99,13 @@ Our manual shows full [read & write examples](https://openpmd-api.readthedocs.io
 ## Dependencies
 
 Required:
-* CMake 3.12.0+
+* CMake 3.15.0+
 * C++14 capable compiler, e.g. g++ 5.0+, clang 5.0+, VS 2017+
 
 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) 2.4.3+ ([new BSD](https://github.com/pybind/pybind11/blob/master/LICENSE))
+* [pybind11](https://github.com/pybind/pybind11) 2.6.1+ ([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))
 
 I/O backends:
@@ -120,7 +120,7 @@ while those can be built either with or without:
 Optional language bindings:
 * Python:
   * Python 3.6 - 3.9
-  * pybind11 2.4.3+
+  * pybind11 2.6.1+
   * numpy 1.15+
   * mpi4py 2.1+
 
@@ -223,7 +223,7 @@ cd openPMD-api-build
 # for options append:
 #   -DopenPMD_USE_...=...
 # e.g. for python support add:
-#   -DopenPMD_USE_PYTHON=ON -DPYTHON_EXECUTABLE=$(which python3)
+#   -DopenPMD_USE_PYTHON=ON
 cmake ../openPMD-api
 
 cmake --build .
@@ -248,7 +248,7 @@ CMake controls options with prefixed `-D`, e.g. `-DopenPMD_USE_MPI=OFF`:
 | `openPMD_USE_INVASIVE_TESTS` | ON/**OFF**       | Enable unit tests that modify source code <sup>1</sup>                       |
 | `openPMD_USE_VERIFY`         | **ON**/OFF       | Enable internal VERIFY (assert) macro independent of build type <sup>2</sup> |
 | `openPMD_INSTALL`            | **ON**/OFF       | Add installation targets                                                     |
-| `PYTHON_EXECUTABLE`          | (first found)    | Path to Python executable                                                    |
+| `Python_EXECUTABLE`          | (newest found)   | Path to Python executable                                                    |
 
 <sup>1</sup> *e.g. changes C++ visibility keywords, breaks MSVC*
 <sup>2</sup> *this includes most pre-/post-condition checks, disabling without specific cause is highly discouraged*
@@ -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      |  2.4.3+ |
+| `openPMD_USE_INTERNAL_PYBIND11` | **ON**/OFF | pybind11      |  2.6.1+ |
 | `openPMD_USE_INTERNAL_JSON`     | **ON**/OFF | NLohmann-JSON |  3.9.1+ |
 
 By default, this will build as a shared library (`libopenPMD.[so|dylib|dll]`) and installs also its headers.

diff --git a/Singularity b/Singularity
@@ -45,7 +45,6 @@ Supported frontends are C++11 and Python3.
         -DopenPMD_USE_ADIOS1=ON  \
         -DopenPMD_USE_ADIOS2=OFF \
         -DopenPMD_USE_PYTHON=ON  \
-        -DPYTHON_EXECUTABLE=$(which python3) \
         -DBUILD_TESTING=OFF      \
         -DCMAKE_INSTALL_PREFIX=/usr/local \
         -DCMAKE_INSTALL_PYTHONDIR=lib/python3.6/dist-packages

diff --git a/docs/source/dev/buildoptions.rst b/docs/source/dev/buildoptions.rst
@@ -20,7 +20,7 @@ CMake Option                   Values          Description
 ``openPMD_USE_INVASIVE_TESTS`` ON/**OFF**      Enable unit tests that modify source code :sup:`1`
 ``openPMD_USE_VERIFY``         **ON**/OFF      Enable internal VERIFY (assert) macro independent of build type :sup:`2`
 ``openPMD_INSTALL``            **ON**/OFF      Add installation targets
-``PYTHON_EXECUTABLE``          (first found)   Path to Python executable
+``Python_EXECUTABLE``          (newest found)  Path to Python executable
 ============================== =============== ========================================================================
 
 :sup:`1` e.g. changes C++ visibility keywords, breaks MSVC
@@ -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        2.4.3+
+``openPMD_USE_INTERNAL_PYBIND11`` **ON**/OFF  No       pybind11        2.6.1+
 ``openPMD_USE_INTERNAL_JSON``     **ON**/OFF  No       NLohmann-JSON   3.9.1+
 ================================= =========== ======== ============= ========
 

diff --git a/docs/source/dev/dependencies.rst b/docs/source/dev/dependencies.rst
@@ -9,7 +9,7 @@ These are currently:
 Required
 --------
 
-* CMake 3.12.0+
+* CMake 3.15.0+
 * C++14 capable compiler, e.g. g++ 5.0+, clang 5.0+, VS 2017+
 
 Shipped internally
@@ -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>`_ 2.4.3+ (`new BSD <https://github.com/pybind/pybind11/blob/master/LICENSE>`_)
+* `pybind11 <https://github.com/pybind/pybind11>`_ 2.6.1+ (`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>`_)
 
 Optional: I/O backends
@@ -40,7 +40,7 @@ Optional: language bindings
 * Python:
 
   * Python 3.6 - 3.9
-  * pybind11 2.4.3+
+  * pybind11 2.6.1+
   * numpy 1.15+
   * mpi4py 2.1+
 

diff --git a/docs/source/install/install.rst b/docs/source/install/install.rst
@@ -138,7 +138,7 @@ Linux & OSX
    # for options append:
    #   -DopenPMD_USE_...=...
    # e.g. for python support add:
-   #   -DopenPMD_USE_PYTHON=ON -DPYTHON_EXECUTABLE=$(which python3)
+   #   -DopenPMD_USE_PYTHON=ON
    cmake ../openPMD-api
 
    cmake --build .

diff --git a/pyproject.toml b/pyproject.toml
@@ -1,2 +1,2 @@
 [build-system]
-requires = ["setuptools>38.6", "wheel", "cmake>=3.12.0,<4.0.0", "pybind11>=2.4.3,<3.0.0"]
+requires = ["setuptools>38.6", "wheel", "cmake>=3.15.0,<4.0.0", "pybind11>=2.6.1,<3.0.0"]
diff --git a/setup.py b/setup.py
@@ -21,16 +21,16 @@ def run(self):
             out = subprocess.check_output(['cmake', '--version'])
         except OSError:
             raise RuntimeError(
-                "CMake 3.12.0+ must be installed to build the following " +
+                "CMake 3.15.0+ must be installed to build the following " +
                 "extensions: " +
                 ", ".join(e.name for e in self.extensions))
 
         cmake_version = LooseVersion(re.search(
             r'version\s*([\d.]+)',
             out.decode()
         ).group(1))
-        if cmake_version < '3.12.0':
-            raise RuntimeError("CMake >= 3.12.0 is required")
+        if cmake_version < '3.15.0':
+            raise RuntimeError("CMake >= 3.15.0 is required")
 
         for ext in self.extensions:
             self.build_extension(ext)
@@ -48,7 +48,7 @@ def build_extension(self, ext):
             os.path.join(extdir, "openpmd_api"),
             # '-DCMAKE_RUNTIME_OUTPUT_DIRECTORY=' + extdir,
             '-DCMAKE_PYTHON_OUTPUT_DIRECTORY=' + extdir,
-            '-DPYTHON_EXECUTABLE=' + sys.executable,
+            '-DPython_ROOT_DIR=' + sys.exec_prefix,
             '-DopenPMD_USE_PYTHON:BOOL=ON',
             # variants
             '-DopenPMD_USE_MPI:BOOL=' + openPMD_USE_MPI,
-Original file line number
+Diff line change
@@ Expand Up / @@ -8,6 +8,7 @@ Upgrade Guide @@
     Building openPMD-api now requires a compiler that supports C++14 or newer.
     Supported Python version are now 3.6 to 3.9.
+    CMake 3.15.0 is now the minimally supported version for CMake.
     Python
     ^^^^^^
@@ Expand Down @@