# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
-# This CMakeLists.txt allows source distributions of the gmxapi Python package
-# to rely on scikit-build for support of various Python packaging systems. The
-# simplest use case is to allow the `setup.py` file to invoke skbuild to
-# configure and run CMake. CMake could be invoked directly by the user or a
-# parent package, but the Python distribution would not be packaged automatically.
-# Reference https://gitlab.com/gromacs/gromacs/-/issues/2896 for additional discussion.
+# This CMakeLists.txt is not intended to be used directly, but either through
+# setup.py or as an inclusion of the full GROMACS project.
+# See https://manual.gromacs.org/current/gmxapi/userguide/install.html for more.
cmake_minimum_required(VERSION 3.16.3)
# This needs to be set before project() in order to pick up toolchain files
# Note that this is the gmxapi._gmxapi Python bindings package version,
# not the C++ API version. It is not essential that it match the pure Python
# package version, but is likely to do so.
-project(gmxapi VERSION 0.3.0)
+project(gmxapi)
# Check if Python package is being built directly or via add_subdirectory
set(GMXAPI_MASTER_PROJECT OFF)
if (CMAKE_CURRENT_SOURCE_DIR STREQUAL CMAKE_SOURCE_DIR)
set(GMXAPI_MASTER_PROJECT ON)
+ if (NOT Python3_FIND_STRATEGY)
+ # If the user provides a hint for the Python installation with Python3_ROOT_DIR,
+ # prevent FindPython3 from overriding the choice with a newer Python version
+ # when CMP0094 is set to OLD.
+ set(Python3_FIND_STRATEGY LOCATION)
+ endif ()
+ if(NOT Python3_FIND_VIRTUALENV)
+ # We advocate using Python venvs to manage package availability, so by default
+ # we want to preferentially discover user-space software.
+ set(Python3_FIND_VIRTUALENV FIRST)
+ endif()
endif()
set(CMAKE_CXX_STANDARD 17)
cmake_policy(SET CMP0074 NEW)
endif()
+find_package(Python3 3.7 COMPONENTS Interpreter Development)
+find_package(pybind11 2.6 CONFIG)
+# If we are not running through setup.py, we may need to look for the pybind11 headers.
+if (NOT pybind11_FOUND)
+ execute_process(
+ COMMAND
+ "${Python3_EXECUTABLE}" -c
+ "import pybind11; print(pybind11.get_cmake_dir())"
+ OUTPUT_VARIABLE _tmp_dir
+ OUTPUT_STRIP_TRAILING_WHITESPACE COMMAND_ECHO STDOUT)
+ list(APPEND CMAKE_PREFIX_PATH "${_tmp_dir}")
+ find_package(pybind11 2.6 CONFIG)
+endif ()
+if (NOT pybind11_FOUND)
+ message(FATAL_ERROR "Python package build dependencies not found with interpreter ${Python3_EXECUTABLE}. "
+ "See https://manual.gromacs.org/current/gmxapi/userguide/install.html")
+endif ()
+
if(GMXAPI_MASTER_PROJECT)
find_package(gmxapi 0.2 REQUIRED
HINTS "$ENV{GROMACS_DIR}"
message(WARNING "Your GROMACS installation does not support custom MD plugins. "
"If you need this feature, please install GROMACS 2021.3 or higher.")
endif ()
+else()
+ # Building as part of the GROMACS master project. GROMACS CMake logic should
+ # not be processing this unless Python3 was appropriately detected.
+ if (NOT Python3_FOUND)
+ message(FATAL_ERROR "Error in CMake script. Please report GROMACS bug.")
+ endif ()
+
+ get_target_property(gmxapi_VERSION gmxapi VERSION)
endif()
+
if(gmxapi_FOUND)
set(_suffix "")
# GROMACS master branch and development branches may have divergent
if(gmxapi_EXPERIMENTAL)
set(_suffix " (unofficial)")
endif()
- message(STATUS "Found gmxapi version ${gmxapi_VERSION}${_suffix}")
endif()
+message(STATUS "Configuring Python package for gmxapi version ${gmxapi_VERSION}${_suffix}")
+
# The Gromacs::gmxapi target could be imported from an existing installation or
# provided as an alias target within the GROMACS build tree.
if (NOT TARGET Gromacs::gmxapi)
message(FATAL_ERROR "Cannot build Python package without GROMACS gmxapi support.")
endif ()
-# TODO: Provide user hints for mpi4py installation.
+# TODO(#3279): Provide user hints for mpi4py installation.
# Note that neither the Python package nor the Gromacs::gmxapi CMake target are
# built with MPI in any case, but they _should_ be built with a C++ compiler
# that is compatible with the available MPI compiler wrappers, and technically
# For convenience, it is fine if libgmxapi and _gmxapi are built with the mpi
# compiler wrapper.
-option(GMXAPI_USE_BUNDLED_PYBIND
- "Use pybind11 headers bundled with this repository. If OFF, CMake does `find_package(pybind11)`."
- ON)
-if(GMXAPI_USE_BUNDLED_PYBIND)
- add_subdirectory(external/pybind)
-else()
- # Reference https://gitlab.com/gromacs/gromacs/-/issues/2896
- find_package(pybind11 2.2 REQUIRED)
-endif()
-
-set(GMXAPI_PYTHON_EXTENSION_SOURCES
- gmxapi/module.cpp
- gmxapi/export_context.cpp
- gmxapi/export_exceptions.cpp
- gmxapi/export_system.cpp
- gmxapi/export_tprfile.cpp
- gmxapi/pycontext.cpp
- gmxapi/pysystem.cpp
- )
-
pybind11_add_module(_gmxapi
- ${GMXAPI_PYTHON_EXTENSION_SOURCES}
+ gmxapi/module.cpp
+ gmxapi/export_context.cpp
+ gmxapi/export_exceptions.cpp
+ gmxapi/export_system.cpp
+ gmxapi/export_tprfile.cpp
+ gmxapi/pycontext.cpp
+ gmxapi/pysystem.cpp
)
if (gmxapi_VERSION VERSION_GREATER_EQUAL 0.2.1)
target_sources(_gmxapi PRIVATE gmxapi/launch_021.cpp)
else()
+ message(WARNING "Found an old gmxapi library version. Please consider updating your GROMACS installation.")
target_sources(_gmxapi PRIVATE gmxapi/launch_020.cpp)
endif()
# RPATH management: make sure build artifacts can find GROMACS library.
set_target_properties(_gmxapi PROPERTIES SKIP_BUILD_RPATH FALSE)
-# Python sources (*.py) will be packaged by scikit-build and setuptools.
-# Note that library targets are built in CMAKE_LIBRARY_OUTPUT_DIRECTORY if not otherwise specified.
-# This may be an unexpected location, whether inherited from the GROMACS build tree
-# or the SKBUILD framework. Note, also, that when scikit-build is invoked with setup.py,
-# the CMake build takes place in a subdirectory of ./_skbuild/.
-set(GMXAPI_PYTHON_STAGING_DIR ${CMAKE_CURRENT_BINARY_DIR}/gmxapi_staging)
-set_target_properties(_gmxapi PROPERTIES
- LIBRARY_OUTPUT_DIRECTORY ${GMXAPI_PYTHON_STAGING_DIR}/gmxapi)
-
if(GMXAPI_MASTER_PROJECT)
# TODO: This requirement is probably overly restrictive.
find_package(GROMACS 2021 REQUIRED
if (NOT _gmx_bindir OR NOT _gmx_executable)
message(FATAL_ERROR "Could not get path for gmx wrapper binary.")
endif ()
-configure_file(gmxapi/gmxconfig.json.in ${GMXAPI_PYTHON_STAGING_DIR}/gmxapi/gmxconfig.json)
+configure_file(gmxapi/gmxconfig.json.in gmxapi/gmxconfig.json)
unset(_gmx_executable)
unset(_gmx_bindir)
unset(_gmx_mpi_type)
-# scikit-build sets SKBUILD when running Python packaging tools through setup.py
-# (e.g. with pip)
-if(SKBUILD)
- # The Python module is being built for a GROMACS installation.
+if (GMXAPI_MASTER_PROJECT)
set_target_properties(_gmxapi PROPERTIES BUILD_WITH_INSTALL_RPATH TRUE)
set_target_properties(_gmxapi PROPERTIES INSTALL_RPATH_USE_LINK_PATH TRUE)
target_link_libraries(_gmxapi PRIVATE Gromacs::gmxapi)
- # By default, scikit-build expects the library to be installed into a directory
- # named for the Python package as in setup.py.
- install(TARGETS _gmxapi LIBRARY DESTINATION gmxapi)
- install(FILES ${GMXAPI_PYTHON_STAGING_DIR}/gmxapi/gmxconfig.json DESTINATION gmxapi)
+ # The Python setup.py sets CMAKE_LIBRARY_OUTPUT_DIRECTORY and will be looking for generated files there.
+ file(COPY ${CMAKE_CURRENT_BINARY_DIR}/gmxapi/gmxconfig.json
+ DESTINATION ${CMAKE_LIBRARY_OUTPUT_DIRECTORY})
else()
- # The Python module is being built against GROMACS in its build tree.
- # Note: we do not have plans to install the staged package when SKBUILD != TRUE
- set_target_properties(_gmxapi PROPERTIES BUILD_WITH_INSTALL_RPATH FALSE)
- target_link_libraries(_gmxapi PRIVATE Gromacs::gmxapi)
-
- # TODO: Determine packaging and installation cases and implementation.
- # Reference https://gitlab.com/gromacs/gromacs/-/issues/2896 for additional discussion.
- # Currently, CMake should be run by scikit-build through setup.py for proper Python packaging.
- # We don't want to install by default in the outer scope of the GROMACS
- # CMake procedure because we could end up trying to install to a system directory
- # the user did not intend, or a user might install a Python-installation-specific
- # package into an overly generic GROMACS path.
+ # The rest of the logic in this conditional is to support the GMX_PYTHON_PACKAGE option
+ # for testing the gmxapi Python packages within a full GROMACS project build_command and.
+ # for building full GROMACS project documentation.
+ set(GMXAPI_PYTHON_STAGING_DIR ${CMAKE_CURRENT_BINARY_DIR}/gmxapi_staging)
# Instead, we should probably build a source package and alert the user of its location.
# We can use CMake to call the Python packaging tools to create an 'sdist'
# source distribution archive to be installed in the GROMACS installation
# easier clean-up, as well.
# TODO: (ref Issue #2896) Build and install 'sdist' with GROMACS.
+ # The Python module is being built against GROMACS in its build tree, so we will not install.
+ set_target_properties(_gmxapi PROPERTIES BUILD_WITH_INSTALL_RPATH FALSE)
+ target_link_libraries(_gmxapi PRIVATE Gromacs::gmxapi)
# However, we can still produce an importable package for documentation builds and
# basic testing in ${CMAKE_CURRENT_BINARY_DIR}/gmxapi_staging
+ set_target_properties(_gmxapi PROPERTIES
+ LIBRARY_OUTPUT_DIRECTORY ${GMXAPI_PYTHON_STAGING_DIR}/gmxapi)
file(GLOB_RECURSE _py_sources
CONFIGURE_DEPENDS
${CMAKE_CURRENT_SOURCE_DIR}/gmxapi/*.py)
file(COPY ${_package_file} DESTINATION ${GMXAPI_PYTHON_STAGING_DIR}/${_relative_dir})
endforeach()
file(COPY setup.py CMakeLists.txt DESTINATION ${GMXAPI_PYTHON_STAGING_DIR})
- # Set CMake variable pybind11_DIR to ${CMAKE_CURRENT_SOURCE_DIR}/external/pybind/tools
- # if re-invoking CMake (including via Python setuptools) for the files in gmxapi_staging.
+ file(COPY ${CMAKE_CURRENT_BINARY_DIR}/gmxapi/gmxconfig.json DESTINATION ${GMXAPI_PYTHON_STAGING_DIR}/gmxapi)
# Unit test and build docs using PYTHONPATH=$CMAKE_CURRENT_BINARY_DIR/gmxapi_staging
set_target_properties(_gmxapi PROPERTIES staging_dir ${GMXAPI_PYTHON_STAGING_DIR})
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff