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35 # This CMakeLists.txt allows source distributions of the gmxapi Python package
36 # to rely on scikit-build for support of various Python packaging systems. The
37 # simplest use case is to allow the `setup.py` file to invoke skbuild to
38 # configure and run CMake. CMake could be invoked directly by the user or a
39 # parent package, but the Python distribution would not be packaged automatically.
40 # Reference https://gitlab.com/gromacs/gromacs/-/issues/2896 for additional discussion.
41 cmake_minimum_required(VERSION 3.13.0)
43 # This needs to be set before project() in order to pick up toolchain files
44 #list(APPEND CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/../../cmake)
46 # OS X deployment target should be >=10.14 for modern C++ compatibility.
47 # Reference https://scikit-build.readthedocs.io/en/latest/generators.html#macosx
48 # and https://github.com/MacPython/wiki/wiki/Spinning-wheels
49 set(CMAKE_OSX_DEPLOYMENT_TARGET 10.14 CACHE STRING
50 "OS X deployment target below 10.14 does not use modern standard library")
51 set(CMAKE_OSX_ARCHITECTURES x86_64 CACHE STRING
52 "OS X should build Python package for 64-bit architecture"
55 # Note that this is the gmxapi._gmxapi Python bindings package version,
56 # not the C++ API version. It is not essential that it match the pure Python
57 # package version, but is likely to do so.
58 project(gmxapi VERSION 0.3.0)
60 # Check if Python package is being built directly or via add_subdirectory
61 set(GMXAPI_MASTER_PROJECT OFF)
62 if (CMAKE_CURRENT_SOURCE_DIR STREQUAL CMAKE_SOURCE_DIR)
63 set(GMXAPI_MASTER_PROJECT ON)
66 set(CMAKE_CXX_STANDARD 17)
67 set(CMAKE_CXX_STANDARD_REQUIRED ON)
69 # Only interpret if() arguments as variables or keywords when unquoted.
70 cmake_policy(SET CMP0054 NEW)
71 # honor the language standard settings for try_compile()
72 cmake_policy(SET CMP0067 NEW)
73 if(POLICY CMP0074) #3.12
74 # Allow gmxapi_ROOT hint.
75 cmake_policy(SET CMP0074 NEW)
78 if(GMXAPI_MASTER_PROJECT)
79 # TODO: Retain compatibility with libgmxapi 0.1 and back down the requirement.
80 find_package(gmxapi 0.2.0 REQUIRED
81 HINTS "$ENV{GROMACS_DIR}"
86 # GROMACS master branch and development branches may have divergent
87 # pre-release APIs. This check allows us to distinguish them and behave
88 # differently if needed. github.com/kassonlab/gromacs-gmxapi devel branch
89 # sets gmxapi_EXPERIMENTAL=TRUE. Upstream GROMACS master branch does not.
90 # Ref: https://github.com/kassonlab/gmxapi/issues/166
91 if(gmxapi_EXPERIMENTAL)
92 set(_suffix " (unofficial)")
94 message(STATUS "Found gmxapi version ${gmxapi_VERSION}${_suffix}")
97 # The Gromacs::gmxapi target could be imported from an existing installation or
98 # provided as an alias target within the GROMACS build tree.
99 if (NOT TARGET Gromacs::gmxapi)
100 message(FATAL_ERROR "Cannot build Python package without GROMACS gmxapi support.")
103 # TODO: Provide user hints for mpi4py installation.
104 # Note that neither the Python package nor the Gromacs::gmxapi CMake target are
105 # built with MPI in any case, but they _should_ be built with a C++ compiler
106 # that is compatible with the available MPI compiler wrappers, and technically
107 # _that_ is what we want to help the user identify when installing mpi4py, even
108 # if libgromacs is not built with MPI support either.
109 # For convenience, it is fine if libgmxapi and _gmxapi are built with the mpi
112 option(GMXAPI_USE_BUNDLED_PYBIND
113 "Use pybind11 headers bundled with this repository. If OFF, CMake does `find_package(pybind11)`."
115 if(GMXAPI_USE_BUNDLED_PYBIND)
116 add_subdirectory(external/pybind)
118 # Reference https://gitlab.com/gromacs/gromacs/-/issues/2896
119 find_package(pybind11 2.2 REQUIRED)
122 set(GMXAPI_PYTHON_EXTENSION_SOURCES
124 gmxapi/export_context.cpp
125 gmxapi/export_exceptions.cpp
126 gmxapi/export_system.cpp
127 gmxapi/export_tprfile.cpp
132 pybind11_add_module(_gmxapi
133 ${GMXAPI_PYTHON_EXTENSION_SOURCES}
136 target_include_directories(_gmxapi PRIVATE
137 ${CMAKE_CURRENT_SOURCE_DIR}/gmxapi
138 ${CMAKE_CURRENT_BINARY_DIR}/gmxapi
141 # RPATH management: make sure build artifacts can find GROMACS library.
142 set_target_properties(_gmxapi PROPERTIES SKIP_BUILD_RPATH FALSE)
144 # Python sources (*.py) will be packaged by scikit-build and setuptools.
145 # Note that library targets are built in CMAKE_LIBRARY_OUTPUT_DIRECTORY if not otherwise specified.
146 # This may be an unexpected location, whether inherited from the GROMACS build tree
147 # or the SKBUILD framework. Note, also, that when scikit-build is invoked with setup.py,
148 # the CMake build takes place in a subdirectory of ./_skbuild/.
149 set(GMXAPI_PYTHON_STAGING_DIR ${CMAKE_CURRENT_BINARY_DIR}/gmxapi_staging)
150 set_target_properties(_gmxapi PROPERTIES
151 LIBRARY_OUTPUT_DIRECTORY ${GMXAPI_PYTHON_STAGING_DIR}/gmxapi)
153 if(GMXAPI_MASTER_PROJECT)
154 # TODO: This requirement is probably overly restrictive.
155 find_package(GROMACS 2021 REQUIRED
156 NAMES gromacs gromacs_mpi
157 HINTS "$ENV{GROMACS_DIR}"
161 # Get details of GROMACS installation needed by the Python package at run time.
163 # Get the MPI capability.
164 get_target_property(_gmx_mpi Gromacs::gmxapi MPI)
165 if (${_gmx_mpi} STREQUAL "library")
166 set(_gmx_mpi_type "\"library\"")
167 elseif(${_gmx_mpi} STREQUAL "tmpi")
168 set(_gmx_mpi_type "\"tmpi\"")
169 elseif(${_gmx_mpi} STREQUAL "none")
170 set(_gmx_mpi_type "null")
172 message(FATAL_ERROR "Unrecognized gmxapi MPI value: ${_gmx_mpi}")
175 # Get the path of the command line entry point and binary install directory.
176 if (NOT TARGET Gromacs::gmx)
177 message(FATAL_ERROR "GROMACS command line tool not found.")
179 get_target_property(_gmx_executable_imported Gromacs::gmx IMPORTED)
180 if (_gmx_executable_imported)
181 get_target_property(_gmx_executable Gromacs::gmx LOCATION)
182 get_filename_component(_gmx_bindir ${_gmx_executable} DIRECTORY)
183 message(STATUS "Imported ${_gmx_bindir} executable.")
184 unset(_gmx_executable_imported)
186 get_target_property(_gmx_bindir Gromacs::gmx RUNTIME_OUTPUT_DIRECTORY)
187 get_target_property(_gmx_executable Gromacs::gmx OUTPUT_NAME)
188 set(_gmx_executable "${_gmx_bindir}/${_gmx_executable}")
189 message(STATUS "Using ${_gmx_executable} from build tree.")
191 if (NOT _gmx_bindir OR NOT _gmx_executable)
192 message(FATAL_ERROR "Could not get path for gmx wrapper binary.")
194 configure_file(gmxapi/gmxconfig.json.in ${GMXAPI_PYTHON_STAGING_DIR}/gmxapi/gmxconfig.json)
195 unset(_gmx_executable)
199 # scikit-build sets SKBUILD when running Python packaging tools through setup.py
202 # The Python module is being built for a GROMACS installation.
203 set_target_properties(_gmxapi PROPERTIES BUILD_WITH_INSTALL_RPATH TRUE)
204 set_target_properties(_gmxapi PROPERTIES INSTALL_RPATH_USE_LINK_PATH TRUE)
205 target_link_libraries(_gmxapi PRIVATE Gromacs::gmxapi)
206 # By default, scikit-build expects the library to be installed into a directory
207 # named for the Python package as in setup.py.
208 install(TARGETS _gmxapi LIBRARY DESTINATION gmxapi)
209 install(FILES ${GMXAPI_PYTHON_STAGING_DIR}/gmxapi/gmxconfig.json DESTINATION gmxapi)
211 # The Python module is being built against GROMACS in its build tree.
212 # Note: we do not have plans to install the staged package when SKBUILD != TRUE
213 set_target_properties(_gmxapi PROPERTIES BUILD_WITH_INSTALL_RPATH FALSE)
214 target_link_libraries(_gmxapi PRIVATE Gromacs::gmxapi)
216 # TODO: Determine packaging and installation cases and implementation.
217 # Reference https://gitlab.com/gromacs/gromacs/-/issues/2896 for additional discussion.
218 # Currently, CMake should be run by scikit-build through setup.py for proper Python packaging.
219 # We don't want to install by default in the outer scope of the GROMACS
220 # CMake procedure because we could end up trying to install to a system directory
221 # the user did not intend, or a user might install a Python-installation-specific
222 # package into an overly generic GROMACS path.
224 # Instead, we should probably build a source package and alert the user of its location.
225 # We can use CMake to call the Python packaging tools to create an 'sdist'
226 # source distribution archive to be installed in the GROMACS installation
227 # destination. We can use the build directory as the working directory for
228 # easier clean-up, as well.
229 # TODO: (ref Issue #2896) Build and install 'sdist' with GROMACS.
231 # However, we can still produce an importable package for documentation builds and
232 # basic testing in ${CMAKE_CURRENT_BINARY_DIR}/gmxapi_staging
233 file(GLOB_RECURSE _py_sources
235 ${CMAKE_CURRENT_SOURCE_DIR}/gmxapi/*.py)
236 foreach(_package_file IN LISTS _py_sources)
237 get_filename_component(_absolute_dir ${_package_file} DIRECTORY)
238 file(RELATIVE_PATH _relative_dir ${CMAKE_CURRENT_SOURCE_DIR} ${_absolute_dir})
239 file(COPY ${_package_file} DESTINATION ${GMXAPI_PYTHON_STAGING_DIR}/${_relative_dir})
241 file(COPY setup.py CMakeLists.txt DESTINATION ${GMXAPI_PYTHON_STAGING_DIR})
242 # Set CMake variable pybind11_DIR to ${CMAKE_CURRENT_SOURCE_DIR}/external/pybind/tools
243 # if re-invoking CMake (including via Python setuptools) for the files in gmxapi_staging.
245 # Unit test and build docs using PYTHONPATH=$CMAKE_CURRENT_BINARY_DIR/gmxapi_staging
246 set_target_properties(_gmxapi PROPERTIES staging_dir ${GMXAPI_PYTHON_STAGING_DIR})
247 # Note: Integration testing for multiple Python versions and/or CMake-driven
248 # sdist preparation could be performed with CMake custom_commands and custom_targets.
251 # When building as part of GROMACS umbrella project, add a testing target
252 # to the `check` target. Normal usage is to first install the Python package,
253 # then run `pytest` on the `tests` directory. Refer to gmxapi package documentation.
254 if(NOT GMXAPI_MASTER_PROJECT)
255 add_subdirectory(test)