2 # This file is part of the GROMACS molecular simulation package.
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5 # Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
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33 # the research papers on the package. Check out http://www.gromacs.org.
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://redmine.gromacs.org/issues/2896 for additional discussion.
41 cmake_minimum_required(VERSION 3.9.6)
43 # This needs to be set before project() in order to pick up toolchain files
44 #list(APPEND CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/../../cmake)
46 # OS X deployment target should be >=10.9 for modern C++ compatibility.
47 # Reference https://scikit-build.readthedocs.io/en/latest/generators.html#macosx
48 # and https://github.com/MacPython/wiki/wiki/Spinning-wheels
49 set(CMAKE_OSX_DEPLOYMENT_TARGET 10.9 CACHE STRING
50 "OS X deployment target below 10.9 does not use modern standard library"
52 set(CMAKE_OSX_ARCHITECTURES x86_64 CACHE STRING
53 "OS X should build Python package for 64-bit architecture"
56 project(gmxapi VERSION 0.1.0)
58 # Check if Python package is being built directly or via add_subdirectory
59 set(GMXAPI_MASTER_PROJECT OFF)
60 if (CMAKE_CURRENT_SOURCE_DIR STREQUAL CMAKE_SOURCE_DIR)
61 set(GMXAPI_MASTER_PROJECT ON)
64 set(CMAKE_CXX_STANDARD 14)
65 set(CMAKE_CXX_STANDARD_REQUIRED ON)
67 # Only interpret if() arguments as variables or keywords when unquoted.
68 cmake_policy(SET CMP0054 NEW)
69 # honor the language standard settings for try_compile()
70 cmake_policy(SET CMP0067 NEW)
71 if(POLICY CMP0074) #3.12
72 # Allow gmxapi_ROOT hint.
73 cmake_policy(SET CMP0074 NEW)
76 if(GMXAPI_MASTER_PROJECT)
77 find_package(gmxapi 0.0.8 REQUIRED
78 HINTS "$ENV{GROMACS_DIR}"
83 # GROMACS master branch and development branches may have divergent
84 # pre-release APIs. This check allows us to distinguish them and behave
85 # differently if needed. github.com/kassonlab/gromacs-gmxapi devel branch
86 # sets gmxapi_EXPERIMENTAL=TRUE. Upstream GROMACS master branch does not.
87 # Ref: https://github.com/kassonlab/gmxapi/issues/166
88 if(gmxapi_EXPERIMENTAL)
89 set(_suffix " (unofficial)")
91 message(STATUS "Found gmxapi version ${gmxapi_VERSION}${_suffix}")
94 # TODO: Provide user hints for mpi4py installation.
95 # Note that neither the Python package nor the Gromacs::gmxapi CMake target are
96 # built with MPI in any case, but they _should_ be built with a C++ compiler
97 # that is compatible with the available MPI compiler wrappers, and technically
98 # _that_ is what we want to help the user identify when installing mpi4py, even
99 # if libgromacs is not built with MPI support either.
100 # For convenience, it is fine if libgmxapi and _gmxapi are built with the mpi
103 option(GMXAPI_USE_BUNDLED_PYBIND
104 "Use pybind11 headers bundled with this repository. If OFF, CMake does `find_package(pybind11)`."
106 if(GMXAPI_USE_BUNDLED_PYBIND)
107 add_subdirectory(external/pybind)
109 # Reference https://redmine.gromacs.org/issues/2896
110 find_package(pybind11 2.2 REQUIRED)
113 set(GMXAPI_PYTHON_EXTENSION_SOURCES
115 gmxapi/export_context.cpp
116 gmxapi/export_exceptions.cpp
117 gmxapi/export_system.cpp
118 gmxapi/export_tprfile.cpp
123 pybind11_add_module(_gmxapi
124 ${GMXAPI_PYTHON_EXTENSION_SOURCES}
127 target_include_directories(_gmxapi PRIVATE
128 ${CMAKE_CURRENT_SOURCE_DIR}/gmxapi
129 ${CMAKE_CURRENT_BINARY_DIR}/gmxapi
132 # RPATH management: make sure build artifacts can find GROMACS library.
133 set_target_properties(_gmxapi PROPERTIES SKIP_BUILD_RPATH FALSE)
135 # Python sources (*.py) will be packaged by scikit-build and setuptools.
136 # Note that library targets are built in CMAKE_LIBRARY_OUTPUT_DIRECTORY if not otherwise specified.
137 # This may be an unexpected location, whether inherited from the GROMACS build tree
138 # or the SKBUILD framework. Note, also, that when scikit-build is invoked with setup.py,
139 # the CMake build takes place in a subdirectory of ./_skbuild/.
140 set(GMXAPI_PYTHON_STAGING_DIR ${CMAKE_CURRENT_BINARY_DIR}/gmxapi_staging)
141 set_target_properties(_gmxapi PROPERTIES
142 LIBRARY_OUTPUT_DIRECTORY ${GMXAPI_PYTHON_STAGING_DIR}/gmxapi)
144 # scikit-build sets SKBUILD when running Python packaging tools through setup.py
147 # The Python module is being built for a GROMACS installation.
148 set_target_properties(_gmxapi PROPERTIES BUILD_WITH_INSTALL_RPATH TRUE)
149 set_target_properties(_gmxapi PROPERTIES INSTALL_RPATH_USE_LINK_PATH TRUE)
150 target_link_libraries(_gmxapi PRIVATE Gromacs::gmxapi)
151 # By default, scikit-build expects the library to be installed into a directory
152 # named for the Python package as in setup.py.
153 install(TARGETS _gmxapi LIBRARY DESTINATION gmxapi)
155 # The Python module is being built against GROMACS in its build tree.
156 # Note: we do not have plans to install the staged package when SKBUILD != TRUE
157 set_target_properties(_gmxapi PROPERTIES BUILD_WITH_INSTALL_RPATH FALSE)
158 target_link_libraries(_gmxapi PRIVATE Gromacs::gmxapi)
160 # TODO: Determine packaging and installation cases and implementation.
161 # Reference https://redmine.gromacs.org/issues/2896 for additional discussion.
162 # Currently, CMake should be run by scikit-build through setup.py for proper Python packaging.
163 # We don't want to install by default in the outer scope of the GROMACS
164 # CMake procedure because we could end up trying to install to a system directory
165 # the user did not intend, or a user might install a Python-installation-specific
166 # package into an overly generic GROMACS path.
168 # Instead, we should probably build a source package and alert the user of its location.
169 # We can use CMake to call the Python packaging tools to create an 'sdist'
170 # source distribution archive to be installed in the GROMACS installation
171 # destination. We can use the build directory as the working directory for
172 # easier clean-up, as well.
173 # TODO: (ref issue #2896) Build and install 'sdist' with GROMACS.
175 # However, we can still produce an importable package for documentation builds and
176 # basic testing in ${CMAKE_CURRENT_BINARY_DIR}/gmxapi_staging
177 if(CMAKE_VERSION VERSION_LESS 3.12)
178 file(GLOB_RECURSE _py_sources
179 ${CMAKE_CURRENT_SOURCE_DIR}/gmxapi/*.py)
181 # CONFIGURE_DEPENDS appears in CMake 3.12 and can help to more robustly detect
182 # the need to update anything depending on the staged package.
183 file(GLOB_RECURSE _py_sources
185 ${CMAKE_CURRENT_SOURCE_DIR}/gmxapi/*.py)
187 foreach(_package_file IN LISTS _py_sources)
188 get_filename_component(_absolute_dir ${_package_file} DIRECTORY)
189 file(RELATIVE_PATH _relative_dir ${CMAKE_CURRENT_SOURCE_DIR} ${_absolute_dir})
190 file(COPY ${_package_file} DESTINATION gmxapi_staging/${_relative_dir})
192 file(COPY setup.py CMakeLists.txt DESTINATION ${GMXAPI_PYTHON_STAGING_DIR})
193 # Set CMake variable pybind11_DIR to ${CMAKE_CURRENT_SOURCE_DIR}/external/pybind/tools
194 # if re-invoking CMake (including via Python setuptools) for the files in gmxapi_staging.
196 # Unit test and build docs using PYTHONPATH=$CMAKE_CURRENT_BINARY_DIR/gmxapi_staging
197 set_target_properties(_gmxapi PROPERTIES staging_dir ${GMXAPI_PYTHON_STAGING_DIR})
198 # Note: Integration testing for multiple Python versions and/or CMake-driven
199 # sdist preparation could be performed with CMake custom_commands and custom_targets.
202 # When building as part of GROMACS umbrella project, add a testing target
203 # to the `check` target. Normal usage is to first install the Python package,
204 # then run `pytest` on the `tests` directory. Refer to gmxapi package documentation.
205 if(NOT GMXAPI_MASTER_PROJECT)
206 add_subdirectory(test)