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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 ${CMAKE_CURRENT_SOURCE_DIR}/../../cmake)
46 # OS X deployment target should be >=10.9 for modern C++ compatibility.
47 # Reference https://scikit-build.readthedocs.io/en/latest/generators.html#macosx
48 # and https://github.com/MacPython/wiki/wiki/Spinning-wheels
49 set(CMAKE_OSX_DEPLOYMENT_TARGET 10.9 CACHE STRING
50 "OS X deployment target below 10.9 does not use modern standard library"
52 set(CMAKE_OSX_ARCHITECTURES x86_64 CACHE STRING
53 "OS X should build Python package for 64-bit architecture"
56 project(gmxapi VERSION 0.1.0)
58 # Check if Python package is being built directly or via add_subdirectory
59 set(GMXAPI_MASTER_PROJECT OFF)
60 if (CMAKE_CURRENT_SOURCE_DIR STREQUAL CMAKE_SOURCE_DIR)
61 set(GMXAPI_MASTER_PROJECT ON)
64 set(CMAKE_CXX_STANDARD 14)
65 set(CMAKE_CXX_STANDARD_REQUIRED ON)
67 # Only interpret if() arguments as variables or keywords when unquoted.
68 cmake_policy(SET CMP0054 NEW)
69 # honor the language standard settings for try_compile()
70 cmake_policy(SET CMP0067 NEW)
72 if(GMXAPI_MASTER_PROJECT)
73 find_package(gmxapi 0.0.8 REQUIRED
74 HINTS "$ENV{GROMACS_DIR}"
79 # GROMACS master branch and development branches may have divergent
80 # pre-release APIs. This check allows us to distinguish them and behave
81 # differently if needed. github.com/kassonlab/gromacs-gmxapi devel branch
82 # sets gmxapi_EXPERIMENTAL=TRUE. Upstream GROMACS master branch does not.
83 # Ref: https://github.com/kassonlab/gmxapi/issues/166
84 if(gmxapi_EXPERIMENTAL)
85 set(_suffix " (unofficial)")
87 message(STATUS "Found gmxapi version ${gmxapi_VERSION}${_suffix}")
90 option(GMXAPI_USE_BUNDLED_PYBIND
91 "Use pybind11 headers bundled with this repository. If OFF, CMake does `find_package(pybind11)`."
93 if(GMXAPI_USE_BUNDLED_PYBIND)
94 add_subdirectory(external/pybind)
96 # Reference https://redmine.gromacs.org/issues/2896
97 find_package(pybind11 2.2 REQUIRED)
100 set(GMXAPI_PYTHON_EXTENSION_SOURCES
102 gmxapi/export_context.cpp
103 gmxapi/export_exceptions.cpp
104 gmxapi/export_system.cpp
105 gmxapi/export_tprfile.cpp
110 pybind11_add_module(_gmxapi
111 ${GMXAPI_PYTHON_EXTENSION_SOURCES}
114 target_include_directories(_gmxapi PRIVATE
115 ${CMAKE_CURRENT_SOURCE_DIR}/gmxapi
116 ${CMAKE_CURRENT_BINARY_DIR}/gmxapi
119 # RPATH management: make sure build artifacts can find GROMACS library.
120 set_target_properties(_gmxapi PROPERTIES SKIP_BUILD_RPATH FALSE)
122 # Python sources (*.py) will be packaged by scikit-build and setuptools.
123 # Note that library targets are built in CMAKE_LIBRARY_OUTPUT_DIRECTORY if not otherwise specified.
124 # This may be an unexpected location, whether inherited from the GROMACS build tree
125 # or the SKBUILD framework. Note, also, that when scikit-build is invoked with setup.py,
126 # the CMake build takes place in a subdirectory of ./_skbuild/.
127 set(GMXAPI_PYTHON_STAGING_DIR ${CMAKE_CURRENT_BINARY_DIR}/gmxapi_staging)
128 set_target_properties(_gmxapi PROPERTIES
129 LIBRARY_OUTPUT_DIRECTORY ${GMXAPI_PYTHON_STAGING_DIR}/gmxapi)
131 # scikit-build sets SKBUILD when running Python packaging tools through setup.py
134 # The Python module is being built for a GROMACS installation.
135 set_target_properties(_gmxapi PROPERTIES BUILD_WITH_INSTALL_RPATH TRUE)
136 set_target_properties(_gmxapi PROPERTIES INSTALL_RPATH_USE_LINK_PATH TRUE)
137 target_link_libraries(_gmxapi PRIVATE Gromacs::gmxapi)
138 # By default, scikit-build expects the library to be installed into a directory
139 # named for the Python package as in setup.py.
140 install(TARGETS _gmxapi LIBRARY DESTINATION gmxapi)
142 # The Python module is being built against GROMACS in its build tree.
143 # Note: we do not have plans to install the staged package when SKBUILD != TRUE
144 set_target_properties(_gmxapi PROPERTIES BUILD_WITH_INSTALL_RPATH FALSE)
145 target_link_libraries(_gmxapi PRIVATE Gromacs::gmxapi)
147 # TODO: Determine packaging and installation cases and implementation.
148 # Reference https://redmine.gromacs.org/issues/2896 for additional discussion.
149 # Currently, CMake should be run by scikit-build through setup.py for proper Python packaging.
150 # We don't want to install by default in the outer scope of the GROMACS
151 # CMake procedure because we could end up trying to install to a system directory
152 # the user did not intend, or a user might install a Python-installation-specific
153 # package into an overly generic GROMACS path.
155 # Instead, we should probably build a source package and alert the user of its location.
156 # We can use CMake to call the Python packaging tools to create an 'sdist'
157 # source distribution archive to be installed in the GROMACS installation
158 # destination. We can use the build directory as the working directory for
159 # easier clean-up, as well.
160 # TODO: (ref issue #2896) Build and install 'sdist' with GROMACS.
162 # However, we can still produce an importable package for documentation builds and
163 # basic testing in ${CMAKE_CURRENT_BINARY_DIR}/gmxapi_staging
164 if(CMAKE_VERSION VERSION_LESS 3.12)
165 file(GLOB_RECURSE _py_sources
166 ${CMAKE_CURRENT_SOURCE_DIR}/gmxapi/*.py)
168 # CONFIGURE_DEPENDS appears in CMake 3.12 and can help to more robustly detect
169 # the need to update anything depending on the staged package.
170 file(GLOB_RECURSE _py_sources
172 ${CMAKE_CURRENT_SOURCE_DIR}/gmxapi/*.py)
174 foreach(_package_file IN LISTS _py_sources)
175 get_filename_component(_absolute_dir ${_package_file} DIRECTORY)
176 file(RELATIVE_PATH _relative_dir ${CMAKE_CURRENT_SOURCE_DIR} ${_absolute_dir})
177 file(COPY ${_package_file} DESTINATION gmxapi_staging/${_relative_dir})
179 file(COPY setup.py CMakeLists.txt DESTINATION gmxapi_staging)
180 # Set CMake variable pybind11_DIR to ${CMAKE_CURRENT_SOURCE_DIR}/external/pybind/tools
181 # if re-invoking CMake (including via Python setuptools) for the files in gmxapi_staging.
183 # Unit test and build docs using PYTHONPATH=$CMAKE_CURRENT_BINARY_DIR/gmxapi_staging/gmxapi
185 # Note: Integration testing for multiple Python versions and/or CMake-driven
186 # sdist preparation could be performed with CMake custom_commands and custom_targets.
189 # When building as part of GROMACS umbrella project, add a testing target
190 # to the `check` target. Normal usage is to first install the Python package,
191 # then run `pytest` on the `tests` directory. Refer to gmxapi package documentation.
192 if(NOT GMXAPI_MASTER_PROJECT)
193 add_subdirectory(test)