2 # This file is part of the GROMACS molecular simulation package.
4 # Copyright (c) 2014,2015,2016,2017,2018, by the GROMACS development team, led by
5 # Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
6 # and including many others, as listed in the AUTHORS file in the
7 # top-level source directory and at http://www.gromacs.org.
9 # GROMACS is free software; you can redistribute it and/or
10 # modify it under the terms of the GNU Lesser General Public License
11 # as published by the Free Software Foundation; either version 2.1
12 # of the License, or (at your option) any later version.
14 # GROMACS is distributed in the hope that it will be useful,
15 # but WITHOUT ANY WARRANTY; without even the implied warranty of
16 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
17 # Lesser General Public License for more details.
19 # You should have received a copy of the GNU Lesser General Public
20 # License along with GROMACS; if not, see
21 # http://www.gnu.org/licenses, or write to the Free Software Foundation,
22 # Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
24 # If you want to redistribute modifications to GROMACS, please
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26 # control is crucial - bugs must be traceable. We will be happy to
27 # consider code for inclusion in the official distribution, but
28 # derived work must not be called official GROMACS. Details are found
29 # in the README & COPYING files - if they are missing, get the
30 # official version at http://www.gromacs.org.
32 # To help us fund GROMACS development, we humbly ask that you cite
33 # the research papers on the package. Check out http://www.gromacs.org.
35 # This directory provides a unified place for building all kinds of
36 # GROMACS documentation. This includes some "static" content (Doxygen
37 # code documentation, reference manual, install guide, old online HTML
38 # images), and content generated from the gmx program for the various
39 # tools (man and HTML pages). It also provides the "webpage" target,
40 # that combines all of the above (except man pages in man format) into
41 # a form suitable for automated deployment to the GROMACS website. It
42 # also provides the INSTALL file for the tarball.
44 # The webpage is mostly built by Sphinx. Variable values for Sphinx
45 # substitutions are configured by CMake (for things like version numbers),
46 # using gmx_configure_version_file(). This happens during build time instead
47 # of configure time, because 1) some of the version variables are only
48 # available during build time, and 2) we don't want to do all the Sphinx setup
49 # during configuration to save some time when not building the content.
50 # All the generated values get put into conf-vars.py (generated from
51 # conf-vars.py.cmakein), which in turn is included by the Sphinx configuration
54 set(SOURCE_MD5SUM "unknown" CACHE STRING
55 "MD5 sum of the source tarball, normally used only for the pre-release webpage build")
56 # REGRESSIONTEST_MD5SUM is set in cmake/gmxVersionInfo.cmake because it is used also in tests/CMakeLists.txt
57 mark_as_advanced(SOURCE_MD5SUM)
59 set(EXPECTED_DOXYGEN_VERSION 1.8.5)
61 set(EXPECTED_SPHINX_VERSION 1.4.1)
63 if (DEFINED PYTHON_EXECUTABLE)
64 # Keep quiet on subsequent runs of cmake
65 set(PythonInterp_FIND_QUIETLY ON)
67 find_package(PythonInterp 2.7)
68 find_package(Sphinx ${EXPECTED_SPHINX_VERSION} QUIET COMPONENTS pygments)
70 # Even if we aren't going to make the full webpage, set up to put all
71 # the documentation output in the same place, for convenience
72 set(HTML_OUTPUT_DIR "${CMAKE_CURRENT_BINARY_DIR}/html")
73 file(MAKE_DIRECTORY ${HTML_OUTPUT_DIR})
75 # The directory from which man pages will be installed; if it remains
76 # empty, they will be silently skipped.
78 if (SOURCE_IS_SOURCE_DISTRIBUTION)
79 # When building from the tarball, install the bundled man pages
80 # (unless overridden).
81 set(MAN_PAGE_DIR ${CMAKE_CURRENT_SOURCE_DIR})
84 add_subdirectory(doxygen)
85 add_subdirectory(manual)
88 # We need to have all the Sphinx input files in a single directory, and
89 # since some of them are generated, we copy everything into the build tree,
91 set(SPHINX_INPUT_DIR ${CMAKE_CURRENT_BINARY_DIR}/sphinx-input)
92 set(SPHINX_EXTENSION_PATH ${CMAKE_CURRENT_SOURCE_DIR})
93 if (SOURCE_MD5SUM STREQUAL "unknown")
94 # But for testing the webpage build (e.g. from the repo) we
95 # need a default value.
96 set(REGRESSIONTEST_MD5SUM_STRING "unknown")
98 # The real build of the webpage happens from the tarball, and
99 # this should be set to the matching MD5 sum.
100 set(REGRESSIONTEST_MD5SUM_STRING "${REGRESSIONTEST_MD5SUM}")
102 set(SPHINX_SOURCE_FILES
106 dev-manual/build-system.rst
107 dev-manual/commitstyle.rst
108 dev-manual/documentation-generation.rst
109 dev-manual/contribute.rst
110 dev-manual/doxygen.rst
111 dev-manual/error-handling.rst
112 dev-manual/formatting.rst
113 dev-manual/gmxtree.rst
114 dev-manual/includestyle.rst
115 dev-manual/jenkins.rst
116 dev-manual/language-features.rst
117 dev-manual/naming.rst
118 dev-manual/overview.rst
119 dev-manual/redmine-states.png
120 dev-manual/relocatable-binaries.rst
121 dev-manual/reportstyle.rst
123 dev-manual/testutils.rst
125 dev-manual/uncrustify.rst
126 fragments/doxygen-links.rst
127 install-guide/index.rst
128 release-notes/index.rst
129 release-notes/2018/2018.1.rst
130 release-notes/2018/major/highlights.rst
131 release-notes/2018/major/features.rst
132 release-notes/2018/major/performance.rst
133 release-notes/2018/major/tools.rst
134 release-notes/2018/major/bugs-fixed.rst
135 release-notes/2018/major/removed-features.rst
136 release-notes/2018/major/portability.rst
137 release-notes/2018/major/miscellaneous.rst
138 release-notes/2016/2016.5.rst
139 release-notes/2016/2016.4.rst
140 release-notes/2016/2016.3.rst
141 release-notes/2016/2016.2.rst
142 release-notes/2016/2016.1.rst
143 release-notes/2016/major/highlights.rst
144 release-notes/2016/major/new-features.rst
145 release-notes/2016/major/performance.rst
146 release-notes/2016/major/tools.rst
147 release-notes/2016/major/bugs-fixed.rst
148 release-notes/2016/major/removed-features.rst
149 release-notes/2016/major/miscellaneous.rst
150 release-notes/older/index.rst
152 user-guide/cutoff-schemes.rst
153 user-guide/getting-started.rst
154 user-guide/force-fields.rst
157 user-guide/floating-point.rst
158 user-guide/system-preparation.rst
159 user-guide/managing-simulations.rst
160 user-guide/mdrun-features.rst
161 user-guide/mdrun-performance.rst
162 user-guide/mdp-options.rst
163 user-guide/run-time-errors.rst
164 user-guide/file-formats.rst
165 user-guide/cmdline.rst
166 user-guide/environment-variables.rst
167 user-guide/terminology.rst
168 user-guide/plotje.gif
174 include(SphinxMacros.cmake)
175 gmx_init_sphinx_setup(${SPHINX_INPUT_DIR})
177 set(SPHINX_CONFIG_VARS_FILE ${SPHINX_INPUT_DIR}/conf-vars.py)
178 gmx_configure_version_file(conf-vars.py.cmakein ${SPHINX_CONFIG_VARS_FILE}
180 SPHINX_EXTENSION_PATH RELENG_PATH
181 EXPECTED_DOXYGEN_VERSION
182 EXPECTED_SPHINX_VERSION
183 CMAKE_MINIMUM_REQUIRED_VERSION REQUIRED_CUDA_VERSION
184 REQUIRED_OPENCL_MIN_VERSION
185 REQUIRED_CUDA_COMPUTE_CAPABILITY REGRESSIONTEST_VERSION
186 SOURCE_MD5SUM REGRESSIONTEST_MD5SUM_STRING
187 GMX_TNG_MINIMUM_REQUIRED_VERSION
188 GMX_LMFIT_MINIMUM_REQUIRED_VERSION
189 COMMENT "Configuring Sphinx configuration file")
190 gmx_add_sphinx_input_file(${SPHINX_CONFIG_VARS_FILE})
191 gmx_add_sphinx_source_files(FILES ${SPHINX_SOURCE_FILES})
192 if (EXISTS ${RELENG_PATH}/docs/FileList.cmake)
193 include(${RELENG_PATH}/docs/FileList.cmake)
194 gmx_add_sphinx_source_files(
195 FROM ${RELENG_PATH}/docs TO dev-manual/releng PREFIX releng/docs/
196 FILES ${RELENG_SPHINX_FILES})
198 gmx_add_sphinx_source_files(FILES
199 dev-manual/releng/index.rst
200 dev-manual/releng/jenkins-howto.rst
201 dev-manual/releng/jenkins-ui.rst
204 gmx_add_sphinx_input_target(sphinx-input)
205 # Remove other rst files from the build tree, since they confuse Sphinx.
206 # Skip generated files in onlinehelp/, and fragments.
207 # The latter do not cause issues with obsolete files, as they
208 # are not considered as Sphinx input files, but will only be
209 # included using an explicit .. include::.
210 gmx_remove_obsolete_sphinx_input_files("^(onlinehelp|fragments)/.*\\\\.rst$")
212 # TODO: Make this remove obsolete .rst files.
213 # TODO: This does not work in cross-compilation scenarios; disable up to
214 # the necessary level.
215 gmx_add_custom_output_target(sphinx-programs OUTPUT STAMP
216 COMMAND ${CMAKE_COMMAND} -E make_directory onlinehelp
217 COMMAND gmx -quiet help -export rst
219 WORKING_DIRECTORY ${SPHINX_INPUT_DIR}
220 COMMENT "Generating reStructuredText help")
221 # This dependency ensures that the directories exist before the
222 # executable tries to write things there.
223 add_dependencies(sphinx-programs sphinx-input)
225 # Make the INSTALL file for CPack for the tarball. This gets put
226 # into the tarball via the CPack rules below, which requires that
227 # the INSTALL file is in a separate directory by itself.
228 set(TEXT_INSTALL_GUIDE_OUTPUT_DIR "install-guide/text")
229 add_custom_target(install-guide
233 -w sphinx-install.log
234 -d ${CMAKE_CURRENT_BINARY_DIR}/install-guide/_doctrees
235 -c ${SPHINX_INPUT_DIR}
236 "${SPHINX_INPUT_DIR}/install-guide"
237 "${TEXT_INSTALL_GUIDE_OUTPUT_DIR}"
239 ${CMAKE_COMMAND} -E rename
240 ${TEXT_INSTALL_GUIDE_OUTPUT_DIR}/index.txt
241 ${TEXT_INSTALL_GUIDE_OUTPUT_DIR}/INSTALL
243 ${CMAKE_CURRENT_BINARY_DIR}
244 COMMENT "Building INSTALL with Sphinx"
247 add_dependencies(install-guide sphinx-input)
248 gmx_cpack_add_generated_source_directory(install-guide/text DESTINATION /)
250 # Sphinx cache with pickled ReST documents
251 set(SPHINX_CACHE_DIR "${CMAKE_CURRENT_BINARY_DIR}/_doctrees")
253 add_custom_target(webpage-sphinx
255 ${CMAKE_COMMAND} -E make_directory ${SPHINX_INPUT_DIR}/_static
260 -d "${SPHINX_CACHE_DIR}"
261 "${SPHINX_INPUT_DIR}"
264 ${CMAKE_CURRENT_BINARY_DIR}
265 COMMENT "Building HTML documentation with Sphinx"
268 add_dependencies(webpage-sphinx sphinx-input sphinx-programs)
270 add_custom_target(man
275 -d ${SPHINX_CACHE_DIR}
278 ${CMAKE_CURRENT_BINARY_DIR}/man
279 COMMENT "Building man pages with Sphinx"
281 add_dependencies(man sphinx-input sphinx-programs)
283 # If requested, install the man pages built by the 'man' target
284 # created above. Nothing will be installed if the user did not
285 # manually build the target.
286 set(MAN_PAGE_DIR ${CMAKE_CURRENT_BINARY_DIR})
289 add_custom_target(webpage-sphinx
290 COMMAND ${CMAKE_COMMAND} -E echo
291 "HTML pages cannot be built because Sphinx version ${EXPECTED_SPHINX_VERSION} is not available"
293 add_custom_target(install-guide
294 COMMAND ${CMAKE_COMMAND} -E echo
295 "INSTALL cannot be built because Sphinx version ${EXPECTED_SPHINX_VERSION} is not available"
297 add_custom_target(man
298 COMMAND ${CMAKE_COMMAND} -E echo
299 "man pages cannot be built because Sphinx version ${EXPECTED_SPHINX_VERSION} is not available"
304 set(MAN_PAGE_DIR ${MAN_PAGE_DIR}/man)
305 # Trailing slash on directory is significant for
306 # install(DIRECTORY). See CMake docs.
307 install(DIRECTORY ${MAN_PAGE_DIR}/
308 DESTINATION ${MAN_INSTALL_DIR}/man1
309 COMPONENT man OPTIONAL
310 FILES_MATCHING PATTERN "*.1")
312 gmx_cpack_add_generated_source_directory(man)
314 # Determine whether we can build all the HTML pages and content linked from
315 # there. If not, construct an informative message if the user tries to
316 # build the target; most people never need to know, unless they've asked for
318 set(HTML_BUILD_IS_POSSIBLE ON)
319 set(HTML_BUILD_NOT_POSSIBLE_REASON)
320 set(HTML_BUILD_WARNINGS)
322 # Next, turn it off if any of the preconditions are unsatisified
323 if (NOT PYTHON_EXECUTABLE)
324 set(HTML_BUILD_IS_POSSIBLE OFF)
325 set(HTML_BUILD_NOT_POSSIBLE_REASON "Python is required")
326 elseif (NOT SPHINX_FOUND)
327 # Hardly anything gets built if Sphinx is not available, so don't bother.
328 set(HTML_BUILD_IS_POSSIBLE OFF)
329 set(HTML_BUILD_NOT_POSSIBLE_REASON "Sphinx version ${EXPECTED_SPHINX_VERSION} is required")
331 if (NOT MANUAL_BUILD_IS_POSSIBLE)
332 list(APPEND HTML_BUILD_WARNINGS
333 "Reference PDF manual was not built, so links to it do not work")
335 if (NOT DOXYGEN_EXECUTABLE)
336 list(APPEND HTML_BUILD_WARNINGS
337 "Doxygen was not available, so links to Doxygen do not work")
339 if (NOT DOXYGEN_DOT_EXECUTABLE)
340 list(APPEND HTML_BUILD_WARNINGS
341 "dot/graphviz was not found, so some graphs are missing")
344 if (HTML_BUILD_IS_POSSIBLE)
345 set(_webpage_target_properties)
346 if (HTML_BUILD_WARNINGS)
347 list(APPEND _webpage_target_properties
348 COMMAND ${CMAKE_COMMAND} -E echo
349 "webpage was built, but with the following limitations:")
350 foreach(_warning ${HTML_BUILD_WARNINGS})
351 list(APPEND _webpage_target_properties
352 COMMAND ${CMAKE_COMMAND} -E echo " - ${_warning}")
356 if (MANUAL_BUILD_IS_POSSIBLE)
357 # Make the PDF reference guide
358 # TODO Try to make the PDF arrive directly in ${HTML_OUTPUT_DIR}
359 # TODO Make this depend on the output of the manual build, so that the
360 # file actually gets copied multiple times.
361 set(_manual_target_location ${HTML_OUTPUT_DIR}/manual-${GMX_VERSION_STRING}.pdf)
363 OUTPUT ${_manual_target_location}
364 COMMAND ${CMAKE_COMMAND}
365 -E remove -f ${_manual_target_location}
366 COMMAND ${CMAKE_COMMAND}
367 -E copy ${CMAKE_CURRENT_BINARY_DIR}/manual/gromacs.pdf ${_manual_target_location}
370 list(APPEND _webpage_target_properties
371 DEPENDS ${_manual_target_location})
374 # The Doxygen configuration in doxygen/Doxyfile-common.cmakein
375 # makes all the Doxygen output directly in
376 # ${HTML_OUTPUT_DIR}/doxygen (and makes the directory if it needs
379 # Add a top-level target that builds everything related to the webpage,
380 # for Jenkins (and possibly others) to use
381 add_custom_target(webpage ${_webpage_target_properties}
382 COMMENT "Building webpage"
384 add_dependencies(webpage webpage-sphinx doxygen-all)
386 add_custom_target(webpage
387 COMMAND ${CMAKE_COMMAND} -E echo
388 "Cannot build webpage because ${HTML_BUILD_NOT_POSSIBLE_REASON}"
389 COMMENT "Webpage build not possible"