2 # This file is part of the GROMACS molecular simulation package.
4 # Copyright (c) 2014,2015,2016,2017,2018,2019, 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
25 # consider that scientific software is very special. Version
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 1.6.1)
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)
70 if (NOT ${PYTHON_VERSION_MAJOR} EQUAL 3)
71 find_package(Sphinx ${EXPECTED_SPHINX_VERSION} QUIET COMPONENTS pygments)
73 MESSAGE(STATUS "Can not build documentation with Python 3")
76 # Even if we aren't going to make the full webpage, set up to put all
77 # the documentation output in the same place, for convenience
78 set(HTML_OUTPUT_DIR "${CMAKE_CURRENT_BINARY_DIR}/html")
79 file(MAKE_DIRECTORY ${HTML_OUTPUT_DIR})
81 # Prepare directories for pdf/tex output
82 set(TEX_OUTPUT_DIR "${CMAKE_CURRENT_BINARY_DIR}/manual")
83 set(SPHINX_LATEX_FILE "${TEX_OUTPUT_DIR}/gromacs.tex")
84 file(MAKE_DIRECTORY ${TEX_OUTPUT_DIR})
86 # The directory from which man pages will be installed; if it remains
87 # empty, they will be silently skipped.
89 if (SOURCE_IS_SOURCE_DISTRIBUTION)
90 # When building from the tarball, install the bundled man pages
91 # (unless overridden).
92 set(MAN_PAGE_DIR ${CMAKE_CURRENT_SOURCE_DIR})
95 add_subdirectory(doxygen)
97 # TODO: Consider whether this could just be replaced by using
98 # GMX_DEVELOPER_BUILD to control this as well.
99 option(GMX_BUILD_MANUAL "Whether to try to configure to build the PDF manual" OFF)
100 mark_as_advanced(GMX_BUILD_MANUAL)
102 set(MANUAL_BUILD_IS_POSSIBLE ON)
103 set(MANUAL_BUILD_NOT_POSSIBLE_REASON)
104 set(NO_IMAGE_CONVERT_REASON)
105 if (NOT GMX_BUILD_MANUAL)
106 # Make sure we only do detection of manual-building dependencies
107 # when the user opted in for that.
108 set(MANUAL_BUILD_IS_POSSIBLE OFF)
109 set(MANUAL_BUILD_NOT_POSSIBLE_REASON "GMX_BUILD_MANUAL is not ON")
110 elseif (BUILD_IS_INSOURCE)
111 # UseLATEX.cmake does not work with an in-source build
112 set(MANUAL_BUILD_IS_POSSIBLE OFF)
113 set(MANUAL_BUILD_NOT_POSSIBLE_REASON "the build is in-source")
115 include(manual/UseLATEX.cmake)
116 if(${PYTHON_VERSION_MAJOR} EQUAL 3)
117 set(MANUAL_BUILD_IS_POSSIBLE OFF)
118 set(MANUAL_BUILD_NOT_POSSIBLE_REASON "We can not build the documentation when using python3")
119 elseif(NOT SPHINX_FOUND)
120 set(MANUAL_BUILD_IS_POSSIBLE OFF)
121 set(MANUAL_BUILD_NOT_POSSIBLE_REASON "Sphinx has not been found and is needed to create the LaTex input files")
122 elseif(NOT PDFLATEX_COMPILER)
123 set(MANUAL_BUILD_IS_POSSIBLE OFF)
124 set(MANUAL_BUILD_NOT_POSSIBLE_REASON "pdflatex is not available")
125 elseif(NOT IMAGE_CONVERT_POSSIBLE)
126 set(MANUAL_BUILD_IS_POSSIBLE OFF)
127 set(MANUAL_BUILD_NOT_POSSIBLE_REASON "a working form of ImageMagick convert is not available")
128 set(NO_IMAGE_CONVERT_REASON "Can not convert files for online or pdf manual")
129 # TODO Later, identify other dependencies like bibtex,
130 # make_index, date, some graphics conversion program,
131 # etc. Perhaps patch UseLATEX.cmake and contribute upstream.
137 # We need to have all the Sphinx input files in a single directory, and
138 # since some of them are generated, we copy everything into the build tree,
140 set(SPHINX_INPUT_DIR ${CMAKE_CURRENT_BINARY_DIR}/sphinx-input)
141 set(SPHINX_EXTENSION_PATH ${CMAKE_CURRENT_SOURCE_DIR})
142 # As the manual build now depends also on Sphinx, the inclusion path needs
143 # to be set after we know the basic information for Sphinx.
144 add_subdirectory(manual)
145 if (SOURCE_MD5SUM STREQUAL "unknown")
146 # But for testing the webpage build (e.g. from the repo) we
147 # need a default value.
148 set(REGRESSIONTEST_MD5SUM_STRING "unknown")
150 # The real build of the webpage happens from the tarball, and
151 # this should be set to the matching MD5 sum.
152 set(REGRESSIONTEST_MD5SUM_STRING "${REGRESSIONTEST_MD5SUM}")
154 # The reference manual still contains the individual sections from the
155 # LaTeX document, with the files below grouped and annotated by chapter.
156 set(REFERENCEMANUAL_SPHINX_FILES_GENERAL
157 # Main index file, preface and introduction.
158 reference-manual/index.rst
159 reference-manual/preface.rst
160 reference-manual/introduction.rst
161 # Definitions and Units chapter
162 reference-manual/definitions.rst
164 reference-manual/topologies.rst
165 reference-manual/topologies/particle-type.rst
166 reference-manual/topologies/parameter-files.rst
167 reference-manual/topologies/molecule-definition.rst
168 reference-manual/topologies/constraint-algorithm-section.rst
169 reference-manual/topologies/pdb2gmx-input-files.rst
170 reference-manual/topologies/topology-file-formats.rst
171 reference-manual/topologies/force-field-organization.rst
172 # File formats chapter
173 reference-manual/file-formats.rst
174 # Run parameters and programs chapter
175 reference-manual/run-parameters.rst
176 # Implementation details chapter
177 reference-manual/details.rst
178 # Averages and fluctations chapter
179 reference-manual/averages.rst
181 reference-manual/references.rst
182 # PNG formated plot files that don't need to be converted into PNG
184 reference-manual/plots/peregrine.png
185 reference-manual/plots/adress.png
186 reference-manual/plots/plotje.png
187 reference-manual/plots/xvgr.png
189 set(REFERENCEMANUAL_SPHINX_FILES_WITH_IMAGES
191 reference-manual/algorithms.rst
192 reference-manual/algorithms/periodic-boundary-conditions.rst
193 reference-manual/algorithms/group-concept.rst
194 reference-manual/algorithms/molecular-dynamics.rst
195 reference-manual/algorithms/shell-molecular-dynamics.rst
196 reference-manual/algorithms/constraint-algorithms.rst
197 reference-manual/algorithms/simulated-annealing.rst
198 reference-manual/algorithms/stochastic-dynamics.rst
199 reference-manual/algorithms/brownian-dynamics.rst
200 reference-manual/algorithms/energy-minimization.rst
201 reference-manual/algorithms/normal-mode-analysis.rst
202 reference-manual/algorithms/free-energy-calculations.rst
203 reference-manual/algorithms/replica-exchange.rst
204 reference-manual/algorithms/essential-dynamics.rst
205 reference-manual/algorithms/expanded-ensemble.rst
206 reference-manual/algorithms/parallelization-domain-decomp.rst
207 # Interaction functions and force fields chapter
208 reference-manual/functions.rst
209 reference-manual/functions/bonded-interactions.rst
210 reference-manual/functions/force-field.rst
211 reference-manual/functions/free-energy-interactions.rst
212 reference-manual/functions/interaction-methods.rst
213 reference-manual/functions/long-range-electrostatics.rst
214 reference-manual/functions/long-range-vdw.rst
215 reference-manual/functions/nonbonded-interactions.rst
216 reference-manual/functions/polarization.rst
217 reference-manual/functions/restraints.rst
218 # Special topics chapter
219 reference-manual/special.rst
220 reference-manual/special/free-energy-implementation.rst
221 reference-manual/special/pulling.rst
222 reference-manual/special/awh.rst
223 reference-manual/special/enforced-rotation.rst
224 reference-manual/special/electric-fields.rst
225 reference-manual/special/comp-electrophys.rst
226 reference-manual/special/free-energy-pmf.rst
227 reference-manual/special/remove-fast-dgf.rst
228 reference-manual/special/viscosity-calculation.rst
229 reference-manual/special/tabulated-interaction-functions.rst
230 reference-manual/special/qmmm.rst
231 reference-manual/special/vmd-imd.rst
232 reference-manual/special/membrane-embedding.rst
233 reference-manual/special/mimic-qmmm.rst
235 reference-manual/analysis.rst
236 reference-manual/analysis/using-groups.rst
237 reference-manual/analysis/looking-at-trajectory.rst
238 reference-manual/analysis/general-properties.rst
239 reference-manual/analysis/radial-distribution-function.rst
240 reference-manual/analysis/correlation-function.rst
241 reference-manual/analysis/curve-fitting.rst
242 reference-manual/analysis/mean-square-displacement.rst
243 reference-manual/analysis/bond-angle-dihedral.rst
244 reference-manual/analysis/radius-of-gyration.rst
245 reference-manual/analysis/rmsd.rst
246 reference-manual/analysis/covariance-analysis.rst
247 reference-manual/analysis/dihedral-pca.rst
248 reference-manual/analysis/protein-related.rst
249 reference-manual/analysis/interface-related.rst)
250 # The image files have also been ordered by the respective
251 # chapter they are included in in the reference manual
252 set(REFERENCEMANUAL_IMAGE_FILES
254 reference-manual/plots/decomp.pdf
255 reference-manual/plots/dih.pdf
256 reference-manual/plots/drift-all.pdf
257 reference-manual/plots/f-angle.pdf
258 reference-manual/plots/f-bond.pdf
259 reference-manual/plots/fp-highres.pdf
260 reference-manual/plots/int-mat.pdf
261 reference-manual/plots/mdpar.pdf
262 reference-manual/plots/parsort.pdf
263 reference-manual/plots/ring.pdf
264 reference-manual/plots/shiftf.pdf
266 reference-manual/algorithms/plots/dd-cells.pdf
267 reference-manual/algorithms/plots/dd-tric.pdf
268 reference-manual/algorithms/plots/flowchart.pdf
269 reference-manual/algorithms/plots/free1.pdf
270 reference-manual/algorithms/plots/free2.pdf
271 reference-manual/algorithms/plots/leapfrog.pdf
272 reference-manual/algorithms/plots/lincs.pdf
273 reference-manual/algorithms/plots/maxwell.pdf
274 reference-manual/algorithms/plots/mpmd-pme.pdf
275 reference-manual/algorithms/plots/nstric.pdf
276 reference-manual/algorithms/plots/par-lincs2.pdf
277 reference-manual/algorithms/plots/pbctric.pdf
278 reference-manual/algorithms/plots/rhododec.pdf
279 reference-manual/algorithms/plots/truncoct.pdf
280 reference-manual/algorithms/plots/verlet-drift.pdf
281 # Interaction functions chapter
282 reference-manual/functions/plots/angle.pdf
283 reference-manual/functions/plots/bstretch.pdf
284 reference-manual/functions/plots/chain.pdf
285 reference-manual/functions/plots/dummies.pdf
286 reference-manual/functions/plots/f-bham.pdf
287 reference-manual/functions/plots/fbposres.pdf
288 reference-manual/functions/plots/f-dih.pdf
289 reference-manual/functions/plots/f-dr.pdf
290 reference-manual/functions/plots/fig-02.pdf
291 reference-manual/functions/plots/fig-04.pdf
292 reference-manual/functions/plots/f-imps.pdf
293 reference-manual/functions/plots/f-lj.pdf
294 reference-manual/functions/plots/f-morse.pdf
295 reference-manual/functions/plots/f-pr.pdf
296 reference-manual/functions/plots/f-rbs.pdf
297 reference-manual/functions/plots/ring-imp.pdf
298 reference-manual/functions/plots/softcore.pdf
299 reference-manual/functions/plots/subst-im.pdf
300 reference-manual/functions/plots/tetra-im.pdf
301 reference-manual/functions/plots/vcrf.pdf
302 reference-manual/functions/plots/vsite-4fdn.pdf
303 # Special topics chapter
304 reference-manual/special/plots/awh-invN.pdf
305 reference-manual/special/plots/awh-pmfs.pdf
306 reference-manual/special/plots/awh-sampleweights.pdf
307 reference-manual/special/plots/awh-traj.pdf
308 reference-manual/special/plots/compelsetup.pdf
309 reference-manual/special/plots/dumaro.pdf
310 reference-manual/special/plots/dumtypes.pdf
311 reference-manual/special/plots/equipotential.pdf
312 reference-manual/special/plots/field.pdf
313 reference-manual/special/plots/gaussians.pdf
314 reference-manual/special/plots/pulldirrel.pdf
315 reference-manual/special/plots/pull.pdf
316 reference-manual/special/plots/pullref.pdf
317 reference-manual/special/plots/rotation.pdf
319 reference-manual/analysis/plots/dih-def.pdf
320 reference-manual/analysis/plots/distm.pdf
321 reference-manual/analysis/plots/dssp.pdf
322 reference-manual/analysis/plots/hbond-insert.pdf
323 reference-manual/analysis/plots/hbond.pdf
324 reference-manual/analysis/plots/hpr-wheel.pdf
325 reference-manual/analysis/plots/msdwater.pdf
326 reference-manual/analysis/plots/ngmxdump.pdf
327 reference-manual/analysis/plots/phipsi.pdf
328 reference-manual/analysis/plots/rama.pdf
329 reference-manual/analysis/plots/rdfO-O.pdf
330 reference-manual/analysis/plots/rdf.pdf
331 reference-manual/analysis/plots/sgangle.pdf
333 set(SPHINX_SOURCE_FILES
338 dev-manual/build-system.rst
339 dev-manual/change-management.rst
340 dev-manual/commitstyle.rst
341 dev-manual/documentation-generation.rst
342 dev-manual/contribute.rst
343 dev-manual/doxygen.rst
344 dev-manual/error-handling.rst
345 dev-manual/formatting.rst
346 dev-manual/gmxtree.rst
347 dev-manual/includestyle.rst
349 dev-manual/jenkins.rst
350 dev-manual/known-issues.rst
351 dev-manual/language-features.rst
352 dev-manual/naming.rst
353 dev-manual/overview.rst
354 dev-manual/physical_validation.rst
355 dev-manual/redmine-states.png
356 dev-manual/relocatable-binaries.rst
357 dev-manual/reportstyle.rst
359 dev-manual/testutils.rst
361 dev-manual/uncrustify.rst
362 fragments/doxygen-links.rst
368 install-guide/index.rst
369 release-notes/index.rst
370 release-notes/2019/2019.5.rst
371 release-notes/2019/2019.4.rst
372 release-notes/2019/2019.3.rst
373 release-notes/2019/2019.2.rst
374 release-notes/2019/2019.1.rst
375 release-notes/2019/major/highlights.rst
376 release-notes/2019/major/features.rst
377 release-notes/2019/major/performance.rst
378 release-notes/2019/major/tools.rst
379 release-notes/2019/major/bugs-fixed.rst
380 release-notes/2019/major/removed-functionality.rst
381 release-notes/2019/major/deprecated-functionality.rst
382 release-notes/2019/major/portability.rst
383 release-notes/2019/major/miscellaneous.rst
384 release-notes/2018/2018.7.rst
385 release-notes/2018/2018.6.rst
386 release-notes/2018/2018.5.rst
387 release-notes/2018/2018.4.rst
388 release-notes/2018/2018.3.rst
389 release-notes/2018/2018.2.rst
390 release-notes/2018/2018.1.rst
391 release-notes/2018/major/highlights.rst
392 release-notes/2018/major/features.rst
393 release-notes/2018/major/performance.rst
394 release-notes/2018/major/tools.rst
395 release-notes/2018/major/bugs-fixed.rst
396 release-notes/2018/major/removed-features.rst
397 release-notes/2018/major/portability.rst
398 release-notes/2018/major/miscellaneous.rst
399 release-notes/2016/2016.5.rst
400 release-notes/2016/2016.4.rst
401 release-notes/2016/2016.3.rst
402 release-notes/2016/2016.2.rst
403 release-notes/2016/2016.1.rst
404 release-notes/2016/major/highlights.rst
405 release-notes/2016/major/new-features.rst
406 release-notes/2016/major/performance.rst
407 release-notes/2016/major/tools.rst
408 release-notes/2016/major/bugs-fixed.rst
409 release-notes/2016/major/removed-features.rst
410 release-notes/2016/major/miscellaneous.rst
411 release-notes/older/index.rst
412 # the entry for user-guide/index.rst should not appear here,
413 # as it will be included conditionally further down depending on
414 # if the documentation will be build with the full reference
416 user-guide/cmdline.rst
417 user-guide/cutoff-schemes.rst
418 user-guide/deprecation-policy.rst
419 user-guide/environment-variables.rst
421 user-guide/floating-point.rst
423 user-guide/force-fields.rst
424 user-guide/getting-started.rst
426 user-guide/managing-simulations.rst
427 user-guide/mdp-options.rst
428 user-guide/mdrun-features.rst
429 user-guide/mdrun-performance.rst
430 user-guide/run-time-errors.rst
431 user-guide/security.rst
432 user-guide/system-preparation.rst
433 user-guide/terminology.rst
436 include(SphinxMacros.cmake)
437 gmx_init_sphinx_setup(${SPHINX_INPUT_DIR})
439 # set temporary variables for doi inclusion
440 # into the manual, plain string + some wrapping
441 # for release builds, and dummy string for non-release
443 if("${GMX_MANUAL_DOI}" STREQUAL "")
444 # empty string means no doi, set dummy text
445 set(GMX_MANUAL_DOI_STRING "This is not a release build of GROMACS, so please reference")
446 set(GMX_MANUAL_DOI_STRING "${GMX_MANUAL_DOI_STRING} one of the GROMACS papers and the base release of the manual.")
448 # release version, set plain old boring string
449 set(GMX_MANUAL_DOI_STRING "Please reference this documentation as https://doi.org/${GMX_MANUAL_DOI}.")
451 # same for source doi, but modify the text
452 if("${GMX_SOURCE_DOI}" STREQUAL "")
453 # empty string means no release build
454 set(GMX_SOURCE_DOI_STRING "This is not a release build of GROMACS. Please reference one of the")
455 set(GMX_SOURCE_DOI_STRING "${GMX_SOURCE_DOI_STRING} GROMACS papers, as well as the base release that this version is built from.")
456 set(GMX_SOURCE_DOI_STRING "${GMX_SOURCE_DOI_STRING} Also, please state what modifcations have been performed or where the version")
457 set(GMX_SOURCE_DOI_STRING "${GMX_SOURCE_DOI_STRING} was sourced from.")
459 # release version, give them a doi url string
460 set(GMX_SOURCE_DOI_STRING "To cite the source code for this release, please cite")
461 set(GMX_SOURCE_DOI_STRING "${GMX_SOURCE_DOI_STRING} https://doi.org/${GMX_SOURCE_DOI}.")
464 if(IMAGE_CONVERT_POSSIBLE)
465 set(IMAGE_CONVERT_STRING "possible")
467 set(IMAGE_CONVERT_STRING "impossible")
470 set(SPHINX_CONFIG_VARS_FILE ${SPHINX_INPUT_DIR}/conf-vars.py)
471 gmx_configure_version_file(conf-vars.py.cmakein ${SPHINX_CONFIG_VARS_FILE}
473 SPHINX_EXTENSION_PATH RELENG_PATH
475 EXPECTED_DOXYGEN_VERSION
476 EXPECTED_SPHINX_VERSION
477 CMAKE_MINIMUM_REQUIRED_VERSION REQUIRED_CUDA_VERSION
478 REQUIRED_OPENCL_MIN_VERSION
479 REQUIRED_CUDA_COMPUTE_CAPABILITY REGRESSIONTEST_VERSION
480 SOURCE_MD5SUM REGRESSIONTEST_MD5SUM_STRING
481 GMX_TNG_MINIMUM_REQUIRED_VERSION
482 GMX_LMFIT_REQUIRED_VERSION
483 GMX_MANUAL_DOI_STRING
484 GMX_SOURCE_DOI_STRING
485 COMMENT "Configuring Sphinx configuration file")
486 gmx_add_sphinx_input_file(${SPHINX_CONFIG_VARS_FILE})
487 gmx_add_sphinx_source_files(FILES ${SPHINX_SOURCE_FILES})
488 if (EXISTS ${RELENG_PATH}/docs/FileList.cmake)
489 include(${RELENG_PATH}/docs/FileList.cmake)
490 gmx_add_sphinx_source_files(
491 FROM ${RELENG_PATH}/docs TO dev-manual/releng PREFIX releng/docs/
492 FILES ${RELENG_SPHINX_FILES})
494 gmx_add_sphinx_source_files(FILES
495 dev-manual/releng/index.rst
496 dev-manual/releng/jenkins-howto.rst
497 dev-manual/releng/jenkins-ui.rst
500 gmx_add_sphinx_source_files(
502 ${REFERENCEMANUAL_SPHINX_FILES_GENERAL})
503 if (IMAGE_CONVERT_POSSIBLE)
504 gmx_add_sphinx_source_files(
506 ${REFERENCEMANUAL_SPHINX_FILES_WITH_IMAGES}
507 ${REFERENCEMANUAL_IMAGE_FILES})
508 gmx_add_sphinx_image_conversion_files(
510 ${REFERENCEMANUAL_IMAGE_FILES})
512 gmx_add_sphinx_input_target(sphinx-input-rst)
513 gmx_add_sphinx_image_conversion_target(sphinx-image-conversion)
514 add_custom_target(sphinx-input)
515 add_dependencies(sphinx-input sphinx-input-rst sphinx-image-conversion)
516 # Remove other rst files from the build tree, since they confuse Sphinx.
517 # Skip generated files in onlinehelp/, and fragments.
518 # The latter do not cause issues with obsolete files, as they
519 # are not considered as Sphinx input files, but will only be
520 # included using an explicit .. include::.
521 gmx_remove_obsolete_sphinx_input_files("^(onlinehelp|fragments)/.*\\\\.rst$")
523 # TODO: Make this remove obsolete .rst files.
524 # TODO: This does not work in cross-compilation scenarios; disable up to
525 # the necessary level.
526 gmx_add_custom_output_target(sphinx-programs OUTPUT STAMP
527 COMMAND ${CMAKE_COMMAND} -E make_directory onlinehelp
528 COMMAND gmx -quiet help -export rst
530 WORKING_DIRECTORY ${SPHINX_INPUT_DIR}
531 COMMENT "Generating reStructuredText help")
532 # This dependency ensures that the directories exist before the
533 # executable tries to write things there.
534 add_dependencies(sphinx-programs sphinx-input)
536 # Make the INSTALL file for CPack for the tarball. This gets put
537 # into the tarball via the CPack rules below, which requires that
538 # the INSTALL file is in a separate directory by itself.
539 set(TEXT_INSTALL_GUIDE_OUTPUT_DIR "install-guide/text")
540 add_custom_target(install-guide
544 -w sphinx-install.log
545 -d ${CMAKE_CURRENT_BINARY_DIR}/install-guide/_doctrees
546 -c ${SPHINX_INPUT_DIR}
547 "${SPHINX_INPUT_DIR}/install-guide"
548 "${TEXT_INSTALL_GUIDE_OUTPUT_DIR}"
550 ${CMAKE_COMMAND} -E rename
551 ${TEXT_INSTALL_GUIDE_OUTPUT_DIR}/index.txt
552 ${TEXT_INSTALL_GUIDE_OUTPUT_DIR}/INSTALL
554 ${CMAKE_CURRENT_BINARY_DIR}
555 COMMENT "Building INSTALL with Sphinx"
558 add_dependencies(install-guide sphinx-input)
559 gmx_cpack_add_generated_source_directory(install-guide/text DESTINATION /)
561 # Sphinx cache with pickled ReST documents
562 set(SPHINX_CACHE_DIR "${CMAKE_CURRENT_BINARY_DIR}/_doctrees")
563 add_custom_target(webpage-sphinx
564 DEPENDS sphinx-programs
566 DEPENDS sphinx-image-conversion
568 ${CMAKE_COMMAND} -E make_directory ${SPHINX_INPUT_DIR}/_static
573 -d "${SPHINX_CACHE_DIR}"
574 "${SPHINX_INPUT_DIR}"
577 ${CMAKE_CURRENT_BINARY_DIR}
578 COMMENT "Building HTML documentation with Sphinx"
582 add_custom_target(man
587 -d ${SPHINX_CACHE_DIR}
590 ${CMAKE_CURRENT_BINARY_DIR}/man
591 COMMENT "Building man pages with Sphinx"
593 add_dependencies(man sphinx-input sphinx-programs)
595 # If requested, install the man pages built by the 'man' target
596 # created above. Nothing will be installed if the user did not
597 # manually build the target.
598 set(MAN_PAGE_DIR ${CMAKE_CURRENT_BINARY_DIR})
602 set(MANUAL_BUILD_IS_POSSIBLE OFF)
603 set(MANUAL_BUILD_NOT_POSSIBLE_REASON "Sphinx expected minimum version ${EXPECTED_SPHINX_VERSION} is not available")
605 add_custom_target(webpage-sphinx
606 COMMAND ${CMAKE_COMMAND} -E echo
607 "HTML pages cannot be built because Sphinx expected minimum version ${EXPECTED_SPHINX_VERSION} is not available"
609 add_custom_target(install-guide
610 COMMAND ${CMAKE_COMMAND} -E echo
611 "INSTALL cannot be built because Sphinx expected minimum version ${EXPECTED_SPHINX_VERSION} is not available"
613 add_custom_target(man
614 COMMAND ${CMAKE_COMMAND} -E echo
615 "man pages cannot be built because Sphinx expected minimum version ${EXPECTED_SPHINX_VERSION} is not available"
617 add_custom_target(sphinx-create-texman
618 COMMAND ${CMAKE_COMMAND} -E echo
619 "Cannot prepare LaTeX input files because Sphinx expected minimum version ${EXPECTED_SPHINX_VERSION} is not available"
621 add_custom_target(manual
622 COMMAND ${CMAKE_COMMAND} -E echo
623 "manual cannot be built because Sphinx expected minimum version ${EXPECTED_SPHINX_VERSION} is not available")
627 set(MAN_PAGE_DIR ${MAN_PAGE_DIR}/man)
628 # Trailing slash on directory is significant for
629 # install(DIRECTORY). See CMake docs.
630 install(DIRECTORY ${MAN_PAGE_DIR}/
631 DESTINATION ${CMAKE_INSTALL_MANDIR}/man1
632 COMPONENT man OPTIONAL
633 FILES_MATCHING PATTERN "*.1")
635 gmx_cpack_add_generated_source_directory(man)
637 # Determine whether we can build all the HTML pages and content linked from
638 # there. If not, construct an informative message if the user tries to
639 # build the target; most people never need to know, unless they've asked for
641 set(HTML_BUILD_IS_POSSIBLE ON)
642 set(HTML_BUILD_NOT_POSSIBLE_REASON)
643 set(HTML_BUILD_WARNINGS)
645 # Next, turn it off if any of the preconditions are unsatisified
646 if (NOT PYTHON_EXECUTABLE)
647 set(HTML_BUILD_IS_POSSIBLE OFF)
648 set(HTML_BUILD_NOT_POSSIBLE_REASON "Python is required")
649 elseif (NOT SPHINX_FOUND)
650 # Hardly anything gets built if Sphinx is not available, so don't bother.
651 set(HTML_BUILD_IS_POSSIBLE OFF)
652 set(HTML_BUILD_NOT_POSSIBLE_REASON "Sphinx expected minimum version ${EXPECTED_SPHINX_VERSION} is required")
654 if (NOT MANUAL_BUILD_IS_POSSIBLE)
655 list(APPEND HTML_BUILD_WARNINGS
656 "Reference PDF manual was not built, so links to it do not work")
658 if (NOT DOXYGEN_EXECUTABLE)
659 list(APPEND HTML_BUILD_WARNINGS
660 "Doxygen was not available, so links to Doxygen do not work")
662 if (NOT DOXYGEN_DOT_EXECUTABLE)
663 list(APPEND HTML_BUILD_WARNINGS
664 "dot/graphviz was not found, so some graphs are missing")
667 if (HTML_BUILD_IS_POSSIBLE)
668 set(_webpage_target_properties)
669 if (HTML_BUILD_WARNINGS)
670 list(APPEND _webpage_target_properties
671 COMMAND ${CMAKE_COMMAND} -E echo
672 "webpage was built, but with the following limitations:")
673 foreach(_warning ${HTML_BUILD_WARNINGS})
674 list(APPEND _webpage_target_properties
675 COMMAND ${CMAKE_COMMAND} -E echo " - ${_warning}")
679 if (MANUAL_BUILD_IS_POSSIBLE)
680 # Make the PDF reference guide
681 # TODO Try to make the PDF arrive directly in ${HTML_OUTPUT_DIR}
682 # TODO Make this depend on the output of the manual build, so that the
683 # file actually gets copied multiple times.
684 set(_manual_target_location ${HTML_OUTPUT_DIR}/manual-${GMX_VERSION_STRING}.pdf)
686 OUTPUT ${_manual_target_location}
687 COMMAND ${CMAKE_COMMAND}
688 -E remove -f ${_manual_target_location}
689 COMMAND ${CMAKE_COMMAND}
690 -E copy ${CMAKE_CURRENT_BINARY_DIR}/manual/gromacs.pdf ${_manual_target_location}
693 list(APPEND _webpage_target_properties
694 DEPENDS ${_manual_target_location})
697 # The Doxygen configuration in doxygen/Doxyfile-common.cmakein
698 # makes all the Doxygen output directly in
699 # ${HTML_OUTPUT_DIR}/doxygen (and makes the directory if it needs
702 # Add a top-level target that builds everything related to the webpage,
703 # for Jenkins (and possibly others) to use
704 add_custom_target(webpage ${_webpage_target_properties}
705 COMMENT "Building webpage"
707 add_dependencies(webpage webpage-sphinx doxygen-all)
709 add_custom_target(webpage
710 COMMAND ${CMAKE_COMMAND} -E echo
711 "Cannot build webpage because ${HTML_BUILD_NOT_POSSIBLE_REASON}"
712 COMMENT "Webpage build not possible"