2 # This file is part of the GROMACS molecular simulation package.
4 # Copyright (c) 2014,2015,2016,2017,2018 by the GROMACS development team.
5 # Copyright (c) 2019,2020, by the GROMACS development team, led by
6 # Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
7 # and including many others, as listed in the AUTHORS file in the
8 # top-level source directory and at http://www.gromacs.org.
10 # GROMACS is free software; you can redistribute it and/or
11 # modify it under the terms of the GNU Lesser General Public License
12 # as published by the Free Software Foundation; either version 2.1
13 # of the License, or (at your option) any later version.
15 # GROMACS is distributed in the hope that it will be useful,
16 # but WITHOUT ANY WARRANTY; without even the implied warranty of
17 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
18 # Lesser General Public License for more details.
20 # You should have received a copy of the GNU Lesser General Public
21 # License along with GROMACS; if not, see
22 # http://www.gnu.org/licenses, or write to the Free Software Foundation,
23 # Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
25 # If you want to redistribute modifications to GROMACS, please
26 # consider that scientific software is very special. Version
27 # control is crucial - bugs must be traceable. We will be happy to
28 # consider code for inclusion in the official distribution, but
29 # derived work must not be called official GROMACS. Details are found
30 # in the README & COPYING files - if they are missing, get the
31 # official version at http://www.gromacs.org.
33 # To help us fund GROMACS development, we humbly ask that you cite
34 # the research papers on the package. Check out http://www.gromacs.org.
36 # This directory provides a unified place for building all kinds of
37 # GROMACS documentation. This includes some "static" content (Doxygen
38 # code documentation, reference manual, install guide, old online HTML
39 # images), and content generated from the gmx program for the various
40 # tools (man and HTML pages). It also provides the "webpage" target,
41 # that combines all of the above (except man pages in man format) into
42 # a form suitable for automated deployment to the GROMACS website. It
43 # also provides the INSTALL file for the tarball.
45 # The webpage is mostly built by Sphinx. Variable values for Sphinx
46 # substitutions are configured by CMake (for things like version numbers),
47 # using gmx_configure_version_file(). This happens during build time instead
48 # of configure time, because 1) some of the version variables are only
49 # available during build time, and 2) we don't want to do all the Sphinx setup
50 # during configuration to save some time when not building the content.
51 # All of the generated values get put into conf.py (generated from
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 # By default, suppress output after first configuration.
64 if(SPHINX_ALREADY_SEARCHED)
65 set(Sphinx_FIND_QUIETLY ON)
67 find_package(Sphinx ${EXPECTED_SPHINX_VERSION} COMPONENTS pygments)
68 set(SPHINX_ALREADY_SEARCHED TRUE CACHE BOOL "True if a search for Sphinx has already been done")
69 mark_as_advanced(SPHINX_ALREADY_SEARCHED)
71 # Even if we aren't going to make the full webpage, set up to put all
72 # the documentation output in the same place, for convenience
73 set(HTML_OUTPUT_DIR "${CMAKE_CURRENT_BINARY_DIR}/html")
74 file(MAKE_DIRECTORY ${HTML_OUTPUT_DIR})
76 # Prepare directories for pdf/tex output
77 set(TEX_OUTPUT_DIR "${CMAKE_CURRENT_BINARY_DIR}/manual")
78 set(SPHINX_LATEX_FILE "${TEX_OUTPUT_DIR}/gromacs.tex")
79 file(MAKE_DIRECTORY ${TEX_OUTPUT_DIR})
81 # The directory from which man pages will be installed; if it remains
82 # empty, they will be silently skipped.
84 if (SOURCE_IS_SOURCE_DISTRIBUTION)
85 # When building from the tarball, install the bundled man pages
86 # (unless overridden).
87 set(MAN_PAGE_DIR ${CMAKE_CURRENT_SOURCE_DIR})
90 add_subdirectory(doxygen)
92 # TODO: Consider whether this could just be replaced by using
93 # GMX_DEVELOPER_BUILD to control this as well.
94 option(GMX_BUILD_MANUAL "Whether to try to configure to build the PDF manual" OFF)
95 mark_as_advanced(GMX_BUILD_MANUAL)
97 set(MANUAL_BUILD_IS_POSSIBLE ON)
98 set(MANUAL_BUILD_NOT_POSSIBLE_REASON)
99 set(NO_IMAGE_CONVERT_REASON)
100 if (NOT GMX_BUILD_MANUAL)
101 # Make sure we only do detection of manual-building dependencies
102 # when the user opted in for that.
103 set(MANUAL_BUILD_IS_POSSIBLE OFF)
104 set(MANUAL_BUILD_NOT_POSSIBLE_REASON "GMX_BUILD_MANUAL is not ON")
105 elseif (BUILD_IS_INSOURCE)
106 # UseLATEX.cmake does not work with an in-source build
107 set(MANUAL_BUILD_IS_POSSIBLE OFF)
108 set(MANUAL_BUILD_NOT_POSSIBLE_REASON "the build is in-source")
110 include(manual/UseLATEX.cmake)
112 set(MANUAL_BUILD_IS_POSSIBLE OFF)
113 set(MANUAL_BUILD_NOT_POSSIBLE_REASON "Sphinx has not been found and is needed to create the LaTex input files")
114 elseif(NOT PDFLATEX_COMPILER)
115 set(MANUAL_BUILD_IS_POSSIBLE OFF)
116 set(MANUAL_BUILD_NOT_POSSIBLE_REASON "pdflatex is not available")
117 elseif(NOT IMAGE_CONVERT_POSSIBLE)
118 set(MANUAL_BUILD_IS_POSSIBLE OFF)
119 set(MANUAL_BUILD_NOT_POSSIBLE_REASON "a working form of ImageMagick convert is not available")
120 set(NO_IMAGE_CONVERT_REASON "Can not convert files for online or pdf manual")
121 # TODO Later, identify other dependencies like bibtex,
122 # make_index, date, some graphics conversion program,
123 # etc. Perhaps patch UseLATEX.cmake and contribute upstream.
129 # We need to have all the Sphinx input files in a single directory, and
130 # since some of them are generated, we copy everything into the build tree,
132 set(SPHINX_INPUT_DIR ${CMAKE_CURRENT_BINARY_DIR}/sphinx-input)
133 set(SPHINX_EXTENSION_PATH ${CMAKE_CURRENT_SOURCE_DIR})
134 # As the manual build now depends also on Sphinx, the inclusion path needs
135 # to be set after we know the basic information for Sphinx.
136 add_subdirectory(manual)
137 if (SOURCE_MD5SUM STREQUAL "unknown")
138 # But for testing the webpage build (e.g. from the repo) we
139 # need a default value.
140 set(REGRESSIONTEST_MD5SUM_STRING "unknown")
142 # The real build of the webpage happens from the tarball, and
143 # this should be set to the matching MD5 sum.
144 set(REGRESSIONTEST_MD5SUM_STRING "${REGRESSIONTEST_MD5SUM}")
146 # The reference manual still contains the individual sections from the
147 # LaTeX document, with the files below grouped and annotated by chapter.
148 set(REFERENCEMANUAL_SPHINX_FILES_GENERAL
149 # Main index file, preface and introduction.
150 reference-manual/index.rst
151 reference-manual/preface.rst
152 reference-manual/introduction.rst
153 # Definitions and Units chapter
154 reference-manual/definitions.rst
156 reference-manual/topologies.rst
157 reference-manual/topologies/particle-type.rst
158 reference-manual/topologies/parameter-files.rst
159 reference-manual/topologies/molecule-definition.rst
160 reference-manual/topologies/constraint-algorithm-section.rst
161 reference-manual/topologies/pdb2gmx-input-files.rst
162 reference-manual/topologies/topology-file-formats.rst
163 reference-manual/topologies/force-field-organization.rst
164 # File formats chapter
165 reference-manual/file-formats.rst
166 # Run parameters and programs chapter
167 reference-manual/run-parameters.rst
168 # Implementation details chapter
169 reference-manual/details.rst
170 # Averages and fluctations chapter
171 reference-manual/averages.rst
173 reference-manual/references.rst
174 # PNG formated plot files that don't need to be converted into PNG
176 reference-manual/plots/peregrine.png
177 reference-manual/plots/adress.png
178 reference-manual/plots/plotje.png
179 reference-manual/plots/xvgr.png
181 set(REFERENCEMANUAL_SPHINX_FILES_WITH_IMAGES
183 reference-manual/algorithms.rst
184 reference-manual/algorithms/periodic-boundary-conditions.rst
185 reference-manual/algorithms/group-concept.rst
186 reference-manual/algorithms/molecular-dynamics.rst
187 reference-manual/algorithms/shell-molecular-dynamics.rst
188 reference-manual/algorithms/constraint-algorithms.rst
189 reference-manual/algorithms/simulated-annealing.rst
190 reference-manual/algorithms/stochastic-dynamics.rst
191 reference-manual/algorithms/brownian-dynamics.rst
192 reference-manual/algorithms/energy-minimization.rst
193 reference-manual/algorithms/normal-mode-analysis.rst
194 reference-manual/algorithms/free-energy-calculations.rst
195 reference-manual/algorithms/replica-exchange.rst
196 reference-manual/algorithms/essential-dynamics.rst
197 reference-manual/algorithms/expanded-ensemble.rst
198 reference-manual/algorithms/parallelization-domain-decomp.rst
199 # Interaction functions and force fields chapter
200 reference-manual/functions.rst
201 reference-manual/functions/bonded-interactions.rst
202 reference-manual/functions/force-field.rst
203 reference-manual/functions/free-energy-interactions.rst
204 reference-manual/functions/interaction-methods.rst
205 reference-manual/functions/long-range-electrostatics.rst
206 reference-manual/functions/long-range-vdw.rst
207 reference-manual/functions/nonbonded-interactions.rst
208 reference-manual/functions/polarization.rst
209 reference-manual/functions/restraints.rst
210 # Special topics chapter
211 reference-manual/special.rst
212 reference-manual/special/free-energy-implementation.rst
213 reference-manual/special/pulling.rst
214 reference-manual/special/awh.rst
215 reference-manual/special/enforced-rotation.rst
216 reference-manual/special/electric-fields.rst
217 reference-manual/special/comp-electrophys.rst
218 reference-manual/special/free-energy-pmf.rst
219 reference-manual/special/remove-fast-dgf.rst
220 reference-manual/special/viscosity-calculation.rst
221 reference-manual/special/tabulated-interaction-functions.rst
222 reference-manual/special/qmmm.rst
223 reference-manual/special/vmd-imd.rst
224 reference-manual/special/membrane-embedding.rst
225 reference-manual/special/mimic-qmmm.rst
226 reference-manual/special/density-guided-simulation.rst
228 reference-manual/analysis.rst
229 reference-manual/analysis/using-groups.rst
230 reference-manual/analysis/looking-at-trajectory.rst
231 reference-manual/analysis/general-properties.rst
232 reference-manual/analysis/radial-distribution-function.rst
233 reference-manual/analysis/correlation-function.rst
234 reference-manual/analysis/curve-fitting.rst
235 reference-manual/analysis/mean-square-displacement.rst
236 reference-manual/analysis/bond-angle-dihedral.rst
237 reference-manual/analysis/radius-of-gyration.rst
238 reference-manual/analysis/rmsd.rst
239 reference-manual/analysis/covariance-analysis.rst
240 reference-manual/analysis/dihedral-pca.rst
241 reference-manual/analysis/hydrogen-bonds.rst
242 reference-manual/analysis/protein-related.rst
243 reference-manual/analysis/interface-related.rst)
244 # The image files have also been ordered by the respective
245 # chapter they are included in in the reference manual
246 set(REFERENCEMANUAL_IMAGE_FILES
248 reference-manual/plots/decomp.pdf
249 reference-manual/plots/dih.pdf
250 reference-manual/plots/drift-all.pdf
251 reference-manual/plots/f-angle.pdf
252 reference-manual/plots/f-bond.pdf
253 reference-manual/plots/fp-highres.pdf
254 reference-manual/plots/int-mat.pdf
255 reference-manual/plots/mdpar.pdf
256 reference-manual/plots/parsort.pdf
257 reference-manual/plots/ring.pdf
258 reference-manual/plots/shiftf.pdf
260 reference-manual/algorithms/plots/dd-cells.pdf
261 reference-manual/algorithms/plots/dd-tric.pdf
262 reference-manual/algorithms/plots/flowchart.pdf
263 reference-manual/algorithms/plots/free1.pdf
264 reference-manual/algorithms/plots/free2.pdf
265 reference-manual/algorithms/plots/leapfrog.pdf
266 reference-manual/algorithms/plots/lincs.pdf
267 reference-manual/algorithms/plots/maxwell.pdf
268 reference-manual/algorithms/plots/mpmd-pme.pdf
269 reference-manual/algorithms/plots/nstric.pdf
270 reference-manual/algorithms/plots/par-lincs2.pdf
271 reference-manual/algorithms/plots/pbctric.pdf
272 reference-manual/algorithms/plots/rhododec.pdf
273 reference-manual/algorithms/plots/truncoct.pdf
274 reference-manual/algorithms/plots/verlet-drift.pdf
275 # Interaction functions chapter
276 reference-manual/functions/plots/angle.pdf
277 reference-manual/functions/plots/bstretch.pdf
278 reference-manual/functions/plots/chain.pdf
279 reference-manual/functions/plots/dummies.pdf
280 reference-manual/functions/plots/f-bham.pdf
281 reference-manual/functions/plots/fbposres.pdf
282 reference-manual/functions/plots/f-dih.pdf
283 reference-manual/functions/plots/f-dr.pdf
284 reference-manual/functions/plots/fig-02.pdf
285 reference-manual/functions/plots/fig-04.pdf
286 reference-manual/functions/plots/f-imps.pdf
287 reference-manual/functions/plots/f-lj.pdf
288 reference-manual/functions/plots/f-morse.pdf
289 reference-manual/functions/plots/f-pr.pdf
290 reference-manual/functions/plots/f-rbs.pdf
291 reference-manual/functions/plots/ring-imp.pdf
292 reference-manual/functions/plots/softcore.pdf
293 reference-manual/functions/plots/subst-im.pdf
294 reference-manual/functions/plots/tetra-im.pdf
295 reference-manual/functions/plots/vcrf.pdf
296 reference-manual/functions/plots/vsite-4fdn.pdf
297 # Special topics chapter
298 reference-manual/special/plots/awh-invN.pdf
299 reference-manual/special/plots/awh-pmfs.pdf
300 reference-manual/special/plots/awh-sampleweights.pdf
301 reference-manual/special/plots/awh-traj.pdf
302 reference-manual/special/plots/compelsetup.pdf
303 reference-manual/special/plots/dumaro.pdf
304 reference-manual/special/plots/dumtypes.pdf
305 reference-manual/special/plots/equipotential.pdf
306 reference-manual/special/plots/field.pdf
307 reference-manual/special/plots/gaussians.pdf
308 reference-manual/special/plots/pulldirrel.pdf
309 reference-manual/special/plots/pull.pdf
310 reference-manual/special/plots/pullref.pdf
311 reference-manual/special/plots/rotation.pdf
313 reference-manual/analysis/plots/dih-def.pdf
314 reference-manual/analysis/plots/distm.pdf
315 reference-manual/analysis/plots/dssp.pdf
316 reference-manual/analysis/plots/hbond-insert.pdf
317 reference-manual/analysis/plots/hbond.pdf
318 reference-manual/analysis/plots/hpr-wheel.pdf
319 reference-manual/analysis/plots/msdwater.pdf
320 reference-manual/analysis/plots/ngmxdump.pdf
321 reference-manual/analysis/plots/phipsi.pdf
322 reference-manual/analysis/plots/rama.pdf
323 reference-manual/analysis/plots/rdfO-O.pdf
324 reference-manual/analysis/plots/rdf.pdf
325 reference-manual/analysis/plots/sgangle.pdf
327 set(SPHINX_SOURCE_FILES
331 dev-manual/build-system.rst
332 dev-manual/change-management.rst
333 dev-manual/commitstyle.rst
334 dev-manual/containers.rst
335 dev-manual/documentation-generation.rst
336 dev-manual/contribute.rst
337 dev-manual/doxygen.rst
338 dev-manual/error-handling.rst
339 dev-manual/formatting.rst
340 dev-manual/gitlab.rst
341 dev-manual/gmxtree.rst
342 dev-manual/includestyle.rst
344 dev-manual/infrastructure.rst
345 dev-manual/jenkins.rst
346 dev-manual/known-issues.rst
347 dev-manual/language-features.rst
348 dev-manual/naming.rst
349 dev-manual/overview.rst
350 dev-manual/physical_validation.rst
351 dev-manual/redmine-states.png
352 dev-manual/relocatable-binaries.rst
353 dev-manual/reportstyle.rst
355 dev-manual/testutils.rst
357 dev-manual/code-formatting.rst
358 fragments/doxygen-links.rst
364 install-guide/index.rst
365 release-notes/index.rst
366 release-notes/2021/major/highlights.rst
367 release-notes/2021/major/features.rst
368 release-notes/2021/major/performance.rst
369 release-notes/2021/major/tools.rst
370 release-notes/2021/major/bugs-fixed.rst
371 release-notes/2021/major/removed-functionality.rst
372 release-notes/2021/major/deprecated-functionality.rst
373 release-notes/2021/major/portability.rst
374 release-notes/2021/major/miscellaneous.rst
375 release-notes/2020/2020.1.rst
376 release-notes/2020/2020.2.rst
377 release-notes/2020/2020.3.rst
378 release-notes/2020/major/highlights.rst
379 release-notes/2020/major/features.rst
380 release-notes/2020/major/performance.rst
381 release-notes/2020/major/tools.rst
382 release-notes/2020/major/bugs-fixed.rst
383 release-notes/2020/major/removed-functionality.rst
384 release-notes/2020/major/deprecated-functionality.rst
385 release-notes/2020/major/portability.rst
386 release-notes/2020/major/miscellaneous.rst
387 release-notes/2019/2019.6.rst
388 release-notes/2019/2019.5.rst
389 release-notes/2019/2019.4.rst
390 release-notes/2019/2019.3.rst
391 release-notes/2019/2019.2.rst
392 release-notes/2019/2019.1.rst
393 release-notes/2019/major/highlights.rst
394 release-notes/2019/major/features.rst
395 release-notes/2019/major/performance.rst
396 release-notes/2019/major/tools.rst
397 release-notes/2019/major/bugs-fixed.rst
398 release-notes/2019/major/removed-functionality.rst
399 release-notes/2019/major/deprecated-functionality.rst
400 release-notes/2019/major/portability.rst
401 release-notes/2019/major/miscellaneous.rst
402 release-notes/2018/2018.7.rst
403 release-notes/2018/2018.6.rst
404 release-notes/2018/2018.5.rst
405 release-notes/2018/2018.4.rst
406 release-notes/2018/2018.3.rst
407 release-notes/2018/2018.2.rst
408 release-notes/2018/2018.1.rst
409 release-notes/2018/major/highlights.rst
410 release-notes/2018/major/features.rst
411 release-notes/2018/major/performance.rst
412 release-notes/2018/major/tools.rst
413 release-notes/2018/major/bugs-fixed.rst
414 release-notes/2018/major/removed-features.rst
415 release-notes/2018/major/portability.rst
416 release-notes/2018/major/miscellaneous.rst
417 release-notes/2016/2016.5.rst
418 release-notes/2016/2016.4.rst
419 release-notes/2016/2016.3.rst
420 release-notes/2016/2016.2.rst
421 release-notes/2016/2016.1.rst
422 release-notes/2016/major/highlights.rst
423 release-notes/2016/major/new-features.rst
424 release-notes/2016/major/performance.rst
425 release-notes/2016/major/tools.rst
426 release-notes/2016/major/bugs-fixed.rst
427 release-notes/2016/major/removed-features.rst
428 release-notes/2016/major/miscellaneous.rst
429 release-notes/older/index.rst
430 # the entry for user-guide/index.rst should not appear here,
431 # as it will be included conditionally further down depending on
432 # if the documentation will be build with the full reference
434 user-guide/cmdline.rst
435 user-guide/deprecation-policy.rst
436 user-guide/environment-variables.rst
438 user-guide/floating-point.rst
440 user-guide/force-fields.rst
441 user-guide/getting-started.rst
443 user-guide/managing-simulations.rst
444 user-guide/mdp-options.rst
445 user-guide/mdrun-features.rst
446 user-guide/mdrun-performance.rst
447 user-guide/run-time-errors.rst
448 user-guide/security.rst
449 user-guide/system-preparation.rst
450 user-guide/terminology.rst
453 include(SphinxMacros.cmake)
454 gmx_init_sphinx_setup(${SPHINX_INPUT_DIR})
456 # set temporary variables for doi inclusion
457 # into the manual, plain string + some wrapping
458 # for release builds, and dummy string for non-release
460 if("${GMX_MANUAL_DOI}" STREQUAL "")
461 # empty string means no doi, set dummy text
462 set(GMX_MANUAL_DOI_STRING "This is not a release build of GROMACS, so please reference")
463 set(GMX_MANUAL_DOI_STRING "${GMX_MANUAL_DOI_STRING} one of the GROMACS papers and the base release of the manual.")
465 # release version, set plain old boring string
466 set(GMX_MANUAL_DOI_STRING "Please reference this documentation as https://doi.org/${GMX_MANUAL_DOI}.")
468 # same for source doi, but modify the text
469 if("${GMX_SOURCE_DOI}" STREQUAL "")
470 # empty string means no release build
471 set(GMX_SOURCE_DOI_STRING "This is not a release build of GROMACS. Please reference one of the")
472 set(GMX_SOURCE_DOI_STRING "${GMX_SOURCE_DOI_STRING} GROMACS papers, as well as the base release that this version is built from.")
473 set(GMX_SOURCE_DOI_STRING "${GMX_SOURCE_DOI_STRING} Also, please state what modifcations have been performed or where the version")
474 set(GMX_SOURCE_DOI_STRING "${GMX_SOURCE_DOI_STRING} was sourced from.")
476 # release version, give them a doi url string
477 set(GMX_SOURCE_DOI_STRING "To cite the source code for this release, please cite")
478 set(GMX_SOURCE_DOI_STRING "${GMX_SOURCE_DOI_STRING} https://doi.org/${GMX_SOURCE_DOI}.")
481 if(IMAGE_CONVERT_POSSIBLE)
482 set(IMAGE_CONVERT_STRING "possible")
484 set(IMAGE_CONVERT_STRING "impossible")
487 set(SPHINX_CONFIG_FILE ${SPHINX_INPUT_DIR}/conf.py)
488 if (GMX_PYTHON_PACKAGE)
489 set(GMXAPI_PYTHON_STAGING_DIR ${CMAKE_BINARY_DIR}/python_packaging/src/gmxapi_staging)
490 # TODO: Resolve circular reference. We would like to get the CMake build-time directory for
491 # the gmxapi Python package from the _gmxapi target, as we do when building sample_restraint.
492 # Instead of the above hard-coded path, how can we do
493 # get_target_property(GMXAPI_PYTHON_STAGING_DIR _gmxapi staging_dir)
497 gmx_configure_version_file(
498 conf.cmakein.py ${SPHINX_CONFIG_FILE}
500 CMAKE_MINIMUM_REQUIRED_VERSION
501 EXPECTED_DOXYGEN_VERSION
502 EXPECTED_SPHINX_VERSION
504 GMX_LMFIT_REQUIRED_VERSION
505 GMX_MANUAL_DOI_STRING
506 GMX_TNG_MINIMUM_REQUIRED_VERSION
507 GMX_SOURCE_DOI_STRING
508 GMXAPI_PYTHON_STAGING_DIR
510 REGRESSIONTEST_VERSION
511 REQUIRED_CUDA_COMPUTE_CAPABILITY
512 REQUIRED_CUDA_VERSION
513 REQUIRED_OPENCL_MIN_VERSION
514 REGRESSIONTEST_MD5SUM_STRING
517 SPHINX_EXTENSION_PATH
518 COMMENT "Configuring Sphinx configuration file")
519 gmx_add_sphinx_input_file(${SPHINX_CONFIG_FILE})
520 gmx_add_sphinx_source_files(FILES ${SPHINX_SOURCE_FILES})
521 if (EXISTS ${RELENG_PATH}/docs/FileList.cmake)
522 include(${RELENG_PATH}/docs/FileList.cmake)
523 gmx_add_sphinx_source_files(
524 FROM ${RELENG_PATH}/docs TO dev-manual/releng PREFIX releng/docs/
525 FILES ${RELENG_SPHINX_FILES})
527 gmx_add_sphinx_source_files(FILES
528 dev-manual/releng/index.rst
532 gmx_add_sphinx_source_files(
535 gmxapi/userguide/install.rst
536 gmxapi/userguide/usage.rst
537 gmxapi/userguide/userguide.rst
540 if (GMX_PYTHON_PACKAGE)
541 gmx_add_sphinx_source_files(
543 gmxapi/userguide/pythonreference.rst
546 gmx_add_sphinx_source_files(
547 FROM ${CMAKE_CURRENT_SOURCE_DIR}/gmxapi/userguide-stub
549 FILES pythonreference.rst
553 gmx_add_sphinx_source_files(
555 ${REFERENCEMANUAL_SPHINX_FILES_GENERAL})
556 if (IMAGE_CONVERT_POSSIBLE)
557 gmx_add_sphinx_source_files(
559 ${REFERENCEMANUAL_SPHINX_FILES_WITH_IMAGES}
560 ${REFERENCEMANUAL_IMAGE_FILES})
561 gmx_add_sphinx_image_conversion_files(
563 ${REFERENCEMANUAL_IMAGE_FILES})
565 gmx_add_sphinx_input_target(sphinx-input-rst)
566 gmx_add_sphinx_image_conversion_target(sphinx-image-conversion)
567 add_custom_target(sphinx-input)
568 add_dependencies(sphinx-input sphinx-input-rst sphinx-image-conversion)
569 if (GMX_PYTHON_PACKAGE)
570 add_dependencies(sphinx-input _gmxapi)
572 # Remove other rst files from the build tree, since they confuse Sphinx.
573 # Skip generated files in onlinehelp/, and fragments.
574 # The latter do not cause issues with obsolete files, as they
575 # are not considered as Sphinx input files, but will only be
576 # included using an explicit .. include::.
577 gmx_remove_obsolete_sphinx_input_files("^(onlinehelp|fragments)/.*\\\\.rst$")
579 # TODO: Make this remove obsolete .rst files.
580 # TODO: This does not work in cross-compilation scenarios; disable up to
581 # the necessary level.
582 gmx_add_custom_output_target(sphinx-programs OUTPUT STAMP
583 COMMAND ${CMAKE_COMMAND} -E make_directory onlinehelp
584 COMMAND gmx -quiet help -export rst
586 WORKING_DIRECTORY ${SPHINX_INPUT_DIR}
587 COMMENT "Generating reStructuredText help")
588 # This dependency ensures that the directories exist before the
589 # executable tries to write things there.
590 add_dependencies(sphinx-programs sphinx-input)
592 # Make the INSTALL file for CPack for the tarball. This gets put
593 # into the tarball via the CPack rules below, which requires that
594 # the INSTALL file is in a separate directory by itself.
595 set(TEXT_INSTALL_GUIDE_OUTPUT_DIR "install-guide/text")
596 add_custom_target(install-guide
600 -w sphinx-install.log
601 -d ${CMAKE_CURRENT_BINARY_DIR}/install-guide/_doctrees
602 -c ${SPHINX_INPUT_DIR}
603 "${SPHINX_INPUT_DIR}/install-guide"
604 "${TEXT_INSTALL_GUIDE_OUTPUT_DIR}"
606 ${CMAKE_COMMAND} -E rename
607 ${TEXT_INSTALL_GUIDE_OUTPUT_DIR}/index.txt
608 ${TEXT_INSTALL_GUIDE_OUTPUT_DIR}/INSTALL
610 ${CMAKE_CURRENT_BINARY_DIR}
611 COMMENT "Building INSTALL with Sphinx"
614 add_dependencies(install-guide sphinx-input)
615 gmx_cpack_add_generated_source_directory(install-guide/text DESTINATION /)
617 # Sphinx cache with pickled ReST documents
618 set(SPHINX_CACHE_DIR "${CMAKE_CURRENT_BINARY_DIR}/_doctrees")
619 set(SPHINX_CONFIG_OVERRIDES "")
620 if (GMX_DEVELOPER_BUILD)
621 set(SPHINX_CONFIG_OVERRIDES "-Dtodo_include_todos=1")
623 add_custom_target(webpage-sphinx
624 DEPENDS sphinx-programs
626 DEPENDS sphinx-image-conversion
629 ${CMAKE_COMMAND} -E make_directory ${SPHINX_INPUT_DIR}/_static
634 -d "${SPHINX_CACHE_DIR}"
635 ${SPHINX_CONFIG_OVERRIDES}
636 "${SPHINX_INPUT_DIR}"
639 ${CMAKE_CURRENT_BINARY_DIR}
640 COMMENT "Building HTML documentation with Sphinx"
644 add_custom_target(man
649 -d ${SPHINX_CACHE_DIR}
652 ${CMAKE_CURRENT_BINARY_DIR}/man
653 COMMENT "Building man pages with Sphinx"
655 add_dependencies(man sphinx-input sphinx-programs)
657 # If requested, install the man pages built by the 'man' target
658 # created above. Nothing will be installed if the user did not
659 # manually build the target.
660 set(MAN_PAGE_DIR ${CMAKE_CURRENT_BINARY_DIR})
664 set(MANUAL_BUILD_IS_POSSIBLE OFF)
665 set(MANUAL_BUILD_NOT_POSSIBLE_REASON "Sphinx expected minimum version ${EXPECTED_SPHINX_VERSION} is not available")
667 add_custom_target(webpage-sphinx
668 COMMAND ${CMAKE_COMMAND} -E echo
669 "HTML pages cannot be built because Sphinx expected minimum version ${EXPECTED_SPHINX_VERSION} is not available"
671 add_custom_target(install-guide
672 COMMAND ${CMAKE_COMMAND} -E echo
673 "INSTALL cannot be built because Sphinx expected minimum version ${EXPECTED_SPHINX_VERSION} is not available"
675 add_custom_target(man
676 COMMAND ${CMAKE_COMMAND} -E echo
677 "man pages cannot be built because Sphinx expected minimum version ${EXPECTED_SPHINX_VERSION} is not available"
679 add_custom_target(sphinx-create-texman
680 COMMAND ${CMAKE_COMMAND} -E echo
681 "Cannot prepare LaTeX input files because Sphinx expected minimum version ${EXPECTED_SPHINX_VERSION} is not available"
683 add_custom_target(manual
684 COMMAND ${CMAKE_COMMAND} -E echo
685 "manual cannot be built because Sphinx expected minimum version ${EXPECTED_SPHINX_VERSION} is not available")
689 set(MAN_PAGE_DIR ${MAN_PAGE_DIR}/man)
690 # Trailing slash on directory is significant for
691 # install(DIRECTORY). See CMake docs.
692 install(DIRECTORY ${MAN_PAGE_DIR}/
693 DESTINATION ${CMAKE_INSTALL_MANDIR}/man1
694 COMPONENT man OPTIONAL
695 FILES_MATCHING PATTERN "*.1")
697 gmx_cpack_add_generated_source_directory(man)
699 # Determine whether we can build all the HTML pages and content linked from
700 # there. If not, construct an informative message if the user tries to
701 # build the target; most people never need to know, unless they've asked for
703 set(HTML_BUILD_IS_POSSIBLE ON)
704 set(HTML_BUILD_NOT_POSSIBLE_REASON)
705 set(HTML_BUILD_WARNINGS)
707 # Next, turn it off if any of the preconditions are unsatisified
708 if (NOT Python3_Interpreter_FOUND)
709 set(HTML_BUILD_IS_POSSIBLE OFF)
710 set(HTML_BUILD_NOT_POSSIBLE_REASON "Python is required")
711 elseif (NOT SPHINX_FOUND)
712 # Hardly anything gets built if Sphinx is not available, so don't bother.
713 set(HTML_BUILD_IS_POSSIBLE OFF)
714 set(HTML_BUILD_NOT_POSSIBLE_REASON "Sphinx expected minimum version ${EXPECTED_SPHINX_VERSION} is required")
716 if (NOT MANUAL_BUILD_IS_POSSIBLE)
717 list(APPEND HTML_BUILD_WARNINGS
718 "Reference PDF manual was not built, so links to it do not work")
720 if (NOT DOXYGEN_EXECUTABLE)
721 list(APPEND HTML_BUILD_WARNINGS
722 "Doxygen was not available, so links to Doxygen do not work")
724 if (NOT DOXYGEN_DOT_EXECUTABLE)
725 list(APPEND HTML_BUILD_WARNINGS
726 "dot/graphviz was not found, so some graphs are missing")
729 if (HTML_BUILD_IS_POSSIBLE)
730 set(_webpage_target_properties)
731 if (HTML_BUILD_WARNINGS)
732 list(APPEND _webpage_target_properties
733 COMMAND ${CMAKE_COMMAND} -E echo
734 "webpage was built, but with the following limitations:")
735 foreach(_warning ${HTML_BUILD_WARNINGS})
736 list(APPEND _webpage_target_properties
737 COMMAND ${CMAKE_COMMAND} -E echo " - ${_warning}")
741 if (MANUAL_BUILD_IS_POSSIBLE)
742 # Make the PDF reference guide
743 # TODO Try to make the PDF arrive directly in ${HTML_OUTPUT_DIR}
744 # TODO Make this depend on the output of the manual build, so that the
745 # file actually gets copied multiple times.
746 set(_manual_target_location ${HTML_OUTPUT_DIR}/manual-${GMX_VERSION_STRING}.pdf)
748 OUTPUT ${_manual_target_location}
749 COMMAND ${CMAKE_COMMAND}
750 -E remove -f ${_manual_target_location}
751 COMMAND ${CMAKE_COMMAND}
752 -E copy ${CMAKE_CURRENT_BINARY_DIR}/manual/gromacs.pdf ${_manual_target_location}
755 list(APPEND _webpage_target_properties
756 DEPENDS ${_manual_target_location})
759 # The Doxygen configuration in doxygen/Doxyfile-common.cmakein
760 # makes all the Doxygen output directly in
761 # ${HTML_OUTPUT_DIR}/doxygen (and makes the directory if it needs
764 # Add a top-level target that builds everything related to the webpage,
765 # for Jenkins (and possibly others) to use
766 add_custom_target(webpage ${_webpage_target_properties}
767 COMMENT "Building webpage"
769 add_dependencies(webpage webpage-sphinx doxygen-all)
771 add_custom_target(webpage
772 COMMAND ${CMAKE_COMMAND} -E echo
773 "Cannot build webpage because ${HTML_BUILD_NOT_POSSIBLE_REASON}"
774 COMMENT "Webpage build not possible"