2 # This file is part of the GROMACS molecular simulation package.
4 # Copyright (c) 2014,2015,2016,2017,2018,2019,2020, 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 # 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
332 dev-manual/build-system.rst
333 dev-manual/change-management.rst
334 dev-manual/commitstyle.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/gmxtree.rst
341 dev-manual/includestyle.rst
343 dev-manual/jenkins.rst
344 dev-manual/known-issues.rst
345 dev-manual/language-features.rst
346 dev-manual/naming.rst
347 dev-manual/overview.rst
348 dev-manual/physical_validation.rst
349 dev-manual/redmine-states.png
350 dev-manual/relocatable-binaries.rst
351 dev-manual/reportstyle.rst
353 dev-manual/testutils.rst
355 dev-manual/code-formatting.rst
356 fragments/doxygen-links.rst
362 install-guide/index.rst
363 release-notes/index.rst
364 release-notes/2020/2020.1.rst
365 release-notes/2020/2020.2.rst
366 release-notes/2020/2020.3.rst
367 release-notes/2020/major/highlights.rst
368 release-notes/2020/major/features.rst
369 release-notes/2020/major/performance.rst
370 release-notes/2020/major/tools.rst
371 release-notes/2020/major/bugs-fixed.rst
372 release-notes/2020/major/removed-functionality.rst
373 release-notes/2020/major/deprecated-functionality.rst
374 release-notes/2020/major/portability.rst
375 release-notes/2020/major/miscellaneous.rst
376 release-notes/2019/2019.6.rst
377 release-notes/2019/2019.5.rst
378 release-notes/2019/2019.4.rst
379 release-notes/2019/2019.3.rst
380 release-notes/2019/2019.2.rst
381 release-notes/2019/2019.1.rst
382 release-notes/2019/major/highlights.rst
383 release-notes/2019/major/features.rst
384 release-notes/2019/major/performance.rst
385 release-notes/2019/major/tools.rst
386 release-notes/2019/major/bugs-fixed.rst
387 release-notes/2019/major/removed-functionality.rst
388 release-notes/2019/major/deprecated-functionality.rst
389 release-notes/2019/major/portability.rst
390 release-notes/2019/major/miscellaneous.rst
391 release-notes/2018/2018.7.rst
392 release-notes/2018/2018.6.rst
393 release-notes/2018/2018.5.rst
394 release-notes/2018/2018.4.rst
395 release-notes/2018/2018.3.rst
396 release-notes/2018/2018.2.rst
397 release-notes/2018/2018.1.rst
398 release-notes/2018/major/highlights.rst
399 release-notes/2018/major/features.rst
400 release-notes/2018/major/performance.rst
401 release-notes/2018/major/tools.rst
402 release-notes/2018/major/bugs-fixed.rst
403 release-notes/2018/major/removed-features.rst
404 release-notes/2018/major/portability.rst
405 release-notes/2018/major/miscellaneous.rst
406 release-notes/2016/2016.5.rst
407 release-notes/2016/2016.4.rst
408 release-notes/2016/2016.3.rst
409 release-notes/2016/2016.2.rst
410 release-notes/2016/2016.1.rst
411 release-notes/2016/major/highlights.rst
412 release-notes/2016/major/new-features.rst
413 release-notes/2016/major/performance.rst
414 release-notes/2016/major/tools.rst
415 release-notes/2016/major/bugs-fixed.rst
416 release-notes/2016/major/removed-features.rst
417 release-notes/2016/major/miscellaneous.rst
418 release-notes/older/index.rst
419 # the entry for user-guide/index.rst should not appear here,
420 # as it will be included conditionally further down depending on
421 # if the documentation will be build with the full reference
423 user-guide/cmdline.rst
424 user-guide/deprecation-policy.rst
425 user-guide/environment-variables.rst
427 user-guide/floating-point.rst
429 user-guide/force-fields.rst
430 user-guide/getting-started.rst
432 user-guide/managing-simulations.rst
433 user-guide/mdp-options.rst
434 user-guide/mdrun-features.rst
435 user-guide/mdrun-performance.rst
436 user-guide/run-time-errors.rst
437 user-guide/security.rst
438 user-guide/system-preparation.rst
439 user-guide/terminology.rst
442 include(SphinxMacros.cmake)
443 gmx_init_sphinx_setup(${SPHINX_INPUT_DIR})
445 # set temporary variables for doi inclusion
446 # into the manual, plain string + some wrapping
447 # for release builds, and dummy string for non-release
449 if("${GMX_MANUAL_DOI}" STREQUAL "")
450 # empty string means no doi, set dummy text
451 set(GMX_MANUAL_DOI_STRING "This is not a release build of GROMACS, so please reference")
452 set(GMX_MANUAL_DOI_STRING "${GMX_MANUAL_DOI_STRING} one of the GROMACS papers and the base release of the manual.")
454 # release version, set plain old boring string
455 set(GMX_MANUAL_DOI_STRING "Please reference this documentation as https://doi.org/${GMX_MANUAL_DOI}.")
457 # same for source doi, but modify the text
458 if("${GMX_SOURCE_DOI}" STREQUAL "")
459 # empty string means no release build
460 set(GMX_SOURCE_DOI_STRING "This is not a release build of GROMACS. Please reference one of the")
461 set(GMX_SOURCE_DOI_STRING "${GMX_SOURCE_DOI_STRING} GROMACS papers, as well as the base release that this version is built from.")
462 set(GMX_SOURCE_DOI_STRING "${GMX_SOURCE_DOI_STRING} Also, please state what modifcations have been performed or where the version")
463 set(GMX_SOURCE_DOI_STRING "${GMX_SOURCE_DOI_STRING} was sourced from.")
465 # release version, give them a doi url string
466 set(GMX_SOURCE_DOI_STRING "To cite the source code for this release, please cite")
467 set(GMX_SOURCE_DOI_STRING "${GMX_SOURCE_DOI_STRING} https://doi.org/${GMX_SOURCE_DOI}.")
470 if(IMAGE_CONVERT_POSSIBLE)
471 set(IMAGE_CONVERT_STRING "possible")
473 set(IMAGE_CONVERT_STRING "impossible")
476 set(SPHINX_CONFIG_VARS_FILE ${SPHINX_INPUT_DIR}/conf-vars.py)
477 if (GMX_PYTHON_PACKAGE)
478 set(GMXAPI_PYTHON_STAGING_DIR ${CMAKE_BINARY_DIR}/python_packaging/src/gmxapi_staging)
479 # TODO: Resolve circular reference. We would like to get the CMake build-time directory for
480 # the gmxapi Python package from the _gmxapi target, as we do when building sample_restraint.
481 # Instead of the above hard-coded path, how can we do
482 # get_target_property(GMXAPI_PYTHON_STAGING_DIR _gmxapi staging_dir)
486 gmx_configure_version_file(conf-vars.py.cmakein ${SPHINX_CONFIG_VARS_FILE}
488 SPHINX_EXTENSION_PATH RELENG_PATH
490 EXPECTED_DOXYGEN_VERSION
491 EXPECTED_SPHINX_VERSION
492 CMAKE_MINIMUM_REQUIRED_VERSION REQUIRED_CUDA_VERSION
493 REQUIRED_OPENCL_MIN_VERSION
494 REQUIRED_CUDA_COMPUTE_CAPABILITY REGRESSIONTEST_VERSION
495 SOURCE_MD5SUM REGRESSIONTEST_MD5SUM_STRING
496 GMX_TNG_MINIMUM_REQUIRED_VERSION
497 GMX_LMFIT_REQUIRED_VERSION
498 GMX_MANUAL_DOI_STRING
499 GMX_SOURCE_DOI_STRING
500 GMXAPI_PYTHON_STAGING_DIR
501 COMMENT "Configuring Sphinx configuration file")
502 gmx_add_sphinx_input_file(${SPHINX_CONFIG_VARS_FILE})
503 gmx_add_sphinx_source_files(FILES ${SPHINX_SOURCE_FILES})
504 if (EXISTS ${RELENG_PATH}/docs/FileList.cmake)
505 include(${RELENG_PATH}/docs/FileList.cmake)
506 gmx_add_sphinx_source_files(
507 FROM ${RELENG_PATH}/docs TO dev-manual/releng PREFIX releng/docs/
508 FILES ${RELENG_SPHINX_FILES})
510 gmx_add_sphinx_source_files(FILES
511 dev-manual/releng/index.rst
515 gmx_add_sphinx_source_files(
518 gmxapi/userguide/install.rst
519 gmxapi/userguide/usage.rst
520 gmxapi/userguide/userguide.rst
523 if (GMX_PYTHON_PACKAGE)
524 gmx_add_sphinx_source_files(
526 gmxapi/userguide/pythonreference.rst
529 gmx_add_sphinx_source_files(
530 FROM ${CMAKE_CURRENT_SOURCE_DIR}/gmxapi/userguide-stub
532 FILES pythonreference.rst
536 gmx_add_sphinx_source_files(
538 ${REFERENCEMANUAL_SPHINX_FILES_GENERAL})
539 if (IMAGE_CONVERT_POSSIBLE)
540 gmx_add_sphinx_source_files(
542 ${REFERENCEMANUAL_SPHINX_FILES_WITH_IMAGES}
543 ${REFERENCEMANUAL_IMAGE_FILES})
544 gmx_add_sphinx_image_conversion_files(
546 ${REFERENCEMANUAL_IMAGE_FILES})
548 gmx_add_sphinx_input_target(sphinx-input-rst)
549 gmx_add_sphinx_image_conversion_target(sphinx-image-conversion)
550 add_custom_target(sphinx-input)
551 add_dependencies(sphinx-input sphinx-input-rst sphinx-image-conversion)
552 if (GMX_PYTHON_PACKAGE)
553 add_dependencies(sphinx-input _gmxapi)
555 # Remove other rst files from the build tree, since they confuse Sphinx.
556 # Skip generated files in onlinehelp/, and fragments.
557 # The latter do not cause issues with obsolete files, as they
558 # are not considered as Sphinx input files, but will only be
559 # included using an explicit .. include::.
560 gmx_remove_obsolete_sphinx_input_files("^(onlinehelp|fragments)/.*\\\\.rst$")
562 # TODO: Make this remove obsolete .rst files.
563 # TODO: This does not work in cross-compilation scenarios; disable up to
564 # the necessary level.
565 gmx_add_custom_output_target(sphinx-programs OUTPUT STAMP
566 COMMAND ${CMAKE_COMMAND} -E make_directory onlinehelp
567 COMMAND gmx -quiet help -export rst
569 WORKING_DIRECTORY ${SPHINX_INPUT_DIR}
570 COMMENT "Generating reStructuredText help")
571 # This dependency ensures that the directories exist before the
572 # executable tries to write things there.
573 add_dependencies(sphinx-programs sphinx-input)
575 # Make the INSTALL file for CPack for the tarball. This gets put
576 # into the tarball via the CPack rules below, which requires that
577 # the INSTALL file is in a separate directory by itself.
578 set(TEXT_INSTALL_GUIDE_OUTPUT_DIR "install-guide/text")
579 add_custom_target(install-guide
583 -w sphinx-install.log
584 -d ${CMAKE_CURRENT_BINARY_DIR}/install-guide/_doctrees
585 -c ${SPHINX_INPUT_DIR}
586 "${SPHINX_INPUT_DIR}/install-guide"
587 "${TEXT_INSTALL_GUIDE_OUTPUT_DIR}"
589 ${CMAKE_COMMAND} -E rename
590 ${TEXT_INSTALL_GUIDE_OUTPUT_DIR}/index.txt
591 ${TEXT_INSTALL_GUIDE_OUTPUT_DIR}/INSTALL
593 ${CMAKE_CURRENT_BINARY_DIR}
594 COMMENT "Building INSTALL with Sphinx"
597 add_dependencies(install-guide sphinx-input)
598 gmx_cpack_add_generated_source_directory(install-guide/text DESTINATION /)
600 # Sphinx cache with pickled ReST documents
601 set(SPHINX_CACHE_DIR "${CMAKE_CURRENT_BINARY_DIR}/_doctrees")
602 add_custom_target(webpage-sphinx
603 DEPENDS sphinx-programs
605 DEPENDS sphinx-image-conversion
608 ${CMAKE_COMMAND} -E make_directory ${SPHINX_INPUT_DIR}/_static
613 -d "${SPHINX_CACHE_DIR}"
614 "${SPHINX_INPUT_DIR}"
617 ${CMAKE_CURRENT_BINARY_DIR}
618 COMMENT "Building HTML documentation with Sphinx"
622 add_custom_target(man
627 -d ${SPHINX_CACHE_DIR}
630 ${CMAKE_CURRENT_BINARY_DIR}/man
631 COMMENT "Building man pages with Sphinx"
633 add_dependencies(man sphinx-input sphinx-programs)
635 # If requested, install the man pages built by the 'man' target
636 # created above. Nothing will be installed if the user did not
637 # manually build the target.
638 set(MAN_PAGE_DIR ${CMAKE_CURRENT_BINARY_DIR})
642 set(MANUAL_BUILD_IS_POSSIBLE OFF)
643 set(MANUAL_BUILD_NOT_POSSIBLE_REASON "Sphinx expected minimum version ${EXPECTED_SPHINX_VERSION} is not available")
645 add_custom_target(webpage-sphinx
646 COMMAND ${CMAKE_COMMAND} -E echo
647 "HTML pages cannot be built because Sphinx expected minimum version ${EXPECTED_SPHINX_VERSION} is not available"
649 add_custom_target(install-guide
650 COMMAND ${CMAKE_COMMAND} -E echo
651 "INSTALL cannot be built because Sphinx expected minimum version ${EXPECTED_SPHINX_VERSION} is not available"
653 add_custom_target(man
654 COMMAND ${CMAKE_COMMAND} -E echo
655 "man pages cannot be built because Sphinx expected minimum version ${EXPECTED_SPHINX_VERSION} is not available"
657 add_custom_target(sphinx-create-texman
658 COMMAND ${CMAKE_COMMAND} -E echo
659 "Cannot prepare LaTeX input files because Sphinx expected minimum version ${EXPECTED_SPHINX_VERSION} is not available"
661 add_custom_target(manual
662 COMMAND ${CMAKE_COMMAND} -E echo
663 "manual cannot be built because Sphinx expected minimum version ${EXPECTED_SPHINX_VERSION} is not available")
667 set(MAN_PAGE_DIR ${MAN_PAGE_DIR}/man)
668 # Trailing slash on directory is significant for
669 # install(DIRECTORY). See CMake docs.
670 install(DIRECTORY ${MAN_PAGE_DIR}/
671 DESTINATION ${CMAKE_INSTALL_MANDIR}/man1
672 COMPONENT man OPTIONAL
673 FILES_MATCHING PATTERN "*.1")
675 gmx_cpack_add_generated_source_directory(man)
677 # Determine whether we can build all the HTML pages and content linked from
678 # there. If not, construct an informative message if the user tries to
679 # build the target; most people never need to know, unless they've asked for
681 set(HTML_BUILD_IS_POSSIBLE ON)
682 set(HTML_BUILD_NOT_POSSIBLE_REASON)
683 set(HTML_BUILD_WARNINGS)
685 # Next, turn it off if any of the preconditions are unsatisified
686 if (NOT PythonInterp_FOUND)
687 set(HTML_BUILD_IS_POSSIBLE OFF)
688 set(HTML_BUILD_NOT_POSSIBLE_REASON "Python is required")
689 elseif (NOT SPHINX_FOUND)
690 # Hardly anything gets built if Sphinx is not available, so don't bother.
691 set(HTML_BUILD_IS_POSSIBLE OFF)
692 set(HTML_BUILD_NOT_POSSIBLE_REASON "Sphinx expected minimum version ${EXPECTED_SPHINX_VERSION} is required")
694 if (NOT MANUAL_BUILD_IS_POSSIBLE)
695 list(APPEND HTML_BUILD_WARNINGS
696 "Reference PDF manual was not built, so links to it do not work")
698 if (NOT DOXYGEN_EXECUTABLE)
699 list(APPEND HTML_BUILD_WARNINGS
700 "Doxygen was not available, so links to Doxygen do not work")
702 if (NOT DOXYGEN_DOT_EXECUTABLE)
703 list(APPEND HTML_BUILD_WARNINGS
704 "dot/graphviz was not found, so some graphs are missing")
707 if (HTML_BUILD_IS_POSSIBLE)
708 set(_webpage_target_properties)
709 if (HTML_BUILD_WARNINGS)
710 list(APPEND _webpage_target_properties
711 COMMAND ${CMAKE_COMMAND} -E echo
712 "webpage was built, but with the following limitations:")
713 foreach(_warning ${HTML_BUILD_WARNINGS})
714 list(APPEND _webpage_target_properties
715 COMMAND ${CMAKE_COMMAND} -E echo " - ${_warning}")
719 if (MANUAL_BUILD_IS_POSSIBLE)
720 # Make the PDF reference guide
721 # TODO Try to make the PDF arrive directly in ${HTML_OUTPUT_DIR}
722 # TODO Make this depend on the output of the manual build, so that the
723 # file actually gets copied multiple times.
724 set(_manual_target_location ${HTML_OUTPUT_DIR}/manual-${GMX_VERSION_STRING}.pdf)
726 OUTPUT ${_manual_target_location}
727 COMMAND ${CMAKE_COMMAND}
728 -E remove -f ${_manual_target_location}
729 COMMAND ${CMAKE_COMMAND}
730 -E copy ${CMAKE_CURRENT_BINARY_DIR}/manual/gromacs.pdf ${_manual_target_location}
733 list(APPEND _webpage_target_properties
734 DEPENDS ${_manual_target_location})
737 # The Doxygen configuration in doxygen/Doxyfile-common.cmakein
738 # makes all the Doxygen output directly in
739 # ${HTML_OUTPUT_DIR}/doxygen (and makes the directory if it needs
742 # Add a top-level target that builds everything related to the webpage,
743 # for Jenkins (and possibly others) to use
744 add_custom_target(webpage ${_webpage_target_properties}
745 COMMENT "Building webpage"
747 add_dependencies(webpage webpage-sphinx doxygen-all)
749 add_custom_target(webpage
750 COMMAND ${CMAKE_COMMAND} -E echo
751 "Cannot build webpage because ${HTML_BUILD_NOT_POSSIBLE_REASON}"
752 COMMENT "Webpage build not possible"