# # This file is part of the GROMACS molecular simulation package. # # Copyright (c) 2014,2015,2016,2017,2018 by the GROMACS development team. # Copyright (c) 2019,2020,2021, by the GROMACS development team, led by # Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, # and including many others, as listed in the AUTHORS file in the # top-level source directory and at http://www.gromacs.org. # # GROMACS is free software; you can redistribute it and/or # modify it under the terms of the GNU Lesser General Public License # as published by the Free Software Foundation; either version 2.1 # of the License, or (at your option) any later version. # # GROMACS is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU # Lesser General Public License for more details. # # You should have received a copy of the GNU Lesser General Public # License along with GROMACS; if not, see # http://www.gnu.org/licenses, or write to the Free Software Foundation, # Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. # # If you want to redistribute modifications to GROMACS, please # consider that scientific software is very special. Version # control is crucial - bugs must be traceable. We will be happy to # consider code for inclusion in the official distribution, but # derived work must not be called official GROMACS. Details are found # in the README & COPYING files - if they are missing, get the # official version at http://www.gromacs.org. # # To help us fund GROMACS development, we humbly ask that you cite # the research papers on the package. Check out http://www.gromacs.org. # This directory provides a unified place for building all kinds of # GROMACS documentation. This includes some "static" content (Doxygen # code documentation, reference manual, install guide, old online HTML # images), and content generated from the gmx program for the various # tools (man and HTML pages). It also provides the "webpage" target, # that combines all of the above (except man pages in man format) into # a form suitable for automated deployment to the GROMACS website. It # also provides the INSTALL file for the tarball. # # The webpage is mostly built by Sphinx. Variable values for Sphinx # substitutions are configured by CMake (for things like version numbers), # using gmx_configure_version_file(). This happens during build time instead # of configure time, because 1) some of the version variables are only # available during build time, and 2) we don't want to do all the Sphinx setup # during configuration to save some time when not building the content. # All of the generated values get put into conf.py (generated from # conf.cmakein.py). set(SOURCE_MD5SUM "unknown" CACHE STRING "MD5 sum of the source tarball, normally used only for the pre-release webpage build") # REGRESSIONTEST_MD5SUM is set in cmake/gmxVersionInfo.cmake because it is used also in tests/CMakeLists.txt mark_as_advanced(SOURCE_MD5SUM) set(EXPECTED_DOXYGEN_VERSION 1.8.5) set(EXPECTED_SPHINX_VERSION 1.6.1) # By default, suppress output after first configuration. if(SPHINX_ALREADY_SEARCHED) set(Sphinx_FIND_QUIETLY ON) endif() find_package(Sphinx ${EXPECTED_SPHINX_VERSION} COMPONENTS pygments) set(SPHINX_ALREADY_SEARCHED TRUE CACHE BOOL "True if a search for Sphinx has already been done") mark_as_advanced(SPHINX_ALREADY_SEARCHED) # Even if we aren't going to make the full webpage, set up to put all # the documentation output in the same place, for convenience set(HTML_OUTPUT_DIR "${CMAKE_CURRENT_BINARY_DIR}/html") file(MAKE_DIRECTORY ${HTML_OUTPUT_DIR}) # Prepare directories for pdf/tex output set(TEX_OUTPUT_DIR "${CMAKE_CURRENT_BINARY_DIR}/manual") set(SPHINX_LATEX_FILE "${TEX_OUTPUT_DIR}/gromacs.tex") file(MAKE_DIRECTORY ${TEX_OUTPUT_DIR}) # The directory from which man pages will be installed; if it remains # empty, they will be silently skipped. set(MAN_PAGE_DIR) if (SOURCE_IS_SOURCE_DISTRIBUTION) # When building from the tarball, install the bundled man pages # (unless overridden). set(MAN_PAGE_DIR ${CMAKE_CURRENT_SOURCE_DIR}) endif() add_subdirectory(doxygen) # TODO: Consider whether this could just be replaced by using # GMX_DEVELOPER_BUILD to control this as well. option(GMX_BUILD_MANUAL "Whether to try to configure to build the PDF manual" OFF) mark_as_advanced(GMX_BUILD_MANUAL) set(MANUAL_BUILD_IS_POSSIBLE ON) set(MANUAL_BUILD_NOT_POSSIBLE_REASON) set(NO_IMAGE_CONVERT_REASON) if (NOT GMX_BUILD_MANUAL) # Make sure we only do detection of manual-building dependencies # when the user opted in for that. set(MANUAL_BUILD_IS_POSSIBLE OFF) set(MANUAL_BUILD_NOT_POSSIBLE_REASON "GMX_BUILD_MANUAL is not ON") elseif (BUILD_IS_INSOURCE) # UseLATEX.cmake does not work with an in-source build set(MANUAL_BUILD_IS_POSSIBLE OFF) set(MANUAL_BUILD_NOT_POSSIBLE_REASON "the build is in-source") else() include(manual/UseLATEX.cmake) if(NOT SPHINX_FOUND) set(MANUAL_BUILD_IS_POSSIBLE OFF) set(MANUAL_BUILD_NOT_POSSIBLE_REASON "Sphinx has not been found and is needed to create the LaTex input files") elseif(NOT PDFLATEX_COMPILER) set(MANUAL_BUILD_IS_POSSIBLE OFF) set(MANUAL_BUILD_NOT_POSSIBLE_REASON "pdflatex is not available") elseif(NOT IMAGE_CONVERT_POSSIBLE) set(MANUAL_BUILD_IS_POSSIBLE OFF) set(MANUAL_BUILD_NOT_POSSIBLE_REASON "a working form of ImageMagick convert is not available") set(NO_IMAGE_CONVERT_REASON "Can not convert files for online or pdf manual") # TODO Later, identify other dependencies like bibtex, # make_index, date, some graphics conversion program, # etc. Perhaps patch UseLATEX.cmake and contribute upstream. endif() endif() if (SPHINX_FOUND) # We need to have all the Sphinx input files in a single directory, and # since some of them are generated, we copy everything into the build tree, # to this directory. set(SPHINX_INPUT_DIR ${CMAKE_CURRENT_BINARY_DIR}/sphinx-input) set(SPHINX_EXTENSION_PATH ${CMAKE_CURRENT_SOURCE_DIR}) # As the manual build now depends also on Sphinx, the inclusion path needs # to be set after we know the basic information for Sphinx. add_subdirectory(manual) if (SOURCE_MD5SUM STREQUAL "unknown") # But for testing the webpage build (e.g. from the repo) we # need a default value. set(REGRESSIONTEST_MD5SUM_STRING "unknown") else() # The real build of the webpage happens from the tarball, and # this should be set to the matching MD5 sum. set(REGRESSIONTEST_MD5SUM_STRING "${REGRESSIONTEST_MD5SUM}") endif() # The reference manual still contains the individual sections from the # LaTeX document, with the files below grouped and annotated by chapter. set(REFERENCEMANUAL_SPHINX_FILES_GENERAL # Main index file, preface and introduction. reference-manual/index.rst reference-manual/preface.rst reference-manual/introduction.rst # Definitions and Units chapter reference-manual/definitions.rst # Topologies chapter reference-manual/topologies.rst reference-manual/topologies/particle-type.rst reference-manual/topologies/parameter-files.rst reference-manual/topologies/molecule-definition.rst reference-manual/topologies/constraint-algorithm-section.rst reference-manual/topologies/pdb2gmx-input-files.rst reference-manual/topologies/topology-file-formats.rst reference-manual/topologies/force-field-organization.rst # File formats chapter reference-manual/file-formats.rst # Run parameters and programs chapter reference-manual/run-parameters.rst # Implementation details chapter reference-manual/details.rst # Averages and fluctations chapter reference-manual/averages.rst # References reference-manual/references.rst # PNG formated plot files that don't need to be converted into PNG # for the web page. reference-manual/plots/GMX_logos/gmx_falcon_blue.png reference-manual/plots/adress.png reference-manual/plots/plotje.png reference-manual/plots/xvgr.png ) set(REFERENCEMANUAL_SPHINX_FILES_WITH_IMAGES # Algorithms chapter reference-manual/algorithms.rst reference-manual/algorithms/periodic-boundary-conditions.rst reference-manual/algorithms/group-concept.rst reference-manual/algorithms/molecular-dynamics.rst reference-manual/algorithms/shell-molecular-dynamics.rst reference-manual/algorithms/constraint-algorithms.rst reference-manual/algorithms/simulated-annealing.rst reference-manual/algorithms/stochastic-dynamics.rst reference-manual/algorithms/brownian-dynamics.rst reference-manual/algorithms/energy-minimization.rst reference-manual/algorithms/normal-mode-analysis.rst reference-manual/algorithms/free-energy-calculations.rst reference-manual/algorithms/replica-exchange.rst reference-manual/algorithms/essential-dynamics.rst reference-manual/algorithms/expanded-ensemble.rst reference-manual/algorithms/parallelization-domain-decomp.rst # Interaction functions and force fields chapter reference-manual/functions.rst reference-manual/functions/bonded-interactions.rst reference-manual/functions/force-field.rst reference-manual/functions/free-energy-interactions.rst reference-manual/functions/interaction-methods.rst reference-manual/functions/long-range-electrostatics.rst reference-manual/functions/long-range-vdw.rst reference-manual/functions/nonbonded-interactions.rst reference-manual/functions/polarization.rst reference-manual/functions/restraints.rst # Special topics chapter reference-manual/special.rst reference-manual/special/free-energy-implementation.rst reference-manual/special/pulling.rst reference-manual/special/awh.rst reference-manual/special/enforced-rotation.rst reference-manual/special/electric-fields.rst reference-manual/special/comp-electrophys.rst reference-manual/special/free-energy-pmf.rst reference-manual/special/remove-fast-dgf.rst reference-manual/special/viscosity-calculation.rst reference-manual/special/tabulated-interaction-functions.rst reference-manual/special/qmmm.rst reference-manual/special/vmd-imd.rst reference-manual/special/membrane-embedding.rst reference-manual/special/mimic-qmmm.rst reference-manual/special/density-guided-simulation.rst # Analysis chapter reference-manual/analysis.rst reference-manual/analysis/using-groups.rst reference-manual/analysis/looking-at-trajectory.rst reference-manual/analysis/general-properties.rst reference-manual/analysis/radial-distribution-function.rst reference-manual/analysis/correlation-function.rst reference-manual/analysis/curve-fitting.rst reference-manual/analysis/mean-square-displacement.rst reference-manual/analysis/bond-angle-dihedral.rst reference-manual/analysis/radius-of-gyration.rst reference-manual/analysis/rmsd.rst reference-manual/analysis/covariance-analysis.rst reference-manual/analysis/dihedral-pca.rst reference-manual/analysis/hydrogen-bonds.rst reference-manual/analysis/protein-related.rst reference-manual/analysis/interface-related.rst) # The image files have also been ordered by the respective # chapter they are included in in the reference manual set(REFERENCEMANUAL_IMAGE_FILES # General folder reference-manual/plots/decomp.pdf reference-manual/plots/dih.pdf reference-manual/plots/drift-all.pdf reference-manual/plots/f-angle.pdf reference-manual/plots/f-bond.pdf reference-manual/plots/fp-highres.pdf reference-manual/plots/int-mat.pdf reference-manual/plots/mdpar.pdf reference-manual/plots/parsort.pdf reference-manual/plots/ring.pdf reference-manual/plots/shiftf.pdf # Algorithms chapter reference-manual/algorithms/plots/dd-cells.pdf reference-manual/algorithms/plots/dd-tric.pdf reference-manual/algorithms/plots/flowchart.pdf reference-manual/algorithms/plots/free1.pdf reference-manual/algorithms/plots/free2.pdf reference-manual/algorithms/plots/leapfrog.pdf reference-manual/algorithms/plots/lincs.pdf reference-manual/algorithms/plots/maxwell.pdf reference-manual/algorithms/plots/mpmd-pme.pdf reference-manual/algorithms/plots/nstric.pdf reference-manual/algorithms/plots/par-lincs2.pdf reference-manual/algorithms/plots/pbctric.pdf reference-manual/algorithms/plots/rhododec.pdf reference-manual/algorithms/plots/truncoct.pdf reference-manual/algorithms/plots/verlet-drift.pdf # Interaction functions chapter reference-manual/functions/plots/angle.pdf reference-manual/functions/plots/bstretch.pdf reference-manual/functions/plots/chain.pdf reference-manual/functions/plots/dummies.pdf reference-manual/functions/plots/f-bham.pdf reference-manual/functions/plots/fbposres.pdf reference-manual/functions/plots/f-dih.pdf reference-manual/functions/plots/f-dr.pdf reference-manual/functions/plots/fig-02.pdf reference-manual/functions/plots/fig-04.pdf reference-manual/functions/plots/f-imps.pdf reference-manual/functions/plots/f-lj.pdf reference-manual/functions/plots/f-morse.pdf reference-manual/functions/plots/f-pr.pdf reference-manual/functions/plots/f-rbs.pdf reference-manual/functions/plots/ring-imp.pdf reference-manual/functions/plots/softcore.pdf reference-manual/functions/plots/gapsys-sc.pdf reference-manual/functions/plots/subst-im.pdf reference-manual/functions/plots/tetra-im.pdf reference-manual/functions/plots/vcrf.pdf reference-manual/functions/plots/vsite-4fdn.pdf # Special topics chapter reference-manual/special/plots/awh-invN.pdf reference-manual/special/plots/awh-pmfs.pdf reference-manual/special/plots/awh-sampleweights.pdf reference-manual/special/plots/awh-traj.pdf reference-manual/special/plots/compelsetup.pdf reference-manual/special/plots/dumaro.pdf reference-manual/special/plots/dumtypes.pdf reference-manual/special/plots/equipotential.pdf reference-manual/special/plots/field.pdf reference-manual/special/plots/gaussians.pdf reference-manual/special/plots/lambda-values.pdf reference-manual/special/plots/pulldirrel.pdf reference-manual/special/plots/pull.pdf reference-manual/special/plots/pullref.pdf reference-manual/special/plots/rotation.pdf # Analysis chapter reference-manual/analysis/plots/dih-def.pdf reference-manual/analysis/plots/distm.pdf reference-manual/analysis/plots/dssp.pdf reference-manual/analysis/plots/hbond-insert.pdf reference-manual/analysis/plots/hbond.pdf reference-manual/analysis/plots/hpr-wheel.pdf reference-manual/analysis/plots/msdwater.pdf reference-manual/analysis/plots/ngmxdump.pdf reference-manual/analysis/plots/phipsi.pdf reference-manual/analysis/plots/rama.pdf reference-manual/analysis/plots/rdfO-O.pdf reference-manual/analysis/plots/rdf.pdf reference-manual/analysis/plots/sgangle.pdf ) set(SPHINX_SOURCE_FILES index.rst download.rst links.dat dev-manual/build-system.rst dev-manual/change-management.rst dev-manual/commitstyle.rst dev-manual/containers.rst dev-manual/documentation-generation.rst dev-manual/contribute.rst dev-manual/doxygen.rst dev-manual/error-handling.rst dev-manual/formatting.rst dev-manual/gitlab-ci.rst dev-manual/gmxtree.rst dev-manual/includestyle.rst dev-manual/index.rst dev-manual/infrastructure.rst dev-manual/jenkins.rst dev-manual/known-issues.rst dev-manual/language-features.rst dev-manual/naming.rst dev-manual/overview.rst dev-manual/physical_validation.rst dev-manual/redmine-states.png dev-manual/relocatable-binaries.rst dev-manual/reportstyle.rst dev-manual/style.rst dev-manual/testutils.rst dev-manual/tools.rst dev-manual/code-formatting.rst fragments/doxygen-links.rst how-to/index.rst how-to/beginners.rst how-to/topology.rst how-to/special.rst how-to/visualize.rst install-guide/index.rst release-notes/index.rst release-notes/2022/major/highlights.rst release-notes/2022/major/features.rst release-notes/2022/major/performance.rst release-notes/2022/major/tools.rst release-notes/2022/major/bugs-fixed.rst release-notes/2022/major/removed-functionality.rst release-notes/2022/major/deprecated-functionality.rst release-notes/2022/major/portability.rst release-notes/2022/major/miscellaneous.rst release-notes/2022/major/api.rst release-notes/2021/2021.4.rst release-notes/2021/2021.3.rst release-notes/2021/2021.2.rst release-notes/2021/2021.1.rst release-notes/2021/major/highlights.rst release-notes/2021/major/features.rst release-notes/2021/major/performance.rst release-notes/2021/major/tools.rst release-notes/2021/major/bugs-fixed.rst release-notes/2021/major/removed-functionality.rst release-notes/2021/major/deprecated-functionality.rst release-notes/2021/major/portability.rst release-notes/2021/major/miscellaneous.rst release-notes/2020/2020.1.rst release-notes/2020/2020.2.rst release-notes/2020/2020.3.rst release-notes/2020/2020.4.rst release-notes/2020/2020.5.rst release-notes/2020/2020.6.rst release-notes/2020/major/highlights.rst release-notes/2020/major/features.rst release-notes/2020/major/performance.rst release-notes/2020/major/tools.rst release-notes/2020/major/bugs-fixed.rst release-notes/2020/major/removed-functionality.rst release-notes/2020/major/deprecated-functionality.rst release-notes/2020/major/portability.rst release-notes/2020/major/miscellaneous.rst release-notes/2019/2019.6.rst release-notes/2019/2019.5.rst release-notes/2019/2019.4.rst release-notes/2019/2019.3.rst release-notes/2019/2019.2.rst release-notes/2019/2019.1.rst release-notes/2019/major/highlights.rst release-notes/2019/major/features.rst release-notes/2019/major/performance.rst release-notes/2019/major/tools.rst release-notes/2019/major/bugs-fixed.rst release-notes/2019/major/removed-functionality.rst release-notes/2019/major/deprecated-functionality.rst release-notes/2019/major/portability.rst release-notes/2019/major/miscellaneous.rst release-notes/2018/2018.7.rst release-notes/2018/2018.6.rst release-notes/2018/2018.5.rst release-notes/2018/2018.4.rst release-notes/2018/2018.3.rst release-notes/2018/2018.2.rst release-notes/2018/2018.1.rst release-notes/2018/major/highlights.rst release-notes/2018/major/features.rst release-notes/2018/major/performance.rst release-notes/2018/major/tools.rst release-notes/2018/major/bugs-fixed.rst release-notes/2018/major/removed-features.rst release-notes/2018/major/portability.rst release-notes/2018/major/miscellaneous.rst release-notes/2016/2016.5.rst release-notes/2016/2016.4.rst release-notes/2016/2016.3.rst release-notes/2016/2016.2.rst release-notes/2016/2016.1.rst release-notes/2016/major/highlights.rst release-notes/2016/major/new-features.rst release-notes/2016/major/performance.rst release-notes/2016/major/tools.rst release-notes/2016/major/bugs-fixed.rst release-notes/2016/major/removed-features.rst release-notes/2016/major/miscellaneous.rst release-notes/older/index.rst # the entry for user-guide/index.rst should not appear here, # as it will be included conditionally further down depending on # if the documentation will be build with the full reference # manual or without. user-guide/cmdline.rst user-guide/deprecation-policy.rst user-guide/environment-variables.rst user-guide/faq.rst user-guide/floating-point.rst user-guide/flow.rst user-guide/force-fields.rst user-guide/getting-started.rst user-guide/index.rst user-guide/known-issues.rst user-guide/managing-simulations.rst user-guide/mdp-options.rst user-guide/mdrun-features.rst user-guide/mdrun-performance.rst user-guide/run-time-errors.rst user-guide/security.rst user-guide/system-preparation.rst user-guide/terminology.rst ) include(SphinxMacros.cmake) gmx_init_sphinx_setup(${SPHINX_INPUT_DIR}) # set temporary variables for doi inclusion # into the manual, plain string + some wrapping # for release builds, and dummy string for non-release # builds if("${GMX_MANUAL_DOI}" STREQUAL "") # empty string means no doi, set dummy text set(GMX_MANUAL_DOI_STRING "This is not a release build of GROMACS, so please reference") set(GMX_MANUAL_DOI_STRING "${GMX_MANUAL_DOI_STRING} one of the GROMACS papers and the base release of the manual.") else() # release version, set plain old boring string set(GMX_MANUAL_DOI_STRING "Please reference this documentation as https://doi.org/${GMX_MANUAL_DOI}.") endif() # same for source doi, but modify the text if("${GMX_SOURCE_DOI}" STREQUAL "") # empty string means no release build set(GMX_SOURCE_DOI_STRING "This is not a release build of GROMACS. Please reference one of the") set(GMX_SOURCE_DOI_STRING "${GMX_SOURCE_DOI_STRING} GROMACS papers, as well as the base release that this version is built from.") set(GMX_SOURCE_DOI_STRING "${GMX_SOURCE_DOI_STRING} Also, please state what modifcations have been performed or where the version") set(GMX_SOURCE_DOI_STRING "${GMX_SOURCE_DOI_STRING} was sourced from.") else() # release version, give them a doi url string set(GMX_SOURCE_DOI_STRING "To cite the source code for this release, please cite") set(GMX_SOURCE_DOI_STRING "${GMX_SOURCE_DOI_STRING} https://doi.org/${GMX_SOURCE_DOI}.") endif() if(IMAGE_CONVERT_POSSIBLE) set(IMAGE_CONVERT_STRING "possible") else() set(IMAGE_CONVERT_STRING "impossible") endif() set(SPHINX_CONFIG_FILE ${SPHINX_INPUT_DIR}/conf.py) if (GMX_PYTHON_PACKAGE) set(GMXAPI_PYTHON_STAGING_DIR ${CMAKE_BINARY_DIR}/python_packaging/src/gmxapi_staging) # TODO: Resolve circular reference. We would like to get the CMake build-time directory for # the gmxapi Python package from the _gmxapi target, as we do when building sample_restraint. # Instead of the above hard-coded path, how can we do # get_target_property(GMXAPI_PYTHON_STAGING_DIR _gmxapi staging_dir) # in this context? endif () gmx_configure_version_file( conf.cmakein.py ${SPHINX_CONFIG_FILE} EXTRA_VARS CMAKE_MINIMUM_REQUIRED_VERSION EXPECTED_DOXYGEN_VERSION EXPECTED_SPHINX_VERSION GMX_ADMIN_DIR GMX_LMFIT_REQUIRED_VERSION GMX_MANUAL_DOI_STRING GMX_TNG_MINIMUM_REQUIRED_VERSION GMX_SOURCE_DOI_STRING GMXAPI_PYTHON_STAGING_DIR IMAGE_CONVERT_STRING REGRESSIONTEST_VERSION REQUIRED_CUDA_COMPUTE_CAPABILITY REQUIRED_CUDA_VERSION REQUIRED_OPENCL_MIN_VERSION REGRESSIONTEST_MD5SUM_STRING RELENG_PATH SOURCE_MD5SUM SPHINX_EXTENSION_PATH COMMENT "Configuring Sphinx configuration file") gmx_add_sphinx_input_file(${SPHINX_CONFIG_FILE}) gmx_add_sphinx_source_files(FILES ${SPHINX_SOURCE_FILES}) if (EXISTS ${RELENG_PATH}/docs/FileList.cmake) include(${RELENG_PATH}/docs/FileList.cmake) gmx_add_sphinx_source_files( FROM ${RELENG_PATH}/docs TO dev-manual/releng PREFIX releng/docs/ FILES ${RELENG_SPHINX_FILES}) else() gmx_add_sphinx_source_files(FILES dev-manual/releng/index.rst ) endif() gmx_add_sphinx_source_files( FILES gmxapi/index.rst gmxapi/userguide/install.rst gmxapi/userguide/usage.rst gmxapi/userguide/userguide.rst ) if (GMX_PYTHON_PACKAGE) gmx_add_sphinx_source_files( FILES gmxapi/userguide/pythonreference.rst ) else() gmx_add_sphinx_source_files( FROM ${CMAKE_CURRENT_SOURCE_DIR}/gmxapi/userguide-stub TO gmxapi/userguide/ FILES pythonreference.rst ) endif () gmx_add_sphinx_source_files( FILES nblib/index.rst nblib/guide-to-writing-MD-programs.rst ) gmx_add_sphinx_source_files( FILES ${REFERENCEMANUAL_SPHINX_FILES_GENERAL}) if (IMAGE_CONVERT_POSSIBLE) gmx_add_sphinx_source_files( FILES ${REFERENCEMANUAL_SPHINX_FILES_WITH_IMAGES} ${REFERENCEMANUAL_IMAGE_FILES}) gmx_add_sphinx_image_conversion_files( FILES ${REFERENCEMANUAL_IMAGE_FILES}) endif() gmx_add_sphinx_input_target(sphinx-input-rst) gmx_add_sphinx_image_conversion_target(sphinx-image-conversion) add_custom_target(sphinx-input) add_dependencies(sphinx-input sphinx-input-rst sphinx-image-conversion) if (GMX_PYTHON_PACKAGE) add_dependencies(sphinx-input _gmxapi) endif() # Remove other rst files from the build tree, since they confuse Sphinx. # Skip generated files in onlinehelp/, and fragments. # The latter do not cause issues with obsolete files, as they # are not considered as Sphinx input files, but will only be # included using an explicit .. include::. gmx_remove_obsolete_sphinx_input_files("^(onlinehelp|fragments)/.*\\\\.rst$") # TODO: Make this remove obsolete .rst files. # TODO: This does not work in cross-compilation scenarios; disable up to # the necessary level. gmx_add_custom_output_target(sphinx-programs OUTPUT STAMP COMMAND ${CMAKE_COMMAND} -E make_directory onlinehelp COMMAND gmx -quiet help -export rst DEPENDS gmx WORKING_DIRECTORY ${SPHINX_INPUT_DIR} COMMENT "Generating reStructuredText help") # This dependency ensures that the directories exist before the # executable tries to write things there. add_dependencies(sphinx-programs sphinx-input) # Make the INSTALL file for CPack for the tarball. This gets put # into the tarball via the CPack rules below, which requires that # the INSTALL file is in a separate directory by itself. set(TEXT_INSTALL_GUIDE_OUTPUT_DIR "install-guide/text") add_custom_target(install-guide COMMAND ${SPHINX_EXECUTABLE} -q -b text -w sphinx-install.log -d ${CMAKE_CURRENT_BINARY_DIR}/install-guide/_doctrees -c ${SPHINX_INPUT_DIR} "${SPHINX_INPUT_DIR}/install-guide" "${TEXT_INSTALL_GUIDE_OUTPUT_DIR}" COMMAND ${CMAKE_COMMAND} -E rename ${TEXT_INSTALL_GUIDE_OUTPUT_DIR}/index.txt ${TEXT_INSTALL_GUIDE_OUTPUT_DIR}/INSTALL WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} COMMENT "Building INSTALL with Sphinx" VERBATIM ) add_dependencies(install-guide sphinx-input) gmx_cpack_add_generated_source_directory(install-guide/text DESTINATION /) # Sphinx cache with pickled ReST documents set(SPHINX_CACHE_DIR "${CMAKE_CURRENT_BINARY_DIR}/_doctrees") set(SPHINX_CONFIG_OVERRIDES "") if (GMX_DEVELOPER_BUILD) set(SPHINX_CONFIG_OVERRIDES "-Dtodo_include_todos=1") endif() add_custom_target(webpage-sphinx DEPENDS sphinx-programs DEPENDS sphinx-input DEPENDS sphinx-image-conversion DEPENDS manual COMMAND ${CMAKE_COMMAND} -E make_directory ${SPHINX_INPUT_DIR}/_static COMMAND ${SPHINX_EXECUTABLE} -q -b html -w sphinx-html.log -d "${SPHINX_CACHE_DIR}" ${SPHINX_CONFIG_OVERRIDES} "${SPHINX_INPUT_DIR}" "${HTML_OUTPUT_DIR}" WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} COMMENT "Building HTML documentation with Sphinx" VERBATIM ) add_custom_target(man COMMAND ${SPHINX_EXECUTABLE} -q -b man -w sphinx-man.log -d ${SPHINX_CACHE_DIR} -t do_man ${SPHINX_INPUT_DIR} ${CMAKE_CURRENT_BINARY_DIR}/man COMMENT "Building man pages with Sphinx" VERBATIM) add_dependencies(man sphinx-input sphinx-programs) if (GMX_BUILD_HELP) # If requested, install the man pages built by the 'man' target # created above. Nothing will be installed if the user did not # manually build the target. set(MAN_PAGE_DIR ${CMAKE_CURRENT_BINARY_DIR}) endif() else() set(MANUAL_BUILD_IS_POSSIBLE OFF) set(MANUAL_BUILD_NOT_POSSIBLE_REASON "Sphinx expected minimum version ${EXPECTED_SPHINX_VERSION} is not available") add_custom_target(webpage-sphinx COMMAND ${CMAKE_COMMAND} -E echo "HTML pages cannot be built because Sphinx expected minimum version ${EXPECTED_SPHINX_VERSION} is not available" VERBATIM) add_custom_target(install-guide COMMAND ${CMAKE_COMMAND} -E echo "INSTALL cannot be built because Sphinx expected minimum version ${EXPECTED_SPHINX_VERSION} is not available" VERBATIM) add_custom_target(man COMMAND ${CMAKE_COMMAND} -E echo "man pages cannot be built because Sphinx expected minimum version ${EXPECTED_SPHINX_VERSION} is not available" VERBATIM) add_custom_target(sphinx-create-texman COMMAND ${CMAKE_COMMAND} -E echo "Cannot prepare LaTeX input files because Sphinx expected minimum version ${EXPECTED_SPHINX_VERSION} is not available" VERBATIM) add_custom_target(manual COMMAND ${CMAKE_COMMAND} -E echo "manual cannot be built because Sphinx expected minimum version ${EXPECTED_SPHINX_VERSION} is not available") endif() if (MAN_PAGE_DIR) set(MAN_PAGE_DIR ${MAN_PAGE_DIR}/man) # Trailing slash on directory is significant for # install(DIRECTORY). See CMake docs. install(DIRECTORY ${MAN_PAGE_DIR}/ DESTINATION ${CMAKE_INSTALL_MANDIR}/man1 COMPONENT man OPTIONAL FILES_MATCHING PATTERN "*.1") endif() gmx_cpack_add_generated_source_directory(man) # Determine whether we can build all the HTML pages and content linked from # there. If not, construct an informative message if the user tries to # build the target; most people never need to know, unless they've asked for # the webpage build. set(HTML_BUILD_IS_POSSIBLE ON) set(HTML_BUILD_NOT_POSSIBLE_REASON) set(HTML_BUILD_WARNINGS) # Next, turn it off if any of the preconditions are unsatisified if (NOT Python3_Interpreter_FOUND) set(HTML_BUILD_IS_POSSIBLE OFF) set(HTML_BUILD_NOT_POSSIBLE_REASON "Python is required") elseif (NOT SPHINX_FOUND) # Hardly anything gets built if Sphinx is not available, so don't bother. set(HTML_BUILD_IS_POSSIBLE OFF) set(HTML_BUILD_NOT_POSSIBLE_REASON "Sphinx expected minimum version ${EXPECTED_SPHINX_VERSION} is required") endif() if (NOT MANUAL_BUILD_IS_POSSIBLE) list(APPEND HTML_BUILD_WARNINGS "Reference PDF manual was not built, so links to it do not work") endif() if (NOT DOXYGEN_EXECUTABLE) list(APPEND HTML_BUILD_WARNINGS "Doxygen was not available, so links to Doxygen do not work") endif() if (NOT DOXYGEN_DOT_EXECUTABLE) list(APPEND HTML_BUILD_WARNINGS "dot/graphviz was not found, so some graphs are missing") endif() if (HTML_BUILD_IS_POSSIBLE) set(_webpage_target_properties) if (HTML_BUILD_WARNINGS) list(APPEND _webpage_target_properties COMMAND ${CMAKE_COMMAND} -E echo "webpage was built, but with the following limitations:") foreach(_warning ${HTML_BUILD_WARNINGS}) list(APPEND _webpage_target_properties COMMAND ${CMAKE_COMMAND} -E echo " - ${_warning}") endforeach() endif() if (MANUAL_BUILD_IS_POSSIBLE) # Make the PDF reference guide # TODO Try to make the PDF arrive directly in ${HTML_OUTPUT_DIR} # TODO Make this depend on the output of the manual build, so that the # file actually gets copied multiple times. set(_manual_target_location ${HTML_OUTPUT_DIR}/manual-${GMX_VERSION_STRING}.pdf) add_custom_command( OUTPUT ${_manual_target_location} COMMAND ${CMAKE_COMMAND} -E remove -f ${_manual_target_location} COMMAND ${CMAKE_COMMAND} -E copy ${CMAKE_CURRENT_BINARY_DIR}/manual/gromacs.pdf ${_manual_target_location} DEPENDS manual VERBATIM) list(APPEND _webpage_target_properties DEPENDS ${_manual_target_location}) endif() # The Doxygen configuration in doxygen/Doxyfile-common.cmakein # makes all the Doxygen output directly in # ${HTML_OUTPUT_DIR}/doxygen (and makes the directory if it needs # to). # Add a top-level target that builds everything related to the webpage, # for CI (and possibly others) to use add_custom_target(webpage ${_webpage_target_properties} COMMENT "Building webpage" VERBATIM) add_dependencies(webpage webpage-sphinx doxygen-all) else() add_custom_target(webpage COMMAND ${CMAKE_COMMAND} -E echo "Cannot build webpage because ${HTML_BUILD_NOT_POSSIBLE_REASON}" COMMENT "Webpage build not possible" VERBATIM) endif()