From: Roland Schulz Date: Sun, 24 Aug 2014 17:36:51 +0000 (-0400) Subject: Merge release-5-0 into master X-Git-Url: http://biod.pnpi.spb.ru/gitweb/?a=commitdiff_plain;h=f62a0e6795372dba0b6dc851fa736980bfd2195c;p=alexxy%2Fgromacs.git Merge release-5-0 into master Conflicts: install-guide/configure-install-guide.cmake.in applied to docs/configure-markdown.cmake.in Moved doxygen/cycle-suppressions.txt -> docs/doxygen/cycle-suppressions.txt docs/CMakeLists.txt: replaced PROJECT_VERSION with GMX_VERSION_STRING Change-Id: I61724a10a5331fdf747edd411dfa2f2256cd3f6b --- f62a0e6795372dba0b6dc851fa736980bfd2195c diff --cc docs/CMakeLists.txt index 0000000000,dd043ecd78..6947156d36 mode 000000,100644..100644 --- a/docs/CMakeLists.txt +++ b/docs/CMakeLists.txt @@@ -1,0 -1,305 +1,305 @@@ + # + # This file is part of the GROMACS molecular simulation package. + # + # Copyright (c) 2014, 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 + # pages), 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. + # + # All of the markdown content is configured, and we'd like to do that + # at build time rather than configure time (for speed, when not + # building markdown content). Also, the way they should be configured + # varies with whether the source is a tarball or repo, and which file + # is being configured. So several *_IS_POSSIBLE variables are used to + # direct the configure-time logic so that all appropriate variables + # are set by the time the configure-markdown.cmake.in file is + # configured, so that later it can do the configuration of all the + # markdown files and the right thing will happen in each case. + + # 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 ${HTML_OUTPUT_DIR}) + + if(${CMAKE_CURRENT_BINARY_DIR} STREQUAL ${CMAKE_CURRENT_SOURCE_DIR}) + set(MARKDOWN_CONFIGURE_IS_POSSIBLE off) + else() + set(MARKDOWN_CONFIGURE_IS_POSSIBLE on) + endif() + find_package(Pandoc) + + # Set up common infrastructure for configuring markdown at build time. + # Do replacement of CMake variables for version strings, etc. The use + # of configure-markdown.cmake defers until build time the + # configuration of markdown files, which could be faster for all the + # configurations that don't make the documentation even though it was + # possible, and helps avoid global re-configures if these files + # change. + set(SCRIPT_TO_CONFIGURE_MARKDOWN ${CMAKE_CURRENT_BINARY_DIR}/configure-markdown.cmake) + configure_file(configure-markdown.cmake.in + ${SCRIPT_TO_CONFIGURE_MARKDOWN} + @ONLY) + + # Makes a custom command to configure a Markdown file found in the + # current source directory with the configure-markdown.make script + # produced above. The result is placed in the current binary directory + # for future use. + function(configure_markdown MARKDOWN_FILE) + add_custom_command( + OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/${MARKDOWN_FILE} + COMMAND ${CMAKE_COMMAND} + -D FILE_TO_CONFIGURE=${CMAKE_CURRENT_SOURCE_DIR}/${MARKDOWN_FILE} + -D CONFIGURED_FILE=${CMAKE_CURRENT_BINARY_DIR}/${MARKDOWN_FILE} + -P ${SCRIPT_TO_CONFIGURE_MARKDOWN} + DEPENDS + ${SCRIPT_TO_CONFIGURE_MARKDOWN} + ${CMAKE_CURRENT_SOURCE_DIR}/${MARKDOWN_FILE} + COMMENT "Configuring Markdown" + VERBATIM + ) + endfunction() + + # Makes a custom command to make single-page HTML from Markdown. Takes + # a NAME argument for an output filename prefix, and a list of full + # paths to input files to concatenate with Pandoc into the HTML + # output. + function(make_markdown_html NAME) + add_custom_command( + OUTPUT ${HTML_OUTPUT_DIR}/${NAME}.html + COMMAND + ${PANDOC_EXECUTABLE} ${ARGN} -o ${HTML_OUTPUT_DIR}/${NAME}.html -s --toc --css buttondown.css + DEPENDS ${ARGN} + VERBATIM + ) + endfunction() + + # Makes a custom command to make PDF from Markdown. Takes a NAME + # argument for an output filename prefix, and a list of full paths to + # input files to concatenate with Pandoc into the PDF. + function(make_markdown_pdf NAME) + add_custom_command( + OUTPUT ${HTML_OUTPUT_DIR}/${NAME}.pdf + COMMAND + ${PANDOC_EXECUTABLE} ${ARGN} -o ${HTML_OUTPUT_DIR}/${NAME}.pdf -s --toc + DEPENDS ${ARGN} + VERBATIM + ) + endfunction() + + # function(make_markdown_multipage_html NAME) + # # Make the multi-page HTML install guide + # + # # TODO This is currently disabled, because the pandoc-specific + # # buttondown.css doesn't work with the different kind of output + # # makeinfo produces. When we understand better how we want to do + # # generation, decide whether we want multi-page HTML output and + # # how to make it work well. + # + # add_custom_command( + # OUTPUT ${HTML_OUTPUT_DIR}/${HTML_DIR}/index.html + # COMMAND + # ${PANDOC_EXECUTABLE} ${ARGN} -o ${NAME}.texi -s + # COMMAND + # ${MAKEINFO_EXECUTABLE} ${NAME}.texi --html -o ${HTML_OUTPUT_DIR}/${NAME} --css-ref buttondown.css + # DEPENDS ${ARGN} + # VERBATIM + # ) + # endfunction() + + add_subdirectory(install-guide) + add_subdirectory(user-guide) + add_subdirectory(man) + add_subdirectory(old-html) + add_subdirectory(doxygen) + + option(GMX_BUILD_WEBPAGE "Whether to try to configure to build the GROMACS static webpages" OFF) + mark_as_advanced(GMX_BUILD_WEBPAGE) + + option(GMX_BUILD_MANUAL "Whether to try to configure to build the PDF manual" ${GMX_BUILD_WEBPAGE}) + mark_as_advanced(GMX_BUILD_MANUAL) + if(GMX_BUILD_MANUAL) + # Make sure we only do detection of manual-building dependencies + # when the user opted in for that. + add_subdirectory(manual) + endif() + + set(HTML_BUILD_IS_POSSIBLE OFF) + # We can only configure to build the webpage if the user asked for it, + # the build is outside of the source dir, and all the components can + # be built. There's no need to be talkative if we fail - most people + # never need to know. + if(GMX_BUILD_WEBPAGE AND + GMX_BUILD_HELP AND + NOT ${CMAKE_BINARY_DIR} STREQUAL ${CMAKE_SOURCE_DIR} AND + MARKDOWN_CONFIGURE_IS_POSSIBLE AND + MANUAL_BUILD_IS_POSSIBLE AND + PANDOC_EXECUTABLE AND + DOXYGEN_EXECUTABLE AND + DOXYGEN_MSCGEN_EXECUTABLE) + set(HTML_BUILD_IS_POSSIBLE ON) + endif() + + if(HTML_BUILD_IS_POSSIBLE) + # For a real build of the webpage, the md5sum of the tarballs must + # already be known, and so we may as well require that the real + # build of the webpage take place from cmake run from the unpacked + # tarball. Then, the *_MD5SUM and *_TARBALL variables will be able + # to be set on the cmake command line (e.g. by a Jenkins job + # configuration), and we can require that they are set. For local + # building of the webpages (e.g. for debugging), those variables + # can be left unset, and if so, the download section will not be + # constructed. + if(NOT SOURCE_IS_SOURCE_DISTRIBUTION) + if (SOURCE_TARBALL AND SOURCE_MD5SUM AND + REGRESSIONTESTS_TARBALL AND REGRESSIONTESTS_MD5SUM) + set(BUILD_DOWNLOAD_SECTION on) + else() + set(BUILD_DOWNLOAD_SECTION off) + endif() + else() + foreach(VAR SOURCE_MD5SUM REGRESSIONTESTS_MD5SUM SOURCE_TARBALL REGRESSIONTESTS_TARBALL) + if(NOT DEFINED ${VAR}) + message(FATAL_ERROR "The build of the webpage requires that ${VAR} is set in the cmake cache, e.g. on the CMake command line") + endif() + endforeach() + set(BUILD_DOWNLOAD_SECTION on) + endif() + + # If building the webpage from the repo, then tarballs may not + # exist, and if so, it would not make sense to build that part of + # the front page from index.md. + if(BUILD_DOWNLOAD_SECTION) + set(DOWNLOAD_SECTION + "# Downloads + -* Source code - [gromacs-${PROJECT_VERSION}.tar.gz](gromacs-${PROJECT_VERSION}.tar.gz) ++* Source code - [gromacs-${GMX_VERSION_STRING}.tar.gz](gromacs-${GMX_VERSION_STRING}.tar.gz) + (md5sum ${SOURCE_MD5SUM}) + Other source code versions may be found at + -* Regression tests - [regressiontests-${PROJECT_VERSION}.tar.gz](regressiontests-${PROJECT_VERSION}.tar.gz) ++* Regression tests - [regressiontests-${GMX_VERSION_STRING}.tar.gz](regressiontests-${GMX_VERSION_STRING}.tar.gz) + (md5sum ${REGRESSIONTESTS_MD5SUM}) + ") + + # Copy the source tarball to the webpage output + add_custom_command( - OUTPUT ${HTML_OUTPUT_DIR}/gromacs-${PROJECT_VERSION}.tar.gz ++ OUTPUT ${HTML_OUTPUT_DIR}/gromacs-${GMX_VERSION_STRING}.tar.gz + COMMAND ${CMAKE_COMMAND} - -E copy ${SOURCE_TARBALL} ${HTML_OUTPUT_DIR}/gromacs-${PROJECT_VERSION}.tar.gz ++ -E copy ${SOURCE_TARBALL} ${HTML_OUTPUT_DIR}/gromacs-${GMX_VERSION_STRING}.tar.gz + VERBATIM + ) + + # Copy the regressiontests tarball to the webpage output + add_custom_command( - OUTPUT ${HTML_OUTPUT_DIR}/regressiontests-${PROJECT_VERSION}.tar.gz ++ OUTPUT ${HTML_OUTPUT_DIR}/regressiontests-${GMX_VERSION_STRING}.tar.gz + COMMAND ${CMAKE_COMMAND} - -E copy ${REGRESSIONTESTS_TARBALL} ${HTML_OUTPUT_DIR}/regressiontests-${PROJECT_VERSION}.tar.gz ++ -E copy ${REGRESSIONTESTS_TARBALL} ${HTML_OUTPUT_DIR}/regressiontests-${GMX_VERSION_STRING}.tar.gz + VERBATIM + ) + else() + set(DOWNLOAD_SECTION "") + endif() + + # Put the CSS in the HTML output directory + add_custom_command( + OUTPUT ${HTML_OUTPUT_DIR}/buttondown.css + COMMAND ${CMAKE_COMMAND} -E copy ${CMAKE_CURRENT_SOURCE_DIR}/buttondown.css ${HTML_OUTPUT_DIR}/buttondown.css + DEPENDS ${CMAKE_CURRENT_SOURCE_DIR}/buttondown.css + VERBATIM + ) + list(APPEND extra_webpage_dependencies ${HTML_OUTPUT_DIR}/buttondown.css) + + # Make the PDF reference guide + # TODO Try to make the PDF arrive directly in ${HTML_OUTPUT_DIR} + add_custom_command( - OUTPUT ${HTML_OUTPUT_DIR}/manual-${PROJECT_VERSION}.pdf ++ OUTPUT ${HTML_OUTPUT_DIR}/manual-${GMX_VERSION_STRING}.pdf + COMMAND ${CMAKE_COMMAND} - -E remove -f ${HTML_OUTPUT_DIR}/manual-${PROJECT_VERSION}.pdf ++ -E remove -f ${HTML_OUTPUT_DIR}/manual-${GMX_VERSION_STRING}.pdf + COMMAND ${CMAKE_COMMAND} - -E copy ${CMAKE_CURRENT_BINARY_DIR}/manual/gromacs.pdf ${HTML_OUTPUT_DIR}/manual-${PROJECT_VERSION}.pdf ++ -E copy ${CMAKE_CURRENT_BINARY_DIR}/manual/gromacs.pdf ${HTML_OUTPUT_DIR}/manual-${GMX_VERSION_STRING}.pdf + # UseLATEX.cmake makes a target called pdf, not ${CMAKE_CURRENT_BINARY_DIR}/manual/gromacs.pdf + DEPENDS pdf + VERBATIM + ) + + # TODO Move content from the "old" html output into the new user + # guide, or delete, as appropriate. + if(NOT SOURCE_IS_SOURCE_DISTRIBUTION) + # TODO If content remains here once the user guide is in + # decent shape, try to make the generated HTML arrive directly + # in ${HTML_OUTPUT_DIR} + add_custom_target(webpage-html + ${CMAKE_COMMAND} -E copy_directory old-html/final ${HTML_OUTPUT_DIR} + ) + add_dependencies(webpage-html html) + else() + # In the source distribution, the html pages are already + # built, so we can avoid making gmx via the html target + add_custom_target(webpage-html + ${CMAKE_COMMAND} -E copy_directory ${CMAKE_CURRENT_SOURCE_DIR}/old-html/final ${HTML_OUTPUT_DIR} + ) + 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 other dependencies for doing the webpage build from the real + # tarball + if(BUILD_DOWNLOAD_SECTION) + list(APPEND extra_webpage_dependencies - ${HTML_OUTPUT_DIR}/gromacs-${PROJECT_VERSION}.tar.gz - ${HTML_OUTPUT_DIR}/regressiontests-${PROJECT_VERSION}.tar.gz ++ ${HTML_OUTPUT_DIR}/gromacs-${GMX_VERSION_STRING}.tar.gz ++ ${HTML_OUTPUT_DIR}/regressiontests-${GMX_VERSION_STRING}.tar.gz + ) + endif() + + configure_markdown(index.md) + make_markdown_html(index ${CMAKE_CURRENT_BINARY_DIR}/index.md) + + # Add a top-level target for the others to hook onto + add_custom_target(webpage + DEPENDS + ${HTML_OUTPUT_DIR}/index.html + install-guide + user-guide - ${HTML_OUTPUT_DIR}/manual-${PROJECT_VERSION}.pdf ++ ${HTML_OUTPUT_DIR}/manual-${GMX_VERSION_STRING}.pdf + ${extra_webpage_dependencies} + VERBATIM + ) + add_dependencies(webpage webpage-html doc-all) + endif() diff --cc docs/configure-markdown.cmake.in index 0000000000,0f99002bea..60a5ab4c56 mode 000000,100644..100644 --- a/docs/configure-markdown.cmake.in +++ b/docs/configure-markdown.cmake.in @@@ -1,0 -1,15 +1,15 @@@ + # Helper script that defers configure_file of markdown until build + # time, so that changes to the files configured here don't trigger a + # global reconfigure + + # Now configure the values for all the variables that might later + # configure any of the markdown files. -set(PROJECT_VERSION "@PROJECT_VERSION@") ++set(PROJECT_VERSION "@GMX_VERSION_STRING@") + set(GMX_CMAKE_MINIMUM_REQUIRED_VERSION "@GMX_CMAKE_MINIMUM_REQUIRED_VERSION@") + set(REQUIRED_CUDA_VERSION "@REQUIRED_CUDA_VERSION@") + set(REQUIRED_CUDA_COMPUTE_CAPABILITY "@REQUIRED_CUDA_COMPUTE_CAPABILITY@") + set(REGRESSIONTEST_VERSION "@REGRESSIONTEST_VERSION@") + set(DOWNLOAD_SECTION "@DOWNLOAD_SECTION@") + + configure_file(${FILE_TO_CONFIGURE} + ${CONFIGURED_FILE} @ONLY) diff --cc docs/doxygen/CMakeLists.txt index 7401e9560c,1e334a4fa8..264f11446e --- a/docs/doxygen/CMakeLists.txt +++ b/docs/doxygen/CMakeLists.txt @@@ -93,10 -93,7 +93,9 @@@ if (DOXYGEN_FOUND "@INCLUDE = ${CMAKE_CURRENT_SOURCE_DIR}/Doxyfile-compact\n") endif() - FILE(COPY index.html DESTINATION ${CMAKE_CURRENT_BINARY_DIR}) configure_file(RunDoxygen.cmake.cmakein RunDoxygen.cmake @ONLY) + gmx_configure_version_file(Doxyfile-version.cmakein Doxyfile-version + TARGET doxygen-version) add_custom_target(doc-full ${CMAKE_COMMAND} -DDOCTYPE=full -P RunDoxygen.cmake WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} diff --cc docs/doxygen/cycle-suppressions.txt index b87e5469ca,0000000000..b87e5469ca mode 100644,000000..100644 --- a/docs/doxygen/cycle-suppressions.txt +++ b/docs/doxygen/cycle-suppressions.txt