From: Mark Abraham Date: Mon, 7 Jul 2014 07:43:13 +0000 (+0200) Subject: Unify documentation for webpage build X-Git-Url: http://biod.pnpi.spb.ru/gitweb/?a=commitdiff_plain;h=9f500c778aa7eb0a8540d70e061ba19ca0768c8f;p=alexxy%2Fgromacs.git Unify documentation for webpage build The new webpage build can be run either from a code repo (for development), or from the unpacked source tarball (for actual deployment). The latter is useful to ensure the documentation reflects the tarball, and because the tarballs and their md5sum values must be available for building the webpage. A Jenkins flow job can build the tarballs and then construct the webpage for automated delivery. The machinery is active only if GMX_BUILD_WEBPAGE is set (and other pieces in place), so will be transparent to normal users. Created configurable top-level index.md inside the new docs top-level directory. Various components have moved into this directory, but each can still be built independently. Imported some basic (but pandoc-specific) CSS from https://gist.github.com/ryangray/1882525 Made a new top-level index.md, and made it build HTML with Pandoc and use the CSS. Later, we can consider making the whole static site build work with some generator, e.g. to make links automatically. Established CMake variables for configuring the webpage build with the names of tarballs and their md5sum values. Builds from the repo don't include this part of the webpage. Moved the install guide into the new docs directory. Minor fixes to header levels. Generated PDF install guide also. Used PANDOC_EXECUTABLE instead of hard-coded "pandoc." Made it use the CSS. Moved reference manual build into the new docs directory, and linked its default setting to GMX_BUILD_WEBPAGE. Moved old html guide content into the new docs directory. This still installs in the old way. Fixed broken links for xpm2ps and grompp. Added rudimentary hdb.html to fix missing link target. Removed text that linked to ancient material that no longer semes to exist. Moved doxygen generation into the new docs directory. The useful output now goes directly to build/docs/html, and logs to build/docs/doxygen. Bumped copyright years to keep uncrustify script happy. Bumped top-level CMakeLists.txt and CPackInit.cmake to check for the new correct paths when building tarballs. Added config file for linkchecker to help automate checking the links all work. Refs #1242 Change-Id: I8e5cf98b2997b76f56b24f45262c9c9eebf9900e --- diff --git a/.gitattributes b/.gitattributes index e9739ac874..46d10516df 100644 --- a/.gitattributes +++ b/.gitattributes @@ -25,11 +25,11 @@ cmake/ThreadMPI.cmake !filter cmake/Platform/BluegeneQ*.cmake !filter cmake/*.c !filter cmake/*.c.cmakein !filter -doxygen/Doxyfile-*.cmakein !filter -doxygen/*.cpp !filter -doxygen/examples/*.cpp filter=uncrustify_only -doxygen/examples/*.c filter=uncrustify_only -manual/UseLATEX.cmake !filter +docs/doxygen/Doxyfile-*.cmakein !filter +docs/doxygen/*.cpp !filter +docs/doxygen/examples/*.cpp filter=uncrustify_only +docs/doxygen/examples/*.c filter=uncrustify_only +docs/manual/UseLATEX.cmake !filter scripts/GMXRC.* !filter scripts/make_gromos_rtp.py !filter src/contrib/* !filter diff --git a/CMakeLists.txt b/CMakeLists.txt index f991ff0cb4..ed24af9615 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -148,7 +148,7 @@ set(CPACK_PROJECT_CONFIG_FILE "${CMAKE_SOURCE_DIR}/CPackInit.cmake") # This variable is a list of pairs of names of source and destination # directories. Most of these are used for content GROMACS generates as # part of the configuration or build. -set(CPACK_SOURCE_INSTALLED_DIRECTORIES "${CMAKE_SOURCE_DIR};/;${CMAKE_BINARY_DIR}/src/programs/completion;src/programs/completion;${CMAKE_BINARY_DIR}/share/man/man1;share/man/man1;${CMAKE_BINARY_DIR}/share/man/man7;share/man/man7;${CMAKE_BINARY_DIR}/share/html/final;share/html/final;${CMAKE_BINARY_DIR}/install-guide/final;/") +set(CPACK_SOURCE_INSTALLED_DIRECTORIES "${CMAKE_SOURCE_DIR};/;${CMAKE_BINARY_DIR}/src/programs/completion;src/programs/completion;${CMAKE_BINARY_DIR}/docs/man/man1;docs/man/man1;${CMAKE_BINARY_DIR}/docs/man/man7;docs/man/man7;${CMAKE_BINARY_DIR}/docs/old-html/final;docs/old-html/final;${CMAKE_BINARY_DIR}/docs/install-guide/final;/") set(CPACK_PACKAGE_CONTACT "gmx-users@gromacs.org") set(CPACK_GMX_BUILD_HELP "${GMX_BUILD_HELP}") #Works even though GMX_BUILD_HELP is defined later because it is off by default. @@ -922,8 +922,7 @@ if (BUILD_TESTING) endif() if (NOT GMX_BUILD_MDRUN_ONLY) - add_subdirectory(doxygen) - add_subdirectory(install-guide) + add_subdirectory(docs) add_subdirectory(share) add_subdirectory(scripts) endif() @@ -953,15 +952,3 @@ ADD_CUSTOM_TARGET(uninstall ########################### set_directory_properties(PROPERTIES ADDITIONAL_MAKE_CLEAN_FILES "install_manifest.txt") - -######################################################################## -# Manual # -######################################################################## - -option(GMX_BUILD_MANUAL "Whether to try to configure to build the PDF manual" OFF) -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() diff --git a/CPackInit.cmake b/CPackInit.cmake index 12be4fdeef..498b034306 100644 --- a/CPackInit.cmake +++ b/CPackInit.cmake @@ -35,11 +35,11 @@ #TODO: add check that source doesn't contain any untracked files if(NOT CPACK_INSTALL_CMAKE_PROJECTS) #building source package get_filename_component(CMAKE_BINARY_DIR ${CPACK_OUTPUT_CONFIG_FILE} PATH) - if (NOT EXISTS "${CMAKE_BINARY_DIR}/share/man/man1/gmx-view.1" OR - NOT EXISTS "${CMAKE_BINARY_DIR}/install-guide/final/INSTALL" OR - NOT EXISTS "${CMAKE_BINARY_DIR}/share/html/final/online.html" OR + if (NOT EXISTS "${CMAKE_BINARY_DIR}/docs/man/man1/gmx-view.1" OR + NOT EXISTS "${CMAKE_BINARY_DIR}/docs/install-guide/final/INSTALL" OR + NOT EXISTS "${CMAKE_BINARY_DIR}/docs/old-html/final/online.html" OR NOT EXISTS "${CMAKE_BINARY_DIR}/src/programs/completion/gmx-completion.bash" OR - NOT EXISTS "${CMAKE_BINARY_DIR}/share/html/final/programs/gmx-view.html") + NOT EXISTS "${CMAKE_BINARY_DIR}/docs/old-html/final/programs/gmx-view.html") message(FATAL_ERROR "To create a complete source package, bash completions, " "man and HTML pages, and INSTALL need to be generated. " diff --git a/docs/CMakeLists.txt b/docs/CMakeLists.txt new file mode 100644 index 0000000000..454758697f --- /dev/null +++ b/docs/CMakeLists.txt @@ -0,0 +1,233 @@ +# +# 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. + +# 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}) + +add_subdirectory(install-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() + +find_package(Pandoc) + +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 + INSTALL_GUIDE_BUILD_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), the *_MD5SUM + # variables need a fallback. + 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 ${VAR} is set in the cmake cache, e.g. on the CMake command line") + endif() + endforeach() + set(BUILD_DOWNLOAD_SECTION on) + endif() + + # If building from the repo, then tarballs may not exist, and if + # so, it would not make sense to build that part of the front + # page. + if(BUILD_DOWNLOAD_SECTION) + set(DOWNLOAD_SECTION +"# Downloads + +* Source code - [gromacs-${PROJECT_VERSION}.tar.gz](gromacs-${PROJECT_VERSION}.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) + (md5sum ${REGRESSIONTESTS_MD5SUM}) +") + + # Copy the source tarball to the webpage output + add_custom_command( + OUTPUT ${HTML_OUTPUT_DIR}/gromacs-${PROJECT_VERSION}.tar.gz + COMMAND ${CMAKE_COMMAND} + -E copy ${SOURCE_TARBALL} ${HTML_OUTPUT_DIR}/gromacs-${PROJECT_VERSION}.tar.gz + VERBATIM + ) + + # Copy the regressiontests tarball to the webpage output + add_custom_command( + OUTPUT ${HTML_OUTPUT_DIR}/regressiontests-${PROJECT_VERSION}.tar.gz + COMMAND ${CMAKE_COMMAND} + -E copy ${REGRESSIONTESTS_TARBALL} ${HTML_OUTPUT_DIR}/regressiontests-${PROJECT_VERSION}.tar.gz + VERBATIM + ) + else() + set(DOWNLOAD_SECTION "") + endif() + + # Do replacement of CMake variables for version strings, etc. + configure_file(configure-html.cmake.in + ${CMAKE_CURRENT_BINARY_DIR}/configure-html.cmake + @ONLY) + + # This defers until build time the configuration of + # index.md, which could be faster + add_custom_command( + OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/index.md + COMMAND ${CMAKE_COMMAND} + -P ${CMAKE_CURRENT_BINARY_DIR}/configure-html.cmake + DEPENDS + ${CMAKE_CURRENT_BINARY_DIR}/configure-html.cmake + ${CMAKE_CURRENT_SOURCE_DIR}/index.md + COMMENT "Configuring index.md" + VERBATIM + ) + + # 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 top-level index.html + add_custom_command( + OUTPUT ${HTML_OUTPUT_DIR}/index.html + COMMAND ${PANDOC_EXECUTABLE} -o ${HTML_OUTPUT_DIR}/index.html index.md -s --css buttondown.css + DEPENDS ${CMAKE_CURRENT_BINARY_DIR}/index.md ${HTML_OUTPUT_DIR}/buttondown.css + VERBATIM + ) + + # 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 + COMMAND ${CMAKE_COMMAND} + -E remove -f ${HTML_OUTPUT_DIR}/manual-${PROJECT_VERSION}.pdf + COMMAND ${CMAKE_COMMAND} + -E copy ${CMAKE_CURRENT_BINARY_DIR}/manual/gromacs.pdf ${HTML_OUTPUT_DIR}/manual-${PROJECT_VERSION}.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 + ) + endif() + + # Add a top-level target for the others to hook onto + add_custom_target(webpage + DEPENDS + ${HTML_OUTPUT_DIR}/index.html + install-guide + ${HTML_OUTPUT_DIR}/install-guide.html + ${HTML_OUTPUT_DIR}/install-guide.pdf + ${HTML_OUTPUT_DIR}/manual-${PROJECT_VERSION}.pdf + ${extra_webpage_dependencies} + VERBATIM + ) + add_dependencies(webpage webpage-html doc-all) +endif() diff --git a/docs/buttondown.css b/docs/buttondown.css new file mode 100644 index 0000000000..89eaa112eb --- /dev/null +++ b/docs/buttondown.css @@ -0,0 +1,453 @@ +/* CSS sourced for GROMACS from https://gist.github.com/ryangray/1882525 + No usage restrictions are asserted there. +*/ +/* + Buttondown + A Markdown/MultiMarkdown/Pandoc HTML output CSS stylesheet + Author: Ryan Gray + Date: 15 Feb 2011 + Revised: 21 Feb 2012 + + General style is clean, with minimal re-definition of the defaults or + overrides of user font settings. The body text and header styles are + left alone except title, author and date classes are centered. A Pandoc TOC + is not printed, URLs are printed after hyperlinks in parentheses. + Block quotes are italicized. Tables are lightly styled with lines above + and below the table and below the header with a boldface header. Code + blocks are line wrapped. + + All elements that Pandoc and MultiMarkdown use should be listed here, even + if the style is empty so you can easily add styling to anything. + + There are some elements in here for HTML5 output of Pandoc, but I have not + gotten around to testing that yet. +*/ + +/* NOTES: + + Stuff tried and failed: + + It seems that specifying font-family:serif in Safari will always use + Times New Roman rather than the user's preferences setting. + + Making the font size different or a fixed value for print in case the screen + font size is making the print font too big: Making font-size different for + print than for screen causes horizontal lines to disappear in math when using + MathJax under Safari. +*/ + +/* ---- Front Matter ---- */ + +/* Pandoc header DIV. Contains .title, .author and .date. Comes before div#TOC. + Only appears if one of those three are in the document. +*/ + +div#header, header + { + /* Put border on bottom. Separates it from TOC or body that comes after it. */ + border-bottom: 1px solid #aaa; + margin-bottom: 0.5em; + } + +.title /* Pandoc title header (h1.title) */ + { + text-align: center; + } + +.author, .date /* Pandoc author(s) and date headers (h2.author and h3.date) */ + { + text-align: center; + } + +/* Pandoc table of contents DIV when using the --toc option. + NOTE: this doesn't support Pandoc's --id-prefix option for #TOC and #header. + Probably would need to use div[id$='TOC'] and div[id$='header'] as selectors. +*/ + +div#TOC, nav#TOC + { + /* Put border on bottom to separate it from body. */ + border-bottom: 1px solid #aaa; + margin-bottom: 0.5em; + } + +@media print + { + div#TOC, nav#TOC + { + /* Don't display TOC in print */ + display: none; + } + } + +/* ---- Headers and sections ---- */ + +h1, h2, h3, h4, h5, h6 +{ + font-family: "Helvetica Neue", Helvetica, "Liberation Sans", Calibri, Arial, sans-serif; /* Sans-serif headers */ + + /* font-family: "Liberation Serif", "Georgia", "Times New Roman", serif; /* Serif headers */ + + page-break-after: avoid; /* Firefox, Chrome, and Safari do not support the property value "avoid" */ +} + +/* Pandoc with --section-divs option */ + +div div, section section /* Nested sections */ + { + margin-left: 2em; /* This will increasingly indent nested header sections */ + } + +p {} + +blockquote + { + font-style: italic; + } + +li /* All list items */ + { + } + +li > p /* Loosely spaced list item */ + { + margin-top: 1em; /* IE: lack of space above a
  • when the item is inside a

    */ + } + +ul /* Whole unordered list */ + { + } + +ul li /* Unordered list item */ + { + } + +ol /* Whole ordered list */ + { + } + +ol li /* Ordered list item */ + { + } + +hr {} + +/* ---- Some span elements --- */ + +sub /* Subscripts. Pandoc: H~2~O */ + { + } + +sup /* Superscripts. Pandoc: The 2^nd^ try. */ + { + } + +em /* Emphasis. Markdown: *emphasis* or _emphasis_ */ + { + } + +em > em /* Emphasis within emphasis: *This is all *emphasized* except that* */ + { + font-style: normal; + } + +strong /* Markdown **strong** or __strong__ */ + { + } + +/* ---- Links (anchors) ---- */ + +a /* All links */ + { + /* Keep links clean. On screen, they are colored; in print, they do nothing anyway. */ + text-decoration: none; + } + +@media screen + { + a:hover + { + /* On hover, we indicate a bit more that it is a link. */ + text-decoration: underline; + } + } + +@media print + { + a { + /* In print, a colored link is useless, so un-style it. */ + color: black; + background: transparent; + } + + a[href^="http://"]:after, a[href^="https://"]:after + { + /* However, links that go somewhere else, might be useful to the reader, + so for http and https links, print the URL after what was the link + text in parens + */ + content: " (" attr(href) ") "; + font-size: 90%; + } + } + +/* ---- Images ---- */ + +img + { + /* Let it be inline left/right where it wants to be, but verticality make + it in the middle to look nicer, but opinions differ, and if in a multi-line + paragraph, it might not be so great. + */ + vertical-align: middle; + } + +div.figure /* Pandoc figure-style image */ + { + /* Center the image and caption */ + margin-left: auto; + margin-right: auto; + text-align: center; + font-style: italic; + } + +p.caption /* Pandoc figure-style caption within div.figure */ + { + /* Inherits div.figure props by default */ + } + +/* ---- Code blocks and spans ---- */ + +pre, code + { + background-color: #fdf7ee; + /* BEGIN word wrap */ + /* Need all the following to word wrap instead of scroll box */ + /* This will override the overflow:auto if present */ + white-space: pre-wrap; /* css-3 */ + white-space: -moz-pre-wrap !important; /* Mozilla, since 1999 */ + white-space: -pre-wrap; /* Opera 4-6 */ + white-space: -o-pre-wrap; /* Opera 7 */ + word-wrap: break-word; /* Internet Explorer 5.5+ */ + /* END word wrap */ + } + +pre /* Code blocks */ + { + /* Distinguish pre blocks from other text by more than the font with a background tint. */ + padding: 0.5em; /* Since we have a background color */ + border-radius: 5px; /* Softens it */ + /* Give it a some definition */ + border: 1px solid #aaa; + /* Set it off left and right, seems to look a bit nicer when we have a background */ + margin-left: 0.5em; + margin-right: 0.5em; + } + +@media screen + { + pre + { + /* On screen, use an auto scroll box for long lines, unless word-wrap is enabled */ + white-space: pre; + overflow: auto; + /* Dotted looks better on screen and solid seems to print better. */ + border: 1px dotted #777; + } + } + +code /* All inline code spans */ + { + } + +p > code, li > code /* Code spans in paragraphs and tight lists */ + { + /* Pad a little from adjacent text */ + padding-left: 2px; + padding-right: 2px; + } + +li > p code /* Code span in a loose list */ + { + /* We have room for some more background color above and below */ + padding: 2px; + } + +/* ---- Math ---- */ + +span.math /* Pandoc inline math default and --jsmath inline math */ + { + /* Tried font-style:italic here, and it messed up MathJax rendering in some browsers. Maybe don't mess with at all. */ + } + +div.math /* Pandoc --jsmath display math */ + { + } + +span.LaTeX /* Pandoc --latexmathml math */ + { + } + +eq /* Pandoc --gladtex math */ + { + } + +/* ---- Tables ---- */ + +/* A clean textbook-like style with horizontal lines above and below and under + the header. Rows highlight on hover to help scanning the table on screen. +*/ + +table + { + border-collapse: collapse; + border-spacing: 0; /* IE 6 */ + + border-bottom: 2pt solid #000; + border-top: 2pt solid #000; /* The caption on top will not have a bottom-border */ + + /* Center */ + margin-left: auto; + margin-right: auto; + } + +thead /* Entire table header */ + { + border-bottom: 1pt solid #000; + background-color: #eee; /* Does this BG print well? */ + } + +tr.header /* Each header row */ + { + } + +tbody /* Entire table body */ + { + } + +/* Table body rows */ + +tr { + } +tr.odd:hover, tr.even:hover /* Use .odd and .even classes to avoid styling rows in other tables */ + { + background-color: #eee; + } + +/* Odd and even rows */ +tr.odd {} +tr.even {} + +td, th /* Table cells and table header cells */ + { + vertical-align: top; /* Word */ + vertical-align: baseline; /* Others */ + padding-left: 0.5em; + padding-right: 0.5em; + padding-top: 0.2em; + padding-bottom: 0.2em; + } + +/* Removes padding on left and right of table for a tight look. Good if thead has no background color*/ +/* +tr td:last-child, tr th:last-child + { + padding-right: 0; + } +tr td:first-child, tr th:first-child + { + padding-left: 0; + } +*/ + +th /* Table header cells */ + { + font-weight: bold; + } + +tfoot /* Table footer (what appears here if caption is on top?) */ + { + } + +caption /* This is for a table caption tag, not the p.caption Pandoc uses in a div.figure */ + { + caption-side: top; + border: none; + font-size: 0.9em; + font-style: italic; + text-align: center; + margin-bottom: 0.3em; /* Good for when on top */ + padding-bottom: 0.2em; + } + +/* ---- Definition lists ---- */ + +dl /* The whole list */ + { + border-top: 2pt solid black; + padding-top: 0.5em; + border-bottom: 2pt solid black; + } + +dt /* Definition term */ + { + font-weight: bold; + } + +dd+dt /* 2nd or greater term in the list */ + { + border-top: 1pt solid black; + padding-top: 0.5em; + } + +dd /* A definition */ + { + margin-bottom: 0.5em; + } + +dd+dd /* 2nd or greater definition of a term */ + { + border-top: 1px solid black; /* To separate multiple definitions */ + } + +/* ---- Footnotes ---- */ + +a.footnote, a.footnoteRef { /* Pandoc, MultiMarkdown footnote links */ + font-size: small; + vertical-align: text-top; +} + +a[href^="#fnref"], a.reversefootnote /* Pandoc, MultiMarkdown, ?? footnote back links */ + { + } + +@media print + { + a[href^="#fnref"], a.reversefootnote /* Pandoc, MultiMarkdown */ + { + /* Don't display these at all in print since the arrow is only something to click on */ + display: none; + } + } + +div.footnotes /* Pandoc footnotes div at end of the document */ + { + } + +div.footnotes li[id^="fn"] /* A footnote item within that div */ + { + } + +/* You can class stuff as "noprint" to not print. + Useful since you can't set this media conditional inside an HTML element's + style attribute (I think), and you don't want to make another stylesheet that + imports this one and adds a class just to do this. +*/ + +@media print + { + .noprint + { + display:none; + } + } diff --git a/docs/configure-html.cmake.in b/docs/configure-html.cmake.in new file mode 100644 index 0000000000..07a2626af7 --- /dev/null +++ b/docs/configure-html.cmake.in @@ -0,0 +1,12 @@ +# Helper script that defers configure_file until build time, so that +# changes to the files configured for the html files don't trigger a +# global reconfigure + +set(SRC_DIR "@CMAKE_CURRENT_SOURCE_DIR@") +set(BIN_DIR "@CMAKE_CURRENT_BINARY_DIR@") + +set(PROJECT_VERSION "@PROJECT_VERSION@") +set(DOWNLOAD_SECTION "@DOWNLOAD_SECTION@") + +configure_file(${SRC_DIR}/index.md + ${BIN_DIR}/index.md @ONLY) diff --git a/doxygen/.gitignore b/docs/doxygen/.gitignore similarity index 100% rename from doxygen/.gitignore rename to docs/doxygen/.gitignore diff --git a/doxygen/CMakeLists.txt b/docs/doxygen/CMakeLists.txt similarity index 99% rename from doxygen/CMakeLists.txt rename to docs/doxygen/CMakeLists.txt index 1d607e28f3..1e334a4fa8 100644 --- a/doxygen/CMakeLists.txt +++ b/docs/doxygen/CMakeLists.txt @@ -93,7 +93,6 @@ 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) add_custom_target(doc-full ${CMAKE_COMMAND} -DDOCTYPE=full -P RunDoxygen.cmake diff --git a/doxygen/Doxyfile-common.cmakein b/docs/doxygen/Doxyfile-common.cmakein similarity index 96% rename from doxygen/Doxyfile-common.cmakein rename to docs/doxygen/Doxyfile-common.cmakein index 344173026f..1ae0a1c340 100644 --- a/doxygen/Doxyfile-common.cmakein +++ b/docs/doxygen/Doxyfile-common.cmakein @@ -10,7 +10,7 @@ FILE_PATTERNS = *.c *.cpp *.h *.md # FILE_PATTERNS += *.cu *.cuh EXAMPLE_PATH = @CMAKE_SOURCE_DIR@ RECURSIVE = YES -EXCLUDE = @CMAKE_SOURCE_DIR@/doxygen/examples \ +EXCLUDE = @CMAKE_CURRENT_SOURCE_DIR@/examples \ @CMAKE_SOURCE_DIR@/src/contrib \ @CMAKE_SOURCE_DIR@/src/external \ @CMAKE_SOURCE_DIR@/src/gromacs/selection/parser.cpp \ @@ -64,3 +64,5 @@ DOT_IMAGE_FORMAT = svg DOT_MULTI_TARGETS = YES # According to Doxygen docs, this is required for svg support on IE HTML_FILE_EXTENSION = .xhtml + +OUTPUT_DIRECTORY = @HTML_OUTPUT_DIR@/doxygen diff --git a/doxygen/Doxyfile-compact b/docs/doxygen/Doxyfile-compact similarity index 100% rename from doxygen/Doxyfile-compact rename to docs/doxygen/Doxyfile-compact diff --git a/doxygen/Doxyfile-full.cmakein b/docs/doxygen/Doxyfile-full.cmakein similarity index 100% rename from doxygen/Doxyfile-full.cmakein rename to docs/doxygen/Doxyfile-full.cmakein diff --git a/doxygen/Doxyfile-lib.cmakein b/docs/doxygen/Doxyfile-lib.cmakein similarity index 100% rename from doxygen/Doxyfile-lib.cmakein rename to docs/doxygen/Doxyfile-lib.cmakein diff --git a/doxygen/Doxyfile-user.cmakein b/docs/doxygen/Doxyfile-user.cmakein similarity index 65% rename from doxygen/Doxyfile-user.cmakein rename to docs/doxygen/Doxyfile-user.cmakein index ba03b00e09..c3ad8ad9a8 100644 --- a/doxygen/Doxyfile-user.cmakein +++ b/docs/doxygen/Doxyfile-user.cmakein @@ -2,10 +2,10 @@ # These pages include documentation that does not belong to the public API # documentation; exclude them from the generated documentation -EXCLUDE += @CMAKE_SOURCE_DIR@/doxygen/doxygen.md -EXCLUDE += @CMAKE_SOURCE_DIR@/doxygen/unittesting.md -EXCLUDE += @CMAKE_SOURCE_DIR@/doxygen/wrapperbinary.md -EXCLUDE += @CMAKE_SOURCE_DIR@/doxygen/simd.md +EXCLUDE += @CMAKE_SOURCE_DIR@/docs/doxygen/doxygen.md +EXCLUDE += @CMAKE_SOURCE_DIR@/docs/doxygen/unittesting.md +EXCLUDE += @CMAKE_SOURCE_DIR@/docs/doxygen/wrapperbinary.md +EXCLUDE += @CMAKE_SOURCE_DIR@/docs/doxygen/simd.md INTERNAL_DOCS = NO HIDE_UNDOC_CLASSES = YES diff --git a/doxygen/Doxyfile-version.cmakein b/docs/doxygen/Doxyfile-version.cmakein similarity index 100% rename from doxygen/Doxyfile-version.cmakein rename to docs/doxygen/Doxyfile-version.cmakein diff --git a/doxygen/Doxyfile-xml.cmakein b/docs/doxygen/Doxyfile-xml.cmakein similarity index 100% rename from doxygen/Doxyfile-xml.cmakein rename to docs/doxygen/Doxyfile-xml.cmakein diff --git a/doxygen/DoxygenLayout.xml b/docs/doxygen/DoxygenLayout.xml similarity index 100% rename from doxygen/DoxygenLayout.xml rename to docs/doxygen/DoxygenLayout.xml diff --git a/doxygen/RunDoxygen.cmake.cmakein b/docs/doxygen/RunDoxygen.cmake.cmakein similarity index 97% rename from doxygen/RunDoxygen.cmake.cmakein rename to docs/doxygen/RunDoxygen.cmake.cmakein index 8b05522dec..4ac1f9bf61 100644 --- a/doxygen/RunDoxygen.cmake.cmakein +++ b/docs/doxygen/RunDoxygen.cmake.cmakein @@ -53,7 +53,7 @@ execute_process(COMMAND ${DOXYGEN_EXECUTABLE} Doxyfile-${DOCTYPE} if (result) message(FATAL_ERROR "Doxygen failed. " "Please run '${DOXYGEN_EXECUTABLE} Doxyfile-${DOCTYPE}' " - "in the doxygen/ subdirectory in the build tree to see the details.") + "in the docs/doxygen/ subdirectory in the build tree to see the details.") endif() file(READ doxygen-${DOCTYPE}.log DOXYGEN_WARNINGS) diff --git a/doxygen/analysisdata.md b/docs/doxygen/analysisdata.md similarity index 100% rename from doxygen/analysisdata.md rename to docs/doxygen/analysisdata.md diff --git a/doxygen/analysisframework.md b/docs/doxygen/analysisframework.md similarity index 100% rename from doxygen/analysisframework.md rename to docs/doxygen/analysisframework.md diff --git a/doxygen/analysistemplate.md b/docs/doxygen/analysistemplate.md similarity index 100% rename from doxygen/analysistemplate.md rename to docs/doxygen/analysistemplate.md diff --git a/doxygen/codelayout.md b/docs/doxygen/codelayout.md similarity index 100% rename from doxygen/codelayout.md rename to docs/doxygen/codelayout.md diff --git a/doxygen/directories.cpp b/docs/doxygen/directories.cpp similarity index 100% rename from doxygen/directories.cpp rename to docs/doxygen/directories.cpp diff --git a/doxygen/doxygen-check.py b/docs/doxygen/doxygen-check.py similarity index 100% rename from doxygen/doxygen-check.py rename to docs/doxygen/doxygen-check.py diff --git a/doxygen/doxygen.md b/docs/doxygen/doxygen.md similarity index 97% rename from doxygen/doxygen.md rename to docs/doxygen/doxygen.md index a173ab76d0..854989caec 100644 --- a/doxygen/doxygen.md +++ b/docs/doxygen/doxygen.md @@ -61,9 +61,10 @@ Building the documentation ========================== If you simply want to see up-to-date documentation, you can go to -http://jenkins.gromacs.org/job/Doxygen_Nightly_master/javadoc/html-lib/index.xhtml +http://jenkins.gromacs.org/job/Documentation_Nightly_master/javadoc/html-lib/index.xhtml to see the documentation for the current development version. -Jenkins also runs Doxygen for all changes pushed to Gerrit for master, and the +Jenkins also runs Doxygen for all changes pushed to Gerrit for +release-5-0 and master branches, and the resulting documentation can be viewed from the link posted by Jenkins. The Doxygen build is marked as unstable if it introduces any Doxygen warnings. @@ -76,7 +77,7 @@ For local work, it is generally a good idea to set `GMX_COMPACT_DOXYGEN=ON` CMake option, which removes some large generated graphs from the documentation and speeds up the process significantly. -All files related to Doxygen reside in the `doxygen/` subdirectory in the source +All files related to Doxygen reside in the `docs/doxygen/` subdirectory in the source and build trees. In a freshly checked out source tree, this directory contains various `Doxyfile-*.cmakein` files. When you run CMake, corresponding files `Doxyfile-user`, `Doxyfile-lib`, and `Doxyfile-full` are generated at the @@ -89,14 +90,15 @@ You can run Doxygen directly with one of the generated files (all output will be produced under the current working directory), or build one of the `doc-user`, `doc-lib`, and `doc-full` targets. The targets run Doxygen in a quieter mode and only show the warnings if there were any, and put the output -under `doxygen/` in the build tree. The `doc-all` target builds all three +under `docs/html/doxygen/` in the build tree, so that the Doxygen build +cooperates with the broader `webpage` target. The `doc-all` target builds all three targets with less typing. The generated documentation is put under `html-user/`, `html-lib/`, and/or -`html-full/` in the output directory. Open `index.xhtml` file from one of +`html-full/`. Open `index.xhtml` file from one of these subdirectories to start browsing (for \Gromacs developers, the `html-lib/` is a reasonable starting point). Log files with all Doxygen -warnings are also produced as `doxygen-*.log`, so you can inspect them after +warnings are also produced as `docs/doxygen/doxygen-*.log`, so you can inspect them after the run. You will need Doxygen 1.8.5 to build the current documentation. Other versions @@ -331,7 +333,7 @@ work even though the script reports absolute paths. Empty lines and lines starting with `#` are ignored. To add suppression for an issue, the line that reports the issue can be copied -into `suppressios.txt`, and the line number (if any) removed. If the +into `suppressions.txt`, and the line number (if any) removed. If the issue does not have a file name (or a pseudo-file) associated, a leading `:` must be added. To cover many similar issues, parts of the line can then be replaced with wildcards. @@ -343,7 +345,7 @@ the number of suppressions. As a side effect, the XML extraction makes Doxygen parse all comments in the code, even if they do not appear in the documentation. This can reveal latent issues in the comments, like invalid Doxygen syntax. The messages from the XML -parsing are stored in `doxygen/doxygen-xml.log` in the build tree, similar to +parsing are stored in `docs/doxygen/doxygen-xml.log` in the build tree, similar to other Doxygen runs. The `doc-check` target requires Python 2.7 (other versions may work, but have @@ -440,7 +442,7 @@ Doxygen pages ------------- The pages that are accessible through navigation from the front page are -written using Markdown and are located under `doxygen/`. Each page should be +written using Markdown and are located under `docs/doxygen/`. Each page should be placed in the page hierarchy by making it a subpage of another page, i.e., it should be referenced once using \c \\subpage. `mainpage.md` is the root of the hierarchy. @@ -463,7 +465,7 @@ module). This header should contain the \c \\defgroup definition for the module. The name of the group should be `module_`name, where _name_ is the name of the subdirectory that hosts the module. -The module should be added to an appropriate group (see `doxygen/misc.cpp` for +The module should be added to an appropriate group (see `docs/doxygen/misc.cpp` for definitions) using \c \\ingroup to organize the "Modules" tab in the generated documentation. @@ -559,7 +561,7 @@ the modules themselves are documented. A brief description is still useful to provide a high-level overview of the source tree on the generated "Files" page. A reference to the module is typically sufficient as a brief description for a directory. All directories are currently documented in -`doxygen/directories.cpp`. +`docs/doxygen/directories.cpp`. Examples diff --git a/doxygen/doxygenxml.py b/docs/doxygen/doxygenxml.py similarity index 100% rename from doxygen/doxygenxml.py rename to docs/doxygen/doxygenxml.py diff --git a/doxygen/examples/doxygen-example-issues.cpp b/docs/doxygen/examples/doxygen-example-issues.cpp similarity index 100% rename from doxygen/examples/doxygen-example-issues.cpp rename to docs/doxygen/examples/doxygen-example-issues.cpp diff --git a/doxygen/examples/doxygen-example-module.cpp b/docs/doxygen/examples/doxygen-example-module.cpp similarity index 100% rename from doxygen/examples/doxygen-example-module.cpp rename to docs/doxygen/examples/doxygen-example-module.cpp diff --git a/doxygen/examples/doxygen-example-scoping.cpp b/docs/doxygen/examples/doxygen-example-scoping.cpp similarity index 100% rename from doxygen/examples/doxygen-example-scoping.cpp rename to docs/doxygen/examples/doxygen-example-scoping.cpp diff --git a/doxygen/examples/doxygen-example.c b/docs/doxygen/examples/doxygen-example.c similarity index 100% rename from doxygen/examples/doxygen-example.c rename to docs/doxygen/examples/doxygen-example.c diff --git a/doxygen/examples/doxygen-example.cpp b/docs/doxygen/examples/doxygen-example.cpp similarity index 100% rename from doxygen/examples/doxygen-example.cpp rename to docs/doxygen/examples/doxygen-example.cpp diff --git a/doxygen/generateGraphs.cmake b/docs/doxygen/generateGraphs.cmake similarity index 100% rename from doxygen/generateGraphs.cmake rename to docs/doxygen/generateGraphs.cmake diff --git a/doxygen/getInstalledHeaders.cmake b/docs/doxygen/getInstalledHeaders.cmake similarity index 100% rename from doxygen/getInstalledHeaders.cmake rename to docs/doxygen/getInstalledHeaders.cmake diff --git a/doxygen/gmxtree.py b/docs/doxygen/gmxtree.py similarity index 99% rename from doxygen/gmxtree.py rename to docs/doxygen/gmxtree.py index 6a8d602a24..c974d13a14 100644 --- a/doxygen/gmxtree.py +++ b/docs/doxygen/gmxtree.py @@ -492,7 +492,7 @@ class GromacsTree(object): If only_files is True, XML data is not loaded for code constructs, but only for files, directories, and their potential parents. """ - xmldir = os.path.join(self._build_root, 'doxygen', 'xml') + xmldir = os.path.join(self._build_root, 'docs', 'html', 'doxygen', 'xml') self._docset = xml.DocumentationSet(xmldir, self._reporter) if only_files: self._docset.load_file_details() diff --git a/doxygen/graphbuilder.py b/docs/doxygen/graphbuilder.py similarity index 100% rename from doxygen/graphbuilder.py rename to docs/doxygen/graphbuilder.py diff --git a/doxygen/mainpage.md b/docs/doxygen/mainpage.md similarity index 100% rename from doxygen/mainpage.md rename to docs/doxygen/mainpage.md diff --git a/doxygen/misc.cpp b/docs/doxygen/misc.cpp similarity index 100% rename from doxygen/misc.cpp rename to docs/doxygen/misc.cpp diff --git a/doxygen/reporter.py b/docs/doxygen/reporter.py similarity index 100% rename from doxygen/reporter.py rename to docs/doxygen/reporter.py diff --git a/doxygen/selections.md b/docs/doxygen/selections.md similarity index 100% rename from doxygen/selections.md rename to docs/doxygen/selections.md diff --git a/doxygen/simd.md b/docs/doxygen/simd.md similarity index 100% rename from doxygen/simd.md rename to docs/doxygen/simd.md diff --git a/doxygen/suppressions.txt b/docs/doxygen/suppressions.txt similarity index 100% rename from doxygen/suppressions.txt rename to docs/doxygen/suppressions.txt diff --git a/doxygen/unittesting.md b/docs/doxygen/unittesting.md similarity index 100% rename from doxygen/unittesting.md rename to docs/doxygen/unittesting.md diff --git a/doxygen/usinglibrary.md b/docs/doxygen/usinglibrary.md similarity index 100% rename from doxygen/usinglibrary.md rename to docs/doxygen/usinglibrary.md diff --git a/doxygen/wrapperbinary.md b/docs/doxygen/wrapperbinary.md similarity index 100% rename from doxygen/wrapperbinary.md rename to docs/doxygen/wrapperbinary.md diff --git a/docs/index.md b/docs/index.md new file mode 100644 index 0000000000..4bdc1180f1 --- /dev/null +++ b/docs/index.md @@ -0,0 +1,30 @@ +% GROMACS @PROJECT_VERSION@ + +@DOWNLOAD_SECTION@ + +[/a/]: # (TODO in release-5-0 branch: consolidate at least some of the material in the Documentation links below into the new user guide, along with all of http://www.gromacs.org/Documentation/Cut-off_schemes, http://www.gromacs.org/Documentation/Acceleration_and_parallelization and http://www.gromacs.org/Documentation/Performance_checklist) + +# Documentation + +* [Installation Guide](install-guide.html) + As [PDF](install-guide.pdf) + +* User Guide - coming soon! + +* [Online Reference](online.html) + +* [Reference manual](manual-@PROJECT_VERSION@.pdf) (PDF format) + +* Answers to [Frequently Asked Questions](http://www.gromacs.org/Documentation/FAQs) + +* Coping with [GROMACS errors](http://www.gromacs.org/Documentation/Errors) + +* Links to [tutorial material](http://www.gromacs.org/Documentation/Tutorials) + +# Documentation for developers + +* [Doxygen code documentation](doxygen/html-lib/index.xhtml) + +* Developer Guide - coming soon (in master branch)! + +[/b/]: # (TODO in master branch: consolidate much of the wiki material into a proper developer guide, and link to it here) diff --git a/install-guide/CMakeLists.txt b/docs/install-guide/CMakeLists.txt similarity index 59% rename from install-guide/CMakeLists.txt rename to docs/install-guide/CMakeLists.txt index fb5faaa7e0..770240d29a 100644 --- a/install-guide/CMakeLists.txt +++ b/docs/install-guide/CMakeLists.txt @@ -43,14 +43,17 @@ endif() if(INSTALL_GUIDE_BUILD_IS_POSSIBLE) # Do replacement of CMake variables for version strings, etc. + # This defers until build time the configuration of + # install-guide.md, which could be faster for all the + # configurations that don't make the install guide even though it + # was possible. configure_file(configure-install-guide.cmake.in ${CMAKE_CURRENT_BINARY_DIR}/configure-install-guide.cmake @ONLY) - # This defers until build time the configuration of - # install-guide.md, which could be faster + # Configure the install-guide.md at build time add_custom_command( - OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/install-guide.md + OUTPUT ${CMAKE_BINARY_DIR}/install-guide.md COMMAND ${CMAKE_COMMAND} -P ${CMAKE_CURRENT_BINARY_DIR}/configure-install-guide.cmake DEPENDS @@ -60,30 +63,65 @@ if(INSTALL_GUIDE_BUILD_IS_POSSIBLE) VERBATIM ) - # Make the HTML install guide - add_custom_command( - OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/install-guide.html - COMMAND pandoc -t html -o ${CMAKE_CURRENT_BINARY_DIR}/install-guide.html install-guide.md -s --toc - DEPENDS ${CMAKE_CURRENT_BINARY_DIR}/install-guide.md - VERBATIM - ) - # Make the INSTALL file for CPack for the tarball. This gets put # into the tarball via the CPack rules in the top-level # CMakeLists.txt add_custom_command( OUTPUT final/INSTALL COMMAND ${CMAKE_COMMAND} -E make_directory final - COMMAND pandoc -t plain -o final/INSTALL install-guide.md - DEPENDS ${CMAKE_CURRENT_BINARY_DIR}/install-guide.md + COMMAND ${PANDOC_EXECUTABLE} -t plain -o final/INSTALL install-guide.md + DEPENDS + ${CMAKE_BINARY_DIR}/install-guide.md VERBATIM ) - # Add a top-level target for the others to hook onto + # Make the single-page HTML install guide + add_custom_command( + OUTPUT ${HTML_OUTPUT_DIR}/install-guide.html + COMMAND + ${PANDOC_EXECUTABLE} install-guide.md -o ${HTML_OUTPUT_DIR}/install-guide.html -s --toc --css buttondown.css + DEPENDS + ${CMAKE_BINARY_DIR}/install-guide.md + VERBATIM + ) + + # Make the PDF install guide + add_custom_command( + OUTPUT ${HTML_OUTPUT_DIR}/install-guide.pdf + COMMAND + ${PANDOC_EXECUTABLE} install-guide.md -o ${HTML_OUTPUT_DIR}/install-guide.pdf -s --toc + DEPENDS + ${CMAKE_BINARY_DIR}/install-guide.md + VERBATIM + ) + + # 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}/index.html + # COMMAND + # ${PANDOC_EXECUTABLE} install-guide.md -o install-guide.texi -s + # COMMAND + # ${MAKEINFO_EXECUTABLE} install-guide.texi --html -o ${HTML_OUTPUT_DIR}/install-guide --css-ref buttondown.css + # DEPENDS + # ${CMAKE_BINARY_DIR}/install-guide.md + # VERBATIM + # ) + + # Add a top-level target for the webpage build to hook onto add_custom_target(install-guide DEPENDS - ${CMAKE_CURRENT_BINARY_DIR}/install-guide.html - final/INSTALL + final/INSTALL + ${HTML_OUTPUT_DIR}/install-guide.html + ${HTML_OUTPUT_DIR}/install-guide.pdf VERBATIM ) endif() + +set(INSTALL_GUIDE_BUILD_IS_POSSIBLE ${INSTALL_GUIDE_BUILD_IS_POSSIBLE} PARENT_SCOPE) diff --git a/install-guide/configure-install-guide.cmake.in b/docs/install-guide/configure-install-guide.cmake.in similarity index 100% rename from install-guide/configure-install-guide.cmake.in rename to docs/install-guide/configure-install-guide.cmake.in diff --git a/install-guide/install-guide.md b/docs/install-guide/install-guide.md similarity index 99% rename from install-guide/install-guide.md rename to docs/install-guide/install-guide.md index 67eb2c7d06..9ab4db6b10 100644 --- a/install-guide/install-guide.md +++ b/docs/install-guide/install-guide.md @@ -1,12 +1,12 @@ % Installation guide for GROMACS @PROJECT_VERSION@ -# Building GROMACS # +# Introduction to building GROMACS # These instructions pertain to building GROMACS @PROJECT_VERSION@. Up-to-date installation instructions may be found at . -# Quick and dirty installation # +## Quick and dirty installation ## 1. Get the latest version of your C and C++ compilers. 2. Check that you have CMake version @GMX_CMAKE_MINIMUM_REQUIRED_VERSION@ or later. @@ -36,7 +36,7 @@ GROMACS, you will have to read further. Sadly, the interactions of hardware, libraries, and compilers are only going to continue to get more complex. -# Typical GROMACS installation # +## Typical GROMACS installation ## As above, and with further details below, but you should consider using the following [CMake options](#using-cmake-command-line-options) with the @@ -55,7 +55,7 @@ appropriate value instead of `xxx` : * `-DGMX_FFT_LIBRARY=xxx` to select whether to use `fftw`, `mkl` or `fftpack` libraries for [FFT support](#fast-fourier-transform-library) * `-DCMAKE_BUILD_TYPE=Debug` to build GROMACS in debug mode -# Building older GROMACS versions # +## Building older GROMACS versions ## For installation instructions for old GROMACS versions, see the documentation at @@ -200,7 +200,7 @@ Many simulations in GROMACS make extensive use of fast Fourier transforms, and a software library to perform these is always required. We recommend [FFTW](http://www.fftw.org) (version 3 or higher only) or -[Intel MKL](http://software.intel.com/en-us/intel-mkl). The choice of +[Intel MKL](https://software.intel.com/en-us/intel-mkl). The choice of library can be set with `cmake -DGMX_FFT_LIBRARY=`, where `` is one of `fftw`, `mkl`, or `fftpack`. FFTPACK is bundled with GROMACS as a fallback, and is acceptable if mdrun performance is @@ -660,11 +660,11 @@ CMakeLists.txt. `share/man/` : Installed man pages go here. -## Building GROMACS ## +## Compiling and linking ## -Once you have configured with `cmake`, you can build GROMACS. It is -expected that the `make` procedure will always complete successfully, -and give few or no warnings. The tests GROMACS makes on the settings +Once you have configured with `cmake`, you can build GROMACS with `make`. +It is expected that this will always complete successfully, and +give few or no warnings. The CMake-time tests GROMACS makes on the settings you choose are pretty extensive, but there are probably a few cases we have not thought of yet. Search the web first for solutions to problems, but if you need help, ask on gmx-users, being sure to @@ -675,7 +675,9 @@ message! If you have a multi-core or multi-CPU machine with `N` processors, then using + $ make -j N + will generally speed things up by quite a bit. Other build generator systems supported by `cmake` (e.g. `ninja`) also work well. diff --git a/docs/linkcheckerrc b/docs/linkcheckerrc new file mode 100644 index 0000000000..888d543445 --- /dev/null +++ b/docs/linkcheckerrc @@ -0,0 +1,8 @@ +# .ini-style config file for linkchecker. Recommended use +# for testing the GROMACS webpage is +# +# linkchecker index.html --ignore-url html-full --ignore-url html-user --ignore-url html-lib -f linkcheckerrc +[filtering] +# This site gives warnings about changed URLs, and suggests +# using... the same URLs. Well done, someone. +ignore=www.ks.uiuc.edu diff --git a/share/man/.gitignore b/docs/man/.gitignore similarity index 100% rename from share/man/.gitignore rename to docs/man/.gitignore diff --git a/share/man/CMakeLists.txt b/docs/man/CMakeLists.txt similarity index 97% rename from share/man/CMakeLists.txt rename to docs/man/CMakeLists.txt index f61222e251..ffcff945a7 100644 --- a/share/man/CMakeLists.txt +++ b/docs/man/CMakeLists.txt @@ -1,7 +1,7 @@ # # This file is part of the GROMACS molecular simulation package. # -# Copyright (c) 2012,2013, by the GROMACS development team, led by +# Copyright (c) 2012,2013,2014, 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. diff --git a/share/man/man7/gromacs.7.in b/docs/man/man7/gromacs.7.in similarity index 100% rename from share/man/man7/gromacs.7.in rename to docs/man/man7/gromacs.7.in diff --git a/manual/CMakeLists.txt b/docs/manual/CMakeLists.txt similarity index 94% rename from manual/CMakeLists.txt rename to docs/manual/CMakeLists.txt index 3628b0133a..0a012e04ff 100644 --- a/manual/CMakeLists.txt +++ b/docs/manual/CMakeLists.txt @@ -77,8 +77,8 @@ if(MANUAL_BUILD_IS_POSSIBLE) # updates in that HTML file without copying files by hand. ADD_CUSTOM_COMMAND(OUTPUT ${output_dir}/mdp_opt.tex - COMMAND ${CMAKE_CURRENT_SOURCE_DIR}/mkmdp ARGS ${CMAKE_SOURCE_DIR}/share/html - DEPENDS mkmdp ${CMAKE_SOURCE_DIR}/share/html/online/mdp_opt.html + COMMAND ${CMAKE_CURRENT_SOURCE_DIR}/mkmdp ARGS ${CMAKE_CURRENT_SOURCE_DIR}/../old-html + DEPENDS mkmdp ${CMAKE_CURRENT_SOURCE_DIR}/../old-html/online/mdp_opt.html ) # Finally, the command to build the manual. @@ -113,3 +113,5 @@ else() # TODO Arrange for the "make manual" target to explain that this can't # be done endif() + +set(MANUAL_BUILD_IS_POSSIBLE ${MANUAL_BUILD_IS_POSSIBLE} PARENT_SCOPE) diff --git a/manual/README b/docs/manual/README similarity index 100% rename from manual/README rename to docs/manual/README diff --git a/manual/UseLATEX.cmake b/docs/manual/UseLATEX.cmake similarity index 100% rename from manual/UseLATEX.cmake rename to docs/manual/UseLATEX.cmake diff --git a/manual/algorithms.tex b/docs/manual/algorithms.tex similarity index 100% rename from manual/algorithms.tex rename to docs/manual/algorithms.tex diff --git a/manual/analyse.tex b/docs/manual/analyse.tex similarity index 100% rename from manual/analyse.tex rename to docs/manual/analyse.tex diff --git a/manual/averages.tex b/docs/manual/averages.tex similarity index 99% rename from manual/averages.tex rename to docs/manual/averages.tex index 36588c1ca2..752cf5b4a6 100644 --- a/manual/averages.tex +++ b/docs/manual/averages.tex @@ -1,7 +1,7 @@ % % This file is part of the GROMACS molecular simulation package. % -% Copyright (c) 2013, by the GROMACS development team, led by +% Copyright (c) 2013,2014, 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. diff --git a/manual/defunits.tex b/docs/manual/defunits.tex similarity index 99% rename from manual/defunits.tex rename to docs/manual/defunits.tex index ee8c0feec6..41d546a859 100644 --- a/manual/defunits.tex +++ b/docs/manual/defunits.tex @@ -1,7 +1,7 @@ % % This file is part of the GROMACS molecular simulation package. % -% Copyright (c) 2013, by the GROMACS development team, led by +% Copyright (c) 2013,2014, 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. diff --git a/manual/fancy.sty b/docs/manual/fancy.sty similarity index 100% rename from manual/fancy.sty rename to docs/manual/fancy.sty diff --git a/manual/files.tex b/docs/manual/files.tex similarity index 100% rename from manual/files.tex rename to docs/manual/files.tex diff --git a/manual/forcefield.tex b/docs/manual/forcefield.tex similarity index 100% rename from manual/forcefield.tex rename to docs/manual/forcefield.tex diff --git a/manual/gmxmanual.cls b/docs/manual/gmxmanual.cls similarity index 100% rename from manual/gmxmanual.cls rename to docs/manual/gmxmanual.cls diff --git a/manual/gromacs.tex b/docs/manual/gromacs.tex similarity index 99% rename from manual/gromacs.tex rename to docs/manual/gromacs.tex index 342c181d86..8a496e6497 100644 --- a/manual/gromacs.tex +++ b/docs/manual/gromacs.tex @@ -1,7 +1,7 @@ % % This file is part of the GROMACS molecular simulation package. % -% Copyright (c) 2013, by the GROMACS development team, led by +% Copyright (c) 2013,2014, 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. diff --git a/manual/here.sty b/docs/manual/here.sty similarity index 100% rename from manual/here.sty rename to docs/manual/here.sty diff --git a/manual/hfill.ist b/docs/manual/hfill.ist similarity index 100% rename from manual/hfill.ist rename to docs/manual/hfill.ist diff --git a/manual/implement.tex b/docs/manual/implement.tex similarity index 100% rename from manual/implement.tex rename to docs/manual/implement.tex diff --git a/manual/index.gmx b/docs/manual/index.gmx similarity index 100% rename from manual/index.gmx rename to docs/manual/index.gmx diff --git a/manual/install.tex b/docs/manual/install.tex similarity index 100% rename from manual/install.tex rename to docs/manual/install.tex diff --git a/manual/intro.tex b/docs/manual/intro.tex similarity index 99% rename from manual/intro.tex rename to docs/manual/intro.tex index 8d431fc2d1..b5f53bb601 100644 --- a/manual/intro.tex +++ b/docs/manual/intro.tex @@ -1,7 +1,7 @@ % % This file is part of the GROMACS molecular simulation package. % -% Copyright (c) 2013, by the GROMACS development team, led by +% Copyright (c) 2013,2014, 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. diff --git a/manual/macros.tex b/docs/manual/macros.tex similarity index 98% rename from manual/macros.tex rename to docs/manual/macros.tex index cd24695efb..ed8442fbb3 100644 --- a/manual/macros.tex +++ b/docs/manual/macros.tex @@ -1,7 +1,7 @@ % % This file is part of the GROMACS molecular simulation package. % -% Copyright (c) 2013, by the GROMACS development team, led by +% Copyright (c) 2013,2014, 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. diff --git a/manual/mkmdp b/docs/manual/mkmdp similarity index 100% rename from manual/mkmdp rename to docs/manual/mkmdp diff --git a/manual/monster.bib b/docs/manual/monster.bib similarity index 100% rename from manual/monster.bib rename to docs/manual/monster.bib diff --git 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share/html/online/dat.html rename to docs/old-html/online/dat.html diff --git a/share/html/online/dlg.html b/docs/old-html/online/dlg.html similarity index 100% rename from share/html/online/dlg.html rename to docs/old-html/online/dlg.html diff --git a/share/html/online/edi.html b/docs/old-html/online/edi.html similarity index 68% rename from share/html/online/edi.html rename to docs/old-html/online/edi.html index 1d5002e3bb..4d619535de 100644 --- a/share/html/online/edi.html +++ b/docs/old-html/online/edi.html @@ -3,6 +3,7 @@ Files with the edi file extension contain information for gmx mdrun to run Molecular Dynamics with Essential Dynamics constraints. -These files can be generated by the program WEDSAM which uses + + diff --git a/share/html/online/edo.html b/docs/old-html/online/edo.html similarity index 100% rename from share/html/online/edo.html rename to docs/old-html/online/edo.html diff --git a/share/html/online/edr.html b/docs/old-html/online/edr.html similarity index 100% rename from share/html/online/edr.html rename to docs/old-html/online/edr.html diff --git a/share/html/online/ene.html b/docs/old-html/online/ene.html similarity index 100% rename from share/html/online/ene.html rename to docs/old-html/online/ene.html diff --git a/share/html/online/eps.html b/docs/old-html/online/eps.html similarity index 100% rename from share/html/online/eps.html rename to docs/old-html/online/eps.html diff --git a/share/html/online/files.html b/docs/old-html/online/files.html similarity index 98% rename from share/html/online/files.html rename to docs/old-html/online/files.html index b27ca53880..ee57c53221 100644 --- a/share/html/online/files.html +++ b/docs/old-html/online/files.html @@ -7,7 +7,7 @@ gmx grompp and gmx convert-tpr

    m2p -
    input for gmx xpm2ps +
    input for gmx xpm2ps

    Structure files

    diff --git a/share/html/online/flow.html b/docs/old-html/online/flow.html similarity index 100% rename from share/html/online/flow.html rename to docs/old-html/online/flow.html diff --git a/share/html/online/g96.html b/docs/old-html/online/g96.html similarity index 100% rename from share/html/online/g96.html rename to docs/old-html/online/g96.html diff --git a/share/html/online/getting_started.html b/docs/old-html/online/getting_started.html similarity index 100% rename from share/html/online/getting_started.html rename to docs/old-html/online/getting_started.html diff --git a/share/html/online/gro.html b/docs/old-html/online/gro.html similarity index 100% rename from share/html/online/gro.html rename to docs/old-html/online/gro.html diff --git a/docs/old-html/online/hdb.html b/docs/old-html/online/hdb.html new file mode 100644 index 0000000000..8dfd3d877c --- /dev/null +++ b/docs/old-html/online/hdb.html @@ -0,0 +1,7 @@ +hdb file format +

    Description

    +The hdb file extension stands for hydrogen database +Such a file is needed by gmx pdb2gmx +when building hydrogen atoms that were either originally missing, or that +were removed with -ignh. + diff --git a/share/html/online/itp.html b/docs/old-html/online/itp.html similarity index 100% rename from share/html/online/itp.html rename to docs/old-html/online/itp.html diff --git a/share/html/online/log.html b/docs/old-html/online/log.html similarity index 100% rename from share/html/online/log.html rename to docs/old-html/online/log.html diff --git a/share/html/online/m2p.html b/docs/old-html/online/m2p.html similarity index 100% rename from share/html/online/m2p.html rename to docs/old-html/online/m2p.html diff --git a/share/html/online/map.html b/docs/old-html/online/map.html similarity index 100% rename from share/html/online/map.html rename to docs/old-html/online/map.html diff --git a/share/html/online/mdp.html b/docs/old-html/online/mdp.html similarity index 98% rename from share/html/online/mdp.html rename to docs/old-html/online/mdp.html index d55efb5372..423c928bbe 100644 --- a/share/html/online/mdp.html +++ b/docs/old-html/online/mdp.html @@ -48,7 +48,7 @@ constraints = all-bonds

    -With this input grompp will produce +With this input grompp will produce an mdout.mdp with all the options and descriptions:

    diff --git a/share/html/online/mdp_opt.html b/docs/old-html/online/mdp_opt.html similarity index 100% rename from share/html/online/mdp_opt.html rename to docs/old-html/online/mdp_opt.html diff --git a/share/html/online/mtx.html b/docs/old-html/online/mtx.html similarity index 100% rename from share/html/online/mtx.html rename to docs/old-html/online/mtx.html diff --git a/share/html/online/ndx.html b/docs/old-html/online/ndx.html similarity index 100% rename from share/html/online/ndx.html rename to docs/old-html/online/ndx.html diff --git a/share/html/online/options.html b/docs/old-html/online/options.html similarity index 100% rename from share/html/online/options.html rename to docs/old-html/online/options.html diff --git a/share/html/online/out.html b/docs/old-html/online/out.html similarity index 100% rename from share/html/online/out.html rename to docs/old-html/online/out.html diff --git a/share/html/online/pdb.html b/docs/old-html/online/pdb.html similarity index 100% rename from share/html/online/pdb.html rename to docs/old-html/online/pdb.html diff --git a/share/html/online/rtp.html b/docs/old-html/online/rtp.html similarity index 100% rename from share/html/online/rtp.html rename to docs/old-html/online/rtp.html diff --git a/share/html/online/style.css b/docs/old-html/online/style.css similarity index 100% rename from share/html/online/style.css rename to docs/old-html/online/style.css diff --git a/share/html/online/tex.html b/docs/old-html/online/tex.html similarity index 100% rename from share/html/online/tex.html rename to docs/old-html/online/tex.html diff --git a/share/html/online/tng.html b/docs/old-html/online/tng.html similarity index 100% rename from share/html/online/tng.html rename to docs/old-html/online/tng.html diff --git a/share/html/online/top.html b/docs/old-html/online/top.html similarity index 100% rename from share/html/online/top.html rename to docs/old-html/online/top.html diff --git a/share/html/online/tpa.html b/docs/old-html/online/tpa.html similarity index 100% rename from share/html/online/tpa.html rename to docs/old-html/online/tpa.html diff --git a/share/html/online/tpb.html b/docs/old-html/online/tpb.html similarity index 100% rename from share/html/online/tpb.html rename to docs/old-html/online/tpb.html diff --git a/share/html/online/tpr.html b/docs/old-html/online/tpr.html similarity index 100% rename from share/html/online/tpr.html rename to docs/old-html/online/tpr.html diff --git a/share/html/online/trj.html b/docs/old-html/online/trj.html similarity index 100% rename from share/html/online/trj.html rename to docs/old-html/online/trj.html diff --git a/share/html/online/trr.html b/docs/old-html/online/trr.html similarity index 100% rename from share/html/online/trr.html rename to docs/old-html/online/trr.html diff --git a/share/html/online/xpm.html b/docs/old-html/online/xpm.html similarity index 100% rename from share/html/online/xpm.html rename to docs/old-html/online/xpm.html diff --git a/share/html/online/xtc.html b/docs/old-html/online/xtc.html similarity index 95% rename from share/html/online/xtc.html rename to docs/old-html/online/xtc.html index 419bafa2d3..acf2c52b1c 100644 --- a/share/html/online/xtc.html +++ b/docs/old-html/online/xtc.html @@ -10,8 +10,8 @@ These are rounded to integer values. Then several other tricks are performed, for instance making use of the fact that atoms close in sequence are usually close in space too (e.g. a water molecule). To this end, the xdr library is extended with a special routine -to write 3-D float coordinates. This routine was written by Frans van Hoesel -as part of an Europort project, and can be obtained through this link. +to write 3-D float coordinates.

    All the data is stored using calls to xdr routines. diff --git a/share/html/online/xvg.html b/docs/old-html/online/xvg.html similarity index 100% rename from share/html/online/xvg.html rename to docs/old-html/online/xvg.html diff --git a/doxygen/index.html b/doxygen/index.html deleted file mode 100644 index 1b546acf4b..0000000000 --- a/doxygen/index.html +++ /dev/null @@ -1,14 +0,0 @@ - - -

    Doxygen documentation for Gromacs

    -

    - Each set of documentation below includes all the information from - the sets above it. -

    - - - diff --git a/share/CMakeLists.txt b/share/CMakeLists.txt index e89e6ff9fe..e82d2d5baa 100644 --- a/share/CMakeLists.txt +++ b/share/CMakeLists.txt @@ -32,8 +32,6 @@ # To help us fund GROMACS development, we humbly ask that you cite # the research papers on the package. Check out http://www.gromacs.org. -add_subdirectory(html) -add_subdirectory(man) add_subdirectory(template) install(FILES README.tutor README_FreeEnergyModifications.txt