Items are packaged into source tarballs so that this is not necessary whenīuilding from a source distribution (since in general, it will not work inĬross-compilation scenarios). The built gmx binary to produce these documentation items. The build system provides targets that then invoke documentation exported from source files For man pages, HTML documentation of command-line options for executables,Īnd for shell completions, the gmx binary has explicit C++ code to export That all the links in the documentation can be resolved correctly. linkchecker linkchecker is used together with the LaTeX Also requires ImageMagick for converting graphics file formats. Sphinx Sphinx at least version 1.6.1 is usedįor building some parts of the documentation from reStructuredText This script shares most of its implementation with the custom checkers, and isĭocumented on the same page: Source tree checker scripts. The generated graph is embedded into the Doxygen documentation: Graph for the code, showing #include dependencies between modules. module dependency graphs GROMACS uses a custom Python script to generate an annotated dependency Separate page (common for several checkers): Source tree checker scripts. Source code (e.g., that a header documented as internal to a module is notĪctually used from outside the module). The script also checks that documentation for a header matches its use in the This is most easily invoked through a check-source target in the build system. GROMACS uses an additional, custom Python script to check for such issues.

Doxygen issue checker Doxygen produces warnings about some incorrect uses and wrongĭocumentation, but there are many common mistakes that it does not detect. The tool is not mandatory, but not having it available will result in warningsĪnd missing graphs. mscgen The Doxygen documentation uses mscgen for building some graphs. Mandatory, but the Doxygen build will produce warnings if it is notĪvailable, and the graphs are omitted from the documentation. graphviz (dot) The Doxygen documentation uses dot from graphviz for building some graphs. ThoroughĮxplanation of the Doxygen setup and instructions for documenting the sourceĬode can be found on a separate page: Using Doxygen. Currently, versionġ.8.5 is required for a warning-free build. Also some other overviewĬontent is laid out by Doxygen from Markdown source files. Doxygen Doxygen is used to extract documentation from The following tools are used in building parts of the documentation. The md5sum values and names of those tarballs, for embedding into the REGRESSIONTESTS_TARBALL CMake variables can be set to pass in SOURCE_TARBALL, REGRESSIONTESTS_MD5SUM, and If built from a release tarball, the SOURCE_MD5SUM, You can browse docs/html/index.html to find everything. Makes the complete GROMACS webpage, requires everything. webpage-sphinx Makes all the components of the GROMACS webpage that require Sphinx, install-guide Makes the INSTALL file for the tarball with Sphinx. doxygen-all Makes the code documentation with Doxygen. man Makes man pages from the wrapper binary with Sphinx. The following make targets are the most useful: manual Builds the PDF reference manual. GMX_BUILD_MDRUN_ONLY is enabled, or when cross-compiling, as it Some documentation cannot be built if the CMake option

To build the man target manually before installing). GMX_BUILD_HELP Option that controls 1) whether shell completions are built automatically,Īnd 2) whether built man pages are installed if available (the user still needs You need to enable at least some of the following CMake options: GMX_BUILD_MANUAL Option needed for trying to build the PDF reference manual The outputs of interest to most developers are generally produced in theĭocs/html/ subdirectory of the build tree. This helpsĮnsure that the functionality and the documentation remain in sync. Wrapper binary, in order to be bundled into the tarball. Also, man pageĭocumentation (and command-line completions) must be built from the Run in order for some documentation to be generated. (particularly when cross-compiling), and yet the code must build and This is quite complex, because the dependencies for building theĭocumentation must not get in the way of building the code

GROMACS documentation, which is aimed primarily at version-specificĭeployment of the complete documentation on the website and in the For now, there are multiple components, formats and tools for the

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