Documentation generation

Building the GROMACS documentation

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

This is quite complex, because the dependencies for building the documentation must not get in the way of building the code (particularly when cross-compiling), and yet the code must build and run in order for some documentation to be generated. Also, man page documentation (and command-line completions) must be built from the wrapper binary, in order to be bundled into the tarball. This helps ensure that the functionality and the documentation remain in sync.

The outputs of interest to most developers are generally produced in the docs/html/ subdirectory of the build tree.

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 (requires LaTeX and ImageMagick). See GMX_BUILD_MANUAL.

GMX_BUILD_HELP

Option that controls 1) whether shell completions are built automatically, and 2) whether built man pages are installed if available (the user still needs to build the man target manually before installing). See GMX_BUILD_HELP.

To include the full Python package documentation with the webpage CMake target (see below), also configure CMake with GMX_PYTHON_PACKAGE=ON, and install Python package dependencies from python_packaging/gmxapi/requirements.txt:

pip install -r python_packaging/gmxapi/requirements.txt

Some documentation cannot be built when cross-compiling, as it requires executing the gmx binary.

The following make targets are the most useful:

manual

Builds the PDF reference manual.

man

Makes man pages from the wrapper binary with Sphinx.

doxygen-all

Makes the code documentation with Doxygen.

install-guide

Makes the INSTALL file for the tarball with Sphinx.

webpage-sphinx

Makes all the components of the GROMACS webpage that require Sphinx, including install guide and user guide.

webpage

Makes the complete GROMACS webpage, requires everything. When complete, you can browse docs/html/index.html to find everything.

If built from a release tarball, the SOURCE_MD5SUM, SOURCE_TARBALL, REGRESSIONTESTS_MD5SUM, and REGRESSIONTESTS_TARBALL CMake variables can be set to pass in the md5sum values and names of those tarballs, for embedding into the final deployment to the GROMACS website.

Needed build tools

The following tools are used in building parts of the documentation. Make sure they are installed before configuring the build system with CMake.

Doxygen

Doxygen is used to extract documentation from source code comments. Also some other overview content is laid out by Doxygen from Markdown source files. Currently, version 1.8.5 is required for a warning-free build. Thorough explanation of the Doxygen setup and instructions for documenting the source code can be found on a separate page: Using Doxygen.

graphviz (dot)

The Doxygen documentation uses dot from graphviz for building some graphs. The tool is not mandatory, but the Doxygen build will produce warnings if it is not available, and the graphs are omitted from the documentation.

mscgen

The Doxygen documentation uses mscgen for building some graphs. As with dot, the tool is not mandatory, but not having it available will result in warnings and missing graphs.

Doxygen issue checker

Doxygen produces warnings about some incorrect uses and wrong documentation, but there are many common mistakes that it does not detect. GROMACS uses an additional, custom Python script to check for such issues. This is most easily invoked through a check-source target in the build system. The script also checks that documentation for a header matches its use in the source code (e.g., that a header documented as internal to a module is not actually used from outside the module). These checks are run in CI. Details for the custom checker are on a separate page (common for several checkers): Source tree checker scripts.

module dependency graphs

GROMACS uses a custom Python script to generate an annotated dependency graph for the code, showing #include dependencies between modules. The generated graph is embedded into the Doxygen documentation: Module dependency graph This script shares most of its implementation with the custom checkers, and is documented on the same page: Source tree checker scripts.

Sphinx

Sphinx; at least version 4.0.0 is used for building some parts of the documentation from reStructuredText source files. To install an appropriate version of sphinx-build and other required Python packages, you can use the requirements.txt file in the docs repository directory. E.g. pip install -r docs/requirements.txt

LaTeX

Also requires ImageMagick for converting graphics file formats.

linkchecker

linkchecker is used together with the docs/linkcheckerrc file to ensure that all the links in the documentation can be resolved correctly.

documentation exported from source files

For man pages, HTML documentation of command-line options for executables, and for shell completions, the gmx binary has explicit C++ code to export the information required. The build system provides targets that then invoke the built gmx binary to produce these documentation items. The generated items are packaged into source tarballs so that this is not necessary when building from a source distribution (since in general, it will not work in cross-compilation scenarios). To build and install these from a git distribution, explicit action is required. See Doxygen documentation on the wrapper binary for some additional details.