# Source tree checker scripts¶

There is a set of Python scripts, currently under docs/doxygen/, that check various aspects of the source tree for consistency. The script is based on producing an abstract representation of the source tree from various sources:

• List of files in the source tree (for overall layout of the source tree)
• List of installed headers (extracted from the generated build system)
• git attributes (to limit the scope of some checks)
• Doxygen XML documentation:
• For tags about public/private nature of documented headers and other constructs
• For actual documented constructs, to check them for consistency
• Hard-coded knowledge about the GROMACS source tree layout

This representation is then used for various purposes:

• Checking Doxygen documentation elements for common mistakes: missing brief descriptions, mismatches in file and class visibility, etc.
• Checking for consistent usage and documentation of headers: e.g., a header that is documented as internal to a module should not be used outside that module.
• Checking for module-level cyclic dependencies
• Checking for consistent style and order of #include directives (see Guidelines for #include directives)
• Actually sorting and reformatting #include directives to adhere to the checked style
• Generating dependency graphs between modules and for files within modules

The checks are run as part of a single check-source target, but are described in separate sections below. In addition to printing the issues to stderr, the script also writes them into docs/doxygen/check-source.log for later inspection. Jenkins runs the checks as part of the Documentation job, and the build is marked unstable if any issues are found.

For correct functionality, the scripts depend on correct usage of Doxygen annotations described in Using Doxygen, in particular the visibility and API definitions in file-level comments.

For some false positives from the script, the suppression mechanism described below is the easiest way to silence the script, but otherwise the goal would be to minimize the number of suppressions.

The scripts require Python 2.7 (other versions may work, but have not been tested).

To understand how the scripts work internally, see comments in the Python source files under docs/doxygen/.

## Checker details¶

The check-source target currently checks for a few different types of issues. These are listed in detail below, mainly related to documentation and include dependencies. Note in particular that the include dependency checks are much stricter for code in modules/directories that are documented with a \defgroup: all undocumented code is assumed to be internal to such modules. The rationale is that such code has gotten some more attention, and some effort should also have been put into defining what is the external interface of the module and documenting it.

• For all Doxygen documentation (currently does not apply for members that do not appear in the documentation):

• If a member has documentation, it should have a brief description.
• A note is issued for in-body documentation for functions, since this is ignored by our current settings.
• If a class has documentation, it should have public documentation only if it appears in an installed header.
• If a class and its containing file has documentation, the class documentation should not be visible if the file documentation is not.
• For all files:

• Consistent usage of

#include "..." // This should be used for GROMACS headers


and

#include <...> // This should be used for system and external headers

• When we again have installed headers, they must not include non-installed headers. Headers should be marked for install within CMakeLists.txt files of their respective modules.

• All source files must include “gmxpre.h” as the first header.

• A source/header file should include “config.h,” “gromacs/simd/simd.h”, or “gromacs/ewald/pme_simd.h” if and only if it uses a macro declared in such files.

• If the file has a git attribute to identify it as a candidate for include sorting, the include sorter described below should not produce any changes (i.e., the file should follow Guidelines for #include directives).

• For documented files:

• Installed headers should have public documentation, and other files should not.
• The API level specified for a file should not be higher than where its documentation is visible. For example, only publicly documented headers should be specified as part of the public API.
• If an \ingroup module_foo exists, it should match the subdirectory that the file is actually part of in the file system.
• If a \defgroup module_foo exists for the subdirectory where the file is, the file should contain \ingroup module_foo.
• Files should not include other files whose documentation visibility is lower (if the included file is not documented, the check is skipped).
• For files that are part of documented modules (\defgroup module_foo exists for the subdirectory), or are explicitly documented to be internal or in the library API:

• Such files should not be included from outside their module if they are undocumented (for documented modules) or are not specified as part of library or public API.
• For all modules:

• There should not be cyclic include dependencies between modules.

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 docs/doxygen/doxygen-xml.log in the build tree, similar to other Doxygen runs.

### Suppressing issues¶

The script is not currently perfect (either because of unfinished implementation, or because Doxygen bugs or incompleteness of the Doxygen XML output), and the current code also contains issues that the script detects, but the authors have not fixed. To allow the script to still be used, doxygen/suppressions.txt contains a list of issues that are filtered out from the report. The syntax is simple:

<file>: <text>


where <file> is a path to the file that reports the message, and <text> is the text reported. Both support * as a wildcard. If <file> is empty, the suppression matches only messages that do not have an associated file. <file> is matched against the trailing portion of the file name to make it work even though the script reports absolute paths. Empty lines and lines starting with # are ignored.

To add a suppression for an issue, the line that reports the issue can be copied 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.

A separate suppression mechanism is in place for cyclic dependencies: to suppress a cycle between moduleA and moduleB, add a line with format

moduleA -> moduleB


into doxygen/cycle-suppressions.txt. This suppresses all cycles that contain the mentioned edge. Since a cycle contains multiple edges, the suppression should be made for the edge that is determined to be an incorrect dependency. This also affects the layout of the include dependency graphs (see below): the suppressed edge is not considered when determining the dependency order, and is shown as invalid in the graph.

## Include order sorting¶

The script checks include ordering according to Guidelines for #include directives. If it is not obvious how the includes should be changed to make the script happy, or bulk changes are needed in multiple files, e.g., because of a header rename or making a previously public header private, it is possible to run a Python script that does the sorting:

docs/doxygen/includesorter.py -S . -B ../build <files>


The script needs to know the location of the source tree (given with -S) and the build tree (given with -B), and sorts the given files. To sort the whole source tree, one can also use:

admin/reformat_all.sh includesort -B=../build


For the sorter to work correctly, the build tree should contain up-to-date list of installed files and Doxygen XML documentation. The former is created automatically when cmake is run, and the latter can be built using the doxygen-xml target.

Note that currently, the sorter script does not change between angle brackets and quotes in include statements.

## Include dependency graphs¶

The same set of Python scripts can also produce include dependency graphs with some additional annotations compared to what, e.g., Doxygen produces for a directory dependency graph. Currently, a module-level graph is automatically built when the Doxygen documentation is built and embedded in the documentation (not in the public API documentation). The graph, together with a legend, is on a separate page: Module dependency graph

The Python script produces the graphs in a format suitable for dot (from the graphviz package) to lay them out. The build system also provides a dep-graphs target that generates PNG files from the intermediate dot files. In addition to the module-level graph, a file-level graph is produced for each module, showing the include dependencies within that module. The file-level graphs can only be viewed as the PNG files, with some explanation of the notation below. Currently, these are mostly for eye candy, but they can also be used for analyzing problematic dependencies to clean up the architecture.

Both the intermediate .dot files and the final PNG files are put under docs/doxygen/depgraphs/ in the build tree.

### File graphs¶

The graphs are written to module_name-deps.dot.png.

Node colors:

light blue