Several tools have their own individual pages and are listed below.
- Using Doxygen
- Change Management
- Automation and Infrastructure
- Release engineering with GitLab
- Source tree checker scripts
- Automatic source code formatting
- Unit testing
- Physical validation
GROMACS change management uses git and GitLab for code uploading and testing as well as issues tracking. (For change submission guidelines, refer to Contribute to GROMACS.)
GROMACS uses git as the version control system. Instructions for setting up git for GROMACS, as well as tips and tricks for its use, can be found in Change Management.
Other basic tutorial material for
gitcan be found on the web.
Bugs and issues, as well as some random features and discussions, are tracked, and all code changes go through a code review system at https://gitlab.com/gromacs/gromacs.
- Build testing
All changes pushed to GitLab are automatically compiled and otherwise checked on various platforms. Automation and Infrastructure documents how builds are automated, providing information on how to replicate the builds (e.g., to diagnose issues). Release engineering with GitLab provides more information on the technical implementation of the builds.
Main tool used in the build system.
packaging for distribution (CPack)
- unit testing (CTest)
GROMACS uses a unit testing framework based on Google C++ Testing Framework (gtest) and CTest. All unit tests are automatically run in GitLab CI for each commit. Details can be found on a separate page on Unit testing.
clang static analyzer
- floating-point exceptions
In debug builds, floating-point exceptions (FPEs) are generated whenever one of the following operations is encountered: division by zero, floating-point overflow, invalid operation (e.g., taking sqrt of a negative number). Such checks are not performed in the following configurations:
any build by Clang with optimizations,
build with SYCL support.
In these configurations, FPEs can be enabled by adding
gmxinvocation. However, FPEs are not supported on Windows and non-x86 Apple hardware. See
api/legacy/include/gromacs/math/utilities.hfor more details.
Code formatting and style#
The tools and scripts listed below are used to automatically check/apply formatting that follows GROMACS style guidelines described on a separate page: Style guidelines.
We use clang-format to enforce a consistent coding style, with the settings recorded in
.clang-formatin the main tree. See Setting up clang-format for details.
The source code linter clang-tidy is used to enforce common restrictions to the code, with the checks collected under
.clang-tidyat the top of the main tree. See Setting up clang-tidy for details.
This Python script adds and formats copyright headers in source files.
copyright.sh(see below) uses the script to check/update copyright years on changed files automatically.
bashscript runs the
copyright.pypython script to enforce correct copyright information in all files that have local changes and checks that they conform to the prescribed style. Optionally, the script can also apply changes to make the files conform. This script is automatically run by the CI to ensure that all commits adhere to Guidelines for code formatting. If the copyright job does not succeed, it means that this script has something to complain. See Automatic source code formatting for details.
This script enforces coding style using clang-format. This script is automatically run by our CI to ensure that all commits adhere to Guidelines for code formatting.
The clang-tidy code correctness restrictions are enforced by this script. The script is also used by the CI to verify the code, in addition to nightly compilations using clang-tidy on the whole tree.
This sample git pre-commit hook can be used if one wants to apply
clang-format.shautomatically before every commit to check for formatting issues. See Automatic source code formatting for details.
- include directive checker
In its present form, the above include sorter script cannot be conveniently applied in the formatting script. To check for issues, it is instead integrated into a
check-sourcebuild target. When this target is built, it also checks for include formatting issues. Internally, it uses the sorter script. This check is run in the CI as part of the Documentation job. Details for the checking mechanism are on a separate page (common for several checkers): Source tree checker scripts.
bashscript runs clang-format/
copyright.py/include sorter on all relevant files in the source tree (or in a particular directory). The script can also produce the list of files where these scripts are applied, for use with other scripts. See Automatic source code formatting for details.
- git attributes
git attributes (specified in
.gitattributesfiles) are used to annotate which files are subject to automatic formatting checks (and for automatic reformatting by the above scripts). See
man gitattributesfor an overview of the mechanism. We use the
filterattribute to specify the type of automatic checking/formatting to apply. Custom attributes are used for specifying some build system dependencies for easier processing in CMake.