Development-time tools¶
Several tools have their own individual pages and are listed below.
Change management¶
GROMACS change management is supported by the following tools. (For change submission guidelines, refer to Contribute to GROMACS.)
- git
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
git
can be found on the web.- GitLab
- 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.
Build system¶
- CMake
- 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 on Jenkins for each commit. Details can be found on a separate page on Unit testing.
clang static analyzer
coverage
regression tests
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.
- clang-format
- We use clang-format to enforce a consistent coding style, with the
settings recorded in
.clang-format
in the main tree. See Setting up clang-format for details. - clang-tidy
- The source code linter clang-tidy is used to enforce common restrictions to the
code, with the checks collected under
.clang-tidy
at the top of the main tree. See Setting up clang-tidy for details. admin/copyright.py
- 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. admin/copyright.sh
- This
bash
script runs thecopyright.py
python 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. admin/clang-format.sh
- 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.
admin/clang-tidy.sh
- 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.
admin/git-pre-commit
- This sample git pre-commit hook can be used if one wants to apply
clang-tidy.sh
,copyright.sh
andclang-format.sh
automatically before every commit to check for formatting issues. See Automatic source code formatting for details. docs/doxygen/includesorter.py
- This Python script sorts and reformats #include directives according to the guidelines at Guidelines for #include directives. Details are documented on a separate page (with the whole suite of Python scripts used for source code checks): Include order sorting.
- 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-source
build 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. admin/reformat_all.sh
- This
bash
script 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
.gitattributes
files) are used to annotate which files are subject to automatic formatting checks (and for automatic reformatting by the above scripts). Seeman gitattributes
for an overview of the mechanism. We use thefilter
attribute 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.