Development-time tools

Several tools have their own individual pages and are listed below.

• Using Doxygen
  • Documentation flavors
  • Building the documentation
  • General guidelines for Doxygen markup
  • GROMACS specifics
  • Documenting specific code constructs
  • Examples
• GROMACS change management
  • Getting started
  • Code Review
  • FAQs
  • More git tips
• Understanding Jenkins builds
  • Pre-submit verification
  • On-demand builds
• Release engineering with GitLab
  • Triggering builds on GitLab
• Source tree checker scripts
  • Checker details
  • Include order sorting
  • Include dependency graphs
• Automatic source code formatting
  • Setting up uncrustify
  • Setting up clang-format
  • What is automatically formatted?
  • Scripts
  • Using git filters
• Unit testing
  • Finding, building and running
  • Unit testing framework
  • Getting started with new tests
• Physical validation
  • Test description
  • Building and testing using the build system
  • Direct usage of the python script
  • Adding new tests

Change management

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.)

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 GROMACS change management.

Other basic tutorial material for git can be found on the web.

GitLab

All code changes go through a code review system at https://gitlab.com/gromacs/gromacs.

Continuous Integration

All changes pushed to GitLab are automatically compiled and otherwise checked on various platforms using a continuous integration system. Release engineering with GitLab provides more information on the technical implementation of the builds.

Issue tracking

Bugs and issues, as well as some random features and discussions, are tracked at https://gitlab.com/gromacs/gromacs/issues.

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.

uncrustify

uncrustify is used for automatic indentation and other formatting of the source code to follow Guidelines for code formatting. All code must remain invariant under uncrustify with the config at admin/uncrustify.cfg. A patched version of uncrustify is used. See Setting up uncrustify for details.

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.

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/uncrustify.sh

This bash script runs uncrustify for 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. It is included only for historical reasons. See Guidelines for code formatting for details.

admin/copyright.sh

This bash script runs the copyright.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 Jenkins 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 Jenkins to ensure that all commits adhere to Guidelines for code formatting.

admin/git-pre-commit

This sample git pre-commit hook can be used if one wants to apply uncrustify.sh and clang-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 Jenkins 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 uncrustify/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). See man gitattributes for an overview of the mechanism. We use the filter 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.

include-what-you-use