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
• Change Management
  • Getting started
  • Labels
  • Code Review
  • More git tips
• Automation and Infrastructure
  • GitLab CI Pipeline Execution
• Release engineering with GitLab
  • Triggering builds on GitLab
• Source tree checker scripts
  • Checker details
  • Include dependency graphs
• Automatic source code formatting
  • Setting up clang-format
  • What is automatically formatted?
  • Setting up clang-tidy
  • Tools
  • Using git filters
  • Hiding formatting commits from git blame
• Unit testing
  • Finding, building and running
  • Unit testing framework
  • Getting started with new tests
  • MPI 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 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 in GitLab CI for each commit. Details can be found on a separate page on Unit testing.

clang static analyzer

coverage

regression tests

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:

• release build,

• any build by Clang with optimizations,

• build with SYCL support.

In these configurations, FPEs can be enabled by adding -fpexcept flag to gmx invocation. However, FPEs are not supported on Windows and non-x86 Apple hardware. See api/legacy/include/gromacs/math/utilities.h for 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.

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 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 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 and clang-format.sh automatically 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-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). 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.