Automatic source code formatting

The source code can be automatically formatted using uncrustify, an automatic source code formatting tool, to follow the guidelines in Guidelines for code formatting. Additionally, Python scripts are used for a few other automatic formatting/checking tasks. The overview tools page contains a list of these tools: Code formatting and style. This page provides more details for uncrustify and copyright scripts.

Jenkins uses these same scripts (in particular, and the check-source target) to enforce that the code stays invariant under such formatting.

Setting up uncrustify

A patched version of uncrustify is used for GROMACS. To set this up, you need to do these (once):

  1. Change to a directory under which you want to build uncrustify and run:

    git clone -b gromacs git://
    cd uncrustify
  2. Copy the binary src/uncrustify into a directory of your choice (/path/to/uncrustify below).

Alternatively, if you are running Linux, you can try whether the binary from works for you.

In order to use the binary for and for the pre-commit hook, you also need to run this in each of your GROMACS repositories:

git config hooks.uncrustifypath /path/to/uncrustify

Alternatively, if you just want to use, you can set the UNCRUSTIFY environment variable to /path/to/uncrustify.

Using the pre-commit hook or git filters needs additional setup; see the respective sections below.

What is automatically formatted?

To identify which files are subject to automatic formatting, the scripts use git filters, specified in .gitattributes files. Only files that have the attribute filter set to one of the below values are processed:

  • filter=uncrustify: uncrustify is run, copyright headers are checked, and include order is enforced
  • filter=uncrustify_only: only uncrustify is run
  • filter=includesort: include order is enforced and copyright headers are checked
  • filter=copyright: only copyright headers are checked

Other files are ignored by and scripts (see below).


This script runs uncrustify and on modified files and reports/applies the results. By default, the current HEAD commit is compared to the work tree, and files that

  1. are different between these two trees and
  2. change under uncrustify and/or have outdated copyright header

are reported. This behavior can be changed by

  1. Specifying an --rev=REV argument, which uses REV instead of HEAD as the base of the comparison. A typical use case is to specify --rev=HEAD^ to check the HEAD commit.

  2. Specifying an action:

    • check-*: reports the files that uncrustify changes
    • diff-*: prints the actual diff of what would change
    • update-*: applies the changes to the repository
    • *-workdir: operates on the working directory (files on disk)
    • *-index: operates on the index of the repository

    For convenience, if you omit the workdir/index suffix, workdir is assumed (i.e., diff equals diff-workdir).

  3. Specifying --uncrustify=off, which does not run uncrustify.

  4. Specifying --copyright=<mode>, which alters the level of copyright checking is done:


    does not check copyright headers at all


    only update copyright year in new-format copyright headers


    in addition to year, add copyright headers to files that do not have any


    in addition to year and add, also update new-format copyright headers if they are broken or outdated


    replace any copyright header with a new-format copyright header


    do all of the above

By default, update-* refuses to update dirty files (i.e., that differ between the disk and the index) to make it easy to revert the changes. This can be overridden by adding a -f/--force option.

git pre-commit hook

If you want to run automatically for changes you make, you can configure a pre-commit hook using admin/git-pre-commit:

  1. Copy the git-pre-commit script to .git/hooks/pre-commit.

  2. Specify the path to uncrustify for the hook if you have not already done so:

    git config hooks.uncrustifypath /path/to/uncrustify
  3. Set the operation mode for the hook:

    git config hooks.uncrustifymode check
    git config hooks.copyrightmode  update

With this configuration, all source files modified in the commit are run through uncrustify and checked for correct copyright headers. If any file would be changed by, the names of those files are reported and the commit is prevented. The issues can be fixed by running manually.

To disable the hook without removing the pre-commit file, you can set

git config hooks.uncrustifymode off
git config hooks.copyrightmode off

To disable it temporarily for a commit, set NO_FORMAT_CHECK environment variable. For example,

NO_FORMAT_CHECK=1 git commit -a

You can also run git commit --no-verify, but that also disables other hooks, such as the Change-Id commit-msg hook used by Gerrit.

Note that when you run git commit --amend, the hook is only run for the changes that are getting amended, not for the whole commit. During a rebase, the hook is not run.

The actual work is done by the admin/ script, which gets run with the check-index action, and with --uncrustify and --copyright getting set according to the git config settings.

This script runs uncrustify,, or the include sorter for all applicable files in the source tree. See -h for the invocation.

The script can also produce the list of files for which these commands would be run. To do this, specify list-files on the command line and use --filter=<type> to specify which command to get the file list for. This can be used together with, e.g., xargs to run other scripts on the same set of files.

For all the operations, it is also possible to apply patters (of the same style that various git commands accept, i.e., src/*.cpp matches all .cpp files recursively under src/). The patterns can be specified with --pattern=<pattern>, and multiple --pattern arguments can be given.

As with, -f/--force is necessary if the working tree and the git index do not match.

Using git filters

An alternative to using a pre-commit hook to automatically apply uncrustify on changes is to use a git filter (does not require, only the .gitattributes file). You can run

git config filter.uncrustify.clean \
    "/path/to/uncrustify -c admin/uncrustify.cfg -q -l cpp"

To configure a filter for all files that specify filter=uncrustify attribute.

The pre-commit hook + manually running gives better/more intuitive control (with the filter, it is possible to have a work tree that is different from HEAD and still have an empty git diff) and provides better performance for changes that modify many files. It is the only way that currently also checks the copyright headers.

The filter allows one to transparently merge branches that have not been run through uncrustify, and is applied more consistently (the pre-commit hook is not run for every commit, e.g., during a rebase).