Automatic source code formatting

The source code can be automatically formatted using clang-format (GROMACS 2020 and later) or uncrustify (GROMACS 2019 and earlier). Both are formatting tools that apply the guidelines in Guidelines for code formatting. Additionally, other 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 clang-format, uncrustify and copyright scripts.

Jenkins uses these same scripts (in particular, clang-format.sh, copyright.sh 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://github.com/rolandschulz/uncrustify.git
   cd uncrustify
   ./configure
   make
   

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 http://redmine.gromacs.org/issues/845 works for you.

In order to use the binary for uncrustify.sh 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 uncrustify.sh, 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.

Note that Jenkins now only allows formatting using clang-format.

Setting up clang-format

GROMACS formatting is enforced with clang-format 7.0.1. clang-format is one of the core clang tools. It may be included in a clang or llvm package from your favorite packaging system or you may find a standalone clang-format package, but you should confirm that the provided command is version 7.0.1 or 7.1.0. Example:

$ clang-format --version
clang-format version 7.1.0 (tags/RELEASE_710/final)

If you use a different version of clang-format, you will likely get different formatting results than the GROMACS continuous integration testing system, and the commits that you push will fail the automated tests.

Note

Refer to LLVM for source and binary downloads. If downloading sources, note that you will need to download both the LLVM source code and the Clang source code. As per the clang INSTALL.txt, place the expanded clang source into a tools/clang subdirectory within the expanded llvm archive, then run CMake against the llvm source directory.

In order to use the installed version of clang-format for clang-format.sh and for the pre-commit hook, you also need to run this in each of your GROMACS repositories:

git config hooks.clangformatpath /path/to/clang-format

Alternatively, if you just want to use clang-format.sh, you can set the CLANG_FORMAT environment variable to /path/to/clang-format.

As above, see the sections below for using the pre-commit hook or git filters.

clang-format discovers which formatting rules to apply from the .clang-format configuration file(s) in project directories, which will be automatically updated (if necessary) when you git pull from the GROMACS repository. For more about the tool and the .clang-format configuration file, visit https://releases.llvm.org/7.0.1/tools/clang/docs/ClangFormat.html

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=complete_formatting: Performs all formatting. Uses clang-format for code formatting.
• filter=uncrustify: uncrustify is run. Deprecated and here for historical reasons.
• filter=clangformat: clang-format 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 uncrustify.sh, clang-format.sh, copyright.sh and reformat_all.sh scripts (see below).

Scripts

copyright.py

This script provides low-level functionality to check and update copyright headers in C/C++ source files, as well as in several other types of files like CMake and Python scripts.

This file is also used as a loadable Python module for kernel generators, and provides the functionality to generate conformant copyright headers for such scripts.

You should rarely need to run this directly, but instead the bash scripts below use it internally. You can run the script with --help option if you want to see what all options it provides if you need to do some maintenance on the copyright headers themselves.

uncrustify.sh

The information for uncrustify is mainly provided for historical reasons, as the actual code formatting is now done using clang-format.

This script runs uncrustify 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

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.

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.

copyright.sh

This script runs copyright.py 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 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 --copyright=<mode>, which alters the level of copyright checking is done:

   off

   does not check copyright headers at all

   year

   only update copyright year in new-format copyright headers

   add

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

   update

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

   replace

   replace any copyright header with a new-format copyright header

   full

   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.

clang-format.sh

This script runs clang-format 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 clang-format

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 clang-format 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 --format=off, which does not run clang-format.

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 uncrustify.sh, copyright.sh and/or clang-format.sh 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 paths to uncrustify and clang-format for the hook if you have not already done so:

   git config hooks.uncrustifypath /path/to/uncrustify
   git config hooks.clangformatpath /path/to/clang-format
   

3. Set the operation modes for the hook:

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

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

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

git config hooks.uncrustifymode off
git config hooks.copyrightmode off
git config hooks.clangformatmode 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/uncrustify.sh, admin/clang-format.sh and admin/copyright.sh scripts, which get run with the check-index action, and with --uncrustify, --copyright and --format getting set according to the git config settings.

reformat_all.sh

This script runs uncrustify, clang-format, copyright.py, or the include sorter for all applicable files in the source tree. See reformat_all.sh -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.

-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 or clang-format on changes is to use a git filter (does not require either of the scripts, only the .gitattributes file). You can run

git config filter.complete_formatting.clean \
    "/path/to/uncrustify -c admin/uncrustify.cfg -q -l cpp"
git config filter.clangformat.clean \
    "/path/to/clang-format -i"

To configure a filter for all files that specify filter=complete_formatting attribute that indicates that all formatting steps should be performed.

The pre-commit hook + manually running the scripts 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 the source checkers, and is applied more consistently (the pre-commit hook is not run for every commit, e.g., during a rebase).