Automatic source code formatting

Python sources can be automatically formatted with Black from Python 3.9.3.

C++ source code can be automatically formatted using clang-format since GROMACS 2020. It automatically applies the guidelines in Guidelines for code formatting and in Guidelines for #include directives. Additionally, other Python scripts are used for a few other automatic formatting/checking tasks. This page provides more details for clang-format, clang-tidy and copyright scripts.

Our CI uses these same scripts (in particular, clang-format.sh, copyright.sh, clang-tidy.sh and the check-source target) to enforce that the code stays invariant under such formatting.

Setting up clang-format

GROMACS formatting is enforced with clang-format 18.0.1. 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 18.0.0 or 18.0.1. Example:

$ clang-format --version
clang-format version 18.0.0

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.

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

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/18.0.1/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.

  Files included here are also passed to the clang-tidy code checker.

• filter=clangformat: clang-format is run. Again also runs clang-tidy.

• filter=includesort: include order is enforced and copyright headers are checked.

• filter=copyright: only copyright headers are checked.

Other files are ignored by clang-tidy.sh, clang-format.sh, copyright.sh and reformat_all.sh scripts (see below).

Setting up clang-tidy

GROMACS source code tidiness checking is enforced with clang-tidy provided alongside clang compiler version 18. clang-tidy 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-tidy or clang-tools package, but you should confirm that the provided command is version 18. Example:

$ clang-tidy --version
  LLVM (http://llvm.org/):
    LLVM version 18.1.3

If you use a different version of clang-tidy, you will likely get different checking 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-tidy for clang-tidy.sh and for the pre-commit hook, you also need to run this in each of your GROMACS repositories:

git config hooks.runclangtidypath /path/to/run-clang-tidy.py

Alternatively, if you just want to use clang-tidy.sh, you can set the RUN_CLANG_TIDY environment variable to /path/to/run-clang-tidy.py.

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

clang-tidy discovers which formatting rules to apply from the .clang-tidy 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-tidy configuration file, visit https://releases.llvm.org/18.1.1/tools/clang/tools/extra/docs/clang-tidy/index.html.

Tools

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.

copyright.sh

This script runs copyright.py on modified files and reports/applies the results. By default, the current HEAD commit on the source branch 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 on the source branch 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.

Since the behaviour of clang-format can change between versions even when using the same options, only clang-format from Clang 18 will give correct results. The path to the correct clang-format binary can be specified via CLANG_FORMAT environment variable or by running git config hooks.clangformatpath /path/to/clang-format-18 in the repository root.

clang-tidy.sh

This script runs the clang-tidy source code checker on modified files and either reports or applies resulting changes. By default, the current HEAD commit on the source branch is compared to the work tree, and files that

1. are different between these two trees and

2. change when applying clang-tidy

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

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.

Black

The Black tool reformats Python files in place, by default. To check and update the entire repository, use the .black.toml config file in the root directory of the repository:

pip install black
black --config .black.toml .

git pre-commit hook

If you want to run copyright.sh, clang-tidy.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 run-clang-tidy and clang-format for the hook if you have not already done so:

   git config hooks.runclangtidypath /path/to/run-clang-tidy.py
   git config hooks.clangformatpath /path/to/clang-format
   

3. Set the operation modes for the hook:

   git config hooks.clangtidymode 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 code formatting tool, are checked with clang-tidy and also checked for correct copyright headers. If any file would be changed by clang-tidy.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.clangtidymode 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.

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/clang-tidy.sh, admin/clang-format.sh and admin/copyright.sh scripts, which get run with the check-index action, and with --copyright and --format getting set according to the git config settings.

reformat_all.sh

This script runs 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 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.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).

Hiding formatting commits from git blame

A large-scale code reformatting, for example, when switching to a new clang-format version, might make the output of git blame/git praise hard to parse, since many lines will be touched by reformatting without any functional change.

A manually-managed list of such formatting-only commits is kept in the .git-blame-ignore-revs file. Please run the following command in the repository root to instruct Git to “skip” the listed commits and instead show the earlier commit from which the line originates

git config blame.ignoreRevsFile .git-blame-ignore-revs

To temporarily disable this option, use git blame --ignore-revs-file= (without any argument).