Automatic source code formatting#
Python sources can be automatically formatted with Black.
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. The overview tools page contains a list of these tools: Code formatting and style. 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 11.0.1. 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 11.0.0 or 11.0.1. Example:
$ clang-format --version
clang-format version 11.0.0
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/11.0.1/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 11. 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 11. Example:
$ clang-tidy --version
LLVM (http://llvm.org/):
LLVM version 11.0.0
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/11.0.0/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
are different between these two trees and
change under have outdated copyright header
are reported. This behavior can be changed by
Specifying an
--rev=REV
argument, which usesREV
instead of HEAD as the base of the comparison. A typical use case is to specify--rev=HEAD^
to check the HEAD commit.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 anyupdate
in addition to
year
andadd
, also update new-format copyright headers if they are broken or outdatedreplace
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
are different between these two trees and
change under clang-format
are reported. This behavior can be changed by
Specifying an
--rev=REV
argument, which usesREV
instead of HEAD as the base of the comparison. A typical use case is to specify--rev=HEAD^
to check the HEAD commit.Specifying an action:
check-*
: reports the files that clang-format changesdiff-*
: prints the actual diff of what would changeupdate-*
: 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
equalsdiff-workdir
).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 11 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-11
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
are different between these two trees and
change when applying clang-tidy
are reported. This behavior can be changed by
Specifying an
--rev=REV
argument, which usesREV
instead of HEAD as the base of the comparison. A typical use case is to specify--rev=HEAD^
to check the HEAD commit.Specifying an action:
check-*
: reports the files that clang-format changesdiff-*
: prints the actual diff of what would changeupdate-*
: 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
equalsdiff-workdir
).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
:
Copy the
git-pre-commit
script to .git/hooks/pre-commit.Specify the paths to
run-clang-tidy
andclang-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
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).