Code formatting

[mabruzzo]

Overview

As a followup to #218, This introduced a basic configuration file for the pre-commit software that calls clang-format and ruff run code-formatting on all new c/c++/python files added to grackle. All existing files will not be touched. (with that said, I tested out the new c/c++ linting on src/clib/utils.c and src/clib/utils.h since they are unlikely to have merge conflicts).

I also added documentation explaining how to locally run this machinery.

We are interested in using pre-commit.ci, which is a continuous integration system designed around pre-commit.

• After we set up pre-commit.ci, a check will appear at the bottom of every PR that specifies whether the configured lints (namely ruff and clang-format) passed or failed.
• pre-commit.ci is free for all open-source software. It also has the nifty feature, where adding a comment that says "pre-commit.ci autofix" to a PR (where the pre-commit.ci check has failed), will trigger pre-commit.ci to add a commit to that PR that fixes the formatting.

yt actually makes use of pre-commit.ci

What we need to do after merging

We will need to go to the pre-commit.ci and enable it for the grackle repository. (I'm happy to try to do that, but I may not have appropriate permissions -- so Britton may ultimately need to do that)

[mabruzzo]

I made a few tweaks based on the work I had done while creating similar a similar PR for Enzo-E (in enzo-project/enzo-e#420)

These changes include:

• modifying .clang-format formatting rules to prevent reordering of include-directives (I think it might be nice to re-enable this, but that's a topic for a different day).
• I moved most excluded files from the .pre-commit-config.yaml file to tool-specific files (.ruff.toml¹ and .clang-format-ignore²). This ensures that the linting tools are aware of the exclusion list, even if you manually invoke the linting tools (outside of pre-commit)
• I improved the documentation.

Footnotes

1. Once we merge Transition Pygrackle from setuptools to scikit-build-core #208, we should move the contents of .ruff.toml into the [tool.ruff] section of the pyproject.toml file that will be introduced. ↩

2. I also needed to bump the clang-format version used during linting (the previously pinned version didn't know about the .clang-format-ignore file) ↩

[mabruzzo]

I added a 3.4 milestone to this (but we can change it). My primary motivation for doing this was Britton's idea that we could start more broadly applying formatting after the next release.