pre-commit → prek

[DimitriPapadopoulos]

Attempt to use prek instead of pre-commit.

This PR switches from pre-commit to prek mostly in CI.

Since prek is a drop-in replacement for pre-commit, either of them can be used on developers' computers, based on the same .pre-commit-config.yaml file, so that developer can change at their pace without disruption.

[gemini-code-assist]

Summary of Changes

Hello, I'm Gemini Code Assist¹! I'm currently reviewing this pull request and will post my feedback shortly. In the meantime, here's a summary to help you and other reviewers quickly get up to speed!

This pull request updates the project's development tooling by replacing pre-commit with prek. The change aims to modernize the pre-commit hook management system, particularly within continuous integration workflows, while maintaining backward compatibility for local developer setups.

Highlights

• Tooling Migration: The project has transitioned from using pre-commit to prek for managing pre-commit hooks, primarily impacting the CI environment.
• Developer Flexibility: Developers can continue to use either prek or pre-commit locally, as prek is designed as a drop-in replacement, ensuring a smooth transition.

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Changelog

• README.md
  • Updated instructions to include prek install alongside pre-commit install for initializing pre-commit hooks.
• pyproject.toml
  • Replaced pre-commit with prek in the dev dependency list.

Ignored Files

• Ignored by pattern: .github/workflows/** (2)
  • .github/workflows/run_precommit.yml
  • .github/workflows/update_precommit_hooks.yml

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[gemini-code-assist]

Code Review

This pull request transitions the project from using pre-commit to prek for pre-commit hooks. The changes update the developer documentation in README.md and the project dependencies in pyproject.toml. My review focuses on ensuring a smooth transition for developers. I've suggested an improvement to the README.md to clarify the change for developers setting up their environment. I've also suggested keeping both pre-commit and prek as development dependencies temporarily to align with the goal of a non-disruptive transition, as mentioned in the pull request description.

_{Note: Security Review has been skipped due to the limited scope of the PR.}

[gemini-code-assist]

This phrasing could be confusing for developers, as pre-commit is no longer installed as a development dependency. It would be clearer to explicitly state that prek is the new default and that pre-commit must be installed separately if a developer wishes to use it.

Suggested change

	Before committing changes, initialize `prek` with `prek install`, or `pre-commit` with `pre-commit install`. This will format code with each commit to keep the style consistent. _Neurodocker_ uses `black` for formatting.
	Before committing changes, initialize `prek` with `prek install` (now a dev dependency), or `pre-commit` (if installed separately) with `pre-commit install`. This will format code with each commit to keep the style consistent. _Neurodocker_ uses `black` for formatting.

[gemini-code-assist]

The PR description mentions that developers can switch at their own pace without disruption. By replacing pre-commit with prek, developers who reinstall their dependencies will lose pre-commit, which could be disruptive to their workflow. To allow for a smoother transition, consider including both pre-commit and prek in the development dependencies for a period of time.

Suggested change

	"prek",
	"pre-commit",
	"prek",