Use `pre-commit`

[qin-yu]

Use pre-commit

• All changes in all commits are manually checked except the co-author-ed 5cf0a745c04f52115afa36ee49f692e59143d179
  • We agreed on Black with line width 120
  • Let's trust the faster alternative Ruff for these 66 reformatted files:

    The Ruff linter is compatible with Black out-of-the-box, as long as the line-length setting is consistent between the two.

• From now on, typos, format, and potential issues are checked by pre-commit hooks:
  • typos: https://github.com/crate-ci/typos (only needed "OME", "ND" and "datas" as exceptions)
  • ruff/ruff-format: https://github.com/astral-sh/ruff-pre-commit (Black-compatible)
  • Codecov: overkill

For contributors

You don't have to do anything because the CI fixes minor problems in new commits. But to check what might happen by yourself:

Either:

• Enable Ruff linter in your IDE
• Enable Ruff or Black formatter in your editor with line length 120

Or:

• cd to the repo root and run pre-commit run --all-files

[qin-yu]

pre-commit.ci shall be installed after merging this PR.

[qin-yu]

This PR includes substantial changes and improvements. Given the current unavailability of the other maintainers, I will proceed with merging it and start the next PR.

[qin-yu]

PS: Using co-author on the great reformatting commit caused GitHub to triple the addition/deletion count in stats.