New pre-commit hooks for everything in code_style.sh ; make code compliant with these hooks

[SamuelMarks]

Description

Many of my contributions have been to improve the overall quality of this codebase through application of automated code-quality tooling. You already have pre-commit hooks; this PR adds everything in your code_style.sh into it; so no longer will people be able to contribute code so low quality it doesn't pass the automated code-quality checking tooling.

Along the way I found and fixed actual errors, like in MaxText/convert_deepseek_unscanned_ckpt.py when the API changed (#1837) and tests didn't pickup the issue but pytype did. Ditto for the required MaxText/sft_trainer.py update from #1327. Also some incorrect types being used (ints vs strings; ints vs np.ndarray; floats vs np.ndarray) and add missing __init__.pys so imports work properly (no pytype module-error).

EDIT: Following internal team-member request, I wrote and executed this script to split this PR up. Don't close this PR, but merge the linked ones first.

fd --exact-depth 2 -Ftd -j1 -x bash -c 'd=${0:2}; d=${d//\//.}; title="[${d}] pytype + pylint + pyink + codespell"; git switch main && git reset --hard && git checkout -b "qa_${d}" && git checkout auto_check_and_precommit_and_bash_code_style_sh "${0}" && git commit --no-verify -S -am "${title}" && git push mine "qa_${d}" ; gh pr create --title "${title}" --body "$(cat -- /tmp/a.md)"' {//}

Tests

N/A

Checklist

Before submitting this PR, please make sure (put X in square brackets):

• I have performed a self-review of my code.
• I have necessary comments in my code, particularly in hard-to-understand areas.
• I have run end-to-end tests tests and provided workload links above if applicable.
• I have made or will make corresponding changes to the doc if needed.

[richjames0]

lgtm pending gemini review. it wasn't working so i just removed and re-added the tag. PTAL before submitting

[NicoGrande]

LGTM

[RissyRan]

@richjames0 & @shralex I think I know the reason now.

This PR is forked version from SamuelMarks:auto_check_and_precommit_and_bash_code_style_sh, and the workflow for gemini-review has rule github.event.pull_request.head.repo.fork == false. This rule is recommended to protect our resources from forked branches (out of control for usage).