Fix typos and add `codespell` pre-commit hook

[BioGeek]

Related issues: N/A

This PR fixes typos found by running codespell on the repsitory.

It also adds a codespell pre-commit hook so that typos are caught faster in the future. I also updated the package versions in the .pre-commit-config.yaml file.

Checks

• [x] a clear description of the PR has been added

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Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 92.30%. Comparing base (a721221) to head (302be48). Report is 14 commits behind head on develop.

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Additional details and impacted files

```diff @@ Coverage Diff @@ ## develop #173 +/- ## ======================================== Coverage 92.30% 92.30% ======================================== Files 125 125 Lines 7485 7485 ======================================== Hits 6909 6909 Misses 576 576 ```

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[Lookatator]

Hi @BioGeek, Thank you very much for the PR!

Because of the merge conflicts and the unsuccessful checks, I transferred all your commits to another internal branch, and solved all issues in that new PR: #194

I will close this PR, and will merge the new one very soon.