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

• a clear description of the PR has been added

[codecov-commenter]

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Codecov Report

All modified and coverable lines are covered by tests ✅

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

@@           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.