Fix typos and add codespell pre-commit hook

[BioGeek]

What?

This PR fixes typos and adds a codespell pre-commit hook.

Why?

Because there were typos in the repsoitory.

How?

I found the typos by running codespell on the repository.

Extra

To catch typos faster in the future, I added a codespell pre-commit hook.
I also:

• updated the packages in the .pre-commit-config.yaml file
• fixed the repo name for the flake8 package
• reformatted a line to fix a line too long flake8 warning
• added a .codespell-ignore.txt to ignore codespell false positives coming from base64 encoded images in the ipynb notebook file.

[OmaymaMahjoub]

Thanks @BioGeek for this initiative 🔥, LGTM!