Refactoring changes and Pytest Integration

[FabianHofmann]

This PR proposes to feed back changes from the OET branch. This mostly include

• refactoring and cleanup
• unit testing script functions

As far as I see, most of these changes are qutie valuable, unit testing is something we should start to do anyway, so this is a good initiative.

For now, I put this PR on draft mode, as I also have some slight reversions that I would like to apply. But having it here allows us to better track overall changes.

Checklist

• I consent to the release of this PR's code under the AGPLv3 license and non-code contributions under CC0-1.0 and CC-BY-4.0.
• I tested my contribution locally and it seems to work fine.
• Code and workflow changes are sufficiently documented.
• Newly introduced dependencies are added to envs/environment.yaml and doc/requirements.txt.
• Changes in configuration options are added in all of config.default.yaml and config.tutorial.yaml.
• Add a test config or line additions to test/ (note tests are changing the config.tutorial.yaml)
• Changes in configuration options are also documented in doc/configtables/*.csv and line references are adjusted in doc/configuration.rst and doc/tutorial.rst.
• A note for the release notes doc/release_notes.rst is amended in the format of previous release notes, including reference to the requested PR.

[davide-f]

Regarding this tracking, I summarize here past discussions in the initiative.

This PR combines multiple different features some of them are quite good in spirit but may be better reviewed one by one.
By clustering the changes, it seemed we could have:

• 1 PR on pathlib, improving on Issue 501 os to pathlib #1017
• 1 PR on unit testing
• various improvements too to styling that can be placed as best and appropriate

Do I miss something?

[ekatef]

Re-opened as #1290. Please feel free to continue a discussion here.

@finozzifa a gentle reminder on the initial review comments mentioned in this comment. As discussed before, addressing the concerns in this comment is a necessary first step to implementing these changes. Thank you!