Add notebooks

[amjjbonvin]

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Checklist

• Tests added for the new code
• Documentation added for the code changes
• Modifications / enhancements are reflected on the haddock3 user-manual
• CHANGELOG.md is updated to incorporate new changes
• Haddock3 version has been incremented in pyproject.toml
• Does not break licensing
• Does not add any dependencies, if it does please add a thorough explanation

Summary of the Pull Request

Added a new directory (notebooks) with a first Jupyter notebook for the antibody-antigen tutorial running on Colab

Related Issue

Closes #1367

[rvhonorato]

I also see this PR is not tied to any issue - please add an issue before merging

[amjjbonvin]

I also see this PR is not tied to any issue - please add an issue before merging

related to issue #1367

[rvhonorato]

so please link it here

[amjjbonvin]

Thanks Rodrigo Those instructions are clear and work perfectly (you do indeed need to isolate in a venv the entire notebook installation to be safe). I will add those to the README file

[amjjbonvin]

PS: But we do have issues with the interactive plots it seems (at least on my laptop / OSX). The section about `Visualizing the scores and their components`: the interactive plots are not showing.

[amjjbonvin]

Updated the README file, linked to the issue.
But we still have the issue that the interactive plots are not showing when running locally (while it works on colab).

[amjjbonvin]

@rvhonorato - as the installation now has the notebooks option, the notebooks tests should only be performed if it was installed with this option. Currently the tests are failing. Can you check/fix it?

[amjjbonvin]

PS: The notebook will have to be updated to use the main version once the notebooks branch will have been merged.

[rvhonorato]

Marking this as a draft because it's not ready yet. The addition of the libnotebooks (and its tests) needs to done in a separate PR, it should then be merged and published to pypi and used here.

The latest changes have tied the execution of this notebook to a git clone which is very error prone and likely to make the notebook unstable.

Once the other PR is merged we can resume work on this one

[rvhonorato]

before merging this it would also be good to check how we can use Binder for it and add it in the repository README - https://mybinder.org