add deeprank module

[rvhonorato]

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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
• Does not break licensing
• Does not add any dependencies, if it does please add a thorough explanation

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[rvhonorato]

@ntxxt I am not exactly sure if you were planning to add deeprank-gnn-esm as a scoring module or something else but anyway I went ahead and got started on it as a scoring module.

I have added the skeleton for the module as well as the unittests, integration tests and necessary updates to the project installation and updates to the continuous integration pipeline.

One thing to note here is that haddock supports python versions 3.9 to 3.14 but deeprank-gnn-esmdoes not support 3.14. Also it seems that deeprank cannot be executed on mac, I opened a PR about it haddocking/deeprank-gnn-esm#32 and once that is merged we can bump deeprank version here to v1.0.1 - for now the tests will skip python3.14 and macos.

deeprank now support python3.14 and can be executed on a mac.

You can get this branch and then pip install -e '.[dev,deeprank-gnn-esm]'

The skeleton should be in place but there are still many things to be done I'll leave it to you to finish it - let me know if there's anything I can help with

[ntxxt]

Great! I was planning to do it but not sure how to handel the dependencies. I will start to look into this next week!

[rvhonorato]

now that we have deeprank-gnn-esm in pypi its very straightforward. since deeprank-gnn-esm has some large dependencies (a few GB) it is better to have it as optional, see how its now defined in the pyproject.toml. I already added the checks in the module to handle it.

The idea is that if you want to use the deeprank module you will install it with pip install haddock3[deeprank-gnn-esm] - same logic as the mpi optional dependency

[rvhonorato]

small update here to the minimum deeprank version and to the ci - now at v1.1.0 that supports both mac and python3.14, see haddocking/deeprank-gnn-esm#32 and haddocking/deeprank-gnn-esm#33