[prodigy] scoring module

[VGPReys]

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Checklist

• Tests added for the new code
• Documentation added for the code changes
• Does not break licensing
• Does not add any dependencies, if it does please add a thorough explanation

Summary of the Pull Request

Add a new scoring module [prodigy].

todo:

• init.py
• prodigy-prot
• prodigy-lig
• Chain reader
• Defaults:
  • shared parameters
  • Chain selection
  • Ligand selection
• installation instructions (pip install prodigy-prot prodigy-lig)
• Fix dependencies issues
• Third party or NOT ?
• Examples:
  • prot-prot
  • fix homotrimer issue
  • prot-lig

[rvhonorato]

I'm guessing you are still working on it - but keep in mind prodigy is also python so it should be used a library, not as a subprocess call

[VGPReys]

I'm guessing you are still working on it - but keep in mind prodigy is also python so it should be used a library, not as a subprocess call

maybe indeed a good idea.

[rvhonorato]

not an idea, it's how it should be done. also keep in mind this could cause a dependency deadlock, so add it as an optional dependency in pyproject.toml

[VGPReys]

It's already not possible to install both prodigy-prot and prodigy-lig within the same haddock3 env, as they both use different python versions.

[rvhonorato]

It's already not possible to install both prodigy-prot and prodigy-lig within the same haddock3 env, as they both use different python versions.

so add it as an optional dependency in pyproject.toml

[rvhonorato]

@VGPReys I've made your life easier by updating the max/min python versions of prodigy and prodigy-lig to match the ones here - so 3.9, 3.10, 3.11 and 3.12, check the latest releases

[VGPReys]

Nice, indeed will simplify the process

[rvhonorato]

Adding this dependencies will be easier after #1099