Major PR refactoring the code and making it easily to read / reuse for processing

[ypriverol]

@rita-gama @DiogoCSTF @leandro-sobral:

Here is the first PR to clean up the project, making it easier for users with no deep-learning background to use it. I think that because it is a big PR, it's better to test before accepting it, rather than pulling my fork and testing it locally. As we discussed offline, we removed all the GenerativePRoteomics towards a cleaner version of the package GainPro

[Copilot]

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[DiogoCSTF]

I have tested and I have only a few points to address:

1. The download function gives the idea that it can download and use any pre-trained model from Hugging Face, and even though it can download any model, the usage part is not so true because the code in it is specific for the GAIN_DANN model. This is something the have into account for that function.

2. When I was running the GAIN-DANN model, I got an error message regarding line 179 in the gainpro.py file.
   I believe what is happening is that you are calling the Data module from our Gain model instead of the DataDANN module, which is specific to the GAIN-DANN model. I believe the same might be happening in lines 185 and 256.

Apart from these, everything seems to be fine

[ypriverol]

@DiogoCSTF Thanks for your review I have tackle you comments.

[Copilot]

Pull request overview

Copilot reviewed 65 out of 81 changed files in this pull request and generated 25 comments.

Comments suppressed due to low confidence (1)

gainpro/model.py:57

• The method parameter should be self instead of cls. This is an instance method, not a class method, so using cls is misleading and incorrect.

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[Copilot]

Pull request overview

Copilot reviewed 65 out of 81 changed files in this pull request and generated 4 comments.

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