Provide base class for dataset loaders

[cthoyt]

Summary

This PR abstracts the essential components of the dataset loader into a base class to allow for future implementations of eager datasets (e.g., all parts of the dataset are already in memory) and for other lazy local dataset loaders.

• [x] Code passes all tests
• [x] Unit tests provided for these changes
• [x] Documentation and docstrings added for these changes

Changes

• Create abstract base class with unimplemented methods for getting drugs, contexts, and labeled triples
• Rename mid-level class to RemoteDatasetLoader

Next steps

The following shows an implementation of an eager dataset, which might be more useful for local datasets.

@dataclass
class EagerDatasetLoader(DatasetLoader):
    """An eager dataset."""

    context_feature_set: ContextFeatureSet
    drug_feature_set: DrugFeatureSet
    labeled_triples: LabeledTriples

    def get_labeled_triples(self) -> LabeledTriples:
        """Get the labeled triples file from the storage."""
        return self.labeled_triples

    def get_context_features(self) -> ContextFeatureSet:
        """Get the context feature set."""
        return self.context_feature_set

    def get_drug_features(self):
        """Get the drug feature set."""
        return self.drug_feature_set

[aminemosbah]

any chance we would load , train and essentially test our own dataset ?

[cthoyt]

@aminemosbah I would suggest looking at https://chemicalx.readthedocs.io/en/latest/api/chemicalx.data.LocalDatasetLoader.html#chemicalx.data.LocalDatasetLoader for loading your own dataset that's already in the right format in a given directory

[aminemosbah]

thx, but i have smiles to predict in a csv file to predict locally , any quick snippet ?

[cthoyt]

@aminemosbah I have in mind a solution for what you want (which is the obvious realistic use case) but this it is blocked #50 and #58. @benedekrozemberczki would love to get your input on #50 ;)

[aminemosbah]

need to hack the dataloader to make it work for local data

[aminemosbah]

here is a possible solution https://chemicalx.readthedocs.io/en/latest/api/chemicalx.data.LocalDatasetLoader.html#chemicalx.data.LocalDatasetLoader