FIX match only dense dataframes

[GeorgWa]

SpecLibBase.available_fragment_dfs() would return ['_fragment_df', '_fragment_intensity_df', '_fragment_mz_df'] on a SpecLibFlat and fail on .remove_unused_fragments().

This makes sure it's really matching _fragment_[attribute_name]_df.

[jalew188]

Looks nice

[GeorgWa]

I discussed the topic a bit with @mo-sameh and we reasoned that there is currently some ambiguity between a SpecLibBase and SpecLibFlat. As the SpecLibFlat is inherited and produced by a SpecLibBase it can still have dense representations (fragment_mz_df, fragment_intensity_df etc.) and inherited functions like remove_unused_fragments which don't operate on the flat representation. This is confusing as one would expect they affect your flat library.

Therefore I made some small changes to this PR:

1. Renaming available_fragment_dfs to available_dense_fragment_dfs to make clear this only returns dense fragments matrices.
2. Returning an empty list on SpecLibFlat.available_dense_fragment_dfs to make clear that dense representations are not supported as part of a SpecLibFlat.
3. Get rid of dense representations when SpecLibBase.parse_base_library is called. If keep_original_frag_dfs is set to true, a deprecation warning is issued.
4. Raise a not implemented error if SpecLibFlat.remove_unused_fragments is called.

I think to handle complexity we have to keep the different library types better separated.

Looking forward to hear your thoughts

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[jalew188]

We should use SpecLibBase as the composite instead of the parent class.

[mo-sameh]

The save/load_hdf functions in flat.py are still using the dense DataFrames.
I agree that there's a need for refactoring the class structures and their relationships. Apart from that, for this PR everything looks good to me.

[GeorgWa]

I agree, or we should have a base class which only handles precursor operations and have this as parent class for SpecLibBase and SpecLibFlat. I think this would be a separate bigger refactoring involving Magnus.

[jalew188]

Yes, let's keep as it is now. You can merge I think

[jalew188]

What about move this into flat_lib? As a base lib must have dense frag dfs

[GeorgWa]

It's only applicable to the dense lib. The flat lib will always return an empty list.

The issue is that it's inherited.