merge DataLinks to MetcalfScoring class

[CunliangGeng]

The role of class DataLinks is to calculate the presence and co-presence for given e.g. GCFs, spectra and strains. The presence matrix are required to compute the Metcalf scores.

This PR merge the role DataLinks to MetCalfScoring and utils to improve the clarity of codebase and to simplify the scoring process.

DataLinks also has a get_common_strains method that will be merged to ObjectLink class in next PR.

Major changes:

• move functions of calculating presence to utils
• merge function of calculating co-presence and raw score to MetcalfScoring
• remove whole linking folder
• remove deprecated and unused code

[CunliangGeng]

• #260
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• dev

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[CunliangGeng]

Merge activity

• Jun 10, 3:24 AM EDT: @CunliangGeng started a stack merge that includes this pull request via Graphite.
• Jun 10, 3:25 AM EDT: @CunliangGeng merged this pull request with Graphite.