Adding the sylph coverage model to yacht

[rtraborn]

Hi @dkoslicki and team!
I created a sylph coverage model from Shaw and Yu, 2024 and added it to yacht, in a branch I named superyacht just for fun.
This is a draft that I'm still testing, so that and other caveats still apply. A few notes:

• The coverage code is in a function called cov_calc, which calculates lambda and ani according as specified by the sylph paper.
• For engineering reasons, I decided to put cov_calc inside get_exclusive_hashes, given that that function provides us with the signature objects needed to make the calculations.
• Because of this, I am passing the output of cov_calc, a pandas dataframe, along with hypothesis_recovery. There are probably good ways to integrate this, and I'll give this some more thought.
• Also, I decided to not incorporate the output of cov_calc more deeply into hypothesis_recovery for now. I have some ideas on what might be the best approach that we could discuss if you'd like. I thought it would be best to share this new branch while I look into this more deeply.
• The script internal_superyacht_test.py is just a script that I have been using to test the new branch, and this can be ignored; I'll remove it once we move towards publication.
• I plan to update the way I instantiated the AdjustStatusLambda enum in a more idiomatic python way this week. It should be a relatively quick fix.
• I did not incorporate the taxonomic reassignment/winner_map routine from sylph, but it's something I would like to add.

I'm going to do more testing this week on additional datasets. Happy to discuss here or via email/video!

[rtraborn]

After some more testing, I just pushed some additional updates to this branch.

• Fixed a typo: corrected to logger.warning in cov_calc.py
• Added missing scipy.special.gamma import to utils.py
• Fixed a few bugs I discovered in binary_search_lambda()
• Replaced print statements with logger.info() for consistency
• Consolidated duplicate constants into utils.py
• Removed a few unused local variables from hypothesis_recovery_src.py

[sonarqubecloud]

Quality Gate passed

Issues
19 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarQube Cloud

[rtraborn]

A small update, but with my most recent commit from last night I made the promised change to the AdjustStatusLambda enum in cov_calc to make it more idiomatically python-like. I think it looks cleaner- thanks to @standage for the flagging this!