BaseSimilarity.matrix method errors if all scores/matches are 0

[tharwood3]

Describe the bug
If the BaseSimilarity.matrix method is given two lists of spectrum objects which all have resulting scores of 0, and the array_type is set to "numpy", the indexing of the numpy score_array produces an error. When array_type is set to "sparse" no error is produced.

To Reproduce
Steps to reproduce the behavior:
Provide the BaseSimilarity.matrix method with two sets of spectra with no matching ions using the default array_type parameter.

Expected behavior
Output should give a numpy array with all zeros in the shape of the score_array.

Screenshots

Desktop (please complete the following information):

• OS: cray_shasta_c
• Version: 5.14.21-150400.24.81_12.0.87

Additional context
Looking at the source code, this seems to be caused from the BaseSimilarity.keep_score method filtering all scores resulting in the idx_row and idx_col lists remaining empty; which causes an error when they are used to index the score_array. Maybe bypass the keep_score method when the array_type == "numpy"?

Please let me know if any additional information is required. Thanks all for building and maintaining MatchMS! It is a great resource for the metabolomics community.