AnnData spatial analysis 1

[camisowers]

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What is the purpose of this PR?

Closes #1105.

How did you implement your changes

Assume that the user will use the AnnData conversion notebook once they have their completed cell table, and use this input for our spatial analyses computations. Functions that were changed to take only anndata_dir as input, rather than the cell table and distance matrix directory path:

• calc_dist_matrix()
• create_neighborhood_matrix()
• generate_cell_distance_analysis()

Notebook updates:

• kmeans (+ tests)
• mixing score

Remaining issues

• [x] Update notebooks
• [x] test_utils function to add dist mats to AnnData table
• [ ] waiting on new ark release

[review-notebook-app[bot]]

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[camisowers]

@alex-l-kong @srivarra Can you guys just take a preliminary look? I'll do a second pass when the notebook tests are running.