Enable clustering by distance matrix input #33
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Adds a mutually exclusive input argument, `--distance-matrix`, to the `pathogen-cluster` command and corresponding logic to load this matrix and find clusters from its using HDBSCAN's precomputed metric option. When an embedding is provided instead, `pathogen-cluster` runs HDBSCAN with the default Euclidean distance metric.
Moves imports of subcommand functions after arguments have been parsed which massively speeds up time to print help output for each command.
Speeds up runtime of individual commands by moving command-specific imports into each command's function, avoiding expensive imports like HDBSCAN when they won't be used.
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Adds a mutually exclusive input argument,
--distance-matrix, to thepathogen-clustercommand and corresponding logic to load this matrix and find clusters from its using HDBSCAN's precomputed metric option. When an embedding is provided instead,pathogen-clusterruns HDBSCAN with the default Euclidean distance metric.