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Update kmeans neighborhood notebook take 2 (#714)

* Update kmeans neighborhood notebook

* Revert start_docker.sh tags

* Revert example data

* merged main

* Revert example data

* Update neighborhood code

* Revert settings.py to avoid problems with tests

* Fix notebook test and remove mantis for now

* Fix tests

* Fix silhouette score function description

* Fix typo in notebook

* Add min_k

* Fix add 1 to generate_cluster_labels

* Breakup lines that removes cells with no neighbors

* Update notebook

* Change silhouette function code

* Add check for min_k

* Add tests

* Change cluster label code

* Add notebook plots

* Change error message to ValueError

73 of 73 new or added lines in 4 files covered. (100.0%)

2969 of 3137 relevant lines covered (94.64%)

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