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I am reopening this PR. I've manually after reset the previous commit history. Looking at the commits, there were too many changes bundled together that I was not able to cherry pick across commits.
In terms of changes, I've simplified the synthetic dataset for unittests and incorporated some of the feedback such as only using the classifier for the unlabeled data and using more informative error messages.
The comments that were ignored were largely centered around unittests that check if a key exists in the AnnData object. These were ignored since the keys are only generated after calling the knn_clustering method and hence could not be checked somewhere else.