Subset of anndata leads to broken graph connectivity

[newmana]

This fixes issue #340 - the cause is that the graph can be disconnected when subsetted and kNN needs to be re-calculated.

Changes:

• Calling pseudotime without a kNN causes an error - requires it to be run first.
• When AnnData is subset the neighbourhood graph can become disconnected and running pseudotime on it creates NaN/Infinite distance nodes - both were kept in the old code - in the new code any node touching these will be removed.
• The fall through if there is equal pseudotime is arbitrary - just picks the node with lowest node number.

Also added some small changes around Xenium data downloading - start of support for zarr in zips and files in subdirectories.