Alright I know what the problem is.
Before creating the viz we drop all rows from the metadata that contain any empty cells. This just so happens to remove all metadata rows with a depth value of anything other than 2. Then when we go to create the viz skbio complains because the depth column has 0 variance (because all values in the column are 2). There is a safeguard that is meant to prevent this, but it is failing because it only checks for 0 variance columns before we remove the rows containing empty cells.
I’ll look into more permanently resolving this issue, but for now if you delete the depth column from the metadata the method should work.