Here we go again...

After further analysis (the trial & error kind), I found out that the error of modified values only occurs in unsorted data. Which makes perfect sense as Python's list.remove picks the first matching item. So the ordering of data plays a role.

As a quick fix …

This is a thumbnail of a visualisation of the separate clustering steps. Open original SVG file for better readability.

The linked image shows the individual steps through the existing clustering algorithm. Each "horizontal line" (the Y-Axis) represents one step of the algorithm. The distance between each "line" represents the level …

It turns out, the test I prepared earlier passes. So the reported issue needs a bit more work. I wanted to avoid the data-set which reproduces the failure because I'm lazy.

I should have known better.

So I will now do a similar manual step through the data-set as I …