SlimTreeSequence() issues

[mshpak76]

I have a pyslim script with the standard syntax for reading in slim tree objects and then converting them to pyslim format, i.e.

_# read in slim tree object
ts = tskit.load("Test.trees")
#convert to pyslim format
ts_new = pyslim.SlimTreeSequence(ts)_

which now throws the error:

ts_new = pyslim.SlimTreeSequence(ts)  AttributeError: module 'pyslim' has no attribute 'SlimTreeSequence'. Did you mean: 'slim_tree_sequence'

I did update to a newer version of pyslim since the last time I used this code, however, I see nothing in the manual about SlimTreeSequence() being deprecated or replaced by an equivalent command (incidentally, replacing SlimTreeSequence() with slim_tree_sequence() gives me the same error, i.e. pyslim has no attribute...

Has there been some subtle change that needs to be implemented in order to convert a tskit ts object into a pyslim object apart from what I have?

[benjeffery]

Have you read https://tskit.dev/pyslim/docs/latest/previous_versions.html?highlight=slimtreesequence
There it says that SlimTreeSequence calls are no longer needed.

[mshpak76]

Thanks. I missed that. One aspect of SlimTreeSequence is that it would rename e.g. p1, p2, p3 (three populations in slim) as pop_0, pop_1, pop_2 (as I called them in my script). In the current version without SlimTreeSequence and the other features, are the original slim population names retained, or is there a new default re-labeling?

[petrelharp]

It's always best to just check directly; here's how you can find out:

for p in ts.populations():
  print(p)