SlimTreeSequence "can't set attribute" errors

[mshpak76]

I have been trying to use SlimTreeSequence() to converts tree sequence files generated by Slim 3.5 into something that pyslim 0.700 could process. I'm getting a generic "can't set attribute" error, suggesting there's a failed linkage to some other library, but I can't figure out what that dependency may be. In case it matters, this is running on Python 3.8.6

Traceback (most recent call last):
File "recapitation_convert_format.py", line 7, in <module>
ts_new = pyslim.SlimTreeSequence(ts)
File "/opt/miniconda3/lib/python3.8/site-packages/pyslim/slim_tree_sequence.py", line 203, in __init__
 self.individual_locations = ts.tables.individuals.location
 AttributeError: can't set attribute

[petrelharp]

Ah - you'll hit this error if you use the new tskit with pyslim 0.700. I recommend using the beta for pyslim 1.0: https://pypi.org/project/pyslim/1.0b1/

Alternatively, just don't use SlimTreeSequence: pretty much all the functionality provided by SlimTreeSequence has been subsumed into tskit now, so you don't need that class at all. Stuff that isn't is now methods, e.g. pyslim.recapitate(ts) instead of SlimTreeSequence(ts).recapitate().

[jahink17]

Hi, it seems that the recapitate() method still includes a call to SlimTreeSequence(recap) at the very end and therefore runs into the same problem as above (i.e. the attribute error) -- at least in the version I'm using. Is there any way to work around this?

Thank you for your help!