Running sleap via import

[katiedunkley]

Hello, I am trying to follow this thread (#436) as I am attempting to import centroid coordinates of individuals into sleap. However, when attempting to import sleap (e.g. on Jupyter/Google collab) I am failing. On Jupyter "import sleap" kills and resets the kernal as a fatal error, whilst with google collab I get the following error: "ImportError: cannot import name '_Union' from 'typing' (/usr/lib/python3.8/typing.py)". I'm working with a Mac with an M1 processor and the sleap GUI works (following the installation guidance). As a side note, I have also tried importing example data (e.g. h5 format, fly from https://zenodo.org/record/3366908#.Y6INIuzP1wQ) from deepposekit and that does not work either (error 'pose missing'), so I am little stuck. Thanks in advance.

[roomrys]

Hi @katiedunkley,

Based on some research, one hypothesis is that there might be a conflict with the python version (python>=3.8) and one of our dependencies cattrs. However, I don't believe that is necessarily the case since I just tested a minimal Colab notebook:

!pip install sleap
exit()

import sleap

with python version 3.8.16 (both in Chrome and Microsoft Edge on Windows 10)

!python -V

resulting in no errors. Although the research example linked above used python v3.8.0....

Do you mind running the !python -V command in Colab (I would think Colab would default to the same python version across browsers/OS's, but just to check our basis). Also, if it isn't too much of a hassle, do you mind posting the full error messages and commands leading up to those errors?

Thanks,
Liezl

[katiedunkley]

Hi Liezl,

Thank you very much for your reply - that seems to be working now - I can import sleap with no errors following the code above. I just tried running the script again (#436) for a sanity check and it doesn't work still but that is using the !pip install sleap==1.1.0a7 which could be where it's going wrong for me. Many thanks for the help.

Best wishes,
Katie