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Recurring TypeError with PrettyTree #48

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auroraab opened this issue Nov 22, 2024 · 1 comment
Open

Recurring TypeError with PrettyTree #48

auroraab opened this issue Nov 22, 2024 · 1 comment

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@auroraab
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Hello! Thank you so much for making and maintaining this wonderful tool. I've been working through the pipeline, and while the code is able to run through the steps in ali_to_anc, I do keep getting an error that seems to be in the PrettyTree script, and the output directories do not have the pdfs with trees in them. I recreated the error on the python API by running the following:

>>> topiary.draw.tree("01_gene-tree")
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/global/home/users/auroraab/.conda/envs/topiary/lib/python3.10/site-packages/topiary/draw/tree.py", line 181, in tree
    pt = PrettyTree(T,
  File "/global/home/users/auroraab/.conda/envs/topiary/lib/python3.10/site-packages/topiary/draw/prettytree.py", line 91, in __init__
    if issubclass(type(T),toytree.tree):
TypeError: issubclass() arg 2 must be a class, a tuple of classes, or a union 

Am I missing a package or something? I installed everything according to the instructions... Is it a python version syntax problem? I am running Python 3.10.8 (which if I remember correctly was necessary for installing some of the accessory programs topiary uses).

Very grateful for any advice you can provide!
Aurora

@cfreye
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cfreye commented Dec 3, 2024

Hi Aurora! I ran into a similar issue and was able to resolve it by installing version 2.0.1 of toytree. Hope this helps!

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