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Incompatible with python >3.8? #16

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joelnitta opened this issue Nov 24, 2021 · 0 comments
Open

Incompatible with python >3.8? #16

joelnitta opened this issue Nov 24, 2021 · 0 comments

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@joelnitta
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I encountered this error when using python v3.10.0

(magus-env) root@39db7c458bba:/wd/MAGUS/example# python3 ../magus.py -d outputs -i unaligned_sequences.txt -o magus_result.txt
Traceback (most recent call last):
  File "/wd/MAGUS/example/../magus.py", line 12, in <module>
    from align.aligner import mainAlignmentTask
  File "/wd/MAGUS/align/aligner.py", line 11, in <module>
    from align.decompose.decomposer import decomposeSequences 
  File "/wd/MAGUS/align/decompose/decomposer.py", line 11, in <module>
    from align.decompose import initial_tree, kmh
  File "/wd/MAGUS/align/decompose/initial_tree.py", line 13, in <module>
    from helpers import sequenceutils, hmmutils, treeutils
  File "/wd/MAGUS/helpers/treeutils.py", line 7, in <module>
    import dendropy
  File "/miniconda3/envs/magus-env/lib/python3.10/site-packages/dendropy/__init__.py", line 24, in <module>
    from dendropy.dataio.nexusprocessing import get_rooting_argument
  File "/miniconda3/envs/magus-env/lib/python3.10/site-packages/dendropy/dataio/__init__.py", line 20, in <module>
    from dendropy.dataio import newickreader
  File "/miniconda3/envs/magus-env/lib/python3.10/site-packages/dendropy/dataio/newickreader.py", line 29, in <module>
    from dendropy.dataio import nexusprocessing
  File "/miniconda3/envs/magus-env/lib/python3.10/site-packages/dendropy/dataio/nexusprocessing.py", line 30, in <module>
    from dendropy.utility import container
  File "/miniconda3/envs/magus-env/lib/python3.10/site-packages/dendropy/utility/container.py", line 356, in <module>
    class CaseInsensitiveDict(collections.MutableMapping):
AttributeError: module 'collections' has no attribute 'MutableMapping'

It seems similar to this issue, and it went away when I used python 3.8. So I'm guessing it's due to the same problem (use of deprecated collections).

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