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support for python 3.10? #1301

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zhang-ivy opened this issue Apr 19, 2023 · 2 comments · May be fixed by #1286
Open

support for python 3.10? #1301

zhang-ivy opened this issue Apr 19, 2023 · 2 comments · May be fixed by #1286

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@zhang-ivy
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zhang-ivy commented Apr 19, 2023 •
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Will yank support python 3.10?

I'm running into errors when running the yank analysis notebook with the CLI using python 3.10.

The first error I get:

Traceback (most recent call last):
  File "/home/zhangi/miniconda3/envs/perses-paper7/bin/yank", line 6, in <module>
    from yank.cli import main
  File "/home/zhangi/miniconda3/envs/perses-paper7/lib/python3.10/site-packages/yank/__init__.py", line 12, in <module>
    from . import utils
  File "/home/zhangi/miniconda3/envs/perses-paper7/lib/python3.10/site-packages/yank/utils.py", line 279, in <module>
    class CombinatorialTree(collections.MutableMapping):
AttributeError: module 'collections' has no attribute 'MutableMapping'

When I run the yank analysis notebook with python 3.9, I see the following warning:

<stdin>:1: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated since Python 3.3, and in 3.10 it will stop working

So it seems like I just need to change collections.MutableMapping to collections.abc.MutableMapping.

When I fix this error in my local version of yank, I get the following error:

TypeError: load() missing 1 required positional argument: 'Loader'

I think this is happening because the yaml file is not being loaded properly here:

yank/Yank/analyze.py

Line 299 in c060590

analysis = yaml.load(f)

These errors are simple enough to fix, but I'm just wondering whether we plan on updating yank to be compatible with python 3.10?
@zhang-ivy
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CC: @jchodera @ijpulidos @mikemhenry

@ijpulidos
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Thanks for reporting this, we should definitely try to support newer python versions.

@ijpulidos ijpulidos linked a pull request Apr 19, 2023 that will close this issue
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Fix/support python 310 choderalab/yank
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@ijpulidos @zhang-ivy