RecursionError: maximum recursion depth exceeded while getting the repr of an object #260
Comments
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Can confirm this problem may be a result of circular import. When installed via conda, the generated script is #!/bin/sh
'''exec' /opt/homebrew/anaconda3/envs/meeko_tutorial/bin/python "$0" "$@"
' '''
# -*- coding: utf-8 -*-
import re
import sys
from meeko.cli.mk_prepare_receptor import main
if __name__ == '__main__':
sys.argv[0] = re.sub(r'(-script\.pyw|\.exe)?$', '', sys.argv[0])
sys.exit(main())This problem is not observed with some other package managers like micromamba. As a walkaround for the time being, you could install meeko via pip or micromamba. We should fix this; we might want to rename the console scripts, or devert the entry points. |
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Hi @ivnsch
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I can't reproduce on linux. @rwxayheee did you observe the recursion error? |
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Hi @diogomart! Yes, I can reproduce this when installed via conda on Mac. |
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Do you know where the circular import happens? |
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It seems like it’s caused by conflict of console script name and the actual script under cli. (You could see the generated script on Mac in my previous comment; it’s like in mk_prepare_receptor it wants to import main from mk_prepare_receptor). Maybe Linux has a console script that is generated differently (and same reason micromamba doesn’t have this issue. To fix this, either changing the console script (entry point) name or creating a different entry point (see the most recent PR) should work. I tested with a locally built conda package.
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From: Diogo ***@***.***>
Sent: Sunday, December 1, 2024 10:59:18 PM
To: forlilab/Meeko ***@***.***>
Cc: Amy He ***@***.***>; Mention ***@***.***>
Subject: Re: [forlilab/Meeko] RecursionError: maximum recursion depth exceeded while getting the repr of an object (Issue #260)
Do you know where the circular import happens?
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I can't reproduce on a Mac either. From the code I don't see a path for recursion. We should meet and figure out where it is happening, I'm afraid it might be something weird like a conflicting installation of an older meeko where we missed an |
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Yes, we can meet and discuss!
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To: forlilab/Meeko ***@***.***>
Cc: Amy He ***@***.***>; Mention ***@***.***>
Subject: Re: [forlilab/Meeko] RecursionError: maximum recursion depth exceeded while getting the repr of an object (Issue #260)
I can't reproduce on a Mac either. From the code I don't see a path for recursion. We should meet and figure out where it is happening, I'm afraid it might be something weird like a conflicting installation of an older meeko where we missed an if __name__ == "__main__" guard.
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Hello @ivnsch I am reaching out to ask for your assistance in reproducing this issue. When I wrote the first reply to you, I could reproduce this but now I couldn't reproduce the exact issue. I'm afraid that #261 may be unnecessary and is not the right way to address this issue. Could you please let us know, if a startover from a new environment solve the issue? When updating or reinstalling a package, some old files might not be removed (renamed) properly, causing unexpected behaviors. I have encountered, and could still produce some other importlib-related issues if I attempted to downgrade or upgrade Meeko with conda in the same environment. I think the reason is that the entry point is not properly updated, while the package body is changing with the version. If this is the case, start over with a new environment and reinstall the required packages should always work. **If so, I will close #261 as unnecessary. ** Before, I was thinking that the problem was literally circular import but now I think it's not. If this is a persistent issue even with a new install in a new environment, could you please provide:
Either way, start over would be the best way to resolve the issue. Please let us know how it goes, and we're more than willing to help ^^ |
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I don't remember what I did to get this working before, but after removing and re-adding the environment (as instructed in https://autodock-vina.readthedocs.io/en/latest/installation.html#), I get the error below installing I stopped working on this (unrelated reasons) so there's no urgency from my side, but can continue debugging if it helps. |
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Alternatively, you could install from conda-forge (e.g. |
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I did a new install again and was able to follow the tutorial's basic docking example. Since I can't reproduce the original issue anymore and there has been no other reports, I'll close it, thanks! |
Hi, I just installed meeko from conda-forge and am following the basic docking for vina tutorial https://meeko.readthedocs.io/en/release/tutorial1.html#for-autodock-vina
and I get
What's wrong? thanks!
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