RecursionError: maximum recursion depth exceeded while getting the repr of an object

[ivnsch]

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

pdb_file="Meeko/example/tutorial1/input_files/1iep_protein.pdb"
mk_prepare_receptor.py --read_pdb $pdb_file -o rec_1iep -p

and I get

  File "<path>/miniconda3/envs/vina/bin/mk_prepare_receptor.py", line 7, in <module>
    from meeko.cli.mk_prepare_receptor import main
  File "<path>/miniconda3/envs/vina/lib/python3.11/site-packages/meeko/__init__.py", line 10, in <module>
# ... 
RecursionError: maximum recursion depth exceeded while getting the repr of an object

What's wrong? thanks!

[rwxayheee]

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.

[rwxayheee]

Hi @ivnsch
Thanks again for reporting this. I opened a PR (#261) but need to talk to other lab members about it. We will need to upload the updated package and it might take a little longer. While we're working on this, there are a few walkaround options:

• micromamba install the current package; micromamba constructs the console scripts differently so we dodged the problem
• pip install from this repository
• (last but not least) conda install from a built package with Use dynamic entry to avoid circular import in generated console scripts when installed via conda #261. I validated the change this way

[diogomart]

I can't reproduce on linux. @rwxayheee did you observe the recursion error?

[rwxayheee]

Hi @diogomart! Yes, I can reproduce this when installed via conda on Mac.

[diogomart]

Do you know where the circular import happens?

[rwxayheee]

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. Get Outlook for iOS<https://aka.ms/o0ukef>

…

________________________________ 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? — Reply to this email directly, view it on GitHub<#260 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AUZKPRRXLC5SRVDWX35JHZ32DQAMNAVCNFSM6AAAAABSZXPYPCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDKMJQG4ZDEMZTHA>. You are receiving this because you were mentioned.Message ID: ***@***.***>

[diogomart]

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.

[rwxayheee]

Yes, we can meet and discuss! Get Outlook for iOS<https://aka.ms/o0ukef>

…

________________________________ From: Diogo ***@***.***> Sent: Monday, December 2, 2024 11:02:30 AM 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. — Reply to this email directly, view it on GitHub<#260 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AUZKPRRYJV7ESKQHS6LFULL2DSVENAVCNFSM6AAAAABSZXPYPCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDKMJSGQ4DCMBRGA>. You are receiving this because you were mentioned.Message ID: ***@***.***>

[rwxayheee]

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:

• Configuration of current environment
  Could you please share with us the output file of pip freeze > requirements.txt?

• Content of the generated script "/miniconda3/envs/vina/bin/mk_prepare_receptor.py"

• Did you possibly install meeko (more than one times) with multiple package managers?
  I encountered some other importlib-related issues when I have attemped to install multiple Meeko in the same environment. See below for how I found out about it. You can use similar commands to check:

(meeko_tutorial_py39) amyhe@Amys-MBP Meeko % conda list meeko
# packages in environment at /Users/amyhe/miniconda3/envs/meeko_tutorial_py39:
#
# Name                    Version                   Build  Channel
meeko                     0.5.1                     dev_0    <develop>
(meeko_tutorial_py39) amyhe@Amys-MBP Meeko % micromamba list | grep meeko
List of packages in environment: "/Users/amyhe/miniconda3/envs/meeko_tutorial_py39"
  meeko                      0.6.0        pyhd8ed1ab_1          conda-forge
(meeko_tutorial_py39) amyhe@Amys-MBP Meeko % pip list | grep meeko
meeko               0.6.0
(meeko_tutorial_py39) amyhe@Amys-MBP Meeko % 

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 ^^