ImportError: cannot import name 'Iterator' from 'collections'

[sophialeeman]

When I run
python /Users/sophialeeman/opt/anaconda3/envs/e3fp/e3fp/conformer/generate.py -s caffeine.smi --num_conf 3 -o ./

I receive the following output:
2022-06-02 09:18:27,522|INFO|num_proc is not specified. 'processes' mode will use all 8 processes
2022-06-02 09:18:27,522|INFO|Parallelizer initialized with mode 'processes' and 8 processors.
2022-06-02 09:18:27,522|INFO|Input type: Detected SMILES file(s)
2022-06-02 09:18:27,522|INFO|Input file number: 1
Traceback (most recent call last):
File "/Users/sophialeeman/opt/anaconda3/envs/e3fp/e3fp/conformer/generate.py", line 601, in
run(**kwargs)
File "/Users/sophialeeman/opt/anaconda3/envs/e3fp/e3fp/conformer/generate.py", line 363, in run
data_iterator = make_data_iterator(
File "/Users/sophialeeman/opt/anaconda3/envs/e3fp_env/lib/python3.10/site-packages/python_utilities/parallel.py", line 66, in make_data_iterator
from collections import Iterator
ImportError: cannot import name 'Iterator' from 'collections' (/Users/sophialeeman/opt/anaconda3/envs/e3fp_env/lib/python3.10/collections/init.py)

Upon further research into this, I've found that others sometimes struggle with Iterator in python 3.10. Are there dependencies in this program that prevent me from using 3.10?

[sethaxen]

Thanks! Indeed it seems we were using aliases that were deprecated in Python 3.3 and are now removed in Python 3.10 (python/cpython#81505). Should be an easy fix.

[sethaxen]

@sophialeeman the issue was that one of our dependencies had not updated for Python 3.10. It has now been updated on pypi and anaconda, so any of the following should work:

If you installed e3fp using conda:

conda update sdaxen_python_utilities

If you installed e3fp using pip (either from pypi or from the master branch of this repo)

pip install --upgrade sdaxen_python_utilities

[sophialeeman]

Thank you so much, Seth!