Installation question

[swbujnowski]

Hi Frank,

I am trying to install SNAF but I am running into trouble. I have started a fresh conda environment with python 3.7 on a Linux system as follows:

$ module load miniforge3/24.5.0-0
(base) $ conda create -p /risapps/rhel8/miniforge3/24.5.0-0/envs/snaf-0.7.0 python=3.7
(base) $ conda activate snaf-0.7.0

But when I issue the pip install command I received the following error:

(snaf-0.7.0) $ pip install git+https://github.com/frankligy/SNAF.git@e23ce39512a1a7f58c74e59b4b7cedc89248b908
Fatal Python error: initsite: Failed to import the site module
Traceback (most recent call last):
File "/risapps/rhel8/miniforge3/24.5.0-0/envs/snaf-0.7.0/lib/python3.7/site.py", line 73, in
import os
File "/risapps/rhel8/miniforge3/24.5.0-0/envs/snaf-0.7.0/lib/python3.7/os.py", line 29, in
from _collections_abc import _check_methods
ImportError: cannot import name '_check_methods' from '_collections_abc' (/risapps/rhel8/miniforge3/24.5.0-0/envs/snaf-0.7.0/lib/python3.7/_collections_abc.py)

Please let me know what I should do next.

Thanks,
Stan

[frankligy]

Hi @swbujnowski,

There's always dozens of possibilities underlying an installation error. I can only offer some guesses from my end. Have you successfully used the this particular miniforge to install other python3 package before? This is to rule out the possibility that this is a corrupted conda environment.

Then, when I use -p for my conda environment, I normally specify the full path of my conda environment when using pip, sometimes when you call pip, it is not calling the actual pip in the isolated env, but not sure if it's the issue here.

/path/to/snaf-0.7.0/bin/python3.7 -m pip install git+https://github.com/frankligy/SNAF.git@e23ce39512a1a7f58c74e59b4b7cedc89248b908

If above two do not solve your problem, maybe just type in the error in the chatGPT or other AI tool and tried some of their suggestions, for instance, test if the python3.7 hasn't properly installed, etc. Because it can really be many different things, sometimes I also need to test around when I am in a new environment.

If it still persists, we can look at that again, but let me know what you have tried and how did them go, because in that way, I can have a better sense of what might have gone wrong.

Best,
Frank