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Bug: Cannot import modules in data_generation_ppi tutorial #577

@lloydtripp

Description

@lloydtripp

Describe the bug

I'm running the docker image and started on the tutorials to make sure everything works. Unfortunately, I'm having issues importing a module "ProteinProteinInterfaceQuery"

All of these imports work from the tutorial

from deeprank2.features import components, contact
from deeprank2.utils.grid import GridSettings, MapMethod
from deeprank2.dataset import GraphDataset
from deeprank2.query import QueryCollection

Just not this
from deeprank2.query import ProteinProteinInterfaceQuery

Environment:

  • OS system: Linux x86_64
  • Version: "FROM --platform=linux/x86_64 condaforge/miniforge3:23.3.1-1"

To Reproduce
Steps/commands/screenshots to reproduce the behaviour:

  1. Git clone deeprank2

  2. Build docker image LSF_DOCKER_VOLUMES="/storage1/fs1/ghaller/Active/lloydt/:/storage1/fs1/ghaller/Active/lloydt/ /home/lloydt:/home/lloydt" bsub -G compute-ghaller -q general-interactive -Is -a 'docker_build(lloydtripp/risdeeprank2:latest)' -- --no-cache -f "/storage1/fs1/ghaller/Active/lloydt/LT4_Pathogenicity-Models/docker/deeprank2" "/storage1/fs1/ghaller/Active/lloydt/LT4_Pathogenicity-Models/docker/deeprank2/"
    2a. Change the first Run comand to have "" at the end of each line

  3. Run image LSF_DOCKER_VOLUMES="/storage1/fs1/ghaller/Active/:/storage1/fs1/ghaller/Active/ /home/$USER:/home/$USER" LSF_DOCKER_PORTS='8888:8888' bsub -G compute-ghaller -Is -R 'rusage[mem=8GB] select[port8888=1]' -n 1 -q general-interactive -a "docker(lloydtripp/risdeeprank2:latest)" /bin/bash

  4. Activate environment and run jupyter server

source activate deeprank2
# Activate Jupyter Server
jupyter notebook --ip=0.0.0.0 --NotebookApp.token='' --NotebookApp.password='' --allow-root
  1. Open jupyter notebook and run first line.

Actual Results or Error Info

ImportError                               Traceback (most recent call last)
Cell In[7], line 11
      9 from deeprank2.dataset import GraphDataset
     10 from deeprank2.query import QueryCollection
---> 11 from deeprank2.query import ProteinProteinInterfaceQuery

ImportError: cannot import name 'ProteinProteinInterfaceQuery' from 'deeprank2.query' (/opt/conda/envs/deeprank2/lib/python3.10/site-packages/deeprank2/query.py)

Additional Context
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