missing modules and problem with notebook paths

[ander-yamamoto]

Hi, I followed the notebook example. I got some problems along the way but I was able to solve them, at least for my environment.

These modules are missing from setup:

• langchain-community
• llama-index-embeddings-huggingface

Also, to solve issue 4 the module

• community
  should be removed from setup.

Steps to replicate the problem and what I did to solve:
I tryed both on windows 10 and ubuntu 22.04

I installed Anaconda3-2024.06, created a new env and installed GraphReasoning.
It installed python 3.12.5

conda create -n GraphReasoning python pip jupyter
conda activate GraphReasoning
pip install git+https://github.com/lamm-mit/GraphReasoning

then I open python and try to import GraphReasoning but I get the error:

• ModuleNotFoundError: Module langchain_community.document_loaders not found. Please install langchain-community to access this module. You can install it using pip install -U langchain-community``

Then I install the missing module

• pip install -U langchain-community

and I open python and try to import GraphReasoning again which throws the error:

• ModuleNotFoundError: No module named 'llama_index.embeddings.huggingface'

After pip install llama-index-embeddings-huggingface , the code import GraphReasoning works on python.

Then I open jupyter notebook example GraphReasoning - Graph Analysis.ipynb
On section "Load graph and embeddings" there is an error:

• HTTPError: 404 Client Error: Not Found for url: https://huggingface.co/lamm-mit/GraphReasoning/resolve/main/GRAPHDATA//BioGraph.graphml

Note the double slash between GRAPHDATA and BioGraph.graphml!
I solved this by replacing every:
f"{data_dir}/{graph_name}" by f"{data_dir}{graph_name}"
f"{data_dir}/{embedding_file}" by f"{data_dir}{embedding_file}"

On Section "Graph statitcs an properties, I get the first graph ok, but the code
describe_communities_with_plots_complex(G, N=6, data_dir=data_dir_output)
give the error from issue 4

• AttributeError: module 'community' has no attribute 'best_partition'

It seems the community module on setup generate a conflict with python-louvain module that is also installed as community:
references:
python-louvain module
Stack overflow
I solved by keeping python-louvain and removing community in setup.py

After these changes, the notebook Graph Analysis.ipynb runs without errors and all graphs are shown.