[BUG] Nano-GraphRAG dependences is NOT working

[someone132s]

Description

I'm installing kotaemon with nano-graphrag and i found it is not woring well. I found the error message like "Nano-GraphRAG dependencies not installed. Try pip install nano-graphrag to install. Nano-GraphRAG retriever pipeline will not work properly." though i have installed the nano-graphrag.

here is my environment:

system: debian12.9
system python3 version: 3.11
kotaemon version: local (perhaps 0.10.2)
koatemon deployment method: docker compose
nano-graphrag version: 0.0.8
nano-graphrag deployment method: pipx install -e .

Otherwise, I tried to uninstall and install the lib hnswlib either before installing nano-graphrag or after installing nano-graphrag, and it's not working as well. I also tried "pip install nano-graphrag" and it's failed due to some incompatible libs.

Reproduction steps

1. install kotaemon with docker first
2. install nano-graphrag with pipx
3. docker compose up kotaemon
4. docker compose logs kotaemon -f

Screenshots

![DESCRIPTION](LINK.png)

Logs

root@Debian12:/opt/kotaemon# docker logs kotaemon_app -f
/app/launch.sh: 20: ollama: not found
[nltk_data] Downloading package punkt_tab to
[nltk_data]     /usr/local/lib/python3.10/site-
[nltk_data]     packages/llama_index/core/_static/nltk_cache...
[nltk_data]   Unzipping tokenizers/punkt_tab.zip.
Nano-GraphRAG dependencies not installed. Try `pip install nano-graphrag` to install. Nano-GraphRAG retriever pipeline will not work properly.
INFO:chromadb.telemetry.product.posthog:Anonymized telemetry enabled. See                     https://docs.trychroma.com/telemetry for more information.
INFO:kotaemon:posthog.capture called with args: ('1b6a3375-cb58-42af-a546-d6d1d1bc1cf4', 'ClientStartEvent', {'batch_size': 1, 'in_colab': False, '$process_person_profile': False, 'chroma_version': '0.5.16', 'server_context': 'None', 'hosted': False, 'chroma_api_impl': 'chromadb.api.segment.SegmentAPI', 'is_persistent': False, 'chroma_server_ssl_enabled': False, 'chroma_server_api_default_path': <APIVersion.V2: '/api/v2'>}), kwargs: {}
INFO:kotaemon:posthog.capture called with args: ('1b6a3375-cb58-42af-a546-d6d1d1bc1cf4', 'ClientCreateCollectionEvent', {'batch_size': 1, 'collection_uuid': 'c7e9a329-2834-4779-9f00-86c2ac2b4a42', '$process_person_profile': False, 'chroma_version': '0.5.16', 'server_context': 'None', 'hosted': False, 'chroma_api_impl': 'chromadb.api.segment.SegmentAPI', 'is_persistent': False, 'chroma_server_ssl_enabled': False, 'chroma_server_api_default_path': <APIVersion.V2: '/api/v2'>}), kwargs: {}
INFO:kotaemon:posthog.capture called with args: ('1b6a3375-cb58-42af-a546-d6d1d1bc1cf4', 'ClientStartEvent', {'batch_size': 1, 'in_colab': False, '$process_person_profile': False, 'chroma_version': '0.5.16', 'server_context': 'None', 'hosted': False, 'chroma_api_impl': 'chromadb.api.segment.SegmentAPI', 'is_persistent': False, 'chroma_server_ssl_enabled': False, 'chroma_server_api_default_path': <APIVersion.V2: '/api/v2'>}), kwargs: {}
INFO:kotaemon:posthog.capture called with args: ('1b6a3375-cb58-42af-a546-d6d1d1bc1cf4', 'ClientCreateCollectionEvent', {'batch_size': 1, 'collection_uuid': '2440597f-a74d-4df2-afb9-baa0d8837469', '$process_person_profile': False, 'chroma_version': '0.5.16', 'server_context': 'None', 'hosted': False, 'chroma_api_impl': 'chromadb.api.segment.SegmentAPI', 'is_persistent': False, 'chroma_server_ssl_enabled': False, 'chroma_server_api_default_path': <APIVersion.V2: '/api/v2'>}), kwargs: {}
INFO:kotaemon:posthog.capture called with args: ('1b6a3375-cb58-42af-a546-d6d1d1bc1cf4', 'ClientStartEvent', {'batch_size': 1, 'in_colab': False, '$process_person_profile': False, 'chroma_version': '0.5.16', 'server_context': 'None', 'hosted': False, 'chroma_api_impl': 'chromadb.api.segment.SegmentAPI', 'is_persistent': False, 'chroma_server_ssl_enabled': False, 'chroma_server_api_default_path': <APIVersion.V2: '/api/v2'>}), kwargs: {}
INFO:kotaemon:posthog.capture called with args: ('1b6a3375-cb58-42af-a546-d6d1d1bc1cf4', 'ClientCreateCollectionEvent', {'batch_size': 1, 'collection_uuid': 'bd86573c-cb44-4695-8614-578a9213f45b', '$process_person_profile': False, 'chroma_version': '0.5.16', 'server_context': 'None', 'hosted': False, 'chroma_api_impl': 'chromadb.api.segment.SegmentAPI', 'is_persistent': False, 'chroma_server_ssl_enabled': False, 'chroma_server_api_default_path': <APIVersion.V2: '/api/v2'>}), kwargs: {}
INFO:matplotlib.font_manager:generated new fontManager
User "admin" already exists
Setting up quick upload event
Running on local URL:  http://0.0.0.0:7860
INFO:httpx:HTTP Request: GET http://localhost:7860/startup-events "HTTP/1.1 200 OK"
INFO:httpx:HTTP Request: HEAD http://localhost:7860/ "HTTP/1.1 200 OK"

To create a public link, set `share=True` in `launch()`.
#################
root@Debian12:/opt/nano-graphrag# pipx uninstall hnswlib
uninstalled hnswlib! ✨ 🌟 ✨
root@Debian12:/opt/nano-graphrag# pipx install hnswlib --include-deps
⚠️  Note: f2py was already on your PATH at /usr/local/bin/f2py
  installed package hnswlib 0.8.0, installed using Python 3.11.2
  These apps are now globally available
    - f2py
    - numpy-config
done! ✨ 🌟 ✨
root@Debian12:/opt/nano-graphrag# pipx install nano-graphrag

root@Debian12:/opt/nano-graphrag# pipx install -e . --include-deps
⚠️  Note: futurize was already on your PATH at /usr/local/bin/futurize
⚠️  Note: pasteurize was already on your PATH at /usr/local/bin/pasteurize
⚠️  Note: openai was already on your PATH at /usr/local/bin/openai
⚠️  Note: httpx was already on your PATH at /usr/local/bin/httpx
⚠️  Note: tqdm was already on your PATH at /usr/local/bin/tqdm
⚠️  Note: normalizer was already on your PATH at /usr/bin/normalizer
⚠️  File exists at /root/.local/bin/f2py and points to /root/.local/pipx/venvs/hnswlib/bin/f2py, not
    /root/.local/pipx/venvs/nano-graphrag/bin/f2py. Not modifying.
⚠️  Note: numba was already on your PATH at /usr/local/bin/numba
⚠️  Note: fonttools was already on your PATH at /usr/local/bin/fonttools
⚠️  Note: pyftmerge was already on your PATH at /usr/local/bin/pyftmerge
⚠️  Note: pyftsubset was already on your PATH at /usr/local/bin/pyftsubset
⚠️  Note: ttx was already on your PATH at /usr/local/bin/ttx
⚠️  Note: datasets-cli was already on your PATH at /usr/local/bin/datasets-cli
⚠️  Note: get_gprof was already on your PATH at /usr/local/bin/get_gprof
⚠️  Note: get_objgraph was already on your PATH at /usr/local/bin/get_objgraph
⚠️  Note: undill was already on your PATH at /usr/local/bin/undill
⚠️  Note: huggingface-cli was already on your PATH at /usr/local/bin/huggingface-cli
⚠️  Note: json_repair was already on your PATH at /usr/local/bin/json_repair
⚠️  Note: litellm was already on your PATH at /usr/local/bin/litellm
⚠️  Note: fastapi was already on your PATH at /usr/local/bin/fastapi
⚠️  Note: gunicorn was already on your PATH at /usr/local/bin/gunicorn
⚠️  Note: jsonschema was already on your PATH at /usr/local/bin/jsonschema
⚠️  Note: dotenv was already on your PATH at /usr/local/bin/dotenv
⚠️  Note: rq was already on your PATH at /usr/local/bin/rq
⚠️  Note: rqinfo was already on your PATH at /usr/local/bin/rqinfo
⚠️  Note: rqworker was already on your PATH at /usr/local/bin/rqworker
⚠️  Note: uvicorn was already on your PATH at /usr/local/bin/uvicorn
⚠️  Note: optuna was already on your PATH at /usr/local/bin/optuna
⚠️  Note: alembic was already on your PATH at /usr/local/bin/alembic
⚠️  Note: mako-render was already on your PATH at /usr/bin/mako-render
⚠️  Note: jp.py was already on your PATH at /usr/local/bin/jp.py
  installed package nano-graphrag 0.0.8.2, installed using Python 3.11.2
  These apps are now globally available
    - alembic
    - datasets-cli
    - distro
    - dotenv
    - fastapi
    - fonttools
    - futurize
    - get_gprof
    - get_objgraph
    - gunicorn
    - httpx
    - huggingface-cli
    - jp.py
    - json_repair
    - jsonschema
    - litellm
    - mako-render
    - normalizer
    - numba
    - openai
    - optuna
    - pasteurize
    - pyftmerge
    - pyftsubset
    - rq
    - rqinfo
    - rqworker
    - tqdm
    - ttx
    - undill
    - uvicorn
    - f2py (symlink missing or pointing to unexpected location)
done! ✨ 🌟 ✨
root@Debian12:/opt/nano-graphrag#

my docker compose file 

services:
  kotaemon:
    image: ghcr.io/cinnamon/kotaemon:main-full
    container_name: kotaemon_app
    environment:
      - GRADIO_SERVER_NAME=0.0.0.0
      - GRADIO_SERVER_PORT=7860
    ports:
      - "8860:7860"
    volumes:
      - ktem_app_data:/app/ktem_app_data
    networks:
      - kotaemon_network
    stdin_open: true
    tty: true

volumes:
  ktem_app_data:
    name: ktem_app_data

networks:
  kotaemon_network:
    name: kotaemon_network
    driver: bridge

Browsers

No response

OS

Linux

Additional information

No response