[Bug]:No dependencies are installed with `uv pip install`

[adamkatav]

Do you need to file an issue?

• [x] I have searched the existing issues and this bug is not already filed.
• [x] I believe this is a legitimate bug, not just a question or feature request.

Describe the bug

I installed lightrag-hku like so:

uv pip install "lightrag-hku[api]"

However only the lightrag-hku package was installed:

Installed 1 package in 5ms
 + lightrag-hku==1.3.2

Works when installing from source except for the following dependecies:

nano-vectordb
ollama

Steps to reproduce

uv venv --python 3.11
. .venv/bin/activate
uv pip install "lightrag-hku[api]"

Expected Behavior

These packages should be installed:

 + aiofiles==24.1.0
 + aiohappyeyeballs==2.6.1
 + aiohttp==3.11.16
 + aiosignal==1.3.2
 + annotated-types==0.7.0
 + anyio==4.9.0
 + anytree==2.13.0
 + ascii-colors==0.7.0
 + asyncpg==0.30.0
 + attrs==25.3.0
 + autograd==1.7.0
 + bcrypt==4.3.0
 + beartype==0.18.5
 + certifi==2025.1.31
 + cffi==1.17.1
 + charset-normalizer==3.4.1
 + click==8.1.8
 + configparser==7.2.0
 + contourpy==1.3.2
 + cryptography==44.0.2
 + cycler==0.12.1
 + distro==1.9.0
 + ecdsa==0.19.1
 + fastapi==0.115.12
 + fonttools==4.57.0
 + frozenlist==1.6.0
 + future==1.0.0
 + gensim==4.3.3
 + graspologic==3.4.1
 + graspologic-native==1.2.5
 + h11==0.14.0
 + httpcore==1.0.8
 + httpx==0.28.1
 + hyppo==0.4.0
 + idna==3.10
 + jiter==0.9.0
 + joblib==1.4.2
 + kiwisolver==1.4.8
 + lightrag-hku==1.3.2 (from git+https://github.com/HKUDS/LightRAG.git@14b4bc96ce31086a807dc9d204a5409e8e812a3b)
 + llvmlite==0.44.0
 + matplotlib==3.10.1
 + multidict==6.4.3
 + nano-vectordb==0.0.4.3
 + networkx==3.4.2
 + numba==0.61.2
 + numpy==1.26.4
 + ollama==0.4.8
 + openai==1.75.0
 + packaging==24.2
 + pandas==2.2.3
 + passlib==1.7.4
 + patsy==1.0.1
 + pillow==11.2.1
 + pipmaster==0.5.4
 + pot==0.9.5
 + propcache==0.3.1
 + pyasn1==0.4.8
 + pycparser==2.22
 + pydantic==2.11.3
 + pydantic-core==2.33.1
 + pyjwt==2.10.1
 + pynndescent==0.5.13
 + pyparsing==3.2.3
 + python-dateutil==2.9.0.post0
 + python-dotenv==1.1.0
 + python-jose==3.4.0
 + python-multipart==0.0.20
 + pytz==2025.2
 + regex==2024.11.6
 + requests==2.32.3
 + rsa==4.9.1
 + scikit-learn==1.6.1
 + scipy==1.12.0
 + seaborn==0.13.2
 + setuptools==78.1.0
 + six==1.17.0
 + smart-open==7.1.0
 + sniffio==1.3.1
 + starlette==0.46.2
 + statsmodels==0.14.4
 + tenacity==9.1.2
 + threadpoolctl==3.6.0
 + tiktoken==0.9.0
 + tqdm==4.67.1
 + typing-extensions==4.13.2
 + typing-inspection==0.4.0
 + tzdata==2025.2
 + umap-learn==0.5.7
 + urllib3==2.4.0
 + uvicorn==0.34.2
 + wrapt==1.17.2
 + xlsxwriter==3.2.3
 + yarl==1.20.0

LightRAG Config Used

Paste your config here

Logs and screenshots

No response

Additional Information

• LightRAG Version: v1.3.2
• Operating System: Arch
• Python Version: 3.11
• Related Issues:

[JaremaPiekutowski]

The same with standard pip installation

[liguochuan00]

This is a huge problem

[danielaskdd]

This problem is solved by v1.3.5

[adamkatav]

This problem is solved by v1.3.5

Thanks! Tough, I have issues with the real time pip installation for 2 reasons:

1. When not running in virtual environment pip cannot install packages without the --break flag
2. uv users don't have pip installed by default. I believe that if pip is a dependency it should be specified as one.

This is my test for installing the latest version (v1.3.6) after manually installing pip:

2025-05-06 14:07:02 - pipmaster.package_manager - INFO - Executing: /tmp/shit/.venv/bin/python3 -m pip install --upgrade ollama
2025-05-06 14:07:05 - pipmaster.package_manager - ERROR - Command failed with exit code 1: /tmp/shit/.venv/bin/python3 -m pip install --upgrade ollama
--- stderr ---
ERROR: Can not perform a '--user' install. User site-packages are not visible in this virtualenv.
Traceback (most recent call last):
  File "/tmp/shit/.venv/bin/lightrag-server", line 10, in <module>
    sys.exit(main())
             ^^^^^^
  File "/tmp/shit/.venv/lib/python3.11/site-packages/lightrag/api/lightrag_server.py", line 627, in main
    app = create_app(global_args)
          ^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/shit/.venv/lib/python3.11/site-packages/lightrag/api/lightrag_server.py", line 198, in create_app
    from lightrag.llm.ollama import ollama_model_complete, ollama_embed
  File "/tmp/shit/.venv/lib/python3.11/site-packages/lightrag/llm/ollama.py", line 17, in <module>
    import ollama
ModuleNotFoundError: No module named 'ollama'

[danielaskdd]

The project is optimize for uv since v1.4.0. Please verify if the issue is resolved with the latest version.