Why uv does not seems to see python packages installed in a different site-packages

[ccoulombe]

Question

Hello,

We have python packages provided from different site-packages, but uv pip list does not seem to see them.

For example, on our HPC systems

module load python/3.13 arrow/21
uv venv --clear TESTY
source TESTY/bin/activate

Then:

(TESTY) $ uv pip list
Using Python 3.13.2 environment at: TESTY

(TESTY) $ pip list | rg pyarrow
pyarrow            21.0.0

The site-packages are listed in $PYTHONPATH.

What am I missing in order for uv to see those packages ?

Thanks

Platform

Linux

Version

0.9.2

[charliermarsh]

uv does not include pip in the virtual environment by default, so pip list is likely showing you packages in some other environment (since it's likely the global pip).

[charliermarsh]

You can run uv venv --seed to include pip if necessary.

[ccoulombe]

Even with a pip installed, it is not showing the packages installed from other site-packages as pip naturally does.

$ module load python/3.13 arrow/21
$ uv venv --seed --clear TESTY
Using CPython 3.13.2 interpreter at: /cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v4/Compiler/gcccore/python/3.13.2/bin/python
Creating virtual environment with seed packages at: TESTY
 + pip==25.2+computecanada
Activate with: source TESTY/bin/activate
$ source TESTY/bin/activate
(TESTY) $ uv pip list
Using Python 3.13.2 environment at: TESTY
Package Version
------- ------------------
pip     25.2+computecanada
(TESTY) $ uv run which pip
/home/coulombc/TESTY/bin/pip
(TESTY) $ which pip
~/TESTY/bin/pip
(TESTY) $ pip list | rg pyarrow
pyarrow            21.0.0
(TESTY) $ uv pip list | rg pyarrow
Using Python 3.13.2 environment at: TESTY
(TESTY) $

It look like it may be an issue related to uv not seeing the PYTHONPATH perhaps?

Thanks!

[charliermarsh]

That sounds right -- is this a duplicate of #2500? We don't read arbitrary locations from sys.path.

[ccoulombe]

Looks like a duplicate yeah.

The packages are available from a different site-package as mentioned, which is not the same as the one from the virtual env.
To be precise, the packages are available from $EBROOTARROW/lib/python3.13/site-packages/ while the virtual env. has $VIRTUAL_ENV/lib/python3.13/site-packages/.

Any quick fix? Thanks