Scvi in R doesn't update to scvi-tools even after uninstalling and reinstalling (I think :) about scvi-tools HOT 3 CLOSED

Can you check that scVI is imported from the same environment in which you are uninstalling it? It would be easier to check that you can uninstall and the import fails and the reinstall.
However, PyPI might create issues in this environment and using a new environment would then be the easiest way to fix it.

from scvi-tools.

Okay, so I tried to check the python environment R is using, which I believe should be this:

`> py_config()
python: /Library/Frameworks/Python.framework/Versions/3.12/bin/python3
libpython: /Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/config-3.12-darwin/libpython3.12.dylib
pythonhome: /Library/Frameworks/Python.framework/Versions/3.12:/Library/Frameworks/Python.framework/Versions/3.12
version: 3.12.1 (v3.12.1:2305ca5144, Dec 7 2023, 17:23:39) [Clang 13.0.0 (clang-1300.0.29.30)]
numpy: /Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/numpy
numpy_version: 1.26.3
scanpy: [NOT FOUND]

NOTE: Python version was forced by use_python() function`

And compared it to the environment I installed scvi-tools in:

/Library/Frameworks/Python.framework/Versions/3.12/bin/python3 -m pip install scvi-tools

Both are the same, so I would say they are the same environment.
But when I try to check what is installed in that environment I don't actually get an answer

`➜ ~ /Library/Frameworks/Python.framework/Versions/3.12/bin/python3 -m pip list

➜ ~ `

So maybe there is indeed something wrong with the environment? ^^>

from scvi-tools.

I created a new environment with Conda, reinstalled scvi-tools and now it works. Thank you for your suggestions and help :))

from scvi-tools.