I just reviewed the PR and I don't see any issues with the code. Launching the notebook the old way (marimo run lvof.py) works as expected. However, when I tested it I ran into an error:

(marimo-lvof) valuing-flexibility-from-water/marimonotebook$ uvx marimo run --sandbox lvof.py
Running in a sandbox: uv run --isolated --no-project --with-requirements /tmp/tmpo3d14tc5.txt marimo run lvof.py

        Running lvof.py ⚡

        URL: http://localhost:2725

Traceback (most recent call last):
  File "/home/fletch/.cache/uv/archive-v0/VDQ8DUT_h_Lhwd4Qnv8KP/lib/python3.12/site-packages/marimo/_runtime/executor.py", line 157, in execute_cell
    exec(cell.body, glbls)
  File "/tmp/marimo_3924777/__marimo__cell_vblA_.py", line 2, in <module>
    import pandas as pd
ModuleNotFoundError: No module named 'pandas'

However, as I said the regular marimo run lvof.py command works, so clearly these dependencies are installed. To double check, this is the output of pip list:

(marimo-lvof) valuing-flexibility-from-water/marimonotebook$ pip list
Package            Version
------------------ ------------
anyio              4.6.0
asttokens          2.4.1
black              23.12.1
click              8.1.7
comm               0.2.1
contourpy          1.2.0
cycler             0.12.1
debugpy            1.8.0
decorator          5.1.1
docutils           0.21.2
exceptiongroup     1.2.0
executing          2.0.1
fonttools          4.47.2
h11                0.14.0
idna               3.10
importlib-metadata 7.0.1
ipykernel          6.29.0
ipython            8.20.0
itsdangerous       2.2.0
jedi               0.19.1
jupyter_client     8.6.0
jupyter_core       5.7.1
kiwisolver         1.4.5
marimo             0.9.1
Markdown           3.5.2
matplotlib         3.8.2
matplotlib-inline  0.1.6
mypy-extensions    1.0.0
nest_asyncio       1.5.9
numpy              1.26.3
packaging          23.2
pandas             2.1.4
parso              0.8.3
pathspec           0.12.1
pexpect            4.8.0
pickleshare        0.7.5
pillow             10.2.0
pip                23.3.2
platformdirs       4.1.0
prompt-toolkit     3.0.42
psutil             5.9.7
ptyprocess         0.7.0
pure-eval          0.2.2
Pygments           2.17.2
pymdown-extensions 10.7
pyparsing          3.1.1
python-dateutil    2.8.2
pytz               2023.3.post1
PyYAML             6.0.1
pyzmq              25.1.2
ruff               0.6.9
setuptools         69.0.3
six                1.16.0
sniffio            1.3.1
stack-data         0.6.2
starlette          0.39.2
tomlkit            0.12.3
tornado            6.3.3
traitlets          5.14.1
typing_extensions  4.9.0
tzdata             2023.4
uv                 0.4.20
uvicorn            0.31.1
wcwidth            0.2.13
websockets         12.0
wheel              0.42.0
zipp               3.17.0

I have no experience with uv, but it seems that is the source of this error. @Haleshot do you have an idea what might be going on here?

As a note, all this is being done inside marimo-lvof conda environment. I updated the dependencies in environment.yml to marimo==0.9.1 and uv==0.4.20 and left the rest of the environment as it was.

I just reviewed the PR and I don't see any issues with the code. Launching the notebook the old way (marimo run lvof.py) works as expected. However, when I tested it I ran into an error:

(marimo-lvof) valuing-flexibility-from-water/marimonotebook$ uvx marimo run --sandbox lvof.py
Running in a sandbox: uv run --isolated --no-project --with-requirements /tmp/tmpo3d14tc5.txt marimo run lvof.py

        Running lvof.py ⚡

        URL: http://localhost:2725

Traceback (most recent call last):
  File "/home/fletch/.cache/uv/archive-v0/VDQ8DUT_h_Lhwd4Qnv8KP/lib/python3.12/site-packages/marimo/_runtime/executor.py", line 157, in execute_cell
    exec(cell.body, glbls)
  File "/tmp/marimo_3924777/__marimo__cell_vblA_.py", line 2, in <module>
    import pandas as pd
ModuleNotFoundError: No module named 'pandas'

I think the issue exists with running the uv command while the conda environment is activated? Can you try it without the conda environment activated? One of the main advantages of of using uvx (when uv is installed) is that marimo will automatically install its dependencies in an isolated virtual environment.

I just recreated the installation steps; created a new conda environment, activated it; used the conda env create -f environment.yml to install packages inside the new environment (ran into some resolvepackagenotfound issues) and ran the uvx marimo run --sandbox lvof.py after cd'ing to marimonotebook folder. It ran for me.

Ah I see. I attempted to run pip install uv and then uvx marimo run --sandbox lvof.py in a fresh terminal, but I ran into a permissions error:

After some googling, it seems uv is not set up to work well with global Python installations that each use their own virtual environment: astral-sh/uv#2059

This is a common set up in academia, such as our lab server. Until this issue is fixed by uv (which it seems they don't view it as worthwhile, so that may be never) I don't think we'll be using it. That's unfortunate because it does seem like it could be useful for package management!

If you feel strongly we should use uv I'm happy to reconsider, but it just seems that if the installation is difficult for me it will cause lots of trouble to our novice users who are more accustomed to conda environments.

Sure; understandable.