Fix Documentation

[t0mdavid-m]

After refactoring the references in the documentation do not fit to the file structure.

[Imama-Kainat]

can i take this issue :)

[Imama-Kainat]

@t0mdavid-m

[t0mdavid-m]

Sure you can give it a go! :) Although I do have concerns this might be a bit more challenging if you are not too familiar with the codebase. Let me know if that is the case!

[Imama-Kainat]

@t0mdavid-m In settings.json, "online_deployment": false is set. Should I update the documentation to reflect that the system is currently not deployed online, or should I keep the explanations for both online and local modes as they are?

[Imama-Kainat]

i have changed the user guide information, in this way .Is it ok?

[Imama-Kainat]

it seems like "online_deployment": false was set intentionally to allow users to create and remove workspaces in local mode.

[Imama-Kainat]

Hi @t0mdavid-m ,

I noticed that the project contains three logo files: in assets
1️⃣ openmslogo.ico (old logo)
2️⃣ OpenMs.png (old logo)
3️⃣ openms_transparent_bg_logo.svg (new logo)

The documentation only refers to openmslogo.ico, but two different logos are being used across the project. Should I:
✔ Update the documentation to use only openms_transparent_bg_logo.svg?
✔ Remove the old logo files (openmslogo.ico & OpenMs.png) if they are no longer needed?
✔ Convert openms_transparent_bg_logo.svg to .ico if an .ico file is still required?

Let me know how you’d like to proceed!

[Imama-Kainat]

current streamlit template assets have old logos

[Imama-Kainat]

@t0mdavid-m @timosachsenberg I noticed that the documentation suggests modifying Streamlit's internal cli.py to add a _main_run_clExplicit() function. However, modifying cli.py can be risky since Streamlit updates might overwrite these changes, potentially breaking the app.

An alternative approach is to use subprocess.run() inside run_app.py like this:

python
Copy
Edit
import subprocess
import sys

def launch_streamlit():
command = [sys.executable, "-m", "streamlit", "run", "app.py"]
subprocess.run(command)

if name == "main":
launch_streamlit()
This avoids modifying cli.py, keeps the app compatible with future Streamlit updates, and works better with PyInstaller for packaging.

[Imama-Kainat]

@t0mdavid-m here it is written that common.py has some utility function but not anyfile is importing it .Tell me need to remove common.py references or reintroduce its usage.