Current env setup issues

[MeWu-IDM]

attempst to fix in branch: mewu/fix-issues

1. devcontainer started but the rstudio and jupyter-lab is not accessible, after manually run

jupyter lab --ip=0.0.0.0 --no-browser --allow-root --NotebookApp.token='' 2>&1 & and rstudio-server restart it seems to work (port 8888 and 8787) until the next restart

2. for github actions, installing the quarto shiny extension is automated in https://github.com/InstituteforDiseaseModeling/data_access_library/blob/mewu/fix-issues/r/install_quarto_extensions.expect but after installation, still getting error in

Could not run /workspace/r/shinylive_demo/shinylive as a JSON filter.
Please make sure the file exists and is executable.

Did you intend 'shinylive' as a Lua filter in an extension?
If so, make sure you've spelled the name of the extension correctly.

The original Pandoc error follows below.
Error running filter /workspace/r/shinylive_demo/shinylive:
Could not find executable /workspace/r/shinylive_demo/shinylive
Error running filter /opt/quarto/share/filters/main.lua:
/opt/quarto/share/filters/main.lua:2639: attempt to call a nil value (global 'crash_with_stack_trace')
stack traceback:
	/opt/quarto/share/filters/main.lua:2218: in function 'fail'
	/opt/quarto/share/filters/main.lua:3797: in field 'Pandoc'
	/opt/quarto/share/filters/main.lua:568: in function 'run_emulated_filter'
	/opt/quarto/share/filters/main.lua:1334: in local 'callback'
	/opt/quarto/share/filters/main.lua:1352: in upvalue 'run_emulated_filter_chain'
	/opt/quarto/share/filters/main.lua:1388: in function </opt/quarto/share/filters/main.lua:1385>
Failed to render /workspace/r/shinylive_demo/simple_example.qmd with execution. Rendering without execution...```

The instruction of quarto is not very clean, right now, I will try to improve but basically  these steps work for me on windows but not on the GA or devcontainer (ubuntu)  https://github.com/InstituteforDiseaseModeling/data_access_library/blob/mewu/fix-issues/r/README.md

3. after rstudio-server restart , I can connect to it (use rstudio as default pwd) but not sure how to set the session default directory to the workspaces (it is annoying for the user to do setwd manually)

 

[DLukacevic-IDM]

I tried running codespace from your branch and after waiting for ~15 min it ran both Rsturdio and Jupyter Lab

[MeWu-IDM]

thanks @DLukacevic-IDM I found a few small issues so I decided to merge this branch to main to get a cleaner start, I used a pre-built image for now to speed up the process and what I have experienced is the
(1) I don't get the port forwarded correctly every time I ran (sometimes it works) and Port label is not showing correctly for me
(2) slow dockerfile (and too big) but for now I workaround it with pre-build image (and added a GA to build this image)
(3) the quarto extension installation still has some issues... I had to install for every folder which is silly but it seems working now https://institutefordiseasemodeling.github.io/data_access_library/r/shinylive_demo/simple_example.html

anyways, I have all the code in main now and they sort of working... when you create your example maybe we can revisit some fragile part mentioned here. feel free to start your new branch from main and add your samples. I will work on documentation the next few days and we can have a team meeting to go over that, Thanks again for your help!