cron tutorial notebooks

[rijobro]

Run tutorial notebooks as cron job. Not sure if github actions syntax is correct.

Status

Ready

Types of changes

• Non-breaking change (fix or new feature that would not break existing functionality).

[wyli]

thanks I'll test it and get back to this PR

[wyli]

the script's syntax is fine now, but some of the notebooks are not ready https://github.com/Project-MONAI/MONAI/runs/2125064870?check_suite_focus=true#step:6:154

[rijobro]

Not sure how to resolve this, I don't see it locally: ERROR: Unexpected bus error encountered in worker. This might be caused by insufficient shared memory (shm).

[wyli]

Not sure how to resolve this, I don't see it locally: ERROR: Unexpected bus error encountered in worker. This might be caused by insufficient shared memory (shm).

I see, I'll try to set --shm-size of the docker container tomorrow

[rijobro]

Tests made it further this time, but still running out of memory: RuntimeError: DataLoader worker (pid 11596) is killed by signal: Bus error. It is possible that dataloader's workers are out of shared memory. Please try to raise your shared memory limit.

[rijobro]

@wyli Committing from a github suggestion seems to make DCO fail...

[wyli]

now having a different issue with the tensorboard magic line: https://github.com/Project-MONAI/MONAI/runs/2130772126?check_suite_focus=true#step:6:298 any idea?

[rijobro]

There's info online about cgi.escape being deprecated in favour of html.escape:

cgi.escape which was deprecated in Python 3.7 and removed in 3.8.

Not sure what that means for solving this problem. Perhaps using python3.7? Or maybe it would be solved with pip install -U <package>, but I'm not sure which package(s) need to be updated -- jupyter?

[wyli]

updating tensorboard resolves that issue. now we have a testing data issue https://github.com/Project-MONAI/MONAI/runs/2132482457?check_suite_focus=true#step:6:317 need to host the zip file for testing?

[rijobro]

@ericspod The current error comes from data in the covid notebook not being automatically download-able from Kaggle. Do you think we could host a copy on Zenodo or somewhere else?

[ericspod]

Yeah that's fine, it's easier that way for sure.

[wyli]

I feel we could merge this after addressing Project-MONAI/tutorials#144, so that these nightly tests would at least give us some useful information about all the tutorials...

[wyli]

thanks, this is a nice follow-up on Project-MONAI/tutorials#101, nightly tutorial tests will be scheduled using this repo's runner https://github.com/Project-MONAI/MONAI/actions/runs/661446080/workflow