When I previously submitted a new tutorial via a PR #1696 , I encountered a timeout issue while verifying the code using runner.sh. Subsequently, I tried to verify other notebooks already in monai/tutorials (e.g., spleen_segmentation_3d.ipynb) using the same method and faced similar issues. However, the timeout problem with these notebooks is sometimes not due to the code itself but because the dataset size is huge, causing the download to take too much time. Therefore, I suggest adding a block in runner.sh to check the time taken for the notebook to download the dataset. Although runner.sh shows the line number of the exit code when a timeout occurs, the timeout issue may not necessarily be caused by that line of code.
To Reproduce
Execute the following commands locally
./runner.sh -t 3d_segmentation/brats_segmentation_3d.ipynb./runner.sh -t 3d_segmentation/spleen_segmentation_3d.ipynb
Expected behavior
There is a section in runner.sh that checks for the presence of "Setup imports" and whether the block following it is for importing various required packages for the notebook.
# if import is used, then it should have the Setup import(s) markdown
if [[ $(${NB_TEST} verify -f "$fname" -k "(^import|[\n\r]import|^from|[\n\r]from)" --type code) == true ]]
then
if [[ $(${NB_TEST} verify -f "$fname" -i $((code_ind + 1)) -k "Setup import") != true ]]; then
print_error_msg "Missing the \"Setup imports\" after the first code cell of file: $fname"
standardized=false
fi
if [[ $(${NB_TEST} verify -f "$fname" -i $((code_ind + 2)) -k "print_config()" --type code) != true ]]; then
print_error_msg "print_config() cannot be found after the \"Setup imports\" markdown cell in file: $fname"
standardized=false
fi
fi
We could use a similar method to add a block of code that checks for the presence of "Download dataset" and measures the download time for the subsequent block. With this update, we can better understand the cause of the timeout when verifying notebooks using runner.sh.
Describe the bug
When I previously submitted a new tutorial via a PR #1696 , I encountered a timeout issue while verifying the code using
runner.sh. Subsequently, I tried to verify other notebooks already in monai/tutorials (e.g.,spleen_segmentation_3d.ipynb) using the same method and faced similar issues. However, the timeout problem with these notebooks is sometimes not due to the code itself but because the dataset size is huge, causing the download to take too much time. Therefore, I suggest adding a block inrunner.shto check the time taken for the notebook to download the dataset. Although runner.sh shows the line number of the exit code when a timeout occurs, the timeout issue may not necessarily be caused by that line of code.To Reproduce Execute the following commands locally
./runner.sh -t 3d_segmentation/brats_segmentation_3d.ipynb./runner.sh -t 3d_segmentation/spleen_segmentation_3d.ipynbExpected behavior
There is a section in
runner.shthat checks for the presence of "Setup imports" and whether the block following it is for importing various required packages for the notebook.We could use a similar method to add a block of code that checks for the presence of "Download dataset" and measures the download time for the subsequent block. With this update, we can better understand the cause of the timeout when verifying notebooks using
runner.sh.