From 7fe65688e92ea2135cba3a494e18a16482969725 Mon Sep 17 00:00:00 2001 From: Wenqi Li <831580+wyli@users.noreply.github.com> Date: Fri, 20 Oct 2023 10:24:46 +0100 Subject: [PATCH] fixes url; workaround to skip 1550 (#1551) temporarily skip the test #1550 while we are improving the premerge runner. ### Checks - [ ] Avoid including large-size files in the PR. - [ ] Clean up long text outputs from code cells in the notebook. - [ ] For security purposes, please check the contents and remove any sensitive info such as user names and private key. - [ ] Ensure (1) hyperlinks and markdown anchors are working (2) use relative paths for tutorial repo files (3) put figure and graphs in the `./figure` folder - [ ] Notebook runs automatically `./runner.sh -t ` Signed-off-by: Wenqi Li --- bundle/README.md | 2 +- runner.sh | 1 + 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/bundle/README.md b/bundle/README.md index 35dd011310..a7abf6ef8d 100644 --- a/bundle/README.md +++ b/bundle/README.md @@ -14,7 +14,7 @@ Start the tutorial notebooks on constructing bundles: 2. [MedNIST Classification](./02_mednist_classification.ipynb): train a network using the bundle for doing a real task. 3. [MedNIST Classification With Best Practices](./03_mednist_classification_v2.ipynb): do the same again but better. 4. [Integrating Existing Code](./04_integrating_code.ipynb): discussion on how to integrate existing, possible non-MONAI, code into a bundle. -5. [Spleen Segmentation using Pytorch Lightning](./05_spleen_segmentation.ipynb): train a segmentation network using MONAI bundle and Pytorch Lightning. +5. [Spleen Segmentation using Pytorch Lightning](./05_spleen_segmentation_lightning.ipynb): train a segmentation network using MONAI bundle and Pytorch Lightning. More advanced topics are covered in this directory: diff --git a/runner.sh b/runner.sh index cecead5f4d..6e3dd0254e 100755 --- a/runner.sh +++ b/runner.sh @@ -124,6 +124,7 @@ skip_run_papermill=("${skip_run_papermill[@]}" .*nuclei_classification_training_ skip_run_papermill=("${skip_run_papermill[@]}" .*nuclick_training_notebook.ipynb*) # https://github.com/Project-MONAI/tutorials/issues/1542 skip_run_papermill=("${skip_run_papermill[@]}" .*nuclei_classification_infer.ipynb*) # https://github.com/Project-MONAI/tutorials/issues/1542 skip_run_papermill=("${skip_run_papermill[@]}" .*nuclick_infer.ipynb*) # https://github.com/Project-MONAI/tutorials/issues/1542 +skip_run_papermill=("${skip_run_papermill[@]}" .*05_spleen_segmentation_lightning.ipynb*) # https://github.com/Project-MONAI/tutorials/issues/1550 # output formatting separator=""