Merge branch 'main' into 1455-lightning-bundle

.pre-commit-config.yaml

@@ -23,7 +23,7 @@ repos:
       - id: detect-private-key
 
   - repo: https://github.com/psf/black
-    rev: "23.3.0"
+    rev: "23.9.1"
     hooks:
       - id: black
       - id: black-jupyter

bundle/README.md

@@ -31,3 +31,8 @@ instantiate necessary components with python program and execute the inference.
 
 * [python bundle workflow](./python_bundle_workflow): step-by-step tutorial examples show how to develop a bundle
 training or inference workflow in Python instead of JSON / YAML configs.
+
+Other tutorials and resources within MONAI on other bundle topics can be found here:
+
+* [MONAI Deploy App SDK](https://github.com/Project-MONAI/monai-deploy-app-sdk/tree/main/notebooks/tutorials) including bundle tutorials
+* [MONAI Label Bundle App](https://github.com/Project-MONAI/MONAILabel/tree/main/sample-apps/monaibundle)

runner.sh

@@ -119,6 +119,11 @@ skip_run_papermill=("${skip_run_papermill[@]}" .*01_bundle_intro.ipynb*)
 skip_run_papermill=("${skip_run_papermill[@]}" .*02_mednist_classification.ipynb*)
 skip_run_papermill=("${skip_run_papermill[@]}" .*03_mednist_classification_v2.ipynb*)
 skip_run_papermill=("${skip_run_papermill[@]}" .*04_integrating_code.ipynb*)
+skip_run_papermill=("${skip_run_papermill[@]}" .*hovernet_torch.ipynb*)  # https://github.com/Project-MONAI/tutorials/issues/1542
+skip_run_papermill=("${skip_run_papermill[@]}" .*nuclei_classification_training_notebook.ipynb*)  # https://github.com/Project-MONAI/tutorials/issues/1542
+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
 
 # output formatting
 separator=""