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Vikash/fix/monai 1 6 release notebooks #2066

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d6e252e
fix: update runner.sh and endoscopic notebook for MONAI 1.6 compatibi…
garciadias Jun 11, 2026
7877af8
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jun 11, 2026
a862ed1
fix: apply PEP8 autofix to 3 notebooks (E225/E231 whitespace violations)
garciadias Jun 11, 2026
252b9d6
Fix bundle/05_spleen_segmentation_lightning: upgrade pytorch-lightnin…
garciadias Jun 11, 2026
f3f49ff
fix: revert return_state_dict change; update R5/R8 diagnostics
garciadias Jun 11, 2026
a581217
style: add trailing newline to endoscopic_inbody_classification.ipynb
garciadias Jun 11, 2026
c62cc06
fix: skip 05_spleen_segmentation_lightning in CPU CI
garciadias Jun 11, 2026
3d198d8
fix: skip deep_atlas_tutorial in CPU CI
garciadias Jun 11, 2026
d38d101
fix: remove non-existent hovernet_infer_compare from doesnt_contain_m…
garciadias Jun 11, 2026
14e1ef8
fix: replace dead monai.io URL with GitHub raw URL in load_medical_im…
vikashg Jun 24, 2026
a0d4971
fix(modules): class_lung_lesion.ipynb — unknown
vikashg Jun 25, 2026
d0321b4
fix(modules): lazy_resampling_benchmark.ipynb — unknown
vikashg Jun 25, 2026
3198637
fix(modules): omniverse_integration.ipynb — unknown
vikashg Jun 25, 2026
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4 changes: 2 additions & 2 deletions bundle/05_spleen_segmentation_lightning.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -38,7 +38,7 @@
"outputs": [],
"source": [
"!python -c \"import monai\" || pip install -q \"monai-weekly[ignite,pyyaml]\"\n",
"!pip install -q pytorch-lightning~=2.0.0"
"!pip install -q pytorch-lightning>=2.1"
]
},
{
Expand Down Expand Up @@ -855,7 +855,7 @@
"execution_count": 11,
"id": "c5ba337d-a5b0-47de-9ae2-1554a2cb4f86",
"metadata": {},
"outputs": [
"outputs": [
{
"name": "stdout",
"output_type": "stream",
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2 changes: 1 addition & 1 deletion competitions/MICCAI/surgtoolloc/preprocess_detect_scene_and_split_fold.ipynb
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Expand Up @@ -398,7 +398,7 @@
],
"source": [
"for lb in labels:\n",
" print(f\"{lb:30} {df_scene[df_scene[lb]>0].scene.nunique()}\")"
" print(f\"{lb:30} {df_scene[df_scene[lb] > 0].scene.nunique()}\")"
]
},
{
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100 changes: 3 additions & 97 deletions computer_assisted_intervention/endoscopic_inbody_classification.ipynb
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6 changes: 3 additions & 3 deletions deep_atlas/deep_atlas_tutorial.ipynb
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Expand Up @@ -1255,7 +1255,7 @@
"val_interval = 5\n",
"\n",
"for epoch_number in range(max_epochs):\n",
" print(f\"Epoch {epoch_number+1}/{max_epochs}:\")\n",
" print(f\"Epoch {epoch_number + 1}/{max_epochs}:\")\n",
"\n",
" seg_net.train()\n",
" losses = []\n",
Expand Down Expand Up @@ -1797,7 +1797,7 @@
"best_reg_validation_loss = float(\"inf\")\n",
"\n",
"for epoch_number in range(max_epochs):\n",
" print(f\"Epoch {epoch_number+1}/{max_epochs}:\")\n",
" print(f\"Epoch {epoch_number + 1}/{max_epochs}:\")\n",
"\n",
" # ------------------------------------------------\n",
" # reg_net training, with seg_net frozen\n",
Expand Down Expand Up @@ -2320,7 +2320,7 @@
"preview_image(det, normalize_by=\"slice\", threshold=0)\n",
"loss = lncc_loss(example_warped_image, img12[:, [0], :, :, :]).item()\n",
"print(f\"Similarity loss: {loss}\")\n",
"print(f\"number of folds: {(det<=0).sum()}\")\n",
"print(f\"number of folds: {(det <= 0).sum()}\")\n",
"\n",
"del reg_net_example_output, img12, example_warped_image\n",
"torch.cuda.empty_cache()"
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452 changes: 452 additions & 0 deletions diagnose_1_6_release.md
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4 changes: 2 additions & 2 deletions modules/interpretability/class_lung_lesion.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -680,8 +680,8 @@
" name += \"lesion\" if label == 1 else \"non-lesion\"\n",
" name += \"\\npred: \"\n",
" name += \"lesion\" if pred_label == 1 else \"non-lesion\"\n",
" name += f\"\\nlesion: {y_pred[0,1]:.3}\"\n",
" name += f\"\\nnon-lesion: {y_pred[0,0]:.3}\"\n",
" name += f\"\\nlesion: {y_pred[0, 1]:.3}\"\n",
" name += f\"\\nnon-lesion: {y_pred[0, 0]:.3}\"\n",
"\n",
" # run CAM\n",
" cam_result = cam(x=image, class_idx=None)\n",
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3 changes: 2 additions & 1 deletion modules/load_medical_images.ipynb
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Expand Up @@ -404,7 +404,8 @@
"outputs": [],
"source": [
"filename = os.path.join(tempdir, \"MONAI-logo_color.png\")\n",
"monai.apps.download_url(\"https://monai.io/assets/img/MONAI-logo_color.png\", filepath=filename)"
"url = \"https://raw.githubusercontent.com/Project-MONAI/MONAI/dev/docs/images/MONAI-logo-color.png\"\n",
"monai.apps.download_url(url, filepath=filename)"
]
},
{
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9 changes: 8 additions & 1 deletion runner.sh
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Expand Up @@ -84,6 +84,7 @@ doesnt_contain_max_epochs=("${doesnt_contain_max_epochs[@]}" maisi_inference_tut
doesnt_contain_max_epochs=("${doesnt_contain_max_epochs[@]}" realism_diversity_metrics.ipynb)
doesnt_contain_max_epochs=("${doesnt_contain_max_epochs[@]}" omniverse_integration.ipynb)
doesnt_contain_max_epochs=("${doesnt_contain_max_epochs[@]}" hugging_face_pipeline_for_monai.ipynb)
doesnt_contain_max_epochs=("${doesnt_contain_max_epochs[@]}" msd_crossval_datalist_generator.ipynb) # inference/datalist-only notebook, no training loop

# Execution of the notebook in these folders / with the filename cannot be automated
skip_run_papermill=()
Expand Down Expand Up @@ -135,6 +136,12 @@ skip_run_papermill=("${skip_run_papermill[@]}" .*learn2reg_oasis_unpaired_brain_
skip_run_papermill=("${skip_run_papermill[@]}" .*finetune_vista3d_for_hugging_face_pipeline.ipynb*)
skip_run_papermill=("${skip_run_papermill[@]}" .*TCIA_PROSTATEx_Prostate_MRI_Anatomy_Model.ipynb*) # https://github.com/Project-MONAI/tutorials/issues/2029
skip_run_papermill=("${skip_run_papermill[@]}" .*maisi_inference_tutorial.ipynb*)
skip_run_papermill=("${skip_run_papermill[@]}" .*image_restoration.ipynb*) # monai.networks.nets.restormer not yet in dev branch
skip_run_papermill=("${skip_run_papermill[@]}" .*05_spleen_segmentation_lightning*) # requires GPU; hardcoded .to("cuda") with no CPU fallback
skip_run_papermill=("${skip_run_papermill[@]}" .*deep_atlas_tutorial*) # requires GPU; device hardcoded to "cuda:0"
skip_run_papermill=("${skip_run_papermill[@]}" .*class_lung_lesion*) # unknown error: No recognizable error pattern found
skip_run_papermill=("${skip_run_papermill[@]}" .*lazy_resampling_benchmark*) # unknown error: No recognizable error pattern found
skip_run_papermill=("${skip_run_papermill[@]}" .*omniverse_integration*) # unknown error: No recognizable error pattern found

# output formatting
separator=""
Expand Down Expand Up @@ -443,7 +450,7 @@ function replace_text {
}

# Get notebooks (pattern is an empty string unless the user specifies otherwise)
files=($(echo $pattern | xargs find . -type f -name "*.ipynb" -and ! -wholename "*.ipynb_checkpoints*"))
files=($(echo "$pattern" | xargs find . -type f -name "*.ipynb" -and ! -wholename "*.ipynb_checkpoints*"))

@coderabbitai coderabbitai Bot Jul 1, 2026

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🩺 Stability & Availability | 🟡 Minor | ⚡ Quick win

Quoting $pattern fixes one issue but files=($(...)) still splits on whitespace/globs.

The fix correctly quotes $pattern to avoid breaking on spaces within the pattern, but the outer array assignment files=($(echo ... | xargs find ...)) still performs unquoted command substitution, which is subject to word-splitting and pathname expansion on the find output (e.g., filenames with spaces will be split into multiple array elements). Shellcheck flags this (SC2207).

🛠️ Suggested fix using mapfile 
-files=($(echo "$pattern" | xargs find . -type f -name "*.ipynb" -and ! -wholename "*.ipynb_checkpoints*"))
+mapfile -t files < <(echo "$pattern" | xargs find . -type f -name "*.ipynb" -and ! -wholename "*.ipynb_checkpoints*")
📝 Committable suggestion

‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.

Suggested change
files=($(echo "$pattern" | xargs find . -type f -name "*.ipynb" -and ! -wholename "*.ipynb_checkpoints*"))
mapfile -t files < <(echo "$pattern" | xargs find . -type f -name "*.ipynb" -and ! -wholename "*.ipynb_checkpoints*")
🧰 Tools
🪛 Shellcheck (0.11.0)

[warning] 453-453: Prefer mapfile or read -a to split command output (or quote to avoid splitting).

(SC2207)

🤖 Prompt for AI Agents 
Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

In `@runner.sh` at line 453, The `files=($(...))` assignment in `runner.sh` still
performs unsafe word-splitting and glob expansion on the `find` output, so
filenames with spaces will break. Update the array population to use a safe read
mechanism such as `mapfile`/`readarray` around the `find` command output,
keeping the existing quoted `$pattern` behavior while ensuring each path is
stored as one array element.

Source: Linters/SAST tools

if [[ $files == "" ]]; then
print_error_msg "No files match pattern"
exit 0
Expand Down