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Fix copyright and guidelines test errors for remaining tutorials #1182

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Merged
merged 7 commits into from
Jan 21, 2023

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mingxin-zheng
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@mingxin-zheng mingxin-zheng commented Jan 20, 2023

Fixes #1181 .

Description

  • Update the guideline test to avoid counting line returns in non-text outputs (for example, html data)

  • Add copyright for all remaining scripts and clean replicates of old copyright info in the following notebooks

    • 2d_classification\mednist_tutorial.ipynb
    • 2d_registration\registration_mednist.ipynb
    • 3d_classification\densenet_training_array.ipynb
    • acceleration\multi_gpu_test.ipynb
    • acceleration\threadbuffer_performance.ipynb
    • acceleration\transform_speed.ipynb
    • modules\TorchIO_MONAI_PyTorch_Lightning.ipynb
    • modules\UNet_input_size_constrains.ipynb
    • multimodal\openi_multilabel_classification_transchex\transchex_openi_multilabel_classification.ipynb
    • experiment_management\spleen_segmentation_aim.ipynb
    • experiment_management\spleen_segmentation_mlflow.ipynb
  • Fix markdown cells for notebooks to match guidelines

    • experiment_management\bundle_integrate_mlflow.ipynb
    • modules\resample_benchmark.ipynb
  • Update the outputs in the following notebooks:

    • 2d_classification\mednist_tutorial.ipynb
    • 2d_registration\registration_mednist.ipynb
    • 3d_classification\densenet_training_array.ipynb

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 <path to .ipynb file>

Signed-off-by: Mingxin Zheng <[email protected]>
Signed-off-by: Mingxin Zheng <[email protected]>
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@mingxin-zheng mingxin-zheng changed the title [WIP] Fix copyright and guidelines test errors for remaining tutorials Fix copyright and guidelines test errors for remaining tutorials Jan 20, 2023
@mingxin-zheng mingxin-zheng requested review from yiheng-wang-nv, Nic-Ma, KumoLiu, binliunls and wyli and removed request for yiheng-wang-nv January 20, 2023 15:01
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Thanks for update, looks good to me.

@mingxin-zheng mingxin-zheng merged commit 4b2771a into Project-MONAI:main Jan 21, 2023
@mingxin-zheng mingxin-zheng deleted the fix-1181-tests branch March 22, 2023 10:05
boneseva pushed a commit to boneseva/MONAI-tutorials that referenced this pull request Apr 21, 2024
…ject-MONAI#1182)

Fixes Project-MONAI#1181 .

### Description

- Update the guideline test to avoid counting line returns in non-text
outputs (for example, html data)
- Add copyright for all remaining scripts and clean replicates of old
copyright info in the following notebooks
  - 2d_classification\mednist_tutorial.ipynb
  - 2d_registration\registration_mednist.ipynb
  - 3d_classification\densenet_training_array.ipynb
  - acceleration\multi_gpu_test.ipynb
  - acceleration\threadbuffer_performance.ipynb
  - acceleration\transform_speed.ipynb
  - modules\TorchIO_MONAI_PyTorch_Lightning.ipynb
  - modules\UNet_input_size_constrains.ipynb
-
multimodal\openi_multilabel_classification_transchex\transchex_openi_multilabel_classification.ipynb
  - experiment_management\spleen_segmentation_aim.ipynb
  - experiment_management\spleen_segmentation_mlflow.ipynb
 
- Fix markdown cells for notebooks to match guidelines
  - experiment_management\bundle_integrate_mlflow.ipynb
  - modules\resample_benchmark.ipynb

- Update the outputs in the following notebooks:
  - 2d_classification\mednist_tutorial.ipynb
  - 2d_registration\registration_mednist.ipynb
  - 3d_classification\densenet_training_array.ipynb
 
### Checks
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [x] Avoid including large-size files in the PR.
- [x] Clean up long text outputs from code cells in the notebook.
- [x] For security purposes, please check the contents and remove any
sensitive info such as user names and private key.
- [x] 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 <path to .ipynb file>`

Signed-off-by: Mingxin Zheng <[email protected]>
Signed-off-by: Mingxin Zheng <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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Update notebooks and scripts to match contributing guidelines
3 participants