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Merged
merged 4 commits into from
Oct 18, 2023
Merged

1455 pl bundle #1547

merged 4 commits into from
Oct 18, 2023

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OeslleLucena
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@OeslleLucena OeslleLucena commented Oct 17, 2023

Fixes #1455 .

Description

A simple Pytorch Lightning bundle tutorial.

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: OeslleLucena <[email protected]>
Signed-off-by: OeslleLucena <[email protected]>
Signed-off-by: OeslleLucena <[email protected]>
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@OeslleLucena OeslleLucena marked this pull request as ready for review October 17, 2023 16:00
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@KumoLiu KumoLiu left a comment

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Thanks for the PR, looks good to me.

@KumoLiu KumoLiu requested review from wyli and ericspod October 18, 2023 02:52
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A few comments to address but it looks good otherwise.

Signed-off-by: OeslleLucena <[email protected]>
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Thanks, it looks good to me.

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wyli commented Oct 18, 2023

btw the bundle workflow in v1.3 tries to add the bundle path to sys.path https://github.com/Project-MONAI/MONAI/blob/0a3cdd9f1403cbad057b96230840ee17cf430dbf/monai/bundle/workflows.py#L307
so perhaps export PYTHONPATH="$bundle_root" is not needed.

also pip install -q "monai-weekly[ignite,pyyaml]" perhaps the ignite is not required by this tutorial

@wyli wyli merged commit 80e96e9 into Project-MONAI:main Oct 18, 2023
boneseva pushed a commit to boneseva/MONAI-tutorials that referenced this pull request Apr 21, 2024
Fixes Project-MONAI#1455  .

### Description
A simple Pytorch Lightning bundle tutorial.

### 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
- [x] Notebook runs automatically `./runner.sh -t <path to .ipynb file>`

---------

Signed-off-by: OeslleLucena <[email protected]>
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Simple example of pytorch Lightning based Pytorch bundle
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