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Segment Template #514

Merged
merged 14 commits into from
Oct 12, 2023
Merged

Segment Template #514

merged 14 commits into from
Oct 12, 2023

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ericspod
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@ericspod ericspod commented Oct 6, 2023

Fixes #513 .

Description

This is the template for segmentation bundles. Users can create their own new bundles by copying and adapting this one.

Multi-GPU support is a work in progress, it doesn't work for me but it should be fine.

Status

Ready

Please ensure all the checkboxes:

  • Codeformat tests passed locally by running ./runtests.sh --codeformat.
  • In-line docstrings updated.
  • Update version and changelog in metadata.json if changing an existing bundle.
  • Please ensure the naming rules in config files meet our requirements (please refer to: CONTRIBUTING.md).
  • Ensure versions of packages such as monai, pytorch and numpy are correct in metadata.json.
  • Descriptions should be consistent with the content, such as eval_metrics of the provided weights and TorchScript modules.
  • Files larger than 25MB are excluded and replaced by providing download links in large_file.yml.
  • Avoid using path that contains personal information within config files (such as use /home/your_name/ for "bundle_root").

ericspod and others added 6 commits October 5, 2023 14:12
Signed-off-by: Eric Kerfoot <[email protected]>
Signed-off-by: Eric Kerfoot <[email protected]>
Signed-off-by: Eric Kerfoot <[email protected]>
Signed-off-by: Eric Kerfoot <[email protected]>
Signed-off-by: Eric Kerfoot <[email protected]>
ericspod and others added 5 commits October 6, 2023 16:19
Signed-off-by: Eric Kerfoot <[email protected]>
Signed-off-by: Eric Kerfoot <[email protected]>
Signed-off-by: Eric Kerfoot <[email protected]>
Signed-off-by: Eric Kerfoot <[email protected]>
@wyli
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wyli commented Oct 11, 2023

/build

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thanks, it looks good to me

@yiheng-wang-nv
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/build

@yiheng-wang-nv
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We may also think about how to check if the whole .yaml files do not have typo or syntax issues. It seems we cannot use similar unit tests on this template bundle.
cc @wyli @KumoLiu @Nic-Ma

@ericspod
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We may also think about how to check if the whole .yaml files do not have typo or syntax issues. It seems we cannot use similar unit tests on this template bundle.

For this we can simply run any YAML file through pyyaml, any JSON file through the in-built json library, and then further check any Python expressions by attempting to parse them with the in-built ast library. This would do a static check without running the code that should be good enough to catch most things.

@ericspod ericspod enabled auto-merge (squash) October 11, 2023 14:36
@wyli
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wyli commented Oct 12, 2023

/build

@ericspod ericspod merged commit 93682e3 into Project-MONAI:dev Oct 12, 2023
4 checks passed
@ericspod ericspod deleted the segment_template branch October 12, 2023 12:14
yiheng-wang-nv pushed a commit to yiheng-wang-nv/model-zoo that referenced this pull request Jul 29, 2024
Fixes Project-MONAI#513 .

### Description
This is the template for segmentation bundles. Users can create their
own new bundles by copying and adapting this one.

Multi-GPU support is a work in progress, it doesn't work for me but it
should be fine.

### Status
**Ready**

### Please ensure all the checkboxes:
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [x] Codeformat tests passed locally by running `./runtests.sh
--codeformat`.
- [ ] In-line docstrings updated.
- [ ] Update `version` and `changelog` in `metadata.json` if changing an
existing bundle.
- [ ] Please ensure the naming rules in config files meet our
requirements (please refer to: `CONTRIBUTING.md`).
- [x] Ensure versions of packages such as `monai`, `pytorch` and `numpy`
are correct in `metadata.json`.
- [x] Descriptions should be consistent with the content, such as
`eval_metrics` of the provided weights and TorchScript modules.
- [x] Files larger than 25MB are excluded and replaced by providing
download links in `large_file.yml`.
- [x] Avoid using path that contains personal information within config
files (such as use `/home/your_name/` for `"bundle_root"`).

---------

Signed-off-by: Eric Kerfoot <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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Segmentation Template For the Model Zoo
3 participants