Deprecate manual changelog (#707)
This commit is contained in:
Fernando Pérez-García
GitHub
Родитель
f1ae24aa69
Коммит
3eaf2f9053
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@ -6,7 +6,5 @@ Please follow the guidelines for PRs contained [here](docs/pull_requests.md). Ch
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- [ ] Add unit tests for all functions that you introduced or modified.
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- [ ] Run PyCharm's code cleanup tools on your Python files.
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- [ ] Link the correct GitHub issue for tracking.
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- [ ] Update the [Changelog](CHANGELOG.md) file: Describe your change in terms of
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Added/Changed/Removed/... in the "Upcoming" section.
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- [ ] When merging your PR, replace the default merge message with a description of your PR,
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and if needed a motivation why that change was required.
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@ -1,46 +0,0 @@
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name: Check Changelog
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# This check ensures that CHANGELOG.md is modified in each PR, and contains a hyperlink to the present PR.
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# To bypass this check, label the PR with "no changelog needed".
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on:
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pull_request:
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jobs:
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check_changelog:
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name: Check Changelog
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runs-on: ubuntu-latest
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if: ${{ contains(github.event.pull_request.labels.*.name, 'no changelog needed') == 0 }}
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steps:
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- name: Get PR number
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run: |
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echo "PR_NUMBER=${{ github.event.pull_request.number }}" >> $GITHUB_ENV
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- uses: actions/checkout@v2
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with:
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fetch-depth: 0
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- name: Check the changelog
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run: |
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set -e
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git config --global core.whitespace cr-at-eol
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changed_files=$(git diff --name-only origin/main)
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if [[ "$changed_files" =~ CHANGELOG\.md ]]
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then
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changelog=$(cat ./CHANGELOG.md)
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if [[ "$changelog" =~ https://github\.com/microsoft/InnerEye-DeepLearning/pull/$PR_NUMBER ]]
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then
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echo "Changelog has been updated and contains the PR number."
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else
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echo "Changelog has been modified, but does not contain a hyperlink the present PR."
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echo "Make sure that there is a changelog entry that links to the present PR."
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echo "If no changelog entry is required for this PR, label the PR with 'no changelog needed'."
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echo "You will need to push another commit to disable this check after adding the label, "
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echo "re-running the github action will simply cause it to fail again"
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exit 1
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fi
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else
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echo "Each PR needs to summarize the changes in CHANGELOG.md, but this PR does not make any"
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echo "changes to that file. The changelog entry must contain a hyperlink to the present PR."
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echo "If no changelog entry is required for this PR, label the PR with 'no changelog needed'."
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echo "You will need to push another commit to disable this check after adding the label, "
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echo "re-running the github action will simply cause it to fail again"
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exit 1
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fi
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51
CHANGELOG.md
51
CHANGELOG.md
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@ -1,17 +1,15 @@
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# Changelog
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All notable changes to this project will be documented in this file.
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Early versions of this toolbox used a manually created changelog.
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As of March 2022, we have switched to using Github's auto-generated changelog.
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If you would like to view the changelog for a particular release, you can do so on the [Releases page](https://github.com/microsoft/InnerEye-DeepLearning/releases).
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Each release contains a link for "Full Changelog".
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The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), and this project adheres
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to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
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## Changelog for Versions before March 2022
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For each Pull Request, the affected code parts should be briefly described and added here in the "Upcoming" section.
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Once a release is done, the "Upcoming" section becomes the release changelog, and a new empty "Upcoming" should be
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created.
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### Upcoming
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## Upcoming
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### Added
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#### Added
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- ([#709](https://github.com/microsoft/InnerEye-DeepLearning/pull/709)) Update hi-ml submodule.
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- ([#667](https://github.com/microsoft/InnerEye-DeepLearning/pull/667)) Automatically and linearly scale the learning rate of the SSL encoder to the number of GPUs.
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@ -58,7 +56,7 @@ jobs that run in AzureML.
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- ([#656](https://github.com/microsoft/InnerEye-DeepLearning/pull/656)) Add subsampling transform and support for MIL mean pooling.
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- ([#679](https://github.com/microsoft/InnerEye-DeepLearning/pull/679)) Add FP and TN slides/tiles to DeepMIL outputs and extend outputs to multi-class problems.
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### Changed
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#### Changed
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- ([#677](https://github.com/microsoft/InnerEye-DeepLearning/pull/677)) Update TorchIO version to include the recent bug fix related to patch-based inference.
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- ([#666](https://github.com/microsoft/InnerEye-DeepLearning/pull/666)) Replace RadIO with TorchIO for patch-based inference.
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@ -98,7 +96,7 @@ gets uploaded to AzureML, by skipping all test folders.
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`autosave_every_n_val_epochs`.
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- ([#632](https://github.com/microsoft/InnerEye-DeepLearning/pull/632)) Nifti test data is no longer stored in Git LFS
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### Fixed
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#### Fixed
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- ([#704](https://github.com/microsoft/InnerEye-DeepLearning/pull/704)) Add submodules to sys.path to fix autodoc's warning.
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- ([#699](https://github.com/microsoft/InnerEye-DeepLearning/pull/699)) Fix Sphinx warnings.
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@ -145,7 +143,8 @@ in inference-only runs when using lightning containers.
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- ([#655](https://github.com/microsoft/InnerEye-DeepLearning/pull/655)) Run pytest on Linux again, but with Ubuntu 20.04
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- ([#674](https://github.com/microsoft/InnerEye-DeepLearning/pull/674)) Fix DeepMIL metrics bug whereby hard labels were used instead of probabilities.
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### Removed
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#### Removed
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- ([#692](https://github.com/microsoft/InnerEye-DeepLearning/pull/692)) Replace InnerEye-DataQuality with a link to commit,
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- ([#577](https://github.com/microsoft/InnerEye-DeepLearning/pull/577)) Removing the monitoring of batch loading time,
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use the `BatchTimeCallback` from `hi-ml` instead
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@ -160,14 +159,14 @@ in inference-only runs when using lightning containers.
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- ([#596](https://github.com/microsoft/InnerEye-DeepLearning/pull/596)) Removed obsolete `TrainGlaucomaCV` from PR build.
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- ([#604](https://github.com/microsoft/InnerEye-DeepLearning/pull/604)) Removed all code that downloads datasets, this is now all handled by hi-ml
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### Deprecated
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#### Deprecated
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- ([#633](https://github.com/microsoft/InnerEye-DeepLearning/pull/633)) Model fields `recovery_checkpoint_save_interval` and `recovery_checkpoints_save_last_k` have been retired.
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Recovery checkpoint handling is now controlled by `autosave_every_n_val_epochs`.
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## 0.3 (2021-06-01)
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### 0.3 (2021-06-01)
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### Added
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#### Added
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- ([#483](https://github.com/microsoft/InnerEye-DeepLearning/pull/483)) Allow cross validation with 'bring your own' Lightning models (without ensemble building).
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- ([#489](https://github.com/microsoft/InnerEye-DeepLearning/pull/489)) Remove portal query for outliers.
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@ -247,7 +246,7 @@ console for easier diagnostics.
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- ([#463](https://github.com/microsoft/InnerEye-DeepLearning/pull/463)) Add arguments `dirs_recursive` and
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`dirs_non_recursive` to `mypy_runner.py` to let users specify a list of directories to run mypy on.
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### Changed
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#### Changed
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- ([#385](https://github.com/microsoft/InnerEye-DeepLearning/pull/385)) Starting an AzureML run now uses the
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`ScriptRunConfig` object, rather than the deprecated `Estimator` object.
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@ -280,7 +279,7 @@ console for easier diagnostics.
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`get_image_transform` (resp. `get_segmentation_transform`). These two functions replace the old
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`get_image_sample_transforms` method. See `docs/building_models.md` for more information on augmentations.
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### Fixed
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#### Fixed
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- ([#422](https://github.com/microsoft/InnerEye-DeepLearning/pull/422)) Documentation - clarified `setting_up_aml.md`
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datastore creation instructions and fixed small typos in `hello_world_model.md`
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@ -294,7 +293,7 @@ console for easier diagnostics.
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- ([#445](https://github.com/microsoft/InnerEye-DeepLearning/pull/445)) Fixed a bug when running inference for
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container models on machines with >1 GPU
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### Removed
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#### Removed
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- ([#439](https://github.com/microsoft/InnerEye-DeepLearning/pull/439)) Deprecated `start_epoch` config argument.
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- ([#450](https://github.com/microsoft/InnerEye-DeepLearning/pull/450)) Delete unused `classification_report.ipynb`.
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@ -304,11 +303,11 @@ console for easier diagnostics.
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RandAugment & Co. The user has now instead complete freedom to specify the set of augmentations to use.
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- ([#468](https://github.com/microsoft/InnerEye-DeepLearning/pull/468)) Removed the `KneeSinglecoil` example model
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### Deprecated
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#### Deprecated
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## 0.2 (2021-01-29)
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### 0.2 (2021-01-29)
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### Added
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#### Added
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- ([#323](https://github.com/microsoft/InnerEye-DeepLearning/pull/323)) There are new model configuration fields
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(and hence, commandline options), in particular for controlling PyTorch Lightning (PL) training:
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@ -327,7 +326,7 @@ console for easier diagnostics.
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config's `get_model_train_test_dataset_splits()` method. See the `InnerEye.ML.utils.split_dataset.DatasetSplits` class
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for details.
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### Changed
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#### Changed
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- ([#323](https://github.com/microsoft/InnerEye-DeepLearning/pull/323)) The codebase has undergone a massive
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refactoring, to use PyTorch Lightning as the foundation for all training. As a consequence of that:
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@ -352,13 +351,13 @@ console for easier diagnostics.
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- ([#427](https://github.com/microsoft/InnerEye-DeepLearning/pull/427)) Move dicom loading function from SimpleITK to
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pydicom. Loading time improved by 30x.
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### Fixed
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#### Fixed
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- When registering a model, it now has a consistent folder structured, described [here](docs/deploy_on_aml.md). This
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folder structure is present irrespective of using InnerEye as a submodule or not. In particular, exactly 1 Conda
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environment will be contained in the model.
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### Removed
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#### Removed
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- The commandline options to control which checkpoint is saved, and which is used for inference, have been removed:
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`save_start_epoch`, `save_step_epochs`, `epochs_to_test`, `test_diff_epochs`, `test_step_epochs`, `test_start_epoch`
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@ -368,8 +367,8 @@ console for easier diagnostics.
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- Removed ability to perform sub-fold cross validation. The parameters `number_of_cross_validation_splits_per_fold`
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and `cross_validation_sub_fold_split_index` have been removed from ScalarModelBase.
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### Deprecated
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#### Deprecated
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## 0.1 (2020-11-13)
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### 0.1 (2020-11-13)
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- This is the baseline release.
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@ -12,7 +12,6 @@ AzureML workspace. A member of the InnerEye team will be happy to assist then.
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by pressing Ctrl+Alt+L, or selecting "Reformat code" in the context menu of the file(s) in the project explorer window.
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Alternatively, you should tick all of "Reformat code", "Rearrange code", "Optimize imports", "Cleanup", "Scan with mypy"
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in the PyCharm version control check-in dialog.
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* Ensure that you modified [CHANGELOG.md](../CHANGELOG.md) and described your PR there.
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* Only publish your PR for review once you have a build that is passing. You can make use of the "Create as Draft"
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feature of GitHub.
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* Link the correct Github issue.
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