Update CHANGELOG.md

CHANGELOG.md

@@ -1,17 +1,16 @@
 # Changelog
 
-All notable changes to this project will be documented in this file.
+Early versions of this toolbox used a manually created changelog.
+As of March 2022, we have switched to using Github's auto-generated changelog.
+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).
+Each release contains a link for "Full Changelog".
 
-The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), and this project adheres
-to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+## Changelog for Versions before March 2022
 
-For each Pull Request, the affected code parts should be briefly described and added here in the "Upcoming" section.
-Once a release is done, the "Upcoming" section becomes the release changelog, and a new empty "Upcoming" should be
-created.
+### Upcoming
 
-## Upcoming
+#### Added
 
-### Added
 - ([#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.
 - ([#689](https://github.com/microsoft/InnerEye-DeepLearning/pull/689)) Show default argument values in help message.
 - ([#671](https://github.com/microsoft/InnerEye-DeepLearning/pull/671)) Remove sequence models and unused variables. Simplify README.
@@ -56,7 +55,7 @@ jobs that run in AzureML.
 - ([#656](https://github.com/microsoft/InnerEye-DeepLearning/pull/656)) Add subsampling transform and support for MIL mean pooling.
 - ([#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.
 
-### Changed
+#### Changed
 
 - ([#677](https://github.com/microsoft/InnerEye-DeepLearning/pull/677)) Update TorchIO version to include the recent bug fix related to patch-based inference.
 - ([#666](https://github.com/microsoft/InnerEye-DeepLearning/pull/666)) Replace RadIO with TorchIO for patch-based inference.
@@ -96,7 +95,7 @@ gets uploaded to AzureML, by skipping all test folders.
  `autosave_every_n_val_epochs`.
 - ([#632](https://github.com/microsoft/InnerEye-DeepLearning/pull/632)) Nifti test data is no longer stored in Git LFS
 
-### Fixed
+#### Fixed
 
 - ([#704](https://github.com/microsoft/InnerEye-DeepLearning/pull/704)) Add submodules to sys.path to fix autodoc's warning.
 - ([#699](https://github.com/microsoft/InnerEye-DeepLearning/pull/699)) Fix Sphinx warnings.
@@ -143,7 +142,8 @@ in inference-only runs when using lightning containers.
 - ([#655](https://github.com/microsoft/InnerEye-DeepLearning/pull/655)) Run pytest on Linux again, but with Ubuntu 20.04
 - ([#674](https://github.com/microsoft/InnerEye-DeepLearning/pull/674)) Fix DeepMIL metrics bug whereby hard labels were used instead of probabilities.
 
-### Removed
+#### Removed
+
 - ([#692](https://github.com/microsoft/InnerEye-DeepLearning/pull/692)) Replace InnerEye-DataQuality with a link to commit,
 - ([#577](https://github.com/microsoft/InnerEye-DeepLearning/pull/577)) Removing the monitoring of batch loading time,
  use the `BatchTimeCallback` from `hi-ml` instead
@@ -158,14 +158,14 @@ in inference-only runs when using lightning containers.
 - ([#596](https://github.com/microsoft/InnerEye-DeepLearning/pull/596)) Removed obsolete `TrainGlaucomaCV` from PR build.
 - ([#604](https://github.com/microsoft/InnerEye-DeepLearning/pull/604)) Removed all code that downloads datasets, this is now all handled by hi-ml
 
-### Deprecated
+#### Deprecated
 
 - ([#633](https://github.com/microsoft/InnerEye-DeepLearning/pull/633)) Model fields `recovery_checkpoint_save_interval` and `recovery_checkpoints_save_last_k` have been retired.
  Recovery checkpoint handling is now controlled by `autosave_every_n_val_epochs`.
 
-## 0.3 (2021-06-01)
+### 0.3 (2021-06-01)
 
-### Added
+#### Added
 
 - ([#483](https://github.com/microsoft/InnerEye-DeepLearning/pull/483)) Allow cross validation with 'bring your own' Lightning models (without ensemble building).
 - ([#489](https://github.com/microsoft/InnerEye-DeepLearning/pull/489)) Remove portal query for outliers.
@@ -245,7 +245,7 @@ console for easier diagnostics.
 - ([#463](https://github.com/microsoft/InnerEye-DeepLearning/pull/463)) Add arguments `dirs_recursive` and
  `dirs_non_recursive` to `mypy_runner.py` to let users specify a list of directories to run mypy on.
 
-### Changed
+#### Changed
 
 - ([#385](https://github.com/microsoft/InnerEye-DeepLearning/pull/385)) Starting an AzureML run now uses the
  `ScriptRunConfig` object, rather than the deprecated `Estimator` object.
@@ -278,7 +278,7 @@ console for easier diagnostics.
  `get_image_transform` (resp. `get_segmentation_transform`). These two functions replace the old
  `get_image_sample_transforms` method. See `docs/building_models.md` for more information on augmentations.
 
-### Fixed
+#### Fixed
 
 - ([#422](https://github.com/microsoft/InnerEye-DeepLearning/pull/422)) Documentation - clarified `setting_up_aml.md`
  datastore creation instructions and fixed small typos in `hello_world_model.md`
@@ -292,7 +292,7 @@ console for easier diagnostics.
 - ([#445](https://github.com/microsoft/InnerEye-DeepLearning/pull/445)) Fixed a bug when running inference for
  container models on machines with >1 GPU
 
-### Removed
+#### Removed
 
 - ([#439](https://github.com/microsoft/InnerEye-DeepLearning/pull/439)) Deprecated `start_epoch` config argument.
 - ([#450](https://github.com/microsoft/InnerEye-DeepLearning/pull/450)) Delete unused `classification_report.ipynb`.
@@ -302,11 +302,11 @@ console for easier diagnostics.
  RandAugment & Co. The user has now instead complete freedom to specify the set of augmentations to use.
 - ([#468](https://github.com/microsoft/InnerEye-DeepLearning/pull/468)) Removed the `KneeSinglecoil` example model
 
-### Deprecated
+#### Deprecated
 
-## 0.2 (2021-01-29)
+### 0.2 (2021-01-29)
 
-### Added
+#### Added
 
 - ([#323](https://github.com/microsoft/InnerEye-DeepLearning/pull/323)) There are new model configuration fields
  (and hence, commandline options), in particular for controlling PyTorch Lightning (PL) training:
@@ -325,7 +325,7 @@ console for easier diagnostics.
  config's `get_model_train_test_dataset_splits()` method. See the `InnerEye.ML.utils.split_dataset.DatasetSplits` class
  for details.
 
-### Changed
+#### Changed
 
 - ([#323](https://github.com/microsoft/InnerEye-DeepLearning/pull/323)) The codebase has undergone a massive
  refactoring, to use PyTorch Lightning as the foundation for all training. As a consequence of that:
@@ -350,13 +350,13 @@ console for easier diagnostics.
 - ([#427](https://github.com/microsoft/InnerEye-DeepLearning/pull/427)) Move dicom loading function from SimpleITK to
  pydicom. Loading time improved by 30x.
 
-### Fixed
+#### Fixed
 
 - When registering a model, it now has a consistent folder structured, described [here](docs/deploy_on_aml.md). This
  folder structure is present irrespective of using InnerEye as a submodule or not. In particular, exactly 1 Conda
  environment will be contained in the model.
 
-### Removed
+#### Removed
 
 - The commandline options to control which checkpoint is saved, and which is used for inference, have been removed:
  `save_start_epoch`, `save_step_epochs`, `epochs_to_test`, `test_diff_epochs`, `test_step_epochs`, `test_start_epoch`
@@ -366,8 +366,8 @@ console for easier diagnostics.
 - Removed ability to perform sub-fold cross validation. The parameters `number_of_cross_validation_splits_per_fold`
  and `cross_validation_sub_fold_split_index` have been removed from ScalarModelBase.
 
-### Deprecated
+#### Deprecated
 
-## 0.1 (2020-11-13)
+### 0.1 (2020-11-13)
 
 - This is the baseline release.