7017 update changelog for v1.3 (Project-MONAI#7048)

Part of Project-MONAI#7017

### Description

- update changelog
- fixes documentation typos

### Types of changes
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [x] Non-breaking change (fix or new feature that would not break
existing functionality).
- [ ] Breaking change (fix or new feature that would cause existing
functionality to change).
- [ ] New tests added to cover the changes.
- [ ] Integration tests passed locally by running `./runtests.sh -f -u
--net --coverage`.
- [ ] Quick tests passed locally by running `./runtests.sh --quick
--unittests --disttests`.
- [ ] In-line docstrings updated.
- [ ] Documentation updated, tested `make html` command in the `docs/`
folder.

---------

Signed-off-by: KumoLiu <[email protected]>
Signed-off-by: Wenqi Li <[email protected]>
Co-authored-by: Wenqi Li <[email protected]>
Co-authored-by: Wenqi Li <[email protected]>

.github/workflows/setupapp.yml

@@ -106,7 +106,7 @@ jobs:
       run: |
         python -m pip list
         python -c 'import torch; print(torch.__version__); print(torch.rand(5,3))'
-        BUILD_MONAI=0 ./runtests.sh --build --quick --unittests --disttests
+        BUILD_MONAI=0 ./runtests.sh --build --quick --unittests
         BUILD_MONAI=1 ./runtests.sh --build --quick --min
         coverage xml --ignore-errors
     - name: Upload coverage

CHANGELOG.md

@@ -5,6 +5,124 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/).
 
 ## [Unreleased]
 
+## [1.3.0] - 2023-10-06
+### Added
+* Intensity transforms `ScaleIntensityFixedMean` and `RandScaleIntensityFixedMean` (#6542)
+* `UltrasoundConfidenceMapTransform` used for computing confidence map from an ultrasound image (#6709)
+* `channel_wise` support in `RandScaleIntensity` and `RandShiftIntensity` (#6793, #7025)
+* `RandSimulateLowResolution` and `RandSimulateLowResolutiond` (#6806)
+* `SignalFillEmptyd` (#7011)
+* Euclidean distance transform `DistanceTransformEDT` with GPU support (#6981)
+* Port loss and metrics from `monai-generative` (#6729, #6836)
+* Support `invert_image` and `retain_stats` in `AdjustContrast` and `RandAdjustContrast` (#6542)
+* New network `DAF3D` and `Quicknat` (#6306)
+* Support `sincos` position embedding (#6986)
+* `ZarrAvgMerger` used for patch inference (#6633)
+* Dataset tracking support to `MLFlowHandler` (#6616)
+* Considering spacing and subvoxel borders in `SurfaceDiceMetric` (#6681)
+* CUCIM support for surface-related metrics (#7008)
+* `loss_fn` support in `IgniteMetric` and renamed it to `IgniteMetricHandler` (#6695)
+* `CallableEventWithFilter` and `Events` options for `trigger_event` in `GarbageCollector` (#6663)
+* Support random sorting option to `GridPatch`, `RandGridPatch`, `GridPatchd` and `RandGridPatchd` (#6701)
+* Support multi-threaded batch sampling in `PatchInferer` (#6139)
+* `SoftclDiceLoss` and `SoftDiceclDiceLoss` (#6763)
+* `HausdorffDTLoss` and `LogHausdorffDTLoss` (#6994)
+* Documentation for `TensorFloat-32` (#6770)
+* Docstring format guide (#6780)
+* `GDSDataset` support for GDS (#6778)
+* PyTorch backend support for `MapLabelValue` (#6872)
+* `filter_func` in `copy_model_state` to filter the weights to be loaded  and `filter_swinunetr` (#6917)
+* `stats_sender` to `MonaiAlgo` for FL stats (#6984)
+* `freeze_layers` to help freeze specific layers (#6970)
+#### misc.
+* Refactor multi-node running command used in `Auto3DSeg` into dedicated functions (#6623)
+* Support str type annotation to `device` in `ToTensorD` (#6737)
+* Improve logging message and file name extenstion in `DataAnalyzer` for `Auto3DSeg` (#6758)
+* Set `data_range` as a property in `SSIMLoss` (#6788)
+* `end_lr` support in `WarmupCosineSchedule` (#6662)
+* Add `ClearML` as optional dependency (#6827)
+* `yandex.disk` support in `download_url` (#6667)
+* Improve config expression error message (#6977)
+### Fixed
+#### transforms
+* Make `convert_box_to_mask` throw errors when box size larger than the image (#6637)
+* Fix lazy mode in `RandAffine` (#6774)
+* Raise `ValueError` when `map_items` is bool in `Compose` (#6882)
+* Improve performance for `NormalizeIntensity` (#6887)
+* Fix mismatched shape in `Spacing` (#6912)
+* Avoid FutureWarning in `CropForeground` (#6934)
+* Fix `Lazy=True` ignored when using `Dataset` call (#6975)
+#### data
+* Fix wrong spacing checking logic in `PydicomReader` and broken link in `ITKReader` (#6660)
+* Fix boolean indexing of batched `MetaTensor` (#6781)
+* Raise warning when multiprocessing in `DataLoader` (#6830)
+* Remove `shuffle` in `DistributedWeightedRandomSampler` (#6886)
+* Fix missing `SegmentDescription` in `PydicomReader` (#6937)
+* Fix reading dicom series error in `ITKReader` (#6943)
+* Fix KeyError in `PydicomReader` (#6946)
+* Update `metatensor_to_itk_image` to accept RAS `MetaTensor` and update default 'space' in `NrrdReader` to `SpaceKeys.LPS` (#7000)
+* Collate common meta dictionary keys (#7054)
+#### metrics and losses
+* Fixed bug in `GeneralizedDiceLoss` when `batch=True` (#6775)
+* Support for `BCEWithLogitsLoss` in `DiceCELoss` (#6924)
+#### networks
+* Use `np.prod` instead of `np.product` (#6639)
+* Fix dimension issue in `MBConvBlock` (#6672)
+* Fix hard-coded `up_kernel_size` in `ViTAutoEnc` (#6735)
+* Remove hard-coded `bias_downsample` in `resnet` (#6848)
+* Fix unused `kernel_size` in `ResBlock` (#6999)
+* Allow for defining reference grid on non-integer coordinates (#7032)
+* Padding option for autoencoder (#7068)
+* Lower peak memory usage for SegResNetDS (#7066)
+#### bundle
+* Set `train_dataset_data` and `dataset_data` to unrequired in BundleProperty (#6607)
+* Set `None` to properties that do not have `REF_ID` (#6607)
+* Fix `AttributeError` for default value in `get_parsed_content` for `ConfigParser` (#6756)
+* Update `monai.bundle.scripts` to support NGC hosting (#6828, #6997)
+* Add `MetaProperties` (#6835)
+* Add `create_workflow` and update `load` function (#6835)
+* Add bundle root directory to Python search directories automatically (#6910)
+* Generate properties for bundle docs automatically (#6918)
+* Move `download_large_files` from model zoo to core (#6958)
+* Bundle syntax `#` as alias of `::` (#6955)
+* Fix bundle download naming issue (#6969, #6963)
+* Simplify the usage of `ckpt_export` (#6965)
+#### engines and handlers
+* Added int options for `iteration_log` and `epoch_log` in `TensorBoardStatsHandler` (#7027)
+#### misc.
+* Fix device fallback error in `DataAnalyzer` (#6658)
+* Add int check for  `current_mode` in `convert_applied_interp_mode` (#6719)
+* Consistent type in `convert_to_contiguous` (#6849)
+* Label `argmax` in `DataAnalyzer` when retry on CPU (#6852)
+* Fix `DataAnalyzer` with `histogram_only=True` (#6874)
+* Fix `AttributeError` in `RankFilter` in single GPU environment (#6895)
+* Remove the default warning on `TORCH_ALLOW_TF32_CUBLAS_OVERRIDE` and add debug print info (#6909)
+* Hide user information in `print_config` (#6913, #6922)
+* Optionally pass coordinates to predictor during sliding window (#6795)
+* Proper ensembling when trained with a sigmoid in `AutoRunner` (#6588)
+* Fixed `test_retinanet` by increasing absolute differences (#6615)
+* Add type check to avoid comparing a np.array with a string in `_check_kwargs_are_present` (#6624)
+* Fix md5 hashing with FIPS mode (#6635)
+* Capture failures from Auto3DSeg related subprocess calls (#6596)
+### Changed
+* Base Docker image upgraded to `nvcr.io/nvidia/pytorch:23.08-py3` from `nvcr.io/nvidia/pytorch:23.03-py3`
+### Deprecated
+* `allow_smaller=True`; `allow_smaller=False` will be the new default in `CropForeground` and `generate_spatial_bounding_box` (#6736)
+* `dropout_prob` in `VNet` in favor of `dropout_prob_down` and `dropout_prob_up` (#6768)
+* `workflow` in `BundleWorkflow` in favor of `workflow_type`(#6768)
+* `pos_embed` in `PatchEmbeddingBlock` in favor of `proj_type`(#6986)
+* `net_name` and `net_kwargs` in `download` in favor of `model`(#7016)
+### Removed
+* `pad_val`, `stride`, `per_channel` and `upsampler` in `OcclusionSensitivity` (#6642)
+* `compute_meaniou` (#7019)
+* `AsChannelFirst`, `AddChannel`and `SplitChannel` (#7019)
+* `create_multigpu_supervised_trainer` and `create_multigpu_supervised_evaluator` (#7019)
+* `runner_id` in `run` (#7019)
+* `data_src_cfg_filename` in `AlgoEnsembleBuilder` (#7019)
+* `get_validation_stats` in `Evaluator` and `get_train_stats` in `Trainer` (#7019)
+* `epoch_interval` and `iteration_interval` in `TensorBoardStatsHandler` (#7019)
+* some self-hosted test (#7041)
+
 ## [1.2.0] - 2023-06-08
 ### Added
 * Various Auto3DSeg enhancements and integration tests including multi-node multi-GPU optimization, major usability improvements
@@ -817,7 +935,8 @@ the postprocessing steps should be used before calling the metrics methods
 
 [highlights]: https://github.com/Project-MONAI/MONAI/blob/master/docs/source/highlights.md
 
-[Unreleased]: https://github.com/Project-MONAI/MONAI/compare/1.2.0...HEAD
+[Unreleased]: https://github.com/Project-MONAI/MONAI/compare/1.3.0...HEAD
+[1.3.0]: https://github.com/Project-MONAI/MONAI/compare/1.2.0...1.3.0
 [1.2.0]: https://github.com/Project-MONAI/MONAI/compare/1.1.0...1.2.0
 [1.1.0]: https://github.com/Project-MONAI/MONAI/compare/1.0.1...1.1.0
 [1.0.1]: https://github.com/Project-MONAI/MONAI/compare/1.0.0...1.0.1

README.md

@@ -63,7 +63,7 @@ Utilizing [the MONAI Bundle format](https://docs.monai.io/en/latest/bundle_intro
 For guidance on making a contribution to MONAI, see the [contributing guidelines](https://github.com/Project-MONAI/MONAI/blob/dev/CONTRIBUTING.md).
 
 ## Community
-Join the conversation on Twitter [@ProjectMONAI](https://twitter.com/ProjectMONAI) or join our [Slack channel](https://forms.gle/QTxJq3hFictp31UM9).
+Join the conversation on Twitter/X [@ProjectMONAI](https://twitter.com/ProjectMONAI) or join our [Slack channel](https://forms.gle/QTxJq3hFictp31UM9).
 
 Ask and answer questions over on [MONAI's GitHub Discussions tab](https://github.com/Project-MONAI/MONAI/discussions).
 

docs/source/whatsnew_1_3.md

@@ -4,7 +4,7 @@
 - Integrating MONAI Generative into MONAI core
 
 
-# Bundle usability enhancements
+## Bundle usability enhancements
 
 Based on the experience of building MONAI model zoo and the feedback from the community,
 MONAI 1.3 provides major enhancements in MONAI Bundle usability. These include:
@@ -16,7 +16,7 @@ MONAI 1.3 provides major enhancements in MONAI Bundle usability. These include:
 For more details please visit [the Bundle tutorials](https://github.com/Project-MONAI/tutorials/tree/main/bundle) and
 [the Model Zoo demos](https://github.com/Project-MONAI/tutorials/tree/main/model_zoo).
 
-# Integrating MONAI Generative into MONAI Core
+## Integrating MONAI Generative into MONAI Core
 
 Main modules developed at [MONAI GenerativeModels](https://github.com/Project-MONAI/GenerativeModels)
 are being ported into the core codebase, allowing for consistent maintenance and release of the key components for generative AI.

monai/metrics/hausdorff_distance.py

@@ -230,9 +230,9 @@ def compute_percent_hausdorff_distance(
     This function is used to compute the directed Hausdorff distance.
     """
 
-    surface_distance: np.ndarray = get_surface_distance(
+    surface_distance: np.ndarray = get_surface_distance(  # type: ignore
         edges_pred, edges_gt, distance_metric=distance_metric, spacing=spacing
-    )  # type: ignore
+    )
 
     # for both pred and gt do not have foreground
     if surface_distance.shape == (0,):

monai/utils/jupyter_utils.py

@@ -163,7 +163,7 @@ def plot_engine_status(
     avg_keys: tuple[str] = (LOSS_NAME,),
     window_fraction: int = 20,
     image_fn: Callable[[str, torch.Tensor], Any] | None = tensor_to_images,
-    fig: plt.Figure = None,
+    fig: plt.Figure | None = None,
     selected_inst: int = 0,
 ) -> tuple[plt.Figure, list]:
     """
@@ -359,7 +359,7 @@ def status(self) -> str:
 
         return ", ".join(msgs)
 
-    def plot_status(self, logger: Any, plot_func: Callable = plot_engine_status) -> plt.Figure:
+    def plot_status(self, logger: Any, plot_func: Callable = plot_engine_status) -> plt.Figure | None:
         """
         Generate a plot of the current status of the contained engine whose loss and metrics were tracked by `logger`.
         The function `plot_func` must accept arguments `title`, `engine`, `logger`, and `fig` which are the plot title,

requirements-dev.txt

@@ -46,7 +46,7 @@ pynrrd
 pre-commit
 pydicom
 h5py
-nni
+nni; platform_system == "Linux"
 optuna
 git+https://github.com/Project-MONAI/MetricsReloaded@monai-support#egg=MetricsReloaded
 onnx>=1.13.0