adds release note v1.1

CHANGELOG.md

@@ -5,6 +5,69 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/).
 
 ## [Unreleased]
 
+## [1.1.0] - 2022-12-19
+### Added
+* Hover-Net based digital pathology workflows including new network, loss, postprocessing, metric, training, and inference modules
+* Various enhancements for Auto3dSeg `AutoRunner` including template caching, selection, and a dry-run mode `nni_dry_run`
+* Various enhancements for Auto3dSeg algo templates including new state-of-the-art configurations, optimized GPU memory utilization
+* New bundle API and configurations to support experiment management including `MLFlowHandler`
+* New `bundle.script` API to support model zoo query and download
+* `LossMetric` metric to compute loss as cumulative metric measurement
+* Transforms and base transform APIs including `RandomizableTrait` and `MedianSmooth`
+* `runtime_cache` option for `CacheDataset` and the derived classes to allow for shared caching on the fly
+* Flexible name formatter for `SaveImage` transform
+* `pending_operations` MetaTensor property and basic APIs for lazy image resampling
+* Contrastive sensitivity for SSIM metric
+* Extensible backbones for `FlexibleUNet`
+* Generalize `SobelGradients` to 3D and any spatial axes
+* `warmup_multiplier` option for `WarmupCosineSchedule`
+* F beta score metric based on confusion matrix metric
+* Support of key overwriting in `Lambdad`
+* Basic premerge tests for Python 3.11
+* Unit and integration tests for CUDA 11.6, 11.7 and A100 GPU
+* `DataAnalyzer` handles minor image-label shape inconsistencies
+### Fixed
+* Review and enhance previously untyped APIs with additional type annotations and casts
+* `switch_endianness` in LoadImage now supports tensor input
+* Reduced memory footprint for various Auto3dSeg tests
+* Issue of `@` in `monai.bundle.ReferenceResolver`
+* Compatibility issue with ITK-Python 5.3 (converting `itkMatrixF44` for default collate)
+* Inconsistent of sform and qform when using different backends for `SaveImage`
+* `MetaTensor.shape` call now returns a `torch.Size` instead of tuple
+* Issue of channel reduction in `GeneralizedDiceLoss`
+* Issue of background handling before softmax in `DiceFocalLoss`
+* Numerical issue of `LocalNormalizedCrossCorrelationLoss`
+* Issue of incompatible view size in `ConfusionMatrixMetric`
+* `NetAdapter` compatibility with Torchscript
+* Issue of `extract_levels` in `RegUNet`
+* Optional `bias_downsample` in `ResNet`
+* `dtype` overflow for `ShiftIntensity` transform
+* Randomized transforms such as `RandCuCIM` now inherit `RandomizableTrait`
+* `fg_indices.size` compatibility issue in `generate_pos_neg_label_crop_centers`
+* Issue when inverting `ToTensor`
+* Issue of capital letters in filename suffixes check in `LoadImage`
+* Minor tensor compatibility issues in `apps.nuclick.transforms`
+* Issue of float16 in `verify_net_in_out`
+* `std` variable type issue for `RandRicianNoise`
+* `DataAnalyzer` accepts `None` as label key and checks empty labels
+* `iter_patch_position` now has a smaller memory footprint
+* `CumulativeAverage` has been refactored and enhanced to allow for simple tracking of metric running stats.
+* Multi-threading issue for `MLFlowHandler`
+### Changed
+* Printing a MetaTensor now generates a less verbose representation
+* `DistributedSampler` raises a ValueError if there are too few devices
+* OpenCV and `VideoDataset` modules are loaded lazily to avoid dependency issues
+* `device` in `monai.engines.Workflow` supports string values
+* `Activations` and `AsDiscrete` take `kwargs` as additional arguments
+* `DataAnalyzer` is now more efficient and writes summary stats before detailed all case stats
+* Base Docker image upgraded to `nvcr.io/nvidia/pytorch:22.10-py3` from `nvcr.io/nvidia/pytorch:22.09-py3`
+* Simplified Conda environment file `environment-dev.yml`
+* Versioneer dependency upgraded to `0.23` from `0.19`
+### Deprecated
+* `NibabelReader` input argument `dtype` is deprecated, the reader will use the original dtype of the image
+### Removed
+* Support for PyTorch 1.7
+
 ## [1.0.1] - 2022-10-24
 ### Fixes
 * DiceCELoss for multichannel targets
@@ -643,7 +706,8 @@ 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/1.0.1...HEAD
+[Unreleased]: https://github.com/Project-MONAI/MONAI/compare/1.1.0...HEAD
+[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
 [1.0.0]: https://github.com/Project-MONAI/MONAI/compare/0.9.1...1.0.0
 [0.9.1]: https://github.com/Project-MONAI/MONAI/compare/0.9.0...0.9.1

README.md

@@ -7,7 +7,7 @@
 [![License](https://img.shields.io/badge/license-Apache%202.0-green.svg)](https://opensource.org/licenses/Apache-2.0)
 [![CI Build](https://github.com/Project-MONAI/MONAI/workflows/build/badge.svg?branch=dev)](https://github.com/Project-MONAI/MONAI/commits/dev)
 [![Documentation Status](https://readthedocs.org/projects/monai/badge/?version=latest)](https://docs.monai.io/en/latest/?badge=latest)
-[![codecov](https://codecov.io/gh/Project-MONAI/MONAI/branch/dev/graph/badge.svg)](https://codecov.io/gh/Project-MONAI/MONAI)
+[![codecov](https://codecov.io/gh/Project-MONAI/MONAI/branch/dev/graph/badge.svg?token=6FTC7U1JJ4)](https://codecov.io/gh/Project-MONAI/MONAI)
 [![PyPI version](https://badge.fury.io/py/monai.svg)](https://badge.fury.io/py/monai)
 [![conda](https://img.shields.io/conda/vn/conda-forge/monai)](https://anaconda.org/conda-forge/monai)
 

tests/test_convert_data_type.py

@@ -31,7 +31,13 @@
 for in_type in TEST_NDARRAYS_ALL + (int, float):
     for out_type in TEST_NDARRAYS_ALL:
         TESTS_LIST.append(
-            ([in_type(np.array(1.0)), in_type(np.array(1.0))], out_type(np.array([1.0, 1.0])), True, None, False)  # type: ignore
+            (
+                [in_type(np.array(1.0)), in_type(np.array(1.0))],  # type: ignore
+                out_type(np.array([1.0, 1.0])),
+                True,
+                None,
+                False,
+            )
         )
         TESTS_LIST.append(
             (
@@ -44,7 +50,13 @@
         )
         if in_type is not float:
             TESTS_LIST.append(
-                ([in_type(np.array(257)), in_type(np.array(1))], out_type(np.array([255, 1])), True, np.uint8, True)  # type: ignore
+                (
+                    [in_type(np.array(257)), in_type(np.array(1))],  # type: ignore
+                    out_type(np.array([255, 1])),
+                    True,
+                    np.uint8,
+                    True,
+                )
             )
             TESTS_LIST.append(
                 (