Merge branch 'dev' into mlflow-sqlite-migration

Author: garciadias

.github/workflows/codeql-analysis.yml

@@ -67,8 +67,8 @@ jobs:
         rm -rf /opt/hostedtoolcache/{node,go,Ruby,Java*}
         ls -al /opt/hostedtoolcache
         rm -rf /usr/share/dotnet/
-        python -m pip install -U pip wheel
-        python -m pip install -r requirements-dev.txt
+        python -m pip install -U --no-build-isolation pip wheel wheel-stub
+        python -m pip install --no-build-isolation -r requirements-dev.txt
         BUILD_MONAI=1 ./runtests.sh --build
 
     - name: Perform CodeQL Analysis

.github/workflows/pythonapp-gpu.yml

@@ -1,14 +1,16 @@
 # Jenkinsfile.monai-premerge
 name: premerge-gpu
 
-# on:
+on:
 #   # quick tests for pull requests and the releasing branches
 #   push:
 #     branches:
 #       - main
 #       - releasing/*
 #   pull_request:
 #     types: [opened, synchronize, closed]
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
 
 concurrency:
   # automatically cancel the previously triggered workflows when there's a newer version

.github/workflows/weekly-preview.yml

@@ -69,7 +69,7 @@ jobs:
         export YEAR_WEEK=$(date +'%y%U')
         echo "Year week for tag is ${YEAR_WEEK}"
         if ! [[ $YEAR_WEEK =~ ^[0-9]{4}$ ]] ; then echo "Wrong 'year week' format.  Should be 4 digits."; exit 1 ; fi
-        git tag "1.6.dev${YEAR_WEEK}"
+        git tag "1.7.dev${YEAR_WEEK}"
         git log -1
         git tag --list
         python setup.py sdist bdist_wheel

CHANGELOG.md

@@ -5,6 +5,67 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/).
 
 ## [Unreleased]
 
+## [1.6.0] - 2026-06-12
+
+## What's Changed
+### Added
+* Add `MAPEMetric` for regression evaluation (#8686)
+* Add `CalibrationErrorMetric` and `CalibrationError` handler (#8707)
+* Add `AUC-Margin Loss` for AUROC optimization (#8719)
+* Add `MCCLoss` (Matthews Correlation Coefficient loss) (#8785)
+* Add `EmbeddingCollapseMetric` for detecting representational collapse (#8815)
+* Add 3D support and confusion matrix output to `PanopticQualityMetric` (#8684)
+* Add `GradientAccumulation` utility for `SupervisedTrainer` (#8763)
+* Add nested dot-notation access to `ConfigParser` (#8858)
+* Add `allow_pickle` argument to relevant loaders (#8875)
+* Add configurable GD-enhancing tumor label in `ConvertToMultiChannelBasedOnBratsClasses` (#8779)
+* Enable global coordinates in spatial crop transforms (#8794)
+* Generalize `TestTimeAugmentation` to non-spatial predictions (#8715)
+* Add parameter to `DiceMetric` and `DiceHelper` classes (#8774)
+* Support additional dtypes in `pad_nd` (#8672)
+
+### Fixed
+* Fix `Invertd` transform (#8651)
+* Fix `PerceptualLoss` errors out after hitting maximum number of downloads (#8652)
+* Prevent implicit conversion of `MetaTensor` to numpy array (#8654)
+* Fix weights in alpha for `FocalLoss` (#8665)
+* Fix align_corners mismatch in `AffineTransform` (#8690)
+* Fix multi-axis shear transform to compose individual shear matrices (#8778)
+* Fix incorrect `truncated` parameter in `make_gaussian_kernel` causing corrupted `LocalNormalizedCrossCorrelationLoss` (#8781, #8783)
+* Fix batch size broadcasting bug in `GeneralizedWassersteinDiceLoss` (#8744)
+* Fix `AutoencoderKLMaisi` forcing CUDA transfer on CPU inputs (#8736)
+* Fix `TrainableBilateralFilter` 3D input validation (#8729)
+* Fix GPU memory leak by checking both image and label tensors for CUDA device (#8708)
+* Fix `compute_shape_offset` non-tuple indexing for PyTorch >=2.9 (#8776, #8812)
+* Fix memory leak in `optional_import` traceback handling (#8782)
+* Fix nested `Compose` `map_items` in forward and inverse paths (#8787)
+* Fix `JukeboxLoss.forward` swapped `input_amplitude` and `target_amplitude` (#8821)
+* Fix `EnsureChannelFirst` to pass `meta_data` when `track_meta` is False (#8835)
+* Fix `RandSimulateLowResolution` to not alter `track_meta` state (#8837)
+* Fix incomplete activation validation in `HausdorffDTLoss` (#8841)
+* Fix `CrossAttentionBlock` instantiated unconditionally (#8848)
+* Fix `GlobalMutualInformationLoss` bin_centers registered as buffer (#8869)
+* Fix `SoftclDiceLoss` and `SoftDiceclDiceLoss` with `DiceLoss`-compatible API (#8703)
+* Fix execution order of activation and masking in `MaskedDiceLoss` (#8704)
+* Fix `load_old_state_dict` key mapping in `AutoencoderKL` (#8786)
+* Fix missing `channel_wise` parameter in `RandScaleIntensityFixedMean` (#8741)
+* Fix NibabelReader eager C-order copy (#8825)
+* Fix `nnUNetV2Runner` to support MIG UUID and respect `CUDA_VISIBLE_DEVICES` (#8716)
+* Fix Auto3DSeg device handling and safe no-grad cleanup (#8801, #8803)
+* Replace deprecated `cuda.cudart` with `cuda.bindings.runtime` (#8790)
+* Replace `Tensor | None` with `Optional[Tensor]` for TorchScript compatibility (#8879)
+* Fix for [GHSA-rghg-q7wp-9767](https://github.com/Project-MONAI/MONAI/security/advisories/GHSA-rghg-q7wp-9767) (#8885)
+
+### Changed
+* Replace `pickle` with JSON in Auto3DSeg algo serialization (#8695)
+* Replace `flake8` with `ruff` and update lint rules (#8692, #8694)
+* Modernize build commands for setuptools 80+ compatibility (#8728)
+* Replace direct `np.random.*` calls with `np.random.RandomState` instances (#8798)
+* Replace `BaseException` with `Exception` across codebase (#8859)
+* Update base Docker image to 25.12 (#8738)
+* Various performance improvements in engine utilities and core data structures (#8747, #8748, #8751)
+* FFT utilities cleanup and update (#8762)
+
 ## [1.5.2] - 2026-01-28
 
 ## What's Changed
@@ -1267,7 +1328,8 @@ 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/1.5.2...HEAD
+[Unreleased]: https://github.com/Project-MONAI/MONAI/compare/1.6.0...HEAD
+[1.6.0]: https://github.com/Project-MONAI/MONAI/compare/1.5.2...1.6.0
 [1.5.2]: https://github.com/Project-MONAI/MONAI/compare/1.5.1...1.5.2
 [1.5.1]: https://github.com/Project-MONAI/MONAI/compare/1.5.0...1.5.1
 [1.5.0]: https://github.com/Project-MONAI/MONAI/compare/1.4.0...1.5.0

CITATION.cff

@@ -6,8 +6,8 @@ title: "MONAI: Medical Open Network for AI"
 abstract: "AI Toolkit for Healthcare Imaging"
 authors:
   - name: "MONAI Consortium"
-date-released: 2026-01-29
-version: "1.5.2"
+date-released: 2026-06-12
+version: "1.6.0"
 identifiers:
   - description: "This DOI represents all versions of MONAI, and will always resolve to the latest one."
     type: doi

CONTRIBUTING.md

@@ -165,7 +165,7 @@ cd docs/
 make html
 ```
 
-The above commands build html documentation, they are used to automatically generate [https://docs.monai.io](https://docs.monai.io).
+The above commands build html documentation, they are used to automatically generate [monai.readthedocs.io](https://monai.readthedocs.io).
 
 The Python code docstring are written in
 [reStructuredText](https://www.sphinx-doc.org/en/master/usage/restructuredtext/basics.html) and

Dockerfile

@@ -26,12 +26,21 @@ RUN if [[ $(uname -m) =~ "aarch64" ]]; then \
 
 WORKDIR /opt/monai
 
+# Patch NVIDIA's pip constraint file:
+#   - keep the base image's numpy pin if present (older images pin numpy==1.26.4 as
+#     their torch was compiled against NumPy 1.x; newer images may ship an empty file)
+#   - add setuptools<71 (setuptools>=71 removed pkg_resources, breaking MetricsReloaded)
+#   - pin urllib3>=2 to prevent inadvertent downgrades by pip-installing legacy packages
+RUN (grep '^numpy' /etc/pip/constraint.txt || true) > /tmp/new_constraints.txt \
+  && printf 'setuptools<71\nurllib3>=2\n' >> /tmp/new_constraints.txt \
+  && cp /tmp/new_constraints.txt /etc/pip/constraint.txt
+
 # install full deps
 COPY requirements.txt requirements-min.txt requirements-dev.txt /tmp/
 RUN cp /tmp/requirements.txt /tmp/req.bak \
   && awk '!/torch/' /tmp/requirements.txt > /tmp/tmp && mv /tmp/tmp /tmp/requirements.txt \
-  && python -m pip install --upgrade --no-cache-dir pip \
-  && python -m pip install --no-cache-dir -r /tmp/requirements-dev.txt
+  && python -m pip install --upgrade --no-cache-dir --no-build-isolation pip wheel wheel-stub \
+  && python -m pip install --no-cache-dir --no-build-isolation -r /tmp/requirements-dev.txt
 
 # compile ext and remove temp files
 # TODO: remark for issue [revise the dockerfile #1276](https://github.com/Project-MONAI/MONAI/issues/1276)

README.md

@@ -59,7 +59,7 @@ Please refer to [the installation guide](https://monai.readthedocs.io/en/latest/
 
 Examples and notebook tutorials are located at [Project-MONAI/tutorials](https://github.com/Project-MONAI/tutorials).
 
-Technical documentation is available at [docs.monai.io](https://docs.monai.io).
+Technical documentation is available at [monai.readthedocs.io](https://monai.readthedocs.io).
 
 ## Docker
 

docs/source/index.rst

@@ -41,7 +41,7 @@ Getting started
 
 Examples and notebook tutorials are located at `Project-MONAI/tutorials <https://github.com/Project-MONAI/tutorials>`_.
 
-Technical documentation is available at `docs.monai.io <https://docs.monai.io>`_.
+Technical documentation is available at `monai.readthedocs.io <https://monai.readthedocs.io>`_.
 
 .. toctree::
    :maxdepth: 1

docs/source/whatsnew.rst

@@ -6,6 +6,7 @@ What's New
 .. toctree::
    :maxdepth: 1
 
+   whatsnew_1_6.md
    whatsnew_1_5_2.md
    whatsnew_1_5_1.md
    whatsnew_1_5.md