Merge branch 'Project-MONAI:dev' into dev

Author: arthurdjn

.coderabbit.yaml

@@ -0,0 +1,53 @@
+# yaml-language-server: $schema=https://coderabbit.ai/integrations/schema.v2.json
+
+# This file configures CodeRabbit with the various options described in https://docs.coderabbit.ai/configure-coderabbit.
+# CodeRabbit also has a set of commands here: https://docs.coderabbit.ai/guides/commands/
+
+language: "en-US"
+early_access: false
+tone_instructions: "Be terse and to the point in all statements and commentary."
+reviews:
+  # chill is less verbose, assertive is more verbose with more nitpick feedback
+  profile: chill
+  high_level_summary: false
+  high_level_summary_placeholder: "@coderabbitai summary"
+  sequence_diagrams: false
+  auto_apply_labels: false
+  suggested_reviewers: false
+  changed_files_summary: false
+  suggested_labels: false
+  abort_on_close: true
+  poem: false
+  path_instructions:
+    - path: '**/*.md'
+      instructions: Remember that documentation must be updated with the latest information.
+    - path: '**/*.rst'
+      instructions: Remember that documentation must be updated with the latest information.
+    - path: '**/*.py'
+      instructions: >-
+        Review the Python code for quality and correctness. Ensure variable names adhere to PEP8 style guides, are
+        sensible and informative in regards to their function, though permitting simple names for loop and comprehension
+        variables. Ensure routine names are meaningful in regards to their function and use verbs, adjectives, and
+        nouns in a semantically appropriate way. Docstrings should be present for all definition which describe each
+        variable, return value, and raised exception in the appropriate section of the Google-style of docstrings.
+        Examine code for logical error or inconsistencies, and suggest what may be changed to addressed these. Suggest
+        any enhancements for code improving efficiency, maintainability, comprehensibility, and correctness. Ensure new
+        or modified definitions will be covered by existing or new unit tests.
+
+  auto_review:
+    # Automatic Review | Automatic code review
+    enabled: true
+    # Review draft PRs/MRs.
+    drafts: false
+    # ignore PRs with these in the title, these sorts of PRs should be drafts anyway
+    ignore_title_keywords:
+    - "WIP"
+    - "DO NOT MERGE"
+
+# opt out for now until it's clear this isn't too much info and is useful
+knowledge_base:
+  opt_out: true
+
+# chat is allowed
+chat:
+  auto_reply: true

.github/workflows/conda.yml

@@ -21,6 +21,7 @@ jobs:
         os: [ubuntu-latest]
         python-version: ["3.9", "3.10"]
     runs-on: ${{ matrix.os }}
+    timeout-minutes: 46 # equal to max + 3*std over the last 600 successful runs
     env:
       QUICKTEST: True
     steps:

.github/workflows/pythonapp-min.yml

@@ -124,7 +124,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        pytorch-version: ['2.4.1', '2.5.1', '2.6.0']  # FIXME: add 'latest' back once PyTorch 2.7 issues are resolved
+        pytorch-version: ['2.5.1', '2.6.0', '2.7.1', '2.8.0']
     timeout-minutes: 40
     steps:
     - uses: actions/checkout@v4
@@ -151,11 +151,7 @@ jobs:
     - name: Install the dependencies
       run: |
         # min. requirements
-        if [ ${{ matrix.pytorch-version }} == "latest" ]; then
-          python -m pip install torch
-        else
-          python -m pip install torch==${{ matrix.pytorch-version }}
-        fi
+        python -m pip install torch==${{ matrix.pytorch-version }}
         python -m pip install -r requirements-min.txt
         python -m pip list
         BUILD_MONAI=0 python setup.py develop  # no compile of extensions

.github/workflows/pythonapp.yml

@@ -94,7 +94,7 @@ jobs:
     - if: runner.os == 'windows'
       name: Install torch cpu from pytorch.org (Windows only)
       run: |
-        python -m pip install torch==2.4.1 torchvision==0.19.1+cpu --index-url https://download.pytorch.org/whl/cpu
+        python -m pip install torch==2.5.1 torchvision==0.20.1+cpu --index-url https://download.pytorch.org/whl/cpu
     - if: runner.os == 'Linux'
       name: Install itk pre-release (Linux only)
       run: |
@@ -103,7 +103,7 @@ jobs:
     - name: Install the dependencies
       run: |
         python -m pip install --user --upgrade pip wheel
-        python -m pip install torch==2.4.1 torchvision==0.19.1
+        python -m pip install torch==2.5.1 torchvision==0.20.1
         cat "requirements-dev.txt"
         python -m pip install -r requirements-dev.txt
         python -m pip list
@@ -155,7 +155,7 @@ jobs:
         # install the latest pytorch for testing
         # however, "pip install monai*.tar.gz" will build cpp/cuda with an isolated
         # fresh torch installation according to pyproject.toml
-        python -m pip install torch>=2.4.1 torchvision
+        python -m pip install torch>=2.5.1 torchvision
     - name: Check packages
       run: |
         pip uninstall monai

.github/workflows/weekly-preview.yml

@@ -66,7 +66,7 @@ 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 "1.5.dev${YEAR_WEEK}"
+        git tag "1.6.dev${YEAR_WEEK}"
         git log -1
         git tag --list
         python setup.py sdist bdist_wheel

CHANGELOG.md

@@ -5,6 +5,103 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/).
 
 ## [Unreleased]
 
+## [1.5.0] - 2025-06-13
+
+## What's Changed
+### Added
+* Add platform-specific constraints to setup.cfg (#8260)
+* Add PythonicWorkflow (#8151)
+* Add SM architecture version check (#8199)
+* Add MedNext implementation (#8004)
+* Added a top button to CONSTRIBUTING.md (#8163)
+* Adding CODEOWNERS (#8457)
+* Restormer Implementation (#8312)
+* Add rectified flow noise scheduler for accelerated diffusion model (#8374)
+* Add prediction type for rflow scheduler (#8386)
+* Add Average Precision to metrics (#8089)
+* Implementation of a Masked Autoencoder for representation learning (#8152)
+* Implement TorchIO transforms wrapper analogous to TorchVision transfo… (#7579)
+* 8328 nnunet bundle integration (#8329)
+* Adding Support Policy + Doc Updates (#8458)
+* Classifier free guidance (#8460)
+
+### Fixed
+* Fix Ruff Numpy2 deprecation rules (#8179)
+* Fix `torch.load()` frequently warning in PersistentDataset and GDSDataset (#8177)
+* Fix the logging of a nested dictionary metric in MLflow (#8169)
+* Fix ImageFilter to allow Gaussian filter without filter_size (#8189)
+* Fix fold_constants, test_handler switched to onnx (#8211)
+* Fix TypeError in meshgrid (#8252)
+* Fix PatchMerging duplicate merging (#8285)
+* Fix test load image issue (#8297)
+* Fix bundle download error from ngc source (#8307)
+* Fix deprecated usage in zarr (#8313, #8477)
+* Fix DataFrame subsets indexing in CSVDataset() (#8351)
+* Fix `packaging` imports in version comparison logic (#8347)
+* Fix CommonKeys docstring (#8342)
+* Fix: correctly apply fftshift to real-valued data inputs (#8407)
+* Fix OptionalImportError: required package `openslide` is not installed (#8419)
+* Fix cosine noise scheduler (#8427)
+* Fix AutoencoderKL docstrings. (#8445)
+* Inverse Threading Fix (#8418)
+* Fix normalize intensity (#8286)
+* Fix path at test onnx trt export (#8361)
+* Fix broken urls (#8481, #8483)
+
+### Changed
+* [DOC] Update README.md (#8157)
+* Streamlined Rearrange in SpatialAttentionBlock (#8130)
+* Optimize VISTA3D (#8123)
+* Skip torch trt convert test with torch newer than or equal to 2.5.0 (#8165)
+* Enable redirection of all loggers by configuring a FileHandler within the bundle (#8142)
+* Apply pyupgrade fixes for Python 3.9+ syntax (#8150)
+* Update base image to 2410 (#8164)
+* TRT support for MAISI (#8153)
+* 8134 Add unit test for responsive inference (#8146)
+* SwinUNETR refactor to accept additional parameters (#8212)
+* Allow an arbitrary mask to be used in the self attention (#8235)
+* Bump codecov/codecov-action from 4 to 5 (#8245)
+* Docs: update brats classes description (#8246)
+* Change default value of `patch_norm` to False in `SwinUNETR` (#8249)
+* Modify Dice, Jaccard and Tversky losses (#8138)
+* Modify Workflow to Allow IterableDataset Inputs (#8263)
+* Enhance download_and_extract (#8216)
+* Relax gpu load check (#8282, #8275)
+* Using LocalStore in Zarr v3 (#8299)
+* Enable gpu load nifti (#8188)
+* update pydicom reader to enable gpu load (#8283)
+* Zarr compression tests only with versions before 3.0 (#8319)
+* Changing utils.py to test_utils.py (#8335)
+* Refactor testd (#8231)
+* Recursive Item Mapping for Nested Lists in Compose  (#8187)
+* Bump min torch to 1.13.1 to mitigate CVE-2022-45907 unsafe usage of eval (#8296)
+* Inferer modification - save_intermediates clashes with latent shape adjustment in latent diffusion inferers (#8343)
+* Solves path problem in test_bundle_trt_export.py (#8357)
+* Modify ControlNet inferer so that it takes in context when the diffus… (#8360)
+* Update monaihosting download method (#8364)
+* Bump torch minimum to mitigate CVE-2024-31580 & CVE-2024-31583 and enable numpy 2 compatibility (#8368)
+* Auto3DSeg algo_template hash update (#8378)
+* Enable Pytorch 2.6 (#8309)
+* Auto3DSeg algo_template hash update (#8393, #8397)
+* Update Dice Metric Docs (#8388)
+* Auto3DSeg algo_template hash update (#8406)
+* Update bundle download API (#8403)
+* Add Skip test in TestTranschex (#8416)
+* Update get latest bundle version function (#8420)
+* Temporarily Restrict setuptools Version to 79.0.1 (#8441)
+* Update default overlap value in occlusion_sensitivity to 0.6 (#8446)
+* Enable code coverage comments on PRs in codecov configuration (#8402)
+* Migrate to modern Python Logger API (#8449)
+
+### Deprecated
+### Removed
+* Remove deprecated functionality for v1.5 (#8430)
+* Remove deprecated `return_state_dict ` in bundle `load` (#8454)
+* Remove deprecated `net_name` in test file (#8461)
+* Remove unused test cases in bundle load (#8463)
+* selfattention block: Remove the fc linear layer if it is not used (#8325)
+* Removed outdated `torch` version checks from transform functions (#8359)
+
 ## [1.4.0] - 2024-10-17
 ## What's Changed
 ### Added
@@ -1132,7 +1229,8 @@ 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/1.4.0...HEAD
+[Unreleased]: https://github.com/Project-MONAI/MONAI/compare/1.5.0...HEAD
+[1.5.0]: https://github.com/Project-MONAI/MONAI/compare/1.4.0...1.5.0
 [1.4.0]: https://github.com/Project-MONAI/MONAI/compare/1.3.2...1.4.0
 [1.3.2]: https://github.com/Project-MONAI/MONAI/compare/1.3.1...1.3.2
 [1.3.1]: https://github.com/Project-MONAI/MONAI/compare/1.3.0...1.3.1

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: 2024-10-17
-version: "1.4.0"
+date-released: 2025-06-13
+version: "1.5.0"
 identifiers:
   - description: "This DOI represents all versions of MONAI, and will always resolve to the latest one."
     type: doi