Merge branch 'Project-MONAI:dev' into model-calibration

.github/workflows/blossom-ci.yml

@@ -29,13 +29,15 @@ jobs:
       args: ${{ env.args }}
 
     # This job only runs for pull request comments
-    if: contains('\
-      Nic-Ma,\
-      wyli,\
-      pxLi,\
-      YanxuanLiu,\
-      KumoLiu,\
-      ', format('{0},', github.actor)) && github.event.comment.body == '/build'
+    if: |
+      github.event.comment.body == '/build' &&
+      (
+        github.actor == 'Nic-Ma' ||
+        github.actor == 'wyli' ||
+        github.actor == 'pxLi' ||
+        github.actor == 'YanxuanLiu' ||
+        github.actor == 'KumoLiu'
+      )
     steps:
       - name: Check if comment is issued by authorized person
         run: blossom-ci

.github/workflows/conda.yml

@@ -32,6 +32,10 @@ jobs:
         maximum-size: 16GB
         disk-root: "D:"
     - uses: actions/checkout@v4
+    - name: Clean up disk space
+      run: |
+        find /opt/hostedtoolcache/* -maxdepth 0 ! -name 'Python' -exec rm -rf {} \;
+        rm -rf /usr/share/dotnet/
     - uses: conda-incubator/setup-miniconda@v3
       with:
         auto-update-conda: true
@@ -56,6 +60,10 @@ jobs:
         conda deactivate
     - name: Test env (CPU ${{ runner.os }})
       shell: bash -el {0}
+      env:
+        NGC_API_KEY: ${{ secrets.NGC_API_KEY }}
+        NGC_ORG: ${{ secrets.NGC_ORG }}
+        NGC_TEAM: ${{ secrets.NGC_TEAM }}
       run: |
         conda activate monai
         $(pwd)/runtests.sh --build --unittests

.github/workflows/cron-ngc-bundle.yml

@@ -18,10 +18,10 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v4
-    - name: Set up Python 3.8
+    - name: Set up Python 3.9
       uses: actions/setup-python@v5
       with:
-        python-version: '3.8'
+        python-version: '3.9'
     - name: cache weekly timestamp
       id: pip-cache
       run: echo "datew=$(date '+%Y-%V')" >> $GITHUB_OUTPUT

.github/workflows/cron.yml

@@ -50,6 +50,10 @@ jobs:
         python -m pip install -r requirements-dev.txt
         python -m pip list
     - name: Run tests report coverage
+      env:
+          NGC_API_KEY: ${{ secrets.NGC_API_KEY }}
+          NGC_ORG: ${{ secrets.NGC_ORG }}
+          NGC_TEAM: ${{ secrets.NGC_TEAM }}
       run: |
         export LAUNCH_DELAY=$[ $RANDOM % 16 * 60 ]
         echo "Sleep $LAUNCH_DELAY"
@@ -94,6 +98,10 @@ jobs:
         python -m pip install -r requirements-dev.txt
         python -m pip list
     - name: Run tests report coverage
+      env:
+        NGC_API_KEY: ${{ secrets.NGC_API_KEY }}
+        NGC_ORG: ${{ secrets.NGC_ORG }}
+        NGC_TEAM: ${{ secrets.NGC_TEAM }}
       run: |
         export LAUNCH_DELAY=$[ $RANDOM % 16 * 60 ]
         echo "Sleep $LAUNCH_DELAY"
@@ -196,6 +204,10 @@ jobs:
     - name: Run tests report coverage
       # The docker image process has done the compilation.
       # BUILD_MONAI=1 is necessary for triggering the USE_COMPILED flag.
+      env:
+        NGC_API_KEY: ${{ secrets.NGC_API_KEY }}
+        NGC_ORG: ${{ secrets.NGC_ORG }}
+        NGC_TEAM: ${{ secrets.NGC_TEAM }}
       run: |
         cd /opt/monai
         nvidia-smi

.github/workflows/docker.yml

@@ -100,3 +100,6 @@ jobs:
       shell: bash
       env:
         QUICKTEST: True
+        NGC_API_KEY: ${{ secrets.NGC_API_KEY }}
+        NGC_ORG: ${{ secrets.NGC_ORG }}
+        NGC_TEAM: ${{ secrets.NGC_TEAM }}

.github/workflows/integration.yml

@@ -68,6 +68,9 @@ jobs:
       shell: bash
       env:
         BUILD_MONAI: 1
+        NGC_API_KEY: ${{ secrets.NGC_API_KEY }}
+        NGC_ORG: ${{ secrets.NGC_ORG }}
+        NGC_TEAM: ${{ secrets.NGC_TEAM }}
       run: ./runtests.sh --build --net
 
     - name: Add reaction

.github/workflows/pythonapp-gpu.yml

@@ -62,7 +62,7 @@ jobs:
         if [ ${{ matrix.environment }} = "PT110+CUDA111" ] || \
           [ ${{ matrix.environment }} = "PT113+CUDA116" ]
         then
-        PYVER=3.8 PYSFX=3 DISTUTILS=python3-distutils && \
+        PYVER=3.9 PYSFX=3 DISTUTILS=python3-distutils && \
         apt-get update && apt-get install -y --no-install-recommends \
           curl \
           pkg-config \

.github/workflows/pythonapp-min.yml

@@ -31,10 +31,10 @@ jobs:
     timeout-minutes: 40
     steps:
     - uses: actions/checkout@v4
-    - name: Set up Python 3.8
+    - name: Set up Python 3.9
       uses: actions/setup-python@v5
       with:
-        python-version: '3.8'
+        python-version: '3.9'
     - name: Prepare pip wheel
       run: |
         which python
@@ -67,13 +67,16 @@ jobs:
       shell: bash
       env:
         QUICKTEST: True
+        NGC_API_KEY: ${{ secrets.NGC_API_KEY }}
+        NGC_ORG: ${{ secrets.NGC_ORG }}
+        NGC_TEAM: ${{ secrets.NGC_TEAM }}
 
   min-dep-py3:  # min dependencies installed tests for different python
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.8', '3.9', '3.10', '3.11']
+        python-version: ['3.9', '3.10', '3.11', '3.12']
     timeout-minutes: 40
     steps:
     - uses: actions/checkout@v4
@@ -112,20 +115,23 @@ jobs:
         ./runtests.sh --min
       env:
         QUICKTEST: True
+        NGC_API_KEY: ${{ secrets.NGC_API_KEY }}
+        NGC_ORG: ${{ secrets.NGC_ORG }}
+        NGC_TEAM: ${{ secrets.NGC_TEAM }}
 
   min-dep-pytorch:  # min dependencies installed tests for different pytorch
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
       matrix:
-        pytorch-version: ['1.9.1', '1.10.2', '1.11.0', '1.12.1', '1.13', 'latest']
+        pytorch-version: ['1.10.2', '1.11.0', '1.12.1', '1.13', '2.0.1', 'latest']
     timeout-minutes: 40
     steps:
     - uses: actions/checkout@v4
-    - name: Set up Python 3.8
+    - name: Set up Python 3.9
       uses: actions/setup-python@v5
       with:
-        python-version: '3.8'
+        python-version: '3.9'
     - name: Prepare pip wheel
       run: |
         which python
@@ -161,3 +167,6 @@ jobs:
         ./runtests.sh --min
       env:
         QUICKTEST: True
+        NGC_API_KEY: ${{ secrets.NGC_API_KEY }}
+        NGC_ORG: ${{ secrets.NGC_ORG }}
+        NGC_TEAM: ${{ secrets.NGC_TEAM }}

.github/workflows/pythonapp.yml

@@ -29,10 +29,10 @@ jobs:
         opt: ["codeformat", "pytype", "mypy"]
     steps:
     - uses: actions/checkout@v4
-    - name: Set up Python 3.8
+    - name: Set up Python 3.9
       uses: actions/setup-python@v5
       with:
-        python-version: '3.8'
+        python-version: '3.9'
     - name: cache weekly timestamp
       id: pip-cache
       run: |
@@ -45,6 +45,7 @@ jobs:
         key: ${{ runner.os }}-pip-${{ steps.pip-cache.outputs.datew }}
     - name: Install dependencies
       run: |
+        find  /opt/hostedtoolcache/* -maxdepth 0 ! -name 'Python' -exec rm -rf {} \;
         python -m pip install --upgrade pip wheel
         python -m pip install -r requirements-dev.txt
     - name: Lint and type check
@@ -130,10 +131,10 @@ jobs:
     - uses: actions/checkout@v4
       with:
         fetch-depth: 0
-    - name: Set up Python 3.8
+    - name: Set up Python 3.9
       uses: actions/setup-python@v5
       with:
-        python-version: '3.8'
+        python-version: '3.9'
     - name: cache weekly timestamp
       id: pip-cache
       run: |
@@ -148,6 +149,7 @@ jobs:
         key: ${{ runner.os }}-pip-${{ steps.pip-cache.outputs.datew }}
     - name: Install dependencies
       run: |
+        find  /opt/hostedtoolcache/* -maxdepth 0 ! -name 'Python' -exec rm -rf {} \;
         python -m pip install --user --upgrade pip setuptools wheel twine
         # install the latest pytorch for testing
         # however, "pip install monai*.tar.gz" will build cpp/cuda with an isolated
@@ -211,10 +213,10 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v4
-    - name: Set up Python 3.8
+    - name: Set up Python 3.9
       uses: actions/setup-python@v5
       with:
-        python-version: '3.8'
+        python-version: '3.9'
     - name: cache weekly timestamp
       id: pip-cache
       run: |

.github/workflows/setupapp.yml

@@ -49,6 +49,10 @@ jobs:
         python -m pip install --upgrade torch torchvision
         python -m pip install -r requirements-dev.txt
     - name: Run unit tests report coverage
+      env:
+        NGC_API_KEY: ${{ secrets.NGC_API_KEY }}
+        NGC_ORG: ${{ secrets.NGC_ORG }}
+        NGC_TEAM: ${{ secrets.NGC_TEAM }}
       run: |
         python -m pip list
         git config --global --add safe.directory /__w/MONAI/MONAI
@@ -77,7 +81,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.8', '3.9', '3.10']
+        python-version: ['3.9', '3.10', '3.11']
     steps:
     - uses: actions/checkout@v4
       with:
@@ -104,6 +108,10 @@ jobs:
         python -m pip install --upgrade pip wheel
         python -m pip install -r requirements-dev.txt
     - name: Run quick tests CPU ubuntu
+      env:
+        NGC_API_KEY: ${{ secrets.NGC_API_KEY }}
+        NGC_ORG: ${{ secrets.NGC_ORG }}
+        NGC_TEAM: ${{ secrets.NGC_TEAM }}
       run: |
         python -m pip list
         python -c 'import torch; print(torch.__version__); print(torch.rand(5,3))'
@@ -119,10 +127,10 @@ jobs:
   install:  # pip install from github url, the default branch is dev
     runs-on: ubuntu-latest
     steps:
-    - name: Set up Python 3.8
+    - name: Set up Python 3.9
       uses: actions/setup-python@v5
       with:
-        python-version: '3.8'
+        python-version: '3.9'
     - name: cache weekly timestamp
       id: pip-cache
       run: |

.pre-commit-config.yaml

@@ -9,7 +9,7 @@ ci:
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v4.6.0
     hooks:
       - id: end-of-file-fixer
       - id: trailing-whitespace

CHANGELOG.md

@@ -5,6 +5,11 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/).
 
 ## [Unreleased]
 
+## [1.3.2] - 2024-06-25
+### Fixed
+#### misc.
+* Updated Numpy version constraint to < 2.0 (#7859)
+
 ## [1.3.1] - 2024-05-17
 ### Added
 * Support for `by_measure` argument in `RemoveSmallObjects` (#7137)
@@ -1035,7 +1040,8 @@ 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/1.3.1...HEAD
+[Unreleased]: https://github.com/Project-MONAI/MONAI/compare/1.3.2...HEAD
+[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
 [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

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: 2024-05-21
-version: "1.3.1"
+date-released: 2024-06-26
+version: "1.3.2"
 identifiers:
   - description: "This DOI represents all versions of MONAI, and will always resolve to the latest one."
     type: doi

CONTRIBUTING.md

@@ -123,7 +123,7 @@ or (for new features that would not break existing functionality):
 ```
 
 It is recommended that the new test `test_[module_name].py` is constructed by using only
-python 3.8+ build-in functions, `torch`, `numpy`, `coverage` (for reporting code coverages) and `parameterized` (for organising test cases) packages.
+python 3.9+ build-in functions, `torch`, `numpy`, `coverage` (for reporting code coverages) and `parameterized` (for organising test cases) packages.
 If it requires any other external packages, please make sure:
 - the packages are listed in [`requirements-dev.txt`](requirements-dev.txt)
 - the new test `test_[module_name].py` is added to the `exclude_cases` in [`./tests/min_tests.py`](./tests/min_tests.py) so that

docs/requirements.txt

@@ -6,7 +6,7 @@ itk>=5.2
 nibabel
 parameterized
 scikit-image>=0.19.0
-scipy>=1.7.1
+scipy>=1.12.0; python_version >= '3.9'
 tensorboard
 commonmark==0.9.1
 recommonmark==0.6.0
@@ -40,3 +40,4 @@ onnx>=1.13.0
 onnxruntime; python_version <= '3.10'
 zarr
 huggingface_hub
+pyamg>=5.0.0

docs/source/apps.rst

@@ -261,3 +261,11 @@ FastMRIReader
 
 .. autoclass:: monai.apps.nnunet.nnUNetV2Runner
   :members:
+
+`Generative AI`
+---------------
+
+`MAISI Utilities`
+~~~~~~~~~~~~~~~~~
+.. automodule:: monai.apps.generation.maisi.utils.morphological_ops
+    :members:

docs/source/engines.rst

@@ -30,6 +30,11 @@ Workflows
 .. autoclass:: GanTrainer
     :members:
 
+`AdversarialTrainer`
+~~~~~~~~~~~~~~~~~~~~
+.. autoclass:: AdversarialTrainer
+    :members:
+
 `Evaluator`
 ~~~~~~~~~~~
 .. autoclass:: Evaluator

docs/source/index.rst

@@ -37,7 +37,7 @@ Features
 Getting started
 ---------------
 
-`MedNIST demo <https://colab.research.google.com/drive/1wy8XUSnNWlhDNazFdvGBHLfdkGvOHBKe>`_ and `MONAI for PyTorch Users <https://colab.research.google.com/drive/1boqy7ENpKrqaJoxFlbHIBnIODAs1Ih1T>`_ are available on Colab.
+`MedNIST demo <https://colab.research.google.com/github/Project-MONAI/tutorials/blob/main/2d_classification/mednist_tutorial.ipynb>`_ and `MONAI for PyTorch Users <https://colab.research.google.com/github/Project-MONAI/tutorials/blob/main/modules/developer_guide.ipynb>`_ are available on Colab.
 
 Examples and notebook tutorials are located at `Project-MONAI/tutorials <https://github.com/Project-MONAI/tutorials>`_.