Merge branch 'Project-MONAI:dev' into dev

.github/workflows/pythonapp.yml

@@ -99,6 +99,7 @@ jobs:
       name: Install itk pre-release (Linux only)
       run: |
         python -m pip install --pre -U itk
+        find  /opt/hostedtoolcache/* -maxdepth 0 ! -name 'Python' -exec rm -rf {} \;
     - name: Install the dependencies
       run: |
         python -m pip install --user --upgrade pip wheel
@@ -150,7 +151,7 @@ jobs:
     - name: Install dependencies
       run: |
         find  /opt/hostedtoolcache/* -maxdepth 0 ! -name 'Python' -exec rm -rf {} \;
-        python -m pip install --user --upgrade pip setuptools wheel twine
+        python -m pip install --user --upgrade pip setuptools wheel twine packaging
         # 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

.github/workflows/release.yml

@@ -24,7 +24,7 @@ jobs:
         python-version: ${{ matrix.python-version }}
     - name: Install setuptools
       run: |
-        python -m pip install --user --upgrade setuptools wheel
+        python -m pip install --user --upgrade setuptools wheel packaging
     - name: Build and test source archive and wheel file
       run: |
         find  /opt/hostedtoolcache/* -maxdepth 0 ! -name 'Python' -exec rm -rf {} \;
@@ -104,7 +104,7 @@ jobs:
         run: |
           find  /opt/hostedtoolcache/* -maxdepth 0 ! -name 'Python' -exec rm -rf {} \;
           git describe
-          python -m pip install --user --upgrade setuptools wheel
+          python -m pip install --user --upgrade setuptools wheel packaging
           python setup.py build
           cat build/lib/monai/_version.py
       - name: Upload version

.github/workflows/weekly-preview.yml

@@ -5,6 +5,39 @@ on:
   - cron: "0 2 * * 0"  # 02:00 of every Sunday
 
 jobs:
+  flake8-py3:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        opt: ["codeformat", "pytype", "mypy"]
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python 3.9
+      uses: actions/setup-python@v5
+      with:
+        python-version: '3.9'
+    - name: cache weekly timestamp
+      id: pip-cache
+      run: |
+        echo "datew=$(date '+%Y-%V')" >> $GITHUB_OUTPUT
+    - name: cache for pip
+      uses: actions/cache@v4
+      id: cache
+      with:
+        path: ~/.cache/pip
+        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
+      run: |
+        # clean up temporary files
+        $(pwd)/runtests.sh --build --clean
+        # Github actions have 2 cores, so parallelize pytype
+        $(pwd)/runtests.sh --build --${{ matrix.opt }} -j 2
+
   packaging:
     if: github.repository == 'Project-MONAI/MONAI'
     runs-on: ubuntu-latest
@@ -19,7 +52,7 @@ jobs:
         python-version: '3.9'
     - name: Install setuptools
       run: |
-        python -m pip install --user --upgrade setuptools wheel
+        python -m pip install --user --upgrade setuptools wheel packaging
     - name: Build distribution
       run: |
         export HEAD_COMMIT_ID=$(git rev-parse HEAD)

README.md

@@ -14,6 +14,7 @@
 [![postmerge](https://img.shields.io/github/checks-status/project-monai/monai/dev?label=postmerge)](https://github.com/Project-MONAI/MONAI/actions?query=branch%3Adev)
 [![Documentation Status](https://readthedocs.org/projects/monai/badge/?version=latest)](https://docs.monai.io/en/latest/)
 [![codecov](https://codecov.io/gh/Project-MONAI/MONAI/branch/dev/graph/badge.svg?token=6FTC7U1JJ4)](https://codecov.io/gh/Project-MONAI/MONAI)
+[![monai Downloads Last Month](https://assets.piptrends.com/get-last-month-downloads-badge/monai.svg 'monai Downloads Last Month by pip Trends')](https://piptrends.com/package/monai)
 
 MONAI is a [PyTorch](https://pytorch.org/)-based, [open-source](https://github.com/Project-MONAI/MONAI/blob/dev/LICENSE) framework for deep learning in healthcare imaging, part of [PyTorch Ecosystem](https://pytorch.org/ecosystem/).
 Its ambitions are:

docs/requirements.txt

@@ -41,3 +41,4 @@ onnxruntime; python_version <= '3.10'
 zarr
 huggingface_hub
 pyamg>=5.0.0
+packaging

docs/source/apps.rst

@@ -248,6 +248,22 @@ FastMRIReader
 ~~~~~~~~~~~~~
 .. autofunction:: monai.apps.reconstruction.complex_utils.complex_conj
 
+`Vista3d`
+---------
+.. automodule:: monai.apps.vista3d.inferer
+.. autofunction:: point_based_window_inferer
+
+.. automodule:: monai.apps.vista3d.transforms
+.. autoclass:: VistaPreTransformd
+    :members:
+.. autoclass:: VistaPostTransformd
+    :members:
+.. autoclass:: Relabeld
+    :members:
+
+.. automodule:: monai.apps.vista3d.sampler
+.. autofunction:: sample_prompt_pairs
+
 `Auto3DSeg`
 -----------
 .. automodule:: monai.apps.auto3dseg
@@ -261,11 +277,3 @@ FastMRIReader
 
 .. autoclass:: monai.apps.nnunet.nnUNetV2Runner
   :members:
-
-`Generative AI`
----------------
-
-`MAISI Utilities`
-~~~~~~~~~~~~~~~~~
-.. automodule:: monai.apps.generation.maisi.utils.morphological_ops
-    :members:

docs/source/installation.md

@@ -254,10 +254,10 @@ Since MONAI v0.2.0, the extras syntax such as `pip install 'monai[nibabel]'` is
 - The options are
 
 ```
-[nibabel, skimage, scipy, pillow, tensorboard, gdown, ignite, torchvision, itk, tqdm, lmdb, psutil, cucim, openslide, pandas, einops, transformers, mlflow, clearml, matplotlib, tensorboardX, tifffile, imagecodecs, pyyaml, fire, jsonschema, ninja, pynrrd, pydicom, h5py, nni, optuna, onnx, onnxruntime, zarr, lpips, pynvml, huggingface_hub]
+[nibabel, skimage, scipy, pillow, tensorboard, gdown, ignite, torchvision, itk, tqdm, lmdb, psutil, cucim, openslide, pandas, einops, transformers, mlflow, clearml, matplotlib, tensorboardX, tifffile, imagecodecs, pyyaml, fire, jsonschema, ninja, pynrrd, pydicom, h5py, nni, optuna, onnx, onnxruntime, zarr, lpips, pynvml, huggingface_hub, segment-anything]
 ```
 
 which correspond to `nibabel`, `scikit-image`,`scipy`, `pillow`, `tensorboard`,
-`gdown`, `pytorch-ignite`, `torchvision`, `itk`, `tqdm`, `lmdb`, `psutil`, `cucim`, `openslide-python`, `pandas`, `einops`, `transformers`, `mlflow`, `clearml`, `matplotlib`, `tensorboardX`, `tifffile`, `imagecodecs`, `pyyaml`, `fire`, `jsonschema`, `ninja`, `pynrrd`, `pydicom`, `h5py`, `nni`, `optuna`, `onnx`, `onnxruntime`, `zarr`, `lpips`, `nvidia-ml-py`, `huggingface_hub` and `pyamg` respectively.
+`gdown`, `pytorch-ignite`, `torchvision`, `itk`, `tqdm`, `lmdb`, `psutil`, `cucim`, `openslide-python`, `pandas`, `einops`, `transformers`, `mlflow`, `clearml`, `matplotlib`, `tensorboardX`, `tifffile`, `imagecodecs`, `pyyaml`, `fire`, `jsonschema`, `ninja`, `pynrrd`, `pydicom`, `h5py`, `nni`, `optuna`, `onnx`, `onnxruntime`, `zarr`, `lpips`, `nvidia-ml-py`, `huggingface_hub`, `pyamg` and `segment-anything` respectively.
 
 - `pip install 'monai[all]'` installs all the optional dependencies.

docs/source/losses.rst

@@ -93,6 +93,11 @@ Segmentation Losses
 .. autoclass:: SoftDiceclDiceLoss
     :members:
 
+`NACLLoss`
+~~~~~~~~~~
+.. autoclass:: NACLLoss
+    :members:
+
 Registration Losses
 -------------------
 

docs/source/networks.rst

@@ -481,6 +481,11 @@ Nets
 .. autoclass:: SegResNetDS
   :members:
 
+`SegResNetDS2`
+~~~~~~~~~~~~~~
+.. autoclass:: SegResNetDS2
+  :members:
+
 `SegResNetVAE`
 ~~~~~~~~~~~~~~
 .. autoclass:: SegResNetVAE
@@ -556,6 +561,11 @@ Nets
 .. autoclass:: UNETR
     :members:
 
+`VISTA3D`
+~~~~~~~~~
+.. autoclass:: VISTA3D
+    :members:
+
 `SwinUNETR`
 ~~~~~~~~~~~
 .. autoclass:: SwinUNETR

docs/source/transforms.rst

@@ -2310,6 +2310,9 @@ Utilities
 .. automodule:: monai.transforms.utils_pytorch_numpy_unification
     :members:
 
+.. automodule:: monai.transforms.utils_morphological_ops
+    :members:
+
 By Categories
 -------------
 .. toctree::

environment-dev.yml

@@ -5,10 +5,10 @@ channels:
   - nvidia
   - conda-forge
 dependencies:
-  - numpy>=1.20
+  - numpy>=1.24,<2.0
   - pytorch>=1.9
   - torchvision
-  - pytorch-cuda=11.6
+  - pytorch-cuda>=11.6
   - pip
   - pip:
     - -r requirements-dev.txt