transformer block local window attention

.github/workflows/chatops.yml

@@ -10,7 +10,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: dispatch
-        uses: peter-evans/[email protected].1
+        uses: peter-evans/[email protected].2
         with:
           token: ${{ secrets.PR_MAINTAIN }}
           reaction-token: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/codeql-analysis.yml

@@ -42,7 +42,7 @@ jobs:
 
     # Initializes the CodeQL tools for scanning.
     - name: Initialize CodeQL
-      uses: github/codeql-action/init@v2
+      uses: github/codeql-action/init@v3
       with:
         languages: ${{ matrix.language }}
         # If you wish to specify custom queries, you can do so here or in a config file.
@@ -72,4 +72,4 @@ jobs:
         BUILD_MONAI=1 ./runtests.sh --build
 
     - name: Perform CodeQL Analysis
-      uses: github/codeql-action/analyze@v2
+      uses: github/codeql-action/analyze@v3

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

@@ -19,7 +19,7 @@ jobs:
     steps:
     - uses: actions/checkout@v4
     - name: Set up Python 3.8
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: '3.8'
     - name: cache weekly timestamp

.github/workflows/docker.yml

@@ -26,7 +26,7 @@ jobs:
           ref: dev
           fetch-depth: 0
       - name: Set up Python 3.9
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: '3.9'
       - shell: bash
@@ -36,7 +36,7 @@ jobs:
           python setup.py build
           cat build/lib/monai/_version.py
       - name: Upload version
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: _version.py
           path: build/lib/monai/_version.py
@@ -56,7 +56,7 @@ jobs:
       with:
         ref: dev
     - name: Download version
-      uses: actions/download-artifact@v3
+      uses: actions/download-artifact@v4
       with:
         name: _version.py
     - name: docker_build

.github/workflows/pythonapp-min.yml

@@ -30,7 +30,7 @@ jobs:
     steps:
     - uses: actions/checkout@v4
     - name: Set up Python 3.8
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: '3.8'
     - name: Prepare pip wheel
@@ -76,7 +76,7 @@ jobs:
     steps:
     - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Prepare pip wheel
@@ -121,7 +121,7 @@ jobs:
     steps:
     - uses: actions/checkout@v4
     - name: Set up Python 3.8
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: '3.8'
     - name: Prepare pip wheel

.github/workflows/pythonapp.yml

@@ -28,7 +28,7 @@ jobs:
     steps:
     - uses: actions/checkout@v4
     - name: Set up Python 3.8
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: '3.8'
     - name: cache weekly timestamp
@@ -69,7 +69,7 @@ jobs:
         disk-root: "D:"
     - uses: actions/checkout@v4
     - name: Set up Python 3.8
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: '3.8'
     - name: Prepare pip wheel
@@ -128,7 +128,7 @@ jobs:
       with:
         fetch-depth: 0
     - name: Set up Python 3.8
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: '3.8'
     - name: cache weekly timestamp
@@ -209,7 +209,7 @@ jobs:
     steps:
     - uses: actions/checkout@v4
     - name: Set up Python 3.8
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: '3.8'
     - name: cache weekly timestamp

.github/workflows/release.yml

@@ -19,7 +19,7 @@ jobs:
       with:
         fetch-depth: 0
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install setuptools
@@ -66,7 +66,7 @@ jobs:
 
     - if: matrix.python-version == '3.9' && startsWith(github.ref, 'refs/tags/')
       name: Upload artifacts
-      uses: actions/upload-artifact@v3
+      uses: actions/upload-artifact@v4
       with:
         name: dist
         path: dist/
@@ -97,7 +97,7 @@ jobs:
         with:
           fetch-depth: 0
       - name: Set up Python 3.9
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: '3.9'
       - shell: bash
@@ -108,7 +108,7 @@ jobs:
           python setup.py build
           cat build/lib/monai/_version.py
       - name: Upload version
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: _version.py
           path: build/lib/monai/_version.py
@@ -125,7 +125,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - name: Download version
-        uses: actions/download-artifact@v3
+        uses: actions/download-artifact@v4
         with:
           name: _version.py
       - name: Set tag

.github/workflows/setupapp.yml

@@ -83,7 +83,7 @@ jobs:
       with:
         fetch-depth: 0
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: cache weekly timestamp
@@ -120,7 +120,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - name: Set up Python 3.8
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: '3.8'
     - name: cache weekly timestamp

.github/workflows/weekly-preview.yml

@@ -14,7 +14,7 @@ jobs:
         ref: dev
         fetch-depth: 0
     - name: Set up Python 3.9
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: '3.9'
     - name: Install setuptools

docs/requirements.txt

@@ -21,7 +21,7 @@ sphinxcontrib-serializinghtml
 sphinx-autodoc-typehints==1.11.1
 pandas
 einops
-transformers<4.22  # https://github.com/Project-MONAI/MONAI/issues/5157
+transformers<4.22; python_version <= '3.10'  # https://github.com/Project-MONAI/MONAI/issues/5157
 mlflow>=1.28.0
 clearml>=1.10.0rc0
 tensorboardX

docs/source/inferers.rst

@@ -49,6 +49,29 @@ Inferers
     :members:
     :special-members: __call__
 
+`DiffusionInferer`
+~~~~~~~~~~~~~~~~~~
+.. autoclass:: DiffusionInferer
+    :members:
+    :special-members: __call__
+
+`LatentDiffusionInferer`
+~~~~~~~~~~~~~~~~~~~~~~~~
+.. autoclass:: LatentDiffusionInferer
+    :members:
+    :special-members: __call__
+
+`ControlNetDiffusionInferer`
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.. autoclass:: ControlNetDiffusionInferer
+    :members:
+    :special-members: __call__
+
+`ControlNetLatentDiffusionInferer`
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.. autoclass:: ControlNetLatentDiffusionInferer
+    :members:
+    :special-members: __call__
 
 Splitters
 ---------

docs/source/losses.rst

@@ -96,6 +96,11 @@ Registration Losses
 .. autoclass:: BendingEnergyLoss
     :members:
 
+`DiffusionLoss`
+~~~~~~~~~~~~~~~
+.. autoclass:: DiffusionLoss
+    :members:
+
 `LocalNormalizedCrossCorrelationLoss`
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 .. autoclass:: LocalNormalizedCrossCorrelationLoss

docs/source/networks.rst

@@ -248,6 +248,12 @@ Blocks
 .. autoclass:: monai.apps.reconstruction.networks.blocks.varnetblock.VarNetBlock
    :members:
 
+`Attention utilities`
+~~~~~~~~~~~~~~~~~~~~~
+.. automodule:: monai.networks.blocks.attention_utils
+.. autofunction:: monai.networks.blocks.attention_utils.get_rel_pos
+.. autofunction:: monai.networks.blocks.attention_utils.add_decomposed_rel_pos
+
 N-Dim Fourier Transform
 ~~~~~~~~~~~~~~~~~~~~~~~~
 .. automodule:: monai.networks.blocks.fft_utils_t
@@ -258,6 +264,11 @@ N-Dim Fourier Transform
 .. autofunction:: monai.networks.blocks.fft_utils_t.fftshift
 .. autofunction:: monai.networks.blocks.fft_utils_t.ifftshift
 
+`SPADE`
+~~~~~~~
+.. autoclass:: monai.networks.blocks.spade_norm.SPADE
+    :members:
+
 Layers
 ------
 
@@ -408,6 +419,13 @@ Layers
 .. autoclass:: LLTM
     :members:
 
+`Vector Quantizer`
+~~~~~~~~~~~~~~~~~~
+.. autoclass:: monai.networks.layers.vector_quantizer.EMAQuantizer
+   :members:
+.. autoclass:: monai.networks.layers.vector_quantizer.VectorQuantizer
+   :members:
+
 `Utilities`
 ~~~~~~~~~~~
 .. automodule:: monai.networks.layers.convutils
@@ -575,6 +593,21 @@ Nets
 .. autoclass:: VNet
   :members:
 
+`DiffusionModelUnet`
+~~~~~~~~~~~~~~~~~~~~
+.. autoclass:: DiffusionModelUNet
+  :members:
+
+`SPADEDiffusionModelUNet`
+~~~~~~~~~~~~~~~~~~~~~~~~~
+.. autoclass:: SPADEDiffusionModelUNet
+  :members:
+
+`ControlNet`
+~~~~~~~~~~~~
+.. autoclass:: ControlNet
+  :members:
+
 `RegUNet`
 ~~~~~~~~~
 .. autoclass:: RegUNet
@@ -595,11 +628,26 @@ Nets
 .. autoclass:: AutoEncoder
   :members:
 
+`AutoEncoderKL`
+~~~~~~~~~~~~~~~
+.. autoclass:: AutoencoderKL
+  :members:
+
+`SPADEAutoencoderKL`
+~~~~~~~~~~~~~~~~~~~~
+.. autoclass:: SPADEAutoencoderKL
+  :members:
+
 `VarAutoEncoder`
 ~~~~~~~~~~~~~~~~
 .. autoclass:: VarAutoEncoder
   :members:
 
+`DecoderOnlyTransformer`
+~~~~~~~~~~~~~~~~~~~~~~~~
+.. autoclass:: DecoderOnlyTransformer
+    :members:
+
 `ViT`
 ~~~~~
 .. autoclass:: ViT
@@ -723,6 +771,39 @@ Nets
 
 .. autoclass:: voxelmorph
 
+`VQ-VAE`
+~~~~~~~~
+.. autoclass:: VQVAE
+   :members:
+
+`PatchGANDiscriminator`
+~~~~~~~~~~~~~~~~~~~~~~~
+.. autoclass:: PatchDiscriminator
+   :members:
+
+.. autoclass:: MultiScalePatchDiscriminator
+   :members:
+
+Diffusion Schedulers
+--------------------
+.. autoclass:: monai.networks.schedulers.Scheduler
+  :members:
+
+`DDPM Scheduler`
+~~~~~~~~~~~~~~~~
+.. autoclass:: monai.networks.schedulers.DDPMScheduler
+   :members:
+
+`DDIM Scheduler`
+~~~~~~~~~~~~~~~~
+.. autoclass:: monai.networks.schedulers.DDIMScheduler
+    :members:
+
+`PNDM Scheduler`
+~~~~~~~~~~~~~~~~
+.. autoclass:: monai.networks.schedulers.PNDMScheduler
+    :members:
+
 Utilities
 ---------
 .. automodule:: monai.networks.utils

docs/source/utils.rst

@@ -81,3 +81,8 @@ Component store
 ---------------
 .. autoclass:: monai.utils.component_store.ComponentStore
   :members:
+
+Ordering
+--------
+.. automodule:: monai.utils.ordering
+  :members: