Merge branch 'dev' into mednext

Author: Suraj Pai

.github/workflows/cron.yml

@@ -13,24 +13,24 @@ jobs:
     strategy:
       matrix:
         environment:
-          - "PT191+CUDA113"
           - "PT110+CUDA113"
-          - "PT113+CUDA113"
-          - "PTLATEST+CUDA121"
+          - "PT113+CUDA118"
+          - "PT210+CUDA121"
+          - "PTLATEST+CUDA124"
         include:
           # https://docs.nvidia.com/deeplearning/frameworks/pytorch-release-notes
           - environment: PT110+CUDA113
             pytorch: "torch==1.10.2 torchvision==0.11.3 --extra-index-url https://download.pytorch.org/whl/cu113"
             base: "nvcr.io/nvidia/pytorch:21.06-py3"  # CUDA 11.3
-          - environment: PT113+CUDA113
-            pytorch: "torch==1.13.1 torchvision==0.14.1 --extra-index-url https://download.pytorch.org/whl/cu113"
-            base: "nvcr.io/nvidia/pytorch:21.06-py3"  # CUDA 11.3
-          - environment: PT113+CUDA122
+          - environment: PT113+CUDA118
             pytorch: "torch==1.13.1 torchvision==0.14.1 --extra-index-url https://download.pytorch.org/whl/cu121"
-            base: "nvcr.io/nvidia/pytorch:23.08-py3"  # CUDA 12.2
+            base: "nvcr.io/nvidia/pytorch:22.10-py3"  # CUDA 11.8
+          - environment: PT210+CUDA121
+            pytorch: "pytorch==2.1.0 torchvision==0.16.0 --extra-index-url https://download.pytorch.org/whl/cu121"
+            base: "nvcr.io/nvidia/pytorch:23.08-py3"  # CUDA 12.1
           - environment: PTLATEST+CUDA124
             pytorch: "-U torch torchvision --extra-index-url https://download.pytorch.org/whl/cu121"
-            base: "nvcr.io/nvidia/pytorch:24.03-py3"  # CUDA 12.4
+            base: "nvcr.io/nvidia/pytorch:24.08-py3"  # CUDA 12.4
     container:
       image: ${{ matrix.base }}
       options: "--gpus all"
@@ -80,7 +80,7 @@ jobs:
     if: github.repository == 'Project-MONAI/MONAI'
     strategy:
       matrix:
-        container: ["pytorch:23.08", "pytorch:24.03"]
+        container: ["pytorch:23.08", "pytorch:24.08"]
     container:
       image: nvcr.io/nvidia/${{ matrix.container }}-py3  # testing with the latest pytorch base image
       options: "--gpus all"
@@ -129,7 +129,7 @@ jobs:
     if: github.repository == 'Project-MONAI/MONAI'
     strategy:
       matrix:
-        container: ["pytorch:24.03"]
+        container: ["pytorch:24.08"]
     container:
       image: nvcr.io/nvidia/${{ matrix.container }}-py3  # testing with the latest pytorch base image
       options: "--gpus all"
@@ -233,7 +233,7 @@ jobs:
     if: github.repository == 'Project-MONAI/MONAI'
     needs: cron-gpu  # so that monai itself is verified first
     container:
-      image: nvcr.io/nvidia/pytorch:24.03-py3  # testing with the latest pytorch base image
+      image: nvcr.io/nvidia/pytorch:24.08-py3  # testing with the latest pytorch base image
       options: "--gpus all --ipc=host"
     runs-on: [self-hosted, linux, x64, integration]
     steps:

.github/workflows/pythonapp-gpu.yml

@@ -44,9 +44,9 @@ jobs:
             pytorch: "-h"  # we explicitly set pytorch to -h to avoid pip install error
             base: "nvcr.io/nvidia/pytorch:23.08-py3"
           - environment: PT210+CUDA121DOCKER
-            # 24.03: 2.3.0a0+40ec155e58.nv24.3
+            # 24.08: 2.3.0a0+40ec155e58.nv24.3
             pytorch: "-h"  # we explicitly set pytorch to -h to avoid pip install error
-            base: "nvcr.io/nvidia/pytorch:24.03-py3"
+            base: "nvcr.io/nvidia/pytorch:24.08-py3"
     container:
       image: ${{ matrix.base }}
       options: --gpus all --env NVIDIA_DISABLE_REQUIRE=true  # workaround for unsatisfied condition: cuda>=11.6

.github/workflows/pythonapp.yml

@@ -151,7 +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)

Dockerfile

@@ -11,7 +11,7 @@
 
 # To build with a different base image
 # please run `docker build` using the `--build-arg PYTORCH_IMAGE=...` flag.
-ARG PYTORCH_IMAGE=nvcr.io/nvidia/pytorch:24.03-py3
+ARG PYTORCH_IMAGE=nvcr.io/nvidia/pytorch:24.08-py3
 FROM ${PYTORCH_IMAGE}
 
 LABEL maintainer="[email protected]"
@@ -56,4 +56,5 @@ RUN apt-get update \
   && rm -rf /var/lib/apt/lists/*
 # append /opt/tools to runtime path for NGC CLI to be accessible from all file system locations
 ENV PATH=${PATH}:/opt/tools
+ENV POLYGRAPHY_AUTOINSTALL_DEPS=1
 WORKDIR /opt/monai

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 +41,5 @@ onnxruntime; python_version <= '3.10'
 zarr
 huggingface_hub
 pyamg>=5.0.0
+packaging
+polygraphy

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/config_syntax.md

@@ -16,6 +16,7 @@ Content:
   - [`$` to evaluate as Python expressions](#to-evaluate-as-python-expressions)
   - [`%` to textually replace configuration elements](#to-textually-replace-configuration-elements)
   - [`_target_` (`_disabled_`, `_desc_`, `_requires_`, `_mode_`) to instantiate a Python object](#instantiate-a-python-object)
+  - [`+` to alter semantics of merging config keys from multiple configuration files](#multiple-config-files)
 - [The command line interface](#the-command-line-interface)
 - [Recommendations](#recommendations)
 
@@ -175,6 +176,47 @@ _Description:_ `_requires_`, `_disabled_`, `_desc_`, and `_mode_` are optional k
   - `"debug"` -- execute with debug prompt and return the return value of ``pdb.runcall(_target_, **kwargs)``,
     see also [`pdb.runcall`](https://docs.python.org/3/library/pdb.html#pdb.runcall).
 
+## Multiple config files
+
+_Description:_ Multiple config files may be specified on the command line.
+The content of those config files is being merged. When same keys are specifiled in more than one config file,
+the value associated with the key is being overridden, in the order config files are specified.
+If the desired behaviour is to merge values from both files, the key in second config file should be prefixed with `+`.
+The value types for the merged contents must match and be both of `dict` or both of `list` type.
+`dict` values will be merged via update(), `list` values - concatenated via extend().
+Here's an example. In this case, "amp" value will be overridden by extra_config.json.
+`imports` and `preprocessing#transforms` lists will be merged. An error would be thrown if the value type in `"+imports"` is not `list`:
+
+config.json:
+```json
+{
+    "amp": "$True"
+    "imports": [
+	"$import torch"
+    ],
+    "preprocessing": {
+        "_target_": "Compose",
+        "transforms": [
+	  "$@t1",
+	  "$@t2"
+        ]
+    },
+}
+```
+
+extra_config.json:
+```json
+{
+    "amp": "$False"
+    "+imports": [
+	"$from monai.networks import trt_compile"
+    ],
+    "+preprocessing#transforms": [
+        "$@t3"
+    ]
+}
+```
+
 ## The command line interface
 
 In addition to the Pythonic APIs, a few command line interfaces (CLI) are provided to interact with the bundle.