Merge pull request #460 from Project-MONAI/dev

merge master

.github/dependabot.yml

@@ -0,0 +1,10 @@
+# Set update schedule for GitHub Actions
+
+version: 2
+updates:
+
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      # Check for updates to GitHub Actions every week
+      interval: "monthly"

.github/workflows/blossom-ci.yml

@@ -49,7 +49,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout code
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
           repository: ${{ fromJson(needs.Authorization.outputs.args).repo }}
           ref: ${{ fromJson(needs.Authorization.outputs.args).ref }}

.github/workflows/chatops.yml

@@ -10,7 +10,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: dispatch
-        uses: peter-evans/slash-command-dispatch@v1.2.0
+        uses: peter-evans/slash-command-dispatch@v3.0.1
         with:
           token: ${{ secrets.PR_MAINTAIN }}
           reaction-token: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/codeql-analysis.yml

@@ -64,6 +64,7 @@ jobs:
 
     - name: Build
       run: |
+        python -m pip install -U pip wheel
         python -m pip install -r requirements-dev.txt
         BUILD_MONAI=1 ./runtests.sh --build
 

.github/workflows/conda.yml

@@ -18,15 +18,15 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [windows-latest, ubuntu-latest]
+        os: [ubuntu-latest]
         python-version: ["3.9"]
     runs-on: ${{ matrix.os }}
     env:
       QUICKTEST: True
     steps:
     - if: runner.os == 'windows'
       name: Config pagefile (Windows only)
-      uses: al-cheb/configure-pagefile-action@v1.2
+      uses: al-cheb/configure-pagefile-action@v1.3
       with:
         minimum-size: 8
         maximum-size: 16

.github/workflows/cron.yml

@@ -17,7 +17,7 @@ jobs:
           - "PT191+CUDA113"
           - "PT110+CUDA113"
           - "PT112+CUDA113"
-          - "PTLATEST+CUDA117"
+          - "PTLATEST+CUDA118"
         include:
           # https://docs.nvidia.com/deeplearning/frameworks/pytorch-release-notes
           - environment: PT182+CUDA102
@@ -32,9 +32,9 @@ jobs:
           - environment: PT112+CUDA113
             pytorch: "torch==1.12.1 torchvision==0.13.1 --extra-index-url https://download.pytorch.org/whl/cu113"
             base: "nvcr.io/nvidia/pytorch:21.06-py3"  # CUDA 11.3
-          - environment: PTLATEST+CUDA117
-            pytorch: "-U torch torchvision --extra-index-url https://download.pytorch.org/whl/cu117"
-            base: "nvcr.io/nvidia/pytorch:22.08-py3"  # CUDA 11.7
+          - environment: PTLATEST+CUDA118
+            pytorch: "-U torch torchvision --extra-index-url https://download.pytorch.org/whl/cu118"
+            base: "nvcr.io/nvidia/pytorch:22.12-py3"  # CUDA 11.8
     container:
       image: ${{ matrix.base }}
       options: "--gpus all"
@@ -119,7 +119,7 @@ jobs:
     if: github.repository == 'Project-MONAI/MONAI'
     strategy:
       matrix:
-        container: ["pytorch:21.02", "pytorch:21.10", "pytorch:22.10"]  # 21.02, 21.10 for backward comp.
+        container: ["pytorch:22.09", "pytorch:22.11", "pytorch:22.12"]
     container:
       image: nvcr.io/nvidia/${{ matrix.container }}-py3  # testing with the latest pytorch base image
       options: "--gpus all"
@@ -164,7 +164,7 @@ jobs:
     if: github.repository == 'Project-MONAI/MONAI'
     strategy:
       matrix:
-        container: ["pytorch:21.02", "pytorch:21.10", "pytorch:22.10"]  # 21.02, 21.10 for backward comp.
+        container: ["pytorch:21.02", "pytorch:21.10", "pytorch:22.12"]  # 21.02, 21.10 for backward comp.
     container:
       image: nvcr.io/nvidia/${{ matrix.container }}-py3  # testing with the latest pytorch base image
       options: "--gpus all"
@@ -264,7 +264,7 @@ jobs:
     if: github.repository == 'Project-MONAI/MONAI'
     needs: cron-gpu  # so that monai itself is verified first
     container:
-      image: nvcr.io/nvidia/pytorch:22.10-py3  # testing with the latest pytorch base image
+      image: nvcr.io/nvidia/pytorch:22.12-py3  # testing with the latest pytorch base image
       options: "--gpus all --ipc=host"
     runs-on: [self-hosted, linux, x64, integration]
     steps:

.github/workflows/docker.yml

@@ -25,17 +25,18 @@ jobs:
         with:
           ref: dev
           fetch-depth: 0
-      - name: Set up Python 3.8
+      - name: Set up Python 3.9
         uses: actions/setup-python@v4
         with:
-          python-version: '3.8'
+          python-version: '3.9'
       - shell: bash
         run: |
           git describe
+          python -m pip install -U pip wheel setuptools
           python setup.py build
           cat build/lib/monai/_version.py
       - name: Upload version
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v3
         with:
           name: _version.py
           path: build/lib/monai/_version.py
@@ -55,18 +56,13 @@ jobs:
       with:
         ref: dev
     - name: Download version
-      uses: actions/download-artifact@v2
+      uses: actions/download-artifact@v3
       with:
         name: _version.py
-    - name: Install Latest Docker
-      run: |
-        curl -fsSL https://download.docker.com/linux/ubuntu/gpg | sudo apt-key add -
-        sudo add-apt-repository "deb [arch=amd64] https://download.docker.com/linux/ubuntu  $(lsb_release -cs)  stable"
-        sudo apt-get update
-        sudo apt-get install docker-ce
     - name: docker_build
       shell: bash
       run: |
+        docker --version
         # get tag info for versioning
         cat _version.py
         mv _version.py monai/

.github/workflows/integration.yml

@@ -34,13 +34,14 @@ jobs:
       run: |
         which python
         python -m pip install --upgrade pip wheel
-        python -m pip uninstall -y torch torchvision
-        python -m pip install torch torchvision --extra-index-url https://download.pytorch.org/whl/cu116
+        python -m pip install --upgrade torch torchvision
         python -m pip install -r requirements-dev.txt
         rm -rf /github/home/.cache/torch/hub/mmars/
     - name: Run integration tests
       run: |
         python -m pip list
+        git config --global --add safe.directory /__w/MONAI/MONAI
+        git clean -ffdx
         nvidia-smi
         export CUDA_VISIBLE_DEVICES=$(python -m tests.utils | tail -n 1)
         echo $CUDA_VISIBLE_DEVICES
@@ -53,7 +54,7 @@ jobs:
         if pgrep python; then pkill python; fi
       shell: bash
     - name: Add reaction
-      uses: peter-evans/create-or-update-comment@v1
+      uses: peter-evans/create-or-update-comment@v2
       if: github.event.pull_request.number != ''
       with:
         token: ${{ secrets.PR_MAINTAIN }}

.github/workflows/pythonapp.yml

@@ -22,6 +22,9 @@ jobs:
   #   - os-latest-pip- (shared)
   flake8-py3:
     runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        opt: ["codeformat", "pytype", "mypy"]
     steps:
     - uses: actions/checkout@v3
     - name: Set up Python 3.8
@@ -46,8 +49,8 @@ jobs:
       run: |
         # clean up temporary files
         $(pwd)/runtests.sh --build --clean
-        # Git hub actions have 2 cores, so parallize pytype
-        $(pwd)/runtests.sh --build --codeformat -j 2
+        # Github actions have 2 cores, so parallelize pytype
+        $(pwd)/runtests.sh --build --${{ matrix.opt }} -j 2
 
   quick-py3:  # full dependencies installed tests for different OS
     runs-on: ${{ matrix.os }}
@@ -59,7 +62,7 @@ jobs:
     steps:
     - if: runner.os == 'windows'
       name: Config pagefile (Windows only)
-      uses: al-cheb/configure-pagefile-action@v1.2
+      uses: al-cheb/configure-pagefile-action@v1.3
       with:
         minimum-size: 8
         maximum-size: 16
@@ -101,8 +104,7 @@ jobs:
         python -m pip list
         python setup.py develop  # test no compile installation
       shell: bash
-    - if: runner.os != 'windows'
-      name: Run compiled (${{ runner.os }})
+    - name: Run compiled (${{ runner.os }})
       run: |
         python setup.py develop --uninstall
         BUILD_MONAI=1 python setup.py develop  # compile the cpp extensions

.github/workflows/release.yml

@@ -65,7 +65,7 @@ jobs:
 
     - if: matrix.python-version == '3.8' && startsWith(github.ref, 'refs/tags/')
       name: Upload artifacts
-      uses: actions/upload-artifact@v1
+      uses: actions/upload-artifact@v3
       with:
         name: dist
         path: dist/
@@ -105,7 +105,7 @@ jobs:
           python setup.py build
           cat build/lib/monai/_version.py
       - name: Upload version
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v3
         with:
           name: _version.py
           path: build/lib/monai/_version.py
@@ -122,7 +122,7 @@ jobs:
     steps:
       - uses: actions/checkout@v3
       - name: Download version
-        uses: actions/download-artifact@v2
+        uses: actions/download-artifact@v3
         with:
           name: _version.py
       - name: Set tag

.github/workflows/weekly-preview.yml

@@ -33,13 +33,13 @@ 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 "1.1.dev${YEAR_WEEK}"
+        git tag "1.2.dev${YEAR_WEEK}"
         git log -1
         git tag --list
         python setup.py sdist bdist_wheel
 
     - name: Publish to PyPI
-      uses: pypa/gh-action-pypi-publish@master
+      uses: pypa/gh-action-pypi-publish@release/v1
       with:
         user: __token__
         password: ${{ secrets.PYPI_TOKEN }}

.gitignore

@@ -135,6 +135,8 @@ tests/testing_data/endo.mp4
 tests/testing_data/ultrasound.avi
 tests/testing_data/train_data_stats.yaml
 tests/testing_data/eval_data_stats.yaml
+tests/testing_data/CT_2D_head_fixed.mha
+tests/testing_data/CT_2D_head_moving.mha
 
 # clang format tool
 .clang-format-bin/

.pre-commit-config.yaml

@@ -9,7 +9,7 @@ ci:
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.3.0
+    rev: v4.4.0
     hooks:
       - id: end-of-file-fixer
       - id: trailing-whitespace
@@ -28,7 +28,7 @@ repos:
       - id: mixed-line-ending
 
   - repo: https://github.com/asottile/pyupgrade
-    rev: v2.38.2
+    rev: v3.3.1
     hooks:
       - id: pyupgrade
         args: [--py37-plus]
@@ -54,11 +54,12 @@ repos:
         exclude: |
           (?x)^(
               monai/__init__.py|
-              docs/source/conf.py
+              docs/source/conf.py|
+              tests/utils.py
           )$
 
   - repo: https://github.com/hadialqattan/pycln
-    rev: v2.1.1
+    rev: v2.1.2
     hooks:
       - id: pycln
         args: [--config=pyproject.toml]

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: 2022-09-16
-version: "1.0.0"
+date-released: 2022-12-19
+version: "1.1.0"
 identifiers:
   - description: "This DOI represents all versions of MONAI, and will always resolve to the latest one."
     type: doi

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:22.10-py3
+ARG PYTORCH_IMAGE=nvcr.io/nvidia/pytorch:22.12-py3
 FROM ${PYTORCH_IMAGE}
 
 LABEL maintainer="monai.contact@gmail.com"

README.md

@@ -51,6 +51,10 @@ Examples and notebook tutorials are located at [Project-MONAI/tutorials](https:/
 
 Technical documentation is available at [docs.monai.io](https://docs.monai.io).
 
+## Citation
+
+If you have used MONAI in your research, please cite us! The citation can be exported from: https://arxiv.org/abs/2211.02701.
+
 ## Model Zoo
 [The MONAI Model Zoo](https://github.com/Project-MONAI/model-zoo) is a place for researchers and data scientists to share the latest and great models from the community.
 Utilizing [the MONAI Bundle format](https://docs.monai.io/en/latest/bundle_intro.html) makes it easy to [get started](https://github.com/Project-MONAI/tutorials/tree/main/model_zoo) building workflows with MONAI.

docs/requirements.txt

@@ -1,11 +1,11 @@
 -f https://download.pytorch.org/whl/cpu/torch-1.12.1%2Bcpu-cp37-cp37m-linux_x86_64.whl
 torch>=1.8
-pytorch-ignite==0.4.10
-numpy>=1.17
+pytorch-ignite==0.4.11
+numpy>=1.20
 itk>=5.2
 nibabel
 parameterized
-scikit-image>=0.14.2
+scikit-image>=0.19.0
 tensorboard
 commonmark==0.9.1
 recommonmark==0.6.0
@@ -21,10 +21,11 @@ sphinx-autodoc-typehints==1.11.1
 pandas
 einops
 transformers<4.22  # https://github.com/Project-MONAI/MONAI/issues/5157
-mlflow
+mlflow>=1.28.0
+clearml >=1.10.0rc0
 tensorboardX
-imagecodecs; platform_system == "Linux"
-tifffile; platform_system == "Linux"
+imagecodecs; platform_system == "Linux" or platform_system == "Darwin"
+tifffile; platform_system == "Linux" or platform_system == "Darwin"
 pyyaml
 fire
 jsonschema

docs/source/applications.md

@@ -76,4 +76,4 @@ The following figure shows the detection training and inference workflows:
 ![detection workflow](../images/detection.png)
 
 ### Reproducing the state-of-the-art Kaggle competition solutions
-[A reimplementation](https://github.com/Project-MONAI/tutorials/tree/master/kaggle/RANZCR/4th_place_solution) of the 4th place solution of RANZCR CLiP - Catheter and Line Position Challenge in Kaggle: https://www.kaggle.com/c/ranzcr-clip-catheter-line-classification
+[A reimplementation](https://github.com/Project-MONAI/tutorials/tree/main/competitions/kaggle/RANZCR/4th_place_solution) of the 4th place solution of RANZCR CLiP - Catheter and Line Position Challenge in Kaggle: https://www.kaggle.com/c/ranzcr-clip-catheter-line-classification

docs/source/bundle.rst

@@ -32,6 +32,7 @@ Model Bundle
 ---------------
 .. autoclass:: ConfigParser
     :members:
+    :special-members:
 
 `Scripts`
 ---------

docs/source/conf.py

@@ -116,8 +116,9 @@ def generate_apidocs(*args):
     "collapse_navigation": True,
     "navigation_depth": 3,
     "show_toc_level": 1,
-    "footer_items": ["copyright"],
+    "footer_start": ["copyright"],
     "navbar_align": "content",
+    "logo": {"image_light": "MONAI-logo-color.png", "image_dark": "MONAI-logo-color.png"},
 }
 html_context = {
     "github_user": "Project-MONAI",