Merge remote-tracking branch 'upstream/dev' into releasing/1.1

Signed-off-by: Wenqi Li <[email protected]>

Author: wyli

.github/workflows/cron-mmar.yml renamed to .github/workflows/cron-ngc-bundle.yml

@@ -1,15 +1,15 @@
-# daily tests for clara mmar models
-name: cron-mmar
+# daily tests for ngc bundles
+name: cron-ngc-bundle
 
 on:
-  # schedule:
-  #   - cron: "0 2 * * *"  # at 02:00 UTC
+  schedule:
+    - cron: "0 2 * * *"  # at 02:00 UTC
   # Allows you to run this workflow manually from the Actions tab
   workflow_dispatch:
 
 concurrency:
   # automatically cancel the previously triggered workflows when there's a newer version
-  group: mmar-tests-${{ github.event.pull_request.number || github.ref }}
+  group: bundle-tests-${{ github.event.pull_request.number || github.ref }}
   cancel-in-progress: true
 
 jobs:
@@ -33,12 +33,12 @@ jobs:
         key: ${{ runner.os }}-pip-${{ steps.pip-cache.outputs.datew }}
     - name: Install dependencies
       run: |
-        rm -rf /github/home/.cache/torch/hub/mmars/
+        rm -rf /github/home/.cache/torch/hub/bundle/
         python -m pip install --upgrade pip wheel
         python -m pip install -r requirements-dev.txt
-    - name: Loading MMARs
+    - name: Loading Bundles
       run: |
         # clean up temporary files
         $(pwd)/runtests.sh --build --clean
         # run tests
-        python -m tests.ngc_mmar_loading
+        python -m tests.ngc_bundle_download

.github/workflows/pythonapp-gpu.yml

@@ -44,7 +44,7 @@ jobs:
             pytorch: "-h"  # we explicitly set pytorch to -h to avoid pip install error
             base: "nvcr.io/nvidia/pytorch:22.09-py3"
           - environment: PT113+CUDA116
-            pytorch: "torch==1.13.0 torchvision==0.14.0"
+            pytorch: "torch==1.13.1 torchvision==0.14.1"
             base: "nvcr.io/nvidia/cuda:11.6.1-devel-ubuntu18.04"
     container:
       image: ${{ matrix.base }}

.github/workflows/pythonapp-min.yml

@@ -52,11 +52,11 @@ jobs:
     - if: runner.os == 'windows'
       name: Install torch cpu from pytorch.org (Windows only)
       run: |
-        python -m pip install torch==1.13+cpu -f https://download.pytorch.org/whl/torch_stable.html
+        python -m pip install torch==1.13.1+cpu -f https://download.pytorch.org/whl/torch_stable.html
     - name: Install the dependencies
       run: |
         # min. requirements
-        python -m pip install torch==1.13
+        python -m pip install torch==1.13.1
         python -m pip install -r requirements-min.txt
         python -m pip list
         BUILD_MONAI=0 python setup.py develop  # no compile of extensions

.github/workflows/pythonapp.yml

@@ -88,14 +88,14 @@ jobs:
     - if: runner.os == 'windows'
       name: Install torch cpu from pytorch.org (Windows only)
       run: |
-        python -m pip install torch==1.13.0+cpu torchvision==0.14.0+cpu -f https://download.pytorch.org/whl/torch_stable.html
+        python -m pip install torch==1.13.1+cpu torchvision==0.14.1+cpu -f https://download.pytorch.org/whl/torch_stable.html
     - if: runner.os == 'Linux'
       name: Install itk pre-release (Linux only)
       run: |
         python -m pip install --pre -U itk
     - name: Install the dependencies
       run: |
-        python -m pip install torch==1.13.0 torchvision==0.14.0
+        python -m pip install torch==1.13.1 torchvision==0.14.1
         cat "requirements-dev.txt"
         python -m pip install -r requirements-dev.txt
         python -m pip list

.github/workflows/setupapp.yml

@@ -100,7 +100,7 @@ jobs:
     - name: Install the dependencies
       run: |
         python -m pip install --upgrade pip wheel
-        python -m pip install torch==1.13.0 torchvision==0.14.0
+        python -m pip install torch==1.13.1 torchvision==0.14.1
         python -m pip install -r requirements-dev.txt
     - name: Run quick tests CPU ubuntu
       run: |

CITATION.cff

@@ -48,8 +48,6 @@ preferred-citation:
     family-names: "Xu"
   - given-names: "Ali"
     family-names: "Hatamizadeh"
-  - given-names: "Andriy"
-    family-names: "Myronenko"
   - given-names: "Wentao"
     family-names: "Zhu"
   - given-names: "Yun"

README.md

@@ -4,12 +4,17 @@
 
 **M**edical **O**pen **N**etwork for **AI**
 
+![Supported Python versions](https://raw.githubusercontent.com/Project-MONAI/MONAI/dev/docs/images/python.svg)
 [![License](https://img.shields.io/badge/license-Apache%202.0-green.svg)](https://opensource.org/licenses/Apache-2.0)
-[![CI Build](https://github.com/Project-MONAI/MONAI/workflows/build/badge.svg?branch=dev)](https://github.com/Project-MONAI/MONAI/commits/dev)
-[![Documentation Status](https://readthedocs.org/projects/monai/badge/?version=latest)](https://docs.monai.io/en/latest/?badge=latest)
-[![codecov](https://codecov.io/gh/Project-MONAI/MONAI/branch/dev/graph/badge.svg?token=6FTC7U1JJ4)](https://codecov.io/gh/Project-MONAI/MONAI)
 [![PyPI version](https://badge.fury.io/py/monai.svg)](https://badge.fury.io/py/monai)
-[![conda](https://img.shields.io/conda/vn/conda-forge/monai)](https://anaconda.org/conda-forge/monai)
+[![docker](https://img.shields.io/badge/docker-pull-green.svg?logo=docker&logoColor=white)](https://hub.docker.com/r/projectmonai/monai)
+[![conda](https://img.shields.io/conda/vn/conda-forge/monai?color=green)](https://anaconda.org/conda-forge/monai)
+
+[![premerge](https://github.com/Project-MONAI/MONAI/actions/workflows/pythonapp.yml/badge.svg?branch=dev)](https://github.com/Project-MONAI/MONAI/actions/workflows/pythonapp.yml)
+[![postmerge](https://img.shields.io/github/checks-status/project-monai/monai/dev?label=postmerge)](https://github.com/Project-MONAI/MONAI/actions?query=branch%3Adev)
+[![docker](https://github.com/Project-MONAI/MONAI/actions/workflows/docker.yml/badge.svg?branch=dev)](https://github.com/Project-MONAI/MONAI/actions/workflows/docker.yml)
+[![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 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: