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Merge remote-tracking branch 'upstream/dev' into releasing/1.1
Signed-off-by: Wenqi Li <[email protected]>
2 parents d865264 + b159ce7 commit a2ec375

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

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

‎.github/workflows/pythonapp-gpu.yml‎

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

‎.github/workflows/pythonapp-min.yml‎

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

‎.github/workflows/pythonapp.yml‎

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

‎.github/workflows/setupapp.yml‎

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

‎CITATION.cff‎

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family-names: "Xu"
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- given-names: "Ali"
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family-names: "Hatamizadeh"
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- given-names: "Andriy"
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family-names: "Myronenko"
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- given-names: "Wentao"
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family-names: "Zhu"
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- given-names: "Yun"

‎README.md‎

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

‎docs/images/exp_mgmt.png‎

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‎docs/images/hovernet_diagram.png‎

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‎docs/images/python.svg‎

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