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Merge pull request #429 from Project-MONAI/dev
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‎.github/workflows/codeql-analysis.yml

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@@ -38,11 +38,11 @@ jobs:
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steps:
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- name: Checkout repository
41-
uses: actions/checkout@v2
41+
uses: actions/checkout@v3
4242

4343
# Initializes the CodeQL tools for scanning.
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- name: Initialize CodeQL
45-
uses: github/codeql-action/init@v1
45+
uses: github/codeql-action/init@v2
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with:
4747
languages: ${{ matrix.language }}
4848
# If you wish to specify custom queries, you can do so here or in a config file.
@@ -53,7 +53,7 @@ jobs:
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# Autobuild attempts to build any compiled languages (C/C++, C#, or Java).
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# If this step fails, then you should remove it and run the build manually (see below)
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# - name: Autobuild
56-
# uses: github/codeql-action/autobuild@v1
56+
# uses: github/codeql-action/autobuild@v2
5757

5858
# ℹ️ Command-line programs to run using the OS shell.
5959
# 📚 https://git.io/JvXDl
@@ -68,4 +68,4 @@ jobs:
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BUILD_MONAI=1 ./runtests.sh --build
6969
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- name: Perform CodeQL Analysis
71-
uses: github/codeql-action/analyze@v1
71+
uses: github/codeql-action/analyze@v2

‎.github/workflows/conda.yml

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@@ -30,7 +30,7 @@ jobs:
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minimum-size: 8
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maximum-size: 16
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disk-root: "D:"
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- uses: actions/checkout@v2
33+
- uses: actions/checkout@v3
3434
- uses: conda-incubator/setup-miniconda@v2
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with:
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auto-update-conda: true

‎.github/workflows/cron-mmar.yml

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Original file line numberDiff line numberDiff line change
@@ -16,16 +16,16 @@ jobs:
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if: github.repository == 'Project-MONAI/MONAI'
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runs-on: ubuntu-latest
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steps:
19-
- uses: actions/checkout@v2
19+
- uses: actions/checkout@v3
2020
- name: Set up Python 3.8
21-
uses: actions/setup-python@v2
21+
uses: actions/setup-python@v3
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with:
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python-version: 3.8
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- name: cache weekly timestamp
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id: pip-cache
2626
run: echo "::set-output name=datew::$(date '+%Y-%V')"
2727
- name: cache for pip
28-
uses: actions/cache@v2
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uses: actions/cache@v3
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id: cache
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with:
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path: ~/.cache/pip

‎.github/workflows/cron.yml

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Original file line numberDiff line numberDiff line change
@@ -15,24 +15,24 @@ jobs:
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runs-on: [self-hosted, linux, x64, common]
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strategy:
1717
matrix:
18-
pytorch-version: [1.6.0, 1.7.1, 1.8.1, 1.9.1, latest]
18+
pytorch-version: [1.7.1, 1.8.1, 1.9.1, 1.10.2, latest]
1919
steps:
20-
- uses: actions/checkout@v2
20+
- uses: actions/checkout@v3
2121
- name: Install the dependencies
2222
run: |
2323
which python
2424
python -m pip install --upgrade pip wheel
2525
python -m pip uninstall -y torch torchvision
2626
if [ ${{ matrix.pytorch-version }} == "latest" ]; then
27-
python -m pip install torch torchvision
28-
elif [ ${{ matrix.pytorch-version }} == "1.6.0" ]; then
29-
python -m pip install torch==1.6.0 torchvision==0.7.0
27+
python -m pip install torch torchvision --extra-index-url https://download.pytorch.org/whl/cu113
3028
elif [ ${{ matrix.pytorch-version }} == "1.7.1" ]; then
31-
python -m pip install torch==1.7.1 torchvision==0.8.2
29+
python -m pip install torch==1.7.1 torchvision==0.8.2 --extra-index-url https://download.pytorch.org/whl/cu113
3230
elif [ ${{ matrix.pytorch-version }} == "1.8.1" ]; then
33-
python -m pip install torch==1.8.1 torchvision==0.9.1
31+
python -m pip install torch==1.8.1 torchvision==0.9.1 --extra-index-url https://download.pytorch.org/whl/cu113
3432
elif [ ${{ matrix.pytorch-version }} == "1.9.1" ]; then
35-
python -m pip install torch==1.9.1 torchvision==0.10.1
33+
python -m pip install torch==1.9.1 torchvision==0.10.1 --extra-index-url https://download.pytorch.org/whl/cu113
34+
elif [ ${{ matrix.pytorch-version }} == "1.10.2" ]; then
35+
python -m pip install torch==1.10.2 torchvision==0.11.3 --extra-index-url https://download.pytorch.org/whl/cu113
3636
fi
3737
python -m pip install -r requirements-dev.txt
3838
python -m pip list
@@ -62,13 +62,13 @@ jobs:
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if: github.repository == 'Project-MONAI/MONAI'
6363
strategy:
6464
matrix:
65-
container: ["pytorch:21.02", "pytorch:21.10", "pytorch:22.03"] # 21.02, 21.10 for backward comp.
65+
container: ["pytorch:21.02", "pytorch:21.10", "pytorch:22.06"] # 21.02, 21.10 for backward comp.
6666
container:
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image: nvcr.io/nvidia/${{ matrix.container }}-py3 # testing with the latest pytorch base image
6868
options: "--gpus all"
6969
runs-on: [self-hosted, linux, x64, common]
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steps:
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- uses: actions/checkout@v2
71+
- uses: actions/checkout@v3
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- name: Install APT dependencies
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run: |
7474
apt-get update
@@ -106,13 +106,13 @@ jobs:
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if: github.repository == 'Project-MONAI/MONAI'
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strategy:
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matrix:
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container: ["pytorch:21.02", "pytorch:21.10", "pytorch:22.03"] # 21.02, 21.10 for backward comp.
109+
container: ["pytorch:21.02", "pytorch:21.10", "pytorch:22.06"] # 21.02, 21.10 for backward comp.
110110
container:
111111
image: nvcr.io/nvidia/${{ matrix.container }}-py3 # testing with the latest pytorch base image
112112
options: "--gpus all"
113113
runs-on: [self-hosted, linux, x64, common]
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steps:
115-
- uses: actions/checkout@v2
115+
- uses: actions/checkout@v3
116116
with:
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fetch-depth: 0
118118
- name: Install the dependencies
@@ -204,11 +204,11 @@ jobs:
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if: github.repository == 'Project-MONAI/MONAI'
205205
needs: cron-gpu # so that monai itself is verified first
206206
container:
207-
image: nvcr.io/nvidia/pytorch:22.03-py3 # testing with the latest pytorch base image
207+
image: nvcr.io/nvidia/pytorch:22.06-py3 # testing with the latest pytorch base image
208208
options: "--gpus all --ipc=host"
209209
runs-on: [self-hosted, linux, x64, common]
210210
steps:
211-
- uses: actions/checkout@v2
211+
- uses: actions/checkout@v3
212212
- name: Install MONAI
213213
id: monai-install
214214
run: |
@@ -223,7 +223,7 @@ jobs:
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- name: Checkout tutorials and install their requirements
224224
run: |
225225
cd /opt
226-
git clone --depth 1 --branch master --single-branch https://github.com/Project-MONAI/tutorials.git # latest commit of master branch
226+
git clone --depth 1 --branch main --single-branch https://github.com/Project-MONAI/tutorials.git # latest commit of main branch
227227
cd tutorials
228228
python -m pip install -r requirements.txt
229229
- name: Run tutorial notebooks

‎.github/workflows/docker.yml

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@@ -19,13 +19,13 @@ jobs:
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if: github.repository == 'Project-MONAI/MONAI'
2020
runs-on: ubuntu-latest
2121
steps:
22-
- uses: actions/checkout@v2
22+
- uses: actions/checkout@v3
2323
# full history so that we can git describe
2424
with:
2525
ref: dev
2626
fetch-depth: 0
2727
- name: Set up Python 3.8
28-
uses: actions/setup-python@v2
28+
uses: actions/setup-python@v3
2929
with:
3030
python-version: 3.8
3131
- shell: bash
@@ -50,7 +50,7 @@ jobs:
5050
needs: versioning_dev
5151
runs-on: ubuntu-latest
5252
steps:
53-
- uses: actions/checkout@v2
53+
- uses: actions/checkout@v3
5454
with:
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ref: dev
5656
- name: Download version

‎.github/workflows/integration.yml

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@@ -7,12 +7,12 @@ on:
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jobs:
88
integration-py3:
99
container:
10-
image: nvcr.io/nvidia/pytorch:21.12-py3 # CUDA 11.5
11-
options: --gpus all
10+
image: nvcr.io/nvidia/pytorch:22.04-py3 # CUDA 11.6
11+
options: --gpus all # shm-size 4g works fine
1212
runs-on: [self-hosted, linux, x64, common]
1313
steps:
1414
# checkout the pull request branch
15-
- uses: actions/checkout@v2
15+
- uses: actions/checkout@v3
1616
with:
1717
token: ${{ secrets.PR_MAINTAIN }}
1818
repository: ${{ github.event.client_payload.pull_request.head.repo.full_name }}
@@ -22,7 +22,7 @@ jobs:
2222
run: |
2323
echo "::set-output name=datew::$(date '+%Y-%V')"
2424
- name: cache for pip
25-
uses: actions/cache@v2
25+
uses: actions/cache@v3
2626
id: cache
2727
with:
2828
path: |
@@ -34,7 +34,7 @@ jobs:
3434
which python
3535
python -m pip install --upgrade pip wheel
3636
python -m pip uninstall -y torch torchvision
37-
python -m pip install torch==1.11.0+cu115 torchvision==0.12.0+cu115 -f https://download.pytorch.org/whl/torch_stable.html
37+
python -m pip install torch==1.12.0+cu116 torchvision==0.13.0+cu116 -f https://download.pytorch.org/whl/torch_stable.html
3838
python -m pip install -r requirements-dev.txt
3939
rm -rf /github/home/.cache/torch/hub/mmars/
4040
- name: Run integration tests

‎.github/workflows/pythonapp-gpu.yml

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Original file line numberDiff line numberDiff line change
@@ -23,16 +23,17 @@ jobs:
2323
- "PT17+CUDA102"
2424
- "PT18+CUDA102"
2525
- "PT18+CUDA112"
26-
- "PT111+CUDA116"
26+
- "PT112+CUDA116"
2727
- "PT110+CUDA102"
28-
- "PT111+CUDA102"
28+
- "PT112+CUDA102"
2929
include:
3030
# https://docs.nvidia.com/deeplearning/frameworks/pytorch-release-notes
3131
- environment: PT17+CUDA102
3232
pytorch: "torch==1.7.1 torchvision==0.8.2"
3333
base: "nvcr.io/nvidia/cuda:10.2-devel-ubuntu18.04"
3434
- environment: PT18+CUDA102
35-
pytorch: "torch==1.8.1 torchvision==0.9.1"
35+
# pytorch 1.8.2 LTS
36+
pytorch: "torch==1.8.2 torchvision==0.9.2 --extra-index-url https://download.pytorch.org/whl/lts/1.8/cu102"
3637
base: "nvcr.io/nvidia/cuda:10.2-devel-ubuntu18.04"
3738
- environment: PT18+CUDA112
3839
# we explicitly set pytorch to -h to avoid pip install error
@@ -44,29 +45,36 @@ jobs:
4445
# 21.10: 1.10.0a0+0aef44c
4546
pytorch: "-h"
4647
base: "nvcr.io/nvidia/pytorch:21.10-py3"
47-
- environment: PT111+CUDA116
48+
- environment: PT112+CUDA116
4849
# we explicitly set pytorch to -h to avoid pip install error
49-
# 22.03: 1.12.0a0+2c916ef
50+
# 22.06: 1.13.0a0+340c412
5051
pytorch: "-h"
51-
base: "nvcr.io/nvidia/pytorch:22.03-py3"
52+
base: "nvcr.io/nvidia/pytorch:22.06-py3"
5253
- environment: PT110+CUDA102
53-
pytorch: "torch==1.10.1 torchvision==0.11.2"
54+
pytorch: "torch==1.10.2 torchvision==0.11.3"
5455
base: "nvcr.io/nvidia/cuda:10.2-devel-ubuntu18.04"
55-
- environment: PT111+CUDA102
56-
pytorch: "torch==1.11.0 torchvision==0.12.0"
56+
- environment: PT112+CUDA102
57+
pytorch: "torch==1.12.0 torchvision==0.13.0"
5758
base: "nvcr.io/nvidia/cuda:10.2-devel-ubuntu18.04"
5859
container:
5960
image: ${{ matrix.base }}
6061
options: --gpus all
6162
runs-on: [self-hosted, linux, x64, common]
6263
steps:
63-
- uses: actions/checkout@v2
64+
- uses: actions/checkout@v3
6465
- name: apt install
6566
run: |
67+
# workaround for https://github.com/Project-MONAI/MONAI/issues/4200
68+
apt-key del 7fa2af80 && rm -rf /etc/apt/sources.list.d/nvidia-ml.list /etc/apt/sources.list.d/cuda.list
69+
apt-get update
70+
apt-get install -y wget
71+
wget https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/cuda-keyring_1.0-1_all.deb
72+
dpkg -i cuda-keyring_1.0-1_all.deb
73+
6674
if [ ${{ matrix.environment }} = "PT17+CUDA102" ] || \
6775
[ ${{ matrix.environment }} = "PT18+CUDA102" ] || \
6876
[ ${{ matrix.environment }} = "PT110+CUDA102" ] || \
69-
[ ${{ matrix.environment }} = "PT111+CUDA102" ]
77+
[ ${{ matrix.environment }} = "PT112+CUDA102" ]
7078
then
7179
PYVER=3.7 PYSFX=3 DISTUTILS=python3-distutils && \
7280
apt-get update && apt-get install -y --no-install-recommends \

‎.github/workflows/pythonapp-min.yml

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Original file line numberDiff line numberDiff line change
@@ -27,9 +27,9 @@ jobs:
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os: [windows-latest, macOS-latest, ubuntu-latest]
2828
timeout-minutes: 40
2929
steps:
30-
- uses: actions/checkout@v2
30+
- uses: actions/checkout@v3
3131
- name: Set up Python 3.8
32-
uses: actions/setup-python@v2
32+
uses: actions/setup-python@v3
3333
with:
3434
python-version: 3.8
3535
- name: Prepare pip wheel
@@ -43,19 +43,19 @@ jobs:
4343
echo "::set-output name=dir::$(pip cache dir)"
4444
shell: bash
4545
- name: cache for pip
46-
uses: actions/cache@v2
46+
uses: actions/cache@v3
4747
id: cache
4848
with:
4949
path: ${{ steps.pip-cache.outputs.dir }}
5050
key: ${{ matrix.os }}-latest-pip-${{ steps.pip-cache.outputs.datew }}
5151
- if: runner.os == 'windows'
5252
name: Install torch cpu from pytorch.org (Windows only)
5353
run: |
54-
python -m pip install torch==1.11.0+cpu -f https://download.pytorch.org/whl/torch_stable.html
54+
python -m pip install torch==1.12.0+cpu -f https://download.pytorch.org/whl/torch_stable.html
5555
- name: Install the dependencies
5656
run: |
5757
# min. requirements
58-
python -m pip install torch==1.11.0
58+
python -m pip install torch==1.12.0
5959
python -m pip install -r requirements-min.txt
6060
python -m pip list
6161
BUILD_MONAI=0 python setup.py develop # no compile of extensions
@@ -77,9 +77,9 @@ jobs:
7777
python-version: [3.7, 3.8, 3.9]
7878
timeout-minutes: 40
7979
steps:
80-
- uses: actions/checkout@v2
80+
- uses: actions/checkout@v3
8181
- name: Set up Python ${{ matrix.python-version }}
82-
uses: actions/setup-python@v2
82+
uses: actions/setup-python@v3
8383
with:
8484
python-version: ${{ matrix.python-version }}
8585
- name: Prepare pip wheel
@@ -93,15 +93,15 @@ jobs:
9393
echo "::set-output name=dir::$(pip cache dir)"
9494
shell: bash
9595
- name: cache for pip
96-
uses: actions/cache@v2
96+
uses: actions/cache@v3
9797
id: cache
9898
with:
9999
path: ${{ steps.pip-cache.outputs.dir }}
100100
key: ubuntu-latest-latest-pip-${{ steps.pip-cache.outputs.datew }}
101101
- name: Install the dependencies
102102
run: |
103103
# min. requirements
104-
python -m pip install torch==1.11.0
104+
python -m pip install torch==1.12.0
105105
python -m pip install -r requirements-min.txt
106106
python -m pip list
107107
BUILD_MONAI=0 python setup.py develop # no compile of extensions
@@ -119,12 +119,12 @@ jobs:
119119
strategy:
120120
fail-fast: false
121121
matrix:
122-
pytorch-version: [1.6.0, 1.7.1, 1.8.1, 1.9.1, 1.10.1, latest]
122+
pytorch-version: [1.7.1, 1.8.2, 1.9.1, 1.10.2, 1.11.0, latest]
123123
timeout-minutes: 40
124124
steps:
125-
- uses: actions/checkout@v2
125+
- uses: actions/checkout@v3
126126
- name: Set up Python 3.8
127-
uses: actions/setup-python@v2
127+
uses: actions/setup-python@v3
128128
with:
129129
python-version: 3.8
130130
- name: Prepare pip wheel
@@ -138,7 +138,7 @@ jobs:
138138
echo "::set-output name=dir::$(pip cache dir)"
139139
shell: bash
140140
- name: cache for pip
141-
uses: actions/cache@v2
141+
uses: actions/cache@v3
142142
id: cache
143143
with:
144144
path: ${{ steps.pip-cache.outputs.dir }}
@@ -148,16 +148,16 @@ jobs:
148148
# min. requirements
149149
if [ ${{ matrix.pytorch-version }} == "latest" ]; then
150150
python -m pip install torch
151-
elif [ ${{ matrix.pytorch-version }} == "1.6.0" ]; then
152-
python -m pip install torch==1.6.0
153151
elif [ ${{ matrix.pytorch-version }} == "1.7.1" ]; then
154152
python -m pip install torch==1.7.1
155-
elif [ ${{ matrix.pytorch-version }} == "1.8.1" ]; then
156-
python -m pip install torch==1.8.1
153+
elif [ ${{ matrix.pytorch-version }} == "1.8.2" ]; then
154+
python -m pip install torch==1.8.2 --extra-index-url https://download.pytorch.org/whl/lts/1.8/cpu
157155
elif [ ${{ matrix.pytorch-version }} == "1.9.1" ]; then
158156
python -m pip install torch==1.9.1
159-
elif [ ${{ matrix.pytorch-version }} == "1.10.1" ]; then
160-
python -m pip install torch==1.10.1
157+
elif [ ${{ matrix.pytorch-version }} == "1.10.2" ]; then
158+
python -m pip install torch==1.10.2
159+
elif [ ${{ matrix.pytorch-version }} == "1.11.0" ]; then
160+
python -m pip install torch==1.11.0
161161
fi
162162
python -m pip install -r requirements-min.txt
163163
python -m pip list

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