merge master

.github/ISSUE_TEMPLATE/question.md

@@ -1,7 +1,7 @@
 ---
-name: Question
-about: Question relating to MONAI
-title: ''
+name: Question (please use the Discussion tab)
+about: https://github.com/Project-MONAI/MONAI/discussions
+title: 'Please use MONAI Discussion tab for questions'
 labels: ''
 assignees: ''
 ---

.github/pull_request_template.md

@@ -12,6 +12,6 @@ A few sentences describing the changes proposed in this pull request.
 - [ ] Breaking change (fix or new feature that would cause existing functionality to change).
 - [ ] New tests added to cover the changes.
 - [ ] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`.
-- [ ] Quick tests passed locally by running `./runtests.sh --quick --unittests`.
+- [ ] Quick tests passed locally by running `./runtests.sh --quick --unittests  --disttests`.
 - [ ] In-line docstrings updated.
 - [ ] Documentation updated, tested `make html` command in the `docs/` folder.

.github/workflows/blossom-ci.yml

@@ -30,7 +30,7 @@ jobs:
 
     # This job only runs for pull request comments
     if: |
-         contains( 'madil90,Nic-Ma,wyli,', format('{0},', github.actor)) &&
+         contains( 'Nic-Ma,wyli,', format('{0},', github.actor)) &&
          github.event.comment.body == '/build'
     steps:
       - name: Check if comment is issued by authorized person

.github/workflows/codeql-analysis.yml

@@ -0,0 +1,71 @@
+# For most projects, this workflow file will not need changing; you simply need
+# to commit it to your repository.
+#
+# You may wish to alter this file to override the set of languages analyzed,
+# or to provide custom queries or build logic.
+#
+# ******** NOTE ********
+# We have attempted to detect the languages in your repository. Please check
+# the `language` matrix defined below to confirm you have the correct set of
+# supported CodeQL languages.
+#
+name: "CodeQL"
+
+on:
+  push:
+    branches: [ dev, main ]
+  pull_request:
+    # The branches below must be a subset of the branches above
+    branches: [ dev ]
+  schedule:
+    - cron: '18 1 * * 0'
+
+jobs:
+  analyze:
+    name: Analyze
+    runs-on: ubuntu-latest
+    permissions:
+      actions: read
+      contents: read
+      security-events: write
+
+    strategy:
+      fail-fast: false
+      matrix:
+        language: [ 'cpp', 'python' ]
+        # CodeQL supports [ 'cpp', 'csharp', 'go', 'java', 'javascript', 'python', 'ruby' ]
+        # Learn more about CodeQL language support at https://git.io/codeql-language-support
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v2
+
+    # Initializes the CodeQL tools for scanning.
+    - name: Initialize CodeQL
+      uses: github/codeql-action/init@v1
+      with:
+        languages: ${{ matrix.language }}
+        # If you wish to specify custom queries, you can do so here or in a config file.
+        # By default, queries listed here will override any specified in a config file.
+        # Prefix the list here with "+" to use these queries and those in the config file.
+        # queries: ./path/to/local/query, your-org/your-repo/queries@main
+
+    # Autobuild attempts to build any compiled languages  (C/C++, C#, or Java).
+    # If this step fails, then you should remove it and run the build manually (see below)
+    # - name: Autobuild
+    #   uses: github/codeql-action/autobuild@v1
+
+    # ℹ️ Command-line programs to run using the OS shell.
+    # 📚 https://git.io/JvXDl
+
+    # ✏️ If the Autobuild fails above, remove it and uncomment the following three lines
+    #    and modify them (or add more) to build your code if your project
+    #    uses a compiled language
+
+    - name: Build
+      run: |
+        python -m pip install -r requirements-dev.txt
+        BUILD_MONAI=1 ./runtests.sh --build
+
+    - name: Perform CodeQL Analysis
+      uses: github/codeql-action/analyze@v1

.github/workflows/conda.yml

@@ -0,0 +1,57 @@
+name: conda
+
+on:
+  schedule:
+    - cron: "0 3 * * *"  # at 03:00 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: conda-tests-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  cron-conda:
+    if: github.repository == 'Project-MONAI/MONAI'
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [windows-latest, macOS-latest, ubuntu-latest]
+        python-version: ["3.7"]
+    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
+      with:
+        minimum-size: 8
+        maximum-size: 16
+        disk-root: "D:"
+    - uses: actions/checkout@v2
+    - uses: conda-incubator/setup-miniconda@v2
+      with:
+        auto-update-conda: true
+        python-version: ${{ matrix.python-version }}
+    - name: Install env (CPU ${{ runner.os }})
+      shell: bash -l {0}
+      run: |
+        conda info
+        conda list
+        conda env create --file environment-dev.yml
+    - if: runner.os == 'windows'
+      name: Windows only install
+      shell: bash -l {0}
+      run: |
+        conda activate monai
+        # this `cpuonly` and -c conda-forge is needed to reduce the paging file size on a github instance
+        conda install pytorch torchvision torchaudio cpuonly -c pytorch -c conda-forge
+        conda deactivate
+    - name: Test env(CPU ${{ runner.os }})
+      shell: bash -l {0}
+      run: |
+        conda activate monai
+        $(pwd)/runtests.sh --build --unittests
+        conda deactivate

.github/workflows/cron-mmar.yml

@@ -0,0 +1,42 @@
+name: cron-mmar
+
+on:
+  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-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  cron-load:
+    if: github.repository == 'Project-MONAI/MONAI'
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python 3.8
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.8
+    - name: cache weekly timestamp
+      id: pip-cache
+      run: echo "::set-output name=datew::$(date '+%Y-%V')"
+    - name: cache for pip
+      uses: actions/cache@v2
+      id: cache
+      with:
+        path: ~/.cache/pip
+        key: ${{ runner.os }}-pip-${{ steps.pip-cache.outputs.datew }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip wheel
+        python -m pip install -r requirements-dev.txt
+    - name: Loading MMARs
+      run: |
+        # clean up temporary files
+        $(pwd)/runtests.sh --build --clean
+        # run tests
+        python -m tests.ngc_mmar_loading

.github/workflows/cron.yml

@@ -10,12 +10,12 @@ jobs:
   cron-gpu:
     if: github.repository == 'Project-MONAI/MONAI'
     container:
-      image: nvcr.io/nvidia/pytorch:20.03-py3  # CUDA 10.2
+      image: nvcr.io/nvidia/pytorch:21.06-py3  # CUDA 11.3
       options: "--gpus all"
     runs-on: [self-hosted, linux, x64, common]
     strategy:
       matrix:
-        pytorch-version: [1.5.1, 1.6.0, 1.7.1, 1.8.1, latest]
+        pytorch-version: [1.6.0, 1.7.1, 1.8.1, 1.9.1, latest]
     steps:
     - uses: actions/checkout@v2
     - name: Install the dependencies
@@ -25,14 +25,14 @@ jobs:
         python -m pip uninstall -y torch torchvision
         if [ ${{ matrix.pytorch-version }} == "latest" ]; then
           python -m pip install torch torchvision
-        elif [ ${{ matrix.pytorch-version }} == "1.5.1" ]; then
-          python -m pip install torch==1.5.1 torchvision==0.6.1
         elif [ ${{ matrix.pytorch-version }} == "1.6.0" ]; then
           python -m pip install torch==1.6.0 torchvision==0.7.0
         elif [ ${{ matrix.pytorch-version }} == "1.7.1" ]; then
           python -m pip install torch==1.7.1 torchvision==0.8.2
         elif [ ${{ matrix.pytorch-version }} == "1.8.1" ]; then
           python -m pip install torch==1.8.1 torchvision==0.9.1
+        elif [ ${{ matrix.pytorch-version }} == "1.9.1" ]; then
+          python -m pip install torch==1.9.1 torchvision==0.10.1
         fi
         python -m pip install -r requirements-dev.txt
         python -m pip list
@@ -48,8 +48,8 @@ jobs:
         python -c $'import torch\na,b=torch.zeros(1,device="cuda:0"),torch.zeros(1,device="cuda:1");\nwhile True:print(a,b)' > /dev/null &
         python -c "import torch; print(torch.__version__); print('{} of GPUs available'.format(torch.cuda.device_count()))"
         python -c 'import torch; print(torch.rand(5, 3, device=torch.device("cuda:0")))'
-        BUILD_MONAI=1 ./runtests.sh --coverage --unittests  # unit tests with coverage report
-        BUILD_MONAI=1 ./runtests.sh --coverage --net  # integration tests with coverage report
+        BUILD_MONAI=1 ./runtests.sh --build --coverage --unittests --disttests  # unit tests with coverage report
+        BUILD_MONAI=1 ./runtests.sh --build --coverage --net  # integration tests with coverage report
         coverage xml
         if pgrep python; then pkill python; fi
     - name: Upload coverage
@@ -62,7 +62,7 @@ jobs:
     if: github.repository == 'Project-MONAI/MONAI'
     strategy:
       matrix:
-        container: ["pytorch:21.02", "pytorch:21.08"]  # 21.02 for backward comp.
+        container: ["pytorch:21.02", "pytorch:22.01"]  # 21.02 for backward comp.
     container:
       image: nvcr.io/nvidia/${{ matrix.container }}-py3  # testing with the latest pytorch base image
       options: "--gpus all"
@@ -91,8 +91,8 @@ jobs:
         python -c $'import torch\na,b=torch.zeros(1,device="cuda:0"),torch.zeros(1,device="cuda:1");\nwhile True:print(a,b)' > /dev/null &
         python -c "import torch; print(torch.__version__); print('{} of GPUs available'.format(torch.cuda.device_count()))"
         python -c 'import torch; print(torch.rand(5, 3, device=torch.device("cuda:0")))'
-        BUILD_MONAI=1 ./runtests.sh --coverage --unittests  # unit tests with coverage report
-        BUILD_MONAI=1 ./runtests.sh --coverage --net  # integration tests with coverage report
+        BUILD_MONAI=1 ./runtests.sh --build --coverage --unittests --disttests  # unit tests with coverage report
+        BUILD_MONAI=1 ./runtests.sh --build --coverage --net  # integration tests with coverage report
         coverage xml
         if pgrep python; then pkill python; fi
     - name: Upload coverage
@@ -106,7 +106,7 @@ jobs:
     if: github.repository == 'Project-MONAI/MONAI'
     strategy:
       matrix:
-        container: ["pytorch:21.02", "pytorch:21.08"]  # 21.02 for backward comp.
+        container: ["pytorch:21.02", "pytorch:22.01"]  # 21.02 for backward comp.
     container:
       image: nvcr.io/nvidia/${{ matrix.container }}-py3  # testing with the latest pytorch base image
       options: "--gpus all"
@@ -173,7 +173,7 @@ jobs:
   cron-docker:
     if: github.repository == 'Project-MONAI/MONAI'
     container:
-      image: localhost:5000/local_monai:dockerhub # use currently latest, locally available dockerhub image
+      image: docker://projectmonai/monai:latest  # this might be slow and has the pull count limitations
       options: "--gpus all"
     runs-on: [self-hosted, linux, x64, common]
     steps:
@@ -190,8 +190,8 @@ jobs:
         python -c "import torch; print(torch.__version__); print('{} of GPUs available'.format(torch.cuda.device_count()))"
         python -c 'import torch; print(torch.rand(5,3, device=torch.device("cuda:0")))'
         ngc --version
-        BUILD_MONAI=1 ./runtests.sh --coverage --pytype --unittests  # unit tests with pytype checks, coverage report
-        BUILD_MONAI=1 ./runtests.sh --coverage --net  # integration tests with coverage report
+        BUILD_MONAI=1 ./runtests.sh --build --coverage --pytype --unittests --disttests  # unit tests with pytype checks, coverage report
+        BUILD_MONAI=1 ./runtests.sh --build --coverage --net  # integration tests with coverage report
         coverage xml
         if pgrep python; then pkill python; fi
     - name: Upload coverage
@@ -204,7 +204,7 @@ jobs:
     if: github.repository == 'Project-MONAI/MONAI'
     needs: cron-gpu  # so that monai itself is verified first
     container:
-      image: nvcr.io/nvidia/pytorch:21.08-py3  # testing with the latest pytorch base image
+      image: nvcr.io/nvidia/pytorch:21.09-py3  # testing with the latest pytorch base image
       options: "--gpus all --ipc=host"
     runs-on: [self-hosted, linux, x64, common]
     steps:
@@ -215,7 +215,7 @@ jobs:
         which python
         python -m pip install --upgrade pip wheel
         python -m pip install -r requirements-dev.txt
-        BUILD_MONAI=0 python setup.py develop  # install monai
+        BUILD_MONAI=1 python setup.py develop  # install monai
         nvidia-smi
         export CUDA_VISIBLE_DEVICES=$(python -m tests.utils)
         echo $CUDA_VISIBLE_DEVICES
@@ -234,5 +234,7 @@ jobs:
         trap 'if pgrep python; then pkill python; fi;' ERR
         python -c $'import torch\na,b=torch.zeros(1,device="cuda:0"),torch.zeros(1,device="cuda:1");\nwhile True:print(a,b)' > /dev/null &
         cd /opt/tutorials
+        python -c 'import monai; monai.config.print_debug_info()'
         $(pwd)/runner.sh
+        python -c 'import monai; monai.config.print_debug_info()'
         if pgrep python; then pkill python; fi