Merge branch 'dev' into mlflow-sqlite-migration

Author: ericspod

.github/workflows/blossom-ci.yml

@@ -51,7 +51,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout code
-        uses: actions/checkout@v4
+        uses: actions/checkout@v7
         with:
           repository: ${{ fromJson(needs.Authorization.outputs.args).repo }}
           ref: ${{ fromJson(needs.Authorization.outputs.args).ref }}

.github/workflows/build_docs.yml

@@ -24,7 +24,7 @@ jobs:
       # minimum supported version of Python
       PYTHON_VER1: '3.10'
     steps:
-    - uses: actions/checkout@v6
+    - uses: actions/checkout@v7
     - name: Set up Python ${{ env.PYTHON_VER1 }}
       uses: actions/setup-python@v6
       with:

.github/workflows/cicd_tests.yml

@@ -66,7 +66,7 @@ jobs:
         sudo rm -rf /opt/ghc /usr/local/.ghcup
         sudo docker system prune -f
 
-    - uses: actions/checkout@v6
+    - uses: actions/checkout@v7
     - name: Set up Python ${{ env.PYTHON_VER1 }}
       uses: actions/setup-python@v6
       with:
@@ -129,7 +129,7 @@ jobs:
         sudo rm -rf /usr/local/lib/android
         sudo rm -rf /opt/ghc /usr/local/.ghcup
         sudo docker system prune -f
-    - uses: actions/checkout@v6
+    - uses: actions/checkout@v7
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v6
       with:
@@ -171,7 +171,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [windows-latest, ubuntu-latest]  # macOS-latest omitted for now for being very slow, see #8864
+        os: [windows-latest, ubuntu-latest, macOS-latest]  # macOS-latest is very slow (#8864), testing install only
     timeout-minutes: 120
     env:
       QUICKTEST: True
@@ -191,7 +191,7 @@ jobs:
         minimum-size: 8GB
         maximum-size: 16GB
         disk-root: "D:"
-    - uses: actions/checkout@v6
+    - uses: actions/checkout@v7
     - name: Set up Python ${{ env.PYTHON_VER1 }}
       uses: actions/setup-python@v6
       with:
@@ -223,19 +223,77 @@ jobs:
         cat "requirements-dev.txt"
         python -m pip install --no-build-isolation -r requirements-dev.txt
         python -m pip list
-        python -m pip install -e .  # test no compile installation
+        python -m pip install --no-build-isolation -e .  # test no compile installation
       shell: bash
     - name: Run compiled (${{ runner.os }})
       run: |
         python -m pip uninstall -y monai
-        BUILD_MONAI=1 python -m pip install -e .  # compile the cpp extensions
+        BUILD_MONAI=1 python -m pip install --no-build-isolation -e .  # compile the cpp extensions
       shell: bash
-    - name: Run quick tests
+    - if: runner.os != 'macOS'
+      name: Run full tests
       run: |
         python -c 'import torch; print(torch.__version__); print(torch.rand(5,3))'
         python -c "import monai; monai.config.print_config()"
         python -m unittest -v
       shell: bash
+    - if: runner.os == 'macOS'
+      name: Run min tests
+      run: |
+        python -c 'import torch; print(torch.__version__); print(torch.rand(5,3))'
+        python -c "import monai; monai.config.print_config()"
+        # TODO: enable large range of macOS tests which don't take a very long time
+        ./runtests.sh --min
+      shell: bash
+
+  hyena-dep:  # Optional HyenaND dependency + the no-CUDA Hyena tests.
+    # nvsubquadratic >= 0.1.1 supports Python >= 3.10 and keeps its CUDA-kernel sdist
+    # (subquadratic-ops-torch-cu12) plus the megatron / dali / timm packages in opt-in
+    # extras, so it installs on a CPU runner.  We still pass ``--no-deps`` deliberately:
+    #   (1) the HyenaND operators import only torch + einops + omegaconf at runtime, so
+    #       skipping the (still batteries-included: datasets/lightning/wandb) core deps
+    #       keeps this job lean; and
+    #   (2) nvsubquadratic pins torch>=2.10,<2.11, which would otherwise upgrade/clash
+    #       with the torch this job (and MONAI's matrix) installs.
+    # CUDA-required Hyena tests skip cleanly here; the GPU surface is covered by
+    # ``.github/workflows/pythonapp-hyena-gpu.yml``.
+    runs-on: ubuntu-latest
+    timeout-minutes: 30
+    steps:
+    - name: Clean unused tools
+      run: |
+        find  /opt/hostedtoolcache/* -maxdepth 0 ! -name 'Python' -exec rm -rf {} \;
+        sudo rm -rf /usr/share/dotnet
+        sudo rm -rf /usr/local/lib/android
+        sudo rm -rf /opt/ghc /usr/local/.ghcup
+        sudo docker system prune -f
+    - uses: actions/checkout@v6
+    - name: Set up Python ${{ env.PYTHON_VER1 }}
+      uses: actions/setup-python@v6
+      with:
+        python-version: ${{ env.PYTHON_VER1 }}
+        cache: 'pip'
+    - name: Install dependencies + nvsubquadratic (no-deps)
+      run: |
+        python -m pip install --upgrade pip wheel
+        python -m pip install torch==${PYTORCH_VER1} torchvision==${TORCHVISION_VER1}
+        python -m pip install --no-build-isolation -r requirements-dev.txt
+        python -m pip install -e .
+        # nvsubquadratic runtime imports need only torch + einops + omegaconf; install
+        # the package itself without its core dependency tree (see job comment above).
+        python -m pip install omegaconf
+        python -m pip install --no-deps 'nvsubquadratic>=0.1.1'
+        python -m pip list
+      shell: bash
+    - name: Run Hyena tests (CUDA-required cases skip cleanly)
+      run: |
+        python -c "from monai.networks.blocks.hyena import is_nvsubquadratic_available; \
+                   assert is_nvsubquadratic_available(), 'nvsubquadratic must be importable'"
+        python -m pytest -v \
+          tests/networks/blocks/test_hyena_block.py \
+          tests/networks/nets/test_hyena_nd_unetr.py \
+          tests/networks/nets/test_swin_unetr.py
+      shell: bash
 
   packaging:  # Test package generation
     runs-on: ubuntu-latest
@@ -249,7 +307,7 @@ jobs:
         sudo rm -rf /usr/local/lib/android
         sudo rm -rf /opt/ghc /usr/local/.ghcup
         sudo docker system prune -f
-    - uses: actions/checkout@v6
+    - uses: actions/checkout@v7
       with:
         fetch-depth: 0
     - name: Set up Python ${{ env.PYTHON_VER1 }}

.github/workflows/codeql-analysis.yml

@@ -38,7 +38,7 @@ jobs:
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v6
+      uses: actions/checkout@v7
 
     # Initializes the CodeQL tools for scanning.
     - name: Initialize CodeQL

.github/workflows/conda.yml

@@ -32,7 +32,7 @@ jobs:
         minimum-size: 8GB
         maximum-size: 16GB
         disk-root: "D:"
-    - uses: actions/checkout@v6
+    - uses: actions/checkout@v7
     - name: Clean up disk space
       run: |
         find /opt/hostedtoolcache/* -maxdepth 0 ! -name 'Python' -exec rm -rf {} \;

.github/workflows/cron-ngc-bundle.yml

@@ -17,7 +17,7 @@ jobs:
     if: github.repository == 'Project-MONAI/MONAI'
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v6
+    - uses: actions/checkout@v7
     - name: Set up Python 3.10
       uses: actions/setup-python@v6
       with:

.github/workflows/cron.yml

@@ -32,7 +32,7 @@ jobs:
       options: "--gpus all"
     runs-on: [self-hosted, linux, x64, common]
     steps:
-    - uses: actions/checkout@v6
+    - uses: actions/checkout@v7
     - name: apt install
       run: |
         apt-get update
@@ -67,7 +67,7 @@ jobs:
         if pgrep python; then pkill python; fi
       shell: bash
     - name: Upload coverage
-      uses: codecov/codecov-action@v6
+      uses: codecov/codecov-action@v7
       with:
         fail_ci_if_error: false
         files: ./coverage.xml
@@ -82,7 +82,7 @@ jobs:
       options: "--gpus all"
     runs-on: [self-hosted, linux, x64, integration]
     steps:
-    - uses: actions/checkout@v6
+    - uses: actions/checkout@v7
     - name: Install APT dependencies
       run: |
         apt-get update
@@ -115,7 +115,7 @@ jobs:
         if pgrep python; then pkill python; fi
       shell: bash
     - name: Upload coverage
-      uses: codecov/codecov-action@v6
+      uses: codecov/codecov-action@v7
       with:
         fail_ci_if_error: false
         files: ./coverage.xml
@@ -131,7 +131,7 @@ jobs:
       options: "--gpus all"
     runs-on: [self-hosted, linux, x64, integration]
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v7
         with:
           fetch-depth: 0
       - name: Install the dependencies
@@ -220,7 +220,7 @@ jobs:
         if pgrep python; then pkill python; fi
       shell: bash
     - name: Upload coverage
-      uses: codecov/codecov-action@v6
+      uses: codecov/codecov-action@v7
       with:
         fail_ci_if_error: false
         files: ./coverage.xml
@@ -233,7 +233,7 @@ jobs:
       options: "--gpus all --ipc=host"
     runs-on: [self-hosted, linux, x64, integration]
     steps:
-    - uses: actions/checkout@v6
+    - uses: actions/checkout@v7
     - name: Install MONAI
       id: monai-install
       run: |

.github/workflows/docker.yml

@@ -21,7 +21,7 @@ jobs:
     if: ${{ false }}  # disable docker build job  project-monai/monai#7450
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v7
         # full history so that we can git describe
         with:
           ref: dev
@@ -53,7 +53,7 @@ jobs:
     needs: versioning_dev
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v6
+    - uses: actions/checkout@v7
       with:
         ref: dev
     - name: Download version

.github/workflows/integration.yml

@@ -13,7 +13,7 @@ jobs:
     runs-on: [self-hosted, linux, x64, command]
     steps:
     # checkout the pull request branch
-    - uses: actions/checkout@v6
+    - uses: actions/checkout@v7
       with:
         token: ${{ secrets.PR_MAINTAIN }}
         repository: ${{ github.event.client_payload.pull_request.head.repo.full_name }}
@@ -22,7 +22,7 @@ jobs:
       id: pip-cache
       run: echo "datew=$(date '+%Y-%V')" >> $GITHUB_OUTPUT
     - name: cache for pip
-      uses: actions/cache@v5
+      uses: actions/cache@v6
       id: cache
       with:
         path: |
@@ -89,7 +89,7 @@ jobs:
     runs-on: [self-hosted, linux, x64, command1]
     steps:
     # checkout the pull request branch
-    - uses: actions/checkout@v6
+    - uses: actions/checkout@v7
       with:
         token: ${{ secrets.PR_MAINTAIN }}
         repository: ${{ github.event.client_payload.pull_request.head.repo.full_name }}
@@ -98,7 +98,7 @@ jobs:
       id: pip-cache
       run: echo "datew=$(date '+%Y-%V')" >> $GITHUB_OUTPUT
     - name: cache for pip
-      uses: actions/cache@v5
+      uses: actions/cache@v6
       id: cache
       with:
         path: |

.github/workflows/pythonapp-gpu.yml

@@ -46,7 +46,7 @@ jobs:
       options: --gpus all --env NVIDIA_DISABLE_REQUIRE=true  # workaround for unsatisfied condition: cuda>=11.6
     runs-on: [self-hosted, linux, x64, common]
     steps:
-    - uses: actions/checkout@v6
+    - uses: actions/checkout@v7
     - name: apt install
       if: github.event.pull_request.merged != true
       run: |
@@ -127,6 +127,6 @@ jobs:
       shell: bash
     - name: Upload coverage
       if: ${{ github.head_ref != 'dev' && github.event.pull_request.merged != true }}
-      uses: codecov/codecov-action@v6
+      uses: codecov/codecov-action@v7
       with:
         files: ./coverage.xml