Merge branch 'dev' into ci-gate-tests-by-change-scan-8971

Signed-off-by: Siddhardha Nanda <99672439+SID-6921@users.noreply.github.com>

Author: SID-6921

.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

@@ -23,8 +23,10 @@ jobs:
     env:
       # minimum supported version of Python
       PYTHON_VER1: '3.10'
+      # force installation of CPU-only PyTorch
+      PIP_EXTRA_INDEX_URL: 'https://download.pytorch.org/whl/cpu'
     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

@@ -100,7 +100,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        opt: ["codeformat", "mypy"]  #  "pytype" omitted for being essentially deprecated, see #8865
+        opt: ["codeformat", "pyrefly"]
     steps:
     - name: Clean unused tools
       run: |
@@ -110,7 +110,7 @@ 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:
@@ -119,13 +119,12 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip wheel
-        python -m pip install --no-build-isolation -r requirements-dev.txt
+        python -m pip install .[all,testing]
     - name: Lint and type check
       run: |
         # clean up temporary files
         $(pwd)/runtests.sh --build --clean
-        # Github actions have multiple cores, so parallelize pytype
-        $(pwd)/runtests.sh --build --${{ matrix.opt }} -j $(nproc --all)
+        $(pwd)/runtests.sh --build --${{ matrix.opt }}
 
   min-dep:  # Test with minumum dependencies installed for different OS, Python, and PyTorch combinations
     needs: changes
@@ -175,7 +174,7 @@ 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 ${{ matrix.python-version }}
       uses: actions/setup-python@v6
       with:
@@ -184,15 +183,14 @@ jobs:
     - name: Prepare pip wheel
       run: |
         which python
-        python -m pip install --upgrade pip wheel
-        python -m pip install --user more-itertools>=8.0
+        python -m pip install --upgrade pip wheel tomli
     - name: Install the minimum dependencies
       run: |
         # min. requirements
         python -m pip install torch==${{ matrix.pytorch-version }}
-        python -m pip install -r requirements-min.txt
+        python monai/config/print_dependencies.py build-system | xargs pip install --no-build-isolation
+        python -m pip install --no-build-isolation .[testing]
         python -m pip list
-        BUILD_MONAI=0 python setup.py develop  # no compile of extensions
       shell: bash
     - if: matrix.os == 'linux-gpu-runner'
       name: Print GPU Info
@@ -219,7 +217,7 @@ 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
@@ -239,7 +237,7 @@ jobs:
         minimum-size: 8GB
         maximum-size: 16GB
         disk-root: "D:"
-    - uses: actions/checkout@v6
+    - uses: actions/checkout@v7
     - name: Set up Python ${{ env.PYTHON_VER1 }}
       uses: actions/setup-python@v6
       with:
@@ -267,30 +265,91 @@ jobs:
       shell: bash
     - name: Install the complete dependencies
       run: |
-        python -m pip install --user --upgrade pip wheel pybind11  # TODO: pybind11 added for macOS, may not be needed
-        cat "requirements-dev.txt"
-        python -m pip install --no-build-isolation -r requirements-dev.txt
+        python -m pip install --user --upgrade pip wheel tomli
+        python monai/config/print_dependencies.py build-system | xargs pip install --no-build-isolation
+        python -m pip install --no-build-isolation .[all,testing]
         python -m pip list
-        python -m pip install -e .  # test no compile installation
       shell: bash
     - name: Run compiled (${{ 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 in-place with -e
+        # ensure extensions were compiled
+        python -c 'import monai._C' > /dev/null
       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 tomli pytest
+        # need a specific version of torch for nvsubquadratic
+        python monai/config/print_dependencies.py build-system | \
+          xargs -d '\n' pip install --no-build-isolation torch==2.10.0 torchvision==0.25.0
+        # # 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 --no-build-isolation omegaconf
+        python -m pip install --no-build-isolation --no-deps 'nvsubquadratic>=0.1.1'
+        python -m pip install --no-build-isolation .[hyena,testing]
+        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
     needs: changes
     if: needs.changes.outputs.run_tests == 'true'
     runs-on: ubuntu-latest
     env:
       QUICKTEST: True
+      INDEX_URL: "https://download.pytorch.org/whl/cpu"
     steps:
     - name: Clean unused tools
       run: |
@@ -299,7 +358,7 @@ 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 ${{ env.PYTHON_VER1 }}
@@ -309,11 +368,10 @@ jobs:
         cache: 'pip'
     - name: Install dependencies
       run: |
-        python -m pip install --user --upgrade pip setuptools wheel twine packaging
+        python -m pip install --user --upgrade pip setuptools wheel twine packaging tomli
         # install the latest pytorch for testing
-        # however, "pip install monai*.tar.gz" will build cpp/cuda with an isolated
-        # fresh torch installation according to pyproject.toml
-        python -m pip install torch==${PYTORCH_VER1} torchvision --extra-index-url https://download.pytorch.org/whl/cpu
+        python monai/config/print_dependencies.py build-system all testing | \
+            xargs -d '\n' pip install --no-build-isolation torch==${PYTORCH_VER1} --extra-index-url $INDEX_URL
     - name: Check packages
       run: |
         python -m pip uninstall -y monai
@@ -342,7 +400,7 @@ jobs:
       working-directory: ${{ steps.mktemp.outputs.tmp_dir }}
       run: |
         # install from wheel
-        python -m pip install monai*.whl --extra-index-url https://download.pytorch.org/whl/cpu
+        python -m pip install --no-build-isolation monai*.whl --extra-index-url $INDEX_URL
         python -c 'import monai; monai.config.print_config()' 2>&1 | grep -iv "unknown"
         python -c 'import monai; print(monai.__file__)'
         python -m pip uninstall -y monai
@@ -352,6 +410,14 @@ jobs:
       run: |
         for name in *.tar.gz; do break; done
         echo $name
-        python -m pip install ${name}[all] --extra-index-url https://download.pytorch.org/whl/cpu
+        python -m pip install --no-build-isolation ${name}[all] --extra-index-url $INDEX_URL
+        python -c 'import monai; monai.config.print_config()' 2>&1 | grep -iv "unknown"
+        python -c 'import monai; print(monai.__file__)'
+        python -m pip uninstall -y monai
+    - name: Install using uv
+      working-directory: ${{ steps.root.outputs.pwd }}
+      run: |
+        pip install uv
+        uv pip install --system --no-build-isolation .[all] --extra-index-url $INDEX_URL
         python -c 'import monai; monai.config.print_config()' 2>&1 | grep -iv "unknown"
         python -c 'import monai; print(monai.__file__)'

.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
@@ -67,8 +67,8 @@ jobs:
         rm -rf /opt/hostedtoolcache/{node,go,Ruby,Java*}
         ls -al /opt/hostedtoolcache
         rm -rf /usr/share/dotnet/
-        python -m pip install -U --no-build-isolation pip wheel wheel-stub
-        python -m pip install --no-build-isolation -r requirements-dev.txt
+        python -m pip install -U pip wheel wheel-stub
+        python -m pip install .[all,testing]
         BUILD_MONAI=1 ./runtests.sh --build
 
     - name: Perform CodeQL Analysis

.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:
@@ -29,8 +29,8 @@ jobs:
     - name: Install dependencies
       run: |
         rm -rf /github/home/.cache/torch/hub/bundle/
-        python -m pip install --no-build-isolation --upgrade pip wheel wheel-stub
-        python -m pip install --no-build-isolation -r requirements-dev.txt
+        python -m pip install -U pip wheel wheel-stub
+        python -m pip install .[all,testing]
     - name: Loading Bundles
       run: |
         # clean up temporary files