Add spatial shape constraints to UNETR docstring and validation

.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

@@ -56,7 +56,7 @@ 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: |
@@ -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:
@@ -75,13 +75,12 @@ 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
     runs-on: ${{ matrix.os }}
@@ -129,7 +128,7 @@ 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 ${{ matrix.python-version }}
       uses: actions/setup-python@v6
       with:
@@ -138,15 +137,14 @@ jobs:
     - name: Prepare pip wheel
       run: |
         which python
-        python -m pip install --upgrade pip wheel
-        python -m pip install --user more-itertools>=8.0
+        python -m pip install --upgrade pip wheel tomli
     - name: Install the minimum dependencies
       run: |
         # min. requirements
         python -m pip install torch==${{ 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
@@ -171,7 +169,7 @@ 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 +189,7 @@ jobs:
         minimum-size: 8GB
         maximum-size: 16GB
         disk-root: "D:"
-    - uses: actions/checkout@v6
+    - uses: actions/checkout@v7
     - name: Set up Python ${{ env.PYTHON_VER1 }}
       uses: actions/setup-python@v6
       with:
@@ -219,28 +217,89 @@ jobs:
       shell: bash
     - name: Install the complete dependencies
       run: |
-        python -m pip install --user --upgrade pip wheel pybind11  # TODO: pybind11 added for macOS, may not be needed
-        cat "requirements-dev.txt"
-        python -m pip install --no-build-isolation -r requirements-dev.txt
+        python -m pip install --user --upgrade pip wheel tomli
+        python monai/config/print_dependencies.py build-system | xargs pip install --no-build-isolation
+        python -m pip install --no-build-isolation .[all,testing]
         python -m pip list
-        python -m pip install -e .  # test no compile installation
       shell: bash
     - name: Run compiled (${{ 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
     runs-on: ubuntu-latest
     env:
       QUICKTEST: True
+      INDEX_URL: "https://download.pytorch.org/whl/cpu"
     steps:
     - name: Clean unused tools
       run: |
@@ -249,7 +308,7 @@ 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 ${{ env.PYTHON_VER1 }}
@@ -259,11 +318,10 @@ jobs:
         cache: 'pip'
     - name: Install dependencies
       run: |
-        python -m pip install --user --upgrade pip setuptools wheel twine packaging
+        python -m pip install --user --upgrade pip setuptools wheel twine packaging tomli
         # install the latest pytorch for testing
-        # however, "pip install monai*.tar.gz" will build cpp/cuda with an isolated
-        # fresh torch installation according to pyproject.toml
-        python -m pip install torch==${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
@@ -292,7 +350,7 @@ 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
@@ -302,6 +360,14 @@ 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

@@ -9,67 +9,110 @@
 # the `language` matrix defined below to confirm you have the correct set of
 # supported CodeQL languages.
 #
-name: "CodeQL"
+name: "CodeQL Advanced"
 
 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'
+    - cron: '0 2 * * 1'  # 2AM Monday
+
+env:
+  PYTHON_VER: '3.11'
+  PYTORCH_VER: '2.8.0'
+  BUILD_MONAI: 1
+  PIP_EXTRA_INDEX_URL: "https://download.pytorch.org/whl/cpu"  # forces CPU PyTorch installation, should be faster
 
 jobs:
   analyze:
-    name: Analyze
+    name: Analyze (${{ matrix.language }})
+    # Runner size impacts CodeQL analysis time. To learn more, please see:
+    #   - https://gh.io/recommended-hardware-resources-for-running-codeql
+    #   - https://gh.io/supported-runners-and-hardware-resources
+    #   - https://gh.io/using-larger-runners (GitHub.com only)
+    # Consider using larger runners or machines with greater resources for possible analysis time improvements.
     runs-on: ubuntu-latest
     permissions:
+      # required for all workflows
+      security-events: write
+
+      # required to fetch internal or private CodeQL packs
+      packages: read
+
+      # only required for workflows in private repositories
       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
-
+        include:
+        - language: actions
+          build-mode: none
+        - language: c-cpp
+          build-mode: none  # TODO: get Cpp building working, autobuild doesn't work and manual fails for inexplicable reasons.
+        - language: python
+          build-mode: none
+        # CodeQL supports the following values keywords for 'language': 'actions', 'c-cpp', 'csharp', 'go', 'java-kotlin', 'javascript-typescript', 'python', 'ruby', 'rust', 'swift'
+        # Use `c-cpp` to analyze code written in C, C++ or both
+        # Use 'java-kotlin' to analyze code written in Java, Kotlin or both
+        # Use 'javascript-typescript' to analyze code written in JavaScript, TypeScript or both
+        # To learn more about changing the languages that are analyzed or customizing the build mode for your analysis,
+        # see https://docs.github.com/en/code-security/code-scanning/creating-an-advanced-setup-for-code-scanning/customizing-your-advanced-setup-for-code-scanning.
+        # If you are analyzing a compiled language, you can modify the 'build-mode' for that language to customize how
+        # your codebase is analyzed, see https://docs.github.com/en/code-security/code-scanning/creating-an-advanced-setup-for-code-scanning/codeql-code-scanning-for-compiled-languages
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v6
+      uses: actions/checkout@v7
+
+    # Add any setup steps before running the `github/codeql-action/init` action.
+    # This includes steps like installing compilers or runtimes (`actions/setup-node`
+    # or others). This is typically only required for manual builds.
+    # - name: Setup runtime (example)
+    #   uses: actions/setup-example@v1
 
     # Initializes the CodeQL tools for scanning.
     - name: Initialize CodeQL
       uses: github/codeql-action/init@v4
       with:
         languages: ${{ matrix.language }}
+        build-mode: ${{ matrix.build-mode }}
         # 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@v2
+        # For more details on CodeQL's query packs, refer to: https://docs.github.com/en/code-security/code-scanning/automatically-scanning-your-code-for-vulnerabilities-and-errors/configuring-code-scanning#using-queries-in-ql-packs
+        # queries: security-extended,security-and-quality
 
+    # If the analyze step fails for one of the languages you are analyzing with
+    # "We were unable to automatically build your code", modify the matrix above
+    # to set the build mode to "manual" for that language. Then modify this step
+    # to build your code.
     # 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
+    # 📚 See https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsrun
+    - name: Set up Python ${{ env.PYTHON_VER }}
+      if: matrix.language == 'c-cpp' && matrix.build-mode == 'manual'
+      uses: actions/setup-python@v6
+      with:
+        python-version: ${{ env.PYTHON_VER }}
+        cache: 'pip'
 
-    - name: Build
+    - name: Run manual build steps
+      if: matrix.language == 'c-cpp' && matrix.build-mode == 'manual'
+      shell: bash
       run: |
         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
-        BUILD_MONAI=1 ./runtests.sh --build
+        sudo rm -rf /usr/share/dotnet/
+        python -m pip install -U pip wheel wheel-stub
+        python -m pip install torch==${PYTORCH_VER} torchvision
+        python -m pip install --user --upgrade pip wheel
+        python monai/config/print_dependencies.py build-system | xargs pip install --no-build-isolation
+        python -m pip install --no-build-isolation .
 
     - name: Perform CodeQL Analysis
       uses: github/codeql-action/analyze@v4
+      with:
+        category: "/language:${{matrix.language}}"

.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 {} \;