Merge branch 'dev' into test/make-nifti-image-temp-cleanup

Author: aymuos15

.github/workflows/build_docs.yml

@@ -23,6 +23,8 @@ 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@v7
     - name: Set up Python ${{ env.PYTHON_VER1 }}

.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: |
@@ -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: ${{ matrix.os }}
@@ -138,15 +137,14 @@ jobs:
     - name: Prepare pip wheel
       run: |
         which python
-        python -m pip install --upgrade pip wheel
-        python -m pip install --user more-itertools>=8.0
+        python -m pip install --upgrade pip wheel tomli
     - name: Install the minimum dependencies
       run: |
         # min. requirements
         python -m pip install torch==${{ 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
@@ -219,16 +217,17 @@ 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 --no-build-isolation -e .  # test no compile installation
       shell: bash
     - name: Run compiled (${{ runner.os }})
       run: |
         python -m pip uninstall -y monai
-        BUILD_MONAI=1 python -m pip install --no-build-isolation -e .  # compile the cpp extensions
+        BUILD_MONAI=1 python -m pip install --no-build-isolation -e .  # compile the cpp extensions in-place with -e
+        # ensure extensions were compiled
+        python -c 'import monai._C' > /dev/null
       shell: bash
     - if: runner.os != 'macOS'
       name: Run full tests
@@ -275,14 +274,15 @@ jobs:
         cache: 'pip'
     - name: Install dependencies + nvsubquadratic (no-deps)
       run: |
-        python -m pip install --upgrade pip wheel
-        python -m pip install torch==${PYTORCH_VER1} torchvision==${TORCHVISION_VER1}
-        python -m pip install --no-build-isolation -r requirements-dev.txt
-        python -m pip install -e .
-        # nvsubquadratic runtime imports need only torch + einops + omegaconf; install
-        # the package itself without its core dependency tree (see job comment above).
-        python -m pip install omegaconf
-        python -m pip install --no-deps 'nvsubquadratic>=0.1.1'
+        python -m pip install --upgrade pip wheel tomli pytest
+        # need a specific version of torch for nvsubquadratic
+        python monai/config/print_dependencies.py build-system | \
+          xargs -d '\n' pip install --no-build-isolation torch==2.10.0 torchvision==0.25.0
+        # # nvsubquadratic runtime imports need only torch + einops + omegaconf; install
+        # # the package itself without its core dependency tree (see job comment above).
+        python -m pip install --no-build-isolation omegaconf
+        python -m pip install --no-build-isolation --no-deps 'nvsubquadratic>=0.1.1'
+        python -m pip install --no-build-isolation .[hyena,testing]
         python -m pip list
       shell: bash
     - name: Run Hyena tests (CUDA-required cases skip cleanly)
@@ -299,6 +299,7 @@ jobs:
     runs-on: ubuntu-latest
     env:
       QUICKTEST: True
+      INDEX_URL: "https://download.pytorch.org/whl/cpu"
     steps:
     - name: Clean unused tools
       run: |
@@ -317,11 +318,10 @@ jobs:
         cache: 'pip'
     - name: Install dependencies
       run: |
-        python -m pip install --user --upgrade pip setuptools wheel twine packaging
+        python -m pip install --user --upgrade pip setuptools wheel twine packaging tomli
         # install the latest pytorch for testing
-        # however, "pip install monai*.tar.gz" will build cpp/cuda with an isolated
-        # fresh torch installation according to pyproject.toml
-        python -m pip install torch==${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
@@ -350,7 +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
@@ -360,6 +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

@@ -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/cron-ngc-bundle.yml

@@ -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

.github/workflows/cron.yml

@@ -43,7 +43,7 @@ jobs:
         python -m pip install --upgrade pip wheel
         python -m pip uninstall -y torch torchvision
         python -m pip install ${{ matrix.pytorch }}
-        python -m pip install -r requirements-dev.txt
+        python -m pip install .[all,testing]
         python -m pip list
     - name: Run tests report coverage
       env:
@@ -91,7 +91,7 @@ jobs:
       run: |
         which python
         python -m pip install --upgrade pip wheel
-        python -m pip install -r requirements-dev.txt
+        python -m pip install .[all,testing]
         python -m pip list
     - name: Run tests report coverage
       env:
@@ -137,7 +137,8 @@ jobs:
       - name: Install the dependencies
         run: |
           which python
-          python -m pip install --upgrade pip wheel twine
+          python -m pip install --upgrade pip wheel twine tomli
+          python monai/config/print_dependencies.py build-system all testing | xargs -d '\n' pip install --no-build-isolation
           python -m pip list
       - name: Run tests report coverage
         shell: bash
@@ -171,7 +172,6 @@ jobs:
           python -c 'import monai; print(monai.__file__)'
 
           # run tests
-          cp $root_dir/requirements*.txt "$tmp_dir"
           cp -r $root_dir/tests "$tmp_dir"
           pwd
           ls -al
@@ -186,7 +186,6 @@ 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 -m pip install -r requirements-dev.txt
           PYTHONPATH="$tmp_dir":$PYTHONPATH BUILD_MONAI=1 python ./tests/runner.py -p 'test_((?!integration).)'  # unit tests
           if pgrep python; then pkill python; fi
 
@@ -214,7 +213,7 @@ 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 --build --coverage --unittests --disttests  # unit tests with pytype checks, coverage report
+        BUILD_MONAI=1 ./runtests.sh --build --coverage --pyrefly --unittests --disttests  # unit tests with pyrefly checks, coverage report
         BUILD_MONAI=1 ./runtests.sh --build --coverage --net  # integration tests with coverage report
         coverage xml --ignore-errors
         if pgrep python; then pkill python; fi
@@ -238,8 +237,8 @@ jobs:
       id: monai-install
       run: |
         which python
-        python -m pip install --upgrade pip wheel
-        python -m pip install -r requirements-dev.txt
+        python -m pip install --upgrade pip wheel tomli
+        python monai/config/print_dependencies.py build-system | xargs -d '\n' pip install --no-cache-dir --no-build-isolation
         BUILD_MONAI=1 python setup.py develop  # install monai
         nvidia-smi
         export CUDA_VISIBLE_DEVICES=$(python -m tests.utils | tail -n 1)

.github/workflows/docker.yml

@@ -69,8 +69,6 @@ jobs:
         cat _version.py
         mv _version.py monai/
 
-        # build "latest": remove flake package as it is not needed on hub.docker.com
-        sed -i '/flake/d' requirements-dev.txt
         docker build -t projectmonai/monai:latest -f Dockerfile .
 
         # distribute as always w/ tag "latest" to hub.docker.com

.github/workflows/integration.yml

@@ -37,8 +37,8 @@ jobs:
         pip uninstall -y monai
         pip uninstall -y monai-weekly
         pip uninstall -y monai-weekly
-        python -m pip install --upgrade torch torchvision torchaudio torchtext
-        python -m pip install -r requirements-dev.txt
+        python monai/config/print_dependencies.py build-system | xargs -d '\n' pip install --no-cache-dir --no-build-isolation
+        python -m pip install --no-build-isolation .[all,testing]
         rm -rf /github/home/.cache/torch/hub/mmars/
     - name: Clean directory
       run: |
@@ -113,8 +113,7 @@ jobs:
         pip uninstall -y monai
         pip uninstall -y monai-weekly
         pip uninstall -y monai-weekly
-        python -m pip install --upgrade torch torchvision torchaudio torchtext
-        python -m pip install -r requirements-dev.txt
+        python -m pip install .[all,testing]
         rm -rf /github/home/.cache/torch/hub/mmars/
     - name: Clean directory
       run: |
@@ -124,7 +123,7 @@ jobs:
         nvidia-smi
         export CUDA_VISIBLE_DEVICES=$(python -m tests.utils -c 1 | tail -n 1)
         echo $CUDA_VISIBLE_DEVICES
-        python -c "import torch; print(torch.__version__); print('{} of GPUs available'.format(torch.cuda.device_count()))"
+        python -c "import torch; print(torch.__version__); print(f'{torch.cuda.device_count()} of GPUs available')"
         python -c 'import torch; print(torch.rand(5,3, device=torch.device("cuda:0")))'
 
     - name: Auto3dseg latest algo

.github/workflows/pythonapp-gpu.yml

@@ -96,7 +96,7 @@ jobs:
         rm -rf $(python -c "from distutils.sysconfig import get_python_lib; print(get_python_lib())")/ruamel*
         rm -rf $(python -c "from distutils.sysconfig import get_python_lib; print(get_python_lib())")/llvmlite*  #6377
         python -m pip install ${{ matrix.pytorch }}
-        python -m pip install -r requirements-dev.txt
+        python -m pip install .[all,testing]
         python -m pip list
     - name: Run quick tests (GPU)
       if: github.event.pull_request.merged != true

.github/workflows/pythonapp-hyena-gpu.yml

@@ -47,8 +47,7 @@ jobs:
       run: |
         python -m pip install --upgrade pip wheel
         python -c "import sys; assert sys.version_info >= (3, 10), f'Python >= 3.10 required for nvsubquadratic, got {sys.version}'"
-        python -m pip install -r requirements-dev.txt
-        python -m pip install -e .
+        python -m pip install -e .[all,testing]
         # Install nvsubquadratic with --no-deps: the default torch_fft path needs only
         # torch + einops + omegaconf, and nvsubquadratic pins torch>=2.10,<2.11 which can
         # clash with the container's torch.  To exercise the accelerated fused CUDA

.github/workflows/release.yml

@@ -22,9 +22,10 @@ jobs:
       uses: actions/setup-python@v6
       with:
         python-version: ${{ matrix.python-version }}
-    - name: Install setuptools
+    - name: Install Dependencies
       run: |
-        python -m pip install --user --upgrade setuptools wheel packaging
+        python -m pip install --user --upgrade setuptools wheel packaging tomli
+        python monai/config/print_dependencies.py build-system all testing | xargs -d '\n' pip install --no-build-isolation
     - name: Build and test source archive and wheel file
       run: |
         find  /opt/hostedtoolcache/* -maxdepth 0 ! -name 'Python' -exec rm -rf {} \;
@@ -55,11 +56,10 @@ jobs:
         # clean up
         cd "$root_dir"
         rm -r "$tmp_dir"
-        rm -rf monai/
         ls -al .
     - name: Quick test installed
       run: |
-        python -m pip install -r requirements-min.txt
+        python -m pip install -e .[testing]
         python -m tests.min_tests
       env:
         QUICKTEST: True
@@ -105,7 +105,8 @@ jobs:
         run: |
           find  /opt/hostedtoolcache/* -maxdepth 0 ! -name 'Python' -exec rm -rf {} \;
           git describe
-          python -m pip install --user --upgrade setuptools wheel packaging
+          python -m pip install --user --upgrade setuptools wheel packaging tomli
+          python monai/config/print_dependencies.py build-system all testing | xargs -d '\n' pip install --no-build-isolation
           python setup.py build
           cat build/lib/monai/_version.py
       - name: Upload version
@@ -159,8 +160,6 @@ jobs:
             echo "unmatched version string, please check the tagging branch."
             exit 1
           fi
-          # remove flake package as it is not needed on hub.docker.com
-          sed -i '/flake/d' requirements-dev.txt
           docker build -t projectmonai/monai:"$RELEASE_VERSION" -f Dockerfile .
           # distribute with a tag to hub.docker.com
           echo "${{ secrets.DOCKER_PW }}" | docker login -u projectmonai --password-stdin