Modernising Build Process

.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

@@ -75,7 +75,7 @@ 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
@@ -138,15 +138,14 @@ 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==${{ matrix.pytorch-version }}
-        python -m pip install -r requirements-min.txt
+        python monai/config/print_dependencies.py build-system | xargs pip install --no-build-isolation
+        python -m pip install --no-build-isolation .[testing]
         python -m pip list
-        BUILD_MONAI=0 python setup.py develop  # no compile of extensions
       shell: bash
     - if: matrix.os == 'linux-gpu-runner'
       name: Print GPU Info
@@ -219,16 +218,15 @@ jobs:
       shell: bash
     - name: Install the complete dependencies
       run: |
-        python -m pip install --user --upgrade pip wheel pybind11  # TODO: pybind11 added for macOS, may not be needed
-        cat "requirements-dev.txt"
-        python -m pip install --no-build-isolation -r requirements-dev.txt
+        python -m pip install --user --upgrade pip wheel tomli
+        python monai/config/print_dependencies.py build-system | xargs pip install --no-build-isolation
+        python -m pip install --no-build-isolation .[all,testing]
         python -m pip list
-        python -m pip install --no-build-isolation -e .  # test no compile installation
       shell: bash
     - name: Run compiled (${{ 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 .  # compile the cpp extensions
       shell: bash
     - if: runner.os != 'macOS'
       name: Run full tests
@@ -275,14 +273,14 @@ jobs:
         cache: 'pip'
     - name: Install dependencies + nvsubquadratic (no-deps)
       run: |
-        python -m pip install --upgrade pip wheel
+        python -m pip install --upgrade pip wheel tomli pytest
+        python monai/config/print_dependencies.py build-system | xargs pip install --no-build-isolation
         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'
+        # # 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 --no-build-isolation .[hyena,testing]
         python -m pip list
       shell: bash
     - name: Run Hyena tests (CUDA-required cases skip cleanly)

.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 ${{ matrix.pytorch }}
-        python -m pip install -r requirements-dev.txt
+        python -m pip install .[all,testing]
         python -m pip list
     - name: Run tests report coverage
       env:
@@ -91,7 +91,7 @@ jobs:
       run: |
         which python
         python -m pip install --upgrade pip wheel
-        python -m pip install -r requirements-dev.txt
+        python -m pip install .[all,testing]
         python -m pip list
     - name: Run tests report coverage
       env:
@@ -137,7 +137,7 @@ jobs:
       - name: Install the dependencies
         run: |
           which python
-          python -m pip install --upgrade pip wheel twine
+          python -m pip install --upgrade pip wheel twine tomli
           python -m pip list
       - name: Run tests report coverage
         shell: bash
@@ -159,6 +159,7 @@ jobs:
           # move packages to a temp dir
           tmp_dir=$(mktemp -d)
           cp dist/monai* "$tmp_dir"
+          python monai/config/print_dependencies.py build-system all testing > "$tmp_dir/requirements.txt"
           rm -r build dist monai.egg-info
           cd "$tmp_dir"
           ls -al
@@ -186,7 +187,7 @@ 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
+          pip install --no-build-isolation -r requirements.txt
           PYTHONPATH="$tmp_dir":$PYTHONPATH BUILD_MONAI=1 python ./tests/runner.py -p 'test_((?!integration).)'  # unit tests
           if pgrep python; then pkill python; fi
 
@@ -238,8 +239,8 @@ 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 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 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

@@ -159,8 +159,6 @@ 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

.github/workflows/weekly-preview.yml

@@ -32,8 +32,8 @@ jobs:
         cache: 'pip'
     - 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 -U pip wheel
+        python -m pip install .[all,testing]
     - name: Lint and type check
       run: |
         # clean up temporary files

Dockerfile

@@ -16,6 +16,8 @@ FROM ${PYTORCH_IMAGE}
 
 LABEL maintainer="monai.contact@gmail.com"
 
+ENV BUILD_MONAI=1
+
 # TODO: remark for issue [revise the dockerfile](https://github.com/zarr-developers/numcodecs/issues/431)
 RUN if [[ $(uname -m) =~ "aarch64" ]]; then \
       export CFLAGS="-O3" && \
@@ -24,36 +26,6 @@ RUN if [[ $(uname -m) =~ "aarch64" ]]; then \
       pip install numcodecs; \
     fi
 
-WORKDIR /opt/monai
-
-# Patch NVIDIA's pip constraint file:
-#   - keep the base image's numpy pin if present (older images pin numpy==1.26.4 as
-#     their torch was compiled against NumPy 1.x; newer images may ship an empty file)
-#   - add setuptools<71 (setuptools>=71 removed pkg_resources, breaking MetricsReloaded)
-#   - pin urllib3>=2 to prevent inadvertent downgrades by pip-installing legacy packages
-RUN (grep '^numpy' /etc/pip/constraint.txt || true) > /tmp/new_constraints.txt \
-  && printf 'setuptools<71\nurllib3>=2\n' >> /tmp/new_constraints.txt \
-  && cp /tmp/new_constraints.txt /etc/pip/constraint.txt
-
-# install full deps
-COPY requirements.txt requirements-min.txt requirements-dev.txt /tmp/
-RUN cp /tmp/requirements.txt /tmp/req.bak \
-  && awk '!/torch/' /tmp/requirements.txt > /tmp/tmp && mv /tmp/tmp /tmp/requirements.txt \
-  && python -m pip install --upgrade --no-cache-dir --no-build-isolation pip wheel wheel-stub \
-  && python -m pip install --no-cache-dir --no-build-isolation -r /tmp/requirements-dev.txt
-
-# compile ext and remove temp files
-# TODO: remark for issue [revise the dockerfile #1276](https://github.com/Project-MONAI/MONAI/issues/1276)
-# please specify exact files and folders to be copied -- else, basically always, the Docker build process cannot cache
-# this or anything below it and always will build from at most here; one file change leads to no caching from here on...
-
-COPY LICENSE CHANGELOG.md CODE_OF_CONDUCT.md CONTRIBUTING.md README.md versioneer.py setup.py setup.cfg runtests.sh MANIFEST.in ./
-COPY tests ./tests
-COPY monai ./monai
-
-RUN BUILD_MONAI=1 FORCE_CUDA=1 python setup.py develop \
-  && rm -rf build __pycache__
-
 # NGC Client
 WORKDIR /opt/tools
 ARG NGC_CLI_URI="https://ngc.nvidia.com/downloads/ngccli_linux.zip"
@@ -68,5 +40,16 @@ RUN apt-get update \
 ENV PATH=${PATH}:/opt/tools
 ENV POLYGRAPHY_AUTOINSTALL_DEPS=1
 
-
 WORKDIR /opt/monai
+
+# TODO: remark for issue [revise the dockerfile #1276](https://github.com/Project-MONAI/MONAI/issues/1276)
+# please specify exact files and folders to be copied -- else, basically always, the Docker build process cannot cache
+# this or anything below it and always will build from at most here; one file change leads to no caching from here on...
+COPY LICENSE CHANGELOG.md CODE_OF_CONDUCT.md CONTRIBUTING.md README.md versioneer.py setup.py pyproject.toml runtests.sh MANIFEST.in ./
+COPY tests ./tests
+COPY monai ./monai
+
+# Need to install build requirements explicitly so that no-build-isolation can be used. This needed to make pip build
+# against the included version of PyTorch, rather than install a new version in the isolated environment.
+RUN python monai/config/print_dependencies.py build-system | xargs pip install --no-cache-dir --no-build-isolation \
+  && FORCE_CUDA=1 pip install --no-cache-dir --no-build-isolation -e .[all,testing]

Dockerfile.slim

@@ -28,9 +28,9 @@ RUN apt update && apt upgrade -y && \
     wget https://developer.download.nvidia.com/compute/cuda/repos/debian12/x86_64/cuda-keyring_1.1-1_all.deb && \
     dpkg -i cuda-keyring_1.1-1_all.deb && \
     apt update && \
-    ${APT_INSTALL} cuda-toolkit-12-9 && \
+    ${APT_INSTALL} cuda-toolkit-13-3 && \
     rm -rf /usr/lib/python*/EXTERNALLY-MANAGED /var/lib/apt/lists/* && \
-    python -m pip install --upgrade --no-cache-dir --no-build-isolation pip
+    python -m pip install --upgrade --no-cache-dir pip
 
 # TODO: remark for issue [revise the dockerfile](https://github.com/zarr-developers/numcodecs/issues/431)
 RUN if [[ $(uname -m) =~ "aarch64" ]]; then \
@@ -46,18 +46,14 @@ RUN wget -q ${NGC_CLI_URI} && unzip ngccli_linux.zip && chmod u+x ngc-cli/ngc &&
 
 WORKDIR /opt/monai
 
-# copy relevant parts of repo
-COPY requirements.txt requirements-min.txt requirements-dev.txt versioneer.py setup.py setup.cfg pyproject.toml ./
-COPY LICENSE CHANGELOG.md CODE_OF_CONDUCT.md CONTRIBUTING.md README.md MANIFEST.in runtests.sh ./
+# TODO: remark for issue [revise the dockerfile #1276](https://github.com/Project-MONAI/MONAI/issues/1276)
+# please specify exact files and folders to be copied -- else, basically always, the Docker build process cannot cache
+# this or anything below it and always will build from at most here; one file change leads to no caching from here on...
+COPY LICENSE CHANGELOG.md CODE_OF_CONDUCT.md CONTRIBUTING.md README.md versioneer.py setup.py pyproject.toml runtests.sh MANIFEST.in ./
 COPY tests ./tests
 COPY monai ./monai
 
-# install full deps
-RUN python -m pip install --no-cache-dir --no-build-isolation -U wheel wheel-stub
-RUN python -m pip install --no-cache-dir --no-build-isolation "torch>=2.8.0,<2.11" -r requirements-dev.txt
-
-# compile ext
-RUN CUDA_HOME=/usr/local/cuda FORCE_CUDA=1 USE_COMPILED=1 BUILD_MONAI=1 python setup.py develop
+RUN BUILD_MONAI=1 FORCE_CUDA=1 pip install --no-cache-dir -e .[all,testing]
 
 # recreate the image without the installed CUDA packages then copy the installed MONAI and Python directories
 FROM ${IMAGE} AS build2

docs/requirements.txt

@@ -33,6 +33,7 @@ pynrrd
 pydicom
 h5py
 nni==2.10.1; platform_system == "Linux" and "arm" not in platform_machine and "aarch" not in platform_machine
+filelock<3.12.0
 optuna
 opencv-python-headless
 onnx>=1.13.0