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==${{ matrix.pytorch-version }}
-        python -m pip install -r requirements-min.txt
+        python monai/config/print_dependencies.py build-system | xargs pip install --no-build-isolation
+        python -m pip install --no-build-isolation .[testing]
         python -m pip list
-        BUILD_MONAI=0 python setup.py develop  # no compile of extensions
       shell: bash
     - if: matrix.os == 'linux-gpu-runner'
       name: Print GPU Info
@@ -175,6 +174,7 @@ jobs:
     timeout-minutes: 120
     env:
       QUICKTEST: True
+      BUILD_MONAI: 1
     steps:
     - if: runner.os == 'Linux'
       name: Clean unused tools
@@ -219,16 +219,17 @@ jobs:
       shell: bash
     - name: Install the complete dependencies
       run: |
-        python -m pip install --user --upgrade pip wheel pybind11  # TODO: pybind11 added for macOS, may not be needed
-        cat "requirements-dev.txt"
-        python -m pip install --no-build-isolation -r requirements-dev.txt
+        python -m pip install --user --upgrade pip wheel tomli
+        python monai/config/print_dependencies.py build-system | xargs pip install --no-build-isolation
+        python -m pip install --no-build-isolation .[all,testing]
         python -m pip list
-        python -m pip install --no-build-isolation -e .  # test no compile installation
       shell: bash
     - name: Run compiled (${{ runner.os }})
       run: |
         python -m pip uninstall -y monai
-        BUILD_MONAI=1 python -m pip install --no-build-isolation -e .  # compile the cpp extensions
+        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 +276,14 @@ 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)
@@ -317,11 +318,13 @@ 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 > requirements.txt
+        pip install --no-build-isolation -r requirements.txt
     - name: Check packages
       run: |
         python -m pip uninstall -y monai

.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
 
@@ -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

.github/workflows/setupapp.yml

@@ -163,9 +163,8 @@ jobs:
       if: github.ref == 'refs/heads/dev'
       run: |
         cd $GITHUB_WORKSPACE
-        rm -rf monai/
         ls -al .
-        python -m pip install -r requirements-min.txt
+        python -m pip install -e .[testing]
         python -m tests.min_tests
       env:
         QUICKTEST: True

.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
@@ -59,12 +59,12 @@ jobs:
     - name: Build distribution
       run: |
         export HEAD_COMMIT_ID=$(git rev-parse HEAD)
-        sed -i 's/name\ =\ monai$/name\ =\ monai-weekly/g' setup.cfg
+        sed -i 's/name\ =\ "monai"$/name\ =\ "monai-weekly"/g' pyproject.toml
         echo "__commit_id__ = \"$HEAD_COMMIT_ID\"" >> monai/__init__.py
-        git diff setup.cfg monai/__init__.py
+        git diff pyproject.toml monai/__init__.py
         git config user.name "CI Builder"
         git config user.email "monai.contact@gmail.com"
-        git add setup.cfg monai/__init__.py
+        git add pyproject.toml monai/__init__.py
         git commit -m "Weekly build at $HEAD_COMMIT_ID"
         export YEAR_WEEK=$(date +'%y%U')
         echo "Year week for tag is ${YEAR_WEEK}"

CONTRIBUTING.md

@@ -57,10 +57,6 @@ Before submitting a pull request, we recommend that all linting should pass, by
 ```bash
 # optionally update the dependencies and dev tools
 python -m pip install -U pip
-python -m pip install -U -r requirements-dev.txt
-
-# run the linting and type checking tools
-./runtests.sh --codeformat
 
 # try to fix the coding style errors automatically
 ./runtests.sh --autofix
@@ -132,7 +128,7 @@ It is recommended that the new test `test_[module_name].py` is constructed by us
 python 3.9+ build-in functions, `torch`, `numpy`, `coverage` (for reporting code coverages) and `parameterized` (for organising test cases) packages.
 If it requires any other external packages, please make sure:
 
-- the packages are listed in [`requirements-dev.txt`](requirements-dev.txt)
+- the packages are listed in [`pyproject.toml`](pyproject.toml)
 - the new test `test_[module_name].py` is added to the `exclude_cases` in [`./tests/min_tests.py`](./tests/min_tests.py) so that
 the minimal CI runner will not execute it.
 
@@ -219,10 +215,8 @@ Integration tests with minimal requirements are deployed to ensure this strategy
 To add new optional dependencies, please communicate with the core team during pull request reviews,
 and add the necessary information (at least) to the following files:
 
-- [setup.cfg](https://github.com/Project-MONAI/MONAI/blob/dev/setup.cfg)  (for package's `[options.extras_require]` config)
-- [requirements-dev.txt](https://github.com/Project-MONAI/MONAI/blob/dev/requirements-dev.txt) (pip requirements file)
+- [pyproject.toml](https://github.com/Project-MONAI/MONAI/blob/dev/pyproject.toml)  (for package's `[project.optional-dependencies]` config)
 - [docs/requirements.txt](https://github.com/Project-MONAI/MONAI/blob/dev/docs/requirements.txt) (docs pip requirements file)
-- [environment-dev.yml](https://github.com/Project-MONAI/MONAI/blob/dev/environment-dev.yml) (conda environment file)
 - [installation.md](https://github.com/Project-MONAI/MONAI/blob/dev/docs/source/installation.md) (documentation)
 
 When writing unit tests that use 3rd-party packages, it is a good practice to always consider
@@ -437,7 +431,7 @@ Do **not** use `[skip ci]` for commits that change:
 
 - Source code in `monai/`
 - Test files in `tests/`
-- Dependencies (`requirements*.txt`, `setup.cfg`, `setup.py`)
+- Dependencies (`pyproject.toml`, `setup.py`, `docs/requirements.txt`)
 - Anything that could affect correctness or compatibility
 
 ### Quick example