feat: replace mypy and pytype with pyrefly for static type analysis

.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: |
@@ -259,7 +259,7 @@ 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<70" wheel twine packaging
         # 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
@@ -291,8 +291,8 @@ jobs:
     - name: Install wheel file
       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
+        # install from wheel (use --no-build-isolation to keep system setuptools with pkg_resources)
+        python -m pip install monai*.whl --no-build-isolation --extra-index-url https://download.pytorch.org/whl/cpu
         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 +302,6 @@ 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 ${name}[all] --no-build-isolation --extra-index-url https://download.pytorch.org/whl/cpu
         python -c 'import monai; monai.config.print_config()' 2>&1 | grep -iv "unknown"
         python -c 'import monai; print(monai.__file__)'

.github/workflows/cron.yml

@@ -214,7 +214,7 @@ 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

.github/workflows/pythonapp.yml

@@ -0,0 +1,213 @@
+# Jenkinsfile.monai-premerge
+name: premerge
+
+permissions:
+  contents: read
+
+on:
+  # quick tests for pull requests and the releasing branches
+  push:
+    branches:
+      - dev
+      - main
+      - releasing/*
+  pull_request:
+    head_ref-ignore:
+      - dev
+
+concurrency:
+  # automatically cancel the previously triggered workflows when there's a newer version
+  group: build-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  # caching of these jobs:
+  #   - docker-py3-pip- (shared)
+  #   - ubuntu py37 pip-
+  #   - os-latest-pip- (shared)
+  flake8-py3:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        opt: ["codeformat", "pyrefly"]
+    steps:
+    - uses: actions/checkout@v6
+    - name: Set up Python ${{ env.PYTHON_VER1 || '3.10' }}
+      uses: actions/setup-python@v6
+      with:
+        python-version: ${{ env.PYTHON_VER1 || '3.10' }}
+        cache: 'pip'
+    - name: Install dependencies
+      run: |
+        find  /opt/hostedtoolcache/* -maxdepth 0 ! -name 'Python' -exec rm -rf {} \;
+        python -m pip install --upgrade pip wheel
+        python -m pip install --no-build-isolation -r requirements-dev.txt
+    - name: Lint and type check
+      run: |
+        # clean up temporary files
+        $(pwd)/runtests.sh --build --clean
+        $(pwd)/runtests.sh --build --${{ matrix.opt }}
+
+  quick-py3:  # full dependencies installed tests for different OS
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [windows-latest, macOS-latest, ubuntu-latest]
+    timeout-minutes: 120
+    steps:
+    - if: runner.os == 'windows'
+      name: Config pagefile (Windows only)
+      uses: al-cheb/configure-pagefile-action@v1.4
+      with:
+        minimum-size: 8GB
+        maximum-size: 16GB
+        disk-root: "D:"
+    - uses: actions/checkout@v6
+    - name: Set up Python ${{ env.PYTHON_VER1 || '3.10' }}
+      uses: actions/setup-python@v6
+      with:
+        python-version: ${{ env.PYTHON_VER1 || '3.10' }}
+        cache: 'pip'
+    - name: Prepare pip wheel
+      run: |
+        which python
+        python -m pip install --upgrade pip wheel
+    - if: runner.os == 'windows'
+      name: Install torch cpu from pytorch.org (Windows only)
+      run: |
+        python -m pip install torch==2.4.1 torchvision==0.19.1+cpu --index-url https://download.pytorch.org/whl/cpu
+      shell: bash
+    - if: runner.os == 'Linux'
+      name: Install itk pre-release (Linux only)
+      run: |
+        python -m pip install --pre -U itk
+        find  /opt/hostedtoolcache/* -maxdepth 0 ! -name 'Python' -exec rm -rf {} \;
+    - name: Install the dependencies
+      run: |
+        python -m pip install --user --upgrade pip wheel
+        TORCH_VER=${{ env.PYTORCH_VER1 || '2.8.0' }}
+        TORCHVISION_VER=${{ env.TORCHVISION_VER1 || '0.23.0' }}
+        if [ "${{ runner.os }}" = "windows" ]; then
+          TORCH_VER="2.4.1"
+          TORCHVISION_VER="0.19.1"
+        fi
+        python -m pip install torch==${TORCH_VER} torchvision==${TORCHVISION_VER}
+        cat "requirements-dev.txt"
+        python -m pip install --no-build-isolation -r requirements-dev.txt
+        python -m pip list
+        BUILD_MONAI=0 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
+      shell: bash
+    - name: Run quick tests (CPU ${{ runner.os }})
+      run: |
+        python -c 'import torch; print(torch.__version__); print(torch.rand(5,3))'
+        python -c "import monai; monai.config.print_config()"
+        # Skip distributed tests on Windows where gloo backend is unsupported
+        ./runtests.sh --unittests --timeout 240
+      env:
+        QUICKTEST: True
+        PROTOCOL_BUFFERS_PYTHON_IMPLEMENTATION: python  # https://github.com/Project-MONAI/MONAI/issues/4354
+
+  packaging:
+    runs-on: ubuntu-latest
+    env:
+      QUICKTEST: True
+      shell: bash
+    steps:
+    - uses: actions/checkout@v6
+      with:
+        fetch-depth: 0
+    - name: Set up Python ${{ env.PYTHON_VER1 || '3.10' }}
+      uses: actions/setup-python@v6
+      with:
+        python-version: ${{ env.PYTHON_VER1 || '3.10' }}
+        cache: 'pip'
+    - name: Install dependencies
+      run: |
+        find  /opt/hostedtoolcache/* -maxdepth 0 ! -name 'Python' -exec rm -rf {} \;
+        python -m pip install --user --upgrade pip "setuptools<70" wheel twine packaging
+        # install the latest pytorch for testing
+        # however, "pip install monai*.tar.gz" will build cpp/cuda with an isolated
+        # fresh torch installation according to pyproject.toml
+        python -m pip install torch==${{ env.PYTORCH_VER1 || '2.8.0' }} torchvision --extra-index-url https://download.pytorch.org/whl/cpu
+    - name: Check packages
+      run: |
+        pip uninstall monai
+        pip list | grep -iv monai
+        git fetch --depth=1 origin +refs/tags/*:refs/tags/*
+        set -e
+
+        # build tar.gz and wheel
+        python setup.py check -m -s
+        python setup.py sdist bdist_wheel
+        python -m twine check dist/*
+    - run: echo "pwd=$PWD" >> $GITHUB_OUTPUT
+      id: root
+    - run: echo "tmp_dir=$(mktemp -d)" >> $GITHUB_OUTPUT
+      id: mktemp
+    - name: Move packages
+      run: |
+        printf ${{ steps.root.outputs.pwd }}
+        printf ${{ steps.mktemp.outputs.tmp_dir }}
+        # move packages to a temp dir
+        cp dist/monai* "${{ steps.mktemp.outputs.tmp_dir }}"
+        rm -r build dist monai.egg-info
+        cd "${{ steps.mktemp.outputs.tmp_dir }}"
+        ls -al
+    - name: Install wheel file
+      working-directory: ${{ steps.mktemp.outputs.tmp_dir }}
+      run: |
+        # install from wheel (use --no-build-isolation to keep system setuptools with pkg_resources)
+        python -m pip install monai*.whl --no-build-isolation
+        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
+        rm monai*.whl
+    - name: Install source archive
+      working-directory: ${{ steps.mktemp.outputs.tmp_dir }}
+      run: |
+        # install from tar.gz (use --no-build-isolation to keep system setuptools with pkg_resources)
+        name=$(ls *.tar.gz | head -n1)
+        echo $name
+        python -m pip install $name[all] --no-build-isolation
+        python -c 'import monai; monai.config.print_config()' 2>&1 | grep -iv "unknown"
+        python -c 'import monai; print(monai.__file__)'
+    - name: Quick test
+      working-directory: ${{ steps.mktemp.outputs.tmp_dir }}
+      run: |
+        # run min tests
+        cp ${{ steps.root.outputs.pwd }}/requirements*.txt .
+        cp -r ${{ steps.root.outputs.pwd }}/tests .
+        ls -al
+        python -m pip install --no-build-isolation -r requirements-dev.txt
+        python -m unittest -v
+      env:
+        PROTOCOL_BUFFERS_PYTHON_IMPLEMENTATION: python  # https://github.com/Project-MONAI/MONAI/issues/4354
+
+  build-docs:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v6
+    - name: Set up Python ${{ env.PYTHON_VER1 || '3.10' }}
+      uses: actions/setup-python@v6
+      with:
+        python-version: ${{ env.PYTHON_VER1 || '3.10' }}
+        cache: 'pip'
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip wheel
+        python -m pip install -r docs/requirements.txt --extra-index-url https://download.pytorch.org/whl/cpu
+    - name: Make html
+      run: |
+        cd docs/
+        make clean
+        make html 2>&1 | tee tmp_log
+        if [[ $(grep -c "ERROR:" tmp_log) != 0 ]]; then echo "found errors"; grep "ERROR:" tmp_log; exit 1; fi
+        sed '/WARNING.*pip/d' tmp_log > tmp_log1; mv tmp_log1 tmp_log  # monai#7133
+        if [[ $(grep -c "WARNING:" tmp_log) != 0 ]]; then echo "found warnings"; grep "WARNING:" tmp_log; exit 1; fi
+      shell: bash

.github/workflows/weekly-preview.yml

@@ -12,7 +12,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        opt: ["codeformat", "mypy"]
+        opt: ["codeformat", "pyrefly"]
     steps:
     - name: Clean unused tools
       run: |

.gitignore

@@ -107,15 +107,11 @@ venv.bak/
 # mkdocs documentation
 /site
 
-# pytype cache
-.pytype/
-
-# mypy
-.mypy_cache/
+# pyrefly cache
+.pyrefly_cache/
 examples/scd_lvsegs.npz
 temp/
 .idea/
-.dmypy.json
 
 *~
 

CONTRIBUTING.md

@@ -38,7 +38,7 @@ Please note that, as per PyTorch, MONAI uses American English spelling. This mea
 ### Preparing pull requests
 
 To ensure the code quality, MONAI relies on several linting tools ([black](https://github.com/psf/black), [isort](https://github.com/timothycrosley/isort), [ruff](https://github.com/astral-sh/ruff)),
-static type analysis tools ([mypy](https://github.com/python/mypy), [pytype](https://github.com/google/pytype)), as well as a set of unit/integration tests.
+static type analysis tools ([pyrefly](https://github.com/facebook/pyrefly)), as well as a set of unit/integration tests.
 
 This section highlights all the necessary preparation steps required before sending a pull request.
 To collaborate efficiently, please read through this section and follow them.

monai/apps/auto3dseg/auto_runner.py

@@ -405,6 +405,7 @@ def inspect_datalist_folds(self, datalist_filename: str) -> int:
 
         datalist = ConfigParser.load_config_file(datalist_filename)
         if "training" not in datalist:
+            # pyrefly: ignore [unnecessary-type-conversion]
             raise ValueError("Datalist files has no training key:" + str(datalist_filename))
 
         fold_list = [int(d["fold"]) for d in datalist["training"] if "fold" in d]
@@ -790,6 +791,7 @@ def _train_algo_in_nni(self, history: list[dict[str, Any]]) -> None:
             nni_config_filename = os.path.abspath(os.path.join(self.work_dir, f"{name}_nni_config.yaml"))
             ConfigParser.export_config_file(nni_config, nni_config_filename, fmt="yaml", default_flow_style=None)
 
+            # pyrefly: ignore [redundant-cast]
             max_trial = min(self.hpo_tasks, cast(int, default_nni_config["maxTrialNumber"]))
             cmd = "nnictl create --config " + nni_config_filename + " --port 8088"
 
@@ -805,6 +807,7 @@ def _train_algo_in_nni(self, history: list[dict[str, Any]]) -> None:
                 n_trainings = len(import_bundle_algo_history(self.work_dir, only_trained=True))
 
             cmd = "nnictl stop --all"
+            # pyrefly: ignore [bad-argument-type]
             run_cmd(cmd.split(), check=True)
             logger.info(f"NNI completes HPO on {name}")
             last_total_tasks = n_trainings

monai/apps/auto3dseg/bundle_gen.py

@@ -344,6 +344,7 @@ def infer(self, image_file):
         config_dir = os.path.join(self.output_path, "configs")
         configs_path = [os.path.join(config_dir, f) for f in os.listdir(config_dir)]
 
+        # pyrefly: ignore [implicit-import]
         spec = importlib.util.spec_from_file_location("InferClass", infer_py)
         infer_class = importlib.util.module_from_spec(spec)  # type: ignore
         sys.modules["InferClass"] = infer_class

monai/apps/auto3dseg/ensemble_builder.py

@@ -337,6 +337,7 @@ def __init__(self, history: Sequence[dict[str, Any]], data_src_cfg_name: str | N
         self.ensemble: AlgoEnsemble
         self.data_src_cfg = ConfigParser(globals=False)
 
+        # pyrefly: ignore [unnecessary-type-conversion]
         if data_src_cfg_name is not None and os.path.exists(str(data_src_cfg_name)):
             self.data_src_cfg.read_config(data_src_cfg_name)
 

monai/apps/deepedit/transforms.py

@@ -434,6 +434,7 @@ def _randomize(self, d, key_label):
         else:
             logger.info(f"Not slice IDs for label: {key_label}")
             sid = None
+        # pyrefly: ignore [unsupported-operation]
         self.sid[key_label] = sid
 
     def __call__(self, data: Mapping[Hashable, np.ndarray]) -> dict[Hashable, np.ndarray]:
@@ -561,6 +562,7 @@ def __init__(
         self.guidance: dict[str, list[list[int]]] = {}
 
     def randomize(self, data=None):
+        # pyrefly: ignore [unsupported-operation]
         probability = data[self.probability]
         self._will_interact = self.R.choice([True, False], p=[probability, 1.0 - probability])
 
@@ -885,6 +887,7 @@ def _randomize(self, d, key_label):
         else:
             logger.info(f"Not slice IDs for label: {key_label}")
             sid = None
+        # pyrefly: ignore [unsupported-operation]
         self.sid[key_label] = sid
 
     def __call__(self, data: Mapping[Hashable, np.ndarray]) -> dict[Hashable, np.ndarray]:

monai/apps/deepgrow/dataset.py

@@ -175,6 +175,7 @@ def _save_data_2d(vol_idx, vol_image, vol_label, dataset_dir, relative_path):
             continue
 
         # For all Labels
+        # pyrefly: ignore [missing-attribute]
         unique_labels = np.unique(label.flatten())
         unique_labels = unique_labels[unique_labels != 0]
         unique_labels_count = max(unique_labels_count, len(unique_labels))

monai/apps/deepgrow/transforms.py

@@ -288,6 +288,7 @@ def __init__(self, guidance: str = "guidance", discrepancy: str = "discrepancy",
         self._will_interact = None
 
     def randomize(self, data=None):
+        # pyrefly: ignore [unsupported-operation]
         probability = data[self.probability]
         self._will_interact = self.R.choice([True, False], p=[probability, 1.0 - probability])
 

monai/apps/detection/networks/retinanet_detector.py

@@ -525,6 +525,7 @@ def forward(
             )
 
         # 4. Generate anchors and store it in self.anchors: List[Tensor]
+        # pyrefly: ignore [bad-argument-type]
         self.generate_anchors(images, head_outputs)
         # num_anchor_locs_per_level: List[int], list of HW or HWD for each level
         num_anchor_locs_per_level = [x.shape[2:].numel() for x in head_outputs[self.cls_key]]
@@ -535,6 +536,7 @@ def forward(
             # reshape to Tensor sized(B, sum(HWA), self.num_classes) for self.cls_key
             # or (B, sum(HWA), 2* self.spatial_dims) for self.box_reg_key
             # A = self.num_anchors_per_loc
+            # pyrefly: ignore [bad-argument-type]
             head_outputs[key] = self._reshape_maps(head_outputs[key])
 
         # 6(1). If during training, return losses