auto updates (#5927)

Signed-off-by: monai-bot <[email protected]>

Signed-off-by: monai-bot <[email protected]>

Author: monai-bot

.github/workflows/pythonapp.yml

@@ -22,6 +22,9 @@ jobs:
   #   - os-latest-pip- (shared)
   flake8-py3:
     runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        opt: ["codeformat", "pytype", "mypy"]
     steps:
     - uses: actions/checkout@v3
     - name: Set up Python 3.8
@@ -46,8 +49,8 @@ jobs:
       run: |
         # clean up temporary files
         $(pwd)/runtests.sh --build --clean
-        # Git hub actions have 2 cores, so parallize pytype
-        $(pwd)/runtests.sh --build --codeformat -j 2
+        # Github actions have 2 cores, so parallelize pytype
+        $(pwd)/runtests.sh --build --${{ matrix.opt }} -j 2
 
   quick-py3:  # full dependencies installed tests for different OS
     runs-on: ${{ matrix.os }}

docs/requirements.txt

@@ -21,7 +21,7 @@ sphinx-autodoc-typehints==1.11.1
 pandas
 einops
 transformers<4.22  # https://github.com/Project-MONAI/MONAI/issues/5157
-mlflow
+mlflow>=1.28.0
 tensorboardX
 imagecodecs; platform_system == "Linux" or platform_system == "Darwin"
 tifffile; platform_system == "Linux" or platform_system == "Darwin"

monai/apps/auto3dseg/auto_runner.py

@@ -223,7 +223,6 @@ def __init__(
         templates_path_or_url: str | None = None,
         **kwargs,
     ):
-
         logger.info(f"AutoRunner using work directory {work_dir}")
         os.makedirs(work_dir, exist_ok=True)
 
@@ -641,7 +640,6 @@ def run(self):
 
         # step 2: algorithm generation
         if self.algo_gen:
-
             if not os.path.isfile(self.datastats_filename):
                 raise ValueError(
                     f"Could not find the datastats file {self.datastats_filename}. "

monai/apps/auto3dseg/bundle_gen.py

@@ -377,9 +377,7 @@ def __init__(
         data_stats_filename: str | None = None,
         data_src_cfg_name: str | None = None,
     ):
-
         if algos is None or isinstance(algos, (list, tuple, str)):
-
             if templates_path_or_url is None:
                 templates_path_or_url = default_algo_zip
 
@@ -404,7 +402,6 @@ def __init__(
         self.algos: Any = []
         if isinstance(algos, dict):
             for algo_name, algo_params in algos.items():
-
                 template_path = os.path.dirname(algo_params.get("template_path", "."))
                 if len(template_path) > 0 and template_path not in sys.path:
                     sys.path.append(template_path)

monai/apps/auto3dseg/data_analyzer.py

@@ -214,7 +214,6 @@ def get_all_case_stats(self, key="training", transform_list=None):
                 Orientationd(keys=keys, axcodes="RAS"),
             ]
             if self.label_key is not None:
-
                 allowed_shape_difference = self.extra_params.pop("allowed_shape_difference", 5)
                 transform_list.append(
                     EnsureSameShaped(
@@ -235,7 +234,6 @@ def get_all_case_stats(self, key="training", transform_list=None):
             warnings.warn("tqdm is not installed. not displaying the caching progress.")
 
         for batch_data in tqdm(dataloader) if has_tqdm else dataloader:
-
             batch_data = batch_data[0]
             batch_data[self.image_key] = batch_data[self.image_key].to(self.device)
 

monai/apps/auto3dseg/ensemble_builder.py

@@ -180,7 +180,6 @@ class AlgoEnsembleBestN(AlgoEnsemble):
     """
 
     def __init__(self, n_best: int = 5):
-
         super().__init__()
         self.n_best = n_best
 
@@ -225,7 +224,6 @@ class AlgoEnsembleBestByFold(AlgoEnsemble):
     """
 
     def __init__(self, n_fold: int = 5):
-
         super().__init__()
         self.n_fold = n_fold
 

monai/apps/auto3dseg/hpo_gen.py

@@ -197,7 +197,6 @@ def generate(self, output_folder: str = ".") -> None:
         if isinstance(self.algo, BundleAlgo):
             self.algo.export_to_disk(output_folder, task_prefix + task_id, fill_with_datastats=False)
         else:
-
             ConfigParser.export_config_file(self.params, write_path)
             logger.info(write_path)
 
@@ -376,7 +375,6 @@ def generate(self, output_folder: str = ".") -> None:
         if isinstance(self.algo, BundleAlgo):
             self.algo.export_to_disk(output_folder, task_prefix + task_id, fill_with_datastats=False)
         else:
-
             ConfigParser.export_config_file(self.params, write_path)
             logger.info(write_path)
 

monai/apps/deepedit/interaction.py

@@ -51,7 +51,6 @@ def __init__(
         click_probability_key: str = "probability",
         max_interactions: int = 1,
     ) -> None:
-
         self.deepgrow_probability = deepgrow_probability
         self.transforms = Compose(transforms) if not isinstance(transforms, Compose) else transforms
         self.train = train

monai/apps/deepedit/transforms.py

@@ -529,7 +529,6 @@ def find_guidance(self, discrepancy):
         return None
 
     def add_guidance(self, guidance, discrepancy, label_names, labels):
-
         # Positive clicks of the segment in the iteration
         pos_discr = discrepancy[0]  # idx 0 is positive discrepancy and idx 1 is negative discrepancy
 

monai/apps/deepgrow/interaction.py

@@ -46,7 +46,6 @@ def __init__(
         train: bool,
         key_probability: str = "probability",
     ) -> None:
-
         if not isinstance(transforms, Compose):
             transforms = Compose(transforms)