[pre-commit.ci] pre-commit autoupdate (#1665)

* [pre-commit.ci] pre-commit autoupdate updates: - [github.com/psf/black: 23.12.1 → 24.3.0](psf/black@23.12.1...24.3.0) - [github.com/psf/black: 23.12.1 → 24.3.0](psf/black@23.12.1...24.3.0) - [github.com/PyCQA/flake8: 6.1.0 → 7.0.0](PyCQA/flake8@6.1.0...7.0.0) - [github.com/pre-commit/mirrors-mypy: v1.8.0 → v1.9.0](pre-commit/mirrors-mypy@v1.8.0...v1.9.0) - [github.com/asottile/pyupgrade: v3.15.0 → v3.15.2](asottile/pyupgrade@v3.15.0...v3.15.2) * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update requirements.txt Signed-off-by: SACHIDANAND ALLE <sachidanand.alle@gmail.com> * Update setup.cfg Signed-off-by: SACHIDANAND ALLE <sachidanand.alle@gmail.com> --------- Signed-off-by: SACHIDANAND ALLE <sachidanand.alle@gmail.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: SACHIDANAND ALLE <sachidanand.alle@gmail.com>
Project-MONAI · Apr 1, 2024 · ba98089 · ba98089
1 parent 6e43aa4
commit ba98089
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Showing 12 changed files with 57 additions and 47 deletions.
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -47,33 +47,33 @@ repos:
     args: ["--line-length=120", "--profile=black", "--check"]
 
 - repo: https://github.com/psf/black
-  rev: 23.12.1
+  rev: 24.3.0
   hooks:
   - id: black
     args: ["--line-length=120"]
 
 - repo: https://github.com/psf/black
-  rev: 23.12.1
+  rev: 24.3.0
   hooks:
   - id: black
     name: black (check)
     args: ["--line-length=120", "--check"]
 
 - repo: https://github.com/PyCQA/flake8
-  rev: 6.1.0
+  rev: 7.0.0
   hooks:
   - id: flake8
     args: ["--count", "--statistics", "--config=setup.cfg"]
 
 - repo: https://github.com/pre-commit/mirrors-mypy
-  rev: v1.8.0
+  rev: v1.9.0
   hooks:
   - id: mypy
     exclude: (^tests/|^plugins/)
     additional_dependencies: [types-PyYAML,types-filelock,types-requests,types-docutils,types-cachetools]
 
 - repo: https://github.com/asottile/pyupgrade
-  rev: v3.15.0
+  rev: v3.15.2
   hooks:
   -   id: pyupgrade
       args: [--py37-plus]
diff --git a/monailabel/endpoints/proxy.py b/monailabel/endpoints/proxy.py
@@ -50,11 +50,11 @@ async def proxy_dicom(request: Request, op: str, path: str):
     prefix = (
         settings.MONAI_LABEL_WADO_PREFIX
         if op == "wado"
-        else settings.MONAI_LABEL_QIDO_PREFIX
-        if op == "qido"
-        else settings.MONAI_LABEL_STOW_PREFIX
-        if op == "stow"
-        else ""
+        else (
+            settings.MONAI_LABEL_QIDO_PREFIX
+            if op == "qido"
+            else settings.MONAI_LABEL_STOW_PREFIX if op == "stow" else ""
+        )
     )
 
     # some version of ohif requests metadata using qido so change it to wado

diff --git a/monailabel/interfaces/utils/transform.py b/monailabel/interfaces/utils/transform.py
@@ -28,11 +28,11 @@ def dump_data(data, level=logging.DEBUG):
                 level,
                 "Data key: {} = {}".format(
                     k,
-                    v.shape
-                    if hasattr(v, "shape")
-                    else v
-                    if type(v) in (int, float, bool, str, dict, tuple, list)
-                    else type(v),
+                    (
+                        v.shape
+                        if hasattr(v, "shape")
+                        else v if type(v) in (int, float, bool, str, dict, tuple, list) else type(v)
+                    ),
                 ),
             )
         logger.log(level, "******************************************************************************")

diff --git a/monailabel/scribbles/transforms.py b/monailabel/scribbles/transforms.py
@@ -146,9 +146,9 @@ def __call__(self, data):
                 cz = int((selected_roi[4] + selected_roi[5]) / 2)
 
                 # add scribbles at center of roi
-                scribbles[
-                    :, cx - offset : cx + offset, cy - offset : cy + offset, cz - offset : cz + offset
-                ] = self.scribbles_fg_label
+                scribbles[:, cx - offset : cx + offset, cy - offset : cy + offset, cz - offset : cz + offset] = (
+                    self.scribbles_fg_label
+                )
 
         # return new scribbles
         d = self._save_data(d, self.scribbles, scribbles)

diff --git a/monailabel/tasks/infer/bundle.py b/monailabel/tasks/infer/bundle.py
@@ -278,15 +278,19 @@ def _get_type(self, name, type):
             (
                 InferType.DEEPEDIT
                 if "deepedit" in name
-                else InferType.DEEPGROW
-                if "deepgrow" in name
-                else InferType.DETECTION
-                if "detection" in name
-                else InferType.SEGMENTATION
-                if "segmentation" in name
-                else InferType.CLASSIFICATION
-                if "classification" in name
-                else InferType.SEGMENTATION
+                else (
+                    InferType.DEEPGROW
+                    if "deepgrow" in name
+                    else (
+                        InferType.DETECTION
+                        if "detection" in name
+                        else (
+                            InferType.SEGMENTATION
+                            if "segmentation" in name
+                            else InferType.CLASSIFICATION if "classification" in name else InferType.SEGMENTATION
+                        )
+                    )
+                )
             )
             if not type
             else type

diff --git a/monailabel/tasks/scoring/epistemic.py b/monailabel/tasks/scoring/epistemic.py
@@ -48,9 +48,7 @@ def infer_seg(self, data, model, roi_size, sw_batch_size):
         pre_transforms = (
             None
             if not self.transforms
-            else self.transforms
-            if isinstance(self.transforms, Compose)
-            else Compose(self.transforms)
+            else self.transforms if isinstance(self.transforms, Compose) else Compose(self.transforms)
         )
         # data = run_transforms(data, pre_transforms, log_prefix="EPISTEMIC-PRE") if pre_transforms else data
         if pre_transforms:

diff --git a/monailabel/tasks/train/basic_train.py b/monailabel/tasks/train/basic_train.py
@@ -235,11 +235,15 @@ def _dataset(self, context, datalist, is_train, replace_rate=0.25):
         dataset = (
             CacheDataset(datalist, transforms)
             if context.dataset_type == "CacheDataset"
-            else SmartCacheDataset(datalist, transforms, replace_rate)
-            if context.dataset_type == "SmartCacheDataset"
-            else PersistentDataset(datalist, transforms, cache_dir=os.path.join(context.cache_dir, "pds"))
-            if context.dataset_type == "PersistentDataset"
-            else Dataset(datalist, transforms)
+            else (
+                SmartCacheDataset(datalist, transforms, replace_rate)
+                if context.dataset_type == "SmartCacheDataset"
+                else (
+                    PersistentDataset(datalist, transforms, cache_dir=os.path.join(context.cache_dir, "pds"))
+                    if context.dataset_type == "PersistentDataset"
+                    else Dataset(datalist, transforms)
+                )
+            )
         )
         return dataset, datalist
 
@@ -681,9 +685,9 @@ def _create_trainer(self, context: Context):
                     save_final=True,
                     final_filename=self._final_filename,
                     save_key_metric=True,
-                    key_metric_filename=f"train_{self._key_metric_filename}"
-                    if context.evaluator
-                    else self._key_metric_filename,
+                    key_metric_filename=(
+                        f"train_{self._key_metric_filename}" if context.evaluator else self._key_metric_filename
+                    ),
                     n_saved=self._n_saved,
                 )
             )

diff --git a/monailabel/tasks/train/bundle.py b/monailabel/tasks/train/bundle.py
@@ -140,9 +140,11 @@ def config(self):
             "val_split": 0.2,  # VALIDATION SPLIT; -1 TO USE DEFAULT FROM BUNDLE
             "multi_gpu": True,  # USE MULTI-GPU
             "gpus": "all",  # COMMA SEPARATE DEVICE INDEX
-            "tracking": ["mlflow", "None"]
-            if self.enable_tracking and settings.MONAI_LABEL_TRACKING_ENABLED
-            else ["None", "mlflow"],
+            "tracking": (
+                ["mlflow", "None"]
+                if self.enable_tracking and settings.MONAI_LABEL_TRACKING_ENABLED
+                else ["None", "mlflow"]
+            ),
             "tracking_uri": settings.MONAI_LABEL_TRACKING_URI,
             "tracking_experiment_name": "",
             "run_id": "",  # bundle run id, if different from default

diff --git a/plugins/slicer/MONAILabelReviewer/MONAILabelReviewer.py b/plugins/slicer/MONAILabelReviewer/MONAILabelReviewer.py
@@ -1463,7 +1463,9 @@ def updateAfterEditingSegmentation(self):
 
         elif setToOverwrite:
             if (imageVersionTag == self.LABEL.FINAL) or (imageVersionTag == self.LABEL.ORIGINAL):
-                warningMessage: str = "Initial Segmentation with label 'final' or 'original' \ncannot be overwritten.\n Please save current edit as new version."
+                warningMessage: str = (
+                    "Initial Segmentation with label 'final' or 'original' \ncannot be overwritten.\n Please save current edit as new version."
+                )
                 slicer.util.warningDisplay(warningMessage)
                 logging.warn(warningMessage)
                 return

diff --git a/requirements.txt b/requirements.txt
@@ -17,7 +17,7 @@ fastapi==0.95.0
 python-multipart==0.0.6
 httpx==0.23.3
 schedule==1.1.0
-dicomweb-client==0.59.1
+dicomweb-client[gcp]==0.59.1
 timeloop==1.0.2
 expiringdict==1.2.2
 expiring_dict==1.1.0

diff --git a/setup.cfg b/setup.cfg
@@ -44,7 +44,7 @@ install_requires =
     requests-toolbelt==0.10.1
     httpx==0.23.3
     schedule==1.1.0
-    dicomweb-client==0.59.1
+    dicomweb-client[gcp]==0.59.1
     timeloop==1.0.2
     expiringdict==1.2.2
     expiring_dict==1.1.0

diff --git a/tests/unit/scribbles/test_transforms_infer.py b/tests/unit/scribbles/test_transforms_infer.py
@@ -273,9 +273,9 @@ def add_scribbles_from_roi(scribbles, roi, scribbles_fg_label, scribbles_bg_labe
         cz = int((roi[4] + roi[5]) / 2)
 
         # add scribbles at center of roi
-        scribbles[
-            :, cx - offset : cx + offset, cy - offset : cy + offset, cz - offset : cz + offset
-        ] = scribbles_fg_label
+        scribbles[:, cx - offset : cx + offset, cy - offset : cy + offset, cz - offset : cz + offset] = (
+            scribbles_fg_label
+        )
 
     return scribbles