9066 Consolidate Black/Isort Into Ruff

.pre-commit-config.yaml

@@ -34,13 +34,20 @@ repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
     rev: v0.16.10
     hooks:
-    -   id: ruff-check
+      - id: ruff-check
         args: ["--fix"]
         exclude: |
           (?x)(
               ^versioneer.py|
               ^monai/_version.py
           )
+      # - id: ruff-format
+      #   args: ["format"]
+      #   exclude: |
+      #     (?x)(
+      #         ^versioneer.py|
+      #         ^monai/_version.py
+      #     )
 
   - repo: https://github.com/psf/black-pre-commit-mirror
     rev: 26.10.0  # Black version, keep synced with MONAI requirements
@@ -54,16 +61,6 @@ repos:
               ^monai/_version.py
           )
 
-  - repo: https://github.com/pycqa/isort
-    rev: 9.0.2  # isort version, keep synced with MONAI requirements
-    hooks:
-      - id: isort
-        name: isort (python)
-        exclude: |
-          (?x)(
-              ^versioneer.py|
-              ^monai/_version.py
-          )
   - repo: local
     hooks:
       - id: dco

docs/source/conf.py

@@ -10,11 +10,11 @@
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 #
+import importlib
+import inspect
 import os
 import subprocess
 import sys
-import importlib
-import inspect
 
 sys.path.insert(0, os.path.abspath(".."))
 sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), "..", "..")))
@@ -59,7 +59,8 @@ def generate_apidocs(*args):
     """Generate API docs automatically by trawling the available modules"""
 
     import pandas as pd
-    from monai.bundle.properties import TrainProperties, InferProperties, MetaProperties
+
+    from monai.bundle.properties import InferProperties, MetaProperties, TrainProperties
 
     csv_file = os.path.join(os.path.dirname(__file__), "train_properties.csv")  # used in mb_properties.rst
     pd.DataFrame.from_dict(TrainProperties, orient="index").iloc[:, :3].to_csv(csv_file)

monai/apps/detection/networks/retinanet_detector.py

@@ -47,8 +47,8 @@
 from torch import Tensor, nn
 
 from monai.apps.detection.networks.retinanet_network import RetinaNet, resnet_fpn_feature_extractor
-from monai.apps.detection.utils.anchor_utils import AnchorGenerator
 from monai.apps.detection.utils.ATSS_matcher import ATSSMatcher
+from monai.apps.detection.utils.anchor_utils import AnchorGenerator
 from monai.apps.detection.utils.box_coder import BoxCoder
 from monai.apps.detection.utils.box_selector import BoxSelector
 from monai.apps.detection.utils.detector_utils import check_training_targets, preprocess_images

monai/apps/pathology/__init__.py

@@ -15,11 +15,11 @@
 from .metrics import LesionFROC
 from .transforms.stain.array import ExtractHEStains, NormalizeHEStains
 from .transforms.stain.dictionary import (
-    ExtractHEStainsd,
     ExtractHEStainsD,
     ExtractHEStainsDict,
-    NormalizeHEStainsd,
+    ExtractHEStainsd,
     NormalizeHEStainsD,
     NormalizeHEStainsDict,
+    NormalizeHEStainsd,
 )
 from .utils import PathologyProbNMS, compute_isolated_tumor_cells, compute_multi_instance_mask

monai/apps/pathology/transforms/__init__.py

@@ -26,45 +26,45 @@
 )
 from .post.dictionary import (
     GenerateDistanceMapD,
-    GenerateDistanceMapd,
     GenerateDistanceMapDict,
+    GenerateDistanceMapd,
     GenerateInstanceBorderD,
-    GenerateInstanceBorderd,
     GenerateInstanceBorderDict,
+    GenerateInstanceBorderd,
     GenerateInstanceCentroidD,
-    GenerateInstanceCentroidd,
     GenerateInstanceCentroidDict,
+    GenerateInstanceCentroidd,
     GenerateInstanceContourD,
-    GenerateInstanceContourd,
     GenerateInstanceContourDict,
+    GenerateInstanceContourd,
     GenerateInstanceTypeD,
-    GenerateInstanceTyped,
     GenerateInstanceTypeDict,
+    GenerateInstanceTyped,
     GenerateSuccinctContourD,
-    GenerateSuccinctContourd,
     GenerateSuccinctContourDict,
+    GenerateSuccinctContourd,
     GenerateWatershedMarkersD,
-    GenerateWatershedMarkersd,
     GenerateWatershedMarkersDict,
+    GenerateWatershedMarkersd,
     GenerateWatershedMaskD,
-    GenerateWatershedMaskd,
     GenerateWatershedMaskDict,
+    GenerateWatershedMaskd,
     HoVerNetInstanceMapPostProcessingD,
-    HoVerNetInstanceMapPostProcessingd,
     HoVerNetInstanceMapPostProcessingDict,
+    HoVerNetInstanceMapPostProcessingd,
     HoVerNetNuclearTypePostProcessingD,
-    HoVerNetNuclearTypePostProcessingd,
     HoVerNetNuclearTypePostProcessingDict,
+    HoVerNetNuclearTypePostProcessingd,
     WatershedD,
-    Watershedd,
     WatershedDict,
+    Watershedd,
 )
 from .stain.array import ExtractHEStains, NormalizeHEStains
 from .stain.dictionary import (
-    ExtractHEStainsd,
     ExtractHEStainsD,
     ExtractHEStainsDict,
-    NormalizeHEStainsd,
+    ExtractHEStainsd,
     NormalizeHEStainsD,
     NormalizeHEStainsDict,
+    NormalizeHEStainsd,
 )

monai/apps/pathology/transforms/post/__init__.py

@@ -26,36 +26,36 @@
 )
 from .dictionary import (
     GenerateDistanceMapD,
-    GenerateDistanceMapd,
     GenerateDistanceMapDict,
+    GenerateDistanceMapd,
     GenerateInstanceBorderD,
-    GenerateInstanceBorderd,
     GenerateInstanceBorderDict,
+    GenerateInstanceBorderd,
     GenerateInstanceCentroidD,
-    GenerateInstanceCentroidd,
     GenerateInstanceCentroidDict,
+    GenerateInstanceCentroidd,
     GenerateInstanceContourD,
-    GenerateInstanceContourd,
     GenerateInstanceContourDict,
+    GenerateInstanceContourd,
     GenerateInstanceTypeD,
-    GenerateInstanceTyped,
     GenerateInstanceTypeDict,
+    GenerateInstanceTyped,
     GenerateSuccinctContourD,
-    GenerateSuccinctContourd,
     GenerateSuccinctContourDict,
+    GenerateSuccinctContourd,
     GenerateWatershedMarkersD,
-    GenerateWatershedMarkersd,
     GenerateWatershedMarkersDict,
+    GenerateWatershedMarkersd,
     GenerateWatershedMaskD,
-    GenerateWatershedMaskd,
     GenerateWatershedMaskDict,
+    GenerateWatershedMaskd,
     HoVerNetInstanceMapPostProcessingD,
-    HoVerNetInstanceMapPostProcessingd,
     HoVerNetInstanceMapPostProcessingDict,
+    HoVerNetInstanceMapPostProcessingd,
     HoVerNetNuclearTypePostProcessingD,
-    HoVerNetNuclearTypePostProcessingd,
     HoVerNetNuclearTypePostProcessingDict,
+    HoVerNetNuclearTypePostProcessingd,
     WatershedD,
-    Watershedd,
     WatershedDict,
+    Watershedd,
 )

monai/apps/pathology/transforms/stain/__init__.py

@@ -13,10 +13,10 @@
 
 from .array import ExtractHEStains, NormalizeHEStains
 from .dictionary import (
-    ExtractHEStainsd,
     ExtractHEStainsD,
     ExtractHEStainsDict,
-    NormalizeHEStainsd,
+    ExtractHEStainsd,
     NormalizeHEStainsD,
     NormalizeHEStainsDict,
+    NormalizeHEStainsd,
 )

monai/data/__init__.py

@@ -28,9 +28,9 @@
 from .dataloader import DataLoader
 from .dataset import (
     ArrayDataset,
+    CSVDataset,
     CacheDataset,
     CacheNTransDataset,
-    CSVDataset,
     Dataset,
     DatasetFunc,
     GDSDataset,
@@ -51,8 +51,8 @@
 from .grid_dataset import GridPatchDataset, PatchDataset, PatchIter, PatchIterd
 from .image_dataset import ImageDataset
 from .image_reader import (
-    ImageReader,
     ITKReader,
+    ImageReader,
     NibabelReader,
     NrrdReader,
     NumpyReader,
@@ -62,8 +62,8 @@
 )
 from .image_writer import (
     SUPPORTED_WRITERS,
-    ImageWriter,
     ITKWriter,
+    ImageWriter,
     NibabelWriter,
     PILWriter,
     logger,

monai/data/image_reader.py

@@ -42,8 +42,8 @@
     import nibabel as nib
     import nrrd
     import pydicom
-    from nibabel.nifti1 import Nifti1Image
     from PIL import Image as PILImage
+    from nibabel.nifti1 import Nifti1Image
 
     has_nrrd = has_itk = has_nib = has_pil = has_pydicom = True
 else:

monai/handlers/classification_saver.py

@@ -19,9 +19,8 @@
 import torch
 
 from monai.data import CSVSaver, decollate_batch
-from monai.utils import IgniteInfo
+from monai.utils import IgniteInfo, evenly_divisible_all_gather, min_version, optional_import, string_list_all_gather
 from monai.utils import ImageMetaKey as Key
-from monai.utils import evenly_divisible_all_gather, min_version, optional_import, string_list_all_gather
 
 idist, _ = optional_import("ignite", IgniteInfo.OPT_IMPORT_VERSION, min_version, "distributed")
 Events, _ = optional_import("ignite.engine", IgniteInfo.OPT_IMPORT_VERSION, min_version, "Events")

monai/handlers/metrics_saver.py

@@ -16,9 +16,8 @@
 
 from monai.data import decollate_batch
 from monai.handlers.utils import write_metrics_reports
-from monai.utils import IgniteInfo
+from monai.utils import IgniteInfo, ensure_tuple, min_version, optional_import, string_list_all_gather
 from monai.utils import ImageMetaKey as Key
-from monai.utils import ensure_tuple, min_version, optional_import, string_list_all_gather
 
 Events, _ = optional_import("ignite.engine", IgniteInfo.OPT_IMPORT_VERSION, min_version, "Events")
 idist, _ = optional_import("ignite", IgniteInfo.OPT_IMPORT_VERSION, min_version, "distributed")

monai/losses/__init__.py

@@ -16,7 +16,7 @@
 from .barlow_twins import BarlowTwinsLoss
 from .boundary_loss import BoundaryLoss
 from .calibration import HardL1ACELoss, SoftL1ACELoss
-from .cldice import SoftclDiceLoss, SoftDiceclDiceLoss
+from .cldice import SoftDiceclDiceLoss, SoftclDiceLoss
 from .contrastive import ContrastiveLoss
 from .deform import BendingEnergyLoss, DiffusionLoss
 from .dice import (

monai/networks/blocks/__init__.py

@@ -21,7 +21,7 @@
 from .crossattention import CrossAttentionBlock
 from .denseblock import ConvDenseBlock, DenseBlock
 from .dints_block import ActiConvNormBlock, FactorizedIncreaseBlock, FactorizedReduceBlock, P3DActiConvNormBlock
-from .downsample import DownSample, Downsample, MaxAvgPool, SubpixelDownsample, SubpixelDownSample, Subpixeldownsample
+from .downsample import DownSample, Downsample, MaxAvgPool, SubpixelDownSample, SubpixelDownsample, Subpixeldownsample
 from .dynunet_block import UnetBasicBlock, UnetOutBlock, UnetResBlock, UnetUpBlock, get_output_padding, get_padding
 from .encoder import BaseEncoder
 from .fcn import FCN, GCN, MCFCN, Refine
@@ -47,10 +47,10 @@
     ResidualSELayer,
     SEBlock,
     SEBottleneck,
-    SEResNetBottleneck,
     SEResNeXtBottleneck,
+    SEResNetBottleneck,
 )
 from .transformerblock import TransformerBlock
 from .unetr_block import UnetrBasicBlock, UnetrPrUpBlock, UnetrUpBlock
-from .upsample import SubpixelUpsample, Subpixelupsample, SubpixelUpSample, Upsample, UpSample
+from .upsample import SubpixelUpSample, SubpixelUpsample, Subpixelupsample, UpSample, Upsample
 from .warp import DVF2DDF, Warp