Merge branch 'main' into fix_patching

.pre-commit-config.yaml

@@ -9,23 +9,23 @@ ci:
 
 repos:
   - repo: https://github.com/abravalheri/validate-pyproject
-    rev: v0.14
+    rev: v0.16
     hooks:
       - id: validate-pyproject
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.0.292
+    rev: v0.4.3
     hooks:
       - id: ruff
         args: [--fix, --target-version, py38]
 
   - repo: https://github.com/psf/black
-    rev: 23.9.1
+    rev: 24.4.2
     hooks:
       - id: black
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.5.1
+    rev: v1.10.0
     hooks:
       - id: mypy
         files: "^src/"
@@ -36,13 +36,13 @@ repos:
 
   # check docstrings
   - repo: https://github.com/numpy/numpydoc
-    rev: v1.6.0
+    rev: v1.7.0
     hooks:
       - id: numpydoc-validation
 
   # jupyter linting and formatting
   - repo: https://github.com/nbQA-dev/nbQA
-    rev: 1.7.0
+    rev: 1.8.5
     hooks:
       - id: nbqa-ruff
         args: [--fix]
@@ -51,6 +51,6 @@ repos:
 
   # strip out jupyter notebooks
   - repo: https://github.com/kynan/nbstripout
-    rev: 0.6.1
+    rev: 0.7.1
     hooks:
       - id: nbstripout

src/careamics/careamist.py

@@ -73,17 +73,15 @@ def __init__(  # numpydoc ignore=GL08
         source: Union[Path, str],
         work_dir: Optional[str] = None,
         experiment_name: str = "CAREamics",
-    ) -> None:
-        ...
+    ) -> None: ...
 
     @overload
     def __init__(  # numpydoc ignore=GL08
         self,
         source: Configuration,
         work_dir: Optional[str] = None,
         experiment_name: str = "CAREamics",
-    ) -> None:
-        ...
+    ) -> None: ...
 
     def __init__(
         self,
@@ -478,8 +476,7 @@ def predict(  # numpydoc ignore=GL08
         source: CAREamicsPredictData,
         *,
         checkpoint: Optional[Literal["best", "last"]] = None,
-    ) -> Union[list, np.ndarray]:
-        ...
+    ) -> Union[list, np.ndarray]: ...
 
     @overload
     def predict(  # numpydoc ignore=GL08
@@ -497,8 +494,7 @@ def predict(  # numpydoc ignore=GL08
         read_source_func: Optional[Callable] = None,
         extension_filter: str = "",
         checkpoint: Optional[Literal["best", "last"]] = None,
-    ) -> Union[list, np.ndarray]:
-        ...
+    ) -> Union[list, np.ndarray]: ...
 
     @overload
     def predict(  # numpydoc ignore=GL08
@@ -514,8 +510,7 @@ def predict(  # numpydoc ignore=GL08
         tta_transforms: bool = True,
         dataloader_params: Optional[Dict] = None,
         checkpoint: Optional[Literal["best", "last"]] = None,
-    ) -> Union[list, np.ndarray]:
-        ...
+    ) -> Union[list, np.ndarray]: ...
 
     def predict(
         self,

src/careamics/config/__init__.py

@@ -1,6 +1,5 @@
 """Configuration module."""
 
-
 __all__ = [
     "AlgorithmConfig",
     "DataConfig",

src/careamics/config/callback_model.py

@@ -1,4 +1,5 @@
 """Checkpoint saving configuration."""
+
 from __future__ import annotations
 
 from datetime import timedelta

src/careamics/config/configuration_factory.py

@@ -493,9 +493,11 @@ def create_n2v_configuration(
     # n2v2 and structn2v
     nv2_transform = {
         "name": SupportedTransform.N2V_MANIPULATE.value,
-        "strategy": SupportedPixelManipulation.MEDIAN.value
-        if use_n2v2
-        else SupportedPixelManipulation.UNIFORM.value,
+        "strategy": (
+            SupportedPixelManipulation.MEDIAN.value
+            if use_n2v2
+            else SupportedPixelManipulation.UNIFORM.value
+        ),
         "roi_size": roi_size,
         "masked_pixel_percentage": masked_pixel_percentage,
         "struct_mask_axis": struct_n2v_axis,

src/careamics/config/configuration_model.py

@@ -1,4 +1,5 @@
 """Pydantic CAREamics configuration."""
+
 from __future__ import annotations
 
 import re

src/careamics/config/data_model.py

@@ -1,4 +1,5 @@
 """Data configuration."""
+
 from __future__ import annotations
 
 from pprint import pformat

src/careamics/config/inference_model.py

@@ -1,4 +1,5 @@
 """Pydantic model representing CAREamics prediction configuration."""
+
 from __future__ import annotations
 
 from typing import Any, List, Literal, Optional, Union

src/careamics/config/references/algorithm_descriptions.py

@@ -1,4 +1,5 @@
 """Descriptions of the algorithms used in CAREmics."""
+
 from pydantic import BaseModel
 
 CUSTOM = "Custom"

src/careamics/config/references/references.py

@@ -1,4 +1,5 @@
 """References for the CAREamics algorithms."""
+
 from bioimageio.spec.generic.v0_3 import CiteEntry
 
 N2VRef = CiteEntry(

src/careamics/config/support/supported_extraction_strategies.py

@@ -3,6 +3,7 @@
 
 This module defines the various extraction strategies available in CAREamics.
 """
+
 from careamics.utils import BaseEnum
 
 

src/careamics/config/training_model.py

@@ -1,4 +1,5 @@
 """Training configuration."""
+
 from __future__ import annotations
 
 from pprint import pformat

src/careamics/config/transformations/n2v_manipulate_model.py

@@ -1,4 +1,5 @@
 """Pydantic model for the N2VManipulate transform."""
+
 from typing import Literal
 
 from pydantic import ConfigDict, Field, field_validator

src/careamics/config/transformations/nd_flip_model.py

@@ -1,4 +1,5 @@
 """Pydantic model for the NDFlip transform."""
+
 from typing import Literal
 
 from pydantic import ConfigDict, Field

src/careamics/config/transformations/normalize_model.py

@@ -1,4 +1,5 @@
 """Pydantic model for the Normalize transform."""
+
 from typing import Literal
 
 from pydantic import ConfigDict, Field

src/careamics/config/transformations/transform_model.py

@@ -1,4 +1,5 @@
 """Parent model for the transforms."""
+
 from typing import Any, Dict
 
 from pydantic import BaseModel, ConfigDict

src/careamics/config/transformations/xy_random_rotate90_model.py

@@ -1,4 +1,5 @@
 """Pydantic model for the XYRandomRotate90 transform."""
+
 from typing import Literal
 
 from pydantic import ConfigDict, Field

src/careamics/config/validators/validator_utils.py

@@ -3,6 +3,7 @@
 
 These functions are used to validate dimensions and axes of inputs.
 """
+
 from typing import List, Optional, Tuple, Union
 
 _AXES = "STCZYX"

src/careamics/conftest.py

@@ -2,6 +2,7 @@
 
 See https://sybil.readthedocs.io/en/latest/use.html#pytest
 """
+
 from pathlib import Path
 
 import pytest

src/careamics/dataset/dataset_utils/__init__.py

@@ -1,6 +1,5 @@
 """Files and arrays utils used in the datasets."""
 
-
 __all__ = [
     "reshape_array",
     "get_files_size",

src/careamics/dataset/dataset_utils/dataset_utils.py

@@ -1,4 +1,5 @@
 """Convenience methods for datasets."""
+
 from typing import List, Tuple
 
 import numpy as np

src/careamics/dataset/in_memory_dataset.py

@@ -1,4 +1,5 @@
 """In-memory dataset module."""
+
 from __future__ import annotations
 
 import copy

src/careamics/dataset/patching/__init__.py

@@ -1,6 +1,5 @@
 """Patching and tiling functions."""
 
-
 __all__ = [
     "get_patch_transform",
 ]

src/careamics/dataset/patching/patch_transform.py

@@ -38,7 +38,9 @@ def get_patch_transform(
         return Aug.Compose(
             transforms,
             # apply image aug to "target"
-            additional_targets={"target": "image"}
-            if (with_target and normalize_mask)  # TODO check this
-            else {},
+            additional_targets=(
+                {"target": "image"}
+                if (with_target and normalize_mask)  # TODO check this
+                else {}
+            ),
         )

src/careamics/dataset/patching/patching.py

@@ -3,6 +3,7 @@
 
 These functions are used to tile images into patches or tiles.
 """
+
 from pathlib import Path
 from typing import Callable, List, Tuple, Union
 

src/careamics/dataset/patching/tiled_patching.py

@@ -43,19 +43,23 @@ def _compute_crop_and_stitch_coords_1d(
             stitch_coords.append(
                 (
                     i + overlap // 2 if i > 0 else 0,
-                    i + tile_size - overlap // 2
-                    if crop_coords[-1][1] < axis_size
-                    else axis_size,
+                    (
+                        i + tile_size - overlap // 2
+                        if crop_coords[-1][1] < axis_size
+                        else axis_size
+                    ),
                 )
             )
 
             # Add the coordinates to crop the overlap from the prediction.
             overlap_crop_coords.append(
                 (
                     overlap // 2 if i > 0 else 0,
-                    tile_size - overlap // 2
-                    if crop_coords[-1][1] < axis_size
-                    else tile_size,
+                    (
+                        tile_size - overlap // 2
+                        if crop_coords[-1][1] < axis_size
+                        else tile_size
+                    ),
                 )
             )
 

src/careamics/lightning_datamodule.py

@@ -1,4 +1,5 @@
 """Training and validation Lightning data modules."""
+
 from pathlib import Path
 from typing import Any, Callable, Dict, List, Literal, Optional, Union
 
@@ -341,9 +342,9 @@ def setup(self, *args: Any, **kwargs: Any) -> None:
                 self.train_dataset = InMemoryDataset(
                     data_config=self.data_config,
                     inputs=self.train_files,
-                    data_target=self.train_target_files
-                    if self.train_data_target
-                    else None,
+                    data_target=(
+                        self.train_target_files if self.train_data_target else None
+                    ),
                     read_source_func=self.read_source_func,
                 )
 
@@ -352,9 +353,9 @@ def setup(self, *args: Any, **kwargs: Any) -> None:
                     self.val_dataset = InMemoryDataset(
                         data_config=self.data_config,
                         inputs=self.val_files,
-                        data_target=self.val_target_files
-                        if self.val_data_target
-                        else None,
+                        data_target=(
+                            self.val_target_files if self.val_data_target else None
+                        ),
                         read_source_func=self.read_source_func,
                     )
                 else:
@@ -370,9 +371,9 @@ def setup(self, *args: Any, **kwargs: Any) -> None:
                 self.train_dataset = PathIterableDataset(
                     data_config=self.data_config,
                     src_files=self.train_files,
-                    target_files=self.train_target_files
-                    if self.train_data_target
-                    else None,
+                    target_files=(
+                        self.train_target_files if self.train_data_target else None
+                    ),
                     read_source_func=self.read_source_func,
                 )
 
@@ -382,9 +383,9 @@ def setup(self, *args: Any, **kwargs: Any) -> None:
                     self.val_dataset = PathIterableDataset(
                         data_config=self.data_config,
                         src_files=self.val_files,
-                        target_files=self.val_target_files
-                        if self.val_data_target
-                        else None,
+                        target_files=(
+                            self.val_target_files if self.val_data_target else None
+                        ),
                         read_source_func=self.read_source_func,
                     )
                 elif len(self.train_files) <= self.val_minimum_split:

src/careamics/lightning_prediction_datamodule.py

@@ -1,4 +1,5 @@
 """Prediction Lightning data modules."""
+
 from pathlib import Path
 from typing import Any, Callable, List, Literal, Optional, Tuple, Union
 

src/careamics/losses/__init__.py

@@ -1,6 +1,5 @@
 """Losses module."""
 
-
 from .loss_factory import loss_factory
 
 # from .noise_model_factory import noise_model_factory as noise_model_factory

src/careamics/losses/loss_factory.py

@@ -3,6 +3,7 @@
 
 This module contains a factory function for creating loss functions.
 """
+
 from typing import Callable, Union
 
 from ..config.support import SupportedLoss

src/careamics/model_io/__init__.py

@@ -1,6 +1,5 @@
 """Model I/O utilities."""
 
-
 __all__ = ["load_pretrained", "export_to_bmz"]
 
 

src/careamics/model_io/bioimage/_readme_factory.py

@@ -1,4 +1,5 @@
 """Functions used to create a README.md file for BMZ export."""
+
 from pathlib import Path
 from typing import Optional
 

src/careamics/model_io/bioimage/bioimage_utils.py

@@ -1,4 +1,5 @@
 """Bioimage.io utils."""
+
 from pathlib import Path
 from typing import Union