ci(pre-commit.ci): autoupdate (#286)

updates: - [github.com/abravalheri/validate-pyproject: v0.22 → v0.23](abravalheri/validate-pyproject@v0.22...v0.23) - [github.com/astral-sh/ruff-pre-commit: v0.7.2 → v0.8.1](astral-sh/ruff-pre-commit@v0.7.2...v0.8.1) - [github.com/kynan/nbstripout: 0.8.0 → 0.8.1](kynan/nbstripout@0.8.0...0.8.1)  --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Joran Deschamps <6367888+jdeschamps@users.noreply.github.com>
CAREamics · Dec 17, 2024 · 04bda28 · 04bda28
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diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -9,12 +9,12 @@ ci:
 
 repos:
   - repo: https://github.com/abravalheri/validate-pyproject
-    rev: v0.22
+    rev: v0.23
     hooks:
       - id: validate-pyproject
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.7.2
+    rev: v0.8.1
     hooks:
       - id: ruff
         exclude: "^src/careamics/lvae_training/.*|^src/careamics/models/lvae/.*|^scripts/.*"
@@ -55,6 +55,6 @@ repos:
 
   # strip out jupyter notebooks
   - repo: https://github.com/kynan/nbstripout
-    rev: 0.8.0
+    rev: 0.8.1
     hooks:
       - id: nbstripout
diff --git a/src/careamics/config/__init__.py b/src/careamics/config/__init__.py
@@ -1,24 +1,24 @@
 """Configuration module."""
 
 __all__ = [
-    "FCNAlgorithmConfig",
-    "VAEAlgorithmConfig",
-    "DataConfig",
-    "Configuration",
     "CheckpointModel",
+    "Configuration",
+    "CustomModel",
+    "DataConfig",
+    "FCNAlgorithmConfig",
+    "GaussianMixtureNMConfig",
     "InferenceConfig",
-    "load_configuration",
-    "save_configuration",
+    "LVAELossConfig",
+    "MultiChannelNMConfig",
     "TrainingConfig",
-    "create_n2v_configuration",
-    "create_n2n_configuration",
+    "VAEAlgorithmConfig",
+    "clear_custom_models",
     "create_care_configuration",
+    "create_n2n_configuration",
+    "create_n2v_configuration",
+    "load_configuration",
     "register_model",
-    "CustomModel",
-    "clear_custom_models",
-    "GaussianMixtureNMConfig",
-    "MultiChannelNMConfig",
-    "LVAELossConfig",
+    "save_configuration",
 ]
 from .architectures import CustomModel, clear_custom_models, register_model
 from .callback_model import CheckpointModel

diff --git a/src/careamics/config/architectures/__init__.py b/src/careamics/config/architectures/__init__.py
@@ -3,8 +3,8 @@
 __all__ = [
     "ArchitectureModel",
     "CustomModel",
-    "UNetModel",
     "LVAEModel",
+    "UNetModel",
     "clear_custom_models",
     "get_custom_model",
     "register_model",

diff --git a/src/careamics/config/references/__init__.py b/src/careamics/config/references/__init__.py
@@ -1,24 +1,24 @@
 """Module containing references to the algorithm used in CAREamics."""
 
 __all__ = [
-    "N2V2Ref",
-    "N2VRef",
-    "StructN2VRef",
-    "N2VDescription",
-    "N2V2Description",
-    "StructN2VDescription",
-    "StructN2V2Description",
+    "CARE",
+    "CUSTOM",
+    "N2N",
     "N2V",
     "N2V2",
     "STRUCT_N2V",
     "STRUCT_N2V2",
-    "CUSTOM",
-    "N2N",
-    "CARE",
     "CAREDescription",
-    "N2NDescription",
     "CARERef",
+    "N2NDescription",
     "N2NRef",
+    "N2V2Description",
+    "N2V2Ref",
+    "N2VDescription",
+    "N2VRef",
+    "StructN2V2Description",
+    "StructN2VDescription",
+    "StructN2VRef",
 ]
 
 from .algorithm_descriptions import (

diff --git a/src/careamics/config/support/__init__.py b/src/careamics/config/support/__init__.py
@@ -5,17 +5,17 @@
 """
 
 __all__ = [
-    "SupportedArchitecture",
     "SupportedActivation",
-    "SupportedOptimizer",
-    "SupportedScheduler",
-    "SupportedLoss",
     "SupportedAlgorithm",
-    "SupportedPixelManipulation",
-    "SupportedTransform",
+    "SupportedArchitecture",
     "SupportedData",
-    "SupportedStructAxis",
     "SupportedLogger",
+    "SupportedLoss",
+    "SupportedOptimizer",
+    "SupportedPixelManipulation",
+    "SupportedScheduler",
+    "SupportedStructAxis",
+    "SupportedTransform",
 ]
 
 

diff --git a/src/careamics/config/transformations/__init__.py b/src/careamics/config/transformations/__init__.py
@@ -1,12 +1,12 @@
 """CAREamics transformation Pydantic models."""
 
 __all__ = [
+    "TRANSFORMS_UNION",
     "N2VManipulateModel",
-    "XYFlipModel",
     "NormalizeModel",
-    "XYRandomRotate90Model",
     "TransformModel",
-    "TRANSFORMS_UNION",
+    "XYFlipModel",
+    "XYRandomRotate90Model",
 ]
 
 

diff --git a/src/careamics/dataset/__init__.py b/src/careamics/dataset/__init__.py
@@ -4,9 +4,9 @@
     "InMemoryDataset",
     "InMemoryPredDataset",
     "InMemoryTiledPredDataset",
-    "PathIterableDataset",
-    "IterableTiledPredDataset",
     "IterablePredDataset",
+    "IterableTiledPredDataset",
+    "PathIterableDataset",
 ]
 
 from .in_memory_dataset import InMemoryDataset

diff --git a/src/careamics/dataset/dataset_utils/__init__.py b/src/careamics/dataset/dataset_utils/__init__.py
@@ -1,13 +1,13 @@
 """Files and arrays utils used in the datasets."""
 
 __all__ = [
-    "reshape_array",
+    "WelfordStatistics",
     "compute_normalization_stats",
     "get_files_size",
+    "iterate_over_files",
     "list_files",
+    "reshape_array",
     "validate_source_target_files",
-    "iterate_over_files",
-    "WelfordStatistics",
 ]
 
 

diff --git a/src/careamics/dataset/tiling/__init__.py b/src/careamics/dataset/tiling/__init__.py
@@ -1,9 +1,9 @@
 """Tiling functions."""
 
 __all__ = [
-    "stitch_prediction",
-    "extract_tiles",
     "collate_tiles",
+    "extract_tiles",
+    "stitch_prediction",
 ]
 
 from .collate_tiles import collate_tiles

diff --git a/src/careamics/file_io/__init__.py b/src/careamics/file_io/__init__.py
@@ -1,13 +1,13 @@
 """Functions relating reading and writing image files."""
 
 __all__ = [
-    "read",
-    "write",
-    "get_read_func",
-    "get_write_func",
     "ReadFunc",
-    "WriteFunc",
     "SupportedWriteType",
+    "WriteFunc",
+    "get_read_func",
+    "get_write_func",
+    "read",
+    "write",
 ]
 
 from . import read, write

diff --git a/src/careamics/file_io/read/__init__.py b/src/careamics/file_io/read/__init__.py
@@ -1,10 +1,10 @@
 """Functions relating to reading image files of different formats."""
 
 __all__ = [
+    "ReadFunc",
     "get_read_func",
     "read_tiff",
     "read_zarr",
-    "ReadFunc",
 ]
 
 from .get_func import ReadFunc, get_read_func

diff --git a/src/careamics/file_io/write/__init__.py b/src/careamics/file_io/write/__init__.py
@@ -1,10 +1,10 @@
 """Functions relating to writing image files of different formats."""
 
 __all__ = [
+    "SupportedWriteType",
+    "WriteFunc",
     "get_write_func",
     "write_tiff",
-    "WriteFunc",
-    "SupportedWriteType",
 ]
 
 from .get_func import (

diff --git a/src/careamics/lightning/__init__.py b/src/careamics/lightning/__init__.py
@@ -2,14 +2,14 @@
 
 __all__ = [
     "FCNModule",
+    "HyperParametersCallback",
+    "PredictDataModule",
+    "ProgressBarCallback",
+    "TrainDataModule",
     "VAEModule",
     "create_careamics_module",
-    "TrainDataModule",
-    "create_train_datamodule",
-    "PredictDataModule",
     "create_predict_datamodule",
-    "HyperParametersCallback",
-    "ProgressBarCallback",
+    "create_train_datamodule",
 ]
 
 from .callbacks import HyperParametersCallback, ProgressBarCallback

diff --git a/src/careamics/lightning/callbacks/__init__.py b/src/careamics/lightning/callbacks/__init__.py
@@ -2,8 +2,8 @@
 
 __all__ = [
     "HyperParametersCallback",
-    "ProgressBarCallback",
     "PredictionWriterCallback",
+    "ProgressBarCallback",
 ]
 
 from .hyperparameters_callback import HyperParametersCallback

diff --git a/src/careamics/lightning/callbacks/prediction_writer_callback/__init__.py b/src/careamics/lightning/callbacks/prediction_writer_callback/__init__.py
@@ -1,12 +1,12 @@
 """A package for the `PredictionWriterCallback` class and utilities."""
 
 __all__ = [
+    "CacheTiles",
     "PredictionWriterCallback",
-    "create_write_strategy",
-    "WriteStrategy",
     "WriteImage",
-    "CacheTiles",
+    "WriteStrategy",
     "WriteTilesZarr",
+    "create_write_strategy",
     "select_write_extension",
     "select_write_func",
 ]

diff --git a/src/careamics/losses/__init__.py b/src/careamics/losses/__init__.py
@@ -1,13 +1,13 @@
 """Losses module."""
 
 __all__ = [
+    "denoisplit_loss",
+    "denoisplit_musplit_loss",
     "loss_factory",
     "mae_loss",
     "mse_loss",
-    "n2v_loss",
-    "denoisplit_loss",
     "musplit_loss",
-    "denoisplit_musplit_loss",
+    "n2v_loss",
 ]
 
 from .fcn.losses import mae_loss, mse_loss, n2v_loss

diff --git a/src/careamics/model_io/__init__.py b/src/careamics/model_io/__init__.py
@@ -1,6 +1,6 @@
 """Model I/O utilities."""
 
-__all__ = ["load_pretrained", "export_to_bmz"]
+__all__ = ["export_to_bmz", "load_pretrained"]
 
 
 from .bmz_io import export_to_bmz

diff --git a/src/careamics/model_io/bioimage/__init__.py b/src/careamics/model_io/bioimage/__init__.py
@@ -1,10 +1,10 @@
 """Bioimage Model Zoo format functions."""
 
 __all__ = [
+    "create_env_text",
     "create_model_description",
     "extract_model_path",
     "get_unzip_path",
-    "create_env_text",
 ]
 
 from .bioimage_utils import create_env_text, get_unzip_path

diff --git a/src/careamics/prediction_utils/__init__.py b/src/careamics/prediction_utils/__init__.py
@@ -1,9 +1,9 @@
 """Package to house various prediction utilies."""
 
 __all__ = [
+    "convert_outputs",
     "stitch_prediction",
     "stitch_prediction_single",
-    "convert_outputs",
 ]
 
 from .prediction_outputs import convert_outputs

diff --git a/src/careamics/transforms/__init__.py b/src/careamics/transforms/__init__.py
@@ -1,14 +1,14 @@
 """Transforms that are used to augment the data."""
 
 __all__ = [
-    "get_all_transforms",
+    "Compose",
+    "Denormalize",
+    "ImageRestorationTTA",
     "N2VManipulate",
+    "Normalize",
     "XYFlip",
     "XYRandomRotate90",
-    "ImageRestorationTTA",
-    "Denormalize",
-    "Normalize",
-    "Compose",
+    "get_all_transforms",
 ]
 
 

diff --git a/src/careamics/utils/__init__.py b/src/careamics/utils/__init__.py
@@ -1,13 +1,13 @@
 """Utils module."""
 
 __all__ = [
-    "cwd",
-    "get_ram_size",
-    "check_path_exists",
     "BaseEnum",
-    "get_logger",
-    "get_careamics_home",
     "autocorrelation",
+    "check_path_exists",
+    "cwd",
+    "get_careamics_home",
+    "get_logger",
+    "get_ram_size",
 ]