(chore): add more doc fixes

src/careamics/config/architectures/architecture_model.py

@@ -18,6 +18,11 @@ def model_dump(self, **kwargs: Any) -> Dict[str, Any]:
         """
         Dump the model as a dictionary, ignoring the architecture keyword.
 
+        Parameters
+        ----------
+        **kwargs : Any
+            Additional keyword arguments from Pydantic BaseModel model_dump method.
+
         Returns
         -------
         dict[str, Any]

src/careamics/config/architectures/custom_model.py

@@ -1,3 +1,5 @@
+"""Custom architecture Pydantic model."""
+
 from __future__ import annotations
 
 from pprint import pformat
@@ -84,6 +86,11 @@ def custom_model_is_known(cls, value: str) -> str:
         value : str
             Name of the custom model as registered using the `@register_model`
             decorator.
+
+        Returns
+        -------
+        str
+            The custom model name.
         """
         # delegate error to get_custom_model
         model = get_custom_model(value)
@@ -134,7 +141,7 @@ def model_dump(self, **kwargs: Any) -> Dict[str, Any]:
 
         Parameters
         ----------
-        kwargs : Any
+        **kwargs : Any
             Additional keyword arguments from Pydantic BaseModel model_dump method.
 
         Returns

src/careamics/config/architectures/register_model.py

@@ -1,3 +1,5 @@
+"""Custom model registration utilities."""
+
 from typing import Callable
 
 from torch.nn import Module
@@ -53,7 +55,7 @@ def add_custom_model(model: Module) -> Module:
         Parameters
         ----------
         model : Module
-            Module class to register
+            Module class to register.
 
         Returns
         -------

src/careamics/config/architectures/unet_model.py

@@ -1,3 +1,5 @@
+"""UNet Pydantic model."""
+
 from __future__ import annotations
 
 from typing import Literal

src/careamics/config/architectures/vae_model.py

@@ -1,3 +1,5 @@
+"""VAE Pydantic model."""
+
 from typing import Literal
 
 from pydantic import (

src/careamics/config/callback_model.py

@@ -1,4 +1,4 @@
-"""Checkpoint saving configuration."""
+"""Callback Pydantic models."""
 
 from __future__ import annotations
 
@@ -13,13 +13,7 @@
 
 
 class CheckpointModel(BaseModel):
-    """_summary_.
-
-    Parameters
-    ----------
-    BaseModel : _type_
-        _description_
-    """
+    """Checkpoint saving callback Pydantic model."""
 
     model_config = ConfigDict(
         validate_assignment=True,
@@ -46,13 +40,7 @@ class CheckpointModel(BaseModel):
 
 
 class EarlyStoppingModel(BaseModel):
-    """_summary_.
-
-    Parameters
-    ----------
-    BaseModel : _type_
-        _description_
-    """
+    """Early stopping callback Pydantic model."""
 
     model_config = ConfigDict(
         validate_assignment=True,

src/careamics/config/configuration_example.py

@@ -1,3 +1,5 @@
+"""Example of configurations."""
+
 from .algorithm_model import AlgorithmConfig
 from .architectures import UNetModel
 from .configuration_model import Configuration
@@ -19,7 +21,7 @@
 
 
 def full_configuration_example() -> Configuration:
-    """Returns a dictionnary representing a full configuration example.
+    """Return a dictionnary representing a full configuration example.
 
     Returns
     -------

src/careamics/config/optimizer_models.py

@@ -1,3 +1,5 @@
+"""Optimizers and schedulers Pydantic models."""
+
 from __future__ import annotations
 
 from typing import Dict, Literal
@@ -19,8 +21,7 @@
 
 
 class OptimizerModel(BaseModel):
-    """
-    Torch optimizer.
+    """Torch optimizer Pydantic model.
 
     Only parameters supported by the corresponding torch optimizer will be taken
     into account. For more details, check:
@@ -115,8 +116,7 @@ def sgd_lr_parameter(self) -> Self:
 
 
 class LrSchedulerModel(BaseModel):
-    """
-    Torch learning rate scheduler.
+    """Torch learning rate scheduler Pydantic model.
 
     Only parameters supported by the corresponding torch lr scheduler will be taken
     into account. For more details, check:

src/careamics/config/support/__init__.py

@@ -14,7 +14,6 @@
     "SupportedPixelManipulation",
     "SupportedTransform",
     "SupportedData",
-    "SupportedExtractionStrategy",
     "SupportedStructAxis",
     "SupportedLogger",
 ]
@@ -24,7 +23,6 @@
 from .supported_algorithms import SupportedAlgorithm
 from .supported_architectures import SupportedArchitecture
 from .supported_data import SupportedData
-from .supported_extraction_strategies import SupportedExtractionStrategy
 from .supported_loggers import SupportedLogger
 from .supported_losses import SupportedLoss
 from .supported_optimizers import SupportedOptimizer, SupportedScheduler

src/careamics/config/support/supported_activations.py

@@ -1,3 +1,5 @@
+"""Activations supported by CAREamics."""
+
 from careamics.utils import BaseEnum
 
 

src/careamics/config/support/supported_algorithms.py

@@ -1,3 +1,5 @@
+"""Algorithms supported by CAREamics."""
+
 from __future__ import annotations
 
 from careamics.utils import BaseEnum
@@ -10,9 +12,9 @@ class SupportedAlgorithm(str, BaseEnum):
     """
 
     N2V = "n2v"
-    CUSTOM = "custom"
     CARE = "care"
     N2N = "n2n"
+    CUSTOM = "custom"
     # PN2V = "pn2v"
     # HDN = "hdn"
     # SEG = "segmentation"

src/careamics/config/support/supported_architectures.py

@@ -1,3 +1,5 @@
+"""Architectures supported by CAREamics."""
+
 from careamics.utils import BaseEnum
 
 

src/careamics/config/support/supported_data.py

@@ -1,3 +1,5 @@
+"""Data supported by CAREamics."""
+
 from __future__ import annotations
 
 from typing import Union

src/careamics/config/support/supported_loggers.py

@@ -1,3 +1,5 @@
+"""Logger supported by CAREamics."""
+
 from careamics.utils import BaseEnum
 
 

src/careamics/config/support/supported_losses.py

@@ -1,3 +1,5 @@
+"""Losses supported by CAREamics."""
+
 from careamics.utils import BaseEnum
 
 

src/careamics/config/support/supported_optimizers.py

@@ -1,3 +1,5 @@
+"""Optimizers and schedulers supported by CAREamics."""
+
 from careamics.utils import BaseEnum
 
 

src/careamics/config/support/supported_pixel_manipulations.py

@@ -1,15 +1,15 @@
+"""Pixel manipulation methods supported by CAREamics."""
+
 from careamics.utils import BaseEnum
 
 
 class SupportedPixelManipulation(str, BaseEnum):
-    """_summary_.
+    """Supported Noise2Void pixel manipulations.
 
     - Uniform: Replace masked pixel value by a (uniformly) randomly selected neighbor
         pixel value.
     - Median: Replace masked pixel value by the mean of the neighborhood.
     """
 
-    # TODO docs
-
     UNIFORM = "uniform"
     MEDIAN = "median"

src/careamics/config/support/supported_struct_axis.py

@@ -1,3 +1,5 @@
+"""StructN2V axes supported by CAREamics."""
+
 from careamics.utils import BaseEnum
 
 

src/careamics/config/support/supported_transforms.py

@@ -1,23 +1,12 @@
+"""Transforms supported by CAREamics."""
+
 from careamics.utils import BaseEnum
 
 
 class SupportedTransform(str, BaseEnum):
-    """Transforms officially supported by CAREamics.
-
-    - Flip: from Albumentations, randomly flip the input horizontally, vertically or
-        both, parameter `p` can be used to set the probability to apply the transform.
-    - XYRandomRotate90: #TODO
-    - Normalize # TODO add details, in particular about the parameters
-    - ManipulateN2V # TODO add details, in particular about the parameters
-    - XYFlip
-
-    Note that while any Albumentations (see https://albumentations.ai/) transform can be
-    used in CAREamics, no check are implemented to verify the compatibility of any other
-    transforms than the ones officially supported.
-    """
+    """Transforms officially supported by CAREamics."""
 
     XY_FLIP = "XYFlip"
     XY_RANDOM_ROTATE90 = "XYRandomRotate90"
     NORMALIZE = "Normalize"
     N2V_MANIPULATE = "N2VManipulate"
-    # CUSTOM = "Custom"

src/careamics/config/tile_information.py

@@ -1,3 +1,5 @@
+"""Pydantic model representing the metadata of a prediction tile."""
+
 from __future__ import annotations
 
 from typing import Optional, Tuple

src/careamics/dataset/dataset_utils/dataset_utils.py

@@ -1,4 +1,4 @@
-"""Convenience methods for datasets."""
+"""Dataset utilities."""
 
 from typing import List, Tuple
 
@@ -17,12 +17,12 @@ def _get_shape_order(
 
     Parameters
     ----------
-    shape_in : Tuple
+    shape_in : Tuple[int, ...]
         Input shape.
-    ref_axes : str
-        Reference axes.
     axes_in : str
         Input axes.
+    ref_axes : str
+        Reference axes.
 
     Returns
     -------

src/careamics/dataset/dataset_utils/file_utils.py

@@ -1,3 +1,5 @@
+"""File utilities."""
+
 from fnmatch import fnmatch
 from pathlib import Path
 from typing import List, Union
@@ -11,8 +13,7 @@
 
 
 def get_files_size(files: List[Path]) -> float:
-    """
-    Get files size in MB.
+    """Get files size in MB.
 
     Parameters
     ----------
@@ -32,7 +33,7 @@ def list_files(
     data_type: Union[str, SupportedData],
     extension_filter: str = "",
 ) -> List[Path]:
-    """Creates a recursive list of files in `data_path`.
+    """Create a recursive list of files in `data_path`.
 
     If `data_path` is a file, its name is validated against the `data_type` using
     `fnmatch`, and the method returns `data_path` itself.

src/careamics/dataset/dataset_utils/read_tiff.py

@@ -1,3 +1,5 @@
+"""Funtions to read tiff images."""
+
 import logging
 from fnmatch import fnmatch
 from pathlib import Path
@@ -19,8 +21,6 @@ def read_tiff(file_path: Path, *args: list, **kwargs: dict) -> np.ndarray:
     ----------
     file_path : Path
         Path to a file.
-    axes : str
-        Description of axes in format STCZYX.
 
     Returns
     -------

src/careamics/dataset/dataset_utils/read_utils.py

@@ -1,3 +1,5 @@
+"""Read function utilities."""
+
 from typing import Callable, Union
 
 from careamics.config.support import SupportedData