careamics 0.0.14__tar.gz → 0.0.16__tar.gz

{careamics-0.0.14 → careamics-0.0.16}/.github/workflows/ci.yml

@@ -27,9 +27,9 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.10", "3.11", "3.12"]
+        python-version: ["3.11", "3.12", "3.13"]
         # https://docs.github.com/en/actions/using-github-hosted-runners/about-github-hosted-runners/about-github-hosted-runners#standard-github-hosted-runners-for-public-repositories
-        platform: [ubuntu-latest, windows-latest] # macos-latest
+        platform: [ubuntu-latest, windows-latest] # macos-latest  
 
     steps:
       - name: 🛑 Cancel Previous Runs

{careamics-0.0.14 → careamics-0.0.16}/.github/workflows/ci_macos.yml

@@ -22,7 +22,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.10", "3.11", "3.12"]
+        python-version: ["3.11", "3.12", "3.13"]
         # https://docs.github.com/en/actions/using-github-hosted-runners/about-github-hosted-runners/about-github-hosted-runners#standard-github-hosted-runners-for-public-repositories
         platform: [macos-latest]
 

{careamics-0.0.14 → careamics-0.0.16}/.github/workflows/codecov.yml

@@ -2,17 +2,14 @@ name: codecov
 
 on:
   push:
-    branches:
-      - main
     tags:
       - "v*"
-  pull_request:
-  workflow_dispatch:
 
 jobs:
-  test:
+  codecov:
     name: ${{ matrix.platform }} (${{ matrix.python-version }})
     runs-on: ${{ matrix.platform }}
+    if: startsWith(github.ref, 'refs/tags/') && github.event_name != 'schedule'
     strategy:
       fail-fast: false
       matrix:
@@ -38,7 +35,7 @@ jobs:
         run: |
           python -m pip install -U pip
           # if running a cron job, we add the --pre flag to test against pre-releases
-          python -m pip install .[dev] ${{ github.event_name == 'schedule' && '--pre' || ''  }}
+          python -m pip install .[dev,czi] ${{ github.event_name == 'schedule' && '--pre' || ''  }}
 
       - name: 🧪 Run Tests
         run: pytest --color=yes --cov --cov-config=pyproject.toml --cov-report=xml --cov-report=term-missing 

{careamics-0.0.14 → careamics-0.0.16}/.pre-commit-config.yaml

@@ -14,11 +14,11 @@ repos:
       - id: validate-pyproject
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.11.12
+    rev: v0.12.11
     hooks:
       - id: ruff
         exclude: "^src/careamics/lvae_training/.*|^src/careamics/models/lvae/.*|^scripts/.*"
-        args: [--fix, --target-version, py310]
+        args: [--fix, --target-version, py311]
 
   - repo: https://github.com/psf/black
     rev: 25.1.0
@@ -26,21 +26,21 @@ repos:
       - id: black
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.16.0
+    rev: v1.17.1
     hooks:
       - id: mypy
         files: "^src/"
         exclude: "^src/careamics/lvae_training/.*|^src/careamics/models/lvae/.*|^src/careamics/config/likelihood_model.py|^src/careamics/losses/loss_factory.py|^src/careamics/losses/lvae/losses.py"
         args: ["--config-file", "mypy.ini"]
         additional_dependencies:
-          - numpy<2.0.0
+          - numpy
           - pydantic
           - types-PyYAML
           - types-setuptools
 
   # check docstrings
   - repo: https://github.com/numpy/numpydoc
-    rev: v1.8.0
+    rev: v1.9.0
     hooks:
       - id: numpydoc-validation
         exclude: "^src/careamics/dataset_ng/.*|^src/careamics/lvae_training/.*|^src/careamics/models/lvae/.*|^src/careamics/losses/lvae/.*|^src/careamics/lightning/dataset_ng/data_module.py|^scripts/.*"

{careamics-0.0.14 → careamics-0.0.16}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: careamics
-Version: 0.0.14
+Version: 0.0.16
 Summary: Toolbox for running N2V and friends.
 Project-URL: homepage, https://careamics.github.io/
 Project-URL: repository, https://github.com/CAREamics/careamics
@@ -10,29 +10,31 @@ License-File: LICENSE
 Classifier: Development Status :: 3 - Alpha
 Classifier: License :: OSI Approved :: BSD License
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
 Classifier: Typing :: Typed
-Requires-Python: >=3.10
-Requires-Dist: bioimageio-core==0.7
-Requires-Dist: matplotlib<=3.10.3
-Requires-Dist: numpy<2.0.0
-Requires-Dist: pillow<=11.2.1
-Requires-Dist: psutil<=7.0.0
+Requires-Python: >=3.11
+Requires-Dist: bioimageio-core>=0.9.0
+Requires-Dist: matplotlib<=3.10.6
+Requires-Dist: numpy>=1.21
+Requires-Dist: numpy>=2.1.0; python_version >= '3.13'
+Requires-Dist: pillow<=11.3.0
+Requires-Dist: psutil<=7.1.0
 Requires-Dist: pydantic<=2.12,>=2.11
-Requires-Dist: pytorch-lightning<=2.5.2,>=2.2
-Requires-Dist: pyyaml!=6.0.0,<=6.0.2
+Requires-Dist: pytorch-lightning<=2.5.5,>=2.2
+Requires-Dist: pyyaml!=6.0.0,<=6.0.3
 Requires-Dist: scikit-image<=0.25.2
-Requires-Dist: tifffile<=2025.5.10
-Requires-Dist: torch<=2.7.1,>=2.0
-Requires-Dist: torchvision<=0.22.1
-Requires-Dist: typer<=0.16.0,>=0.12.3
-Requires-Dist: xarray<2025.3.0
-Requires-Dist: zarr<3.0.0
+Requires-Dist: tifffile<=2025.9.30
+Requires-Dist: torch<=2.8.0,>=2.0
+Requires-Dist: torchvision<=0.23.0
+Requires-Dist: typer<=0.19.2,>=0.12.3
+Requires-Dist: validators<=0.35.0
+Requires-Dist: zarr<4.0.0,>=3.0.0
 Provides-Extra: czi
 Requires-Dist: pylibczirw<6.0.0,>=4.1.2; extra == 'czi'
 Provides-Extra: dev
+Requires-Dist: ml-dtypes>=0.5.0; extra == 'dev'
 Requires-Dist: onnx; extra == 'dev'
 Requires-Dist: pre-commit; extra == 'dev'
 Requires-Dist: pytest; extra == 'dev'

{careamics-0.0.14 → careamics-0.0.16}/pyproject.toml

@@ -20,7 +20,7 @@ name = "careamics"
 dynamic = ["version"]
 description = "Toolbox for running N2V and friends."
 readme = "README.md"
-requires-python = ">=3.10"
+requires-python = ">=3.11"
 license = { text = "BSD-3-Clause" }
 authors = [
     { name = 'CAREamics team', email = 'rse@fht.org' },
@@ -34,28 +34,29 @@ authors = [
 classifiers = [
     "Development Status :: 3 - Alpha",
     "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
     "License :: OSI Approved :: BSD License",
     "Typing :: Typed",
 ]
 dependencies = [
-    'numpy<2.0.0',
-    'torch>=2.0,<=2.7.1',
-    'torchvision<=0.22.1',
-    'bioimageio.core==0.7',
-    'tifffile<=2025.5.10',
-    'psutil<=7.0.0',
+    "numpy>=1.21",
+    "numpy>=2.1.0; python_version>='3.13'", # prevents ml_dtypes conflict in py313
+    'torch>=2.0,<=2.8.0',
+    'torchvision<=0.23.0',
+    'bioimageio.core>=0.9.0',
+    'tifffile<=2025.9.30',
+    'psutil<=7.1.0',
     'pydantic>=2.11,<=2.12',
-    'pytorch_lightning>=2.2,<=2.5.2',
-    'pyyaml<=6.0.2,!=6.0.0',
-    'typer>=0.12.3,<=0.16.0',
+    'pytorch_lightning>=2.2,<=2.5.5',
+    'pyyaml!=6.0.0,<=6.0.3',
+    'typer>=0.12.3,<=0.19.2',
     'scikit-image<=0.25.2',
-    'zarr<3.0.0',
-    'pillow<=11.2.1',
-    'matplotlib<=3.10.3',
-    'xarray<2025.3.0',
+    'zarr>=3.0.0,<4.0.0',
+    'pillow<=11.3.0',
+    'matplotlib<=3.10.6',
+    'validators<=0.35.0'
 ]
 
 [project.optional-dependencies]
@@ -68,8 +69,11 @@ dev = [
     "pre-commit",
     "pytest",
     "pytest-cov",
-    "onnx",
     "sybil",      # doctesting
+
+    # libraries used in some tests
+    "onnx",
+    "ml_dtypes>=0.5.0" # required by onnx, causes issues in gh runners with py313
 ]
 
 # notebooks

{careamics-0.0.14 → careamics-0.0.16}/src/careamics/careamist.py

@@ -2,7 +2,7 @@
 
 from collections.abc import Callable
 from pathlib import Path
-from typing import Any, Literal, Optional, Union, overload
+from typing import Any, Literal, Union, overload
 
 import numpy as np
 from numpy.typing import NDArray
@@ -79,8 +79,8 @@ class CAREamist:
     def __init__(  # numpydoc ignore=GL08
         self,
         source: Union[Path, str],
-        work_dir: Optional[Union[Path, str]] = None,
-        callbacks: Optional[list[Callback]] = None,
+        work_dir: Union[Path, str] | None = None,
+        callbacks: list[Callback] | None = None,
         enable_progress_bar: bool = True,
     ) -> None: ...
 
@@ -88,16 +88,16 @@ class CAREamist:
     def __init__(  # numpydoc ignore=GL08
         self,
         source: Configuration,
-        work_dir: Optional[Union[Path, str]] = None,
-        callbacks: Optional[list[Callback]] = None,
+        work_dir: Union[Path, str] | None = None,
+        callbacks: list[Callback] | None = None,
         enable_progress_bar: bool = True,
     ) -> None: ...
 
     def __init__(
         self,
         source: Union[Path, str, Configuration],
-        work_dir: Optional[Union[Path, str]] = None,
-        callbacks: Optional[list[Callback]] = None,
+        work_dir: Union[Path, str] | None = None,
+        callbacks: list[Callback] | None = None,
         enable_progress_bar: bool = True,
     ) -> None:
         """
@@ -208,25 +208,19 @@ class CAREamist:
 
         # instantiate trainer
         self.trainer = Trainer(
-            max_epochs=self.cfg.training_config.num_epochs,
-            precision=self.cfg.training_config.precision,
-            max_steps=self.cfg.training_config.max_steps,
-            check_val_every_n_epoch=self.cfg.training_config.check_val_every_n_epoch,
             enable_progress_bar=enable_progress_bar,
-            accumulate_grad_batches=self.cfg.training_config.accumulate_grad_batches,
-            gradient_clip_val=self.cfg.training_config.gradient_clip_val,
-            gradient_clip_algorithm=self.cfg.training_config.gradient_clip_algorithm,
             callbacks=self.callbacks,
             default_root_dir=self.work_dir,
             logger=experiment_logger,
+            **self.cfg.training_config.lightning_trainer_config or {},
         )
 
         # place holder for the datamodules
-        self.train_datamodule: Optional[TrainDataModule] = None
-        self.pred_datamodule: Optional[PredictDataModule] = None
+        self.train_datamodule: TrainDataModule | None = None
+        self.pred_datamodule: PredictDataModule | None = None
 
     def _define_callbacks(
-        self, callbacks: Optional[list[Callback]], enable_progress_bar: bool
+        self, callbacks: list[Callback] | None, enable_progress_bar: bool
     ) -> None:
         """Define the callbacks for the training loop.
 
@@ -264,7 +258,7 @@ class CAREamist:
                 HyperParametersCallback(self.cfg),
                 ModelCheckpoint(
                     dirpath=self.work_dir / Path("checkpoints"),
-                    filename=self.cfg.experiment_name,
+                    filename=f"{self.cfg.experiment_name}_{{epoch:02d}}_step_{{step}}",
                     **self.cfg.training_config.checkpoint_callback.model_dump(),
                 ),
             ]
@@ -288,11 +282,11 @@ class CAREamist:
     def train(
         self,
         *,
-        datamodule: Optional[TrainDataModule] = None,
-        train_source: Optional[Union[Path, str, NDArray]] = None,
-        val_source: Optional[Union[Path, str, NDArray]] = None,
-        train_target: Optional[Union[Path, str, NDArray]] = None,
-        val_target: Optional[Union[Path, str, NDArray]] = None,
+        datamodule: TrainDataModule | None = None,
+        train_source: Union[Path, str, NDArray] | None = None,
+        val_source: Union[Path, str, NDArray] | None = None,
+        train_target: Union[Path, str, NDArray] | None = None,
+        val_target: Union[Path, str, NDArray] | None = None,
         use_in_memory: bool = True,
         val_percentage: float = 0.1,
         val_minimum_split: int = 1,
@@ -443,9 +437,9 @@ class CAREamist:
     def _train_on_array(
         self,
         train_data: NDArray,
-        val_data: Optional[NDArray] = None,
-        train_target: Optional[NDArray] = None,
-        val_target: Optional[NDArray] = None,
+        val_data: NDArray | None = None,
+        train_target: NDArray | None = None,
+        val_target: NDArray | None = None,
         val_percentage: float = 0.1,
         val_minimum_split: int = 5,
     ) -> None:
@@ -484,9 +478,9 @@ class CAREamist:
     def _train_on_path(
         self,
         path_to_train_data: Union[Path, str],
-        path_to_val_data: Optional[Union[Path, str]] = None,
-        path_to_train_target: Optional[Union[Path, str]] = None,
-        path_to_val_target: Optional[Union[Path, str]] = None,
+        path_to_val_data: Union[Path, str] | None = None,
+        path_to_train_target: Union[Path, str] | None = None,
+        path_to_val_target: Union[Path, str] | None = None,
         use_in_memory: bool = True,
         val_percentage: float = 0.1,
         val_minimum_split: int = 1,
@@ -549,13 +543,13 @@ class CAREamist:
         source: Union[Path, str],
         *,
         batch_size: int = 1,
-        tile_size: Optional[tuple[int, ...]] = None,
-        tile_overlap: Optional[tuple[int, ...]] = (48, 48),
-        axes: Optional[str] = None,
-        data_type: Optional[Literal["tiff", "custom"]] = None,
+        tile_size: tuple[int, ...] | None = None,
+        tile_overlap: tuple[int, ...] | None = (48, 48),
+        axes: str | None = None,
+        data_type: Literal["tiff", "custom"] | None = None,
         tta_transforms: bool = False,
-        dataloader_params: Optional[dict] = None,
-        read_source_func: Optional[Callable] = None,
+        dataloader_params: dict | None = None,
+        read_source_func: Callable | None = None,
         extension_filter: str = "",
     ) -> Union[list[NDArray], NDArray]: ...
 
@@ -565,12 +559,12 @@ class CAREamist:
         source: NDArray,
         *,
         batch_size: int = 1,
-        tile_size: Optional[tuple[int, ...]] = None,
-        tile_overlap: Optional[tuple[int, ...]] = (48, 48),
-        axes: Optional[str] = None,
-        data_type: Optional[Literal["array"]] = None,
+        tile_size: tuple[int, ...] | None = None,
+        tile_overlap: tuple[int, ...] | None = (48, 48),
+        axes: str | None = None,
+        data_type: Literal["array"] | None = None,
         tta_transforms: bool = False,
-        dataloader_params: Optional[dict] = None,
+        dataloader_params: dict | None = None,
     ) -> Union[list[NDArray], NDArray]: ...
 
     def predict(
@@ -578,13 +572,13 @@ class CAREamist:
         source: Union[PredictDataModule, Path, str, NDArray],
         *,
         batch_size: int = 1,
-        tile_size: Optional[tuple[int, ...]] = None,
-        tile_overlap: Optional[tuple[int, ...]] = (48, 48),
-        axes: Optional[str] = None,
-        data_type: Optional[Literal["array", "tiff", "custom"]] = None,
+        tile_size: tuple[int, ...] | None = None,
+        tile_overlap: tuple[int, ...] | None = (48, 48),
+        axes: str | None = None,
+        data_type: Literal["array", "tiff", "custom"] | None = None,
         tta_transforms: bool = False,
-        dataloader_params: Optional[dict] = None,
-        read_source_func: Optional[Callable] = None,
+        dataloader_params: dict | None = None,
+        read_source_func: Callable | None = None,
         extension_filter: str = "",
         **kwargs: Any,
     ) -> Union[list[NDArray], NDArray]:
@@ -704,18 +698,18 @@ class CAREamist:
         source: Union[PredictDataModule, Path, str],
         *,
         batch_size: int = 1,
-        tile_size: Optional[tuple[int, ...]] = None,
-        tile_overlap: Optional[tuple[int, ...]] = (48, 48),
-        axes: Optional[str] = None,
-        data_type: Optional[Literal["tiff", "custom"]] = None,
+        tile_size: tuple[int, ...] | None = None,
+        tile_overlap: tuple[int, ...] | None = (48, 48),
+        axes: str | None = None,
+        data_type: Literal["tiff", "custom"] | None = None,
         tta_transforms: bool = False,
-        dataloader_params: Optional[dict] = None,
-        read_source_func: Optional[Callable] = None,
+        dataloader_params: dict | None = None,
+        read_source_func: Callable | None = None,
         extension_filter: str = "",
         write_type: Literal["tiff", "custom"] = "tiff",
-        write_extension: Optional[str] = None,
-        write_func: Optional[WriteFunc] = None,
-        write_func_kwargs: Optional[dict[str, Any]] = None,
+        write_extension: str | None = None,
+        write_func: WriteFunc | None = None,
+        write_func_kwargs: dict[str, Any] | None = None,
         prediction_dir: Union[Path, str] = "predictions",
         **kwargs,
     ) -> None:
@@ -823,12 +817,12 @@ class CAREamist:
 
         # extract file names
         source_path: Union[Path, str, NDArray]
-        source_data_type: Literal["array", "tiff", "custom"]
+        source_data_type: Literal["array", "tiff", "czi", "custom"]
         if isinstance(source, PredictDataModule):
             source_path = source.pred_data
             source_data_type = source.data_type
             extension_filter = source.extension_filter
-        elif isinstance(source, str | Path):
+        elif isinstance(source, (str | Path)):
             source_path = source
             source_data_type = data_type or self.cfg.data_config.data_type
             extension_filter = SupportedData.get_extension_pattern(
@@ -841,7 +835,7 @@ class CAREamist:
             raise ValueError(
                 "Predicting to disk is not supported for input type 'array'."
             )
-        assert isinstance(source_path, str | Path)  # because data_type != "array"
+        assert isinstance(source_path, (Path | str))  # because data_type != "array"
         source_path = Path(source_path)
 
         file_paths = list_files(source_path, source_data_type, extension_filter)
@@ -879,14 +873,14 @@ class CAREamist:
 
     def export_to_bmz(
         self,
-        path_to_archive: Union[Path, str],
+        path_to_archive: Union[Path | str],
         friendly_model_name: str,
         input_array: NDArray,
         authors: list[dict],
         general_description: str,
         data_description: str,
-        covers: Optional[list[Union[Path, str]]] = None,
-        channel_names: Optional[list[str]] = None,
+        covers: list[Union[Path, str]] | None = None,
+        channel_names: list[str] | None = None,
         model_version: str = "0.1.0",
     ) -> None:
         """Export the model to the BioImage Model Zoo format.

{careamics-0.0.14 → careamics-0.0.16}/src/careamics/cli/conf.py

@@ -3,7 +3,7 @@
 import sys
 from dataclasses import dataclass
 from pathlib import Path
-from typing import Annotated, Optional
+from typing import Annotated
 
 import click
 import typer
@@ -116,7 +116,11 @@ def care(  # numpydoc ignore=PR01
         ),
     ],
     batch_size: Annotated[int, typer.Option(help="Batch size.")],
-    num_epochs: Annotated[int, typer.Option(help="Number of epochs.")],
+    num_epochs: Annotated[int, typer.Option(help="Number of epochs.")] = 100,
+    num_steps: Annotated[
+        int | None,
+        typer.Option(help="Number of batches per epoch (limit_train_batches)."),
+    ] = None,
     data_type: Annotated[
         click.Choice,
         typer.Option(click_type=click.Choice(["tiff"]), help="Type of the data."),
@@ -135,10 +139,10 @@ def care(  # numpydoc ignore=PR01
         ),
     ] = "mae",
     n_channels_in: Annotated[
-        Optional[int], typer.Option(help="Number of channels in")
+        int | None, typer.Option(help="Number of channels in")
     ] = None,
     n_channels_out: Annotated[
-        Optional[int], typer.Option(help="Number of channels out")
+        int | None, typer.Option(help="Number of channels out")
     ] = None,
     logger: Annotated[
         click.Choice,
@@ -175,6 +179,7 @@ def care(  # numpydoc ignore=PR01
         patch_size=patch_size,
         batch_size=batch_size,
         num_epochs=num_epochs,
+        num_steps=num_steps,
         # TODO: fix choosing augmentations
         augmentations=None if use_augmentations else [],
         independent_channels=independent_channels,
@@ -203,7 +208,11 @@ def n2n(  # numpydoc ignore=PR01
         ),
     ],
     batch_size: Annotated[int, typer.Option(help="Batch size.")],
-    num_epochs: Annotated[int, typer.Option(help="Number of epochs.")],
+    num_epochs: Annotated[int, typer.Option(help="Number of epochs.")] = 100,
+    num_steps: Annotated[
+        int | None,
+        typer.Option(help="Number of batches per epoch (limit_train_batches)."),
+    ] = None,
     data_type: Annotated[
         click.Choice,
         typer.Option(click_type=click.Choice(["tiff"]), help="Type of the data."),
@@ -222,10 +231,10 @@ def n2n(  # numpydoc ignore=PR01
         ),
     ] = "mae",
     n_channels_in: Annotated[
-        Optional[int], typer.Option(help="Number of channels in")
+        int | None, typer.Option(help="Number of channels in")
     ] = None,
     n_channels_out: Annotated[
-        Optional[int], typer.Option(help="Number of channels out")
+        int | None, typer.Option(help="Number of channels out")
     ] = None,
     logger: Annotated[
         click.Choice,
@@ -259,6 +268,7 @@ def n2n(  # numpydoc ignore=PR01
         patch_size=patch_size,
         batch_size=batch_size,
         num_epochs=num_epochs,
+        num_steps=num_steps,
         # TODO: fix choosing augmentations
         augmentations=None if use_augmentations else [],
         independent_channels=independent_channels,
@@ -287,7 +297,11 @@ def n2v(  # numpydoc ignore=PR01
         ),
     ],
     batch_size: Annotated[int, typer.Option(help="Batch size.")],
-    num_epochs: Annotated[int, typer.Option(help="Number of epochs.")],
+    num_epochs: Annotated[int, typer.Option(help="Number of epochs.")] = 100,
+    num_steps: Annotated[
+        int | None,
+        typer.Option(help="Number of batches per epoch (limit_train_batches)."),
+    ] = None,
     data_type: Annotated[
         click.Choice,
         typer.Option(click_type=click.Choice(["tiff"]), help="Type of the data."),
@@ -300,7 +314,7 @@ def n2v(  # numpydoc ignore=PR01
     ] = True,
     use_n2v2: Annotated[bool, typer.Option(help="Whether to use N2V2")] = False,
     n_channels: Annotated[
-        Optional[int], typer.Option(help="Number of channels (in and out)")
+        int | None, typer.Option(help="Number of channels (in and out)")
     ] = None,
     roi_size: Annotated[int, typer.Option(help="N2V pixel manipulation area.")] = 11,
     masked_pixel_percentage: Annotated[
@@ -364,6 +378,7 @@ def n2v(  # numpydoc ignore=PR01
         patch_size=patch_size,
         batch_size=batch_size,
         num_epochs=num_epochs,
+        num_steps=num_steps,
         # TODO: fix choosing augmentations
         augmentations=None if use_augmentations else [],
         independent_channels=independent_channels,

{careamics-0.0.14 → careamics-0.0.16}/src/careamics/cli/main.py

@@ -7,7 +7,7 @@ its implementation is contained in the conf.py file.
 """
 
 from pathlib import Path
-from typing import Annotated, Optional
+from typing import Annotated
 
 import click
 import typer
@@ -47,7 +47,7 @@ def train(  # numpydoc ignore=PR01
         ),
     ],
     train_target: Annotated[
-        Optional[Path],
+        Path | None,
         typer.Option(
             "--train-target",
             "-tt",
@@ -58,7 +58,7 @@ def train(  # numpydoc ignore=PR01
         ),
     ] = None,
     val_source: Annotated[
-        Optional[Path],
+        Path | None,
         typer.Option(
             "--val-source",
             "-vs",
@@ -69,7 +69,7 @@ def train(  # numpydoc ignore=PR01
         ),
     ] = None,
     val_target: Annotated[
-        Optional[Path],
+        Path | None,
         typer.Option(
             "--val-target",
             "-vt",
@@ -96,7 +96,7 @@ def train(  # numpydoc ignore=PR01
         typer.Option(help="Minimum number of files to use for validation,"),
     ] = 1,
     work_dir: Annotated[
-        Optional[Path],
+        Path | None,
         typer.Option(
             "--work-dir",
             "-wd",
@@ -142,7 +142,7 @@ def predict(  # numpydoc ignore=PR01
     ],
     batch_size: Annotated[int, typer.Option(help="Batch size.")] = 1,
     tile_size: Annotated[
-        Optional[click.Tuple],
+        click.Tuple | None,
         typer.Option(
             help=(
                 "Size of the tiles to use for prediction, (if the data "
@@ -164,7 +164,7 @@ def predict(  # numpydoc ignore=PR01
         ),
     ] = (48, 48, -1),
     axes: Annotated[
-        Optional[str],
+        str | None,
         typer.Option(
             help="Axes of the input data. If unused the data is assumed to have the "
             "same axes as the original training data."
@@ -190,7 +190,7 @@ def predict(  # numpydoc ignore=PR01
     ] = "tiff",
     # TODO: could make dataloader_params as json, necessary?
     work_dir: Annotated[
-        Optional[Path],
+        Path | None,
         typer.Option(
             "--work-dir",
             "-wd",

{careamics-0.0.14 → careamics-0.0.16}/src/careamics/cli/utils.py

@@ -1,11 +1,9 @@
 """Utility functions for the CAREamics CLI."""
 
-from typing import Optional
-
 
 def handle_2D_3D_callback(
-    value: Optional[tuple[int, int, int]],
-) -> Optional[tuple[int, ...]]:
+    value: tuple[int, int, int] | None,
+) -> tuple[int, ...] | None:
     """
     Callback for options that require 2D or 3D inputs.