careamics 0.0.13__tar.gz → 0.0.15__tar.gz

{careamics-0.0.13 → careamics-0.0.15}/.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-0.0.13 → careamics-0.0.15}/.pre-commit-config.yaml

@@ -14,7 +14,7 @@ repos:
       - id: validate-pyproject
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.11.12
+    rev: v0.12.2
     hooks:
       - id: ruff
         exclude: "^src/careamics/lvae_training/.*|^src/careamics/models/lvae/.*|^scripts/.*"
@@ -26,7 +26,7 @@ repos:
       - id: black
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.16.0
+    rev: v1.16.1
     hooks:
       - id: mypy
         files: "^src/"
@@ -40,7 +40,7 @@ repos:
 
   # 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-0.0.13 → careamics-0.0.15}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: careamics
-Version: 0.0.13
+Version: 0.0.15
 Summary: Toolbox for running N2V and friends.
 Project-URL: homepage, https://careamics.github.io/
 Project-URL: repository, https://github.com/CAREamics/careamics
@@ -15,7 +15,7 @@ Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Typing :: Typed
 Requires-Python: >=3.10
-Requires-Dist: bioimageio-core==0.7
+Requires-Dist: bioimageio-core==0.9.0
 Requires-Dist: matplotlib<=3.10.3
 Requires-Dist: numpy<2.0.0
 Requires-Dist: pillow<=11.2.1
@@ -28,7 +28,6 @@ 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
 Provides-Extra: czi
 Requires-Dist: pylibczirw<6.0.0,>=4.1.2; extra == 'czi'

{careamics-0.0.13 → careamics-0.0.15}/pyproject.toml

@@ -44,7 +44,7 @@ dependencies = [
     'numpy<2.0.0',
     'torch>=2.0,<=2.7.1',
     'torchvision<=0.22.1',
-    'bioimageio.core==0.7',
+    'bioimageio.core==0.9.0',
     'tifffile<=2025.5.10',
     'psutil<=7.0.0',
     'pydantic>=2.11,<=2.12',
@@ -55,7 +55,6 @@ dependencies = [
     'zarr<3.0.0',
     'pillow<=11.2.1',
     'matplotlib<=3.10.3',
-    'xarray<2025.3.0',
 ]
 
 [project.optional-dependencies]

{careamics-0.0.13 → careamics-0.0.15}/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:
         """
@@ -222,11 +222,11 @@ class CAREamist:
         )
 
         # 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.
 
@@ -288,11 +288,11 @@ 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 +443,9 @@ 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 +484,9 @@ 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 +549,13 @@ 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 +565,12 @@ 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 +578,13 @@ 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 +704,18 @@ 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:
@@ -885,8 +885,8 @@ class CAREamist:
         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-0.0.13 → careamics-0.0.15}/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
@@ -135,10 +135,10 @@ 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,
@@ -222,10 +222,10 @@ 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,
@@ -300,7 +300,7 @@ 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[

{careamics-0.0.13 → careamics-0.0.15}/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-0.0.13 → careamics-0.0.15}/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.
 

{careamics-0.0.13 → careamics-0.0.15}/src/careamics/config/algorithms/vae_algorithm_model.py

@@ -3,7 +3,7 @@
 from __future__ import annotations
 
 from pprint import pformat
-from typing import Literal, Optional
+from typing import Literal
 
 from pydantic import BaseModel, ConfigDict, model_validator
 from typing_extensions import Self
@@ -45,9 +45,9 @@ class VAEBasedAlgorithm(BaseModel):
     # NOTE: these are all configs (pydantic models)
     loss: LVAELossConfig
     model: LVAEModel
-    noise_model: Optional[MultiChannelNMConfig] = None
-    noise_model_likelihood: Optional[NMLikelihoodConfig] = None
-    gaussian_likelihood: Optional[GaussianLikelihoodConfig] = None
+    noise_model: MultiChannelNMConfig | None = None
+    noise_model_likelihood: NMLikelihoodConfig | None = None
+    gaussian_likelihood: GaussianLikelihoodConfig | None = None
 
     # Optional fields
     optimizer: OptimizerModel = OptimizerModel()

{careamics-0.0.13 → careamics-0.0.15}/src/careamics/config/callback_model.py

@@ -3,7 +3,7 @@
 from __future__ import annotations
 
 from datetime import timedelta
-from typing import Literal, Optional
+from typing import Literal
 
 from pydantic import (
     BaseModel,
@@ -33,7 +33,7 @@ class CheckpointModel(BaseModel):
     save_weights_only: bool = Field(default=False)
     """When `True`, only the model's weights will be saved (model.save_weights)."""
 
-    save_last: Optional[Literal[True, False, "link"]] = Field(default=True)
+    save_last: Literal[True, False, "link"] | None = Field(default=True)
     """When `True`, saves a last.ckpt copy whenever a checkpoint file gets saved."""
 
     save_top_k: int = Field(default=3, ge=-1, le=100)
@@ -51,13 +51,13 @@ class CheckpointModel(BaseModel):
     auto_insert_metric_name: bool = Field(default=False)
     """When `True`, the checkpoints filenames will contain the metric name."""
 
-    every_n_train_steps: Optional[int] = Field(default=None, ge=1, le=1000)
+    every_n_train_steps: int | None = Field(default=None, ge=1, le=1000)
     """Number of training steps between checkpoints."""
 
-    train_time_interval: Optional[timedelta] = Field(default=None)
+    train_time_interval: timedelta | None = Field(default=None)
     """Checkpoints are monitored at the specified time interval."""
 
-    every_n_epochs: Optional[int] = Field(default=None, ge=1, le=100)
+    every_n_epochs: int | None = Field(default=None, ge=1, le=100)
     """Number of epochs between checkpoints."""
 
 
@@ -96,14 +96,14 @@ class EarlyStoppingModel(BaseModel):
     """When `True`, stops training when the monitored quantity becomes `NaN` or
     `inf`."""
 
-    stopping_threshold: Optional[float] = Field(default=None)
+    stopping_threshold: float | None = Field(default=None)
     """Stop training immediately once the monitored quantity reaches this threshold."""
 
-    divergence_threshold: Optional[float] = Field(default=None)
+    divergence_threshold: float | None = Field(default=None)
     """Stop training as soon as the monitored quantity becomes worse than this
     threshold."""
 
-    check_on_train_epoch_end: Optional[bool] = Field(default=False)
+    check_on_train_epoch_end: bool | None = Field(default=False)
     """Whether to run early stopping at the end of the training epoch. If this is
     `False`, then the check runs at the end of the validation."""