careamics 0.0.16__tar.gz → 0.0.17__tar.gz

{careamics-0.0.16 → careamics-0.0.17}/.github/dependabot.yml

@@ -7,5 +7,5 @@ updates:
       interval: "daily"
       time: "08:00"
     ignore:
-      - dependency-name: "numpy"
       - dependency-name: "zarr"
+      - dependency-name: "torchmetrics"

careamics-0.0.17/.github/workflows/ci.yml

@@ -0,0 +1,98 @@
+name: CI
+
+on:
+  push:
+    branches:
+      - main
+    tags:
+      - "v*"
+  pull_request:
+  workflow_dispatch:
+  schedule:
+    # run every week (for --pre release tests)
+    - cron: "0 0 * * 0"
+
+jobs:
+  check-manifest:
+    # check-manifest is a tool that checks that all files in version control are
+    # included in the sdist (unless explicitly excluded)
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - run: pipx run check-manifest
+
+  test:
+    name: ${{ matrix.platform }} (${{ matrix.python-version }})
+    runs-on: ${{ matrix.platform }}
+    strategy:
+      fail-fast: false
+      matrix:
+        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 ]
+
+    steps:
+      - name: 🛑 Cancel Previous Runs
+        uses: styfle/cancel-workflow-action@0.11.0
+        with:
+          access_token: ${{ github.token }}
+
+      - uses: actions/checkout@v5
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
+        with:
+          # Install a specific version of uv.
+          version: "0.9.0"
+          enable-cache: true
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install the project
+        run: uv sync --all-extras --dev
+
+      - name: 🧪 Run tests
+        run: uv run pytest --color=yes -m "not lvae"
+
+
+  deploy:
+    name: Release
+    needs: test
+    if: success() && startsWith(github.ref, 'refs/tags/') && github.event_name != 'schedule'
+    runs-on: ubuntu-latest
+
+    permissions:
+      # IMPORTANT: this permission is mandatory for trusted publishing
+      id-token: write
+
+      # This permission allows writing releases
+      contents: write
+
+    steps:
+      - uses: actions/checkout@v5
+        with:
+          fetch-depth: 0
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
+        with:
+          # Install a specific version of uv.
+          version: "0.9.0"
+          enable-cache: true
+          python-version: 3.12
+
+      - name: Build
+        run: uv build
+
+      # Check that basic features work and we didn't miss to include crucial files
+      - name: Smoke test (wheel)
+        run: uv run --isolated --no-project --with dist/*.whl tests/smoke_test.py
+
+      - name: Smoke test (source distribution)
+        run: uv run --isolated --no-project --with dist/*.tar.gz tests/smoke_test.py
+        
+      - name: Publish
+        run: uv publish
+
+      - uses: softprops/action-gh-release@v2
+        with:
+          generate_release_notes: true

careamics-0.0.17/.github/workflows/ci_lvae.yml

@@ -0,0 +1,45 @@
+name: CI-lvae-uv
+
+on:
+  push:
+    branches:
+      - main
+    tags:
+      - "v*"
+  pull_request:
+  workflow_dispatch:
+  schedule:
+    # run every week (for --pre release tests)
+    - cron: "0 0 * * 0"
+
+jobs:
+  test:
+    name: LVAE py3.12 (ubuntu-latest)
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.12"]
+
+    steps:
+      - name: 🛑 Cancel Previous Runs
+        uses: styfle/cancel-workflow-action@0.11.0
+        with:
+          access_token: ${{ github.token }}
+
+      - uses: actions/checkout@v5
+            
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
+        with:
+          # Install a specific version of uv.
+          version: "0.9.0"
+          enable-cache: true
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install the project
+        run: uv sync --all-extras --dev
+
+      - name: 🧪 Run tests
+        # does not run doctests
+        run: uv run pytest tests --color=yes -m lvae

careamics-0.0.17/.github/workflows/codecov.yml

@@ -0,0 +1,43 @@
+name: codecov
+
+on:
+  push:
+    tags:
+      - "v*"
+
+jobs:
+  codecov:
+    name: codecov update
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.12"]
+
+    steps:
+      - name: 🛑 Cancel Previous Runs
+        uses: styfle/cancel-workflow-action@0.11.0
+        with:
+          access_token: ${{ github.token }}
+
+      - name: Checkout code
+        uses: actions/checkout@v5
+  
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
+        with:
+          # Install a specific version of uv.
+          version: "0.9.0"
+          enable-cache: true
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install the project
+        run: uv sync --all-extras --dev
+
+      - name: 🧪 Run Tests
+        run: uv run pytest --color=yes --cov --cov-config=pyproject.toml --cov-report=xml --cov-report=term-missing 
+
+      - name: Coverage
+        uses: codecov/codecov-action@v5
+        with:
+          version: v0.7.3

{careamics-0.0.16 → careamics-0.0.17}/.pre-commit-config.yaml

@@ -14,19 +14,18 @@ repos:
       - id: validate-pyproject
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.12.11
+    rev: v0.13.3
     hooks:
       - id: ruff
         exclude: "^src/careamics/lvae_training/.*|^src/careamics/models/lvae/.*|^scripts/.*"
-        args: [--fix, --target-version, py311]
 
-  - repo: https://github.com/psf/black
-    rev: 25.1.0
+  - repo: https://github.com/psf/black-pre-commit-mirror
+    rev: 25.9.0
     hooks:
       - id: black
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.17.1
+    rev: v1.18.2
     hooks:
       - id: mypy
         files: "^src/"

{careamics-0.0.16 → careamics-0.0.17}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: careamics
-Version: 0.0.16
+Version: 0.0.17
 Summary: Toolbox for running N2V and friends.
 Project-URL: homepage, https://careamics.github.io/
 Project-URL: repository, https://github.com/CAREamics/careamics
@@ -16,30 +16,24 @@ Classifier: Programming Language :: Python :: 3.13
 Classifier: Typing :: Typed
 Requires-Python: >=3.11
 Requires-Dist: bioimageio-core>=0.9.0
-Requires-Dist: matplotlib<=3.10.6
+Requires-Dist: matplotlib<=3.10.7
 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: pydantic<=2.12.2,>=2.11
 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<=2025.9.30
+Requires-Dist: tifffile<=2025.10.4
 Requires-Dist: torch<=2.8.0,>=2.0
+Requires-Dist: torchmetrics<1.5.0,>=0.11.0
 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'
-Requires-Dist: pytest-cov; extra == 'dev'
-Requires-Dist: sybil; extra == 'dev'
 Provides-Extra: examples
 Requires-Dist: careamics-portfolio; extra == 'examples'
 Requires-Dist: jupyter; extra == 'examples'

{careamics-0.0.16 → careamics-0.0.17}/pyproject.toml

@@ -46,17 +46,18 @@ dependencies = [
     'torch>=2.0,<=2.8.0',
     'torchvision<=0.23.0',
     'bioimageio.core>=0.9.0',
-    'tifffile<=2025.9.30',
+    'tifffile<=2025.10.4',
     'psutil<=7.1.0',
-    'pydantic>=2.11,<=2.12',
+    'pydantic>=2.11,<=2.12.2',
     '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,<4.0.0',
     'pillow<=11.3.0',
-    'matplotlib<=3.10.6',
-    'validators<=0.35.0'
+    'matplotlib<=3.10.7',
+    'validators<=0.35.0',
+    'torchmetrics>=0.11.0,<1.5.0' # 1.5.0 causes `data_range` mandatory parameter issues
 ]
 
 [project.optional-dependencies]
@@ -64,6 +65,14 @@ dependencies = [
 # czi format
 czi = ['pylibCZIrw>=4.1.2,<6.0.0']
 
+# notebooks
+examples = ["jupyter", "careamics-portfolio"]
+
+# loggers
+wandb = ["wandb"]
+tensorboard = ["tensorboard", "protobuf==5.29.1"]
+
+[dependency-groups]
 # development dependencies and tooling
 dev = [
     "pre-commit",
@@ -76,13 +85,6 @@ dev = [
     "ml_dtypes>=0.5.0" # required by onnx, causes issues in gh runners with py313
 ]
 
-# notebooks
-examples = ["jupyter", "careamics-portfolio"]
-
-# loggers
-wandb = ["wandb"]
-tensorboard = ["tensorboard", "protobuf==5.29.1"]
-
 [project.urls]
 homepage = "https://careamics.github.io/"
 repository = "https://github.com/CAREamics/careamics"
@@ -93,8 +95,9 @@ careamics = "careamics.cli.main:run"
 
 # https://beta.ruff.rs/docs
 [tool.ruff]
+fix = true
 line-length = 88
-target-version = "py310"
+target-version = "py311" # is this needed? see .pre-commit-config.yaml
 src = ["src"]
 lint.select = [
     "E",  # style errors

{careamics-0.0.16 → careamics-0.0.17}/src/careamics/careamist.py

@@ -41,6 +41,7 @@ logger = get_logger(__name__)
 LOGGER_TYPES = list[Union[TensorBoardLogger, WandbLogger, CSVLogger]]
 
 
+# TODO type ignore have been added because of the czi data type in data configuration
 class CAREamist:
     """Main CAREamics class, allowing training and prediction using various algorithms.
 
@@ -674,7 +675,7 @@ class CAREamist:
         # create the prediction
         self.pred_datamodule = create_predict_datamodule(
             pred_data=source,
-            data_type=data_type or self.cfg.data_config.data_type,
+            data_type=data_type or self.cfg.data_config.data_type,  # type: ignore
             axes=axes or self.cfg.data_config.axes,
             image_means=self.cfg.data_config.image_means,
             image_stds=self.cfg.data_config.image_stds,
@@ -817,14 +818,16 @@ class CAREamist:
 
         # extract file names
         source_path: Union[Path, str, NDArray]
-        source_data_type: Literal["array", "tiff", "czi", "custom"]
+        source_data_type: Literal["array", "tiff", "custom"]
         if isinstance(source, PredictDataModule):
             source_path = source.pred_data
-            source_data_type = source.data_type
+            source_data_type = source.data_type  # type: ignore
             extension_filter = source.extension_filter
         elif isinstance(source, (str | Path)):
             source_path = source
-            source_data_type = data_type or self.cfg.data_config.data_type
+            source_data_type = (
+                data_type or self.cfg.data_config.data_type  # type: ignore
+            )
             extension_filter = SupportedData.get_extension_pattern(
                 SupportedData(source_data_type)
             )

{careamics-0.0.16 → careamics-0.0.17}/src/careamics/config/configuration.py

@@ -3,14 +3,12 @@
 from __future__ import annotations
 
 import re
-from collections.abc import Callable
 from pprint import pformat
 from typing import Any, Literal, Self, Union
 
 import numpy as np
 from bioimageio.spec.generic.v0_3 import CiteEntry
 from pydantic import BaseModel, ConfigDict, Field, field_validator, model_validator
-from pydantic.main import IncEx
 
 from careamics.config.algorithms import (
     CAREAlgorithm,
@@ -343,19 +341,7 @@ class Configuration(BaseModel):
 
     def model_dump(
         self,
-        *,
-        mode: Literal["json", "python"] | str = "python",
-        include: IncEx | None = None,
-        exclude: IncEx | None = None,
-        context: Any | None = None,
-        by_alias: bool | None = False,
-        exclude_unset: bool = False,
-        exclude_defaults: bool = False,
-        exclude_none: bool = True,
-        round_trip: bool = False,
-        warnings: bool | Literal["none", "warn", "error"] = True,
-        fallback: Callable[[Any], Any] | None = None,
-        serialize_as_any: bool = False,
+        **kwargs: Any,
     ) -> dict[str, Any]:
         """
         Override model_dump method in order to set default values.
@@ -365,50 +351,15 @@ class Configuration(BaseModel):
 
         Parameters
         ----------
-        mode : Literal['json', 'python'] | str, default='python'
-            The serialization format.
-        include : Any | None, default=None
-            Attributes to include.
-        exclude : Any | None, default=None
-            Attributes to exclude.
-        context : Any | None, default=None
-            Additional context to pass to the serialization functions.
-        by_alias : bool, default=False
-            Whether to use attribute aliases.
-        exclude_unset : bool, default=False
-            Whether to exclude fields that are not set.
-        exclude_defaults : bool, default=False
-            Whether to exclude fields that have default values.
-        exclude_none : bool, default=true
-            Whether to exclude fields that have None values.
-        round_trip : bool, default=False
-            Whether to dump and load the data to ensure that the output is a valid
-            representation.
-        warnings : bool | Literal['none', 'warn', 'error'], default=True
-            Whether to emit warnings.
-        fallback : Callable[[Any], Any] | None, default=None
-            A function to call when an unknown value is encountered.
-        serialize_as_any : bool, default=False
-            Whether to serialize all types as Any.
+        **kwargs : Any
+            Additional arguments to pass to the parent model_dump method.
 
         Returns
         -------
         dict
             Dictionary containing the model parameters.
         """
-        dictionary = super().model_dump(
-            mode=mode,
-            include=include,
-            exclude=exclude,
-            context=context,
-            by_alias=by_alias,
-            exclude_unset=exclude_unset,
-            exclude_defaults=exclude_defaults,
-            exclude_none=exclude_none,
-            round_trip=round_trip,
-            warnings=warnings,
-            fallback=fallback,
-            serialize_as_any=serialize_as_any,
-        )
+        if "exclude_none" not in kwargs:
+            kwargs["exclude_none"] = True
 
-        return dictionary
+        return super().model_dump(**kwargs)

{careamics-0.0.16 → careamics-0.0.17}/src/careamics/config/configuration_factories.py

@@ -311,6 +311,10 @@ def _create_microsplit_data_configuration(
         Axes of the data.
     patch_size : list of int
         Size of the patches along the spatial dimensions.
+    grid_size : int
+        Grid size for patch extraction.
+    multiscale_count : int
+        Number of LC scales.
     batch_size : int
         Batch size.
     augmentations : list of transforms
@@ -1610,6 +1614,12 @@ def get_likelihood_config(
 ]:
     """Get the likelihood configuration for split models.
 
+    Returns a tuple containing the following optional entries:
+        - GaussianLikelihoodConfig: Gaussian likelihood configuration for musplit losses
+        - MultiChannelNMConfig: Multi-channel noise model configuration for denoisplit
+        losses
+        - NMLikelihoodConfig: Noise model likelihood configuration for denoisplit losses
+
     Parameters
     ----------
     loss_type : Literal["musplit", "denoisplit", "denoisplit_musplit"]
@@ -1629,15 +1639,12 @@ def get_likelihood_config(
 
     Returns
     -------
-    tuple[GaussianLikelihoodConfig | None, MultiChannelNMConfig | None,
-    NMLikelihoodConfig | None]
-        A tuple containing the likelihood and noise model configurations for the
-        specified loss type.
-
-        - GaussianLikelihoodConfig: Gaussian likelihood configuration for musplit losses
-        - MultiChannelNMConfig: Multi-channel noise model configuration for denoisplit
-        losses
-        - NMLikelihoodConfig: Noise model likelihood configuration for denoisplit losses
+    GaussianLikelihoodConfig or None
+        Configuration for the Gaussian likelihood model.
+    MultiChannelNMConfig or None
+        Configuration for the multi-channel noise model.
+    NMLikelihoodConfig or None
+        Configuration for the noise model likelihood.
 
     Raises
     ------
@@ -1647,7 +1654,7 @@ def get_likelihood_config(
     # gaussian likelihood
     if loss_type in ["musplit", "denoisplit_musplit"]:
         # if predict_logvar is None:
-        #     raise ValueError(f"predict_logvar is required for loss_type '{loss_type}'")
+        #    raise ValueError(f"predict_logvar is required for loss_type '{loss_type}'")
         # TODO validators should be in pydantic models
         gaussian_lik_config = GaussianLikelihoodConfig(
             predict_logvar=predict_logvar,
@@ -1903,7 +1910,7 @@ def create_microsplit_configuration(
     decoder_dropout: float = 0.0,
     nonlinearity: Literal[
         "None", "Sigmoid", "Softmax", "Tanh", "ReLU", "LeakyReLU", "ELU"
-    ] = "ReLU",
+    ] = "ReLU",  # TODO do we need all these?
     analytical_kl: bool = False,
     predict_logvar: Literal["pixelwise"] = "pixelwise",
     logvar_lowerbound: Union[float, None] = None,
@@ -1943,8 +1950,11 @@ def create_microsplit_configuration(
         Strides for the decoder convolutional layers, by default (2, 2).
     multiscale_count : int, optional
         Number of multiscale levels, by default 1.
+    grid_size : int, optional
+        Size of the grid for the lateral context, by default 32.
     z_dims : tuple[int, ...], optional
-        List of latent dimensions for each hierarchy level in the LVAE, by default (128, 128).
+        List of latent dimensions for each hierarchy level in the LVAE, by default
+        (128, 128).
     output_channels : int, optional
         Number of output channels for the model, by default 1.
     encoder_n_filters : int, optional

{careamics-0.0.16 → careamics-0.0.17}/src/careamics/config/data/data_model.py

@@ -207,13 +207,12 @@ class DataConfig(BaseModel):
 
     @field_validator("train_dataloader_params", "val_dataloader_params", mode="before")
     @classmethod
-    def set_default_dataloader_params(
+    def set_default_pin_memory(
         cls, dataloader_params: dict[str, Any]
     ) -> dict[str, Any]:
         """
-        Set default dataloader parameters if not provided.
+        Set default pin_memory for dataloader parameters if not provided.
 
-        - If 'num_workers' is not set, it defaults to the number of available CPU cores.
         - If 'pin_memory' is not set, it defaults to True if CUDA is available.
 
         Parameters
@@ -224,21 +223,62 @@ class DataConfig(BaseModel):
         Returns
         -------
         dict of {str: Any}
-            The dataloader parameters with defaults applied.
+            The dataloader parameters with pin_memory default applied.
+        """
+        if "pin_memory" not in dataloader_params:
+            import torch
+
+            dataloader_params["pin_memory"] = torch.cuda.is_available()
+
+        return dataloader_params
+
+    @field_validator("train_dataloader_params", mode="before")
+    @classmethod
+    def set_default_train_workers(
+        cls, dataloader_params: dict[str, Any]
+    ) -> dict[str, Any]:
+        """
+        Set default num_workers for training dataloader if not provided.
+
+        - If 'num_workers' is not set, it defaults to the number of available CPU cores.
+
+        Parameters
+        ----------
+        dataloader_params : dict of {str: Any}
+            The training dataloader parameters.
+
+        Returns
+        -------
+        dict of {str: Any}
+            The dataloader parameters with num_workers default applied.
         """
         if "num_workers" not in dataloader_params:
-            # Use 1 worker during tests, otherwise use all available CPU cores
+            # Use 0 workers during tests, otherwise use all available CPU cores
             if "pytest" in sys.modules:
                 dataloader_params["num_workers"] = 0
             else:
                 dataloader_params["num_workers"] = os.cpu_count()
 
-        if "pin_memory" not in dataloader_params:
-            import torch
+        return dataloader_params
 
-            dataloader_params["pin_memory"] = torch.cuda.is_available()
+    @model_validator(mode="after")
+    def set_val_workers_to_match_train(self: Self) -> Self:
+        """
+        Set validation dataloader num_workers to match training dataloader.
 
-        return dataloader_params
+        If num_workers is not specified in val_dataloader_params, it will be set to the
+        same value as train_dataloader_params["num_workers"].
+
+        Returns
+        -------
+        Self
+            Validated data model with synchronized num_workers.
+        """
+        if "num_workers" not in self.val_dataloader_params:
+            self.val_dataloader_params["num_workers"] = self.train_dataloader_params[
+                "num_workers"
+            ]
+        return self
 
     @field_validator("train_dataloader_params")
     @classmethod