Merge remote-tracking branch 'origin/main' into splits_prediction_refac

.github/dependabot.yml

@@ -8,3 +8,4 @@ updates:
       time: "08:00"
     ignore:
       - dependency-name: "numpy"
+      - dependency-name: "zarr"

.github/pull_request_template.md

@@ -1,33 +1,80 @@
-### Description
+## Description
 
-Please provide a brief description of the changes in this PR. Include any relevant context or background information.
+<!-- This section provides the necessary background and information for reviewers to
+understand the code and have the correct mindset when examining changes. -->
 
-- **What**: Clearly and concisely describe what changes you have made.
-- **Why**: Explain the reasoning behind these changes. What problem are you solving? Why is this change necessary?
-- **How**: Describe how you implemented these changes. Provide an overview of the approach and any important implementation details.
+> [!NOTE]  
+> **tldr**: <!-- Write a one sentence summary. -->
 
-### Changes Made
 
-- **Added**: List new features or files added.
-- **Modified**: Describe existing features or files modified.
-- **Removed**: Detail features or files that were removed.
+### Background - why do we need this PR?
 
-### Related Issues
+<!-- What problem are you solving? Describe in a few sentences the state before
+this PR. Use code examples if useful. -->
 
-Link to any related issues or discussions. Use keywords like "Fixes", "Resolves", or "Closes" to link to issues automatically.
+### Overview - what changed?
 
-- Fixes #
-- Resolves #
-- Closes #
+<!-- What aspects and mechanisms of the code base changed? Describe only the general 
+idea and overarching features. -->
+
+### Implementation - how did you implement the changes?
+
+<!-- How did you solve the issue technically? Explain why you chose this approach and 
+provide code examples if applicable (e.g. change in the API for users). -->
+
+
+## Changes Made
+
+<!-- This section highlights the important features and files that reviewers should
+pay attention to when reviewing. Only list important features or files, this is useful for 
+reviewers to correctly assess how deeply the modifications impact the code base.
+
+For instance:
+
+### New features or files
+- `NewClass` added to `new_file.py`
+- `new_function` added to `existing_file.py`
+
+...
+-->
+
+### New features or files
+
+<!-- List new features or files added. -->
+-
 
-### Breaking changes
+### Modified features or files
+
+<!-- List important modified features or files. -->
+-
+
+### Removed features or files
+
+<!-- List removed features or files. -->
+-
+
+## How has this been tested?
+
+<!-- Describe the tests that you ran to verify your changes. This can be a short 
+description of the tests added to the PR or code snippet to reproduce the change
+in behaviour. -->
+
+
+## Related Issues
+
+<!-- Link to any related issues or discussions. Use keywords like "Fixes", "Resolves",
+or "Closes" to link to issues automatically. -->
+
+- Resolves #
 
-Describe any breaking change.
+## Breaking changes
 
+<!-- Describe any breaking changes introduced by this PR. -->
 
-### Additional Notes and Examples
+## Additional Notes and Examples
 
-Include any additional notes or context that reviewers should be aware of, including snippets of code illustrating your new feature.
+<!-- Provide any additional information that will help reviewers understand the
+changes. This can be links to documentations, forum posts, past discussions etc. -->
 
 ---
 

.pre-commit-config.yaml

@@ -14,7 +14,7 @@ repos:
       - id: validate-pyproject
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.8.1
+    rev: v0.8.6
     hooks:
       - id: ruff
         exclude: "^src/careamics/lvae_training/.*|^src/careamics/models/lvae/.*|^scripts/.*"
@@ -26,14 +26,15 @@ repos:
       - id: black
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.13.0
+    rev: v1.14.1
     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
+          - numpy<2.0.0
+          - pydantic
           - types-PyYAML
           - types-setuptools
 

mypy.ini

@@ -1,5 +1,6 @@
 [mypy]
 ignore_missing_imports = True
+plugins = pydantic.mypy
 
 [mypy-careamics.lvae_training.*]
 follow_imports = skip

pyproject.toml

@@ -43,18 +43,20 @@ classifiers = [
 ]
 dependencies = [
     'numpy<2.0.0',
-    'torch>=2.0,<=2.5.1',
+    'torch>=2.0,<=2.6.0',
+    'torchvision<=0.21.0',
     'torchvision<=0.20.1',
     'bioimageio.core==0.7',
-    'tifffile<=2024.12.12',
-    'psutil<=6.1',
+    'tifffile<=2025.1.10',
+    'psutil<=6.1.1',
     'pydantic>=2.5,<2.11',
-    'pytorch_lightning>=2.2,<=2.4',
+    'pytorch_lightning>=2.2,<=2.5.0.post0',
     'pyyaml<=6.0.2,!=6.0.0',
     'typer>=0.12.3,<=0.15.1',
-    'scikit-image<=0.25.0',
+    'scikit-image<=0.25.1',
     'zarr<3.0.0',
-    'pillow<=11.0.0',
+    'pillow<=11.1.0',
+    'matplotlib<=3.10.0'
 ]
 
 [project.optional-dependencies]

src/careamics/__init__.py

@@ -7,7 +7,22 @@
 except PackageNotFoundError:
     __version__ = "uninstalled"
 
-__all__ = ["CAREamist", "Configuration", "load_configuration", "save_configuration"]
+__all__ = [
+    "CAREamist",
+    "Configuration",
+    "algorithm_factory",
+    "configuration_factory",
+    "data_factory",
+    "load_configuration",
+    "save_configuration",
+]
 
 from .careamist import CAREamist
-from .config import Configuration, load_configuration, save_configuration
+from .config import (
+    Configuration,
+    algorithm_factory,
+    configuration_factory,
+    data_factory,
+    load_configuration,
+    save_configuration,
+)

src/careamics/careamist.py

@@ -13,7 +13,7 @@
 )
 from pytorch_lightning.loggers import CSVLogger, TensorBoardLogger, WandbLogger
 
-from careamics.config import Configuration, FCNAlgorithmConfig, load_configuration
+from careamics.config import Configuration, UNetBasedAlgorithm, load_configuration
 from careamics.config.support import (
     SupportedAlgorithm,
     SupportedArchitecture,
@@ -137,7 +137,7 @@ def __init__(
             self.cfg = source
 
             # instantiate model
-            if isinstance(self.cfg.algorithm_config, FCNAlgorithmConfig):
+            if isinstance(self.cfg.algorithm_config, UNetBasedAlgorithm):
                 self.model = FCNModule(
                     algorithm_config=self.cfg.algorithm_config,
                 )
@@ -157,7 +157,8 @@ def __init__(
                 self.cfg = load_configuration(source)
 
                 # instantiate model
-                if isinstance(self.cfg.algorithm_config, FCNAlgorithmConfig):
+                # TODO call model factory here
+                if isinstance(self.cfg.algorithm_config, UNetBasedAlgorithm):
                     self.model = FCNModule(
                         algorithm_config=self.cfg.algorithm_config,
                     )  # type: ignore

src/careamics/config/__init__.py

@@ -1,41 +1,63 @@
-"""Configuration module."""
+"""CAREamics Pydantic configuration models.
+
+To maintain clarity at the module level, we follow the following naming conventions:
+`*_model` is specific for sub-configurations (e.g. architecture, data, algorithm),
+while `*_configuration` is reserved for the main configuration models, including the
+`Configuration` base class and its algorithm-specific child classes.
+"""
 
 __all__ = [
+    "CAREAlgorithm",
+    "CAREConfiguration",
     "CheckpointModel",
     "Configuration",
-    "CustomModel",
     "DataConfig",
-    "FCNAlgorithmConfig",
     "GaussianMixtureNMConfig",
+    "GeneralDataConfig",
     "InferenceConfig",
     "LVAELossConfig",
     "MultiChannelNMConfig",
+    "N2NAlgorithm",
+    "N2NConfiguration",
+    "N2VAlgorithm",
+    "N2VConfiguration",
+    "N2VDataConfig",
     "TrainingConfig",
-    "VAEAlgorithmConfig",
-    "clear_custom_models",
+    "UNetBasedAlgorithm",
+    "VAEBasedAlgorithm",
+    "algorithm_factory",
+    "configuration_factory",
     "create_care_configuration",
     "create_n2n_configuration",
     "create_n2v_configuration",
+    "data_factory",
     "load_configuration",
-    "register_model",
     "save_configuration",
 ]
-from .architectures import CustomModel, clear_custom_models, register_model
+
+from .algorithms import (
+    CAREAlgorithm,
+    N2NAlgorithm,
+    N2VAlgorithm,
+    UNetBasedAlgorithm,
+    VAEBasedAlgorithm,
+)
 from .callback_model import CheckpointModel
-from .configuration_factory import (
+from .care_configuration import CAREConfiguration
+from .configuration import Configuration
+from .configuration_factories import (
+    algorithm_factory,
+    configuration_factory,
     create_care_configuration,
     create_n2n_configuration,
     create_n2v_configuration,
+    data_factory,
 )
-from .configuration_model import (
-    Configuration,
-    load_configuration,
-    save_configuration,
-)
-from .data_model import DataConfig
-from .fcn_algorithm_model import FCNAlgorithmConfig
+from .configuration_io import load_configuration, save_configuration
+from .data import DataConfig, GeneralDataConfig, N2VDataConfig
 from .inference_model import InferenceConfig
 from .loss_model import LVAELossConfig
+from .n2n_configuration import N2NConfiguration
+from .n2v_configuration import N2VConfiguration
 from .nm_model import GaussianMixtureNMConfig, MultiChannelNMConfig
 from .training_model import TrainingConfig
-from .vae_algorithm_model import VAEAlgorithmConfig

src/careamics/config/algorithms/__init__.py

@@ -0,0 +1,15 @@
+"""Algorithm configurations."""
+
+__all__ = [
+    "CAREAlgorithm",
+    "N2NAlgorithm",
+    "N2VAlgorithm",
+    "UNetBasedAlgorithm",
+    "VAEBasedAlgorithm",
+]
+
+from .care_algorithm_model import CAREAlgorithm
+from .n2n_algorithm_model import N2NAlgorithm
+from .n2v_algorithm_model import N2VAlgorithm
+from .unet_algorithm_model import UNetBasedAlgorithm
+from .vae_algorithm_model import VAEBasedAlgorithm

src/careamics/config/algorithms/care_algorithm_model.py

@@ -0,0 +1,38 @@
+"""CARE algorithm configuration."""
+
+from typing import Annotated, Literal
+
+from pydantic import AfterValidator
+
+from careamics.config.architectures import UNetModel
+from careamics.config.validators import (
+    model_without_final_activation,
+    model_without_n2v2,
+)
+
+from .unet_algorithm_model import UNetBasedAlgorithm
+
+
+class CAREAlgorithm(UNetBasedAlgorithm):
+    """CARE algorithm configuration.
+
+    Attributes
+    ----------
+    algorithm : "care"
+        CARE Algorithm name.
+    loss : {"mae", "mse"}
+        CARE-compatible loss function.
+    """
+
+    algorithm: Literal["care"] = "care"
+    """CARE Algorithm name."""
+
+    loss: Literal["mae", "mse"] = "mae"
+    """CARE-compatible loss function."""
+
+    model: Annotated[
+        UNetModel,
+        AfterValidator(model_without_n2v2),
+        AfterValidator(model_without_final_activation),
+    ]
+    """UNet without a final activation function and without the `n2v2` modifications."""

src/careamics/config/algorithms/n2n_algorithm_model.py

@@ -0,0 +1,30 @@
+"""N2N Algorithm configuration."""
+
+from typing import Annotated, Literal
+
+from pydantic import AfterValidator
+
+from careamics.config.architectures import UNetModel
+from careamics.config.validators import (
+    model_without_final_activation,
+    model_without_n2v2,
+)
+
+from .unet_algorithm_model import UNetBasedAlgorithm
+
+
+class N2NAlgorithm(UNetBasedAlgorithm):
+    """Noise2Noise Algorithm configuration."""
+
+    algorithm: Literal["n2n"] = "n2n"
+    """N2N Algorithm name."""
+
+    loss: Literal["mae", "mse"] = "mae"
+    """N2N-compatible loss function."""
+
+    model: Annotated[
+        UNetModel,
+        AfterValidator(model_without_n2v2),
+        AfterValidator(model_without_final_activation),
+    ]
+    """UNet without a final activation function and without the `n2v2` modifications."""