Merge branch 'main' into iz/feat/separate_norm

.github/workflows/ci.yml

@@ -27,7 +27,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
         # 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, macos-13, windows-latest]
 

.pre-commit-config.yaml

@@ -9,12 +9,12 @@ ci:
 
 repos:
   - repo: https://github.com/abravalheri/validate-pyproject
-    rev: v0.16
+    rev: v0.18
     hooks:
       - id: validate-pyproject
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.4.3
+    rev: v0.4.7
     hooks:
       - id: ruff
         args: [--fix, --target-version, py38]
@@ -40,14 +40,14 @@ repos:
     hooks:
       - id: numpydoc-validation
 
-  # jupyter linting and formatting
-  - repo: https://github.com/nbQA-dev/nbQA
-    rev: 1.8.5
-    hooks:
-      - id: nbqa-ruff
-        args: [--fix]
-      - id: nbqa-black
-      #- id: nbqa-mypy
+  # # jupyter linting and formatting
+  # - repo: https://github.com/nbQA-dev/nbQA
+  #   rev: 1.8.5
+  #   hooks:
+  #     - id: nbqa-ruff
+  #       args: [--fix]
+  #     - id: nbqa-black
+  #     #- id: nbqa-mypy
 
   # strip out jupyter notebooks
   - repo: https://github.com/kynan/nbstripout

README.md

@@ -4,7 +4,7 @@
   </a>
 </p>
 
-# CAREamics Restoration
+# CAREamics
 
 [![License](https://img.shields.io/pypi/l/careamics.svg?color=green)](https://github.com/CAREamics/careamics/blob/main/LICENSE)
 [![PyPI](https://img.shields.io/pypi/v/careamics.svg?color=green)](https://pypi.org/project/careamics)
@@ -31,4 +31,4 @@ tutorials on how to best apply these methods in a scientific context.
 
 ## Installation and use
 
-Check out the [documentation](https://careamics.github.io/) for installation instructions and guides!
+Check out the [documentation](https://careamics.github.io/) for installation instructions and guides!

examples/2D/n2v/example_BSD68_lightning.ipynb

@@ -18,11 +18,7 @@
     "    CAREamicsPredictDataModule,\n",
     "    CAREamicsTrainDataModule,\n",
     ")\n",
-<<<<<<< Updated upstream
     "from careamics.lightning_prediction import CAREamicsPredictionLoop\n",
-=======
-    "from careamics.lightning_prediction import CAREamicsFiring\n",
->>>>>>> Stashed changes
     "from careamics.utils.metrics import psnr"
    ]
   },
@@ -172,11 +168,7 @@
     "train_data_module = CAREamicsTrainDataModule(\n",
     "    train_data=train_path,\n",
     "    val_data=val_path,\n",
-<<<<<<< Updated upstream
     "    data_type=\"tiff\",  # to use np.ndarray, set data_type to \"array\"\n",
-=======
-    "    data_type=\"tiff\",\n",
->>>>>>> Stashed changes
     "    patch_size=(64, 64),\n",
     "    axes=\"SYX\",\n",
     "    batch_size=128,\n",

pyproject.toml

@@ -33,6 +33,7 @@ classifiers = [
     "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
     "License :: OSI Approved :: BSD License",
     "Typing :: Typed",
 ]
@@ -73,7 +74,7 @@ repository = "https://github.com/CAREamics/careamics"
 line-length = 88
 target-version = "py38"
 src = ["src"]
-select = [
+lint.select = [
     "E",  # style errors
     "W",  # style warnings
     "F",  # flakes
@@ -86,7 +87,7 @@ select = [
     "A001", # flake8-builtins
     "RUF",  # ruff-specific rules
 ]
-ignore = [
+lint.ignore = [
     "D100", # Missing docstring in public module
     "D107", # Missing docstring in __init__
     "D203", # 1 blank line required before class docstring
@@ -103,13 +104,12 @@ ignore = [
     "UP006", # Replace typing.List by list, mandatory for py3.8
     "UP007", # Replace Union by |, mandatory for py3.9
 ]
-ignore-init-module-imports = true
 show-fixes = true
 
-[tool.ruff.pydocstyle]
+[tool.ruff.lint.pydocstyle]
 convention = "numpy"
 
-[tool.ruff.per-file-ignores]
+[tool.ruff.lint.per-file-ignores]
 "tests/*.py" = ["D", "S"]
 "setup.py" = ["D"]
 

src/careamics/callbacks/hyperparameters_callback.py

@@ -1,3 +1,5 @@
+"""Callback saving CAREamics configuration as hyperparameters in the model."""
+
 from pytorch_lightning import LightningModule, Trainer
 from pytorch_lightning.callbacks import Callback
 
@@ -11,13 +13,18 @@ class HyperParametersCallback(Callback):
     This allows saving the configuration as dictionnary in the checkpoints, and
     loading it subsequently in a CAREamist instance.
 
+    Parameters
+    ----------
+    config : Configuration
+        CAREamics configuration to be saved as hyperparameter in the model.
+
     Attributes
     ----------
     config : Configuration
         CAREamics configuration to be saved as hyperparameter in the model.
     """
 
-    def __init__(self, config: Configuration):
+    def __init__(self, config: Configuration) -> None:
         """
         Constructor.
 
@@ -28,14 +35,14 @@ def __init__(self, config: Configuration):
         """
         self.config = config
 
-    def on_train_start(self, trainer: Trainer, pl_module: LightningModule):
+    def on_train_start(self, trainer: Trainer, pl_module: LightningModule) -> None:
         """
         Update the hyperparameters of the model with the configuration on train start.
 
         Parameters
         ----------
         trainer : Trainer
-            PyTorch Lightning trainer.
+            PyTorch Lightning trainer, unused.
         pl_module : LightningModule
             PyTorch Lightning module.
         """

src/careamics/callbacks/progress_bar_callback.py

@@ -1,3 +1,5 @@
+"""Progressbar callback."""
+
 import sys
 from typing import Dict, Union
 
@@ -10,7 +12,13 @@ class ProgressBarCallback(TQDMProgressBar):
     """Progress bar for training and validation steps."""
 
     def init_train_tqdm(self) -> tqdm:
-        """Override this to customize the tqdm bar for training."""
+        """Override this to customize the tqdm bar for training.
+
+        Returns
+        -------
+        tqdm
+            A tqdm bar.
+        """
         bar = tqdm(
             desc="Training",
             position=(2 * self.process_position),
@@ -23,7 +31,13 @@ def init_train_tqdm(self) -> tqdm:
         return bar
 
     def init_validation_tqdm(self) -> tqdm:
-        """Override this to customize the tqdm bar for validation."""
+        """Override this to customize the tqdm bar for validation.
+
+        Returns
+        -------
+        tqdm
+            A tqdm bar.
+        """
         # The main progress bar doesn't exist in `trainer.validate()`
         has_main_bar = self.train_progress_bar is not None
         bar = tqdm(
@@ -37,7 +51,13 @@ def init_validation_tqdm(self) -> tqdm:
         return bar
 
     def init_test_tqdm(self) -> tqdm:
-        """Override this to customize the tqdm bar for testing."""
+        """Override this to customize the tqdm bar for testing.
+
+        Returns
+        -------
+        tqdm
+            A tqdm bar.
+        """
         bar = tqdm(
             desc="Testing",
             position=(2 * self.process_position),
@@ -52,6 +72,19 @@ def init_test_tqdm(self) -> tqdm:
     def get_metrics(
         self, trainer: Trainer, pl_module: LightningModule
     ) -> Dict[str, Union[int, str, float, Dict[str, float]]]:
-        """Override this to customize the metrics displayed in the progress bar."""
+        """Override this to customize the metrics displayed in the progress bar.
+
+        Parameters
+        ----------
+        trainer : Trainer
+            The trainer object.
+        pl_module : LightningModule
+            The LightningModule object, unused.
+
+        Returns
+        -------
+        dict
+            A dictionary with the metrics to display in the progress bar.
+        """
         pbar_metrics = trainer.progress_bar_metrics
         return {**pbar_metrics}