careamics 0.0.12__tar.gz → 0.0.13__tar.gz

{careamics-0.0.12 → careamics-0.0.13}/.github/ISSUE_TEMPLATE/bug_report.md

@@ -30,7 +30,7 @@ Error message:
 <!-- Please fill in the following information, you can check the package versions using `conda list` -->
 > [!IMPORTANT]
 > - OS: [e.g. iOS]
-> - Python version [e.g. 3.9]
+> - Python version [e.g. 3.12]
 > - PyTorch version [e.g. 2.3]
 > - PyTorch lightning version [e.g. 2.4]
 > - CAREamics version [e.g. 0.0.4]

{careamics-0.0.12 → careamics-0.0.13}/.github/workflows/ci.yml

@@ -27,9 +27,9 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["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]
+        platform: [ubuntu-latest, windows-latest] # macos-latest
 
     steps:
       - name: 🛑 Cancel Previous Runs
@@ -40,17 +40,19 @@ jobs:
       - uses: actions/checkout@v3
 
       - name: 🐍 Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
+          # architecture: ${{ matrix.platform == 'macos-latest' && 'arm64' || 'x64' }}
           cache-dependency-path: "pyproject.toml"
           cache: "pip"
 
       - name: Install Dependencies
         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 -m "not lvae"
@@ -90,7 +92,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
-          python-version: "3.9"
+          python-version: "3.12"
 
       - name: Build
         run: |

careamics-0.0.13/.github/workflows/ci_macos.yml

@@ -0,0 +1,67 @@
+# This CI runs the tests that do not fail on gh macos-latest runner due to the MPS
+# backend. Once the MPS backend is fixed on gh side, this workflow can be removed
+# and merged back once again with the main CI workflow.
+name: CI-macOS
+
+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: ${{ matrix.platform }} (${{ matrix.python-version }})
+    runs-on: ${{ matrix.platform }}
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["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: [macos-latest]
+
+    steps:
+      - name: 🛑 Cancel Previous Runs
+        uses: styfle/cancel-workflow-action@0.11.0
+        with:
+          access_token: ${{ github.token }}
+
+      - uses: actions/checkout@v3
+
+      - name: 🐍 Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          architecture: ${{ matrix.platform == 'macos-latest' && 'arm64' || 'x64' }} # force arm64 architecture
+          cache-dependency-path: "pyproject.toml"
+          cache: "pip"
+
+      - name: Install Dependencies
+        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' || ''  }}
+
+      - name: 🧪 Run Tests
+        run: pytest --color=yes -m "not lvae and not mps_gh_fail"
+
+      # If something goes wrong with --pre tests, we can open an issue in the repo
+      - name: 📝 Report --pre Failures
+        if: failure() && github.event_name == 'schedule'
+        uses: JasonEtco/create-an-issue@v2
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          PLATFORM: ${{ matrix.platform }}
+          PYTHON: ${{ matrix.python-version }}
+          RUN_ID: ${{ github.run_id }}
+          TITLE: "[test-bot] pip install --pre is failing"
+        with:
+          filename: .github/TEST_FAIL_TEMPLATE.md
+          update_existing: true

{careamics-0.0.12 → careamics-0.0.13}/.github/workflows/codecov.yml

@@ -16,7 +16,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.9"]
+        python-version: ["3.12"]
         platform: [ubuntu-latest]
 
     steps:

{careamics-0.0.12 → careamics-0.0.13}/.github/workflows/lvae.yml

@@ -19,8 +19,8 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.9"]
-        platform: [ubuntu-latest, windows-latest]
+        python-version: ["3.12"]
+        platform: [ubuntu-latest]
 
     steps:
       - name: 🛑 Cancel Previous Runs

{careamics-0.0.12 → careamics-0.0.13}/.pre-commit-config.yaml

@@ -9,24 +9,24 @@ ci:
 
 repos:
   - repo: https://github.com/abravalheri/validate-pyproject
-    rev: v0.23
+    rev: v0.24.1
     hooks:
       - id: validate-pyproject
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.8.6
+    rev: v0.11.12
     hooks:
       - id: ruff
         exclude: "^src/careamics/lvae_training/.*|^src/careamics/models/lvae/.*|^scripts/.*"
-        args: [--fix, --target-version, py39]
+        args: [--fix, --target-version, py310]
 
   - repo: https://github.com/psf/black
-    rev: 24.10.0
+    rev: 25.1.0
     hooks:
       - id: black
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.14.1
+    rev: v1.16.0
     hooks:
       - id: mypy
         files: "^src/"
@@ -43,7 +43,8 @@ repos:
     rev: v1.8.0
     hooks:
       - id: numpydoc-validation
-        exclude: "^src/careamics/dataset_ng/.*|^src/careamics/lvae_training/.*|^src/careamics/models/lvae/.*|^src/careamics/losses/lvae/.*|^scripts/.*"
+        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/.*"
+        # regarding src/careamics/lightning/dataset_ng/data_module.py: https://github.com/numpy/numpydoc/issues/559
 
   # # jupyter linting and formatting
   # - repo: https://github.com/nbQA-dev/nbQA

{careamics-0.0.12 → careamics-0.0.13}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: careamics
-Version: 0.0.12
+Version: 0.0.13
 Summary: Toolbox for running N2V and friends.
 Project-URL: homepage, https://careamics.github.io/
 Project-URL: repository, https://github.com/CAREamics/careamics
@@ -10,27 +10,28 @@ License-File: LICENSE
 Classifier: Development Status :: 3 - Alpha
 Classifier: License :: OSI Approved :: BSD License
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Typing :: Typed
-Requires-Python: >=3.9
+Requires-Python: >=3.10
 Requires-Dist: bioimageio-core==0.7
-Requires-Dist: matplotlib<=3.10.1
+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-Dist: pydantic<=2.12,>=2.11
-Requires-Dist: pytorch-lightning<=2.5.0.post0,>=2.2
+Requires-Dist: pytorch-lightning<=2.5.2,>=2.2
 Requires-Dist: pyyaml!=6.0.0,<=6.0.2
 Requires-Dist: scikit-image<=0.25.2
-Requires-Dist: tifffile<=2025.3.13
-Requires-Dist: torch<=2.6.0,>=2.0
-Requires-Dist: torchvision<=0.21.0
-Requires-Dist: typer<=0.15.2,>=0.12.3
+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'
 Provides-Extra: dev
 Requires-Dist: onnx; extra == 'dev'
 Requires-Dist: pre-commit; extra == 'dev'

{careamics-0.0.12 → careamics-0.0.13}/pyproject.toml

@@ -20,7 +20,7 @@ name = "careamics"
 dynamic = ["version"]
 description = "Toolbox for running N2V and friends."
 readme = "README.md"
-requires-python = ">=3.9"
+requires-python = ">=3.10"
 license = { text = "BSD-3-Clause" }
 authors = [
     { name = 'CAREamics team', email = 'rse@fht.org' },
@@ -34,7 +34,6 @@ authors = [
 classifiers = [
     "Development Status :: 3 - Alpha",
     "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
@@ -43,23 +42,27 @@ classifiers = [
 ]
 dependencies = [
     'numpy<2.0.0',
-    'torch>=2.0,<=2.6.0',
-    'torchvision<=0.21.0',
+    'torch>=2.0,<=2.7.1',
+    'torchvision<=0.22.1',
     'bioimageio.core==0.7',
-    'tifffile<=2025.3.13',
+    'tifffile<=2025.5.10',
     'psutil<=7.0.0',
     'pydantic>=2.11,<=2.12',
-    'pytorch_lightning>=2.2,<=2.5.0.post0',
+    'pytorch_lightning>=2.2,<=2.5.2',
     'pyyaml<=6.0.2,!=6.0.0',
-    'typer>=0.12.3,<=0.15.2',
+    'typer>=0.12.3,<=0.16.0',
     'scikit-image<=0.25.2',
     'zarr<3.0.0',
     'pillow<=11.2.1',
-    'matplotlib<=3.10.1',
-    'xarray<2025.3.0'
+    'matplotlib<=3.10.3',
+    'xarray<2025.3.0',
 ]
 
 [project.optional-dependencies]
+
+# czi format
+czi = ['pylibCZIrw>=4.1.2,<6.0.0']
+
 # development dependencies and tooling
 dev = [
     "pre-commit",
@@ -87,7 +90,7 @@ careamics = "careamics.cli.main:run"
 # https://beta.ruff.rs/docs
 [tool.ruff]
 line-length = 88
-target-version = "py39"
+target-version = "py310"
 src = ["src"]
 lint.select = [
     "E",  # style errors
@@ -134,6 +137,7 @@ line-length = 88
 
 # https://mypy.readthedocs.io/en/stable/config_file.html
 [tool.mypy]
+# plugins = ["pydantic.mypy"]
 files = "src/**/"
 strict = false
 # allow_untyped_defs = false
@@ -141,6 +145,12 @@ strict = false
 # disallow_any_generics = false
 # ignore_missing_imports = false
 
+# https://docs.pydantic.dev/latest/integrations/mypy/
+# [tool.pydantic-mypy]
+# init_forbid_extra = true
+# init_typed = true
+# warn_required_dynamic_aliases = true
+
 
 # https://docs.pytest.org/en/6.2.x/customize.html
 [tool.pytest.ini_options]
@@ -155,6 +165,8 @@ addopts = "-p no:doctest"
 markers = [
     # "gpu: marks tests as requiring gpu",
     "lvae: marks tests as testing lvae",
+    "mps_gh_fail: marks tests as failing on Github macos-latest runner",
+    "czi: marks tests using czi files",
 ]
 
 # https://coverage.readthedocs.io/en/6.4/config.html

{careamics-0.0.12 → careamics-0.0.13}/src/careamics/careamist.py

@@ -1,7 +1,8 @@
 """A class to train, predict and export models in CAREamics."""
 
+from collections.abc import Callable
 from pathlib import Path
-from typing import Any, Callable, Literal, Optional, Union, overload
+from typing import Any, Literal, Optional, Union, overload
 
 import numpy as np
 from numpy.typing import NDArray
@@ -827,7 +828,7 @@ class CAREamist:
             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(
@@ -840,7 +841,7 @@ class CAREamist:
             raise ValueError(
                 "Predicting to disk is not supported for input type 'array'."
             )
-        assert isinstance(source_path, (Path, str))  # because data_type != "array"
+        assert isinstance(source_path, str | Path)  # because data_type != "array"
         source_path = Path(source_path)
 
         file_paths = list_files(source_path, source_data_type, extension_filter)

{careamics-0.0.12 → careamics-0.0.13}/src/careamics/cli/utils.py

@@ -4,7 +4,7 @@ from typing import Optional
 
 
 def handle_2D_3D_callback(
-    value: Optional[tuple[int, int, int]]
+    value: Optional[tuple[int, int, int]],
 ) -> Optional[tuple[int, ...]]:
     """
     Callback for options that require 2D or 3D inputs.

{careamics-0.0.12 → careamics-0.0.13}/src/careamics/config/algorithms/n2v_algorithm_model.py

@@ -1,4 +1,4 @@
-""""N2V Algorithm configuration."""
+"""N2V Algorithm configuration."""
 
 from typing import Annotated, Literal
 

{careamics-0.0.12 → careamics-0.0.13}/src/careamics/config/architectures/unet_model.py

@@ -63,6 +63,9 @@ class UNetModel(ArchitectureModel):
     """Whether information is processed independently in each channel, used to train
     channels independently."""
 
+    use_batch_norm: bool = Field(default=True, validate_default=True)
+    """Whether to use batch normalization in the model."""
+
     @field_validator("num_channels_init")
     @classmethod
     def validate_num_channels_init(cls, num_channels_init: int) -> int:

{careamics-0.0.12 → careamics-0.0.13}/src/careamics/config/callback_model.py

@@ -22,52 +22,42 @@ class CheckpointModel(BaseModel):
     https://lightning.ai/docs/pytorch/stable/api/lightning.pytorch.callbacks.ModelCheckpoint.html#modelcheckpoint
     """
 
-    model_config = ConfigDict(
-        validate_assignment=True,
-    )
+    model_config = ConfigDict(validate_assignment=True, validate_default=True)
 
-    monitor: Literal["val_loss"] = Field(default="val_loss", validate_default=True)
-    """Quantity to monitor."""
+    monitor: Literal["val_loss"] = Field(default="val_loss")
+    """Quantity to monitor, currently only `val_loss`."""
 
-    verbose: bool = Field(default=False, validate_default=True)
+    verbose: bool = Field(default=False)
     """Verbosity mode."""
 
-    save_weights_only: bool = Field(default=False, validate_default=True)
+    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, validate_default=True
-    )
+    save_last: Optional[Literal[True, False, "link"]] = 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=10, validate_default=True)
+    save_top_k: int = Field(default=3, ge=-1, le=100)
     """If `save_top_k == kz, the best k models according to the quantity monitored
     will be saved. If `save_top_k == 0`, no models are saved. if `save_top_k == -1`,
     all models are saved."""
 
-    mode: Literal["min", "max"] = Field(default="min", validate_default=True)
+    mode: Literal["min", "max"] = Field(default="min")
     """One of {min, max}. If `save_top_k != 0`, the decision to overwrite the current
     save file is made based on either the maximization or the minimization of the
     monitored quantity. For 'val_acc', this should be 'max', for 'val_loss' this should
     be 'min', etc.
     """
 
-    auto_insert_metric_name: bool = Field(default=False, validate_default=True)
+    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=10, validate_default=True
-    )
+    every_n_train_steps: Optional[int] = Field(default=None, ge=1, le=1000)
     """Number of training steps between checkpoints."""
 
-    train_time_interval: Optional[timedelta] = Field(
-        default=None, validate_default=True
-    )
+    train_time_interval: Optional[timedelta] = Field(default=None)
     """Checkpoints are monitored at the specified time interval."""
 
-    every_n_epochs: Optional[int] = Field(
-        default=None, ge=1, le=10, validate_default=True
-    )
+    every_n_epochs: Optional[int] = Field(default=None, ge=1, le=100)
     """Number of epochs between checkpoints."""
 
 
@@ -83,41 +73,40 @@ class EarlyStoppingModel(BaseModel):
 
     model_config = ConfigDict(
         validate_assignment=True,
+        validate_default=True,
     )
 
-    monitor: Literal["val_loss"] = Field(default="val_loss", validate_default=True)
+    monitor: Literal["val_loss"] = Field(default="val_loss")
     """Quantity to monitor."""
 
-    min_delta: float = Field(default=0.0, ge=0.0, le=1.0, validate_default=True)
+    min_delta: float = Field(default=0.0, ge=0.0, le=1.0)
     """Minimum change in the monitored quantity to qualify as an improvement, i.e. an
     absolute change of less than or equal to min_delta, will count as no improvement."""
 
-    patience: int = Field(default=3, ge=1, le=10, validate_default=True)
+    patience: int = Field(default=3, ge=1, le=10)
     """Number of checks with no improvement after which training will be stopped."""
 
-    verbose: bool = Field(default=False, validate_default=True)
+    verbose: bool = Field(default=False)
     """Verbosity mode."""
 
-    mode: Literal["min", "max", "auto"] = Field(default="min", validate_default=True)
+    mode: Literal["min", "max", "auto"] = Field(default="min")
     """One of {min, max, auto}."""
 
-    check_finite: bool = Field(default=True, validate_default=True)
+    check_finite: bool = Field(default=True)
     """When `True`, stops training when the monitored quantity becomes `NaN` or
     `inf`."""
 
-    stopping_threshold: Optional[float] = Field(default=None, validate_default=True)
+    stopping_threshold: Optional[float] = Field(default=None)
     """Stop training immediately once the monitored quantity reaches this threshold."""
 
-    divergence_threshold: Optional[float] = Field(default=None, validate_default=True)
+    divergence_threshold: Optional[float] = 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, validate_default=True
-    )
+    check_on_train_epoch_end: Optional[bool] = 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."""
 
-    log_rank_zero_only: bool = Field(default=False, validate_default=True)
+    log_rank_zero_only: bool = Field(default=False)
     """When set `True`, logs the status of the early stopping callback only for rank 0
     process."""

{careamics-0.0.12 → careamics-0.0.13}/src/careamics/config/configuration.py

@@ -3,9 +3,11 @@
 from __future__ import annotations
 
 import re
+from collections.abc import Callable
 from pprint import pformat
-from typing import Any, Callable, Literal, Union
+from typing import Any, Literal, 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
@@ -183,6 +185,50 @@ class Configuration(BaseModel):
 
         return name
 
+    @model_validator(mode="after")
+    def validate_n2v_mask_pixel_perc(self: Self) -> Self:
+        """
+        Validate that there will always be at least one blind-spot pixel in every patch.
+
+        The probability of creating a blind-spot pixel is a function of the chosen
+        masked pixel percentage and patch size.
+
+        Returns
+        -------
+        Self
+            Validated configuration.
+
+        Raises
+        ------
+        ValueError
+            If the probability of masking a pixel within a patch is less than 1 for the
+            chosen masked pixel percentage and patch size.
+        """
+        # No validation needed for non n2v algorithms
+        if not isinstance(self.algorithm_config, N2VAlgorithm):
+            return self
+
+        mask_pixel_perc = self.algorithm_config.n2v_config.masked_pixel_percentage
+        patch_size = self.data_config.patch_size
+        expected_area_per_pixel = 1 / (mask_pixel_perc / 100)
+
+        n_dims = 3 if self.algorithm_config.model.is_3D() else 2
+        patch_size_lower_bound = int(np.ceil(expected_area_per_pixel ** (1 / n_dims)))
+        required_patch_size = tuple(
+            2 ** int(np.ceil(np.log2(patch_size_lower_bound))) for _ in range(n_dims)
+        )
+        required_mask_pixel_perc = (1 / np.prod(patch_size)) * 100
+        if expected_area_per_pixel > np.prod(patch_size):
+            raise ValueError(
+                "The probability of creating a blind-spot pixel within a patch is "
+                f"below 1, for a patch size of {patch_size} with a masked pixel "
+                f"percentage of {mask_pixel_perc}%. Either increase the patch size to "
+                f"{required_patch_size} or increase the masked pixel percentage to "
+                f"at least {required_mask_pixel_perc}%."
+            )
+
+        return self
+
     @model_validator(mode="after")
     def validate_3D(self: Self) -> Self:
         """