ci: [pre-commit.ci] pre-commit autoupdate (#1222)

updates: - [github.com/astral-sh/ruff-pre-commit: v0.7.0 → v0.8.2](astral-sh/ruff-pre-commit@v0.7.0...v0.8.2) - [github.com/executablebooks/mdformat: 0.7.18 → 0.7.19](hukkin/mdformat@0.7.18...0.7.19) - [github.com/pre-commit/mirrors-mypy: v1.12.1 → v1.13.0](pre-commit/mirrors-mypy@v1.12.1...v1.13.0)  ## Summary by Sourcery CI: - Update pre-commit hooks for ruff-pre-commit from v0.7.0 to v0.7.1 and mirrors-mypy from v1.12.1 to v1.13.0. --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Grzegorz Bokota <bokota+github@gmail.com>
4DNucleome · Dec 10, 2024 · 287f452 · 287f452
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diff --git a/.napari/DESCRIPTION.md b/.napari/DESCRIPTION.md
@@ -61,7 +61,7 @@ The list of available measurements could be extensible using the PartSeg plugin
 ![Simple Measurement](https://i.imgur.com/Rnq6lF5.png)
 
 Set of measurements that could be calculated per component respecting data voxel size.
-In comparison to  *Measurement* list of available measures is limited to ones that do not need
+In comparison to *Measurement* list of available measures is limited to ones that do not need
 *Mask* information and could be calculated per component.
 
 This widget is equivalent to the PartSeg ROI Mask Simple Measurement window.

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -17,7 +17,7 @@ repos:
     - id: debug-statements
     - id: mixed-line-ending
 -   repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.7.0
+    rev: v0.8.2
     hooks:
       - id: ruff
 -   repo: https://github.com/pre-commit/pygrep-hooks
@@ -36,7 +36,7 @@ repos:
           - mdformat-toc
 
 -   repo: https://github.com/pre-commit/mirrors-mypy
-    rev: 'v1.12.1'  # Use the sha / tag you want to point at
+    rev: 'v1.13.0'  # Use the sha / tag you want to point at
     hooks:
     -   id: mypy
         files: ^package/PartSegImage/.+\.py

diff --git a/changelog.md b/changelog.md
@@ -100,9 +100,9 @@ This release drop support for python 3.8 and napari below 0.4.19.
 - Fix coverage files upload by enable hidden files upload ([#1186](https://github.com/4DNucleome/PartSeg/pull/1186))
 - \[pre-commit.ci\] pre-commit autoupdate ([#1184](https://github.com/4DNucleome/PartSeg/pull/1184))
 - Use PyQt6 in pre-tests ([#1196](https://github.com/4DNucleome/PartSeg/pull/1196))
-- Add missed code from  #1191 ([#1197](https://github.com/4DNucleome/PartSeg/pull/1197))
+- Add missed code from #1191 ([#1197](https://github.com/4DNucleome/PartSeg/pull/1197))
 - \[pre-commit.ci\] pre-commit autoupdate ([#1189](https://github.com/4DNucleome/PartSeg/pull/1189))
-- Auto add "skip check PR title"  label in update dependencies PR ([#1199](https://github.com/4DNucleome/PartSeg/pull/1199))
+- Auto add "skip check PR title" label in update dependencies PR ([#1199](https://github.com/4DNucleome/PartSeg/pull/1199))
 
 ### Build
 
@@ -172,7 +172,7 @@ This release drop support for python 3.8 and napari below 0.4.19.
 - Move coverage back to main workflow ([#1055](https://github.com/4DNucleome/PartSeg/pull/1055))
 - \[pre-commit.ci\] pre-commit autoupdate ([#1056](https://github.com/4DNucleome/PartSeg/pull/1056))
 - \[pre-commit.ci\] pre-commit autoupdate ([#1059](https://github.com/4DNucleome/PartSeg/pull/1059))
-- Update `actions/upload-artifact` and  `actions/download-artifact` from 3 to 4 ([#1062](https://github.com/4DNucleome/PartSeg/pull/1062))
+- Update `actions/upload-artifact` and `actions/download-artifact` from 3 to 4 ([#1062](https://github.com/4DNucleome/PartSeg/pull/1062))
 - \[pre-commit.ci\] pre-commit autoupdate ([#1064](https://github.com/4DNucleome/PartSeg/pull/1064))
 - Group actions update ([#1065](https://github.com/4DNucleome/PartSeg/pull/1065))
 - \[pre-commit.ci\] pre-commit autoupdate ([#1068](https://github.com/4DNucleome/PartSeg/pull/1068))
@@ -253,7 +253,7 @@ This release drop support for python 3.8 and napari below 0.4.19.
 ### 🐛 Bug Fixes
 
 - Fix possible problem of double registration napari plugin in PartSeg bundle ([#974](https://github.com/4DNucleome/PartSeg/pull/974))
-- Bump OS versions for part of testing workflows.  ([#977](https://github.com/4DNucleome/PartSeg/pull/977))
+- Bump OS versions for part of testing workflows. ([#977](https://github.com/4DNucleome/PartSeg/pull/977))
 - Bump os version for main tests workflow. ([#979](https://github.com/4DNucleome/PartSeg/pull/979))
 - Ensure that the module `PartSegCore.channel_class` is present in bundle ([#980](https://github.com/4DNucleome/PartSeg/pull/980))
 - Lower npe2 schema version to work with older napari version ([#981](https://github.com/4DNucleome/PartSeg/pull/981))
@@ -472,11 +472,11 @@ This release drop support for python 3.8 and napari below 0.4.19.
 
 ### 🚜 Refactor
 
-- Clean potential vulnerabilities  ([#630](https://github.com/4DNucleome/PartSeg/pull/630))
+- Clean potential vulnerabilities ([#630](https://github.com/4DNucleome/PartSeg/pull/630))
 
 ### 🧪 Testing
 
-- Add more tests for common GUI elements  ([#622](https://github.com/4DNucleome/PartSeg/pull/622))
+- Add more tests for common GUI elements ([#622](https://github.com/4DNucleome/PartSeg/pull/622))
 - Report coverage per package. ([#639](https://github.com/4DNucleome/PartSeg/pull/639))
 - Update conda environment to not use PyQt5 in test ([#646](https://github.com/4DNucleome/PartSeg/pull/646))
 - Add tests files to calculate coverage ([#655](https://github.com/4DNucleome/PartSeg/pull/655))
@@ -714,13 +714,13 @@ This release drop support for python 3.8 and napari below 0.4.19.
 
 ### Features
 
-- Add CellFromNucleusFlow "Cell from nucleus flow" cell segmentation method  (#367)
+- Add CellFromNucleusFlow "Cell from nucleus flow" cell segmentation method (#367)
 - When cutting components in PartSeg ROI mask allow not masking outer data (#379)
 - Theme selection in GUI (#381)
 - Allow return points from ROI extraction algorithm (#382)
 - Add measurement to get ROI annotation by name. (#386)
 - PartSeg ROI extraction algorithms as napari plugins (#387)
-- Add  Pearson, Mander's, Intensity, Spearman colocalization measurements (#392)
+- Add Pearson, Mander's, Intensity, Spearman colocalization measurements (#392)
 - Separate standalone napari settings from PartSeg embedded napari settings (#397)
 
 ### Performance
@@ -921,7 +921,7 @@ This release drop support for python 3.8 and napari below 0.4.19.
 ## 0.9.6
 
 - fix bug in loading project with mask
-- upgrade PyInstaller version (bug  GHSA-7fcj-pq9j-wh2r)
+- upgrade PyInstaller version (bug GHSA-7fcj-pq9j-wh2r)
 
 ## 0.9.5
 

diff --git a/package/PartSeg/__init__.py b/package/PartSeg/__init__.py
@@ -14,12 +14,12 @@
 ANALYSIS_NAME = "ROI Analysis"
 
 __all__ = (
+    "ANALYSIS_NAME",
+    "APP_LAB",
+    "APP_NAME",
+    "MASK_NAME",
     "__author__",
-    "parsed_version",
     "__version__",
     "changelog",
-    "APP_NAME",
-    "MASK_NAME",
-    "APP_LAB",
-    "ANALYSIS_NAME",
+    "parsed_version",
 )
diff --git a/package/PartSeg/common_gui/algorithms_description.py b/package/PartSeg/common_gui/algorithms_description.py
@@ -165,7 +165,7 @@ def from_algorithm_property(cls, ob: typing.Union[str, AlgorithmProperty]):
                 mgi_options=ob.mgi_options,
             )
         if isinstance(ob, str):
-            if ob.lower() == "hline" or len(ob) > 5 and all(x == "-" for x in ob):
+            if ob.lower() == "hline" or (len(ob) > 5 and all(x == "-" for x in ob)):
                 return Hline()
             return QLabel(ob)
         raise ValueError(f"unknown parameter type {type(ob)} of {ob}")

diff --git a/package/PartSeg/plugins/napari_widgets/__init__.py b/package/PartSeg/plugins/napari_widgets/__init__.py
@@ -18,21 +18,21 @@
 from PartSeg.plugins.napari_widgets.search_label_widget import SearchLabel
 
 __all__ = (
-    "PartSegGUILauncher",
     "BorderSmooth",
     "ConnectedComponents",
     "CopyLabelsWidget",
     "DoubleThreshold",
-    "NoiseFilter",
-    "SplitCoreObjects",
-    "Threshold",
-    "Watershed",
     "ImageColormap",
     "LabelSelector",
     "LayerMetadata",
     "MaskCreate",
+    "NoiseFilter",
+    "PartSegGUILauncher",
     "ROIAnalysisExtraction",
     "ROIMaskExtraction",
     "SearchLabel",
     "SettingsEditor",
+    "SplitCoreObjects",
+    "Threshold",
+    "Watershed",
 )
diff --git a/package/PartSeg/state_store.py b/package/PartSeg/state_store.py
@@ -35,14 +35,14 @@
 sentry_url = os.environ.get("PARTSEG_SENTRY_URL", "https://d4118280b73d4ee3a0222d0b17637687@sentry.io/1309302")
 
 __all__ = (
-    "auto_report",
     "always_report",
-    "custom_plugin_load",
+    "auto_report",
     "check_for_updates",
+    "custom_plugin_load",
     "develop",
     "report_errors",
-    "save_suffix",
     "save_folder",
+    "save_suffix",
     "sentry_url",
     "show_error_dialog",
 )
diff --git a/package/PartSegCore/__init__.py b/package/PartSegCore/__init__.py
@@ -1,3 +1,3 @@
 from PartSegCore.universal_const import UNIT_SCALE, Units
 
-__all__ = ("Units", "UNIT_SCALE")
+__all__ = ("UNIT_SCALE", "Units")
diff --git a/package/PartSegCore/analysis/__init__.py b/package/PartSegCore/analysis/__init__.py
@@ -7,11 +7,11 @@
 from PartSegCore.analysis.measurement_calculation import MEASUREMENT_DICT
 
 __all__ = (
+    "MEASUREMENT_DICT",
     "AnalysisAlgorithmSelection",
     "ProjectTuple",
     "SegmentationPipeline",
     "SegmentationPipelineElement",
-    "MEASUREMENT_DICT",
     "load_metadata",
 )
 

diff --git a/package/PartSegCore/analysis/load_functions.py b/package/PartSegCore/analysis/load_functions.py
@@ -41,15 +41,15 @@
 from PartSegImage import GenericImageReader
 
 __all__ = [
-    "LoadStackImage",
+    "LoadImageForBatch",
     "LoadImageMask",
-    "LoadProject",
     "LoadMask",
-    "load_dict",
-    "load_metadata",
     "LoadMaskSegmentation",
     "LoadProfileFromJSON",
-    "LoadImageForBatch",
+    "LoadProject",
+    "LoadStackImage",
+    "load_dict",
+    "load_metadata",
 ]
 
 from PartSegImage.image import Image

diff --git a/package/PartSegCore/analysis/save_functions.py b/package/PartSegCore/analysis/save_functions.py
@@ -19,12 +19,12 @@
 from PartSegImage import Channel, Image, ImageWriter
 
 __all__ = [
-    "SaveProject",
-    "SaveCmap",
-    "SaveXYZ",
-    "SaveAsTiff",
     "SaveAsNumpy",
+    "SaveAsTiff",
+    "SaveCmap",
     "SaveProfilesToJSON",
+    "SaveProject",
+    "SaveXYZ",
     "save_dict",
 ]
 

diff --git a/package/PartSegCore/image_transforming/__init__.py b/package/PartSegCore/image_transforming/__init__.py
@@ -8,11 +8,11 @@
 image_transform_dict = Register(CombineChannels, ImageProjection, InterpolateImage, SwapTimeStack)
 
 __all__ = (
-    "image_transform_dict",
     "CombineChannels",
     "CombineMode",
     "ImageProjection",
     "InterpolateImage",
     "SwapTimeStack",
     "TransformBase",
+    "image_transform_dict",
 )
diff --git a/package/PartSegCore/segmentation/__init__.py b/package/PartSegCore/segmentation/__init__.py
@@ -13,12 +13,12 @@
 from PartSegCore.segmentation.watershed import BaseWatershed
 
 __all__ = [
-    "ROIExtractionAlgorithm",
+    "BaseThreshold",
     "BaseWatershed",
     "NoiseFilteringBase",
-    "BaseThreshold",
-    "RestartableAlgorithm",
+    "ROIExtractionAlgorithm",
     "ROIExtractionResult",
+    "RestartableAlgorithm",
     "StackAlgorithm",
 ]
 

diff --git a/package/PartSegImage/__init__.py b/package/PartSegImage/__init__.py
@@ -19,15 +19,15 @@
     "Channel",
     "ChannelInfo",
     "ChannelInfoFull",
-    "Image",
-    "TiffImageReader",
+    "CziImageReader",
+    "GenericImageReader",
     "IMAGEJImageWriter",
+    "Image",
     "ImageWriter",
-    "TiffFileException",
-    "CziImageReader",
-    "OifImagReader",
     "ObsepImageReader",
-    "GenericImageReader",
+    "OifImagReader",
+    "TiffFileException",
+    "TiffImageReader",
 )
 
 if os.path.basename(sys.argv[0]) in ["sphinx-build", "sphinx-build.exe"]:  # pragma: no cover

diff --git a/package/PartSegImage/image.py b/package/PartSegImage/image.py
@@ -709,9 +709,9 @@ def clip_array(self, array: np.ndarray, **kwargs: int | slice) -> np.ndarray:
         array = self.fit_array_to_image(array)
         slices: list[int | slice] = [slice(None) for _ in range(len(self.array_axis_order))]
         axis_pos = self.get_array_axis_positions()
-        for name in kwargs:
+        for name, value in kwargs.items():
             if (n := name.upper()) in axis_pos:
-                slices[axis_pos[n]] = kwargs[name]
+                slices[axis_pos[n]] = value
         return array[tuple(slices)]
 
     def get_channel(self, num: int | str | Channel) -> np.ndarray:

diff --git a/pyproject.toml b/pyproject.toml
@@ -335,7 +335,6 @@ select = [
 ]
 ignore = ["A003", "SIM108", "ARG002", "ARG003", "ARG004", "PLR2004",
     "PLR0913", # should be re-enabled in a future version
-    "ANN101", "ANN102",
 ]
 
 [tool.ruff.lint.isort]

diff --git a/tutorials/tutorial-batch-processing/tutorial-batch.md b/tutorials/tutorial-batch-processing/tutorial-batch.md
@@ -10,11 +10,11 @@ To open window for batch processing use marked button or use *Batch processing*
 
 1. Select how the mask file for segmentation will be recognized.
 
-   a.  In section *Use mask from*, Select *File* tab.
+   a. In section *Use mask from*, Select *File* tab.
 
    b. Select *Suffix*.
 
-   c. Input “\_mask” in  *Use suffix* field. (All masks created by the *ROI Mask* component of Partseg have `_mask` suffix)
+   c. Input “\_mask” in *Use suffix* field. (All masks created by the *ROI Mask* component of Partseg have `_mask` suffix)
 
    d. Confirm with the "Add mask" button
 
@@ -36,11 +36,11 @@ To open window for batch processing use marked button or use *Batch processing*
 
    b. All measurements within the selected set are visible in the *information* section
 
-   c.  Select channel (x) and units (um) that will be used in quantification.
+   c. Select channel (x) and units (um) that will be used in quantification.
 
-   d.  Confirm with the "Add Set of measurements" button
+   d. Confirm with the "Add Set of measurements" button
 
-   e.  The segmentation profile is now added to the workflow (3c).
+   e. The segmentation profile is now added to the workflow (3c).
 
 4. Save created Workflow under the chosen name (e.g. *Chromosome1_batch*) with the "Save" button.
 

diff --git a/tutorials/tutorial-chromosome-1/tutorial-chromosome1_16.md b/tutorials/tutorial-chromosome-1/tutorial-chromosome1_16.md
@@ -118,7 +118,7 @@ In order to quantify features of chromosome 1 territory segmentation of FISH spe
 
 8. Execute segmentation
 
-9. Save segmentation profile with name "chromosome1_prof" (more details in [interface documentation](<>))  **TODO**
+9. Save segmentation profile with name "chromosome1_prof" (more details in [interface documentation](<>)) **TODO**
 
 Some background signal is always present in FISH, however specific signal is much brighter.
 As an example nucleus with two separate chromosome 1 territories is shown,