ci: [pre-commit.ci] pre-commit autoupdate (#1068)

<!--pre-commit.ci start-->
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.1.14 →
v0.2.0](astral-sh/ruff-pre-commit@v0.1.14...v0.2.0)
<!--pre-commit.ci end-->

<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->

## Summary by CodeRabbit

- **Refactor**
- Improved code robustness by utilizing the `get` method for dictionary
access across several modules. This enhances error handling and code
readability.
- **Bug Fixes**
- Adjusted data type handling in file attribute management for
consistency and reliability.
- **Chores**
- Updated the version of a development tool to enhance the setup
configuration formatting process.

<!-- end of auto-generated comment: release notes by coderabbit.ai -->

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Grzegorz Bokota <[email protected]>

.pre-commit-config.yaml

@@ -25,7 +25,7 @@ repos:
     - id: setup-cfg-fmt
       args: ["--include-version-classifiers", "--max-py-version", "3.11"]
 -   repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.1.14
+    rev: v0.2.0
     hooks:
       - id: ruff
 -   repo: https://github.com/asottile/pyupgrade

package/PartSeg/_roi_mask/main_window.py

@@ -97,7 +97,7 @@ def prev_mask(self):
             history.roi_extraction_parameters["selected"],
             history.roi_extraction_parameters["parameters"],
         )
-        self.settings.mask = seg["mask"] if "mask" in seg else None
+        self.settings.mask = seg.get("mask")
         self.close()
 
 

package/PartSeg/common_gui/algorithms_description.py

@@ -572,7 +572,7 @@ def algorithm_choose(self, name):
         if name not in self.widgets_dict:
             if name not in self.property.possible_values:
                 return
-            start_dict = {} if name not in self.starting_values else self.starting_values[name]
+            start_dict = self.starting_values.get(name, {})
             self.widgets_dict[name] = self._get_form_widget(self.property.possible_values[name], start_dict)
 
             self.layout().addWidget(self.widgets_dict[name])

package/PartSegCore/analysis/load_functions.py

@@ -100,7 +100,7 @@ def load_project_from_tar(tar_file, file_path):
 
     if version == Version("1.0"):
         seg_dict = np.load(tar_to_buff(tar_file, "segmentation.npz"))
-        mask = seg_dict["mask"] if "mask" in seg_dict else None
+        mask = seg_dict.get("mask")
         roi = seg_dict["segmentation"]
     else:
         roi = tifffile.imread(tar_to_buff(tar_file, "segmentation.tif"))

package/PartSegCore/analysis/save_functions.py

@@ -122,14 +122,14 @@ def _save_cmap(
             meta_group.attrs[key] = val
 
     grp = cmap_file["Chimera"]
-    grp.attrs["CLASS"] = np.string_("GROUP")
-    grp.attrs["TITLE"] = np.string_("")
-    grp.attrs["VERSION"] = np.string_("1.0")
+    grp.attrs["CLASS"] = np.bytes_("GROUP")
+    grp.attrs["TITLE"] = np.bytes_("")
+    grp.attrs["VERSION"] = np.bytes_("1.0")
 
     grp = cmap_file["Chimera/image1"]
-    grp.attrs["CLASS"] = np.string_("GROUP")
-    grp.attrs["TITLE"] = np.string_("")
-    grp.attrs["VERSION"] = np.string_("1.0")
+    grp.attrs["CLASS"] = np.bytes_("GROUP")
+    grp.attrs["TITLE"] = np.bytes_("")
+    grp.attrs["VERSION"] = np.bytes_("1.0")
     grp.attrs["step"] = np.array(spacing, dtype=np.float32)[::-1] * UNIT_SCALE[cmap_profile["units"].value]
 
     return cmap_file

package/PartSegCore/mask/io_functions.py

@@ -293,11 +293,11 @@ def load_stack_segmentation_from_tar(tar_file: tarfile.TarFile, file_path: str,
     step_changed(6)
     return MaskProjectTuple(
         file_path=file_path,
-        image=metadata["base_file"] if "base_file" in metadata else None,
+        image=metadata.get("base_file"),
         roi_info=roi_info,
         selected_components=metadata["components"],
         mask=mask,
-        roi_extraction_parameters=metadata["parameters"] if "parameters" in metadata else None,
+        roi_extraction_parameters=metadata.get("parameters"),
         history=history,
         spacing=([10 ** (-9), *list(spacing)]) if spacing is not None else None,
         frame_thickness=metadata.get("frame_thickness", FRAME_THICKNESS),

package/PartSegCore/project_info.py

@@ -72,7 +72,7 @@ def get_roi_info_and_mask(self) -> Tuple[ROIInfo, Optional[np.ndarray]]:
         self.arrays.seek(0)
         alternative = {name: array for name, array in seg.items() if name not in {"roi", "mask"}}
         roi_info = ROIInfo(seg["roi"], annotations=self.annotations, alternative=alternative)
-        mask = seg["mask"] if "mask" in seg else None
+        mask = seg.get("mask")
         return roi_info, mask
 
 

package/PartSegCore/utils.py

@@ -169,7 +169,7 @@ def __setitem__(self, k, v) -> None:
         if k in self._dict and isinstance(self._dict[k], EventedDict):
             self._dict[k].setted.disconnect(self._propagate_setitem)
             self._dict[k].deleted.disconnect(self._propagate_del)
-        old_value = self._dict[k] if k in self._dict else None
+        old_value = self._dict.get(k)
         with suppress(ValueError):
             if old_value == v:
                 return

pyproject.toml

@@ -33,6 +33,11 @@ exclude = '''
 
 [tool.ruff]
 line-length = 120
+exclude = ["examples/call_simple_threshold.py"]
+target-version = "py38"
+fix = true
+
+[tool.ruff.lint]
 select = [
     "F", # Pyflakes
     "E", "W", # pycodestyle
@@ -65,22 +70,19 @@ select = [
 ignore = ["A003", "SIM108", "ARG002", "ARG003", "ARG004", "PLR2004",
     "PLR0913" # should be reenabled in future version
 ]
-exclude = ["examples/call_simple_threshold.py"]
-target-version = "py38"
-fix = true
 
-[tool.ruff.isort]
+[tool.ruff.lint.isort]
 known-first-party=['PartSeg', 'PartSegData','PartSegCore','PartSegImage', 'PartSegCore_compiled_backend']
 
-[tool.ruff.flake8-tidy-imports]
+[tool.ruff.lint.flake8-tidy-imports]
 # Disallow all relative imports.
 ban-relative-imports = "all"
 
-[tool.ruff.mccabe]
+[tool.ruff.lint.mccabe]
 # Unlike Flake8, default to a complexity level of 10.
 max-complexity = 15
 
-[tool.ruff.per-file-ignores]
+[tool.ruff.lint.per-file-ignores]
 "docs/conf.py" = ["A001"]
 "package/tests/**" = ["ARG", "PLC1901", "S101", "RUF012"]
 "package/PartSegCore/sphinx/*" = ["ARG"]