Apply non esentail parts of better serialization PR #462 (#533)

Co-authored-by: Sourcery AI <>
Co-authored-by: sourcery-ai[bot] <58596630+sourcery-ai[bot]@users.noreply.github.com>

.github/workflows/test_prereleases.yml

@@ -69,21 +69,10 @@ jobs:
 
       - name: Test with tox linux
         # run tests using pip install --pre
-        if: runner.os == 'Linux'
         uses: GabrielBB/xvfb-action@v1
         timeout-minutes: 60
         with:
-          run: tox -v --pre
-        env:
-          PLATFORM: ${{ matrix.platform }}
-          PYVISTA_OFF_SCREEN: True  # required for opengl on windows
-          NAPARI: None
-
-      - name: Test with tox linux
-        # run tests using pip install --pre
-        if: runner.os != 'Linux'
-        timeout-minutes: 60
-        run: tox -v --pre
+          run: python -m tox -v --pre
         env:
           PLATFORM: ${{ matrix.platform }}
           PYVISTA_OFF_SCREEN: True  # required for opengl on windows

.github/workflows/tests.yml

@@ -74,21 +74,10 @@ jobs:
 
     - name: Test with tox linux
       # run tests using pip install --pre
-      if: runner.os == 'Linux'
       uses: GabrielBB/xvfb-action@v1
       timeout-minutes: 60
       with:
-        run: tox
-      env:
-        PLATFORM: ${{ matrix.platform }}
-        PYVISTA_OFF_SCREEN: True  # required for opengl on windows
-        NAPARI: None
-
-    - name: Test with tox linux
-      # run tests using pip install --pre
-      if: runner.os != 'Linux'
-      timeout-minutes: 60
-      run: tox
+        run: python -m tox
       env:
         PLATFORM: ${{ matrix.platform }}
         PYVISTA_OFF_SCREEN: True  # required for opengl on windows
@@ -136,7 +125,7 @@ jobs:
         # run tests using pip install --pre
         uses: GabrielBB/xvfb-action@v1
         with:
-          run: tox -e py38-PyQt5-all
+          run: python -m tox -e py38-PyQt5-all
         timeout-minutes: 60
 
   test_coverage:
@@ -168,7 +157,7 @@ jobs:
       - name: Test with tox
         uses: GabrielBB/xvfb-action@v1
         with:
-          run: tox -e py38-PyQt5-coverage
+          run: python -m tox -e py38-PyQt5-coverage
         timeout-minutes: 60
 
       - uses: codecov/codecov-action@v1
@@ -200,5 +189,5 @@ jobs:
       - name: Test with tox
         uses: GabrielBB/xvfb-action@v1
         with:
-          run: tox -e py37-PyQt5-minimal
+          run: python -m tox -e py37-PyQt5-minimal
         timeout-minutes: 60

MANIFEST.in

@@ -38,3 +38,4 @@ exclude dist/**
 exclude dist/**.swp
 exclude cliff.toml
 exclude runtime.txt
+exclude .sourcery.yaml

package/PartSeg/_roi_analysis/main_window.py

@@ -278,7 +278,7 @@ def save_profile(self):
                 QMessageBox.No,
             ):
                 continue
-            resp = ROIExtractionProfile(text, widget.name, widget.get_values())
+            resp = ROIExtractionProfile(name=text, algorithm=widget.name, values=widget.get_values())
             self._settings.roi_profiles[text] = resp
             self._settings.dump()
             break

package/PartSeg/_roi_analysis/prepare_plan_widget.py

@@ -468,9 +468,9 @@ def change_segmentation_table(self):
         index = self.segment_stack.currentIndex()
         text = self.segment_stack.tabText(index)
         if self.update_element_chk.isChecked():
-            self.chose_profile_btn.setText("Replace " + text)
+            self.chose_profile_btn.setText(f"Replace {text}")
         else:
-            self.chose_profile_btn.setText("Add " + text)
+            self.chose_profile_btn.setText(f"Add {text}")
         self.segment_profile.setCurrentItem(None)
         self.pipeline_profile.setCurrentItem(None)
 
@@ -800,9 +800,12 @@ def refresh_profiles(self, list_widget: QListWidget, new_values: typing.List[str
 
     @contextmanager
     def enable_protect(self):
+        previous = self.protect
         self.protect = True
-        yield
-        self.protect = False
+        try:
+            yield
+        finally:
+            self.protect = previous
 
     def _refresh_measurement(self):
         new_measurements = list(sorted(self.settings.measurement_profiles.keys(), key=str.lower))
@@ -1125,7 +1128,7 @@ def delete_plan(self):
         if self.calculate_plans.currentItem() is None:
             return
         text = str(self.calculate_plans.currentItem().text())
-        if text == "":
+        if not text:
             return
         if text in self.settings.batch_plans:
             del self.settings.batch_plans[text]
@@ -1135,7 +1138,7 @@ def edit_plan(self):
         if self.calculate_plans.currentItem() is None:
             return
         text = str(self.calculate_plans.currentItem().text())
-        if text == "":
+        if not text:
             return
         if text in self.settings.batch_plans:
             self.plan_to_edit = self.settings.batch_plans[text]

package/PartSeg/_roi_mask/simple_measurements.py

@@ -84,7 +84,7 @@ def calculate(self):
             QMessageBox.warning(self, "No measurement", "Select at least one measurement")
             return
 
-        profile = MeasurementProfile("", [MeasurementEntry(x.name, x) for x in to_calculate])
+        profile = MeasurementProfile("", [MeasurementEntry(name=x.name, calculation_tree=x) for x in to_calculate])
 
         dial = ExecuteFunctionDialog(
             profile.calculate,

package/PartSeg/common_backend/base_argparser.py

@@ -25,9 +25,9 @@ def proper_suffix(val: str):
 
     :raise argparse.ArgumentTypeError: on validation error
     """
-    if len(val) > 0 and not val.isalnum():
-        raise argparse.ArgumentTypeError(f"suffix '{val}' need to contains only alpha numeric characters")
-    return val
+    if not val or val.isalnum():
+        return val
+    raise argparse.ArgumentTypeError(f"suffix '{val}' need to contains only alpha numeric characters")
 
 
 def proper_path(val: str):
@@ -40,8 +40,9 @@ def proper_path(val: str):
         return val
     try:
         os.makedirs(val)
-    except OSError:
-        raise argparse.ArgumentTypeError(f" Path {val} is not a valid path in this system")
+    except OSError as e:
+        raise argparse.ArgumentTypeError(f" Path {val} is not a valid path in this system") from e
+
     return val
 
 
@@ -105,8 +106,9 @@ def parse_args(self, args: Optional[Sequence[str]] = None, namespace: Optional[a
         state_store.develop = args.develop
         state_store.save_suffix = args.save_suffix[0]
         state_store.save_folder = os.path.abspath(
-            args.save_directory[0] + ("_" + state_store.save_suffix if state_store.save_suffix else "")
+            args.save_directory[0] + (f"_{state_store.save_suffix}" if state_store.save_suffix else "")
         )
+
         if args.no_report and args.no_dialog:
             _setup_sentry()
         sys.excepthook = my_excepthook
@@ -129,6 +131,4 @@ def _setup_sentry():  # pragma: no cover
 
 
 def safe_repr(val):
-    if isinstance(val, np.ndarray):
-        return numpy_repr(val)
-    return _safe_repr(val)
+    return numpy_repr(val) if isinstance(val, np.ndarray) else _safe_repr(val)

package/PartSeg/common_backend/base_settings.py

@@ -176,8 +176,8 @@ def roi(self, val: Union[np.ndarray, ROIInfo]):
                 self._roi_info = ROIInfo(self.image.fit_array_to_image(val))
             else:
                 self._roi_info = val.fit_to_image(self.image)
-        except ValueError:
-            raise ValueError(ROI_NOT_FIT)
+        except ValueError as e:
+            raise ValueError(ROI_NOT_FIT) from e
         self._additional_layers = {}
         self.roi_changed.emit(self._roi_info)
 
@@ -540,8 +540,8 @@ def set_segmentation_result(self, result: ROIExtractionResult):
         # Fixme not use EventedDict here
         try:
             roi_info = result.roi_info.fit_to_image(self.image)
-        except ValueError:  # pragma: no cover
-            raise ValueError(ROI_NOT_FIT)
+        except ValueError as e:  # pragma: no cover
+            raise ValueError(ROI_NOT_FIT) from e
         if result.points is not None:
             self.points = result.points
         self._roi_info = roi_info
@@ -601,8 +601,8 @@ def mask(self, value):
         try:
             self._image.set_mask(value)
             self.mask_changed.emit()
-        except ValueError:
-            raise ValueError("mask do not fit to image")
+        except ValueError as e:
+            raise ValueError("mask do not fit to image") from e
 
     def get_save_list(self) -> List[SaveSettingsDescription]:
         """List of files in which program save the state."""
@@ -618,7 +618,7 @@ def get_path_history(self) -> List[str]:
         """
         res = self.get(DIR_HISTORY, [])[:]
         for name in self.save_locations_keys:
-            val = self.get("io." + name, str(Path.home()))
+            val = self.get(f"io.{name}", str(Path.home()))
             if val not in res:
                 res = res + [val]
         return res
@@ -698,9 +698,7 @@ def load_part(cls, file_path):
         data = cls.load_metadata(file_path)
         bad_key = []
         if isinstance(data, MutableMapping) and not check_loaded_dict(data):
-            for k, v in data.items():
-                if not check_loaded_dict(v):
-                    bad_key.append(k)
+            bad_key.extend(k for k, v in data.items() if not check_loaded_dict(v))
             for el in bad_key:
                 del data[el]
         elif isinstance(data, ProfileDict) and not data.verify_data():
@@ -762,7 +760,7 @@ def load(self, folder_path: Union[Path, str, None] = None):
                 if error:
                     timestamp = datetime.today().strftime("%Y-%m-%d_%H_%M_%S")
                     base_path, ext = os.path.splitext(file_path)
-                    os.rename(file_path, base_path + "_" + timestamp + ext)
+                    os.rename(file_path, f"{base_path}_{timestamp}{ext}")
 
         if errors_list:
             logger.error(errors_list)

package/PartSeg/common_gui/algorithms_description.py

@@ -467,12 +467,9 @@ def algorithm_choose(self, name):
             if name not in self.property.possible_values:
                 return
             start_dict = {} if name not in self.starting_values else self.starting_values[name]
-            try:
-                self.widgets_dict[name] = FormWidget(
-                    self.property.possible_values[name].get_fields(), start_values=start_dict
-                )
-            except KeyError as e:
-                raise e
+            self.widgets_dict[name] = FormWidget(
+                self.property.possible_values[name].get_fields(), start_values=start_dict
+            )
             self.widgets_dict[name].layout().setContentsMargins(0, 0, 0, 0)
             self.layout().addWidget(self.widgets_dict[name])
             self.widgets_dict[name].value_changed.connect(self.values_changed)
@@ -633,7 +630,7 @@ def enable_selector(self):
             el.setEnabled(True)
 
     def get_segmentation_profile(self) -> ROIExtractionProfile:
-        return ROIExtractionProfile("", self.algorithm.get_name(), self.get_values())
+        return ROIExtractionProfile(name="", algorithm=self.algorithm.get_name(), values=self.get_values())
 
 
 class AlgorithmChooseBase(QWidget):
@@ -738,7 +735,7 @@ def current_widget(self) -> InteractiveAlgorithmSettingsWidget:
 
     def current_parameters(self) -> ROIExtractionProfile:
         widget = self.current_widget()
-        return ROIExtractionProfile("", widget.name, widget.get_values())
+        return ROIExtractionProfile(name="", algorithm=widget.name, values=widget.get_values())
 
     def get_info_text(self):
         return self.current_widget().algorithm_thread.get_info_text()

package/PartSeg/plugins/napari_widgets/roi_extraction_algorithms.py

@@ -172,7 +172,7 @@ def save_action(self):
                 QMessageBox.No,
             ):
                 break  # pragma: no cover
-        resp = ROIExtractionProfile(text, widget.name, widget.get_values())
+        resp = ROIExtractionProfile(name=text, algorithm=widget.name, values=widget.get_values())
         profiles[text] = resp
         self.settings.dump()
         self.profile_combo_box.addItem(text)

package/PartSeg/plugins/napari_widgets/simple_measurement_widget.py

@@ -67,7 +67,7 @@ def _calculate(self, event=None):
             warnings.warn("No measurement. Select at least one measurement")
             return
 
-        profile = MeasurementProfile("", [MeasurementEntry(x.name, x) for x in to_calculate])
+        profile = MeasurementProfile("", [MeasurementEntry(name=x.name, calculation_tree=x) for x in to_calculate])
 
         data_layer = self.image_choice.value or self.labels_choice.value
 

package/PartSegCore/analysis/calculation_plan.py

@@ -705,9 +705,9 @@ def dict_load(cls, data_dict):
             res_plan.current_pos = pos[:-1]
             try:
                 res_plan.add_step(CalculationPlan.correct_name[el["type"]](**el["values"]))
-            except TypeError as e:
+            except TypeError:
                 logging.warning(el["type"])
-                raise e
+                raise
         res_plan.changes = []
         return res_plan
 
@@ -743,8 +743,8 @@ def get_el_name(el):
         if isinstance(el, Save):
             base = el.short_name
             if el.directory:
-                return f"Save {base} in directory with name " + el.suffix
-            return "Save " + base + " with suffix " + el.suffix if el.suffix != "" else "Save " + base
+                return f"Save {base} in directory with name {el.suffix}"
+            return f"Save {base} with suffix {el.suffix}" if el.suffix != "" else f"Save {base}"
 
         if isinstance(el, MaskIntersection):
             if el.name == "":

package/PartSegCore/analysis/load_functions.py

@@ -228,7 +228,7 @@ def load(
             metadata = {"default_spacing": (10**-6, 10**-6, 10**-6)}
         if len(load_locations) == 1:
             new_path, ext = os.path.splitext(load_locations[0])
-            new_path += "_mask" + ext
+            new_path += f"_mask{ext}"
             if not os.path.exists(new_path):
                 raise ValueError("Cannot determine mask file. It need to have '_mask' suffix.")
             load_locations.append(load_locations)
@@ -243,7 +243,7 @@ def load(
     @classmethod
     def get_next_file(cls, file_paths: typing.List[str]):
         base, ext = os.path.splitext(file_paths[0])
-        return base + "_mask" + ext
+        return f"{base}_mask{ext}"
 
 
 class LoadMask(LoadBase):
@@ -349,9 +349,9 @@ def update_segmentation_pipeline_element(cls, data: SegmentationPipelineElement)
     @classmethod
     def update_segmentation_pipeline(cls, data: SegmentationPipeline) -> SegmentationPipeline:
         return SegmentationPipeline(
-            data.name,
-            cls.update_segmentation_profile(data.segmentation),
-            [cls.update_segmentation_pipeline_element(x) for x in data.mask_history],
+            name=data.name,
+            segmentaion=cls.update_segmentation_profile(data.segmentation),
+            mask_history=[cls.update_segmentation_pipeline_element(x) for x in data.mask_history],
         )
 
     @classmethod
@@ -426,9 +426,7 @@ def load(
         data = load_metadata(load_locations[0])
         bad_key = []
         if isinstance(data, typing.MutableMapping) and not check_loaded_dict(data):
-            for k, v in data.items():
-                if not check_loaded_dict(v):
-                    bad_key.append(k)
+            bad_key.extend(k for k, v in data.items() if not check_loaded_dict(v))
             for el in bad_key:
                 del data[el]
         elif isinstance(data, ProfileDict) and not data.verify_data():
@@ -452,9 +450,9 @@ def load_metadata(data: typing.Union[str, Path]):
 
 def update_algorithm_dict(dkt):
     if "name" in dkt:
-        profile = ROIExtractionProfile("", dkt["name"], dkt["values"])
+        profile = ROIExtractionProfile(name="", algorithm=dkt["name"], values=dkt["values"])
     elif "algorithm_name" in dkt:
-        profile = ROIExtractionProfile("", dkt["algorithm_name"], dkt["values"])
+        profile = ROIExtractionProfile(name="", algorithm=dkt["algorithm_name"], values=dkt["values"])
     else:
         return dkt
     profile = UpdateLoadedMetadataAnalysis.recursive_update(profile)