Docstrings and tweaks of ScanWorflow refactor

src/openflexure_microscope_server/scan_directories.py

@@ -59,7 +59,7 @@ class BaseScanData(BaseModel):
         ScanWorkflow
     * HistoricScanData which has the workflow specific data loaded as a dictionary.
 
-    Sepearating historic and active data allows workflows to use any BaseModel for its
+    Separating historic and active data allows workflows to use any BaseModel for its
     settings, but for the data to be reloaded even if that model has updated or is not
     available. Historic scan data loaded from disk is used for stitching and for
     creating a ScanInfo object for  communicating with the UI. These uses are clearly

src/openflexure_microscope_server/things/autofocus.py

@@ -567,7 +567,7 @@ class AutofocusThing(lt.Thing):
         """Capture a series of images checking that sharpest image central.
 
         This is part of run_smart_stack. This is the actual z_stackng stacking method
-        called by the action run_smart_stack. The action also handles reseting,
+        called by the action run_smart_stack. The action also handles resetting,
         autofocussing, and retrying.
 
         The images are separated in z offset by stack_parameters.stack_dz, as they

src/openflexure_microscope_server/things/scan_workflows.py

@@ -40,13 +40,13 @@ SettingModelType = TypeVar("SettingModelType", bound=BaseModel)
 class ScanWorkflow(Generic[SettingModelType], lt.Thing):
     """A base class for all Scanworkflows.
 
-    Scan workflows set the behaviour of a scan, inclduing the background detection,
+    Scan workflows set the behaviour of a scan, including the background detection,
-    scan planning, aquisition routine.
+    scan planning, acquisition routine.
     """
 
     _settings_model: type[SettingModelType]
 
-    # All workdlows must have a set class for scan planning
+    # All workflows must have a set class for scan planning
     _planner_cls: type[ScanPlanner]
 
     # All workflows set a save resolution
@@ -98,19 +98,19 @@ class ScanWorkflow(Generic[SettingModelType], lt.Thing):
             "Each specific ScanWorkflow must implement a ``new_scan_planner`` method."
         )
 
-    def aquisition_routine(
+    def acquisition_routine(
         self, settings: SettingModelType, xyz_pos: tuple[int, int, int]
     ) -> tuple[bool, Optional[int]]:
-        """Overload to set the aquisition routine that happens at each scan site."""
+        """Overload to set the acquisition routine that happens at each scan site."""
         raise NotImplementedError(
-            "Each specific ScanWorkflow must implement an aquisition routine"
+            "Each specific ScanWorkflow must implement an acquisition routine"
         )
 
 
 class HistoScanSettingsModel(BaseModel):
     """The settings for a scan with the HistoScanWorkflow.
 
-    This includes settings caluclated when starting. This will be held by smart scan
+    This includes settings calculated when starting. This will be held by smart scan
     during a scan and serialised to disk.
     """
 
@@ -188,7 +188,7 @@ class HistoScanWorkflow(ScanWorkflow[HistoScanSettingsModel]):
     * 200 for 20x
     """
 
-    # The noqa statment is because scan_name is unused but is needed for equivalence
+    # The noqa statement is because scan_name is unused but is needed for equivalence
     # with other workflows that may want to validate the scan name.
     def check_before_start(self, scan_name: str) -> None:  # noqa: ARG002
         """Before starting a scan, check that background and camera-stage-mapping are set.
@@ -389,13 +389,13 @@ class HistoScanWorkflow(ScanWorkflow[HistoScanSettingsModel]):
             planner_settings=planner_settings,
         )
 
-    def aquisition_routine(
+    def acquisition_routine(
         self, settings: HistoScanSettingsModel, xyz_pos: tuple[int, int, int]
     ) -> tuple[bool, Optional[int]]:
-        """Perform aquisition routine. This is run at each scan location.
+        """Perform acquisition routine. This is run at each scan location.
 
         :param settings: The settings for this scan as a HistoScanSettingsModel
-        :param xyz_position: The current position as a tuple or 3 ints.
+        :param xyz_pos: The current position as a tuple or 3 ints.
         :return: A tuple of whether an image was taken, and the z-position for focus.
             If failed to find focus, returns for the focus z-position.
         """

src/openflexure_microscope_server/things/smart_scan.py

@@ -179,8 +179,8 @@ class SmartScanThing(lt.Thing):
     def sample_scan(self, scan_name: str = "") -> None:
         """Move the stage to cover an area, taking images.
 
-        Depending on the way the stage moves depends on the selected worflow.
+        Depending on the way the stage moves depends on the selected workflow.
-        If images overlap for a scan workdlow then the images can be stitched together
+        If images overlap for a scan workflow then the images can be stitched together
         into a larger composite image.
         """
         got_lock = self._scan_lock.acquire(timeout=0.1)
@@ -383,7 +383,7 @@ class SmartScanThing(lt.Thing):
                 new_pos_xyz[1],
                 self._stage.position["z"],
             )
-            imaged, focus_height = workflow.aquisition_routine(
+            imaged, focus_height = workflow.acquisition_routine(
                 workflow_settings, current_pos_xyz
             )