Update stiching to differentiate bwtween stitchers that use a thread and those that block

src/openflexure_microscope_server/stitching.py

@@ -44,7 +44,12 @@ def validate_command(cmd: list[str]):
 
 
 class BaseStitcher:
-    """A base stitching class for all stitchers. Don't initialise this directly."""
+    """A base stitching class for all stitchers. Don't initialise this directly.
+
+    The base class has no way to run the command. Child classes should either implement
+    a ``start``, ``running``, and ``wait`` methods if they stitch in a thread, or ``run``
+    if they stitch in this thread and return once complete.
+    """
 
     def __init__(self, images_dir: str, *, overlap: float, correlation_resize: float):
         """Initialise a stitcher.
@@ -104,15 +109,6 @@ class BaseStitcher:
                 "Invalid directory path: Contains unsafe characters."
             )
 
-    def start(self) -> None:
-        """Start stitching a stitching process.
-
-        This should be overridden by any child class.
-        """
-        raise NotImplementedError(
-            "Child stitchers should implement their own ``start`` method."
-        )
-
 
 class PreviewStitcher(BaseStitcher):
     """A stitcher for stitching an ongoing scan in preview mode.
@@ -262,7 +258,7 @@ class FinalStitcher(BaseStitcher):
                 )
         return overlap, correlation_resize
 
-    def start(
+    def run(
         self,
         cancel: lt.deps.CancelHook,
     ) -> None:

src/openflexure_microscope_server/things/smart_scan.py

@@ -715,7 +715,7 @@ class SmartScanThing(lt.Thing):
         )
         try:
             # start the final stitch, providing the cancel hook to allow aborting
-            final_stitcher.start(cancel)
+            final_stitcher.run(cancel)
         except lt.exceptions.InvocationCancelledError:
             # Sleep for 1 second just to allow invocation logs to pass to user.
             time.sleep(1)

tests/test_stitching.py

@@ -54,9 +54,6 @@ def test_base_stitcher():
         ]
         stitcher = BaseStitcher(FAKE_DIR, overlap=overlap, correlation_resize=0.5)
         assert stitcher.command == expected_command
-        # check that a BaseStitcher can't start
-        with pytest.raises(NotImplementedError):
-            stitcher.start()
 
 
 def test_preview_stitcher_command():
@@ -227,7 +224,7 @@ def test_final_stitching_command(caplog, mocker):
             FAKE_DIR, logger=LOGGER, overlap=0.1, correlation_resize=0.5
         )
         # For the final stitcher it will always complete before returning.
-        stitcher.start(cancel=lt.deps.CancelHook(id=uuid.uuid4()))
+        stitcher.run(cancel=lt.deps.CancelHook(id=uuid.uuid4()))
         # The mock command logs the inputs (but not the initial command) and the
         # stitcher logs # "Stitching complete" when it ends.
         assert len(caplog.records) == len(FINAL_EXPECTED_COMMAND)
@@ -250,7 +247,7 @@ def test_final_stitching_command_cancelled(caplog, mocker):
         cancel_hook = lt.deps.CancelHook(id=uuid.uuid4())
 
         # Start stitching in a thread.
-        thread = threading.Thread(target=stitcher.start, kwargs={"cancel": cancel_hook})
+        thread = threading.Thread(target=stitcher.run, kwargs={"cancel": cancel_hook})
         thread.start()
         # Sleep long enough for at least 1 log.
         sleep(0.5)
@@ -273,4 +270,4 @@ def test_final_stitching_command_error(caplog, mocker):
         # than echo.
         stitcher._extra_args = ["ERROR"]
         with pytest.raises(ChildProcessError):
-            stitcher.start(cancel=lt.deps.CancelHook(id=uuid.uuid4()))
+            stitcher.run(cancel=lt.deps.CancelHook(id=uuid.uuid4()))