src/aare/gui/main_window.py

@@ -1024,6 +1024,7 @@ class MainWindow(QMainWindow):
         )
 
         self.job_list_panel.auto_scan.connect(self.daq.automated_scan)
+        self.job_list_panel.auto_scan.connect(self.data_collection.auto_scan_started)
 
         self.job_list_panel.unmount.connect(self.daq.unmount)
         self.job_list_panel.unmount_then_park_and_dry.connect(self.daq.unmount_then_park_and_dry)
@@ -1148,6 +1149,7 @@ class MainWindow(QMainWindow):
 
         self.daq.automated_scan_done.connect(self.job_list_panel.automated_scan_done)
         self.daq.automated_scan_done.connect(self._mark_scan_result)
+        self.daq.automated_scan_done.connect(self.data_collection.auto_scan_finished)
         self.daq.automation_critical_failure.connect(self._on_automation_critical_failure)
         self.daq.manual_collection_critical_failure.connect(
             self._on_manual_collection_critical_failure

src/aare/gui/panels/data_collection_settings.py

@@ -195,6 +195,9 @@ class DataCollectionSettings(QFrame):
         # startup must not trigger an auto-centering (hardware would move
         # uninvited on every restart).
         self._status_seen = False
+        # Set on mount, fired once the hw lock frees (see _track_sample).
+        self._center_after_mount_pending = False
+        self._auto_scans_in_flight = 0
 
         self._tab_bar.currentChanged.connect(self._stack.setCurrentIndex)
         self._tab_bar.currentChanged.connect(self._on_tab_changed)
@@ -242,23 +245,48 @@ class DataCollectionSettings(QFrame):
         self.raster.update_daq_status(s)
         self.screening.update_daq_status(s)
         self.simple.update_daq_status(s)
-        self._track_sample(None if s.sample is None else s.sample.db_id)
+        self._track_sample(None if s.sample is None else s.sample.db_id, s.busy)
 
-    def _track_sample(self, db_id: int | None):
+    def _track_sample(self, db_id: int | None, busy: bool = False):
         # Separate from update_daq_status so tests can drive mount detection
         # without building a full DAQStatusModel.
         if db_id is None:
             # Forget on unmount so remounting the same sample counts as a
             # fresh mount below.
             self._sample_id = None
+            self._center_after_mount_pending = False
         elif db_id != self._sample_id:
             self._sample_id = db_id
             self._tab_bar.setCurrentIndex(0)
-            if self._status_seen and self.auto_center_after_mount.isChecked():
-                # Reuse the button wiring (clicked -> daq.center_loop in
-                # main_window) instead of a second signal path.
-                self.find_tip.click()
+            self._center_after_mount_pending = (
+                self._status_seen
+                and self.auto_center_after_mount.isChecked()
+                and not self._auto_scans_in_flight
+            )
         self._status_seen = True
+        # The server publishes the new sample while the mount still holds the
+        # hw lock, and /alc/center_loop refuses (non-blocking lock) while busy,
+        # so firing on the id change alone was silently rejected. Wait for idle.
+        if self._center_after_mount_pending and not busy:
+            self._center_after_mount_pending = False
+            # Reuse the button wiring (clicked -> daq.center_loop in
+            # main_window) instead of a second signal path.
+            self.find_tip.click()
+
+    # Queue automation centers each sample itself and frees the hw lock
+    # between samples; a GUI centering in that gap could steal the lock from
+    # the next /scan/auto. Tracks the request, not the queue's running flag,
+    # because Pause flips that flag while the current sample is still running.
+    # A counter, since the queue sends the next scan before the settings panel
+    # sees the previous one's done signal.
+    @Slot()
+    def auto_scan_started(self):
+        self._auto_scans_in_flight += 1
+        self._center_after_mount_pending = False
+
+    @Slot()
+    def auto_scan_finished(self):
+        self._auto_scans_in_flight = max(0, self._auto_scans_in_flight - 1)
 
     @Slot(int)
     def _on_tab_changed(self, idx: int):

tests/unit/gui/test_data_collection_settings.py

@@ -353,6 +353,59 @@ def test_auto_center_fires_on_mount_only_when_armed(settings_panel):
     assert len(clicks) == 3
 
 
+def test_auto_center_waits_for_mount_to_release_hw_lock(settings_panel):
+    # Server shows the new sample while the mount still holds the hw lock;
+    # center_loop would be refused then, so the click must wait for idle.
+    clicks = []
+    settings_panel.find_tip.clicked.connect(lambda: clicks.append(1))
+    settings_panel.auto_center_after_mount.setChecked(True)
+    settings_panel._track_sample(1)
+    settings_panel._track_sample(None)
+
+    settings_panel._track_sample(2, busy=True)
+    settings_panel._track_sample(2, busy=True)
+    assert not clicks
+    settings_panel._track_sample(2, busy=False)
+    assert len(clicks) == 1
+    settings_panel._track_sample(2, busy=False)
+    assert len(clicks) == 1
+
+    # Unmount before the lock frees drops the pending centering.
+    settings_panel._track_sample(3, busy=True)
+    settings_panel._track_sample(None, busy=False)
+    assert len(clicks) == 1
+
+
+def test_auto_center_skipped_while_auto_scan_in_flight(settings_panel):
+    # Automation centers itself and frees the lock between samples; a GUI
+    # centering there could steal the lock from the next /scan/auto.
+    clicks = []
+    settings_panel.find_tip.clicked.connect(lambda: clicks.append(1))
+    settings_panel.auto_center_after_mount.setChecked(True)
+    settings_panel._track_sample(1)
+
+    # Queue sends the next scan before the settings panel sees the previous one
+    # finish (signal order in main_window): must still count as in flight.
+    settings_panel.auto_scan_started()
+    settings_panel.auto_scan_started()
+    settings_panel.auto_scan_finished()
+    settings_panel._track_sample(2, busy=True)
+    settings_panel._track_sample(2, busy=False)
+    assert not clicks
+
+    # Pause mid-sample: the current scan still runs to completion, so no
+    # centering until its request is done and a later manual mount happens.
+    settings_panel._track_sample(3, busy=True)
+    settings_panel.auto_scan_finished()
+    settings_panel._track_sample(3, busy=False)
+    assert not clicks
+
+    settings_panel._track_sample(None)
+    settings_panel._track_sample(4, busy=True)
+    settings_panel._track_sample(4, busy=False)
+    assert len(clicks) == 1
+
+
 # ---------------------------------------------------------------------------
 # Pending color while typing (movestate property, committed on Enter/focus-out)
 # ---------------------------------------------------------------------------