fix/stop LamNI per-sub-tomogram scilog entries

LamNI's tomo_scan() wrote a separate scilog entry ("Starting subtomo:
N...") every time the sub-tomogram number changed -- 8 extra entries
per tomo_type-1 scan, and one per sub-tomogram traversed for types 2/3
-- leftover behavior carried over from omny.py during the flomni->lamni
port. Flomni itself never does this: it only writes at scan start (PDF
report) and scan end (timing summary). Removed the three
_write_subtomo_to_scilog() call sites and the now-unused method so
LamNI's scilog behavior matches Flomni's.

Also fixed a stale test (test_tomo_queue_reacquire_rejects_when_another_job_is_incomplete)
that encoded the old, buggy tomo_queue_reacquire() invariant (rejecting
on ANY other job being incomplete/running) rather than the fixed one
from the prior commit (only an EARLIER job is a real conflict) --
split it into two tests covering both directions.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>

csaxs_bec/bec_ipython_client/plugins/LamNI/lamni.py

@@ -771,17 +771,6 @@ class LamNI(TomoQueueMixin, LamNIAlignmentMixin, LamNIOpticsMixin, LamniGuiTools
         except Exception:
             logger.warning("Failed to write to scilog.")
 
-    def _write_subtomo_to_scilog(self, subtomo_number):
-        bec = builtins.__dict__.get("bec")
-        if self.tomo_id > 0:
-            tags = ["BEC_subtomo", self.sample_name, f"tomo_id_{self.tomo_id}"]
-        else:
-            tags = ["BEC_subtomo", self.sample_name]
-        self.write_to_scilog(
-            f"Starting subtomo: {subtomo_number}. First scan number: {bec.queue.next_scan_number}.",
-            tags,
-        )
-
     _TIMING_LOG_DIR = "~/data/raw/logs/timing_statistics"
     _TIMING_SETUP = "lamni"
     _PROJECTION_TIMING_LOG = "projection_timing_log.jsonl"
@@ -1306,8 +1295,6 @@ class LamNI(TomoQueueMixin, LamNIAlignmentMixin, LamNIOpticsMixin, LamniGuiTools
 
     def sub_tomo_scan(self, subtomo_number, start_angle=None):
         """Perform one sub-tomogram (tomo_type 1 only)."""
-        self._write_subtomo_to_scilog(subtomo_number)
-
         angles, N = self._subtomo_angle_plan(
             subtomo_number, self.tomo_angle_stepsize, start_angle=start_angle
         )
@@ -1564,7 +1551,6 @@ class LamNI(TomoQueueMixin, LamNIAlignmentMixin, LamNIOpticsMixin, LamniGuiTools
                             ii, self.golden_ratio_bunch_size, maxangle=360, reverse=True
                         )
                         if previous_subtomo_number != subtomo_number:
-                            self._write_subtomo_to_scilog(subtomo_number)
                             if (
                                 subtomo_number % 2 == 1
                                 and ii > 10
@@ -1603,7 +1589,6 @@ class LamNI(TomoQueueMixin, LamNIAlignmentMixin, LamNIOpticsMixin, LamniGuiTools
                             ii, int(360 / self.tomo_angle_stepsize), maxangle=360, reverse=True
                         )
                         if previous_subtomo_number != subtomo_number:
-                            self._write_subtomo_to_scilog(subtomo_number)
                             if (
                                 subtomo_number % 2 == 1
                                 and ii > 10

tests/tests_bec_ipython_client/test_lamni_tomo_angles.py

@@ -46,7 +46,6 @@ def make_lamni(tomo_angle_stepsize: float) -> LamNI:
     obj._progress_proxy = _ProgressProxy(obj.client)
     obj.tomo_angle_stepsize = tomo_angle_stepsize
     obj.tomo_id = -1
-    obj._write_subtomo_to_scilog = lambda subtomo_number: None
     return obj
 
 

tests/tests_bec_ipython_client/test_tomo_queue_reacquire.py

@@ -82,7 +82,6 @@ def make_flomni():
 def test_lamni_resolve_type1_projection_matches_sub_tomo_scan(stepsize):
     lamni = make_lamni()
     lamni.tomo_angle_stepsize = stepsize
-    lamni._write_subtomo_to_scilog = lambda subtomo_number: None
     recorded = {}
     lamni._tomo_scan_at_angle = lambda angle, subtomo_number: recorded.__setitem__(
         lamni.progress["projection"], (subtomo_number, angle)
@@ -219,7 +218,21 @@ def test_tomo_queue_reacquire_rejects_command_job():
         lamni.tomo_queue_reacquire(0, projection_number=0)
 
 
-def test_tomo_queue_reacquire_rejects_when_another_job_is_incomplete():
+def test_tomo_queue_reacquire_rejects_when_an_earlier_job_is_incomplete():
+    lamni = make_lamni()
+    lamni.tomo_type = 1
+    lamni.tomo_angle_stepsize = 10.0
+    i0 = lamni.tomo_queue_add(label="job0")
+    i1 = lamni.tomo_queue_add(label="job1")
+    lamni._tomo_queue_proxy.update(i0, status="incomplete")
+
+    with pytest.raises(TomoQueueError):
+        lamni.tomo_queue_reacquire(i1, projection_number=0)
+
+
+def test_tomo_queue_reacquire_allows_a_later_job_being_incomplete():
+    # A later job's own status doesn't matter -- it gets reset to
+    # "pending" by this call anyway, so it's not a real conflict.
     lamni = make_lamni()
     lamni.tomo_type = 1
     lamni.tomo_angle_stepsize = 10.0
@@ -227,8 +240,11 @@ def test_tomo_queue_reacquire_rejects_when_another_job_is_incomplete():
     i1 = lamni.tomo_queue_add(label="job1")
     lamni._tomo_queue_proxy.update(i1, status="incomplete")
 
-    with pytest.raises(TomoQueueError):
-        lamni.tomo_queue_reacquire(i0, projection_number=0)
+    lamni.tomo_queue_reacquire(i0, projection_number=0)
+
+    jobs = lamni._tomo_queue_proxy.as_list()
+    assert jobs[i0]["status"] == "incomplete"
+    assert jobs[i1]["status"] == "pending"
 
 
 def test_tomo_queue_reacquire_allows_targeting_the_incomplete_job_itself():