clock-expire: exclude active tasks

* Active tasks should not be considered for clock-expiry.
  Closes #6025
* Manually triggered tasks should not be considered for clock-expiry.
  Implements proposal point 10
  https://cylc.github.io/cylc-admin/proposal-optional-output-extension.html#proposal

cylc/flow/task_pool.py

@@ -2161,10 +2161,25 @@ def spawn_parentless_sequential_xtriggers(self):
     def clock_expire_tasks(self):
         """Expire any tasks past their clock-expiry time."""
         for itask in self.get_tasks():
-            if not itask.clock_expire():
-                continue
-            self.task_events_mgr.process_message(
-                itask, logging.WARNING, TASK_OUTPUT_EXPIRED)
+            if (
+                # force triggered tasks can not clock-expire
+                # see proposal point 10:
+                # https://cylc.github.io/cylc-admin/proposal-optional-output-extension.html#proposal
+                not itask.is_manual_submit
+
+                # only waiting tasks can clock-expire
+                # see https://github.com/cylc/cylc-flow/issues/6025
+                # (note retrying tasks will be in the waiting state)
+                and itask.state(TASK_STATUS_WAITING)
+
+                # check if this task is clock expired
+                and itask.clock_expire()
+            ):
+                self.task_events_mgr.process_message(
+                    itask,
+                    logging.WARNING,
+                    TASK_OUTPUT_EXPIRED,
+                )
 
     def task_succeeded(self, id_):
         """Return True if task with id_ is in the succeeded state."""

tests/integration/test_optional_outputs.py

@@ -44,6 +44,7 @@
     TASK_STATUS_EXPIRED,
     TASK_STATUS_PREPARING,
     TASK_STATUS_WAITING,
+    TASK_STATUSES_ACTIVE,
 )
 
 if TYPE_CHECKING:
@@ -378,3 +379,65 @@ async def test_clock_expire_partially_satisfied_task(
 
         # the task should now be in the expired state
         assert e.state(TASK_STATUS_EXPIRED)
+
+
+async def test_clock_expiry(
+    flow,
+    scheduler,
+    start,
+):
+    """Waiting tasks should be considered for clock-expiry.
+
+    Tests two things:
+
+    * Manually triggered tasks should not be considered for clock-expiry.
+
+      Tests proposal point 10:
+      https://cylc.github.io/cylc-admin/proposal-optional-output-extension.html#proposal
+
+    * Active tasks should not be considered for clock-expiry.
+
+      Closes https://github.com/cylc/cylc-flow/issues/6025
+    """
+    id_ = flow({
+        'scheduling': {
+            'initial cycle point': '2000',
+            'runahead limit': 'P1',
+            'special tasks': {
+                'clock-expire': 'x'
+            },
+            'graph': {
+                'P1Y': 'x'
+            },
+        },
+    })
+    schd = scheduler(id_)
+    async with start(schd):
+        # the first task (waiting)
+        one = schd.pool.get_task(ISO8601Point('20000101T0000Z'), 'x')
+        assert one
+
+        # the second task (preparing)
+        two = schd.pool.get_task(ISO8601Point('20010101T0000Z'), 'x')
+        assert two
+        two.state_reset(TASK_STATUS_PREPARING)
+
+        # the third task (force-triggered)
+        schd.pool.force_trigger_tasks(['20100101T0000Z/x'], ['1'])
+        three = schd.pool.get_task(ISO8601Point('20100101T0000Z'), 'x')
+        assert three
+
+        # check for expiry
+        schd.pool.clock_expire_tasks()
+
+        # the first task should be expired (it was waiting)
+        assert one.state(TASK_STATUS_EXPIRED)
+        assert one.state.outputs.is_message_complete(TASK_OUTPUT_EXPIRED)
+
+        # the second task should *not* be expired (it was active)
+        assert not two.state(TASK_STATUS_EXPIRED)
+        assert not two.state.outputs.is_message_complete(TASK_OUTPUT_EXPIRED)
+
+        # the third task should *not* be expired (it was a manual submit)
+        assert not three.state(TASK_STATUS_EXPIRED)
+        assert not three.state.outputs.is_message_complete(TASK_OUTPUT_EXPIRED)