Merge branch 'master' into fix-poll-on-restart

CHANGES.md

@@ -100,6 +100,12 @@ access to information on configured platforms.
 [#4658](https://github.com/cylc/cylc-flow/pull/4658) - At restart, only poll
 tasks recorded as active at shutdown.
 
+[#4667](https://github.com/cylc/cylc-flow/pull/4667) - Check manually triggered
+tasks are not already preparing for job submission.
+
+[#4640](https://github.com/cylc/cylc-flow/pull/4640) - Fix manual triggering of
+runahead-limited parentless tasks.
+
 [#4566](https://github.com/cylc/cylc-flow/pull/4566) - Fix `cylc scan`
 invocation for remote scheduler host on a shared filesystem.
 

cylc/flow/broadcast_mgr.py

@@ -65,7 +65,7 @@ def check_ext_triggers(self, itask, ext_trigger_queue):
         """Get queued ext trigger messages and try to satisfy itask.
 
         Ext-triggers are pushed by the remote end, so we can check for
-        new messages and satisfy dependendent tasks at the same time.
+        new messages and satisfy dependent tasks at the same time.
         Return True if itask has a newly satisfied ext-trigger.
         """
         while not ext_trigger_queue.empty():

cylc/flow/cfgspec/globalcfg.py

@@ -166,7 +166,7 @@
 
         A workflow will stall if there are no tasks ready to run and no
         waiting external triggers, but the presence of incomplete
-        tasks or unsatisified prerequisites shows the workflow did not run to
+        tasks or unsatisfied prerequisites shows the workflow did not run to
         completion. The stall timer turns off on any post-stall task activity.
         It resets on restarting a stalled workflow.
 
@@ -388,7 +388,7 @@
                 .. versionchanged:: 8.0.0
 
                    {REPLACES}``[suite servers]run ports``.
-                   It can no longer be used to definine a non-contiguous port
+                   It can no longer be used to define a non-contiguous port
                    range.
             ''')
             Conf('condemned', VDR.V_ABSOLUTE_HOST_LIST, desc=f'''
@@ -1173,7 +1173,7 @@
             Conf('clean job submission environment', VDR.V_BOOLEAN, False,
                  desc='''
                 Job submission subprocesses inherit their parent environment by
-                default. Remote jobs inherit the default non-interative shell
+                default. Remote jobs inherit the default non-interactive shell
                 environment for their platform. Jobs on the scheduler host
                 inherit the scheduler environment (unless their job runner
                 prevents this).

cylc/flow/cfgspec/workflow.py

@@ -623,13 +623,14 @@ def get_script_common_text(this: str, example: Optional[str] = None):
         ''')
         Conf('cycling mode', VDR.V_STRING, Calendar.MODE_GREGORIAN,
              options=list(Calendar.MODES) + ['integer'], desc='''
-            Choice of integer cycling or one of several calendars.
-
-            Cylc runs using the proleptic Gregorian calendar by default.
-            This allows you to run the workflow with the 360 day
-            calendar (12 months of 30 days in a year) OR integer cycling. It
-            also supports use of the 365 (never a leap year) and 366 (always a
-            leap year) calendars.
+            Choice of :term:`integer cycling` or one of several
+            :term:`datetime cycling` calendars.
+
+            Cylc runs workflows using the proleptic Gregorian calendar
+            by default. This setting allows you to instead choose
+            integer cycling, or one of the other supported non-Gregorian
+            datetime calendars: 360 day (12 months of 30 days in a year),
+            365 day (never a leap year) and 366 day (always a leap year).
         ''')
         Conf('runahead limit', VDR.V_STRING, 'P5', desc='''
             How many cycles ahead of the slowest tasks the fastest may run.
@@ -977,6 +978,16 @@ def get_script_common_text(this: str, example: Optional[str] = None):
 
                 If no parents are listed default is ``root``.
             ''')
+            Conf('script', VDR.V_STRING, desc=dedent('''
+                The main custom script invoked from the task job script.
+
+                It can be an external command or script, or inlined scripting.
+
+                See :ref:`Task Job Script Variables` for the list of variables
+                available in the task execution environment.
+            ''') + get_script_common_text(
+                this='script', example='my_script.sh'
+            ))
             Conf('init-script', VDR.V_STRING, desc=dedent('''
                 Custom script invoked by the task job script before the task
                 execution environment is configured.
@@ -1036,13 +1047,6 @@ def get_script_common_text(this: str, example: Optional[str] = None):
                 this='pre-script',
                 example='echo "Hello from workflow ${CYLC_WORKFLOW_ID}!"'
             ))
-            Conf('script', VDR.V_STRING, desc=dedent('''
-                The main custom script invoked from the task job script.
-
-                It can be an external command or script, or inlined scripting.
-            ''') + get_script_common_text(
-                this='script', example='my_script.sh'
-            ))
             Conf('post-script', VDR.V_STRING, desc=dedent('''
                 Custom script invoked by the task job script immediately
                 after :cylc:conf:`[..]script`.
@@ -1126,7 +1130,7 @@ def get_script_common_text(this: str, example: Optional[str] = None):
             with Conf('meta', desc=r'''
                 Metadata for the task or task family.
 
-                The ``meta`` section containins metadata items for this task or
+                The ``meta`` section contains metadata items for this task or
                 family namespace. The items ``title``, ``description`` and
                 ``URL`` are pre-defined and are used by Cylc. Others can be
                 user-defined and passed to task event handlers to be

cylc/flow/etc/tutorial/runtime-tutorial/etc/met-office-sites.dat

@@ -0,0 +1 @@
+../../cylc-forecasting-workflow/etc/met-office-sites.dat

cylc/flow/main_loop/__init__.py

@@ -142,7 +142,7 @@ async def my_startup_coroutine(schd, state):
 ^^^^^^^^^^^
 
 Coroutines must be decorated using one of the main loop decorators. The
-choise of decorator effects when the coroutine is called and what
+choice of decorator effects when the coroutine is called and what
 arguments are provided to it.
 
 The available event types are:

cylc/flow/network/server.py

@@ -370,7 +370,7 @@ def get_graph_raw(
                 Task identifier for the dependency of
                 an edge.
             right (str):
-                Task identifier for the dependant task
+                Task identifier for the dependent task
                 of an edge.
             is_suicide (bool):
                 True if edge represents a suicide trigger.

cylc/flow/parsec/validate.py

@@ -116,7 +116,7 @@ class ParsecValidator:
         ),
         V_RANGE: (
             'integer range',
-            'An integer range specified by a minumum and maximum value.',
+            'An integer range specified by a minimum and maximum value.',
             {
                 '1..5': 'The numbers 1 to 5 inclusive.',
             }

cylc/flow/scripts/dump.py

@@ -267,7 +267,7 @@ def main(_, options: 'Values', workflow_id: str) -> None:
                                 item['name'],
                                 item['cyclePoint'],
                                 item['state']]
-                        values.append('held' if item['isHeld'] else 'unheld')
+                        values.append('held' if item['isHeld'] else 'not-held')
                         values.append('queued' if item['isQueued']
                                       else 'not-queued')
                         values.append('runahead' if item['isRunahead']

cylc/flow/task_pool.py

@@ -538,7 +538,9 @@ def load_db_tasks_to_hold(self):
             self.workflow_db_mgr.pri_dao.select_tasks_to_hold()
         )
 
-    def spawn_successor(self, itask: TaskProxy) -> Optional[TaskProxy]:
+    def spawn_successor_if_parentless(
+            self, itask: TaskProxy
+    ) -> Optional[TaskProxy]:
         """Spawn next-cycle instance of itask if parentless.
 
         This includes:
@@ -597,17 +599,15 @@ def release_runahead_task(
             # implicit prev-instance parent
             return
 
-        if not itask.flow_nums:
-            # No reflow
-            return
-
-        if not runahead_limit_point:
-            return
-
-        # Autospawn successor of itask if parentless.
-        n_task = self.spawn_successor(itask)
-        if n_task and n_task.point <= runahead_limit_point:
-            self.release_runahead_task(n_task, runahead_limit_point)
+        # Autospawn successor of itask if parentless and reflowing.
+        if itask.flow_nums:
+            n_task = self.spawn_successor_if_parentless(itask)
+            if (
+                n_task and
+                runahead_limit_point and
+                n_task.point <= runahead_limit_point
+            ):
+                self.release_runahead_task(n_task, runahead_limit_point)
 
     def remove(self, itask, reason=""):
         """Remove a task from the pool (e.g. after a reload)."""
@@ -1425,9 +1425,9 @@ def force_trigger_tasks(
                 # In pool already
                 itasks.append(itask)
 
-        # trigger tasks
+        # trigger tasks if not already preparing or active
         for itask in itasks:
-            if itask.state(*TASK_STATUSES_ACTIVE):
+            if itask.state(TASK_STATUS_PREPARING, *TASK_STATUSES_ACTIVE):
                 LOG.warning(f"[{itask}] ignoring trigger - already active")
                 continue
             itask.is_manual_submit = True

tests/flakyfunctional/hold-release/14-hold-kill/flow.cylc

@@ -14,7 +14,7 @@
             sleep 10  # sleep, should still be held after 10 seconds
             cylc dump -s -t "${CYLC_WORKFLOW_ID}" >'cylc-dump.out'
             diff -u 'cylc-dump.out' - <<'__OUT__'
-            1, killer, running, unheld, not-queued, not-runahead
+            1, killer, running, not-held, not-queued, not-runahead
             1, sleeper, waiting, held, not-queued, not-runahead
             __OUT__
             cylc release "${CYLC_WORKFLOW_ID}//1/sleeper"

tests/functional/cli/05-colour.t

@@ -20,6 +20,9 @@
 # Uses the "script" command to make stdout log file look like a terminal.
 
 . "$(dirname "$0")/test_header"
+if [[ "$OSTYPE" != "linux-gnu"* ]]; then
+    skip_all "Tests not compatibile with $OSTYPE"
+fi
 set_test_number 8
 
 ANSI='\e\['

tests/functional/spawn-on-demand/13-trigger-runahead.t

@@ -0,0 +1,25 @@
+#!/usr/bin/env bash
+# THIS FILE IS PART OF THE CYLC WORKFLOW ENGINE.
+# Copyright (C) NIWA & British Crown (Met Office) & Contributors.
+# 
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#-------------------------------------------------------------------------------
+
+# Check correct behaviour if a parentless task is manually triggered whilst
+# runahead-limited. See GitHub #4619.
+
+. "$(dirname "$0")/test_header"
+set_test_number 2
+reftest
+exit

tests/functional/spawn-on-demand/13-trigger-runahead/flow.cylc

@@ -0,0 +1,21 @@
+# This workflow should behave the same as if foo.1 did not trigger foo.2.
+
+[scheduling]
+   cycling mode = integer
+   initial cycle point = 1
+   final cycle point = 3
+   runahead limit = P1
+   [[graph]]
+      P1 = foo
+[runtime]
+   [[foo]]
+      script = """
+         cylc__job__wait_cylc_message_started
+         if ((CYLC_TASK_CYCLE_POINT == 1)); then
+            expected="foo, 1, running, not-held, not-queued, not-runahead
+foo, 2, waiting, not-held, not-queued, runahead"
+            diff <(cylc dump -t "${CYLC_WORKFLOW_NAME}") <(echo "$expected")
+            # Force trigger next instance while it is runahead limited.
+            cylc trigger $CYLC_WORKFLOW_NAME//2/foo
+         fi
+      """

tests/functional/spawn-on-demand/13-trigger-runahead/reference.log

@@ -0,0 +1,5 @@
+Initial point: 1
+Final point: 3
+1/foo -triggered off []
+2/foo -triggered off []
+3/foo -triggered off []

tests/integration/test_task_pool.py

@@ -23,6 +23,13 @@
 from cylc.flow.cycling import PointBase
 from cylc.flow.cycling.integer import IntegerPoint
 from cylc.flow.scheduler import Scheduler
+from cylc.flow.task_state import (
+    TASK_STATUS_WAITING,
+    TASK_STATUS_PREPARING,
+    TASK_STATUS_SUBMITTED,
+    TASK_STATUS_RUNNING,
+    TASK_STATUS_SUCCEEDED,
+)
 
 
 # NOTE: foo & bar have no parents so at start-up (even with the workflow
@@ -405,3 +412,29 @@ async def test_hold_point(
 
     assert task_pool.tasks_to_hold == set()
     assert db_select(example_flow, True, 'tasks_to_hold') == []
+
+
+@pytest.mark.parametrize(
+    'status,should_trigger',
+    [
+        (TASK_STATUS_WAITING, True),
+        (TASK_STATUS_PREPARING, False),
+        (TASK_STATUS_SUBMITTED, False),
+        (TASK_STATUS_RUNNING, False),
+        (TASK_STATUS_SUCCEEDED, True),
+    ]
+)
+async def test_trigger_states(status, should_trigger, one, run):
+    """It should only trigger tasks in compatible states."""
+
+    async with run(one):
+        task = one.pool.filter_task_proxies('1/a')[0][0]
+
+        # reset task a to the provided state
+        task.state.reset(status)
+
+        # try triggering the task
+        one.pool.force_trigger_tasks('1/a')
+
+        # check whether the task triggered
+        assert task.is_manual_submit == should_trigger