Merge 'upstream/8.6.x' into paused-trigger-platform

Author: MetRonnie

changes.d/6261.feat.md

@@ -0,0 +1 @@
+Allow a workflow to be restarted by `cylc vr` even if there are no changes to reinstall.

changes.d/7007.fix.md

@@ -0,0 +1 @@
+Fix bug where cylc play --pause would resume a paused workflow.

changes.d/7041.fix.md

@@ -0,0 +1 @@
+Removed spurious "tasks not killable" warnings for `cylc stop --kill`.

changes.d/7054.fix.md

@@ -0,0 +1,3 @@
+Fix an issue where job submission could fail with the message
+`No such file or directory` when tasks were triggered while the workflow was
+paused.

cylc/flow/cfgspec/workflow.py

@@ -488,7 +488,7 @@ def get_script_common_text(this: str, example: Optional[str] = None):
                     default = None
                 elif item.endswith("handlers"):
                     desc = desc + '\n\n' + dedent(f'''
-                        Examples:
+                        .. rubric:: Examples:
 
                         .. code-block:: cylc
 
@@ -548,7 +548,7 @@ def get_script_common_text(this: str, example: Optional[str] = None):
         Conf('<parameter>', VDR.V_PARAMETER_LIST, desc='''
             A custom parameter to use in a workflow.
 
-            Examples:
+            .. rubric:: Examples:
 
             - ``run = control, test1, test2``
             - ``mem = 1..5``  (equivalent to ``1, 2, 3, 4, 5``).
@@ -623,6 +623,24 @@ def get_script_common_text(this: str, example: Optional[str] = None):
 
             This item can be overridden on the command line using
             ``cylc play --initial-cycle-point`` or ``--icp``.
+
+            .. rubric:: Examples:
+
+            ``2000-01-01T00:00Z``
+               The 1st of January at midnight.
+            ``2000``
+               Shorthand for ``2000-01-01T00:00``.
+            ``now``
+               The exact time when the workflow is started. By default this is
+               to the minute, e.g: ``2001-02-03T12:34``.
+            ``previous(T-00)``
+               The hour when the workflow was started. I.e, The time when the
+               workflow is started with the minute cut off.
+            ``previous(T00)``
+               The day when the workflow was started. I.e, the time when the
+               workflow was started with the hour and minute cut off.
+            ``next(T00)``
+               The day after the workflow was started (at midnight).
         ''')
         # NOTE: final cycle point is not a V_CYCLE_POINT to allow expressions
         # such as '+P1Y' (relative to initial cycle point)
@@ -635,11 +653,16 @@ def get_script_common_text(this: str, example: Optional[str] = None):
             This item can be overridden on the command line using
             ``cylc play --final-cycle-point`` or ``--fcp``.
 
-            Examples:
+            .. rubric:: Examples:
 
-            - ``2000`` - Shorthand for ``2000-01-01T00:00``.
-            - ``+P1D`` - The initial cycle point plus one day.
-            - ``2000 +P1D +P1Y`` - The year ``2000`` plus one day and one year.
+            ``2000-01-01T00:00Z``
+               The 1st of January at midnight.
+            ``2000``
+               Shorthand for ``2000-01-01T00:00``.
+            ``+P1D``
+               The initial cycle point plus one day.
+            ``2000 +P1D +P1Y``
+               The year ``2000`` plus one day and one year.
         ''')
         Conf('initial cycle point constraints', VDR.V_STRING_LIST,
              desc=CYCLE_POINT_CONSTRAINTS.format('initial') + dedent('''
@@ -676,7 +699,7 @@ def get_script_common_text(this: str, example: Optional[str] = None):
                choosing not to run that part of the graph. You can play
                the workflow and continue.
 
-            Examples:
+            .. rubric:: Examples:
 
             - ``2000`` - Shorthand for ``2000-01-01T00:00``.
             - ``+P1D`` - The initial cycle point plus one day.
@@ -717,7 +740,7 @@ def get_script_common_text(this: str, example: Optional[str] = None):
             value instead, in which case the number of cycles
             within the interval depends on the cycling intervals present.
 
-            Examples:
+            .. rubric:: Examples:
 
             ``P0``
                 Only one cycle can be active at a time.
@@ -831,7 +854,7 @@ def get_script_common_text(this: str, example: Optional[str] = None):
 
                    :ref:`ClockExpireTasks`.
 
-                Examples:
+                .. rubric:: Examples:
 
                 ``foo(PT1H)`` - expire task ``foo`` if the current wall clock
                 time has reached 1 hour after the task's cycle point.
@@ -1035,7 +1058,7 @@ def get_script_common_text(this: str, example: Optional[str] = None):
 
                See :ref:`task namespace rules. <namespace-names>`
 
-            Examples of legal values:
+            ..rubric:: Examples:
 
             - ``[foo]``
             - ``[foo, bar, baz]``

cylc/flow/config.py

@@ -1036,27 +1036,27 @@ def _check_circular_helper(x2ys, y2xs):
                     del y2xs[y01]
             del x2ys[sx01]
 
-    def _check_sequence_bounds(self):
-        """Check bounds of sequences against the start point."""
+    def _check_sequence_bounds(self) -> None:
+        """Check bounds of sequences against the initial cycle point."""
         out_of_bounds = [
             str(seq)
             for seq in self.sequences
-            if seq.get_first_point(self.start_point) is None
+            if seq.get_first_point(self.initial_point) is None
         ]
         if out_of_bounds:
             if len(out_of_bounds) > 1:
                 # avoid spamming users with multiple warnings
                 out_of_bounds_str = '\n'.join(
-                    wrap(', '.join(out_of_bounds), 70))
+                    wrap(', '.join(out_of_bounds), 70)
+                )
                 msg = (
-                    "multiple sequences out of bounds for"
-                    " initial cycle point "
-                    f"{self.start_point}:\n{out_of_bounds_str}"
+                    "multiple sequences out of bounds for initial cycle point "
+                    f"{self.initial_point}:\n{out_of_bounds_str}"
                 )
             else:
                 msg = (
                     f"{out_of_bounds[0]}: sequence out of bounds for "
-                    f"initial cycle point {self.start_point}"
+                    f"initial cycle point {self.initial_point}"
                 )
             LOG.warning(msg)
 

cylc/flow/scheduler.py

@@ -1505,8 +1505,8 @@ async def workflow_shutdown(self):
             self.time_next_kill is not None
             and time() > self.time_next_kill
         ):
-            await commands.run_cmd(commands.poll_tasks(self, ['*/*']))
-            await commands.run_cmd(commands.kill_tasks(self, ['*/*']))
+            self.task_job_mgr.poll_task_jobs(self.pool.get_tasks())
+            self.kill_tasks(self.pool.get_tasks(), warn=False)
             self.time_next_kill = time() + self.INTERVAL_STOP_KILL
 
         # Is the workflow set to auto stop [+restart] now ...

cylc/flow/scheduler_cli.py

@@ -495,6 +495,11 @@ async def _resume(workflow_id, options):
         LOG.critical('Cannot tell if the workflow is running')
         sys.exit(1)
     else:
+        # It's running but the user has specified --pause:
+        if options.paused_start:
+            LOG.warning('Workflow already running: Remove --pause to resume.')
+            sys.exit(0)
+
         # It's running: resume it and exit.
         print("Resuming already-running workflow")
         mutation_kwargs = {

cylc/flow/scripts/validate_reinstall.py

@@ -18,12 +18,17 @@
 
 """cylc validate-reinstall [OPTIONS] ARGS
 
-Validate, reinstall and apply changes to a workflow.
+Validate, reinstall, and reload or restart a workflow.
 
-Validate and reinstall a workflow then either:
+This command updates a workflow to reflect any new changes made in the workflow
+source directory since it was installed.
 
-* "Reload" the workflow (if it is running),
-* or "play" it (if it is stopped).
+The workflow will be reinstalled, then either:
+* Reloaded (if the workflow is running),
+* or restarted (if it is stopped).
+
+Cylc will show you the list of files changed and prompt for confirmation before
+reinstalling. Use the '--yes' option to bypass this.
 
 This command is equivalent to:
   $ cylc validate myworkflow --against-source
@@ -77,10 +82,8 @@
     RELOAD_OPTIONS,
     run as cylc_reload
 )
-from cylc.flow.terminal import cli_function
-from cylc.flow.workflow_files import (
-    get_workflow_run_dir,
-)
+from cylc.flow.terminal import cli_function, is_terminal
+from cylc.flow.workflow_files import get_workflow_run_dir
 
 
 CYLC_ROSE_OPTIONS = COP.get_cylc_rose_options()
@@ -94,6 +97,8 @@
     modify={'cylc-rose': 'validate, install'}
 )
 
+_input = input  # to enable testing
+
 
 def get_option_parser() -> COP:
     parser = COP(
@@ -191,32 +196,56 @@ async def vr_cli(
     # against source option:
     options.against_source = Path(get_workflow_run_dir(workflow_id))
 
-    # Run cylc validate
+    # Run "cylc validate"
     log_subcommand('validate --against-source', workflow_id)
     await cylc_validate(parser, options, workflow_id)
 
     # Unset options that do not apply after validation:
     delattr(options, 'against_source')
     delattr(options, 'is_validate')
 
+    # Run "cylc reinstall"
     log_subcommand('reinstall', workflow_id)
     reinstall_ok = await cylc_reinstall(
-        options, workflow_id,
+        options,
+        workflow_id,
         [],
         print_reload_tip=False
     )
 
     if not reinstall_ok:
-        # No changes, OR user said No to the reinstall prompt: abort.
-        return False
-
-    # Run reload if workflow is running or paused:
+        # No changes OR user said No to the reinstall prompt.
+
+        # If not a terminal and not --yes do nothing.
+        if not is_terminal() and not options.skip_interactive:
+            return False
+
+        # Else if not --yes, prompt user to continue or not.
+        if not options.skip_interactive:
+            usr = None
+            if not workflow_running:
+                # No changes to install, and the workflow is not running.
+                # Can still restart with no changes.
+                action = "Restart"
+            else:
+                # No changes to install, and the workflow is running.
+                # Reload is probably pointless, but not necessarily (the user
+                # could modify the run dir and do 'vr' to restart or reload).
+                action = "Reload"
+            while usr not in ['y', 'n']:
+                usr = _input(
+                    cparse(f'<bold>{action} anyway?</bold> [y/n]: ')
+                ).lower()
+                if usr == 'n':
+                    return False
+
+    # Run "cylc reload" (if workflow is running or paused)
     if workflow_running:
         log_subcommand('reload', workflow_id)
         await cylc_reload(options, workflow_id)
         return True
 
-    # run play anyway, to play a stopped workflow:
+    # Run "cylc play" (if workflow is stopped)
     else:
         set_timestamps(LOG, options.log_timestamp)
         cleanup_sysargv(

cylc/flow/task_job_mgr.py

@@ -222,7 +222,9 @@ def kill_prep_task(self, itask: 'TaskProxy') -> None:
         self._set_retry_timers(itask)
         self._prep_submit_task_job_error(itask, '(killed in job prep)', '')
 
-    def poll_task_jobs(self, itasks, msg=None):
+    def poll_task_jobs(
+        self, itasks: 'Iterable[TaskProxy]', msg: str | None = None
+    ):
         """Poll jobs of specified tasks.
 
         This method uses _poll_task_jobs_callback() and