Merge branch 'main' into revert_chgres_cube

docs/sections/user_guide/cli/drivers/filter_topo/help.out

@@ -12,6 +12,8 @@ Optional arguments:
 
 Positional arguments:
   TASK
+    filtered_output_file
+      The filtered output file staged from raw input
     input_grid_file
       The input grid file
     namelist_file

docs/sections/user_guide/cli/drivers/filter_topo/show-schema.out

@@ -6,7 +6,7 @@
         "config": {
           "additionalProperties": false,
           "properties": {
-            "input_grid_file": {
+            "filtered_orog": {
               "type": "string"
 ...
         "rundir"

docs/sections/user_guide/cli/drivers/orog_gsl/help.out

@@ -12,6 +12,8 @@ Optional arguments:
 
 Positional arguments:
   TASK
+    input_config_file
+      The input config file
     input_grid_file
       The input grid file
     provisioned_rundir

docs/sections/user_guide/cli/drivers/shave/help.out

@@ -12,6 +12,8 @@ Optional arguments:
 
 Positional arguments:
   TASK
+    input_config_file
+      The input config file
     provisioned_rundir
       Run directory provisioned with all required content
     run

docs/sections/user_guide/yaml/components/filter_topo.rst

@@ -20,10 +20,18 @@ config:
 
 Configuration parameters for the ``orog_gsl`` component.
 
+  **filtered_orog:**
+
+  Name of the filtered output file.
+
   **input_grid_file:**
 
   Path to the tiled input grid file.
 
+  **input_raw_orog:**
+
+  Path to the raw orography file. The output of the ``orog`` driver.
+
 namelist:
 ^^^^^^^^^
 

docs/sections/user_guide/yaml/components/shave.rst

@@ -27,7 +27,7 @@ Describes the required parameters to run a ``shave`` configuration.
 
   Name of the grid file with extra points to be shaved.
 
-  **nh4:**
+  **nhalo:**
 
   The number of halo rows/columns.
 
@@ -39,6 +39,10 @@ Describes the required parameters to run a ``shave`` configuration.
 
   The j/y dimensions of the compute domain (not including halo)
 
+  **output_grid_file:**
+
+  The path to the output file.
+
 rundir:
 ^^^^^^^
 

docs/sections/user_guide/yaml/rocoto.rst

@@ -86,12 +86,30 @@ In the example, the resulting log would appear in the XML file as:
 
 .. code-block:: xml
 
-   <log>
-     <cyclestr>/some/path/to/&FOO;</cyclestr>
-   </log>
+   <log><cyclestr>/some/path/to/&FOO;</cyclestr></log>
 
 The ``attrs:`` block is optional within the ``cyclestr:`` block and can be used to specify the cycle offset.
 
+Wherever a ``cyclestr:`` block is accepted, a YAML sequence mixing text and ``cyclestr:`` blocks may also be provided. For example,
+
+.. code-block:: yaml
+
+   log:
+     - cyclestr:
+         value: "%Y%m%d%H"
+     - -through-
+     - cyclestr:
+         attrs:
+           offset: "06:00:00"
+         value: "%Y%m%d%H"
+     - .log
+
+would be rendered as
+
+.. code-block:: xml
+
+   <log><cyclestr>%Y%m%d%H</cyclestr>-through-<cyclestr offset="06:00:00">%Y%m%d%H</cyclestr>.log</log>
+
 Tasks Section
 -------------
 

docs/shared/filter_topo.yaml

@@ -1,6 +1,8 @@
 filter_topo:
   config:
+    filtered_orog: C403_filtered_orog.tile7.nc
     input_grid_file: /path/to/C403_grid.tile7.halo6.nc
+    input_raw_orog: /path/to/out.oro.nc
   execution:
     batchargs:
       cores: 1

docs/shared/orog.yaml

@@ -4,12 +4,12 @@ orog:
       cores: 1
       walltime: 00:05:00
     executable: /path/to/orog
-    files_to_link:
-      fort.15: /path/to/fix/thirty.second.antarctic.new.bin
-      landcover30.fixed: /path/to/fix/landcover30.fixed
-      fort.235: /path/to/fix/gmted2010.30sec.int
-    grid_file: /path/to/netcdf/grid/file
-    rundir: /path/to/run/dir
+  files_to_link:
+    fort.15: /path/to/fix/thirty.second.antarctic.new.bin
+    landcover30.fixed: /path/to/fix/landcover30.fixed
+    fort.235: /path/to/fix/gmted2010.30sec.int
+  grid_file: /path/to/netcdf/grid/file
+  rundir: /path/to/run/dir
 platform:
   account: me
   scheduler: slurm

docs/shared/shave.yaml

@@ -1,9 +1,10 @@
 shave:
   config:
     input_grid_file: /path/to/input/grid/file
-    nh4: 1
+    nhalo: 0
     nx: 214
     ny: 128
+    output_grid_file: /path/to/C403_oro_data.tile7.halo0.nc
   execution:
     batchargs:
       cores: 1

src/uwtools/drivers/driver.py

@@ -49,7 +49,7 @@ def __init__(
         dry_run: bool = False,
         key_path: Optional[list[str]] = None,
         schema_file: Optional[Path] = None,
-        controller: Optional[str] = None,
+        controller: Optional[list[str]] = None,
     ) -> None:
         config_input = config if isinstance(config, YAMLConfig) else YAMLConfig(config=config)
         config_input.dereference(
@@ -65,8 +65,7 @@ def __init__(
             self._config: dict = self._config_intermediate[self.driver_name()]
         except KeyError as e:
             raise UWConfigError("Required '%s' block missing in config" % self.driver_name()) from e
-        if controller:
-            self._config[STR.rundir] = self._config_intermediate[controller][STR.rundir]
+        self._delegate(controller, STR.rundir)
         self.schema_file = schema_file
         self._validate()
         dryrun(enable=dry_run)
@@ -167,6 +166,19 @@ def _create_user_updated_config(
         else:
             log.debug(f"Failed to validate {path}")
 
+    def _delegate(self, controller: Optional[list[str]], config_key: str) -> None:
+        """
+        Selectively delegate config to controller.
+
+        :param controller: Key(s) leading to block in config controlling run-time values.
+        :param config_key: Name of config item to delegate to controller.
+        """
+        if controller:
+            val = self._config_intermediate[controller[0]]
+            for key in controller[1:]:
+                val = val[key]
+            self._config[config_key] = val[config_key]
+
     # Public helper methods
 
     @classmethod
@@ -241,7 +253,7 @@ def __init__(
         dry_run: bool = False,
         key_path: Optional[list[str]] = None,
         schema_file: Optional[Path] = None,
-        controller: Optional[str] = None,
+        controller: Optional[list[str]] = None,
     ):
         super().__init__(
             cycle=cycle,
@@ -274,7 +286,7 @@ def __init__(
         dry_run: bool = False,
         key_path: Optional[list[str]] = None,
         schema_file: Optional[Path] = None,
-        controller: Optional[str] = None,
+        controller: Optional[list[str]] = None,
     ):
         super().__init__(
             cycle=cycle,
@@ -314,7 +326,7 @@ def __init__(
         dry_run: bool = False,
         key_path: Optional[list[str]] = None,
         schema_file: Optional[Path] = None,
-        controller: Optional[str] = None,
+        controller: Optional[list[str]] = None,
     ):
         super().__init__(
             config=config,
@@ -339,7 +351,7 @@ def __init__(
         key_path: Optional[list[str]] = None,
         batch: bool = False,
         schema_file: Optional[Path] = None,
-        controller: Optional[str] = None,
+        controller: Optional[list[str]] = None,
     ):
         super().__init__(
             cycle=cycle,
@@ -351,8 +363,7 @@ def __init__(
             controller=controller,
         )
         self._batch = batch
-        if controller:
-            self._config[STR.execution] = self.config_full[controller][STR.execution]
+        self._delegate(controller, STR.execution)
 
     # Workflow tasks
 
@@ -541,7 +552,7 @@ def __init__(
         key_path: Optional[list[str]] = None,
         batch: bool = False,
         schema_file: Optional[Path] = None,
-        controller: Optional[str] = None,
+        controller: Optional[list[str]] = None,
     ):
         super().__init__(
             cycle=cycle,
@@ -576,7 +587,7 @@ def __init__(
         key_path: Optional[list[str]] = None,
         batch: bool = False,
         schema_file: Optional[Path] = None,
-        controller: Optional[str] = None,
+        controller: Optional[list[str]] = None,
     ):
         super().__init__(
             cycle=cycle,
@@ -618,7 +629,7 @@ def __init__(
         key_path: Optional[list[str]] = None,
         batch: bool = False,
         schema_file: Optional[Path] = None,
-        controller: Optional[str] = None,
+        controller: Optional[list[str]] = None,
     ):
         super().__init__(
             config=config,
@@ -650,7 +661,7 @@ def _add_docstring(class_: type, omit: Optional[list[str]] = None) -> None:
     :param key_path: Keys leading through the config to the driver's configuration block.
     :param batch: Run component via the batch system?
     :param schema_file: Path to schema file to use to validate an external driver.
-    :param controller: Name of block in config controlling run-time values.
+    :param controller: Key(s) leading to block in config controlling run-time values.
     """
     setattr(
         class_,

src/uwtools/drivers/filter_topo.py

@@ -10,7 +10,7 @@
 from uwtools.drivers.driver import DriverTimeInvariant
 from uwtools.drivers.support import set_driver_docstring
 from uwtools.strings import STR
-from uwtools.utils.tasks import symlink
+from uwtools.utils.tasks import filecopy, symlink
 
 
 class FilterTopo(DriverTimeInvariant):
@@ -27,10 +27,21 @@ def input_grid_file(self):
         """
         src = Path(self.config["config"]["input_grid_file"])
         dst = Path(self.config[STR.rundir], src.name)
-        yield self.taskname("Input grid")
+        yield self.taskname(f"Input grid {str(src)}")
         yield asset(dst, dst.is_file)
         yield symlink(target=src, linkname=dst)
 
+    @task
+    def filtered_output_file(self):
+        """
+        The filtered output file staged from raw input.
+        """
+        src = Path(self.config["config"]["input_raw_orog"])
+        dst = self.rundir / self.config["config"]["filtered_orog"]
+        yield self.taskname(f"Raw orog input {str(dst)}")
+        yield asset(dst, dst.is_file)
+        yield filecopy(src=src, dst=dst)
+
     @task
     def namelist_file(self):
         """
@@ -56,6 +67,7 @@ def provisioned_rundir(self):
         yield self.taskname("provisioned run directory")
         yield [
             self.input_grid_file(),
+            self.filtered_output_file(),
             self.namelist_file(),
             self.runscript(),
         ]

src/uwtools/drivers/orog.py

@@ -37,7 +37,7 @@ def grid_file(self):
         The input grid file.
         """
         grid_file = Path(self.config["grid_file"])
-        yield self.taskname("Input grid file")
+        yield self.taskname(f"Input grid file {grid_file}")
         yield asset(grid_file, grid_file.is_file) if str(grid_file) != "none" else None
 
     @task
@@ -62,8 +62,9 @@ def input_config_file(self):
                 "blat",
             ]
             inputs = " ".join([str(inputs[i]) for i in ordered_entries])
-        outgrid = self.config["grid_file"]
-        orogfile = self.config.get("orog_file")
+        outgrid = "'{}'".format(self.config["grid_file"])
+        if orogfile := self.config.get("orog_file"):
+            orogfile = "'{}'".format(orogfile)
         mask_only = ".true." if self.config.get("mask") else ".false."
         merge_file = self.config.get("merge", "none")  # string none is intentional
         content = [i for i in [inputs, outgrid, orogfile, mask_only, merge_file] if i is not None]
@@ -82,6 +83,22 @@ def provisioned_rundir(self):
             self.runscript(),
         ]
 
+    @task
+    def runscript(self):
+        """
+        The runscript.
+        """
+        path = self._runscript_path
+        yield self.taskname(path.name)
+        yield asset(path, path.is_file)
+        yield None
+        envvars = {
+            "KMP_AFFINITY": "disabled",
+            "OMP_NUM_THREADS": self.config.get(STR.execution, {}).get(STR.threads, 1),
+            "OMP_STACKSIZE": "2048m",
+        }
+        self._write_runscript(path=path, envvars=envvars)
+
     # Public helper methods
 
     @classmethod