adjustments for pr

benkozi · Feb 6, 2025 · f75abba · f75abba
1 parent 13d5a9d
commit f75abba
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Showing 7 changed files with 38 additions and 18 deletions.
diff --git a/doc/Makefile b/doc/Makefile
@@ -1,7 +1,6 @@
 # Makefile for Sphinx documentation
 
-#tdk: add back in -W --keep-going
-SPHINXOPTS    = -a -n
+SPHINXOPTS    = -a -n #-W
 SPHINXBUILD   = sphinx-build
 SOURCEDIR     = .
 BUILDDIR      = build
@@ -15,7 +14,7 @@ help:
 
 doc:
 	make clean
-# 	$(MAKE) linkcheck #tdk:uncomm
+	$(MAKE) linkcheck
 	$(MAKE) html
 
 linkcheck:
@@ -25,4 +24,4 @@ linkcheck:
 # "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS).
 
 %: Makefile
-	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) -w $(BUILDDIR)/warnings.log
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) -w $(BUILDDIR)/warnings.log
diff --git a/doc/conf.py b/doc/conf.py
@@ -268,10 +268,24 @@ def setup(app):
 
 # -- Options for autodoc extension ---------------------------------------
 
-autodoc_mock_imports = ["f90nml","cartopy","mpl_toolkits.basemap","fill_jinja_template",
-   "matplotlib","numpy","uwtools","mpl_toolkits","metplus","esmpy","netCDF4","pandas","xarray",
-   "mpi4py","pydantic","typer"
-   ]
+autodoc_mock_imports = [
+    "f90nml",
+    "cartopy",
+    "mpl_toolkits.basemap",
+    "fill_jinja_template",
+    "matplotlib",
+    "numpy",
+    "uwtools",
+    "mpl_toolkits",
+    "metplus",
+    "esmpy",
+    "netCDF4",
+    "pandas",
+    "xarray",
+    "mpi4py",
+    "pydantic",
+    "typer",
+]
 
 logger = logging.getLogger(__name__)
 

diff --git a/scripts/exsrw_smoke_dust.sh b/scripts/exsrw_smoke_dust.sh
@@ -127,8 +127,7 @@ else
 
   # Copy Smoke file to COMOUT
   cp -p ${DATA_SHARE}/${smokeFile} ${COMOUT}
-  cp -p ${DATA_SHARE}/${smokeFile} ${DATA} #tdk:pr: is this copy of the file needed?
-#  cp -p ${DATA}/${smokeFile} ${COMOUT} #tdk: is this the correct method?
+  cp -p ${DATA_SHARE}/${smokeFile} ${DATA}
 fi
 #
 #-----------------------------------------------------------------------

diff --git a/tests/test_python/test_smoke_dust/test_core/test_regrid.py b/tests/test_python/test_smoke_dust/test_core/test_regrid.py
@@ -176,7 +176,6 @@ def test_run(
         tmp_path: Path,
     ) -> None:
         """Test the regrid processor."""
-        # tdk:story: add MPI testing
         spy1 = mocker.spy(SmokeDustRegridProcessor, "_run_impl_")
         regrid_processor = SmokeDustRegridProcessor(data_for_test.context)
         regrid_processor.run(data_for_test.preprocessor.forecast_metadata)

diff --git a/ush/config.smoke_dust.yaml b/ush/config.smoke_dust.yaml
@@ -37,7 +37,6 @@ task_get_extrn_ics:
   EXTRN_MDL_NAME_ICS: RAP
   EXTRN_MDL_ICS_OFFSET_HRS: 0
   USE_USER_STAGED_EXTRN_FILES: true
-  #tdk:pr: can we use overlays to parameterize these?
   EXTRN_MDL_SOURCE_BASEDIR_ICS: /scratch2/NAGAPE/epic/SRW-AQM_DATA/data_smoke_dust/RAP_DATA_SD/${yyyymmddhh} # hera
 #  EXTRN_MDL_SOURCE_BASEDIR_ICS: /work/noaa/epic/SRW-AQM_DATA/input_model_data/RAP/${yyyymmddhh} # orion/hercules
 #  EXTRN_MDL_SOURCE_BASEDIR_ICS: /gpfs/f6/bil-fire8/world-shared/UFS_SRW_data/develop/input_model_data/RAP/${yyyymmddhh} # gaea-c6
@@ -61,9 +60,9 @@ task_run_fcst:
   QUILTING: true
   PRINT_ESMF: false
   DO_FCST_RESTART: false
-#task_run_post: #tdk:rm maybe?
-#  POST_OUTPUT_DOMAIN_NAME: conus3km
-#  USE_CUSTOM_POST_CONFIG_FILE: false
+task_run_post:
+  POST_OUTPUT_DOMAIN_NAME: conus3km
+  USE_CUSTOM_POST_CONFIG_FILE: false
 global:
   DO_ENSEMBLE: false
   NUM_ENS_MEMBERS: 2
@@ -75,4 +74,4 @@ smoke_dust_parm:
   PERSISTENCE: false
   RAVE_QA_FILTER: none
   EXIT_ON_ERROR: true
-  LOG_LEVEL: info
+  LOG_LEVEL: info
diff --git a/ush/config_defaults.yaml b/ush/config_defaults.yaml
@@ -2867,7 +2867,18 @@ smoke_dust_parm:
   #
   # SMOKE_DUST_FILE_PREFIX:
   # Prefix of Smoke and Dust file name
-  #tdk:doc
+  #
+  # RAVE_QA_FILTER:
+  # Apply RAVE QA filtering to source RAVE fields.
+  #   none: No filtering applied
+  #   high: QA flag values < 2 set to zero.
+  #
+  # EXIT_ON_ERROR:
+  # If true, raise and exception in the preprocessor when an error occurs. If false, create a
+  # dummy emissions file, log the error, and continue.
+  #
+  # LOG_LEVEL:
+  # Logging level for the preprocessor: info or debug
   #
   #-----------------------------------------------------------------------
   #

diff --git a/ush/smoke_dust/core/cycle.py b/ush/smoke_dust/core/cycle.py
@@ -154,7 +154,6 @@ def create_start_datetime(self) -> dt.datetime:
         return self._context.fcst_datetime - dt.timedelta(days=1, hours=1)
 
     def process_emissions(self, forecast_metadata: pd.DataFrame) -> None:
-        # tdk:story: figure out restart file copying
         # pylint: disable=too-many-statements
         self.log("process_emissions: enter")