maybe ready to move out of draft [ci skip]

.github/workflows/python_tests.yaml

@@ -24,21 +24,22 @@ jobs:
       - name: Install Micromamba and srw_app environment
         uses: mamba-org/setup-micromamba@v1
         with:
-          environment-file: environment.yml
-          environment-name: srw_app
+          environment-file: sd_environment.yml
+          environment-name: srw_sd
           init-shell: bash
           cache-downloads: true
           cache-environment: true
 
       - name: Lint the python code
         run: |
-          micromamba activate srw_app
+          micromamba activate srw_sd
           export PYTHONPATH=$(pwd)/ush
           pylint --ignore-imports=yes tests/test_python/
           pylint ush/create_*.py
           pylint ush/generate_FV3LAM_wflow.py
           pylint ush/set_fv3nml*.py
           pylint ush/update_input_nml.py
+          pylint ush/smoke_dust
 
       - name: Checkout externals
         run: |
@@ -47,15 +48,16 @@ jobs:
       - name: Run python unittests
         run: |
           # exclude test_retrieve_data that is tested in functional test
-          micromamba activate srw_app
+          micromamba activate srw_sd
           export UNIT_TEST=True
           export PYTHONPATH=$(pwd)/ush
           python -m unittest tests/test_python/*.py
+          export PYTHONPATH=${PYTHONPATH}:$(pwd)/tests
+          python -m pytest tests/test_python/test_smoke_dust
 
       - name: Run python functional tests
         run: |
-          micromamba activate srw_app
+          micromamba activate srw_sd
           export CI=true
           export PYTHONPATH=${PWD}/ush
           python3 -m unittest tests/test_python/test_retrieve_data.py
-

doc/Makefile

@@ -1,6 +1,6 @@
 # Makefile for Sphinx documentation
 
-#tdk: add back in -W
+#tdk: add back in -W --keep-going
 SPHINXOPTS    = -a -n
 SPHINXBUILD   = sphinx-build
 SOURCEDIR     = .

doc/conf.py

@@ -36,9 +36,22 @@
 
 numfig = True
 
-nitpick_ignore = [('py:class', 'obj'),('py:class', 
-                   'yaml.dumper.Dumper'),('py:class', 
-                   'xml.etree.ElementTree'),('py:class', 'Basemap'),]
+nitpick_ignore = [
+    ('py:class', 'obj'),
+    ('py:class', 'yaml.dumper.Dumper'),
+    ('py:class', 'xml.etree.ElementTree'),
+    ('py:class', 'Basemap'),
+    ('py:class', 'numpy.ma.MaskedArray'),
+    ('py:class', 'esmpy.Field'),
+    ('py:class', 'pandas.DataFrame'),
+    ('py:class', 'netCDF4.Variable'),
+    ('py:class', 'pandas.DatetimeIndex'),
+    ('py:class', 'netCDF4.Dataset'),
+    ('py:class', 'numpy.ndarray'),
+    ('py:class', 'pydantic.BaseModel'),
+    ('py:class', 'esmpy.Grid'),
+    ('py:class', 'esmpy.StaggerLoc'),
+]
 
 # -- General configuration ---------------------------------------------------
 
@@ -52,7 +65,6 @@
     'sphinx.ext.mathjax',
     'sphinx.ext.napoleon',
     'sphinxcontrib.bibtex',
-    'sphinxcontrib.autodoc_pydantic',
 ]
 
 bibtex_bibfiles = ['references.bib']
@@ -322,6 +334,3 @@ def warn_undocumented_members(app, what, name, obj, options, lines):
 # the purpose of building the documentation, METplus is loaded by including "metplus" in
 # the autodoc_mock_imports list above, not via use of the METPLUS_ROOT environment variable.
 os.environ["METPLUS_ROOT"] = ""
-
-# Configuration related to autodoc_pydantic
-autodoc_pydantic_model_show_validator_summary = False

sd_environment.yml

@@ -14,4 +14,5 @@ dependencies:
   - scipy=1.10.*
   - uwtools=2.3.*
   - xarray=2022.11.*
-  - typer=0.15.*
+  - typer=0.15.*
+  - sphinx=7.4.*

ush/smoke_dust/core/context.py

@@ -9,7 +9,7 @@
 from typing import Union, Annotated, Any
 
 from mpi4py import MPI
-from pydantic import BaseModel, model_validator, BeforeValidator
+from pydantic import BaseModel, model_validator, BeforeValidator, Field
 
 from smoke_dust.core.common import open_nc
 
@@ -29,8 +29,8 @@ class PredefinedGrid(StrEnum):
 class EbbDCycle(StrEnum):
     """Emission forecast cycle method.
 
-    * `1`: Estimate emissions and fire radiative power.
-    * `2`: In addition to `1`, also create inputs to forecast hourly wildfire potential.
+    * ``1``: Estimate emissions and fire radiative power.
+    * ``2``: In addition to `1`, also create inputs to forecast hourly wildfire potential.
     """
 
     ONE = "1"
@@ -43,8 +43,9 @@ class RaveQaFilter(StrEnum):
     Quality assurance flag filtering to apply to input RAVE data. RAVE QA filter values range from
     one to three.
 
-    * `none`: Do not apply any QA filtering.
-    * `high`: QA flag values less than `2` are set to zero for derived fire radiative energy fields.
+    * ``none``: Do not apply any QA filtering.
+    * ``high``: QA flag values less than `2` are set to zero for derived fire radiative energy
+        fields.
     """
 
     NONE = "none"
@@ -123,21 +124,43 @@ class SmokeDustContext(BaseModel):
     """Context object for smoke/dust."""
 
     # Values provided via command-line
-    staticdir: ReadPathType
-    ravedir: ReadPathType
-    intp_dir: WritePathType
-    predef_grid: PredefinedGrid
-    ebb_dcycle: EbbDCycle
-    restart_interval: Annotated[tuple[int, ...], BeforeValidator(_format_restart_interval_)]
-    persistence: bool
-    rave_qa_filter: RaveQaFilter
-    exit_on_error: bool
-    log_level: LogLevel
-    regrid_in_memory: bool = False
+    staticdir: ReadPathType = Field(description="Path to smoke and dust fixed files.")
+    ravedir: ReadPathType = Field(
+        description="Path to the directory containing RAVE data files (hourly)."
+    )
+    intp_dir: WritePathType = Field(
+        description="Path to the directory containing interpolated RAVE data files."
+    )
+    predef_grid: PredefinedGrid = Field(
+        description="SRW predefined grid to use as the forecast domain."
+    )
+    ebb_dcycle: EbbDCycle = Field(description="The forecast cycle to run.")
+    restart_interval: Annotated[tuple[int, ...], BeforeValidator(_format_restart_interval_)] = (
+        Field(
+            description="Restart intervals used for restart file search. For example '6 12 18 24'."
+        )
+    )
+    persistence: bool = Field(
+        description="If true, use satellite observations from the previous day. Otherwise, use "
+        "observations from the same day."
+    )
+    rave_qa_filter: RaveQaFilter = Field(
+        description="Filter level for RAVE QA flags when regridding fields."
+    )
+    exit_on_error: bool = Field(
+        description="If false, log errors and write a dummy emissions file but do not raise an "
+        "exception."
+    )
+    log_level: LogLevel = Field(description="Logging level for the preprocessor")
+    regrid_in_memory: bool = Field(
+        description="If true, do esmpy regridding in-memory as opposed to reading from the fixed "
+        "weight file.",
+        default=False,
+    )
 
     # Values provided via environment
-    current_day: str
-    nwges_dir: ReadPathType
+    current_day: str = Field(description="The forecast date for the start of the cycle.")
+    nwges_dir: ReadPathType = Field(description="Directory containing restart files.")
 
     # Fixed parameters
     should_calc_desc_stats: bool = False

ush/smoke_dust/generate_emissions.py

@@ -4,7 +4,7 @@
 Python script for fire emissions preprocessing from RAVE FRP and FRE (Li et al.,2022)
 Author: [email protected]
 """
-
+import os
 import sys
 from enum import StrEnum, unique
 from pathlib import Path
@@ -25,7 +25,7 @@
 
 # pylint: enable=wrong-import-position
 
-
+os.environ["NO_COLOR"] = "1"
 app = typer.Typer(pretty_exceptions_enable=False)