Refactor Jill's initial PR for maintainability

add testing script and cfg file

Move METRICS_DEFAULT_VALUE to /driver/__init__.py

Refactor `default_viewer.py` and `main.py`

Move `run_native_grid_test.py` to `debug/968-native-grid-vis`

Refactor `lat_lon_native_parameter.py` and `core_parameter.py`
- Update type annotations, re-order methods in `LatLonNativeParameter` class

Add a comment for granulation in `core_parser.py`

Extract code from LatLonNativeDriver into NativeDataset class
- Move `TimeSlice` and  `TimeSelection` into `type_annotations.py` and update all references

Add type annotations and comments

Add fixme and todo comments in driver and plotter

Update run script to use single run

Author: chengzhuzhang

auxiliary_tools/debug/968-native-grid-vis/TGCLDLWP.cfg

@@ -0,0 +1,11 @@
+[#]
+sets = ["lat_lon_native"]
+case_id = "model_vs_model"
+variables = ["TGCLDLWP"]
+seasons = ["ANN", "01", "02", "03", "04", "05", "06", "07", "08", "09", "10", "11", "12", "DJF", "MAM", "JJA", "SON"]
+regions = ["global", "30S30N-150E90W"]
+#test_colormap = "Blues"
+#reference_colormap = "Blues"
+diff_colormap = "RdBu"
+#contour_levels = [  1.25892541,   2.26754313,   4.08423865,   7.35642254, 13.25019355,  23.86589787,  42.98662347,  77.42636827, 139.45832492, 251.18864315]
+diff_levels = [-35, -30, -25, -20, -15, -10, -5, 5, 10, 15, 20, 25, 30, 35]

auxiliary_tools/debug/968-native-grid-vis/run_lat_lon_native.cfg

@@ -0,0 +1,11 @@
+[#]
+sets = ["lat_lon_native"]
+case_id = "model_vs_model"
+variables = ["PRECT"]
+seasons = ["ANN", "01", "02", "03", "04", "05", "06", "07", "08", "09", "10", "11", "12", "DJF", "MAM", "JJA", "SON"]
+regions = ["global", "60S60N", "30S30N-150E90W"]
+test_colormap = "WhiteBlueGreenYellowRed.rgb"
+reference_colormap = "WhiteBlueGreenYellowRed.rgb"
+diff_colormap = "BrBG"
+contour_levels = [0.5, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 14, 15, 16]
+diff_levels = [-2.5, -2, -1.5, -1, -0.5, -0.25, 0.25, 0.5, 1, 1.5, 2, 2.5]

auxiliary_tools/debug/968-native-grid-vis/run_lat_lon_native.py

@@ -0,0 +1,77 @@
+#!/usr/bin/env python3
+"""
+This script runs e3sm_diags with the lat_lon_native set to visualize native grid data.
+"""
+
+import os
+import sys
+
+from e3sm_diags.parameter.lat_lon_native_parameter import LatLonNativeParameter
+from e3sm_diags.run import runner
+
+# Create parameter object
+param = LatLonNativeParameter()
+
+# Basic parameters
+param.results_dir = "/lcrc/group/e3sm/public_html/diagnostic_output/ac.tvo/tests/lat_lon_native_file"
+# Create results directory if it doesn't exist
+if not os.path.exists(param.results_dir):
+    os.makedirs(param.results_dir)
+
+
+# Model data
+
+##(1)
+#param.test_data_path = "/home/ac.zhang40/test"
+#param.test_name = "v3.LR.amip_0101"
+#param.short_test_name = "v3.LR.amip_0101"
+#param.reference_data_path = "/home/ac.zhang40/test"
+#param.ref_name = "v3.HR.test4"
+#param.short_ref_name = "v3.HR.test4"
+#param.seasons = ["DJF"]
+
+
+##(2)
+#param.test_data_path = "/home/ac.zhang40/test"
+#param.test_file = "v3.LR.amip_0101_DJF_climo.nc"
+#param.short_test_name = "v3.LR.amip_0101"
+#param.reference_data_path = "/home/ac.zhang40/test"
+#param.ref_file = "v3.HR.test4_DJF_climo.nc"
+#param.short_ref_name = "v3.HR.test4"
+#param.seasons = ["DJF"]
+##(3)
+param.test_data_path = "/lcrc/group/e3sm2/ac.wlin/E3SMv3/v3.LR.historical_0051/archive/atm/hist"
+param.test_file = "v3.LR.historical_0051.eam.h0.1989-12.nc"
+#param.short_test_name = "v3.LR.amip_0101"
+param.reference_data_path = "/lcrc/group/e3sm2/ac.wlin/E3SMv3/v3.LR.historical_0051/archive/atm/hist"
+param.ref_file = "v3.LR.historical_0051.eam.h0.1989-12.nc"
+#param.reference_data_path = "/lcrc/group/e3sm2/ac.jwolfe/E3SMv3_dev/20250404.wcycl1850.ne120pg2_r025_RRSwISC6to18E3r5.test4.chrysalis/archive/atm/hist/"
+#param.ref_file = "20250404.wcycl1850.ne120pg2_r025_RRSwISC6to18E3r5.test4.chrysalis.eam.h0.0018-12.nc"
+param.short_ref_name = "v3.HR.test4"
+#param.seasons = ["DJF"]
+param.time_slices=["0"]
+
+
+param.case_id = "model_vs_model"
+
+
+# Native grid settings
+param.test_grid_file = "/lcrc/group/e3sm/diagnostics/grids/ne30pg2.nc"
+param.ref_grid_file = "/lcrc/group/e3sm/diagnostics/grids/ne30pg2.nc"
+#param.ref_grid_file = "/lcrc/group/e3sm/diagnostics/grids/ne120pg2.nc"
+
+param.split_periodic_elements = True
+param.antialiased = False
+
+# param.model_only = True
+param.run_type = "model_vs_model"
+
+# Run the single diagnostic, comment out for complete diagnostics.
+cfg_path = "auxiliary_tools/debug/968-native-grid-vis/run_lat_lon_native.cfg"
+
+sys.argv.extend(["--diags", cfg_path])
+
+runner.sets_to_run = ["lat_lon_native"]
+runner.run_diags([param])
+
+

run_native_grid_test.py renamed to auxiliary_tools/debug/968-native-grid-vis/run_native_grid_test.py

@@ -9,3 +9,9 @@
 # The keys for the land and ocean fraction variables in the
 # `LAND_OCEAN_MASK_PATH` file.
 FRAC_REGION_KEYS = {"land": ("LANDFRAC", "landfrac"), "ocean": ("OCNFRAC", "ocnfrac")}
+
+# The default value for metrics if it is not calculated. This value was
+# preserved from the legacy CDAT codebase because the viewer expects this
+# value for metrics that aren't calculated.
+# TODO: Update `lat_lon_viewer.py` to handle missing metrics with None value.
+METRICS_DEFAULT_VALUE = 999.999

e3sm_diags/driver/__init__.py

@@ -4,6 +4,7 @@
 
 import xarray as xr
 
+from e3sm_diags.driver import METRICS_DEFAULT_VALUE
 from e3sm_diags.driver.utils.climo_xr import ClimoFreq
 from e3sm_diags.driver.utils.dataset_xr import Dataset
 from e3sm_diags.driver.utils.io import _save_data_metrics_and_plots
@@ -25,12 +26,6 @@
 if TYPE_CHECKING:
     from e3sm_diags.parameter.core_parameter import CoreParameter
 
-# The default value for metrics if it is not calculated. This value was
-# preserved from the legacy CDAT codebase because the viewer expects this
-# value for metrics that aren't calculated.
-# TODO: Update `lat_lon_viewer.py` to handle missing metrics with None value.
-METRICS_DEFAULT_VALUE = 999.999
-
 
 def run_diag(parameter: CoreParameter) -> CoreParameter:
     """Get metrics for the lat_lon diagnostic set.