Add IODA and Increment comparisons

docs/examples/comparison_workflows.md

@@ -21,3 +21,34 @@ comparison_experiment_paths:
 These experiments should have matching assimilation window parameters. By default in this suite, start and end cycle points are not specified, in which case Swell will parse the two experiments to find the matching cycle times between the two. Alternatively, start and end cycle points can be set manually.
 
 The experiment can then be created using `swell create compare_variational_marine -o override.yaml` or `swell create compare_variational_atmosphere -o override`, depending on the type of experiments being compared. Launching the experiment will run tasks analyzing the jedi log and generating plots using Eva for increments. Comparison of the log analysis will be placed under the comparison suite's directory in a file named `jedi_log_comparison.txt`, while the eva plots will be located under the cycle directory for each cycle.
+
+## Comparing IODA observations
+The task `CompareIodaObservations` compares IODA files between experiments by checking for equality in standard IODA fields for simulated variables, including:
+
+```
+EffectiveError0
+EffectiveError1
+EffectiveQC0
+EffectiveQC1
+ObsBias0
+ObsBias1
+ObsValue
+PreQC
+hofx
+hofx0,
+hofx1
+oman
+ombg
+```
+
+Which variables are compared depends on the parameter `ioda_fields_for_comparison`. By default, `hofx` will be compared for hofx experiments, and `hofx0` and `hofx1` for variational and fgat suites. If a mismatch in data field length or average is detected, this task will fail.
+
+The `CleanCycle` task may clear observation files depending on the setting for `clean_patterns` in `experiment.yaml`. To use this task, ensure that `clean_patterns` is set correctly in the comparison experiments.
+
+## Comparing Increment files
+`CompareIncrement` compares increment values between experiments. By default, `geos_atmosphere` suites will compare `Salt, Temp, and ave_ssh`, `geos_atmosphere` will compare `ps, ts, ua, va, t, q`, and `geos_cf` suites compare `NO2`. Data fields will be checked to ensure they share the same size, and an average will be taken to check for equality 
+
+
+The `CleanCycle` task may clear observation files depending on the setting for `clean_patterns` in `
+experiment.yaml`. To use this task, ensure that `clean_patterns` is set correctly in the comparison
+experiments.

src/swell/suites/compare/flow.cylc

@@ -41,9 +41,12 @@
             {% for path in comparison_experiment_paths %}
             JediOopsLogParser-{{model_component}}-{{ loop.index0 }}
             {% endfor %}
-            JediLogComparison-{{model_component}}[^]:fail? => EvaComparisonIncrement-{{model_component}} => PublishComparisons => comparison_fail
-            JediLogComparison-{{model_component}}[^]:fail? => EvaComparisonJediLog-{{model_component}} => PublishComparisons => comparison_fail
-	    JediLogComparison-{{model_component}}[^]:fail? => EvaComparisonObservations-{{model_component}} => PublishComparisons => comparison_fail
+            CompareIodaObservations-{{model_component}}? & CompareIncrement-{{model_component}}? & JediLogComparison-{{model_component}}[^]? => Pass
+
+            CompareIodaObservations-{{model_component}}:fail? => EvaComparisonObservations-{{model_component}}? => PublishComparisons?
+            CompareIncrement-{{model_component}}:fail? => EvaComparisonIncrement-{{model_component}} => PublishComparisons?
+            JediLogComparison-{{model_component}}[^]:fail? => EvaComparisonJediLog-{{model_component}} => PublishComparisons?
+            PublishComparisons? => comparison_fail?
         {% endif %}
         {% endfor %}
         """
@@ -69,12 +72,30 @@
         script = "exit 1"
 
     {% for model_component in model_components %}
+    [[Pass]]
+        script = """
+            cylc set $CYLC_WORKFLOW_ID//$datetime/EvaComparisonIncrement-{{model_component}} --out skip
+            cylc set $CYLC_WORKFLOW_ID//$datetime/EvaComparisonJediLog-{{model_component}} --out skip
+            cylc set $CYLC_WORKFLOW_ID//$datetime/EvaComparisonObservations-{{model_component}} --out skip
+            cylc set $CYLC_WORKFLOW_ID//$datetime/PublishComparisons --out skip
+            cylc set $CYLC_WORKFLOW_ID//$datetime/comparison_fail --out skip
+        """
+
+    [[CompareIncrement-{{model_component}}]]
+        script = "swell task CompareIncrement $config -d $datetime -m {{model_component}}"
+
     [[EvaComparisonIncrement-{{model_component}}]]
         script = "swell task EvaComparisonIncrement $config -d $datetime -m {{model_component}}"
 
     [[EvaComparisonJediLog-{{model_component}}]]
         script = "swell task EvaComparisonJediLog $config -d $datetime -m {{model_component}}"
 
+    [[PublishComparisons]]
+         script = "swell task PublishComparisons $config -d $datetime -m {{model_component}}"
+
+    [[CompareIodaObservations-{{model_component}}]]
+        script = "swell task CompareIodaObservations $config -d $datetime -m {{model_component}}"
+
     [[EvaComparisonObservations-{{model_component}}]]
         script = "swell task EvaComparisonObservations $config -d $datetime -m {{model_component}}"
         platform = {{platform}}
@@ -84,9 +105,6 @@
             --{{key}} = {{value}}
         {%- endfor %}
 
-    [[PublishComparisons]]
-         script = "swell task PublishComparisons $config -d $datetime -m {{model_component}}"
-
     {% if comparison_experiment_paths is mapping %}
     {% for path in comparison_experiment_paths.values() %}
     [[JediOopsLogParser-{{model_component}}-{{ loop.index0 }}]]

src/swell/suites/compare/suite_config.py

@@ -30,6 +30,9 @@ class SuiteConfig(QuestionContainer, Enum):
             qd.cycle_times(default_value=[None], widget_type=WidgetType.STRING_CHECK_LIST),
             qd.model_components(),
             qd.runahead_limit(),
+            qd.ioda_fields_for_comparison(['hofx0/{variable}',
+                                           'hofx1/{variable}']),
+            qd.observations([]),
         ]
     )
 
@@ -41,6 +44,21 @@ class SuiteConfig(QuestionContainer, Enum):
             compare,
             qd.comparison_log_type('variational'),
             qd.model_components(['geos_marine']),
+            qd.observations([
+                "adt_cryosat2n",
+                "adt_jason3",
+                "adt_saral",
+                "adt_sentinel3a",
+                "adt_sentinel3b",
+                "insitu_profile_argo",
+                "sst_ostia",
+                "sss_smos",
+                "sss_smapv5",
+                "sst_abi_g16_l3c",
+                "sst_gmi_l3u",
+                "sst_viirs_n20_l3u",
+                "temp_profile_xbt"
+            ])
         ]
     )
 
@@ -52,6 +70,42 @@ class SuiteConfig(QuestionContainer, Enum):
             compare,
             qd.comparison_log_type('variational'),
             qd.model_components(['geos_atmosphere']),
+            qd.observations([
+                "aircraft_temperature",
+                "aircraft_wind",
+                "airs_aqua",
+                "amsr2_gcom-w1",
+                "amsua_aqua",
+                "amsua_metop-b",
+                "amsua_metop-c",
+                "amsua_n15",
+                "amsua_n18",
+                "amsua_n19",
+                "atms_n20",
+                "atms_npp",
+                "avhrr3_metop-b",
+                "avhrr3_n18",
+                "avhrr3_n19",
+                "cris-fsr_n20",
+                "cris-fsr_npp",
+                "gmi_gpm",
+                "gps",
+                "iasi_metop-b",
+                "iasi_metop-c",
+                "mhs_metop-b",
+                "mhs_metop-c",
+                "mhs_n19",
+                "mls55_aura",
+                "omi_aura",
+                "ompsnm_npp",
+                "pibal",
+                "satwind",
+                "scatwind",
+                "sfcship",
+                "sfc",
+                "sondes",
+                "ssmis_f17"
+            ])
         ]
     )
 
@@ -63,6 +117,10 @@ class SuiteConfig(QuestionContainer, Enum):
             compare,
             qd.comparison_log_type('variational'),
             qd.model_components(['geos_cf']),
+            qd.observations([
+                "tempo_no2_tropo",
+                "tropomi_s5p_no2_tropo",
+            ])
         ]
     )
 
@@ -74,6 +132,95 @@ class SuiteConfig(QuestionContainer, Enum):
             compare,
             qd.comparison_log_type('fgat'),
             qd.model_components(['geos_marine']),
+            qd.observations([
+                "adt_cryosat2n",
+                "adt_jason3",
+                "adt_jason3n",
+                "adt_saral",
+                "adt_sentinel3a",
+                "adt_sentinel3b",
+                "adt_sentinel6a",
+                "adt_swot_nadir",
+                "insitu_profile_argo",
+                "insitu_profile_ctd",
+                "insitu_profile_pirata",
+                "insitu_profile_rama",
+                "insitu_profile_tao",
+                "icec_amsr2_north",
+                "icec_amsr2_south",
+                "icec_nsidc_nh",
+                "icec_nsidc_sh",
+                "sst_ostia",
+                "sss_smos",
+                "sss_smapv5",
+                "sst_abi_g16_l3c",
+                "sst_avhrrf_mb_l3u",
+                "sst_avhrrf_mc_l3u",
+                "sst_viirs_n20_l3u",
+                "sst_viirs_npp_l3u",
+                "temp_profile_xbt"
+            ])
+        ]
+    )
+
+    # --------------------------------------------------------------------------------------------------
+
+    compare_hofx = QuestionList(
+        list_name="compare_hofx",
+        questions=[
+            compare,
+            qd.comparison_log_type('hofx'),
+            qd.model_components(['geos_atmosphere']),
+            qd.ioda_fields_for_comparison(['hofx/{variable}']),
+            qd.observations([
+                "aircraft_temperature",
+                "aircraft_wind",
+                "airs_aqua",
+                "amsr2_gcom-w1",
+                "amsua_aqua",
+                "amsua_metop-b",
+                "amsua_metop-c",
+                "amsua_n15",
+                "amsua_n18",
+                "amsua_n19",
+                "atms_n20",
+                "atms_npp",
+                "avhrr3_metop-b",
+                "avhrr3_n18",
+                "avhrr3_n19",
+                "cris-fsr_n20",
+                "cris-fsr_npp",
+                "gmi_gpm",
+                "gps",
+                "iasi_metop-b",
+                "iasi_metop-c",
+                "mhs_metop-b",
+                "mhs_metop-c",
+                "mhs_n19",
+                "mls55_aura",
+                "omi_aura",
+                "ompsnm_npp",
+                "pibal",
+                "satwind",
+                "scatwind",
+                "sfcship",
+                "sfc",
+                "sondes",
+                "ssmis_f17"
+            ]),
+            qd.mock_experiment(True)
+        ]
+    )
+
+    # --------------------------------------------------------------------------------------------------
+
+    compare_hofx_cf = QuestionList(
+        list_name="compare_hofx_cf",
+        questions=[
+            compare,
+            qd.comparison_log_type('hofx'),
+            qd.ioda_fields_for_comparison(['hofx/{variable}']),
+            qd.model_components(['geos_cf']),
         ]
     )
 

src/swell/suites/hofx_cf/suite_config.py

@@ -30,16 +30,21 @@ class SuiteConfig(QuestionContainer, Enum):
             qd.final_cycle_point("2023-08-05T18:00:00Z"),
             qd.jedi_build_method("use_existing"),
             qd.model_components(['geos_cf']),
-            qd.check_for_obs(False)  # don't check empty for empty obs
+            qd.check_for_obs(False),  # don't check empty for empty obs
+            qd.clean_patterns([])
         ],
 
         geos_cf=[
         ]
     )
 
+    # --------------------------------------------------------------------------------------------------
+
     hofx_cf_tier1 = QuestionList(
         list_name="hofx_cf_tier1",
         questions=[
              hofx_cf
         ]
     )
+
+# --------------------------------------------------------------------------------------------------