updated HAB schema (#65)

* updated HAB schema

* precommit

Author: kthyng

docs/tutorial.md

@@ -65,7 +65,7 @@ m = ptm.OpenDriftModel(drift_model="HarmfulAlgalBloom", lon = -89.8, lat = 29.08
                        ocean_model="TXLA",
                        start_time="2009-11-19T12:00",
                        ocean_model_local=False,
-                       species_type="Pseudo_nitzschia",
+                       species_type="Pseudo nitzschia",
                        plots={'spaghetti': {}})
 ```
 

docs/whats_new.md

@@ -1,6 +1,11 @@
 # What's New
 
-## Unreleased
+## v2.0.2 (Decemeber 5, 2025)
+
+* Changed "name" of `HarmfulAlgalBloom` `species_type` enum to be an abbreviation "PN" and the value for the initial species to be "Pseudo nitzschia" instead of "Pseudo_nitzschia".
+* Added to the `HarmfulAlgalBloom` schema to have a "oneOf" output containing the preset values associated with a `species_type` in the description.
+
+## v2.0.0 (December 4, 2025)
 
 * Added a new model scenario: `HarmfalAlgalBloom`.
 * Fix a bug for running backward in time.

particle_tracking_manager/models/opendrift/config_opendrift.py

@@ -30,6 +30,7 @@
     SPECIES_HAB_DEFAULTS,
     SPECIES_HAB_MANAGER_DEFAULTS,
     HABParameters,
+    _species_descriptions,
 )
 
 
@@ -770,12 +771,22 @@ class HarmfulAlgalBloomModelConfig(HABParameters, OceanDriftModelConfig):
     """Harmful algal bloom model configuration for OpenDrift."""
 
     drift_model: DriftModelEnum = DriftModelEnum.HarmfulAlgalBloom
-
+    # import pdb; pdb.set_trace()
     species_type: HABSpeciesTypeEnum = Field(
-        default=HABSpeciesTypeEnum("Pseudo_nitzschia"),
+        default=HABSpeciesTypeEnum.PN,
         description="HarmfulAlgalBloom species category for this simulation. This option maps to individual properties which can instead be set manually if desired.",
         title="HAB Species Type",
-        json_schema_extra={"ptm_level": 1},
+        json_schema_extra={
+            "ptm_level": 1,
+            "oneOf": [
+                {
+                    "const": species.name,
+                    "title": species.value,
+                    "description": _species_descriptions[species.value],
+                }
+                for species in HABSpeciesTypeEnum
+            ],
+        },
     )
 
     # # new field: full parameter bundle for the HAB species
@@ -824,7 +835,7 @@ def apply_species_defaults(cls, data: Any) -> Any:
             return data
 
         # Ensure species_type has some value in raw input
-        data.setdefault("species_type", HABSpeciesTypeEnum("Pseudo_nitzschia"))
+        data.setdefault("species_type", HABSpeciesTypeEnum.PN)
         species = data["species_type"]
 
         # -------- HAB param defaults (flattened) --------

particle_tracking_manager/models/opendrift/enums/species_types.py

@@ -8,7 +8,7 @@
 class HABSpeciesTypeEnum(str, Enum):
     """Enum for species types used in HarmfulAlgalBloom model in OpenDrift."""
 
-    Pseudo_nitzschia = "Pseudo_nitzschia"
+    PN = "Pseudo nitzschia"
     custom = "custom"  # for fully user-specified params
 
 
@@ -20,6 +20,7 @@ class HABParameters(BaseModel):
         title="Cell death below this temperature",
         ge=-5.0,
         le=40.0,
+        default=3.0,
         json_schema_extra={
             "units": "degrees",
             "od_mapping": "hab:temperature_death_min",
@@ -32,6 +33,7 @@ class HABParameters(BaseModel):
         title="Cell death above this temperature",
         ge=-5.0,
         le=40.0,
+        default=22.0,
         json_schema_extra={
             "units": "degrees",
             "od_mapping": "hab:temperature_death_max",
@@ -44,6 +46,7 @@ class HABParameters(BaseModel):
         title="High mortality rate",
         ge=0.0,
         le=10.0,
+        default=1.0,
         json_schema_extra={
             "units": "days^-1",
             "od_mapping": "hab:mortality_rate_high",
@@ -56,6 +59,7 @@ class HABParameters(BaseModel):
         title="Cell death below this salinity",
         ge=0.0,
         le=50.0,
+        default=25.0,
         json_schema_extra={
             "units": "psu",
             "od_mapping": "hab:salinity_death_min",
@@ -68,6 +72,7 @@ class HABParameters(BaseModel):
         title="Cell death above this salinity",
         ge=0.0,
         le=50.0,
+        default=36.0,
         json_schema_extra={
             "units": "psu",
             "od_mapping": "hab:salinity_death_max",
@@ -78,7 +83,7 @@ class HABParameters(BaseModel):
 
 # Species default for HarmfulAlgalBloom model
 SPECIES_HAB_DEFAULTS: dict[HABSpeciesTypeEnum, HABParameters] = {
-    HABSpeciesTypeEnum.Pseudo_nitzschia: HABParameters(
+    HABSpeciesTypeEnum.PN: HABParameters(
         temperature_death_min=3.0,
         temperature_death_max=22.0,
         mortality_rate_high=1.0,
@@ -91,10 +96,24 @@ class HABParameters(BaseModel):
 
 # Other config defaults per species (z, do3D, etc.)
 SPECIES_HAB_MANAGER_DEFAULTS: dict[HABSpeciesTypeEnum, dict[str, object]] = {
-    HABSpeciesTypeEnum.Pseudo_nitzschia: {
+    HABSpeciesTypeEnum.PN: {
         "z": -1.0,
         "do3D": False,
     },
     # HABSpeciesTypeEnum.Alexandrium: {"do3D": True, ...},
     # HABSpeciesTypeEnum.Dinophysis: {...},
 }
+
+# this is for the schema
+_species_descriptions = {
+    species.value: "Defaults: "
+    + ", ".join(
+        [
+            f"{key}={value}"
+            for key, value in SPECIES_HAB_DEFAULTS[species].model_dump().items()
+        ]
+    )
+    for species in HABSpeciesTypeEnum
+    if species != "custom"
+}
+_species_descriptions["custom"] = "Custom species with user-defined parameters."

tests/test_config_opendrift.py

@@ -286,25 +286,25 @@ def test_HarmfulAlgalBloom_species_type():
     """Make sure species_type parameter works as expected."""
     m = HarmfulAlgalBloomModelConfig(
         drift_model="HarmfulAlgalBloom",
-        species_type="Pseudo_nitzschia",
+        species_type="Pseudo nitzschia",
         steps=1,
     )
-    assert m.species_type == "Pseudo_nitzschia"
+    assert m.species_type == "Pseudo nitzschia"
     assert (
         m.temperature_death_min
-        == SPECIES_HAB_DEFAULTS["Pseudo_nitzschia"].temperature_death_min
+        == SPECIES_HAB_DEFAULTS["Pseudo nitzschia"].temperature_death_min
     )
     assert (
         m.temperature_death_max
-        == SPECIES_HAB_DEFAULTS["Pseudo_nitzschia"].temperature_death_max
+        == SPECIES_HAB_DEFAULTS["Pseudo nitzschia"].temperature_death_max
     )
     assert (
         m.salinity_death_min
-        == SPECIES_HAB_DEFAULTS["Pseudo_nitzschia"].salinity_death_min
+        == SPECIES_HAB_DEFAULTS["Pseudo nitzschia"].salinity_death_min
     )
     assert (
         m.salinity_death_max
-        == SPECIES_HAB_DEFAULTS["Pseudo_nitzschia"].salinity_death_max
+        == SPECIES_HAB_DEFAULTS["Pseudo nitzschia"].salinity_death_max
     )
 
 

tests/test_opendrift.py

@@ -291,7 +291,7 @@ def test_HarmfulAlgalBloom_seeding():
 
     m = OpenDriftModel(
         drift_model="HarmfulAlgalBloom",
-        species_type="Pseudo_nitzschia",
+        species_type="Pseudo nitzschia",
         temperature_death_min=1,
         lon=-151,
         lat=60,