just wrapping up

Author: kthyng

docs/environment.yml

@@ -3,17 +3,16 @@ channels:
   - conda-forge
   - nodefaults
 dependencies:
-   - python=3.10
+   - python>=3.11
    # If your docs code examples depend on other packages add them here
    - adios_db
    - aiohttp
    - appdirs
    - cmocean
    - fastparquet
-   - geojson_pydantic
    - numpy
    - xarray
-   - kerchunk
+   - kerchunk==0.2.7
    - numpydoc
    - opendrift==1.13.0
    # These are needed for the docs themselves

docs/tutorial.md

@@ -211,7 +211,7 @@ There are also specific seeding options for this model:
 
 ```{code-cell} ipython3
 m = ptm.OpenDriftModel(drift_model="OpenOil", lon=-89.85, lat=28.08, number=10, steps=45,
-                       z=-10, do3D=True, oil_type='Cook Inlet [2003] (EC00561)',
+                       z=-10, do3D=True, oil_type='Cook Inlet [2003]',
                        start_time="2009-11-19T12:00", ocean_model="TXLA",
                        ocean_model_local=False,
                        )
@@ -220,12 +220,14 @@ m.o.set_config('environment:constant:x_wind', -1)
 m.o.set_config('environment:constant:y_wind', 1)
 ```
 
-List available oil types from NOAA's ADIOS database:
+List available oil types from NOAA's ADIOS database (or check the database online):
 
 ```{code-cell} ipython3
 ptm.OpenOilModelConfig.model_json_schema()["$defs"]["OilTypeEnum"]["enum"]
 ```
 
+You can instead refer to the `oil_type` by its id, for example in this case `oil_tye='EC00561'` would work.
+
 The configuration parameters for this simulation are:
 
 ```{code-cell} ipython3

docs/whats_new.md

@@ -1,6 +1,6 @@
 # What's New
 
-## Unreleased
+## v0.12.0 (April 9, 2025)
 
 * Suffix for parquet file format is now ".parquet" instead of ".parq".
 * Added a method to run plots from saved OpenDrift output file; also available in CLI. Updated docs.
@@ -16,8 +16,11 @@
     * can run plots from a parquet or netcdf output file now
     * can't run idealized simulations using `OpenDrift` directly in PTM anymore but this could be added back in if needed
     * updated docs
-    * property plot now requires keyword "variable" instead of "prop"
+    * property plot now requires keyword "variable" instead of "prop" (this change is from `OpenDrift`)
     * most configuration parameters are under `m.config` now instead of just `m`, if `m` represents a Manager instance.
+    * a geojson dict can be input but it is not fully working at the moment
+    * `oil_type` can be input as the name or the id from the adios database.
+    * `.model_json_schema()` is overridden in `OpenDriftConfig` to include a bit of custom code to modify the `oil_type` output in the JSON schema "properties" area. This shouldn't affect anything other than it being available if people want that.
 
 
 ## v0.11.1 (February 4, 2025)

environment.yml

@@ -9,7 +9,7 @@ dependencies:
   - aiohttp
   - appdirs
   - fastparquet
-  - geojson_pydantic
+  # - geojson_pydantic
   - jupyter
   - jupyterlab
   - kerchunk

particle_tracking_manager/__init__.py

@@ -17,4 +17,5 @@
     OpenDriftConfig,
     OpenOilModelConfig,
 )
+from .models.opendrift.enums import ModifyOilTypeJsonSchema
 from .models.opendrift.opendrift import OpenDriftModel

particle_tracking_manager/config_misc.py

@@ -65,7 +65,9 @@ def assign_output_file_if_needed(value: str | None) -> str:
     @field_validator("output_file", mode="after")
     def clean_output_file(value: str) -> str:
         """Clean the output file name by removing extensions."""
-        value = value.replace(".nc", "").replace(".parquet", "").replace(".parq", "")
+        value = (
+            str(value).replace(".nc", "").replace(".parquet", "").replace(".parq", "")
+        )
         return value
 
     @model_validator(mode="after")

particle_tracking_manager/config_the_manager.py

@@ -11,7 +11,7 @@
 # Third-party imports
 import pandas as pd
 
-from geojson import GeoJSON
+# from geojson import GeoJSON
 from pydantic import BaseModel, Field, computed_field, model_validator
 
 # Local imports

particle_tracking_manager/models/opendrift/config_opendrift.py

@@ -7,7 +7,7 @@
 from pathlib import Path
 
 # Third-party imports
-from pydantic import Field, model_validator
+from pydantic import Field, field_validator, model_validator
 from pydantic.fields import FieldInfo
 from typing_extensions import Self
 
@@ -18,6 +18,7 @@
     DiffusivityModelEnum,
     DriftModelEnum,
     DropletSizeDistributionEnum,
+    ModifyOilTypeJsonSchema,
     ObjectTypeEnum,
     OilTypeEnum,
     PlotTypeEnum,
@@ -165,6 +166,13 @@ class OpenDriftConfig(TheManagerConfig):
         "extra": "forbid",
     }
 
+    @classmethod
+    def model_json_schema(cls, **kwargs) -> dict:
+        """Override the method to customize the JSON schema to include customization of oil_type."""
+        return super().model_json_schema(
+            schema_generator=ModifyOilTypeJsonSchema, **kwargs
+        )
+
     @model_validator(mode="after")
     def check_interpolator_filename(self) -> Self:
         """Check if interpolator_filename is set correctly."""
@@ -479,7 +487,7 @@ class OpenOilModelConfig(OceanDriftModelConfig):
     drift_model: DriftModelEnum = DriftModelEnum.OpenOil  # .value
 
     oil_type: OilTypeEnum = Field(
-        default=OilTypeEnum.GENERIC_BUNKER_C_AD04012,  # .value,
+        default=OilTypeEnum("GENERIC BUNKER C"),  # .value,
         description="Oil type to be used for the simulation, from the NOAA ADIOS database.",
         title="Oil Type",
         json_schema_extra={"od_mapping": "seed:oil_type", "ptm_level": 1},
@@ -650,6 +658,24 @@ class OpenOilModelConfig(OceanDriftModelConfig):
     #         self.oil_type = self.oil_type_input.split(" (")[0]
     #     return self
 
+    # @model_validator(mode="before")
+    # def validate_oil_type_by_id_from_name(cls, values):
+    #     """Validate oil type by id from name."""
+    #     name_id = values.get('oil_type')
+    #     if name_id not in OceanModelEnum.__members__:
+    #         raise ValueError(f"Invalid ocean model name_id: {name_id}")
+    #     return values
+
+    @field_validator("oil_type", mode="before")
+    def map_oil_type_to_id(cls, v):
+        """Map oil type to enum name (which is the oil type id)."""
+        if v in OilTypeEnum.__members__:  # Check if it matches a name
+            return OilTypeEnum[v]
+        for enum_member in OilTypeEnum:  # Check if it matches a value
+            if enum_member.value == v:
+                return enum_member
+        raise ValueError(f"Invalid value or name '{v}' for OilTypeEnum")
+
 
 class LarvalFishModelConfig(OceanDriftModelConfig):
     """Larval fish model configuration for OpenDrift."""