New biogeochemistry features

src/virtualship/cli/_fetch.py

@@ -87,7 +87,7 @@ def _fetch(path: str | Path, username: str | None, password: str | None) -> None
 
     if (
         (
-            {"XBT", "CTD", "SHIP_UNDERWATER_ST"}
+            {"XBT", "CTD", "CDT_BGC", "SHIP_UNDERWATER_ST"}
             & set(instrument.name for instrument in instruments_in_schedule)
         )
         or ship_config.ship_underwater_st_config is not None
@@ -144,7 +144,6 @@ def _fetch(path: str | Path, username: str | None, password: str | None) -> None
             shutil.rmtree(download_folder)
             raise e
 
-        complete_download(download_folder)
         click.echo("Ship data download based on space-time region completed.")
 
     if InstrumentType.DRIFTER in instruments_in_schedule:
@@ -187,7 +186,6 @@ def _fetch(path: str | Path, username: str | None, password: str | None) -> None
             shutil.rmtree(download_folder)
             raise e
 
-        complete_download(download_folder)
         click.echo("Drifter data download based on space-time region completed.")
 
     if InstrumentType.ARGO_FLOAT in instruments_in_schedule:
@@ -235,9 +233,53 @@ def _fetch(path: str | Path, username: str | None, password: str | None) -> None
             shutil.rmtree(download_folder)
             raise e
 
-        complete_download(download_folder)
         click.echo("Argo_float data download based on space-time region completed.")
 
+    if InstrumentType.CTD_BGC in instruments_in_schedule:
+        print("CTD_BGC data will be downloaded. Please wait...")
+
+        ctd_bgc_download_dict = {
+            "o2data": {
+                "dataset_id": "cmems_mod_glo_bgc-bio_anfc_0.25deg_P1D-m",
+                "variables": ["o2"],
+                "output_filename": "ctd_bgc_o2.nc",
+            },
+            "chlorodata": {
+                "dataset_id": "cmems_mod_glo_bgc-pft_anfc_0.25deg_P1D-m",
+                "variables": ["chl"],
+                "output_filename": "ctd_bgc_chloro.nc",
+            },
+        }
+
+        # Iterate over all datasets and download each based on space_time_region
+        try:
+            for dataset in ctd_bgc_download_dict.values():
+                copernicusmarine.subset(
+                    dataset_id=dataset["dataset_id"],
+                    variables=dataset["variables"],
+                    minimum_longitude=spatial_range.minimum_longitude - 3.0,
+                    maximum_longitude=spatial_range.maximum_longitude + 3.0,
+                    minimum_latitude=spatial_range.minimum_latitude - 3.0,
+                    maximum_latitude=spatial_range.maximum_latitude + 3.0,
+                    start_datetime=start_datetime,
+                    end_datetime=end_datetime + timedelta(days=21),
+                    minimum_depth=abs(1),
+                    maximum_depth=abs(spatial_range.maximum_depth),
+                    output_filename=dataset["output_filename"],
+                    output_directory=download_folder,
+                    username=username,
+                    password=password,
+                    overwrite=True,
+                    coordinates_selection_method="outside",
+                )
+        except InvalidUsernameOrPassword as e:
+            shutil.rmtree(download_folder)
+            raise e
+
+        click.echo("CTD_BGC data download based on space-time region completed.")
+
+    complete_download(download_folder)
+
 
 def _hash(s: str, *, length: int) -> str:
     """Create a hash of a string."""

src/virtualship/expedition/ship_config.py

@@ -17,9 +17,10 @@
 
 
 class InstrumentType(Enum):
-    """Types of instruments."""
+    """Types of the instruments."""
 
     CTD = "CTD"
+    CTD_BGC = "CTD_BGC"
     DRIFTER = "DRIFTER"
     ARGO_FLOAT = "ARGO_FLOAT"
     XBT = "XBT"
@@ -80,6 +81,28 @@ def _validate_stationkeeping_time(cls, value: int | float | timedelta) -> timede
         return _validate_numeric_mins_to_timedelta(value)
 
 
+class CTD_BGCConfig(pydantic.BaseModel):
+    """Configuration for CTD_BGC instrument."""
+
+    stationkeeping_time: timedelta = pydantic.Field(
+        serialization_alias="stationkeeping_time_minutes",
+        validation_alias="stationkeeping_time_minutes",
+        gt=timedelta(),
+    )
+    min_depth_meter: float = pydantic.Field(le=0.0)
+    max_depth_meter: float = pydantic.Field(le=0.0)
+
+    model_config = pydantic.ConfigDict(populate_by_name=True)
+
+    @pydantic.field_serializer("stationkeeping_time")
+    def _serialize_stationkeeping_time(self, value: timedelta, _info):
+        return value.total_seconds() / 60.0
+
+    @pydantic.field_validator("stationkeeping_time", mode="before")
+    def _validate_stationkeeping_time(cls, value: int | float | timedelta) -> timedelta:
+        return _validate_numeric_mins_to_timedelta(value)
+
+
 class ShipUnderwaterSTConfig(pydantic.BaseModel):
     """Configuration for underwater ST."""
 
@@ -159,6 +182,13 @@ class ShipConfig(pydantic.BaseModel):
     If None, no CTDs can be cast.
     """
 
+    ctd_bgc_config: CTD_BGCConfig | None = None
+    """
+    CTD_BGC configuration.
+
+    If None, no BGC CTDs can be cast.
+    """
+
     ship_underwater_st_config: ShipUnderwaterSTConfig | None = None
     """
     Ship underwater salinity temperature measurementconfiguration.
@@ -239,6 +269,7 @@ def verify(self, schedule: Schedule) -> None:
             "DRIFTER",
             "XBT",
             "CTD",
+            "CTD_BGC",
         ]:  # TODO make instrument names consistent capitals or lowercase throughout codebase
             if hasattr(self, instrument.lower() + "_config") and not any(
                 instrument == schedule_instrument.name
@@ -248,6 +279,7 @@ def verify(self, schedule: Schedule) -> None:
                 setattr(self, instrument.lower() + "_config", None)
 
         # verify instruments in schedule have configuration
+        # TODO: the ConfigError message could be improved to explain that the **schedule** file has X instrument but the **ship_config** file does not
         for instrument in instruments_in_schedule:
             try:
                 InstrumentType(instrument)
@@ -266,6 +298,12 @@ def verify(self, schedule: Schedule) -> None:
                 raise ConfigError(
                     "Planning has a waypoint with CTD instrument, but configuration does not configure CTDs."
                 )
+            if instrument == InstrumentType.CTD_BGC and (
+                not hasattr(self, "ctd_bgc_config") or self.ctd_bgc_config is None
+            ):
+                raise ConfigError(
+                    "Planning has a waypoint with CTD_BGC instrument, but configuration does not configure CTD_BGCs."
+                )
             if instrument == InstrumentType.DRIFTER and (
                 not hasattr(self, "drifter_config") or self.drifter_config is None
             ):

src/virtualship/static/ship_config.yaml

@@ -14,6 +14,10 @@ ctd_config:
   max_depth_meter: -2000.0
   min_depth_meter: -11.0
   stationkeeping_time_minutes: 20.0
+ctd_bgc_config:
+  max_depth_meter: -2000.0
+  min_depth_meter: -11.0
+  stationkeeping_time_minutes: 20.0
 drifter_config:
   depth_meter: 0.0
   lifetime_minutes: 60480.0

src/virtualship/utils.py

@@ -156,6 +156,7 @@ def mfp_to_yaml(coordinates_file_path: str, yaml_output_path: str):  # noqa: D41
     instrument_max_depths = {
         "XBT": 2000,
         "CTD": 5000,
+        "CTD_BGC": 5000,
         "DRIFTER": 1,
         "ARGO_FLOAT": 2000,
     }