New biogeochemistry features

src/virtualship/cli/_fetch.py

@@ -38,6 +38,8 @@ def _fetch(path: str | Path, username: str | None, password: str | None) -> None
     be provided on prompt, via command line arguments, or via a YAML config file. Run
     `virtualship fetch` on an expedition for more info.
     """
+    from virtualship.expedition.ship_config import InstrumentType
+
     if sum([username is None, password is None]) == 1:
         raise ValueError("Both username and password must be provided when using CLI.")
 
@@ -85,13 +87,13 @@ 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 hasattr(ship_config, "ship_underwater_st_config")
-        or hasattr(ship_config, "adcp_config")
+        or ship_config.ship_underwater_st_config is not None
+        or ship_config.adcp_config is not None
     ):
-        print("Ship data will be downloaded")
+        print("Ship data will be downloaded. Please wait...")
 
         # Define all ship datasets to download, including bathymetry
         download_dict = {
@@ -142,11 +144,10 @@ 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 "DRIFTER" in instruments_in_schedule:
-        print("Drifter data will be downloaded")
+    if InstrumentType.DRIFTER in instruments_in_schedule:
+        print("Drifter data will be downloaded. Please wait...")
         drifter_download_dict = {
             "UVdata": {
                 "dataset_id": "cmems_mod_glo_phy-cur_anfc_0.083deg_PT6H-i",
@@ -185,11 +186,10 @@ 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 "ARGO_FLOAT" in instruments_in_schedule:
-        print("Argo float data will be downloaded")
+    if InstrumentType.ARGO_FLOAT in instruments_in_schedule:
+        print("Argo float data will be downloaded. Please wait...")
         argo_download_dict = {
             "UVdata": {
                 "dataset_id": "cmems_mod_glo_phy-cur_anfc_0.083deg_PT6H-i",
@@ -233,9 +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/__init__.py

@@ -2,8 +2,7 @@
 
 from .do_expedition import do_expedition
 from .input_data import InputData
-from .instrument_type import InstrumentType
-from .schedule import Schedule
+from .schedule import Schedule, Waypoint
 from .ship_config import (
     ADCPConfig,
     ArgoFloatConfig,
@@ -13,7 +12,6 @@
     ShipUnderwaterSTConfig,
 )
 from .space_time_region import SpaceTimeRegion
-from .waypoint import Waypoint
 
 __all__ = [
     "ADCPConfig",

src/virtualship/expedition/checkpoint.py

@@ -7,8 +7,8 @@
 import pydantic
 import yaml
 
-from .instrument_type import InstrumentType
 from .schedule import Schedule
+from .ship_config import InstrumentType
 
 
 class _YamlDumper(yaml.SafeDumper):

src/virtualship/expedition/schedule.py

@@ -3,22 +3,37 @@
 from __future__ import annotations
 
 import itertools
-from datetime import timedelta
+from datetime import datetime, timedelta
 from pathlib import Path
 
 import pydantic
 import pyproj
 import yaml
 from parcels import FieldSet
 
+from ..location import Location
 from .input_data import InputData
-from .instrument_type import InstrumentType
+from .ship_config import InstrumentType
 from .space_time_region import SpaceTimeRegion
-from .waypoint import Waypoint
 
 projection: pyproj.Geod = pyproj.Geod(ellps="WGS84")
 
 
+class Waypoint(pydantic.BaseModel):
+    """A Waypoint to sail to with an optional time and an optional instrument."""
+
+    location: Location
+    time: datetime | None = None
+    instrument: InstrumentType | list[InstrumentType] | None = None
+
+    @pydantic.field_serializer("instrument")
+    def serialize_instrument(self, instrument):
+        """Ensure InstrumentType is serialized as a string (or list of strings)."""
+        if isinstance(instrument, list):
+            return [inst.value for inst in instrument]
+        return instrument.value if instrument else None
+
+
 class Schedule(pydantic.BaseModel):
     """Schedule of the virtual ship."""
 

src/virtualship/expedition/ship_config.py

@@ -3,15 +3,27 @@
 from __future__ import annotations
 
 from datetime import timedelta
+from enum import Enum
 from pathlib import Path
+from typing import TYPE_CHECKING
 
 import pydantic
 import yaml
 
 from virtualship.utils import _validate_numeric_mins_to_timedelta
 
-from .instrument_type import InstrumentType
-from .schedule import Schedule
+if TYPE_CHECKING:
+    from .schedule import Schedule
+
+
+class InstrumentType(Enum):
+    """Types of instruments."""
+
+    CTD = "CTD"
+    CTD_BGC = "CTD_BGC"
+    DRIFTER = "DRIFTER"
+    ARGO_FLOAT = "ARGO_FLOAT"
+    XBT = "XBT"
 
 
 class ArgoFloatConfig(pydantic.BaseModel):
@@ -69,6 +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."""
 
@@ -148,6 +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.
@@ -228,6 +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
@@ -237,6 +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)
@@ -255,6 +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/expedition/simulate_schedule.py

@@ -13,10 +13,8 @@
 from ..instruments.xbt import XBT
 from ..location import Location
 from ..spacetime import Spacetime
-from .instrument_type import InstrumentType
-from .schedule import Schedule
-from .ship_config import ShipConfig
-from .waypoint import Waypoint
+from .schedule import Schedule, Waypoint
+from .ship_config import InstrumentType, ShipConfig
 
 
 @dataclass

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

@@ -139,14 +139,13 @@ def mfp_to_yaml(coordinates_file_path: str, yaml_output_path: str):  # noqa: D41
 
     """
     # Importing Schedule and related models from expedition module
-    from virtualship.expedition.instrument_type import InstrumentType
-    from virtualship.expedition.schedule import Schedule
+    from virtualship.expedition.schedule import Location, Schedule, Waypoint
+    from virtualship.expedition.ship_config import InstrumentType
     from virtualship.expedition.space_time_region import (
         SpaceTimeRegion,
         SpatialRange,
         TimeRange,
     )
-    from virtualship.expedition.waypoint import Location, Waypoint
 
     # Read data from file
     coordinates_data = load_coordinates(coordinates_file_path)
@@ -157,6 +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,
     }

tests/expedition/test_schedule.py

@@ -5,9 +5,8 @@
 import pytest
 
 from virtualship import Location
-from virtualship.expedition import Waypoint
 from virtualship.expedition.do_expedition import _load_input_data
-from virtualship.expedition.schedule import Schedule, ScheduleError
+from virtualship.expedition.schedule import Schedule, ScheduleError, Waypoint
 from virtualship.utils import _get_ship_config
 
 projection = pyproj.Geod(ellps="WGS84")

tests/test_mfp_to_yaml.py

@@ -3,8 +3,8 @@
 import pandas as pd
 import pytest
 
-from virtualship.expedition.instrument_type import InstrumentType
 from virtualship.expedition.schedule import Schedule
+from virtualship.expedition.ship_config import InstrumentType
 from virtualship.utils import mfp_to_yaml