From 221a0edfc446b92869111ac3424458e5d1c9a15c Mon Sep 17 00:00:00 2001
From: j-atkins <106238905+j-atkins@users.noreply.github.com>
Date: Wed, 30 Apr 2025 15:13:08 +0200
Subject: [PATCH 01/15] update init command to use CTD_BGC as new instrument
 when making schedule

---
 src/virtualship/expedition/instrument_type.py | 1 +
 src/virtualship/utils.py                      | 1 +
 2 files changed, 2 insertions(+)

diff --git a/src/virtualship/expedition/instrument_type.py b/src/virtualship/expedition/instrument_type.py
index 82360c7b..43ffe68d 100644
--- a/src/virtualship/expedition/instrument_type.py
+++ b/src/virtualship/expedition/instrument_type.py
@@ -7,6 +7,7 @@ class InstrumentType(Enum):
     """Types of instruments."""
 
     CTD = "CTD"
+    CTD_BGC = "CTD_BGC"
     DRIFTER = "DRIFTER"
     ARGO_FLOAT = "ARGO_FLOAT"
     XBT = "XBT"
diff --git a/src/virtualship/utils.py b/src/virtualship/utils.py
index c798a3dd..848d5d63 100644
--- a/src/virtualship/utils.py
+++ b/src/virtualship/utils.py
@@ -157,6 +157,7 @@ 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,
     }

From ff28801f877af66907862aa30ff51aea1f37b961 Mon Sep 17 00:00:00 2001
From: j-atkins <106238905+j-atkins@users.noreply.github.com>
Date: Thu, 1 May 2025 14:51:06 +0200
Subject: [PATCH 02/15] update example ship_config file to also include CTD_BGC
 instrument config

---
 src/virtualship/static/ship_config.yaml | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/src/virtualship/static/ship_config.yaml b/src/virtualship/static/ship_config.yaml
index 5066e38d..34d6c6ea 100644
--- a/src/virtualship/static/ship_config.yaml
+++ b/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

From 9464a17d6aac6e6a3a4297d3c16c7177d2f1096d Mon Sep 17 00:00:00 2001
From: Jamie Atkins <106238905+j-atkins@users.noreply.github.com>
Date: Fri, 2 May 2025 13:28:46 +0200
Subject: [PATCH 03/15] Prevent fetch from downloading unnecessary data and
 skipping data download for certain instruments (#175)

* fixes for over-extensive data downloads and skipping certain instruments

* fixes based on PR feedback #175
---
 src/virtualship/cli/_fetch.py | 16 +++++++++-------
 1 file changed, 9 insertions(+), 7 deletions(-)

diff --git a/src/virtualship/cli/_fetch.py b/src/virtualship/cli/_fetch.py
index 340edfd9..16712d38 100644
--- a/src/virtualship/cli/_fetch.py
+++ b/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.instrument_type import InstrumentType
+
     if sum([username is None, password is None]) == 1:
         raise ValueError("Both username and password must be provided when using CLI.")
 
@@ -88,10 +90,10 @@ def _fetch(path: str | Path, username: str | None, password: str | None) -> None
             {"XBT", "CTD", "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 = {
@@ -145,8 +147,8 @@ def _fetch(path: str | Path, username: str | None, password: str | None) -> None
         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",
@@ -188,8 +190,8 @@ def _fetch(path: str | Path, username: str | None, password: str | None) -> None
         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",

From 91a28d633fefa1947fe1b3d8ae3d946cd3d3a763 Mon Sep 17 00:00:00 2001
From: Vecko <36369090+VeckoTheGecko@users.noreply.github.com>
Date: Fri, 2 May 2025 15:38:29 +0200
Subject: [PATCH 04/15] Managing conflicts on branch. Move InstrumentType to
 ship_config.py

---
 src/virtualship/cli/_fetch.py                   |  2 +-
 src/virtualship/expedition/__init__.py          |  1 -
 src/virtualship/expedition/checkpoint.py        |  2 +-
 src/virtualship/expedition/instrument_type.py   | 13 -------------
 src/virtualship/expedition/schedule.py          |  2 +-
 src/virtualship/expedition/ship_config.py       | 15 +++++++++++++--
 src/virtualship/expedition/simulate_schedule.py |  3 +--
 src/virtualship/expedition/waypoint.py          | 10 ++++++----
 src/virtualship/utils.py                        |  2 +-
 tests/test_mfp_to_yaml.py                       |  2 +-
 10 files changed, 25 insertions(+), 27 deletions(-)
 delete mode 100644 src/virtualship/expedition/instrument_type.py

diff --git a/src/virtualship/cli/_fetch.py b/src/virtualship/cli/_fetch.py
index 16712d38..2e09dec2 100644
--- a/src/virtualship/cli/_fetch.py
+++ b/src/virtualship/cli/_fetch.py
@@ -38,7 +38,7 @@ 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.instrument_type import InstrumentType
+    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.")
diff --git a/src/virtualship/expedition/__init__.py b/src/virtualship/expedition/__init__.py
index 9137f7b1..831371bd 100644
--- a/src/virtualship/expedition/__init__.py
+++ b/src/virtualship/expedition/__init__.py
@@ -2,7 +2,6 @@
 
 from .do_expedition import do_expedition
 from .input_data import InputData
-from .instrument_type import InstrumentType
 from .schedule import Schedule
 from .ship_config import (
     ADCPConfig,
diff --git a/src/virtualship/expedition/checkpoint.py b/src/virtualship/expedition/checkpoint.py
index 75dd2356..be6079ef 100644
--- a/src/virtualship/expedition/checkpoint.py
+++ b/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):
diff --git a/src/virtualship/expedition/instrument_type.py b/src/virtualship/expedition/instrument_type.py
deleted file mode 100644
index 43ffe68d..00000000
--- a/src/virtualship/expedition/instrument_type.py
+++ /dev/null
@@ -1,13 +0,0 @@
-"""InstrumentType Enum."""
-
-from enum import Enum
-
-
-class InstrumentType(Enum):
-    """Types of instruments."""
-
-    CTD = "CTD"
-    CTD_BGC = "CTD_BGC"
-    DRIFTER = "DRIFTER"
-    ARGO_FLOAT = "ARGO_FLOAT"
-    XBT = "XBT"
diff --git a/src/virtualship/expedition/schedule.py b/src/virtualship/expedition/schedule.py
index 6c3bbfd1..5658f8d2 100644
--- a/src/virtualship/expedition/schedule.py
+++ b/src/virtualship/expedition/schedule.py
@@ -12,7 +12,7 @@
 from parcels import FieldSet
 
 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
 
diff --git a/src/virtualship/expedition/ship_config.py b/src/virtualship/expedition/ship_config.py
index b411443f..4f238b36 100644
--- a/src/virtualship/expedition/ship_config.py
+++ b/src/virtualship/expedition/ship_config.py
@@ -3,15 +3,26 @@
 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"
+    DRIFTER = "DRIFTER"
+    ARGO_FLOAT = "ARGO_FLOAT"
+    XBT = "XBT"
 
 
 class ArgoFloatConfig(pydantic.BaseModel):
diff --git a/src/virtualship/expedition/simulate_schedule.py b/src/virtualship/expedition/simulate_schedule.py
index fadfd2aa..db22bd71 100644
--- a/src/virtualship/expedition/simulate_schedule.py
+++ b/src/virtualship/expedition/simulate_schedule.py
@@ -13,9 +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 .ship_config import InstrumentType, ShipConfig
 from .waypoint import Waypoint
 
 
diff --git a/src/virtualship/expedition/waypoint.py b/src/virtualship/expedition/waypoint.py
index 018ccecb..9fb08a52 100644
--- a/src/virtualship/expedition/waypoint.py
+++ b/src/virtualship/expedition/waypoint.py
@@ -1,21 +1,23 @@
 """Waypoint class."""
 
+from __future__ import annotations
+
 from datetime import datetime
 
-from pydantic import BaseModel, field_serializer
+import pydantic
 
 from ..location import Location
-from .instrument_type import InstrumentType
+from .ship_config import InstrumentType
 
 
-class Waypoint(BaseModel):
+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
 
-    @field_serializer("instrument")
+    @pydantic.field_serializer("instrument")
     def serialize_instrument(self, instrument):
         """Ensure InstrumentType is serialized as a string (or list of strings)."""
         if isinstance(instrument, list):
diff --git a/src/virtualship/utils.py b/src/virtualship/utils.py
index 848d5d63..5aa85f26 100644
--- a/src/virtualship/utils.py
+++ b/src/virtualship/utils.py
@@ -139,8 +139,8 @@ 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.ship_config import InstrumentType
     from virtualship.expedition.space_time_region import (
         SpaceTimeRegion,
         SpatialRange,
diff --git a/tests/test_mfp_to_yaml.py b/tests/test_mfp_to_yaml.py
index a3175185..3ef511f5 100644
--- a/tests/test_mfp_to_yaml.py
+++ b/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
 
 

From 1ae51d3f41bded49cff2eb4bc07f0cace0fbc21e Mon Sep 17 00:00:00 2001
From: Vecko <36369090+VeckoTheGecko@users.noreply.github.com>
Date: Fri, 2 May 2025 15:48:37 +0200
Subject: [PATCH 05/15] Move Waypoint to schedule.py

---
 src/virtualship/expedition/__init__.py        |  3 +--
 src/virtualship/expedition/schedule.py        | 19 ++++++++++++--
 .../expedition/simulate_schedule.py           |  3 +--
 src/virtualship/expedition/waypoint.py        | 25 -------------------
 src/virtualship/utils.py                      |  3 +--
 tests/expedition/test_schedule.py             |  3 +--
 6 files changed, 21 insertions(+), 35 deletions(-)
 delete mode 100644 src/virtualship/expedition/waypoint.py

diff --git a/src/virtualship/expedition/__init__.py b/src/virtualship/expedition/__init__.py
index 831371bd..74403732 100644
--- a/src/virtualship/expedition/__init__.py
+++ b/src/virtualship/expedition/__init__.py
@@ -2,7 +2,7 @@
 
 from .do_expedition import do_expedition
 from .input_data import InputData
-from .schedule import Schedule
+from .schedule import Schedule, Waypoint
 from .ship_config import (
     ADCPConfig,
     ArgoFloatConfig,
@@ -12,7 +12,6 @@
     ShipUnderwaterSTConfig,
 )
 from .space_time_region import SpaceTimeRegion
-from .waypoint import Waypoint
 
 __all__ = [
     "ADCPConfig",
diff --git a/src/virtualship/expedition/schedule.py b/src/virtualship/expedition/schedule.py
index 5658f8d2..79f14758 100644
--- a/src/virtualship/expedition/schedule.py
+++ b/src/virtualship/expedition/schedule.py
@@ -3,7 +3,7 @@
 from __future__ import annotations
 
 import itertools
-from datetime import timedelta
+from datetime import datetime, timedelta
 from pathlib import Path
 
 import pydantic
@@ -11,14 +11,29 @@
 import yaml
 from parcels import FieldSet
 
+from ..location import Location
 from .input_data import InputData
 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."""
 
diff --git a/src/virtualship/expedition/simulate_schedule.py b/src/virtualship/expedition/simulate_schedule.py
index db22bd71..df36b8b2 100644
--- a/src/virtualship/expedition/simulate_schedule.py
+++ b/src/virtualship/expedition/simulate_schedule.py
@@ -13,9 +13,8 @@
 from ..instruments.xbt import XBT
 from ..location import Location
 from ..spacetime import Spacetime
-from .schedule import Schedule
+from .schedule import Schedule, Waypoint
 from .ship_config import InstrumentType, ShipConfig
-from .waypoint import Waypoint
 
 
 @dataclass
diff --git a/src/virtualship/expedition/waypoint.py b/src/virtualship/expedition/waypoint.py
deleted file mode 100644
index 9fb08a52..00000000
--- a/src/virtualship/expedition/waypoint.py
+++ /dev/null
@@ -1,25 +0,0 @@
-"""Waypoint class."""
-
-from __future__ import annotations
-
-from datetime import datetime
-
-import pydantic
-
-from ..location import Location
-from .ship_config import InstrumentType
-
-
-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
diff --git a/src/virtualship/utils.py b/src/virtualship/utils.py
index 5aa85f26..6dbbb49c 100644
--- a/src/virtualship/utils.py
+++ b/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.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)
diff --git a/tests/expedition/test_schedule.py b/tests/expedition/test_schedule.py
index 50c35d2f..eabcbd9a 100644
--- a/tests/expedition/test_schedule.py
+++ b/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")

From 3aed6850e46492e9e9293f8da827753fb332b8c0 Mon Sep 17 00:00:00 2001
From: j-atkins <106238905+j-atkins@users.noreply.github.com>
Date: Wed, 30 Apr 2025 15:13:08 +0200
Subject: [PATCH 06/15] update init command to use CTD_BGC as new instrument
 when making schedule

---
 src/virtualship/expedition/ship_config.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/virtualship/expedition/ship_config.py b/src/virtualship/expedition/ship_config.py
index 4f238b36..062b3784 100644
--- a/src/virtualship/expedition/ship_config.py
+++ b/src/virtualship/expedition/ship_config.py
@@ -20,6 +20,7 @@ class InstrumentType(Enum):
     """Types of instruments."""
 
     CTD = "CTD"
+    CTD_BGC = "CTD_BGC"
     DRIFTER = "DRIFTER"
     ARGO_FLOAT = "ARGO_FLOAT"
     XBT = "XBT"

From 938052c9aaeae148d2b0eb3d43d5193cf3cb9087 Mon Sep 17 00:00:00 2001
From: j-atkins <106238905+j-atkins@users.noreply.github.com>
Date: Fri, 9 May 2025 10:54:57 +0200
Subject: [PATCH 07/15] add configuration for CTD_BGC

---
 src/virtualship/expedition/ship_config.py | 37 +++++++++++++++++++++++
 1 file changed, 37 insertions(+)

diff --git a/src/virtualship/expedition/ship_config.py b/src/virtualship/expedition/ship_config.py
index 062b3784..c22b673e 100644
--- a/src/virtualship/expedition/ship_config.py
+++ b/src/virtualship/expedition/ship_config.py
@@ -81,6 +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."""
 
@@ -160,6 +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.
@@ -240,6 +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
@@ -249,6 +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)
@@ -267,6 +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
             ):

From 21ad1c68b1426343bfcb7ae824d94b887bdba9b2 Mon Sep 17 00:00:00 2001
From: j-atkins <106238905+j-atkins@users.noreply.github.com>
Date: Fri, 9 May 2025 11:09:45 +0200
Subject: [PATCH 08/15] add bgc data download option for CTD_BGC instrument

---
 src/virtualship/cli/_fetch.py | 44 +++++++++++++++++++++++++++++++++++
 1 file changed, 44 insertions(+)

diff --git a/src/virtualship/cli/_fetch.py b/src/virtualship/cli/_fetch.py
index 2e09dec2..386e6623 100644
--- a/src/virtualship/cli/_fetch.py
+++ b/src/virtualship/cli/_fetch.py
@@ -238,6 +238,50 @@ def _fetch(path: str | Path, username: str | None, password: str | None) -> None
         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
+
+        complete_download(download_folder)
+        click.echo("CTD_BGC data download based on space-time region completed.")
+
 
 def _hash(s: str, *, length: int) -> str:
     """Create a hash of a string."""

From 956e395412541abd0796fb31220279d64aae7a9a Mon Sep 17 00:00:00 2001
From: j-atkins <106238905+j-atkins@users.noreply.github.com>
Date: Fri, 9 May 2025 16:47:44 +0200
Subject: [PATCH 09/15] add CTD_BGC to instruments which prompts ship data
 download

---
 src/virtualship/cli/_fetch.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/virtualship/cli/_fetch.py b/src/virtualship/cli/_fetch.py
index 386e6623..b1cfde2a 100644
--- a/src/virtualship/cli/_fetch.py
+++ b/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

From b2b7858a3ddd738baf3fe98d52f963f114160efe Mon Sep 17 00:00:00 2001
From: Vecko <36369090+VeckoTheGecko@users.noreply.github.com>
Date: Thu, 15 May 2025 10:33:04 +0200
Subject: [PATCH 10/15] Review feedback on complete_download

---
 src/virtualship/cli/_fetch.py | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/src/virtualship/cli/_fetch.py b/src/virtualship/cli/_fetch.py
index b1cfde2a..f07c5b92 100644
--- a/src/virtualship/cli/_fetch.py
+++ b/src/virtualship/cli/_fetch.py
@@ -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:
@@ -235,7 +233,6 @@ def _fetch(path: str | Path, username: str | None, password: str | None) -> None
             shutil.rmtree(download_folder)
             raise e
 
-        complete_download(download_folder)
         click.echo("Argo_float data download based on space-time region completed.")
 
     if InstrumentType.CTD_BGC in instruments_in_schedule:
@@ -279,9 +276,10 @@ def _fetch(path: str | Path, username: str | None, password: str | None) -> None
             shutil.rmtree(download_folder)
             raise e
 
-        complete_download(download_folder)
         click.echo("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."""

From fda781979c84539936645a87b7bf2e8174562005 Mon Sep 17 00:00:00 2001
From: j-atkins <106238905+j-atkins@users.noreply.github.com>
Date: Mon, 12 May 2025 15:47:14 +0200
Subject: [PATCH 11/15] bgc input data .nc files for testing

---
 .../expedition_dir/input_data/ctd_bgc_chloro.nc | Bin 0 -> 23313 bytes
 .../expedition_dir/input_data/ctd_bgc_o2.nc     | Bin 0 -> 23323 bytes
 2 files changed, 0 insertions(+), 0 deletions(-)
 create mode 100644 tests/expedition/expedition_dir/input_data/ctd_bgc_chloro.nc
 create mode 100644 tests/expedition/expedition_dir/input_data/ctd_bgc_o2.nc

diff --git a/tests/expedition/expedition_dir/input_data/ctd_bgc_chloro.nc b/tests/expedition/expedition_dir/input_data/ctd_bgc_chloro.nc
new file mode 100644
index 0000000000000000000000000000000000000000..efdc51d381ee74b0fefbdac6c097852fd71e55c3
GIT binary patch
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diff --git a/tests/expedition/expedition_dir/input_data/ctd_bgc_o2.nc b/tests/expedition/expedition_dir/input_data/ctd_bgc_o2.nc
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literal 0
HcmV?d00001


From bd31d15441ce6863fe7cae54694385cf6df2d7e9 Mon Sep 17 00:00:00 2001
From: j-atkins <106238905+j-atkins@users.noreply.github.com>
Date: Mon, 12 May 2025 15:54:03 +0200
Subject: [PATCH 12/15] add CTD_BGC to static/example schedule (also necessary
 for ship_config test)

---
 src/virtualship/static/schedule.yaml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/virtualship/static/schedule.yaml b/src/virtualship/static/schedule.yaml
index d15736d0..7cb39423 100644
--- a/src/virtualship/static/schedule.yaml
+++ b/src/virtualship/static/schedule.yaml
@@ -12,6 +12,7 @@ space_time_region:
 waypoints:
   - instrument:
       - CTD
+      - CTD_BGC
     location:
       latitude: 0
       longitude: 0

From 2449163b438f446107fef33957c3e18721613c27 Mon Sep 17 00:00:00 2001
From: j-atkins <106238905+j-atkins@users.noreply.github.com>
Date: Tue, 13 May 2025 09:48:42 +0200
Subject: [PATCH 13/15] update test suite for new bgc sampling using ctd_bgc

---
 .../expedition_dir/ship_config.yaml           |   4 +
 tests/expedition/test_ship_config.py          |  12 ++
 tests/expedition/test_simulate_schedule.py    |   1 +
 tests/instruments/test_ctd_bgc.py             | 137 ++++++++++++++++++
 4 files changed, 154 insertions(+)
 create mode 100644 tests/instruments/test_ctd_bgc.py

diff --git a/tests/expedition/expedition_dir/ship_config.yaml b/tests/expedition/expedition_dir/ship_config.yaml
index 09f40c0a..1bae9d1d 100644
--- a/tests/expedition/expedition_dir/ship_config.yaml
+++ b/tests/expedition/expedition_dir/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: 40320.0
diff --git a/tests/expedition/test_ship_config.py b/tests/expedition/test_ship_config.py
index 44bfd524..920058d2 100644
--- a/tests/expedition/test_ship_config.py
+++ b/tests/expedition/test_ship_config.py
@@ -50,6 +50,12 @@ def ship_config_no_ctd(ship_config):
     return ship_config
 
 
+@pytest.fixture
+def ship_config_no_ctd_bgc(ship_config):
+    delattr(ship_config, "ctd_bgc_config")
+    return ship_config
+
+
 @pytest.fixture
 def ship_config_no_argo_float(ship_config):
     delattr(ship_config, "argo_float_config")
@@ -91,6 +97,12 @@ def test_verify_ship_config_no_instrument(ship_config, schedule_no_xbt) -> None:
             "Planning has a waypoint with CTD instrument, but configuration does not configure CTD.",
             id="ShipConfigNoCTD",
         ),
+        pytest.param(
+            "ship_config_no_ctd_bgc",
+            ConfigError,
+            "Planning has a waypoint with CTD_BGC instrument, but configuration does not configure CTD_BGCs.",
+            id="ShipConfigNoCTD_BGC",
+        ),
         pytest.param(
             "ship_config_no_argo_float",
             ConfigError,
diff --git a/tests/expedition/test_simulate_schedule.py b/tests/expedition/test_simulate_schedule.py
index 6381b805..8c42097b 100644
--- a/tests/expedition/test_simulate_schedule.py
+++ b/tests/expedition/test_simulate_schedule.py
@@ -53,4 +53,5 @@ def test_time_in_minutes_in_ship_schedule() -> None:
     ship_config = ShipConfig.from_yaml("expedition_dir/ship_config.yaml")
     assert ship_config.adcp_config.period == timedelta(minutes=5)
     assert ship_config.ctd_config.stationkeeping_time == timedelta(minutes=20)
+    assert ship_config.ctd_bgc_config.stationkeeping_time == timedelta(minutes=20)
     assert ship_config.ship_underwater_st_config.period == timedelta(minutes=5)
diff --git a/tests/instruments/test_ctd_bgc.py b/tests/instruments/test_ctd_bgc.py
new file mode 100644
index 00000000..8083c580
--- /dev/null
+++ b/tests/instruments/test_ctd_bgc.py
@@ -0,0 +1,137 @@
+"""
+Test the simulation of CTD_BGC instruments.
+
+Fields are kept static over time and time component of CTD_BGC measurements is not tested because it's tricky to provide expected measurements.
+"""
+
+import datetime
+from datetime import timedelta
+
+import numpy as np
+import xarray as xr
+from parcels import Field, FieldSet
+
+from virtualship import Location, Spacetime
+from virtualship.instruments.ctd_bgc import CTD_BGC, simulate_ctd_bgc
+
+
+def test_simulate_ctd_bgcs(tmpdir) -> None:
+    # arbitrary time offset for the dummy fieldset
+    base_time = datetime.datetime.strptime("1950-01-01", "%Y-%m-%d")
+
+    # where to cast CTD_BGCs
+    ctd_bgcs = [
+        CTD_BGC(
+            spacetime=Spacetime(
+                location=Location(latitude=0, longitude=1),
+                time=base_time + datetime.timedelta(hours=0),
+            ),
+            min_depth=0,
+            max_depth=float("-inf"),
+        ),
+        CTD_BGC(
+            spacetime=Spacetime(
+                location=Location(latitude=1, longitude=0),
+                time=base_time,
+            ),
+            min_depth=0,
+            max_depth=float("-inf"),
+        ),
+    ]
+
+    # expected observations for ctd_bgcs at surface and at maximum depth
+    ctd_bgc_exp = [
+        {
+            "surface": {
+                "o2": 9,
+                "chl": 10,
+                "lat": ctd_bgcs[0].spacetime.location.lat,
+                "lon": ctd_bgcs[0].spacetime.location.lon,
+            },
+            "maxdepth": {
+                "o2": 11,
+                "chl": 12,
+                "lat": ctd_bgcs[0].spacetime.location.lat,
+                "lon": ctd_bgcs[0].spacetime.location.lon,
+            },
+        },
+        {
+            "surface": {
+                "o2": 9,
+                "chl": 10,
+                "lat": ctd_bgcs[1].spacetime.location.lat,
+                "lon": ctd_bgcs[1].spacetime.location.lon,
+            },
+            "maxdepth": {
+                "o2": 11,
+                "chl": 12,
+                "lat": ctd_bgcs[1].spacetime.location.lat,
+                "lon": ctd_bgcs[1].spacetime.location.lon,
+            },
+        },
+    ]
+
+    # create fieldset based on the expected observations
+    # indices are time, depth, latitude, longitude
+    u = np.zeros((2, 2, 2, 2))
+    v = np.zeros((2, 2, 2, 2))
+    o2 = np.zeros((2, 2, 2, 2))  # o2 field
+    chl = np.zeros((2, 2, 2, 2))  # chl field
+
+    o2[:, 1, 0, 1] = ctd_bgc_exp[0]["surface"]["o2"]
+    o2[:, 0, 0, 1] = ctd_bgc_exp[0]["maxdepth"]["o2"]
+    o2[:, 1, 1, 0] = ctd_bgc_exp[1]["surface"]["o2"]
+    o2[:, 0, 1, 0] = ctd_bgc_exp[1]["maxdepth"]["o2"]
+
+    chl[:, 1, 0, 1] = ctd_bgc_exp[0]["surface"]["chl"]
+    chl[:, 0, 0, 1] = ctd_bgc_exp[0]["maxdepth"]["chl"]
+    chl[:, 1, 1, 0] = ctd_bgc_exp[1]["surface"]["chl"]
+    chl[:, 0, 1, 0] = ctd_bgc_exp[1]["maxdepth"]["chl"]
+
+    fieldset = FieldSet.from_data(
+        {"V": v, "U": u, "o2": o2, "chl": chl},
+        {
+            "time": [
+                np.datetime64(base_time + datetime.timedelta(hours=0)),
+                np.datetime64(base_time + datetime.timedelta(hours=1)),
+            ],
+            "depth": [-1000, 0],
+            "lat": [0, 1],
+            "lon": [0, 1],
+        },
+    )
+    fieldset.add_field(Field("bathymetry", [-1000], lon=0, lat=0))
+
+    # perform simulation
+    out_path = tmpdir.join("out.zarr")
+
+    simulate_ctd_bgc(
+        ctd_bgcs=ctd_bgcs,
+        fieldset=fieldset,
+        out_path=out_path,
+        outputdt=timedelta(seconds=10),
+    )
+
+    # test if output is as expected
+    results = xr.open_zarr(out_path)
+
+    assert len(results.trajectory) == len(ctd_bgcs)
+
+    for ctd_i, (traj, exp_bothloc) in enumerate(
+        zip(results.trajectory, ctd_bgc_exp, strict=True)
+    ):
+        obs_surface = results.sel(trajectory=traj, obs=0)
+        min_index = np.argmin(results.sel(trajectory=traj)["z"].data)
+        obs_maxdepth = results.sel(trajectory=traj, obs=min_index)
+
+        for obs, loc in [
+            (obs_surface, "surface"),
+            (obs_maxdepth, "maxdepth"),
+        ]:
+            exp = exp_bothloc[loc]
+            for var in ["o2", "chl", "lat", "lon"]:
+                obs_value = obs[var].values.item()
+                exp_value = exp[var]
+                assert np.isclose(obs_value, exp_value), (
+                    f"Observation incorrect {ctd_i=} {loc=} {var=} {obs_value=} {exp_value=}."
+                )

From d73401180660b7dd542113c9354547bda09b9cce Mon Sep 17 00:00:00 2001
From: j-atkins <106238905+j-atkins@users.noreply.github.com>
Date: Tue, 13 May 2025 09:53:01 +0200
Subject: [PATCH 14/15] new ctd_bgc instrument

---
 src/virtualship/instruments/ctd_bgc.py | 143 +++++++++++++++++++++++++
 1 file changed, 143 insertions(+)
 create mode 100644 src/virtualship/instruments/ctd_bgc.py

diff --git a/src/virtualship/instruments/ctd_bgc.py b/src/virtualship/instruments/ctd_bgc.py
new file mode 100644
index 00000000..cb218e3a
--- /dev/null
+++ b/src/virtualship/instruments/ctd_bgc.py
@@ -0,0 +1,143 @@
+"""CTD_BGC instrument."""
+
+from dataclasses import dataclass
+from datetime import timedelta
+from pathlib import Path
+
+import numpy as np
+from parcels import FieldSet, JITParticle, ParticleSet, Variable
+
+from ..spacetime import Spacetime
+
+
+@dataclass
+class CTD_BGC:
+    """Configuration for a single BGC CTD."""
+
+    spacetime: Spacetime
+    min_depth: float
+    max_depth: float
+
+
+_CTD_BGCParticle = JITParticle.add_variables(
+    [
+        Variable("o2", dtype=np.float32, initial=np.nan),
+        Variable("chl", dtype=np.float32, initial=np.nan),
+        Variable("raising", dtype=np.int8, initial=0.0),  # bool. 0 is False, 1 is True.
+        Variable("max_depth", dtype=np.float32),
+        Variable("min_depth", dtype=np.float32),
+        Variable("winch_speed", dtype=np.float32),
+    ]
+)
+
+
+def _sample_o2(particle, fieldset, time):
+    particle.o2 = fieldset.o2[time, particle.depth, particle.lat, particle.lon]
+
+
+def _sample_chlorophyll(particle, fieldset, time):
+    particle.chl = fieldset.chl[time, particle.depth, particle.lat, particle.lon]
+
+
+def _ctd_bgc_cast(particle, fieldset, time):
+    # lowering
+    if particle.raising == 0:
+        particle_ddepth = -particle.winch_speed * particle.dt
+        if particle.depth + particle_ddepth < particle.max_depth:
+            particle.raising = 1
+            particle_ddepth = -particle_ddepth
+    # raising
+    else:
+        particle_ddepth = particle.winch_speed * particle.dt
+        if particle.depth + particle_ddepth > particle.min_depth:
+            particle.delete()
+
+
+def simulate_ctd_bgc(
+    fieldset: FieldSet,
+    out_path: str | Path,
+    ctd_bgcs: list[CTD_BGC],
+    outputdt: timedelta,
+) -> None:
+    """
+    Use Parcels to simulate a set of BGC CTDs in a fieldset.
+
+    :param fieldset: The fieldset to simulate the BGC CTDs in.
+    :param out_path: The path to write the results to.
+    :param ctds: A list of BGC CTDs to simulate.
+    :param outputdt: Interval which dictates the update frequency of file output during simulation
+    :raises ValueError: Whenever provided BGC CTDs, fieldset, are not compatible with this function.
+    """
+    WINCH_SPEED = 1.0  # sink and rise speed in m/s
+    DT = 10.0  # dt of CTD simulation integrator
+
+    if len(ctd_bgcs) == 0:
+        print(
+            "No BGC CTDs provided. Parcels currently crashes when providing an empty particle set, so no BGC CTD simulation will be done and no files will be created."
+        )
+        # TODO when Parcels supports it this check can be removed.
+        return
+
+    fieldset_starttime = fieldset.time_origin.fulltime(fieldset.U.grid.time_full[0])
+    fieldset_endtime = fieldset.time_origin.fulltime(fieldset.U.grid.time_full[-1])
+
+    # deploy time for all ctds should be later than fieldset start time
+    if not all(
+        [
+            np.datetime64(ctd_bgc.spacetime.time) >= fieldset_starttime
+            for ctd_bgc in ctd_bgcs
+        ]
+    ):
+        raise ValueError("BGC CTD deployed before fieldset starts.")
+
+    # depth the bgc ctd will go to. shallowest between bgc ctd max depth and bathymetry.
+    max_depths = [
+        max(
+            ctd_bgc.max_depth,
+            fieldset.bathymetry.eval(
+                z=0,
+                y=ctd_bgc.spacetime.location.lat,
+                x=ctd_bgc.spacetime.location.lon,
+                time=0,
+            ),
+        )
+        for ctd_bgc in ctd_bgcs
+    ]
+
+    # CTD depth can not be too shallow, because kernel would break.
+    # This shallow is not useful anyway, no need to support.
+    if not all([max_depth <= -DT * WINCH_SPEED for max_depth in max_depths]):
+        raise ValueError(
+            f"BGC CTD max_depth or bathymetry shallower than maximum {-DT * WINCH_SPEED}"
+        )
+
+    # define parcel particles
+    ctd_bgc_particleset = ParticleSet(
+        fieldset=fieldset,
+        pclass=_CTD_BGCParticle,
+        lon=[ctd_bgc.spacetime.location.lon for ctd_bgc in ctd_bgcs],
+        lat=[ctd_bgc.spacetime.location.lat for ctd_bgc in ctd_bgcs],
+        depth=[ctd_bgc.min_depth for ctd_bgc in ctd_bgcs],
+        time=[ctd_bgc.spacetime.time for ctd_bgc in ctd_bgcs],
+        max_depth=max_depths,
+        min_depth=[ctd_bgc.min_depth for ctd_bgc in ctd_bgcs],
+        winch_speed=[WINCH_SPEED for _ in ctd_bgcs],
+    )
+
+    # define output file for the simulation
+    out_file = ctd_bgc_particleset.ParticleFile(name=out_path, outputdt=outputdt)
+
+    # execute simulation
+    ctd_bgc_particleset.execute(
+        [_sample_o2, _sample_chlorophyll, _ctd_bgc_cast],
+        endtime=fieldset_endtime,
+        dt=DT,
+        verbose_progress=False,
+        output_file=out_file,
+    )
+
+    # there should be no particles left, as they delete themselves when they resurface
+    if len(ctd_bgc_particleset.particledata) != 0:
+        raise ValueError(
+            "Simulation ended before BGC CTD resurfaced. This most likely means the field time dimension did not match the simulation time span."
+        )

From 09e9d872cfa11706787f95984a617d967dcec25c Mon Sep 17 00:00:00 2001
From: j-atkins <106238905+j-atkins@users.noreply.github.com>
Date: Tue, 13 May 2025 09:59:33 +0200
Subject: [PATCH 15/15] add ctd_bgc sampling capability to virtualship run
 execution

---
 src/virtualship/expedition/__init__.py        |  2 +
 src/virtualship/expedition/do_expedition.py   |  1 +
 src/virtualship/expedition/input_data.py      | 50 +++++++++++++++++++
 .../expedition/simulate_measurements.py       | 14 ++++++
 .../expedition/simulate_schedule.py           | 12 +++++
 5 files changed, 79 insertions(+)

diff --git a/src/virtualship/expedition/__init__.py b/src/virtualship/expedition/__init__.py
index 74403732..65b7cf11 100644
--- a/src/virtualship/expedition/__init__.py
+++ b/src/virtualship/expedition/__init__.py
@@ -6,6 +6,7 @@
 from .ship_config import (
     ADCPConfig,
     ArgoFloatConfig,
+    CTD_BGCConfig,
     CTDConfig,
     DrifterConfig,
     ShipConfig,
@@ -17,6 +18,7 @@
     "ADCPConfig",
     "ArgoFloatConfig",
     "CTDConfig",
+    "CTD_BGCConfig",
     "DrifterConfig",
     "InputData",
     "InstrumentType",
diff --git a/src/virtualship/expedition/do_expedition.py b/src/virtualship/expedition/do_expedition.py
index 97a66f7f..a4243361 100644
--- a/src/virtualship/expedition/do_expedition.py
+++ b/src/virtualship/expedition/do_expedition.py
@@ -136,6 +136,7 @@ def _load_input_data(
         load_adcp=ship_config.adcp_config is not None,
         load_argo_float=ship_config.argo_float_config is not None,
         load_ctd=ship_config.ctd_config is not None,
+        load_ctd_bgc=ship_config.ctd_bgc_config is not None,
         load_drifter=ship_config.drifter_config is not None,
         load_xbt=ship_config.xbt_config is not None,
         load_ship_underwater_st=ship_config.ship_underwater_st_config is not None,
diff --git a/src/virtualship/expedition/input_data.py b/src/virtualship/expedition/input_data.py
index 554efb78..ca99f7e8 100644
--- a/src/virtualship/expedition/input_data.py
+++ b/src/virtualship/expedition/input_data.py
@@ -15,6 +15,7 @@ class InputData:
     adcp_fieldset: FieldSet | None
     argo_float_fieldset: FieldSet | None
     ctd_fieldset: FieldSet | None
+    ctd_bgc_fieldset: FieldSet | None
     drifter_fieldset: FieldSet | None
     xbt_fieldset: FieldSet | None
     ship_underwater_st_fieldset: FieldSet | None
@@ -26,6 +27,7 @@ def load(
         load_adcp: bool,
         load_argo_float: bool,
         load_ctd: bool,
+        load_ctd_bgc: bool,
         load_drifter: bool,
         load_xbt: bool,
         load_ship_underwater_st: bool,
@@ -39,6 +41,7 @@ def load(
         :param load_adcp: Whether to load the ADCP fieldset.
         :param load_argo_float: Whether to load the argo float fieldset.
         :param load_ctd: Whether to load the CTD fieldset.
+        :param load_ctd_bgc: Whether to load the CTD BGC fieldset.
         :param load_drifter: Whether to load the drifter fieldset.
         :param load_ship_underwater_st: Whether to load the ship underwater ST fieldset.
         :returns: An instance of this class with loaded fieldsets.
@@ -51,6 +54,10 @@ def load(
             argo_float_fieldset = cls._load_argo_float_fieldset(directory)
         else:
             argo_float_fieldset = None
+        if load_ctd_bgc:
+            ctd_bgc_fieldset = cls._load_ctd_bgc_fieldset(directory)
+        else:
+            ctd_bgc_fieldset = None
         if load_adcp or load_ctd or load_ship_underwater_st or load_xbt:
             ship_fieldset = cls._load_ship_fieldset(directory)
         if load_adcp:
@@ -74,6 +81,7 @@ def load(
             adcp_fieldset=adcp_fieldset,
             argo_float_fieldset=argo_float_fieldset,
             ctd_fieldset=ctd_fieldset,
+            ctd_bgc_fieldset=ctd_bgc_fieldset,
             drifter_fieldset=drifter_fieldset,
             xbt_fieldset=xbt_fieldset,
             ship_underwater_st_fieldset=ship_underwater_st_fieldset,
@@ -122,6 +130,48 @@ def _load_ship_fieldset(cls, directory: Path) -> FieldSet:
 
         return fieldset
 
+    @classmethod
+    def _load_ctd_bgc_fieldset(cls, directory: Path) -> FieldSet:
+        filenames = {
+            "U": directory.joinpath("ship_uv.nc"),
+            "V": directory.joinpath("ship_uv.nc"),
+            "o2": directory.joinpath("ctd_bgc_o2.nc"),
+            "chl": directory.joinpath("ctd_bgc_chloro.nc"),
+        }
+        variables = {"U": "uo", "V": "vo", "o2": "o2", "chl": "chl"}
+        dimensions = {
+            "lon": "longitude",
+            "lat": "latitude",
+            "time": "time",
+            "depth": "depth",
+        }
+
+        fieldset = FieldSet.from_netcdf(
+            filenames, variables, dimensions, allow_time_extrapolation=True
+        )
+        fieldset.o2.interp_method = "linear_invdist_land_tracer"
+        fieldset.chl.interp_method = "linear_invdist_land_tracer"
+
+        # make depth negative
+        for g in fieldset.gridset.grids:
+            g.negate_depth()
+
+        # add bathymetry data
+        bathymetry_file = directory.joinpath("bathymetry.nc")
+        bathymetry_variables = ("bathymetry", "deptho")
+        bathymetry_dimensions = {"lon": "longitude", "lat": "latitude"}
+        bathymetry_field = Field.from_netcdf(
+            bathymetry_file, bathymetry_variables, bathymetry_dimensions
+        )
+        # make depth negative
+        bathymetry_field.data = -bathymetry_field.data
+        fieldset.add_field(bathymetry_field)
+
+        # read in data already
+        fieldset.computeTimeChunk(0, 1)
+
+        return fieldset
+
     @classmethod
     def _load_drifter_fieldset(cls, directory: Path) -> FieldSet:
         filenames = {
diff --git a/src/virtualship/expedition/simulate_measurements.py b/src/virtualship/expedition/simulate_measurements.py
index bf28c989..c7cd8746 100644
--- a/src/virtualship/expedition/simulate_measurements.py
+++ b/src/virtualship/expedition/simulate_measurements.py
@@ -6,6 +6,7 @@
 from ..instruments.adcp import simulate_adcp
 from ..instruments.argo_float import simulate_argo_floats
 from ..instruments.ctd import simulate_ctd
+from ..instruments.ctd_bgc import simulate_ctd_bgc
 from ..instruments.drifter import simulate_drifters
 from ..instruments.ship_underwater_st import simulate_ship_underwater_st
 from ..instruments.xbt import simulate_xbt
@@ -75,6 +76,19 @@ def simulate_measurements(
             outputdt=timedelta(seconds=10),
         )
 
+    if len(measurements.ctd_bgcs) > 0:
+        print("Simulating BGC CTD casts.")
+        if ship_config.ctd_bgc_config is None:
+            raise RuntimeError("No configuration for CTD_BGC provided.")
+        if input_data.ctd_bgc_fieldset is None:
+            raise RuntimeError("No fieldset for CTD_BGC provided.")
+        simulate_ctd_bgc(
+            out_path=expedition_dir.joinpath("results", "ctd_bgc.zarr"),
+            fieldset=input_data.ctd_bgc_fieldset,
+            ctd_bgcs=measurements.ctd_bgcs,
+            outputdt=timedelta(seconds=10),
+        )
+
     if len(measurements.drifters) > 0:
         print("Simulating drifters")
         if ship_config.drifter_config is None:
diff --git a/src/virtualship/expedition/simulate_schedule.py b/src/virtualship/expedition/simulate_schedule.py
index df36b8b2..596d16a2 100644
--- a/src/virtualship/expedition/simulate_schedule.py
+++ b/src/virtualship/expedition/simulate_schedule.py
@@ -9,6 +9,7 @@
 
 from ..instruments.argo_float import ArgoFloat
 from ..instruments.ctd import CTD
+from ..instruments.ctd_bgc import CTD_BGC
 from ..instruments.drifter import Drifter
 from ..instruments.xbt import XBT
 from ..location import Location
@@ -42,6 +43,7 @@ class MeasurementsToSimulate:
     argo_floats: list[ArgoFloat] = field(default_factory=list, init=False)
     drifters: list[Drifter] = field(default_factory=list, init=False)
     ctds: list[CTD] = field(default_factory=list, init=False)
+    ctd_bgcs: list[CTD_BGC] = field(default_factory=list, init=False)
     xbts: list[XBT] = field(default_factory=list, init=False)
 
 
@@ -102,6 +104,7 @@ def simulate(self) -> ScheduleOk | ScheduleProblem:
             # check if waypoint was reached in time
             if waypoint.time is not None and self._time > waypoint.time:
                 print(
+                    # TODO: I think this should be wp_i + 1, not wp_i; otherwise it will be off by one
                     f"Waypoint {wp_i} could not be reached in time. Current time: {self._time}. Waypoint time: {waypoint.time}."
                 )
                 return ScheduleProblem(self._time, wp_i)
@@ -251,6 +254,15 @@ def _make_measurements(self, waypoint: Waypoint) -> timedelta:
                     )
                 )
                 time_costs.append(self._ship_config.ctd_config.stationkeeping_time)
+            elif instrument is InstrumentType.CTD_BGC:
+                self._measurements_to_simulate.ctd_bgcs.append(
+                    CTD_BGC(
+                        spacetime=Spacetime(self._location, self._time),
+                        min_depth=self._ship_config.ctd_bgc_config.min_depth_meter,
+                        max_depth=self._ship_config.ctd_bgc_config.max_depth_meter,
+                    )
+                )
+                time_costs.append(self._ship_config.ctd_bgc_config.stationkeeping_time)
             elif instrument is InstrumentType.DRIFTER:
                 self._measurements_to_simulate.drifters.append(
                     Drifter(