Parcels-code · j-atkins · May 4, 2026 · May 4, 2026 · May 4, 2026 · May 4, 2026
diff --git a/docs/user-guide/assignments/Research_Proposal_only.ipynb b/docs/user-guide/assignments/Research_Proposal_only.ipynb
@@ -176,7 +176,7 @@
     "\n",
     "Please provide a scheme with number of necessary work and in-transit days within the working areas and station times. This can be downloaded from [the NIOZ MFP website](https://nioz.marinefacilitiesplanning.com/cruiselocationplanning#) using the Export button on the right.\n",
     "\n",
-    "Please indicate at each station what instruments you want to deploy (CTD, Argo float, drifter, XBT) and take the deployment time into account. If you plan to use Argo floats, please give the required depth and cycle duration. In case of the CTD the deployment time depends on the depth of the ocean. \n",
+    "Please indicate at each station what instruments you want to deploy (CTD, Argo float, drifter, XBT) and take the deployment time into account. If you plan to use Argo floats, please give the required depth and cycle duration.\n",
     "\n",
     "Here is some sample code to sample the depth using the bathymetry data that the Virtual Ship will also use. "
    ]

diff --git a/docs/user-guide/assignments/Research_proposal_intro.ipynb b/docs/user-guide/assignments/Research_proposal_intro.ipynb
@@ -97,11 +97,6 @@
     "\n",
     "In total, therefore, you can expect a CTD deployment to take approximately 50 minutes.\n",
     "\n",
-    "<!-- TODO: this note can be removed when CTD and CTD_BGC are combined to one instrument -->\n",
-    "<div class=\"alert alert-block alert-info\"> \n",
-    "**Note**: If you are deploying CTDs in both standard and biogeochemical configurations (`CTD` and `CTD_BGC`) in your [VirtualShip expeditions](./Sail_the_ship.ipynb), you only need to factor in the 50 minutes **once** per waypoint, as both can be deployed on the same cast.\n",
-    "</div>\n",
-    "\n",
     "<iframe width=\"560\" height=\"315\" src=\"https://www.youtube.com/embed/7N2UsPDczTw\" title=\"YouTube video player\" frameborder=\"0\" allow=\"accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture\" allowfullscreen></iframe>"
    ]
   },

diff --git a/docs/user-guide/assignments/Sail_the_ship.ipynb b/docs/user-guide/assignments/Sail_the_ship.ipynb
@@ -212,10 +212,6 @@
     "\n",
     "<div class=\"alert alert-block alert-info\"> \n",
     "**Note**: On pressing _Save Changes_ the tool will check the selections are valid (for example that the ship will be able to reach each waypoint in time). If they are, the changes will be saved to the `expedition.yaml` file, ready for the next steps. If your selections are invalid you should be provided with information on how to fix them.\n",
-    "</div>\n",
-    "\n",
-    "<div class=\"alert alert-block alert-warning\"> \n",
-    "**Caution**: The `virtualship plan` tool will check that the ship can reach each waypoint according to the prescribed ship speed (10 knots). However, before the ultimate simulation step (i.e. step 6 below) there will be a final, automated check that the schedule also accounts for the time taken to conduct the measurements at each site (e.g. a CTD cast in deeper waters will take longer). Therefore, we recommend to take this extra time into account at this stage of the planning by estimating how long each measurement will take and adding this time on.\n",
     "</div>"
    ]
   },

diff --git a/docs/user-guide/assignments/Virtualship_research_proposal.ipynb b/docs/user-guide/assignments/Virtualship_research_proposal.ipynb
@@ -132,7 +132,7 @@
    "source": [
     "7. **Scientific work program**\n",
     "\n",
-    "Please upload a screenshot of the MFP website inlcuding port of departure and arrival, all stations (and transects) and total time. Please indicate at each station what instruments you want to deploy (CTD, Argo float, drifter, XBT) and take the deployment time into account. If you plan to use Argo floats, please give the required depth and cycle duration. In case of the CTD the deployment time depends on the depth of the ocean. Note that transit times from the port of departure to the first station and from the last station in the working area to the port of arrival are regarded as work days at sea, so they are deducted from your (three-week) availability. "
+    "Please upload a screenshot of the MFP website inlcuding port of departure and arrival, all stations (and transects) and total time. Please indicate at each station what instruments you want to deploy (CTD, Argo float, drifter, XBT) and take the deployment time into account. If you plan to use Argo floats, please give the required depth and cycle duration. Note that transit times from the port of departure to the first station and from the last station in the working area to the port of arrival are regarded as work days at sea, so they are deducted from your (three-week) availability. "
    ]
   },
   {

diff --git a/docs/user-guide/quickstart.md b/docs/user-guide/quickstart.md
@@ -124,10 +124,6 @@ When you are happy with your ship configuration and schedule plan, press _Save C
 On pressing _Save Changes_ the tool will check the selections are valid (for example that the ship will be able to reach each waypoint in time). If they are, the changes will be saved to the `expedition.yaml` file, ready for the next steps. If your selections are invalid you should be provided with information on how to fix them.
 ```
 
-```{caution}
-The `virtualship plan` tool will check that the ship can reach each waypoint according to the prescribed ship speed. However, before the ultimate [simulation step](#run-the-expedition) there will be a final, automated check that the schedule also accounts for the time taken to conduct the measurements at each site (e.g. a CTD cast in deeper waters will take longer). Therefore, we recommend to take this extra time into account at this stage of the planning by estimating how long each measurement will take and adding this time on.
-```
-
 ## 4) Run the expedition
 
 You are now ready to run your virtual expedition! This stage will simulate the measurements taken by the instruments you selected at each waypoint in your expedition schedule, using input data sourced from the [Copernicus Marine Data Store](https://data.marine.copernicus.eu/products).

diff --git a/docs/user-guide/tutorials/CTD_transects.ipynb b/docs/user-guide/tutorials/CTD_transects.ipynb
@@ -9,7 +9,7 @@
     "\n",
     "This notebook demonstrates a simple plotting exercise for CTD data across a transect, using the output of a VirtualShip expedition. There are example plots embedded at the end, but these will ultimately be replaced by your own versions as you work through the notebook.\n",
     "\n",
-    "We can plot physical (temperature, salinity) or biogeochemical data (oxygen, chlorophyll, primary production, phytoplankton, nutrients, pH) as measured by the VirtualShip `CTD` and `CTD_BGC` instruments, respectively.\n",
+    "We can plot physical (temperature, salinity) or biogeochemical data (oxygen, chlorophyll, primary production, phytoplankton, nutrients, pH) as measured by the VirtualShip `CTD` instrument.\n",
     "\n",
     "The plot(s) we will produce are simple plots which follow the trajectory of the expedition as a function of distance from the first waypoint, and are intended to be a starting point for your analysis. \n",
     "\n",
@@ -82,13 +82,11 @@
    "source": [
     "#### Variable choice\n",
     "\n",
-    "You should now consider which variable from your CTD casts you would like to plot. Which ones are available to you will depend on whether you have used the `CTD` (physical variables) or `CTD_BGC` (biogeochemical) instrument, or both. Below is a list of all valid variable choices for both instruments...\n",
+    "You should now consider which variable from your CTD casts you would like to plot. Which ones are available to you will depend on which sensors you deployed the `CTD` instrument with (via the `virtualship plan` tool and/or your `expedition.yaml` file). Below is the full list of valid variable choices...\n",
     "\n",
-    "`CTD` (physical):\n",
+    "`CTD`:\n",
     "- \"temperature\"\n",
     "- \"salinity\"\n",
-    "\n",
-    "`CTD_BGC` (biogeochemical):\n",
     "- \"oxygen\"\n",
     "- \"nitrate\"\n",
     "- \"phosphate\"\n",
@@ -191,15 +189,13 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 76,
+   "execution_count": null,
    "id": "13f4664b",
    "metadata": {},
    "outputs": [],
    "source": [
     "# load CTD data\n",
-    "filename = (\n",
-    "    \"ctd.zarr\" if plot_variable in [\"temperature\", \"salinity\"] else \"ctd_bgc.zarr\"\n",
-    ")\n",
+    "filename = \"ctd.zarr\"\n",
     "ctd_ds = xr.open_dataset(f\"{data_dir}/{filename}\")\n",
     "if ctd_ds[\"trajectory\"].size <= 1:\n",
     "    raise ValueError(\"Number of waypoints must be > 1\")"
@@ -482,7 +478,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.9"
+   "version": "3.12.12"
   }
  },
  "nbformat": 4,

diff --git a/docs/user-guide/tutorials/working_with_expedition_yaml.md b/docs/user-guide/tutorials/working_with_expedition_yaml.md
@@ -29,7 +29,6 @@ schedule: # <-- 1. expedition schedule section
   waypoints:
     - instrument: # <-- Waypoint 1
         - CTD
-        - CTD_BGC
         - ARGO_FLOAT
         - DRIFTER
       location:
@@ -53,7 +52,6 @@ instruments_config: # <-- 2. instrument configuration section
   ship_underwater_st_config:
     period_minutes: 5.0
   argo_float_config: ...
-  ctd_bgc_config: ...
   ctd_config: ...
   drifter_config: ...
   xbt_config: ...
@@ -75,7 +73,7 @@ This section contains a list of `waypoints` that define the expedition's route.
 - **Instruments (`instrument`)**: A list of instruments to be deployed at that waypoint. Add or remove instruments by adding or deleting entries on _new lines_. The instrument selection can also be left empty (i.e., no instruments deployed at that waypoint) by setting the parameter to: `instrument: null`.
 
 ```{tip}
-Full list of instruments supported for deployment at waypoints (case-sensitive): `CTD`, `CTD_BGC`, `DRIFTER`, `ARGO_FLOAT`, `XBT` (or `null`).
+Full list of instruments supported for deployment at waypoints (case-sensitive): `CTD`, `DRIFTER`, `ARGO_FLOAT`, `XBT` (or `null`).
 ```
 
 ```{tip}

diff --git a/src/virtualship/cli/_plan.py b/src/virtualship/cli/_plan.py
@@ -32,7 +32,6 @@
 from virtualship.models import (
     ADCPConfig,
     ArgoFloatConfig,
-    CTD_BGCConfig,
     CTDConfig,
     DrifterConfig,
     Expedition,
@@ -109,15 +108,6 @@ def log_exception_to_file(
             {"name": "stationkeeping_time", "minutes": True},
         ],
     },
-    "ctd_bgc_config": {
-        "class": CTD_BGCConfig,
-        "title": "CTD-BGC",
-        "attributes": [
-            {"name": "max_depth_meter"},
-            {"name": "min_depth_meter"},
-            {"name": "stationkeeping_time", "minutes": True},
-        ],
-    },
     "xbt_config": {
         "class": XBTConfig,
         "title": "XBT",

diff --git a/src/virtualship/expedition/simulate_schedule.py b/src/virtualship/expedition/simulate_schedule.py
@@ -10,7 +10,6 @@
 
 from virtualship.instruments.argo_float import ArgoFloat
 from virtualship.instruments.ctd import CTD
-from virtualship.instruments.ctd_bgc import CTD_BGC
 from virtualship.instruments.drifter import Drifter
 from virtualship.instruments.types import InstrumentType
 from virtualship.instruments.xbt import XBT
@@ -53,7 +52,6 @@ class MeasurementsToSimulate:
         InstrumentType.ARGO_FLOAT: "argo_floats",
         InstrumentType.DRIFTER: "drifters",
         InstrumentType.CTD: "ctds",
-        InstrumentType.CTD_BGC: "ctd_bgcs",
         InstrumentType.XBT: "xbts",
     }
 
@@ -67,7 +65,6 @@ def get_attr_for_instrumenttype(cls, instrument_type):
     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)
 
 
@@ -265,12 +262,6 @@ def _make_measurements(self, waypoint: Waypoint) -> timedelta:
         # time costs of each measurement
         time_costs = [timedelta()]
 
-        # check if both CTD and CTD_BGC are present
-        # TODO: this can be avoided if CTD and CTD_BGC are merged into a single instrument
-        both_ctd_and_bgc = (
-            InstrumentType.CTD in instruments and InstrumentType.CTD_BGC in instruments
-        )
-
         for instrument in instruments:
             if instrument is InstrumentType.ARGO_FLOAT:
                 self._measurements_to_simulate.argo_floats.append(
@@ -302,20 +293,7 @@ def _make_measurements(self, waypoint: Waypoint) -> timedelta:
                 time_costs.append(
                     self._expedition.instruments_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._expedition.instruments_config.ctd_bgc_config.min_depth_meter,
-                        max_depth=self._expedition.instruments_config.ctd_bgc_config.max_depth_meter,
-                    )
-                )
-                if both_ctd_and_bgc:  # only need to add time cost once if both CTD and CTD_BGC are being taken; in reality they would be done on the same instrument
-                    pass
-                else:
-                    time_costs.append(
-                        self._expedition.instruments_config.ctd_bgc_config.stationkeeping_time
-                    )
+
             elif instrument is InstrumentType.DRIFTER:
                 self._measurements_to_simulate.drifters.append(
                     Drifter(

diff --git a/src/virtualship/instruments/__init__.py b/src/virtualship/instruments/__init__.py
@@ -4,7 +4,6 @@
     adcp,
     argo_float,
     ctd,
-    ctd_bgc,
     drifter,
     ship_underwater_st,
     xbt,
@@ -14,7 +13,6 @@
     "adcp",
     "argo_float",
     "ctd",
-    "ctd_bgc",
     "drifter",
     "ship_underwater_st",
     "xbt",

diff --git a/src/virtualship/instruments/ctd.py b/src/virtualship/instruments/ctd.py
@@ -49,6 +49,8 @@ class CTD:
 # SECTION: Kernels
 # =====================================================
 
+## physical variables
+
 
 def _sample_temperature(particle, fieldset, time):
     particle.temperature = fieldset.T[time, particle.depth, particle.lat, particle.lon]
@@ -58,6 +60,40 @@ def _sample_salinity(particle, fieldset, time):
     particle.salinity = fieldset.S[time, particle.depth, particle.lat, particle.lon]
 
 
+## bgc variables
+
+
+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 _sample_nitrate(particle, fieldset, time):
+    particle.no3 = fieldset.no3[time, particle.depth, particle.lat, particle.lon]
+
+
+def _sample_phosphate(particle, fieldset, time):
+    particle.po4 = fieldset.po4[time, particle.depth, particle.lat, particle.lon]
+
+
+def _sample_ph(particle, fieldset, time):
+    particle.ph = fieldset.ph[time, particle.depth, particle.lat, particle.lon]
+
+
+def _sample_phytoplankton(particle, fieldset, time):
+    particle.phyc = fieldset.phyc[time, particle.depth, particle.lat, particle.lon]
+
+
+def _sample_primary_production(particle, fieldset, time):
+    particle.nppv = fieldset.nppv[time, particle.depth, particle.lat, particle.lon]
+
+
+## cast
+
+
 def _ctd_cast(particle, fieldset, time):
     # lowering
     if particle.raising == 0:
@@ -84,6 +120,13 @@ class CTDInstrument(Instrument):
     sensor_kernels: ClassVar[dict[SensorType, Callable]] = {
         SensorType.TEMPERATURE: _sample_temperature,
         SensorType.SALINITY: _sample_salinity,
+        SensorType.OXYGEN: _sample_o2,
+        SensorType.CHLOROPHYLL: _sample_chlorophyll,
+        SensorType.NITRATE: _sample_nitrate,
+        SensorType.PHOSPHATE: _sample_phosphate,
+        SensorType.PH: _sample_ph,
+        SensorType.PHYTOPLANKTON: _sample_phytoplankton,
+        SensorType.PRIMARY_PRODUCTION: _sample_primary_production,
     }
 
     def __init__(self, expedition, from_data):