53 interactive loop

meta.yaml

@@ -5,6 +5,10 @@ package:
 source:
   path: virtual_ship
 
+build:
+  entry_points:
+    - do_expedition = virtual_ship.cli.do_expedition:main
+
 requirements:
   run:
     - python >=3.8

pyproject.toml

@@ -30,6 +30,7 @@ dependencies = [
     "sortedcontainers == 2.4.0",
     "opensimplex == 0.4.5",
     "numpy >=1, < 2",
+    "pydantic >=2, <3",
 ]
 
 [project.urls]
@@ -61,6 +62,9 @@ dev = [
     "sortedcontainers-stubs == 2.4.2",
 ]
 
+[project.scripts]
+do_expedition = "virtual_ship.cli.do_expedition:main"
+
 [tool.isort]
 profile = "black"
 skip_gitignore = true

scripts/download_data.py

@@ -0,0 +1,136 @@
+"""
+Download data required to run expeditions.
+
+This is a very crude script, here just as long as we do not properly incorporate it into the library.
+"""
+
+import copernicusmarine
+import datetime
+
+if __name__ == "__main__":
+    datadir = "input_data"
+    username = input("username: ")
+    password = input("password: ")
+
+    copernicusmarine.subset(
+        dataset_id="cmems_mod_glo_phy_my_0.083deg_static",
+        force_dataset_part="bathy",
+        variables=["deptho"],
+        minimum_longitude=-0.01,
+        maximum_longitude=0.01,
+        minimum_latitude=-0.01,
+        maximum_latitude=0.01,
+        minimum_depth=0.49402499198913574,
+        maximum_depth=5727.9169921875,
+        output_filename="bathymetry.nc",
+        output_directory=datadir,
+        username=username,
+        password=password,
+        force_download=True,
+    )
+
+    download_dict = {
+        "UVdata": {
+            "dataset_id": "cmems_mod_glo_phy-cur_anfc_0.083deg_PT6H-i",
+            "variables": ["uo", "vo"],
+            "output_filename": "default_uv.nc",
+        },
+        "Sdata": {
+            "dataset_id": "cmems_mod_glo_phy-so_anfc_0.083deg_PT6H-i",
+            "variables": ["so"],
+            "output_filename": "default_s.nc",
+        },
+        "Tdata": {
+            "dataset_id": "cmems_mod_glo_phy-thetao_anfc_0.083deg_PT6H-i",
+            "variables": ["thetao"],
+            "output_filename": "default_t.nc",
+        },
+    }
+
+    for dataset in download_dict:
+        copernicusmarine.subset(
+            dataset_id=download_dict[dataset]["dataset_id"],
+            variables=download_dict[dataset]["variables"],
+            minimum_longitude=-0.01,
+            maximum_longitude=0.01,
+            minimum_latitude=-0.01,
+            maximum_latitude=0.01,
+            start_datetime=datetime.datetime.strptime("2023-01-01", "%Y-%m-%d"),
+            end_datetime=datetime.datetime.strptime("2023-01-02", "%Y-%m-%d"),
+            minimum_depth=0.49402499198913574,
+            maximum_depth=5727.9169921875,
+            output_filename=download_dict[dataset]["output_filename"],
+            output_directory=datadir,
+            username=username,
+            password=password,
+            force_download=True,
+        )
+
+    download_dict = {
+        "UVdata": {
+            "dataset_id": "cmems_mod_glo_phy-cur_anfc_0.083deg_PT6H-i",
+            "variables": ["uo", "vo"],
+            "output_filename": "drifter_uv.nc",
+        },
+        "Tdata": {
+            "dataset_id": "cmems_mod_glo_phy-thetao_anfc_0.083deg_PT6H-i",
+            "variables": ["thetao"],
+            "output_filename": "drifter_t.nc",
+        },
+    }
+
+    for dataset in download_dict:
+        copernicusmarine.subset(
+            dataset_id=download_dict[dataset]["dataset_id"],
+            variables=download_dict[dataset]["variables"],
+            minimum_longitude=-0.01,
+            maximum_longitude=0.01,
+            minimum_latitude=-0.01,
+            maximum_latitude=0.01,
+            start_datetime=datetime.datetime.strptime("2023-01-01", "%Y-%m-%d"),
+            end_datetime=datetime.datetime.strptime("2023-01-02", "%Y-%m-%d"),
+            minimum_depth=0.49402499198913574,
+            maximum_depth=0.49402499198913574,
+            output_filename=download_dict[dataset]["output_filename"],
+            output_directory=datadir,
+            username=username,
+            password=password,
+            force_download=True,
+        )
+
+    download_dict = {
+        "UVdata": {
+            "dataset_id": "cmems_mod_glo_phy-cur_anfc_0.083deg_PT6H-i",
+            "variables": ["uo", "vo"],
+            "output_filename": "argo_float_uv.nc",
+        },
+        "Sdata": {
+            "dataset_id": "cmems_mod_glo_phy-so_anfc_0.083deg_PT6H-i",
+            "variables": ["so"],
+            "output_filename": "argo_float_s.nc",
+        },
+        "Tdata": {
+            "dataset_id": "cmems_mod_glo_phy-thetao_anfc_0.083deg_PT6H-i",
+            "variables": ["thetao"],
+            "output_filename": "argo_float_t.nc",
+        },
+    }
+
+    for dataset in download_dict:
+        copernicusmarine.subset(
+            dataset_id=download_dict[dataset]["dataset_id"],
+            variables=download_dict[dataset]["variables"],
+            minimum_longitude=-0.01,
+            maximum_longitude=0.01,
+            minimum_latitude=-0.01,
+            maximum_latitude=0.01,
+            start_datetime=datetime.datetime.strptime("2023-01-01", "%Y-%m-%d"),
+            end_datetime=datetime.datetime.strptime("2023-01-02", "%Y-%m-%d"),
+            minimum_depth=0.49402499198913574,
+            maximum_depth=5727.9169921875,
+            output_filename=download_dict[dataset]["output_filename"],
+            output_directory=datadir,
+            username=username,
+            password=password,
+            force_download=True,
+        )

tests/expedition/expedition_dir/.gitignore

@@ -0,0 +1 @@
+results/

tests/expedition/expedition_dir/input_data/.gitignore

@@ -0,0 +1,9 @@
+!argo_float_s.nc
+!argo_float_t.nc
+!argo_float_uv.nc
+!bathymetry.nc
+!default_s.nc
+!default_t.nc
+!default_uv.nc
+!drifter_t.nc
+!drifter_uv.nc

tests/expedition/expedition_dir/schedule.yaml

@@ -0,0 +1,16 @@
+waypoints:
+- instrument: CTD
+  location:
+    latitude: 0
+    longitude: 0
+  time: 2023-01-01 00:00:00
+- instrument: DRIFTER
+  location:
+    latitude: 0.01
+    longitude: 0.01
+  time: 2023-01-01 01:00:00
+- instrument: ARGO_FLOAT
+  location:
+    latitude: 0.02
+    longitude: 0.02
+  time: 2023-01-01 02:00:00

tests/expedition/expedition_dir/ship_config.yaml

@@ -0,0 +1,21 @@
+ship_speed_meter_per_second: 5.14
+adcp_config:
+  num_bins: 40
+  max_depth_meter: -1000.0
+  period_minutes: 5.0
+argo_float_config:
+  cycle_days: 10.0
+  drift_days: 9.0
+  drift_depth_meter: -1000.0
+  max_depth_meter: -2000.0
+  min_depth_meter: 0.0
+  vertical_speed_meter_per_second: -0.1
+ctd_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
+ship_underwater_st_config:
+  period_minutes: 5.0

tests/expedition/test_do_expedition.py

@@ -0,0 +1,9 @@
+from pytest import CaptureFixture
+
+from virtual_ship.expedition import do_expedition
+
+
+def test_do_expedition(capfd: CaptureFixture) -> None:
+    do_expedition("expedition_dir")
+    out, _ = capfd.readouterr()
+    assert "This expedition took" in out, "Expedition did not complete successfully."

tests/expedition/test_schedule.py

@@ -0,0 +1,26 @@
+from datetime import datetime, timedelta
+
+import py
+
+from virtual_ship import Location
+from virtual_ship.expedition import Schedule, Waypoint
+
+
+def test_schedule(tmpdir: py.path.LocalPath) -> None:
+    out_path = tmpdir.join("schedule.yaml")
+
+    # arbitrary time for testing
+    base_time = datetime.strptime("1950-01-01", "%Y-%m-%d")
+
+    schedule = Schedule(
+        waypoints=[
+            Waypoint(Location(0, 0), time=base_time, instrument=None),
+            Waypoint(
+                Location(1, 1), time=base_time + timedelta(hours=1), instrument=None
+            ),
+        ]
+    )
+    schedule.to_yaml(out_path)
+
+    schedule2 = Schedule.from_yaml(out_path)
+    assert schedule == schedule2

tests/expedition/test_simulate_schedule.py

@@ -0,0 +1,48 @@
+from datetime import datetime, timedelta
+
+import pyproj
+
+from virtual_ship import Location
+from virtual_ship.expedition import Schedule, ShipConfig, Waypoint
+from virtual_ship.expedition.simulate_schedule import (
+    ScheduleOk,
+    ScheduleProblem,
+    simulate_schedule,
+)
+
+
+def test_simulate_schedule_feasible() -> None:
+    """Test schedule with two waypoints that can be reached within time is OK."""
+    base_time = datetime.strptime("2022-01-01T00:00:00", "%Y-%m-%dT%H:%M:%S")
+
+    projection = pyproj.Geod(ellps="WGS84")
+    ship_config = ShipConfig.from_yaml("expedition_dir/ship_config.yaml")
+    ship_config.ship_speed_meter_per_second = 5.14
+    schedule = Schedule(
+        waypoints=[
+            Waypoint(Location(0, 0), base_time),
+            Waypoint(Location(0.01, 0), base_time + timedelta(days=1)),
+        ]
+    )
+
+    result = simulate_schedule(projection, ship_config, schedule)
+
+    assert isinstance(result, ScheduleOk)
+
+
+def test_simulate_schedule_too_far() -> None:
+    """Test schedule with two waypoints that are very far away and cannot be reached in time is not OK."""
+    base_time = datetime.strptime("2022-01-01T00:00:00", "%Y-%m-%dT%H:%M:%S")
+
+    projection = pyproj.Geod(ellps="WGS84")
+    ship_config = ShipConfig.from_yaml("expedition_dir/ship_config.yaml")
+    schedule = Schedule(
+        waypoints=[
+            Waypoint(Location(0, 0), base_time),
+            Waypoint(Location(1.0, 0), base_time + timedelta(minutes=1)),
+        ]
+    )
+
+    result = simulate_schedule(projection, ship_config, schedule)
+
+    assert isinstance(result, ScheduleProblem)

tests/instruments/test_ship_underwater_st.py

@@ -27,15 +27,15 @@ def test_simulate_ship_underwater_st(tmpdir: py.path.LocalPath) -> None:
     # expected observations at sample points
     expected_obs = [
         {
-            "salinity": 5,
-            "temperature": 6,
+            "S": 5,
+            "T": 6,
             "lat": sample_points[0].location.lat,
             "lon": sample_points[0].location.lon,
             "time": base_time + datetime.timedelta(seconds=0),
         },
         {
-            "salinity": 7,
-            "temperature": 8,
+            "S": 7,
+            "T": 8,
             "lat": sample_points[1].location.lat,
             "lon": sample_points[1].location.lon,
             "time": base_time + datetime.timedelta(seconds=1),
@@ -45,19 +45,19 @@ def test_simulate_ship_underwater_st(tmpdir: py.path.LocalPath) -> None:
     # create fieldset based on the expected observations
     # indices are time, latitude, longitude
     salinity = np.zeros((2, 2, 2))
-    salinity[0, 0, 0] = expected_obs[0]["salinity"]
-    salinity[1, 1, 1] = expected_obs[1]["salinity"]
+    salinity[0, 0, 0] = expected_obs[0]["S"]
+    salinity[1, 1, 1] = expected_obs[1]["S"]
 
     temperature = np.zeros((2, 2, 2))
-    temperature[0, 0, 0] = expected_obs[0]["temperature"]
-    temperature[1, 1, 1] = expected_obs[1]["temperature"]
+    temperature[0, 0, 0] = expected_obs[0]["T"]
+    temperature[1, 1, 1] = expected_obs[1]["T"]
 
     fieldset = FieldSet.from_data(
         {
             "V": np.zeros((2, 2, 2)),
             "U": np.zeros((2, 2, 2)),
-            "salinity": salinity,
-            "temperature": temperature,
+            "S": salinity,
+            "T": temperature,
         },
         {
             "lat": np.array([expected_obs[0]["lat"], expected_obs[1]["lat"]]),
@@ -95,7 +95,7 @@ def test_simulate_ship_underwater_st(tmpdir: py.path.LocalPath) -> None:
         zip(results.sel(trajectory=traj).obs, expected_obs, strict=True)
     ):
         obs = results.sel(trajectory=traj, obs=obs_i)
-        for var in ["salinity", "temperature", "lat", "lon"]:
+        for var in ["S", "T", "lat", "lon"]:
             obs_value = obs[var].values.item()
             exp_value = exp[var]
             assert np.isclose(