Basic test

.github/workflows/codetools.yml

@@ -31,3 +31,15 @@ jobs:
         run: black --diff --check ./$PACKAGE
       - name: isort
         run: isort --check-only --diff ./$PACKAGE
+
+  tests:
+    runs-on: ubuntu-20.04
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/[email protected]
+        with:
+          python-version: 3.12
+      - name: install
+        run: pip install ".[dev]"
+      - name: run_tests
+        run: pytest --cov=virtual_ship tests

.gitignore

@@ -172,3 +172,5 @@ cython_debug/
 
 # Auto generated by setuptools scm
 virtual_ship/_version_setup.py
+
+.vscode/

pyproject.toml

@@ -30,6 +30,16 @@ dependencies = [
     "parcels >= 3, < 4",
     "scipy >= 1, < 2",
     "xarray >= 2023, < 2024",
+    # The packages below are parcels packages not included in their distribution requirements.
+    "numpy >= 1, < 2",
+    "cgen >= 2020, < 2021",
+    "dask >= 2023, < 2025",
+    "cftime >= 1, < 2",
+    "psutil >= 1, < 2",
+    "netCDF4 >= 1, < 2",
+    "zarr >= 2, < 3",
+    "tqdm >= 4, < 5",
+    "pymbolic >= 2022, < 2023",
 ]
 
 [project.urls]
@@ -53,6 +63,9 @@ dev = [
     "isort == 5.13.2",
     "pydocstyle == 6.3.0",
     "sort-all == 1.2.0",
+    "pytest == 8.2.0",
+    "pytest-cov == 5.0.0",
+    "codecov == 2.1.13",
 ]
 
 [tool.isort]

tests.sh

@@ -0,0 +1,5 @@
+#!/bin/sh
+
+# Runs the tests and creates a code coverage report.
+
+pytest --cov=virtual_ship --cov-report=html tests

tests/conftest.py

@@ -0,0 +1,7 @@
+import pytest
+
+
+# Set the working directory for each test to the directory of that test.
+@pytest.fixture(autouse=True)
+def change_test_dir(request, monkeypatch):
+    monkeypatch.chdir(request.fspath.dirname)

tests/instruments/test_argo.py

@@ -0,0 +1,40 @@
+"""Test the simulation of argos."""
+
+from virtual_ship.instruments.argo import simulate_argos, Argo
+from virtual_ship.instruments.location import Location
+from parcels import FieldSet
+import numpy as np
+
+
+def test_simulate_argos() -> None:
+    DRIFT_DEPTH = -1000
+    MAX_DEPTH = -2000
+    VERTICLE_SPEED = -0.10
+    CYCLE_DAYS = 10
+    DRIFT_DAYS = 9
+
+    fieldset = FieldSet.from_data(
+        {"U": 0, "V": 0, "T": 0, "S": 0},
+        {
+            "lon": 0,
+            "lat": 0,
+            "time": [np.datetime64("1950-01-01") + np.timedelta64(632160, "h")],
+        },
+    )
+
+    min_depth = -fieldset.U.depth[0]
+
+    argos = [
+        Argo(
+            location=Location(latitude=0, longitude=0),
+            deployment_time=0,
+            min_depth=min_depth,
+            max_depth=MAX_DEPTH,
+            drift_depth=DRIFT_DEPTH,
+            vertical_speed=VERTICLE_SPEED,
+            cycle_days=CYCLE_DAYS,
+            drift_days=DRIFT_DAYS,
+        )
+    ]
+
+    simulate_argos(argos=argos, fieldset=fieldset, out_file_name="test")

tests/sailship_config.json

@@ -0,0 +1,40 @@
+{
+    "region_of_interest": {
+        "North": 64,
+        "East": -23,
+        "South": 59,
+        "West": -43
+      },
+    "requested_ship_time": {
+        "start": "2022-01-01T00:00:00",
+        "end": "2022-01-2T00:00:00"
+      },
+    "route_coordinates": [
+      [-23.071289, 63.743631], [-23.081289, 63.743631], [-23.091289, 63.743631]
+    ],
+    "underway_data": true,
+    "ADCP_data": false,
+    "ADCP_settings": {
+        "max_depth": -1000,
+        "bin_size_m": 24
+      },
+    "CTD_locations": [
+      [-23.071289, 63.743631]
+    ],
+    "CTD_settings": {
+        "max_depth": "max"
+      },
+    "drifter_deploylocations": [
+
+    ],
+    "argo_deploylocations": [
+      [-23.081289, 63.743631]
+    ],
+    "argo_characteristics": {
+      "driftdepth": -1000,
+      "maxdepth": -2000,
+      "vertical_speed": -0.10, 
+      "cycle_days" : 10, 
+      "drift_days": 9
+    }
+  }

tests/test_sailship.py

@@ -0,0 +1,42 @@
+"""Performs a complete cruise with virtual ship."""
+
+from virtual_ship.virtual_ship_configuration import VirtualShipConfiguration
+from virtual_ship.sailship import sailship
+from parcels import FieldSet
+import numpy as np
+
+
+def test_sailship() -> None:
+    ctd_fieldset = FieldSet.from_data(
+        {"U": 0, "V": 0, "S": 0, "T": 0, "bathymetry": 0},
+        {"lon": 0, "lat": 0},
+    )
+    ctd_fieldset.add_constant("maxtime", ctd_fieldset.U.grid.time_full[-1])
+    ctd_fieldset.add_constant("mindepth", -ctd_fieldset.U.depth[0])
+    ctd_fieldset.add_constant("max_depth", -ctd_fieldset.U.depth[-1])
+
+    drifter_fieldset = FieldSet.from_data(
+        {
+            "U": 0,
+            "V": 0,
+        },
+        {"lon": 0, "lat": 0},
+    )
+
+    argo_fieldset = FieldSet.from_data(
+        {"U": 0, "V": 0, "T": 0, "S": 0},
+        {
+            "lon": 0,
+            "lat": 0,
+            "time": [np.datetime64("1950-01-01") + np.timedelta64(632160, "h")],
+        },
+    )
+
+    config = VirtualShipConfiguration(
+        "sailship_config.json",
+        ctd_fieldset=ctd_fieldset,
+        drifter_fieldset=drifter_fieldset,
+        argo_fieldset=argo_fieldset,
+    )
+
+    sailship(config)