Basic test (#33)

    Created test framework
    Added test that runs sail_ship complete. No assertions yet; just to see if it runs.
    Seperated Argo simulation as a seperate module in instruments/argo. Created test for it; similarly without assertions.
    Added tests to CI. Full code coverage is not generated or uploaded anywhere yet. Just runs the tests and sees how that goes.

.github/workflows/codetools.yml

@@ -4,6 +4,7 @@ on: [push, pull_request]
 
 env:
   PACKAGE: virtual_ship
+  TESTS: tests
 
 jobs:
   codetools:
@@ -19,7 +20,7 @@ jobs:
       - name: install
         run: pip install ".[dev]"
       - name: flake8
-        run: flake8 ./$PACKAGE
+        run: flake8 ./$PACKAGE ./$TESTS
       - name: pydocstyle
         run: pydocstyle ./$PACKAGE
       - name: sort-all
@@ -28,6 +29,18 @@ jobs:
           [[ -z $(git status -s) ]]
           git checkout -- .
       - name: black
-        run: black --diff --check ./$PACKAGE
+        run: black --diff --check ./$PACKAGE ./$TESTS
       - name: isort
-        run: isort --check-only --diff ./$PACKAGE
+        run: isort --check-only --diff ./$PACKAGE ./$TESTS
+
+  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/

codetools.sh

@@ -9,11 +9,12 @@ set -e
 cd "$(dirname "$0")"
 
 PACKAGE=virtual_ship
+TESTS=tests
 
 echo "--------------"
 echo "flake8"
 echo "--------------"
-flake8 ./$PACKAGE
+flake8 ./$PACKAGE ./$TESTS
 # darglint is ran as a plugin for flake8.
 
 echo "--------------"
@@ -29,10 +30,10 @@ find ./$PACKAGE -type f -name '__init__.py' -print0 | xargs -0 sort-all
 echo "--------------"
 echo "black"
 echo "--------------"
-black ./$PACKAGE
+black ./$PACKAGE ./$TESTS
 
 echo "--------------"
 echo "isort"
 echo "--------------"
-isort ./$PACKAGE
+isort ./$PACKAGE ./$TESTS
 

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 +1,48 @@
+"""Test the simulation of Argo floats."""
+
+from datetime import timedelta
+
+import numpy as np
+from parcels import FieldSet
+
+from virtual_ship.instruments import Location
+from virtual_ship.instruments.argo_float import ArgoFloat, simulate_argo_floats
+
+
+def test_simulate_argo_floats() -> 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]
+
+    argo_floats = [
+        ArgoFloat(
+            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_argo_floats(
+        argo_floats=argo_floats,
+        fieldset=fieldset,
+        out_file_name="test",
+        outputdt=timedelta(minutes=5),
+    )

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 +1,43 @@
+"""Performs a complete cruise with virtual ship."""
+
+import numpy as np
+from parcels import FieldSet
+
+from virtual_ship.sailship import sailship
+from virtual_ship.virtual_ship_configuration import VirtualShipConfiguration
+
+
+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_float_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_float_fieldset=argo_float_fieldset,
+    )
+
+    sailship(config)

virtual_ship/__init__.py

@@ -1 +1,5 @@
 """Code for the Virtual Ship Classroom, where Marine Scientists can combine Copernicus Marine Data with an OceanParcels ship to go on a virtual expedition."""
+
+from . import instruments, sailship
+
+__all__ = ["instruments", "sailship"]